AlwaysBreakAfterReturnType: None
AlwaysBreakBeforeMultilineStrings: true
AlwaysBreakTemplateDeclarations: true
-BinPackArguments: true
+BinPackArguments: false
BinPackParameters: false
BraceWrapping:
AfterClass: true
- nightly-deploy
# Release work for packaging code
- release-package
- # Release checksum verification
- - release-verify
# Configure code for release builds
- release-configure
# Release work for packaging code
- release-build
# Tests for release code
- release-tests
+ # Release checksum verification
+ - release-verify
# Prepare for deploying artifacts
- release-prepare-deploy
# Deploy stage for release builds
- local: '/admin/gitlab-ci/global.gitlab-ci.yml'
- local: '/admin/gitlab-ci/rules.gitlab-ci.yml'
# gmxapi Python package.
- - local: '/admin/gitlab-ci/python-gmxapi.gitlab-ci.yml'
+ - local: '/admin/gitlab-ci/python-gmxapi01.gitlab-ci.yml'
+ - local: '/admin/gitlab-ci/python-gmxapi02.gitlab-ci.yml'
+ - local: '/admin/gitlab-ci/python-gmxapi03.gitlab-ci.yml'
# Further API validation and usability of sample gmxapi extension package.
- local: '/admin/gitlab-ci/sample_restraint.gitlab-ci.yml'
# API regression testing using sample gmxapi extension package.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-cmake_minimum_required(VERSION 3.13)
+cmake_minimum_required(VERSION 3.16.3)
cmake_policy(SET CMP0074 NEW) # From CMake 3.12
cmake_policy(SET CMP0068 NEW) # From CMake-3.9
set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
-# Fujitsu only has SIMD in double precision, so this will be faster
-gmx_set_boolean(GMX_DOUBLE_DEFAULT GMX_TARGET_FUJITSU_SPARC64)
-option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" ${GMX_DOUBLE_DEFAULT})
-option(GMX_RELAXED_DOUBLE_PRECISION "Accept single precision 1/sqrt(x) when using Fujitsu HPC-ACE SIMD" OFF)
-mark_as_advanced(GMX_RELAXED_DOUBLE_PRECISION)
+option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" OFF)
option(GMX_MPI "Build a parallel (message-passing) version of GROMACS" OFF)
option(GMX_THREAD_MPI "Build a thread-MPI-based multithreaded version of GROMACS (not compatible with MPI)" ON)
-gmx_dependent_option(
- GMX_MPI_IN_PLACE
- "Enable MPI_IN_PLACE for MPIs that have it defined"
- ON
- GMX_MPI)
-mark_as_advanced(GMX_MPI_IN_PLACE)
option(GMX_MIMIC "Enable MiMiC QM/MM interface (CPMD is required)" OFF)
GMX_SIMD
"SIMD instruction set for CPU kernels and compiler optimization"
"AUTO"
- AUTO None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 AVX2_128 AVX_512 AVX_512_KNL MIC ARM_NEON ARM_NEON_ASIMD ARM_SVE IBM_VMX IBM_VSX Sparc64_HPC_ACE Reference)
+ AUTO None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 AVX2_128 AVX_512 AVX_512_KNL ARM_NEON_ASIMD ARM_SVE IBM_VSX Reference)
-if(GMX_TARGET_MIC)
- set(GMX_FFT_LIBRARY_DEFAULT "mkl")
-else()
- set(GMX_FFT_LIBRARY_DEFAULT "fftw3")
-endif()
+set(GMX_FFT_LIBRARY_DEFAULT "fftw3")
gmx_option_multichoice(
GMX_FFT_LIBRARY
option(GMX_USE_TNG "Use the TNG library for trajectory I/O" ON)
-option(GMX_BUILD_MDRUN_ONLY "Build and install only the mdrun binary" OFF)
-
option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
mark_as_advanced(GMX_CYCLE_SUBCOUNTERS)
# want such variables to always have a definition, because #if is more
# robust than #ifdef. So, we put this value on the compiler command
# line in all cases.
-#
-# GMX_RELAXED_DOUBLE_PRECISION does not need to be handled here,
-# because no installed header needs it
if(GMX_DOUBLE)
set(GMX_DOUBLE_VALUE 1)
else()
gmx_set_boolean(GMX_USE_NICE "HAVE_UNISTD_H AND HAVE_NICE")
-# Management of GROMACS options for specific toolchains should go
-# here. Because the initial settings for some of the main options have
-# already happened, but things like library detection and MPI compiler
-# feature detection have not, the docstrings for any over-rides of
-# GROMACS defaults or user settings will make sense. Also, any
-# toolchain-related reasons for choosing whether to detect various
-# things can be sorted out now, before the detection takes place.
-if(GMX_TARGET_FUJITSU_SPARC64)
- include(gmxManageFujitsuSparc64)
-endif()
-
########################################################################
#Process MPI settings
########################################################################
if(GMX_THREAD_MPI)
# enable MPI functions
tmpi_enable()
- set(MPI_IN_PLACE_EXISTS 1)
endif()
# If atomics are manually disabled a define is needed because atomics.h doesn't depend on config.h
if (TMPI_ATOMICS_DISABLED)
message(WARNING "To use GPU acceleration efficiently, mdrun requires OpenMP multi-threading, which is currently not enabled.")
endif()
+ if (GMX_OPENCL_NB_CLUSTER_SIZE)
+ message(WARNING "GMX_OPENCL_NB_CLUSTER_SIZE is deprecated, use GMX_GPU_NB_CLUSTER_SIZE instead")
+ endif()
+ if (GMX_OPENCL_NB_CLUSTER_SIZE AND GMX_GPU_NB_CLUSTER_SIZE)
+ if (NOT ${GMX_OPENCL_NB_CLUSTER_SIZE} EQUAL ${GMX_GPU_NB_CLUSTER_SIZE})
+ message(FATAL_ERROR "Mismatching values passed to GMX_OPENCL_NB_CLUSTER_SIZE and GMX_GPU_NB_CLUSTER_SIZE; the former is deprecated, use only the latter!")
+ endif()
+ endif()
+ # Only OpenCL and SYCL support changing the default cluster size
+ if (${_gmx_gpu_uppercase} STREQUAL "CUDA")
+ if (GMX_GPU_NB_CLUSTER_SIZE AND NOT "${GMX_GPU_NB_CLUSTER_SIZE}" EQUAL 8)
+ message(FATAL_ERROR "Setting GMX_GPU_NB_CLUSTER_SIZE is not supported in CUDA (the default GMX_GPU_NB_CLUSTER_SIZE=8 is used)")
+ endif()
+ else()
+ # use the legacy GMX_OPENCL_NB_CLUSTER_SIZE variable if set, otherwise set the defaults
+ if (GMX_OPENCL_NB_CLUSTER_SIZE)
+ set(_gmx_gpu_nb_cluster_size_value ${GMX_OPENCL_NB_CLUSTER_SIZE})
+ else()
+ # default cluster size is 8 with OpenCL and 4 with SYCL for now
+ if(${_gmx_gpu_uppercase} STREQUAL "OPENCL")
+ set(_gmx_gpu_nb_cluster_size_value 8)
+ else()
+ set(_gmx_gpu_nb_cluster_size_value 4)
+ endif()
+ endif()
+ set(GMX_GPU_NB_CLUSTER_SIZE ${_gmx_gpu_nb_cluster_size_value} CACHE STRING "Cluster size used by the nonbonded kernel. Set to 4 for Intel GPUs.")
+ mark_as_advanced(GMX_GPU_NB_CLUSTER_SIZE)
+ endif()
+
+endif()
+
+# For build with CUDA and Lib-MPI, check if underlying MPI implementation is CUDA-aware
+# CUDA-aware MPI allows direct GPU communication without staging data through host
+if(GMX_GPU_CUDA AND GMX_LIB_MPI)
+ include(gmxManageCudaAwareMPI)
+else()
+ set(HAVE_CUDA_AWARE_MPI 0)
endif()
if(CYGWIN)
# Our own GROMACS tests
########################################################################
-include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src)
include_directories(SYSTEM ${CMAKE_SOURCE_DIR}/src/external)
-# Required for config.h, maybe should only be set in src/CMakeLists.txt
-include_directories(BEFORE ${CMAKE_BINARY_DIR}/src)
include(gmxTestInlineASM)
gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
"Set GMX_BUILD_HELP=OFF or do an out-of-source build to proceed.")
endif()
+if (GMX_BUILD_FOR_COVERAGE)
+ # Set flags for coverage build here instead having to do so manually
+ set(CMAKE_C_FLAGS "-g --coverage")
+ set(CMAKE_CXX_FLAGS "-g --coverage")
+endif()
+
# # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
# these are set after everything else
if (NOT GMX_SKIP_DEFAULT_CFLAGS)
#Simpler to always install.
install(FILES COPYING DESTINATION ${GMX_INSTALL_GMXDATADIR} COMPONENT data)
-if (GMX_BUILD_FOR_COVERAGE)
- # Code heavy with asserts makes conditional coverage close to useless metric,
- # as by design most of the false branches are impossible to trigger in
- # correctly functioning code. And the benefit of testing those that could
- # be triggered by using an API against its specification isn't usually
- # worth the effort.
- add_definitions(-DNDEBUG -DGMX_DISABLE_ASSERTS)
-endif()
-
if (BUILD_TESTING)
include(tests/CheckTarget.cmake)
endif()
option(GMX_PYTHON_PACKAGE "Configure gmxapi Python package" OFF)
mark_as_advanced(GMX_PYTHON_PACKAGE)
-if (NOT GMX_BUILD_MDRUN_ONLY)
- find_package(ImageMagick QUIET COMPONENTS convert)
- include(gmxTestImageMagick)
- GMX_TEST_IMAGEMAGICK(IMAGE_CONVERT_POSSIBLE)
- # TODO: Resolve circular dependency between docs, gromacs, and python_packaging
- add_subdirectory(docs)
- add_subdirectory(share)
- add_subdirectory(scripts)
-endif()
+find_package(ImageMagick QUIET COMPONENTS convert)
+include(gmxTestImageMagick)
+GMX_TEST_IMAGEMAGICK(IMAGE_CONVERT_POSSIBLE)
+# TODO: Resolve circular dependency between docs, gromacs, and python_packaging
+add_subdirectory(docs)
+add_subdirectory(share)
+add_subdirectory(scripts)
add_subdirectory(api)
add_subdirectory(src)
add_subdirectory(tests)
endif()
-if(GMX_PYTHON_PACKAGE AND NOT GMX_BUILD_MDRUN_ONLY)
+if(GMX_PYTHON_PACKAGE)
add_subdirectory(python_packaging)
endif()
--- /dev/null
+#!/usr/bin/env bash
+#
+# Build, install, and test the gmxapi 0.2 Python package developed with
+# GROMACS 2021.
+#
+# This script assumes an activated Python venv with the
+# gmxapi dependencies already installed, with `python` resolvable by the shell
+# to the appropriate Python interpreter.
+#
+# This script is intended to support automated GROMACS testing infrastructure,
+# and may be removed without notice.
+#
+# WARNING: This script assumes OpenMPI mpiexec. Syntax for launch wrappers from
+# other implementations will need different syntax, and we should get a
+# MPIRUNNER from the environment, or something.
+
+# Make sure the script errors if any commands error.
+set -e
+
+# Create "sdist" source distribution archive.
+pushd python_packaging/src
+ # TODO: Remove extraneous environment variable with resolution of #3273
+ # Ref: https://redmine.gromacs.org/issues/3273
+ GMXTOOLCHAINDIR=$INSTALL_DIR/share/cmake/gromacs \
+ python setup.py sdist
+ # TODO: Identify SDIST
+
+ # Build and install from sdist.
+ # Note that tool chain may be provided differently in GROMACS 2020 and 2021.
+ GMXTOOLCHAINDIR=$INSTALL_DIR/share/cmake/gromacs \
+ python -m pip install \
+ --no-cache-dir \
+ --no-deps \
+ --no-index \
+ --no-build-isolation \
+ dist/gmxapi*
+ # TODO: Build and install from $SDIST instead of wildcard.
+
+popd
+
+# Run Python unit tests.
+python -m pytest python_packaging/src/test --junitxml=$PY_UNIT_TEST_XML --threads=2
+
+# Note: Multiple pytest processes getting --junitxml output file argument
+# may cause problems, so we set the option on only one of the launched processes.
+# See also Multiple Instruction Multiple Data Model for OpenMPI mpirun:
+# https://www.open-mpi.org/doc/v3.0/man1/mpiexec.1.php
+PROGRAM=(`which python` -m mpi4py -m pytest \
+ -p no:cacheprovider \
+ $PWD/python_packaging/src/test \
+ --threads=1)
+# shellcheck disable=SC2068
+if [ -x `which mpiexec` ]; then
+ PYTHONDONTWRITEBYTECODE=1 \
+ mpiexec --allow-run-as-root \
+ -x OMP_NUM_THREADS=1 \
+ --mca opal_warn_on_missing_libcuda 0 \
+ --mca orte_base_help_aggregate 0 \
+ -n 1 ${PROGRAM[@]} --junitxml=$PLUGIN_MPI_TEST_XML : \
+ -n 1 ${PROGRAM[@]}
+fi
+
+# Run Python acceptance tests.
+python -m pytest python_packaging/test --junitxml=$PY_ACCEPTANCE_TEST_XML --threads=2
+
+# Note: Multiple pytest processes getting --junitxml output file argument
+# may cause problems, so we set the option on only one of the launched processes.
+# See also Multiple Instruction Multiple Data Model for OpenMPI mpirun:
+# https://www.open-mpi.org/doc/v3.0/man1/mpiexec.1.php
+PROGRAM=(`which python` -m mpi4py -m pytest \
+ -p no:cacheprovider \
+ $PWD/python_packaging/test \
+ --threads=1)
+# shellcheck disable=SC2068
+if [ -x `which mpiexec` ]; then
+ PYTHONDONTWRITEBYTECODE=1 \
+ mpiexec --allow-run-as-root \
+ -x OMP_NUM_THREADS=1 \
+ --mca opal_warn_on_missing_libcuda 0 \
+ --mca orte_base_help_aggregate 0 \
+ -n 1 ${PROGRAM[@]} --junitxml=$PLUGIN_MPI_TEST_XML : \
+ -n 1 ${PROGRAM[@]}
+fi
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
if [ -z "$CLANG_FORMAT" ]
then
echo "Please set the path to clang-format using the git hook"
- echo "git config hooks.clangformatpath /path/to/clang-format"
+ echo "git config hooks.clangformatpath /path/to/clang-format-11"
echo "or by setting an environment variable, e.g."
- echo "CLANG_FORMAT=/path/to/clang-format"
+ echo "CLANG_FORMAT=/path/to/clang-format-11"
echo "See docs/dev-manual/code-formatting.rst for how to get clang-format."
exit 2
fi
if ! which "$CLANG_FORMAT" 1>/dev/null
then
- echo "clang-format not found: $CLANG_FORMAT"
+ echo "clang-format-11 not found: $CLANG_FORMAT"
exit 2
fi
fi
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2020, by the GROMACS development team, led by
+# Copyright (c) 2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
echo "Please set the path to run-clang-tidy using the git hook"
echo "git config hooks.runclangtidypath /path/to/run-clang-tidy-9.py"
echo "or by setting an environment variable, e.g."
- echo "RUN_CLANG_TIDY=/path/to/run-clang-tidy-9.py"
+ echo "RUN_CLANG_TIDY=/path/to/run-clang-tidy-11.py"
exit 2
fi
if ! which "$RUN_CLANG_TIDY" 1>/dev/null
then
- echo "run-clang-tidy-9.py not found: $RUN_CLANG_TIDY"
+ echo "run-clang-tidy-11.py not found: $RUN_CLANG_TIDY"
exit 2
fi
fi
args[${#args[@]}]="--gcc 8 --cuda 11.0 --clfft --mpi openmpi"
args[${#args[@]}]="--gcc 7 --cuda 10.2 --clfft --mpi openmpi --ubuntu 18.04"
args[${#args[@]}]="--llvm 8 --tsan"
+args[${#args[@]}]="--llvm 11 --tsan"
args[${#args[@]}]="--llvm 8 --cuda 10.0 --clfft --mpi openmpi"
args[${#args[@]}]="--llvm 8 --cuda 10.1 --clfft --mpi openmpi"
args[${#args[@]}]="--llvm 8 --cuda 11.0 --clfft --mpi openmpi"
args[${#args[@]}]="--llvm 9 --clfft --mpi openmpi --ubuntu 18.04"
args[${#args[@]}]="--oneapi 2021.1.1"
-args[${#args[@]}]="--llvm --doxygen"
+args[${#args[@]}]="--llvm --doxygen --mpi openmpi --venvs 3.7.7"
+args[${#args[@]}]="--llvm 11 --cuda 11.2.1 --hipsycl 2bc21b677a --ubuntu 20.04"
echo "Building the following images."
for arg_string in "${args[@]}"; do
for arg_string in "${args[@]}"; do
# shellcheck disable=SC2086
- tag=$(python3 -m utility $arg_string):release-2021
+ tag=$(python3 -m utility $arg_string)
tags[${#tags[@]}]=$tag
# shellcheck disable=SC2086
python3 $SCRIPT $arg_string | docker build -t $tag -
def get_llvm_packages(args) -> typing.Iterable[str]:
# If we use the package version of LLVM, we need to install extra packages for it.
if (args.llvm is not None) and (args.tsan is None):
- return ['libomp-dev',
- 'libomp5',
- 'clang-format-' + str(args.llvm),
- 'clang-tidy-' + str(args.llvm)]
+ packages = [f'libomp-{args.llvm}-dev',
+ f'libomp5-{args.llvm}',
+ 'clang-format-' + str(args.llvm),
+ 'clang-tidy-' + str(args.llvm)]
+ if args.hipsycl is not None:
+ packages += [f'llvm-{args.llvm}-dev',
+ f'libclang-{args.llvm}-dev',
+ f'lld-{args.llvm}']
+ return packages
else:
return []
def get_compiler(args, compiler_build_stage: hpccm.Stage = None) -> bb_base:
# Compiler
- if args.icc is not None:
- raise RuntimeError('Intel compiler toolchain recipe not implemented yet')
-
if args.llvm is not None:
# Build our own version instead to get TSAN + OMP
if args.tsan is not None:
compiler = compiler_build_stage.runtime(_from='oneapi')
# Prepare the toolchain (needed only for builds done within the Dockerfile, e.g.
# OpenMPI builds, which don't currently work for other reasons)
- oneapi_toolchain = hpccm.toolchain(CC='/opt/intel/oneapi/compiler/latest/linux/bin/intel64/icc',
- CXX='/opt/intel/oneapi/compiler/latest/linux/bin/intel64/icpc')
+ oneapi_toolchain = hpccm.toolchain(CC=f'/opt/intel/oneapi/compiler/{args.oneapi}/linux/bin/intel64/icx',
+ CXX=f'/opt/intel/oneapi/compiler/{args.oneapi}/linux/bin/intel64/icpx')
setattr(compiler, 'toolchain', oneapi_toolchain)
else:
else:
return None
+def get_hipsycl(args):
+ if args.hipsycl is None:
+ return None
+ if args.llvm is None:
+ raise RuntimeError('Can not build hipSYCL without llvm')
+
+ cmake_opts = [f'-DLLVM_DIR=/usr/lib/llvm-{args.llvm}/cmake',
+ f'-DCLANG_EXECUTABLE_PATH=/usr/bin/clang++-{args.llvm}',
+ '-DCMAKE_PREFIX_PATH=/opt/rocm/lib/cmake',
+ '-DWITH_ROCM_BACKEND=ON']
+ if args.cuda is not None:
+ cmake_opts += [f'-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda',
+ '-DWITH_CUDA_BACKEND=ON']
+
+ postinstall = [
+ # https://github.com/illuhad/hipSYCL/issues/361#issuecomment-718943645
+ 'for f in /opt/rocm/amdgcn/bitcode/*.bc; do ln -s "$f" "/opt/rocm/lib/$(basename $f .bc).amdgcn.bc"; done'
+ ]
+ if args.cuda is not None:
+ postinstall += [
+ # https://github.com/illuhad/hipSYCL/issues/410#issuecomment-743301929
+ f'sed s/_OPENMP/__OPENMP_NVPTX__/ -i /usr/lib/llvm-{args.llvm}/lib/clang/*/include/__clang_cuda_complex_builtins.h',
+ # Not needed unless we're building with CUDA 11.x, but no harm in doing always
+ f'ln -s /usr/local/cuda/compat/* /usr/local/cuda/lib64/'
+ ]
+
+ return hpccm.building_blocks.generic_cmake(
+ repository='https://github.com/illuhad/hipSYCL.git',
+ directory='/var/tmp/hipSYCL',
+ prefix='/usr/local', recursive=True, commit=args.hipsycl,
+ cmake_opts=['-DCMAKE_BUILD_TYPE=Release', *cmake_opts],
+ postinstall=postinstall)
def add_tsan_compiler_build_stage(input_args, output_stages: typing.Mapping[str, hpccm.Stage]):
"""Isolate the expensive TSAN preparation stage.
This stage is isolated so that its installed components are minimized in the
final image (chiefly /opt/intel) and its environment setup script can be
sourced. This also helps with rebuild time and final image size.
-
- Note that the ICC compiler inside oneAPI on linux also needs
- gcc to build other components and provide libstdc++.
"""
if not isinstance(output_stages, collections.abc.MutableMapping):
raise RuntimeError('Need output_stages container.')
apt_keys=['https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB'],
apt_repositories=['deb https://apt.repos.intel.com/oneapi all main'],
# Add minimal packages (not the whole HPC toolkit!)
- ospackages=['intel-oneapi-dpcpp-cpp-{}'.format(version),
- 'intel-oneapi-openmp-{}'.format(version),
- 'intel-oneapi-mkl-{}'.format(version),
- 'intel-oneapi-mkl-devel-{}'.format(version)]
+ ospackages=[f'intel-oneapi-dpcpp-cpp-{version}',
+ f'intel-oneapi-openmp-{version}',
+ f'intel-oneapi-mkl-{version}',
+ f'intel-oneapi-mkl-devel-{version}']
)
# Ensure that all bash shells on the final container will have access to oneAPI
oneapi_stage += hpccm.primitives.shell(
- commands=['echo "source /opt/intel/oneapi/setvars.sh" >> /etc/bash.bashrc']
+ commands=['echo "source /opt/intel/oneapi/setvars.sh" >> /etc/bash.bashrc',
+ 'unlink /opt/intel/oneapi/compiler/latest',
+ f'ln -sf /opt/intel/oneapi/compiler/{version} /opt/intel/oneapi/compiler/latest']
)
setattr(oneapi_stage, 'runtime', oneapi_runtime)
pyenv = '$HOME/.pyenv/bin/pyenv'
- py_ver = '{}.{}'.format(major, minor)
- venv_path = '$HOME/venv/py{}'.format(py_ver)
- commands = ['$({pyenv} prefix `{pyenv} whence python{py_ver}`)/bin/python -m venv {path}'.format(
- pyenv=pyenv,
- py_ver=py_ver,
- path=venv_path
- )]
-
- commands.append('{path}/bin/python -m pip install --upgrade pip setuptools'.format(
- path=venv_path
- ))
+ py_ver = f'{major}.{minor}'
+ venv_path = f'$HOME/venv/py{py_ver}'
+ commands = [f'$({pyenv} prefix `{pyenv} whence python{py_ver}`)/bin/python -m venv {venv_path}']
+
+ commands.append(f'{venv_path}/bin/python -m pip install --upgrade pip setuptools')
# Install dependencies for building and testing gmxapi Python package.
# WARNING: Please keep this list synchronized with python_packaging/requirements-test.txt
# TODO: Get requirements.txt from an input argument.
- commands.append("""{path}/bin/python -m pip install --upgrade \
- 'cmake>=3.13' \
+ commands.append(f"""{venv_path}/bin/python -m pip install --upgrade \
+ 'cmake>=3.16.3' \
'flake8>=3.7.7' \
+ 'gcovr>=4.2' \
'mpi4py>=3.0.3' \
'networkx>=2.0' \
'numpy>=1' \
'pip>=10.1' \
+ 'Pygments>=2.2.0' \
'pytest>=3.9' \
'setuptools>=42' \
- 'scikit-build>=0.10'""".format(path=venv_path))
+ 'scikit-build>=0.10' \
+ 'Sphinx>=1.6.3' \
+ 'sphinxcontrib-plantuml>=0.14'""")
# TODO: Remove 'importlib_resources' dependency when Python >=3.7 is required.
if minor == 6:
- commands.append("""{path}/bin/python -m pip install --upgrade \
- 'importlib_resources'""".format(path=venv_path))
+ commands.append(f"""{venv_path}/bin/python -m pip install --upgrade \
+ 'importlib_resources'""")
return commands
"""echo 'eval "$(pyenv init -)"' >> $HOME/.bashrc""",
"""echo 'eval "$(pyenv virtualenv-init -)"' >> $HOME/.bashrc"""])
pyenv = '$HOME/.pyenv/bin/pyenv'
- commands = ['PYTHON_CONFIGURE_OPTS="--enable-shared" {pyenv} install -s {version}'.format(
- pyenv=pyenv,
- version=str(version))]
+ commands = [f'PYTHON_CONFIGURE_OPTS="--enable-shared" {pyenv} install -s {version}']
stage += hpccm.primitives.shell(commands=commands)
commands = prepare_venv(version)
return
output_stages['main'] += hpccm.primitives.shell(
commands=['sed -i \'/\"XPS\"/d;/\"PDF\"/d;/\"PS\"/d;/\"EPS\"/d;/disable ghostscript format types/d\' /etc/ImageMagick-6/policy.xml'])
- output_stages['main'] += hpccm.building_blocks.pip(pip='pip3', packages=['sphinx==1.6.1', 'gcovr'])
if input_args.doxygen == '1.8.5':
doxygen_commit = 'ed4ed873ab0e7f15116e2052119a6729d4589f7a'
output_stages['main'] += hpccm.building_blocks.generic_autotools(
'--static'])
else:
version = input_args.doxygen
- archive_name = 'doxygen-{}.linux.bin.tar.gz'.format(version)
- archive_url = 'https://sourceforge.net/projects/doxygen/files/rel-{}/{}'.format(
- version,
- archive_name
- )
- binary_path = 'doxygen-{}/bin/doxygen'.format(version)
+ archive_name = f'doxygen-{version}.linux.bin.tar.gz'
+ archive_url = f'https://sourceforge.net/projects/doxygen/files/rel-{version}/{archive_name}'
+ binary_path = f'doxygen-{version}/bin/doxygen'
commands = [
'mkdir doxygen && cd doxygen',
- 'wget {}'.format(archive_url),
- 'tar xf {} {}'.format(archive_name, binary_path),
- 'cp {} /usr/local/bin/'.format(binary_path),
+ f'wget {archive_url}',
+ f'tar xf {archive_name} {binary_path}',
+ f'cp {binary_path} /usr/local/bin/',
'cd .. && rm -rf doxygen'
]
output_stages['main'] += hpccm.primitives.shell(commands=commands)
for i, cmake in enumerate(args.cmake):
building_blocks['cmake' + str(i)] = hpccm.building_blocks.cmake(
eula=True,
- prefix='/usr/local/cmake-{}'.format(cmake),
+ prefix=f'/usr/local/cmake-{cmake}',
version=cmake)
# Install additional packages early in the build to optimize Docker build layer cache.
os_packages += _docs_extra_packages
if args.oneapi is not None:
os_packages += ['lsb-release']
+ if args.hipsycl is not None:
+ os_packages += ['libboost-fiber-dev']
building_blocks['extra_packages'] = hpccm.building_blocks.packages(
ospackages=os_packages,
apt_ppas=['ppa:intel-opencl/intel-opencl'],
apt_repositories=['deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ xenial main']
)
+ if args.cuda is not None and args.llvm is not None:
+ # Hack to tell clang what version of CUDA we're using
+ # based on https://github.com/llvm/llvm-project/blob/1fdec59bffc11ae37eb51a1b9869f0696bfd5312/clang/lib/Driver/ToolChains/Cuda.cpp#L43
+ cuda_version_split = args.cuda.split('.')
+ # LLVM requires having the version in x.y.z format, while args.cuda be be either x.y or x.y.z
+ cuda_version_str = '{}.{}.{}'.format(
+ cuda_version_split[0],
+ cuda_version_split[1],
+ cuda_version_split[2] if len(cuda_version_split) > 2 else 0
+ )
+ building_blocks['cuda-clang-workaround'] = hpccm.primitives.shell(commands=[
+ f'echo "CUDA Version {cuda_version_str}" > /usr/local/cuda/version.txt'
+ ])
+
building_blocks['clfft'] = get_clfft(args)
+ building_blocks['hipSYCL'] = get_hipsycl(args)
+
# Add Python environments to MPI images, only, so we don't have to worry
# about whether to install mpi4py.
if args.mpi is not None and len(args.venvs) > 0:
stages['main'] += bb
# We always add Python3 and Pip
- stages['main'] += hpccm.building_blocks.python(python3=True, python2=False, devel=True)
- stages['main'] += hpccm.building_blocks.pip(upgrade=True, pip='pip3',
- packages=['pytest', 'networkx', 'numpy'])
+ stages['main'] += hpccm.building_blocks.python(python3=True, python2=False)
# Add documentation requirements (doxygen and sphinx + misc).
if args.doxygen is not None:
Instead, inherit from it with the *parents* argument to :py:class:`argparse.ArgumentParser`
"""
-parser.add_argument('--cmake', nargs='*', type=str, default=['3.13.0', '3.15.7', '3.17.2'],
+parser.add_argument('--cmake', nargs='*', type=str, default=['3.16.3', '3.17.2', '3.18.4'], # new minimum required versions
help='Selection of CMake version to provide to base image')
compiler_group = parser.add_mutually_exclusive_group()
compiler_group.add_argument('--llvm', type=str, nargs='?', const='7', default=None,
help='Select LLVM compiler tool chain. '
'Some checking is implemented to avoid incompatible combinations')
-compiler_group.add_argument('--icc', type=int, nargs='?', const=19, default=None,
- help='Select Intel compiler tool chain. '
- 'Some checking is implemented to avoid incompatible combinations')
# TODO currently the installation merely gets the latest beta version of oneAPI,
# not a specific version. GROMACS probably doesn't need to address that until
# oneAPI makes an official release. Also, the resulting container is a mix
parser.add_argument('--tsan', type=str, nargs='?', const='llvm', default=None,
help='Build special compiler versions with TSAN OpenMP support')
+parser.add_argument('--hipsycl', type=str, nargs='?', default=None,
+ help='Select hipSYCL repository tag/commit/branch.')
+
parser.add_argument('--clfft', type=str, nargs='?', const='master', default=None,
help='Add external clFFT libraries to the build image')
if version is not None:
elements.append(distro + '-' + version)
break
- for compiler in ('icc', 'llvm', 'gcc'):
+ for compiler in ('llvm', 'gcc'):
version = getattr(configuration, compiler, None)
if version is not None:
elements.append(compiler + '-' + str(version).split('.')[0])
break
- for gpusdk in ('cuda',):
+ for gpusdk in ('cuda', 'hipsycl'):
version = getattr(configuration, gpusdk, None)
if version is not None:
elements.append(gpusdk + '-' + version)
if [ -z "$runclangtidy_path" ]
then
echo "Please set the path to run-clang-tidy using 'git config hooks.runclangtidypath'."
- echo "Note that you need at least clang-tidy-9."
+ echo "Note that you should use clang-tidy-11 to get the same checking as in CI."
exit 1
fi
export RUN_CLANG_TIDY="$runclangtidy_path"
- .variables:default
- .rules:nightly-only-for-release
cache: {}
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs
stage: configure-build
variables:
KUBERNETES_CPU_LIMIT: 1
- .variables:default
- .rules:merge-and-post-merge-acceptance
cache: {}
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs
stage: configure-build
variables:
KUBERNETES_CPU_LIMIT: 1
KUBERNETES_CPU_REQUEST: 1
KUBERNETES_MEMORY_REQUEST: 2Gi
- # Always clone the default version for this branch, 2021 in this case
+ # Always clone the default version for this branch, master in this case
script:
- - export REGTESTBRANCH=release-2021
+ - export REGTESTBRANCH=master
- if [[ ! -z $REGRESSIONTESTBRANCH ]] ; then
export REGTESTBRANCH=$REGRESSIONTESTBRANCH ;
echo "Using $REGTESTBRANCH instead of default" ;
cache: {}
# Docker image uploaded to dockerhub by user eriklindahl
# TODO: Get DockerFile for admin/dockerfiles
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs
stage: release-package
variables:
KUBERNETES_CPU_LIMIT: 1
- if [[ $GROMACS_RELEASE != "true" ]] ; then
REGTESTNAME=$REGTESTNAME-dev ;
fi
- - export REGTESTBRANCH=release-2021
+ - export REGTESTBRANCH=master
- if [[ $CI_COMMIT_REF_NAME == "master" || $CI_COMMIT_REF_NAME == "release-20"[1-2][0-9] ]] ; then
export REGTESTBRANCH=$CI_COMMIT_REF_NAME ;
fi
- .use-ccache
- .before_script:default
- .docs:build
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs
variables:
KUBERNETES_CPU_LIMIT: 4
KUBERNETES_CPU_REQUEST: 2
when: always
expire_in: 1 week
paths:
- - $BUILD_DIR/*log
+ - $BUILD_DIR/*logs
+ - $BUILD_DIR/bin
+ - $BUILD_DIR/lib
- gromacs*tar.gz
archive:build:
variables:
BUILD_DIR: build-package
-release-verify:
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs:release-2021
+checksum-verify:
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs
stage: release-verify
extends:
- .variables:default
KUBERNETES_CPU_LIMIT: 1
KUBERNETES_CPU_REQUEST: 1
KUBERNETES_MEMORY_REQUEST: 2Gi
+ BUILD_DIR: build-package
script:
+ - VALID_BUILD=true
- VERSION=`cat version.json |
python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
- - if [[ $GROMACS_RELEASE != "true" ]] ; then
- VERSION=$VERSION-dev ;
+ - if [[ "$GROMACS_RELEASE" != "true" ]] ; then
+ VERSION="$VERSION"-dev ;
fi
- REGTEST_COMPARE=`cat version.json |
python3 -c "import json,sys; print(json.load(sys.stdin)['regressiontest-md5sum'])"`
- - SOURCENAME=gromacs-$VERSION
- - SOURCETARBALL=$SOURCENAME.tar.gz
- - SOURCE_MD5SUM=`md5sum $SOURCETARBALL | awk '{print $1}'`
- - REGTESTNAME=regressiontests-$VERSION
- - REGTESTTARBALL=$REGTESTNAME.tar.gz
- - REGTEST_MD5SUM=`md5sum $REGTESTTARBALL | awk '{print $1}'`
+ - SOURCENAME=gromacs-"$VERSION"
+ - SOURCETARBALL="$SOURCENAME".tar.gz
+ - SOURCE_MD5SUM=`md5sum "$SOURCETARBALL" | awk '{print $1}'`
+ - REGTESTNAME=regressiontests-"$VERSION"
+ - REGTESTTARBALL="$REGTESTNAME".tar.gz
+ - REGTEST_MD5SUM=`md5sum "$REGTESTTARBALL" | awk '{print $1}'`
- echo "$SOURCETARBALL md5sum = $SOURCE_MD5SUM"
- echo "$REGTESTTARBALL md5sum = $REGTEST_MD5SUM"
- echo "$REGTESTTARBALL reference md5sum = $REGTEST_COMPARE"
- - if [[ $REGTEST_COMPARE != $REGTEST_MD5SUM && $GROMACS_RELEASE == "true" ]] ; then
+ - if [[ "$REGTEST_COMPARE" != "$REGTEST_MD5SUM" && "$GROMACS_RELEASE" == "true" ]] ; then
echo "Mismatch in regressiontest md5sums";
+ VALID_BUILD=false;
+ fi
+ - if [[ "$VALID_BUILD" != "true" ]] ; then
exit 1;
fi
dependencies:
- regressiontests:package
- prepare-release-version
+version-verify:
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs
+ stage: release-verify
+ extends:
+ - .variables:default
+ - .rules:nightly-only-for-release
+ cache: {}
+
+ variables:
+ KUBERNETES_CPU_LIMIT: 1
+ KUBERNETES_CPU_REQUEST: 1
+ KUBERNETES_MEMORY_REQUEST: 2Gi
+ BUILD_DIR: release-doc-builds
+ script:
+ - VALID_BUILD=true
+ - VERSION=`cat version.json |
+ python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
+ - if [[ "$GROMACS_RELEASE" != "true" ]] ; then
+ VERSION="$VERSION"-dev ;
+ fi
+ - VERSION_FROM_BINARY=`"${BUILD_DIR}"/bin/gmx --version | grep "GROMACS version" | awk '{print $3}'`
+ - echo "Version name from CMake = $VERSION"
+ - echo "Version name from binary = $VERSION_FROM_BINARY"
+ - if [[ "$VERSION" != "$VERSION_FROM_BINARY" && "$GROMACS_RELEASE" == "true" ]] ; then
+ echo "Version names don't match";
+ VALID_BUILD=false;
+ fi
+ - if [[ "$VALID_BUILD" != "true" ]] ; then
+ exit 1;
+ fi
+ dependencies:
+ - webpage:dependencies
+ - prepare-release-version
+
archive:nightly-webpage:
extends:
- .webpage:build
- job: webpage:build
variables:
BUILD_DIR: build-docs
+ before_script:
+ - eval $(ssh-agent -s)
+ - echo "$SSH_PRIVATE_KEY" | tr -d '\r' | ssh-add -
+ - mkdir -p ~/.ssh
+ - chmod 700 ~/.ssh
+ - ssh-keyscan manual.gromacs.org > ~/.ssh/known_hosts # Force overwrite the known hosts so we only have that one key in it.
+ - chmod 644 ~/.ssh/known_hosts
script:
- tar czf webpage.tar.gz $BUILD_DIR/docs/html/
+ - rsync --chmod=u+rwX,g+rwX,o+rX -av $BUILD_DIR/docs/html/* $BUILD_DIR/docs/html/.[a-z]* pbauer@manual.gromacs.org:/var/www/manual/nightly/
artifacts:
when: always
- .gromacs:base:configure
- .before_script:default
# TODO (#3480) this should be organized more like the current documentation.py script
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs
stage: configure-build
cache: {}
variables:
mkdir $BUILD_DIR ;
fi
- cd $BUILD_DIR
+ # Running CMake with the venv activated should not be strictly necessary,
+ # but helps to find and cache self-consistent Python and Sphinx details
+ # without additional hinting. Once CMakeCache.txt exists, the later stages
+ # should work fine without reactivating the venv.
+ - source /root/venv/py3.7/bin/activate
- cmake ..
-DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
$CMAKE_COMPILER_SCRIPT
- .before_script:default
- .rules:nightly-only-for-release
# TODO (#3480) this should be organized more like the current documentation.py script
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs
stage: release-configure
cache: {}
variables:
mkdir $RELEASE_BUILD_DIR ;
fi
- cd $RELEASE_BUILD_DIR
+ - source /root/venv/py3.7/bin/activate
- cmake ../$RELEASE_SOURCE/
-DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
$CMAKE_COMPILER_SCRIPT
.docs:build:
# TODO (#3480) this should be organized more like the current documentation.py script
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs
script:
- cd $BUILD_DIR
- cmake --build . --target gmx -- -j8
- .gromacs:base:build
- .before_script:default
# TODO (#3480) this should be organized more like the current documentation.py script
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs
cache: {}
variables:
KUBERNETES_CPU_LIMIT: 4
KUBERNETES_MEMORY_LIMIT: 8Gi
KUBERNETES_EXTENDED_RESOURCE_NAME: ""
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 0
- CACHE_FALLBACK_KEY: "$CI_JOB_NAME-$CI_JOB_STAGE-release-2021"
+ CACHE_FALLBACK_KEY: "$CI_JOB_NAME-$CI_JOB_STAGE-master"
BUILD_DIR: build
INSTALL_DIR: install
CMAKE_GMXAPI_OPTIONS: ""
# Base definition for using oneAPI.
.use-oneapi:base:
variables:
- # Use the HPC variants of icc and icpc so that OpenMP is active
+ # Use the HPC clang-based compiler variants so that OpenMP is active
CMAKE_COMPILER_SCRIPT: -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx -DCMAKE_INCLUDE_PATH=/opt/intel/oneapi/compiler/latest/linux/include/sycl -DCMAKE_PREFIX_PATH=/opt/intel/oneapi/compiler/latest/linux
CMAKE_EXTRA_OPTIONS: -DGMX_FFT_LIBRARY=mkl
before_script:
- mkdir -p ccache
- export CCACHE_BASEDIR=${PWD}
- export CCACHE_DIR=${PWD}/ccache
-
-# Base definition for using the classic Intel compiler
-.use-icc-oneapi:base:
- variables:
- CMAKE_COMPILER_SCRIPT: -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc #-DCMAKE_PREFIX_PATH=/opt/intel/oneapi/compiler/latest/linux
- CMAKE_EXTRA_OPTIONS: -DGMX_FFT_LIBRARY=mkl
- before_script:
- # Necessary to override gitlab default 'set -e' which breaks Intel's
- # setvar.sh script
- - set +e
- - source /opt/intel/oneapi/setvars.sh
- - set -e
- - mkdir -p ccache
-# - export CCACHE_BASEDIR=${PWD}
-# - export CCACHE_DIR=${PWD}/ccache
# OS: Ubuntu oldest supported
# Compiler: Clang
# Build type: Debug
+# CMake: oldest supported
# GPU: no
# SIMD: no
# Scope: configure, build, unit tests
- .use-clang:base
- .rules:basic-push
stage: pre-build
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
KUBERNETES_CPU_LIMIT: 8
KUBERNETES_CPU_REQUEST: 4
KUBERNETES_MEMORY_REQUEST: 8Gi
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-8.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-9-mpi.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-9-release.gitlab-ci.yml'
+ - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-11-cuda-11.2.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-ASAN.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-static-analyzer.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-TSAN.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-UBSAN.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-10.gitlab-ci.yml'
+ - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-10-coverage.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-7-cuda-10.2.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-8-cuda-11.0.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-8-cuda-11.0-release.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-9-release.gitlab-ci.yml'
- - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.icc-2021.1.gitlab-ci.yml'
+ - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.hipsycl-dev.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.oneapi-2021.1.1-opencl.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.oneapi-2021.1.1-opencl-release.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.oneapi-2021.1.1-sycl.gitlab-ci.yml'
--- /dev/null
+# Test goal: Clang-CUDA build
+# Test intents (should change rarely and conservatively):
+# OS: Ubuntu newest supported
+# GPU: Clang CUDA
+# HW: NVIDIA GPU
+# Scope: configure, build, unit tests, regression tests
+# Test implementation choices (free to change as needed):
+# OS: Ubuntu 20.04
+# Build type: RelWithDebInfo
+# Compiler: Clang 11
+# MPI: thread_MPI
+# GPU: Clang CUDA 11.2, CUDA 11.2
+# SIMD: AVX2_256, no kernels
+# FFT: FFTW3
+# Parallelism nt/ntomp: 4/2 (unit tests)
+# Parallelism nt/ntomp: 2/1 (regression tests)
+
+gromacs:clang-11-cuda-11.2:configure:
+ extends:
+ - .gromacs:base:configure
+ - .use-clang:base
+ - .use-cuda
+ - .rules:post-merge-acceptance
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-11-cuda-11.2.1-hipsycl-2bc21b677a
+ variables:
+ CMAKE: /usr/local/cmake-3.17.2/bin/cmake
+ CMAKE_SIMD_OPTIONS: "-DGMX_USE_SIMD_KERNELS=off"
+ CMAKE_EXTRA_OPTIONS: "-DGMX_CLANG_CUDA=ON"
+ CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithDebInfo"
+ COMPILER_MAJOR_VERSION: 11
+
+gromacs:clang-11-cuda-11.2:build:
+ extends:
+ - .variables:default
+ - .gromacs:base:build
+ - .use-clang:base
+ - .use-ccache
+ - .rules:post-merge-acceptance
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-11-cuda-11.2.1-hipsycl-2bc21b677a
+ variables:
+ CMAKE: /usr/local/cmake-3.17.2/bin/cmake
+ needs:
+ - job: gromacs:clang-11-cuda-11.2:configure
+
+gromacs:clang-11-cuda-11.2:test:
+ extends:
+ - .gromacs:base:test
+ - .rules:post-merge-acceptance
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-11-cuda-11.2.1-hipsycl-2bc21b677a
+ variables:
+ CMAKE: /usr/local/cmake-3.17.2/bin/cmake
+ KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
+ KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
+ tags:
+ - k8s-scilifelab
+ needs:
+ - job: gromacs:clang-11-cuda-11.2:build
+
+gromacs:clang-11-cuda-11.2:regressiontest:
+ extends:
+ - .gromacs:base:regressiontest
+ - .rules:post-merge-acceptance
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-11-cuda-11.2.1-hipsycl-2bc21b677a
+ variables:
+ CMAKE: /usr/local/cmake-3.17.2/bin/cmake
+ KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
+ KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
+ REGRESSIONTEST_PME_RANK_NUMBER: 0
+ REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
+ REGRESSIONTEST_OMP_RANK_NUMBER: 1
+ tags:
+ - k8s-scilifelab
+ needs:
+ - job: gromacs:clang-11-cuda-11.2:build
+ - job: regressiontests:prepare
\ No newline at end of file
- .use-clang:base
- .use-cuda
- .rules:merge-and-post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
CMAKE_SIMD_OPTIONS: "-DGMX_USE_SIMD_KERNELS=off"
CMAKE_EXTRA_OPTIONS: "-DGMX_CLANG_CUDA=ON"
CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithDebInfo"
- .use-clang:base
- .use-ccache
- .rules:merge-and-post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
needs:
- job: gromacs:clang-8-cuda-10.0:configure
extends:
- .gromacs:base:test
- .rules:post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
tags:
extends:
- .gromacs:base:regressiontest
- .rules:post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
REGRESSIONTEST_PME_RANK_NUMBER: 0
- .use-clang:base
- .use-cuda
- .rules:nightly-only-for-release
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.1:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.1
variables:
COMPILER_MAJOR_VERSION: 8
RELEASE_BUILD_DIR: release-builds-clang
stage: release-build
variables:
BUILD_DIR: release-builds-clang
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.1:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.1
needs:
- job: gromacs:clang-8-cuda-10.1:release:configure
- .gromacs:base:test
- .rules:nightly-only-for-release
stage: release-tests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.1:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.1
variables:
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
- .gromacs:base:regressiontest
- .rules:nightly-only-for-release
stage: release-tests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.1:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.1
variables:
BUILD_DIR: release-builds-clang
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
- .gromacs:base:configure
- .use-clang:base
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
variables:
COMPILER_MAJOR_VERSION: 8
- .before_script:default
- .use-ccache
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
needs:
- job: gromacs:clang-8:configure
extends:
- .gromacs:base:test
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
needs:
- job: gromacs:clang-8:build
extends:
- .gromacs:base:regressiontest
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
tags:
- k8s-scilifelab
needs:
# SIMD: AVX2_256
# FFT: FFTW3
# Parallelism np/ntomp: 4/2
+# Subcyclecounting: Active
gromacs:clang-9-mpi:configure:
extends:
- .use-clang:base
- .use-mpi
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.17.2/bin/cmake
COMPILER_MAJOR_VERSION: 9
CMAKE_PRECISION_OPTIONS: -DGMX_DOUBLE=ON
+ CMAKE_EXTRA_OPTIONS: -DGMX_CYCLE_SUBCOUNTERS=ON
gromacs:clang-9-mpi:build:
# Test using configuration: gromacs:clang-9-mpi:configure
- .before_script:default
- .use-ccache
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.17.2/bin/cmake
needs:
- job: gromacs:clang-9-mpi:configure
extends:
- .gromacs:base:test
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.17.2/bin/cmake
tags:
- k8s-scilifelab
needs:
extends:
- .gromacs:base:regressiontest
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.17.2/bin/cmake
REGRESSIONTEST_DOUBLE: "-double"
REGRESSIONTEST_PARALLEL: "-np"
tags:
- .use-clang:base
- .use-mpi
- .rules:nightly-only-for-release
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
COMPILER_MAJOR_VERSION: 9
RELEASE_BUILD_DIR: release-builds-clang
CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
- .rules:nightly-only-for-release
stage: release-build
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
BUILD_DIR: release-builds-clang
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
needs:
- job: gromacs:clang-9:release:configure
- .gromacs:base:test
- .rules:nightly-only-for-release
stage: release-tests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
BUILD_DIR: release-builds-clang
needs:
- job: gromacs:clang-9:release:configure
- .gromacs:base:regressiontest
- .rules:nightly-only-for-release
stage: release-tests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
BUILD_DIR: release-builds-clang
REGRESSIONTEST_DOUBLE: "-double"
REGRESSIONTEST_PARALLEL: "-np"
# Scope: configure, build, unit tests, regression tests
# Test implementation choices (free to change as needed):
# OS: Ubuntu 18.04
-# Compiler: Clang 8
+# Compiler: Clang 11
# MPI: thread_MPI
# SIMD: AVX2_256
# FFT: FFTW3
- .gromacs:base:configure
- .use-clang:base
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
- COMPILER_MAJOR_VERSION: 8
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
+ COMPILER_MAJOR_VERSION: 11
CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=ASAN"
gromacs:clang-ASAN:build:
- .use-clang:base
- .use-ccache
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
tags:
- k8s-scilifelab
needs:
- .gromacs:base:test
- .use-clang:base
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
CTEST_RUN_MODE: "ExperimentalMemCheck"
tags:
- k8s-scilifelab
- .gromacs:base:regressiontest
- .use-clang:base
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
tags:
- k8s-scilifelab
needs:
# Scope: configure, build, unit tests, regression tests
# Test implementation choices (free to change as needed):
# OS: Ubuntu 18.04
-# Compiler: Clang 8
+# Compiler: Clang 11
# MPI: thread_MPI
# SIMD: AVX2_256
# FFT: FFTW3
- .gromacs:base:configure
- .use-clang:base
- .rules:merge-and-post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
- COMPILER_MAJOR_VERSION: 8
+ CMAKE: /usr/local/cmake-3.17.2/bin/cmake
+ COMPILER_MAJOR_VERSION: 11
CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=TSAN"
gromacs:clang-TSAN:build:
- .use-clang:base
- .use-ccache
- .rules:merge-and-post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.17.2/bin/cmake
needs:
- job: gromacs:clang-TSAN:configure
extends:
- .gromacs:base:test
- .rules:post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.17.2/bin/cmake
needs:
- job: gromacs:clang-TSAN:build
extends:
- .gromacs:base:regressiontest
- .rules:post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.17.2/bin/cmake
tags:
- k8s-scilifelab
needs:
# Scope: configure, build, unit tests
# Test implementation choices (free to change as needed):
# OS: Ubuntu 18.04
-# Compiler: Clang 8
+# Compiler: Clang 11
# MPI: thread_MPI
# SIMD: AVX2_256
# FFT: FFTW3
- .gromacs:base:configure
- .use-clang:base
- .rules:merge-and-post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
- COMPILER_MAJOR_VERSION: 8
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
+ COMPILER_MAJOR_VERSION: 11
CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=UBSAN"
gromacs:clang-UBSAN:build:
- .use-clang:base
- .use-ccache
- .rules:merge-and-post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
tags:
- k8s-scilifelab
needs:
- .gromacs:base:test
- .use-clang:base
- .rules:post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
tags:
- k8s-scilifelab
needs:
- .gromacs:base:configure
- .use-clang:base
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
CMAKE_COMPILER_SCRIPT: "-DCMAKE_CXX_COMPILER=/usr/local/libexec/c++-analyzer -DCMAKE_C_COMPILER=gcc"
CMAKE_EXTRA_OPTIONS: "-DGMX_CLANG_ANALYZER=ON -DGMX_OPENMP=OFF -DGMX_USE_RDTSCP=OFF -DGMX_FFT_LIBRARY=fftpack -DGMX_DEVELOPER_BUILD=ON"
CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
- .use-clang:base
- .use-ccache
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
tags:
- k8s-scilifelab
needs:
--- /dev/null
+# Test goal: code coverage with newest GCC
+# Test intents (should change rarely and conservatively):
+# OS: Ubuntu newest supported
+# Compiler: GCC newest supported
+# GPU: no
+# Scope: configure, build, unit tests, coverage
+# Test implementation choices (free to change as needed):
+# OS: Ubuntu 20.04
+# Build type: Debug
+# Compiler: GCC 10
+# MPI: thread_MPI
+# SIMD: AVX2_256
+# Parallelism nt/ntomp: 4/2 (unit tests)
+
+gromacs:gcc-10:coverage:configure:
+ extends:
+ - .gromacs:base:configure
+ - .use-gcc:base
+ - .rules:post-merge-acceptance
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10
+ variables:
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
+ CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
+ CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_FOR_COVERAGE=ON"
+ COMPILER_MAJOR_VERSION: 10
+
+gromacs:gcc-10:coverage:build:
+ extends:
+ - .variables:default
+ - .gromacs:base:build
+ - .before_script:default
+ - .use-ccache
+ - .rules:post-merge-acceptance
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10
+ variables:
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
+ needs:
+ - job: gromacs:gcc-10:coverage:configure
+
+gromacs:gcc-10:coverage:test:
+ extends:
+ - .gromacs:base:test
+ - .rules:post-merge-acceptance
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10
+ variables:
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
+ tags:
+ - k8s-scilifelab
+ needs:
+ - job: gromacs:gcc-10:coverage:build
+ artifacts:
+ paths:
+ - $BUILD_DIR
+
+gromacs:coverage:analyse:
+ variables:
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
+ VENVPATH: "/root/venv/py3.7"
+ GCOVR_GENERAL_OPTIONS: "-r ../ /. --gcov-executable=gcov-10 --exclude-unreachable-branches --exclude-throw-branches -j$KUBERNETES_CPU_LIMIT"
+ GCOVR_EXCLUDE_OPTIONS: "--exclude-directories '^src/external/.*' --exclude-directories '^src/gromacs/selection/.*' --exclude-directories '.*tests.*"
+ extends:
+ - .variables:default
+ - .rules:post-merge-acceptance
+ stage: post-test
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10
+ needs:
+ - job: gromacs:gcc-10:coverage:build
+ - job: gromacs:gcc-10:coverage:test
+
+ tags:
+ - k8s-scilifelab
+ script:
+ - echo ${GCOVR_GENERAL_OPTIONS}
+ - echo ${GCOVR_EXCLUDE_OPTIONS}
+ - source $VENVPATH/bin/activate
+ - mkdir public
+ - outputdir=`pwd`/public
+ - cd $BUILD_DIR
+ # run gcovr to write to stdout for GitLab pipeline grep.
+ - gcovr ${GCOVR_GENERAL_OPTIONS} ${GCOVR_EXCLUDE_OPTIONS}
+ # run gcovr to generate xml output. keep the generated files to produce the html output later.
+ # the invocations need to be separate due to a crash in gcovr where files can not be found.
+ - gcovr ${GCOVR_GENERAL_OPTIONS} ${GCOVR_EXCLUDE_OPTIONS} --xml $outputdir/cobertura-coverage.xml --xml-pretty --keep
+ # final gcovr run, using the generated files to produce nice looking html output
+ - gcovr ${GCOVR_GENERAL_OPTIONS} ${GCOVR_EXCLUDE_OPTIONS} --html $outputdir/coverage.html --use-gcov-files
+ artifacts:
+ paths:
+ - public/
+ reports:
+ cobertura: public/cobertura-coverage.xml
- .use-gcc:base
- .use-opencl
- .rules:merge-and-post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON"
COMPILER_MAJOR_VERSION: 10
- .before_script:default
- .use-ccache
- .rules:merge-and-post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
needs:
- job: gromacs:gcc-10:configure
extends:
- .gromacs:base:test
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
extends:
- .gromacs:base:regressiontest
- .rules:post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
REGRESSIONTEST_PME_RANK_NUMBER: 0
- .use-gcc:base
- .use-cuda
- .rules:merge-and-post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.17.2/bin/cmake
CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
COMPILER_MAJOR_VERSION: 7
- .before_script:default
- .use-ccache
- .rules:merge-and-post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.17.2/bin/cmake
needs:
- job: gromacs:gcc-7-cuda-10.2:configure
extends:
- .gromacs:base:test
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.17.2/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
tags:
extends:
- .gromacs:base:test
- .rules:post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.17.2/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
GMX_GPU_DD_COMMS: 1
extends:
- .gromacs:base:regressiontest
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.17.2/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
REGRESSIONTEST_PME_RANK_NUMBER: 0
extends:
- .gromacs:base:regressiontest
- .rules:post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.17.2/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 2
REGRESSIONTEST_PME_RANK_NUMBER: 0
extends:
- .gromacs:base:regressiontest
- .rules:post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2
variables:
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 2
-# Test goal: GCC with newest CUDA; Mdrun-only build
+# Test goal: GCC with newest CUDA
# Test intents (should change rarely and conservatively):
# OS: Ubuntu oldest supported
# GPU: CUDA newest supported
# HW: NVIDIA GPU
-# Features: Mdrun-only build
+# CMake: oldest supported
# Scope: configure, build, unit tests
# Test implementation choices (free to change as needed):
# OS: Ubuntu 18.04
- .use-mpi
- .use-cuda
- .rules:nightly-only-for-release
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
COMPILER_MAJOR_VERSION: 8
RELEASE_BUILD_DIR: release-builds-gcc
- CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_MDRUN_ONLY=ON"
CMAKE_BUILD_TYPE_OPTIONS : "-DCMAKE_BUILD_TYPE=RelWithAssert"
CMAKE_REGRESSIONTEST_OPTIONS: ""
dependencies:
- .rules:nightly-only-for-release
stage: release-build
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
BUILD_DIR: release-builds-gcc
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
needs:
- job: gromacs:gcc-8-cuda-11.0:release:configure
- .gromacs:base:test
- .rules:nightly-only-for-release
stage: release-tests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
BUILD_DIR: release-builds-gcc
- .use-cuda
- .use-mpi
- .rules:merge-and-post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
COMPILER_MAJOR_VERSION: 8
- .before_script:default
- .use-ccache
- .rules:merge-and-post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
needs:
- job: gromacs:gcc-8-cuda-11.0:configureMPI
extends:
- .gromacs:base:regressiontest
- .rules:post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 2
REGRESSIONTEST_PME_RANK_NUMBER: 0
# MPI: thread_MPI
# SIMD: AVX2_256
# FFT: FFTW3
-# Parallelism nt/ntomp: 4/2
+# Parallelism nt/ntomp: 4/2 (unit tests)
+# Parallelism nt/ntomp: 2/1 (regression tests)
gromacs:gcc-9:release:configure:
extends:
- .use-gcc:base
- .use-opencl
- .rules:nightly-only-for-release
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-9:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-9
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
COMPILER_MAJOR_VERSION: 9
RELEASE_BUILD_DIR: release-builds-gcc
CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
- .rules:nightly-only-for-release
stage: release-build
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
BUILD_DIR: release-builds-gcc
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-9:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-9
needs:
- job: gromacs:gcc-9:release:configure
- .gromacs:base:test
- .rules:nightly-only-for-release
stage: release-tests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-9:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-9
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
BUILD_DIR: release-builds-gcc
KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
- .gromacs:base:regressiontest
- .rules:nightly-only-for-release
stage: release-tests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-9:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-9
variables:
- CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
BUILD_DIR: release-builds-gcc
KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
+ REGRESSIONTEST_PME_RANK_NUMBER: 0
+ REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
+ REGRESSIONTEST_OMP_RANK_NUMBER: 1
LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
tags:
- k8s-scilifelab
--- /dev/null
+# Test goal: build with hipSYCL (both CUDA and ROCm backends) to check SYCL code compatibility
+# Test intents (should change rarely and conservatively):
+# OS: Ubuntu newest supported
+# Compiler: Clang newest supported
+# GPU: hipSYCL
+# Scope: configure, build
+# Test implementation choices (free to change as needed):
+# OS: Ubuntu 20.04
+# Build type: RelWithAssert
+# Compiler: Clang 11
+# MPI: thread_MPI
+# SIMD: AVX2_256
+
+gromacs:hipsycl-dev:configure:
+ extends:
+ - .gromacs:base:configure
+ - .use-clang:base
+ - .use-sycl
+ - .rules:merge-and-post-merge-acceptance
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-11-cuda-11.2.1-hipsycl-2bc21b677a
+ variables:
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
+ CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
+ CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
+ CMAKE_GPU_OPTIONS: "-DGMX_GPU=SYCL -DGMX_SYCL_HIPSYCL=ON -DHIPSYCL_TARGETS='cuda:sm_60,sm_61,sm_70,sm_75;hip:gfx900'"
+ # Unset COMPILER_LAUNCHER (previously set to ccache) because it conflicts with hipSYCL's syclcc-launcher
+ CMAKE_EXTRA_OPTIONS: "-DCMAKE_C_COMPILER_LAUNCHER= -DCMAKE_CXX_COMPILER_LAUNCHER="
+ COMPILER_MAJOR_VERSION: 11
+
+gromacs:hipsycl-dev:build:
+ extends:
+ - .variables:default
+ - .gromacs:base:build
+ - .before_script:default
+ # Not using ccache because it plays poorly with syclcc-launcher
+ - .rules:merge-and-post-merge-acceptance
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-11-cuda-11.2.1-hipsycl-2bc21b677a
+ variables:
+ CMAKE: /usr/local/cmake-3.18.4/bin/cmake
+ tags:
+ - k8s-scilifelab
+ needs:
+ - job: gromacs:hipsycl-dev:configure
+
+++ /dev/null
-# Test goal: Newest ICC CPU-only build
-# Test intents (should change rarely and conservatively):
-# OS: Ubuntu oldest supported
-# Compiler: ICC newest supported
-# FFT: MKL
-# GPU: no
-# Scope: configure, build, unit tests, regression tests
-# Test implementation choices (free to change as needed):
-# OS: Ubuntu 18.04
-# Build type: Debug
-# Compiler: ICC 2021.1
-# MPI: thread_MPI
-# SIMD: AVX2_256
-# Parallelism nt/ntomp: 4/2
-
-gromacs:icc-2021.1:configure:
- # Test SIMD: AVX2_256
- # Test FFT: MKL
- # Test scope: configure
- extends:
- - .gromacs:base:configure
- - .use-icc-oneapi:base
- - .rules:merge-and-post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1:release-2021
- variables:
- CMAKE: /usr/local/cmake-3.17.2/bin/cmake
- COMPILER_MAJOR_VERSION: 2021
-
-gromacs:icc-2021.1:build:
- extends:
- - .variables:default
- - .gromacs:base:build
- - .use-icc-oneapi:base
- - .rules:post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1:release-2021
- variables:
- CMAKE: /usr/local/cmake-3.17.2/bin/cmake
- needs:
- - job: gromacs:icc-2021.1:configure
-
-gromacs:icc-2021.1:test:
- extends:
- - .gromacs:base:test
- - .use-icc-oneapi:base
- - .rules:post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1:release-2021
- variables:
- CMAKE: /usr/local/cmake-3.17.2/bin/cmake
- needs:
- - job: gromacs:icc-2021.1:build
-
-gromacs:icc-2021.1:regressiontest:
- extends:
- - .gromacs:base:regressiontest
- - .use-icc-oneapi:base
- - .rules:post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1:release-2021
- variables:
- CMAKE: /usr/local/cmake-3.17.2/bin/cmake
- needs:
- - job: gromacs:icc-2021.1:build
- - job: regressiontests:prepare
-
- .use-oneapi:base
- .use-opencl
- .rules:nightly-only-for-release
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
COMPILER_MAJOR_VERSION: 2021
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
BUILD_DIR: release-builds-oneapi
COMPILER_MAJOR_VERSION: 2021
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1
needs:
- job: gromacs:oneapi-2021.1.1-opencl:release:configure
- .use-oneapi:base
- .rules:nightly-only-for-release
stage: release-tests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
BUILD_DIR: release-builds-oneapi
- .use-oneapi:base
- .rules:nightly-only-for-release
stage: release-tests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
BUILD_DIR: release-builds-oneapi
- .use-oneapi:base
- .use-opencl
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
COMPILER_MAJOR_VERSION: 2021
- .use-ccache
- .use-oneapi:base
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
needs:
- .gromacs:base:test
- .use-oneapi:base
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
needs:
- .gromacs:base:regressiontest
- .use-oneapi:base
- .rules:merge-requests
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
needs:
- .use-oneapi:base
- .use-sycl
- .rules:merge-and-post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
COMPILER_MAJOR_VERSION: 2021
- .use-ccache
- .use-oneapi:base
- .rules:merge-and-post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
needs:
- .gromacs:base:test
- .use-oneapi:base
- .rules:post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
needs:
- .gromacs:base:regressiontest
- .use-oneapi:base
- .rules:post-merge-acceptance
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1.1
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
needs:
- .gromacs:base:configure
- .use-clang:base
- .rules:basic-push
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
- COMPILER_MAJOR_VERSION: 9
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
+ COMPILER_MAJOR_VERSION: 11
BUILD_DIR: build-clang-tidy
CMAKE_EXTRA_OPTIONS: -DCLANG_TIDY=clang-tidy-$COMPILER_MAJOR_VERSION -DGMX_CLANG_TIDY=ON -DGMX_COMPILER_WARNINGS=ON -DCMAKE_EXPORT_COMPILE_COMMANDS=ON
- .gromacs:base:configure
- .use-clang:base
- .rules:nightly-not-for-release
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
- COMPILER_MAJOR_VERSION: 9
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
+ COMPILER_MAJOR_VERSION: 11
BUILD_DIR: build-clang-tidy
CMAKE_EXTRA_OPTIONS: -DCLANG_TIDY=clang-tidy-$COMPILER_MAJOR_VERSION -DGMX_CLANG_TIDY=ON -DGMX_COMPILER_WARNINGS=ON
- .variables:default
- .rules:nightly-not-for-release
stage: source-check
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
needs:
- job: clang-tidy:configure-schedule
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
BUILD_DIR: build-clang-tidy
clang-tidy:test:
- .variables:default
- .rules:basic-push
stage: source-check
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
needs:
- job: clang-tidy:configure-push
variables:
- CMAKE: /usr/local/cmake-3.15.7/bin/cmake
- COMPILER_MAJOR_VERSION: 9
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
+ COMPILER_MAJOR_VERSION: 11
BUILD_DIR: build-clang-tidy
EXTRA_INSTALLS: clang-tidy-$COMPILER_MAJOR_VERSION
KUBERNETES_CPU_LIMIT: 4
# Make sure that a Python interpreter can be found for `/bin/env python`
- test -x /usr/bin/python || update-alternatives --install /usr/bin/python python /usr/bin/python3 1
# TODO (issue #3272) `master` is not appropriate for use on release-xxxx branches, how should we handle that?
- - REV=$(git fetch -q https://gitlab.com/gromacs/gromacs.git release-2021 && git show -s --pretty=format:"%h" `git merge-base FETCH_HEAD HEAD`)
+ - REV=$(git fetch -q https://gitlab.com/gromacs/gromacs.git master && git show -s --pretty=format:"%h" `git merge-base FETCH_HEAD HEAD`)
- HEAD_REV=$(git show -s --pretty=format:"%h" HEAD)
- if [[ "$REV" == "$HEAD_REV" ]] ; then
REV="HEAD~1" ;
- .rules:basic-push
cache: {}
stage: pre-build
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
variables:
- COMPILER_MAJOR_VERSION: 7
+ COMPILER_MAJOR_VERSION: 11
KUBERNETES_CPU_LIMIT: 1
KUBERNETES_CPU_REQUEST: 1
KUBERNETES_MEMORY_REQUEST: 2Gi
EXTRA_INSTALLS: clang-format-$COMPILER_MAJOR_VERSION
script:
- - REV=$(git fetch -q https://gitlab.com/gromacs/gromacs.git release-2021 && git show -s --pretty=format:"%h" `git merge-base FETCH_HEAD HEAD`)
+ # TODO (issue #3272) `master` is not appropriate for use on release-xxxx branches, how should we handle that?
+ - REV=$(git fetch -q https://gitlab.com/gromacs/gromacs.git master && git show -s --pretty=format:"%h" `git merge-base FETCH_HEAD HEAD`)
- HEAD_REV=$(git show -s --pretty=format:"%h" HEAD)
- if [[ "$REV" == "$HEAD_REV" ]] ; then
REV="HEAD~1" ;
- .rules:basic-push
cache: {}
stage: pre-build
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-11-tsan
variables:
KUBERNETES_CPU_LIMIT: 1
KUBERNETES_CPU_REQUEST: 1
KUBERNETES_MEMORY_REQUEST: 2Gi
script:
- - REV=$(git fetch -q https://gitlab.com/gromacs/gromacs.git release-2021 && git show -s --pretty=format:"%h" `git merge-base FETCH_HEAD HEAD`)
+ - REV=$(git fetch -q https://gitlab.com/gromacs/gromacs.git master && git show -s --pretty=format:"%h" `git merge-base FETCH_HEAD HEAD`)
- HEAD_REV=$(git show -s --pretty=format:"%h" HEAD)
- if [[ "$REV" == "$HEAD_REV" ]] ; then
REV="HEAD~1" ;
- .variables:default
- .use-clang:base
stage: test
- image: ${CI_REGISTRY}/gromacs/gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
variables:
KUBERNETES_CPU_LIMIT: 2
KUBERNETES_CPU_REQUEST: 2
extends:
- .variables:default
- .use-clang:base
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10
stage: test
variables:
KUBERNETES_CPU_LIMIT: 2
--- /dev/null
+#
+# Jobs to test gmxapi client (Python) packages
+#
+
+.gmxapi-0.2:gcc-10:gmx2021:
+ extends:
+ - .variables:default
+ - .use-clang:base
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10
+ stage: test
+ variables:
+ KUBERNETES_CPU_LIMIT: 2
+ KUBERNETES_CPU_REQUEST: 2
+ KUBERNETES_MEMORY_LIMIT: 2Gi
+ KUBERNETES_MEMORY_REQUEST: 2Gi
+ PY_UNIT_TEST_XML: $CI_PROJECT_DIR/py-JUnitTestResults.xml
+ PY_MPI_UNIT_TEST_XML: $CI_PROJECT_DIR/py-mpi-JUnitTestResults.xml
+ PY_ACCEPTANCE_TEST_XML: $CI_PROJECT_DIR/gmxapi-acceptance-JUnitTestResults.xml
+ PY_MPI_ACCEPTANCE_TEST_XML: $CI_PROJECT_DIR/gmxapi-acceptance-mpi-JUnitTestResults.xml
+ script:
+ - source $INSTALL_DIR/bin/GMXRC
+ - source $VENVPATH/bin/activate && INSTALL_DIR=$PWD/$INSTALL_DIR OMP_NUM_THREADS=1 bash admin/ci-scripts/build-and-test-py-gmxapi-0.2.sh
+ artifacts:
+ reports:
+ junit:
+ - $PY_UNIT_TEST_XML
+ - $PY_MPI_UNIT_TEST_XML
+ - $PY_ACCEPTANCE_TEST_XML
+ - $PY_MPI_ACCEPTANCE_TEST_XML
+ when: always
+ expire_in: 1 week
+ tags:
+ - k8s-scilifelab
+ # The dependency means we need to use the same tag restriction as upstream.
+ needs:
+ - job: gromacs:gcc-10:build
+ artifacts: true
+
+gmxapi-0.2:gcc-10:gmx2021:py-3.6.10:
+ extends:
+ - .gmxapi-0.2:gcc-10:gmx2021
+ - .rules:merge-requests:release-2021
+ variables:
+ VENVPATH: "/root/venv/py3.6"
+ PY_VER: "3.6.10"
+
+gmxapi-0.2:gcc-10:gmx2021:py-3.7.7:
+ extends:
+ - .gmxapi-0.2:gcc-10:gmx2021
+ - .rules:merge-requests:release-2021
+ variables:
+ VENVPATH: "/root/venv/py3.7"
+ PY_VER: "3.7.7"
+
+gmxapi-0.2:gcc-10:gmx2021:py-3.8.2:
+ extends:
+ - .gmxapi-0.2:gcc-10:gmx2021
+ - .rules:merge-requests:release-2021
+ variables:
+ VENVPATH: "/root/venv/py3.8"
+ PY_VER: "3.8.2"
--- /dev/null
+#
+# Jobs to test gmxapi client (Python) packages
+#
+
+.gmxapi-0.3:gcc-10:gmx2022:
+ extends:
+ - .variables:default
+ - .use-clang:base
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10
+ stage: test
+ variables:
+ KUBERNETES_CPU_LIMIT: 2
+ KUBERNETES_CPU_REQUEST: 2
+ KUBERNETES_MEMORY_LIMIT: 2Gi
+ KUBERNETES_MEMORY_REQUEST: 2Gi
+ PY_UNIT_TEST_XML: $CI_PROJECT_DIR/py-JUnitTestResults.xml
+ PY_MPI_UNIT_TEST_XML: $CI_PROJECT_DIR/py-mpi-JUnitTestResults.xml
+ PY_ACCEPTANCE_TEST_XML: $CI_PROJECT_DIR/gmxapi-acceptance-JUnitTestResults.xml
+ PY_MPI_ACCEPTANCE_TEST_XML: $CI_PROJECT_DIR/gmxapi-acceptance-mpi-JUnitTestResults.xml
+ script:
+ - source $INSTALL_DIR/bin/GMXRC
+ - source $VENVPATH/bin/activate && INSTALL_DIR=$PWD/$INSTALL_DIR OMP_NUM_THREADS=1 bash admin/ci-scripts/build-and-test-py-gmxapi-0.3.sh
+ artifacts:
+ reports:
+ junit:
+ - $PY_UNIT_TEST_XML
+ - $PY_MPI_UNIT_TEST_XML
+ - $PY_ACCEPTANCE_TEST_XML
+ - $PY_MPI_ACCEPTANCE_TEST_XML
+ when: always
+ expire_in: 1 week
+ tags:
+ - k8s-scilifelab
+ # The dependency means we need to use the same tag restriction as upstream.
+ needs:
+ - job: gromacs:gcc-10:build
+ artifacts: true
+
+gmxapi-0.3:gcc-10:gmx2022:py-3.7.7:
+ extends:
+ - .gmxapi-0.3:gcc-10:gmx2022
+ - .rules:merge-requests:master
+ variables:
+ VENVPATH: "/root/venv/py3.7"
+ PY_VER: "3.7.7"
+
+gmxapi-0.3:gcc-10:gmx2022:py-3.8.2:
+ extends:
+ - .gmxapi-0.3:gcc-10:gmx2022
+ - .rules:merge-requests:master
+ variables:
+ VENVPATH: "/root/venv/py3.8"
+ PY_VER: "3.8.2"
.rules-element:if-post-merge-acceptance-or-mr-then-always: &if-post-merge-acceptance-or-mr-then-always
if: '$CI_PIPELINE_SOURCE == "merge_request_event" ||
($CI_PIPELINE_SOURCE == "push" &&
- $CI_COMMIT_REF_NAME == "release-2021")'
+ $CI_COMMIT_REF_NAME == "master")'
when: always
# Include job only for post submit push
.rules-element:if-post-merge-acceptance-then-always: &if-post-merge-acceptance-then-always
if: '$CI_PIPELINE_SOURCE == "push" &&
- $CI_COMMIT_REF_NAME == "release-2021"'
+ $CI_COMMIT_REF_NAME == "master"'
when: always
# When composing a rule set, note that the first matching rule is applied.
- *if-schedule-then-always
- *if-mr-then-always
-# Jobs that run for merge requests and schedules for branch `release-2020`,
+# Jobs that run for merge requests and schedules for branch `release-2021`,
# but not when GROMACS_RELEASE is set.
# Excludes non-gromacs projects.
-.rules:merge-requests:release-2020:
+.rules:merge-requests:release-2021:
rules:
- *if-not-gromacs-then-never
- *if-release-then-never
- *if-post-merge-acceptance-then-never
- # This next rule catches "push" and other events in branches other than `release-2020`
- # but allows merge_request_events for merge requests targeting `release-2020`.
+ # This next rule catches "push" and other events in branches other than `release-2021`
+ # but allows merge_request_events for merge requests targeting `release-2021`.
# This rule is before "web" so the web interface won't include jobs that can't succeed
# (and would not ordinarily be run). Such jobs are hard to identify in a way that is
# sufficiently general for a global rules definition.
# If extra coverage is needed through a web-triggered job in merge request branches,
# we could provide an additional short-circuiting rule based on an environment variable
# to be provided through the web interface.
- - if: '$CI_MERGE_REQUEST_TARGET_BRANCH_NAME != "release-2020" && $CI_COMMIT_REF_NAME != "release-2020"'
+ - if: '$CI_MERGE_REQUEST_TARGET_BRANCH_NAME != "release-2021" && $CI_COMMIT_REF_NAME != "release-2021"'
when: never
- *if-web-then-always
- *if-schedule-then-always
- *if-mr-then-always
-# Jobs that run for merge requests and schedules for branch `release-2021`,
+# Jobs that run for merge requests and schedules for branch `release-2020`,
# but not when GROMACS_RELEASE is set.
# Excludes non-gromacs projects.
-.rules:merge-requests:release-2021:
+.rules:merge-requests:release-2020:
rules:
- *if-not-gromacs-then-never
- *if-release-then-never
- *if-post-merge-acceptance-then-never
- # This next rule catches "push" and other events in branches other than `release-2021`
- # but allows merge_request_events for merge requests targeting `release-2021`.
+ # This next rule catches "push" and other events in branches other than `release-2020`
+ # but allows merge_request_events for merge requests targeting `release-2020`.
# This rule is before "web" so the web interface won't include jobs that can't succeed
# (and would not ordinarily be run). Such jobs are hard to identify in a way that is
# sufficiently general for a global rules definition.
# If extra coverage is needed through a web-triggered job in merge request branches,
# we could provide an additional short-circuiting rule based on an environment variable
# to be provided through the web interface.
- - if: '$CI_MERGE_REQUEST_TARGET_BRANCH_NAME != "release-2021" && $CI_COMMIT_REF_NAME != "release-2021"'
+ - if: '$CI_MERGE_REQUEST_TARGET_BRANCH_NAME != "release-2020" && $CI_COMMIT_REF_NAME != "release-2020"'
when: never
- *if-web-then-always
- *if-schedule-then-always
extends:
- .variables:default
- .use-clang:base
- image: ${CI_REGISTRY}/gromacs/gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
stage: test
variables:
KUBERNETES_CPU_LIMIT: 2
extends:
- .variables:default
- .use-clang:base
- image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10:release-2021
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10
stage: test
variables:
KUBERNETES_CPU_LIMIT: 2
leak:atoms_to_constraints
leak:atoms_to_settles
leak:balance_fep_lists
-leak:cpp_opts
-leak:dd_init_bondeds
+leak:dd_make_reverse_top
+leak:makeBondedLinks
leak:dd_make_local_constraints
leak:dd_move_f
leak:dd_partition_system
leak:do_edsam
leak:do_inputrec
leak:do_single_flood
-leak:get_ir
-leak:get_zone_pulse_cgs
+leak:get_zone_pulse_groups
leak:gmx::DomainDecompositionBuilder::Impl::build
leak:gmx_check
leak:gmx_make_edi
-leak:gmx_mtop_ilistloop_init
-leak:gmx_pme_init
leak:gmx_pme_receive_f
-leak:init_buffer_flags
-leak:init_disres
leak:init_dfhist_state
leak:init_df_history
+leak:init_disres
leak:init_edsam
leak:init_ekinstate
-leak:init_interaction_const
-leak:init_orires
leak:init_rot
leak:init_swapcoords
leak:make_bondeds_zone
leak:make_dd_indices
leak:make_exclusions_zone
leak:make_fep_list
-leak:make_ljpme_c6grid
leak:make_pull_groups
-leak:make_reverse_top
leak:make_rotation_groups
-leak:make_swap_groups
leak:make_tables
leak:mdoutf_write_to_trajectory_files
# Stack trace does not report a function beyond gmx_srenew_impl, so the file is suppressed instead.
leak:pairlist.cpp
leak:read_rotparams
-leak:set_ddgrid_parameters
leak:set_reference_positions
leak:set_state_entries
leak:visitOption
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# The legacy public API headers may still be installed,
+# but may be removed or changed without warning.
+add_subdirectory(legacy)
# Activate targets for new C++ API components and docs.
-if(GMX_NATIVE_WINDOWS OR GMX_BUILD_MDRUN_ONLY)
+if(GMX_NATIVE_WINDOWS)
# GMXAPI has not been tested in Microsoft environments.
- # GMXAPI relies on libgromacs and is incompatible with an `mdrun`-only build.
# GMXAPI requires position-independent code
set(_GMXAPI_DEFAULT OFF)
else()
endif()
# Activate targets NBLIB
-if(GMX_NATIVE_WINDOWS OR GMX_BUILD_MDRUN_ONLY OR NOT BUILD_SHARED_LIBS OR CMAKE_CXX_COMPILER_ID MATCHES "Intel")
+if(GMX_NATIVE_WINDOWS OR NOT BUILD_SHARED_LIBS)
# NBLIB has not been tested in Microsoft environments.
- # NBLIB relies on libgromacs and is incompatible with an `mdrun`-only build.
# NBLIB requires position-independent code
- # NBLIB causes an ICE in icc 19.1.2.20200623
set(_NBLIB_DEFAULT OFF)
else()
set(_NBLIB_DEFAULT ON)
# be tagged. Official GROMACS releases should be mappable to a distinct gmxapi
# release string. For roadmap details, see https://gitlab.com/gromacs/gromacs/-/issues/2585
set(GMXAPI_MAJOR 0)
-set(GMXAPI_MINOR 2)
+set(GMXAPI_MINOR 3)
set(GMXAPI_PATCH 0)
set(GMXAPI_RELEASE ${GMXAPI_MAJOR}.${GMXAPI_MINOR}.${GMXAPI_PATCH})
# Do not target_link_options(gmxapi PRIVATE ${MPI_LINKER_FLAGS})
# because the root CMakeLists.txt sets CMAKE_SHARED_LINKER_FLAGS.
target_compile_options(gmxapi PUBLIC ${MPI_COMPILE_FLAGS})
- target_link_libraries(gmxapi PUBLIC ${MPI_C_LIBRARIES})
+ target_link_libraries(gmxapi PUBLIC ${MPI_CXX_LIBRARIES})
elseif(GMX_THREAD_MPI)
# GROMACS is built with its internal thread-MPI implementation.
set(_gmx_mpi_type "tmpi")
)
target_link_libraries(gmxapi PRIVATE libgromacs)
+target_link_libraries(gmxapi PRIVATE common)
+# TODO: Explicitly link specific modules: mdlib, mdtypes, utility, commandline
+target_link_libraries(gmxapi PRIVATE legacy_modules)
################################################
@PACKAGE_INIT@
# Refer to CMake docs for information on more elaborate use of this stub file:
# https://cmake.org/cmake/help/v3.4/module/CMakePackageConfigHelpers.html#command:configure_package_config_file
+include(CMakeFindDependencyMacro)
+@_gmxapi_find_dependencies@
include("${CMAKE_CURRENT_LIST_DIR}/gmxapi.cmake")
check_required_components(gmxapi)
set_property(TARGET Gromacs::gmxapi PROPERTY MPI "@_mpi@")
SimulationContext simulationContext(communicator, multiSimDirectoryNames);
- StartingBehavior startingBehavior = StartingBehavior::NewSimulation;
- LogFilePtr logFileGuard = nullptr;
- gmx_multisim_t* ms = simulationContext.multiSimulation_.get();
- std::tie(startingBehavior, logFileGuard) = handleRestart(
- findIsSimulationMasterRank(ms, simulationContext.simulationCommunicator_),
- simulationContext.simulationCommunicator_, ms, options.mdrunOptions.appendingBehavior,
- ssize(options.filenames), options.filenames.data());
+ StartingBehavior startingBehavior = StartingBehavior::NewSimulation;
+ LogFilePtr logFileGuard = nullptr;
+ gmx_multisim_t* ms = simulationContext.multiSimulation_.get();
+ std::tie(startingBehavior, logFileGuard) =
+ handleRestart(findIsSimulationMasterRank(ms, simulationContext.simulationCommunicator_),
+ simulationContext.simulationCommunicator_,
+ ms,
+ options.mdrunOptions.appendingBehavior,
+ ssize(options.filenames),
+ options.filenames.data());
auto builder = MdrunnerBuilder(std::move(mdModules),
compat::not_null<SimulationContext*>(&simulationContext));
builder.addLogFile(logFileGuard.get());
// Note, creation is not mature enough to be exposed in the external API yet.
- launchedSession = createSession(shared_from_this(), std::move(builder),
- std::move(simulationContext), std::move(logFileGuard));
+ launchedSession = createSession(
+ shared_from_this(), std::move(builder), std::move(simulationContext), std::move(logFileGuard));
// Clean up argv once builder is no longer in use
// TODO: Remove long-lived references to argv so this is no longer necessary.
auto& callCounter = manager_->called_.at(name_);
callCounter.store(true);
using pairType = typename decltype(manager_->called_)::value_type;
- if (std::all_of(manager_->called_.cbegin(), manager_->called_.cend(),
- [](const pairType& p) { return p.second.load(); }))
+ if (std::all_of(manager_->called_.cbegin(), manager_->called_.cend(), [](const pairType& p) {
+ return p.second.load();
+ }))
{
*manager_->state_ = gmx::StopSignal::stopAtNextNSStep;
}
{
// We should be able to get a communicator (or subcommunicator) through the
// Context.
- return std::make_unique<SessionImpl>(std::move(context), std::move(runnerBuilder),
- std::move(simulationContext), std::move(logFilehandle));
+ return std::make_unique<SessionImpl>(std::move(context),
+ std::move(runnerBuilder),
+ std::move(simulationContext),
+ std::move(logFilehandle));
}
SessionImpl::SessionImpl(std::shared_ptr<ContextImpl> context,
gmx::SimulationContext&& simulationContext,
gmx::LogFilePtr logFilehandle)
{
- auto newSession = SessionImpl::create(std::move(context), std::move(runnerBuilder),
- std::move(simulationContext), std::move(logFilehandle));
+ auto newSession = SessionImpl::create(std::move(context),
+ std::move(runnerBuilder),
+ std::move(simulationContext),
+ std::move(logFilehandle));
auto launchedSession = std::make_shared<Session>(std::move(newSession));
return launchedSession;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const auto& inputRecord = tprFile->inputRecord();
const auto& writeState = tprFile->state();
const auto& writeTopology = tprFile->molecularTopology();
- write_tpx_state(filename.c_str(), &inputRecord, &writeState, &writeTopology);
+ write_tpx_state(filename.c_str(), &inputRecord, &writeState, writeTopology);
}
TprReadHandle::TprReadHandle(TprContents&& tprFile) :
{
return false;
}
- gmxapicompat::writeTprFile(
- outFile, *gmxapicompat::getMdParams(input), *gmxapicompat::getStructureSource(input),
- *gmxapicompat::getSimulationState(input), *gmxapicompat::getTopologySource(input));
+ gmxapicompat::writeTprFile(outFile,
+ *gmxapicompat::getMdParams(input),
+ *gmxapicompat::getStructureSource(input),
+ *gmxapicompat::getSimulationState(input),
+ *gmxapicompat::getTopologySource(input));
return true;
}
irInstance.nsteps = lround((endTime - run_t) / irInstance.delta_t);
- write_tpx_state(outFile.c_str(), &irInstance, &state, &mtop);
+ write_tpx_state(outFile.c_str(), &irInstance, &state, mtop);
success = true;
return success;
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-# the name of the target operating system
-set(CMAKE_SYSTEM_NAME Linux CACHE STRING "Cross-compiling for Fujitsu Sparc64")
-# Set the identification to the same value we would get on the nodes (uname -m)
-set(CMAKE_SYSTEM_PROCESSOR "s64fx")
+# The legacy installed API consists of headers that are not considered
+# to be maintainable in terms of a stable API specification. These headers
+# will no longer be available to install in a future release.
-set_property(GLOBAL PROPERTY TARGET_SUPPORTS_SHARED_LIBS FALSE)
+# Note: Any usage requirements that should be transitive should be added to
+# this INTERFACE target. Compiler and linker options (that do not need to
+# be propagated when linking to the `common` target) can be added directly
+# to the `common` target.
+add_library(legacy_api INTERFACE)
+target_include_directories(legacy_api INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/include>
+ $<INSTALL_INTERFACE:include>)
-# set the compiler
-set(CMAKE_C_COMPILER fccpx)
-set(CMAKE_CXX_COMPILER FCCpx)
+configure_file(version.h.cmakein include/gromacs/version.h)
-# Prevent CMake from adding GNU-specific linker flags (-rdynamic)
-# A patch has been submitted to make CMake itself handle this in the future
-set(CMAKE_C_COMPILER_ID "Fujitsu" CACHE STRING "Fujitsu C cross-compiler" FORCE)
-set(CMAKE_CXX_COMPILER_ID "Fujitsu" CACHE STRING "Fujitsu C++ cross-compiler" FORCE)
+# Allow an export target for legacy_api since it is a dependency of the
+# installable libgromacs target.
+install(TARGETS legacy_api
+ EXPORT libgromacs
+ INCLUDES DESTINATION include)
-# FindOpenMP.cmake does not try -Kopenmp,but the package will try specific
-# flags based on the compier ID.
-set(OMP_FLAG_Fujitsu "-Kopenmp")
+if(GMX_INSTALL_LEGACY_API)
+ # Install public header directories.
+ install(DIRECTORY include/gromacs
+ DESTINATION include)
+
+ # Install "configured" files from the build tree.
+ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/include/gromacs/version.h
+ DESTINATION include/gromacs)
+endif()
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void write_sto_conf_mtop(const char* outfile,
const char* title,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const rvec x[],
const rvec* v,
PbcType pbcType,
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct t_symtab;
struct t_topology;
enum class PbcType : int;
+enum class PdbRecordType : int;
typedef struct gmx_conect_t* gmx_conect;
*
* Returns the number of characters printed.
*/
-int gmx_fprintf_pdb_atomline(FILE* fp,
- enum PDB_record record,
- int atom_seq_number,
- const char* atom_name,
- char alternate_location,
- const char* res_name,
- char chain_id,
- int res_seq_number,
- char res_insertion_code,
- real x,
- real y,
- real z,
- real occupancy,
- real b_factor,
- const char* element);
+int gmx_fprintf_pdb_atomline(FILE* fp,
+ PdbRecordType record,
+ int atom_seq_number,
+ const char* atom_name,
+ char alternate_location,
+ const char* res_name,
+ char chain_id,
+ int res_seq_number,
+ char res_insertion_code,
+ real x,
+ real y,
+ real z,
+ real occupancy,
+ real b_factor,
+ const char* element);
/* Enumerated value for indexing an uij entry (anisotropic temperature factors) */
enum
*/
TpxFileHeader readTpxHeader(const char* fileName, bool canReadTopologyOnly);
-void write_tpx_state(const char* fn, const t_inputrec* ir, const t_state* state, const gmx_mtop_t* mtop);
+void write_tpx_state(const char* fn, const t_inputrec* ir, const t_state* state, const gmx_mtop_t& mtop);
/* Write a file, and close it again.
*/
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
t_trxstatus* in,
const char* infile,
int natoms,
- const struct gmx_mtop_t* mtop,
+ const gmx_mtop_t* mtop,
gmx::ArrayRef<const int> index,
const char* index_group_name);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2018,2019,2020 by the GROMACS development team.
+ * Copyright (c) 2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return static_cast<int>(rint(x));
}
+//! \brief Check whether \p v is an integer power of 2.
+template<typename T, typename = std::enable_if_t<std::is_integral<T>::value>>
+#if defined(__NVCC__) && !defined(__CUDACC_RELAXED_CONSTEXPR__)
+/* In CUDA 11, a constexpr function cannot be called from a function with incompatible execution
+ * space, unless --expt-relaxed-constexpr flag is set */
+__host__ __device__
+#endif
+ static inline constexpr bool
+ isPowerOfTwo(const T v)
+{
+ return (v > 0) && ((v & (v - 1)) == 0);
+}
+
} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2012,2014,2015,2018,2019, The GROMACS development team.
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_MATH_UNITS_H
+#define GMX_MATH_UNITS_H
+
+#include <cmath>
+
+/*
+ * Physical constants to be used in Gromacs.
+ * No constants (apart from 0, 1 or 2) should
+ * be anywhere else in the code.
+ */
+
+#ifndef M_PI
+# define M_PI 3.14159265358979323846
+#endif
+
+#ifndef M_PI_2
+# define M_PI_2 1.57079632679489661923
+#endif
+
+#ifndef M_2PI
+# define M_2PI 6.28318530717958647692
+#endif
+
+#ifndef M_SQRT2
+# define M_SQRT2 sqrt(2.0)
+#endif
+
+#ifndef M_1_PI
+# define M_1_PI 0.31830988618379067154
+#endif
+
+#ifndef M_FLOAT_1_SQRTPI /* used in GPU kernels */
+/* 1.0 / sqrt(M_PI) */
+# define M_FLOAT_1_SQRTPI 0.564189583547756f
+#endif
+
+#ifndef M_1_SQRTPI
+/* 1.0 / sqrt(M_PI) */
+# define M_1_SQRTPI 0.564189583547756
+#endif
+
+#ifndef M_2_SQRTPI
+/* 2.0 / sqrt(M_PI) */
+# define M_2_SQRTPI 1.128379167095513
+#endif
+
+namespace gmx
+{
+
+constexpr double c_angstrom = 1e-10;
+constexpr double c_kilo = 1e3;
+constexpr double c_nano = 1e-9;
+constexpr double c_pico = 1e-12;
+constexpr double c_nm2A = c_nano / c_angstrom;
+constexpr double c_cal2Joule = 4.184; /* Exact definition of the calorie */
+constexpr double c_electronCharge = 1.602176634e-19; /* Exact definition, Coulomb NIST 2018 CODATA */
+
+constexpr double c_amu = 1.66053906660e-27; /* kg, NIST 2018 CODATA */
+constexpr double c_boltzmann = 1.380649e-23; /* (J/K, Exact definition, NIST 2018 CODATA */
+constexpr double c_avogadro = 6.02214076e23; /* 1/mol, Exact definition, NIST 2018 CODATA */
+constexpr double c_universalGasConstant = c_boltzmann * c_avogadro; /* (J/(mol K)) */
+constexpr double c_boltz = c_universalGasConstant / c_kilo; /* (kJ/(mol K)) */
+constexpr double c_faraday = c_electronCharge * c_avogadro; /* (C/mol) */
+constexpr double c_planck1 = 6.62607015e-34; /* J/Hz, Exact definition, NIST 2018 CODATA */
+constexpr double c_planck = (c_planck1 * c_avogadro / (c_pico * c_kilo)); /* (kJ/mol) ps */
+
+constexpr double c_epsilon0Si = 8.8541878128e-12; /* F/m, NIST 2018 CODATA */
+/* Epsilon in our MD units: (e^2 / Na (kJ nm)) == (e^2 mol/(kJ nm)) */
+constexpr double c_epsilon0 =
+ ((c_epsilon0Si * c_nano * c_kilo) / (c_electronCharge * c_electronCharge * c_avogadro));
+
+constexpr double c_speedOfLight =
+ 2.99792458e05; /* units of nm/ps, Exact definition, NIST 2018 CODATA */
+
+constexpr double c_rydberg = 1.0973731568160e-02; /* nm^-1, NIST 2018 CODATA */
+
+constexpr double c_one4PiEps0 = (1.0 / (4.0 * M_PI * c_epsilon0));
+
+/* Pressure in MD units is:
+ * 1 bar = 1e5 Pa = 1e5 kg m^-1 s^-2 = 1e-28 kg nm^-1 ps^-2 = 1e-28 / amu amu nm^1 ps ^2
+ */
+constexpr double c_barMdunits = (1e5 * c_nano * c_pico * c_pico / c_amu);
+constexpr double c_presfac = 1.0 / c_barMdunits;
+
+/* c_debye2Enm should be (1e-21*c_pico)/(c_speedOfLight*c_electronCharge*c_nano*c_nano),
+ * but we need to factor out some of the exponents to avoid single-precision overflows.
+ */
+constexpr double c_debye2Enm = (1e-15 / (c_speedOfLight * c_electronCharge));
+constexpr double c_enm2Debye = 1.0 / c_debye2Enm;
+
+/* to convert from a acceleration in (e V)/(amu nm) */
+/* c_fieldfac is also Faraday's constant and c_electronCharge/(1e6 amu) */
+constexpr double c_fieldfac = c_faraday / c_kilo;
+
+/* to convert AU to MD units: */
+constexpr double c_hartree2Kj = ((2.0 * c_rydberg * c_planck * c_speedOfLight) / c_avogadro);
+constexpr double c_bohr2Nm = 0.0529177210903; /* nm^-1, NIST 2018 CODATA */
+constexpr double c_hartreeBohr2Md = (c_hartree2Kj * c_avogadro / c_bohr2Nm);
+
+constexpr double c_rad2Deg = 180.0 / M_PI;
+constexpr double c_deg2Rad = M_PI / 180.0;
+} // namespace gmx
+
+/* The four basic units */
+#define unit_length "nm"
+#define unit_time "ps"
+#define unit_mass "u"
+#define unit_energy "kJ/mol"
+
+/* Temperature unit, T in this unit times c_boltz give energy in unit_energy */
+#define unit_temp_K "K"
+
+/* Charge unit, electron charge, involves c_one4PiEps0 */
+#define unit_charge_e "e"
+
+/* Pressure unit, pressure in basic units times c_presfac gives this unit */
+#define unit_pres_bar "bar"
+
+/* Dipole unit, debye, conversion from the unit_charge_e involves c_enm2Debye */
+#define unit_dipole_D "D"
+
+/* Derived units from basic units only */
+#define unit_vel unit_length "/" unit_time
+#define unit_volume unit_length "^3"
+#define unit_invtime "1/" unit_time
+
+/* Other derived units */
+#define unit_surft_bar unit_pres_bar " " unit_length
+
+/* SI units, conversion from basic units involves c_nano, c_pico and amu */
+#define unit_length_SI "m"
+#define unit_time_SI "s"
+#define unit_mass_SI "kg"
+
+#define unit_density_SI unit_mass_SI "/" unit_length_SI "^3"
+#define unit_invvisc_SI unit_length_SI " " unit_time_SI "/" unit_mass_SI
+
+#endif
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_MATH_UTILITIES_H
#include <limits.h>
+#include <stdint.h>
#include <cmath>
-#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/real.h"
-
-#ifndef M_PI
-# define M_PI 3.14159265358979323846
-#endif
-
-#ifndef M_PI_2
-# define M_PI_2 1.57079632679489661923
-#endif
-
-#ifndef M_2PI
-# define M_2PI 6.28318530717958647692
-#endif
-
-#ifndef M_SQRT2
-# define M_SQRT2 sqrt(2.0)
-#endif
-
-#ifndef M_1_PI
-# define M_1_PI 0.31830988618379067154
-#endif
-
-#ifndef M_FLOAT_1_SQRTPI /* used in GPU kernels */
-/* 1.0 / sqrt(M_PI) */
-# define M_FLOAT_1_SQRTPI 0.564189583547756f
-#endif
-
-#ifndef M_1_SQRTPI
-/* 1.0 / sqrt(M_PI) */
-# define M_1_SQRTPI 0.564189583547756
-#endif
-
-#ifndef M_2_SQRTPI
-/* 2.0 / sqrt(M_PI) */
-# define M_2_SQRTPI 1.128379167095513
-#endif
-
/*! \brief Enum to select safe or highly unsafe (faster) math functions.
*
* Normally all the Gromacs math functions should apply reasonable care with
*
* \return False iff overflow occurred
*/
-gmx_bool check_int_multiply_for_overflow(int64_t a, int64_t b, int64_t* result);
+bool check_int_multiply_for_overflow(int64_t a, int64_t b, int64_t* result);
/*! \brief Enable floating-point exceptions if supported on OS
*
*/
int gmx_fedisableexcept();
+/*! \brief Return true if the current build should enable floating-point exceptions by default.
+ *
+ * Currently, it returns true unless any of the following conditions are met:
+ * - release build,
+ * - SYCL build (Intel IGC, at least 1.0.5964, raises FP exceptions in JIT compilation),
+ * - - See https://github.com/intel/intel-graphics-compiler/issues/164
+ * - compilers with known buggy FP exception support (clang with any optimization)
+ * or suspected buggy FP exception support (gcc 7.* with optimization).
+ *
+ * Note that this function does not check whether the build/OS supports FP exceptions.
+ *
+ * \returns true if we should enable FP exceptions by default.
+ */
+bool gmxShouldEnableFPExceptions();
+
#endif
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
ValueType& operator[](int i) { return x_[i]; }
//! Indexing operator to make the class work as the raw array.
ValueType operator[](int i) const { return x_[i]; }
+ //! Return whether all elements compare equal
+ bool operator==(const BasicVector<ValueType>& right)
+ {
+ return x_[0] == right[0] && x_[1] == right[1] && x_[2] == right[2];
+ }
+ //! Return whether any elements compare unequal
+ bool operator!=(const BasicVector<ValueType>& right)
+ {
+ return x_[0] != right[0] || x_[1] != right[1] || x_[2] != right[2];
+ }
//! Allow inplace addition for BasicVector
BasicVector<ValueType>& operator+=(const BasicVector<ValueType>& right)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#ifndef gmx_unused
# ifdef __GNUC__
-/* GCC, clang, and some ICC pretending to be GCC */
-# define gmx_unused __attribute__((unused))
-# elif (defined(__INTEL_COMPILER) || defined(__ECC)) && !defined(_MSC_VER)
-/* ICC on *nix */
+/* GCC, clang, and any pretending to be or based on them */
# define gmx_unused __attribute__((unused))
# elif defined(__PGI)
/* Portland group compilers */
*/
#define GMX_UNUSED_VALUE(value) (void)value
+#if defined(__GNUC__) && !defined(__clang__)
+# define DO_PRAGMA(x) _Pragma(# x)
+# define GCC_DIAGNOSTIC_IGNORE(warning) \
+ _Pragma("GCC diagnostic push") DO_PRAGMA(GCC diagnostic ignored #warning)
+# define GCC_DIAGNOSTIC_RESET _Pragma("GCC diagnostic pop")
+#else
+//! Ignore specified clang warning until GCC_DIAGNOSTIC_RESET
+# define GCC_DIAGNOSTIC_IGNORE(warning)
+//! Reset all diagnostics to default
+# define GCC_DIAGNOSTIC_RESET
+#endif
+
#ifdef __clang__
# define DO_PRAGMA(x) _Pragma(# x)
# define CLANG_DIAGNOSTIC_IGNORE(warning) \
# define MSVC_DIAGNOSTIC_RESET
#endif
-#ifdef __INTEL_COMPILER
-//! Ignore unused loop variable warning - it was used until the compiler removes the use!
-# define DO_PRAGMA(x) _Pragma(# x)
-# define INTEL_DIAGNOSTIC_IGNORE(id) DO_PRAGMA(warning push) DO_PRAGMA(warning(disable : id))
-# define INTEL_DIAGNOSTIC_RESET DO_PRAGMA(warning pop)
-#else
-//! Ignore specified diagnostic message from Intel compiler.
-# define INTEL_DIAGNOSTIC_IGNORE(id)
-//! Reset the diagnostic message setting.
-# define INTEL_DIAGNOSTIC_RESET
-#endif
-
namespace gmx
{
namespace internal
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
# define GMX_CURRENT_FUNCTION __FUNCSIG__
-#elif (defined(__INTEL_COMPILER) && (__INTEL_COMPILER >= 600)) \
- || (defined(__IBMCPP__) && (__IBMCPP__ >= 500))
+#elif (defined(__IBMCPP__) && (__IBMCPP__ >= 500))
# define GMX_CURRENT_FUNCTION __FUNCTION__
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2011-2018, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_UTILITY_GMXASSERT_H
#define GMX_UTILITY_GMXASSERT_H
-#include "gromacs/utility/basedefinitions.h"
-
#include "current_function.h"
//! \addtogroup module_utility
# define GMX_RELEASE_ASSERT(condition, msg)
#else
# ifdef _MSC_VER
-# define GMX_RELEASE_ASSERT(condition, msg) \
- ((void)((condition) ? (void)0 \
- : ::gmx::internal::assertHandler(#condition, msg, GMX_CURRENT_FUNCTION, \
- __FILE__, __LINE__)))
+# define GMX_RELEASE_ASSERT(condition, msg) \
+ ((void)((condition) ? (void)0 \
+ : ::gmx::internal::assertHandler( \
+ #condition, msg, GMX_CURRENT_FUNCTION, __FILE__, __LINE__)))
# else
// Use an "immediately invoked function expression" to allow being
// used in constexpr context with older GCC versions
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
ArrayRef<T> front()
{
GMX_ASSERT(size() > 0, "Must contain a list if front() is called");
- auto beginPtr = elements_.data();
- auto endPtr = beginPtr + listRanges_[1];
+ auto* beginPtr = elements_.data();
+ auto* endPtr = beginPtr + listRanges_[1];
return { beginPtr, endPtr };
}
/*! \brief Returns a reference to the final list
//! Appends a ListOfLists at the end and increments the appended elements by \p offset
void appendListOfLists(const ListOfLists& listOfLists, const T offset = 0)
{
- listRanges_.insert(listRanges_.end(), listOfLists.listRanges_.begin() + 1,
- listOfLists.listRanges_.end());
+ listRanges_.insert(
+ listRanges_.end(), listOfLists.listRanges_.begin() + 1, listOfLists.listRanges_.end());
const int oldNumElements = elements_.size();
for (std::size_t i = listRanges_.size() - listOfLists.size(); i < listRanges_.size(); i++)
{
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2012,2014,2020, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief
+ * Version information for software that links to \Gromacs.
+ *
+ * \if libapi
+ * This include file will be configured by CMake and contains version
+ * information. It is not used by \Gromacs, but intended for software that
+ * links to \Gromacs.
+ * The values come from the main CMakeLists.txt.
+ * \endif
+ *
+ * This file exists from 4.6 onward, and can be included as
+ * `<gromacs/version.h>`. In 4.6, it is also included by
+ * `<gromacs/typedefs.h>, but that header has already moved in 5.0.
+ *
+ * This header defines two values, the \Gromacs version, and the API version.
+ * The versions are in numerical form, where, for example, version
+ * 4.6.1 would be 40601.
+ *
+ * The API version is defined in ::GMX_API_VERSION, and denotes the
+ * version of the programmer interface, i.e. the installed header files
+ * and compatible library.
+ *
+ * Programs written against the \Gromacs library can use this file
+ * to provide some backward compatibility even though parts of the API
+ * change. For example:
+ * \code
+ #include <gromacs/version.h>
+ #if (GMX_API_VERSION < 50000)
+ .... <do pre-5.0 stuff>
+ #else
+ .... <do post-5.0 stuff>
+ #endif
+ \endcode
+ * where version.h is included directly. For code that must be compatible
+ * between 4.5 and 4.6, an interim solution is to include typedefs.h, which
+ * includes this file:
+ * \code
+ #include <gromacs/typedefs.h>
+ #if !defined(GMX_API_VERSION) || (GMX_API_VERSION < 40600)
+ .... <do 4.5 specific stuff>
+ #elif (GMX_API_VERSION < 40700)
+ .... <do 4.6 specific stuff>
+ #endif
+ \endcode
+ *
+ * \inpublicapi
+ */
+#ifndef GMX_VERSION_H
+#define GMX_VERSION_H
+
+/*! \brief
+ * API version of this set of \Gromacs headers.
+ *
+ * If there are multiple versions of \Gromacs that work with the same set of
+ * headers, then this version is not updated between the versions, even though
+ * ::GMX_VERSION is.
+ * For 4.6 and 5.0 (and likely for some time in the future as well), this
+ * tracks the exact \Gromacs version.
+ */
+#define GMX_API_VERSION @GMX_API_VERSION@
+
+/*! \brief
+ * Exact \Gromacs version of this set of headers.
+ *
+ * This specifies the version number of the actual \Gromacs library that
+ * installed these headers.
+ */
+#define GMX_VERSION @GMX_VERSION_NUMERIC@
+
+#endif
target_link_libraries(nblib PRIVATE libgromacs)
target_include_directories(nblib PRIVATE ${PROJECT_SOURCE_DIR}/api)
include_directories(BEFORE ${CMAKE_SOURCE_DIR}/api)
+target_link_libraries(nblib PRIVATE common)
+# There are transitive dependencies on the legacy GROMACS headers.
+target_link_libraries(nblib PUBLIC legacy_api)
+# TODO: Explicitly link specific modules.
+target_link_libraries(nblib PRIVATE legacy_modules)
install(TARGETS nblib
EXPORT nblib
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx::ArrayRef<gmx::RVec> forceOutput)
{
// update the coordinates in the backend
- nbv_->convertCoordinates(gmx::AtomLocality::Local, false, coordinateInput);
+ nbv_->convertCoordinates(gmx::AtomLocality::Local, coordinateInput);
- nbv_->dispatchNonbondedKernel(gmx::InteractionLocality::Local, *interactionConst_, *stepWork_,
- enbvClearFYes, *forcerec_, enerd_.get(), nrnb_.get());
+ nbv_->dispatchNonbondedKernel(
+ gmx::InteractionLocality::Local,
+ *interactionConst_,
+ *stepWork_,
+ enbvClearFYes,
+ forcerec_->shift_vec,
+ enerd_->grpp.energyGroupPairTerms[forcerec_->haveBuckingham ? NonBondedEnergyTerms::BuckinghamSR
+ : NonBondedEnergyTerms::LJSR],
+ enerd_->grpp.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR],
+ nrnb_.get());
nbv_->atomdata_add_nbat_f_to_f(gmx::AtomLocality::All, forceOutput);
}
const real particleDensity = coordinates.size() / det(legacyBox);
- nbnxn_put_on_grid(nbv_.get(), legacyBox, 0, lowerCorner, upperCorner, nullptr,
- { 0, int(coordinates.size()) }, particleDensity, particleInfoAllVdw,
- coordinates, 0, nullptr);
+ nbnxn_put_on_grid(nbv_.get(),
+ legacyBox,
+ 0,
+ lowerCorner,
+ upperCorner,
+ nullptr,
+ { 0, int(coordinates.size()) },
+ particleDensity,
+ particleInfoAllVdw,
+ coordinates,
+ 0,
+ nullptr);
}
} // namespace nblib
void NbvSetupUtil::setExecutionContext(const NBKernelOptions& options)
{
// Todo: find a more general way to initialize hardware
- gmx_omp_nthreads_set(emntPairsearch, options.numOpenMPThreads);
- gmx_omp_nthreads_set(emntNonbonded, options.numOpenMPThreads);
+ gmx_omp_nthreads_set(ModuleMultiThread::Pairsearch, options.numOpenMPThreads);
+ gmx_omp_nthreads_set(ModuleMultiThread::Nonbonded, options.numOpenMPThreads);
}
Nbnxm::KernelSetup NbvSetupUtil::getKernelSetup(const NBKernelOptions& options)
Nbnxm::KernelSetup kernelSetup = getKernelSetup(options);
PairlistParams pairlistParams(kernelSetup.kernelType, false, options.pairlistCutoff, false);
- Nbnxm::GridSet gridSet(PbcType::Xyz, false, nullptr, nullptr, pairlistParams.pairlistType,
- false, numThreads, pinPolicy);
- auto pairlistSets = std::make_unique<PairlistSets>(pairlistParams, false, 0);
- auto pairSearch =
- std::make_unique<PairSearch>(PbcType::Xyz, false, nullptr, nullptr,
- pairlistParams.pairlistType, false, numThreads, pinPolicy);
-
- auto atomData = std::make_unique<nbnxn_atomdata_t>(pinPolicy);
-
- // Needs to be called with the number of unique ParticleTypes
- nbnxn_atomdata_init(gmx::MDLogger(), atomData.get(), kernelSetup.kernelType, combinationRule,
- numParticleTypes, nonbondedParameters_, 1, numThreads);
+ Nbnxm::GridSet gridSet(
+ PbcType::Xyz, false, nullptr, nullptr, pairlistParams.pairlistType, false, numThreads, pinPolicy);
+ auto pairlistSets = std::make_unique<PairlistSets>(pairlistParams, false, 0);
+ auto pairSearch = std::make_unique<PairSearch>(
+ PbcType::Xyz, false, nullptr, nullptr, pairlistParams.pairlistType, false, numThreads, pinPolicy);
+
+ auto atomData = std::make_unique<nbnxn_atomdata_t>(pinPolicy,
+ gmx::MDLogger(),
+ kernelSetup.kernelType,
+ combinationRule,
+ numParticleTypes,
+ nonbondedParameters_,
+ 1,
+ numThreads);
// Put everything together
- auto nbv = std::make_unique<nonbonded_verlet_t>(std::move(pairlistSets), std::move(pairSearch),
- std::move(atomData), kernelSetup, nullptr,
- nullWallcycle);
+ auto nbv = std::make_unique<nonbonded_verlet_t>(
+ std::move(pairlistSets), std::move(pairSearch), std::move(atomData), kernelSetup, nullptr, nullptr);
gmxForceCalculator_->nbv_ = std::move(nbv);
}
void NbvSetupUtil::setupInteractionConst(const NBKernelOptions& options)
{
- gmxForceCalculator_->interactionConst_->vdwtype = evdwCUT;
- gmxForceCalculator_->interactionConst_->vdw_modifier = eintmodPOTSHIFT;
+ gmxForceCalculator_->interactionConst_->vdwtype = VanDerWaalsType::Cut;
+ gmxForceCalculator_->interactionConst_->vdw_modifier = InteractionModifiers::PotShift;
gmxForceCalculator_->interactionConst_->rvdw = options.pairlistCutoff;
switch (options.coulombType)
{
- case CoulombType::Pme: gmxForceCalculator_->interactionConst_->eeltype = eelPME; break;
- case CoulombType::Cutoff: gmxForceCalculator_->interactionConst_->eeltype = eelCUT; break;
+ case CoulombType::Pme:
+ gmxForceCalculator_->interactionConst_->eeltype = CoulombInteractionType::Pme;
+ break;
+ case CoulombType::Cutoff:
+ gmxForceCalculator_->interactionConst_->eeltype = CoulombInteractionType::Cut;
+ break;
case CoulombType::ReactionField:
- gmxForceCalculator_->interactionConst_->eeltype = eelRF;
+ gmxForceCalculator_->interactionConst_->eeltype = CoulombInteractionType::RF;
break;
case CoulombType::Count: throw InputException("Unsupported electrostatic interaction");
}
- gmxForceCalculator_->interactionConst_->coulomb_modifier = eintmodPOTSHIFT;
+ gmxForceCalculator_->interactionConst_->coulomb_modifier = InteractionModifiers::PotShift;
gmxForceCalculator_->interactionConst_->rcoulomb = options.pairlistCutoff;
- // Note: values correspond to ic->coulomb_modifier = eintmodPOTSHIFT
+ // Note: values correspond to ic->coulomb_modifier = InteractionModifiers::PotShift
gmxForceCalculator_->interactionConst_->dispersion_shift.cpot =
-1.0 / gmx::power6(gmxForceCalculator_->interactionConst_->rvdw);
gmxForceCalculator_->interactionConst_->repulsion_shift.cpot =
// These are the initialized values but we leave them here so that later
// these can become options.
- gmxForceCalculator_->interactionConst_->epsilon_r = 1.0;
- gmxForceCalculator_->interactionConst_->epsilon_rf = 1.0;
+ gmxForceCalculator_->interactionConst_->epsilon_r = 1.0;
+ gmxForceCalculator_->interactionConst_->reactionFieldPermitivity = 1.0;
/* Set the Coulomb energy conversion factor */
if (gmxForceCalculator_->interactionConst_->epsilon_r != 0)
gmxForceCalculator_->interactionConst_->epsfac = 0;
}
- calc_rffac(nullptr, gmxForceCalculator_->interactionConst_->epsilon_r,
- gmxForceCalculator_->interactionConst_->epsilon_rf,
+ calc_rffac(nullptr,
+ gmxForceCalculator_->interactionConst_->epsilon_r,
+ gmxForceCalculator_->interactionConst_->reactionFieldPermitivity,
gmxForceCalculator_->interactionConst_->rcoulomb,
- &gmxForceCalculator_->interactionConst_->k_rf,
- &gmxForceCalculator_->interactionConst_->c_rf);
+ &gmxForceCalculator_->interactionConst_->reactionFieldCoefficient,
+ &gmxForceCalculator_->interactionConst_->reactionFieldShift);
if (EEL_PME_EWALD(gmxForceCalculator_->interactionConst_->eeltype))
{
{
assert((gmxForceCalculator_->forcerec_ && "Forcerec not initialized"));
gmxForceCalculator_->forcerec_->nbfp = nonbondedParameters_;
- snew(gmxForceCalculator_->forcerec_->shift_vec, numShiftVectors);
+ gmxForceCalculator_->forcerec_->shift_vec.resize(numShiftVectors);
calc_shifts(box, gmxForceCalculator_->forcerec_->shift_vec);
}
{
gmx::ListOfLists<int> exclusions(std::move(exclusionLists.ListRanges),
std::move(exclusionLists.ListElements));
- gmxForceCalculator_->nbv_->constructPairlist(gmx::InteractionLocality::Local, exclusions, 0,
- gmxForceCalculator_->nrnb_.get());
+ gmxForceCalculator_->nbv_->constructPairlist(
+ gmx::InteractionLocality::Local, exclusions, 0, gmxForceCalculator_->nrnb_.get());
}
std::string message = formatString(
"Attempting to add nonbonded interaction parameters between the particle types "
"{} {} twice",
- particleTypeName1.value(), particleTypeName2.value());
+ particleTypeName1.value(),
+ particleTypeName2.value());
throw InputException(message);
}
}
C6 c6_combo{ combineNonbondedParameters(c6_1, c6_2, combinationRule_) };
C12 c12_combo{ combineNonbondedParameters(c12_1, c12_2, combinationRule_) };
- nonbondedParameters_.setInteractions(particleType1.first, particleType2.first, c6_combo,
- c12_combo);
+ nonbondedParameters_.setInteractions(
+ particleType1.first, particleType2.first, c6_combo, c12_combo);
}
}
if (nonbondedParameters_.count(interactionKey) == 0)
{
std::string message = formatString("Missing interaction between {} {}",
- particleTypeName1.value(), particleTypeName2.value());
+ particleTypeName1.value(),
+ particleTypeName2.value());
throw InputException(message);
}
}
for (const auto& keyval : other.twoParticlesInteractionsMap_)
{
- add(std::get<0>(keyval.first), std::get<1>(keyval.first), std::get<0>(keyval.second),
+ add(std::get<0>(keyval.first),
+ std::get<1>(keyval.first),
+ std::get<0>(keyval.second),
std::get<1>(keyval.second));
}
}
TEST(NBlibTest, BondTypesOperatorEqualWorks)
{
- auto bondList3 = std::make_tuple(HarmonicBondType(), G96BondType(), FENEBondType(),
- HalfAttractiveQuarticBondType());
+ auto bondList3 = std::make_tuple(
+ HarmonicBondType(), G96BondType(), FENEBondType(), HalfAttractiveQuarticBondType());
for_each_tuple([](const auto& b) { test_detail::testTwoParameterBondEquality(b); }, bondList3);
auto bondList4 = std::make_tuple(CubicBondType(), MorseBondType());
TEST(NBlibTest, BondTypesLessThanWorks)
{
- auto bondList3 = std::make_tuple(HarmonicBondType(), G96BondType(), FENEBondType(),
- HalfAttractiveQuarticBondType());
+ auto bondList3 = std::make_tuple(
+ HarmonicBondType(), G96BondType(), FENEBondType(), HalfAttractiveQuarticBondType());
for_each_tuple([](const auto& b) { test_detail::testTwoParameterBondLessThan(b); }, bondList3);
auto bondList4 = std::make_tuple(CubicBondType(), MorseBondType());
for (int m = 0; m < dimSize; ++m)
{
EXPECT_FLOAT_DOUBLE_EQ_TOL(
- forces[i][m], refForcesFloat[i][m], refForcesDouble[i][m],
+ forces[i][m],
+ refForcesFloat[i][m],
+ refForcesDouble[i][m],
// Todo: why does the tolerance need to be so low?
gmx::test::relativeToleranceAsFloatingPoint(refForcesDouble[i][m], 5e-5));
}
{
for (size_t i = 0; i < energies.size(); ++i)
{
- EXPECT_REAL_EQ_TOL(energies[i], refEnergies[i],
+ EXPECT_REAL_EQ_TOL(energies[i],
+ refEnergies[i],
gmx::test::relativeToleranceAsFloatingPoint(refEnergies[i], 1e-5));
}
}
{
for (size_t m = 0; m < dimSize; ++m)
{
- EXPECT_REAL_EQ_TOL(refMasterBuffer[i][m], masterBuffer[i][m],
- gmx::test::defaultRealTolerance());
+ EXPECT_REAL_EQ_TOL(
+ refMasterBuffer[i][m], masterBuffer[i][m], gmx::test::defaultRealTolerance());
}
}
using InteractionContainerType = std::decay_t<decltype(interactionElement)>;
using InteractionType = typename InteractionContainerType::type;
- std::sort(begin(interactionElement.indices), end(interactionElement.indices),
+ std::sort(begin(interactionElement.indices),
+ end(interactionElement.indices),
interactionSortKey<InteractionType>);
};
+ name_.value());
}
- addInteractionImpl(interaction, particleI.particleName(), residueName(particleI),
- particleJ.particleName(), residueName(particleJ));
+ addInteractionImpl(interaction,
+ particleI.particleName(),
+ residueName(particleI),
+ particleJ.particleName(),
+ residueName(particleJ));
}
void Molecule::addInteraction(const ParticleIdentifier& particleI,
+ name_.value());
}
- addInteractionImpl(interaction, particleI.particleName(), residueName(particleI),
- particleJ.particleName(), residueName(particleJ), particleK.particleName(),
+ addInteractionImpl(interaction,
+ particleI.particleName(),
+ residueName(particleI),
+ particleJ.particleName(),
+ residueName(particleJ),
+ particleK.particleName(),
residueName(particleK));
}
+ name_.value());
}
- addInteractionImpl(interaction, particleI.particleName(), residueName(particleI),
- particleJ.particleName(), residueName(particleJ), particleK.particleName(),
- residueName(particleK), particleL.particleName(), residueName(particleL));
+ addInteractionImpl(interaction,
+ particleI.particleName(),
+ residueName(particleI),
+ particleJ.particleName(),
+ residueName(particleJ),
+ particleK.particleName(),
+ residueName(particleK),
+ particleL.particleName(),
+ residueName(particleL));
}
void Molecule::addInteraction(const ParticleIdentifier& particleI,
+ name_.value());
}
- addInteractionImpl(interaction, particleI.particleName(), residueName(particleI),
- particleJ.particleName(), residueName(particleJ), particleK.particleName(),
- residueName(particleK), particleL.particleName(), residueName(particleL),
- particleM.particleName(), residueName(particleM));
+ addInteractionImpl(interaction,
+ particleI.particleName(),
+ residueName(particleI),
+ particleJ.particleName(),
+ residueName(particleJ),
+ particleK.particleName(),
+ residueName(particleK),
+ particleL.particleName(),
+ residueName(particleL),
+ particleM.particleName(),
+ residueName(particleM));
}
}
// duplication for the swapped pair happens in getExclusions()
- exclusionsByName_.emplace_back(std::make_tuple(particle.particleName(), residueName(particle),
+ exclusionsByName_.emplace_back(std::make_tuple(particle.particleName(),
+ residueName(particle),
particleToExclude.particleName(),
residueName(particleToExclude)));
}
const std::string& residueName2 = std::get<3>(tup);
// look up first index (binary search)
- auto it1 = std::lower_bound(std::begin(indexKey), std::end(indexKey),
- std::make_tuple(particleName1, residueName2, 0), sortKey);
+ auto it1 = std::lower_bound(std::begin(indexKey),
+ std::end(indexKey),
+ std::make_tuple(particleName1, residueName2, 0),
+ sortKey);
// make sure we have the (particleName,residueName) combo
if (it1 == std::end(indexKey) or std::get<0>(*it1) != particleName1 or std::get<1>(*it1) != residueName1)
int firstIndex = std::get<2>(*it1);
// look up second index (binary search)
- auto it2 = std::lower_bound(std::begin(indexKey), std::end(indexKey),
- std::make_tuple(particleName2, residueName2, 0), sortKey);
+ auto it2 = std::lower_bound(std::begin(indexKey),
+ std::end(indexKey),
+ std::make_tuple(particleName2, residueName2, 0),
+ sortKey);
// make sure we have the (particleName,residueName) combo
if (it2 == std::end(indexKey) or std::get<0>(*it2) != particleName2 or std::get<1>(*it2) != residueName2)
// TODO: use string format function once we have it
if (moleculeName.value() == residueName.value())
{
- printf("No particle %s in residue %s in molecule %s found\n", particleName.value().c_str(),
- residueName.value().c_str(), moleculeName.value().c_str());
+ printf("No particle %s in residue %s in molecule %s found\n",
+ particleName.value().c_str(),
+ residueName.value().c_str(),
+ moleculeName.value().c_str());
}
else
{
- printf("No particle %s in molecule %s found\n", particleName.value().c_str(),
+ printf("No particle %s in molecule %s found\n",
+ particleName.value().c_str(),
moleculeName.value().c_str());
}
gmx::ArrayRef<nblib::Vec3> userForces(simState.forces());
forceCalculator.compute(simState.coordinates(), userForces);
// Print some diagnostic info
- printf(" final forces on particle 0: x %4f y %4f z %4f\n", userForces[0][0], userForces[0][1],
+ printf(" final forces on particle 0: x %4f y %4f z %4f\n",
+ userForces[0][0],
+ userForces[0][1],
userForces[0][2]);
// User may modify forces stored in simState.forces() if needed
// Print some diagnostic info
- printf("initial position of particle 0: x %4f y %4f z %4f\n", simState.coordinates()[0][0],
- simState.coordinates()[0][1], simState.coordinates()[0][2]);
+ printf("initial position of particle 0: x %4f y %4f z %4f\n",
+ simState.coordinates()[0][0],
+ simState.coordinates()[0][1],
+ simState.coordinates()[0][2]);
// Integrate with a time step of 1 fs
integrator.integrate(1.0, simState.coordinates(), simState.velocities(), simState.forces());
// Print some diagnostic info
- printf(" final position of particle 0: x %4f y %4f z %4f\n", simState.coordinates()[0][0],
- simState.coordinates()[0][1], simState.coordinates()[0][2]);
+ printf(" final position of particle 0: x %4f y %4f z %4f\n",
+ simState.coordinates()[0][0],
+ simState.coordinates()[0][1],
+ simState.coordinates()[0][2]);
return 0;
}
ForceCalculator forceCalculator(simulationState, options);
// The listed force calculator is also initialized with the required arguments
- ListedForceCalculator listedForceCalculator(topology.getInteractionData(),
- topology.numParticles(), 4, box);
+ ListedForceCalculator listedForceCalculator(
+ topology.getInteractionData(), topology.numParticles(), 4, box);
// Integrator is initialized with an array of inverse masses (constructed from topology) and
// the bounding box
LeapFrog integrator(topology, box);
// Print some diagnostic info
- printf("initial position of particle 0: x %4f y %4f z %4f\n", simulationState.coordinates()[0][0],
- simulationState.coordinates()[0][1], simulationState.coordinates()[0][2]);
+ printf("initial position of particle 0: x %4f y %4f z %4f\n",
+ simulationState.coordinates()[0][0],
+ simulationState.coordinates()[0][1],
+ simulationState.coordinates()[0][2]);
// MD Loop
int numSteps = 2;
listedForceCalculator.compute(simulationState.coordinates(), simulationState.forces());
// Integrate with a time step of 1 fs, positions, velocities and forces
- integrator.integrate(1.0, simulationState.coordinates(), simulationState.velocities(),
- simulationState.forces());
+ integrator.integrate(
+ 1.0, simulationState.coordinates(), simulationState.velocities(), simulationState.forces());
}
- printf(" final position of particle 9: x %4f y %4f z %4f\n", simulationState.coordinates()[9][0],
- simulationState.coordinates()[9][1], simulationState.coordinates()[9][2]);
+ printf(" final position of particle 9: x %4f y %4f z %4f\n",
+ simulationState.coordinates()[9][0],
+ simulationState.coordinates()[9][1],
+ simulationState.coordinates()[9][2]);
return 0;
} // main
#include <vector>
#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/arrayref.h"
#include "nblib/exception.h"
#include "nblib/simulationstate.h"
#include "nblib/simulationstateimpl.h"
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2020, by the GROMACS development team, led by
+# Copyright (c) 2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
)
target_include_directories(nblib_test_infrastructure PRIVATE ${PROJECT_SOURCE_DIR}/api)
target_include_directories(nblib_test_infrastructure SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
+target_link_libraries(nblib_test_infrastructure PRIVATE legacy_api)
+# TODO: Explicitly link specific modules: math,
+target_link_libraries(nblib_test_infrastructure PRIVATE legacy_modules)
set(testname "NbLibSetupTests")
set(exename "nblib-setup-test")
*/
#include "nblib/integrator.h"
#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/arrayref.h"
#include "nblib/molecules.h"
#include "nblib/particletype.h"
#include "nblib/simulationstate.h"
<< formatString(
"Coordinate {} of atom {} is different from analytical solution "
"at step {}.",
- d, i, step);
+ d,
+ i,
+ step);
EXPECT_REAL_EQ_TOL(vAnalytical[d], simulationState.velocities()[i][d], tolerance)
<< formatString(
"Velocity component {} of atom {} is different from analytical "
"solution at step {}.",
- d, i, step);
+ d,
+ i,
+ step);
}
- integrator.integrate(dt, simulationState.coordinates(), simulationState.velocities(),
+ integrator.integrate(dt,
+ simulationState.coordinates(),
+ simulationState.velocities(),
simulationState.forces());
}
}
EXPECT_REAL_EQ_TOL(c12_1, nbfp.getC12(atom1.name(), atom1.name()), gmx::test::defaultRealTolerance());
//! geometric comb rule for c6
- EXPECT_REAL_EQ_TOL(std::sqrt(c6_1 * c6_2), nbfp.getC6(atom1.name(), atom2.name()),
+ EXPECT_REAL_EQ_TOL(std::sqrt(c6_1 * c6_2),
+ nbfp.getC6(atom1.name(), atom2.name()),
gmx::test::defaultRealTolerance());
//! + symmetric pair
- EXPECT_REAL_EQ_TOL(std::sqrt(c6_1 * c6_2), nbfp.getC6(atom2.name(), atom1.name()),
+ EXPECT_REAL_EQ_TOL(std::sqrt(c6_1 * c6_2),
+ nbfp.getC6(atom2.name(), atom1.name()),
gmx::test::defaultRealTolerance());
//! geometric comb rule for c12
- EXPECT_REAL_EQ_TOL(std::sqrt(c12_1 * c12_2), nbfp.getC12(atom1.name(), atom2.name()),
+ EXPECT_REAL_EQ_TOL(std::sqrt(c12_1 * c12_2),
+ nbfp.getC12(atom1.name(), atom2.name()),
gmx::test::defaultRealTolerance());
//! + symmetric par
- EXPECT_REAL_EQ_TOL(std::sqrt(c12_1 * c12_2), nbfp.getC12(atom2.name(), atom1.name()),
+ EXPECT_REAL_EQ_TOL(std::sqrt(c12_1 * c12_2),
+ nbfp.getC12(atom2.name(), atom1.name()),
gmx::test::defaultRealTolerance());
//! explicit pairwise interaction c6
EXPECT_REAL_EQ_TOL(c6comb, nbfp.getC6(atom3.name(), atom2.name()), gmx::test::defaultRealTolerance());
//! explicit pairwise interaction c12
- EXPECT_REAL_EQ_TOL(c12comb, nbfp.getC12(atom2.name(), atom3.name()),
- gmx::test::defaultRealTolerance());
- EXPECT_REAL_EQ_TOL(c12comb, nbfp.getC12(atom3.name(), atom2.name()),
- gmx::test::defaultRealTolerance());
+ EXPECT_REAL_EQ_TOL(
+ c12comb, nbfp.getC12(atom2.name(), atom3.name()), gmx::test::defaultRealTolerance());
+ EXPECT_REAL_EQ_TOL(
+ c12comb, nbfp.getC12(atom3.name(), atom2.name()), gmx::test::defaultRealTolerance());
ParticleType atom4(ParticleTypeName("a4"), Mass(1));
interactions.add(atom3.name(), atom4.name(), C6(1), C12(2));
auto nbfp = interactions.generateTable();
- EXPECT_REAL_EQ_TOL(std::sqrt(c6_3 * c6_4), nbfp.getC6(atom3.name(), atom4.name()),
- gmx::test::defaultRealTolerance());
- EXPECT_REAL_EQ_TOL(std::sqrt(c12_3 * c12_4), nbfp.getC12(atom3.name(), atom4.name()),
- gmx::test::defaultRealTolerance());
- EXPECT_REAL_EQ_TOL(c6_override, nbfp.getC6(atom4.name(), atom5.name()),
+ EXPECT_REAL_EQ_TOL(std::sqrt(c6_3 * c6_4),
+ nbfp.getC6(atom3.name(), atom4.name()),
gmx::test::defaultRealTolerance());
- EXPECT_REAL_EQ_TOL(c12_override, nbfp.getC12(atom4.name(), atom5.name()),
+ EXPECT_REAL_EQ_TOL(std::sqrt(c12_3 * c12_4),
+ nbfp.getC12(atom3.name(), atom4.name()),
gmx::test::defaultRealTolerance());
+ EXPECT_REAL_EQ_TOL(
+ c6_override, nbfp.getC6(atom4.name(), atom5.name()), gmx::test::defaultRealTolerance());
+ EXPECT_REAL_EQ_TOL(
+ c12_override, nbfp.getC12(atom4.name(), atom5.name()), gmx::test::defaultRealTolerance());
}
} // namespace
{
gmx::ArrayRef<Vec3> forces(simState.forces());
forceCalculator.compute(simState.coordinates(), simState.forces());
- EXPECT_NO_THROW(integrator.integrate(1.0, simState.coordinates(), simState.velocities(),
- simState.forces()));
+ EXPECT_NO_THROW(integrator.integrate(
+ 1.0, simState.coordinates(), simState.velocities(), simState.forces()));
}
}
std::vector<std::string> typeNames = { "Ow", "H" };
for (const auto& name : typeNames)
{
- interactions.add(ParticleTypeName(name), library.c6(ParticleName(name)),
- library.c12(ParticleName(name)));
+ interactions.add(
+ ParticleTypeName(name), library.c6(ParticleName(name)), library.c12(ParticleName(name)));
}
// Add some molecules to the topology
std::vector<std::string> typeNames = { "Ow", "H", "OMet", "CMet" };
for (const auto& name : typeNames)
{
- interactions.add(ParticleTypeName(name), library.c6(ParticleName(name)),
- library.c12(ParticleName(name)));
+ interactions.add(
+ ParticleTypeName(name), library.c6(ParticleName(name)), library.c12(ParticleName(name)));
}
// Add some molecules to the topology
ParticleLibrary library;
ParticleTypesInteractions nbinteractions;
- nbinteractions.add(ParticleTypeName("Ar"), library.c6(ParticleName("Ar")),
- library.c12(ParticleName("Ar")));
+ nbinteractions.add(
+ ParticleTypeName("Ar"), library.c6(ParticleName("Ar")), library.c12(ParticleName("Ar")));
Molecule argonMolecule(MoleculeName("AR"));
argonMolecule.addParticle(ParticleName("AR"), library.type("Ar"));
WaterTopologyBuilder waters;
Topology watersTopology = waters.buildTopology(2);
- EXPECT_EQ(0, watersTopology.sequenceID(MoleculeName("SOL"), 0, ResidueName("SOL"),
- ParticleName("Oxygen")));
+ EXPECT_EQ(0, watersTopology.sequenceID(MoleculeName("SOL"), 0, ResidueName("SOL"), ParticleName("Oxygen")));
EXPECT_EQ(1, watersTopology.sequenceID(MoleculeName("SOL"), 0, ResidueName("SOL"), ParticleName("H1")));
EXPECT_EQ(2, watersTopology.sequenceID(MoleculeName("SOL"), 0, ResidueName("SOL"), ParticleName("H2")));
- EXPECT_EQ(3, watersTopology.sequenceID(MoleculeName("SOL"), 1, ResidueName("SOL"),
- ParticleName("Oxygen")));
+ EXPECT_EQ(3, watersTopology.sequenceID(MoleculeName("SOL"), 1, ResidueName("SOL"), ParticleName("Oxygen")));
EXPECT_EQ(4, watersTopology.sequenceID(MoleculeName("SOL"), 1, ResidueName("SOL"), ParticleName("H1")));
EXPECT_EQ(5, watersTopology.sequenceID(MoleculeName("SOL"), 1, ResidueName("SOL"), ParticleName("H2")));
}
std::vector<HarmonicBondType> bondsTest;
// use the expansionArray (bondsExpansion) to expand to the full list if bonds
- std::transform(begin(bondsExpansion), end(bondsExpansion), std::back_inserter(bondsTest),
+ std::transform(begin(bondsExpansion),
+ end(bondsExpansion),
+ std::back_inserter(bondsTest),
[&bonds](size_t i) { return bonds[i]; });
std::vector<HarmonicBondType> waterBonds =
#undef SORT
/// \endcond
- EXPECT_TRUE(std::equal(begin(interactions_reference), end(interactions_reference),
- begin(interactions_test)));
+ EXPECT_TRUE(std::equal(
+ begin(interactions_reference), end(interactions_reference), begin(interactions_test)));
}
TEST(NBlibTest, TopologyListedInteractionsMultipleTypes)
int MeH1 = topology.sequenceID(MoleculeName("MeOH"), 0, ResidueName("MeOH"), ParticleName("H3"));
std::vector<CubicBondType> cubicBondsReference{ testBond };
- std::vector<InteractionIndex<CubicBondType>> cubicIndicesReference{ { std::min(H1, H2),
- std::max(H1, H2), 0 } };
+ std::vector<InteractionIndex<CubicBondType>> cubicIndicesReference{
+ { std::min(H1, H2), std::max(H1, H2), 0 }
+ };
EXPECT_EQ(cubicBondsReference, cubicBonds.parameters);
EXPECT_EQ(cubicIndicesReference, cubicBonds.indices);
{
auto offsetExclusions = offsetGmxBlock(exclusionBlockPerMolecule, particleNumberOffset);
- std::copy(std::begin(offsetExclusions), std::end(offsetExclusions),
+ std::copy(std::begin(offsetExclusions),
+ std::end(offsetExclusions),
std::back_inserter(exclusionBlockGlobal));
particleNumberOffset += molecule.numParticlesInMolecule();
// combine stage 1 + 2 expansion arrays
std::vector<size_t> expansionArray(expansionArrayStage1.size());
- std::transform(begin(expansionArrayStage1), end(expansionArrayStage1), begin(expansionArray),
+ std::transform(begin(expansionArrayStage1),
+ end(expansionArrayStage1),
+ begin(expansionArray),
[& S2 = expansionArrayStage2](size_t S1Element) { return S2[S1Element]; });
// add data about InteractionType instances
// coordinateIndices contains the particle sequence IDs of all interaction coordinates of type <BondType>
auto coordinateIndices = detail::sequenceIDs<InteractionType>(this->molecules_, particleSequencer);
// zip coordinateIndices(i,j,...) + expansionArray(k) -> interactionDataElement.indices(i,j,...,k)
- std::transform(begin(coordinateIndices), end(coordinateIndices), begin(expansionArray),
+ std::transform(begin(coordinateIndices),
+ end(coordinateIndices),
+ begin(expansionArray),
begin(interactionDataElement.indices),
[](auto coordinateIndex, auto interactionIndex) {
std::array<int, coordinateIndex.size() + 1> ret{ 0 };
{
std::string message =
formatString("Missing nonbonded interaction parameters for pair {} {}",
- particleType1.first, particleType2.first);
+ particleType1.first,
+ particleType2.first);
throw InputException(message);
}
}
// shift particle numbers by offset
for (auto& localBlock : inBlock)
{
- std::transform(std::begin(localBlock.atomNumber), std::end(localBlock.atomNumber),
- std::begin(localBlock.atomNumber), [offset](auto i) { return i + offset; });
+ std::transform(std::begin(localBlock.atomNumber),
+ std::end(localBlock.atomNumber),
+ std::begin(localBlock.atomNumber),
+ [offset](auto i) { return i + offset; });
}
return inBlock;
fprintf(debug,
"Velocities were taken from a Maxwell distribution\n"
"Initial generated temperature: %12.5e (scaled to: %12.5e)\n",
- temp, tempi);
+ temp,
+ tempi);
}
return velocities;
message(FATAL_ERROR "${GMX_GPLUSPLUS_PATH}/include/c++ doesn't exist even though it should. "
"Please report to developers.")
endif()
- else() #Intel
- if (${GMX_GPLUSPLUS_VERSION} VERSION_GREATER_EQUAL 7 AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 19)
- message(FATAL_ERROR "ICC versions below 19 don't support GCC versions above 6.")
- endif ()
endif()
# Set up to use the libstdc++ from that g++. Note that we checked
# we will not override any user settings here.
if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" OR CMAKE_CXX_COMPILER_ID MATCHES "IntelLLVM")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --gcc-toolchain=${GMX_GPLUSPLUS_PATH}")
- else() #Intel
- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -gcc-name=${GMX_GPLUSPLUS_PATH}")
endif()
endif()
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2016,2018, by the GROMACS development team, led by
+# Copyright (c) 2016,2018,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# library built in the main project.
if (LMFIT_FOUND)
add_library(lmfit INTERFACE IMPORTED)
- set_target_properties(lmfit PROPERTIES
- INTERFACE_INCLUDE_DIRECTORIES "${LMFIT_INCLUDE_DIR}"
- INTERFACE_LINK_LIBRARIES "${LMFIT_LIBRARY}"
- )
+ target_link_libraries(lmfit INTERFACE "${LMFIT_LIBRARY}")
+ target_include_directories(lmfit SYSTEM BEFORE INTERFACE "${LMFIT_INCLUDE_DIR}")
endif()
cmake_pop_check_state()
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2018, by the GROMACS development team, led by
+# Copyright (c) 2018,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# that was found was actually built in this project.
if(clFFT_FOUND)
add_library(clFFT INTERFACE IMPORTED)
- # When we depend on cmake 3.11, this work-around (specific to
- # imported targets) can be done more simply by using the normal
- # target_include_directories() and target_link_libraries()
- set_target_properties(clFFT PROPERTIES
- INTERFACE_INCLUDE_DIRECTORIES "${clFFT_INCLUDE_DIR}"
- INTERFACE_LINK_LIBRARIES "${clFFT_LIBRARY};${CMAKE_DL_LIBS}"
- )
+ target_link_libraries(clFFT INTERFACE "${clFFT_LIBRARY}" "${CMAKE_DL_LIBS}")
+ target_include_directories(clFFT SYSTEM BEFORE INTERFACE "${clFFT_INCLUDE_DIR}")
endif()
+++ /dev/null
-int main()
-{
-#if defined (__FUJITSU) && ( defined(__sparc) || defined(__sparcv9) ) && ( defined(__LP64__) || defined(__arch64) )
- return 0;
-#else
-#error This compiler is not targetting Fujitsu Sparc64
-#endif
-}
+++ /dev/null
-int main()
-{
-#ifdef __MIC__
- return 0;
-#else
-#error This compiler is not targetting MIC
-#endif
-}
list(APPEND ${SRC_VARIABLE} ${SRC_ROOT}/winthreads.cpp)
endif ()
- if (TMPI_CXX_LIB)
- list(APPEND ${SRC_VARIABLE} ${SRC_ROOT}/system_error.cpp)
- endif ()
-
if (TMPI_ENABLED)
list(APPEND ${SRC_VARIABLE}
${SRC_ROOT}/alltoall.cpp ${SRC_ROOT}/p2p_protocol.cpp
GMX_TEST_CXXFLAG(CXXFLAGS_NOINLINE "-fno-inline" GMXC_CXXFLAGS_DEBUG)
endif()
- # icc
- if (CMAKE_C_COMPILER_ID STREQUAL "Intel")
- if (NOT WIN32)
- if(NOT GMX_OPENMP)
-# 3180: unrecognized OpenMP #pragma
- GMX_TEST_CFLAG(CFLAGS_PRAGMA "-wd3180" GMXC_CFLAGS)
- endif()
- if (GMX_COMPILER_WARNINGS)
-# -w3 enables a lot of useful diagnostics but we don't care about all. -wd disables some selectively.
-# 177: function/variable ".." was declared but never referenced
-# 280: selector expression is constant
-# 411: class defines no constructor to initialize the following (incorrect for struct, initializer list works)
-# 593: variable ".." was set but never used
-# 981: operands are evaluated in unspecified order
-#1418: external function definition with no prior declaration
-#1419: external declaration in primary source file
-#1572: floating-point equality and inequality comparisons are unreliable
-#1599: declaration hides variable ".."
-#2259: non-pointer conversion from ".." to ".." may lose significant bits
-#2415: variable ".." of static storage duration was declared but never referenced
-#2547: ".." was specified as both a system and non-system include directory
-#2557: comparison between signed and unsigned operands
-#3280: declaration hides member ".."
-#11074: Inlining inhibited by limit max-size(/max-total-size)
-#11076: To get full report use -opt-report=3 -opt-report-phase ipo (shown for previous remark)
- GMX_TEST_CFLAG(CFLAGS_WARN "-w3;-wd177;-wd280;-wd411;-wd593;-wd981;-wd1418;-wd1419;-wd1572;-wd1599;-wd2259;-wd2415;-wd2547;-wd2557;-wd3280;-wd11074;-wd11076" GMXC_CFLAGS)
- endif()
- GMX_TEST_CFLAG(CFLAGS_STDGNU "-std=gnu99" GMXC_CFLAGS)
- GMX_TEST_CFLAG(CFLAGS_OPT "-ip;-funroll-all-loops;-alias-const;-ansi-alias;-no-prec-div;-fimf-domain-exclusion=14;-qoverride-limits" GMXC_CFLAGS_RELEASE)
- GMX_TEST_CFLAG(CFLAGS_DEBUG "-O0" GMXC_CFLAGS_DEBUG) #icc defaults to -O2 even with -g
- # The "except" fp-model requires something other than the
- # default "fast" model, so we test and use it with
- # "precise".
- GMX_TEST_CFLAG(CFLAGS_FP_MODEL_RELASSERT "-fp-model=except;-fp-model=precise" GMXC_CFLAGS_RELWITHASSERT)
- else()
- if(NOT GMX_OPENMP)
- GMX_TEST_CFLAG(CFLAGS_PRAGMA "/wd3180" GMXC_CFLAGS)
- endif()
- if (GMX_COMPILER_WARNINGS)
-#only on Windows
-#161: unrecognized pragma
-#1786 function was declared deprecated (is issued for stdlib function such as strncpy which have a _s version)
-GMX_TEST_CFLAG(CFLAGS_WARN "/W3;/wd161;/wd177;/wd411;/wd593;/wd981;/wd1418;/wd1419;/wd1572;/wd1599;/wd1786;/wd2259;/wd2415;/wd2547;/wd2557;/wd3280" GMXC_CFLAGS)
- endif()
- GMX_TEST_CFLAG(CFLAGS_OPT "/Qip" GMXC_CFLAGS_RELEASE)
- endif()
- endif()
-
- if (CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
- if (NOT WIN32)
- if(NOT GMX_OPENMP)
- GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "-wd3180" GMXC_CXXFLAGS)
- endif()
- if (GMX_COMPILER_WARNINGS)
-#All but the following warnings are identical for the C-compiler (see above)
-# 304: access control not specified
-# 383: value copied to temporary, reference to temporary used
-# 444: destructor for base class ".." is not virtual
-# 869: was never referenced (false positives)
-#2282: unrecognized GCC pragma
-#2621: attribute "unused" does not apply here
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN "-w3;-wd177;-wd280;-wd304;-wd383;-wd411;-wd444;-wd869;-wd981;-wd1418;-wd1572;-wd1599;-wd2259;-wd2547;-wd2621;-wd3280;-wd11074;-wd11076;-wd2282" GMXC_CXXFLAGS)
- endif()
- GMX_TEST_CXXFLAG(CXXFLAGS_OPT "-ip;-funroll-all-loops;-alias-const;-ansi-alias;-no-prec-div;-fimf-domain-exclusion=14;-qoverride-limits" GMXC_CXXFLAGS_RELEASE)
- GMX_TEST_CXXFLAG(CXXFLAGS_DEBUG "-O0" GMXC_CXXFLAGS_DEBUG)
- # The "except" fp-model requires something other than the
- # default "fast" model, so we test and use it with
- # "precise".
- GMX_TEST_CXXFLAG(CXXFLAGS_FP_MODEL_RELASSERT "-fp-model=except;-fp-model=precise" GMXC_CXXFLAGS_RELWITHASSERT)
- else()
- if(NOT GMX_OPENMP)
- GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "/wd3180" GMXC_CFLAGS)
- endif()
- if (GMX_COMPILER_WARNINGS)
-#161: unrecognized pragma
-#809: exception specification for virtual function X is incompatible with that of overridden function
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/W3;/wd161;/wd177;/wd280;/wd304;/wd383;/wd411;/wd444;/wd809;/wd869;/wd981;/wd1418;/wd1572;/wd1599;/wd1786;/wd2259;/wd2547;/wd3280;/wd11074;/wd11076;/wd2282" GMXC_CXXFLAGS)
- endif()
- GMX_TEST_CXXFLAG(CXXFLAGS_OPT "/Qip" GMXC_CXXFLAGS_RELEASE)
- endif()
- endif()
-
# PGI
# Inter-procedural analysis causes pgcc/pgc++ to crash when linking the library with PGI release 15.7.
if (CMAKE_C_COMPILER_ID MATCHES "PGI")
endif()
endif()
- # Fujitsu compilers on PrimeHPC/Sparc64
- if(${CMAKE_C_COMPILER_ID} MATCHES Fujitsu OR
- (${CMAKE_C_COMPILER_ID} MATCHES unknown AND ${CMAKE_C_COMPILER} MATCHES ^fcc))
- GMX_TEST_CFLAG(CFLAG_GNUCOMPAT "-Xg;-w" GMXC_CFLAGS)
- GMX_TEST_CFLAG(CFLAG_OPT "-Kfast,reduction,swp,simd=2,uxsimd,fsimple;-x100" GMXC_CFLAGS)
- endif()
-
- if(${CMAKE_CXX_COMPILER_ID} MATCHES Fujitsu OR
- (${CMAKE_CXX_COMPILER_ID} MATCHES unknown AND ${CMAKE_CXX_COMPILER} MATCHES ^FCC))
- GMX_TEST_CXXFLAG(CXXFLAG_GNUCOMPAT "-Xg;-w" GMXC_CXXFLAGS)
- GMX_TEST_CXXFLAG(CXXFLAG_OPT "-Kfast,reduction,swp,simd=2,uxsimd,fsimple;-x100" GMXC_CXXFLAGS)
- endif()
-
endmacro()
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
-# Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
else()
if(CPU_DETECTION_FEATURES MATCHES " vsx ")
set(OUTPUT_SIMD "IBM_VSX")
- elseif(CPU_DETECTION_FEATURES MATCHES " vmx ")
- set(OUTPUT_SIMD "IBM_VMX")
elseif(CPU_DETECTION_FEATURES MATCHES " sve ")
set(OUTPUT_SIMD "ARM_SVE")
elseif(CPU_DETECTION_FEATURES MATCHES " neon_asimd ")
set(OUTPUT_SIMD "ARM_NEON_ASIMD")
- elseif(CPU_DETECTION_FEATURES MATCHES " neon " AND NOT GMX_DOUBLE)
- set(OUTPUT_SIMD "ARM_NEON")
endif()
endif()
if (NOT SUGGEST_SIMD_QUIETLY)
function(gmx_detect_simd _suggested_simd)
if(GMX_SIMD STREQUAL "AUTO")
- if(GMX_TARGET_FUJITSU_SPARC64)
- # HPC-ACE is always present. In the future we
- # should add detection for HPC-ACE2 here.
- set(${_suggested_simd} "Sparc64_HPC_ACE")
- elseif(GMX_TARGET_MIC)
- set(${_suggested_simd} "MIC")
- else()
- gmx_suggest_simd(${_suggested_simd})
- endif()
+ gmx_suggest_simd(${_suggested_simd})
string(TOUPPER "${${_suggested_simd}}" ${_suggested_simd})
set(${_suggested_simd} ${${_suggested_simd}} PARENT_SCOPE)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014,2016,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2016,2018,2019,2020, by the GROMACS development team.
+# Copyright (c) 2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
try_compile(GMX_TARGET_X86 ${CMAKE_BINARY_DIR}
"${CMAKE_SOURCE_DIR}/cmake/TestX86.cpp")
endif()
- if (NOT DEFINED GMX_TARGET_MIC)
- try_compile(GMX_TARGET_MIC ${CMAKE_BINARY_DIR}
- "${CMAKE_SOURCE_DIR}/cmake/TestMIC.cpp")
- endif()
- if (GMX_TARGET_MIC)
- message(STATUS "The Intel MIC KNC target is deprecated")
- endif()
- if (NOT DEFINED GMX_TARGET_FUJITSU_SPARC64)
- try_compile(GMX_TARGET_FUJITSU_SPARC64 ${CMAKE_BINARY_DIR}
- "${CMAKE_SOURCE_DIR}/cmake/TestFujitsuSparc64.cpp")
- endif()
- if (GMX_TARGET_FUJITSU_SPARC64)
- message(STATUS "The Fujitsu Sparc64 target is deprecated")
- endif()
endfunction()
# version of GROMACS is in use.
set(RELEASE_CHECKSUM_FILE "${PROJECT_SOURCE_DIR}/src/reference_checksum")
if(NOT VERSION_STRING_OF_FORK OR "${VERSION_STRING_OF_FORK}" STREQUAL "")
- if(EXISTS ${RELEASE_CHECKSUM_FILE} AND PYTHON_EXECUTABLE)
+ if(NOT EXISTS ${RELEASE_CHECKSUM_FILE})
+ set(GMX_VERSION_STRING_FULL "${GMX_VERSION_STRING_FULL}-UNCHECKED")
+ set(GMX_RELEASE_SOURCE_FILE_CHECKSUM "NoChecksumFile")
+ set(GMX_CURRENT_SOURCE_FILE_CHECKSUM "NoChecksumFile")
+ message(WARNING "Could not valdiate the GROMACS source due to missing reference checksum file.")
+ elseif(NOT PYTHON_EXECUTABLE)
+ set(GMX_VERSION_STRING_FULL "${GMX_VERSION_STRING_FULL}-UNCHECKED")
+ set(GMX_RELEASE_SOURCE_FILE_CHECKSUM "NoPythonAvailable")
+ set(GMX_CURRENT_SOURCE_FILE_CHECKSUM "NoPythonAvailable")
+ message(STATUS "Could not calculate checksum of source files without Python")
+ else()
file(READ ${RELEASE_CHECKSUM_FILE} GMX_RELEASE_SOURCE_FILE_CHECKSUM)
string(STRIP ${GMX_RELEASE_SOURCE_FILE_CHECKSUM} GMX_RELEASE_SOURCE_FILE_CHECKSUM)
set(CHECKSUM_RESULT_FILE "${CMAKE_CURRENT_BINARY_DIR}/computed_checksum")
set(GMX_VERSION_STRING_FULL "${GMX_VERSION_STRING_FULL}-MODIFIED")
message(STATUS "The source code for this GROMACS installation is different from the officially released version.")
endif()
- elseif(PYTHON_EXECUTABLE)
- set(GMX_VERSION_STRING_FULL "${GMX_VERSION_STRING_FULL}-UNCHECKED")
- set(GMX_RELEASE_SOURCE_FILE_CHECKSUM "NoChecksumFile")
- set(GMX_CURRENT_SOURCE_FILE_CHECKSUM "NoChecksumFile")
- message(WARNING "Could not valdiate the GROMACS source due to missing reference checksum file.")
- else()
- set(GMX_VERSION_STRING_FULL "${GMX_VERSION_STRING_FULL}-UNCHECKED")
- set(GMX_RELEASE_SOURCE_FILE_CHECKSUM "NoPythonAvailable")
- set(GMX_CURRENT_SOURCE_FILE_CHECKSUM "NoPythonAvailable")
- message(STATUS "Could not calculate checksum of source files without Python")
endif()
endif()
else()
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
message(WARNING "Values passed in GMX_CUDA_TARGET_COMPUTE will be ignored; clang will by default include PTX in the binary.")
endif()
+if (CUDA_VERSION VERSION_GREATER 10.1)
+ # At the time of writing, the latest versions are Clang 11 and CUDA 11.2.
+ if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 11.0)
+ # We don't know about the future Clang versions, but so far Clang 12 docs state that only CUDA versions 7.0-10.1 are supported.
+ set(_support_status "likely incompatible")
+ else()
+ if (CUDA_VERSION VERSION_GREATER 11.2)
+ # No idea about future CUDA versions.
+ set(_support_status "officially incompatible")
+ else()
+ # Our experience and multiple reports on the internet indicate that it works just fine.
+ set(_support_status "officially incompatible (but generally working)")
+ endif()
+ endif()
+ message(NOTICE "Using ${_support_status} version of CUDA with Clang.")
+ message(NOTICE "If Clang fails to recognize CUDA version, consider creating doing "
+ "`echo \"CUDA Version ${CUDA_VERSION}\" | sudo tee \"${CUDA_TOOLKIT_ROOT_DIR}/version.txt\"`")
+ list(APPEND _CUDA_CLANG_FLAGS "-Wno-unknown-cuda-version")
+
+endif()
+
if (GMX_CUDA_TARGET_SM)
set(_CUDA_CLANG_GENCODE_FLAGS)
set(_target_sm_list ${GMX_CUDA_TARGET_SM})
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_${_target}")
endforeach()
else()
- list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_30")
+ if (CUDA_VERSION VERSION_LESS 11.0)
+ list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_30")
+ endif()
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_35")
# clang 6.0 + CUDA 9.0 seems to have issues generating code for sm_37
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 6.0 OR CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 6.0.999)
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_60")
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_61")
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_70")
- # Enable this when clang (8.0 ?) introduces sm_75 support
- #if (NOT CUDA_VERSION VERSION_LESS 10.0)
- # list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_75")
+ if (NOT CUDA_VERSION VERSION_LESS 10.0)
+ list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_75")
+ endif()
+ # Enable this when clang (12.0 ?) properly recognizes CUDA 11.0
+ #if(NOT CUDA_VERSION VERSION_LESS 11.0)
+ # list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_80")
+ #endif()
+ # Enable this when clang (12.0 ?) introduces sm_86 support
+ #if(NOT CUDA_VERSION VERSION_LESS 11.1)
+ # list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_86")
#endif()
endif()
if (GMX_CUDA_TARGET_SM)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2009,2011,2012,2014,2015 by the GROMACS development team.
-# Copyright (c) 2016,2020, by the GROMACS development team, led by
+# Copyright (c) 2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-# - Define macro to check if MPI_IN_PLACE exists
+# - Define function to check if underlying MPI is CUDA-aware
#
-# GMX_TEST_MPI_IN_PLACE(VARIABLE)
+# GMX_TEST_CUDA_AWARE_MPI()
#
-# VARIABLE will be set to true if MPI_IN_PLACE exists
+# GMX_TEST_CUDA_AWARE_MPI puts HAVE_CUDA_AWARE_MPI variable in cache
#
-
-include(CheckCSourceCompiles)
-MACRO(GMX_TEST_MPI_IN_PLACE VARIABLE)
- if(NOT DEFINED MPI_IN_PLACE_COMPILE_OK)
- MESSAGE(STATUS "Checking for MPI_IN_PLACE")
-
- if(CMAKE_VERSION VERSION_LESS 3.12)
- foreach(_FLAG ${MPI_COMPILE_FLAGS})
- set(CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS} ${_FLAG}")
- endforeach()
- else()
- list(JOIN MPI_COMPILE_FLAGS " " CMAKE_REQUIRED_FLAGS)
- endif()
+include(CheckCXXSourceCompiles)
+function(GMX_TEST_CUDA_AWARE_MPI)
+ if (NOT DEFINED HAVE_CUDA_AWARE_MPI)
+ MESSAGE(STATUS "Checking for CUDA_AWARE_MPI")
+ list(JOIN MPI_COMPILE_FLAGS " " CMAKE_REQUIRED_FLAGS)
set(CMAKE_REQUIRED_INCLUDES ${MPI_INCLUDE_PATH})
set(CMAKE_REQUIRED_LIBRARIES ${MPI_LIBRARIES})
+ # cannot use check_include_file here as mpi.h needs to be included
+ # before mpi-ext.h for compilation, check_include_file doesn't support
+ # this use-case
check_cxx_source_compiles(
"#include <mpi.h>
-int main(void) {
- void* buf;
- MPI_Allreduce(MPI_IN_PLACE, buf, 10, MPI_FLOAT, MPI_SUM, MPI_COMM_WORLD);
-}" MPI_IN_PLACE_COMPILE_OK)
+ #include <mpi-ext.h>
+ int main(void)
+ {
+ #if defined(MPIX_CUDA_AWARE_SUPPORT) && (MPIX_CUDA_AWARE_SUPPORT==1)
+ return 0;
+ #else
+ #error MPI implementation isn't CUDA-aware
+ #endif
+ }" HAVE_CUDA_AWARE_MPI)
- if(MPI_IN_PLACE_COMPILE_OK)
- MESSAGE(STATUS "Checking for MPI_IN_PLACE - yes")
+ if(HAVE_CUDA_AWARE_MPI)
+ MESSAGE(STATUS "Checking for CUDA_AWARE_MPI - yes")
else()
- MESSAGE(STATUS "Checking for MPI_IN_PLACE - no")
+ MESSAGE(STATUS "Checking for CUDA_AWARE_MPI - no")
+ MESSAGE(WARNING "GROMACS cannot determine if underlying MPI is CUDA-aware, "
+ "for better multi-GPU performance consider using a more recent CUDA-aware MPI.")
endif()
- set(MPI_IN_PLACE_COMPILE_OK "${MPI_IN_PLACE_COMPILE_OK}" CACHE INTERNAL "Result of mpi_in_place check")
- set(CMAKE_REQUIRED_FLAGS)
- set(CMAKE_REQUIRED_INCLUDES)
- set(CMAKE_REQUIRED_LIBRARIES)
endif()
- if (MPI_IN_PLACE_COMPILE_OK)
- set(${VARIABLE} ${MPI_IN_PLACE_COMPILE_OK}
- "Result of test for MPI_IN_PLACE")
- endif()
-ENDMACRO(GMX_TEST_MPI_IN_PLACE VARIABLE)
+endfunction()
+
+# Test if CUDA-aware MPI is supported
+gmx_test_cuda_aware_mpi()
+
# all their stuff. It's not easy if you only want some of their
# stuff...
set(MKL_MANUALLY FALSE)
-if (GMX_FFT_LIBRARY STREQUAL "MKL" AND
- NOT ((CMAKE_C_COMPILER_ID MATCHES "Intel" AND CMAKE_C_COMPILER_VERSION VERSION_GREATER "11")
- OR GMX_INTEL_LLVM))
+if (GMX_FFT_LIBRARY STREQUAL "MKL" AND NOT GMX_INTEL_LLVM)
# The user will have to provide the set of magic libraries in
# MKL_LIBRARIES (see below), which we cache (non-advanced), so that they
# don't have to keep specifying it, and can easily see that
set(FFT_LIBRARIES ${${FFTW}_LIBRARIES})
elseif(${GMX_FFT_LIBRARY} STREQUAL "MKL")
- # Intel 11 and up makes life somewhat easy if you just want to use
+ # Intel compilers make life somewhat easy if you just want to use
# all their stuff. It's not easy if you only want some of their
# stuff...
if (NOT MKL_MANUALLY)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014,2016,2020, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2016,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# these. If the libraries are not in a standard location, the user can
# indicate a search path with CMAKE_PREFIX_PATH.
#
-# However, if we are using icc+mkl (so a build command that includes
+# However, if we are using icpx+mkl (so a build command that includes
# -mkl), then it is probably painful to try to link some other BLAS or
# LAPACK. In that case, we use the BLAS & LAPACK provided by MKL. In
# principle, we could offer a more configurable behaviour if/when
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
-# Copyright (c) 2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# If CMAKE_C_COMPILER is not a MPI wrapper. Try to find MPI using cmake module as fall-back.
if(NOT MPI_FOUND)
find_package(MPI)
- if(MPI_C_FOUND)
- set(MPI_COMPILE_FLAGS ${MPI_C_COMPILE_FLAGS})
+ if (MPI_CXX_VERSION VERSION_LESS 2.0)
+ message(FATAL_ERROR "MPI version 2.0 or higher is required. Please update your MPI library.")
+ endif()
+ if(MPI_CXX_FOUND)
+ set(MPI_COMPILE_FLAGS ${MPI_CXX_COMPILE_FLAGS})
separate_arguments(MPI_COMPILE_FLAGS)
- set(MPI_LINKER_FLAGS ${MPI_C_LINK_FLAGS})
- separate_arguments(MPI_C_LINK_FLAGS)
- include_directories(SYSTEM ${MPI_C_INCLUDE_PATH})
- list(APPEND GMX_COMMON_LIBRARIES ${MPI_C_LIBRARIES})
+ set(MPI_LINKER_FLAGS ${MPI_CXX_LINK_FLAGS})
+ separate_arguments(MPI_CXX_LINK_FLAGS)
+ include_directories(SYSTEM ${MPI_CXX_INCLUDE_PATH})
+ list(APPEND GMX_COMMON_LIBRARIES ${MPI_CXX_LIBRARIES})
endif()
- set(MPI_FOUND ${MPI_C_FOUND})
+ set(MPI_FOUND ${MPI_CXX_FOUND})
else()
# The following defaults are based on FindMPI.cmake in cmake
# 3.1.2. (That package does not actually do any detection of the
endif()
if(MPI_FOUND)
- include(gmxTestMPI_IN_PLACE)
- if (GMX_MPI_IN_PLACE)
- gmx_test_mpi_in_place(MPI_IN_PLACE_EXISTS)
- endif()
-
# Find path of the mpi compilers
- if (${MPI_C_FOUND})
- get_filename_component(_mpi_c_compiler_path "${MPI_C_COMPILER}" PATH)
+ if (${MPI_CXX_FOUND})
+ get_filename_component(_mpi_c_compiler_path "${MPI_CXX_COMPILER}" PATH)
get_filename_component(_mpiexec_path "${MPIEXEC}" PATH)
else()
get_filename_component(_cmake_c_compiler_path "${CMAKE_C_COMPILER}" PATH)
message(FATAL_ERROR
"MPI support requested, but no MPI compiler found. Either set the "
"C-compiler (CMAKE_C_COMPILER) to the MPI compiler (often called mpicc), "
- "or set the variables reported missing for MPI_C above.")
+ "or set the variables reported missing for MPI_CXX above.")
endif()
set(GMX_LIB_MPI 1)
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2012,2013,2014,2015,2018 by the GROMACS development team.
-# Copyright (c) 2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
message(FATAL_ERROR "The OpenCL implementation is only supported on 64-bit platforms.")
endif()
-set(GMX_OPENCL_NB_CLUSTER_SIZE 8 CACHE STRING "Cluster size used by nonbonded OpenCL kernel. Set to 4 for Intel GPUs.")
-mark_as_advanced(GMX_OPENCL_NB_CLUSTER_SIZE)
-
set(GMX_INSTALL_OCLDIR ${GMX_INSTALL_GMXDATADIR}/opencl)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2020, by the GROMACS development team, led by
+# Copyright (c) 2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
set(GMX_GPU_SYCL ON)
+# CMake issue tracking the efforts to make a universal upstream module:
+# https://gitlab.kitware.com/cmake/cmake/-/issues/21711
+
+option(GMX_SYCL_HIPSYCL "Use hipSYCL instead of Intel/Clang for SYCL compilation" OFF)
+
if(GMX_DOUBLE)
message(FATAL_ERROR "SYCL acceleration is not available in double precision")
endif()
include(gmxFindFlagsForSource)
-if(CMAKE_CXX_COMPILER MATCHES "dpcpp")
- # At least Intel dpcpp defaults to having SYCL enabled for all code. This leads to two problems:
- #
- # 1. Compiles take ~3x longer, since every file has to be compiled for multiple targets.
- # 2. We get a ton of warnings for the device-specific pass when the compiler sees our SIMD code.
- #
- # To avoid this, we attempt to find a flag to disable SYCL for non-SYCL files. Unfortunately,
- # when using gmx_find_flag_for_source() that includes calling check_cxx_compiler_flag(),
- # this in turn exposes a bug in dpcpp, where an object file compiles with -fno-sycl leads to
- # a failed link stage (when the same flag is not used). Since none of this is critical, we handle
- # it by merely checking if it works to compile a source fils with this flag, and choking if SYCL
- # is still enabled.
-
- if(NOT CHECK_DISABLE_SYCL_CXX_FLAGS_QUIETLY)
- message(STATUS "Checking for flags to disable SYCL")
- endif()
-
- gmx_check_source_compiles_with_flags(
- "int main() { return 0; }"
- "-fno-sycl"
- "CXX"
- DISABLE_SYCL_CXX_FLAGS_RESULT)
-
- if(DISABLE_SYCL_CXX_FLAGS_RESULT)
- set(DISABLE_SYCL_CXX_FLAGS "-fno-sycl")
+if(GMX_SYCL_HIPSYCL)
+ if(NOT CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+ message(FATAL_ERROR "hipSYCL can only be built with Clang++ compiler")
endif()
- if(NOT CHECK_DISABLE_SYCL_CXX_FLAGS_QUIETLY)
+ set(HIPSYCL_CLANG "${CMAKE_CXX_COMPILER}")
+ # -Wno-unknown-cuda-version because Clang-11 complains about CUDA 11.0-11.2, despite working fine with them.
+ # -Wno-unknown-attributes because hipSYCL does not support reqd_sub_group_size (because it can only do some sub group sizes).
+ # --hipsycl-explicit-multipass is needed when building for both CUDA and HIP.
+ set(HIPSYCL_SYCLCC_EXTRA_ARGS "-Wno-unknown-cuda-version -Wno-unknown-attributes --hipsycl-explicit-multipass")
+ find_package(hipsycl REQUIRED)
+else()
+ if(CMAKE_CXX_COMPILER MATCHES "dpcpp")
+ # At least Intel dpcpp defaults to having SYCL enabled for all code. This leads to two problems:
+ #
+ # 1. Compiles take ~3x longer, since every file has to be compiled for multiple targets.
+ # 2. We get a ton of warnings for the device-specific pass when the compiler sees our SIMD code.
+ #
+ # To avoid this, we attempt to find a flag to disable SYCL for non-SYCL files. Unfortunately,
+ # when using gmx_find_flag_for_source() that includes calling check_cxx_compiler_flag(),
+ # this in turn exposes a bug in dpcpp, where an object file compiles with -fno-sycl leads to
+ # a failed link stage (when the same flag is not used). Since none of this is critical, we handle
+ # it by merely checking if it works to compile a source fils with this flag, and choking if SYCL
+ # is still enabled.
+
+ if(NOT CHECK_DISABLE_SYCL_CXX_FLAGS_QUIETLY)
+ message(STATUS "Checking for flags to disable SYCL")
+ endif()
+
+ gmx_check_source_compiles_with_flags(
+ "int main() { return 0; }"
+ "-fno-sycl"
+ "CXX"
+ DISABLE_SYCL_CXX_FLAGS_RESULT)
+
if(DISABLE_SYCL_CXX_FLAGS_RESULT)
- message(STATUS "Checking for flags to disable SYCL - -fno-sycl")
- else()
- message(WARNING "Cannot find flags to disable SYCL for non-SYCL hardware-specific C++ code. Expect many warnings, but they are likely benign.")
+ set(DISABLE_SYCL_CXX_FLAGS "-fno-sycl")
+ endif()
+ if(NOT CHECK_DISABLE_SYCL_CXX_FLAGS_QUIETLY)
+ if(DISABLE_SYCL_CXX_FLAGS_RESULT)
+ message(STATUS "Checking for flags to disable SYCL - -fno-sycl")
+ else()
+ message(WARNING "Cannot find flags to disable SYCL for non-SYCL hardware-specific C++ code. Expect many warnings, but they are likely benign.")
+ endif()
+ set(CHECK_DISABLE_SYCL_CXX_FLAGS_QUIETLY 1 CACHE INTERNAL "Keep quiet on future calls to detect no-SYCL flags" FORCE)
endif()
- set(CHECK_DISABLE_SYCL_CXX_FLAGS_QUIETLY 1 CACHE INTERNAL "Keep quiet on future calls to detect no-SYCL flags" FORCE)
endif()
-endif()
-
-# Find the flags to enable (or re-enable) SYCL with Intel extensions. In case we turned it off above,
-# it's important that we check the combination of both flags, to make sure the second one re-enables SYCL.
-if(NOT CHECK_SYCL_CXX_FLAGS_QUIETLY)
- message(STATUS "Checking for flags to enable SYCL")
-endif()
-gmx_find_flag_for_source(SYCL_CXX_FLAGS_RESULT
- "#include <CL/sycl.hpp>
- namespace sycl = cl::sycl;
- int main(){
- constexpr int length = 1000;
- sycl::queue q(sycl::default_selector{});
- // Check USM extension
- sycl::usm_allocator<int, sycl::usm::alloc::shared> q_alloc{q};
- std::vector<int, sycl::usm_allocator<int, sycl::usm::alloc::shared>> v(q_alloc);
- v.reserve(length);
- for(int i = 0; i < length ; i++) { v.push_back(i); }
- q.parallel_for<class whatever>(sycl::range<1>{length}, [=, ptr = v.data()] (sycl::id<1> i){ ptr[i] *= 2; }).wait();
- return 0;
- }
- " "CXX" DISABLE_SYCL_CXX_FLAGS SYCL_CXX_FLAGS "-fsycl")
-
-if(NOT CHECK_SYCL_CXX_FLAGS_QUIETLY)
- if(SYCL_CXX_FLAGS_RESULT)
- message(STATUS "Checking for flags to enable SYCL - ${SYCL_CXX_FLAGS}")
+
+ # Find the flags to enable (or re-enable) SYCL with Intel extensions. In case we turned it off above,
+ # it's important that we check the combination of both flags, to make sure the second one re-enables SYCL.
+ if(NOT CHECK_SYCL_CXX_FLAGS_QUIETLY)
+ message(STATUS "Checking for flags to enable SYCL")
+ endif()
+ gmx_find_flag_for_source(SYCL_CXX_FLAGS_RESULT
+ "#include <CL/sycl.hpp>
+ namespace sycl = cl::sycl;
+ int main(){
+ sycl::queue q(sycl::default_selector{});
+ return 0;
+ }
+ " "CXX" DISABLE_SYCL_CXX_FLAGS SYCL_CXX_FLAGS "-fsycl -fsycl-device-code-split=per_kernel")
+
+ if(NOT CHECK_SYCL_CXX_FLAGS_QUIETLY)
+ if(SYCL_CXX_FLAGS_RESULT)
+ message(STATUS "Checking for flags to enable SYCL - ${SYCL_CXX_FLAGS}")
+ endif()
+ set(CHECK_SYCL_CXX_FLAGS_QUIETLY 1 CACHE INTERNAL "Keep quiet on future calls to detect SYCL flags" FORCE)
+ endif()
+
+ if(NOT SYCL_CXX_FLAGS_RESULT)
+ message(FATAL_ERROR "Cannot compile with SYCL Intel compiler. Try a different compiler or disable SYCL.")
endif()
- set(CHECK_SYCL_CXX_FLAGS_QUIETLY 1 CACHE INTERNAL "Keep quiet on future calls to detect SYCL flags" FORCE)
-endif()
-if(NOT SYCL_CXX_FLAGS_RESULT)
- message(ERROR "Cannot compile SYCL with Intel extensions. Try a different compiler or disable SYCL.")
+ # Add function wrapper similar to the one used by ComputeCPP and hipSYCL
+ function(add_sycl_to_target)
+ cmake_parse_arguments(
+ PARSE_ARGV 0 # No positional arguments
+ ARGS # Prefix for the resulting variables
+ "" # No options
+ "TARGET" # One-value keyword
+ "SOURCES" # Multi-value keyword
+ )
+ set_source_files_properties(${ARGS_SOURCES} PROPERTIES COMPILE_FLAGS "${SYCL_CXX_FLAGS}")
+ target_link_libraries(${ARGS_TARGET} PRIVATE ${SYCL_CXX_FLAGS})
+ endfunction(add_sycl_to_target)
endif()
########################################################################
# Determine the defaults (this block has no effect if the variables have
# already been set)
-if((APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD|GNU") AND NOT GMX_BUILD_MDRUN_ONLY)
+if((APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD|GNU"))
# Maybe Solaris should be here? Patch this if you know!
SET(SHARED_LIBS_DEFAULT ON)
elseif(WIN32)
set(GMX_PREFER_STATIC_LIBS_DEFAULT ON)
endif()
-if(BUILD_SHARED_LIBS AND GMX_BUILD_MDRUN_ONLY)
- message(WARNING "Both BUILD_SHARED_LIBS and GMX_BUILD_MDRUN_ONLY are set. Generally, an mdrun-only build should prefer to use static libraries, which is the default if you make a fresh build tree. You may be re-using an old build tree, and so may wish to set BUILD_SHARED_LIBS=off yourself.")
-endif()
-
if (UNIX)
set(GMX_PREFER_STATIC_LIBS_DESCRIPTION
"When finding libraries prefer static archives (it will only work if static versions of external dependencies are available and found)")
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
-# Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
set(SIMD_STATUS_MESSAGE "Enabling 256-bit AVX2 SIMD instructions using CXX flags: ${SIMD_AVX2_CXX_FLAGS}")
endif()
-elseif(GMX_SIMD_ACTIVE STREQUAL "MIC")
- # No flags needed. Not testing.
- set(GMX_SIMD_X86_MIC 1)
- set(SIMD_STATUS_MESSAGE "Enabling MIC (Xeon Phi) SIMD instructions without special flags. This SIMD support is deprecated.")
-
elseif(GMX_SIMD_ACTIVE STREQUAL "AVX_512")
gmx_find_simd_avx_512_flags(SIMD_AVX_512_C_SUPPORTED SIMD_AVX_512_CXX_SUPPORTED
set(GMX_SIMD_X86_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling 512-bit AVX-512-KNL SIMD instructions using CXX flags: ${SIMD_AVX_512_KNL_CXX_FLAGS}")
-elseif(GMX_SIMD_ACTIVE STREQUAL "ARM_NEON")
-
- if (GMX_DOUBLE)
- message(FATAL_ERROR "ARM_NEON SIMD support is not available for a double precision build because the architecture lacks double-precision support")
- endif()
-
- gmx_find_simd_arm_neon_flags(SIMD_ARM_NEON_C_SUPPORTED SIMD_ARM_NEON_CXX_SUPPORTED
- SIMD_ARM_NEON_C_FLAGS SIMD_ARM_NEON_CXX_FLAGS)
-
- if(NOT SIMD_ARM_NEON_C_SUPPORTED OR NOT SIMD_ARM_NEON_CXX_SUPPORTED)
- gmx_give_fatal_error_when_simd_support_not_found("ARM NEON" "disable SIMD support (slower)" "${SUGGEST_BINUTILS_UPDATE}")
- endif()
-
- # If multiple flags are neeed, make them into a list
- string(REPLACE " " ";" SIMD_C_FLAGS ${SIMD_ARM_NEON_C_FLAGS})
- string(REPLACE " " ";" SIMD_CXX_FLAGS ${SIMD_ARM_NEON_CXX_FLAGS})
- set(GMX_SIMD_${GMX_SIMD_ACTIVE} 1)
- set(SIMD_STATUS_MESSAGE "Enabling 32-bit ARM NEON SIMD instructions using CXX flags: ${SIMD_ARM_NEON_CXX_FLAGS}. This SIMD support is deprecated.")
-
elseif(GMX_SIMD_ACTIVE STREQUAL "ARM_NEON_ASIMD")
gmx_find_simd_arm_neon_asimd_flags(SIMD_ARM_NEON_ASIMD_C_SUPPORTED SIMD_ARM_NEON_ASIMD_CXX_SUPPORTED
elseif(GMX_SIMD_ACTIVE STREQUAL "ARM_SVE")
- # Note that GMX_RELAXED_DOUBLE_PRECISION is enabled by default in the top-level CMakeLists.txt
gmx_option_multichoice(
GMX_SIMD_ARM_SVE_LENGTH
"SVE vector length in bits"
set(GMX_SIMD_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling ARM (AArch64) SVE Advanced SIMD instructions using CXX flags: ${SIMD_ARM_SVE_CXX_FLAGS}")
-elseif(GMX_SIMD_ACTIVE STREQUAL "IBM_VMX")
-
- gmx_find_simd_ibm_vmx_flags(SIMD_IBM_VMX_C_SUPPORTED SIMD_IBM_VMX_CXX_SUPPORTED
- SIMD_IBM_VMX_C_FLAGS SIMD_IBM_VMX_CXX_FLAGS)
-
- if(NOT SIMD_IBM_VMX_C_SUPPORTED OR NOT SIMD_IBM_VMX_CXX_SUPPORTED)
- gmx_give_fatal_error_when_simd_support_not_found("IBM VMX" "disable SIMD support (slower)" "${SUGGEST_BINUTILS_UPDATE}")
- endif()
-
- # If multiple flags are neeed, make them into a list
- string(REPLACE " " ";" SIMD_C_FLAGS ${SIMD_IBM_VMX_C_FLAGS})
- string(REPLACE " " ";" SIMD_CXX_FLAGS ${SIMD_IBM_VMX_CXX_FLAGS})
- set(GMX_SIMD_${GMX_SIMD_ACTIVE} 1)
- set(SIMD_STATUS_MESSAGE "Enabling IBM VMX SIMD instructions using CXX flags: ${SIMD_IBM_VMX_CXX_FLAGS}. This SIMD support is deprecated.")
-
elseif(GMX_SIMD_ACTIVE STREQUAL "IBM_VSX")
# IBM_VSX and gcc > 9 do not work together, so we need to prevent people from
set(GMX_SIMD_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling IBM VSX SIMD instructions using CXX flags: ${SIMD_IBM_VSX_CXX_FLAGS}")
-elseif(GMX_SIMD_ACTIVE STREQUAL "SPARC64_HPC_ACE")
-
- # Note that GMX_RELAXED_DOUBLE_PRECISION is enabled by default in the top-level CMakeLists.txt
-
- set(GMX_SIMD_${GMX_SIMD_ACTIVE} 1)
- set(SIMD_STATUS_MESSAGE "Enabling Sparc64 HPC-ACE SIMD instructions without special flags. This SIMD support is deprecated.")
-
elseif(GMX_SIMD_ACTIVE STREQUAL "REFERENCE")
# NB: This file handles settings for the SIMD module, so in the interest
# By default, 32-bit windows cannot pass SIMD (SSE/AVX) arguments in registers,
# and even on 64-bit (all platforms) it is only used for a handful of arguments.
-# The __vectorcall (MSVC, from MSVC2013) or __regcall (ICC) calling conventions
-# enable this, which is critical to enable 32-bit SIMD and improves performance
+# The __vectorcall (MSVC, from MSVC2013) calling convention
+# enables this, which is critical to enable 32-bit SIMD and improves performance
# for 64-bit SIMD.
# Check if the compiler supports one of these, and in that case set gmx_simdcall
# to that string. If we do not have any such calling convention modifier, set it
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
endif()
endif()
unset(SUFFIXES_CHANGED)
-
-if (GMX_BUILD_MDRUN_ONLY)
- set(GMX_LIBS_SUFFIX "_mdrun${GMX_LIBS_SUFFIX}")
-endif()
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2020, by the GROMACS development team, led by
+# Copyright (c) 2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
set(Python3_FIND_QUIETLY ON)
set(PythonInterp_FIND_QUIETLY ON)
endif()
-if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.15)
- if (NOT Python3_FIND_STRATEGY)
- # If the user provides a hint for the Python installation with Python3_ROOT_DIR,
- # prevent FindPython3 from overriding the choice with a newer Python version
- # when CMP0094 is set to OLD.
- set(Python3_FIND_STRATEGY LOCATION)
- endif ()
- if(NOT Python3_FIND_VIRTUALENV)
- # We advocate using Python venvs to manage package availability, so by default
- # we want to preferentially discover user-space software.
- set(Python3_FIND_VIRTUALENV FIRST)
- endif()
-else()
- if(NOT Python3_FIND_REGISTRY)
- # We advocate using Python venvs to manage package availability, so by default
- # we want to preferentially discover user-space software.
- set(Python3_FIND_REGISTRY LAST)
- endif()
- # Make package discovery consistent with Unix behavior and our documented
- # suggestions for installing dependencies.
- set(CMAKE_FIND_FRAMEWORK LAST)
+if (NOT Python3_FIND_STRATEGY)
+ # If the user provides a hint for the Python installation with Python3_ROOT_DIR,
+ # prevent FindPython3 from overriding the choice with a newer Python version
+ # when CMP0094 is set to OLD.
+ set(Python3_FIND_STRATEGY LOCATION)
endif ()
+if(NOT Python3_FIND_VIRTUALENV)
+ # We advocate using Python venvs to manage package availability, so by default
+ # we want to preferentially discover user-space software.
+ set(Python3_FIND_VIRTUALENV FIRST)
+endif()
if(GMX_PYTHON_PACKAGE)
find_package(Python3 3.6 COMPONENTS Interpreter Development)
if (NOT Python3_FOUND OR NOT Python3_Development_FOUND)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# AVX2
function(gmx_find_simd_avx2_flags C_FLAGS_RESULT CXX_FLAGS_RESULT C_FLAGS_VARIABLE CXX_FLAGS_VARIABLE)
find_x86_toolchain_flags(TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS)
- # For our "AVX2_256" support we would ideally want to enable the instructions
- # we want to use, '-mavx2 -mfma'. icc (v16-18) does not allow doing that and
- # instead, it requires the '-march=core-avx2' flag to be used. Annoyingly, it does
- # however accept the former flags but it is not silent about it issuing warnings
- # that can't be disabled.
- # At the same time Intel's -march=core-avx2 flag is not rejected by gcc/clang either
- # (though they're at least silent). However, -march=core-avx2 is an undocumented
- # flag with unclear behavior in gcc/clang (and might enable some arch-specific optimizations).
- # For this reason, and because we can't distinguish compilers just based on checking flag
- # compatibility, we need to treat the Intel and gcc/clang separately.
- if (CMAKE_C_COMPILER_ID MATCHES "Intel")
- set(TOOLCHAIN_FLAG_FOR_AVX2 "-march=core-avx2")
- else()
- set(TOOLCHAIN_FLAG_FOR_AVX2 "-mavx2 -mfma")
- endif()
gmx_find_flags(SIMD_AVX2_C_FLAGS_RESULT SIMD_AVX2_CXX_FLAGS_RESULT
"#include<immintrin.h>
int main(){__m256i x=_mm256_set1_epi32(5);x=_mm256_add_epi32(x,x);return _mm256_movemask_epi8(x);}"
TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS
SIMD_AVX2_C_FLAGS SIMD_AVX2_CXX_FLAGS
- "${TOOLCHAIN_FLAG_FOR_AVX2}" "-mavx2" "/arch:AVX2" "-hgnu")
+ "-mavx2 -mfma" "-mavx2" "/arch:AVX2" "-hgnu")
if(${SIMD_AVX2_C_FLAGS_RESULT})
set(${C_FLAGS_VARIABLE} "${TOOLCHAIN_C_FLAGS} ${SIMD_AVX2_C_FLAGS}" CACHE INTERNAL "C flags required for AVX2 instructions")
return idata[0]*(int)(_mm512_cmp_ps_mask(x,y,_CMP_LT_OS));}"
TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS
SIMD_AVX_512_C_FLAGS SIMD_AVX_512_CXX_FLAGS
- "-xCORE-AVX512 -qopt-zmm-usage=high" "-xCORE-AVX512" "-mavx512f -mfma" "-mavx512f" "/arch:AVX512" "-hgnu") #ICC should use ZMM if code anyhow uses ZMM
+ "-xCORE-AVX512 -qopt-zmm-usage=high" "-xCORE-AVX512" "-mavx512f -mfma" "-mavx512f" "/arch:AVX512" "-hgnu")
if(${SIMD_AVX_512_C_FLAGS_RESULT})
set(${C_FLAGS_VARIABLE} "${TOOLCHAIN_C_FLAGS} ${SIMD_AVX_512_C_FLAGS}" CACHE INTERNAL "C flags required for AVX-512 instructions")
endfunction()
-# Arm Neon (32-bit ARM)
-function(gmx_find_simd_arm_neon_flags C_FLAGS_RESULT CXX_FLAGS_RESULT C_FLAGS_VARIABLE CXX_FLAGS_VARIABLE)
-
- gmx_find_flags(SIMD_ARM_NEON_C_FLAGS_RESULT SIMD_ARM_NEON_CXX_FLAGS_RESULT
- "#include<arm_neon.h>
- int main(){float32x4_t x=vdupq_n_f32(0.5);x=vmlaq_f32(x,x,x);return vgetq_lane_f32(x,0)>0;}"
- TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS
- SIMD_ARM_NEON_C_FLAGS SIMD_ARM_NEON_CXX_FLAGS
- "-mfpu=neon-vfpv4" "-mfpu=neon" "")
-
- if(${SIMD_ARM_NEON_C_FLAGS_RESULT})
- set(${C_FLAGS_VARIABLE} "${TOOLCHAIN_C_FLAGS} ${SIMD_ARM_NEON_C_FLAGS}" CACHE INTERNAL "C flags required for Arm Neon instructions")
- endif()
- if(${SIMD_ARM_NEON_CXX_FLAGS_RESULT})
- set(${CXX_FLAGS_VARIABLE} "${TOOLCHAIN_CXX_FLAGS} ${SIMD_ARM_NEON_CXX_FLAGS}" CACHE INTERNAL "C++ flags required for Arm Neon instructions")
- endif()
- set(${C_FLAGS_RESULT} ${SIMD_ARM_NEON_C_FLAGS_RESULT} CACHE INTERNAL "Result of test for Arm Neon C flags" FORCE)
- set(${CXX_FLAGS_RESULT} ${SIMD_ARM_NEON_CXX_FLAGS_RESULT} CACHE INTERNAL "Result of test for Arm Neon C++ flags" FORCE)
-endfunction()
-
# Arm Neon Asimd (64-bit ARM)
function(gmx_find_simd_arm_neon_asimd_flags C_FLAGS_RESULT CXX_FLAGS_RESULT C_FLAGS_VARIABLE CXX_FLAGS_VARIABLE)
set(${CXX_FLAGS_RESULT} ${SIMD_ARM_SVE_CXX_FLAGS_RESULT} CACHE INTERNAL "Result of test for Arm SVE C++ flags" FORCE)
endfunction()
-# IBM VMX (power6)
-function(gmx_find_simd_ibm_vmx_flags C_FLAGS_RESULT CXX_FLAGS_RESULT C_FLAGS_VARIABLE CXX_FLAGS_VARIABLE)
-
- gmx_find_flags(SIMD_IBM_VMX_C_FLAGS_RESULT SIMD_IBM_VMX_CXX_FLAGS_RESULT
- "#include<altivec.h>
- int main(){vector float x,y=vec_ctf(vec_splat_s32(1),0);x=vec_madd(y,y,y);return vec_all_ge(y,x);}"
- TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS
- SIMD_IBM_VMX_C_FLAGS SIMD_IBM_VMX_CXX_FLAGS
- "-maltivec -mabi=altivec" "-qarch=auto -qaltivec")
-
- if(${SIMD_IBM_VMX_C_FLAGS_RESULT})
- set(${C_FLAGS_VARIABLE} "${TOOLCHAIN_C_FLAGS} ${SIMD_IBM_VMX_C_FLAGS}" CACHE INTERNAL "C flags required for IBM VMX instructions")
- endif()
- if(${SIMD_IBM_VMX_CXX_FLAGS_RESULT})
- set(${CXX_FLAGS_VARIABLE} "${TOOLCHAIN_CXX_FLAGS} ${SIMD_IBM_VMX_CXX_FLAGS}" CACHE INTERNAL "C++ flags required for IBM VMX instructions")
- endif()
- set(${C_FLAGS_RESULT} ${SIMD_IBM_VMX_C_FLAGS_RESULT} CACHE INTERNAL "Result of test for IBM VMX C flags" FORCE)
- set(${CXX_FLAGS_RESULT} ${SIMD_IBM_VMX_CXX_FLAGS_RESULT} CACHE INTERNAL "Result of test for IBM VMX C++ flags" FORCE)
-endfunction()
-
# IBM VSX (power7 and later)
function(gmx_find_simd_ibm_vsx_flags C_FLAGS_RESULT CXX_FLAGS_RESULT C_FLAGS_VARIABLE CXX_FLAGS_VARIABLE)
find_power_vsx_toolchain_flags(TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS)
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5)
set(cxx_required_version "Clang 5")
endif()
- elseif(CMAKE_CXX_COMPILER_ID MATCHES "Intel")
- if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 19.1)
- set(cxx_required_version "Intel Compiler 2017")
- endif()
else()
message(WARNING "You are using an unsupported compiler. Please make sure it fully supports C++17.")
endif()
"Earlier versions don't have full C++17 support.")
endif()
+ if (CMAKE_CXX_COMPILER_ID MATCHES "Intel")
+ message(WARNING "The Intel classic compiler is no longer supported. It may pass the tests, but is not tested by the GROMACS developers. Use the clang-based compiler from oneAPI, or gcc")
+ endif()
+
if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "XL")
check_cxx_source_compiles(
"// Test in-class array initalizers used with constructor initializer lists
endif()
endif()
if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "PGI")
- message(WARNING "Currently tested PGI compiler versions (up to 15.7) generate binaries that do not pass all regression test, and the generated binaries are significantly slower than with GCC, ICC or Clang. For now we do not recommend PGI beyond development testing - make sure to run the regressiontests.")
+ message(WARNING "Currently tested PGI compiler versions (up to 15.7) generate binaries that do not pass all regression test, and the generated binaries are significantly slower than with GCC or Clang. For now we do not recommend PGI beyond development testing - make sure to run the regressiontests.")
endif()
endmacro(gmx_test_compiler_problems)
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2009,2010,2012,2013,2014 by the GROMACS development team.
-# Copyright (c) 2015,2020, by the GROMACS development team, led by
+# Copyright (c) 2015,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# GROMACS 2019 4
# GROMACS 2020 5
# GROMACS 2021 6
+# GROMACS 2022 7
# LIBRARY_SOVERSION_MINOR so minor version for the built libraries.
# Should be increased for each release that changes only the implementation.
# In GROMACS, the typical policy is to increase it for each patch version
# The GROMACS convention is that these are the version number of the next
# release that is going to be made from this branch.
-set(GMX_VERSION_MAJOR 2021)
-set(GMX_VERSION_PATCH 3)
+set(GMX_VERSION_MAJOR 2022)
+set(GMX_VERSION_PATCH 0)
# The suffix, on the other hand, is used mainly for betas and release
# candidates, where it signifies the most recent such release from
# this branch; it will be empty before the first such release, as well
# here. The important thing is to minimize the chance of third-party
# code being able to dynamically link with a version of libgromacs
# that might not work.
-set(LIBRARY_SOVERSION_MAJOR 6)
+set(LIBRARY_SOVERSION_MAJOR 7)
set(LIBRARY_SOVERSION_MINOR 0)
set(LIBRARY_VERSION ${LIBRARY_SOVERSION_MAJOR}.${LIBRARY_SOVERSION_MINOR}.0)
endif()
set(REGRESSIONTEST_VERSION "${GMX_VERSION_STRING}")
-set(REGRESSIONTEST_BRANCH "release-2021")
+set(REGRESSIONTEST_BRANCH "master")
# Run the regressiontests packaging job with the correct pakage
# version string, and the release box checked, in order to have it
# build the regressiontests tarball with all the right naming. The
dev-manual/doxygen.rst
dev-manual/error-handling.rst
dev-manual/formatting.rst
- dev-manual/gitlab.rst
+ dev-manual/gitlab-ci.rst
dev-manual/gmxtree.rst
dev-manual/includestyle.rst
dev-manual/index.rst
how-to/visualize.rst
install-guide/index.rst
release-notes/index.rst
+ release-notes/2022/major/highlights.rst
+ release-notes/2022/major/features.rst
+ release-notes/2022/major/performance.rst
+ release-notes/2022/major/tools.rst
+ release-notes/2022/major/bugs-fixed.rst
+ release-notes/2022/major/removed-functionality.rst
+ release-notes/2022/major/deprecated-functionality.rst
+ release-notes/2022/major/portability.rst
+ release-notes/2022/major/miscellaneous.rst
+ release-notes/2022/major/api.rst
release-notes/2021/2021.3.rst
release-notes/2021/2021.2.rst
release-notes/2021/2021.1.rst
.. todo:: This could likely be replaced by a (yet another) build type.
-.. cmake:: GMX_BUILD_MDRUN_ONLY
-
- If set ``ON``, the build system is configured to only build and install a
- single :file:`mdrun` executable. To be fully functional, the installed
- :file:`mdrun` requires a standard |Gromacs| installation (with
- ``GMX_BUILD_MDRUN_ONLY=OFF``) in the same installation prefix, as the
- mdrun-only build does not install any data files or scripts, only the
- binary. This is intended for cases where one wants to/needs to compile one
- or more instances of :file:`mdrun` with different build options (e.g., MPI
- or SIMD) than the full installation with the other utilities.
- Defaults to ``OFF``, in which case a single :file:`gmx` executable is built
- and installed, together with all the supporting files. :command:`mdrun` can
- be executed as :command:`gmx mdrun`.
-
.. cmake:: GMX_BUILD_OWN_FFTW
.. cmake:: GMX_BUILD_SHARED_EXE
unaffected by this setting. See reference manual for further
information.
-.. cmake:: GMX_RELAXED_DOUBLE_PRECISION
-
- Permit a double-precision configuration to compute some quantities
- to single-precision accuracy. Particularly on architectures where
- only double-precision SIMD is available (e.g. Sparc machines such
- as the K computer), it is faster to default to ``GMX_DOUBLE=ON``
- and use SIMD than to use ``GMX_DOUBLE=OFF`` and use no
- SIMD. However, if the user does not need full double precision,
- then some optimizations can achieve the equivalent of
- single-precision results (e.g. fewer Newton-Raphson iterations for
- a reciprocal square root computation).
-
.. cmake:: GMX_EXTRAE
.. cmake:: GMX_EXTERNAL_BLAS
headers fall in this category. See Doxygen documentation for
:file:`gmxpre.h`.
- All the above files get generated in :file:`src/`.
+ The above files are available through the INTERFACE_INCLUDE_DIR of
+ the ``common`` CMake target. I.e. to ``#include "config.h"``, be sure to
+ ``target_link_libraries(mymodule PRIVATE common)``
Additionally, the following file is generated by the build system:
Good names: documentation_UpdateDevelopersDocsTOGitLab, nbnxm_MakeNbnxmGPUIntoClass, pme_FEPPMEGPU.
Bad names: branch1234, mybranch, test, etc
+Labels
+======
+
+Labels <https://docs.gitlab.com/ee/user/project/labels.html>`__ help developers by allowing additional filtering of issues and merge requests.
+
+The GROMACS project `defines many labels <https://gitlab.com/gromacs/gromacs/-/labels>`__.
+
+.. Note: labeling guidelines TBD. See https://gitlab.com/gromacs/gromacs/-/issues/3949 and open new issues as appropriate.
+
+In general:
+
+* Ongoing categorizations to help specify the GROMACS component or development area use the ``#7F8C8D`` color.
+* Specific features or subproject areas targeting an upcoming release use the ``#8E44AD`` background color.
+
+When creating a new label, please provide a short description
+so that people can understand what the label is intended to convey,
+and when they should apply it to their own issues or merge requests.
+
+.. Best practices and labeling policies can be proposed as changes to this document. See https://gitlab.com/gromacs/gromacs/-/issues/3949
+
Code Review
===========
The reviewing workflow is the following:
-#. https://gitlab.com/gromacs/gromacs/-/issues shows all open changes
+#. https://gitlab.com/gromacs/gromacs/-/merge_requests shows all open changes
#. A change needs two approvals to go in, of which one approval has to come from
a member of either GMX Core or GMX Developers.
#. Usually a patch goes through several cycles of voting, commenting and
Steps:
-1. Create a `personal access token <https://docs.gitlab.com/ee/user/profile/personal_access_tokens.html>`__
- with ``write_registry`` scope. Save the hash!
-2. Authenticate from the command line with ``docker login registry.gitlab.com -u <token name> -p <hash>``
+1. Create a `personal access token <https://gitlab.com/-/profile/personal_access_tokens>`__ (`docs <https://docs.gitlab.com/ee/user/profile/personal_access_tokens.html>`__)
+ with ``write_registry`` and ``read_registry`` scopes. Save the hash!
+2. Authenticate from the command line with ``docker login registry.gitlab.com -u <user name> -p <hash>``
3. ``docker push registry.gitlab.com/gromacs/gromacs/<imagename>``
Refer to :file:`buildall.sh` in the ``master`` branch for the set of images
currently built.
-Within :doc:`pipeline jobs <gitlab>`, jobs specify a Docker image with the *image* property.
+Within :doc:`pipeline jobs <gitlab-ci>`, jobs specify a Docker image with the *image* property.
For image naming convention, see :py:func:`utility.image_name`.
Images from the GitLab registry
are easily accessible with the same identifier as above.
to build the ``man`` target manually before installing). See
:cmake:`GMX_BUILD_HELP`.
-Some documentation cannot be built if the CMake option
-``GMX_BUILD_MDRUN_ONLY`` is enabled, or when cross-compiling, as it
+Some documentation cannot be built when cross-compiling, as it
requires executing the ``gmx`` binary.
The following make targets are the most useful:
Error handling
==============
-To make |Gromacs| behave like a proper library, we need to change the
-way errors etc. are handled. Basically, the library should not print
-out anything to stdio/stderr unless it is part of the API
-specification, and even then, there should be a way for the user to
-suppress the output. Also, the library should normally not terminate
-the program without the user having control over this. There are
-different types of errors, which also affects the handling. Different
-cases are discussed separately below, split by the way they are
-handled. These guidelines are starting to take their final form,
-although details may still change.
-
-* For programming errors, i.e., errors that should never occur if the
- program is correctly written, it's acceptable to assert and
- terminate the program. This applies to both errors in the library
- and errors in user code or user input that calls the library.
- Older code tends to still use ``assert()`` calls, but new
- code should prefer more expressive functionality such as
- ``GMX_RELEASE_ASSERT()``. This version of the macro will result
- in asserts that are still present when the build type is Release,
- which is what we want by default. In performance-sensitive parts
- of the code, it is acceptable to rather use ``GMX_ASSERT()`` to
- avoid the performance penalty of a branch when the code is compiled
- for production use. By default, Jenkins builds the RelWithAssert
- build type.
-* For some errors it might be feasible to recover gracefully and
- continue execution. In this case, your APIs should be defined
- so that the API-user/programmer does not have to check separately
- whether the problem was due to a programming error, but it's
- better to e.g. use exceptions for recoverable errors and
- asserts for programming errors.
-* Exceptions should only be used for unexpected errors, e.g., out of
+To make |Gromacs| behave like a proper library, we need to handle
+errors in a consistent and predictable way. In this section, "user"
+refers to the end user of |Gromacs| whether via some command-line
+tool, or a workflow, or a call to a public API. There are different
+types of errors, and the handling reflects this. This section is a work
+in progress, particularly as the broader C++ community is a long way
+from consensus in these areas.
+
+Brief summary on which method to use
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+More detailed rules and rationale are written below, but in short, when a reason
+exists that code is unable to do its job:
+
+* If the reason can be checked at compile-time, then use ``static_assert``.
+* If the reason is normal in context, then express that in the types used
+ (e.g. return ``std::optional``) and document that this is normal.
+* If the reason is that an internal invariant or pre-condition is violated (e.g.
+ unexpected null pointer passed) on a hot code path, then use ``GMX_ASSERT``.
+* Otherwise, if the reason is that an internal invariant or pre-condition is violated
+ then use ``GMX_RELEASE_ASSERT``.
+* Otherwise, (typically an error returned from system call or GPU SDK, bad user
+ input), then use ``GMX_THROW``.
+
+Guiding principles
+^^^^^^^^^^^^^^^^^^
+
+* |Gromacs| should adopt approaches that have achieved consensus
+ elsewhere, e.g. in the `C++ Core Guidelines
+ <http://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines>`_. In
+ particular, be guided by `its section on error handling
+ <https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#S-errors>`_
+* The library should not print out anything to stdio/stderr unless it
+ is part of the API specification, and even then, there should be a
+ way for the user to suppress or redirect the output.
+* The library should normally not terminate the program without
+ the user having control over this.
+* Design interfaces of functions, classes, modules, and libraries so
+ that values passed at run time are valid. Pass const references or
+ ``not_null`` pointers rather than raw pointers. Return objects where
+ possible. Use e.g. class enums for the type of passed
+ values. Consider such enums as template parameters, rather than
+ passing run-time values. Refactor existing interfaces to improve
+ such aspects when starting new work in an area.
+* Check user input at API boundaries and establish invariants as soon
+ as possible, e.g. by expressing the user's choice in the type
+ system. These form the pre-conditions that error handling will rely
+ on.
+* Use assertions to validate invariants and pre-conditions. There is value in
+ using a different technique for checking such violations in order to make
+ the reason for the check clear to the maintainer.
+
+Specific rules
+^^^^^^^^^^^^^^
+
+* Use ``static_assert`` wherever possible to detect errors at compile
+ time.
+* Throw *exceptions* to indicate that a function can't do its assigned
+ task, per the `C++ Core Guidelines E.2
+ <https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#Re-throw>`_.
+ In particular, constructors should throw when they cannot construct
+ a valid object, per `C++ Core Guidelines C.42
+ <https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#Re-invariant>`_.
+ However, recognize that in some cases the underlying reason is that
+ some other component has not set up the correct pre-condition, and
+ such cases should be handled with assertions (see below).
+* At API boundaries, the assigned task of some code will be to
+ validate the input, and that code should express failure to validate
+ by throwing.
+* Many programming errors violate pre-conditions of other
+ functions. Until there is language support for contracts, the best
+ that can be done is to check these with *assertions*. Note that only
+ one component should have the responsibility for validating any
+ particular input from the user, and other components should rely
+ upon that validation in their pre-conditions.
+* When asserting, use ``GMX_RELEASE_ASSERT`` by default. This macro
+ will run its check in all build configurations, including
+ ``Release``.
+* When asserting in cases where the code is called in an inner loop of
+ e.g. the MD step, ``GMX_ASSERT`` can be used. This macro will run
+ its check only when ``NDEBUG`` is not defined, including the
+ ``RelWithAssert`` build configuration (which is the default build
+ type used in CI).
+* It can be appropriate to provide both checked and unchecked
+ interfaces, as ``std::vector`` does with ``at()`` and
+ ``operator[]``, respectively. Note that even the latter is checked
+ if you build e.g. ``libstdc++`` in the right configuration!
+* When calling low-level APIs (including C and C++ standard
+ libraries, GPU SDKs) always check for success/failure. Generally the
+ correct thing to do upon failure will be to throw, perhaps including
+ a descriptive string obtained from an error code with another API
+ call.
+* Do catch exceptions from lower-level components
memory or file system IO errors. As a general guideline, incorrect
user input should not produce an untrapped exception resulting
in execution termination telling the user an exception occured.
Instead, you should catch exceptions in an earlier stack frame,
make a suitable decision about diagnostic messages, and then
- decide how execution should be terminated.
+ decide whether execution should be terminated (if that is in the
+ scope of the code making the decision) and, if so, how to terminate.
* There is a global list of possible exceptions in
- ``src/gromacs/utility/exceptions.h``, and the library should throw
- one of these when it fails, possibly providing a more detailed
- description of the reason for the failure. The types of exceptions
- can be extended, and currently include:
+ ``api/legacy/include/gromacs/utility/exceptions.h``, and the library
+ should throw one of these when it fails, possibly providing a more
+ detailed description of the reason for the failure. The types of
+ exceptions can be extended, and currently include:
- Out of memory (e.g. ``std::bad_alloc``)
avoid propagating them to caller code.
* Avoid using exceptions to propagate errors across regions that start
- or join threads with OpenMP, since OpenMP cannot make guarantees about
- whether exceptions are caught or if the program will crash.
- Currently we catch all exceptions before we leave an OpenMP threaded region.
- If you throw an exception, make sure that it is caught and handled appropriately
- in the same thread/OpenMP section.
+ or join threads with OpenMP, since OpenMP cannot make guarantees
+ about whether exceptions are caught or if the program will crash.
+ Currently we catch all exceptions before we leave an OpenMP threaded
+ region. If you throw an exception, make sure that it is caught and
+ handled appropriately in the same thread/OpenMP section.
+* Avoid using exceptions to propagate errors within regions where
+ non-blocking API calls (e.g. to MPI or GPU SDKs) have been made,
+ because the possible advantage of catching at a higher level and
+ continuing execution is absent when the partner in the API call
+ may be left blocked.
* There are also cases where a library routine wants to report a
warning or a non-fatal error, but is still able to continue
processing. In this case you should try to collect all issues and
accessing data should typically also be callable when no such data is
available, but still return through normal means. If the failure is not
normal, it is OK to rather throw an exception.
+* Error handling with ``gmx_fatal``, ``gmx_warning``, ``gmx_incons``,
+ ``gmx_comm`` etc. is deprecated and should generally be refactored
+ to throw or assert according to the above guidelines.
+* There is currently no attempt made to check for error states on
+ other MPI ranks during the simulation and provide a coordinated
+ recovery. However setup code should do such checks routinely.
+* We use ``GMX_RELEASE_ASSERT`` and ``GMX_ASSERT`` rather
+ than ``assert`` to ensure that non-immediate strings can be
+ used to describe the problem when the error is reported.
+ This is particularly useful when troubleshooting issues where
+ missing test coverage leads users to uncover such errors.
+
For coding guidelines to make this all work, see :ref:`implementing exceptions`.
Avoid using *before-script* directly, and be cautious
about nested *extends* overriding multiple *before_script* definitions.
- cache
+ job cache
There is no global default, but jobs that build software will likely
set *cache*. To explicitly unset *cache* directives, specify a job
parameter of ``cache: {}``.
must be added. To cover many similar issues, parts of the line can then be
replaced with wildcards.
-A separate suppression mechanism is in place for cyclic dependencies: to
-suppress a cycle between moduleA and moduleB, add a line with format ::
-
- moduleA -> moduleB
-
-into ``doxygen/cycle-suppressions.txt``. This suppresses all cycles that contain
-the mentioned edge. Since a cycle contains multiple edges, the suppression
-should be made for the edge that is determined to be an incorrect dependency.
-This also affects the layout of the include dependency graphs (see below): the
-suppressed edge is not considered when determining the dependency order, and is
-shown as invalid in the graph.
-
.. _dev-include-sorter:
Include order sorting
1. Each *source* file should include ``gmxpre.h`` first.
2. If a *source* file has a corresponding header, it should be included next.
If the header is in the same directory as the source, then it is included
- without any path (i.e., relative to the source), otherwise relative to
- ``src/`` (the latter case should be rare).
+ without any path (i.e., relative to the source). Otherwise, the canonical
+ include path of ``libraryname/modulename/header.h`` is used.
3. If the file depends on defines from ``config.h``, that comes next.
4. This is followed by standard C/C++ headers, grouped as follows:
``<gtest/gtest.h>``.
6. |Gromacs|-specific libraries from ``src/external/``, such as
``"thread_mpi/threads.h"``.
-7. |Gromacs|-specific headers that are not internal to the including module,
- included with a path relative to ``src/``.
-8. In *test* files, headers not internal to the module, but specific to
- testing code, are in a separate block at this point, paths relative to
- ``src/``.
-9. Finally, |Gromacs| headers that are internal to the including module are
- included using a relative path (but never with a path starting with ``../``;
- such headers go into group 7 instead). For test files, this group contains
- headers that are internal to tests for that module.
+7. |Gromacs| headers that are not part of the including module.
+8. Public |Gromacs| headers that are part of the including module.
+9. Finally, |Gromacs| headers that are internal to the including module,
+ executable, or test target
+ (typically at the same path as the source file).
All |Gromacs| headers are included with quotes (``"gromacs/utility/path.h"``),
other headers with angle brackets (``<stdio.h>``). Headers under ``src/external/``
cases. Trailing comments on the same line as #include statements are
preserved and do not affect the checker/sorter.
-The includestyle used to differentiate between header files that were declared
-to be part of the module and not used outside the module, and those that were
-either not part of a module, used in other modules, or installed.
-As the possibility of installation has been removed (for now), changes to the
-previous organization might occur where such installed files were implicitly
-marked as being used outside of a module even though they were not used within
-|Gromacs| outside their module.
-
As part of the effort to build a proper API, a new scheme of separating between
public, library and module functionality in header files is planned.
-
-The guidelines are enforced by an automatic checker script that can also
-sort/reformat include statements to follow the guidelines.
-See :doc:`gmxtree` for details.
+See also :doc:`gmxtree` and
+`API restructuring issues <https://gitlab.com/gromacs/gromacs/-/issues?label_name%5B%5D=API+restructuring>`__
+for details.
Enforcing a consistent order and style has a few advantages:
first. With this order, the person working on the header is most likely to
see these problems instead of someone else seeing them later when
refactoring unrelated code.
-* Consistent usage of paths in #include directives makes it easy to use
+* Consistent usage of paths in ``#include`` directives makes it easy to use
``grep`` to find all uses of a header, as well as all include dependencies
between two modules.
* An automatic script can be used to re-establish clean code after
:maxdepth: 2
jenkins
- gitlab
+ gitlab-ci
containers
* Member variables are named with a trailing underscore.
* Accessors for a variable ``foo_`` are named ``foo()`` and ``setFoo()``.
* Global variables are named with a ``g_`` prefix.
-* Static class variables are named with a ``s_`` prefix.
-* Static ``constexpr`` class members are named with a ``sc_`` prefix.
+* Global and file-static variables are named with a ``g_`` prefix.
+* Static class and function variables are named with an ``s_`` prefix.
+* Static ``constexpr`` file, class, or function members are named with a ``sc_`` prefix.
* Global constants are often named with a ``c_`` prefix.
* If the main responsibility of a file is to implement a particular class,
then the name of the file should match that class, except for possible
typically including a verb for boolean variables, like ``foundAtom``.
* Prefer class enums over regular ones, so that unexpected conversions to
int do not happen.
+* Name functions to convert class enum values to strings as ``enumValueToString``.
* When using a non-class enum, prefer to include the name of the enumeration type
as a base in the name of enum values, e.g., ``HelpOutputFormat_Console``,
in particular for settings exposed to other modules.
The following figure shows a high-level view of components of what gets built
from the source code under :file:`src/` and how the code is organized.
+Arrows indicate the direction of dependencies.
The build system is described in detail in :doc:`build-system`.
With default options, the green and white components are built as part of the
-default target. If ``GMX_BUILD_MDRUN_ONLY`` is ``ON``, then the blue and white
-components are built instead; :file:`libgromacs_mdrun` is built from a subset
-of the code used for :file:`libgromacs`.
+default target.
The gray parts are for testing, and are by default only built as part of the
``tests`` target, but if ``GMX_DEVELOPER_BUILD`` is ``ON``, then these are
included in the default build target.
label="externals\nsrc/external/", group=common, style=rounded
]
gtest [
- label="Google Test & Mock\nsrc/external/gmock-1.7.0/", group=test
+ label="Google Test & Mock\nsrc/external/googletest/", group=test
style="rounded,filled", fillcolor="0 0 0.9"
]
}
libgromacs [
label="libgromacs\nsrc/gromacs/", group=gmx, fillcolor="0.33 0.3 1"
]
- libgromacs_mdrun [
- label="libgromacs_mdrun\nsrc/gromacs/", group=mdrun, fillcolor="0.66 0.3 1"
- ]
}
testutils [
label="testutils\nsrc/testutils/", group=test
style="rounded,filled", fillcolor="0 0 0.9"
]
- mdrun_objlib [
- label="mdrun object lib.\nsrc/programs/mdrun/", group=common, style=rouded
- ]
subgraph {
rank = same
gmx [
label="gmx\nsrc/programs/", group=gmx, fillcolor="0.33 0.3 1"
]
- mdrun [
- label="mdrun\nsrc/programs/", group=mdrun, fillcolor="0.66 0.3 1"
- ]
tests [
label="test binaries\nsrc/.../tests/", group=test
style="rounded,filled", fillcolor="0 0 0.9"
]
gmx -> template [ style=invis, constraint=no ]
- template -> mdrun [ style=invis, constraint=no ]
}
libgromacs -> externals
- libgromacs_mdrun -> externals
- mdrun_objlib -> libgromacs
gmx -> libgromacs
- gmx -> mdrun_objlib
- mdrun -> libgromacs_mdrun
- mdrun -> mdrun_objlib
testutils -> externals
testutils -> gtest
testutils -> libgromacs
tests -> gtest
tests -> libgromacs
- tests -> mdrun_objlib
tests -> testutils
template -> libgromacs
- template -> mdrun_objlib [ style=invis ]
- mdrun_objlib -> externals [ style=invis ]
-
All the source code (except for the analysis template) is under the
:file:`src/` directory. Only a few files related to the build system are
included at the root level. All actual code is in subdirectories:
This is the main part of the code, and is organized into further subdirectories
as *modules*. See below for details.
:file:`src/programs/`
- |Gromacs| executables are built from code under this directory.
- Although some build options can change this, there is typically only a single
- binary, :file:`gmx`, built.
+ The |Gromacs| executable ``gmx`` is built from code under this directory.
+ Also found here is some of the driver code for the ``mdrun`` module called
+ by ``gmx``, the whole of the ``gmx view`` visualization module, and numerous
+ end-to-end tests of ``gmx mdrun``.
:file:`src/{...}/tests/`
Various subdirectories under :file:`src/` contain a subdirectory named
necessary for that file. You can use the public API header if you
really require everything declared in it.
-intra-module/intra-file.
-
See :doc:`naming` for some common naming patterns for files that can help
locating declarations.
regression tests
+floating-point exceptions
+ In debug builds, floating-point exceptions (FPEs) are generated whenever one of the
+ following operations is encountered: division by zero, floating-point overflow,
+ invalid operation (e.g., taking sqrt of a negative number).
+ Such checks are *not* performed in the following configurations:
+
+ - release build,
+ - any build by GCC 7.x or Clang with optimizations,
+ - build with SYCL support.
+
+ In these configurations, FPEs can be enabled by adding ``-fpexcept`` flag to ``gmx``
+ invocation. However, FPEs are not supported on Windows and non-x86 Apple hardware.
+ See ``api/legacy/include/gromacs/math/utilities.h`` for more details.
+
.. _dev-formatting-tools:
Code formatting and style
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
-# Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
COMMAND ${Python3_EXECUTABLE}
${CMAKE_CURRENT_SOURCE_DIR}/graphbuilder.py
-S ${CMAKE_SOURCE_DIR} -B ${CMAKE_BINARY_DIR}
- --ignore-cycles ${CMAKE_CURRENT_SOURCE_DIR}/cycle-suppressions.txt
-o ${DEPGRAPH_DIR}
DEPENDS doxygen-xml ${INSTALLED_HEADER_FILE}
${CMAKE_CURRENT_SOURCE_DIR}/doxygenxml.py
${CMAKE_CURRENT_SOURCE_DIR}/gmxtree.py
${CMAKE_CURRENT_SOURCE_DIR}/graphbuilder.py
- ${CMAKE_CURRENT_SOURCE_DIR}/cycle-suppressions.txt
COMMENT "Generating include dependency graphs for dot"
USES_TERMINAL)
${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/check-source.py
-S ${CMAKE_SOURCE_DIR} -B ${CMAKE_BINARY_DIR}
-l ${CMAKE_CURRENT_BINARY_DIR}/check-source.log
- --ignore ${CMAKE_CURRENT_SOURCE_DIR}/suppressions.txt
- --ignore-cycles ${CMAKE_CURRENT_SOURCE_DIR}/cycle-suppressions.txt)
+ --ignore ${CMAKE_CURRENT_SOURCE_DIR}/suppressions.txt)
add_custom_target(check-source COMMAND ${check_source_command}
COMMENT "Checking source code for various issues" VERBATIM USES_TERMINAL)
add_custom_target(check-source-fast COMMAND ${check_source_command}
LAYOUT_FILE = @CMAKE_CURRENT_SOURCE_DIR@/DoxygenLayout.xml
INPUT = @CMAKE_CURRENT_SOURCE_DIR@ \
@CMAKE_SOURCE_DIR@/src \
+ @CMAKE_SOURCE_DIR@/api/legacy/include \
@CMAKE_SOURCE_DIR@/share/template
FILE_PATTERNS = *.c *.cpp *.h *.md
# CUDA files could be included like this, but currently produce a lot of
EXCLUDE_SYMBOLS += MOCK_METHOD* MOCK_CONST_METHOD*
FULL_PATH_NAMES = YES
STRIP_FROM_PATH = @CMAKE_SOURCE_DIR@
-STRIP_FROM_INC_PATH = @CMAKE_SOURCE_DIR@/src
+STRIP_FROM_INC_PATH = @CMAKE_SOURCE_DIR@/src \
+ @CMAKE_SOURCE_DIR@/src/include \
+ @CMAKE_SOURCE_DIR@/src/gromacs/*/include \
+ @CMAKE_SOURCE_DIR@/api/legacy/include
INCLUDE_PATH = @CMAKE_SOURCE_DIR@/src
HAVE_DOT = @DOXYGEN_DOT_FOUND@
DOT_PATH = @DOXYGEN_DOT_PATH@
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015,2018,2019, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2018,2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
if member.has_inbody_description():
reporter.doc_note(member, "has in-body comments, which are ignored")
-def check_cycles(graph, reporter):
- """Check cyclic dependencies in a dependency graph.
-
- The graph parameter provides the graph to check. It should be an object
- that has three methods:
- iternodes():
- Return the list of nodes in the graph.
- iteredges(node):
- Return the list of edges from a given node.
- The list should contain (node, edge) pairs, where node is an object
- returned by iternodes() and edge is any object.
- report_cycle(cycle, reporter):
- Process a found cycle. cycle contains a list of (node, edge) pairs
- that describe the cycle. edge is the edge object that leads _to_
- the node in the cycle.
-
- This is implemented using an extended DFS-based strongly connected
- component (SCC) search, written using a stack instead of recursion.
- The base algorithm is Tarjan's SCC search:
- http://en.wikipedia.org/wiki/Tarjan's_strongly_connected_components_algorithm
-
- Each back edge that is encountered during the search is reported as a
- cycle. Additionally, if a cross edge is encountered that is within the
- current SCC, the target node and all its children in the current SCC will
- be visited again to find all cycles. All steps except cycle detection are
- omitted for such re-traversal.
-
- To avoid duplicates from cycles that do not include all nodes in an SCC,
- a cycle is only reported if the target of the back edge is still active
- in the search, i.e., all edges from it have not yet been traversed.
- """
- # The DFS stack; next node is always popped from the end.
- # Stores (node, edge) pairs.
- # edge is None for start nodes and for post-order processing.
- dfsstack = []
- for node in graph.iternodes():
- dfsstack.append((node, None))
- # Stack of visited nodes that have not yet been assigned to a strongly
- # connected component.
- visitstack = []
- # List of nodes in the DFS recursion stack.
- currlist = []
- # Set of nodes in currlist for more efficient searching.
- currset = set()
- # Counter for initializing preorder.
- visit_count = 0
- # DFS pre-order for nodes: initialized when a node is first encountered
- # in the search.
- preorder = dict()
- # Lowest pre-order index reachable from this node.
- # Initialized to pre-order, and updated during post-order processing.
- linkorder = dict()
- # Set to True for a node when first encountered, and set to False when
- # a strongly connected component has been processed.
- in_progress = dict()
- # The DFS search
- while dfsstack:
- currnode, curredge = dfsstack.pop()
- # curredge is None if this is a start node or post-order traversal.
- # currlist is empty if this is a start node.
- if curredge is None and currlist:
- # All children visited: post-order processing.
- done = currlist.pop()[0]
- assert done == currnode
- currset.remove(currnode)
- # If this is the first time this node is encountered, fill
- # linkorder and check for strongly connected components.
- if linkorder[currnode] == preorder[currnode]:
- children = [x for x, dummy in graph.iteredges(currnode) if in_progress[x]]
- if children:
- linkorder[currnode] = min([linkorder[x] for x in children])
- if preorder[currnode] <= linkorder[currnode]:
- # This is a root of a strongly connected component.
- while visitstack:
- node = visitstack.pop()
- in_progress[node] = False
- if node == currnode:
- break
- else:
- assert False
- continue
- if currnode not in preorder:
- # First encounter of this node: pre-order processing.
- preorder[currnode] = visit_count
- linkorder[currnode] = visit_count
- visitstack.append(currnode)
- visit_count += 1
- in_progress[currnode] = True
- elif not in_progress[currnode]:
- # Do not enter processed components again.
- continue
- currlist.append((currnode, curredge))
- currset.add(currnode)
- # add entry for post-order traversal
- dfsstack.append((currnode, None))
- for nextnode, edge in graph.iteredges(currnode):
- if nextnode not in preorder:
- # Not seen previously: push
- dfsstack.append((nextnode, edge))
- else:
- # If an already visited node is in the same component, it is
- # either part of a cycle, or we need to traverse it again to
- # find all cycles.
- if in_progress[nextnode]:
- if nextnode not in currset:
- dfsstack.append((nextnode, edge))
- # Only report cycles to nodes that haven't been processed
- # yet to avoid duplicates.
- elif linkorder[nextnode] == preorder[nextnode]:
- for index, node in enumerate(currlist):
- if node[0] == nextnode:
- cycle = [(nextnode, edge)]
- cycle.extend(currlist[index+1:])
- graph.report_cycle(cycle, reporter)
- break
- else:
- assert False
-
-class ModuleDependencyGraph(object):
-
- """Module dependency graph representation for check_cycles().
-
- In the reported graph, the nodes are gmxtree.Module objects and the edges
- are gmxtree.ModuleDependency objects.
- """
-
- def __init__(self, tree):
- self._tree = tree
-
- def iternodes(self):
- return self._tree.get_modules()
-
- def iteredges(self, module):
- for dependency in module.get_dependencies():
- if not dependency.is_test_only_dependency():
- yield (dependency.get_other_module(), dependency)
-
- def report_cycle(self, cycle, reporter):
- if any([x[1].is_cycle_suppressed() for x in cycle]):
- # TODO: Report unused suppressions.
- return
- modulelist = ' -> '.join([x[0].get_name()[7:] for x in cycle])
- summary = 'module-level cyclic dependency: ' + modulelist
- reporter.cyclic_issue(summary)
-
def check_all(tree, reporter, check_ignored):
"""Do all checks for the GROMACS tree."""
- includesorter = IncludeSorter()
- for fileobj in tree.get_files():
- if isinstance(fileobj, gmxtree.GeneratorSourceFile):
- continue
- check_file(fileobj, tree, reporter)
- for includedfile in fileobj.get_includes():
- check_include(fileobj, includedfile, reporter)
- if fileobj.should_includes_be_sorted():
- is_sorted, details = includesorter.check_sorted(fileobj)
- if not is_sorted:
- details.append("You can use includesorter.py to do the sorting automatically; see docs/dev-manual/gmxtree.rst")
- reporter.code_issue(fileobj,
- "include style/order is not consistent; see docs/dev-manual/includestyle.rst", details)
+ # Include sorting is disabled pending resolution of
+ # https://gitlab.com/gromacs/gromacs/-/issues/3288 and
+ # https://gitlab.com/gromacs/gromacs/-/issues/3659
+ # includesorter = IncludeSorter()
+ # for fileobj in tree.get_files():
+ # if isinstance(fileobj, gmxtree.GeneratorSourceFile):
+ # continue
+ # check_file(fileobj, tree, reporter)
+ # for includedfile in fileobj.get_includes():
+ # check_include(fileobj, includedfile, reporter)
+ # if fileobj.should_includes_be_sorted():
+ # is_sorted, details = includesorter.check_sorted(fileobj)
+ # if not is_sorted:
+ # details.append("You can use includesorter.py to do the sorting automatically; see docs/dev-manual/gmxtree.rst")
+ # reporter.code_issue(fileobj,
+ # "include style/order is not consistent; see docs/dev-manual/includestyle.rst", details)
for classobj in tree.get_classes():
check_class(classobj, reporter)
for memberobj in tree.get_members():
check_member(memberobj, reporter, check_ignored)
- check_cycles(ModuleDependencyGraph(tree), reporter)
- tree.report_unused_cycle_suppressions(reporter)
-
def main():
"""Run the checking script."""
parser = OptionParser()
help='Write issues into a given log file in addition to stderr')
parser.add_option('--ignore',
help='Set file with patterns for messages to ignore')
- parser.add_option('--ignore-cycles',
- help='Set file with module dependencies to ignore in cycles')
parser.add_option('--check-ignored', action='store_true',
help='Issue notes for comments ignored by Doxygen')
parser.add_option('-q', '--quiet', action='store_true',
if not options.quiet:
sys.stderr.write('Finding config.h and other preprocessor macro uses...\n')
tree.find_define_file_uses()
- if options.ignore_cycles:
- tree.load_cycle_suppression_list(options.ignore_cycles)
if not options.quiet:
sys.stderr.write('Reading Doxygen XML files...\n')
tree.load_xml()
+++ /dev/null
-# Order (or more generally, edge selection) is significant (see gmxtree.md);
-# "moduleA -> moduleB" means that moduleA should not depend on moduleB, and is
-# a problem to be addressed at some point.
-
-domdec -> imd
-domdec -> ewald
-domdec -> mdlib
-domdec -> pulling
-fileio -> gmxlib
-mdlib -> essentialdynamics
-mdlib -> imd
-mdlib -> ewald
-mdlib -> pulling
-nbnxm -> domdec
-nbnxm -> mdlib
-simd -> hardware
-gpu_utils -> hardware
-listed_forces -> mdlib
-utility -> math
-
-# modular simulator uses shellfc from mdrun, but is later included in mdrun by simulator builder
-modularsimulator -> mdrun
-
-# Cycle counters in timing use comrec for the set up, which is in the mdtypes. This introduces
-# cyclic dependencies if the cycle counting is used anywhere in mdtypes.
-timing -> mdtypes
-
-# awh has dependencies in mdlib and pulling that need resolving.
-mdlib -> applied_forces
To include a notification for your module
* Add the function signature for the callback function to the
- `MdModulesNotifier` in `mdmodulenotification.h`,
+ `MDModulesNotifiers` in `mdmodulesnotifiers.h`,
```C++
- registerMdModulesNotification<...,
+ BuildMDModulesNotifier<...,
YourCallbackSignature,
...,
```
(keep alphabetical order for ease of git merge)
-* Hand the notifier_ member of the MdModules Implementation class to your
+* Hand the notifier_ member of the MDModules Implementation class to your
builder createYourModule(¬ifier_)
* Add the function you want to subscribe with in the builder,
builder->add<ForceElement>();
// We have a full state here (positions(t), velocities(t-dt/2), forces(t)
builder->add<StatePropagatorData::Element>();
- if (legacySimulatorData_->inputrec->etc == etcVRESCALE)
+ if (legacySimulatorData_->inputrec->etc == TemperatureCoupling::VRescale)
{
- builder->add<VRescaleThermostat>(-1, VRescaleThermostatUseFullStepKE::No);
+ builder->add<VRescaleThermostat>(-1,
+ VRescaleThermostatUseFullStepKE::No,
+ PropagatorTag("LeapFrogPropagator"));
}
- builder->add<Propagator<IntegrationStep::LeapFrog>>(legacySimulatorData_->inputrec->delta_t,
- RegisterWithThermostat::True,
- RegisterWithBarostat::True);
+ builder->add<Propagator<IntegrationStage::LeapFrog>>(PropagatorTag("LeapFrogPropagator"),
+ legacySimulatorData_->inputrec->delta_t);
if (legacySimulatorData_->constr)
{
builder->add<ConstraintsElement<ConstraintVariable::Positions>>();
builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>>();
// We have the energies at time t here
builder->add<EnergyData::Element>();
- if (legacySimulatorData_->inputrec->epc == epcPARRINELLORAHMAN)
+ if (legacySimulatorData_->inputrec->epc == PressureCoupling::ParrinelloRahman)
{
- builder->add<ParrinelloRahmanBarostat>(-1);
+ builder->add<ParrinelloRahmanBarostat>(-1, PropagatorTag("LeapFrogPropagator"));
}
}
}
time step of PositionsOnly.
The propagators also allow to implement temperature and pressure coupling
-schemes by offering (templated) scaling of the velocities.
+schemes by offering (templated) scaling of the velocities. In order to
+link temperature / pressure coupling objects to the propagators, the
+propagator objects have a tag (of strong type `PropagatorTag`). The
+temperature and pressure coupling objects can then connect to the
+matching propagator by comparing their target tag to the different
+propagators. Giving the propagators their tags and informing the
+temperature and pressure coupling algorithms which propagator they are
+connecting to is in the responsibility of the simulation algorithm
+builder.
#### `CompositeSimulatorElement`
The composite simulator element takes a list of elements and implements
structure, changing the function signature of all checkpoint-related functions,
and write a corresponding low-level routine interacting with the XDR library.
-**The MdModule approach:** To allow for modules to write checkpoints, the legacy
+**The MDModule approach:** To allow for modules to write checkpoints, the legacy
checkpoint was extended by a KVTree. When writing to checkpoint, this tree gets
filled (via callbacks) by the single modules, and then serialized. When reading,
the KVTree gets deserialized, and then distributed to the modules which can read
##### Modular simulator design
-The MdModule checks off almost all requirements to a modularized checkpointing format.
+The MDModule checks off almost all requirements to a modularized checkpointing format.
The proposed design is therefore an evolved form of this approach. Notably, two
improvements include
* Hide the implementation details of the data structure holding the data (currently,
Checking for key existence seems rather to be a lazy way to circumvent versioning,
and is therefore discouraged.
-**Callback method:** The modular simulator and MdModules don't use the exact same
+**Callback method:** The modular simulator and MDModules don't use the exact same
way of communicating with clients. The two methods could be unified if needed.
The only _fundamental_ difference is that modular simulator clients need to identify
-with a unique key to receive their dedicated sub-data, while MdModules all read from
-and write to the same KV-tree. MdModules could be adapted to that by either requiring
+with a unique key to receive their dedicated sub-data, while MDModules all read from
+and write to the same KV-tree. MDModules could be adapted to that by either requiring
a unique key from the modules, or by using the same `CheckpointData` for all modules
-and using a single unique key (something like "MdModules") to register that object
+and using a single unique key (something like "MDModules") to register that object
with the global checkpoint.
**Performance:** One of the major differences between the new approach and the legacy
Finally, for some architectures with large or very large SIMD width (e.g. AVX
with 8 elements in single precision, or AVX-512 with 16), the nonbonded
kernels can become inefficient. Since all such architectures presently known
-(AVX, AVX2, MIC, AVX512) also provide extensive support for accessing
+(AVX, AVX2, AVX512) also provide extensive support for accessing
parts of the register, we optionally define a handful of routines to
perform load, store, and reduce operations based on half-SIMD-width data,
which can improve performance. It is only useful for wide implementations,
-# The script is currently a bit too eager
-share/template/template.cpp: error: source file documentation appears outside full documentation
-# The parser in the script is not clever enough
-src/gromacs/version.h: warning: includes local file as <gromacs/version.h>
-
-# These are OK
-src/gromacs/linearalgebra/eigensolver.cpp: warning: should include "config.h"
-src/gromacs/linearalgebra/gmx_arpack.cpp: warning: should include "config.h"
-src/gromacs/linearalgebra/gmx_blas/*: warning: does not include "gmxpre.h" first
-src/gromacs/linearalgebra/gmx_blas/*: warning: should include "config.h"
-src/gromacs/linearalgebra/gmx_lapack/*: warning: does not include "gmxpre.h" first
-src/gromacs/linearalgebra/gmx_lapack/*: warning: should include "config.h"
-src/gromacs/utility/baseversion-gen.cpp: warning: does not include "gmxpre.h" first
-
-# Exclude header files that are used for inlining code; the responsibility for
-# making the right #includes should be on the source file that uses these.
-# TODO: # Stop using the preprocessor for meta-programming!
-src/gromacs/ewald/pme_simd4.h: warning: should include "pme_simd.h"
-src/gromacs/ewald/pme_spline_work.cpp: warning: includes "simd.h" unnecessarily
-src/gromacs/ewald/pme_spline_work.h: warning: includes "simd.h" unnecessarily
-src/gromacs/ewald/pme_spread.cpp: warning: includes "simd.h" unnecessarily
-src/gromacs/nbnxm/boundingboxes.h: warning: includes "simd.h" unnecessarily
-src/gromacs/nbnxm/kernels_simd_2xmm/kernel_inner.h: warning: should include "simd.h"
-src/gromacs/nbnxm/kernels_simd_2xmm/kernel_outer.h: warning: should include "simd.h"
-src/gromacs/nbnxm/kernels_simd_4xm/kernel_inner.h: warning: should include "simd.h"
-src/gromacs/nbnxm/kernels_simd_4xm/kernel_outer.h: warning: should include "simd.h"
-src/gromacs/nbnxm/pairlist_simd_2xmm.h: warning: should include "simd.h"
-src/gromacs/nbnxm/pairlist_simd_4xm.h: warning: should include "simd.h"
-
-# This module name doesn't really fall into any currently used pattern; needs some thought
-: error: no matching directory for module: module_mdrun_integration_tests
-
-# These would be nice to fix, but can wait for later / deletion / rewrites
-src/gromacs/nbnxm/kernels_simd_2xmm/kernel_common.h: warning: should include "nbnxm_simd.h"
-src/gromacs/nbnxm/kernels_simd_4xm/kernel_common.h: warning: should include "nbnxm_simd.h"
-
# This seems to be a false positive
src/gromacs/nbnxm/cuda/nbnxm_cuda_types.h: error: NbnxmGpu: is in internal file(s), but appears in public documentation
+# doxygen has problems with the template construct in this file
+src/gromacs/modularsimulator/signallers.h: error: build: is documented, but does not have brief description
+
# False positive caused by forward-declaration of BasicVector in src/testutils/refdata.h
-src/gromacs/math/vectypes.h: error: gmx::BasicVector: is in library file(s), but appears in public documentation
+src/testutils/refdata.h: error: gmx::BasicVector: is in library file(s), but appears in public documentation
-# Temporary while we change the SIMD implementation
-src/gromacs/simd/impl_sparc64_hpc_ace/impl_sparc64_hpc_ace_common.h: warning: should include "simd.h"
+#
+# All following suppressions are disabled while the include checker
+# is temporarily disabled pending resolution of
+# https://gitlab.com/gromacs/gromacs/-/issues/3288 and
+# https://gitlab.com/gromacs/gromacs/-/issues/3659
+#
-src/gromacs/simd/tests/scalar.cpp: warning: includes "simd.h" unnecessarily
-src/gromacs/simd/tests/scalar_math.cpp: warning: includes "simd.h" unnecessarily
-src/gromacs/simd/tests/scalar_util.cpp: warning: includes "simd.h" unnecessarily
-src/gromacs/tables/cubicsplinetable.h: warning: includes "simd.h" unnecessarily
-src/gromacs/tables/quadraticsplinetable.h: warning: includes "simd.h" unnecessarily
+# # The script is currently a bit too eager
+# share/template/template.cpp: error: source file documentation appears outside full documentation
+# # The parser in the script is not clever enough
+# src/gromacs/version.h: warning: includes local file as <gromacs/version.h>
-# These are specific to Folding@Home, and easiest to suppress here
-src/gmxpre.h: warning: includes non-local file as "swindirect.h"
+# # These are OK
+# src/gromacs/linearalgebra/eigensolver.cpp: warning: should include "config.h"
+# src/gromacs/linearalgebra/gmx_arpack.cpp: warning: should include "config.h"
+# src/gromacs/linearalgebra/gmx_blas/*: warning: does not include "gmxpre.h" first
+# src/gromacs/linearalgebra/gmx_blas/*: warning: should include "config.h"
+# src/gromacs/linearalgebra/gmx_lapack/*: warning: does not include "gmxpre.h" first
+# src/gromacs/linearalgebra/gmx_lapack/*: warning: should include "config.h"
+# src/gromacs/utility/baseversion-gen.cpp: warning: does not include "gmxpre.h" first
-# New external API (see https://gitlab.com/gromacs/gromacs/-/issues/2586) has some unresolved
-# conflicts with previous definitions of public API, installed API, and other things
-# described or implemented in check-source.py, gmxtree.py, gmxtree.rst, and others
-# TODO: resolve definitions, update testing heuristics, and activate policy checks
-# for src/api/cpp files.
-src/api/cpp/*: *
+# # Exclude header files that are used for inlining code; the responsibility for
+# # making the right #includes should be on the source file that uses these.
+# # TODO: # Stop using the preprocessor for meta-programming!
+# src/gromacs/ewald/pme_simd4.h: warning: should include "pme_simd.h"
+# src/gromacs/ewald/pme_spline_work.cpp: warning: includes "simd.h" unnecessarily
+# src/gromacs/ewald/pme_spline_work.h: warning: includes "simd.h" unnecessarily
+# src/gromacs/ewald/pme_spread.cpp: warning: includes "simd.h" unnecessarily
+# src/gromacs/nbnxm/boundingboxes.h: warning: includes "simd.h" unnecessarily
+# src/gromacs/nbnxm/kernels_simd_2xmm/kernel_inner.h: warning: should include "simd.h"
+# src/gromacs/nbnxm/kernels_simd_2xmm/kernel_outer.h: warning: should include "simd.h"
+# src/gromacs/nbnxm/kernels_simd_4xm/kernel_inner.h: warning: should include "simd.h"
+# src/gromacs/nbnxm/kernels_simd_4xm/kernel_outer.h: warning: should include "simd.h"
+# src/gromacs/nbnxm/pairlist_simd_2xmm.h: warning: should include "simd.h"
+# src/gromacs/nbnxm/pairlist_simd_4xm.h: warning: should include "simd.h"
-# doxygen has problems with the template construct in this file
-src/gromacs/modularsimulator/signallers.h: error: build: is documented, but does not have brief description
+# # This module name doesn't really fall into any currently used pattern; needs some thought
+# : error: no matching directory for module: module_mdrun_integration_tests
+
+# # These would be nice to fix, but can wait for later / deletion / rewrites
+# src/gromacs/nbnxm/kernels_simd_2xmm/kernel_common.h: warning: should include "nbnxm_simd.h"
+# src/gromacs/nbnxm/kernels_simd_4xm/kernel_common.h: warning: should include "nbnxm_simd.h"
+
+
+# # Temporary while we change the SIMD implementation
+# src/gromacs/simd/impl_sparc64_hpc_ace/impl_sparc64_hpc_ace_common.h: warning: should include "simd.h"
+
+# src/gromacs/simd/tests/scalar.cpp: warning: includes "simd.h" unnecessarily
+# src/gromacs/simd/tests/scalar_math.cpp: warning: includes "simd.h" unnecessarily
+# src/gromacs/simd/tests/scalar_util.cpp: warning: includes "simd.h" unnecessarily
+# src/gromacs/tables/cubicsplinetable.h: warning: includes "simd.h" unnecessarily
+# src/gromacs/tables/quadraticsplinetable.h: warning: includes "simd.h" unnecessarily
+
+# # These are specific to Folding@Home, and easiest to suppress here
+# src/gmxpre.h: warning: includes non-local file as "swindirect.h"
+
+# # New external API (see https://gitlab.com/gromacs/gromacs/-/issues/2586) has some unresolved
+# # conflicts with previous definitions of public API, installed API, and other things
+# # described or implemented in check-source.py, gmxtree.py, gmxtree.rst, and others
+# # TODO: resolve definitions, update testing heuristics, and activate policy checks
+# # for src/api/cpp files.
+# src/api/cpp/*: *
}
To check the status or error output of a command line operation, refer to the
-``returncode`` and ``erroroutput`` outputs.
+``returncode`` and ``stderr`` outputs.
To access the results from the output file arguments, use the command line flags
as keys in the ``file`` dictionary output.
On a cluster where users are expected to be running across multiple
nodes using MPI, make one installation similar to the above, and
-another using ``-DGMX_MPI=on`` and which is `building only
-mdrun`_, because that is the only component of |Gromacs| that uses
-MPI. The latter will install a single simulation engine binary,
-i.e. ``mdrun_mpi`` when the default suffix is used. Hence it is safe
+another using ``-DGMX_MPI=on``.
+The latter will install binaries and libraries named using
+a default suffix of ``_mpi`` ie ``gmx_mpi``. Hence it is safe
and common practice to install this into the same location where
the non-MPI build is installed.
* ``-DCMAKE_C_COMPILER=xxx`` equal to the name of the C99 `Compiler`_ you wish to use (or the environment variable ``CC``)
* ``-DCMAKE_CXX_COMPILER=xxx`` equal to the name of the C++17 `compiler`_ you wish to use (or the environment variable ``CXX``)
-* ``-DGMX_MPI=on`` to build using `MPI support`_ (generally good to combine with `building only mdrun`_)
+* ``-DGMX_MPI=on`` to build using `MPI support`_
* ``-DGMX_GPU=CUDA`` to build with NVIDIA CUDA support enabled.
* ``-DGMX_GPU=OpenCL`` to build with OpenCL_ support enabled.
* ``-DGMX_SIMD=xxx`` to specify the level of `SIMD support`_ of the node on which |Gromacs| will run
-* ``-DGMX_BUILD_MDRUN_ONLY=on`` for `building only mdrun`_, e.g. for compute cluster back-end nodes
* ``-DGMX_DOUBLE=on`` to build |Gromacs| in double precision (slower, and not normally useful)
* ``-DCMAKE_PREFIX_PATH=xxx`` to add a non-standard location for CMake to `search for libraries, headers or programs`_
* ``-DCMAKE_INSTALL_PREFIX=xxx`` to install |Gromacs| to a `non-standard location`_ (default ``/usr/local/gromacs``)
compiler versions are
* GNU (gcc/libstdc++) 7
-* Intel (icc) 19.1
* LLVM (clang/libc++) 5
* Microsoft (MSVC) 2017 15.7
not offer competitive performance. We recommend against PGI because
the performance with C++ is very bad.
+The Intel classic compiler (icc/icpc) is no longer supported in
+|Gromacs|. Use Intel's newer clang-based compiler from oneAPI, or
+gcc.
+
The xlc compiler is not supported and version 16.1 does not compile on
POWER architectures for |Gromacs|\ -\ |version|. We recommend to use
the gcc compiler instead, as it is being extensively tested.
compiler also manages the standard library library via compiler flags,
these will be honored. For configuration of other compilers, read on.
-On Linux, both the Intel and clang compiler use the libstdc++ which
+On Linux, the clang compilers use the libstdc++ which
comes with gcc as the default C++ library. For |Gromacs|, we require
the compiler to support libstc++ version 7.1 or higher. To select a
particular libstdc++ library, provide the path to g++ with
``-DGMX_GPLUSPLUS_PATH=/path/to/g++``.
-On Windows with the Intel compiler, the MSVC standard library is used,
-and at least MSVC 2017 15.7 is required. Load the environment variables with
-vcvarsall.bat.
-
To build with clang and llvm's libcxx standard library, use
``-DCMAKE_CXX_FLAGS=-stdlib=libc++``.
-If you are running on Mac OS X, the best option is the Intel
-compiler. Both clang and gcc will work, but they produce lower
-performance and each have some shortcomings. clang 3.8 now offers
-support for OpenMP, and so may provide decent performance.
+If you are running on Mac OS X, the best option is gcc. The Apple
+clang compiler provided by MacPorts will work, but does not support
+OpenMP, so will probably not provide best performance.
For all non-x86 platforms, your best option is typically to use gcc or
the vendor's default or recommended compiler, and check for
in order to enable this.
If you wish to run in parallel on multiple machines across a network,
-you will need to have
-
-* an MPI library installed that supports the MPI 1.3
- standard, and
-* wrapper compilers that will compile code using that library.
+you will need to have an MPI library installed that supports the MPI
+2.0 standard. That's true for any MPI library version released since
+about 2009, but the |Gromacs| team recommends the latest version (for
+best performance) of either your vendor's library, OpenMPI_ or MPICH_.
To compile with MPI set your compiler to the normal (non-MPI) compiler
and add ``-DGMX_MPI=on`` to the cmake options. It is possible to set
the compiler to the MPI compiler wrapper but it is neither necessary
nor recommended.
-The |Gromacs| team recommends OpenMPI_ version
-1.6 (or higher), MPICH_ version 1.4.1 (or
-higher), or your hardware vendor's MPI installation. The most recent
-version of either of these is likely to be the best. More specialized
-networks might depend on accelerations only available in the vendor's
-library. LAM-MPI_ might work, but since it has
-been deprecated for years, it is not supported.
-
-For example, depending on your actual MPI library, use ``cmake
--DMPI_C_COMPILER=mpicc -DGMX_MPI=on``.
+CUDA-Aware MPI support
+~~~~~~~~~~~~~~~~~~~~~~
+In simulations using multiple NVIDIA GPUs, an MPI implementation with CUDA support
+(also called "CUDA-aware") allows communication to be performed directly between the
+distinct GPU memory spaces without staging through CPU memory, often
+resulting in higher bandwidth and lower latency communication. For
+more details, see `Introduction to CUDA-aware MPI
+<https://developer.nvidia.com/blog/introduction-cuda-aware-mpi/>`_.
+
+To use CUDA-aware MPI for direct GPU communication we recommend
+using the latest OpenMPI version (>=4.1.0) with the latest UCX version
+(>=1.10), since most GROMACS internal testing on CUDA-aware support has
+been performed using these versions. OpenMPI with CUDA-aware support can
+be built following the procedure in `these OpenMPI build instructions
+<https://www.open-mpi.org/faq/?category=buildcuda>`_.
+
+With ``GPU_MPI=ON``, GROMACS attempts to automatically detect CUDA support
+in the underlying MPI library at compile time, and enables direct GPU
+communication when this is detected. However, there are some cases when
+GROMACS may fail to detect existing CUDA-aware support, in which case
+it can be manually enabled by setting environment variable ``GMX_FORCE_CUDA_AWARE_MPI=1``
+at runtime (although such cases still lack substantial
+testing, so we urge the user to carefully check correctness of results
+against those using default build options, and report any issues).
CMake
^^^^^
Additionally, with GPU accelerated runs ``AVX2_256`` can also be
faster on high-end Skylake CPUs with both 512-bit FMA units enabled.
9. ``AVX_512_KNL`` Knights Landing Xeon Phi processors
-10. ``Sparc64_HPC_ACE`` Fujitsu machines like the K computer have this.
-11. ``IBM_VMX`` Power6 and similar Altivec processors have this.
-12. ``IBM_VSX`` Power7, Power8, Power9 and later have this.
-13. ``ARM_NEON`` 32-bit ARMv7 with NEON support.
-14. ``ARM_NEON_ASIMD`` 64-bit ARMv8 and later.
-15. ``ARM_SVE`` 64-bit ARMv8 and later with the Scalable Vector Extensions (SVE).
+10. ``IBM_VSX`` Power7, Power8, Power9 and later have this.
+11. ``ARM_NEON_ASIMD`` 64-bit ARMv8 and later.
+12. ``ARM_SVE`` 64-bit ARMv8 and later with the Scalable Vector Extensions (SVE).
The SVE vector length is fixed at CMake configure time. The default vector
length is automatically detected, and this can be changed via the
``GMX_SIMD_ARM_SVE_LENGTH`` CMake variable.
cmake .. -DGMX_GPU=OpenCL
To build with support for Intel integrated GPUs, it is required
-to add ``-DGMX_OPENCL_NB_CLUSTER_SIZE=4`` to the cmake command line,
+to add ``-DGMX_GPU_NB_CLUSTER_SIZE=4`` to the cmake command line,
so that the GPU kernels match the characteristics of the hardware.
The `Neo driver <https://github.com/intel/compute-runtime/releases>`_
is recommended.
mdrun) that run slowly on the new hardware. Building two full
installations and locally managing how to call the correct one
(e.g. using a module system) is the recommended
-approach. Alternatively, as at the moment the |Gromacs| tools do not
-make strong use of SIMD acceleration, it can be convenient to create
-an installation with tools portable across different x86 machines, but
-with separate mdrun binaries for each architecture. To achieve this,
+approach. Alternatively, one can use different suffixes to install
+several versions of |Gromacs| in the same location. To achieve this,
one can first build a full installation with the
least-common-denominator SIMD instruction set, e.g. ``-DGMX_SIMD=SSE2``,
-then build separate mdrun binaries for each architecture present in
+in order for simple commands like ``gmx grompp`` to work on all machines,
+then build specialized ``gmx`` binaries for each architecture present in
the heterogeneous environment. By using custom binary and library
-suffixes for the mdrun-only builds, these can be installed to the
-same location as the "generic" tools installation.
-`Building just the mdrun binary`_ is possible by setting the
-``-DGMX_BUILD_MDRUN_ONLY=ON`` option.
+suffixes (with CMake variables ``-DGMX_BINARY_SUFFIX=xxx`` and
+``-DGMX_LIBS_SUFFIX=xxx``), these can be installed to the same
+location.
Linear algebra libraries
~~~~~~~~~~~~~~~~~~~~~~~~
.. _building just the mdrun binary:
-Building only mdrun
-~~~~~~~~~~~~~~~~~~~
-
-This is now deprecated, but still supported with the ``cmake`` option
-``-DGMX_BUILD_MDRUN_ONLY=ON``, which will build a different version of
-``libgromacs`` and the ``mdrun`` program. Naturally, now ``make
-install`` installs only those products. By default, mdrun-only builds
-will default to static linking against |Gromacs| libraries, because
-this is generally a good idea for the targets for which an mdrun-only
-build is desirable.
-
Installing |Gromacs|
^^^^^^^^^^^^^^^^^^^^
your hardware, and the output of ``gmx mdrun -version`` (which contains
valuable diagnostic information in the header).
-Testing for MDRUN_ONLY executables
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-A build with ``-DGMX_BUILD_MDRUN_ONLY`` cannot be tested with
-``make check`` from the build tree, because most of the tests
-require a full build to run things like ``grompp``. To test such an
-mdrun fully requires installing it to the same location as a normal
-build of |Gromacs|, downloading the regression tests tarball manually
-as described above, sourcing the correct ``GMXRC`` and running the
-perl script manually. For example, from your |Gromacs| source
-directory:
-
-::
-
- mkdir build-normal
- cd build-normal
- # First, build and install normally to allow full testing of the standalone simulator.
- cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/your/installation/prefix/here
- make -j 4
- make install
- cd ..
- mkdir build-mdrun-only
- cd build-mdrun-only
- # Next, build and install the GMX_BUILD_MDRUN_ONLY version (optional).
- cmake .. -DGMX_MPI=ON -DGMX_BUILD_MDRUN_ONLY=ON -DCMAKE_INSTALL_PREFIX=/your/installation/prefix/here
- make -j 4
- make install
- cd /to/your/unpacked/regressiontests
- source /your/installation/prefix/here/bin/GMXRC
- ./gmxtest.pl all -np 2
-
Non-standard suffix
~~~~~~~~~~~~~~~~~~~
-If your mdrun program has been suffixed in a non-standard way, then
-the ``./gmxtest.pl -mdrun`` option will let you specify that name to the
+If your ``gmx`` program has been suffixed in a non-standard way, then
+the ``./gmxtest.pl -suffix`` option will let you specify that suffix to the
test machinery. You can use ``./gmxtest.pl -double`` to test the
double-precision version. You can use ``./gmxtest.pl -crosscompiling``
to stop the test harness attempting to check that the programs can
does not currently compile |Gromacs| correctly, perhaps because the
thread-MPI atomics are incorrectly implemented in |Gromacs|).
-Fujitsu PRIMEHPC
-^^^^^^^^^^^^^^^^
-
-This is the architecture of the K computer, which uses Fujitsu
-Sparc64VIIIfx chips. On this platform, |Gromacs| has
-accelerated group kernels using the HPC-ACE instructions, no
-accelerated Verlet kernels, and a custom build toolchain. Since this
-particular chip only does double precision SIMD, the default setup
-is to build |Gromacs| in double. Since most users only need single, we have added
-an option GMX_RELAXED_DOUBLE_PRECISION to accept single precision square root
-accuracy in the group kernels; unless you know that you really need 15 digits
-of accuracy in each individual force, we strongly recommend you use this. Note
-that all summation and other operations are still done in double.
-
-The recommended configuration is to use
-
-::
-
- cmake .. -DCMAKE_TOOLCHAIN_FILE=Toolchain-Fujitsu-Sparc64-mpi.cmake \
- -DCMAKE_PREFIX_PATH=/your/fftw/installation/prefix \
- -DCMAKE_INSTALL_PREFIX=/where/gromacs/should/be/installed \
- -DGMX_MPI=ON \
- -DGMX_BUILD_MDRUN_ONLY=ON \
- -DGMX_RELAXED_DOUBLE_PRECISION=ON
- make
- make install
-
Intel Xeon Phi
^^^^^^^^^^^^^^
Xeon Phi processors, hosted or self-hosted, are supported.
-Only symmetric (aka native) mode is supported on Knights Corner. The
-performance depends among other factors on the system size, and for
-now the performance might not be faster than CPUs. When building for it,
-the recommended configuration is
-
-::
-
- cmake .. -DCMAKE_TOOLCHAIN_FILE=Platform/XeonPhi
- make
- make install
-
-
The Knights Landing-based Xeon Phi processors behave like standard x86 nodes,
but support a special SIMD instruction set. When cross-compiling for such nodes,
use the ``AVX_512_KNL`` SIMD flavor.
gcc versions 7 and 8,
clang versions 8 and 9,
and
-a beta version of oneAPI containing Intel's compiler.
+a version of oneAPI containing Intel's clang-based compiler.
For this testing, we use Ubuntu 18.04 or 20.04 operating system.
Other compiler, library, and OS versions are tested less frequently.
For details, you can have a look at the
simulation, and afterward use position restraints in conjunction
with constant pressure.
-accelerate group
-
- On each atom in an “accelerate group” an acceleration
- :math:`\mathbf{a}^g` is imposed. This is equivalent to
- an external force. This feature makes it possible to drive the
- system into a non-equilibrium state and enables the performance of
- non-equilibrium MD and hence to obtain transport properties.
- (Deprecated)
-
energy-monitor group
Mutual interactions between all energy-monitor groups are compiled
The types of virtual sites supported in |Gromacs| are given in the list
below. Constructing atoms in virtual sites can be virtual sites
themselves, but only if they are higher in the list, i.e. virtual sites
-can be constructed from “particles” that are simpler virtual sites.
+can be constructed from “particles” that are simpler virtual sites. The
+virtual site velocities are reported, but not used in the integration
+of the virtual site positions.
-- On top of an atom. This allows giving an atom multiple atom types and
+On top of an atom
+~~~~~~~~~~~~~~~~~
+
+- This allows giving an atom multiple atom types and
with that also assigned multiple, different bonded interactions. This
- can espically be of use in free-energy calculations.
+ can especially be of use in free-energy calculations.
- The coordinates of the virtual site equal that of the constructing atom:
.. math:: \mathbf{F}_i ~=~ \mathbf{F}_{s}
:label: eqnvsite1force
-- As a linear combination of two atoms
- (:numref:`Fig. %s <fig-vsites>` 2):
+- The velocity of the virtual site equals that of the constructing atom:
+
+ .. math:: \mathbf{v}_s ~=~ \mathbf{v}_i
+ :label: eqnvsite1vel
+
+As a linear combination of two atoms (:numref:`Fig. %s <fig-vsites>` 2)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- The weights are calculated as
.. math:: w_i = 1 - a ~,~~ w_j = a
:label: eqnvsitelin2atom
- In this case the virtual site is on the line through atoms :math:`i`
and :math:`j`.
-- On the line through two atoms, with a fixed distance
- (:numref:`Fig. %s <fig-vsites>` 2fd):
+- The velocity of the virtual site is a linear combination of the
+ velocities of the constructing atoms
+
+On the line through two atoms, with a fixed distance (:numref:`Fig. %s <fig-vsites>` 2fd)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- The position is calculated as:
.. math:: \mathbf{r}_s ~=~ \mathbf{r}_i + a \frac{ \mathbf{r}_{ij} }
{ | \mathbf{r}_{ij} | }
\end{array}
:label: eqnvsite2fdforce
-- As a linear combination of three atoms
- (:numref:`Fig. %s <fig-vsites>` 3):
+- The velocity is calculated as:
+
+ .. math:: \mathbf{v}_{s} = \mathbf{v}_{i} + \frac{a}{|\mathbf{r}_{ij}|}
+ \left(\mathbf{v}_{ij} - \mathbf{r}_{ij}
+ \frac{\mathbf{v}_{ij}\cdot\mathbf{r}_{ij}}
+ {|\mathbf{r}_{ij}|^2}\right)
+ :label: eqnvsite2fdatomvel
+
+As a linear combination of three atoms (:numref:`Fig. %s <fig-vsites>` 3)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- The weights are calculated as:
.. math:: w_i = 1 - a - b ~,~~ w_j = a ~,~~ w_k = b
:label: eqnvsitelin3atom
- In this case the virtual site is in the plane of the other three
particles.
-- In the plane of three atoms, with a fixed distance
- (:numref:`Fig. %s <fig-vsites>` 3fd):
+In the plane of three atoms, with a fixed distance (:numref:`Fig. %s <fig-vsites>` 3fd)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- .. math:: \mathbf{r}_s ~=~ \mathbf{r}_i + b \frac{ (1 - a) \mathbf{r}_{ij} + a \mathbf{r}_{jk} }
- { | (1 - a) \mathbf{r}_{ij} + a \mathbf{r}_{jk} | }
+- The position is calculated as:
+
+ .. math:: \mathbf{r}_s ~=~ \mathbf{r}_i + b \frac{ \mathbf{r}_{ijk} } { | \mathbf{r}_{ijk} | }
+ ~\mbox{ where }~
+ \mathbf{r}_{ijk} ~=~ (1 - a) \mathbf{r}_{ij} + a \mathbf{r}_{jk}
:label: eqnvsiteplane3atom
- In this case the virtual site is in the plane of the other three
\end{array}
:label: eqnvsiteplane3atomforce
-- In the plane of three atoms, with a fixed angle and
- distance (:numref:`Fig. %s <fig-vsites>` 3fad):
+- The velocity is calculated as:
+
+ .. math:: \mathbf{v}_{s} ~=~ \mathbf{v}_{i} +
+ \frac{b}{|\mathbf{r}_{ijk}|}
+ \left(\dot{\mathbf{r}}_{ijk} -
+ \mathbf{r}_{ijk}\frac{\dot{\mathbf{r}}_{ijk}\cdot\mathbf{r}_{ijk}}
+ {|\mathbf{r}_{ijk}|^2}\right)
+ :label: eqnvsiteplane3atomvel
+
+In the plane of three atoms, with a fixed angle and distance (:numref:`Fig. %s <fig-vsites>` 3fad)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- The position is calculated as:
.. math:: \mathbf{r}_s ~=~ \mathbf{r}_i +
d \cos \theta \frac{\mathbf{r}_{ij}}{ | \mathbf{r}_{ij} | } +
\end{array}
:label: eqnvsite2fadFforce
-- As a non-linear combination of three atoms, out of
- plane (:numref:`Fig. %s <fig-vsites>` 3out):
+- The velocity is calculated as:
+
+ .. math:: \mathbf{v}_{s} &= \mathbf{v}_{i} + d\cos\theta\ \frac{\delta}{\delta t}\frac{\mathbf{r}_{ij}}{|\mathbf{r}_{ij}|} +
+ d\sin\theta\ \frac{\delta}{\delta t}\frac{\mathbf{r}_{\perp}}{|\mathbf{r}_{\perp}|} \\
+ ~\mbox{where}~&\\
+ \frac{\delta}{\delta t}\frac{\mathbf{r}_{ij}}{|\mathbf{r}_{ij}|} &=
+ \frac{1}{|\mathbf{r}_{ij}|}\left(\mathbf{v}_{ij} - \mathbf{r}_{ij}
+ \frac{\mathbf{v}_{ij}\cdot\mathbf{r}_{ij}}{|\mathbf{r}_{ij}|^2}\right)\\
+ \frac{\delta}{\delta t}\frac{\mathbf{r}_{\perp}}{|\mathbf{r}_{\perp}|} &=
+ \frac{1}{|\mathbf{r}_{\perp}|}
+ \left(\dot{\mathbf{r}}_{\perp} - \mathbf{r}_{\perp}\frac{\dot{\mathbf{r}}_{\perp}\cdot\mathbf{r}_{\perp}}{|\mathbf{r}_{\perp}|^2}\right)\\
+ \dot{\mathbf{r}}_\perp &= \mathbf{v}_{jk} - \mathbf{r}_{ij}
+ \frac{|\mathbf{r}_{ij}|^2(\mathbf{v}_{ij}\cdot\mathbf{r}_{jk} + \mathbf{r}_{ij}\cdot\mathbf{v}_{jk}) -
+ (\mathbf{r}_{ij}\cdot\mathbf{r}_{jk})(2\mathbf{r}_{ij}\cdot\mathbf{v}_{ij})} {|\mathbf{r}_{ij}|^4} -
+ \frac{\mathbf{r}_{ij}\cdot\mathbf{r}_{jk}}{|\mathbf{r}_{ij}|^2}\ \mathbf{v}_{ij}
+ :label: eqnvsite2fadvel
+
+As a non-linear combination of three atoms, out of plane (:numref:`Fig. %s <fig-vsites>` 3out)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- The position is calculated as:
.. math:: \mathbf{r}_s ~=~ \mathbf{r}_i + a \mathbf{r}_{ij} + b \mathbf{r}_{ik} +
c (\mathbf{r}_{ij} \times \mathbf{r}_{ik})
\end{array}
:label: eqnvsitenonlin3atomforce
-- From four atoms, with a fixed distance, see
- separate :numref:`Fig. %s <fig-vsite4fdn>`. This construction is a bit complex,
+- The velocity is calculated as:
+
+ .. math:: \mathbf{v}_{s} ~=~ \mathbf{v}_{i} + \frac{c}{|\mathbf{r}_{m}|}\left(\dot{\mathbf{r}}_{m} -
+ \mathbf{r}_{m} \frac{\dot{\mathbf{r}}_{m}\cdot\mathbf{r}_{m}}{|\mathbf{r}_{m}|^2}\right)
+ :label: eqnvsitenonlin3atomvel
+
+From four atoms, with a fixed distance, see separate :numref:`Fig. %s <fig-vsite4fdn>`
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+- This construction is a bit complex,
in particular since the previous type (4fd) could be unstable which
forced us to introduce a more elaborate construction:
The new 4fdn virtual site construction, which is stable even when
all constructing atoms are in the same plane.
--
+- The position is calculated as
+
.. math:: \begin{aligned}
\mathbf{r}_{ja} &=& a\, \mathbf{r}_{ik} - \mathbf{r}_{ij} = a\, (\mathbf{x}_k - \mathbf{x}_i) - (\mathbf{x}_j - \mathbf{x}_i) \nonumber \\
\mathbf{r}_{jb} &=& b\, \mathbf{r}_{il} - \mathbf{r}_{ij} = b\, (\mathbf{x}_l - \mathbf{x}_i) - (\mathbf{x}_j - \mathbf{x}_i) \nonumber \\
\mathbf{r}_m &=& \mathbf{r}_{ja} \times \mathbf{r}_{jb} \nonumber \\
- \mathbf{x}_s &=& \mathbf{x}_i + c \frac{\mathbf{r}_m}{ | \mathbf{r}_m | }
+ \mathbf{r}_s &=& \mathbf{r}_i + c \frac{\mathbf{r}_m}{ | \mathbf{r}_m | }
\end{aligned}
:label: eqnvsite
+- The velocity is calculated as:
+
+ .. math:: \mathbf{v}_{s} = \mathbf{v}_{i} + \frac{c}{|\mathbf{r}_{m}|}\left(\dot{\mathbf{r}}_{m} - \mathbf{r}_{m} \frac{\dot{\mathbf{r}}_{m}\cdot\mathbf{r}_{m}}{|\mathbf{r}_{m}|^2}\right)\\
+ ~\mbox{where}~&\\
+ \dot{\mathbf{r}}_{m} &= \dot{\mathbf{r}}_{ja} \times \mathbf{r}_{jb} + \mathbf{r}_{ja} \times \dot{\mathbf{r}}_{jb}
+ :label: eqnvsitevel
+
- In this case the virtual site is at a distance of :math:`|c|` from
:math:`i`, while :math:`a` and :math:`b` are parameters. **Note**
that the vectors :math:`\mathbf{r}_{ik}` and :math:`\mathbf{r}_{ij}`
value 1), but it should not be used for new simulations. All current
|Gromacs| tools will automatically generate type 4fdn instead.
-- A linear combination of :math:`N` atoms with relative
- weights :math:`a_i`. The weight for atom :math:`i` is:
+A linear combination of :math:`N` atoms with relative weights :math:`a_i`
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- The weight for atom :math:`i` is:
.. math:: w_i = a_i \left(\sum_{j=1}^N a_j \right)^{-1}
:label: eqnvsiterelweight
-.. _anticipated-changes:
-
.. Note to developers!
Please use """"""" to underline the individual entries for fixed issues in the subfolders,
otherwise the formatting on the webpage is messed up.
--- /dev/null
+Changes to the API
+^^^^^^^^^^^^^^^^^^
+
+.. Note to developers!
+ Please use """"""" to underline the individual entries for fixed issues in the subfolders,
+ otherwise the formatting on the webpage is messed up.
+ Also, please use the syntax :issue:`number` to reference issues on GitLab, without the
+ a space between the colon and number!
+
+Remove physical constant conversion functions
+"""""""""""""""""""""""""""""""""""""""""""""
+
+Legacy conversion functions for physical constants from and to the |Gromacs|
+representation have been removed as they didn't see any use in the library.
+
+
--- /dev/null
+Bugs fixed
+^^^^^^^^^^
+
+Fixed slight inaccuracies when using virtual sites with pressure coupling
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+Virtual sites were reconstructed after the system was propagated, but before
+scaling due to pressure coupling. For virtual site types which are not a linear
+combination of other atoms, this is not completely correct. Since the scaling
+due to pressure coupling is very small in healthy simulations, the resulting
+inaccuracies are expected to have been extremely minor, and in most cases
+undetectable.
+
+:issue:`3866`
+
+.. Note to developers!
+ Please use """"""" to underline the individual entries for fixed issues in the subfolders,
+ otherwise the formatting on the webpage is messed up.
+ Also, please use the syntax :issue:`number` to reference issues on GitLab, without the
+ a space between the colon and number!
+
--- /dev/null
+.. _anticipated-changes:
+
+.. Note to developers!
+ Please use """"""" to underline the individual entries for fixed issues in the subfolders,
+ otherwise the formatting on the webpage is messed up.
+ Also, please use the syntax :issue:`number` to reference issues on GitLab, without the
+ a space between the colon and number!
+
+Changes anticipated to |Gromacs| 2022 functionality
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Functionality deprecated in |Gromacs| 2022
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+GMX_OPENCL_NB_CLUSTER_SIZE CMake variable deprecated in favor of GMX_GPU_NB_CLUSTER_SIZE
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+Both OpenCL and SYCL support different cluster sizes, so GMX_GPU_NB_CLUSTER_SIZE should
+be used going forward.
--- /dev/null
+New and improved features
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. Note to developers!
+ Please use """"""" to underline the individual entries for fixed issues in the subfolders,
+ otherwise the formatting on the webpage is messed up.
+ Also, please use the syntax :issue:`number` to reference issues on GitLab, without the
+ a space between the colon and number!
+
--- /dev/null
+Highlights
+^^^^^^^^^^
+
+|Gromacs| 2022 was released on INSERT DATE HERE. Patch releases may
+have been made since then, please use the updated versions! Here are
+some highlights of what you can expect, along with more detail in the
+links below!
+
+As always, we've got several useful performance improvements, with or
+without GPUs, all enabled and automated by default. In addition,
+several new features are available for running simulations. We are extremely
+interested in your feedback on how well the new release works on your
+simulations and hardware. The new features are:
+
+* Cool quotes music play list
+
+
+.. Note to developers!
+ Please use """"""" to underline the individual entries for fixed issues in the subfolders,
+ otherwise the formatting on the webpage is messed up.
+ Also, please use the syntax :issue:`number` to reference issues on GitLab, without the
+ a space between the colon and number!
--- /dev/null
+Miscellaneous
+^^^^^^^^^^^^^
+
+.. Note to developers!
+ Please use """"""" to underline the individual entries for fixed issues in the subfolders,
+ otherwise the formatting on the webpage is messed up.
+ Also, please use the syntax :issue:`number` to reference issues on GitLab, without the
+ a space between the colon and number!
+
--- /dev/null
+Performance improvements
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. Note to developers!
+ Please use """"""" to underline the individual entries for fixed issues in the subfolders,
+ otherwise the formatting on the webpage is messed up.
+ Also, please use the syntax :issue:`number` to reference issues on GitLab, without the
+ a space between the colon and number!
+
+Dynamic pairlist generation for energy minimization
+"""""""""""""""""""""""""""""""""""""""""""""""""""
+
+With energy minimization, the pairlist, and domain decomposition when running
+in parallel, is now performed when at least one atom has moved more than the
+half the pairlist buffer size. The pairlist used to be constructed every step.
--- /dev/null
+Portability
+^^^^^^^^^^^
+
+Intel classic compiler (icc/icpc) no longer supported
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+We now support the Intel clang-based compiler from oneAPI (icx/icpx)
+instead. Please use it, or gcc.
+
+:issue:`3893`
--- /dev/null
+Removed functionality
+^^^^^^^^^^^^^^^^^^^^^
+
+Removed constant-acceleration groups support
+""""""""""""""""""""""""""""""""""""""""""""
+This code has been broken since before GROMACS 4.6, so it has been
+removed.
+
+:issue:`1354`
+
+.. Note to developers!
+ Please use """"""" to underline the individual entries for fixed issues in the subfolders,
+ otherwise the formatting on the webpage is messed up.
+ Also, please use the syntax :issue:`number` to reference issues on GitLab, without the
+ a space between the colon and number!
+
+Removed mdrun-only build configuration
+""""""""""""""""""""""""""""""""""""""
+
+The need for the mdrun-only build of |Gromacs| has expired, as it has
+the same set of dependencies as regular |Gromacs|. It was deprecated
+in GROMACS 2021. Removing it will simplify maintenance, testing,
+documentation, installation, and teaching new users.
+
+:issue:`3808`
+
+Removed support for x86 MIC, ARMv7, Sparc64 HPC-ACE, and IBM VMX SIMD
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+These platforms are dead in HPC and so are no longer supported. The
+KNL platform is unaffected by this change.
+
+:issue:`3891`
+
+Removed deprecated environment variables
+""""""""""""""""""""""""""""""""""""""""
+
+The following environment variables were removed after being deprecated
+in favor of better-named alternatives:
+
+* ``GMX_CUDA_NB_ANA_EWALD`` and ``GMX_OCL_NB_ANA_EWALD`` (use ``GMX_GPU_NB_ANA_EWALD``)
+* ``GMX_CUDA_NB_TAB_EWALD`` and ``GMX_OCL_NB_TAB_EWALD`` (use ``GMX_GPU_NB_TAB_EWALD``)
+* ``GMX_CUDA_NB_EWALD_TWINCUT`` and ``GMX_OCL_NB_EWALD_TWINCUT`` (use ``GMX_GPU_NB_EWALD_TWINCUT``)
+
+:issue:`3803`
+
+Removed the ability for gmx wham to read .pdo files
+"""""""""""""""""""""""""""""""""""""""""""""""""""
+
+Files in .pdo format were written by |Gromacs| versions prior to 4.0.
+That is so long ago that being able to read them is no longer
+relevant, so this capability was deprecated in version 2021. If you do
+need to read such files, please use an older version of |Gromacs|.
--- /dev/null
+Improvements to |Gromacs| tools
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. Note to developers!
+ Please use """"""" to underline the individual entries for fixed issues in the subfolders,
+ otherwise the formatting on the webpage is messed up.
+ Also, please use the syntax :issue:`number` to reference issues on GitLab, without the
+ a space between the colon and number!
+
+gmx msd has been migrated to the trajectoryanalysis framework
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+The tool now uses the |Gromacs| selection syntax. Rather than piping selections via stdin,
+selections are now made using the "-sel" option.
+
+This migration comes with about a 20% speedup in execution time.
+
+TODO: Modify/Delete this segment as features are added back in.
+Some rarely used features have yet to be migrated, including:
+
+- Mass weighting of MSDs cannot currently be turned on or off. It is set to on when -mol is set, otherwise off.
+- The -tensor option is not yet implemented.
+- System COM removal with -rmcomm has not yet been implemented.
+- B-factor writing using the -pdb option is not yet supported.
+
+:issue:`2368`
\ No newline at end of file
functionality supported, whereas patch releases contain only fixes for
issues identified in the corresponding major releases.
-Two versions of |Gromacs| are under active maintenance, the 2021
-series and the 2020 series. In the latter, only highly conservative
+Two versions of |Gromacs| are under active maintenance, the 2022
+series and the 2021 series. In the latter, only highly conservative
fixes will be made, and only to address issues that affect scientific
correctness. Naturally, some of those releases will be made after the
-year 2020 ends, but we keep 2019 in the name so users understand how
+year 2021 ends, but we keep 2021 in the name so users understand how
up to date their version is. Such fixes will also be incorporated into
-the 2021 release series, as appropriate. Around the time the 2022
-release is made, the 2020 series will no longer be maintained.
+the 2022 release series, as appropriate. Around the time the 2023
+release is made, the 2021 series will no longer be maintained.
Where issue numbers are reported in these release notes, more details
can be found on the `issue tracker`_ at that issue number.
-|Gromacs| 2021 series
+|Gromacs| 2022 series
---------------------
.. todolist::
2021/2021.1
+Major release
+^^^^^^^^^^^^^
+
+.. toctree::
+ :maxdepth: 1
+
+ 2022/major/highlights
+ 2022/major/features
+ 2022/major/performance
+ 2022/major/api
+ 2022/major/tools
+ 2022/major/bugs-fixed
+ 2022/major/deprecated-functionality
+ 2022/major/removed-functionality
+ 2022/major/portability
+ 2022/major/miscellaneous
+
+
+|Gromacs| 2021 series
+---------------------
+
Major release
^^^^^^^^^^^^^
2021/major/portability
2021/major/miscellaneous
+
+Older (unmaintained) |Gromacs| series
+-------------------------------------------------------
+
|Gromacs| 2020 series
---------------------
2019/major/portability
2019/major/miscellaneous
-Older (unmaintained) |Gromacs| series
--------------------------------------------------------
-
|Gromacs| 2018 series
---------------------
|Gromacs| includes many tools for preparing, running and analyzing
molecular dynamics simulations. These are all structured as part of a single
:command:`gmx` wrapper binary, and invoked with commands like :command:`gmx grompp`.
-:ref:`mdrun <gmx mdrun>` is the only other binary that
-:ref:`can be built <building just the mdrun binary>`; in the normal
-build it can be run with :command:`gmx mdrun`. Documentation for these can
+or :command:`gmx mdrun`. Documentation for these can
be found at the respective sections below, as well as on man pages (e.g.,
:manpage:`gmx-grompp(1)`) and with :samp:`gmx help {command}` or
:samp:`gmx {command} -h`.
(for coordinate and force buffers) directly on GPU memory spaces, without the staging of data through CPU
memory, where possible.
+``GMX_GPU_SYCL_NO_SYNCHRONIZE``
+ disable synchronizations between different GPU streams in SYCL build, instead relying on SYCL runtime to
+ do scheduling based on data dependencies. Experimental.
+
``GMX_CYCLE_ALL``
times all code during runs. Incompatible with threads.
by mdrun. Values should be between the pruning frequency value
(1 for CPU and 2 for GPU) and :mdp:`nstlist` ``- 1``.
-``GMX_USE_TREEREDUCE``
- use tree reduction for nbnxn force reduction. Potentially faster for large number of
- OpenMP threads (if memory locality is important).
-
.. _opencl-management:
OpenCL management
terminal residues (NXXX and CXXX) as :ref:`rtp` entries that are normally renamed. Setting
this environment variable disables this renaming.
-``GMX_PATH_GZIP``
- ``gunzip`` executable, used by :ref:`gmx wham`.
-
``GMX_FONT``
name of X11 font used by :ref:`gmx view`.
#. Do I need to compile all utilities with MPI?
- With one rarely-used exception (:ref:`pme_error <gmx pme_error>`), only the
- :ref:`mdrun <gmx mdrun>` binary is able to use the :ref:`MPI <mpi-support>`
+ With one rarely-used exception (:ref:`pme_error <gmx pme_error>`), only
+ :ref:`mdrun <gmx mdrun>` is able to use the :ref:`MPI <mpi-support>`
parallelism. So you only need to use the ``-DGMX_MPI=on`` flag
when :ref:`configuring <configure-cmake>` for a build intended to run
- the main simulation engine :ref:`mdrun <gmx mdrun>`.
+ the main simulation engine :ref:`mdrun <gmx mdrun>`. Generally that
+ is desirable when running on a multi-node cluster, and necessary
+ when using multi-simulation algorithms. Usually also installing a
+ build of GROMACS configured without MPI is convenient for users.
#. Should my version be compiled using double precision?
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Once the run input file is available, we can start the simulation. The
-program which starts the simulation is called :ref:`gmx mdrun` (or
-sometimes just mdrun, or mdrun_mpi). The only input file of :ref:`gmx mdrun`
+program which starts the simulation is called :ref:`gmx mdrun`.
+The only input file of :ref:`gmx mdrun`
that you usually need in order to start a run is the run input
file (:ref:`tpr` file). The typical output files of :ref:`gmx mdrun` are the
trajectory file (:ref:`trr` file), a logfile (:ref:`log` file), and perhaps a
a minimum value and :ref:`gmx mdrun` might increase it, unless
it is set to 1. With parallel simulations and/or non-bonded
force calculation on the GPU, a value of 20 or 40 often gives
- the best performance.
+ the best performance. With energy minimization this parameter
+ is not used as the pair list is updated when at least one atom
+ has moved by more than half the pair list buffer size.
.. mdp-value:: 0
Non-equilibrium MD
^^^^^^^^^^^^^^^^^^
-.. mdp:: acc-grps
-
- groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
- in groups Protein and Sol will experience constant acceleration as
- specified in the :mdp:`accelerate` line. (Deprecated)
-
-.. mdp:: accelerate
-
- (0) [nm ps\ :sup:`-2`]
- acceleration for :mdp:`acc-grps`; x, y and z for each group
- (*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has
- constant acceleration of 0.1 nm ps\ :sup:`-2` in X direction, second group
- the opposite). (Deprecated)
-
.. mdp:: freezegrps
Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
:ref:`configuring |Gromacs| with an external MPI library <mpi-support>`
so that the set of
simulations can communicate. The ``n`` simulations within the set can
-use internal MPI parallelism also, so that ``mpirun -np x mdrun_mpi``
+use internal MPI parallelism also, so that ``mpirun -np x gmx_mpi mdrun``
for ``x`` a multiple of ``n`` will use ``x/n`` ranks per simulation.
There are two ways of organizing files when running such
This requires configuring |Gromacs| to build with an external MPI
library. By default, this :ref:`mdrun <gmx mdrun>` executable is run with
-:ref:`mdrun_mpi`. All of the considerations for running single-node
+``gmx_mpi mdrun``. All of the considerations for running single-node
:ref:`mdrun <gmx mdrun>` still apply, except that ``-ntmpi`` and ``-nt`` cause a fatal
error, and instead the number of ranks is controlled by the
MPI environment.
mpirun -np 16 gmx_mpi mdrun
-Starts :ref:`mdrun_mpi` with 16 ranks, which are mapped to
+Starts :ref:`gmx mdrun` with 16 ranks, which are mapped to
the hardware by the MPI library, e.g. as specified
in an MPI hostfile. The available cores will be
automatically split among ranks using OpenMP threads,
mpirun -np 16 gmx_mpi mdrun -npme 5
-Starts :ref:`mdrun_mpi` with 16 ranks, as above, and
+Starts :ref:`gmx mdrun` with 16 ranks, as above, and
require that 5 of them are dedicated to the PME
component.
mpirun -np 11 gmx_mpi mdrun -ntomp 2 -npme 6 -ntomp_pme 1
-Starts :ref:`mdrun_mpi` with 11 ranks, as above, and
+Starts :ref:`gmx mdrun` with 11 ranks, as above, and
require that six of them are dedicated to the PME
component with one OpenMP thread each. The remaining
five do the PP component, with two OpenMP threads
mpirun -np 4 gmx_mpi mdrun -ntomp 6 -nb gpu -gputasks 00
-Starts :ref:`mdrun_mpi` on a machine with two nodes, using
+Starts :ref:`gmx mdrun` on a machine with two nodes, using
four total ranks, each rank with six OpenMP threads,
and both ranks on a node sharing GPU with ID 0.
mpirun -np 8 gmx_mpi mdrun -ntomp 3 -gputasks 0000
Using a same/similar hardware as above,
-starts :ref:`mdrun_mpi` on a machine with two nodes, using
+starts :ref:`gmx mdrun` on a machine with two nodes, using
eight total ranks, each rank with three OpenMP threads,
and all four ranks on a node sharing GPU with ID 0.
This may or may not be faster than the previous setup
mpirun -np 20 gmx_mpi mdrun -ntomp 4 -gputasks 00
-Starts :ref:`mdrun_mpi` with 20 ranks, and assigns the CPU cores evenly
+Starts :ref:`gmx mdrun` with 20 ranks, and assigns the CPU cores evenly
across ranks each to one OpenMP thread. This setup is likely to be
suitable when there are ten nodes, each with one GPU, and each node
has two sockets each of four cores.
mpirun -np 10 gmx_mpi mdrun -gpu_id 1
-Starts :ref:`mdrun_mpi` with 20 ranks, and assigns the CPU cores evenly
+Starts :ref:`gmx mdrun` with 20 ranks, and assigns the CPU cores evenly
across ranks each to one OpenMP thread. This setup is likely to be
suitable when there are ten nodes, each with two GPUs, but another
job on each node is using GPU 0. The job scheduler should set the
mpirun -np 20 gmx_mpi mdrun -gpu_id 01
-Starts :ref:`mdrun_mpi` with 20 ranks. This setup is likely
+Starts :ref:`gmx mdrun` with 20 ranks. This setup is likely
to be suitable when there are ten nodes, each with two
GPUs, but there is no need to specify ``-gpu_id`` for the
normal case where all the GPUs on the node are available
* Don't use double precision unless you're absolute sure you need it.
* Compile the FFTW library (yourself) with the correct flags on x86 (in most
cases, the correct flags are automatically configured).
-* On x86, use gcc or icc as the compiler (not pgi or the Cray compiler).
+* On x86, use gcc as the compiler (not icc, pgi or the Cray compiler).
* On POWER, use gcc instead of IBM's xlc.
* Use a new compiler version, especially for gcc (e.g. from version 5 to 6
the performance of the compiled code improved a lot).
# Python package requirements for complete build, installation, and testing of
# gmxapi functionality.
-cmake>=3.13
+cmake>=3.16.3
flake8>=3.7.7
networkx>=2.0
numpy>=1
-cmake_minimum_required(VERSION 3.13.0)
+cmake_minimum_required(VERSION 3.16.3)
# If you are using this repository as a template, you should probably change the
# project name and adopt your own versioning scheme.
project(sample_restraint VERSION 0.0.8)
# If building with setuptools, CMake will not be performing the install
set_target_properties(gmxapi_extension_ensemblepotential PROPERTIES BUILD_WITH_INSTALL_RPATH TRUE)
-target_link_libraries(gmxapi_extension_ensemblepotential PRIVATE Gromacs::gmxapi)
+target_link_libraries(gmxapi_extension_ensemblepotential PUBLIC Gromacs::libgromacs Gromacs::gmxapi)
add_executable(gmxapi_extension_library-test test_binding.cpp)
add_dependencies(gmxapi_extension_library-test gmxapi_extension_spc2_water_box)
target_include_directories(gmxapi_extension_library-test PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
-target_link_libraries(gmxapi_extension_library-test Gromacs::gmxapi GTest::Main)
+target_link_libraries(gmxapi_extension_library-test Gromacs::libgromacs Gromacs::gmxapi GTest::Main)
gtest_add_tests(TARGET gmxapi_extension_library-test
TEST_LIST BasicPlugin)
assert os.path.exists(topfile)
if solvate.output.returncode.result() != 0:
- logging.debug(solvate.output.erroroutput.result())
+ logging.debug(solvate.output.stderr.result())
raise RuntimeError('solvate failed in spc_water_box testing fixture.')
# Choose an exactly representable dt of 2^-9 ps (approximately 0.002)
output_files={'-o': tprfile})
tprfilename = grompp.output.file['-o'].result()
if grompp.output.returncode.result() != 0:
- logging.debug(grompp.output.erroroutput.result())
+ logging.debug(grompp.output.stderr.result())
raise RuntimeError('grompp failed in spc_water_box testing fixture.')
# TODO: more inspection of grompp errors...
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# configure and run CMake. CMake could be invoked directly by the user or a
# parent package, but the Python distribution would not be packaged automatically.
# Reference https://gitlab.com/gromacs/gromacs/-/issues/2896 for additional discussion.
-cmake_minimum_required(VERSION 3.13.0)
+cmake_minimum_required(VERSION 3.16.3)
# This needs to be set before project() in order to pick up toolchain files
#list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/../../cmake)
# Note that this is the gmxapi._gmxapi Python bindings package version,
# not the C++ API version. It is not essential that it match the pure Python
# package version, but is likely to do so.
-project(gmxapi VERSION 0.2.0)
+project(gmxapi VERSION 0.3.0)
# Check if Python package is being built directly or via add_subdirectory
set(GMXAPI_MASTER_PROJECT OFF)
# * provides `output` publishing proxy to the inner function and
# * produce a result with attributes for
# * file: mapping of output flags to output filenames
-# * erroroutput: text results in case of error
+# * stdout: process STDOUT
+# * stderr: porcess STDERR
# * returncode: integer return code of wrapped command
#
# Note that the existence of the 'file' output map is expressed here, but
#
# TODO: Operation returns the output object when called with the shorter signature.
#
-@gmx.function_wrapper(output={'erroroutput': str, 'returncode': int})
+@gmx.function_wrapper(output={'stdout': str,
+ 'stderr': str,
+ 'returncode': int})
def cli(command: NDArray, shell: bool, output: OutputCollectionDescription, stdin: str = ''):
"""Execute a command line program in a subprocess.
>>> my_filename = "somefilename"
>>> result = cli(('exe', '--origin', 1.0, 2.0, 3.0, '-f', my_filename), shell=False)
>>> assert hasattr(result, 'file')
- >>> assert hasattr(result, 'erroroutput')
+ >>> assert hasattr(result, 'stdout')
+ >>> assert hasattr(result, 'stderr')
>>> assert hasattr(result, 'returncode')
Returns:
- A data structure with attributes for each of the results `file`, `erroroutput`, and `returncode`
+ A data structure with attributes for each of the results `file`, `stdout`, `stderr`, and `returncode`
Result object attributes:
* `file`: the mapping of CLI flags to filename strings resulting from the `output` kwarg
- * `erroroutput`: A string of error output (if any) if the process failed.
+ * `stdout`: A string mapping from process STDOUT.
+ * `stderr`: A string mapping from process STDERR; it will be the
+ error output (if any) if the process failed.
* `returncode`: return code of the subprocess.
"""
- # Note: we could make provisions for stdio filehandles in a future version. E.g.
- # * STDOUT is available if a consuming operation is bound to `output.stdout`.
- # * STDERR is available if a consuming operation is bound to `output.stderr`.
- # * Otherwise, STDOUT and/or STDERR is(are) closed when command is called.
-
# In the operation implementation, we expect the `shell` parameter to be intercepted by the
# wrapper and set to False.
if shell:
# TODO: (FR9) Can OS input/output filehandles be a responsibility of
# the code providing 'resources'?
- erroroutput = ''
+ stdout = ''
+ stderr = ''
logger.debug('executing subprocess')
try:
completed_process = subprocess.run(command,
input=stdin,
check=True,
stdout=subprocess.PIPE,
- stderr=subprocess.STDOUT,
+ stderr=subprocess.PIPE,
encoding='utf-8',
universal_newlines=True
)
returncode = completed_process.returncode
# TODO: Resource management code should manage a safe data object for `output`.
- for line in completed_process.stdout.split('\n'):
- logger.debug(line)
+ logger.debug('STDOUT:')
+ if completed_process.stderr is not None:
+ for line in completed_process.stdout.split('\n'):
+ logger.debug(line)
+ else:
+ logger.debug('STDOUT is empty')
+ logger.debug('STDERR:')
+ if completed_process.stderr is not None:
+ for line in completed_process.stderr.split('\n'):
+ logger.debug(line)
+ else:
+ logger.debug('STDERR is empty')
+
+ stdout = completed_process.stdout
+ stderr = completed_process.stderr
+
except subprocess.CalledProcessError as e:
- logger.info("commandline operation had non-zero return status when calling {}".format(e.cmd))
- erroroutput = e.output
+ logger.info("commandline operation had non-zero return status"
+ "when calling {}".format(e.cmd))
+ stdout = e.stdout
+ stderr = e.stderr
returncode = e.returncode
+
# Publish outputs.
- output.erroroutput = erroroutput
+ output.stdout = stdout
+ output.stderr = stderr
output.returncode = returncode
The output node of the resulting operation handle contains
* ``file``: the mapping of CLI flags to filename strings resulting from the ``output_files`` kwarg
- * ``erroroutput``: A string of error output (if any) if the process failed.
+ * ``stdout``: A string mapping from process STDOUT.
+ * ``stderr``: A string mapping from process STDERR; it will be the
+ error output (if any) if the process failed.
* ``returncode``: return code of the subprocess.
"""
#
# TODO: (FR4+) Characterize the `file` dictionary key type:
# explicitly sequences rather than maybe-string/maybe-sequence-of-strings
- @gmx.function_wrapper(output={'erroroutput': str, 'returncode': int, 'file': dict})
- def merged_ops(erroroutput: str = None, returncode: int = None, file: dict = None,
+ @gmx.function_wrapper(output={'stdout': str,
+ 'stderr': str,
+ 'returncode': int,
+ 'file': dict})
+ def merged_ops(stdout: str = None,
+ stderr: str = None,
+ returncode: int = None,
+ file: dict = None,
output: OutputCollectionDescription = None):
- assert erroroutput is not None
+ assert stdout is not None
+ assert stderr is not None
assert returncode is not None
assert file is not None
assert output is not None
output.returncode = returncode
- output.erroroutput = erroroutput
+ output.stdout = stdout
+ output.stderr = stderr
if returncode == 0:
output.file = file
else:
# TODO: ``label`` kwarg
# TODO: input fingerprinting
cli_result = cli(**cli_args)
- merged_result = merged_ops(erroroutput=cli_result.output.erroroutput,
+ merged_result = merged_ops(stdout=cli_result.output.stdout,
+ stderr=cli_result.output.stderr,
returncode=cli_result.output.returncode,
file=output_files,
**kwargs)
// Add argument type before it is used for more sensible automatic bindings behavior.
py::class_<MDArgs, std::unique_ptr<MDArgs>> mdargs(m, "MDArgs");
mdargs.def(py::init(), "Create an empty MDArgs object.");
- mdargs.def("set", [](MDArgs* self, const py::dict& params) { setMDArgs(self, params); },
+ mdargs.def("set",
+ [](MDArgs* self, const py::dict& params) { setMDArgs(self, params); },
"Assign parameters in MDArgs from Python dict.");
// Export execution context class
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct UnknownExceptionPlaceHolder
{
};
- static py::exception<UnknownExceptionPlaceHolder> unknownException(m, "UnknownException",
- baseException.ptr());
+ static py::exception<UnknownExceptionPlaceHolder> unknownException(
+ m, "UnknownException", baseException.ptr());
unknownException.doc() =
"GROMACS library produced an exception that is "
"not mapped in gmxapi or which should have been "
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
// required to maintain and to pass to the API.
py::class_<::gmxapi::Session, std::shared_ptr<::gmxapi::Session>> session(m, "MDSession");
session.def("run", &::gmxapi::Session::run, "Run the simulation workflow");
- session.def("close", &::gmxapi::Session::close,
+ session.def("close",
+ &::gmxapi::Session::close,
"Shut down the execution environment and close the session.");
// Export system container class
"Launch the configured workflow in the provided context.");
// Module-level function
- m.def("from_tpr", &gmxpy::from_tpr,
+ m.def("from_tpr",
+ &gmxpy::from_tpr,
"Return a system container initialized from the given input record.");
}
[](GmxMdParams* self, const std::string& key, int64_t value) {
gmxapicompat::setParam(self, key, value);
},
- py::arg("key").none(false), py::arg("value").none(false),
+ py::arg("key").none(false),
+ py::arg("value").none(false),
"Use a dictionary to update simulation parameters.");
mdparams.def("set",
[](GmxMdParams* self, const std::string& key, double value) {
gmxapicompat::setParam(self, key, value);
},
- py::arg("key").none(false), py::arg("value").none(false),
+ py::arg("key").none(false),
+ py::arg("value").none(false),
"Use a dictionary to update simulation parameters.");
mdparams.def("set",
[](GmxMdParams* self, const std::string& key, py::none) {
// unsetParam(self, key);
},
- py::arg("key").none(false), py::arg("value"),
+ py::arg("key").none(false),
+ py::arg("value"),
"Use a dictionary to update simulation parameters.");
return params;
});
- module.def("read_tprfile", &readTprFile, py::arg("filename"),
+ module.def("read_tprfile",
+ &readTprFile,
+ py::arg("filename"),
"Get a handle to a TPR file resource for a given file name.");
module.def("write_tprfile",
auto topology = gmxapicompat::getTopologySource(tprReadHandle);
gmxapicompat::writeTprFile(filename, *params, *structure, *state, *topology);
},
- py::arg("filename").none(false), py::arg("parameters"),
+ py::arg("filename").none(false),
+ py::arg("parameters"),
"Write a new TPR file with the provided data.");
module.def("copy_tprfile",
[](const gmxapicompat::TprReadHandle& input, std::string outFile) {
return gmxapicompat::copy_tprfile(input, outFile);
},
- py::arg("source"), py::arg("destination"),
+ py::arg("source"),
+ py::arg("destination"),
"Copy a TPR file from ``source`` to ``destination``.");
module.def("rewrite_tprfile",
[](std::string input, std::string output, double end_time) {
return gmxapicompat::rewrite_tprfile(input, output, end_time);
},
- py::arg("source"), py::arg("destination"), py::arg("end_time"),
+ py::arg("source"),
+ py::arg("destination"),
+ py::arg("end_time"),
"Copy a TPR file from ``source`` to ``destination``, replacing `nsteps` with "
"``end_time``.");
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
export_exceptions(m);
// Export core bindings
- m.def("has_feature", &gmxapi::Version::hasFeature,
+ m.def("has_feature",
+ &gmxapi::Version::hasFeature,
"Check the gmxapi library for a named feature.");
py::class_<::gmxapi::Status> gmx_status(m, "Status", "Holds status for API operations.");
# TODO: Version management policy and procedures.
_major = 0
-_minor = 2
+_minor = 3
_micro = 0
_suffix = ''
name='gmxapi',
# TODO: single-source version information (currently repeated in gmxapi/version.py and CMakeLists.txt)
- version='0.2.0',
+ version='0.3.0a1',
python_requires='>=3.6',
install_requires=['networkx>=2.0',
'numpy>=1'],
assert os.path.exists(topfile)
if solvate.output.returncode.result() != 0:
- logging.debug(solvate.output.erroroutput.result())
+ logging.debug(solvate.output.stderr.result())
raise RuntimeError('solvate failed in spc_water_box testing fixture.')
# Choose an exactly representable dt of 2^-9 ps (approximately 0.002)
output_files={'-o': tprfile})
tprfilename = grompp.output.file['-o'].result()
if grompp.output.returncode.result() != 0:
- logging.debug(grompp.output.erroroutput.result())
+ logging.debug(grompp.output.stderr.result())
raise RuntimeError('grompp failed in spc_water_box testing fixture.')
# TODO: more inspection of grompp errors...
command = shutil.which('true')
operation = commandline.cli(command=[command], shell=False)
- # Note: 'stdout' and 'stderr' not mapped.
# Note: getitem not implemented.
- # assert not 'stdout' in operation.output
- # assert not 'stderr' in operation.output
- assert not hasattr(operation.output, 'stdout')
- assert not hasattr(operation.output, 'stderr')
-
- # Check for the attributes that we _do_ expect.
- assert hasattr(operation.output, 'erroroutput')
+ # assert 'stdout' in operation.output
+ # assert 'stderr' in operation.output
+ assert hasattr(operation.output, 'stdout')
+ assert hasattr(operation.output, 'stderr')
+ assert not hasattr(operation.output, 'erroroutput')
assert hasattr(operation.output, 'returncode')
operation.run()
def test_true(self):
operation = commandline.commandline_operation(executable='true')
- # Note: 'stdout' and 'stderr' not mapped.
# Note: getitem not implemented.
- # assert not 'stdout' in operation.output
- # assert not 'stderr' in operation.output
- assert not hasattr(operation.output, 'stdout')
- assert not hasattr(operation.output, 'stderr')
+ # assert 'stdout' in operation.output
+ # assert 'stderr' in operation.output
+ assert not hasattr(operation.output, 'erroroutput')
assert hasattr(operation.output, 'file')
- assert hasattr(operation.output, 'erroroutput')
+ assert hasattr(operation.output, 'stdout')
+ assert hasattr(operation.output, 'stderr')
assert hasattr(operation.output, 'returncode')
assert operation.output.returncode.result() == 0
assert operation.output.returncode.result() == 1
def test_echo(self):
- # TODO: (FR5+) do we want to pipeline or checkpoint stdout somehow?
+ # TODO: (#3549) Check stdout, stderr.
operation = commandline.commandline_operation(executable='echo',
arguments=['hi there'])
assert operation.output.returncode.result() == 0
# This should be removable once object libraries can directly use target_link_libraries
# with CMake 3.12, #3290
target_include_directories(template SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
-target_link_libraries(template libgromacs ${GMX_EXE_LINKER_FLAGS})
+target_link_libraries(template libgromacs legacy_modules ${GMX_EXE_LINKER_FLAGS})
set(DOCUMENTATION_HTTP_URL_BASE
http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc)
-cmake_minimum_required(VERSION 3.9.6)
+cmake_minimum_required(VERSION 3.16.3)
project(template CXX)
-set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)
settings->setHelpText(desc);
options->addOption(FileNameOption("o")
- .filetype(eftPlot).outputFile()
+ .filetype(OptionFileType::Plot).outputFile()
.store(&fnDist_).defaultBasename("avedist")
.description("Average distances from reference group"));
# We need to use underscores for readability for our legacy types
# and command-line parameter names
#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
bugprone-*,misc-*,readability-*,performance-*,mpi-*,
-readability-inconsistent-declaration-parameter-name,
-cppcoreguidelines-macro-usage,
-cppcoreguidelines-narrowing-conversions,
-bugprone-narrowing-conversions,
- -google-readability-avoid-underscore-in-googletest-name
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion
HeaderFilterRegex: .*
CheckOptions:
- key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
-readability-magic-numbers,
-cppcoreguidelines-macro-usage,
-cppcoreguidelines-narrowing-conversions,
- -bugprone-narrowing-conversions
+ -cppcoreguidelines-init-variables,
+ -bugprone-narrowing-conversions,
+ -misc-no-recursion
HeaderFilterRegex: .*
CheckOptions:
- key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
# CMAKE_BUILD_TYPE is #included into buildinfo.h and populates the
# fields e.g. printed to the log file.
file(GENERATE
- OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/compilerflaginfo-$<CONFIG>-$<COMPILE_LANGUAGE>.h
+ OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/include/compilerflaginfo-$<CONFIG>-$<COMPILE_LANGUAGE>.h
INPUT ${CMAKE_CURRENT_SOURCE_DIR}/compilerflaginfo.h.cmakein
CONDITION $<CONFIG:${CMAKE_BUILD_TYPE}>
)
mark_as_advanced(CLANG_TIDY_EXE)
endif()
+# Create a basic target for the `src` section of the build tree to capture
+# the library-level shared details through CMake infrastructure. It is not
+# installed or exported, so it must only be used as a PRIVATE dependency by
+# installed targets.
+# Initially, this is just an INTERFACE target to provide include directory.
+# It should also absorb global variables and compiler/linker details to be
+# provided as transitive usage requirements.
+# It could expand to aggregate the module targets in the future.
+add_library(common INTERFACE)
+target_include_directories(common INTERFACE
+ ${CMAKE_CURRENT_SOURCE_DIR}/include
+ ${CMAKE_CURRENT_BINARY_DIR}/include)
+
add_subdirectory(external)
if (BUILD_TESTING)
# header file in both of the make stages. That's slow, and is useless
# busy work for ccache, too.
string(TOUPPER "${CMAKE_BUILD_TYPE}" CMAKE_BUILD_TYPE_UPPER)
-configure_file(config.h.cmakein config.h)
-configure_file(gmxpre-config.h.cmakein gmxpre-config.h)
+configure_file(config.h.cmakein include/config.h)
+configure_file(gmxpre-config.h.cmakein include/gmxpre-config.h)
set(CMAKE_BUILD_CONFIGURATION_C_FLAGS ${CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE_UPPER}})
set(CMAKE_BUILD_CONFIGURATION_CXX_FLAGS ${CMAKE_CXX_FLAGS_${CMAKE_BUILD_TYPE_UPPER}})
-configure_file(buildinfo.h.cmakein buildinfo.h ESCAPE_QUOTES)
+configure_file(buildinfo.h.cmakein include/buildinfo.h ESCAPE_QUOTES)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# Activate targets for new C++ API components and docs.
if (GMXAPI)
- if (GMX_BUILD_MDRUN_ONLY)
- message(FATAL_ERROR "GMXAPI relies on libgromacs and is incompatible with GMX_BUILD_MDRUN_ONLY.")
- endif()
if(NOT ${BUILD_SHARED_LIBS})
# Note: this conditional should check for the existence of a libgromacs target supporting PIC
# using the POSITION_INDEPENDENT_CODE property, but for now the only facility we have is the global
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
#include "gromacs/math/vectypes.h"
#include "gromacs/restraint/restraintpotential.h"
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/classhelpers.h"
namespace gmxapi
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
auto session = system.launch(context);
// Try to simulate an interrupt signal to catch.
- gmx_set_stop_condition(gmx_stop_cond_next_ns);
+ gmx_set_stop_condition(StopCondition::NextNS);
- session->run();
+ auto status = session->run();
+ EXPECT_FALSE(status.success());
// If this assertion fails, it is not an error, but it indicates expected behavior has
// changed and we need to consider the impact of whatever changes caused this.
- EXPECT_NE(gmx_get_stop_condition(), gmx_stop_cond_none);
+ EXPECT_NE(gmx_get_stop_condition(), StopCondition::None);
session->close();
} // allow system and session to be destroyed.
// changed and we need to consider the impact of whatever changes caused this.
// We are expecting that the libgromacs state has retained the stop condition from the
// previously issued SIGINT
- EXPECT_NE(gmx_get_stop_condition(), gmx_stop_cond_none);
+ EXPECT_NE(gmx_get_stop_condition(), StopCondition::None);
auto session = system.launch(context);
// Launching a session should clear the stop condition.
- EXPECT_EQ(gmx_get_stop_condition(), gmx_stop_cond_none);
+ EXPECT_EQ(gmx_get_stop_condition(), StopCondition::None);
- session->run();
+ auto status = session->run();
+ EXPECT_TRUE(status.success());
// Stop condition should still be clear.
- EXPECT_EQ(gmx_get_stop_condition(), gmx_stop_cond_none);
+ EXPECT_EQ(gmx_get_stop_condition(), StopCondition::None);
session->close();
}
"tau-t = 1\n"
"ref-t = 298\n"
"compressed-x-grps = Sol\n",
- steps, getTestStepSize()));
+ steps,
+ getTestStepSize()));
EXPECT_EQ(0, runner_.callGromppOnThisRank());
}
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# Test code relies on exported and globally accessible variables.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
*
* Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* AVX2 128-bit SIMD instruction set level was selected */
#cmakedefine01 GMX_SIMD_X86_AVX2_128
-/* MIC (Xeon Phi) SIMD instruction set level was selected */
-#cmakedefine01 GMX_SIMD_X86_MIC
-
/* AVX-512F foundation level instruction SIMD */
#cmakedefine01 GMX_SIMD_X86_AVX_512
/* AVX-512ER foundation level instruction SIMD */
#cmakedefine01 GMX_SIMD_X86_AVX_512_KNL
-/* 32-bit ARM NEON SIMD instruction set level was selected */
-#cmakedefine01 GMX_SIMD_ARM_NEON
-
/* ARM (AArch64) NEON Advanced SIMD instruction set level was selected */
#cmakedefine01 GMX_SIMD_ARM_NEON_ASIMD
/* SVE vector length */
#define GMX_SIMD_ARM_SVE_LENGTH_VALUE @GMX_SIMD_ARM_SVE_LENGTH_VALUE@
-/* IBM VMX was selected as SIMD instructions (Power 6 and later) */
-#cmakedefine01 GMX_SIMD_IBM_VMX
-
/* IBM VSX was selected as SIMD instructions (Power 7 and later) */
#cmakedefine01 GMX_SIMD_IBM_VSX
-/* Fujitsu Sparc64 HPC-ACE SIMD acceleration */
-#cmakedefine01 GMX_SIMD_SPARC64_HPC_ACE
-
/* Reference SIMD implementation for testing */
#cmakedefine01 GMX_SIMD_REFERENCE
/* Whether NBNXM and other SIMD kernels should be compiled */
#cmakedefine01 GMX_USE_SIMD_KERNELS
-/* Whether a double-precision configuration may target accuracy equivalent to single precision */
-#cmakedefine01 GMX_RELAXED_DOUBLE_PRECISION
-
/* Integer byte order is big endian. */
#cmakedefine01 GMX_INTEGER_BIG_ENDIAN
(MPI or thread_mpi) */
#define GMX_MPI (GMX_LIB_MPI || GMX_THREAD_MPI)
-/* MPI_IN_PLACE exists for collective operations */
-#cmakedefine01 MPI_IN_PLACE_EXISTS
-
/* Use OpenMP multithreading */
#cmakedefine01 GMX_OPENMP
/* Define if SYCL GPU acceleration is compiled */
#cmakedefine01 GMX_GPU_SYCL
+/* Define if hipSYCL is used for SYCL support (otherwise DPCPP is assumed) */
+#cmakedefine01 GMX_SYCL_HIPSYCL
+
+/* Define if Intel's DPCPP is used (default unless hipSYCL is chosen) */
+#define GMX_SYCL_DPCPP (!GMX_SYCL_HIPSYCL)
+
/* Use a single compilation unit when compiling the CUDA (non-bonded) kernels. */
#cmakedefine01 GMX_CUDA_NB_SINGLE_COMPILATION_UNIT
-/* Cluster size used by nonbonded OpenCL kernel. Should be 8 for NVIDIA/AMD and 4 for Intel */
-#define GMX_OPENCL_NB_CLUSTER_SIZE @GMX_OPENCL_NB_CLUSTER_SIZE@
+/* Use CUDA-aware MPI. */
+#cmakedefine01 HAVE_CUDA_AWARE_MPI
+
+/* Cluster size used by nonbonded kernel. Should be 8 for NVIDIA/AMD and 4 for Intel */
+#define GMX_GPU_NB_CLUSTER_SIZE @GMX_GPU_NB_CLUSTER_SIZE@
/* Define constants for build types (starting at 1 to make sure undefined values don't match) */
#define CMAKE_BUILD_TYPE_DEBUG 1
#cmakedefine01 HAVE_FSEEKO
/* Define to 1 if _fseeki64 (and presumably _fseeki64) exists and is declared. */
+//NOLINTNEXTLINE(bugprone-reserved-identifier)
#cmakedefine01 HAVE__FSEEKI64
/* Have io.h (windows)*/
#cmakedefine01 HAVE_MEMALIGN
/* Define to 1 if you have the MSVC _aligned_malloc() function. */
+//NOLINTNEXTLINE(bugprone-reserved-identifier)
#cmakedefine01 HAVE__ALIGNED_MALLOC
/* Define to 1 if you have the clock_gettime() function. */
#cmakedefine01 HAVE_FSYNC
/* Define to 1 if you have the Windows _commit() function. */
+//NOLINTNEXTLINE(bugprone-reserved-identifier)
#cmakedefine01 HAVE__COMMIT
/* Define to 1 if you have the fileno() function. */
#cmakedefine01 HAVE_FILENO
/* Define to 1 if you have the _fileno() function. */
+//NOLINTNEXTLINE(bugprone-reserved-identifier)
#cmakedefine01 HAVE__FILENO
/* Define to 1 if you have the sigaction() function. */
* malloc.h or xmmintrin.h, and 0 otherwise. Note that you need to
* conditionally include the three headers too before using _mm_malloc().
*/
+//NOLINTNEXTLINE(bugprone-reserved-identifier)
#cmakedefine01 HAVE__MM_MALLOC
/* Define if SIGUSR1 is present */
# We don't want any checks at all for external code, but that leads to
# clang-tidy complaining that it is being run with no checks. So we
# let it use a single check that is irrelevant for GROMACS.
-Checks: -clang-analyzer*,zircon-temporary-objects
+Checks: -clang-analyzer*,zircon-temporary-objects, -cppcoreguidelines*
#else
/* older versions of gcc don't support atomic intrinsics */
-#ifndef __MIC__
#define tMPI_Atomic_memory_barrier() __asm__ __volatile__("sfence;" : : : "memory")
-#else
-/* MIC is in-order and does not need nor support sfense */
-#define tMPI_Atomic_memory_barrier() __asm__ __volatile__("" ::: "memory")
-#endif
#define TMPI_ATOMIC_HAVE_NATIVE_FETCH_ADD
static inline int tMPI_Atomic_fetch_add(tMPI_Atomic_t *a, int i)
+++ /dev/null
-/*
- This source code file is part of thread_mpi.
- Written by Sander Pronk, Erik Lindahl, and possibly others.
-
- Copyright (c) 2009, Sander Pronk, Erik Lindahl.
- All rights reserved.
-
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are met:
- 1) Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- 2) Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in the
- documentation and/or other materials provided with the distribution.
- 3) Neither the name of the copyright holders nor the
- names of its contributors may be used to endorse or promote products
- derived from this software without specific prior written permission.
-
- THIS SOFTWARE IS PROVIDED BY US ''AS IS'' AND ANY
- EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- DISCLAIMED. IN NO EVENT SHALL WE BE LIABLE FOR ANY
- DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
- ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
- If you want to redistribute modifications, please consider that
- scientific software is very special. Version control is crucial -
- bugs must be traceable. We will be happy to consider code for
- inclusion in the official distribution, but derived work should not
- be called official thread_mpi. Details are found in the README & COPYING
- files.
- */
-
-/** \file
- *
- * \brief mutex objects with C++11 API compatibility.
- *
- * This header contains classes mutex and lock_guard, used in C++ mutex
- * implementations safe for exceptions.
- */
-
-#ifndef TMPI_MUTEX_H_
-#define TMPI_MUTEX_H_
-
-#include "visibility.h"
-#include "system_error.h"
-#include "threads.h"
-
-namespace tMPI
-{
-/*! \brief A lock guard class that allows for the simple management of
- mutexes. C++11 compatible.
-
- In C++, mutexes would normally have to be unlocked with explicit
- exception handlers and unlock statements. This class automates that
- by handling the mutex unlock in a destructor. The constructor locks
- the mutex.
-
- Usage example:
- tMPI::mutex mtx;
- void do_count()
- {
- tMPI::lock_guard<tMPI::mutex> lock(mtx);
- count += 1;
- }
- */
-template <class Mutex> class TMPI_EXPORT lock_guard
-{
- public:
- //! Lockable type that this lock operates on.
- typedef Mutex mutex_type;
- /*! \brief The constructor, which locks the mutex.
-
- \param m The exisiting (globally accessible) mutex to lock. */
- explicit lock_guard(mutex_type &m) : m_(m)
- {
- m_.lock();
- }
- //lock_guard(mutex_type &m, adopt_lock_t t);
-
- /*! \brief The destructor, which unlocks the mutex */
- ~lock_guard()
- {
- m_.unlock();
- }
- private:
- // forbid copy constructor & assignment
- lock_guard(const lock_guard &l);
- lock_guard &operator=(const lock_guard &l);
-
- mutex_type &m_;
-};
-
-/*! \brief A basic mutex class with C++11 compatibility. */
-class TMPI_EXPORT mutex
-{
- public:
- //! Type of the native mutex handle.
- typedef tMPI_Thread_mutex_t* native_handle_type;
-
- /*! \brief The constructor.
-
- Throws a tMPI::system_error exception upon failure. */
- mutex()
- {
- int ret = tMPI_Thread_mutex_init(&handle_);
- if (ret)
- {
- throw system_error(ret);
- }
- }
-
- /*! \brief The destructor.*/
- ~mutex()
- {
- tMPI_Thread_mutex_destroy(&handle_);
- }
-
- /*! \brief The lock function.
-
- Throws a tMPI::system_error exception upon failure. */
- void lock()
- {
- int ret = tMPI_Thread_mutex_lock(&handle_);
- if (ret)
- {
- throw system_error(ret);
- }
- }
-
- /*! \brief The try_lock function.
-
- \return true if the lock was locked successfully, false if
- another thread owned it, and implementation-specific if
- already held by this thread. Do not rely on the return code
- if the calling thread could already hold this lock. */
- bool try_lock()
- {
- if (tMPI_Thread_mutex_trylock(&handle_))
- {
- return false;
- }
- return true;
- }
-
- /*! \brief The unlock function.
-
- Throws a tMPI::system_error exception upon failure. */
- void unlock()
- {
- int ret = tMPI_Thread_mutex_unlock(&handle_);
- if (ret)
- {
- throw system_error(ret);
- }
- }
-
- //! Returns the native handle for this mutex.
- native_handle_type native_handle() { return &handle_; }
- private:
- // forbid copy constructor & assignment
- mutex(const mutex &m);
- mutex &operator=(const mutex &m);
-
- tMPI_Thread_mutex_t handle_;
-};
-}
-
-#endif /* TMPI_MUTEX_H_ */
+++ /dev/null
-/*
- This source code file is part of thread_mpi.
- Written by Sander Pronk, Erik Lindahl, and possibly others.
-
- Copyright (c) 2009, Sander Pronk, Erik Lindahl.
- All rights reserved.
-
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are met:
- 1) Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- 2) Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in the
- documentation and/or other materials provided with the distribution.
- 3) Neither the name of the copyright holders nor the
- names of its contributors may be used to endorse or promote products
- derived from this software without specific prior written permission.
-
- THIS SOFTWARE IS PROVIDED BY US ''AS IS'' AND ANY
- EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- DISCLAIMED. IN NO EVENT SHALL WE BE LIABLE FOR ANY
- DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
- ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
- If you want to redistribute modifications, please consider that
- scientific software is very special. Version control is crucial -
- bugs must be traceable. We will be happy to consider code for
- inclusion in the official distribution, but derived work should not
- be called official thread_mpi. Details are found in the README & COPYING
- files.
- */
-
-/** \file
- * \brief A C++11 compatible system_error class for reporting exceptions
- *
- * This header contains class definitions for system_error.
- */
-
-#ifndef TMPI_SYSTEM_ERROR_H_
-#define TMPI_SYSTEM_ERROR_H_
-
-#include <stdexcept>
-
-#include "visibility.h"
-
-namespace tMPI
-{
-/*! \brief Subset of the C++11 system_error class
-
- Only contains the errno-based constructor. */
-class system_error : public std::runtime_error
-{
- public:
- //! Type to represent error codes within this class.
- typedef int error_code;
-
- //system_error(error_code ec, const std::string& what_arg);
- //system_error(error_code ec, const char* what_arg);
- /*! \brief Constuctor that takes an system error number */
- explicit system_error(error_code ec);
-
- /*! \brief Returns the error code */
- const error_code &code() const
- {
- return ec_;
- }
- private:
- error_code ec_;
-};
-}
-
-#endif /* TMPI_SYSTEM_ERROR_H_ */
+++ /dev/null
-/*
- This source code file is part of thread_mpi.
- Written by Sander Pronk, Erik Lindahl, and possibly others.
-
- Copyright (c) 2009, Sander Pronk, Erik Lindahl.
- All rights reserved.
-
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are met:
- 1) Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- 2) Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in the
- documentation and/or other materials provided with the distribution.
- 3) Neither the name of the copyright holders nor the
- names of its contributors may be used to endorse or promote products
- derived from this software without specific prior written permission.
-
- THIS SOFTWARE IS PROVIDED BY US ''AS IS'' AND ANY
- EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- DISCLAIMED. IN NO EVENT SHALL WE BE LIABLE FOR ANY
- DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
- ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
- If you want to redistribute modifications, please consider that
- scientific software is very special. Version control is crucial -
- bugs must be traceable. We will be happy to consider code for
- inclusion in the official distribution, but derived work should not
- be called official thread_mpi. Details are found in the README & COPYING
- files.
- */
-
-#include <cerrno>
-#include <cstring>
-#include <cstdlib>
-#include <stdexcept>
-#include <string>
-#include "thread_mpi/system_error.h"
-
-tMPI::system_error::system_error(error_code ec)
- : runtime_error(std::string(std::strerror(ec))), ec_(ec)
-{
-}
This source code file is part of thread_mpi.
Written by Sander Pronk, Erik Lindahl, and possibly others.
- Copyright (c) 2009,2018, Sander Pronk, Erik Lindahl.
+ Copyright (c) 2009,2018,2021, Sander Pronk, Erik Lindahl.
All rights reserved.
Redistribution and use in source and binary forms, with or without
tMPI_Thread_barrier_destroy(&(g->barrier));
tMPI_Thread_mutex_destroy(&(g->timer_mutex));
tMPI_Thread_mutex_destroy(&(g->comm_link_lock));
+ for (int i = 0; i < g->N_usertypes; i++)
+ {
+ tMPI_Free(g->usertypes[i]->comps);
+ tMPI_Free(g->usertypes[i]);
+ }
+ tMPI_Free(g->usertypes);
}
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
-# Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,2017,2018,2019 by the GROMACS development team.
+# Copyright (c) 2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
add_subdirectory(compat)
add_subdirectory(mimic)
add_subdirectory(modularsimulator)
-if (NOT GMX_BUILD_MDRUN_ONLY)
- add_subdirectory(gmxana)
- add_subdirectory(gmxpreprocess)
- add_subdirectory(correlationfunctions)
- add_subdirectory(statistics)
- add_subdirectory(analysisdata)
- add_subdirectory(coordinateio)
- add_subdirectory(trajectoryanalysis)
- add_subdirectory(energyanalysis)
- add_subdirectory(tools)
-endif()
+add_subdirectory(gmxana)
+add_subdirectory(gmxpreprocess)
+add_subdirectory(correlationfunctions)
+add_subdirectory(statistics)
+add_subdirectory(analysisdata)
+add_subdirectory(coordinateio)
+add_subdirectory(trajectoryanalysis)
+add_subdirectory(energyanalysis)
+add_subdirectory(tools)
get_property(PROPERTY_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES} ${PROPERTY_SOURCES})
endif()
list(APPEND libgromacs_object_library_dependencies thread_mpi)
-configure_file(version.h.cmakein version.h)
if(GMX_INSTALL_LEGACY_API)
install(FILES
- ${CMAKE_CURRENT_BINARY_DIR}/version.h
analysisdata.h
options.h
selection.h
else()
add_library(libgromacs ${LIBGROMACS_SOURCES})
endif()
+target_link_libraries(libgromacs PRIVATE $<BUILD_INTERFACE:common>)
+# As long as the libgromacs target has source files that reference headers from
+# modules that don't provide CMake targets, libgromacs needs to use `src/`
+# amongst its include directories (to support `#include "gromacs/module/header.h"`).
+add_library(legacy_modules INTERFACE)
+target_include_directories(legacy_modules INTERFACE $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/src>)
+target_link_libraries(libgromacs PRIVATE $<BUILD_INTERFACE:legacy_modules>)
# Add these contents first because linking their tests can take a lot
# of time, so we want lots of parallel work still available after
set_target_properties(${object_library} PROPERTIES POSITION_INDEPENDENT_CODE true)
endif()
target_include_directories(${object_library} SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
+ target_link_libraries(${object_library} PRIVATE common)
# Add the sources from the object libraries to the main library.
target_sources(libgromacs PRIVATE $<TARGET_OBJECTS:${object_library}>)
# Only add the -fsycl flag to sources that really need it
if (GMX_GPU_SYCL)
get_property(SYCL_SOURCES GLOBAL PROPERTY SYCL_SOURCES)
- set_source_files_properties(${SYCL_SOURCES} PROPERTIES COMPILE_FLAGS "${SYCL_CXX_FLAGS}")
+ add_sycl_to_target(TARGET libgromacs SOURCES ${SYCL_SOURCES})
endif()
gmx_setup_tng_for_libgromacs()
PUBLIC
${GMX_PUBLIC_LIBRARIES}
)
+target_link_libraries(libgromacs PUBLIC legacy_api)
+# Dependencies from libgromacs to the modules are set up here, but
+# once the add_subdirectory() commands are re-ordered then
+# responsibility for setting this up will move to the respective
+# modules.
+target_link_libraries(libgromacs PRIVATE
+ $<BUILD_INTERFACE:analysisdata>
+ $<BUILD_INTERFACE:applied_forces>
+ $<BUILD_INTERFACE:commandline>
+ $<BUILD_INTERFACE:compat>
+ $<BUILD_INTERFACE:coordinateio>
+ $<BUILD_INTERFACE:correlationfunctions>
+ $<BUILD_INTERFACE:domdec>
+# $<BUILD_INTERFACE:energyanalysis>
+ $<BUILD_INTERFACE:essentialdynamics>
+ $<BUILD_INTERFACE:ewald>
+ $<BUILD_INTERFACE:fft>
+ $<BUILD_INTERFACE:fileio>
+ $<BUILD_INTERFACE:gmxana>
+ $<BUILD_INTERFACE:gmxlib>
+ $<BUILD_INTERFACE:gmxpreprocess>
+ $<BUILD_INTERFACE:gpu_utils>
+ $<BUILD_INTERFACE:hardware>
+ $<BUILD_INTERFACE:imd>
+ $<BUILD_INTERFACE:linearalgebra>
+ $<BUILD_INTERFACE:listed_forces>
+ $<BUILD_INTERFACE:math>
+ $<BUILD_INTERFACE:mdlib>
+ $<BUILD_INTERFACE:mdrun>
+ $<BUILD_INTERFACE:mdrunutility>
+ $<BUILD_INTERFACE:mdspan>
+ $<BUILD_INTERFACE:mdtypes>
+ $<BUILD_INTERFACE:mimic>
+ $<BUILD_INTERFACE:modularsimulator>
+ $<BUILD_INTERFACE:nbnxm>
+ $<BUILD_INTERFACE:onlinehelp>
+ $<BUILD_INTERFACE:options>
+ $<BUILD_INTERFACE:pbcutil>
+ $<BUILD_INTERFACE:pulling>
+ $<BUILD_INTERFACE:random>
+ $<BUILD_INTERFACE:restraint>
+ $<BUILD_INTERFACE:selection>
+ $<BUILD_INTERFACE:simd>
+ $<BUILD_INTERFACE:statistics>
+ $<BUILD_INTERFACE:swap>
+ $<BUILD_INTERFACE:tables>
+ $<BUILD_INTERFACE:taskassignment>
+ $<BUILD_INTERFACE:timing>
+ $<BUILD_INTERFACE:tools>
+ $<BUILD_INTERFACE:topology>
+ $<BUILD_INTERFACE:trajectory>
+ $<BUILD_INTERFACE:trajectoryanalysis>
+ $<BUILD_INTERFACE:utility>
+ )
if (GMX_OPENMP)
target_link_libraries(libgromacs PUBLIC OpenMP::OpenMP_CXX)
endif()
target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-w>)
endif()
-# Only install the library in mdrun-only mode if it is actually necessary
-# for the binary
-if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
+# TODO: Stop installing libgromacs. Possibly allow installation during deprecation period with GMX_INSTALL_LEGACY_API.
+if (BUILD_SHARED_LIBS)
install(TARGETS libgromacs
EXPORT libgromacs
LIBRARY
if(GMX_INSTALL_LEGACY_API)
target_compile_features(libgromacs INTERFACE cxx_std_${CMAKE_CXX_STANDARD})
endif()
- add_library(Gromacs::libgromacs ALIAS libgromacs)
endif()
+add_library(Gromacs::libgromacs ALIAS libgromacs)
-if (NOT GMX_BUILD_MDRUN_ONLY)
- include(InstallLibInfo.cmake)
-endif()
+include(InstallLibInfo.cmake)
# Technically, the user could want to do this for an OpenCL build
# using the CUDA runtime, but currently there's no reason to want to
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+add_library(analysisdata INTERFACE)
file(GLOB ANALYSISDATA_SOURCES *.cpp modules/*.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${ANALYSISDATA_SOURCES} PARENT_SCOPE)
DESTINATION include/gromacs/analysisdata)
endif()
+# Source files have the following private module dependencies.
+target_link_libraries(analysisdata PRIVATE
+# gmxlib
+# math
+# mdtypes
+# tng_io
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(analysisdata PUBLIC
+target_include_directories(analysisdata INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(analysisdata PUBLIC
+target_link_libraries(analysisdata INTERFACE
+ legacy_api
+ )
+
+# TODO: when analysisdata is an OBJECT target
+#target_link_libraries(analysisdata PUBLIC legacy_api)
+#target_link_libraries(analysisdata PRIVATE common)
+
+# Module dependencies
+# analysisdata interfaces convey transitive dependence on these modules.
+#target_link_libraries(analysisdata PUBLIC
+target_link_libraries(analysisdata INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(analysisdata PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(analysisdata PRIVATE legacy_modules)
add_subdirectory(modules)
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
- * Copyright (c) 2015,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <memory>
-#include "gromacs/utility/classhelpers.h"
-
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
friend class AnalysisDataHandle;
};
AnalysisDataFrameHeader header(i, xvalue(i), 0);
modules.notifyFrameStart(header);
modules.notifyPointsAdd(AnalysisDataPointSetRef(
- header, pointSetInfo_,
- makeConstArrayRef(value_).subArray(i * columnCount(), columnCount())));
+ header, pointSetInfo_, makeConstArrayRef(value_).subArray(i * columnCount(), columnCount())));
modules.notifyFrameFinish(header);
}
modules.notifyDataFinish();
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/flags.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/real.h"
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* calls the notification functions in \p module as if the module had
* been registered to the data object when the data was added.
*/
- void presentData(AbstractAnalysisData* data, IAnalysisDataModule* module);
+ void presentData(AbstractAnalysisData* data, IAnalysisDataModule* module) const;
//! List of modules added to the data.
ModuleList modules_;
}
}
-void AnalysisDataModuleManager::Impl::presentData(AbstractAnalysisData* data, IAnalysisDataModule* module)
+void AnalysisDataModuleManager::Impl::presentData(AbstractAnalysisData* data, IAnalysisDataModule* module) const
{
if (state_ == eNotStarted)
{
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
- * Copyright (c) 2015,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_ANALYSISDATA_DATAMODULEMANAGER_H
#define GMX_ANALYSISDATA_DATAMODULEMANAGER_H
+#include <memory>
+
#include "gromacs/analysisdata/abstractdata.h"
-#include "gromacs/utility/classhelpers.h"
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/analysisdata/dataframe.h"
#include "gromacs/analysisdata/datamodulemanager.h"
#include "gromacs/analysisdata/paralleloptions.h"
+#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
{
GMX_RELEASE_ASSERT(data_ != nullptr, "Invalid frame accessed");
const AbstractAnalysisData& baseData = data_->baseData();
- GMX_RELEASE_ASSERT(index >= 0 && index < baseData.dataSetCount(),
- "Out of range data set index");
+ GMX_RELEASE_ASSERT(index >= 0 && index < baseData.dataSetCount(), "Out of range data set index");
GMX_RELEASE_ASSERT(!baseData.isMultipoint() || !bPointSetInProgress_,
"Point sets in multipoint data cannot span data sets");
currentDataSet_ = index;
{
firstColumn = 0;
}
- data_->addPointSet(currentDataSet_, firstColumn,
- makeConstArrayRef(values_).subArray(begin, end - begin));
+ data_->addPointSet(
+ currentDataSet_, firstColumn, makeConstArrayRef(values_).subArray(begin, end - begin));
}
clearValues();
}
AnalysisDataStorageFrame& AnalysisDataStorage::startFrame(const AnalysisDataFrameHeader& header)
{
GMX_ASSERT(header.isValid(), "Invalid header");
- internal::AnalysisDataStorageFrameData* storedFrame;
+ internal::AnalysisDataStorageFrameData* storedFrame = nullptr;
if (impl_->storeAll())
{
size_t size = header.index() + 1;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_ANALYSISDATA_DATASTORAGE_H
#define GMX_ANALYSISDATA_DATASTORAGE_H
+#include <memory>
#include <vector>
#include "gromacs/analysisdata/dataframe.h"
private:
typedef internal::AnalysisDataStorageImpl Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
- * Copyright (c) 2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_ANALYSISDATA_MODULES_AVERAGE_H
#define GMX_ANALYSISDATA_MODULES_AVERAGE_H
+#include <memory>
#include <vector>
#include "gromacs/analysisdata/abstractdata.h"
#include "gromacs/analysisdata/arraydata.h"
#include "gromacs/analysisdata/datamodule.h"
-#include "gromacs/utility/classhelpers.h"
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
//! Smart pointer to manage an AnalysisDataAverageModule object.
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
//! Smart pointer to manage an AnalysisDataFrameAverageModule object.
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return;
}
- int step, i;
-
if (_impl->nstored == 2)
{
if (_impl->histm)
AnalysisDataFrameHeader header(_impl->nstored - 2, _impl->t, 0);
moduleManager().notifyFrameStart(header);
- for (i = _impl->ci - _impl->nmax, step = 1; step < _impl->nstored && i != _impl->ci;
+ for (int i = _impl->ci - _impl->nmax, step = 1; step < _impl->nstored && i != _impl->ci;
i -= _impl->nmax, ++step)
{
if (i < 0)
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
- * Copyright (c) 2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
class Impl;
- PrivateImplPointer<Impl> _impl;
+ std::unique_ptr<Impl> _impl;
};
//! Smart pointer to manage an AnalysisDataDisplacementModule object.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/real.h"
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
- * Copyright (c) 2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
AverageHistogramPointer AbstractAverageHistogram::resampleDoubleBinWidth(bool bIntegerBins) const
{
- int nbins;
- if (bIntegerBins)
- {
- nbins = (rowCount() + 1) / 2;
- }
- else
- {
- nbins = rowCount() / 2;
- }
+ const int nbins = bIntegerBins ? (rowCount() + 1) / 2 : rowCount() / 2;
AverageHistogramPointer dest(new StaticAverageHistogram(
histogramFromBins(settings().firstEdge(), nbins, 2 * xstep()).integerBins(bIntegerBins)));
dest->setColumnCount(columnCount());
dest->allocateValues();
- int i, j;
- for (i = j = 0; i < nbins; ++i)
+ for (int i = 0, j = 0; i < nbins; ++i)
{
const bool bFirstHalfBin = (bIntegerBins && i == 0);
for (int c = 0; c < columnCount(); ++c)
{
- real v1, v2;
- real e1, e2;
- if (bFirstHalfBin)
- {
- v1 = value(0, c).value();
- e1 = value(0, c).error();
- v2 = 0;
- e2 = 0;
- }
- else
- {
- v1 = value(j, c).value();
- e1 = value(j, c).error();
- v2 = value(j + 1, c).value();
- e2 = value(j + 1, c).error();
- }
+ const real v1 = bFirstHalfBin ? value(0, c).value() : value(j, c).value();
+ const real v2 = bFirstHalfBin ? 0 : value(j + 1, c).value();
+ const real e1 = bFirstHalfBin ? value(0, c).error() : value(j, c).error();
+ const real e2 = bFirstHalfBin ? 0 : value(j + 1, c).error();
dest->value(i, c).setValue(v1 + v2, std::sqrt(e1 * e1 + e2 * e2));
}
if (bFirstHalfBin)
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
- * Copyright (c) 2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
// Copy and assign disallowed by base.
};
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
// Copy and assign disallowed by base.
};
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
// Copy and assign disallowed by base.
};
// if explicitly requested.
std::vector<Impl::LifetimeHistogram>::iterator histogram;
for (histogram = impl_->lifetimeHistograms_.begin();
- histogram != impl_->lifetimeHistograms_.end(); ++histogram)
+ histogram != impl_->lifetimeHistograms_.end();
+ ++histogram)
{
Impl::LifetimeHistogram::iterator shorter, longer;
for (shorter = histogram->begin(); shorter != histogram->end(); ++shorter)
setColumnCount(impl_->lifetimeHistograms_.size());
std::vector<Impl::LifetimeHistogram>::const_iterator histogram;
size_t maxLifetime = 1;
- for (histogram = impl_->lifetimeHistograms_.begin();
- histogram != impl_->lifetimeHistograms_.end(); ++histogram)
+ for (histogram = impl_->lifetimeHistograms_.begin(); histogram != impl_->lifetimeHistograms_.end();
+ ++histogram)
{
maxLifetime = std::max(maxLifetime, histogram->size());
}
// Fill up the output data from the histograms.
allocateValues();
int column = 0;
- for (histogram = impl_->lifetimeHistograms_.begin();
- histogram != impl_->lifetimeHistograms_.end(); ++histogram, ++column)
+ for (histogram = impl_->lifetimeHistograms_.begin(); histogram != impl_->lifetimeHistograms_.end();
+ ++histogram, ++column)
{
int row = 0;
Impl::LifetimeHistogram::const_iterator i;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_ANALYSISDATA_MODULES_LIFETIME_H
#define GMX_ANALYSISDATA_MODULES_LIFETIME_H
+#include <memory>
+
#include "gromacs/analysisdata/arraydata.h"
#include "gromacs/analysisdata/datamodule.h"
-#include "gromacs/utility/classhelpers.h"
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
//! Smart pointer to manage an AnalysisDataLifetimeModule object.
* Technically this duplicates a definition in pargs.cpp for legacy
* support code, but as the latter will go away and the alternatives
* are ugly, the duplication is acceptable. */
-const gmx::EnumerationArray<XvgFormat, const char*> c_xvgFormatNames = { { "xmgrace", "xmgr",
- "none" } };
+const gmx::EnumerationArray<XvgFormat, const char*> c_xvgFormatNames = {
+ { "xmgrace", "xmgr", "none" }
+};
void AnalysisDataPlotSettings::initOptions(IOptionsContainer* options)
{
gmx_output_env_t* oenv;
output_env_init(&oenv, getProgramContext(), timeUnit, FALSE, xvgFormat, 0);
const unique_cptr<gmx_output_env_t, output_env_done> oenvGuard(oenv);
- impl_->fp_ = xvgropen(impl_->filename_.c_str(), impl_->title_.c_str(), impl_->xlabel_,
- impl_->ylabel_, oenv);
+ impl_->fp_ = xvgropen(
+ impl_->filename_.c_str(), impl_->title_.c_str(), impl_->xlabel_, impl_->ylabel_, oenv);
const SelectionCollection* selections = impl_->settings_.selectionCollection();
if (selections != nullptr && output_env_get_xvg_format(oenv) != XvgFormat::None)
{
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
- * Copyright (c) 2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/analysisdata/datamodule.h"
#include "gromacs/options/timeunitmanager.h"
-#include "gromacs/utility/classhelpers.h"
enum class XvgFormat : int;
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
gmx_add_unit_test_library(analysisdata-test-shared
datatest.cpp
mock_datamodule.cpp)
+target_link_libraries(analysisdata-test-shared PRIVATE legacy_api)
gmx_add_unit_test(AnalysisDataUnitTests analysisdata-test
CPP_SOURCE_FILES
{
if (points.hasError(j))
{
- handle.setPoint(j + points.firstColumn(), points.y(j), points.error(j),
+ handle.setPoint(j + points.firstColumn(),
+ points.y(j),
+ points.error(j),
AnalysisDataTestInputPointSet::present(j));
}
else
{
- handle.setPoint(j + points.firstColumn(), points.y(j),
+ handle.setPoint(j + points.firstColumn(),
+ points.y(j),
AnalysisDataTestInputPointSet::present(j));
}
}
for (int ps = 0; ps < frame.pointSetCount(); ++ps)
{
const AnalysisDataTestInputPointSet& points = frame.pointSet(ps);
- StaticDataPointsChecker checker(&frame, &points, 0,
- data.columnCount(points.dataSetIndex()));
+ StaticDataPointsChecker checker(
+ &frame, &points, 0, data.columnCount(points.dataSetIndex()));
EXPECT_CALL(*this, pointsAdded(Property(&AnalysisDataPointSetRef::frameIndex, row)))
.WillOnce(Invoke(checker));
}
for (int ps = 0; ps < frame.pointSetCount(); ++ps)
{
const AnalysisDataTestInputPointSet& points = frame.pointSet(ps);
- StaticDataPointsChecker checker(&frame, &points, 0,
- data.columnCount(points.dataSetIndex()));
+ StaticDataPointsChecker checker(
+ &frame, &points, 0, data.columnCount(points.dataSetIndex()));
EXPECT_CALL(*this, pointsAdded(_)).WillOnce(Invoke(checker));
}
EXPECT_CALL(*this, frameFinished(_)).WillOnce(Invoke(StaticDataFrameHeaderChecker(&frame)));
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2011,2012,2013,2014,2015 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/analysisdata/dataframe.h"
#include "gromacs/analysisdata/datamodule.h"
#include "gromacs/analysisdata/paralleloptions.h"
-#include "gromacs/utility/classhelpers.h"
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
//! Smart pointer to manage an MockAnalysisDataModule object.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(applied_forces INTERFACE)
+
+# Source files have the following private module dependencies.
+target_link_libraries(applied_forces PRIVATE
+ # gmxlib
+ # math
+ # mdtypes
+ # tng_io
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(applied_forces PUBLIC
+target_include_directories(applied_forces INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(applied_forces PUBLIC
+target_link_libraries(applied_forces INTERFACE
+ legacy_api
+ )
+
+# TODO: when fileio is an OBJECT target
+#target_link_libraries(applied_forces PUBLIC legacy_api)
+#target_link_libraries(applied_forces PRIVATE common)
+
+# Module dependencies
+# This module convey transitive dependence on these modules.
+#target_link_libraries(applied_forces PUBLIC
+target_link_libraries(applied_forces INTERFACE
+ # utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(applied_forces PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(applied_forces PRIVATE legacy_modules)
+
gmx_add_libgromacs_sources(
electricfield.cpp
)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstring>
#include <algorithm>
+#include <vector>
#include "gromacs/fileio/enxio.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/mdrunutility/multisim.h"
#include "gromacs/mdtypes/awh_history.h"
#include "gromacs/mdtypes/awh_params.h"
*/
static bool anyDimUsesPull(const AwhBiasParams& awhBiasParams)
{
- for (int d = 0; d < awhBiasParams.ndim; d++)
- {
- const AwhDimParams& awhDimParams = awhBiasParams.dimParams[d];
- if (awhDimParams.eCoordProvider == eawhcoordproviderPULL)
- {
- return true;
- }
- }
- return false;
+ return std::any_of(
+ awhBiasParams.dimParams().begin(), awhBiasParams.dimParams().end(), [](const auto& awhDimParam) {
+ return awhDimParam.coordinateProvider() == AwhCoordinateProviderType::Pull;
+ });
}
/*! \brief Checks whether any dimension uses pulling as a coordinate provider.
*/
static bool anyDimUsesPull(const AwhParams& awhParams)
{
- for (int k = 0; k < awhParams.numBias; k++)
- {
- const AwhBiasParams& awhBiasParams = awhParams.awhBiasParams[k];
- if (anyDimUsesPull(awhBiasParams))
- {
- return true;
- }
- }
- return false;
+ return std::any_of(awhParams.awhBiasParams().begin(),
+ awhParams.awhBiasParams().end(),
+ [](const auto& awhBiasParam) { return anyDimUsesPull(awhBiasParam); });
}
/*! \brief Checks whether any dimension uses pulling as a coordinate provider.
*/
static bool anyDimUsesPull(const ArrayRef<BiasCoupledToSystem> biasCoupledToSystem)
{
- for (const auto& biasCts : biasCoupledToSystem)
- {
- if (!biasCts.pullCoordIndex_.empty())
- {
- return true;
- }
- }
- return false;
+ return std::any_of(biasCoupledToSystem.begin(), biasCoupledToSystem.end(), [](const auto& biasCts) {
+ return !biasCts.pullCoordIndex_.empty();
+ });
}
BiasCoupledToSystem::BiasCoupledToSystem(Bias bias, const std::vector<int>& pullCoordIndex) :
pull_t* pull_work,
int numFepLambdaStates,
int fepLambdaState) :
- seed_(awhParams.seed),
- nstout_(awhParams.nstOut),
+ seed_(awhParams.seed()),
+ nstout_(awhParams.nstout()),
commRecord_(commRecord),
multiSimRecord_(multiSimRecord),
pull_(pull_work),
}
int numSharingSimulations = 1;
- if (awhParams.shareBiasMultisim && isMultiSim(multiSimRecord_))
+ if (awhParams.shareBiasMultisim() && isMultiSim(multiSimRecord_))
{
numSharingSimulations = multiSimRecord_->numSimulations_;
}
/* Initialize all the biases */
- const double beta = 1 / (BOLTZ * inputRecord.opts.ref_t[0]);
- for (int k = 0; k < awhParams.numBias; k++)
+ const double beta = 1 / (gmx::c_boltz * inputRecord.opts.ref_t[0]);
+ const auto& awhBiasParams = awhParams.awhBiasParams();
+ for (int k = 0; k < gmx::ssize(awhBiasParams); k++)
{
- const AwhBiasParams& awhBiasParams = awhParams.awhBiasParams[k];
-
std::vector<int> pullCoordIndex;
std::vector<DimParams> dimParams;
- for (int d = 0; d < awhBiasParams.ndim; d++)
+ for (const auto& awhDimParam : awhBiasParams[k].dimParams())
{
- const AwhDimParams& awhDimParams = awhBiasParams.dimParams[d];
- if (awhDimParams.eCoordProvider != eawhcoordproviderPULL
- && awhDimParams.eCoordProvider != eawhcoordproviderFREE_ENERGY_LAMBDA)
+ if (awhDimParam.coordinateProvider() != AwhCoordinateProviderType::Pull
+ && awhDimParam.coordinateProvider() != AwhCoordinateProviderType::FreeEnergyLambda)
{
GMX_THROW(
InvalidInputError("Currently only the pull code and lambda are supported "
"as coordinate providers"));
}
- if (awhDimParams.eCoordProvider == eawhcoordproviderPULL)
+ if (awhDimParam.coordinateProvider() == AwhCoordinateProviderType::Pull)
{
- const t_pull_coord& pullCoord = inputRecord.pull->coord[awhDimParams.coordIndex];
- if (pullCoord.eGeom == epullgDIRPBC)
+ const t_pull_coord& pullCoord = inputRecord.pull->coord[awhDimParam.coordinateIndex()];
+ if (pullCoord.eGeom == PullGroupGeometry::DirectionPBC)
{
GMX_THROW(InvalidInputError(
"Pull geometry 'direction-periodic' is not supported by AWH"));
}
- double conversionFactor = pull_coordinate_is_angletype(&pullCoord) ? DEG2RAD : 1;
- pullCoordIndex.push_back(awhDimParams.coordIndex);
- dimParams.push_back(DimParams::pullDimParams(conversionFactor,
- awhDimParams.forceConstant, beta));
+ double conversionFactor = pull_conversion_factor_userinput2internal(pullCoord);
+ pullCoordIndex.push_back(awhDimParam.coordinateIndex());
+ dimParams.emplace_back(DimParams::pullDimParams(
+ conversionFactor, awhDimParam.forceConstant(), beta));
}
else
{
/* Construct the bias and couple it to the system. */
Bias::ThisRankWillDoIO thisRankWillDoIO =
(MASTER(commRecord_) ? Bias::ThisRankWillDoIO::Yes : Bias::ThisRankWillDoIO::No);
- biasCoupledToSystem_.emplace_back(
- Bias(k, awhParams, awhParams.awhBiasParams[k], dimParams, beta, inputRecord.delta_t,
- numSharingSimulations, biasInitFilename, thisRankWillDoIO),
- pullCoordIndex);
+ biasCoupledToSystem_.emplace_back(Bias(k,
+ awhParams,
+ awhBiasParams[k],
+ dimParams,
+ beta,
+ inputRecord.delta_t,
+ numSharingSimulations,
+ biasInitFilename,
+ thisRankWillDoIO),
+ pullCoordIndex);
biasCoupledToSystem_.back().bias_.printInitializationToLog(fplog);
}
}
real Awh::applyBiasForcesAndUpdateBias(PbcType pbcType,
- const real* masses,
+ ArrayRef<const real> masses,
ArrayRef<const double> neighborLambdaEnergies,
ArrayRef<const double> neighborLambdaDhdl,
const matrix box,
GMX_ASSERT(forceWithVirial, "Need a valid ForceWithVirial object");
}
- wallcycle_start(wallcycle, ewcAWH);
+ wallcycle_start(wallcycle, WallCycleCounter::Awh);
t_pbc pbc;
set_pbc(&pbc, pbcType, box);
/* Note: In the near future this call will be split in calls
* to supports bias sharing within a single simulation.
*/
- gmx::ArrayRef<const double> biasForce = biasCts.bias_.calcForceAndUpdateBias(
- coordValue, neighborLambdaEnergies, neighborLambdaDhdl, &biasPotential,
- &biasPotentialJump, commRecord_, multiSimRecord_, t, step, seed_, fplog);
+ gmx::ArrayRef<const double> biasForce =
+ biasCts.bias_.calcForceAndUpdateBias(coordValue,
+ neighborLambdaEnergies,
+ neighborLambdaDhdl,
+ &biasPotential,
+ &biasPotentialJump,
+ commRecord_,
+ multiSimRecord_,
+ t,
+ step,
+ seed_,
+ fplog);
awhPotential += biasPotential;
{
if (biasCts.bias_.dimParams()[d].isPullDimension())
{
- apply_external_pull_coord_force(pull_, biasCts.pullCoordIndex_[d - numLambdaDimsCounted],
- biasForce[d], masses, forceWithVirial);
+ apply_external_pull_coord_force(pull_,
+ biasCts.pullCoordIndex_[d - numLambdaDimsCounted],
+ biasForce[d],
+ masses,
+ forceWithVirial);
}
else
{
}
}
- wallcycle_stop(wallcycle, ewcAWH);
+ wallcycle_stop(wallcycle, WallCycleCounter::Awh);
return MASTER(commRecord_) ? static_cast<real>(awhPotential) : 0;
}
{
GMX_RELEASE_ASSERT(!anyDimUsesPull(awhParams) || pull_work, "Need a valid pull object");
- for (int k = 0; k < awhParams.numBias; k++)
+ for (const auto& biasParam : awhParams.awhBiasParams())
{
- const AwhBiasParams& biasParams = awhParams.awhBiasParams[k];
-
- for (int d = 0; d < biasParams.ndim; d++)
+ for (const auto& dimParam : biasParam.dimParams())
{
- if (biasParams.dimParams[d].eCoordProvider == eawhcoordproviderPULL)
+ if (dimParam.coordinateProvider() == AwhCoordinateProviderType::Pull)
{
- register_external_pull_potential(pull_work, biasParams.dimParams[d].coordIndex,
- Awh::externalPotentialString());
+ register_external_pull_potential(
+ pull_work, dimParam.coordinateIndex(), Awh::externalPotentialString());
}
}
}
/* Get the total number of energy subblocks that AWH needs */
int numSubblocks = 0;
- for (auto& biasCoupledToSystem : biasCoupledToSystem_)
+ for (const auto& biasCoupledToSystem : biasCoupledToSystem_)
{
numSubblocks += biasCoupledToSystem.bias_.numEnergySubblocksToWrite();
}
/* Transfer AWH data blocks to energy sub blocks */
int energySubblockCount = 0;
- for (auto& biasCoupledToSystem : biasCoupledToSystem_)
+ for (const auto& biasCoupledToSystem : biasCoupledToSystem_)
{
energySubblockCount += biasCoupledToSystem.bias_.writeToEnergySubblocks(
&(awhEnergyBlock->sub[energySubblockCount]));
bool Awh::hasFepLambdaDimension() const
{
return std::any_of(
- std::begin(biasCoupledToSystem_), std::end(biasCoupledToSystem_),
+ std::begin(biasCoupledToSystem_),
+ std::end(biasCoupledToSystem_),
[](const auto& coupledBias) { return coupledBias.bias_.hasFepLambdaDimension(); });
}
/* Check whether the bias(es) that has/have a FEP lambda dimension should sample coordinates
* this step. Since the biases may have different sampleCoordStep it is necessary to check
* this combination. */
- for (const auto& biasCts : biasCoupledToSystem_)
- {
- if (biasCts.bias_.hasFepLambdaDimension() && biasCts.bias_.isSampleCoordStep(step))
- {
- return true;
- }
- }
- return false;
+ return std::any_of(biasCoupledToSystem_.begin(), biasCoupledToSystem_.end(), [step](const auto& biasCts) {
+ return biasCts.bias_.hasFepLambdaDimension() && biasCts.bias_.isSampleCoordStep(step);
+ });
}
std::unique_ptr<Awh> prepareAwhModule(FILE* fplog,
GMX_THROW(InvalidInputError("AWH biasing does not support shell particles."));
}
- auto awh = std::make_unique<Awh>(
- fplog, inputRecord, commRecord, multiSimRecord, *inputRecord.awhParams, biasInitFilename,
- pull_work, inputRecord.fepvals->n_lambda, inputRecord.fepvals->init_fep_state);
+ auto awh = std::make_unique<Awh>(fplog,
+ inputRecord,
+ commRecord,
+ multiSimRecord,
+ *inputRecord.awhParams,
+ biasInitFilename,
+ pull_work,
+ inputRecord.fepvals->n_lambda,
+ inputRecord.fepvals->init_fep_state);
if (startingFromCheckpoint)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
template<typename>
class ArrayRef;
struct AwhHistory;
-struct AwhParams;
+class AwhParams;
class Bias;
struct BiasCoupledToSystem;
class ForceWithVirial;
* \returns the potential energy for the bias.
*/
real applyBiasForcesAndUpdateBias(PbcType pbcType,
- const real* masses,
+ ArrayRef<const real> masses,
ArrayRef<const double> neighborLambdaEnergies,
ArrayRef<const double> neighborLambdaDhdl,
const matrix box,
*/
bool isOutputStep(int64_t step) const;
-private:
std::vector<BiasCoupledToSystem> biasCoupledToSystem_; /**< AWH biases and definitions of their coupling to the system. */
const int64_t seed_; /**< Random seed for MC jumping with umbrella type bias potential. */
const int nstout_; /**< Interval in steps for writing to energy file. */
state_.doSkippedUpdatesInNeighborhood(params_, grid_);
}
convolvedBias = state_.updateProbabilityWeightsAndConvolvedBias(
- dimParams_, grid_, moveUmbrella ? neighborLambdaEnergies : ArrayRef<const double>{},
- &probWeightNeighbor);
+ dimParams_, grid_, moveUmbrella ? neighborLambdaEnergies : ArrayRef<const double>{}, &probWeightNeighbor);
if (isSampleCoordStep)
{
double potential;
if (params_.convolveForce)
{
- state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor,
+ state_.calcConvolvedForce(dimParams_,
+ grid_,
+ probWeightNeighbor,
moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{},
- tempForce_, biasForce_);
+ tempForce_,
+ biasForce_);
potential = -convolvedBias * params_.invBeta;
}
"AWH bias grid point for the umbrella reference value is outside of the "
"target region.");
potential = state_.calcUmbrellaForceAndPotential(
- dimParams_, grid_, coordState.umbrellaGridpoint(),
- moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{}, biasForce_);
+ dimParams_,
+ grid_,
+ coordState.umbrellaGridpoint(),
+ moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{},
+ biasForce_);
/* Moving the umbrella results in a force correction and
* a new potential. The umbrella center is sampled as often as
*/
if (moveUmbrella)
{
- double newPotential =
- state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, neighborLambdaDhdl,
- biasForce_, step, seed, params_.biasIndex);
- *potentialJump = newPotential - potential;
+ const bool onlySampleUmbrellaGridpoint = false;
+ double newPotential = state_.moveUmbrella(dimParams_,
+ grid_,
+ probWeightNeighbor,
+ neighborLambdaDhdl,
+ biasForce_,
+ step,
+ seed,
+ params_.biasIndex,
+ onlySampleUmbrellaGridpoint);
+ *potentialJump = newPotential - potential;
}
}
/* Update the free energy estimates and bias and other history dependent method parameters */
if (params_.isUpdateFreeEnergyStep(step))
{
- state_.updateFreeEnergyAndAddSamplesToHistogram(dimParams_, grid_, params_, commRecord, ms,
- t, step, fplog, &updateList_);
+ state_.updateFreeEnergyAndAddSamplesToHistogram(
+ dimParams_, grid_, params_, commRecord, ms, t, step, fplog, &updateList_);
if (params_.convolveForce)
{
*potentialJump = newPotential - potential;
}
}
+ /* If there is a lambda axis it is still controlled using an umbrella even if the force
+ * is convolved in the other dimensions. */
+ if (moveUmbrella && params_.convolveForce && grid_.hasLambdaAxis())
+ {
+ const bool onlySampleUmbrellaGridpoint = true;
+ state_.moveUmbrella(dimParams_,
+ grid_,
+ probWeightNeighbor,
+ neighborLambdaDhdl,
+ biasForce_,
+ step,
+ seed,
+ params_.biasIndex,
+ onlySampleUmbrellaGridpoint);
+ }
/* Return the potential. */
*awhPotential = potential;
* \param[in] pointState The state of the points in a bias.
* \returns the total sample count.
*/
-static int64_t countSamples(const std::vector<PointState>& pointState)
+static int64_t countSamples(ArrayRef<const PointState> pointState)
{
double numSamples = 0;
for (const PointState& point : pointState)
"The number of AWH updates in the checkpoint file (%" PRId64
") does not match the total number of AWH samples divided by the number of samples "
"per update for %d sharing AWH bias(es) (%" PRId64 "/%d=%" PRId64 ")",
- numUpdatesExpected, params.numSharedUpdate, numSamples,
- params.numSamplesUpdateFreeEnergy_ * params.numSharedUpdate, numUpdatesFromSamples);
+ numUpdatesExpected,
+ params.numSharedUpdate,
+ numSamples,
+ params.numSamplesUpdateFreeEnergy_ * params.numSharedUpdate,
+ numUpdatesFromSamples);
mesg += " Maybe you changed AWH parameters.";
/* Unfortunately we currently do not store the number of simulations
* sharing the bias or the state to checkpoint. But we can hint at
mesg += gmx::formatString(
" Or the run you continued from used %" PRId64
" sharing simulations, whereas you now specified %d sharing simulations.",
- numUpdatesFromSamples / state.histogramSize().numUpdates(), params.numSharedUpdate);
+ numUpdatesFromSamples / state.histogramSize().numUpdates(),
+ params.numSharedUpdate);
}
GMX_THROW(InvalidInputError(mesg));
}
Bias::Bias(int biasIndexInCollection,
const AwhParams& awhParams,
const AwhBiasParams& awhBiasParams,
- const std::vector<DimParams>& dimParamsInit,
+ ArrayRef<const DimParams> dimParamsInit,
double beta,
double mdTimeStep,
int numSharingSimulations,
const std::string& biasInitFilename,
ThisRankWillDoIO thisRankWillDoIO,
BiasParams::DisableUpdateSkips disableUpdateSkips) :
- dimParams_(dimParamsInit),
- grid_(dimParamsInit, awhBiasParams.dimParams),
+ dimParams_(dimParamsInit.begin(), dimParamsInit.end()),
+ grid_(dimParamsInit, awhBiasParams.dimParams()),
params_(awhParams,
awhBiasParams,
dimParams_,
/* For a global update updateList covers all points, so reserve that */
updateList_.reserve(grid_.numPoints());
- state_.initGridPointState(awhBiasParams, dimParams_, grid_, params_, biasInitFilename, awhParams.numBias);
+ state_.initGridPointState(
+ awhBiasParams, dimParams_, grid_, params_, biasInitFilename, awhParams.numBias());
if (thisRankDoesIO_)
{
*/
double blockLength = 0;
/* Construct the force correlation object. */
- forceCorrelationGrid_ = std::make_unique<CorrelationGrid>(
- state_.points().size(), ndim(), blockLength,
- CorrelationGrid::BlockLengthMeasure::Time, awhParams.nstSampleCoord * mdTimeStep);
+ forceCorrelationGrid_ =
+ std::make_unique<CorrelationGrid>(state_.points().size(),
+ ndim(),
+ blockLength,
+ CorrelationGrid::BlockLengthMeasure::Time,
+ awhParams.nstSampleCoord() * mdTimeStep);
writer_ = std::make_unique<BiasWriter>(*this);
}
fprintf(fplog,
"%s initial force correlation block length = %g %s"
"%s force correlation number of blocks = %d",
- prefix.c_str(), forceCorrelationGrid().getBlockLength(),
+ prefix.c_str(),
+ forceCorrelationGrid().getBlockLength(),
forceCorrelationGrid().blockLengthMeasure == CorrelationGrid::BlockLengthMeasure::Weight
? ""
: "ps",
- prefix.c_str(), forceCorrelationGrid().getNumBlocks());
+ prefix.c_str(),
+ forceCorrelationGrid().getNumBlocks());
}
}
We actually add the force normalized by beta which has the units of 1/length. This means that the
resulting correlation time integral is directly in units of friction time/length^2 which is really what
we're interested in. */
- state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, neighborLambdaDhdl,
- forceFromNeighbor);
+ state_.calcUmbrellaForceAndPotential(
+ dimParams_, grid_, indexNeighbor, neighborLambdaDhdl, forceFromNeighbor);
/* Note: we might want to give a whole list of data to add instead and have this loop in the data adding function */
forceCorrelationGrid_->addData(indexNeighbor, weightNeighbor, forceFromNeighbor, t);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
struct AwhBiasHistory;
-struct AwhBiasParams;
+class AwhBiasParams;
struct AwhHistory;
-struct AwhParams;
+class AwhParams;
struct AwhPointStateHistory;
class CorrelationGrid;
class BiasGrid;
Bias(int biasIndexInCollection,
const AwhParams& awhParams,
const AwhBiasParams& awhBiasParams,
- const std::vector<DimParams>& dimParams,
+ ArrayRef<const DimParams> dimParams,
double beta,
double mdTimeStep,
int numSharingSimulations,
/*! \brief Returns the dimension parameters.
*/
- inline const std::vector<DimParams>& dimParams() const { return dimParams_; }
+ inline ArrayRef<const DimParams> dimParams() const { return dimParams_; }
//! Returns the bias parameters
inline const BiasParams& params() const { return params_; }
*/
bool hasFepLambdaDimension() const
{
- return std::any_of(std::begin(dimParams_), std::end(dimParams_),
- [](const auto& dimParam) { return dimParam.isFepLambdaDimension(); });
+ return std::any_of(std::begin(dimParams_), std::end(dimParams_), [](const auto& dimParam) {
+ return dimParam.isFepLambdaDimension();
+ });
}
/*! \brief
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
/*! \brief
- * Modify x so that it is periodic in [-period/2, +period/2).
+ * Return x so that it is periodic in [-period/2, +period/2).
*
* x is modified by shifting its value by a +/- a period if
* needed. Thus, it is assumed that x is at most one period
* away from this interval. For period = 0, x is not modified.
*
- * \param[in,out] x Pointer to the value to modify.
- * \param[in] period The period, or 0 if not periodic.
+ * \param[in] x Pointer to the value to modify.
+ * \param[in] period The period, or 0 if not periodic.
+ * \returns Value that is within the period.
*/
-void centerPeriodicValueAroundZero(double* x, double period)
+double centerPeriodicValueAroundZero(const double x, double period)
{
GMX_ASSERT(period >= 0, "Periodic should not be negative");
const double halfPeriod = period * 0.5;
- if (*x >= halfPeriod)
+ double valueInPeriod = x;
+
+ if (valueInPeriod >= halfPeriod)
{
- *x -= period;
+ valueInPeriod -= period;
}
- else if (*x < -halfPeriod)
+ else if (valueInPeriod < -halfPeriod)
{
- *x += period;
+ valueInPeriod += period;
}
+ return valueInPeriod;
}
/*! \brief
if (period > 0)
{
- centerPeriodicValueAroundZero(&dev, period);
+ dev = centerPeriodicValueAroundZero(dev, period);
}
return dev;
* \param[in] indexMulti Multidimensional grid point index to convert to a linear one.
* \returns the linear index.
*/
-int multiDimGridIndexToLinear(const std::vector<GridAxis>& axis, const awh_ivec indexMulti)
+int multiDimGridIndexToLinear(ArrayRef<const GridAxis> axis, const awh_ivec indexMulti)
{
awh_ivec numPointsDim = { 0 };
* \param[in] axis The grid axes.
* \returns true if the value is in the grid.
*/
-static bool valueIsInGrid(const awh_dvec value, const std::vector<GridAxis>& axis)
+static bool valueIsInGrid(const awh_dvec value, ArrayRef<const GridAxis> axis)
{
/* For each dimension get the one-dimensional index and check if it is in range. */
for (size_t d = 0; d < axis.size(); d++)
* \param[in] axis The grid axes.
* \returns the point index nearest to the value.
*/
-static int getNearestIndexInGrid(const awh_dvec value, const std::vector<GridAxis>& axis)
+static int getNearestIndexInGrid(const awh_dvec value, ArrayRef<const GridAxis> axis)
{
awh_ivec indexMulti;
if (axis_[d].period() > 0)
{
/* Do we always want the values to be centered around 0 ? */
- centerPeriodicValueAroundZero(&point.coordValue[d], axis_[d].period());
+ point.coordValue[d] =
+ centerPeriodicValueAroundZero(point.coordValue[d], axis_[d].period());
}
point.index[d] = indexWork[d];
}
}
-BiasGrid::BiasGrid(const std::vector<DimParams>& dimParams, const AwhDimParams* awhDimParams)
+BiasGrid::BiasGrid(ArrayRef<const DimParams> dimParams, ArrayRef<const AwhDimParams> awhDimParams)
{
+ GMX_RELEASE_ASSERT(dimParams.size() == awhDimParams.size(), "Dimensions needs to be equal");
/* Define the discretization along each dimension */
awh_dvec period;
int numPoints = 1;
- for (size_t d = 0; d < dimParams.size(); d++)
+ for (int d = 0; d < gmx::ssize(awhDimParams); d++)
{
- double origin = dimParams[d].scaleUserInputToInternal(awhDimParams[d].origin);
- double end = dimParams[d].scaleUserInputToInternal(awhDimParams[d].end);
- if (awhDimParams[d].eCoordProvider == eawhcoordproviderPULL)
+ double origin = dimParams[d].scaleUserInputToInternal(awhDimParams[d].origin());
+ double end = dimParams[d].scaleUserInputToInternal(awhDimParams[d].end());
+ if (awhDimParams[d].coordinateProvider() == AwhCoordinateProviderType::Pull)
{
- period[d] = dimParams[d].scaleUserInputToInternal(awhDimParams[d].period);
+ period[d] = dimParams[d].scaleUserInputToInternal(awhDimParams[d].period());
static_assert(
c_numPointsPerSigma >= 1.0,
"The number of points per sigma should be at least 1.0 to get a uniformly "
std::string mesg = gmx::formatString(
"Could not extract data properly from %s. Wrong data format?"
"\n\n%s",
- dataFilename.c_str(), correctFormatMessage.c_str());
+ dataFilename.c_str(),
+ correctFormatMessage.c_str());
GMX_THROW(InvalidInputError(mesg));
}
}
else
{
- axis_.emplace_back(data[d][0], data[d][numDataPoints - 1], grid.axis(d).period(),
- numPoints[d], false);
+ axis_.emplace_back(
+ data[d][0], data[d][numDataPoints - 1], grid.axis(d).period(), numPoints[d], false);
}
}
"%s does not contain data for all coordinate values. "
"Make sure your input data covers the whole sampling domain "
"and is correctly formatted. \n\n%s",
- dataFilename.c_str(), correctFormatMessage.c_str());
+ dataFilename.c_str(),
+ correctFormatMessage.c_str());
GMX_THROW(InvalidInputError(mesg));
}
(*gridpointToDatapoint)[m] = getNearestIndexInGrid(grid.point(m).coordValue, axis_);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <optional>
#include <string>
+#include "gromacs/utility/arrayref.h"
+
#include "dimparams.h" /* This is needed for awh_dvec */
namespace gmx
{
-struct AwhDimParams;
+class AwhDimParams;
/*! \internal
* \brief An axis, i.e. dimension, of the grid.
* coordinate living on the grid (determines the grid spacing).
* \param[in] awhDimParams Dimension params from inputrec.
*/
- BiasGrid(const std::vector<DimParams>& dimParams, const AwhDimParams* awhDimParams);
+ BiasGrid(ArrayRef<const DimParams> dimParams, ArrayRef<const AwhDimParams> awhDimParams);
/*! \brief Returns the number of points in the grid.
*
*
* \returns a constant reference to the grid axes.
*/
- const std::vector<GridAxis>& axis() const { return axis_; }
+ ArrayRef<const GridAxis> axis() const { return axis_; }
/*! \brief Returns a grid axis.
*
*/
bool hasLambdaAxis() const
{
- return std::any_of(std::begin(axis_), std::end(axis_),
- [](const auto& axis) { return axis.isFepLambdaAxis(); });
+ return std::any_of(std::begin(axis_), std::end(axis_), [](const auto& axis) {
+ return axis.isFepLambdaAxis();
+ });
}
/*! \brief
* (this could be made a user-option but there is most likely no big need
* for tweaking this for most users).
*/
- switch (awhBiasParams.eTarget)
+ switch (awhBiasParams.targetDistribution())
{
- case eawhtargetCONSTANT: numStepsUpdateTarget = 0; break;
- case eawhtargetCUTOFF:
- case eawhtargetBOLTZMANN:
+ case AwhTargetType::Constant: numStepsUpdateTarget = 0; break;
+ case AwhTargetType::Cutoff:
+ case AwhTargetType::Boltzmann:
/* Updating the target generally requires updating the whole grid so to keep the cost
down we generally update the target less often than the free energy (unless the free
energy update step is set to > 100 samples). */
- numStepsUpdateTarget = std::max(100 % awhParams.numSamplesUpdateFreeEnergy,
- awhParams.numSamplesUpdateFreeEnergy)
- * awhParams.nstSampleCoord;
+ numStepsUpdateTarget = std::max(100 % awhParams.numSamplesUpdateFreeEnergy(),
+ awhParams.numSamplesUpdateFreeEnergy())
+ * awhParams.nstSampleCoord();
break;
- case eawhtargetLOCALBOLTZMANN:
+ case AwhTargetType::LocalBoltzmann:
/* The target distribution is set equal to the reference histogram which is updated every free energy update.
So the target has to be updated at the same time. This leads to a global update each time because it is
assumed that a target distribution update can take any form. This is a bit unfortunate for a "local"
target distribution. One could avoid the global update by making a local target update function (and
postponing target updates for non-local points as for the free energy update). We avoid such additions
for now and accept that this target type always does global updates. */
- numStepsUpdateTarget = awhParams.numSamplesUpdateFreeEnergy * awhParams.nstSampleCoord;
+ numStepsUpdateTarget = awhParams.numSamplesUpdateFreeEnergy() * awhParams.nstSampleCoord();
break;
default: GMX_RELEASE_ASSERT(false, "Unknown AWH target type"); break;
}
* \param[in] gridAxis The BiasGrid axes.
* \returns the check interval in steps.
*/
-int64_t calcCheckCoveringInterval(const AwhParams& awhParams,
- const std::vector<DimParams>& dimParams,
- const std::vector<GridAxis>& gridAxis)
+int64_t calcCheckCoveringInterval(const AwhParams& awhParams,
+ ArrayRef<const DimParams> dimParams,
+ ArrayRef<const GridAxis> gridAxis)
{
/* Each sample will have a width of sigma. To cover the axis a
minimum number of samples of width sigma is required. */
/* Convert to number of steps using the sampling frequency. The
check interval should be a multiple of the update step
interval. */
- int numStepsUpdate = awhParams.numSamplesUpdateFreeEnergy * awhParams.nstSampleCoord;
- GMX_RELEASE_ASSERT(awhParams.numSamplesUpdateFreeEnergy > 0,
+ int numStepsUpdate = awhParams.numSamplesUpdateFreeEnergy() * awhParams.nstSampleCoord();
+ GMX_RELEASE_ASSERT(awhParams.numSamplesUpdateFreeEnergy() > 0,
"When checking for AWH coverings, the number of samples per AWH update need "
"to be > 0.");
- int numUpdatesCheck = std::max(1, minNumSamplesCover / awhParams.numSamplesUpdateFreeEnergy);
+ int numUpdatesCheck = std::max(1, minNumSamplesCover / awhParams.numSamplesUpdateFreeEnergy());
int numStepsCheck = numUpdatesCheck * numStepsUpdate;
GMX_RELEASE_ASSERT(numStepsCheck % numStepsUpdate == 0,
* \param[in] samplingTimestep Sampling frequency of probability weights.
* \returns estimate of initial histogram size.
*/
-double getInitialHistogramSizeEstimate(const AwhBiasParams& awhBiasParams,
- const std::vector<GridAxis>& gridAxis,
- double beta,
- double samplingTimestep)
+double getInitialHistogramSizeEstimate(const AwhBiasParams& awhBiasParams,
+ ArrayRef<const GridAxis> gridAxis,
+ double beta,
+ double samplingTimestep)
{
/* Get diffusion factor */
double maxCrossingTime = 0.;
std::vector<double> x;
+ const auto awhDimParams = awhBiasParams.dimParams();
for (size_t d = 0; d < gridAxis.size(); d++)
{
- GMX_RELEASE_ASSERT(awhBiasParams.dimParams[d].diffusion > 0, "We need positive diffusion");
+ GMX_RELEASE_ASSERT(awhDimParams[d].diffusion() > 0, "We need positive diffusion");
// With diffusion it takes on average T = L^2/2D time to cross length L
double axisLength = gridAxis[d].isFepLambdaAxis() ? 1.0 : gridAxis[d].length();
- double crossingTime = (axisLength * axisLength) / (2 * awhBiasParams.dimParams[d].diffusion);
+ double crossingTime = (axisLength * axisLength) / (2 * awhDimParams[d].diffusion());
maxCrossingTime = std::max(maxCrossingTime, crossingTime);
}
GMX_RELEASE_ASSERT(maxCrossingTime > 0, "We need at least one dimension with non-zero length");
- double errorInitialInKT = beta * awhBiasParams.errorInitial;
+ double errorInitialInKT = beta * awhBiasParams.initialErrorEstimate();
double histogramSize = maxCrossingTime / (gmx::square(errorInitialInKT) * samplingTimestep);
return histogramSize;
int numShared = 1;
- if (awhBiasParams.shareGroup > 0)
+ if (awhBiasParams.shareGroup() > 0)
{
/* We do not yet support sharing within a simulation */
int numSharedWithinThisSimulation = 1;
} // namespace
-BiasParams::BiasParams(const AwhParams& awhParams,
- const AwhBiasParams& awhBiasParams,
- const std::vector<DimParams>& dimParams,
- double beta,
- double mdTimeStep,
- DisableUpdateSkips disableUpdateSkips,
- int numSharingSimulations,
- const std::vector<GridAxis>& gridAxis,
- int biasIndex) :
+BiasParams::BiasParams(const AwhParams& awhParams,
+ const AwhBiasParams& awhBiasParams,
+ ArrayRef<const DimParams> dimParams,
+ double beta,
+ double mdTimeStep,
+ DisableUpdateSkips disableUpdateSkips,
+ int numSharingSimulations,
+ ArrayRef<const GridAxis> gridAxis,
+ int biasIndex) :
invBeta(beta > 0 ? 1 / beta : 0),
- numStepsSampleCoord_(awhParams.nstSampleCoord),
- numSamplesUpdateFreeEnergy_(awhParams.numSamplesUpdateFreeEnergy),
+ numStepsSampleCoord_(awhParams.nstSampleCoord()),
+ numSamplesUpdateFreeEnergy_(awhParams.numSamplesUpdateFreeEnergy()),
numStepsUpdateTarget_(calcTargetUpdateInterval(awhParams, awhBiasParams)),
numStepsCheckCovering_(calcCheckCoveringInterval(awhParams, dimParams, gridAxis)),
- eTarget(awhBiasParams.eTarget),
- freeEnergyCutoffInKT(beta * awhBiasParams.targetCutoff),
- temperatureScaleFactor(awhBiasParams.targetBetaScaling),
- idealWeighthistUpdate(eTarget != eawhtargetLOCALBOLTZMANN),
+ eTarget(awhBiasParams.targetDistribution()),
+ freeEnergyCutoffInKT(beta * awhBiasParams.targetCutoff()),
+ temperatureScaleFactor(awhBiasParams.targetBetaScaling()),
+ idealWeighthistUpdate(eTarget != AwhTargetType::LocalBoltzmann),
numSharedUpdate(getNumSharedUpdate(awhBiasParams, numSharingSimulations)),
updateWeight(numSamplesUpdateFreeEnergy_ * numSharedUpdate),
- localWeightScaling(eTarget == eawhtargetLOCALBOLTZMANN ? temperatureScaleFactor : 1),
- initialErrorInKT(beta * awhBiasParams.errorInitial),
+ localWeightScaling(eTarget == AwhTargetType::LocalBoltzmann ? temperatureScaleFactor : 1),
+ initialErrorInKT(beta * awhBiasParams.initialErrorEstimate()),
initialHistogramSize(
getInitialHistogramSizeEstimate(awhBiasParams, gridAxis, beta, numStepsSampleCoord_ * mdTimeStep)),
- convolveForce(awhParams.ePotential == eawhpotentialCONVOLVED),
+ convolveForce(awhParams.potential() == AwhPotentialType::Convolved),
biasIndex(biasIndex),
disableUpdateSkips_(disableUpdateSkips == DisableUpdateSkips::yes)
{
GMX_THROW(InvalidInputError("To use AWH, the beta=1/(k_B T) should be > 0"));
}
- for (int d = 0; d < awhBiasParams.ndim; d++)
+ const auto& awhDimParams = awhBiasParams.dimParams();
+ for (int d = 0; d < gmx::ssize(awhDimParams); d++)
{
/* The spacing in FEP dimensions is 1. The calculated coverRadius will be in lambda states
* (cf points in other dimensions). */
- double coverRadiusInNm = 0.5 * awhBiasParams.dimParams[d].coverDiameter;
+ double coverRadiusInNm = 0.5 * awhDimParams[d].coverDiameter();
double spacing = gridAxis[d].spacing();
coverRadius_[d] = spacing > 0 ? static_cast<int>(std::round(coverRadiusInNm / spacing)) : 0;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
namespace gmx
{
-struct AwhBiasParams;
-struct AwhParams;
+template<typename>
+class ArrayRef;
+class AwhBiasParams;
+class AwhParams;
struct DimParams;
class GridAxis;
+enum class AwhTargetType : int;
/*! \internal \brief Constant parameters for the bias.
*/
* \param[in] disableUpdateSkips If to disable update skips, useful for testing.
* \param[in] biasIndex Index of the bias.
*/
- BiasParams(const AwhParams& awhParams,
- const AwhBiasParams& awhBiasParams,
- const std::vector<DimParams>& dimParams,
- double beta,
- double mdTimeStep,
- DisableUpdateSkips disableUpdateSkips,
- int numSharingSimulations,
- const std::vector<GridAxis>& gridAxis,
- int biasIndex);
+ BiasParams(const AwhParams& awhParams,
+ const AwhBiasParams& awhBiasParams,
+ ArrayRef<const DimParams> dimParams,
+ double beta,
+ double mdTimeStep,
+ DisableUpdateSkips disableUpdateSkips,
+ int numSharingSimulations,
+ ArrayRef<const GridAxis> gridAxis,
+ int biasIndex);
/* Data members */
const double invBeta; /**< 1/beta = kT in kJ/mol */
const int64_t numStepsUpdateTarget_; /**< Number of steps per updating the target distribution. */
const int64_t numStepsCheckCovering_; /**< Number of steps per checking for covering. */
public:
- const int eTarget; /**< Type of target distribution. */
- const double freeEnergyCutoffInKT; /**< Free energy cut-off in kT for cut-off target distribution. */
- const double temperatureScaleFactor; /**< Temperature scaling factor for temperature scaled targed distributions. */
- const bool idealWeighthistUpdate; /**< Update reference weighthistogram using the target distribution? Otherwise use the realized distribution. */
+ const AwhTargetType eTarget; /**< Type of target distribution. */
+ const double freeEnergyCutoffInKT; /**< Free energy cut-off in kT for cut-off target distribution. */
+ const double temperatureScaleFactor; /**< Temperature scaling factor for temperature scaled targed distributions. */
+ const bool idealWeighthistUpdate; /**< Update reference weighthistogram using the target distribution? Otherwise use the realized distribution. */
const int numSharedUpdate; /**< The number of (multi-)simulations sharing the bias update */
const double updateWeight; /**< The probability weight accumulated for each update. */
const double localWeightScaling; /**< Scaling factor applied to a sample before adding it to the reference weight histogram (= 1, usually). */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdrunutility/multisim.h"
#include "gromacs/mdtypes/awh_params.h"
#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/stringutil.h"
{
bool haveSharing = false;
- for (int k = 0; k < awhParams.numBias; k++)
+ const auto awhBiasParams = awhParams.awhBiasParams();
+ for (auto awhBiasParamIt = awhBiasParams.begin(); awhBiasParamIt != awhBiasParams.end(); ++awhBiasParamIt)
{
- int shareGroup = awhParams.awhBiasParams[k].shareGroup;
+ int shareGroup = awhBiasParamIt->shareGroup();
if (shareGroup > 0)
{
- for (int i = k + 1; i < awhParams.numBias; i++)
+ for (auto awhBiasParamIt2 = awhBiasParamIt + 1; awhBiasParamIt2 != awhBiasParams.end();
+ ++awhBiasParamIt2)
{
- if (awhParams.awhBiasParams[i].shareGroup == shareGroup)
+ if (awhBiasParamIt2->shareGroup() == shareGroup)
{
haveSharing = true;
}
return haveSharing;
}
-void biasesAreCompatibleForSharingBetweenSimulations(const AwhParams& awhParams,
- const std::vector<size_t>& pointSize,
- const gmx_multisim_t* multiSimComm)
+void biasesAreCompatibleForSharingBetweenSimulations(const AwhParams& awhParams,
+ ArrayRef<const size_t> pointSize,
+ const gmx_multisim_t* multiSimComm)
{
const int numSim = multiSimComm->numSimulations_;
* biases in order over the ranks and it does not restrict possibilities.
*/
int numShare = 0;
- for (int b = 0; b < awhParams.numBias; b++)
+ for (const auto& awhBiasParam : awhParams.awhBiasParams())
{
- int group = awhParams.awhBiasParams[b].shareGroup;
+ int group = awhBiasParam.shareGroup();
if (group > 0)
{
numShare++;
}
std::vector<int> intervals(numSim * 2);
- intervals[numSim * 0 + multiSimComm->simulationIndex_] = awhParams.nstSampleCoord;
- intervals[numSim * 1 + multiSimComm->simulationIndex_] = awhParams.numSamplesUpdateFreeEnergy;
+ intervals[numSim * 0 + multiSimComm->simulationIndex_] = awhParams.nstSampleCoord();
+ intervals[numSim * 1 + multiSimComm->simulationIndex_] = awhParams.numSamplesUpdateFreeEnergy();
gmx_sumi_sim(intervals.size(), intervals.data(), multiSimComm);
for (int sim = 1; sim < numSim; sim++)
{
/* Check the point sizes. This is a sufficient condition for running
* as shared multi-sim run. No physics checks are performed here.
*/
- for (int b = 0; b < awhParams.numBias; b++)
+ const auto& awhBiasParams = awhParams.awhBiasParams();
+ for (int b = 0; b < gmx::ssize(awhBiasParams); b++)
{
- if (awhParams.awhBiasParams[b].shareGroup > 0)
+ if (awhBiasParams[b].shareGroup() > 0)
{
std::vector<int64_t> pointSizes(numSim);
pointSizes[multiSimComm->simulationIndex_] = pointSize[b];
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
namespace gmx
{
-struct AwhParams;
+template<typename>
+class ArrayRef;
+class AwhParams;
/*! \brief Returns if any bias is sharing within a simulation.
*
* \param[in] pointSize Vector of grid-point sizes for each bias.
* \param[in] multiSimComm Struct for multi-simulation communication.
*/
-void biasesAreCompatibleForSharingBetweenSimulations(const AwhParams& awhParams,
- const std::vector<size_t>& pointSize,
- const gmx_multisim_t* multiSimComm);
+void biasesAreCompatibleForSharingBetweenSimulations(const AwhParams& awhParams,
+ ArrayRef<const size_t> pointSize,
+ const gmx_multisim_t* multiSimComm);
} // namespace gmx
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxlib/network.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/mdrunutility/multisim.h"
#include "gromacs/mdtypes/awh_history.h"
* \param[in] gridpointIndex The index of the current grid point.
* \returns the log of the biased probability weight.
*/
-double biasedLogWeightFromPoint(const std::vector<DimParams>& dimParams,
- const std::vector<PointState>& points,
- const BiasGrid& grid,
- int pointIndex,
- double pointBias,
- const awh_dvec value,
- gmx::ArrayRef<const double> neighborLambdaEnergies,
- int gridpointIndex)
+double biasedLogWeightFromPoint(ArrayRef<const DimParams> dimParams,
+ ArrayRef<const PointState> points,
+ const BiasGrid& grid,
+ int pointIndex,
+ double pointBias,
+ const awh_dvec value,
+ ArrayRef<const double> neighborLambdaEnergies,
+ int gridpointIndex)
{
double logWeight = detail::c_largeNegativeExponent;
* \returns The calculated marginal distribution in a 1D array with
* as many elements as there are points along the axis of interest.
*/
-std::vector<double> calculateFELambdaMarginalDistribution(const BiasGrid& grid,
- gmx::ArrayRef<const int> neighbors,
- gmx::ArrayRef<const double> probWeightNeighbor)
+std::vector<double> calculateFELambdaMarginalDistribution(const BiasGrid& grid,
+ ArrayRef<const int> neighbors,
+ ArrayRef<const double> probWeightNeighbor)
{
const std::optional<int> lambdaAxisIndex = grid.lambdaAxisIndex();
GMX_RELEASE_ASSERT(lambdaAxisIndex,
} // namespace
-void BiasState::calcConvolvedPmf(const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
- std::vector<float>* convolvedPmf) const
+void BiasState::calcConvolvedPmf(ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
+ std::vector<float>* convolvedPmf) const
{
size_t numPoints = grid.numPoints();
{
double freeEnergyWeights = 0;
const GridPoint& point = grid.point(m);
- for (auto& neighbor : point.neighbor)
+ for (const auto& neighbor : point.neighbor)
{
/* Do not convolve the bias along a lambda axis - only use the pmf from the current point */
if (!pointsHaveDifferentLambda(grid, m, neighbor))
/* Add the convolved PMF weights for the neighbors of this point.
Note that this function only adds point within the target > 0 region.
Sum weights, take the logarithm last to get the free energy. */
- double logWeight = biasedLogWeightFromPoint(dimParams, points_, grid, neighbor,
- biasNeighbor, point.coordValue, {}, m);
+ double logWeight = biasedLogWeightFromPoint(
+ dimParams, points_, grid, neighbor, biasNeighbor, point.coordValue, {}, m);
freeEnergyWeights += std::exp(logWeight);
}
}
* \param[in,out] pointState The state of all points.
* \param[in] params The bias parameters.
*/
-void updateTargetDistribution(
gmx::ArrayRef<PointState> pointState, const BiasParams& params)
+void updateTargetDistribution(ArrayRef<PointState> pointState, const BiasParams& params)
{
double freeEnergyCutoff = 0;
- if (params.eTarget == eawhtargetCUTOFF)
+ if (params.eTarget == AwhTargetType::Cutoff)
{
freeEnergyCutoff = freeEnergyMinimumValue(pointState) + params.freeEnergyCutoffInKT;
}
/* Sum up the histograms and get their normalization */
double sumVisits = 0;
double sumWeights = 0;
- for (auto& pointState : points_)
+ for (const auto& pointState : points_)
{
if (pointState.inTargetRegion())
{
"If you are not certain about your settings you might want to increase your "
"pull force constant or "
"modify your sampling region.\n",
- biasIndex + 1, t, pointValueString.c_str(), maxHistogramRatio);
+ biasIndex + 1,
+ t,
+ pointValueString.c_str(),
+ maxHistogramRatio);
gmx::TextLineWrapper wrapper;
wrapper.settings().setLineLength(c_linewidth);
fprintf(fplog, "%s", wrapper.wrapToString(warningMessage).c_str());
return numWarnings;
}
-double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
- int point,
- ArrayRef<const double> neighborLambdaDhdl,
- gmx::ArrayRef<double> force) const
+double BiasState::calcUmbrellaForceAndPotential(ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
+ int point,
+ ArrayRef<const double> neighborLambdaDhdl,
+ ArrayRef<double> force) const
{
double potential = 0;
for (size_t d = 0; d < dimParams.size(); d++)
return potential;
}
-void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
- gmx::ArrayRef<const double> probWeightNeighbor,
- ArrayRef<const double> neighborLambdaDhdl,
- gmx::ArrayRef<double> forceWorkBuffer,
- gmx::ArrayRef<double> force) const
+void BiasState::calcConvolvedForce(ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
+ ArrayRef<const double> probWeightNeighbor,
+ ArrayRef<const double> neighborLambdaDhdl,
+ ArrayRef<double> forceWorkBuffer,
+ ArrayRef<double> force) const
{
for (size_t d = 0; d < dimParams.size(); d++)
{
}
}
-double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
- gmx::ArrayRef<const double> probWeightNeighbor,
- ArrayRef<const double> neighborLambdaDhdl,
- gmx::ArrayRef<double> biasForce,
- int64_t step,
- int64_t seed,
- int indexSeed)
+double BiasState::moveUmbrella(ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
+ ArrayRef<const double> probWeightNeighbor,
+ ArrayRef<const double> neighborLambdaDhdl,
+ ArrayRef<double> biasForce,
+ int64_t step,
+ int64_t seed,
+ int indexSeed,
+ bool onlySampleUmbrellaGridpoint)
{
/* Generate and set a new coordinate reference value */
- coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
- step, seed, indexSeed);
+ coordState_.sampleUmbrellaGridpoint(
+ grid, coordState_.gridpointIndex(), probWeightNeighbor, step, seed, indexSeed);
+
+ if (onlySampleUmbrellaGridpoint)
+ {
+ return 0;
+ }
std::vector<double> newForce(dimParams.size());
double newPotential = calcUmbrellaForceAndPotential(
/* In between global updates the reference histogram size is kept constant so we trivially
know what the histogram size was at the time of the skipped update. */
double histogramSize = histogramSize_.histogramSize();
- setHistogramUpdateScaleFactors(params, histogramSize, histogramSize, weightHistScaling,
- logPmfSumScaling);
+ setHistogramUpdateScaleFactors(
+ params, histogramSize, histogramSize, weightHistScaling, logPmfSumScaling);
}
else
{
/* For each neighbor point of the center point, refresh its state by adding the results of all past, skipped updates. */
const std::vector<int>& neighbors = grid.point(coordState_.gridpointIndex()).neighbor;
- for (auto& neighbor : neighbors)
+ for (const auto& neighbor : neighbors)
{
bool didUpdate = points_[neighbor].performPreviouslySkippedUpdates(
params, histogramSize_.numUpdates(), weightHistScaling, logPmfsumScaling);
* last update. \param[in] endUpdatelist The end of the rectangular that has been sampled since
* last update. \param[in,out] updateList Local update list to set (assumed >= npoints long).
*/
-void makeLocalUpdateList(const BiasGrid& grid,
- const std::vector<PointState>& points,
- const awh_ivec originUpdatelist,
- const awh_ivec endUpdatelist,
- std::vector<int>* updateList)
+void makeLocalUpdateList(const BiasGrid& grid,
+ ArrayRef<const PointState> points,
+ const awh_ivec originUpdatelist,
+ const awh_ivec endUpdatelist,
+ std::vector<int>* updateList)
{
awh_ivec origin;
awh_ivec numPoints;
} // namespace
-bool BiasState::isSamplingRegionCovered(const BiasParams& params,
- const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
- const t_commrec* commRecord,
- const gmx_multisim_t* multiSimComm) const
+bool BiasState::isSamplingRegionCovered(const BiasParams& params,
+ ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
+ const t_commrec* commRecord,
+ const gmx_multisim_t* multiSimComm) const
{
/* Allocate and initialize arrays: one for checking visits along each dimension,
one for keeping track of which points to check and one for the covered points.
/* Set the free energy cutoff */
double maxFreeEnergy = GMX_FLOAT_MAX;
- if (params.eTarget == eawhtargetCUTOFF)
+ if (params.eTarget == AwhTargetType::Cutoff)
{
maxFreeEnergy = freeEnergyMinimumValue(points_) + params.freeEnergyCutoffInKT;
}
/* Label each point along each dimension as covered or not. */
for (int d = 0; d < grid.numDimensions(); d++)
{
- labelCoveredPoints(checkDim[d].visited, checkDim[d].checkCovering, grid.axis(d).numPoints(),
- grid.axis(d).numPointsInPeriod(), params.coverRadius()[d], checkDim[d].covered);
+ labelCoveredPoints(checkDim[d].visited,
+ checkDim[d].checkCovering,
+ grid.axis(d).numPoints(),
+ grid.axis(d).numPointsInPeriod(),
+ params.coverRadius()[d],
+ checkDim[d].covered);
}
/* Now check for global covering. Each dimension needs to be covered separately.
{
sumOverSimulations(
gmx::arrayRefFromArray(checkDim[d].covered.data(), grid.axis(d).numPoints()),
- commRecord, multiSimComm);
+ commRecord,
+ multiSimComm);
}
}
}
}
-void BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
- const BiasParams& params,
- const t_commrec* commRecord,
- const gmx_multisim_t* multiSimComm,
- double t,
- int64_t step,
- FILE* fplog,
- std::vector<int>* updateList)
+void BiasState::updateFreeEnergyAndAddSamplesToHistogram(ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
+ const BiasParams& params,
+ const t_commrec* commRecord,
+ const gmx_multisim_t* multiSimComm,
+ double t,
+ int64_t step,
+ FILE* fplog,
+ std::vector<int>* updateList)
{
/* Note hat updateList is only used in this scope and is always
* re-initialized. We do not use a local vector, because that would
/* Update target distribution? */
bool needToUpdateTargetDistribution =
- (params.eTarget != eawhtargetCONSTANT && params.isUpdateTargetStep(step));
+ (params.eTarget != AwhTargetType::Constant && params.isUpdateTargetStep(step));
/* In the initial stage, the histogram grows dynamically as a function of the number of coverings. */
bool detectedCovering = false;
}
/* The weighthistogram size after this update. */
- double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
- weightSumCovering_, fplog);
+ double newHistogramSize = histogramSize_.newHistogramSize(
+ params, t, detectedCovering, points_, weightSumCovering_, fplog);
/* Make the update list. Usually we try to only update local points,
* but if the update has non-trivial or non-deterministic effects
}
double weightHistScalingNew;
double logPmfsumScalingNew;
- setHistogramUpdateScaleFactors(params, newHistogramSize, histogramSize_.histogramSize(),
- &weightHistScalingNew, &logPmfsumScalingNew);
+ setHistogramUpdateScaleFactors(
+ params, newHistogramSize, histogramSize_.histogramSize(), &weightHistScalingNew, &logPmfsumScalingNew);
/* Update free energy and reference weight histogram for points in the update list. */
for (int pointIndex : *updateList)
/* Do updates from previous update steps that were skipped because this point was at that time non-local. */
if (params.skipUpdates())
{
- pointStateToUpdate->performPreviouslySkippedUpdates(params, histogramSize_.numUpdates(),
- weightHistScalingSkipped,
- logPmfsumScalingSkipped);
+ pointStateToUpdate->performPreviouslySkippedUpdates(
+ params, histogramSize_.numUpdates(), weightHistScalingSkipped, logPmfsumScalingSkipped);
}
/* Now do an update with new sampling data. */
- pointStateToUpdate->updateWithNewSampling(params, histogramSize_.numUpdates(),
- weightHistScalingNew, logPmfsumScalingNew);
+ pointStateToUpdate->updateWithNewSampling(
+ params, histogramSize_.numUpdates(), weightHistScalingNew, logPmfsumScalingNew);
}
/* Only update the histogram size after we are done with the local point updates */
histogramSize_.incrementNumUpdates();
}
-double BiasState::updateProbabilityWeightsAndConvolvedBias(const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
- gmx::ArrayRef<const double> neighborLambdaEnergies,
+double BiasState::updateProbabilityWeightsAndConvolvedBias(ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
+ ArrayRef<const double> neighborLambdaEnergies,
std::vector<double, AlignedAllocator<double>>* weight) const
{
/* Only neighbors of the current coordinate value will have a non-negligible chance of getting sampled */
if (n < neighbors.size())
{
const int neighbor = neighbors[n];
- (*weight)[n] = biasedLogWeightFromPoint(
- dimParams, points_, grid, neighbor, points_[neighbor].bias(),
- coordState_.coordValue(), neighborLambdaEnergies, coordState_.gridpointIndex());
+ (*weight)[n] = biasedLogWeightFromPoint(dimParams,
+ points_,
+ grid,
+ neighbor,
+ points_[neighbor].bias(),
+ coordState_.coordValue(),
+ neighborLambdaEnergies,
+ coordState_.gridpointIndex());
}
else
{
return std::log(weightSum);
}
-double BiasState::calcConvolvedBias(const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
- const awh_dvec& coordValue) const
+double BiasState::calcConvolvedBias(ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
+ const awh_dvec& coordValue) const
{
int point = grid.nearestIndex(coordValue);
const GridPoint& gridPoint = grid.point(point);
{
continue;
}
- double logWeight = biasedLogWeightFromPoint(dimParams, points_, grid, neighbor,
- points_[neighbor].bias(), coordValue, {}, point);
+ double logWeight = biasedLogWeightFromPoint(
+ dimParams, points_, grid, neighbor, points_[neighbor].bias(), coordValue, {}, point);
weightSum += std::exp(logWeight);
}
std::vector<double> lambdaMarginalDistribution =
calculateFELambdaMarginalDistribution(grid, neighbors, probWeightNeighbor);
- awh_dvec coordValueAlongLambda = { coordState_.coordValue()[0], coordState_.coordValue()[1],
- coordState_.coordValue()[2], coordState_.coordValue()[3] };
+ awh_dvec coordValueAlongLambda = { coordState_.coordValue()[0],
+ coordState_.coordValue()[1],
+ coordState_.coordValue()[2],
+ coordState_.coordValue()[3] };
for (size_t i = 0; i < neighbors.size(); i++)
{
const int neighbor = neighbors[i];
gmx_bcast(points_.size() * sizeof(PointState), points_.data(), commRecord->mpi_comm_mygroup);
- gmx_bcast(weightSumCovering_.size() * sizeof(double), weightSumCovering_.data(),
- commRecord->mpi_comm_mygroup);
+ gmx_bcast(weightSumCovering_.size() * sizeof(double), weightSumCovering_.data(), commRecord->mpi_comm_mygroup);
gmx_bcast(sizeof(histogramSize_), &histogramSize_, commRecord->mpi_comm_mygroup);
}
-void BiasState::setFreeEnergyToConvolvedPmf(const std::vector<DimParams>& dimParams, const BiasGrid& grid)
+void BiasState::setFreeEnergyToConvolvedPmf(ArrayRef<const DimParams> dimParams, const BiasGrid& grid)
{
std::vector<float> convolvedPmf;
* \param[in] biasIndex The index of the bias.
* \param[in,out] pointState The state of the points in this bias.
*/
-static void readUserPmfAndTargetDistribution(const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
- const std::string& filename,
- int numBias,
- int biasIndex,
- std::vector<PointState>* pointState)
+static void readUserPmfAndTargetDistribution(ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
+ const std::string& filename,
+ int numBias,
+ int biasIndex,
+ std::vector<PointState>* pointState)
{
/* Read the PMF and target distribution.
From the PMF, the convolved PMF, or the reference value free energy, can be calculated
if (numRows <= 0)
{
- std::string mesg = gmx::formatString("%s is empty!.\n\n%s", filename.c_str(),
- correctFormatMessage.c_str());
+ std::string mesg = gmx::formatString(
+ "%s is empty!.\n\n%s", filename.c_str(), correctFormatMessage.c_str());
GMX_THROW(InvalidInputError(mesg));
}
std::string mesg = gmx::formatString(
"%s contains too few data points (%d)."
"The minimum number of points is 2.",
- filename.c_str(), numRows);
+ filename.c_str(),
+ numRows);
GMX_THROW(InvalidInputError(mesg));
}
std::string mesg = gmx::formatString(
"The number of columns in %s should be at least %d."
"\n\n%s",
- filename.c_str(), numColumnsMin, correctFormatMessage.c_str());
+ filename.c_str(),
+ numColumnsMin,
+ correctFormatMessage.c_str());
GMX_THROW(InvalidInputError(mesg));
}
std::string mesg = gmx::formatString(
"Found %d trailing zero data rows in %s. Please remove trailing empty lines and "
"try again.",
- numZeroRows, filename.c_str());
+ numZeroRows,
+ filename.c_str());
GMX_THROW(InvalidInputError(mesg));
}
if (target < 0)
{
std::string mesg = gmx::formatString(
- "Target distribution weight at point %zu (%g) in %s is negative.", m, target,
+ "Target distribution weight at point %zu (%g) in %s is negative.",
+ m,
+ target,
filename.c_str());
GMX_THROW(InvalidInputError(mesg));
}
{
std::string mesg =
gmx::formatString("The target weights given in column %d in %s are all 0",
- columnIndexTarget, filename.c_str());
+ columnIndexTarget,
+ filename.c_str());
GMX_THROW(InvalidInputError(mesg));
}
}
}
-void BiasState::initGridPointState(const AwhBiasParams& awhBiasParams,
- const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
- const BiasParams& params,
- const std::string& filename,
- int numBias)
+void BiasState::initGridPointState(const AwhBiasParams& awhBiasParams,
+ ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
+ const BiasParams& params,
+ const std::string& filename,
+ int numBias)
{
/* Modify PMF, free energy and the constant target distribution factor
* to user input values if there is data given.
*/
- if (awhBiasParams.bUserData)
+ if (awhBiasParams.userPMFEstimate())
{
readUserPmfAndTargetDistribution(dimParams, grid, filename, numBias, params.biasIndex, &points_);
setFreeEnergyToConvolvedPmf(dimParams, grid);
}
/* The local Boltzmann distribution is special because the target distribution is updated as a function of the reference weighthistogram. */
- GMX_RELEASE_ASSERT(params.eTarget != eawhtargetLOCALBOLTZMANN || points_[0].weightSumRef() != 0,
+ GMX_RELEASE_ASSERT(params.eTarget != AwhTargetType::LocalBoltzmann || points_[0].weightSumRef() != 0,
"AWH reference weight histogram not initialized properly with local "
"Boltzmann target distribution.");
normalizePmf(params.numSharedUpdate);
}
-BiasState::BiasState(const AwhBiasParams& awhBiasParams,
- double histogramSizeInitial,
- const std::vector<DimParams>& dimParams,
- const BiasGrid& grid) :
+BiasState::BiasState(const AwhBiasParams& awhBiasParams,
+ double histogramSizeInitial,
+ ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid) :
coordState_(awhBiasParams, dimParams, grid),
points_(grid.numPoints()),
weightSumCovering_(grid.numPoints()),
template<typename>
class ArrayRef;
struct AwhBiasHistory;
-struct AwhBiasParams;
class BiasParams;
class BiasGrid;
class GridAxis;
* \param[in] dimParams The dimension parameters.
* \param[in] grid The bias grid.
*/
- BiasState(const AwhBiasParams& awhBiasParams,
- double histogramSizeInitial,
- const std::vector<DimParams>& dimParams,
- const BiasGrid& grid);
+ BiasState(const AwhBiasParams& awhBiasParams,
+ double histogramSizeInitial,
+ ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid);
/*! \brief
* Restore the bias state from history.
* \param[in] grid The grid.
* \param[in,out] convolvedPmf Array returned will be of the same length as the AWH grid to store the convolved PMF in.
*/
- void calcConvolvedPmf(const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
- std::vector<float>* convolvedPmf) const;
+ void calcConvolvedPmf(ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
+ std::vector<float>* convolvedPmf) const;
/*! \brief
* Convolves the PMF and sets the initial free energy to its convolution.
* \param[in] dimParams The bias dimensions parameters
* \param[in] grid The bias grid.
*/
- void setFreeEnergyToConvolvedPmf(const std::vector<DimParams>& dimParams, const BiasGrid& grid);
+ void setFreeEnergyToConvolvedPmf(ArrayRef<const DimParams> dimParams, const BiasGrid& grid);
/*! \brief
* Normalize the PMF histogram.
* \param[in] filename Name of file to read PMF and target from.
* \param[in] numBias The number of biases.
*/
- void initGridPointState(const AwhBiasParams& awhBiasParams,
- const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
- const BiasParams& params,
- const std::string& filename,
- int numBias);
+ void initGridPointState(const AwhBiasParams& awhBiasParams,
+ ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
+ const BiasParams& params,
+ const std::string& filename,
+ int numBias);
/*! \brief
* Performs statistical checks on the collected histograms and warns if issues are detected.
* \param[in,out] force Force vector to set.
* Returns the umbrella potential.
*/
- double calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
- int point,
- ArrayRef<const double> neighborLambdaDhdl,
- gmx::ArrayRef<double> force) const;
+ double calcUmbrellaForceAndPotential(ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
+ int point,
+ ArrayRef<const double> neighborLambdaDhdl,
+ ArrayRef<double> force) const;
/*! \brief
* Calculates and sets the convolved force acting on the coordinate.
* \param[in] forceWorkBuffer Force work buffer, values only used internally.
* \param[in,out] force Bias force vector to set.
*/
- void calcConvolvedForce(const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
- gmx::ArrayRef<const double> probWeightNeighbor,
- ArrayRef<const double> neighborLambdaDhdl,
- gmx::ArrayRef<double> forceWorkBuffer,
- gmx::ArrayRef<double> force) const;
+ void calcConvolvedForce(ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
+ ArrayRef<const double> probWeightNeighbor,
+ ArrayRef<const double> neighborLambdaDhdl,
+ ArrayRef<double> forceWorkBuffer,
+ ArrayRef<double> force) const;
/*! \brief
* Move the center point of the umbrella potential.
* \param[in] step Step number, needed for the random number generator.
* \param[in] seed Random seed.
* \param[in] indexSeed Second random seed, should be the bias Index.
+ * \param[in] onlySampleUmbrellaGridpoint Only sample the umbrella gridpoint without calculating
+ * force and potential.
* \returns the new potential value.
*/
- double moveUmbrella(const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
- gmx::ArrayRef<const double> probWeightNeighbor,
- ArrayRef<const double> neighborLambdaDhdl,
- gmx::ArrayRef<double> biasForce,
- int64_t step,
- int64_t seed,
- int indexSeed);
+ double moveUmbrella(ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
+ ArrayRef<const double> probWeightNeighbor,
+ ArrayRef<const double> neighborLambdaDhdl,
+ ArrayRef<double> biasForce,
+ int64_t step,
+ int64_t seed,
+ int indexSeed,
+ bool onlySampleUmbrellaGridpoint);
private:
/*! \brief
* \param[in] multiSimComm Struct for multi-simulation communication.
* \returns true if covered.
*/
- bool isSamplingRegionCovered(const BiasParams& params,
- const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
- const t_commrec* commRecord,
- const gmx_multisim_t* multiSimComm) const;
+ bool isSamplingRegionCovered(const BiasParams& params,
+ ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
+ const t_commrec* commRecord,
+ const gmx_multisim_t* multiSimComm) const;
/*! \brief
* Return the new reference weight histogram size for the current update.
* \param[in,out] fplog Log file.
* \param[in,out] updateList Work space to store a temporary list.
*/
- void updateFreeEnergyAndAddSamplesToHistogram(const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
- const BiasParams& params,
- const t_commrec* commRecord,
- const gmx_multisim_t* ms,
- double t,
- int64_t step,
- FILE* fplog,
- std::vector<int>* updateList);
+ void updateFreeEnergyAndAddSamplesToHistogram(ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
+ const BiasParams& params,
+ const t_commrec* commRecord,
+ const gmx_multisim_t* ms,
+ double t,
+ int64_t step,
+ FILE* fplog,
+ std::vector<int>* updateList);
/*! \brief
* Update the probability weights and the convolved bias.
* \returns the convolved bias.
*/
- double updateProbabilityWeightsAndConvolvedBias(const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
+ double updateProbabilityWeightsAndConvolvedBias(ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
ArrayRef<const double> neighborLambdaEnergies,
std::vector<double, AlignedAllocator<double>>* weight) const;
* \param[in] grid The grid.
* \param[in] probWeightNeighbor Probability weights of the neighbors.
*/
- void sampleProbabilityWeights(const BiasGrid& grid, gmx::ArrayRef<const double> probWeightNeighbor);
+ void sampleProbabilityWeights(const BiasGrid& grid, ArrayRef<const double> probWeightNeighbor);
/*! \brief
* Sample the reaction coordinate and PMF for future updates or analysis.
*/
void sampleCoordAndPmf(const std::vector<DimParams>& dimParams,
const BiasGrid& grid,
- gmx::ArrayRef<const double> probWeightNeighbor,
+ ArrayRef<const double> probWeightNeighbor,
double convolvedBias);
/*! \brief
* Calculates the convolved bias for a given coordinate value.
* \param[in] coordValue Coordinate value.
* \returns the convolved bias >= -GMX_FLOAT_MAX.
*/
- double calcConvolvedBias(const std::vector<DimParams>& dimParams,
- const BiasGrid& grid,
- const awh_dvec& coordValue) const;
+ double calcConvolvedBias(ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid,
+ const awh_dvec& coordValue) const;
/*! \brief
* Fills the given array with PMF values.
*
* \param[out] pmf Array(ref) to be filled with the PMF values, should have the same size as the bias grid.
*/
- void getPmf(gmx::ArrayRef<float> /*pmf*/) const;
+ void getPmf(ArrayRef<float> /*pmf*/) const;
/*! \brief Returns the current coordinate state.
*/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
for (size_t b = 0; b < block_.size(); b++)
{
- sub[b].type = xdr_datatype_float;
+ sub[b].type = XdrDataType::Float;
sub[b].nr = block_[b].data().size();
sub[b].fval = block_[b].data().data();
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
void prepareBiasOutput(const Bias& bias);
-private:
std::vector<AwhEnergyBlock> block_; /**< The data blocks */
std::map<AwhOutputEntryType, int> outputTypeToBlock_; /**< Start block index for each variable, -1 when variable should not be written */
};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
namespace gmx
{
-CoordState::CoordState(const AwhBiasParams& awhBiasParams,
- const std::vector<DimParams>& dimParams,
- const BiasGrid& grid)
+CoordState::CoordState(const AwhBiasParams& awhBiasParams,
+ ArrayRef<const DimParams> dimParams,
+ const BiasGrid& grid)
{
- for (size_t d = 0; d < dimParams.size(); d++)
+ GMX_RELEASE_ASSERT(awhBiasParams.ndim() == dimParams.ssize(),
+ "Need to have identical size for dimensions");
+ const auto& awhDimParams = awhBiasParams.dimParams();
+ for (int d = 0; d < gmx::ssize(awhDimParams); d++)
{
- coordValue_[d] = dimParams[d].scaleUserInputToInternal(awhBiasParams.dimParams[d].coordValueInit);
+ coordValue_[d] = dimParams[d].scaleUserInputToInternal(awhDimParams[d].initialCoordinate());
}
/* The grid-point index is always the nearest point to the coordinate.
"Coordinate %d of an AWH bias has a value %f which is more than %d sigma "
"out of the AWH range of [%f, %f]. You seem to have an unstable reaction "
"coordinate setup or an unequilibrated system.",
- dim + 1, coordValue[dim], c_marginInSigma, axis.origin(),
+ dim + 1,
+ coordValue[dim],
+ c_marginInSigma,
+ axis.origin(),
axis.origin() + axis.length());
GMX_THROW(SimulationInstabilityError(mesg));
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
template<typename>
class ArrayRef;
-struct AwhBiasParams;
+class AwhBiasParams;
struct AwhBiasStateHistory;
class BiasParams;
class BiasGrid;
* \param[in] dimParams The dimension Parameters.
* \param[in] grid The grid.
*/
- CoordState(const AwhBiasParams& awhBiasParams,
- const std::vector<DimParams>& dimParams,
- const BiasGrid& grid);
+ CoordState(const AwhBiasParams& awhBiasParams, ArrayRef<const DimParams> dimParams, const BiasGrid& grid);
/*! \brief
* Sample a new umbrella reference point given the current coordinate value.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "correlationgrid.h"
-#include "gromacs/math/utilities.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
namespace gmx
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
int getNumBlocks() const;
-public:
const double dtSample; /**< Time in between samples. */
const BlockLengthMeasure blockLengthMeasure; /**< The measure for the block length. */
private:
{
CorrelationGridHistory correlationGridHistory;
- initCorrelationGridHistory(&correlationGridHistory, correlationGrid.tensors().size(),
- correlationGrid.tensorSize(), correlationGrid.blockDataListSize());
+ initCorrelationGridHistory(&correlationGridHistory,
+ correlationGrid.tensors().size(),
+ correlationGrid.tensorSize(),
+ correlationGrid.blockDataListSize());
return correlationGridHistory;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* Builder function for pull dimension parameters.
*
* \param[in] conversionFactor Conversion factor from user coordinate units to bias internal
- * units (=DEG2RAD for angles).
+ * units (=c_deg2Rad for angles).
* \param[in] forceConstant The harmonic force constant.
* \param[in] beta 1/(k_B T).
*/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
HistogramSize::HistogramSize(const AwhBiasParams& awhBiasParams, double histogramSizeInitial) :
numUpdates_(0),
histogramSize_(histogramSizeInitial),
- inInitialStage_(awhBiasParams.eGrowth == eawhgrowthEXP_LINEAR),
- equilibrateHistogram_(awhBiasParams.equilibrateHistogram),
+ inInitialStage_(awhBiasParams.growthType() == AwhHistogramGrowthType::ExponentialLinear),
+ equilibrateHistogram_(awhBiasParams.equilibrateHistogram()),
logScaledSampleWeight_(0),
maxLogScaledSampleWeight_(0),
havePrintedAboutCovering_(false)
* \param[in] pointStates The state of the bias points.
* \returns true if the histogram is equilibrated.
*/
-bool histogramIsEquilibrated(const std::vector<PointState>& pointStates)
+bool histogramIsEquilibrated(ArrayRef<const PointState> pointStates)
{
/* Get the total weight of the total weight histogram; needed for normalization. */
double totalWeight = 0;
int numTargetPoints = 0;
- for (auto& pointState : pointStates)
+ for (const auto& pointState : pointStates)
{
if (!pointState.inTargetRegion())
{
/* Sum up weight of points that do or don't pass the check. */
double equilibratedWeight = 0;
double notEquilibratedWeight = 0;
- for (auto& pointState : pointStates)
+ for (const auto& pointState : pointStates)
{
double targetWeight = pointState.target();
double sampledWeight = pointState.weightSumTot() * inverseTotalWeight;
} // namespace
-double HistogramSize::newHistogramSize(const BiasParams& params,
- double t,
- bool covered,
- const std::vector<PointState>& pointStates,
- ArrayRef<double> weightsumCovering,
- FILE* fplog)
+double HistogramSize::newHistogramSize(const BiasParams& params,
+ double t,
+ bool covered,
+ ArrayRef<const PointState> pointStates,
+ ArrayRef<double> weightsumCovering,
+ FILE* fplog)
{
double newHistogramSize;
if (inInitialStage_)
}
else if (!havePrintedAboutCovering_)
{
- fprintf(fplog, "%s covered but histogram not equilibrated at t = %g ps.\n",
- prefix.c_str(), t);
+ fprintf(fplog,
+ "%s covered but histogram not equilibrated at t = %g ps.\n",
+ prefix.c_str(),
+ t);
havePrintedAboutCovering_ = true; /* Just print once. */
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
template<typename>
class ArrayRef;
struct AwhBiasStateHistory;
-struct AwhBiasParams;
+class AwhBiasParams;
class BiasParams;
class PointState;
* \param[in,out] fplog Log file.
* \returns the new histogram size.
*/
- double newHistogramSize(const BiasParams& params,
- double t,
- bool covered,
- const std::vector<PointState>& pointStates,
- ArrayRef<double> weightsumCovering,
- FILE* fplog);
+ double newHistogramSize(const BiasParams& params,
+ double t,
+ bool covered,
+ ArrayRef<const PointState> pointStates,
+ ArrayRef<double> weightsumCovering,
+ FILE* fplog);
/*! \brief Restores the histogram size from history.
*
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
switch (params.eTarget)
{
- case eawhtargetCONSTANT: target_ = 1; break;
- case eawhtargetCUTOFF:
+ case AwhTargetType::Constant: target_ = 1; break;
+ case AwhTargetType::Cutoff:
{
double df = freeEnergy_ - freeEnergyCutoff;
target_ = 1 / (1 + std::exp(df));
break;
}
- case eawhtargetBOLTZMANN:
+ case AwhTargetType::Boltzmann:
target_ = std::exp(-params.temperatureScaleFactor * freeEnergy_);
break;
- case eawhtargetLOCALBOLTZMANN: target_ = weightSumRef_; break;
+ case AwhTargetType::LocalBoltzmann: target_ = weightSumRef_; break;
+ default: GMX_RELEASE_ASSERT(false, "Unhandled enum");
}
/* All target types can be modulated by a constant factor. */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+
#include "gmxpre.h"
#include "read_params.h"
+#include <algorithm>
+
#include "gromacs/applied_forces/awh/awh.h"
#include "gromacs/fileio/readinp.h"
#include "gromacs/fileio/warninp.h"
#include "gromacs/random/seed.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/iserializer.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
namespace gmx
{
-const char* eawhtarget_names[eawhtargetNR + 1] = { "constant", "cutoff", "boltzmann",
- "local-boltzmann", nullptr };
+const char* enumValueToString(AwhTargetType enumValue)
+{
+ constexpr gmx::EnumerationArray<AwhTargetType, const char*> awhTargetTypeNames = {
+ "constant", "cutoff", "boltzmann", "local-boltzmann"
+ };
+ return awhTargetTypeNames[enumValue];
+}
-const char* eawhgrowth_names[eawhgrowthNR + 1] = { "exp-linear", "linear", nullptr };
+const char* enumValueToString(AwhHistogramGrowthType enumValue)
+{
+ constexpr gmx::EnumerationArray<AwhHistogramGrowthType, const char*> awhHistogramGrowthTypeNames = {
+ "exp-linear", "linear"
+ };
+ return awhHistogramGrowthTypeNames[enumValue];
+}
-const char* eawhpotential_names[eawhpotentialNR + 1] = { "convolved", "umbrella", nullptr };
+const char* enumValueToString(AwhPotentialType enumValue)
+{
+ constexpr gmx::EnumerationArray<AwhPotentialType, const char*> awhPotentialTypeNames = {
+ "convolved", "umbrella"
+ };
+ return awhPotentialTypeNames[enumValue];
+}
-const char* eawhcoordprovider_names[eawhcoordproviderNR + 1] = { "pull", "fep-lambda", nullptr };
+const char* enumValueToString(AwhCoordinateProviderType enumValue)
+{
+ constexpr gmx::EnumerationArray<AwhCoordinateProviderType, const char*> awhCoordinateProviderTypeNames = {
+ "pull", "fep-lambda"
+ };
+ return awhCoordinateProviderTypeNames[enumValue];
+}
namespace
{
bool usesPull = false;
bool usesFep = false;
- for (int b = 0; b < inputrec.awhParams->numBias; b++)
+ for (const auto& awhBiasParam : inputrec.awhParams->awhBiasParams())
{
- const auto& biasParams = inputrec.awhParams->awhBiasParams[b];
- for (int d = 0; d < biasParams.ndim; d++)
+ for (const auto& dimParam : awhBiasParam.dimParams())
{
- switch (biasParams.dimParams[d].eCoordProvider)
+ switch (dimParam.coordinateProvider())
{
- case eawhcoordproviderPULL: usesPull = true; break;
- case eawhcoordproviderFREE_ENERGY_LAMBDA: usesFep = true; break;
+ case AwhCoordinateProviderType::Pull: usesPull = true; break;
+ case AwhCoordinateProviderType::FreeEnergyLambda: usesFep = true; break;
default: GMX_RELEASE_ASSERT(false, "Unsupported coord provider");
}
}
"computed at the slow MTS level");
}
- if (inputrec.awhParams->nstSampleCoord % inputrec.mtsLevels[awhMtsLevel].stepFactor != 0)
+ if (inputrec.awhParams->nstSampleCoord() % inputrec.mtsLevels[awhMtsLevel].stepFactor != 0)
{
warning_error(wi,
"With MTS applied to AWH, awh-nstsample should be a multiple of mts-factor");
* \param[in,out] wi Struct for bookeeping warnings.
*/
void checkPullDimParams(const std::string& prefix,
- AwhDimParams* dimParams,
+ const AwhDimParams& dimParams,
const pull_params_t& pull_params,
warninp_t wi)
{
- if (dimParams->coordIndex < 0)
+ if (dimParams.coordinateIndex() < 0)
{
gmx_fatal(FARGS,
"Failed to read a valid coordinate index for %s-coord-index. "
"Note that the pull coordinate indexing starts at 1.",
prefix.c_str());
}
- if (dimParams->coordIndex >= pull_params.ncoord)
+ if (dimParams.coordinateIndex() >= pull_params.ncoord)
{
gmx_fatal(FARGS,
"The given AWH coordinate index (%d) is larger than the number of pull "
"coordinates (%d)",
- dimParams->coordIndex + 1, pull_params.ncoord);
+ dimParams.coordinateIndex() + 1,
+ pull_params.ncoord);
}
- if (pull_params.coord[dimParams->coordIndex].rate != 0)
+ if (pull_params.coord[dimParams.coordinateIndex()].rate != 0)
{
auto message = formatString(
"Setting pull-coord%d-rate (%g) is incompatible with AWH biasing this coordinate",
- dimParams->coordIndex + 1, pull_params.coord[dimParams->coordIndex].rate);
+ dimParams.coordinateIndex() + 1,
+ pull_params.coord[dimParams.coordinateIndex()].rate);
warning_error(wi, message);
}
- if (gmx_within_tol(dimParams->end - dimParams->origin, 0, GMX_REAL_EPS))
+ if (gmx_within_tol(dimParams.end() - dimParams.origin(), 0, GMX_REAL_EPS))
{
auto message = formatString(
"The given interval length given by %s-start (%g) and %s-end (%g) is zero. "
"This will result in only one point along this axis in the coordinate value grid.",
- prefix.c_str(), dimParams->origin, prefix.c_str(), dimParams->end);
+ prefix.c_str(),
+ dimParams.origin(),
+ prefix.c_str(),
+ dimParams.end());
warning(wi, message);
}
- if (dimParams->forceConstant <= 0)
+ if (dimParams.forceConstant() <= 0)
{
warning_error(wi, "The force AWH bias force constant should be > 0");
}
/* Grid params for each axis */
- int eGeom = pull_params.coord[dimParams->coordIndex].eGeom;
+ PullGroupGeometry eGeom = pull_params.coord[dimParams.coordinateIndex()].eGeom;
/* Check that the requested interval is in allowed range */
- if (eGeom == epullgDIST)
+ if (eGeom == PullGroupGeometry::Distance)
{
- if (dimParams->origin < 0 || dimParams->end < 0)
+ if (dimParams.origin() < 0 || dimParams.end() < 0)
{
gmx_fatal(FARGS,
"%s-start (%g) or %s-end (%g) set to a negative value. With pull "
"geometry distance coordinate values are non-negative. "
"Perhaps you want to use geometry %s instead?",
- prefix.c_str(), dimParams->origin, prefix.c_str(), dimParams->end,
- EPULLGEOM(epullgDIR));
+ prefix.c_str(),
+ dimParams.origin(),
+ prefix.c_str(),
+ dimParams.end(),
+ enumValueToString(PullGroupGeometry::Direction));
}
}
- else if (eGeom == epullgANGLE || eGeom == epullgANGLEAXIS)
+ else if (eGeom == PullGroupGeometry::Angle || eGeom == PullGroupGeometry::AngleAxis)
{
- if (dimParams->origin < 0 || dimParams->end > 180)
+ if (dimParams.origin() < 0 || dimParams.end() > 180)
{
gmx_fatal(FARGS,
"%s-start (%g) and %s-end (%g) are outside of the allowed range "
"0 to 180 deg for pull geometries %s and %s ",
- prefix.c_str(), dimParams->origin, prefix.c_str(), dimParams->end,
- EPULLGEOM(epullgANGLE), EPULLGEOM(epullgANGLEAXIS));
+ prefix.c_str(),
+ dimParams.origin(),
+ prefix.c_str(),
+ dimParams.end(),
+ enumValueToString(PullGroupGeometry::Angle),
+ enumValueToString(PullGroupGeometry::AngleAxis));
}
}
- else if (eGeom == epullgDIHEDRAL)
+ else if (eGeom == PullGroupGeometry::Dihedral)
{
- if (dimParams->origin < -180 || dimParams->end > 180)
+ if (dimParams.origin() < -180 || dimParams.end() > 180)
{
gmx_fatal(FARGS,
"%s-start (%g) and %s-end (%g) are outside of the allowed range "
"-180 to 180 deg for pull geometry %s. ",
- prefix.c_str(), dimParams->origin, prefix.c_str(), dimParams->end,
- EPULLGEOM(epullgDIHEDRAL));
+ prefix.c_str(),
+ dimParams.origin(),
+ prefix.c_str(),
+ dimParams.end(),
+ enumValueToString(PullGroupGeometry::Dihedral));
}
}
}
* \param[in] efep This is the type of FEP calculation (efep enumerator).
* \param[in,out] wi Struct for bookeeping warnings.
*/
-void checkFepLambdaDimParams(const std::string& prefix,
- const AwhDimParams* dimParams,
- const t_lambda* lambdaParams,
- const int efep,
- warninp_t wi)
+void checkFepLambdaDimParams(const std::string& prefix,
+ const AwhDimParams& dimParams,
+ const t_lambda* lambdaParams,
+ const FreeEnergyPerturbationType efep,
+ warninp_t wi)
{
std::string opt;
"When running AWH coupled to the free energy lambda state all lambda states "
"should be used as neighbors in order to get correct probabilities, i.e. "
"calc-lambda-neighbors (%d) must be %d.",
- lambdaParams->lambda_neighbors, -1);
+ lambdaParams->lambda_neighbors,
+ -1);
}
- if (efep == efepSLOWGROWTH || lambdaParams->delta_lambda != 0)
+ if (efep == FreeEnergyPerturbationType::SlowGrowth || lambdaParams->delta_lambda != 0)
{
gmx_fatal(FARGS,
"AWH coupled to the free energy lambda state is not compatible with slow-growth "
"and delta-lambda must be 0.");
}
- if (efep == efepEXPANDED)
+ if (efep == FreeEnergyPerturbationType::Expanded)
{
gmx_fatal(FARGS,
"AWH is not treated like other expanded ensemble methods. Do not use expanded.");
}
- if (dimParams->origin < 0)
+ if (dimParams.origin() < 0)
{
opt = prefix + "-start";
gmx_fatal(FARGS,
"When running AWH coupled to the free energy lambda state the lower lambda state "
"for AWH, %s (%.0f), must be >= 0.",
- opt.c_str(), dimParams->origin);
+ opt.c_str(),
+ dimParams.origin());
}
- if (dimParams->end >= lambdaParams->n_lambda)
+ if (dimParams.end() >= lambdaParams->n_lambda)
{
opt = prefix + "-end";
gmx_fatal(FARGS,
"When running AWH coupled to the free energy lambda state the upper lambda state "
"for AWH, %s (%.0f), must be < n_lambda (%d).",
- opt.c_str(), dimParams->origin, lambdaParams->n_lambda);
+ opt.c_str(),
+ dimParams.origin(),
+ lambdaParams->n_lambda);
}
- if (gmx_within_tol(dimParams->end - dimParams->origin, 0, GMX_REAL_EPS))
+ if (gmx_within_tol(dimParams.end() - dimParams.origin(), 0, GMX_REAL_EPS))
{
auto message = formatString(
"The given interval length given by %s-start (%g) and %s-end (%g) is zero. "
"This will result in only one lambda point along this free energy lambda state "
"axis in the coordinate value grid.",
- prefix.c_str(), dimParams->origin, prefix.c_str(), dimParams->end);
+ prefix.c_str(),
+ dimParams.origin(),
+ prefix.c_str(),
+ dimParams.end());
warning(wi, message);
}
- if (dimParams->forceConstant != 0)
+ if (dimParams.forceConstant() != 0)
{
warning_error(
wi,
}
}
-/*! \brief
- * Read parameters of an AWH bias dimension.
- *
- * \param[in,out] inp Input file entries.
- * \param[in] prefix Prefix for dimension parameters.
- * \param[in,out] dimParams AWH dimensional parameters.
- * \param[in,out] wi Struct for bookeeping warnings.
- * \param[in] bComment True if comments should be printed.
- */
-void readDimParams(std::vector<t_inpfile>* inp,
- const std::string& prefix,
- AwhDimParams* dimParams,
- warninp_t wi,
- bool bComment)
-{
- std::string opt;
- if (bComment)
- {
- printStringNoNewline(
- inp,
- "The provider of the reaction coordinate, "
- "currently only 'pull' and 'fep-lambda' (free energy lambda state) is supported");
- }
- opt = prefix + "-coord-provider";
- dimParams->eCoordProvider = get_eeenum(inp, opt, eawhcoordprovider_names, wi);
-
- if (bComment)
- {
- printStringNoNewline(inp, "The coordinate index for this dimension");
- }
- opt = prefix + "-coord-index";
- int coordIndexInput;
- coordIndexInput = get_eint(inp, opt, 1, wi);
-
- /* The pull coordinate indices start at 1 in the input file, at 0 internally */
- dimParams->coordIndex = coordIndexInput - 1;
-
- if (bComment)
- {
- printStringNoNewline(inp, "Start and end values for each coordinate dimension");
- }
- opt = prefix + "-start";
- dimParams->origin = get_ereal(inp, opt, 0., wi);
- opt = prefix + "-end";
- dimParams->end = get_ereal(inp, opt, 0., wi);
-
- if (bComment)
- {
- printStringNoNewline(
- inp, "The force constant for this coordinate (kJ/mol/nm^2 or kJ/mol/rad^2)");
- }
- opt = prefix + "-force-constant";
- dimParams->forceConstant = get_ereal(inp, opt, 0, wi);
-
- if (bComment)
- {
- printStringNoNewline(inp, "Estimated diffusion constant (nm^2/ps, rad^2/ps or ps^-1)");
- }
- opt = prefix + "-diffusion";
- dimParams->diffusion = get_ereal(inp, opt, 0, wi);
-
- if (bComment)
- {
- printStringNoNewline(inp,
- "Diameter that needs to be sampled around a point before it is "
- "considered covered. In FEP dimensions the cover diameter is "
- "specified in lambda states.");
- }
- opt = prefix + "-cover-diameter";
- dimParams->coverDiameter = get_ereal(inp, opt, 0, wi);
-}
-
/*! \brief
* Check the parameters of an AWH bias dimension.
*
* \param[in] ir Input parameter struct.
* \param[in,out] wi Struct for bookeeping warnings.
*/
-void checkDimParams(const std::string& prefix, AwhDimParams* dimParams, const t_inputrec* ir, warninp_t wi)
+void checkDimParams(const std::string& prefix, const AwhDimParams& dimParams, const t_inputrec& ir, warninp_t wi)
{
- if (dimParams->eCoordProvider == eawhcoordproviderPULL)
+ if (dimParams.coordinateProvider() == AwhCoordinateProviderType::Pull)
{
- if (!ir->bPull)
+ if (!ir.bPull)
{
gmx_fatal(FARGS,
"AWH biasing along a pull dimension is only compatible with COM pulling "
"turned on");
}
- checkPullDimParams(prefix, dimParams, *ir->pull, wi);
+ checkPullDimParams(prefix, dimParams, *ir.pull, wi);
}
- else if (dimParams->eCoordProvider == eawhcoordproviderFREE_ENERGY_LAMBDA)
+ else if (dimParams.coordinateProvider() == AwhCoordinateProviderType::FreeEnergyLambda)
{
- if (ir->efep == efepNO)
+ if (ir.efep == FreeEnergyPerturbationType::No)
{
gmx_fatal(FARGS,
"AWH biasing along a free energy lambda state dimension is only compatible "
"with free energy turned on");
}
- checkFepLambdaDimParams(prefix, dimParams, ir->fepvals, ir->efep, wi);
+ checkFepLambdaDimParams(prefix, dimParams, ir.fepvals.get(), ir.efep, wi);
}
else
{
}
}
-/*! \brief
- * Check consistency of input at the AWH bias level.
- *
- * \param[in] awhBiasParams AWH bias parameters.
- * \param[in,out] wi Struct for bookkeeping warnings.
- */
-void checkInputConsistencyAwhBias(const AwhBiasParams& awhBiasParams, warninp_t wi)
-{
- /* Covering diameter and sharing warning. */
- for (int d = 0; d < awhBiasParams.ndim; d++)
- {
- double coverDiameter = awhBiasParams.dimParams[d].coverDiameter;
- if (awhBiasParams.shareGroup <= 0 && coverDiameter > 0)
- {
- warning(wi,
- "The covering diameter is only relevant to set for bias sharing simulations.");
- }
- }
-}
-
-/*! \brief
- * Read parameters of an AWH bias.
- *
- * \param[in,out] inp Input file entries.
- * \param[in,out] awhBiasParams AWH dimensional parameters.
- * \param[in] prefix Prefix for bias parameters.
- * \param[in,out] wi Struct for bookeeping warnings.
- * \param[in] bComment True if comments should be printed.
- */
-void readBiasParams(std::vector<t_inpfile>* inp,
- AwhBiasParams* awhBiasParams,
- const std::string& prefix,
- warninp_t wi,
- bool bComment)
-{
- if (bComment)
- {
- printStringNoNewline(inp, "Estimated initial PMF error (kJ/mol)");
- }
-
- std::string opt = prefix + "-error-init";
- awhBiasParams->errorInitial = get_ereal(inp, opt, 10, wi);
-
- if (bComment)
- {
- printStringNoNewline(inp,
- "Growth rate of the reference histogram determining the bias update "
- "size: exp-linear or linear");
- }
- opt = prefix + "-growth";
- awhBiasParams->eGrowth = get_eeenum(inp, opt, eawhgrowth_names, wi);
-
- if (bComment)
- {
- printStringNoNewline(inp,
- "Start the simulation by equilibrating histogram towards the target "
- "distribution: no or yes");
- }
- opt = prefix + "-equilibrate-histogram";
- awhBiasParams->equilibrateHistogram = (get_eeenum(inp, opt, yesno_names, wi) != 0);
-
- if (bComment)
- {
- printStringNoNewline(
- inp, "Target distribution type: constant, cutoff, boltzmann or local-boltzmann");
- }
- opt = prefix + "-target";
- awhBiasParams->eTarget = get_eeenum(inp, opt, eawhtarget_names, wi);
-
- if (bComment)
- {
- printStringNoNewline(inp,
- "Boltzmann beta scaling factor for target distribution types "
- "'boltzmann' and 'boltzmann-local'");
- }
- opt = prefix + "-target-beta-scaling";
- awhBiasParams->targetBetaScaling = get_ereal(inp, opt, 0, wi);
-
- if (bComment)
- {
- printStringNoNewline(inp, "Free energy cutoff value for target distribution type 'cutoff'");
- }
- opt = prefix + "-target-cutoff";
- awhBiasParams->targetCutoff = get_ereal(inp, opt, 0, wi);
-
- if (bComment)
- {
- printStringNoNewline(inp, "Initialize PMF and target with user data: no or yes");
- }
- opt = prefix + "-user-data";
- awhBiasParams->bUserData = get_eeenum(inp, opt, yesno_names, wi);
-
- if (bComment)
- {
- printStringNoNewline(inp, "Group index to share the bias with, 0 means not shared");
- }
- opt = prefix + "-share-group";
- awhBiasParams->shareGroup = get_eint(inp, opt, 0, wi);
-
- if (bComment)
- {
- printStringNoNewline(inp, "Dimensionality of the coordinate");
- }
- opt = prefix + "-ndim";
- awhBiasParams->ndim = get_eint(inp, opt, 0, wi);
-
- /* Check this before starting to read the AWH dimension parameters. */
- if (awhBiasParams->ndim <= 0 || awhBiasParams->ndim > c_biasMaxNumDim)
- {
- gmx_fatal(FARGS, "%s (%d) needs to be > 0 and at most %d\n", opt.c_str(),
- awhBiasParams->ndim, c_biasMaxNumDim);
- }
- snew(awhBiasParams->dimParams, awhBiasParams->ndim);
- for (int d = 0; d < awhBiasParams->ndim; d++)
- {
- bComment = bComment && d == 0;
- std::string prefixdim = prefix + formatString("-dim%d", d + 1);
- readDimParams(inp, prefixdim, &awhBiasParams->dimParams[d], wi, bComment);
- }
-}
-
/*! \brief
* Check the parameters of an AWH bias.
*
* \param[in] ir Input parameter struct.
* \param[in,out] wi Struct for bookeeping warnings.
*/
-void checkBiasParams(const AwhBiasParams* awhBiasParams, const std::string& prefix, const t_inputrec* ir, warninp_t wi)
+void checkBiasParams(const AwhBiasParams& awhBiasParams, const std::string& prefix, const t_inputrec& ir, warninp_t wi)
{
std::string opt = prefix + "-error-init";
- if (awhBiasParams->errorInitial <= 0)
+ if (awhBiasParams.initialErrorEstimate() <= 0)
{
gmx_fatal(FARGS, "%s needs to be > 0.", opt.c_str());
}
opt = prefix + "-equilibrate-histogram";
- if (awhBiasParams->equilibrateHistogram && awhBiasParams->eGrowth != eawhgrowthEXP_LINEAR)
+ if (awhBiasParams.equilibrateHistogram()
+ && awhBiasParams.growthType() != AwhHistogramGrowthType::ExponentialLinear)
{
auto message =
formatString("Option %s will only have an effect for histogram growth type '%s'.",
- opt.c_str(), EAWHGROWTH(eawhgrowthEXP_LINEAR));
+ opt.c_str(),
+ enumValueToString(AwhHistogramGrowthType::ExponentialLinear));
warning(wi, message);
}
- if ((awhBiasParams->eTarget == eawhtargetLOCALBOLTZMANN)
- && (awhBiasParams->eGrowth == eawhgrowthEXP_LINEAR))
+ if ((awhBiasParams.targetDistribution() == AwhTargetType::LocalBoltzmann)
+ && (awhBiasParams.growthType() == AwhHistogramGrowthType::ExponentialLinear))
{
auto message = formatString(
"Target type '%s' combined with histogram growth type '%s' is not "
"expected to give stable bias updates. You probably want to use growth type "
"'%s' instead.",
- EAWHTARGET(eawhtargetLOCALBOLTZMANN), EAWHGROWTH(eawhgrowthEXP_LINEAR),
- EAWHGROWTH(eawhgrowthLINEAR));
+ enumValueToString(AwhTargetType::LocalBoltzmann),
+ enumValueToString(AwhHistogramGrowthType::ExponentialLinear),
+ enumValueToString(AwhHistogramGrowthType::Linear));
warning(wi, message);
}
opt = prefix + "-target-beta-scaling";
- switch (awhBiasParams->eTarget)
+ switch (awhBiasParams.targetDistribution())
{
- case eawhtargetBOLTZMANN:
- case eawhtargetLOCALBOLTZMANN:
- if (awhBiasParams->targetBetaScaling < 0 || awhBiasParams->targetBetaScaling > 1)
+ case AwhTargetType::Boltzmann:
+ case AwhTargetType::LocalBoltzmann:
+ if (awhBiasParams.targetBetaScaling() < 0 || awhBiasParams.targetBetaScaling() > 1)
{
- gmx_fatal(FARGS, "%s = %g is not useful for target type %s.", opt.c_str(),
- awhBiasParams->targetBetaScaling, EAWHTARGET(awhBiasParams->eTarget));
+ gmx_fatal(FARGS,
+ "%s = %g is not useful for target type %s.",
+ opt.c_str(),
+ awhBiasParams.targetBetaScaling(),
+ enumValueToString(awhBiasParams.targetDistribution()));
}
break;
default:
- if (awhBiasParams->targetBetaScaling != 0)
+ if (awhBiasParams.targetBetaScaling() != 0)
{
gmx_fatal(
FARGS,
"Value for %s (%g) set explicitly but will not be used for target type %s.",
- opt.c_str(), awhBiasParams->targetBetaScaling,
- EAWHTARGET(awhBiasParams->eTarget));
+ opt.c_str(),
+ awhBiasParams.targetBetaScaling(),
+ enumValueToString(awhBiasParams.targetDistribution()));
}
break;
}
opt = prefix + "-target-cutoff";
- switch (awhBiasParams->eTarget)
+ switch (awhBiasParams.targetDistribution())
{
- case eawhtargetCUTOFF:
- if (awhBiasParams->targetCutoff <= 0)
+ case AwhTargetType::Cutoff:
+ if (awhBiasParams.targetCutoff() <= 0)
{
- gmx_fatal(FARGS, "%s = %g is not useful for target type %s.", opt.c_str(),
- awhBiasParams->targetCutoff, EAWHTARGET(awhBiasParams->eTarget));
+ gmx_fatal(FARGS,
+ "%s = %g is not useful for target type %s.",
+ opt.c_str(),
+ awhBiasParams.targetCutoff(),
+ enumValueToString(awhBiasParams.targetDistribution()));
}
break;
default:
- if (awhBiasParams->targetCutoff != 0)
+ if (awhBiasParams.targetCutoff() != 0)
{
gmx_fatal(
FARGS,
"Value for %s (%g) set explicitly but will not be used for target type %s.",
- opt.c_str(), awhBiasParams->targetCutoff, EAWHTARGET(awhBiasParams->eTarget));
+ opt.c_str(),
+ awhBiasParams.targetCutoff(),
+ enumValueToString(awhBiasParams.targetDistribution()));
}
break;
}
opt = prefix + "-share-group";
- if (awhBiasParams->shareGroup < 0)
+ if (awhBiasParams.shareGroup() < 0)
{
warning_error(wi, "AWH bias share-group should be >= 0");
}
opt = prefix + "-ndim";
- if (awhBiasParams->ndim <= 0 || awhBiasParams->ndim > c_biasMaxNumDim)
+ if (awhBiasParams.ndim() <= 0 || awhBiasParams.ndim() > c_biasMaxNumDim)
{
- gmx_fatal(FARGS, "%s (%d) needs to be > 0 and at most %d\n", opt.c_str(),
- awhBiasParams->ndim, c_biasMaxNumDim);
+ gmx_fatal(FARGS, "%s (%d) needs to be > 0 and at most %d\n", opt.c_str(), awhBiasParams.ndim(), c_biasMaxNumDim);
}
- if (awhBiasParams->ndim > 2)
+ if (awhBiasParams.ndim() > 2)
{
warning_note(wi,
"For awh-dim > 2 the estimate based on the diffusion and the initial error is "
"currently only a rough guideline."
" You should verify its usefulness for your system before production runs!");
}
- for (int d = 0; d < awhBiasParams->ndim; d++)
+ for (int d = 0; d < awhBiasParams.ndim(); d++)
{
std::string prefixdim = prefix + formatString("-dim%d", d + 1);
- checkDimParams(prefixdim, &awhBiasParams->dimParams[d], ir, wi);
+ checkDimParams(prefixdim, awhBiasParams.dimParams()[d], ir, wi);
}
+}
- /* Check consistencies here that cannot be checked at read time at a lower level. */
- checkInputConsistencyAwhBias(*awhBiasParams, wi);
+/*! \brief
+ * Check consistency of input at the AWH bias level.
+ *
+ * \param[in] awhBiasParams AWH bias parameters.
+ * \param[in,out] wi Struct for bookkeeping warnings.
+ */
+void checkInputConsistencyAwhBias(const AwhBiasParams& awhBiasParams, warninp_t wi)
+{
+ /* Covering diameter and sharing warning. */
+ auto awhBiasDimensionParams = awhBiasParams.dimParams();
+ for (const auto& dimensionParam : awhBiasDimensionParams)
+ {
+ double coverDiameter = dimensionParam.coverDiameter();
+ if (awhBiasParams.shareGroup() <= 0 && coverDiameter > 0)
+ {
+ warning(wi,
+ "The covering diameter is only relevant to set for bias sharing simulations.");
+ }
+ }
}
/*! \brief
* Check that we have a shared bias when requesting multisim sharing.
*/
bool haveSharedBias = false;
- for (int k1 = 0; k1 < awhParams.numBias; k1++)
+ auto awhBiasParams = awhParams.awhBiasParams();
+ for (int k1 = 0; k1 < awhParams.numBias(); k1++)
{
- const AwhBiasParams& awhBiasParams1 = awhParams.awhBiasParams[k1];
+ const AwhBiasParams& awhBiasParams1 = awhBiasParams[k1];
- if (awhBiasParams1.shareGroup > 0)
+ if (awhBiasParams1.shareGroup() > 0)
{
haveSharedBias = true;
}
/* k1 is the reference AWH, k2 is the AWH we compare with (can be equal to k1) */
- for (int k2 = k1; k2 < awhParams.numBias; k2++)
+ for (int k2 = k1; k2 < awhParams.numBias(); k2++)
{
- for (int d1 = 0; d1 < awhBiasParams1.ndim; d1++)
+ const AwhBiasParams& awhBiasParams2 = awhBiasParams[k2];
+ const auto& dimParams1 = awhBiasParams1.dimParams();
+ const auto& dimParams2 = awhBiasParams2.dimParams();
+ for (int d1 = 0; d1 < gmx::ssize(dimParams1); d1++)
{
- if (awhBiasParams1.dimParams[d1].eCoordProvider == eawhcoordproviderFREE_ENERGY_LAMBDA)
+ if (dimParams1[d1].coordinateProvider() == AwhCoordinateProviderType::FreeEnergyLambda)
{
continue;
}
- const AwhBiasParams& awhBiasParams2 = awhParams.awhBiasParams[k2];
-
/* d1 is the reference dimension of the reference AWH. d2 is the dim index of the AWH to compare with. */
- for (int d2 = 0; d2 < awhBiasParams2.ndim; d2++)
+ for (int d2 = 0; d2 < gmx::ssize(dimParams2); d2++)
{
- if (awhBiasParams2.dimParams[d2].eCoordProvider == eawhcoordproviderFREE_ENERGY_LAMBDA)
+ if (dimParams2[d2].coordinateProvider() == AwhCoordinateProviderType::FreeEnergyLambda)
{
continue;
}
/* Give an error if (d1, k1) is different from (d2, k2) but the pull coordinate is the same */
if ((d1 != d2 || k1 != k2)
- && (awhBiasParams1.dimParams[d1].coordIndex == awhBiasParams2.dimParams[d2].coordIndex))
+ && (dimParams1[d1].coordinateIndex() == dimParams2[d2].coordinateIndex()))
{
char errormsg[STRLEN];
sprintf(errormsg,
"dimensions (awh%d-dim%d and awh%d-dim%d). "
"If this is really what you want to do you will have to duplicate "
"this pull coordinate.",
- awhBiasParams1.dimParams[d1].coordIndex + 1, k1 + 1, d1 + 1, k2 + 1,
+ dimParams1[d1].coordinateIndex() + 1,
+ k1 + 1,
+ d1 + 1,
+ k2 + 1,
d2 + 1);
gmx_fatal(FARGS, "%s", errormsg);
}
}
}
- if (awhParams.shareBiasMultisim && !haveSharedBias)
+ if (awhParams.shareBiasMultisim() && !haveSharedBias)
{
warning(wi,
"Sharing of biases over multiple simulations is requested, but no bias is marked "
"this (yet)");
}
}
+
} // namespace
-AwhParams* readAwhParams(std::vector<t_inpfile>* inp, warninp_t wi)
+AwhDimParams::AwhDimParams(std::vector<t_inpfile>* inp, const std::string& prefix, warninp_t wi, bool bComment)
+{
+ std::string opt;
+ if (bComment)
+ {
+ printStringNoNewline(
+ inp,
+ "The provider of the reaction coordinate, "
+ "currently only 'pull' and 'fep-lambda' (free energy lambda state) is supported");
+ }
+
+ opt = prefix + "-coord-provider";
+ eCoordProvider_ = getEnum<AwhCoordinateProviderType>(inp, opt.c_str(), wi);
+
+ if (bComment)
+ {
+ printStringNoNewline(inp, "The coordinate index for this dimension");
+ }
+ opt = prefix + "-coord-index";
+ int coordIndexInput;
+ coordIndexInput = get_eint(inp, opt, 1, wi);
+ if (coordIndexInput < 1)
+ {
+ gmx_fatal(FARGS,
+ "Failed to read a valid coordinate index for %s. "
+ "Note that the pull coordinate indexing starts at 1.",
+ opt.c_str());
+ }
+
+ /* The pull coordinate indices start at 1 in the input file, at 0 internally */
+ coordIndex_ = coordIndexInput - 1;
+
+ if (bComment)
+ {
+ printStringNoNewline(inp, "Start and end values for each coordinate dimension");
+ }
+
+ opt = prefix + "-start";
+ origin_ = get_ereal(inp, opt, 0., wi);
+
+ opt = prefix + "-end";
+ end_ = get_ereal(inp, opt, 0., wi);
+
+ if (bComment)
+ {
+ printStringNoNewline(
+ inp, "The force constant for this coordinate (kJ/mol/nm^2 or kJ/mol/rad^2)");
+ }
+ opt = prefix + "-force-constant";
+ forceConstant_ = get_ereal(inp, opt, 0, wi);
+
+ if (bComment)
+ {
+ printStringNoNewline(inp, "Estimated diffusion constant (nm^2/ps or rad^2/ps or ps^-1)");
+ }
+ opt = prefix + "-diffusion";
+ double diffusionValue = get_ereal(inp, opt, 0, wi);
+ if (diffusionValue <= 0)
+ {
+ const double diffusion_default = 1e-5;
+ auto message = formatString(
+ "%s not explicitly set by user. You can choose to use a default "
+ "value (%g nm^2/ps or rad^2/ps) but this may very well be "
+ "non-optimal for your system!",
+ opt.c_str(),
+ diffusion_default);
+ warning(wi, message);
+ diffusionValue = diffusion_default;
+ }
+ diffusion_ = diffusionValue;
+
+ if (bComment)
+ {
+ printStringNoNewline(inp,
+ "Diameter that needs to be sampled around a point before it is "
+ "considered covered. In FEP dimensions the cover diameter is "
+ "specified in lambda states.");
+ }
+ opt = prefix + "-cover-diameter";
+ coverDiameter_ = get_ereal(inp, opt, 0, wi);
+}
+
+AwhDimParams::AwhDimParams(ISerializer* serializer)
+{
+ GMX_RELEASE_ASSERT(serializer->reading(),
+ "Can not use writing serializer for creating datastructure");
+ serializer->doEnumAsInt(&eCoordProvider_);
+ serializer->doInt(&coordIndex_);
+ serializer->doDouble(&origin_);
+ serializer->doDouble(&end_);
+ serializer->doDouble(&period_);
+ serializer->doDouble(&forceConstant_);
+ serializer->doDouble(&diffusion_);
+ serializer->doDouble(&coordValueInit_);
+ serializer->doDouble(&coverDiameter_);
+}
+
+void AwhDimParams::serialize(ISerializer* serializer)
+{
+ GMX_RELEASE_ASSERT(!serializer->reading(),
+ "Can not use reading serializer for writing datastructure");
+ serializer->doEnumAsInt(&eCoordProvider_);
+ serializer->doInt(&coordIndex_);
+ serializer->doDouble(&origin_);
+ serializer->doDouble(&end_);
+ serializer->doDouble(&period_);
+ serializer->doDouble(&forceConstant_);
+ serializer->doDouble(&diffusion_);
+ serializer->doDouble(&coordValueInit_);
+ serializer->doDouble(&coverDiameter_);
+}
+
+AwhBiasParams::AwhBiasParams(std::vector<t_inpfile>* inp, const std::string& prefix, warninp_t wi, bool bComment)
+{
+ if (bComment)
+ {
+ printStringNoNewline(inp, "Estimated initial PMF error (kJ/mol)");
+ }
+
+ std::string opt = prefix + "-error-init";
+ errorInitial_ = get_ereal(inp, opt, 10, wi);
+
+ if (bComment)
+ {
+ printStringNoNewline(inp,
+ "Growth rate of the reference histogram determining the bias update "
+ "size: exp-linear or linear");
+ }
+ opt = prefix + "-growth";
+ eGrowth_ = getEnum<AwhHistogramGrowthType>(inp, opt.c_str(), wi);
+
+ if (bComment)
+ {
+ printStringNoNewline(inp,
+ "Start the simulation by equilibrating histogram towards the target "
+ "distribution: no or yes");
+ }
+ opt = prefix + "-equilibrate-histogram";
+ equilibrateHistogram_ = (getEnum<Boolean>(inp, opt.c_str(), wi) != Boolean::No);
+
+ if (bComment)
+ {
+ printStringNoNewline(
+ inp, "Target distribution type: constant, cutoff, boltzmann or local-boltzmann");
+ }
+ opt = prefix + "-target";
+ eTarget_ = getEnum<AwhTargetType>(inp, opt.c_str(), wi);
+
+ if (bComment)
+ {
+ printStringNoNewline(inp,
+ "Boltzmann beta scaling factor for target distribution types "
+ "'boltzmann' and 'boltzmann-local'");
+ }
+ opt = prefix + "-target-beta-scaling";
+ targetBetaScaling_ = get_ereal(inp, opt, 0, wi);
+
+ if (bComment)
+ {
+ printStringNoNewline(inp, "Free energy cutoff value for target distribution type 'cutoff'");
+ }
+ opt = prefix + "-target-cutoff";
+ targetCutoff_ = get_ereal(inp, opt, 0, wi);
+
+ if (bComment)
+ {
+ printStringNoNewline(inp, "Initialize PMF and target with user data: no or yes");
+ }
+ opt = prefix + "-user-data";
+ bUserData_ = getEnum<Boolean>(inp, opt.c_str(), wi) != Boolean::No;
+
+ if (bComment)
+ {
+ printStringNoNewline(inp, "Group index to share the bias with, 0 means not shared");
+ }
+ opt = prefix + "-share-group";
+ shareGroup_ = get_eint(inp, opt, 0, wi);
+
+ if (bComment)
+ {
+ printStringNoNewline(inp, "Dimensionality of the coordinate");
+ }
+ opt = prefix + "-ndim";
+ int ndim = get_eint(inp, opt, 0, wi);
+
+ /* Check this before starting to read the AWH dimension parameters. */
+ if (ndim <= 0 || ndim > c_biasMaxNumDim)
+ {
+ gmx_fatal(FARGS, "%s (%d) needs to be > 0 and at most %d\n", opt.c_str(), ndim, c_biasMaxNumDim);
+ }
+ for (int d = 0; d < ndim; d++)
+ {
+ bComment = bComment && d == 0;
+ std::string prefixdim = prefix + formatString("-dim%d", d + 1);
+ dimParams_.emplace_back(inp, prefixdim, wi, bComment);
+ }
+}
+
+AwhBiasParams::AwhBiasParams(ISerializer* serializer)
+{
+ GMX_RELEASE_ASSERT(serializer->reading(),
+ "Can not use writing serializer to create datastructure");
+ serializer->doEnumAsInt(&eTarget_);
+ serializer->doDouble(&targetBetaScaling_);
+ serializer->doDouble(&targetCutoff_);
+ serializer->doEnumAsInt(&eGrowth_);
+ int temp = 0;
+ serializer->doInt(&temp);
+ bUserData_ = static_cast<bool>(temp);
+ serializer->doDouble(&errorInitial_);
+ int numDimensions = dimParams_.size();
+ serializer->doInt(&numDimensions);
+ serializer->doInt(&shareGroup_);
+ serializer->doBool(&equilibrateHistogram_);
+
+ for (int k = 0; k < numDimensions; k++)
+ {
+ dimParams_.emplace_back(serializer);
+ }
+ /* Check consistencies here that cannot be checked at read time at a lower level. */
+ checkInputConsistencyAwhBias(*this, nullptr);
+}
+
+void AwhBiasParams::serialize(ISerializer* serializer)
+{
+ GMX_RELEASE_ASSERT(!serializer->reading(),
+ "Can not use reading serializer to write datastructure");
+ serializer->doEnumAsInt(&eTarget_);
+ serializer->doDouble(&targetBetaScaling_);
+ serializer->doDouble(&targetCutoff_);
+ serializer->doEnumAsInt(&eGrowth_);
+ int temp = static_cast<int>(bUserData_);
+ serializer->doInt(&temp);
+ serializer->doDouble(&errorInitial_);
+ int numDimensions = ndim();
+ serializer->doInt(&numDimensions);
+ serializer->doInt(&shareGroup_);
+ serializer->doBool(&equilibrateHistogram_);
+
+ for (int k = 0; k < numDimensions; k++)
+ {
+ dimParams_[k].serialize(serializer);
+ }
+}
+
+AwhParams::AwhParams(std::vector<t_inpfile>* inp, warninp_t wi)
{
- AwhParams* awhParams;
- snew(awhParams, 1);
std::string opt;
/* Parameters common for all biases */
printStringNoNewline(inp, "The way to apply the biasing potential: convolved or umbrella");
- opt = "awh-potential";
- awhParams->ePotential = get_eeenum(inp, opt, eawhpotential_names, wi);
+ opt = "awh-potential";
+ potentialEnum_ = getEnum<AwhPotentialType>(inp, opt.c_str(), wi);
printStringNoNewline(inp,
"The random seed used for sampling the umbrella center in the case of "
"umbrella type potential");
- opt = "awh-seed";
- awhParams->seed = get_eint(inp, opt, -1, wi);
- if (awhParams->seed == -1)
+ opt = "awh-seed";
+ seed_ = get_eint(inp, opt, -1, wi);
+ if (seed_ == -1)
{
- awhParams->seed = static_cast<int>(gmx::makeRandomSeed());
- fprintf(stderr, "Setting the AWH bias MC random seed to %" PRId64 "\n", awhParams->seed);
+ seed_ = static_cast<int>(gmx::makeRandomSeed());
+ fprintf(stderr, "Setting the AWH bias MC random seed to %" PRId64 "\n", seed_);
}
printStringNoNewline(inp, "Data output interval in number of steps");
- opt = "awh-nstout";
- awhParams->nstOut = get_eint(inp, opt, 100000, wi);
+ opt = "awh-nstout";
+ nstOut_ = get_eint(inp, opt, 100000, wi);
printStringNoNewline(inp, "Coordinate sampling interval in number of steps");
- opt = "awh-nstsample";
- awhParams->nstSampleCoord = get_eint(inp, opt, 10, wi);
+ opt = "awh-nstsample";
+ nstSampleCoord_ = get_eint(inp, opt, 10, wi);
printStringNoNewline(inp, "Free energy and bias update interval in number of samples");
- opt = "awh-nsamples-update";
- awhParams->numSamplesUpdateFreeEnergy = get_eint(inp, opt, 10, wi);
+ opt = "awh-nsamples-update";
+ numSamplesUpdateFreeEnergy_ = get_eint(inp, opt, 10, wi);
printStringNoNewline(
inp, "When true, biases with share-group>0 are shared between multiple simulations");
- opt = "awh-share-multisim";
- awhParams->shareBiasMultisim = (get_eeenum(inp, opt, yesno_names, wi) != 0);
+ opt = "awh-share-multisim";
+ shareBiasMultisim_ = (getEnum<Boolean>(inp, opt.c_str(), wi) != Boolean::No);
printStringNoNewline(inp, "The number of independent AWH biases");
- opt = "awh-nbias";
- awhParams->numBias = get_eint(inp, opt, 1, wi);
+ opt = "awh-nbias";
+ int numBias = get_eint(inp, opt, 1, wi);
/* Check this before starting to read the AWH biases. */
- if (awhParams->numBias <= 0)
+ if (numBias <= 0)
{
gmx_fatal(FARGS, "%s needs to be an integer > 0", opt.c_str());
}
/* Read the parameters specific to each AWH bias */
- snew(awhParams->awhBiasParams, awhParams->numBias);
-
- for (int k = 0; k < awhParams->numBias; k++)
+ for (int k = 0; k < numBias; k++)
{
bool bComment = (k == 0);
std::string prefixawh = formatString("awh%d", k + 1);
- readBiasParams(inp, &awhParams->awhBiasParams[k], prefixawh, wi, bComment);
+ awhBiasParams_.emplace_back(inp, prefixawh, wi, bComment);
}
-
- return awhParams;
+ checkInputConsistencyAwh(*this, wi);
}
-void checkAwhParams(const AwhParams* awhParams, const t_inputrec* ir, warninp_t wi)
+AwhParams::AwhParams(ISerializer* serializer)
{
- std::string opt;
-
- checkMtsConsistency(*ir, wi);
-
- opt = "awh-nstout";
- if (awhParams->nstOut <= 0)
- {
- auto message = formatString("Not writing AWH output with AWH (%s = %d) does not make sense",
- opt.c_str(), awhParams->nstOut);
- warning_error(wi, message);
- }
- /* This restriction can be removed by changing a flag of print_ebin() */
- if (ir->nstenergy == 0 || awhParams->nstOut % ir->nstenergy != 0)
- {
- auto message = formatString("%s (%d) should be a multiple of nstenergy (%d)", opt.c_str(),
- awhParams->nstOut, ir->nstenergy);
- warning_error(wi, message);
- }
-
- opt = "awh-nsamples-update";
- if (awhParams->numSamplesUpdateFreeEnergy <= 0)
- {
- warning_error(wi, opt + " needs to be an integer > 0");
- }
-
- bool haveFepLambdaDim = false;
- for (int k = 0; k < awhParams->numBias; k++)
- {
- std::string prefixawh = formatString("awh%d", k + 1);
- checkBiasParams(&awhParams->awhBiasParams[k], prefixawh, ir, wi);
- /* Check if there is a FEP lambda dimension. */
- for (int l = 0; l < awhParams->awhBiasParams[k].ndim; l++)
+ GMX_RELEASE_ASSERT(serializer->reading(),
+ "Can not use writing serializer to read AWH parameters");
+ int numberOfBiases = awhBiasParams_.size();
+ serializer->doInt(&numberOfBiases);
+ serializer->doInt(&nstOut_);
+ serializer->doInt64(&seed_);
+ serializer->doInt(&nstSampleCoord_);
+ serializer->doInt(&numSamplesUpdateFreeEnergy_);
+ serializer->doEnumAsInt(&potentialEnum_);
+ serializer->doBool(&shareBiasMultisim_);
+
+ if (numberOfBiases > 0)
+ {
+ for (int k = 0; k < numberOfBiases; k++)
{
- if (awhParams->awhBiasParams[k].dimParams[l].eCoordProvider == eawhcoordproviderFREE_ENERGY_LAMBDA)
- {
- haveFepLambdaDim = true;
- break;
- }
+ awhBiasParams_.emplace_back(serializer);
}
}
+ checkInputConsistencyAwh(*this, nullptr);
+}
- if (haveFepLambdaDim)
- {
- if (awhParams->nstSampleCoord % ir->nstcalcenergy != 0)
- {
- opt = "awh-nstsample";
- auto message = formatString(
- "%s (%d) should be a multiple of nstcalcenergy (%d) when using AWH for "
- "sampling an FEP lambda dimension",
- opt.c_str(), awhParams->nstSampleCoord, ir->nstcalcenergy);
- warning_error(wi, message);
- }
- if (awhParams->ePotential != eawhpotentialUMBRELLA)
+void AwhParams::serialize(ISerializer* serializer)
+{
+ GMX_RELEASE_ASSERT(!serializer->reading(),
+ "Can not use reading serializer to write AWH parameters");
+ int numberOfBiases = numBias();
+ serializer->doInt(&numberOfBiases);
+ serializer->doInt(&nstOut_);
+ serializer->doInt64(&seed_);
+ serializer->doInt(&nstSampleCoord_);
+ serializer->doInt(&numSamplesUpdateFreeEnergy_);
+ serializer->doEnumAsInt(&potentialEnum_);
+ serializer->doBool(&shareBiasMultisim_);
+
+ if (numberOfBiases > 0)
+ {
+ for (int k = 0; k < numberOfBiases; k++)
{
- opt = "awh-potential";
- auto message = formatString(
- "%s (%s) must be set to %s when using AWH for sampling an FEP lambda dimension",
- opt.c_str(), eawhpotential_names[awhParams->ePotential],
- eawhpotential_names[eawhpotentialUMBRELLA]);
- warning_error(wi, message);
+ awhBiasParams_[k].serialize(serializer);
}
}
-
- /* Do a final consistency check before returning */
- checkInputConsistencyAwh(*awhParams, wi);
-
- if (ir->init_step != 0)
- {
- warning_error(wi, "With AWH init-step should be 0");
- }
}
/*! \brief
{
double period = 0;
- if (pullCoordParams.eGeom == epullgDIR)
+ if (pullCoordParams.eGeom == PullGroupGeometry::Direction)
{
const real margin = 0.001;
// Make dims periodic when the interval covers > 95%
gmx_fatal(FARGS,
"The AWH interval (%f nm) for a pull coordinate is larger than the "
"box size (%f nm)",
- intervalLength, boxLength);
+ intervalLength,
+ boxLength);
}
if (intervalLength > periodicFraction * boxLength)
}
}
}
- else if (pullCoordParams.eGeom == epullgDIHEDRAL)
+ else if (pullCoordParams.eGeom == PullGroupGeometry::Dihedral)
{
/* The dihedral angle is periodic in -180 to 180 deg */
period = 360;
* \param[in] awhParams AWH parameters.
* \param[in,out] wi Struct for bookeeping warnings.
*/
-static void checkInputConsistencyInterval(const AwhParams* awhParams, warninp_t wi)
+static void checkInputConsistencyInterval(const AwhParams& awhParams, warninp_t wi)
{
- for (int k = 0; k < awhParams->numBias; k++)
+ const auto& awhBiasParams = awhParams.awhBiasParams();
+ for (int k = 0; k < gmx::ssize(awhBiasParams); k++)
{
- AwhBiasParams* awhBiasParams = &awhParams->awhBiasParams[k];
- for (int d = 0; d < awhBiasParams->ndim; d++)
+ const auto& dimParams = awhBiasParams[k].dimParams();
+ for (int d = 0; d < gmx::ssize(dimParams); d++)
{
- AwhDimParams* dimParams = &awhBiasParams->dimParams[d];
- int coordIndex = dimParams->coordIndex;
- double origin = dimParams->origin, end = dimParams->end, period = dimParams->period;
- double coordValueInit = dimParams->coordValueInit;
+ int coordIndex = dimParams[d].coordinateIndex();
+ double origin = dimParams[d].origin(), end = dimParams[d].end(),
+ period = dimParams[d].period();
+ double coordValueInit = dimParams[d].initialCoordinate();
if ((period == 0) && (origin > end))
{
gmx_fatal(FARGS,
"For the non-periodic pull coordinates awh%d-dim%d-start (%f) cannot be "
"larger than awh%d-dim%d-end (%f)",
- k + 1, d + 1, origin, k + 1, d + 1, end);
+ k + 1,
+ d + 1,
+ origin,
+ k + 1,
+ d + 1,
+ end);
}
/* Currently we assume symmetric periodic intervals, meaning we use [-period/2, period/2] as the reference interval.
"values in between "
"minus half a period and plus half a period, i.e. in the interval [%.8g, "
"%.8g].",
- k + 1, d + 1, origin, k + 1, d + 1, end, period, -0.5 * period, 0.5 * period);
+ k + 1,
+ d + 1,
+ origin,
+ k + 1,
+ d + 1,
+ end,
+ period,
+ -0.5 * period,
+ 0.5 * period);
}
/* Warn if the pull initial coordinate value is not in the grid */
"(%.8g). "
"This can lead to large initial forces pulling the coordinate towards the "
"sampling interval.",
- coordValueInit, coordIndex + 1, k + 1, d + 1, origin, k + 1, d + 1, end);
+ coordValueInit,
+ coordIndex + 1,
+ k + 1,
+ d + 1,
+ origin,
+ k + 1,
+ d + 1,
+ end);
warning(wi, message);
}
}
static void setStateDependentAwhPullDimParams(AwhDimParams* dimParams,
const int biasIndex,
const int dimIndex,
- const pull_params_t* pull_params,
+ const pull_params_t& pull_params,
pull_t* pull_work,
const t_pbc& pbc,
const tensor& compressibility,
warninp_t wi)
{
- const t_pull_coord& pullCoordParams = pull_params->coord[dimParams->coordIndex];
+ const t_pull_coord& pullCoordParams = pull_params.coord[dimParams->coordinateIndex()];
- if (pullCoordParams.eGeom == epullgDIRPBC)
+ if (pullCoordParams.eGeom == PullGroupGeometry::DirectionPBC)
{
gmx_fatal(FARGS,
"AWH does not support pull geometry '%s'. "
"If the maximum distance between the groups is always "
"less than half the box size, "
"you can use geometry '%s' instead.",
- EPULLGEOM(epullgDIRPBC), EPULLGEOM(epullgDIR));
+ enumValueToString(PullGroupGeometry::DirectionPBC),
+ enumValueToString(PullGroupGeometry::Direction));
}
- dimParams->period = get_pull_coord_period(pullCoordParams, pbc, dimParams->end - dimParams->origin);
+ dimParams->setPeriod(
+ get_pull_coord_period(pullCoordParams, pbc, dimParams->end() - dimParams->origin()));
// We would like to check for scaling, but we don't have the full inputrec available here
- if (dimParams->period > 0
- && !(pullCoordParams.eGeom == epullgANGLE || pullCoordParams.eGeom == epullgDIHEDRAL))
+ if (dimParams->period() > 0
+ && !(pullCoordParams.eGeom == PullGroupGeometry::Angle
+ || pullCoordParams.eGeom == PullGroupGeometry::Dihedral))
{
bool coordIsScaled = false;
for (int d2 = 0; d2 < DIM; d2++)
{
std::string mesg = gmx::formatString(
"AWH dimension %d of bias %d is periodic with pull geometry '%s', "
- "while you should are applying pressure scaling to the "
+ "while you should be applying pressure scaling to the "
"corresponding box vector, this is not supported.",
- dimIndex + 1, biasIndex + 1, EPULLGEOM(pullCoordParams.eGeom));
+ dimIndex + 1,
+ biasIndex + 1,
+ enumValueToString(pullCoordParams.eGeom));
warning(wi, mesg.c_str());
}
}
/* The initial coordinate value, converted to external user units. */
- dimParams->coordValueInit = get_pull_coord_value(pull_work, dimParams->coordIndex, &pbc);
-
- dimParams->coordValueInit *= pull_conversion_factor_internal2userinput(&pullCoordParams);
+ double initialCoordinate = get_pull_coord_value(pull_work, dimParams->coordinateIndex(), &pbc);
+ initialCoordinate *= pull_conversion_factor_internal2userinput(pullCoordParams);
+ dimParams->setInitialCoordinate(initialCoordinate);
}
void setStateDependentAwhParams(AwhParams* awhParams,
t_pbc pbc;
set_pbc(&pbc, pbcType, box);
- for (int k = 0; k < awhParams->numBias; k++)
+ auto awhBiasParams = awhParams->awhBiasParams();
+ for (int k = 0; k < awhParams->numBias(); k++)
{
- AwhBiasParams* awhBiasParams = &awhParams->awhBiasParams[k];
- for (int d = 0; d < awhBiasParams->ndim; d++)
+ auto awhBiasDimensionParams = awhBiasParams[k].dimParams();
+ for (int d = 0; d < awhBiasParams[k].ndim(); d++)
{
- AwhDimParams* dimParams = &awhBiasParams->dimParams[d];
- if (dimParams->eCoordProvider == eawhcoordproviderPULL)
+ AwhDimParams* dimParams = &awhBiasDimensionParams[d];
+ if (dimParams->coordinateProvider() == AwhCoordinateProviderType::Pull)
{
- setStateDependentAwhPullDimParams(dimParams, k, d, &pull_params, pull_work, pbc,
- compressibility, wi);
+ setStateDependentAwhPullDimParams(
+ dimParams, k, d, pull_params, pull_work, pbc, compressibility, wi);
}
else
{
- dimParams->coordValueInit = initLambda;
+ dimParams->setInitialCoordinate(initLambda);
checkFepLambdaDimDecouplingConsistency(mtop, wi);
}
}
}
- checkInputConsistencyInterval(awhParams, wi);
+ checkInputConsistencyInterval(*awhParams, wi);
/* Register AWH as external potential with pull (for AWH dimensions that use pull as
* reaction coordinate provider) to check consistency. */
Awh::registerAwhWithPull(*awhParams, pull_work);
}
+void checkAwhParams(const AwhParams& awhParams, const t_inputrec& ir, warninp_t wi)
+{
+ std::string opt;
+ checkMtsConsistency(ir, wi);
+
+ opt = "awh-nstout";
+ if (awhParams.nstout() <= 0)
+ {
+ auto message = formatString("Not writing AWH output with AWH (%s = %d) does not make sense",
+ opt.c_str(),
+ awhParams.nstout());
+ warning_error(wi, message);
+ }
+ /* This restriction can be removed by changing a flag of print_ebin() */
+ if (ir.nstenergy == 0 || awhParams.nstout() % ir.nstenergy != 0)
+ {
+ auto message = formatString(
+ "%s (%d) should be a multiple of nstenergy (%d)", opt.c_str(), awhParams.nstout(), ir.nstenergy);
+ warning_error(wi, message);
+ }
+
+ opt = "awh-nsamples-update";
+ if (awhParams.numSamplesUpdateFreeEnergy() <= 0)
+ {
+ warning_error(wi, opt + " needs to be an integer > 0");
+ }
+
+ bool haveFepLambdaDim = false;
+ const auto awhBiasParams = awhParams.awhBiasParams();
+ for (int k = 0; k < awhParams.numBias() && !haveFepLambdaDim; k++)
+ {
+ std::string prefixawh = formatString("awh%d", k + 1);
+ checkBiasParams(awhBiasParams[k], prefixawh, ir, wi);
+ /* Check if there is a FEP lambda dimension. */
+ const auto dimParams = awhBiasParams[k].dimParams();
+ haveFepLambdaDim = std::any_of(dimParams.begin(), dimParams.end(), [](const auto& dimParam) {
+ return dimParam.coordinateProvider() == AwhCoordinateProviderType::FreeEnergyLambda;
+ });
+ }
+
+ if (haveFepLambdaDim)
+ {
+ if (awhParams.nstSampleCoord() % ir.nstcalcenergy != 0)
+ {
+ opt = "awh-nstsample";
+ auto message = formatString(
+ "%s (%d) should be a multiple of nstcalcenergy (%d) when using AWH for "
+ "sampling an FEP lambda dimension",
+ opt.c_str(),
+ awhParams.nstSampleCoord(),
+ ir.nstcalcenergy);
+ warning_error(wi, message);
+ }
+ if (awhParams.potential() != AwhPotentialType::Umbrella)
+ {
+ opt = "awh-potential";
+ auto message = formatString(
+ "%s (%s) must be set to %s when using AWH for sampling an FEP lambda dimension",
+ opt.c_str(),
+ enumValueToString(awhParams.potential()),
+ enumValueToString(AwhPotentialType::Umbrella));
+ warning_error(wi, message);
+ }
+ }
+
+ if (ir.init_step != 0)
+ {
+ warning_error(wi, "With AWH init-step should be 0");
+ }
+}
+
} // namespace gmx
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
namespace gmx
{
-struct AwhParams;
-/*! \brief Allocate and initialize the AWH parameters with values from the input file.
- *
- * \param[in,out] inp Input file entries.
- * \param[in,out] wi Struct for bookeeping warnings.
- * \returns AWH parameters.
- */
-AwhParams* readAwhParams(std::vector<t_inpfile>* inp, warninp_t wi);
+class AwhParams;
+class ISerializer;
/*! \brief Check the AWH parameters.
*
- * \param[in,out] awhParams The AWH parameters.
+ * \param[in] awhParams The AWH parameters.
* \param[in] inputrec Input parameter struct.
* \param[in,out] wi Struct for bookeeping warnings.
*/
-void checkAwhParams(const AwhParams* awhParams, const t_inputrec* inputrec, warninp_t wi);
+void checkAwhParams(const AwhParams& awhParams, const t_inputrec& inputrec, warninp_t wi);
/*! \brief
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2017,2020, by the GROMACS development team, led by
+# Copyright (c) 2017,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
gmx_add_unit_test(AwhTest awh-test
CPP_SOURCE_FILES
+ awh_setup.cpp
bias.cpp
biasgrid.cpp
biasstate.cpp
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "awh_setup.h"
+
+#include <cmath>
+
+#include <memory>
+#include <tuple>
+#include <vector>
+
+#include <gmock/gmock.h>
+#include <gmock/gmock-matchers.h>
+#include <gtest/gtest.h>
+
+#include "gromacs/applied_forces/awh/bias.h"
+#include "gromacs/applied_forces/awh/correlationgrid.h"
+#include "gromacs/applied_forces/awh/pointstate.h"
+#include "gromacs/mdtypes/awh_params.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/inmemoryserializer.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+namespace gmx
+{
+
+namespace test
+{
+
+using ::testing::Eq;
+using ::testing::Pointwise;
+
+std::vector<char> awhDimParamSerialized(AwhCoordinateProviderType inputCoordinateProvider,
+ int inputCoordIndex,
+ double inputOrigin,
+ double inputEnd,
+ double inputPeriod,
+ double inputDiffusion)
+{
+ AwhCoordinateProviderType eCoordProvider = inputCoordinateProvider;
+ int coordIndex = inputCoordIndex;
+ double forceConstant = 10;
+ double period = inputPeriod;
+ double diffusion = inputDiffusion;
+ double origin = inputOrigin;
+ double end = inputEnd;
+ double coordValueInit = inputOrigin;
+ double coverDiameter = 0;
+
+ gmx::InMemorySerializer serializer;
+ serializer.doEnumAsInt(&eCoordProvider);
+ serializer.doInt(&coordIndex);
+ serializer.doDouble(&origin);
+ serializer.doDouble(&end);
+ serializer.doDouble(&period);
+ serializer.doDouble(&forceConstant);
+ serializer.doDouble(&diffusion);
+ serializer.doDouble(&coordValueInit);
+ serializer.doDouble(&coverDiameter);
+ return serializer.finishAndGetBuffer();
+}
+
+/*! \internal \brief
+ * Prepare a memory buffer with serialized AwhBiasParams.
+ *
+ * \param[in] eawhgrowth Way to grow potential.
+ * \param[in] beta Value for 1/(kB*T).
+ * \param[in] inputErrorScaling Factor for initial error scaling.
+ * \param[in] dimensionParameterBuffers Buffers containing the dimension parameters.
+ * \param[in] inputUserData If there is a user provided PMF estimate.
+ */
+static std::vector<char> awhBiasParamSerialized(AwhHistogramGrowthType eawhgrowth,
+ double beta,
+ double inputErrorScaling,
+ ArrayRef<const std::vector<char>> dimensionParameterBuffers,
+ bool inputUserData)
+{
+ int ndim = dimensionParameterBuffers.size();
+ AwhTargetType eTarget = AwhTargetType::Constant;
+ double targetBetaScaling = 0;
+ double targetCutoff = 0;
+ AwhHistogramGrowthType eGrowth = eawhgrowth;
+ bool bUserData = inputUserData;
+ double errorInitial = inputErrorScaling / beta;
+ int shareGroup = 0;
+ bool equilibrateHistogram = false;
+
+ gmx::InMemorySerializer serializer;
+ serializer.doEnumAsInt(&eTarget);
+ serializer.doDouble(&targetBetaScaling);
+ serializer.doDouble(&targetCutoff);
+ serializer.doEnumAsInt(&eGrowth);
+ int temp = static_cast<int>(bUserData);
+ serializer.doInt(&temp);
+ serializer.doDouble(&errorInitial);
+ serializer.doInt(&ndim);
+ serializer.doInt(&shareGroup);
+ serializer.doBool(&equilibrateHistogram);
+
+ auto awhDimBuffer = awhDimParamSerialized();
+ auto awhBiasBuffer = serializer.finishAndGetBuffer();
+ for (const auto& dimParamBuffer : dimensionParameterBuffers)
+ {
+ awhBiasBuffer.insert(awhBiasBuffer.end(), dimParamBuffer.begin(), dimParamBuffer.end());
+ }
+ return awhBiasBuffer;
+}
+
+/*! \internal \brief
+ * Prepare a memory buffer with serialized AwhParams.
+ *
+ * \param[in] eawhgrowth Way to grow potential.
+ * \param[in] eawhpotential Which potential to use.
+ * \param[in] beta Value for 1/(kB*T).
+ * \param[in] inputErrorScaling Factor for initial error scaling.
+ * \param[in] inputSeed Seed value to use.
+ * \param[in] dimensionParameterBuffers Buffers containing the dimension parameters.
+ * \param[in] inputUserData If there is a user provided PMF estimate.
+ */
+static std::vector<char> awhParamSerialized(AwhHistogramGrowthType eawhgrowth,
+ AwhPotentialType eawhpotential,
+ double beta,
+ double inputErrorScaling,
+ int64_t inputSeed,
+ ArrayRef<const std::vector<char>> dimensionParameterBuffers,
+ bool inputUserData)
+{
+ int numBias = 1;
+ int64_t seed = inputSeed;
+ int nstOut = 0;
+ int nstSampleCoord = 1;
+ int numSamplesUpdateFreeEnergy = 10;
+ AwhPotentialType ePotential = eawhpotential;
+ bool shareBiasMultisim = false;
+
+ gmx::InMemorySerializer serializer;
+ serializer.doInt(&numBias);
+ serializer.doInt(&nstOut);
+ serializer.doInt64(&seed);
+ serializer.doInt(&nstSampleCoord);
+ serializer.doInt(&numSamplesUpdateFreeEnergy);
+ serializer.doEnumAsInt(&ePotential);
+ serializer.doBool(&shareBiasMultisim);
+
+ auto awhParamBuffer = serializer.finishAndGetBuffer();
+ auto awhBiasBuffer = awhBiasParamSerialized(
+ eawhgrowth, beta, inputErrorScaling, dimensionParameterBuffers, inputUserData);
+
+ awhParamBuffer.insert(awhParamBuffer.end(), awhBiasBuffer.begin(), awhBiasBuffer.end());
+
+ return awhParamBuffer;
+}
+
+AwhTestParameters::AwhTestParameters(ISerializer* serializer) : awhParams(serializer) {}
+/*! \brief
+ * Helper function to set up the C-style AWH parameters for the test.
+ *
+ * Builds the test input data from serialized data.
+ */
+AwhTestParameters getAwhTestParameters(AwhHistogramGrowthType eawhgrowth,
+ AwhPotentialType eawhpotential,
+ ArrayRef<const std::vector<char>> dimensionParameterBuffers,
+ bool inputUserData,
+ double beta,
+ bool useAwhFep,
+ double inputErrorScaling,
+ int numFepLambdaStates)
+{
+ double convFactor = 1;
+ double k = 1000;
+ int64_t seed = 93471803;
+
+ auto awhParamBuffer = awhParamSerialized(
+ eawhgrowth, eawhpotential, beta, inputErrorScaling, seed, dimensionParameterBuffers, inputUserData);
+ gmx::InMemoryDeserializer deserializer(awhParamBuffer, false);
+ AwhTestParameters params(&deserializer);
+
+ params.beta = beta;
+
+ if (useAwhFep)
+ {
+ params.dimParams.emplace_back(DimParams::fepLambdaDimParams(numFepLambdaStates, params.beta));
+ }
+ else
+ {
+ params.dimParams.emplace_back(DimParams::pullDimParams(convFactor, k, params.beta));
+ }
+ return params;
+}
+
+TEST(SerializationTest, CanSerializeDimParams)
+{
+ auto awhDimBuffer = awhDimParamSerialized();
+ gmx::InMemoryDeserializer deserializer(awhDimBuffer, false);
+ AwhDimParams awhDimParams(&deserializer);
+ EXPECT_EQ(awhDimParams.coordinateProvider(), AwhCoordinateProviderType::Pull);
+ EXPECT_EQ(awhDimParams.coordinateIndex(), 0);
+ EXPECT_FLOAT_EQ(awhDimParams.forceConstant(), 10);
+ EXPECT_FLOAT_EQ(awhDimParams.period(), 0);
+ EXPECT_FLOAT_EQ(awhDimParams.diffusion(), 0.34690997);
+ EXPECT_FLOAT_EQ(awhDimParams.origin(), 0.5);
+ EXPECT_FLOAT_EQ(awhDimParams.end(), 1.5);
+ EXPECT_FLOAT_EQ(awhDimParams.initialCoordinate(), awhDimParams.origin());
+ EXPECT_FLOAT_EQ(awhDimParams.coverDiameter(), 0);
+
+ gmx::InMemorySerializer serializer;
+ awhDimParams.serialize(&serializer);
+ EXPECT_THAT(awhDimBuffer, Pointwise(Eq(), serializer.finishAndGetBuffer()));
+}
+
+TEST(SerializationTest, CanSerializeBiasParams)
+{
+ auto awhDimBuffer = awhDimParamSerialized();
+ auto awhDimArrayRef = gmx::arrayRefFromArray(&awhDimBuffer, 1);
+ auto awhBiasBuffer = awhBiasParamSerialized(
+ AwhHistogramGrowthType::ExponentialLinear, 0.4, 0.5, awhDimArrayRef, false);
+ gmx::InMemoryDeserializer deserializer(awhBiasBuffer, false);
+ AwhBiasParams awhBiasParams(&deserializer);
+ EXPECT_EQ(awhBiasParams.ndim(), 1);
+ EXPECT_EQ(awhBiasParams.targetDistribution(), AwhTargetType::Constant);
+ EXPECT_FLOAT_EQ(awhBiasParams.targetBetaScaling(), 0);
+ EXPECT_FLOAT_EQ(awhBiasParams.targetCutoff(), 0);
+ EXPECT_EQ(awhBiasParams.growthType(), AwhHistogramGrowthType::ExponentialLinear);
+ EXPECT_EQ(awhBiasParams.userPMFEstimate(), 0);
+ EXPECT_FLOAT_EQ(awhBiasParams.initialErrorEstimate(), 0.5 / 0.4);
+ EXPECT_EQ(awhBiasParams.shareGroup(), 0);
+ EXPECT_EQ(awhBiasParams.equilibrateHistogram(), false);
+ const auto& awhDimParams = awhBiasParams.dimParams()[0];
+ EXPECT_EQ(awhDimParams.coordinateProvider(), AwhCoordinateProviderType::Pull);
+ EXPECT_EQ(awhDimParams.coordinateIndex(), 0);
+ EXPECT_FLOAT_EQ(awhDimParams.forceConstant(), 10);
+ EXPECT_FLOAT_EQ(awhDimParams.period(), 0);
+ EXPECT_FLOAT_EQ(awhDimParams.diffusion(), 0.34690997);
+ EXPECT_FLOAT_EQ(awhDimParams.origin(), 0.5);
+ EXPECT_FLOAT_EQ(awhDimParams.end(), 1.5);
+ EXPECT_FLOAT_EQ(awhDimParams.initialCoordinate(), awhDimParams.origin());
+ EXPECT_FLOAT_EQ(awhDimParams.coverDiameter(), 0);
+
+ gmx::InMemorySerializer serializer;
+ awhBiasParams.serialize(&serializer);
+ EXPECT_THAT(awhBiasBuffer, Pointwise(Eq(), serializer.finishAndGetBuffer()));
+}
+
+TEST(SerializationTest, CanSerializeAwhParams)
+{
+ auto awhDimBuffer = awhDimParamSerialized();
+ auto awhDimArrayRef = gmx::arrayRefFromArray(&awhDimBuffer, 1);
+ auto awhParamBuffer = awhParamSerialized(
+ AwhHistogramGrowthType::ExponentialLinear, AwhPotentialType::Convolved, 0.4, 0.5, 1337, awhDimArrayRef, false);
+ gmx::InMemoryDeserializer deserializer(awhParamBuffer, false);
+ AwhParams awhParams(&deserializer);
+ EXPECT_EQ(awhParams.numBias(), 1);
+ EXPECT_EQ(awhParams.seed(), 1337);
+ EXPECT_EQ(awhParams.nstout(), 0);
+ EXPECT_EQ(awhParams.nstSampleCoord(), 1);
+ EXPECT_EQ(awhParams.numSamplesUpdateFreeEnergy(), 10);
+ EXPECT_EQ(awhParams.potential(), AwhPotentialType::Convolved);
+ EXPECT_EQ(awhParams.shareBiasMultisim(), false);
+ const auto& awhBiasParams = awhParams.awhBiasParams()[0];
+ EXPECT_EQ(awhBiasParams.ndim(), 1);
+ EXPECT_EQ(awhBiasParams.targetDistribution(), AwhTargetType::Constant);
+ EXPECT_FLOAT_EQ(awhBiasParams.targetBetaScaling(), 0);
+ EXPECT_FLOAT_EQ(awhBiasParams.targetCutoff(), 0);
+ EXPECT_EQ(awhBiasParams.growthType(), AwhHistogramGrowthType::ExponentialLinear);
+ EXPECT_EQ(awhBiasParams.userPMFEstimate(), 0);
+ EXPECT_FLOAT_EQ(awhBiasParams.initialErrorEstimate(), 0.5 / 0.4);
+ EXPECT_EQ(awhBiasParams.shareGroup(), 0);
+ EXPECT_EQ(awhBiasParams.equilibrateHistogram(), false);
+ const auto& awhDimParams = awhBiasParams.dimParams()[0];
+ EXPECT_EQ(awhDimParams.coordinateProvider(), AwhCoordinateProviderType::Pull);
+ EXPECT_EQ(awhDimParams.coordinateIndex(), 0);
+ EXPECT_FLOAT_EQ(awhDimParams.forceConstant(), 10);
+ EXPECT_FLOAT_EQ(awhDimParams.period(), 0);
+ EXPECT_FLOAT_EQ(awhDimParams.diffusion(), 0.34690997);
+ EXPECT_FLOAT_EQ(awhDimParams.origin(), 0.5);
+ EXPECT_FLOAT_EQ(awhDimParams.end(), 1.5);
+ EXPECT_FLOAT_EQ(awhDimParams.initialCoordinate(), awhDimParams.origin());
+ EXPECT_FLOAT_EQ(awhDimParams.coverDiameter(), 0);
+
+ gmx::InMemorySerializer serializer;
+ awhParams.serialize(&serializer);
+ EXPECT_THAT(awhParamBuffer, Pointwise(Eq(), serializer.finishAndGetBuffer()));
+}
+
+} // namespace test
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_AWH_TEST_SETUP_H
+#define GMX_AWH_TEST_SETUP_H
+
+#include "gmxpre.h"
+
+#include <memory>
+#include <vector>
+
+#include "gromacs/applied_forces/awh/bias.h"
+#include "gromacs/mdtypes/awh_params.h"
+
+namespace gmx
+{
+
+template<typename>
+class ArrayRef;
+
+namespace test
+{
+
+/*! \internal \brief
+ * Prepare a memory buffer with serialized AwhDimParams.
+ */
+std::vector<char> awhDimParamSerialized(
+ AwhCoordinateProviderType inputCoordinateProvider = AwhCoordinateProviderType::Pull,
+ int inputCoordIndex = 0,
+ double inputOrigin = 0.5,
+ double inputEnd = 1.5,
+ double inputPeriod = 0,
+ // Correction for removal of GaussianGeometryFactor/2 in histogram size
+ double inputDiffusion = 0.1 / (0.144129616073222 * 2));
+
+/*! \internal \brief
+ * Struct that gathers all input for setting up and using a Bias
+ */
+struct AwhTestParameters
+{
+ explicit AwhTestParameters(ISerializer* serializer);
+ //! Move constructor
+ AwhTestParameters(AwhTestParameters&& o) noexcept :
+ beta(o.beta),
+ awhParams(std::move(o.awhParams)),
+ dimParams(std::move(o.dimParams))
+ {
+ }
+ //! 1/(kB*T).
+ double beta;
+
+ //! AWH parameters, this is the struct to actually use.
+ AwhParams awhParams;
+ //! Dimension parameters for setting up Bias.
+ std::vector<DimParams> dimParams;
+};
+
+/*! \brief
+ * Helper function to set up the C-style AWH parameters for the test.
+ *
+ * Builds the test input data from serialized data.
+ */
+AwhTestParameters getAwhTestParameters(AwhHistogramGrowthType eawhgrowth,
+ AwhPotentialType eawhpotential,
+ ArrayRef<const std::vector<char>> dimensionParameterBuffers,
+ bool inputUserData,
+ double beta,
+ bool useAwhFep,
+ double inputErrorScaling,
+ int numFepLambdaStates);
+
+} // namespace test
+} // namespace gmx
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
#include <gmock/gmock.h>
+#include <gmock/gmock-matchers.h>
#include <gtest/gtest.h>
#include "gromacs/applied_forces/awh/correlationgrid.h"
#include "gromacs/applied_forces/awh/pointstate.h"
#include "gromacs/mdtypes/awh_params.h"
+#include "gromacs/utility/inmemoryserializer.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/applied_forces/awh/tests/awh_setup.h"
#include "testutils/refdata.h"
#include "testutils/testasserts.h"
namespace test
{
-/*! \internal \brief
- * Struct that gathers all input for setting up and using a Bias
- */
-struct AwhTestParameters
-{
- AwhTestParameters() = default;
- //! Move constructor
- AwhTestParameters(AwhTestParameters&& o) noexcept :
- beta(o.beta),
- awhDimParams(o.awhDimParams),
- awhBiasParams(o.awhBiasParams),
- awhParams(o.awhParams),
- dimParams(std::move(o.dimParams))
- {
- awhBiasParams.dimParams = &awhDimParams;
- awhParams.awhBiasParams = &awhBiasParams;
- }
- double beta; //!< 1/(kB*T)
-
- AwhDimParams awhDimParams; //!< Dimension parameters pointed to by \p awhBiasParams
- AwhBiasParams awhBiasParams; //!< Bias parameters pointed to by \[ awhParams
- AwhParams awhParams; //!< AWH parameters, this is the struct to actually use
-
- std::vector<DimParams> dimParams; //!< Dimension parameters for setting up Bias
-};
-
-//! Helper function to set up the C-style AWH parameters for the test
-static AwhTestParameters getAwhTestParameters(int eawhgrowth, int eawhpotential)
-{
- AwhTestParameters params;
-
- params.beta = 0.4;
-
- AwhDimParams& awhDimParams = params.awhDimParams;
-
- awhDimParams.period = 0;
- // Correction for removal of GaussianGeometryFactor/2 in histogram size
- awhDimParams.diffusion = 0.1 / (0.144129616073222 * 2);
- awhDimParams.origin = 0.5;
- awhDimParams.end = 1.5;
- awhDimParams.coordValueInit = awhDimParams.origin;
- awhDimParams.coverDiameter = 0;
- awhDimParams.eCoordProvider = eawhcoordproviderPULL;
-
- AwhBiasParams& awhBiasParams = params.awhBiasParams;
-
- awhBiasParams.ndim = 1;
- awhBiasParams.dimParams = &awhDimParams;
- awhBiasParams.eTarget = eawhtargetCONSTANT;
- awhBiasParams.targetBetaScaling = 0;
- awhBiasParams.targetCutoff = 0;
- awhBiasParams.eGrowth = eawhgrowth;
- awhBiasParams.bUserData = FALSE;
- awhBiasParams.errorInitial = 0.5 / params.beta;
- awhBiasParams.shareGroup = 0;
- awhBiasParams.equilibrateHistogram = FALSE;
-
- double convFactor = 1;
- double k = 1000;
- int64_t seed = 93471803;
-
- params.dimParams.push_back(DimParams::pullDimParams(convFactor, k, params.beta));
-
- AwhParams& awhParams = params.awhParams;
-
- awhParams.numBias = 1;
- awhParams.awhBiasParams = &awhBiasParams;
- awhParams.seed = seed;
- awhParams.nstOut = 0;
- awhParams.nstSampleCoord = 1;
- awhParams.numSamplesUpdateFreeEnergy = 10;
- awhParams.ePotential = eawhpotential;
- awhParams.shareBiasMultisim = FALSE;
-
- return params;
-}
-
//! Database of 21 test coordinates that represent a trajectory */
-const double g_coords[] = { 0.62, 0.70, 0.68, 0.80, 0.93, 0.87, 1.16, 1.14, 0.95, 0.89, 0.91,
- 0.86, 0.88, 0.79, 0.75, 0.82, 0.74, 0.70, 0.68, 0.71, 0.73 };
+constexpr double g_coords[] = { 0.62, 0.70, 0.68, 0.80, 0.93, 0.87, 1.16, 1.14, 0.95, 0.89, 0.91,
+ 0.86, 0.88, 0.79, 0.75, 0.82, 0.74, 0.70, 0.68, 0.71, 0.73 };
//! Convenience typedef: growth type enum, potential type enum, disable update skips
-typedef std::tuple<int, int, BiasParams::DisableUpdateSkips> BiasTestParameters;
+typedef std::tuple<AwhHistogramGrowthType, AwhPotentialType, BiasParams::DisableUpdateSkips> BiasTestParameters;
/*! \brief Test fixture for testing Bias updates
*/
class BiasTest : public ::testing::TestWithParam<BiasTestParameters>
{
+private:
+ //! Storage for test parameters.
+ std::unique_ptr<AwhTestParameters> params_;
+
public:
//! Random seed for AWH MC sampling
int64_t seed_;
-
//! Coordinates representing a trajectory in time
std::vector<double> coordinates_;
//! The awh Bias
* and disableUpdateSkips do not affect the point state.
* But the reference data will also ensure this.
*/
- int eawhgrowth;
- int eawhpotential;
+ AwhHistogramGrowthType eawhgrowth;
+ AwhPotentialType eawhpotential;
BiasParams::DisableUpdateSkips disableUpdateSkips;
std::tie(eawhgrowth, eawhpotential, disableUpdateSkips) = GetParam();
* The idea is to, among other things, have part of the interval
* not covered by samples.
*/
- const AwhTestParameters params = getAwhTestParameters(eawhgrowth, eawhpotential);
+ auto awhDimBuffer = awhDimParamSerialized();
+ auto awhDimArrayRef = gmx::arrayRefFromArray(&awhDimBuffer, 1);
+ params_ = std::make_unique<AwhTestParameters>(getAwhTestParameters(
+ eawhgrowth, eawhpotential, awhDimArrayRef, false, 0.4, false, 0.5, 0));
- seed_ = params.awhParams.seed;
+ seed_ = params_->awhParams.seed();
- double mdTimeStep = 0.1;
+ constexpr double mdTimeStep = 0.1;
int numSamples = coordinates_.size() - 1; // No sample taken at step 0
- GMX_RELEASE_ASSERT(numSamples % params.awhParams.numSamplesUpdateFreeEnergy == 0,
+ GMX_RELEASE_ASSERT(numSamples % params_->awhParams.numSamplesUpdateFreeEnergy() == 0,
"This test is intended to reproduce the situation when the might need "
"to write output during a normal AWH run, therefore the number of "
"samples should be a multiple of the free-energy update interval (but "
"the test should also runs fine without this condition).");
- bias_ = std::make_unique<Bias>(-1, params.awhParams, params.awhBiasParams, params.dimParams,
- params.beta, mdTimeStep, 1, "", Bias::ThisRankWillDoIO::No,
+ bias_ = std::make_unique<Bias>(-1,
+ params_->awhParams,
+ params_->awhParams.awhBiasParams()[0],
+ params_->dimParams,
+ params_->beta,
+ mdTimeStep,
+ 1,
+ "",
+ Bias::ThisRankWillDoIO::No,
disableUpdateSkips);
}
};
awh_dvec coordValue = { coord, 0, 0, 0 };
double potential = 0;
- gmx::ArrayRef<const double> biasForce =
- bias.calcForceAndUpdateBias(coordValue, {}, {}, &potential, &potentialJump, nullptr,
- nullptr, step, step, seed_, nullptr);
+ gmx::ArrayRef<const double> biasForce = bias.calcForceAndUpdateBias(
+ coordValue, {}, {}, &potential, &potentialJump, nullptr, nullptr, step, step, seed_, nullptr);
force.push_back(biasForce[0]);
pot.push_back(potential);
}
std::vector<double> pointBias, logPmfsum;
- for (auto& point : bias.state().points())
+ for (const auto& point : bias.state().points())
{
pointBias.push_back(point.bias());
logPmfsum.push_back(point.logPmfSum());
*/
INSTANTIATE_TEST_CASE_P(WithParameters,
BiasTest,
- ::testing::Combine(::testing::Values(eawhgrowthLINEAR, eawhgrowthEXP_LINEAR),
- ::testing::Values(eawhpotentialUMBRELLA, eawhpotentialCONVOLVED),
+ ::testing::Combine(::testing::Values(AwhHistogramGrowthType::Linear,
+ AwhHistogramGrowthType::ExponentialLinear),
+ ::testing::Values(AwhPotentialType::Umbrella,
+ AwhPotentialType::Convolved),
::testing::Values(BiasParams::DisableUpdateSkips::yes,
BiasParams::DisableUpdateSkips::no)));
// Test that we detect coverings and exit the initial stage at the correct step
TEST(BiasTest, DetectsCovering)
{
- const AwhTestParameters params = getAwhTestParameters(eawhgrowthEXP_LINEAR, eawhpotentialCONVOLVED);
- const AwhDimParams& awhDimParams = params.awhParams.awhBiasParams[0].dimParams[0];
-
- const double mdTimeStep = 0.1;
-
- Bias bias(-1, params.awhParams, params.awhBiasParams, params.dimParams, params.beta, mdTimeStep,
- 1, "", Bias::ThisRankWillDoIO::No);
+ const std::vector<char> serializedAwhParametersPerDim = awhDimParamSerialized();
+ auto awhDimArrayRef = gmx::arrayRefFromArray(&serializedAwhParametersPerDim, 1);
+ const AwhTestParameters params = getAwhTestParameters(AwhHistogramGrowthType::ExponentialLinear,
+ AwhPotentialType::Convolved,
+ awhDimArrayRef,
+ false,
+ 0.4,
+ false,
+ 0.5,
+ 0);
+ const AwhDimParams& awhDimParams = params.awhParams.awhBiasParams()[0].dimParams()[0];
+
+ constexpr double mdTimeStep = 0.1;
+
+ Bias bias(-1,
+ params.awhParams,
+ params.awhParams.awhBiasParams()[0],
+ params.dimParams,
+ params.beta,
+ mdTimeStep,
+ 1,
+ "",
+ Bias::ThisRankWillDoIO::No);
/* We use a trajectory of the sum of two sines to cover the reaction
* coordinate range in a semi-realistic way. The period is 4*pi=12.57.
* We get out of the initial stage after 4 coverings at step 300.
*/
- const int64_t exitStepRef = 300;
- const double midPoint = 0.5 * (awhDimParams.end + awhDimParams.origin);
- const double halfWidth = 0.5 * (awhDimParams.end - awhDimParams.origin);
+ constexpr int64_t exitStepRef = 300;
+ const double midPoint = 0.5 * (awhDimParams.end() + awhDimParams.origin());
+ const double halfWidth = 0.5 * (awhDimParams.end() - awhDimParams.origin());
bool inInitialStage = bias.state().inInitialStage();
/* Normally this loop exits at exitStepRef, but we extend with failure */
awh_dvec coordValue = { coord, 0, 0, 0 };
double potential = 0;
double potentialJump = 0;
- bias.calcForceAndUpdateBias(coordValue, {}, {}, &potential, &potentialJump, nullptr,
- nullptr, step, step, params.awhParams.seed, nullptr);
+ bias.calcForceAndUpdateBias(coordValue,
+ {},
+ {},
+ &potential,
+ &potentialJump,
+ nullptr,
+ nullptr,
+ step,
+ step,
+ params.awhParams.seed(),
+ nullptr);
inInitialStage = bias.state().inInitialStage();
if (!inInitialStage)
#include "gromacs/mdtypes/awh_params.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/applied_forces/awh/tests/awh_setup.h"
#include "testutils/refdata.h"
#include "testutils/testasserts.h"
{
//! The number of lambda states to use in the tests.
-const int numLambdaStates = 16;
+static constexpr int c_numLambdaStates = 16;
-/*! \internal \brief
- * Struct that gathers all input for setting up and using a Bias
- */
-struct AwhFepLambdaStateTestParameters
-{
- AwhFepLambdaStateTestParameters() = default;
- //! Move constructor
- AwhFepLambdaStateTestParameters(AwhFepLambdaStateTestParameters&& o) noexcept :
- beta(o.beta),
- awhDimParams(o.awhDimParams),
- awhBiasParams(o.awhBiasParams),
- awhParams(o.awhParams),
- dimParams(std::move(o.dimParams))
- {
- awhBiasParams.dimParams = &awhDimParams;
- awhParams.awhBiasParams = &awhBiasParams;
- }
- double beta; //!< 1/(kB*T)
-
- AwhDimParams awhDimParams; //!< Dimension parameters pointed to by \p awhBiasParams
- AwhBiasParams awhBiasParams; //!< Bias parameters pointed to by \[ awhParams
- AwhParams awhParams; //!< AWH parameters, this is the struct to actually use
-
- std::vector<DimParams> dimParams; //!< Dimension parameters for setting up Bias
-};
-
-//! Helper function to set up the C-style AWH parameters for the test
-static AwhFepLambdaStateTestParameters getAwhFepLambdaTestParameters(int eawhgrowth, int eawhpotential)
-{
- AwhFepLambdaStateTestParameters params;
-
- params.beta = 0.4;
-
- AwhDimParams& awhDimParams = params.awhDimParams;
-
- awhDimParams.period = 0;
- // Correction for removal of GaussianGeometryFactor/2 in histogram size
- awhDimParams.diffusion = 1e-4 / (0.12927243028700 * 2);
- awhDimParams.origin = 0;
- awhDimParams.end = numLambdaStates - 1;
- awhDimParams.coordValueInit = awhDimParams.origin;
- awhDimParams.coverDiameter = 0;
- awhDimParams.eCoordProvider = eawhcoordproviderFREE_ENERGY_LAMBDA;
-
- AwhBiasParams& awhBiasParams = params.awhBiasParams;
-
- awhBiasParams.ndim = 1;
- awhBiasParams.dimParams = &awhDimParams;
- awhBiasParams.eTarget = eawhtargetCONSTANT;
- awhBiasParams.targetBetaScaling = 0;
- awhBiasParams.targetCutoff = 0;
- awhBiasParams.eGrowth = eawhgrowth;
- awhBiasParams.bUserData = FALSE;
- awhBiasParams.errorInitial = 1.0 / params.beta;
- awhBiasParams.shareGroup = 0;
- awhBiasParams.equilibrateHistogram = FALSE;
-
- int64_t seed = 93471803;
-
- params.dimParams.push_back(DimParams::fepLambdaDimParams(numLambdaStates, params.beta));
-
- AwhParams& awhParams = params.awhParams;
-
- awhParams.numBias = 1;
- awhParams.awhBiasParams = &awhBiasParams;
- awhParams.seed = seed;
- awhParams.nstOut = 0;
- awhParams.nstSampleCoord = 1;
- awhParams.numSamplesUpdateFreeEnergy = 10;
- awhParams.ePotential = eawhpotential;
- awhParams.shareBiasMultisim = FALSE;
-
- return params;
-}
//! Convenience typedef: growth type enum, potential type enum, disable update skips
-typedef std::tuple<int, int, BiasParams::DisableUpdateSkips> BiasTestParameters;
+typedef std::tuple<AwhHistogramGrowthType, AwhPotentialType, BiasParams::DisableUpdateSkips> BiasTestParameters;
/*! \brief Test fixture for testing Bias updates
*/
class BiasFepLambdaStateTest : public ::testing::TestWithParam<BiasTestParameters>
{
+private:
+ //! Storage for test parameters.
+ std::unique_ptr<AwhTestParameters> params_;
+
public:
//! Random seed for AWH MC sampling
int64_t seed_;
* and disableUpdateSkips do not affect the point state.
* But the reference data will also ensure this.
*/
- int eawhgrowth;
- int eawhpotential;
+ AwhHistogramGrowthType eawhgrowth;
+ AwhPotentialType eawhpotential;
BiasParams::DisableUpdateSkips disableUpdateSkips;
std::tie(eawhgrowth, eawhpotential, disableUpdateSkips) = GetParam();
/* Set up a basic AWH setup with a single, 1D bias with parameters
* such that we can measure the effects of different parameters.
*/
- const AwhFepLambdaStateTestParameters params =
- getAwhFepLambdaTestParameters(eawhgrowth, eawhpotential);
-
- seed_ = params.awhParams.seed;
+ constexpr AwhCoordinateProviderType coordinateProvider = AwhCoordinateProviderType::FreeEnergyLambda;
+ constexpr int coordIndex = 0;
+ constexpr double origin = 0;
+ constexpr double end = c_numLambdaStates - 1;
+ constexpr double period = 0;
+ // Correction for removal of GaussianGeometryFactor/2 in histogram size
+ constexpr double diffusion = 1e-4 / (0.12927243028700 * 2);
+ const auto awhDimBuffer =
+ awhDimParamSerialized(coordinateProvider, coordIndex, origin, end, period, diffusion);
+ const auto awhDimArrayRef = gmx::arrayRefFromArray(&awhDimBuffer, 1);
+ params_ = std::make_unique<AwhTestParameters>(getAwhTestParameters(
+ eawhgrowth, eawhpotential, awhDimArrayRef, false, 0.4, true, 1.0, c_numLambdaStates));
+
+ seed_ = params_->awhParams.seed();
double mdTimeStep = 0.1;
- bias_ = std::make_unique<Bias>(-1, params.awhParams, params.awhBiasParams, params.dimParams,
- params.beta, mdTimeStep, 1, "", Bias::ThisRankWillDoIO::No,
+ bias_ = std::make_unique<Bias>(-1,
+ params_->awhParams,
+ params_->awhParams.awhBiasParams()[0],
+ params_->dimParams,
+ params_->beta,
+ mdTimeStep,
+ 1,
+ "",
+ Bias::ThisRankWillDoIO::No,
disableUpdateSkips);
}
};
int nSteps = 501;
/* Some energies to use as base values (to which some noise is added later on). */
- std::vector<double> neighborLambdaEnergies(numLambdaStates);
- std::vector<double> neighborLambdaDhdl(numLambdaStates);
+ std::vector<double> neighborLambdaEnergies(c_numLambdaStates);
+ std::vector<double> neighborLambdaDhdl(c_numLambdaStates);
const double magnitude = 12.0;
- for (int i = 0; i < numLambdaStates; i++)
+ for (int i = 0; i < c_numLambdaStates; i++)
{
neighborLambdaEnergies[i] = magnitude * std::sin(i * 0.1);
neighborLambdaDhdl[i] = magnitude * std::cos(i * 0.1);
int umbrellaGridpointIndex = bias.state().coordState().umbrellaGridpoint();
awh_dvec coordValue = { bias.getGridCoordValue(umbrellaGridpointIndex)[0], 0, 0, 0 };
double potential = 0;
- gmx::ArrayRef<const double> biasForce = bias.calcForceAndUpdateBias(
- coordValue, neighborLambdaEnergies, neighborLambdaDhdl, &potential, &potentialJump,
- nullptr, nullptr, step * mdTimeStep, step, seed_, nullptr);
+ gmx::ArrayRef<const double> biasForce = bias.calcForceAndUpdateBias(coordValue,
+ neighborLambdaEnergies,
+ neighborLambdaDhdl,
+ &potential,
+ &potentialJump,
+ nullptr,
+ nullptr,
+ step * mdTimeStep,
+ step,
+ seed_,
+ nullptr);
force.push_back(biasForce[0]);
pot.push_back(potential);
}
std::vector<double> pointBias, logPmfsum;
- for (auto& point : bias.state().points())
+ for (const auto& point : bias.state().points())
{
pointBias.push_back(point.bias());
logPmfsum.push_back(point.logPmfSum());
*/
INSTANTIATE_TEST_CASE_P(WithParameters,
BiasFepLambdaStateTest,
- ::testing::Combine(::testing::Values(eawhgrowthLINEAR, eawhgrowthEXP_LINEAR),
- ::testing::Values(eawhpotentialUMBRELLA),
+ ::testing::Combine(::testing::Values(AwhHistogramGrowthType::Linear,
+ AwhHistogramGrowthType::ExponentialLinear),
+ ::testing::Values(AwhPotentialType::Umbrella),
::testing::Values(BiasParams::DisableUpdateSkips::yes,
BiasParams::DisableUpdateSkips::no)));
// Test that we detect coverings and exit the initial stage at the correct step
TEST(BiasFepLambdaStateTest, DetectsCovering)
{
- const AwhFepLambdaStateTestParameters params =
- getAwhFepLambdaTestParameters(eawhgrowthEXP_LINEAR, eawhpotentialUMBRELLA);
+ constexpr AwhCoordinateProviderType coordinateProvider = AwhCoordinateProviderType::FreeEnergyLambda;
+ constexpr int coordIndex = 0;
+ constexpr double origin = 0;
+ constexpr double end = c_numLambdaStates - 1;
+ constexpr double period = 0;
+ constexpr double diffusion = 1e-4 / (0.12927243028700 * 2);
+ auto awhDimBuffer =
+ awhDimParamSerialized(coordinateProvider, coordIndex, origin, end, period, diffusion);
+ auto awhDimArrayRef = gmx::arrayRefFromArray(&awhDimBuffer, 1);
+ const AwhTestParameters params(getAwhTestParameters(AwhHistogramGrowthType::ExponentialLinear,
+ AwhPotentialType::Umbrella,
+ awhDimArrayRef,
+ false,
+ 0.4,
+ true,
+ 1.0,
+ c_numLambdaStates));
const double mdTimeStep = 0.1;
- Bias bias(-1, params.awhParams, params.awhBiasParams, params.dimParams, params.beta, mdTimeStep,
- 1, "", Bias::ThisRankWillDoIO::No);
+ Bias bias(-1,
+ params.awhParams,
+ params.awhParams.awhBiasParams()[0],
+ params.dimParams,
+ params.beta,
+ mdTimeStep,
+ 1,
+ "",
+ Bias::ThisRankWillDoIO::No);
const int64_t exitStepRef = 320;
bool inInitialStage = bias.state().inInitialStage();
/* Some energies to use as base values (to which some noise is added later on). */
- std::vector<double> neighborLambdaEnergies(numLambdaStates);
- std::vector<double> neighborLambdaDhdl(numLambdaStates);
+ std::vector<double> neighborLambdaEnergies(c_numLambdaStates);
+ std::vector<double> neighborLambdaDhdl(c_numLambdaStates);
const double magnitude = 12.0;
- for (int i = 0; i < numLambdaStates; i++)
+ for (int i = 0; i < c_numLambdaStates; i++)
{
neighborLambdaEnergies[i] = magnitude * std::sin(i * 0.1);
neighborLambdaDhdl[i] = magnitude * std::cos(i * 0.1);
double potential = 0;
double potentialJump = 0;
- bias.calcForceAndUpdateBias(coordValue, neighborLambdaEnergies, neighborLambdaDhdl,
- &potential, &potentialJump, nullptr, nullptr, step, step,
- params.awhParams.seed, nullptr);
+ bias.calcForceAndUpdateBias(coordValue,
+ neighborLambdaEnergies,
+ neighborLambdaDhdl,
+ &potential,
+ &potentialJump,
+ nullptr,
+ nullptr,
+ step,
+ step,
+ params.awhParams.seed(),
+ nullptr);
inInitialStage = bias.state().inInitialStage();
if (!inInitialStage)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/awh_params.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/inmemoryserializer.h"
+#include "gromacs/applied_forces/awh/tests/awh_setup.h"
#include "testutils/testasserts.h"
namespace gmx
*/
const int numDim = 2;
- std::vector<AwhDimParams> awhDimParams(numDim);
-
- awhDimParams[0].origin = -5;
- awhDimParams[0].end = 5;
- awhDimParams[0].period = 10;
-
- awhDimParams[1].origin = 0.5;
- awhDimParams[1].end = 2.0;
- awhDimParams[1].period = 0;
+ std::vector<AwhDimParams> awhDimParams;
+ AwhCoordinateProviderType coordinateProvider = AwhCoordinateProviderType::Pull;
+ double diffusion = 0.1;
+ {
+ int coordIndex = 0;
+ double origin = -5;
+ double end = 5;
+ double period = 10;
+ auto awhDimBuffer =
+ awhDimParamSerialized(coordinateProvider, coordIndex, origin, end, period, diffusion);
+ gmx::InMemoryDeserializer serializer(awhDimBuffer, false);
+ awhDimParams.emplace_back(AwhDimParams(&serializer));
+ }
+ {
+ int coordIndex = 1;
+ double origin = 0.5;
+ double end = 2;
+ double period = 0;
+ auto awhDimBuffer =
+ awhDimParamSerialized(coordinateProvider, coordIndex, origin, end, period, diffusion);
+ gmx::InMemoryDeserializer serializer(awhDimBuffer, false);
+ awhDimParams.emplace_back(AwhDimParams(&serializer));
+ }
const real conversionFactor = 1;
const real beta = 3.0;
dimParams.push_back(DimParams::pullDimParams(conversionFactor, 1 / (beta * 0.7 * 0.7), beta));
dimParams.push_back(DimParams::pullDimParams(conversionFactor, 1 / (beta * 0.1 * 0.1), beta));
- BiasGrid grid(dimParams, awhDimParams.data());
+ BiasGrid grid(dimParams, awhDimParams);
const int numPoints = grid.numPoints();
haveCorrectNumNeighbors = false;
}
- for (auto& j : point.neighbor)
+ for (const auto& j : point.neighbor)
{
if (j >= 0 && j < numPoints)
{
}
/* Clear the marked points in the checking grid */
- for (auto& neighbor : point.neighbor)
+ for (const auto& neighbor : point.neighbor)
{
if (neighbor >= 0 && neighbor < numPoints)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/applied_forces/awh/tests/awh_setup.h"
#include "testutils/testasserts.h"
#include "testutils/testfilemanager.h"
namespace test
{
-/*! \internal \brief
- * Struct that gathers all input for setting up and using a Bias
- */
-struct AwhTestParameters
-{
- double beta; //!< 1/(kB*T)
-
- AwhDimParams awhDimParams[2]; //!< Dimension parameters pointed to by \p awhBiasParams
- AwhBiasParams awhBiasParams; //!< Bias parameters pointed to by \[ awhParams
- AwhParams awhParams; //!< AWH parameters, this is the struct to actually use
-};
-
-//! Helper function to set up the C-style AWH parameters for the test
-static AwhTestParameters getAwhTestParameters()
-{
- AwhTestParameters params;
-
- params.beta = 1.0;
-
- AwhParams& awhParams = params.awhParams;
- snew(params.awhParams.awhBiasParams, 1);
- AwhBiasParams& awhBiasParams = params.awhParams.awhBiasParams[0];
- snew(awhBiasParams.dimParams, 2);
-
- AwhDimParams& awhDimParams0 = awhBiasParams.dimParams[0];
-
- awhDimParams0.period = 0;
- awhDimParams0.diffusion = 0.1;
- awhDimParams0.origin = 0.5;
- awhDimParams0.end = 1.5;
- awhDimParams0.coordValueInit = awhDimParams0.origin;
- awhDimParams0.coverDiameter = 0;
- awhDimParams0.eCoordProvider = eawhcoordproviderPULL;
-
- AwhDimParams& awhDimParams1 = awhBiasParams.dimParams[1];
-
- awhDimParams1.period = 0;
- awhDimParams1.diffusion = 0.1;
- awhDimParams1.origin = 0.8;
- awhDimParams1.end = 1.3;
- awhDimParams1.coordValueInit = awhDimParams1.origin;
- awhDimParams1.coverDiameter = 0;
- awhDimParams1.eCoordProvider = eawhcoordproviderPULL;
-
- awhBiasParams.ndim = 2;
- awhBiasParams.eTarget = eawhtargetCONSTANT;
- awhBiasParams.targetBetaScaling = 0;
- awhBiasParams.targetCutoff = 0;
- awhBiasParams.eGrowth = eawhgrowthLINEAR;
- awhBiasParams.bUserData = TRUE;
- awhBiasParams.errorInitial = 0.5;
- awhBiasParams.shareGroup = 0;
- awhBiasParams.equilibrateHistogram = FALSE;
-
- awhParams.numBias = 1;
- awhParams.seed = 93471803;
- awhParams.nstOut = 0;
- awhParams.nstSampleCoord = 1;
- awhParams.numSamplesUpdateFreeEnergy = 10;
- awhParams.ePotential = eawhpotentialCONVOLVED;
- awhParams.shareBiasMultisim = FALSE;
-
- return params;
-}
-
/*! \brief Test fixture for testing Bias updates
*/
class BiasStateTest : public ::testing::TestWithParam<const char*>
{
+private:
+ std::unique_ptr<AwhTestParameters> params_;
+
public:
std::unique_ptr<BiasState> biasState_; //!< The bias state
BiasStateTest()
{
- AwhTestParameters params = getAwhTestParameters();
- const AwhParams& awhParams = params.awhParams;
- const AwhBiasParams& awhBiasParams = awhParams.awhBiasParams[0];
+ std::vector<std::vector<char>> awhDimParameters;
+ AwhCoordinateProviderType coordinateProvider = AwhCoordinateProviderType::Pull;
+ double diffusion = 0.1;
+ {
+ int coordIndex = 0;
+ double origin = 0.5;
+ double end = 1.5;
+ double period = 0;
+ awhDimParameters.emplace_back(awhDimParamSerialized(
+ coordinateProvider, coordIndex, origin, end, period, diffusion));
+ }
+ {
+ int coordIndex = 1;
+ double origin = 0.8;
+ double end = 1.3;
+ double period = 0;
+ awhDimParameters.emplace_back(awhDimParamSerialized(
+ coordinateProvider, coordIndex, origin, end, period, diffusion));
+ }
+ params_ = std::make_unique<AwhTestParameters>(getAwhTestParameters(
+ AwhHistogramGrowthType::Linear, AwhPotentialType::Convolved, awhDimParameters, true, 1.0, false, 0.5, 0));
+ const AwhParams& awhParams = params_->awhParams;
+ const AwhBiasParams& awhBiasParams = awhParams.awhBiasParams()[0];
std::vector<DimParams> dimParams;
- dimParams.push_back(DimParams::pullDimParams(1.0, 15.0, params.beta));
- dimParams.push_back(DimParams::pullDimParams(1.0, 15.0, params.beta));
- BiasGrid grid(dimParams, awhBiasParams.dimParams);
- BiasParams biasParams(awhParams, awhBiasParams, dimParams, 1.0, 1.0,
- BiasParams::DisableUpdateSkips::no, 1, grid.axis(), 0);
+ dimParams.push_back(DimParams::pullDimParams(1.0, 15.0, params_->beta));
+ dimParams.push_back(DimParams::pullDimParams(1.0, 15.0, params_->beta));
+ BiasGrid grid(dimParams, awhBiasParams.dimParams());
+ BiasParams biasParams(
+ awhParams, awhBiasParams, dimParams, 1.0, 1.0, BiasParams::DisableUpdateSkips::no, 1, grid.axis(), 0);
biasState_ = std::make_unique<BiasState>(awhBiasParams, 1.0, dimParams, grid);
// Here we initialize the grid point state using the input file
std::string filename = gmx::test::TestFileManager::getInputFilePath(GetParam());
- biasState_->initGridPointState(awhBiasParams, dimParams, grid, biasParams, filename,
- params.awhParams.numBias);
-
- sfree(params.awhParams.awhBiasParams[0].dimParams);
- sfree(params.awhParams.awhBiasParams);
+ biasState_->initGridPointState(
+ awhBiasParams, dimParams, grid, biasParams, filename, params_->awhParams.numBias());
}
};
#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/keyvaluetreebuilder.h"
-#include "gromacs/utility/mdmodulenotification.h"
+#include "gromacs/utility/mdmodulesnotifiers.h"
#include "densityfittingforceprovider.h"
#include "densityfittingoptions.h"
* the DensityFitting class needs access to parameters that become available
* only during simulation setup.
*
- * This class collects these parameters via MdModuleNotifications in the
+ * This class collects these parameters via MDModulesNotifiers in the
* simulation setup phase and provides a check if all necessary parameters have
* been provided.
*/
GMX_THROW(InternalError("Need to set reference density before normalizing it."));
}
- const real sumOfDensityData = std::accumulate(begin(referenceDensity_->asView()),
- end(referenceDensity_->asView()), 0.);
+ const real sumOfDensityData = std::accumulate(
+ begin(referenceDensity_->asView()), end(referenceDensity_->asView()), 0.);
for (float& referenceDensityVoxel : referenceDensity_->asView())
{
referenceDensityVoxel /= sumOfDensityData;
}
}
- /*! \brief Set the periodic boundary condition via MdModuleNotifier.
+ /*! \brief Set the periodic boundary condition via MDModuleNotifier.
*
* The pbc type is wrapped in PeriodicBoundaryConditionType to
- * allow the MdModuleNotifier to statically distinguish the callback
+ * allow the MDModuleNotifier to statically distinguish the callback
* function type from other 'int' function callbacks.
*
* \param[in] pbcType enumerates the periodic boundary condition.
void setSimulationTimeStep(double timeStep) { simulationTimeStep_ = timeStep; }
//! Return the simulation time step
- double simulationTimeStep() { return simulationTimeStep_; }
+ double simulationTimeStep() const { return simulationTimeStep_; }
private:
//! The reference density to fit to
/*! \brief Request to be notified during pre-processing.
*
- * \param[in] notifier allows the module to subscribe to notifications from MdModules.
+ * \param[in] notifiers allows the module to subscribe to notifications from MDModules.
*
* The density fitting code subscribes to these notifications:
* - setting atom group indices in the densityFittingOptions_ from an
* key-value-tree during pre-processing by a function taking a
* KeyValueTreeObjectBuilder as parameter
*/
- void subscribeToPreProcessingNotifications(MdModulesNotifier* notifier) override
+ void subscribeToPreProcessingNotifications(MDModulesNotifiers* notifiers) override
{
- // Callbacks for several kinds of MdModuleNotification are created
+ // Callbacks for several kinds of MDModulesNotifier are created
// and subscribed, and will be dispatched correctly at run time
// based on the type of the parameter required by the lambda.
const auto setFitGroupIndicesFunction = [this](const IndexGroupsAndNames& indexGroupsAndNames) {
densityFittingOptions_.setFitGroupIndices(indexGroupsAndNames);
};
- notifier->preProcessingNotifications_.subscribe(setFitGroupIndicesFunction);
+ notifiers->preProcessingNotifier_.subscribe(setFitGroupIndicesFunction);
// Writing internal parameters during pre-processing
const auto writeInternalParametersFunction = [this](KeyValueTreeObjectBuilder treeBuilder) {
densityFittingOptions_.writeInternalParametersToKvt(treeBuilder);
};
- notifier->preProcessingNotifications_.subscribe(writeInternalParametersFunction);
+ notifiers->preProcessingNotifier_.subscribe(writeInternalParametersFunction);
// Checking for consistency with all .mdp options
const auto checkEnergyCaluclationFrequencyFunction =
[this](EnergyCalculationFrequencyErrors* energyCalculationFrequencyErrors) {
densityFittingOptions_.checkEnergyCaluclationFrequency(energyCalculationFrequencyErrors);
};
- notifier->preProcessingNotifications_.subscribe(checkEnergyCaluclationFrequencyFunction);
+ notifiers->preProcessingNotifier_.subscribe(checkEnergyCaluclationFrequencyFunction);
}
/*! \brief Request to be notified.
* - the type of periodic boundary conditions that are used
* by taking a PeriodicBoundaryConditionType as parameter
* - the writing of checkpoint data
- * by taking a MdModulesWriteCheckpointData as parameter
+ * by taking a MDModulesWriteCheckpointData as parameter
* - the reading of checkpoint data
- * by taking a MdModulesCheckpointReadingDataOnMaster as parameter
+ * by taking a MDModulesCheckpointReadingDataOnMaster as parameter
* - the broadcasting of checkpoint data
- * by taking MdModulesCheckpointReadingBroadcast as parameter
+ * by taking MDModulesCheckpointReadingBroadcast as parameter
*/
- void subscribeToSimulationSetupNotifications(MdModulesNotifier* notifier) override
+ void subscribeToSimulationSetupNotifications(MDModulesNotifiers* notifiers) override
{
if (!densityFittingOptions_.active())
{
const auto readInternalParametersFunction = [this](const KeyValueTreeObject& tree) {
densityFittingOptions_.readInternalParametersFromKvt(tree);
};
- notifier->simulationSetupNotifications_.subscribe(readInternalParametersFunction);
+ notifiers->simulationSetupNotifier_.subscribe(readInternalParametersFunction);
// constructing local atom sets during simulation setup
const auto setLocalAtomSetFunction = [this](LocalAtomSetManager* localAtomSetManager) {
this->constructLocalAtomSet(localAtomSetManager);
};
- notifier->simulationSetupNotifications_.subscribe(setLocalAtomSetFunction);
+ notifiers->simulationSetupNotifier_.subscribe(setLocalAtomSetFunction);
// constructing local atom sets during simulation setup
const auto setPeriodicBoundaryContionsFunction = [this](const PbcType& pbc) {
this->densityFittingSimulationParameters_.setPeriodicBoundaryConditionType(pbc);
};
- notifier->simulationSetupNotifications_.subscribe(setPeriodicBoundaryContionsFunction);
+ notifiers->simulationSetupNotifier_.subscribe(setPeriodicBoundaryContionsFunction);
// setting the simulation time step
const auto setSimulationTimeStepFunction = [this](const SimulationTimeStep& simulationTimeStep) {
this->densityFittingSimulationParameters_.setSimulationTimeStep(simulationTimeStep.delta_t);
};
- notifier->simulationSetupNotifications_.subscribe(setSimulationTimeStepFunction);
+ notifiers->simulationSetupNotifier_.subscribe(setSimulationTimeStepFunction);
// adding output to energy file
const auto requestEnergyOutput =
- [this](MdModulesEnergyOutputToDensityFittingRequestChecker* energyOutputRequest) {
+ [this](MDModulesEnergyOutputToDensityFittingRequestChecker* energyOutputRequest) {
this->setEnergyOutputRequest(energyOutputRequest);
};
- notifier->simulationSetupNotifications_.subscribe(requestEnergyOutput);
+ notifiers->simulationSetupNotifier_.subscribe(requestEnergyOutput);
// writing checkpoint data
- const auto checkpointDataWriting = [this](MdModulesWriteCheckpointData checkpointData) {
+ const auto checkpointDataWriting = [this](MDModulesWriteCheckpointData checkpointData) {
forceProvider_->writeCheckpointData(checkpointData, DensityFittingModuleInfo::name_);
};
- notifier->checkpointingNotifications_.subscribe(checkpointDataWriting);
+ notifiers->checkpointingNotifier_.subscribe(checkpointDataWriting);
// reading checkpoint data
- const auto checkpointDataReading = [this](MdModulesCheckpointReadingDataOnMaster checkpointData) {
+ const auto checkpointDataReading = [this](MDModulesCheckpointReadingDataOnMaster checkpointData) {
densityFittingState_.readState(checkpointData.checkpointedData_,
DensityFittingModuleInfo::name_);
};
- notifier->checkpointingNotifications_.subscribe(checkpointDataReading);
+ notifiers->checkpointingNotifier_.subscribe(checkpointDataReading);
// broadcasting checkpoint data
- const auto checkpointDataBroadcast = [this](MdModulesCheckpointReadingBroadcast checkpointData) {
+ const auto checkpointDataBroadcast = [this](MDModulesCheckpointReadingBroadcast checkpointData) {
densityFittingState_.broadcastState(checkpointData.communicator_, checkpointData.isParallelRun_);
};
- notifier->checkpointingNotifications_.subscribe(checkpointDataBroadcast);
+ notifiers->checkpointingNotifier_.subscribe(checkpointDataBroadcast);
}
//! From IMDModule
densityFittingSimulationParameters_.normalizeReferenceDensity();
}
forceProvider_ = std::make_unique<DensityFittingForceProvider>(
- parameters, densityFittingSimulationParameters_.referenceDensity(),
+ parameters,
+ densityFittingSimulationParameters_.referenceDensity(),
densityFittingSimulationParameters_.transformationToDensityLattice(),
densityFittingSimulationParameters_.localAtomSet(),
densityFittingSimulationParameters_.periodicBoundaryConditionType(),
- densityFittingSimulationParameters_.simulationTimeStep(), densityFittingState_);
+ densityFittingSimulationParameters_.simulationTimeStep(),
+ densityFittingState_);
forceProviders->addForceProvider(forceProvider_.get());
}
}
/*! \brief Set up the local atom sets that are used by this module.
*
- * \note When density fitting is set up with MdModuleNotification in
+ * \note When density fitting is set up with MDModulesNotifier in
* the constructor, this function is called back.
*
* \param[in] localAtomSetManager the manager to add local atom sets.
/*! \brief Request energy output to energy file during simulation.
*/
- void setEnergyOutputRequest(MdModulesEnergyOutputToDensityFittingRequestChecker* energyOutputRequest)
+ void setEnergyOutputRequest(MDModulesEnergyOutputToDensityFittingRequestChecker* energyOutputRequest)
{
energyOutputRequest->energyOutputToDensityFitting_ = densityFittingOptions_.active();
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <algorithm>
#include <vector>
-#include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/arrayref.h"
namespace gmx
DensityFittingAmplitudeLookupImpl(const DensityFittingAmplitudeLookupImpl&) = default;
virtual ~DensityFittingAmplitudeLookupImpl() = default;
- virtual const std::vector<real>& operator()(const t_mdatoms& atoms, ArrayRef<const int> localIndex) = 0;
- virtual std::unique_ptr<DensityFittingAmplitudeLookupImpl> clone() = 0;
+ virtual const std::vector<real>& operator()(ArrayRef<const real> /*chargeA*/,
+ ArrayRef<const real> /*massT*/,
+ ArrayRef<const int> localIndex) = 0;
+ virtual std::unique_ptr<DensityFittingAmplitudeLookupImpl> clone() = 0;
};
namespace
UnitAmplitudes(const UnitAmplitudes&) = default;
~UnitAmplitudes() override = default;
std::unique_ptr<DensityFittingAmplitudeLookupImpl> clone() override;
- const std::vector<real>& operator()(const t_mdatoms& atoms, ArrayRef<const int> localIndex) override;
+ const std::vector<real>& operator()(ArrayRef<const real> /*chargeA*/,
+ ArrayRef<const real> /*massT*/,
+ ArrayRef<const int> localIndex) override;
private:
std::vector<real> amplitude_;
return std::make_unique<UnitAmplitudes>(*this);
};
-const std::vector<real>& UnitAmplitudes::operator()(const t_mdatoms& /*atoms*/, ArrayRef<const int> localIndex)
+const std::vector<real>& UnitAmplitudes::operator()(ArrayRef<const real> /*chargeA*/,
+ ArrayRef<const real> /*massT*/,
+ ArrayRef<const int> localIndex)
{
if (amplitude_.size() != localIndex.size())
{
ChargesAsAmplitudes(const ChargesAsAmplitudes&) = default;
~ChargesAsAmplitudes() override = default;
std::unique_ptr<DensityFittingAmplitudeLookupImpl> clone() override;
- const std::vector<real>& operator()(const t_mdatoms& atoms, ArrayRef<const int> localIndex) override;
+ const std::vector<real>& operator()(ArrayRef<const real> chargeA,
+ ArrayRef<const real> /*massT*/,
+ ArrayRef<const int> localIndex) override;
private:
std::vector<real> amplitude_;
return std::make_unique<ChargesAsAmplitudes>(*this);
};
-const std::vector<real>& ChargesAsAmplitudes::operator()(const t_mdatoms& atoms, ArrayRef<const int> localIndex)
+const std::vector<real>& ChargesAsAmplitudes::operator()(ArrayRef<const real> chargeA,
+ ArrayRef<const real> /*massT*/,
+ ArrayRef<const int> localIndex)
{
if (amplitude_.size() != localIndex.size())
{
amplitude_.resize(localIndex.size());
}
- std::transform(std::begin(localIndex), std::end(localIndex), std::begin(amplitude_),
- [&atoms](gmx::index index) { return atoms.chargeA[index]; });
+ std::transform(std::begin(localIndex),
+ std::end(localIndex),
+ std::begin(amplitude_),
+ [&chargeA](gmx::index index) { return chargeA[index]; });
return amplitude_;
}
MassesAsAmplitudes(const MassesAsAmplitudes&) = default;
~MassesAsAmplitudes() override = default;
std::unique_ptr<DensityFittingAmplitudeLookupImpl> clone() override;
- const std::vector<real>& operator()(const t_mdatoms& atoms, ArrayRef<const int> localIndex) override;
+ const std::vector<real>& operator()(ArrayRef<const real> /*chargeA*/,
+ ArrayRef<const real> massT,
+ ArrayRef<const int> localIndex) override;
private:
std::vector<real> amplitude_;
return std::make_unique<MassesAsAmplitudes>(*this);
};
-const std::vector<real>& MassesAsAmplitudes::operator()(const t_mdatoms& atoms, ArrayRef<const int> localIndex)
+const std::vector<real>& MassesAsAmplitudes::operator()(ArrayRef<const real> /*chargeA*/,
+ ArrayRef<const real> massT,
+ ArrayRef<const int> localIndex)
{
if (amplitude_.size() != localIndex.size())
{
amplitude_.resize(localIndex.size());
}
- std::transform(std::begin(localIndex), std::end(localIndex), std::begin(amplitude_),
- [&atoms](gmx::index index) { return atoms.massT[index]; });
+ std::transform(std::begin(localIndex),
+ std::end(localIndex),
+ std::begin(amplitude_),
+ [&massT](gmx::index index) { return massT[index]; });
return amplitude_;
}
}
}
-const std::vector<real>& DensityFittingAmplitudeLookup::operator()(const t_mdatoms& atoms,
- ArrayRef<const int> localIndex)
+const std::vector<real>& DensityFittingAmplitudeLookup::operator()(ArrayRef<const real> chargeA,
+ ArrayRef<const real> massT,
+ ArrayRef<const int> localIndex)
{
- return (*impl_)(atoms, localIndex);
+ return (*impl_)(chargeA, massT, localIndex);
}
DensityFittingAmplitudeLookup::~DensityFittingAmplitudeLookup() = default;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/real.h"
-struct t_mdatoms;
-
namespace gmx
{
//! Move assignment
DensityFittingAmplitudeLookup& operator=(DensityFittingAmplitudeLookup&& other) noexcept;
/*! \brief Return the amplitudes for spreading atoms of a given local index.
- * \param[in] atoms the atom information
+ * \param[in] chargeA Atom charges
+ * \param[in] massT Atom masses.
* \param[in] localIndex the local atom indices
* \returns amplitudes
*/
- const std::vector<real>& operator()(const t_mdatoms& atoms, ArrayRef<const int> localIndex);
+ const std::vector<real>& operator()(ArrayRef<const real> chargeA,
+ ArrayRef<const real> massT,
+ ArrayRef<const int> localIndex);
private:
std::unique_ptr<DensityFittingAmplitudeLookupImpl> impl_;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
RVec sigmaInLatticeCoordinates{ sigma, sigma, sigma };
scaleToLattice(&sigmaInLatticeCoordinates);
- return { DVec{ sigmaInLatticeCoordinates[XX], sigmaInLatticeCoordinates[YY],
- sigmaInLatticeCoordinates[ZZ] },
+ return { DVec{ sigmaInLatticeCoordinates[XX], sigmaInLatticeCoordinates[YY], sigmaInLatticeCoordinates[ZZ] },
nSigma };
}
void DensityFittingForceProviderState::writeState(KeyValueTreeObjectBuilder kvtBuilder,
const std::string& identifier) const
{
- writeKvtCheckpointValue(stepsSinceLastCalculation_, stepsSinceLastCalculationName_, identifier,
- kvtBuilder);
- writeKvtCheckpointValue(adaptiveForceConstantScale_, adaptiveForceConstantScaleName_,
- identifier, kvtBuilder);
+ writeKvtCheckpointValue(
+ stepsSinceLastCalculation_, stepsSinceLastCalculationName_, identifier, kvtBuilder);
+ writeKvtCheckpointValue(
+ adaptiveForceConstantScale_, adaptiveForceConstantScaleName_, identifier, kvtBuilder);
KeyValueTreeObjectBuilder exponentialMovingAverageKvtEntry =
kvtBuilder.addObject(identifier + "-" + exponentialMovingAverageStateName_);
const std::string& identifier)
{
readKvtCheckpointValue(compat::make_not_null(&stepsSinceLastCalculation_),
- stepsSinceLastCalculationName_, identifier, kvtData);
+ stepsSinceLastCalculationName_,
+ identifier,
+ kvtData);
readKvtCheckpointValue(compat::make_not_null(&adaptiveForceConstantScale_),
- adaptiveForceConstantScaleName_, identifier, kvtData);
+ adaptiveForceConstantScaleName_,
+ identifier,
+ kvtData);
if (kvtData.keyExists(identifier + "-" + exponentialMovingAverageStateName_))
{
transformedCoordinates_.resize(localAtomSet_.numAtomsLocal());
// pick and copy atom coordinates
- std::transform(std::cbegin(localAtomSet_.localIndex()), std::cend(localAtomSet_.localIndex()),
+ std::transform(std::cbegin(localAtomSet_.localIndex()),
+ std::cend(localAtomSet_.localIndex()),
std::begin(transformedCoordinates_),
[&forceProviderInput](int index) { return forceProviderInput.x_[index]; });
// spread atoms on grid
gaussTransform_.setZero();
- std::vector<real> amplitudes =
- amplitudeLookup_(forceProviderInput.mdatoms_, localAtomSet_.localIndex());
+ std::vector<real> amplitudes = amplitudeLookup_(
+ forceProviderInput.chargeA_, forceProviderInput.massT_, localAtomSet_.localIndex());
if (parameters_.normalizeDensities_)
{
{
// \todo update to real once GaussTransform class returns real
gmx_sumf(gaussTransform_.view().mapping().required_span_size(),
- gaussTransform_.view().data(), &forceProviderInput.cr_);
+ gaussTransform_.view().data(),
+ &forceProviderInput.cr_);
}
// calculate grid derivative
// calculate forces
forces_.resize(localAtomSet_.numAtomsLocal());
std::transform(
- std::begin(transformedCoordinates_), std::end(transformedCoordinates_), std::begin(amplitudes),
- std::begin(forces_), [&densityDerivative, this](const RVec r, real amplitude) {
+ std::begin(transformedCoordinates_),
+ std::end(transformedCoordinates_),
+ std::begin(amplitudes),
+ std::begin(forces_),
+ [&densityDerivative, this](const RVec r, real amplitude) {
return densityFittingForce_.evaluateForce({ r, amplitude }, densityDerivative);
});
impl_->calculateForces(forceProviderInput, forceProviderOutput);
}
-void DensityFittingForceProvider::writeCheckpointData(MdModulesWriteCheckpointData checkpointWriting,
+void DensityFittingForceProvider::writeCheckpointData(MDModulesWriteCheckpointData checkpointWriting,
const std::string& moduleName)
{
impl_->stateToCheckpoint().writeState(checkpointWriting.builder_, moduleName);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/exponentialmovingaverage.h"
#include "gromacs/mdspan/extensions.h"
#include "gromacs/mdtypes/iforceprovider.h"
-#include "gromacs/utility/classhelpers.h"
enum class PbcType : int;
* \note The provided state to checkpoint has to change if checkpointing
* is moved before the force provider call in the MD-loop.
*/
- void writeCheckpointData(MdModulesWriteCheckpointData checkpointWriting, const std::string& moduleName);
+ void writeCheckpointData(MDModulesWriteCheckpointData checkpointWriting, const std::string& moduleName);
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/keyvaluetreebuilder.h"
#include "gromacs/utility/keyvaluetreetransform.h"
-#include "gromacs/utility/mdmodulenotification.h"
+#include "gromacs/utility/mdmodulesnotifiers.h"
#include "gromacs/utility/strconvert.h"
#include "densityfittingamplitudelookup.h"
const auto& stringIdentityTransform = [](std::string s) { return s; };
densityfittingMdpTransformFromString<bool>(rules, &fromStdString<bool>, c_activeTag_);
densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform, c_groupTag_);
- densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform,
- c_similarityMeasureTag_);
+ densityfittingMdpTransformFromString<std::string>(
+ rules, stringIdentityTransform, c_similarityMeasureTag_);
densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform, c_amplitudeMethodTag_);
densityfittingMdpTransformFromString<real>(rules, &fromStdString<real>, c_forceConstantTag_);
- densityfittingMdpTransformFromString<real>(rules, &fromStdString<real>,
- c_gaussianTransformSpreadingWidthTag_);
+ densityfittingMdpTransformFromString<real>(
+ rules, &fromStdString<real>, c_gaussianTransformSpreadingWidthTag_);
densityfittingMdpTransformFromString<real>(
rules, &fromStdString<real>, c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_);
- densityfittingMdpTransformFromString<std::string>(rules, stringIdentityTransform,
- c_referenceDensityFileNameTag_);
- densityfittingMdpTransformFromString<std::int64_t>(rules, &fromStdString<std::int64_t>,
- c_everyNStepsTag_);
+ densityfittingMdpTransformFromString<std::string>(
+ rules, stringIdentityTransform, c_referenceDensityFileNameTag_);
+ densityfittingMdpTransformFromString<std::int64_t>(
+ rules, &fromStdString<std::int64_t>, c_everyNStepsTag_);
densityfittingMdpTransformFromString<bool>(rules, &fromStdString<bool>, c_normalizeDensitiesTag_);
densityfittingMdpTransformFromString<bool>(rules, &fromStdString<bool>, c_adaptiveForceScalingTag_);
- densityfittingMdpTransformFromString<real>(rules, &fromStdString<real>,
- c_adaptiveForceScalingTimeConstantTag_);
+ densityfittingMdpTransformFromString<real>(
+ rules, &fromStdString<real>, c_adaptiveForceScalingTimeConstantTag_);
const auto& stringRVecToStringRVecWithCheck = [](const std::string& str) {
return stringIdentityTransformWithArrayCheck<real, 3>(
- str, "Reading three real values as vector while parsing the .mdp input failed in "
- + DensityFittingModuleInfo::name_ + ".");
+ str,
+ "Reading three real values as vector while parsing the .mdp input failed in "
+ + DensityFittingModuleInfo::name_ + ".");
};
- densityfittingMdpTransformFromString<std::string>(rules, stringRVecToStringRVecWithCheck,
- c_translationTag_);
+ densityfittingMdpTransformFromString<std::string>(
+ rules, stringRVecToStringRVecWithCheck, c_translationTag_);
const auto& stringMatrixToStringMatrixWithCheck = [](const std::string& str) {
return stringIdentityTransformWithArrayCheck<real, 9>(
- str, "Reading nine real values as vector while parsing the .mdp input failed in "
- + DensityFittingModuleInfo::name_ + ".");
+ str,
+ "Reading nine real values as vector while parsing the .mdp input failed in "
+ + DensityFittingModuleInfo::name_ + ".");
};
- densityfittingMdpTransformFromString<std::string>(rules, stringMatrixToStringMatrixWithCheck,
- c_transformationMatrixTag_);
+ densityfittingMdpTransformFromString<std::string>(
+ rules, stringMatrixToStringMatrixWithCheck, c_transformationMatrixTag_);
}
//! Name the methods that may be used to evaluate similarity between densities
"cross-correlation",
c_similarityMeasureTag_);
addDensityFittingMdpOutputValue<std::string>(
- builder, c_densitySimilarityMeasureMethodNames[parameters_.similarityMeasureMethod_],
+ builder,
+ c_densitySimilarityMeasureMethodNames[parameters_.similarityMeasureMethod_],
c_similarityMeasureTag_);
addDensityFittingMdpOutputValueComment(
- builder, "; Atom amplitude for spreading onto grid: unity, mass, or charge",
- c_amplitudeMethodTag_);
+ builder, "; Atom amplitude for spreading onto grid: unity, mass, or charge", c_amplitudeMethodTag_);
addDensityFittingMdpOutputValue<std::string>(
- builder, c_densityFittingAmplitudeMethodNames[parameters_.amplitudeLookupMethod_],
+ builder,
+ c_densityFittingAmplitudeMethodNames[parameters_.amplitudeLookupMethod_],
c_amplitudeMethodTag_);
addDensityFittingMdpOutputValue(builder, parameters_.forceConstant_, c_forceConstantTag_);
- addDensityFittingMdpOutputValue(builder, parameters_.gaussianTransformSpreadingWidth_,
+ addDensityFittingMdpOutputValue(builder,
+ parameters_.gaussianTransformSpreadingWidth_,
c_gaussianTransformSpreadingWidthTag_);
- addDensityFittingMdpOutputValue(builder, parameters_.gaussianTransformSpreadingRangeInMultiplesOfWidth_,
+ addDensityFittingMdpOutputValue(builder,
+ parameters_.gaussianTransformSpreadingRangeInMultiplesOfWidth_,
c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag_);
addDensityFittingMdpOutputValueComment(builder,
"; Reference density file location as absolute path "
addDensityFittingMdpOutputValueComment(
builder, "; Normalize the sum of density voxel values to one", c_normalizeDensitiesTag_);
addDensityFittingMdpOutputValue(builder, parameters_.normalizeDensities_, c_normalizeDensitiesTag_);
- addDensityFittingMdpOutputValueComment(builder, "; Apply adaptive force scaling",
- c_adaptiveForceScalingTag_);
- addDensityFittingMdpOutputValue(builder, parameters_.adaptiveForceScaling_,
- c_adaptiveForceScalingTag_);
+ addDensityFittingMdpOutputValueComment(
+ builder, "; Apply adaptive force scaling", c_adaptiveForceScalingTag_);
+ addDensityFittingMdpOutputValue(
+ builder, parameters_.adaptiveForceScaling_, c_adaptiveForceScalingTag_);
addDensityFittingMdpOutputValueComment(builder,
"; Time constant for adaptive force scaling in ps",
c_adaptiveForceScalingTimeConstantTag_);
- addDensityFittingMdpOutputValue(builder, parameters_.adaptiveForceScalingTimeConstant_,
+ addDensityFittingMdpOutputValue(builder,
+ parameters_.adaptiveForceScalingTimeConstant_,
c_adaptiveForceScalingTimeConstantTag_);
}
}
}
auto kvtIndexArray = tree[DensityFittingModuleInfo::name_ + "-" + c_groupTag_].asArray().values();
parameters_.indices_.resize(kvtIndexArray.size());
- std::transform(std::begin(kvtIndexArray), std::end(kvtIndexArray), std::begin(parameters_.indices_),
+ std::transform(std::begin(kvtIndexArray),
+ std::end(kvtIndexArray),
+ std::begin(parameters_.indices_),
[](const KeyValueTreeValue& val) { return val.cast<std::int64_t>(); });
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! The time constant for the adaptive force scaling in ps
real adaptiveForceScalingTimeConstant_ = 4;
//! Translation of the structure, so that the coordinates that are fitted are x+translation
- std::string translationString_ = "";
+ std::string translationString_;
//! Linear transformation of the structure, so that the coordinates that are fitted are Matrix * x
- std::string transformationMatrixString_ = "";
+ std::string transformationMatrixString_;
};
/*!\brief Check if two structs holding density fitting parameters are equal.
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/options/treesupport.h"
#include "gromacs/utility/keyvaluetreebuilder.h"
#include "gromacs/utility/keyvaluetreetransform.h"
-#include "gromacs/utility/mdmodulenotification.h"
+#include "gromacs/utility/mdmodulesnotifiers.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringcompare.h"
public:
void addMdpOptionDensityFittingActive()
{
- mdpValueBuilder_.rootObject().addValue("density-guided-simulation-active",
- std::string("yes"));
+ mdpValueBuilder_.rootObject().addValue("density-guided-simulation-active", std::string("yes"));
}
void addMdpOptionReferenceDensity()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
class DensityFittingAmplitudeLookupTest : public ::testing::Test
{
-public:
- DensityFittingAmplitudeLookupTest()
- {
- atoms_.nr = numberOfAtoms_;
- atoms_.massT = masses_.data();
- atoms_.chargeA = charges_.data();
- }
-
protected:
int numberOfAtoms_ = 3;
std::vector<real> masses_ = { 2, 3, 4 };
TEST_F(DensityFittingAmplitudeLookupTest, Unity)
{
DensityFittingAmplitudeLookup lookup(DensityFittingAmplitudeMethod::Unity);
- const auto lookupResult = lookup(atoms_, lookupIndices_);
+ const auto lookupResult = lookup(charges_, masses_, lookupIndices_);
EXPECT_EQ(lookupResult[0], 1);
EXPECT_EQ(lookupResult[1], 1);
}
TEST_F(DensityFittingAmplitudeLookupTest, Charge)
{
DensityFittingAmplitudeLookup lookup(DensityFittingAmplitudeMethod::Charge);
- const auto lookupResult = lookup(atoms_, lookupIndices_);
+ const auto lookupResult = lookup(charges_, masses_, lookupIndices_);
EXPECT_EQ(lookupResult[0], 30);
EXPECT_EQ(lookupResult[1], 40);
}
TEST_F(DensityFittingAmplitudeLookupTest, Masses)
{
DensityFittingAmplitudeLookup lookup(DensityFittingAmplitudeMethod::Mass);
- const auto lookupResult = lookup(atoms_, lookupIndices_);
+ const auto lookupResult = lookup(charges_, masses_, lookupIndices_);
EXPECT_EQ(lookupResult[0], 3);
EXPECT_EQ(lookupResult[1], 4);
}
{
DensityFittingAmplitudeLookup lookup(DensityFittingAmplitudeMethod::Unity);
DensityFittingAmplitudeLookup lookupCopied = lookup;
- const auto lookupResult = lookupCopied(atoms_, lookupIndices_);
+ const auto lookupResult = lookupCopied(charges_, masses_, lookupIndices_);
EXPECT_EQ(lookupResult[0], 1);
EXPECT_EQ(lookupResult[1], 1);
}
{
DensityFittingAmplitudeLookup lookup(DensityFittingAmplitudeMethod::Unity);
DensityFittingAmplitudeLookup lookupCopied(lookup);
- const auto lookupResult = lookupCopied(atoms_, lookupIndices_);
+ const auto lookupResult = lookupCopied(charges_, masses_, lookupIndices_);
EXPECT_EQ(lookupResult[0], 1);
EXPECT_EQ(lookupResult[1], 1);
}
{
DensityFittingAmplitudeLookup lookup(DensityFittingAmplitudeMethod::Unity);
DensityFittingAmplitudeLookup lookupCopied = std::move(lookup);
- const auto lookupResult = lookupCopied(atoms_, lookupIndices_);
+ const auto lookupResult = lookupCopied(charges_, masses_, lookupIndices_);
EXPECT_EQ(lookupResult[0], 1);
EXPECT_EQ(lookupResult[1], 1);
}
{
DensityFittingAmplitudeLookup lookup(DensityFittingAmplitudeMethod::Unity);
DensityFittingAmplitudeLookup lookupCopied(std::move(lookup));
- const auto lookupResult = lookupCopied(atoms_, lookupIndices_);
+ const auto lookupResult = lookupCopied(charges_, masses_, lookupIndices_);
EXPECT_EQ(lookupResult[0], 1);
EXPECT_EQ(lookupResult[1], 1);
}
{
// Prepare MDP inputs
KeyValueTreeBuilder mdpValueBuilder;
- mdpValueBuilder.rootObject().addValue("density-guided-simulation-active",
- std::string("yes"));
+ mdpValueBuilder.rootObject().addValue("density-guided-simulation-active", std::string("yes"));
return mdpValueBuilder.build();
}
{
done_blocka(&defaultGroups_);
stupid_fill_blocka(&defaultGroups_, 3);
- std::vector<std::string> groupNames = { "A", "protein", "C" };
- const char* const namesAsConstChar[3] = { groupNames[0].c_str(), groupNames[1].c_str(),
+ std::vector<std::string> groupNames = { "A", "protein", "C" };
+ const char* const namesAsConstChar[3] = { groupNames[0].c_str(),
+ groupNames[1].c_str(),
groupNames[2].c_str() };
return { defaultGroups_, namesAsConstChar };
}
{
done_blocka(&defaultGroups_);
stupid_fill_blocka(&defaultGroups_, 3);
- std::vector<std::string> groupNames = { "protein", "C", "A" };
- const char* const namesAsConstChar[3] = { groupNames[0].c_str(), groupNames[1].c_str(),
+ std::vector<std::string> groupNames = { "protein", "C", "A" };
+ const char* const namesAsConstChar[3] = { groupNames[0].c_str(),
+ groupNames[1].c_str(),
groupNames[2].c_str() };
return { defaultGroups_, namesAsConstChar };
}
#include "gromacs/mdtypes/imdmodule.h"
#include "gromacs/mdtypes/imdoutputprovider.h"
#include "gromacs/mdtypes/imdpoptionprovider.h"
-#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/ioptionscontainerwithsections.h"
#include "gromacs/options/optionsection.h"
void calculateForces(const ForceProviderInput& forceProviderInput,
ForceProviderOutput* forceProviderOutput) override;
- void subscribeToSimulationSetupNotifications(MdModulesNotifier* /* notifier */) override {}
- void subscribeToPreProcessingNotifications(MdModulesNotifier* /* notifier */) override {}
+ void subscribeToSimulationSetupNotifications(MDModulesNotifiers* /* notifiers */) override {}
+ void subscribeToPreProcessingNotifications(MDModulesNotifiers* /* notifiers */) override {}
private:
//! Return whether or not to apply a field
}
else
{
- fpField_ = xvgropen(opt2fn("-field", nfile, fnm), "Applied electric field",
- "Time (ps)", "E (V/nm)", oenv);
+ fpField_ = xvgropen(opt2fn("-field", nfile, fnm),
+ "Applied electric field",
+ "Time (ps)",
+ "E (V/nm)",
+ oenv);
}
}
}
{
if (isActive())
{
- const t_mdatoms& mdatoms = forceProviderInput.mdatoms_;
- const double t = forceProviderInput.t_;
- const t_commrec& cr = forceProviderInput.cr_;
+ const double t = forceProviderInput.t_;
+ const t_commrec& cr = forceProviderInput.cr_;
// NOTE: The non-conservative electric field does not have a virial
ArrayRef<RVec> f = forceProviderOutput->forceWithVirial_.force_;
+ auto chargeA = forceProviderInput.chargeA_;
for (int m = 0; (m < DIM); m++)
{
- const real fieldStrength = FIELDFAC * field(m, t);
+ const real fieldStrength = gmx::c_fieldfac * field(m, t);
if (fieldStrength != 0)
{
// TODO: Check parallellism
- for (int i = 0; i < mdatoms.homenr; ++i)
+ for (int i = 0; i < forceProviderInput.homenr_; ++i)
{
// NOTE: Not correct with perturbed charges
- f[i][m] += mdatoms.chargeA[i] * fieldStrength;
+ f[i][m] += chargeA[i] * fieldStrength;
}
}
}
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
// Prepare a ForceProviderInput
- t_mdatoms md;
- std::vector<real> chargeA{ 1 };
- md.homenr = ssize(chargeA);
- md.chargeA = chargeA.data();
+ std::vector<real> chargeA{ 1 };
t_commrec cr;
matrix boxDummy = { { 0, 0, 0 }, { 0, 0, 0 }, { 0, 0, 0 } };
- ForceProviderInput forceProviderInput({}, md, 0.0, boxDummy, cr);
+ ForceProviderInput forceProviderInput({}, ssize(chargeA), chargeA, {}, 0.0, boxDummy, cr);
// Prepare a ForceProviderOutput
PaddedVector<RVec> f = { { 0, 0, 0 } };
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2019, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2019,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+add_library(commandline INTERFACE)
file(GLOB COMMANDLINE_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${COMMANDLINE_SOURCES} PARENT_SCOPE)
+# Source files have the following private module dependencies.
+target_link_libraries(commandline PRIVATE
+# gmxlib
+# math
+# mdtypes
+# tng_io
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(commandline PUBLIC
+target_include_directories(commandline INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(commandline PUBLIC
+target_link_libraries(commandline INTERFACE
+ legacy_api
+ )
+
+# TODO: when commandline is an OBJECT target
+#target_link_libraries(commandline PUBLIC legacy_api)
+#target_link_libraries(commandline PRIVATE common)
+
+# Module dependencies
+# commandline interfaces convey transitive dependence on these modules.
+#target_link_libraries(commandline PUBLIC
+target_link_libraries(commandline INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(commandline PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(commandline PRIVATE legacy_modules)
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* \ingroup module_commandline
*/
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
const CommandLineHelpContext* g_globalContext = nullptr;
} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_COMMANDLINE_CMDLINEHELPCONTEXT_H
#define GMX_COMMANDLINE_CMDLINEHELPCONTEXT_H
+#include <memory>
#include <string>
#include "gromacs/onlinehelp/helpwritercontext.h"
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
GMX_DISALLOW_ASSIGN(CommandLineHelpContext);
};
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/options/options.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/baseversion.h"
+#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fileredirector.h"
#include "gromacs/utility/gmxassert.h"
while (linksFile.readLine(&line))
{
links_.addLink("[REF]." + line + "[ref]",
- formatString(":ref:`.%s <%s>`", line.c_str(), line.c_str()), line);
+ formatString(":ref:`.%s <%s>`", line.c_str(), line.c_str()),
+ line);
links_.addLink("[REF]" + line + "[ref]", formatString(":ref:`%s`", line.c_str()), line);
}
linksFile.close();
{
indexFile_ = std::make_unique<TextWriter>(
outputRedirector_->openTextOutputFile("fragments/byname.rst"));
- indexFile_->writeLine(formatString("* :doc:`%s </onlinehelp/%s>` - %s", binaryName_.c_str(),
- binaryName_.c_str(), RootHelpText::title));
+ indexFile_->writeLine(formatString(
+ "* :doc:`%s </onlinehelp/%s>` - %s", binaryName_.c_str(), binaryName_.c_str(), RootHelpText::title));
manPagesFile_ =
std::make_unique<TextWriter>(outputRedirector_->openTextOutputFile("conf-man.py"));
manPagesFile_->writeLine("man_pages = [");
outputRedirector_->openTextOutputFile("onlinehelp/" + tag + ".rst");
TextWriter writer(file);
writer.writeLine(formatString(".. _%s:", displayName.c_str()));
- if (displayName == binaryName_ + " mdrun")
- {
- // Make an extra link target for the convenience of
- // MPI-specific documentation
- writer.writeLine(".. _mdrun_mpi:");
- }
writer.ensureEmptyLine();
CommandLineHelpContext context(&writer, eHelpOutputFormat_Rst, &links_, binaryName_);
" More information about |Gromacs| is available at <http://www.gromacs.org/>.");
file->close();
- indexFile_->writeLine(formatString("* :doc:`%s </onlinehelp/%s>` - %s", displayName.c_str(),
- tag.c_str(), module.shortDescription()));
+ indexFile_->writeLine(formatString(
+ "* :doc:`%s </onlinehelp/%s>` - %s", displayName.c_str(), tag.c_str(), module.shortDescription()));
manPagesFile_->writeLine(formatString(" ('onlinehelp/%s', '%s', \"%s\", '', 1),",
- tag.c_str(), tag.c_str(), module.shortDescription()));
+ tag.c_str(),
+ tag.c_str(),
+ module.shortDescription()));
}
void HelpExportReStructuredText::finishModuleExport()
indexFile_.reset();
// TODO: Generalize.
manPagesFile_->writeLine(formatString(" ('onlinehelp/%s', '%s', '%s', '', 1)",
- binaryName_.c_str(), binaryName_.c_str(), RootHelpText::title));
+ binaryName_.c_str(),
+ binaryName_.c_str(),
+ RootHelpText::title));
manPagesFile_->writeLine("]");
manPagesFile_->close();
manPagesFile_.reset();
GMX_RELEASE_ASSERT(dashPos != std::string::npos,
"There should always be at least one dash in the tag");
displayName[dashPos] = ' ';
- indexFile_->writeLine(formatString(":doc:`%s </onlinehelp/%s>`\n %s", displayName.c_str(),
- tag.c_str(), module->second));
+ indexFile_->writeLine(formatString(
+ ":doc:`%s </onlinehelp/%s>`\n %s", displayName.c_str(), tag.c_str(), module->second));
manPagesFile_->writeLine(formatString(":manpage:`%s(1)`\n %s", tag.c_str(), module->second));
}
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_COMMANDLINE_CMDLINEHELPMODULE_H
#define GMX_COMMANDLINE_CMDLINEHELPMODULE_H
+#include <memory>
+
#include "gromacs/commandline/cmdlinemodule.h"
#include "gromacs/onlinehelp/ihelptopic.h"
-#include "gromacs/utility/classhelpers.h"
#include "cmdlinemodulemanager_impl.h"
private:
typedef CommandLineHelpModuleImpl Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
SynopsisFormatter synopsisFormatter(writerContext);
synopsisFormatter.start(context.moduleDisplayName());
filter.formatSelected(OptionsFilter::eSelectInputFileOptions, &synopsisFormatter, impl_->options_);
- filter.formatSelected(OptionsFilter::eSelectInputOutputFileOptions, &synopsisFormatter,
- impl_->options_);
+ filter.formatSelected(
+ OptionsFilter::eSelectInputOutputFileOptions, &synopsisFormatter, impl_->options_);
filter.formatSelected(OptionsFilter::eSelectOutputFileOptions, &synopsisFormatter, impl_->options_);
filter.formatSelected(OptionsFilter::eSelectOtherOptions, &synopsisFormatter, impl_->options_);
synopsisFormatter.finish();
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
- * Copyright (c) 2015,2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_COMMANDLINE_CMDLINEHELPWRITER_H
#define GMX_COMMANDLINE_CMDLINEHELPWRITER_H
+#include <memory>
#include <string>
-#include "gromacs/utility/classhelpers.h"
-
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
// These never release ownership.
//! Global context instance initialized in initForCommandLine().
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
std::unique_ptr<CommandLineProgramContext> g_commandLineContext;
//! Global library data file finder that respects GMXLIB.
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
std::unique_ptr<DataFileFinder> g_libFileFinder;
/*! \brief
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_COMMANDLINE_CMDLINEMODULE_H
#define GMX_COMMANDLINE_CMDLINEMODULE_H
-#include "gromacs/utility/classhelpers.h"
+#include <memory>
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
/*! \brief
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <memory>
#include "gromacs/onlinehelp/ihelptopic.h"
-#include "gromacs/utility/classhelpers.h"
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
/*! \libinternal \brief
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
- * Copyright (c) 2016,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_COMMANDLINE_CMDLINEPARSER_H
#define GMX_COMMANDLINE_CMDLINEPARSER_H
+#include <memory>
#include <string>
#include <vector>
-#include "gromacs/utility/classhelpers.h"
-
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdlib>
#include <cstring>
+#include <mutex>
#include <string>
#include <vector>
#include "buildinfo.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
-#include "gromacs/utility/mutex.h"
#include "gromacs/utility/path.h"
#include "gromacs/utility/stringutil.h"
mutable std::string fullBinaryPath_;
mutable std::string installationPrefix_;
mutable bool bSourceLayout_;
- mutable Mutex binaryPathMutex_;
+ mutable std::mutex binaryPathMutex_;
};
CommandLineProgramContext::Impl::Impl() : programName_("GROMACS"), bSourceLayout_(false) {}
const char* CommandLineProgramContext::fullBinaryPath() const
{
- lock_guard<Mutex> lock(impl_->binaryPathMutex_);
+ std::lock_guard<std::mutex> lock(impl_->binaryPathMutex_);
impl_->findBinaryPath();
return impl_->fullBinaryPath_.c_str();
}
InstallationPrefixInfo CommandLineProgramContext::installationPrefix() const
{
- lock_guard<Mutex> lock(impl_->binaryPathMutex_);
+ std::lock_guard<std::mutex> lock(impl_->binaryPathMutex_);
if (impl_->installationPrefix_.empty())
{
impl_->findBinaryPath();
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
#include <vector>
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/programcontext.h"
namespace gmx
* Returns the full path of the running binary.
*
* \throws std::bad_alloc if out of memory.
- * \throws tMPI::system_error on thread synchronization errors.
*
* Returns argv[0] if there was an error in finding the absolute path.
*/
* Returns the installation prefix (for finding \Gromacs data files).
*
* \throws std::bad_alloc if out of memory.
- * \throws tMPI::system_error on thread synchronization errors.
*
* Returns a hardcoded path set during configuration time if there is
* an error in finding the library data files.
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
#include "gromacs/fileio/filetypes.h"
-#include "gromacs/utility/basedefinitions.h"
//! \addtogroup module_commandline
#define ftp2FILE(ftp, nfile, fnm, mode) gmx_ffopen(ftp2fn(ftp, nfile, fnm), mode)
//! Returns TRUE when this file type has been found on the cmd-line.
-gmx_bool ftp2bSet(int ftp, int nfile, const t_filenm fnm[]);
+bool ftp2bSet(int ftp, int nfile, const t_filenm fnm[]);
//! Returns TRUE when this option has been found on the cmd-line.
-gmx_bool opt2bSet(const char* opt, int nfile, const t_filenm fnm[]);
+bool opt2bSet(const char* opt, int nfile, const t_filenm fnm[]);
/*! \brief
* Returns the file name belonging top cmd-line option opt, or NULL when
const char* ftp2fn_null(int ftp, int nfile, const t_filenm fnm[]);
//! Returns whether or not this filenm is optional.
-gmx_bool is_optional(const t_filenm* fnm);
+bool is_optional(const t_filenm* fnm);
//! Returns whether or not this filenm is output.
-gmx_bool is_output(const t_filenm* fnm);
+bool is_output(const t_filenm* fnm);
//! Returns whether or not this filenm is set.
-gmx_bool is_set(const t_filenm* fnm);
+bool is_set(const t_filenm* fnm);
/*! \brief Return whether \c filename might have been produced by mdrun -noappend.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
//! Names for XvgFormat
-const gmx::EnumerationArray<XvgFormat, const char*> c_xvgFormatNames = { { "xmgrace", "xmgr",
- "none" } };
+const gmx::EnumerationArray<XvgFormat, const char*> c_xvgFormatNames = {
+ { "xmgrace", "xmgr", "none" }
+};
/*! \brief Returns the default xvg format, as modified by GMX_VIEW_XVG
* if that environment variable is set.
/* Extract Time info from arguments */
if (bBeginTimeSet)
{
- setTimeValue(TBEGIN, tbegin);
+ setTimeValue(TimeControl::Begin, tbegin);
}
if (bEndTimeSet)
{
- setTimeValue(TEND, tend);
+ setTimeValue(TimeControl::End, tend);
}
if (bDtSet)
{
- setTimeValue(TDELTA, tdelta);
+ setTimeValue(TimeControl::Delta, tdelta);
}
adapter.copyValues();
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/commandline/filenm.h"
#include "gromacs/fileio/oenv.h"
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
struct gmx_output_env_t;
*/
const char** c;
/** Boolean value for etBOOL. */
- gmx_bool* b;
+ bool* b;
/** Vector value for etRVEC. */
rvec* rv;
} u;
*
* \p option must specify a valid argument in \p pa of the correct type.
*/
-gmx_bool opt2parg_bool(const char* option, int nparg, t_pargs pa[]);
+bool opt2parg_bool(const char* option, int nparg, t_pargs pa[]);
/*! \brief
* Returns value of an etREAL/etTIME option.
*
* \p option must specify a valid argument in \p pa.
*/
-gmx_bool opt2parg_bSet(const char* option, int nparg, const t_pargs* pa);
+bool opt2parg_bSet(const char* option, int nparg, const t_pargs* pa);
/** Add option -w to view output files (must be implemented in program). */
*
* \see gmx_run_cmain().
*/
-gmx_bool parse_common_args(int* argc,
- char* argv[],
- unsigned long Flags,
- int nfile,
- t_filenm fnm[],
- int npargs,
- t_pargs* pa,
- int ndesc,
- const char** desc,
- int nbugs,
- const char** bugs,
- gmx_output_env_t** oenv);
+bool parse_common_args(int* argc,
+ char* argv[],
+ unsigned long Flags,
+ int nfile,
+ t_filenm fnm[],
+ int npargs,
+ t_pargs* pa,
+ int ndesc,
+ const char** desc,
+ int nbugs,
+ const char** bugs,
+ gmx_output_env_t** oenv);
/*! \} */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_COMMANDLINE_SHELLCOMPLETIONS_H
#define GMX_COMMANDLINE_SHELLCOMPLETIONS_H
+#include <memory>
#include <string>
#include <vector>
-#include "gromacs/utility/classhelpers.h"
-
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
gmx::StringOutputStream stream;
gmx::TextWriter streamWriter(&stream);
- gmx::CommandLineHelpContext context(&streamWriter, gmx::eHelpOutputFormat_Console, nullptr,
- "test");
+ gmx::CommandLineHelpContext context(
+ &streamWriter, gmx::eHelpOutputFormat_Console, nullptr, "test");
context.setShowHidden(bHidden_);
writer->writeHelp(context);
stream.close();
std::string filename;
options.addOption(FileNameOption("f")
.description("Input file description")
- .filetype(eftTrajectory)
+ .filetype(OptionFileType::Trajectory)
.inputFile()
.required()
.defaultBasename("traj"));
options.addOption(FileNameOption("mult")
.description("Multiple file description")
- .filetype(eftTrajectory)
+ .filetype(OptionFileType::Trajectory)
.inputFile()
.multiValue()
.defaultBasename("traj"));
options.addOption(FileNameOption("lib")
.description("Library file description")
- .filetype(eftGenericData)
+ .filetype(OptionFileType::GenericData)
.inputFile()
.libraryFile()
.defaultBasename("libdata"));
options.addOption(FileNameOption("io")
.store(&filename)
.description("Input/Output file description")
- .filetype(eftGenericData)
+ .filetype(OptionFileType::GenericData)
.inputOutputFile()
.defaultBasename("inout"));
- options.addOption(
- FileNameOption("o").description("Output file description").filetype(eftPlot).outputFile());
+ options.addOption(FileNameOption("o")
+ .description("Output file description")
+ .filetype(OptionFileType::Plot)
+ .outputFile());
CommandLineHelpWriter writer(options);
bHidden_ = true;
*/
TEST_F(CommandLineHelpWriterTest, HandlesLongFileOptions)
{
- using gmx::eftGenericData;
- using gmx::eftTrajectory;
using gmx::FileNameOption;
+ using gmx::OptionFileType;
gmx::Options options;
options.addOption(FileNameOption("f")
.description("File name option with a long value")
- .filetype(eftTrajectory)
+ .filetype(OptionFileType::Trajectory)
.inputFile()
.required()
.defaultBasename("path/to/long/trajectory/name"));
options.addOption(FileNameOption("f2")
.description("File name option with a long value")
- .filetype(eftTrajectory)
+ .filetype(OptionFileType::Trajectory)
.inputFile()
.required()
.defaultBasename("path/to/long/trajectory"));
options.addOption(FileNameOption("lib")
.description("File name option with a long value and type")
- .filetype(eftTrajectory)
+ .filetype(OptionFileType::Trajectory)
.inputFile()
.libraryFile()
.defaultBasename("path/to/long/trajectory/name"));
options.addOption(FileNameOption("longfileopt")
.description("File name option with a long name")
- .filetype(eftGenericData)
+ .filetype(OptionFileType::GenericData)
.inputFile()
.defaultBasename("deffile"));
options.addOption(FileNameOption("longfileopt2")
.description("File name option with multiple long fields")
- .filetype(eftGenericData)
+ .filetype(OptionFileType::GenericData)
.inputFile()
.libraryFile()
.defaultBasename("path/to/long/file/name"));
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void CommandLineModuleManagerTestBase::initManager(const CommandLine& args, const char* realBinaryName)
{
GMX_RELEASE_ASSERT(impl_ == nullptr, "initManager() called more than once in test");
- impl_.reset(new Impl(args, realBinaryName));
+ impl_ = std::make_unique<Impl>(args, realBinaryName);
}
MockModule& CommandLineModuleManagerTestBase::addModule(const char* name, const char* description)
{
std::unique_ptr<MockOptionsModule> modulePtr(new MockOptionsModule());
MockOptionsModule* module = modulePtr.get();
- gmx::ICommandLineOptionsModule::registerModuleDirect(&manager(), name, description,
- std::move(modulePtr));
+ gmx::ICommandLineOptionsModule::registerModuleDirect(
+ &manager(), name, description, std::move(modulePtr));
return *module;
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_COMMANDLINE_CMDLINEMODULEMANAGERTEST_H
#define GMX_COMMANDLINE_CMDLINEMODULEMANAGERTEST_H
+#include <memory>
#include <string>
#include <gmock/gmock.h>
#include "gromacs/commandline/cmdlinehelpcontext.h"
#include "gromacs/commandline/cmdlinemodule.h"
#include "gromacs/commandline/cmdlineoptionsmodule.h"
-#include "gromacs/utility/classhelpers.h"
#include "testutils/stringtest.h"
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace test
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void parseFromArgs(unsigned long flags, gmx::ArrayRef<t_filenm> fnm, gmx::ArrayRef<t_pargs> pa)
{
fileCount_ = fnm.size();
- bool bOk = parse_common_args(&args_.argc(), args_.argv(), flags, fnm.size(), fnm.data(),
- pa.size(), pa.data(), 0, nullptr, 0, nullptr, &oenv_);
+ bool bOk = parse_common_args(
+ &args_.argc(), args_.argv(), flags, fnm.size(), fnm.data(), pa.size(), pa.data(), 0, nullptr, 0, nullptr, &oenv_);
EXPECT_TRUE(bOk);
}
void parseFromArray(gmx::ArrayRef<const char* const> cmdline,
EXPECT_TRUE(value3);
}
+TEST_F(ParseCommonArgsTest, ParsesBooleanArgsToValuesOfSuitableEnum)
+{
+ enum class LikeBool : bool
+ {
+ No = false,
+ Yes = true
+ };
+ // Set up the default values
+ LikeBool value1 = LikeBool::No;
+ LikeBool value2 = LikeBool::No;
+ LikeBool value3 = LikeBool::No;
+ LikeBool value4 = LikeBool::Yes;
+ LikeBool value5 = LikeBool::Yes;
+ LikeBool value6 = LikeBool::Yes;
+ // Set up 6 options
+ t_pargs pa[] = { { "-b1", FALSE, etBOOL, { &value1 }, "Description" },
+ { "-b2", FALSE, etBOOL, { &value2 }, "Description" },
+ { "-b3", FALSE, etBOOL, { &value3 }, "Description" },
+ { "-b4", FALSE, etBOOL, { &value4 }, "Description" },
+ { "-b5", FALSE, etBOOL, { &value5 }, "Description" },
+ { "-b6", FALSE, etBOOL, { &value6 }, "Description" } };
+ // Set some to yes and no, leave some as default
+ const char* const cmdline[] = { "test", "-b1", "-nob2", "-b4", "-nob5" };
+
+ parseFromArray(cmdline, 0, {}, pa);
+ // Expetactions
+ EXPECT_EQ(value1, LikeBool::Yes) << "set to yes";
+ EXPECT_EQ(value2, LikeBool::No) << "set to no";
+ EXPECT_EQ(value3, LikeBool::No) << "preserves the default of no";
+ EXPECT_EQ(value4, LikeBool::Yes) << "set to yes";
+ EXPECT_EQ(value5, LikeBool::No) << "set to no";
+ EXPECT_EQ(value6, LikeBool::Yes) << "preserves the default of yes";
+}
+
TEST_F(ParseCommonArgsTest, ParsesVectorArgs)
{
rvec value1 = { 0, 0, 0 }, value2 = { 0, 0, 0 }, value3 = { 1, 2, 3 };
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdlib>
#include <cstring>
+#include <array>
+#include <type_traits>
+
#include "gromacs/commandline/filenm.h"
#include "gromacs/fileio/oenv.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
-static const int can_view_ftp[] = { 0, efEPS, efXPM, efXVG, efPDB };
-#define NVIEW asize(can_view_ftp)
-static const char* view_program[] = { nullptr, "ghostview", "display", nullptr, "xterm -e rasmol" };
+static constexpr std::array<int, 5> canViewFileType = { 0, efEPS, efXPM, efXVG, efPDB };
+
+static constexpr int numberOfPossibleFiles = canViewFileType.size();
static int can_view(int ftp)
{
- int i;
-
- for (i = 1; i < NVIEW; i++)
+ for (int i = 1; i < numberOfPossibleFiles; i++)
{
- if (ftp == can_view_ftp[i])
+ if (ftp == canViewFileType[i])
{
return i;
}
void do_view(const gmx_output_env_t* oenv, const char* fn, const char* opts)
{
+ std::array<const char*, 5> viewProgram = {
+ nullptr, "ghostview", "display", nullptr, "xterm -e rasmol"
+ };
char buf[STRLEN], env[STRLEN];
const char* cmd;
int ftp, n;
{
if (!(cmd = getenv(env)))
{
- cmd = view_program[n];
+ cmd = viewProgram[n];
}
}
else
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2018,2019, by the GROMACS development team, led by
+# Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+add_library(compat INTERFACE)
+
+# Source files have the following private module dependencies.
+target_link_libraries(compat PRIVATE
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(compat PUBLIC
+target_include_directories(compat INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(compat PUBLIC
+target_link_libraries(compat INTERFACE
+ legacy_api
+ )
+
+# TODO: when compat is an OBJECT target
+#target_link_libraries(compat PUBLIC legacy_api)
+#target_link_libraries(compat PRIVATE common)
+
+# Module dependencies
+# compat interfaces convey transitive dependence on these modules.
+#target_link_libraries(compat PUBLIC
+target_link_libraries(compat INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(compat PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(compat PRIVATE legacy_modules)
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! Contract-assurance macros that work like a simple version of the GSL ones
//! \{
-#if !defined(__INTEL_COMPILER) || !(__INTEL_COMPILER == 1800 && __INTEL_COMPILER_UPDATE == 0)
-# define Expects(cond) GMX_ASSERT((cond), "Precondition violation")
-# define Ensures(cond) GMX_ASSERT((cond), "Postcondition violation")
-#else
-// icc 18.0.0 in a RelWithAssert build has an ICE, even if we directly
-// embed the contents of GMX_ASSERT, so it seems the lambda in
-// GMX_ASSERT is too complex for it in this use case.
-# define Expects(cond)
-# define Ensures(cond)
-#endif
+#define Expects(cond) GMX_ASSERT((cond), "Precondition violation")
+#define Ensures(cond) GMX_ASSERT((cond), "Postcondition violation")
//! \}
/*! \libinternal
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
not_null<std::shared_ptr<int>> sharedPointer(std::make_shared<int>(10));
#ifndef NDEBUG
-/* The workaround here is needed because the intel implementation
- * will not trigger the assert when using the pointer without
- * a valid object. This was needed due to an internal error
- * being triggered instead with the compiler under this condition.
- *
- * Death tests can also not be used safely in a parallel environment.
- */
-# if !defined(__INTEL_COMPILER) || !(__INTEL_COMPILER == 1800 && __INTEL_COMPILER_UPDATE == 0)
int* nullPointer = nullptr;
GMX_EXPECT_DEATH_IF_SUPPORTED(not_null<int*> invalidNullPointer(nullPointer), "");
-# endif
#endif
int value = 20;
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2019, by the GROMACS development team, led by
+# Copyright (c) 2019,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(coordinateio INTERFACE)
file(GLOB COORDINATEIO_SOURCES *.cpp outputadapters/*.cpp)
-
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${COORDINATEIO_SOURCES} PARENT_SCOPE)
+# Source files have the following dependencies on library infrastructure.
+#target_link_libraries(coordinateio PRIVATE
+# common
+# legacy_modules
+#)
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(coordinateio PUBLIC
+target_include_directories(coordinateio INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(coordinateio PUBLIC
+target_link_libraries(coordinateio INTERFACE
+ legacy_api
+ )
+
+# TODO: when coordinateio is an OBJECT target
+#target_link_libraries(coordinateio PUBLIC legacy_api)
+#target_link_libraries(coordinateio PRIVATE common)
+
+# Module dependencies
+# coordinateio interfaces convey transitive dependence on these modules.
+#target_link_libraries(coordinateio PUBLIC
+target_link_libraries(coordinateio INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(coordinateio PRIVATE NOTHING)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(coordinateio PRIVATE legacy_modules)
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
if (sel.isValid())
{
GMX_ASSERT(sel.hasOnlyAtoms(), "Can only work with selections consisting out of atoms");
- return trjtools_gmx_prepare_tng_writing(name.c_str(), filemode[0],
+ return trjtools_gmx_prepare_tng_writing(name.c_str(),
+ filemode[0],
nullptr, // infile_, //how to get the input file here?
- nullptr, sel.atomCount(), mtop, sel.atomIndices(),
+ nullptr,
+ sel.atomCount(),
+ mtop,
+ sel.atomIndices(),
sel.name());
}
else
{
- return trjtools_gmx_prepare_tng_writing(name.c_str(), filemode[0],
+ return trjtools_gmx_prepare_tng_writing(name.c_str(),
+ filemode[0],
nullptr, // infile_, //how to get the input file here?
- nullptr, mtop->natoms, mtop, get_atom_index(mtop),
+ nullptr,
+ mtop->natoms,
+ mtop,
+ get_atom_index(*mtop),
"System");
}
}
{
localF_.resize(input.natoms);
}
- deepCopy_t_trxframe(input, &local, localX_.data(), localV_.data(), localF_.data(),
- localIndex_.data());
+ deepCopy_t_trxframe(
+ input, &local, localX_.data(), localV_.data(), localF_.data(), localIndex_.data());
for (const auto& outputAdapter : outputAdapters_.getAdapters())
{
if (outputAdapter)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
bool OutputAdapterContainer::isEmpty() const
{
- return std::none_of(outputAdapters_.begin(), outputAdapters_.end(),
- [](const auto& adapter) { return adapter != nullptr; });
+ return std::none_of(outputAdapters_.begin(), outputAdapters_.end(), [](const auto& adapter) {
+ return adapter != nullptr;
+ });
}
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/coordinateio/ioutputadapter.h"
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/enumerationhelpers.h"
namespace gmx
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const Selection& selection,
OutputRequirements requirements)
{
- return createTrajectoryFrameWriter(topology.mtop(), selection, filename,
+ return createTrajectoryFrameWriter(topology.mtop(),
+ selection,
+ filename,
topology.hasTopology() ? topology.copyAtoms() : nullptr,
requirements);
}
* \param[in] requirements Requirements for adding to the object.
* \returns The newly created object.
*/
- TrajectoryFrameWriterPointer runTest(const char* filename, const OutputRequirements& requirements)
+ TrajectoryFrameWriterPointer runTest(const char* filename, const OutputRequirements& requirements) const
{
return createMinimalTrajectoryFrameWriter(filename, dummyTopology_, dummySelection_, requirements);
}
#if GMX_USE_TNG
"spc2-traj.tng",
#endif
- "spc2-traj.xtc", "spc2-traj.g96" };
+ "spc2-traj.xtc",
+ "spc2-traj.g96" };
//! Names here work for setVelocity module
const char* const setVelocitySupported[] = {
};
//! Names here don't work for setForce module
-const char* const setForceUnSupported[] = { "spc2-traj.xtc", "spc2-traj.pdb", "spc2-traj.gro",
+const char* const setForceUnSupported[] = { "spc2-traj.xtc",
+ "spc2-traj.pdb",
+ "spc2-traj.gro",
"spc2-traj.g96" };
//! Names here work for setPrecision module
};
//! Names here don't work for setPrecision module
-const char* const setPrecisionUnSupported[] = { "spc2-traj.trr", "spc2-traj.pdb", "spc2-traj.gro",
+const char* const setPrecisionUnSupported[] = { "spc2-traj.trr",
+ "spc2-traj.pdb",
+ "spc2-traj.gro",
"spc2-traj.g96" };
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2016,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(correlationfunctions INTERFACE)
+
file(GLOB GMXCORRFUNC_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${GMXCORRFUNC_SOURCES} PARENT_SCOPE)
+
+# Source files have the following private module dependencies.
+target_link_libraries(correlationfunctions PRIVATE
+ # gmxlib
+ # math
+ # mdtypes
+ # tng_io
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(correlationfunctions PUBLIC
+target_include_directories(correlationfunctions INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(correlationfunctions PUBLIC
+target_link_libraries(correlationfunctions INTERFACE
+ legacy_api
+ )
+
+# TODO: when fileio is an OBJECT target
+#target_link_libraries(correlationfunctions PUBLIC legacy_api)
+#target_link_libraries(correlationfunctions PRIVATE common)
+
+# Module dependencies
+# This module convey transitive dependence on these modules.
+#target_link_libraries(correlationfunctions PUBLIC
+target_link_libraries(correlationfunctions INTERFACE
+ # utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(correlationfunctions PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(correlationfunctions PRIVATE legacy_modules)
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
} t_acf;
/*! \brief Global variable set true if initialization routines are called. */
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static gmx_bool bACFinit = FALSE;
/*! \brief Data structure for storing command line variables. */
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static t_acf acf;
enum
}
if (debug)
{
- fprintf(debug, "Starting do_ac_core: nframes=%d, nout=%d, nrestart=%d,mode=%lu\n", nframes,
- nout, nrestart, mode);
+ fprintf(debug, "Starting do_ac_core: nframes=%d, nout=%d, nrestart=%d,mode=%lu\n", nframes, nout, nrestart, mode);
}
for (j = 0; (j < nout); j++)
if (cth - 1.0 > 1.0e-15)
{
- printf("j: %d, k: %d, xj:(%g,%g,%g), xk:(%g,%g,%g)\n", j, k, xj[XX], xj[YY],
- xj[ZZ], xk[XX], xk[YY], xk[ZZ]);
+ printf("j: %d, k: %d, xj:(%g,%g,%g), xk:(%g,%g,%g)\n",
+ j,
+ k,
+ xj[XX],
+ xj[YY],
+ xj[ZZ],
+ xk[XX],
+ xk[YY],
+ xk[ZZ]);
}
mmm = 1;
if (MODE(eacP2))
/* Print flags and parameters */
if (bVerbose)
{
- printf("Will calculate %s of %d thingies for %d frames\n",
- title ? title : "autocorrelation", nitem, nframes);
- printf("bAver = %s, bFour = %s bNormalize= %s\n", gmx::boolToString(bAver),
- gmx::boolToString(bFour), gmx::boolToString(bNormalize));
+ printf("Will calculate %s of %d thingies for %d frames\n", title ? title : "autocorrelation", nitem, nframes);
+ printf("bAver = %s, bFour = %s bNormalize= %s\n",
+ gmx::boolToString(bAver),
+ gmx::boolToString(bFour),
+ gmx::boolToString(bNormalize));
printf("mode = %lu, dt = %g, nrestart = %d\n", mode, dt, nrestart);
}
/* Allocate temp arrays */
{
Ctav /= nitem;
Ct2av /= nitem;
- printf("Average correlation time %.3f Std. Dev. %.3f Error %.3f (ps)\n", Ctav,
+ printf("Average correlation time %.3f Std. Dev. %.3f Error %.3f (ps)\n",
+ Ctav,
std::sqrt((Ct2av - gmx::square(Ctav))),
std::sqrt((Ct2av - gmx::square(Ctav)) / (nitem - 1)));
}
}
/*! \brief Legend for selecting Legendre polynomials. */
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static const char* Leg[] = { nullptr, "0", "1", "2", "3", nullptr };
t_pargs* add_acf_pargs(int* npargs, t_pargs* pa)
default: break;
}
- low_do_autocorr(fn, oenv, title, nframes, nitem, acf.nout, c1, dt, mode, acf.nrestart, bAver,
- acf.bNormalize, bDebugMode(), acf.tbeginfit, acf.tendfit, acf.fitfn);
+ low_do_autocorr(fn,
+ oenv,
+ title,
+ nframes,
+ nitem,
+ acf.nout,
+ c1,
+ dt,
+ mode,
+ acf.nrestart,
+ bAver,
+ acf.bNormalize,
+ bDebugMode(),
+ acf.tbeginfit,
+ acf.tendfit,
+ acf.fitfn);
}
int get_acfnout()
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013-2019, by the GROMACS development team, led by
+ * Copyright (c) 2013-2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* hence there are many more NULL field (which have to be at the end of
* the array).
*/
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
const char* s_ffn[effnNR + 2] = { nullptr, "none", "exp", "aexp", "exp_exp", "exp5", "exp7",
"exp9", nullptr, nullptr, nullptr, nullptr, nullptr };
// clang-format off
// needed because clang-format wants to break the lines below
/*! \brief Long description for each fitting function type */
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static const char* longs_ffn[effnNR]
= { "no fit",
"y = exp(-x/|a0|)",
}
/*! \brief array of fitting functions corresponding to the pre-defined types */
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
t_lmcurve lmcurves[effnNR + 1] = { lmc_exp_one_parm, lmc_exp_one_parm, lmc_exp_two_parm,
lmc_exp_exp, lmc_exp_5_parm, lmc_exp_7_parm,
lmc_exp_9_parm, lmc_vac_2_parm, lmc_erffit,
double yfit = lmcurves[eFitFn](x[i], fitparms);
chi2 += gmx::square(y[i] - yfit);
}
- fprintf(fp, "There are %d data points, %d parameters, %s chi2 = %g\nparams:", nfitpnts,
- effnNparams(eFitFn), label, chi2);
+ fprintf(fp,
+ "There are %d data points, %d parameters, %s chi2 = %g\nparams:",
+ nfitpnts,
+ effnNparams(eFitFn),
+ label,
+ chi2);
for (i = 0; (i < effnNparams(eFitFn)); i++)
{
fprintf(fp, " %10g", fitparms[i]);
if (debug)
{
fprintf(debug, "There are %d points to fit %d vars!\n", ndata, effnNparams(eFitFn));
- fprintf(debug, "Fit to function %d from %g through %g, dt=%g\n", eFitFn, begintimefit,
- endtimefit, dt);
+ fprintf(debug, "Fit to function %d from %g through %g, dt=%g\n", eFitFn, begintimefit, endtimefit, dt);
}
snew(x, ndata);
if (bPrint)
{
- printf("COR: Correlation time (plain integral from %6.3f to %6.3f ps) = %8.5f ps\n", 0.0,
- dt * nf_int, sum);
+ printf("COR: Correlation time (plain integral from %6.3f to %6.3f ps) = %8.5f ps\n", 0.0, dt * nf_int, sum);
printf("COR: Relaxation times are computed as fit to an exponential:\n");
printf("COR: %s\n", effnDescription(fitfn));
printf("COR: Fit to correlation function from %6.3f ps to %6.3f ps, results in a\n",
- tbeginfit, std::min(ncorr * dt, tendfit));
+ tbeginfit,
+ std::min(ncorr * dt, tendfit));
}
tStart = 0;
if (bPrint)
{
- printf("COR:%11s%11s%11s%11s%11s%11s%11s\n", "Fit from", "Integral", "Tail Value",
- "Sum (ps)", " a1 (ps)", (effnNparams(fitfn) >= 2) ? " a2 ()" : "",
+ printf("COR:%11s%11s%11s%11s%11s%11s%11s\n",
+ "Fit from",
+ "Integral",
+ "Tail Value",
+ "Sum (ps)",
+ " a1 (ps)",
+ (effnNparams(fitfn) >= 2) ? " a2 ()" : "",
(effnNparams(fitfn) >= 3) ? " a3 (ps)" : "");
}
nf_int = std::min(ncorr, static_cast<int>((tStart + 1e-4) / dt));
sum = print_and_integrate(debug, nf_int, dt, c1, nullptr, 1);
- tail_corr = do_lmfit(ncorr, c1, sig, dt, nullptr, tStart, tendfit, oenv, bDebugMode(),
- fitfn, fitparm, 0, nullptr);
- sumtot = sum + tail_corr;
+ tail_corr = do_lmfit(
+ ncorr, c1, sig, dt, nullptr, tStart, tendfit, oenv, bDebugMode(), fitfn, fitparm, 0, nullptr);
+ sumtot = sum + tail_corr;
if (fit && ((jmax == 1) || (j == 1)))
{
double mfp[3];
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* This is exported for now in order to use when
* calling parse_common_args.
*/
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
extern const char* s_ffn[effnNR + 2];
/*! \brief
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
chisq = gmx::square(status->fnorm);
if (bVerbose)
{
- printf("status: fnorm = %g, nfev = %d, userbreak = %d\noutcome = %s\n", status->fnorm,
- status->nfev, status->userbreak, lm_infmsg[status->outcome]);
+ printf("status: fnorm = %g, nfev = %d, userbreak = %d\noutcome = %s\n",
+ status->fnorm,
+ status->nfev,
+ status->userbreak,
+ lm_infmsg[status->outcome]);
}
if (bVerbose)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int eFitFn,
int nfix);
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
extern t_lmcurve lmcurves[effnNR + 1];
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
if ((*c)[i].size() != ndata)
{
char buf[256];
- snprintf(buf, sizeof(buf), "Vectors of different lengths supplied (%d %d)",
- static_cast<int>((*c)[i].size()), static_cast<int>(ndata));
+ snprintf(buf,
+ sizeof(buf),
+ "Vectors of different lengths supplied (%d %d)",
+ static_cast<int>((*c)[i].size()),
+ static_cast<int>(ndata));
GMX_THROW(gmx::InconsistentInputError(buf));
}
}
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
}
}
real* ptr = result.data();
- low_do_autocorr(nullptr, nullptr, nullptr, nrFrames_, 1, get_acfnout(), &ptr,
- data_->getDt(), mode, nrRestart, bAverage, bNormalize, bVerbose,
- data_->getStartTime(), data_->getEndTime(), effnNONE);
+ low_do_autocorr(nullptr,
+ nullptr,
+ nullptr,
+ nrFrames_,
+ 1,
+ get_acfnout(),
+ &ptr,
+ data_->getDt(),
+ mode,
+ nrRestart,
+ bAverage,
+ bNormalize,
+ bVerbose,
+ data_->getStartTime(),
+ data_->getEndTime(),
+ effnNONE);
double testResult = 0;
for (int i = 0; i < get_acfnout(); i++)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_CORRELATIONDATASET_H
#define GMX_CORRELATIONDATASET_H
+#include <memory>
#include <string>
#include <vector>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
GMX_THROW(InvalidInputError("testType out of range"));
}
output_env_init_default(&oenv);
- do_lmfit(data_[testType].nrLines_, &(data_[testType].y_[0]), nullptr, data_[testType].dt_,
- &(data_[testType].x_[0]), data_[testType].startTime_, data_[testType].endTime_,
- oenv, false, type, result, 0, nullptr);
+ do_lmfit(data_[testType].nrLines_,
+ &(data_[testType].y_[0]),
+ nullptr,
+ data_[testType].dt_,
+ &(data_[testType].x_[0]),
+ data_[testType].startTime_,
+ data_[testType].endTime_,
+ oenv,
+ false,
+ type,
+ result,
+ 0,
+ nullptr);
output_env_done(oenv);
checker_.setDefaultTolerance(test::relativeToleranceAsFloatingPoint(1, tolerance));
checker_.checkSequenceArray(nfitparm, result, "result");
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(domdec INTERFACE)
file(GLOB DOMDEC_SOURCES *.cpp)
if(GMX_GPU_CUDA)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${DOMDEC_SOURCES} ${DOMDEC_CUDA_SOURCES} PARENT_SCOPE)
+# Source files have the following dependencies on library infrastructure.
+#target_link_libraries(domdec PRIVATE
+# common
+# legacy_modules
+#)
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(domdec PUBLIC
+target_include_directories(domdec INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(domdec PUBLIC
+target_link_libraries(domdec INTERFACE
+ legacy_api
+ )
+
+# TODO: when domdec is an OBJECT target
+#target_link_libraries(domdec PUBLIC legacy_api)
+#target_link_libraries(domdec PRIVATE common)
+
+# Module dependencies
+# domdec interfaces convey transitive dependence on these modules.
+#target_link_libraries(domdec PUBLIC
+target_link_libraries(domdec INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(domdec PRIVATE NOTHING)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(domdec PRIVATE legacy_modules)
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2009,2010,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_network.h"
#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/domdec/nsgrid.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
-#include "gromacs/mdlib/nsgrid.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/pbcutil/pbc.h"
/*! \brief Determines if dimensions require triclinic treatment and stores this info in ddbox */
static void set_tric_dir(const ivec* dd_nc, gmx_ddbox_t* ddbox, const matrix box)
{
- int npbcdim, d, i, j;
- rvec *v, *normal;
- real dep, inv_skew_fac2;
-
- npbcdim = ddbox->npbcdim;
- normal = ddbox->normal;
- for (d = 0; d < DIM; d++)
+ int npbcdim = ddbox->npbcdim;
+ rvec* normal = ddbox->normal;
+ for (int d = 0; d < DIM; d++)
{
ddbox->tric_dir[d] = 0;
- for (j = d + 1; j < npbcdim; j++)
+ for (int j = d + 1; j < npbcdim; j++)
{
if (box[j][d] != 0)
{
"Domain decomposition has not been implemented for box vectors that "
"have non-zero components in directions that do not use domain "
"decomposition: ncells = %d %d %d, box vector[%d] = %f %f %f",
- (*dd_nc)[XX], (*dd_nc)[YY], (*dd_nc)[ZZ], j + 1, box[j][XX],
- box[j][YY], box[j][ZZ]);
+ (*dd_nc)[XX],
+ (*dd_nc)[YY],
+ (*dd_nc)[ZZ],
+ j + 1,
+ box[j][XX],
+ box[j][YY],
+ box[j][ZZ]);
}
}
}
*/
if (ddbox->tric_dir[d])
{
- inv_skew_fac2 = 1;
- v = ddbox->v[d];
+ real inv_skew_fac2 = 1;
+ rvec* v = ddbox->v[d];
if (d == XX || d == YY)
{
/* Normalize such that the "diagonal" is 1 */
svmul(1 / box[d + 1][d + 1], box[d + 1], v[d + 1]);
- for (i = 0; i < d; i++)
+ for (int i = 0; i < d; i++)
{
v[d + 1][i] = 0;
}
/* Normalize such that the "diagonal" is 1 */
svmul(1 / box[d + 2][d + 2], box[d + 2], v[d + 2]);
/* Set v[d+2][d+1] to zero by shifting along v[d+1] */
- dep = v[d + 2][d + 1] / v[d + 1][d + 1];
- for (i = 0; i < DIM; i++)
+ const real dep = v[d + 2][d + 1] / v[d + 1][d + 1];
+ for (int i = 0; i < DIM; i++)
{
v[d + 2][i] -= dep * v[d + 1][i];
}
if (debug)
{
fprintf(debug, "box[%d] %.3f %.3f %.3f\n", d, box[d][XX], box[d][YY], box[d][ZZ]);
- for (i = d + 1; i < DIM; i++)
+ for (int i = d + 1; i < DIM; i++)
{
fprintf(debug, " v[%d] %.3f %.3f %.3f\n", i, v[i][XX], v[i][YY], v[i][ZZ]);
}
}
ddbox->skew_fac[d] = 1.0 / std::sqrt(inv_skew_fac2);
/* Set the normal vector length to skew_fac */
- dep = ddbox->skew_fac[d] / norm(normal[d]);
+ const real dep = ddbox->skew_fac[d] / norm(normal[d]);
svmul(dep, normal[d], normal[d]);
if (debug)
{
fprintf(debug, "skew_fac[%d] = %f\n", d, ddbox->skew_fac[d]);
- fprintf(debug, "normal[%d] %.3f %.3f %.3f\n", d, normal[d][XX], normal[d][YY],
- normal[d][ZZ]);
+ fprintf(debug, "normal[%d] %.3f %.3f %.3f\n", d, normal[d][XX], normal[d][YY], normal[d][ZZ]);
}
}
else
{
ddbox->skew_fac[d] = 1;
- for (i = 0; i < DIM; i++)
+ for (int i = 0; i < DIM; i++)
{
clear_rvec(ddbox->v[d][i]);
ddbox->v[d][i][i] = 1;
gmx_ddbox_t* ddbox)
{
rvec av, stddev;
- real b0, b1;
- int d;
ddbox->npbcdim = numPbcDimensions;
ddbox->nboundeddim = numBoundedDimensions;
- for (d = 0; d < numBoundedDimensions; d++)
+ for (int d = 0; d < numBoundedDimensions; d++)
{
ddbox->box0[d] = 0;
ddbox->box_size[d] = box[d][d];
{
calc_pos_av_stddev(x, av, stddev, mpiCommunicator);
- /* GRID_STDDEV_FAC * stddev
+ /* c_gridStdDevFactor * stddev
* gives a uniform load for a rectangular block of cg's.
* For a sphere it is not a bad approximation for 4x1x1 up to 4x2x2.
*/
- for (d = ddbox->nboundeddim; d < DIM; d++)
+ for (int d = ddbox->nboundeddim; d < DIM; d++)
{
- b0 = av[d] - GRID_STDDEV_FAC * stddev[d];
- b1 = av[d] + GRID_STDDEV_FAC * stddev[d];
+ const real b0 = av[d] - c_gridStdDevFactor * stddev[d];
+ const real b1 = av[d] + c_gridStdDevFactor * stddev[d];
if (debug)
{
fprintf(debug, "Setting global DD grid boundaries to %f - %f\n", b0, b1);
gmx::ArrayRef<const gmx::RVec> xRef = constArrayRefFromArray(
x.data(), masterRankHasTheSystemState ? x.size() : dd.comm->atomRanges.numHomeAtoms());
- low_set_ddbox(dd.unitCellInfo.npbcdim, dd.unitCellInfo.numBoundedDimensions, &dd.numCells,
- box, calculateUnboundedSize, xRef,
- needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr, ddbox);
+ low_set_ddbox(dd.unitCellInfo.npbcdim,
+ dd.unitCellInfo.numBoundedDimensions,
+ &dd.numCells,
+ box,
+ calculateUnboundedSize,
+ xRef,
+ needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr,
+ ddbox);
}
if (masterRankHasTheSystemState)
{
if (ddRole == DDRole::Master)
{
- low_set_ddbox(numPbcDimensions(ir.pbcType), inputrec2nboundeddim(&ir), dd_nc, box, true, x,
- nullptr, ddbox);
+ low_set_ddbox(
+ numPbcDimensions(ir.pbcType), inputrec2nboundeddim(&ir), dd_nc, box, true, x, nullptr, ddbox);
}
gmx_bcast(sizeof(gmx_ddbox_t), ddbox, communicator);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_DOMDEC_BUILDER_H
#define GMX_DOMDEC_BUILDER_H
+#include <memory>
+
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/classhelpers.h"
struct gmx_domdec_t;
struct gmx_mtop_t;
private:
class Impl;
//! Pimpl to hide implementation details
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const gmx_ddbox_t* ddbox,
const real* cellFrac)
{
- gmx_domdec_comm_t* comm;
- int nc, ns, s;
- int * xmin, *xmax;
- real range, pme_boundary;
- int sh;
+ int sh = 0;
- comm = dd->comm;
- nc = dd->numCells[ddpme->dim];
- ns = ddpme->nslab;
+ gmx_domdec_comm_t* comm = dd->comm;
+ const int nc = dd->numCells[ddpme->dim];
+ const int ns = ddpme->nslab;
if (!ddpme->dim_match)
{
/* We need to check for all pme nodes which nodes they
* could possibly need to communicate with.
*/
- xmin = ddpme->pp_min;
- xmax = ddpme->pp_max;
+ const int* xmin = ddpme->pp_min;
+ const int* xmax = ddpme->pp_max;
/* Allow for atoms to be maximally 2/3 times the cut-off
* out of their DD cell. This is a reasonable balance between
* between performance and support for most charge-group/cut-off
* combinations.
*/
- range = 2.0 / 3.0 * comm->systemInfo.cutoff / ddbox->box_size[ddpme->dim];
+ real range = 2.0 / 3.0 * comm->systemInfo.cutoff / ddbox->box_size[ddpme->dim];
/* Avoid extra communication when we are exactly at a boundary */
range *= 0.999;
sh = 1;
- for (s = 0; s < ns; s++)
+ for (int s = 0; s < ns; s++)
{
/* PME slab s spreads atoms between box frac. s/ns and (s+1)/ns */
- pme_boundary = static_cast<real>(s) / ns;
+ real pme_boundary = static_cast<real>(s) / ns;
while (sh + 1 < ns
&& ((s - (sh + 1) >= 0 && cellFrac[xmax[s - (sh + 1)] + 1] + range > pme_boundary)
|| (s - (sh + 1) < 0 && cellFrac[xmax[s - (sh + 1) + ns] + 1] - 1 + range > pme_boundary)))
static void check_box_size(const gmx_domdec_t* dd, const gmx_ddbox_t* ddbox)
{
- int d, dim;
-
- for (d = 0; d < dd->ndim; d++)
+ for (int d = 0; d < dd->ndim; d++)
{
- dim = dd->dim[d];
+ const int dim = dd->dim[d];
if (dim < ddbox->nboundeddim
&& ddbox->box_size[dim] * ddbox->skew_fac[dim]
< dd->numCells[dim] * dd->comm->cellsize_limit * DD_CELL_MARGIN)
FARGS,
"The %c-size of the box (%f) times the triclinic skew factor (%f) is smaller "
"than the number of DD cells (%d) times the smallest allowed cell size (%f)\n",
- dim2char(dim), ddbox->box_size[dim], ddbox->skew_fac[dim], dd->numCells[dim],
+ dim2char(dim),
+ ddbox->box_size[dim],
+ ddbox->skew_fac[dim],
+ dd->numCells[dim],
dd->comm->cellsize_limit);
}
}
real grid_jump_limit(const gmx_domdec_comm_t* comm, real cutoff, int dim_ind)
{
- real grid_jump_limit;
-
/* The distance between the boundaries of cells at distance
* x+-1,y+-1 or y+-1,z+-1 is limited by the cut-off restrictions
* and by the fact that cells should not be shifted by more than
* half their size, such that cg's only shift by one cell
* at redecomposition.
*/
- grid_jump_limit = comm->cellsize_limit;
+ real grid_jump_limit = comm->cellsize_limit;
if (!comm->bVacDLBNoLimit)
{
if (comm->bPMELoadBalDLBLimits)
*/
static real cellsize_min_dlb(gmx_domdec_comm_t* comm, int dim_ind, int dim)
{
- real cellsize_min;
-
- cellsize_min = comm->cellsize_min[dim];
+ real cellsize_min = comm->cellsize_min[dim];
if (!comm->bVacDLBNoLimit)
{
"The box size in direction %c (%f) times the triclinic skew factor (%f) is too "
"small for a cut-off of %f with %d domain decomposition cells, use 1 or more "
"than %d %s or increase the box size in this direction",
- dim2char(d), ddbox->box_size[d], ddbox->skew_fac[d], comm->systemInfo.cutoff,
- dd->numCells[d], dd->numCells[d], dd->nnodes > dd->numCells[d] ? "cells" : "ranks");
+ dim2char(d),
+ ddbox->box_size[d],
+ ddbox->skew_fac[d],
+ comm->systemInfo.cutoff,
+ dd->numCells[d],
+ dd->numCells[d],
+ dd->nnodes > dd->numCells[d] ? "cells" : "ranks");
if (setmode == setcellsizeslbLOCAL)
{
DDRankSetup& ddRankSetup = comm->ddRankSetup;
for (int d = 0; d < ddRankSetup.npmedecompdim; d++)
{
- set_pme_maxshift(dd, &ddRankSetup.ddpme[d], comm->slb_frac[dd->dim[d]] == nullptr, ddbox,
+ set_pme_maxshift(dd,
+ &ddRankSetup.ddpme[d],
+ comm->slb_frac[dd->dim[d]] == nullptr,
+ ddbox,
ddRankSetup.ddpme[d].slb_dim_f);
}
real cellsize_limit_f,
int range[])
{
- gmx_domdec_comm_t* comm;
- real halfway, cellsize_limit_f_i, region_size;
- gmx_bool bLastHi = FALSE;
- int nrange[] = { range[0], range[1] };
+ gmx_bool bLastHi = FALSE;
+ int nrange[] = { range[0], range[1] };
- region_size = rowMaster->cellFrac[range[1]] - rowMaster->cellFrac[range[0]];
+ const real region_size = rowMaster->cellFrac[range[1]] - rowMaster->cellFrac[range[0]];
GMX_ASSERT(region_size >= (range[1] - range[0]) * cellsize_limit_f,
"The region should fit all cells at minimum size");
- comm = dd->comm;
+ gmx_domdec_comm_t* comm = dd->comm;
const int ncd = dd->numCells[dim];
{
rowMaster->isCellMin[i] = false;
}
- int nmin = 0;
- int nmin_old;
+ int nmin = 0;
+ int nmin_old = 0;
do
{
nmin_old = nmin;
if (!rowMaster->isCellMin[i])
{
cell_size[i] *= fac;
- if (!dimHasPbc && (i == 0 || i == dd->numCells[dim] - 1))
- {
- cellsize_limit_f_i = 0;
- }
- else
- {
- cellsize_limit_f_i = cellsize_limit_f;
- }
+ const real cellsize_limit_f_i =
+ (!dimHasPbc && (i == 0 || i == dd->numCells[dim] - 1)) ? 0 : cellsize_limit_f;
if (cell_size[i] < cellsize_limit_f_i)
{
rowMaster->isCellMin[i] = true;
gmx_fatal(FARGS,
"step %s: the dynamic load balancing could not balance dimension %c: box size "
"%f, triclinic skew factor %f, #cells %d, minimum cell size %f\n",
- gmx_step_str(step, buf), dim2char(dim), ddbox->box_size[dim],
- ddbox->skew_fac[dim], ncd, comm->cellsize_min[dim]);
+ gmx_step_str(step, buf),
+ dim2char(dim),
+ ddbox->box_size[dim],
+ ddbox->skew_fac[dim],
+ ncd,
+ comm->cellsize_min[dim]);
}
rowMaster->dlbIsLimited = (nmin > 0) || (range[0] > 0) || (range[1] < ncd);
*/
for (int i = range[0] + 1; i < range[1]; i++)
{
- halfway = 0.5 * (rowMaster->oldCellFrac[i] + rowMaster->oldCellFrac[i - 1]);
+ real halfway = 0.5 * (rowMaster->oldCellFrac[i] + rowMaster->oldCellFrac[i - 1]);
if (rowMaster->cellFrac[i] < halfway)
{
rowMaster->cellFrac[i] = halfway;
rowMaster->cellFrac[i] = 0.5 * (bounds.boundMin + bounds.boundMax);
nrange[0] = range[0];
nrange[1] = i;
- dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, rowMaster, ddbox, bUniform,
- step, cellsize_limit_f, nrange);
+ dd_cell_sizes_dlb_root_enforce_limits(
+ dd, d, dim, rowMaster, ddbox, bUniform, step, cellsize_limit_f, nrange);
nrange[0] = i;
nrange[1] = range[1];
- dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, rowMaster, ddbox, bUniform,
- step, cellsize_limit_f, nrange);
+ dd_cell_sizes_dlb_root_enforce_limits(
+ dd, d, dim, rowMaster, ddbox, bUniform, step, cellsize_limit_f, nrange);
return;
}
if (nrange[1] < range[1]) /* found a LimLo before */
{
rowMaster->cellFrac[nrange[1]] = rowMaster->bounds[nrange[1]].boundMin;
- dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, rowMaster, ddbox, bUniform,
- step, cellsize_limit_f, nrange);
+ dd_cell_sizes_dlb_root_enforce_limits(
+ dd, d, dim, rowMaster, ddbox, bUniform, step, cellsize_limit_f, nrange);
nrange[0] = nrange[1];
}
rowMaster->cellFrac[i] = rowMaster->bounds[i].boundMax;
nrange[1] = i;
- dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, rowMaster, ddbox, bUniform,
- step, cellsize_limit_f, nrange);
+ dd_cell_sizes_dlb_root_enforce_limits(
+ dd, d, dim, rowMaster, ddbox, bUniform, step, cellsize_limit_f, nrange);
nrange[0] = i;
nrange[1] = range[1];
}
if (nrange[1] < range[1]) /* found last a LimLo */
{
rowMaster->cellFrac[nrange[1]] = rowMaster->bounds[nrange[1]].boundMin;
- dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, rowMaster, ddbox, bUniform, step,
- cellsize_limit_f, nrange);
+ dd_cell_sizes_dlb_root_enforce_limits(
+ dd, d, dim, rowMaster, ddbox, bUniform, step, cellsize_limit_f, nrange);
nrange[0] = nrange[1];
nrange[1] = range[1];
- dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, rowMaster, ddbox, bUniform, step,
- cellsize_limit_f, nrange);
+ dd_cell_sizes_dlb_root_enforce_limits(
+ dd, d, dim, rowMaster, ddbox, bUniform, step, cellsize_limit_f, nrange);
}
else if (nrange[0] > range[0]) /* found at least one LimHi */
{
- dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, rowMaster, ddbox, bUniform, step,
- cellsize_limit_f, nrange);
+ dd_cell_sizes_dlb_root_enforce_limits(
+ dd, d, dim, rowMaster, ddbox, bUniform, step, cellsize_limit_f, nrange);
}
}
}
{
real load_aver = comm->load[d].sum_m / ncd;
real change_max = 0;
- real load_i;
- real change;
for (int i = 0; i < ncd; i++)
{
/* Determine the relative imbalance of cell i */
- load_i = comm->load[d].load[i * comm->load[d].nload + 2];
- real imbalance = (load_i - load_aver) / (load_aver > 0 ? load_aver : 1);
+ const real load_i = comm->load[d].load[i * comm->load[d].nload + 2];
+ const real imbalance = (load_i - load_aver) / (load_aver > 0 ? load_aver : 1);
/* Determine the change of the cell size using underrelaxation */
- change = -c_relax * imbalance;
- change_max = std::max(change_max, std::max(change, -change));
+ const real change = -c_relax * imbalance;
+ change_max = std::max(change_max, std::max(change, -change));
}
/* Limit the amount of scaling.
* We need to use the same rescaling for all cells in one row,
for (int i = 0; i < ncd; i++)
{
/* Determine the relative imbalance of cell i */
- load_i = comm->load[d].load[i * comm->load[d].nload + 2];
- real imbalance = (load_i - load_aver) / (load_aver > 0 ? load_aver : 1);
+ const real load_i = comm->load[d].load[i * comm->load[d].nload + 2];
+ const real imbalance = (load_i - load_aver) / (load_aver > 0 ? load_aver : 1);
/* Determine the change of the cell size using underrelaxation */
- change = -sc * imbalance;
+ const real change = -sc * imbalance;
cell_size[i] = (rowMaster->cellFrac[i + 1] - rowMaster->cellFrac[i]) * (1 + change);
}
}
}
if (debug)
{
- fprintf(debug, "dim %d boundary %d %.3f < %.3f < %.3f < %.3f < %.3f\n", d, i,
- boundsNeighbor.cellFracLowerMax + dist_min_f, bounds.boundMin,
- rowMaster->cellFrac[i], bounds.boundMax, bounds.cellFracUpperMin - dist_min_f);
+ fprintf(debug,
+ "dim %d boundary %d %.3f < %.3f < %.3f < %.3f < %.3f\n",
+ d,
+ i,
+ boundsNeighbor.cellFracLowerMax + dist_min_f,
+ bounds.boundMin,
+ rowMaster->cellFrac[i],
+ bounds.boundMax,
+ bounds.cellFracUpperMin - dist_min_f);
}
}
}
range[1] = ncd;
rowMaster->cellFrac[0] = 0;
rowMaster->cellFrac[ncd] = 1;
- dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, rowMaster, ddbox, bUniform, step,
- cellsize_limit_f, range);
+ dd_cell_sizes_dlb_root_enforce_limits(
+ dd, d, dim, rowMaster, ddbox, bUniform, step, cellsize_limit_f, range);
/* After the checks above, the cells should obey the cut-off
{
if (debug)
{
- fprintf(debug, "Relative bounds dim %d cell %d: %f %f\n", dim, i,
- rowMaster->cellFrac[i], rowMaster->cellFrac[i + 1]);
+ fprintf(debug,
+ "Relative bounds dim %d cell %d: %f %f\n",
+ dim,
+ i,
+ rowMaster->cellFrac[i],
+ rowMaster->cellFrac[i + 1]);
}
if ((bPBC || (i != 0 && i != dd->numCells[dim] - 1))
&& rowMaster->cellFrac[i + 1] - rowMaster->cellFrac[i] < cellsize_limit_f / DD_CELL_MARGIN)
{
char buf[22];
- fprintf(stderr, "\nWARNING step %s: direction %c, cell %d too small: %f\n",
- gmx_step_str(step, buf), dim2char(dim), i,
+ fprintf(stderr,
+ "\nWARNING step %s: direction %c, cell %d too small: %f\n",
+ gmx_step_str(step, buf),
+ dim2char(dim),
+ i,
(rowMaster->cellFrac[i + 1] - rowMaster->cellFrac[i]) * ddbox->box_size[dim]
* ddbox->skew_fac[dim]);
}
/* Each node would only need to know two fractions,
* but it is probably cheaper to broadcast the whole array.
*/
- MPI_Bcast(cellFracRow.data(), ddCellFractionBufferSize(dd, d) * sizeof(real), MPI_BYTE, 0,
+ MPI_Bcast(cellFracRow.data(),
+ ddCellFractionBufferSize(dd, d) * sizeof(real),
+ MPI_BYTE,
+ 0,
comm.mpi_comm_load[d]);
#endif
/* Copy the fractions for this dimension from the buffer */
static void set_dd_cell_sizes_dlb_nochange(gmx_domdec_t* dd, const gmx_ddbox_t* ddbox)
{
- int d;
-
/* This function assumes the box is static and should therefore
* not be called when the box has changed since the last
* call to dd_partition_system.
*/
- for (d = 0; d < dd->ndim; d++)
+ for (int d = 0; d < dd->ndim; d++)
{
relative_to_absolute_cell_bounds(dd, ddbox, d);
}
gmx_bool bUniform,
gmx_bool bDoDLB,
int64_t step,
- gmx_wallcycle_t wcycle)
+ gmx_wallcycle* wcycle)
{
- gmx_domdec_comm_t* comm;
- int dim;
-
- comm = dd->comm;
+ gmx_domdec_comm_t* comm = dd->comm;
if (bDoDLB)
{
- wallcycle_start(wcycle, ewcDDCOMMBOUND);
+ wallcycle_start(wcycle, WallCycleCounter::DDCommBound);
set_dd_cell_sizes_dlb_change(dd, ddbox, bDynamicBox, bUniform, step);
- wallcycle_stop(wcycle, ewcDDCOMMBOUND);
+ wallcycle_stop(wcycle, WallCycleCounter::DDCommBound);
}
else if (bDynamicBox)
{
}
/* Set the dimensions for which no DD is used */
- for (dim = 0; dim < DIM; dim++)
+ for (int dim = 0; dim < DIM; dim++)
{
if (dd->numCells[dim] == 1)
{
gmx_bool bUniform,
gmx_bool bDoDLB,
int64_t step,
- gmx_wallcycle_t wcycle)
+ gmx_wallcycle* wcycle)
{
gmx_domdec_comm_t* comm = dd->comm;
fprintf(debug,
"Changing the number of halo communication pulses along dim %c from %d "
"to %d\n",
- dim2char(dd->dim[d]), cd.numPulses(), numPulsesDim);
+ dim2char(dd->dim[d]),
+ cd.numPulses(),
+ numPulsesDim);
}
cd.ind.resize(numPulsesDim);
}
{
for (int d = 0; d < DIM; d++)
{
- fprintf(debug, "cell_x[%d] %f - %f skew_fac %f\n", d, comm->cell_x0[d],
- comm->cell_x1[d], ddbox->skew_fac[d]);
+ fprintf(debug,
+ "cell_x[%d] %f - %f skew_fac %f\n",
+ d,
+ comm->cell_x0[d],
+ comm->cell_x1[d],
+ ddbox->skew_fac[d]);
}
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx_bool bUniform,
gmx_bool bDoDLB,
int64_t step,
- gmx_wallcycle_t wcycle);
+ gmx_wallcycle* wcycle);
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/domdec/domdec_network.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/state.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "atomdistribution.h"
}
/* Collect the charge group indices on the master */
- dd_gatherv(dd, atomGroups.size() * sizeof(int), atomGroups.data(),
+ dd_gatherv(dd,
+ atomGroups.size() * sizeof(int),
+ atomGroups.data(),
DDMASTER(dd) ? ma->intBuffer.data() : nullptr,
DDMASTER(dd) ? ma->intBuffer.data() + dd->nnodes : nullptr,
DDMASTER(dd) ? ma->atomGroups.data() : nullptr);
#if GMX_MPI
const int numHomeAtoms = dd->comm->atomRanges.numHomeAtoms();
MPI_Send(const_cast<void*>(static_cast<const void*>(lv.data())),
- numHomeAtoms * sizeof(rvec), MPI_BYTE, dd->masterrank, dd->rank, dd->mpi_comm_all);
+ numHomeAtoms * sizeof(rvec),
+ MPI_BYTE,
+ dd->masterrank,
+ dd->rank,
+ dd->mpi_comm_all);
#endif
}
else
}
#if GMX_MPI
- MPI_Recv(ma.rvecBuffer.data(), domainGroups.numAtoms * sizeof(rvec), MPI_BYTE, rank,
- rank, dd->mpi_comm_all, MPI_STATUS_IGNORE);
+ MPI_Recv(ma.rvecBuffer.data(),
+ domainGroups.numAtoms * sizeof(rvec),
+ MPI_BYTE,
+ rank,
+ rank,
+ dd->mpi_comm_all,
+ MPI_STATUS_IGNORE);
#endif
int localAtom = 0;
for (const int& globalAtom : domainGroups.atomGroups)
}
const int numHomeAtoms = dd->comm->atomRanges.numHomeAtoms();
- dd_gatherv(dd, numHomeAtoms * sizeof(rvec), lv.data(), recvCounts, displacements,
+ dd_gatherv(dd,
+ numHomeAtoms * sizeof(rvec),
+ lv.data(),
+ recvCounts,
+ displacements,
DDMASTER(dd) ? dd->ma->rvecBuffer.data() : nullptr);
if (DDMASTER(dd))
GMX_RELEASE_ASSERT(state->nhchainlength == nh,
"The global and local Nose-Hoover chain lengths should match");
- for (int i = 0; i < efptNR; i++)
+ for (auto i : gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real>::keys())
{
state->lambda[i] = state_local->lambda[i];
}
state->baros_integral = state_local->baros_integral;
state->pull_com_prev_step = state_local->pull_com_prev_step;
}
- if (state_local->flags & (1 << estX))
+ if (state_local->flags & enumValueToBitMask(StateEntry::X))
{
auto globalXRef = state ? state->x : gmx::ArrayRef<gmx::RVec>();
- dd_collect_vec(dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl,
- state_local->x, globalXRef);
+ dd_collect_vec(dd,
+ state_local->ddp_count,
+ state_local->ddp_count_cg_gl,
+ state_local->cg_gl,
+ state_local->x,
+ globalXRef);
}
- if (state_local->flags & (1 << estV))
+ if (state_local->flags & enumValueToBitMask(StateEntry::V))
{
auto globalVRef = state ? state->v : gmx::ArrayRef<gmx::RVec>();
- dd_collect_vec(dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl,
- state_local->v, globalVRef);
+ dd_collect_vec(dd,
+ state_local->ddp_count,
+ state_local->ddp_count_cg_gl,
+ state_local->cg_gl,
+ state_local->v,
+ globalVRef);
}
- if (state_local->flags & (1 << estCGP))
+ if (state_local->flags & enumValueToBitMask(StateEntry::Cgp))
{
auto globalCgpRef = state ? state->cg_p : gmx::ArrayRef<gmx::RVec>();
- dd_collect_vec(dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl,
- state_local->cg_p, globalCgpRef);
+ dd_collect_vec(dd,
+ state_local->ddp_count,
+ state_local->ddp_count_cg_gl,
+ state_local->cg_gl,
+ state_local->cg_p,
+ globalCgpRef);
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/df_history.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/logger.h"
"The index count and number of indices should match");
#if GMX_MPI
- MPI_Send(buffer.data(), domainGroups.numAtoms * sizeof(gmx::RVec), MPI_BYTE, rank,
- rank, dd->mpi_comm_all);
+ MPI_Send(buffer.data(), domainGroups.numAtoms * sizeof(gmx::RVec), MPI_BYTE, rank, rank, dd->mpi_comm_all);
#endif
}
}
{
#if GMX_MPI
int numHomeAtoms = dd->comm->atomRanges.numHomeAtoms();
- MPI_Recv(localVec.data(), numHomeAtoms * sizeof(gmx::RVec), MPI_BYTE, dd->masterrank,
- MPI_ANY_TAG, dd->mpi_comm_all, MPI_STATUS_IGNORE);
+ MPI_Recv(localVec.data(),
+ numHomeAtoms * sizeof(gmx::RVec),
+ MPI_BYTE,
+ dd->masterrank,
+ MPI_ANY_TAG,
+ dd->mpi_comm_all,
+ MPI_STATUS_IGNORE);
#endif
}
}
}
int numHomeAtoms = dd->comm->atomRanges.numHomeAtoms();
- dd_scatterv(dd, sendCounts, displacements, DDMASTER(dd) ? dd->ma->rvecBuffer.data() : nullptr,
- numHomeAtoms * sizeof(gmx::RVec), localVec.data());
+ dd_scatterv(dd,
+ sendCounts,
+ displacements,
+ DDMASTER(dd) ? dd->ma->rvecBuffer.data() : nullptr,
+ numHomeAtoms * sizeof(gmx::RVec),
+ localVec.data());
}
static void distributeVec(gmx_domdec_t* dd,
GMX_RELEASE_ASSERT(state->nhchainlength == nh,
"The global and local Nose-Hoover chain lengths should match");
- for (int i = 0; i < efptNR; i++)
+ for (auto i : gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real>::keys())
{
state_local->lambda[i] = state->lambda[i];
}
}
state_local->baros_integral = state->baros_integral;
}
- dd_bcast(dd, ((efptNR) * sizeof(real)), state_local->lambda.data());
+ dd_bcast(dd,
+ (static_cast<int>(FreeEnergyPerturbationCouplingType::Count) * sizeof(real)),
+ state_local->lambda.data());
dd_bcast(dd, sizeof(int), &state_local->fep_state);
dd_bcast(dd, sizeof(real), &state_local->veta);
dd_bcast(dd, sizeof(real), &state_local->vol0);
state_change_natoms(state_local, dd->comm->atomRanges.numHomeAtoms());
- if (state_local->flags & (1 << estX))
+ if (state_local->flags & enumValueToBitMask(StateEntry::X))
{
distributeVec(dd, DDMASTER(dd) ? state->x : gmx::ArrayRef<const gmx::RVec>(), state_local->x);
}
- if (state_local->flags & (1 << estV))
+ if (state_local->flags & enumValueToBitMask(StateEntry::V))
{
distributeVec(dd, DDMASTER(dd) ? state->v : gmx::ArrayRef<const gmx::RVec>(), state_local->v);
}
- if (state_local->flags & (1 << estCGP))
+ if (state_local->flags & enumValueToBitMask(StateEntry::Cgp))
{
distributeVec(dd, DDMASTER(dd) ? state->cg_p : gmx::ArrayRef<const gmx::RVec>(), state_local->cg_p);
}
const matrix box,
rvec* pos)
{
- /* Set the reference location cg_cm for assigning the group */
+ /* Set the reference location for assigning the group */
rvec cog;
int numAtoms = atomEnd - atomBegin;
if (numAtoms == 1)
for (const gmx_molblock_t& molblock : mtop.molblock)
{
const auto& updateGrouping =
- dd->comm->systemInfo.updateGroupingPerMoleculetype[molblock.type];
+ dd->comm->systemInfo.updateGroupingsPerMoleculeType[molblock.type];
for (int mol = 0; mol < molblock.nmol; mol++)
{
for (int g = 0; g < updateGrouping.numBlocks(); g++)
{
- const auto& block = updateGrouping.block(g);
- const int atomBegin = atomOffset + block.begin();
- const int atomEnd = atomOffset + block.end();
- const int domainIndex =
- computeAtomGroupDomainIndex(*dd, ddbox, triclinicCorrectionMatrix,
- cellBoundaries, atomBegin, atomEnd, box, pos);
+ const auto& block = updateGrouping.block(g);
+ const int atomBegin = atomOffset + block.begin();
+ const int atomEnd = atomOffset + block.end();
+ const int domainIndex = computeAtomGroupDomainIndex(
+ *dd, ddbox, triclinicCorrectionMatrix, cellBoundaries, atomBegin, atomEnd, box, pos);
for (int atomIndex : block)
{
/* Compute the center of geometry for all atoms */
for (int atom = 0; atom < mtop.natoms; atom++)
{
- int domainIndex = computeAtomGroupDomainIndex(*dd, ddbox, triclinicCorrectionMatrix,
- cellBoundaries, atom, atom + 1, box, pos);
+ int domainIndex = computeAtomGroupDomainIndex(
+ *dd, ddbox, triclinicCorrectionMatrix, cellBoundaries, atom, atom + 1, box, pos);
indices[domainIndex].push_back(atom);
ma.domainGroups[domainIndex].numAtoms += 1;
{
// Use double for the sums to avoid natoms^2 overflowing
// (65537^2 > 2^32)
- int nat_sum, nat_min, nat_max;
- double nat2_sum;
-
- nat_sum = 0;
- nat2_sum = 0;
- nat_min = ma.domainGroups[0].numAtoms;
- nat_max = ma.domainGroups[0].numAtoms;
+ int nat_sum = 0;
+ double nat2_sum = 0;
+ int nat_min = ma.domainGroups[0].numAtoms;
+ int nat_max = ma.domainGroups[0].numAtoms;
for (int rank = 0; rank < dd->nnodes; rank++)
{
int numAtoms = ma.domainGroups[rank].numAtoms;
GMX_LOG(mdlog.info)
.appendTextFormatted(
"Atom distribution over %d domains: av %d stddev %d min %d max %d",
- dd->nnodes, nat_sum,
+ dd->nnodes,
+ nat_sum,
gmx::roundToInt(std::sqrt(nat2_sum - gmx::square(static_cast<double>(nat_sum)))),
- nat_min, nat_max);
+ nat_min,
+ nat_max);
}
return indices;
const gmx_ddbox_t* ddbox,
rvec pos[])
{
- AtomDistribution* ma = dd->ma.get();
- int * ibuf, buf2[2] = { 0, 0 };
+ AtomDistribution* ma = dd->ma.get();
+ int * ibuf = nullptr, buf2[2] = { 0, 0 };
gmx_bool bMaster = DDMASTER(dd);
std::vector<std::vector<int>> groupIndices;
ma->intBuffer[rank] = groupIndices[rank].size() * sizeof(int);
ma->intBuffer[dd->nnodes + rank] = groupOffset * sizeof(int);
- ma->atomGroups.insert(ma->atomGroups.end(), groupIndices[rank].begin(),
- groupIndices[rank].end());
+ ma->atomGroups.insert(
+ ma->atomGroups.end(), groupIndices[rank].begin(), groupIndices[rank].end());
ma->domainGroups[rank].atomGroups = gmx::constArrayRefFromArray(
ma->atomGroups.data() + groupOffset, groupIndices[rank].size());
}
}
- dd_scatterv(dd, bMaster ? ma->intBuffer.data() : nullptr,
+ dd_scatterv(dd,
+ bMaster ? ma->intBuffer.data() : nullptr,
bMaster ? ma->intBuffer.data() + dd->nnodes : nullptr,
- bMaster ? ma->atomGroups.data() : nullptr, dd->ncg_home * sizeof(int),
+ bMaster ? ma->atomGroups.data() : nullptr,
+ dd->ncg_home * sizeof(int),
dd->globalAtomGroupIndices.data());
if (debug)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! Accumulates flop counts for force calculations.
static double force_flop_count(const t_nrnb* nrnb)
{
- int i;
- double sum;
- const char* name;
-
- sum = 0;
- for (i = 0; i < eNR_NBKERNEL_FREE_ENERGY; i++)
+ double sum = 0;
+ for (int i = 0; i < eNR_NBKERNEL_FREE_ENERGY; i++)
{
/* To get closer to the real timings, we half the count
* for the normal loops and again half it for water loops.
*/
- name = nrnb_str(i);
+ const char* name = nrnb_str(i);
if (strstr(name, "W3") != nullptr || strstr(name, "W4") != nullptr)
{
sum += nrnb->n[i] * 0.25 * cost_nrnb(i);
sum += nrnb->n[i] * 0.50 * cost_nrnb(i);
}
}
- for (i = eNR_NBKERNEL_FREE_ENERGY; i <= eNR_NB14; i++)
+ for (int i = eNR_NBKERNEL_FREE_ENERGY; i <= eNR_NB14; i++)
{
- name = nrnb_str(i);
+ const char* name = nrnb_str(i);
if (strstr(name, "W3") != nullptr || strstr(name, "W4") != nullptr)
{
sum += nrnb->n[i] * cost_nrnb(i);
}
}
- for (i = eNR_BONDS; i <= eNR_WALLS; i++)
+ for (int i = eNR_BONDS; i <= eNR_WALLS; i++)
{
sum += nrnb->n[i] * cost_nrnb(i);
}
void clear_dd_cycle_counts(gmx_domdec_t* dd)
{
- int i;
-
- for (i = 0; i < ddCyclNr; i++)
+ for (int i = 0; i < ddCyclNr; i++)
{
dd->comm->cycl[i] = 0;
dd->comm->cycl_n[i] = 0;
* Copyright (c) 2005,2006,2007,2008,2009 by the GROMACS development team.
* Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
* Copyright (c) 2015,2016,2017,2018,2019 by the GROMACS development team.
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
using gmx::DlbOption;
using gmx::DomdecOptions;
-static const char* edlbs_names[int(DlbState::nr)] = { "off", "off", "auto", "locked", "on", "on" };
+static const char* enumValueToString(DlbState enumValue)
+{
+ static constexpr gmx::EnumerationArray<DlbState, const char*> dlbStateNames = {
+ "off", "off", "auto", "locked", "on", "on"
+ };
+ return dlbStateNames[enumValue];
+}
/* The size per atom group of the cggl_flag buffer in gmx_domdec_comm_t */
#define DD_CGIBS 2
int ddglatnr(const gmx_domdec_t* dd, int i)
{
- int atnr;
+ int atnr = 0;
if (dd == nullptr)
{
{
gmx_fatal(FARGS,
"glatnr called with %d, which is larger than the local number of atoms (%d)",
- i, dd->comm->atomRanges.numAtomsTotal());
+ i,
+ dd->comm->atomRanges.numAtomsTotal());
}
atnr = dd->globalAtomIndices[i] + 1;
}
return atnr;
}
-gmx::ArrayRef<const gmx::RangePartitioning> getUpdateGroupingPerMoleculetype(const gmx_domdec_t& dd)
+gmx::ArrayRef<const gmx::RangePartitioning> getUpdateGroupingsPerMoleculeType(const gmx_domdec_t& dd)
{
GMX_RELEASE_ASSERT(dd.comm, "Need a valid dd.comm");
- return dd.comm->systemInfo.updateGroupingPerMoleculetype;
+ return dd.comm->systemInfo.updateGroupingsPerMoleculeType;
}
-void dd_store_state(gmx_domdec_t* dd, t_state* state)
+void dd_store_state(const gmx_domdec_t& dd, t_state* state)
{
- int i;
-
- if (state->ddp_count != dd->ddp_count)
+ if (state->ddp_count != dd.ddp_count)
{
gmx_incons("The MD state does not match the domain decomposition state");
}
- state->cg_gl.resize(dd->ncg_home);
- for (i = 0; i < dd->ncg_home; i++)
+ state->cg_gl.resize(dd.ncg_home);
+ for (int i = 0; i < dd.ncg_home; i++)
{
- state->cg_gl[i] = dd->globalAtomGroupIndices[i];
+ state->cg_gl[i] = dd.globalAtomGroupIndices[i];
}
- state->ddp_count_cg_gl = dd->ddp_count;
+ state->ddp_count_cg_gl = dd.ddp_count;
}
gmx_domdec_zones_t* domdec_zones(gmx_domdec_t* dd)
return dd.comm->atomRanges.numHomeAtoms();
}
-int dd_natoms_mdatoms(const gmx_domdec_t* dd)
+int dd_natoms_mdatoms(const gmx_domdec_t& dd)
{
/* We currently set mdatoms entries for all atoms:
* local + non-local + communicated for vsite + constraints
*/
- return dd->comm->atomRanges.numAtomsTotal();
+ return dd.comm->atomRanges.numAtomsTotal();
}
-int dd_natoms_vsite(const gmx_domdec_t* dd)
+int dd_natoms_vsite(const gmx_domdec_t& dd)
{
- return dd->comm->atomRanges.end(DDAtomRanges::Type::Vsites);
+ return dd.comm->atomRanges.end(DDAtomRanges::Type::Vsites);
}
-void dd_get_constraint_range(const gmx_domdec_t* dd, int* at_start, int* at_end)
+void dd_get_constraint_range(const gmx_domdec_t& dd, int* at_start, int* at_end)
{
- *at_start = dd->comm->atomRanges.start(DDAtomRanges::Type::Constraints);
- *at_end = dd->comm->atomRanges.end(DDAtomRanges::Type::Constraints);
+ *at_start = dd.comm->atomRanges.start(DDAtomRanges::Type::Constraints);
+ *at_end = dd.comm->atomRanges.end(DDAtomRanges::Type::Constraints);
}
void dd_move_x(gmx_domdec_t* dd, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_wallcycle* wcycle)
{
- wallcycle_start(wcycle, ewcMOVEX);
+ wallcycle_start(wcycle, WallCycleCounter::MoveX);
- int nzone, nat_tot;
- gmx_domdec_comm_t* comm;
- gmx_domdec_comm_dim_t* cd;
- rvec shift = { 0, 0, 0 };
- gmx_bool bPBC, bScrew;
+ rvec shift = { 0, 0, 0 };
- comm = dd->comm;
+ gmx_domdec_comm_t* comm = dd->comm;
- nzone = 1;
- nat_tot = comm->atomRanges.numHomeAtoms();
+ int nzone = 1;
+ int nat_tot = comm->atomRanges.numHomeAtoms();
for (int d = 0; d < dd->ndim; d++)
{
- bPBC = (dd->ci[dd->dim[d]] == 0);
- bScrew = (bPBC && dd->unitCellInfo.haveScrewPBC && dd->dim[d] == XX);
+ const bool bPBC = (dd->ci[dd->dim[d]] == 0);
+ const bool bScrew = (bPBC && dd->unitCellInfo.haveScrewPBC && dd->dim[d] == XX);
if (bPBC)
{
copy_rvec(box[dd->dim[d]], shift);
}
- cd = &comm->cd[d];
+ gmx_domdec_comm_dim_t* cd = &comm->cd[d];
for (const gmx_domdec_ind_t& ind : cd->ind)
{
DDBufferAccess<gmx::RVec> sendBufferAccess(comm->rvecBuffer, ind.nsend[nzone + 1]);
nzone += nzone;
}
- wallcycle_stop(wcycle, ewcMOVEX);
+ wallcycle_stop(wcycle, WallCycleCounter::MoveX);
}
void dd_move_f(gmx_domdec_t* dd, gmx::ForceWithShiftForces* forceWithShiftForces, gmx_wallcycle* wcycle)
{
- wallcycle_start(wcycle, ewcMOVEF);
+ wallcycle_start(wcycle, WallCycleCounter::MoveF);
gmx::ArrayRef<gmx::RVec> f = forceWithShiftForces->force();
gmx::ArrayRef<gmx::RVec> fshift = forceWithShiftForces->shiftForces();
/* Determine which shift vector we need */
ivec vis = { 0, 0, 0 };
vis[dd->dim[d]] = 1;
- const int is = IVEC2IS(vis);
+ const int is = gmx::ivecToShiftIndex(vis);
/* Loop over the pulses */
const gmx_domdec_comm_dim_t& cd = comm.cd[d];
}
nzone /= 2;
}
- wallcycle_stop(wcycle, ewcMOVEF);
+ wallcycle_stop(wcycle, WallCycleCounter::MoveF);
}
/* Convenience function for extracting a real buffer from an rvec buffer
void dd_atom_spread_real(gmx_domdec_t* dd, real v[])
{
- int nzone, nat_tot;
- gmx_domdec_comm_t* comm;
- gmx_domdec_comm_dim_t* cd;
-
- comm = dd->comm;
+ gmx_domdec_comm_t* comm = dd->comm;
- nzone = 1;
- nat_tot = comm->atomRanges.numHomeAtoms();
+ int nzone = 1;
+ int nat_tot = comm->atomRanges.numHomeAtoms();
for (int d = 0; d < dd->ndim; d++)
{
- cd = &comm->cd[d];
+ gmx_domdec_comm_dim_t* cd = &comm->cd[d];
for (const gmx_domdec_ind_t& ind : cd->ind)
{
/* Note: We provision for RVec instead of real, so a factor of 3
void dd_atom_sum_real(gmx_domdec_t* dd, real v[])
{
- int nzone, nat_tot;
- gmx_domdec_comm_t* comm;
- gmx_domdec_comm_dim_t* cd;
-
- comm = dd->comm;
+ gmx_domdec_comm_t* comm = dd->comm;
- nzone = comm->zones.n / 2;
- nat_tot = comm->atomRanges.end(DDAtomRanges::Type::Zones);
+ int nzone = comm->zones.n / 2;
+ int nat_tot = comm->atomRanges.end(DDAtomRanges::Type::Zones);
for (int d = dd->ndim - 1; d >= 0; d--)
{
- cd = &comm->cd[d];
+ gmx_domdec_comm_dim_t* cd = &comm->cd[d];
for (int p = cd->numPulses() - 1; p >= 0; p--)
{
const gmx_domdec_ind_t& ind = cd->ind[p];
real dd_cutoff_twobody(const gmx_domdec_t* dd)
{
- real r_mb;
-
- r_mb = dd_cutoff_multibody(dd);
+ const real r_mb = dd_cutoff_multibody(dd);
return std::max(dd->comm->systemInfo.cutoff, r_mb);
}
return pmeRanks;
}
-static int gmx_ddcoord2pmeindex(const t_commrec* cr, int x, int y, int z)
+static int gmx_ddcoord2pmeindex(const gmx_domdec_t& dd, int x, int y, int z)
{
- gmx_domdec_t* dd;
- ivec coords;
- int slab;
+ ivec coords;
- dd = cr->dd;
- coords[XX] = x;
- coords[YY] = y;
- coords[ZZ] = z;
- slab = ddindex2pmeindex(dd->comm->ddRankSetup, dd_index(dd->numCells, coords));
+ coords[XX] = x;
+ coords[YY] = y;
+ coords[ZZ] = z;
+ const int slab = ddindex2pmeindex(dd.comm->ddRankSetup, dd_index(dd.numCells, coords));
return slab;
}
{
if (cr->dd->comm->ddRankSetup.usePmeOnlyRanks)
{
- nodeid = ddindex + gmx_ddcoord2pmeindex(cr, x, y, z);
+ nodeid = ddindex + gmx_ddcoord2pmeindex(*cr->dd, x, y, z);
}
else
{
else
{
/* The slab corresponds to the nodeid in the PME group */
- if (gmx_ddcoord2pmeindex(cr, x, y, z) == pmenodeid)
+ if (gmx_ddcoord2pmeindex(*cr->dd, x, y, z) == pmenodeid)
{
ddranks.push_back(ddcoord2simnodeid(cr, x, y, z));
}
static gmx_bool receive_vir_ener(const gmx_domdec_t* dd, gmx::ArrayRef<const int> pmeRanks, const t_commrec* cr)
{
- gmx_bool bReceive = TRUE;
+ bool bReceive = true;
const DDRankSetup& ddRankSetup = dd->comm->ddRankSetup;
if (ddRankSetup.usePmeOnlyRanks)
coords[cartSetup.cartpmedim]++;
if (coords[cartSetup.cartpmedim] < dd->numCells[cartSetup.cartpmedim])
{
- int rank;
+ int rank = 0;
MPI_Cart_rank(cr->mpi_comm_mysim, coords, &rank);
if (dd_simnode2pmenode(ddRankSetup, cartSetup, pmeRanks, cr, rank) == pmenode)
{
static void set_slb_pme_dim_f(gmx_domdec_t* dd, int dim, real** dim_f)
{
- gmx_domdec_comm_t* comm;
- int i;
-
- comm = dd->comm;
+ gmx_domdec_comm_t* comm = dd->comm;
snew(*dim_f, dd->numCells[dim] + 1);
(*dim_f)[0] = 0;
- for (i = 1; i < dd->numCells[dim]; i++)
+ for (int i = 1; i < dd->numCells[dim]; i++)
{
if (comm->slb_frac[dim])
{
*/
if (dimind == 0 || xyz[XX] == dd->ci[XX])
{
- const int pmeindex = ddindex2pmeindex(ddRankSetup, i);
- int slab;
- if (dimind == 0)
- {
- slab = pmeindex / nso;
- }
- else
- {
- slab = pmeindex % ddpme->nslab;
- }
+ const int pmeindex = ddindex2pmeindex(ddRankSetup, i);
+ const int slab = (dimind == 0) ? (pmeindex / nso) : (pmeindex % ddpme->nslab);
ddpme->pp_min[slab] = std::min(ddpme->pp_min[slab], xyz[dimind]);
ddpme->pp_max[slab] = std::max(ddpme->pp_max[slab], xyz[dimind]);
}
set_slb_pme_dim_f(dd, ddpme->dim, &ddpme->slb_dim_f);
}
-int dd_pme_maxshift_x(const gmx_domdec_t* dd)
+int dd_pme_maxshift_x(const gmx_domdec_t& dd)
{
- const DDRankSetup& ddRankSetup = dd->comm->ddRankSetup;
+ const DDRankSetup& ddRankSetup = dd.comm->ddRankSetup;
if (ddRankSetup.ddpme[0].dim == XX)
{
}
}
-int dd_pme_maxshift_y(const gmx_domdec_t* dd)
+int dd_pme_maxshift_y(const gmx_domdec_t& dd)
{
- const DDRankSetup& ddRankSetup = dd->comm->ddRankSetup;
+ const DDRankSetup& ddRankSetup = dd.comm->ddRankSetup;
if (ddRankSetup.ddpme[0].dim == YY)
{
}
}
-bool ddHaveSplitConstraints(const gmx_domdec_t& dd)
+bool ddMayHaveSplitConstraints(const gmx_domdec_t& dd)
{
- return dd.comm->systemInfo.haveSplitConstraints;
+ return dd.comm->systemInfo.mayHaveSplitConstraints;
}
bool ddUsesUpdateGroups(const gmx_domdec_t& dd)
#if GMX_MPI
static void make_load_communicator(gmx_domdec_t* dd, int dim_ind, ivec loc)
{
- MPI_Comm c_row;
- int dim, i, rank;
+ MPI_Comm c_row = MPI_COMM_NULL;
ivec loc_c;
- gmx_bool bPartOfGroup = FALSE;
+ bool bPartOfGroup = false;
- dim = dd->dim[dim_ind];
+ const int dim = dd->dim[dim_ind];
copy_ivec(loc, loc_c);
- for (i = 0; i < dd->numCells[dim]; i++)
+ for (int i = 0; i < dd->numCells[dim]; i++)
{
- loc_c[dim] = i;
- rank = dd_index(dd->numCells, loc_c);
+ loc_c[dim] = i;
+ const int rank = dd_index(dd->numCells, loc_c);
if (rank == dd->rank)
{
/* This process is part of the group */
void dd_setup_dlb_resource_sharing(const t_commrec* cr, int gpu_id)
{
#if GMX_MPI
- int physicalnode_id_hash;
- gmx_domdec_t* dd;
- MPI_Comm mpi_comm_pp_physicalnode;
+ MPI_Comm mpi_comm_pp_physicalnode = MPI_COMM_NULL;
if (!thisRankHasDuty(cr, DUTY_PP) || gpu_id < 0)
{
return;
}
- physicalnode_id_hash = gmx_physicalnode_id_hash();
+ const int physicalnode_id_hash = gmx_physicalnode_id_hash();
- dd = cr->dd;
+ gmx_domdec_t* dd = cr->dd;
if (debug)
{
fprintf(debug, "dd_setup_dd_dlb_gpu_sharing:\n");
- fprintf(debug, "DD PP rank %d physical node hash %d gpu_id %d\n", dd->rank,
- physicalnode_id_hash, gpu_id);
+ fprintf(debug, "DD PP rank %d physical node hash %d gpu_id %d\n", dd->rank, physicalnode_id_hash, gpu_id);
}
/* Split the PP communicator over the physical nodes */
/* TODO: See if we should store this (before), as it's also used for
static void make_load_communicators(gmx_domdec_t gmx_unused* dd)
{
#if GMX_MPI
- int dim0, dim1, i, j;
ivec loc;
if (debug)
make_load_communicator(dd, 0, loc);
if (dd->ndim > 1)
{
- dim0 = dd->dim[0];
- for (i = 0; i < dd->numCells[dim0]; i++)
+ const int dim0 = dd->dim[0];
+ for (int i = 0; i < dd->numCells[dim0]; i++)
{
loc[dim0] = i;
make_load_communicator(dd, 1, loc);
}
if (dd->ndim > 2)
{
- dim0 = dd->dim[0];
- for (i = 0; i < dd->numCells[dim0]; i++)
+ const int dim0 = dd->dim[0];
+ for (int i = 0; i < dd->numCells[dim0]; i++)
{
- loc[dim0] = i;
- dim1 = dd->dim[1];
- for (j = 0; j < dd->numCells[dim1]; j++)
+ loc[dim0] = i;
+ const int dim1 = dd->dim[1];
+ for (int j = 0; j < dd->numCells[dim1]; j++)
{
loc[dim1] = j;
make_load_communicator(dd, 2, loc);
/*! \brief Sets up the relation between neighboring domains and zones */
static void setup_neighbor_relations(gmx_domdec_t* dd)
{
- int d, dim, m;
- ivec tmp, s;
- gmx_domdec_zones_t* zones;
+ ivec tmp, s;
GMX_ASSERT((dd->ndim >= 0) && (dd->ndim <= DIM), "Must have valid number of dimensions for DD");
- for (d = 0; d < dd->ndim; d++)
+ for (int d = 0; d < dd->ndim; d++)
{
- dim = dd->dim[d];
+ const int dim = dd->dim[d];
copy_ivec(dd->ci, tmp);
tmp[dim] = (tmp[dim] + 1) % dd->numCells[dim];
dd->neighbor[d][0] = ddcoord2ddnodeid(dd, tmp);
dd->neighbor[d][1] = ddcoord2ddnodeid(dd, tmp);
if (debug)
{
- fprintf(debug, "DD rank %d neighbor ranks in dir %d are + %d - %d\n", dd->rank, dim,
- dd->neighbor[d][0], dd->neighbor[d][1]);
+ fprintf(debug,
+ "DD rank %d neighbor ranks in dir %d are + %d - %d\n",
+ dd->rank,
+ dim,
+ dd->neighbor[d][0],
+ dd->neighbor[d][1]);
}
}
int nizone = (1 << std::max(dd->ndim - 1, 0));
assert(nizone >= 1 && nizone <= DD_MAXIZONE);
- zones = &dd->comm->zones;
+ gmx_domdec_zones_t* zones = &dd->comm->zones;
for (int i = 0; i < nzone; i++)
{
- m = 0;
+ int m = 0;
clear_ivec(zones->shift[i]);
- for (d = 0; d < dd->ndim; d++)
+ for (int d = 0; d < dd->ndim; d++)
{
zones->shift[i][dd->dim[d]] = dd_zo[i][m++];
}
zones->n = nzone;
for (int i = 0; i < nzone; i++)
{
- for (d = 0; d < DIM; d++)
+ for (int d = 0; d < DIM; d++)
{
s[d] = dd->ci[d] - zones->shift[i][d];
if (s[d] < 0)
*/
iZone.jZoneRange = gmx::Range<int>(std::min(ddNonbondedZonePairRanges[iZoneIndex][1], nzone),
std::min(ddNonbondedZonePairRanges[iZoneIndex][2], nzone));
- for (dim = 0; dim < DIM; dim++)
+ for (int dim = 0; dim < DIM; dim++)
{
if (dd->numCells[dim] == 1)
{
/* Set up cartesian communication for the particle-particle part */
GMX_LOG(mdlog.info)
.appendTextFormatted("Will use a Cartesian communicator: %d x %d x %d",
- dd->numCells[XX], dd->numCells[YY], dd->numCells[ZZ]);
+ dd->numCells[XX],
+ dd->numCells[YY],
+ dd->numCells[ZZ]);
ivec periods;
for (int i = 0; i < DIM; i++)
{
periods[i] = TRUE;
}
- MPI_Comm comm_cart;
- MPI_Cart_create(cr->mpi_comm_mygroup, DIM, dd->numCells, periods, static_cast<int>(reorder),
- &comm_cart);
+ MPI_Comm comm_cart = MPI_COMM_NULL;
+ MPI_Cart_create(cr->mpi_comm_mygroup, DIM, dd->numCells, periods, static_cast<int>(reorder), &comm_cart);
/* We overwrite the old communicator with the new cartesian one */
cr->mpi_comm_mygroup = comm_cart;
}
/* Get the rank of the DD master,
* above we made sure that the master node is a PP node.
*/
- int rank;
- if (MASTER(cr))
- {
- rank = dd->rank;
- }
- else
- {
- rank = 0;
- }
+ int rank = MASTER(cr) ? dd->rank : 0;
MPI_Allreduce(&rank, &dd->masterrank, 1, MPI_INT, MPI_SUM, dd->mpi_comm_all);
}
else if (cartSetup.bCartesianPP)
buf[dd_index(dd->numCells, dd->ci)] = cr->sim_nodeid;
}
/* Communicate the ddindex to simulation nodeid index */
- MPI_Allreduce(buf.data(), cartSetup.ddindex2simnodeid.data(), dd->nnodes, MPI_INT, MPI_SUM,
- cr->mpi_comm_mysim);
+ MPI_Allreduce(buf.data(), cartSetup.ddindex2simnodeid.data(), dd->nnodes, MPI_INT, MPI_SUM, cr->mpi_comm_mysim);
/* Determine the master coordinates and rank.
* The DD master should be the same node as the master of this sim.
#endif
GMX_LOG(mdlog.info)
- .appendTextFormatted("Domain decomposition rank %d, coordinates %d %d %d\n", dd->rank,
- dd->ci[XX], dd->ci[YY], dd->ci[ZZ]);
+ .appendTextFormatted("Domain decomposition rank %d, coordinates %d %d %d\n",
+ dd->rank,
+ dd->ci[XX],
+ dd->ci[YY],
+ dd->ci[ZZ]);
if (debug)
{
- fprintf(debug, "Domain decomposition rank %d, coordinates %d %d %d\n\n", dd->rank,
- dd->ci[XX], dd->ci[YY], dd->ci[ZZ]);
+ fprintf(debug,
+ "Domain decomposition rank %d, coordinates %d %d %d\n\n",
+ dd->rank,
+ dd->ci[XX],
+ dd->ci[YY],
+ dd->ci[ZZ]);
}
}
buf[dd_index(dd->numCells, dd->ci)] = cr->sim_nodeid;
}
/* Communicate the ddindex to simulation nodeid index */
- MPI_Allreduce(buf.data(), cartSetup.ddindex2simnodeid.data(), dd->nnodes, MPI_INT, MPI_SUM,
- cr->mpi_comm_mysim);
+ MPI_Allreduce(buf.data(), cartSetup.ddindex2simnodeid.data(), dd->nnodes, MPI_INT, MPI_SUM, cr->mpi_comm_mysim);
}
#else
GMX_UNUSED_VALUE(dd);
.appendTextFormatted(
"Number of PME-only ranks (%d) is not a multiple of nx*ny (%d*%d) or "
"nx*nz (%d*%d)",
- ddRankSetup.numRanksDoingPme, numDDCells[XX], numDDCells[YY],
- numDDCells[XX], numDDCells[ZZ]);
+ ddRankSetup.numRanksDoingPme,
+ numDDCells[XX],
+ numDDCells[YY],
+ numDDCells[XX],
+ numDDCells[ZZ]);
GMX_LOG(mdlog.info)
.appendText("Will not use a Cartesian communicator for PP <-> PME\n");
}
if (cartSetup.bCartesianPP_PME)
{
#if GMX_MPI
- int rank;
+ int rank = 0;
ivec periods;
GMX_LOG(mdlog.info)
.appendTextFormatted(
"Will use a Cartesian communicator for PP <-> PME: %d x %d x %d",
- cartSetup.ntot[XX], cartSetup.ntot[YY], cartSetup.ntot[ZZ]);
+ cartSetup.ntot[XX],
+ cartSetup.ntot[YY],
+ cartSetup.ntot[ZZ]);
for (int i = 0; i < DIM; i++)
{
periods[i] = TRUE;
}
- MPI_Comm comm_cart;
- MPI_Cart_create(cr->mpi_comm_mysim, DIM, cartSetup.ntot, periods, static_cast<int>(reorder),
- &comm_cart);
+ MPI_Comm comm_cart = MPI_COMM_NULL;
+ MPI_Cart_create(cr->mpi_comm_mysim, DIM, cartSetup.ntot, periods, static_cast<int>(reorder), &comm_cart);
MPI_Comm_rank(comm_cart, &rank);
if (MASTER(cr) && rank != 0)
{
MPI_Cart_coords(cr->mpi_comm_mysim, cr->sim_nodeid, DIM, ddCellIndex);
GMX_LOG(mdlog.info)
- .appendTextFormatted("Cartesian rank %d, coordinates %d %d %d\n", cr->sim_nodeid,
- ddCellIndex[XX], ddCellIndex[YY], ddCellIndex[ZZ]);
+ .appendTextFormatted("Cartesian rank %d, coordinates %d %d %d\n",
+ cr->sim_nodeid,
+ ddCellIndex[XX],
+ ddCellIndex[YY],
+ ddCellIndex[ZZ]);
if (ddCellIndex[cartSetup.cartpmedim] < numDDCells[cartSetup.cartpmedim])
{
}
/* Split the sim communicator into PP and PME only nodes */
- MPI_Comm_split(cr->mpi_comm_mysim, getThisRankDuties(cr),
- dd_index(cartSetup.ntot, ddCellIndex), &cr->mpi_comm_mygroup);
+ MPI_Comm_split(cr->mpi_comm_mysim,
+ getThisRankDuties(cr),
+ dd_index(cartSetup.ntot, ddCellIndex),
+ &cr->mpi_comm_mygroup);
#else
GMX_UNUSED_VALUE(ddCellIndex);
#endif
if (ddRankSetup.usePmeOnlyRanks)
{
/* Split the communicator into a PP and PME part */
- cartSetup = split_communicator(mdlog, cr, ddRankOrder, ddSettings.useCartesianReorder,
- ddRankSetup, ddCellIndex, pmeRanks);
+ cartSetup = split_communicator(
+ mdlog, cr, ddRankOrder, ddSettings.useCartesianReorder, ddRankSetup, ddCellIndex, pmeRanks);
}
else
{
dd->pme_receive_vir_ener = receive_vir_ener(dd, pmeRanks, cr);
if (debug)
{
- fprintf(debug, "My pme_nodeid %d receive ener %s\n", dd->pme_nodeid,
+ fprintf(debug,
+ "My pme_nodeid %d receive ener %s\n",
+ dd->pme_nodeid,
gmx::boolToString(dd->pme_receive_vir_ener));
}
}
static real* get_slb_frac(const gmx::MDLogger& mdlog, const char* dir, int nc, const char* size_string)
{
- real * slb_frac, tot;
- int i, n;
- double dbl;
-
- slb_frac = nullptr;
+ real* slb_frac = nullptr;
if (nc > 1 && size_string != nullptr)
{
GMX_LOG(mdlog.info).appendTextFormatted("Using static load balancing for the %s direction", dir);
snew(slb_frac, nc);
- tot = 0;
- for (i = 0; i < nc; i++)
+ real tot = 0;
+ for (int i = 0; i < nc; i++)
{
- dbl = 0;
+ double dbl = 0;
+ int n = 0;
sscanf(size_string, "%20lf%n", &dbl, &n);
if (dbl == 0)
{
gmx_fatal(FARGS,
"Incorrect or not enough DD cell size entries for direction %s: '%s'",
- dir, size_string);
+ dir,
+ size_string);
}
slb_frac[i] = dbl;
size_string += n;
}
/* Normalize */
std::string relativeCellSizes = "Relative cell sizes:";
- for (i = 0; i < nc; i++)
+ for (int i = 0; i < nc; i++)
{
slb_frac[i] /= tot;
relativeCellSizes += gmx::formatString(" %5.3f", slb_frac[i]);
return slb_frac;
}
-static int multi_body_bondeds_count(const gmx_mtop_t* mtop)
+static int multi_body_bondeds_count(const gmx_mtop_t& mtop)
{
- int n = 0;
- gmx_mtop_ilistloop_t iloop = gmx_mtop_ilistloop_init(mtop);
- int nmol;
- while (const InteractionLists* ilists = gmx_mtop_ilistloop_next(iloop, &nmol))
+ int n = 0;
+ for (const auto ilists : IListRange(mtop))
{
- for (auto& ilist : extractILists(*ilists, IF_BOND))
+ for (auto& ilist : extractILists(ilists.list(), IF_BOND))
{
if (NRAL(ilist.functionType) > 2)
{
- n += nmol * (ilist.iatoms.size() / ilistStride(ilist));
+ n += ilists.nmol() * (ilist.iatoms.size() / ilistStride(ilist));
}
}
}
static int dd_getenv(const gmx::MDLogger& mdlog, const char* env_var, int def)
{
- char* val;
- int nst;
-
- nst = def;
- val = getenv(env_var);
+ int nst = def;
+ char* val = getenv(env_var);
if (val)
{
if (sscanf(val, "%20d", &nst) <= 0)
return nst;
}
-static void check_dd_restrictions(const gmx_domdec_t* dd, const t_inputrec* ir, const gmx::MDLogger& mdlog)
+static void check_dd_restrictions(const gmx_domdec_t* dd, const t_inputrec& inputrec, const gmx::MDLogger& mdlog)
{
- if (ir->pbcType == PbcType::Screw
+ if (inputrec.pbcType == PbcType::Screw
&& (dd->numCells[XX] == 1 || dd->numCells[YY] > 1 || dd->numCells[ZZ] > 1))
{
- gmx_fatal(FARGS, "With pbc=%s can only do domain decomposition in the x-direction",
- c_pbcTypeNames[ir->pbcType].c_str());
+ gmx_fatal(FARGS,
+ "With pbc=%s can only do domain decomposition in the x-direction",
+ c_pbcTypeNames[inputrec.pbcType].c_str());
}
- if (ir->nstlist == 0)
+ if (inputrec.nstlist == 0)
{
gmx_fatal(FARGS, "Domain decomposition does not work with nstlist=0");
}
- if (ir->comm_mode == ecmANGULAR && ir->pbcType != PbcType::No)
+ if (inputrec.comm_mode == ComRemovalAlgorithm::Angular && inputrec.pbcType != PbcType::No)
{
GMX_LOG(mdlog.warning)
.appendText(
* \param [in] dlbOption Enum value for the DLB option.
* \param [in] bRecordLoad True if the load balancer is recording load information.
* \param [in] mdrunOptions Options for mdrun.
- * \param [in] ir Pointer mdrun to input parameters.
+ * \param [in] inputrec Pointer mdrun to input parameters.
* \returns DLB initial/startup state.
*/
static DlbState determineInitialDlbState(const gmx::MDLogger& mdlog,
DlbOption dlbOption,
gmx_bool bRecordLoad,
const gmx::MdrunOptions& mdrunOptions,
- const t_inputrec* ir)
+ const t_inputrec& inputrec)
{
DlbState dlbState = DlbState::offCanTurnOn;
}
/* Unsupported integrators */
- if (!EI_DYNAMICS(ir->eI))
+ if (!EI_DYNAMICS(inputrec.eI))
{
- auto reasonStr = gmx::formatString(
- "it is only supported with dynamics, not with integrator '%s'.", EI(ir->eI));
+ auto reasonStr =
+ gmx::formatString("it is only supported with dynamics, not with integrator '%s'.",
+ enumValueToString(inputrec.eI));
return forceDlbOffOrBail(dlbState, reasonStr, mdlog);
}
"ensured.",
mdlog);
default:
- gmx_fatal(FARGS, "Death horror: undefined case (%d) for load balancing choice",
+ gmx_fatal(FARGS,
+ "Death horror: undefined case (%d) for load balancing choice",
static_cast<int>(dlbState));
}
}
/* Returns whether mtop contains constraints and/or vsites */
static bool systemHasConstraintsOrVsites(const gmx_mtop_t& mtop)
{
- auto ilistLoop = gmx_mtop_ilistloop_init(mtop);
- int nmol;
- while (const InteractionLists* ilists = gmx_mtop_ilistloop_next(ilistLoop, &nmol))
- {
- if (!extractILists(*ilists, IF_CONSTRAINT | IF_VSITE).empty())
- {
- return true;
- }
- }
-
- return false;
+ return std::any_of(IListRange(mtop).begin(), IListRange(mtop).end(), [](const auto ilist) {
+ return !extractILists(ilist.list(), IF_CONSTRAINT | IF_VSITE).empty();
+ });
}
static void setupUpdateGroups(const gmx::MDLogger& mdlog,
return;
}
- systemInfo->updateGroupingPerMoleculetype = gmx::makeUpdateGroups(mtop);
- systemInfo->useUpdateGroups = (!systemInfo->updateGroupingPerMoleculetype.empty()
+ systemInfo->updateGroupingsPerMoleculeType = gmx::makeUpdateGroupingsPerMoleculeType(mtop);
+ systemInfo->useUpdateGroups = (!systemInfo->updateGroupingsPerMoleculeType.empty()
&& getenv("GMX_NO_UPDATEGROUPS") == nullptr);
if (systemInfo->useUpdateGroups)
for (const auto& molblock : mtop.molblock)
{
numUpdateGroups += molblock.nmol
- * systemInfo->updateGroupingPerMoleculetype[molblock.type].numBlocks();
+ * systemInfo->updateGroupingsPerMoleculeType[molblock.type].numBlocks();
}
systemInfo->maxUpdateGroupRadius = computeMaxUpdateGroupRadius(
- mtop, systemInfo->updateGroupingPerMoleculetype, maxReferenceTemperature(inputrec));
+ mtop, systemInfo->updateGroupingsPerMoleculeType, maxReferenceTemperature(inputrec));
/* To use update groups, the large domain-to-domain cutoff distance
* should be compatible with the box size.
.appendTextFormatted(
"Using update groups, nr %d, average size %.1f atoms, max. radius %.3f "
"nm\n",
- numUpdateGroups, mtop.natoms / static_cast<double>(numUpdateGroups),
+ numUpdateGroups,
+ mtop.natoms / static_cast<double>(numUpdateGroups),
systemInfo->maxUpdateGroupRadius);
}
else
.appendTextFormatted(
"The combination of rlist and box size prohibits the use of update "
"groups\n");
- systemInfo->updateGroupingPerMoleculetype.clear();
+ systemInfo->updateGroupingsPerMoleculeType.clear();
}
}
}
/* Returns whether molecules are always whole, i.e. not broken by PBC */
static bool moleculesAreAlwaysWhole(const gmx_mtop_t& mtop,
const bool useUpdateGroups,
- gmx::ArrayRef<const gmx::RangePartitioning> updateGroupingPerMoleculetype)
+ gmx::ArrayRef<const gmx::RangePartitioning> updateGroupingsPerMoleculeType)
{
if (useUpdateGroups)
{
- GMX_RELEASE_ASSERT(updateGroupingPerMoleculetype.size() == mtop.moltype.size(),
+ GMX_RELEASE_ASSERT(updateGroupingsPerMoleculeType.size() == mtop.moltype.size(),
"Need one grouping per moltype");
for (size_t mol = 0; mol < mtop.moltype.size(); mol++)
{
- if (updateGroupingPerMoleculetype[mol].numBlocks() > 1)
+ if (updateGroupingsPerMoleculeType[mol].numBlocks() > 1)
{
return false;
}
/* We need to decide on update groups early, as this affects communication distances */
systemInfo.useUpdateGroups = false;
- if (ir.cutoff_scheme == ecutsVERLET)
+ if (ir.cutoff_scheme == CutoffScheme::Verlet)
{
real cutoffMargin = std::sqrt(max_cutoff2(ir.pbcType, box)) - ir.rlist;
setupUpdateGroups(mdlog, mtop, ir, cutoffMargin, &systemInfo);
}
systemInfo.moleculesAreAlwaysWhole = moleculesAreAlwaysWhole(
- mtop, systemInfo.useUpdateGroups, systemInfo.updateGroupingPerMoleculetype);
+ mtop, systemInfo.useUpdateGroups, systemInfo.updateGroupingsPerMoleculeType);
systemInfo.haveInterDomainBondeds =
(!systemInfo.moleculesAreAlwaysWhole || mtop.bIntermolecularInteractions);
systemInfo.haveInterDomainMultiBodyBondeds =
- (systemInfo.haveInterDomainBondeds && multi_body_bondeds_count(&mtop) > 0);
+ (systemInfo.haveInterDomainBondeds && multi_body_bondeds_count(mtop) > 0);
if (systemInfo.useUpdateGroups)
{
- systemInfo.haveSplitConstraints = false;
- systemInfo.haveSplitSettles = false;
+ systemInfo.mayHaveSplitConstraints = false;
+ systemInfo.mayHaveSplitSettles = false;
}
else
{
- systemInfo.haveSplitConstraints = (gmx_mtop_ftype_count(mtop, F_CONSTR) > 0
- || gmx_mtop_ftype_count(mtop, F_CONSTRNC) > 0);
- systemInfo.haveSplitSettles = (gmx_mtop_ftype_count(mtop, F_SETTLE) > 0);
+ systemInfo.mayHaveSplitConstraints = (gmx_mtop_ftype_count(mtop, F_CONSTR) > 0
+ || gmx_mtop_ftype_count(mtop, F_CONSTRNC) > 0);
+ systemInfo.mayHaveSplitSettles = (gmx_mtop_ftype_count(mtop, F_SETTLE) > 0);
}
if (ir.rlist == 0)
*/
constexpr real c_chanceThatAtomMovesBeyondDomain = 1e-12;
const real limitForAtomDisplacement = minCellSizeForAtomDisplacement(
- mtop, ir, systemInfo.updateGroupingPerMoleculetype, c_chanceThatAtomMovesBeyondDomain);
+ mtop, ir, systemInfo.updateGroupingsPerMoleculeType, c_chanceThatAtomMovesBeyondDomain);
GMX_LOG(mdlog.info).appendTextFormatted("Minimum cell size due to atom displacement: %.3f nm", limitForAtomDisplacement);
systemInfo.cellsizeLimit = std::max(systemInfo.cellsizeLimit, limitForAtomDisplacement);
}
else
{
- real r_2b, r_mb;
+ real r_2b = 0;
+ real r_mb = 0;
if (ddRole == DDRole::Master)
{
- dd_bonded_cg_distance(mdlog, &mtop, &ir, xGlobal, box,
- options.checkBondedInteractions, &r_2b, &r_mb);
+ dd_bonded_cg_distance(mdlog, mtop, ir, xGlobal, box, options.ddBondedChecking, &r_2b, &r_mb);
}
gmx_bcast(sizeof(r_2b), &r_2b, communicator);
gmx_bcast(sizeof(r_mb), &r_mb, communicator);
}
systemInfo.constraintCommunicationRange = 0;
- if (systemInfo.haveSplitConstraints && options.constraintCommunicationRange <= 0)
+ if (systemInfo.mayHaveSplitConstraints && options.constraintCommunicationRange <= 0)
{
/* There is a cell size limit due to the constraints (P-LINCS) */
systemInfo.constraintCommunicationRange = gmx::constr_r_max(mdlog, &mtop, &ir);
{
if (options.numCells[XX] <= 0 && (ddGridSetup.numDomains[XX] == 0))
{
- char buf[STRLEN];
- gmx_bool bC = (systemInfo.haveSplitConstraints
- && systemInfo.constraintCommunicationRange > systemInfo.minCutoffForMultiBody);
- sprintf(buf, "Change the number of ranks or mdrun option %s%s%s", !bC ? "-rdd" : "-rcon",
- ddSettings.initialDlbState != DlbState::offUser ? " or -dds" : "",
- bC ? " or your LINCS settings" : "");
-
- gmx_fatal_collective(FARGS, communicator, ddRole == DDRole::Master,
+ const bool bC = (systemInfo.mayHaveSplitConstraints
+ && systemInfo.constraintCommunicationRange > systemInfo.minCutoffForMultiBody);
+ std::string message =
+ gmx::formatString("Change the number of ranks or mdrun option %s%s%s",
+ !bC ? "-rdd" : "-rcon",
+ ddSettings.initialDlbState != DlbState::offUser ? " or -dds" : "",
+ bC ? " or your LINCS settings" : "");
+
+ gmx_fatal_collective(FARGS,
+ communicator,
+ ddRole == DDRole::Master,
"There is no domain decomposition for %d ranks that is compatible "
"with the given box and a minimum cell size of %g nm\n"
"%s\n"
"Look in the log file for details on the domain decomposition",
- numNodes - ddGridSetup.numPmeOnlyRanks, cellsizeLimit, buf);
+ numNodes - ddGridSetup.numPmeOnlyRanks,
+ cellsizeLimit,
+ message.c_str());
}
const real acs = average_cellsize_min(ddbox, ddGridSetup.numDomains);
else
{
gmx_fatal_collective(
- FARGS, communicator, ddRole == DDRole::Master,
+ FARGS,
+ communicator,
+ ddRole == DDRole::Master,
"The initial cell size (%f) is smaller than the cell size limit (%f), change "
"options -dd, -rdd or -rcon, see the log file for details",
- acs, cellsizeLimit);
+ acs,
+ cellsizeLimit);
}
}
ddGridSetup.numDomains[XX] * ddGridSetup.numDomains[YY] * ddGridSetup.numDomains[ZZ];
if (numNodes - numPPRanks != ddGridSetup.numPmeOnlyRanks)
{
- gmx_fatal_collective(FARGS, communicator, ddRole == DDRole::Master,
+ gmx_fatal_collective(FARGS,
+ communicator,
+ ddRole == DDRole::Master,
"The size of the domain decomposition grid (%d) does not match the "
"number of PP ranks (%d). The total number of ranks is %d",
- numPPRanks, numNodes - ddGridSetup.numPmeOnlyRanks, numNodes);
+ numPPRanks,
+ numNodes - ddGridSetup.numPmeOnlyRanks,
+ numNodes);
}
if (ddGridSetup.numPmeOnlyRanks > numPPRanks)
{
- gmx_fatal_collective(FARGS, communicator, ddRole == DDRole::Master,
+ gmx_fatal_collective(FARGS,
+ communicator,
+ ddRole == DDRole::Master,
"The number of separate PME ranks (%d) is larger than the number of "
"PP ranks (%d), this is not supported.",
- ddGridSetup.numPmeOnlyRanks, numPPRanks);
+ ddGridSetup.numPmeOnlyRanks,
+ numPPRanks);
}
}
{
GMX_LOG(mdlog.info)
.appendTextFormatted("Domain decomposition grid %d x %d x %d, separate PME ranks %d",
- ddGridSetup.numDomains[XX], ddGridSetup.numDomains[YY],
- ddGridSetup.numDomains[ZZ], ddGridSetup.numPmeOnlyRanks);
+ ddGridSetup.numDomains[XX],
+ ddGridSetup.numDomains[YY],
+ ddGridSetup.numDomains[ZZ],
+ ddGridSetup.numPmeOnlyRanks);
DDRankSetup ddRankSetup;
}
GMX_LOG(mdlog.info)
.appendTextFormatted("PME domain decomposition: %d x %d x %d",
- ddRankSetup.npmenodes_x, ddRankSetup.npmenodes_y, 1);
+ ddRankSetup.npmenodes_x,
+ ddRankSetup.npmenodes_y,
+ 1);
}
else
{
const DDSystemInfo& systemInfo,
const DDGridSetup& ddGridSetup,
const int numPPRanks,
- const gmx_mtop_t* mtop,
- const t_inputrec* ir,
+ const gmx_mtop_t& mtop,
+ const t_inputrec& ir,
const gmx_ddbox_t& ddbox)
{
gmx_domdec_comm_t* comm = dd->comm;
* but that is not yet available here. But this anyhow only
* affect performance up to the second dd_partition_system call.
*/
- const int homeAtomCountEstimate = mtop->natoms / numPPRanks;
+ const int homeAtomCountEstimate = mtop.natoms / numPPRanks;
comm->updateGroupsCog = std::make_unique<gmx::UpdateGroupsCog>(
- *mtop, systemInfo.updateGroupingPerMoleculetype, maxReferenceTemperature(*ir),
- homeAtomCountEstimate);
+ mtop, systemInfo.updateGroupingsPerMoleculeType, maxReferenceTemperature(ir), homeAtomCountEstimate);
}
/* Set the DD setup given by ddGridSetup */
fprintf(debug,
"Bonded atom communication beyond the cut-off: %s\n"
"cellsize limit %f\n",
- gmx::boolToString(systemInfo.filterBondedCommunication), comm->cellsize_limit);
+ gmx::boolToString(systemInfo.filterBondedCommunication),
+ comm->cellsize_limit);
}
if (ddRole == DDRole::Master)
}
}
-void dd_init_bondeds(FILE* fplog,
- gmx_domdec_t* dd,
- const gmx_mtop_t& mtop,
- const gmx::VirtualSitesHandler* vsite,
- const t_inputrec* ir,
- gmx_bool bBCheck,
- gmx::ArrayRef<cginfo_mb_t> cginfo_mb)
-{
- gmx_domdec_comm_t* comm;
-
- dd_make_reverse_top(fplog, dd, &mtop, vsite, ir, bBCheck);
-
- comm = dd->comm;
-
- if (comm->systemInfo.filterBondedCommunication)
- {
- /* Communicate atoms beyond the cut-off for bonded interactions */
- comm->bondedLinks = makeBondedLinks(mtop, cginfo_mb);
- }
- else
- {
- /* Only communicate atoms based on cut-off */
- comm->bondedLinks = nullptr;
- }
-}
-
static void writeSettings(gmx::TextWriter* log,
gmx_domdec_t* dd,
- const gmx_mtop_t* mtop,
- const t_inputrec* ir,
+ const gmx_mtop_t& mtop,
+ const t_inputrec& ir,
gmx_bool bDynLoadBal,
real dlb_scale,
const gmx_ddbox_t* ddbox)
{
- gmx_domdec_comm_t* comm;
- int d;
- ivec np;
- real limit, shrink;
-
- comm = dd->comm;
+ gmx_domdec_comm_t* comm = dd->comm;
if (bDynLoadBal)
{
log->writeString("The maximum number of communication pulses is:");
- for (d = 0; d < dd->ndim; d++)
+ for (int d = 0; d < dd->ndim; d++)
{
log->writeStringFormatted(" %c %d", dim2char(dd->dim[d]), comm->cd[d].np_dlb);
}
comm->cellsize_limit);
log->writeLineFormatted("The requested allowed shrink of DD cells (option -dds) is: %.2f", dlb_scale);
log->writeString("The allowed shrink of domain decomposition cells is:");
- for (d = 0; d < DIM; d++)
+ for (int d = 0; d < DIM; d++)
{
if (dd->numCells[d] > 1)
{
- if (d >= ddbox->npbcdim && dd->numCells[d] == 2)
- {
- shrink = 0;
- }
- else
- {
- shrink = comm->cellsize_min_dlb[d]
- / (ddbox->box_size[d] * ddbox->skew_fac[d] / dd->numCells[d]);
- }
+ const real shrink =
+ (d >= ddbox->npbcdim && dd->numCells[d] == 2)
+ ? 0
+ : comm->cellsize_min_dlb[d]
+ / (ddbox->box_size[d] * ddbox->skew_fac[d] / dd->numCells[d]);
log->writeStringFormatted(" %c %.2f", dim2char(d), shrink);
}
}
}
else
{
+ ivec np;
set_dd_cell_sizes_slb(dd, ddbox, setcellsizeslbPULSE_ONLY, np);
log->writeString("The initial number of communication pulses is:");
- for (d = 0; d < dd->ndim; d++)
+ for (int d = 0; d < dd->ndim; d++)
{
log->writeStringFormatted(" %c %d", dim2char(dd->dim[d]), np[dd->dim[d]]);
}
log->ensureLineBreak();
log->writeString("The initial domain decomposition cell size is:");
- for (d = 0; d < DIM; d++)
+ for (int d = 0; d < DIM; d++)
{
if (dd->numCells[d] > 1)
{
}
const bool haveInterDomainVsites =
- (countInterUpdategroupVsites(*mtop, comm->systemInfo.updateGroupingPerMoleculetype) != 0);
+ (countInterUpdategroupVsites(mtop, comm->systemInfo.updateGroupingsPerMoleculeType) != 0);
if (comm->systemInfo.haveInterDomainBondeds || haveInterDomainVsites
- || comm->systemInfo.haveSplitConstraints || comm->systemInfo.haveSplitSettles)
+ || comm->systemInfo.mayHaveSplitConstraints || comm->systemInfo.mayHaveSplitSettles)
{
std::string decompUnits;
if (comm->systemInfo.useUpdateGroups)
log->writeLineFormatted("The maximum allowed distance for %s involved in interactions is:",
decompUnits.c_str());
- log->writeLineFormatted("%40s %-7s %6.3f nm", "non-bonded interactions", "",
- comm->systemInfo.cutoff);
+ log->writeLineFormatted(
+ "%40s %-7s %6.3f nm", "non-bonded interactions", "", comm->systemInfo.cutoff);
+ real limit = 0;
if (bDynLoadBal)
{
limit = dd->comm->cellsize_limit;
"deformation)");
}
limit = dd->comm->cellsize_min[XX];
- for (d = 1; d < DIM; d++)
+ for (int d = 1; d < DIM; d++)
{
limit = std::min(limit, dd->comm->cellsize_min[d]);
}
if (comm->systemInfo.haveInterDomainBondeds)
{
- log->writeLineFormatted("%40s %-7s %6.3f nm", "two-body bonded interactions", "(-rdd)",
+ log->writeLineFormatted("%40s %-7s %6.3f nm",
+ "two-body bonded interactions",
+ "(-rdd)",
std::max(comm->systemInfo.cutoff, comm->cutoff_mbody));
- log->writeLineFormatted("%40s %-7s %6.3f nm", "multi-body bonded interactions",
+ log->writeLineFormatted("%40s %-7s %6.3f nm",
+ "multi-body bonded interactions",
"(-rdd)",
(comm->systemInfo.filterBondedCommunication || isDlbOn(dd->comm))
? comm->cutoff_mbody
{
log->writeLineFormatted("%40s %-7s %6.3f nm", "virtual site constructions", "(-rcon)", limit);
}
- if (comm->systemInfo.haveSplitConstraints || comm->systemInfo.haveSplitSettles)
+ if (comm->systemInfo.mayHaveSplitConstraints || comm->systemInfo.mayHaveSplitSettles)
{
std::string separation =
- gmx::formatString("atoms separated by up to %d constraints", 1 + ir->nProjOrder);
+ gmx::formatString("atoms separated by up to %d constraints", 1 + ir.nProjOrder);
log->writeLineFormatted("%40s %-7s %6.3f nm\n", separation.c_str(), "(-rcon)", limit);
}
log->ensureLineBreak();
static void logSettings(const gmx::MDLogger& mdlog,
gmx_domdec_t* dd,
- const gmx_mtop_t* mtop,
- const t_inputrec* ir,
+ const gmx_mtop_t& mtop,
+ const t_inputrec& ir,
real dlb_scale,
const gmx_ddbox_t* ddbox)
{
static void set_cell_limits_dlb(const gmx::MDLogger& mdlog,
gmx_domdec_t* dd,
real dlb_scale,
- const t_inputrec* ir,
+ const t_inputrec& inputrec,
const gmx_ddbox_t* ddbox)
{
- gmx_domdec_comm_t* comm;
- int d, dim, npulse, npulse_d_max, npulse_d;
- gmx_bool bNoCutOff;
+ int npulse = 0;
+ int npulse_d_max = 0;
+ int npulse_d = 0;
- comm = dd->comm;
+ gmx_domdec_comm_t* comm = dd->comm;
- bNoCutOff = (ir->rvdw == 0 || ir->rcoulomb == 0);
+ bool bNoCutOff = (inputrec.rvdw == 0 || inputrec.rcoulomb == 0);
/* Determine the maximum number of comm. pulses in one dimension */
{
/* See if we can do with less pulses, based on dlb_scale */
npulse_d_max = 0;
- for (d = 0; d < dd->ndim; d++)
+ for (int d = 0; d < dd->ndim; d++)
{
- dim = dd->dim[d];
+ int dim = dd->dim[d];
npulse_d = static_cast<int>(
1
+ dd->numCells[dim] * comm->systemInfo.cutoff
}
/* This env var can override npulse */
- d = dd_getenv(mdlog, "GMX_DD_NPULSE", 0);
- if (d > 0)
+ const int ddPulseEnv = dd_getenv(mdlog, "GMX_DD_NPULSE", 0);
+ if (ddPulseEnv > 0)
{
- npulse = d;
+ npulse = ddPulseEnv;
}
comm->maxpulse = 1;
- comm->bVacDLBNoLimit = (ir->pbcType == PbcType::No);
- for (d = 0; d < dd->ndim; d++)
+ comm->bVacDLBNoLimit = (inputrec.pbcType == PbcType::No);
+ for (int d = 0; d < dd->ndim; d++)
{
comm->cd[d].np_dlb = std::min(npulse, dd->numCells[dd->dim[d]] - 1);
comm->maxpulse = std::max(comm->maxpulse, comm->cd[d].np_dlb);
}
comm->cellsize_limit = std::max(comm->cellsize_limit, comm->cutoff_mbody);
/* Set the minimum cell size for each DD dimension */
- for (d = 0; d < dd->ndim; d++)
+ for (int d = 0; d < dd->ndim; d++)
{
if (comm->bVacDLBNoLimit || comm->cd[d].np_dlb * comm->cellsize_limit >= comm->systemInfo.cutoff)
{
return dd.comm->systemInfo.moleculesAreAlwaysWhole;
}
-gmx_bool dd_bonded_molpbc(const gmx_domdec_t* dd, PbcType pbcType)
+bool dd_bonded_molpbc(const gmx_domdec_t& dd, PbcType pbcType)
{
/* If each molecule is a single charge group
* or we use domain decomposition for each periodic dimension,
* we do not need to take pbc into account for the bonded interactions.
*/
- return (pbcType != PbcType::No && dd->comm->systemInfo.haveInterDomainBondeds
- && !(dd->numCells[XX] > 1 && dd->numCells[YY] > 1
- && (dd->numCells[ZZ] > 1 || pbcType == PbcType::XY)));
+ return (pbcType != PbcType::No && dd.comm->systemInfo.haveInterDomainBondeds
+ && !(dd.numCells[XX] > 1 && dd.numCells[YY] > 1
+ && (dd.numCells[ZZ] > 1 || pbcType == PbcType::XY)));
}
/*! \brief Sets grid size limits and PP-PME setup, prints settings to log */
static void set_ddgrid_parameters(const gmx::MDLogger& mdlog,
gmx_domdec_t* dd,
real dlb_scale,
- const gmx_mtop_t* mtop,
- const t_inputrec* ir,
+ const gmx_mtop_t& mtop,
+ const t_inputrec& inputrec,
const gmx_ddbox_t* ddbox)
{
gmx_domdec_comm_t* comm = dd->comm;
DDRankSetup& ddRankSetup = comm->ddRankSetup;
- if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
+ if (EEL_PME(inputrec.coulombtype) || EVDW_PME(inputrec.vdwtype))
{
init_ddpme(dd, &ddRankSetup.ddpme[0], 0);
if (ddRankSetup.npmedecompdim >= 2)
ddRankSetup.numRanksDoingPme = 0;
if (dd->pme_nodeid >= 0)
{
- gmx_fatal_collective(FARGS, dd->mpi_comm_all, DDMASTER(dd),
+ gmx_fatal_collective(FARGS,
+ dd->mpi_comm_all,
+ DDMASTER(dd),
"Can not have separate PME ranks without PME electrostatics");
}
}
}
if (!isDlbDisabled(comm))
{
- set_cell_limits_dlb(mdlog, dd, dlb_scale, ir, ddbox);
+ set_cell_limits_dlb(mdlog, dd, dlb_scale, inputrec, ddbox);
}
- logSettings(mdlog, dd, mtop, ir, dlb_scale, ddbox);
+ logSettings(mdlog, dd, mtop, inputrec, dlb_scale, ddbox);
- real vol_frac;
- if (ir->pbcType == PbcType::No)
- {
- vol_frac = 1 - 1 / static_cast<double>(dd->nnodes);
- }
- else
- {
- vol_frac = (1 + comm_box_frac(dd->numCells, comm->systemInfo.cutoff, *ddbox))
- / static_cast<double>(dd->nnodes);
- }
+ const real vol_frac = (inputrec.pbcType == PbcType::No)
+ ? (1 - 1 / static_cast<double>(dd->nnodes))
+ : ((1 + comm_box_frac(dd->numCells, comm->systemInfo.cutoff, *ddbox))
+ / static_cast<double>(dd->nnodes));
if (debug)
{
fprintf(debug, "Volume fraction for all DD zones: %f\n", vol_frac);
}
- int natoms_tot = mtop->natoms;
+ int natoms_tot = mtop.natoms;
dd->ga2la = new gmx_ga2la_t(natoms_tot, static_cast<int>(vol_frac * natoms_tot));
}
ddSettings.recordLoad = (wallcycle_have_counter() && recload > 0);
}
- ddSettings.initialDlbState = determineInitialDlbState(mdlog, options.dlbOption,
- ddSettings.recordLoad, mdrunOptions, &ir);
+ ddSettings.initialDlbState =
+ determineInitialDlbState(mdlog, options.dlbOption, ddSettings.recordLoad, mdrunOptions, ir);
GMX_LOG(mdlog.info)
.appendTextFormatted("Dynamic load balancing: %s",
- edlbs_names[static_cast<int>(ddSettings.initialDlbState)]);
+ enumValueToString(ddSettings.initialDlbState));
return ddSettings;
}
gmx_domdec_t::gmx_domdec_t(const t_inputrec& ir) : unitCellInfo(ir) {}
+gmx_domdec_t::~gmx_domdec_t() = default;
+
namespace gmx
{
srand(1 + cr_->rankInDefaultCommunicator);
}
- systemInfo_ = getSystemInfo(mdlog_, MASTER(cr_) ? DDRole::Master : DDRole::Agent,
- cr->mpiDefaultCommunicator, options_, mtop_, ir_, box, xGlobal);
+ systemInfo_ = getSystemInfo(mdlog_,
+ MASTER(cr_) ? DDRole::Master : DDRole::Agent,
+ cr->mpiDefaultCommunicator,
+ options_,
+ mtop_,
+ ir_,
+ box,
+ xGlobal);
const int numRanksRequested = cr_->sizeOfDefaultCommunicator;
const bool checkForLargePrimeFactors = (options_.numCells[0] <= 0);
- checkForValidRankCountRequests(numRanksRequested, EEL_PME(ir_.coulombtype),
- options_.numPmeRanks, checkForLargePrimeFactors);
+ checkForValidRankCountRequests(
+ numRanksRequested, EEL_PME(ir_.coulombtype), options_.numPmeRanks, checkForLargePrimeFactors);
// DD grid setup uses a more different cell size limit for
// automated setup than the one in systemInfo_. The latter is used
// in set_dd_limits() to configure DLB, for example.
const real gridSetupCellsizeLimit =
- getDDGridSetupCellSizeLimit(mdlog_, !isDlbDisabled(ddSettings_.initialDlbState),
- options_.dlbScaling, ir_, systemInfo_.cellsizeLimit);
- ddGridSetup_ =
- getDDGridSetup(mdlog_, MASTER(cr_) ? DDRole::Master : DDRole::Agent,
- cr->mpiDefaultCommunicator, numRanksRequested, options_, ddSettings_,
- systemInfo_, gridSetupCellsizeLimit, mtop_, ir_, box, xGlobal, &ddbox_);
- checkDDGridSetup(ddGridSetup_, MASTER(cr_) ? DDRole::Master : DDRole::Agent,
- cr->mpiDefaultCommunicator, cr->sizeOfDefaultCommunicator, options_,
- ddSettings_, systemInfo_, gridSetupCellsizeLimit, ddbox_);
+ getDDGridSetupCellSizeLimit(mdlog_,
+ !isDlbDisabled(ddSettings_.initialDlbState),
+ options_.dlbScaling,
+ ir_,
+ systemInfo_.cellsizeLimit);
+ ddGridSetup_ = getDDGridSetup(mdlog_,
+ MASTER(cr_) ? DDRole::Master : DDRole::Agent,
+ cr->mpiDefaultCommunicator,
+ numRanksRequested,
+ options_,
+ ddSettings_,
+ systemInfo_,
+ gridSetupCellsizeLimit,
+ mtop_,
+ ir_,
+ box,
+ xGlobal,
+ &ddbox_);
+ checkDDGridSetup(ddGridSetup_,
+ MASTER(cr_) ? DDRole::Master : DDRole::Agent,
+ cr->mpiDefaultCommunicator,
+ cr->sizeOfDefaultCommunicator,
+ options_,
+ ddSettings_,
+ systemInfo_,
+ gridSetupCellsizeLimit,
+ ddbox_);
cr_->npmenodes = ddGridSetup_.numPmeOnlyRanks;
ddRankSetup_ = getDDRankSetup(mdlog_, cr_->sizeOfDefaultCommunicator, ddGridSetup_, ir_);
/* Generate the group communicator, also decides the duty of each rank */
- cartSetup_ = makeGroupCommunicators(mdlog_, ddSettings_, options_.rankOrder, ddRankSetup_, cr_,
- ddCellIndex_, &pmeRanks_);
+ cartSetup_ = makeGroupCommunicators(
+ mdlog_, ddSettings_, options_.rankOrder, ddRankSetup_, cr_, ddCellIndex_, &pmeRanks_);
}
gmx_domdec_t* DomainDecompositionBuilder::Impl::build(LocalAtomSetManager* atomSets)
dd->comm->ddRankSetup = ddRankSetup_;
dd->comm->cartesianRankSetup = cartSetup_;
- set_dd_limits(mdlog_, MASTER(cr_) ? DDRole::Master : DDRole::Agent, dd, options_, ddSettings_,
- systemInfo_, ddGridSetup_, ddRankSetup_.numPPRanks, &mtop_, &ir_, ddbox_);
+ set_dd_limits(mdlog_,
+ MASTER(cr_) ? DDRole::Master : DDRole::Agent,
+ dd,
+ options_,
+ ddSettings_,
+ systemInfo_,
+ ddGridSetup_,
+ ddRankSetup_.numPPRanks,
+ mtop_,
+ ir_,
+ ddbox_);
setupGroupCommunication(mdlog_, ddSettings_, pmeRanks_, cr_, mtop_.natoms, dd);
if (thisRankHasDuty(cr_, DUTY_PP))
{
- set_ddgrid_parameters(mdlog_, dd, options_.dlbScaling, &mtop_, &ir_, &ddbox_);
+ set_ddgrid_parameters(mdlog_, dd, options_.dlbScaling, mtop_, ir_, &ddbox_);
setup_neighbor_relations(dd);
}
/* Set overallocation to avoid frequent reallocation of arrays */
- set_over_alloc_dd(TRUE);
+ set_over_alloc_dd(true);
dd->atomSets = atomSets;
static gmx_bool test_dd_cutoff(const t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
{
gmx_ddbox_t ddbox;
- int d, dim, np;
- real inv_cell_size;
- int LocallyLimited;
+ int LocallyLimited = 0;
const auto* dd = cr->dd;
LocallyLimited = 0;
- for (d = 0; d < dd->ndim; d++)
+ for (int d = 0; d < dd->ndim; d++)
{
- dim = dd->dim[d];
+ const int dim = dd->dim[d];
- inv_cell_size = DD_CELL_MARGIN * dd->numCells[dim] / ddbox.box_size[dim];
+ real inv_cell_size = DD_CELL_MARGIN * dd->numCells[dim] / ddbox.box_size[dim];
if (dd->unitCellInfo.ddBoxIsDynamic)
{
inv_cell_size *= DD_PRES_SCALE_MARGIN;
}
- np = 1 + static_cast<int>(cutoffRequested * inv_cell_size * ddbox.skew_fac[dim]);
+ const int np = 1 + static_cast<int>(cutoffRequested * inv_cell_size * ddbox.skew_fac[dim]);
if (!isDlbDisabled(dd->comm) && (dim < ddbox.npbcdim) && (dd->comm->cd[d].np_dlb > 0))
{
/* If DLB is not active yet, we don't need to check the grid jumps.
* Actually we shouldn't, because then the grid jump data is not set.
*/
- if (isDlbOn(dd->comm) && check_grid_jump(0, dd, cutoffRequested, &ddbox, FALSE))
+ if (isDlbOn(dd->comm) && gmx::check_grid_jump(0, dd, cutoffRequested, &ddbox, FALSE))
{
LocallyLimited = 1;
}
return TRUE;
}
-gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
+bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
{
- gmx_bool bCutoffAllowed;
-
- bCutoffAllowed = test_dd_cutoff(cr, box, x, cutoffRequested);
+ bool bCutoffAllowed = test_dd_cutoff(cr, box, x, cutoffRequested);
if (bCutoffAllowed)
{
for (int pulse = cr.dd->gpuHaloExchange[d].size(); pulse < cr.dd->comm->cd[d].numPulses(); pulse++)
{
cr.dd->gpuHaloExchange[d].push_back(std::make_unique<gmx::GpuHaloExchange>(
- cr.dd, d, cr.mpi_comm_mysim, deviceStreamManager.context(),
+ cr.dd,
+ d,
+ cr.mpi_comm_mygroup,
+ deviceStreamManager.context(),
deviceStreamManager.stream(gmx::DeviceStreamType::NonBondedLocal),
- deviceStreamManager.stream(gmx::DeviceStreamType::NonBondedNonLocal), pulse, wcycle));
+ deviceStreamManager.stream(gmx::DeviceStreamType::NonBondedNonLocal),
+ pulse,
+ wcycle));
}
}
}
*
* Copyright (c) 2005 - 2014, The GROMACS development team.
* Copyright (c) 2015,2016,2017,2018,2019 by the GROMACS development team.
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
struct cginfo_mb_t;
struct gmx_domdec_zones_t;
struct gmx_localtop_t;
struct gmx_mtop_t;
-struct t_block;
-struct t_blocka;
struct t_commrec;
struct t_forcerec;
struct t_inputrec;
class MDLogger;
class RangePartitioning;
class VirtualSitesHandler;
+template<typename>
+class ArrayRef;
+enum class DDBondedChecking : bool;
} // namespace gmx
/*! \brief Returns the global topology atom number belonging to local atom index i.
int ddglatnr(const gmx_domdec_t* dd, int i);
/*! \brief Returns a list of update group partitioning for each molecule type or empty when update groups are not used */
-gmx::ArrayRef<const gmx::RangePartitioning> getUpdateGroupingPerMoleculetype(const gmx_domdec_t& dd);
+gmx::ArrayRef<const gmx::RangePartitioning> getUpdateGroupingsPerMoleculeType(const gmx_domdec_t& dd);
/*! \brief Store the global cg indices of the home cgs in state,
*
* This means it can be reset, even after a new DD partitioning.
*/
-void dd_store_state(struct gmx_domdec_t* dd, t_state* state);
+void dd_store_state(const gmx_domdec_t& dd, t_state* state);
/*! \brief Returns a pointer to the gmx_domdec_zones_t struct */
struct gmx_domdec_zones_t* domdec_zones(struct gmx_domdec_t* dd);
int dd_numHomeAtoms(const gmx_domdec_t& dd);
/*! \brief Returns the atom range in the local state for atoms that need to be present in mdatoms */
-int dd_natoms_mdatoms(const gmx_domdec_t* dd);
+int dd_natoms_mdatoms(const gmx_domdec_t& dd);
/*! \brief Returns the atom range in the local state for atoms involved in virtual sites */
-int dd_natoms_vsite(const gmx_domdec_t* dd);
+int dd_natoms_vsite(const gmx_domdec_t& dd);
/*! \brief Sets the atom range for atom in the local state for atoms received in constraints communication */
-void dd_get_constraint_range(const gmx_domdec_t* dd, int* at_start, int* at_end);
+void dd_get_constraint_range(const gmx_domdec_t& dd, int* at_start, int* at_end);
/*! \libinternal \brief Struct for passing around the number of PME domains */
struct NumPmeDomains
std::vector<int> get_pme_ddranks(const t_commrec* cr, int pmenodeid);
/*! \brief Returns the maximum shift for coordinate communication in PME, dim x */
-int dd_pme_maxshift_x(const gmx_domdec_t* dd);
+int dd_pme_maxshift_x(const gmx_domdec_t& dd);
/*! \brief Returns the maximum shift for coordinate communication in PME, dim y */
-int dd_pme_maxshift_y(const gmx_domdec_t* dd);
+int dd_pme_maxshift_y(const gmx_domdec_t& dd);
-/*! \brief Return whether constraints, not including settles, cross domain boundaries */
-bool ddHaveSplitConstraints(const gmx_domdec_t& dd);
+/*! \brief Return whether constraints, not including settles, may cross domain boundaries */
+bool ddMayHaveSplitConstraints(const gmx_domdec_t& dd);
/*! \brief Return whether update groups are used */
bool ddUsesUpdateGroups(const gmx_domdec_t& dd);
-/*! \brief Initialize data structures for bonded interactions */
-void dd_init_bondeds(FILE* fplog,
- gmx_domdec_t* dd,
- const gmx_mtop_t& mtop,
- const gmx::VirtualSitesHandler* vsite,
- const t_inputrec* ir,
- gmx_bool bBCheck,
- gmx::ArrayRef<cginfo_mb_t> cginfo_mb);
-
/*! \brief Returns whether molecules are always whole, i.e. not broken by PBC */
bool dd_moleculesAreAlwaysWhole(const gmx_domdec_t& dd);
/*! \brief Returns if we need to do pbc for calculating bonded interactions */
-gmx_bool dd_bonded_molpbc(const gmx_domdec_t* dd, PbcType pbcType);
+bool dd_bonded_molpbc(const gmx_domdec_t& dd, PbcType pbcType);
/*! \brief Change the DD non-bonded communication cut-off.
*
* \param[in] x Position vector, used for computing the dimensions of the system
* \param[in] cutoffRequested The requested atom to atom cut-off distance, usually the pair-list cutoff distance
*/
-gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested);
+bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested);
/*! \brief Set up communication for averaging GPU wait times over domains
*
const matrix box,
gmx::ArrayRef<gmx::RVec> x0,
gmx::ArrayRef<gmx::RVec> x1,
- gmx_bool bX1IsCoord);
+ bool bX1IsCoord);
/*! \brief Communicates the coordinates involved in virtual sites */
void dd_move_x_vsites(const gmx_domdec_t& dd, const matrix box, rvec* x);
+/*! \brief Communicates the positions and velocities involved in virtual sites */
+void dd_move_x_and_v_vsites(const gmx_domdec_t& dd, const matrix box, rvec* x, rvec* v);
/*! \brief Returns the local atom count array for all constraints
*
[[noreturn]] void dd_print_missing_interactions(const gmx::MDLogger& mdlog,
t_commrec* cr,
int local_count,
- const gmx_mtop_t* top_global,
+ const gmx_mtop_t& top_global,
const gmx_localtop_t* top_local,
gmx::ArrayRef<const gmx::RVec> x,
const matrix box);
/*! \brief Generate and store the reverse topology */
void dd_make_reverse_top(FILE* fplog,
gmx_domdec_t* dd,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const gmx::VirtualSitesHandler* vsite,
- const t_inputrec* ir,
- gmx_bool bBCheck);
+ const t_inputrec& inputrec,
+ gmx::DDBondedChecking ddBondedChecking);
+
+/*! \brief Return whether the total bonded interaction count across
+ * domains should be checked this step. */
+bool shouldCheckNumberOfBondedInteractions(const gmx_domdec_t& dd);
+
+//! Return the number of bonded interactions in this domain.
+int numBondedInteractions(const gmx_domdec_t& dd);
+
+/*! \brief Set total bonded interaction count across domains. */
+void setNumberOfBondedInteractionsOverAllDomains(const gmx_domdec_t& dd, int newValue);
+
+/*! \brief Check whether bonded interactions are missing from the reverse topology
+ * produced by domain decomposition.
+ *
+ * Must only be called when DD is active.
+ *
+ * \param[in] mdlog Logger
+ * \param[in] cr Communication object
+ * \param[in] top_global Global topology for the error message
+ * \param[in] top_local Local topology for the error message
+ * \param[in] x Position vector for the error message
+ * \param[in] box Box matrix for the error message
+ */
+void checkNumberOfBondedInteractions(const gmx::MDLogger& mdlog,
+ t_commrec* cr,
+ const gmx_mtop_t& top_global,
+ const gmx_localtop_t* top_local,
+ gmx::ArrayRef<const gmx::RVec> x,
+ const matrix box);
/*! \brief Generate the local topology and virtual site data */
-void dd_make_local_top(struct gmx_domdec_t* dd,
- struct gmx_domdec_zones_t* zones,
- int npbcdim,
- matrix box,
- rvec cellsize_min,
- const ivec npulse,
- t_forcerec* fr,
- rvec* cgcm_or_x,
- const gmx_mtop_t& top,
- gmx_localtop_t* ltop);
+void dd_make_local_top(struct gmx_domdec_t* dd,
+ struct gmx_domdec_zones_t* zones,
+ int npbcdim,
+ matrix box,
+ rvec cellsize_min,
+ const ivec npulse,
+ t_forcerec* fr,
+ gmx::ArrayRef<const gmx::RVec> coordinates,
+ const gmx_mtop_t& top,
+ gmx_localtop_t* ltop);
/*! \brief Sort ltop->ilist when we are doing free energy. */
-void dd_sort_local_top(gmx_domdec_t* dd, const t_mdatoms* mdatoms, gmx_localtop_t* ltop);
+void dd_sort_local_top(const gmx_domdec_t& dd, const t_mdatoms* mdatoms, gmx_localtop_t* ltop);
/*! \brief Construct local state */
-void dd_init_local_state(struct gmx_domdec_t* dd, const t_state* state_global, t_state* local_state);
+void dd_init_local_state(const gmx_domdec_t& dd, const t_state* state_global, t_state* local_state);
/*! \brief Generate a list of links between atoms that are linked by bonded interactions
*
* Also stores whether atoms are linked in \p cginfo_mb.
*/
-t_blocka* makeBondedLinks(const gmx_mtop_t& mtop, gmx::ArrayRef<cginfo_mb_t> cginfo_mb);
+void makeBondedLinks(gmx_domdec_t* dd, const gmx_mtop_t& mtop, gmx::ArrayRef<cginfo_mb_t> cginfo_mb);
/*! \brief Calculate the maximum distance involved in 2-body and multi-body bonded interactions */
void dd_bonded_cg_distance(const gmx::MDLogger& mdlog,
- const gmx_mtop_t* mtop,
- const t_inputrec* ir,
+ const gmx_mtop_t& mtop,
+ const t_inputrec& ir,
gmx::ArrayRef<const gmx::RVec> x,
const matrix box,
- gmx_bool bBCheck,
+ gmx::DDBondedChecking ddBondedChecking,
real* r_2b,
real* r_mb);
*
* Copyright (c) 2006,2007,2008,2009,2010 by the GROMACS development team.
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const matrix box,
gmx::ArrayRef<gmx::RVec> x0,
gmx::ArrayRef<gmx::RVec> x1,
- gmx_bool bX1IsCoord)
+ bool bX1IsCoord)
{
if (dd->constraint_comm)
{
- dd_move_x_specat(dd, dd->constraint_comm, box, as_rvec_array(x0.data()),
- as_rvec_array(x1.data()), bX1IsCoord);
+ dd_move_x_specat(
+ dd, dd->constraint_comm, box, as_rvec_array(x0.data()), as_rvec_array(x1.data()), bX1IsCoord);
ddReopenBalanceRegionCpu(dd);
}
{
/* Walk further */
const int* iap = constr_iatomptr(ia1, ia2, coni);
- int b;
- if (a == iap[1])
- {
- b = iap[2];
- }
- else
- {
- b = iap[1];
- }
+ const int b = (a == iap[1]) ? iap[2] : iap[1];
if (!ga2la.findHome(offset + b))
{
- walk_out(coni, con_offset, b, offset, nrec - 1, ia1, ia2, at2con, ga2la, FALSE,
- dc, dcc, il_local, ireq);
+ walk_out(coni, con_offset, b, offset, nrec - 1, ia1, ia2, at2con, ga2la, FALSE, dc, dcc, il_local, ireq);
}
}
}
/*! \brief Looks up SETTLE constraints for a range of charge-groups */
static void atoms_to_settles(gmx_domdec_t* dd,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const int* cginfo,
gmx::ArrayRef<const std::vector<int>> at2settle_mt,
int cg_start,
{
if (GET_CGINFO_SETTLE(cginfo[a]))
{
- int a_gl = dd->globalAtomIndices[a];
- int a_mol;
+ int a_gl = dd->globalAtomIndices[a];
+ int a_mol = 0;
mtopGetMolblockIndex(mtop, a_gl, &mb, nullptr, &a_mol);
- const gmx_molblock_t* molb = &mtop->molblock[mb];
+ const gmx_molblock_t* molb = &mtop.molblock[mb];
int settle = at2settle_mt[molb->type][a_mol];
if (settle >= 0)
{
int offset = a_gl - a_mol;
- const int* ia1 = mtop->moltype[molb->type].ilist[F_SETTLE].iatoms.data();
+ const int* ia1 = mtop.moltype[molb->type].ilist[F_SETTLE].iatoms.data();
int a_gls[3];
gmx_bool bAssign = FALSE;
/*! \brief Looks up constraint for the local atoms */
static void atoms_to_constraints(gmx_domdec_t* dd,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const int* cginfo,
gmx::ArrayRef<const ListOfLists<int>> at2con_mt,
int nrec,
{
if (GET_CGINFO_CONSTR(cginfo[a]))
{
- int a_gl = dd->globalAtomIndices[a];
- int molnr, a_mol;
+ int a_gl = dd->globalAtomIndices[a];
+ int molnr = 0;
+ int a_mol = 0;
mtopGetMolblockIndex(mtop, a_gl, &mb, &molnr, &a_mol);
- const gmx_molblock_t& molb = mtop->molblock[mb];
+ const gmx_molblock_t& molb = mtop.molblock[mb];
- gmx::ArrayRef<const int> ia1 = mtop->moltype[molb.type].ilist[F_CONSTR].iatoms;
- gmx::ArrayRef<const int> ia2 = mtop->moltype[molb.type].ilist[F_CONSTRNC].iatoms;
+ gmx::ArrayRef<const int> ia1 = mtop.moltype[molb.type].ilist[F_CONSTR].iatoms;
+ gmx::ArrayRef<const int> ia2 = mtop.moltype[molb.type].ilist[F_CONSTRNC].iatoms;
/* Calculate the global constraint number offset for the molecule.
* This is only required for the global index to make sure
const auto& at2con = at2con_mt[molb.type];
for (const int con : at2con[a_mol])
{
- const int* iap = constr_iatomptr(ia1, ia2, con);
- int b_mol;
+ const int* iap = constr_iatomptr(ia1, ia2, con);
+ int b_mol = 0;
if (a_mol == iap[1])
{
b_mol = iap[2];
* Therefore we call walk_out with nrec recursions to go
* after this first call.
*/
- walk_out(con, con_offset, b_mol, offset, nrec, ia1, ia2, at2con, ga2la, TRUE,
- dc, dcc, ilc_local, ireq);
+ walk_out(con, con_offset, b_mol, offset, nrec, ia1, ia2, at2con, ga2la, TRUE, dc, dcc, ilc_local, ireq);
}
}
}
if (debug)
{
- fprintf(debug, "Constraints: home %3d border %3d atoms: %3zu\n", nhome, dc->ncon - nhome,
+ fprintf(debug,
+ "Constraints: home %3d border %3d atoms: %3zu\n",
+ nhome,
+ dc->ncon - nhome,
dd->constraint_comm ? ireq->size() : 0);
}
}
int dd_make_local_constraints(gmx_domdec_t* dd,
int at_start,
- const struct gmx_mtop_t* mtop,
+ const struct gmx_mtop_t& mtop,
const int* cginfo,
gmx::Constraints* constr,
int nrec,
gmx::ArrayRef<InteractionList> il_local)
{
- gmx_domdec_constraints_t* dc;
- InteractionList * ilc_local, *ils_local;
- gmx::HashedMap<int>* ga2la_specat;
- int at_end, i, j;
-
// This code should not be called unless this condition is true,
// because that's the only time init_domdec_constraints is
// called...
- GMX_RELEASE_ASSERT(dd->comm->systemInfo.haveSplitConstraints || dd->comm->systemInfo.haveSplitSettles,
+ GMX_RELEASE_ASSERT(dd->comm->systemInfo.mayHaveSplitConstraints || dd->comm->systemInfo.mayHaveSplitSettles,
"dd_make_local_constraints called when there are no local constraints");
// ... and init_domdec_constraints always sets
// dd->constraint_comm...
// true. dd->constraint_comm is unilaterally dereferenced before
// the call to atoms_to_settles.
- dc = dd->constraints;
+ gmx_domdec_constraints_t* dc = dd->constraints;
- ilc_local = &il_local[F_CONSTR];
- ils_local = &il_local[F_SETTLE];
+ InteractionList* ilc_local = &il_local[F_CONSTR];
+ InteractionList* ils_local = &il_local[F_SETTLE];
dc->ncon = 0;
gmx::ArrayRef<const ListOfLists<int>> at2con_mt;
gmx::ArrayRef<const std::vector<int>> at2settle_mt;
/* When settle works inside charge groups, we assigned them already */
- if (dd->comm->systemInfo.haveSplitSettles)
+ if (dd->comm->systemInfo.mayHaveSplitSettles)
{
// TODO Perhaps gmx_domdec_constraints_t should keep a valid constr?
GMX_RELEASE_ASSERT(constr != nullptr, "Must have valid constraints object");
}
else
{
- int t0_set;
-
/* Do the constraints, if present, on the first thread.
* Do the settles on all other threads.
*/
- t0_set = ((!at2con_mt.empty() && dc->nthread > 1) ? 1 : 0);
+ const int t0_set = ((!at2con_mt.empty() && dc->nthread > 1) ? 1 : 0);
#pragma omp parallel for num_threads(dc->nthread) schedule(static)
for (int thread = 0; thread < dc->nthread; thread++)
if (thread >= t0_set)
{
- int cg0, cg1;
- InteractionList* ilst;
-
/* Distribute the settle check+assignments over
* dc->nthread or dc->nthread-1 threads.
*/
- cg0 = (dd->ncg_home * (thread - t0_set)) / (dc->nthread - t0_set);
- cg1 = (dd->ncg_home * (thread - t0_set + 1)) / (dc->nthread - t0_set);
+ const int cg0 = (dd->ncg_home * (thread - t0_set)) / (dc->nthread - t0_set);
+ const int cg1 = (dd->ncg_home * (thread - t0_set + 1)) / (dc->nthread - t0_set);
- if (thread == t0_set)
- {
- ilst = ils_local;
- }
- else
- {
- ilst = &dc->ils[thread];
- }
+ InteractionList* ilst = (thread == t0_set) ? ils_local : &dc->ils[thread];
ilst->clear();
std::vector<int>& ireqt = dc->requestedGlobalAtomIndices[thread];
}
}
+ int at_end = 0;
if (dd->constraint_comm)
{
- int nral1;
-
- at_end = setup_specat_communication(dd, ireq, dd->constraint_comm, dd->constraints->ga2la.get(),
- at_start, 2, "constraint", " or lincs-order");
+ at_end = setup_specat_communication(dd,
+ ireq,
+ dd->constraint_comm,
+ dd->constraints->ga2la.get(),
+ at_start,
+ 2,
+ "constraint",
+ " or lincs-order");
/* Fill in the missing indices */
- ga2la_specat = dd->constraints->ga2la.get();
+ gmx::HashedMap<int>* ga2la_specat = dd->constraints->ga2la.get();
- nral1 = 1 + NRAL(F_CONSTR);
- for (i = 0; i < ilc_local->size(); i += nral1)
+ int nral1 = 1 + NRAL(F_CONSTR);
+ for (int i = 0; i < ilc_local->size(); i += nral1)
{
int* iap = ilc_local->iatoms.data() + i;
- for (j = 1; j < nral1; j++)
+ for (int j = 1; j < nral1; j++)
{
if (iap[j] < 0)
{
}
nral1 = 1 + NRAL(F_SETTLE);
- for (i = 0; i < ils_local->size(); i += nral1)
+ for (int i = 0; i < ils_local->size(); i += nral1)
{
int* iap = ils_local->iatoms.data() + i;
- for (j = 1; j < nral1; j++)
+ for (int j = 1; j < nral1; j++)
{
if (iap[j] < 0)
{
return at_end;
}
-void init_domdec_constraints(gmx_domdec_t* dd, const gmx_mtop_t* mtop)
+void init_domdec_constraints(gmx_domdec_t* dd, const gmx_mtop_t& mtop)
{
- gmx_domdec_constraints_t* dc;
- const gmx_molblock_t* molb;
-
if (debug)
{
fprintf(debug, "Begin init_domdec_constraints\n");
}
- dd->constraints = new gmx_domdec_constraints_t;
- dc = dd->constraints;
+ dd->constraints = new gmx_domdec_constraints_t;
+ gmx_domdec_constraints_t* dc = dd->constraints;
- dc->molb_con_offset.resize(mtop->molblock.size());
- dc->molb_ncon_mol.resize(mtop->molblock.size());
+ dc->molb_con_offset.resize(mtop.molblock.size());
+ dc->molb_ncon_mol.resize(mtop.molblock.size());
int ncon = 0;
- for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
+ for (size_t mb = 0; mb < mtop.molblock.size(); mb++)
{
- molb = &mtop->molblock[mb];
- dc->molb_con_offset[mb] = ncon;
- dc->molb_ncon_mol[mb] = mtop->moltype[molb->type].ilist[F_CONSTR].size() / 3
- + mtop->moltype[molb->type].ilist[F_CONSTRNC].size() / 3;
+ const gmx_molblock_t* molb = &mtop.molblock[mb];
+ dc->molb_con_offset[mb] = ncon;
+ dc->molb_ncon_mol[mb] = mtop.moltype[molb->type].ilist[F_CONSTR].size() / 3
+ + mtop.moltype[molb->type].ilist[F_CONSTRNC].size() / 3;
ncon += molb->nmol * dc->molb_ncon_mol[mb];
}
/* Use a hash table for the global to local index.
* The number of keys is a rough estimate, it will be optimized later.
*/
- int numKeysEstimate = std::min(mtop->natoms / 20, mtop->natoms / (2 * dd->nnodes));
+ int numKeysEstimate = std::min(mtop.natoms / 20, mtop.natoms / (2 * dd->nnodes));
dc->ga2la = std::make_unique<gmx::HashedMap<int>>(numKeysEstimate);
- dc->nthread = gmx_omp_nthreads_get(emntDomdec);
+ dc->nthread = gmx_omp_nthreads_get(ModuleMultiThread::Domdec);
dc->ils.resize(dc->nthread);
dd->constraint_comm = new gmx_domdec_specat_comm_t;
*
* Copyright (c) 2005,2006,2007,2008,2009 by the GROMACS development team.
* Copyright (c) 2010,2012,2013,2014,2015 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*! \brief Sets up communication and atom indices for all local+connected constraints */
int dd_make_local_constraints(struct gmx_domdec_t* dd,
int at_start,
- const struct gmx_mtop_t* mtop,
+ const struct gmx_mtop_t& mtop,
const int* cginfo,
gmx::Constraints* constr,
int nrec,
gmx::ArrayRef<InteractionList> il_local);
/*! \brief Initializes the data structures for constraint communication */
-void init_domdec_constraints(gmx_domdec_t* dd, const gmx_mtop_t* mtop);
+void init_domdec_constraints(gmx_domdec_t* dd, const gmx_mtop_t& mtop);
#endif
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
offTemporarilyLocked, /**< DLB is off and temporarily can't turn on */
onCanTurnOff, /**< DLB is on and can turn off when slow */
onUser, /**< DLB is permanently on per user request */
- nr /**< The number of DLB states */
+ Count /**< The number of DLB states */
};
/*! \brief The PME domain decomposition for one dimension */
//! True when update groups are used
bool useUpdateGroups = false;
//! Update atom grouping for each molecule type
- std::vector<gmx::RangePartitioning> updateGroupingPerMoleculetype;
+ std::vector<gmx::RangePartitioning> updateGroupingsPerMoleculeType;
//! The maximum radius over all update groups
real maxUpdateGroupRadius;
real cellsizeLimit = 0;
//! Can atoms connected by constraints be assigned to different domains?
- bool haveSplitConstraints = false;
+ bool mayHaveSplitConstraints = false;
//! Can atoms connected by settles be assigned to different domains?
- bool haveSplitSettles = false;
+ bool mayHaveSplitSettles = false;
//! Estimated communication range needed for constraints
real constraintCommunicationRange = 0;
/**< Cut-off for multi-body interactions, also 2-body bonded when \p cutoff_mody > \p cutoff */
real cutoff_mbody = 0;
/**< The minimum guaranteed cell-size, Cartesian indexing */
- rvec cellsize_min = {};
+ gmx::RVec cellsize_min = { 0, 0, 0 };
/**< The minimum guaranteed cell-size with dlb=auto */
- rvec cellsize_min_dlb = {};
+ gmx::RVec cellsize_min_dlb = { 0, 0, 0 };
/**< The lower limit for the DD cell size with DLB */
real cellsize_limit = 0;
/**< Effectively no NB cut-off limit with DLB for systems without PBC? */
- gmx_bool bVacDLBNoLimit = false;
+ bool bVacDLBNoLimit = false;
/** With PME load balancing we set limits on DLB */
- gmx_bool bPMELoadBalDLBLimits = false;
+ bool bPMELoadBalDLBLimits = false;
/** DLB needs to take into account that we want to allow this maximum
* cut-off (for PME load balancing), this could limit cell boundaries.
*/
real PMELoadBal_max_cutoff = 0;
/**< box lower corner, required with dim's without pbc and -gcom */
- rvec box0 = {};
+ gmx::RVec box0 = { 0, 0, 0 };
/**< box size, required with dim's without pbc and -gcom */
- rvec box_size = {};
+ gmx::RVec box_size = { 0, 0, 0 };
/**< The DD cell lower corner, in triclinic space */
- rvec cell_x0 = {};
+ gmx::RVec cell_x0 = { 0, 0, 0 };
/**< The DD cell upper corner, in triclinic space */
- rvec cell_x1 = {};
+ gmx::RVec cell_x1 = { 0, 0, 0 };
/**< The old \p cell_x0, to check cg displacements */
- rvec old_cell_x0 = {};
+ gmx::RVec old_cell_x0 = { 0, 0, 0 };
/**< The old \p cell_x1, to check cg displacements */
- rvec old_cell_x1 = {};
+ gmx::RVec old_cell_x1 = { 0, 0, 0 };
/** The communication setup and charge group boundaries for the zones */
gmx_domdec_zones_t zones;
* dynamic load balancing.
*/
/**< Zone limits for dim 1 with staggered grids */
- gmx_ddzone_t zone_d1[2];
+ std::array<gmx_ddzone_t, 2> zone_d1;
/**< Zone limits for dim 2 with staggered grids */
gmx_ddzone_t zone_d2[2][2];
/** The coordinate/force communication setup and indices */
- gmx_domdec_comm_dim_t cd[DIM];
+ std::array<gmx_domdec_comm_dim_t, DIM> cd;
/** Restricts the maximum number of cells to communicate with in one dimension
*
* Dynamic load balancing is not permitted to change sizes if it
int64_t master_cg_ddp_count = 0;
/** The number of cg's received from the direct neighbors */
- int zone_ncg1[DD_MAXZONE] = { 0 };
+ std::array<int, DD_MAXZONE> zone_ncg1 = { 0 };
/** The atom ranges in the local state */
DDAtomRanges atomRanges;
/* Cycle counters over nstlist steps */
/**< Total cycles counted */
- float cycl[ddCyclNr] = {};
+ std::array<float, ddCyclNr> cycl = { 0 };
/**< The number of cycle recordings */
- int cycl_n[ddCyclNr] = {};
+ std::array<int, ddCyclNr> cycl_n = { 0 };
/**< The maximum cycle count */
- float cycl_max[ddCyclNr] = {};
+ std::array<float, ddCyclNr> cycl_max = { 0 };
/**< Total flops counted */
double flop = 0.0;
/**< The number of flop recordings */
/**< Max \p load_sum over the ranks */
double load_max = 0.0;
/**< Was load balancing limited, per DD dim */
- ivec load_lim = {};
+ gmx::IVec load_lim = { 0, 0, 0 };
/**< Total time on PP done during PME overlap time */
double load_mdf = 0.0;
/**< Total time on our PME-only rank */
/*! \endcond */
+//! \internal \brief Reverse topology class
+struct gmx_reverse_top_t
+{
+ //! Constructor
+ gmx_reverse_top_t(const gmx_mtop_t& mtop, bool useFreeEnergy, const ReverseTopOptions& reverseTopOptions);
+ //! Destructor
+ ~gmx_reverse_top_t();
+
+ //! Private implementation definition
+ struct Impl;
+ //! Private implementation declaration
+ std::unique_ptr<Impl> impl_;
+};
+
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2008-2019, by the GROMACS development team, led by
+ * Copyright (c) 2008-2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
MPI_Status mpiStatus;
if (numElementsToSend > 0 && numElementsToReceive > 0)
{
- MPI_Sendrecv(sendBuffer, numElementsToSend * sizeof(T), MPI_BYTE, sendRank, mpiTag,
- receiveBuffer, numElementsToReceive * sizeof(T), MPI_BYTE, receiveRank, mpiTag,
- dd->mpi_comm_all, &mpiStatus);
+ MPI_Sendrecv(sendBuffer,
+ numElementsToSend * sizeof(T),
+ MPI_BYTE,
+ sendRank,
+ mpiTag,
+ receiveBuffer,
+ numElementsToReceive * sizeof(T),
+ MPI_BYTE,
+ receiveRank,
+ mpiTag,
+ dd->mpi_comm_all,
+ &mpiStatus);
}
else if (numElementsToSend > 0)
{
}
else if (numElementsToReceive > 0)
{
- MPI_Recv(receiveBuffer, numElementsToReceive * sizeof(T), MPI_BYTE, receiveRank, mpiTag,
- dd->mpi_comm_all, &mpiStatus);
+ MPI_Recv(receiveBuffer, numElementsToReceive * sizeof(T), MPI_BYTE, receiveRank, mpiTag, dd->mpi_comm_all, &mpiStatus);
}
#else // GMX_MPI
GMX_UNUSED_VALUE(dd);
gmx::ArrayRef<T> sendBuffer,
gmx::ArrayRef<T> receiveBuffer)
{
- ddSendrecv(dd, ddDimensionIndex, direction, sendBuffer.data(), sendBuffer.size(),
- receiveBuffer.data(), receiveBuffer.size());
+ ddSendrecv(dd,
+ ddDimensionIndex,
+ direction,
+ sendBuffer.data(),
+ sendBuffer.size(),
+ receiveBuffer.data(),
+ receiveBuffer.size());
}
//! Specialization of extern template for int
int gmx_unused n_r_bw)
{
#if GMX_MPI
- int rank_fw, rank_bw, nreq;
MPI_Request req[4];
MPI_Status stat[4];
- rank_fw = dd->neighbor[ddimind][0];
- rank_bw = dd->neighbor[ddimind][1];
+ int rank_fw = dd->neighbor[ddimind][0];
+ int rank_bw = dd->neighbor[ddimind][1];
if (!dd->comm->ddSettings.useSendRecv2)
{
* are slower.
* SendRecv2 can be turned on with the env.var. GMX_DD_SENDRECV2
*/
- nreq = 0;
+ int nreq = 0;
if (n_r_fw)
{
- MPI_Irecv(buf_r_fw[0], n_r_fw * sizeof(rvec), MPI_BYTE, rank_bw, 0, dd->mpi_comm_all,
- &req[nreq++]);
+ MPI_Irecv(buf_r_fw[0], n_r_fw * sizeof(rvec), MPI_BYTE, rank_bw, 0, dd->mpi_comm_all, &req[nreq++]);
}
if (n_r_bw)
{
- MPI_Irecv(buf_r_bw[0], n_r_bw * sizeof(rvec), MPI_BYTE, rank_fw, 1, dd->mpi_comm_all,
- &req[nreq++]);
+ MPI_Irecv(buf_r_bw[0], n_r_bw * sizeof(rvec), MPI_BYTE, rank_fw, 1, dd->mpi_comm_all, &req[nreq++]);
}
if (n_s_fw)
{
- MPI_Isend(buf_s_fw[0], n_s_fw * sizeof(rvec), MPI_BYTE, rank_fw, 0, dd->mpi_comm_all,
- &req[nreq++]);
+ MPI_Isend(buf_s_fw[0], n_s_fw * sizeof(rvec), MPI_BYTE, rank_fw, 0, dd->mpi_comm_all, &req[nreq++]);
}
if (n_s_bw)
{
- MPI_Isend(buf_s_bw[0], n_s_bw * sizeof(rvec), MPI_BYTE, rank_bw, 1, dd->mpi_comm_all,
- &req[nreq++]);
+ MPI_Isend(buf_s_bw[0], n_s_bw * sizeof(rvec), MPI_BYTE, rank_bw, 1, dd->mpi_comm_all, &req[nreq++]);
}
if (nreq)
{
* with a single full-duplex network connection per machine.
*/
/* Forward */
- MPI_Sendrecv(buf_s_fw[0], n_s_fw * sizeof(rvec), MPI_BYTE, rank_fw, 0, buf_r_fw[0],
- n_r_fw * sizeof(rvec), MPI_BYTE, rank_bw, 0, dd->mpi_comm_all, &stat[0]);
+ MPI_Sendrecv(buf_s_fw[0],
+ n_s_fw * sizeof(rvec),
+ MPI_BYTE,
+ rank_fw,
+ 0,
+ buf_r_fw[0],
+ n_r_fw * sizeof(rvec),
+ MPI_BYTE,
+ rank_bw,
+ 0,
+ dd->mpi_comm_all,
+ &stat[0]);
/* Backward */
- MPI_Sendrecv(buf_s_bw[0], n_s_bw * sizeof(rvec), MPI_BYTE, rank_bw, 0, buf_r_bw[0],
- n_r_bw * sizeof(rvec), MPI_BYTE, rank_fw, 0, dd->mpi_comm_all, &stat[0]);
+ MPI_Sendrecv(buf_s_bw[0],
+ n_s_bw * sizeof(rvec),
+ MPI_BYTE,
+ rank_bw,
+ 0,
+ buf_r_bw[0],
+ n_r_bw * sizeof(rvec),
+ MPI_BYTE,
+ rank_fw,
+ 0,
+ dd->mpi_comm_all,
+ &stat[0]);
}
#endif
}
if (dd->nnodes > 1)
{
/* Some MPI implementions don't specify const */
- MPI_Scatter(const_cast<void*>(src), nbytes, MPI_BYTE, dest, nbytes, MPI_BYTE,
- DDMASTERRANK(dd), dd->mpi_comm_all);
+ MPI_Scatter(const_cast<void*>(src), nbytes, MPI_BYTE, dest, nbytes, MPI_BYTE, DDMASTERRANK(dd), dd->mpi_comm_all);
}
else
#endif
{
#if GMX_MPI
/* Some MPI implementions don't specify const */
- MPI_Gather(const_cast<void*>(src), nbytes, MPI_BYTE, dest, nbytes, MPI_BYTE, DDMASTERRANK(dd),
- dd->mpi_comm_all);
+ MPI_Gather(const_cast<void*>(src), nbytes, MPI_BYTE, dest, nbytes, MPI_BYTE, DDMASTERRANK(dd), dd->mpi_comm_all);
#endif
}
void* rbuf)
{
#if GMX_MPI
- int dum;
+ int dum = 0;
if (dd->nnodes > 1)
{
rbuf = &dum;
}
/* Some MPI implementions don't specify const */
- MPI_Scatterv(const_cast<void*>(sbuf), scounts, disps, MPI_BYTE, rbuf, rcount, MPI_BYTE,
- DDMASTERRANK(dd), dd->mpi_comm_all);
+ MPI_Scatterv(
+ const_cast<void*>(sbuf), scounts, disps, MPI_BYTE, rbuf, rcount, MPI_BYTE, DDMASTERRANK(dd), dd->mpi_comm_all);
}
else
#endif
void gmx_unused* rbuf)
{
#if GMX_MPI
- int dum;
+ int dum = 0;
if (scount == 0)
{
sbuf = &dum;
}
/* Some MPI implementions don't specify const */
- MPI_Gatherv(const_cast<void*>(sbuf), scount, MPI_BYTE, rbuf, rcounts, disps, MPI_BYTE,
- DDMASTERRANK(dd), dd->mpi_comm_all);
+ MPI_Gatherv(
+ const_cast<void*>(sbuf), scount, MPI_BYTE, rbuf, rcounts, disps, MPI_BYTE, DDMASTERRANK(dd), dd->mpi_comm_all);
#endif
}
*
* Copyright (c) 2008,2009,2010,2011,2012 by the GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cmath>
#include <cstdio>
+#include <numeric>
+
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/domdec/options.h"
#include "gromacs/ewald/pme.h"
#include "gromacs/gmxlib/network.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/perf_est.h"
return div.back();
}
-/*! \brief Compute largest common divisor of \p n1 and \b n2 */
-static int lcd(int n1, int n2)
-{
- int d, i;
-
- d = 1;
- for (i = 2; (i <= n1 && i <= n2); i++)
- {
- if (n1 % i == 0 && n2 % i == 0)
- {
- d = i;
- }
- }
-
- return d;
-}
-
/*! \brief Returns TRUE when there are enough PME ranks for the ratio */
static gmx_bool fits_pme_ratio(int nrank_tot, int nrank_pme, float ratio)
{
* The factor of 2 allows for a maximum ratio of 2^2=4
* between nx_pme and ny_pme.
*/
- if (lcd(ntot - npme, npme) * 2 < npme_root2)
+ if (std::gcd(ntot - npme, npme) * 2 < npme_root2)
{
return FALSE;
}
const matrix box,
int nrank_tot)
{
- float ratio;
- int npme;
-
- ratio = pme_load_estimate(mtop, ir, box);
+ float ratio = pme_load_estimate(mtop, ir, box);
GMX_LOG(mdlog.info).appendTextFormatted("Guess for relative PME load: %.2f", ratio);
* We start with a minimum PME node fraction of 1/16
* and avoid ratios which lead to large prime factors in nnodes-npme.
*/
- npme = (nrank_tot + 15) / 16;
+ int npme = (nrank_tot + 15) / 16;
while (npme <= nrank_tot / 3)
{
if (nrank_tot % npme == 0)
"grid_y=%d).\n"
"Use the -npme option of mdrun or change the number of ranks or the PME grid "
"dimensions, see the manual for details.",
- ratio, gmx::roundToInt(0.95 * ratio * nrank_tot), nrank_tot / 2, ir.nkx, ir.nky);
+ ratio,
+ gmx::roundToInt(0.95 * ratio * nrank_tot),
+ nrank_tot / 2,
+ ir.nkx,
+ ir.nky);
}
else
{
.appendTextFormatted(
"Will use %d particle-particle and %d PME only ranks\n"
"This is a guess, check the performance at the end of the log file",
- nrank_tot - npme, npme);
+ nrank_tot - npme,
+ npme);
}
return npme;
real comm_box_frac(const gmx::IVec& dd_nc, real cutoff, const gmx_ddbox_t& ddbox)
{
- int i, j, k;
rvec nw;
- real comm_vol;
- for (i = 0; i < DIM; i++)
+ for (int i = 0; i < DIM; i++)
{
real bt = ddbox.box_size[i] * ddbox.skew_fac[i];
nw[i] = dd_nc[i] * cutoff / bt;
}
- comm_vol = 0;
- for (i = 0; i < DIM; i++)
+ real comm_vol = 0;
+ for (int i = 0; i < DIM; i++)
{
if (dd_nc[i] > 1)
{
comm_vol += nw[i];
- for (j = i + 1; j < DIM; j++)
+ for (int j = i + 1; j < DIM; j++)
{
if (dd_nc[j] > 1)
{
comm_vol += nw[i] * nw[j] * M_PI / 4;
- for (k = j + 1; k < DIM; k++)
+ for (int k = j + 1; k < DIM; k++)
{
if (dd_nc[k] > 1)
{
/*! \brief Return whether the DD inhomogeneous in the z direction */
static gmx_bool inhomogeneous_z(const t_inputrec& ir)
{
- return ((EEL_PME(ir.coulombtype) || ir.coulombtype == eelEWALD) && ir.pbcType == PbcType::Xyz
- && ir.ewald_geometry == eewg3DC);
+ return ((EEL_PME(ir.coulombtype) || ir.coulombtype == CoulombInteractionType::Ewald)
+ && ir.pbcType == PbcType::Xyz && ir.ewald_geometry == EwaldGeometry::ThreeDC);
}
/*! \brief Estimate cost of PME FFT communication
static float comm_pme_cost_vol(int npme, int a, int b, int c)
{
/* We use a float here, since an integer might overflow */
- float comm_vol;
-
- comm_vol = npme - 1;
+ float comm_vol = npme - 1;
comm_vol *= npme;
comm_vol *= div_up(a, npme);
comm_vol *= div_up(b, npme);
const gmx::IVec& nc)
{
gmx::IVec npme = { 1, 1, 1 };
- int i, j, nk, overlap;
rvec bt;
- float comm_vol, comm_vol_xf, comm_pme, cost_pbcdx;
/* This is the cost of a pbc_dx call relative to the cost
* of communicating the coordinate and force of an atom.
* This will be machine dependent.
*/
float pbcdx_rect_fac = 0.1;
float pbcdx_tric_fac = 0.2;
- float temp;
/* Check the DD algorithm restrictions */
if ((ir.pbcType == PbcType::XY && ir.nwall < 2 && nc[ZZ] > 1)
assert(ddbox.npbcdim <= DIM);
/* Check if the triclinic requirements are met */
- for (i = 0; i < DIM; i++)
+ for (int i = 0; i < DIM; i++)
{
- for (j = i + 1; j < ddbox.npbcdim; j++)
+ for (int j = i + 1; j < ddbox.npbcdim; j++)
{
- if (box[j][i] != 0 || ir.deform[j][i] != 0 || (ir.epc != epcNO && ir.compress[j][i] != 0))
+ if (box[j][i] != 0 || ir.deform[j][i] != 0
+ || (ir.epc != PressureCoupling::No && ir.compress[j][i] != 0))
{
if (nc[j] > 1 && nc[i] == 1)
{
}
}
- for (i = 0; i < DIM; i++)
+ for (int i = 0; i < DIM; i++)
{
bt[i] = ddbox.box_size[i] * ddbox.skew_fac[i];
*/
bool useThreads = true;
bool errorsAreFatal = false;
- if (!gmx_pme_check_restrictions(ir.pme_order, ir.nkx, ir.nky, ir.nkz, npme_x, useThreads,
- errorsAreFatal))
+ if (!gmx_pme_check_restrictions(
+ ir.pme_order, ir.nkx, ir.nky, ir.nkz, npme_x, useThreads, errorsAreFatal))
{
return -1;
}
* for the smallest index, so the decomposition does not
* depend sensitively on the rounding of the box elements.
*/
- for (i = 0; i < DIM; i++)
+ for (int i = 0; i < DIM; i++)
{
- for (j = i + 1; j < DIM; j++)
+ for (int j = i + 1; j < DIM; j++)
{
/* Check if the box size is nearly identical,
* in that case we prefer nx > ny and ny > nz.
* and the "back"-communication cost is identical to the forward cost.
*/
- comm_vol = comm_box_frac(nc, cutoff, ddbox);
+ float comm_vol = comm_box_frac(nc, cutoff, ddbox);
- comm_pme = 0;
- for (i = 0; i < 2; i++)
+ float comm_pme = 0;
+ for (int i = 0; i < 2; i++)
{
/* Determine the largest volume for PME x/f redistribution */
if (nc[i] % npme[i] != 0)
{
- if (nc[i] > npme[i])
- {
- comm_vol_xf = (npme[i] == 2 ? 1.0 / 3.0 : 0.5);
- }
- else
- {
- comm_vol_xf = 1.0 - lcd(nc[i], npme[i]) / static_cast<double>(npme[i]);
- }
+ float comm_vol_xf =
+ (nc[i] > npme[i]) ? (npme[i] == 2 ? 1.0 / 3.0 : 0.5)
+ : (1.0 - std::gcd(nc[i], npme[i]) / static_cast<double>(npme[i]));
comm_pme += 3 * natoms * comm_vol_xf;
}
/* Grid overlap communication */
if (npme[i] > 1)
{
- nk = (i == 0 ? ir.nkx : ir.nky);
- overlap = (nk % npme[i] == 0 ? ir.pme_order - 1 : ir.pme_order);
- temp = npme[i];
+ const int nk = (i == 0 ? ir.nkx : ir.nky);
+ const int overlap = (nk % npme[i] == 0 ? ir.pme_order - 1 : ir.pme_order);
+ float temp = npme[i];
temp *= overlap;
temp *= ir.nkx;
temp *= ir.nky;
comm_pme += comm_pme_cost_vol(npme[XX], ir.nkx, ir.nky, ir.nkz);
/* Add cost of pbc_dx for bondeds */
- cost_pbcdx = 0;
+ float cost_pbcdx = 0;
if ((nc[XX] == 1 || nc[YY] == 1) || (nc[ZZ] == 1 && ir.pbcType != PbcType::XY))
{
if ((ddbox.tric_dir[XX] && nc[XX] == 1) || (ddbox.tric_dir[YY] && nc[YY] == 1))
if (debug)
{
- fprintf(debug, "nc %2d %2d %2d %2d %2d vol pp %6.4f pbcdx %6.4f pme %9.3e tot %9.3e\n",
- nc[XX], nc[YY], nc[ZZ], npme[XX], npme[YY], comm_vol, cost_pbcdx,
- comm_pme / (3 * natoms), comm_vol + cost_pbcdx + comm_pme / (3 * natoms));
+ fprintf(debug,
+ "nc %2d %2d %2d %2d %2d vol pp %6.4f pbcdx %6.4f pme %9.3e tot %9.3e\n",
+ nc[XX],
+ nc[YY],
+ nc[ZZ],
+ npme[XX],
+ npme[YY],
+ comm_vol,
+ cost_pbcdx,
+ comm_pme / (3 * natoms),
+ comm_vol + cost_pbcdx + comm_pme / (3 * natoms));
}
return 3 * natoms * (comm_vol + cost_pbcdx) + comm_pme;
gmx::IVec* irTryPtr,
gmx::IVec* opt)
{
- int x, y, i;
- float ce;
gmx::IVec& ir_try = *irTryPtr;
if (ndiv == 0)
{
- ce = comm_cost_est(limit, cutoff, box, ddbox, natoms, ir, pbcdxr, npme, ir_try);
+ const float ce = comm_cost_est(limit, cutoff, box, ddbox, natoms, ir, pbcdxr, npme, ir_try);
if (ce >= 0
&& ((*opt)[XX] == 0
|| ce < comm_cost_est(limit, cutoff, box, ddbox, natoms, ir, pbcdxr, npme, *opt)))
return;
}
- for (x = mdiv[0]; x >= 0; x--)
+ for (int x = mdiv[0]; x >= 0; x--)
{
- for (i = 0; i < x; i++)
+ for (int i = 0; i < x; i++)
{
ir_try[XX] *= div[0];
}
- for (y = mdiv[0] - x; y >= 0; y--)
+ for (int y = mdiv[0] - x; y >= 0; y--)
{
- for (i = 0; i < y; i++)
+ for (int i = 0; i < y; i++)
{
ir_try[YY] *= div[0];
}
- for (i = 0; i < mdiv[0] - x - y; i++)
+ for (int i = 0; i < mdiv[0] - x - y; i++)
{
ir_try[ZZ] *= div[0];
}
/* recurse */
- assign_factors(limit, cutoff, box, ddbox, natoms, ir, pbcdxr, npme, ndiv - 1, div + 1,
- mdiv + 1, irTryPtr, opt);
+ assign_factors(
+ limit, cutoff, box, ddbox, natoms, ir, pbcdxr, npme, ndiv - 1, div + 1, mdiv + 1, irTryPtr, opt);
- for (i = 0; i < mdiv[0] - x - y; i++)
+ for (int i = 0; i < mdiv[0] - x - y; i++)
{
ir_try[ZZ] /= div[0];
}
- for (i = 0; i < y; i++)
+ for (int i = 0; i < y; i++)
{
ir_try[YY] /= div[0];
}
}
- for (i = 0; i < x; i++)
+ for (int i = 0; i < x; i++)
{
ir_try[XX] /= div[0];
}
const t_inputrec& ir,
const DDSystemInfo& systemInfo)
{
- double pbcdxr;
+ double pbcdxr = 0;
const int numPPRanks = numRanksRequested - numPmeOnlyRanks;
GMX_LOG(mdlog.info)
.appendTextFormatted(
"Optimizing the DD grid for %d cells with a minimum initial size of %.3f nm",
- numPPRanks, cellSizeLimit);
+ numPPRanks,
+ cellSizeLimit);
if (inhomogeneous_z(ir))
{
GMX_LOG(mdlog.info)
.appendTextFormatted(
"Ewald_geometry=%s: assuming inhomogeneous particle distribution in z, "
"will not decompose in z.",
- eewg_names[ir.ewald_geometry]);
+ enumValueToString(ir.ewald_geometry));
}
gmx::IVec itry = { 1, 1, 1 };
gmx::IVec numDomains = { 0, 0, 0 };
- assign_factors(cellSizeLimit, systemInfo.cutoff, box, ddbox, mtop.natoms, ir, pbcdxr,
- numRanksDoingPmeWork, div.size(), div.data(), mdiv.data(), &itry, &numDomains);
+ assign_factors(cellSizeLimit,
+ systemInfo.cutoff,
+ box,
+ ddbox,
+ mtop.natoms,
+ ir,
+ pbcdxr,
+ numRanksDoingPmeWork,
+ div.size(),
+ div.data(),
+ mdiv.data(),
+ &itry,
+ &numDomains);
return numDomains;
}
}
GMX_LOG(mdlog.info)
.appendTextFormatted(
- "Scaling the initial minimum size with 1/%g (option -dds) = %g", dlb_scale,
- 1 / dlb_scale);
+ "Scaling the initial minimum size with 1/%g (option -dds) = %g", dlb_scale, 1 / dlb_scale);
cellSizeLimit /= dlb_scale;
}
- else if (ir.epc != epcNO)
+ else if (ir.epc != PressureCoupling::No)
{
GMX_LOG(mdlog.info)
.appendTextFormatted(
gmx_fatal(FARGS,
"Cannot have %d separate PME ranks with only %d PP ranks, choose fewer or no "
"separate PME ranks",
- numPmeRanksRequested, numPPRanksRequested);
+ numPmeRanksRequested,
+ numPPRanksRequested);
}
}
"contains a large prime factor %d. In most cases this will lead to "
"bad performance. Choose a number with smaller prime factors or "
"set the decomposition (option -dd) manually.",
- numPPRanksRequested, largestDivisor);
+ numPPRanksRequested,
+ largestDivisor);
}
}
}
const matrix box,
const int numRanksRequested)
{
- int numPmeOnlyRanks;
- const char* extraMessage = "";
+ int numPmeOnlyRanks = 0;
+ const char* extraMessage = "";
if (options.numCells[XX] > 0)
{
if (ddRole == DDRole::Master)
{
- numDomains = optimizeDDCells(mdlog, numRanksRequested, numPmeOnlyRanks, cellSizeLimit,
- mtop, box, *ddbox, ir, systemInfo);
+ numDomains = optimizeDDCells(
+ mdlog, numRanksRequested, numPmeOnlyRanks, cellSizeLimit, mtop, box, *ddbox, ir, systemInfo);
}
}
*
* Copyright (c) 2006,2007,2008,2009,2010 by the GROMACS development team.
* Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void dd_move_f_specat(const gmx_domdec_t* dd, gmx_domdec_specat_comm_t* spac, rvec* f, rvec* fshift)
{
- gmx_specatsend_t* spas;
- rvec* vbuf;
- int n, n0, n1, dim, dir;
- ivec vis;
- int is;
- gmx_bool bPBC, bScrew;
+ ivec vis;
- n = spac->at_end;
+ int n = spac->at_end;
for (int d = dd->ndim - 1; d >= 0; d--)
{
- dim = dd->dim[d];
+ const int dim = dd->dim[d];
if (dd->numCells[dim] > 2)
{
/* Pulse the grid forward and backward */
- spas = spac->spas[d];
- n0 = spas[0].nrecv;
- n1 = spas[1].nrecv;
+ gmx_specatsend_t* spas = spac->spas[d];
+ int n0 = spas[0].nrecv;
+ int n1 = spas[1].nrecv;
n -= n1 + n0;
- vbuf = as_rvec_array(spac->vbuf.data());
+ rvec* vbuf = as_rvec_array(spac->vbuf.data());
/* Send and receive the coordinates */
- dd_sendrecv2_rvec(dd, d, f + n + n1, n0, vbuf, spas[0].a.size(), f + n, n1,
- vbuf + spas[0].a.size(), spas[1].a.size());
- for (dir = 0; dir < 2; dir++)
+ dd_sendrecv2_rvec(dd,
+ d,
+ f + n + n1,
+ n0,
+ vbuf,
+ spas[0].a.size(),
+ f + n,
+ n1,
+ vbuf + spas[0].a.size(),
+ spas[1].a.size());
+ for (int dir = 0; dir < 2; dir++)
{
- bPBC = ((dir == 0 && dd->ci[dim] == 0)
- || (dir == 1 && dd->ci[dim] == dd->numCells[dim] - 1));
- bScrew = (bPBC && dd->unitCellInfo.haveScrewPBC && dim == XX);
+ bool bPBC = ((dir == 0 && dd->ci[dim] == 0)
+ || (dir == 1 && dd->ci[dim] == dd->numCells[dim] - 1));
+ bool bScrew = (bPBC && dd->unitCellInfo.haveScrewPBC && dim == XX);
- spas = &spac->spas[d][dir];
+ gmx_specatsend_t* spas = &spac->spas[d][dir];
/* Sum the buffer into the required forces */
if (!bPBC || (!bScrew && fshift == nullptr))
{
{
clear_ivec(vis);
vis[dim] = (dir == 0 ? 1 : -1);
- is = IVEC2IS(vis);
+ int is = gmx::ivecToShiftIndex(vis);
if (!bScrew)
{
/* Sum and add to shift forces */
else
{
/* Two cells, so we only need to communicate one way */
- spas = &spac->spas[d][0];
+ gmx_specatsend_t* spas = &spac->spas[d][0];
n -= spas->nrecv;
/* Send and receive the coordinates */
- ddSendrecv(dd, d, dddirForward, f + n, spas->nrecv, as_rvec_array(spac->vbuf.data()),
- spas->a.size());
+ ddSendrecv(dd, d, dddirForward, f + n, spas->nrecv, as_rvec_array(spac->vbuf.data()), spas->a.size());
/* Sum the buffer into the required forces */
if (dd->unitCellInfo.haveScrewPBC && dim == XX
&& (dd->ci[dim] == 0 || dd->ci[dim] == dd->numCells[dim] - 1))
rvec* x1,
gmx_bool bX1IsCoord)
{
- gmx_specatsend_t* spas;
- int nvec, v, n, nn, ns0, ns1, nr0, nr1, nr, d, dim, dir, i;
- gmx_bool bPBC, bScrew = FALSE;
- rvec shift = { 0, 0, 0 };
+ rvec shift = { 0, 0, 0 };
- nvec = 1;
+ int nvec = 1;
if (x1 != nullptr)
{
nvec++;
}
- n = spac->at_start;
- for (d = 0; d < dd->ndim; d++)
+ int n = spac->at_start;
+ for (int d = 0; d < dd->ndim; d++)
{
- dim = dd->dim[d];
+ int dim = dd->dim[d];
if (dd->numCells[dim] > 2)
{
/* Pulse the grid forward and backward */
rvec* vbuf = as_rvec_array(spac->vbuf.data());
- for (dir = 0; dir < 2; dir++)
+ for (int dir = 0; dir < 2; dir++)
{
+ bool bPBC = false;
+ bool bScrew = false;
if (dir == 0 && dd->ci[dim] == 0)
{
- bPBC = TRUE;
+ bPBC = true;
bScrew = (dd->unitCellInfo.haveScrewPBC && dim == XX);
copy_rvec(box[dim], shift);
}
else if (dir == 1 && dd->ci[dim] == dd->numCells[dim] - 1)
{
- bPBC = TRUE;
+ bPBC = true;
bScrew = (dd->unitCellInfo.haveScrewPBC && dim == XX);
- for (i = 0; i < DIM; i++)
+ for (int i = 0; i < DIM; i++)
{
shift[i] = -box[dim][i];
}
}
- else
- {
- bPBC = FALSE;
- bScrew = FALSE;
- }
- spas = &spac->spas[d][dir];
- for (v = 0; v < nvec; v++)
+ gmx_specatsend_t* spas = &spac->spas[d][dir];
+ for (int v = 0; v < nvec; v++)
{
rvec* x = (v == 0 ? x0 : x1);
/* Copy the required coordinates to the send buffer */
}
}
/* Send and receive the coordinates */
- spas = spac->spas[d];
- ns0 = spas[0].a.size();
- nr0 = spas[0].nrecv;
- ns1 = spas[1].a.size();
- nr1 = spas[1].nrecv;
+ gmx_specatsend_t* spas = spac->spas[d];
+ int ns0 = spas[0].a.size();
+ int nr0 = spas[0].nrecv;
+ int ns1 = spas[1].a.size();
+ int nr1 = spas[1].nrecv;
if (nvec == 1)
{
rvec* vbuf = as_rvec_array(spac->vbuf.data());
rvec* vbuf = as_rvec_array(spac->vbuf.data());
/* Communicate both vectors in one buffer */
rvec* rbuf = as_rvec_array(spac->vbuf2.data());
- dd_sendrecv2_rvec(dd, d, vbuf + 2 * ns0, 2 * ns1, rbuf, 2 * nr1, vbuf, 2 * ns0,
- rbuf + 2 * nr1, 2 * nr0);
+ dd_sendrecv2_rvec(
+ dd, d, vbuf + 2 * ns0, 2 * ns1, rbuf, 2 * nr1, vbuf, 2 * ns0, rbuf + 2 * nr1, 2 * nr0);
/* Split the buffer into the two vectors */
- nn = n;
- for (dir = 1; dir >= 0; dir--)
+ int nn = n;
+ for (int dir = 1; dir >= 0; dir--)
{
- nr = spas[dir].nrecv;
- for (v = 0; v < 2; v++)
+ int nr = spas[dir].nrecv;
+ for (int v = 0; v < 2; v++)
{
rvec* x = (v == 0 ? x0 : x1);
- for (i = 0; i < nr; i++)
+ for (int i = 0; i < nr; i++)
{
copy_rvec(*rbuf, x[nn + i]);
rbuf++;
}
else
{
- spas = &spac->spas[d][0];
+ gmx_specatsend_t* spas = &spac->spas[d][0];
/* Copy the required coordinates to the send buffer */
rvec* vbuf = as_rvec_array(spac->vbuf.data());
- for (v = 0; v < nvec; v++)
+ for (int v = 0; v < nvec; v++)
{
rvec* x = (v == 0 ? x0 : x1);
if (dd->unitCellInfo.haveScrewPBC && dim == XX
rvec* rbuf = as_rvec_array(spac->vbuf2.data());
ddSendrecv(dd, d, dddirBackward, vbuf, 2 * spas->a.size(), rbuf, 2 * spas->nrecv);
/* Split the buffer into the two vectors */
- nr = spas[0].nrecv;
- for (v = 0; v < 2; v++)
+ int nr = spas[0].nrecv;
+ for (int v = 0; v < 2; v++)
{
rvec* x = (v == 0 ? x0 : x1);
- for (i = 0; i < nr; i++)
+ for (int i = 0; i < nr; i++)
{
copy_rvec(*rbuf, x[n + i]);
rbuf++;
const char* specat_type,
const char* add_err)
{
- int nsend[2], nlast, nsend_zero[2] = { 0, 0 }, *nsend_ptr;
- int dim, ndir, nr, ns, nrecv_local, n0, start, buf[2];
- int nat_tot_specat, nat_tot_prev;
- gmx_bool bPBC;
- gmx_specatsend_t* spas;
+ int nsend[2], nsend_zero[2] = { 0, 0 };
+ int buf[2];
if (debug)
{
const int numRequested = ireq->size();
nsend[0] = ireq->size();
nsend[1] = nsend[0];
- nlast = nsend[1];
+ int nlast = nsend[1];
for (int d = dd->ndim - 1; d >= 0; d--)
{
/* Pulse the grid forward and backward */
- dim = dd->dim[d];
- bPBC = (dim < dd->unitCellInfo.npbcdim);
- if (dd->numCells[dim] == 2)
- {
- /* Only 2 cells, so we only need to communicate once */
- ndir = 1;
- }
- else
- {
- ndir = 2;
- }
+ int dim = dd->dim[d];
+ bool bPBC = (dim < dd->unitCellInfo.npbcdim);
+ const int ndir = (dd->numCells[dim] == 2)
+ ?
+ /* Only 2 cells, so we only need to communicate once */
+ 1
+ : 2;
+ int* nsend_ptr = nullptr;
for (int dir = 0; dir < ndir; dir++)
{
if (!bPBC && dd->numCells[dim] > 2
nsend_ptr = nsend;
}
/* Communicate the number of indices */
- ddSendrecv(dd, d, dir == 0 ? dddirForward : dddirBackward, nsend_ptr, 2,
- spac->nreq[d][dir], 2);
- nr = spac->nreq[d][dir][1];
+ ddSendrecv(dd, d, dir == 0 ? dddirForward : dddirBackward, nsend_ptr, 2, spac->nreq[d][dir], 2);
+ int nr = spac->nreq[d][dir][1];
ireq->resize(nlast + nr);
/* Communicate the indices */
- ddSendrecv(dd, d, dir == 0 ? dddirForward : dddirBackward, ireq->data(), nsend_ptr[1],
- ireq->data() + nlast, nr);
+ ddSendrecv(dd,
+ d,
+ dir == 0 ? dddirForward : dddirBackward,
+ ireq->data(),
+ nsend_ptr[1],
+ ireq->data() + nlast,
+ nr);
nlast += nr;
}
nsend[1] = nlast;
}
/* Search for the requested atoms and communicate the indices we have */
- nat_tot_specat = at_start;
- nrecv_local = 0;
+ int nat_tot_specat = at_start;
+ int nrecv_local = 0;
for (int d = 0; d < dd->ndim; d++)
{
/* Pulse the grid forward and backward */
- if (dd->dim[d] >= dd->unitCellInfo.npbcdim || dd->numCells[dd->dim[d]] > 2)
- {
- ndir = 2;
- }
- else
- {
- ndir = 1;
- }
- nat_tot_prev = nat_tot_specat;
+ const int ndir = (dd->dim[d] >= dd->unitCellInfo.npbcdim || dd->numCells[dd->dim[d]] > 2) ? 2 : 1;
+ int nat_tot_prev = nat_tot_specat;
for (int dir = ndir - 1; dir >= 0; dir--)
{
/* To avoid cost of clearing by resize(), we only increase size */
/* Note: resize initializes new elements to false, which is actually needed here */
spac->sendAtom.resize(nat_tot_specat);
}
- spas = &spac->spas[d][dir];
- n0 = spac->nreq[d][dir][0];
- nr = spac->nreq[d][dir][1];
+ gmx_specatsend_t* spas = &spac->spas[d][dir];
+ const int n0 = spac->nreq[d][dir][0];
+ const int nr = spac->nreq[d][dir][1];
if (debug)
{
fprintf(debug, "dim=%d, dir=%d, searching for %d atoms\n", d, dir, nr);
}
- start = nlast - nr;
+ const int start = nlast - nr;
spas->a.clear();
spac->ibuf.clear();
nsend[0] = 0;
for (int i = 0; i < nr; i++)
{
const int indr = (*ireq)[start + i];
- int ind;
+ int ind = 0;
/* Check if this is a home atom and if so ind will be set */
if (const int* homeIndex = dd->ga2la->findHome(indr))
{
fprintf(debug,
"Send to rank %d, %d (%d) indices, "
"receive from rank %d, %d (%d) indices\n",
- dd->neighbor[d][1 - dir], nsend[1], nsend[0], dd->neighbor[d][dir], buf[1],
+ dd->neighbor[d][1 - dir],
+ nsend[1],
+ nsend[0],
+ dd->neighbor[d][dir],
+ buf[1],
buf[0]);
if (gmx_debug_at)
{
spas->nrecv = buf[1];
dd->globalAtomIndices.resize(nat_tot_specat + spas->nrecv);
/* Send and receive the indices */
- ddSendrecv(dd, d, dir == 0 ? dddirBackward : dddirForward, spac->ibuf.data(),
- spac->ibuf.size(), dd->globalAtomIndices.data() + nat_tot_specat, spas->nrecv);
+ ddSendrecv(dd,
+ d,
+ dir == 0 ? dddirBackward : dddirForward,
+ spac->ibuf.data(),
+ spac->ibuf.size(),
+ dd->globalAtomIndices.data() + nat_tot_specat,
+ spas->nrecv);
nat_tot_specat += spas->nrecv;
}
/* Increase the x/f communication buffer sizes, when necessary */
- ns = spac->spas[d][0].a.size();
- nr = spac->spas[d][0].nrecv;
+ int ns = spac->spas[d][0].a.size();
+ int nr = spac->spas[d][0].nrecv;
if (ndir == 2)
{
ns += spac->spas[d][1].a.size();
{
if (debug)
{
- fprintf(debug, "Requested %d, received %d (tot recv %d)\n", numRequested, nrecv_local,
+ fprintf(debug,
+ "Requested %d, received %d (tot recv %d)\n",
+ numRequested,
+ nrecv_local,
nat_tot_specat - at_start);
if (gmx_debug_at)
{
fprintf(debug, "\n");
}
}
- fprintf(stderr, "\nDD cell %d %d %d: Neighboring cells do not have atoms:", dd->ci[XX],
- dd->ci[YY], dd->ci[ZZ]);
+ fprintf(stderr,
+ "\nDD cell %d %d %d: Neighboring cells do not have atoms:",
+ dd->ci[XX],
+ dd->ci[YY],
+ dd->ci[ZZ]);
for (int i = 0; i < numRequested; i++)
{
if (!ga2la_specat->find((*ireq)[i]))
"%ss from the neighboring cells. This probably means your %s lengths are too "
"long compared to the domain decomposition cell size. Decrease the number of "
"domain decomposition grid cells%s%s.",
- dd->ci[XX], dd->ci[YY], dd->ci[ZZ], nrecv_local, numRequested, specat_type,
- specat_type, add_err, dd_dlb_is_on(dd) ? " or use the -rcon option of mdrun" : "");
+ dd->ci[XX],
+ dd->ci[YY],
+ dd->ci[ZZ],
+ nrecv_local,
+ numRequested,
+ specat_type,
+ specat_type,
+ add_err,
+ dd_dlb_is_on(dd) ? " or use the -rcon option of mdrun" : "");
}
spac->at_start = at_start;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/block.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/range.h"
#include "gromacs/utility/real.h"
struct gmx_domdec_specat_comm_t;
class gmx_ga2la_t;
struct gmx_pme_comm_n_box_t;
-struct gmx_reverse_top_t;
struct t_inputrec;
+struct gmx_reverse_top_t;
+struct gmx_mtop_t;
+struct ReverseTopOptions;
namespace gmx
{
/* The number of zones including the home zone */
int n = 0;
/* The shift of the zones with respect to the home zone */
- ivec shift[DD_MAXZONE] = {};
+ std::array<ivec, DD_MAXZONE> shift;
/* The charge group boundaries for the zones */
- int cg_range[DD_MAXZONE + 1] = {};
+ std::array<int, DD_MAXZONE + 1> cg_range;
/* The pair interaction zone and atom ranges per each i-zone */
std::vector<DDPairInteractionRanges> iZones;
/* Boundaries of the zones */
- gmx_domdec_zone_size_t size[DD_MAXZONE];
+ std::array<gmx_domdec_zone_size_t, DD_MAXZONE> size;
/* The cg density of the home zone */
real dens_zone0 = 0;
};
{ //NOLINT(clang-analyzer-optin.performance.Padding)
//! Constructor, only partial for now
gmx_domdec_t(const t_inputrec& ir);
+ ~gmx_domdec_t();
/* The DD particle-particle nodes only */
/* The communication setup within the communicator all
std::unique_ptr<AtomDistribution> ma;
/* Global atom number to interaction list */
- gmx_reverse_top_t* reverse_top = nullptr;
- int nbonded_global = 0;
- int nbonded_local = 0;
+ std::unique_ptr<gmx_reverse_top_t> reverse_top;
/* Whether we have non-self exclusion */
bool haveExclusions = false;
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2006 - 2014, The GROMACS development team.
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <algorithm>
#include <memory>
+#include <optional>
#include <string>
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_network.h"
#include "gromacs/domdec/ga2la.h"
+#include "gromacs/domdec/options.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/forcerec.h"
#include "dump.h"
using gmx::ArrayRef;
+using gmx::DDBondedChecking;
using gmx::ListOfLists;
using gmx::RVec;
InteractionDefinitions idef; /**< Partial local topology */
std::unique_ptr<gmx::VsitePbc> vsitePbc = nullptr; /**< vsite PBC structure */
- int nbonded = 0; /**< The number of bondeds in this struct */
- ListOfLists<int> excl; /**< List of exclusions */
- int excl_count = 0; /**< The total exclusion count for \p excl */
+ int numBondedInteractions = 0; /**< The number of bonded interactions observed */
+ ListOfLists<int> excl; /**< List of exclusions */
};
-/*! \brief Struct for the reverse topology: links bonded interactions to atomsx */
-struct gmx_reverse_top_t
+/*! \brief Options for setting up gmx_reverse_top_t */
+struct ReverseTopOptions
{
+ //! Constructor, constraints and settles are not including with a single argument
+ ReverseTopOptions(DDBondedChecking ddBondedChecking,
+ bool includeConstraints = false,
+ bool includeSettles = false) :
+ ddBondedChecking(ddBondedChecking),
+ includeConstraints(includeConstraints),
+ includeSettles(includeSettles)
+ {
+ }
+
+ //! \brief For which bonded interactions to check assignments
+ const DDBondedChecking ddBondedChecking;
+ //! \brief Whether constraints are stored in this reverse top
+ const bool includeConstraints;
+ //! \brief Whether settles are stored in this reverse top
+ const bool includeSettles;
+};
+
+/*! \brief Struct for the reverse topology: links bonded interactions to atoms */
+struct gmx_reverse_top_t::Impl
+{
+ //! Constructs a reverse topology from \p mtop
+ Impl(const gmx_mtop_t& mtop, bool useFreeEnergy, const ReverseTopOptions& reverseTopOptions);
+
//! @cond Doxygen_Suppress
- //! \brief Are there constraints in this revserse top?
- bool bConstr = false;
- //! \brief Are there settles in this revserse top?
- bool bSettle = false;
- //! \brief All bonded interactions have to be assigned?
- bool bBCheck = false;
+ //! Options for the setup of this reverse topology
+ const ReverseTopOptions options;
+ //! Are there interaction of type F_POSRES and/or F_FBPOSRES
+ bool havePositionRestraints;
//! \brief Are there bondeds/exclusions between atoms?
bool bInterAtomicInteractions = false;
//! \brief Reverse ilist for all moltypes
//! \brief Intermolecular reverse ilist
reverse_ilist_t ril_intermol;
+ /*! \brief Data to help check reverse topology construction
+ *
+ * Partitioning could incorrectly miss a bonded interaction.
+ * However, checking for that requires a global communication
+ * stage, which does not otherwise happen during partitioning. So,
+ * for performance, we do that alongside the first global energy
+ * reduction after a new DD is made. These variables handle
+ * whether the check happens, its input for this domain, output
+ * across all domains, and the expected value it should match. */
+ /*! \{ */
+ /*! \brief Number of bonded interactions found in the reverse
+ * topology for this domain. */
+ int numBondedInteractions = 0;
+ /*! \brief Whether to check at the next global communication
+ * stage the total number of bonded interactions found.
+ *
+ * Cleared after that number is found. */
+ bool shouldCheckNumberOfBondedInteractions = false;
+ /*! \brief The total number of bonded interactions found in
+ * the reverse topology across all domains.
+ *
+ * Only has a value after reduction across all ranks, which is
+ * removed when it is again time to check after a new
+ * partition. */
+ std::optional<int> numBondedInteractionsOverAllDomains;
+ //! The number of bonded interactions computed from the full topology
+ int expectedNumGlobalBondedInteractions = 0;
+ /*! \} */
+
/* Work data structures for multi-threading */
//! \brief Thread work array for local topology generation
std::vector<thread_work_t> th_work;
//! @endcond
};
+
/*! \brief Returns the number of atom entries for il in gmx_reverse_top_t */
static int nral_rt(int ftype)
{
- int nral;
-
- nral = NRAL(ftype);
+ int nral = NRAL(ftype);
if (interaction_function[ftype].flags & IF_VSITE)
{
/* With vsites the reverse topology contains an extra entry
}
/*! \brief Return whether interactions of type \p ftype need to be assigned exactly once */
-static gmx_bool dd_check_ftype(int ftype, gmx_bool bBCheck, gmx_bool bConstr, gmx_bool bSettle)
+static gmx_bool dd_check_ftype(const int ftype, const ReverseTopOptions rtOptions)
{
return ((((interaction_function[ftype].flags & IF_BOND) != 0U)
&& ((interaction_function[ftype].flags & IF_VSITE) == 0U)
- && (bBCheck || ((interaction_function[ftype].flags & IF_LIMZERO) == 0U)))
- || (bConstr && (ftype == F_CONSTR || ftype == F_CONSTRNC)) || (bSettle && ftype == F_SETTLE));
+ && ((rtOptions.ddBondedChecking == DDBondedChecking::All)
+ || ((interaction_function[ftype].flags & IF_LIMZERO) == 0U)))
+ || (rtOptions.includeConstraints && (ftype == F_CONSTR || ftype == F_CONSTRNC))
+ || (rtOptions.includeSettles && ftype == F_SETTLE));
}
/*! \brief Checks whether interactions have been assigned for one function type
for (int ftype = 0; ftype < F_NRE; ftype++)
{
- if (dd_check_ftype(ftype, rt.bBCheck, rt.bConstr, rt.bSettle))
+ if (dd_check_ftype(ftype, rt.impl_->options))
{
- flagInteractionsForType(ftype, idef.il[ftype], ril, atomRange, numAtomsPerMolecule,
- cr->dd->globalAtomIndices, isAssigned);
+ flagInteractionsForType(
+ ftype, idef.il[ftype], ril, atomRange, numAtomsPerMolecule, cr->dd->globalAtomIndices, isAssigned);
}
}
numMissingToPrint);
}
log.writeStringFormatted("%20s atoms", interaction_function[ftype].longname);
- int a;
- for (a = 0; a < nral; a++)
+ int a = 0;
+ for (; a < nral; a++)
{
log.writeStringFormatted("%5d", ril.il[j_mol + 2 + a] + 1);
}
a++;
}
log.writeString(" global");
- for (a = 0; a < nral; a++)
+ for (int a = 0; a < nral; a++)
{
- log.writeStringFormatted("%6d", atomRange.begin() + mol * numAtomsPerMolecule
- + ril.il[j_mol + 2 + a] + 1);
+ log.writeStringFormatted("%6d",
+ atomRange.begin() + mol * numAtomsPerMolecule
+ + ril.il[j_mol + 2 + a] + 1);
}
log.ensureLineBreak();
}
a_end = a_start + molb.nmol * moltype.atoms.nr;
const gmx::Range<int> atomRange(a_start, a_end);
- auto warning = printMissingInteractionsMolblock(cr, rt, *(moltype.name), rt.ril_mt[molb.type],
- atomRange, moltype.atoms.nr, molb.nmol, idef);
+ auto warning = printMissingInteractionsMolblock(
+ cr, rt, *(moltype.name), rt.impl_->ril_mt[molb.type], atomRange, moltype.atoms.nr, molb.nmol, idef);
GMX_LOG(mdlog.warning).appendText(warning);
}
}
-void dd_print_missing_interactions(const gmx::MDLogger& mdlog,
- t_commrec* cr,
- int local_count,
- const gmx_mtop_t* top_global,
- const gmx_localtop_t* top_local,
+void dd_print_missing_interactions(const gmx::MDLogger& mdlog,
+ t_commrec* cr,
+ int numBondedInteractionsOverAllDomains,
+ const gmx_mtop_t& top_global,
+ const gmx_localtop_t* top_local,
gmx::ArrayRef<const gmx::RVec> x,
const matrix box)
{
- int ndiff_tot, cl[F_NRE], n, ndiff, rest_global, rest_local;
- int ftype, nral;
- gmx_domdec_t* dd;
-
- dd = cr->dd;
+ int cl[F_NRE];
+ gmx_domdec_t* dd = cr->dd;
GMX_LOG(mdlog.warning)
.appendText(
"Not all bonded interactions have been properly assigned to the domain "
"decomposition cells");
- ndiff_tot = local_count - dd->nbonded_global;
+ const int ndiff_tot = numBondedInteractionsOverAllDomains
+ - dd->reverse_top->impl_->expectedNumGlobalBondedInteractions;
- for (ftype = 0; ftype < F_NRE; ftype++)
+ for (int ftype = 0; ftype < F_NRE; ftype++)
{
- nral = NRAL(ftype);
- cl[ftype] = top_local->idef.il[ftype].size() / (1 + nral);
+ const int nral = NRAL(ftype);
+ cl[ftype] = top_local->idef.il[ftype].size() / (1 + nral);
}
gmx_sumi(F_NRE, cl, cr);
if (DDMASTER(dd))
{
GMX_LOG(mdlog.warning).appendText("A list of missing interactions:");
- rest_global = dd->nbonded_global;
- rest_local = local_count;
- for (ftype = 0; ftype < F_NRE; ftype++)
+ int rest_global = dd->reverse_top->impl_->expectedNumGlobalBondedInteractions;
+ int rest = numBondedInteractionsOverAllDomains;
+ for (int ftype = 0; ftype < F_NRE; ftype++)
{
/* In the reverse and local top all constraints are merged
* into F_CONSTR. So in the if statement we skip F_CONSTRNC
* and add these constraints when doing F_CONSTR.
*/
- if (((interaction_function[ftype].flags & IF_BOND)
- && (dd->reverse_top->bBCheck || !(interaction_function[ftype].flags & IF_LIMZERO)))
- || (dd->reverse_top->bConstr && ftype == F_CONSTR)
- || (dd->reverse_top->bSettle && ftype == F_SETTLE))
+ if (dd_check_ftype(ftype, dd->reverse_top->impl_->options) && ftype != F_CONSTRNC)
{
- n = gmx_mtop_ftype_count(top_global, ftype);
+ int n = gmx_mtop_ftype_count(top_global, ftype);
if (ftype == F_CONSTR)
{
n += gmx_mtop_ftype_count(top_global, F_CONSTRNC);
}
- ndiff = cl[ftype] - n;
+ int ndiff = cl[ftype] - n;
if (ndiff != 0)
{
GMX_LOG(mdlog.warning)
.appendTextFormatted("%20s of %6d missing %6d",
- interaction_function[ftype].longname, n, -ndiff);
+ interaction_function[ftype].longname,
+ n,
+ -ndiff);
}
rest_global -= n;
- rest_local -= cl[ftype];
+ rest -= cl[ftype];
}
}
- ndiff = rest_local - rest_global;
+ int ndiff = rest - rest_global;
if (ndiff != 0)
{
GMX_LOG(mdlog.warning).appendTextFormatted("%20s of %6d missing %6d", "exclusions", rest_global, -ndiff);
}
}
- printMissingInteractionsAtoms(mdlog, cr, *top_global, top_local->idef);
+ printMissingInteractionsAtoms(mdlog, cr, top_global, top_local->idef);
write_dd_pdb("dd_dump_err", 0, "dump", top_global, cr, -1, as_rvec_array(x.data()), box);
std::string errorMessage;
"involved moved further apart than the multi-body cut-off distance (%g nm) or the "
"two-body cut-off distance (%g nm), see option -rdd, for pairs and tabulated bonds "
"also see option -ddcheck",
- -ndiff_tot, cr->dd->nbonded_global, dd_cutoff_multibody(dd), dd_cutoff_twobody(dd));
+ -ndiff_tot,
+ dd->reverse_top->impl_->expectedNumGlobalBondedInteractions,
+ dd_cutoff_multibody(dd),
+ dd_cutoff_twobody(dd));
}
gmx_fatal_collective(FARGS, cr->mpi_comm_mygroup, MASTER(cr), "%s", errorMessage.c_str());
}
/*! \brief Return global topology molecule information for global atom index \p i_gl */
-static void global_atomnr_to_moltype_ind(const gmx_reverse_top_t* rt, int i_gl, int* mb, int* mt, int* mol, int* i_mol)
+static void global_atomnr_to_moltype_ind(ArrayRef<const MolblockIndices> molblockIndices,
+ int i_gl,
+ int* mb,
+ int* mt,
+ int* mol,
+ int* i_mol)
{
- const MolblockIndices* mbi = rt->mbi.data();
+ const MolblockIndices* mbi = molblockIndices.data();
int start = 0;
- int end = rt->mbi.size(); /* exclusive */
- int mid;
+ int end = molblockIndices.size(); /* exclusive */
+ int mid = 0;
/* binary search for molblock_ind */
while (TRUE)
return maxNumExcls;
}
+//! Options for linking atoms in make_reverse_ilist
+enum class AtomLinkRule
+{
+ FirstAtom, //!< Link all interactions to the first atom in the atom list
+ AllAtomsInBondeds //!< Link bonded interactions to all atoms involved, don't link vsites
+};
+
/*! \brief Run the reverse ilist generation and store it in r_il when \p bAssign = TRUE */
static int low_make_reverse_ilist(const InteractionLists& il_mt,
const t_atom* atom,
int* count,
- gmx_bool bConstr,
- gmx_bool bSettle,
- gmx_bool bBCheck,
+ const ReverseTopOptions& rtOptions,
gmx::ArrayRef<const int> r_index,
gmx::ArrayRef<int> r_il,
- gmx_bool bLinkToAllAtoms,
- gmx_bool bAssign)
+ const AtomLinkRule atomLinkRule,
+ const bool assignReverseIlist)
{
- int ftype, j, nlink, link;
- int a;
- int nint;
+ const bool includeConstraints = rtOptions.includeConstraints;
+ const bool includeSettles = rtOptions.includeSettles;
+ const DDBondedChecking ddBondedChecking = rtOptions.ddBondedChecking;
+
+ int nint = 0;
- nint = 0;
- for (ftype = 0; ftype < F_NRE; ftype++)
+ for (int ftype = 0; ftype < F_NRE; ftype++)
{
if ((interaction_function[ftype].flags & (IF_BOND | IF_VSITE))
- || (bConstr && (ftype == F_CONSTR || ftype == F_CONSTRNC)) || (bSettle && ftype == F_SETTLE))
+ || (includeConstraints && (ftype == F_CONSTR || ftype == F_CONSTRNC))
+ || (includeSettles && ftype == F_SETTLE))
{
- const bool bVSite = ((interaction_function[ftype].flags & IF_VSITE) != 0U);
- const int nral = NRAL(ftype);
- const auto& il = il_mt[ftype];
+ const bool isVSite = ((interaction_function[ftype].flags & IF_VSITE) != 0U);
+ const int nral = NRAL(ftype);
+ const auto& il = il_mt[ftype];
for (int i = 0; i < il.size(); i += 1 + nral)
{
const int* ia = il.iatoms.data() + i;
- if (bLinkToAllAtoms)
+ // Virtual sites should not be linked for bonded interactions
+ const int nlink = (atomLinkRule == AtomLinkRule::FirstAtom) ? 1 : (isVSite ? 0 : nral);
+ for (int link = 0; link < nlink; link++)
{
- if (bVSite)
- {
- /* We don't need the virtual sites for the cg-links */
- nlink = 0;
- }
- else
- {
- nlink = nral;
- }
- }
- else
- {
- /* Couple to the first atom in the interaction */
- nlink = 1;
- }
- for (link = 0; link < nlink; link++)
- {
- a = ia[1 + link];
- if (bAssign)
+ const int a = ia[1 + link];
+ if (assignReverseIlist)
{
GMX_ASSERT(!r_il.empty(), "with bAssign not allowed to be empty");
GMX_ASSERT(!r_index.empty(), "with bAssign not allowed to be empty");
r_il[r_index[a] + count[a]] = (ftype == F_CONSTRNC ? F_CONSTR : ftype);
r_il[r_index[a] + count[a] + 1] = ia[0];
- for (j = 1; j < 1 + nral; j++)
+ for (int j = 1; j < 1 + nral; j++)
{
/* Store the molecular atom number */
r_il[r_index[a] + count[a] + 1 + j] = ia[j];
}
if (interaction_function[ftype].flags & IF_VSITE)
{
- if (bAssign)
+ if (assignReverseIlist)
{
/* Add an entry to iatoms for storing
* which of the constructing atoms are
* vsites again.
*/
r_il[r_index[a] + count[a] + 2 + nral] = 0;
- for (j = 2; j < 1 + nral; j++)
+ for (int j = 2; j < 1 + nral; j++)
{
- if (atom[ia[j]].ptype == eptVSite)
+ if (atom[ia[j]].ptype == ParticleType::VSite)
{
r_il[r_index[a] + count[a] + 2 + nral] |= (2 << j);
}
* uniquely assigned and can be assigned
* to multiple nodes with recursive vsites.
*/
- if (bBCheck || !(interaction_function[ftype].flags & IF_LIMZERO))
+ if (ddBondedChecking == DDBondedChecking::All
+ || !(interaction_function[ftype].flags & IF_LIMZERO))
{
nint++;
}
}
/*! \brief Make the reverse ilist: a list of bonded interactions linked to atoms */
-static int make_reverse_ilist(const InteractionLists& ilist,
- const t_atoms* atoms,
- gmx_bool bConstr,
- gmx_bool bSettle,
- gmx_bool bBCheck,
- gmx_bool bLinkToAllAtoms,
- reverse_ilist_t* ril_mt)
+static int make_reverse_ilist(const InteractionLists& ilist,
+ const t_atoms* atoms,
+ const ReverseTopOptions& rtOptions,
+ const AtomLinkRule atomLinkRule,
+ reverse_ilist_t* ril_mt)
{
- int nat_mt, *count, i, nint_mt;
-
/* Count the interactions */
- nat_mt = atoms->nr;
- snew(count, nat_mt);
- low_make_reverse_ilist(ilist, atoms->atom, count, bConstr, bSettle, bBCheck, {}, {},
- bLinkToAllAtoms, FALSE);
+ const int nat_mt = atoms->nr;
+ std::vector<int> count(nat_mt);
+ low_make_reverse_ilist(ilist, atoms->atom, count.data(), rtOptions, {}, {}, atomLinkRule, FALSE);
ril_mt->index.push_back(0);
- for (i = 0; i < nat_mt; i++)
+ for (int i = 0; i < nat_mt; i++)
{
ril_mt->index.push_back(ril_mt->index[i] + count[i]);
count[i] = 0;
ril_mt->il.resize(ril_mt->index[nat_mt]);
/* Store the interactions */
- nint_mt = low_make_reverse_ilist(ilist, atoms->atom, count, bConstr, bSettle, bBCheck,
- ril_mt->index, ril_mt->il, bLinkToAllAtoms, TRUE);
-
- sfree(count);
+ int nint_mt = low_make_reverse_ilist(
+ ilist, atoms->atom, count.data(), rtOptions, ril_mt->index, ril_mt->il, atomLinkRule, TRUE);
ril_mt->numAtomsInMolecule = atoms->nr;
return nint_mt;
}
-/*! \brief Generate the reverse topology */
-static gmx_reverse_top_t make_reverse_top(const gmx_mtop_t* mtop,
- gmx_bool bFE,
- gmx_bool bConstr,
- gmx_bool bSettle,
- gmx_bool bBCheck,
- int* nint)
+gmx_reverse_top_t::gmx_reverse_top_t(const gmx_mtop_t& mtop,
+ bool useFreeEnergy,
+ const ReverseTopOptions& reverseTopOptions) :
+ impl_(std::make_unique<Impl>(mtop, useFreeEnergy, reverseTopOptions))
{
- gmx_reverse_top_t rt;
+}
- /* Should we include constraints (for SHAKE) in rt? */
- rt.bConstr = bConstr;
- rt.bSettle = bSettle;
- rt.bBCheck = bBCheck;
+gmx_reverse_top_t::~gmx_reverse_top_t() {}
- rt.bInterAtomicInteractions = mtop->bIntermolecularInteractions;
- rt.ril_mt.resize(mtop->moltype.size());
- rt.ril_mt_tot_size = 0;
+/*! \brief Generate the reverse topology */
+gmx_reverse_top_t::Impl::Impl(const gmx_mtop_t& mtop,
+ const bool useFreeEnergy,
+ const ReverseTopOptions& reverseTopOptions) :
+ options(reverseTopOptions),
+ havePositionRestraints(
+ gmx_mtop_ftype_count(mtop, F_POSRES) + gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0),
+ bInterAtomicInteractions(mtop.bIntermolecularInteractions)
+{
+ bInterAtomicInteractions = mtop.bIntermolecularInteractions;
+ ril_mt.resize(mtop.moltype.size());
+ ril_mt_tot_size = 0;
std::vector<int> nint_mt;
- for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
+ for (size_t mt = 0; mt < mtop.moltype.size(); mt++)
{
- const gmx_moltype_t& molt = mtop->moltype[mt];
+ const gmx_moltype_t& molt = mtop.moltype[mt];
if (molt.atoms.nr > 1)
{
- rt.bInterAtomicInteractions = true;
+ bInterAtomicInteractions = true;
}
/* Make the atom to interaction list for this molecule type */
int numberOfInteractions = make_reverse_ilist(
- molt.ilist, &molt.atoms, rt.bConstr, rt.bSettle, rt.bBCheck, FALSE, &rt.ril_mt[mt]);
+ molt.ilist, &molt.atoms, options, AtomLinkRule::FirstAtom, &ril_mt[mt]);
nint_mt.push_back(numberOfInteractions);
- rt.ril_mt_tot_size += rt.ril_mt[mt].index[molt.atoms.nr];
+ ril_mt_tot_size += ril_mt[mt].index[molt.atoms.nr];
}
if (debug)
{
- fprintf(debug, "The total size of the atom to interaction index is %d integers\n",
- rt.ril_mt_tot_size);
+ fprintf(debug, "The total size of the atom to interaction index is %d integers\n", ril_mt_tot_size);
}
- *nint = 0;
- for (const gmx_molblock_t& molblock : mtop->molblock)
+ expectedNumGlobalBondedInteractions = 0;
+ for (const gmx_molblock_t& molblock : mtop.molblock)
{
- *nint += molblock.nmol * nint_mt[molblock.type];
+ expectedNumGlobalBondedInteractions += molblock.nmol * nint_mt[molblock.type];
}
/* Make an intermolecular reverse top, if necessary */
- rt.bIntermolecularInteractions = mtop->bIntermolecularInteractions;
- if (rt.bIntermolecularInteractions)
+ bIntermolecularInteractions = mtop.bIntermolecularInteractions;
+ if (bIntermolecularInteractions)
{
t_atoms atoms_global;
- atoms_global.nr = mtop->natoms;
+ atoms_global.nr = mtop.natoms;
atoms_global.atom = nullptr; /* Only used with virtual sites */
- GMX_RELEASE_ASSERT(mtop->intermolecular_ilist,
+ GMX_RELEASE_ASSERT(mtop.intermolecular_ilist,
"We should have an ilist when intermolecular interactions are on");
- *nint += make_reverse_ilist(*mtop->intermolecular_ilist, &atoms_global, rt.bConstr,
- rt.bSettle, rt.bBCheck, FALSE, &rt.ril_intermol);
+ expectedNumGlobalBondedInteractions += make_reverse_ilist(
+ *mtop.intermolecular_ilist, &atoms_global, options, AtomLinkRule::FirstAtom, &ril_intermol);
}
- if (bFE && gmx_mtop_bondeds_free_energy(mtop))
+ if (useFreeEnergy && gmx_mtop_bondeds_free_energy(&mtop))
{
- rt.ilsort = ilsortFE_UNSORTED;
+ ilsort = ilsortFE_UNSORTED;
}
else
{
- rt.ilsort = ilsortNO_FE;
+ ilsort = ilsortNO_FE;
}
/* Make a molblock index for fast searching */
int i = 0;
- for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
+ for (size_t mb = 0; mb < mtop.molblock.size(); mb++)
{
- const gmx_molblock_t& molb = mtop->molblock[mb];
- const int numAtomsPerMol = mtop->moltype[molb.type].atoms.nr;
- MolblockIndices mbi;
- mbi.a_start = i;
+ const gmx_molblock_t& molb = mtop.molblock[mb];
+ const int numAtomsPerMol = mtop.moltype[molb.type].atoms.nr;
+ MolblockIndices mbiMolblock;
+ mbiMolblock.a_start = i;
i += molb.nmol * numAtomsPerMol;
- mbi.a_end = i;
- mbi.natoms_mol = numAtomsPerMol;
- mbi.type = molb.type;
- rt.mbi.push_back(mbi);
+ mbiMolblock.a_end = i;
+ mbiMolblock.natoms_mol = numAtomsPerMol;
+ mbiMolblock.type = molb.type;
+ mbi.push_back(mbiMolblock);
}
- for (int th = 0; th < gmx_omp_nthreads_get(emntDomdec); th++)
+ for (int th = 0; th < gmx_omp_nthreads_get(ModuleMultiThread::Domdec); th++)
{
- rt.th_work.emplace_back(mtop->ffparams);
+ th_work.emplace_back(mtop.ffparams);
}
-
- return rt;
}
void dd_make_reverse_top(FILE* fplog,
gmx_domdec_t* dd,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const gmx::VirtualSitesHandler* vsite,
- const t_inputrec* ir,
- gmx_bool bBCheck)
+ const t_inputrec& inputrec,
+ const DDBondedChecking ddBondedChecking)
{
if (fplog)
{
* Otherwise we need to assign them to multiple domains and set up
* the parallel version constraint algorithm(s).
*/
+ GMX_RELEASE_ASSERT(ddBondedChecking == DDBondedChecking::ExcludeZeroLimit
+ || ddBondedChecking == DDBondedChecking::All,
+ "Invalid enum value for mdrun -ddcheck");
+ const ReverseTopOptions rtOptions(ddBondedChecking,
+ !dd->comm->systemInfo.mayHaveSplitConstraints,
+ !dd->comm->systemInfo.mayHaveSplitSettles);
- dd->reverse_top = new gmx_reverse_top_t;
- *dd->reverse_top =
- make_reverse_top(mtop, ir->efep != efepNO, !dd->comm->systemInfo.haveSplitConstraints,
- !dd->comm->systemInfo.haveSplitSettles, bBCheck, &dd->nbonded_global);
+ dd->reverse_top = std::make_unique<gmx_reverse_top_t>(
+ mtop, inputrec.efep != FreeEnergyPerturbationType::No, rtOptions);
dd->haveExclusions = false;
- for (const gmx_molblock_t& molb : mtop->molblock)
+ for (const gmx_molblock_t& molb : mtop.molblock)
{
- const int maxNumExclusionsPerAtom = getMaxNumExclusionsPerAtom(mtop->moltype[molb.type].excls);
+ const int maxNumExclusionsPerAtom = getMaxNumExclusionsPerAtom(mtop.moltype[molb.type].excls);
// We checked above that max 1 exclusion means only self exclusions
if (maxNumExclusionsPerAtom > 1)
{
}
}
- if (vsite && vsite->numInterUpdategroupVirtualSites() > 0)
+ const int numInterUpdategroupVirtualSites =
+ (vsite == nullptr ? 0 : vsite->numInterUpdategroupVirtualSites());
+ if (numInterUpdategroupVirtualSites > 0)
{
if (fplog)
{
fprintf(fplog,
"There are %d inter update-group virtual sites,\n"
- "will an extra communication step for selected coordinates and forces\n",
- vsite->numInterUpdategroupVirtualSites());
+ "will perform an extra communication step for selected coordinates and "
+ "forces\n",
+ numInterUpdategroupVirtualSites);
}
- init_domdec_vsites(dd, vsite->numInterUpdategroupVirtualSites());
+ init_domdec_vsites(dd, numInterUpdategroupVirtualSites);
}
- if (dd->comm->systemInfo.haveSplitConstraints || dd->comm->systemInfo.haveSplitSettles)
+ if (dd->comm->systemInfo.mayHaveSplitConstraints || dd->comm->systemInfo.mayHaveSplitSettles)
{
init_domdec_constraints(dd, mtop);
}
static void add_posres(int mol,
int a_mol,
int numAtomsInMolecule,
- const gmx_molblock_t* molb,
- t_iatom* iatoms,
+ const gmx_molblock_t& molb,
+ gmx::ArrayRef<int> iatoms,
const t_iparams* ip_in,
InteractionDefinitions* idef)
{
/* Get the position restraint coordinates from the molblock */
const int a_molb = mol * numAtomsInMolecule + a_mol;
- GMX_ASSERT(a_molb < ssize(molb->posres_xA),
+ GMX_ASSERT(a_molb < ssize(molb.posres_xA),
"We need a sufficient number of position restraint coordinates");
/* Copy the force constants */
t_iparams ip = ip_in[iatoms[0]];
- ip.posres.pos0A[XX] = molb->posres_xA[a_molb][XX];
- ip.posres.pos0A[YY] = molb->posres_xA[a_molb][YY];
- ip.posres.pos0A[ZZ] = molb->posres_xA[a_molb][ZZ];
- if (!molb->posres_xB.empty())
+ ip.posres.pos0A[XX] = molb.posres_xA[a_molb][XX];
+ ip.posres.pos0A[YY] = molb.posres_xA[a_molb][YY];
+ ip.posres.pos0A[ZZ] = molb.posres_xA[a_molb][ZZ];
+ if (!molb.posres_xB.empty())
{
- ip.posres.pos0B[XX] = molb->posres_xB[a_molb][XX];
- ip.posres.pos0B[YY] = molb->posres_xB[a_molb][YY];
- ip.posres.pos0B[ZZ] = molb->posres_xB[a_molb][ZZ];
+ ip.posres.pos0B[XX] = molb.posres_xB[a_molb][XX];
+ ip.posres.pos0B[YY] = molb.posres_xB[a_molb][YY];
+ ip.posres.pos0B[ZZ] = molb.posres_xB[a_molb][ZZ];
}
else
{
static void add_fbposres(int mol,
int a_mol,
int numAtomsInMolecule,
- const gmx_molblock_t* molb,
- t_iatom* iatoms,
+ const gmx_molblock_t& molb,
+ gmx::ArrayRef<int> iatoms,
const t_iparams* ip_in,
InteractionDefinitions* idef)
{
/* Get the position restraint coordinats from the molblock */
const int a_molb = mol * numAtomsInMolecule + a_mol;
- GMX_ASSERT(a_molb < ssize(molb->posres_xA),
+ GMX_ASSERT(a_molb < ssize(molb.posres_xA),
"We need a sufficient number of position restraint coordinates");
/* Copy the force constants */
t_iparams ip = ip_in[iatoms[0]];
/* Take reference positions from A position of normal posres */
- ip.fbposres.pos0[XX] = molb->posres_xA[a_molb][XX];
- ip.fbposres.pos0[YY] = molb->posres_xA[a_molb][YY];
- ip.fbposres.pos0[ZZ] = molb->posres_xA[a_molb][ZZ];
+ ip.fbposres.pos0[XX] = molb.posres_xA[a_molb][XX];
+ ip.fbposres.pos0[YY] = molb.posres_xA[a_molb][YY];
+ ip.fbposres.pos0[ZZ] = molb.posres_xA[a_molb][ZZ];
/* Note: no B-type for flat-bottom posres */
const t_iatom* iatoms,
InteractionDefinitions* idef)
{
- int k;
t_iatom tiatoms[1 + MAXATOMLIST];
- int j, ftype_r, nral_r;
/* Add this interaction to the local topology */
add_ifunc_for_vsites(tiatoms, ga2la, nral, bHomeA, a, a_gl, a_mol, iatoms, &idef->il[ftype]);
if (iatoms[1 + nral])
{
/* Check for recursion */
- for (k = 2; k < 1 + nral; k++)
+ for (int k = 2; k < 1 + nral; k++)
{
if ((iatoms[1 + nral] & (2 << k)) && (tiatoms[k] < 0))
{
/* This construction atoms is a vsite and not a home atom */
if (gmx_debug_at)
{
- fprintf(debug, "Constructing atom %d of vsite atom %d is a vsite and non-home\n",
- iatoms[k] + 1, a_mol + 1);
+ fprintf(debug,
+ "Constructing atom %d of vsite atom %d is a vsite and non-home\n",
+ iatoms[k] + 1,
+ a_mol + 1);
}
/* Find the vsite construction */
/* Check all interactions assigned to this atom */
- j = index[iatoms[k]];
+ int j = index[iatoms[k]];
while (j < index[iatoms[k] + 1])
{
- ftype_r = rtil[j++];
- nral_r = NRAL(ftype_r);
+ int ftype_r = rtil[j++];
+ int nral_r = NRAL(ftype_r);
if (interaction_function[ftype_r].flags & IF_VSITE)
{
/* Add this vsite (recursion) */
- add_vsite(ga2la, index, rtil, ftype_r, nral_r, FALSE, -1,
- a_gl + iatoms[k] - iatoms[1], iatoms[k], rtil.data() + j, idef);
+ add_vsite(ga2la,
+ index,
+ rtil,
+ ftype_r,
+ nral_r,
+ FALSE,
+ -1,
+ a_gl + iatoms[k] - iatoms[1],
+ iatoms[k],
+ rtil.data() + j,
+ idef);
}
j += 1 + nral_rt(ftype_r);
}
}
/*! \brief Returns the squared distance between atoms \p i and \p j */
-static real dd_dist2(t_pbc* pbc_null, const rvec* x, const int i, int j)
+static real dd_dist2(const t_pbc* pbc_null, ArrayRef<const RVec> coordinates, const int i, const int j)
{
rvec dx;
if (pbc_null)
{
- pbc_dx_aiuc(pbc_null, x[i], x[j], dx);
+ pbc_dx_aiuc(pbc_null, coordinates[i], coordinates[j], dx);
}
else
{
- rvec_sub(x[i], x[j], dx);
+ rvec_sub(coordinates[i], coordinates[j], dx);
}
return norm2(dx);
/*! \brief Append t_idef structures 1 to nsrc in src to *dest */
static void combine_idef(InteractionDefinitions* dest, gmx::ArrayRef<const thread_work_t> src)
{
- int ftype;
-
- for (ftype = 0; ftype < F_NRE; ftype++)
+ for (int ftype = 0; ftype < F_NRE; ftype++)
{
int n = 0;
for (gmx::index s = 1; s < src.ssize(); s++)
}
}
-/*! \brief Check and when available assign bonded interactions for local atom i
+//! Options for assigning interactions for atoms
+enum class InteractionConnectivity
+{
+ Intramolecular, //!< Only intra-molecular interactions
+ Intermolecular //!< Only inter-molecular interactions
+};
+
+/*! \brief Determine whether the local domain has responsibility for
+ * any of the bonded interactions for local atom \p atomIndex
+ * and assign those to the local domain.
+ *
+ * \returns The total number of bonded interactions for this atom for
+ * which this domain is responsible.
*/
-static inline void check_assign_interactions_atom(int i,
- int i_gl,
- int mol,
- int i_mol,
- int numAtomsInMolecule,
- gmx::ArrayRef<const int> index,
- gmx::ArrayRef<const int> rtil,
- gmx_bool bInterMolInteractions,
- int ind_start,
- int ind_end,
- const gmx_domdec_t* dd,
- const gmx_domdec_zones_t* zones,
- const gmx_molblock_t* molb,
- gmx_bool bRCheckMB,
- const ivec rcheck,
- gmx_bool bRCheck2B,
- real rc2,
- t_pbc* pbc_null,
- rvec* cg_cm,
- const t_iparams* ip_in,
- InteractionDefinitions* idef,
- int iz,
- gmx_bool bBCheck,
- int* nbonded_local)
+template<InteractionConnectivity interactionConnectivity>
+static inline int assignInteractionsForAtom(const int atomIndex,
+ const int globalAtomIndex,
+ const int atomIndexInMolecule,
+ gmx::ArrayRef<const int> index,
+ gmx::ArrayRef<const int> rtil,
+ const int ind_start,
+ const int ind_end,
+ const gmx_ga2la_t& ga2la,
+ const gmx_domdec_zones_t* zones,
+ const bool checkDistanceMultiBody,
+ const ivec rcheck,
+ const bool checkDistanceTwoBody,
+ const real cutoffSquared,
+ const t_pbc* pbc_null,
+ ArrayRef<const RVec> coordinates,
+ InteractionDefinitions* idef,
+ const int iz,
+ const DDBondedChecking ddBondedChecking)
{
gmx::ArrayRef<const DDPairInteractionRanges> iZones = zones->iZones;
+ int numBondedInteractions = 0;
+
int j = ind_start;
while (j < ind_end)
{
const int nral = NRAL(ftype);
if (interaction_function[ftype].flags & IF_VSITE)
{
- assert(!bInterMolInteractions);
+ GMX_ASSERT(interactionConnectivity == InteractionConnectivity::Intramolecular,
+ "All vsites should be intramolecular");
+
/* The vsite construction goes where the vsite itself is */
if (iz == 0)
{
- add_vsite(*dd->ga2la, index, rtil, ftype, nral, TRUE, i, i_gl, i_mol, iatoms.data(), idef);
+ add_vsite(ga2la,
+ index,
+ rtil,
+ ftype,
+ nral,
+ TRUE,
+ atomIndex,
+ globalAtomIndex,
+ atomIndexInMolecule,
+ iatoms.data(),
+ idef);
}
}
else
{
- gmx_bool bUse;
+ bool bUse = false;
/* Copy the type */
tiatoms[0] = iatoms[0];
if (nral == 1)
{
- assert(!bInterMolInteractions);
- /* Assign single-body interactions to the home zone */
- if (iz == 0)
- {
- bUse = TRUE;
- tiatoms[1] = i;
- if (ftype == F_POSRES)
- {
- add_posres(mol, i_mol, numAtomsInMolecule, molb, tiatoms, ip_in, idef);
- }
- else if (ftype == F_FBPOSRES)
- {
- add_fbposres(mol, i_mol, numAtomsInMolecule, molb, tiatoms, ip_in, idef);
- }
- }
- else
+ GMX_ASSERT(interactionConnectivity == InteractionConnectivity::Intramolecular,
+ "All interactions that involve a single atom are intramolecular");
+
+ /* Assign single-body interactions to the home zone.
+ * Position restraints are not handled here, but separately.
+ */
+ if (iz == 0 && !(ftype == F_POSRES || ftype == F_FBPOSRES))
{
- bUse = FALSE;
+ bUse = true;
+ tiatoms[1] = atomIndex;
}
}
else if (nral == 2)
/* This is a two-body interaction, we can assign
* analogous to the non-bonded assignments.
*/
- int k_gl;
-
- if (!bInterMolInteractions)
- {
- /* Get the global index using the offset in the molecule */
- k_gl = i_gl + iatoms[2] - i_mol;
- }
- else
- {
- k_gl = iatoms[2];
- }
- if (const auto* entry = dd->ga2la->find(k_gl))
+ const int k_gl = (interactionConnectivity == InteractionConnectivity::Intramolecular)
+ ?
+ /* Get the global index using the offset in the molecule */
+ (globalAtomIndex + iatoms[2] - atomIndexInMolecule)
+ : iatoms[2];
+ if (const auto* entry = ga2la.find(k_gl))
{
int kz = entry->cell;
if (kz >= zones->n)
GMX_ASSERT(ftype != F_CONSTR || (iz == 0 && kz == 0),
"Constraint assigned here should only involve home atoms");
- tiatoms[1] = i;
+ tiatoms[1] = atomIndex;
tiatoms[2] = entry->la;
/* If necessary check the cgcm distance */
- if (bRCheck2B && dd_dist2(pbc_null, cg_cm, tiatoms[1], tiatoms[2]) >= rc2)
+ if (checkDistanceTwoBody
+ && dd_dist2(pbc_null, coordinates, tiatoms[1], tiatoms[2]) >= cutoffSquared)
{
- bUse = FALSE;
+ bUse = false;
}
}
}
else
{
/* Assign this multi-body bonded interaction to
- * the local node if we have all the atoms involved
+ * the local domain if we have all the atoms involved
* (local or communicated) and the minimum zone shift
* in each dimension is zero, for dimensions
* with 2 DD cells an extra check may be necessary.
*/
ivec k_zero, k_plus;
- int k;
-
- bUse = TRUE;
+ bUse = true;
clear_ivec(k_zero);
clear_ivec(k_plus);
- for (k = 1; k <= nral && bUse; k++)
+ for (int k = 1; k <= nral && bUse; k++)
{
- int k_gl;
- if (!bInterMolInteractions)
- {
- /* Get the global index using the offset in the molecule */
- k_gl = i_gl + iatoms[k] - i_mol;
- }
- else
- {
- k_gl = iatoms[k];
- }
- const auto* entry = dd->ga2la->find(k_gl);
+ const int k_gl =
+ (interactionConnectivity == InteractionConnectivity::Intramolecular)
+ ?
+ /* Get the global index using the offset in the molecule */
+ (globalAtomIndex + iatoms[k] - atomIndexInMolecule)
+ : iatoms[k];
+ const auto* entry = ga2la.find(k_gl);
if (entry == nullptr || entry->cell >= zones->n)
{
/* We do not have this atom of this interaction
}
else
{
- int d;
-
tiatoms[k] = entry->la;
- for (d = 0; d < DIM; d++)
+ for (int d = 0; d < DIM; d++)
{
if (zones->shift[entry->cell][d] == 0)
{
}
}
bUse = (bUse && (k_zero[XX] != 0) && (k_zero[YY] != 0) && (k_zero[ZZ] != 0));
- if (bRCheckMB)
+ if (checkDistanceMultiBody)
{
- int d;
-
- for (d = 0; (d < DIM && bUse); d++)
+ for (int d = 0; (d < DIM && bUse); d++)
{
- /* Check if the cg_cm distance falls within
+ /* Check if the distance falls within
* the cut-off to avoid possible multiple
* assignments of bonded interactions.
*/
if (rcheck[d] && k_plus[d]
- && dd_dist2(pbc_null, cg_cm, tiatoms[k_zero[d]], tiatoms[k_plus[d]]) >= rc2)
+ && dd_dist2(pbc_null, coordinates, tiatoms[k_zero[d]], tiatoms[k_plus[d]])
+ >= cutoffSquared)
{
bUse = FALSE;
}
/* Sum so we can check in global_stat
* if we have everything.
*/
- if (bBCheck || !(interaction_function[ftype].flags & IF_LIMZERO))
+ if (ddBondedChecking == DDBondedChecking::All
+ || !(interaction_function[ftype].flags & IF_LIMZERO))
{
- (*nbonded_local)++;
+ numBondedInteractions++;
}
}
}
j += 1 + nral_rt(ftype);
}
+
+ return numBondedInteractions;
+}
+
+/*! \brief Determine whether the local domain has responsibility for
+ * any of the position restraints for local atom \p atomIndex
+ * and assign those to the local domain.
+ *
+ * \returns The total number of bonded interactions for this atom for
+ * which this domain is responsible.
+ */
+static inline int assignPositionRestraintsForAtom(const int atomIndex,
+ const int mol,
+ const int atomIndexInMolecule,
+ const int numAtomsInMolecule,
+ gmx::ArrayRef<const int> rtil,
+ const int ind_start,
+ const int ind_end,
+ const gmx_molblock_t& molb,
+ const t_iparams* ip_in,
+ InteractionDefinitions* idef)
+{
+ constexpr int nral = 1;
+
+ int numBondedInteractions = 0;
+
+ int j = ind_start;
+ while (j < ind_end)
+ {
+ const int ftype = rtil[j++];
+ auto iatoms = gmx::constArrayRefFromArray(rtil.data() + j, rtil.size() - j);
+
+ if (ftype == F_POSRES || ftype == F_FBPOSRES)
+ {
+ std::array<int, 1 + nral> tiatoms = { iatoms[0], atomIndex };
+ if (ftype == F_POSRES)
+ {
+ add_posres(mol, atomIndexInMolecule, numAtomsInMolecule, molb, tiatoms, ip_in, idef);
+ }
+ else
+ {
+ add_fbposres(mol, atomIndexInMolecule, numAtomsInMolecule, molb, tiatoms, ip_in, idef);
+ }
+ idef->il[ftype].push_back(tiatoms[0], nral, tiatoms.data() + 1);
+ numBondedInteractions++;
+ }
+ j += 1 + nral_rt(ftype);
+ }
+
+ return numBondedInteractions;
}
/*! \brief This function looks up and assigns bonded interactions for zone iz.
* With thread parallelizing each thread acts on a different atom range:
* at_start to at_end.
*/
-static int make_bondeds_zone(gmx_domdec_t* dd,
+static int make_bondeds_zone(gmx_reverse_top_t* rt,
+ ArrayRef<const int> globalAtomIndices,
+ const gmx_ga2la_t& ga2la,
const gmx_domdec_zones_t* zones,
const std::vector<gmx_molblock_t>& molb,
- gmx_bool bRCheckMB,
- ivec rcheck,
- gmx_bool bRCheck2B,
- real rc2,
- t_pbc* pbc_null,
- rvec* cg_cm,
+ const bool checkDistanceMultiBody,
+ const ivec rcheck,
+ const bool checkDistanceTwoBody,
+ const real cutoffSquared,
+ const t_pbc* pbc_null,
+ ArrayRef<const RVec> coordinates,
const t_iparams* ip_in,
InteractionDefinitions* idef,
int izone,
const gmx::Range<int>& atomRange)
{
- int mb, mt, mol, i_mol;
- gmx_bool bBCheck;
- gmx_reverse_top_t* rt;
- int nbonded_local;
-
- rt = dd->reverse_top;
+ int mb = 0;
+ int mt = 0;
+ int mol = 0;
+ int atomIndexInMolecule = 0;
- bBCheck = rt->bBCheck;
+ const auto ddBondedChecking = rt->impl_->options.ddBondedChecking;
- nbonded_local = 0;
+ int numBondedInteractions = 0;
for (int i : atomRange)
{
/* Get the global atom number */
- const int i_gl = dd->globalAtomIndices[i];
- global_atomnr_to_moltype_ind(rt, i_gl, &mb, &mt, &mol, &i_mol);
+ const int globalAtomIndex = globalAtomIndices[i];
+ global_atomnr_to_moltype_ind(rt->impl_->mbi, globalAtomIndex, &mb, &mt, &mol, &atomIndexInMolecule);
/* Check all intramolecular interactions assigned to this atom */
- gmx::ArrayRef<const int> index = rt->ril_mt[mt].index;
- gmx::ArrayRef<const t_iatom> rtil = rt->ril_mt[mt].il;
-
- check_assign_interactions_atom(i, i_gl, mol, i_mol, rt->ril_mt[mt].numAtomsInMolecule,
- index, rtil, FALSE, index[i_mol], index[i_mol + 1], dd,
- zones, &molb[mb], bRCheckMB, rcheck, bRCheck2B, rc2,
- pbc_null, cg_cm, ip_in, idef, izone, bBCheck, &nbonded_local);
-
+ gmx::ArrayRef<const int> index = rt->impl_->ril_mt[mt].index;
+ gmx::ArrayRef<const t_iatom> rtil = rt->impl_->ril_mt[mt].il;
+
+ numBondedInteractions += assignInteractionsForAtom<InteractionConnectivity::Intramolecular>(
+ i,
+ globalAtomIndex,
+ atomIndexInMolecule,
+ index,
+ rtil,
+ index[atomIndexInMolecule],
+ index[atomIndexInMolecule + 1],
+ ga2la,
+ zones,
+ checkDistanceMultiBody,
+ rcheck,
+ checkDistanceTwoBody,
+ cutoffSquared,
+ pbc_null,
+ coordinates,
+ idef,
+ izone,
+ ddBondedChecking);
+
+ // Assign position restraints, when present, for the home zone
+ if (izone == 0 && rt->impl_->havePositionRestraints)
+ {
+ numBondedInteractions +=
+ assignPositionRestraintsForAtom(i,
+ mol,
+ atomIndexInMolecule,
+ rt->impl_->ril_mt[mt].numAtomsInMolecule,
+ rtil,
+ index[atomIndexInMolecule],
+ index[atomIndexInMolecule + 1],
+ molb[mb],
+ ip_in,
+ idef);
+ }
- if (rt->bIntermolecularInteractions)
+ if (rt->impl_->bIntermolecularInteractions)
{
/* Check all intermolecular interactions assigned to this atom */
- index = rt->ril_intermol.index;
- rtil = rt->ril_intermol.il;
-
- check_assign_interactions_atom(i, i_gl, mol, i_mol, rt->ril_mt[mt].numAtomsInMolecule,
- index, rtil, TRUE, index[i_gl], index[i_gl + 1], dd, zones,
- &molb[mb], bRCheckMB, rcheck, bRCheck2B, rc2, pbc_null,
- cg_cm, ip_in, idef, izone, bBCheck, &nbonded_local);
+ index = rt->impl_->ril_intermol.index;
+ rtil = rt->impl_->ril_intermol.il;
+
+ numBondedInteractions += assignInteractionsForAtom<InteractionConnectivity::Intermolecular>(
+ i,
+ -1, // not used
+ -1, // not used
+ index,
+ rtil,
+ index[globalAtomIndex],
+ index[globalAtomIndex + 1],
+ ga2la,
+ zones,
+ checkDistanceMultiBody,
+ rcheck,
+ checkDistanceTwoBody,
+ cutoffSquared,
+ pbc_null,
+ coordinates,
+ idef,
+ izone,
+ ddBondedChecking);
}
}
- return nbonded_local;
+ return numBondedInteractions;
}
/*! \brief Set the exclusion data for i-zone \p iz */
-static void make_exclusions_zone(gmx_domdec_t* dd,
+static void make_exclusions_zone(ArrayRef<const int> globalAtomIndices,
+ const gmx_ga2la_t& ga2la,
gmx_domdec_zones_t* zones,
+ ArrayRef<const MolblockIndices> molblockIndices,
const std::vector<gmx_moltype_t>& moltype,
const int* cginfo,
ListOfLists<int>* lexcls,
int at_end,
const gmx::ArrayRef<const int> intermolecularExclusionGroup)
{
- const gmx_ga2la_t& ga2la = *dd->ga2la;
-
const auto& jAtomRange = zones->iZones[iz].jAtomRange;
const gmx::index oldNumLists = lexcls->ssize();
if (GET_CGINFO_EXCL_INTER(cginfo[at]))
{
- int a_gl, mb, mt, mol, a_mol;
+ int mb = 0;
+ int mt = 0;
+ int mol = 0;
+ int a_mol = 0;
/* Copy the exclusions from the global top */
- a_gl = dd->globalAtomIndices[at];
- global_atomnr_to_moltype_ind(dd->reverse_top, a_gl, &mb, &mt, &mol, &a_mol);
+ int a_gl = globalAtomIndices[at];
+ global_atomnr_to_moltype_ind(molblockIndices, a_gl, &mb, &mt, &mol, &a_mol);
const auto excls = moltype[mt].excls[a_mol];
for (const int aj_mol : excls)
{
bool isExcludedAtom = !intermolecularExclusionGroup.empty()
&& std::find(intermolecularExclusionGroup.begin(),
- intermolecularExclusionGroup.end(), dd->globalAtomIndices[at])
+ intermolecularExclusionGroup.end(),
+ globalAtomIndices[at])
!= intermolecularExclusionGroup.end();
if (isExcludedAtom)
{
for (int qmAtomGlobalIndex : intermolecularExclusionGroup)
{
- if (const auto* entry = dd->ga2la->find(qmAtomGlobalIndex))
+ if (const auto* entry = ga2la.find(qmAtomGlobalIndex))
{
exclusionsForAtom.push_back(entry->la);
}
}
/*! \brief Generate and store all required local bonded interactions in \p idef and local exclusions in \p lexcls */
-static int make_local_bondeds_excls(gmx_domdec_t* dd,
- gmx_domdec_zones_t* zones,
- const gmx_mtop_t* mtop,
- const int* cginfo,
- gmx_bool bRCheckMB,
- ivec rcheck,
- gmx_bool bRCheck2B,
- real rc,
- t_pbc* pbc_null,
- rvec* cg_cm,
- InteractionDefinitions* idef,
- ListOfLists<int>* lexcls,
- int* excl_count)
+static void make_local_bondeds_excls(gmx_domdec_t* dd,
+ gmx_domdec_zones_t* zones,
+ const gmx_mtop_t& mtop,
+ const int* cginfo,
+ const bool checkDistanceMultiBody,
+ const ivec rcheck,
+ const gmx_bool checkDistanceTwoBody,
+ const real cutoff,
+ const t_pbc* pbc_null,
+ ArrayRef<const RVec> coordinates,
+ InteractionDefinitions* idef,
+ ListOfLists<int>* lexcls)
{
- int nzone_bondeds;
- int cg0, cg1;
- real rc2;
- int nbonded_local;
- gmx_reverse_top_t* rt;
+ int nzone_bondeds = 0;
- if (dd->reverse_top->bInterAtomicInteractions)
+ if (dd->reverse_top->impl_->bInterAtomicInteractions)
{
nzone_bondeds = zones->n;
}
/* We only use exclusions from i-zones to i- and j-zones */
const int numIZonesForExclusions = (dd->haveExclusions ? zones->iZones.size() : 0);
- rt = dd->reverse_top;
+ gmx_reverse_top_t* rt = dd->reverse_top.get();
- rc2 = rc * rc;
+ const real cutoffSquared = gmx::square(cutoff);
/* Clear the counts */
idef->clear();
- nbonded_local = 0;
+ dd->reverse_top->impl_->numBondedInteractions = 0;
lexcls->clear();
- *excl_count = 0;
for (int izone = 0; izone < nzone_bondeds; izone++)
{
- cg0 = zones->cg_range[izone];
- cg1 = zones->cg_range[izone + 1];
+ const int cg0 = zones->cg_range[izone];
+ const int cg1 = zones->cg_range[izone + 1];
- const int numThreads = rt->th_work.size();
+ const int numThreads = rt->impl_->th_work.size();
#pragma omp parallel for num_threads(numThreads) schedule(static)
for (int thread = 0; thread < numThreads; thread++)
{
try
{
- int cg0t, cg1t;
- InteractionDefinitions* idef_t;
+ InteractionDefinitions* idef_t = nullptr;
- cg0t = cg0 + ((cg1 - cg0) * thread) / numThreads;
- cg1t = cg0 + ((cg1 - cg0) * (thread + 1)) / numThreads;
+ int cg0t = cg0 + ((cg1 - cg0) * thread) / numThreads;
+ int cg1t = cg0 + ((cg1 - cg0) * (thread + 1)) / numThreads;
if (thread == 0)
{
}
else
{
- idef_t = &rt->th_work[thread].idef;
+ idef_t = &rt->impl_->th_work[thread].idef;
idef_t->clear();
}
- rt->th_work[thread].nbonded = make_bondeds_zone(
- dd, zones, mtop->molblock, bRCheckMB, rcheck, bRCheck2B, rc2, pbc_null,
- cg_cm, idef->iparams.data(), idef_t, izone, gmx::Range<int>(cg0t, cg1t));
+ rt->impl_->th_work[thread].numBondedInteractions =
+ make_bondeds_zone(rt,
+ dd->globalAtomIndices,
+ *dd->ga2la,
+ zones,
+ mtop.molblock,
+ checkDistanceMultiBody,
+ rcheck,
+ checkDistanceTwoBody,
+ cutoffSquared,
+ pbc_null,
+ coordinates,
+ idef->iparams.data(),
+ idef_t,
+ izone,
+ gmx::Range<int>(cg0t, cg1t));
if (izone < numIZonesForExclusions)
{
- ListOfLists<int>* excl_t;
+ ListOfLists<int>* excl_t = nullptr;
if (thread == 0)
{
// Thread 0 stores exclusions directly in the final storage
else
{
// Threads > 0 store in temporary storage, starting at list index 0
- excl_t = &rt->th_work[thread].excl;
+ excl_t = &rt->impl_->th_work[thread].excl;
excl_t->clear();
}
/* No charge groups and no distance check required */
- make_exclusions_zone(dd, zones, mtop->moltype, cginfo, excl_t, izone, cg0t,
- cg1t, mtop->intermolecularExclusionGroup);
+ make_exclusions_zone(dd->globalAtomIndices,
+ *dd->ga2la,
+ zones,
+ rt->impl_->mbi,
+ mtop.moltype,
+ cginfo,
+ excl_t,
+ izone,
+ cg0t,
+ cg1t,
+ mtop.intermolecularExclusionGroup);
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- if (rt->th_work.size() > 1)
+ if (rt->impl_->th_work.size() > 1)
{
- combine_idef(idef, rt->th_work);
+ combine_idef(idef, rt->impl_->th_work);
}
- for (const thread_work_t& th_work : rt->th_work)
+ for (const thread_work_t& th_work : rt->impl_->th_work)
{
- nbonded_local += th_work.nbonded;
+ dd->reverse_top->impl_->numBondedInteractions += th_work.numBondedInteractions;
}
if (izone < numIZonesForExclusions)
{
- for (std::size_t th = 1; th < rt->th_work.size(); th++)
+ for (std::size_t th = 1; th < rt->impl_->th_work.size(); th++)
{
- lexcls->appendListOfLists(rt->th_work[th].excl);
- }
- for (const thread_work_t& th_work : rt->th_work)
- {
- *excl_count += th_work.excl_count;
+ lexcls->appendListOfLists(rt->impl_->th_work[th].excl);
}
}
}
+ // Note that it's possible for this to still be true from the last
+ // time it was set, e.g. if repartitioning was triggered before
+ // global communication that would have acted on the true
+ // value. This could happen for example when replica exchange took
+ // place soon after a partition.
+ dd->reverse_top->impl_->shouldCheckNumberOfBondedInteractions = true;
+ // Clear the old global value, which is now invalid
+ dd->reverse_top->impl_->numBondedInteractionsOverAllDomains.reset();
+
if (debug)
{
- fprintf(debug, "We have %d exclusions, check count %d\n", lexcls->numElements(), *excl_count);
+ fprintf(debug, "We have %d exclusions\n", lexcls->numElements());
}
+}
- return nbonded_local;
+bool shouldCheckNumberOfBondedInteractions(const gmx_domdec_t& dd)
+{
+ return dd.reverse_top->impl_->shouldCheckNumberOfBondedInteractions;
}
-void dd_make_local_top(gmx_domdec_t* dd,
- gmx_domdec_zones_t* zones,
- int npbcdim,
- matrix box,
- rvec cellsize_min,
- const ivec npulse,
- t_forcerec* fr,
- rvec* cgcm_or_x,
- const gmx_mtop_t& mtop,
- gmx_localtop_t* ltop)
+int numBondedInteractions(const gmx_domdec_t& dd)
{
- gmx_bool bRCheckMB, bRCheck2B;
- real rc = -1;
- ivec rcheck;
- int d, nexcl;
- t_pbc pbc, *pbc_null = nullptr;
+ return dd.reverse_top->impl_->numBondedInteractions;
+}
+
+void setNumberOfBondedInteractionsOverAllDomains(const gmx_domdec_t& dd, int newValue)
+{
+ GMX_RELEASE_ASSERT(!dd.reverse_top->impl_->numBondedInteractionsOverAllDomains.has_value(),
+ "Cannot set number of bonded interactions because it is already set");
+ dd.reverse_top->impl_->numBondedInteractionsOverAllDomains.emplace(newValue);
+}
+
+void checkNumberOfBondedInteractions(const gmx::MDLogger& mdlog,
+ t_commrec* cr,
+ const gmx_mtop_t& top_global,
+ const gmx_localtop_t* top_local,
+ gmx::ArrayRef<const gmx::RVec> x,
+ const matrix box)
+{
+ GMX_RELEASE_ASSERT(
+ DOMAINDECOMP(cr),
+ "No need to check number of bonded interactions when not using domain decomposition");
+ if (cr->dd->reverse_top->impl_->shouldCheckNumberOfBondedInteractions)
+ {
+ GMX_RELEASE_ASSERT(cr->dd->reverse_top->impl_->numBondedInteractionsOverAllDomains.has_value(),
+ "The check for the total number of bonded interactions requires the "
+ "value to have been reduced across all domains");
+ if (cr->dd->reverse_top->impl_->numBondedInteractionsOverAllDomains.value()
+ != cr->dd->reverse_top->impl_->expectedNumGlobalBondedInteractions)
+ {
+ dd_print_missing_interactions(
+ mdlog,
+ cr,
+ cr->dd->reverse_top->impl_->numBondedInteractionsOverAllDomains.value(),
+ top_global,
+ top_local,
+ x,
+ box); // Does not return
+ }
+ // Now that the value is set and the check complete, future
+ // global communication should not compute the value until
+ // after the next partitioning.
+ cr->dd->reverse_top->impl_->shouldCheckNumberOfBondedInteractions = false;
+ }
+}
+
+void dd_make_local_top(gmx_domdec_t* dd,
+ gmx_domdec_zones_t* zones,
+ int npbcdim,
+ matrix box,
+ rvec cellsize_min,
+ const ivec npulse,
+ t_forcerec* fr,
+ ArrayRef<const RVec> coordinates,
+ const gmx_mtop_t& mtop,
+ gmx_localtop_t* ltop)
+{
+ real rc = -1;
+ ivec rcheck;
+ t_pbc pbc, *pbc_null = nullptr;
if (debug)
{
fprintf(debug, "Making local topology\n");
}
- bRCheckMB = FALSE;
- bRCheck2B = FALSE;
+ bool checkDistanceMultiBody = false;
+ bool checkDistanceTwoBody = false;
- if (dd->reverse_top->bInterAtomicInteractions)
+ if (dd->reverse_top->impl_->bInterAtomicInteractions)
{
/* We need to check to which cell bondeds should be assigned */
rc = dd_cutoff_twobody(dd);
fprintf(debug, "Two-body bonded cut-off distance is %g\n", rc);
}
- /* Should we check cg_cm distances when assigning bonded interactions? */
- for (d = 0; d < DIM; d++)
+ /* Should we check distances when assigning bonded interactions? */
+ for (int d = 0; d < DIM; d++)
{
rcheck[d] = FALSE;
/* Only need to check for dimensions where the part of the box
{
if (dd->numCells[d] == 2)
{
- rcheck[d] = TRUE;
- bRCheckMB = TRUE;
+ rcheck[d] = TRUE;
+ checkDistanceMultiBody = TRUE;
}
/* Check for interactions between two atoms,
* where we can allow interactions up to the cut-off,
* instead of up to the smallest cell dimension.
*/
- bRCheck2B = TRUE;
+ checkDistanceTwoBody = TRUE;
}
if (debug)
{
- fprintf(debug, "dim %d cellmin %f bonded rcheck[%d] = %d, bRCheck2B = %s\n", d,
- cellsize_min[d], d, rcheck[d], gmx::boolToString(bRCheck2B));
+ fprintf(debug,
+ "dim %d cellmin %f bonded rcheck[%d] = %d, checkDistanceTwoBody = %s\n",
+ d,
+ cellsize_min[d],
+ d,
+ rcheck[d],
+ gmx::boolToString(checkDistanceTwoBody));
}
}
- if (bRCheckMB || bRCheck2B)
+ if (checkDistanceMultiBody || checkDistanceTwoBody)
{
if (fr->bMolPBC)
{
}
}
- dd->nbonded_local = make_local_bondeds_excls(dd, zones, &mtop, fr->cginfo.data(), bRCheckMB,
- rcheck, bRCheck2B, rc, pbc_null, cgcm_or_x,
- <op->idef, <op->excls, &nexcl);
+ make_local_bondeds_excls(dd,
+ zones,
+ mtop,
+ fr->cginfo.data(),
+ checkDistanceMultiBody,
+ rcheck,
+ checkDistanceTwoBody,
+ rc,
+ pbc_null,
+ coordinates,
+ <op->idef,
+ <op->excls);
/* The ilist is not sorted yet,
* we can only do this when we have the charge arrays.
ltop->idef.ilsort = ilsortUNKNOWN;
}
-void dd_sort_local_top(gmx_domdec_t* dd, const t_mdatoms* mdatoms, gmx_localtop_t* ltop)
+void dd_sort_local_top(const gmx_domdec_t& dd, const t_mdatoms* mdatoms, gmx_localtop_t* ltop)
{
- if (dd->reverse_top->ilsort == ilsortNO_FE)
+ if (dd.reverse_top->impl_->ilsort == ilsortNO_FE)
{
ltop->idef.ilsort = ilsortNO_FE;
}
}
}
-void dd_init_local_state(gmx_domdec_t* dd, const t_state* state_global, t_state* state_local)
+void dd_init_local_state(const gmx_domdec_t& dd, const t_state* state_global, t_state* state_local)
{
int buf[NITEM_DD_INIT_LOCAL_STATE];
buf[3] = state_global->nhchainlength;
buf[4] = state_global->dfhist ? state_global->dfhist->nlambda : 0;
}
- dd_bcast(dd, NITEM_DD_INIT_LOCAL_STATE * sizeof(int), buf);
+ dd_bcast(&dd, NITEM_DD_INIT_LOCAL_STATE * sizeof(int), buf);
init_gtc_state(state_local, buf[1], buf[2], buf[3]);
init_dfhist_state(state_local, buf[4]);
/*! \brief Check if a link is stored in \p link between charge groups \p cg_gl and \p cg_gl_j and if not so, store a link */
static void check_link(t_blocka* link, int cg_gl, int cg_gl_j)
{
- int k;
- gmx_bool bFound;
-
- bFound = FALSE;
- for (k = link->index[cg_gl]; k < link->index[cg_gl + 1]; k++)
+ bool bFound = false;
+ for (int k = link->index[cg_gl]; k < link->index[cg_gl + 1]; k++)
{
GMX_RELEASE_ASSERT(link->a, "Inconsistent NULL pointer while making charge-group links");
if (link->a[k] == cg_gl_j)
}
}
-t_blocka* makeBondedLinks(const gmx_mtop_t& mtop, gmx::ArrayRef<cginfo_mb_t> cginfo_mb)
+void makeBondedLinks(gmx_domdec_t* dd, const gmx_mtop_t& mtop, gmx::ArrayRef<cginfo_mb_t> cginfo_mb)
{
- t_blocka* link;
- cginfo_mb_t* cgi_mb;
+
+ if (!dd->comm->systemInfo.filterBondedCommunication)
+ {
+ /* Only communicate atoms based on cut-off */
+ dd->comm->bondedLinks = nullptr;
+ return;
+ }
+
+ t_blocka* link = nullptr;
/* For each atom make a list of other atoms in the system
* that a linked to it via bonded interactions
GMX_RELEASE_ASSERT(mtop.intermolecular_ilist,
"We should have an ilist when intermolecular interactions are on");
- make_reverse_ilist(*mtop.intermolecular_ilist, &atoms, FALSE, FALSE, FALSE, TRUE, &ril_intermol);
+ ReverseTopOptions rtOptions(DDBondedChecking::ExcludeZeroLimit);
+ make_reverse_ilist(
+ *mtop.intermolecular_ilist, &atoms, rtOptions, AtomLinkRule::AllAtomsInBondeds, &ril_intermol);
}
snew(link, 1);
* to all atoms, not only the first atom as in gmx_reverse_top.
* The constraints are discarded here.
*/
- reverse_ilist_t ril;
- make_reverse_ilist(molt.ilist, &molt.atoms, FALSE, FALSE, FALSE, TRUE, &ril);
+ ReverseTopOptions rtOptions(DDBondedChecking::ExcludeZeroLimit);
+ reverse_ilist_t ril;
+ make_reverse_ilist(molt.ilist, &molt.atoms, rtOptions, AtomLinkRule::AllAtomsInBondeds, &ril);
- cgi_mb = &cginfo_mb[mb];
+ cginfo_mb_t* cgi_mb = &cginfo_mb[mb];
- int mol;
+ int mol = 0;
for (mol = 0; mol < (mtop.bIntermolecularInteractions ? molb.nmol : 1); mol++)
{
for (int a = 0; a < molt.atoms.nr; a++)
if (debug)
{
- fprintf(debug, "molecule type '%s' %d atoms has %d atom links through bonded interac.\n",
- *molt.name, molt.atoms.nr, nlink_mol);
+ fprintf(debug,
+ "molecule type '%s' %d atoms has %d atom links through bonded interac.\n",
+ *molt.name,
+ molt.atoms.nr,
+ nlink_mol);
}
if (molb.nmol > mol)
fprintf(debug, "Of the %d atoms %d are linked via bonded interactions\n", mtop.natoms, ncgi);
}
- return link;
+ dd->comm->bondedLinks = link;
}
typedef struct
}
/*! \brief Set the distance, function type and atom indices for the longest distance between atoms of molecule type \p molt for two-body and multi-body bonded interactions */
-static void bonded_cg_distance_mol(const gmx_moltype_t* molt,
- gmx_bool bBCheck,
- gmx_bool bExcl,
- ArrayRef<const RVec> x,
- bonded_distance_t* bd_2b,
- bonded_distance_t* bd_mb)
+static void bonded_cg_distance_mol(const gmx_moltype_t* molt,
+ const DDBondedChecking ddBondedChecking,
+ gmx_bool bExcl,
+ ArrayRef<const RVec> x,
+ bonded_distance_t* bd_2b,
+ bonded_distance_t* bd_mb)
{
+ const ReverseTopOptions rtOptions(ddBondedChecking);
+
for (int ftype = 0; ftype < F_NRE; ftype++)
{
- if (dd_check_ftype(ftype, bBCheck, FALSE, FALSE))
+ if (dd_check_ftype(ftype, rtOptions))
{
const auto& il = molt->ilist[ftype];
int nral = NRAL(ftype);
{
real rij2 = distance2(x[atomI], x[atomJ]);
- update_max_bonded_distance(rij2, ftype, atomI, atomJ,
- (nral == 2) ? bd_2b : bd_mb);
+ update_max_bonded_distance(
+ rij2, ftype, atomI, atomJ, (nral == 2) ? bd_2b : bd_mb);
}
}
}
/*! \brief Set the distance, function type and atom indices for the longest atom distance involved in intermolecular interactions for two-body and multi-body bonded interactions */
static void bonded_distance_intermol(const InteractionLists& ilists_intermol,
- gmx_bool bBCheck,
+ const DDBondedChecking ddBondedChecking,
ArrayRef<const RVec> x,
PbcType pbcType,
const matrix box,
set_pbc(&pbc, pbcType, box);
+ const ReverseTopOptions rtOptions(ddBondedChecking);
+
for (int ftype = 0; ftype < F_NRE; ftype++)
{
- if (dd_check_ftype(ftype, bBCheck, FALSE, FALSE))
+ if (dd_check_ftype(ftype, rtOptions))
{
const auto& il = ilists_intermol[ftype];
int nral = NRAL(ftype);
for (int aj = ai + 1; aj < nral; aj++)
{
rvec dx;
- real rij2;
int atom_j = il.iatoms[i + 1 + aj];
pbc_dx(&pbc, x[atom_i], x[atom_j], dx);
- rij2 = norm2(dx);
+ const real rij2 = norm2(dx);
update_max_bonded_distance(rij2, ftype, atom_i, atom_j, (nral == 2) ? bd_2b : bd_mb);
}
ArrayRef<const RVec> x,
ArrayRef<RVec> xs)
{
- int n, i;
-
if (pbcType != PbcType::No)
{
mk_mshift(nullptr, graph, pbcType, box, as_rvec_array(x.data()));
* unchanged, just to be 100% sure that we do not affect
* binary reproducibility of simulations.
*/
- n = molt->atoms.nr;
- for (i = 0; i < n; i++)
+ for (int i = 0; i < molt->atoms.nr; i++)
{
copy_rvec(x[i], xs[i]);
}
}
}
-void dd_bonded_cg_distance(const gmx::MDLogger& mdlog,
- const gmx_mtop_t* mtop,
- const t_inputrec* ir,
- ArrayRef<const RVec> x,
- const matrix box,
- gmx_bool bBCheck,
- real* r_2b,
- real* r_mb)
+void dd_bonded_cg_distance(const gmx::MDLogger& mdlog,
+ const gmx_mtop_t& mtop,
+ const t_inputrec& inputrec,
+ ArrayRef<const RVec> x,
+ const matrix box,
+ const DDBondedChecking ddBondedChecking,
+ real* r_2b,
+ real* r_mb)
{
- gmx_bool bExclRequired;
- int at_offset;
bonded_distance_t bd_2b = { 0, -1, -1, -1 };
bonded_distance_t bd_mb = { 0, -1, -1, -1 };
- bExclRequired = inputrecExclForces(ir);
+ bool bExclRequired = inputrecExclForces(&inputrec);
- *r_2b = 0;
- *r_mb = 0;
- at_offset = 0;
- for (const gmx_molblock_t& molb : mtop->molblock)
+ *r_2b = 0;
+ *r_mb = 0;
+ int at_offset = 0;
+ for (const gmx_molblock_t& molb : mtop.molblock)
{
- const gmx_moltype_t& molt = mtop->moltype[molb.type];
+ const gmx_moltype_t& molt = mtop.moltype[molb.type];
if (molt.atoms.nr == 1 || molb.nmol == 0)
{
at_offset += molb.nmol * molt.atoms.nr;
else
{
t_graph graph;
- if (ir->pbcType != PbcType::No)
+ if (inputrec.pbcType != PbcType::No)
{
graph = mk_graph_moltype(molt);
}
std::vector<RVec> xs(molt.atoms.nr);
for (int mol = 0; mol < molb.nmol; mol++)
{
- getWholeMoleculeCoordinates(&molt, &mtop->ffparams, ir->pbcType, &graph, box,
- x.subArray(at_offset, molt.atoms.nr), xs);
+ getWholeMoleculeCoordinates(&molt,
+ &mtop.ffparams,
+ inputrec.pbcType,
+ &graph,
+ box,
+ x.subArray(at_offset, molt.atoms.nr),
+ xs);
bonded_distance_t bd_mol_2b = { 0, -1, -1, -1 };
bonded_distance_t bd_mol_mb = { 0, -1, -1, -1 };
- bonded_cg_distance_mol(&molt, bBCheck, bExclRequired, xs, &bd_mol_2b, &bd_mol_mb);
+ bonded_cg_distance_mol(&molt, ddBondedChecking, bExclRequired, xs, &bd_mol_2b, &bd_mol_mb);
/* Process the mol data adding the atom index offset */
- update_max_bonded_distance(bd_mol_2b.r2, bd_mol_2b.ftype, at_offset + bd_mol_2b.a1,
- at_offset + bd_mol_2b.a2, &bd_2b);
- update_max_bonded_distance(bd_mol_mb.r2, bd_mol_mb.ftype, at_offset + bd_mol_mb.a1,
- at_offset + bd_mol_mb.a2, &bd_mb);
+ update_max_bonded_distance(bd_mol_2b.r2,
+ bd_mol_2b.ftype,
+ at_offset + bd_mol_2b.a1,
+ at_offset + bd_mol_2b.a2,
+ &bd_2b);
+ update_max_bonded_distance(bd_mol_mb.r2,
+ bd_mol_mb.ftype,
+ at_offset + bd_mol_mb.a1,
+ at_offset + bd_mol_mb.a2,
+ &bd_mb);
at_offset += molt.atoms.nr;
}
}
}
- if (mtop->bIntermolecularInteractions)
+ if (mtop.bIntermolecularInteractions)
{
- GMX_RELEASE_ASSERT(mtop->intermolecular_ilist,
+ GMX_RELEASE_ASSERT(mtop.intermolecular_ilist,
"We should have an ilist when intermolecular interactions are on");
- bonded_distance_intermol(*mtop->intermolecular_ilist, bBCheck, x, ir->pbcType, box, &bd_2b, &bd_mb);
+ bonded_distance_intermol(
+ *mtop.intermolecular_ilist, ddBondedChecking, x, inputrec.pbcType, box, &bd_2b, &bd_mb);
}
*r_2b = sqrt(bd_2b.r2);
{
GMX_LOG(mdlog.info)
.appendTextFormatted(
- " two-body bonded interactions: %5.3f nm, %s, atoms %d %d", *r_2b,
+ " two-body bonded interactions: %5.3f nm, %s, atoms %d %d",
+ *r_2b,
(bd_2b.ftype >= 0) ? interaction_function[bd_2b.ftype].longname : "Exclusion",
- bd_2b.a1 + 1, bd_2b.a2 + 1);
+ bd_2b.a1 + 1,
+ bd_2b.a2 + 1);
}
if (*r_mb > 0)
{
GMX_LOG(mdlog.info)
.appendTextFormatted(
- " multi-body bonded interactions: %5.3f nm, %s, atoms %d %d", *r_mb,
- interaction_function[bd_mb.ftype].longname, bd_mb.a1 + 1, bd_mb.a2 + 1);
+ " multi-body bonded interactions: %5.3f nm, %s, atoms %d %d",
+ *r_mb,
+ interaction_function[bd_mb.ftype].longname,
+ bd_mb.a1 + 1,
+ bd_mb.a2 + 1);
}
}
}
*
* Copyright (c) 2006,2007,2008,2009,2010 by the GROMACS development team.
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
}
+void dd_move_x_and_v_vsites(const gmx_domdec_t& dd, const matrix box, rvec* x, rvec* v)
+{
+ if (dd.vsite_comm)
+ {
+ dd_move_x_specat(&dd, dd.vsite_comm, box, x, v, FALSE);
+ }
+}
+
void dd_clear_local_vsite_indices(gmx_domdec_t* dd)
{
if (dd->vsite_comm)
}
}
- int at_end = setup_specat_communication(dd, &ireq, dd->vsite_comm, ga2la_specat, at_start, 1,
- "vsite", "");
+ int at_end = setup_specat_communication(
+ dd, &ireq, dd->vsite_comm, ga2la_specat, at_start, 2, "vsite", "");
/* Fill in the missing indices */
for (int ftype = 0; ftype < F_NRE; ftype++)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
cx[YY] = grid_r[i * 2 + y][YY];
cx[ZZ] = grid_r[i * 2 + z][ZZ];
mvmul(tric, cx, r);
- gmx_fprintf_pdb_atomline(out, epdbATOM, a++, "CA", ' ', "GLY", ' ', i + 1, ' ',
- 10 * r[XX], 10 * r[YY], 10 * r[ZZ], 1.0, vol, "");
+ gmx_fprintf_pdb_atomline(out,
+ PdbRecordType::Atom,
+ a++,
+ "CA",
+ ' ',
+ "GLY",
+ ' ',
+ i + 1,
+ ' ',
+ 10 * r[XX],
+ 10 * r[YY],
+ 10 * r[ZZ],
+ 1.0,
+ vol,
+ "");
}
}
}
void write_dd_pdb(const char* fn,
int64_t step,
const char* title,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const t_commrec* cr,
int natoms,
const rvec x[],
{
b = dd->comm->zones.n + 1;
}
- gmx_fprintf_pdb_atomline(out, epdbATOM, ii + 1, atomname, ' ', resname, ' ', resnr, ' ',
- 10 * x[i][XX], 10 * x[i][YY], 10 * x[i][ZZ], 1.0, b, "");
+ gmx_fprintf_pdb_atomline(out,
+ PdbRecordType::Atom,
+ ii + 1,
+ atomname,
+ ' ',
+ resname,
+ ' ',
+ resnr,
+ ' ',
+ 10 * x[i][XX],
+ 10 * x[i][YY],
+ 10 * x[i][ZZ],
+ 1.0,
+ b,
+ "");
}
fprintf(out, "TER\n");
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void write_dd_pdb(const char* fn,
int64_t step,
const char* title,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const t_commrec* cr,
int natoms,
const rvec x[],
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_DOMDEC_GPUHALOEXCHANGE_H
#define GMX_DOMDEC_GPUHALOEXCHANGE_H
+#include <memory>
+
#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/gmxmpi.h"
struct gmx_domdec_t;
* after the local coordinates buffer operations (where the
* coordinates are copied to the device and hence the \c
* coordinatesReadyOnDeviceEvent is recorded). Force Halo exchange
- * will be performed in \c streamNonLocal (also potentally
- * with buffer clearing in \c streamLocal)and the \c
+ * will be performed in \c streamNonLocal and the \c
* communicateHaloForces method must be called after the
* non-local buffer operations, after the local force buffer
* has been copied to the GPU (if CPU forces are present), and
private:
class Impl;
- gmx::PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void GpuHaloExchange::Impl::reinitHalo(float3* d_coordinatesBuffer, float3* d_forcesBuffer)
{
- wallcycle_start(wcycle_, ewcDOMDEC);
- wallcycle_sub_start(wcycle_, ewcsDD_GPU);
+ wallcycle_start(wcycle_, WallCycleCounter::Domdec);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::DDGpu);
d_x_ = d_coordinatesBuffer;
d_f_ = d_forcesBuffer;
xSendSize_ = newSize;
#if GMX_MPI
- MPI_Sendrecv(&xSendSize_, sizeof(int), MPI_BYTE, sendRankX_, 0, &xRecvSize_, sizeof(int),
- MPI_BYTE, recvRankX_, 0, mpi_comm_mysim_, MPI_STATUS_IGNORE);
+ MPI_Sendrecv(&xSendSize_,
+ sizeof(int),
+ MPI_BYTE,
+ sendRankX_,
+ 0,
+ &xRecvSize_,
+ sizeof(int),
+ MPI_BYTE,
+ recvRankX_,
+ 0,
+ mpi_comm_mysim_,
+ MPI_STATUS_IGNORE);
#endif
fSendSize_ = xRecvSize_;
fRecvSize_ = xSendSize_;
"halo exchange index mapping array");
std::copy(ind.index.begin(), ind.index.end(), h_indexMap_.begin());
- copyToDeviceBuffer(&d_indexMap_, h_indexMap_.data(), 0, newSize, nonLocalStream_,
- GpuApiCallBehavior::Async, nullptr);
+ copyToDeviceBuffer(
+ &d_indexMap_, h_indexMap_.data(), 0, newSize, nonLocalStream_, GpuApiCallBehavior::Async, nullptr);
}
- // This rank will push data to its neighbor, so needs to know
- // the remote receive address and similarly send its receive
- // address to other neighbour. We can do this here in reinit fn
- // since the pointers will not change until the next NS step.
- // Coordinates buffer:
- void* recvPtr = static_cast<void*>(&d_x_[atomOffset_]);
#if GMX_MPI
- MPI_Sendrecv(&recvPtr, sizeof(void*), MPI_BYTE, recvRankX_, 0, &remoteXPtr_, sizeof(void*),
- MPI_BYTE, sendRankX_, 0, mpi_comm_mysim_, MPI_STATUS_IGNORE);
-
- // Force buffer:
- recvPtr = static_cast<void*>(d_recvBuf_);
- MPI_Sendrecv(&recvPtr, sizeof(void*), MPI_BYTE, recvRankF_, 0, &remoteFPtr_, sizeof(void*),
- MPI_BYTE, sendRankF_, 0, mpi_comm_mysim_, MPI_STATUS_IGNORE);
+ // Exchange of remote addresses from neighboring ranks is needed only with CUDA-direct as cudamemcpy needs both src/dst pointer
+ // MPI calls such as MPI_send doesn't worry about receiving address, that is taken care by MPI_recv call in neighboring rank
+ if (GMX_THREAD_MPI)
+ {
+ // This rank will push data to its neighbor, so needs to know
+ // the remote receive address and similarly send its receive
+ // address to other neighbour. We can do this here in reinit fn
+ // since the pointers will not change until the next NS step.
+
+ // Coordinates buffer:
+ float3* recvPtr = &d_x_[atomOffset_];
+ MPI_Sendrecv(&recvPtr,
+ sizeof(void*),
+ MPI_BYTE,
+ recvRankX_,
+ 0,
+ &remoteXPtr_,
+ sizeof(void*),
+ MPI_BYTE,
+ sendRankX_,
+ 0,
+ mpi_comm_mysim_,
+ MPI_STATUS_IGNORE);
+
+ // Force buffer:
+ recvPtr = d_recvBuf_;
+ MPI_Sendrecv(&recvPtr,
+ sizeof(void*),
+ MPI_BYTE,
+ recvRankF_,
+ 0,
+ &remoteFPtr_,
+ sizeof(void*),
+ MPI_BYTE,
+ sendRankF_,
+ 0,
+ mpi_comm_mysim_,
+ MPI_STATUS_IGNORE);
+ }
#endif
- wallcycle_sub_stop(wcycle_, ewcsDD_GPU);
- wallcycle_stop(wcycle_, ewcDOMDEC);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::DDGpu);
+ wallcycle_stop(wcycle_, WallCycleCounter::Domdec);
return;
}
+void GpuHaloExchange::Impl::enqueueWaitRemoteCoordinatesReadyEvent(GpuEventSynchronizer* coordinatesReadyOnDeviceEvent)
+{
+ GMX_ASSERT(coordinatesReadyOnDeviceEvent != nullptr,
+ "Co-ordinate Halo exchange requires valid co-ordinate ready event");
+
+ // Wait for event from receiving task that remote coordinates are ready, and enqueue that event to stream used
+ // for subsequent data push. This avoids a race condition with the remote data being written in the previous timestep.
+ // Similarly send event to task that will push data to this task.
+ GpuEventSynchronizer* remoteCoordinatesReadyOnDeviceEvent;
+ MPI_Sendrecv(&coordinatesReadyOnDeviceEvent,
+ sizeof(GpuEventSynchronizer*),
+ MPI_BYTE,
+ recvRankX_,
+ 0,
+ &remoteCoordinatesReadyOnDeviceEvent,
+ sizeof(GpuEventSynchronizer*),
+ MPI_BYTE,
+ sendRankX_,
+ 0,
+ mpi_comm_mysim_,
+ MPI_STATUS_IGNORE);
+ remoteCoordinatesReadyOnDeviceEvent->enqueueWaitEvent(nonLocalStream_);
+}
+
void GpuHaloExchange::Impl::communicateHaloCoordinates(const matrix box,
GpuEventSynchronizer* coordinatesReadyOnDeviceEvent)
{
- wallcycle_start(wcycle_, ewcLAUNCH_GPU);
+ wallcycle_start(wcycle_, WallCycleCounter::LaunchGpu);
if (pulse_ == 0)
{
// ensure stream waits until coordinate data is available on device
coordinatesReadyOnDeviceEvent->enqueueWaitEvent(nonLocalStream_);
}
- wallcycle_sub_start(wcycle_, ewcsLAUNCH_GPU_MOVEX);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::LaunchGpuMoveX);
// launch kernel to pack send buffer
KernelLaunchConfig config;
// is used every step to pass the shift vector as an argument of
// the packing kernel.
const int boxDimensionIndex = dd_->dim[dimIndex_];
- const float3 coordinateShift{ box[boxDimensionIndex][XX], box[boxDimensionIndex][YY],
+ const float3 coordinateShift{ box[boxDimensionIndex][XX],
+ box[boxDimensionIndex][YY],
box[boxDimensionIndex][ZZ] };
// Avoid launching kernel when there is no work to do
{
auto kernelFn = usePBC_ ? packSendBufKernel<true> : packSendBufKernel<false>;
- const auto kernelArgs = prepareGpuKernelArguments(kernelFn, config, &sendBuf, &d_x,
- &indexMap, &size, &coordinateShift);
+ const auto kernelArgs = prepareGpuKernelArguments(
+ kernelFn, config, &sendBuf, &d_x, &indexMap, &size, &coordinateShift);
- launchGpuKernel(kernelFn, config, nonLocalStream_, nullptr,
- "Domdec GPU Apply X Halo Exchange", kernelArgs);
+ launchGpuKernel(
+ kernelFn, config, nonLocalStream_, nullptr, "Domdec GPU Apply X Halo Exchange", kernelArgs);
}
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_GPU_MOVEX);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchGpuMoveX);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
// Consider time spent in communicateHaloData as Comm.X counter
// ToDo: We need further refinement here as communicateHaloData includes launch time for cudamemcpyasync
- wallcycle_start(wcycle_, ewcMOVEX);
+ wallcycle_start(wcycle_, WallCycleCounter::MoveX);
+
+ // wait for remote co-ordinates is implicit with process-MPI as non-local stream is synchronized before MPI calls
+ // and MPI_Waitall call makes sure both neighboring ranks' non-local stream is synchronized before data transfer is initiated
+ if (GMX_THREAD_MPI && pulse_ == 0)
+ {
+ enqueueWaitRemoteCoordinatesReadyEvent(coordinatesReadyOnDeviceEvent);
+ }
- communicateHaloData(d_x_, HaloQuantity::HaloCoordinates, coordinatesReadyOnDeviceEvent);
+ float3* recvPtr = GMX_THREAD_MPI ? remoteXPtr_ : &d_x_[atomOffset_];
+ communicateHaloData(d_sendBuf_, xSendSize_, sendRankX_, recvPtr, xRecvSize_, recvRankX_);
- wallcycle_stop(wcycle_, ewcMOVEX);
+ wallcycle_stop(wcycle_, WallCycleCounter::MoveX);
return;
}
{
// Consider time spent in communicateHaloData as Comm.F counter
// ToDo: We need further refinement here as communicateHaloData includes launch time for cudamemcpyasync
- wallcycle_start(wcycle_, ewcMOVEF);
+ wallcycle_start(wcycle_, WallCycleCounter::MoveF);
+
+ float3* recvPtr = GMX_THREAD_MPI ? remoteFPtr_ : d_recvBuf_;
// Communicate halo data (in non-local stream)
- communicateHaloData(d_f_, HaloQuantity::HaloForces, nullptr);
+ communicateHaloData(&(d_f_[atomOffset_]), fSendSize_, sendRankF_, recvPtr, fRecvSize_, recvRankF_);
- wallcycle_stop(wcycle_, ewcMOVEF);
+ wallcycle_stop(wcycle_, WallCycleCounter::MoveF);
- wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU);
- wallcycle_sub_start(wcycle_, ewcsLAUNCH_GPU_MOVEF);
+ wallcycle_start_nocount(wcycle_, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::LaunchGpuMoveF);
float3* d_f = d_f_;
// If this is the last pulse and index (noting the force halo
// activities
if ((pulse_ == (dd_->comm->cd[dimIndex_].numPulses() - 1)) && (dimIndex_ == (dd_->ndim - 1)))
{
- if (!accumulateForces)
- {
- // Clear local portion of force array (in local stream)
- cudaMemsetAsync(d_f, 0, numHomeAtoms_ * sizeof(rvec), localStream_.stream());
- }
-
// ensure non-local stream waits for local stream, due to dependence on
// the previous H2D copy of CPU forces (if accumulateForces is true)
- // or the above clearing.
- // TODO remove this dependency on localStream - edmine Issue #3093
+ // or local force clearing.
GpuEventSynchronizer eventLocal;
eventLocal.markEvent(localStream_);
eventLocal.enqueueWaitEvent(nonLocalStream_);
const auto kernelArgs =
prepareGpuKernelArguments(kernelFn, config, &d_f, &recvBuf, &indexMap, &size);
- launchGpuKernel(kernelFn, config, nonLocalStream_, nullptr,
- "Domdec GPU Apply F Halo Exchange", kernelArgs);
+ launchGpuKernel(
+ kernelFn, config, nonLocalStream_, nullptr, "Domdec GPU Apply F Halo Exchange", kernelArgs);
}
if (pulse_ == 0)
fReadyOnDevice_.markEvent(nonLocalStream_);
}
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_GPU_MOVEF);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchGpuMoveF);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
}
-
-void GpuHaloExchange::Impl::communicateHaloData(float3* d_ptr,
- HaloQuantity haloQuantity,
- GpuEventSynchronizer* coordinatesReadyOnDeviceEvent)
+void GpuHaloExchange::Impl::communicateHaloData(float3* sendPtr,
+ int sendSize,
+ int sendRank,
+ float3* recvPtr,
+ int recvSize,
+ int recvRank)
{
-
- void* sendPtr;
- int sendSize;
- void* remotePtr;
- int sendRank;
- int recvRank;
-
- if (haloQuantity == HaloQuantity::HaloCoordinates)
+ if (GMX_THREAD_MPI)
{
- sendPtr = static_cast<void*>(d_sendBuf_);
- sendSize = xSendSize_;
- remotePtr = remoteXPtr_;
- sendRank = sendRankX_;
- recvRank = recvRankX_;
-
-#if GMX_MPI
- // Wait for event from receiving task that remote coordinates are ready, and enqueue that event to stream used
- // for subsequent data push. This avoids a race condition with the remote data being written in the previous timestep.
- // Similarly send event to task that will push data to this task.
- GpuEventSynchronizer* remoteCoordinatesReadyOnDeviceEvent;
- MPI_Sendrecv(&coordinatesReadyOnDeviceEvent, sizeof(GpuEventSynchronizer*), MPI_BYTE,
- recvRank, 0, &remoteCoordinatesReadyOnDeviceEvent, sizeof(GpuEventSynchronizer*),
- MPI_BYTE, sendRank, 0, mpi_comm_mysim_, MPI_STATUS_IGNORE);
- remoteCoordinatesReadyOnDeviceEvent->enqueueWaitEvent(nonLocalStream_);
-#else
- GMX_UNUSED_VALUE(coordinatesReadyOnDeviceEvent);
-#endif
+ // no need to explicitly sync with GMX_THREAD_MPI as all operations are
+ // anyway launched in correct stream
+ communicateHaloDataWithCudaDirect(sendPtr, sendSize, sendRank, recvPtr, recvRank);
}
else
{
- sendPtr = static_cast<void*>(&(d_ptr[atomOffset_]));
- sendSize = fSendSize_;
- remotePtr = remoteFPtr_;
- sendRank = sendRankF_;
- recvRank = recvRankF_;
+ communicateHaloDataWithCudaMPI(sendPtr, sendSize, sendRank, recvPtr, recvSize, recvRank);
}
+}
- communicateHaloDataWithCudaDirect(sendPtr, sendSize, sendRank, remotePtr, recvRank);
+void GpuHaloExchange::Impl::communicateHaloDataWithCudaMPI(float3* sendPtr,
+ int sendSize,
+ int sendRank,
+ float3* recvPtr,
+ int recvSize,
+ int recvRank)
+{
+ // no need to wait for haloDataReadyOnDevice event if this rank is not sending any data
+ if (sendSize > 0)
+ {
+ // wait for non local stream to complete all outstanding
+ // activities, to ensure that buffer is up-to-date in GPU memory
+ // before transferring to remote rank
+
+ // ToDo: Replace stream synchronize with event synchronize
+ nonLocalStream_.synchronize();
+ }
+
+ // perform halo exchange directly in device buffers
+#if GMX_MPI
+ MPI_Request request;
+
+ // recv remote data into halo region
+ MPI_Irecv(recvPtr, recvSize * DIM, MPI_FLOAT, recvRank, 0, mpi_comm_mysim_, &request);
+
+ // send data to remote halo region
+ MPI_Send(sendPtr, sendSize * DIM, MPI_FLOAT, sendRank, 0, mpi_comm_mysim_);
+
+ MPI_Wait(&request, MPI_STATUS_IGNORE);
+#endif
}
-void GpuHaloExchange::Impl::communicateHaloDataWithCudaDirect(void* sendPtr,
- int sendSize,
- int sendRank,
- void* remotePtr,
- int recvRank)
+void GpuHaloExchange::Impl::communicateHaloDataWithCudaDirect(float3* sendPtr,
+ int sendSize,
+ int sendRank,
+ float3* remotePtr,
+ int recvRank)
{
cudaError_t stat;
// send data to neighbor, if any data exists to send
if (sendSize > 0)
{
- stat = cudaMemcpyAsync(remotePtr, sendPtr, sendSize * DIM * sizeof(float),
- cudaMemcpyDeviceToDevice, nonLocalStream_.stream());
+ stat = cudaMemcpyAsync(remotePtr,
+ sendPtr,
+ sendSize * DIM * sizeof(float),
+ cudaMemcpyDeviceToDevice,
+ nonLocalStream_.stream());
CU_RET_ERR(stat, "cudaMemcpyAsync on GPU Domdec CUDA direct data transfer failed");
}
// to its stream.
GpuEventSynchronizer* haloDataTransferRemote;
+ GMX_ASSERT(haloDataTransferLaunched_ != nullptr,
+ "Halo exchange requires valid event to synchronize data transfer initiated in "
+ "remote rank");
haloDataTransferLaunched_->markEvent(nonLocalStream_);
- MPI_Sendrecv(&haloDataTransferLaunched_, sizeof(GpuEventSynchronizer*), MPI_BYTE, sendRank, 0,
- &haloDataTransferRemote, sizeof(GpuEventSynchronizer*), MPI_BYTE, recvRank, 0,
- mpi_comm_mysim_, MPI_STATUS_IGNORE);
+ MPI_Sendrecv(&haloDataTransferLaunched_,
+ sizeof(GpuEventSynchronizer*),
+ MPI_BYTE,
+ sendRank,
+ 0,
+ &haloDataTransferRemote,
+ sizeof(GpuEventSynchronizer*),
+ MPI_BYTE,
+ recvRank,
+ 0,
+ mpi_comm_mysim_,
+ MPI_STATUS_IGNORE);
haloDataTransferRemote->enqueueWaitEvent(nonLocalStream_);
#else
sendRankF_(dd->neighbor[dimIndex][0]),
recvRankF_(dd->neighbor[dimIndex][1]),
usePBC_(dd->ci[dd->dim[dimIndex]] == 0),
- haloDataTransferLaunched_(new GpuEventSynchronizer()),
+ haloDataTransferLaunched_(GMX_THREAD_MPI ? new GpuEventSynchronizer() : nullptr),
mpi_comm_mysim_(mpi_comm_mysim),
deviceContext_(deviceContext),
localStream_(localStream),
pulse_(pulse),
wcycle_(wcycle)
{
-
- GMX_RELEASE_ASSERT(GMX_THREAD_MPI,
- "GPU Halo exchange is currently only supported with thread-MPI enabled");
-
if (usePBC_ && dd->unitCellInfo.haveScrewPBC)
{
gmx_fatal(FARGS, "Error: screw is not yet supported in GPU halo exchange\n");
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
private:
/*! \brief Data transfer wrapper for GPU halo exchange
- * \param [inout] d_ptr pointer to coordinates or force buffer in GPU memory
- * \param [in] haloQuantity switch on whether X or F halo exchange is being performed
- * \param [in] coordinatesReadyOnDeviceEvent event recorded when coordinates have been copied to device
+ * \param [in] sendPtr send buffer address
+ * \param [in] sendSize number of elements to send
+ * \param [in] sendRank rank of destination
+ * \param [in] recvPtr receive buffer address
+ * \param [in] recvSize number of elements to receive
+ * \param [in] recvRank rank of source
*/
- void communicateHaloData(float3* d_ptr,
- HaloQuantity haloQuantity,
- GpuEventSynchronizer* coordinatesReadyOnDeviceEvent);
+ void communicateHaloData(float3* sendPtr, int sendSize, int sendRank, float3* recvPtr, int recvSize, int recvRank);
/*! \brief Data transfer for GPU halo exchange using CUDA memcopies
* \param [inout] sendPtr address to send data from
* \param [in] sendSize number of atoms to be sent
* \param [in] sendRank rank to send data to
- * \param [inout] remotePtr remote address to recv data
+ * \param [in] remotePtr remote address to recv data
* \param [in] recvRank rank to recv data from
*/
- void communicateHaloDataWithCudaDirect(void* sendPtr, int sendSize, int sendRank, void* remotePtr, int recvRank);
+ void communicateHaloDataWithCudaDirect(float3* sendPtr, int sendSize, int sendRank, float3* remotePtr, int recvRank);
+
+ /*! \brief Data transfer wrapper for GPU halo exchange using MPI_send and MPI_Recv
+ * \param [in] sendPtr send buffer address
+ * \param [in] sendSize number of elements to send
+ * \param [in] sendRank rank of destination
+ * \param [in] recvPtr receive buffer address
+ * \param [in] recvSize number of elements to receive
+ * \param [in] recvRank rank of source
+ */
+ void communicateHaloDataWithCudaMPI(float3* sendPtr,
+ int sendSize,
+ int sendRank,
+ float3* recvPtr,
+ int recvSize,
+ int recvRank);
+
+ /*! \brief Exchange coordinate-ready event with neighbor ranks and enqueue wait in non-local
+ * stream \param [in] eventSync event recorded when coordinates/forces are ready to device
+ */
+ void enqueueWaitRemoteCoordinatesReadyEvent(GpuEventSynchronizer* coordinatesReadyOnDeviceEvent);
//! Domain decomposition object
gmx_domdec_t* dd_ = nullptr;
//! number of home atoms - offset of local halo region
int numHomeAtoms_ = 0;
//! remote GPU coordinates buffer pointer for pushing data
- void* remoteXPtr_ = nullptr;
+ float3* remoteXPtr_ = nullptr;
//! remote GPU force buffer pointer for pushing data
- void* remoteFPtr_ = nullptr;
+ float3* remoteFPtr_ = nullptr;
//! Periodic Boundary Conditions for this rank
bool usePBC_ = false;
//! force shift buffer on device
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <memory>
#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/classhelpers.h"
class gmx_ga2la_t;
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
* for initialization and atom-data setup.
*/
void mdAlgorithmsSetupAtomData(const t_commrec* cr,
- const t_inputrec* ir,
+ const t_inputrec& inputrec,
const gmx_mtop_t& top_global,
gmx_localtop_t* top,
t_forcerec* fr,
if (usingDomDec)
{
- numAtomIndex = dd_natoms_mdatoms(cr->dd);
+ numAtomIndex = dd_natoms_mdatoms(*cr->dd);
numHomeAtoms = dd_numHomeAtoms(*cr->dd);
- numTotalAtoms = dd_natoms_mdatoms(cr->dd);
+ numTotalAtoms = dd_natoms_mdatoms(*cr->dd);
}
else
{
force->resize(numTotalAtoms);
}
- atoms2md(&top_global, ir, numAtomIndex,
- usingDomDec ? cr->dd->globalAtomIndices : std::vector<int>(), numHomeAtoms, mdAtoms);
+ atoms2md(top_global,
+ inputrec,
+ numAtomIndex,
+ usingDomDec ? cr->dd->globalAtomIndices : std::vector<int>(),
+ numHomeAtoms,
+ mdAtoms);
- auto mdatoms = mdAtoms->mdatoms();
+ t_mdatoms* mdatoms = mdAtoms->mdatoms();
if (usingDomDec)
{
- dd_sort_local_top(cr->dd, mdatoms, top);
+ dd_sort_local_top(*cr->dd, mdatoms, top);
}
else
{
- gmx_mtop_generate_local_top(top_global, top, ir->efep != efepNO);
+ gmx_mtop_generate_local_top(top_global, top, inputrec.efep != FreeEnergyPerturbationType::No);
}
if (vsite)
{
- vsite->setVirtualSites(top->idef.il, *mdatoms);
+ vsite->setVirtualSites(top->idef.il,
+ mdatoms->nr,
+ mdatoms->homenr,
+ gmx::arrayRefFromArray(mdatoms->ptype, mdatoms->nr));
}
/* Note that with DD only flexible constraints, not shells, are supported
*/
if (!usingDomDec && shellfc)
{
- make_local_shells(cr, mdatoms, shellfc);
+ make_local_shells(cr, *mdatoms, shellfc);
}
for (auto& listedForces : fr->listedForces)
* For PME-only ranks, gmx_pmeonly() has its own call to gmx_pme_reinit_atoms().
*/
const int numPmeAtoms = numHomeAtoms - fr->n_tpi;
- gmx_pme_reinit_atoms(fr->pmedata, numPmeAtoms, mdatoms->chargeA, mdatoms->chargeB);
+ gmx_pme_reinit_atoms(fr->pmedata,
+ numPmeAtoms,
+ mdatoms->chargeA ? gmx::arrayRefFromArray(mdatoms->chargeA, mdatoms->nr)
+ : gmx::ArrayRef<real>{},
+ mdatoms->chargeB ? gmx::arrayRefFromArray(mdatoms->chargeB, mdatoms->nr)
+ : gmx::ArrayRef<real>{});
}
if (constr)
{
- constr->setConstraints(top, mdatoms->nr, mdatoms->homenr, mdatoms->massT, mdatoms->invmass,
- mdatoms->nMassPerturbed != 0, mdatoms->lambda, mdatoms->cFREEZE);
+ constr->setConstraints(top,
+ mdatoms->nr,
+ mdatoms->homenr,
+ gmx::arrayRefFromArray(mdatoms->massT, mdatoms->nr),
+ gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
+ mdatoms->nMassPerturbed != 0,
+ mdatoms->lambda,
+ mdatoms->cFREEZE ? gmx::arrayRefFromArray(mdatoms->cFREEZE, mdatoms->nr)
+ : gmx::ArrayRef<const unsigned short>());
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \param[in] md The MD atom data
* \param[in,out] shfc The shell/flexible-constraint data
*/
-void make_local_shells(const t_commrec* cr, const t_mdatoms* md, gmx_shellfc_t* shfc);
+void make_local_shells(const t_commrec* cr, const t_mdatoms& md, gmx_shellfc_t* shfc);
/*! \brief Sets atom data for several MD algorithms
*
* This is called at the start of serial runs and during domain decomposition.
*
* \param[in] cr Communication record
- * \param[in] ir Input parameter record
+ * \param[in] inputrec Input parameter record
* \param[in] top_global The global topology
* \param[in,out] top The local topology
* \param[in,out] fr The force calculation parameter/data record
* \param[in,out] shellfc The shell/flexible-constraint data, can be NULL
*/
void mdAlgorithmsSetupAtomData(const t_commrec* cr,
- const t_inputrec* ir,
+ const t_inputrec& inputrec,
const gmx_mtop_t& top_global,
gmx_localtop_t* top,
t_forcerec* fr,
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/* This file is completely threadsafe - keep it that way! */
+#include "gmxpre.h"
+
+#include "nsgrid.h"
+
+#include <cmath>
+#include <cstdio>
+
+#include "gromacs/domdec/dlb.h"
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+
+/*! \brief The extent of the neighborsearch grid is a bit larger than sqrt(3)
+ * to account for less dense regions at the edges of the system.
+ */
+constexpr real c_stdDevFactor = 2.0;
+
+/***********************************
+ * Grid Routines
+ ***********************************/
+
+static void calc_x_av_stddev(int n, rvec* x, rvec av, rvec stddev)
+{
+ dvec s1, s2;
+ int i, d;
+
+ clear_dvec(s1);
+ clear_dvec(s2);
+
+ for (i = 0; i < n; i++)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ s1[d] += x[i][d];
+ s2[d] += x[i][d] * x[i][d];
+ }
+ }
+
+ dsvmul(1.0 / n, s1, s1);
+ dsvmul(1.0 / n, s2, s2);
+
+ for (d = 0; d < DIM; d++)
+ {
+ av[d] = s1[d];
+ stddev[d] = std::sqrt(s2[d] - s1[d] * s1[d]);
+ }
+}
+
+static void get_nsgrid_boundaries_vac(real av, real stddev, real* bound0, real* bound1, real* bdens0, real* bdens1)
+{
+ /* Set the grid to 2 times the standard deviation of
+ * the charge group centers in both directions.
+ * For a uniform bounded distribution the width is sqrt(3)*stddev,
+ * so all charge groups fall within the width.
+ * For a sphere stddev is r/sqrt(5): 99.2% falls within the width.
+ * For a Gaussian distribution 98% fall within the width.
+ */
+ *bound0 = av - c_stdDevFactor * stddev;
+ *bound1 = av + c_stdDevFactor * stddev;
+
+ *bdens0 = av - c_gridStdDevFactor * stddev;
+ *bdens1 = av + c_gridStdDevFactor * stddev;
+}
+
+static void dd_box_bounds_to_ns_bounds(real box0, real box_size, real* gr0, real* gr1)
+{
+ real av, stddev;
+
+ /* Redetermine av and stddev from the DD box boundaries */
+ av = box0 + 0.5 * box_size;
+ stddev = 0.5 * box_size / c_gridStdDevFactor;
+
+ *gr0 = av - c_stdDevFactor * stddev;
+ *gr1 = av + c_stdDevFactor * stddev;
+}
+
+void get_nsgrid_boundaries(int nboundeddim,
+ matrix box,
+ gmx_domdec_t* dd,
+ gmx_ddbox_t* ddbox,
+ gmx::RVec* gr0,
+ gmx::RVec* gr1,
+ int ncg,
+ rvec* cgcm,
+ rvec grid_x0,
+ rvec grid_x1)
+{
+ rvec av, stddev;
+ real vol, bdens0, bdens1;
+ int d;
+
+ if (nboundeddim < DIM)
+ {
+ calc_x_av_stddev(ncg, cgcm, av, stddev);
+ }
+
+ vol = 1;
+ for (d = 0; d < DIM; d++)
+ {
+ if (d < nboundeddim)
+ {
+ grid_x0[d] = (gr0 != nullptr ? (*gr0)[d] : 0);
+ grid_x1[d] = (gr1 != nullptr ? (*gr1)[d] : box[d][d]);
+ vol *= (grid_x1[d] - grid_x0[d]);
+ }
+ else
+ {
+ if (ddbox == nullptr)
+ {
+ get_nsgrid_boundaries_vac(av[d], stddev[d], &grid_x0[d], &grid_x1[d], &bdens0, &bdens1);
+ }
+ else
+ {
+ /* Temporary fix which uses global ddbox boundaries
+ * for unbounded dimensions.
+ * Should be replaced by local boundaries, which makes
+ * the ns grid smaller and does not require global comm.
+ */
+ dd_box_bounds_to_ns_bounds(ddbox->box0[d], ddbox->box_size[d], &grid_x0[d], &grid_x1[d]);
+ bdens0 = grid_x0[d];
+ bdens1 = grid_x1[d];
+ }
+ /* Check for a DD cell not at a lower edge */
+ if (dd != nullptr && gr0 != nullptr && dd->ci[d] > 0)
+ {
+ grid_x0[d] = (*gr0)[d];
+ bdens0 = (*gr0)[d];
+ }
+ /* Check for a DD cell not at a higher edge */
+ if (dd != nullptr && gr1 != nullptr && dd->ci[d] < dd->numCells[d] - 1)
+ {
+ grid_x1[d] = (*gr1)[d];
+ bdens1 = (*gr1)[d];
+ }
+ vol *= (bdens1 - bdens0);
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "Set grid boundaries dim %d: %f %f\n", d, grid_x0[d], grid_x1[d]);
+ }
+ }
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015,2019,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_MDLIB_NSGRID_H
+#define GMX_MDLIB_NSGRID_H
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
+
+struct gmx_domdec_t;
+struct gmx_ddbox_t;
+
+/*! \brief Used when estimating the interaction density.
+ *
+ * c_gridStdDevFactor * stddev estimates the interaction density. The
+ * value sqrt(3) == 1.73205080757 gives a uniform load for a
+ * rectangular 3D block of charge groups. For a sphere, it is not a
+ * bad approximation for 4x1x1 up to 4x2x2.
+ *
+ * \todo It would be nicer to use sqrt(3) here, when all code that
+ * includes this file is in C++, which will let us cope with the
+ * std::sqrt<T> on Windows. */
+constexpr real c_gridStdDevFactor = 1.73205080757;
+
+void get_nsgrid_boundaries(int nboundeddim,
+ matrix box,
+ struct gmx_domdec_t* dd,
+ gmx_ddbox_t* ddbox,
+ gmx::RVec* gr0,
+ gmx::RVec* gr1,
+ int ncg,
+ rvec* cgcm,
+ rvec grid_x0,
+ rvec grid_x1);
+/* Return the ns grid boundaries grid_x0 and grid_x1
+ * and the estimate for the grid density.
+ * For non-bounded dimensions the boundaries are determined
+ * from the average and std.dev. of cgcm.
+ * The are determined from box, unless gr0!=NULL or gr1!=NULL,
+ * then they are taken from gr0 or gr1.
+ * With dd and unbounded dimensions, the proper grid borders for cells
+ * on the edges are determined from cgcm.
+ */
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
Count //!< The number of options
};
+/*! \brief Options for checking bonded interactions.
+ *
+ * These values must match the bool false and true used for mdrun -ddcheck */
+enum class DDBondedChecking : bool
+{
+ ExcludeZeroLimit = false, //!< Do not check bonded interactions that go to 0 for large distances
+ All = true //!< Check all bonded interactions
+};
+
/*! \libinternal \brief Structure containing all (command line) options for the domain decomposition */
struct DomdecOptions
{
- //! If true, check that all bonded interactions have been assigned to exactly one domain/rank.
- bool checkBondedInteractions = true;
+ //! Style of bonded-interaction checking
+ DDBondedChecking ddBondedChecking = DDBondedChecking::All;
//! If true, don't communicate all atoms between the non-bonded cut-off and the larger bonded cut-off, but only those that have non-local bonded interactions. This significantly reduces the communication volume.
bool useBondedCommunication = true;
//! The domain decomposition grid cell count, 0 means let domdec choose based on the number of ranks.
#include "gmxpre.h"
+#include "gromacs/utility/arrayref.h"
#include "partition.h"
#include "config.h"
#include "gromacs/domdec/ga2la.h"
#include "gromacs/domdec/localatomsetmanager.h"
#include "gromacs/domdec/mdsetup.h"
+#include "gromacs/domdec/nsgrid.h"
#include "gromacs/ewald/pme_pp.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/mdlib/forcerec.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdlib/mdatoms.h"
-#include "gromacs/mdlib/nsgrid.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/forcerec.h"
fprintf(fp,
"zone d0 %d d1 %d d2 %d min0 %6.3f max1 %6.3f mch0 %6.3f mch1 %6.3f p1_0 %6.3f p1_1 "
"%6.3f\n",
- d, i, j, zone->min0, zone->max1, zone->mch0, zone->mch0, zone->p1_0, zone->p1_1);
+ d,
+ i,
+ j,
+ zone->min0,
+ zone->max1,
+ zone->mch0,
+ zone->mch0,
+ zone->p1_0,
+ zone->p1_1);
}
/*! \brief Using the home grid size as input in cell_ns_x0 and cell_ns_x1
"Here we expect gmx_ddzone_t to consist of c_ddzoneNumReals reals (only)");
int numReals = numElementsInBuffer * c_ddzoneNumReals;
- ddSendrecv(dd, d, dddirBackward, gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
+ ddSendrecv(dd,
+ d,
+ dddirBackward,
+ gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
rvec dh = { 0 };
cellsizes[d].fracUpperMin = extr_s[d - 1][1];
if (debug)
{
- fprintf(debug, "Cell fraction d %d, max0 %f, min1 %f\n", d, cellsizes[d].fracLowerMax,
+ fprintf(debug,
+ "Cell fraction d %d, max0 %f, min1 %f\n",
+ d,
+ cellsizes[d].fracLowerMax,
cellsizes[d].fracUpperMin);
}
}
static void make_dd_indices(gmx_domdec_t* dd, const int atomStart)
{
const int numZones = dd->comm->zones.n;
- const int* zone2cg = dd->comm->zones.cg_range;
- const int* zone_ncg1 = dd->comm->zone_ncg1;
+ gmx::ArrayRef<const int> zone2cg = dd->comm->zones.cg_range;
+ gmx::ArrayRef<const int> zone_ncg1 = dd->comm->zone_ncg1;
gmx::ArrayRef<const int> globalAtomGroupIndices = dd->globalAtomGroupIndices;
std::vector<int>& globalAtomIndices = dd->globalAtomIndices;
int globalAtomIndex = dd->globalAtomIndices[a];
if (have[globalAtomIndex] > 0)
{
- fprintf(stderr, "DD rank %d: global atom %d occurs twice: index %d and %d\n",
- dd->rank, globalAtomIndex + 1, have[globalAtomIndex], a + 1);
+ fprintf(stderr,
+ "DD rank %d: global atom %d occurs twice: index %d and %d\n",
+ dd->rank,
+ globalAtomIndex + 1,
+ have[globalAtomIndex],
+ a + 1);
}
else
{
int ngl = 0;
for (int i = 0; i < natoms_sys; i++)
{
- if (const auto entry = dd->ga2la->find(i))
+ if (const auto* entry = dd->ga2la->find(i))
{
const int a = entry->la;
if (a >= numAtomsInZones)
fprintf(stderr,
"DD rank %d: global atom %d marked as local atom %d, which is larger than "
"nat_tot (%d)\n",
- dd->rank, i + 1, a + 1, numAtomsInZones);
+ dd->rank,
+ i + 1,
+ a + 1,
+ numAtomsInZones);
nerr++;
}
else
fprintf(stderr,
"DD rank %d: global atom %d marked as local atom %d, which has global "
"atom index %d\n",
- dd->rank, i + 1, a + 1, dd->globalAtomIndices[a] + 1);
+ dd->rank,
+ i + 1,
+ a + 1,
+ dd->globalAtomIndices[a] + 1);
nerr++;
}
}
}
if (ngl != numAtomsInZones)
{
- fprintf(stderr, "DD rank %d, %s: %d global atom indices, %d local atoms\n", dd->rank, where,
- ngl, numAtomsInZones);
+ fprintf(stderr, "DD rank %d, %s: %d global atom indices, %d local atoms\n", dd->rank, where, ngl, numAtomsInZones);
}
for (int a = 0; a < numAtomsInZones; a++)
{
if (have[a] == 0)
{
- fprintf(stderr, "DD rank %d, %s: local atom %d, global %d has no global index\n",
- dd->rank, where, a + 1, dd->globalAtomIndices[a] + 1);
+ fprintf(stderr,
+ "DD rank %d, %s: local atom %d, global %d has no global index\n",
+ dd->rank,
+ where,
+ a + 1,
+ dd->globalAtomIndices[a] + 1);
}
}
}
}
-bool check_grid_jump(int64_t step, const gmx_domdec_t* dd, real cutoff, const gmx_ddbox_t* ddbox, gmx_bool bFatal)
-{
- gmx_domdec_comm_t* comm = dd->comm;
- bool invalid = false;
-
- for (int d = 1; d < dd->ndim; d++)
- {
- const DDCellsizesWithDlb& cellsizes = comm->cellsizesWithDlb[d];
- const int dim = dd->dim[d];
- const real limit = grid_jump_limit(comm, cutoff, d);
- real bfac = ddbox->box_size[dim];
- if (ddbox->tric_dir[dim])
- {
- bfac *= ddbox->skew_fac[dim];
- }
- if ((cellsizes.fracUpper - cellsizes.fracLowerMax) * bfac < limit
- || (cellsizes.fracLower - cellsizes.fracUpperMin) * bfac > -limit)
- {
- invalid = true;
-
- if (bFatal)
- {
- char buf[22];
-
- /* This error should never be triggered under normal
- * circumstances, but you never know ...
- */
- gmx_fatal(FARGS,
- "step %s: The domain decomposition grid has shifted too much in the "
- "%c-direction around cell %d %d %d. This should not have happened. "
- "Running with fewer ranks might avoid this issue.",
- gmx_step_str(step, buf), dim2char(dim), dd->ci[XX], dd->ci[YY], dd->ci[ZZ]);
- }
- }
- }
-
- return invalid;
-}
//! Return the duration of force calculations on this rank.
static float dd_force_load(gmx_domdec_comm_t* comm)
{
"step %s: The %c-size (%f) times the triclinic skew factor (%f) is smaller "
"than the smallest allowed cell size (%f) for domain decomposition grid cell "
"%d %d %d",
- gmx_step_str(step, buf), dim2char(dim),
- comm->cell_x1[dim] - comm->cell_x0[dim], ddbox->skew_fac[dim],
- dd->comm->cellsize_min[dim], dd->ci[XX], dd->ci[YY], dd->ci[ZZ]);
+ gmx_step_str(step, buf),
+ dim2char(dim),
+ comm->cell_x1[dim] - comm->cell_x0[dim],
+ ddbox->skew_fac[dim],
+ dd->comm->cellsize_min[dim],
+ dd->ci[XX],
+ dd->ci[YY],
+ dd->ci[ZZ]);
}
}
dd_move_cellx(dd, ddbox, cell_ns_x0, cell_ns_x1);
if (isDlbOn(dd->comm) && dd->ndim > 1)
{
- check_grid_jump(step, dd, dd->comm->systemInfo.cutoff, ddbox, TRUE);
+ gmx::check_grid_jump(step, dd, dd->comm->systemInfo.cutoff, ddbox, TRUE);
}
}
}
//! Compute and communicate to determine the load distribution across PP ranks.
-static void get_load_distribution(gmx_domdec_t* dd, gmx_wallcycle_t wcycle)
+static void get_load_distribution(gmx_domdec_t* dd, gmx_wallcycle* wcycle)
{
gmx_domdec_comm_t* comm;
domdec_load_t* load;
fprintf(debug, "get_load_distribution start\n");
}
- wallcycle_start(wcycle, ewcDDCOMMLOAD);
+ wallcycle_start(wcycle, WallCycleCounter::DDCommLoad);
comm = dd->comm;
comm->load[0].pme = comm->cycl[ddCyclPME];
}
+ // Either we have DLB off, or we have it on and the array is large enough
+ GMX_ASSERT(!isDlbOn(dd->comm) || static_cast<int>(dd->comm->cellsizesWithDlb.size()) == dd->ndim,
+ "DLB cell sizes data not set up properly ");
for (int d = dd->ndim - 1; d >= 0; d--)
{
- const DDCellsizesWithDlb* cellsizes = (isDlbOn(dd->comm) ? &comm->cellsizesWithDlb[d] : nullptr);
- const int dim = dd->dim[d];
+ const int dim = dd->dim[d];
/* Check if we participate in the communication in this dimension */
if (d == dd->ndim - 1 || (dd->ci[dd->dim[d + 1]] == 0 && dd->ci[dd->dim[dd->ndim - 1]] == 0))
{
load = &comm->load[d];
if (isDlbOn(dd->comm))
{
- cell_frac = cellsizes->fracUpper - cellsizes->fracLower;
+ cell_frac = comm->cellsizesWithDlb[d].fracUpper - comm->cellsizesWithDlb[d].fracLower;
}
int pos = 0;
if (d == dd->ndim - 1)
sbuf[pos++] = cell_frac;
if (d > 0)
{
- sbuf[pos++] = cellsizes->fracLowerMax;
- sbuf[pos++] = cellsizes->fracUpperMin;
+ sbuf[pos++] = comm->cellsizesWithDlb[d].fracLowerMax;
+ sbuf[pos++] = comm->cellsizesWithDlb[d].fracUpperMin;
}
}
if (bSepPME)
sbuf[pos++] = comm->load[d + 1].flags;
if (d > 0)
{
- sbuf[pos++] = cellsizes->fracLowerMax;
- sbuf[pos++] = cellsizes->fracUpperMin;
+ sbuf[pos++] = comm->cellsizesWithDlb[d].fracLowerMax;
+ sbuf[pos++] = comm->cellsizesWithDlb[d].fracUpperMin;
}
}
if (bSepPME)
* The communicators are setup such that the root always has rank 0.
*/
#if GMX_MPI
- MPI_Gather(sbuf, load->nload * sizeof(float), MPI_BYTE, load->load,
- load->nload * sizeof(float), MPI_BYTE, 0, comm->mpi_comm_load[d]);
+ MPI_Gather(sbuf,
+ load->nload * sizeof(float),
+ MPI_BYTE,
+ load->load,
+ load->nload * sizeof(float),
+ MPI_BYTE,
+ 0,
+ comm->mpi_comm_load[d]);
#endif
if (dd->ci[dim] == dd->master_ci[dim])
{
if (isDlbOn(comm))
{
- rowMaster = cellsizes->rowMaster.get();
+ rowMaster = comm->cellsizesWithDlb[d].rowMaster.get();
}
load->sum = 0;
load->max = 0;
}
}
- wallcycle_stop(wcycle, ewcDDCOMMLOAD);
+ wallcycle_stop(wcycle, WallCycleCounter::DDCommLoad);
if (debug)
{
sprintf(buf, " Average PME mesh/force load: %5.3f\n", pmeForceRatio);
fprintf(fplog, "%s", buf);
fprintf(stderr, "%s", buf);
- sprintf(buf, " Part of the total run time spent waiting due to PP/PME imbalance: %.1f %%\n",
+ sprintf(buf,
+ " Part of the total run time spent waiting due to PP/PME imbalance: %.1f %%\n",
std::fabs(lossFractionPme) * 100);
fprintf(fplog, "%s", buf);
fprintf(stderr, "%s", buf);
" had %s work to do than the PP ranks.\n"
" You might want to %s the number of PME ranks\n"
" or %s the cut-off and the grid spacing.\n",
- std::fabs(lossFractionPme * 100), (lossFractionPme < 0) ? "less" : "more",
+ std::fabs(lossFractionPme * 100),
+ (lossFractionPme < 0) ? "less" : "more",
(lossFractionPme < 0) ? "decrease" : "increase",
(lossFractionPme < 0) ? "decrease" : "increase");
fprintf(fplog, "%s\n", buf);
"step %s Measured %.1f %% performance loss due to load imbalance, "
"but the minimum cell size is smaller than 1.05 times the cell size limit. "
"Will no longer try dynamic load balancing.",
- gmx::toString(step).c_str(), dd_force_imb_perf_loss(dd) * 100);
+ gmx::toString(step).c_str(),
+ dd_force_imb_perf_loss(dd) * 100);
comm->dlbState = DlbState::offForever;
return;
.appendTextFormatted(
"step %s Turning on dynamic load balancing, because the performance loss due "
"to load imbalance is %.1f %%.",
- gmx::toString(step).c_str(), dd_force_imb_perf_loss(dd) * 100);
+ gmx::toString(step).c_str(),
+ dd_force_imb_perf_loss(dd) * 100);
comm->dlbState = DlbState::onCanTurnOff;
/* Store the non-DLB performance, so we can check if DLB actually
}
}
-/*! \brief Add the atom groups we need to send in this pulse from this
- * zone to \p localAtomGroups and \p work. */
-static void get_zone_pulse_cgs(gmx_domdec_t* dd,
- int zonei,
- int zone,
- int cg0,
- int cg1,
- gmx::ArrayRef<const int> globalAtomGroupIndices,
- int dim,
- int dim_ind,
- int dim0,
- int dim1,
- int dim2,
- real r_comm2,
- real r_bcomm2,
- matrix box,
- bool distanceIsTriclinic,
- rvec* normal,
- real skew_fac2_d,
- real skew_fac_01,
- rvec* v_d,
- rvec* v_0,
- rvec* v_1,
- const dd_corners_t* c,
- const rvec sf2_round,
- gmx_bool bDistBonded,
- gmx_bool bBondComm,
- gmx_bool bDist2B,
- gmx_bool bDistMB,
- rvec* cg_cm,
- gmx::ArrayRef<const int> cginfo,
- std::vector<int>* localAtomGroups,
- dd_comm_setup_work_t* work)
+/*! \brief Add the atom groups and coordinates we need to send in this
+ * pulse from this zone to \p localAtomGroups and \p work. */
+static void get_zone_pulse_groups(gmx_domdec_t* dd,
+ int zonei,
+ int zone,
+ int cg0,
+ int cg1,
+ gmx::ArrayRef<const int> globalAtomGroupIndices,
+ int dim,
+ int dim_ind,
+ int dim0,
+ int dim1,
+ int dim2,
+ real r_comm2,
+ real r_bcomm2,
+ matrix box,
+ bool distanceIsTriclinic,
+ rvec* normal,
+ real skew_fac2_d,
+ real skew_fac_01,
+ rvec* v_d,
+ rvec* v_0,
+ rvec* v_1,
+ const dd_corners_t* c,
+ const rvec sf2_round,
+ gmx_bool bDistBonded,
+ gmx_bool bBondComm,
+ gmx_bool bDist2B,
+ gmx_bool bDistMB,
+ gmx::ArrayRef<const gmx::RVec> coordinates,
+ gmx::ArrayRef<const int> cginfo,
+ std::vector<int>* localAtomGroups,
+ dd_comm_setup_work_t* work)
{
gmx_domdec_comm_t* comm;
gmx_bool bScrew;
if (!distanceIsTriclinic)
{
/* Rectangular direction, easy */
- r = cg_cm[cg][dim] - c->c[dim_ind][zone];
+ r = coordinates[cg][dim] - c->c[dim_ind][zone];
if (r > 0)
{
r2 += r * r;
}
if (bDistMB_pulse)
{
- r = cg_cm[cg][dim] - c->bc[dim_ind];
+ r = coordinates[cg][dim] - c->bc[dim_ind];
if (r > 0)
{
rb2 += r * r;
*/
if (dim_ind >= 1 && (zonei == 1 || zonei == 2))
{
- r = cg_cm[cg][dim0] - c->cr0;
+ r = coordinates[cg][dim0] - c->cr0;
/* This is the first dimension, so always r >= 0 */
r2 += r * r;
if (bDistMB_pulse)
}
if (dim_ind == 2 && (zonei == 2 || zonei == 3))
{
- r = cg_cm[cg][dim1] - c->cr1[zone];
+ r = coordinates[cg][dim1] - c->cr1[zone];
if (r > 0)
{
r2 += r * r;
}
if (bDistMB_pulse)
{
- r = cg_cm[cg][dim1] - c->bcr1;
+ r = coordinates[cg][dim1] - c->bcr1;
if (r > 0)
{
rb2 += r * r;
*/
if (dim_ind >= 1 && (zonei == 1 || zonei == 2))
{
- rn[dim0] = cg_cm[cg][dim0] - c->cr0;
+ rn[dim0] = coordinates[cg][dim0] - c->cr0;
for (i = dim0 + 1; i < DIM; i++)
{
- rn[dim0] -= cg_cm[cg][i] * v_0[i][dim0];
+ rn[dim0] -= coordinates[cg][i] * v_0[i][dim0];
}
r2 = rn[dim0] * rn[dim0] * sf2_round[dim0];
if (bDistMB_pulse)
if (dim_ind == 2 && (zonei == 2 || zonei == 3))
{
GMX_ASSERT(dim1 >= 0 && dim1 < DIM, "Must have a valid dimension index");
- rn[dim1] += cg_cm[cg][dim1] - c->cr1[zone];
+ rn[dim1] += coordinates[cg][dim1] - c->cr1[zone];
tric_sh = 0;
for (i = dim1 + 1; i < DIM; i++)
{
- tric_sh -= cg_cm[cg][i] * v_1[i][dim1];
+ tric_sh -= coordinates[cg][i] * v_1[i][dim1];
}
rn[dim1] += tric_sh;
if (rn[dim1] > 0)
}
if (bDistMB_pulse)
{
- rb[dim1] += cg_cm[cg][dim1] - c->bcr1 + tric_sh;
+ rb[dim1] += coordinates[cg][dim1] - c->bcr1 + tric_sh;
if (rb[dim1] > 0)
{
rb2 += rb[dim1] * rb[dim1] * sf2_round[dim1];
}
}
/* The distance along the communication direction */
- rn[dim] += cg_cm[cg][dim] - c->c[dim_ind][zone];
+ rn[dim] += coordinates[cg][dim] - c->c[dim_ind][zone];
tric_sh = 0;
for (i = dim + 1; i < DIM; i++)
{
- tric_sh -= cg_cm[cg][i] * v_d[i][dim];
+ tric_sh -= coordinates[cg][i] * v_d[i][dim];
}
rn[dim] += tric_sh;
if (rn[dim] > 0)
{
clear_rvec(rb);
GMX_ASSERT(dim >= 0 && dim < DIM, "Must have a valid dimension index");
- rb[dim] += cg_cm[cg][dim] - c->bc[dim_ind] + tric_sh;
+ rb[dim] += coordinates[cg][dim] - c->bc[dim_ind] + tric_sh;
if (rb[dim] > 0)
{
rb2 += rb[dim] * rb[dim] * skew_fac2_d;
rvec posPbc;
if (dd->ci[dim] == 0)
{
- /* Correct cg_cm for pbc */
- rvec_add(cg_cm[cg], box[dim], posPbc);
+ /* Correct coordinates for pbc */
+ rvec_add(coordinates[cg], box[dim], posPbc);
if (bScrew)
{
posPbc[YY] = box[YY][YY] - posPbc[YY];
}
else
{
- copy_rvec(cg_cm[cg], posPbc);
+ copy_rvec(coordinates[cg], posPbc);
}
vbuf.emplace_back(posPbc[XX], posPbc[YY], posPbc[ZZ]);
* This can not be done in init_domain_decomposition,
* as the numbers of threads is determined later.
*/
- int numThreads = gmx_omp_nthreads_get(emntDomdec);
+ int numThreads = gmx_omp_nthreads_get(ModuleMultiThread::Domdec);
comm->dth.resize(numThreads);
}
v_1 = ddbox->v[dim1];
}
- zone_cg_range = zones->cg_range;
+ zone_cg_range = zones->cg_range.data();
gmx::ArrayRef<cginfo_mb_t> cginfo_mb = fr->cginfo_mb;
zone_cg_range[0] = 0;
int cg0_th = cg0 + ((cg1 - cg0) * th) / numThreads;
int cg1_th = cg0 + ((cg1 - cg0) * (th + 1)) / numThreads;
- /* Get the cg's for this pulse in this zone */
- get_zone_pulse_cgs(dd, zonei, zone, cg0_th, cg1_th, dd->globalAtomGroupIndices,
- dim, dim_ind, dim0, dim1, dim2, r_comm2, r_bcomm2, box,
- distanceIsTriclinic, normal, skew_fac2_d, skew_fac_01,
- v_d, v_0, v_1, &corners, sf2_round, bDistBonded, bBondComm,
- bDist2B, bDistMB, state->x.rvec_array(), fr->cginfo,
- th == 0 ? &ind->index : &work.localAtomGroupBuffer, &work);
+ /* Get the atom groups and coordinates for this pulse in this zone */
+ get_zone_pulse_groups(dd,
+ zonei,
+ zone,
+ cg0_th,
+ cg1_th,
+ dd->globalAtomGroupIndices,
+ dim,
+ dim_ind,
+ dim0,
+ dim1,
+ dim2,
+ r_comm2,
+ r_bcomm2,
+ box,
+ distanceIsTriclinic,
+ normal,
+ skew_fac2_d,
+ skew_fac_01,
+ v_d,
+ v_0,
+ v_1,
+ &corners,
+ sf2_round,
+ bDistBonded,
+ bBondComm,
+ bDist2B,
+ bDistMB,
+ state->x,
+ fr->cginfo,
+ th == 0 ? &ind->index : &work.localAtomGroupBuffer,
+ &work);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
} // END
{
const dd_comm_setup_work_t& dth = comm->dth[th];
- ind->index.insert(ind->index.end(), dth.localAtomGroupBuffer.begin(),
+ ind->index.insert(ind->index.end(),
+ dth.localAtomGroupBuffer.begin(),
dth.localAtomGroupBuffer.end());
- atomGroups.insert(atomGroups.end(), dth.atomGroupBuffer.begin(),
- dth.atomGroupBuffer.end());
- positions.insert(positions.end(), dth.positionBuffer.begin(),
- dth.positionBuffer.end());
+ atomGroups.insert(
+ atomGroups.end(), dth.atomGroupBuffer.begin(), dth.atomGroupBuffer.end());
+ positions.insert(
+ positions.end(), dth.positionBuffer.begin(), dth.positionBuffer.end());
comm->dth[0].nat += dth.nat;
ind->nsend[zone] += dth.nsend_zone;
}
}
ddSendrecv<int>(dd, dim_ind, dddirBackward, work.atomGroupBuffer, integerBufferRef);
- /* Make space for cg_cm */
+ /* Make space for cginfo */
dd_resize_atominfo_and_state(fr, state, pos_cg + ind->nrecv[nzone]);
/* Communicate the coordinates */
else
{
/* This part of the code is never executed with bBondComm. */
- merge_cg_buffers(nzone, cd, p, zone_cg_range, dd->globalAtomGroupIndices,
- integerBufferRef.data(), state->x, rvecBufferRef, fr->cginfo_mb,
+ merge_cg_buffers(nzone,
+ cd,
+ p,
+ zone_cg_range,
+ dd->globalAtomGroupIndices,
+ integerBufferRef.data(),
+ state->x,
+ rvecBufferRef,
+ fr->cginfo_mb,
fr->cginfo);
pos_cg += ind->nrecv[nzone];
}
{
for (z = zone_start; z < zone_end; z++)
{
- fprintf(debug, "zone %d %6.3f - %6.3f %6.3f - %6.3f %6.3f - %6.3f\n", z,
- zones->size[z].x0[XX], zones->size[z].x1[XX], zones->size[z].x0[YY],
- zones->size[z].x1[YY], zones->size[z].x0[ZZ], zones->size[z].x1[ZZ]);
- fprintf(debug, "zone %d bb %6.3f - %6.3f %6.3f - %6.3f %6.3f - %6.3f\n", z,
- zones->size[z].bb_x0[XX], zones->size[z].bb_x1[XX], zones->size[z].bb_x0[YY],
- zones->size[z].bb_x1[YY], zones->size[z].bb_x0[ZZ], zones->size[z].bb_x1[ZZ]);
+ fprintf(debug,
+ "zone %d %6.3f - %6.3f %6.3f - %6.3f %6.3f - %6.3f\n",
+ z,
+ zones->size[z].x0[XX],
+ zones->size[z].x1[XX],
+ zones->size[z].x0[YY],
+ zones->size[z].x1[YY],
+ zones->size[z].x0[ZZ],
+ zones->size[z].x1[ZZ]);
+ fprintf(debug,
+ "zone %d bb %6.3f - %6.3f %6.3f - %6.3f %6.3f - %6.3f\n",
+ z,
+ zones->size[z].bb_x0[XX],
+ zones->size[z].bb_x1[XX],
+ zones->size[z].bb_x0[YY],
+ zones->size[z].bb_x1[YY],
+ zones->size[z].bb_x0[ZZ],
+ zones->size[z].bb_x1[ZZ]);
}
}
}
gmx::ArrayRef<const gmx_cgsort_t> cgsort = sort->sorted;
GMX_RELEASE_ASSERT(cgsort.ssize() == dd->ncg_home, "We should sort all the home atom groups");
- if (state->flags & (1 << estX))
+ if (state->flags & enumValueToBitMask(StateEntry::X))
{
orderVector(cgsort, makeArrayRef(state->x), rvecBuffer.buffer);
}
- if (state->flags & (1 << estV))
+ if (state->flags & enumValueToBitMask(StateEntry::V))
{
orderVector(cgsort, makeArrayRef(state->v), rvecBuffer.buffer);
}
- if (state->flags & (1 << estCGP))
+ if (state->flags & enumValueToBitMask(StateEntry::Cgp))
{
orderVector(cgsort, makeArrayRef(state->cg_p), rvecBuffer.buffer);
}
comm->load_pme = 0;
}
-void print_dd_statistics(const t_commrec* cr, const t_inputrec* ir, FILE* fplog)
+namespace gmx
+{
+
+bool check_grid_jump(int64_t step, const gmx_domdec_t* dd, real cutoff, const gmx_ddbox_t* ddbox, bool bFatal)
+{
+ gmx_domdec_comm_t* comm = dd->comm;
+ bool invalid = false;
+
+ for (int d = 1; d < dd->ndim; d++)
+ {
+ const DDCellsizesWithDlb& cellsizes = comm->cellsizesWithDlb[d];
+ const int dim = dd->dim[d];
+ const real limit = grid_jump_limit(comm, cutoff, d);
+ real bfac = ddbox->box_size[dim];
+ if (ddbox->tric_dir[dim])
+ {
+ bfac *= ddbox->skew_fac[dim];
+ }
+ if ((cellsizes.fracUpper - cellsizes.fracLowerMax) * bfac < limit
+ || (cellsizes.fracLower - cellsizes.fracUpperMin) * bfac > -limit)
+ {
+ invalid = true;
+
+ if (bFatal)
+ {
+ char buf[22];
+
+ /* This error should never be triggered under normal
+ * circumstances, but you never know ...
+ */
+ gmx_fatal(FARGS,
+ "step %s: The domain decomposition grid has shifted too much in the "
+ "%c-direction around cell %d %d %d. This should not have happened. "
+ "Running with fewer ranks might avoid this issue.",
+ gmx_step_str(step, buf),
+ dim2char(dim),
+ dd->ci[XX],
+ dd->ci[YY],
+ dd->ci[ZZ]);
+ }
+ }
+ }
+
+ return invalid;
+}
+
+void print_dd_statistics(const t_commrec* cr, const t_inputrec& inputrec, FILE* fplog)
{
gmx_domdec_comm_t* comm = cr->dd->comm;
case DDAtomRanges::Type::Vsites:
if (cr->dd->vsite_comm)
{
- fprintf(fplog, " av. #atoms communicated per step for vsites: %d x %.1f\n",
- (EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD) ? 3 : 2, av);
+ fprintf(fplog,
+ " av. #atoms communicated per step for vsites: %d x %.1f\n",
+ (EEL_PME(inputrec.coulombtype)
+ || inputrec.coulombtype == CoulombInteractionType::Ewald)
+ ? 3
+ : 2,
+ av);
}
break;
case DDAtomRanges::Type::Constraints:
if (cr->dd->constraint_comm)
{
- fprintf(fplog, " av. #atoms communicated per step for LINCS: %d x %.1f\n",
- 1 + ir->nLincsIter, av);
+ fprintf(fplog,
+ " av. #atoms communicated per step for LINCS: %d x %.1f\n",
+ 1 + inputrec.nLincsIter,
+ av);
}
break;
default: gmx_incons(" Unknown type for DD statistics");
}
fprintf(fplog, "\n");
- if (comm->ddSettings.recordLoad && EI_DYNAMICS(ir->eI))
+ if (comm->ddSettings.recordLoad && EI_DYNAMICS(inputrec.eI))
{
print_dd_load_av(fplog, cr->dd);
}
const gmx::MDLogger& mdlog,
int64_t step,
const t_commrec* cr,
- gmx_bool bMasterState,
+ bool bMasterState,
int nstglobalcomm,
t_state* state_global,
const gmx_mtop_t& top_global,
- const t_inputrec* ir,
+ const t_inputrec& inputrec,
gmx::ImdSession* imdSession,
pull_t* pull_work,
t_state* state_local,
gmx::Constraints* constr,
t_nrnb* nrnb,
gmx_wallcycle* wcycle,
- gmx_bool bVerbose)
+ bool bVerbose)
{
- gmx_domdec_t* dd;
- gmx_domdec_comm_t* comm;
- gmx_ddbox_t ddbox = { 0 };
- int64_t step_pcoupl;
- rvec cell_ns_x0, cell_ns_x1;
- int ncgindex_set, ncg_moved, nat_f_novirsum;
- gmx_bool bBoxChanged, bNStGlobalComm, bDoDLB, bCheckWhetherToTurnDlbOn, bLogLoad;
- gmx_bool bRedist;
- ivec np;
- real grid_density;
- char sbuf[22];
-
- wallcycle_start(wcycle, ewcDOMDEC);
-
- dd = cr->dd;
- comm = dd->comm;
+ gmx_ddbox_t ddbox = { 0 };
+ int ncgindex_set;
+ char sbuf[22];
+
+ wallcycle_start(wcycle, WallCycleCounter::Domdec);
+
+ gmx_domdec_t* dd = cr->dd;
+ gmx_domdec_comm_t* comm = dd->comm;
// TODO if the update code becomes accessible here, use
// upd->deform for this logic.
- bBoxChanged = (bMasterState || inputrecDeform(ir));
- if (ir->epc != epcNO)
+ bool bBoxChanged = (bMasterState || inputrecDeform(&inputrec));
+ if (inputrec.epc != PressureCoupling::No)
{
/* With nstpcouple > 1 pressure coupling happens.
* one step after calculating the pressure.
* We need to determine the last step in which p-coupling occurred.
* MRS -- need to validate this for vv?
*/
- int n = ir->nstpcouple;
+ int n = inputrec.nstpcouple;
+ int64_t step_pcoupl;
if (n == 1)
{
step_pcoupl = step - 1;
}
if (step_pcoupl >= comm->partition_step)
{
- bBoxChanged = TRUE;
+ bBoxChanged = true;
}
}
- bNStGlobalComm = (step % nstglobalcomm == 0);
-
+ bool bNStGlobalComm = (step % nstglobalcomm == 0);
+ bool bDoDLB;
if (!isDlbOn(comm))
{
- bDoDLB = FALSE;
+ bDoDLB = false;
}
else
{
* Since it requires (possibly expensive) global communication,
* we might want to do DLB less frequently.
*/
- if (bBoxChanged || ir->epc != epcNO)
+ if (bBoxChanged || inputrec.epc != PressureCoupling::No)
{
bDoDLB = bBoxChanged;
}
/* Check if we have recorded loads on the nodes */
if (comm->ddSettings.recordLoad && dd_load_count(comm) > 0)
{
- bCheckWhetherToTurnDlbOn = dd_dlb_get_should_check_whether_to_turn_dlb_on(dd);
+ bool bCheckWhetherToTurnDlbOn = dd_dlb_get_should_check_whether_to_turn_dlb_on(dd);
/* Print load every nstlog, first and last step to the log file */
- bLogLoad = ((ir->nstlog > 0 && step % ir->nstlog == 0) || comm->n_load_collect == 0
- || (ir->nsteps >= 0 && (step + ir->nstlist > ir->init_step + ir->nsteps)));
+ bool bLogLoad = ((inputrec.nstlog > 0 && step % inputrec.nstlog == 0) || comm->n_load_collect == 0
+ || (inputrec.nsteps >= 0
+ && (step + inputrec.nstlist > inputrec.init_step + inputrec.nsteps)));
/* Avoid extra communication due to verbose screen output
* when nstglobalcomm is set.
*/
if (bDoDLB || bLogLoad || bCheckWhetherToTurnDlbOn
- || (bVerbose && (ir->nstlist == 0 || nstglobalcomm <= ir->nstlist)))
+ || (bVerbose && (inputrec.nstlist == 0 || nstglobalcomm <= inputrec.nstlist)))
{
get_load_distribution(dd, wcycle);
if (DDMASTER(dd))
if (comm->dlbState == DlbState::onCanTurnOff
&& dd->comm->n_load_have % c_checkTurnDlbOffInterval == c_checkTurnDlbOffInterval - 1)
{
- gmx_bool turnOffDlb;
+ bool turnOffDlb;
if (DDMASTER(dd))
{
/* If the running averaged cycles with DLB are more
{
/* To turn off DLB, we need to redistribute the atoms */
dd_collect_state(dd, state_local, state_global);
- bMasterState = TRUE;
+ bMasterState = true;
turn_off_dlb(mdlog, dd, step);
}
}
}
else if (bCheckWhetherToTurnDlbOn)
{
- gmx_bool turnOffDlbForever = FALSE;
- gmx_bool turnOnDlb = FALSE;
+ bool turnOffDlbForever = false;
+ bool turnOnDlb = false;
/* Since the timings are node dependent, the master decides */
if (DDMASTER(dd))
if (comm->dlbSlowerPartitioningCount > 0
&& dd->ddp_count < comm->dlbSlowerPartitioningCount + 10 * c_checkTurnDlbOnInterval)
{
- turnOffDlbForever = TRUE;
+ turnOffDlbForever = true;
}
comm->haveTurnedOffDlb = false;
/* Register when we last measured DLB slowdown */
*/
if (comm->ddRankSetup.usePmeOnlyRanks && dd_pme_f_ratio(dd) > 1 - DD_PERF_LOSS_DLB_ON)
{
- turnOnDlb = FALSE;
+ turnOnDlb = false;
}
else
{
}
struct
{
- gmx_bool turnOffDlbForever;
- gmx_bool turnOnDlb;
+ bool turnOffDlbForever;
+ bool turnOnDlb;
} bools{ turnOffDlbForever, turnOnDlb };
dd_bcast(dd, sizeof(bools), &bools);
if (bools.turnOffDlbForever)
else if (bools.turnOnDlb)
{
turn_on_dlb(mdlog, dd, step);
- bDoDLB = TRUE;
+ bDoDLB = true;
}
}
}
comm->n_load_have++;
}
- bRedist = FALSE;
+ bool bRedist = false;
if (bMasterState)
{
/* Clear the old state */
gmx_fatal(FARGS,
"Internal inconsistency state_local->ddp_count (%d) > dd->ddp_count (%" PRId64
")",
- state_local->ddp_count, dd->ddp_count);
+ state_local->ddp_count,
+ dd->ddp_count);
}
if (state_local->ddp_count_cg_gl != state_local->ddp_count)
gmx_fatal(FARGS,
"Internal inconsistency state_local->ddp_count_cg_gl (%d) != "
"state_local->ddp_count (%d)",
- state_local->ddp_count_cg_gl, state_local->ddp_count);
+ state_local->ddp_count_cg_gl,
+ state_local->ddp_count);
}
/* Clear the old state */
}
set_ddbox(*dd, bMasterState, state_local->box, bNStGlobalComm, state_local->x, &ddbox);
- bBoxChanged = TRUE;
- bRedist = TRUE;
+ bBoxChanged = true;
+ bRedist = true;
}
/* Copy needed for dim's without pbc when avoiding communication */
copy_rvec(ddbox.box0, comm->box0);
* Thus we need to keep track of how many charge groups will move for
* obtaining correct local charge group / atom counts.
*/
- ncg_moved = 0;
+ int ncg_moved = 0;
if (bRedist)
{
- wallcycle_sub_start(wcycle, ewcsDD_REDIST);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::DDRedist);
ncgindex_set = dd->ncg_home;
dd_redistribute_cg(fplog, step, dd, ddbox.tric_dir, state_local, fr, nrnb, &ncg_moved);
state_local->x);
}
- wallcycle_sub_stop(wcycle, ewcsDD_REDIST);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::DDRedist);
}
- // TODO: Integrate this code in the nbnxm module
- get_nsgrid_boundaries(ddbox.nboundeddim, state_local->box, dd, &ddbox, &comm->cell_x0,
- &comm->cell_x1, dd->ncg_home, as_rvec_array(state_local->x.data()),
- cell_ns_x0, cell_ns_x1, &grid_density);
+ RVec cell_ns_x0, cell_ns_x1;
+ get_nsgrid_boundaries(ddbox.nboundeddim,
+ state_local->box,
+ dd,
+ &ddbox,
+ &comm->cell_x0,
+ &comm->cell_x1,
+ dd->ncg_home,
+ as_rvec_array(state_local->x.data()),
+ cell_ns_x0,
+ cell_ns_x1);
if (bBoxChanged)
{
if (bSortCG)
{
- wallcycle_sub_start(wcycle, ewcsDD_GRID);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::DDGrid);
/* Sort the state on charge group position.
* This enables exact restarts from this step.
set_zones_size(dd, state_local->box, &ddbox, 0, 1, ncg_moved);
- nbnxn_put_on_grid(fr->nbv.get(), state_local->box, 0, comm->zones.size[0].bb_x0,
- comm->zones.size[0].bb_x1, comm->updateGroupsCog.get(),
- { 0, dd->ncg_home }, comm->zones.dens_zone0, fr->cginfo, state_local->x,
- ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr);
+ nbnxn_put_on_grid(fr->nbv.get(),
+ state_local->box,
+ 0,
+ comm->zones.size[0].bb_x0,
+ comm->zones.size[0].bb_x1,
+ comm->updateGroupsCog.get(),
+ { 0, dd->ncg_home },
+ comm->zones.dens_zone0,
+ fr->cginfo,
+ state_local->x,
+ ncg_moved,
+ bRedist ? comm->movedBuffer.data() : nullptr);
if (debug)
{
- fprintf(debug, "Step %s, sorting the %d home charge groups\n", gmx_step_str(step, sbuf),
- dd->ncg_home);
+ fprintf(debug, "Step %s, sorting the %d home charge groups\n", gmx_step_str(step, sbuf), dd->ncg_home);
}
dd_sort_state(dd, fr, state_local);
dd->ga2la->clear();
ncgindex_set = 0;
- wallcycle_sub_stop(wcycle, ewcsDD_GRID);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::DDGrid);
}
else
{
/* With the group scheme the sorting array is part of the DD state,
* but it just got out of sync, so mark as invalid by emptying it.
*/
- if (ir->cutoff_scheme == ecutsGROUP)
+ if (inputrec.cutoff_scheme == CutoffScheme::Group)
{
comm->sort->sorted.clear();
}
comm->updateGroupsCog->clear();
}
- wallcycle_sub_start(wcycle, ewcsDD_SETUPCOMM);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::DDSetupComm);
/* Set the induces for the home atoms */
set_zones_ncg_home(dd);
/* When bSortCG=true, we have already set the size for zone 0 */
set_zones_size(dd, state_local->box, &ddbox, bSortCG ? 1 : 0, comm->zones.n, 0);
- wallcycle_sub_stop(wcycle, ewcsDD_SETUPCOMM);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::DDSetupComm);
/*
write_dd_pdb("dd_home",step,"dump",top_global,cr,
-1,state_local->x.rvec_array(),state_local->box);
*/
- wallcycle_sub_start(wcycle, ewcsDD_MAKETOP);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::DDMakeTop);
/* Extract a local topology from the global topology */
+ IVec numPulses;
for (int i = 0; i < dd->ndim; i++)
{
- np[dd->dim[i]] = comm->cd[i].numPulses();
+ numPulses[dd->dim[i]] = comm->cd[i].numPulses();
}
- dd_make_local_top(dd, &comm->zones, dd->unitCellInfo.npbcdim, state_local->box,
- comm->cellsize_min, np, fr, state_local->x.rvec_array(), top_global, top_local);
+ dd_make_local_top(dd,
+ &comm->zones,
+ dd->unitCellInfo.npbcdim,
+ state_local->box,
+ comm->cellsize_min,
+ numPulses,
+ fr,
+ state_local->x,
+ top_global,
+ top_local);
- wallcycle_sub_stop(wcycle, ewcsDD_MAKETOP);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::DDMakeTop);
- wallcycle_sub_start(wcycle, ewcsDD_MAKECONSTR);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::DDMakeConstr);
/* Set up the special atom communication */
int n = comm->atomRanges.end(DDAtomRanges::Type::Zones);
for (int i = static_cast<int>(DDAtomRanges::Type::Zones) + 1;
- i < static_cast<int>(DDAtomRanges::Type::Number); i++)
+ i < static_cast<int>(DDAtomRanges::Type::Number);
+ i++)
{
auto range = static_cast<DDAtomRanges::Type>(i);
switch (range)
}
break;
case DDAtomRanges::Type::Constraints:
- if (dd->comm->systemInfo.haveSplitConstraints || dd->comm->systemInfo.haveSplitSettles)
+ if (dd->comm->systemInfo.mayHaveSplitConstraints || dd->comm->systemInfo.mayHaveSplitSettles)
{
/* Only for inter-cg constraints we need special code */
- n = dd_make_local_constraints(dd, n, &top_global, fr->cginfo.data(), constr,
- ir->nProjOrder, top_local->idef.il);
+ n = dd_make_local_constraints(dd,
+ n,
+ top_global,
+ fr->cginfo.data(),
+ constr,
+ inputrec.nProjOrder,
+ top_local->idef.il);
}
break;
default: gmx_incons("Unknown special atom type setup");
comm->atomRanges.setEnd(range, n);
}
- wallcycle_sub_stop(wcycle, ewcsDD_MAKECONSTR);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::DDMakeConstr);
- wallcycle_sub_start(wcycle, ewcsDD_TOPOTHER);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::DDTopOther);
/* Make space for the extra coordinates for virtual site
* or constraint communication.
state_change_natoms(state_local, state_local->natoms);
+ int nat_f_novirsum;
if (vsite && vsite->numInterUpdategroupVirtualSites())
{
nat_f_novirsum = comm->atomRanges.end(DDAtomRanges::Type::Vsites);
}
else
{
- if (EEL_FULL(ir->coulombtype) && dd->haveExclusions)
+ if (EEL_FULL(inputrec.coulombtype) && dd->haveExclusions)
{
nat_f_novirsum = comm->atomRanges.end(DDAtomRanges::Type::Zones);
}
* allocation, zeroing and copying, but this is probably not worth
* the complications and checking.
*/
- forcerec_set_ranges(fr, comm->atomRanges.end(DDAtomRanges::Type::Zones),
- comm->atomRanges.end(DDAtomRanges::Type::Constraints), nat_f_novirsum);
+ forcerec_set_ranges(fr,
+ comm->atomRanges.end(DDAtomRanges::Type::Zones),
+ comm->atomRanges.end(DDAtomRanges::Type::Constraints),
+ nat_f_novirsum);
/* Update atom data for mdatoms and several algorithms */
- mdAlgorithmsSetupAtomData(cr, ir, top_global, top_local, fr, f, mdAtoms, constr, vsite, nullptr);
+ mdAlgorithmsSetupAtomData(cr, inputrec, top_global, top_local, fr, f, mdAtoms, constr, vsite, nullptr);
- auto mdatoms = mdAtoms->mdatoms();
+ auto* mdatoms = mdAtoms->mdatoms();
if (!thisRankHasDuty(cr, DUTY_PME))
{
/* Send the charges and/or c6/sigmas to our PME only node */
- gmx_pme_send_parameters(cr, fr->ic, mdatoms->nChargePerturbed != 0,
- mdatoms->nTypePerturbed != 0, mdatoms->chargeA, mdatoms->chargeB,
- mdatoms->sqrt_c6A, mdatoms->sqrt_c6B, mdatoms->sigmaA,
- mdatoms->sigmaB, dd_pme_maxshift_x(dd), dd_pme_maxshift_y(dd));
+ gmx_pme_send_parameters(
+ cr,
+ *fr->ic,
+ mdatoms->nChargePerturbed != 0,
+ mdatoms->nTypePerturbed != 0,
+ mdatoms->chargeA ? gmx::arrayRefFromArray(mdatoms->chargeA, mdatoms->nr)
+ : gmx::ArrayRef<real>{},
+ mdatoms->chargeB ? gmx::arrayRefFromArray(mdatoms->chargeB, mdatoms->nr)
+ : gmx::ArrayRef<real>{},
+ mdatoms->sqrt_c6A ? gmx::arrayRefFromArray(mdatoms->sqrt_c6A, mdatoms->nr)
+ : gmx::ArrayRef<real>{},
+ mdatoms->sqrt_c6B ? gmx::arrayRefFromArray(mdatoms->sqrt_c6B, mdatoms->nr)
+ : gmx::ArrayRef<real>{},
+ mdatoms->sigmaA ? gmx::arrayRefFromArray(mdatoms->sigmaA, mdatoms->nr)
+ : gmx::ArrayRef<real>{},
+ mdatoms->sigmaB ? gmx::arrayRefFromArray(mdatoms->sigmaB, mdatoms->nr)
+ : gmx::ArrayRef<real>{},
+ dd_pme_maxshift_x(*dd),
+ dd_pme_maxshift_y(*dd));
}
if (dd->atomSets != nullptr)
}
// The pull group construction can need the atom sets updated above
- if (ir->bPull)
+ if (inputrec.bPull)
{
/* Update the local pull groups */
dd_make_local_pull_groups(cr, pull_work);
}
- /* Update the local atoms to be communicated via the IMD protocol if bIMD is TRUE. */
+ /* Update the local atoms to be communicated via the IMD protocol if bIMD is true. */
imdSession->dd_make_local_IMD_atoms(dd);
add_dd_statistics(dd);
*/
dd_move_x_vsites(*dd, state_local->box, state_local->x.rvec_array());
- wallcycle_sub_stop(wcycle, ewcsDD_TOPOTHER);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::DDTopOther);
if (comm->ddSettings.nstDDDump > 0 && step % comm->ddSettings.nstDDDump == 0)
{
- dd_move_x(dd, state_local->box, state_local->x, nullWallcycle);
- write_dd_pdb("dd_dump", step, "dump", &top_global, cr, -1, state_local->x.rvec_array(),
+ dd_move_x(dd, state_local->box, state_local->x, nullptr);
+ write_dd_pdb("dd_dump",
+ step,
+ "dump",
+ top_global,
+ cr,
+ -1,
+ state_local->x.rvec_array(),
state_local->box);
}
check_index_consistency(dd, top_global.natoms, "after partitioning");
}
- wallcycle_stop(wcycle, ewcDOMDEC);
+ wallcycle_stop(wcycle, WallCycleCounter::Domdec);
}
-/*! \brief Check whether bonded interactions are missing, if appropriate */
-void checkNumberOfBondedInteractions(const gmx::MDLogger& mdlog,
- t_commrec* cr,
- int totalNumberOfBondedInteractions,
- const gmx_mtop_t* top_global,
- const gmx_localtop_t* top_local,
- gmx::ArrayRef<const gmx::RVec> x,
- const matrix box,
- bool* shouldCheckNumberOfBondedInteractions)
-{
- if (*shouldCheckNumberOfBondedInteractions)
- {
- if (totalNumberOfBondedInteractions != cr->dd->nbonded_global)
- {
- dd_print_missing_interactions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
- top_local, x, box); // Does not return
- }
- *shouldCheckNumberOfBondedInteractions = false;
- }
-}
+} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
struct gmx_ddbox_t;
class MDAtoms;
class MDLogger;
class VirtualSitesHandler;
-} // namespace gmx
//! Check whether the DD grid has moved too far for correctness.
-bool check_grid_jump(int64_t step, const gmx_domdec_t* dd, real cutoff, const gmx_ddbox_t* ddbox, gmx_bool bFatal);
+bool check_grid_jump(int64_t step, const gmx_domdec_t* dd, real cutoff, const gmx_ddbox_t* ddbox, bool bFatal);
/*! \brief Print statistics for domain decomposition communication */
-void print_dd_statistics(const t_commrec* cr, const t_inputrec* ir, FILE* fplog);
+void print_dd_statistics(const t_commrec* cr, const t_inputrec& inputrec, FILE* fplog);
/*! \brief Partition the system over the nodes.
*
* \param[in] nstglobalcomm Will globals be computed on this step
* \param[in] state_global Global state
* \param[in] top_global Global topology
- * \param[in] ir Input record
+ * \param[in] inputrec Input record
* \param[in] imdSession IMD handle
* \param[in] pull_work Pulling data
* \param[in] state_local Local state
const gmx::MDLogger& mdlog,
int64_t step,
const t_commrec* cr,
- gmx_bool bMasterState,
+ bool bMasterState,
int nstglobalcomm,
t_state* state_global,
const gmx_mtop_t& top_global,
- const t_inputrec* ir,
+ const t_inputrec& inputrec,
gmx::ImdSession* imdSession,
pull_t* pull_work,
t_state* state_local,
gmx::Constraints* constr,
t_nrnb* nrnb,
gmx_wallcycle* wcycle,
- gmx_bool bVerbose);
-
-/*! \brief Check whether bonded interactions are missing, if appropriate
- *
- * \param[in] mdlog Logger
- * \param[in] cr Communication object
- * \param[in] totalNumberOfBondedInteractions Result of the global reduction over the number of bonds treated in each domain
- * \param[in] top_global Global topology for the error message
- * \param[in] top_local Local topology for the error message
- * \param[in] x Position vector for the error message
- * \param[in] box Box matrix for the error message
- * \param[in,out] shouldCheckNumberOfBondedInteractions Whether we should do the check. Always set to false.
- */
-void checkNumberOfBondedInteractions(const gmx::MDLogger& mdlog,
- t_commrec* cr,
- int totalNumberOfBondedInteractions,
- const gmx_mtop_t* top_global,
- const gmx_localtop_t* top_local,
- gmx::ArrayRef<const gmx::RVec> x,
- const matrix box,
- bool* shouldCheckNumberOfBondedInteractions);
+ bool bVerbose);
+} // namespace gmx
#endif
* Copyright (c) 2005,2006,2007,2008,2009 by the GROMACS development team.
* Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
* Copyright (c) 2015,2016,2017,2018,2019 by the GROMACS development team.
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
-#include "gromacs/mdlib/nsgrid.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/nblist.h"
#include "gromacs/mdtypes/state.h"
mesg += gmx::formatString(" in direction %c\n", dim2char(dim));
fprintf(fplog, "%s", mesg.c_str());
- fprintf(fplog, "distance out of cell %f\n",
+ fprintf(fplog,
+ "distance out of cell %f\n",
dir == 1 ? pos_d - comm->cell_x1[dim] : pos_d - comm->cell_x0[dim]);
if (bHaveCgcmOld)
{
fprintf(fplog, "Old coordinates: %8.3f %8.3f %8.3f\n", cm_old[XX], cm_old[YY], cm_old[ZZ]);
}
fprintf(fplog, "New coordinates: %8.3f %8.3f %8.3f\n", cm_new[XX], cm_new[YY], cm_new[ZZ]);
- fprintf(fplog, "Old cell boundaries in direction %c: %8.3f %8.3f\n", dim2char(dim),
- comm->old_cell_x0[dim], comm->old_cell_x1[dim]);
- fprintf(fplog, "New cell boundaries in direction %c: %8.3f %8.3f\n", dim2char(dim),
- comm->cell_x0[dim], comm->cell_x1[dim]);
+ fprintf(fplog,
+ "Old cell boundaries in direction %c: %8.3f %8.3f\n",
+ dim2char(dim),
+ comm->old_cell_x0[dim],
+ comm->old_cell_x1[dim]);
+ fprintf(fplog,
+ "New cell boundaries in direction %c: %8.3f %8.3f\n",
+ dim2char(dim),
+ comm->cell_x0[dim],
+ comm->cell_x1[dim]);
}
[[noreturn]] static void cg_move_error(FILE* fplog,
static void rotate_state_atom(t_state* state, int a)
{
- if (state->flags & (1 << estX))
+ if (state->flags & enumValueToBitMask(StateEntry::X))
{
auto x = makeArrayRef(state->x);
/* Rotate the complete state; for a rectangular box only */
x[a][YY] = state->box[YY][YY] - x[a][YY];
x[a][ZZ] = state->box[ZZ][ZZ] - x[a][ZZ];
}
- if (state->flags & (1 << estV))
+ if (state->flags & enumValueToBitMask(StateEntry::V))
{
auto v = makeArrayRef(state->v);
v[a][YY] = -v[a][YY];
v[a][ZZ] = -v[a][ZZ];
}
- if (state->flags & (1 << estCGP))
+ if (state->flags & enumValueToBitMask(StateEntry::Cgp))
{
auto cg_p = makeArrayRef(state->cg_p);
cg_p[a][YY] = -cg_p[a][YY];
{
if (pos_d >= moveLimits.upper[d])
{
- cg_move_error(fplog, dd, step, a, d, 1, false, moveLimits.distance[d],
- cm_new, cm_new, pos_d);
+ cg_move_error(
+ fplog, dd, step, a, d, 1, false, moveLimits.distance[d], cm_new, cm_new, pos_d);
}
dev[d] = 1;
if (dd->ci[d] == dd->numCells[d] - 1)
{
if (pos_d < moveLimits.lower[d])
{
- cg_move_error(fplog, dd, step, a, d, -1, false, moveLimits.distance[d],
- cm_new, cm_new, pos_d);
+ cg_move_error(
+ fplog, dd, step, a, d, -1, false, moveLimits.distance[d], cm_new, cm_new, pos_d);
}
dev[d] = -1;
if (dd->ci[d] == 0)
{
if (pos_d >= moveLimits.upper[d])
{
- cg_move_error(fplog, dd, step, g, d, 1, true, moveLimits.distance[d],
- cogOld, cog, pos_d);
+ cg_move_error(
+ fplog, dd, step, g, d, 1, true, moveLimits.distance[d], cogOld, cog, pos_d);
}
dev[d] = 1;
if (dd->ci[d] == dd->numCells[d] - 1)
{
if (pos_d < moveLimits.lower[d])
{
- cg_move_error(fplog, dd, step, g, d, -1, true, moveLimits.distance[d],
- cogOld, cog, pos_d);
+ cg_move_error(
+ fplog, dd, step, g, d, -1, true, moveLimits.distance[d], cogOld, cog, pos_d);
}
dev[d] = -1;
if (dd->ci[d] == 0)
}
// Positions are always present, so there's nothing to flag
- bool bV = (state->flags & (1 << estV)) != 0;
- bool bCGP = (state->flags & (1 << estCGP)) != 0;
+ bool bV = (state->flags & enumValueToBitMask(StateEntry::V)) != 0;
+ bool bCGP = (state->flags & enumValueToBitMask(StateEntry::Cgp)) != 0;
DDBufferAccess<int> moveBuffer(comm->intBuffer, dd->ncg_home);
gmx::ArrayRef<int> move = moveBuffer.buffer;
matrix tcm;
make_tric_corr_matrix(npbcdim, state->box, tcm);
- const int nthread = gmx_omp_nthreads_get(emntDomdec);
+ const int nthread = gmx_omp_nthreads_get(ModuleMultiThread::Domdec);
/* Compute the center of geometry for all home charge groups
* and put them in the box and determine where they should go.
{
const auto& updateGroupsCog = *comm->updateGroupsCog;
const int numGroups = updateGroupsCog.numCogs();
- calcGroupMove(fplog, step, dd, state, tric_dir, tcm, cell_x0, cell_x1, moveLimits,
- (thread * numGroups) / nthread, ((thread + 1) * numGroups) / nthread,
+ calcGroupMove(fplog,
+ step,
+ dd,
+ state,
+ tric_dir,
+ tcm,
+ cell_x0,
+ cell_x1,
+ moveLimits,
+ (thread * numGroups) / nthread,
+ ((thread + 1) * numGroups) / nthread,
pbcAndFlags);
/* We need a barrier as atoms below can be in a COG of a different thread */
#pragma omp barrier
const int numHomeAtoms = comm->atomRanges.numHomeAtoms();
- applyPbcAndSetMoveFlags(updateGroupsCog, pbcAndFlags, (thread * numHomeAtoms) / nthread,
- ((thread + 1) * numHomeAtoms) / nthread, state->x, move);
+ applyPbcAndSetMoveFlags(updateGroupsCog,
+ pbcAndFlags,
+ (thread * numHomeAtoms) / nthread,
+ ((thread + 1) * numHomeAtoms) / nthread,
+ state->x,
+ move);
}
else
{
/* Here we handle single atoms or charge groups */
- calc_cg_move(fplog, step, dd, state, tric_dir, tcm, cell_x0, cell_x1, moveLimits,
+ calc_cg_move(fplog,
+ step,
+ dd,
+ state,
+ tric_dir,
+ tcm,
+ cell_x0,
+ cell_x1,
+ moveLimits,
(thread * dd->ncg_home) / nthread,
- ((thread + 1) * dd->ncg_home) / nthread, move);
+ ((thread + 1) * dd->ncg_home) / nthread,
+ move);
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
flagBuffer.resize((ncg_recv + rbuf[0]) * DD_CGIBS);
/* Communicate the charge group indices, sizes and flags */
- ddSendrecv(dd, d, dir, comm->cggl_flag[cdd].data(), sbuf[0] * DD_CGIBS,
- flagBuffer.buffer.data() + ncg_recv * DD_CGIBS, rbuf[0] * DD_CGIBS);
+ ddSendrecv(dd,
+ d,
+ dir,
+ comm->cggl_flag[cdd].data(),
+ sbuf[0] * DD_CGIBS,
+ flagBuffer.buffer.data() + ncg_recv * DD_CGIBS,
+ rbuf[0] * DD_CGIBS);
const int nvs = ncg[cdd] + nat[cdd] * nvec;
const int i = rbuf[0] + rbuf[1] * nvec;
rvecBuffer.resize(nvr + i);
/* Communicate cgcm and state */
- ddSendrecv(dd, d, dir, as_rvec_array(comm->cgcm_state[cdd].data()), nvs,
- as_rvec_array(rvecBuffer.buffer.data()) + nvr, i);
+ ddSendrecv(dd,
+ d,
+ dir,
+ as_rvec_array(comm->cgcm_state[cdd].data()),
+ nvs,
+ as_rvec_array(rvecBuffer.buffer.data()) + nvr,
+ i);
ncg_recv += rbuf[0];
nvr += i;
}
|| ((flag & DD_FLAG_BW(d)) && cog[dim] < cell_x0[dim]))
{
rvec pos = { cog[0], cog[1], cog[2] };
- cg_move_error(fplog, dd, step, cg, dim, (flag & DD_FLAG_FW(d)) ? 1 : 0, false,
- 0, pos, pos, pos[dim]);
+ cg_move_error(
+ fplog, dd, step, cg, dim, (flag & DD_FLAG_FW(d)) ? 1 : 0, false, 0, pos, pos, pos[dim]);
}
}
}
/* Copy from the receive to the send buffers */
memcpy(comm->cggl_flag[mc].data() + ncg[mc] * DD_CGIBS,
- flagBuffer.buffer.data() + cg * DD_CGIBS, DD_CGIBS * sizeof(int));
- memcpy(comm->cgcm_state[mc][nvr], rvecBuffer.buffer.data() + buf_pos,
+ flagBuffer.buffer.data() + cg * DD_CGIBS,
+ DD_CGIBS * sizeof(int));
+ memcpy(comm->cgcm_state[mc][nvr],
+ rvecBuffer.buffer.data() + buf_pos,
(1 + nrcg * nvec) * sizeof(rvec));
buf_pos += 1 + nrcg * nvec;
ncg[mc] += 1;
if (debug)
{
- fprintf(debug, "Finished repartitioning: cgs moved out %d, new home %d\n", *ncg_moved,
+ fprintf(debug,
+ "Finished repartitioning: cgs moved out %d, new home %d\n",
+ *ncg_moved,
dd->ncg_home - *ncg_moved);
}
}
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
{
for (int pulse = 0; pulse < dd->comm->cd[d].numPulses(); pulse++)
{
- gpuHaloExchange[d].push_back(GpuHaloExchange(dd, d, MPI_COMM_WORLD, deviceContext,
- deviceStream, deviceStream, pulse, nullptr));
+ gpuHaloExchange[d].push_back(GpuHaloExchange(
+ dd, d, MPI_COMM_WORLD, deviceContext, deviceStream, deviceStream, pulse, nullptr));
}
}
haloCompletedEvent.waitForEvent();
// Copy results back to host
- copyFromDeviceBuffer(h_x->data(), &d_x, 0, numAtomsTotal, deviceStream,
- GpuApiCallBehavior::Sync, nullptr);
+ copyFromDeviceBuffer(
+ h_x->data(), &d_x, 0, numAtomsTotal, deviceStream, GpuApiCallBehavior::Sync, nullptr);
freeDeviceBuffer(d_x);
#else
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+add_library(essentialdynamics INTERFACE)
+
file(GLOB ESSENTIALDYNAMICS_SOURCES *.cpp)
+
+# Source files have the following private module dependencies.
+target_link_libraries(essentialdynamics PRIVATE
+ # gmxlib
+ # math
+ # mdtypes
+ # tng_io
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(essentialdynamics PUBLIC
+target_include_directories(essentialdynamics INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(essentialdynamics PUBLIC
+target_link_libraries(essentialdynamics INTERFACE
+ legacy_api
+ )
+
+# TODO: when fileio is an OBJECT target
+#target_link_libraries(fileio PUBLIC legacy_api)
+#target_link_libraries(fileio PRIVATE common)
+
+# Module dependencies
+# fileio interfaces convey transitive dependence on these modules.
+#target_link_libraries(essentialdynamics PUBLIC
+target_link_libraries(essentialdynamics INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(essentialdynamics PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(essentialdynamics PRIVATE legacy_modules)
+
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${ESSENTIALDYNAMICS_SOURCES} PARENT_SCOPE)
if (BUILD_TESTING)
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/linearalgebra/nrjac.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
rad += gmx::square((vec.refproj[i] - vec.xproj[i]));
}
- return rad = sqrt(rad);
+ return sqrt(rad);
}
} // namespace
}
-static void do_single_flood(FILE* edo,
- const rvec x[],
- rvec force[],
- t_edpar* edi,
- int64_t step,
- const matrix box,
- const t_commrec* cr,
- gmx_bool bNS) /* Are we in a neighbor searching step? */
+static void do_single_flood(FILE* edo,
+ gmx::ArrayRef<const gmx::RVec> coords,
+ gmx::ArrayRef<gmx::RVec> force,
+ t_edpar* edi,
+ int64_t step,
+ const matrix box,
+ const t_commrec* cr,
+ gmx_bool bNS) /* Are we in a neighbor searching step? */
{
int i;
matrix rotmat; /* rotation matrix */
/* Broadcast the positions of the AVERAGE structure such that they are known on
* every processor. Each node contributes its local positions x and stores them in
* the collective ED array buf->xcoll */
- communicate_group_positions(cr, buf->xcoll, buf->shifts_xcoll, buf->extra_shifts_xcoll, bNS, x,
- edi->sav.nr, edi->sav.nr_loc, edi->sav.anrs_loc, edi->sav.c_ind,
- edi->sav.x_old, box);
+ communicate_group_positions(cr,
+ buf->xcoll,
+ buf->shifts_xcoll,
+ buf->extra_shifts_xcoll,
+ bNS,
+ as_rvec_array(coords.data()),
+ edi->sav.nr,
+ edi->sav.nr_loc,
+ edi->sav.anrs_loc,
+ edi->sav.c_ind,
+ edi->sav.x_old,
+ box);
/* Only assembly REFERENCE positions if their indices differ from the average ones */
if (!edi->bRefEqAv)
{
- communicate_group_positions(cr, buf->xc_ref, buf->shifts_xc_ref, buf->extra_shifts_xc_ref,
- bNS, x, edi->sref.nr, edi->sref.nr_loc, edi->sref.anrs_loc,
- edi->sref.c_ind, edi->sref.x_old, box);
+ communicate_group_positions(cr,
+ buf->xc_ref,
+ buf->shifts_xc_ref,
+ buf->extra_shifts_xc_ref,
+ bNS,
+ as_rvec_array(coords.data()),
+ edi->sref.nr,
+ edi->sref.nr_loc,
+ edi->sref.anrs_loc,
+ edi->sref.c_ind,
+ edi->sref.x_old,
+ box);
}
/* If bUpdateShifts was TRUE, the shifts have just been updated in get_positions.
/* Main flooding routine, called from do_force */
-extern void do_flood(const t_commrec* cr,
- const t_inputrec* ir,
- const rvec x[],
- rvec force[],
- gmx_edsam* ed,
- const matrix box,
- int64_t step,
- gmx_bool bNS)
+void do_flood(const t_commrec* cr,
+ const t_inputrec& ir,
+ gmx::ArrayRef<const gmx::RVec> coords,
+ gmx::ArrayRef<gmx::RVec> force,
+ gmx_edsam* ed,
+ const matrix box,
+ int64_t step,
+ bool bNS)
{
/* Write time to edo, when required. Output the time anyhow since we need
* it in the output file for ED constraints. */
if (MASTER(cr) && do_per_step(step, ed->edpar.begin()->outfrq))
{
- fprintf(ed->edo, "\n%12f", ir->init_t + step * ir->delta_t);
+ fprintf(ed->edo, "\n%12f", ir.init_t + step * ir.delta_t);
}
if (ed->eEDtype != EssentialDynamicsType::Flooding)
/* Call flooding for one matrix */
if (edi.flood.vecs.neig)
{
- do_single_flood(ed->edo, x, force, &edi, step, box, cr, bNS);
+ do_single_flood(ed->edo, coords, force, &edi, step, box, cr, bNS);
}
}
}
/* If in any of the ED groups we find a flooding vector, flooding is turned on */
ed->eEDtype = EssentialDynamicsType::Flooding;
- fprintf(stderr, "ED: Flooding %d eigenvector%s.\n", edi->flood.vecs.neig,
+ fprintf(stderr,
+ "ED: Flooding %d eigenvector%s.\n",
+ edi->flood.vecs.neig,
edi->flood.vecs.neig > 1 ? "s" : "");
if (edi->flood.bConstForce)
{
edi->flood.vecs.fproj[i] = edi->flood.vecs.stpsz[i];
- fprintf(stderr, "ED: applying on eigenvector %d a constant force of %g\n",
- edi->flood.vecs.ieig[i], edi->flood.vecs.fproj[i]);
+ fprintf(stderr,
+ "ED: applying on eigenvector %d a constant force of %g\n",
+ edi->flood.vecs.ieig[i],
+ edi->flood.vecs.fproj[i]);
}
}
}
const gmx_output_env_t* oenv,
const t_commrec* cr)
{
- auto edHandle = std::make_unique<gmx::EssentialDynamics>();
- auto ed = edHandle->getLegacyED();
+ auto edHandle = std::make_unique<gmx::EssentialDynamics>();
+ auto* ed = edHandle->getLegacyED();
/* We want to perform ED (this switch might later be upgraded to EssentialDynamicsType::Flooding) */
ed->eEDtype = EssentialDynamicsType::EDSampling;
}
else
{
- ed->edo = xvgropen(edoFileName, "Essential dynamics / flooding output", "Time (ps)",
- "RMSDs (nm), projections on EVs (nm), ...", oenv);
+ ed->edo = xvgropen(edoFileName,
+ "Essential dynamics / flooding output",
+ "Time (ps)",
+ "RMSDs (nm), projections on EVs (nm), ...",
+ oenv);
/* Make a descriptive legend */
write_edo_legend(ed, EDstate->nED, oenv);
* There, also memory is allocated */
s->nalloc_loc = 0; /* allocation size of s->anrs_loc */
snew_bc(MASTER(cr), s->x_old, s->nr); /* To be able to always make the ED molecule whole, ... */
- nblock_bc(cr->mpi_comm_mygroup, s->nr,
- s->x_old); /* ... keep track of shift changes with the help of old coords */
+ nblock_bc(cr->mpi_comm_mygroup, s->nr, s->x_old); /* ... keep track of shift changes with the help of old coords */
}
/* broadcast masses for the reference structure (for mass-weighted fitting) */
block_bc(cr->mpi_comm_mygroup, edi);
/* Broadcast positions */
- bc_ed_positions(cr, &(edi.sref),
- EssentialDynamicsStructure::Reference); /* reference positions (don't broadcast masses) */
- bc_ed_positions(cr, &(edi.sav),
- EssentialDynamicsStructure::Average); /* average positions (do broadcast masses as well) */
+ bc_ed_positions(cr, &(edi.sref), EssentialDynamicsStructure::Reference); /* reference positions (don't broadcast masses) */
+ bc_ed_positions(cr, &(edi.sav), EssentialDynamicsStructure::Average); /* average positions (do broadcast masses as well) */
bc_ed_positions(cr, &(edi.star), EssentialDynamicsStructure::Target); /* target positions */
bc_ed_positions(cr, &(edi.sori), EssentialDynamicsStructure::Origin); /* origin positions */
/* init-routine called for every *.edi-cycle, initialises t_edpar structure */
-static void init_edi(const gmx_mtop_t* mtop, t_edpar* edi)
+static void init_edi(const gmx_mtop_t& mtop, t_edpar* edi)
{
int i;
real totalmass = 0.0;
">0.\n"
"Either make the covariance analysis non-mass-weighted, or exclude massless\n"
"atoms from the reference structure by creating a proper index group.\n",
- i, edi->sref.anrs[i] + 1, edi->sref.m[i]);
+ i,
+ edi->sref.anrs[i] + 1,
+ edi->sref.m[i]);
}
totalmass += edi->sref.m[i];
">0.\n"
"Either make the covariance analysis non-mass-weighted, or exclude massless\n"
"atoms from the average structure by creating a proper index group.\n",
- i, edi->sav.anrs[i] + 1, edi->sav.m[i]);
+ i,
+ edi->sav.anrs[i] + 1,
+ edi->sav.m[i]);
}
}
gmx_fatal(FARGS,
"Could not find input parameter %s at expected position in edsam input-file "
"(.edi)\nline read instead is %s",
- label, line);
+ label,
+ line);
}
}
double stepSize = 0.;
double referenceProjection = 0.;
double referenceSlope = 0.;
- const int nscan = sscanf(line, max_ev_fmt_dlflflf, &numEigenVectors, &stepSize,
- &referenceProjection, &referenceSlope);
+ const int nscan = sscanf(
+ line, max_ev_fmt_dlflflf, &numEigenVectors, &stepSize, &referenceProjection, &referenceSlope);
/* Zero out values which were not scanned */
switch (nscan)
{
edi.nini = read_edint(in, &bEOF);
if (edi.nini != nr_mdatoms)
{
- gmx_fatal(FARGS, "Nr of atoms in %s (%d) does not match nr of md atoms (%d)", fn, edi.nini,
- nr_mdatoms);
+ gmx_fatal(FARGS, "Nr of atoms in %s (%d) does not match nr of md atoms (%d)", fn, edi.nini, nr_mdatoms);
}
/* Done checking. For the rest we blindly trust the input */
bool bHaveReference = false;
if (edi.flood.bHarmonic)
{
- bHaveReference = readEdVecWithReferenceProjection(in, edi.sav.nr, &edi.flood.vecs,
+ bHaveReference = readEdVecWithReferenceProjection(in,
+ edi.sav.nr,
+ &edi.flood.vecs,
&edi.flood.initialReferenceProjection,
&edi.flood.referenceProjectionSlope);
}
gmx_fatal(FARGS, "No complete ED data set found in edi file %s.", fn);
}
- fprintf(stderr, "ED: Found %zu ED group%s.\n", essentialDynamicsParameters.size(),
+ fprintf(stderr,
+ "ED: Found %zu ED group%s.\n",
+ essentialDynamicsParameters.size(),
essentialDynamicsParameters.size() > 1 ? "s" : "");
/* Close the .edi file again */
* if their indices differ from the average ones */
if (!edi.bRefEqAv)
{
- dd_make_local_group_indices(dd->ga2la, edi.sref.nr, edi.sref.anrs, &edi.sref.nr_loc,
- &edi.sref.anrs_loc, &edi.sref.nalloc_loc, edi.sref.c_ind);
+ dd_make_local_group_indices(dd->ga2la,
+ edi.sref.nr,
+ edi.sref.anrs,
+ &edi.sref.nr_loc,
+ &edi.sref.anrs_loc,
+ &edi.sref.nalloc_loc,
+ edi.sref.c_ind);
}
/* Local atoms of the average structure (on these ED will be performed) */
- dd_make_local_group_indices(dd->ga2la, edi.sav.nr, edi.sav.anrs, &edi.sav.nr_loc,
- &edi.sav.anrs_loc, &edi.sav.nalloc_loc, edi.sav.c_ind);
+ dd_make_local_group_indices(dd->ga2la,
+ edi.sav.nr,
+ edi.sav.anrs,
+ &edi.sav.nr_loc,
+ &edi.sav.anrs_loc,
+ &edi.sav.nalloc_loc,
+ edi.sav.c_ind);
/* Indicate that the ED shift vectors for this structure need to be updated
* at the next call to communicate_group_positions, since obviously we are in a NS step */
gmx_fatal(FARGS,
"The number of reference structure atoms in ED group %c is\n"
"not the same in .cpt (NREF=%d) and .edi (NREF=%d) files!\n",
- get_EDgroupChar(edinum + 1, 0), EDstate->nref[edinum], ed.edpar[edinum].sref.nr);
+ get_EDgroupChar(edinum + 1, 0),
+ EDstate->nref[edinum],
+ ed.edpar[edinum].sref.nr);
}
if (EDstate->nav[edinum] != ed.edpar[edinum].sav.nr)
{
gmx_fatal(FARGS,
"The number of average structure atoms in ED group %c is\n"
"not the same in .cpt (NREF=%d) and .edi (NREF=%d) files!\n",
- get_EDgroupChar(edinum + 1, 0), EDstate->nav[edinum], ed.edpar[edinum].sav.nr);
+ get_EDgroupChar(edinum + 1, 0),
+ EDstate->nav[edinum],
+ ed.edpar[edinum].sav.nr);
}
}
"The number of essential dynamics / flooding groups is not consistent.\n"
"There are %d ED groups in the .cpt file, but %zu in the .edi file!\n"
"Are you sure this is the correct .edi file?\n",
- EDstate->nED, ed.edpar.size());
+ EDstate->nED,
+ ed.edpar.size());
}
}
auto edi = ed->edpar.begin();
- fprintf(ed->edo, "# Output will be written every %d step%s\n", edi->outfrq,
- edi->outfrq != 1 ? "s" : "");
+ fprintf(ed->edo, "# Output will be written every %d step%s\n", edi->outfrq, edi->outfrq != 1 ? "s" : "");
for (nr_edi = 1; nr_edi <= nED; nr_edi++)
{
fprintf(ed->edo, "#\n");
- fprintf(ed->edo, "# Summary of applied con/restraints for the ED group %c\n",
+ fprintf(ed->edo,
+ "# Summary of applied con/restraints for the ED group %c\n",
get_EDgroupChar(nr_edi, nED));
fprintf(ed->edo, "# Atoms in average structure: %d\n", edi->sav.nr);
- fprintf(ed->edo, "# monitor : %d vec%s\n", edi->vecs.mon.neig,
- edi->vecs.mon.neig != 1 ? "s" : "");
- fprintf(ed->edo, "# LINFIX : %d vec%s\n", edi->vecs.linfix.neig,
+ fprintf(ed->edo, "# monitor : %d vec%s\n", edi->vecs.mon.neig, edi->vecs.mon.neig != 1 ? "s" : "");
+ fprintf(ed->edo,
+ "# LINFIX : %d vec%s\n",
+ edi->vecs.linfix.neig,
edi->vecs.linfix.neig != 1 ? "s" : "");
- fprintf(ed->edo, "# LINACC : %d vec%s\n", edi->vecs.linacc.neig,
+ fprintf(ed->edo,
+ "# LINACC : %d vec%s\n",
+ edi->vecs.linacc.neig,
edi->vecs.linacc.neig != 1 ? "s" : "");
- fprintf(ed->edo, "# RADFIX : %d vec%s\n", edi->vecs.radfix.neig,
+ fprintf(ed->edo,
+ "# RADFIX : %d vec%s\n",
+ edi->vecs.radfix.neig,
edi->vecs.radfix.neig != 1 ? "s" : "");
- fprintf(ed->edo, "# RADACC : %d vec%s\n", edi->vecs.radacc.neig,
+ fprintf(ed->edo,
+ "# RADACC : %d vec%s\n",
+ edi->vecs.radacc.neig,
edi->vecs.radacc.neig != 1 ? "s" : "");
- fprintf(ed->edo, "# RADCON : %d vec%s\n", edi->vecs.radcon.neig,
+ fprintf(ed->edo,
+ "# RADCON : %d vec%s\n",
+ edi->vecs.radcon.neig,
edi->vecs.radcon.neig != 1 ? "s" : "");
- fprintf(ed->edo, "# FLOODING : %d vec%s ", edi->flood.vecs.neig,
- edi->flood.vecs.neig != 1 ? "s" : "");
+ fprintf(ed->edo, "# FLOODING : %d vec%s ", edi->flood.vecs.neig, edi->flood.vecs.neig != 1 ? "s" : "");
if (edi->flood.vecs.neig)
{
nice_legend(&setname, &nsets, &LegendStr, "RMSD to ref", "nm", get_EDgroupChar(nr_edi, nED));
/* Essential dynamics, projections on eigenvectors */
- nice_legend_evec(&setname, &nsets, &LegendStr, &edi->vecs.mon,
- get_EDgroupChar(nr_edi, nED), "MON");
- nice_legend_evec(&setname, &nsets, &LegendStr, &edi->vecs.linfix,
- get_EDgroupChar(nr_edi, nED), "LINFIX");
- nice_legend_evec(&setname, &nsets, &LegendStr, &edi->vecs.linacc,
- get_EDgroupChar(nr_edi, nED), "LINACC");
- nice_legend_evec(&setname, &nsets, &LegendStr, &edi->vecs.radfix,
- get_EDgroupChar(nr_edi, nED), "RADFIX");
+ nice_legend_evec(&setname,
+ &nsets,
+ &LegendStr,
+ &edi->vecs.mon,
+ get_EDgroupChar(nr_edi, nED),
+ "MON");
+ nice_legend_evec(&setname,
+ &nsets,
+ &LegendStr,
+ &edi->vecs.linfix,
+ get_EDgroupChar(nr_edi, nED),
+ "LINFIX");
+ nice_legend_evec(&setname,
+ &nsets,
+ &LegendStr,
+ &edi->vecs.linacc,
+ get_EDgroupChar(nr_edi, nED),
+ "LINACC");
+ nice_legend_evec(&setname,
+ &nsets,
+ &LegendStr,
+ &edi->vecs.radfix,
+ get_EDgroupChar(nr_edi, nED),
+ "RADFIX");
if (edi->vecs.radfix.neig)
{
- nice_legend(&setname, &nsets, &LegendStr, "RADFIX radius", "nm",
- get_EDgroupChar(nr_edi, nED));
+ nice_legend(&setname, &nsets, &LegendStr, "RADFIX radius", "nm", get_EDgroupChar(nr_edi, nED));
}
- nice_legend_evec(&setname, &nsets, &LegendStr, &edi->vecs.radacc,
- get_EDgroupChar(nr_edi, nED), "RADACC");
+ nice_legend_evec(&setname,
+ &nsets,
+ &LegendStr,
+ &edi->vecs.radacc,
+ get_EDgroupChar(nr_edi, nED),
+ "RADACC");
if (edi->vecs.radacc.neig)
{
- nice_legend(&setname, &nsets, &LegendStr, "RADACC radius", "nm",
- get_EDgroupChar(nr_edi, nED));
+ nice_legend(&setname, &nsets, &LegendStr, "RADACC radius", "nm", get_EDgroupChar(nr_edi, nED));
}
- nice_legend_evec(&setname, &nsets, &LegendStr, &edi->vecs.radcon,
- get_EDgroupChar(nr_edi, nED), "RADCON");
+ nice_legend_evec(&setname,
+ &nsets,
+ &LegendStr,
+ &edi->vecs.radcon,
+ get_EDgroupChar(nr_edi, nED),
+ "RADCON");
if (edi->vecs.radcon.neig)
{
- nice_legend(&setname, &nsets, &LegendStr, "RADCON radius", "nm",
- get_EDgroupChar(nr_edi, nED));
+ nice_legend(&setname, &nsets, &LegendStr, "RADCON radius", "nm", get_EDgroupChar(nr_edi, nED));
}
}
++edi;
fprintf(ed->edo,
"#\n"
"# Legend for %d column%s of flooding plus %d column%s of essential dynamics data:\n",
- n_flood, 1 == n_flood ? "" : "s", n_edsam, 1 == n_edsam ? "" : "s");
+ n_flood,
+ 1 == n_flood ? "" : "s",
+ n_edsam,
+ 1 == n_edsam ? "" : "s");
fprintf(ed->edo, "%s", LegendStr);
sfree(LegendStr);
std::unique_ptr<gmx::EssentialDynamics> init_edsam(const gmx::MDLogger& mdlog,
const char* ediFileName,
const char* edoFileName,
- const gmx_mtop_t* mtop,
- const t_inputrec* ir,
+ const gmx_mtop_t& mtop,
+ const t_inputrec& ir,
const t_commrec* cr,
gmx::Constraints* constr,
const t_state* globalState,
"gmx grompp and the related .mdp options may change also.");
/* Open input and output files, allocate space for ED data structure */
- auto edHandle = ed_open(mtop->natoms, oh, ediFileName, edoFileName, startingBehavior, oenv, cr);
- auto ed = edHandle->getLegacyED();
+ auto edHandle = ed_open(mtop.natoms, oh, ediFileName, edoFileName, startingBehavior, oenv, cr);
+ auto* ed = edHandle->getLegacyED();
GMX_RELEASE_ASSERT(constr != nullptr, "Must have valid constraints object");
constr->saveEdsamPointer(ed);
for (auto& edi : ed->edpar)
{
init_edi(mtop, &edi);
- init_flood(&edi, ed, ir->delta_t);
+ init_flood(&edi, ed, ir.delta_t);
}
}
if (!EDstate->bFromCpt)
{
/* Remove PBC, make molecule(s) subject to ED whole. */
- snew(x_pbc, mtop->natoms);
- copy_rvecn(globalState->x.rvec_array(), x_pbc, 0, mtop->natoms);
- do_pbc_first_mtop(nullptr, ir->pbcType, globalState->box, mtop, x_pbc);
+ snew(x_pbc, mtop.natoms);
+ copy_rvecn(globalState->x.rvec_array(), x_pbc, 0, mtop.natoms);
+ do_pbc_first_mtop(nullptr, ir.pbcType, globalState->box, &mtop, x_pbc);
}
/* Reset pointer to first ED data set which contains the actual ED data */
auto edi = ed->edpar.begin();
/* Output how well we fit to the reference at the start */
translate_and_rotate(xfit, edi->sref.nr, fit_transvec, fit_rotmat);
- fprintf(stderr, "ED: Initial RMSD from reference after fit = %f nm",
+ fprintf(stderr,
+ "ED: Initial RMSD from reference after fit = %f nm",
rmsd_from_structure(xfit, &edi->sref));
if (EDstate->nED > 1)
{
{
for (i = 0; i < edi->flood.vecs.neig; i++)
{
- fprintf(stdout, "ED: EV %d flooding potential center: %11.4e",
- edi->flood.vecs.ieig[i], edi->flood.vecs.refproj[i]);
+ fprintf(stdout,
+ "ED: EV %d flooding potential center: %11.4e",
+ edi->flood.vecs.ieig[i],
+ edi->flood.vecs.refproj[i]);
if (edi->flood.bHarmonic)
{
- fprintf(stdout, " (adding %11.4e/timestep)",
- edi->flood.referenceProjectionSlope[i]);
+ fprintf(stdout, " (adding %11.4e/timestep)", edi->flood.referenceProjectionSlope[i]);
}
fprintf(stdout, "\n");
}
}
-void do_edsam(const t_inputrec* ir, int64_t step, const t_commrec* cr, rvec xs[], rvec v[], const matrix box, gmx_edsam* ed)
+void do_edsam(const t_inputrec* ir,
+ int64_t step,
+ const t_commrec* cr,
+ gmx::ArrayRef<gmx::RVec> coords,
+ gmx::ArrayRef<gmx::RVec> velocities,
+ const matrix box,
+ gmx_edsam* ed)
{
int i, edinr, iupdate = 500;
matrix rotmat; /* rotation matrix */
* the collective buf->xcoll array. Note that for edinr > 1
* xs could already have been modified by an earlier ED */
- communicate_group_positions(cr, buf->xcoll, buf->shifts_xcoll, buf->extra_shifts_xcoll,
- PAR(cr) ? buf->bUpdateShifts : TRUE, xs, edi.sav.nr, edi.sav.nr_loc,
- edi.sav.anrs_loc, edi.sav.c_ind, edi.sav.x_old, box);
+ communicate_group_positions(cr,
+ buf->xcoll,
+ buf->shifts_xcoll,
+ buf->extra_shifts_xcoll,
+ PAR(cr) ? buf->bUpdateShifts : TRUE,
+ as_rvec_array(coords.data()),
+ edi.sav.nr,
+ edi.sav.nr_loc,
+ edi.sav.anrs_loc,
+ edi.sav.c_ind,
+ edi.sav.x_old,
+ box);
/* Only assembly reference positions if their indices differ from the average ones */
if (!edi.bRefEqAv)
{
- communicate_group_positions(
- cr, buf->xc_ref, buf->shifts_xc_ref, buf->extra_shifts_xc_ref,
- PAR(cr) ? buf->bUpdateShifts : TRUE, xs, edi.sref.nr, edi.sref.nr_loc,
- edi.sref.anrs_loc, edi.sref.c_ind, edi.sref.x_old, box);
+ communicate_group_positions(cr,
+ buf->xc_ref,
+ buf->shifts_xc_ref,
+ buf->extra_shifts_xc_ref,
+ PAR(cr) ? buf->bUpdateShifts : TRUE,
+ as_rvec_array(coords.data()),
+ edi.sref.nr,
+ edi.sref.nr_loc,
+ edi.sref.anrs_loc,
+ edi.sref.c_ind,
+ edi.sref.x_old,
+ box);
}
/* If bUpdateShifts was TRUE then the shifts have just been updated in communicate_group_positions.
for (i = 0; i < edi.sav.nr_loc; i++)
{
/* Unshift local ED coordinate and store in x_unsh */
- ed_unshift_single_coord(box, buf->xcoll[edi.sav.c_ind[i]],
- buf->shifts_xcoll[edi.sav.c_ind[i]], x_unsh);
+ ed_unshift_single_coord(
+ box, buf->xcoll[edi.sav.c_ind[i]], buf->shifts_xcoll[edi.sav.c_ind[i]], x_unsh);
/* dx is the ED correction to the positions: */
- rvec_sub(x_unsh, xs[edi.sav.anrs_loc[i]], dx);
+ rvec_sub(x_unsh, coords[edi.sav.anrs_loc[i]], dx);
- if (v != nullptr)
+ if (!velocities.empty())
{
/* dv is the ED correction to the velocity: */
svmul(dt_1, dx, dv);
/* apply the velocity correction: */
- rvec_inc(v[edi.sav.anrs_loc[i]], dv);
+ rvec_inc(velocities[edi.sav.anrs_loc[i]], dv);
}
/* Finally apply the position correction due to ED: */
- copy_rvec(x_unsh, xs[edi.sav.anrs_loc[i]]);
+ copy_rvec(x_unsh, coords[edi.sav.anrs_loc[i]]);
}
}
} /* END of if ( bNeedDoEdsam(edi) ) */
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <memory>
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/classhelpers.h"
/*! \brief Abstract type for essential dynamics
*
{
enum class StartingBehavior;
class Constraints;
+template<typename>
+class ArrayRef;
+
class EssentialDynamics
{
public:
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
class MDLogger;
} // namespace gmx
* \param ir MD input parameter record.
* \param step Number of the time step.
* \param cr Data needed for MPI communication.
- * \param xs The local positions on this processor.
- * \param v The local velocities.
+ * \param coords The local positions on this processor.
+ * \param velocities The local velocities.
* \param box The simulation box.
* \param ed The essential dynamics data.
*/
-void do_edsam(const t_inputrec* ir,
- int64_t step,
- const t_commrec* cr,
- rvec xs[],
- rvec v[],
- const matrix box,
- gmx_edsam* ed);
+void do_edsam(const t_inputrec* ir,
+ int64_t step,
+ const t_commrec* cr,
+ gmx::ArrayRef<gmx::RVec> coords,
+ gmx::ArrayRef<gmx::RVec> velocities,
+ const matrix box,
+ gmx_edsam* ed);
/*! \brief Initializes the essential dynamics and flooding module.
std::unique_ptr<gmx::EssentialDynamics> init_edsam(const gmx::MDLogger& mdlog,
const char* ediFileName,
const char* edoFileName,
- const gmx_mtop_t* mtop,
- const t_inputrec* ir,
+ const gmx_mtop_t& mtop,
+ const t_inputrec& ir,
const t_commrec* cr,
gmx::Constraints* constr,
const t_state* globalState,
*
* \param cr Data needed for MPI communication.
* \param ir MD input parameter record.
- * \param x Positions on the local processor.
+ * \param coords Positions on the local processor.
* \param force Forcefield forces to which the flooding forces are added.
* \param ed The essential dynamics data.
* \param box The simulation box.
* \param step Number of the time step.
* \param bNS Are we in a neighbor searching step?
*/
-void do_flood(const t_commrec* cr,
- const t_inputrec* ir,
- const rvec x[],
- rvec force[],
- gmx_edsam* ed,
- const matrix box,
- int64_t step,
- gmx_bool bNS);
+void do_flood(const t_commrec* cr,
+ const t_inputrec& ir,
+ gmx::ArrayRef<const gmx::RVec> coords,
+ gmx::ArrayRef<gmx::RVec> force,
+ gmx_edsam* ed,
+ const matrix box,
+ int64_t step,
+ bool bNS);
#endif
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
-# Copyright (c) 2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(ewald INTERFACE)
gmx_add_libgromacs_sources(
calculate_spline_moduli.cpp
ewald.cpp
# Must add these files so they can include device_information.h
pme_gpu_internal.cpp
pme_gpu_timings.cpp
- )
+ )
elseif (GMX_GPU_OPENCL)
gmx_add_libgromacs_sources(
# OpenCL-specific sources
elseif (GMX_GPU_SYCL)
# SYCL-TODO: proper implementation
gmx_add_libgromacs_sources(
- pme_gpu_program_impl.cpp
+ # Files that implement stubs
+ pme_gpu_sycl_stubs.cpp
+ # GPU-specific sources
+ pme_gpu.cpp
+ pme_gpu_internal.cpp
+ pme_gpu_timings.cpp
)
_gmx_add_files_to_property(SYCL_SOURCES
- pme_gpu_program_impl.cpp
+ pme_gpu_internal.cpp
pme_gpu_program.cpp
+ pme_gpu_sycl_stubs.cpp
+ pme_gpu_timings.cpp
)
else()
gmx_add_libgromacs_sources(
)
endif()
+# Source files have the following private module dependencies.
+target_link_libraries(ewald PRIVATE
+ # gmxlib
+ # math
+ # mdtypes
+ # tng_io
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(ewald PUBLIC
+target_include_directories(ewald INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(ewald PUBLIC
+target_link_libraries(ewald INTERFACE
+ legacy_api
+ )
+
+# TODO: when fileio is an OBJECT target
+#target_link_libraries(ewald PUBLIC legacy_api)
+#target_link_libraries(ewald PRIVATE common)
+
+# Module dependencies
+# This module convey transitive dependence on these modules.
+#target_link_libraries(ewald PUBLIC
+target_link_libraries(ewald INTERFACE
+ # utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(ewald PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(ewald PRIVATE legacy_modules)
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <algorithm>
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/utility/exceptions.h"
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-struct gmx_ewald_tab_t
-{
- int nx, ny, nz, kmax;
- cvec** eir;
- t_complex *tab_xy, *tab_qxyz;
-};
+using cvec = std::array<t_complex, DIM>;
-void init_ewald_tab(struct gmx_ewald_tab_t** et, const t_inputrec* ir, FILE* fp)
+gmx_ewald_tab_t::gmx_ewald_tab_t(const t_inputrec& ir, FILE* fp)
{
- snew(*et, 1);
if (fp)
{
fprintf(fp, "Will do ordinary reciprocal space Ewald sum.\n");
}
- (*et)->nx = ir->nkx + 1;
- (*et)->ny = ir->nky + 1;
- (*et)->nz = ir->nkz + 1;
- (*et)->kmax = std::max((*et)->nx, std::max((*et)->ny, (*et)->nz));
- (*et)->eir = nullptr;
- (*et)->tab_xy = nullptr;
- (*et)->tab_qxyz = nullptr;
+ nx = ir.nkx + 1;
+ ny = ir.nky + 1;
+ nz = ir.nkz + 1;
+ kmax = std::max(nx, std::max(ny, nz));
}
+gmx_ewald_tab_t::~gmx_ewald_tab_t() = default;
+
//! Calculates wave vectors.
static void calc_lll(const rvec box, rvec lll)
{
}
//! Make tables for the structure factor parts
-static void tabulateStructureFactors(int natom, const rvec x[], int kmax, cvec** eir, const rvec lll)
+static void tabulateStructureFactors(int natom, gmx::ArrayRef<const gmx::RVec> x, int kmax, cvec** eir, const rvec lll)
{
int i, j, m;
}
}
-real do_ewald(const t_inputrec* ir,
- const rvec x[],
- rvec f[],
- const real chargeA[],
- const real chargeB[],
- const matrix box,
- const t_commrec* cr,
- int natoms,
- matrix lrvir,
- real ewaldcoeff,
- real lambda,
- real* dvdlambda,
- gmx_ewald_tab_t* et)
+real do_ewald(const t_inputrec& ir,
+ gmx::ArrayRef<const gmx::RVec> x,
+ gmx::ArrayRef<gmx::RVec> f,
+ gmx::ArrayRef<const real> chargeA,
+ gmx::ArrayRef<const real> chargeB,
+ const matrix box,
+ const t_commrec* cr,
+ int natoms,
+ matrix lrvir,
+ real ewaldcoeff,
+ real lambda,
+ real* dvdlambda,
+ gmx_ewald_tab_t* et)
{
- real factor = -1.0 / (4 * ewaldcoeff * ewaldcoeff);
- const real* charge;
- real energy_AB[2], energy;
- rvec lll;
- int lowiy, lowiz, ix, iy, iz, n, q;
- real tmp, cs, ss, ak, akv, mx, my, mz, m2, scale;
- gmx_bool bFreeEnergy;
+ real factor = -1.0 / (4 * ewaldcoeff * ewaldcoeff);
+ real energy_AB[2], energy;
+ rvec lll;
+ int lowiy, lowiz, ix, iy, iz, n, q;
+ real tmp, cs, ss, ak, akv, mx, my, mz, m2, scale;
+ cvec** eir;
+ bool bFreeEnergy;
if (cr != nullptr)
{
/* Scale box with Ewald wall factor */
matrix scaledBox;
- EwaldBoxZScaler boxScaler(*ir);
+ EwaldBoxZScaler boxScaler(ir);
boxScaler.scaleBox(box, scaledBox);
rvec boxDiag;
}
/* 1/(Vol*e0) */
- real scaleRecip = 4.0 * M_PI / (boxDiag[XX] * boxDiag[YY] * boxDiag[ZZ]) * ONE_4PI_EPS0 / ir->epsilon_r;
+ real scaleRecip =
+ 4.0 * M_PI / (boxDiag[XX] * boxDiag[YY] * boxDiag[ZZ]) * gmx::c_one4PiEps0 / ir.epsilon_r;
- if (!et->eir) /* allocate if we need to */
+ snew(eir, et->kmax);
+ for (n = 0; n < et->kmax; n++)
{
- snew(et->eir, et->kmax);
- for (n = 0; n < et->kmax; n++)
- {
- snew(et->eir[n], natoms);
- }
- snew(et->tab_xy, natoms);
- snew(et->tab_qxyz, natoms);
+ snew(eir[n], natoms);
}
+ et->tab_xy.resize(natoms);
+ et->tab_qxyz.resize(natoms);
- bFreeEnergy = (ir->efep != efepNO);
+ bFreeEnergy = (ir.efep != FreeEnergyPerturbationType::No);
clear_mat(lrvir);
calc_lll(boxDiag, lll);
- tabulateStructureFactors(natoms, x, et->kmax, et->eir, lll);
+ tabulateStructureFactors(natoms, x, et->kmax, eir, lll);
+ gmx::ArrayRef<const real> charge;
for (q = 0; q < (bFreeEnergy ? 2 : 1); q++)
{
if (!bFreeEnergy)
{
for (n = 0; n < natoms; n++)
{
- et->tab_xy[n] = cmul(et->eir[ix][n][XX], et->eir[iy][n][YY]);
+ et->tab_xy[n] = cmul(eir[ix][n][XX], eir[iy][n][YY]);
}
}
else
{
for (n = 0; n < natoms; n++)
{
- et->tab_xy[n] = cmul(et->eir[ix][n][XX], conjugate(et->eir[-iy][n][YY]));
+ et->tab_xy[n] = cmul(eir[ix][n][XX], conjugate(eir[-iy][n][YY]));
}
}
for (iz = lowiz; iz < et->nz; iz++)
{
for (n = 0; n < natoms; n++)
{
- et->tab_qxyz[n] = rcmul(charge[n], cmul(et->tab_xy[n], et->eir[iz][n][ZZ]));
+ et->tab_qxyz[n] = rcmul(charge[n], cmul(et->tab_xy[n], eir[iz][n][ZZ]));
}
}
else
{
for (n = 0; n < natoms; n++)
{
- et->tab_qxyz[n] = rcmul(
- charge[n], cmul(et->tab_xy[n], conjugate(et->eir[-iz][n][ZZ])));
+ et->tab_qxyz[n] =
+ rcmul(charge[n], cmul(et->tab_xy[n], conjugate(eir[-iz][n][ZZ])));
}
}
/* Apply charge correction */
vol = box[XX][XX] * box[YY][YY] * box[ZZ][ZZ];
- fac = M_PI * ONE_4PI_EPS0
+ fac = M_PI * gmx::c_one4PiEps0
/ (fr->ic->epsilon_r * 2.0 * vol * vol * gmx::square(fr->ic->ewaldcoeff_q));
qs2A = fr->qsum[0] * fr->qsum[0];
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <stdio.h>
+#include <vector>
+
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/real.h"
struct t_commrec;
struct t_forcerec;
struct t_inputrec;
+struct t_complex;
+
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
+struct gmx_ewald_tab_t
+{
+ gmx_ewald_tab_t(const t_inputrec& ir, FILE* fp);
+
+ ~gmx_ewald_tab_t();
-/* Forward declaration of type for managing Ewald tables */
-struct gmx_ewald_tab_t;
+ int nx;
+ int ny;
+ int nz;
+ int kmax;
-/*! \brief Initialize the tables used in the Ewald long-ranged part */
-void init_ewald_tab(struct gmx_ewald_tab_t** et, const t_inputrec* ir, FILE* fp);
+ std::vector<t_complex> tab_xy;
+ std::vector<t_complex> tab_qxyz;
+};
/*! \brief Do the long-ranged part of an Ewald calculation */
-real do_ewald(const t_inputrec* ir,
- const rvec x[],
- rvec f[],
- const real chargeA[],
- const real chargeB[],
- const matrix box,
- const t_commrec* cr,
- int natoms,
- matrix lrvir,
- real ewaldcoeff,
- real lambda,
- real* dvdlambda,
- gmx_ewald_tab_t* et);
+real do_ewald(const t_inputrec& ir,
+ gmx::ArrayRef<const gmx::RVec> x,
+ gmx::ArrayRef<gmx::RVec> f,
+ gmx::ArrayRef<const real> chargeA,
+ gmx::ArrayRef<const real> chargeB,
+ const matrix box,
+ const t_commrec* cr,
+ int natoms,
+ matrix lrvir,
+ real ewaldcoeff,
+ real lambda,
+ real* dvdlambda,
+ gmx_ewald_tab_t* et);
/*! \brief Calculate the correction to the Ewald sum, due to a net system
* charge.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2017,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \param[in] box The current box matrix
* \param[out] scaledBox Scaled copy of the box matrix.
*/
- void scaleBox(const matrix box, matrix scaledBox)
+ void scaleBox(const matrix box, matrix scaledBox) const
{
GMX_ASSERT(box, "invalid source box pointer");
GMX_ASSERT(scaledBox, "invalid target box pointer");
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* perturbations. The parameter vectors for LJ-PME are likewise
* undefined when LJ-PME is not active. This works because
* bHaveChargeOrTypePerturbed handles the control flow. */
-void ewald_LRcorrection(const int numAtomsLocal,
- const t_commrec* cr,
- int numThreads,
- int thread,
- const t_forcerec& fr,
- const t_inputrec& ir,
- const real* chargeA,
- const real* chargeB,
- gmx_bool bHaveChargePerturbed,
- const rvec x[],
- const matrix box,
- const rvec mu_tot[],
- rvec* f,
- real* Vcorr_q,
- real lambda_q,
- real* dvdlambda_q)
+void ewald_LRcorrection(const int numAtomsLocal,
+ const t_commrec* cr,
+ int numThreads,
+ int thread,
+ const t_forcerec& fr,
+ const t_inputrec& ir,
+ gmx::ArrayRef<const real> chargeA,
+ gmx::ArrayRef<const real> chargeB,
+ bool bHaveChargePerturbed,
+ gmx::ArrayRef<const gmx::RVec> x,
+ const matrix box,
+ gmx::ArrayRef<const gmx::RVec> mu_tot,
+ gmx::ArrayRef<gmx::RVec> f,
+ real* Vcorr_q,
+ real lambda_q,
+ real* dvdlambda_q)
{
/* We need to correct only self interactions */
const int start = (numAtomsLocal * thread) / numThreads;
EwaldBoxZScaler boxScaler(ir);
boxScaler.scaleBox(box, scaledBox);
- one_4pi_eps = ONE_4PI_EPS0 / fr.ic->epsilon_r;
+ one_4pi_eps = gmx::c_one4PiEps0 / fr.ic->epsilon_r;
Vexcl_q = 0;
dvdl_excl_q = 0;
Vdipole[0] = 0;
*/
for (i = 0; (i < DIM); i++)
{
- mutot[0][i] = mu_tot[0][i] * DEBYE2ENM;
- mutot[1][i] = mu_tot[1][i] * DEBYE2ENM;
+ mutot[0][i] = mu_tot[0][i] * gmx::c_debye2Enm;
+ mutot[1][i] = mu_tot[1][i] * gmx::c_debye2Enm;
dipcorrA[i] = 0;
dipcorrB[i] = 0;
}
real boxVolume = scaledBox[XX][XX] * scaledBox[YY][YY] * scaledBox[ZZ][ZZ];
switch (ir.ewald_geometry)
{
- case eewg3D:
+ case EwaldGeometry::ThreeD:
if (ir.epsilon_surface != 0)
{
- dipole_coeff = 2 * M_PI * ONE_4PI_EPS0
+ dipole_coeff = 2 * M_PI * gmx::c_one4PiEps0
/ ((2 * ir.epsilon_surface + fr.ic->epsilon_r) * boxVolume);
for (i = 0; (i < DIM); i++)
{
}
}
break;
- case eewg3DC:
+ case EwaldGeometry::ThreeDC:
dipole_coeff = 2 * M_PI * one_4pi_eps / boxVolume;
dipcorrA[ZZ] = 2 * dipole_coeff * mutot[0][ZZ];
dipcorrB[ZZ] = 2 * dipole_coeff * mutot[1][ZZ];
*/
if (dipole_coeff != 0)
{
- if (ir.ewald_geometry == eewg3D)
+ if (ir.ewald_geometry == EwaldGeometry::ThreeD)
{
Vdipole[q] = dipole_coeff * iprod(mutot[q], mutot[q]);
}
- else if (ir.ewald_geometry == eewg3DC)
+ else if (ir.ewald_geometry == EwaldGeometry::ThreeDC)
{
Vdipole[q] = dipole_coeff * mutot[q][ZZ] * mutot[q][ZZ];
* We could implement a reduction over threads,
* but this case is rarely used.
*/
- const real* qPtr = (q == 0 ? chargeA : chargeB);
- real sumQZ2 = 0;
+ gmx::ArrayRef<const real> charge = (q == 0 ? chargeA : chargeB);
+ real sumQZ2 = 0;
for (int i = 0; i < numAtomsLocal; i++)
{
- sumQZ2 += qPtr[i] * x[i][ZZ] * x[i][ZZ];
+ sumQZ2 += charge[i] * x[i][ZZ] * x[i][ZZ];
}
Vdipole[q] -= dipole_coeff * fr.qsum[q]
* (sumQZ2 + fr.qsum[q] * box[ZZ][ZZ] * box[ZZ][ZZ] / 12);
if (debug)
{
fprintf(debug, "Long Range corrections for Ewald interactions:\n");
- fprintf(debug, "q2sum = %g, Vself_q=%g\n", L1_q * fr.q2sum[0] + lambda_q * fr.q2sum[1],
+ fprintf(debug,
+ "q2sum = %g, Vself_q=%g\n",
+ L1_q * fr.q2sum[0] + lambda_q * fr.q2sum[1],
L1_q * Vself_q[0] + lambda_q * Vself_q[1]);
fprintf(debug, "Electrostatic Long Range correction: Vexcl=%g\n", Vexcl_q);
if (MASTER(cr) && thread == 0)
{
- if (ir.epsilon_surface > 0 || ir.ewald_geometry == eewg3DC)
+ if (ir.epsilon_surface > 0 || ir.ewald_geometry == EwaldGeometry::ThreeDC)
{
- fprintf(debug, "Total dipole correction: Vdipole=%g\n",
+ fprintf(debug,
+ "Total dipole correction: Vdipole=%g\n",
L1_q * Vdipole[0] + lambda_q * Vdipole[1]);
}
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_EWALD_LONG_RANGE_CORRECTION_H
#include "gromacs/math/vectypes.h"
-#include "gromacs/topology/block.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
struct t_commrec;
struct t_forcerec;
struct t_inputrec;
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
/*! \brief Calculate long-range Ewald correction terms.
*
* Calculate correction for electrostatic surface dipole terms.
*/
-void ewald_LRcorrection(int numAtomsLocal,
- const t_commrec* cr,
- int numThreads,
- int thread,
- const t_forcerec& fr,
- const t_inputrec& ir,
- const real* chargeA,
- const real* chargeB,
- gmx_bool bHaveChargePerturbed,
- const rvec x[],
- const matrix box,
- const rvec mu_tot[],
- rvec* f,
- real* Vcorr_q,
- real lambda_q,
- real* dvdlambda_q);
+void ewald_LRcorrection(int numAtomsLocal,
+ const t_commrec* cr,
+ int numThreads,
+ int thread,
+ const t_forcerec& fr,
+ const t_inputrec& ir,
+ gmx::ArrayRef<const real> chargeA,
+ gmx::ArrayRef<const real> chargeB,
+ bool bHaveChargePerturbed,
+ gmx::ArrayRef<const gmx::RVec> x,
+ const matrix box,
+ gmx::ArrayRef<const gmx::RVec> mu_tot,
+ gmx::ArrayRef<gmx::RVec> f,
+ real* Vcorr_q,
+ real lambda_q,
+ real* dvdlambda_q);
#endif
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
MPI_Status stat;
for (size_t b = 0; b < ol->comm_data.size(); b++)
{
- MPI_Sendrecv(&ol->send_size, 1, MPI_INT, ol->comm_data[b].send_id, b, &ol->comm_data[b].recv_size,
- 1, MPI_INT, ol->comm_data[b].recv_id, b, ol->mpi_comm, &stat);
+ MPI_Sendrecv(&ol->send_size,
+ 1,
+ MPI_INT,
+ ol->comm_data[b].send_id,
+ b,
+ &ol->comm_data[b].recv_size,
+ 1,
+ MPI_INT,
+ ol->comm_data[b].recv_id,
+ b,
+ ol->mpi_comm,
+ &stat);
}
#endif
std::string message = gmx::formatString(
"pme_order (%d) is larger than the maximum allowed value (%d). Modify and "
"recompile the code if you really need such a high order.",
- pme_order, PME_ORDER_MAX);
+ pme_order,
+ PME_ORDER_MAX);
GMX_THROW(gmx::InconsistentInputError(message));
}
"threads, the number of grid lines per rank along x should be >= pme_order (%d) "
"or = pmeorder-1. To resolve this issue, use fewer ranks along x (and possibly "
"more along y and/or z) by specifying -dd manually.",
- nkx / static_cast<double>(numPmeDomainsAlongX), pme_order);
+ nkx / static_cast<double>(numPmeDomainsAlongX),
+ pme_order);
}
return true;
pme->ndecompdim = 2;
#if GMX_MPI
- MPI_Comm_split(pme->mpi_comm, pme->nodeid % numPmeDomains.y, pme->nodeid,
+ MPI_Comm_split(pme->mpi_comm,
+ pme->nodeid % numPmeDomains.y,
+ pme->nodeid,
&pme->mpi_comm_d[0]); /* My communicator along major dimension */
- MPI_Comm_split(pme->mpi_comm, pme->nodeid / numPmeDomains.y, pme->nodeid,
+ MPI_Comm_split(pme->mpi_comm,
+ pme->nodeid / numPmeDomains.y,
+ pme->nodeid,
&pme->mpi_comm_d[1]); /* My communicator along minor dimension */
MPI_Comm_rank(pme->mpi_comm_d[0], &pme->nodeid_major);
* not calculating free-energy for Coulomb and/or LJ while gmx_pme_init()
* configures with free-energy, but that has never been tested.
*/
- pme->doCoulomb = EEL_PME(ir->coulombtype);
- pme->doLJ = EVDW_PME(ir->vdwtype);
- pme->bFEP_q = ((ir->efep != efepNO) && bFreeEnergy_q);
- pme->bFEP_lj = ((ir->efep != efepNO) && bFreeEnergy_lj);
- pme->bFEP = (pme->bFEP_q || pme->bFEP_lj);
- pme->nkx = ir->nkx;
- pme->nky = ir->nky;
- pme->nkz = ir->nkz;
- pme->bP3M = (ir->coulombtype == eelP3M_AD || getenv("GMX_PME_P3M") != nullptr);
+ pme->doCoulomb = EEL_PME(ir->coulombtype);
+ pme->doLJ = EVDW_PME(ir->vdwtype);
+ pme->bFEP_q = ((ir->efep != FreeEnergyPerturbationType::No) && bFreeEnergy_q);
+ pme->bFEP_lj = ((ir->efep != FreeEnergyPerturbationType::No) && bFreeEnergy_lj);
+ pme->bFEP = (pme->bFEP_q || pme->bFEP_lj);
+ pme->nkx = ir->nkx;
+ pme->nky = ir->nky;
+ pme->nkz = ir->nkz;
+ pme->bP3M = (ir->coulombtype == CoulombInteractionType::P3mAD || getenv("GMX_PME_P3M") != nullptr);
pme->pme_order = ir->pme_order;
pme->ewaldcoeff_q = ewaldcoeff_q;
pme->ewaldcoeff_lj = ewaldcoeff_lj;
pme->boxScaler = new EwaldBoxZScaler(*ir);
/* If we violate restrictions, generate a fatal error here */
- gmx_pme_check_restrictions(pme->pme_order, pme->nkx, pme->nky, pme->nkz, pme->nnodes_major,
- pme->bUseThreads, true);
+ gmx_pme_check_restrictions(
+ pme->pme_order, pme->nkx, pme->nky, pme->nkz, pme->nnodes_major, pme->bUseThreads, true);
if (pme->nnodes > 1)
{
" and PME grid_y (%d) and grid_z (%d) should be divisible by "
"#PME_ranks_y "
"(%d)",
- gmx::roundToInt((imbal - 1) * 100), pme->nkx, pme->nky,
- pme->nnodes_major, pme->nky, pme->nkz, pme->nnodes_minor);
+ gmx::roundToInt((imbal - 1) * 100),
+ pme->nkx,
+ pme->nky,
+ pme->nnodes_major,
+ pme->nky,
+ pme->nkz,
+ pme->nnodes_minor);
}
}
* y is always copied through a buffer: we don't need padding in z,
* but we do need the overlap in x because of the communication order.
*/
- init_overlap_comm(&pme->overlap[0], pme->pme_order, pme->mpi_comm_d[0], pme->nnodes_major,
- pme->nodeid_major, pme->nkx,
+ init_overlap_comm(&pme->overlap[0],
+ pme->pme_order,
+ pme->mpi_comm_d[0],
+ pme->nnodes_major,
+ pme->nodeid_major,
+ pme->nkx,
(div_round_up(pme->nky, pme->nnodes_minor) + pme->pme_order)
* (pme->nkz + pme->pme_order - 1));
* We do this with an offset buffer of equal size, so we need to allocate
* extra for the offset. That's what the (+1)*pme->nkz is for.
*/
- init_overlap_comm(&pme->overlap[1], pme->pme_order, pme->mpi_comm_d[1], pme->nnodes_minor,
- pme->nodeid_minor, pme->nky,
+ init_overlap_comm(&pme->overlap[1],
+ pme->pme_order,
+ pme->mpi_comm_d[1],
+ pme->nnodes_minor,
+ pme->nodeid_minor,
+ pme->nky,
(div_round_up(pme->nkx, pme->nnodes_major) + pme->pme_order + 1) * pme->nkz);
/* Double-check for a limitation of the (current) sum_fftgrid_dd code.
pme->pmegrid_start_iy = pme->overlap[1].s2g0[pme->nodeid_minor];
pme->pmegrid_start_iz = 0;
- make_gridindex_to_localindex(pme->nkx, pme->pmegrid_start_ix,
- pme->pmegrid_nx - (pme->pme_order - 1), &pme->nnx, &pme->fshx);
- make_gridindex_to_localindex(pme->nky, pme->pmegrid_start_iy,
- pme->pmegrid_ny - (pme->pme_order - 1), &pme->nny, &pme->fshy);
- make_gridindex_to_localindex(pme->nkz, pme->pmegrid_start_iz, pme->pmegrid_nz_base, &pme->nnz,
- &pme->fshz);
+ make_gridindex_to_localindex(
+ pme->nkx, pme->pmegrid_start_ix, pme->pmegrid_nx - (pme->pme_order - 1), &pme->nnx, &pme->fshx);
+ make_gridindex_to_localindex(
+ pme->nky, pme->pmegrid_start_iy, pme->pmegrid_ny - (pme->pme_order - 1), &pme->nny, &pme->fshy);
+ make_gridindex_to_localindex(
+ pme->nkz, pme->pmegrid_start_iz, pme->pmegrid_nz_base, &pme->nnz, &pme->fshz);
pme->spline_work = make_pme_spline_work(pme->pme_order);
*/
if (pme->doLJ)
{
- pme->ngrids = ((ir->ljpme_combination_rule == eljpmeLB) ? DO_Q_AND_LJ_LB : DO_Q_AND_LJ);
+ pme->ngrids = ((ir->ljpme_combination_rule == LongRangeVdW::LB) ? DO_Q_AND_LJ_LB : DO_Q_AND_LJ);
}
else
{
{
if ((i < DO_Q && pme->doCoulomb && (i == 0 || bFreeEnergy_q))
|| (i >= DO_Q && pme->doLJ
- && (i == 2 || bFreeEnergy_lj || ir->ljpme_combination_rule == eljpmeLB)))
+ && (i == 2 || bFreeEnergy_lj || ir->ljpme_combination_rule == LongRangeVdW::LB)))
{
- pmegrids_init(&pme->pmegrid[i], pme->pmegrid_nx, pme->pmegrid_ny, pme->pmegrid_nz,
- pme->pmegrid_nz_base, pme->pme_order, pme->bUseThreads, pme->nthread,
+ pmegrids_init(&pme->pmegrid[i],
+ pme->pmegrid_nx,
+ pme->pmegrid_ny,
+ pme->pmegrid_nz,
+ pme->pmegrid_nz_base,
+ pme->pme_order,
+ pme->bUseThreads,
+ pme->nthread,
pme->overlap[0].s2g1[pme->nodeid_major]
- pme->overlap[0].s2g0[pme->nodeid_major + 1],
pme->overlap[1].s2g1[pme->nodeid_minor]
const auto allocateRealGridForGpu = (pme->runMode == PmeRunMode::Mixed)
? gmx::PinningPolicy::PinnedIfSupported
: gmx::PinningPolicy::CannotBePinned;
- gmx_parallel_3dfft_init(&pme->pfft_setup[i], ndata, &pme->fftgrid[i], &pme->cfftgrid[i],
- pme->mpi_comm_d, bReproducible, pme->nthread, allocateRealGridForGpu);
+ gmx_parallel_3dfft_init(&pme->pfft_setup[i],
+ ndata,
+ &pme->fftgrid[i],
+ &pme->cfftgrid[i],
+ pme->mpi_comm_d,
+ bReproducible,
+ pme->nthread,
+ allocateRealGridForGpu);
}
}
const gmx::MDLogger dummyLogger;
GMX_ASSERT(pmedata, "Invalid PME pointer");
NumPmeDomains numPmeDomains = { pme_src->nnodes_major, pme_src->nnodes_minor };
- *pmedata = gmx_pme_init(cr, numPmeDomains, &irc, pme_src->bFEP_q, pme_src->bFEP_lj, FALSE,
- ewaldcoeff_q, ewaldcoeff_lj, pme_src->nthread, pme_src->runMode,
- pme_src->gpu, nullptr, nullptr, nullptr, dummyLogger);
+ *pmedata = gmx_pme_init(cr,
+ numPmeDomains,
+ &irc,
+ pme_src->bFEP_q,
+ pme_src->bFEP_lj,
+ FALSE,
+ ewaldcoeff_q,
+ ewaldcoeff_lj,
+ pme_src->nthread,
+ pme_src->runMode,
+ pme_src->gpu,
+ nullptr,
+ nullptr,
+ nullptr,
+ dummyLogger);
/* When running PME on the CPU not using domain decomposition,
* the atom data is allocated once only in gmx_pme_(re)init().
*/
if (!pme_src->gpu && pme_src->nnodes == 1)
{
- gmx_pme_reinit_atoms(*pmedata, pme_src->atc[0].numAtoms(), nullptr, nullptr);
+ gmx_pme_reinit_atoms(*pmedata, pme_src->atc[0].numAtoms(), {}, {});
}
// TODO this is mostly passing around current values
}
/* We would like to reuse the fft grids, but that's harder */
}
-void gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q, real* V)
+real gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q)
{
pmegrids_t* grid;
/* Only calculate the spline coefficients, don't actually spread */
spread_on_grid(pme, atc, nullptr, TRUE, FALSE, pme->fftgrid[PME_GRID_QA], FALSE, PME_GRID_QA);
- *V = gather_energy_bsplines(pme, grid->grid.grid, atc);
+ return gather_energy_bsplines(pme, grid->grid.grid, atc);
}
/*! \brief Calculate initial Lorentz-Berthelot coefficients for LJ-PME */
-static void calc_initial_lb_coeffs(gmx::ArrayRef<real> coefficient, const real* local_c6, const real* local_sigma)
+static void calc_initial_lb_coeffs(gmx::ArrayRef<real> coefficient,
+ gmx::ArrayRef<const real> local_c6,
+ gmx::ArrayRef<const real> local_sigma)
{
for (gmx::index i = 0; i < coefficient.ssize(); ++i)
{
}
/*! \brief Calculate next Lorentz-Berthelot coefficients for LJ-PME */
-static void calc_next_lb_coeffs(gmx::ArrayRef<real> coefficient, const real* local_sigma)
+static void calc_next_lb_coeffs(gmx::ArrayRef<real> coefficient, gmx::ArrayRef<const real> local_sigma)
{
for (gmx::index i = 0; i < coefficient.ssize(); ++i)
{
int gmx_pme_do(struct gmx_pme_t* pme,
gmx::ArrayRef<const gmx::RVec> coordinates,
gmx::ArrayRef<gmx::RVec> forces,
- real chargeA[],
- real chargeB[],
- real c6A[],
- real c6B[],
- real sigmaA[],
- real sigmaB[],
+ gmx::ArrayRef<const real> chargeA,
+ gmx::ArrayRef<const real> chargeB,
+ gmx::ArrayRef<const real> c6A,
+ gmx::ArrayRef<const real> c6B,
+ gmx::ArrayRef<const real> sigmaA,
+ gmx::ArrayRef<const real> sigmaB,
const matrix box,
const t_commrec* cr,
int maxshift_x,
GMX_ASSERT(pme->runMode == PmeRunMode::CPU,
"gmx_pme_do should not be called on the GPU PME run.");
- int d, npme, grid_index, max_grid_index;
- PmeAtomComm& atc = pme->atc[0];
- pmegrids_t* pmegrid = nullptr;
- real* grid = nullptr;
- real* coefficient = nullptr;
- PmeOutput output[2]; // The second is used for the B state with FEP
- real scale, lambda;
- gmx_bool bClearF;
- gmx_parallel_3dfft_t pfft_setup;
- real* fftgrid;
- t_complex* cfftgrid;
- int thread;
- gmx_bool bFirst, bDoSplines;
- int fep_state;
- int fep_states_lj = pme->bFEP_lj ? 2 : 1;
+ int d, npme, grid_index, max_grid_index;
+ PmeAtomComm& atc = pme->atc[0];
+ pmegrids_t* pmegrid = nullptr;
+ real* grid = nullptr;
+ gmx::ArrayRef<const real> coefficient;
+ PmeOutput output[2]; // The second is used for the B state with FEP
+ real scale, lambda;
+ gmx_bool bClearF;
+ gmx_parallel_3dfft_t pfft_setup;
+ real* fftgrid;
+ t_complex* cfftgrid;
+ int thread;
+ gmx_bool bFirst, bDoSplines;
+ int fep_state;
+ int fep_states_lj = pme->bFEP_lj ? 2 : 1;
// There's no support for computing energy without virial, or vice versa
const bool computeEnergyAndVirial = (stepWork.computeEnergy || stepWork.computeVirial);
*/
/* If we are doing LJ-PME with LB, we only do Q here */
- max_grid_index = (pme->ljpme_combination_rule == eljpmeLB) ? DO_Q : DO_Q_AND_LJ;
+ max_grid_index = (pme->ljpme_combination_rule == LongRangeVdW::LB) ? DO_Q : DO_Q_AND_LJ;
for (grid_index = 0; grid_index < max_grid_index; ++grid_index)
{
if (pme->nnodes == 1)
{
- atc.coefficient = gmx::arrayRefFromArray(coefficient, coordinates.size());
+ atc.coefficient = coefficient;
}
else
{
- wallcycle_start(wcycle, ewcPME_REDISTXF);
+ wallcycle_start(wcycle, WallCycleCounter::PmeRedistXF);
do_redist_pos_coeffs(pme, cr, bFirst, coordinates, coefficient);
- wallcycle_stop(wcycle, ewcPME_REDISTXF);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeRedistXF);
}
if (debug)
fprintf(debug, "Rank= %6d, pme local particles=%6d\n", cr->nodeid, atc.numAtoms());
}
- wallcycle_start(wcycle, ewcPME_SPREAD);
+ wallcycle_start(wcycle, WallCycleCounter::PmeSpread);
/* Spread the coefficients on a grid */
spread_on_grid(pme, &atc, pmegrid, bFirst, TRUE, fftgrid, bDoSplines, grid_index);
copy_pmegrid_to_fftgrid(pme, grid, fftgrid, grid_index);
}
- wallcycle_stop(wcycle, ewcPME_SPREAD);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeSpread);
/* TODO If the OpenMP and single-threaded implementations
converge, then spread_on_grid() and
/* do 3d-fft */
if (thread == 0)
{
- wallcycle_start(wcycle, ewcPME_FFT);
+ wallcycle_start(wcycle, WallCycleCounter::PmeFft);
}
gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_REAL_TO_COMPLEX, thread, wcycle);
if (thread == 0)
{
- wallcycle_stop(wcycle, ewcPME_FFT);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeFft);
}
/* solve in k-space for our local cells */
if (thread == 0)
{
- wallcycle_start(wcycle, (grid_index < DO_Q ? ewcPME_SOLVE : ewcLJPME));
+ wallcycle_start(
+ wcycle,
+ (grid_index < DO_Q ? WallCycleCounter::PmeSolve : WallCycleCounter::LJPme));
}
if (grid_index < DO_Q)
{
- loop_count = solve_pme_yzx(
- pme, cfftgrid, scaledBox[XX][XX] * scaledBox[YY][YY] * scaledBox[ZZ][ZZ],
- computeEnergyAndVirial, pme->nthread, thread);
+ loop_count = solve_pme_yzx(pme,
+ cfftgrid,
+ scaledBox[XX][XX] * scaledBox[YY][YY] * scaledBox[ZZ][ZZ],
+ computeEnergyAndVirial,
+ pme->nthread,
+ thread);
}
else
{
loop_count =
- solve_pme_lj_yzx(pme, &cfftgrid, FALSE,
+ solve_pme_lj_yzx(pme,
+ &cfftgrid,
+ FALSE,
scaledBox[XX][XX] * scaledBox[YY][YY] * scaledBox[ZZ][ZZ],
- computeEnergyAndVirial, pme->nthread, thread);
+ computeEnergyAndVirial,
+ pme->nthread,
+ thread);
}
if (thread == 0)
{
- wallcycle_stop(wcycle, (grid_index < DO_Q ? ewcPME_SOLVE : ewcLJPME));
+ wallcycle_stop(
+ wcycle,
+ (grid_index < DO_Q ? WallCycleCounter::PmeSolve : WallCycleCounter::LJPme));
inc_nrnb(nrnb, eNR_SOLVEPME, loop_count);
}
/* do 3d-invfft */
if (thread == 0)
{
- wallcycle_start(wcycle, ewcPME_FFT);
+ wallcycle_start(wcycle, WallCycleCounter::PmeFft);
}
gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_COMPLEX_TO_REAL, thread, wcycle);
if (thread == 0)
{
- wallcycle_stop(wcycle, ewcPME_FFT);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeFft);
if (pme->nodeid == 0)
/* Note: this wallcycle region is closed below
outside an OpenMP region, so take care if
refactoring code here. */
- wallcycle_start(wcycle, ewcPME_GATHER);
+ wallcycle_start(wcycle, WallCycleCounter::PmeGather);
}
copy_fftgrid_to_pmegrid(pme, fftgrid, grid, grid_index, pme->nthread, thread);
{
try
{
- gather_f_bsplines(pme, grid, bClearF, &atc, &atc.spline[thread],
+ gather_f_bsplines(pme,
+ grid,
+ bClearF,
+ &atc,
+ &atc.spline[thread],
pme->bFEP ? (grid_index % 2 == 0 ? 1.0 - lambda : lambda) : 1.0);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- inc_nrnb(nrnb, eNR_GATHERFBSP,
- pme->pme_order * pme->pme_order * pme->pme_order * atc.numAtoms());
+ inc_nrnb(nrnb, eNR_GATHERFBSP, pme->pme_order * pme->pme_order * pme->pme_order * atc.numAtoms());
/* Note: this wallcycle region is opened above inside an OpenMP
region, so take care if refactoring code here. */
- wallcycle_stop(wcycle, ewcPME_GATHER);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeGather);
}
if (computeEnergyAndVirial)
/* For Lorentz-Berthelot combination rules in LJ-PME, we need to calculate
* seven terms. */
- if (pme->doLJ && pme->ljpme_combination_rule == eljpmeLB)
+ if (pme->doLJ && pme->ljpme_combination_rule == LongRangeVdW::LB)
{
/* Loop over A- and B-state if we are doing FEP */
for (fep_state = 0; fep_state < fep_states_lj; ++fep_state)
{
- real *local_c6 = nullptr, *local_sigma = nullptr, *RedistC6 = nullptr, *RedistSigma = nullptr;
- gmx::ArrayRef<real> coefficientBuffer;
+ std::vector<real> local_c6;
+ std::vector<real> local_sigma;
+ gmx::ArrayRef<const real> RedistC6;
+ gmx::ArrayRef<const real> RedistSigma;
+ gmx::ArrayRef<real> coefficientBuffer;
if (pme->nnodes == 1)
{
pme->lb_buf1.resize(atc.numAtoms());
switch (fep_state)
{
case 0:
- local_c6 = c6A;
- local_sigma = sigmaA;
+ local_c6.assign(c6A.begin(), c6A.end());
+ local_sigma.assign(sigmaA.begin(), sigmaA.end());
break;
case 1:
- local_c6 = c6B;
- local_sigma = sigmaB;
+ local_c6.assign(c6B.begin(), c6B.end());
+ local_sigma.assign(sigmaB.begin(), sigmaB.end());
break;
default: gmx_incons("Trying to access wrong FEP-state in LJ-PME routine");
}
break;
default: gmx_incons("Trying to access wrong FEP-state in LJ-PME routine");
}
- wallcycle_start(wcycle, ewcPME_REDISTXF);
+ wallcycle_start(wcycle, WallCycleCounter::PmeRedistXF);
do_redist_pos_coeffs(pme, cr, bFirst, coordinates, RedistC6);
pme->lb_buf1.resize(atc.numAtoms());
pme->lb_buf2.resize(atc.numAtoms());
- local_c6 = pme->lb_buf1.data();
+ local_c6.assign(pme->lb_buf1.begin(), pme->lb_buf1.end());
for (int i = 0; i < atc.numAtoms(); ++i)
{
local_c6[i] = atc.coefficient[i];
}
do_redist_pos_coeffs(pme, cr, FALSE, coordinates, RedistSigma);
- local_sigma = pme->lb_buf2.data();
+ local_sigma.assign(pme->lb_buf2.begin(), pme->lb_buf2.end());
for (int i = 0; i < atc.numAtoms(); ++i)
{
local_sigma[i] = atc.coefficient[i];
}
- wallcycle_stop(wcycle, ewcPME_REDISTXF);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeRedistXF);
}
atc.coefficient = coefficientBuffer;
calc_initial_lb_coeffs(coefficientBuffer, local_c6, local_sigma);
calc_next_lb_coeffs(coefficientBuffer, local_sigma);
grid = pmegrid->grid.grid;
- wallcycle_start(wcycle, ewcPME_SPREAD);
+ wallcycle_start(wcycle, WallCycleCounter::PmeSpread);
/* Spread the c6 on a grid */
spread_on_grid(pme, &atc, pmegrid, bFirst, TRUE, fftgrid, bDoSplines, grid_index);
inc_nrnb(nrnb, eNR_WEIGHTS, DIM * atc.numAtoms());
}
- inc_nrnb(nrnb, eNR_SPREADBSP,
+ inc_nrnb(nrnb,
+ eNR_SPREADBSP,
pme->pme_order * pme->pme_order * pme->pme_order * atc.numAtoms());
if (pme->nthread == 1)
{
}
copy_pmegrid_to_fftgrid(pme, grid, fftgrid, grid_index);
}
- wallcycle_stop(wcycle, ewcPME_SPREAD);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeSpread);
/*Here we start a large thread parallel region*/
#pragma omp parallel num_threads(pme->nthread) private(thread)
/* do 3d-fft */
if (thread == 0)
{
- wallcycle_start(wcycle, ewcPME_FFT);
+ wallcycle_start(wcycle, WallCycleCounter::PmeFft);
}
gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_REAL_TO_COMPLEX, thread, wcycle);
if (thread == 0)
{
- wallcycle_stop(wcycle, ewcPME_FFT);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeFft);
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
thread = gmx_omp_get_thread_num();
if (thread == 0)
{
- wallcycle_start(wcycle, ewcLJPME);
+ wallcycle_start(wcycle, WallCycleCounter::LJPme);
}
loop_count =
- solve_pme_lj_yzx(pme, &pme->cfftgrid[2], TRUE,
+ solve_pme_lj_yzx(pme,
+ &pme->cfftgrid[2],
+ TRUE,
scaledBox[XX][XX] * scaledBox[YY][YY] * scaledBox[ZZ][ZZ],
- computeEnergyAndVirial, pme->nthread, thread);
+ computeEnergyAndVirial,
+ pme->nthread,
+ thread);
if (thread == 0)
{
- wallcycle_stop(wcycle, ewcLJPME);
+ wallcycle_stop(wcycle, WallCycleCounter::LJPme);
inc_nrnb(nrnb, eNR_SOLVEPME, loop_count);
}
}
/* do 3d-invfft */
if (thread == 0)
{
- wallcycle_start(wcycle, ewcPME_FFT);
+ wallcycle_start(wcycle, WallCycleCounter::PmeFft);
}
gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_COMPLEX_TO_REAL, thread, wcycle);
if (thread == 0)
{
- wallcycle_stop(wcycle, ewcPME_FFT);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeFft);
if (pme->nodeid == 0)
npme = static_cast<int>(ntot * std::log(ntot) / std::log(2.0));
inc_nrnb(nrnb, eNR_FFT, 2 * npme);
}
- wallcycle_start(wcycle, ewcPME_GATHER);
+ wallcycle_start(wcycle, WallCycleCounter::PmeGather);
}
copy_fftgrid_to_pmegrid(pme, fftgrid, grid, grid_index, pme->nthread, thread);
{
try
{
- gather_f_bsplines(pme, grid, bClearF, &pme->atc[0],
- &pme->atc[0].spline[thread], scale);
+ gather_f_bsplines(
+ pme, grid, bClearF, &pme->atc[0], &pme->atc[0].spline[thread], scale);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- inc_nrnb(nrnb, eNR_GATHERFBSP,
+ inc_nrnb(nrnb,
+ eNR_GATHERFBSP,
pme->pme_order * pme->pme_order * pme->pme_order * pme->atc[0].numAtoms());
}
- wallcycle_stop(wcycle, ewcPME_GATHER);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeGather);
bFirst = FALSE;
} /* for (grid_index = 8; grid_index >= 2; --grid_index) */
} /* for (fep_state = 0; fep_state < fep_states_lj; ++fep_state) */
- } /* if (pme->doLJ && pme->ljpme_combination_rule == eljpmeLB) */
+ } /* if (pme->doLJ && pme->ljpme_combination_rule == LongRangeVdW::LB) */
if (stepWork.computeForces && pme->nnodes > 1)
{
- wallcycle_start(wcycle, ewcPME_REDISTXF);
+ wallcycle_start(wcycle, WallCycleCounter::PmeRedistXF);
for (d = 0; d < pme->ndecompdim; d++)
{
gmx::ArrayRef<gmx::RVec> forcesRef;
}
}
- wallcycle_stop(wcycle, ewcPME_REDISTXF);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeRedistXF);
}
if (computeEnergyAndVirial)
delete pme;
}
-void gmx_pme_reinit_atoms(gmx_pme_t* pme, const int numAtoms, const real* chargesA, const real* chargesB)
+void gmx_pme_reinit_atoms(gmx_pme_t* pme,
+ const int numAtoms,
+ gmx::ArrayRef<const real> chargesA,
+ gmx::ArrayRef<const real> chargesB)
{
if (pme->gpu != nullptr)
{
- GMX_ASSERT(!(pme->bFEP_q && chargesB == nullptr),
+ GMX_ASSERT(!(pme->bFEP_q && !chargesB.empty()),
"B state charges must be specified if running Coulomb FEP on the GPU");
- pme_gpu_reinit_atoms(pme->gpu, numAtoms, chargesA, pme->bFEP_q ? chargesB : nullptr);
+ pme_gpu_reinit_atoms(pme->gpu, numAtoms, chargesA.data(), pme->bFEP_q ? chargesB.data() : nullptr);
}
else
{
{
return (pme.nkx == grid_size[XX] && pme.nky == grid_size[YY] && pme.nkz == grid_size[ZZ]);
}
+
+void gmx::SeparatePmeRanksPermitted::disablePmeRanks(const std::string& reason)
+{
+ permitSeparatePmeRanks_ = false;
+
+ if (!reason.empty())
+ {
+ reasons_.push_back(reason);
+ }
+}
+
+bool gmx::SeparatePmeRanksPermitted::permitSeparatePmeRanks() const
+{
+ return permitSeparatePmeRanks_;
+}
+
+std::string gmx::SeparatePmeRanksPermitted::reasonsWhyDisabled() const
+{
+ return joinStrings(reasons_, "; ");
+}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_EWALD_PME_H
#include <string>
+#include <vector>
#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/gpu_utils/gpu_macros.h"
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
struct gmx_hw_info_t;
class MDLogger;
enum class PinningPolicy : int;
class StepWorkload;
+
+/*! \libinternal \brief Class for managing usage of separate PME-only ranks
+ *
+ * Used for checking if some parts of the code could not use PME-only ranks
+ *
+ */
+class SeparatePmeRanksPermitted
+{
+public:
+ //! Disables PME ranks permitted flag with a reason
+ void disablePmeRanks(const std::string& reason);
+ //! Return status of PME ranks usage
+ bool permitSeparatePmeRanks() const;
+ //! Returns all reasons, for not using PME ranks
+ std::string reasonsWhyDisabled() const;
+
+private:
+ //! Flag that informs whether simualtion could use dedicated PME ranks
+ bool permitSeparatePmeRanks_ = true;
+ //! Storage for all reasons, why PME ranks could not be used
+ std::vector<std::string> reasons_;
+};
+
} // namespace gmx
enum
int gmx_pme_do(struct gmx_pme_t* pme,
gmx::ArrayRef<const gmx::RVec> coordinates,
gmx::ArrayRef<gmx::RVec> forces,
- real chargeA[],
- real chargeB[],
- real c6A[],
- real c6B[],
- real sigmaA[],
- real sigmaB[],
+ gmx::ArrayRef<const real> chargeA,
+ gmx::ArrayRef<const real> chargeB,
+ gmx::ArrayRef<const real> c6A,
+ gmx::ArrayRef<const real> c6B,
+ gmx::ArrayRef<const real> sigmaA,
+ gmx::ArrayRef<const real> sigmaB,
const matrix box,
const t_commrec* cr,
int maxshift_x,
* pme struct. Currently does not work in parallel or with free
* energy.
*/
-void gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q, real* V);
+real gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q);
/*! \brief
* This function updates the local atom data on GPU after DD (charges, coordinates, etc.).
* \param[in] chargesB The pointer to the array of particle charges in state B. Only used if
* charges are perturbed and can otherwise be nullptr.
*/
-void gmx_pme_reinit_atoms(gmx_pme_t* pme, int numAtoms, const real* chargesA, const real* chargesB);
+void gmx_pme_reinit_atoms(gmx_pme_t* pme,
+ int numAtoms,
+ gmx::ArrayRef<const real> chargesA,
+ gmx::ArrayRef<const real> chargesB);
/* A block of PME GPU functions */
* \param[in] pme The PME data structure.
* \returns Pointer to force data
*/
-GPU_FUNC_QUALIFIER void* pme_gpu_get_device_f(const gmx_pme_t* GPU_FUNC_ARGUMENT(pme))
- GPU_FUNC_TERM_WITH_RETURN(nullptr);
+GPU_FUNC_QUALIFIER DeviceBuffer<gmx::RVec> pme_gpu_get_device_f(const gmx_pme_t* GPU_FUNC_ARGUMENT(pme))
+ GPU_FUNC_TERM_WITH_RETURN(DeviceBuffer<gmx::RVec>{});
/*! \brief Get pointer to the device synchronizer object that allows syncing on PME force calculation completion
* \param[in] pme The PME data structure.
- * \returns Pointer to sychronizer
+ * \returns Pointer to synchronizer
*/
GPU_FUNC_QUALIFIER GpuEventSynchronizer* pme_gpu_get_f_ready_synchronizer(const gmx_pme_t* GPU_FUNC_ARGUMENT(pme))
GPU_FUNC_TERM_WITH_RETURN(nullptr);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_PMECOORDINATERECEIVERGPU_H
#define GMX_PMECOORDINATERECEIVERGPU_H
+#include <memory>
+
#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/gmxmpi.h"
class DeviceStream;
/*! \brief
- * launch receive of coordinate data from PP rank
- * \param[in] ppRank PP rank to send data
+ * Receive coordinate synchronizer pointer from the PP ranks.
+ * \param[in] ppRank PP rank to receive the synchronizer from.
+ */
+ void receiveCoordinatesSynchronizerFromPpCudaDirect(int ppRank);
+
+ /*! \brief
+ * Used for lib MPI, receives co-ordinates from PP ranks
+ * \param[in] recvbuf coordinates buffer in GPU memory
+ * \param[in] numAtoms starting element in buffer
+ * \param[in] numBytes number of bytes to transfer
+ * \param[in] ppRank PP rank to send data
*/
- void launchReceiveCoordinatesFromPpCudaDirect(int ppRank);
+ void launchReceiveCoordinatesFromPpCudaMpi(DeviceBuffer<RVec> recvbuf, int numAtoms, int numBytes, int ppRank);
/*! \brief
- * enqueue wait for coordinate data from PP ranks
+ * For lib MPI, wait for coordinates from PP ranks
+ * For thread MPI, enqueue PP co-ordinate transfer event into PME stream
*/
- void enqueueWaitReceiveCoordinatesFromPpCudaDirect();
+ void synchronizeOnCoordinatesFromPpRanks();
private:
class Impl;
- gmx::PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"correct implementation.");
}
-void PmeCoordinateReceiverGpu::launchReceiveCoordinatesFromPpCudaDirect(int /* ppRank */)
+void PmeCoordinateReceiverGpu::receiveCoordinatesSynchronizerFromPpCudaDirect(int /* ppRank */)
{
GMX_ASSERT(!impl_,
"A CPU stub for PME-PP GPU communication was called instead of the correct "
"implementation.");
}
-void PmeCoordinateReceiverGpu::enqueueWaitReceiveCoordinatesFromPpCudaDirect()
+void PmeCoordinateReceiverGpu::launchReceiveCoordinatesFromPpCudaMpi(DeviceBuffer<RVec> /* recvbuf */,
+ int /* numAtoms */,
+ int /* numBytes */,
+ int /* ppRank */)
+{
+ GMX_ASSERT(!impl_,
+ "A CPU stub for PME-PP GPU communication was called instead of the correct "
+ "implementation.");
+}
+
+void PmeCoordinateReceiverGpu::synchronizeOnCoordinatesFromPpRanks()
{
GMX_ASSERT(!impl_,
"A CPU stub for PME-PP GPU communication was called instead of the correct "
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "gromacs/ewald/pme_pp_communication.h"
#include "pme_coordinate_receiver_gpu_impl.h"
#include "config.h"
comm_(comm),
ppRanks_(ppRanks)
{
- GMX_RELEASE_ASSERT(
- GMX_THREAD_MPI,
- "PME-PP GPU Communication is currently only supported with thread-MPI enabled");
request_.resize(ppRanks.size());
ppSync_.resize(ppRanks.size());
}
void PmeCoordinateReceiverGpu::Impl::sendCoordinateBufferAddressToPpRanks(DeviceBuffer<RVec> d_x)
{
-
- int ind_start = 0;
- int ind_end = 0;
- for (const auto& receiver : ppRanks_)
+ // Need to send address to PP rank only for thread-MPI as PP rank pushes data using cudamemcpy
+ if (GMX_THREAD_MPI)
{
- ind_start = ind_end;
- ind_end = ind_start + receiver.numAtoms;
-
- // Data will be transferred directly from GPU.
- void* sendBuf = reinterpret_cast<void*>(&d_x[ind_start]);
+ int ind_start = 0;
+ int ind_end = 0;
+ for (const auto& receiver : ppRanks_)
+ {
+ ind_start = ind_end;
+ ind_end = ind_start + receiver.numAtoms;
+ // Data will be transferred directly from GPU.
+ void* sendBuf = reinterpret_cast<void*>(&d_x[ind_start]);
#if GMX_MPI
- MPI_Send(&sendBuf, sizeof(void**), MPI_BYTE, receiver.rankId, 0, comm_);
+ MPI_Send(&sendBuf, sizeof(void**), MPI_BYTE, receiver.rankId, 0, comm_);
#else
- GMX_UNUSED_VALUE(sendBuf);
+ GMX_UNUSED_VALUE(sendBuf);
#endif
+ }
}
}
-/*! \brief Receive coordinate data directly using CUDA memory copy */
-void PmeCoordinateReceiverGpu::Impl::launchReceiveCoordinatesFromPpCudaDirect(int ppRank)
+/*! \brief Receive coordinate synchronizer pointer from the PP ranks. */
+void PmeCoordinateReceiverGpu::Impl::receiveCoordinatesSynchronizerFromPpCudaDirect(int ppRank)
{
+ GMX_ASSERT(GMX_THREAD_MPI,
+ "receiveCoordinatesSynchronizerFromPpCudaDirect is expected to be called only for "
+ "Thread-MPI");
+
// Data will be pushed directly from PP task
#if GMX_MPI
// Receive event from PP task
- MPI_Irecv(&ppSync_[recvCount_], sizeof(GpuEventSynchronizer*), MPI_BYTE, ppRank, 0, comm_,
- &request_[recvCount_]);
+ MPI_Irecv(&ppSync_[recvCount_], sizeof(GpuEventSynchronizer*), MPI_BYTE, ppRank, 0, comm_, &request_[recvCount_]);
recvCount_++;
#else
GMX_UNUSED_VALUE(ppRank);
#endif
}
-void PmeCoordinateReceiverGpu::Impl::enqueueWaitReceiveCoordinatesFromPpCudaDirect()
+/*! \brief Receive coordinate data using CUDA-aware MPI */
+void PmeCoordinateReceiverGpu::Impl::launchReceiveCoordinatesFromPpCudaMpi(DeviceBuffer<RVec> recvbuf,
+ int numAtoms,
+ int numBytes,
+ int ppRank)
+{
+ GMX_ASSERT(GMX_LIB_MPI,
+ "launchReceiveCoordinatesFromPpCudaMpi is expected to be called only for Lib-MPI");
+
+#if GMX_MPI
+ MPI_Irecv(&recvbuf[numAtoms], numBytes, MPI_BYTE, ppRank, eCommType_COORD_GPU, comm_, &request_[recvCount_++]);
+#else
+ GMX_UNUSED_VALUE(recvbuf);
+ GMX_UNUSED_VALUE(numAtoms);
+ GMX_UNUSED_VALUE(numBytes);
+ GMX_UNUSED_VALUE(ppRank);
+#endif
+}
+
+void PmeCoordinateReceiverGpu::Impl::synchronizeOnCoordinatesFromPpRanks()
{
if (recvCount_ > 0)
{
- // ensure PME calculation doesn't commence until coordinate data has been transferred
+ // ensure PME calculation doesn't commence until coordinate data/remote events
+ // has been transferred
#if GMX_MPI
MPI_Waitall(recvCount_, request_.data(), MPI_STATUS_IGNORE);
#endif
- for (int i = 0; i < recvCount_; i++)
+
+ // Make PME stream wait on PP to PME data trasnfer events
+ if (GMX_THREAD_MPI)
{
- ppSync_[i]->enqueueWaitEvent(pmeStream_);
+ for (int i = 0; i < recvCount_; i++)
+ {
+ ppSync_[i]->enqueueWaitEvent(pmeStream_);
+ }
}
+
// reset receive counter
recvCount_ = 0;
}
impl_->sendCoordinateBufferAddressToPpRanks(d_x);
}
-void PmeCoordinateReceiverGpu::launchReceiveCoordinatesFromPpCudaDirect(int ppRank)
+void PmeCoordinateReceiverGpu::receiveCoordinatesSynchronizerFromPpCudaDirect(int ppRank)
+{
+ impl_->receiveCoordinatesSynchronizerFromPpCudaDirect(ppRank);
+}
+
+void PmeCoordinateReceiverGpu::launchReceiveCoordinatesFromPpCudaMpi(DeviceBuffer<RVec> recvbuf,
+ int numAtoms,
+ int numBytes,
+ int ppRank)
{
- impl_->launchReceiveCoordinatesFromPpCudaDirect(ppRank);
+ impl_->launchReceiveCoordinatesFromPpCudaMpi(recvbuf, numAtoms, numBytes, ppRank);
}
-void PmeCoordinateReceiverGpu::enqueueWaitReceiveCoordinatesFromPpCudaDirect()
+void PmeCoordinateReceiverGpu::synchronizeOnCoordinatesFromPpRanks()
{
- impl_->enqueueWaitReceiveCoordinatesFromPpCudaDirect();
+ impl_->synchronizeOnCoordinatesFromPpRanks();
}
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void sendCoordinateBufferAddressToPpRanks(DeviceBuffer<RVec> d_x);
/*! \brief
- * launch receive of coordinate data from PP rank
- * \param[in] ppRank PP rank to send data
+ * Receive coordinate synchronizer pointer from the PP ranks.
+ * \param[in] ppRank PP rank to receive the synchronizer from.
*/
- void launchReceiveCoordinatesFromPpCudaDirect(int ppRank);
+ void receiveCoordinatesSynchronizerFromPpCudaDirect(int ppRank);
/*! \brief
- * enqueue wait for coordinate data from PP ranks
+ * Used for lib MPI, receives co-ordinates from PP ranks
+ * \param[in] recvbuf coordinates buffer in GPU memory
+ * \param[in] numAtoms starting element in buffer
+ * \param[in] numBytes number of bytes to transfer
+ * \param[in] ppRank PP rank to send data
*/
- void enqueueWaitReceiveCoordinatesFromPpCudaDirect();
+ void launchReceiveCoordinatesFromPpCudaMpi(DeviceBuffer<RVec> recvbuf, int numAtoms, int numBytes, int ppRank);
+
+ /*! \brief
+ * For lib MPI, wait for coordinates from PP ranks
+ * For thread MPI, enqueue PP co-ordinate transfer event into PME stream
+ */
+ void synchronizeOnCoordinatesFromPpRanks();
private:
//! CUDA stream for PME operations
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_PMEFORCESENDERGPU_H
#define GMX_PMEFORCESENDERGPU_H
+#include <memory>
+
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/classhelpers.h"
+#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/utility/gmxmpi.h"
-class DeviceStream;
+class GpuEventSynchronizer;
/*! \libinternal
* \brief Contains information about the PP ranks that partner this PME rank. */
public:
/*! \brief Creates PME GPU Force sender object
- * \param[in] pmeStream CUDA stream used for PME computations
+ * \param[in] pmeForcesReady Event synchronizer marked when PME forces are ready on the GPU
* \param[in] comm Communicator used for simulation
* \param[in] ppRanks List of PP ranks
*/
- PmeForceSenderGpu(
const DeviceStream& pmeStream, MPI_Comm comm, gmx::ArrayRef<PpRanks> ppRanks);
+ PmeForceSenderGpu(
GpuEventSynchronizer* pmeForcesReady, MPI_Comm comm, gmx::ArrayRef<PpRanks> ppRanks);
~PmeForceSenderGpu();
/*! \brief
* Initialization of GPU PME Force sender
* \param[in] d_f force buffer in GPU memory
*/
- void sendForceBufferAddressToPpRanks(rvec* d_f);
+ void sendForceBufferAddressToPpRanks(DeviceBuffer<RVec> d_f);
/*! \brief
- * Send PP data to PP rank
+ * Send force synchronizer to PP rank (used with Thread-MPI)
* \param[in] ppRank PP rank to receive data
*/
- void sendFToPpCudaDirect(int ppRank);
+ void sendFSynchronizerToPpCudaDirect(int ppRank);
+
+ /*! \brief
+ * Send force to PP rank (used with Lib-MPI)
+ * \param[in] sendbuf force buffer in GPU memory
+ * \param[in] offset starting element in buffer
+ * \param[in] numBytes number of bytes to transfer
+ * \param[in] ppRank PP rank to receive data
+ * \param[in] request MPI request to track asynchronous MPI call status
+ */
+ void sendFToPpCudaMpi(DeviceBuffer<RVec> sendbuf, int offset, int numBytes, int ppRank, MPI_Request* request);
private:
class Impl;
- gmx::PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "config.h"
#include "gromacs/ewald/pme_force_sender_gpu.h"
+#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/gmxassert.h"
};
/*!\brief Constructor stub. */
-PmeForceSenderGpu::PmeForceSenderGpu(const DeviceStream& /*pmeStream */,
+PmeForceSenderGpu::PmeForceSenderGpu(GpuEventSynchronizer* /*pmeForcesReady */,
MPI_Comm /* comm */,
gmx::ArrayRef<PpRanks> /* ppRanks */) :
impl_(nullptr)
PmeForceSenderGpu::~PmeForceSenderGpu() = default;
/*!\brief init PME-PP GPU communication stub */
-void PmeForceSenderGpu::sendForceBufferAddressToPpRanks(rvec* /* d_f */)
+void PmeForceSenderGpu::sendForceBufferAddressToPpRanks(DeviceBuffer<RVec> /* d_f */)
{
GMX_ASSERT(!impl_,
"A CPU stub for PME-PP GPU communication initialization was called instead of the "
"correct implementation.");
}
-void PmeForceSenderGpu::sendFToPpCudaDirect(int /* ppRank */)
+void PmeForceSenderGpu::sendFSynchronizerToPpCudaDirect(int /* ppRank */)
+{
+ GMX_ASSERT(!impl_,
+ "A CPU stub for PME-PP GPU communication was called instead of the correct "
+ "implementation.");
+}
+
+void PmeForceSenderGpu::sendFToPpCudaMpi(DeviceBuffer<RVec> /* sendbuf */,
+ int /* offset */,
+ int /* numBytes */,
+ int /* ppRank */,
+ MPI_Request* /* request */)
{
GMX_ASSERT(!impl_,
"A CPU stub for PME-PP GPU communication was called instead of the correct "
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
/*! \brief Create PME-PP GPU communication object */
-PmeForceSenderGpu::Impl::Impl(const DeviceStream& pmeStream, MPI_Comm comm, gmx::ArrayRef<PpRanks> ppRanks) :
- pmeStream_(pmeStream),
+PmeForceSenderGpu::Impl::Impl(GpuEventSynchronizer* pmeForcesReady,
+ MPI_Comm comm,
+ gmx::ArrayRef<PpRanks> ppRanks) :
+ pmeForcesReady_(pmeForcesReady),
comm_(comm),
ppRanks_(ppRanks)
{
- GMX_RELEASE_ASSERT(
- GMX_THREAD_MPI,
- "PME-PP GPU Communication is currently only supported with thread-MPI enabled");
}
PmeForceSenderGpu::Impl::~Impl() = default;
/*! \brief sends force buffer address to PP ranks */
-void PmeForceSenderGpu::Impl::sendForceBufferAddressToPpRanks(rvec* d_f)
+void PmeForceSenderGpu::Impl::sendForceBufferAddressToPpRanks(DeviceBuffer<Float3> d_f)
{
+ // Need to send address to PP rank only for thread-MPI as PP rank pulls
+ // data using cudamemcpy
+ if (!GMX_THREAD_MPI)
+ {
+ return;
+ }
+#if GMX_MPI
int ind_start = 0;
int ind_end = 0;
for (const auto& receiver : ppRanks_)
ind_end = ind_start + receiver.numAtoms;
// Data will be transferred directly from GPU.
- void* sendBuf = reinterpret_cast<void*>(&d_f[ind_start]);
+ Float3* sendBuf = &d_f[ind_start];
-#if GMX_MPI
- MPI_Send(&sendBuf, sizeof(void**), MPI_BYTE, receiver.rankId, 0, comm_);
+ MPI_Send(&sendBuf, sizeof(Float3*), MPI_BYTE, receiver.rankId, 0, comm_);
+ }
#else
- GMX_UNUSED_VALUE(sendBuf);
+ GMX_UNUSED_VALUE(d_f);
#endif
- }
}
-/*! \brief Send PME data directly using CUDA memory copy */
-void PmeForceSenderGpu::Impl::sendFToPpCudaDirect(int ppRank)
+/*! \brief Send PME synchronizer directly using CUDA memory copy */
+void PmeForceSenderGpu::Impl::sendFSynchronizerToPpCudaDirect(int ppRank)
{
- // Data will be pulled directly from PP task
+ GMX_ASSERT(GMX_THREAD_MPI,
+ "sendFSynchronizerToPpCudaDirect is expected to be called only for Thread-MPI");
- // Record and send event to ensure PME force calcs are completed before PP task pulls data
- pmeSync_.markEvent(pmeStream_);
- GpuEventSynchronizer* pmeSyncPtr = &pmeSync_;
+ // Data will be pulled directly from PP task
#if GMX_MPI
// TODO Using MPI_Isend would be more efficient, particularly when
// sending to multiple PP ranks
- MPI_Send(&pmeSyncPtr, sizeof(GpuEventSynchronizer*), MPI_BYTE, ppRank, 0, comm_);
+ MPI_Send(&pmeForcesReady_, sizeof(GpuEventSynchronizer*), MPI_BYTE, ppRank, 0, comm_);
#else
- GMX_UNUSED_VALUE(pmeSyncPtr);
GMX_UNUSED_VALUE(ppRank);
#endif
}
-PmeForceSenderGpu::PmeForceSenderGpu(const DeviceStream& pmeStream,
+/*! \brief Send PME data directly using CUDA-aware MPI */
+void PmeForceSenderGpu::Impl::sendFToPpCudaMpi(DeviceBuffer<RVec> sendbuf,
+ int offset,
+ int numBytes,
+ int ppRank,
+ MPI_Request* request)
+{
+ GMX_ASSERT(GMX_LIB_MPI, "sendFToPpCudaMpi is expected to be called only for Lib-MPI");
+
+#if GMX_MPI
+ // if using GPU direct comm with CUDA-aware MPI, make sure forces are ready on device
+ // before sending it to PP ranks
+ pmeForcesReady_->waitForEvent();
+
+ MPI_Isend(sendbuf[offset], numBytes, MPI_BYTE, ppRank, 0, comm_, request);
+
+#else
+ GMX_UNUSED_VALUE(sendbuf);
+ GMX_UNUSED_VALUE(offset);
+ GMX_UNUSED_VALUE(numBytes);
+ GMX_UNUSED_VALUE(ppRank);
+ GMX_UNUSED_VALUE(request);
+#endif
+}
+
+PmeForceSenderGpu::PmeForceSenderGpu(GpuEventSynchronizer* pmeForcesReady,
MPI_Comm comm,
gmx::ArrayRef<PpRanks> ppRanks) :
- impl_(new Impl(pmeStream, comm, ppRanks))
+ impl_(new Impl(pmeForcesReady, comm, ppRanks))
{
}
PmeForceSenderGpu::~PmeForceSenderGpu() = default;
-void PmeForceSenderGpu::sendForceBufferAddressToPpRanks(rvec* d_f)
+void PmeForceSenderGpu::sendForceBufferAddressToPpRanks(DeviceBuffer<RVec> d_f)
{
impl_->sendForceBufferAddressToPpRanks(d_f);
}
-void PmeForceSenderGpu::sendFToPpCudaDirect(int ppRank)
+void PmeForceSenderGpu::sendFSynchronizerToPpCudaDirect(int ppRank)
+{
+ impl_->sendFSynchronizerToPpCudaDirect(ppRank);
+}
+
+void PmeForceSenderGpu::sendFToPpCudaMpi(DeviceBuffer<RVec> sendbuf,
+ int offset,
+ int numBytes,
+ int ppRank,
+ MPI_Request* request)
{
- impl_->sendFToPpCudaDirect(ppRank);
+ impl_->sendFToPpCudaMpi(sendbuf, offset, numBytes, ppRank, request);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_PMEFORCESENDERGPU_IMPL_H
#include "gromacs/ewald/pme_force_sender_gpu.h"
-#include "gromacs/gpu_utils/gpueventsynchronizer.cuh"
+#include "gromacs/gpu_utils/devicebuffer_datatype.h"
+#include "gromacs/gpu_utils/gputraits.h"
#include "gromacs/utility/arrayref.h"
+class GpuEventSynchronizer;
+
namespace gmx
{
public:
/*! \brief Creates PME GPU Force sender object
- * \param[in] pmeStream CUDA stream used for PME computations
+ * \param[in] pmeForcesReady Event synchronizer marked when PME forces are ready on the GPU
* \param[in] comm Communicator used for simulation
* \param[in] ppRanks List of PP ranks
*/
- Impl(
const DeviceStream& pmeStream, MPI_Comm comm, gmx::ArrayRef<PpRanks> ppRanks);
+ Impl(
GpuEventSynchronizer* pmeForcesReady, MPI_Comm comm, gmx::ArrayRef<PpRanks> ppRanks);
~Impl();
/*! \brief
* sends force buffer address to PP rank
* \param[in] d_f force buffer in GPU memory
*/
- void sendForceBufferAddressToPpRanks(rvec* d_f);
+ void sendForceBufferAddressToPpRanks(DeviceBuffer<Float3> d_f);
/*! \brief
- * Send PP data to PP rank
+ * Send force synchronizer to PP rank (used with Thread-MPI)
* \param[in] ppRank PP rank to receive data
*/
- void sendFToPpCudaDirect(int ppRank);
+ void sendFSynchronizerToPpCudaDirect(int ppRank);
+
+ /*! \brief
+ * Send force to PP rank (used with Lib-MPI)
+ * \param[in] sendbuf force buffer in GPU memory
+ * \param[in] offset starting element in buffer
+ * \param[in] numBytes number of bytes to transfer
+ * \param[in] ppRank PP rank to receive data
+ * \param[in] request MPI request to track asynchronous MPI call status
+ */
+ void sendFToPpCudaMpi(DeviceBuffer<RVec> sendbuf, int offset, int numBytes, int ppRank, MPI_Request* request);
private:
- //! CUDA stream for PME operations
- const DeviceStream& pmeStream_;
- //! Event triggered when to allow remote PP stream to syn with pme stream
- GpuEventSynchronizer pmeSync_;
+ //! Event indicating when PME forces are ready on the GPU in order for PP stream to sync with the PME stream
+ GpuEventSynchronizer* pmeForcesReady_;
//! communicator for simulation
MPI_Comm comm_;
//! list of PP ranks
if (chargeCheck)
{
- sumForceComponents(&fx, &fy, &fz, ixBase, nx, pny, pnz, constOffset, splineIndexBase, tdy,
- tdz, sm_splineParams, gm_gridA);
+ sumForceComponents(
+ &fx, &fy, &fz, ixBase, nx, pny, pnz, constOffset, splineIndexBase, tdy, tdz, sm_splineParams, gm_gridA);
}
// Reduction of partial force contributions
__local float sm_forceReduction[totalSharedMemory];
__local float* sm_forceTemp[DIM];
- reduce_atom_forces(sm_forces, atomIndexLocal, splineIndex, lineIndex,
- kernelParams.grid.realGridSizeFP, fx, fy, fz, sm_forceReduction, sm_forceTemp);
+ reduce_atom_forces(sm_forces,
+ atomIndexLocal,
+ splineIndex,
+ lineIndex,
+ kernelParams.grid.realGridSizeFP,
+ fx,
+ fy,
+ fz,
+ sm_forceReduction,
+ sm_forceTemp);
barrier(CLK_LOCAL_MEM_FENCE);
/* Calculating the final forces with no component branching, atomsPerBlock threads */
const float scale = kernelParams.current.scale;
if (forceIndexLocal < atomsPerBlock)
{
- calculateAndStoreGridForces(sm_forces, forceIndexLocal, forceIndexGlobal,
- kernelParams.current.recipBox, scale, gm_coefficientsA);
+ calculateAndStoreGridForces(
+ sm_forces, forceIndexLocal, forceIndexGlobal, kernelParams.current.recipBox, scale, gm_coefficientsA);
}
#if !defined(_AMD_SOURCE_) && !defined(_NVIDIA_SOURCE_)
chargeCheck = pme_gpu_check_atom_charge(gm_coefficientsB[atomIndexGlobal]);
if (chargeCheck)
{
- sumForceComponents(&fx, &fy, &fz, ixBase, nx, pny, pnz, constOffset, splineIndexBase,
- tdy, tdz, sm_splineParams, gm_gridB);
+ sumForceComponents(
+ &fx, &fy, &fz, ixBase, nx, pny, pnz, constOffset, splineIndexBase, tdy, tdz, sm_splineParams, gm_gridB);
}
- reduce_atom_forces(sm_forces, atomIndexLocal, splineIndex, lineIndex,
- kernelParams.grid.realGridSizeFP, fx, fy, fz, sm_forceReduction, sm_forceTemp);
+ reduce_atom_forces(sm_forces,
+ atomIndexLocal,
+ splineIndex,
+ lineIndex,
+ kernelParams.grid.realGridSizeFP,
+ fx,
+ fy,
+ fz,
+ sm_forceReduction,
+ sm_forceTemp);
barrier(CLK_LOCAL_MEM_FENCE);
if (forceIndexLocal < atomsPerBlock)
{
- calculateAndStoreGridForces(sm_forces, forceIndexLocal, forceIndexGlobal,
- kernelParams.current.recipBox, 1.0F - scale, gm_coefficientsB);
+ calculateAndStoreGridForces(sm_forces,
+ forceIndexLocal,
+ forceIndexGlobal,
+ kernelParams.current.recipBox,
+ 1.0F - scale,
+ gm_coefficientsB);
}
#if !defined(_AMD_SOURCE_) && !defined(_NVIDIA_SOURCE_)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020 by the GROMACS development team.
+ * Copyright (c) 2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
float& fy,
float& fz)
{
- if (!(order & (order - 1))) // Only for orders of power of 2
+ if (gmx::isPowerOfTwo(order)) // Only for orders of power of 2
{
const unsigned int activeMask = c_fullWarpMask;
const float* __restrict__ gm_coefficientsB = kernelParams.atoms.d_coefficients[1];
const float* __restrict__ gm_gridA = kernelParams.grid.d_realGrid[0];
const float* __restrict__ gm_gridB = kernelParams.grid.d_realGrid[1];
- float* __restrict__ gm_forces = kernelParams.atoms.d_forces;
+ static_assert(sizeof(*kernelParams.atoms.d_forces) == 3 * sizeof(float));
+ float* __restrict__ gm_forces = reinterpret_cast<float*>(kernelParams.atoms.d_forces);
/* Global memory pointers for readGlobal */
const float* __restrict__ gm_theta = kernelParams.atoms.d_theta;
const int ithyMax = (threadsPerAtom == ThreadsPerAtom::Order) ? order : threadIdx.y + 1;
if (chargeCheck)
{
- sumForceComponents<order, atomsPerWarp, wrapX, wrapY>(
- &fx, &fy, &fz, ithyMin, ithyMax, ixBase, iz, nx, ny, pny, pnz, atomIndexLocal,
- splineIndexBase, tdz, sm_gridlineIndices, sm_theta, sm_dtheta, gm_gridA);
+ sumForceComponents<order, atomsPerWarp, wrapX, wrapY>(&fx,
+ &fy,
+ &fz,
+ ithyMin,
+ ithyMax,
+ ixBase,
+ iz,
+ nx,
+ ny,
+ pny,
+ pnz,
+ atomIndexLocal,
+ splineIndexBase,
+ tdz,
+ sm_gridlineIndices,
+ sm_theta,
+ sm_dtheta,
+ gm_gridA);
}
// Reduction of partial force contributions
__shared__ float3 sm_forces[atomsPerBlock];
- reduce_atom_forces<order, atomDataSize, blockSize>(sm_forces, atomIndexLocal, splineIndex, lineIndex,
- kernelParams.grid.realGridSizeFP, fx, fy, fz);
+ reduce_atom_forces<order, atomDataSize, blockSize>(
+ sm_forces, atomIndexLocal, splineIndex, lineIndex, kernelParams.grid.realGridSizeFP, fx, fy, fz);
__syncthreads();
/* Calculating the final forces with no component branching, atomsPerBlock threads */
const float scale = kernelParams.current.scale;
if (forceIndexLocal < atomsPerBlock)
{
- calculateAndStoreGridForces(sm_forces, forceIndexLocal, forceIndexGlobal,
- kernelParams.current.recipBox, scale, gm_coefficientsA);
+ calculateAndStoreGridForces(
+ sm_forces, forceIndexLocal, forceIndexGlobal, kernelParams.current.recipBox, scale, gm_coefficientsA);
}
__syncwarp();
const int chargeCheck = pme_gpu_check_atom_charge(gm_coefficientsB[atomIndexGlobal]);
if (chargeCheck)
{
- sumForceComponents<order, atomsPerWarp, wrapX, wrapY>(
- &fx, &fy, &fz, ithyMin, ithyMax, ixBase, iz, nx, ny, pny, pnz, atomIndexLocal,
- splineIndexBase, tdz, sm_gridlineIndices, sm_theta, sm_dtheta, gm_gridB);
+ sumForceComponents<order, atomsPerWarp, wrapX, wrapY>(&fx,
+ &fy,
+ &fz,
+ ithyMin,
+ ithyMax,
+ ixBase,
+ iz,
+ nx,
+ ny,
+ pny,
+ pnz,
+ atomIndexLocal,
+ splineIndexBase,
+ tdz,
+ sm_gridlineIndices,
+ sm_theta,
+ sm_dtheta,
+ gm_gridB);
}
// Reduction of partial force contributions
- reduce_atom_forces<order, atomDataSize, blockSize>(sm_forces, atomIndexLocal, splineIndex,
- lineIndex, kernelParams.grid.realGridSizeFP,
- fx, fy, fz);
+ reduce_atom_forces<order, atomDataSize, blockSize>(
+ sm_forces, atomIndexLocal, splineIndex, lineIndex, kernelParams.grid.realGridSizeFP, fx, fy, fz);
__syncthreads();
/* Calculating the final forces with no component branching, atomsPerBlock threads */
if (forceIndexLocal < atomsPerBlock)
{
- calculateAndStoreGridForces(sm_forces, forceIndexLocal, forceIndexGlobal,
- kernelParams.current.recipBox, 1.0F - scale, gm_coefficientsB);
+ calculateAndStoreGridForces(sm_forces,
+ forceIndexLocal,
+ forceIndexGlobal,
+ kernelParams.current.recipBox,
+ 1.0F - scale,
+ gm_coefficientsB);
}
__syncwarp();
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void inline parallel_3dfft_execute_gpu_wrapper(gmx_pme_t* pme,
const int gridIndex,
enum gmx_fft_direction dir,
- gmx_wallcycle_t wcycle)
+ gmx_wallcycle* wcycle)
{
if (pme_gpu_settings(pme->gpu).performGPUFFT)
{
- wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
- wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_PME);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start_nocount(wcycle, WallCycleSubCounter::LaunchGpuPme);
pme_gpu_3dfft(pme->gpu, dir, gridIndex);
- wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_PME);
- wallcycle_stop(wcycle, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuPme);
+ wallcycle_stop(wcycle, WallCycleCounter::LaunchGpu);
}
else
{
- wallcycle_start(wcycle, ewcPME_FFT_MIXED_MODE);
+ wallcycle_start(wcycle, WallCycleCounter::PmeFftMixedMode);
#pragma omp parallel for num_threads(pme->nthread) schedule(static)
for (int thread = 0; thread < pme->nthread; thread++)
{
gmx_parallel_3dfft_execute(pme->pfft_setup[gridIndex], dir, thread, wcycle);
}
- wallcycle_stop(wcycle, ewcPME_FFT_MIXED_MODE);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeFftMixedMode);
}
}
if (stepWork.haveDynamicBox || shouldUpdateBox) // || is to make the first computation always update
{
- wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
- wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_PME);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start_nocount(wcycle, WallCycleSubCounter::LaunchGpuPme);
pme_gpu_update_input_box(pmeGpu, box);
- wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_PME);
- wallcycle_stop(wcycle, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuPme);
+ wallcycle_stop(wcycle, WallCycleCounter::LaunchGpu);
if (!pme_gpu_settings(pmeGpu).performGPUSolve)
{
/* Spread the coefficients on a grid */
const bool computeSplines = true;
const bool spreadCharges = true;
- wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
- wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_PME);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start_nocount(wcycle, WallCycleSubCounter::LaunchGpuPme);
pme_gpu_spread(pmeGpu, xReadyOnDevice, fftgrids, computeSplines, spreadCharges, lambdaQ);
- wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_PME);
- wallcycle_stop(wcycle, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuPme);
+ wallcycle_stop(wcycle, WallCycleCounter::LaunchGpu);
}
void pme_gpu_launch_complex_transforms(gmx_pme_t* pme, gmx_wallcycle* wcycle, const gmx::StepWorkload& stepWork)
const bool computeEnergyAndVirial = stepWork.computeEnergy || stepWork.computeVirial;
if (!settings.performGPUFFT)
{
- wallcycle_start(wcycle, ewcWAIT_GPU_PME_SPREAD);
+ wallcycle_start(wcycle, WallCycleCounter::WaitGpuPmeSpread);
pme_gpu_sync_spread_grid(pme->gpu);
- wallcycle_stop(wcycle, ewcWAIT_GPU_PME_SPREAD);
+ wallcycle_stop(wcycle, WallCycleCounter::WaitGpuPmeSpread);
}
try
{
const auto gridOrdering =
settings.useDecomposition ? GridOrdering::YZX : GridOrdering::XYZ;
- wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
- wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_PME);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start_nocount(wcycle, WallCycleSubCounter::LaunchGpuPme);
pme_gpu_solve(pmeGpu, gridIndex, cfftgrid, gridOrdering, computeEnergyAndVirial);
- wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_PME);
- wallcycle_stop(wcycle, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuPme);
+ wallcycle_stop(wcycle, WallCycleCounter::LaunchGpu);
}
else
{
- wallcycle_start(wcycle, ewcPME_SOLVE_MIXED_MODE);
+ wallcycle_start(wcycle, WallCycleCounter::PmeSolveMixedMode);
#pragma omp parallel for num_threads(pme->nthread) schedule(static)
for (int thread = 0; thread < pme->nthread; thread++)
{
- solve_pme_yzx(pme, cfftgrid, pme->boxVolume, computeEnergyAndVirial,
- pme->nthread, thread);
+ solve_pme_yzx(pme, cfftgrid, pme->boxVolume, computeEnergyAndVirial, pme->nthread, thread);
}
- wallcycle_stop(wcycle, ewcPME_SOLVE_MIXED_MODE);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeSolveMixedMode);
}
parallel_3dfft_execute_gpu_wrapper(pme, gridIndex, GMX_FFT_COMPLEX_TO_REAL, wcycle);
return;
}
- wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
- wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_PME);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start_nocount(wcycle, WallCycleSubCounter::LaunchGpuPme);
float** fftgrids = pme->fftgrid;
pme_gpu_gather(pme->gpu, fftgrids, lambdaQ);
- wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_PME);
- wallcycle_stop(wcycle, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuPme);
+ wallcycle_stop(wcycle, WallCycleCounter::LaunchGpu);
}
//! Accumulate the \c forcesToAdd to \c f, using the available threads.
{
const int end = forceToAdd.size();
- int gmx_unused nt = gmx_omp_nthreads_get(emntPME);
+ int gmx_unused nt = gmx_omp_nthreads_get(ModuleMultiThread::Pme);
#pragma omp parallel for num_threads(nt) schedule(static)
for (int i = 0; i < end; i++)
{
gmx::ForceWithVirial* forceWithVirial,
gmx_enerdata_t* enerd)
{
- wallcycle_start(wcycle, ewcPME_GPU_F_REDUCTION);
+ wallcycle_start(wcycle, WallCycleCounter::PmeGpuFReduction);
GMX_ASSERT(forceWithVirial, "Invalid force pointer");
if (computeEnergyAndVirial)
GMX_ASSERT(enerd, "Invalid energy output manager");
forceWithVirial->addVirialContribution(output.coulombVirial_);
enerd->term[F_COUL_RECIP] += output.coulombEnergy_;
- enerd->dvdl_lin[efptCOUL] += output.coulombDvdl_;
+ enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Coul] += output.coulombDvdl_;
}
if (output.haveForceOutput_)
{
sum_forces(forceWithVirial->force_, output.forces_);
}
- wallcycle_stop(wcycle, ewcPME_GPU_F_REDUCTION);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeGpuFReduction);
}
bool pme_gpu_try_finish_task(gmx_pme_t* pme,
// TODO: implement c_streamQuerySupported with an additional GpuEventSynchronizer per stream (#2521)
if ((completionKind == GpuTaskCompletion::Check) && c_streamQuerySupported)
{
- wallcycle_start_nocount(wcycle, ewcWAIT_GPU_PME_GATHER);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::WaitGpuPmeGather);
// Query the PME stream for completion of all tasks enqueued and
// if we're not done, stop the timer before early return.
const bool pmeGpuDone = pme_gpu_stream_query(pme->gpu);
- wallcycle_stop(wcycle, ewcWAIT_GPU_PME_GATHER);
+ wallcycle_stop(wcycle, WallCycleCounter::WaitGpuPmeGather);
if (!pmeGpuDone)
{
needToSynchronize = false;
}
- wallcycle_start(wcycle, ewcWAIT_GPU_PME_GATHER);
+ wallcycle_start(wcycle, WallCycleCounter::WaitGpuPmeGather);
// If the above check passed, then there is no need to make an
// explicit synchronization call.
if (needToSynchronize)
pme_gpu_update_timings(pme->gpu);
// There's no support for computing energy without virial, or vice versa
const bool computeEnergyAndVirial = stepWork.computeEnergy || stepWork.computeVirial;
- PmeOutput output = pme_gpu_getOutput(*pme, computeEnergyAndVirial,
- pme->gpu->common->ngrids > 1 ? lambdaQ : 1.0);
- wallcycle_stop(wcycle, ewcWAIT_GPU_PME_GATHER);
+ PmeOutput output = pme_gpu_getOutput(
+ *pme, computeEnergyAndVirial, pme->gpu->common->ngrids > 1 ? lambdaQ : 1.0);
+ wallcycle_stop(wcycle, WallCycleCounter::WaitGpuPmeGather);
GMX_ASSERT(pme->gpu->settings.useGpuForceReduction == !output.haveForceOutput_,
"When forces are reduced on the CPU, there needs to be force output");
{
GMX_ASSERT(pme_gpu_active(pme), "This should be a GPU run of PME but it is not enabled.");
- wallcycle_start(wcycle, ewcWAIT_GPU_PME_GATHER);
+ wallcycle_start(wcycle, WallCycleCounter::WaitGpuPmeGather);
// Synchronize the whole PME stream at once, including D2H result transfers
// if there are outputs we need to wait for at this step; we still call getOutputs
pme_gpu_synchronize(pme->gpu);
}
- PmeOutput output = pme_gpu_getOutput(*pme, computeEnergyAndVirial,
- pme->gpu->common->ngrids > 1 ? lambdaQ : 1.0);
- wallcycle_stop(wcycle, ewcWAIT_GPU_PME_GATHER);
+ PmeOutput output = pme_gpu_getOutput(
+ *pme, computeEnergyAndVirial, pme->gpu->common->ngrids > 1 ? lambdaQ : 1.0);
+ wallcycle_stop(wcycle, WallCycleCounter::WaitGpuPmeGather);
return output;
}
{
GMX_ASSERT(pme_gpu_active(pme), "This should be a GPU run of PME but it is not enabled.");
- wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
- wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_PME);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start_nocount(wcycle, WallCycleSubCounter::LaunchGpuPme);
pme_gpu_update_timings(pme->gpu);
pme_gpu_clear_grids(pme->gpu);
pme_gpu_clear_energy_virial(pme->gpu);
- wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_PME);
- wallcycle_stop(wcycle, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuPme);
+ wallcycle_stop(wcycle, WallCycleCounter::LaunchGpu);
}
-void* pme_gpu_get_device_f(const gmx_pme_t* pme)
+DeviceBuffer<gmx::RVec> pme_gpu_get_device_f(const gmx_pme_t* pme)
{
if (!pme || !pme_gpu_active(pme))
{
- return nullptr;
+ return DeviceBuffer<gmx::RVec>{};
}
return pme_gpu_get_kernelparam_forces(pme->gpu);
}
*/
const int rank = 3, batch = 1;
- result = cufftPlanMany(&planR2C_, rank, realGridSize, realGridSizePadded, 1, realGridSizePaddedTotal,
- complexGridSizePadded, 1, complexGridSizePaddedTotal, CUFFT_R2C, batch);
+ result = cufftPlanMany(&planR2C_,
+ rank,
+ realGridSize,
+ realGridSizePadded,
+ 1,
+ realGridSizePaddedTotal,
+ complexGridSizePadded,
+ 1,
+ complexGridSizePaddedTotal,
+ CUFFT_R2C,
+ batch);
handleCufftError(result, "cufftPlanMany R2C plan failure");
- result = cufftPlanMany(&planC2R_, rank, realGridSize, complexGridSizePadded, 1,
- complexGridSizePaddedTotal, realGridSizePadded, 1,
- realGridSizePaddedTotal, CUFFT_C2R, batch);
+ result = cufftPlanMany(&planC2R_,
+ rank,
+ realGridSize,
+ complexGridSizePadded,
+ 1,
+ complexGridSizePaddedTotal,
+ realGridSizePadded,
+ 1,
+ realGridSizePaddedTotal,
+ CUFFT_C2R,
+ batch);
handleCufftError(result, "cufftPlanMany C2R plan failure");
cudaStream_t stream = pmeGpu->archSpecific->pmeStream_.stream();
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team.
+ * Copyright (c) 2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
# include "gromacs/gpu_utils/gmxopencl.h"
# include "gromacs/gpu_utils/gputraits_ocl.h"
+#elif GMX_GPU_SYCL
+# include "gromacs/gpu_utils/gputraits_sycl.h"
#endif
#include "gromacs/fft/fft.h" // for the enum gmx_fft_direction
// clFFT expects row-major, so dimensions/strides are reversed (ZYX instead of XYZ)
std::array<size_t, DIM> realGridDimensions = { realGridSize[ZZ], realGridSize[YY], realGridSize[XX] };
- std::array<size_t, DIM> realGridStrides = { 1, realGridSizePadded[ZZ],
+ std::array<size_t, DIM> realGridStrides = { 1,
+ realGridSizePadded[ZZ],
realGridSizePadded[YY] * realGridSizePadded[ZZ] };
- std::array<size_t, DIM> complexGridStrides = { 1, complexGridSizePadded[ZZ],
- complexGridSizePadded[YY] * complexGridSizePadded[ZZ] };
+ std::array<size_t, DIM> complexGridStrides = {
+ 1, complexGridSizePadded[ZZ], complexGridSizePadded[YY] * complexGridSizePadded[ZZ]
+ };
constexpr clfftDim dims = CLFFT_3D;
handleClfftError(clfftCreateDefaultPlan(&planR2C_, context, dims, realGridDimensions.data()),
GMX_THROW(
gmx::NotImplementedError("The chosen 3D-FFT case is not implemented on GPUs"));
}
- handleClfftError(clfftEnqueueTransform(plan, direction, deviceStreams_.size(),
- deviceStreams_.data(), waitEvents.size(), waitEvents.data(),
- timingEvent, inputGrids, outputGrids, tempBuffer),
+ handleClfftError(clfftEnqueueTransform(plan,
+ direction,
+ deviceStreams_.size(),
+ deviceStreams_.data(),
+ waitEvents.size(),
+ waitEvents.data(),
+ timingEvent,
+ inputGrids,
+ outputGrids,
+ tempBuffer),
"clFFT execution failure");
}
// TODO have shared table for both parameters to share the fetch, as index is always same?
// TODO compare texture/LDG performance
- sm_fractCoords[sharedMemoryIndex] +=
- fetchFromParamLookupTable(kernelParams.grid.d_fractShiftsTable,
- kernelParams.fractShiftsTableTexture, tableIndex);
+ sm_fractCoords[sharedMemoryIndex] += fetchFromParamLookupTable(
+ kernelParams.grid.d_fractShiftsTable, kernelParams.fractShiftsTableTexture, tableIndex);
sm_gridlineIndices[sharedMemoryIndex] =
fetchFromParamLookupTable(kernelParams.grid.d_gridlineIndicesTable,
- kernelParams.gridlineIndicesTableTexture, tableIndex);
+ kernelParams.gridlineIndicesTableTexture,
+ tableIndex);
if (writeGlobal)
{
gm_gridlineIndices[atomIndexOffset * DIM + sharedMemoryIndex] =
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team.
+ * Copyright (c) 2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gpu_utils/device_context.h"
#include "gromacs/gpu_utils/device_stream.h"
#include "gromacs/gpu_utils/gpu_utils.h"
+#include "gromacs/gpu_utils/pmalloc.h"
+#if GMX_GPU_SYCL
+# include "gromacs/gpu_utils/syclutils.h"
+#endif
#include "gromacs/hardware/device_information.h"
#include "gromacs/math/invertmatrix.h"
#include "gromacs/math/units.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/ewald/pme.h"
#if GMX_GPU_CUDA
-# include "gromacs/gpu_utils/pmalloc_cuda.h"
-
# include "pme.cuh"
-#elif GMX_GPU_OPENCL
-# include "gromacs/gpu_utils/gmxopencl.h"
#endif
-#include "gromacs/ewald/pme.h"
-
#include "pme_gpu_3dfft.h"
#include "pme_gpu_calculate_splines.h"
#include "pme_gpu_constants.h"
for (int gridIndex = 0; gridIndex < pmeGpu->common->ngrids; gridIndex++)
{
allocateDeviceBuffer(&pmeGpu->kernelParams->constants.d_virialAndEnergy[gridIndex],
- c_virialAndEnergyCount, pmeGpu->archSpecific->deviceContext_);
+ c_virialAndEnergyCount,
+ pmeGpu->archSpecific->deviceContext_);
pmalloc(reinterpret_cast<void**>(&pmeGpu->staging.h_virialAndEnergy[gridIndex]), energyAndVirialSize);
}
}
{
for (int gridIndex = 0; gridIndex < pmeGpu->common->ngrids; gridIndex++)
{
- clearDeviceBufferAsync(&pmeGpu->kernelParams->constants.d_virialAndEnergy[gridIndex], 0,
- c_virialAndEnergyCount, pmeGpu->archSpecific->pmeStream_);
+ clearDeviceBufferAsync(&pmeGpu->kernelParams->constants.d_virialAndEnergy[gridIndex],
+ 0,
+ c_virialAndEnergyCount,
+ pmeGpu->archSpecific->pmeStream_);
}
}
GMX_ASSERT(gridIndex < pmeGpu->common->ngrids,
"Invalid combination of gridIndex and number of grids");
- const int splineValuesOffset[DIM] = { 0, pmeGpu->kernelParams->grid.realGridSize[XX],
+ const int splineValuesOffset[DIM] = { 0,
+ pmeGpu->kernelParams->grid.realGridSize[XX],
pmeGpu->kernelParams->grid.realGridSize[XX]
+ pmeGpu->kernelParams->grid.realGridSize[YY] };
memcpy(&pmeGpu->kernelParams->grid.splineValuesOffset, &splineValuesOffset, sizeof(splineValuesOffset));
+ pmeGpu->kernelParams->grid.realGridSize[ZZ];
const bool shouldRealloc = (newSplineValuesSize > pmeGpu->archSpecific->splineValuesSize[gridIndex]);
reallocateDeviceBuffer(&pmeGpu->kernelParams->grid.d_splineModuli[gridIndex],
- newSplineValuesSize, &pmeGpu->archSpecific->splineValuesSize[gridIndex],
+ newSplineValuesSize,
+ &pmeGpu->archSpecific->splineValuesSize[gridIndex],
&pmeGpu->archSpecific->splineValuesCapacity[gridIndex],
pmeGpu->archSpecific->deviceContext_);
if (shouldRealloc)
for (int i = 0; i < DIM; i++)
{
memcpy(pmeGpu->staging.h_splineModuli[gridIndex] + splineValuesOffset[i],
- pmeGpu->common->bsp_mod[i].data(), pmeGpu->common->bsp_mod[i].size() * sizeof(float));
+ pmeGpu->common->bsp_mod[i].data(),
+ pmeGpu->common->bsp_mod[i].size() * sizeof(float));
}
/* TODO: pin original buffer instead! */
copyToDeviceBuffer(&pmeGpu->kernelParams->grid.d_splineModuli[gridIndex],
- pmeGpu->staging.h_splineModuli[gridIndex], 0, newSplineValuesSize,
- pmeGpu->archSpecific->pmeStream_, pmeGpu->settings.transferKind, nullptr);
+ pmeGpu->staging.h_splineModuli[gridIndex],
+ 0,
+ newSplineValuesSize,
+ pmeGpu->archSpecific->pmeStream_,
+ pmeGpu->settings.transferKind,
+ nullptr);
}
void pme_gpu_free_bspline_values(const PmeGpu* pmeGpu)
void pme_gpu_realloc_forces(PmeGpu* pmeGpu)
{
- const size_t newForcesSize = pmeGpu->nAtomsAlloc * DIM;
+ const size_t newForcesSize = pmeGpu->nAtomsAlloc;
GMX_ASSERT(newForcesSize > 0, "Bad number of atoms in PME GPU");
- reallocateDeviceBuffer(&pmeGpu->kernelParams->atoms.d_forces, newForcesSize,
- &pmeGpu->archSpecific->forcesSize, &pmeGpu->archSpecific->forcesSizeAlloc,
+ reallocateDeviceBuffer(&pmeGpu->kernelParams->atoms.d_forces,
+ newForcesSize,
+ &pmeGpu->archSpecific->forcesSize,
+ &pmeGpu->archSpecific->forcesSizeAlloc,
pmeGpu->archSpecific->deviceContext_);
pmeGpu->staging.h_forces.reserveWithPadding(pmeGpu->nAtomsAlloc);
pmeGpu->staging.h_forces.resizeWithPadding(pmeGpu->kernelParams->atoms.nAtoms);
void pme_gpu_copy_input_forces(PmeGpu* pmeGpu)
{
GMX_ASSERT(pmeGpu->kernelParams->atoms.nAtoms > 0, "Bad number of atoms in PME GPU");
- float* h_forcesFloat = reinterpret_cast<float*>(pmeGpu->staging.h_forces.data());
- copyToDeviceBuffer(&pmeGpu->kernelParams->atoms.d_forces, h_forcesFloat, 0,
- DIM * pmeGpu->kernelParams->atoms.nAtoms, pmeGpu->archSpecific->pmeStream_,
- pmeGpu->settings.transferKind, nullptr);
+ copyToDeviceBuffer(&pmeGpu->kernelParams->atoms.d_forces,
+ pmeGpu->staging.h_forces.data(),
+ 0,
+ pmeGpu->kernelParams->atoms.nAtoms,
+ pmeGpu->archSpecific->pmeStream_,
+ pmeGpu->settings.transferKind,
+ nullptr);
}
void pme_gpu_copy_output_forces(PmeGpu* pmeGpu)
{
GMX_ASSERT(pmeGpu->kernelParams->atoms.nAtoms > 0, "Bad number of atoms in PME GPU");
- float* h_forcesFloat = reinterpret_cast<float*>(pmeGpu->staging.h_forces.data());
- copyFromDeviceBuffer(h_forcesFloat, &pmeGpu->kernelParams->atoms.d_forces, 0,
- DIM * pmeGpu->kernelParams->atoms.nAtoms, pmeGpu->archSpecific->pmeStream_,
- pmeGpu->settings.transferKind, nullptr);
+ copyFromDeviceBuffer(pmeGpu->staging.h_forces.data(),
+ &pmeGpu->kernelParams->atoms.d_forces,
+ 0,
+ pmeGpu->kernelParams->atoms.nAtoms,
+ pmeGpu->archSpecific->pmeStream_,
+ pmeGpu->settings.transferKind,
+ nullptr);
}
void pme_gpu_realloc_and_copy_input_coefficients(const PmeGpu* pmeGpu,
const size_t newCoefficientsSize = pmeGpu->nAtomsAlloc;
GMX_ASSERT(newCoefficientsSize > 0, "Bad number of atoms in PME GPU");
reallocateDeviceBuffer(&pmeGpu->kernelParams->atoms.d_coefficients[gridIndex],
- newCoefficientsSize, &pmeGpu->archSpecific->coefficientsSize[gridIndex],
+ newCoefficientsSize,
+ &pmeGpu->archSpecific->coefficientsSize[gridIndex],
&pmeGpu->archSpecific->coefficientsCapacity[gridIndex],
pmeGpu->archSpecific->deviceContext_);
copyToDeviceBuffer(&pmeGpu->kernelParams->atoms.d_coefficients[gridIndex],
- const_cast<float*>(h_coefficients), 0, pmeGpu->kernelParams->atoms.nAtoms,
- pmeGpu->archSpecific->pmeStream_, pmeGpu->settings.transferKind, nullptr);
+ const_cast<float*>(h_coefficients),
+ 0,
+ pmeGpu->kernelParams->atoms.nAtoms,
+ pmeGpu->archSpecific->pmeStream_,
+ pmeGpu->settings.transferKind,
+ nullptr);
const size_t paddingIndex = pmeGpu->kernelParams->atoms.nAtoms;
const size_t paddingCount = pmeGpu->nAtomsAlloc - paddingIndex;
if (paddingCount > 0)
{
- clearDeviceBufferAsync(&pmeGpu->kernelParams->atoms.d_coefficients[gridIndex], paddingIndex,
- paddingCount, pmeGpu->archSpecific->pmeStream_);
+ clearDeviceBufferAsync(&pmeGpu->kernelParams->atoms.d_coefficients[gridIndex],
+ paddingIndex,
+ paddingCount,
+ pmeGpu->archSpecific->pmeStream_);
}
}
const bool shouldRealloc = (newSplineDataSize > pmeGpu->archSpecific->splineDataSize);
int currentSizeTemp = pmeGpu->archSpecific->splineDataSize;
int currentSizeTempAlloc = pmeGpu->archSpecific->splineDataSizeAlloc;
- reallocateDeviceBuffer(&pmeGpu->kernelParams->atoms.d_theta, newSplineDataSize, ¤tSizeTemp,
- ¤tSizeTempAlloc, pmeGpu->archSpecific->deviceContext_);
- reallocateDeviceBuffer(&pmeGpu->kernelParams->atoms.d_dtheta, newSplineDataSize,
- &pmeGpu->archSpecific->splineDataSize, &pmeGpu->archSpecific->splineDataSizeAlloc,
+ reallocateDeviceBuffer(&pmeGpu->kernelParams->atoms.d_theta,
+ newSplineDataSize,
+ ¤tSizeTemp,
+ ¤tSizeTempAlloc,
+ pmeGpu->archSpecific->deviceContext_);
+ reallocateDeviceBuffer(&pmeGpu->kernelParams->atoms.d_dtheta,
+ newSplineDataSize,
+ &pmeGpu->archSpecific->splineDataSize,
+ &pmeGpu->archSpecific->splineDataSizeAlloc,
pmeGpu->archSpecific->deviceContext_);
// the host side reallocation
if (shouldRealloc)
{
const size_t newIndicesSize = DIM * pmeGpu->nAtomsAlloc;
GMX_ASSERT(newIndicesSize > 0, "Bad number of atoms in PME GPU");
- reallocateDeviceBuffer(&pmeGpu->kernelParams->atoms.d_gridlineIndices, newIndicesSize,
+ reallocateDeviceBuffer(&pmeGpu->kernelParams->atoms.d_gridlineIndices,
+ newIndicesSize,
&pmeGpu->archSpecific->gridlineIndicesSize,
&pmeGpu->archSpecific->gridlineIndicesSizeAlloc,
pmeGpu->archSpecific->deviceContext_);
if (pmeGpu->archSpecific->performOutOfPlaceFFT)
{
/* 2 separate grids */
- reallocateDeviceBuffer(&kernelParamsPtr->grid.d_fourierGrid[gridIndex], newComplexGridSize,
+ reallocateDeviceBuffer(&kernelParamsPtr->grid.d_fourierGrid[gridIndex],
+ newComplexGridSize,
&pmeGpu->archSpecific->complexGridSize[gridIndex],
&pmeGpu->archSpecific->complexGridCapacity[gridIndex],
pmeGpu->archSpecific->deviceContext_);
- reallocateDeviceBuffer(&kernelParamsPtr->grid.d_realGrid[gridIndex], newRealGridSize,
+ reallocateDeviceBuffer(&kernelParamsPtr->grid.d_realGrid[gridIndex],
+ newRealGridSize,
&pmeGpu->archSpecific->realGridSize[gridIndex],
&pmeGpu->archSpecific->realGridCapacity[gridIndex],
pmeGpu->archSpecific->deviceContext_);
{
/* A single buffer so that any grid will fit */
const int newGridsSize = std::max(newRealGridSize, newComplexGridSize);
- reallocateDeviceBuffer(&kernelParamsPtr->grid.d_realGrid[gridIndex], newGridsSize,
+ reallocateDeviceBuffer(&kernelParamsPtr->grid.d_realGrid[gridIndex],
+ newGridsSize,
&pmeGpu->archSpecific->realGridSize[gridIndex],
&pmeGpu->archSpecific->realGridCapacity[gridIndex],
pmeGpu->archSpecific->deviceContext_);
{
for (int gridIndex = 0; gridIndex < pmeGpu->common->ngrids; gridIndex++)
{
- clearDeviceBufferAsync(&pmeGpu->kernelParams->grid.d_realGrid[gridIndex], 0,
+ clearDeviceBufferAsync(&pmeGpu->kernelParams->grid.d_realGrid[gridIndex],
+ 0,
pmeGpu->archSpecific->realGridSize[gridIndex],
pmeGpu->archSpecific->pmeStream_);
}
const int newFractShiftsSize = cellCount * (nx + ny + nz);
initParamLookupTable(&kernelParamsPtr->grid.d_fractShiftsTable,
- &kernelParamsPtr->fractShiftsTableTexture, pmeGpu->common->fsh.data(),
- newFractShiftsSize, pmeGpu->archSpecific->deviceContext_);
+ &kernelParamsPtr->fractShiftsTableTexture,
+ pmeGpu->common->fsh.data(),
+ newFractShiftsSize,
+ pmeGpu->archSpecific->deviceContext_);
initParamLookupTable(&kernelParamsPtr->grid.d_gridlineIndicesTable,
- &kernelParamsPtr->gridlineIndicesTableTexture, pmeGpu->common->nn.data(),
- newFractShiftsSize, pmeGpu->archSpecific->deviceContext_);
+ &kernelParamsPtr->gridlineIndicesTableTexture,
+ pmeGpu->common->nn.data(),
+ newFractShiftsSize,
+ pmeGpu->archSpecific->deviceContext_);
}
void pme_gpu_free_fract_shifts(const PmeGpu* pmeGpu)
kernelParamsPtr->fractShiftsTableTexture);
destroyParamLookupTable(&kernelParamsPtr->grid.d_gridlineIndicesTable,
kernelParamsPtr->gridlineIndicesTableTexture);
-#elif GMX_GPU_OPENCL
+#elif GMX_GPU_OPENCL || GMX_GPU_SYCL
freeDeviceBuffer(&kernelParamsPtr->grid.d_fractShiftsTable);
freeDeviceBuffer(&kernelParamsPtr->grid.d_gridlineIndicesTable);
#endif
void pme_gpu_copy_input_gather_grid(const PmeGpu* pmeGpu, const float* h_grid, const int gridIndex)
{
- copyToDeviceBuffer(&pmeGpu->kernelParams->grid.d_realGrid[gridIndex], h_grid, 0,
+ copyToDeviceBuffer(&pmeGpu->kernelParams->grid.d_realGrid[gridIndex],
+ h_grid,
+ 0,
pmeGpu->archSpecific->realGridSize[gridIndex],
- pmeGpu->archSpecific->pmeStream_, pmeGpu->settings.transferKind, nullptr);
+ pmeGpu->archSpecific->pmeStream_,
+ pmeGpu->settings.transferKind,
+ nullptr);
}
void pme_gpu_copy_output_spread_grid(const PmeGpu* pmeGpu, float* h_grid, const int gridIndex)
{
- copyFromDeviceBuffer(h_grid, &pmeGpu->kernelParams->grid.d_realGrid[gridIndex], 0,
+ copyFromDeviceBuffer(h_grid,
+ &pmeGpu->kernelParams->grid.d_realGrid[gridIndex],
+ 0,
pmeGpu->archSpecific->realGridSize[gridIndex],
- pmeGpu->archSpecific->pmeStream_, pmeGpu->settings.transferKind, nullptr);
+ pmeGpu->archSpecific->pmeStream_,
+ pmeGpu->settings.transferKind,
+ nullptr);
pmeGpu->archSpecific->syncSpreadGridD2H.markEvent(pmeGpu->archSpecific->pmeStream_);
}
{
const size_t splinesCount = DIM * pmeGpu->nAtomsAlloc * pmeGpu->common->pme_order;
auto* kernelParamsPtr = pmeGpu->kernelParams.get();
- copyFromDeviceBuffer(pmeGpu->staging.h_dtheta, &kernelParamsPtr->atoms.d_dtheta, 0, splinesCount,
- pmeGpu->archSpecific->pmeStream_, pmeGpu->settings.transferKind, nullptr);
- copyFromDeviceBuffer(pmeGpu->staging.h_theta, &kernelParamsPtr->atoms.d_theta, 0, splinesCount,
- pmeGpu->archSpecific->pmeStream_, pmeGpu->settings.transferKind, nullptr);
- copyFromDeviceBuffer(pmeGpu->staging.h_gridlineIndices, &kernelParamsPtr->atoms.d_gridlineIndices,
- 0, kernelParamsPtr->atoms.nAtoms * DIM, pmeGpu->archSpecific->pmeStream_,
- pmeGpu->settings.transferKind, nullptr);
+ copyFromDeviceBuffer(pmeGpu->staging.h_dtheta,
+ &kernelParamsPtr->atoms.d_dtheta,
+ 0,
+ splinesCount,
+ pmeGpu->archSpecific->pmeStream_,
+ pmeGpu->settings.transferKind,
+ nullptr);
+ copyFromDeviceBuffer(pmeGpu->staging.h_theta,
+ &kernelParamsPtr->atoms.d_theta,
+ 0,
+ splinesCount,
+ pmeGpu->archSpecific->pmeStream_,
+ pmeGpu->settings.transferKind,
+ nullptr);
+ copyFromDeviceBuffer(pmeGpu->staging.h_gridlineIndices,
+ &kernelParamsPtr->atoms.d_gridlineIndices,
+ 0,
+ kernelParamsPtr->atoms.nAtoms * DIM,
+ pmeGpu->archSpecific->pmeStream_,
+ pmeGpu->settings.transferKind,
+ nullptr);
}
void pme_gpu_copy_input_gather_atom_data(const PmeGpu* pmeGpu)
auto* kernelParamsPtr = pmeGpu->kernelParams.get();
// TODO: could clear only the padding and not the whole thing, but this is a test-exclusive code anyway
- clearDeviceBufferAsync(&kernelParamsPtr->atoms.d_gridlineIndices, 0, pmeGpu->nAtomsAlloc * DIM,
+ clearDeviceBufferAsync(&kernelParamsPtr->atoms.d_gridlineIndices,
+ 0,
+ pmeGpu->nAtomsAlloc * DIM,
pmeGpu->archSpecific->pmeStream_);
- clearDeviceBufferAsync(&kernelParamsPtr->atoms.d_dtheta, 0,
+ clearDeviceBufferAsync(&kernelParamsPtr->atoms.d_dtheta,
+ 0,
pmeGpu->nAtomsAlloc * pmeGpu->common->pme_order * DIM,
pmeGpu->archSpecific->pmeStream_);
- clearDeviceBufferAsync(&kernelParamsPtr->atoms.d_theta, 0,
+ clearDeviceBufferAsync(&kernelParamsPtr->atoms.d_theta,
+ 0,
pmeGpu->nAtomsAlloc * pmeGpu->common->pme_order * DIM,
pmeGpu->archSpecific->pmeStream_);
- copyToDeviceBuffer(&kernelParamsPtr->atoms.d_dtheta, pmeGpu->staging.h_dtheta, 0, splinesCount,
- pmeGpu->archSpecific->pmeStream_, pmeGpu->settings.transferKind, nullptr);
- copyToDeviceBuffer(&kernelParamsPtr->atoms.d_theta, pmeGpu->staging.h_theta, 0, splinesCount,
- pmeGpu->archSpecific->pmeStream_, pmeGpu->settings.transferKind, nullptr);
- copyToDeviceBuffer(&kernelParamsPtr->atoms.d_gridlineIndices, pmeGpu->staging.h_gridlineIndices,
- 0, kernelParamsPtr->atoms.nAtoms * DIM, pmeGpu->archSpecific->pmeStream_,
- pmeGpu->settings.transferKind, nullptr);
+ copyToDeviceBuffer(&kernelParamsPtr->atoms.d_dtheta,
+ pmeGpu->staging.h_dtheta,
+ 0,
+ splinesCount,
+ pmeGpu->archSpecific->pmeStream_,
+ pmeGpu->settings.transferKind,
+ nullptr);
+ copyToDeviceBuffer(&kernelParamsPtr->atoms.d_theta,
+ pmeGpu->staging.h_theta,
+ 0,
+ splinesCount,
+ pmeGpu->archSpecific->pmeStream_,
+ pmeGpu->settings.transferKind,
+ nullptr);
+ copyToDeviceBuffer(&kernelParamsPtr->atoms.d_gridlineIndices,
+ pmeGpu->staging.h_gridlineIndices,
+ 0,
+ kernelParamsPtr->atoms.nAtoms * DIM,
+ pmeGpu->archSpecific->pmeStream_,
+ pmeGpu->settings.transferKind,
+ nullptr);
}
void pme_gpu_sync_spread_grid(const PmeGpu* pmeGpu)
GMX_ASSERT(pmeGpu->common->epsilon_r != 0.0F, "PME GPU: bad electrostatic coefficient");
auto* kernelParamsPtr = pme_gpu_get_kernel_params_base_ptr(pmeGpu);
- kernelParamsPtr->constants.elFactor = ONE_4PI_EPS0 / pmeGpu->common->epsilon_r;
+ kernelParamsPtr->constants.elFactor = gmx::c_one4PiEps0 / pmeGpu->common->epsilon_r;
}
void pme_gpu_get_real_grid_sizes(const PmeGpu* pmeGpu, gmx::IVec* gridSize, gmx::IVec* paddedGridSize)
* In CUDA result can be nullptr stub, per GpuRegionTimer implementation.
*
* \param[in] pmeGpu The PME GPU data structure.
- * \param[in] PMEStageId The PME GPU stage gtPME_ index from the enum in src/gromacs/timing/gpu_timing.h
+ * \param[in] pmeStageId The PME GPU stage gtPME_ index from the enum in src/gromacs/timing/gpu_timing.h
*/
-static CommandEvent* pme_gpu_fetch_timing_event(const PmeGpu* pmeGpu, size_t PMEStageId)
+static CommandEvent* pme_gpu_fetch_timing_event(const PmeGpu* pmeGpu, PmeStage pmeStageId)
{
CommandEvent* timingEvent = nullptr;
if (pme_gpu_timings_enabled(pmeGpu))
{
- GMX_ASSERT(PMEStageId < pmeGpu->archSpecific->timingEvents.size(),
- "Wrong PME GPU timing event index");
- timingEvent = pmeGpu->archSpecific->timingEvents[PMEStageId].fetchNextEvent();
+ GMX_ASSERT(pmeStageId < PmeStage::Count, "Wrong PME GPU timing event index");
+ timingEvent = pmeGpu->archSpecific->timingEvents[pmeStageId].fetchNextEvent();
}
return timingEvent;
}
void pme_gpu_3dfft(const PmeGpu* pmeGpu, gmx_fft_direction dir, const int grid_index)
{
- int timerId = (dir == GMX_FFT_REAL_TO_COMPLEX) ? gtPME_FFT_R2C : gtPME_FFT_C2R;
+ PmeStage timerId = (dir == GMX_FFT_REAL_TO_COMPLEX) ? PmeStage::FftTransformR2C
+ : PmeStage::FftTransformC2R;
pme_gpu_start_timing(pmeGpu, timerId);
pmeGpu->archSpecific->fftSetup[grid_index]->perform3dFft(
config.gridSize[0] = dimGrid.first;
config.gridSize[1] = dimGrid.second;
- int timingId;
+ PmeStage timingId;
PmeGpuProgramImpl::PmeKernelHandle kernelPtr = nullptr;
if (computeSplines)
{
if (spreadCharges)
{
- timingId = gtPME_SPLINEANDSPREAD;
- kernelPtr = selectSplineAndSpreadKernelPtr(pmeGpu, pmeGpu->settings.threadsPerAtom,
+ timingId = PmeStage::SplineAndSpread;
+ kernelPtr = selectSplineAndSpreadKernelPtr(pmeGpu,
+ pmeGpu->settings.threadsPerAtom,
writeGlobal || (!recalculateSplines),
pmeGpu->common->ngrids);
}
else
{
- timingId = gtPME_SPLINE;
- kernelPtr = selectSplineKernelPtr(pmeGpu, pmeGpu->settings.threadsPerAtom,
+ timingId = PmeStage::Spline;
+ kernelPtr = selectSplineKernelPtr(pmeGpu,
+ pmeGpu->settings.threadsPerAtom,
writeGlobal || (!recalculateSplines),
pmeGpu->common->ngrids);
}
}
else
{
- timingId = gtPME_SPREAD;
- kernelPtr = selectSpreadKernelPtr(pmeGpu, pmeGpu->settings.threadsPerAtom,
- writeGlobal || (!recalculateSplines), pmeGpu->common->ngrids);
+ timingId = PmeStage::Spread;
+ kernelPtr = selectSpreadKernelPtr(pmeGpu,
+ pmeGpu->settings.threadsPerAtom,
+ writeGlobal || (!recalculateSplines),
+ pmeGpu->common->ngrids);
}
#if c_canEmbedBuffers
const auto kernelArgs = prepareGpuKernelArguments(kernelPtr, config, kernelParamsPtr);
#else
- const auto kernelArgs = prepareGpuKernelArguments(
- kernelPtr, config, kernelParamsPtr, &kernelParamsPtr->atoms.d_theta,
- &kernelParamsPtr->atoms.d_dtheta, &kernelParamsPtr->atoms.d_gridlineIndices,
- &kernelParamsPtr->grid.d_realGrid[FEP_STATE_A], &kernelParamsPtr->grid.d_realGrid[FEP_STATE_B],
- &kernelParamsPtr->grid.d_fractShiftsTable, &kernelParamsPtr->grid.d_gridlineIndicesTable,
- &kernelParamsPtr->atoms.d_coefficients[FEP_STATE_A],
- &kernelParamsPtr->atoms.d_coefficients[FEP_STATE_B], &kernelParamsPtr->atoms.d_coordinates);
+ const auto kernelArgs =
+ prepareGpuKernelArguments(kernelPtr,
+ config,
+ kernelParamsPtr,
+ &kernelParamsPtr->atoms.d_theta,
+ &kernelParamsPtr->atoms.d_dtheta,
+ &kernelParamsPtr->atoms.d_gridlineIndices,
+ &kernelParamsPtr->grid.d_realGrid[FEP_STATE_A],
+ &kernelParamsPtr->grid.d_realGrid[FEP_STATE_B],
+ &kernelParamsPtr->grid.d_fractShiftsTable,
+ &kernelParamsPtr->grid.d_gridlineIndicesTable,
+ &kernelParamsPtr->atoms.d_coefficients[FEP_STATE_A],
+ &kernelParamsPtr->atoms.d_coefficients[FEP_STATE_B],
+ &kernelParamsPtr->atoms.d_coordinates);
#endif
- launchGpuKernel(kernelPtr, config, pmeGpu->archSpecific->pmeStream_, timingEvent,
- "PME spline/spread", kernelArgs);
+ launchGpuKernel(
+ kernelPtr, config, pmeGpu->archSpecific->pmeStream_, timingEvent, "PME spline/spread", kernelArgs);
pme_gpu_stop_timing(pmeGpu, timingId);
const auto& settings = pmeGpu->settings;
float* h_gridFloat = reinterpret_cast<float*>(h_grid);
if (copyInputAndOutputGrid)
{
- copyToDeviceBuffer(&kernelParamsPtr->grid.d_fourierGrid[gridIndex], h_gridFloat, 0,
+ copyToDeviceBuffer(&kernelParamsPtr->grid.d_fourierGrid[gridIndex],
+ h_gridFloat,
+ 0,
pmeGpu->archSpecific->complexGridSize[gridIndex],
- pmeGpu->archSpecific->pmeStream_, pmeGpu->settings.transferKind, nullptr);
+ pmeGpu->archSpecific->pmeStream_,
+ pmeGpu->settings.transferKind,
+ nullptr);
}
int majorDim = -1, middleDim = -1, minorDim = -1;
/ gridLinesPerBlock;
config.gridSize[2] = pmeGpu->kernelParams->grid.complexGridSize[majorDim];
- int timingId = gtPME_SOLVE;
+ PmeStage timingId = PmeStage::Solve;
PmeGpuProgramImpl::PmeKernelHandle kernelPtr = nullptr;
if (gridOrdering == GridOrdering::YZX)
{
#if c_canEmbedBuffers
const auto kernelArgs = prepareGpuKernelArguments(kernelPtr, config, kernelParamsPtr);
#else
- const auto kernelArgs = prepareGpuKernelArguments(
- kernelPtr, config, kernelParamsPtr, &kernelParamsPtr->grid.d_splineModuli[gridIndex],
- &kernelParamsPtr->constants.d_virialAndEnergy[gridIndex],
- &kernelParamsPtr->grid.d_fourierGrid[gridIndex]);
+ const auto kernelArgs =
+ prepareGpuKernelArguments(kernelPtr,
+ config,
+ kernelParamsPtr,
+ &kernelParamsPtr->grid.d_splineModuli[gridIndex],
+ &kernelParamsPtr->constants.d_virialAndEnergy[gridIndex],
+ &kernelParamsPtr->grid.d_fourierGrid[gridIndex]);
#endif
- launchGpuKernel(kernelPtr, config, pmeGpu->archSpecific->pmeStream_, timingEvent, "PME solve",
- kernelArgs);
+ launchGpuKernel(kernelPtr, config, pmeGpu->archSpecific->pmeStream_, timingEvent, "PME solve", kernelArgs);
pme_gpu_stop_timing(pmeGpu, timingId);
if (computeEnergyAndVirial)
{
copyFromDeviceBuffer(pmeGpu->staging.h_virialAndEnergy[gridIndex],
- &kernelParamsPtr->constants.d_virialAndEnergy[gridIndex], 0,
- c_virialAndEnergyCount, pmeGpu->archSpecific->pmeStream_,
- pmeGpu->settings.transferKind, nullptr);
+ &kernelParamsPtr->constants.d_virialAndEnergy[gridIndex],
+ 0,
+ c_virialAndEnergyCount,
+ pmeGpu->archSpecific->pmeStream_,
+ pmeGpu->settings.transferKind,
+ nullptr);
}
if (copyInputAndOutputGrid)
{
- copyFromDeviceBuffer(h_gridFloat, &kernelParamsPtr->grid.d_fourierGrid[gridIndex], 0,
+ copyFromDeviceBuffer(h_gridFloat,
+ &kernelParamsPtr->grid.d_fourierGrid[gridIndex],
+ 0,
pmeGpu->archSpecific->complexGridSize[gridIndex],
- pmeGpu->archSpecific->pmeStream_, pmeGpu->settings.transferKind, nullptr);
+ pmeGpu->archSpecific->pmeStream_,
+ pmeGpu->settings.transferKind,
+ nullptr);
}
}
// TODO test different cache configs
- int timingId = gtPME_GATHER;
+ PmeStage timingId = PmeStage::Gather;
PmeGpuProgramImpl::PmeKernelHandle kernelPtr =
- selectGatherKernelPtr(pmeGpu, pmeGpu->settings.threadsPerAtom,
- readGlobal || (!recalculateSplines), pmeGpu->common->ngrids);
+ selectGatherKernelPtr(pmeGpu,
+ pmeGpu->settings.threadsPerAtom,
+ readGlobal || (!recalculateSplines),
+ pmeGpu->common->ngrids);
// TODO design kernel selection getters and make PmeGpu a friend of PmeGpuProgramImpl
pme_gpu_start_timing(pmeGpu, timingId);
#if c_canEmbedBuffers
const auto kernelArgs = prepareGpuKernelArguments(kernelPtr, config, kernelParamsPtr);
#else
- const auto kernelArgs = prepareGpuKernelArguments(
- kernelPtr, config, kernelParamsPtr, &kernelParamsPtr->atoms.d_coefficients[FEP_STATE_A],
- &kernelParamsPtr->atoms.d_coefficients[FEP_STATE_B],
- &kernelParamsPtr->grid.d_realGrid[FEP_STATE_A], &kernelParamsPtr->grid.d_realGrid[FEP_STATE_B],
- &kernelParamsPtr->atoms.d_theta, &kernelParamsPtr->atoms.d_dtheta,
- &kernelParamsPtr->atoms.d_gridlineIndices, &kernelParamsPtr->atoms.d_forces);
+ const auto kernelArgs =
+ prepareGpuKernelArguments(kernelPtr,
+ config,
+ kernelParamsPtr,
+ &kernelParamsPtr->atoms.d_coefficients[FEP_STATE_A],
+ &kernelParamsPtr->atoms.d_coefficients[FEP_STATE_B],
+ &kernelParamsPtr->grid.d_realGrid[FEP_STATE_A],
+ &kernelParamsPtr->grid.d_realGrid[FEP_STATE_B],
+ &kernelParamsPtr->atoms.d_theta,
+ &kernelParamsPtr->atoms.d_dtheta,
+ &kernelParamsPtr->atoms.d_gridlineIndices,
+ &kernelParamsPtr->atoms.d_forces);
#endif
- launchGpuKernel(kernelPtr, config, pmeGpu->archSpecific->pmeStream_, timingEvent, "PME gather",
- kernelArgs);
+ launchGpuKernel(kernelPtr, config, pmeGpu->archSpecific->pmeStream_, timingEvent, "PME gather", kernelArgs);
pme_gpu_stop_timing(pmeGpu, timingId);
if (pmeGpu->settings.useGpuForceReduction)
}
}
-void* pme_gpu_get_kernelparam_forces(const PmeGpu* pmeGpu)
+DeviceBuffer<gmx::RVec> pme_gpu_get_kernelparam_forces(const PmeGpu* pmeGpu)
{
if (pmeGpu && pmeGpu->kernelParams)
{
}
else
{
- return nullptr;
+ return DeviceBuffer<gmx::RVec>{};
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \param[in] pmeGpu The PME GPU structure.
* \returns Pointer to force data
*/
-GPU_FUNC_QUALIFIER void* pme_gpu_get_kernelparam_forces(const PmeGpu* GPU_FUNC_ARGUMENT(pmeGpu))
- GPU_FUNC_TERM_WITH_RETURN(nullptr);
+GPU_FUNC_QUALIFIER DeviceBuffer<gmx::RVec> pme_gpu_get_kernelparam_forces(const PmeGpu* GPU_FUNC_ARGUMENT(pmeGpu))
+ GPU_FUNC_TERM_WITH_RETURN(DeviceBuffer<gmx::RVec>{});
/*! \brief Return pointer to the sync object triggered after the PME force calculation completion
* \param[in] pmeGpu The PME GPU structure.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! PME CUDA kernels forward declarations. Kernels are documented in their respective files.
template<int order, bool computeSplines, bool spreadCharges, bool wrapX, bool wrapY, int mode, bool writeGlobal, ThreadsPerAtom threadsPerAtom>
-void pme_spline_and_spread_kernel(const PmeGpuCudaKernelParams kernelParams);
+__global__ void pme_spline_and_spread_kernel(const PmeGpuCudaKernelParams kernelParams);
// Add extern declarations to inform that there will be a definition
// provided in another translation unit.
// clang-format off
-extern template void
+extern template void __global__
pme_spline_and_spread_kernel<c_pmeOrder, true, true, c_wrapX, c_wrapY, 1, true, ThreadsPerAtom::Order>(const PmeGpuCudaKernelParams);
-extern template void
+extern template void __global__
pme_spline_and_spread_kernel<c_pmeOrder, true, true, c_wrapX, c_wrapY, 1, true, ThreadsPerAtom::OrderSquared>(const PmeGpuCudaKernelParams);
-extern template void
+extern template void __global__
pme_spline_and_spread_kernel<c_pmeOrder, true, false, c_wrapX, c_wrapY, 1, true, ThreadsPerAtom::Order>(const PmeGpuCudaKernelParams);
-extern template void
+extern template void __global__
pme_spline_and_spread_kernel<c_pmeOrder, true, false, c_wrapX, c_wrapY, 1, true, ThreadsPerAtom::OrderSquared>(const PmeGpuCudaKernelParams);
-extern template void
+extern template __global__ void
pme_spline_and_spread_kernel<c_pmeOrder, false, true, c_wrapX, c_wrapY, 1, true, ThreadsPerAtom::Order>(const PmeGpuCudaKernelParams);
-extern template void
+extern template __global__ void
pme_spline_and_spread_kernel<c_pmeOrder, false, true, c_wrapX, c_wrapY, 1, true, ThreadsPerAtom::OrderSquared>(const PmeGpuCudaKernelParams);
-extern template void
+extern template __global__ void
pme_spline_and_spread_kernel<c_pmeOrder, true, true, c_wrapX, c_wrapY, 1, false, ThreadsPerAtom::Order>(const PmeGpuCudaKernelParams);
-extern template void
+extern template __global__ void
pme_spline_and_spread_kernel<c_pmeOrder, true, true, c_wrapX, c_wrapY, 1, false, ThreadsPerAtom::OrderSquared>(const PmeGpuCudaKernelParams);
-extern template void
+extern template __global__ void
pme_spline_and_spread_kernel<c_pmeOrder, true, true, c_wrapX, c_wrapY, 2, true, ThreadsPerAtom::Order>(const PmeGpuCudaKernelParams);
-extern template void
+extern template __global__ void
pme_spline_and_spread_kernel<c_pmeOrder, true, true, c_wrapX, c_wrapY, 2, true, ThreadsPerAtom::OrderSquared>(const PmeGpuCudaKernelParams);
-extern template void
+extern template __global__ void
pme_spline_and_spread_kernel<c_pmeOrder, true, false, c_wrapX, c_wrapY, 2, true, ThreadsPerAtom::Order>(const PmeGpuCudaKernelParams);
-extern template void
+extern template __global__ void
pme_spline_and_spread_kernel<c_pmeOrder, true, false, c_wrapX, c_wrapY, 2, true, ThreadsPerAtom::OrderSquared>(const PmeGpuCudaKernelParams);
-extern template void
+extern template __global__ void
pme_spline_and_spread_kernel<c_pmeOrder, false, true, c_wrapX, c_wrapY, 2, true, ThreadsPerAtom::Order>(const PmeGpuCudaKernelParams);
-extern template void
+extern template __global__ void
pme_spline_and_spread_kernel<c_pmeOrder, false, true, c_wrapX, c_wrapY, 2, true, ThreadsPerAtom::OrderSquared>(const PmeGpuCudaKernelParams);
-extern template void
+extern template __global__ void
pme_spline_and_spread_kernel<c_pmeOrder, true, true, c_wrapX, c_wrapY, 2, false, ThreadsPerAtom::Order>(const PmeGpuCudaKernelParams);
-extern template void
+extern template __global__ void
pme_spline_and_spread_kernel<c_pmeOrder, true, true, c_wrapX, c_wrapY, 2, false, ThreadsPerAtom::OrderSquared>(const PmeGpuCudaKernelParams);
template<GridOrdering gridOrdering, bool computeEnergyAndVirial, const int gridIndex> /* It is significantly slower to pass gridIndex as a kernel parameter */
-void pme_solve_kernel(const PmeGpuCudaKernelParams kernelParams);
+__global__ void pme_solve_kernel(const PmeGpuCudaKernelParams kernelParams);
// Add extern declarations to inform that there will be a definition
// provided in another translation unit.
// clang-format off
-extern template void pme_solve_kernel<GridOrdering::XYZ, false, c_stateA>(const PmeGpuCudaKernelParams);
-extern template void pme_solve_kernel<GridOrdering::XYZ, true, c_stateA>(const PmeGpuCudaKernelParams);
-extern template void pme_solve_kernel<GridOrdering::YZX, false, c_stateA>(const PmeGpuCudaKernelParams);
-extern template void pme_solve_kernel<GridOrdering::YZX, true, c_stateA>(const PmeGpuCudaKernelParams);
-extern template void pme_solve_kernel<GridOrdering::XYZ, false, c_stateB>(const PmeGpuCudaKernelParams);
-extern template void pme_solve_kernel<GridOrdering::XYZ, true, c_stateB>(const PmeGpuCudaKernelParams);
-extern template void pme_solve_kernel<GridOrdering::YZX, false, c_stateB>(const PmeGpuCudaKernelParams);
-extern template void pme_solve_kernel<GridOrdering::YZX, true, c_stateB>(const PmeGpuCudaKernelParams);
+extern template __global__ void pme_solve_kernel<GridOrdering::XYZ, false, c_stateA>(const PmeGpuCudaKernelParams);
+extern template __global__ void pme_solve_kernel<GridOrdering::XYZ, true, c_stateA>(const PmeGpuCudaKernelParams);
+extern template __global__ void pme_solve_kernel<GridOrdering::YZX, false, c_stateA>(const PmeGpuCudaKernelParams);
+extern template __global__ void pme_solve_kernel<GridOrdering::YZX, true, c_stateA>(const PmeGpuCudaKernelParams);
+extern template __global__ void pme_solve_kernel<GridOrdering::XYZ, false, c_stateB>(const PmeGpuCudaKernelParams);
+extern template __global__ void pme_solve_kernel<GridOrdering::XYZ, true, c_stateB>(const PmeGpuCudaKernelParams);
+extern template __global__ void pme_solve_kernel<GridOrdering::YZX, false, c_stateB>(const PmeGpuCudaKernelParams);
+extern template __global__ void pme_solve_kernel<GridOrdering::YZX, true, c_stateB>(const PmeGpuCudaKernelParams);
// clang-format on
template<int order, bool wrapX, bool wrapY, int nGrids, bool readGlobal, ThreadsPerAtom threadsPerAtom>
-void pme_gather_kernel(const PmeGpuCudaKernelParams kernelParams);
+__global__ void pme_gather_kernel(const PmeGpuCudaKernelParams kernelParams);
// Add extern declarations to inform that there will be a definition
// provided in another translation unit.
// clang-format off
-extern template void pme_gather_kernel<c_pmeOrder, c_wrapX, c_wrapY, 1, true, ThreadsPerAtom::Order> (const PmeGpuCudaKernelParams);
-extern template void pme_gather_kernel<c_pmeOrder, c_wrapX, c_wrapY, 1, false, ThreadsPerAtom::Order> (const PmeGpuCudaKernelParams);
-extern template void pme_gather_kernel<c_pmeOrder, c_wrapX, c_wrapY, 1, true, ThreadsPerAtom::OrderSquared> (const PmeGpuCudaKernelParams);
-extern template void pme_gather_kernel<c_pmeOrder, c_wrapX, c_wrapY, 1, false, ThreadsPerAtom::OrderSquared>(const PmeGpuCudaKernelParams);
-extern template void pme_gather_kernel<c_pmeOrder, c_wrapX, c_wrapY, 2, true, ThreadsPerAtom::Order> (const PmeGpuCudaKernelParams);
-extern template void pme_gather_kernel<c_pmeOrder, c_wrapX, c_wrapY, 2, false, ThreadsPerAtom::Order> (const PmeGpuCudaKernelParams);
-extern template void pme_gather_kernel<c_pmeOrder, c_wrapX, c_wrapY, 2, true, ThreadsPerAtom::OrderSquared> (const PmeGpuCudaKernelParams);
-extern template void pme_gather_kernel<c_pmeOrder, c_wrapX, c_wrapY, 2, false, ThreadsPerAtom::OrderSquared> (const PmeGpuCudaKernelParams);
+extern template __global__ void pme_gather_kernel<c_pmeOrder, c_wrapX, c_wrapY, 1, true, ThreadsPerAtom::Order> (const PmeGpuCudaKernelParams);
+extern template __global__ void pme_gather_kernel<c_pmeOrder, c_wrapX, c_wrapY, 1, false, ThreadsPerAtom::Order> (const PmeGpuCudaKernelParams);
+extern template __global__ void pme_gather_kernel<c_pmeOrder, c_wrapX, c_wrapY, 1, true, ThreadsPerAtom::OrderSquared> (const PmeGpuCudaKernelParams);
+extern template __global__ void pme_gather_kernel<c_pmeOrder, c_wrapX, c_wrapY, 1, false, ThreadsPerAtom::OrderSquared>(const PmeGpuCudaKernelParams);
+extern template __global__ void pme_gather_kernel<c_pmeOrder, c_wrapX, c_wrapY, 2, true, ThreadsPerAtom::Order> (const PmeGpuCudaKernelParams);
+extern template __global__ void pme_gather_kernel<c_pmeOrder, c_wrapX, c_wrapY, 2, false, ThreadsPerAtom::Order> (const PmeGpuCudaKernelParams);
+extern template __global__ void pme_gather_kernel<c_pmeOrder, c_wrapX, c_wrapY, 2, true, ThreadsPerAtom::OrderSquared> (const PmeGpuCudaKernelParams);
+extern template __global__ void pme_gather_kernel<c_pmeOrder, c_wrapX, c_wrapY, 2, false, ThreadsPerAtom::OrderSquared> (const PmeGpuCudaKernelParams);
// clang-format on
PmeGpuProgramImpl::PmeGpuProgramImpl(const DeviceContext& deviceContext) :
// clang-format on
}
-PmeGpuProgramImpl::~PmeGpuProgramImpl() {}
+PmeGpuProgramImpl::~PmeGpuProgramImpl() = default;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "config.h"
+#include <memory>
+
#include "gromacs/gpu_utils/device_context.h"
#include "gromacs/utility/classhelpers.h"
PmeGpuProgramImpl() = delete;
//! Constructor for the given device
explicit PmeGpuProgramImpl(const DeviceContext& deviceContext);
+ // NOLINTNEXTLINE(performance-trivially-destructible)
~PmeGpuProgramImpl();
GMX_DISALLOW_COPY_AND_ASSIGN(PmeGpuProgramImpl);
stat |= clReleaseKernel(solveYZXKernelB);
stat |= clReleaseKernel(solveYZXEnergyKernelB);
GMX_ASSERT(stat == CL_SUCCESS,
- gmx::formatString("Failed to release PME OpenCL resources %d: %s", stat,
+ gmx::formatString("Failed to release PME OpenCL resources %d: %s",
+ stat,
ocl_get_error_string(stat).c_str())
.c_str());
}
"PME OpenCL kernels require >=%d execution width, but the %s kernel "
"has been compiled for the device %s to a %d width and therefore it can not "
"execute correctly.",
- minKernelWarpSize, kernelName, deviceInfo.device_name, kernelWarpSize);
+ minKernelWarpSize,
+ kernelName,
+ deviceInfo.device_name,
+ kernelWarpSize);
GMX_THROW(gmx::InternalError(errorString));
}
}
"-DDIM=%d -DXX=%d -DYY=%d -DZZ=%d "
// decomposition parameter placeholders
"-DwrapX=true -DwrapY=true ",
- warpSize_, c_pmeGpuOrder, c_pmeGpuOrder * c_pmeGpuOrder,
- static_cast<float>(c_pmeMaxUnitcellShift), static_cast<int>(c_skipNeutralAtoms),
- c_virialAndEnergyCount, spreadWorkGroupSize, solveMaxWorkGroupSize,
- gatherWorkGroupSize, DIM, XX, YY, ZZ);
+ warpSize_,
+ c_pmeGpuOrder,
+ c_pmeGpuOrder * c_pmeGpuOrder,
+ static_cast<float>(c_pmeMaxUnitcellShift),
+ static_cast<int>(c_skipNeutralAtoms),
+ c_virialAndEnergyCount,
+ spreadWorkGroupSize,
+ solveMaxWorkGroupSize,
+ gatherWorkGroupSize,
+ DIM,
+ XX,
+ YY,
+ ZZ);
try
{
/* TODO when we have a proper MPI-aware logging module,
the log output here should be written there */
- program = gmx::ocl::compileProgram(stderr, "gromacs/ewald", "pme_program.cl",
- commonDefines, deviceContext_.context(),
- deviceInfo.oclDeviceId, deviceInfo.deviceVendor);
+ program = gmx::ocl::compileProgram(stderr,
+ "gromacs/ewald",
+ "pme_program.cl",
+ commonDefines,
+ deviceContext_.context(),
+ deviceInfo.oclDeviceId,
+ deviceInfo.deviceVendor);
}
catch (gmx::GromacsException& e)
{
{
const std::string errorString = gmx::formatString(
"Failed to create kernels for PME on GPU #%s:\n OpenCL error %d: %s",
- deviceInfo.device_name, clError, ocl_get_error_string(clError).c_str());
+ deviceInfo.device_name,
+ clError,
+ ocl_get_error_string(clError).c_str());
GMX_THROW(gmx::InternalError(errorString));
}
kernels.resize(actualKernelCount);
std::array<char, 100> kernelNamesBuffer;
for (const auto& kernel : kernels)
{
- clError = clGetKernelInfo(kernel, CL_KERNEL_FUNCTION_NAME, kernelNamesBuffer.size(),
- kernelNamesBuffer.data(), nullptr);
+ clError = clGetKernelInfo(
+ kernel, CL_KERNEL_FUNCTION_NAME, kernelNamesBuffer.size(), kernelNamesBuffer.data(), nullptr);
if (clError != CL_SUCCESS)
{
const std::string errorString = gmx::formatString(
"Failed to parse kernels for PME on GPU #%s:\n OpenCL error %d: %s",
- deviceInfo.device_name, clError, ocl_get_error_string(clError).c_str());
+ deviceInfo.device_name,
+ clError,
+ ocl_get_error_string(clError).c_str());
GMX_THROW(gmx::InternalError(errorString));
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _nb_kernel_h_
-#define _nb_kernel_h_
-#include <stdio.h>
+/*! \internal \file
+ * \brief Implements stubs of high-level PME GPU functions for SYCL.
+ *
+ * \author Andrey Alekseenko <al42and@gmail.com>
+ *
+ * \ingroup module_ewald
+ */
+#include "gmxpre.h"
-#include "gromacs/gmxlib/nrnb.h"
-#include "gromacs/math/vectypes.h"
-#include "gromacs/mdtypes/nblist.h"
-#include "gromacs/utility/real.h"
+#include "gromacs/ewald/ewald_utils.h"
-struct t_blocka;
-struct t_mdatoms;
+#include "pme_gpu_3dfft.h"
+#include "pme_gpu_internal.h"
+#include "pme_gpu_program_impl.h"
-/* Structure to collect kernel data not available in forcerec or mdatoms structures.
- * This is only used inside the nonbonded module.
- */
-typedef struct
+PmeGpuProgramImpl::PmeGpuProgramImpl(const DeviceContext& deviceContext) :
+ deviceContext_(deviceContext),
+ warpSize_(0),
+ spreadWorkGroupSize(0),
+ gatherWorkGroupSize(0),
+ solveMaxWorkGroupSize(0)
{
- int flags;
- const struct t_blocka* exclusions;
- const real* lambda;
- real* dvdl;
+ // SYCL-TODO
+}
- /* pointers to tables */
- t_forcetable* table_elec;
- t_forcetable* table_vdw;
- t_forcetable* table_elec_vdw;
+PmeGpuProgramImpl::~PmeGpuProgramImpl() = default;
- /* potentials */
- real* energygrp_elec;
- real* energygrp_vdw;
-} nb_kernel_data_t;
+// [[noreturn]] attributes must be added in the common headers, so it's easier to silence the warning here
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wmissing-noreturn"
+GpuParallel3dFft::GpuParallel3dFft(PmeGpu const* /*pmeGpu*/, int /*gridIndex*/)
+{
+ GMX_THROW(gmx::NotImplementedError("PME is not implemented in SYCL"));
+}
+
+GpuParallel3dFft::~GpuParallel3dFft() = default;
-typedef void nb_kernel_t(t_nblist* gmx_restrict nlist,
- rvec* gmx_restrict x,
- rvec* gmx_restrict f,
- struct t_forcerec* gmx_restrict fr,
- t_mdatoms* gmx_restrict mdatoms,
- nb_kernel_data_t* gmx_restrict kernel_data,
- t_nrnb* gmx_restrict nrnb);
+void GpuParallel3dFft::perform3dFft(gmx_fft_direction /*dir*/, CommandEvent* /*timingEvent*/)
+{
+ GMX_THROW(gmx::NotImplementedError("Not implemented on SYCL yet"));
+}
-#endif /* _nb_kernel_h_ */
+#pragma clang diagnostic pop
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return pmeGpu->archSpecific->useTiming;
}
-void pme_gpu_start_timing(const PmeGpu* pmeGpu, size_t PMEStageId)
+void pme_gpu_start_timing(const PmeGpu* pmeGpu, PmeStage pmeStageId)
{
if (pme_gpu_timings_enabled(pmeGpu))
{
- GMX_ASSERT(PMEStageId < pmeGpu->archSpecific->timingEvents.size(),
- "Wrong PME GPU timing event index");
- pmeGpu->archSpecific->timingEvents[PMEStageId].openTimingRegion(pmeGpu->archSpecific->pmeStream_);
+ GMX_ASSERT(pmeStageId < PmeStage::Count, "Wrong PME GPU timing event index");
+ pmeGpu->archSpecific->timingEvents[pmeStageId].openTimingRegion(pmeGpu->archSpecific->pmeStream_);
}
}
-void pme_gpu_stop_timing(const PmeGpu* pmeGpu, size_t PMEStageId)
+void pme_gpu_stop_timing(const PmeGpu* pmeGpu, PmeStage pmeStageId)
{
if (pme_gpu_timings_enabled(pmeGpu))
{
- GMX_ASSERT(PMEStageId < pmeGpu->archSpecific->timingEvents.size(),
- "Wrong PME GPU timing event index");
- pmeGpu->archSpecific->timingEvents[PMEStageId].closeTimingRegion(pmeGpu->archSpecific->pmeStream_);
+ GMX_ASSERT(pmeStageId < PmeStage::Count, "Wrong PME GPU timing event index");
+ pmeGpu->archSpecific->timingEvents[pmeStageId].closeTimingRegion(pmeGpu->archSpecific->pmeStream_);
}
}
if (pme_gpu_timings_enabled(pmeGpu))
{
GMX_RELEASE_ASSERT(timings, "Null GPU timing pointer");
- for (size_t i = 0; i < pmeGpu->archSpecific->timingEvents.size(); i++)
+ for (auto key : keysOf(timings->timing))
{
- timings->timing[i].t = pmeGpu->archSpecific->timingEvents[i].getTotalTime();
- timings->timing[i].c = pmeGpu->archSpecific->timingEvents[i].getCallCount();
+ timings->timing[key].t = pmeGpu->archSpecific->timingEvents[key].getTotalTime();
+ timings->timing[key].c = pmeGpu->archSpecific->timingEvents[key].getCallCount();
}
}
}
{
if (pme_gpu_timings_enabled(pmeGpu))
{
- for (const size_t& activeTimer : pmeGpu->archSpecific->activeTimers)
+ for (const auto& activeTimer : pmeGpu->archSpecific->activeTimers)
{
pmeGpu->archSpecific->timingEvents[activeTimer].getLastRangeTime();
}
if (pme_gpu_timings_enabled(pmeGpu))
{
pmeGpu->archSpecific->activeTimers.clear();
- pmeGpu->archSpecific->activeTimers.insert(gtPME_SPLINEANDSPREAD);
+ pmeGpu->archSpecific->activeTimers.insert(PmeStage::SplineAndSpread);
const auto& settings = pme_gpu_settings(pmeGpu);
// TODO: no separate gtPME_SPLINE and gtPME_SPREAD as they are not used currently
if (settings.performGPUFFT)
{
- pmeGpu->archSpecific->activeTimers.insert(gtPME_FFT_C2R);
- pmeGpu->archSpecific->activeTimers.insert(gtPME_FFT_R2C);
+ pmeGpu->archSpecific->activeTimers.insert(PmeStage::FftTransformC2R);
+ pmeGpu->archSpecific->activeTimers.insert(PmeStage::FftTransformR2C);
}
if (settings.performGPUSolve)
{
- pmeGpu->archSpecific->activeTimers.insert(gtPME_SOLVE);
+ pmeGpu->archSpecific->activeTimers.insert(PmeStage::Solve);
}
if (settings.performGPUGather)
{
- pmeGpu->archSpecific->activeTimers.insert(gtPME_GATHER);
+ pmeGpu->archSpecific->activeTimers.insert(PmeStage::Gather);
}
}
}
{
if (pme_gpu_timings_enabled(pmeGpu))
{
- for (size_t i = 0; i < pmeGpu->archSpecific->timingEvents.size(); i++)
+ for (auto key : keysOf(pmeGpu->archSpecific->timingEvents))
{
- pmeGpu->archSpecific->timingEvents[i].reset();
+ pmeGpu->archSpecific->timingEvents[key].reset();
}
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct gmx_wallclock_gpu_pme_t;
struct PmeGpu;
+enum class PmeStage : int;
+
/*! \libinternal \brief
* Starts timing the certain PME GPU stage during a single computation (if timings are enabled).
*
* \param[in] pmeGpu The PME GPU data structure.
- * \param[in] PMEStageId The PME GPU stage gtPME_ index from the enum in src/gromacs/timing/gpu_timing.h
+ * \param[in] pmeStageId The PME GPU stage gtPME_ index from the enum in src/gromacs/timing/gpu_timing.h
*/
-void pme_gpu_start_timing(const PmeGpu* pmeGpu, size_t PMEStageId);
+void pme_gpu_start_timing(const PmeGpu* pmeGpu, PmeStage pmeStageId);
/*! \libinternal \brief
* Stops timing the certain PME GPU stage during a single computation (if timings are enabled).
*
* \param[in] pmeGpu The PME GPU data structure.
- * \param[in] PMEStageId The PME GPU stage gtPME_ index from the enum in src/gromacs/timing/gpu_timing.h
+ * \param[in] pmeStageId The PME GPU stage gtPME_ index from the enum in src/gromacs/timing/gpu_timing.h
*/
-void pme_gpu_stop_timing(const PmeGpu* pmeGpu, size_t PMEStageId);
+void pme_gpu_stop_timing(const PmeGpu* pmeGpu, PmeStage pmeStageId);
/*! \brief
* Tells if CUDA-based performance tracking is enabled for PME.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
struct PmeGpuConstParams
{
- /*! \brief Electrostatics coefficient = ONE_4PI_EPS0 / pme->epsilon_r */
+ /*! \brief Electrostatics coefficient = c_one4PiEps0 / pme->epsilon_r */
float elFactor;
/*! \brief Virial and energy GPU array. Size is c_virialAndEnergyCount (7) floats.
* The element order is virxx, viryy, virzz, virxy, virxz, viryz, energy. */
* The forces change and need to be copied from (and possibly to) the GPU for every PME
* computation, but reallocation happens only at DD.
*/
- HIDE_FROM_OPENCL_COMPILER(DeviceBuffer<float>) d_forces;
+ HIDE_FROM_OPENCL_COMPILER(DeviceBuffer<gmx::RVec>) d_forces;
/*! \brief Global GPU memory array handle with ivec atom gridline indices.
* Computed on GPU in the spline calculation part.
*/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct PmeGpuCudaKernelParams;
/*! \brief A typedef for including the GPU kernel arguments data by pointer */
typedef PmeGpuCudaKernelParams PmeGpuKernelParams;
-#elif GMX_GPU_OPENCL
+#elif GMX_GPU_OPENCL || GMX_GPU_SYCL
struct PmeGpuKernelParamsBase;
/*! \brief A typedef for including the GPU kernel arguments data by pointer */
typedef PmeGpuKernelParamsBase PmeGpuKernelParams;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define PMEGPUTYPESHOSTIMPL_H
#include "config.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include <array>
#include <set>
#elif GMX_GPU_OPENCL
# include "gromacs/gpu_utils/gpueventsynchronizer_ocl.h"
# include "gromacs/gpu_utils/gpuregiontimer_ocl.h"
+#elif GMX_GPU_SYCL
+# include "gromacs/gpu_utils/gpueventsynchronizer_sycl.h"
+# include "gromacs/gpu_utils/gpuregiontimer_sycl.h"
#endif
#include "gromacs/timing/gpu_timing.h" // for gtPME_EVENT_COUNT
std::vector<std::unique_ptr<GpuParallel3dFft>> fftSetup;
//! All the timers one might use
- std::array<GpuRegionTimer, gtPME_EVENT_COUNT> timingEvents;
+ gmx::EnumerationArray<PmeStage, GpuRegionTimer> timingEvents;
//! Indices of timingEvents actually used
- std::set<size_t> activeTimers;
+ std::set<PmeStage> activeTimers;
/* GPU arrays element counts (not the arrays sizes in bytes!).
* They might be larger than the actual meaningful data sizes.
/* Copy data to contiguous send buffer */
if (debug)
{
- fprintf(debug, "PME send rank %d %d -> %d grid start %d Communicating %d to %d\n",
- pme->nodeid, overlap->nodeid, send_id, pme->pmegrid_start_iy,
+ fprintf(debug,
+ "PME send rank %d %d -> %d grid start %d Communicating %d to %d\n",
+ pme->nodeid,
+ overlap->nodeid,
+ send_id,
+ pme->pmegrid_start_iy,
send_index0 - pme->pmegrid_start_iy,
send_index0 - pme->pmegrid_start_iy + send_nindex);
}
datasize = pme->pmegrid_nx * pme->nkz;
- MPI_Sendrecv(overlap->sendbuf.data(), send_nindex * datasize, GMX_MPI_REAL, send_id, ipulse,
- overlap->recvbuf.data(), recv_nindex * datasize, GMX_MPI_REAL, recv_id, ipulse,
- overlap->mpi_comm, &stat);
+ MPI_Sendrecv(overlap->sendbuf.data(),
+ send_nindex * datasize,
+ GMX_MPI_REAL,
+ send_id,
+ ipulse,
+ overlap->recvbuf.data(),
+ recv_nindex * datasize,
+ GMX_MPI_REAL,
+ recv_id,
+ ipulse,
+ overlap->mpi_comm,
+ &stat);
/* Get data from contiguous recv buffer */
if (debug)
{
- fprintf(debug, "PME recv rank %d %d <- %d grid start %d Communicating %d to %d\n",
- pme->nodeid, overlap->nodeid, recv_id, pme->pmegrid_start_iy,
+ fprintf(debug,
+ "PME recv rank %d %d <- %d grid start %d Communicating %d to %d\n",
+ pme->nodeid,
+ overlap->nodeid,
+ recv_id,
+ pme->pmegrid_start_iy,
recv_index0 - pme->pmegrid_start_iy,
recv_index0 - pme->pmegrid_start_iy + recv_nindex);
}
if (debug)
{
- fprintf(debug, "PME send rank %d %d -> %d grid start %d Communicating %d to %d\n",
- pme->nodeid, overlap->nodeid, send_id, pme->pmegrid_start_ix,
+ fprintf(debug,
+ "PME send rank %d %d -> %d grid start %d Communicating %d to %d\n",
+ pme->nodeid,
+ overlap->nodeid,
+ send_id,
+ pme->pmegrid_start_ix,
send_index0 - pme->pmegrid_start_ix,
send_index0 - pme->pmegrid_start_ix + send_nindex);
- fprintf(debug, "PME recv rank %d %d <- %d grid start %d Communicating %d to %d\n",
- pme->nodeid, overlap->nodeid, recv_id, pme->pmegrid_start_ix,
+ fprintf(debug,
+ "PME recv rank %d %d <- %d grid start %d Communicating %d to %d\n",
+ pme->nodeid,
+ overlap->nodeid,
+ recv_id,
+ pme->pmegrid_start_ix,
recv_index0 - pme->pmegrid_start_ix,
recv_index0 - pme->pmegrid_start_ix + recv_nindex);
}
- MPI_Sendrecv(sendptr, send_nindex * datasize, GMX_MPI_REAL, send_id, ipulse, recvptr,
- recv_nindex * datasize, GMX_MPI_REAL, recv_id, ipulse, overlap->mpi_comm, &stat);
+ MPI_Sendrecv(sendptr,
+ send_nindex * datasize,
+ GMX_MPI_REAL,
+ send_id,
+ ipulse,
+ recvptr,
+ recv_nindex * datasize,
+ GMX_MPI_REAL,
+ recv_id,
+ ipulse,
+ overlap->mpi_comm,
+ &stat);
/* ADD data from contiguous recv buffer */
if (direction == GMX_SUM_GRID_FORWARD)
int pmeidx, fftidx;
/* Dimensions should be identical for A/B grid, so we just use A here */
- gmx_parallel_3dfft_real_limits(pme->pfft_setup[grid_index], local_fft_ndata, local_fft_offset,
- local_fft_size);
+ gmx_parallel_3dfft_real_limits(
+ pme->pfft_setup[grid_index], local_fft_ndata, local_fft_offset, local_fft_size);
local_pme_size[0] = pme->pmegrid_nx;
local_pme_size[1] = pme->pmegrid_ny;
val = 100 * pmegrid[pmeidx];
if (pmegrid[pmeidx] != 0)
{
- gmx_fprintf_pdb_atomline(fp, epdbATOM, pmeidx, "CA", ' ', "GLY", ' ', pmeidx,
- ' ', 5.0 * ix, 5.0 * iy, 5.0 * iz, 1.0, val, "");
+ gmx_fprintf_pdb_atomline(fp,
+ epdbATOM,
+ pmeidx,
+ "CA",
+ ' ',
+ "GLY",
+ ' ',
+ pmeidx,
+ ' ',
+ 5.0 * ix,
+ 5.0 * iy,
+ 5.0 * iz,
+ 1.0,
+ val,
+ "");
}
if (pmegrid[pmeidx] != 0)
{
- fprintf(fp2, "%-12s %5d %5d %5d %12.5e\n", "qgrid",
- pme->pmegrid_start_ix + ix, pme->pmegrid_start_iy + iy,
- pme->pmegrid_start_iz + iz, pmegrid[pmeidx]);
+ fprintf(fp2,
+ "%-12s %5d %5d %5d %12.5e\n",
+ "qgrid",
+ pme->pmegrid_start_ix + ix,
+ pme->pmegrid_start_iy + iy,
+ pme->pmegrid_start_iz + iz,
+ pmegrid[pmeidx]);
}
#endif
}
c1 = omp_cyc_start();
#endif
/* Dimensions should be identical for A/B grid, so we just use A here */
- gmx_parallel_3dfft_real_limits(pme->pfft_setup[grid_index], local_fft_ndata, local_fft_offset,
- local_fft_size);
+ gmx_parallel_3dfft_real_limits(
+ pme->pfft_setup[grid_index], local_fft_ndata, local_fft_offset, local_fft_size);
local_pme_size[0] = pme->pmegrid_nx;
local_pme_size[1] = pme->pmegrid_ny;
gmx_fatal(FARGS,
"PME grid thread division (%d x %d x %d) does not match the total number of "
"threads (%d)",
- nsub[XX], nsub[YY], nsub[ZZ], nthread);
+ nsub[XX],
+ nsub[YY],
+ nsub[ZZ],
+ nthread);
}
}
if (debug)
{
- fprintf(debug, "pmegrid thread local division: %d x %d x %d\n", grids->nc[XX],
- grids->nc[YY], grids->nc[ZZ]);
- fprintf(debug, "pmegrid %d %d %d max thread pmegrid %d %d %d\n", nx, ny, nz, nst[XX],
- nst[YY], nst[ZZ]);
+ fprintf(debug,
+ "pmegrid thread local division: %d x %d x %d\n",
+ grids->nc[XX],
+ grids->nc[YY],
+ grids->nc[ZZ]);
+ fprintf(debug, "pmegrid %d %d %d max thread pmegrid %d %d %d\n", nx, ny, nz, nst[XX], nst[YY], nst[ZZ]);
}
snew(grids->grid_th, grids->nthread);
t = 0;
gridsize = nst[XX] * nst[YY] * nst[ZZ];
set_gridsize_alignment(&gridsize, pme_order);
- snew_aligned(grids->grid_all, grids->nthread * gridsize + (grids->nthread + 1) * GMX_CACHE_SEP,
+ snew_aligned(grids->grid_all,
+ grids->nthread * gridsize + (grids->nthread + 1) * GMX_CACHE_SEP,
SIMD4_ALIGNMENT);
for (x = 0; x < grids->nc[XX]; x++)
{
for (z = 0; z < grids->nc[ZZ]; z++)
{
- pmegrid_init(&grids->grid_th[t], x, y, z, (n[XX] * (x)) / grids->nc[XX],
- (n[YY] * (y)) / grids->nc[YY], (n[ZZ] * (z)) / grids->nc[ZZ],
- (n[XX] * (x + 1)) / grids->nc[XX], (n[YY] * (y + 1)) / grids->nc[YY],
- (n[ZZ] * (z + 1)) / grids->nc[ZZ], TRUE, pme_order,
+ pmegrid_init(&grids->grid_th[t],
+ x,
+ y,
+ z,
+ (n[XX] * (x)) / grids->nc[XX],
+ (n[YY] * (y)) / grids->nc[YY],
+ (n[ZZ] * (z)) / grids->nc[ZZ],
+ (n[XX] * (x + 1)) / grids->nc[XX],
+ (n[YY] * (y + 1)) / grids->nc[YY],
+ (n[ZZ] * (z + 1)) / grids->nc[ZZ],
+ TRUE,
+ pme_order,
grids->grid_all + GMX_CACHE_SEP + t * (gridsize + GMX_CACHE_SEP));
t++;
}
}
if (debug != nullptr)
{
- fprintf(debug, "pmegrid thread grid communication range in %c: %d\n", 'x' + d,
+ fprintf(debug,
+ "pmegrid thread grid communication range in %c: %d\n",
+ 'x' + d,
grids->nthread_comm[d]);
}
/* It should be possible to make grids->nthread_comm[d]==grids->nc[d]
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct PmeGpu;
enum class PmeRunMode;
+enum class LongRangeVdW : int;
//@{
//! Grid indices for A state for charge and Lennard-Jones C6
class EwaldBoxZScaler* boxScaler; /**< The scaling data Ewald uses with walls (set at pme_init constant for the entire run) */
- int ljpme_combination_rule; /* Type of combination rule in LJ-PME */
+ LongRangeVdW ljpme_combination_rule; /* Type of combination rule in LJ-PME */
int ngrids; /* number of grids we maintain for pmegrid, (c)fftgrid and pfft_setups*/
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "pme_load_balancing.h"
#include <cassert>
const double c_startupTimeDelay = 5.0;
/*! \brief Enumeration whose values describe the effect limiting the load balancing */
-enum epmelb
+enum class PmeLoadBalancingLimit : int
{
- epmelblimNO,
- epmelblimBOX,
- epmelblimDD,
- epmelblimPMEGRID,
- epmelblimMAXSCALING,
- epmelblimNR
+ No,
+ Box,
+ DD,
+ PmeGrid,
+ MaxScaling,
+ Count
};
-/*! \brief Descriptive strings matching ::epmelb */
-static const char* pmelblim_str[epmelblimNR] = { "no", "box size", "domain decompostion",
- "PME grid restriction",
- "maximum allowed grid scaling" };
+/*! \brief Descriptive strings for PmeLoadBalancingLimit \c enumValue */
+static const char* enumValueToString(PmeLoadBalancingLimit enumValue)
+{
+ constexpr gmx::EnumerationArray<PmeLoadBalancingLimit, const char*> pmeLoadBalancingLimitNames = {
+ "no",
+ "box size",
+ "domain decompostion",
+ "PME grid restriction",
+ "maximum allowed grid scaling"
+ };
+ return pmeLoadBalancingLimitNames[enumValue];
+}
struct pme_load_balancing_t
{
int lower_limit; /**< don't go below this setup index */
int start; /**< start of setup index range to consider in stage>0 */
int end; /**< end of setup index range to consider in stage>0 */
- int elimited; /**< was the balancing limited, uses enum above */
- int cutoff_scheme; /**< Verlet or group cut-offs */
+ PmeLoadBalancingLimit elimited; /**< was the balancing limited, uses enum above */
+ CutoffScheme cutoff_scheme; /**< Verlet or group cut-offs */
int stage; /**< the current stage */
if (!pme_lb->bSepPMERanks)
{
- GMX_RELEASE_ASSERT(pmedata,
- "On ranks doing both PP and PME we need a valid pmedata object");
+ GMX_RELEASE_ASSERT(pmedata, "On ranks doing both PP and PME we need a valid pmedata object");
pme_lb->setup[0].pmedata = pmedata;
}
pme_lb->lower_limit = 0;
pme_lb->start = 0;
pme_lb->end = 0;
- pme_lb->elimited = epmelblimNO;
+ pme_lb->elimited = PmeLoadBalancingLimit::No;
pme_lb->cycles_n = 0;
pme_lb->cycles_c = 0;
fac *= 1.01;
clear_ivec(set.grid);
- sp = calcFftGrid(nullptr, pme_lb->box_start, fac * pme_lb->setup[pme_lb->cur].spacing,
- minimalPmeGridSize(pme_order), &set.grid[XX], &set.grid[YY], &set.grid[ZZ]);
+ sp = calcFftGrid(nullptr,
+ pme_lb->box_start,
+ fac * pme_lb->setup[pme_lb->cur].spacing,
+ minimalPmeGridSize(pme_order),
+ &set.grid[XX],
+ &set.grid[YY],
+ &set.grid[ZZ]);
/* As here we can't easily check if one of the PME ranks
* uses threading, we do a conservative grid check.
* This means we can't use pme_order or less grid lines
* per PME rank along x, which is not a strong restriction.
*/
- grid_ok = gmx_pme_check_restrictions(pme_order, set.grid[XX], set.grid[YY], set.grid[ZZ],
- numPmeDomains.x, true, false);
+ grid_ok = gmx_pme_check_restrictions(
+ pme_order, set.grid[XX], set.grid[YY], set.grid[ZZ], numPmeDomains.x, true, false);
} while (sp <= 1.001 * pme_lb->setup[pme_lb->cur].spacing || !grid_ok);
set.rcut_coulomb = pme_lb->cut_spacing * sp;
set.rcut_coulomb = pme_lb->rcut_coulomb_start;
}
- if (pme_lb->cutoff_scheme == ecutsVERLET)
+ if (pme_lb->cutoff_scheme == CutoffScheme::Verlet)
{
/* Never decrease the Coulomb and VdW list buffers */
set.rlistOuter = std::max(set.rcut_coulomb + pme_lb->rbufOuter_coulomb,
if (debug)
{
- fprintf(debug, "PME loadbal: grid %d %d %d, coulomb cutoff %f\n", set.grid[XX],
- set.grid[YY], set.grid[ZZ], set.rcut_coulomb);
+ fprintf(debug,
+ "PME loadbal: grid %d %d %d, coulomb cutoff %f\n",
+ set.grid[XX],
+ set.grid[YY],
+ set.grid[ZZ],
+ set.rcut_coulomb);
}
pme_lb->setup.push_back(set);
return TRUE;
/*! \brief Print the PME grid */
static void print_grid(FILE* fp_err, FILE* fp_log, const char* pre, const char* desc, const pme_setup_t* set, double cycles)
{
- auto buf = gmx::formatString("%-11s%10s pme grid %d %d %d, coulomb cutoff %.3f", pre, desc,
- set->grid[XX], set->grid[YY], set->grid[ZZ], set->rcut_coulomb);
+ auto buf = gmx::formatString("%-11s%10s pme grid %d %d %d, coulomb cutoff %.3f",
+ pre,
+ desc,
+ set->grid[XX],
+ set->grid[YY],
+ set->grid[ZZ],
+ set->rcut_coulomb);
if (cycles >= 0)
{
buf += gmx::formatString(": %.1f M-cycles", cycles * 1e-6);
{
auto buf = gmx::formatString(
"step %4s: the %s limits the PME load balancing to a coulomb cut-off of %.3f",
- gmx::int64ToString(step).c_str(), pmelblim_str[pme_lb->elimited],
+ gmx::int64ToString(step).c_str(),
+ enumValueToString(pme_lb->elimited),
pme_lb->setup[pme_loadbal_end(pme_lb) - 1].rcut_coulomb);
if (fp_err != nullptr)
{
"is more than %f\n"
"Increased the number stages to %d"
" and ignoring the previous performance\n",
- set->grid[XX], set->grid[YY], set->grid[ZZ], set->cycles * 1e-6,
- cycles * 1e-6, maxFluctuationAccepted, pme_lb->nstage);
+ set->grid[XX],
+ set->grid[YY],
+ set->grid[ZZ],
+ set->cycles * 1e-6,
+ cycles * 1e-6,
+ maxFluctuationAccepted,
+ pme_lb->nstage);
}
}
set->cycles = std::min(set->cycles, cycles);
if (!OK)
{
- pme_lb->elimited = epmelblimPMEGRID;
+ pme_lb->elimited = PmeLoadBalancingLimit::PmeGrid;
}
}
&& pme_lb->setup[pme_lb->cur + 1].spacing > c_maxSpacingScaling * pme_lb->setup[0].spacing)
{
OK = FALSE;
- pme_lb->elimited = epmelblimMAXSCALING;
+ pme_lb->elimited = PmeLoadBalancingLimit::MaxScaling;
}
if (OK && ir.pbcType != PbcType::No)
<= max_cutoff2(ir.pbcType, box));
if (!OK)
{
- pme_lb->elimited = epmelblimBOX;
+ pme_lb->elimited = PmeLoadBalancingLimit::Box;
}
}
{
/* Failed: do not use this setup */
pme_lb->cur--;
- pme_lb->elimited = epmelblimDD;
+ pme_lb->elimited = PmeLoadBalancingLimit::DD;
}
}
}
/* Limit the range to below the current cut-off, scan from start */
pme_lb->end = pme_lb->cur;
pme_lb->cur = pme_lb->start;
- pme_lb->elimited = epmelblimDD;
+ pme_lb->elimited = PmeLoadBalancingLimit::DD;
print_loadbal_limited(fp_err, fp_log, step, pme_lb);
}
}
nbv->changePairlistRadii(set->rlistOuter, set->rlistInner);
ic->ewaldcoeff_q = set->ewaldcoeff_q;
/* TODO: centralize the code that sets the potentials shifts */
- if (ic->coulomb_modifier == eintmodPOTSHIFT)
+ if (ic->coulomb_modifier == InteractionModifiers::PotShift)
{
GMX_RELEASE_ASSERT(ic->rcoulomb != 0, "Cutoff radius cannot be zero");
ic->sh_ewald = std::erfc(ic->ewaldcoeff_q * ic->rcoulomb) / ic->rcoulomb;
/* We have PME for both Coulomb and VdW, set rvdw equal to rcoulomb */
ic->rvdw = set->rcut_coulomb;
ic->ewaldcoeff_lj = set->ewaldcoeff_lj;
- if (ic->vdw_modifier == eintmodPOTSHIFT)
+ if (ic->vdw_modifier == InteractionModifiers::PotShift)
{
real crc2;
/* We always re-initialize the tables whether they are used or not */
init_interaction_const_tables(nullptr, ic, set->rlistOuter, ir.tabext);
- Nbnxm::gpu_pme_loadbal_update_param(nbv, ic);
+ Nbnxm::gpu_pme_loadbal_update_param(nbv, *ic);
if (!pme_lb->bSepPMERanks)
{
/* Generate a new PME data structure,
* copying part of the old pointers.
*/
- gmx_pme_reinit(&set->pmedata, cr, pme_lb->setup[0].pmedata, &ir, set->grid,
- set->ewaldcoeff_q, set->ewaldcoeff_lj);
+ gmx_pme_reinit(
+ &set->pmedata, cr, pme_lb->setup[0].pmedata, &ir, set->grid, set->ewaldcoeff_q, set->ewaldcoeff_lj);
}
*pmedata = set->pmedata;
}
t_forcerec* fr,
const matrix box,
gmx::ArrayRef<const gmx::RVec> x,
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle* wcycle,
int64_t step,
int64_t step_rel,
gmx_bool* bPrinting,
n_prev = pme_lb->cycles_n;
cycles_prev = pme_lb->cycles_c;
- wallcycle_get(wcycle, ewcSTEP, &pme_lb->cycles_n, &pme_lb->cycles_c);
+ wallcycle_get(wcycle, WallCycleCounter::Step, &pme_lb->cycles_n, &pme_lb->cycles_c);
/* Before the first step we haven't done any steps yet.
* Also handle cases where ir.init_step % ir.nstlist != 0.
* since init_step might not be a multiple of nstlist,
* but the first data collected is skipped anyhow.
*/
- pme_load_balance(pme_lb, cr, fp_err, fp_log, mdlog, ir, box, x,
- pme_lb->cycles_c - cycles_prev, fr->ic, fr->nbv.get(), &fr->pmedata, step);
+ pme_load_balance(pme_lb,
+ cr,
+ fp_err,
+ fp_log,
+ mdlog,
+ ir,
+ box,
+ x,
+ pme_lb->cycles_c - cycles_prev,
+ fr->ic.get(),
+ fr->nbv.get(),
+ &fr->pmedata,
+ step);
/* Update deprecated rlist in forcerec to stay in sync with fr->nbv */
fr->rlist = fr->nbv->pairlistOuterRadius();
- if (ir.eDispCorr != edispcNO)
+ if (ir.eDispCorr != DispersionCorrectionType::No)
{
fr->dispersionCorrection->setParameters(*fr->ic);
}
/*! \brief Print one load-balancing setting */
static void print_pme_loadbal_setting(FILE* fplog, const char* name, const pme_setup_t* setup)
{
- fprintf(fplog, " %-7s %6.3f nm %6.3f nm %3d %3d %3d %5.3f nm %5.3f nm\n", name,
- setup->rcut_coulomb, setup->rlistInner, setup->grid[XX], setup->grid[YY],
- setup->grid[ZZ], setup->spacing, 1 / setup->ewaldcoeff_q);
+ fprintf(fplog,
+ " %-7s %6.3f nm %6.3f nm %3d %3d %3d %5.3f nm %5.3f nm\n",
+ name,
+ setup->rcut_coulomb,
+ setup->rlistInner,
+ setup->grid[XX],
+ setup->grid[YY],
+ setup->grid[ZZ],
+ setup->spacing,
+ 1 / setup->ewaldcoeff_q);
}
/*! \brief Print all load-balancing settings */
fprintf(fplog, " P P - P M E L O A D B A L A N C I N G\n");
fprintf(fplog, "\n");
/* Here we only warn when the optimal setting is the last one */
- if (pme_lb->elimited != epmelblimNO && pme_lb->cur == pme_loadbal_end(pme_lb) - 1)
+ if (pme_lb->elimited != PmeLoadBalancingLimit::No && pme_lb->cur == pme_loadbal_end(pme_lb) - 1)
{
- fprintf(fplog, " NOTE: The PP/PME load balancing was limited by the %s,\n",
- pmelblim_str[pme_lb->elimited]);
+ fprintf(fplog,
+ " NOTE: The PP/PME load balancing was limited by the %s,\n",
+ enumValueToString(pme_lb->elimited));
fprintf(fplog, " you might not have reached a good load balance.\n");
- if (pme_lb->elimited == epmelblimDD)
+ if (pme_lb->elimited == PmeLoadBalancingLimit::DD)
{
fprintf(fplog, " Try different mdrun -dd settings or lower the -dds value.\n");
}
void pme_loadbal_done(pme_load_balancing_t* pme_lb, FILE* fplog, const gmx::MDLogger& mdlog, gmx_bool bNonBondedOnGPU)
{
- if (fplog != nullptr && (pme_lb->cur > 0 || pme_lb->elimited != epmelblimNO))
+ if (fplog != nullptr && (pme_lb->cur > 0 || pme_lb->elimited != PmeLoadBalancingLimit::No))
{
print_pme_loadbal_settings(pme_lb, fplog, mdlog, bNonBondedOnGPU);
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* Process the cycles measured over the last nstlist steps and then
* either continue balancing or check if we need to trigger balancing.
- * Should be called after the ewcSTEP cycle counter has been stopped.
+ * Should be called after the WallCycleCounter::Step cycle counter has been stopped.
* Returns if the load balancing is printing to fp_err.
*/
void pme_loadbal_do(pme_load_balancing_t* pme_lb,
t_forcerec* fr,
const matrix box,
gmx::ArrayRef<const gmx::RVec> x,
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle* wcycle,
int64_t step,
int64_t step_rel,
gmx_bool* bPrinting,
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "pme_output.h"
#include "pme_pp_communication.h"
-/*! \brief environment variable to enable GPU P2P communication */
-static const bool c_enableGpuPmePpComms =
- GMX_GPU_CUDA && GMX_THREAD_MPI && (getenv("GMX_GPU_PME_PP_COMMS") != nullptr);
-
/*! \brief Master PP-PME communication data structure */
struct gmx_pme_pp
{
return pme_pp;
}
-static void reset_pmeonly_counters(gmx_wallcycle_t wcycle,
+static void reset_pmeonly_counters(gmx_wallcycle* wcycle,
gmx_walltime_accounting_t walltime_accounting,
t_nrnb* nrnb,
int64_t step,
bool useGpuForPme)
{
/* Reset all the counters related to performance over the run */
- wallcycle_stop(wcycle, ewcRUN);
+ wallcycle_stop(wcycle, WallCycleCounter::Run);
wallcycle_reset_all(wcycle);
*nrnb = { 0 };
- wallcycle_start(wcycle, ewcRUN);
+ wallcycle_start(wcycle, WallCycleCounter::Run);
walltime_accounting_reset_time(walltime_accounting, step);
if (useGpuForPme)
cnb.flags = 0;
/* Receive the send count, box and time step from the peer PP node */
- MPI_Recv(&cnb, sizeof(cnb), MPI_BYTE, pme_pp->peerRankId, eCommType_CNB,
- pme_pp->mpi_comm_mysim, MPI_STATUS_IGNORE);
+ MPI_Recv(&cnb, sizeof(cnb), MPI_BYTE, pme_pp->peerRankId, eCommType_CNB, pme_pp->mpi_comm_mysim, MPI_STATUS_IGNORE);
/* We accumulate all received flags */
flags |= cnb.flags;
if (debug)
{
- fprintf(debug, "PME only rank receiving:%s%s%s%s%s\n",
+ fprintf(debug,
+ "PME only rank receiving:%s%s%s%s%s\n",
(cnb.flags & PP_PME_CHARGE) ? " charges" : "",
(cnb.flags & PP_PME_COORD) ? " coordinates" : "",
(cnb.flags & PP_PME_FINISH) ? " finish" : "",
}
else
{
- MPI_Irecv(&sender.numAtoms, sizeof(sender.numAtoms), MPI_BYTE, sender.rankId,
- eCommType_CNB, pme_pp->mpi_comm_mysim, &pme_pp->req[messages++]);
+ MPI_Irecv(&sender.numAtoms,
+ sizeof(sender.numAtoms),
+ MPI_BYTE,
+ sender.rankId,
+ eCommType_CNB,
+ pme_pp->mpi_comm_mysim,
+ &pme_pp->req[messages++]);
}
}
MPI_Waitall(messages, pme_pp->req.data(), pme_pp->stat.data());
{
if (sender.numAtoms > 0)
{
- MPI_Irecv(bufferPtr + nat, sender.numAtoms * sizeof(real), MPI_BYTE,
- sender.rankId, q, pme_pp->mpi_comm_mysim, &pme_pp->req[messages++]);
+ MPI_Irecv(bufferPtr + nat,
+ sender.numAtoms * sizeof(real),
+ MPI_BYTE,
+ sender.rankId,
+ q,
+ pme_pp->mpi_comm_mysim,
+ &pme_pp->req[messages++]);
nat += sender.numAtoms;
if (debug)
{
- fprintf(debug, "Received from PP rank %d: %d %s\n", sender.rankId,
+ fprintf(debug,
+ "Received from PP rank %d: %d %s\n",
+ sender.rankId,
sender.numAtoms,
(q == eCommType_ChargeA || q == eCommType_ChargeB) ? "charges"
: "params");
{
if (atomSetChanged)
{
- gmx_pme_reinit_atoms(pme, nat, pme_pp->chargeA.data(), pme_pp->chargeB.data());
+ gmx_pme_reinit_atoms(pme, nat, pme_pp->chargeA, pme_pp->chargeB);
if (useGpuForPme)
{
stateGpu->reinit(nat, nat);
// This rank will have its data accessed directly by PP rank, so needs to send the remote addresses.
pme_pp->pmeCoordinateReceiverGpu->sendCoordinateBufferAddressToPpRanks(
stateGpu->getCoordinates());
- pme_pp->pmeForceSenderGpu->sendForceBufferAddressToPpRanks(
- reinterpret_cast<rvec*>(pme_gpu_get_device_f(pme)));
+ pme_pp->pmeForceSenderGpu->sendForceBufferAddressToPpRanks(pme_gpu_get_device_f(pme));
}
}
{
if (pme_pp->useGpuDirectComm)
{
- pme_pp->pmeCoordinateReceiverGpu->launchReceiveCoordinatesFromPpCudaDirect(
- sender.rankId);
+ if (GMX_THREAD_MPI)
+ {
+ pme_pp->pmeCoordinateReceiverGpu->receiveCoordinatesSynchronizerFromPpCudaDirect(
+ sender.rankId);
+ }
+ else
+ {
+ pme_pp->pmeCoordinateReceiverGpu->launchReceiveCoordinatesFromPpCudaMpi(
+ stateGpu->getCoordinates(), nat, sender.numAtoms * sizeof(rvec), sender.rankId);
+ }
}
else
{
- MPI_Irecv(pme_pp->x[nat], sender.numAtoms * sizeof(rvec), MPI_BYTE, sender.rankId,
- eCommType_COORD, pme_pp->mpi_comm_mysim, &pme_pp->req[messages++]);
+ MPI_Irecv(pme_pp->x[nat],
+ sender.numAtoms * sizeof(rvec),
+ MPI_BYTE,
+ sender.rankId,
+ eCommType_COORD,
+ pme_pp->mpi_comm_mysim,
+ &pme_pp->req[messages++]);
}
nat += sender.numAtoms;
if (debug)
fprintf(debug,
"Received from PP rank %d: %d "
"coordinates\n",
- sender.rankId, sender.numAtoms);
+ sender.rankId,
+ sender.numAtoms);
}
}
}
if (pme_pp->useGpuDirectComm)
{
- pme_pp->pmeCoordinateReceiverGpu->enqueueWaitReceiveCoordinatesFromPpCudaDirect();
+ pme_pp->pmeCoordinateReceiverGpu->synchronizeOnCoordinatesFromPpRanks();
}
status = pmerecvqxX;
return status;
}
-#if GMX_MPI
-/*! \brief Send force data to PP ranks */
-static void sendFToPP(void* sendbuf, PpRanks receiver, gmx_pme_pp* pme_pp, int* messages)
-{
-
- if (pme_pp->useGpuDirectComm)
- {
- GMX_ASSERT((pme_pp->pmeForceSenderGpu != nullptr),
- "The use of GPU direct communication for PME-PP is enabled, "
- "but the PME GPU force reciever object does not exist");
-
- pme_pp->pmeForceSenderGpu->sendFToPpCudaDirect(receiver.rankId);
- }
- else
- {
- // Send using MPI
- MPI_Isend(sendbuf, receiver.numAtoms * sizeof(rvec), MPI_BYTE, receiver.rankId, 0,
- pme_pp->mpi_comm_mysim, &pme_pp->req[*messages]);
- *messages = *messages + 1;
- }
-}
-#endif
-
/*! \brief Send the PME mesh force, virial and energy to the PP-only ranks. */
static void gmx_pme_send_force_vir_ener(const gmx_pme_t& pme,
gmx_pme_pp* pme_pp,
ind_end = 0;
for (const auto& receiver : pme_pp->ppRanks)
{
- ind_start = ind_end;
- ind_end = ind_start + receiver.numAtoms;
- void* sendbuf = const_cast<void*>(static_cast<const void*>(output.forces_[ind_start]));
+ ind_start = ind_end;
+ ind_end = ind_start + receiver.numAtoms;
if (pme_pp->useGpuDirectComm)
{
- // Data will be transferred directly from GPU.
- rvec* d_f = reinterpret_cast<rvec*>(pme_gpu_get_device_f(&pme));
- sendbuf = reinterpret_cast<void*>(&d_f[ind_start]);
+ GMX_ASSERT((pme_pp->pmeForceSenderGpu != nullptr),
+ "The use of GPU direct communication for PME-PP is enabled, "
+ "but the PME GPU force reciever object does not exist");
+
+ if (GMX_THREAD_MPI)
+ {
+ pme_pp->pmeForceSenderGpu->sendFSynchronizerToPpCudaDirect(receiver.rankId);
+ }
+ else
+ {
+ pme_pp->pmeForceSenderGpu->sendFToPpCudaMpi(pme_gpu_get_device_f(&pme),
+ ind_start,
+ receiver.numAtoms * sizeof(rvec),
+ receiver.rankId,
+ &pme_pp->req[messages]);
+
+ messages++;
+ }
+ }
+ else
+ {
+ void* sendbuf = const_cast<void*>(static_cast<const void*>(output.forces_[ind_start]));
+ // Send using MPI
+ MPI_Isend(sendbuf,
+ receiver.numAtoms * sizeof(rvec),
+ MPI_BYTE,
+ receiver.rankId,
+ 0,
+ pme_pp->mpi_comm_mysim,
+ &pme_pp->req[messages]);
+ messages++;
}
- sendFToPP(sendbuf, receiver, pme_pp, &messages);
}
/* send virial and energy to our last PP node */
{
fprintf(debug, "PME rank sending to PP rank %d: virial and energy\n", pme_pp->peerRankId);
}
- MPI_Isend(&cve, sizeof(cve), MPI_BYTE, pme_pp->peerRankId, 1, pme_pp->mpi_comm_mysim,
- &pme_pp->req[messages++]);
+ MPI_Isend(&cve, sizeof(cve), MPI_BYTE, pme_pp->peerRankId, 1, pme_pp->mpi_comm_mysim, &pme_pp->req[messages++]);
/* Wait for the forces to arrive */
MPI_Waitall(messages, pme_pp->req.data(), pme_pp->stat.data());
gmx_walltime_accounting_t walltime_accounting,
t_inputrec* ir,
PmeRunMode runMode,
+ bool useGpuPmePpCommunication,
const gmx::DeviceStreamManager* deviceStreamManager)
{
int ret;
"Device stream can not be nullptr when using GPU in PME-only rank");
changePinningPolicy(&pme_pp->chargeA, pme_get_pinning_policy());
changePinningPolicy(&pme_pp->x, pme_get_pinning_policy());
- if (c_enableGpuPmePpComms)
+ if (useGpuPmePpCommunication)
{
pme_pp->pmeCoordinateReceiverGpu = std::make_unique<gmx::PmeCoordinateReceiverGpu>(
- deviceStreamManager->stream(gmx::DeviceStreamType::Pme), pme_pp->mpi_comm_mysim,
+ deviceStreamManager->stream(gmx::DeviceStreamType::Pme),
+ pme_pp->mpi_comm_mysim,
pme_pp->ppRanks);
pme_pp->pmeForceSenderGpu = std::make_unique<gmx::PmeForceSenderGpu>(
- deviceStreamManager->stream(gmx::DeviceStreamType::Pme), pme_pp->mpi_comm_mysim,
- pme_pp->ppRanks);
+ pme_gpu_get_f_ready_synchronizer(pme), pme_pp->mpi_comm_mysim, pme_pp->ppRanks);
}
// TODO: Special PME-only constructor is used here. There is no mechanism to prevent from using the other constructor here.
// This should be made safer.
stateGpu = std::make_unique<gmx::StatePropagatorDataGpu>(
- &deviceStreamManager->stream(gmx::DeviceStreamType::Pme), deviceStreamManager->context(),
- GpuApiCallBehavior::Async, pme_gpu_get_block_size(pme), wcycle);
+ &deviceStreamManager->stream(gmx::DeviceStreamType::Pme),
+ deviceStreamManager->context(),
+ GpuApiCallBehavior::Async,
+ pme_gpu_get_block_size(pme),
+ wcycle);
}
clear_nrnb(mynrnb);
/* Domain decomposition */
ivec newGridSize;
real ewaldcoeff_q = 0, ewaldcoeff_lj = 0;
- ret = gmx_pme_recv_coeffs_coords(pme, pme_pp.get(), &natoms, box, &maxshift_x, &maxshift_y,
- &lambda_q, &lambda_lj, &computeEnergyAndVirial, &step,
- &newGridSize, &ewaldcoeff_q, &ewaldcoeff_lj,
- useGpuForPme, stateGpu.get(), runMode);
+ ret = gmx_pme_recv_coeffs_coords(pme,
+ pme_pp.get(),
+ &natoms,
+ box,
+ &maxshift_x,
+ &maxshift_y,
+ &lambda_q,
+ &lambda_lj,
+ &computeEnergyAndVirial,
+ &step,
+ &newGridSize,
+ &ewaldcoeff_q,
+ &ewaldcoeff_lj,
+ useGpuForPme,
+ stateGpu.get(),
+ runMode);
if (ret == pmerecvqxSWITCHGRID)
{
if (count == 0)
{
- wallcycle_start(wcycle, ewcRUN);
+ wallcycle_start(wcycle, WallCycleCounter::Run);
walltime_accounting_start_time(walltime_accounting);
}
- wallcycle_start(wcycle, ewcPMEMESH);
+ wallcycle_start(wcycle, WallCycleCounter::PmeMesh);
dvdlambda_q = 0;
dvdlambda_lj = 0;
GMX_ASSERT(pme_pp->x.size() == static_cast<size_t>(natoms),
"The coordinate buffer should have size natoms");
- gmx_pme_do(pme, pme_pp->x, pme_pp->f, pme_pp->chargeA.data(), pme_pp->chargeB.data(),
- pme_pp->sqrt_c6A.data(), pme_pp->sqrt_c6B.data(), pme_pp->sigmaA.data(),
- pme_pp->sigmaB.data(), box, cr, maxshift_x, maxshift_y, mynrnb, wcycle,
- output.coulombVirial_, output.lennardJonesVirial_, &output.coulombEnergy_,
- &output.lennardJonesEnergy_, lambda_q, lambda_lj, &dvdlambda_q,
- &dvdlambda_lj, stepWork);
+ gmx_pme_do(pme,
+ pme_pp->x,
+ pme_pp->f,
+ pme_pp->chargeA,
+ pme_pp->chargeB,
+ pme_pp->sqrt_c6A,
+ pme_pp->sqrt_c6B,
+ pme_pp->sigmaA,
+ pme_pp->sigmaB,
+ box,
+ cr,
+ maxshift_x,
+ maxshift_y,
+ mynrnb,
+ wcycle,
+ output.coulombVirial_,
+ output.lennardJonesVirial_,
+ &output.coulombEnergy_,
+ &output.lennardJonesEnergy_,
+ lambda_q,
+ lambda_lj,
+ &dvdlambda_q,
+ &dvdlambda_lj,
+ stepWork);
output.forces_ = pme_pp->f;
}
- cycles = wallcycle_stop(wcycle, ewcPMEMESH);
+ cycles = wallcycle_stop(wcycle, WallCycleCounter::PmeMesh);
gmx_pme_send_force_vir_ener(*pme, pme_pp.get(), output, dvdlambda_q, dvdlambda_lj, cycles);
count++;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx_walltime_accounting_t walltime_accounting,
t_inputrec* ir,
PmeRunMode runMode,
+ bool useGpuPmePpCommunication,
const gmx::DeviceStreamManager* deviceStreamManager);
#endif
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
/*! \brief Send data to PME ranks */
-static void gmx_pme_send_coeffs_coords(t_forcerec* fr,
- const t_commrec* cr,
- unsigned int flags,
- real gmx_unused* chargeA,
- real gmx_unused* chargeB,
- real gmx_unused* c6A,
- real gmx_unused* c6B,
- real gmx_unused* sigmaA,
- real gmx_unused* sigmaB,
- const matrix box,
+static void gmx_pme_send_coeffs_coords(t_forcerec* fr,
+ const t_commrec* cr,
+ unsigned int flags,
+ gmx::ArrayRef<real> chargeA,
+ gmx::ArrayRef<real> chargeB,
+ gmx::ArrayRef<real> c6A,
+ gmx::ArrayRef<real> c6B,
+ gmx::ArrayRef<real> sigmaA,
+ gmx::ArrayRef<real> sigmaB,
+ const matrix box,
const rvec gmx_unused* x,
real lambda_q,
real lambda_lj,
if (debug)
{
- fprintf(debug, "PP rank %d sending to PME rank %d: %d%s%s%s%s\n", cr->sim_nodeid, dd->pme_nodeid,
- n, (flags & PP_PME_CHARGE) ? " charges" : "", (flags & PP_PME_SQRTC6) ? " sqrtC6" : "",
- (flags & PP_PME_SIGMA) ? " sigma" : "", (flags & PP_PME_COORD) ? " coordinates" : "");
+ fprintf(debug,
+ "PP rank %d sending to PME rank %d: %d%s%s%s%s\n",
+ cr->sim_nodeid,
+ dd->pme_nodeid,
+ n,
+ (flags & PP_PME_CHARGE) ? " charges" : "",
+ (flags & PP_PME_SQRTC6) ? " sqrtC6" : "",
+ (flags & PP_PME_SIGMA) ? " sigma" : "",
+ (flags & PP_PME_COORD) ? " coordinates" : "");
}
if (useGpuPmePpComms)
copy_mat(box, cnb->box);
}
#if GMX_MPI
- MPI_Isend(cnb, sizeof(*cnb), MPI_BYTE, dd->pme_nodeid, eCommType_CNB, cr->mpi_comm_mysim,
+ MPI_Isend(cnb,
+ sizeof(*cnb),
+ MPI_BYTE,
+ dd->pme_nodeid,
+ eCommType_CNB,
+ cr->mpi_comm_mysim,
&dd->req_pme[dd->nreq_pme++]);
#endif
}
{
#if GMX_MPI
/* Communicate only the number of atoms */
- MPI_Isend(&n, sizeof(n), MPI_BYTE, dd->pme_nodeid, eCommType_CNB, cr->mpi_comm_mysim,
+ MPI_Isend(&n,
+ sizeof(n),
+ MPI_BYTE,
+ dd->pme_nodeid,
+ eCommType_CNB,
+ cr->mpi_comm_mysim,
&dd->req_pme[dd->nreq_pme++]);
#endif
}
{
if (flags & PP_PME_CHARGE)
{
- MPI_Isend(chargeA, n * sizeof(real), MPI_BYTE, dd->pme_nodeid, eCommType_ChargeA,
- cr->mpi_comm_mysim, &dd->req_pme[dd->nreq_pme++]);
+ MPI_Isend(chargeA.data(),
+ n * sizeof(real),
+ MPI_BYTE,
+ dd->pme_nodeid,
+ eCommType_ChargeA,
+ cr->mpi_comm_mysim,
+ &dd->req_pme[dd->nreq_pme++]);
}
if (flags & PP_PME_CHARGEB)
{
- MPI_Isend(chargeB, n * sizeof(real), MPI_BYTE, dd->pme_nodeid, eCommType_ChargeB,
- cr->mpi_comm_mysim, &dd->req_pme[dd->nreq_pme++]);
+ MPI_Isend(chargeB.data(),
+ n * sizeof(real),
+ MPI_BYTE,
+ dd->pme_nodeid,
+ eCommType_ChargeB,
+ cr->mpi_comm_mysim,
+ &dd->req_pme[dd->nreq_pme++]);
}
if (flags & PP_PME_SQRTC6)
{
- MPI_Isend(c6A, n * sizeof(real), MPI_BYTE, dd->pme_nodeid, eCommType_SQRTC6A,
- cr->mpi_comm_mysim, &dd->req_pme[dd->nreq_pme++]);
+ MPI_Isend(c6A.data(),
+ n * sizeof(real),
+ MPI_BYTE,
+ dd->pme_nodeid,
+ eCommType_SQRTC6A,
+ cr->mpi_comm_mysim,
+ &dd->req_pme[dd->nreq_pme++]);
}
if (flags & PP_PME_SQRTC6B)
{
- MPI_Isend(c6B, n * sizeof(real), MPI_BYTE, dd->pme_nodeid, eCommType_SQRTC6B,
- cr->mpi_comm_mysim, &dd->req_pme[dd->nreq_pme++]);
+ MPI_Isend(c6B.data(),
+ n * sizeof(real),
+ MPI_BYTE,
+ dd->pme_nodeid,
+ eCommType_SQRTC6B,
+ cr->mpi_comm_mysim,
+ &dd->req_pme[dd->nreq_pme++]);
}
if (flags & PP_PME_SIGMA)
{
- MPI_Isend(sigmaA, n * sizeof(real), MPI_BYTE, dd->pme_nodeid, eCommType_SigmaA,
- cr->mpi_comm_mysim, &dd->req_pme[dd->nreq_pme++]);
+ MPI_Isend(sigmaA.data(),
+ n * sizeof(real),
+ MPI_BYTE,
+ dd->pme_nodeid,
+ eCommType_SigmaA,
+ cr->mpi_comm_mysim,
+ &dd->req_pme[dd->nreq_pme++]);
}
if (flags & PP_PME_SIGMAB)
{
- MPI_Isend(sigmaB, n * sizeof(real), MPI_BYTE, dd->pme_nodeid, eCommType_SigmaB,
- cr->mpi_comm_mysim, &dd->req_pme[dd->nreq_pme++]);
+ MPI_Isend(sigmaB.data(),
+ n * sizeof(real),
+ MPI_BYTE,
+ dd->pme_nodeid,
+ eCommType_SigmaB,
+ cr->mpi_comm_mysim,
+ &dd->req_pme[dd->nreq_pme++]);
}
if (flags & PP_PME_COORD)
{
real* xRealPtr = const_cast<real*>(x[0]);
if (useGpuPmePpComms && (fr != nullptr))
{
- void* sendPtr = sendCoordinatesFromGpu
- ? static_cast<void*>(fr->stateGpu->getCoordinates())
- : static_cast<void*>(xRealPtr);
- fr->pmePpCommGpu->sendCoordinatesToPmeCudaDirect(sendPtr, n, sendCoordinatesFromGpu,
- coordinatesReadyOnDeviceEvent);
+ if (sendCoordinatesFromGpu)
+ {
+ fr->pmePpCommGpu->sendCoordinatesToPmeFromGpu(
+ fr->stateGpu->getCoordinates(), n, coordinatesReadyOnDeviceEvent);
+ }
+ else
+ {
+ fr->pmePpCommGpu->sendCoordinatesToPmeFromCpu(
+ reinterpret_cast<gmx::RVec*>(xRealPtr), n, coordinatesReadyOnDeviceEvent);
+ }
}
else
{
- MPI_Isend(xRealPtr, n * sizeof(rvec), MPI_BYTE, dd->pme_nodeid, eCommType_COORD,
- cr->mpi_comm_mysim, &dd->req_pme[dd->nreq_pme++]);
+ MPI_Isend(xRealPtr,
+ n * sizeof(rvec),
+ MPI_BYTE,
+ dd->pme_nodeid,
+ eCommType_COORD,
+ cr->mpi_comm_mysim,
+ &dd->req_pme[dd->nreq_pme++]);
}
}
}
#else
GMX_UNUSED_VALUE(fr);
+ GMX_UNUSED_VALUE(chargeA);
+ GMX_UNUSED_VALUE(chargeB);
+ GMX_UNUSED_VALUE(c6A);
+ GMX_UNUSED_VALUE(c6B);
+ GMX_UNUSED_VALUE(sigmaA);
+ GMX_UNUSED_VALUE(sigmaB);
GMX_UNUSED_VALUE(reinitGpuPmePpComms);
GMX_UNUSED_VALUE(sendCoordinatesFromGpu);
GMX_UNUSED_VALUE(coordinatesReadyOnDeviceEvent);
}
void gmx_pme_send_parameters(const t_commrec* cr,
- const interaction_const_t* ic,
- gmx_bool bFreeEnergy_q,
- gmx_bool bFreeEnergy_lj,
- real* chargeA,
- real* chargeB,
- real* sqrt_c6A,
- real* sqrt_c6B,
- real* sigmaA,
- real* sigmaB,
+ const interaction_const_t& interactionConst,
+ bool bFreeEnergy_q,
+ bool bFreeEnergy_lj,
+ gmx::ArrayRef<real> chargeA,
+ gmx::ArrayRef<real> chargeB,
+ gmx::ArrayRef<real> sqrt_c6A,
+ gmx::ArrayRef<real> sqrt_c6B,
+ gmx::ArrayRef<real> sigmaA,
+ gmx::ArrayRef<real> sigmaB,
int maxshift_x,
int maxshift_y)
{
unsigned int flags = 0;
- if (EEL_PME(ic->eeltype))
+ if (EEL_PME(interactionConst.eeltype))
{
flags |= PP_PME_CHARGE;
}
- if (EVDW_PME(ic->vdwtype))
+ if (EVDW_PME(interactionConst.vdwtype))
{
flags |= (PP_PME_SQRTC6 | PP_PME_SIGMA);
}
flags |= (flags << 1);
}
- gmx_pme_send_coeffs_coords(nullptr, cr, flags, chargeA, chargeB, sqrt_c6A, sqrt_c6B, sigmaA,
- sigmaB, nullptr, nullptr, 0, 0, maxshift_x, maxshift_y, -1, false,
- false, false, nullptr);
+ gmx_pme_send_coeffs_coords(nullptr,
+ cr,
+ flags,
+ chargeA,
+ chargeB,
+ sqrt_c6A,
+ sqrt_c6B,
+ sigmaA,
+ sigmaB,
+ nullptr,
+ nullptr,
+ 0,
+ 0,
+ maxshift_x,
+ maxshift_y,
+ -1,
+ false,
+ false,
+ false,
+ nullptr);
}
void gmx_pme_send_coordinates(t_forcerec* fr,
GpuEventSynchronizer* coordinatesReadyOnDeviceEvent,
gmx_wallcycle* wcycle)
{
- wallcycle_start(wcycle, ewcPP_PMESENDX);
+ wallcycle_start(wcycle, WallCycleCounter::PpPmeSendX);
unsigned int flags = PP_PME_COORD;
if (computeEnergyAndVirial)
{
flags |= PP_PME_ENER_VIR;
}
- gmx_pme_send_coeffs_coords(fr, cr, flags, nullptr, nullptr, nullptr, nullptr, nullptr, nullptr,
- box, x, lambda_q, lambda_lj, 0, 0, step, useGpuPmePpComms,
- receiveCoordinateAddressFromPme, sendCoordinatesFromGpu,
+ gmx_pme_send_coeffs_coords(fr,
+ cr,
+ flags,
+ {},
+ {},
+ {},
+ {},
+ {},
+ {},
+ box,
+ x,
+ lambda_q,
+ lambda_lj,
+ 0,
+ 0,
+ step,
+ useGpuPmePpComms,
+ receiveCoordinateAddressFromPme,
+ sendCoordinatesFromGpu,
coordinatesReadyOnDeviceEvent);
- wallcycle_stop(wcycle, ewcPP_PMESENDX);
+ wallcycle_stop(wcycle, WallCycleCounter::PpPmeSendX);
}
void gmx_pme_send_finish(const t_commrec* cr)
{
unsigned int flags = PP_PME_FINISH;
- gmx_pme_send_coeffs_coords(nullptr, cr, flags, nullptr, nullptr, nullptr, nullptr, nullptr, nullptr,
- nullptr, nullptr, 0, 0, 0, 0, -1, false, false, false, nullptr);
+ gmx_pme_send_coeffs_coords(
+ nullptr, cr, flags, {}, {}, {}, {}, {}, {}, nullptr, nullptr, 0, 0, 0, 0, -1, false, false, false, nullptr);
}
void gmx_pme_send_switchgrid(const t_commrec* cr, ivec grid_size, real ewaldcoeff_q, real ewaldcoeff_lj)
{
if (debug)
{
- fprintf(debug, "PP rank %d receiving from PME rank %d: virial and energy\n",
- cr->sim_nodeid, cr->dd->pme_nodeid);
+ fprintf(debug,
+ "PP rank %d receiving from PME rank %d: virial and energy\n",
+ cr->sim_nodeid,
+ cr->dd->pme_nodeid);
}
#if GMX_MPI
MPI_Recv(&cve, sizeof(cve), MPI_BYTE, cr->dd->pme_nodeid, 1, cr->mpi_comm_mysim, MPI_STATUS_IGNORE);
*dvdlambda_lj += cve.dvdlambda_lj;
*pme_cycles = cve.cycles;
- if (cve.stop_cond != gmx_stop_cond_none)
+ if (cve.stop_cond != StopCondition::None)
{
gmx_set_stop_condition(cve.stop_cond);
}
if (useGpuPmePpComms)
{
GMX_ASSERT(pmePpCommGpu != nullptr, "Need valid pmePpCommGpu");
- // Receive directly using CUDA memory copy
- pmePpCommGpu->receiveForceFromPmeCudaDirect(recvptr, n, receivePmeForceToGpu);
+ // Receive forces from PME rank
+ pmePpCommGpu->receiveForceFromPme(static_cast<gmx::RVec*>(recvptr), n, receivePmeForceToGpu);
}
else
{
// Receive data using MPI
#if GMX_MPI
- MPI_Recv(recvptr, n * sizeof(rvec), MPI_BYTE, cr->dd->pme_nodeid, 0, cr->mpi_comm_mysim,
- MPI_STATUS_IGNORE);
+ MPI_Recv(recvptr, n * sizeof(rvec), MPI_BYTE, cr->dd->pme_nodeid, 0, cr->mpi_comm_mysim, MPI_STATUS_IGNORE);
#else
GMX_UNUSED_VALUE(cr);
#endif
void* recvptr = reinterpret_cast<void*>(buffer.data());
recvFFromPme(pmePpCommGpu, recvptr, natoms, cr, useGpuPmePpComms, receivePmeForceToGpu);
- int nt = gmx_omp_nthreads_get_simple_rvec_task(emntDefault, natoms);
+ int nt = gmx_omp_nthreads_get_simple_rvec_task(ModuleMultiThread::Default, natoms);
gmx::ArrayRef<gmx::RVec> f = forceWithVirial->force_;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
class ForceWithVirial;
class PmePpCommGpu;
+template<typename>
+class ArrayRef;
} // namespace gmx
/*! \brief Send the charges and maxshift to out PME-only node. */
void gmx_pme_send_parameters(const t_commrec* cr,
- const interaction_const_t* ic,
+ const interaction_const_t& interactionConst,
gmx_bool bFreeEnergy_q,
gmx_bool bFreeEnergy_lj,
- real* chargeA,
- real* chargeB,
- real* sqrt_c6A,
- real* sqrt_c6B,
- real* sigmaA,
- real* sigmaB,
+ gmx::ArrayRef<real> chargeA,
+ gmx::ArrayRef<real> chargeB,
+ gmx::ArrayRef<real> sqrt_c6A,
+ gmx::ArrayRef<real> sqrt_c6B,
+ gmx::ArrayRef<real> sigmaA,
+ gmx::ArrayRef<real> sigmaB,
int maxshift_x,
int maxshift_y);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_PME_PP_COMM_GPU_H
#define GMX_PME_PP_COMM_GPU_H
-#include "gromacs/utility/classhelpers.h"
+#include <memory>
+
+#include "gromacs/gpu_utils/devicebuffer_datatype.h"
+#include "gromacs/math/vectypes.h"
#include "gromacs/utility/gmxmpi.h"
class DeviceContext;
* \param[in] recvSize Number of elements to receive
* \param[in] recvPmeForceToGpu Whether receive is to GPU, otherwise CPU
*/
- void receiveForceFromPmeCudaDirect(void* recvPtr, int recvSize, bool recvPmeForceToGpu);
+ void receiveForceFromPme(RVec* recvPtr, int recvSize, bool recvPmeForceToGpu);
/*! \brief Push coordinates buffer directly to GPU memory on PME task
* \param[in] sendPtr Buffer with coordinate data
* \param[in] sendSize Number of elements to send
- * \param[in] sendPmeCoordinatesFromGpu Whether send is from GPU, otherwise CPU
* \param[in] coordinatesReadyOnDeviceEvent Event recorded when coordinates are available on device
*/
- void sendCoordinatesToPmeCudaDirect(void* sendPtr,
- int sendSize,
- bool sendPmeCoordinatesFromGpu,
- GpuEventSynchronizer* coordinatesReadyOnDeviceEvent);
+ void sendCoordinatesToPmeFromGpu(DeviceBuffer<RVec> sendPtr,
+ int sendSize,
+ GpuEventSynchronizer* coordinatesReadyOnDeviceEvent);
+
+ /*! \brief Push coordinates buffer from host memory directly to GPU memory on PME task
+ * \param[in] sendPtr Buffer with coordinate data
+ * \param[in] sendSize Number of elements to send
+ * \param[in] coordinatesReadyOnDeviceEvent Event recorded when coordinates are available on device
+ */
+ void sendCoordinatesToPmeFromCpu(RVec* sendPtr,
+ int sendSize,
+ GpuEventSynchronizer* coordinatesReadyOnDeviceEvent);
/*! \brief
* Return pointer to buffer used for staging PME force on GPU
*/
- void* getGpuForceStagingPtr();
+ DeviceBuffer<gmx::RVec> getGpuForceStagingPtr();
/*! \brief
* Return pointer to event recorded when forces are ready
private:
class Impl;
- gmx::PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"correct implementation.");
}
-void PmePpCommGpu::receiveForceFromPmeCudaDirect(void* /* recvPtr */,
- int /* recvSize */,
- bool /* receivePmeForceToGpu */)
+void PmePpCommGpu::receiveForceFromPme(RVec* /* recvPtr */, int /* recvSize */, bool /* receivePmeForceToGpu */)
{
GMX_ASSERT(!impl_,
"A CPU stub for PME-PP GPU communication was called instead of the correct "
"implementation.");
}
-void PmePpCommGpu::sendCoordinatesToPmeCudaDirect(void* /* sendPtr */,
- int /* sendSize */,
- bool /* sendPmeCoordinatesFromGpu */,
- GpuEventSynchronizer* /* coordinatesOnDeviceEvent */)
+void PmePpCommGpu::sendCoordinatesToPmeFromGpu(DeviceBuffer<RVec> /* sendPtr */,
+ int /* sendSize */,
+ GpuEventSynchronizer* /* coordinatesOnDeviceEvent */)
{
GMX_ASSERT(!impl_,
"A CPU stub for PME-PP GPU communication was called instead of the correct "
"implementation.");
}
-void* PmePpCommGpu::getGpuForceStagingPtr()
+void PmePpCommGpu::sendCoordinatesToPmeFromCpu(RVec* /* sendPtr */,
+ int /* sendSize */,
+ GpuEventSynchronizer* /* coordinatesOnDeviceEvent */)
{
GMX_ASSERT(!impl_,
"A CPU stub for PME-PP GPU communication was called instead of the correct "
"implementation.");
- return nullptr;
+}
+
+DeviceBuffer<gmx::RVec> PmePpCommGpu::getGpuForceStagingPtr()
+{
+ GMX_ASSERT(!impl_,
+ "A CPU stub for PME-PP GPU communication was called instead of the correct "
+ "implementation.");
+ return DeviceBuffer<gmx::RVec>{};
}
GpuEventSynchronizer* PmePpCommGpu::getForcesReadySynchronizer()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "gromacs/ewald/pme_pp_communication.h"
#include "pme_pp_comm_gpu_impl.h"
#include "config.h"
#include "gromacs/gpu_utils/device_stream.h"
#include "gromacs/gpu_utils/devicebuffer.h"
#include "gromacs/gpu_utils/gpueventsynchronizer.cuh"
+#include "gromacs/gpu_utils/typecasts.cuh"
#include "gromacs/utility/gmxmpi.h"
namespace gmx
deviceContext_(deviceContext),
pmePpCommStream_(deviceStream),
comm_(comm),
- pmeRank_(pmeRank)
+ pmeRank_(pmeRank),
+ d_pmeForces_(nullptr)
{
- GMX_RELEASE_ASSERT(
- GMX_THREAD_MPI,
- "PME-PP GPU Communication is currently only supported with thread-MPI enabled");
}
PmePpCommGpu::Impl::~Impl() = default;
{
// This rank will access PME rank memory directly, so needs to receive the remote PME buffer addresses.
#if GMX_MPI
- MPI_Recv(&remotePmeXBuffer_, sizeof(void**), MPI_BYTE, pmeRank_, 0, comm_, MPI_STATUS_IGNORE);
- MPI_Recv(&remotePmeFBuffer_, sizeof(void**), MPI_BYTE, pmeRank_, 0, comm_, MPI_STATUS_IGNORE);
+
+ if (GMX_THREAD_MPI)
+ {
+ // receive device buffer address from PME rank
+ MPI_Recv(&remotePmeXBuffer_, sizeof(float3*), MPI_BYTE, pmeRank_, 0, comm_, MPI_STATUS_IGNORE);
+ MPI_Recv(&remotePmeFBuffer_, sizeof(float3*), MPI_BYTE, pmeRank_, 0, comm_, MPI_STATUS_IGNORE);
+ }
+
+#endif
// Reallocate buffer used for staging PME force on GPU
reallocateDeviceBuffer(&d_pmeForces_, size, &d_pmeForcesSize_, &d_pmeForcesSizeAlloc_, deviceContext_);
-#else
- GMX_UNUSED_VALUE(size);
-#endif
return;
}
-// TODO make this asynchronous by splitting into this into
-// launchRecvForceFromPmeCudaDirect() and sycnRecvForceFromPmeCudaDirect()
-void PmePpCommGpu::Impl::receiveForceFromPmeCudaDirect(void* recvPtr, int recvSize, bool receivePmeForceToGpu)
+void PmePpCommGpu::Impl::receiveForceFromPmeCudaDirect(float3* pmeForcePtr, int recvSize, bool receivePmeForceToGpu)
{
#if GMX_MPI
// Receive event from PME task and add to stream, to ensure pull of data doesn't
GpuEventSynchronizer* pmeSync;
MPI_Recv(&pmeSync, sizeof(GpuEventSynchronizer*), MPI_BYTE, pmeRank_, 0, comm_, MPI_STATUS_IGNORE);
pmeSync->enqueueWaitEvent(pmePpCommStream_);
+#endif
// Pull force data from remote GPU
- void* pmeForcePtr = receivePmeForceToGpu ? static_cast<void*>(d_pmeForces_) : recvPtr;
- cudaError_t stat = cudaMemcpyAsync(pmeForcePtr, remotePmeFBuffer_, recvSize * DIM * sizeof(float),
- cudaMemcpyDefault, pmePpCommStream_.stream());
+ cudaError_t stat = cudaMemcpyAsync(pmeForcePtr,
+ remotePmeFBuffer_,
+ recvSize * DIM * sizeof(float),
+ cudaMemcpyDefault,
+ pmePpCommStream_.stream());
CU_RET_ERR(stat, "cudaMemcpyAsync on Recv from PME CUDA direct data transfer failed");
if (receivePmeForceToGpu)
{
// Ensure CPU waits for PME forces to be copied before reducing
// them with other forces on the CPU
- cudaStreamSynchronize(pmePpCommStream_.stream());
+ pmePpCommStream_.synchronize();
}
+}
+
+void PmePpCommGpu::Impl::receiveForceFromPmeCudaMpi(float3* pmeForcePtr, int recvSize)
+{
+#if GMX_MPI
+ MPI_Recv(pmeForcePtr, recvSize * DIM, MPI_FLOAT, pmeRank_, 0, comm_, MPI_STATUS_IGNORE);
#else
- GMX_UNUSED_VALUE(recvPtr);
+ GMX_UNUSED_VALUE(pmeForcePtr);
GMX_UNUSED_VALUE(recvSize);
- GMX_UNUSED_VALUE(receivePmeForceToGpu);
#endif
}
-void PmePpCommGpu::Impl::sendCoordinatesToPmeCudaDirect(void* sendPtr,
- int sendSize,
- bool gmx_unused sendPmeCoordinatesFromGpu,
+void PmePpCommGpu::Impl::receiveForceFromPme(float3* recvPtr, int recvSize, bool receivePmeForceToGpu)
+{
+ float3* pmeForcePtr = receivePmeForceToGpu ? asFloat3(d_pmeForces_) : recvPtr;
+ if (GMX_THREAD_MPI)
+ {
+ receiveForceFromPmeCudaDirect(pmeForcePtr, recvSize, receivePmeForceToGpu);
+ }
+ else
+ {
+ receiveForceFromPmeCudaMpi(pmeForcePtr, recvSize);
+ }
+}
+
+void PmePpCommGpu::Impl::sendCoordinatesToPmeCudaDirect(float3* sendPtr,
+ int sendSize,
GpuEventSynchronizer* coordinatesReadyOnDeviceEvent)
{
-#if GMX_MPI
// ensure stream waits until coordinate data is available on device
coordinatesReadyOnDeviceEvent->enqueueWaitEvent(pmePpCommStream_);
- cudaError_t stat = cudaMemcpyAsync(remotePmeXBuffer_, sendPtr, sendSize * DIM * sizeof(float),
- cudaMemcpyDefault, pmePpCommStream_.stream());
+ cudaError_t stat = cudaMemcpyAsync(remotePmeXBuffer_,
+ sendPtr,
+ sendSize * DIM * sizeof(float),
+ cudaMemcpyDefault,
+ pmePpCommStream_.stream());
CU_RET_ERR(stat, "cudaMemcpyAsync on Send to PME CUDA direct data transfer failed");
+#if GMX_MPI
// Record and send event to allow PME task to sync to above transfer before commencing force calculations
pmeCoordinatesSynchronizer_.markEvent(pmePpCommStream_);
GpuEventSynchronizer* pmeSync = &pmeCoordinatesSynchronizer_;
MPI_Send(&pmeSync, sizeof(GpuEventSynchronizer*), MPI_BYTE, pmeRank_, 0, comm_);
+#endif
+}
+
+void PmePpCommGpu::Impl::sendCoordinatesToPmeCudaMpi(float3* sendPtr,
+ int sendSize,
+ GpuEventSynchronizer* coordinatesReadyOnDeviceEvent)
+{
+ // ensure coordinate data is available on device before we start transfer
+ coordinatesReadyOnDeviceEvent->waitForEvent();
+
+#if GMX_MPI
+ float3* sendptr_x = sendPtr;
+
+ MPI_Send(sendptr_x, sendSize * DIM, MPI_FLOAT, pmeRank_, eCommType_COORD_GPU, comm_);
#else
GMX_UNUSED_VALUE(sendPtr);
GMX_UNUSED_VALUE(sendSize);
- GMX_UNUSED_VALUE(sendPmeCoordinatesFromGpu);
- GMX_UNUSED_VALUE(coordinatesReadyOnDeviceEvent);
#endif
}
-void* PmePpCommGpu::Impl::getGpuForceStagingPtr()
+
+void PmePpCommGpu::Impl::sendCoordinatesToPme(float3* sendPtr,
+ int sendSize,
+ GpuEventSynchronizer* coordinatesReadyOnDeviceEvent)
+{
+ if (GMX_THREAD_MPI)
+ {
+ sendCoordinatesToPmeCudaDirect(sendPtr, sendSize, coordinatesReadyOnDeviceEvent);
+ }
+ else
+ {
+ sendCoordinatesToPmeCudaMpi(sendPtr, sendSize, coordinatesReadyOnDeviceEvent);
+ }
+}
+DeviceBuffer<Float3> PmePpCommGpu::Impl::getGpuForceStagingPtr()
{
- return static_cast<void*>(d_pmeForces_);
+ return d_pmeForces_;
}
GpuEventSynchronizer* PmePpCommGpu::Impl::getForcesReadySynchronizer()
{
- return &forcesReadySynchronizer_;
+ if (GMX_THREAD_MPI)
+ {
+ return &forcesReadySynchronizer_;
+ }
+ else
+ {
+ return nullptr;
+ }
}
PmePpCommGpu::PmePpCommGpu(MPI_Comm comm,
impl_->reinit(size);
}
-void PmePpCommGpu::receiveForceFromPmeCudaDirect(void* recvPtr, int recvSize, bool receivePmeForceToGpu)
+void PmePpCommGpu::receiveForceFromPme(RVec* recvPtr, int recvSize, bool receivePmeForceToGpu)
+{
+ impl_->receiveForceFromPme(asFloat3(recvPtr), recvSize, receivePmeForceToGpu);
+}
+
+void PmePpCommGpu::sendCoordinatesToPmeFromGpu(DeviceBuffer<RVec> sendPtr,
+ int sendSize,
+ GpuEventSynchronizer* coordinatesReadyOnDeviceEvent)
{
- impl_->receiveForceFromPmeCudaDirect(recvPtr, recvSize, receivePmeForceToGpu);
+ impl_->sendCoordinatesToPme(asFloat3(sendPtr), sendSize, coordinatesReadyOnDeviceEvent);
}
-void PmePpCommGpu::sendCoordinatesToPmeCudaDirect(void* sendPtr,
- int sendSize,
- bool sendPmeCoordinatesFromGpu,
- GpuEventSynchronizer* coordinatesReadyOnDeviceEvent)
+void PmePpCommGpu::sendCoordinatesToPmeFromCpu(RVec* sendPtr,
+ int sendSize,
+ GpuEventSynchronizer* coordinatesReadyOnDeviceEvent)
{
- impl_->sendCoordinatesToPmeCudaDirect(sendPtr, sendSize, sendPmeCoordinatesFromGpu,
- coordinatesReadyOnDeviceEvent);
+ impl_->sendCoordinatesToPme(asFloat3(sendPtr), sendSize, coordinatesReadyOnDeviceEvent);
}
-void* PmePpCommGpu::getGpuForceStagingPtr()
+DeviceBuffer<Float3> PmePpCommGpu::getGpuForceStagingPtr()
{
return impl_->getGpuForceStagingPtr();
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*! \brief Pull force buffer directly from GPU memory on PME
* rank to either GPU or CPU memory on PP task using CUDA
- * Memory copy.
+ * Memory copy or CUDA-aware MPI.
*
* recvPtr should be in GPU or CPU memory if recvPmeForceToGpu
* is true or false, respectively. If receiving to GPU, this
* \param[in] recvSize Number of elements to receive
* \param[in] receivePmeForceToGpu Whether receive is to GPU, otherwise CPU
*/
- void receiveForceFromPmeCudaDirect(void* recvPtr, int recvSize, bool receivePmeForceToGpu);
+ void receiveForceFromPme(float3* recvPtr, int recvSize, bool receivePmeForceToGpu);
/*! \brief Push coordinates buffer directly to GPU memory on PME
* task, from either GPU or CPU memory on PP task using CUDA
- * Memory copy. sendPtr should be in GPU or CPU memory if
- * sendPmeCoordinatesFromGpu is true or false respectively. If
- * sending from GPU, this method should be called after the
- * local GPU coordinate buffer operations. The remote PME task will
- * automatically wait for data to be copied before commencing PME force calculations.
+ * Memory copy or CUDA-aware MPI. If sending from GPU, this method should
+ * be called after the local GPU coordinate buffer operations.
+ * The remote PME task will automatically wait for data to be copied
+ * before commencing PME force calculations.
* \param[in] sendPtr Buffer with coordinate data
* \param[in] sendSize Number of elements to send
- * \param[in] sendPmeCoordinatesFromGpu Whether send is from GPU, otherwise CPU
* \param[in] coordinatesReadyOnDeviceEvent Event recorded when coordinates are available on device
*/
- void sendCoordinatesToPmeCudaDirect(void* sendPtr,
- int sendSize,
- bool sendPmeCoordinatesFromGpu,
- GpuEventSynchronizer* coordinatesReadyOnDeviceEvent);
+ void sendCoordinatesToPme(float3* sendPtr, int sendSize, GpuEventSynchronizer* coordinatesReadyOnDeviceEvent);
/*! \brief
* Return pointer to buffer used for staging PME force on GPU
*/
- void* getGpuForceStagingPtr();
+ DeviceBuffer<Float3> getGpuForceStagingPtr();
/*! \brief
* Return pointer to event recorded when forces are ready
*/
GpuEventSynchronizer* getForcesReadySynchronizer();
+private:
+ /*! \brief Pull force buffer directly from GPU memory on PME
+ * rank to either GPU or CPU memory on PP task using CUDA
+ * Memory copy. This method is used with Thread-MPI.
+ * \param[out] recvPtr CPU buffer to receive PME force data
+ * \param[in] recvSize Number of elements to receive
+ * \param[in] receivePmeForceToGpu Whether receive is to GPU, otherwise CPU
+ */
+ void receiveForceFromPmeCudaDirect(float3* recvPtr, int recvSize, bool receivePmeForceToGpu);
+
+ /*! \brief Pull force buffer directly from GPU memory on PME
+ * rank to either GPU or CPU memory on PP task using CUDA-aware
+ * MPI. This method is used with process-MPI.
+ * \param[out] recvPtr CPU buffer to receive PME force data
+ * \param[in] recvSize Number of elements to receive
+ */
+ void receiveForceFromPmeCudaMpi(float3* recvPtr, int recvSize);
+
+ /*! \brief Push coordinates buffer directly to GPU memory on PME
+ * task, from either GPU or CPU memory on PP task using CUDA Memory copy.
+ * This method is used with Thread-MPI.
+ * \param[in] sendPtr Buffer with coordinate data
+ * \param[in] sendSize Number of elements to send
+ * \param[in] coordinatesReadyOnDeviceEvent Event recorded when coordinates are available on device
+ */
+ void sendCoordinatesToPmeCudaDirect(float3* sendPtr,
+ int sendSize,
+ GpuEventSynchronizer* coordinatesReadyOnDeviceEvent);
+
+ /*! \brief Push coordinates buffer directly to GPU memory on PME
+ * task, from either GPU or CPU memory on PP task using CUDA-aware MPI.
+ * This method is used with process-MPI.
+ * \param[in] sendPtr Buffer with coordinate data
+ * \param[in] sendSize Number of elements to send
+ * \param[in] coordinatesReadyOnDeviceEvent Event recorded when coordinates are available on device
+ */
+ void sendCoordinatesToPmeCudaMpi(float3* sendPtr,
+ int sendSize,
+ GpuEventSynchronizer* coordinatesReadyOnDeviceEvent);
+
private:
//! GPU context handle (not used in CUDA)
const DeviceContext& deviceContext_;
//! Handle for CUDA stream used for the communication operations in this class
const DeviceStream& pmePpCommStream_;
//! Remote location of PME coordinate data buffer
- void* remotePmeXBuffer_ = nullptr;
+ float3* remotePmeXBuffer_ = nullptr;
//! Remote location of PME force data buffer
- void* remotePmeFBuffer_ = nullptr;
+ float3* remotePmeFBuffer_ = nullptr;
//! communicator for simulation
MPI_Comm comm_;
//! Rank of PME task
int pmeRank_ = -1;
//! Buffer for staging PME force on GPU
- rvec* d_pmeForces_ = nullptr;
+ DeviceBuffer<gmx::RVec> d_pmeForces_;
//! number of atoms in PME force staging array
int d_pmeForcesSize_ = -1;
//! number of atoms allocated in recvbuf array
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
eCommType_SigmaB,
eCommType_NR,
eCommType_COORD,
+ eCommType_COORD_GPU,
eCommType_CNB
};
real dvdlambda_q;
real dvdlambda_lj;
//@}
- float cycles; /**< Counter of CPU cycles used */
- gmx_stop_cond_t stop_cond; /**< Flag used in responding to an external signal to terminate */
+ float cycles; /**< Counter of CPU cycles used */
+ StopCondition stop_cond; /**< Flag used in responding to an external signal to terminate */
};
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
try
{
const int natoms = x.ssize();
- pme_calc_pidx(natoms * thread / nthread, natoms * (thread + 1) / nthread, recipbox, x,
- atc, atc->count_thread[thread].data());
+ pme_calc_pidx(natoms * thread / nthread,
+ natoms * (thread + 1) / nthread,
+ recipbox,
+ x,
+ atc,
+ atc->count_thread[thread].data());
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
if (nbyte_s > 0 && nbyte_r > 0)
{
- MPI_Sendrecv(buf_s, nbyte_s, MPI_BYTE, dest, shift, buf_r, nbyte_r, MPI_BYTE, src, shift,
- atc->mpi_comm, &stat);
+ MPI_Sendrecv(
+ buf_s, nbyte_s, MPI_BYTE, dest, shift, buf_r, nbyte_r, MPI_BYTE, src, shift, atc->mpi_comm, &stat);
}
else if (nbyte_s > 0)
{
static void dd_pmeredist_pos_coeffs(gmx_pme_t* pme,
const gmx_bool bX,
gmx::ArrayRef<const gmx::RVec> x,
- const real* data,
+ gmx::ArrayRef<const real> data,
PmeAtomComm* atc)
{
int nnodes_comm, i, local_pos, buf_pos, node;
"%zd particles communicated to PME rank %d are more than 2/3 times the cut-off "
"out of the domain decomposition cell of their charge group in dimension %c.\n"
"This usually means that your system is not well equilibrated.",
- x.ssize() - (sendCount[atc->nodeid] + nsend), pme->nodeid, 'x' + atc->dimind);
+ x.ssize() - (sendCount[atc->nodeid] + nsend),
+ pme->nodeid,
+ 'x' + atc->dimind);
}
if (nsend > pme->buf_nalloc)
/* Communicate the count */
if (debug)
{
- fprintf(debug, "dimind %d PME rank %d send to rank %d: %d\n", atc->dimind,
- atc->nodeid, commnode, scount);
+ fprintf(debug, "dimind %d PME rank %d send to rank %d: %d\n", atc->dimind, atc->nodeid, commnode, scount);
}
- pme_dd_sendrecv(atc, FALSE, i, &scount, sizeof(int), &atc->slabCommSetup[i].rcount,
- sizeof(int));
+ pme_dd_sendrecv(
+ atc, FALSE, i, &scount, sizeof(int), &atc->slabCommSetup[i].rcount, sizeof(int));
numAtoms += atc->slabCommSetup[i].rcount;
}
if (bX)
{
/* Communicate the coordinates */
- pme_dd_sendrecv(atc, FALSE, i, pme->bufv + buf_pos, scount * sizeof(rvec),
- atc->xBuffer.data() + local_pos, rcount * sizeof(rvec));
+ pme_dd_sendrecv(atc,
+ FALSE,
+ i,
+ pme->bufv + buf_pos,
+ scount * sizeof(rvec),
+ atc->xBuffer.data() + local_pos,
+ rcount * sizeof(rvec));
}
/* Communicate the coefficients */
- pme_dd_sendrecv(atc, FALSE, i, pme->bufr + buf_pos, scount * sizeof(real),
- atc->coefficientBuffer.data() + local_pos, rcount * sizeof(real));
+ pme_dd_sendrecv(atc,
+ FALSE,
+ i,
+ pme->bufr + buf_pos,
+ scount * sizeof(real),
+ atc->coefficientBuffer.data() + local_pos,
+ rcount * sizeof(real));
buf_pos += scount;
local_pos += atc->slabCommSetup[i].rcount;
}
if (scount > 0 || rcount > 0)
{
/* Communicate the forces */
- pme_dd_sendrecv(atc, TRUE, i, atc->f.data() + local_pos, scount * sizeof(rvec),
- pme->bufv + buf_pos, rcount * sizeof(rvec));
+ pme_dd_sendrecv(atc,
+ TRUE,
+ i,
+ atc->f.data() + local_pos,
+ scount * sizeof(rvec),
+ pme->bufv + buf_pos,
+ rcount * sizeof(rvec));
local_pos += scount;
}
atc->slabCommSetup[commnode].buf_index = buf_pos;
const t_commrec* cr,
gmx_bool bFirst,
gmx::ArrayRef<const gmx::RVec> x,
- const real* data)
+ gmx::ArrayRef<const real> data)
{
for (int d = pme->ndecompdim - 1; d >= 0; d--)
{
gmx::ArrayRef<const gmx::RVec> xRef;
- const real* param_d;
+ gmx::ArrayRef<const real> param_d;
if (d == pme->ndecompdim - 1)
{
/* Start out with the local coordinates and charges */
/* Redistribute the data collected along the previous dimension */
const PmeAtomComm& atc = pme->atc[d + 1];
xRef = atc.x;
- param_d = atc.coefficient.data();
+ param_d = atc.coefficient;
}
PmeAtomComm& atc = pme->atc[d];
atc.pd.resize(xRef.size());
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const t_commrec* cr,
gmx_bool bFirst,
gmx::ArrayRef<const gmx::RVec> x,
- const real* data);
+ gmx::ArrayRef<const real> data);
#endif
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
template<unsigned int factor>
static size_t roundUpToMultipleOfFactor(size_t number)
{
- static_assert(factor > 0 && (factor & (factor - 1)) == 0,
- "factor should be >0 and a power of 2");
+ static_assert(gmx::isPowerOfTwo(factor));
/* We need to add a most factor-1 and because factor is a power of 2,
* we get the result by masking out the bits corresponding to factor-1.
static void reallocSimdAlignedAndPadded(real** ptr, int unpaddedNumElements)
{
sfree_aligned(*ptr);
- snew_aligned(*ptr, roundUpToMultipleOfFactor<c_simdWidth>(unpaddedNumElements),
+ snew_aligned(*ptr,
+ roundUpToMultipleOfFactor<c_simdWidth>(unpaddedNumElements),
c_simdWidth * sizeof(real));
}
ivec local_ndata, local_offset, local_size;
real elfac;
- elfac = ONE_4PI_EPS0 / pme->epsilon_r;
+ elfac = gmx::c_one4PiEps0 / pme->epsilon_r;
nx = pme->nkx;
ny = pme->nky;
nz = pme->nkz;
/* Dimensions should be identical for A/B grid, so we just use A here */
- gmx_parallel_3dfft_complex_limits(pme->pfft_setup[PME_GRID_QA], complex_order, local_ndata,
- local_offset, local_size);
+ gmx_parallel_3dfft_complex_limits(
+ pme->pfft_setup[PME_GRID_QA], complex_order, local_ndata, local_offset, local_size);
rxx = pme->recipbox[XX][XX];
ryx = pme->recipbox[YY][XX];
}
calc_exponentials_q(
- kxstart, kxend, elfac,
+ kxstart,
+ kxend,
+ elfac,
ArrayRef<PME_T>(denom, denom + roundUpToMultipleOfFactor<c_simdWidth>(kxend)),
ArrayRef<PME_T>(tmp1, tmp1 + roundUpToMultipleOfFactor<c_simdWidth>(kxend)),
ArrayRef<PME_T>(eterm, eterm + roundUpToMultipleOfFactor<c_simdWidth>(kxend)));
}
calc_exponentials_q(
- kxstart, kxend, elfac,
+ kxstart,
+ kxend,
+ elfac,
ArrayRef<PME_T>(denom, denom + roundUpToMultipleOfFactor<c_simdWidth>(kxend)),
ArrayRef<PME_T>(tmp1, tmp1 + roundUpToMultipleOfFactor<c_simdWidth>(kxend)),
ArrayRef<PME_T>(eterm, eterm + roundUpToMultipleOfFactor<c_simdWidth>(kxend)));
nz = pme->nkz;
/* Dimensions should be identical for A/B grid, so we just use A here */
- gmx_parallel_3dfft_complex_limits(pme->pfft_setup[PME_GRID_C6A], complex_order, local_ndata,
- local_offset, local_size);
+ gmx_parallel_3dfft_complex_limits(
+ pme->pfft_setup[PME_GRID_C6A], complex_order, local_ndata, local_offset, local_size);
rxx = pme->recipbox[XX][XX];
ryx = pme->recipbox[YY][XX];
ryy = pme->recipbox[YY][YY];
}
calc_exponentials_lj(
- kxstart, kxend,
+ kxstart,
+ kxend,
ArrayRef<PME_T>(tmp1, tmp1 + roundUpToMultipleOfFactor<c_simdWidth>(kxend)),
ArrayRef<PME_T>(tmp2, tmp2 + roundUpToMultipleOfFactor<c_simdWidth>(kxend)),
ArrayRef<PME_T>(denom, denom + roundUpToMultipleOfFactor<c_simdWidth>(kxend)));
}
calc_exponentials_lj(
- kxstart, kxend,
+ kxstart,
+ kxend,
ArrayRef<PME_T>(tmp1, tmp1 + roundUpToMultipleOfFactor<c_simdWidth>(kxend)),
ArrayRef<PME_T>(tmp2, tmp2 + roundUpToMultipleOfFactor<c_simdWidth>(kxend)),
ArrayRef<PME_T>(denom, denom + roundUpToMultipleOfFactor<c_simdWidth>(kxend)));
pme_gpu_stage_atom_data(sm_coordinates, gm_coordinates, DIM);
barrier(CLK_LOCAL_MEM_FENCE);
- calculate_splines(kernelParams, atomIndexOffset, sm_coordinates, sm_coefficients, sm_theta,
- sm_gridlineIndices, sm_fractCoords, gm_theta, gm_dtheta,
- gm_gridlineIndices, gm_fractShiftsTable, gm_gridlineIndicesTable);
+ calculate_splines(kernelParams,
+ atomIndexOffset,
+ sm_coordinates,
+ sm_coefficients,
+ sm_theta,
+ sm_gridlineIndices,
+ sm_fractCoords,
+ gm_theta,
+ gm_dtheta,
+ gm_gridlineIndices,
+ gm_fractShiftsTable,
+ gm_gridlineIndicesTable);
#if !defined(_AMD_SOURCE_) && !defined(_NVIDIA_SOURCE_)
/* This is only here for execution of e.g. 32-sized warps on 16-wide hardware; this was
* __syncwarp() in CUDA. #2519
/* Spline data - only thetas (dthetas will only be needed in gather) */
pme_gpu_stage_atom_data(sm_theta, gm_theta, DIM * order);
/* Gridline indices - they're actually int and not float, but C99 is angry about overloads */
- pme_gpu_stage_atom_data((__local float*)sm_gridlineIndices,
- (__global const float*)gm_gridlineIndices, DIM);
+ pme_gpu_stage_atom_data(
+ (__local float*)sm_gridlineIndices, (__global const float*)gm_gridlineIndices, DIM);
barrier(CLK_LOCAL_MEM_FENCE);
}
int d;
real* grid_th;
- gmx_parallel_3dfft_real_limits(pme->pfft_setup[grid_index], local_fft_ndata, local_fft_offset,
- local_fft_size);
+ gmx_parallel_3dfft_real_limits(
+ pme->pfft_setup[grid_index], local_fft_ndata, local_fft_offset, local_fft_size);
fft_my = local_fft_size[YY];
fft_mz = local_fft_size[ZZ];
const real* grid_th;
real* commbuf = nullptr;
- gmx_parallel_3dfft_real_limits(pme->pfft_setup[grid_index], local_fft_ndata, local_fft_offset,
- local_fft_size);
+ gmx_parallel_3dfft_real_limits(
+ pme->pfft_setup[grid_index], local_fft_ndata, local_fft_offset, local_fft_size);
fft_nx = local_fft_ndata[XX];
fft_ny = local_fft_ndata[YY];
fft_nz = local_fft_ndata[ZZ];
#ifdef DEBUG_PME_REDUCE
printf("n%d t%d add %d %2d %2d %2d %2d %2d %2d %2d-%2d %2d-%2d, %2d-%2d "
"%2d-%2d, %2d-%2d %2d-%2d\n",
- pme->nodeid, thread, thread_f, pme->pmegrid_start_ix, pme->pmegrid_start_iy,
- pme->pmegrid_start_iz, sx, sy, sz, offx - ox, tx1 - ox, offx, tx1, offy - oy,
- ty1 - oy, offy, ty1, offz - oz, tz1 - oz, offz, tz1);
+ pme->nodeid,
+ thread,
+ thread_f,
+ pme->pmegrid_start_ix,
+ pme->pmegrid_start_iy,
+ pme->pmegrid_start_iz,
+ sx,
+ sy,
+ sz,
+ offx - ox,
+ tx1 - ox,
+ offx,
+ tx1,
+ offy - oy,
+ ty1 - oy,
+ offy,
+ ty1,
+ offz - oz,
+ tz1 - oz,
+ offz,
+ tz1);
#endif
if (!(bCommX || bCommY))
* communication setup.
*/
- gmx_parallel_3dfft_real_limits(pme->pfft_setup[grid_index], local_fft_ndata, local_fft_offset,
- local_fft_size);
+ gmx_parallel_3dfft_real_limits(
+ pme->pfft_setup[grid_index], local_fft_ndata, local_fft_offset, local_fft_size);
if (pme->nnodes_minor > 1)
{
if (debug != nullptr)
{
- fprintf(debug, "PME fftgrid comm y %2d x %2d x %2d\n", local_fft_ndata[XX],
- send_nindex, local_fft_ndata[ZZ]);
+ fprintf(debug,
+ "PME fftgrid comm y %2d x %2d x %2d\n",
+ local_fft_ndata[XX],
+ send_nindex,
+ local_fft_ndata[ZZ]);
}
#if GMX_MPI
int send_id = overlap->comm_data[ipulse].send_id;
int recv_id = overlap->comm_data[ipulse].recv_id;
- MPI_Sendrecv(sendptr, send_size_y * datasize, GMX_MPI_REAL, send_id, ipulse, recvptr,
- recv_size_y * datasize, GMX_MPI_REAL, recv_id, ipulse, overlap->mpi_comm, &stat);
+ MPI_Sendrecv(sendptr,
+ send_size_y * datasize,
+ GMX_MPI_REAL,
+ send_id,
+ ipulse,
+ recvptr,
+ recv_size_y * datasize,
+ GMX_MPI_REAL,
+ recv_id,
+ ipulse,
+ overlap->mpi_comm,
+ &stat);
#endif
for (x = 0; x < local_fft_ndata[XX]; x++)
if (debug != nullptr)
{
- fprintf(debug, "PME fftgrid comm x %2d x %2d x %2d\n", send_nindex, local_fft_ndata[YY],
+ fprintf(debug,
+ "PME fftgrid comm x %2d x %2d x %2d\n",
+ send_nindex,
+ local_fft_ndata[YY],
local_fft_ndata[ZZ]);
}
int recv_id = overlap->comm_data[ipulse].recv_id;
auto* sendptr = const_cast<real*>(overlap->sendbuf.data());
auto* recvptr = const_cast<real*>(overlap->recvbuf.data());
- MPI_Sendrecv(sendptr, send_nindex * datasize, GMX_MPI_REAL, send_id, ipulse, recvptr,
- recv_nindex * datasize, GMX_MPI_REAL, recv_id, ipulse, overlap->mpi_comm, &stat);
+ MPI_Sendrecv(sendptr,
+ send_nindex * datasize,
+ GMX_MPI_REAL,
+ send_id,
+ ipulse,
+ recvptr,
+ recv_nindex * datasize,
+ GMX_MPI_REAL,
+ recv_id,
+ ipulse,
+ overlap->mpi_comm,
+ &stat);
#endif
for (x = 0; x < recv_nindex; x++)
if (bCalcSplines)
{
- make_bsplines(spline->theta.coefficients, spline->dtheta.coefficients,
- pme->pme_order, as_rvec_array(atc->fractx.data()), spline->n,
- spline->ind.data(), atc->coefficient.data(), bDoSplines);
+ make_bsplines(spline->theta.coefficients,
+ spline->dtheta.coefficients,
+ pme->pme_order,
+ as_rvec_array(atc->fractx.data()),
+ spline->n,
+ spline->ind.data(),
+ atc->coefficient.data(),
+ bDoSplines);
}
if (bSpread)
{
try
{
- reduce_threadgrid_overlap(pme, grids, thread, fftgrid,
+ reduce_threadgrid_overlap(pme,
+ grids,
+ thread,
+ fftgrid,
const_cast<real*>(pme->overlap[0].sendbuf.data()),
- const_cast<real*>(pme->overlap[1].sendbuf.data()), grid_index);
+ const_cast<real*>(pme->overlap[1].sendbuf.data()),
+ grid_index);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
/* Spreading */
if (spreadCharges)
{
- spread_charges<order, wrapX, wrapY, 0, threadsPerAtom>(kernelParams, &atomCharge,
- sm_gridlineIndices, sm_theta);
+ spread_charges<order, wrapX, wrapY, 0, threadsPerAtom>(
+ kernelParams, &atomCharge, sm_gridlineIndices, sm_theta);
}
if (numGrids == 2)
{
}
if (spreadCharges)
{
- spread_charges<order, wrapX, wrapY, 1, threadsPerAtom>(kernelParams, &atomCharge,
- sm_gridlineIndices, sm_theta);
+ spread_charges<order, wrapX, wrapY, 1, threadsPerAtom>(
+ kernelParams, &atomCharge, sm_gridlineIndices, sm_theta);
}
}
}
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2016,2017,2020, by the GROMACS development team, led by
+# Copyright (c) 2016,2017,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
pmesolvetest.cpp
pmesplinespreadtest.cpp
pmetestcommon.cpp
+ pme.cpp
)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for functionality of the pme related classes:
+ * class SeparatePmeRanksPermitted
+ *
+ * \author Dmitry Morozov <dmitry.morozov@jyu.fi>
+ * \ingroup module_ewald
+ */
+#include "gmxpre.h"
+
+#include <gtest/gtest.h>
+
+#include "gromacs/utility/real.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringcompare.h"
+
+#include "testutils/testasserts.h"
+#include "testutils/testmatchers.h"
+
+#include "pmetestcommon.h"
+
+namespace gmx
+{
+
+namespace test
+{
+
+class SeparatePmeRanksPermittedTest : public ::testing::Test
+{
+public:
+ void disableFirstReason() { separatePmeRanksPermitted_.disablePmeRanks("First reason"); }
+
+ void disableSecondReason() { separatePmeRanksPermitted_.disablePmeRanks("Second reason"); }
+
+ void disableEmptyReason() { separatePmeRanksPermitted_.disablePmeRanks(""); }
+
+protected:
+ SeparatePmeRanksPermitted separatePmeRanksPermitted_;
+};
+
+TEST_F(SeparatePmeRanksPermittedTest, ZeroPmeDisableReasons)
+{
+ // Expect that SeparatePmeRanksPermitted is enabled by default
+ EXPECT_TRUE(separatePmeRanksPermitted_.permitSeparatePmeRanks());
+}
+
+TEST_F(SeparatePmeRanksPermittedTest, CanBeDisabled)
+{
+ // Test if disablePmeRanks works
+ EXPECT_NO_THROW(disableFirstReason(););
+}
+
+TEST_F(SeparatePmeRanksPermittedTest, OneDisableReasonFlag)
+{
+ disableFirstReason();
+
+ // Expect that SeparatePmeRanksPermitted is disabled now
+ EXPECT_FALSE(separatePmeRanksPermitted_.permitSeparatePmeRanks());
+}
+
+TEST_F(SeparatePmeRanksPermittedTest, OneDisableReasonText)
+{
+ disableFirstReason();
+
+ // Expect that reasonsWhyDisabled works with one reason
+ EXPECT_TRUE(separatePmeRanksPermitted_.reasonsWhyDisabled() == "First reason");
+}
+
+TEST_F(SeparatePmeRanksPermittedTest, TwoDisableReasonText)
+{
+ disableFirstReason();
+ disableSecondReason();
+
+ // Expect that reasonsWhyDisabled works with two reasons
+ EXPECT_TRUE(separatePmeRanksPermitted_.reasonsWhyDisabled() == "First reason; Second reason");
+}
+
+TEST_F(SeparatePmeRanksPermittedTest, EmptyDisableReasonText)
+{
+ disableEmptyReason();
+
+ // Expect that reasonsWhyDisabled works with empty reason
+ EXPECT_TRUE(separatePmeRanksPermitted_.reasonsWhyDisabled().empty());
+}
+
+} // namespace test
+
+} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* Describing the test in case it fails */
SCOPED_TRACE(formatString(
"Testing B-spline moduli creation (%s) for PME order %d, grid size %d %d %d",
- (moduliType == ModuliType::P3M) ? "P3M" : "plain", pmeOrder, gridSize[XX],
- gridSize[YY], gridSize[ZZ]));
+ (moduliType == ModuliType::P3M) ? "P3M" : "plain",
+ pmeOrder,
+ gridSize[XX],
+ gridSize[YY],
+ gridSize[ZZ]));
/* Storing the input where it's needed */
t_inputrec inputRec;
inputRec.nkx = gridSize[XX];
inputRec.nky = gridSize[YY];
inputRec.nkz = gridSize[ZZ];
- inputRec.coulombtype = (moduliType == ModuliType::P3M) ? eelP3M_AD : eelPME;
- inputRec.pme_order = pmeOrder;
+ inputRec.coulombtype = (moduliType == ModuliType::P3M) ? CoulombInteractionType::P3mAD
+ : CoulombInteractionType::Pme;
+ inputRec.pme_order = pmeOrder;
/* PME initialization call which checks the inputs and computes the B-spline moduli according to the grid sizes. */
PmeSafePointer pme = pmeInitEmpty(&inputRec);
BSplineModuliInputParameters{ IVec{ 64, 2, 64 }, sanePmeOrder, ModuliType::PME },
/* Invalid interpolation orders */
BSplineModuliInputParameters{
- saneGridSize, 8 + 1, ModuliType::P3M // P3M only supports orders up to 8
+ saneGridSize,
+ 8 + 1,
+ ModuliType::P3M // P3M only supports orders up to 8
},
BSplineModuliInputParameters{ saneGridSize, PME_ORDER_MAX + 1, ModuliType::PME },
};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
inputRec.nky = gridSize[YY];
inputRec.nkz = gridSize[ZZ];
inputRec.pme_order = pmeOrder;
- inputRec.coulombtype = eelPME;
+ inputRec.coulombtype = CoulombInteractionType::Pme;
inputRec.epsilon_r = 1.0;
TestReferenceData refData;
SCOPED_TRACE(
formatString("Testing force gathering on %s for PME grid size %d %d %d"
", order %d, %zu atoms",
- pmeTestHardwareContext->description().c_str(), gridSize[XX],
- gridSize[YY], gridSize[ZZ], pmeOrder, atomCount));
-
- PmeSafePointer pmeSafe =
- pmeInitWrapper(&inputRec, codePath, pmeTestHardwareContext->deviceContext(),
- pmeTestHardwareContext->deviceStream(),
- pmeTestHardwareContext->pmeGpuProgram(), box);
+ pmeTestHardwareContext->description().c_str(),
+ gridSize[XX],
+ gridSize[YY],
+ gridSize[ZZ],
+ pmeOrder,
+ atomCount));
+
+ PmeSafePointer pmeSafe = pmeInitWrapper(&inputRec,
+ codePath,
+ pmeTestHardwareContext->deviceContext(),
+ pmeTestHardwareContext->deviceStream(),
+ pmeTestHardwareContext->pmeGpuProgram(),
+ box);
std::unique_ptr<StatePropagatorDataGpu> stateGpu =
(codePath == CodePath::GPU)
? makeStatePropagatorDataGpu(*pmeSafe.get(),
pmeTestHardwareContext->deviceStream())
: nullptr;
- pmeInitAtoms(pmeSafe.get(), stateGpu.get(), codePath, inputAtomData.coordinates,
+ pmeInitAtoms(pmeSafe.get(),
+ stateGpu.get(),
+ codePath,
+ inputAtomData.coordinates,
inputAtomData.charges);
/* Setting some more inputs */
pmeSetGridLineIndices(pmeSafe.get(), codePath, inputAtomData.gridLineIndices);
for (int dimIndex = 0; dimIndex < DIM; dimIndex++)
{
- pmeSetSplineData(pmeSafe.get(), codePath, inputAtomSplineData.splineValues[dimIndex],
- PmeSplineDataType::Values, dimIndex);
- pmeSetSplineData(pmeSafe.get(), codePath, inputAtomSplineData.splineDerivatives[dimIndex],
- PmeSplineDataType::Derivatives, dimIndex);
+ pmeSetSplineData(pmeSafe.get(),
+ codePath,
+ inputAtomSplineData.splineValues[dimIndex],
+ PmeSplineDataType::Values,
+ dimIndex);
+ pmeSetSplineData(pmeSafe.get(),
+ codePath,
+ inputAtomSplineData.splineDerivatives[dimIndex],
+ PmeSplineDataType::Derivatives,
+ dimIndex);
}
/* Explicitly copying the sample forces to be able to modify them */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
inputRec.nky = gridSize[YY];
inputRec.nkz = gridSize[ZZ];
inputRec.pme_order = 4;
- inputRec.coulombtype = eelPME;
+ inputRec.coulombtype = CoulombInteractionType::Pme;
inputRec.epsilon_r = epsilon_r;
switch (method)
{
case PmeSolveAlgorithm::Coulomb: break;
- case PmeSolveAlgorithm::LennardJones: inputRec.vdwtype = evdwPME; break;
+ case PmeSolveAlgorithm::LennardJones: inputRec.vdwtype = VanDerWaalsType::Pme; break;
default: GMX_THROW(InternalError("Unknown PME solver"));
}
if (!supportedInput)
{
/* Testing the failure for the unsupported input */
- EXPECT_THROW_GMX(pmeInitWrapper(&inputRec, codePath, nullptr, nullptr, nullptr, box,
- ewaldCoeff_q, ewaldCoeff_lj),
- NotImplementedError);
+ EXPECT_THROW_GMX(
+ pmeInitWrapper(&inputRec, codePath, nullptr, nullptr, nullptr, box, ewaldCoeff_q, ewaldCoeff_lj),
+ NotImplementedError);
continue;
}
"Testing solving (%s, %s, %s energy/virial) on %s for PME grid "
"size %d %d %d, Ewald coefficients %g %g",
(method == PmeSolveAlgorithm::LennardJones) ? "Lennard-Jones" : "Coulomb",
- gridOrdering.second.c_str(), computeEnergyAndVirial ? "with" : "without",
- pmeTestHardwareContext->description().c_str(), gridSize[XX],
- gridSize[YY], gridSize[ZZ], ewaldCoeff_q, ewaldCoeff_lj));
+ gridOrdering.second.c_str(),
+ computeEnergyAndVirial ? "with" : "without",
+ pmeTestHardwareContext->description().c_str(),
+ gridSize[XX],
+ gridSize[YY],
+ gridSize[ZZ],
+ ewaldCoeff_q,
+ ewaldCoeff_lj));
/* Running the test */
- PmeSafePointer pmeSafe = pmeInitWrapper(
- &inputRec, codePath, pmeTestHardwareContext->deviceContext(),
- pmeTestHardwareContext->deviceStream(),
- pmeTestHardwareContext->pmeGpuProgram(), box, ewaldCoeff_q, ewaldCoeff_lj);
+ PmeSafePointer pmeSafe = pmeInitWrapper(&inputRec,
+ codePath,
+ pmeTestHardwareContext->deviceContext(),
+ pmeTestHardwareContext->deviceStream(),
+ pmeTestHardwareContext->pmeGpuProgram(),
+ box,
+ ewaldCoeff_q,
+ ewaldCoeff_lj);
pmeSetComplexGrid(pmeSafe.get(), codePath, gridOrdering.first, nonZeroGridValues);
const real cellVolume = box[0] * box[4] * box[8];
// FIXME - this is box[XX][XX] * box[YY][YY] * box[ZZ][ZZ], should be stored in the PME structure
- pmePerformSolve(pmeSafe.get(), codePath, method, cellVolume, gridOrdering.first,
- computeEnergyAndVirial);
+ pmePerformSolve(pmeSafe.get(), codePath, method, cellVolume, gridOrdering.first, computeEnergyAndVirial);
pmeFinalizeTest(pmeSafe.get(), codePath);
/* Check the outputs */
const uint64_t splineModuliDoublePrecisionUlps =
getSplineModuliDoublePrecisionUlps(inputRec.pme_order + 1);
auto gridTolerance = relativeToleranceAsPrecisionDependentUlp(
- gridValuesMagnitude, gridUlpToleranceFactor * c_splineModuliSinglePrecisionUlps,
+ gridValuesMagnitude,
+ gridUlpToleranceFactor * c_splineModuliSinglePrecisionUlps,
gridUlpToleranceFactor * splineModuliDoublePrecisionUlps);
gridValuesChecker.setDefaultTolerance(gridTolerance);
// TODO This factor is arbitrary, do a proper error-propagation analysis
uint64_t energyUlpToleranceFactor = gridUlpToleranceFactor * 2;
auto energyTolerance = relativeToleranceAsPrecisionDependentUlp(
- energyMagnitude, energyUlpToleranceFactor * c_splineModuliSinglePrecisionUlps,
+ energyMagnitude,
+ energyUlpToleranceFactor * c_splineModuliSinglePrecisionUlps,
energyUlpToleranceFactor * splineModuliDoublePrecisionUlps);
TestReferenceChecker energyChecker(checker);
energyChecker.setDefaultTolerance(energyTolerance);
// TODO This factor is arbitrary, do a proper error-propagation analysis
uint64_t virialUlpToleranceFactor = energyUlpToleranceFactor * 2;
auto virialTolerance = relativeToleranceAsPrecisionDependentUlp(
- virialMagnitude, virialUlpToleranceFactor * c_splineModuliSinglePrecisionUlps,
+ virialMagnitude,
+ virialUlpToleranceFactor * c_splineModuliSinglePrecisionUlps,
virialUlpToleranceFactor * splineModuliDoublePrecisionUlps);
TestReferenceChecker virialChecker(
checker.checkCompound("Matrix", "Virial"));
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
inputRec.nky = gridSize[YY];
inputRec.nkz = gridSize[ZZ];
inputRec.pme_order = pmeOrder;
- inputRec.coulombtype = eelPME;
+ inputRec.coulombtype = CoulombInteractionType::Pme;
inputRec.epsilon_r = 1.0;
const std::map<PmeSplineAndSpreadOptions, std::string> optionsToTest = {
{
/* Describing the test uniquely in case it fails */
- SCOPED_TRACE(formatString(
- "Testing %s on %s for PME grid size %d %d %d"
- ", order %d, %zu atoms",
- option.second.c_str(), pmeTestHardwareContext->description().c_str(),
- gridSize[XX], gridSize[YY], gridSize[ZZ], pmeOrder, atomCount));
+ SCOPED_TRACE(
+ formatString("Testing %s on %s for PME grid size %d %d %d"
+ ", order %d, %zu atoms",
+ option.second.c_str(),
+ pmeTestHardwareContext->description().c_str(),
+ gridSize[XX],
+ gridSize[YY],
+ gridSize[ZZ],
+ pmeOrder,
+ atomCount));
/* Running the test */
- PmeSafePointer pmeSafe =
- pmeInitWrapper(&inputRec, codePath, pmeTestHardwareContext->deviceContext(),
- pmeTestHardwareContext->deviceStream(),
- pmeTestHardwareContext->pmeGpuProgram(), box);
+ PmeSafePointer pmeSafe = pmeInitWrapper(&inputRec,
+ codePath,
+ pmeTestHardwareContext->deviceContext(),
+ pmeTestHardwareContext->deviceStream(),
+ pmeTestHardwareContext->pmeGpuProgram(),
+ box);
std::unique_ptr<StatePropagatorDataGpu> stateGpu =
(codePath == CodePath::GPU)
? makeStatePropagatorDataGpu(*pmeSafe.get(),
{
auto splineValuesDim =
pmeGetSplineData(pmeSafe.get(), codePath, PmeSplineDataType::Values, i);
- splineValuesChecker.checkSequence(splineValuesDim.begin(),
- splineValuesDim.end(), dimString[i]);
+ splineValuesChecker.checkSequence(
+ splineValuesDim.begin(), splineValuesDim.end(), dimString[i]);
}
/* Spline derivatives */
/* Particle gridline indices */
auto gridLineIndices = pmeGetGridlineIndices(pmeSafe.get(), codePath);
- rootChecker.checkSequence(gridLineIndices.begin(), gridLineIndices.end(),
- "Gridline indices");
+ rootChecker.checkSequence(
+ gridLineIndices.begin(), gridLineIndices.end(), "Gridline indices");
}
if (spreadCharges)
//! Random coordinate vectors
CoordinatesVector const c_sampleCoordinatesFull{ { 5.59F, 1.37F, 0.95F },
{
- 16.0F, 1.02F, 0.22F // 2 box lengths in x
+ 16.0F,
+ 1.02F,
+ 0.22F // 2 box lengths in x
},
{ 0.034F, 1.65F, 0.22F },
{ 0.33F, 0.92F, 1.56F },
{ 1.16F, 0.75F, 0.39F },
{ 0.5F, 1.63F, 1.14F },
{
- 16.0001F, 1.52F, 1.19F // > 2 box lengths in x
+ 16.0001F,
+ 1.52F,
+ 1.19F // > 2 box lengths in x
},
{
- 1.43F, 1.1F, 4.1F // > 2 box lengths in z
+ 1.43F,
+ 1.1F,
+ 4.1F // > 2 box lengths in z
},
{
- -1.08F, 1.19F, 0.08F // negative x
+ -1.08F,
+ 1.19F,
+ 0.08F // negative x
},
{ 1.6F, 0.93F, 0.53F },
{
- 1.32F, -1.48F, 0.16F // negative y
+ 1.32F,
+ -1.48F,
+ 0.16F // negative y
},
{ 0.87F, 0.0F, 0.33F },
{
- 0.95F, 7.7F, -0.48F // > 2 box lengths in y, negative z
+ 0.95F,
+ 7.7F,
+ -0.48F // > 2 box lengths in y, negative z
},
{ 1.23F, 0.91F, 0.68F },
{ 0.19F, 1.45F, 0.94F },
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const auto runMode = (mode == CodePath::CPU) ? PmeRunMode::CPU : PmeRunMode::Mixed;
t_commrec dummyCommrec = { 0 };
NumPmeDomains numPmeDomains = { 1, 1 };
- gmx_pme_t* pmeDataRaw = gmx_pme_init(&dummyCommrec, numPmeDomains, inputRec, false, false, true,
- ewaldCoeff_q, ewaldCoeff_lj, 1, runMode, nullptr,
- deviceContext, deviceStream, pmeGpuProgram, dummyLogger);
+ gmx_pme_t* pmeDataRaw = gmx_pme_init(&dummyCommrec,
+ numPmeDomains,
+ inputRec,
+ false,
+ false,
+ true,
+ ewaldCoeff_q,
+ ewaldCoeff_lj,
+ 1,
+ runMode,
+ nullptr,
+ deviceContext,
+ deviceStream,
+ pmeGpuProgram,
+ dummyLogger);
PmeSafePointer pme(pmeDataRaw); // taking ownership
// TODO get rid of this with proper matrix type
// TODO: Pin the host buffer and use async memory copies
// TODO: Special constructor for PME-only rank / PME-tests is used here. There should be a mechanism to
// restrict one from using other constructor here.
- return std::make_unique<StatePropagatorDataGpu>(deviceStream, *deviceContext, GpuApiCallBehavior::Sync,
- pme_gpu_get_block_size(&pme), nullptr);
+ return std::make_unique<StatePropagatorDataGpu>(
+ deviceStream, *deviceContext, GpuApiCallBehavior::Sync, pme_gpu_get_block_size(&pme), nullptr);
}
//! PME initialization with atom data
atc = &(pme->atc[0]);
atc->x = coordinates;
atc->coefficient = charges;
- gmx_pme_reinit_atoms(pme, atomCount, charges.data(), nullptr);
+ gmx_pme_reinit_atoms(pme, atomCount, charges, {});
/* With decomposition there would be more boilerplate atc code here, e.g. do_redist_pos_coeffs */
break;
atc = &(pme->atc[0]);
// We need to set atc->n for passing the size in the tests
atc->setNumAtoms(atomCount);
- gmx_pme_reinit_atoms(pme, atomCount, charges.data(), nullptr);
+ gmx_pme_reinit_atoms(pme, atomCount, charges, {});
stateGpu->reinit(atomCount, atomCount);
stateGpu->copyCoordinatesToGpu(arrayRefFromArray(coordinates.data(), coordinates.size()),
switch (mode)
{
case CodePath::CPU:
- gmx_parallel_3dfft_real_limits(pme->pfft_setup[gridIndex], gridSize, gridOffsetUnused,
- paddedGridSize);
+ gmx_parallel_3dfft_real_limits(
+ pme->pfft_setup[gridIndex], gridSize, gridOffsetUnused, paddedGridSize);
break;
case CodePath::GPU:
{
const size_t gridIndex = 0;
IVec gridOffsetUnused, complexOrderUnused;
- gmx_parallel_3dfft_complex_limits(pme->pfft_setup[gridIndex], complexOrderUnused, gridSize,
- gridOffsetUnused, paddedGridSize); // TODO: what about YZX ordering?
+ gmx_parallel_3dfft_complex_limits(
+ pme->pfft_setup[gridIndex], complexOrderUnused, gridSize, gridOffsetUnused, paddedGridSize); // TODO: what about YZX ordering?
}
//! Getting the PME grid memory buffer and its sizes - template definition
IVec& /*unused*/) //NOLINT(google-runtime-references)
{
GMX_THROW(InternalError("Deleted function call"));
- // explicitly deleting general template does not compile in clang/icc, see https://llvm.org/bugs/show_bug.cgi?id=17537
+ // explicitly deleting general template does not compile in clang, see https://llvm.org/bugs/show_bug.cgi?id=17537
}
//! Getting the PME real grid memory buffer and its sizes
switch (mode)
{
case CodePath::CPU:
- spread_on_grid(pme, atc, &pme->pmegrid[gridIndex], computeSplines, spreadCharges,
+ spread_on_grid(pme,
+ atc,
+ &pme->pmegrid[gridIndex],
+ computeSplines,
+ spreadCharges,
fftgrid != nullptr ? fftgrid[gridIndex] : nullptr,
- computeSplinesForZeroCharges, gridIndex);
+ computeSplinesForZeroCharges,
+ gridIndex);
if (spreadCharges && !pme->bUseThreads)
{
wrap_periodic_pmegrid(pme, pmegrid);
break;
case PmeSolveAlgorithm::LennardJones:
- solve_pme_lj_yzx(pme, &h_grid, useLorentzBerthelot, cellVolume,
- computeEnergyAndVirial, pme->nthread, threadIndex);
+ solve_pme_lj_yzx(pme,
+ &h_grid,
+ useLorentzBerthelot,
+ cellVolume,
+ computeEnergyAndVirial,
+ pme->nthread,
+ threadIndex);
break;
default: GMX_THROW(InternalError("Test not implemented for this mode"));
switch (mode)
{
case CodePath::GPU:
- memcpy(pme_gpu_staging(pme->gpu).h_gridlineIndices, gridLineIndices.data(),
+ memcpy(pme_gpu_staging(pme->gpu).h_gridlineIndices,
+ gridLineIndices.data(),
atomCount * sizeof(gridLineIndices[0]));
break;
{
case CodePath::GPU: // intentional absence of break, the grid will be copied from the host buffer in testing mode
case CodePath::CPU:
- std::memset(grid, 0,
- paddedGridSize[XX] * paddedGridSize[YY] * paddedGridSize[ZZ] * sizeof(ValueType));
+ std::memset(grid, 0, paddedGridSize[XX] * paddedGridSize[YY] * paddedGridSize[ZZ] * sizeof(ValueType));
for (const auto& gridValue : gridValues)
{
for (int i = 0; i < DIM; i++)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015,2018,2019,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(fft INTERFACE)
+
gmx_add_libgromacs_sources(
calcgrid.cpp
fft.cpp
gmx_add_libgromacs_sources(fft_mkl.cpp)
endif()
+# Source files have the following private module dependencies.
+target_link_libraries(fft PRIVATE
+ # gmxlib
+ # math
+ # mdtypes
+ # tng_io
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(fft PUBLIC
+target_include_directories(fft INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(fft PUBLIC
+target_link_libraries(fft INTERFACE
+ legacy_api
+ )
+
+# TODO: when fft is an OBJECT target
+#target_link_libraries(fft PUBLIC legacy_api)
+#target_link_libraries(fft PRIVATE common)
+
+# Module dependencies
+# This module convey transitive dependence on these modules.
+#target_link_libraries(fft PUBLIC
+target_link_libraries(fft INTERFACE
+ # utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(fft PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(fft PRIVATE legacy_modules)
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
{
if (nullptr != fp)
{
- fprintf(fp, "Calculating fourier grid dimensions for%s%s%s\n", *nx > 0 ? "" : " X",
- *ny > 0 ? "" : " Y", *nz > 0 ? "" : " Z");
+ fprintf(fp,
+ "Calculating fourier grid dimensions for%s%s%s\n",
+ *nx > 0 ? "" : " X",
+ *ny > 0 ? "" : " Y",
+ *nz > 0 ? "" : " Z");
}
}
*nz = n[ZZ];
if (nullptr != fp)
{
- fprintf(fp, "Using a fourier grid of %dx%dx%d, spacing %.3f %.3f %.3f\n", *nx, *ny, *nz,
- spacing[XX], spacing[YY], spacing[ZZ]);
+ fprintf(fp,
+ "Using a fourier grid of %dx%dx%d, spacing %.3f %.3f %.3f\n",
+ *nx,
+ *ny,
+ *nz,
+ spacing[XX],
+ spacing[YY],
+ spacing[ZZ]);
}
return max_spacing;
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2009-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#if GMX_FFT_FFTW3
+# include <mutex>
+
# include "gromacs/utility/exceptions.h"
-# include "gromacs/utility/mutex.h"
+
/* none of the fftw3 calls, except execute(), are thread-safe, so
we need to serialize them with this mutex. */
-static gmx::Mutex big_fftw_mutex;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static std::mutex big_fftw_mutex;
# define FFTW_LOCK \
try \
{ \
fprintf(debug,
"FFT5D: N: %d, M: %d, K: %d, P: %dx%d, real2complex: %d, backward: %d, order "
"yz: %d, debug %d\n",
- NG, MG, KG, P[0], P[1], int((flags & FFT5D_REALCOMPLEX) > 0),
- int((flags & FFT5D_BACKWARD) > 0), int((flags & FFT5D_ORDER_YZ) > 0),
+ NG,
+ MG,
+ KG,
+ P[0],
+ P[1],
+ int((flags & FFT5D_REALCOMPLEX) > 0),
+ int((flags & FFT5D_BACKWARD) > 0),
+ int((flags & FFT5D_ORDER_YZ) > 0),
int((flags & FFT5D_DEBUG) > 0));
}
/* The check below is not correct, one prime factor 11 or 13 is ok.
# endif
if ((flags & FFT5D_REALCOMPLEX) && !(flags & FFT5D_BACKWARD))
{
- plan->p3d = FFTW(plan_guru_dft_r2c)(/*rank*/ 3, dims,
- /*howmany*/ 0, /*howmany_dims*/ nullptr,
+ plan->p3d = FFTW(plan_guru_dft_r2c)(/*rank*/ 3,
+ dims,
+ /*howmany*/ 0,
+ /*howmany_dims*/ nullptr,
reinterpret_cast<real*>(lin),
reinterpret_cast<FFTW(complex)*>(lout),
/*flags*/ fftwflags);
}
else if ((flags & FFT5D_REALCOMPLEX) && (flags & FFT5D_BACKWARD))
{
- plan->p3d = FFTW(plan_guru_dft_c2r)(/*rank*/ 3, dims,
- /*howmany*/ 0, /*howmany_dims*/ nullptr,
+ plan->p3d = FFTW(plan_guru_dft_c2r)(/*rank*/ 3,
+ dims,
+ /*howmany*/ 0,
+ /*howmany_dims*/ nullptr,
reinterpret_cast<FFTW(complex)*>(lin),
reinterpret_cast<real*>(lout),
/*flags*/ fftwflags);
else
{
plan->p3d = FFTW(plan_guru_dft)(
- /*rank*/ 3, dims,
- /*howmany*/ 0, /*howmany_dims*/ nullptr, reinterpret_cast<FFTW(complex)*>(lin),
+ /*rank*/ 3,
+ dims,
+ /*howmany*/ 0,
+ /*howmany_dims*/ nullptr,
+ reinterpret_cast<FFTW(complex)*>(lin),
reinterpret_cast<FFTW(complex)*>(lout),
- /*sign*/ (flags & FFT5D_BACKWARD) ? 1 : -1, /*flags*/ fftwflags);
+ /*sign*/ (flags & FFT5D_BACKWARD) ? 1 : -1,
+ /*flags*/ fftwflags);
}
# ifdef FFT5D_THREADS
# ifdef FFT5D_FFTW_THREADS
{
if (debug)
{
- fprintf(debug, "FFT5D: Plan s %d rC %d M %d pK %d C %d lsize %d\n", s, rC[s], M[s],
- pK[s], C[s], lsize);
+ fprintf(debug, "FFT5D: Plan s %d rC %d M %d pK %d C %d lsize %d\n", s, rC[s], M[s], pK[s], C[s], lsize);
}
plan->p1d[s] = static_cast<gmx_fft_t*>(malloc(sizeof(gmx_fft_t) * nthreads));
|| ((flags & FFT5D_BACKWARD) && s == 2)))
{
gmx_fft_init_many_1d_real(
- &plan->p1d[s][t], rC[s], tsize,
+ &plan->p1d[s][t],
+ rC[s],
+ tsize,
(flags & FFT5D_NOMEASURE) ? GMX_FFT_FLAG_CONSERVATIVE : 0);
}
else
{
- gmx_fft_init_many_1d(&plan->p1d[s][t], C[s], tsize,
+ gmx_fft_init_many_1d(&plan->p1d[s][t],
+ C[s],
+ tsize,
(flags & FFT5D_NOMEASURE) ? GMX_FFT_FLAG_CONSERVATIVE : 0);
}
}
{
if ((s == 0 && !(flags & FFT5D_ORDER_YZ)) || (s == 1 && (flags & FFT5D_ORDER_YZ)))
{
- plan->mpip[s] = FFTW(mpi_plan_many_transpose)(nP[s], nP[s], N[s] * K[s] * pM[s] * 2, 1,
- 1, (real*)lout2, (real*)lout3,
- plan->cart[s], FFTW_PATIENT);
+ plan->mpip[s] = FFTW(mpi_plan_many_transpose)(
+ nP[s], nP[s], N[s] * K[s] * pM[s] * 2, 1, 1, (real*)lout2, (real*)lout3, plan->cart[s], FFTW_PATIENT);
}
else
{
- plan->mpip[s] = FFTW(mpi_plan_many_transpose)(nP[s], nP[s], N[s] * pK[s] * M[s] * 2, 1,
- 1, (real*)lout2, (real*)lout3,
- plan->cart[s], FFTW_PATIENT);
+ plan->mpip[s] = FFTW(mpi_plan_many_transpose)(
+ nP[s], nP[s], N[s] * pK[s] * M[s] * 2, 1, 1, (real*)lout2, (real*)lout3, plan->cart[s], FFTW_PATIENT);
}
}
FFTW_UNLOCK;
{
for (l = 0; l < ll; l++)
{
- fprintf(debug, "%f ",
+ fprintf(debug,
+ "%f ",
reinterpret_cast<const real*>(
lin)[(z * xs[2] + y * xs[1]) * 2 + (x * xs[0]) * ll + l]);
}
gmx_fft_many_1d_real(p1d[s][thread],
(plan->flags & FFT5D_BACKWARD) ? GMX_FFT_COMPLEX_TO_REAL
: GMX_FFT_REAL_TO_COMPLEX,
- lin + tstart, fftout + tstart);
+ lin + tstart,
+ fftout + tstart);
}
else
{
gmx_fft_many_1d(p1d[s][thread],
(plan->flags & FFT5D_BACKWARD) ? GMX_FFT_BACKWARD : GMX_FFT_FORWARD,
- lin + tstart, fftout + tstart);
+ lin + tstart,
+ fftout + tstart);
}
#ifdef NOGMX
{
tend = ((thread + 1) * pM[s] * pK[s] / plan->nthreads);
tstart /= C[s];
- splitaxes(lout2, lout, N[s], M[s], K[s], pM[s], P[s], C[s], iNout[s], oNout[s],
- tstart % pM[s], tstart / pM[s], tend % pM[s], tend / pM[s]);
+ splitaxes(lout2,
+ lout,
+ N[s],
+ M[s],
+ K[s],
+ pM[s],
+ P[s],
+ C[s],
+ iNout[s],
+ oNout[s],
+ tstart % pM[s],
+ tstart / pM[s],
+ tend % pM[s],
+ tend / pM[s]);
}
#pragma omp barrier /*barrier required before AllToAll (all input has to be their) - before timing to make timing more acurate*/
#ifdef NOGMX
time = MPI_Wtime();
}
#else
- wallcycle_start(times, ewcPME_FFTCOMM);
+ wallcycle_start(times, WallCycleCounter::PmeFftComm);
#endif
#ifdef FFT5D_MPI_TRANSPOSE
FFTW(execute)(mpip[s]);
{
MPI_Alltoall(reinterpret_cast<real*>(lout2),
N[s] * pM[s] * K[s] * sizeof(t_complex) / sizeof(real),
- GMX_MPI_REAL, reinterpret_cast<real*>(lout3),
+ GMX_MPI_REAL,
+ reinterpret_cast<real*>(lout3),
N[s] * pM[s] * K[s] * sizeof(t_complex) / sizeof(real),
- GMX_MPI_REAL, cart[s]);
+ GMX_MPI_REAL,
+ cart[s]);
}
else
{
MPI_Alltoall(reinterpret_cast<real*>(lout2),
N[s] * M[s] * pK[s] * sizeof(t_complex) / sizeof(real),
- GMX_MPI_REAL, reinterpret_cast<real*>(lout3),
+ GMX_MPI_REAL,
+ reinterpret_cast<real*>(lout3),
N[s] * M[s] * pK[s] * sizeof(t_complex) / sizeof(real),
- GMX_MPI_REAL, cart[s]);
+ GMX_MPI_REAL,
+ cart[s]);
}
# else
GMX_RELEASE_ASSERT(false, "Invalid call to fft5d_execute");
time_mpi[s] = MPI_Wtime() - time;
}
#else
- wallcycle_stop(times, ewcPME_FFTCOMM);
+ wallcycle_stop(times, WallCycleCounter::PmeFftComm);
#endif
} /*master*/
} /* bPrallelDim */
{
tstart = (thread * pM[s] * pN[s] / plan->nthreads);
tend = ((thread + 1) * pM[s] * pN[s] / plan->nthreads);
- joinAxesTrans13(lin, joinin, N[s], pM[s], K[s], pM[s], P[s], C[s + 1], iNin[s + 1],
- oNin[s + 1], tstart % pM[s], tstart / pM[s], tend % pM[s], tend / pM[s]);
+ joinAxesTrans13(lin,
+ joinin,
+ N[s],
+ pM[s],
+ K[s],
+ pM[s],
+ P[s],
+ C[s + 1],
+ iNin[s + 1],
+ oNin[s + 1],
+ tstart % pM[s],
+ tstart / pM[s],
+ tend % pM[s],
+ tend / pM[s]);
}
}
else
{
tstart = (thread * pK[s] * pN[s] / plan->nthreads);
tend = ((thread + 1) * pK[s] * pN[s] / plan->nthreads);
- joinAxesTrans12(lin, joinin, N[s], M[s], pK[s], pN[s], P[s], C[s + 1], iNin[s + 1],
- oNin[s + 1], tstart % pN[s], tstart / pN[s], tend % pN[s], tend / pN[s]);
+ joinAxesTrans12(lin,
+ joinin,
+ N[s],
+ M[s],
+ pK[s],
+ pN[s],
+ P[s],
+ C[s + 1],
+ iNin[s + 1],
+ oNin[s + 1],
+ tstart % pN[s],
+ tstart / pN[s],
+ tend % pN[s],
+ tend / pN[s]);
}
}
{
gmx_fft_many_1d_real(p1d[s][thread],
(plan->flags & FFT5D_BACKWARD) ? GMX_FFT_COMPLEX_TO_REAL : GMX_FFT_REAL_TO_COMPLEX,
- lin + tstart, lout + tstart);
+ lin + tstart,
+ lout + tstart);
}
else
{
- gmx_fft_many_1d(p1d[s][thread], (plan->flags & FFT5D_BACKWARD) ? GMX_FFT_BACKWARD : GMX_FFT_FORWARD,
- lin + tstart, lout + tstart);
+ gmx_fft_many_1d(p1d[s][thread],
+ (plan->flags & FFT5D_BACKWARD) ? GMX_FFT_BACKWARD : GMX_FFT_FORWARD,
+ lin + tstart,
+ lout + tstart);
}
/* ------------ END FFT ---------*/
if (std::fabs(a - b) > 2 * NG[0] * NG[1] * NG[2] * GMX_REAL_EPS)
{
printf("result incorrect on %d,%d at %d,%d,%d: FFT5D:%f reference:%f\n",
- coor[0], coor[1], x, y, z, a, b);
+ coor[0],
+ coor[1],
+ x,
+ y,
+ z,
+ a,
+ b);
}
/* assert(fabs(a-b)<2*NG[0]*NG[1]*NG[2]*GMX_REAL_EPS);*/
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2009-2017, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
typedef struct fft5d_time_t* fft5d_time;
#else
# include "gromacs/timing/wallcycle.h"
-typedef gmx_wallcycle_t fft5d_time;
+typedef gmx_wallcycle* fft5d_time;
#endif
namespace gmx
*
* Copyright (c) 1991-2003 David van der Spoel, Erik Lindahl, University of Groningen.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cerrno>
#include <cstdlib>
+#include <mutex>
+
#include <fftw3.h>
#include "gromacs/fft/fft.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/mutex.h"
#if GMX_DOUBLE
# define FFTWPREFIX(name) fftw_##name
/* none of the fftw3 calls, except execute(), are thread-safe, so
we need to serialize them with this mutex. */
-static gmx::Mutex big_fftw_mutex;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static std::mutex big_fftw_mutex;
#define FFTW_LOCK \
try \
{ \
fftw_complex *out, const int *onembed,
int ostride, int odist,
int sign, unsigned flags */
- fft->plan[0][0][0] = FFTWPREFIX(plan_many_dft)(1, &nx, howmany, up1, &nx, 1, nx, up2, &nx, 1,
- nx, FFTW_BACKWARD, fftw_flags);
- fft->plan[0][0][1] = FFTWPREFIX(plan_many_dft)(1, &nx, howmany, up1, &nx, 1, nx, up2, &nx, 1,
- nx, FFTW_FORWARD, fftw_flags);
- fft->plan[0][1][0] = FFTWPREFIX(plan_many_dft)(1, &nx, howmany, up1, &nx, 1, nx, up1, &nx, 1,
- nx, FFTW_BACKWARD, fftw_flags);
- fft->plan[0][1][1] = FFTWPREFIX(plan_many_dft)(1, &nx, howmany, up1, &nx, 1, nx, up1, &nx, 1,
- nx, FFTW_FORWARD, fftw_flags);
- fft->plan[1][0][0] = FFTWPREFIX(plan_many_dft)(1, &nx, howmany, p1, &nx, 1, nx, p2, &nx, 1, nx,
- FFTW_BACKWARD, fftw_flags);
- fft->plan[1][0][1] = FFTWPREFIX(plan_many_dft)(1, &nx, howmany, p1, &nx, 1, nx, p2, &nx, 1, nx,
- FFTW_FORWARD, fftw_flags);
- fft->plan[1][1][0] = FFTWPREFIX(plan_many_dft)(1, &nx, howmany, p1, &nx, 1, nx, p1, &nx, 1, nx,
- FFTW_BACKWARD, fftw_flags);
- fft->plan[1][1][1] = FFTWPREFIX(plan_many_dft)(1, &nx, howmany, p1, &nx, 1, nx, p1, &nx, 1, nx,
- FFTW_FORWARD, fftw_flags);
+ fft->plan[0][0][0] = FFTWPREFIX(plan_many_dft)(
+ 1, &nx, howmany, up1, &nx, 1, nx, up2, &nx, 1, nx, FFTW_BACKWARD, fftw_flags);
+ fft->plan[0][0][1] = FFTWPREFIX(plan_many_dft)(
+ 1, &nx, howmany, up1, &nx, 1, nx, up2, &nx, 1, nx, FFTW_FORWARD, fftw_flags);
+ fft->plan[0][1][0] = FFTWPREFIX(plan_many_dft)(
+ 1, &nx, howmany, up1, &nx, 1, nx, up1, &nx, 1, nx, FFTW_BACKWARD, fftw_flags);
+ fft->plan[0][1][1] = FFTWPREFIX(plan_many_dft)(
+ 1, &nx, howmany, up1, &nx, 1, nx, up1, &nx, 1, nx, FFTW_FORWARD, fftw_flags);
+ fft->plan[1][0][0] = FFTWPREFIX(plan_many_dft)(
+ 1, &nx, howmany, p1, &nx, 1, nx, p2, &nx, 1, nx, FFTW_BACKWARD, fftw_flags);
+ fft->plan[1][0][1] = FFTWPREFIX(plan_many_dft)(
+ 1, &nx, howmany, p1, &nx, 1, nx, p2, &nx, 1, nx, FFTW_FORWARD, fftw_flags);
+ fft->plan[1][1][0] = FFTWPREFIX(plan_many_dft)(
+ 1, &nx, howmany, p1, &nx, 1, nx, p1, &nx, 1, nx, FFTW_BACKWARD, fftw_flags);
+ fft->plan[1][1][1] = FFTWPREFIX(plan_many_dft)(
+ 1, &nx, howmany, p1, &nx, 1, nx, p1, &nx, 1, nx, FFTW_FORWARD, fftw_flags);
for (i = 0; i < 2; i++)
{
fftw_complex *out, const int *onembed,
int ostride, int odist,
unsigned flag */
- fft->plan[0][0][1] = FFTWPREFIX(plan_many_dft_r2c)(
- 1, &nx, howmany, up1, nullptr, 1, (nx / 2 + 1) * 2,
- reinterpret_cast<FFTWPREFIX(complex)*>(up2), nullptr, 1, (nx / 2 + 1), fftw_flags);
- fft->plan[0][1][1] = FFTWPREFIX(plan_many_dft_r2c)(
- 1, &nx, howmany, up1, nullptr, 1, (nx / 2 + 1) * 2,
- reinterpret_cast<FFTWPREFIX(complex)*>(up1), nullptr, 1, (nx / 2 + 1), fftw_flags);
- fft->plan[1][0][1] = FFTWPREFIX(plan_many_dft_r2c)(
- 1, &nx, howmany, p1, nullptr, 1, (nx / 2 + 1) * 2,
- reinterpret_cast<FFTWPREFIX(complex)*>(p2), nullptr, 1, (nx / 2 + 1), fftw_flags);
- fft->plan[1][1][1] = FFTWPREFIX(plan_many_dft_r2c)(
- 1, &nx, howmany, p1, nullptr, 1, (nx / 2 + 1) * 2,
- reinterpret_cast<FFTWPREFIX(complex)*>(p1), nullptr, 1, (nx / 2 + 1), fftw_flags);
-
- fft->plan[0][0][0] = FFTWPREFIX(plan_many_dft_c2r)(
- 1, &nx, howmany, reinterpret_cast<FFTWPREFIX(complex)*>(up1), nullptr, 1, (nx / 2 + 1),
- up2, nullptr, 1, (nx / 2 + 1) * 2, fftw_flags);
- fft->plan[0][1][0] = FFTWPREFIX(plan_many_dft_c2r)(
- 1, &nx, howmany, reinterpret_cast<FFTWPREFIX(complex)*>(up1), nullptr, 1, (nx / 2 + 1),
- up1, nullptr, 1, (nx / 2 + 1) * 2, fftw_flags);
- fft->plan[1][0][0] = FFTWPREFIX(plan_many_dft_c2r)(
- 1, &nx, howmany, reinterpret_cast<FFTWPREFIX(complex)*>(p1), nullptr, 1, (nx / 2 + 1),
- p2, nullptr, 1, (nx / 2 + 1) * 2, fftw_flags);
- fft->plan[1][1][0] = FFTWPREFIX(plan_many_dft_c2r)(
- 1, &nx, howmany, reinterpret_cast<FFTWPREFIX(complex)*>(p1), nullptr, 1, (nx / 2 + 1),
- p1, nullptr, 1, (nx / 2 + 1) * 2, fftw_flags);
+ fft->plan[0][0][1] = FFTWPREFIX(plan_many_dft_r2c)(1,
+ &nx,
+ howmany,
+ up1,
+ nullptr,
+ 1,
+ (nx / 2 + 1) * 2,
+ reinterpret_cast<FFTWPREFIX(complex)*>(up2),
+ nullptr,
+ 1,
+ (nx / 2 + 1),
+ fftw_flags);
+ fft->plan[0][1][1] = FFTWPREFIX(plan_many_dft_r2c)(1,
+ &nx,
+ howmany,
+ up1,
+ nullptr,
+ 1,
+ (nx / 2 + 1) * 2,
+ reinterpret_cast<FFTWPREFIX(complex)*>(up1),
+ nullptr,
+ 1,
+ (nx / 2 + 1),
+ fftw_flags);
+ fft->plan[1][0][1] = FFTWPREFIX(plan_many_dft_r2c)(1,
+ &nx,
+ howmany,
+ p1,
+ nullptr,
+ 1,
+ (nx / 2 + 1) * 2,
+ reinterpret_cast<FFTWPREFIX(complex)*>(p2),
+ nullptr,
+ 1,
+ (nx / 2 + 1),
+ fftw_flags);
+ fft->plan[1][1][1] = FFTWPREFIX(plan_many_dft_r2c)(1,
+ &nx,
+ howmany,
+ p1,
+ nullptr,
+ 1,
+ (nx / 2 + 1) * 2,
+ reinterpret_cast<FFTWPREFIX(complex)*>(p1),
+ nullptr,
+ 1,
+ (nx / 2 + 1),
+ fftw_flags);
+
+ fft->plan[0][0][0] = FFTWPREFIX(plan_many_dft_c2r)(1,
+ &nx,
+ howmany,
+ reinterpret_cast<FFTWPREFIX(complex)*>(up1),
+ nullptr,
+ 1,
+ (nx / 2 + 1),
+ up2,
+ nullptr,
+ 1,
+ (nx / 2 + 1) * 2,
+ fftw_flags);
+ fft->plan[0][1][0] = FFTWPREFIX(plan_many_dft_c2r)(1,
+ &nx,
+ howmany,
+ reinterpret_cast<FFTWPREFIX(complex)*>(up1),
+ nullptr,
+ 1,
+ (nx / 2 + 1),
+ up1,
+ nullptr,
+ 1,
+ (nx / 2 + 1) * 2,
+ fftw_flags);
+ fft->plan[1][0][0] = FFTWPREFIX(plan_many_dft_c2r)(1,
+ &nx,
+ howmany,
+ reinterpret_cast<FFTWPREFIX(complex)*>(p1),
+ nullptr,
+ 1,
+ (nx / 2 + 1),
+ p2,
+ nullptr,
+ 1,
+ (nx / 2 + 1) * 2,
+ fftw_flags);
+ fft->plan[1][1][0] = FFTWPREFIX(plan_many_dft_c2r)(1,
+ &nx,
+ howmany,
+ reinterpret_cast<FFTWPREFIX(complex)*>(p1),
+ nullptr,
+ 1,
+ (nx / 2 + 1),
+ p1,
+ nullptr,
+ 1,
+ (nx / 2 + 1) * 2,
+ fftw_flags);
for (i = 0; i < 2; i++)
{
}
FFTWPREFIX(execute_dft)
- (fft->plan[aligned][inplace][isforward], static_cast<FFTWPREFIX(complex)*>(in_data),
+ (fft->plan[aligned][inplace][isforward],
+ static_cast<FFTWPREFIX(complex)*>(in_data),
static_cast<FFTWPREFIX(complex)*>(out_data));
return 0;
if (isforward)
{
FFTWPREFIX(execute_dft_r2c)
- (fft->plan[aligned][inplace][isforward], static_cast<real*>(in_data),
+ (fft->plan[aligned][inplace][isforward],
+ static_cast<real*>(in_data),
static_cast<FFTWPREFIX(complex)*>(out_data));
}
else
{
FFTWPREFIX(execute_dft_c2r)
- (fft->plan[aligned][inplace][isforward], static_cast<FFTWPREFIX(complex)*>(in_data),
+ (fft->plan[aligned][inplace][isforward],
+ static_cast<FFTWPREFIX(complex)*>(in_data),
static_cast<real*>(out_data));
}
if (isforward)
{
FFTWPREFIX(execute_dft_r2c)
- (fft->plan[aligned][inplace][isforward], static_cast<real*>(in_data),
+ (fft->plan[aligned][inplace][isforward],
+ static_cast<real*>(in_data),
static_cast<FFTWPREFIX(complex)*>(out_data));
}
else
{
FFTWPREFIX(execute_dft_c2r)
- (fft->plan[aligned][inplace][isforward], static_cast<FFTWPREFIX(complex)*>(in_data),
+ (fft->plan[aligned][inplace][isforward],
+ static_cast<FFTWPREFIX(complex)*>(in_data),
static_cast<real*>(out_data));
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2005 David van der Spoel, Erik Lindahl, University of Groningen.
- * Copyright (c) 2013,2014,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
Kb = M; /* currently always true because ORDER_YZ always set */
}
- (*pfft_setup)->p1 = fft5d_plan_3d(rN, M, K, rcomm, flags, reinterpret_cast<t_complex**>(real_data),
- complex_data, &buf1, &buf2, nthreads, realGridAllocation);
+ (*pfft_setup)->p1 = fft5d_plan_3d(
+ rN, M, K, rcomm, flags, reinterpret_cast<t_complex**>(real_data), complex_data, &buf1, &buf2, nthreads, realGridAllocation);
- (*pfft_setup)->p2 = fft5d_plan_3d(
- Nb, Mb, Kb, rcomm, (flags | FFT5D_BACKWARD | FFT5D_NOMALLOC) ^ FFT5D_ORDER_YZ,
- complex_data, reinterpret_cast<t_complex**>(real_data), &buf1, &buf2, nthreads);
+ (*pfft_setup)->p2 = fft5d_plan_3d(Nb,
+ Mb,
+ Kb,
+ rcomm,
+ (flags | FFT5D_BACKWARD | FFT5D_NOMALLOC) ^ FFT5D_ORDER_YZ,
+ complex_data,
+ reinterpret_cast<t_complex**>(real_data),
+ &buf1,
+ &buf2,
+ nthreads);
return static_cast<int>((*pfft_setup)->p1 != nullptr && (*pfft_setup)->p2 != nullptr);
}
int gmx_parallel_3dfft_execute(gmx_parallel_3dfft_t pfft_setup,
enum gmx_fft_direction dir,
int thread,
- gmx_wallcycle_t wcycle)
+ gmx_wallcycle* wcycle)
{
if (((pfft_setup->p1->flags & FFT5D_REALCOMPLEX) == 0)
^ (dir == GMX_FFT_FORWARD || dir == GMX_FFT_BACKWARD))
{
- gmx_fatal(FARGS,
- "Invalid transform. Plan and execution don't match regarding reel/complex");
+ gmx_fatal(FARGS, "Invalid transform. Plan and execution don't match regarding reel/complex");
}
if (dir == GMX_FFT_FORWARD || dir == GMX_FFT_REAL_TO_COMPLEX)
{
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2005 David van der Spoel, Erik Lindahl, University of Groningen.
- * Copyright (c) 2013,2014,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2017,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int gmx_parallel_3dfft_execute(gmx_parallel_3dfft_t pfft_setup,
enum gmx_fft_direction dir,
int thread,
- gmx_wallcycle_t wcycle);
+ gmx_wallcycle* wcycle);
/*! \brief Release all data in parallel fft setup
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
gmx_parallel_3dfft_execute(fft_, GMX_FFT_COMPLEX_TO_REAL, 0, nullptr);
for (int i = 0; i < ndata[0] * ndata[1]; i++) // check sequence but skip unused data
{
- checker_.checkSequenceArray(ndata[2], rdata + i * rsize[2],
- gmx::formatString("backward %d", i).c_str());
+ checker_.checkSequenceArray(
+ ndata[2], rdata + i * rsize[2], gmx::formatString("backward %d", i).c_str());
}
}
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(fileio INTERFACE)
file(GLOB FILEIO_SOURCES *.cpp)
if(GMX_USE_PLUGINS)
list(FILTER FILEIO_SOURCES EXCLUDE REGEX ".*vmdio.cpp$")
endif()
-target_sources(libgromacs PRIVATE ${FILEIO_SOURCES})
+# Source files have the following private module dependencies.
+target_link_libraries(fileio PRIVATE
+# gmxlib
+# math
+# mdtypes
+# tng_io
+ )
-if(GMX_INSTALL_LEGACY_API)
- install(FILES
- oenv.h
- confio.h
- pdbio.h
- tpxio.h
- trxio.h
- filetypes.h
- DESTINATION include/gromacs/fileio)
-endif()
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(fileio PUBLIC
+target_include_directories(fileio INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(fileio PUBLIC
+target_link_libraries(fileio INTERFACE
+ legacy_api
+ )
+
+# TODO: when fileio is an OBJECT target
+#target_link_libraries(fileio PUBLIC legacy_api)
+#target_link_libraries(fileio PRIVATE common)
+
+# Module dependencies
+# fileio interfaces convey transitive dependence on these modules.
+#target_link_libraries(fileio PUBLIC
+target_link_libraries(fileio INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(fileio PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(fileio PRIVATE legacy_modules)
+
+target_sources(libgromacs PRIVATE ${FILEIO_SOURCES})
if (BUILD_TESTING)
add_subdirectory(tests)
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/baseversion.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/keyvaluetree.h"
#include "gromacs/utility/keyvaluetreebuilder.h"
#include "gromacs/utility/keyvaluetreeserializer.h"
-#include "gromacs/utility/mdmodulenotification.h"
+#include "gromacs/utility/mdmodulesnotifiers.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/sysinfo.h"
cptv_RemoveBuildMachineInformation, /**< remove functionality that makes mdrun builds non-reproducible */
cptv_ComPrevStepAsPullGroupReference, /**< Allow using COM of previous step as pull group PBC reference */
cptv_PullAverage, /**< Added possibility to output average pull force and position */
- cptv_MdModules, /**< Added checkpointing for MdModules */
+ cptv_MDModules, /**< Added checkpointing for MDModules */
cptv_ModularSimulator, /**< Added checkpointing for modular simulator */
cptv_Count /**< the total number of cptv versions */
};
* the correct code path. */
static const int cpt_version = cptv_Count - 1;
+const char* enumValueToString(StateEntry enumValue)
+{
+ static constexpr gmx::EnumerationArray<StateEntry, const char*> stateEntryNames = {
+ "FE-lambda",
+ "box",
+ "box-rel",
+ "box-v",
+ "pres_prev",
+ "nosehoover-xi",
+ "thermostat-integral",
+ "x",
+ "v",
+ "sdx-unsupported",
+ "CGp",
+ "LD-rng-unsupported",
+ "LD-rng-i-unsupported",
+ "disre_initf",
+ "disre_rm3tav",
+ "orire_initf",
+ "orire_Dtav",
+ "svir_prev",
+ "nosehoover-vxi",
+ "v_eta",
+ "vol0",
+ "nhpres_xi",
+ "nhpres_vxi",
+ "fvir_prev",
+ "fep_state",
+ "MC-rng-unsupported",
+ "MC-rng-i-unsupported",
+ "barostat-integral"
+ };
+ return stateEntryNames[enumValue];
+}
-const char* est_names[estNR] = { "FE-lambda",
- "box",
- "box-rel",
- "box-v",
- "pres_prev",
- "nosehoover-xi",
- "thermostat-integral",
- "x",
- "v",
- "sdx-unsupported",
- "CGp",
- "LD-rng-unsupported",
- "LD-rng-i-unsupported",
- "disre_initf",
- "disre_rm3tav",
- "orire_initf",
- "orire_Dtav",
- "svir_prev",
- "nosehoover-vxi",
- "v_eta",
- "vol0",
- "nhpres_xi",
- "nhpres_vxi",
- "fvir_prev",
- "fep_state",
- "MC-rng-unsupported",
- "MC-rng-i-unsupported",
- "barostat-integral" };
-
-enum
-{
- eeksEKIN_N,
- eeksEKINH,
- eeksDEKINDL,
- eeksMVCOS,
- eeksEKINF,
- eeksEKINO,
- eeksEKINSCALEF,
- eeksEKINSCALEH,
- eeksVSCALE,
- eeksEKINTOTAL,
- eeksNR
+enum class StateKineticEntry : int
+{
+ EkinNumber,
+ EkinHalfStep,
+ DEkinDLambda,
+ Mvcos,
+ EkinFullStep,
+ EkinHalfStepOld,
+ EkinNoseHooverScaleFullStep,
+ EkinNoseHooverScaleHalfStep,
+ VelocityScale,
+ EkinTotal,
+ Count
};
-static const char* eeks_names[eeksNR] = { "Ekin_n", "Ekinh", "dEkindlambda",
- "mv_cos", "Ekinf", "Ekinh_old",
- "EkinScaleF_NHC", "EkinScaleH_NHC", "Vscale_NHC",
- "Ekin_Total" };
-
-enum
-{
- eenhENERGY_N,
- eenhENERGY_AVER,
- eenhENERGY_SUM,
- eenhENERGY_NSUM,
- eenhENERGY_SUM_SIM,
- eenhENERGY_NSUM_SIM,
- eenhENERGY_NSTEPS,
- eenhENERGY_NSTEPS_SIM,
- eenhENERGY_DELTA_H_NN,
- eenhENERGY_DELTA_H_LIST,
- eenhENERGY_DELTA_H_STARTTIME,
- eenhENERGY_DELTA_H_STARTLAMBDA,
- eenhNR
+static const char* enumValueToString(StateKineticEntry enumValue)
+{
+ static constexpr gmx::EnumerationArray<StateKineticEntry, const char*> stateKineticEntryNames = {
+ "Ekin_n", "Ekinh", "dEkindlambda", "mv_cos", "Ekinf",
+ "Ekinh_old", "EkinScaleF_NHC", "EkinScaleH_NHC", "Vscale_NHC", "Ekin_Total"
+ };
+ return stateKineticEntryNames[enumValue];
+}
+
+enum class StateEnergyEntry : int
+{
+ N,
+ Aver,
+ Sum,
+ NumSum,
+ SumSim,
+ NumSumSim,
+ NumSteps,
+ NumStepsSim,
+ DeltaHNN,
+ DeltaHList,
+ DeltaHStartTime,
+ DeltaHStartLambda,
+ Count
};
-enum
+enum class StatePullEntry : int
{
- epullhPULL_NUMCOORDINATES,
- epullhPULL_NUMGROUPS,
- epullhPULL_NUMVALUESINXSUM,
- epullhPULL_NUMVALUESINFSUM,
- epullhNR
+ NumCoordinates,
+ NumGroups,
+ NumValuesInXSum,
+ NumValuesInFSum,
+ Count
};
-enum
+enum class StatePullCoordEntry : int
{
- epullcoordh_VALUE_REF_SUM,
- epullcoordh_VALUE_SUM,
- epullcoordh_DR01_SUM,
- epullcoordh_DR23_SUM,
- epullcoordh_DR45_SUM,
- epullcoordh_FSCAL_SUM,
- epullcoordh_DYNAX_SUM,
- epullcoordh_NR
+ ValueReferenceSum,
+ ValueSum,
+ DR01Sum,
+ DR23Sum,
+ DR45Sum,
+ FScalarSum,
+ DynaxSum,
+ Count
};
-enum
+static const char* enumValueToString(StatePullCoordEntry enumValue)
+{
+ static constexpr gmx::EnumerationArray<StatePullCoordEntry, const char*> statePullCoordEntryNames = {
+ "reference-sum", "sum", "dr01-sum", "dr23-sum", "dr45-sum", "fscal-sum", "dynax-sum"
+ };
+ return statePullCoordEntryNames[enumValue];
+}
+
+enum class StatePullGroupEntry : int
{
- epullgrouph_X_SUM,
- epullgrouph_NR
+ XSum,
+ Count
};
-static const char* eenh_names[eenhNR] = { "energy_n",
- "energy_aver",
- "energy_sum",
- "energy_nsum",
- "energy_sum_sim",
- "energy_nsum_sim",
- "energy_nsteps",
- "energy_nsteps_sim",
- "energy_delta_h_nn",
- "energy_delta_h_list",
- "energy_delta_h_start_time",
- "energy_delta_h_start_lambda" };
-
-static const char* ePullhNames[epullhNR] = { "pullhistory_numcoordinates", "pullhistory_numgroups",
- "pullhistory_numvaluesinxsum",
- "pullhistory_numvaluesinfsum" };
+static const char* enumValueToString(StatePullGroupEntry enumValue)
+{
+ static constexpr gmx::EnumerationArray<StatePullGroupEntry, const char*> statePullGroupEntryNames = {
+ "coordinate-sum"
+ };
+ return statePullGroupEntryNames[enumValue];
+}
+
+static const char* enumValueToString(StateEnergyEntry enumValue)
+{
+ static constexpr gmx::EnumerationArray<StateEnergyEntry, const char*> stateEnergyEntryNames = {
+ "energy_n",
+ "energy_aver",
+ "energy_sum",
+ "energy_nsum",
+ "energy_sum_sim",
+ "energy_nsum_sim",
+ "energy_nsteps",
+ "energy_nsteps_sim",
+ "energy_delta_h_nn",
+ "energy_delta_h_list",
+ "energy_delta_h_start_time",
+ "energy_delta_h_start_lambda"
+ };
+ return stateEnergyEntryNames[enumValue];
+}
+
+static const char* enumValueToString(StatePullEntry enumValue)
+{
+ static constexpr gmx::EnumerationArray<StatePullEntry, const char*> statePullEntryNames = {
+ "pullhistory_numcoordinates",
+ "pullhistory_numgroups",
+ "pullhistory_numvaluesinxsum",
+ "pullhistory_numvaluesinfsum"
+ };
+ return statePullEntryNames[enumValue];
+}
/* free energy history variables -- need to be preserved over checkpoint */
-enum
-{
- edfhBEQUIL,
- edfhNATLAMBDA,
- edfhWLHISTO,
- edfhWLDELTA,
- edfhSUMWEIGHTS,
- edfhSUMDG,
- edfhSUMMINVAR,
- edfhSUMVAR,
- edfhACCUMP,
- edfhACCUMM,
- edfhACCUMP2,
- edfhACCUMM2,
- edfhTIJ,
- edfhTIJEMP,
- edfhNR
-};
-/* free energy history variable names */
-static const char* edfh_names[edfhNR] = { "bEquilibrated",
- "N_at_state",
- "Wang-Landau Histogram",
- "Wang-Landau Delta",
- "Weights",
- "Free Energies",
- "minvar",
- "variance",
- "accumulated_plus",
- "accumulated_minus",
- "accumulated_plus_2",
- "accumulated_minus_2",
- "Tij",
- "Tij_empirical" };
-
-/* AWH biasing history variables */
-enum
-{
- eawhhIN_INITIAL,
- eawhhEQUILIBRATEHISTOGRAM,
- eawhhHISTSIZE,
- eawhhNPOINTS,
- eawhhCOORDPOINT,
- eawhhUMBRELLAGRIDPOINT,
- eawhhUPDATELIST,
- eawhhLOGSCALEDSAMPLEWEIGHT,
- eawhhNUMUPDATES,
- eawhhFORCECORRELATIONGRID,
- eawhhNR
+enum class StateFepEntry : int
+{
+ IsEquilibrated,
+ NumAtLambda,
+ WangLandauHistogram,
+ WangLandauDelta,
+ SumWeights,
+ SumDG,
+ SumMinVar,
+ SumVar,
+ Accump,
+ Accumm,
+ Accump2,
+ Accumm2,
+ Tij,
+ TijEmp,
+ Count
};
-static const char* eawhh_names[eawhhNR] = { "awh_in_initial", "awh_equilibrateHistogram",
- "awh_histsize", "awh_npoints",
- "awh_coordpoint", "awh_umbrellaGridpoint",
- "awh_updatelist", "awh_logScaledSampleWeight",
- "awh_numupdates", "awh_forceCorrelationGrid" };
+//! free energy history names
+static const char* enumValueToString(StateFepEntry enumValue)
+{
+ static constexpr gmx::EnumerationArray<StateFepEntry, const char*> stateFepEntryNames = {
+ "bEquilibrated",
+ "N_at_state",
+ "Wang-Landau Histogram",
+ "Wang-Landau Delta",
+ "Weights",
+ "Free Energies",
+ "minvar",
+ "variance",
+ "accumulated_plus",
+ "accumulated_minus",
+ "accumulated_plus_2",
+ "accumulated_minus_2",
+ "Tij",
+ "Tij_empirical"
+ };
+ return stateFepEntryNames[enumValue];
+}
-enum
-{
- epullsPREVSTEPCOM,
- epullsNR
+//! AWH biasing history variables
+enum class StateAwhEntry : int
+{
+ InInitial,
+ EquilibrateHistogram,
+ HistogramSize,
+ NumPoints,
+ CoordPoint,
+ UmbrellaGridPoint,
+ UpdateList,
+ LogScaledSampleWeight,
+ NumUpdates,
+ ForceCorrelationGrid,
+ Count
};
-static const char* epull_prev_step_com_names[epullsNR] = { "Pull groups prev step COM" };
+static const char* enumValueToString(StateAwhEntry enumValue)
+{
+ static constexpr gmx::EnumerationArray<StateAwhEntry, const char*> stateAwhEntryNames = {
+ "awh_in_initial", "awh_equilibrateHistogram", "awh_histsize", "awh_npoints",
+ "awh_coordpoint", "awh_umbrellaGridpoint", "awh_updatelist", "awh_logScaledSampleWeight",
+ "awh_numupdates", "awh_forceCorrelationGrid"
+ };
+ return stateAwhEntryNames[enumValue];
+}
+enum class StatePullCommunicationEntry : int
+{
+ PreviousStepCom,
+ Count
+};
//! Higher level vector element type, only used for formatting checkpoint dumps
enum class CptElementType
matrix3x3 //!< float[3][3] or double[3][3], not linked to precision of type real
};
-//! \brief Parts of the checkpoint state, only used for reporting
-enum class StatePart
-{
- microState, //!< The microstate of the simulated system
- kineticEnergy, //!< Kinetic energy, needed for T/P-coupling state
- energyHistory, //!< Energy observable statistics
- freeEnergyHistory, //!< Free-energy state and observable statistics
- accWeightHistogram, //!< Accelerated weight histogram method state
- pullState, //!< COM of previous step.
- pullHistory //!< Pull history statistics (sums since last written output)
-};
-
-//! \brief Return the name of a checkpoint entry based on part and part entry
-static const char* entryName(StatePart part, int ecpt)
-{
- switch (part)
- {
- case StatePart::microState: return est_names[ecpt];
- case StatePart::kineticEnergy: return eeks_names[ecpt];
- case StatePart::energyHistory: return eenh_names[ecpt];
- case StatePart::freeEnergyHistory: return edfh_names[ecpt];
- case StatePart::accWeightHistogram: return eawhh_names[ecpt];
- case StatePart::pullState: return epull_prev_step_com_names[ecpt];
- case StatePart::pullHistory: return ePullhNames[ecpt];
- }
-
- return nullptr;
-}
-
static void cp_warning(FILE* fp)
{
fprintf(fp, "\nWARNING: Checkpoint file is corrupted or truncated\n\n");
return 0;
}
+template<typename EnumType>
+static int do_cpt_enum_as_int(XDR* xd, const char* desc, EnumType* enumValue, FILE* list)
+{
+ static_assert(std::is_same<std::underlying_type_t<EnumType>, int>::value,
+ "Only enums with underlying type int are supported.");
+ auto castedValue = static_cast<int>(*enumValue);
+ if (xdr_int(xd, &castedValue) == 0)
+ {
+ return -1;
+ }
+ *enumValue = static_cast<EnumType>(castedValue);
+ if (list)
+ {
+ fprintf(list, "%s = %d\n", desc, castedValue);
+ }
+ return 0;
+}
+
+template<typename EnumType>
+static int do_cpt_n_enum_as_int(XDR* xd, const char* desc, int n, EnumType* enumValue, FILE* list)
+{
+ bool_t res = 1;
+ for (int j = 0; j < n && res; j++)
+ {
+ res &= do_cpt_enum_as_int<EnumType>(xd, desc, &enumValue[j], list);
+ }
+ if (res == 0)
+ {
+ return -1;
+ }
+
+ return 0;
+}
+
static void do_cpt_int_err(XDR* xd, const char* desc, int* i, FILE* list)
{
if (do_cpt_int(xd, desc, i, list) < 0)
template<>
struct xdr_type<int>
{
- static const int value = xdr_datatype_int;
+ static const XdrDataType value = XdrDataType::Int;
};
template<>
struct xdr_type<float>
{
- static const int value = xdr_datatype_float;
+ static const XdrDataType value = XdrDataType::Float;
};
template<>
struct xdr_type<double>
{
- static const int value = xdr_datatype_double;
+ static const XdrDataType value = XdrDataType::Double;
};
-//! \brief Returns size in byte of an xdr_datatype
-static inline unsigned int sizeOfXdrType(int xdrType)
+//! \brief Returns size in byte of an XdrDataType
+static inline unsigned int sizeOfXdrType(XdrDataType xdrType)
{
switch (xdrType)
{
- case xdr_datatype_int: return sizeof(int);
- case xdr_datatype_float: return sizeof(float);
- case xdr_datatype_double: return sizeof(double);
+ case XdrDataType::Int: return sizeof(int);
+ case XdrDataType::Float: return sizeof(float);
+ case XdrDataType::Double: return sizeof(double);
default: GMX_RELEASE_ASSERT(false, "XDR data type not implemented");
}
}
//! \brief Returns the XDR process function for i/o of an XDR type
-static inline xdrproc_t xdrProc(int xdrType)
+static inline xdrproc_t xdrProc(XdrDataType xdrType)
{
switch (xdrType)
{
- case xdr_datatype_int: return reinterpret_cast<xdrproc_t>(xdr_int);
- case xdr_datatype_float: return reinterpret_cast<xdrproc_t>(xdr_float);
- case xdr_datatype_double: return reinterpret_cast<xdrproc_t>(xdr_double);
+ case XdrDataType::Int: return reinterpret_cast<xdrproc_t>(xdr_int);
+ case XdrDataType::Float: return reinterpret_cast<xdrproc_t>(xdr_float);
+ case XdrDataType::Double: return reinterpret_cast<xdrproc_t>(xdr_double);
default: GMX_RELEASE_ASSERT(false, "XDR data type not implemented");
}
* The formatting of the printing is set by \p cptElementType.
* When list==NULL only reads the elements.
*/
-static bool_t listXdrVector(XDR* xd, StatePart part, int ecpt, int nf, int xdrType, FILE* list, CptElementType cptElementType)
+template<typename Enum>
+static bool_t listXdrVector(XDR* xd, Enum ecpt, int nf, XdrDataType xdrType, FILE* list, CptElementType cptElementType)
{
bool_t res = 0;
{
switch (xdrType)
{
- case xdr_datatype_int:
- pr_ivec(list, 0, entryName(part, ecpt), reinterpret_cast<const int*>(data.data()), nf, TRUE);
+ case XdrDataType::Int:
+ pr_ivec(list, 0, enumValueToString(ecpt), reinterpret_cast<const int*>(data.data()), nf, TRUE);
break;
- case xdr_datatype_float:
+ case XdrDataType::Float:
#if !GMX_DOUBLE
if (cptElementType == CptElementType::real3)
{
- pr_rvecs(list, 0, entryName(part, ecpt),
- reinterpret_cast<const rvec*>(data.data()), nf / 3);
+ pr_rvecs(list, 0, enumValueToString(ecpt), reinterpret_cast<const rvec*>(data.data()), nf / 3);
}
else
#endif
{
/* Note: With double precision code dumping a single precision rvec will produce float iso rvec print, but that's a minor annoyance */
- pr_fvec(list, 0, entryName(part, ecpt),
- reinterpret_cast<const float*>(data.data()), nf, TRUE);
+ pr_fvec(list, 0, enumValueToString(ecpt), reinterpret_cast<const float*>(data.data()), nf, TRUE);
}
break;
- case xdr_datatype_double:
+ case XdrDataType::Double:
#if GMX_DOUBLE
if (cptElementType == CptElementType::real3)
{
- pr_rvecs(list, 0, entryName(part, ecpt),
- reinterpret_cast<const rvec*>(data.data()), nf / 3);
+ pr_rvecs(list, 0, enumValueToString(ecpt), reinterpret_cast<const rvec*>(data.data()), nf / 3);
}
else
#endif
{
/* Note: With single precision code dumping a double precision rvec will produce float iso rvec print, but that's a minor annoyance */
- pr_dvec(list, 0, entryName(part, ecpt),
- reinterpret_cast<const double*>(data.data()), nf, TRUE);
+ pr_dvec(list, 0, enumValueToString(ecpt), reinterpret_cast<const double*>(data.data()), nf, TRUE);
}
break;
default: GMX_RELEASE_ASSERT(false, "Data type not implemented for listing");
* If nval n<0, *nptr (with v) or vector->size() is used. On read using v,
* the value is stored in nptr
*/
-template<typename T, typename AllocatorType>
+template<typename T, typename AllocatorType, typename Enum>
static int doVectorLow(XDR* xd,
- StatePart part,
- int ecpt,
+ Enum ecpt,
int sflags,
int nval,
int* nptr,
return -1;
}
/* Read/write the element data type */
- constexpr int xdrTypeInTheCode = xdr_type<T>::value;
- int xdrTypeInTheFile = xdrTypeInTheCode;
- res = xdr_int(xd, &xdrTypeInTheFile);
+ constexpr XdrDataType xdrTypeInTheCode = xdr_type<T>::value;
+ XdrDataType xdrTypeInTheFile = xdrTypeInTheCode;
+ int xdrTypeInTheFileAsInt = static_cast<int>(xdrTypeInTheFile);
+ res = xdr_int(xd, &xdrTypeInTheFileAsInt);
+ xdrTypeInTheFile = static_cast<XdrDataType>(xdrTypeInTheFileAsInt);
if (res == 0)
{
return -1;
}
- if (list == nullptr && (sflags & (1 << ecpt)))
+ if (list == nullptr && (sflags & enumValueToBitMask(ecpt)))
{
if (nval >= 0)
{
{
gmx_fatal(FARGS,
"Count mismatch for state entry %s, code count is %d, file count is %d\n",
- entryName(part, ecpt), nval, numElemInTheFile);
+ enumValueToString(ecpt),
+ nval,
+ numElemInTheFile);
}
}
else if (nptr != nullptr)
if (!typesMatch)
{
char buf[STRLEN];
- sprintf(buf, "mismatch for state entry %s, code precision is %s, file precision is %s",
- entryName(part, ecpt), xdr_datatype_names[xdrTypeInTheCode],
- xdr_datatype_names[xdrTypeInTheFile]);
+ sprintf(buf,
+ "mismatch for state entry %s, code precision is %s, file precision is %s",
+ enumValueToString(ecpt),
+ enumValueToString(xdrTypeInTheCode),
+ enumValueToString(xdrTypeInTheFile));
/* Matching int and real should never occur, but check anyhow */
- if (xdrTypeInTheFile == xdr_datatype_int || xdrTypeInTheCode == xdr_datatype_int)
+ if (xdrTypeInTheFile == XdrDataType::Int || xdrTypeInTheCode == XdrDataType::Int)
{
gmx_fatal(FARGS,
- "Type %s: incompatible checkpoint formats or corrupted checkpoint file.", buf);
+ "Type %s: incompatible checkpoint formats or corrupted checkpoint file.",
+ buf);
}
}
{
snew(vChar, numElemInTheFile * sizeOfXdrType(xdrTypeInTheFile));
}
- res = xdr_vector(xd, vChar, numElemInTheFile, sizeOfXdrType(xdrTypeInTheFile),
- xdrProc(xdrTypeInTheFile));
+ res = xdr_vector(
+ xd, vChar, numElemInTheFile, sizeOfXdrType(xdrTypeInTheFile), xdrProc(xdrTypeInTheFile));
if (res == 0)
{
return -1;
}
else
{
- res = listXdrVector(xd, part, ecpt, numElemInTheFile, xdrTypeInTheFile, list, cptElementType);
+ res = listXdrVector(xd, ecpt, numElemInTheFile, xdrTypeInTheFile, list, cptElementType);
}
return 0;
}
//! \brief Read/Write a std::vector, on read checks the number of elements matches \p numElements, if specified.
-template<typename T>
-static int
-doVector(XDR* xd, StatePart part, int ecpt, int sflags, std::vector<T>* vector, FILE* list, int numElements = -1)
+template<typename T, typename Enum>
+static int doVector(XDR* xd, Enum ecpt, int sflags, std::vector<T>* vector, FILE* list, int numElements = -1)
{
- return doVectorLow<T>(xd, part, ecpt, sflags, numElements, nullptr, nullptr, vector, list,
- CptElementType::real);
+ return doVectorLow<T>(
+ xd, ecpt, sflags, numElements, nullptr, nullptr, vector, list, CptElementType::real);
}
//! \brief Read/Write an ArrayRef<real>.
-static int doRealArrayRef(XDR* xd, StatePart part, int ecpt, int sflags, gmx::ArrayRef<real> vector, FILE* list)
+template<typename Enum>
+static int doRealArrayRef(XDR* xd, Enum ecpt, int sflags, gmx::ArrayRef<real> vector, FILE* list)
{
real* v_real = vector.data();
- return doVectorLow<real, std::allocator<real>>(xd, part, ecpt, sflags, vector.size(), nullptr,
- &v_real, nullptr, list, CptElementType::real);
+ return doVectorLow<real, std::allocator<real>>(
+ xd, ecpt, sflags, vector.size(), nullptr, &v_real, nullptr, list, CptElementType::real);
}
//! Convert from view of RVec to view of real.
}
//! \brief Read/Write a PaddedVector whose value_type is RVec.
-template<typename PaddedVectorOfRVecType>
-static int
-doRvecVector(XDR* xd, StatePart part, int ecpt, int sflags, PaddedVectorOfRVecType* v, int numAtoms, FILE* list)
+template<typename PaddedVectorOfRVecType, typename Enum>
+static int doRvecVector(XDR* xd, Enum ecpt, int sflags, PaddedVectorOfRVecType* v, int numAtoms, FILE* list)
{
const int numReals = numAtoms * DIM;
if (list == nullptr)
{
GMX_RELEASE_ASSERT(
- sflags & (1 << ecpt),
+ sflags & enumValueToBitMask(ecpt),
"When not listing, the flag for the entry should be set when requesting i/o");
GMX_RELEASE_ASSERT(v->size() == numAtoms, "v should have sufficient size for numAtoms");
- return doRealArrayRef(xd, part, ecpt, sflags, realArrayRefFromRVecArrayRef(makeArrayRef(*v)), list);
+ return doRealArrayRef(xd, ecpt, sflags, realArrayRefFromRVecArrayRef(makeArrayRef(*v)), list);
}
else
{
// allocator from RVec to real.
using realAllocator =
typename std::allocator_traits<typename PaddedVectorOfRVecType::allocator_type>::template rebind_alloc<real>;
- return doVectorLow<real, realAllocator>(xd, part, ecpt, sflags, numReals, nullptr, nullptr,
- nullptr, list, CptElementType::real);
+ return doVectorLow<real, realAllocator>(
+ xd, ecpt, sflags, numReals, nullptr, nullptr, nullptr, list, CptElementType::real);
}
}
* but on reading it assumes that n matches the value in the checkpoint file,
* a fatal error is generated when this is not the case.
*/
-static int do_cpte_reals(XDR* xd, StatePart part, int ecpt, int sflags, int n, real** v, FILE* list)
+template<typename Enum>
+static int do_cpte_reals(XDR* xd, Enum ecpt, int sflags, int n, real** v, FILE* list)
{
- return doVectorLow<real, std::allocator<real>>(xd, part, ecpt, sflags, n, nullptr, v, nullptr,
- list, CptElementType::real);
+ return doVectorLow<real, std::allocator<real>>(
+ xd, ecpt, sflags, n, nullptr, v, nullptr, list, CptElementType::real);
}
-/* This function does the same as do_cpte_reals,
- * except that on reading it ignores the passed value of *n
- * and stores the value read from the checkpoint file in *n.
- */
-static int do_cpte_n_reals(XDR* xd, StatePart part, int ecpt, int sflags, int* n, real** v, FILE* list)
+template<typename Enum>
+static int do_cpte_real(XDR* xd, Enum ecpt, int sflags, real* r, FILE* list)
{
- return doVectorLow<real, std::allocator<real>>(xd, part, ecpt, sflags, -1, n, v, nullptr, list,
- CptElementType::real);
+ return doVectorLow<real, std::allocator<real>>(
+ xd, ecpt, sflags, 1, nullptr, &r, nullptr, list, CptElementType::real);
}
-static int do_cpte_real(XDR* xd, StatePart part, int ecpt, int sflags, real* r, FILE* list)
+template<typename Enum>
+static int do_cpte_ints(XDR* xd, Enum ecpt, int sflags, int n, int** v, FILE* list)
{
- return doVectorLow<real, std::allocator<real>>(xd, part, ecpt, sflags, 1, nullptr, &r, nullptr,
- list, CptElementType::real);
+ return doVectorLow<int, std::allocator<int>>(
+ xd, ecpt, sflags, n, nullptr, v, nullptr, list, CptElementType::integer);
}
-static int do_cpte_ints(XDR* xd, StatePart part, int ecpt, int sflags, int n, int** v, FILE* list)
+template<typename Enum>
+static int do_cpte_int(XDR* xd, Enum ecpt, int sflags, int* i, FILE* list)
{
- return doVectorLow<int, std::allocator<int>>(xd, part, ecpt, sflags, n, nullptr, v, nullptr,
- list, CptElementType::integer);
+ return do_cpte_ints(xd, ecpt, sflags, 1, &i, list);
}
-static int do_cpte_int(XDR* xd, StatePart part, int ecpt, int sflags, int* i, FILE* list)
-{
- return do_cpte_ints(xd, part, ecpt, sflags, 1, &i, list);
-}
-
-static int do_cpte_bool(XDR* xd, StatePart part, int ecpt, int sflags, bool* b, FILE* list)
+template<typename Enum>
+static int do_cpte_bool(XDR* xd, Enum ecpt, int sflags, bool* b, FILE* list)
{
int i = static_cast<int>(*b);
- int ret = do_cpte_int(xd, part, ecpt, sflags, &i, list);
+ int ret = do_cpte_int(xd, ecpt, sflags, &i, list);
*b = (i != 0);
return ret;
}
-static int do_cpte_doubles(XDR* xd, StatePart part, int ecpt, int sflags, int n, double** v, FILE* list)
+template<typename Enum>
+static int do_cpte_doubles(XDR* xd, Enum ecpt, int sflags, int n, double** v, FILE* list)
{
- return doVectorLow<double, std::allocator<double>>(xd, part, ecpt, sflags, n, nullptr, v,
- nullptr, list, CptElementType::real);
+ return doVectorLow<double, std::allocator<double>>(
+ xd, ecpt, sflags, n, nullptr, v, nullptr, list, CptElementType::real);
}
-static int do_cpte_double(XDR* xd, StatePart part, int ecpt, int sflags, double* r, FILE* list)
+template<typename Enum>
+static int do_cpte_double(XDR* xd, Enum ecpt, int sflags, double* r, FILE* list)
{
- return do_cpte_doubles(xd, part, ecpt, sflags, 1, &r, list);
+ return do_cpte_doubles(xd, ecpt, sflags, 1, &r, list);
}
-static int do_cpte_matrix(XDR* xd, StatePart part, int ecpt, int sflags, matrix v, FILE* list)
+template<typename Enum>
+static int do_cpte_matrix(XDR* xd, Enum ecpt, int sflags, matrix v, FILE* list)
{
real* vr;
int ret;
vr = &(v[0][0]);
- ret = doVectorLow<real, std::allocator<real>>(xd, part, ecpt, sflags, DIM * DIM, nullptr, &vr,
- nullptr, nullptr, CptElementType::matrix3x3);
+ ret = doVectorLow<real, std::allocator<real>>(
+ xd, ecpt, sflags, DIM * DIM, nullptr, &vr, nullptr, nullptr, CptElementType::matrix3x3);
if (list && ret == 0)
{
- pr_rvecs(list, 0, entryName(part, ecpt), v, DIM);
+ pr_rvecs(list, 0, enumValueToString(ecpt), v, DIM);
}
return ret;
}
-
-static int do_cpte_nmatrix(XDR* xd, StatePart part, int ecpt, int sflags, int n, real** v, FILE* list)
+template<typename Enum>
+static int do_cpte_nmatrix(XDR* xd, Enum ecpt, int sflags, int n, real** v, FILE* list)
{
int i;
int ret, reti;
}
for (i = 0; i < n; i++)
{
- reti = doVectorLow<real, std::allocator<real>>(xd, part, ecpt, sflags, n, nullptr, &(v[i]),
- nullptr, nullptr, CptElementType::matrix3x3);
+ reti = doVectorLow<real, std::allocator<real>>(
+ xd, ecpt, sflags, n, nullptr, &(v[i]), nullptr, nullptr, CptElementType::matrix3x3);
if (list && reti == 0)
{
- sprintf(name, "%s[%d]", entryName(part, ecpt), i);
+ sprintf(name, "%s[%d]", enumValueToString(ecpt), i);
pr_reals(list, 0, name, v[i], n);
}
if (reti != 0)
return ret;
}
-static int do_cpte_matrices(XDR* xd, StatePart part, int ecpt, int sflags, int n, matrix** v, FILE* list)
+template<typename Enum>
+static int do_cpte_matrices(XDR* xd, Enum ecpt, int sflags, int n, matrix** v, FILE* list)
{
bool_t res = 0;
matrix *vp, *va = nullptr;
}
if (list == nullptr && nf != n)
{
- gmx_fatal(FARGS, "Count mismatch for state entry %s, code count is %d, file count is %d\n",
- entryName(part, ecpt), n, nf);
+ gmx_fatal(FARGS,
+ "Count mismatch for state entry %s, code count is %d, file count is %d\n",
+ enumValueToString(ecpt),
+ n,
+ nf);
}
- if (list || !(sflags & (1 << ecpt)))
+ if (list || !(sflags & enumValueToBitMask(ecpt)))
{
snew(va, nf);
vp = va;
}
}
}
- ret = doVectorLow<real, std::allocator<real>>(xd, part, ecpt, sflags, nf * DIM * DIM, nullptr,
- &vr, nullptr, nullptr, CptElementType::matrix3x3);
+ ret = doVectorLow<real, std::allocator<real>>(
+ xd, ecpt, sflags, nf * DIM * DIM, nullptr, &vr, nullptr, nullptr, CptElementType::matrix3x3);
for (i = 0; i < nf; i++)
{
for (j = 0; j < DIM; j++)
{
for (i = 0; i < nf; i++)
{
- pr_rvecs(list, 0, entryName(part, ecpt), vp[i], DIM);
+ pr_rvecs(list, 0, enumValueToString(ecpt), vp[i], DIM);
}
}
if (va)
gmx_fatal(FARGS,
"Start of file magic number mismatch, checkpoint file has %d, should be %d\n"
"The checkpoint file is corrupted or not a checkpoint file",
- magic, CPT_MAGIC1);
+ magic,
+ CPT_MAGIC1);
}
char fhost[255];
if (!bRead)
{
gmx_fatal(FARGS,
"Attempting to read a checkpoint file of version %d with code of version %d\n",
- contents->file_version, cpt_version);
+ contents->file_version,
+ cpt_version);
}
if (contents->file_version >= 13)
{
{
contents->nlambda = 0;
}
- do_cpt_int_err(xd, "integrator", &contents->eIntegrator, list);
+ {
+ int integrator = static_cast<int>(contents->eIntegrator);
+ do_cpt_int_err(xd, "integrator", &integrator, list);
+ if (bRead)
+ {
+ contents->eIntegrator = static_cast<IntegrationAlgorithm>(integrator);
+ }
+ }
if (contents->file_version >= 3)
{
do_cpt_int_err(xd, "simulation part #", &contents->simulation_part, list);
}
else
{
- contents->flags_eks = 0;
- contents->flags_enh = (contents->flags_state >> (estORIRE_DTAV + 1));
+ contents->flags_eks = 0;
+ contents->flags_enh = (contents->flags_state >> (static_cast<int>(StateEntry::OrireDtav) + 1));
contents->flags_state = (contents->flags_state
- & ~((1 << (estORIRE_DTAV + 1)) | (1 << (estORIRE_DTAV + 2))
- | (1 << (estORIRE_DTAV + 3))));
+ & ~((1 << (static_cast<int>(StateEntry::OrireDtav) + 1))
+ | (1 << (static_cast<int>(StateEntry::OrireDtav) + 2))
+ | (1 << (static_cast<int>(StateEntry::OrireDtav) + 3))));
}
if (contents->file_version >= 14)
{
if (contents->file_version >= 16)
{
- do_cpt_int_err(xd, "swap", &contents->eSwapCoords, list);
+ int swapState = static_cast<int>(contents->eSwapCoords);
+ do_cpt_int_err(xd, "swap", &swapState, list);
+ if (bRead)
+ {
+ contents->eSwapCoords = static_cast<SwapType>(swapState);
+ }
}
else
{
- contents->eSwapCoords = eswapNO;
+ contents->eSwapCoords = SwapType::No;
}
if (contents->file_version >= 17)
if (contents->file_version >= cptv_ModularSimulator)
{
- do_cpt_bool_err(xd, "Is modular simulator checkpoint",
- &contents->isModularSimulatorCheckpoint, list);
+ do_cpt_bool_err(
+ xd, "Is modular simulator checkpoint", &contents->isModularSimulatorCheckpoint, list);
}
else
{
static int do_cpt_state(XDR* xd, int fflags, t_state* state, FILE* list)
{
- int ret = 0;
- const StatePart part = StatePart::microState;
- const int sflags = state->flags;
+ int ret = 0;
+ const int sflags = state->flags;
// If reading, state->natoms was probably just read, so
// allocations need to be managed. If writing, this won't change
// anything that matters.
+ using StateFlags = gmx::EnumerationArray<StateEntry, bool>;
state_change_natoms(state, state->natoms);
- for (int i = 0; (i < estNR && ret == 0); i++)
+ for (auto i = StateFlags::keys().begin(); (i != StateFlags::keys().end() && ret == 0); i++)
{
- if (fflags & (1 << i))
+ if (fflags & enumValueToBitMask(*i))
{
- switch (i)
+ switch (*i)
{
- case estLAMBDA:
- ret = doRealArrayRef(
- xd, part, i, sflags,
- gmx::arrayRefFromArray<real>(state->lambda.data(), state->lambda.size()),
- list);
+ case StateEntry::Lambda:
+ ret = doRealArrayRef(xd, *i, sflags, state->lambda, list);
+ break;
+ case StateEntry::FepState:
+ ret = do_cpte_int(xd, *i, sflags, &state->fep_state, list);
break;
- case estFEPSTATE:
- ret = do_cpte_int(xd, part, i, sflags, &state->fep_state, list);
+ case StateEntry::Box: ret = do_cpte_matrix(xd, *i, sflags, state->box, list); break;
+ case StateEntry::BoxRel:
+ ret = do_cpte_matrix(xd, *i, sflags, state->box_rel, list);
break;
- case estBOX: ret = do_cpte_matrix(xd, part, i, sflags, state->box, list); break;
- case estBOX_REL:
- ret = do_cpte_matrix(xd, part, i, sflags, state->box_rel, list);
+ case StateEntry::BoxV:
+ ret = do_cpte_matrix(xd, *i, sflags, state->boxv, list);
break;
- case estBOXV: ret = do_cpte_matrix(xd, part, i, sflags, state->boxv, list); break;
- case estPRES_PREV:
- ret = do_cpte_matrix(xd, part, i, sflags, state->pres_prev, list);
+ case StateEntry::PressurePrevious:
+ ret = do_cpte_matrix(xd, *i, sflags, state->pres_prev, list);
break;
- case estSVIR_PREV:
- ret = do_cpte_matrix(xd, part, i, sflags, state->svir_prev, list);
+ case StateEntry::SVirPrev:
+ ret = do_cpte_matrix(xd, *i, sflags, state->svir_prev, list);
break;
- case estFVIR_PREV:
- ret = do_cpte_matrix(xd, part, i, sflags, state->fvir_prev, list);
+ case StateEntry::FVirPrev:
+ ret = do_cpte_matrix(xd, *i, sflags, state->fvir_prev, list);
break;
- case estNH_XI:
- ret = doVector<double>(xd, part, i, sflags, &state->nosehoover_xi, list);
+ case StateEntry::Nhxi:
+ ret = doVector<double>(xd, *i, sflags, &state->nosehoover_xi, list);
break;
- case estNH_VXI:
- ret = doVector<double>(xd, part, i, sflags, &state->nosehoover_vxi, list);
+ case StateEntry::Nhvxi:
+ ret = doVector<double>(xd, *i, sflags, &state->nosehoover_vxi, list);
break;
- case estNHPRES_XI:
- ret = doVector<double>(xd, part, i, sflags, &state->nhpres_xi, list);
+ case StateEntry::Nhpresxi:
+ ret = doVector<double>(xd, *i, sflags, &state->nhpres_xi, list);
break;
- case estNHPRES_VXI:
- ret = doVector<double>(xd, part, i, sflags, &state->nhpres_vxi, list);
+ case StateEntry::Nhpresvxi:
+ ret = doVector<double>(xd, *i, sflags, &state->nhpres_vxi, list);
break;
- case estTHERM_INT:
- ret = doVector<double>(xd, part, i, sflags, &state->therm_integral, list);
+ case StateEntry::ThermInt:
+ ret = doVector<double>(xd, *i, sflags, &state->therm_integral, list);
break;
- case estBAROS_INT:
- ret = do_cpte_double(xd, part, i, sflags, &state->baros_integral, list);
+ case StateEntry::BarosInt:
+ ret = do_cpte_double(xd, *i, sflags, &state->baros_integral, list);
break;
- case estVETA: ret = do_cpte_real(xd, part, i, sflags, &state->veta, list); break;
- case estVOL0: ret = do_cpte_real(xd, part, i, sflags, &state->vol0, list); break;
- case estX:
- ret = doRvecVector(xd, part, i, sflags, &state->x, state->natoms, list);
+ case StateEntry::Veta:
+ ret = do_cpte_real(xd, *i, sflags, &state->veta, list);
break;
- case estV:
- ret = doRvecVector(xd, part, i, sflags, &state->v, state->natoms, list);
+ case StateEntry::Vol0:
+ ret = do_cpte_real(xd, *i, sflags, &state->vol0, list);
+ break;
+ case StateEntry::X:
+ ret = doRvecVector(xd, *i, sflags, &state->x, state->natoms, list);
+ break;
+ case StateEntry::V:
+ ret = doRvecVector(xd, *i, sflags, &state->v, state->natoms, list);
break;
/* The RNG entries are no longer written,
* the next 4 lines are only for reading old files.
* It's OK that three case statements fall through.
*/
- case estLD_RNG_NOTSUPPORTED:
- case estLD_RNGI_NOTSUPPORTED:
- case estMC_RNG_NOTSUPPORTED:
- case estMC_RNGI_NOTSUPPORTED:
- ret = do_cpte_ints(xd, part, i, sflags, 0, nullptr, list);
+ case StateEntry::LDRngNotSupported:
+ case StateEntry::LDRngINotSupported:
+ case StateEntry::MCRngNotSupported:
+ case StateEntry::MCRngINotSupported:
+ ret = do_cpte_ints(xd, *i, sflags, 0, nullptr, list);
break;
- case estDISRE_INITF:
- ret = do_cpte_real(xd, part, i, sflags, &state->hist.disre_initf, list);
+ case StateEntry::DisreInitF:
+ ret = do_cpte_real(xd, *i, sflags, &state->hist.disre_initf, list);
break;
- case estDISRE_RM3TAV:
- ret = do_cpte_n_reals(xd, part, i, sflags, &state->hist.ndisrepairs,
- &state->hist.disre_rm3tav, list);
+ case StateEntry::DisreRm3Tav:
+ ret = doVector<real>(xd, *i, sflags, &state->hist.disre_rm3tav, list);
break;
- case estORIRE_INITF:
- ret = do_cpte_real(xd, part, i, sflags, &state->hist.orire_initf, list);
+ case StateEntry::OrireInitF:
+ ret = do_cpte_real(xd, *i, sflags, &state->hist.orire_initf, list);
break;
- case estORIRE_DTAV:
- ret = do_cpte_n_reals(xd, part, i, sflags, &state->hist.norire_Dtav,
- &state->hist.orire_Dtav, list);
+ case StateEntry::OrireDtav:
+ ret = doVector<real>(xd, *i, sflags, &state->hist.orire_Dtav, list);
break;
- case estPULLCOMPREVSTEP:
- ret = doVector<double>(xd, part, i, sflags, &state->pull_com_prev_step, list);
+ case StateEntry::PullComPrevStep:
+ ret = doVector<double>(xd, *i, sflags, &state->pull_com_prev_step, list);
break;
default:
gmx_fatal(FARGS,
"Unknown state entry %d\n"
"You are reading a checkpoint file written by different code, which "
"is not supported",
- i);
+ enumValueToBitMask(*i));
}
}
}
{
int ret = 0;
- const StatePart part = StatePart::kineticEnergy;
- for (int i = 0; (i < eeksNR && ret == 0); i++)
+ using StateFlags = gmx::EnumerationArray<StateKineticEntry, bool>;
+ for (auto i = StateFlags::keys().begin(); (i != StateFlags::keys().end() && ret == 0); i++)
{
- if (fflags & (1 << i))
+ if (fflags & enumValueToBitMask(*i))
{
- switch (i)
+ switch (*i)
{
- case eeksEKIN_N:
- ret = do_cpte_int(xd, part, i, fflags, &ekins->ekin_n, list);
+ case StateKineticEntry::EkinNumber:
+ ret = do_cpte_int(xd, *i, fflags, &ekins->ekin_n, list);
break;
- case eeksEKINH:
- ret = do_cpte_matrices(xd, part, i, fflags, ekins->ekin_n, &ekins->ekinh, list);
+ case StateKineticEntry::EkinHalfStep:
+ ret = do_cpte_matrices(xd, *i, fflags, ekins->ekin_n, &ekins->ekinh, list);
break;
- case eeksEKINF:
- ret = do_cpte_matrices(xd, part, i, fflags, ekins->ekin_n, &ekins->ekinf, list);
+ case StateKineticEntry::EkinFullStep:
+ ret = do_cpte_matrices(xd, *i, fflags, ekins->ekin_n, &ekins->ekinf, list);
break;
- case eeksEKINO:
- ret = do_cpte_matrices(xd, part, i, fflags, ekins->ekin_n, &ekins->ekinh_old, list);
+ case StateKineticEntry::EkinHalfStepOld:
+ ret = do_cpte_matrices(xd, *i, fflags, ekins->ekin_n, &ekins->ekinh_old, list);
break;
- case eeksEKINTOTAL:
- ret = do_cpte_matrix(xd, part, i, fflags, ekins->ekin_total, list);
+ case StateKineticEntry::EkinTotal:
+ ret = do_cpte_matrix(xd, *i, fflags, ekins->ekin_total, list);
break;
- case eeksEKINSCALEF:
- ret = doVector<double>(xd, part, i, fflags, &ekins->ekinscalef_nhc, list);
+ case StateKineticEntry::EkinNoseHooverScaleFullStep:
+ ret = doVector<double>(xd, *i, fflags, &ekins->ekinscalef_nhc, list);
break;
- case eeksVSCALE:
- ret = doVector<double>(xd, part, i, fflags, &ekins->vscale_nhc, list);
+ case StateKineticEntry::VelocityScale:
+ ret = doVector<double>(xd, *i, fflags, &ekins->vscale_nhc, list);
break;
- case eeksEKINSCALEH:
- ret = doVector<double>(xd, part, i, fflags, &ekins->ekinscaleh_nhc, list);
+ case StateKineticEntry::EkinNoseHooverScaleHalfStep:
+ ret = doVector<double>(xd, *i, fflags, &ekins->ekinscaleh_nhc, list);
break;
- case eeksDEKINDL:
- ret = do_cpte_real(xd, part, i, fflags, &ekins->dekindl, list);
+ case StateKineticEntry::DEkinDLambda:
+ ret = do_cpte_real(xd, *i, fflags, &ekins->dekindl, list);
+ break;
+ case StateKineticEntry::Mvcos:
+ ret = do_cpte_real(xd, *i, fflags, &ekins->mvcos, list);
break;
- case eeksMVCOS: ret = do_cpte_real(xd, part, i, fflags, &ekins->mvcos, list); break;
default:
gmx_fatal(FARGS,
"Unknown ekin data state entry %d\n"
"You are probably reading a new checkpoint file with old code",
- i);
+ enumValueToBitMask(*i));
}
}
}
}
-static int do_cpt_swapstate(XDR* xd, gmx_bool bRead, int eSwapCoords, swaphistory_t* swapstate, FILE* list)
+static int do_cpt_swapstate(XDR* xd, gmx_bool bRead, SwapType eSwapCoords, swaphistory_t* swapstate, FILE* list)
{
int swap_cpt_version = 2;
- if (eSwapCoords == eswapNO)
+ if (eSwapCoords == SwapType::No)
{
return 0;
}
snew(swapstate->ionType, swapstate->nIonTypes);
}
- for (int ic = 0; ic < eCompNR; ic++)
+ for (auto ic : gmx::EnumerationWrapper<Compartment>{})
{
for (int ii = 0; ii < swapstate->nIonTypes; ii++)
{
}
/* Ion flux per channel */
- for (int ic = 0; ic < eChanNR; ic++)
+ for (auto ic : gmx::EnumerationWrapper<Channel>{})
{
for (int ii = 0; ii < swapstate->nIonTypes; ii++)
{
snew(gs->comp_from, gs->nMol);
}
- do_cpt_u_chars(xd, "channel history", gs->nMol, gs->channel_label, list);
- do_cpt_u_chars(xd, "domain history", gs->nMol, gs->comp_from, list);
+ do_cpt_n_enum_as_int<ChannelHistory>(xd, "channel history", gs->nMol, gs->channel_label, list);
+ do_cpt_n_enum_as_int<Domain>(xd, "domain history", gs->nMol, gs->comp_from, list);
}
/* Save the last known whole positions to checkpoint
* file to be able to also make multimeric channels whole in PBC */
- do_cpt_int_err(xd, "Ch0 atoms", &swapstate->nat[eChan0], list);
- do_cpt_int_err(xd, "Ch1 atoms", &swapstate->nat[eChan1], list);
+ do_cpt_int_err(xd, "Ch0 atoms", &swapstate->nat[Channel::Zero], list);
+ do_cpt_int_err(xd, "Ch1 atoms", &swapstate->nat[Channel::One], list);
if (bRead)
{
- snew(swapstate->xc_old_whole[eChan0], swapstate->nat[eChan0]);
- snew(swapstate->xc_old_whole[eChan1], swapstate->nat[eChan1]);
- do_cpt_n_rvecs_err(xd, "Ch0 whole x", swapstate->nat[eChan0], swapstate->xc_old_whole[eChan0], list);
- do_cpt_n_rvecs_err(xd, "Ch1 whole x", swapstate->nat[eChan1], swapstate->xc_old_whole[eChan1], list);
+ snew(swapstate->xc_old_whole[Channel::Zero], swapstate->nat[Channel::Zero]);
+ snew(swapstate->xc_old_whole[Channel::One], swapstate->nat[Channel::One]);
+ do_cpt_n_rvecs_err(
+ xd, "Ch0 whole x", swapstate->nat[Channel::Zero], swapstate->xc_old_whole[Channel::Zero], list);
+ do_cpt_n_rvecs_err(
+ xd, "Ch1 whole x", swapstate->nat[Channel::One], swapstate->xc_old_whole[Channel::One], list);
}
else
{
- do_cpt_n_rvecs_err(xd, "Ch0 whole x", swapstate->nat[eChan0],
- *swapstate->xc_old_whole_p[eChan0], list);
- do_cpt_n_rvecs_err(xd, "Ch1 whole x", swapstate->nat[eChan1],
- *swapstate->xc_old_whole_p[eChan1], list);
+ do_cpt_n_rvecs_err(xd,
+ "Ch0 whole x",
+ swapstate->nat[Channel::Zero],
+ *swapstate->xc_old_whole_p[Channel::Zero],
+ list);
+ do_cpt_n_rvecs_err(
+ xd, "Ch1 whole x", swapstate->nat[Channel::One], *swapstate->xc_old_whole_p[Channel::One], list);
}
return 0;
return ret;
}
- GMX_RELEASE_ASSERT(enerhist != nullptr,
- "With energy history, we need a valid enerhist pointer");
+ GMX_RELEASE_ASSERT(enerhist != nullptr, "With energy history, we need a valid enerhist pointer");
/* This is stored/read for backward compatibility */
int energyHistoryNumEnergies = 0;
}
delta_h_history_t* deltaH = enerhist->deltaHForeignLambdas.get();
- const StatePart part = StatePart::energyHistory;
- for (int i = 0; (i < eenhNR && ret == 0); i++)
+ using StateFlags = gmx::EnumerationArray<StateEnergyEntry, bool>;
+ for (auto i = StateFlags::keys().begin(); (i != StateFlags::keys().end() && ret == 0); i++)
{
- if (fflags & (1 << i))
+ if (fflags & enumValueToBitMask(*i))
{
- switch (i)
+ switch (*i)
{
- case eenhENERGY_N:
- ret = do_cpte_int(xd, part, i, fflags, &energyHistoryNumEnergies, list);
+ case StateEnergyEntry::N:
+ ret = do_cpte_int(xd, *i, fflags, &energyHistoryNumEnergies, list);
break;
- case eenhENERGY_AVER:
- ret = doVector<double>(xd, part, i, fflags, &enerhist->ener_ave, list);
+ case StateEnergyEntry::Aver:
+ ret = doVector<double>(xd, *i, fflags, &enerhist->ener_ave, list);
break;
- case eenhENERGY_SUM:
- ret = doVector<double>(xd, part, i, fflags, &enerhist->ener_sum, list);
+ case StateEnergyEntry::Sum:
+ ret = doVector<double>(xd, *i, fflags, &enerhist->ener_sum, list);
break;
- case eenhENERGY_NSUM:
- do_cpt_step_err(xd, eenh_names[i], &enerhist->nsum, list);
+ case StateEnergyEntry::NumSum:
+ do_cpt_step_err(xd, enumValueToString(*i), &enerhist->nsum, list);
break;
- case eenhENERGY_SUM_SIM:
- ret = doVector<double>(xd, part, i, fflags, &enerhist->ener_sum_sim, list);
+ case StateEnergyEntry::SumSim:
+ ret = doVector<double>(xd, *i, fflags, &enerhist->ener_sum_sim, list);
break;
- case eenhENERGY_NSUM_SIM:
- do_cpt_step_err(xd, eenh_names[i], &enerhist->nsum_sim, list);
+ case StateEnergyEntry::NumSumSim:
+ do_cpt_step_err(xd, enumValueToString(*i), &enerhist->nsum_sim, list);
break;
- case eenhENERGY_NSTEPS:
- do_cpt_step_err(xd, eenh_names[i], &enerhist->nsteps, list);
+ case StateEnergyEntry::NumSteps:
+ do_cpt_step_err(xd, enumValueToString(*i), &enerhist->nsteps, list);
break;
- case eenhENERGY_NSTEPS_SIM:
- do_cpt_step_err(xd, eenh_names[i], &enerhist->nsteps_sim, list);
+ case StateEnergyEntry::NumStepsSim:
+ do_cpt_step_err(xd, enumValueToString(*i), &enerhist->nsteps_sim, list);
break;
- case eenhENERGY_DELTA_H_NN:
+ case StateEnergyEntry::DeltaHNN:
{
int numDeltaH = 0;
if (!bRead && deltaH != nullptr)
{
numDeltaH = deltaH->dh.size();
}
- do_cpt_int_err(xd, eenh_names[i], &numDeltaH, list);
+ do_cpt_int_err(xd, enumValueToString(*i), &numDeltaH, list);
if (bRead)
{
if (deltaH == nullptr)
}
break;
}
- case eenhENERGY_DELTA_H_LIST:
+ case StateEnergyEntry::DeltaHList:
for (auto dh : deltaH->dh)
{
- ret = doVector<real>(xd, part, i, fflags, &dh, list);
+ ret = doVector<real>(xd, *i, fflags, &dh, list);
}
break;
- case eenhENERGY_DELTA_H_STARTTIME:
- ret = do_cpte_double(xd, part, i, fflags, &(deltaH->start_time), list);
+ case StateEnergyEntry::DeltaHStartTime:
+ ret = do_cpte_double(xd, *i, fflags, &(deltaH->start_time), list);
break;
- case eenhENERGY_DELTA_H_STARTLAMBDA:
- ret = do_cpte_double(xd, part, i, fflags, &(deltaH->start_lambda), list);
+ case StateEnergyEntry::DeltaHStartLambda:
+ ret = do_cpte_double(xd, *i, fflags, &(deltaH->start_lambda), list);
break;
default:
gmx_fatal(FARGS,
"Unknown energy history entry %d\n"
"You are probably reading a new checkpoint file with old code",
- i);
+ enumValueToBitMask(*i));
}
}
}
- if ((fflags & (1 << eenhENERGY_SUM)) && !(fflags & (1 << eenhENERGY_SUM_SIM)))
+ if ((fflags & enumValueToBitMask(StateEnergyEntry::Sum))
+ && !(fflags & enumValueToBitMask(StateEnergyEntry::SumSim)))
{
/* Assume we have an old file format and copy sum to sum_sim */
enerhist->ener_sum_sim = enerhist->ener_sum;
}
- if ((fflags & (1 << eenhENERGY_NSUM)) && !(fflags & (1 << eenhENERGY_NSTEPS)))
+ if ((fflags & enumValueToBitMask(StateEnergyEntry::NumSum))
+ && !(fflags & enumValueToBitMask(StateEnergyEntry::NumSteps)))
{
/* Assume we have an old file format and copy nsum to nsteps */
enerhist->nsteps = enerhist->nsum;
}
- if ((fflags & (1 << eenhENERGY_NSUM_SIM)) && !(fflags & (1 << eenhENERGY_NSTEPS_SIM)))
+ if ((fflags & enumValueToBitMask(StateEnergyEntry::NumSumSim))
+ && !(fflags & enumValueToBitMask(StateEnergyEntry::NumStepsSim)))
{
/* Assume we have an old file format and copy nsum to nsteps */
enerhist->nsteps_sim = enerhist->nsum_sim;
return ret;
}
-static int doCptPullCoordHist(XDR* xd, PullCoordinateHistory* pullCoordHist, const StatePart part, FILE* list)
+static int doCptPullCoordHist(XDR* xd, PullCoordinateHistory* pullCoordHist, FILE* list)
{
int ret = 0;
int flags = 0;
- flags |= ((1 << epullcoordh_VALUE_REF_SUM) | (1 << epullcoordh_VALUE_SUM)
- | (1 << epullcoordh_DR01_SUM) | (1 << epullcoordh_DR23_SUM)
- | (1 << epullcoordh_DR45_SUM) | (1 << epullcoordh_FSCAL_SUM));
+ flags |= (enumValueToBitMask(StatePullCoordEntry::ValueReferenceSum)
+ | enumValueToBitMask(StatePullCoordEntry::ValueSum)
+ | enumValueToBitMask(StatePullCoordEntry::DR01Sum)
+ | enumValueToBitMask(StatePullCoordEntry::DR23Sum)
+ | enumValueToBitMask(StatePullCoordEntry::DR45Sum)
+ | enumValueToBitMask(StatePullCoordEntry::FScalarSum));
- for (int i = 0; i < epullcoordh_NR && ret == 0; i++)
+ using StateFlags = gmx::EnumerationArray<StatePullCoordEntry, bool>;
+ for (auto i = StateFlags::keys().begin(); (i != StateFlags::keys().end() && ret == 0); i++)
{
- switch (i)
+ switch (*i)
{
- case epullcoordh_VALUE_REF_SUM:
- ret = do_cpte_double(xd, part, i, flags, &(pullCoordHist->valueRef), list);
+ case StatePullCoordEntry::ValueReferenceSum:
+ ret = do_cpte_double(xd, *i, flags, &(pullCoordHist->valueRef), list);
break;
- case epullcoordh_VALUE_SUM:
- ret = do_cpte_double(xd, part, i, flags, &(pullCoordHist->value), list);
+ case StatePullCoordEntry::ValueSum:
+ ret = do_cpte_double(xd, *i, flags, &(pullCoordHist->value), list);
break;
- case epullcoordh_DR01_SUM:
+ case StatePullCoordEntry::DR01Sum:
for (int j = 0; j < DIM && ret == 0; j++)
{
- ret = do_cpte_double(xd, part, i, flags, &(pullCoordHist->dr01[j]), list);
+ ret = do_cpte_double(xd, *i, flags, &(pullCoordHist->dr01[j]), list);
}
break;
- case epullcoordh_DR23_SUM:
+ case StatePullCoordEntry::DR23Sum:
for (int j = 0; j < DIM && ret == 0; j++)
{
- ret = do_cpte_double(xd, part, i, flags, &(pullCoordHist->dr23[j]), list);
+ ret = do_cpte_double(xd, *i, flags, &(pullCoordHist->dr23[j]), list);
}
break;
- case epullcoordh_DR45_SUM:
+ case StatePullCoordEntry::DR45Sum:
for (int j = 0; j < DIM && ret == 0; j++)
{
- ret = do_cpte_double(xd, part, i, flags, &(pullCoordHist->dr45[j]), list);
+ ret = do_cpte_double(xd, *i, flags, &(pullCoordHist->dr45[j]), list);
}
break;
- case epullcoordh_FSCAL_SUM:
- ret = do_cpte_double(xd, part, i, flags, &(pullCoordHist->scalarForce), list);
+ case StatePullCoordEntry::FScalarSum:
+ ret = do_cpte_double(xd, *i, flags, &(pullCoordHist->scalarForce), list);
break;
- case epullcoordh_DYNAX_SUM:
+ case StatePullCoordEntry::DynaxSum:
for (int j = 0; j < DIM && ret == 0; j++)
{
- ret = do_cpte_double(xd, part, i, flags, &(pullCoordHist->dynaX[j]), list);
+ ret = do_cpte_double(xd, *i, flags, &(pullCoordHist->dynaX[j]), list);
}
break;
+ default:
+ gmx_fatal(FARGS, "Unhandled StatePullCoordEntry enum value: %d", enumValueToBitMask(*i));
}
}
return ret;
}
-static int doCptPullGroupHist(XDR* xd, PullGroupHistory* pullGroupHist, const StatePart part, FILE* list)
+static int doCptPullGroupHist(XDR* xd, PullGroupHistory* pullGroupHist, FILE* list)
{
int ret = 0;
int flags = 0;
- flags |= ((1 << epullgrouph_X_SUM));
+ flags |= (enumValueToBitMask(StatePullGroupEntry::XSum));
- for (int i = 0; i < epullgrouph_NR; i++)
+ using StateFlags = gmx::EnumerationArray<StatePullGroupEntry, bool>;
+ for (auto i = StateFlags::keys().begin(); (i != StateFlags::keys().end() && ret == 0); i++)
{
- switch (i)
+ switch (*i)
{
- case epullgrouph_X_SUM:
+ case StatePullGroupEntry::XSum:
for (int j = 0; j < DIM && ret == 0; j++)
{
- ret = do_cpte_double(xd, part, i, flags, &(pullGroupHist->x[j]), list);
+ ret = do_cpte_double(xd, *i, flags, &(pullGroupHist->x[j]), list);
}
break;
+ default: gmx_fatal(FARGS, "Unhandled pull group state entry");
}
}
}
-static int doCptPullHist(XDR* xd, gmx_bool bRead, int fflags, PullHistory* pullHist, const StatePart part, FILE* list)
+static int doCptPullHist(XDR* xd, gmx_bool bRead, int fflags, PullHistory* pullHist, FILE* list)
{
int ret = 0;
int pullHistoryNumCoordinates = 0;
GMX_RELEASE_ASSERT(fflags == 0, "Without pull history, all flags should be off");
}
- for (int i = 0; (i < epullhNR && ret == 0); i++)
+ using StateFlags = gmx::EnumerationArray<StatePullEntry, bool>;
+ for (auto i = StateFlags::keys().begin(); (i != StateFlags::keys().end() && ret == 0); i++)
{
- if (fflags & (1 << i))
+ if (fflags & (1 << enumValueToBitMask(*i)))
{
- switch (i)
+ switch (*i)
{
- case epullhPULL_NUMCOORDINATES:
- ret = do_cpte_int(xd, part, i, fflags, &pullHistoryNumCoordinates, list);
+ case StatePullEntry::NumCoordinates:
+ ret = do_cpte_int(xd, *i, fflags, &pullHistoryNumCoordinates, list);
break;
- case epullhPULL_NUMGROUPS:
- do_cpt_int_err(xd, eenh_names[i], &pullHistoryNumGroups, list);
+ case StatePullEntry::NumGroups:
+ do_cpt_int_err(xd, enumValueToString(*i), &pullHistoryNumGroups, list);
break;
- case epullhPULL_NUMVALUESINXSUM:
- do_cpt_int_err(xd, eenh_names[i], &pullHist->numValuesInXSum, list);
+ case StatePullEntry::NumValuesInXSum:
+ do_cpt_int_err(xd, enumValueToString(*i), &pullHist->numValuesInXSum, list);
break;
- case epullhPULL_NUMVALUESINFSUM:
- do_cpt_int_err(xd, eenh_names[i], &pullHist->numValuesInFSum, list);
+ case StatePullEntry::NumValuesInFSum:
+ do_cpt_int_err(xd, enumValueToString(*i), &pullHist->numValuesInFSum, list);
break;
default:
gmx_fatal(FARGS,
"Unknown pull history entry %d\n"
"You are probably reading a new checkpoint file with old code",
- i);
+ enumValueToBitMask(*i));
}
}
}
{
for (size_t i = 0; i < pullHist->pullCoordinateSums.size() && ret == 0; i++)
{
- ret = doCptPullCoordHist(xd, &(pullHist->pullCoordinateSums[i]), part, list);
+ ret = doCptPullCoordHist(xd, &(pullHist->pullCoordinateSums[i]), list);
}
for (size_t i = 0; i < pullHist->pullGroupSums.size() && ret == 0; i++)
{
- ret = doCptPullGroupHist(xd, &(pullHist->pullGroupSums[i]), part, list);
+ ret = doCptPullGroupHist(xd, &(pullHist->pullGroupSums[i]), list);
}
}
}
df_history_t* dfhist = *dfhistPtr;
- const StatePart part = StatePart::freeEnergyHistory;
- for (int i = 0; (i < edfhNR && ret == 0); i++)
+ using StateFlags = gmx::EnumerationArray<StateFepEntry, bool>;
+ for (auto i = StateFlags::keys().begin(); (i != StateFlags::keys().end() && ret == 0); i++)
{
- if (fflags & (1 << i))
+ if (fflags & enumValueToBitMask(*i))
{
- switch (i)
+ switch (*i)
{
- case edfhBEQUIL:
- ret = do_cpte_bool(xd, part, i, fflags, &dfhist->bEquil, list);
+ case StateFepEntry::IsEquilibrated:
+ ret = do_cpte_bool(xd, *i, fflags, &dfhist->bEquil, list);
break;
- case edfhNATLAMBDA:
- ret = do_cpte_ints(xd, part, i, fflags, nlambda, &dfhist->n_at_lam, list);
+ case StateFepEntry::NumAtLambda:
+ ret = do_cpte_ints(xd, *i, fflags, nlambda, &dfhist->n_at_lam, list);
break;
- case edfhWLHISTO:
- ret = do_cpte_reals(xd, part, i, fflags, nlambda, &dfhist->wl_histo, list);
+ case StateFepEntry::WangLandauHistogram:
+ ret = do_cpte_reals(xd, *i, fflags, nlambda, &dfhist->wl_histo, list);
break;
- case edfhWLDELTA:
- ret = do_cpte_real(xd, part, i, fflags, &dfhist->wl_delta, list);
+ case StateFepEntry::WangLandauDelta:
+ ret = do_cpte_real(xd, *i, fflags, &dfhist->wl_delta, list);
break;
- case edfhSUMWEIGHTS:
- ret = do_cpte_reals(xd, part, i, fflags, nlambda, &dfhist->sum_weights, list);
+ case StateFepEntry::SumWeights:
+ ret = do_cpte_reals(xd, *i, fflags, nlambda, &dfhist->sum_weights, list);
break;
- case edfhSUMDG:
- ret = do_cpte_reals(xd, part, i, fflags, nlambda, &dfhist->sum_dg, list);
+ case StateFepEntry::SumDG:
+ ret = do_cpte_reals(xd, *i, fflags, nlambda, &dfhist->sum_dg, list);
break;
- case edfhSUMMINVAR:
- ret = do_cpte_reals(xd, part, i, fflags, nlambda, &dfhist->sum_minvar, list);
+ case StateFepEntry::SumMinVar:
+ ret = do_cpte_reals(xd, *i, fflags, nlambda, &dfhist->sum_minvar, list);
break;
- case edfhSUMVAR:
- ret = do_cpte_reals(xd, part, i, fflags, nlambda, &dfhist->sum_variance, list);
+ case StateFepEntry::SumVar:
+ ret = do_cpte_reals(xd, *i, fflags, nlambda, &dfhist->sum_variance, list);
break;
- case edfhACCUMP:
- ret = do_cpte_nmatrix(xd, part, i, fflags, nlambda, dfhist->accum_p, list);
+ case StateFepEntry::Accump:
+ ret = do_cpte_nmatrix(xd, *i, fflags, nlambda, dfhist->accum_p, list);
break;
- case edfhACCUMM:
- ret = do_cpte_nmatrix(xd, part, i, fflags, nlambda, dfhist->accum_m, list);
+ case StateFepEntry::Accumm:
+ ret = do_cpte_nmatrix(xd, *i, fflags, nlambda, dfhist->accum_m, list);
break;
- case edfhACCUMP2:
- ret = do_cpte_nmatrix(xd, part, i, fflags, nlambda, dfhist->accum_p2, list);
+ case StateFepEntry::Accump2:
+ ret = do_cpte_nmatrix(xd, *i, fflags, nlambda, dfhist->accum_p2, list);
break;
- case edfhACCUMM2:
- ret = do_cpte_nmatrix(xd, part, i, fflags, nlambda, dfhist->accum_m2, list);
+ case StateFepEntry::Accumm2:
+ ret = do_cpte_nmatrix(xd, *i, fflags, nlambda, dfhist->accum_m2, list);
break;
- case edfhTIJ:
- ret = do_cpte_nmatrix(xd, part, i, fflags, nlambda, dfhist->Tij, list);
+ case StateFepEntry::Tij:
+ ret = do_cpte_nmatrix(xd, *i, fflags, nlambda, dfhist->Tij, list);
break;
- case edfhTIJEMP:
- ret = do_cpte_nmatrix(xd, part, i, fflags, nlambda, dfhist->Tij_empirical, list);
+ case StateFepEntry::TijEmp:
+ ret = do_cpte_nmatrix(xd, *i, fflags, nlambda, dfhist->Tij_empirical, list);
break;
default:
gmx_fatal(FARGS,
"Unknown df history entry %d\n"
"You are probably reading a new checkpoint file with old code",
- i);
+ enumValueToBitMask(*i));
}
}
}
gmx_unused int fflags,
gmx::CorrelationGridHistory* corrGrid,
FILE* list,
- int eawhh)
+ StateAwhEntry eawhh)
{
int ret = 0;
- do_cpt_int_err(xd, eawhh_names[eawhh], &(corrGrid->numCorrelationTensors), list);
- do_cpt_int_err(xd, eawhh_names[eawhh], &(corrGrid->tensorSize), list);
- do_cpt_int_err(xd, eawhh_names[eawhh], &(corrGrid->blockDataListSize), list);
+ do_cpt_int_err(xd, enumValueToString(eawhh), &(corrGrid->numCorrelationTensors), list);
+ do_cpt_int_err(xd, enumValueToString(eawhh), &(corrGrid->tensorSize), list);
+ do_cpt_int_err(xd, enumValueToString(eawhh), &(corrGrid->blockDataListSize), list);
if (bRead)
{
- initCorrelationGridHistory(corrGrid, corrGrid->numCorrelationTensors, corrGrid->tensorSize,
- corrGrid->blockDataListSize);
+ initCorrelationGridHistory(
+ corrGrid, corrGrid->numCorrelationTensors, corrGrid->tensorSize, corrGrid->blockDataListSize);
}
for (gmx::CorrelationBlockDataHistory& blockData : corrGrid->blockDataBuffer)
{
- do_cpt_double_err(xd, eawhh_names[eawhh], &(blockData.blockSumWeight), list);
- do_cpt_double_err(xd, eawhh_names[eawhh], &(blockData.blockSumSquareWeight), list);
- do_cpt_double_err(xd, eawhh_names[eawhh], &(blockData.blockSumWeightX), list);
- do_cpt_double_err(xd, eawhh_names[eawhh], &(blockData.blockSumWeightY), list);
- do_cpt_double_err(xd, eawhh_names[eawhh], &(blockData.sumOverBlocksSquareBlockWeight), list);
- do_cpt_double_err(xd, eawhh_names[eawhh], &(blockData.sumOverBlocksBlockSquareWeight), list);
- do_cpt_double_err(xd, eawhh_names[eawhh], &(blockData.sumOverBlocksBlockWeightBlockWeightX), list);
- do_cpt_double_err(xd, eawhh_names[eawhh], &(blockData.sumOverBlocksBlockWeightBlockWeightY), list);
- do_cpt_double_err(xd, eawhh_names[eawhh], &(blockData.blockLength), list);
- do_cpt_int_err(xd, eawhh_names[eawhh], &(blockData.previousBlockIndex), list);
- do_cpt_double_err(xd, eawhh_names[eawhh], &(blockData.correlationIntegral), list);
+ do_cpt_double_err(xd, enumValueToString(eawhh), &(blockData.blockSumWeight), list);
+ do_cpt_double_err(xd, enumValueToString(eawhh), &(blockData.blockSumSquareWeight), list);
+ do_cpt_double_err(xd, enumValueToString(eawhh), &(blockData.blockSumWeightX), list);
+ do_cpt_double_err(xd, enumValueToString(eawhh), &(blockData.blockSumWeightY), list);
+ do_cpt_double_err(xd, enumValueToString(eawhh), &(blockData.sumOverBlocksSquareBlockWeight), list);
+ do_cpt_double_err(xd, enumValueToString(eawhh), &(blockData.sumOverBlocksBlockSquareWeight), list);
+ do_cpt_double_err(
+ xd, enumValueToString(eawhh), &(blockData.sumOverBlocksBlockWeightBlockWeightX), list);
+ do_cpt_double_err(
+ xd, enumValueToString(eawhh), &(blockData.sumOverBlocksBlockWeightBlockWeightY), list);
+ do_cpt_double_err(xd, enumValueToString(eawhh), &(blockData.blockLength), list);
+ do_cpt_int_err(xd, enumValueToString(eawhh), &(blockData.previousBlockIndex), list);
+ do_cpt_double_err(xd, enumValueToString(eawhh), &(blockData.correlationIntegral), list);
}
return ret;
int ret = 0;
gmx::AwhBiasStateHistory* state = &biasHistory->state;
- for (int i = 0; (i < eawhhNR && ret == 0); i++)
+ using StateFlags = gmx::EnumerationArray<StateAwhEntry, bool>;
+ for (auto i = StateFlags::keys().begin(); (i != StateFlags::keys().end() && ret == 0); i++)
{
- if (fflags & (1 << i))
+ if (fflags & enumValueToBitMask(*i))
{
- switch (i)
+ switch (*i)
{
- case eawhhIN_INITIAL:
- do_cpt_bool_err(xd, eawhh_names[i], &state->in_initial, list);
+ case StateAwhEntry::InInitial:
+ do_cpt_bool_err(xd, enumValueToString(*i), &state->in_initial, list);
break;
- case eawhhEQUILIBRATEHISTOGRAM:
- do_cpt_bool_err(xd, eawhh_names[i], &state->equilibrateHistogram, list);
+ case StateAwhEntry::EquilibrateHistogram:
+ do_cpt_bool_err(xd, enumValueToString(*i), &state->equilibrateHistogram, list);
break;
- case eawhhHISTSIZE:
- do_cpt_double_err(xd, eawhh_names[i], &state->histSize, list);
+ case StateAwhEntry::HistogramSize:
+ do_cpt_double_err(xd, enumValueToString(*i), &state->histSize, list);
break;
- case eawhhNPOINTS:
+ case StateAwhEntry::NumPoints:
{
int numPoints;
if (!bRead)
{
numPoints = biasHistory->pointState.size();
}
- do_cpt_int_err(xd, eawhh_names[i], &numPoints, list);
+ do_cpt_int_err(xd, enumValueToString(*i), &numPoints, list);
if (bRead)
{
biasHistory->pointState.resize(numPoints);
}
}
break;
- case eawhhCOORDPOINT:
+ case StateAwhEntry::CoordPoint:
for (auto& psh : biasHistory->pointState)
{
- do_cpt_double_err(xd, eawhh_names[i], &psh.target, list);
- do_cpt_double_err(xd, eawhh_names[i], &psh.free_energy, list);
- do_cpt_double_err(xd, eawhh_names[i], &psh.bias, list);
- do_cpt_double_err(xd, eawhh_names[i], &psh.weightsum_iteration, list);
- do_cpt_double_err(xd, eawhh_names[i], &psh.weightsum_covering, list);
- do_cpt_double_err(xd, eawhh_names[i], &psh.weightsum_tot, list);
- do_cpt_double_err(xd, eawhh_names[i], &psh.weightsum_ref, list);
- do_cpt_step_err(xd, eawhh_names[i], &psh.last_update_index, list);
- do_cpt_double_err(xd, eawhh_names[i], &psh.log_pmfsum, list);
- do_cpt_double_err(xd, eawhh_names[i], &psh.visits_iteration, list);
- do_cpt_double_err(xd, eawhh_names[i], &psh.visits_tot, list);
+ do_cpt_double_err(xd, enumValueToString(*i), &psh.target, list);
+ do_cpt_double_err(xd, enumValueToString(*i), &psh.free_energy, list);
+ do_cpt_double_err(xd, enumValueToString(*i), &psh.bias, list);
+ do_cpt_double_err(xd, enumValueToString(*i), &psh.weightsum_iteration, list);
+ do_cpt_double_err(xd, enumValueToString(*i), &psh.weightsum_covering, list);
+ do_cpt_double_err(xd, enumValueToString(*i), &psh.weightsum_tot, list);
+ do_cpt_double_err(xd, enumValueToString(*i), &psh.weightsum_ref, list);
+ do_cpt_step_err(xd, enumValueToString(*i), &psh.last_update_index, list);
+ do_cpt_double_err(xd, enumValueToString(*i), &psh.log_pmfsum, list);
+ do_cpt_double_err(xd, enumValueToString(*i), &psh.visits_iteration, list);
+ do_cpt_double_err(xd, enumValueToString(*i), &psh.visits_tot, list);
}
break;
- case eawhhUMBRELLAGRIDPOINT:
- do_cpt_int_err(xd, eawhh_names[i], &(state->umbrellaGridpoint), list);
+ case StateAwhEntry::UmbrellaGridPoint:
+ do_cpt_int_err(xd, enumValueToString(*i), &(state->umbrellaGridpoint), list);
break;
- case eawhhUPDATELIST:
- do_cpt_int_err(xd, eawhh_names[i], &(state->origin_index_updatelist), list);
- do_cpt_int_err(xd, eawhh_names[i], &(state->end_index_updatelist), list);
+ case StateAwhEntry::UpdateList:
+ do_cpt_int_err(xd, enumValueToString(*i), &(state->origin_index_updatelist), list);
+ do_cpt_int_err(xd, enumValueToString(*i), &(state->end_index_updatelist), list);
break;
- case eawhhLOGSCALEDSAMPLEWEIGHT:
- do_cpt_double_err(xd, eawhh_names[i], &(state->logScaledSampleWeight), list);
- do_cpt_double_err(xd, eawhh_names[i], &(state->maxLogScaledSampleWeight), list);
+ case StateAwhEntry::LogScaledSampleWeight:
+ do_cpt_double_err(xd, enumValueToString(*i), &(state->logScaledSampleWeight), list);
+ do_cpt_double_err(xd, enumValueToString(*i), &(state->maxLogScaledSampleWeight), list);
break;
- case eawhhNUMUPDATES:
- do_cpt_step_err(xd, eawhh_names[i], &(state->numUpdates), list);
+ case StateAwhEntry::NumUpdates:
+ do_cpt_step_err(xd, enumValueToString(*i), &(state->numUpdates), list);
break;
- case eawhhFORCECORRELATIONGRID:
- ret = do_cpt_correlation_grid(xd, bRead, fflags,
- &biasHistory->forceCorrelationGrid, list, i);
+ case StateAwhEntry::ForceCorrelationGrid:
+ ret = do_cpt_correlation_grid(
+ xd, bRead, fflags, &biasHistory->forceCorrelationGrid, list, *i);
break;
- default: gmx_fatal(FARGS, "Unknown awh history entry %d\n", i);
+ default: gmx_fatal(FARGS, "Unknown awh history entry %d\n", enumValueToBitMask(*i));
}
}
}
return ret;
}
-static void do_cpt_mdmodules(int fileVersion,
- t_fileio* checkpointFileHandle,
- const gmx::MdModulesNotifier& mdModulesNotifier,
- FILE* outputFile)
+static void do_cpt_mdmodules(int fileVersion,
+ t_fileio* checkpointFileHandle,
+ const gmx::MDModulesNotifiers& mdModulesNotifiers,
+ FILE* outputFile)
{
- if (fileVersion >= cptv_MdModules)
+ if (fileVersion >= cptv_MDModules)
{
gmx::FileIOXdrSerializer serializer(checkpointFileHandle);
gmx::KeyValueTreeObject mdModuleCheckpointParameterTree =
gmx::TextWriter textWriter(outputFile);
gmx::dumpKeyValueTree(&textWriter, mdModuleCheckpointParameterTree);
}
- gmx::MdModulesCheckpointReadingDataOnMaster mdModuleCheckpointReadingDataOnMaster = {
+ gmx::MDModulesCheckpointReadingDataOnMaster mdModuleCheckpointReadingDataOnMaster = {
mdModuleCheckpointParameterTree, fileVersion
};
- mdModulesNotifier.checkpointingNotifications_.notify(mdModuleCheckpointReadingDataOnMaster);
+ mdModulesNotifiers.checkpointingNotifier_.notify(mdModuleCheckpointReadingDataOnMaster);
}
}
{
return -1;
}
- if (do_cpt_u_chars(xd, "file_checksum", outputfile.checksum.size(),
- outputfile.checksum.data(), list)
+ if (do_cpt_u_chars(xd, "file_checksum", outputfile.checksum.size(), outputfile.checksum.data(), list)
!= 0)
{
return -1;
void write_checkpoint_data(t_fileio* fp,
CheckpointHeaderContents headerContents,
gmx_bool bExpanded,
- int elamstats,
+ LambdaWeightCalculation elamstats,
t_state* state,
ObservablesHistory* observablesHistory,
- const gmx::MdModulesNotifier& mdModulesNotifier,
+ const gmx::MDModulesNotifiers& mdModulesNotifiers,
std::vector<gmx_file_position_t>* outputfiles,
gmx::WriteCheckpointDataHolder* modularSimulatorCheckpointData)
{
headerContents.flags_eks = 0;
if (state->ekinstate.bUpToDate)
{
- headerContents.flags_eks = ((1 << eeksEKIN_N) | (1 << eeksEKINH) | (1 << eeksEKINF)
- | (1 << eeksEKINO) | (1 << eeksEKINSCALEF) | (1 << eeksEKINSCALEH)
- | (1 << eeksVSCALE) | (1 << eeksDEKINDL) | (1 << eeksMVCOS));
+ headerContents.flags_eks = (enumValueToBitMask(StateKineticEntry::EkinNumber)
+ | enumValueToBitMask(StateKineticEntry::EkinHalfStep)
+ | enumValueToBitMask(StateKineticEntry::EkinFullStep)
+ | enumValueToBitMask(StateKineticEntry::EkinHalfStepOld)
+ | enumValueToBitMask(StateKineticEntry::EkinNoseHooverScaleFullStep)
+ | enumValueToBitMask(StateKineticEntry::EkinNoseHooverScaleHalfStep)
+ | enumValueToBitMask(StateKineticEntry::VelocityScale)
+ | enumValueToBitMask(StateKineticEntry::DEkinDLambda)
+ | enumValueToBitMask(StateKineticEntry::Mvcos));
}
headerContents.isModularSimulatorCheckpoint = !modularSimulatorCheckpointData->empty();
headerContents.flags_enh = 0;
if (enerhist != nullptr && (enerhist->nsum > 0 || enerhist->nsum_sim > 0))
{
- headerContents.flags_enh |=
- (1 << eenhENERGY_N) | (1 << eenhENERGY_NSTEPS) | (1 << eenhENERGY_NSTEPS_SIM);
+ headerContents.flags_enh |= enumValueToBitMask(StateEnergyEntry::N)
+ | enumValueToBitMask(StateEnergyEntry::NumSteps)
+ | enumValueToBitMask(StateEnergyEntry::NumStepsSim);
if (enerhist->nsum > 0)
{
- headerContents.flags_enh |=
- ((1 << eenhENERGY_AVER) | (1 << eenhENERGY_SUM) | (1 << eenhENERGY_NSUM));
+ headerContents.flags_enh |= (enumValueToBitMask(StateEnergyEntry::Aver)
+ | enumValueToBitMask(StateEnergyEntry::Sum)
+ | enumValueToBitMask(StateEnergyEntry::NumSum));
}
if (enerhist->nsum_sim > 0)
{
- headerContents.flags_enh |= ((1 << eenhENERGY_SUM_SIM) | (1 << eenhENERGY_NSUM_SIM));
+ headerContents.flags_enh |= (enumValueToBitMask(StateEnergyEntry::SumSim)
+ | enumValueToBitMask(StateEnergyEntry::NumSumSim));
}
if (enerhist->deltaHForeignLambdas != nullptr)
{
- headerContents.flags_enh |=
- ((1 << eenhENERGY_DELTA_H_NN) | (1 << eenhENERGY_DELTA_H_LIST)
- | (1 << eenhENERGY_DELTA_H_STARTTIME) | (1 << eenhENERGY_DELTA_H_STARTLAMBDA));
+ headerContents.flags_enh |= (enumValueToBitMask(StateEnergyEntry::DeltaHNN)
+ | enumValueToBitMask(StateEnergyEntry::DeltaHList)
+ | enumValueToBitMask(StateEnergyEntry::DeltaHStartTime)
+ | enumValueToBitMask(StateEnergyEntry::DeltaHStartLambda));
}
}
headerContents.flagsPullHistory = 0;
if (pullHist != nullptr && (pullHist->numValuesInXSum > 0 || pullHist->numValuesInFSum > 0))
{
- headerContents.flagsPullHistory |= (1 << epullhPULL_NUMCOORDINATES);
- headerContents.flagsPullHistory |= ((1 << epullhPULL_NUMGROUPS) | (1 << epullhPULL_NUMVALUESINXSUM)
- | (1 << epullhPULL_NUMVALUESINFSUM));
+ headerContents.flagsPullHistory |= enumValueToBitMask(StatePullEntry::NumCoordinates);
+ headerContents.flagsPullHistory |= (enumValueToBitMask(StatePullEntry::NumGroups)
+ | enumValueToBitMask(StatePullEntry::NumValuesInXSum)
+ | enumValueToBitMask(StatePullEntry::NumValuesInFSum));
}
headerContents.flags_dfh = 0;
if (bExpanded)
{
- headerContents.flags_dfh = ((1 << edfhBEQUIL) | (1 << edfhNATLAMBDA) | (1 << edfhSUMWEIGHTS)
- | (1 << edfhSUMDG) | (1 << edfhTIJ) | (1 << edfhTIJEMP));
+ headerContents.flags_dfh =
+ (enumValueToBitMask(StateFepEntry::IsEquilibrated)
+ | enumValueToBitMask(StateFepEntry::NumAtLambda)
+ | enumValueToBitMask(StateFepEntry::SumWeights) | enumValueToBitMask(StateFepEntry::SumDG)
+ | enumValueToBitMask(StateFepEntry::Tij) | enumValueToBitMask(StateFepEntry::TijEmp));
if (EWL(elamstats))
{
- headerContents.flags_dfh |= ((1 << edfhWLDELTA) | (1 << edfhWLHISTO));
+ headerContents.flags_dfh |= (enumValueToBitMask(StateFepEntry::WangLandauDelta)
+ | enumValueToBitMask(StateFepEntry::WangLandauHistogram));
}
- if ((elamstats == elamstatsMINVAR) || (elamstats == elamstatsBARKER)
- || (elamstats == elamstatsMETROPOLIS))
+ if ((elamstats == LambdaWeightCalculation::Minvar) || (elamstats == LambdaWeightCalculation::Barker)
+ || (elamstats == LambdaWeightCalculation::Metropolis))
{
- headerContents.flags_dfh |= ((1 << edfhACCUMP) | (1 << edfhACCUMM) | (1 << edfhACCUMP2)
- | (1 << edfhACCUMM2) | (1 << edfhSUMMINVAR) | (1 << edfhSUMVAR));
+ headerContents.flags_dfh |= (enumValueToBitMask(StateFepEntry::Accump)
+ | enumValueToBitMask(StateFepEntry::Accumm)
+ | enumValueToBitMask(StateFepEntry::Accump2)
+ | enumValueToBitMask(StateFepEntry::Accumm2)
+ | enumValueToBitMask(StateFepEntry::SumMinVar)
+ | enumValueToBitMask(StateFepEntry::SumVar));
}
}
headerContents.flags_awhh = 0;
if (state->awhHistory != nullptr && !state->awhHistory->bias.empty())
{
- headerContents.flags_awhh |=
- ((1 << eawhhIN_INITIAL) | (1 << eawhhEQUILIBRATEHISTOGRAM) | (1 << eawhhHISTSIZE)
- | (1 << eawhhNPOINTS) | (1 << eawhhCOORDPOINT) | (1 << eawhhUMBRELLAGRIDPOINT)
- | (1 << eawhhUPDATELIST) | (1 << eawhhLOGSCALEDSAMPLEWEIGHT)
- | (1 << eawhhNUMUPDATES) | (1 << eawhhFORCECORRELATIONGRID));
+ headerContents.flags_awhh |= (enumValueToBitMask(StateAwhEntry::InInitial)
+ | enumValueToBitMask(StateAwhEntry::EquilibrateHistogram)
+ | enumValueToBitMask(StateAwhEntry::HistogramSize)
+ | enumValueToBitMask(StateAwhEntry::NumPoints)
+ | enumValueToBitMask(StateAwhEntry::CoordPoint)
+ | enumValueToBitMask(StateAwhEntry::UmbrellaGridPoint)
+ | enumValueToBitMask(StateAwhEntry::UpdateList)
+ | enumValueToBitMask(StateAwhEntry::LogScaledSampleWeight)
+ | enumValueToBitMask(StateAwhEntry::NumUpdates)
+ | enumValueToBitMask(StateAwhEntry::ForceCorrelationGrid));
}
do_cpt_header(gmx_fio_getxdr(fp), FALSE, nullptr, &headerContents);
if ((do_cpt_state(gmx_fio_getxdr(fp), state->flags, state, nullptr) < 0)
|| (do_cpt_ekinstate(gmx_fio_getxdr(fp), headerContents.flags_eks, &state->ekinstate, nullptr) < 0)
|| (do_cpt_enerhist(gmx_fio_getxdr(fp), FALSE, headerContents.flags_enh, enerhist, nullptr) < 0)
- || (doCptPullHist(gmx_fio_getxdr(fp), FALSE, headerContents.flagsPullHistory, pullHist,
- StatePart::pullHistory, nullptr)
- < 0)
- || (do_cpt_df_hist(gmx_fio_getxdr(fp), headerContents.flags_dfh, headerContents.nlambda,
- &state->dfhist, nullptr)
+ || (doCptPullHist(gmx_fio_getxdr(fp), FALSE, headerContents.flagsPullHistory, pullHist, nullptr) < 0)
+ || (do_cpt_df_hist(gmx_fio_getxdr(fp), headerContents.flags_dfh, headerContents.nlambda, &state->dfhist, nullptr)
< 0)
- || (do_cpt_EDstate(gmx_fio_getxdr(fp), FALSE, headerContents.nED,
- observablesHistory->edsamHistory.get(), nullptr)
+ || (do_cpt_EDstate(
+ gmx_fio_getxdr(fp), FALSE, headerContents.nED, observablesHistory->edsamHistory.get(), nullptr)
< 0)
|| (do_cpt_awh(gmx_fio_getxdr(fp), FALSE, headerContents.flags_awhh, state->awhHistory.get(), nullptr) < 0)
- || (do_cpt_swapstate(gmx_fio_getxdr(fp), FALSE, headerContents.eSwapCoords,
- observablesHistory->swapHistory.get(), nullptr)
+ || (do_cpt_swapstate(gmx_fio_getxdr(fp),
+ FALSE,
+ headerContents.eSwapCoords,
+ observablesHistory->swapHistory.get(),
+ nullptr)
< 0)
|| (do_cpt_files(gmx_fio_getxdr(fp), FALSE, outputfiles, nullptr, headerContents.file_version) < 0))
{
gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
}
- // Checkpointing MdModules
+ // Checkpointing MDModules
{
gmx::KeyValueTreeBuilder builder;
- gmx::MdModulesWriteCheckpointData mdModulesWriteCheckpoint = { builder.rootObject(),
+ gmx::MDModulesWriteCheckpointData mdModulesWriteCheckpoint = { builder.rootObject(),
headerContents.file_version };
- mdModulesNotifier.checkpointingNotifications_.notify(mdModulesWriteCheckpoint);
+ mdModulesNotifiers.checkpointingNotifier_.notify(mdModulesWriteCheckpoint);
auto tree = builder.build();
gmx::FileIOXdrSerializer serializer(fp);
gmx::serializeKeyValueTree(tree, &serializer);
if (reproducibilityRequested)
{
- check_string(fplog, "Program name", gmx::getProgramContext().fullBinaryPath(),
- headerContents.fprog, &mm);
+ check_string(
+ fplog, "Program name", gmx::getProgramContext().fullBinaryPath(), headerContents.fprog, &mm);
check_int(fplog, "#ranks", cr->nnodes, headerContents.nnodes, &mm);
}
t_fileio* logfio,
const t_commrec* cr,
const ivec dd_nc,
- int eIntegrator,
+ IntegrationAlgorithm eIntegrator,
int* init_fep_state,
CheckpointHeaderContents* headerContents,
t_state* state,
ObservablesHistory* observablesHistory,
gmx_bool reproducibilityRequested,
- const gmx::MdModulesNotifier& mdModulesNotifier,
+ const gmx::MDModulesNotifiers& mdModulesNotifiers,
gmx::ReadCheckpointDataHolder* modularSimulatorCheckpointData,
bool useModularSimulator)
{
gmx_fatal(FARGS,
"Checkpoint file is for a system of %d atoms, while the current system consists "
"of %d atoms",
- headerContents->natoms, state->natoms);
+ headerContents->natoms,
+ state->natoms);
}
if (headerContents->ngtc != state->ngtc)
{
gmx_fatal(FARGS,
"Checkpoint file is for a system of %d T-coupling groups, while the current "
"system consists of %d T-coupling groups",
- headerContents->ngtc, state->ngtc);
+ headerContents->ngtc,
+ state->ngtc);
}
if (headerContents->nnhpres != state->nnhpres)
{
gmx_fatal(FARGS,
"Checkpoint file is for a system of %d NH-pressure-coupling variables, while the "
"current system consists of %d NH-pressure-coupling variables",
- headerContents->nnhpres, state->nnhpres);
+ headerContents->nnhpres,
+ state->nnhpres);
}
int nlambdaHistory = (state->dfhist ? state->dfhist->nlambda : 0);
gmx_fatal(FARGS,
"Checkpoint file is for a system with %d lambda states, while the current system "
"consists of %d lambda states",
- headerContents->nlambda, nlambdaHistory);
+ headerContents->nlambda,
+ nlambdaHistory);
}
- init_gtc_state(state, state->ngtc, state->nnhpres,
+ init_gtc_state(state,
+ state->ngtc,
+ state->nnhpres,
headerContents->nhchainlength); /* need to keep this here to keep the tpr format working */
/* write over whatever was read; we use the number of Nose-Hoover chains from the checkpoint */
{
cp_error();
}
- state->ekinstate.hasReadEkinState = (((headerContents->flags_eks & (1 << eeksEKINH)) != 0)
- || ((headerContents->flags_eks & (1 << eeksEKINF)) != 0)
- || ((headerContents->flags_eks & (1 << eeksEKINO)) != 0)
- || (((headerContents->flags_eks & (1 << eeksEKINSCALEF))
- | (headerContents->flags_eks & (1 << eeksEKINSCALEH))
- | (headerContents->flags_eks & (1 << eeksVSCALE)))
- != 0));
+ state->ekinstate.hasReadEkinState =
+ (((headerContents->flags_eks & enumValueToBitMask(StateKineticEntry::EkinHalfStep)) != 0)
+ || ((headerContents->flags_eks & enumValueToBitMask(StateKineticEntry::EkinFullStep)) != 0)
+ || ((headerContents->flags_eks & enumValueToBitMask(StateKineticEntry::EkinHalfStepOld)) != 0)
+ || (((headerContents->flags_eks & enumValueToBitMask(StateKineticEntry::EkinNoseHooverScaleFullStep))
+ | (headerContents->flags_eks & enumValueToBitMask(StateKineticEntry::EkinNoseHooverScaleHalfStep))
+ | (headerContents->flags_eks & enumValueToBitMask(StateKineticEntry::VelocityScale)))
+ != 0));
if (headerContents->flags_enh && observablesHistory->energyHistory == nullptr)
{
observablesHistory->energyHistory = std::make_unique<energyhistory_t>();
}
- ret = do_cpt_enerhist(gmx_fio_getxdr(fp), TRUE, headerContents->flags_enh,
- observablesHistory->energyHistory.get(), nullptr);
+ ret = do_cpt_enerhist(
+ gmx_fio_getxdr(fp), TRUE, headerContents->flags_enh, observablesHistory->energyHistory.get(), nullptr);
if (ret)
{
cp_error();
{
observablesHistory->pullHistory = std::make_unique<PullHistory>();
}
- ret = doCptPullHist(gmx_fio_getxdr(fp), TRUE, headerContents->flagsPullHistory,
- observablesHistory->pullHistory.get(), StatePart::pullHistory, nullptr);
+ ret = doCptPullHist(gmx_fio_getxdr(fp),
+ TRUE,
+ headerContents->flagsPullHistory,
+ observablesHistory->pullHistory.get(),
+ nullptr);
if (ret)
{
cp_error();
"Continuing from checkpoint files written before GROMACS 4.5 is not supported");
}
- ret = do_cpt_df_hist(gmx_fio_getxdr(fp), headerContents->flags_dfh, headerContents->nlambda,
- &state->dfhist, nullptr);
+ ret = do_cpt_df_hist(
+ gmx_fio_getxdr(fp), headerContents->flags_dfh, headerContents->nlambda, &state->dfhist, nullptr);
if (ret)
{
cp_error();
{
observablesHistory->edsamHistory = std::make_unique<edsamhistory_t>(edsamhistory_t{});
}
- ret = do_cpt_EDstate(gmx_fio_getxdr(fp), TRUE, headerContents->nED,
- observablesHistory->edsamHistory.get(), nullptr);
+ ret = do_cpt_EDstate(
+ gmx_fio_getxdr(fp), TRUE, headerContents->nED, observablesHistory->edsamHistory.get(), nullptr);
if (ret)
{
cp_error();
cp_error();
}
- if (headerContents->eSwapCoords != eswapNO && observablesHistory->swapHistory == nullptr)
+ if (headerContents->eSwapCoords != SwapType::No && observablesHistory->swapHistory == nullptr)
{
observablesHistory->swapHistory = std::make_unique<swaphistory_t>(swaphistory_t{});
}
- ret = do_cpt_swapstate(gmx_fio_getxdr(fp), TRUE, headerContents->eSwapCoords,
- observablesHistory->swapHistory.get(), nullptr);
+ ret = do_cpt_swapstate(
+ gmx_fio_getxdr(fp), TRUE, headerContents->eSwapCoords, observablesHistory->swapHistory.get(), nullptr);
if (ret)
{
cp_error();
{
cp_error();
}
- do_cpt_mdmodules(headerContents->file_version, fp, mdModulesNotifier, nullptr);
+ do_cpt_mdmodules(headerContents->file_version, fp, mdModulesNotifiers, nullptr);
if (headerContents->file_version >= cptv_ModularSimulator)
{
gmx::FileIOXdrSerializer serializer(fp);
t_state* state,
ObservablesHistory* observablesHistory,
gmx_bool reproducibilityRequested,
- const gmx::MdModulesNotifier& mdModulesNotifier,
+ const gmx::MDModulesNotifiers& mdModulesNotifiers,
gmx::ReadCheckpointDataHolder* modularSimulatorCheckpointData,
bool useModularSimulator)
{
if (SIMMASTER(cr))
{
/* Read the state from the checkpoint file */
- read_checkpoint(fn, logfio, cr, dd_nc, ir->eI, &(ir->fepvals->init_fep_state),
- &headerContents, state, observablesHistory, reproducibilityRequested,
- mdModulesNotifier, modularSimulatorCheckpointData, useModularSimulator);
+ read_checkpoint(fn,
+ logfio,
+ cr,
+ dd_nc,
+ ir->eI,
+ &(ir->fepvals->init_fep_state),
+ &headerContents,
+ state,
+ observablesHistory,
+ reproducibilityRequested,
+ mdModulesNotifiers,
+ modularSimulatorCheckpointData,
+ useModularSimulator);
}
if (PAR(cr))
{
gmx_bcast(sizeof(headerContents.step), &headerContents.step, cr->mpiDefaultCommunicator);
- gmx::MdModulesCheckpointReadingBroadcast broadcastCheckPointData = {
+ gmx::MDModulesCheckpointReadingBroadcast broadcastCheckPointData = {
cr->mpiDefaultCommunicator, PAR(cr), headerContents.file_version
};
- mdModulesNotifier.checkpointingNotifications_.notify(broadcastCheckPointData);
+ mdModulesNotifiers.checkpointingNotifier_.notify(broadcastCheckPointData);
}
ir->bContinuation = TRUE;
if (ir->nsteps >= 0)
cp_error();
}
PullHistory pullHist = {};
- ret = doCptPullHist(gmx_fio_getxdr(fp), TRUE, headerContents.flagsPullHistory, &pullHist,
- StatePart::pullHistory, nullptr);
+ ret = doCptPullHist(gmx_fio_getxdr(fp), TRUE, headerContents.flagsPullHistory, &pullHist, nullptr);
if (ret)
{
cp_error();
}
- ret = do_cpt_df_hist(gmx_fio_getxdr(fp), headerContents.flags_dfh, headerContents.nlambda,
- &state->dfhist, nullptr);
+ ret = do_cpt_df_hist(
+ gmx_fio_getxdr(fp), headerContents.flags_dfh, headerContents.nlambda, &state->dfhist, nullptr);
if (ret)
{
cp_error();
{
cp_error();
}
- gmx::MdModulesNotifier mdModuleNotifier;
- do_cpt_mdmodules(headerContents.file_version, fp, mdModuleNotifier, nullptr);
+ gmx::MDModulesNotifiers mdModuleNotifiers;
+ do_cpt_mdmodules(headerContents.file_version, fp, mdModuleNotifiers, nullptr);
if (headerContents.file_version >= cptv_ModularSimulator)
{
// Store modular checkpoint data into modularSimulatorCheckpointData
fr->bTime = TRUE;
fr->time = headerContents.t;
fr->bLambda = TRUE;
- fr->lambda = state.lambda[efptFEP];
+ fr->lambda = state.lambda[FreeEnergyPerturbationCouplingType::Fep];
fr->fep_state = state.fep_state;
fr->bAtoms = FALSE;
- fr->bX = ((state.flags & (1 << estX)) != 0);
+ fr->bX = ((state.flags & enumValueToBitMask(StateEntry::X)) != 0);
if (fr->bX)
{
fr->x = makeRvecArray(state.x, state.natoms);
}
- fr->bV = ((state.flags & (1 << estV)) != 0);
+ fr->bV = ((state.flags & enumValueToBitMask(StateEntry::V)) != 0);
if (fr->bV)
{
fr->v = makeRvecArray(state.v, state.natoms);
}
fr->bF = FALSE;
- fr->bBox = ((state.flags & (1 << estBOX)) != 0);
+ fr->bBox = ((state.flags & enumValueToBitMask(StateEntry::Box)) != 0);
if (fr->bBox)
{
copy_mat(state.box, fr->box);
if (ret == 0)
{
PullHistory pullHist = {};
- ret = doCptPullHist(gmx_fio_getxdr(fp), TRUE, headerContents.flagsPullHistory, &pullHist,
- StatePart::pullHistory, out);
+ ret = doCptPullHist(gmx_fio_getxdr(fp), TRUE, headerContents.flagsPullHistory, &pullHist, out);
}
if (ret == 0)
{
- ret = do_cpt_df_hist(gmx_fio_getxdr(fp), headerContents.flags_dfh, headerContents.nlambda,
- &state.dfhist, out);
+ ret = do_cpt_df_hist(
+ gmx_fio_getxdr(fp), headerContents.flags_dfh, headerContents.nlambda, &state.dfhist, out);
}
if (ret == 0)
std::vector<gmx_file_position_t> outputfiles;
ret = do_cpt_files(gmx_fio_getxdr(fp), TRUE, &outputfiles, out, headerContents.file_version);
}
- gmx::MdModulesNotifier mdModuleNotifier;
- do_cpt_mdmodules(headerContents.file_version, fp, mdModuleNotifier, out);
+ gmx::MDModulesNotifiers mdModuleNotifiers;
+ do_cpt_mdmodules(headerContents.file_version, fp, mdModuleNotifiers, out);
if (headerContents.file_version >= cptv_ModularSimulator)
{
gmx::FileIOXdrSerializer serializer(fp);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _checkpoint_h
-#define _checkpoint_h
+#ifndef GMX_FILEIO_CHECKPOINT_H
+#define GMX_FILEIO_CHECKPOINT_H
#include <cstdio>
struct t_inputrec;
class t_state;
struct t_trxframe;
+enum class IntegrationAlgorithm : int;
+enum class SwapType : int;
+enum class LambdaWeightCalculation : int;
namespace gmx
{
-struct MdModulesNotifier;
+struct MDModulesNotifiers;
class KeyValueTreeObject;
class ReadCheckpointDataHolder;
class WriteCheckpointDataHolder;
KeyValueTreeObjectBuilder kvtBuilder);
/*! \libinternal
- * \brief Provides the MdModules with the checkpointed data on the master rank.
+ * \brief Provides the MDModules with the checkpointed data on the master rank.
*/
-struct MdModulesCheckpointReadingDataOnMaster
+struct MDModulesCheckpointReadingDataOnMaster
{
- //! The data of the MdModules that is stored in the checkpoint file
+ //! The data of the MDModules that is stored in the checkpoint file
const KeyValueTreeObject& checkpointedData_;
//! The version of the read ceckpoint file
int checkpointFileVersion_;
};
/*! \libinternal
- * \brief Provides the MdModules with the communication record to broadcast.
+ * \brief Provides the MDModules with the communication record to broadcast.
*/
-struct MdModulesCheckpointReadingBroadcast
+struct MDModulesCheckpointReadingBroadcast
{
//! The communicator
MPI_Comm communicator_;
int checkpointFileVersion_;
};
-/*! \libinternal \brief Writing the MdModules data to a checkpoint file.
+/*! \libinternal \brief Writing the MDModules data to a checkpoint file.
*/
-struct MdModulesWriteCheckpointData
+struct MDModulesWriteCheckpointData
{
- //! Builder for the Key-Value-Tree to store the MdModule checkpoint data
+ //! Builder for the Key-Value-Tree to store the MDModule checkpoint data
KeyValueTreeObjectBuilder builder_;
//! The version of the read file version
int checkpointFileVersion_;
//! Time string.
char ftime[CPTSTRLEN];
//! Which integrator is in use.
- int eIntegrator;
+ IntegrationAlgorithm eIntegrator;
//! Which part of the simulation this is.
int simulation_part;
//! Which step the checkpoint is at.
//! Essential dynamics states.
int nED;
//! Enum for coordinate swapping.
- int eSwapCoords;
+ SwapType eSwapCoords;
//! Whether the checkpoint was written by modular simulator.
bool isModularSimulatorCheckpoint = false;
};
void write_checkpoint_data(t_fileio* fp,
CheckpointHeaderContents headerContents,
gmx_bool bExpanded,
- int elamstats,
+ LambdaWeightCalculation elamstats,
t_state* state,
ObservablesHistory* observablesHistory,
- const gmx::MdModulesNotifier& notifier,
+ const gmx::MDModulesNotifiers& mdModulesNotifiers,
std::vector<gmx_file_position_t>* outputfiles,
gmx::WriteCheckpointDataHolder* modularSimulatorCheckpointData);
t_state* state,
ObservablesHistory* observablesHistory,
gmx_bool reproducibilityRequested,
- const gmx::MdModulesNotifier& mdModulesNotifier,
+ const gmx::MDModulesNotifiers& mdModulesNotifiers,
gmx::ReadCheckpointDataHolder* modularSimulatorCheckpointData,
bool useModularSimulator);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "confio.h"
+#include "gromacs/fileio/confio.h"
#include <cstdio>
#include <cstring>
case efENT:
case efPQR:
out = gmx_fio_fopen(outfile, "w");
- write_pdbfile_indexed(out, title, atoms, x, pbcType, box, ' ', -1, nindex, index,
- nullptr, ftp == efPQR);
+ write_pdbfile_indexed(
+ out, title, atoms, x, pbcType, box, ' ', -1, nindex, index, nullptr, ftp == efPQR);
gmx_fio_fclose(out);
break;
case efESP:
void write_sto_conf_mtop(const char* outfile,
const char* title,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const rvec x[],
const rvec* v,
PbcType pbcType,
{
// We always assign a new chain number, but only assign a chain id
// characters for larger molecules.
- int chainIdToAssign;
+ char chainIdToAssign;
if (endAtomIndex - startAtomIndex >= s_chainMinAtoms && !outOfIds_)
{
/* Set the chain id for the output */
readConfAndTopology(infile, &haveTopology, &mtop, pbcType, x, v, box);
*symtab = mtop.symtab;
*name = gmx_strdup(*mtop.name);
- *atoms = gmx_mtop_global_atoms(&mtop);
+ *atoms = gmx_mtop_global_atoms(mtop);
gmx::RangePartitioning molecules = gmx_mtop_molecules(mtop);
makeChainIdentifiersAfterTprReading(atoms, molecules);
snew(*v, header.natoms);
}
int natoms;
- PbcType pbcType_tmp = read_tpx(infile, nullptr, box, &natoms, (x == nullptr) ? nullptr : *x,
- (v == nullptr) ? nullptr : *v, mtop);
+ PbcType pbcType_tmp = read_tpx(
+ infile, nullptr, box, &natoms, (x == nullptr) ? nullptr : *x, (v == nullptr) ? nullptr : *v, mtop);
if (pbcType != nullptr)
{
*pbcType = pbcType_tmp;
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* This number should be increased whenever the file format changes! */
static const int enx_version = 5;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
const char* enx_block_id_name[] = { "Averaged orientation restraints",
"Instantaneous orientation restraints",
"Orientation restraint order tensor(s)",
{
sb->nr = 0;
#if GMX_DOUBLE
- sb->type = xdr_datatype_double;
+ sb->type = XdrDataType::Double;
#else
- sb->type = xdr_datatype_float;
+ sb->type = XdrDataType::Float;
#endif
sb->fval = nullptr;
sb->dval = nullptr;
/* allocate the appropriate amount of memory */
switch (sb->type)
{
- case xdr_datatype_float:
+ case XdrDataType::Float:
if (sb->nr > sb->fval_alloc)
{
srenew(sb->fval, sb->nr);
sb->fval_alloc = sb->nr;
}
break;
- case xdr_datatype_double:
+ case XdrDataType::Double:
if (sb->nr > sb->dval_alloc)
{
srenew(sb->dval, sb->nr);
sb->dval_alloc = sb->nr;
}
break;
- case xdr_datatype_int:
+ case XdrDataType::Int:
if (sb->nr > sb->ival_alloc)
{
srenew(sb->ival, sb->nr);
sb->ival_alloc = sb->nr;
}
break;
- case xdr_datatype_int64:
+ case XdrDataType::Int64:
if (sb->nr > sb->lval_alloc)
{
srenew(sb->lval, sb->nr);
sb->lval_alloc = sb->nr;
}
break;
- case xdr_datatype_char:
+ case XdrDataType::Char:
if (sb->nr > sb->cval_alloc)
{
srenew(sb->cval, sb->nr);
sb->cval_alloc = sb->nr;
}
break;
- case xdr_datatype_string:
+ case XdrDataType::String:
if (sb->nr > sb->sval_alloc)
{
int i;
}
else
{
- gmx_fatal(FARGS, "%s\n%s", msg,
+ gmx_fatal(FARGS,
+ "%s\n%s",
+ msg,
"If you want to use the correct frames before the corrupted frame and avoid this "
"fatal error set the env.var. GMX_ENX_NO_FATAL");
}
xdr_int(xdr, &file_version);
if (file_version > enx_version)
{
- gmx_fatal(FARGS, "reading tpx file (%s) version %d with version %d program",
- gmx_fio_getname(ef->fio), file_version, enx_version);
+ gmx_fatal(FARGS,
+ "reading tpx file (%s) version %d with version %d program",
+ gmx_fio_getname(ef->fio),
+ file_version,
+ enx_version);
}
xdr_int(xdr, nre);
}
int ndisre = 0;
int startb = 0;
#if !GMX_DOUBLE
- xdr_datatype dtreal = xdr_datatype_float;
+ XdrDataType xdrDataType = XdrDataType::Float;
#else
- xdr_datatype dtreal = xdr_datatype_double;
+ XdrDataType xdrDataType = XdrDataType::Double;
#endif
if (bWrongPrecision)
}
if (*bOK && *file_version > enx_version)
{
- gmx_fatal(FARGS, "reading tpx file (%s) version %d with version %d program",
- gmx_fio_getname(ef->fio), *file_version, enx_version);
+ gmx_fatal(FARGS,
+ "reading tpx file (%s) version %d with version %d program",
+ gmx_fio_getname(ef->fio),
+ *file_version,
+ enx_version);
}
if (!gmx_fio_do_double(ef->fio, fr->t))
{
fr->block[0].id = enxDISRE;
fr->block[0].sub[0].nr = ndisre;
fr->block[0].sub[1].nr = ndisre;
- fr->block[0].sub[0].type = dtreal;
- fr->block[0].sub[1].type = dtreal;
+ fr->block[0].sub[0].type = xdrDataType;
+ fr->block[0].sub[1].type = xdrDataType;
startb++;
}
{
gmx_incons("Writing an old version .edr file with too many subblocks");
}
- if (fr->block[b].sub[0].type != dtreal)
+ if (fr->block[b].sub[0].type != xdrDataType)
{
gmx_incons("Writing an old version .edr file the wrong subblock type");
}
}
fr->block[b].id = b - startb;
fr->block[b].sub[0].nr = nrint;
- fr->block[b].sub[0].type = dtreal;
+ fr->block[b].sub[0].type = xdrDataType;
}
else
{
for (i = 0; i < nsub; i++)
{
t_enxsubblock* sub = &(fr->block[b].sub[i]); /* shortcut */
- int typenr = sub->type;
+ int typenr = static_cast<int>(sub->type);
*bOK = *bOK && gmx_fio_do_int(ef->fio, typenr);
*bOK = *bOK && gmx_fio_do_int(ef->fio, sub->nr);
- sub->type = static_cast<xdr_datatype>(typenr);
+ sub->type = static_cast<XdrDataType>(typenr);
}
}
}
{
if (bRead)
{
- fprintf(stderr, "\rLast energy frame read %d time %8.3f ", ef->framenr - 1,
- ef->frametime);
+ fprintf(stderr, "\rLast energy frame read %d time %8.3f ", ef->framenr - 1, ef->frametime);
fflush(stderr);
if (!bOK)
{
- fprintf(stderr, "\nWARNING: Incomplete energy frame: nr %d time %8.3f\n",
- ef->framenr, fr->t);
+ fprintf(stderr, "\nWARNING: Incomplete energy frame: nr %d time %8.3f\n", ef->framenr, fr->t);
}
}
else
}
if (!((fr->step >= 0) && bSane) && bRead)
{
- fprintf(stderr, "\nWARNING: there may be something wrong with energy file %s\n",
+ fprintf(stderr,
+ "\nWARNING: there may be something wrong with energy file %s\n",
gmx_fio_getname(ef->fio));
- fprintf(stderr, "Found: step=%" PRId64 ", nre=%d, nblock=%d, time=%g.\n", fr->step, fr->nre,
- fr->nblock, fr->t);
+ fprintf(stderr,
+ "Found: step=%" PRId64 ", nre=%d, nblock=%d, time=%g.\n",
+ fr->step,
+ fr->nre,
+ fr->nblock,
+ fr->t);
}
if (bRead && fr->nre > fr->e_alloc)
{
/* read/write data */
switch (sub->type)
{
- case xdr_datatype_float:
+ case XdrDataType::Float:
bOK1 = gmx_fio_ndo_float(ef->fio, sub->fval, sub->nr);
break;
- case xdr_datatype_double:
+ case XdrDataType::Double:
bOK1 = gmx_fio_ndo_double(ef->fio, sub->dval, sub->nr);
break;
- case xdr_datatype_int: bOK1 = gmx_fio_ndo_int(ef->fio, sub->ival, sub->nr); break;
- case xdr_datatype_int64:
+ case XdrDataType::Int: bOK1 = gmx_fio_ndo_int(ef->fio, sub->ival, sub->nr); break;
+ case XdrDataType::Int64:
bOK1 = gmx_fio_ndo_int64(ef->fio, sub->lval, sub->nr);
break;
- case xdr_datatype_char:
+ case XdrDataType::Char:
bOK1 = gmx_fio_ndo_uchar(ef->fio, sub->cval, sub->nr);
break;
- case xdr_datatype_string:
+ case XdrDataType::String:
bOK1 = gmx_fio_ndo_string(ef->fio, sub->sval, sub->nr);
break;
default:
}
npcoupl = TRICLINIC(ir->compress) ? 6 : 3;
- if (ir->epc == epcPARRINELLORAHMAN)
+ if (ir->epc == PressureCoupling::ParrinelloRahman)
{
clear_mat(state->boxv);
for (i = 0; i < npcoupl; i++)
fprintf(stderr, "\nREAD %d BOX VELOCITIES FROM %s\n\n", npcoupl, fn);
}
- if (ir->etc == etcNOSEHOOVER)
+ if (ir->etc == TemperatureCoupling::NoseHoover)
{
char cns[20];
}
if (!equal_real(e1[ind1[i]].e, e2[ind2[i]].e, ftol_i, abstol_i))
{
- fprintf(fp, "%-15s step %3d: %12g, step %3d: %12g\n", enm1[ind1[i]].name, step1,
- e1[ind1[i]].e, step2, e2[ind2[i]].e);
+ fprintf(fp,
+ "%-15s step %3d: %12g, step %3d: %12g\n",
+ enm1[ind1[i]].name,
+ step1,
+ e1[ind1[i]].e,
+ step2,
+ e2[ind2[i]].e);
}
}
{
switch (s1->type)
{
- case xdr_datatype_float:
+ case XdrDataType::Float:
for (k = 0; k < s1->nr; k++)
{
cmp_float(stdout, buf, i, s1->fval[k], s2->fval[k], ftol, abstol);
}
break;
- case xdr_datatype_double:
+ case XdrDataType::Double:
for (k = 0; k < s1->nr; k++)
{
cmp_double(stdout, buf, i, s1->dval[k], s2->dval[k], ftol, abstol);
}
break;
- case xdr_datatype_int:
+ case XdrDataType::Int:
for (k = 0; k < s1->nr; k++)
{
cmp_int(stdout, buf, i, s1->ival[k], s2->ival[k]);
}
break;
- case xdr_datatype_int64:
+ case XdrDataType::Int64:
for (k = 0; k < s1->nr; k++)
{
cmp_int64(stdout, buf, s1->lval[k], s2->lval[k]);
}
break;
- case xdr_datatype_char:
+ case XdrDataType::Char:
for (k = 0; k < s1->nr; k++)
{
cmp_uc(stdout, buf, i, s1->cval[k], s2->cval[k]);
}
break;
- case xdr_datatype_string:
+ case XdrDataType::String:
for (k = 0; k < s1->nr; k++)
{
cmp_str(stdout, buf, i, s1->sval[k], s2->sval[k]);
/* cmp_int(stdout,"nre",-1,fr1->nre,fr2->nre); */
if ((fr1->nre >= nre) && (fr2->nre >= nre))
{
- cmp_energies(stdout, fr1->step, fr1->step, fr1->ener, fr2->ener, enm1, ftol, abstol,
- nre, ind1, ind2, maxener);
+ cmp_energies(
+ stdout, fr1->step, fr1->step, fr1->ener, fr2->ener, enm1, ftol, abstol, nre, ind1, ind2, maxener);
}
/*cmp_disres(fr1,fr2,ftol,abstol);*/
cmp_eblocks(fr1, fr2, ftol, abstol);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
/* names for the above enum */
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
extern const char* enx_block_id_name[];
has a number of values of a single data type in a .edr file. */
struct t_enxsubblock
{
- int nr; /* number of items in subblock */
- xdr_datatype type; /* the block type */
+ int nr; /* number of items in subblock */
+ XdrDataType type; /* the block type */
/* the values: pointers for each type */
float* fval;
}
else
{
- sprintf(buf, "T%c%c", 'A' + atoms->atom[i].type / 26,
- 'A' + atoms->atom[i].type % 26);
+ sprintf(buf, "T%c%c", 'A' + atoms->atom[i].type / 26, 'A' + atoms->atom[i].type % 26);
}
t_atoms_set_resinfo(atoms, i, symtab, buf, i, ' ', 0, ' ');
}
gmx_fatal(FARGS,
"Internal inconsistency in Espresso routines, read %d atoms, expected %d "
"atoms",
- i, atoms->nr);
+ i,
+ atoms->nr);
}
}
else if (level == 1 && std::strcmp(word, "variable") == 0 && !bFoundVariable)
{
j = i;
}
- fprintf(out, "\t{%d %f %f %f %hu %g", j, x[j][XX], x[j][YY], x[j][ZZ], atoms->atom[j].type,
+ fprintf(out,
+ "\t{%d %f %f %f %hu %g",
+ j,
+ x[j][XX],
+ x[j][YY],
+ x[j][ZZ],
+ atoms->atom[j].type,
atoms->atom[j].q);
if (v)
{
*/
#include "gmxpre.h"
-#include "filetypes.h"
+#include "gromacs/fileio/filetypes.h"
#include <cstring>
{ eftGEN, ".???", "trajout", "-f", "Trajectory", NTROS, tros },
{ eftGEN, ".???", "traj", nullptr, "Full precision trajectory", NTRNS, trns },
{ eftXDR, ".trr", "traj", nullptr, "Trajectory in portable xdr format" },
- { eftGEN, ".???", "traj_comp", nullptr,
- "Compressed trajectory (tng format or portable xdr format)", NTRCOMPRESSED, trcompressed },
+ { eftGEN,
+ ".???",
+ "traj_comp",
+ nullptr,
+ "Compressed trajectory (tng format or portable xdr format)",
+ NTRCOMPRESSED,
+ trcompressed },
{ eftXDR, ".xtc", "traj", nullptr, "Compressed trajectory (portable xdr format): xtc" },
{ eftTNG, ".tng", "traj", nullptr, "Trajectory file (tng format)" },
{ eftXDR, ".edr", "ener", nullptr, "Energy file" },
}
if ((nwanted != -1) && (natoms >= nwanted))
{
- gmx_fatal(FARGS, "Found more coordinates (%d) in %s than expected %d\n", natoms,
- infile, nwanted);
+ gmx_fatal(FARGS, "Found more coordinates (%d) in %s than expected %d\n", natoms, infile, nwanted);
}
if (atoms)
{
newres++;
if (newres >= atoms->nr)
{
- gmx_fatal(FARGS, "More residues than atoms in %s (natoms = %d)", infile,
- atoms->nr);
+ gmx_fatal(FARGS, "More residues than atoms in %s (natoms = %d)", infile, atoms->nr);
}
atoms->atom[natoms].resind = newres;
if (newres + 1 > atoms->nres)
}
if ((nwanted != -1) && natoms != nwanted)
{
- fprintf(stderr, "Warning: found less coordinates (%d) in %s than expected %d\n", natoms,
- infile, nwanted);
+ fprintf(stderr, "Warning: found less coordinates (%d) in %s than expected %d\n", natoms, infile, nwanted);
}
}
}
if ((nwanted != -1) && (natoms >= nwanted))
{
- gmx_fatal(FARGS, "Found more velocities (%d) in %s than expected %d\n", natoms,
- infile, nwanted);
+ gmx_fatal(FARGS, "Found more velocities (%d) in %s than expected %d\n", natoms, infile, nwanted);
}
if (fr->v)
{
}
if ((nwanted != -1) && (natoms != nwanted))
{
- fprintf(stderr, "Warning: found less velocities (%d) in %s than expected %d\n", natoms,
- infile, nwanted);
+ fprintf(stderr, "Warning: found less velocities (%d) in %s than expected %d\n", natoms, infile, nwanted);
}
}
bEnd = (strncmp(line, "END", 3) == 0);
if (!bEnd && (line[0] != '#'))
{
- nbp = sscanf(line, "%15lf%15lf%15lf%15lf%15lf%15lf%15lf%15lf%15lf", &db1, &db2,
- &db3, &db4, &db5, &db6, &db7, &db8, &db9);
+ nbp = sscanf(line,
+ "%15lf%15lf%15lf%15lf%15lf%15lf%15lf%15lf%15lf",
+ &db1,
+ &db2,
+ &db3,
+ &db4,
+ &db5,
+ &db6,
+ &db7,
+ &db8,
+ &db9);
if (nbp < 3)
{
gmx_fatal(FARGS, "Found a BOX line, but no box in %s", infile);
{
a = i;
}
- fprintf(out, "%5d %-5s %-5s%7d%15.9f%15.9f%15.9f\n",
+ fprintf(out,
+ "%5d %-5s %-5s%7d%15.9f%15.9f%15.9f\n",
(atoms->resinfo[atoms->atom[a].resind].nr) % 100000,
- *atoms->resinfo[atoms->atom[a].resind].name, *atoms->atomname[a],
- (i + 1) % 10000000, fr->x[a][XX], fr->x[a][YY], fr->x[a][ZZ]);
+ *atoms->resinfo[atoms->atom[a].resind].name,
+ *atoms->atomname[a],
+ (i + 1) % 10000000,
+ fr->x[a][XX],
+ fr->x[a][YY],
+ fr->x[a][ZZ]);
}
}
else
{
a = i;
}
- fprintf(out, "%5d %-5s %-5s%7d%15.9f%15.9f%15.9f\n",
+ fprintf(out,
+ "%5d %-5s %-5s%7d%15.9f%15.9f%15.9f\n",
(atoms->resinfo[atoms->atom[a].resind].nr) % 100000,
- *atoms->resinfo[atoms->atom[a].resind].name, *atoms->atomname[a],
- (i + 1) % 10000000, fr->v[a][XX], fr->v[a][YY], fr->v[a][ZZ]);
+ *atoms->resinfo[atoms->atom[a].resind].name,
+ *atoms->atomname[a],
+ (i + 1) % 10000000,
+ fr->v[a][XX],
+ fr->v[a][YY],
+ fr->v[a][ZZ]);
}
}
else
if ((fr->box[XX][YY] != 0.0F) || (fr->box[XX][ZZ] != 0.0F) || (fr->box[YY][XX] != 0.0F)
|| (fr->box[YY][ZZ] != 0.0F) || (fr->box[ZZ][XX] != 0.0F) || (fr->box[ZZ][YY] != 0.0F))
{
- fprintf(out, "%15.9f%15.9f%15.9f%15.9f%15.9f%15.9f", fr->box[XX][YY], fr->box[XX][ZZ],
- fr->box[YY][XX], fr->box[YY][ZZ], fr->box[ZZ][XX], fr->box[ZZ][YY]);
+ fprintf(out,
+ "%15.9f%15.9f%15.9f%15.9f%15.9f%15.9f",
+ fr->box[XX][YY],
+ fr->box[XX][ZZ],
+ fr->box[YY][XX],
+ fr->box[YY][ZZ],
+ fr->box[ZZ][XX],
+ fr->box[ZZ][YY]);
}
fprintf(out, "\n");
fprintf(out, "END\n");
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
#include <cstring>
+#include <mutex>
#include <vector>
#if HAVE_IO_H
#include "gromacs/fileio/md5.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
-#include "gromacs/utility/mutex.h"
#include "gromacs/utility/smalloc.h"
#include "gmxfio_impl.h"
/* the list of open files is a linked list, with a dummy element at its head;
it is initialized when the first file is opened. */
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static t_fileio* open_files = nullptr;
opening and closing of files, or during global operations like
iterating along all open files. All these cases should be rare
during the simulation. */
-static gmx::Mutex open_file_mutex;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static std::mutex open_file_mutex;
-using Lock = gmx::lock_guard<gmx::Mutex>;
+using Lock = std::lock_guard<std::mutex>;
/******************************************************************
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/xdrf.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
#include "gmxfio_impl.h"
/* Enumerated for data types in files */
-enum
-{
- eioREAL,
- eioFLOAT,
- eioDOUBLE,
- eioINT,
- eioINT32,
- eioINT64,
- eioUCHAR,
- eioCHAR,
- eioNCHAR,
- eioNUCHAR,
- eioUSHORT,
- eioRVEC,
- eioNRVEC,
- eioIVEC,
- eioSTRING,
- eioOPAQUE,
- eioNR
+enum class InputOutputType : int
+{
+ Real,
+ Float,
+ Double,
+ Int,
+ Int32,
+ Int64,
+ UnsignedChar,
+ Char,
+ CharArray,
+ UnsignedCharArray,
+ UnsignedShort,
+ RVec,
+ RVecArray,
+ IVec,
+ String,
+ Opaque,
+ Count
};
-static const char* eioNames[eioNR] = { "REAL", "FLOAT", "DOUBLE", "INT", "INT32", "INT64",
- "UCHAR", "CHAR", "NCHAR", "NUCHAR", "USHORT", "RVEC",
- "NRVEC", "IVEC", "STRING", "OPAQUE" };
+static const char* enumValueToString(InputOutputType enumValue)
+{
+ constexpr gmx::EnumerationArray<InputOutputType, const char*> ioTypeNames = {
+ "REAL", "FLOAT", "DOUBLE", "INT", "INT32", "INT64", "UCHAR", "CHAR",
+ "NCHAR", "NUCHAR", "USHORT", "RVEC", "NRVEC", "IVEC", "STRING", "OPAQUE"
+ };
+ return ioTypeNames[enumValue];
+}
void gmx_fio_setprecision(t_fileio* fio, gmx_bool bDouble)
{
}
/* check the number of items given against the type */
-static void gmx_fio_check_nitem(int eio, std::size_t nitem, const char* file, int line)
+static void gmx_fio_check_nitem(InputOutputType eio, std::size_t nitem, const char* file, int line)
{
if ((nitem != 1)
- && !((eio == eioNRVEC) || (eio == eioNUCHAR) || (eio == eioNCHAR) || (eio == eioOPAQUE)))
+ && !((eio == InputOutputType::RVecArray) || (eio == InputOutputType::UnsignedCharArray)
+ || (eio == InputOutputType::CharArray) || (eio == InputOutputType::Opaque)))
{
gmx_fatal(FARGS,
"nitem may differ from 1 only for %s, %s, %s or %s, not for %s"
"(%s, %d)",
- eioNames[eioNUCHAR], eioNames[eioNRVEC], eioNames[eioNCHAR], eioNames[eioOPAQUE],
- eioNames[eio], file, line);
+ enumValueToString(InputOutputType::UnsignedCharArray),
+ enumValueToString(InputOutputType::RVecArray),
+ enumValueToString(InputOutputType::CharArray),
+ enumValueToString(InputOutputType::Opaque),
+ enumValueToString(eio),
+ file,
+ line);
}
}
/* output a data type error. */
-[[noreturn]] static void gmx_fio_fe(t_fileio* fio, int eio, const char* desc, const char* srcfile, int line)
+[[noreturn]] static void
+gmx_fio_fe(t_fileio* fio, InputOutputType eio, const char* desc, const char* srcfile, int line)
{
- gmx_fatal(FARGS, "Trying to %s %s type %d (%s), src %s, line %d", fio->bRead ? "read" : "write",
- desc, eio, ((eio >= 0) && (eio < eioNR)) ? eioNames[eio] : "unknown", srcfile, line);
+ gmx_fatal(FARGS,
+ "Trying to %s %s type %d (%s), src %s, line %d",
+ fio->bRead ? "read" : "write",
+ desc,
+ static_cast<int>(eio),
+ ((eio >= InputOutputType::Real) && (eio < InputOutputType::Count)) ? enumValueToString(eio)
+ : "unknown",
+ srcfile,
+ line);
}
/* This is the part that reads xdr files. */
-
-static gmx_bool
-do_xdr(t_fileio* fio, void* item, std::size_t nitem, int eio, const char* desc, const char* srcfile, int line)
+static gmx_bool do_xdr(t_fileio* fio,
+ void* item,
+ std::size_t nitem,
+ InputOutputType eio,
+ const char* desc,
+ const char* srcfile,
+ int line)
{
unsigned char ucdum, *ucptr;
char cdum, *cptr;
gmx_fio_check_nitem(eio, nitem, srcfile, line);
switch (eio)
{
- case eioREAL:
+ case InputOutputType::Real:
if (fio->bDouble)
{
if (item && !fio->bRead)
}
}
break;
- case eioFLOAT:
+ case InputOutputType::Float:
if (item && !fio->bRead)
{
f = *(static_cast<float*>(item));
*(static_cast<float*>(item)) = f;
}
break;
- case eioDOUBLE:
+ case InputOutputType::Double:
if (item && !fio->bRead)
{
d = *(static_cast<double*>(item));
*(static_cast<double*>(item)) = d;
}
break;
- case eioINT:
+ case InputOutputType::Int:
if (item && !fio->bRead)
{
idum = *static_cast<int*>(item);
*static_cast<int*>(item) = idum;
}
break;
- case eioINT32:
+ case InputOutputType::Int32:
if (item && !fio->bRead)
{
s32dum = *static_cast<int32_t*>(item);
*static_cast<int32_t*>(item) = s32dum;
}
break;
- case eioINT64:
+ case InputOutputType::Int64:
if (item && !fio->bRead)
{
s64dum = *static_cast<int64_t*>(item);
*static_cast<int64_t*>(item) = s64dum;
}
break;
- case eioUCHAR:
+ case InputOutputType::UnsignedChar:
if (item && !fio->bRead)
{
ucdum = *static_cast<unsigned char*>(item);
*static_cast<unsigned char*>(item) = ucdum;
}
break;
- case eioCHAR:
+ case InputOutputType::Char:
if (item && !fio->bRead)
{
cdum = *static_cast<char*>(item);
*static_cast<char*>(item) = cdum;
}
break;
- case eioNCHAR:
+ case InputOutputType::CharArray:
cptr = static_cast<char*>(item);
GMX_RELEASE_ASSERT(nitem < static_cast<std::size_t>(std::numeric_limits<int>::max()),
"The XDR interface cannot handle array lengths > 2^31");
- res = xdr_vector(fio->xdr, cptr, static_cast<int>(nitem),
+ res = xdr_vector(fio->xdr,
+ cptr,
+ static_cast<int>(nitem),
static_cast<unsigned int>(sizeof(char)),
reinterpret_cast<xdrproc_t>(xdr_char));
break;
- case eioNUCHAR:
+ case InputOutputType::UnsignedCharArray:
ucptr = static_cast<unsigned char*>(item);
GMX_RELEASE_ASSERT(nitem < static_cast<std::size_t>(std::numeric_limits<int>::max()),
"The XDR interface cannot handle array lengths > 2^31");
- res = xdr_vector(fio->xdr, reinterpret_cast<char*>(ucptr), static_cast<int>(nitem),
+ res = xdr_vector(fio->xdr,
+ reinterpret_cast<char*>(ucptr),
+ static_cast<int>(nitem),
static_cast<unsigned int>(sizeof(unsigned char)),
reinterpret_cast<xdrproc_t>(xdr_u_char));
break;
- case eioUSHORT:
+ case InputOutputType::UnsignedShort:
if (item && !fio->bRead)
{
us = *static_cast<unsigned short*>(item);
*static_cast<unsigned short*>(item) = us;
}
break;
- case eioRVEC:
+ case InputOutputType::RVec:
if (fio->bDouble)
{
if (item && !fio->bRead)
dvec[m] = (static_cast<real*>(item))[m];
}
}
- res = xdr_vector(fio->xdr, reinterpret_cast<char*>(dvec), DIM,
+ res = xdr_vector(fio->xdr,
+ reinterpret_cast<char*>(dvec),
+ DIM,
static_cast<unsigned int>(sizeof(double)),
reinterpret_cast<xdrproc_t>(xdr_double));
if (item)
fvec[m] = (static_cast<real*>(item))[m];
}
}
- res = xdr_vector(fio->xdr, reinterpret_cast<char*>(fvec), DIM,
+ res = xdr_vector(fio->xdr,
+ reinterpret_cast<char*>(fvec),
+ DIM,
static_cast<unsigned int>(sizeof(float)),
reinterpret_cast<xdrproc_t>(xdr_float));
if (item)
}
}
break;
- case eioNRVEC:
+ case InputOutputType::RVecArray:
ptr = nullptr;
res = 1;
for (std::size_t j = 0; j < nitem && res; j++)
{
ptr = (static_cast<rvec*>(item))[j];
}
- res = static_cast<bool_t>(do_xdr(fio, ptr, 1, eioRVEC, desc, srcfile, line));
+ res = static_cast<bool_t>(do_xdr(fio, ptr, 1, InputOutputType::RVec, desc, srcfile, line));
}
break;
- case eioIVEC:
+ case InputOutputType::IVec:
iptr = static_cast<int*>(item);
res = 1;
for (m = 0; (m < DIM) && res; m++)
}
}
break;
- case eioSTRING:
+ case InputOutputType::String:
{
char* cptr;
int slen;
gmx_fatal(FARGS,
"wrong string length %d for string %s"
" (source %s, line %d)",
- slen, desc, srcfile, line);
+ slen,
+ desc,
+ srcfile,
+ line);
}
if (!item && fio->bRead)
{
}
break;
}
- case eioOPAQUE:
+ case InputOutputType::Opaque:
{
if (item == nullptr && nitem > 0)
{
gmx_bool ret;
void* it = const_cast<char*>(item); /* ugh.. */
gmx_fio_lock(fio);
- ret = do_xdr(fio, it, 1, eioSTRING, desc, srcfile, line);
+ ret = do_xdr(fio, it, 1, InputOutputType::String, desc, srcfile, line);
gmx_fio_unlock(fio);
return ret;
}
{
gmx_bool ret;
gmx_fio_lock(fio);
- ret = do_xdr(fio, item, 1, eioREAL, desc, srcfile, line);
+ ret = do_xdr(fio, item, 1, InputOutputType::Real, desc, srcfile, line);
gmx_fio_unlock(fio);
return ret;
}
{
gmx_bool ret;
gmx_fio_lock(fio);
- ret = do_xdr(fio, item, 1, eioFLOAT, desc, srcfile, line);
+ ret = do_xdr(fio, item, 1, InputOutputType::Float, desc, srcfile, line);
gmx_fio_unlock(fio);
return ret;
}
{
gmx_bool ret;
gmx_fio_lock(fio);
- ret = do_xdr(fio, item, 1, eioDOUBLE, desc, srcfile, line);
+ ret = do_xdr(fio, item, 1, InputOutputType::Double, desc, srcfile, line);
gmx_fio_unlock(fio);
return ret;
}
if (fio->bRead)
{
int itmp = 0;
- ret = do_xdr(fio, &itmp, 1, eioINT, desc, srcfile, line);
+ ret = do_xdr(fio, &itmp, 1, InputOutputType::Int, desc, srcfile, line);
*item = (itmp != 0);
}
else
{
int itmp = static_cast<int>(*item);
- ret = do_xdr(fio, &itmp, 1, eioINT, desc, srcfile, line);
+ ret = do_xdr(fio, &itmp, 1, InputOutputType::Int, desc, srcfile, line);
}
gmx_fio_unlock(fio);
return ret;
{
gmx_bool ret;
gmx_fio_lock(fio);
- ret = do_xdr(fio, item, 1, eioINT, desc, srcfile, line);
+ ret = do_xdr(fio, item, 1, InputOutputType::Int, desc, srcfile, line);
gmx_fio_unlock(fio);
return ret;
}
{
gmx_bool ret;
gmx_fio_lock(fio);
- ret = do_xdr(fio, item, 1, eioINT32, desc, srcfile, line);
+ ret = do_xdr(fio, item, 1, InputOutputType::Int32, desc, srcfile, line);
gmx_fio_unlock(fio);
return ret;
}
{
gmx_bool ret;
gmx_fio_lock(fio);
- ret = do_xdr(fio, item, 1, eioINT64, desc, srcfile, line);
+ ret = do_xdr(fio, item, 1, InputOutputType::Int64, desc, srcfile, line);
gmx_fio_unlock(fio);
return ret;
}
{
gmx_bool ret;
gmx_fio_lock(fio);
- ret = do_xdr(fio, item, 1, eioUCHAR, desc, srcfile, line);
+ ret = do_xdr(fio, item, 1, InputOutputType::UnsignedChar, desc, srcfile, line);
gmx_fio_unlock(fio);
return ret;
}
{
gmx_bool ret;
gmx_fio_lock(fio);
- ret = do_xdr(fio, item, 1, eioCHAR, desc, srcfile, line);
+ ret = do_xdr(fio, item, 1, InputOutputType::Char, desc, srcfile, line);
gmx_fio_unlock(fio);
return ret;
}
{
gmx_bool ret;
gmx_fio_lock(fio);
- ret = do_xdr(fio, item, 1, eioUSHORT, desc, srcfile, line);
+ ret = do_xdr(fio, item, 1, InputOutputType::UnsignedShort, desc, srcfile, line);
gmx_fio_unlock(fio);
return ret;
}
{
gmx_bool ret;
gmx_fio_lock(fio);
- ret = do_xdr(fio, item, 1, eioRVEC, desc, srcfile, line);
+ ret = do_xdr(fio, item, 1, InputOutputType::RVec, desc, srcfile, line);
gmx_fio_unlock(fio);
return ret;
}
{
gmx_bool ret;
gmx_fio_lock(fio);
- ret = do_xdr(fio, item, 1, eioIVEC, desc, srcfile, line);
+ ret = do_xdr(fio, item, 1, InputOutputType::IVec, desc, srcfile, line);
gmx_fio_unlock(fio);
return ret;
}
{
gmx_bool ret;
gmx_fio_lock(fio);
- ret = do_xdr(fio, item, 1, eioSTRING, desc, srcfile, line);
+ ret = do_xdr(fio, item, 1, InputOutputType::String, desc, srcfile, line);
gmx_fio_unlock(fio);
return ret;
}
{
gmx_bool ret;
gmx_fio_lock(fio);
- ret = do_xdr(fio, data, size, eioOPAQUE, desc, srcfile, line);
+ ret = do_xdr(fio, data, size, InputOutputType::Opaque, desc, srcfile, line);
gmx_fio_unlock(fio);
return ret;
}
gmx_fio_lock(fio);
for (i = 0; i < n; i++)
{
- ret = ret && do_xdr(fio, &(item[i]), 1, eioREAL, desc, srcfile, line);
+ ret = ret && do_xdr(fio, &(item[i]), 1, InputOutputType::Real, desc, srcfile, line);
}
gmx_fio_unlock(fio);
return ret;
gmx_fio_lock(fio);
for (i = 0; i < n; i++)
{
- ret = ret && do_xdr(fio, &(item[i]), 1, eioFLOAT, desc, srcfile, line);
+ ret = ret && do_xdr(fio, &(item[i]), 1, InputOutputType::Float, desc, srcfile, line);
}
gmx_fio_unlock(fio);
return ret;
gmx_fio_lock(fio);
for (i = 0; i < n; i++)
{
- ret = ret && do_xdr(fio, &(item[i]), 1, eioDOUBLE, desc, srcfile, line);
+ ret = ret && do_xdr(fio, &(item[i]), 1, InputOutputType::Double, desc, srcfile, line);
}
gmx_fio_unlock(fio);
return ret;
if (fio->bRead)
{
int itmp = 0;
- ret = ret && do_xdr(fio, &itmp, 1, eioINT, desc, srcfile, line);
+ ret = ret && do_xdr(fio, &itmp, 1, InputOutputType::Int, desc, srcfile, line);
item[i] = (itmp != 0);
}
else
{
int itmp = static_cast<int>(item[i]);
- ret = ret && do_xdr(fio, &itmp, 1, eioINT, desc, srcfile, line);
+ ret = ret && do_xdr(fio, &itmp, 1, InputOutputType::Int, desc, srcfile, line);
}
}
gmx_fio_unlock(fio);
gmx_fio_lock(fio);
for (i = 0; i < n; i++)
{
- ret = ret && do_xdr(fio, &(item[i]), 1, eioINT, desc, srcfile, line);
+ ret = ret && do_xdr(fio, &(item[i]), 1, InputOutputType::Int, desc, srcfile, line);
}
gmx_fio_unlock(fio);
return ret;
gmx_fio_lock(fio);
for (i = 0; i < n; i++)
{
- ret = ret && do_xdr(fio, &(item[i]), 1, eioINT64, desc, srcfile, line);
+ ret = ret && do_xdr(fio, &(item[i]), 1, InputOutputType::Int64, desc, srcfile, line);
}
gmx_fio_unlock(fio);
return ret;
{
gmx_bool ret = TRUE;
gmx_fio_lock(fio);
- ret = ret && do_xdr(fio, item, n, eioNUCHAR, desc, srcfile, line);
+ ret = ret && do_xdr(fio, item, n, InputOutputType::UnsignedCharArray, desc, srcfile, line);
gmx_fio_unlock(fio);
return ret;
}
{
gmx_bool ret = TRUE;
gmx_fio_lock(fio);
- ret = ret && do_xdr(fio, item, n, eioNCHAR, desc, srcfile, line);
+ ret = ret && do_xdr(fio, item, n, InputOutputType::CharArray, desc, srcfile, line);
gmx_fio_unlock(fio);
return ret;
}
gmx_fio_lock(fio);
for (i = 0; i < n; i++)
{
- ret = ret && do_xdr(fio, &(item[i]), 1, eioUSHORT, desc, srcfile, line);
+ ret = ret && do_xdr(fio, &(item[i]), 1, InputOutputType::UnsignedShort, desc, srcfile, line);
}
gmx_fio_unlock(fio);
return ret;
{
gmx_bool ret = TRUE;
gmx_fio_lock(fio);
- ret = ret && do_xdr(fio, item, n, eioNRVEC, desc, srcfile, line);
+ ret = ret && do_xdr(fio, item, n, InputOutputType::RVecArray, desc, srcfile, line);
gmx_fio_unlock(fio);
return ret;
}
gmx_fio_lock(fio);
for (i = 0; i < n; i++)
{
- ret = ret && do_xdr(fio, &(item[i]), 1, eioIVEC, desc, srcfile, line);
+ ret = ret && do_xdr(fio, &(item[i]), 1, InputOutputType::IVec, desc, srcfile, line);
}
gmx_fio_unlock(fio);
return ret;
gmx_fio_lock(fio);
for (i = 0; i < n; i++)
{
- ret = ret && do_xdr(fio, &(item[i]), 1, eioSTRING, desc, srcfile, line);
+ ret = ret && do_xdr(fio, &(item[i]), 1, InputOutputType::String, desc, srcfile, line);
}
gmx_fio_unlock(fio);
return ret;
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
fprintf(stderr,
"Warning: gro file contains less atoms (%d) than expected"
" (%d)\n",
- natoms, atoms->nr);
+ natoms,
+ atoms->nr);
}
atoms->haveMass = FALSE;
{
box[m][m] = (xmax[m] - xmin[m]);
}
- fprintf(stderr, "Generated a cubic box %8.3f x %8.3f x %8.3f\n", box[XX][XX], box[YY][YY],
- box[ZZ][ZZ]);
+ fprintf(stderr, "Generated a cubic box %8.3f x %8.3f x %8.3f\n", box[XX][XX], box[YY][YY], box[ZZ][ZZ]);
}
else
{
gmx_fatal(FARGS,
"Number of atoms in gro frame (%d) doesn't match the number in the previous "
"frame (%d)",
- atoms.nr, fr->natoms);
+ atoms.nr,
+ fr->natoms);
}
return TRUE;
if ((box[XX][YY] != 0.0F) || (box[XX][ZZ] != 0.0F) || (box[YY][XX] != 0.0F)
|| (box[YY][ZZ] != 0.0F) || (box[ZZ][XX] != 0.0F) || (box[ZZ][YY] != 0.0F))
{
- fprintf(out, "%10.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f\n", box[XX][XX],
- box[YY][YY], box[ZZ][ZZ], box[XX][YY], box[XX][ZZ], box[YY][XX], box[YY][ZZ],
- box[ZZ][XX], box[ZZ][YY]);
+ fprintf(out,
+ "%10.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f\n",
+ box[XX][XX],
+ box[YY][YY],
+ box[ZZ][ZZ],
+ box[XX][YY],
+ box[XX][ZZ],
+ box[YY][XX],
+ box[YY][ZZ],
+ box[ZZ][XX],
+ box[ZZ][YY]);
}
else
{
fflush(out);
}
-void write_hconf_mtop(FILE* out, const char* title, const gmx_mtop_t* mtop, const rvec* x, const rvec* v, const matrix box)
+void write_hconf_mtop(FILE* out, const char* title, const gmx_mtop_t& mtop, const rvec* x, const rvec* v, const matrix box)
{
fprintf(out, "%s\n", (title && title[0]) ? title : gmx::bromacs().c_str());
- fprintf(out, "%5d\n", mtop->natoms);
+ fprintf(out, "%5d\n", mtop.natoms);
const char* format = get_hconf_format(v != nullptr);
- for (const AtomProxy atomP : AtomRange(*mtop))
+ for (const AtomProxy atomP : AtomRange(mtop))
{
int i = atomP.globalAtomNumber();
int residueNumber = atomP.residueNumber();
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const rvec* v,
const matrix box);
-void write_hconf_mtop(FILE* out, const char* title, const gmx_mtop_t* mtop, const rvec* x, const rvec* v, const matrix box);
+void write_hconf_mtop(FILE* out, const char* title, const gmx_mtop_t& mtop, const rvec* x, const rvec* v, const matrix box);
void write_hconf_p(FILE* out, const char* title, const t_atoms* atoms, const rvec* x, const rvec* v, const matrix box);
/* Write a Gromos file with precision ndec: number of decimal places in x,
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/xdr_datatype.h"
#include "gromacs/fileio/xdrf.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/futil.h"
/* This is just for clarity - it can never be anything but 4! */
#define XDR_INT_SIZE 4
-/* same order as the definition of xdr_datatype */
-const char* xdr_datatype_names[] = { "int", "float", "double", "large int", "char", "string" };
+/* Human-friendly names for XdrDataType enum class */
+const char* enumValueToString(XdrDataType enumValue)
+{
+ constexpr gmx::EnumerationArray<XdrDataType, const char*> xdrDataTypeNames = {
+ "int", "float", "double", "large int", "char", "string"
+ };
+ return xdrDataTypeNames[enumValue];
+}
/*___________________________________________________________________________
fprintf(stderr,
"major breakdown in sendints num %u doesn't "
"match size %u\n",
- nums[i], sizes[i]);
+ nums[i],
+ sizes[i]);
exit(1);
}
/* use one step multiply */
*/
if (*size <= 9)
{
- return (xdr_vector(xdrs, reinterpret_cast<char*>(fp), static_cast<unsigned int>(size3),
+ return (xdr_vector(xdrs,
+ reinterpret_cast<char*>(fp),
+ static_cast<unsigned int>(size3),
static_cast<unsigned int>(sizeof(*fp)),
reinterpret_cast<xdrproc_t>(xdr_float)));
}
fprintf(stderr,
"wrong number of coordinates in xdr3dfcoord; "
"%d arg vs %d in file",
- *size, lsize);
+ *size,
+ lsize);
}
*size = lsize;
size3 = *size * 3;
if (*size <= 9)
{
*precision = -1;
- return (xdr_vector(xdrs, reinterpret_cast<char*>(fp), static_cast<unsigned int>(size3),
+ return (xdr_vector(xdrs,
+ reinterpret_cast<char*>(fp),
+ static_cast<unsigned int>(size3),
static_cast<unsigned int>(sizeof(*fp)),
reinterpret_cast<xdrproc_t>(xdr_float)));
}
gmx_fatal(FARGS,
"Not enough lines in colormap file %s"
"(should be %d, found only %d)",
- fn, n + 1, i);
+ fn,
+ n + 1,
+ i);
}
sscanf(line, "%s%s%lf%lf%lf", code, desc, &r, &g, &b);
m[i].code.c1 = code[0];
fprintf(out, "%d\n", n);
for (i = 0; (i < n); i++)
{
- fprintf(out, "%c%c %20s %10g %10g %10g\n", map[i].code.c1 ? map[i].code.c1 : ' ',
- map[i].code.c2 ? map[i].code.c2 : ' ', map[i].desc, map[i].rgb.r, map[i].rgb.g,
+ fprintf(out,
+ "%c%c %20s %10g %10g %10g\n",
+ map[i].code.c1 ? map[i].code.c1 : ' ',
+ map[i].code.c2 ? map[i].code.c2 : ' ',
+ map[i].desc,
+ map[i].rgb.r,
+ map[i].rgb.g,
map[i].rgb.b);
}
}
if (debug)
{
- fprintf(debug, "%s %s %s %s\n", mm.title.c_str(), mm.legend.c_str(), mm.label_x.c_str(),
+ fprintf(debug,
+ "%s %s %s %s\n",
+ mm.title.c_str(),
+ mm.legend.c_str(),
+ mm.label_x.c_str(),
mm.label_y.c_str());
}
gmx_fatal(FARGS,
"Number of read colors map entries (%d) does not match the number in the header "
"(%d)",
- m, nmap);
+ m,
+ nmap);
}
/* Read axes, if there are any */
fprintf(stderr,
"Could not convert matrix to reals,\n"
"color map entry %zd has a non-real description: \"%s\"\n",
- i, in->map[i].desc);
+ i,
+ in->map[i].desc);
return nullptr;
}
rmap[i] = tmp;
if (*nlevels > NMAP * NMAP)
{
- fprintf(stderr, "Warning, too many levels (%d) in matrix, using %d only\n", *nlevels,
+ fprintf(stderr,
+ "Warning, too many levels (%d) in matrix, using %d only\n",
+ *nlevels,
static_cast<int>(NMAP * NMAP));
*nlevels = NMAP * NMAP;
}
r = rlo.r + (i * (rmid.r - rlo.r) / clev_lo);
g = rlo.g + (i * (rmid.g - rlo.g) / clev_lo);
b = rlo.b + (i * (rmid.b - rlo.b) / clev_lo);
- fprintf(out, "\"%c%c c #%02X%02X%02X \" /* \"%.3g\" */,\n", mapper[i % NMAP],
+ fprintf(out,
+ "\"%c%c c #%02X%02X%02X \" /* \"%.3g\" */,\n",
+ mapper[i % NMAP],
(*nlevels <= NMAP) ? ' ' : mapper[i / NMAP],
static_cast<unsigned int>(std::round(255 * r)),
static_cast<unsigned int>(std::round(255 * g)),
- static_cast<unsigned int>(std::round(255 * b)), ((nmid - i) * lo + i * mid) / clev_lo);
+ static_cast<unsigned int>(std::round(255 * b)),
+ ((nmid - i) * lo + i * mid) / clev_lo);
}
for (i = 0; (i < (*nlevels - nmid)); i++)
{
r = rmid.r + (i * (rhi.r - rmid.r) / clev_hi);
g = rmid.g + (i * (rhi.g - rmid.g) / clev_hi);
b = rmid.b + (i * (rhi.b - rmid.b) / clev_hi);
- fprintf(out, "\"%c%c c #%02X%02X%02X \" /* \"%.3g\" */,\n", mapper[(i + nmid) % NMAP],
+ fprintf(out,
+ "\"%c%c c #%02X%02X%02X \" /* \"%.3g\" */,\n",
+ mapper[(i + nmid) % NMAP],
(*nlevels <= NMAP) ? ' ' : mapper[(i + nmid) / NMAP],
static_cast<unsigned int>(std::round(255 * r)),
static_cast<unsigned int>(std::round(255 * g)),
r = rlo.r + fac * (rhi.r - rlo.r);
g = rlo.g + fac * (rhi.g - rlo.g);
b = rlo.b + fac * (rhi.b - rlo.b);
- fprintf(out, "\"%c%c c #%02X%02X%02X \" /* \"%.3g\" */,\n", mapper[(i + i0) % NMAP],
+ fprintf(out,
+ "\"%c%c c #%02X%02X%02X \" /* \"%.3g\" */,\n",
+ mapper[(i + i0) % NMAP],
(nlevel <= NMAP) ? ' ' : mapper[(i + i0) / NMAP],
static_cast<unsigned int>(std::round(255 * r)),
static_cast<unsigned int>(std::round(255 * g)),
- static_cast<unsigned int>(std::round(255 * b)), lo + fac * (hi - lo));
+ static_cast<unsigned int>(std::round(255 * b)),
+ lo + fac * (hi - lo));
}
}
n = *nlevel;
for (i = 0; (i < n); i++)
{
- fprintf(out, "\"%c%c c #%02X%02X%02X \" /* \"%3d\" */,\n", mapper[(i + i0) % NMAP],
+ fprintf(out,
+ "\"%c%c c #%02X%02X%02X \" /* \"%3d\" */,\n",
+ mapper[(i + i0) % NMAP],
(n <= NMAP) ? ' ' : mapper[(i + i0) / NMAP],
static_cast<unsigned int>(round(255 * rgbd[i].r)),
static_cast<unsigned int>(round(255 * rgbd[i].g)),
- static_cast<unsigned int>(round(255 * rgbd[i].b)), i);
+ static_cast<unsigned int>(round(255 * rgbd[i].b)),
+ i);
}
}
if (*nlevels > NMAP * NMAP)
{
- fprintf(stderr, "Warning, too many levels (%d) in matrix, using %d only\n", *nlevels,
+ fprintf(stderr,
+ "Warning, too many levels (%d) in matrix, using %d only\n",
+ *nlevels,
static_cast<int>(NMAP * NMAP));
*nlevels = NMAP * NMAP;
}
r = (nlo * rlo.r + i * rhi.r) * invlevel;
g = (nlo * rlo.g + i * rhi.g) * invlevel;
b = (nlo * rlo.b + i * rhi.b) * invlevel;
- fprintf(out, "\"%c%c c #%02X%02X%02X \" /* \"%.3g\" */,\n", mapper[i % NMAP],
+ fprintf(out,
+ "\"%c%c c #%02X%02X%02X \" /* \"%.3g\" */,\n",
+ mapper[i % NMAP],
(*nlevels <= NMAP) ? ' ' : mapper[i / NMAP],
static_cast<unsigned int>(std::round(255 * r)),
static_cast<unsigned int>(std::round(255 * g)),
- static_cast<unsigned int>(std::round(255 * b)), (nlo * lo + i * hi) * invlevel);
+ static_cast<unsigned int>(std::round(255 * b)),
+ (nlo * lo + i * hi) * invlevel);
}
}
gmx_fatal(FARGS,
"Range checking i = %d, j = %d, c = %d, bot = %d, top = %d "
"matrix[i,j] = %f",
- i, j, c, nlevel_bot, nlevel_top, mat[i][j]);
+ i,
+ j,
+ c,
+ nlevel_bot,
+ nlevel_top,
+ mat[i][j]);
}
}
else if (i > j)
gmx_fatal(FARGS,
"Range checking i = %d, j = %d, c = %d, bot = %d, top = %d "
"matrix[i,j] = %f",
- i, j, c, nlevel_bot, nlevel_top, mat[i][j]);
+ i,
+ j,
+ c,
+ nlevel_bot,
+ nlevel_top,
+ mat[i][j]);
}
}
else
fprintf(out, "\"%d %d %zu %d\",\n", m.nx, m.ny, m.map.size(), bOneChar ? 1 : 2);
for (const auto& map : m.map)
{
- fprintf(out, "\"%c%c c #%02X%02X%02X \" /* \"%s\" */,\n", map.code.c1,
- bOneChar ? ' ' : map.code.c2, static_cast<unsigned int>(round(map.rgb.r * 255)),
+ fprintf(out,
+ "\"%c%c c #%02X%02X%02X \" /* \"%s\" */,\n",
+ map.code.c1,
+ bOneChar ? ' ' : map.code.c2,
+ static_cast<unsigned int>(round(map.rgb.r * 255)),
static_cast<unsigned int>(round(map.rgb.g * 255)),
- static_cast<unsigned int>(round(map.rgb.b * 255)), map.desc);
+ static_cast<unsigned int>(round(map.rgb.b * 255)),
+ map.desc);
}
writeXpmAxis(out, "x", m.axis_x);
writeXpmAxis(out, "y", m.axis_y);
}
write_xpm_header(out, title, legend, label_x, label_y, FALSE);
- write_xpm_map_split(out, n_x, n_y, nlevel_top, lo_top, hi_top, rlo_top, rhi_top, bDiscreteColor,
- nlevel_bot, lo_bot, hi_bot, rlo_bot, rhi_bot);
+ write_xpm_map_split(
+ out, n_x, n_y, nlevel_top, lo_top, hi_top, rlo_top, rhi_top, bDiscreteColor, nlevel_bot, lo_bot, hi_bot, rlo_bot, rhi_bot);
writeXpmAxis(out, "x", ArrayRef<real>(axis_x, axis_x + n_x + ((flags & MAT_SPATIAL_X) != 0U ? 1 : 0)));
writeXpmAxis(out, "y", ArrayRef<real>(axis_y, axis_y + n_y + ((flags & MAT_SPATIAL_Y) != 0U ? 1 : 0)));
write_xpm_data_split(out, n_x, n_y, mat, lo_top, hi_top, *nlevel_top, lo_bot, hi_bot, *nlevel_bot);
gmx_fseek(gmx_fio_getfp(mrcFile), 0, SEEK_SET);
// Read whole file into buffer the size of the file
std::vector<char> fileContentBuffer(fileSize);
- size_t readSize = fread(fileContentBuffer.data(), sizeof(char), fileContentBuffer.size(),
- gmx_fio_getfp(mrcFile));
+ size_t readSize = fread(
+ fileContentBuffer.data(), sizeof(char), fileContentBuffer.size(), gmx_fio_getfp(mrcFile));
gmx_fio_close(mrcFile);
if (fileContentBuffer.size() != readSize)
{
MultiDimArray<std::vector<float>, dynamicExtents3D> result(
getDynamicExtents3D(impl_->reader().header()));
- std::copy(std::begin(impl_->reader().constView()), std::end(impl_->reader().constView()),
+ std::copy(std::begin(impl_->reader().constView()),
+ std::end(impl_->reader().constView()),
begin(result.asView()));
return result;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \inlibraryapi
* \ingroup module_fileio
*/
+#include <memory>
#include <string>
#include <vector>
#include "gromacs/math/multidimarray.h"
#include "gromacs/mdspan/extensions.h"
-#include "gromacs/utility/classhelpers.h"
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
/*! \libinternal \brief Read an mrc density map from a given file.
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
/*! \libinternal \brief Write an mrc/ccp4 file that contains float values.
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
template<typename Container>
bool anyLargerThanValue(Container values, typename Container::value_type boundaryValue)
{
- return std::any_of(std::begin(values), std::end(values),
- [boundaryValue](auto v) { return v > boundaryValue; });
+ return std::any_of(std::begin(values), std::end(values), [boundaryValue](auto v) {
+ return v > boundaryValue;
+ });
}
} // namespace
RVec scale = { header.extent_[XX] / (header.cellLength_[XX] * c_AAtoNmConversion),
header.extent_[YY] / (header.cellLength_[YY] * c_AAtoNmConversion),
header.extent_[ZZ] / (header.cellLength_[ZZ] * c_AAtoNmConversion) };
- const RVec emdbOrigin{ header.userDefinedFloat_[12], header.userDefinedFloat_[13],
+ const RVec emdbOrigin{ header.userDefinedFloat_[12],
+ header.userDefinedFloat_[13],
header.userDefinedFloat_[14] };
RVec translation;
if (emdbOrigin[XX] == 0. && emdbOrigin[YY] == 0. && emdbOrigin[ZZ] == 0.)
}
else
{
- translation = { -emdbOrigin[XX] * c_AAtoNmConversion, -emdbOrigin[YY] * c_AAtoNmConversion,
+ translation = { -emdbOrigin[XX] * c_AAtoNmConversion,
+ -emdbOrigin[YY] * c_AAtoNmConversion,
-emdbOrigin[ZZ] * c_AAtoNmConversion };
}
return { scale, translation };
dynamicExtents3D getDynamicExtents3D(const MrcDensityMapHeader& header)
{
- return { header.numColumnRowSection_[ZZ], header.numColumnRowSection_[YY],
+ return { header.numColumnRowSection_[ZZ],
+ header.numColumnRowSection_[YY],
header.numColumnRowSection_[XX] };
};
}
gmx_fio_do_int(fio, prec);
- fprintf(stderr, "Reading %s precision matrix generated by GROMACS %s\n",
- (prec == 1) ? "double" : "single", gmxver);
+ fprintf(stderr,
+ "Reading %s precision matrix generated by GROMACS %s\n",
+ (prec == 1) ? "double" : "single",
+ gmxver);
gmx_fio_do_int(fio, i);
*nrow = i;
*/
#include "gmxpre.h"
-#include "oenv.h"
+#include "gromacs/fileio/oenv.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/exceptions.h"
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "pdbio.h"
+#include "gromacs/fileio/pdbio.h"
+#include <algorithm>
#include <cctype>
#include <cmath>
#include <cstdlib>
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/atomprop.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/coolstuff.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/snprintf.h"
+#include "gromacs/utility/stringtoenumvalueconverter.h"
typedef struct
{
gmx_conection_t* conect;
} gmx_conect_t;
-static const char* pdbtp[epdbNR] = { "ATOM ", "HETATM", "ANISOU", "CRYST1", "COMPND", "MODEL",
- "ENDMDL", "TER", "HEADER", "TITLE", "REMARK", "CONECT" };
+const char* enumValueToString(PdbRecordType enumValue)
+{
+ static constexpr gmx::EnumerationArray<PdbRecordType, const char*> pdbRecordTypeName = {
+ "ATOM ", "HETATM", "ANISOU", "CRYST1", "COMPND", "MODEL",
+ "ENDMDL", "TER", "HEADER", "TITLE", "REMARK", "CONECT"
+ };
+ return pdbRecordTypeName[enumValue];
+}
#define REMARK_SIM_BOX "REMARK THIS IS A SIMULATION BOX"
if (norm2(box[YY]) * norm2(box[ZZ]) != 0)
{
- alpha = RAD2DEG * gmx_angle(box[YY], box[ZZ]);
+ alpha = gmx::c_rad2Deg * gmx_angle(box[YY], box[ZZ]);
}
else
{
}
if (norm2(box[XX]) * norm2(box[ZZ]) != 0)
{
- beta = RAD2DEG * gmx_angle(box[XX], box[ZZ]);
+ beta = gmx::c_rad2Deg * gmx_angle(box[XX], box[ZZ]);
}
else
{
}
if (norm2(box[XX]) * norm2(box[YY]) != 0)
{
- gamma = RAD2DEG * gmx_angle(box[XX], box[YY]);
+ gamma = gmx::c_rad2Deg * gmx_angle(box[XX], box[YY]);
}
else
{
fprintf(out, "REMARK THIS IS A SIMULATION BOX\n");
if (pbcType != PbcType::Screw)
{
- fprintf(out, "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n", 10 * norm(box[XX]),
- 10 * norm(box[YY]), 10 * norm(box[ZZ]), alpha, beta, gamma, "P 1", 1);
+ fprintf(out,
+ "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n",
+ 10 * norm(box[XX]),
+ 10 * norm(box[YY]),
+ 10 * norm(box[ZZ]),
+ alpha,
+ beta,
+ gamma,
+ "P 1",
+ 1);
}
else
{
/* Double the a-vector length and write the correct space group */
- fprintf(out, "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n", 20 * norm(box[XX]),
- 10 * norm(box[YY]), 10 * norm(box[ZZ]), alpha, beta, gamma, "P 21 1 1", 1);
+ fprintf(out,
+ "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n",
+ 20 * norm(box[XX]),
+ 10 * norm(box[YY]),
+ 10 * norm(box[ZZ]),
+ alpha,
+ beta,
+ gamma,
+ "P 21 1 1",
+ 1);
}
}
{
if (alpha != 90.0)
{
- cosa = std::cos(alpha * DEG2RAD);
+ cosa = std::cos(alpha * gmx::c_deg2Rad);
}
else
{
}
if (beta != 90.0)
{
- cosb = std::cos(beta * DEG2RAD);
+ cosb = std::cos(beta * gmx::c_deg2Rad);
}
else
{
}
if (gamma != 90.0)
{
- cosg = std::cos(gamma * DEG2RAD);
- sing = std::sin(gamma * DEG2RAD);
+ cosg = std::cos(gamma * gmx::c_deg2Rad);
+ sing = std::sin(gamma * gmx::c_deg2Rad);
}
else
{
}
}
-static int gmx_fprintf_pqr_atomline(FILE* fp,
- enum PDB_record record,
- int atom_seq_number,
- const char* atom_name,
- const char* res_name,
- char chain_id,
- int res_seq_number,
- real x,
- real y,
- real z,
- real occupancy,
- real b_factor)
+static int gmx_fprintf_pqr_atomline(FILE* fp,
+ PdbRecordType record,
+ int atom_seq_number,
+ const char* atom_name,
+ const char* res_name,
+ char chain_id,
+ int res_seq_number,
+ real x,
+ real y,
+ real z,
+ real occupancy,
+ real b_factor)
{
- GMX_RELEASE_ASSERT(record == epdbATOM || record == epdbHETATM,
+ GMX_RELEASE_ASSERT(record == PdbRecordType::Atom || record == PdbRecordType::Hetatm,
"Can only print PQR atom lines as ATOM or HETATM records");
/* Check atom name */
atom_seq_number = atom_seq_number % 100000;
res_seq_number = res_seq_number % 10000;
- int n = fprintf(fp, "%-6s%5d %-4.4s%4.4s%c%4d %8.3f %8.3f %8.3f %6.2f %6.2f\n", pdbtp[record],
- atom_seq_number, atom_name, res_name, chain_id, res_seq_number, x, y, z,
- occupancy, b_factor);
+ int n = fprintf(fp,
+ "%-6s%5d %-4.4s%4.4s%c%4d %8.3f %8.3f %8.3f %6.2f %6.2f\n",
+ enumValueToString(record),
+ atom_seq_number,
+ atom_name,
+ res_name,
+ chain_id,
+ res_seq_number,
+ x,
+ y,
+ z,
+ occupancy,
+ b_factor);
return n;
}
gmx_conect conect,
bool usePqrFormat)
{
- gmx_conect_t* gc = static_cast<gmx_conect_t*>(conect);
- enum PDB_record type;
- char altloc;
- real occup, bfac;
- gmx_bool bOccup;
+ gmx_conect_t* gc = static_cast<gmx_conect_t*>(conect);
+ PdbRecordType type;
+ char altloc;
+ real occup, bfac;
+ gmx_bool bOccup;
fprintf(out, "TITLE %s\n", (title && title[0]) ? title : gmx::bromacs().c_str());
{
gmx_pdbinfo_init_default(&pdbinfo);
}
- type = static_cast<enum PDB_record>(pdbinfo.type);
+ type = pdbinfo.type;
altloc = pdbinfo.altloc;
if (!isalnum(altloc))
{
bfac = pdbinfo.bfac;
if (!usePqrFormat)
{
- gmx_fprintf_pdb_atomline(out, type, i + 1, nm.c_str(), altloc, resnm.c_str(), ch, resnr,
- resic, 10 * x[i][XX], 10 * x[i][YY], 10 * x[i][ZZ], occup,
- bfac, atoms->atom[i].elem);
+ gmx_fprintf_pdb_atomline(out,
+ type,
+ i + 1,
+ nm.c_str(),
+ altloc,
+ resnm.c_str(),
+ ch,
+ resnr,
+ resic,
+ 10 * x[i][XX],
+ 10 * x[i][YY],
+ 10 * x[i][ZZ],
+ occup,
+ bfac,
+ atoms->atom[i].elem);
if (atoms->pdbinfo && atoms->pdbinfo[i].bAnisotropic)
{
- fprintf(out, "ANISOU%5d %-4.4s%4.4s%c%4d%c %7d%7d%7d%7d%7d%7d\n", (i + 1) % 100000,
- nm.c_str(), resnm.c_str(), ch, resnr, (resic == '\0') ? ' ' : resic,
- atoms->pdbinfo[i].uij[0], atoms->pdbinfo[i].uij[1], atoms->pdbinfo[i].uij[2],
- atoms->pdbinfo[i].uij[3], atoms->pdbinfo[i].uij[4], atoms->pdbinfo[i].uij[5]);
+ fprintf(out,
+ "ANISOU%5d %-4.4s%4.4s%c%4d%c %7d%7d%7d%7d%7d%7d\n",
+ (i + 1) % 100000,
+ nm.c_str(),
+ resnm.c_str(),
+ ch,
+ resnr,
+ (resic == '\0') ? ' ' : resic,
+ atoms->pdbinfo[i].uij[0],
+ atoms->pdbinfo[i].uij[1],
+ atoms->pdbinfo[i].uij[2],
+ atoms->pdbinfo[i].uij[3],
+ atoms->pdbinfo[i].uij[4],
+ atoms->pdbinfo[i].uij[5]);
}
}
else
{
- gmx_fprintf_pqr_atomline(out, type, i + 1, nm.c_str(), resnm.c_str(), ch, resnr,
- 10 * x[i][XX], 10 * x[i][YY], 10 * x[i][ZZ], occup, bfac);
+ gmx_fprintf_pqr_atomline(out,
+ type,
+ i + 1,
+ nm.c_str(),
+ resnm.c_str(),
+ ch,
+ resnr,
+ 10 * x[i][XX],
+ 10 * x[i][YY],
+ 10 * x[i][ZZ],
+ occup,
+ bfac);
}
}
{
index[i] = i;
}
- write_pdbfile_indexed(out, title, atoms, x, pbcType, box, chainid, model_nr, atoms->nr, index,
- conect, false);
+ write_pdbfile_indexed(
+ out, title, atoms, x, pbcType, box, chainid, model_nr, atoms->nr, index, conect, false);
sfree(index);
}
-static int line2type(const char* line)
-{
- int k;
- char type[8];
-
- for (k = 0; (k < 6); k++)
- {
- type[k] = line[k];
- }
- type[k] = '\0';
-
- for (k = 0; (k < epdbNR); k++)
- {
- if (std::strncmp(type, pdbtp[k], strlen(pdbtp[k])) == 0)
- {
- break;
- }
- }
-
- return k;
-}
-
static void read_anisou(char line[], int natom, t_atoms* atoms)
{
int i, j, k, atomnr;
}
else
{
- if (sscanf(line + 29, "%d%d%d%d%d%d", &atoms->pdbinfo[i].uij[U11], &atoms->pdbinfo[i].uij[U22],
- &atoms->pdbinfo[i].uij[U33], &atoms->pdbinfo[i].uij[U12],
- &atoms->pdbinfo[i].uij[U13], &atoms->pdbinfo[i].uij[U23])
+ if (sscanf(line + 29,
+ "%d%d%d%d%d%d",
+ &atoms->pdbinfo[i].uij[U11],
+ &atoms->pdbinfo[i].uij[U22],
+ &atoms->pdbinfo[i].uij[U33],
+ &atoms->pdbinfo[i].uij[U12],
+ &atoms->pdbinfo[i].uij[U13],
+ &atoms->pdbinfo[i].uij[U23])
== 6)
{
atoms->pdbinfo[i].bAnisotropic = TRUE;
atomNumberSet = true;
}
}
- std::string buf;
+ static constexpr size_t sc_maxElementNameLength = 3;
+ static_assert(sizeof(atoms->atom[i].elem) >= sc_maxElementNameLength + 1);
+ std::string element;
if (atomNumberSet)
{
atoms->atom[i].atomnumber = atomnumber;
- buf = aps->elementFromAtomNumber(atomnumber);
+ element = aps->elementFromAtomNumber(atomnumber);
if (debug)
{
fprintf(debug, "Atomnumber for atom '%s' is %d\n", anm, atomnumber);
}
}
- buf.resize(3);
- std::strncpy(atoms->atom[i].elem, buf.c_str(), 4);
+ element.resize(sc_maxElementNameLength);
+ std::strcpy(atoms->atom[i].elem, element.c_str());
}
}
-static int read_atom(t_symtab* symtab, const char line[], int type, int natom, t_atoms* atoms, rvec x[], int chainnum)
+static int
+read_atom(t_symtab* symtab, const char line[], PdbRecordType type, int natom, t_atoms* atoms, rvec x[], int chainnum)
{
t_atom* atomn;
int j, k;
gmx_bool bCOMPND;
gmx_bool bConnWarn = FALSE;
char line[STRLEN + 1];
- int line_type;
char * c, *d;
int natom, chainnum;
gmx_bool bStop = FALSE;
title[0] = '\0';
natom = 0;
chainnum = 0;
+ static const gmx::StringToEnumValueConverter<PdbRecordType, enumValueToString, gmx::StringCompareType::Exact, gmx::StripStrings::Yes>
+ sc_pdbRecordTypeIdentifier;
while (!bStop && (fgets2(line, STRLEN, in) != nullptr))
{
- line_type = line2type(line);
+ // Convert line to a null-terminated string, then take a substring of at most 6 chars
+ std::string lineAsString(line);
+ std::optional<PdbRecordType> line_type =
+ sc_pdbRecordTypeIdentifier.valueFrom(lineAsString.substr(0, 6));
+ if (!line_type)
+ {
+ // Skip this line because it does not start with a
+ // recognized leading string describing a PDB record type.
+ continue;
+ }
- switch (line_type)
+ switch (line_type.value())
{
- case epdbATOM:
- case epdbHETATM:
- natom = read_atom(symtab, line, line_type, natom, atoms, x, chainnum);
+ case PdbRecordType::Atom:
+ case PdbRecordType::Hetatm:
+ natom = read_atom(symtab, line, line_type.value(), natom, atoms, x, chainnum);
break;
- case epdbANISOU:
+ case PdbRecordType::Anisou:
if (atoms->havePdbInfo)
{
read_anisou(line, natom, atoms);
}
break;
- case epdbCRYST1: read_cryst1(line, pbcType, box); break;
+ case PdbRecordType::Cryst1: read_cryst1(line, pbcType, box); break;
- case epdbTITLE:
- case epdbHEADER:
+ case PdbRecordType::Title:
+ case PdbRecordType::Header:
if (std::strlen(line) > 6)
{
c = line + 6;
}
break;
- case epdbCOMPND:
+ case PdbRecordType::Compound:
if ((!std::strstr(line, ": ")) || (std::strstr(line + 6, "MOLECULE:")))
{
if (!(c = std::strstr(line + 6, "MOLECULE:")))
}
break;
- case epdbTER: chainnum++; break;
+ case PdbRecordType::Ter: chainnum++; break;
- case epdbMODEL:
+ case PdbRecordType::Model:
if (model_nr)
{
sscanf(line, "%*s%d", model_nr);
}
break;
- case epdbENDMDL: bStop = TRUE; break;
- case epdbCONECT:
+ case PdbRecordType::EndModel: bStop = TRUE; break;
+ case PdbRecordType::Conect:
if (gc)
{
gmx_conect_addline(gc, line);
return gc;
}
-int gmx_fprintf_pdb_atomline(FILE* fp,
- enum PDB_record record,
- int atom_seq_number,
- const char* atom_name,
- char alternate_location,
- const char* res_name,
- char chain_id,
- int res_seq_number,
- char res_insertion_code,
- real x,
- real y,
- real z,
- real occupancy,
- real b_factor,
- const char* element)
+int gmx_fprintf_pdb_atomline(FILE* fp,
+ PdbRecordType record,
+ int atom_seq_number,
+ const char* atom_name,
+ char alternate_location,
+ const char* res_name,
+ char chain_id,
+ int res_seq_number,
+ char res_insertion_code,
+ real x,
+ real y,
+ real z,
+ real occupancy,
+ real b_factor,
+ const char* element)
{
char tmp_atomname[6], tmp_resname[6];
gmx_bool start_name_in_col13;
int n;
- if (record != epdbATOM && record != epdbHETATM)
+ if (record != PdbRecordType::Atom && record != PdbRecordType::Hetatm)
{
gmx_fatal(FARGS, "Can only print PDB atom lines as ATOM or HETATM records");
}
atom_seq_number = atom_seq_number % 100000;
res_seq_number = res_seq_number % 10000;
- n = fprintf(fp, "%-6s%5d %-4.4s%c%4.4s%c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f %2s\n",
- pdbtp[record], atom_seq_number, tmp_atomname, alternate_location, tmp_resname,
- chain_id, res_seq_number, res_insertion_code, x, y, z, occupancy, b_factor,
+ n = fprintf(fp,
+ "%-6s%5d %-4.4s%c%4.4s%c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f %2s\n",
+ enumValueToString(record),
+ atom_seq_number,
+ tmp_atomname,
+ alternate_location,
+ tmp_resname,
+ chain_id,
+ res_seq_number,
+ res_insertion_code,
+ x,
+ y,
+ z,
+ occupancy,
+ b_factor,
(element != nullptr) ? element : "");
return n;
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/binaryinformation.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/keyvaluetreebuilder.h"
{
gmx::KeyValueTreeBuilder builder;
auto root = builder.rootObject();
- for (auto& local : inp)
+ for (const auto& local : inp)
{
root.addValue<std::string>(local.name_, !local.value_.empty() ? local.value_ : "");
}
}
else
{
- writer.writeLine(formatString("%-24s = %s", local.name_.c_str(),
+ writer.writeLine(formatString("%-24s = %s",
+ local.name_.c_str(),
!local.value_.empty() ? local.value_.c_str() : ""));
}
}
gmx_fatal(FARGS,
"A parameter is present with both the old name '%s' and the new name "
"'%s'.",
- local.name_.c_str(), inp[foundIndex].name_.c_str());
+ local.name_.c_str(),
+ inp[foundIndex].name_.c_str());
}
local.name_.assign(new_entry);
}
}
-static int get_einp(std::vector<t_inpfile>* inp, const char* name)
+int get_einp(std::vector<t_inpfile>* inp, const char* name)
{
std::vector<t_inpfile>& inpRef = *inp;
bool notfound = false;
sprintf(warn_buf,
"Right hand side '%s' for parameter '%s' in parameter file is not an integer "
"value\n",
- inpRef[ii].value_.c_str(), inpRef[ii].name_.c_str());
+ inpRef[ii].value_.c_str(),
+ inpRef[ii].name_.c_str());
warning_error(wi, warn_buf);
}
sprintf(warn_buf,
"Right hand side '%s' for parameter '%s' in parameter file is not an integer "
"value\n",
- inpRef[ii].value_.c_str(), inpRef[ii].name_.c_str());
+ inpRef[ii].value_.c_str(),
+ inpRef[ii].name_.c_str());
warning_error(wi, warn_buf);
}
sprintf(warn_buf,
"Right hand side '%s' for parameter '%s' in parameter file is not a real "
"value\n",
- inpRef[ii].value_.c_str(), inpRef[ii].name_.c_str());
+ inpRef[ii].value_.c_str(),
+ inpRef[ii].name_.c_str());
warning_error(wi, warn_buf);
}
if (defs[i] == nullptr)
{
- n += sprintf(buf, "Invalid enum '%s' for variable %s, using '%s'\n",
- inpRef[ii].value_.c_str(), name, defs[0]);
+ n += sprintf(buf,
+ "Invalid enum '%s' for variable %s, using '%s'\n",
+ inpRef[ii].value_.c_str(),
+ name,
+ defs[0]);
n += sprintf(buf + n, "Next time use one of:");
int j = 0;
while (defs[j])
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <utility>
#include <vector>
+#include "gromacs/fileio/warninp.h"
#include "gromacs/utility/basedefinitions.h"
-
-struct warninp;
-typedef warninp* warninp_t;
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/enumerationhelpers.h"
+#include "gromacs/utility/stringutil.h"
namespace gmx
{
int get_eenum(std::vector<t_inpfile>* inp, const char* name, const char** defs);
/* defs must be NULL terminated */
+//! Get index of option `name`. Exposed here so that `getEnum` can access it.
+int get_einp(std::vector<t_inpfile>* inp, const char* name);
+
+/*! \brief Read option from input and return corresponding enum value
+ *
+ * If the option is not set, return the first value of the enum as default.
+ * Defined here so we don't need to instantiate the templates in the source file.
+ *
+ * \tparam EnumType The type of enum to be returned
+ * \param[in] inp The input file vector
+ * \param[in] name The name of the option to be read
+ * \param[out] wi Handler for context-sensitive warnings.
+ * \return Enum value corresponding to read input
+ */
+template<typename EnumType>
+EnumType getEnum(std::vector<t_inpfile>* inp, const char* name, warninp* wi)
+{
+ // If there's no valid option, we'll use the EnumType::Default.
+ // Note, this assumes the enum is zero based, which is also assumed by
+ // EnumerationWrapper and EnumerationArray.
+ const auto defaultEnumValue = EnumType::Default;
+ const auto& defaultName = enumValueToString(defaultEnumValue);
+ // Get index of option in input
+ const auto ii = get_einp(inp, name);
+ if (ii == -1)
+ {
+ // If the option wasn't set, we return EnumType::Default
+ inp->back().value_.assign(defaultName);
+ return defaultEnumValue;
+ }
+
+ // Check if option string can be mapped to a valid enum value.
+ //
+ // Note that this cannot be replaced with
+ // StringToEnumValueConverter until all instantiations of this
+ // function have a matching enumValueToString, and all of the
+ // latter are in the same namespace. Currently some of those
+ // function declarations are in gmx namespace and some are not.
+ const auto* optionString = (*inp)[ii].value_.c_str();
+ for (auto enumValue : gmx::EnumerationWrapper<EnumType>{})
+ {
+ if (gmx_strcasecmp_min(enumValueToString(enumValue), optionString) == 0)
+ {
+ return enumValue;
+ }
+ }
+
+ // If we get here, the option set is invalid. Print error.
+ std::string errorMessage = gmx::formatString(
+ "Invalid enum '%s' for variable %s, using '%s'\n", optionString, name, defaultName);
+ errorMessage += gmx::formatString("Next time, use one of:");
+ for (auto enumValue : gmx::EnumerationWrapper<EnumType>{})
+ {
+ errorMessage += gmx::formatString(" '%s'", enumValueToString(enumValue));
+ }
+ if (wi != nullptr)
+ {
+ warning_error(wi, errorMessage);
+ }
+ else
+ {
+ fprintf(stderr, "%s\n", errorMessage.c_str());
+ }
+ (*inp)[ii].value_.assign(defaultName);
+ return defaultEnumValue;
+}
+
+
//! Replace for macro CCTYPE, prints comment string after newline
void printStringNewline(std::vector<t_inpfile>* inp, const char* line);
//! Replace for macro CTYPE, prints comment string
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
${tng_sources}
xvgio.cpp
)
+target_link_libraries(fileio-test PRIVATE legacy_api)
void writeReferenceFile()
{
- write_sto_conf(referenceFilename_.c_str(), *refTop_->name, &refTop_->atoms,
- as_rvec_array(refX_.data()), nullptr, PbcType::Unset, refBox_);
+ write_sto_conf(referenceFilename_.c_str(),
+ *refTop_->name,
+ &refTop_->atoms,
+ as_rvec_array(refX_.data()),
+ nullptr,
+ PbcType::Unset,
+ refBox_);
}
void readReferenceFileTps()
void writeTestFileAndTest()
{
- write_sto_conf(testFilename_.c_str(), *testTop_->name, &testTop_->atoms, testX_, nullptr,
- PbcType::Unset, testBox_);
+ write_sto_conf(
+ testFilename_.c_str(), *testTop_->name, &testTop_->atoms, testX_, nullptr, PbcType::Unset, testBox_);
testFilesEqual(referenceFilename_, testFilename_);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
class FileMD5Test : public ::testing::Test
{
public:
- void prepareFile(int lengthInBytes)
+ void prepareFile(int lengthInBytes) const
{
// Fill some memory with some arbitrary bits.
std::vector<char> data(lengthInBytes);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
TestReferenceData refData;
TestReferenceChecker checker(refData.rootChecker());
- checker.checkSequence(begin(densityData.asConstView()), end(densityData.asConstView()),
+ checker.checkSequence(begin(densityData.asConstView()),
+ end(densityData.asConstView()),
"data ellipsoid density");
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void useStringAsXvgFile(const std::string& xvgString) { referenceContents_ = xvgString; }
- void writeXvgFile()
+ void writeXvgFile() const
{
gmx::TextWriter::writeFileFromString(referenceFilename(), referenceContents());
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "timecontrol.h"
-#include "thread_mpi/threads.h"
+#include <mutex>
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/fatalerror.h"
Please keep it that way. */
/* Globals for trajectory input */
-typedef struct
+struct t_timecontrol
{
- real t;
- gmx_bool bSet;
-} t_timecontrol;
+ t_timecontrol(real inputT, bool inputSet) : t(inputT), bSet(inputSet) {}
+ real t;
+ bool bSet;
+};
-static t_timecontrol timecontrol[TNR] = { { 0, FALSE }, { 0, FALSE }, { 0, FALSE } };
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static gmx::EnumerationArray<TimeControl, t_timecontrol> timecontrol = { t_timecontrol(0, false),
+ t_timecontrol(0, false),
+ t_timecontrol(0, false) };
-static tMPI_Thread_mutex_t tc_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static std::mutex g_timeControlMutex;
-gmx_bool bTimeSet(int tcontrol)
+gmx_bool bTimeSet(TimeControl tcontrol)
{
gmx_bool ret;
- tMPI_Thread_mutex_lock(&tc_mutex);
- range_check(tcontrol, 0, TNR);
+ const std::lock_guard<std::mutex> lock(g_timeControlMutex);
ret = timecontrol[tcontrol].bSet;
- tMPI_Thread_mutex_unlock(&tc_mutex);
return ret;
}
-real rTimeValue(int tcontrol)
+real rTimeValue(TimeControl tcontrol)
{
real ret;
- tMPI_Thread_mutex_lock(&tc_mutex);
- range_check(tcontrol, 0, TNR);
+ const std::lock_guard<std::mutex> lock(g_timeControlMutex);
ret = timecontrol[tcontrol].t;
- tMPI_Thread_mutex_unlock(&tc_mutex);
return ret;
}
-void setTimeValue(int tcontrol, real value)
+void setTimeValue(TimeControl tcontrol, real value)
{
- tMPI_Thread_mutex_lock(&tc_mutex);
- range_check(tcontrol, 0, TNR);
+ const std::lock_guard<std::mutex> lock(g_timeControlMutex);
timecontrol[tcontrol].t = value;
timecontrol[tcontrol].bSet = TRUE;
- tMPI_Thread_mutex_unlock(&tc_mutex);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* The code below is to facilitate controlled begin and end of
* trajectory reading.
*/
-enum
+enum class TimeControl : int
{
- TBEGIN,
- TEND,
- TDELTA,
- TNR
+ Begin,
+ End,
+ Delta,
+ Count
};
-gmx_bool bTimeSet(int tcontrol);
+bool bTimeSet(TimeControl tcontrol);
-real rTimeValue(int tcontrol);
+real rTimeValue(TimeControl tcontrol);
-void setTimeValue(int tcontrol, real value);
+void setTimeValue(TimeControl tcontrol, real value);
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
# if GMX_DOUBLE
precisionString = " (double precision)";
# endif
- sprintf(programInfo, "%.100s %.128s%.24s", gmx::getProgramContext().displayName(),
- gmx_version(), precisionString);
+ sprintf(programInfo, "%.100s %.128s%.24s", gmx::getProgramContext().displayName(), gmx_version(), precisionString);
if (mode == 'w')
{
tng_first_program_name_set(*tng, programInfo);
* number the latter should be used. Wait for TNG 2.0*/
tng_chain_residue_add(tng, tngChain, *resInfo->name, &tngRes);
}
- tng_residue_atom_add(tng, tngRes, *(atoms->atomname[atomIndex]),
- *(atoms->atomtype[atomIndex]), &tngAtom);
+ tng_residue_atom_add(
+ tng, tngRes, *(atoms->atomname[atomIndex]), *(atoms->atomtype[atomIndex]), &tngAtom);
}
}
tng_molecule_cnt_set(tng, *tngMol, numMolecules);
}
for (int molCounter = 1; molCounter < molBlock.nmol; molCounter++)
{
- std::copy_n(atomCharges.end() - molType->atoms.nr, molType->atoms.nr,
+ std::copy_n(atomCharges.end() - molType->atoms.nr,
+ molType->atoms.nr,
std::back_inserter(atomCharges));
- std::copy_n(atomMasses.end() - molType->atoms.nr, molType->atoms.nr,
- std::back_inserter(atomMasses));
+ std::copy_n(atomMasses.end() - molType->atoms.nr, molType->atoms.nr, std::back_inserter(atomMasses));
}
}
/* Write the TNG data blocks. */
- tng_particle_data_block_add(tng, TNG_TRAJ_PARTIAL_CHARGES, "PARTIAL CHARGES", datatype,
- TNG_NON_TRAJECTORY_BLOCK, 1, 1, 1, 0, mtop->natoms,
- TNG_GZIP_COMPRESSION, atomCharges.data());
- tng_particle_data_block_add(tng, TNG_TRAJ_MASSES, "ATOM MASSES", datatype, TNG_NON_TRAJECTORY_BLOCK,
- 1, 1, 1, 0, mtop->natoms, TNG_GZIP_COMPRESSION, atomMasses.data());
+ tng_particle_data_block_add(tng,
+ TNG_TRAJ_PARTIAL_CHARGES,
+ "PARTIAL CHARGES",
+ datatype,
+ TNG_NON_TRAJECTORY_BLOCK,
+ 1,
+ 1,
+ 1,
+ 0,
+ mtop->natoms,
+ TNG_GZIP_COMPRESSION,
+ atomCharges.data());
+ tng_particle_data_block_add(tng,
+ TNG_TRAJ_MASSES,
+ "ATOM MASSES",
+ datatype,
+ TNG_NON_TRAJECTORY_BLOCK,
+ 1,
+ 1,
+ 1,
+ 0,
+ mtop->natoms,
+ TNG_GZIP_COMPRESSION,
+ atomMasses.data());
}
/*! \libinternal \brief Compute greatest common divisor of n1 and n2
/* Define pointers to specific writing functions depending on if we
* write float or double data */
typedef tng_function_status (*set_writing_interval_func_pointer)(
- tng_trajectory_t, const int64_t, const int64_t, const int64_t, const char*, const char,
- const char);
+ tng_trajectory_t, const int64_t, const int64_t, const int64_t, const char*, const char, const char);
# if GMX_DOUBLE
set_writing_interval_func_pointer set_writing_interval = tng_util_generic_write_interval_double_set;
# else
}
if (xout)
{
- set_writing_interval(tng, xout, 3, TNG_TRAJ_POSITIONS, "POSITIONS", TNG_PARTICLE_BLOCK_DATA,
- compression);
+ set_writing_interval(
+ tng, xout, 3, TNG_TRAJ_POSITIONS, "POSITIONS", TNG_PARTICLE_BLOCK_DATA, compression);
/* TODO: if/when we write energies to TNG also, reconsider how
* and when box information is written, because GROMACS
* behaviour pre-5.0 was to write the box with every
}
if (vout)
{
- set_writing_interval(tng, vout, 3, TNG_TRAJ_VELOCITIES, "VELOCITIES",
- TNG_PARTICLE_BLOCK_DATA, compression);
+ set_writing_interval(
+ tng, vout, 3, TNG_TRAJ_VELOCITIES, "VELOCITIES", TNG_PARTICLE_BLOCK_DATA, compression);
gcd = greatest_common_divisor_if_positive(gcd, vout);
if (lowest < 0 || vout < lowest)
}
if (fout)
{
- set_writing_interval(tng, fout, 3, TNG_TRAJ_FORCES, "FORCES", TNG_PARTICLE_BLOCK_DATA,
- TNG_GZIP_COMPRESSION);
+ set_writing_interval(
+ tng, fout, 3, TNG_TRAJ_FORCES, "FORCES", TNG_PARTICLE_BLOCK_DATA, TNG_GZIP_COMPRESSION);
gcd = greatest_common_divisor_if_positive(gcd, fout);
if (lowest < 0 || fout < lowest)
{
/* Lambdas and box shape written at an interval of the lowest common
denominator of other output */
- set_writing_interval(tng, gcd, 1, TNG_GMX_LAMBDA, "LAMBDAS", TNG_NON_PARTICLE_BLOCK_DATA,
- TNG_GZIP_COMPRESSION);
+ set_writing_interval(
+ tng, gcd, 1, TNG_GMX_LAMBDA, "LAMBDAS", TNG_NON_PARTICLE_BLOCK_DATA, TNG_GZIP_COMPRESSION);
- set_writing_interval(tng, gcd, 9, TNG_TRAJ_BOX_SHAPE, "BOX SHAPE",
- TNG_NON_PARTICLE_BLOCK_DATA, TNG_GZIP_COMPRESSION);
+ set_writing_interval(
+ tng, gcd, 9, TNG_TRAJ_BOX_SHAPE, "BOX SHAPE", TNG_NON_PARTICLE_BLOCK_DATA, TNG_GZIP_COMPRESSION);
gmx_tng->lambdaOutputInterval = gcd;
gmx_tng->boxOutputInterval = gcd;
if (gcd < lowest / 10)
"The lowest common denominator of trajectory output is "
"every %d step(s), whereas the shortest output interval "
"is every %d steps.",
- gcd, lowest);
+ gcd,
+ lowest);
}
}
}
#if GMX_USE_TNG
gmx_tng_add_mtop(gmx_tng, mtop);
set_writing_intervals(gmx_tng, FALSE, ir);
- tng_time_per_frame_set(gmx_tng->tng, ir->delta_t * PICO);
+ tng_time_per_frame_set(gmx_tng->tng, ir->delta_t * gmx::c_pico);
gmx_tng->timePerFrameIsSet = true;
#else
GMX_UNUSED_VALUE(gmx_tng);
* original residue IDs - otherwise there might be conflicts. */
tng_chain_residue_add(tng, chain, res_name, &res);
}
- tng_residue_atom_w_id_add(tng, res, *(atoms->atomname[atomIndex]),
- *(atoms->atomtype[atomIndex]), atom_offset + atomIndex, &atom);
+ tng_residue_atom_w_id_add(tng,
+ res,
+ *(atoms->atomname[atomIndex]),
+ *(atoms->atomtype[atomIndex]),
+ atom_offset + atomIndex,
+ &atom);
bAtomsAdded = TRUE;
}
/* Add bonds. */
int atom1, atom2;
atom1 = ilist.iatoms[l] + atom_offset;
atom2 = ilist.iatoms[l + 1] + atom_offset;
- if (getGroupType(mtop->groups,
- SimulationAtomGroupType::CompressedPositionOutput, atom1)
+ if (getGroupType(mtop->groups, SimulationAtomGroupType::CompressedPositionOutput, atom1)
== 0
- && getGroupType(mtop->groups,
- SimulationAtomGroupType::CompressedPositionOutput, atom2)
+ && getGroupType(mtop->groups, SimulationAtomGroupType::CompressedPositionOutput, atom2)
== 0)
{
- tng_molecule_bond_add(tng, mol, ilist.iatoms[l],
- ilist.iatoms[l + 1], &tngBond);
+ tng_molecule_bond_add(
+ tng, mol, ilist.iatoms[l], ilist.iatoms[l + 1], &tngBond);
}
}
}
gmx_tng_add_mtop(gmx_tng, mtop);
add_selection_groups(gmx_tng, mtop);
set_writing_intervals(gmx_tng, TRUE, ir);
- tng_time_per_frame_set(gmx_tng->tng, ir->delta_t * PICO);
+ tng_time_per_frame_set(gmx_tng->tng, ir->delta_t * gmx::c_pico);
gmx_tng->timePerFrameIsSet = true;
gmx_tng_set_compression_precision(gmx_tng, ir->x_compression_precision);
#else
const rvec* f)
{
#if GMX_USE_TNG
- typedef tng_function_status (*write_data_func_pointer)(
- tng_trajectory_t, const int64_t, const double, const real*, const int64_t,
- const int64_t, const char*, const char, const char);
+ typedef tng_function_status (*write_data_func_pointer)(tng_trajectory_t,
+ const int64_t,
+ const double,
+ const real*,
+ const int64_t,
+ const int64_t,
+ const char*,
+ const char,
+ const char);
# if GMX_DOUBLE
static write_data_func_pointer write_data = tng_util_generic_with_time_double_write;
# else
static write_data_func_pointer write_data = tng_util_generic_with_time_write;
# endif
- double elapsedSeconds = elapsedPicoSeconds * PICO;
+ double elapsedSeconds = elapsedPicoSeconds * gmx::c_pico;
int64_t nParticles;
char compression;
{
GMX_ASSERT(box, "Need a non-NULL box if positions are written");
- if (write_data(tng, step, elapsedSeconds, reinterpret_cast<const real*>(x), 3,
- TNG_TRAJ_POSITIONS, "POSITIONS", TNG_PARTICLE_BLOCK_DATA, compression)
+ if (write_data(tng,
+ step,
+ elapsedSeconds,
+ reinterpret_cast<const real*>(x),
+ 3,
+ TNG_TRAJ_POSITIONS,
+ "POSITIONS",
+ TNG_PARTICLE_BLOCK_DATA,
+ compression)
!= TNG_SUCCESS)
{
gmx_file("Cannot write TNG trajectory frame; maybe you are out of disk space?");
if (v)
{
- if (write_data(tng, step, elapsedSeconds, reinterpret_cast<const real*>(v), 3,
- TNG_TRAJ_VELOCITIES, "VELOCITIES", TNG_PARTICLE_BLOCK_DATA, compression)
+ if (write_data(tng,
+ step,
+ elapsedSeconds,
+ reinterpret_cast<const real*>(v),
+ 3,
+ TNG_TRAJ_VELOCITIES,
+ "VELOCITIES",
+ TNG_PARTICLE_BLOCK_DATA,
+ compression)
!= TNG_SUCCESS)
{
gmx_file("Cannot write TNG trajectory frame; maybe you are out of disk space?");
{
/* TNG-MF1 compression only compresses positions and velocities. Use lossless
* compression for forces regardless of output mode */
- if (write_data(tng, step, elapsedSeconds, reinterpret_cast<const real*>(f), 3,
- TNG_TRAJ_FORCES, "FORCES", TNG_PARTICLE_BLOCK_DATA, TNG_GZIP_COMPRESSION)
+ if (write_data(tng,
+ step,
+ elapsedSeconds,
+ reinterpret_cast<const real*>(f),
+ 3,
+ TNG_TRAJ_FORCES,
+ "FORCES",
+ TNG_PARTICLE_BLOCK_DATA,
+ TNG_GZIP_COMPRESSION)
!= TNG_SUCCESS)
{
gmx_file("Cannot write TNG trajectory frame; maybe you are out of disk space?");
{
/* TNG-MF1 compression only compresses positions and velocities. Use lossless
* compression for box shape regardless of output mode */
- if (write_data(tng, step, elapsedSeconds, reinterpret_cast<const real*>(box), 9,
- TNG_TRAJ_BOX_SHAPE, "BOX SHAPE", TNG_NON_PARTICLE_BLOCK_DATA, TNG_GZIP_COMPRESSION)
+ if (write_data(tng,
+ step,
+ elapsedSeconds,
+ reinterpret_cast<const real*>(box),
+ 9,
+ TNG_TRAJ_BOX_SHAPE,
+ "BOX SHAPE",
+ TNG_NON_PARTICLE_BLOCK_DATA,
+ TNG_GZIP_COMPRESSION)
!= TNG_SUCCESS)
{
gmx_file("Cannot write TNG trajectory frame; maybe you are out of disk space?");
{
/* TNG-MF1 compression only compresses positions and velocities. Use lossless
* compression for lambda regardless of output mode */
- if (write_data(tng, step, elapsedSeconds, reinterpret_cast<const real*>(&lambda), 1,
- TNG_GMX_LAMBDA, "LAMBDAS", TNG_NON_PARTICLE_BLOCK_DATA, TNG_GZIP_COMPRESSION)
+ if (write_data(tng,
+ step,
+ elapsedSeconds,
+ reinterpret_cast<const real*>(&lambda),
+ 1,
+ TNG_GMX_LAMBDA,
+ "LAMBDAS",
+ TNG_NON_PARTICLE_BLOCK_DATA,
+ TNG_GZIP_COMPRESSION)
!= TNG_SUCCESS)
{
gmx_file("Cannot write TNG trajectory frame; maybe you are out of disk space?");
tng_num_frames_get(tng, &nFrames);
tng_util_time_of_frame_get(tng, nFrames - 1, &time);
- fTime = time / PICO;
+ fTime = time / gmx::c_pico;
return fTime;
#else
GMX_UNUSED_VALUE(gmx_tng);
#if GMX_USE_TNG
tng_trajectory_t* input = (gmx_tng_input && *gmx_tng_input) ? &(*gmx_tng_input)->tng : nullptr;
/* FIXME after 5.0: Currently only standard block types are read */
- const int defaultNumIds = 5;
- static int64_t fallbackIds[defaultNumIds] = { TNG_TRAJ_BOX_SHAPE, TNG_TRAJ_POSITIONS,
- TNG_TRAJ_VELOCITIES, TNG_TRAJ_FORCES, TNG_GMX_LAMBDA };
- static char fallbackNames[defaultNumIds][32] = { "BOX SHAPE", "POSITIONS", "VELOCITIES",
- "FORCES", "LAMBDAS" };
+ const int defaultNumIds = 5;
+ static int64_t fallbackIds[defaultNumIds] = {
+ TNG_TRAJ_BOX_SHAPE, TNG_TRAJ_POSITIONS, TNG_TRAJ_VELOCITIES, TNG_TRAJ_FORCES, TNG_GMX_LAMBDA
+ };
+ static char fallbackNames[defaultNumIds][32] = {
+ "BOX SHAPE", "POSITIONS", "VELOCITIES", "FORCES", "LAMBDAS"
+ };
typedef tng_function_status (*set_writing_interval_func_pointer)(
- tng_trajectory_t, const int64_t, const int64_t, const int64_t, const char*, const char,
- const char);
+ tng_trajectory_t, const int64_t, const int64_t, const int64_t, const char*, const char, const char);
# if GMX_DOUBLE
set_writing_interval_func_pointer set_writing_interval = tng_util_generic_write_interval_double_set;
# else
{
case TNG_TRAJ_POSITIONS:
case TNG_TRAJ_VELOCITIES:
- set_writing_interval(*output, interval, 3, fallbackIds[i], fallbackNames[i],
- TNG_PARTICLE_BLOCK_DATA, compression_type);
+ set_writing_interval(*output,
+ interval,
+ 3,
+ fallbackIds[i],
+ fallbackNames[i],
+ TNG_PARTICLE_BLOCK_DATA,
+ compression_type);
break;
case TNG_TRAJ_FORCES:
- set_writing_interval(*output, interval, 3, fallbackIds[i], fallbackNames[i],
- TNG_PARTICLE_BLOCK_DATA, TNG_GZIP_COMPRESSION);
+ set_writing_interval(*output,
+ interval,
+ 3,
+ fallbackIds[i],
+ fallbackNames[i],
+ TNG_PARTICLE_BLOCK_DATA,
+ TNG_GZIP_COMPRESSION);
break;
case TNG_TRAJ_BOX_SHAPE:
- set_writing_interval(*output, interval, 9, fallbackIds[i], fallbackNames[i],
- TNG_NON_PARTICLE_BLOCK_DATA, TNG_GZIP_COMPRESSION);
+ set_writing_interval(*output,
+ interval,
+ 9,
+ fallbackIds[i],
+ fallbackNames[i],
+ TNG_NON_PARTICLE_BLOCK_DATA,
+ TNG_GZIP_COMPRESSION);
(*gmx_tng_output)->boxOutputInterval = interval;
break;
case TNG_GMX_LAMBDA:
- set_writing_interval(*output, interval, 1, fallbackIds[i], fallbackNames[i],
- TNG_NON_PARTICLE_BLOCK_DATA, TNG_GZIP_COMPRESSION);
+ set_writing_interval(*output,
+ interval,
+ 1,
+ fallbackIds[i],
+ fallbackNames[i],
+ TNG_NON_PARTICLE_BLOCK_DATA,
+ TNG_GZIP_COMPRESSION);
(*gmx_tng_output)->lambdaOutputInterval = interval;
break;
default: continue;
{
natoms = frame->natoms;
}
- gmx_fwrite_tng(gmx_tng_output, TRUE, frame->step, frame->time, 0, frame->box, natoms, frame->x,
- frame->v, frame->f);
+ gmx_fwrite_tng(
+ gmx_tng_output, TRUE, frame->step, frame->time, 0, frame->box, natoms, frame->x, frame->v, frame->f);
#else
GMX_UNUSED_VALUE(gmx_tng_output);
GMX_UNUSED_VALUE(frame);
// GROMACS expects distances in nm
switch (exp)
{
- case 9: distanceScaleFactor = NANO / NANO; break;
- case 10: distanceScaleFactor = NANO / ANGSTROM; break;
+ case 9: distanceScaleFactor = gmx::c_nano / gmx::c_nano; break;
+ case 10: distanceScaleFactor = gmx::c_nano / gmx::c_angstrom; break;
default: distanceScaleFactor = pow(10.0, exp + 9.0);
}
double frameTime = -1.0;
int size, blockDependency;
double prec;
- const int defaultNumIds = 5;
- static int64_t fallbackRequestedIds[defaultNumIds] = { TNG_TRAJ_BOX_SHAPE, TNG_TRAJ_POSITIONS,
- TNG_TRAJ_VELOCITIES, TNG_TRAJ_FORCES,
- TNG_GMX_LAMBDA };
+ const int defaultNumIds = 5;
+ static int64_t fallbackRequestedIds[defaultNumIds] = {
+ TNG_TRAJ_BOX_SHAPE, TNG_TRAJ_POSITIONS, TNG_TRAJ_VELOCITIES, TNG_TRAJ_FORCES, TNG_GMX_LAMBDA
+ };
fr->bStep = FALSE;
tng_data_block_dependency_get(input, blockId, &blockDependency);
if (blockDependency & TNG_PARTICLE_DEPENDENT)
{
- stat = tng_util_particle_data_next_frame_read(input, blockId, &values, &datatype,
- &frameNumber, &frameTime);
+ stat = tng_util_particle_data_next_frame_read(
+ input, blockId, &values, &datatype, &frameNumber, &frameTime);
}
else
{
- stat = tng_util_non_particle_data_next_frame_read(input, blockId, &values, &datatype,
- &frameNumber, &frameTime);
+ stat = tng_util_non_particle_data_next_frame_read(
+ input, blockId, &values, &datatype, &frameNumber, &frameTime);
}
if (stat == TNG_CRITICAL)
{
{
convert_array_to_real_array(reinterpret_cast<char*>(values) + size * i * DIM,
reinterpret_cast<real*>(fr->box[i]),
- getDistanceScaleFactor(gmx_tng_input), 1, DIM, datatype);
+ getDistanceScaleFactor(gmx_tng_input),
+ 1,
+ DIM,
+ datatype);
}
fr->bBox = TRUE;
break;
case TNG_TRAJ_POSITIONS:
srenew(fr->x, fr->natoms);
- convert_array_to_real_array(values, reinterpret_cast<real*>(fr->x),
- getDistanceScaleFactor(gmx_tng_input), fr->natoms, DIM,
+ convert_array_to_real_array(values,
+ reinterpret_cast<real*>(fr->x),
+ getDistanceScaleFactor(gmx_tng_input),
+ fr->natoms,
+ DIM,
datatype);
fr->bX = TRUE;
tng_util_frame_current_compression_get(input, blockId, &codecId, &prec);
break;
case TNG_TRAJ_VELOCITIES:
srenew(fr->v, fr->natoms);
- convert_array_to_real_array(values, reinterpret_cast<real*>(fr->v),
- getDistanceScaleFactor(gmx_tng_input), fr->natoms, DIM,
+ convert_array_to_real_array(values,
+ reinterpret_cast<real*>(fr->v),
+ getDistanceScaleFactor(gmx_tng_input),
+ fr->natoms,
+ DIM,
datatype);
fr->bV = TRUE;
tng_util_frame_current_compression_get(input, blockId, &codecId, &prec);
break;
case TNG_TRAJ_FORCES:
srenew(fr->f, fr->natoms);
- convert_array_to_real_array(values, reinterpret_cast<real*>(fr->f),
- getDistanceScaleFactor(gmx_tng_input), fr->natoms, DIM,
+ convert_array_to_real_array(values,
+ reinterpret_cast<real*>(fr->f),
+ getDistanceScaleFactor(gmx_tng_input),
+ fr->natoms,
+ DIM,
datatype);
fr->bF = TRUE;
break;
fr->bStep = TRUE;
// Convert the time to ps
- fr->time = frameTime / PICO;
+ fr->time = frameTime / gmx::c_pico;
fr->bTime = (frameTime > 0);
// TODO This does not leak, but is not exception safe.
}
tng_num_particles_get(input, &nAtoms);
- stat = tng_particle_data_vector_get(input, TNG_TRAJ_PARTIAL_CHARGES, &data, &nFramesRead,
- &strideLength, &nParticlesRead, &nValuesPerFrameRead, &datatype);
+ stat = tng_particle_data_vector_get(input,
+ TNG_TRAJ_PARTIAL_CHARGES,
+ &data,
+ &nFramesRead,
+ &strideLength,
+ &nParticlesRead,
+ &nValuesPerFrameRead,
+ &datatype);
if (stat == TNG_SUCCESS)
{
atomCharges.resize(nAtoms);
}
}
- stat = tng_particle_data_vector_get(input, TNG_TRAJ_MASSES, &data, &nFramesRead, &strideLength,
- &nParticlesRead, &nValuesPerFrameRead, &datatype);
+ stat = tng_particle_data_vector_get(
+ input, TNG_TRAJ_MASSES, &data, &nFramesRead, &strideLength, &nParticlesRead, &nValuesPerFrameRead, &datatype);
if (stat == TNG_SUCCESS)
{
atomMasses.resize(nAtoms);
if (blockDependency & TNG_PARTICLE_DEPENDENT)
{
tng_num_particles_get(input, nAtoms);
- stat = tng_util_particle_data_next_frame_read(input, blockId, &data, &datatype, frameNumber,
- frameTime);
+ stat = tng_util_particle_data_next_frame_read(
+ input, blockId, &data, &datatype, frameNumber, frameTime);
}
else
{
*nAtoms = 1; /* There are not actually any atoms, but it is used for
allocating memory */
- stat = tng_util_non_particle_data_next_frame_read(input, blockId, &data, &datatype,
- frameNumber, frameTime);
+ stat = tng_util_non_particle_data_next_frame_read(
+ input, blockId, &data, &datatype, frameNumber, frameTime);
}
if (stat == TNG_CRITICAL)
{
gmx_file("Cannot read next frame of TNG file");
}
srenew(*values, sizeof(real) * *nValuesPerFrame * *nAtoms);
- convert_array_to_real_array(data, *values, getDistanceScaleFactor(gmx_tng_input), *nAtoms,
- *nValuesPerFrame, datatype);
+ convert_array_to_real_array(
+ data, *values, getDistanceScaleFactor(gmx_tng_input), *nAtoms, *nValuesPerFrame, datatype);
tng_util_frame_current_compression_get(input, blockId, &codecId, &localPrec);
/* This file is completely threadsafe - keep it that way! */
-#include "tpxio.h"
+#include "gromacs/fileio/tpxio.h"
#include <cstdio>
#include <cstdlib>
#include <memory>
#include <vector>
+#include "gromacs/applied_forces/awh/read_params.h"
#include "gromacs/fileio/filetypes.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/gmxfio_xdr.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/inmemoryserializer.h"
+#include "gromacs/utility/iserializer.h"
#include "gromacs/utility/keyvaluetreebuilder.h"
#include "gromacs/utility/keyvaluetreeserializer.h"
#include "gromacs/utility/smalloc.h"
* merging with mainstream GROMACS, set this tag string back to
* TPX_TAG_RELEASE, and instead add an element to tpxv.
*/
-static const char* tpx_tag = TPX_TAG_RELEASE;
+static const std::string tpx_tag = TPX_TAG_RELEASE;
/*! \brief Enum of values that describe the contents of a tpr file
* whose format matches a version number
tpxv_StoreNonBondedInteractionExclusionGroup, /**< Store the non bonded interaction exclusion group in the topology */
tpxv_VSite1, /**< Added 1 type virtual site */
tpxv_MTS, /**< Added multiple time stepping */
- tpxv_Count /**< the total number of tpxv versions */
+ tpxv_RemovedConstantAcceleration, /**< Removed support for constant acceleration NEMD. */
+ tpxv_Count /**< the total number of tpxv versions */
};
/*! \brief Version number of the file format written to run input
static void do_pull_coord(gmx::ISerializer* serializer,
t_pull_coord* pcrd,
int file_version,
- int ePullOld,
- int eGeomOld,
+ PullingAlgorithm ePullOld,
+ PullGroupGeometry eGeomOld,
ivec dimOld)
{
if (file_version >= tpxv_PullCoordNGroup)
{
- serializer->doInt(&pcrd->eType);
+ serializer->doEnumAsInt(&pcrd->eType);
if (file_version >= tpxv_PullExternalPotential)
{
- if (pcrd->eType == epullEXTERNAL)
+ if (pcrd->eType == PullingAlgorithm::External)
{
std::string buf;
if (serializer->reading())
* changing the tpx version. This requires checks when printing the
* geometry string and a check and fatal_error in init_pull.
*/
- serializer->doInt(&pcrd->eGeom);
+ serializer->doEnumAsInt(&pcrd->eGeom);
serializer->doInt(&pcrd->ngroup);
if (pcrd->ngroup <= c_pullCoordNgroupMax)
{
serializer->doInt(&pcrd->group[1]);
if (file_version >= tpxv_PullCoordTypeGeom)
{
- pcrd->ngroup = (pcrd->eGeom == epullgDIRRELATIVE ? 4 : 2);
- serializer->doInt(&pcrd->eType);
- serializer->doInt(&pcrd->eGeom);
+ pcrd->ngroup = (pcrd->eGeom == PullGroupGeometry::DirectionRelative ? 4 : 2);
+ serializer->doEnumAsInt(&pcrd->eType);
+ serializer->doEnumAsInt(&pcrd->eGeom);
if (pcrd->ngroup == 4)
{
serializer->doInt(&pcrd->group[2]);
{
if (n_lambda > 0)
{
- if (serializer->reading())
- {
- snew(expand->init_lambda_weights, n_lambda);
- }
- serializer->doRealArray(expand->init_lambda_weights, n_lambda);
+ expand->init_lambda_weights.resize(n_lambda);
+ serializer->doRealArray(expand->init_lambda_weights.data(), n_lambda);
serializer->doBool(&expand->bInit_weights);
}
serializer->doInt(&expand->nstexpanded);
- serializer->doInt(&expand->elmcmove);
- serializer->doInt(&expand->elamstats);
+ serializer->doEnumAsInt(&expand->elmcmove);
+ serializer->doEnumAsInt(&expand->elamstats);
serializer->doInt(&expand->lmc_repeats);
serializer->doInt(&expand->gibbsdeltalam);
serializer->doInt(&expand->lmc_forced_nstart);
serializer->doReal(&expand->wl_ratio);
serializer->doReal(&expand->init_wl_delta);
serializer->doBool(&expand->bWLoneovert);
- serializer->doInt(&expand->elmceq);
+ serializer->doEnumAsInt(&expand->elmceq);
serializer->doInt(&expand->equil_steps);
serializer->doInt(&expand->equil_samples);
serializer->doInt(&expand->equil_n_at_lam);
{
if (file_version >= 79)
{
- serializer->doInt(&simtemp->eSimTempScale);
+ serializer->doEnumAsInt(&simtemp->eSimTempScale);
serializer->doReal(&simtemp->simtemp_high);
serializer->doReal(&simtemp->simtemp_low);
if (n_lambda > 0)
{
if (serializer->reading())
{
- snew(simtemp->temperatures, n_lambda);
+ simtemp->temperatures.resize(n_lambda);
}
- serializer->doRealArray(simtemp->temperatures, n_lambda);
+ serializer->doRealArray(simtemp->temperatures.data(), n_lambda);
}
}
}
static void do_fepvals(gmx::ISerializer* serializer, t_lambda* fepvals, int file_version)
{
/* i is defined in the ndo_double macro; use g to iterate. */
- int g;
real rdum;
/* free energy values */
if (file_version >= 79)
{
serializer->doInt(&fepvals->n_lambda);
- if (serializer->reading())
- {
- snew(fepvals->all_lambda, efptNR);
- }
- for (g = 0; g < efptNR; g++)
+ for (auto g : keysOf(fepvals->all_lambda))
{
if (fepvals->n_lambda > 0)
{
- if (serializer->reading())
- {
- snew(fepvals->all_lambda[g], fepvals->n_lambda);
- }
- serializer->doDoubleArray(fepvals->all_lambda[g], fepvals->n_lambda);
- serializer->doBoolArray(fepvals->separate_dvdl, efptNR);
+ fepvals->all_lambda[g].resize(fepvals->n_lambda);
+ serializer->doDoubleArray(fepvals->all_lambda[g].data(), fepvals->n_lambda);
+ serializer->doBoolArray(fepvals->separate_dvdl.begin(), fepvals->separate_dvdl.size());
}
else if (fepvals->init_lambda >= 0)
{
- fepvals->separate_dvdl[efptFEP] = TRUE;
+ fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
}
}
}
serializer->doInt(&fepvals->n_lambda);
if (serializer->reading())
{
- int g;
-
- snew(fepvals->all_lambda, efptNR);
/* still allocate the all_lambda array's contents. */
- for (g = 0; g < efptNR; g++)
+ for (auto g : keysOf(fepvals->all_lambda))
{
if (fepvals->n_lambda > 0)
{
- snew(fepvals->all_lambda[g], fepvals->n_lambda);
+ fepvals->all_lambda[g].resize(fepvals->n_lambda);
}
}
}
- serializer->doDoubleArray(fepvals->all_lambda[efptFEP], fepvals->n_lambda);
+ serializer->doDoubleArray(fepvals->all_lambda[FreeEnergyPerturbationCouplingType::Fep].data(),
+ fepvals->n_lambda);
if (fepvals->init_lambda >= 0)
{
- int g, h;
-
- fepvals->separate_dvdl[efptFEP] = TRUE;
+ fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
if (serializer->reading())
{
/* copy the contents of the efptFEP lambda component to all
the other components */
- for (g = 0; g < efptNR; g++)
+ for (auto g : keysOf(fepvals->all_lambda))
{
- for (h = 0; h < fepvals->n_lambda; h++)
+ for (int h = 0; h < fepvals->n_lambda; h++)
{
- if (g != efptFEP)
+ if (g != FreeEnergyPerturbationCouplingType::Fep)
{
- fepvals->all_lambda[g][h] = fepvals->all_lambda[efptFEP][h];
+ fepvals->all_lambda[g][h] =
+ fepvals->all_lambda[FreeEnergyPerturbationCouplingType::Fep][h];
}
}
}
}
else
{
- fepvals->n_lambda = 0;
- fepvals->all_lambda = nullptr;
+ fepvals->n_lambda = 0;
if (fepvals->init_lambda >= 0)
{
- fepvals->separate_dvdl[efptFEP] = TRUE;
+ fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
}
}
serializer->doReal(&fepvals->sc_alpha);
if (file_version >= 73)
{
- serializer->doInt(&fepvals->separate_dhdl_file);
- serializer->doInt(&fepvals->dhdl_derivatives);
+ serializer->doEnumAsInt(&fepvals->separate_dhdl_file);
+ serializer->doEnumAsInt(&fepvals->dhdl_derivatives);
}
else
{
- fepvals->separate_dhdl_file = esepdhdlfileYES;
- fepvals->dhdl_derivatives = edhdlderivativesYES;
+ fepvals->separate_dhdl_file = SeparateDhdlFile::Yes;
+ fepvals->dhdl_derivatives = DhDlDerivativeCalculation::Yes;
}
if (file_version >= 71)
{
}
if (file_version >= 79)
{
- serializer->doInt(&fepvals->edHdLPrintEnergy);
+ serializer->doEnumAsInt(&fepvals->edHdLPrintEnergy);
}
else
{
- fepvals->edHdLPrintEnergy = edHdLPrintEnergyNO;
+ fepvals->edHdLPrintEnergy = FreeEnergyPrintEnergy::No;
}
/* handle lambda_neighbors */
}
}
-static void do_awhBias(gmx::ISerializer* serializer, gmx::AwhBiasParams* awhBiasParams, int gmx_unused file_version)
-{
- serializer->doInt(&awhBiasParams->eTarget);
- serializer->doDouble(&awhBiasParams->targetBetaScaling);
- serializer->doDouble(&awhBiasParams->targetCutoff);
- serializer->doInt(&awhBiasParams->eGrowth);
- serializer->doInt(&awhBiasParams->bUserData);
- serializer->doDouble(&awhBiasParams->errorInitial);
- serializer->doInt(&awhBiasParams->ndim);
- serializer->doInt(&awhBiasParams->shareGroup);
- serializer->doBool(&awhBiasParams->equilibrateHistogram);
-
- if (serializer->reading())
- {
- snew(awhBiasParams->dimParams, awhBiasParams->ndim);
- }
-
- for (int d = 0; d < awhBiasParams->ndim; d++)
- {
- gmx::AwhDimParams* dimParams = &awhBiasParams->dimParams[d];
-
- serializer->doInt(&dimParams->eCoordProvider);
- serializer->doInt(&dimParams->coordIndex);
- serializer->doDouble(&dimParams->origin);
- serializer->doDouble(&dimParams->end);
- serializer->doDouble(&dimParams->period);
- serializer->doDouble(&dimParams->forceConstant);
- serializer->doDouble(&dimParams->diffusion);
- serializer->doDouble(&dimParams->coordValueInit);
- serializer->doDouble(&dimParams->coverDiameter);
- }
-}
-
-static void do_awh(gmx::ISerializer* serializer, gmx::AwhParams* awhParams, int gmx_unused file_version)
+static void do_pull(gmx::ISerializer* serializer, pull_params_t* pull, int file_version, PullingAlgorithm ePullOld)
{
- serializer->doInt(&awhParams->numBias);
- serializer->doInt(&awhParams->nstOut);
- serializer->doInt64(&awhParams->seed);
- serializer->doInt(&awhParams->nstSampleCoord);
- serializer->doInt(&awhParams->numSamplesUpdateFreeEnergy);
- serializer->doInt(&awhParams->ePotential);
- serializer->doBool(&awhParams->shareBiasMultisim);
-
- if (awhParams->numBias > 0)
- {
- if (serializer->reading())
- {
- snew(awhParams->awhBiasParams, awhParams->numBias);
- }
-
- for (int k = 0; k < awhParams->numBias; k++)
- {
- do_awhBias(serializer, &awhParams->awhBiasParams[k], file_version);
- }
- }
-}
-
-static void do_pull(gmx::ISerializer* serializer, pull_params_t* pull, int file_version, int ePullOld)
-{
- int eGeomOld = -1;
- ivec dimOld;
- int g;
+ PullGroupGeometry eGeomOld = PullGroupGeometry::Count;
+ ivec dimOld;
+ int g;
if (file_version >= 95)
{
{
real dum;
- serializer->doInt(&eGeomOld);
+ serializer->doEnumAsInt(&eGeomOld);
serializer->doIvec(&dimOld);
/* The inner cylinder radius, now removed */
serializer->doReal(&dum);
if (file_version < 95)
{
/* epullgPOS for position pulling, before epullgDIRPBC was removed */
- if (eGeomOld == epullgDIRPBC)
+ if (eGeomOld == PullGroupGeometry::DirectionPBC)
{
gmx_fatal(FARGS, "pull-geometry=position is no longer supported");
}
- if (eGeomOld > epullgDIRPBC)
+ if (eGeomOld > PullGroupGeometry::DirectionPBC)
{
- eGeomOld -= 1;
+ switch (eGeomOld)
+ {
+ case (PullGroupGeometry::DirectionRelative):
+ eGeomOld = PullGroupGeometry::DirectionPBC;
+ break;
+ case (PullGroupGeometry::Angle):
+ eGeomOld = PullGroupGeometry::DirectionRelative;
+ break;
+ case (PullGroupGeometry::Dihedral): eGeomOld = PullGroupGeometry::Angle; break;
+ case (PullGroupGeometry::AngleAxis): eGeomOld = PullGroupGeometry::Dihedral; break;
+ case (PullGroupGeometry::Count): eGeomOld = PullGroupGeometry::AngleAxis; break;
+ default: GMX_RELEASE_ASSERT(false, "Unhandled old pull type");
+ }
}
for (g = 0; g < pull->ngroup; g++)
for (g = 0; g < pull->ncoord; g++)
{
do_pull_coord(serializer, &pull->coord[g], file_version, ePullOld, eGeomOld, dimOld);
+ if (serializer->reading())
+ {
+ pull->coord[g].coordIndex = g;
+ }
}
}
if (file_version >= tpxv_PullAverage)
static void do_rotgrp(gmx::ISerializer* serializer, t_rotgrp* rotg)
{
- serializer->doInt(&rotg->eType);
- serializer->doInt(&rotg->bMassW);
+ serializer->doEnumAsInt(&rotg->eType);
+ if (serializer->reading())
+ {
+ int temp = 0;
+ serializer->doInt(&temp);
+ rotg->bMassW = static_cast<bool>(temp);
+ }
+ else
+ {
+ int temp = static_cast<int>(rotg->bMassW);
+ serializer->doInt(&temp);
+ }
serializer->doInt(&rotg->nat);
if (serializer->reading())
{
serializer->doReal(&rotg->slab_dist);
serializer->doReal(&rotg->min_gaussian);
serializer->doReal(&rotg->eps);
- serializer->doInt(&rotg->eFittype);
+ serializer->doEnumAsInt(&rotg->eFittype);
serializer->doInt(&rotg->PotAngle_nstep);
serializer->doReal(&rotg->PotAngle_step);
}
serializer->doIntArray(g->ind, g->nat);
/* Requested counts for compartments A and B */
- serializer->doIntArray(g->nmolReq, eCompNR);
+ serializer->doIntArray(g->nmolReq.data(), static_cast<int>(Compartment::Count));
}
static void do_swapcoords_tpx(gmx::ISerializer* serializer, t_swapcoords* swap, int file_version)
swap->ngrp = 5;
snew(swap->grp, swap->ngrp);
- swap->grp[eGrpSplit0].molname = gmx_strdup("split0"); // group 0: split0
- swap->grp[eGrpSplit1].molname = gmx_strdup("split1"); // group 1: split1
- swap->grp[eGrpSolvent].molname = gmx_strdup("solvent"); // group 2: solvent
- swap->grp[3].molname = gmx_strdup("anions"); // group 3: anions
- swap->grp[4].molname = gmx_strdup("cations"); // group 4: cations
+ swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname = gmx_strdup("split0"); // group 0: split0
+ swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname = gmx_strdup("split1"); // group 1: split1
+ swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].molname =
+ gmx_strdup("solvent"); // group 2: solvent
+ swap->grp[3].molname = gmx_strdup("anions"); // group 3: anions
+ swap->grp[4].molname = gmx_strdup("cations"); // group 4: cations
serializer->doInt(&swap->grp[3].nat);
- serializer->doInt(&swap->grp[eGrpSolvent].nat);
- serializer->doInt(&swap->grp[eGrpSplit0].nat);
+ serializer->doInt(&swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].nat);
+ serializer->doInt(&swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].nat);
serializer->doBool(&swap->massw_split[eChannel0]);
- serializer->doInt(&swap->grp[eGrpSplit1].nat);
+ serializer->doInt(&swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].nat);
serializer->doBool(&swap->massw_split[eChannel1]);
serializer->doInt(&swap->nstswap);
serializer->doInt(&swap->nAverage);
// The order[] array keeps compatibility with older .tpr files
// by reading in the groups in the classic order
{
- const int order[4] = { 3, eGrpSolvent, eGrpSplit0, eGrpSplit1 };
+ const int order[4] = { 3,
+ static_cast<int>(SwapGroupSplittingType::Solvent),
+ static_cast<int>(SwapGroupSplittingType::Split0),
+ static_cast<int>(SwapGroupSplittingType::Split1) };
for (int ig = 0; ig < 4; ig++)
{
gmx::KeyValueTreeObjectBuilder paramsObj = paramsBuilder.rootObject();
/* Basic inputrec stuff */
- serializer->doInt(&ir->eI);
+ serializer->doEnumAsInt(&ir->eI);
if (file_version >= 62)
{
serializer->doInt64(&ir->nsteps);
}
if (file_version >= 81)
{
- serializer->doInt(&ir->cutoff_scheme);
+ serializer->doEnumAsInt(&ir->cutoff_scheme);
if (file_version < 94)
{
- ir->cutoff_scheme = 1 - ir->cutoff_scheme;
+ // Need to invert the scheme order
+ switch (ir->cutoff_scheme)
+ {
+ case (CutoffScheme::Group): ir->cutoff_scheme = CutoffScheme::Verlet; break;
+ case (CutoffScheme::Verlet): ir->cutoff_scheme = CutoffScheme::Group; break;
+ default: GMX_RELEASE_ASSERT(false, "Unhandled cutoff scheme type");
+ }
}
}
else
{
- ir->cutoff_scheme = ecutsGROUP;
+ ir->cutoff_scheme = CutoffScheme::Group;
}
serializer->doInt(&idum); /* used to be ns_type; not used anymore */
serializer->doInt(&ir->nstlist);
serializer->doReal(&ir->rtpi);
serializer->doInt(&ir->nstcomm);
- serializer->doInt(&ir->comm_mode);
+ serializer->doEnumAsInt(&ir->comm_mode);
/* ignore nstcheckpoint */
if (file_version < tpxv_RemoveObsoleteParameters1)
int dummy_nstcalclr = -1;
serializer->doInt(&dummy_nstcalclr);
}
- serializer->doInt(&ir->coulombtype);
+ serializer->doEnumAsInt(&ir->coulombtype);
if (file_version >= 81)
{
- serializer->doInt(&ir->coulomb_modifier);
+ serializer->doEnumAsInt(&ir->coulomb_modifier);
}
else
{
- ir->coulomb_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
+ ir->coulomb_modifier = (ir->cutoff_scheme == CutoffScheme::Verlet ? InteractionModifiers::PotShift
+ : InteractionModifiers::None);
}
serializer->doReal(&ir->rcoulomb_switch);
serializer->doReal(&ir->rcoulomb);
- serializer->doInt(&ir->vdwtype);
+ serializer->doEnumAsInt(&ir->vdwtype);
if (file_version >= 81)
{
- serializer->doInt(&ir->vdw_modifier);
+ serializer->doEnumAsInt(&ir->vdw_modifier);
}
else
{
- ir->vdw_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
+ ir->vdw_modifier = (ir->cutoff_scheme == CutoffScheme::Verlet ? InteractionModifiers::PotShift
+ : InteractionModifiers::None);
}
serializer->doReal(&ir->rvdw_switch);
serializer->doReal(&ir->rvdw);
- serializer->doInt(&ir->eDispCorr);
+ serializer->doEnumAsInt(&ir->eDispCorr);
serializer->doReal(&ir->epsilon_r);
serializer->doReal(&ir->epsilon_rf);
serializer->doReal(&ir->tabext);
{
ir->ewald_rtol_lj = ir->ewald_rtol;
}
- serializer->doInt(&ir->ewald_geometry);
+ serializer->doEnumAsInt(&ir->ewald_geometry);
serializer->doReal(&ir->epsilon_surface);
/* ignore bOptFFT */
if (file_version >= 93)
{
- serializer->doInt(&ir->ljpme_combination_rule);
+ serializer->doEnumAsInt(&ir->ljpme_combination_rule);
}
serializer->doBool(&ir->bContinuation);
- serializer->doInt(&ir->etc);
+ serializer->doEnumAsInt(&ir->etc);
/* before version 18, ir->etc was a gmx_bool (ir->btc),
* but the values 0 and 1 still mean no and
* berendsen temperature coupling, respectively.
{
ir->nsttcouple = ir->nstcalcenergy;
}
- serializer->doInt(&ir->epc);
- serializer->doInt(&ir->epct);
+ serializer->doEnumAsInt(&ir->epc);
+ serializer->doEnumAsInt(&ir->epct);
if (file_version >= 71)
{
serializer->doInt(&ir->nstpcouple);
serializer->doRvec(&ir->compress[XX]);
serializer->doRvec(&ir->compress[YY]);
serializer->doRvec(&ir->compress[ZZ]);
- serializer->doInt(&ir->refcoord_scaling);
+ serializer->doEnumAsInt(&ir->refcoord_scaling);
serializer->doRvec(&ir->posres_com);
serializer->doRvec(&ir->posres_comB);
serializer->doReal(&ir->shake_tol);
- serializer->doInt(&ir->efep);
- do_fepvals(serializer, ir->fepvals, file_version);
+ serializer->doEnumAsInt(&ir->efep);
+ if (serializer->reading())
+ {
+ ir->fepvals = std::make_unique<t_lambda>();
+ }
+ do_fepvals(serializer, ir->fepvals.get(), file_version);
if (file_version >= 79)
{
}
if (ir->bSimTemp)
{
- do_simtempvals(serializer, ir->simtempvals, ir->fepvals->n_lambda, file_version);
+ if (serializer->reading())
+ {
+ ir->simtempvals = std::make_unique<t_simtemp>();
+ }
+ do_simtempvals(serializer, ir->simtempvals.get(), ir->fepvals->n_lambda, file_version);
}
if (file_version >= 79)
}
if (ir->bExpanded)
{
- do_expandedvals(serializer, ir->expandedvals, ir->fepvals, file_version);
+ if (serializer->reading())
+ {
+ ir->expandedvals = std::make_unique<t_expanded>();
+ }
+ do_expandedvals(serializer, ir->expandedvals.get(), ir->fepvals.get(), file_version);
}
- serializer->doInt(&ir->eDisre);
- serializer->doInt(&ir->eDisreWeighting);
+ serializer->doEnumAsInt(&ir->eDisre);
+ serializer->doEnumAsInt(&ir->eDisreWeighting);
serializer->doBool(&ir->bDisreMixed);
serializer->doReal(&ir->dr_fc);
serializer->doReal(&ir->dr_tau);
serializer->doBool(&ir->bShakeSOR);
serializer->doInt(&ir->niter);
serializer->doReal(&ir->fc_stepsize);
- serializer->doInt(&ir->eConstrAlg);
+ serializer->doEnumAsInt(&ir->eConstrAlg);
serializer->doInt(&ir->nProjOrder);
serializer->doReal(&ir->LincsWarnAngle);
serializer->doInt(&ir->nLincsIter);
/* pull stuff */
{
- int ePullOld = 0;
+ PullingAlgorithm ePullOld = PullingAlgorithm::Umbrella;
if (file_version >= tpxv_PullCoordTypeGeom)
{
}
else
{
- serializer->doInt(&ePullOld);
- ir->bPull = (ePullOld > 0);
+ serializer->doEnumAsInt(&ePullOld);
+ ir->bPull = (ePullOld != PullingAlgorithm::Umbrella);
/* We removed the first ePull=ePullNo for the enum */
- ePullOld -= 1;
+ switch (ePullOld)
+ {
+ case (PullingAlgorithm::Umbrella): break; // this is equal to not using pulling
+ case (PullingAlgorithm::Constraint): ePullOld = PullingAlgorithm::Umbrella; break;
+ case (PullingAlgorithm::ConstantForce):
+ ePullOld = PullingAlgorithm::Constraint;
+ break;
+ case (PullingAlgorithm::FlatBottom):
+ ePullOld = PullingAlgorithm::ConstantForce;
+ break;
+ case (PullingAlgorithm::FlatBottomHigh):
+ ePullOld = PullingAlgorithm::FlatBottom;
+ break;
+ case (PullingAlgorithm::External):
+ ePullOld = PullingAlgorithm::FlatBottomHigh;
+ break;
+ case (PullingAlgorithm::Count): ePullOld = PullingAlgorithm::External; break;
+ default: GMX_RELEASE_ASSERT(false, "Unhandled old pull algorithm");
+ }
}
if (ir->bPull)
{
{
if (serializer->reading())
{
- snew(ir->awhParams, 1);
+ ir->awhParams = std::make_unique<gmx::AwhParams>(serializer);
+ }
+ else
+ {
+ ir->awhParams->serialize(serializer);
}
- do_awh(serializer, ir->awhParams, file_version);
}
}
else
{
ir->opts.nhchainlength = 1;
}
- serializer->doInt(&ir->opts.ngacc);
+ int removedOptsNgacc = 0;
+ if (serializer->reading() && file_version < tpxv_RemovedConstantAcceleration)
+ {
+ serializer->doInt(&removedOptsNgacc);
+ }
serializer->doInt(&ir->opts.ngfrz);
serializer->doInt(&ir->opts.ngener);
snew(ir->opts.anneal_temp, ir->opts.ngtc);
snew(ir->opts.tau_t, ir->opts.ngtc);
snew(ir->opts.nFreeze, ir->opts.ngfrz);
- snew(ir->opts.acc, ir->opts.ngacc);
snew(ir->opts.egp_flags, ir->opts.ngener * ir->opts.ngener);
}
if (ir->opts.ngtc > 0)
{
serializer->doIvecArray(ir->opts.nFreeze, ir->opts.ngfrz);
}
- if (ir->opts.ngacc > 0)
+ if (serializer->reading() && file_version < tpxv_RemovedConstantAcceleration && removedOptsNgacc > 0)
+ {
+ std::vector<gmx::RVec> dummy;
+ dummy.resize(removedOptsNgacc);
+ serializer->doRvecArray(reinterpret_cast<rvec*>(dummy.data()), removedOptsNgacc);
+ ir->useConstantAcceleration = std::any_of(dummy.begin(), dummy.end(), [](const gmx::RVec& vec) {
+ return vec[XX] != 0.0 || vec[YY] != 0.0 || vec[ZZ] != 0.0;
+ });
+ }
+ else
{
- serializer->doRvecArray(ir->opts.acc, ir->opts.ngacc);
+ ir->useConstantAcceleration = false;
}
serializer->doIntArray(ir->opts.egp_flags, ir->opts.ngener * ir->opts.ngener);
/* First read the lists with annealing and npoints for each group */
- serializer->doIntArray(ir->opts.annealing, ir->opts.ngtc);
+ serializer->doEnumArrayAsInt(ir->opts.annealing, ir->opts.ngtc);
serializer->doIntArray(ir->opts.anneal_npoints, ir->opts.ngtc);
for (j = 0; j < (ir->opts.ngtc); j++)
{
/* Walls */
{
serializer->doInt(&ir->nwall);
- serializer->doInt(&ir->wall_type);
+ serializer->doEnumAsInt(&ir->wall_type);
serializer->doReal(&ir->wall_r_linpot);
serializer->doInt(&ir->wall_atomtype[0]);
serializer->doInt(&ir->wall_atomtype[1]);
/* Swap ions */
if (file_version >= tpxv_ComputationalElectrophysiology)
{
- serializer->doInt(&ir->eSwapCoords);
- if (ir->eSwapCoords != eswapNO)
+ serializer->doEnumAsInt(&ir->eSwapCoords);
+ if (ir->eSwapCoords != SwapType::No)
{
if (serializer->reading())
{
serializer->doInt(&iparams->cmap.cmapB);
break;
default:
- gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d", ftype,
- interaction_function[ftype].name, __FILE__, __LINE__);
+ gmx_fatal(FARGS,
+ "unknown function type %d (%s) in %s line %d",
+ ftype,
+ interaction_function[ftype].name,
+ __FILE__,
+ __LINE__);
}
}
serializer->doReal(&atom->qB);
serializer->doUShort(&atom->type);
serializer->doUShort(&atom->typeB);
- serializer->doInt(&atom->ptype);
+ serializer->doEnumAsInt(&atom->ptype);
serializer->doInt(&atom->resind);
serializer->doInt(&atom->atomnumber);
if (serializer->reading())
static void set_disres_npair(gmx_mtop_t* mtop)
{
- gmx_mtop_ilistloop_t iloop;
- int nmol;
-
gmx::ArrayRef<t_iparams> ip = mtop->ffparams.iparams;
- iloop = gmx_mtop_ilistloop_init(mtop);
- while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
+ for (const auto ilist : IListRange(*mtop))
{
- const InteractionList& il = (*ilist)[F_DISRES];
+ const InteractionList& il = ilist.list()[F_DISRES];
if (!il.empty())
{
}
do_groups(serializer, &mtop->groups, &(mtop->symtab));
+ if (file_version < tpxv_RemovedConstantAcceleration)
+ {
+ mtop->groups.groups[SimulationAtomGroupType::AccelerationUnused].clear();
+ mtop->groups.groupNumbers[SimulationAtomGroupType::AccelerationUnused].clear();
+ }
mtop->haveMoleculeIndices = true;
gmx_fatal(FARGS,
"Unknown precision in file %s: real is %d bytes "
"instead of %zu or %zu",
- filename, precision, sizeof(float), sizeof(double));
+ filename,
+ precision,
+ sizeof(float),
+ sizeof(double));
}
gmx_fio_setprecision(fio, tpx->isDouble);
- fprintf(stderr, "Reading file %s, %s (%s precision)\n", filename, buf.c_str(),
+ fprintf(stderr,
+ "Reading file %s, %s (%s precision)\n",
+ filename,
+ buf.c_str(),
tpx->isDouble ? "double" : "single");
}
else
serializer->doString(&buf);
gmx_fio_setprecision(fio, tpx->isDouble);
serializer->doInt(&precision);
- fileTag = gmx::formatString("%s", tpx_tag);
+ fileTag = tpx_tag;
}
/* Check versions! */
if (fileTag != tpx_tag)
{
- fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n", fileTag.c_str(), tpx_tag);
+ fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n", fileTag.c_str(), tpx_tag.c_str());
/* We only support reading tpx files with the same tag as the code
* or tpx files with the release tag and with lower version number.
gmx_fatal(FARGS,
"tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' "
"with program for tpx version %d, tag '%s'",
- filename, tpx->fileVersion, fileTag.c_str(), tpx_version, tpx_tag);
+ filename,
+ tpx->fileVersion,
+ fileTag.c_str(),
+ tpx_version,
+ tpx_tag.c_str());
}
}
}
|| ((tpx->fileVersion > tpx_version) && !TopOnlyOK) || (tpx->fileGeneration > tpx_generation)
|| tpx_version == 80) /*80 was used by both 5.0-dev and 4.6-dev*/
{
- gmx_fatal(FARGS, "reading tpx file (%s) version %d with version %d program", filename,
- tpx->fileVersion, tpx_version);
+ gmx_fatal(FARGS,
+ "reading tpx file (%s) version %d with version %d program",
+ filename,
+ tpx->fileVersion,
+ tpx_version);
}
serializer->doInt(&tpx->natoms);
// of the tpx file.
if (tpx->bX)
{
- state->flags |= (1 << estX);
+ state->flags |= enumValueToBitMask(StateEntry::X);
}
if (tpx->bV)
{
- state->flags |= (1 << estV);
+ state->flags |= enumValueToBitMask(StateEntry::V);
}
state_change_natoms(state, tpx->natoms);
}
{
if (serializer->reading())
{
- state->flags |= (1 << estX);
+ state->flags |= enumValueToBitMask(StateEntry::X);
}
serializer->doRvecArray(x, tpx->natoms);
}
{
if (serializer->reading())
{
- state->flags |= (1 << estV);
+ state->flags |= enumValueToBitMask(StateEntry::V);
}
if (!v)
{
{
if (tpx->fileVersion < 57)
{
- if (!mtop->moltype[0].ilist[F_DISRES].empty())
- {
- ir->eDisre = edrSimple;
- }
- else
- {
- ir->eDisre = edrNone;
- }
+ ir->eDisre = !mtop->moltype[0].ilist[F_DISRES].empty()
+ ? DistanceRestraintRefinement::Simple
+ : DistanceRestraintRefinement::None;
}
}
}
header.natoms = state.natoms;
header.ngtc = state.ngtc;
header.fep_state = state.fep_state;
- header.lambda = state.lambda[efptFEP];
+ header.lambda = state.lambda[FreeEnergyPerturbationCouplingType::Fep];
header.bIr = ir != nullptr;
header.bTop = mtop != nullptr;
- header.bX = (state.flags & (1 << estX)) != 0;
- header.bV = (state.flags & (1 << estV)) != 0;
+ header.bX = (state.flags & enumValueToBitMask(StateEntry::X)) != 0;
+ header.bV = (state.flags & enumValueToBitMask(StateEntry::V)) != 0;
header.bF = false;
header.bBox = true;
header.fileVersion = tpx_version;
return tpx;
}
-void write_tpx_state(const char* fn, const t_inputrec* ir, const t_state* state, const gmx_mtop_t* mtop)
+void write_tpx_state(const char* fn, const t_inputrec* ir, const t_state* state, const gmx_mtop_t& mtop)
{
/* To write a state, we first need to write the state information to a buffer before
* we append the raw bytes to the file. For this, the header information needs to be
t_fileio* fio;
- TpxFileHeader tpx = populateTpxHeader(*state, ir, mtop);
+ TpxFileHeader tpx = populateTpxHeader(*state, ir, &mtop);
// Long-term we should move to use little endian in files to avoid extra byte swapping,
// but since we just used the default XDR format (which is big endian) for the TPR
// header it would cause third-party libraries reading our raw data to tear their hair
// TPR file for now - and thus we ask the serializer to swap if this host is little endian.
gmx::InMemorySerializer tprBodySerializer(gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
- do_tpx_body(&tprBodySerializer, &tpx, const_cast<t_inputrec*>(ir), const_cast<t_state*>(state),
- nullptr, nullptr, const_cast<gmx_mtop_t*>(mtop));
+ do_tpx_body(&tprBodySerializer,
+ &tpx,
+ const_cast<t_inputrec*>(ir),
+ const_cast<t_state*>(state),
+ nullptr,
+ nullptr,
+ const_cast<gmx_mtop_t*>(&mtop));
std::vector<char> tprBody = tprBodySerializer.finishAndGetBuffer();
tpx.sizeOfTprBody = tprBody.size();
const rvec* f)
{
t_fileio* fio = gmx_trr_open(fn, "w");
- do_trr_frame(fio, false, &step, &t, &lambda, const_cast<rvec*>(box), &natoms,
- const_cast<rvec*>(x), const_cast<rvec*>(v), const_cast<rvec*>(f));
+ do_trr_frame(fio,
+ false,
+ &step,
+ &t,
+ &lambda,
+ const_cast<rvec*>(box),
+ &natoms,
+ const_cast<rvec*>(x),
+ const_cast<rvec*>(v),
+ const_cast<rvec*>(f));
gmx_trr_close(fio);
}
const rvec* v,
const rvec* f)
{
- if (!do_trr_frame(fio, false, &step, &t, &lambda, const_cast<rvec*>(box), &natoms,
- const_cast<rvec*>(x), const_cast<rvec*>(v), const_cast<rvec*>(f)))
+ if (!do_trr_frame(fio,
+ false,
+ &step,
+ &t,
+ &lambda,
+ const_cast<rvec*>(box),
+ &natoms,
+ const_cast<rvec*>(x),
+ const_cast<rvec*>(v),
+ const_cast<rvec*>(f)))
{
gmx_file("Cannot write trajectory frame; maybe you are out of disk space?");
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "trxio.h"
+#include "gromacs/fileio/trxio.h"
#include "config.h"
struct t_trxstatus
{
int flags; /* flags for read_first/next_frame */
- int __frame;
+ int currentFrame;
real t0; /* time of the first frame, needed *
* for skipping frames with -dt */
real tf; /* internal frame time */
#endif
r = -1;
- if ((!bTimeSet(TBEGIN) || (t >= rTimeValue(TBEGIN))) && (!bTimeSet(TEND) || (t <= rTimeValue(TEND))))
+ if ((!bTimeSet(TimeControl::Begin) || (t >= rTimeValue(TimeControl::Begin)))
+ && (!bTimeSet(TimeControl::End) || (t <= rTimeValue(TimeControl::End))))
{
- if (bTimeSet(TDELTA) && !bRmod_fd(t, t0, rTimeValue(TDELTA), bDouble))
+ if (bTimeSet(TimeControl::Delta) && !bRmod_fd(t, t0, rTimeValue(TimeControl::Delta), bDouble))
{
r = -1;
}
r = 0;
}
}
- else if (bTimeSet(TEND) && (t >= rTimeValue(TEND)))
+ else if (bTimeSet(TimeControl::End) && (t >= rTimeValue(TimeControl::End)))
{
r = 1;
}
if (debug)
{
- fprintf(debug, "t=%g, t0=%g, b=%g, e=%g, dt=%g: r=%d\n", t, t0, rTimeValue(TBEGIN),
- rTimeValue(TEND), rTimeValue(TDELTA), r);
+ fprintf(debug,
+ "t=%g, t0=%g, b=%g, e=%g, dt=%g: r=%d\n",
+ t,
+ t0,
+ rTimeValue(TimeControl::Begin),
+ rTimeValue(TimeControl::End),
+ rTimeValue(TimeControl::Delta),
+ r);
}
return r;
}
static void initcount(t_trxstatus* status)
{
- status->__frame = -1;
+ status->currentFrame = -1;
}
static void status_init(t_trxstatus* status)
status->flags = 0;
status->xframe = nullptr;
status->fio = nullptr;
- status->__frame = -1;
+ status->currentFrame = -1;
status->t0 = 0;
status->tf = 0;
status->persistent_line = nullptr;
int nframes_read(t_trxstatus* status)
{
- return status->__frame;
+ return status->currentFrame;
}
static void printcount_(t_trxstatus* status, const gmx_output_env_t* oenv, const char* l, real t)
{
- if ((status->__frame < 2 * SKIP1 || status->__frame % SKIP1 == 0)
- && (status->__frame < 2 * SKIP2 || status->__frame % SKIP2 == 0)
- && (status->__frame < 2 * SKIP3 || status->__frame % SKIP3 == 0)
+ if ((status->currentFrame < 2 * SKIP1 || status->currentFrame % SKIP1 == 0)
+ && (status->currentFrame < 2 * SKIP2 || status->currentFrame % SKIP2 == 0)
+ && (status->currentFrame < 2 * SKIP3 || status->currentFrame % SKIP3 == 0)
&& output_env_get_trajectory_io_verbosity(oenv) != 0)
{
- fprintf(stderr, "\r%-14s %6d time %8.3f ", l, status->__frame, output_env_conv_time(oenv, t));
+ fprintf(stderr, "\r%-14s %6d time %8.3f ", l, status->currentFrame, output_env_conv_time(oenv, t));
fflush(stderr);
}
}
static void printcount(t_trxstatus* status, const gmx_output_env_t* oenv, real t, gmx_bool bSkip)
{
- status->__frame++;
+ status->currentFrame++;
printcount_(status, oenv, bSkip ? "Skipping frame" : "Reading frame", t);
}
{
if (fr->not_ok & HEADER_NOT_OK)
{
- fprintf(stderr, "WARNING: Incomplete header: nr %d time %g\n", status->__frame + 1, fr->time);
+ fprintf(stderr, "WARNING: Incomplete header: nr %d time %g\n", status->currentFrame + 1, fr->time);
}
else if (fr->not_ok)
{
- fprintf(stderr, "WARNING: Incomplete frame: nr %d time %g\n", status->__frame + 1, fr->time);
+ fprintf(stderr, "WARNING: Incomplete frame: nr %d time %g\n", status->currentFrame + 1, fr->time);
}
fflush(stderr);
}
if (filetype == efXTC)
{
- lasttime = xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio), gmx_fio_getxdr(stfio),
- status->natoms, &bOK);
+ lasttime = xdr_xtc_get_last_frame_time(
+ gmx_fio_getfp(stfio), gmx_fio_getxdr(stfio), status->natoms, &bOK);
if (!bOK)
{
gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported.");
case efTNG: gmx_write_tng_from_trxframe(status->tng, fr, nind); break;
case efXTC: write_xtc(status->fio, nind, fr->step, fr->time, fr->box, xout, prec); break;
case efTRR:
- gmx_trr_write_frame(status->fio, nframes_read(status), fr->time, fr->step, fr->box,
- nind, xout, vout, fout);
+ gmx_trr_write_frame(
+ status->fio, nframes_read(status), fr->time, fr->step, fr->box, nind, xout, vout, fout);
break;
case efGRO:
case efPDB:
sprintf(title, "frame t= %.3f", fr->time);
if (ftp == efGRO)
{
- write_hconf_indexed_p(gmx_fio_getfp(status->fio), title, fr->atoms, nind, ind,
- fr->x, fr->bV ? fr->v : nullptr, fr->box);
+ write_hconf_indexed_p(gmx_fio_getfp(status->fio),
+ title,
+ fr->atoms,
+ nind,
+ ind,
+ fr->x,
+ fr->bV ? fr->v : nullptr,
+ fr->box);
}
else
{
- write_pdbfile_indexed(gmx_fio_getfp(status->fio), title, fr->atoms, fr->x,
- PbcType::Unset, fr->box, ' ', fr->step, nind, ind, gc, FALSE);
+ write_pdbfile_indexed(gmx_fio_getfp(status->fio),
+ title,
+ fr->atoms,
+ fr->x,
+ PbcType::Unset,
+ fr->box,
+ ' ',
+ fr->step,
+ nind,
+ ind,
+ gc,
+ FALSE);
}
break;
case efG96:
if (in != nullptr)
{
- gmx_prepare_tng_writing(filename, filemode, &in->tng, &out->tng, natoms, mtop, index,
- index_group_name);
+ gmx_prepare_tng_writing(
+ filename, filemode, &in->tng, &out->tng, natoms, mtop, index, index_group_name);
}
else if ((infile) && (efTNG == fn2ftp(infile)))
{
gmx_tng_trajectory_t tng_in;
gmx_tng_open(infile, 'r', &tng_in);
- gmx_prepare_tng_writing(filename, filemode, &tng_in, &out->tng, natoms, mtop, index,
- index_group_name);
+ gmx_prepare_tng_writing(
+ filename, filemode, &tng_in, &out->tng, natoms, mtop, index, index_group_name);
}
else
{
// we start from a file that is not a tng file or have been unable to load the
// input file, so we need to populate the fields independently of it
- gmx_prepare_tng_writing(filename, filemode, nullptr, &out->tng, natoms, mtop, index,
- index_group_name);
+ gmx_prepare_tng_writing(
+ filename, filemode, nullptr, &out->tng, natoms, mtop, index, index_group_name);
}
return out;
}
default:
if (!fr->bX)
{
- gmx_fatal(FARGS, "Need coordinates to write a %s trajectory",
+ gmx_fatal(FARGS,
+ "Need coordinates to write a %s trajectory",
ftp2ext(gmx_fio_getftp(status->fio)));
}
break;
write_xtc(status->fio, fr->natoms, fr->step, fr->time, fr->box, fr->x, prec);
break;
case efTRR:
- gmx_trr_write_frame(status->fio, fr->step, fr->time, fr->lambda, fr->box, fr->natoms,
- fr->bX ? fr->x : nullptr, fr->bV ? fr->v : nullptr,
+ gmx_trr_write_frame(status->fio,
+ fr->step,
+ fr->time,
+ fr->lambda,
+ fr->box,
+ fr->natoms,
+ fr->bX ? fr->x : nullptr,
+ fr->bV ? fr->v : nullptr,
fr->bF ? fr->f : nullptr);
break;
case efGRO:
case efENT:
if (!fr->bAtoms)
{
- gmx_fatal(FARGS, "Can not write a %s file without atom names",
+ gmx_fatal(FARGS,
+ "Can not write a %s file without atom names",
ftp2ext(gmx_fio_getftp(status->fio)));
}
sprintf(title, "frame t= %.3f", fr->time);
if (gmx_fio_getftp(status->fio) == efGRO)
{
- write_hconf_p(gmx_fio_getfp(status->fio), title, fr->atoms, fr->x,
- fr->bV ? fr->v : nullptr, fr->box);
+ write_hconf_p(
+ gmx_fio_getfp(status->fio), title, fr->atoms, fr->x, fr->bV ? fr->v : nullptr, fr->box);
}
else
{
- write_pdbfile(gmx_fio_getfp(status->fio), title, fr->atoms, fr->x,
- fr->bPBC ? fr->pbcType : PbcType::Unset, fr->box, ' ', fr->step, gc);
+ write_pdbfile(gmx_fio_getfp(status->fio),
+ title,
+ fr->atoms,
+ fr->x,
+ fr->bPBC ? fr->pbcType : PbcType::Unset,
+ fr->box,
+ ' ',
+ fr->step,
+ gc);
}
break;
case efG96: write_g96_conf(gmx_fio_getfp(status->fio), title, fr, -1, nullptr); break;
default:
- gmx_fatal(FARGS, "Sorry, write_trxframe can not write %s",
- ftp2ext(gmx_fio_getftp(status->fio)));
+ gmx_fatal(FARGS, "Sorry, write_trxframe can not write %s", ftp2ext(gmx_fio_getftp(status->fio)));
}
return 0;
{
if (na != fr->natoms)
{
- gmx_fatal(FARGS, "Number of atoms in pdb frame %d is %d instead of %d",
- nframes_read(status), na, fr->natoms);
+ gmx_fatal(FARGS,
+ "Number of atoms in pdb frame %d is %d instead of %d",
+ nframes_read(status),
+ na,
+ fr->natoms);
}
return TRUE;
}
case efG96:
{
t_symtab* symtab = nullptr;
- read_g96_conf(gmx_fio_getfp(status->fio), nullptr, nullptr, fr, symtab,
- status->persistent_line);
+ read_g96_conf(gmx_fio_getfp(status->fio), nullptr, nullptr, fr, symtab, status->persistent_line);
bRet = (fr->natoms > 0);
break;
}
case efXTC:
- if (bTimeSet(TBEGIN) && (status->tf < rTimeValue(TBEGIN)))
+ if (bTimeSet(TimeControl::Begin) && (status->tf < rTimeValue(TimeControl::Begin)))
{
- if (xtc_seek_time(status->fio, rTimeValue(TBEGIN), fr->natoms, TRUE))
+ if (xtc_seek_time(status->fio, rTimeValue(TimeControl::Begin), fr->natoms, TRUE))
{
gmx_fatal(FARGS,
"Specified frame (time %f) doesn't exist or file "
"corrupt/inconsistent.",
- rTimeValue(TBEGIN));
+ rTimeValue(TimeControl::Begin));
}
initcount(status);
}
- bRet = (read_next_xtc(status->fio, fr->natoms, &fr->step, &fr->time, fr->box, fr->x,
- &fr->prec, &bOK)
+ bRet = (read_next_xtc(
+ status->fio, fr->natoms, &fr->step, &fr->time, fr->box, fr->x, &fr->prec, &bOK)
!= 0);
fr->bPrec = (bRet && fr->prec > 0);
fr->bStep = bRet;
#if GMX_USE_PLUGINS
bRet = read_next_vmd_frame(status->vmdplugin, fr);
#else
- gmx_fatal(FARGS, "DEATH HORROR in read_next_frame ftp=%s,status=%s",
- ftp2ext(gmx_fio_getftp(status->fio)), gmx_fio_getname(status->fio));
+ gmx_fatal(FARGS,
+ "DEATH HORROR in read_next_frame ftp=%s,status=%s",
+ ftp2ext(gmx_fio_getftp(status->fio)),
+ gmx_fio_getname(status->fio));
#endif
}
status->tf = fr->time;
{
if (debug)
{
- fprintf(debug, "\nUnable to open dynamic library %s.\n%s\n", fullpath,
- vmddlerror()); /*only to debug because of stdc++ erros */
+ fprintf(debug, "\nUnable to open dynamic library %s.\n%s\n", fullpath, vmddlerror()); /*only to debug because of stdc++ erros */
}
return 0;
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
if (wi->lineno != -1)
{
- fprintf(stderr, "\n%s %d [file %s, line %d]:\n%s\n\n", wtype, n, wi->filenm.c_str(),
- wi->lineno, temp2);
+ fprintf(stderr, "\n%s %d [file %s, line %d]:\n%s\n\n", wtype, n, wi->filenm.c_str(), wi->lineno, temp2);
}
else
{
print_warn_count("note", wi->nwarn_note);
print_warn_count("warning", wi->nwarn_warn);
- gmx_fatal(f_errno, file, line, "There %s %d error%s in input file(s)",
- (wi->nwarn_error == 1) ? "was" : "were", wi->nwarn_error, (wi->nwarn_error == 1) ? "" : "s");
+ gmx_fatal(f_errno,
+ file,
+ line,
+ "There %s %d error%s in input file(s)",
+ (wi->nwarn_error == 1) ? "was" : "were",
+ wi->nwarn_error,
+ (wi->nwarn_error == 1) ? "" : "s");
}
void check_warning_error(warninp_t wi, int f_errno, const char* file, int line)
if (wi->maxwarn >= 0 && wi->nwarn_warn > wi->maxwarn)
{
- gmx_fatal(f_errno, file, line,
+ gmx_fatal(f_errno,
+ file,
+ line,
"Too many warnings (%d).\n"
"If you are sure all warnings are harmless, use the -maxwarn option.",
wi->nwarn_warn);
delete wi;
}
-void _too_few(warninp_t wi, const char* fn, int line)
+void too_few_function(warninp_t wi, const char* fn, int line)
{
char buf[STRLEN];
warning(wi, buf);
}
-void _incorrect_n_param(warninp_t wi, const char* fn, int line)
+void incorrect_n_param_function(warninp_t wi, const char* fn, int line)
{
char buf[STRLEN];
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2010,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void free_warning(warninp_t wi);
/* Frees the data structure pointed to by wi. */
-void _too_few(warninp_t wi, const char* fn, int line);
-#define too_few(wi) _too_few(wi, __FILE__, __LINE__)
+void too_few_function(warninp_t wi, const char* fn, int line);
+#define too_few(wi) too_few_function(wi, __FILE__, __LINE__)
/* Issue a warning stating 'Too few parameters' */
-void _incorrect_n_param(warninp_t wi, const char* fn, int line);
-#define incorrect_n_param(wi) _incorrect_n_param(wi, __FILE__, __LINE__)
+void incorrect_n_param_function(warninp_t wi, const char* fn, int line);
+#define incorrect_n_param(wi) incorrect_n_param_function(wi, __FILE__, __LINE__)
/* Issue a warning stating 'Incorrect number of parameters' */
#endif
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "writeps.h"
#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
using namespace gmx;
-const char* fontnm[efontNR] = {
- "Times-Roman", "Times-Italic", "Times-Bold", "Times-BoldItalic",
- "Helvetica", "Helvetica-Oblique", "Helvetica-Bold", "Helvetica-BoldOblique",
- "Courier", "Courier-Oblique", "Courier-Bold", "Courier-BoldOblique"
-};
+const char* enumValueToString(Fonts enumValue)
+{
+ gmx::EnumerationArray<Fonts, const char*> fontNames = {
+ "Times-Roman", "Times-Italic", "Times-Bold", "Times-BoldItalic",
+ "Helvetica", "Helvetica-Oblique", "Helvetica-Bold", "Helvetica-BoldOblique",
+ "Courier", "Courier-Oblique", "Courier-Bold", "Courier-BoldOblique"
+ };
+ return fontNames[enumValue];
+}
t_psdata ps_open(const char* fn, real x1, real y1, real x2, real y2)
{
fprintf(ps->fp,
"/by {def currentpoint "
"%g y r %g %g r %g y neg r %g %g r f y add moveto} bind def\n",
- 0.0, xbox, 0.0, 0.0, -xbox, 0.0);
+ 0.0,
+ xbox,
+ 0.0,
+ 0.0,
+ -xbox,
+ 0.0);
/* macro bn is used in ps_rgb_nbox to draw rectangular boxes */
}
fprintf(ps->fp,
"/b {currentpoint "
"%g %g r %g %g r %g %g r %g %g r f %g add moveto} bind def\n",
- 0.0, ybox, xbox, 0.0, 0.0, -ybox, -xbox, 0.0, ybox);
+ 0.0,
+ ybox,
+ xbox,
+ 0.0,
+ 0.0,
+ -ybox,
+ -xbox,
+ 0.0,
+ ybox);
/* macro b is used in search_col to define macro B */
}
void ps_arcslice(t_psdata* ps, real xc, real yc, real rad1, real rad2, real a0, real a1)
{
- fprintf(ps->fp, "newpath %g %g %g %g %g arc %g %g %g %g %g arcn closepath s\n", xc, yc, rad1,
- a0, a1, xc, yc, rad2, a1, a0);
+ fprintf(ps->fp, "newpath %g %g %g %g %g arc %g %g %g %g %g arcn closepath s\n", xc, yc, rad1, a0, a1, xc, yc, rad2, a1, a0);
}
void ps_fillarcslice(t_psdata* ps, real xc, real yc, real rad1, real rad2, real a0, real a1)
{
- fprintf(ps->fp, "newpath %g %g %g %g %g arc %g %g %g %g %g arcn closepath f\n", xc, yc, rad1,
- a0, a1, xc, yc, rad2, a1, a0);
+ fprintf(ps->fp, "newpath %g %g %g %g %g arc %g %g %g %g %g arcn closepath f\n", xc, yc, rad1, a0, a1, xc, yc, rad2, a1, a0);
}
void ps_circle(t_psdata* ps, real x1, real y1, real rad)
ps_arc(ps, x1, y1, rad, 0, 360);
}
-void ps_font(t_psdata* ps, int font, real size)
+void ps_font(t_psdata* ps, Fonts font, real size)
{
- if ((font < 0) || (font > efontNR))
+ if (font == Fonts::Count)
{
- fprintf(stderr, "Invalid Font: %d, using %s\n", font, fontnm[0]);
- font = 0;
+ fprintf(stderr, "Invalid Font: %d, using %s\n", static_cast<int>(font), enumValueToString(Fonts::Times));
+ font = Fonts::Times;
}
- fprintf(ps->fp, "/%s findfont\n", fontnm[font]);
+ fprintf(ps->fp, "/%s findfont\n", enumValueToString(font));
fprintf(ps->fp, "%g scalefont setfont\n", size);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
eYBottom
} eYPos;
-enum
+enum class Fonts : int
{
- efontTIMES,
- efontTIMESITALIC,
- efontTIMESBOLD,
- efontTIMESBOLDITALIC,
- efontHELV,
- efontHELVITALIC,
- efontHELVBOLD,
- efontHELVBOLDITALIC,
- efontCOUR,
- efontCOURITALIC,
- efontCOURBOLD,
- efontCOURBOLDITALIC,
- efontNR
+ Times,
+ TimesItalic,
+ TimesBold,
+ TimesBoldItalic,
+ Helvetica,
+ HelveticaItalic,
+ HelveticaBold,
+ HelveticaBoldItalic,
+ Courier,
+ CourierItalic,
+ CourierBold,
+ CourierBoldItalic,
+ Count
};
};
-extern const char* fontnm[efontNR];
+const char* enumValueToString(Fonts enumValue);
t_psdata ps_open(const char* fn, real x1, real y1, real x2, real y2);
void ps_circle(t_psdata* ps, real x1, real y1, real rad);
-void ps_font(t_psdata* ps, int font, real size);
+void ps_font(t_psdata* ps, Fonts font, real size);
void ps_strfont(t_psdata* ps, char* font, real size);
void ps_text(t_psdata* ps, real x1, real y1, const std::string& str);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* the xdr data types; note that there is no data type 'real' because
here we deal with the types as they are actually written to disk. */
-typedef enum
+enum class XdrDataType : int
{
- xdr_datatype_int,
- xdr_datatype_float,
- xdr_datatype_double,
- xdr_datatype_int64,
- xdr_datatype_char,
- xdr_datatype_string
-} xdr_datatype;
+ Int,
+ Float,
+ Double,
+ Int64,
+ Char,
+ String,
+ Count
+};
-/* names corresponding to the xdr_datatype enum */
-extern const char* xdr_datatype_names[];
+/* names corresponding to the XdrDataType enum */
+const char* enumValueToString(XdrDataType enumValue);
#endif
fprintf(debug,
"\nXTC error: read/write of %s failed, "
"source file %s, line %d\n",
- str, file, line);
+ str,
+ file,
+ line);
}
return 0;
}
}
/* write data */
- bOK = xtc_coord(xd, &natoms, const_cast<rvec*>(box), const_cast<rvec*>(x), &prec,
- FALSE); /* bOK will be 1 if writing went well */
+ bOK = xtc_coord(xd, &natoms, const_cast<rvec*>(box), const_cast<rvec*>(x), &prec, FALSE); /* bOK will be 1 if writing went well */
if (bOK)
{
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "xvgr.h"
+#include <array>
#include <cassert>
#include <cctype>
#include <cstring>
gmx_fatal(FARGS,
"Output buffer length in xvgstr (%d) too small to process xvg input string "
"'%s'",
- buflen, gmx.c_str());
+ buflen,
+ gmx.c_str());
}
if (gmx[g] == '\\')
{
"@ world ymin %g\n"
"@ world xmax %g\n"
"@ world ymax %g\n",
- xmin, ymin, xmax, ymax);
+ xmin,
+ ymin,
+ xmax,
+ ymax);
}
}
{
if (output_env_get_xvg_format(oenv) == XvgFormat::Xmgr)
{
- fprintf(out, "@ legend string %d \"%s\"\n", i + nr_first,
+ fprintf(out,
+ "@ legend string %d \"%s\"\n",
+ i + nr_first,
xvgrstr(setname[i], oenv, buf, STRLEN));
}
else
{
- fprintf(out, "@ s%d legend \"%s\"\n", i + nr_first,
- xvgrstr(setname[i], oenv, buf, STRLEN));
+ fprintf(out, "@ s%d legend \"%s\"\n", i + nr_first, xvgrstr(setname[i], oenv, buf, STRLEN));
}
}
}
}
}
-static const char* LocTypeStr[] = { "view", "world" };
-static const char* BoxFillStr[] = { "none", "color", "pattern" };
+static constexpr std::array<const char*, 2> LocTypeStr = { "view", "world" };
+static constexpr std::array<const char*, 3> BoxFillStr = { "none", "color", "pattern" };
void xvgr_box(FILE* out,
int LocType,
fprintf(stderr,
"Invalid line in %s:\n%s"
"Using zeros for the last %d sets\n",
- fn, line0, narg - a);
+ fn,
+ line0,
+ narg - a);
}
n++;
}
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014,2015,2017,2019, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015,2017,2019,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(gmxana INTERFACE)
+
file(GLOB GMXANA_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${GMXANA_SOURCES} PARENT_SCOPE)
+# Source files have the following private module dependencies.
+target_link_libraries(gmxana PRIVATE
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(gmxana PUBLIC
+target_include_directories(gmxana INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(gmxana PUBLIC
+target_link_libraries(gmxana INTERFACE
+ legacy_api
+ )
+
+# TODO: when gmxana is an OBJECT target
+#target_link_libraries(gmxana PUBLIC legacy_api)
+#target_link_libraries(gmxana PRIVATE common)
+
+# Module dependencies
+# gmxana interfaces convey transitive dependence on these modules.
+#target_link_libraries(gmxana PUBLIC
+target_link_libraries(gmxana INTERFACE
+ utility
+ )
+
if(BUILD_TESTING)
add_subdirectory(tests)
endif()
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/listed_forces/bonded.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vecdump.h"
#include "gromacs/pbcutil/pbc.h"
static int calc_Nbin(real phi, int multiplicity, real core_frac)
{
- static const real r360 = 360 * DEG2RAD;
+ static const real r360 = 360 * gmx::c_deg2Rad;
real rot_width, core_width, core_offset, low, hi;
int bin;
/* with multiplicity 3 and core_frac 0.5
{
low = ((bin - 1) * rot_width) + core_offset;
hi = ((bin - 1) * rot_width) + core_offset + core_width;
- low *= DEG2RAD;
- hi *= DEG2RAD;
+ low *= gmx::c_deg2Rad;
+ hi *= gmx::c_deg2Rad;
if ((phi > low) && (phi < hi))
{
return bin;
multiplicity[k] = 3;
}
- low_ana_dih_trans(TRUE, fn_trans, TRUE, fn_histo, maxchi, dih, nlist, dlist, nframes, nangles,
- grpname, multiplicity, time, bRb, 0.5, oenv);
+ low_ana_dih_trans(
+ TRUE, fn_trans, TRUE, fn_histo, maxchi, dih, nlist, dlist, nframes, nangles, grpname, multiplicity, time, bRb, 0.5, oenv);
sfree(dlist);
sfree(multiplicity);
}
if (bAll)
{
/* print cuml rotamer vs time */
- print_one(oenv, "chiproduct", dlist[i].name, "chi product for",
- "cumulative rotamer", nframes, time, chi_prtrj);
+ print_one(oenv, "chiproduct", dlist[i].name, "chi product for", "cumulative rotamer", nframes, time, chi_prtrj);
}
/* make a histogram pf culm. rotamer occupancy too */
for (i = ix = 0; (ix < n3); i++, ix += 3)
{
- ang[i] = bond_angle(x_s[index[ix]], x_s[index[ix + 1]], x_s[index[ix + 2]], pbc, r_ij, r_kj,
- &costh, &t1, &t2);
+ ang[i] = bond_angle(
+ x_s[index[ix]], x_s[index[ix + 1]], x_s[index[ix + 2]], pbc, r_ij, r_kj, &costh, &t1, &t2);
}
if (debug)
{
- fprintf(debug, "Angle[0]=%g, costh=%g, index0 = %d, %d, %d\n", ang[0], costh, index[0],
- index[1], index[2]);
+ fprintf(debug, "Angle[0]=%g, costh=%g, index0 = %d, %d, %d\n", ang[0], costh, index[0], index[1], index[2]);
pr_rvec(debug, 0, "rij", r_ij, DIM, TRUE);
pr_rvec(debug, 0, "rkj", r_kj, DIM, TRUE);
}
for (i = 0; i < nangles; i++)
{
- angle = angles[i] * RAD2DEG;
+ angle = angles[i] * gmx::c_rad2Deg;
if (angle > 135 && angle < 225)
{
for (i = ix = 0; (ix < n4); i++, ix += 4)
{
- aaa = dih_angle(x_s[index[ix]], x_s[index[ix + 1]], x_s[index[ix + 2]], x_s[index[ix + 3]],
- pbc, r_ij, r_kj, r_kl, m, n, &t1, &t2, &t3);
+ aaa = dih_angle(x_s[index[ix]],
+ x_s[index[ix + 1]],
+ x_s[index[ix + 2]],
+ x_s[index[ix + 3]],
+ pbc,
+ r_ij,
+ r_kj,
+ r_kl,
+ m,
+ n,
+ &t1,
+ &t2,
+ &t3);
ang[i] = aaa; /* not taking into account ryckaert bellemans yet */
}
dx = npoints / (maxx - minx);
if (debug)
{
- fprintf(debug, "Histogramming: ndata=%d, nhisto=%d, minx=%g,maxx=%g,dx=%g\n", ndata,
- npoints, minx, maxx, dx);
+ fprintf(debug, "Histogramming: ndata=%d, nhisto=%d, minx=%g,maxx=%g,dx=%g\n", ndata, npoints, minx, maxx, dx);
}
for (i = 0; (i < ndata); i++)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_GMXANA_ANGLE_CORRECTION_H
#define GMX_GMXANA_ANGLE_CORRECTION_H
-#include "gromacs/math/units.h"
+#include "gromacs/utility/real.h"
/*! \brief
* Return the angle in radians after correcting to be within range of -PI < \p angle < PI.
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2013,2014,2015 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _binsearch_h
-#define _binsearch_h
+#ifndef GMX_GMXANA_BINSEARCH_H
+#define GMX_GMXANA_BINSEARCH_H
#include "gromacs/utility/real.h"
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "cluster_methods.h"
+
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/cmat.h"
+#include "gromacs/linearalgebra/eigensolver.h"
+#include "gromacs/random/threefry.h"
+#include "gromacs/random/uniformintdistribution.h"
+#include "gromacs/random/uniformrealdistribution.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
+
+void mc_optimize(FILE* log, t_mat* m, real* time, int maxiter, int nrandom, int seed, real kT, const char* conv, gmx_output_env_t* oenv)
+{
+ FILE* fp = nullptr;
+ real ecur, enext, emin, prob, enorm;
+ int i, j, iswap, jswap, nn, nuphill = 0;
+ t_mat* minimum;
+
+ if (seed == 0)
+ {
+ seed = static_cast<int>(gmx::makeRandomSeed());
+ }
+ gmx::DefaultRandomEngine rng(seed);
+
+ if (m->n1 != m->nn)
+ {
+ fprintf(stderr, "Can not do Monte Carlo optimization with a non-square matrix.\n");
+ return;
+ }
+ printf("\nDoing Monte Carlo optimization to find the smoothest trajectory\n");
+ printf("by reordering the frames to minimize the path between the two structures\n");
+ printf("that have the largest pairwise RMSD.\n");
+ printf("Using random seed %d.\n", seed);
+
+ iswap = jswap = -1;
+ enorm = m->mat[0][0];
+ for (i = 0; (i < m->n1); i++)
+ {
+ for (j = 0; (j < m->nn); j++)
+ {
+ if (m->mat[i][j] > enorm)
+ {
+ enorm = m->mat[i][j];
+ iswap = i;
+ jswap = j;
+ }
+ }
+ }
+ if ((iswap == -1) || (jswap == -1))
+ {
+ fprintf(stderr, "Matrix contains identical values in all fields\n");
+ return;
+ }
+ swap_rows(m, 0, iswap);
+ swap_rows(m, m->n1 - 1, jswap);
+ emin = ecur = mat_energy(m);
+ printf("Largest distance %g between %d and %d. Energy: %g.\n", enorm, iswap, jswap, emin);
+
+ nn = m->nn;
+
+ /* Initiate and store global minimum */
+ minimum = init_mat(nn, m->b1D);
+ minimum->nn = nn;
+ copy_t_mat(minimum, m);
+
+ if (nullptr != conv)
+ {
+ fp = xvgropen(conv, "Convergence of the MC optimization", "Energy", "Step", oenv);
+ }
+
+ gmx::UniformIntDistribution<int> intDistNN(1, nn - 2); // [1,nn-2]
+ gmx::UniformRealDistribution<real> realDistOne; // [0,1)
+
+ for (i = 0; (i < maxiter); i++)
+ {
+ /* Generate new swapping candidates */
+ do
+ {
+ iswap = intDistNN(rng);
+ jswap = intDistNN(rng);
+ } while ((iswap == jswap) || (iswap >= nn - 1) || (jswap >= nn - 1));
+
+ /* Apply swap and compute energy */
+ swap_rows(m, iswap, jswap);
+ enext = mat_energy(m);
+
+ /* Compute probability */
+ prob = 0;
+ if ((enext < ecur) || (i < nrandom))
+ {
+ prob = 1;
+ if (enext < emin)
+ {
+ /* Store global minimum */
+ copy_t_mat(minimum, m);
+ emin = enext;
+ }
+ }
+ else if (kT > 0)
+ {
+ /* Try Monte Carlo step */
+ prob = std::exp(-(enext - ecur) / (enorm * kT));
+ }
+
+ if (prob == 1 || realDistOne(rng) < prob)
+ {
+ if (enext > ecur)
+ {
+ nuphill++;
+ }
+
+ fprintf(log, "Iter: %d Swapped %4d and %4d (energy: %g prob: %g)\n", i, iswap, jswap, enext, prob);
+ if (nullptr != fp)
+ {
+ fprintf(fp, "%6d %10g\n", i, enext);
+ }
+ ecur = enext;
+ }
+ else
+ {
+ swap_rows(m, jswap, iswap);
+ }
+ }
+ fprintf(log, "%d uphill steps were taken during optimization\n", nuphill);
+
+ /* Now swap the matrix to get it into global minimum mode */
+ copy_t_mat(m, minimum);
+
+ fprintf(log, "Global minimum energy %g\n", mat_energy(minimum));
+ fprintf(log, "Global minimum energy %g\n", mat_energy(m));
+ fprintf(log, "Swapped time and frame indices and RMSD to next neighbor:\n");
+ for (i = 0; (i < m->nn); i++)
+ {
+ fprintf(log,
+ "%10g %5d %10g\n",
+ time[m->m_ind[i]],
+ m->m_ind[i],
+ (i < m->nn - 1) ? m->mat[m->m_ind[i]][m->m_ind[i + 1]] : 0);
+ }
+
+ if (nullptr != fp)
+ {
+ xvgrclose(fp);
+ }
+}
+
+static bool rms_dist_comp(const t_dist& a, const t_dist& b)
+{
+ return a.dist < b.dist;
+}
+
+static bool clust_id_comp(const t_clustid& a, const t_clustid& b)
+{
+ return a.clust < b.clust;
+}
+
+static bool nrnb_comp(const t_nnb& a, const t_nnb& b)
+{
+ /* return b<a, we want highest first */
+ return b.nr < a.nr;
+}
+
+void gather(t_mat* m, real cutoff, t_clusters* clust)
+{
+ t_clustid* c;
+ t_dist* d;
+ int i, j, k, nn, cid, n1, diff;
+ gmx_bool bChange;
+
+ /* First we sort the entries in the RMSD matrix */
+ n1 = m->nn;
+ nn = ((n1 - 1) * n1) / 2;
+ snew(d, nn);
+ for (i = k = 0; (i < n1); i++)
+ {
+ for (j = i + 1; (j < n1); j++, k++)
+ {
+ d[k].i = i;
+ d[k].j = j;
+ d[k].dist = m->mat[i][j];
+ }
+ }
+ if (k != nn)
+ {
+ gmx_incons("gather algortihm");
+ }
+ std::sort(d, d + nn, rms_dist_comp);
+
+ /* Now we make a cluster index for all of the conformations */
+ c = new_clustid(n1);
+
+ /* Now we check the closest structures, and equalize their cluster numbers */
+ fprintf(stderr, "Linking structures ");
+ do
+ {
+ fprintf(stderr, "*");
+ bChange = FALSE;
+ for (k = 0; (k < nn) && (d[k].dist < cutoff); k++)
+ {
+ diff = c[d[k].j].clust - c[d[k].i].clust;
+ if (diff)
+ {
+ bChange = TRUE;
+ if (diff > 0)
+ {
+ c[d[k].j].clust = c[d[k].i].clust;
+ }
+ else
+ {
+ c[d[k].i].clust = c[d[k].j].clust;
+ }
+ }
+ }
+ } while (bChange);
+ fprintf(stderr, "\nSorting and renumbering clusters\n");
+ /* Sort on cluster number */
+ std::sort(c, c + n1, clust_id_comp);
+
+ /* Renumber clusters */
+ cid = 1;
+ for (k = 1; k < n1; k++)
+ {
+ if (c[k].clust != c[k - 1].clust)
+ {
+ c[k - 1].clust = cid;
+ cid++;
+ }
+ else
+ {
+ c[k - 1].clust = cid;
+ }
+ }
+ c[k - 1].clust = cid;
+ if (debug)
+ {
+ for (k = 0; (k < n1); k++)
+ {
+ fprintf(debug, "Cluster index for conformation %d: %d\n", c[k].conf, c[k].clust);
+ }
+ }
+ clust->ncl = cid;
+ for (k = 0; k < n1; k++)
+ {
+ clust->cl[c[k].conf] = c[k].clust;
+ }
+
+ sfree(c);
+ sfree(d);
+}
+
+static gmx_bool jp_same(int** nnb, int i, int j, int P)
+{
+ gmx_bool bIn;
+ int k, ii, jj, pp;
+
+ bIn = FALSE;
+ for (k = 0; nnb[i][k] >= 0; k++)
+ {
+ bIn = bIn || (nnb[i][k] == j);
+ }
+ if (!bIn)
+ {
+ return FALSE;
+ }
+
+ bIn = FALSE;
+ for (k = 0; nnb[j][k] >= 0; k++)
+ {
+ bIn = bIn || (nnb[j][k] == i);
+ }
+ if (!bIn)
+ {
+ return FALSE;
+ }
+
+ pp = 0;
+ for (ii = 0; nnb[i][ii] >= 0; ii++)
+ {
+ for (jj = 0; nnb[j][jj] >= 0; jj++)
+ {
+ if ((nnb[i][ii] == nnb[j][jj]) && (nnb[i][ii] != -1))
+ {
+ pp++;
+ }
+ }
+ }
+
+ return (pp >= P);
+}
+
+void jarvis_patrick(int n1, real** mat, int M, int P, real rmsdcut, t_clusters* clust)
+{
+ t_dist* row;
+ t_clustid* c;
+ int** nnb;
+ int i, j, k, cid, diff, maxval;
+ gmx_bool bChange;
+ real** mcpy = nullptr;
+
+ if (rmsdcut < 0)
+ {
+ rmsdcut = 10000;
+ }
+
+ /* First we sort the entries in the RMSD matrix row by row.
+ * This gives us the nearest neighbor list.
+ */
+ snew(nnb, n1);
+ snew(row, n1);
+ for (i = 0; (i < n1); i++)
+ {
+ for (j = 0; (j < n1); j++)
+ {
+ row[j].j = j;
+ row[j].dist = mat[i][j];
+ }
+ std::sort(row, row + n1, rms_dist_comp);
+ if (M > 0)
+ {
+ /* Put the M nearest neighbors in the list */
+ snew(nnb[i], M + 1);
+ for (j = k = 0; (k < M) && (j < n1) && (mat[i][row[j].j] < rmsdcut); j++)
+ {
+ if (row[j].j != i)
+ {
+ nnb[i][k] = row[j].j;
+ k++;
+ }
+ }
+ nnb[i][k] = -1;
+ }
+ else
+ {
+ /* Put all neighbors nearer than rmsdcut in the list */
+ maxval = 0;
+ k = 0;
+ for (j = 0; (j < n1) && (mat[i][row[j].j] < rmsdcut); j++)
+ {
+ if (row[j].j != i)
+ {
+ if (k >= maxval)
+ {
+ maxval += 10;
+ srenew(nnb[i], maxval);
+ }
+ nnb[i][k] = row[j].j;
+ k++;
+ }
+ }
+ if (k == maxval)
+ {
+ srenew(nnb[i], maxval + 1);
+ }
+ nnb[i][k] = -1;
+ }
+ }
+ sfree(row);
+ if (debug)
+ {
+ fprintf(debug, "Nearest neighborlist. M = %d, P = %d\n", M, P);
+ for (i = 0; (i < n1); i++)
+ {
+ fprintf(debug, "i:%5d nbs:", i);
+ for (j = 0; nnb[i][j] >= 0; j++)
+ {
+ fprintf(debug, "%5d[%5.3f]", nnb[i][j], mat[i][nnb[i][j]]);
+ }
+ fprintf(debug, "\n");
+ }
+ }
+
+ c = new_clustid(n1);
+ fprintf(stderr, "Linking structures ");
+ /* Use mcpy for temporary storage of booleans */
+ mcpy = mk_matrix(n1, n1, FALSE);
+ for (i = 0; i < n1; i++)
+ {
+ for (j = i + 1; j < n1; j++)
+ {
+ mcpy[i][j] = static_cast<real>(jp_same(nnb, i, j, P));
+ }
+ }
+ do
+ {
+ fprintf(stderr, "*");
+ bChange = FALSE;
+ for (i = 0; i < n1; i++)
+ {
+ for (j = i + 1; j < n1; j++)
+ {
+ if (mcpy[i][j] != 0.0F)
+ {
+ diff = c[j].clust - c[i].clust;
+ if (diff)
+ {
+ bChange = TRUE;
+ if (diff > 0)
+ {
+ c[j].clust = c[i].clust;
+ }
+ else
+ {
+ c[i].clust = c[j].clust;
+ }
+ }
+ }
+ }
+ }
+ } while (bChange);
+
+ fprintf(stderr, "\nSorting and renumbering clusters\n");
+ /* Sort on cluster number */
+ std::sort(c, c + n1, clust_id_comp);
+
+ /* Renumber clusters */
+ cid = 1;
+ for (k = 1; k < n1; k++)
+ {
+ if (c[k].clust != c[k - 1].clust)
+ {
+ c[k - 1].clust = cid;
+ cid++;
+ }
+ else
+ {
+ c[k - 1].clust = cid;
+ }
+ }
+ c[k - 1].clust = cid;
+ clust->ncl = cid;
+ for (k = 0; k < n1; k++)
+ {
+ clust->cl[c[k].conf] = c[k].clust;
+ }
+ if (debug)
+ {
+ for (k = 0; (k < n1); k++)
+ {
+ fprintf(debug, "Cluster index for conformation %d: %d\n", c[k].conf, c[k].clust);
+ }
+ }
+
+ done_matrix(n1, &mcpy);
+
+ sfree(c);
+ for (i = 0; (i < n1); i++)
+ {
+ sfree(nnb[i]);
+ }
+ sfree(nnb);
+}
+
+static void dump_nnb(FILE* fp, const char* title, int n1, t_nnb* nnb)
+{
+ int i, j;
+
+ /* dump neighbor list */
+ fprintf(fp, "%s", title);
+ for (i = 0; (i < n1); i++)
+ {
+ fprintf(fp, "i:%5d #:%5d nbs:", i, nnb[i].nr);
+ for (j = 0; j < nnb[i].nr; j++)
+ {
+ fprintf(fp, "%5d", nnb[i].nb[j]);
+ }
+ fprintf(fp, "\n");
+ }
+}
+
+void gromos(int n1, real** mat, real rmsdcut, t_clusters* clust)
+{
+ t_nnb* nnb;
+ int i, j, k, j1, maxval;
+
+ /* Put all neighbors nearer than rmsdcut in the list */
+ fprintf(stderr, "Making list of neighbors within cutoff ");
+ snew(nnb, n1);
+ for (i = 0; (i < n1); i++)
+ {
+ maxval = 0;
+ k = 0;
+ /* put all neighbors within cut-off in list */
+ for (j = 0; j < n1; j++)
+ {
+ if (mat[i][j] < rmsdcut)
+ {
+ if (k >= maxval)
+ {
+ maxval += 10;
+ srenew(nnb[i].nb, maxval);
+ }
+ nnb[i].nb[k] = j;
+ k++;
+ }
+ }
+ /* store nr of neighbors, we'll need that */
+ nnb[i].nr = k;
+ if (i % (1 + n1 / 100) == 0)
+ {
+ fprintf(stderr, "%3d%%\b\b\b\b", (i * 100 + 1) / n1);
+ }
+ }
+ fprintf(stderr, "%3d%%\n", 100);
+
+ /* sort neighbor list on number of neighbors, largest first */
+ std::sort(nnb, nnb + n1, nrnb_comp);
+
+ if (debug)
+ {
+ dump_nnb(debug, "Nearest neighborlist after sort.\n", n1, nnb);
+ }
+
+ /* turn first structure with all its neighbors (largest) into cluster
+ remove them from pool of structures and repeat for all remaining */
+ fprintf(stderr, "Finding clusters %4d", 0);
+ /* cluster id's start at 1: */
+ k = 1;
+ while (nnb[0].nr)
+ {
+ /* set cluster id (k) for first item in neighborlist */
+ for (j = 0; j < nnb[0].nr; j++)
+ {
+ clust->cl[nnb[0].nb[j]] = k;
+ }
+ /* mark as done */
+ nnb[0].nr = 0;
+ sfree(nnb[0].nb);
+
+ /* adjust number of neighbors for others, taking removals into account: */
+ for (i = 1; i < n1 && nnb[i].nr; i++)
+ {
+ j1 = 0;
+ for (j = 0; j < nnb[i].nr; j++)
+ {
+ /* if this neighbor wasn't removed */
+ if (clust->cl[nnb[i].nb[j]] == 0)
+ {
+ /* shift the rest (j1<=j) */
+ nnb[i].nb[j1] = nnb[i].nb[j];
+ /* next */
+ j1++;
+ }
+ }
+ /* now j1 is the new number of neighbors */
+ nnb[i].nr = j1;
+ }
+ /* sort again on nnb[].nr, because we have new # neighbors: */
+ /* but we only need to sort upto i, i.e. when nnb[].nr>0 */
+ std::sort(nnb, nnb + i, nrnb_comp);
+
+ fprintf(stderr, "\b\b\b\b%4d", k);
+ /* new cluster id */
+ k++;
+ }
+ fprintf(stderr, "\n");
+ sfree(nnb);
+ if (debug)
+ {
+ fprintf(debug, "Clusters (%d):\n", k);
+ for (i = 0; i < n1; i++)
+ {
+ fprintf(debug, " %3d", clust->cl[i]);
+ }
+ fprintf(debug, "\n");
+ }
+
+ clust->ncl = k - 1;
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef GMX_GMXANA_CLUSTER_METHODS_H
+#define GMX_GMXANA_CLUSTER_METHODS_H
+
+#include <stdio.h>
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
+struct gmx_output_env_t;
+struct t_mat;
+
+struct t_clusters
+{
+ int ncl;
+ int* cl;
+};
+
+struct t_nnb
+{
+ int nr;
+ int* nb;
+};
+
+
+void mc_optimize(FILE* log,
+ t_mat* m,
+ real* time,
+ int maxiter,
+ int nrandom,
+ int seed,
+ real kT,
+ const char* conv,
+ gmx_output_env_t* oenv);
+
+void gather(t_mat* m, real cutoff, t_clusters* clust);
+
+void jarvis_patrick(int n1, real** mat, int M, int P, real rmsdcut, t_clusters* clust);
+
+void gromos(int n1, real** mat, real rmsdcut, t_clusters* clust);
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _cmat_h
-#define _cmat_h
+#ifndef GMX_GMXANA_CMAT_H
+#define GMX_GMXANA_CMAT_H
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
int conf, clust;
} t_clustid;
-typedef struct
+struct t_mat
{
int n1, nn;
int* m_ind;
real minrms, maxrms, sumrms;
real* erow;
real** mat;
-} t_mat;
+};
/* The matrix is indexed using the matrix index */
#define EROW(m, i) m->erow[i]
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2013,2014,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2011,2013,2014,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _dens_filter_h
-#define _dens_filter_h
+#ifndef GMX_GMXANA_DENS_FILTER_H
+#define GMX_GMXANA_DENS_FILTER_H
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
fprintf(debug,
"Could not find N atom but could find other atoms"
" in residue %s%d\n",
- thisres, ires + r0);
+ thisres,
+ ires + r0);
}
}
fprintf(stderr, "\n");
}
if (bPhi)
{
- fprintf(fp, " Phi [%5d,%5d,%5d,%5d]",
- (dl[i].atm.H == -1) ? 1 + dl[i].atm.minC : 1 + dl[i].atm.H, 1 + dl[i].atm.N,
- 1 + dl[i].atm.Cn[1], 1 + dl[i].atm.C);
+ fprintf(fp,
+ " Phi [%5d,%5d,%5d,%5d]",
+ (dl[i].atm.H == -1) ? 1 + dl[i].atm.minC : 1 + dl[i].atm.H,
+ 1 + dl[i].atm.N,
+ 1 + dl[i].atm.Cn[1],
+ 1 + dl[i].atm.C);
pr_props(fp, &dl[i], edPhi, dt);
}
if (bPsi)
{
- fprintf(fp, " Psi [%5d,%5d,%5d,%5d]", 1 + dl[i].atm.N, 1 + dl[i].atm.Cn[1],
- 1 + dl[i].atm.C, 1 + dl[i].atm.O);
+ fprintf(fp,
+ " Psi [%5d,%5d,%5d,%5d]",
+ 1 + dl[i].atm.N,
+ 1 + dl[i].atm.Cn[1],
+ 1 + dl[i].atm.C,
+ 1 + dl[i].atm.O);
pr_props(fp, &dl[i], edPsi, dt);
}
if (bOmega && has_dihedral(edOmega, &(dl[i])))
{
- fprintf(fp, " Omega [%5d,%5d,%5d,%5d]", 1 + dl[i].atm.minCalpha, 1 + dl[i].atm.minC,
- 1 + dl[i].atm.N, 1 + dl[i].atm.Cn[1]);
+ fprintf(fp,
+ " Omega [%5d,%5d,%5d,%5d]",
+ 1 + dl[i].atm.minCalpha,
+ 1 + dl[i].atm.minC,
+ 1 + dl[i].atm.N,
+ 1 + dl[i].atm.Cn[1]);
pr_props(fp, &dl[i], edOmega, dt);
}
for (Xi = 0; Xi < MAXCHI; Xi++)
{
if (bChi && (Xi < maxchi) && (dl[i].atm.Cn[Xi + 3] != -1))
{
- fprintf(fp, " Chi%d[%5d,%5d,%5d,%5d]", Xi + 1, 1 + dl[i].atm.Cn[Xi],
- 1 + dl[i].atm.Cn[Xi + 1], 1 + dl[i].atm.Cn[Xi + 2], 1 + dl[i].atm.Cn[Xi + 3]);
+ fprintf(fp,
+ " Chi%d[%5d,%5d,%5d,%5d]",
+ Xi + 1,
+ 1 + dl[i].atm.Cn[Xi],
+ 1 + dl[i].atm.Cn[Xi + 1],
+ 1 + dl[i].atm.Cn[Xi + 2],
+ 1 + dl[i].atm.Cn[Xi + 3]);
pr_props(fp, &dl[i], Xi + edChi1, dt); /* Xi+2 was wrong here */
}
}
*bFit = (head.lambda > -0.5);
if (*bFit)
{
- fprintf(stderr, "Read %smass weighted reference structure with %d atoms from %s\n",
- *bDMR ? "" : "non ", *natoms, file);
+ fprintf(stderr,
+ "Read %smass weighted reference structure with %d atoms from %s\n",
+ *bDMR ? "" : "non ",
+ *natoms,
+ file);
}
else
{
}
else
{
- fprintf(stderr, "Read %smass weighted average/minimum structure with %d atoms from %s\n",
- *bDMA ? "" : "non ", *natoms, file);
+ fprintf(stderr,
+ "Read %smass weighted average/minimum structure with %d atoms from %s\n",
+ *bDMA ? "" : "non ",
+ *natoms,
+ file);
}
snew(x, *natoms);
clear_mat(zerobox);
snew(x, natoms);
- fprintf(stderr, "\nWriting %saverage structure & eigenvectors %d--%d to %s\n",
- (WriteXref == eWXR_YES) ? "reference, " : "", begin, end, trrname);
+ fprintf(stderr,
+ "\nWriting %saverage structure & eigenvectors %d--%d to %s\n",
+ (WriteXref == eWXR_YES) ? "reference, " : "",
+ begin,
+ end,
+ trrname);
trrout = gmx_trr_open(trrname, "w");
if (WriteXref == eWXR_YES)
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _eigio_h
-#define _eigio_h
+#ifndef GMX_GMXANA_EIGIO_H
+#define GMX_GMXANA_EIGIO_H
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.h"
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "fitahx.h"
#include <cmath>
+#include <vector>
#include "gromacs/math/do_fit.h"
#include "gromacs/math/vec.h"
+#include "gromacs/math/vectypes.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
real fit_ahx(int nres, t_bb bb[], int natoms, int nall, int allindex[], rvec x[], int nca, int caindex[], gmx_bool bFit)
{
- static rvec* xref = nullptr;
- static real* mass = nullptr;
- const real d = 0.15; /* Rise per residue (nm) */
- const real tw = 1.745; /* Twist per residue (rad) */
- const real rad = 0.23; /* Radius of the helix (nm) */
- real phi0, trms, rms;
- rvec dx, xcm;
- int ai, i, nmass;
+ static std::vector<gmx::RVec> xref;
+ static std::vector<real> mass;
+ const real d = 0.15; /* Rise per residue (nm) */
+ const real tw = 1.745; /* Twist per residue (rad) */
+ const real rad = 0.23; /* Radius of the helix (nm) */
+ real phi0, trms, rms;
+ rvec dx, xcm;
+ int ai, i, nmass;
if (nca < 3)
{
gmx_fatal(FARGS, "Need at least 3 Calphas to fit to, (now %d)...\n", nca);
}
- if (xref == nullptr)
+ if (xref.empty())
{
- snew(xref, natoms);
- snew(mass, natoms);
+ xref.resize(natoms);
+ mass.resize(natoms);
}
phi0 = 0;
for (i = 0; (i < nca); i++)
mass[ai] = 10.0;
/*#define DEBUG*/
#ifdef DEBUG
- fprintf(stderr, "%5d %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n", ai, x[ai][XX], x[ai][YY],
- x[ai][ZZ], xref[ai][XX], xref[ai][YY], xref[ai][ZZ]);
+ fprintf(stderr,
+ "%5d %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n",
+ ai,
+ x[ai][XX],
+ x[ai][YY],
+ x[ai][ZZ],
+ xref[ai][XX],
+ xref[ai][YY],
+ xref[ai][ZZ]);
#endif
phi0 += tw;
}
/* Center the referece around the origin */
- my_calc_xcm(nca, caindex, xref, xcm);
- my_sub_xcm(nca, caindex, xref, xcm);
+ my_calc_xcm(nca, caindex, as_rvec_array(xref.data()), xcm);
+ my_sub_xcm(nca, caindex, as_rvec_array(xref.data()), xcm);
if (bFit)
{
/* Now call the fitting routine */
if (bFit)
{
- do_fit(natoms, mass, xref, x);
+ do_fit(natoms, mass.data(), as_rvec_array(xref.data()), x);
}
/* Reset masses and calc rms */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _fitahx_h
-#define _fitahx_h
+#ifndef GMX_GMXANA_FITAHX_H
+#define GMX_GMXANA_FITAHX_H
#include "gromacs/gmxana/hxprops.h"
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _gmx_ana_h
-# define _gmx_ana_h
+#ifndef GMX_GMXANA_GMX_ANA_H
+# define GMX_GMXANA_GMX_ANA_H
int gmx_analyze(int argc, char* argv[]);
int gmx_mindist(int argc, char* argv[]);
-int gmx_msd(int argc, char* argv[]);
-
int gmx_nmeig(int argc, char* argv[]);
int gmx_nmens(int argc, char* argv[]);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "thermochemistry.h"
-static const char* proj_unit;
-
static real tick_spacing(real range, int minticks)
{
real sp;
fprintf(stdout, "Trace of the two matrices: %g and %g\n", sum1, sum2);
if (neig1 != n || neig2 != n)
{
- fprintf(stdout, "this is %d%% and %d%% of the total trace\n",
- gmx::roundToInt(100 * sum1 / trace1), gmx::roundToInt(100 * sum2 / trace2));
+ fprintf(stdout,
+ "this is %d%% and %d%% of the total trace\n",
+ gmx::roundToInt(100 * sum1 / trace1),
+ gmx::roundToInt(100 * sum2 / trace2));
}
fprintf(stdout, "Square root of the traces: %g and %g\n", std::sqrt(sum1), std::sqrt(sum2));
rhi.b = 0;
nlevels = 41;
out = gmx_ffopen(matfile, "w");
- write_xpm(out, 0, "Eigenvector inner-products", "in.prod.", "run 1", "run 2", nx, ny, t_x, t_y,
- mat, 0.0, maxval, rlo, rhi, &nlevels);
+ write_xpm(out, 0, "Eigenvector inner-products", "in.prod.", "run 1", "run 2", nx, ny, t_x, t_y, mat, 0.0, maxval, rlo, rhi, &nlevels);
gmx_ffclose(out);
}
const char* twodplotfile,
const char* threedplotfile,
const char* filterfile,
+ const char* projUnit,
int skip,
const char* extremefile,
gmx_bool bExtrAll,
gmx_fatal(FARGS,
"the number of atoms in your trajectory (%d) is larger than the number of "
"atoms in your structure file (%d)",
- nat, atoms->nr);
+ nat,
+ atoms->nr);
}
snew(all_at, nat);
sprintf(str, "vec %d", eignr[outvec[v]] + 1);
ylabel[v] = gmx_strdup(str);
}
- sprintf(str, "projection on eigenvectors (%s)", proj_unit);
- write_xvgr_graphs(projfile, noutvec, 1, str, nullptr, output_env_get_xvgr_tlabel(oenv),
- ylabel, nframes, inprod[noutvec], inprod, nullptr,
- output_env_get_time_factor(oenv), FALSE, bSplit, oenv);
+ sprintf(str, "projection on eigenvectors (%s)", projUnit);
+ write_xvgr_graphs(projfile,
+ noutvec,
+ 1,
+ str,
+ nullptr,
+ output_env_get_xvgr_tlabel(oenv),
+ ylabel,
+ nframes,
+ inprod[noutvec],
+ inprod,
+ nullptr,
+ output_env_get_time_factor(oenv),
+ FALSE,
+ bSplit,
+ oenv);
}
if (twodplotfile)
{
- sprintf(str, "projection on eigenvector %d (%s)", eignr[outvec[0]] + 1, proj_unit);
- sprintf(str2, "projection on eigenvector %d (%s)", eignr[outvec[noutvec - 1]] + 1, proj_unit);
+ sprintf(str, "projection on eigenvector %d (%s)", eignr[outvec[0]] + 1, projUnit);
+ sprintf(str2, "projection on eigenvector %d (%s)", eignr[outvec[noutvec - 1]] + 1, projUnit);
xvgrout = xvgropen(twodplotfile, "2D projection of trajectory", str, str2, oenv);
for (i = 0; i < nframes; i++)
{
"You have selected four or more eigenvectors:\n"
"fourth eigenvector will be plotted "
"in bfactor field of pdb file\n");
- sprintf(str, "4D proj. of traj. on eigenv. %d, %d, %d and %d", eignr[outvec[0]] + 1,
- eignr[outvec[1]] + 1, eignr[outvec[2]] + 1, eignr[outvec[3]] + 1);
+ sprintf(str,
+ "4D proj. of traj. on eigenv. %d, %d, %d and %d",
+ eignr[outvec[0]] + 1,
+ eignr[outvec[1]] + 1,
+ eignr[outvec[2]] + 1,
+ eignr[outvec[3]] + 1);
}
else
{
- sprintf(str, "3D proj. of traj. on eigenv. %d, %d and %d", eignr[outvec[0]] + 1,
- eignr[outvec[1]] + 1, eignr[outvec[2]] + 1);
+ sprintf(str,
+ "3D proj. of traj. on eigenv. %d, %d and %d",
+ eignr[outvec[0]] + 1,
+ eignr[outvec[1]] + 1,
+ eignr[outvec[2]] + 1);
}
init_t_atoms(&atoms, nframes, FALSE);
snew(x, nframes);
fprintf(out, "TER\n");
j = 0;
}
- gmx_fprintf_pdb_atomline(out, epdbATOM, i + 1, "C", ' ', "PRJ", ' ', j + 1, ' ',
- 10 * x[i][XX], 10 * x[i][YY], 10 * x[i][ZZ], 1.0,
- 10 * b[i], "");
+ gmx_fprintf_pdb_atomline(out,
+ PdbRecordType::Atom,
+ i + 1,
+ "C",
+ ' ',
+ "PRJ",
+ ' ',
+ j + 1,
+ ' ',
+ 10 * x[i][XX],
+ 10 * x[i][YY],
+ 10 * x[i][ZZ],
+ 1.0,
+ 10 * b[i],
+ "");
if (j > 0)
{
fprintf(out, "CONECT%5d%5d\n", i, i + 1);
}
pmin[v] = inprod[v][imin];
pmax[v] = inprod[v][imax];
- fprintf(stderr, "%7d %10.6f %10d %10.6f %10d\n", eignr[outvec[v]] + 1, pmin[v],
- imin, pmax[v], imax);
+ fprintf(stderr, "%7d %10.6f %10d %10.6f %10d\n", eignr[outvec[v]] + 1, pmin[v], imin, pmax[v], imax);
}
}
else
}
}
}
- write_xvgr_graphs(outfile, noutvec, 4, "Eigenvector components",
- "black: total, red: x, green: y, blue: z", "Atom number", ylabel, natoms, x,
- nullptr, y, 1, FALSE, FALSE, oenv);
+ write_xvgr_graphs(outfile,
+ noutvec,
+ 4,
+ "Eigenvector components",
+ "black: total, red: x, green: y, blue: z",
+ "Atom number",
+ ylabel,
+ natoms,
+ x,
+ nullptr,
+ y,
+ 1,
+ FALSE,
+ FALSE,
+ oenv);
fprintf(stderr, "\n");
}
v = outvec[g];
if (eignr[v] >= neig)
{
- gmx_fatal(FARGS, "Selected vector %d is larger than the number of eigenvalues (%d)",
- eignr[v] + 1, neig);
+ gmx_fatal(FARGS,
+ "Selected vector %d is larger than the number of eigenvalues (%d)",
+ eignr[v] + 1,
+ neig);
}
sprintf(str, "vec %d", eignr[v] + 1);
ylabel[g] = gmx_strdup(str);
y[g][i] = std::sqrt(eigval[eignr[v]] * norm2(eigvec[v][i])) / sqrtm[i];
}
}
- write_xvgr_graphs(outfile, noutvec, 1, "RMS fluctuation (nm) ", nullptr, "Atom number", ylabel,
- natoms, x, y, nullptr, 1, TRUE, FALSE, oenv);
+ write_xvgr_graphs(
+ outfile, noutvec, 1, "RMS fluctuation (nm) ", nullptr, "Atom number", ylabel, natoms, x, y, nullptr, 1, TRUE, FALSE, oenv);
fprintf(stderr, "\n");
}
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW, NFILE, fnm,
- NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW, NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
bCompare = (Vec2File != nullptr) || (Eig2File != nullptr);
bPDB3D = fn2ftp(ThreeDPlotFile) == efPDB;
- read_eigenvectors(VecFile, &natoms, &bFit1, &xref1, &bDMR1, &xav1, &bDMA1, &nvec1, &eignr1,
- &eigvec1, &eigval1);
+ read_eigenvectors(
+ VecFile, &natoms, &bFit1, &xref1, &bDMR1, &xav1, &bDMA1, &nvec1, &eignr1, &eigvec1, &eigval1);
neig1 = std::min(nvec1, DIM * natoms);
if (nvec1 != DIM * natoms)
{
fprintf(stderr,
"Warning: number of eigenvectors %d does not match three times\n"
"the number of atoms %d in %s. Using %d eigenvectors.\n\n",
- nvec1, natoms, VecFile, neig1);
+ nvec1,
+ natoms,
+ VecFile,
+ neig1);
}
/* Overwrite eigenvalues from separate files if the user provides them */
{
fprintf(stderr,
"Warning: number of eigenvalues in xvg file (%d) does not mtch trr file (%d)\n",
- neig1, natoms);
+ neig1,
+ natoms);
}
neig1 = neig_tmp;
srenew(eigval1, neig1);
eigval1[j] = xvgdata[1][j];
if (debug && (eigval1[j] != tmp))
{
- fprintf(debug, "Replacing eigenvalue %d. From trr: %10g, from xvg: %10g\n", j, tmp,
- eigval1[j]);
+ fprintf(debug, "Replacing eigenvalue %d. From trr: %10g, from xvg: %10g\n", j, tmp, eigval1[j]);
}
}
for (j = 0; j < i; j++)
gmx_fatal(FARGS, "Need a second eigenvector file to do this analysis.");
}
int natoms2;
- read_eigenvectors(Vec2File, &natoms2, &bFit2, &xref2, &bDMR2, &xav2, &bDMA2, &nvec2,
- &eignr2, &eigvec2, &eigval2);
+ read_eigenvectors(
+ Vec2File, &natoms2, &bFit2, &xref2, &bDMR2, &xav2, &bDMA2, &nvec2, &eignr2, &eigvec2, &eigval2);
neig2 = std::min(nvec2, DIM * natoms2);
if (neig2 != neig1)
gmx_fatal(FARGS,
"you selected a group with %d elements instead of %d, your selection "
"does not fit the reference structure in the eigenvector file.",
- nfit, natoms);
+ nfit,
+ natoms);
}
for (i = 0; (i < nfit); i++)
{
}
snew(sqrtm, natoms);
+ std::string projUnit;
if (bM && bDMA1)
{
- proj_unit = "u\\S1/2\\Nnm";
+ projUnit = "u\\S1/2\\Nnm";
for (i = 0; (i < natoms); i++)
{
sqrtm[i] = std::sqrt(atoms->atom[index[i]].m);
}
else
{
- proj_unit = "nm";
+ projUnit = "nm";
for (i = 0; (i < natoms); i++)
{
sqrtm[i] = 1.0;
if (bProj)
{
- project(bTraj ? opt2fn("-f", NFILE, fnm) : nullptr, bTop ? &top : nullptr, pbcType, topbox,
- ProjOnVecFile, TwoDPlotFile, ThreeDPlotFile, FilterFile, skip, ExtremeFile,
- bFirstLastSet, max, nextr, atoms, natoms, index, bFit1, xrefp, nfit, ifit, w_rls,
- sqrtm, xav1, eignr1, eigvec1, noutvec, outvec, bSplit, oenv);
+ project(bTraj ? opt2fn("-f", NFILE, fnm) : nullptr,
+ bTop ? &top : nullptr,
+ pbcType,
+ topbox,
+ ProjOnVecFile,
+ TwoDPlotFile,
+ ThreeDPlotFile,
+ FilterFile,
+ projUnit.c_str(),
+ skip,
+ ExtremeFile,
+ bFirstLastSet,
+ max,
+ nextr,
+ atoms,
+ natoms,
+ index,
+ bFit1,
+ xrefp,
+ nfit,
+ ifit,
+ w_rls,
+ sqrtm,
+ xav1,
+ eignr1,
+ eigvec1,
+ noutvec,
+ outvec,
+ bSplit,
+ oenv);
}
if (OverlapFile)
if (InpMatFile)
{
- inprod_matrix(InpMatFile, natoms, nvec1, eignr1, eigvec1, nvec2, eignr2, eigvec2,
- bFirstLastSet, noutvec, outvec);
+ inprod_matrix(
+ InpMatFile, natoms, nvec1, eignr1, eigvec1, nvec2, eignr2, eigvec2, bFirstLastSet, noutvec, outvec);
}
if (bCompare)
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxana/gstat.h"
#include "gromacs/linearalgebra/matrix.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/statistics/statistics.h"
static void regression_analysis(int n, gmx_bool bXYdy, real* x, int nset, real** val)
{
- real S, chi2, a, b, da, db, r = 0;
- int ok;
+ real S, chi2, a, b, da, db, r = 0;
+ StatisticsStatus ok;
if (bXYdy || (nset == 1))
{
printf("(use option -xydy).\n\n");
if (bXYdy)
{
- if ((ok = lsq_y_ax_b_error(n, x, val[0], val[1], &a, &b, &da, &db, &r, &S)) != estatsOK)
+ if ((ok = lsq_y_ax_b_error(n, x, val[0], val[1], &a, &b, &da, &db, &r, &S))
+ != StatisticsStatus::Ok)
{
- gmx_fatal(FARGS, "Error fitting the data: %s", gmx_stats_message(ok));
+ gmx_stats_message(ok);
}
}
else
{
- if ((ok = lsq_y_ax_b(n, x, val[0], &a, &b, &r, &S)) != estatsOK)
+ if ((ok = lsq_y_ax_b(n, x, val[0], &a, &b, &r, &S)) != StatisticsStatus::Ok)
{
- gmx_fatal(FARGS, "Error fitting the data: %s", gmx_stats_message(ok));
+ gmx_stats_message(ok);
}
}
chi2 = gmx::square((n - 2) * S);
fprintf(stdout,
"Errorbars: discarding %d points on both sides: %d%%"
" interval\n",
- edge, gmx::roundToInt(100. * (nset - 2 * edge) / nset));
+ edge,
+ gmx::roundToInt(100. * (nset - 2 * edge) / nset));
}
else
{
* to halfway between tau1_est and the total time (on log scale).
*/
fitparm[2] = std::sqrt(tau1_est * (n - 1) * dt);
- do_lmfit(nbs, ybs, fitsig, 0, tbs, 0, dt * n, oenv, bDebugMode(), effnERREST,
- fitparm, 0, nullptr);
+ do_lmfit(nbs, ybs, fitsig, 0, tbs, 0, dt * n, oenv, bDebugMode(), effnERREST, fitparm, 0, nullptr);
}
if (bSingleExpFit || fitparm[0] < 0 || fitparm[2] < 0 || fitparm[1] < 0
|| (fitparm[1] > 1 && !bAllowNegLTCorr) || fitparm[2] > (n - 1) * dt)
{
fprintf(stdout, "a fitted parameter is negative\n");
}
- fprintf(stdout, "invalid fit: e.e. %g a %g tau1 %g tau2 %g\n",
- optimal_error_estimate(sig[s], fitparm, n * dt), fitparm[1], fitparm[0],
+ fprintf(stdout,
+ "invalid fit: e.e. %g a %g tau1 %g tau2 %g\n",
+ optimal_error_estimate(sig[s], fitparm, n * dt),
+ fitparm[1],
+ fitparm[0],
fitparm[2]);
/* Do a fit with tau2 fixed at the total time.
* One could also choose any other large value for tau2.
fitparm[1] = 0.95;
fitparm[2] = (n - 1) * dt;
fprintf(stdout, "Will fix tau2 at the total time: %g\n", fitparm[2]);
- do_lmfit(nbs, ybs, fitsig, 0, tbs, 0, dt * n, oenv, bDebugMode(), effnERREST,
- fitparm, 4, nullptr);
+ do_lmfit(nbs, ybs, fitsig, 0, tbs, 0, dt * n, oenv, bDebugMode(), effnERREST, fitparm, 4, nullptr);
}
if (bSingleExpFit || fitparm[0] < 0 || fitparm[1] < 0 || (fitparm[1] > 1 && !bAllowNegLTCorr))
{
if (!bSingleExpFit)
{
fprintf(stdout, "a fitted parameter is negative\n");
- fprintf(stdout, "invalid fit: e.e. %g a %g tau1 %g tau2 %g\n",
- optimal_error_estimate(sig[s], fitparm, n * dt), fitparm[1],
- fitparm[0], fitparm[2]);
+ fprintf(stdout,
+ "invalid fit: e.e. %g a %g tau1 %g tau2 %g\n",
+ optimal_error_estimate(sig[s], fitparm, n * dt),
+ fitparm[1],
+ fitparm[0],
+ fitparm[2]);
}
/* Do a single exponential fit */
fprintf(stderr, "Will use a single exponential fit for set %d\n", s + 1);
fitparm[0] = tau1_est;
fitparm[1] = 1.0;
fitparm[2] = 0.0;
- do_lmfit(nbs, ybs, fitsig, 0, tbs, 0, dt * n, oenv, bDebugMode(), effnERREST,
- fitparm, 6, nullptr);
+ do_lmfit(nbs, ybs, fitsig, 0, tbs, 0, dt * n, oenv, bDebugMode(), effnERREST, fitparm, 6, nullptr);
}
}
ee = optimal_error_estimate(sig[s], fitparm, n * dt);
if (output_env_get_xvg_format(oenv) == XvgFormat::Xmgr)
{
fprintf(fp, "@ legend string %d \"av %f\"\n", 2 * s, av[s]);
- fprintf(fp, "@ legend string %d \"ee %6g\"\n", 2 * s + 1,
+ fprintf(fp,
+ "@ legend string %d \"ee %6g\"\n",
+ 2 * s + 1,
optimal_error_estimate(sig[s], fitparm, n * dt));
}
else if (output_env_get_xvg_format(oenv) == XvgFormat::Xmgrace)
{
fprintf(fp, "@ s%d legend \"av %f\"\n", 2 * s, av[s]);
- fprintf(fp, "@ s%d legend \"ee %6g\"\n", 2 * s + 1,
- optimal_error_estimate(sig[s], fitparm, n * dt));
+ fprintf(fp, "@ s%d legend \"ee %6g\"\n", 2 * s + 1, optimal_error_estimate(sig[s], fitparm, n * dt));
}
for (i = 0; i < nbs; i++)
{
- fprintf(fp, "%g %g %g\n", tbs[i], sig[s] * std::sqrt(ybs[i] / (n * dt)),
+ fprintf(fp,
+ "%g %g %g\n",
+ tbs[i],
+ sig[s] * std::sqrt(ybs[i] / (n * dt)),
sig[s] * std::sqrt(fit_function(effnERREST, fitparm, tbs[i]) / (n * dt)));
}
fitsig[i] = 1;
}
}
- low_do_autocorr(nullptr, oenv, nullptr, n, 1, -1, &ac, dt, eacNormal, 1, FALSE, TRUE,
- FALSE, 0, 0, effnNONE);
+ low_do_autocorr(
+ nullptr, oenv, nullptr, n, 1, -1, &ac, dt, eacNormal, 1, FALSE, TRUE, FALSE, 0, 0, effnNONE);
fitlen = n / nb_min;
ac_fit[0] = 0.5 * acint;
ac_fit[1] = 0.95;
ac_fit[2] = 10 * acint;
- do_lmfit(n / nb_min, ac, fitsig, dt, nullptr, 0, fitlen * dt, oenv, bDebugMode(),
- effnEXPEXP, ac_fit, 0, nullptr);
+ do_lmfit(n / nb_min, ac, fitsig, dt, nullptr, 0, fitlen * dt, oenv, bDebugMode(), effnEXPEXP, ac_fit, 0, nullptr);
ac_fit[3] = 1 - ac_fit[1];
- fprintf(stdout, "Set %3d: ac erest %g a %g tau1 %g tau2 %g\n", s + 1,
- optimal_error_estimate(sig[s], ac_fit, n * dt), ac_fit[1], ac_fit[0], ac_fit[2]);
+ fprintf(stdout,
+ "Set %3d: ac erest %g a %g tau1 %g tau2 %g\n",
+ s + 1,
+ optimal_error_estimate(sig[s], ac_fit, n * dt),
+ ac_fit[1],
+ ac_fit[0],
+ ac_fit[2]);
fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
for (i = 0; i < nbs; i++)
{
- fprintf(fp, "%g %g\n", tbs[i],
+ fprintf(fp,
+ "%g %g\n",
+ tbs[i],
sig[s] * std::sqrt(fit_function(effnERREST, ac_fit, tbs[i])) / (n * dt));
}
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, npargs, ppa, asize(desc), desc, 0,
- nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW, NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
{
sfree(ppa);
return 0;
fitfile = opt2fn_null("-g", NFILE, fnm);
}
- val = read_xvg_time(opt2fn("-f", NFILE, fnm), bHaveT, opt2parg_bSet("-b", npargs, ppa), tb,
- opt2parg_bSet("-e", npargs, ppa), te, nsets_in, &nset, &n, &dt, &t);
+ val = read_xvg_time(opt2fn("-f", NFILE, fnm),
+ bHaveT,
+ opt2parg_bSet("-b", npargs, ppa),
+ tb,
+ opt2parg_bSet("-e", npargs, ppa),
+ te,
+ nsets_in,
+ &nset,
+ &n,
+ &dt,
+ &t);
printf("Read %d sets of %d points, dt = %g\n\n", nset, n, dt);
if (bDer)
if (fitfile != nullptr)
{
- print_fitted_function(fitfile, opt2fn_null("-fitted", NFILE, fnm), bXYdy, nset, n, t, val,
- npargs, ppa, oenv);
+ print_fitted_function(
+ fitfile, opt2fn_null("-fitted", NFILE, fnm), bXYdy, nset, n, t, val, npargs, ppa, oenv);
}
printf(" std. dev. relative deviation of\n");
{
error = 0;
}
- printf("SS%d %13.6e %12.6e %12.6e %6.3f %6.3f\n", s + 1, av[s], sig[s], error,
+ printf("SS%d %13.6e %12.6e %12.6e %6.3f %6.3f\n",
+ s + 1,
+ av[s],
+ sig[s],
+ error,
sig[s] != 0.0 ? cum3 / (sig[s] * sig[s] * sig[s] * std::sqrt(8 / M_PI)) : 0,
sig[s] != 0.0 ? cum4 / (sig[s] * sig[s] * sig[s] * sig[s] * 3) - 1 : 0);
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxana/gstat.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/topology/index.h"
#include "gromacs/utility/arraysize.h"
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, npargs, ppa,
- asize(desc), desc, asize(bugs), bugs, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
sfree(ppa);
return 0;
gmx_fatal(FARGS,
"number of index elements not multiple of %d, "
"these can not be %s\n",
- mult, (mult == 3) ? "angle triplets" : "dihedral quadruplets");
+ mult,
+ (mult == 3) ? "angle triplets" : "dihedral quadruplets");
}
snew(angstat, maxangstat);
- read_ang_dih(ftp2fn(efTRX, NFILE, fnm), (mult == 3),
- bALL || bCorr || bTrans || opt2bSet("-or", NFILE, fnm), bRb, bPBC, maxangstat,
- angstat, &nframes, &time, isize, index, &trans_frac, &aver_angle, dih, oenv);
+ read_ang_dih(ftp2fn(efTRX, NFILE, fnm),
+ (mult == 3),
+ bALL || bCorr || bTrans || opt2bSet("-or", NFILE, fnm),
+ bRb,
+ bPBC,
+ maxangstat,
+ angstat,
+ &nframes,
+ &time,
+ isize,
+ index,
+ &trans_frac,
+ &aver_angle,
+ dih,
+ oenv);
dt = (time[nframes - 1] - time[0]) / (nframes - 1);
out = xvgropen(opt2fn("-ov", NFILE, fnm), title, "Time (ps)", "Angle (degrees)", oenv);
for (i = 0; (i < nframes); i++)
{
- fprintf(out, "%10.5f %8.3f", time[i], aver_angle[i] * RAD2DEG);
+ fprintf(out, "%10.5f %8.3f", time[i], aver_angle[i] * gmx::c_rad2Deg);
if (bALL)
{
for (j = 0; (j < nangles); j++)
if (bPBC)
{
real dd = dih[j][i];
- fprintf(out, " %8.3f", std::atan2(std::sin(dd), std::cos(dd)) * RAD2DEG);
+ fprintf(out, " %8.3f", std::atan2(std::sin(dd), std::cos(dd)) * gmx::c_rad2Deg);
}
else
{
- fprintf(out, " %8.3f", dih[j][i] * RAD2DEG);
+ fprintf(out, " %8.3f", dih[j][i] * gmx::c_rad2Deg);
}
}
}
if (bTrans)
{
- ana_dih_trans(opt2fn("-ot", NFILE, fnm), opt2fn("-oh", NFILE, fnm), dih, nframes, nangles,
- grpname, time, bRb, oenv);
+ ana_dih_trans(
+ opt2fn("-ot", NFILE, fnm), opt2fn("-oh", NFILE, fnm), dih, nframes, nangles, grpname, time, bRb, oenv);
}
if (bCorr)
if (bChandler)
{
- real dval, sixty = DEG2RAD * 60;
+ real dval, sixty = gmx::c_deg2Rad * 60;
gmx_bool bTest;
for (i = 0; (i < nangles); i++)
{
mode = eacCos;
}
- do_autocorr(opt2fn("-oc", NFILE, fnm), oenv, "Dihedral Autocorrelation Function",
- nframes, nangles, dih, dt, mode, bAverCorr);
+ do_autocorr(opt2fn("-oc", NFILE, fnm),
+ oenv,
+ "Dihedral Autocorrelation Function",
+ nframes,
+ nangles,
+ dih,
+ dt,
+ mode,
+ bAverCorr);
}
}
}
aver /= nframes;
double aversig = correctRadianAngleRange(aver);
- aversig *= RAD2DEG;
- aver *= RAD2DEG;
+ aversig *= gmx::c_rad2Deg;
+ aver *= gmx::c_rad2Deg;
printf(" < angle > = %g\n", aversig);
if (mult == 3)
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <memory>
#include <string>
+#include "gromacs/applied_forces/awh/read_params.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/gmxfio.h"
*/
void initializeAwhOutputFile(int subBlockStart,
int numSubBlocks,
- const AwhBiasParams* awhBiasParams,
+ const AwhBiasParams& awhBiasParams,
AwhGraphSelection graphSelection,
EnergyUnit energyUnit,
real kTValue);
*/
void initializeFrictionOutputFile(int subBlockStart,
int numSubBlocks,
- const AwhBiasParams* awhBiasParams,
+ const AwhBiasParams& awhBiasParams,
EnergyUnit energyUnit,
real kTValue);
{
public:
//! Constructor
- AwhReader(const AwhParams* awhParams,
+ AwhReader(const AwhParams& awhParams,
int numFileOptions,
const t_filenm* filenames,
AwhGraphSelection awhGraphSelection,
constexpr int maxAwhGraphs = 6;
/*! \brief Constructs a legend for a standard awh output file */
-std::vector<std::string> makeLegend(const AwhBiasParams* awhBiasParams,
+std::vector<std::string> makeLegend(const AwhBiasParams& awhBiasParams,
OutputFileType outputFileType,
size_t numLegend)
{
- const std::array<std::string, maxAwhGraphs> legendBase = {
- { "PMF", "Coord bias", "Coord distr", "Ref value distr", "Target ref value distr",
- "Friction metric" }
- };
+ const std::array<std::string, maxAwhGraphs> legendBase = { { "PMF",
+ "Coord bias",
+ "Coord distr",
+ "Ref value distr",
+ "Target ref value distr",
+ "Friction metric" } };
std::vector<std::string> legend;
/* Give legends to dimensions higher than the first */
- for (int d = 1; d < awhBiasParams->ndim; d++)
+ for (int d = 1; d < awhBiasParams.ndim(); d++)
{
legend.push_back(gmx::formatString("dim%d", d));
}
}
break;
case OutputFileType::Friction:
- for (int i0 = 0; i0 < awhBiasParams->ndim; i0++)
+ for (int i0 = 0; i0 < awhBiasParams.ndim(); i0++)
{
for (int i1 = 0; i1 <= i0; i1++)
{
void OutputFile::initializeAwhOutputFile(int subblockStart,
int numSubBlocks,
- const AwhBiasParams* awhBiasParams,
+ const AwhBiasParams& awhBiasParams,
AwhGraphSelection graphSelection,
EnergyUnit energyUnit,
real kTValue)
{
/* The first subblock with actual graph y-values is index 1 + ndim */
- numDim_ = awhBiasParams->ndim;
+ numDim_ = awhBiasParams.ndim();
firstGraphSubBlock_ = subblockStart + 1 + numDim_;
if (graphSelection == AwhGraphSelection::All)
{
yLabel_ = useKTForEnergy_ ? "(k\\sB\\NT)" : "(kJ/mol)";
if (graphSelection == AwhGraphSelection::All)
{
- yLabel_ += gmx::formatString(", (nm\\S-%d\\N or rad\\S-%d\\N), (-)", awhBiasParams->ndim,
- awhBiasParams->ndim);
+ yLabel_ += gmx::formatString(
+ ", (nm\\S-%d\\N or rad\\S-%d\\N), (-)", awhBiasParams.ndim(), awhBiasParams.ndim());
}
}
/*! \brief Initializes the output file setup for the fricion output (note that the filename is not set here). */
void OutputFile::initializeFrictionOutputFile(int subBlockStart,
int numSubBlocks,
- const AwhBiasParams* awhBiasParams,
+ const AwhBiasParams& awhBiasParams,
EnergyUnit energyUnit,
real kTValue)
{
/* The first subblock with actual graph y-values is index 1 + ndim */
- numDim_ = awhBiasParams->ndim;
+ numDim_ = awhBiasParams.ndim();
int numTensorElements = (numDim_ * (numDim_ + 1)) / 2;
/* The friction tensor elements are always the last subblocks */
}
}
-AwhReader::AwhReader(const AwhParams* awhParams,
+AwhReader::AwhReader(const AwhParams& awhParams,
int numFileOptions,
const t_filenm* filenames,
AwhGraphSelection awhGraphSelection,
/* Keep track of the first subblock of this AWH */
int subblockStart = 0;
- for (int k = 0; k < awhParams->numBias; k++)
+ for (int k = 0; k < awhParams.numBias(); k++)
{
- AwhBiasParams* awhBiasParams = &awhParams->awhBiasParams[k];
+ const AwhBiasParams& awhBiasParams = awhParams.awhBiasParams()[k];
int numSubBlocks = static_cast<int>(block->sub[subblockStart].fval[0]);
std::unique_ptr<OutputFile> awhOutputFile(new OutputFile(
- opt2fn("-o", numFileOptions, filenames), "AWH", awhParams->numBias, k));
+ opt2fn("-o", numFileOptions, filenames), "AWH", awhParams.numBias(), k));
- awhOutputFile->initializeAwhOutputFile(subblockStart, numSubBlocks, awhBiasParams,
- awhGraphSelection, energyUnit, kT);
+ awhOutputFile->initializeAwhOutputFile(
+ subblockStart, numSubBlocks, awhBiasParams, awhGraphSelection, energyUnit, kT);
std::unique_ptr<OutputFile> frictionOutputFile;
if (outputFriction)
{
frictionOutputFile = std::make_unique<OutputFile>(
- opt2fn("-fric", numFileOptions, filenames), "Friction tensor", awhParams->numBias, k);
+ opt2fn("-fric", numFileOptions, filenames), "Friction tensor", awhParams.numBias(), k);
- frictionOutputFile->initializeFrictionOutputFile(subblockStart, numSubBlocks,
- awhBiasParams, energyUnit, kT);
+ frictionOutputFile->initializeFrictionOutputFile(
+ subblockStart, numSubBlocks, awhBiasParams, energyUnit, kT);
}
- biasOutputSetups_.emplace_back(BiasOutputSetup(subblockStart, std::move(awhOutputFile),
- std::move(frictionOutputFile)));
+ biasOutputSetups_.emplace_back(BiasOutputSetup(
+ subblockStart, std::move(awhOutputFile), std::move(frictionOutputFile)));
subblockStart += numSubBlocks;
}
FILE* fpAwh = awhOutputFile.openBiasOutputFile(time, oenv);
/* Now do the actual printing. Metadata in first subblock is treated separately. */
- fprintf(fpAwh, "# AWH metadata: target error = %.2f kT = %.2f kJ/mol\n",
- block.sub[subStart].fval[1], block.sub[subStart].fval[1] * kT_);
+ fprintf(fpAwh,
+ "# AWH metadata: target error = %.2f kT = %.2f kJ/mol\n",
+ block.sub[subStart].fval[1],
+ block.sub[subStart].fval[1] * kT_);
fprintf(fpAwh, "# AWH metadata: log sample weight = %4.2f\n", block.sub[subStart].fval[2]);
{ efXVG, "-o", "awh", ffWRITE },
{ efXVG, "-fric", "friction", ffOPTWR } };
const int nfile = asize(fnm);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END, nfile, fnm,
- asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc,
+ argv,
+ PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END,
+ nfile,
+ fnm,
+ asize(pa),
+ pa,
+ asize(desc),
+ desc,
+ 0,
+ nullptr,
+ &oenv))
{
return 0;
}
AwhGraphSelection awhGraphSelection =
(moreGraphs ? AwhGraphSelection::All : AwhGraphSelection::Pmf);
EnergyUnit energyUnit = (kTUnit ? EnergyUnit::KT : EnergyUnit::KJPerMol);
- awhReader = std::make_unique<AwhReader>(ir.awhParams, nfile, fnm, awhGraphSelection,
- energyUnit, BOLTZ * ir.opts.ref_t[0], block);
+ awhReader = std::make_unique<AwhReader>(*ir.awhParams,
+ nfile,
+ fnm,
+ awhGraphSelection,
+ energyUnit,
+ gmx::c_boltz * ir.opts.ref_t[0],
+ block);
}
awhReader->processAwhFrame(*block, frame->t, oenv);
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
GMX_ASSERT(sc->next->s, "Next not properly initialized!");
if (sc->temp != s->temp)
{
- gmx_fatal(FARGS, "Temperatures in files %s and %s are not the same!", s->filename,
+ gmx_fatal(FARGS,
+ "Temperatures in files %s and %s are not the same!",
+ s->filename,
sc->next->s[0]->filename);
}
if (!lambda_vec_same(sc->native_lambda, s->native_lambda))
{
- gmx_fatal(FARGS, "Native lambda in files %s and %s are not the same (and they should be)!",
- s->filename, sc->next->s[0]->filename);
+ gmx_fatal(FARGS,
+ "Native lambda in files %s and %s are not the same (and they should be)!",
+ s->filename,
+ sc->next->s[0]->filename);
}
if (!lambda_vec_same(sc->foreign_lambda, s->foreign_lambda))
{
- gmx_fatal(FARGS, "Foreign lambda in files %s and %s are not the same (and they should be)!",
- s->filename, sc->next->s[0]->filename);
+ gmx_fatal(FARGS,
+ "Foreign lambda in files %s and %s are not the same (and they should be)!",
+ s->filename,
+ sc->next->s[0]->filename);
}
/* check if there's room */
"them.\nAlternatively, use the -extp option if (and only if) the "
"Hamiltonian\ndepends linearly on lambda, which is NOT normally the "
"case.\n\n%s\n%s\n",
- descX, descY);
+ descX,
+ descY);
}
/* normal delta H */
gmx_fatal(FARGS,
"Could not find a set for foreign lambda (state X below)\nin the files for "
"main lambda (state Y below)\n\n%s\n%s\n",
- descX, descY);
+ descX,
+ descY);
}
if (!sc)
{
gmx_fatal(FARGS,
"Could not find a set for foreign lambda (state X below)\nin the files for "
"main lambda (state Y below)\n\n%s\n%s\n",
- descX, descY);
+ descX,
+ descY);
}
br->a = scprev;
br->b = sc;
double DG0, DG1, DG2, dDG1;
double n1, n2; /* numbers of samples as doubles */
- kT = BOLTZ * temp;
+ kT = gmx::c_boltz * temp;
beta = 1 / kT;
/* count the numbers of samples */
double Wfac1, Wfac2;
double n1, n2;
- kT = BOLTZ * temp;
+ kT = gmx::c_boltz * temp;
beta = 1 / kT;
/* count the numbers of samples */
double Wfac1, Wfac2;
double n1, n2;
- kT = BOLTZ * temp;
+ kT = gmx::c_boltz * temp;
beta = 1 / kT;
/* count the numbers of samples */
if (!lambda_components_check(lc, 0, "", 0))
{
gmx_fatal(FARGS,
- "lambda vector components in %s don't match those previously read", fn);
+ "lambda vector components in %s don't match those previously read",
+ fn);
}
}
else
snew(s, barsim->nset);
for (i = 0; i < barsim->nset; i++)
{
- samples_init(s + i, &(barsim->native_lambda), &(barsim->lambda[i]), barsim->temp,
- lambda_vec_same(&(barsim->native_lambda), &(barsim->lambda[i])), fn);
+ samples_init(s + i,
+ &(barsim->native_lambda),
+ &(barsim->lambda[i]),
+ barsim->temp,
+ lambda_vec_same(&(barsim->native_lambda), &(barsim->lambda[i])),
+ fn);
s[i].du = barsim->y[i];
s[i].ndu = barsim->np[i];
s[i].t = barsim->t;
char buf[STRLEN];
lambda_vec_print(s[0].native_lambda, buf, FALSE);
- printf("%s: %.1f - %.1f; lambda = %s\n dH/dl & foreign lambdas:\n", fn, s[0].t[0],
- s[0].t[s[0].ndu - 1], buf);
+ printf("%s: %.1f - %.1f; lambda = %s\n dH/dl & foreign lambdas:\n",
+ fn,
+ s[0].t[0],
+ s[0].t[s[0].ndu - 1],
+ buf);
for (i = 0; i < barsim->nset; i++)
{
lambda_vec_print(s[i].foreign_lambda, buf, TRUE);
int startj;
/* check the block types etc. */
- if ((blk->nsub < 3) || (blk->sub[0].type != xdr_datatype_int) || (blk->sub[1].type != xdr_datatype_double)
- || ((blk->sub[2].type != xdr_datatype_float) && (blk->sub[2].type != xdr_datatype_double))
+ if ((blk->nsub < 3) || (blk->sub[0].type != XdrDataType::Int)
+ || (blk->sub[1].type != XdrDataType::Double)
+ || ((blk->sub[2].type != XdrDataType::Float) && (blk->sub[2].type != XdrDataType::Double))
|| (blk->sub[0].nr < 1) || (blk->sub[1].nr < 1))
{
gmx_fatal(FARGS, "Unexpected/corrupted block data in file %s around time %f.", filename, start_time);
/* and copy the data*/
for (j = 0; j < blk->sub[2].nr; j++)
{
- if (blk->sub[2].type == xdr_datatype_float)
+ if (blk->sub[2].type == XdrDataType::Float)
{
s->du[startj + j] = blk->sub[2].fval[j];
}
int nbins[2];
/* check the block types etc. */
- if ((blk->nsub < 2) || (blk->sub[0].type != xdr_datatype_double)
- || (blk->sub[1].type != xdr_datatype_int64) || (blk->sub[0].nr < 2) || (blk->sub[1].nr < 2))
+ if ((blk->nsub < 2) || (blk->sub[0].type != XdrDataType::Double)
+ || (blk->sub[1].type != XdrDataType::Int64) || (blk->sub[0].nr < 2) || (blk->sub[1].nr < 2))
{
gmx_fatal(FARGS, "Unexpected/corrupted block data in file %s around time %f", filename, start_time);
}
if (fr->block[i].id == enxDHCOLL)
{
nlam++;
- if ((fr->block[i].nsub < 1) || (fr->block[i].sub[0].type != xdr_datatype_double)
+ if ((fr->block[i].nsub < 1) || (fr->block[i].sub[0].type != XdrDataType::Double)
|| (fr->block[i].sub[0].nr < 5))
{
gmx_fatal(FARGS, "Unexpected block data in file %s", fn);
if ((*temp != rtemp) && (*temp > 0))
{
gmx_fatal(FARGS,
- "Temperature in file %s different from earlier files or setting\n", fn);
+ "Temperature in file %s different from earlier files or setting\n",
+ fn);
}
*temp = rtemp;
n_lambda_vec = fr->block[i].sub[1].ival[1];
for (j = 0; j < n_lambda_vec; j++)
{
- const char* name = efpt_singular_names[fr->block[i].sub[1].ival[1 + j]];
+ const char* name =
+ enumValueToStringSingular(static_cast<FreeEnergyPerturbationCouplingType>(
+ fr->block[i].sub[1].ival[1 + j]));
if (check)
{
/* check the components */
gmx_fatal(FARGS,
"Native lambda not constant in file %s: started at %f, and becomes %f at "
"time %f",
- fn, native_lambda->val[0], start_lambda.val[0], start_time);
+ fn,
+ native_lambda->val[0],
+ start_lambda.val[0],
+ start_time);
}
/* check the number of samples against the previous number */
if (((nblocks_raw + nblocks_hist) != nsamples) || (nlam != 1))
{
- gmx_fatal(FARGS, "Unexpected block count in %s: was %d, now %d\n", fn, nsamples + 1,
+ gmx_fatal(FARGS,
+ "Unexpected block count in %s: was %d, now %d\n",
+ fn,
+ nsamples + 1,
nblocks_raw + nblocks_hist + nlam);
}
/* check whether last iterations's end time matches with
if (type == dhbtDH || type == dhbtDHDL)
{
int ndu;
- read_edr_rawdh_block(&(samples_rawdh[k]), &ndu, &(fr->block[i]), start_time,
- delta_time, native_lambda, rtemp, &last_t, fn);
+ read_edr_rawdh_block(&(samples_rawdh[k]),
+ &ndu,
+ &(fr->block[i]),
+ start_time,
+ delta_time,
+ native_lambda,
+ rtemp,
+ &last_t,
+ fn);
npts[k] += ndu;
if (samples_rawdh[k])
{
int j;
int nb = 0;
samples_t* s; /* this is where the data will go */
- s = read_edr_hist_block(&nb, &(fr->block[i]), start_time, delta_time,
- native_lambda, rtemp, &last_t, fn);
+ s = read_edr_hist_block(
+ &nb, &(fr->block[i]), start_time, delta_time, native_lambda, rtemp, &last_t, fn);
nhists[k] += nb;
if (nb > 0)
{
double sum_histrange_err = 0.; /* histogram range error */
double stat_err = 0.; /* statistical error */
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa, asize(desc), desc,
- 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
if (opt2bSet("-o", NFILE, fnm))
{
sprintf(buf, "%s (%s)", "\\DeltaG", "kT");
- fpb = xvgropen_type(opt2fn("-o", NFILE, fnm), "Free energy differences", "\\lambda", buf,
- exvggtXYDY, oenv);
+ fpb = xvgropen_type(
+ opt2fn("-o", NFILE, fnm), "Free energy differences", "\\lambda", buf, exvggtXYDY, oenv);
}
fpi = nullptr;
}
/* print results in kT */
- kT = BOLTZ * temp;
+ kT = gmx::c_boltz * temp;
printf("\nTemperature: %g K\n", temp);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cmath>
#include <cstring>
+#include <vector>
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/rmpbc.h"
#include "gromacs/topology/index.h"
static void dump_axes(t_trxstatus* status, t_trxframe* fr, t_atoms* outat, t_bundle* bun)
{
- t_trxframe frout;
- static rvec* xout = nullptr;
- int i;
+ t_trxframe frout;
+ static std::vector<gmx::RVec> xout;
+ int i;
GMX_ASSERT(outat->nr >= bun->n, "");
- if (xout == nullptr)
+ if (xout.empty())
{
- snew(xout, outat->nr);
+ xout.resize(outat->nr);
}
for (i = 0; i < bun->n; i++)
frout.bAtoms = TRUE;
frout.natoms = outat->nr;
frout.atoms = outat;
- frout.x = xout;
+ frout.x = as_rvec_array(xout.data());
write_trxframe(status, &frout, nullptr);
}
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
snew(bun.dir, n);
snew(bun.len, n);
- flen = xvgropen(opt2fn("-ol", NFILE, fnm), "Axis lengths", output_env_get_xvgr_tlabel(oenv),
- "(nm)", oenv);
- fdist = xvgropen(opt2fn("-od", NFILE, fnm), "Distance of axis centers",
- output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
- fz = xvgropen(opt2fn("-oz", NFILE, fnm), "Z-shift of axis centers",
- output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
- ftilt = xvgropen(opt2fn("-ot", NFILE, fnm), "Axis tilts", output_env_get_xvgr_tlabel(oenv),
- "(degrees)", oenv);
- ftiltr = xvgropen(opt2fn("-otr", NFILE, fnm), "Radial axis tilts",
- output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
- ftiltl = xvgropen(opt2fn("-otl", NFILE, fnm), "Lateral axis tilts",
- output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
+ flen = xvgropen(
+ opt2fn("-ol", NFILE, fnm), "Axis lengths", output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
+ fdist = xvgropen(opt2fn("-od", NFILE, fnm),
+ "Distance of axis centers",
+ output_env_get_xvgr_tlabel(oenv),
+ "(nm)",
+ oenv);
+ fz = xvgropen(opt2fn("-oz", NFILE, fnm),
+ "Z-shift of axis centers",
+ output_env_get_xvgr_tlabel(oenv),
+ "(nm)",
+ oenv);
+ ftilt = xvgropen(
+ opt2fn("-ot", NFILE, fnm), "Axis tilts", output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
+ ftiltr = xvgropen(opt2fn("-otr", NFILE, fnm),
+ "Radial axis tilts",
+ output_env_get_xvgr_tlabel(oenv),
+ "(degrees)",
+ oenv);
+ ftiltl = xvgropen(opt2fn("-otl", NFILE, fnm),
+ "Lateral axis tilts",
+ output_env_get_xvgr_tlabel(oenv),
+ "(degrees)",
+ oenv);
if (bKink)
{
- fkink = xvgropen(opt2fn("-ok", NFILE, fnm), "Kink angles", output_env_get_xvgr_tlabel(oenv),
- "(degrees)", oenv);
- fkinkr = xvgropen(opt2fn("-okr", NFILE, fnm), "Radial kink angles",
- output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
+ fkink = xvgropen(opt2fn("-ok", NFILE, fnm),
+ "Kink angles",
+ output_env_get_xvgr_tlabel(oenv),
+ "(degrees)",
+ oenv);
+ fkinkr = xvgropen(opt2fn("-okr", NFILE, fnm),
+ "Radial kink angles",
+ output_env_get_xvgr_tlabel(oenv),
+ "(degrees)",
+ oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fkinkr, "@ subtitle \"+ = ) ( - = ( )\"\n");
}
- fkinkl = xvgropen(opt2fn("-okl", NFILE, fnm), "Lateral kink angles",
- output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
+ fkinkl = xvgropen(opt2fn("-okl", NFILE, fnm),
+ "Lateral kink angles",
+ output_env_get_xvgr_tlabel(oenv),
+ "(degrees)",
+ oenv);
}
if (opt2bSet("-oa", NFILE, fnm))
fprintf(flen, " %6g", bun.len[i]);
fprintf(fdist, " %6g", norm(bun.mid[i]));
fprintf(fz, " %6g", bun.mid[i][ZZ]);
- fprintf(ftilt, " %6g", RAD2DEG * acos(bun.dir[i][ZZ]));
+ fprintf(ftilt, " %6g", gmx::c_rad2Deg * acos(bun.dir[i][ZZ]));
comp = bun.mid[i][XX] * bun.dir[i][XX] + bun.mid[i][YY] * bun.dir[i][YY];
- fprintf(ftiltr, " %6g", RAD2DEG * std::asin(comp / std::hypot(comp, bun.dir[i][ZZ])));
+ fprintf(ftiltr, " %6g", gmx::c_rad2Deg * std::asin(comp / std::hypot(comp, bun.dir[i][ZZ])));
comp = bun.mid[i][YY] * bun.dir[i][XX] - bun.mid[i][XX] * bun.dir[i][YY];
- fprintf(ftiltl, " %6g", RAD2DEG * std::asin(comp / std::hypot(comp, bun.dir[i][ZZ])));
+ fprintf(ftiltl, " %6g", gmx::c_rad2Deg * std::asin(comp / std::hypot(comp, bun.dir[i][ZZ])));
if (bKink)
{
rvec_sub(bun.end[0][i], bun.end[2][i], va);
rvec_sub(bun.end[2][i], bun.end[1][i], vb);
unitv(va, va);
unitv(vb, vb);
- fprintf(fkink, " %6g", RAD2DEG * acos(iprod(va, vb)));
+ fprintf(fkink, " %6g", gmx::c_rad2Deg * acos(iprod(va, vb)));
cprod(va, vb, vc);
copy_rvec(bun.mid[i], vr);
vr[ZZ] = 0;
unitv(vr, vr);
- fprintf(fkinkr, " %6g", RAD2DEG * std::asin(iprod(vc, vr)));
+ fprintf(fkinkr, " %6g", gmx::c_rad2Deg * std::asin(iprod(vc, vr)));
vl[XX] = vr[YY];
vl[YY] = -vr[XX];
vl[ZZ] = 0;
- fprintf(fkinkl, " %6g", RAD2DEG * std::asin(iprod(vc, vl)));
+ fprintf(fkinkl, " %6g", gmx::c_rad2Deg * std::asin(iprod(vc, vl)));
}
}
fprintf(flen, "\n");
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define NPP asize(map)
int x, y;
-#define INDEX(ppp) (((static_cast<int>(360 + (ppp)*RAD2DEG)) % 360) / 6)
+#define INDEX(ppp) (((static_cast<int>(360 + (ppp)*gmx::c_rad2Deg)) % 360) / 6)
x = INDEX(phi);
y = INDEX(psi);
#undef INDEX
}
else if (debug)
{
- fprintf(debug, "Res. %d has imcomplete occupancy or bfacs > %g\n",
- dlist[i].resnr, bfac_max);
+ fprintf(debug, "Res. %d has imcomplete occupancy or bfacs > %g\n", dlist[i].resnr, bfac_max);
}
}
else
break;
default:
sprintf(hisfile, "histo-chi%d%s", Dih - NONCHI + 1, residue_name);
- sprintf(title, "\\xc\\f{}\\s%d\\N Distribution for %s", Dih - NONCHI + 1,
- residue_name);
+ sprintf(title, "\\xc\\f{}\\s%d\\N Distribution for %s", Dih - NONCHI + 1, residue_name);
}
std::strcpy(hhisfile, hisfile);
std::strcat(hhisfile, ".xvg");
Psi = dlist[i].j0[edPsi];
for (j = 0; (j < nf); j++)
{
- phi = RAD2DEG * dih[Phi][j];
- psi = RAD2DEG * dih[Psi][j];
+ phi = gmx::c_rad2Deg * dih[Phi][j];
+ psi = gmx::c_rad2Deg * dih[Psi][j];
fprintf(fp, "%10g %10g\n", phi, psi);
if (bViol)
{
- fprintf(gp, "%d\n", static_cast<int>(!bAllowed(dih[Phi][j], RAD2DEG * dih[Psi][j])));
+ fprintf(gp,
+ "%d\n",
+ static_cast<int>(!bAllowed(dih[Phi][j], gmx::c_rad2Deg * dih[Psi][j])));
}
if (bOm)
{
- omega = RAD2DEG * dih[Om][j];
+ omega = gmx::c_rad2Deg * dih[Om][j];
mat[static_cast<int>(((phi * NMAT) / 360) + gmx::exactDiv(NMAT, 2))]
[static_cast<int>(((psi * NMAT) / 360) + gmx::exactDiv(NMAT, 2))] += omega;
}
lo += 180;
hi += 180;
nlevels = 20;
- write_xpm3(fp, 0, "Omega/Ramachandran Plot", "Deg", "Phi", "Psi", NMAT, NMAT, axis,
- axis, mat, lo, 180.0, hi, rlo, rmid, rhi, &nlevels);
+ write_xpm3(fp,
+ 0,
+ "Omega/Ramachandran Plot",
+ "Deg",
+ "Phi",
+ "Psi",
+ NMAT,
+ NMAT,
+ axis,
+ axis,
+ mat,
+ lo,
+ 180.0,
+ hi,
+ rlo,
+ rmid,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
for (j = 0; (j < NMAT); j++)
{
if ((has_dihedral(edChi1, &(dlist[i]))) && (has_dihedral(edChi2, &(dlist[i]))))
{
sprintf(fn, "ramaX1X2%s.xvg", dlist[i].name);
- fp = rama_file(fn, "\\8c\\4\\s1\\N-\\8c\\4\\s2\\N Ramachandran Plot",
- "\\8c\\4\\s1\\N (deg)", "\\8c\\4\\s2\\N (deg)", oenv);
+ fp = rama_file(fn,
+ "\\8c\\4\\s1\\N-\\8c\\4\\s2\\N Ramachandran Plot",
+ "\\8c\\4\\s1\\N (deg)",
+ "\\8c\\4\\s2\\N (deg)",
+ oenv);
Xi1 = dlist[i].j0[edChi1];
Xi2 = dlist[i].j0[edChi2];
for (j = 0; (j < nf); j++)
{
- fprintf(fp, "%10g %10g\n", RAD2DEG * dih[Xi1][j], RAD2DEG * dih[Xi2][j]);
+ fprintf(fp, "%10g %10g\n", gmx::c_rad2Deg * dih[Xi1][j], gmx::c_rad2Deg * dih[Xi2][j]);
}
xvgrclose(fp);
}
z0 *= 10.0; /* nm -> angstrom */
for (i = 0; (i < 10); i++)
{
- gmx_fprintf_pdb_atomline(fp, epdbATOM, atoms->nr + 1 + i, "CA", ' ', "LEG", ' ',
- atoms->nres + 1, ' ', x0, y0, z0 + (1.2 * i), 0.0, -0.1 * i,
+ gmx_fprintf_pdb_atomline(fp,
+ PdbRecordType::Atom,
+ atoms->nr + 1 + i,
+ "CA",
+ ' ',
+ "LEG",
+ ' ',
+ atoms->nres + 1,
+ ' ',
+ x0,
+ y0,
+ z0 + (1.2 * i),
+ 0.0,
+ -0.1 * i,
"");
}
gmx_ffclose(fp);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, npargs, ppa,
- asize(desc), desc, asize(bugs), bugs, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
sfree(ppa);
return 0;
snew(dih, ndih);
/* COMPUTE ALL DIHEDRALS! */
- read_ang_dih(ftp2fn(efTRX, NFILE, fnm), FALSE, TRUE, FALSE, bPBC, 1, &idum, &nf, &time, isize,
- index, &trans_frac, &aver_angle, dih, oenv);
+ read_ang_dih(
+ ftp2fn(efTRX, NFILE, fnm), FALSE, TRUE, FALSE, bPBC, 1, &idum, &nf, &time, isize, index, &trans_frac, &aver_angle, dih, oenv);
dt = (time[nf - 1] - time[0]) / (nf - 1); /* might want this for corr or n. transit*/
if (bCorr)
}
/* Histogramming & J coupling constants & calc of S2 order params */
- histogramming(log, nbin, &rt, nf, maxchi, dih, nlist, dlist, index, bPhi, bPsi, bOmega, bChi,
- bNormHisto, bSSHisto, ftp2fn(efDAT, NFILE, fnm), bfac_max, &atoms, bDo_jc,
- opt2fn("-jc", NFILE, fnm), oenv);
+ histogramming(log,
+ nbin,
+ &rt,
+ nf,
+ maxchi,
+ dih,
+ nlist,
+ dlist,
+ index,
+ bPhi,
+ bPsi,
+ bOmega,
+ bChi,
+ bNormHisto,
+ bSSHisto,
+ ftp2fn(efDAT, NFILE, fnm),
+ bfac_max,
+ &atoms,
+ bDo_jc,
+ opt2fn("-jc", NFILE, fnm),
+ oenv);
/* transitions
*
}
- low_ana_dih_trans(bDo_ot, opt2fn("-ot", NFILE, fnm), bDo_oh, opt2fn("-oh", NFILE, fnm), maxchi, dih,
- nlist, dlist, nf, nactdih, grpname, multiplicity, time, FALSE, core_frac, oenv);
+ low_ana_dih_trans(bDo_ot,
+ opt2fn("-ot", NFILE, fnm),
+ bDo_oh,
+ opt2fn("-oh", NFILE, fnm),
+ maxchi,
+ dih,
+ nlist,
+ dlist,
+ nf,
+ nactdih,
+ grpname,
+ multiplicity,
+ time,
+ FALSE,
+ core_frac,
+ oenv);
/* Order parameters */
- order_params(log, opt2fn("-o", NFILE, fnm), maxchi, nlist, dlist, ftp2fn_null(efPDB, NFILE, fnm),
- bfac_init, &atoms, x, pbcType, box, bPhi, bPsi, bChi, oenv);
+ order_params(log,
+ opt2fn("-o", NFILE, fnm),
+ maxchi,
+ nlist,
+ dlist,
+ ftp2fn_null(efPDB, NFILE, fnm),
+ bfac_init,
+ &atoms,
+ x,
+ pbcType,
+ box,
+ bPhi,
+ bPsi,
+ bChi,
+ oenv);
/* Print ramachandran maps! */
if (bRama)
}
mk_chi_lookup(chi_lookup, maxchi, nlist, dlist);
- get_chi_product_traj(dih, nf, nactdih, maxchi, dlist, time, chi_lookup, multiplicity, FALSE,
- bNormHisto, core_frac, bAll, opt2fn("-cp", NFILE, fnm), oenv);
+ get_chi_product_traj(dih,
+ nf,
+ nactdih,
+ maxchi,
+ dlist,
+ time,
+ chi_lookup,
+ multiplicity,
+ FALSE,
+ bNormHisto,
+ core_frac,
+ bAll,
+ opt2fn("-cp", NFILE, fnm),
+ oenv);
for (i = 0; i < nlist; i++)
{
/* Correlation comes last because it messes up the angles */
if (bCorr)
{
- do_dihcorr(opt2fn("-corr", NFILE, fnm), nf, ndih, dih, dt, nlist, dlist, time, maxchi, bPhi,
- bPsi, bChi, bOmega, oenv);
+ do_dihcorr(opt2fn("-corr", NFILE, fnm), nf, ndih, dih, dt, nlist, dlist, time, maxchi, bPhi, bPsi, bChi, bOmega, oenv);
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/cluster_methods.h"
#include "gromacs/gmxana/cmat.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/linearalgebra/eigensolver.h"
lo_ffprintf(fp1, fp2, buf);
}
-typedef struct
-{
- int ncl;
- int* cl;
-} t_clusters;
-
-typedef struct
-{
- int nr;
- int* nb;
-} t_nnb;
-
-static void mc_optimize(FILE* log,
- t_mat* m,
- real* time,
- int maxiter,
- int nrandom,
- int seed,
- real kT,
- const char* conv,
- gmx_output_env_t* oenv)
-{
- FILE* fp = nullptr;
- real ecur, enext, emin, prob, enorm;
- int i, j, iswap, jswap, nn, nuphill = 0;
- t_mat* minimum;
-
- if (seed == 0)
- {
- seed = static_cast<int>(gmx::makeRandomSeed());
- }
- gmx::DefaultRandomEngine rng(seed);
-
- if (m->n1 != m->nn)
- {
- fprintf(stderr, "Can not do Monte Carlo optimization with a non-square matrix.\n");
- return;
- }
- printf("\nDoing Monte Carlo optimization to find the smoothest trajectory\n");
- printf("by reordering the frames to minimize the path between the two structures\n");
- printf("that have the largest pairwise RMSD.\n");
- printf("Using random seed %d.\n", seed);
-
- iswap = jswap = -1;
- enorm = m->mat[0][0];
- for (i = 0; (i < m->n1); i++)
- {
- for (j = 0; (j < m->nn); j++)
- {
- if (m->mat[i][j] > enorm)
- {
- enorm = m->mat[i][j];
- iswap = i;
- jswap = j;
- }
- }
- }
- if ((iswap == -1) || (jswap == -1))
- {
- fprintf(stderr, "Matrix contains identical values in all fields\n");
- return;
- }
- swap_rows(m, 0, iswap);
- swap_rows(m, m->n1 - 1, jswap);
- emin = ecur = mat_energy(m);
- printf("Largest distance %g between %d and %d. Energy: %g.\n", enorm, iswap, jswap, emin);
-
- nn = m->nn;
-
- /* Initiate and store global minimum */
- minimum = init_mat(nn, m->b1D);
- minimum->nn = nn;
- copy_t_mat(minimum, m);
-
- if (nullptr != conv)
- {
- fp = xvgropen(conv, "Convergence of the MC optimization", "Energy", "Step", oenv);
- }
-
- gmx::UniformIntDistribution<int> intDistNN(1, nn - 2); // [1,nn-2]
- gmx::UniformRealDistribution<real> realDistOne; // [0,1)
-
- for (i = 0; (i < maxiter); i++)
- {
- /* Generate new swapping candidates */
- do
- {
- iswap = intDistNN(rng);
- jswap = intDistNN(rng);
- } while ((iswap == jswap) || (iswap >= nn - 1) || (jswap >= nn - 1));
-
- /* Apply swap and compute energy */
- swap_rows(m, iswap, jswap);
- enext = mat_energy(m);
-
- /* Compute probability */
- prob = 0;
- if ((enext < ecur) || (i < nrandom))
- {
- prob = 1;
- if (enext < emin)
- {
- /* Store global minimum */
- copy_t_mat(minimum, m);
- emin = enext;
- }
- }
- else if (kT > 0)
- {
- /* Try Monte Carlo step */
- prob = std::exp(-(enext - ecur) / (enorm * kT));
- }
-
- if (prob == 1 || realDistOne(rng) < prob)
- {
- if (enext > ecur)
- {
- nuphill++;
- }
-
- fprintf(log, "Iter: %d Swapped %4d and %4d (energy: %g prob: %g)\n", i, iswap, jswap,
- enext, prob);
- if (nullptr != fp)
- {
- fprintf(fp, "%6d %10g\n", i, enext);
- }
- ecur = enext;
- }
- else
- {
- swap_rows(m, jswap, iswap);
- }
- }
- fprintf(log, "%d uphill steps were taken during optimization\n", nuphill);
-
- /* Now swap the matrix to get it into global minimum mode */
- copy_t_mat(m, minimum);
-
- fprintf(log, "Global minimum energy %g\n", mat_energy(minimum));
- fprintf(log, "Global minimum energy %g\n", mat_energy(m));
- fprintf(log, "Swapped time and frame indices and RMSD to next neighbor:\n");
- for (i = 0; (i < m->nn); i++)
- {
- fprintf(log, "%10g %5d %10g\n", time[m->m_ind[i]], m->m_ind[i],
- (i < m->nn - 1) ? m->mat[m->m_ind[i]][m->m_ind[i + 1]] : 0);
- }
-
- if (nullptr != fp)
- {
- xvgrclose(fp);
- }
-}
-
static void calc_dist(int nind, rvec x[], real** d)
{
int i, j;
return std::sqrt(r2);
}
-static bool rms_dist_comp(const t_dist& a, const t_dist& b)
-{
- return a.dist < b.dist;
-}
-
-static bool clust_id_comp(const t_clustid& a, const t_clustid& b)
-{
- return a.clust < b.clust;
-}
-
-static bool nrnb_comp(const t_nnb& a, const t_nnb& b)
-{
- /* return b<a, we want highest first */
- return b.nr < a.nr;
-}
-
-static void gather(t_mat* m, real cutoff, t_clusters* clust)
-{
- t_clustid* c;
- t_dist* d;
- int i, j, k, nn, cid, n1, diff;
- gmx_bool bChange;
-
- /* First we sort the entries in the RMSD matrix */
- n1 = m->nn;
- nn = ((n1 - 1) * n1) / 2;
- snew(d, nn);
- for (i = k = 0; (i < n1); i++)
- {
- for (j = i + 1; (j < n1); j++, k++)
- {
- d[k].i = i;
- d[k].j = j;
- d[k].dist = m->mat[i][j];
- }
- }
- if (k != nn)
- {
- gmx_incons("gather algortihm");
- }
- std::sort(d, d + nn, rms_dist_comp);
-
- /* Now we make a cluster index for all of the conformations */
- c = new_clustid(n1);
-
- /* Now we check the closest structures, and equalize their cluster numbers */
- fprintf(stderr, "Linking structures ");
- do
- {
- fprintf(stderr, "*");
- bChange = FALSE;
- for (k = 0; (k < nn) && (d[k].dist < cutoff); k++)
- {
- diff = c[d[k].j].clust - c[d[k].i].clust;
- if (diff)
- {
- bChange = TRUE;
- if (diff > 0)
- {
- c[d[k].j].clust = c[d[k].i].clust;
- }
- else
- {
- c[d[k].i].clust = c[d[k].j].clust;
- }
- }
- }
- } while (bChange);
- fprintf(stderr, "\nSorting and renumbering clusters\n");
- /* Sort on cluster number */
- std::sort(c, c + n1, clust_id_comp);
-
- /* Renumber clusters */
- cid = 1;
- for (k = 1; k < n1; k++)
- {
- if (c[k].clust != c[k - 1].clust)
- {
- c[k - 1].clust = cid;
- cid++;
- }
- else
- {
- c[k - 1].clust = cid;
- }
- }
- c[k - 1].clust = cid;
- if (debug)
- {
- for (k = 0; (k < n1); k++)
- {
- fprintf(debug, "Cluster index for conformation %d: %d\n", c[k].conf, c[k].clust);
- }
- }
- clust->ncl = cid;
- for (k = 0; k < n1; k++)
- {
- clust->cl[c[k].conf] = c[k].clust;
- }
-
- sfree(c);
- sfree(d);
-}
-
-static gmx_bool jp_same(int** nnb, int i, int j, int P)
-{
- gmx_bool bIn;
- int k, ii, jj, pp;
-
- bIn = FALSE;
- for (k = 0; nnb[i][k] >= 0; k++)
- {
- bIn = bIn || (nnb[i][k] == j);
- }
- if (!bIn)
- {
- return FALSE;
- }
-
- bIn = FALSE;
- for (k = 0; nnb[j][k] >= 0; k++)
- {
- bIn = bIn || (nnb[j][k] == i);
- }
- if (!bIn)
- {
- return FALSE;
- }
-
- pp = 0;
- for (ii = 0; nnb[i][ii] >= 0; ii++)
- {
- for (jj = 0; nnb[j][jj] >= 0; jj++)
- {
- if ((nnb[i][ii] == nnb[j][jj]) && (nnb[i][ii] != -1))
- {
- pp++;
- }
- }
- }
-
- return (pp >= P);
-}
-
-static void jarvis_patrick(int n1, real** mat, int M, int P, real rmsdcut, t_clusters* clust)
-{
- t_dist* row;
- t_clustid* c;
- int** nnb;
- int i, j, k, cid, diff, maxval;
- gmx_bool bChange;
- real** mcpy = nullptr;
-
- if (rmsdcut < 0)
- {
- rmsdcut = 10000;
- }
-
- /* First we sort the entries in the RMSD matrix row by row.
- * This gives us the nearest neighbor list.
- */
- snew(nnb, n1);
- snew(row, n1);
- for (i = 0; (i < n1); i++)
- {
- for (j = 0; (j < n1); j++)
- {
- row[j].j = j;
- row[j].dist = mat[i][j];
- }
- std::sort(row, row + n1, rms_dist_comp);
- if (M > 0)
- {
- /* Put the M nearest neighbors in the list */
- snew(nnb[i], M + 1);
- for (j = k = 0; (k < M) && (j < n1) && (mat[i][row[j].j] < rmsdcut); j++)
- {
- if (row[j].j != i)
- {
- nnb[i][k] = row[j].j;
- k++;
- }
- }
- nnb[i][k] = -1;
- }
- else
- {
- /* Put all neighbors nearer than rmsdcut in the list */
- maxval = 0;
- k = 0;
- for (j = 0; (j < n1) && (mat[i][row[j].j] < rmsdcut); j++)
- {
- if (row[j].j != i)
- {
- if (k >= maxval)
- {
- maxval += 10;
- srenew(nnb[i], maxval);
- }
- nnb[i][k] = row[j].j;
- k++;
- }
- }
- if (k == maxval)
- {
- srenew(nnb[i], maxval + 1);
- }
- nnb[i][k] = -1;
- }
- }
- sfree(row);
- if (debug)
- {
- fprintf(debug, "Nearest neighborlist. M = %d, P = %d\n", M, P);
- for (i = 0; (i < n1); i++)
- {
- fprintf(debug, "i:%5d nbs:", i);
- for (j = 0; nnb[i][j] >= 0; j++)
- {
- fprintf(debug, "%5d[%5.3f]", nnb[i][j], mat[i][nnb[i][j]]);
- }
- fprintf(debug, "\n");
- }
- }
-
- c = new_clustid(n1);
- fprintf(stderr, "Linking structures ");
- /* Use mcpy for temporary storage of booleans */
- mcpy = mk_matrix(n1, n1, FALSE);
- for (i = 0; i < n1; i++)
- {
- for (j = i + 1; j < n1; j++)
- {
- mcpy[i][j] = static_cast<real>(jp_same(nnb, i, j, P));
- }
- }
- do
- {
- fprintf(stderr, "*");
- bChange = FALSE;
- for (i = 0; i < n1; i++)
- {
- for (j = i + 1; j < n1; j++)
- {
- if (mcpy[i][j] != 0.0F)
- {
- diff = c[j].clust - c[i].clust;
- if (diff)
- {
- bChange = TRUE;
- if (diff > 0)
- {
- c[j].clust = c[i].clust;
- }
- else
- {
- c[i].clust = c[j].clust;
- }
- }
- }
- }
- }
- } while (bChange);
-
- fprintf(stderr, "\nSorting and renumbering clusters\n");
- /* Sort on cluster number */
- std::sort(c, c + n1, clust_id_comp);
-
- /* Renumber clusters */
- cid = 1;
- for (k = 1; k < n1; k++)
- {
- if (c[k].clust != c[k - 1].clust)
- {
- c[k - 1].clust = cid;
- cid++;
- }
- else
- {
- c[k - 1].clust = cid;
- }
- }
- c[k - 1].clust = cid;
- clust->ncl = cid;
- for (k = 0; k < n1; k++)
- {
- clust->cl[c[k].conf] = c[k].clust;
- }
- if (debug)
- {
- for (k = 0; (k < n1); k++)
- {
- fprintf(debug, "Cluster index for conformation %d: %d\n", c[k].conf, c[k].clust);
- }
- }
-
- done_matrix(n1, &mcpy);
-
- sfree(c);
- for (i = 0; (i < n1); i++)
- {
- sfree(nnb[i]);
- }
- sfree(nnb);
-}
-
-static void dump_nnb(FILE* fp, const char* title, int n1, t_nnb* nnb)
-{
- int i, j;
-
- /* dump neighbor list */
- fprintf(fp, "%s", title);
- for (i = 0; (i < n1); i++)
- {
- fprintf(fp, "i:%5d #:%5d nbs:", i, nnb[i].nr);
- for (j = 0; j < nnb[i].nr; j++)
- {
- fprintf(fp, "%5d", nnb[i].nb[j]);
- }
- fprintf(fp, "\n");
- }
-}
-
-static void gromos(int n1, real** mat, real rmsdcut, t_clusters* clust)
-{
- t_nnb* nnb;
- int i, j, k, j1, maxval;
-
- /* Put all neighbors nearer than rmsdcut in the list */
- fprintf(stderr, "Making list of neighbors within cutoff ");
- snew(nnb, n1);
- for (i = 0; (i < n1); i++)
- {
- maxval = 0;
- k = 0;
- /* put all neighbors within cut-off in list */
- for (j = 0; j < n1; j++)
- {
- if (mat[i][j] < rmsdcut)
- {
- if (k >= maxval)
- {
- maxval += 10;
- srenew(nnb[i].nb, maxval);
- }
- nnb[i].nb[k] = j;
- k++;
- }
- }
- /* store nr of neighbors, we'll need that */
- nnb[i].nr = k;
- if (i % (1 + n1 / 100) == 0)
- {
- fprintf(stderr, "%3d%%\b\b\b\b", (i * 100 + 1) / n1);
- }
- }
- fprintf(stderr, "%3d%%\n", 100);
-
- /* sort neighbor list on number of neighbors, largest first */
- std::sort(nnb, nnb + n1, nrnb_comp);
-
- if (debug)
- {
- dump_nnb(debug, "Nearest neighborlist after sort.\n", n1, nnb);
- }
-
- /* turn first structure with all its neighbors (largest) into cluster
- remove them from pool of structures and repeat for all remaining */
- fprintf(stderr, "Finding clusters %4d", 0);
- /* cluster id's start at 1: */
- k = 1;
- while (nnb[0].nr)
- {
- /* set cluster id (k) for first item in neighborlist */
- for (j = 0; j < nnb[0].nr; j++)
- {
- clust->cl[nnb[0].nb[j]] = k;
- }
- /* mark as done */
- nnb[0].nr = 0;
- sfree(nnb[0].nb);
-
- /* adjust number of neighbors for others, taking removals into account: */
- for (i = 1; i < n1 && nnb[i].nr; i++)
- {
- j1 = 0;
- for (j = 0; j < nnb[i].nr; j++)
- {
- /* if this neighbor wasn't removed */
- if (clust->cl[nnb[i].nb[j]] == 0)
- {
- /* shift the rest (j1<=j) */
- nnb[i].nb[j1] = nnb[i].nb[j];
- /* next */
- j1++;
- }
- }
- /* now j1 is the new number of neighbors */
- nnb[i].nr = j1;
- }
- /* sort again on nnb[].nr, because we have new # neighbors: */
- /* but we only need to sort upto i, i.e. when nnb[].nr>0 */
- std::sort(nnb, nnb + i, nrnb_comp);
-
- fprintf(stderr, "\b\b\b\b%4d", k);
- /* new cluster id */
- k++;
- }
- fprintf(stderr, "\n");
- sfree(nnb);
- if (debug)
- {
- fprintf(debug, "Clusters (%d):\n", k);
- for (i = 0; i < n1; i++)
- {
- fprintf(debug, " %3d", clust->cl[i]);
- }
- fprintf(debug, "\n");
- }
-
- clust->ncl = k - 1;
-}
-
static rvec** read_whole_trj(const char* fn,
int isize,
const int index[],
trans[clust->cl[i] - 1][clust->cl[i - 1] - 1]));
}
}
- ffprintf_dd(stderr, log, buf,
+ ffprintf_dd(stderr,
+ log,
+ buf,
"Counted %d transitions in total, "
"max %d between two specific clusters\n",
- ntranst, maxtrans);
+ ntranst,
+ maxtrans);
if (transfn)
{
fp = gmx_ffopen(transfn, "w");
i = std::min(maxtrans + 1, 80);
- write_xpm(fp, 0, "Cluster Transitions", "# transitions", "from cluster", "to cluster",
- clust->ncl, clust->ncl, axis, axis, trans, 0, maxtrans, rlo, rhi, &i);
+ write_xpm(fp,
+ 0,
+ "Cluster Transitions",
+ "# transitions",
+ "from cluster",
+ "to cluster",
+ clust->ncl,
+ clust->ncl,
+ axis,
+ axis,
+ trans,
+ 0,
+ maxtrans,
+ rlo,
+ rhi,
+ &i);
gmx_ffclose(fp);
}
if (ntransfn)
trxsfn = parse_filename(trxfn, std::max(write_ncl, clust->ncl));
snew(bWrite, nf);
}
- ffprintf_ss(stderr, log, buf, "Writing %s structure for each cluster to %s\n",
- bAverage ? "average" : "middle", trxfn);
+ ffprintf_ss(stderr,
+ log,
+ buf,
+ "Writing %s structure for each cluster to %s\n",
+ bAverage ? "average" : "middle",
+ trxfn);
if (write_ncl)
{
/* find out what we want to tell the user:
}
snew(structure, nf);
- fprintf(log, "\n%3s | %3s %4s | %6s %4s | cluster members\n", "cl.", "#st", "rmsd", "middle",
+ fprintf(log,
+ "\n%3s | %3s %4s | %6s %4s | cluster members\n",
+ "cl.",
+ "#st",
+ "rmsd",
+ "middle",
"rmsd");
for (cl = 1; cl <= clust->ncl; cl++)
{
}
if (bWrite[i])
{
- write_trx(trxsout, iosize, outidx, atoms, i, time[structure[i]],
- boxes[structure[i]], xx[structure[i]], nullptr, nullptr);
+ write_trx(trxsout,
+ iosize,
+ outidx,
+ atoms,
+ i,
+ time[structure[i]],
+ boxes[structure[i]],
+ xx[structure[i]],
+ nullptr,
+ nullptr);
}
}
close_trx(trxsout);
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm,
- asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc,
+ argv,
+ PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
+ NFILE,
+ fnm,
+ asize(pa),
+ pa,
+ asize(desc),
+ desc,
+ 0,
+ nullptr,
+ &oenv))
{
return 0;
}
}
if (bReadMat && output_env_get_time_factor(oenv) != 1)
{
- fprintf(stderr, "\nWarning: assuming the time unit in %s is %s\n",
- opt2fn("-dm", NFILE, fnm), output_env_get_time_unit(oenv).c_str());
+ fprintf(stderr,
+ "\nWarning: assuming the time unit in %s is %s\n",
+ opt2fn("-dm", NFILE, fnm),
+ output_env_get_time_unit(oenv).c_str());
}
if (trx_out_fn && !bReadTraj)
{
gmx_fatal(FARGS,
"Matrix size (%dx%d) does not match the number of "
"frames (%d)",
- readmat[0].nx, readmat[0].ny, nf);
+ readmat[0].nx,
+ readmat[0].ny,
+ nf);
}
nf = readmat[0].nx;
fprintf(stderr,
"WARNING: rmsd cutoff %g is outside range of rmsd values "
"%g to %g\n",
- rmsdcut, rms->minrms, rms->maxrms);
+ rmsdcut,
+ rms->minrms,
+ rms->maxrms);
}
if (bAnalyze && (rmsmin < rms->minrms))
{
eigensolver(eigenvectors, nf, 0, nf, eigenvalues, rms->mat[0]);
sfree(eigenvectors);
- fp = xvgropen(opt2fn("-ev", NFILE, fnm), "RMSD matrix Eigenvalues", "Eigenvector index",
- "Eigenvalues (nm\\S2\\N)", oenv);
+ fp = xvgropen(opt2fn("-ev", NFILE, fnm),
+ "RMSD matrix Eigenvalues",
+ "Eigenvector index",
+ "Eigenvalues (nm\\S2\\N)",
+ oenv);
for (i = 0; (i < nf); i++)
{
fprintf(fp, "%10d %10g\n", i, eigenvalues[i]);
copy_rvec(xtps[index[i]], usextps[i]);
}
useatoms.nr = isize;
- analyze_clusters(nf, &clust, rms->mat, isize, &useatoms, usextps, mass, xx, time, boxes,
- frameindices, ifsize, fitidx, iosize, outidx,
- bReadTraj ? trx_out_fn : nullptr, opt2fn_null("-sz", NFILE, fnm),
- opt2fn_null("-tr", NFILE, fnm), opt2fn_null("-ntr", NFILE, fnm),
- opt2fn_null("-clid", NFILE, fnm), opt2fn_null("-clndx", NFILE, fnm),
- bAverage, write_ncl, write_nst, rmsmin, bFit, log, rlo_bot, rhi_bot, oenv);
+ analyze_clusters(nf,
+ &clust,
+ rms->mat,
+ isize,
+ &useatoms,
+ usextps,
+ mass,
+ xx,
+ time,
+ boxes,
+ frameindices,
+ ifsize,
+ fitidx,
+ iosize,
+ outidx,
+ bReadTraj ? trx_out_fn : nullptr,
+ opt2fn_null("-sz", NFILE, fnm),
+ opt2fn_null("-tr", NFILE, fnm),
+ opt2fn_null("-ntr", NFILE, fnm),
+ opt2fn_null("-clid", NFILE, fnm),
+ opt2fn_null("-clndx", NFILE, fnm),
+ bAverage,
+ write_ncl,
+ write_nst,
+ rmsmin,
+ bFit,
+ log,
+ rlo_bot,
+ rhi_bot,
+ oenv);
sfree(boxes);
sfree(frameindices);
}
fprintf(stderr, "Writing rms distance/clustering matrix ");
if (bReadMat)
{
- write_xpm(fp, 0, readmat[0].title, readmat[0].legend, readmat[0].label_x,
- readmat[0].label_y, nf, nf, readmat[0].axis_x.data(), readmat[0].axis_y.data(),
- rms->mat, 0.0, rms->maxrms, rlo_top, rhi_top, &nlevels);
+ write_xpm(fp,
+ 0,
+ readmat[0].title,
+ readmat[0].legend,
+ readmat[0].label_x,
+ readmat[0].label_y,
+ nf,
+ nf,
+ readmat[0].axis_x.data(),
+ readmat[0].axis_y.data(),
+ rms->mat,
+ 0.0,
+ rms->maxrms,
+ rlo_top,
+ rhi_top,
+ &nlevels);
}
else
{
auto title = gmx::formatString("RMS%sDeviation / Cluster Index", bRMSdist ? " Distance " : " ");
if (minstruct > 1)
{
- write_xpm_split(fp, 0, title, "RMSD (nm)", timeLabel, timeLabel, nf, nf, time, time,
- rms->mat, 0.0, rms->maxrms, &nlevels, rlo_top, rhi_top, 0.0, ncluster,
- &ncluster, TRUE, rlo_bot, rhi_bot);
+ write_xpm_split(fp,
+ 0,
+ title,
+ "RMSD (nm)",
+ timeLabel,
+ timeLabel,
+ nf,
+ nf,
+ time,
+ time,
+ rms->mat,
+ 0.0,
+ rms->maxrms,
+ &nlevels,
+ rlo_top,
+ rhi_top,
+ 0.0,
+ ncluster,
+ &ncluster,
+ TRUE,
+ rlo_bot,
+ rhi_bot);
}
else
{
- write_xpm(fp, 0, title, "RMSD (nm)", timeLabel, timeLabel, nf, nf, time, time, rms->mat,
- 0.0, rms->maxrms, rlo_top, rhi_top, &nlevels);
+ write_xpm(fp,
+ 0,
+ title,
+ "RMSD (nm)",
+ timeLabel,
+ timeLabel,
+ nf,
+ nf,
+ time,
+ time,
+ rms->mat,
+ 0.0,
+ rms->maxrms,
+ rlo_top,
+ rhi_top,
+ &nlevels);
}
}
fprintf(stderr, "\n");
fp = opt2FILE("-om", NFILE, fnm, "w");
auto timeLabel = output_env_get_time_label(oenv);
auto title = gmx::formatString("RMS%sDeviation", bRMSdist ? " Distance " : " ");
- write_xpm(fp, 0, title, "RMSD (nm)", timeLabel, timeLabel, nf, nf, time, time, orig->mat,
- 0.0, orig->maxrms, rlo_top, rhi_top, &nlevels);
+ write_xpm(fp,
+ 0,
+ title,
+ "RMSD (nm)",
+ timeLabel,
+ timeLabel,
+ nf,
+ nf,
+ time,
+ time,
+ orig->mat,
+ 0.0,
+ orig->maxrms,
+ rlo_top,
+ rhi_top,
+ &nlevels);
gmx_ffclose(fp);
done_mat(&orig);
sfree(orig);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2007, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* Topology stuff */
t_trxframe fr;
TpxFileHeader tpxh;
- gmx_mtop_t* mtop = nullptr;
+ gmx_mtop_t mtop;
PbcType pbcType = PbcType::Unset;
int ii, jj;
real temp, tfac;
if (tpr)
{
- mtop = new gmx_mtop_t;
tpxh = readTpxHeader(tpr, true);
if (tpxh.natoms != natoms)
{
gmx_fatal(FARGS, "tpr (%d atoms) and trajectory (%d atoms) do not match!", tpxh.natoms, natoms);
}
- pbcType = read_tpx(tpr, nullptr, nullptr, &natoms, nullptr, nullptr, mtop);
+ pbcType = read_tpx(tpr, nullptr, nullptr, &natoms, nullptr, nullptr, &mtop);
}
if (ndf <= -1)
{
{
printf("Using molecules rather than atoms. Not reading index file %s\n", ndx);
}
- GMX_RELEASE_ASSERT(mtop != nullptr, "Trying to access mtop->mols from NULL mtop pointer");
- mols = gmx_mtop_molecules(*mtop);
+ GMX_RELEASE_ASSERT(tpr, "Cannot access topology without having read it from TPR");
+ mols = gmx_mtop_molecules(mtop);
/* Make dummy index */
nindex = mols.numBlocks();
{
if (clust_size[cj] <= 0)
{
- gmx_fatal(FARGS, "negative cluster size %d for element %d",
- clust_size[cj], cj);
+ gmx_fatal(FARGS,
+ "negative cluster size %d for element %d",
+ clust_size[cj],
+ cj);
}
clust_size[cj]--;
clust_index[k] = ci;
ekin += 0.5 * m * iprod(v[ai], v[ai]);
}
}
- temp = (ekin * 2.0) / (3.0 * tfac * max_clust_size * BOLTZ);
+ temp = (ekin * 2.0) / (3.0 * tfac * max_clust_size * gmx::c_boltz);
fprintf(tp, "%10.3f %10.3f\n", frameTime, temp);
}
}
fprintf(stderr, "cmid: %g, cmax: %g, max_size: %d\n", cmid, cmax, max_size);
cmid = 1;
fp = gmx_ffopen(xpm, "w");
- write_xpm3(fp, 0, "Cluster size distribution", "# clusters", timeLabel, "Size", n_x, max_size,
- t_x, t_y, cs_dist, 0, cmid, cmax, rlo, rmid, rhi, &nlevels);
+ write_xpm3(fp,
+ 0,
+ "Cluster size distribution",
+ "# clusters",
+ timeLabel,
+ "Size",
+ n_x,
+ max_size,
+ t_x,
+ t_y,
+ cs_dist,
+ 0,
+ cmid,
+ cmax,
+ rlo,
+ rmid,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
cmid = 100.0;
cmax = 0.0;
}
fprintf(stderr, "cmid: %g, cmax: %g, max_size: %d\n", cmid, cmax, max_size);
fp = gmx_ffopen(xpmw, "w");
- write_xpm3(fp, 0, "Weighted cluster size distribution", "Fraction", timeLabel, "Size", n_x,
- max_size, t_x, t_y, cs_dist, 0, cmid, cmax, rlo, rmid, rhi, &nlevels);
+ write_xpm3(fp,
+ 0,
+ "Weighted cluster size distribution",
+ "Fraction",
+ timeLabel,
+ "Size",
+ n_x,
+ max_size,
+ t_x,
+ t_y,
+ cs_dist,
+ 0,
+ cmid,
+ cmax,
+ rlo,
+ rmid,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
- delete mtop;
sfree(t_x);
sfree(t_y);
for (i = 0; (i < n_x); i++)
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm,
- NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
gmx_fatal(FARGS, "You need a tpr file for the -mol option");
}
- clust_size(fnNDX, ftp2fn(efTRX, NFILE, fnm), opt2fn("-o", NFILE, fnm), opt2fn("-ow", NFILE, fnm),
- opt2fn("-nc", NFILE, fnm), opt2fn("-ac", NFILE, fnm), opt2fn("-mc", NFILE, fnm),
- opt2fn("-hc", NFILE, fnm), opt2fn("-temp", NFILE, fnm), opt2fn("-mcn", NFILE, fnm),
- bMol, bPBC, fnTPR, cutoff, nskip, nlevels, rgblo, rgbhi, ndf, oenv);
+ clust_size(fnNDX,
+ ftp2fn(efTRX, NFILE, fnm),
+ opt2fn("-o", NFILE, fnm),
+ opt2fn("-ow", NFILE, fnm),
+ opt2fn("-nc", NFILE, fnm),
+ opt2fn("-ac", NFILE, fnm),
+ opt2fn("-mc", NFILE, fnm),
+ opt2fn("-hc", NFILE, fnm),
+ opt2fn("-temp", NFILE, fnm),
+ opt2fn("-mcn", NFILE, fnm),
+ bMol,
+ bPBC,
+ fnTPR,
+ cutoff,
+ nskip,
+ nlevels,
+ rgblo,
+ rgbhi,
+ ndf,
+ oenv);
output_env_done(oenv);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/math/do_fit.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/rmpbc.h"
{
if (debug)
{
- fprintf(debug, "%d.%d.%dX%sX%s", dx, rr1, rr2, *resinfo1[index1[rr1 + 1]].name,
+ fprintf(debug,
+ "%d.%d.%dX%sX%s",
+ dx,
+ rr1,
+ rr2,
+ *resinfo1[index1[rr1 + 1]].name,
*resinfo2[index2[rr2 + 1]].name);
}
dx = 1;
}
if (debug)
{
- fprintf(debug, " -> %s%d-%s%d %s%d-%s%d", *resinfo1[rnr1].name, rnr1, *atnms1[index1[i1]],
- index1[i1], *resinfo2[rnr2].name, rnr2, *atnms2[index2[i2]], index2[i2]);
+ fprintf(debug,
+ " -> %s%d-%s%d %s%d-%s%d",
+ *resinfo1[rnr1].name,
+ rnr1,
+ *atnms1[index1[i1]],
+ index1[i1],
+ *resinfo2[rnr2].name,
+ rnr2,
+ *atnms2[index2[i2]],
+ index2[i2]);
}
m1 = find_res_end(i1, *isize1, index1, atoms1);
m2 = find_res_end(i2, *isize2, index2, atoms2);
real* msds;
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa, asize(desc), desc,
- 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
if (matchndxfile)
{
fp = gmx_ffopen(matchndxfile, "w");
- fprintf(fp, "; Matching atoms between %s from %s and %s from %s\n", groupnames1,
- conf1file, groupnames2, conf2file);
+ fprintf(fp,
+ "; Matching atoms between %s from %s and %s from %s\n",
+ groupnames1,
+ conf1file,
+ groupnames2,
+ conf2file);
fprintf(fp, "[ Match_%s_%s ]\n", conf1file, groupnames1);
for (i = 0; i < isize1; i++)
{
{
if (warn < 20)
{
- fprintf(stderr, "Warning: atomnames at index %d don't match: %d %s, %d %s\n", i + 1,
- index1[i] + 1, name1, index2[i] + 1, name2);
+ fprintf(stderr,
+ "Warning: atomnames at index %d don't match: %d %s, %d %s\n",
+ i + 1,
+ index1[i] + 1,
+ name1,
+ index2[i] + 1,
+ name2);
}
warn++;
}
/* Avoid segfaults when writing the pdb-file */
for (i = 0; i < atoms1->nr; i++)
{
- atoms1->pdbinfo[i].type = eptAtom;
+ atoms1->pdbinfo[i].type = PdbRecordType::Atom;
atoms1->pdbinfo[i].occup = 1.00;
atoms1->pdbinfo[i].bAnisotropic = FALSE;
if (bBfac)
for (i = 0; i < atoms2->nr; i++)
{
- atoms2->pdbinfo[i].type = eptAtom;
+ atoms2->pdbinfo[i].type = PdbRecordType::Atom;
atoms2->pdbinfo[i].occup = 1.00;
atoms2->pdbinfo[i].bAnisotropic = FALSE;
if (bBfac)
default:
if (bBfac)
{
- fprintf(stderr, "WARNING: cannot write B-factor values to %s file\n",
+ fprintf(stderr,
+ "WARNING: cannot write B-factor values to %s file\n",
ftp2ext(fn2ftp(outfile)));
}
if (!bOne)
{
- fprintf(stderr, "WARNING: cannot write the reference structure to %s file\n",
+ fprintf(stderr,
+ "WARNING: cannot write the reference structure to %s file\n",
ftp2ext(fn2ftp(outfile)));
}
write_sto_conf(outfile, *top2->name, atoms2, x2, v2, pbcType2, box2);
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
fprintf(stderr,
"\nWARNING: number of atoms in structure file (%d) and trajectory (%d) do not "
"match\n",
- natoms, nat);
+ natoms,
+ nat);
}
gmx::throwErrorIfIndexOutOfBounds({ ifit, ifit + nfit }, nat, "fitting");
gmx::throwErrorIfIndexOutOfBounds({ index, index + natoms }, nat, "analysis");
xread[index[i]][d] = xav[i][d];
}
}
- write_sto_conf_indexed(opt2fn("-av", NFILE, fnm), "Average structure", atoms, xread, nullptr,
- PbcType::No, zerobox, natoms, index);
+ write_sto_conf_indexed(
+ opt2fn("-av", NFILE, fnm), "Average structure", atoms, xread, nullptr, PbcType::No, zerobox, natoms, index);
sfree(xread);
- fprintf(stderr, "Constructing covariance matrix (%dx%d) ...\n", static_cast<int>(ndim),
+ fprintf(stderr,
+ "Constructing covariance matrix (%dx%d) ...\n",
+ static_cast<int>(ndim),
static_cast<int>(ndim));
nframes = 0;
nat = read_first_x(oenv, &status, trxfile, &t, &xread, box);
{
for (i = 0; i < ndim; i += 3)
{
- fprintf(out, "%g %g %g\n", mat[ndim * j + i], mat[ndim * j + i + 1],
- mat[ndim * j + i + 2]);
+ fprintf(out, "%g %g %g\n", mat[ndim * j + i], mat[ndim * j + i + 1], mat[ndim * j + i + 2]);
}
}
gmx_ffclose(out);
rhi.b = 0;
out = gmx_ffopen(xpmfile, "w");
nlevels = 80;
- write_xpm3(out, 0, "Covariance", bM ? "u nm^2" : "nm^2", "dim", "dim", ndim, ndim, axis,
- axis, mat2, min, 0.0, max, rlo, rmi, rhi, &nlevels);
+ write_xpm3(out,
+ 0,
+ "Covariance",
+ bM ? "u nm^2" : "nm^2",
+ "dim",
+ "dim",
+ ndim,
+ ndim,
+ axis,
+ axis,
+ mat2,
+ min,
+ 0.0,
+ max,
+ rlo,
+ rmi,
+ rhi,
+ &nlevels);
gmx_ffclose(out);
sfree(axis);
sfree(mat2);
rhi.b = 0;
out = gmx_ffopen(xpmafile, "w");
nlevels = 80;
- write_xpm3(out, 0, "Covariance", bM ? "u nm^2" : "nm^2", "atom", "atom", ndim / DIM,
- ndim / DIM, axis, axis, mat2, min, 0.0, max, rlo, rmi, rhi, &nlevels);
+ write_xpm3(out,
+ 0,
+ "Covariance",
+ bM ? "u nm^2" : "nm^2",
+ "atom",
+ "atom",
+ ndim / DIM,
+ ndim / DIM,
+ axis,
+ axis,
+ mat2,
+ min,
+ 0.0,
+ max,
+ rlo,
+ rmi,
+ rhi,
+ &nlevels);
gmx_ffclose(out);
sfree(axis);
for (i = 0; i < ndim / DIM; i++)
if (nframes - 1 < ndim)
{
end = nframes - 1;
- fprintf(stderr,
- "\nWARNING: there are fewer frames in your trajectory than there are\n");
+ fprintf(stderr, "\nWARNING: there are fewer frames in your trajectory than there are\n");
fprintf(stderr, "degrees of freedom in your system. Only generating the first\n");
fprintf(stderr, "%d out of %d eigenvectors and eigenvalues.\n", end, static_cast<int>(ndim));
}
WriteXref = eWXR_NOFIT;
}
- write_eigenvectors(eigvecfile, natoms, mat, TRUE, 1, end, WriteXref, x, bDiffMass1, xproj, bM,
- eigenvalues);
+ write_eigenvectors(
+ eigvecfile, natoms, mat, TRUE, 1, end, WriteXref, x, bDiffMass1, xproj, bM, eigenvalues);
out = gmx_ffopen(logfile, "w");
fprintf(out, "Working directory: %s\n\n", str);
- fprintf(out, "Read %d frames from %s (time %g to %g %s)\n", nframes, trxfile,
- output_env_conv_time(oenv, tstart), output_env_conv_time(oenv, tend),
+ fprintf(out,
+ "Read %d frames from %s (time %g to %g %s)\n",
+ nframes,
+ trxfile,
+ output_env_conv_time(oenv, tstart),
+ output_env_conv_time(oenv, tend),
output_env_get_time_unit(oenv).c_str());
if (bFit)
{
{
fprintf(out, "Fit is %smass weighted\n", bDiffMass1 ? "" : "non-");
}
- fprintf(out, "Diagonalized the %dx%d covariance matrix\n", static_cast<int>(ndim),
- static_cast<int>(ndim));
+ fprintf(out, "Diagonalized the %dx%d covariance matrix\n", static_cast<int>(ndim), static_cast<int>(ndim));
fprintf(out, "Trace of the covariance matrix before diagonalizing: %g\n", trace);
fprintf(out, "Trace of the covariance matrix after diagonalizing: %g\n\n", sum);
*
* Copyright (c) 2008,2009,2010,2011,2012 by the GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
-#define EPSI0 (EPSILON0 * E_CHARGE * E_CHARGE * AVOGADRO / (KILO * NANO)) /* EPSILON0 in SI units */
+constexpr double EPSI0 = (gmx::c_epsilon0 * gmx::c_electronCharge * gmx::c_electronCharge * gmx::c_avogadro
+ / (gmx::c_kilo * gmx::c_nano)); /* c_epsilon0 in SI units */
static void index_atom2mol(int* n, int* index, t_block* mols)
{
mj2 += iprod(mtrans[nfr], mtrans[nfr]);
md2 += iprod(mu[nfr], mu[nfr]);
- fprintf(fmj, "%.3f\t%8.5f\t%8.5f\t%8.5f\t%8.5f\t%8.5f\n", time[nfr], mtrans[nfr][XX],
- mtrans[nfr][YY], mtrans[nfr][ZZ], mj2 / refr, norm(mja_tmp) / refr);
- fprintf(fmd, "%.3f\t%8.5f\t%8.5f\t%8.5f\t%8.5f\t%8.5f\n", time[nfr], mu[nfr][XX],
- mu[nfr][YY], mu[nfr][ZZ], md2 / refr, norm(mdvec) / refr);
+ fprintf(fmj,
+ "%.3f\t%8.5f\t%8.5f\t%8.5f\t%8.5f\t%8.5f\n",
+ time[nfr],
+ mtrans[nfr][XX],
+ mtrans[nfr][YY],
+ mtrans[nfr][ZZ],
+ mj2 / refr,
+ norm(mja_tmp) / refr);
+ fprintf(fmd,
+ "%.3f\t%8.5f\t%8.5f\t%8.5f\t%8.5f\t%8.5f\n",
+ time[nfr],
+ mu[nfr][XX],
+ mu[nfr][YY],
+ mu[nfr][ZZ],
+ md2 / refr,
+ norm(mdvec) / refr);
nfr++;
volume_av /= refr;
prefactor = 1.0;
- prefactor /= 3.0 * EPSILON0 * volume_av * BOLTZ * temp;
+ prefactor /= 3.0 * gmx::c_epsilon0 * volume_av * gmx::c_boltz * temp;
- prefactorav = E_CHARGE * E_CHARGE;
- prefactorav /= volume_av * BOLTZMANN * temp * NANO * 6.0;
+ prefactorav = gmx::c_electronCharge * gmx::c_electronCharge;
+ prefactorav /= volume_av * gmx::c_boltzmann * temp * gmx::c_nano * 6.0;
fprintf(stderr, "Prefactor fit E-H: 1 / 6.0*V*k_B*T: %g\n", prefactorav);
printf("\n\nAverage translational dipole moment M_J [enm] after %d frames (|M|^2): %f %f %f "
"(%f)\n",
- nfr, mja_tmp[XX], mja_tmp[YY], mja_tmp[ZZ], mj2);
+ nfr,
+ mja_tmp[XX],
+ mja_tmp[YY],
+ mja_tmp[ZZ],
+ mj2);
printf("\n\nAverage molecular dipole moment M_D [enm] after %d frames (|M|^2): %f %f %f (%f)\n",
- nfr, mdvec[XX], mdvec[YY], mdvec[ZZ], md2);
+ nfr,
+ mdvec[XX],
+ mdvec[YY],
+ mdvec[ZZ],
+ md2);
if (v0 != nullptr)
{
{
printf("\nCalculating current autocorrelation ... \n");
- sgk = calc_cacf(outf, prefactorav / PICO, cacf, time, nvfr, vfr, ie, nshift);
+ sgk = calc_cacf(outf, prefactorav / gmx::c_pico, cacf, time, nvfr, vfr, ie, nshift);
if (ie > ii)
{
dk_f = calceps(prefactor, md2 - mdav2, mj2 - mj, mjd - mjdav, eps_rf, FALSE);
fprintf(stderr, "\n\nFluctuations:\n epsilon=%f\n\n", dk_f);
- fprintf(stderr, "\n deltaM_D , deltaM_J, deltaM_JD: (%f, %f, %f)\n", md2 - mdav2, mj2 - mj,
- mjd - mjdav);
+ fprintf(stderr, "\n deltaM_D , deltaM_J, deltaM_JD: (%f, %f, %f)\n", md2 - mdav2, mj2 - mj, mjd - mjdav);
fprintf(stderr, "\n********************************************\n");
if (bINT)
{
if (bACF && (ii < nvfr))
{
fprintf(stderr, "Integral and integrated fit to the current acf yields at t=%f:\n", time[vfr[ii]]);
- fprintf(stderr, "sigma=%8.3f (pure integral: %.3f)\n",
- sgk - malt * std::pow(time[vfr[ii]], sigma), sgk);
+ fprintf(stderr, "sigma=%8.3f (pure integral: %.3f)\n", sgk - malt * std::pow(time[vfr[ii]], sigma), sgk);
}
if (ei > bi)
/* At first the arguments will be parsed and the system information processed */
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
{
if (bACF)
{
- outf = xvgropen(opt2fn("-caf", NFILE, fnm), "Current autocorrelation function",
- output_env_get_xvgr_tlabel(oenv), "ACF (e nm/ps)\\S2", oenv);
+ outf = xvgropen(opt2fn("-caf", NFILE, fnm),
+ "Current autocorrelation function",
+ output_env_get_xvgr_tlabel(oenv),
+ "ACF (e nm/ps)\\S2",
+ oenv);
fprintf(outf, "# time\t acf\t average \t std.dev\n");
}
- fcur = xvgropen(opt2fn("-o", NFILE, fnm), "Current", output_env_get_xvgr_tlabel(oenv),
- "J(t) (e nm/ps)", oenv);
+ fcur = xvgropen(opt2fn("-o", NFILE, fnm),
+ "Current",
+ output_env_get_xvgr_tlabel(oenv),
+ "J(t) (e nm/ps)",
+ oenv);
fprintf(fcur, "# time\t Jx\t Jy \t J_z \n");
if (bINT)
{
mcor = xvgropen(opt2fn("-mc", NFILE, fnm),
"M\\sD\\N - current autocorrelation function",
output_env_get_xvgr_tlabel(oenv),
- "< M\\sD\\N (0)\\c7\\CJ(t) > (e nm/ps)\\S2", oenv);
+ "< M\\sD\\N (0)\\c7\\CJ(t) > (e nm/ps)\\S2",
+ oenv);
fprintf(mcor, "# time\t M_D(0) J(t) acf \t Integral acf\n");
}
}
- fmj = xvgropen(opt2fn("-mj", NFILE, fnm), "Averaged translational part of M",
- output_env_get_xvgr_tlabel(oenv), "< M\\sJ\\N > (enm)", oenv);
+ fmj = xvgropen(opt2fn("-mj", NFILE, fnm),
+ "Averaged translational part of M",
+ output_env_get_xvgr_tlabel(oenv),
+ "< M\\sJ\\N > (enm)",
+ oenv);
fprintf(fmj, "# time\t x\t y \t z \t average of M_J^2 \t std.dev\n");
- fmd = xvgropen(opt2fn("-md", NFILE, fnm), "Averaged rotational part of M",
- output_env_get_xvgr_tlabel(oenv), "< M\\sD\\N > (enm)", oenv);
+ fmd = xvgropen(opt2fn("-md", NFILE, fnm),
+ "Averaged rotational part of M",
+ output_env_get_xvgr_tlabel(oenv),
+ "< M\\sD\\N > (enm)",
+ oenv);
fprintf(fmd, "# time\t x\t y \t z \t average of M_D^2 \t std.dev\n");
fmjdsp = xvgropen(
- opt2fn("-dsp", NFILE, fnm), "MSD of the squared translational dipole moment M",
+ opt2fn("-dsp", NFILE, fnm),
+ "MSD of the squared translational dipole moment M",
output_env_get_xvgr_tlabel(oenv),
- "<|M\\sJ\\N(t)-M\\sJ\\N(0)|\\S2\\N > / 6.0*V*k\\sB\\N*T / Sm\\S-1\\Nps\\S-1\\N", oenv);
+ "<|M\\sJ\\N(t)-M\\sJ\\N(0)|\\S2\\N > / 6.0*V*k\\sB\\N*T / Sm\\S-1\\Nps\\S-1\\N",
+ oenv);
/* System information is read and prepared, dielectric() processes the frames
* and calculates the requested quantities */
- dielectric(fmj, fmd, outf, fcur, mcor, fmjdsp, bNoJump, bACF, bINT, pbcType, top, fr, temp, bfit, efit,
- bvit, evit, status, isize, nmols, nshift, index0, indexm, mass2, qmol, eps_rf, oenv);
+ dielectric(fmj,
+ fmd,
+ outf,
+ fcur,
+ mcor,
+ fmjdsp,
+ bNoJump,
+ bACF,
+ bINT,
+ pbcType,
+ top,
+ fr,
+ temp,
+ bfit,
+ efit,
+ bvit,
+ evit,
+ status,
+ isize,
+ nmols,
+ nshift,
+ index0,
+ indexm,
+ mass2,
+ qmol,
+ eps_rf,
+ oenv);
xvgrclose(fmj);
xvgrclose(fmd);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
i = index_center[k];
if (i >= atoms->nr)
{
- gmx_fatal(FARGS, "Index %d refers to atom %d, which is larger than natoms (%d).", k + 1,
- i + 1, atoms->nr);
+ gmx_fatal(FARGS,
+ "Index %d refers to atom %d, which is larger than natoms (%d).",
+ k + 1,
+ i + 1,
+ atoms->nr);
}
mm = atoms->atom[i].m;
tmass += mm;
/* now find the number of electrons. This is not efficient. */
found = static_cast<t_electron*>(
- bsearch(&sought, eltab, nr, sizeof(t_electron),
+ bsearch(&sought,
+ eltab,
+ nr,
+ sizeof(t_electron),
reinterpret_cast<int (*)(const void*, const void*)>(compare)));
if (found == nullptr)
{
- fprintf(stderr, "Couldn't find %s. Add it to the .dat file\n",
+ fprintf(stderr,
+ "Couldn't find %s. Add it to the .dat file\n",
*(top->atoms.atomname[index[n][i]]));
}
else
}
if (dens_opt[0][0] == 'm')
{
- fprintf(den, " %12g", ddd * AMU / (NANO * NANO * NANO));
+ fprintf(den, " %12g", ddd * gmx::c_amu / (gmx::c_nano * gmx::c_nano * gmx::c_nano));
}
else
{
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, asize(bugs), bugs, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
nr_electrons = get_electrons(&el_tab, ftp2fn(efDAT, NFILE, fnm));
fprintf(stderr, "Read %d atomtypes from datafile\n", nr_electrons);
- calc_electron_density(ftp2fn(efTRX, NFILE, fnm), index, ngx, &density, &nslices, top,
- pbcType, axis, ngrps, &slWidth, el_tab, nr_electrons, bCenter,
- index_center, ncenter, bRelative, oenv);
+ calc_electron_density(ftp2fn(efTRX, NFILE, fnm),
+ index,
+ ngx,
+ &density,
+ &nslices,
+ top,
+ pbcType,
+ axis,
+ ngrps,
+ &slWidth,
+ el_tab,
+ nr_electrons,
+ bCenter,
+ index_center,
+ ncenter,
+ bRelative,
+ oenv);
}
else
{
- calc_density(ftp2fn(efTRX, NFILE, fnm), index, ngx, &density, &nslices, top, pbcType, axis,
- ngrps, &slWidth, bCenter, index_center, ncenter, bRelative, oenv, dens_opt);
- }
-
- plot_density(density, opt2fn("-o", NFILE, fnm), nslices, ngrps, grpname, slWidth, dens_opt,
- bCenter, bRelative, bSymmetrize, oenv);
+ calc_density(ftp2fn(efTRX, NFILE, fnm),
+ index,
+ ngx,
+ &density,
+ &nslices,
+ top,
+ pbcType,
+ axis,
+ ngrps,
+ &slWidth,
+ bCenter,
+ index_center,
+ ncenter,
+ bRelative,
+ oenv,
+ dens_opt);
+ }
+
+ plot_density(
+ density, opt2fn("-o", NFILE, fnm), nslices, ngrps, grpname, slWidth, dens_opt, bCenter, bRelative, bSymmetrize, oenv);
do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy"); /* view xvgr file */
return 0;
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/trxio.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxana/gstat.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
npargs = asize(pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, npargs, pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, npargs, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
else
{
fp = gmx_ffopen(ftp2fn(efXPM, NFILE, fnm), "w");
- write_xpm(fp, MAT_SPATIAL_X | MAT_SPATIAL_Y, buf, unit, bRadial ? "axial (nm)" : label[c1],
- bRadial ? "r (nm)" : label[c2], n1, n2, tickx, tickz, grid, dmin, maxgrid, rlo,
- rhi, &nlev);
+ write_xpm(fp,
+ MAT_SPATIAL_X | MAT_SPATIAL_Y,
+ buf,
+ unit,
+ bRadial ? "axial (nm)" : label[c1],
+ bRadial ? "r (nm)" : label[c2],
+ n1,
+ n2,
+ tickx,
+ tickz,
+ grid,
+ dmin,
+ maxgrid,
+ rlo,
+ rhi,
+ &nlev);
gmx_ffclose(fp);
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*yslices = 1;
}
}
- fprintf(stderr, "\nDividing the box in %5d x %5d x %5d slices with binw %f along axis %d\n",
- *xslices, *yslices, *zslices, bw, axis);
+ fprintf(stderr,
+ "\nDividing the box in %5d x %5d x %5d slices with binw %f along axis %d\n",
+ *xslices,
+ *yslices,
+ *zslices,
+ bw,
+ axis);
/****Start trajectory processing***/
(*Densdevel)[*tblock] = Densslice;
}
- dscale = (*xslices) * (*yslices) * (*zslices) * AMU
- / (box[ax1][ax1] * box[ax2][ax2] * box[axis][axis] * nsttblock * (NANO * NANO * NANO));
+ dscale = (*xslices) * (*yslices) * (*zslices) * gmx::c_amu
+ / (box[ax1][ax1] * box[ax2][ax2] * box[axis][axis] * nsttblock
+ * (gmx::c_nano * gmx::c_nano * gmx::c_nano));
if (bCenter)
{
if (debug)
{
- xvg = xvgropen("DensprofileonZ.xvg", "Averaged Densityprofile on Z", "z[nm]",
- "Density[kg/m^3]", oenv);
+ xvg = xvgropen(
+ "DensprofileonZ.xvg", "Averaged Densityprofile on Z", "z[nm]", "Density[kg/m^3]", oenv);
for (k = 0; k < zslices; k++)
{
fprintf(xvg, "%4f.3 %8f.4\n", k * binwidth, zDensavg[k]);
/*Fit average density in z over whole trajectory to obtain tentative fit-parameters in fit1 and fit2*/
/*Fit 1st half of box*/
- do_lmfit(zslices, zDensavg, sigma1, binwidth, nullptr, startpoint, splitpoint, oenv, FALSE,
- effnERF, beginfit1, 8, nullptr);
+ do_lmfit(zslices, zDensavg, sigma1, binwidth, nullptr, startpoint, splitpoint, oenv, FALSE, effnERF, beginfit1, 8, nullptr);
/*Fit 2nd half of box*/
- do_lmfit(zslices, zDensavg, sigma2, binwidth, nullptr, splitpoint, endpoint, oenv, FALSE,
- effnERF, beginfit2, 8, nullptr);
+ do_lmfit(zslices, zDensavg, sigma2, binwidth, nullptr, splitpoint, endpoint, oenv, FALSE, effnERF, beginfit2, 8, nullptr);
/*Initialise the const arrays for storing the average fit parameters*/
avgfit1 = beginfit1;
fit2[k] = avgfit2[k];
}
/*Now fit and store in structures in row-major order int[n][i][j]*/
- do_lmfit(zslices, Densmap[n][i][j], sigma1, binwidth, nullptr, startpoint,
- splitpoint, oenv, FALSE, effnERF, fit1, 0, nullptr);
+ do_lmfit(zslices,
+ Densmap[n][i][j],
+ sigma1,
+ binwidth,
+ nullptr,
+ startpoint,
+ splitpoint,
+ oenv,
+ FALSE,
+ effnERF,
+ fit1,
+ 0,
+ nullptr);
int1[n][j + (yslices * i)]->Z = fit1[2];
int1[n][j + (yslices * i)]->t = fit1[3];
- do_lmfit(zslices, Densmap[n][i][j], sigma2, binwidth, nullptr, splitpoint,
- endpoint, oenv, FALSE, effnERF, fit2, 0, nullptr);
+ do_lmfit(zslices,
+ Densmap[n][i][j],
+ sigma2,
+ binwidth,
+ nullptr,
+ splitpoint,
+ endpoint,
+ oenv,
+ FALSE,
+ effnERF,
+ fit2,
+ 0,
+ nullptr);
int2[n][j + (yslices * i)]->Z = fit2[2];
int2[n][j + (yslices * i)]->t = fit2[3];
}
}
}
- write_xpm(xpmfile1, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks,
- profile1, min1, max1, lo, hi, &maplevels);
- write_xpm(xpmfile2, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks,
- profile2, min2, max2, lo, hi, &maplevels);
+ write_xpm(xpmfile1, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks, profile1, min1, max1, lo, hi, &maplevels);
+ write_xpm(xpmfile2, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks, profile2, min2, max2, lo, hi, &maplevels);
}
gmx_ffclose(xpmfile1);
{
for (j = 0; j < ybins; j++)
{
- fprintf(raw1, "%i %i %8.5f %6.4f\n", i, j, (int1[n][j + ybins * i])->Z,
+ fprintf(raw1,
+ "%i %i %8.5f %6.4f\n",
+ i,
+ j,
+ (int1[n][j + ybins * i])->Z,
(int1[n][j + ybins * i])->t);
- fprintf(raw2, "%i %i %8.5f %6.4f\n", i, j, (int2[n][j + ybins * i])->Z,
+ fprintf(raw2,
+ "%i %i %8.5f %6.4f\n",
+ i,
+ j,
+ (int2[n][j + ybins * i])->Z,
(int2[n][j + ybins * i])->t);
}
}
{ efTPR, "-s", nullptr, ffREAD }, /* this is for the topology */
{ efTRX, "-f", nullptr, ffREAD }, /* and this for the trajectory */
{ efNDX, "-n", nullptr, ffREAD }, /* this is to select groups */
- { efDAT, "-o", "Density4D",
- ffOPTWR }, /* This is for outputting the entire 4D densityfield in binary format */
- { efOUT, "-or", nullptr,
- ffOPTWRMULT }, /* This is for writing out the entire information in the t_interf arrays */
- { efXPM, "-og", "interface",
- ffOPTWRMULT }, /* This is for writing out the interface meshes - one xpm-file per tblock*/
+ { efDAT, "-o", "Density4D", ffOPTWR }, /* This is for outputting the entire 4D densityfield in binary format */
+ { efOUT, "-or", nullptr, ffOPTWRMULT }, /* This is for writing out the entire information in the t_interf arrays */
+ { efXPM, "-og", "interface", ffOPTWRMULT }, /* This is for writing out the interface meshes - one xpm-file per tblock*/
{ efOUT, "-Spect", "intfspect", ffOPTWRMULT }, /* This is for the trajectory averaged Fourier-spectra*/
};
/* This is the routine responsible for adding default options,
* calling the X/motif interface, etc. */
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
get_index(&top->atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, ngx, index, grpname);
- density_in_time(ftp2fn(efTRX, NFILE, fnm), index, ngx, binw, binwz, nsttblock, &Densmap,
- &xslices, &yslices, &zslices, &tblock, top, pbcType, axis, bCenter, b1d, oenv);
+ density_in_time(ftp2fn(efTRX, NFILE, fnm),
+ index,
+ ngx,
+ binw,
+ binwz,
+ nsttblock,
+ &Densmap,
+ &xslices,
+ &yslices,
+ &zslices,
+ &tblock,
+ top,
+ pbcType,
+ axis,
+ bCenter,
+ b1d,
+ oenv);
if (ftorder > 0)
{
outputfield(opt2fn("-o", NFILE, fnm), Densmap, xslices, yslices, zslices, tblock);
}
- interfaces_txy(Densmap, xslices, yslices, zslices, tblock, binwz, eMeth, dens1, dens2, &surf1,
- &surf2, oenv);
+ interfaces_txy(
+ Densmap, xslices, yslices, zslices, tblock, binwz, eMeth, dens1, dens2, &surf1, &surf2, oenv);
if (bGraph)
{
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxana/gstat.h"
#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/fatalerror.h"
fprintf(fp, "%10.5e %10.5e %10.5e\n", nu, kw.re, kw.im);
fprintf(cp, "%10.5e %10.5e\n", kw.re, kw.im);
}
- printf("MAXEPS = %10.5e at frequency %10.5e GHz (tauD = %8.1f ps)\n", maxeps, numax,
+ printf("MAXEPS = %10.5e at frequency %10.5e GHz (tauD = %8.1f ps)\n",
+ maxeps,
+ numax,
1000 / (2 * M_PI * numax));
xvgrclose(fp);
xvgrclose(cp);
{ "-nsmooth", FALSE, etINT, { &nsmooth }, "Number of points for smoothing" }
};
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
}
printf("DATA INTEGRAL: %5.1f, tauD(old) = %5.1f ps, "
"tau_slope = %5.1f, tau_slope,D = %5.1f ps\n",
- integral, integral * rffac, fitparms[0], fitparms[0] * rffac);
+ integral,
+ integral * rffac,
+ fitparms[0],
+ fitparms[0] * rffac);
- printf("tau_D from tau1 = %8.3g , eps(Infty) = %8.3f\n", fitparms[0] * (1 + fitparms[1] * lambda),
+ printf("tau_D from tau1 = %8.3g , eps(Infty) = %8.3f\n",
+ fitparms[0] * (1 + fitparms[1] * lambda),
1 + ((1 - fitparms[1]) * (eps0 - 1)) / (1 + fitparms[1] * lambda));
fitintegral = numerical_deriv(nx, y[0], y[1], y[3], y[4], y[5], tendInt, nsmooth);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
-#define e2d(x) ENM2DEBYE*(x)
-#define EANG2CM (E_CHARGE * 1.0e-10) /* e Angstrom to Coulomb meter */
-#define CM2D (SPEED_OF_LIGHT * 1.0e+24) /* Coulomb meter to Debye */
+#define e2d(x) gmx::c_enm2Debye*(x)
+constexpr double EANG2CM = gmx::c_electronCharge * 1.0e-10; /* e Angstrom to Coulomb meter */
+constexpr double CM2D = gmx::c_speedOfLight * 1.0e+24; /* Coulomb meter to Debye */
typedef struct
{
copy_rvec(xcm[grp1][j], xk);
rvec_add(xj, mu[gi], xi);
rvec_add(xk, mu[gj], xl);
- phi = dih_angle(xi, xj, xk, xl, &pbc, r_ij, r_kj, r_kl, mm, nn, /* out */
- &t1, &t2, &t3);
+ phi = dih_angle(xi,
+ xj,
+ xk,
+ xl,
+ &pbc,
+ r_ij,
+ r_kj,
+ r_kl,
+ mm,
+ nn, /* out */
+ &t1,
+ &t2,
+ &t3);
cosa = std::cos(phi);
}
else
fprintf(debug ? debug : stderr,
"mu[%d] = %5.2f %5.2f %5.2f |mi| = %5.2f, mu[%d] = %5.2f %5.2f %5.2f "
"|mj| = %5.2f rr = %5.2f cosa = %5.2f\n",
- gi, mu[gi][XX], mu[gi][YY], mu[gi][ZZ], norm(mu[gi]), gj, mu[gj][XX],
- mu[gj][YY], mu[gj][ZZ], norm(mu[gj]), rr, cosa);
+ gi,
+ mu[gi][XX],
+ mu[gi][YY],
+ mu[gi][ZZ],
+ norm(mu[gi]),
+ gj,
+ mu[gj][XX],
+ mu[gj][YY],
+ mu[gj][ZZ],
+ norm(mu[gj]),
+ rr,
+ cosa);
}
add2gkr(gb, rr, cosa, phi);
/*2.0*j/(gb->ny-1.0)-1.0;*/
}
out = gmx_ffopen(cmap, "w");
- write_xpm(out, 0, "Dipole Orientation Distribution", "Fraction", "r (nm)", gb->bPhi ? "Phi" : "Alpha",
- gb->nx, gb->ny, xaxis, yaxis, gb->cmap, 0, hi, rlo, rhi, nlevels);
+ write_xpm(out,
+ 0,
+ "Dipole Orientation Distribution",
+ "Fraction",
+ "r (nm)",
+ gb->bPhi ? "Phi" : "Alpha",
+ gb->nx,
+ gb->ny,
+ xaxis,
+ yaxis,
+ gb->cmap,
+ 0,
+ hi,
+ rlo,
+ rhi,
+ nlevels);
gmx_ffclose(out);
sfree(xaxis);
sfree(yaxis);
{
cosav = 0;
}
- ener = -0.5 * cosav * ONE_4PI_EPS0 / (x1 * x1 * x1);
+ ener = -0.5 * cosav * gmx::c_one4PiEps0 / (x1 * x1 * x1);
fprintf(fp, "%10.5e %12.5e %12.5e %12.5e %12.5e %12.5e\n", x1, Gkr, cosav, hOO, gOO, ener);
fprintf(stderr,
"Something strange: expected %d entries in energy file at step %s\n(time %g) but "
"found %d entries\n",
- nre, gmx_step_str(fr->step, buf), fr->t, fr->nre);
+ nre,
+ gmx_step_str(fr->step, buf),
+ fr->t,
+ fr->nre);
}
if (bCont)
double eps_0 = 8.854187817e-12; /* epsilon_0 in C^2 J^-1 m^-1 */
double fac = 1.112650021e-59; /* converts Debye^2 to C^2 m^2 */
- A = M_diff * fac / (3 * eps_0 * volume * NANO * NANO * NANO * BOLTZMANN * temp);
+ A = M_diff * fac
+ / (3 * eps_0 * volume * gmx::c_nano * gmx::c_nano * gmx::c_nano * gmx::c_boltzmann * temp);
if (epsRF == 0.0)
{
char buf[STRLEN];
int i;
real mutot;
- const char* leg_dim[4] = { "\\f{12}m\\f{4}\\sX\\N", "\\f{12}m\\f{4}\\sY\\N",
- "\\f{12}m\\f{4}\\sZ\\N", "\\f{12}m\\f{4}\\stot\\N" };
+ const char* leg_dim[4] = { "\\f{12}m\\f{4}\\sX\\N",
+ "\\f{12}m\\f{4}\\sY\\N",
+ "\\f{12}m\\f{4}\\sZ\\N",
+ "\\f{12}m\\f{4}\\stot\\N" };
sprintf(buf, "Box-%c (nm)", 'X' + idim);
fp = xvgropen(fn, "Average dipole moment per slab", buf, "\\f{12}m\\f{4} (D)", oenv);
for (i = 0; (i < nslice); i++)
{
mutot = norm(slab_dipole[i]) / nframes;
- fprintf(fp, "%10.3f %10.3f %10.3f %10.3f %10.3f\n",
- ((i + 0.5) * box[idim][idim]) / nslice, slab_dipole[i][XX] / nframes,
- slab_dipole[i][YY] / nframes, slab_dipole[i][ZZ] / nframes, mutot);
+ fprintf(fp,
+ "%10.3f %10.3f %10.3f %10.3f %10.3f\n",
+ ((i + 0.5) * box[idim][idim]) / nslice,
+ slab_dipole[i][XX] / nframes,
+ slab_dipole[i][YY] / nframes,
+ slab_dipole[i][ZZ] / nframes,
+ mutot);
}
xvgrclose(fp);
do_view(oenv, fn, "-autoscale xy -nxy");
#define NLEGMTOT asize(leg_mtot)
const char* leg_eps[] = { "epsilon", "G\\sk", "g\\sk" };
#define NLEGEPS asize(leg_eps)
- const char* leg_aver[] = { "< |M|\\S2\\N >", "< |M| >\\S2\\N", "< |M|\\S2\\N > - < |M| >\\S2\\N",
+ const char* leg_aver[] = { "< |M|\\S2\\N >",
+ "< |M| >\\S2\\N",
+ "< |M|\\S2\\N > - < |M| >\\S2\\N",
"< |M| >\\S2\\N / < |M|\\S2\\N >" };
#define NLEGAVER asize(leg_aver)
- const char* leg_cosaver[] = { "\\f{4}<|cos\\f{12}q\\f{4}\\sij\\N|>", "RMSD cos",
+ const char* leg_cosaver[] = { "\\f{4}<|cos\\f{12}q\\f{4}\\sij\\N|>",
+ "RMSD cos",
"\\f{4}<|cos\\f{12}q\\f{4}\\siX\\N|>",
"\\f{4}<|cos\\f{12}q\\f{4}\\siY\\N|>",
"\\f{4}<|cos\\f{12}q\\f{4}\\siZ\\N|>" };
mulsq = gmx_stats_init();
/* Open all the files */
- outmtot = xvgropen(out_mtot, "Total dipole moment of the simulation box vs. time", "Time (ps)",
- "Total Dipole Moment (Debye)", oenv);
+ outmtot = xvgropen(out_mtot,
+ "Total dipole moment of the simulation box vs. time",
+ "Time (ps)",
+ "Total Dipole Moment (Debye)",
+ oenv);
outeps = xvgropen(out_eps, "Epsilon and Kirkwood factors", "Time (ps)", "", oenv);
outaver = xvgropen(out_aver, "Total dipole moment", "Time (ps)", "D", oenv);
if (bSlab)
}
if (cosaver)
{
- caver = xvgropen(cosaver, bPairs ? "Average pair orientation" : "Average absolute dipole orientation",
- "Time (ps)", "", oenv);
+ caver = xvgropen(cosaver,
+ bPairs ? "Average pair orientation" : "Average absolute dipole orientation",
+ "Time (ps)",
+ "",
+ oenv);
xvgr_legend(caver, NLEGCOSAVER, bPairs ? leg_cosaver : &(leg_cosaver[1]), oenv);
}
{
fprintf(dip3d,
"set arrow %d from %f, %f, %f to %f, %f, %f lt %d # %d %d\n",
- i + 1, x[ind0][XX], x[ind0][YY], x[ind0][ZZ],
- x[ind0][XX] + dipole[i][XX] / 25, x[ind0][YY] + dipole[i][YY] / 25,
- x[ind0][ZZ] + dipole[i][ZZ] / 25, ncolour, ind0, i);
+ i + 1,
+ x[ind0][XX],
+ x[ind0][YY],
+ x[ind0][ZZ],
+ x[ind0][XX] + dipole[i][XX] / 25,
+ x[ind0][YY] + dipole[i][YY] / 25,
+ x[ind0][ZZ] + dipole[i][ZZ] / 25,
+ ncolour,
+ ind0,
+ i);
}
}
} /* End loop of all molecules in frame */
+ gmx::square(dipaxis[ZZ] - 0.5));
if (bPairs)
{
- fprintf(caver, "%10.3e %10.3e %10.3e %10.3e %10.3e %10.3e\n", t, dd, rms_cos,
- dipaxis[XX], dipaxis[YY], dipaxis[ZZ]);
+ fprintf(caver,
+ "%10.3e %10.3e %10.3e %10.3e %10.3e %10.3e\n",
+ t,
+ dd,
+ rms_cos,
+ dipaxis[XX],
+ dipaxis[YY],
+ dipaxis[ZZ]);
}
else
{
- fprintf(caver, "%10.3e %10.3e %10.3e %10.3e %10.3e\n", t, rms_cos, dipaxis[XX],
- dipaxis[YY], dipaxis[ZZ]);
+ fprintf(caver,
+ "%10.3e %10.3e %10.3e %10.3e %10.3e\n",
+ t,
+ rms_cos,
+ dipaxis[XX],
+ dipaxis[YY],
+ dipaxis[ZZ]);
}
}
*/
if ((skip == 0) || ((teller % skip) == 0))
{
- fprintf(outmtot, "%10g %12.8e %12.8e %12.8e %12.8e\n", t, M_av[XX], M_av[YY], M_av[ZZ],
+ fprintf(outmtot,
+ "%10g %12.8e %12.8e %12.8e %12.8e\n",
+ t,
+ M_av[XX],
+ M_av[YY],
+ M_av[ZZ],
std::sqrt(M_av2[XX] + M_av2[YY] + M_av2[ZZ]));
}
* the two. Here M is sum mu_i. Further write the finite system
* Kirkwood G factor and epsilon.
*/
- fprintf(outaver, "%10g %10.3e %10.3e %10.3e %10.3e\n", t, M2_ave, M_ave2, M_diff,
- M_ave2 / M2_ave);
+ fprintf(outaver, "%10g %10.3e %10.3e %10.3e %10.3e\n", t, M2_ave, M_ave2, M_diff, M_ave2 / M2_ave);
if (fnadip)
{
if (bTotal)
{
- do_autocorr(corf, oenv, "Autocorrelation Function of Total Dipole", teller, 1,
- muall, dt, mode, TRUE);
+ do_autocorr(
+ corf, oenv, "Autocorrelation Function of Total Dipole", teller, 1, muall, dt, mode, TRUE);
}
else
{
- do_autocorr(corf, oenv, "Dipole Autocorrelation Function", teller, gnx_tot, muall,
- dt, mode, std::strcmp(corrtype, "molsep") != 0);
+ do_autocorr(corf,
+ oenv,
+ "Dipole Autocorrelation Function",
+ teller,
+ gnx_tot,
+ muall,
+ dt,
+ mode,
+ std::strcmp(corrtype, "molsep") != 0);
}
}
}
}
if (m == mols->nr)
{
- gmx_fatal(FARGS, "index[%d]=%d does not correspond to the first atom of a molecule",
- i + 1, index[i] + 1);
+ gmx_fatal(FARGS,
+ "index[%d]=%d does not correspond to the first atom of a molecule",
+ i + 1,
+ index[i] + 1);
}
for (j = mols->index[m]; j < mols->index[m + 1]; j++)
{
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, npargs, ppa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
{
sfree(ppa);
return 0;
}
nFF[0] = nFA;
nFF[1] = nFB;
- do_dip(top, pbcType, det(box), ftp2fn(efTRX, NFILE, fnm), opt2fn("-o", NFILE, fnm),
- opt2fn("-eps", NFILE, fnm), opt2fn("-a", NFILE, fnm), opt2fn("-d", NFILE, fnm),
- opt2fn_null("-cos", NFILE, fnm), opt2fn_null("-dip3d", NFILE, fnm),
- opt2fn_null("-adip", NFILE, fnm), bPairs, corrtype[0], opt2fn("-c", NFILE, fnm), bGkr,
- opt2fn("-g", NFILE, fnm), bPhi, &nlevels, ndegrees, ncos, opt2fn("-cmap", NFILE, fnm),
- rcmax, bQuad, bMU, opt2fn("-en", NFILE, fnm), gnx, grpindex, mu_max, mu_aver, epsilonRF,
- temp, nFF, skip, bSlab, nslices, axtitle, opt2fn("-slab", NFILE, fnm), oenv);
+ do_dip(top,
+ pbcType,
+ det(box),
+ ftp2fn(efTRX, NFILE, fnm),
+ opt2fn("-o", NFILE, fnm),
+ opt2fn("-eps", NFILE, fnm),
+ opt2fn("-a", NFILE, fnm),
+ opt2fn("-d", NFILE, fnm),
+ opt2fn_null("-cos", NFILE, fnm),
+ opt2fn_null("-dip3d", NFILE, fnm),
+ opt2fn_null("-adip", NFILE, fnm),
+ bPairs,
+ corrtype[0],
+ opt2fn("-c", NFILE, fnm),
+ bGkr,
+ opt2fn("-g", NFILE, fnm),
+ bPhi,
+ &nlevels,
+ ndegrees,
+ ncos,
+ opt2fn("-cmap", NFILE, fnm),
+ rcmax,
+ bQuad,
+ bMU,
+ opt2fn("-en", NFILE, fnm),
+ gnx,
+ grpindex,
+ mu_max,
+ mu_aver,
+ epsilonRF,
+ temp,
+ nFF,
+ skip,
+ bSlab,
+ nslices,
+ axtitle,
+ opt2fn("-slab", NFILE, fnm),
+ oenv);
do_view(oenv, opt2fn("-o", NFILE, fnm), "-autoscale xy -nxy");
do_view(oenv, opt2fn("-eps", NFILE, fnm), "-autoscale xy -nxy");
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
real v;
} t_toppop;
-static t_toppop* top = nullptr;
-static int ntop = 0;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static t_toppop* top = nullptr;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static int ntop = 0;
typedef struct
{
gmx_fatal(FARGS,
"Label mismatch in distance restrains. Label for restraint %d is %d, "
"expected it to be either %d or %d",
- i / nat, label, label_old, label_old + 1);
+ i / nat,
+ label,
+ label_old,
+ label_old + 1);
}
}
- // Set up t_fcdata, only needed for calling ta_disres()
- t_fcdata fcd;
- fcd.disres = disresdata;
-
// Get offset for label index
label_old = forceparams[forceatoms[0]].disres.label;
for (i = 0; (i < disres.size());)
dr[clust_id].aver_3[ndr] += drt;
dr[clust_id].aver_6[ndr] += disresdata->Rt_6[label];
- snew(fshift, SHIFTS);
- ta_disres(n, &forceatoms[i], forceparams.data(), x, f, fshift, pbc, lam, &dvdl, nullptr,
- &fcd, nullptr);
+ snew(fshift, gmx::c_numShiftVectors);
+ ta_disres(n, &forceatoms[i], forceparams.data(), x, f, fshift, pbc, lam, &dvdl, {}, nullptr, disresdata, nullptr, nullptr);
sfree(fshift);
viol = disresdata->sumviol;
{
break;
}
- fprintf(log, "%6d%5s%8.3f%8.3f%8.3f%8.3f%8.3f%8.3f%8.3f\n", drs[i].label,
- yesno_names[drs[i].bCore], drs[i].up1, drs[i].r, drs[i].rT3, drs[i].rT6,
- drs[i].viol, drs[i].violT3, drs[i].violT6);
+ fprintf(log,
+ "%6d%5s%8.3f%8.3f%8.3f%8.3f%8.3f%8.3f%8.3f\n",
+ drs[i].label,
+ booleanValueToString(drs[i].bCore),
+ drs[i].up1,
+ drs[i].r,
+ drs[i].rT3,
+ drs[i].rT6,
+ drs[i].viol,
+ drs[i].violT3,
+ drs[i].violT6);
}
}
dump_viol(log, dd.nres, drs, FALSE);
fprintf(log, "+++ Sorted by linear averaged violations: +++\n");
- std::sort(drs, drs + dd.nres,
- [](const t_dr_stats& a, const t_dr_stats& b) { return a.viol > b.viol; }); // Reverse sort
+ std::sort(drs, drs + dd.nres, [](const t_dr_stats& a, const t_dr_stats& b) {
+ return a.viol > b.viol;
+ }); // Reverse sort
dump_viol(log, dd.nres, drs, TRUE);
dump_dump(log, dd.nres, drs);
gmx_fatal(FARGS,
"Inconsistency in cluster %s.\n"
"Found %d frames in trajectory rather than the expected %d\n",
- clust_name[k], dr[k].nframes, clust->index[k + 1] - clust->index[k]);
+ clust_name[k],
+ dr[k].nframes,
+ clust->index[k + 1] - clust->index[k]);
}
if (!clust_name[k])
{
{
mmm++;
}
- fprintf(fp, "%-10s%6d%8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n", clust_name[k],
- dr[k].nframes, sumV, maxV, sumVT3, maxVT3, sumVT6, maxVT6);
+ fprintf(fp,
+ "%-10s%6d%8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n",
+ clust_name[k],
+ dr[k].nframes,
+ sumV,
+ maxV,
+ sumVT3,
+ maxVT3,
+ sumVT6,
+ maxVT6);
}
fflush(fp);
sfree(drs);
{
printf("Warning: the maxdr that you have specified (%g) is smaller than\nthe largest "
"value in your simulation (%g)\n",
- max_dr, hi);
+ max_dr,
+ hi);
}
hi = max_dr;
}
printf("Highest level in the matrix will be %g\n", hi);
fp = gmx_ffopen(fn, "w");
- write_xpm(fp, 0, "Distance Violations", "<V> (nm)", "Residue", "Residue", n_res, n_res, t_res,
- t_res, matrix, 0, hi, rlo, rhi, &nlevels);
+ write_xpm(fp,
+ 0,
+ "Distance Violations",
+ "<V> (nm)",
+ "Residue",
+ "Residue",
+ n_res,
+ n_res,
+ t_res,
+ t_res,
+ matrix,
+ 0,
+ hi,
+ rlo,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
}
{ efNDX, "-c", "clust", ffOPTRD }, { efXPM, "-x", "matrix", ffOPTWR } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
}
gmx_localtop_t top(topInfo.mtop()->ffparams);
- gmx_mtop_generate_local_top(*topInfo.mtop(), &top, ir->efep != efepNO);
+ gmx_mtop_generate_local_top(*topInfo.mtop(), &top, ir->efep != FreeEnergyPerturbationType::No);
const InteractionDefinitions& idef = top.idef;
pbc_null = nullptr;
ir->dr_tau = 0.0;
t_disresdata disresdata;
- init_disres(fplog, topInfo.mtop(), ir, DisResRunMode::AnalysisTool, DDRole::Master,
- NumRanks::Single, MPI_COMM_NULL, nullptr, &disresdata, nullptr, FALSE);
+ init_disres(fplog,
+ *topInfo.mtop(),
+ ir,
+ DisResRunMode::AnalysisTool,
+ DDRole::Master,
+ NumRanks::Single,
+ MPI_COMM_NULL,
+ nullptr,
+ &disresdata,
+ nullptr,
+ FALSE);
int natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
snew(f, 5 * natoms);
}
auto mdAtoms = gmx::makeMDAtoms(fplog, *topInfo.mtop(), *ir, false);
- atoms2md(topInfo.mtop(), ir, -1, {}, ntopatoms, mdAtoms.get());
+ atoms2md(*topInfo.mtop(), *ir, -1, {}, ntopatoms, mdAtoms.get());
update_mdatoms(mdAtoms->mdatoms(), ir->fepvals->init_lambda);
if (ir->pbcType != PbcType::No)
{
}
my_clust = clust->inv_clust[j];
range_check(my_clust, 0, clust->clust->nr);
- check_viol(fplog, idef.il[F_DISRES], idef.iparams, x, f, pbc_null, dr_clust, my_clust,
- isize, index, vvindex, &disresdata);
+ check_viol(
+ fplog, idef.il[F_DISRES], idef.iparams, x, f, pbc_null, dr_clust, my_clust, isize, index, vvindex, &disresdata);
}
else
{
- check_viol(fplog, idef.il[F_DISRES], idef.iparams, x, f, pbc_null, &dr, 0, isize, index,
- vvindex, &disresdata);
+ check_viol(fplog, idef.il[F_DISRES], idef.iparams, x, f, pbc_null, &dr, 0, isize, index, vvindex, &disresdata);
}
if (bPDB)
{
if (clust)
{
- dump_clust_stats(fplog, disresdata, idef.il[F_DISRES], idef.iparams, clust->clust, dr_clust,
- clust->grpname, isize, index);
+ dump_clust_stats(
+ fplog, disresdata, idef.il[F_DISRES], idef.iparams, clust->clust, dr_clust, clust->grpname, isize, index);
}
else
{
- dump_stats(fplog, j, disresdata, idef.il[F_DISRES], idef.iparams, &dr, isize, index,
- bPDB ? atoms.get() : nullptr);
+ dump_stats(fplog, j, disresdata, idef.il[F_DISRES], idef.iparams, &dr, isize, index, bPDB ? atoms.get() : nullptr);
if (bPDB)
{
- write_sto_conf(opt2fn("-q", NFILE, fnm), "Coloured by average violation in Angstrom",
- atoms.get(), xav, nullptr, ir->pbcType, box);
+ write_sto_conf(opt2fn("-q", NFILE, fnm),
+ "Coloured by average violation in Angstrom",
+ atoms.get(),
+ xav,
+ nullptr,
+ ir->pbcType,
+ box);
}
- dump_disre_matrix(opt2fn_null("-x", NFILE, fnm), &dr, disresdata.nres, j, idef,
- topInfo.mtop(), max_dr, nlevels, bThird);
+ dump_disre_matrix(
+ opt2fn_null("-x", NFILE, fnm), &dr, disresdata.nres, j, idef, topInfo.mtop(), max_dr, nlevels, bThird);
xvgrclose(out);
xvgrclose(aver);
xvgrclose(numv);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#if HAVE_PIPES || GMX_NATIVE_WINDOWS
sprintf(dssp, "%s -i %s %s", strings.dptr.c_str(), strings.pdbfile.c_str(), redirectionString.c_str());
#else
- sprintf(dssp, "%s -i %s -o %s > %s %s", strings.dptr.c_str(), strings.pdbfile.c_str(),
- strings.tmpfile.c_str(), NULL_DEVICE, redirectionString.c_str());
+ sprintf(dssp,
+ "%s -i %s -o %s > %s %s",
+ strings.dptr.c_str(),
+ strings.pdbfile.c_str(),
+ strings.tmpfile.c_str(),
+ NULL_DEVICE,
+ redirectionString.c_str());
#endif
}
int average_area[],
const gmx_output_env_t* oenv)
{
- static gmx_bool bFirst = TRUE;
- static char* ssbuf;
- char buf[STRLEN + 1];
- char SSTP;
- int nr, iacc, nresidues;
- int naccf, naccb; /* Count hydrophobic and hydrophilic residues */
- real iaccf, iaccb;
+ static gmx_bool bFirst = TRUE;
+ static std::string ssbuf;
+ char buf[STRLEN + 1];
+ char SSTP;
+ int nr, iacc, nresidues;
+ int naccf, naccb; /* Count hydrophobic and hydrophilic residues */
+ real iaccf, iaccb;
/* Skip header */
* we allocate 2*nres-1, since for each chain there is a
* separating line in the temp file. (At most each residue
* could have been defined as a separate chain.) */
- snew(ssbuf, 2 * nres - 1);
+ ssbuf.resize(2 * nres - 1);
}
iaccb = iaccf = 0;
{
if (nullptr != acc)
{
- fprintf(stderr, "%d residues were classified as hydrophobic and %d as hydrophilic.\n",
- naccb, naccf);
+ fprintf(stderr, "%d residues were classified as hydrophobic and %d as hydrophilic.\n", naccb, naccf);
}
mat->title = "Secondary structure";
if (i != j)
{
fprintf(stderr,
- "Not all residues were recognized (%d from %d), the result may be inaccurate!\n", j, i);
+ "Not all residues were recognized (%d from %d), the result may be inaccurate!\n",
+ j,
+ i);
}
for (i = 0; (i < n_surf); i++)
}
else
{
- fprintf(stderr, "Residue %s not found in surface database (%s)\n",
- *atoms->resinfo[i].name, surffn);
+ fprintf(stderr, "Residue %s not found in surface database (%s)\n", *atoms->resinfo[i].name, surffn);
}
}
}
}
fp = gmx_ffopen(fn, "w");
nlev = static_cast<int>(hi - lo + 1);
- write_xpm(fp, 0, "Solvent Accessible Surface", "Surface (A^2)", "Time", "Residue Index",
- nframe, nres, mat->axis_x.data(), mat->axis_y.data(), accr, lo, hi, rlo, rhi, &nlev);
+ write_xpm(fp,
+ 0,
+ "Solvent Accessible Surface",
+ "Surface (A^2)",
+ "Time",
+ "Residue Index",
+ nframe,
+ nres,
+ mat->axis_x.data(),
+ mat->axis_y.data(),
+ accr,
+ lo,
+ hi,
+ rlo,
+ rhi,
+ &nlev);
gmx_ffclose(fp);
}
}
leg.emplace_back(m.desc);
}
- fp = xvgropen(outfile, "Secondary Structure", output_env_get_xvgr_tlabel(oenv),
- "Number of Residues", oenv);
+ fp = xvgropen(
+ outfile, "Secondary Structure", output_env_get_xvgr_tlabel(oenv), "Number of Residues", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"Structure = ");
int gmx_do_dssp(int argc, char* argv[])
{
const char* desc[] = {
- "[THISMODULE] ", "reads a trajectory file and computes the secondary structure for",
- "each time frame ", "calling the dssp program. If you do not have the dssp program,",
+ "[THISMODULE] ",
+ "reads a trajectory file and computes the secondary structure for",
+ "each time frame ",
+ "calling the dssp program. If you do not have the dssp program,",
"get it from http://swift.cmbi.ru.nl/gv/dssp. [THISMODULE] assumes ",
"that the dssp executable is located in ",
// NOLINTNEXTLINE(bugprone-suspicious-missing-comma)
"[TT]" GMX_DSSP_PROGRAM_PATH "[tt]. If this is not the case, then you should",
- "set an environment variable [TT]DSSP[tt] pointing to the dssp", "executable, e.g.: [PAR]",
+ "set an environment variable [TT]DSSP[tt] pointing to the dssp",
+ "executable, e.g.: [PAR]",
"[TT]setenv DSSP /opt/dssp/bin/dssp[tt][PAR]",
"Since version 2.0.0, dssp is invoked with a syntax that differs",
"from earlier versions. If you have an older version of dssp,",
"[REF].xpm[ref] matrix file. This file can be visualized with for instance",
"[TT]xv[tt] and can be converted to postscript with [TT]xpm2ps[tt].",
"Individual chains are separated by light grey lines in the [REF].xpm[ref] and",
- "postscript files.", "The number of residues with each secondary structure type and the",
+ "postscript files.",
+ "The number of residues with each secondary structure type and the",
"total secondary structure ([TT]-sss[tt]) count as a function of",
"time are also written to file ([TT]-sc[tt]).[PAR]",
"Solvent accessible surface (SAS) per residue can be calculated, both in",
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT, NFILE, fnm,
- asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc,
+ argv,
+ PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT,
+ NFILE,
+ fnm,
+ asize(pa),
+ pa,
+ asize(desc),
+ desc,
+ 0,
+ nullptr,
+ &oenv))
{
return 0;
}
if (fnTArea)
{
- fTArea = xvgropen(fnTArea, "Solvent Accessible Surface Area",
- output_env_get_xvgr_tlabel(oenv), "Area (nm\\S2\\N)", oenv);
+ fTArea = xvgropen(fnTArea,
+ "Solvent Accessible Surface Area",
+ output_env_get_xvgr_tlabel(oenv),
+ "Area (nm\\S2\\N)",
+ oenv);
xvgr_legend(fTArea, 2, leg, oenv);
}
else
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2011-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
double fy = f * y;
- return BOLTZ * (std::log(calc_compress(fy)) + fy * (3 * fy - 4) / gmx::square(1 - fy));
+ return gmx::c_boltz * (std::log(calc_compress(fy)) + fy * (3 * fy - 4) / gmx::square(1 - fy));
}
static real wCsolid(real nu, real beta)
{
- real bhn = beta * PLANCK * nu;
+ real bhn = beta * gmx::c_planck * nu;
real ebn, koko;
if (bhn == 0)
static real wSsolid(real nu, real beta)
{
- real bhn = beta * PLANCK * nu;
+ real bhn = beta * gmx::c_planck * nu;
if (bhn == 0)
{
static real wAsolid(real nu, real beta)
{
- real bhn = beta * PLANCK * nu;
+ real bhn = beta * gmx::c_planck * nu;
if (bhn == 0)
{
static real wEsolid(real nu, real beta)
{
- real bhn = beta * PLANCK * nu;
+ real bhn = beta * gmx::c_planck * nu;
if (bhn == 0)
{
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, npargs, ppa,
- asize(desc), desc, asize(bugs), bugs, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
sfree(ppa);
return 0;
}
- beta = 1 / (Temp * BOLTZ);
+ beta = 1 / (Temp * gmx::c_boltz);
fplog = gmx_fio_fopen(ftp2fn(efLOG, NFILE, fnm), "w");
fprintf(fplog, "Doing density of states analysis based on trajectory.\n");
if (nframes < min_frames)
{
- gmx_fatal(FARGS, "You need at least %d frames in the trajectory and you only have %d.",
- min_frames, nframes);
+ gmx_fatal(FARGS, "You need at least %d frames in the trajectory and you only have %d.", min_frames, nframes);
}
dt = (t1 - t0) / (nframes - 1);
if (nV > 0)
normalizeAutocorrelation = opt2parg_bool("-normalize", npargs, ppa);
/* Note that we always disable normalization here, regardless of user settings */
- low_do_autocorr(nullptr, oenv, nullptr, nframes, gnx, nframes, c1, dt, eacNormal, 0, FALSE,
- FALSE, FALSE, -1, -1, 0);
+ low_do_autocorr(
+ nullptr, oenv, nullptr, nframes, gnx, nframes, c1, dt, eacNormal, 0, FALSE, FALSE, FALSE, -1, -1, 0);
snew(dos, DOS_NR);
for (j = 0; (j < DOS_NR); j++)
{
}
}
- fp = xvgropen(opt2fn("-vacf", NFILE, fnm), "Velocity autocorrelation function", "Time (ps)",
- "C(t)", oenv);
+ fp = xvgropen(
+ opt2fn("-vacf", NFILE, fnm), "Velocity autocorrelation function", "Time (ps)", "C(t)", oenv);
snew(tt, nframes / 2);
invNormalize = normalizeAutocorrelation ? 1.0 / dos[VACF][0] : 1.0;
}
xvgrclose(fp);
- fp = xvgropen(opt2fn("-mvacf", NFILE, fnm), "Mass-weighted velocity autocorrelation function",
- "Time (ps)", "C(t)", oenv);
+ fp = xvgropen(opt2fn("-mvacf", NFILE, fnm),
+ "Mass-weighted velocity autocorrelation function",
+ "Time (ps)",
+ "C(t)",
+ oenv);
invNormalize = normalizeAutocorrelation ? 1.0 / dos[VACF][0] : 1.0;
DoS0 = dos[DOS][0];
/* Note this eqn. is incorrect in Pascal2011a! */
- Delta = ((2 * DoS0 / (9 * Natom)) * std::sqrt(M_PI * BOLTZ * Temp * Natom / tmass)
+ Delta = ((2 * DoS0 / (9 * Natom)) * std::sqrt(M_PI * gmx::c_boltz * Temp * Natom / tmass)
* std::pow((Natom / V), 1.0 / 3.0) * std::pow(6.0 / M_PI, 2.0 / 3.0));
f = calc_fluidicity(Delta, toler);
y = calc_y(f, Delta, toler);
z = calc_compress(y);
- Sig = BOLTZ
- * (5.0 / 2.0 + std::log(2 * M_PI * BOLTZ * Temp / (gmx::square(PLANCK)) * V / (f * Natom)));
+ Sig = gmx::c_boltz
+ * (5.0 / 2.0
+ + std::log(2 * M_PI * gmx::c_boltz * Temp / (gmx::square(gmx::c_planck)) * V / (f * Natom)));
Shs = Sig + calc_Shs(f, y);
- rho = (tmass * AMU) / (V * NANO * NANO * NANO);
+ rho = (tmass * gmx::c_amu) / (V * gmx::c_nano * gmx::c_nano * gmx::c_nano);
sigHS = std::cbrt(6 * y * V / (M_PI * Natom));
fprintf(fplog, "System = \"%s\"\n", *top.name);
fprintf(fplog, "DoSTot = %g\n", dostot);
/* Now compute solid (2) and diffusive (3) components */
- fp = xvgropen(opt2fn("-dos", NFILE, fnm), "Density of states",
- bRecip ? "E (cm\\S-1\\N)" : "\\f{12}n\\f{4} (1/ps)", "\\f{4}S(\\f{12}n\\f{4})", oenv);
+ fp = xvgropen(opt2fn("-dos", NFILE, fnm),
+ "Density of states",
+ bRecip ? "E (cm\\S-1\\N)" : "\\f{12}n\\f{4} (1/ps)",
+ "\\f{4}S(\\f{12}n\\f{4})",
+ oenv);
xvgr_legend(fp, asize(DoSlegend), DoSlegend, oenv);
- recip_fac = bRecip ? (1e7 / SPEED_OF_LIGHT) : 1.0;
+ recip_fac = bRecip ? (1e7 / gmx::c_speedOfLight) : 1.0;
for (j = 0; (j < nframes / 4); j++)
{
dos[DOS_DIFF][j] = DoS0 / (1 + gmx::square(DoS0 * M_PI * nu[j] / (6 * f * Natom)));
dos[DOS_SOLID][j] = dos[DOS][j] - dos[DOS_DIFF][j];
- fprintf(fp, "%10g %10g %10g %10g\n", recip_fac * nu[j], dos[DOS][j] / recip_fac,
- dos[DOS_SOLID][j] / recip_fac, dos[DOS_DIFF][j] / recip_fac);
+ fprintf(fp,
+ "%10g %10g %10g %10g\n",
+ recip_fac * nu[j],
+ dos[DOS][j] / recip_fac,
+ dos[DOS_SOLID][j] / recip_fac,
+ dos[DOS_DIFF][j] / recip_fac);
}
xvgrclose(fp);
/* Finally analyze the results! */
wCdiff = 0.5;
- wSdiff = Shs / (3 * BOLTZ); /* Is this correct? */
+ wSdiff = Shs / (3 * gmx::c_boltz); /* Is this correct? */
wEdiff = 0.5;
wAdiff = wEdiff - wSdiff;
for (j = 0; (j < nframes / 4); j++)
fprintf(fplog, "Diffusion coefficient from VACF %g 10^-5 cm^2/s\n", DiffCoeff);
fprintf(fplog, "Diffusion coefficient from DoS %g 10^-5 cm^2/s\n", 1000 * DoS0 / (12 * tmass * beta));
- cP = BOLTZ * evaluate_integral(nframes / 4, nu, dos[DOS_CP], nullptr, int{ nframes / 4 }, &stddev);
+ cP = gmx::c_boltz
+ * evaluate_integral(nframes / 4, nu, dos[DOS_CP], nullptr, int{ nframes / 4 }, &stddev);
fprintf(fplog, "Heat capacity %g J/mol K\n", 1000 * cP / Nmol);
fprintf(fplog, "\nArrivederci!\n");
gmx_fio_fclose(fplog);
rrange, krange, rincr, kincr, Rfrac;
int rkcount = 0, rblocksallocated = 0, kblocksallocated = 0;
- if (!parse_common_args(&argc, argv, PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc,
+ argv,
+ PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT,
+ NFILE,
+ fnm,
+ NPA,
+ pa,
+ asize(desc),
+ desc,
+ 0,
+ nullptr,
+ &oenv))
{
return 0;
}
if (bRKout)
{
- rkfp = xvgropen(out_xvgrkfile, "Distance and \\f{Symbol}k\\f{}\\S2\\N trajectory",
- "Time (ps)", "Distance (nm) / \\f{Symbol}k\\f{}\\S2\\N", oenv);
+ rkfp = xvgropen(out_xvgrkfile,
+ "Distance and \\f{Symbol}k\\f{}\\S2\\N trajectory",
+ "Time (ps)",
+ "Distance (nm) / \\f{Symbol}k\\f{}\\S2\\N",
+ oenv);
xvgr_legend(rkfp, 2, rkleg, oenv);
}
if (bInstEffout)
{
- iefp = xvgropen(out_xvginstefffile, "Instantaneous RET Efficiency", "Time (ps)",
- "RET Efficiency", oenv);
+ iefp = xvgropen(out_xvginstefffile,
+ "Instantaneous RET Efficiency",
+ "Time (ps)",
+ "RET Efficiency",
+ oenv);
xvgr_legend(iefp, 1, ieleg, oenv);
}
{
rhist[i] /= rkcount * rrange / histbins;
}
- rhfp = xvgropen(out_xvgrhistfile, "Distance Distribution", "R (nm)",
- "Normalized Probability", oenv);
+ rhfp = xvgropen(out_xvgrhistfile,
+ "Distance Distribution",
+ "R (nm)",
+ "Normalized Probability",
+ oenv);
}
else
{
- rhfp = xvgropen(out_xvgrhistfile, "Distance Distribution", "R (nm)",
- "Probability", oenv);
+ rhfp = xvgropen(
+ out_xvgrhistfile, "Distance Distribution", "R (nm)", "Probability", oenv);
}
xvgr_legend(rhfp, 1, rhleg, oenv);
for (i = 0; i < histbins; i++)
{
khist[i] /= rkcount * krange / histbins;
}
- khfp = xvgropen(out_xvgkhistfile, "\\f{Symbol}k\\f{}\\S2\\N Distribution",
- "\\f{Symbol}k\\f{}\\S2\\N", "Normalized Probability", oenv);
+ khfp = xvgropen(out_xvgkhistfile,
+ "\\f{Symbol}k\\f{}\\S2\\N Distribution",
+ "\\f{Symbol}k\\f{}\\S2\\N",
+ "Normalized Probability",
+ oenv);
}
else
{
- khfp = xvgropen(out_xvgkhistfile, "\\f{Symbol}k\\f{}\\S2\\N Distribution",
- "\\f{Symbol}k\\f{}\\S2\\N", "Probability", oenv);
+ khfp = xvgropen(out_xvgkhistfile,
+ "\\f{Symbol}k\\f{}\\S2\\N Distribution",
+ "\\f{Symbol}k\\f{}\\S2\\N",
+ "Probability",
+ oenv);
}
xvgr_legend(khfp, 1, khleg, oenv);
for (i = 0; i < histbins; i++)
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return -1;
}
+// The non-bonded energy terms accumulated for energy group pairs. These were superseded elsewhere
+// by NonBondedEnergyTerms but not updated here due to the need for refactoring here first.
+enum
+{
+ egCOULSR,
+ egLJSR,
+ egBHAMSR,
+ egCOUL14,
+ egLJ14,
+ egNR
+};
+
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static const char* egrp_nm[egNR + 1] = { "Coul-SR", "LJ-SR", "Buck-SR", "Coul-14", "LJ-14", nullptr };
+
+
int gmx_enemat(int argc, char* argv[])
{
const char* desc[] = {
{ efXVG, "-etot", "energy", ffWRITE } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
fprintf(stderr,
"WARNING! could not find group %s (%d,%d) "
"in energy file\n",
- groupname, i, j);
+ groupname,
+ i,
+ j);
}
else
{
fprintf(stderr,
"Will build energy half-matrix of %d groups, %d elements, "
"over %d frames\n",
- ngroups, nset, nenergy);
+ ngroups,
+ nset,
+ nenergy);
snew(emat, egNR + egSP);
for (j = 0; (j < egNR + egSP); j++)
}
eaver[i] /= nenergy;
}
- beta = 1.0 / (BOLTZ * reftemp);
+ beta = 1.0 / (gmx::c_boltz * reftemp);
snew(efree, ngroups);
snew(edif, ngroups);
for (i = 0; (i < ngroups); i++)
fprintf(stderr,
"Matrix of %s energy is uniform at %f "
"(will not produce output).\n",
- egrp_nm[m], emax);
+ egrp_nm[m],
+ emax);
}
else
{
out = gmx_ffopen(fn, "w");
if (emin >= emid)
{
- write_xpm(out, 0, label, "Energy (kJ/mol)", "Residue Index",
- "Residue Index", ngroups, ngroups, groupnr, groupnr, emat[m],
- emid, emax, rmid, rhi, &nlevels);
+ write_xpm(out,
+ 0,
+ label,
+ "Energy (kJ/mol)",
+ "Residue Index",
+ "Residue Index",
+ ngroups,
+ ngroups,
+ groupnr,
+ groupnr,
+ emat[m],
+ emid,
+ emax,
+ rmid,
+ rhi,
+ &nlevels);
}
else if (emax <= emid)
{
- write_xpm(out, 0, label, "Energy (kJ/mol)", "Residue Index",
- "Residue Index", ngroups, ngroups, groupnr, groupnr, emat[m],
- emin, emid, rlo, rmid, &nlevels);
+ write_xpm(out,
+ 0,
+ label,
+ "Energy (kJ/mol)",
+ "Residue Index",
+ "Residue Index",
+ ngroups,
+ ngroups,
+ groupnr,
+ groupnr,
+ emat[m],
+ emin,
+ emid,
+ rlo,
+ rmid,
+ &nlevels);
}
else
{
- write_xpm3(out, 0, label, "Energy (kJ/mol)", "Residue Index",
- "Residue Index", ngroups, ngroups, groupnr, groupnr, emat[m],
- emin, emid, emax, rlo, rmid, rhi, &nlevels);
+ write_xpm3(out,
+ 0,
+ label,
+ "Energy (kJ/mol)",
+ "Residue Index",
+ "Residue Index",
+ ngroups,
+ ngroups,
+ groupnr,
+ groupnr,
+ emat[m],
+ emin,
+ emid,
+ emax,
+ rlo,
+ rmid,
+ rhi,
+ &nlevels);
}
gmx_ffclose(out);
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
avold[i] = 0;
}
fp0 = xvgropen(fni, "Shear viscosity integral", "Time (ps)", "(kg m\\S-1\\N s\\S-1\\N ps)", oenv);
- fp1 = xvgropen(fn, "Shear viscosity using Einstein relation", "Time (ps)",
- "(kg m\\S-1\\N s\\S-1\\N)", oenv);
+ fp1 = xvgropen(
+ fn, "Shear viscosity using Einstein relation", "Time (ps)", "(kg m\\S-1\\N s\\S-1\\N)", oenv);
for (i = 0; i < nf4; i++)
{
for (m = 0; m <= nsets; m++)
}
}
/* Convert to SI for the viscosity */
- fac = (V * NANO * NANO * NANO * PICO * 1e10) / (2 * BOLTZMANN * T) / (nint - i);
+ fac = (V * gmx::c_nano * gmx::c_nano * gmx::c_nano * gmx::c_pico * 1e10)
+ / (2 * gmx::c_boltzmann * T) / (nint - i);
fprintf(fp0, "%10g", i * dt);
for (m = 0; (m <= nsets); m++)
{
if (debug)
{
char buf1[STEPSTRSIZE], buf2[STEPSTRSIZE];
- fprintf(debug, "Requested %d blocks, we have %d blocks, min %s nsteps %s\n", nb,
- eee[nb].b, gmx_step_str(eee[nb].nst_min, buf1), gmx_step_str(edat->nsteps, buf2));
+ fprintf(debug,
+ "Requested %d blocks, we have %d blocks, min %s nsteps %s\n",
+ nb,
+ eee[nb].b,
+ gmx_step_str(eee[nb].nst_min, buf1),
+ gmx_step_str(edat->nsteps, buf2));
}
if (eee[nb].b == nb && 5 * nb * eee[nb].nst_min >= 4 * edat->nsteps)
{
const char* my_ener[] = { "Volume", "Enthalpy", "Temperature", "Total Energy" };
int ii[eNR];
- NANO3 = NANO * NANO * NANO;
+ NANO3 = gmx::c_nano * gmx::c_nano * gmx::c_nano;
if (!bDriftCorr)
{
fprintf(fp,
{
vv = edat->s[ii[eVol]].av * NANO3;
varv = gmx::square(edat->s[ii[eVol]].rmsd * NANO3);
- kappa = (varv / vv) / (BOLTZMANN * tt);
+ kappa = (varv / vv) / (gmx::c_boltzmann * tt);
}
/* Enthalpy */
hh = varh = NOTSET;
if ((ii[eEnth] < nset) && (ii[eTemp] < nset))
{
- hh = KILO * edat->s[ii[eEnth]].av / AVOGADRO;
- varh = gmx::square(KILO * edat->s[ii[eEnth]].rmsd / AVOGADRO);
- cp = AVOGADRO * ((varh / nmol) / (BOLTZMANN * tt * tt));
+ hh = gmx::c_kilo * edat->s[ii[eEnth]].av / gmx::c_avogadro;
+ varh = gmx::square(gmx::c_kilo * edat->s[ii[eEnth]].rmsd / gmx::c_avogadro);
+ cp = gmx::c_avogadro * ((varh / nmol) / (gmx::c_boltzmann * tt * tt));
}
/* Total energy */
if ((ii[eEtot] < nset) && (hh == NOTSET) && (tt != NOTSET))
by checking whether the enthalpy was computed.
*/
varet = gmx::square(edat->s[ii[eEtot]].rmsd);
- cv = KILO * ((varet / nmol) / (BOLTZ * tt * tt));
+ cv = gmx::c_kilo * ((varet / nmol) / (gmx::c_boltz * tt * tt));
}
/* Alpha, dcp */
if ((ii[eVol] < nset) && (ii[eEnth] < nset) && (ii[eTemp] < nset))
for (j = 0; (j < edat->nframes); j++)
{
v = edat->s[ii[eVol]].ener[j] * NANO3;
- h = KILO * edat->s[ii[eEnth]].ener[j] / AVOGADRO;
+ h = gmx::c_kilo * edat->s[ii[eEnth]].ener[j] / gmx::c_avogadro;
v_sum += v;
h_sum += h;
vh_sum += (v * h);
vh_aver = vh_sum / edat->nframes;
v_aver = v_sum / edat->nframes;
h_aver = h_sum / edat->nframes;
- alpha = (vh_aver - v_aver * h_aver) / (v_aver * BOLTZMANN * tt * tt);
- dcp = (v_aver * AVOGADRO / nmol) * tt * gmx::square(alpha) / (kappa);
+ alpha = (vh_aver - v_aver * h_aver) / (v_aver * gmx::c_boltzmann * tt * tt);
+ dcp = (v_aver * gmx::c_avogadro / nmol) * tt * gmx::square(alpha) / (kappa);
}
if (tt != NOTSET)
{
if (varv != NOTSET)
{
- fprintf(fp, "varv = %10g (m^6)\n", varv * AVOGADRO / nmol);
+ fprintf(fp, "varv = %10g (m^6)\n", varv * gmx::c_avogadro / nmol);
}
}
if (vv != NOTSET)
{
- fprintf(fp, "Volume = %10g m^3/mol\n", vv * AVOGADRO / nmol);
+ fprintf(fp, "Volume = %10g m^3/mol\n", vv * gmx::c_avogadro / nmol);
}
if (varh != NOTSET)
{
- fprintf(fp, "Enthalpy = %10g kJ/mol\n",
- hh * AVOGADRO / (KILO * nmol));
+ fprintf(fp,
+ "Enthalpy = %10g kJ/mol\n",
+ hh * gmx::c_avogadro / (gmx::c_kilo * nmol));
}
if (alpha != NOTSET)
{
/* Calculate the time difference */
delta_t = t - start_t;
- fprintf(stdout, "\nStatistics over %s steps [ %.4f through %.4f ps ], %d data sets\n",
- gmx_step_str(nsteps, buf), start_t, t, nset);
+ fprintf(stdout,
+ "\nStatistics over %s steps [ %.4f through %.4f ps ], %d data sets\n",
+ gmx_step_str(nsteps, buf),
+ start_t,
+ t,
+ nset);
calc_averages(nset, edat, nbmin, nbmax);
fprintf(stdout, " '%s'", leg[i]);
}
}
- fprintf(stdout, " %s has statistics over %d points (frames)\n",
- nnotexact == 1 ? "is" : "are", edat->nframes);
+ fprintf(stdout,
+ " %s has statistics over %d points (frames)\n",
+ nnotexact == 1 ? "is" : "are",
+ edat->nframes);
fprintf(stdout, "All other statistics are over %s points\n", gmx_step_str(edat->npoints, buf));
}
fprintf(stdout, "\n");
- fprintf(stdout, "%-24s %10s %10s %10s %10s", "Energy", "Average", "Err.Est.", "RMSD",
+ fprintf(stdout,
+ "%-24s %10s %10s %10s %10s",
+ "Energy",
+ "Average",
+ "Err.Est.",
+ "RMSD",
"Tot-Drift");
if (bFee)
{
expEtot = 0;
if (bFee)
{
- beta = 1.0 / (BOLTZ * reftemp);
+ beta = 1.0 / (gmx::c_boltz * reftemp);
snew(fee, nset);
}
for (i = 0; (i < nset); i++)
{
totaldrift = (edat->nsteps - 1) * esum->s[0].slope;
ee_pr(esum->s[0].ee / nmol, sizeof(eebuf), eebuf);
- fprintf(stdout, "%-24s %10g %10s %10s %10g (%s)", "Total", esum->s[0].av / nmol, eebuf,
- "--", totaldrift / nmol, enm[set[0]].unit);
+ fprintf(stdout,
+ "%-24s %10g %10s %10s %10g (%s)",
+ "Total",
+ esum->s[0].av / nmol,
+ eebuf,
+ "--",
+ totaldrift / nmol,
+ enm[set[0]].unit);
/* pr_aver,pr_stddev,a,totaldrift */
if (bFee)
{
- fprintf(stdout, " %10g %10g\n", std::log(expEtot) / beta + esum->s[0].av / nmol,
+ fprintf(stdout,
+ " %10g %10g\n",
+ std::log(expEtot) / beta + esum->s[0].av / nmol,
std::log(expEtot) / beta);
}
else
/*do_autocorr(corrfn,buf,nenergy,3,eneset,Dt,eacNormal,TRUE);*/
/* Do it for shear viscosity */
std::strcpy(buf, "Shear Viscosity");
- low_do_autocorr(corrfn, oenv, buf, edat->nframes, 3, (edat->nframes + 1) / 2, eneset,
- Dt, eacNormal, 1, TRUE, FALSE, FALSE, 0.0, 0.0, 0);
+ low_do_autocorr(corrfn,
+ oenv,
+ buf,
+ edat->nframes,
+ 3,
+ (edat->nframes + 1) / 2,
+ eneset,
+ Dt,
+ eacNormal,
+ 1,
+ TRUE,
+ FALSE,
+ FALSE,
+ 0.0,
+ 0.0,
+ 0);
/* Now for bulk viscosity */
std::strcpy(buf, "Bulk Viscosity");
- low_do_autocorr(corrfn, oenv, buf, edat->nframes, 1, (edat->nframes + 1) / 2,
- &(eneset[11]), Dt, eacNormal, 1, TRUE, FALSE, FALSE, 0.0, 0.0, 0);
-
- factor = (Vaver * 1e-26 / (BOLTZMANN * Temp)) * Dt;
+ low_do_autocorr(corrfn,
+ oenv,
+ buf,
+ edat->nframes,
+ 1,
+ (edat->nframes + 1) / 2,
+ &(eneset[11]),
+ Dt,
+ eacNormal,
+ 1,
+ TRUE,
+ FALSE,
+ FALSE,
+ 0.0,
+ 0.0,
+ 0);
+
+ factor = (Vaver * 1e-26 / (gmx::c_boltzmann * Temp)) * Dt;
fp = xvgropen(visfn, buf, "Time (ps)", "\\8h\\4 (cp)", oenv);
xvgr_legend(fp, asize(leg), leg, oenv);
#if 0
do_autocorr(corrfn, oenv, buf, edat->nframes,
bSum ? 1 : nset,
- bSum ? &edat->s[nset-1].ener : eneset,
+ bSum ? &edat->s[nset-1].energyGroupPairTerms : eneset,
(delta_t/edat->nframes), eacNormal, FALSE);
#endif
}
if (fr->t != time[nenergy2])
{
- fprintf(stderr, "\nWARNING time mismatch %g!=%g at frame %s\n", fr->t,
- time[nenergy2], gmx_step_str(fr->step, buf));
+ fprintf(stderr,
+ "\nWARNING time mismatch %g!=%g at frame %s\n",
+ fr->t,
+ time[nenergy2],
+ gmx_step_str(fr->step, buf));
}
for (i = 0; i < nset; i++)
{
fp = nullptr;
if (runavgfn)
{
- fp = xvgropen(runavgfn, "Running average free energy difference", "Time (" unit_time ")",
- "\\8D\\4E (" unit_energy ")", oenv);
+ fp = xvgropen(runavgfn,
+ "Running average free energy difference",
+ "Time (" unit_time ")",
+ "\\8D\\4E (" unit_energy ")",
+ oenv);
xvgr_legend(fp, asize(ravgleg), ravgleg, oenv);
}
fprintf(stdout, "\n%-24s %10s\n", "Energy", "dF = -kT ln < exp(-(EB-EA)/kT) >A");
sum = 0;
- beta = 1.0 / (BOLTZ * reftemp);
+ beta = 1.0 / (gmx::c_boltz * reftemp);
for (i = 0; i < nset; i++)
{
if (gmx_strcasecmp(leg[i], enm[set[i]].name) != 0)
sum += std::exp(-dE * beta);
if (fp)
{
- fprintf(fp, "%10g %10g %10g\n", time[j], dE, -BOLTZ * reftemp * std::log(sum / (j + 1)));
+ fprintf(fp, "%10g %10g %10g\n", time[j], dE, -gmx::c_boltz * reftemp * std::log(sum / (j + 1)));
}
}
- aver = -BOLTZ * reftemp * std::log(sum / nenergy);
+ aver = -gmx::c_boltz * reftemp * std::log(sum / nenergy);
fprintf(stdout, "%-24s %10g\n", leg[i], aver);
}
if (fp)
else if (fr->block[i].id == enxDHCOLL)
{
nblock_dhcoll++;
- if ((fr->block[i].nsub < 1) || (fr->block[i].sub[0].type != xdr_datatype_double)
+ if ((fr->block[i].nsub < 1) || (fr->block[i].sub[0].type != XdrDataType::Double)
|| (fr->block[i].sub[0].nr < 5))
{
gmx_fatal(FARGS, "Unexpected block data");
for (j = 0; j < n_lambda_vec; j++)
{
native_lambda_vec[j] = fr->block[i].sub[0].dval[5 + j];
- lambda_components[j] = efpt_singular_names[fr->block[i].sub[1].ival[2 + j]];
+ lambda_components[j] =
+ enumValueToStringSingular(static_cast<FreeEnergyPerturbationCouplingType>(
+ fr->block[i].sub[1].ival[2 + j]));
}
}
}
int nhist, derivative;
/* check the block types etc. */
- if ((blk->nsub < 2) || (blk->sub[0].type != xdr_datatype_double)
- || (blk->sub[1].type != xdr_datatype_int64) || (blk->sub[0].nr < 2)
+ if ((blk->nsub < 2) || (blk->sub[0].type != XdrDataType::Double)
+ || (blk->sub[1].type != XdrDataType::Int64) || (blk->sub[0].nr < 2)
|| (blk->sub[1].nr < 2))
{
gmx_fatal(FARGS, "Unexpected block data in file");
if (!derivative)
{
- sprintf(legend, "N(%s(%s=%g) | %s=%g)", deltag, lambda, foreign_lambda,
- lambda, start_lambda);
+ sprintf(legend, "N(%s(%s=%g) | %s=%g)", deltag, lambda, foreign_lambda, lambda, start_lambda);
}
else
{
if (blk->id == enxDH)
{
double value;
- if (blk->sub[2].type == xdr_datatype_float)
+ if (blk->sub[2].type == XdrDataType::Float)
{
value = blk->sub[2].fval[i];
}
if (j == 1 && ir->bExpanded)
{
- fprintf(*fp_dhdl, "%4d",
- static_cast<int>(value)); /* if expanded ensembles and zero, this is a state value, it's an integer. We need a cleaner conditional than if j==1! */
+ fprintf(*fp_dhdl, "%4d", static_cast<int>(value)); /* if expanded ensembles and zero, this is a state value, it's an integer. We need a cleaner conditional than if j==1! */
}
else
{
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END, NFILE, fnm,
- npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END, NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
{
sfree(ppa);
return 0;
}
if (bDHDL)
{
- do_dhdl(fr, ir, &fp_dhdl, opt2fn("-odh", NFILE, fnm), bDp, &dh_blocks, &dh_hists,
- &dh_samples, &dh_lambdas, oenv);
+ do_dhdl(fr, ir, &fp_dhdl, opt2fn("-odh", NFILE, fnm), bDp, &dh_blocks, &dh_hists, &dh_samples, &dh_lambdas, oenv);
}
/*******************************************
else
{
double dt = (frame[cur].t - start_t) / (edat.nframes - 1);
- analyse_ener(opt2bSet("-corr", NFILE, fnm), opt2fn("-corr", NFILE, fnm),
- opt2fn("-evisco", NFILE, fnm), opt2fn("-eviscoi", NFILE, fnm), bFee, bSum,
- bFluct, bVisco, opt2fn("-vis", NFILE, fnm), nmol, start_step, start_t,
- frame[cur].step, frame[cur].t, reftemp, &edat, nset, set, bIsEner, leg, enm,
- Vaver, ezero, nbmin, nbmax, oenv);
+ analyse_ener(opt2bSet("-corr", NFILE, fnm),
+ opt2fn("-corr", NFILE, fnm),
+ opt2fn("-evisco", NFILE, fnm),
+ opt2fn("-eviscoi", NFILE, fnm),
+ bFee,
+ bSum,
+ bFluct,
+ bVisco,
+ opt2fn("-vis", NFILE, fnm),
+ nmol,
+ start_step,
+ start_t,
+ frame[cur].step,
+ frame[cur].t,
+ reftemp,
+ &edat,
+ nset,
+ set,
+ bIsEner,
+ leg,
+ enm,
+ Vaver,
+ ezero,
+ nbmin,
+ nbmax,
+ oenv);
if (bFluctProps)
{
calc_fluctuation_props(stdout, bDriftCorr, dt, nset, nmol, leg, &edat, nbmin, nbmax);
}
if (opt2bSet("-f2", NFILE, fnm))
{
- fec(opt2fn("-f2", NFILE, fnm), opt2fn("-ravg", NFILE, fnm), reftemp, nset, set, leg, &edat,
- time, oenv);
+ fec(opt2fn("-f2", NFILE, fnm), opt2fn("-ravg", NFILE, fnm), reftemp, nset, set, leg, &edat, time, oenv);
}
// Clean up!
done_enerdata_t(nset, &edat);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxana/princ.h"
#include "gromacs/math/do_fit.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
{ efTRO, "-oh", "highpass", ffOPTWR } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
}
if (outl && (bLowAll || fr % nf == nf - 1))
{
- write_trx(outl, nat, ind, topfile ? &(top.atoms) : nullptr, 0, t[nf - 1],
- bFit ? topbox : boxf, xf, nullptr, nullptr);
+ write_trx(outl,
+ nat,
+ ind,
+ topfile ? &(top.atoms) : nullptr,
+ 0,
+ t[nf - 1],
+ bFit ? topbox : boxf,
+ xf,
+ nullptr,
+ nullptr);
}
if (outh)
{
boxf[j][d] = topbox[j][d] + box[nf - 1][j][d] - boxf[j][d];
}
}
- write_trx(outh, nat, ind, topfile ? &(top.atoms) : nullptr, 0, t[nf - 1],
- bFit ? topbox : boxf, xf, nullptr, nullptr);
+ write_trx(outh,
+ nat,
+ ind,
+ topfile ? &(top.atoms) : nullptr,
+ 0,
+ t[nf - 1],
+ bFit ? topbox : boxf,
+ xf,
+ nullptr,
+ nullptr);
}
}
/* Cycle all the pointer and the box by one */
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cmath>
#include <cstring>
+#include <vector>
#include "gromacs/commandline/pargs.h"
#include "gromacs/commandline/viewit.h"
#include "gromacs/gmxana/gstat.h"
#include "gromacs/gmxana/princ.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/rmpbc.h"
static void calc_gyro_z(rvec x[], matrix box, int gnx, const int index[], t_atom atom[], int nz, real time, FILE* out)
{
- static dvec* inertia = nullptr;
- static double* tm = nullptr;
- int i, ii, j, zi;
- real zf, w, sdet, e1, e2;
+ static std::vector<gmx::DVec> inertia;
+ static std::vector<double> tm;
+ int i, ii, j, zi;
+ real zf, w, sdet, e1, e2;
- if (inertia == nullptr)
+ if (inertia.empty())
{
- snew(inertia, nz);
- snew(tm, nz);
+ inertia.resize(nz);
+ tm.resize(nz);
}
for (i = 0; i < nz; i++)
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, npargs, ppa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
{
sfree(ppa);
return 0;
t0 = t;
if (bQ)
{
- out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Radius of Charge (total and around axes)",
- "Time (ps)", "Rg (nm)", oenv);
+ out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
+ "Radius of Charge (total and around axes)",
+ "Time (ps)",
+ "Rg (nm)",
+ oenv);
}
else if (bMOI)
{
- out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Moments of inertia (total and around axes)",
- "Time (ps)", "I (a.m.u. nm\\S2\\N)", oenv);
+ out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
+ "Moments of inertia (total and around axes)",
+ "Time (ps)",
+ "I (a.m.u. nm\\S2\\N)",
+ oenv);
}
else
{
- out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Radius of gyration (total and around axes)",
- "Time (ps)", "Rg (nm)", oenv);
+ out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
+ "Radius of gyration (total and around axes)",
+ "Time (ps)",
+ "Rg (nm)",
+ oenv);
}
if (bMOI)
{
tm = sub_xcm(nz == 0 ? x_s : x, nam, index + mol * nam, top.atoms.atom, xcm, bQ);
if (nz == 0)
{
- gyro += calc_gyro(x_s, nam, index + mol * nam, top.atoms.atom, tm, gvec1, d1, bQ,
- bRot, bMOI, trans);
+ gyro += calc_gyro(
+ x_s, nam, index + mol * nam, top.atoms.atom, tm, gvec1, d1, bQ, bRot, bMOI, trans);
}
else
{
{
int mode = eacVector;
- do_autocorr(opt2fn("-acf", NFILE, fnm), oenv, "Moment of inertia vector ACF", j, 3,
- moi_trans, (t - t0) / j, mode, FALSE);
+ do_autocorr(opt2fn("-acf", NFILE, fnm),
+ oenv,
+ "Moment of inertia vector ACF",
+ j,
+ 3,
+ moi_trans,
+ (t - t0) / j,
+ mode,
+ FALSE);
do_view(oenv, opt2fn("-acf", NFILE, fnm), "-nxy");
}
for (slice = 0; slice < nslices; slice++)
{
- fprintf(ord, "%8.3f %8.3f %8.3f %8.3f %e\n", slWidth * slice, factor * dipole[slice][XX],
- factor * dipole[slice][YY], factor * dipole[slice][ZZ], order[slice]);
+ fprintf(ord,
+ "%8.3f %8.3f %8.3f %8.3f %e\n",
+ slWidth * slice,
+ factor * dipole[slice][XX],
+ factor * dipole[slice][YY],
+ factor * dipole[slice][ZZ],
+ order[slice]);
}
xvgrclose(ord);
#define NFILE asize(fnm)
// Parse the user input in argv into pa
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, asize(bugs), bugs, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
rd_index(opt2fn("-nm", NFILE, fnm), 1, &nmic, &micelle, &micname);
}
- calc_h2order(ftp2fn(efTRX, NFILE, fnm), index, ngx, &slDipole, &slOrder, &slWidth, &nslices,
- top, pbcType, axis, bMicel, micelle, nmic, oenv);
+ calc_h2order(ftp2fn(efTRX, NFILE, fnm),
+ index,
+ ngx,
+ &slDipole,
+ &slOrder,
+ &slWidth,
+ &nslices,
+ top,
+ pbcType,
+ axis,
+ bMicel,
+ micelle,
+ nmic,
+ oenv);
h2order_plot(slDipole, slOrder, opt2fn("-o", NFILE, fnm), nslices, slWidth, oenv);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxana/gstat.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/pbcutil/pbc.h"
#define max_hx 7
typedef int t_hx[max_hx];
#define NRHXTYPES max_hx
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static const char* hxtypenames[NRHXTYPES] = { "n-n", "n-n+1", "n-n+2", "n-n+3",
"n-n+4", "n-n+5", "n-n>6" };
#define MAXHH 4
static const unsigned char c_donorMask = (1 << 1);
static const unsigned char c_inGroupMask = (1 << 2);
-
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static const char* grpnames[grNR] = { "0", "1", "I" };
-
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static gmx_bool bDebug = FALSE;
#define HB_NO 0
#define OFFSET(frame) ((frame) / 32)
#define MASK(frame) (1 << ((frame) % 32))
-static void _set_hb(unsigned int hbexist[], unsigned int frame, gmx_bool bValue)
+static void set_hb_function(unsigned int hbexist[], unsigned int frame, gmx_bool bValue)
{
if (bValue)
{
gmx_fatal(FARGS, "Incomprehensible iValue %d in set_hb", ihb);
}
- _set_hb(ghptr, frame - hb->hbmap[id][ia]->n0, TRUE);
+ set_hb_function(ghptr, frame - hb->hbmap[id][ia]->n0, TRUE);
}
static void add_ff(t_hbdata* hbd, int id, int h, int ia, int frame, int ihb)
}
}
-static int _acceptor_index(t_acceptors* a, int grp, int i, const char* file, int line)
+static int acceptor_index_function(t_acceptors* a, int grp, int i, const char* file, int line)
{
int ai = a->aptr[i];
{
if (debug && bDebug)
{
- fprintf(debug, "Acc. group inconsist.. grp[%d] = %d, grp = %d (%s, %d)\n", ai,
- a->grp[ai], grp, file, line);
+ fprintf(debug, "Acc. group inconsist.. grp[%d] = %d, grp = %d (%s, %d)\n", ai, a->grp[ai], grp, file, line);
}
return NOTSET;
}
return ai;
}
}
-#define acceptor_index(a, grp, i) _acceptor_index(a, grp, i, __FILE__, __LINE__)
+#define acceptor_index(a, grp, i) acceptor_index_function(a, grp, i, __FILE__, __LINE__)
-static int _donor_index(t_donors* d, int grp, int i, const char* file, int line)
+static int donor_index_function(t_donors* d, int grp, int i, const char* file, int line)
{
int di = d->dptr[i];
{
if (debug && bDebug)
{
- fprintf(debug, "Don. group inconsist.. grp[%d] = %d, grp = %d (%s, %d)\n", di,
- d->grp[di], grp, file, line);
+ fprintf(debug, "Don. group inconsist.. grp[%d] = %d, grp = %d (%s, %d)\n", di, d->grp[di], grp, file, line);
}
return NOTSET;
}
return di;
}
}
-#define donor_index(d, grp, i) _donor_index(d, grp, i, __FILE__, __LINE__)
+#define donor_index(d, grp, i) donor_index_function(d, grp, i, __FILE__, __LINE__)
static gmx_bool isInterchangable(t_hbdata* hb, int d, int a, int grpa, int grpd)
{
}
else if (grpd != hb->d.grp[id])
{
- gmx_fatal(FARGS, "Inconsistent donor groups, %d instead of %d, atom %d", grpd,
- hb->d.grp[id], d + 1);
+ gmx_fatal(FARGS, "Inconsistent donor groups, %d instead of %d, atom %d", grpd, hb->d.grp[id], d + 1);
}
if ((ia = hb->a.aptr[a]) == NOTSET)
{
}
else if (grpa != hb->a.grp[ia])
{
- gmx_fatal(FARGS, "Inconsistent acceptor groups, %d instead of %d, atom %d", grpa,
- hb->a.grp[ia], a + 1);
+ gmx_fatal(FARGS, "Inconsistent acceptor groups, %d instead of %d, atom %d", grpa, hb->a.grp[ia], a + 1);
}
if (bMerge)
}
else if (grpd != hb->d.grp[id])
{
- gmx_fatal(FARGS, "Inconsistent donor groups, %d instead of %d, atom %d", grpd,
- hb->d.grp[id], d + 1);
+ gmx_fatal(FARGS,
+ "Inconsistent donor groups, %d instead of %d, atom %d",
+ grpd,
+ hb->d.grp[id],
+ d + 1);
}
if ((ia = hb->a.aptr[a]) == NOTSET)
{
}
else if (grpa != hb->a.grp[ia])
{
- gmx_fatal(FARGS, "Inconsistent acceptor groups, %d instead of %d, atom %d", grpa,
- hb->a.grp[ia], a + 1);
+ gmx_fatal(FARGS,
+ "Inconsistent acceptor groups, %d instead of %d, atom %d",
+ grpa,
+ hb->a.grp[ia],
+ a + 1);
}
}
}
}
else
{
- printf("\nWill do grid-search on %dx%dx%d grid, rcut=%3.8f\n", ngrid[XX], ngrid[YY],
- ngrid[ZZ], rcut);
+ printf("\nWill do grid-search on %dx%dx%d grid, rcut=%3.8f\n", ngrid[XX], ngrid[YY], ngrid[ZZ], rcut);
}
if (((ngrid[XX] * ngrid[YY] * ngrid[ZZ]) * sizeof(grid)) > INT_MAX)
{
"the maximum of %zu. "
"You are likely either using a box that is too large (box dimensions are %3.8f "
"nm x%3.8f nm x%3.8f nm) or a cutoff (%3.8f nm) that is too small.",
- ngrid[XX], ngrid[YY], ngrid[ZZ], INT_MAX / sizeof(grid), box[XX][XX], box[YY][YY],
- box[ZZ][ZZ], rcut);
+ ngrid[XX],
+ ngrid[YY],
+ ngrid[ZZ],
+ INT_MAX / sizeof(grid),
+ box[XX][XX],
+ box[YY][YY],
+ box[ZZ][ZZ],
+ rcut);
}
snew(grid, ngrid[ZZ]);
for (z = 0; z < ngrid[ZZ]; z++)
/* Copy temp array to target array */
for (m = 0; (m <= nnframes); m++)
{
- _set_hb(hb0->h[0], m, htmp[m]);
- _set_hb(hb0->g[0], m, gtmp[m]);
+ set_hb_function(hb0->h[0], m, htmp[m]);
+ set_hb_function(hb0->g[0], m, gtmp[m]);
}
/* Set scalar variables */
}
else
{
- fp = xvgropen(fn, "Uninterrupted hydrogen bond lifetime", output_env_get_xvgr_tlabel(oenv),
- "()", oenv);
+ fp = xvgropen(
+ fn, "Uninterrupted hydrogen bond lifetime", output_env_get_xvgr_tlabel(oenv), "()", oenv);
}
xvgr_legend(fp, asize(leg), leg, oenv);
{
real kbt;
- kbt = BOLTZ * temp;
+ kbt = gmx::c_boltz * temp;
if (tau <= 0)
{
return -666;
}
else
{
- return kbt * std::log(kbt * tau / PLANCK);
+ return kbt * std::log(kbt * tau / gmx::c_planck);
}
}
{
chi2 += gmx::square(k * ct[i] - kp * nt[i] - kt[i]);
}
- compute_weighted_rates(n, t, ct, nt, kt, sigma_ct, sigma_nt, sigma_kt, &k, &kp,
- &sigma_k, &sigma_kp, fit_start);
+ compute_weighted_rates(
+ n, t, ct, nt, kt, sigma_ct, sigma_nt, sigma_kt, &k, &kp, &sigma_k, &sigma_kp, fit_start);
Q = 0; /* quality_of_fit(chi2, 2);*/
- ddg = BOLTZ * temp * sigma_k / k;
+ ddg = gmx::c_boltz * temp * sigma_k / k;
printf("Fitting paramaters chi^2 = %10g, Quality of fit = %10g\n", chi2, Q);
printf("The Rate and Delta G are followed by an error estimate\n");
printf("----------------------------------------------------------\n"
"Type Rate (1/ps) Sigma Time (ps) DG (kJ/mol) Sigma\n");
- printf("Forward %10.3f %6.2f %8.3f %10.3f %6.2f\n", k, sigma_k, 1 / k,
- calc_dg(1 / k, temp), ddg);
- ddg = BOLTZ * temp * sigma_kp / kp;
- printf("Backward %10.3f %6.2f %8.3f %10.3f %6.2f\n", kp, sigma_kp, 1 / kp,
- calc_dg(1 / kp, temp), ddg);
+ printf("Forward %10.3f %6.2f %8.3f %10.3f %6.2f\n",
+ k,
+ sigma_k,
+ 1 / k,
+ calc_dg(1 / k, temp),
+ ddg);
+ ddg = gmx::c_boltz * temp * sigma_kp / kp;
+ printf("Backward %10.3f %6.2f %8.3f %10.3f %6.2f\n",
+ kp,
+ sigma_kp,
+ 1 / kp,
+ calc_dg(1 / kp, temp),
+ ddg);
}
else
{
if (sc2 > 0)
{
kow = 2 * sck / sc2;
- printf("One-way %10.3f %s%8.3f %10.3f\n", kow, bError ? " " : "", 1 / kow,
+ printf("One-way %10.3f %s%8.3f %10.3f\n",
+ kow,
+ bError ? " " : "",
+ 1 / kow,
calc_dg(1 / kow, temp));
}
else
{
printf(" - Numerical problems computing HB thermodynamics:\n"
"sc2 = %g sn2 = %g sk2 = %g sck = %g snk = %g scn = %g\n",
- sc2, sn2, sk2, sck, snk, scn);
+ sc2,
+ sn2,
+ sk2,
+ sck,
+ snk,
+ scn);
}
/* Determine integral of the correlation function */
tau_hb = evaluate_integral(n, t, ct, nullptr, (t[n - 1] - t[0]) / 2, &dtau);
- printf("Integral %10.3f %s%8.3f %10.3f\n", 1 / tau_hb, bError ? " " : "", tau_hb,
+ printf("Integral %10.3f %s%8.3f %10.3f\n",
+ 1 / tau_hb,
+ bError ? " " : "",
+ tau_hb,
calc_dg(tau_hb, temp));
e_1 = std::exp(-1.0);
for (i = 0; (i < n - 2); i++)
{
/* Determine tau_relax from linear interpolation */
tau_rlx = t[i] - t[0] + (e_1 - ct[i]) * (t[i + 1] - t[i]) / (ct[i + 1] - ct[i]);
- printf("Relaxation %10.3f %8.3f %s%10.3f\n", 1 / tau_rlx, tau_rlx,
- bError ? " " : "", calc_dg(tau_rlx, temp));
+ printf("Relaxation %10.3f %8.3f %s%10.3f\n",
+ 1 / tau_rlx,
+ tau_rlx,
+ bError ? " " : "",
+ calc_dg(tau_rlx, temp));
}
}
else
FILE* fp;
int i, j, k, m, ihb, idist, n2, nn;
- const char* legLuzar[] = { "Ac\\sfin sys\\v{}\\z{}(t)", "Ac(t)", "Cc\\scontact,hb\\v{}\\z{}(t)",
+ const char* legLuzar[] = { "Ac\\sfin sys\\v{}\\z{}(t)",
+ "Ac(t)",
+ "Cc\\scontact,hb\\v{}\\z{}(t)",
"-dAc\\sfs\\v{}\\z{}/dt" };
- gmx_bool bNorm = FALSE;
- double nhb = 0;
- real * rhbex = nullptr, *ht, *gt, *ght, *dght, *kt;
- real * ct, tail, tail2, dtail, *cct;
- const real tol = 1e-3;
- int nframes = hb->nframes;
+ gmx_bool bNorm = FALSE;
+ double nhb = 0;
+ real * rhbex = nullptr, *ht, *gt, *ght, *dght, *kt;
+ real * ct, tail, tail2, dtail, *cct;
+ const real tol = 1e-3;
+ int nframes = hb->nframes;
unsigned int **h = nullptr, **g = nullptr;
int nh, nhbonds, nhydro;
t_hbond* hbh;
}
/* The autocorrelation function is normalized after summation only */
- low_do_autocorr(nullptr, oenv, nullptr, nframes, 1, -1, &rhbex,
- hb->time[1] - hb->time[0], eacNormal, 1, FALSE, bNorm, FALSE, 0,
- -1, 0);
+ low_do_autocorr(nullptr,
+ oenv,
+ nullptr,
+ nframes,
+ 1,
+ -1,
+ &rhbex,
+ hb->time[1] - hb->time[0],
+ eacNormal,
+ 1,
+ FALSE,
+ bNorm,
+ FALSE,
+ 0,
+ -1,
+ 0);
/* Cross correlation analysis for thermodynamics */
for (j = nframes; (j < n2); j++)
printf("\nWARNING: Correlation function is probably not long enough\n"
"because the standard deviation in the tail of C(t) > %g\n"
"Tail value (average C(t) over second half of acf): %g +/- %g\n",
- tol, tail, dtail);
+ tol,
+ tail,
+ dtail);
}
for (j = 0; (j < nn); j++)
{
for (j = 0; (j < nn); j++)
{
- fprintf(fp, "%10g %10g %10g %10g %10g\n", hb->time[j] - hb->time[0], ct[j], cct[j],
- ght[j], kt[j]);
+ fprintf(fp, "%10g %10g %10g %10g %10g\n", hb->time[j] - hb->time[0], ct[j], cct[j], ght[j], kt[j]);
}
xvgrclose(fp);
"If you set [TT]-shell[tt], you will be asked for an additional index group",
"which should contain exactly one atom. In this case, only hydrogen",
- "bonds between atoms within the shell distance from the one atom are", "considered.[PAR]",
+ "bonds between atoms within the shell distance from the one atom are",
+ "considered.[PAR]",
"With option -ac, rate constants for hydrogen bonding can be derived with the",
"model of Luzar and Chandler (Nature 379:55, 1996; J. Chem. Phys. 113:23, 2000).",
"n(t) can be defined as either all pairs that are not within contact distance r at time t",
"(corresponding to leaving the -r2 option at the default value 0) or all pairs that",
"are within distance r2 (corresponding to setting a second cut-off value with option -r2).",
- "See mentioned literature for more details and definitions.", "[PAR]",
+ "See mentioned literature for more details and definitions.",
+ "[PAR]",
/* "It is also possible to analyse specific hydrogen bonds with",
"[TT]-sel[tt]. This index file must contain a group of atom triplets",
"note also that no check is made for the types of atoms.[PAR]",
*/
- "[BB]Output:[bb]", "", " * [TT]-num[tt]: number of hydrogen bonds as a function of time.",
+ "[BB]Output:[bb]",
+ "",
+ " * [TT]-num[tt]: number of hydrogen bonds as a function of time.",
" * [TT]-ac[tt]: average over all autocorrelations of the existence",
" functions (either 0 or 1) of all hydrogen bonds.",
" * [TT]-dist[tt]: distance distribution of all hydrogen bonds.",
" all solvent atoms involved in insertion.",
" * [TT]-hbm[tt]: existence matrix for all hydrogen bonds over all",
" frames, this also contains information on solvent insertion",
- " into hydrogen bonds. Ordering is identical to that in [TT]-hbn[tt]", " index file.",
+ " into hydrogen bonds. Ordering is identical to that in [TT]-hbn[tt]",
+ " index file.",
" * [TT]-dan[tt]: write out the number of donors and acceptors analyzed for",
" each timeframe. This is especially useful when using [TT]-shell[tt].",
" * [TT]-nhbdist[tt]: compute the number of HBonds per hydrogen in order to",
- " compare results to Raman Spectroscopy.", "",
+ " compare results to Raman Spectroscopy.",
+ "",
"Note: options [TT]-ac[tt], [TT]-life[tt], [TT]-hbn[tt] and [TT]-hbm[tt]",
"require an amount of memory proportional to the total numbers of donors",
"times the total number of acceptors in the selected group(s)."
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm, npargs, ppa,
- asize(desc), desc, asize(bugs), bugs, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
sfree(ppa);
return 0;
/* process input */
bSelected = FALSE;
- ccut = std::cos(acut * DEG2RAD);
+ ccut = std::cos(acut * gmx::c_deg2Rad);
if (bContact)
{
if (opt2bSet("-nhbdist", NFILE, fnm))
{
const char* leg[MAXHH + 1] = { "0 HBs", "1 HB", "2 HBs", "3 HBs", "Total" };
- fpnhb = xvgropen(opt2fn("-nhbdist", NFILE, fnm), "Number of donor-H with N HBs",
- output_env_get_xvgr_tlabel(oenv), "N", oenv);
+ fpnhb = xvgropen(opt2fn("-nhbdist", NFILE, fnm),
+ "Number of donor-H with N HBs",
+ output_env_get_xvgr_tlabel(oenv),
+ "N",
+ oenv);
xvgr_legend(fpnhb, asize(leg), leg, oenv);
}
{
if (ISINGRP(datable[index[1][i]]))
{
- gmx_fatal(FARGS, "Partial overlap between groups '%s' and '%s'", grpnames[0],
- grpnames[1]);
+ gmx_fatal(FARGS, "Partial overlap between groups '%s' and '%s'", grpnames[0], grpnames[1]);
}
}
}
{
printf("Calculating %s "
"between %s (%d atoms) and %s (%d atoms)\n",
- bContact ? "contacts" : "hydrogen bonds", grpnames[0], isize[0], grpnames[1],
+ bContact ? "contacts" : "hydrogen bonds",
+ grpnames[0],
+ isize[0],
+ grpnames[1],
isize[1]);
}
else
{
- fprintf(stderr, "Calculating %s in %s (%d atoms)\n",
- bContact ? "contacts" : "hydrogen bonds", grpnames[0], isize[0]);
+ fprintf(stderr,
+ "Calculating %s in %s (%d atoms)\n",
+ bContact ? "contacts" : "hydrogen bonds",
+ grpnames[0],
+ isize[0]);
}
}
sfree(datable);
gen_datable(index[i], isize[i], datable, top.atoms.nr);
if (bContact)
{
- search_acceptors(&top, isize[i], index[i], &hb->a, i, bNitAcc, TRUE,
- (bTwo && (i == gr0)) || !bTwo, datable);
- search_donors(&top, isize[i], index[i], &hb->d, i, TRUE,
- (bTwo && (i == gr1)) || !bTwo, datable);
+ search_acceptors(
+ &top, isize[i], index[i], &hb->a, i, bNitAcc, TRUE, (bTwo && (i == gr0)) || !bTwo, datable);
+ search_donors(&top, isize[i], index[i], &hb->d, i, TRUE, (bTwo && (i == gr1)) || !bTwo, datable);
}
else
{
shatom = shidx[0];
printf("Will calculate hydrogen bonds within a shell "
"of %g nm around atom %i\n",
- rshell, shatom + 1);
+ rshell,
+ shatom + 1);
}
/* Analyze trajectory */
snew(rdist, nrbin + 1);
#if !GMX_OPENMP
-# define __ADIST adist
-# define __RDIST rdist
-# define __HBDATA hb
-#else /* GMX_OPENMP ================================================== \
- * Set up the OpenMP stuff, | \
- * like the number of threads and such | \
- * Also start the parallel loop. | \
- */
-# define __ADIST p_adist[threadNr]
-# define __RDIST p_rdist[threadNr]
-# define __HBDATA p_hb[threadNr]
+# define __ADIST adist // NOLINT(bugprone-reserved-identifier)
+# define __RDIST rdist // NOLINT(bugprone-reserved-identifier)
+# define __HBDATA hb // NOLINT(bugprone-reserved-identifier)
+#else /* GMX_OPENMP ================================================== \
+ * Set up the OpenMP stuff, | \
+ * like the number of threads and such | \
+ * Also start the parallel loop. | \
+ */
+# define __ADIST p_adist[threadNr] // NOLINT(bugprone-reserved-identifier)
+# define __RDIST p_rdist[threadNr] // NOLINT(bugprone-reserved-identifier)
+# define __HBDATA p_hb[threadNr] // NOLINT(bugprone-reserved-identifier)
#endif
if (bOMP)
{
/* Make a thread pool here,
* instead of forking anew at every frame. */
-#pragma omp parallel firstprivate(i) private( \
- j, h, ii, hh, xi, yi, zi, xj, yj, zj, threadNr, dist, ang, icell, jcell, grp, ogrp, ai, \
- aj, xjj, yjj, zjj, ihb, resdist, k, bTric, bEdge_xjj, bEdge_yjj) default(shared)
+#pragma omp parallel firstprivate(i) private(j, \
+ h, \
+ ii, \
+ hh, \
+ xi, \
+ yi, \
+ zi, \
+ xj, \
+ yj, \
+ zj, \
+ threadNr, \
+ dist, \
+ ang, \
+ icell, \
+ jcell, \
+ grp, \
+ ogrp, \
+ ai, \
+ aj, \
+ xjj, \
+ yjj, \
+ zjj, \
+ ihb, \
+ resdist, \
+ k, \
+ bTric, \
+ bEdge_xjj, \
+ bEdge_yjj) default(shared)
{ /* Start of parallel region */
if (bOMP)
{
{
try
{
- build_grid(hb, x, x[shatom], bBox, box, hbox, (rcut > r2cut) ? rcut : r2cut,
- rshell, ngrid, grid);
+ build_grid(hb, x, x[shatom], bBox, box, hbox, (rcut > r2cut) ? rcut : r2cut, rshell, ngrid, grid);
reset_nhbonds(&(hb->d));
if (debug && bDebug)
int dd = index[0][i];
int aa = index[0][i + 2];
/* int */ hh = index[0][i + 1];
- ihb = is_hbond(hb, ii, ii, dd, aa, rcut, r2cut, ccut, x, bBox, box,
- hbox, &dist, &ang, bDA, &h, bContact, bMerge);
+ ihb = is_hbond(
+ hb, ii, ii, dd, aa, rcut, r2cut, ccut, x, bBox, box, hbox, &dist, &ang, bDA, &h, bContact, bMerge);
if (ihb)
{
/* loop over all adjacent gridcells (xj,yj,zj) */
for (zjj = grid_loop_begin(ngrid[ZZ], zi, bTric, FALSE);
- zjj <= grid_loop_end(ngrid[ZZ], zi, bTric, FALSE); zjj++)
+ zjj <= grid_loop_end(ngrid[ZZ], zi, bTric, FALSE);
+ zjj++)
{
zj = grid_mod(zjj, ngrid[ZZ]);
bEdge_yjj = (zj == 0) || (zj == ngrid[ZZ] - 1);
j = jcell->atoms[aj];
/* check if this once was a h-bond */
- ihb = is_hbond(__HBDATA, grp, ogrp, i, j,
- rcut, r2cut, ccut, x, bBox,
- box, hbox, &dist, &ang, bDA,
- &h, bContact, bMerge);
+ ihb = is_hbond(__HBDATA,
+ grp,
+ ogrp,
+ i,
+ j,
+ rcut,
+ r2cut,
+ ccut,
+ x,
+ bBox,
+ box,
+ hbox,
+ &dist,
+ &ang,
+ bDA,
+ &h,
+ bContact,
+ bMerge);
if (ihb)
{
/* add to index if not already there */
/* Add a hbond */
- add_hbond(__HBDATA, i, j, h, grp, ogrp,
- nframes, bMerge, ihb, bContact);
+ add_hbond(__HBDATA, i, j, h, grp, ogrp, nframes, bMerge, ihb, bContact);
/* make angle and distance distributions */
if (ihb == hbHB && !bContact)
"for an hbond: %f",
dist);
}
- ang *= RAD2DEG;
+ ang *= gmx::c_rad2Deg;
__ADIST[static_cast<int>(ang / abin)]++;
__RDIST[static_cast<int>(dist / rbin)]++;
if (!bTwo)
{
gmx_fatal(
FARGS,
- "Invalid donor %d", i);
+ "Invalid donor %d",
+ i);
}
if (acceptor_index(&hb->a, ogrp, j)
== NOTSET)
if (nframes < 2 && (opt2bSet("-ac", NFILE, fnm) || opt2bSet("-life", NFILE, fnm)))
{
- gmx_fatal(FARGS,
- "Cannot calculate autocorrelation of life times with less than two frames");
+ gmx_fatal(FARGS, "Cannot calculate autocorrelation of life times with less than two frames");
}
free_grid(ngrid, &grid);
{
printf("Found %d different %s in trajectory\n"
"Found %d different atom-pairs within %s distance\n",
- hb->nrhb, bContact ? "contacts" : "hydrogen bonds", hb->nrdist,
+ hb->nrhb,
+ bContact ? "contacts" : "hydrogen bonds",
+ hb->nrdist,
(r2cut > 0) ? "second cut-off" : "hydrogen bonding");
if (bMerge)
/* Print out number of hbonds and distances */
aver_nhb = 0;
aver_dist = 0;
- fp = xvgropen(opt2fn("-num", NFILE, fnm), bContact ? "Contacts" : "Hydrogen Bonds",
- output_env_get_xvgr_tlabel(oenv), "Number", oenv);
+ fp = xvgropen(opt2fn("-num", NFILE, fnm),
+ bContact ? "Contacts" : "Hydrogen Bonds",
+ output_env_get_xvgr_tlabel(oenv),
+ "Number",
+ oenv);
snew(leg, 2);
snew(leg[0], STRLEN);
snew(leg[1], STRLEN);
sum += rdist[i];
}
- fp = xvgropen(opt2fn("-dist", NFILE, fnm), "Hydrogen Bond Distribution",
+ fp = xvgropen(opt2fn("-dist", NFILE, fnm),
+ "Hydrogen Bond Distribution",
bDA ? "Donor - Acceptor Distance (nm)" : "Hydrogen - Acceptor Distance (nm)",
- "", oenv);
+ "",
+ oenv);
for (i = 0; i < nrbin; i++)
{
fprintf(fp, "%10g %10g\n", (i + 0.5) * rbin, rdist[i] / (rbin * sum));
sum += adist[i];
}
- fp = xvgropen(opt2fn("-ang", NFILE, fnm), "Hydrogen Bond Distribution",
- "Hydrogen - Donor - Acceptor Angle (\\SO\\N)", "", oenv);
+ fp = xvgropen(opt2fn("-ang", NFILE, fnm),
+ "Hydrogen Bond Distribution",
+ "Hydrogen - Donor - Acceptor Angle (\\SO\\N)",
+ "",
+ oenv);
for (i = 0; i < nabin; i++)
{
fprintf(fp, "%10g %10g\n", (i + 0.5) * abin, adist[i] / (abin * sum));
/* Print HB in alpha-helix */
if (opt2bSet("-hx", NFILE, fnm))
{
- fp = xvgropen(opt2fn("-hx", NFILE, fnm), "Hydrogen Bonds", output_env_get_xvgr_tlabel(oenv),
- "Count", oenv);
+ fp = xvgropen(opt2fn("-hx", NFILE, fnm),
+ "Hydrogen Bonds",
+ output_env_get_xvgr_tlabel(oenv),
+ "Count",
+ oenv);
xvgr_legend(fp, NRHXTYPES, hxtypenames, oenv);
for (i = 0; i < nframes; i++)
{
}
printf("Average number of %s per timeframe %.3f out of %g possible\n",
- bContact ? "contacts" : "hbonds", bContact ? aver_dist : aver_nhb, max_nhb);
+ bContact ? "contacts" : "hbonds",
+ bContact ? aver_dist : aver_nhb,
+ max_nhb);
/* Do Autocorrelation etc. */
if (hb->bHBmap)
}
if (opt2bSet("-ac", NFILE, fnm))
{
- do_hbac(opt2fn("-ac", NFILE, fnm), hb, nDump, bMerge, bContact, fit_start, temp,
- r2cut > 0, oenv, nThreads);
+ do_hbac(opt2fn("-ac", NFILE, fnm), hb, nDump, bMerge, bContact, fit_start, temp, r2cut > 0, oenv, nThreads);
}
if (opt2bSet("-life", NFILE, fnm))
{
#define USE_THIS_GROUP(j) (((j) == gr0) || (bTwo && ((j) == gr1)))
- fp = xvgropen(opt2fn("-dan", NFILE, fnm), "Donors and Acceptors",
- output_env_get_xvgr_tlabel(oenv), "Count", oenv);
+ fp = xvgropen(opt2fn("-dan", NFILE, fnm),
+ "Donors and Acceptors",
+ output_env_get_xvgr_tlabel(oenv),
+ "Count",
+ oenv);
nleg = (bTwo ? 2 : 1) * 2;
snew(legnames, nleg);
i = 0;
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
gmx_fatal(FARGS,
"Sorry can only run when the number of atoms in the run input file (%d) is equal "
"to the number in the trajectory (%d)",
- top->atoms.nr, natoms);
+ top->atoms.nr,
+ natoms);
}
- bb = mkbbind(ftp2fn(efNDX, NFILE, fnm), &nres, &nbb, r0, &nall, &allindex, top->atoms.atomname,
- top->atoms.atom, top->atoms.resinfo);
+ bb = mkbbind(ftp2fn(efNDX, NFILE, fnm),
+ &nres,
+ &nbb,
+ r0,
+ &nall,
+ &allindex,
+ top->atoms.atomname,
+ top->atoms.atom,
+ top->atoms.resinfo);
snew(bbindex, natoms);
snew(caindex, nres);
if (teller == 1)
{
- write_sto_conf(opt2fn("-cz", NFILE, fnm), "Helix fitted to Z-Axis", &(top->atoms),
- x, nullptr, pbcType, box);
+ write_sto_conf(
+ opt2fn("-cz", NFILE, fnm), "Helix fitted to Z-Axis", &(top->atoms), x, nullptr, pbcType, box);
}
xf[efhRAD].val = radius(xf[efhRAD].fp2, nca, caindex, x);
}
av_phipsi(xf[efhPHI].fp, xf[efhPSI].fp, xf[efhPHI].fp2, xf[efhPSI].fp2, t, nres, bb);
- av_hblen(xf[efhHB3].fp, xf[efhHB3].fp2, xf[efhHB4].fp, xf[efhHB4].fp2, xf[efhHB5].fp,
- xf[efhHB5].fp2, t, nres, bb);
+ av_hblen(xf[efhHB3].fp,
+ xf[efhHB3].fp2,
+ xf[efhHB4].fp,
+ xf[efhHB4].fp2,
+ xf[efhHB5].fp,
+ xf[efhHB5].fp2,
+ t,
+ nres,
+ bb);
}
} while (read_next_x(oenv, status, &t, x, box));
fprintf(stderr, "\n");
fprintf(xf[efhRMSA].fp, "%10d %10g\n", r0 + i, bb[i].rmsa / bb[i].nrms);
}
fprintf(xf[efhAHX].fp, "%10d %10g\n", r0 + i, (bb[i].nhx * 100.0) / static_cast<real>(teller));
- fprintf(xf[efhJCA].fp, "%10d %10g\n", r0 + i,
- 140.3 + (bb[i].jcaha / static_cast<double>(teller)));
+ fprintf(xf[efhJCA].fp, "%10d %10g\n", r0 + i, 140.3 + (bb[i].jcaha / static_cast<double>(teller)));
}
for (i = 0; (i < efhNR); i++)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxana/gstat.h"
#include "gromacs/math/do_fit.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm, NPA, pa, asize(desc), desc, 0,
- nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME, NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
if (bIncremental)
{
- fptilt = xvgropen(opt2fn("-otilt", NFILE, fnm), "Incremental local helix tilt", "Time(ps)",
- "Tilt (degrees)", oenv);
- fprotation = xvgropen(opt2fn("-orot", NFILE, fnm), "Incremental local helix rotation",
- "Time(ps)", "Rotation (degrees)", oenv);
+ fptilt = xvgropen(opt2fn("-otilt", NFILE, fnm),
+ "Incremental local helix tilt",
+ "Time(ps)",
+ "Tilt (degrees)",
+ oenv);
+ fprotation = xvgropen(opt2fn("-orot", NFILE, fnm),
+ "Incremental local helix rotation",
+ "Time(ps)",
+ "Rotation (degrees)",
+ oenv);
}
else
{
- fptilt = xvgropen(opt2fn("-otilt", NFILE, fnm), "Cumulative local helix tilt", "Time(ps)",
- "Tilt (degrees)", oenv);
- fprotation = xvgropen(opt2fn("-orot", NFILE, fnm), "Cumulative local helix rotation",
- "Time(ps)", "Rotation (degrees)", oenv);
+ fptilt = xvgropen(opt2fn("-otilt", NFILE, fnm),
+ "Cumulative local helix tilt",
+ "Time(ps)",
+ "Tilt (degrees)",
+ oenv);
+ fprotation = xvgropen(opt2fn("-orot", NFILE, fnm),
+ "Cumulative local helix rotation",
+ "Time(ps)",
+ "Rotation (degrees)",
+ oenv);
}
clear_rvecs(3, unitaxes);
rvec_sub(bSC ? x_SC[i] : x_CA[i], residueorigin[i], residuevector[i]);
svmul(1.0 / norm(residuevector[i]), residuevector[i], residuevector[i]);
cprod(residuehelixaxis[i], residuevector[i], axis3[i]);
- fprintf(fpaxis, "%15.12g %15.12g %15.12g ", residuehelixaxis[i][0],
- residuehelixaxis[i][1], residuehelixaxis[i][2]);
- fprintf(fpcenter, "%15.12g %15.12g %15.12g ", residueorigin[i][0],
- residueorigin[i][1], residueorigin[i][2]);
+ fprintf(fpaxis,
+ "%15.12g %15.12g %15.12g ",
+ residuehelixaxis[i][0],
+ residuehelixaxis[i][1],
+ residuehelixaxis[i][2]);
+ fprintf(fpcenter,
+ "%15.12g %15.12g %15.12g ",
+ residueorigin[i][0],
+ residueorigin[i][1],
+ residueorigin[i][2]);
fprintf(fprise, "%15.12g ", residuerise[i]);
fprintf(fpradius, "%15.12g ", residueradius[i]);
}
}
- find_tetra_order_grid(top, pbcType, natoms, box, x, isize[0], index[0], &sg, &sk, *nslicex,
- *nslicey, nslicez, sg_grid, sk_grid);
+ find_tetra_order_grid(
+ top, pbcType, natoms, box, x, isize[0], index[0], &sg, &sk, *nslicex, *nslicey, nslicez, sg_grid, sk_grid);
GMX_RELEASE_ASSERT(sk_fravg != nullptr, "Trying to dereference NULL sk_fravg pointer");
for (i = 0; i < *nslicex; i++)
{
/*Debugging for printing out the entire order parameter meshes.*/
if (debug)
{
- fpsg = xvgropen("sg_ang_mesh", "S\\sg\\N Angle Order Parameter / Meshpoint", "(nm)",
- "S\\sg\\N", oenv);
- fpsk = xvgropen("sk_dist_mesh", "S\\sk\\N Distance Order Parameter / Meshpoint", "(nm)",
- "S\\sk\\N", oenv);
+ fpsg = xvgropen(
+ "sg_ang_mesh", "S\\sg\\N Angle Order Parameter / Meshpoint", "(nm)", "S\\sg\\N", oenv);
+ fpsk = xvgropen(
+ "sk_dist_mesh", "S\\sk\\N Distance Order Parameter / Meshpoint", "(nm)", "S\\sk\\N", oenv);
for (n = 0; n < (*nframes); n++)
{
fprintf(fpsg, "%i\n", n);
{
for (k = 0; k < nslicez; k++)
{
- fprintf(fpsg, "%4f %4f %4f %8f\n", (i + 0.5) * box[XX][XX] / (*nslicex),
+ fprintf(fpsg,
+ "%4f %4f %4f %8f\n",
+ (i + 0.5) * box[XX][XX] / (*nslicex),
(j + 0.5) * box[YY][YY] / (*nslicey),
- (k + 0.5) * box[ZZ][ZZ] / nslicez, sg_4d[n][i][j][k]);
- fprintf(fpsk, "%4f %4f %4f %8f\n", (i + 0.5) * box[XX][XX] / (*nslicex),
+ (k + 0.5) * box[ZZ][ZZ] / nslicez,
+ sg_4d[n][i][j][k]);
+ fprintf(fpsk,
+ "%4f %4f %4f %8f\n",
+ (i + 0.5) * box[XX][XX] / (*nslicex),
(j + 0.5) * box[YY][YY] / (*nslicey),
- (k + 0.5) * box[ZZ][ZZ] / nslicez, sk_4d[n][i][j][k]);
+ (k + 0.5) * box[ZZ][ZZ] / nslicez,
+ sk_4d[n][i][j][k]);
}
}
}
}
}
- write_xpm(xpmfile1, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks,
- profile1, min1, max1, lo, hi, &maplevels);
- write_xpm(xpmfile2, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks,
- profile2, min2, max2, lo, hi, &maplevels);
+ write_xpm(xpmfile1, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks, profile1, min1, max1, lo, hi, &maplevels);
+ write_xpm(xpmfile2, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks, profile2, min2, max2, lo, hi, &maplevels);
}
gmx_ffclose(xpmfile1);
const char * ndxfnm, *tpsfnm, *trxfnm;
gmx_output_env_t* oenv;
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
{
gmx_fatal(FARGS, "No or not correct number (2) of output-files: %td", intfn.ssize());
}
- calc_tetra_order_interface(ndxfnm, tpsfnm, trxfnm, binwidth, nsttblock, &frames, &xslices,
- &yslices, sg1, sg2, &intfpos, oenv);
+ calc_tetra_order_interface(
+ ndxfnm, tpsfnm, trxfnm, binwidth, nsttblock, &frames, &xslices, &yslices, sg1, sg2, &intfpos, oenv);
writesurftoxpms(intfpos, frames, xslices, yslices, binwidth, intfn, nlevels);
if (bFourier)
t_filenm fnm[] = { { efEDR, "-f", "ener", ffREAD }, { efXVG, "-o", "lie", ffWRITE } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, NPA, pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
ld = analyze_names(nre, enm, ligand);
snew(fr, 1);
- out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "LIE free energy estimate", "Time (ps)",
- "DGbind (kJ/mol)", oenv);
+ out = xvgropen(
+ ftp2fn(efXVG, NFILE, fnm), "LIE free energy estimate", "Time (ps)", "DGbind (kJ/mol)", oenv);
while (do_enx(fp, fr))
{
ct = check_times(fr->t);
if (nframes > 0)
{
- printf("DGbind = %.3f (%.3f)\n", lieaver / nframes,
+ printf("DGbind = %.3f (%.3f)\n",
+ lieaver / nframes,
std::sqrt(lieav2 / nframes - gmx::square(lieaver / nframes)));
}
/* format error occured */
case sError:
- gmx_fatal(FARGS, "Error in the list of eigenvectors for %s at pos %td with char %c",
- listname, pos - startpos, *(pos - 1));
+ gmx_fatal(FARGS,
+ "Error in the list of eigenvectors for %s at pos %td with char %c",
+ listname,
+ pos - startpos,
+ *(pos - 1));
/* logical error occured */
case sZero:
gmx_fatal(FARGS,
"Error in the list of eigenvectors for %s at pos %td: eigenvector 0 is "
"not valid",
- listname, pos - startpos);
+ listname,
+ pos - startpos);
case sSmaller:
gmx_fatal(FARGS,
"Error in the list of eigenvectors for %s at pos %td: second index %d is "
"not bigger than %d",
- listname, pos - startpos, end_number, number);
+ listname,
+ pos - startpos,
+ end_number,
+ number);
}
++pos; /* read next character */
} /*scanner has finished */
gmx_fatal(FARGS,
"Selected eigenvector %d is higher than maximum number %d of available "
"eigenvectors",
- eig_list[n], nvec);
+ eig_list[n],
+ nvec);
}
copy_rvec(eigvecs[eig_list[n] - 1][i], x);
fprintf(fp, "%8.5f %8.5f %8.5f\n", x[XX], x[YY], x[ZZ]);
/* write edi-file */
/*Header*/
- fprintf(fp, "#MAGIC\n %d \n#NINI\n %d\n#FITMAS\n %d\n#ANALYSIS_MAS\n %d\n", MAGIC, edpars->nini,
- int(edpars->fitmas), int(edpars->pcamas));
- fprintf(fp, "#OUTFRQ\n %d\n#MAXLEN\n %d\n#SLOPECRIT\n %f\n", edpars->outfrq, edpars->maxedsteps,
- edpars->slope);
+ fprintf(fp,
+ "#MAGIC\n %d \n#NINI\n %d\n#FITMAS\n %d\n#ANALYSIS_MAS\n %d\n",
+ MAGIC,
+ edpars->nini,
+ int(edpars->fitmas),
+ int(edpars->pcamas));
+ fprintf(fp, "#OUTFRQ\n %d\n#MAXLEN\n %d\n#SLOPECRIT\n %f\n", edpars->outfrq, edpars->maxedsteps, edpars->slope);
fprintf(fp,
"#PRESTEPS\n %d\n#DELTA_F0\n %f\n#INIT_DELTA_F\n %f\n#TAU\n %f\n#EFL_NULL\n "
"%f\n#ALPHA2\n %f\n#KT\n %f\n#HARMONIC\n %d\n#CONST_FORCE_FLOODING\n %d\n",
- edpars->presteps, edpars->flood.deltaF0, edpars->flood.deltaF, edpars->flood.tau,
- edpars->flood.constEfl, edpars->flood.alpha2, edpars->flood.kT,
- int(edpars->flood.bHarmonic), int(edpars->flood.bConstForce));
+ edpars->presteps,
+ edpars->flood.deltaF0,
+ edpars->flood.deltaF,
+ edpars->flood.tau,
+ edpars->flood.constEfl,
+ edpars->flood.alpha2,
+ edpars->flood.kT,
+ int(edpars->flood.bHarmonic),
+ int(edpars->flood.bConstForce));
/* Average and reference positions */
write_t_edx(fp, edpars->sref, "NREF, XREF");
/*Eigenvectors */
write_eigvec(fp, edpars->ned, eig_listen[evMON], eigvecs, nvec, "COMPONENTS GROUP 1", nullptr);
- write_eigvec(fp, edpars->ned, eig_listen[evLINFIX], eigvecs, nvec, "COMPONENTS GROUP 2",
- evStepList[evLINFIX]);
- write_eigvec(fp, edpars->ned, eig_listen[evLINACC], eigvecs, nvec, "COMPONENTS GROUP 3",
- evStepList[evLINACC]);
- write_eigvec(fp, edpars->ned, eig_listen[evRADFIX], eigvecs, nvec, "COMPONENTS GROUP 4",
- evStepList[evRADFIX]);
+ write_eigvec(fp, edpars->ned, eig_listen[evLINFIX], eigvecs, nvec, "COMPONENTS GROUP 2", evStepList[evLINFIX]);
+ write_eigvec(fp, edpars->ned, eig_listen[evLINACC], eigvecs, nvec, "COMPONENTS GROUP 3", evStepList[evLINACC]);
+ write_eigvec(fp, edpars->ned, eig_listen[evRADFIX], eigvecs, nvec, "COMPONENTS GROUP 4", evStepList[evRADFIX]);
write_eigvec(fp, edpars->ned, eig_listen[evRADACC], eigvecs, nvec, "COMPONENTS GROUP 5", nullptr);
write_eigvec(fp, edpars->ned, eig_listen[evRADCON], eigvecs, nvec, "COMPONENTS GROUP 6", nullptr);
- write_eigvec(fp, edpars->ned, eig_listen[evFLOOD], eigvecs, nvec, "COMPONENTS GROUP 7",
- evStepList[evFLOOD]);
+ write_eigvec(fp, edpars->ned, eig_listen[evFLOOD], eigvecs, nvec, "COMPONENTS GROUP 7", evStepList[evFLOOD]);
/*Target and Origin positions */
ntar = read_conffile(StructureFile, &xtar);
printf("Select an index group of %d elements that corresponds to the atoms in the structure "
"file %s\n",
- ntar, StructureFile);
+ ntar,
+ StructureFile);
get_index(atoms, IndexFile, 1, &ngro, &igro, &grpname);
if (ngro != ntar)
{
if (opt2parg_bSet(evOptions[ev_class], NPA, pa))
{
/*get list of eigenvectors*/
- nvecs = sscan_list(&(listen[ev_class]), opt2parg_str(evOptions[ev_class], NPA, pa),
- evOptions[ev_class]);
+ nvecs = sscan_list(
+ &(listen[ev_class]), opt2parg_str(evOptions[ev_class], NPA, pa), evOptions[ev_class]);
if (ev_class < evStepNr - 2)
{
/*if apropriate get list of stepsizes for these eigenvectors*/
if (opt2parg_bSet(evStepOptions[ev_class], NPA, pa))
{
- evStepList[ev_class] = scan_vecparams(opt2parg_str(evStepOptions[ev_class], NPA, pa),
- evStepOptions[ev_class], nvecs);
+ evStepList[ev_class] = scan_vecparams(
+ opt2parg_str(evStepOptions[ev_class], NPA, pa), evStepOptions[ev_class], nvecs);
}
else /*if list is not given fill with zeros */
{
EigvecFile = opt2fn("-f", NFILE, fnm);
/*read eigenvectors from eigvec.trr*/
- read_eigenvectors(EigvecFile, &nav, &bFit1, &xref1, &edi_params.fitmas, &xav1,
- &edi_params.pcamas, &nvec1, &eignr1, &eigvec1, &eigval1);
+ read_eigenvectors(
+ EigvecFile, &nav, &bFit1, &xref1, &edi_params.fitmas, &xav1, &edi_params.pcamas, &nvec1, &eignr1, &eigvec1, &eigval1);
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &pbcType, &xtop, nullptr, topbox, false);
atoms = &top.atoms;
if (listen[evFLOOD][0] != 0)
{
- read_eigenvalues(listen[evFLOOD], opt2fn("-eig", NFILE, fnm), evStepList[evFLOOD],
- bHesse, kB * T, nav);
+ read_eigenvalues(
+ listen[evFLOOD], opt2fn("-eig", NFILE, fnm), evStepList[evFLOOD], bHesse, kB * T, nav);
}
edi_params.flood.tau = tau;
gmx_output_env_t* oenv;
gmx_rmpbc_t gpbc = nullptr;
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm, asize(pa), pa, asize(desc), desc,
- 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
useatoms.resinfo[i] = top.atoms.resinfo[prevres];
if (debug)
{
- fprintf(debug, "New residue: atom %5s %5s %6d, index entry %5d, newres %5d\n",
+ fprintf(debug,
+ "New residue: atom %5s %5s %6d, index entry %5d, newres %5d\n",
*(top.atoms.resinfo[top.atoms.atom[ii].resind].name),
- *(top.atoms.atomname[ii]), ii, i, newres);
+ *(top.atoms.atomname[ii]),
+ ii,
+ i,
+ newres);
}
}
useatoms.atom[i].resind = newres;
if (bFrames)
{
sprintf(label, "t=%.0f ps", t);
- write_xpm(out, 0, label, "Distance (nm)", "Residue Index", "Residue Index", nres, nres,
- resnr, resnr, mdmat, 0, truncate, rlo, rhi, &nlevels);
+ write_xpm(out,
+ 0,
+ label,
+ "Distance (nm)",
+ "Residue Index",
+ "Residue Index",
+ nres,
+ nres,
+ resnr,
+ resnr,
+ mdmat,
+ 0,
+ truncate,
+ rlo,
+ rhi,
+ &nlevels);
}
} while (read_next_x(oenv, status, &t, x, box));
fprintf(stderr, "\n");
totmdmat[i][j] /= nframes;
}
}
- write_xpm(opt2FILE("-mean", NFILE, fnm, "w"), 0, "Mean smallest distance", "Distance (nm)",
- "Residue Index", "Residue Index", nres, nres, resnr, resnr, totmdmat, 0, truncate,
- rlo, rhi, &nlevels);
+ write_xpm(opt2FILE("-mean", NFILE, fnm, "w"),
+ 0,
+ "Mean smallest distance",
+ "Distance (nm)",
+ "Residue Index",
+ "Residue Index",
+ nres,
+ nres,
+ resnr,
+ resnr,
+ totmdmat,
+ 0,
+ truncate,
+ rlo,
+ rhi,
+ &nlevels);
if (bCalcN)
{
snew(legend[i], STRLEN);
}
tot_nmat(nres, natoms, nframes, totnmat, tot_n, mean_n);
- fp = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Increase in number of contacts", "Residue",
- "Ratio", oenv);
+ fp = xvgropen(
+ ftp2fn(efXVG, NFILE, fnm), "Increase in number of contacts", "Residue", "Ratio", oenv);
sprintf(legend[0], "Total/mean");
sprintf(legend[1], "Total");
sprintf(legend[2], "Mean");
{
ratio = tot_n[i] / mean_n[i];
}
- fprintf(fp, "%3d %8.3f %3d %8.3f %3d %8.3f\n", i + 1, ratio, tot_n[i], mean_n[i],
- natm[i], mean_n[i] / natm[i]);
+ fprintf(fp,
+ "%3d %8.3f %3d %8.3f %3d %8.3f\n",
+ i + 1,
+ ratio,
+ tot_n[i],
+ mean_n[i],
+ natm[i],
+ mean_n[i] / natm[i]);
}
xvgrclose(fp);
}
check_index(nullptr, n, index, nullptr, natoms);
- out = xvgropen(outfn, "Minimum distance to periodic image", output_env_get_time_label(oenv),
- "Distance (nm)", oenv);
+ out = xvgropen(outfn,
+ "Minimum distance to periodic image",
+ output_env_get_time_label(oenv),
+ "Distance (nm)",
+ oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(out, "@ subtitle \"and maximum internal distance\"\n");
{
fprintf(out, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
- fprintf(out, "\t%g\t%6.3f %6.3f %6.3f %6.3f %6.3f\n", output_env_conv_time(oenv, t), rmin,
- rmax, norm(box[0]), norm(box[1]), norm(box[2]));
+ fprintf(out,
+ "\t%g\t%6.3f %6.3f %6.3f %6.3f %6.3f\n",
+ output_env_conv_time(oenv, t),
+ rmin,
+ rmax,
+ norm(box[0]),
+ norm(box[1]),
+ norm(box[2]));
bFirst = FALSE;
} while (read_next_x(oenv, status, &t, x, box));
fprintf(stdout,
"\nThe shortest periodic distance is %g (nm) at time %g (%s),\n"
"between atoms %d and %d\n",
- rmint, output_env_conv_time(oenv, tmint), output_env_get_time_unit(oenv).c_str(),
- index[ind_mini] + 1, index[ind_minj] + 1);
+ rmint,
+ output_env_conv_time(oenv, tmint),
+ output_env_get_time_unit(oenv).c_str(),
+ index[ind_mini] + 1,
+ index[ind_minj] + 1);
}
static void calc_dist(real rcut,
for (j = 0; j < nres; j++)
{
- fprintf(respertime, "%s%d ",
+ fprintf(respertime,
+ "%s%d ",
*(atoms->resinfo[atoms->atom[index[0][residue[j]]].resind].name),
atoms->atom[index[0][residue[j]]].resind);
}
{
if (ng == 1)
{
- calc_dist(rcut, bPBC, pbcType, box, x0, gnx[0], gnx[0], index[0], index[0], bGroup,
- &dmin, &dmax, &nmin, &nmax, &min1, &min2, &max1, &max2);
+ calc_dist(rcut,
+ bPBC,
+ pbcType,
+ box,
+ x0,
+ gnx[0],
+ gnx[0],
+ index[0],
+ index[0],
+ bGroup,
+ &dmin,
+ &dmax,
+ &nmin,
+ &nmax,
+ &min1,
+ &min2,
+ &max1,
+ &max2);
fprintf(dist, " %12e", bMin ? dmin : dmax);
if (num)
{
{
for (k = i + 1; (k < ng); k++)
{
- calc_dist(rcut, bPBC, pbcType, box, x0, gnx[i], gnx[k], index[i], index[k],
- bGroup, &dmin, &dmax, &nmin, &nmax, &min1, &min2, &max1, &max2);
+ calc_dist(rcut,
+ bPBC,
+ pbcType,
+ box,
+ x0,
+ gnx[i],
+ gnx[k],
+ index[i],
+ index[k],
+ bGroup,
+ &dmin,
+ &dmax,
+ &nmin,
+ &nmax,
+ &min1,
+ &min2,
+ &max1,
+ &max2);
fprintf(dist, " %12e", bMin ? dmin : dmax);
if (num)
{
GMX_RELEASE_ASSERT(ng > 1, "Must have more than one group when not using -matrix");
for (i = 1; (i < ng); i++)
{
- calc_dist(rcut, bPBC, pbcType, box, x0, gnx[0], gnx[i], index[0], index[i], bGroup,
- &dmin, &dmax, &nmin, &nmax, &min1, &min2, &max1, &max2);
+ calc_dist(rcut,
+ bPBC,
+ pbcType,
+ box,
+ x0,
+ gnx[0],
+ gnx[i],
+ index[0],
+ index[i],
+ bGroup,
+ &dmin,
+ &dmax,
+ &nmin,
+ &nmax,
+ &min1,
+ &min2,
+ &max1,
+ &max2);
fprintf(dist, " %12e", bMin ? dmin : dmax);
if (num)
{
{
for (j = 0; j < nres; j++)
{
- calc_dist(rcut, bPBC, pbcType, box, x0, residue[j + 1] - residue[j], gnx[i],
- &(index[0][residue[j]]), index[i], bGroup, &dmin, &dmax, &nmin,
- &nmax, &min1r, &min2r, &max1r, &max2r);
+ calc_dist(rcut,
+ bPBC,
+ pbcType,
+ box,
+ x0,
+ residue[j + 1] - residue[j],
+ gnx[i],
+ &(index[0][residue[j]]),
+ index[i],
+ bGroup,
+ &dmin,
+ &dmax,
+ &nmin,
+ &nmax,
+ &min1r,
+ &min2r,
+ &max1r,
+ &max2r);
mindres[i - 1][j] = std::min(mindres[i - 1][j], dmin);
maxdres[i - 1][j] = std::max(maxdres[i - 1][j], dmax);
}
{
if (atm)
{
- fprintf(atm, "%12e %12d %12d\n", output_env_conv_time(oenv, t),
- 1 + (bMin ? min1 : max1), 1 + (bMin ? min2 : max2));
+ fprintf(atm,
+ "%12e %12d %12d\n",
+ output_env_conv_time(oenv, t),
+ 1 + (bMin ? min1 : max1),
+ 1 + (bMin ? min2 : max2));
}
}
{ efTRO, "-ox", "mindist", ffOPTWR }, { efXVG, "-or", "mindistres", ffOPTWR } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm,
- asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc,
+ argv,
+ PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
+ NFILE,
+ fnm,
+ asize(pa),
+ pa,
+ asize(desc),
+ desc,
+ 0,
+ nullptr,
+ &oenv))
{
return 0;
}
}
else
{
- dist_plot(trxfnm, atmfnm, distfnm, numfnm, resfnm, oxfnm, rcutoff, bMat,
- top ? &(top->atoms) : nullptr, ng, index, gnx, grpname, bSplit, !bMax, nres,
- residues, bPBC, pbcType, bGroup, bEachResEachTime, bPrintResName, oenv);
+ dist_plot(trxfnm,
+ atmfnm,
+ distfnm,
+ numfnm,
+ resfnm,
+ oxfnm,
+ rcutoff,
+ bMat,
+ top ? &(top->atoms) : nullptr,
+ ng,
+ index,
+ gnx,
+ grpname,
+ bSplit,
+ !bMax,
+ nres,
+ residues,
+ bPBC,
+ pbcType,
+ bGroup,
+ bEachResEachTime,
+ bPrintResName,
+ oenv);
}
do_view(oenv, distfnm, "-nxy");
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "gmxpre.h"
-
-#include <cmath>
-#include <cstring>
-
-#include <memory>
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/commandline/viewit.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/gmxana/gmx_ana.h"
-#include "gromacs/gmxana/gstat.h"
-#include "gromacs/math/functions.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/math/vectypes.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gromacs/statistics/statistics.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/topology/topology.h"
-#include "gromacs/utility/arraysize.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/utility/gmxassert.h"
-#include "gromacs/utility/smalloc.h"
-
-static constexpr double diffusionConversionFactor = 1000.0; /* Convert nm^2/ps to 10e-5 cm^2/s */
-/* NORMAL = total diffusion coefficient (default). X,Y,Z is diffusion
- coefficient in X,Y,Z direction. LATERAL is diffusion coefficient in
- plane perpendicular to axis
- */
-typedef enum
-{
- NOT_USED,
- NORMAL,
- X,
- Y,
- Z,
- LATERAL
-} msd_type;
-
-// TODO : Group related fields into a struct
-struct t_corr
-{
- real t0; /* start time and time increment between */
- real delta_t; /* time between restart points */
- real beginfit, /* the begin/end time for fits as reals between */
- endfit; /* 0 and 1 */
- real dim_factor; /* the dimensionality factor for the diffusion
- constant */
- std::vector<std::vector<real>> data; /* the displacement data. First index is the group
- number, second is frame number */
- std::vector<real> time; /* frame time */
- std::vector<real> mass; /* masses for mass-weighted msd */
- matrix** datam;
- std::vector<std::vector<gmx::RVec>> x0; /* original positions */
- std::vector<gmx::RVec> com; /* center of mass correction for each frame */
- gmx_stats_t** lsq; /* fitting stats for individual molecule msds */
- msd_type type; /* the type of msd to calculate (lateral, etc.)*/
- int axis; /* the axis along which to calculate */
- int ncoords;
- int nrestart; /* number of restart points */
- int nmol; /* number of molecules (for bMol) */
- int nframes; /* number of frames */
- int nlast;
- int ngrp; /* number of groups to use for msd calculation */
- std::vector<int> n_offs;
- std::vector<std::vector<int>> ndata; /* the number of msds (particles/mols) per data
- point. */
- t_corr(int nrgrp,
- int type,
- int axis,
- real dim_factor,
- int nrmol,
- gmx_bool bTen,
- gmx_bool bMass,
- real dt,
- const t_topology* top,
- real beginfit,
- real endfit) :
- t0(0),
- delta_t(dt),
- beginfit((1 - 2 * GMX_REAL_EPS) * beginfit),
- endfit((1 + 2 * GMX_REAL_EPS) * endfit),
- dim_factor(dim_factor),
- data(nrgrp, std::vector<real>()),
- datam(nullptr),
- lsq(nullptr),
- type(static_cast<msd_type>(type)),
- axis(axis),
- ncoords(0),
- nrestart(0),
- nmol(nrmol),
- nframes(0),
- nlast(0),
- ngrp(nrgrp),
- ndata(nrgrp, std::vector<int>())
- {
-
- if (bTen)
- {
- snew(datam, nrgrp);
- for (int i = 0; i < nrgrp; i++)
- {
- datam[i] = nullptr;
- }
- }
-
- if (nmol > 0)
- {
- mass.resize(nmol, 1);
- }
- else
- {
- if (bMass)
- {
- const t_atoms* atoms = &top->atoms;
- mass.resize(atoms->nr);
- for (int i = 0; (i < atoms->nr); i++)
- {
- mass[i] = atoms->atom[i].m;
- }
- }
- }
- }
- ~t_corr()
- {
- for (int i = 0; i < nrestart; i++)
- {
- for (int j = 0; j < nmol; j++)
- {
- gmx_stats_free(lsq[i][j]);
- }
- }
- sfree(lsq);
- }
-};
-
-typedef real
-t_calc_func(t_corr* curr, int nx, const int index[], int nx0, rvec xc[], const rvec dcom, gmx_bool bTen, matrix mat);
-
-static real thistime(t_corr* curr)
-{
- return curr->time[curr->nframes];
-}
-
-static int in_data(t_corr* curr, int nx00)
-{
- return curr->nframes - curr->n_offs[nx00];
-}
-
-static void corr_print(t_corr* curr,
- gmx_bool bTen,
- const char* fn,
- const char* title,
- const char* yaxis,
- real msdtime,
- real beginfit,
- real endfit,
- real* DD,
- real* SigmaD,
- char* grpname[],
- const gmx_output_env_t* oenv)
-{
- FILE* out;
- int i, j;
-
- out = xvgropen(fn, title, output_env_get_xvgr_tlabel(oenv), yaxis, oenv);
- if (DD)
- {
- fprintf(out, "# MSD gathered over %g %s with %d restarts\n", msdtime,
- output_env_get_time_unit(oenv).c_str(), curr->nrestart);
- fprintf(out, "# Diffusion constants fitted from time %g to %g %s\n", beginfit, endfit,
- output_env_get_time_unit(oenv).c_str());
- for (i = 0; i < curr->ngrp; i++)
- {
- fprintf(out, "# D[%10s] = %.4f (+/- %.4f) (1e-5 cm^2/s)\n", grpname[i], DD[i], SigmaD[i]);
- }
- }
- for (i = 0; i < curr->nframes; i++)
- {
- fprintf(out, "%10g", output_env_conv_time(oenv, curr->time[i]));
- for (j = 0; j < curr->ngrp; j++)
- {
- fprintf(out, " %10g", curr->data[j][i]);
- if (bTen)
- {
- fprintf(out, " %10g %10g %10g %10g %10g %10g", curr->datam[j][i][XX][XX],
- curr->datam[j][i][YY][YY], curr->datam[j][i][ZZ][ZZ], curr->datam[j][i][YY][XX],
- curr->datam[j][i][ZZ][XX], curr->datam[j][i][ZZ][YY]);
- }
- }
- fprintf(out, "\n");
- }
- xvgrclose(out);
-}
-
-/* called from corr_loop, to do the main calculations */
-static void
-calc_corr(t_corr* curr, int nr, int nx, int index[], rvec xc[], gmx_bool bRmCOMM, rvec com, t_calc_func* calc1, gmx_bool bTen)
-{
- int nx0;
- real g;
- matrix mat;
- rvec dcom;
-
- /* Check for new starting point */
- if (curr->nlast < curr->nrestart)
- {
- if ((thistime(curr) >= (curr->nlast * curr->delta_t)) && (nr == 0))
- {
- std::memcpy(curr->x0[curr->nlast].data()->as_vec(), xc, curr->ncoords * sizeof(xc[0]));
- curr->n_offs[curr->nlast] = curr->nframes;
- copy_rvec(com, curr->com[curr->nlast]);
- curr->nlast++;
- }
- }
-
- /* nx0 appears to be the number of new starting points,
- * so for all starting points, call calc1.
- */
- for (nx0 = 0; (nx0 < curr->nlast); nx0++)
- {
- if (bRmCOMM)
- {
- rvec_sub(com, curr->com[nx0], dcom);
- }
- else
- {
- clear_rvec(dcom);
- }
- g = calc1(curr, nx, index, nx0, xc, dcom, bTen, mat);
-#ifdef DEBUG2
- printf("g[%d]=%g\n", nx0, g);
-#endif
- curr->data[nr][in_data(curr, nx0)] += g;
- if (bTen)
- {
- m_add(curr->datam[nr][in_data(curr, nx0)], mat, curr->datam[nr][in_data(curr, nx0)]);
- }
- curr->ndata[nr][in_data(curr, nx0)]++;
- }
-}
-
-/* the non-mass-weighted mean-squared displacement calculation */
-static real
-calc1_norm(t_corr* curr, int nx, const int index[], int nx0, rvec xc[], const rvec dcom, gmx_bool bTen, matrix mat)
-{
- int i, ix, m, m2;
- real g, r, r2;
- rvec rv;
-
- g = 0.0;
- clear_mat(mat);
-
- for (i = 0; (i < nx); i++)
- {
- ix = index[i];
- r2 = 0.0;
- switch (curr->type)
- {
- case NORMAL:
- for (m = 0; (m < DIM); m++)
- {
- rv[m] = xc[ix][m] - curr->x0[nx0][ix][m] - dcom[m];
- r2 += rv[m] * rv[m];
- if (bTen)
- {
- for (m2 = 0; m2 <= m; m2++)
- {
- mat[m][m2] += rv[m] * rv[m2];
- }
- }
- }
- break;
- case X:
- case Y:
- case Z:
- r = xc[ix][curr->type - X] - curr->x0[nx0][ix][curr->type - X] - dcom[curr->type - X];
- r2 += r * r;
- break;
- case LATERAL:
- for (m = 0; (m < DIM); m++)
- {
- if (m != curr->axis)
- {
- r = xc[ix][m] - curr->x0[nx0][ix][m] - dcom[m];
- r2 += r * r;
- }
- }
- break;
- default: gmx_fatal(FARGS, "Error: did not expect option value %d", curr->type);
- }
- g += r2;
- }
- g /= nx;
- msmul(mat, 1.0 / nx, mat);
-
- return g;
-}
-
-/* calculate the com of molecules in x and put it into xa */
-static void
-calc_mol_com(int nmol, const int* molindex, const t_block* mols, const t_atoms* atoms, rvec* x, rvec* xa)
-{
- int m, mol, i, d;
- rvec xm;
- real mass, mtot;
-
- for (m = 0; m < nmol; m++)
- {
- mol = molindex[m];
- clear_rvec(xm);
- mtot = 0;
- for (i = mols->index[mol]; i < mols->index[mol + 1]; i++)
- {
- mass = atoms->atom[i].m;
- for (d = 0; d < DIM; d++)
- {
- xm[d] += mass * x[i][d];
- }
- mtot += mass;
- }
- svmul(1 / mtot, xm, xa[m]);
- }
-}
-
-static real calc_one_mw(t_corr* curr, int ix, int nx0, rvec xc[], real* tm, const rvec dcom, gmx_bool bTen, matrix mat)
-{
- real r2, r, mm;
- rvec rv;
- int m, m2;
-
- mm = curr->mass[ix];
- if (mm == 0)
- {
- return 0;
- }
- (*tm) += mm;
- r2 = 0.0;
- switch (curr->type)
- {
- case NORMAL:
- for (m = 0; (m < DIM); m++)
- {
- rv[m] = xc[ix][m] - curr->x0[nx0][ix][m] - dcom[m];
- r2 += mm * rv[m] * rv[m];
- if (bTen)
- {
- for (m2 = 0; m2 <= m; m2++)
- {
- mat[m][m2] += mm * rv[m] * rv[m2];
- }
- }
- }
- break;
- case X:
- case Y:
- case Z:
- r = xc[ix][curr->type - X] - curr->x0[nx0][ix][curr->type - X] - dcom[curr->type - X];
- r2 = mm * r * r;
- break;
- case LATERAL:
- for (m = 0; (m < DIM); m++)
- {
- if (m != curr->axis)
- {
- r = xc[ix][m] - curr->x0[nx0][ix][m] - dcom[m];
- r2 += mm * r * r;
- }
- }
- break;
- default: gmx_fatal(FARGS, "Options got screwed. Did not expect value %d\n", curr->type);
- } /* end switch */
- return r2;
-}
-
-/* the normal, mass-weighted mean-squared displacement calcuation */
-static real calc1_mw(t_corr* curr, int nx, const int index[], int nx0, rvec xc[], const rvec dcom, gmx_bool bTen, matrix mat)
-{
- int i;
- real g, tm;
-
- g = tm = 0.0;
- clear_mat(mat);
- for (i = 0; (i < nx); i++)
- {
- g += calc_one_mw(curr, index[i], nx0, xc, &tm, dcom, bTen, mat);
- }
-
- g /= tm;
- if (bTen)
- {
- msmul(mat, 1 / tm, mat);
- }
-
- return g;
-}
-
-/* prepare the coordinates by removing periodic boundary crossings.
- gnx = the number of atoms/molecules
- index = the indices
- xcur = the current coordinates
- xprev = the previous coordinates
- box = the box matrix */
-static void prep_data(gmx_bool bMol, int gnx, const int index[], rvec xcur[], rvec xprev[], matrix box)
-{
- int i, m, ind;
- rvec hbox;
-
- /* Remove periodicity */
- for (m = 0; (m < DIM); m++)
- {
- hbox[m] = 0.5 * box[m][m];
- }
-
- for (i = 0; (i < gnx); i++)
- {
- if (bMol)
- {
- ind = i;
- }
- else
- {
- ind = index[i];
- }
-
- for (m = DIM - 1; m >= 0; m--)
- {
- if (hbox[m] == 0)
- {
- continue;
- }
- while (xcur[ind][m] - xprev[ind][m] <= -hbox[m])
- {
- rvec_inc(xcur[ind], box[m]);
- }
- while (xcur[ind][m] - xprev[ind][m] > hbox[m])
- {
- rvec_dec(xcur[ind], box[m]);
- }
- }
- }
-}
-
-/* calculate the center of mass for a group
- gnx = the number of atoms/molecules
- index = the indices
- xcur = the current coordinates
- xprev = the previous coordinates
- box = the box matrix
- atoms = atom data (for mass)
- com(output) = center of mass */
-static void
-calc_com(gmx_bool bMol, int gnx, int index[], rvec xcur[], rvec xprev[], matrix box, const t_atoms* atoms, rvec com)
-{
- int i, m, ind;
- real mass;
- double tmass;
- dvec sx;
-
- clear_dvec(sx);
- tmass = 0;
-
- prep_data(bMol, gnx, index, xcur, xprev, box);
- for (i = 0; (i < gnx); i++)
- {
- if (bMol)
- {
- ind = i;
- }
- else
- {
- ind = index[i];
- }
-
-
- mass = atoms->atom[ind].m;
- for (m = 0; m < DIM; m++)
- {
- sx[m] += mass * xcur[ind][m];
- }
- tmass += mass;
- }
- for (m = 0; m < DIM; m++)
- {
- com[m] = sx[m] / tmass;
- }
-}
-
-
-static real calc1_mol(t_corr* curr,
- int nx,
- const int gmx_unused index[],
- int nx0,
- rvec xc[],
- const rvec dcom,
- gmx_bool bTen,
- matrix mat)
-{
- int i;
- real g, tm, gtot, tt;
-
- tt = curr->time[in_data(curr, nx0)];
- gtot = 0;
- tm = 0;
- clear_mat(mat);
- for (i = 0; (i < nx); i++)
- {
- g = calc_one_mw(curr, i, nx0, xc, &tm, dcom, bTen, mat);
- /* We don't need to normalize as the mass was set to 1 */
- gtot += g;
- if (tt >= curr->beginfit && (curr->endfit < 0 || tt <= curr->endfit))
- {
- gmx_stats_add_point(curr->lsq[nx0][i], tt, g, 0, 0);
- }
- }
- msmul(mat, 1.0 / nx, mat);
-
- return gtot / nx;
-}
-
-static void printmol(t_corr* curr,
- const char* fn,
- const char* fn_pdb,
- const int* molindex,
- const t_topology* top,
- rvec* x,
- PbcType pbcType,
- matrix box,
- const gmx_output_env_t* oenv)
-{
- FILE* out;
- gmx_stats_t lsq1;
- int i, j;
- real a, b, D, Dav, D2av, VarD, sqrtD, sqrtD_max, scale;
- t_pdbinfo* pdbinfo = nullptr;
- const int* mol2a = nullptr;
-
- out = xvgropen(fn, "Diffusion Coefficients / Molecule", "Molecule", "D (1e-5 cm^2/s)", oenv);
-
- if (fn_pdb)
- {
- pdbinfo = top->atoms.pdbinfo;
- mol2a = top->mols.index;
- }
-
- Dav = D2av = 0;
- sqrtD_max = 0;
- for (i = 0; (i < curr->nmol); i++)
- {
- lsq1 = gmx_stats_init();
- for (j = 0; (j < curr->nrestart); j++)
- {
- real xx, yy, dx, dy;
-
- while (gmx_stats_get_point(curr->lsq[j][i], &xx, &yy, &dx, &dy, 0) == estatsOK)
- {
- gmx_stats_add_point(lsq1, xx, yy, dx, dy);
- }
- }
- gmx_stats_get_ab(lsq1, elsqWEIGHT_NONE, &a, &b, nullptr, nullptr, nullptr, nullptr);
- gmx_stats_free(lsq1);
- D = a * diffusionConversionFactor / curr->dim_factor;
- if (D < 0)
- {
- D = 0;
- }
- Dav += D;
- D2av += gmx::square(D);
- fprintf(out, "%10d %10g\n", i, D);
- if (pdbinfo)
- {
- sqrtD = std::sqrt(D);
- if (sqrtD > sqrtD_max)
- {
- sqrtD_max = sqrtD;
- }
- for (j = mol2a[molindex[i]]; j < mol2a[molindex[i] + 1]; j++)
- {
- pdbinfo[j].bfac = sqrtD;
- }
- }
- }
- xvgrclose(out);
- fprintf(stdout, "Wrote per-molecule output to %s\n", fn);
- do_view(oenv, fn, "-graphtype bar");
-
- /* Compute variance, stddev and error */
- Dav /= curr->nmol;
- D2av /= curr->nmol;
- VarD = D2av - gmx::square(Dav);
- printf("<D> = %.4f Std. Dev. = %.4f Error = %.4f\n", Dav, std::sqrt(VarD),
- std::sqrt(VarD / curr->nmol));
-
- if (fn_pdb && x)
- {
- scale = 1;
- while (scale * sqrtD_max > 10)
- {
- scale *= 0.1;
- }
- while (scale * sqrtD_max < 0.1)
- {
- scale *= 10;
- }
- GMX_RELEASE_ASSERT(pdbinfo != nullptr, "Internal error - pdbinfo not set for PDB input");
- for (i = 0; i < top->atoms.nr; i++)
- {
- pdbinfo[i].bfac *= scale;
- }
- write_sto_conf(fn_pdb, "molecular MSD", &top->atoms, x, nullptr, pbcType, box);
- fprintf(stdout, "Wrote frame for -tpdb to %s\n", fn_pdb);
- }
-}
-
-/* this is the main loop for the correlation type functions
- * fx and nx are file pointers to things like read_first_x and
- * read_next_x
- */
-static int corr_loop(t_corr* curr,
- const char* fn,
- const t_topology* top,
- PbcType pbcType,
- gmx_bool bMol,
- int gnx[],
- int* index[],
- t_calc_func* calc1,
- gmx_bool bTen,
- gmx::ArrayRef<const int> gnx_com,
- int* index_com[],
- real dt,
- real t_pdb,
- rvec** x_pdb,
- matrix box_pdb,
- const gmx_output_env_t* oenv)
-{
- rvec* x[2]; /* the coordinates to read */
- rvec* xa[2]; /* the coordinates to calculate displacements for */
- rvec com = { 0 };
- real t, t_prev = 0;
- int natoms, i, j, cur = 0, maxframes = 0;
- t_trxstatus* status;
-#define prev (1 - cur)
- matrix box;
- gmx_bool bFirst;
- gmx_rmpbc_t gpbc = nullptr;
-
- natoms = read_first_x(oenv, &status, fn, &curr->t0, &(x[cur]), box);
-#ifdef DEBUG
- fprintf(stderr, "Read %d atoms for first frame\n", natoms);
-#endif
- if ((!gnx_com.empty()) && natoms < top->atoms.nr)
- {
- fprintf(stderr,
- "WARNING: The trajectory only contains part of the system (%d of %d atoms) and "
- "therefore the COM motion of only this part of the system will be removed\n",
- natoms, top->atoms.nr);
- }
-
- snew(x[prev], natoms);
-
- // if com is requested, the data structure needs to be large enough to do this
- // to prevent overflow
- if (bMol && gnx_com.empty())
- {
- curr->ncoords = curr->nmol;
- snew(xa[0], curr->ncoords);
- snew(xa[1], curr->ncoords);
- }
- else
- {
- curr->ncoords = natoms;
- xa[0] = x[0];
- xa[1] = x[1];
- }
-
- bFirst = TRUE;
- t = curr->t0;
- if (x_pdb)
- {
- *x_pdb = nullptr;
- }
-
- if (bMol)
- {
- gpbc = gmx_rmpbc_init(&top->idef, pbcType, natoms);
- }
-
- /* the loop over all frames */
- do
- {
- if (x_pdb
- && ((bFirst && t_pdb < t)
- || (!bFirst && t_pdb > t - 0.5 * (t - t_prev) && t_pdb < t + 0.5 * (t - t_prev))))
- {
- if (*x_pdb == nullptr)
- {
- snew(*x_pdb, natoms);
- }
- for (i = 0; i < natoms; i++)
- {
- copy_rvec(x[cur][i], (*x_pdb)[i]);
- }
- copy_mat(box, box_pdb);
- }
-
-
- /* check whether we've reached a restart point */
- if (bRmod(t, curr->t0, dt))
- {
- curr->nrestart++;
-
- curr->x0.resize(curr->nrestart);
- curr->x0[curr->nrestart - 1].resize(curr->ncoords);
- curr->com.resize(curr->nrestart);
- curr->n_offs.resize(curr->nrestart);
- srenew(curr->lsq, curr->nrestart);
- snew(curr->lsq[curr->nrestart - 1], curr->nmol);
- for (i = 0; i < curr->nmol; i++)
- {
- curr->lsq[curr->nrestart - 1][i] = gmx_stats_init();
- }
-
- if (debug)
- {
- fprintf(debug, "Extended data structures because of new restart %d\n", curr->nrestart);
- }
- }
- /* create or extend the frame-based arrays */
- if (curr->nframes >= maxframes - 1)
- {
- if (maxframes == 0)
- {
- for (i = 0; (i < curr->ngrp); i++)
- {
- if (bTen)
- {
- curr->datam[i] = nullptr;
- }
- }
- }
- maxframes += 10;
- for (i = 0; (i < curr->ngrp); i++)
- {
- curr->ndata[i].resize(maxframes);
- curr->data[i].resize(maxframes);
- if (bTen)
- {
- srenew(curr->datam[i], maxframes);
- }
- for (j = maxframes - 10; j < maxframes; j++)
- {
- curr->ndata[i][j] = 0;
- curr->data[i][j] = 0;
- if (bTen)
- {
- clear_mat(curr->datam[i][j]);
- }
- }
- }
- curr->time.resize(maxframes);
- }
-
- /* set the time */
- curr->time[curr->nframes] = t - curr->t0;
-
- /* make the molecules whole */
- if (bMol)
- {
- gmx_rmpbc(gpbc, natoms, box, x[cur]);
- }
-
- /* calculate the molecules' centers of masses and put them into xa */
- // NOTE and WARNING! If above both COM removal and individual molecules have been
- // requested, x and xa point to the same memory, and the coordinate
- // data becomes overwritten by the molecule data.
- if (bMol)
- {
- calc_mol_com(gnx[0], index[0], &top->mols, &top->atoms, x[cur], xa[cur]);
- }
-
- /* for the first frame, the previous frame is a copy of the first frame */
- if (bFirst)
- {
- std::memcpy(xa[prev], xa[cur], curr->ncoords * sizeof(xa[prev][0]));
- bFirst = FALSE;
- }
-
- /* first remove the periodic boundary condition crossings */
- for (i = 0; i < curr->ngrp; i++)
- {
- prep_data(bMol, gnx[i], index[i], xa[cur], xa[prev], box);
- }
-
- /* calculate the center of mass */
- if (!gnx_com.empty())
- {
- GMX_RELEASE_ASSERT(index_com != nullptr,
- "Center-of-mass removal must have valid index group");
- calc_com(bMol, gnx_com[0], index_com[0], xa[cur], xa[prev], box, &top->atoms, com);
- }
-
- /* loop over all groups in index file */
- for (i = 0; (i < curr->ngrp); i++)
- {
- /* calculate something useful, like mean square displacements */
- calc_corr(curr, i, gnx[i], index[i], xa[cur], (!gnx_com.empty()), com, calc1, bTen);
- }
- cur = prev;
- t_prev = t;
-
- curr->nframes++;
- } while (read_next_x(oenv, status, &t, x[cur], box));
- fprintf(stderr, "\nUsed %d restart points spaced %g %s over %g %s\n\n", curr->nrestart,
- output_env_conv_time(oenv, dt), output_env_get_time_unit(oenv).c_str(),
- output_env_conv_time(oenv, curr->time[curr->nframes - 1]),
- output_env_get_time_unit(oenv).c_str());
-
- if (bMol)
- {
- gmx_rmpbc_done(gpbc);
- }
-
- close_trx(status);
-
- return natoms;
-}
-
-static void index_atom2mol(int* n, int* index, const t_block* mols)
-{
- int nat, i, nmol, mol, j;
-
- nat = *n;
- i = 0;
- nmol = 0;
- mol = 0;
- while (i < nat)
- {
- while (index[i] > mols->index[mol])
- {
- mol++;
- if (mol >= mols->nr)
- {
- gmx_fatal(FARGS, "Atom index out of range: %d", index[i] + 1);
- }
- }
- for (j = mols->index[mol]; j < mols->index[mol + 1]; j++)
- {
- if (i >= nat || index[i] != j)
- {
- gmx_fatal(FARGS, "The index group does not consist of whole molecules");
- }
- i++;
- }
- index[nmol++] = mol;
- }
-
- fprintf(stderr, "Split group of %d atoms into %d molecules\n", nat, nmol);
-
- *n = nmol;
-}
-
-static void do_corr(const char* trx_file,
- const char* ndx_file,
- const char* msd_file,
- const char* mol_file,
- const char* pdb_file,
- real t_pdb,
- int nrgrp,
- t_topology* top,
- PbcType pbcType,
- gmx_bool bTen,
- gmx_bool bMW,
- gmx_bool bRmCOMM,
- int type,
- real dim_factor,
- int axis,
- real dt,
- real beginfit,
- real endfit,
- const gmx_output_env_t* oenv)
-{
- std::unique_ptr<t_corr> msd;
- std::vector<int> gnx, gnx_com; /* the selected groups' sizes */
- int** index; /* selected groups' indices */
- char** grpname;
- int i, i0, i1, j, N, nat_trx;
- std::vector<real> SigmaD, DD;
- real a, a2, b, r, chi2;
- rvec* x = nullptr;
- matrix box;
- int** index_com = nullptr; /* the COM removal group atom indices */
- char** grpname_com = nullptr; /* the COM removal group name */
-
- gnx.resize(nrgrp);
- snew(index, nrgrp);
- snew(grpname, nrgrp);
-
- fprintf(stderr, "\nSelect a group to calculate mean squared displacement for:\n");
- get_index(&top->atoms, ndx_file, nrgrp, gnx.data(), index, grpname);
-
- if (bRmCOMM)
- {
- gnx_com.resize(1);
- snew(index_com, 1);
- snew(grpname_com, 1);
-
- fprintf(stderr, "\nNow select a group for center of mass removal:\n");
- get_index(&top->atoms, ndx_file, 1, gnx_com.data(), index_com, grpname_com);
- }
-
- if (mol_file)
- {
- index_atom2mol(&gnx[0], index[0], &top->mols);
- }
-
- msd = std::make_unique<t_corr>(nrgrp, type, axis, dim_factor, mol_file == nullptr ? 0 : gnx[0],
- bTen, bMW, dt, top, beginfit, endfit);
-
- nat_trx = corr_loop(msd.get(), trx_file, top, pbcType, mol_file ? gnx[0] != 0 : false, gnx.data(),
- index, (mol_file != nullptr) ? calc1_mol : (bMW ? calc1_mw : calc1_norm),
- bTen, gnx_com, index_com, dt, t_pdb, pdb_file ? &x : nullptr, box, oenv);
-
- /* Correct for the number of points */
- for (j = 0; (j < msd->ngrp); j++)
- {
- for (i = 0; (i < msd->nframes); i++)
- {
- msd->data[j][i] /= msd->ndata[j][i];
- if (bTen)
- {
- msmul(msd->datam[j][i], 1.0 / msd->ndata[j][i], msd->datam[j][i]);
- }
- }
- }
-
- if (mol_file)
- {
- if (pdb_file && x == nullptr)
- {
- fprintf(stderr,
- "\nNo frame found need time tpdb = %g ps\n"
- "Can not write %s\n\n",
- t_pdb, pdb_file);
- }
- i = top->atoms.nr;
- top->atoms.nr = nat_trx;
- if (pdb_file && top->atoms.pdbinfo == nullptr)
- {
- snew(top->atoms.pdbinfo, top->atoms.nr);
- }
- printmol(msd.get(), mol_file, pdb_file, index[0], top, x, pbcType, box, oenv);
- top->atoms.nr = i;
- }
-
- if (beginfit == -1)
- {
- i0 = gmx::roundToInt(0.1 * (msd->nframes - 1));
- beginfit = msd->time[i0];
- }
- else
- {
- for (i0 = 0; i0 < msd->nframes && msd->time[i0] < beginfit; i0++) {}
- }
-
- if (endfit == -1)
- {
- i1 = gmx::roundToInt(0.9 * (msd->nframes - 1)) + 1;
- endfit = msd->time[i1 - 1];
- }
- else
- {
- for (i1 = i0; i1 < msd->nframes && msd->time[i1] <= endfit; i1++) {}
- }
- fprintf(stdout, "Fitting from %g to %g %s\n\n", beginfit, endfit,
- output_env_get_time_unit(oenv).c_str());
-
- N = i1 - i0;
- if (N <= 2)
- {
- fprintf(stdout,
- "Not enough points for fitting (%d).\n"
- "Can not determine the diffusion constant.\n",
- N);
- }
- else
- {
- DD.resize(msd->ngrp);
- SigmaD.resize(msd->ngrp);
- for (j = 0; j < msd->ngrp; j++)
- {
- if (N >= 4)
- {
- lsq_y_ax_b(N / 2, &(msd->time[i0]), &(msd->data[j][i0]), &a, &b, &r, &chi2);
- lsq_y_ax_b(N / 2, &(msd->time[i0 + N / 2]), &(msd->data[j][i0 + N / 2]), &a2, &b, &r, &chi2);
- SigmaD[j] = std::abs(a - a2);
- }
- else
- {
- SigmaD[j] = 0;
- }
- lsq_y_ax_b(N, &(msd->time[i0]), &(msd->data[j][i0]), &(DD[j]), &b, &r, &chi2);
- DD[j] *= diffusionConversionFactor / msd->dim_factor;
- SigmaD[j] *= diffusionConversionFactor / msd->dim_factor;
- if (DD[j] > 0.01 && DD[j] < 1e4)
- {
- fprintf(stdout, "D[%10s] %.4f (+/- %.4f) 1e-5 cm^2/s\n", grpname[j], DD[j], SigmaD[j]);
- }
- else
- {
- fprintf(stdout, "D[%10s] %.4g (+/- %.4g) 1e-5 cm^2/s\n", grpname[j], DD[j], SigmaD[j]);
- }
- }
- }
- /* Print mean square displacement */
- corr_print(msd.get(), bTen, msd_file, "Mean Square Displacement", "MSD (nm\\S2\\N)",
- msd->time[msd->nframes - 1], beginfit, endfit, DD.data(), SigmaD.data(), grpname, oenv);
-}
-
-int gmx_msd(int argc, char* argv[])
-{
- const char* desc[] = {
- "[THISMODULE] computes the mean square displacement (MSD) of atoms from",
- "a set of initial positions. This provides an easy way to compute",
- "the diffusion constant using the Einstein relation.",
- "The time between the reference points for the MSD calculation",
- "is set with [TT]-trestart[tt].",
- "The diffusion constant is calculated by least squares fitting a",
- "straight line (D*t + c) through the MSD(t) from [TT]-beginfit[tt] to",
- "[TT]-endfit[tt] (note that t is time from the reference positions,",
- "not simulation time). An error estimate given, which is the difference",
- "of the diffusion coefficients obtained from fits over the two halves",
- "of the fit interval.[PAR]",
- "There are three, mutually exclusive, options to determine different",
- "types of mean square displacement: [TT]-type[tt], [TT]-lateral[tt]",
- "and [TT]-ten[tt]. Option [TT]-ten[tt] writes the full MSD tensor for",
- "each group, the order in the output is: trace xx yy zz yx zx zy.[PAR]",
- "If [TT]-mol[tt] is set, [THISMODULE] plots the MSD for individual molecules",
- "(including making molecules whole across periodic boundaries): ",
- "for each individual molecule a diffusion constant is computed for ",
- "its center of mass. The chosen index group will be split into ",
- "molecules.[PAR]",
- "The default way to calculate a MSD is by using mass-weighted averages.",
- "This can be turned off with [TT]-nomw[tt].[PAR]",
- "With the option [TT]-rmcomm[tt], the center of mass motion of a ",
- "specific group can be removed. For trajectories produced with ",
- "GROMACS this is usually not necessary, ",
- "as [gmx-mdrun] usually already removes the center of mass motion.",
- "When you use this option be sure that the whole system is stored",
- "in the trajectory file.[PAR]",
- "The diffusion coefficient is determined by linear regression of the MSD.",
- "When [TT]-beginfit[tt] is -1, fitting starts at 10%",
- "and when [TT]-endfit[tt] is -1, fitting goes to 90%.",
- "Using this option one also gets an accurate error estimate",
- "based on the statistics between individual molecules.",
- "Note that this diffusion coefficient and error estimate are only",
- "accurate when the MSD is completely linear between",
- "[TT]-beginfit[tt] and [TT]-endfit[tt].[PAR]",
- "Option [TT]-pdb[tt] writes a [REF].pdb[ref] file with the coordinates of the frame",
- "at time [TT]-tpdb[tt] with in the B-factor field the square root of",
- "the diffusion coefficient of the molecule.",
- "This option implies option [TT]-mol[tt]."
- };
- static const char* normtype[] = { nullptr, "no", "x", "y", "z", nullptr };
- static const char* axtitle[] = { nullptr, "no", "x", "y", "z", nullptr };
- static int ngroup = 1;
- static real dt = 10;
- static real t_pdb = 0;
- static real beginfit = -1;
- static real endfit = -1;
- static gmx_bool bTen = FALSE;
- static gmx_bool bMW = TRUE;
- static gmx_bool bRmCOMM = FALSE;
- t_pargs pa[] = {
- { "-type", FALSE, etENUM, { normtype }, "Compute diffusion coefficient in one direction" },
- { "-lateral",
- FALSE,
- etENUM,
- { axtitle },
- "Calculate the lateral diffusion in a plane perpendicular to" },
- { "-ten", FALSE, etBOOL, { &bTen }, "Calculate the full tensor" },
- { "-ngroup", FALSE, etINT, { &ngroup }, "Number of groups to calculate MSD for" },
- { "-mw", FALSE, etBOOL, { &bMW }, "Mass weighted MSD" },
- { "-rmcomm", FALSE, etBOOL, { &bRmCOMM }, "Remove center of mass motion" },
- { "-tpdb", FALSE, etTIME, { &t_pdb }, "The frame to use for option [TT]-pdb[tt] (%t)" },
- { "-trestart", FALSE, etTIME, { &dt }, "Time between restarting points in trajectory (%t)" },
- { "-beginfit",
- FALSE,
- etTIME,
- { &beginfit },
- "Start time for fitting the MSD (%t), -1 is 10%" },
- { "-endfit", FALSE, etTIME, { &endfit }, "End time for fitting the MSD (%t), -1 is 90%" }
- };
-
- t_filenm fnm[] = {
- { efTRX, nullptr, nullptr, ffREAD }, { efTPS, nullptr, nullptr, ffREAD },
- { efNDX, nullptr, nullptr, ffOPTRD }, { efXVG, nullptr, "msd", ffWRITE },
- { efXVG, "-mol", "diff_mol", ffOPTWR }, { efPDB, "-pdb", "diff_mol", ffOPTWR }
- };
-#define NFILE asize(fnm)
-
- t_topology top;
- PbcType pbcType;
- matrix box;
- const char * trx_file, *tps_file, *ndx_file, *msd_file, *mol_file, *pdb_file;
- rvec* xdum;
- gmx_bool bTop;
- int axis, type;
- real dim_factor;
- gmx_output_env_t* oenv;
-
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END | PCA_TIME_UNIT,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
- {
- return 0;
- }
- trx_file = ftp2fn_null(efTRX, NFILE, fnm);
- tps_file = ftp2fn_null(efTPS, NFILE, fnm);
- ndx_file = ftp2fn_null(efNDX, NFILE, fnm);
- msd_file = ftp2fn_null(efXVG, NFILE, fnm);
- pdb_file = opt2fn_null("-pdb", NFILE, fnm);
- if (pdb_file)
- {
- mol_file = opt2fn("-mol", NFILE, fnm);
- }
- else
- {
- mol_file = opt2fn_null("-mol", NFILE, fnm);
- }
-
- if (ngroup < 1)
- {
- gmx_fatal(FARGS, "Must have at least 1 group (now %d)", ngroup);
- }
- if (mol_file && ngroup > 1)
- {
- gmx_fatal(FARGS, "With molecular msd can only have 1 group (now %d)", ngroup);
- }
-
-
- if (mol_file)
- {
- bMW = TRUE;
- fprintf(stderr, "Calculating diffusion coefficients for molecules.\n");
- }
-
- GMX_RELEASE_ASSERT(normtype[0] != nullptr, "Options inconsistency; normtype[0] is NULL");
- GMX_RELEASE_ASSERT(axtitle[0] != nullptr, "Options inconsistency; axtitle[0] is NULL");
-
- if (normtype[0][0] != 'n')
- {
- type = normtype[0][0] - 'x' + X; /* See defines above */
- dim_factor = 2.0;
- }
- else
- {
- type = NORMAL;
- dim_factor = 6.0;
- }
- if ((type == NORMAL) && (axtitle[0][0] != 'n'))
- {
- type = LATERAL;
- dim_factor = 4.0;
- axis = (axtitle[0][0] - 'x'); /* See defines above */
- }
- else
- {
- axis = 0;
- }
-
- if (bTen && type != NORMAL)
- {
- gmx_fatal(FARGS, "Can only calculate the full tensor for 3D msd");
- }
-
- bTop = read_tps_conf(tps_file, &top, &pbcType, &xdum, nullptr, box, bMW || bRmCOMM);
- if (mol_file && !bTop)
- {
- gmx_fatal(FARGS, "Could not read a topology from %s. Try a tpr file instead.", tps_file);
- }
-
- do_corr(trx_file, ndx_file, msd_file, mol_file, pdb_file, t_pdb, ngroup, &top, pbcType, bTen,
- bMW, bRmCOMM, type, dim_factor, axis, dt, beginfit, endfit, oenv);
-
- done_top(&top);
- view_all(oenv, NFILE, fnm);
-
- return 0;
-}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static double cv_corr(double nu, double T)
{
- double x = PLANCK * nu / (BOLTZ * T);
+ double x = gmx::c_planck * nu / (gmx::c_boltz * T);
double ex = std::exp(x);
if (nu <= 0)
{
- return BOLTZ * KILO;
+ return gmx::c_boltz * gmx::c_kilo;
}
else
{
- return BOLTZ * KILO * (ex * gmx::square(x) / gmx::square(ex - 1) - 1);
+ return gmx::c_boltz * gmx::c_kilo * (ex * gmx::square(x) / gmx::square(ex - 1) - 1);
}
}
static double u_corr(double nu, double T)
{
- double x = PLANCK * nu / (BOLTZ * T);
+ double x = gmx::c_planck * nu / (gmx::c_boltz * T);
double ex = std::exp(x);
if (nu <= 0)
{
- return BOLTZ * T;
+ return gmx::c_boltz * T;
}
else
{
- return BOLTZ * T * (0.5 * x - 1 + x / (ex - 1));
+ return gmx::c_boltz * T * (0.5 * x - 1 + x / (ex - 1));
}
}
gmx_fatal(FARGS,
"You asked to store %d eigenvectors of size %d, which requires more than the "
"supported %d elements; %sdecrease -last",
- numVector, nrow, INT_MAX, ignoreBegin ? "" : "increase -first and/or ");
+ numVector,
+ nrow,
+ INT_MAX,
+ ignoreBegin ? "" : "increase -first and/or ");
}
real* eigenvectors;
*/
static double calcTranslationalHeatCapacity()
{
- return RGAS * 1.5;
+ return gmx::c_universalGasConstant * 1.5;
}
/*! \brief Compute internal energy due to translational motion
*/
static double calcTranslationalInternalEnergy(double T)
{
- return BOLTZ * T * 1.5;
+ return gmx::c_boltz * T * 1.5;
}
/*! \brief Compute heat capacity due to rotational motion
{
if (linear)
{
- return BOLTZ * T;
+ return gmx::c_boltz * T;
}
else
{
- return BOLTZ * T * 1.5;
+ return gmx::c_boltz * T * 1.5;
}
}
{
if (linear)
{
- return RGAS;
+ return gmx::c_universalGasConstant;
}
else
{
- return RGAS * 1.5;
+ return gmx::c_universalGasConstant * 1.5;
}
}
principal_comp(index.size(), index.data(), top.atoms.atom, as_rvec_array(x_com.data()), trans, inertia);
bool linear = (inertia[XX] / inertia[YY] < linear_toler && inertia[XX] / inertia[ZZ] < linear_toler);
// (kJ/mol ps)^2/(Dalton nm^2 kJ/mol K) =
- // KILO kg m^2 ps^2/(s^2 mol g/mol nm^2 K) =
- // KILO^2 10^18 / 10^24 K = 1/K
- double rot_const = gmx::square(PLANCK) / (8 * gmx::square(M_PI) * BOLTZ);
+ // c_kilo kg m^2 ps^2/(s^2 mol g/mol nm^2 K) =
+ // c_kilo^2 10^18 / 10^24 K = 1/K
+ double rot_const = gmx::square(gmx::c_planck) / (8 * gmx::square(M_PI) * gmx::c_boltz);
// Rotational temperature (1/K)
rvec theta = { 0, 0, 0 };
if (linear)
{
nharm = get_nharm(&mtop);
}
- std::vector<int> atom_index = get_atom_index(&mtop);
+ std::vector<int> atom_index = get_atom_index(mtop);
top = gmx_mtop_t_to_t_topology(&mtop, true);
gmx_fatal(FARGS,
"Hessian size is %d x %d, which is larger than the maximum allowed %d "
"elements.",
- nrow, ncol, INT_MAX);
+ nrow,
+ ncol,
+ INT_MAX);
}
snew(full_hessian, hessianSize);
for (i = 0; i < nrow * ncol; i++)
/* now write the output */
fprintf(stderr, "Writing eigenvalues...\n");
- out = xvgropen(opt2fn("-ol", NFILE, fnm), "Eigenvalues", "Eigenvalue index",
- "Eigenvalue [Gromacs units]", oenv);
+ out = xvgropen(opt2fn("-ol", NFILE, fnm),
+ "Eigenvalues",
+ "Eigenvalue index",
+ "Eigenvalue [Gromacs units]",
+ oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
if (bM)
}
printf("Writing eigenfrequencies - negative eigenvalues will be set to zero.\n");
- out = xvgropen(opt2fn("-of", NFILE, fnm), "Eigenfrequencies", "Eigenvector index",
- "Wavenumber [cm\\S-1\\N]", oenv);
+ out = xvgropen(opt2fn("-of", NFILE, fnm),
+ "Eigenfrequencies",
+ "Eigenvector index",
+ "Wavenumber [cm\\S-1\\N]",
+ oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
if (bM)
snew(spectrum, maxspec);
spec = xvgropen(opt2fn("-os", NFILE, fnm),
"Vibrational spectrum based on harmonic approximation",
- "\\f{12}w\\f{4} (cm\\S-1\\N)", "Intensity [Gromacs units]", oenv);
+ "\\f{12}w\\f{4} (cm\\S-1\\N)",
+ "Intensity [Gromacs units]",
+ oenv);
for (i = 0; (i < maxspec); i++)
{
spectrum[i] = 0;
* light. Do this by first converting to omega^2 (units 1/s), take the square
* root, and finally divide by the speed of light (nm/ps in gromacs).
*/
- factor_gmx_to_omega2 = 1.0E21 / (AVOGADRO * AMU);
- factor_omega_to_wavenumber = 1.0E-5 / (2.0 * M_PI * SPEED_OF_LIGHT);
+ factor_gmx_to_omega2 = 1.0E21 / (gmx::c_avogadro * gmx::c_amu);
+ factor_omega_to_wavenumber = 1.0E-5 / (2.0 * M_PI * gmx::c_speedOfLight);
value = 0;
for (i = begin; (i <= end); i++)
qu = u_corr(nu, T);
if (i > end - nharm)
{
- qcv += BOLTZ * KILO;
- qu += BOLTZ * T;
+ qcv += gmx::c_boltz * gmx::c_kilo;
+ qu += gmx::c_boltz * T;
}
fprintf(qc, "%6d %15g %15g\n", i, qcv, qu);
qcvtot += qcv;
/* The sparse matrix diagonalization store all eigenvectors up to end */
eigenvectorPtr = eigenvectors + (begin - 1) * atom_index.size();
}
- write_eigenvectors(opt2fn("-v", NFILE, fnm), atom_index.size(), eigenvectorPtr, FALSE, begin,
- end, eWXR_NO, nullptr, FALSE, top_x, bM, eigenvalues);
+ write_eigenvectors(opt2fn("-v", NFILE, fnm),
+ atom_index.size(),
+ eigenvectorPtr,
+ FALSE,
+ begin,
+ end,
+ eWXR_NO,
+ nullptr,
+ FALSE,
+ top_x,
+ bM,
+ eigenvalues);
if (begin == 1)
{
- analyzeThermochemistry(stdout, top, top_x, atom_index, eigenvalues, T, P, sigma_r,
- scale_factor, linear_toler);
+ analyzeThermochemistry(
+ stdout, top, top_x, atom_index, eigenvalues, T, P, sigma_r, scale_factor, linear_toler);
please_cite(stdout, "Spoel2018a");
}
else
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
indexfile = ftp2fn_null(efNDX, NFILE, fnm);
- read_eigenvectors(opt2fn("-v", NFILE, fnm), &natoms, &bFit, &xref, &bDMR, &xav, &bDMA, &nvec,
- &eignr, &eigvec, &eigval);
+ read_eigenvectors(
+ opt2fn("-v", NFILE, fnm), &natoms, &bFit, &xref, &bDMR, &xav, &bDMA, &nvec, &eignr, &eigvec, &eigval);
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &pbcType, &xtop, nullptr, box, bDMA);
atoms = &top.atoms;
/* (r-0.5) n times: var_n = n * var_1 = n/12
n=4: var_n = 1/3, so multiply with 3 */
- rfac = std::sqrt(3.0 * BOLTZ * temp / eigval[iout[j]]);
+ rfac = std::sqrt(3.0 * gmx::c_boltz * temp / eigval[iout[j]]);
rhalf = 2.0 * rfac;
rfac = rfac / im;
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strconvert.h"
-static real minthird = -1.0 / 3.0, minsixth = -1.0 / 6.0;
+static constexpr real minthird = -1.0 / 3.0, minsixth = -1.0 / 6.0;
static double mypow(double x, double y)
{
static real blk_value(t_enxblock* blk, int sub, int index)
{
range_check(index, 0, blk->sub[sub].nr);
- if (blk->sub[sub].type == xdr_datatype_float)
+ if (blk->sub[sub].type == XdrDataType::Float)
{
return blk->sub[sub].fval[index];
}
- else if (blk->sub[sub].type == xdr_datatype_double)
+ else if (blk->sub[sub].type == XdrDataType::Double)
{
return blk->sub[sub].dval[index];
}
int npargs;
npargs = asize(pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END, NFILE, fnm,
- npargs, pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END, NFILE, fnm, npargs, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
}
if (bORT)
{
- fort = xvgropen(opt2fn("-ort", NFILE, fnm), "Calculated orientations",
- "Time (ps)", "", oenv);
+ fort = xvgropen(
+ opt2fn("-ort", NFILE, fnm), "Calculated orientations", "Time (ps)", "", oenv);
if (bOrinst && output_env_get_print_xvgr_codes(oenv))
{
fprintf(fort, "%s", orinst_sub);
}
if (bODT)
{
- fodt = xvgropen(opt2fn("-odt", NFILE, fnm), "Orientation restraint deviation",
- "Time (ps)", "", oenv);
+ fodt = xvgropen(opt2fn("-odt", NFILE, fnm),
+ "Orientation restraint deviation",
+ "Time (ps)",
+ "",
+ oenv);
if (bOrinst && output_env_get_print_xvgr_codes(oenv))
{
fprintf(fodt, "%s", orinst_sub);
{
topInfo.fillFromInputFile(ftp2fn(efTPR, NFILE, fnm));
top = std::make_unique<gmx_localtop_t>(topInfo.mtop()->ffparams);
- gmx_mtop_generate_local_top(*topInfo.mtop(), top.get(), ir->efep != efepNO);
+ gmx_mtop_generate_local_top(
+ *topInfo.mtop(), top.get(), ir->efep != FreeEnergyPerturbationType::No);
}
nbounds = get_bounds(&bounds, &index, &pair, &npairs, top->idef);
snew(violaver, npairs);
xvgr_legend(out_disre, 2, drleg, oenv);
if (bDRAll)
{
- fp_pairs = xvgropen(opt2fn("-pairs", NFILE, fnm), "Pair Distances", "Time (ps)",
- "Distance (nm)", oenv);
+ fp_pairs = xvgropen(
+ opt2fn("-pairs", NFILE, fnm), "Pair Distances", "Time (ps)", "Distance (nm)", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp_pairs, "@ subtitle \"averaged (tau=%g) and instantaneous\"\n", ir->dr_tau);
gmx_fatal(FARGS,
"Number of disre pairs in the energy file (%d) does not match the "
"number in the run input file (%d)\n",
- ndisre, ilist.size() / 3);
+ ndisre,
+ ilist.size() / 3);
}
snew(pairleg, ndisre);
int molb = 0;
snew(pairleg[i], 30);
j = fa[3 * i + 1];
k = fa[3 * i + 2];
- mtopGetAtomAndResidueName(topInfo.mtop(), j, &molb, &anm_j, &resnr_j, &resnm_j, nullptr);
- mtopGetAtomAndResidueName(topInfo.mtop(), k, &molb, &anm_k, &resnr_k, &resnm_k, nullptr);
- sprintf(pairleg[i], "%d %s %d %s (%d)", resnr_j, anm_j, resnr_k, anm_k,
+ GMX_ASSERT(topInfo.hasTopology(), "Need to have a valid topology");
+ mtopGetAtomAndResidueName(*topInfo.mtop(), j, &molb, &anm_j, &resnr_j, &resnm_j, nullptr);
+ mtopGetAtomAndResidueName(*topInfo.mtop(), k, &molb, &anm_k, &resnr_k, &resnm_k, nullptr);
+ sprintf(pairleg[i],
+ "%d %s %d %s (%d)",
+ resnr_j,
+ anm_j,
+ resnr_k,
+ anm_k,
ip[fa[3 * i]].disres.label);
}
set = select_it(ndisre, pairleg, &nset);
}
/* Subtract bounds from distances, to calculate violations */
- calc_violations(disre_rt, disre_rm3tav, nbounds, pair, bounds, violaver,
- &sumt, &sumaver);
+ calc_violations(
+ disre_rt, disre_rm3tav, nbounds, pair, bounds, violaver, &sumt, &sumaver);
fprintf(out_disre, " %8.4f %8.4f\n", sumaver, sumt);
if (bDRAll)
gmx_fatal(FARGS,
"Number of orientation restraints in energy file (%d) does "
"not match with the topology (%d)",
- blk->sub[0].nr, nor);
+ blk->sub[0].nr,
+ nor);
}
if (bORA || bODA)
{
gmx_fatal(FARGS,
"Number of orientation experiments in energy file (%d) does "
"not match with the topology (%d)",
- blk->sub[0].nr / 12, nex);
+ blk->sub[0].nr / 12,
+ nex);
}
fprintf(foten, " %10f", fr.t);
for (i = 0; i < nex; i++)
}
if (bORA)
{
- FILE* out = xvgropen(opt2fn("-ora", NFILE, fnm), "Average calculated orientations",
- "Restraint label", "", oenv);
+ FILE* out = xvgropen(
+ opt2fn("-ora", NFILE, fnm), "Average calculated orientations", "Restraint label", "", oenv);
if (bOrinst && output_env_get_print_xvgr_codes(oenv))
{
fprintf(out, "%s", orinst_sub);
}
if (bODA)
{
- FILE* out = xvgropen(opt2fn("-oda", NFILE, fnm), "Average restraint deviation",
- "Restraint label", "", oenv);
+ FILE* out = xvgropen(
+ opt2fn("-oda", NFILE, fnm), "Average restraint deviation", "Restraint label", "", oenv);
if (bOrinst && output_env_get_print_xvgr_codes(oenv))
{
fprintf(out, "%s", orinst_sub);
}
if (bODR)
{
- FILE* out = xvgropen(opt2fn("-odr", NFILE, fnm), "RMS orientation restraint deviations",
- "Restraint label", "", oenv);
+ FILE* out = xvgropen(opt2fn("-odr", NFILE, fnm),
+ "RMS orientation restraint deviations",
+ "Restraint label",
+ "",
+ oenv);
if (bOrinst && output_env_get_print_xvgr_codes(oenv))
{
fprintf(out, "%s", orinst_sub);
if (bDisRe)
{
- analyse_disre(opt2fn("-viol", NFILE, fnm), teller_disre, violaver, bounds, index, pair,
- nbounds, oenv);
+ analyse_disre(opt2fn("-viol", NFILE, fnm), teller_disre, violaver, bounds, index, pair, nbounds, oenv);
}
{
const char* nxy = "-nxy";
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return 0;
}
- read_eigenvectors(opt2fn("-v", NFILE, fnm), &natoms, &bFit, &xref, &bDMR, &xav, &bDMA, &nvec,
- &eignr, &eigvec, &eigval);
+ read_eigenvectors(
+ opt2fn("-v", NFILE, fnm), &natoms, &bFit, &xref, &bDMR, &xav, &bDMA, &nvec, &eignr, &eigvec, &eigval);
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &pbcType, &xtop, nullptr, box, bDMA);
/* Derive amplitude from temperature and eigenvalue if we can */
/* Convert eigenvalue to angular frequency, in units s^(-1) */
- omega = std::sqrt(eigval[kmode] * 1.0E21 / (AVOGADRO * AMU));
+ omega = std::sqrt(eigval[kmode] * 1.0E21 / (gmx::c_avogadro * gmx::c_amu));
/* Harmonic motion will be x=x0 + A*sin(omega*t)*eigenvec.
* The velocity is thus:
*
/* Convert Ekin from amu*(nm/s)^2 to J, i.e., kg*(m/s)^2
* This will also be proportional to A^2
*/
- Ekin *= AMU * 1E-18;
+ Ekin *= gmx::c_amu * 1E-18;
/* Set the amplitude so the energy is kT/2 */
- amplitude[i] = std::sqrt(0.5 * BOLTZMANN * temp / Ekin);
+ amplitude[i] = std::sqrt(0.5 * gmx::c_boltzmann * temp / Ekin);
}
else
{
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxana/gstat.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
nframes = 0;
do
{
- find_nearest_neighbours(pbcType, natoms, box, x, isize[0], index[0], &sg, &sk, nslice,
- slice_dim, sg_slice, sk_slice, gpbc);
+ find_nearest_neighbours(
+ pbcType, natoms, box, x, isize[0], index[0], &sg, &sk, nslice, slice_dim, sg_slice, sk_slice, gpbc);
for (i = 0; (i < nslice); i++)
{
sg_slice_tot[i] += sg_slice[i];
fpsk = xvgropen(skslfn, "S\\sk\\N Distance Order Parameter / Slab", "(nm)", "S\\sk\\N", oenv);
for (i = 0; (i < nslice); i++)
{
- fprintf(fpsg, "%10g %10g\n", (i + 0.5) * box[slice_dim][slice_dim] / nslice,
+ fprintf(fpsg,
+ "%10g %10g\n",
+ (i + 0.5) * box[slice_dim][slice_dim] / nslice,
sg_slice_tot[i] / static_cast<real>(nframes));
- fprintf(fpsk, "%10g %10g\n", (i + 0.5) * box[slice_dim][slice_dim] / nslice,
+ fprintf(fpsk,
+ "%10g %10g\n",
+ (i + 0.5) * box[slice_dim][slice_dim] / nslice,
sk_slice_tot[i] / static_cast<real>(nframes));
}
xvgrclose(fpsg);
fprintf(stderr, "Using following groups: \n");
for (i = 0; i < ngrps; i++)
{
- fprintf(stderr, "Groupname: %s First atomname: %s First atomnr %d\n", groups[i],
- *(top->atoms.atomname[a[index[i]]]), a[index[i]]);
+ fprintf(stderr,
+ "Groupname: %s First atomname: %s First atomnr %d\n",
+ groups[i],
+ *(top->atoms.atomname[a[index[i]]]),
+ a[index[i]]);
}
fprintf(stderr, "\n");
}
fprintf(stderr,
"WARNING: distance between atoms %d and "
"%d > 0.3 nm (%f). Index file might be corrupt.\n",
- a, b, length);
+ a,
+ b,
+ length);
}
}
for (i = 1; i < ngrps - 1; i++)
{
svmul(1.0 / nr_frames, (*order)[i], (*order)[i]);
- fprintf(stderr, "Atom %d Tensor: x=%g , y=%g, z=%g\n", i, (*order)[i][XX], (*order)[i][YY],
+ fprintf(stderr,
+ "Atom %d Tensor: x=%g , y=%g, z=%g\n",
+ i,
+ (*order)[i][XX],
+ (*order)[i][YY],
(*order)[i][ZZ]);
if (bSliced || permolecule)
{
if (bUnsat)
{
- fprintf(stderr, "Average angle between double bond and normal: %f\n",
+ fprintf(stderr,
+ "Average angle between double bond and normal: %f\n",
180 * sdbangle / (nr_frames * static_cast<real>(size) * M_PI));
}
slOrd = xvgropen(bfile, buf, "Molecule", "S", oenv);
for (atom = 1; atom < ngrps - 1; atom++)
{
- fprintf(ord, "%12d %12g\n", atom,
+ fprintf(ord,
+ "%12d %12g\n",
+ atom,
-1.0 * (2.0 / 3.0 * order[atom][XX] + 1.0 / 3.0 * order[atom][YY]));
}
{
S += slOrder[slice][atom];
}
- fprintf(slOrd, "%12g %12g\n", static_cast<real>(slice) * slWidth,
- S / static_cast<real>(atom));
+ fprintf(slOrd, "%12g %12g\n", static_cast<real>(slice) * slWidth, S / static_cast<real>(atom));
}
}
else
for (atom = 1; atom < ngrps - 1; atom++)
{
- fprintf(ord, "%12d %12g %12g %12g\n", atom, order[atom][XX], order[atom][YY],
- order[atom][ZZ]);
- fprintf(slOrd, "%12d %12g\n", atom,
+ fprintf(ord, "%12d %12g %12g %12g\n", atom, order[atom][XX], order[atom][YY], order[atom][ZZ]);
+ fprintf(slOrd,
+ "%12d %12g\n",
+ atom,
-1.0 * (2.0 / 3.0 * order[atom][XX] + 1.0 / 3.0 * order[atom][YY]));
}
}
/*initialize PDBinfo*/
for (i = 0; i < useatoms.nr; ++i)
{
- useatoms.pdbinfo[i].type = 0;
+ useatoms.pdbinfo[i].type = PdbRecordType::Atom;
useatoms.pdbinfo[i].occup = 0.0;
useatoms.pdbinfo[i].bfac = 0.0;
useatoms.pdbinfo[i].bAnisotropic = FALSE;
}
}
- write_sto_conf(opt2fn("-ob", nfile, fnm), "Order parameters", &useatoms, frout.x, nullptr,
- frout.pbcType, frout.box);
+ write_sto_conf(
+ opt2fn("-ob", nfile, fnm), "Order parameters", &useatoms, frout.x, nullptr, frout.pbcType, frout.box);
sfree(frout.x);
done_atom(&useatoms);
const char * sgfnm, *skfnm, *ndxfnm, *tpsfnm, *trxfnm;
gmx_output_env_t* oenv;
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
/* If either of theoptions is set we compute both */
sgfnm = opt2fn("-Sg", NFILE, fnm);
skfnm = opt2fn("-Sk", NFILE, fnm);
- calc_tetra_order_parm(ndxfnm, tpsfnm, trxfnm, sgfnm, skfnm, nslices, axis,
- opt2fn("-Sgsl", NFILE, fnm), opt2fn("-Sksl", NFILE, fnm), oenv);
+ calc_tetra_order_parm(ndxfnm,
+ tpsfnm,
+ trxfnm,
+ sgfnm,
+ skfnm,
+ nslices,
+ axis,
+ opt2fn("-Sgsl", NFILE, fnm),
+ opt2fn("-Sksl", NFILE, fnm),
+ oenv);
/* view xvgr files */
do_view(oenv, opt2fn("-Sg", NFILE, fnm), nullptr);
do_view(oenv, opt2fn("-Sk", NFILE, fnm), nullptr);
/* show atomtypes, to check if index file is correct */
print_types(index, a, ngrps, grpname, top);
- calc_order(ftp2fn(efTRX, NFILE, fnm), index, a, &order, &slOrder, &slWidth, nslices,
- bSliced, bUnsat, top, pbcType, ngrps, axis, permolecule, radial, distcalc,
- opt2fn_null("-nr", NFILE, fnm), &distvals, oenv);
+ calc_order(ftp2fn(efTRX, NFILE, fnm),
+ index,
+ a,
+ &order,
+ &slOrder,
+ &slWidth,
+ nslices,
+ bSliced,
+ bUnsat,
+ top,
+ pbcType,
+ ngrps,
+ axis,
+ permolecule,
+ radial,
+ distcalc,
+ opt2fn_null("-nr", NFILE, fnm),
+ &distvals,
+ oenv);
if (radial)
{
ngrps--; /*don't print the last group--was used for
center-of-mass determination*/
}
- order_plot(order, slOrder, opt2fn("-o", NFILE, fnm), opt2fn("-os", NFILE, fnm),
- opt2fn("-od", NFILE, fnm), ngrps, nslices, slWidth, bSzonly, permolecule,
- distvals, oenv);
+ order_plot(order,
+ slOrder,
+ opt2fn("-o", NFILE, fnm),
+ opt2fn("-os", NFILE, fnm),
+ opt2fn("-od", NFILE, fnm),
+ ngrps,
+ nslices,
+ slWidth,
+ bSzonly,
+ permolecule,
+ distvals,
+ oenv);
if (opt2bSet("-ob", NFILE, fnm))
{
char ** legp, buf[STRLEN];
gmx_rmpbc_t gpbc = nullptr;
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm,
- asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc,
+ argv,
+ PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
+ NFILE,
+ fnm,
+ asize(pa),
+ pa,
+ asize(desc),
+ desc,
+ 0,
+ nullptr,
+ &oenv))
{
return 0;
}
if (opt2bSet("-v", NFILE, fnm))
{
- outv = xvgropen(opt2fn("-v", NFILE, fnm), "Principal components",
- output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
+ outv = xvgropen(opt2fn("-v", NFILE, fnm),
+ "Principal components",
+ output_env_get_xvgr_tlabel(oenv),
+ "(nm)",
+ oenv);
snew(legp, DIM * DIM);
for (d = 0; d < DIM; d++)
{
if (opt2bSet("-p", NFILE, fnm))
{
- outp = xvgropen(opt2fn("-p", NFILE, fnm), "Persistence length",
- output_env_get_xvgr_tlabel(oenv), "bonds", oenv);
+ outp = xvgropen(opt2fn("-p", NFILE, fnm),
+ "Persistence length",
+ output_env_get_xvgr_tlabel(oenv),
+ "bonds",
+ oenv);
snew(bond, nat_max - 1);
snew(sum_inp, nat_min / 2);
snew(ninp, nat_min / 2);
if (opt2bSet("-i", NFILE, fnm))
{
- outi = xvgropen(opt2fn("-i", NFILE, fnm), "Internal distances", "n",
- "<R\\S2\\N(n)>/n (nm\\S2\\N)", oenv);
- i = index[molind[1] - 1] - index[molind[0]]; /* Length of polymer -1 */
+ outi = xvgropen(
+ opt2fn("-i", NFILE, fnm), "Internal distances", "n", "<R\\S2\\N(n)>/n (nm\\S2\\N)", oenv);
+ i = index[molind[1] - 1] - index[molind[0]]; /* Length of polymer -1 */
snew(intd, i);
}
else
gyro_eigen(gyr_all, eig, eigv, ord);
- fprintf(out, "%10.3f %8.4f %8.4f %8.4f %8.4f %8.4f", t * output_env_get_time_factor(oenv),
- std::sqrt(sum_eed2), sqrt(sum_gyro), std::sqrt(eig[ord[0]]), std::sqrt(eig[ord[1]]),
+ fprintf(out,
+ "%10.3f %8.4f %8.4f %8.4f %8.4f %8.4f",
+ t * output_env_get_time_factor(oenv),
+ std::sqrt(sum_eed2),
+ sqrt(sum_gyro),
+ std::sqrt(eig[ord[0]]),
+ std::sqrt(eig[ord[1]]),
std::sqrt(eig[ord[2]]));
if (bPC)
{
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxana/princ.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/rmpbc.h"
/* This probably sucks but it seems to work. */
/****************************************************************************/
-static int ce = 0, cb = 0;
-
/* this routine integrates the array data and returns the resulting array */
/* routine uses simple trapezoid rule */
-static void p_integrate(double* result, const double data[], int ndata, double slWidth)
+static void p_integrate(double* result, const double data[], int ndata, double slWidth, int cb, int ce)
{
int i, slice;
double sum;
double fudge_z,
gmx_bool bSpherical,
gmx_bool bCorrect,
+ int cb,
+ int ce,
const gmx_output_env_t* oenv)
{
rvec* x0; /* coordinates without pbc */
gmx_fatal(FARGS,
"You selected a group with %d atoms, but only %d atoms\n"
"were found in the trajectory.\n",
- gnx[n], natoms);
+ gnx[n],
+ natoms);
}
for (i = 0; i < gnx[n]; i++) /* loop over all atoms in index file */
{
for (n = 0; n < nr_grps; n++)
{
/* integrate twice to get field and potential */
- p_integrate((*slField)[n], (*slCharge)[n], *nslices, *slWidth);
+ p_integrate((*slField)[n], (*slCharge)[n], *nslices, *slWidth, cb, ce);
}
for (n = 0; n < nr_grps; n++)
{
- p_integrate((*slPotential)[n], (*slField)[n], *nslices, *slWidth);
+ p_integrate((*slPotential)[n], (*slField)[n], *nslices, *slWidth, cb, ce);
}
/* Now correct for eps0 and in spherical case for r*/
int nr_grps,
const char* const grpname[],
double slWidth,
+ int cb,
+ int ce,
const gmx_output_env_t* oenv)
{
FILE *pot, /* xvgr file with potential */
static gmx_bool bSpherical = FALSE; /* default is bilayer types */
static real fudge_z = 0; /* translate coordinates */
static gmx_bool bCorrect = false;
+ int cb = 0;
+ int ce = 0;
t_pargs pa[] = {
{ "-d",
FALSE,
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, asize(bugs), bugs, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
rd_index(ftp2fn(efNDX, NFILE, fnm), ngrps, ngx, index, grpname);
- calc_potential(ftp2fn(efTRX, NFILE, fnm), index, ngx, &potential, &charge, &field, &nslices,
- top, pbcType, axis, ngrps, &slWidth, fudge_z, bSpherical, bCorrect, oenv);
-
- plot_potential(potential, charge, field, opt2fn("-o", NFILE, fnm), opt2fn("-oc", NFILE, fnm),
- opt2fn("-of", NFILE, fnm), nslices, ngrps, grpname, slWidth, oenv);
+ calc_potential(ftp2fn(efTRX, NFILE, fnm),
+ index,
+ ngx,
+ &potential,
+ &charge,
+ &field,
+ &nslices,
+ top,
+ pbcType,
+ axis,
+ ngrps,
+ &slWidth,
+ fudge_z,
+ bSpherical,
+ bCorrect,
+ cb,
+ ce,
+ oenv);
+
+ plot_potential(potential,
+ charge,
+ field,
+ opt2fn("-o", NFILE, fnm),
+ opt2fn("-oc", NFILE, fnm),
+ opt2fn("-of", NFILE, fnm),
+ nslices,
+ ngrps,
+ grpname,
+ slWidth,
+ cb,
+ ce,
+ oenv);
do_view(oenv, opt2fn("-o", NFILE, fnm), nullptr); /* view xvgr file */
do_view(oenv, opt2fn("-oc", NFILE, fnm), nullptr); /* view xvgr file */
{ efXVG, "-om", "moi", ffWRITE } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW, NFILE, fnm,
- asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc,
+ argv,
+ PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
+ NFILE,
+ fnm,
+ asize(pa),
+ pa,
+ asize(desc),
+ desc,
+ 0,
+ nullptr,
+ &oenv))
{
return 0;
}
sprintf(legend[i], "%c component", 'X' + i);
}
- axis1 = xvgropen(opt2fn("-a1", NFILE, fnm), "Principal axis 1 (major axis)",
- output_env_get_xvgr_tlabel(oenv), "Component (nm)", oenv);
+ axis1 = xvgropen(opt2fn("-a1", NFILE, fnm),
+ "Principal axis 1 (major axis)",
+ output_env_get_xvgr_tlabel(oenv),
+ "Component (nm)",
+ oenv);
xvgr_legend(axis1, DIM, legend, oenv);
- axis2 = xvgropen(opt2fn("-a2", NFILE, fnm), "Principal axis 2 (middle axis)",
- output_env_get_xvgr_tlabel(oenv), "Component (nm)", oenv);
+ axis2 = xvgropen(opt2fn("-a2", NFILE, fnm),
+ "Principal axis 2 (middle axis)",
+ output_env_get_xvgr_tlabel(oenv),
+ "Component (nm)",
+ oenv);
xvgr_legend(axis2, DIM, legend, oenv);
- axis3 = xvgropen(opt2fn("-a3", NFILE, fnm), "Principal axis 3 (minor axis)",
- output_env_get_xvgr_tlabel(oenv), "Component (nm)", oenv);
+ axis3 = xvgropen(opt2fn("-a3", NFILE, fnm),
+ "Principal axis 3 (minor axis)",
+ output_env_get_xvgr_tlabel(oenv),
+ "Component (nm)",
+ oenv);
xvgr_legend(axis3, DIM, legend, oenv);
sprintf(legend[XX], "Axis 1 (major)");
sprintf(legend[YY], "Axis 2 (middle)");
sprintf(legend[ZZ], "Axis 3 (minor)");
- fmoi = xvgropen(opt2fn("-om", NFILE, fnm), "Moments of inertia around inertial axes",
- output_env_get_xvgr_tlabel(oenv), "I (au nm\\S2\\N)", oenv);
+ fmoi = xvgropen(opt2fn("-om", NFILE, fnm),
+ "Moments of inertia around inertial axes",
+ output_env_get_xvgr_tlabel(oenv),
+ "I (au nm\\S2\\N)",
+ oenv);
xvgr_legend(fmoi, DIM, legend, oenv);
for (i = 0; i < DIM; i++)
calc_principal_axes(&top, x, index, gnx, axes, moi);
- fprintf(axis1, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[XX][XX], axes[XX][YY],
- axes[XX][ZZ]);
- fprintf(axis2, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[YY][XX], axes[YY][YY],
- axes[YY][ZZ]);
- fprintf(axis3, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[ZZ][XX], axes[ZZ][YY],
- axes[ZZ][ZZ]);
+ fprintf(axis1, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[XX][XX], axes[XX][YY], axes[XX][ZZ]);
+ fprintf(axis2, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[YY][XX], axes[YY][YY], axes[YY][ZZ]);
+ fprintf(axis3, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[ZZ][XX], axes[ZZ][YY], axes[ZZ][ZZ]);
fprintf(fmoi, "%15.10f %15.10f %15.10f %15.10f\n", t, moi[XX], moi[YY], moi[ZZ]);
} while (read_next_x(oenv, status, &t, x, box));
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxana/nrama.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/futil.h"
for (i = 0; (i < xr->npp); i++)
{
- phi = xr->dih[xr->pp[i].iphi].ang * RAD2DEG;
- psi = xr->dih[xr->pp[i].ipsi].ang * RAD2DEG;
+ phi = xr->dih[xr->pp[i].iphi].ang * gmx::c_rad2Deg;
+ psi = xr->dih[xr->pp[i].ipsi].ang * gmx::c_rad2Deg;
fprintf(out, "%g %g %s\n", phi, psi, xr->pp[i].label);
}
}
{ efXVG, nullptr, "rama", ffWRITE } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, 0, nullptr,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, 0, nullptr, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxana/princ.h"
#include "gromacs/math/do_fit.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/rmpbc.h"
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW, NFILE, fnm,
- asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc,
+ argv,
+ PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
+ NFILE,
+ fnm,
+ asize(pa),
+ pa,
+ asize(desc),
+ desc,
+ 0,
+ nullptr,
+ &oenv))
{
return 0;
}
natoms_trx = read_first_x(oenv, &status, opt2fn("-f", NFILE, fnm), &t, &x, box);
if (natoms_trx != top.atoms.nr)
{
- fprintf(stderr, "\nWARNING: topology has %d atoms, whereas trajectory has %d\n",
- top.atoms.nr, natoms_trx);
+ fprintf(stderr, "\nWARNING: topology has %d atoms, whereas trajectory has %d\n", top.atoms.nr, natoms_trx);
}
natoms = std::min(top.atoms.nr, natoms_trx);
if (bMat || bBond || bPrev)
gmx_fatal(FARGS,
"Second trajectory (%d atoms) does not match the first one"
" (%d atoms)",
- natoms_trx2, natoms_trx);
+ natoms_trx2,
+ natoms_trx);
}
frame2 = 0;
do
{
if (bFile2 || (i < j))
{
- rmsd_mat[i][j] = calc_similar_ind(ewhat != ewRMSD, irms[0], ind_rms_m,
- w_rms_m, mat_x[i], mat_x2_j);
+ rmsd_mat[i][j] = calc_similar_ind(
+ ewhat != ewRMSD, irms[0], ind_rms_m, w_rms_m, mat_x[i], mat_x2_j);
if (rmsd_mat[i][j] > rmsd_max)
{
rmsd_max = rmsd_mat[i][j];
fprintf(stderr, "Min and Max value set to resp. %f and %f\n", rmsd_min, rmsd_max);
}
sprintf(buf, "%s %s matrix", gn_rms[0], whatname[ewhat]);
- write_xpm(opt2FILE("-m", NFILE, fnm, "w"), 0, buf, whatlabel[ewhat],
- output_env_get_time_label(oenv), output_env_get_time_label(oenv), tel_mat,
- tel_mat2, axis, axis2, rmsd_mat, rmsd_min, rmsd_max, rlo, rhi, &nlevels);
+ write_xpm(opt2FILE("-m", NFILE, fnm, "w"),
+ 0,
+ buf,
+ whatlabel[ewhat],
+ output_env_get_time_label(oenv),
+ output_env_get_time_label(oenv),
+ tel_mat,
+ tel_mat2,
+ axis,
+ axis2,
+ rmsd_mat,
+ rmsd_min,
+ rmsd_max,
+ rlo,
+ rhi,
+ &nlevels);
/* Print the distribution of RMSD values */
if (opt2bSet("-dist", NFILE, fnm))
{
}
sprintf(buf, "%s %s vs. delta t", gn_rms[0], whatname[ewhat]);
fp = gmx_ffopen("delta.xpm", "w");
- write_xpm(fp, 0, buf, "density", output_env_get_time_label(oenv), whatlabel[ewhat],
- delta_xsize, del_lev + 1, del_xaxis, del_yaxis, delta, 0.0, delta_max,
- rlo, rhi, &nlevels);
+ write_xpm(fp,
+ 0,
+ buf,
+ "density",
+ output_env_get_time_label(oenv),
+ whatlabel[ewhat],
+ delta_xsize,
+ del_lev + 1,
+ del_xaxis,
+ del_yaxis,
+ delta,
+ 0.0,
+ delta_max,
+ rlo,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
}
if (opt2bSet("-bin", NFILE, fnm))
fprintf(stderr,
"Bond angle Min and Max set to:\n"
"Min. angle: %f, Max. angle: %f\n",
- bond_min, bond_max);
+ bond_min,
+ bond_max);
}
rlo.r = 1;
rlo.g = 1;
rhi.g = 0;
rhi.b = 0;
sprintf(buf, "%s av. bond angle deviation", gn_rms[0]);
- write_xpm(opt2FILE("-bm", NFILE, fnm, "w"), 0, buf, "degrees",
- output_env_get_time_label(oenv), output_env_get_time_label(oenv), tel_mat,
- tel_mat2, axis, axis2, bond_mat, bond_min, bond_max, rlo, rhi, &nlevels);
+ write_xpm(opt2FILE("-bm", NFILE, fnm, "w"),
+ 0,
+ buf,
+ "degrees",
+ output_env_get_time_label(oenv),
+ output_env_get_time_label(oenv),
+ tel_mat,
+ tel_mat2,
+ axis,
+ axis2,
+ bond_mat,
+ bond_min,
+ bond_max,
+ rlo,
+ rhi,
+ &nlevels);
}
}
}
else
{
- sprintf(buf, "%s with frame %g %s ago", whatxvgname[ewhat], time[prev * freq] - time[0],
+ sprintf(buf,
+ "%s with frame %g %s ago",
+ whatxvgname[ewhat],
+ time[prev * freq] - time[0],
output_env_get_time_label(oenv).c_str());
}
- fp = xvgropen(opt2fn("-o", NFILE, fnm), buf, output_env_get_xvgr_tlabel(oenv),
- whatxvglabel[ewhat], oenv);
+ fp = xvgropen(opt2fn("-o", NFILE, fnm), buf, output_env_get_xvgr_tlabel(oenv), whatxvglabel[ewhat], oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
- fprintf(fp, "@ subtitle \"%s%s after %s%s%s\"\n", (nrms == 1) ? "" : "of ", gn_rms[0],
- fitgraphlabel[efit], bFit ? " to " : "", bFit ? gn_fit : "");
+ fprintf(fp,
+ "@ subtitle \"%s%s after %s%s%s\"\n",
+ (nrms == 1) ? "" : "of ",
+ gn_rms[0],
+ fitgraphlabel[efit],
+ bFit ? " to " : "",
+ bFit ? gn_fit : "");
}
if (nrms != 1)
{
{
if (output_env_get_print_xvgr_codes(oenv))
{
- fprintf(fp, "@ subtitle \"of %s after lsq fit to mirror of %s\"\n", gn_rms[0],
- bFit ? gn_fit : "");
+ fprintf(fp, "@ subtitle \"of %s after lsq fit to mirror of %s\"\n", gn_rms[0], bFit ? gn_fit : "");
}
}
else
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
}
-static char Hnum[] = "123";
+static const char Hnum[] = "123";
typedef struct
{
j = i + 1;
rnri = atoms->atom[index[i]].resind;
rnrj = atoms->atom[index[j]].resind;
- bEquiv = is_equiv(neq, equiv, &nnm[i], rnri, *atoms->resinfo[rnri].name,
- *atoms->atomname[index[i]], rnrj, *atoms->resinfo[rnrj].name,
+ bEquiv = is_equiv(neq,
+ equiv,
+ &nnm[i],
+ rnri,
+ *atoms->resinfo[rnri].name,
+ *atoms->atomname[index[i]],
+ rnrj,
+ *atoms->resinfo[rnrj].name,
*atoms->atomname[index[j]]);
if (nnm[i] && bEquiv)
{
for (i = 0; i < isize; i++)
{
rnri = atoms->atom[index[i]].resind;
- fprintf(debug, "%s %s %d -> %s\n", *atoms->atomname[index[i]],
- *atoms->resinfo[rnri].name, rnri, nnm[i] ? nnm[i] : "");
+ fprintf(debug,
+ "%s %s %d -> %s\n",
+ *atoms->atomname[index[i]],
+ *atoms->resinfo[rnri].name,
+ rnri,
+ nnm[i] ? nnm[i] : "");
}
}
/* dump group definitions */
if (debug)
{
- fprintf(debug, "%d %d %d %d %s %s %d\n", i, gi, noe_gr[gi].ianr, noe_gr[gi].anr,
- noe_gr[gi].aname, noe_gr[gi].rname, noe_gr[gi].rnr);
+ fprintf(debug,
+ "%d %d %d %d %s %s %d\n",
+ i,
+ gi,
+ noe_gr[gi].ianr,
+ noe_gr[gi].anr,
+ noe_gr[gi].aname,
+ noe_gr[gi].rname,
+ noe_gr[gi].rnr);
}
}
}
t_noe_gr gri, grj;
min3 = min6 = 1e6;
- fprintf(fp, ";%4s %3s %4s %4s%3s %4s %4s %4s %4s%3s %5s %5s %8s %2s %2s %s\n", "ianr", "anr",
- "anm", "rnm", "rnr", "ianr", "anr", "anm", "rnm", "rnr", "1/r^3", "1/r^6", "intnsty",
- "Dr", "Da", "scale");
+ fprintf(fp,
+ ";%4s %3s %4s %4s%3s %4s %4s %4s %4s%3s %5s %5s %8s %2s %2s %s\n",
+ "ianr",
+ "anr",
+ "anm",
+ "rnm",
+ "rnr",
+ "ianr",
+ "anr",
+ "anm",
+ "rnm",
+ "rnr",
+ "1/r^3",
+ "1/r^6",
+ "intnsty",
+ "Dr",
+ "Da",
+ "scale");
for (i = 0; i < gnr; i++)
{
gri = noe_gr[i];
{
std::strcpy(b6, "-");
}
- fprintf(fp, "%4d %4d %4s %4s%3d %4d %4d %4s %4s%3d %5s %5s %8d %2d %2s %s\n",
- gri.ianr + 1, gri.anr + 1, gri.aname, gri.rname, gri.rnr + 1, grj.ianr + 1,
- grj.anr + 1, grj.aname, grj.rname, grj.rnr + 1, b3, b6,
- gmx::roundToInt(noe[i][j].i_6), grj.rnr - gri.rnr, buf, noe2scale(r3, r6, rmax));
+ fprintf(fp,
+ "%4d %4d %4s %4s%3d %4d %4d %4s %4s%3d %5s %5s %8d %2d %2s %s\n",
+ gri.ianr + 1,
+ gri.anr + 1,
+ gri.aname,
+ gri.rname,
+ gri.rnr + 1,
+ grj.ianr + 1,
+ grj.anr + 1,
+ grj.aname,
+ grj.rname,
+ grj.rnr + 1,
+ b3,
+ b6,
+ gmx::roundToInt(noe[i][j].i_6),
+ grj.rnr - gri.rnr,
+ buf,
+ noe2scale(r3, r6, rmax));
}
}
}
fprintf(stdout,
"NOTE: no 1/r^%d averaged distances found below %g, "
"smallest was %g\n",
- i, rmax, MINI);
+ i,
+ rmax,
+ MINI);
}
else
{
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
/* make list of noe atom groups */
snew(noe_index, isize + 1);
snew(noe_gr, isize);
- gnr = analyze_noe_equivalent(opt2fn_null("-equiv", NFILE, fnm), atoms, isize, index, bSumH,
- noe_index, noe_gr);
+ gnr = analyze_noe_equivalent(
+ opt2fn_null("-equiv", NFILE, fnm), atoms, isize, index, bSumH, noe_index, noe_gr);
fprintf(stdout, "Found %d non-equivalent atom-groups in %d atoms\n", gnr, isize);
/* make half matrix of of noe-group distances from atom distances */
snew(noe, gnr);
if (bRMS)
{
- write_xpm(opt2FILE("-rms", NFILE, fnm, "w"), 0, "RMS of distance", "RMS (nm)", "Atom Index",
- "Atom Index", isize, isize, resnr, resnr, rms, 0.0, rmsmax, rlo, rhi, &nlevels);
+ write_xpm(opt2FILE("-rms", NFILE, fnm, "w"),
+ 0,
+ "RMS of distance",
+ "RMS (nm)",
+ "Atom Index",
+ "Atom Index",
+ isize,
+ isize,
+ resnr,
+ resnr,
+ rms,
+ 0.0,
+ rmsmax,
+ rlo,
+ rhi,
+ &nlevels);
}
if (bScale)
{
- write_xpm(opt2FILE("-scl", NFILE, fnm, "w"), 0, "Relative RMS", "RMS", "Atom Index",
- "Atom Index", isize, isize, resnr, resnr, rmsc, 0.0, rmscmax, rlo, rhi, &nlevels);
+ write_xpm(opt2FILE("-scl", NFILE, fnm, "w"),
+ 0,
+ "Relative RMS",
+ "RMS",
+ "Atom Index",
+ "Atom Index",
+ isize,
+ isize,
+ resnr,
+ resnr,
+ rmsc,
+ 0.0,
+ rmscmax,
+ rlo,
+ rhi,
+ &nlevels);
}
if (bMean)
{
- write_xpm(opt2FILE("-mean", NFILE, fnm, "w"), 0, "Mean Distance", "Distance (nm)",
- "Atom Index", "Atom Index", isize, isize, resnr, resnr, mean, 0.0, meanmax, rlo,
- rhi, &nlevels);
+ write_xpm(opt2FILE("-mean", NFILE, fnm, "w"),
+ 0,
+ "Mean Distance",
+ "Distance (nm)",
+ "Atom Index",
+ "Atom Index",
+ isize,
+ isize,
+ resnr,
+ resnr,
+ mean,
+ 0.0,
+ meanmax,
+ rlo,
+ rhi,
+ &nlevels);
}
if (bNMR3)
{
- write_xpm(opt2FILE("-nmr3", NFILE, fnm, "w"), 0, "1/r^3 averaged distances",
- "Distance (nm)", "Atom Index", "Atom Index", isize, isize, resnr, resnr, dtot1_3,
- 0.0, max1_3, rlo, rhi, &nlevels);
+ write_xpm(opt2FILE("-nmr3", NFILE, fnm, "w"),
+ 0,
+ "1/r^3 averaged distances",
+ "Distance (nm)",
+ "Atom Index",
+ "Atom Index",
+ isize,
+ isize,
+ resnr,
+ resnr,
+ dtot1_3,
+ 0.0,
+ max1_3,
+ rlo,
+ rhi,
+ &nlevels);
}
if (bNMR6)
{
- write_xpm(opt2FILE("-nmr6", NFILE, fnm, "w"), 0, "1/r^6 averaged distances",
- "Distance (nm)", "Atom Index", "Atom Index", isize, isize, resnr, resnr, dtot1_6,
- 0.0, max1_6, rlo, rhi, &nlevels);
+ write_xpm(opt2FILE("-nmr6", NFILE, fnm, "w"),
+ 0,
+ "1/r^6 averaged distances",
+ "Distance (nm)",
+ "Atom Index",
+ "Atom Index",
+ isize,
+ isize,
+ resnr,
+ resnr,
+ dtot1_6,
+ 0.0,
+ max1_6,
+ rlo,
+ rhi,
+ &nlevels);
}
if (bNOE)
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/linearalgebra/eigensolver.h"
#include "gromacs/math/do_fit.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/rmpbc.h"
{ efXVG, "-oc", "correl", ffOPTWR }, { efLOG, "-dir", "rmsf", ffOPTWR } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pargs),
- pargs, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pargs), pargs, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
|| top.atoms.atom[index[i]].resind != top.atoms.atom[index[i + 1]].resind)
{
resind = top.atoms.atom[index[i]].resind;
- pdb_bfac = find_pdb_bfac(pdbatoms, &top.atoms.resinfo[resind],
- *(top.atoms.atomname[index[i]]));
+ pdb_bfac = find_pdb_bfac(
+ pdbatoms, &top.atoms.resinfo[resind], *(top.atoms.atomname[index[i]]));
- fprintf(fp, "%5d %10.5f %10.5f\n",
+ fprintf(fp,
+ "%5d %10.5f %10.5f\n",
bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i] + 1,
- rmsf[i] * bfac, pdb_bfac);
+ rmsf[i] * bfac,
+ pdb_bfac);
}
}
xvgrclose(fp);
if (!bRes || i + 1 == isize
|| top.atoms.atom[index[i]].resind != top.atoms.atom[index[i + 1]].resind)
{
- fprintf(fp, "%5d %8.4f\n",
+ fprintf(fp,
+ "%5d %8.4f\n",
bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i] + 1,
std::sqrt(rmsf[i]));
}
if (!bRes || i + 1 == isize
|| top.atoms.atom[index[i]].resind != top.atoms.atom[index[i + 1]].resind)
{
- fprintf(fp, "%5d %8.4f\n",
+ fprintf(fp,
+ "%5d %8.4f\n",
bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i] + 1,
std::sqrt(rmsf[i]));
}
{
rvec_inc(pdbx[index[i]], xcm);
}
- write_sto_conf_indexed(opt2fn("-oq", NFILE, fnm), title, pdbatoms, pdbx, nullptr, pbcType,
- pdbbox, isize, index);
+ write_sto_conf_indexed(
+ opt2fn("-oq", NFILE, fnm), title, pdbatoms, pdbx, nullptr, pbcType, pdbbox, isize, index);
}
if (opt2bSet("-ox", NFILE, fnm))
{
}
}
/* Write a .pdb file with B-factors and optionally anisou records */
- write_sto_conf_indexed(opt2fn("-ox", NFILE, fnm), title, pdbatoms, bFactorX, nullptr,
- pbcType, pdbbox, isize, index);
+ write_sto_conf_indexed(
+ opt2fn("-ox", NFILE, fnm), title, pdbatoms, bFactorX, nullptr, pbcType, pdbbox, isize, index);
sfree(bFactorX);
}
if (bAniso)
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, npargs, ppa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
{
sfree(ppa);
return 0;
mode = eacVector;
- do_autocorr(ftp2fn(efXVG, NFILE, fnm), oenv, "Rotational Correlation Function", teller,
- nvec, c1, dt, mode, bAver);
+ do_autocorr(
+ ftp2fn(efXVG, NFILE, fnm), oenv, "Rotational Correlation Function", teller, nvec, c1, dt, mode, bAver);
}
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), nullptr);
{
gmx_fatal(FARGS,
"Atom index (%d) is larger than the number of atoms in the trajecory (%d)",
- index[a] + 1, natoms);
+ index[a] + 1,
+ natoms);
}
w_rls[a] = (bMW ? top->atoms.atom[index[a]].m : 1.0);
tot_mass += w_rls[a];
{ efXVG, nullptr, "rotmat", ffWRITE } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
GMX_RELEASE_ASSERT(reffit[0] != nullptr, "Options inconsistency; reffit[0] is NULL");
if (reffit[0][0] != 'n')
{
- get_refx(oenv, ftp2fn(efTRX, NFILE, fnm), reffit[0][2] == 'z' ? 3 : 2, skip, gnx, index,
- bMW, &top, pbcType, x_ref);
+ get_refx(oenv, ftp2fn(efTRX, NFILE, fnm), reffit[0][2] == 'z' ? 3 : 2, skip, gnx, index, bMW, &top, pbcType, x_ref);
}
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
{
gmx_fatal(FARGS,
"Atom index (%d) is larger than the number of atoms in the trajecory (%d)",
- index[i] + 1, natoms);
+ index[i] + 1,
+ natoms);
}
w_rls[index[i]] = (bMW ? top.atoms.atom[index[i]].m : 1.0);
}
calc_fit_R(DIM, natoms, w_rls, x_ref, x, R);
- fprintf(out, "%7g %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f\n", t, R[XX][XX],
- R[XX][YY], R[XX][ZZ], R[YY][XX], R[YY][YY], R[YY][ZZ], R[ZZ][XX], R[ZZ][YY], R[ZZ][ZZ]);
+ fprintf(out,
+ "%7g %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f\n",
+ t,
+ R[XX][XX],
+ R[XX][YY],
+ R[XX][ZZ],
+ R[YY][XX],
+ R[YY][YY],
+ R[YY][ZZ],
+ R[ZZ][XX],
+ R[ZZ][YY],
+ R[ZZ][ZZ]);
} while (read_next_x(oenv, status, &t, x, box));
gmx_rmpbc_done(gpbc);
matrix box;
gmx_output_env_t* oenv;
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm, asize(pa), pa, asize(desc), desc,
- 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
nthreads = gmx_omp_get_max_threads();
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
fnTRX = ftp2fn(efTRX, NFILE, fnm);
gnsf = gmx_neutronstructurefactors_init(fnDAT);
- fprintf(stderr, "Read %d atom names from %s with neutron scattering parameters\n\n",
- gnsf->nratoms, fnDAT);
+ fprintf(stderr, "Read %d atom names from %s with neutron scattering parameters\n\n", gnsf->nratoms, fnDAT);
snew(top, 1);
snew(grpname, 1);
natoms = read_first_x(oenv, &status, fnTRX, &t, &x, box);
if (natoms != top->atoms.nr)
{
- fprintf(stderr, "\nWARNING: number of atoms in tpx (%d) and trajectory (%d) do not match\n",
- natoms, top->atoms.nr);
+ fprintf(stderr,
+ "\nWARNING: number of atoms in tpx (%d) and trajectory (%d) do not match\n",
+ natoms,
+ top->atoms.nr);
}
do
snew(pr, 1);
}
/* realy calc p(r) */
- prframecurrent = calc_radial_distribution_histogram(gsans, x, box, index, isize, binwidth,
- bMC, bNORM, mcover, seed);
+ prframecurrent = calc_radial_distribution_histogram(
+ gsans, x, box, index, isize, binwidth, bMC, bNORM, mcover, seed);
/* copy prframecurrent -> pr and summ up pr->gr[i] */
/* allocate and/or resize memory for pr->gr[i] and pr->r[i] */
if (pr->gr == nullptr)
auto fnmdup = filenames;
sprintf(suffix, "-t%.2f", t);
add_suffix_to_output_names(fnmdup.data(), NFILE, suffix);
- fp = xvgropen(opt2fn_null("-prframe", NFILE, fnmdup.data()), hdr, "Distance (nm)",
- "Probability", oenv);
+ fp = xvgropen(opt2fn_null("-prframe", NFILE, fnmdup.data()),
+ hdr,
+ "Distance (nm)",
+ "Probability",
+ oenv);
for (i = 0; i < prframecurrent->grn; i++)
{
fprintf(fp, "%10.6f%10.6f\n", prframecurrent->r[i], prframecurrent->gr[i]);
auto fnmdup = filenames;
sprintf(suffix, "-t%.2f", t);
add_suffix_to_output_names(fnmdup.data(), NFILE, suffix);
- fp = xvgropen(opt2fn_null("-sqframe", NFILE, fnmdup.data()), hdr, "q (nm^-1)",
- "s(q)/s(0)", oenv);
+ fp = xvgropen(
+ opt2fn_null("-sqframe", NFILE, fnmdup.data()), hdr, "q (nm^-1)", "s(q)/s(0)", oenv);
for (i = 0; i < sqframecurrent->qn; i++)
{
fprintf(fp, "%10.6f%10.6f\n", sqframecurrent->q[i], sqframecurrent->s[i]);
{ efXVG, "-sq", "sq", ffWRITE },
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm, NPA, pa, asize(desc), desc, 0,
- nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME, NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
fnDAT = ftp2fn(efDAT, NFILE, fnm);
fnNDX = ftp2fn_null(efNDX, NFILE, fnm);
- do_scattering_intensity(fnTPS, fnNDX, opt2fn("-sq", NFILE, fnm), fnTRX, fnDAT, start_q, end_q,
- energy, ngroups, oenv);
+ do_scattering_intensity(
+ fnTPS, fnNDX, opt2fn("-sq", NFILE, fnm), fnTRX, fnDAT, start_q, end_q, energy, ngroups, oenv);
please_cite(stdout, "Cromer1968a");
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxana/gstat.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arraysize.h"
fprintf(fp, "\n 2 !NTITLE\n");
fprintf(fp, " REMARKS Energy Landscape from GROMACS\n");
fprintf(fp, " REMARKS DATE: 2004-12-21 \n");
- fprintf(fp, " %7d %7d %7d %7d %7d %7d %7d %7d %7d\n", map->Nx, map->dmin[0], map->dmax[0],
- map->Ny, map->dmin[1], map->dmax[1], map->Nz, map->dmin[2], map->dmax[2]);
- fprintf(fp, "%12.5E%12.5E%12.5E%12.5E%12.5E%12.5E\n", map->cell[0], map->cell[1], map->cell[2],
- map->cell[3], map->cell[4], map->cell[5]);
+ fprintf(fp,
+ " %7d %7d %7d %7d %7d %7d %7d %7d %7d\n",
+ map->Nx,
+ map->dmin[0],
+ map->dmax[0],
+ map->Ny,
+ map->dmin[1],
+ map->dmax[1],
+ map->Nz,
+ map->dmin[2],
+ map->dmax[2]);
+ fprintf(fp,
+ "%12.5E%12.5E%12.5E%12.5E%12.5E%12.5E\n",
+ map->cell[0],
+ map->cell[1],
+ map->cell[2],
+ map->cell[3],
+ map->cell[4],
+ map->cell[5]);
fprintf(fp, "ZYX\n");
z = map->dmin[2];
fprintf(fp,
"Minimum %d at index "
"%" PRId64 " energy %10.3f\n",
- num, min->index, min->ener);
+ num,
+ min->index,
+ min->ener);
}
static inline void add_minimum(FILE* fp, int num, const t_minimum* min, t_minimum* mm)
this_min.index = index3(ibox, i, j, k);
this_min.ener = W[this_min.index];
if (is_local_minimum_from_below(&this_min, i, 0, index3(ibox, i - 1, j, k), W)
- && is_local_minimum_from_above(&this_min, i, ibox[0] - 1,
- index3(ibox, i + 1, j, k), W)
+ && is_local_minimum_from_above(
+ &this_min, i, ibox[0] - 1, index3(ibox, i + 1, j, k), W)
&& is_local_minimum_from_below(&this_min, j, 0, index3(ibox, i, j - 1, k), W)
- && is_local_minimum_from_above(&this_min, j, ibox[1] - 1,
- index3(ibox, i, j + 1, k), W)
+ && is_local_minimum_from_above(
+ &this_min, j, ibox[1] - 1, index3(ibox, i, j + 1, k), W)
&& is_local_minimum_from_below(&this_min, k, 0, index3(ibox, i, j, k - 1), W)
- && is_local_minimum_from_above(&this_min, k, ibox[2] - 1,
- index3(ibox, i, j, k + 1), W))
+ && is_local_minimum_from_above(
+ &this_min, k, ibox[2] - 1, index3(ibox, i, j, k + 1), W))
{
add_minimum(fp, nmin, &this_min, mm);
nmin++;
int index = this_point[i];
this_point[i]--;
bMin = bMin
- && is_local_minimum_from_below(&this_min, index, 0,
- indexn(ndim, ibox, this_point), W);
+ && is_local_minimum_from_below(
+ &this_min, index, 0, indexn(ndim, ibox, this_point), W);
this_point[i] += 2;
bMin = bMin
- && is_local_minimum_from_above(&this_min, index, ibox[i] - 1,
- indexn(ndim, ibox, this_point), W);
+ && is_local_minimum_from_above(
+ &this_min, index, ibox[i] - 1, indexn(ndim, ibox, this_point), W);
this_point[i]--;
}
if (bMin)
{
if (max_eig[i] > xmax[i])
{
- gmx_warning("Your xmax[%d] value %f is smaller than the largest data point %f", i,
- xmax[i], max_eig[i]);
+ gmx_warning("Your xmax[%d] value %f is smaller than the largest data point %f",
+ i,
+ xmax[i],
+ max_eig[i]);
}
max_eig[i] = xmax[i];
}
{
if (min_eig[i] < xmin[i])
{
- gmx_warning("Your xmin[%d] value %f is larger than the smallest data point %f", i,
- xmin[i], min_eig[i]);
+ gmx_warning("Your xmin[%d] value %f is larger than the smallest data point %f",
+ i,
+ xmin[i],
+ min_eig[i]);
}
min_eig[i] = xmin[i];
}
bfac[i] = ibox[i] / (max_eig[i] - min_eig[i]);
}
/* Do the binning */
- bref = 1 / (BOLTZ * Tref);
+ bref = 1 / (gmx::c_boltz * Tref);
snew(bE, n);
if (bGE || nenerT == 2)
{
}
else
{
- bE[j] = (bref - 1 / (BOLTZ * enerT[1][j])) * enerT[0][j];
+ bE[j] = (bref - 1 / (gmx::c_boltz * enerT[1][j])) * enerT[0][j];
}
Emin = std::min(Emin, static_cast<double>(bE[j]));
}
}
else if (idim[i] == -1)
{
- efac /= std::sin(DEG2RAD * eig[i][j]);
+ efac /= std::sin(gmx::c_deg2Rad * eig[i][j]);
}
}
/* Update the probability */
if (P[i] != 0)
{
Pmax = std::max(P[i], Pmax);
- W[i] = -BOLTZ * Tref * std::log(P[i]);
+ W[i] = -gmx::c_boltz * Tref * std::log(P[i]);
if (W[i] < Wmin)
{
Wmin = W[i];
SS[i] = &(S[i * ibox[1]]);
}
fp = gmx_ffopen(xpmP, "w");
- write_xpm(fp, flags, "Probability Distribution", "", "PC1", "PC2", ibox[0], ibox[1], axis_x,
- axis_y, PP, 0, Pmax, rlo, rhi, &nlevels);
+ write_xpm(fp,
+ flags,
+ "Probability Distribution",
+ "",
+ "PC1",
+ "PC2",
+ ibox[0],
+ ibox[1],
+ axis_x,
+ axis_y,
+ PP,
+ 0,
+ Pmax,
+ rlo,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
fp = gmx_ffopen(xpm, "w");
- write_xpm(fp, flags, "Gibbs Energy Landscape", "G (kJ/mol)", "PC1", "PC2", ibox[0], ibox[1],
- axis_x, axis_y, WW, 0, gmax, rlo, rhi, &nlevels);
+ write_xpm(fp,
+ flags,
+ "Gibbs Energy Landscape",
+ "G (kJ/mol)",
+ "PC1",
+ "PC2",
+ ibox[0],
+ ibox[1],
+ axis_x,
+ axis_y,
+ WW,
+ 0,
+ gmax,
+ rlo,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
fp = gmx_ffopen(xpm2, "w");
- write_xpm(fp, flags, "Enthalpy Landscape", "H (kJ/mol)", "PC1", "PC2", ibox[0], ibox[1],
- axis_x, axis_y, EE, emin ? *emin : Emin, emax ? *emax : Einf, rlo, rhi, &nlevels);
+ write_xpm(fp,
+ flags,
+ "Enthalpy Landscape",
+ "H (kJ/mol)",
+ "PC1",
+ "PC2",
+ ibox[0],
+ ibox[1],
+ axis_x,
+ axis_y,
+ EE,
+ emin ? *emin : Emin,
+ emax ? *emax : Einf,
+ rlo,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
fp = gmx_ffopen(xpm3, "w");
- write_xpm(fp, flags, "Entropy Landscape", "TDS (kJ/mol)", "PC1", "PC2", ibox[0], ibox[1],
- axis_x, axis_y, SS, 0, Sinf, rlo, rhi, &nlevels);
+ write_xpm(fp,
+ flags,
+ "Entropy Landscape",
+ "TDS (kJ/mol)",
+ "PC1",
+ "PC2",
+ ibox[0],
+ ibox[1],
+ axis_x,
+ axis_y,
+ SS,
+ 0,
+ Sinf,
+ rlo,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
}
else if (neig == 3)
index = index3(ibox, i, j, k);
if (P[index] > 0)
{
- fprintf(fp, "%-6s%5d %-4.4s%3.3s %4d %8.3f%8.3f%8.3f%6.2f%6.2f\n",
- "ATOM", (index + 1) % 10000, "H", "H", (index + 1) % 10000, xxx[XX],
- xxx[YY], xxx[ZZ], 1.0, W[index]);
+ fprintf(fp,
+ "%-6s%5d %-4.4s%3.3s %4d %8.3f%8.3f%8.3f%6.2f%6.2f\n",
+ "ATOM",
+ (index + 1) % 10000,
+ "H",
+ "H",
+ (index + 1) % 10000,
+ xxx[XX],
+ xxx[YY],
+ xxx[ZZ],
+ 1.0,
+ W[index]);
}
}
}
sprintf(buf, "%s", xpm);
sprintf(&buf[std::strlen(xpm) - 4], "12.xpm");
fp = gmx_ffopen(buf, "w");
- write_xpm(fp, flags, "Gibbs Energy Landscape", "W (kJ/mol)", "PC1", "PC2", ibox[0], ibox[1],
- axis_x, axis_y, WW, 0, gmax, rlo, rhi, &nlevels);
+ write_xpm(fp,
+ flags,
+ "Gibbs Energy Landscape",
+ "W (kJ/mol)",
+ "PC1",
+ "PC2",
+ ibox[0],
+ ibox[1],
+ axis_x,
+ axis_y,
+ WW,
+ 0,
+ gmax,
+ rlo,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
for (i = 0; (i < ibox[0]); i++)
{
}
sprintf(&buf[std::strlen(xpm) - 4], "13.xpm");
fp = gmx_ffopen(buf, "w");
- write_xpm(fp, flags, "SHAM Energy Landscape", "kJ/mol", "PC1", "PC3", ibox[0], ibox[2],
- axis_x, axis_z, WW, 0, gmax, rlo, rhi, &nlevels);
+ write_xpm(fp,
+ flags,
+ "SHAM Energy Landscape",
+ "kJ/mol",
+ "PC1",
+ "PC3",
+ ibox[0],
+ ibox[2],
+ axis_x,
+ axis_z,
+ WW,
+ 0,
+ gmax,
+ rlo,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
for (i = 0; (i < ibox[1]); i++)
{
}
sprintf(&buf[std::strlen(xpm) - 4], "23.xpm");
fp = gmx_ffopen(buf, "w");
- write_xpm(fp, flags, "SHAM Energy Landscape", "kJ/mol", "PC2", "PC3", ibox[1], ibox[2],
- axis_y, axis_z, WW, 0, gmax, rlo, rhi, &nlevels);
+ write_xpm(fp,
+ flags,
+ "SHAM Energy Landscape",
+ "kJ/mol",
+ "PC2",
+ "PC3",
+ ibox[1],
+ ibox[2],
+ axis_y,
+ axis_z,
+ WW,
+ 0,
+ gmax,
+ rlo,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
sfree(buf);
}
int npargs;
npargs = asize(pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, npargs, pa, asize(desc), desc, 0,
- nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW, NFILE, fnm, npargs, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
- val = read_xvg_time(opt2fn("-f", NFILE, fnm), bHaveT, opt2parg_bSet("-b", npargs, pa), tb - ttol,
- opt2parg_bSet("-e", npargs, pa), te + ttol, nsets_in, &nset, &n, &dt, &t);
+ val = read_xvg_time(opt2fn("-f", NFILE, fnm),
+ bHaveT,
+ opt2parg_bSet("-b", npargs, pa),
+ tb - ttol,
+ opt2parg_bSet("-e", npargs, pa),
+ te + ttol,
+ nsets_in,
+ &nset,
+ &n,
+ &dt,
+ &t);
printf("Read %d sets of %d points, dt = %g\n\n", nset, n, dt);
fn_ge = opt2fn_null("-ge", NFILE, fnm);
if (fn_ge || fn_ene)
{
- et_val = read_xvg_time(fn_ge ? fn_ge : fn_ene, bHaveT, opt2parg_bSet("-b", npargs, pa),
- tb - ttol, opt2parg_bSet("-e", npargs, pa), te + ttol, 1, &e_nset,
- &e_n, &e_dt, &e_t);
+ et_val = read_xvg_time(fn_ge ? fn_ge : fn_ene,
+ bHaveT,
+ opt2parg_bSet("-b", npargs, pa),
+ tb - ttol,
+ opt2parg_bSet("-e", npargs, pa),
+ te + ttol,
+ 1,
+ &e_nset,
+ &e_n,
+ &e_dt,
+ &e_t);
if (fn_ge)
{
if (e_nset != 1)
if (e_nset != 1 && e_nset != 2)
{
gmx_fatal(FARGS,
- "Can only handle one energy component or one energy and one T in %s", fn_ene);
+ "Can only handle one energy component or one energy and one T in %s",
+ fn_ene);
}
}
if (e_n != n)
{
- gmx_fatal(FARGS, "Number of energies (%d) does not match number of entries (%d) in %s",
- e_n, n, opt2fn("-f", NFILE, fnm));
+ gmx_fatal(FARGS,
+ "Number of energies (%d) does not match number of entries (%d) in %s",
+ e_n,
+ n,
+ opt2fn("-f", NFILE, fnm));
}
}
else
}
/* The number of grid points fits in a int64_t. */
- do_sham(opt2fn("-dist", NFILE, fnm), opt2fn("-bin", NFILE, fnm), opt2fn("-lp", NFILE, fnm),
- opt2fn("-ls", NFILE, fnm), opt2fn("-lsh", NFILE, fnm), opt2fn("-lss", NFILE, fnm),
- opt2fn("-ls3", NFILE, fnm), opt2fn("-g", NFILE, fnm), n, nset, val, fn_ge != nullptr,
- e_nset, et_val, Tref, pmax, gmax, opt2parg_bSet("-emin", NPA, pa) ? &emin : nullptr,
- opt2parg_bSet("-emax", NPA, pa) ? &emax : nullptr, nlevels, pmin, idim, ibox,
- opt2parg_bSet("-xmin", NPA, pa), rmin, opt2parg_bSet("-xmax", NPA, pa), rmax);
+ do_sham(opt2fn("-dist", NFILE, fnm),
+ opt2fn("-bin", NFILE, fnm),
+ opt2fn("-lp", NFILE, fnm),
+ opt2fn("-ls", NFILE, fnm),
+ opt2fn("-lsh", NFILE, fnm),
+ opt2fn("-lss", NFILE, fnm),
+ opt2fn("-ls3", NFILE, fnm),
+ opt2fn("-g", NFILE, fnm),
+ n,
+ nset,
+ val,
+ fn_ge != nullptr,
+ e_nset,
+ et_val,
+ Tref,
+ pmax,
+ gmax,
+ opt2parg_bSet("-emin", NPA, pa) ? &emin : nullptr,
+ opt2parg_bSet("-emax", NPA, pa) ? &emax : nullptr,
+ nlevels,
+ pmin,
+ idim,
+ ibox,
+ opt2parg_bSet("-xmin", NPA, pa),
+ rmin,
+ opt2parg_bSet("-xmax", NPA, pa),
+ rmax);
return 0;
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static real pot(real x, real qq, real c6, real cn, int npow)
{
- return cn * pow(x, -npow) - c6 / gmx::power6(x) + qq * ONE_4PI_EPS0 / x;
+ return cn * pow(x, -npow) - c6 / gmx::power6(x) + qq * gmx::c_one4PiEps0 / x;
}
static real bhpot(real x, real A, real B, real C)
static real dpot(real x, real qq, real c6, real cn, int npow)
{
return -(npow * cn * std::pow(x, -npow - 1) - 6 * c6 / (x * gmx::power6(x))
- + qq * ONE_4PI_EPS0 / gmx::square(x));
+ + qq * gmx::c_one4PiEps0 / gmx::square(x));
}
int gmx_sigeps(int argc, char* argv[])
int cur = 0;
#define next (1 - cur)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa, asize(desc), desc,
- 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
{
minimum = oldx + dp[cur] * (x - oldx) / (dp[cur] - dp[next]);
mval = pot(minimum, qq, c6, cn, npow);
- printf("Van der Waals + Coulomb minimum at r = %g (nm). Value = %g (kJ/mol)\n",
- minimum, mval);
+ printf("Van der Waals + Coulomb minimum at r = %g (nm). Value = %g (kJ/mol)\n", minimum, mval);
}
}
cur = next;
{ efXVG, "-co", "scum", ffWRITE }, { efXVG, "-rc", "scount", ffWRITE } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
xvgr_legend(fp, 2, legr, oenv);
for (i = 0; i < nrbin; i++)
{
- fprintf(fp, "%g %g %g\n", (i + 0.5) * rbinw, histn[i] ? histi1[i] / histn[i] : 0,
+ fprintf(fp,
+ "%g %g %g\n",
+ (i + 0.5) * rbinw,
+ histn[i] ? histi1[i] / histn[i] : 0,
histn[i] ? histi2[i] / histn[i] : 0);
}
xvgrclose(fp);
/* This is the routine responsible for adding default options,
* calling the X/motif interface, etc. */
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, asize(bugs), bugs, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
{
printf("There was an item outside of the allocated memory. Increase the value "
"given with the -nab option.\n");
- printf("Memory was allocated for [%f,%f,%f]\tto\t[%f,%f,%f]\n", MINBIN[XX],
- MINBIN[YY], MINBIN[ZZ], MAXBIN[XX], MAXBIN[YY], MAXBIN[ZZ]);
- printf("Memory was required for [%f,%f,%f]\n", fr.x[index[i]][XX],
- fr.x[index[i]][YY], fr.x[index[i]][ZZ]);
+ printf("Memory was allocated for [%f,%f,%f]\tto\t[%f,%f,%f]\n",
+ MINBIN[XX],
+ MINBIN[YY],
+ MINBIN[ZZ],
+ MAXBIN[XX],
+ MAXBIN[YY],
+ MAXBIN[ZZ]);
+ printf("Memory was required for [%f,%f,%f]\n",
+ fr.x[index[i]][XX],
+ fr.x[index[i]][YY],
+ fr.x[index[i]][ZZ]);
exit(1);
}
x = static_cast<int>(std::ceil((fr.x[index[i]][XX] - MINBIN[XX]) / rBINWIDTH));
flp = gmx_ffopen("grid.cube", "w");
fprintf(flp, "Spatial Distribution Function\n");
fprintf(flp, "test\n");
- fprintf(flp, "%5d%12.6f%12.6f%12.6f\n", nidxp,
+ fprintf(flp,
+ "%5d%12.6f%12.6f%12.6f\n",
+ nidxp,
(MINBIN[XX] + (minx + iIGNOREOUTER) * rBINWIDTH) * 10. / bohr,
(MINBIN[YY] + (miny + iIGNOREOUTER) * rBINWIDTH) * 10. / bohr,
(MINBIN[ZZ] + (minz + iIGNOREOUTER) * rBINWIDTH) * 10. / bohr);
- fprintf(flp, "%5d%12.6f%12.6f%12.6f\n", maxx - minx + 1 - (2 * iIGNOREOUTER),
- rBINWIDTH * 10. / bohr, 0., 0.);
- fprintf(flp, "%5d%12.6f%12.6f%12.6f\n", maxy - miny + 1 - (2 * iIGNOREOUTER), 0.,
- rBINWIDTH * 10. / bohr, 0.);
- fprintf(flp, "%5d%12.6f%12.6f%12.6f\n", maxz - minz + 1 - (2 * iIGNOREOUTER), 0., 0.,
- rBINWIDTH * 10. / bohr);
+ fprintf(flp, "%5d%12.6f%12.6f%12.6f\n", maxx - minx + 1 - (2 * iIGNOREOUTER), rBINWIDTH * 10. / bohr, 0., 0.);
+ fprintf(flp, "%5d%12.6f%12.6f%12.6f\n", maxy - miny + 1 - (2 * iIGNOREOUTER), 0., rBINWIDTH * 10. / bohr, 0.);
+ fprintf(flp, "%5d%12.6f%12.6f%12.6f\n", maxz - minz + 1 - (2 * iIGNOREOUTER), 0., 0., rBINWIDTH * 10. / bohr);
for (i = 0; i < nidxp; i++)
{
v = 2;
{
v = 16;
}
- fprintf(flp, "%5d%12.6f%12.6f%12.6f%12.6f\n", v, 0., fr.x[indexp[i]][XX] * 10.0 / bohr,
- fr.x[indexp[i]][YY] * 10.0 / bohr, fr.x[indexp[i]][ZZ] * 10.0 / bohr);
+ fprintf(flp,
+ "%5d%12.6f%12.6f%12.6f%12.6f\n",
+ v,
+ 0.,
+ fr.x[indexp[i]][XX] * 10.0 / bohr,
+ fr.x[indexp[i]][YY] * 10.0 / bohr,
+ fr.x[indexp[i]][ZZ] * 10.0 / bohr);
}
tot = 0;
if (bCALCDIV)
{
printf("Counts per frame in all %d cubes divided by %le\n", numcu, 1.0 / norm);
- printf("Normalized data: average %le, min %le, max %le\n", 1.0, minval * norm / numfr,
+ printf("Normalized data: average %le, min %le, max %le\n",
+ 1.0,
+ minval * norm / numfr,
maxval * norm / numfr);
}
else
{
printf("grid.cube contains counts per frame in all %d cubes\n", numcu);
- printf("Raw data: average %le, min %le, max %le\n", 1.0 / norm,
- static_cast<double>(minval) / numfr, static_cast<double>(maxval) / numfr);
+ printf("Raw data: average %le, min %le, max %le\n",
+ 1.0 / norm,
+ static_cast<double>(minval) / numfr,
+ static_cast<double>(maxval) / numfr);
}
return 0;
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
if (m == mols->nr)
{
- gmx_fatal(FARGS, "index[%d]=%d does not correspond to the first atom of a molecule",
- i + 1, index[i] + 1);
+ gmx_fatal(FARGS,
+ "index[%d]=%d does not correspond to the first atom of a molecule",
+ i + 1,
+ index[i] + 1);
}
for (j = mols->index[m]; j < mols->index[m + 1]; j++)
{
{ efXVG, nullptr, "scdist", ffWRITE } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
}
unitv(dir, dir);
- svmul(ENM2DEBYE, dip, dip);
+ svmul(gmx::c_enm2Debye, dip, dip);
dip2 = norm2(dip);
sdip += std::sqrt(dip2);
sdip2 += dip2;
sfree(x);
close_trx(status);
- fprintf(stderr, "Average number of molecules within %g nm is %.1f\n", rmax,
- static_cast<real>(ntot) / nf);
+ fprintf(stderr, "Average number of molecules within %g nm is %.1f\n", rmax, static_cast<real>(ntot) / nf);
if (ntot > 0)
{
sdip /= ntot;
sdip2 /= ntot;
sinp /= ntot;
sdinp /= ntot;
- fprintf(stderr, "Average dipole: %f (D), std.dev. %f\n", sdip,
+ fprintf(stderr,
+ "Average dipole: %f (D), std.dev. %f\n",
+ sdip,
std::sqrt(sdip2 - gmx::square(sdip)));
fprintf(stderr, "Average radial component of the dipole: %f (D)\n", sinp);
fprintf(stderr, "Average radial component of the polarization: %f (D)\n", sdinp);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define NKC0 4
static const int kset_c[NKC + 1] = { 0, 3, 9, 13, 16, 19, NK };
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static rvec v0[NK] = { { 1, 0, 0 }, { 0, 1, 0 }, { 0, 0, 1 }, { 1, 1, 0 }, { 1, -1, 0 },
{ 1, 0, 1 }, { 1, 0, -1 }, { 0, 1, 1 }, { 0, 1, -1 }, { 1, 1, 1 },
{ 1, 1, -1 }, { 1, -1, 1 }, { -1, 1, 1 }, { 2, 0, 0 }, { 0, 2, 0 },
{ 0, 0, 2 }, { 3, 0, 0 }, { 0, 3, 0 }, { 0, 0, 3 }, { 4, 0, 0 },
{ 0, 4, 0 }, { 0, 0, 4 } };
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static rvec v1[NK] = { { 0, 1, 0 }, { 0, 0, 1 }, { 1, 0, 0 }, { 0, 0, 1 }, { 0, 0, 1 },
{ 0, 1, 0 }, { 0, 1, 0 }, { 1, 0, 0 }, { 1, 0, 0 }, { 1, -1, 0 },
{ 1, -1, 0 }, { 1, 0, -1 }, { 0, 1, -1 }, { 0, 1, 0 }, { 0, 0, 1 },
{ 1, 0, 0 }, { 0, 1, 0 }, { 0, 0, 1 }, { 1, 0, 0 }, { 0, 1, 0 },
{ 0, 0, 1 }, { 1, 0, 0 } };
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static rvec v2[NK] = { { 0, 0, 1 }, { 1, 0, 0 }, { 0, 1, 0 }, { 1, -1, 0 }, { 1, 1, 0 },
{ 1, 0, -1 }, { 1, 0, 1 }, { 0, 1, -1 }, { 0, 1, 1 }, { 1, 1, -2 },
{ 1, 1, 2 }, { 1, 2, 1 }, { 2, 1, 1 }, { 0, 0, 1 }, { 1, 0, 0 },
sig[i] = std::exp(0.5 * i * dt / wt);
}
- low_do_autocorr(fn_tca, oenv, "Transverse Current Autocorrelation Functions", nframes, ntc,
- ncorr, tc, dt, eacNormal, 1, FALSE, FALSE, FALSE, 0, 0, 0);
+ low_do_autocorr(fn_tca,
+ oenv,
+ "Transverse Current Autocorrelation Functions",
+ nframes,
+ ntc,
+ ncorr,
+ tc,
+ dt,
+ eacNormal,
+ 1,
+ FALSE,
+ FALSE,
+ FALSE,
+ 0,
+ 0,
+ 0);
do_view(oenv, fn_tca, "-nxy");
fp = xvgropen(fn_tc, "Transverse Current Autocorrelation Functions", "Time (ps)", "TCAF", oenv);
tcaf[k][0] = 1.0;
fitparms[0] = 1;
fitparms[1] = 1;
- do_lmfit(ncorr, tcaf[k], sig, dt, nullptr, 0, ncorr * dt, oenv, bDebugMode(), effnVAC,
- fitparms, 0, nullptr);
- eta = 1000 * fitparms[1] * rho / (4 * fitparms[0] * PICO * norm2(kfac[k]) / (NANO * NANO));
+ do_lmfit(ncorr, tcaf[k], sig, dt, nullptr, 0, ncorr * dt, oenv, bDebugMode(), effnVAC, fitparms, 0, nullptr);
+ eta = 1000 * fitparms[1] * rho
+ / (4 * fitparms[0] * gmx::c_pico * norm2(kfac[k]) / (gmx::c_nano * gmx::c_nano));
fprintf(stdout, "k %6.3f tau %6.3f eta %8.5f 10^-3 kg/(m s)\n", norm(kfac[k]), fitparms[0], eta);
fprintf(fp_vk, "%6.3f %g\n", norm(kfac[k]), eta);
for (i = 0; i < ncorr; i++)
tcafc[k][0] = 1.0;
fitparms[0] = 1;
fitparms[1] = 1;
- do_lmfit(ncorr, tcafc[k], sig, dt, nullptr, 0, ncorr * dt, oenv, bDebugMode(), effnVAC,
- fitparms, 0, nullptr);
+ do_lmfit(ncorr, tcafc[k], sig, dt, nullptr, 0, ncorr * dt, oenv, bDebugMode(), effnVAC, fitparms, 0, nullptr);
eta = 1000 * fitparms[1] * rho
- / (4 * fitparms[0] * PICO * norm2(kfac[kset_c[k]]) / (NANO * NANO));
- fprintf(stdout, "k %6.3f tau %6.3f Omega %6.3f eta %8.5f 10^-3 kg/(m s)\n",
- norm(kfac[kset_c[k]]), fitparms[0], fitparms[1], eta);
+ / (4 * fitparms[0] * gmx::c_pico * norm2(kfac[kset_c[k]]) / (gmx::c_nano * gmx::c_nano));
+ fprintf(stdout,
+ "k %6.3f tau %6.3f Omega %6.3f eta %8.5f 10^-3 kg/(m s)\n",
+ norm(kfac[kset_c[k]]),
+ fitparms[0],
+ fitparms[1],
+ eta);
fprintf(fp_vk, "%6.3f %g\n", norm(kfac[kset_c[k]]), eta);
for (i = 0; i < ncorr; i++)
{
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, npargs, ppa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
{
sfree(ppa);
return 0;
dt = (t1 - t0) / (nframes - 1);
- rho *= sysmass / nframes * AMU / (NANO * NANO * NANO);
+ rho *= sysmass / nframes * gmx::c_amu / (gmx::c_nano * gmx::c_nano * gmx::c_nano);
fprintf(stdout, "Density = %g (kg/m^3)\n", rho);
- process_tcaf(nframes, dt, nkc, tc, kfac, rho, wt, opt2fn_null("-ot", NFILE, fnm),
- opt2fn("-oa", NFILE, fnm), opt2fn("-o", NFILE, fnm), opt2fn("-of", NFILE, fnm),
- opt2fn_null("-oc", NFILE, fnm), opt2fn("-ov", NFILE, fnm), oenv);
+ process_tcaf(nframes,
+ dt,
+ nkc,
+ tc,
+ kfac,
+ rho,
+ wt,
+ opt2fn_null("-ot", NFILE, fnm),
+ opt2fn("-oa", NFILE, fnm),
+ opt2fn("-o", NFILE, fnm),
+ opt2fn("-of", NFILE, fnm),
+ opt2fn_null("-oc", NFILE, fnm),
+ opt2fn("-ov", NFILE, fnm),
+ oenv);
return 0;
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <algorithm>
#include <string>
+#include <vector>
#include "gromacs/commandline/pargs.h"
#include "gromacs/commandline/viewit.h"
gmx_bool bDim[],
const char* sffmt)
{
- static rvec* xav = nullptr;
+ static std::vector<gmx::RVec> xav;
if (bCom)
{
- if (xav == nullptr)
+ if (xav.empty())
{
- snew(xav, ngrps);
+ xav.resize(ngrps);
}
- average_data(x, xav, mass, ngrps, isize, index);
- low_print_data(fp, time, xav, ngrps, nullptr, bDim, sffmt);
+ average_data(x, as_rvec_array(xav.data()), mass, ngrps, isize, index);
+ low_print_data(fp, time, as_rvec_array(xav.data()), ngrps, nullptr, bDim, sffmt);
}
else
{
int isize[],
int** index)
{
- static rvec* xav = nullptr;
+ static std::vector<gmx::RVec> xav;
+ // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static t_atoms* atoms = nullptr;
t_trxframe fr_av;
int i;
if (bCom)
{
- if (xav == nullptr)
+ if (xav.empty())
{
- snew(xav, ngrps);
+ xav.resize(ngrps);
snew(atoms, 1);
*atoms = *fr->atoms;
snew(atoms->atom, ngrps);
atoms->atomname[i] = fr->atoms->atomname[index[i][0]];
}
}
- average_data(fr->x, xav, mass, ngrps, isize, index);
+ average_data(fr->x, as_rvec_array(xav.data()), mass, ngrps, isize, index);
fr_av = *fr;
fr_av.natoms = ngrps;
fr_av.atoms = atoms;
- fr_av.x = xav;
+ fr_av.x = as_rvec_array(xav.data());
write_trxframe(status, &fr_av, nullptr);
}
else
ekin2 += mass[j] * norm2(v[j]);
}
- return ekin2 / (3 * isize * BOLTZ);
+ return ekin2 / (3 * isize * gmx::c_boltz);
}
static void remove_jump(matrix box, int natoms, rvec xp[], rvec x[])
fp = xvgropen(xname, title, "Atom", "Spatial component", oenv);
for (i = 0; i < isize; i++)
{
- fprintf(fp, "%-5d %10.3f %10.3f %10.3f\n", 1 + i, sum[index[i]][XX],
- sum[index[i]][YY], sum[index[i]][ZZ]);
+ fprintf(fp,
+ "%-5d %10.3f %10.3f %10.3f\n",
+ 1 + i,
+ sum[index[i]][XX],
+ sum[index[i]][YY],
+ sum[index[i]][ZZ]);
}
xvgrclose(fp);
max = 0;
}
}
- printf("Maximum %s is %g on atom %d %s, res. %s %d\n", title, std::sqrt(max), maxi + 1,
- *(atoms->atomname[maxi]), *(atoms->resinfo[atoms->atom[maxi].resind].name),
+ printf("Maximum %s is %g on atom %d %s, res. %s %d\n",
+ title,
+ std::sqrt(max),
+ maxi + 1,
+ *(atoms->atomname[maxi]),
+ *(atoms->resinfo[atoms->atom[maxi].resind].name),
atoms->resinfo[atoms->atom[maxi].resind].nr);
if (atoms->pdbinfo == nullptr)
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW, NFILE, fnm,
- asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc,
+ argv,
+ PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
+ NFILE,
+ fnm,
+ asize(pa),
+ pa,
+ asize(desc),
+ desc,
+ 0,
+ nullptr,
+ &oenv))
{
return 0;
}
}
std::string sffmt6 = gmx::formatString("%s%s%s%s%s%s", sffmt, sffmt, sffmt, sffmt, sffmt, sffmt);
- bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &pbcType, &xtop, nullptr, topbox,
+ bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm),
+ &top,
+ &pbcType,
+ &xtop,
+ nullptr,
+ topbox,
bCom && (bOX || bOXT || bOV || bOT || bEKT || bEKR));
sfree(xtop);
if ((bMol || bCV || bCF) && !bTop)
{
if (index0[0][i] < 0 || index0[0][i] >= mols->nr)
{
- gmx_fatal(FARGS, "Molecule index (%d) is out of range (%d-%d)", index0[0][i] + 1, 1,
- mols->nr);
+ gmx_fatal(FARGS, "Molecule index (%d) is out of range (%d-%d)", index0[0][i] + 1, 1, mols->nr);
}
isize[i] = atndx[index0[0][i] + 1] - atndx[index0[0][i]];
snew(index[i], isize[i]);
if (bOX)
{
flags = flags | TRX_READ_X;
- outx = xvgropen(opt2fn("-ox", NFILE, fnm), bCom ? "Center of mass" : "Coordinate", label,
- "Coordinate (nm)", oenv);
+ outx = xvgropen(opt2fn("-ox", NFILE, fnm),
+ bCom ? "Center of mass" : "Coordinate",
+ label,
+ "Coordinate (nm)",
+ oenv);
make_legend(outx, ngroups, isize0[0], index0[0], grpname, bCom, bMol, bDim, oenv);
}
if (bOXT)
if (bOV)
{
flags = flags | TRX_READ_V;
- outv = xvgropen(opt2fn("-ov", NFILE, fnm), bCom ? "Center of mass velocity" : "Velocity",
- label, "Velocity (nm/ps)", oenv);
+ outv = xvgropen(opt2fn("-ov", NFILE, fnm),
+ bCom ? "Center of mass velocity" : "Velocity",
+ label,
+ "Velocity (nm/ps)",
+ oenv);
make_legend(outv, ngroups, isize0[0], index0[0], grpname, bCom, bMol, bDim, oenv);
}
if (bOF)
{
flags = flags | TRX_READ_F;
- outf = xvgropen(opt2fn("-of", NFILE, fnm), "Force", label,
- "Force (kJ mol\\S-1\\N nm\\S-1\\N)", oenv);
+ outf = xvgropen(
+ opt2fn("-of", NFILE, fnm), "Force", label, "Force (kJ mol\\S-1\\N nm\\S-1\\N)", oenv);
make_legend(outf, ngroups, isize0[0], index0[0], grpname, bCom, bMol, bDim, oenv);
}
if (bOB)
bDum[ZZ] = FALSE;
bDum[DIM] = TRUE;
flags = flags | TRX_READ_V;
- outekt = xvgropen(opt2fn("-ekt", NFILE, fnm), "Center of mass translation", label,
- "Energy (kJ mol\\S-1\\N)", oenv);
+ outekt = xvgropen(opt2fn("-ekt", NFILE, fnm),
+ "Center of mass translation",
+ label,
+ "Energy (kJ mol\\S-1\\N)",
+ oenv);
make_legend(outekt, ngroups, isize[0], index[0], grpname, bCom, bMol, bDum, oenv);
}
if (bEKR)
bDum[ZZ] = FALSE;
bDum[DIM] = TRUE;
flags = flags | TRX_READ_X | TRX_READ_V;
- outekr = xvgropen(opt2fn("-ekr", NFILE, fnm), "Center of mass rotation", label,
- "Energy (kJ mol\\S-1\\N)", oenv);
+ outekr = xvgropen(opt2fn("-ekr", NFILE, fnm),
+ "Center of mass rotation",
+ label,
+ "Energy (kJ mol\\S-1\\N)",
+ oenv);
make_legend(outekr, ngroups, isize[0], index[0], grpname, bCom, bMol, bDum, oenv);
}
if (bVD)
if (bOB && fr.bBox)
{
fprintf(outb, "\t%g", fr.time);
- fprintf(outb, sffmt6.c_str(), fr.box[XX][XX], fr.box[YY][YY], fr.box[ZZ][ZZ],
- fr.box[YY][XX], fr.box[ZZ][XX], fr.box[ZZ][YY]);
+ fprintf(outb,
+ sffmt6.c_str(),
+ fr.box[XX][XX],
+ fr.box[YY][YY],
+ fr.box[ZZ][ZZ],
+ fr.box[YY][XX],
+ fr.box[ZZ][XX],
+ fr.box[ZZ][YY]);
fprintf(outb, "\n");
}
if (bOT && fr.bV)
}
if (bCV)
{
- write_pdb_bfac(opt2fn("-cv", NFILE, fnm), opt2fn("-av", NFILE, fnm), "average velocity",
- &(top.atoms), pbcType, topbox, isize[0], index[0], nr_xfr, sumx, nr_vfr,
- sumv, bDim, scale, oenv);
+ write_pdb_bfac(opt2fn("-cv", NFILE, fnm),
+ opt2fn("-av", NFILE, fnm),
+ "average velocity",
+ &(top.atoms),
+ pbcType,
+ topbox,
+ isize[0],
+ index[0],
+ nr_xfr,
+ sumx,
+ nr_vfr,
+ sumv,
+ bDim,
+ scale,
+ oenv);
}
if (bCF)
{
- write_pdb_bfac(opt2fn("-cf", NFILE, fnm), opt2fn("-af", NFILE, fnm), "average force",
- &(top.atoms), pbcType, topbox, isize[0], index[0], nr_xfr, sumx, nr_ffr,
- sumf, bDim, scale, oenv);
+ write_pdb_bfac(opt2fn("-cf", NFILE, fnm),
+ opt2fn("-af", NFILE, fnm),
+ "average force",
+ &(top.atoms),
+ pbcType,
+ topbox,
+ isize[0],
+ index[0],
+ nr_xfr,
+ sumx,
+ nr_ffr,
+ sumf,
+ bDim,
+ scale,
+ oenv);
}
/* view it */
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
real d2;
} t_order;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static t_order* order;
static int ocomp(const void* a, const void* b)
{ efXVG, "-nshell", "nshell", ffOPTWR } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm, asize(pa), pa, asize(desc), desc,
- 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
if ((isize_sol % na) != 0)
{
- gmx_fatal(FARGS, "Number of atoms in the molecule group (%d) is not a multiple of na (%d)",
- isize[1], na);
+ gmx_fatal(FARGS,
+ "Number of atoms in the molecule group (%d) is not a multiple of na (%d)",
+ isize[1],
+ na);
}
nwat = isize_sol / na;
FILE* fp;
t_rgb rlo = { 1, 1, 1 }, rhi = { 0, 0, 0 };
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
ticky[i] = i * rbin;
}
fp = gmx_ffopen(matfile, "w");
- write_xpm(fp, MAT_SPATIAL_Y, "Van Hove function", "G (1/nm)",
- sbin == 0 ? "time (ps)" : "sqrt(time) (ps^1/2)", "r (nm)", mat_nx, nbin, tickx,
- ticky, mat, 0, matmax, rlo, rhi, &nlev);
+ write_xpm(fp,
+ MAT_SPATIAL_Y,
+ "Van Hove function",
+ "G (1/nm)",
+ sbin == 0 ? "time (ps)" : "sqrt(time) (ps^1/2)",
+ "r (nm)",
+ mat_nx,
+ nbin,
+ tickx,
+ ticky,
+ mat,
+ 0,
+ matmax,
+ rlo,
+ rhi,
+ &nlev);
gmx_ffclose(fp);
}
fprintf(fp, "%g", i * rbin);
for (fbin = 0; fbin < nr; fbin++)
{
- fprintf(fp, " %g",
+ fprintf(fp,
+ " %g",
static_cast<real>(pr[fbin][i]
/ (rcount[fbin] * isize * rbin * (i == 0 ? 0.5 : 1.0))));
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
gmx_fatal(FARGS, "Invalid fft return status %d", status);
}
- fp = xvgropen(fn, "Vibrational Power Spectrum",
- bRecip ? "\\f{12}w\\f{4} (cm\\S-1\\N)" : "\\f{12}n\\f{4} (ps\\S-1\\N)", "a.u.", oenv);
+ fp = xvgropen(fn,
+ "Vibrational Power Spectrum",
+ bRecip ? "\\f{12}w\\f{4} (cm\\S-1\\N)" : "\\f{12}n\\f{4} (ps\\S-1\\N)",
+ "a.u.",
+ oenv);
/* This is difficult.
* The length of the ACF is dt (as passed to this routine).
* We pass the vacf with N time steps from 0 to dt.
* The timestep between saving the trajectory is
* 1e7 is to convert nanometer to cm
*/
- recip_fac = bRecip ? (1e7 / SPEED_OF_LIGHT) : 1.0;
+ recip_fac = bRecip ? (1e7 / gmx::c_speedOfLight) : 1.0;
for (i = 0; (i < n); i += 2)
{
nu = i / (2 * dt);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, npargs, ppa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
{
sfree(ppa);
return 0;
{
/* Compute time step between frames */
dt = (t1 - t0) / (counter - 1);
- do_autocorr(opt2fn("-o", NFILE, fnm), oenv,
+ do_autocorr(opt2fn("-o", NFILE, fnm),
+ oenv,
bMass ? "Momentum Autocorrelation Function" : "Velocity Autocorrelation Function",
- counter, gnx, c1, dt, eacVector, TRUE);
+ counter,
+ gnx,
+ c1,
+ dt,
+ eacVector,
+ TRUE);
do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstring>
#include <algorithm>
-#include <sstream>
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/tpxio.h"
enNr
};
/*! \brief
- * enum for type of input files (pdos, tpr, or pullf)
+ * enum for type of input files (tpr or pullx/pullf)
*/
enum
{
whamin_unknown,
whamin_tpr,
whamin_pullxf,
- whamin_pdo
};
/*! \brief enum for bootstrapping method
//! Parameters of one pull coodinate
typedef struct
{
- int pull_type; //!< such as constraint, umbrella, ...
- int geometry; //!< such as distance, direction, cylinder
- int ngroup; //!< the number of pull groups involved
- ivec dim; //!< pull dimension with geometry distance
- int ndim; //!< nr of pull_dim != 0
- real k; //!< force constants in tpr file
- real init_dist; //!< reference displacement
- char coord_unit[256]; //!< unit of the displacement
+ PullingAlgorithm pull_type; //!< such as constraint, umbrella, ...
+ PullGroupGeometry geometry; //!< such as distance, direction, cylinder
+ int ngroup; //!< the number of pull groups involved
+ ivec dim; //!< pull dimension with geometry distance
+ int ndim; //!< nr of pull_dim != 0
+ real k; //!< force constants in tpr file
+ real init_dist; //!< reference displacement
+ char coord_unit[256]; //!< unit of the displacement
} t_pullcoord;
//! Parameters of the umbrella potentials
gmx_bool bPrintComp; //!< Components of pull distance written to pullx.xvg ?
/*!\}*/
- /*!
- * \name Using PDO files common until gromacs 3.x
- */
- /*!\{*/
- int nSkip;
- char Reference[256];
- int nPull;
- int nDim;
- ivec Dims;
- char PullName[4][256];
- double UmbPos[4][3];
- double UmbCons[4][3];
- /*!\}*/
} t_UmbrellaHeader;
//! Data in the umbrella histograms
typedef struct
{
- int nPull; //!< nr of pull groups in this pdo or pullf/x file
+ int nPull; //!< nr of pull groups in this pullf/pullx file
double** Histo; //!< nPull histograms
double** cum; //!< nPull cumulative distribution functions
int nBin; //!< nr of bins. identical to opt->bins
*/
/*!\{*/
const char *fnTpr, *fnPullf, *fnCoordSel;
- const char *fnPdo, *fnPullx; //!< file names of input
- gmx_bool bTpr, bPullf, bPdo, bPullx; //!< input file types given?
- real tmin, tmax, dt; //!< only read input within tmin and tmax with dt
+ const char* fnPullx; //!< file names of input
+ gmx_bool bTpr, bPullf, bPullx; //!< input file types given?
+ real tmin, tmax, dt; //!< only read input within tmin and tmax with dt
gmx_bool bInitPotByIntegration; //!< before WHAM, guess potential by force integration. Yields 1.5 to 2 times faster convergence
int stepUpdateContrib; //!< update contribution table every ... iterations. Accelerates WHAM.
opt->tabX[i] = y[0][i];
opt->tabY[i] = y[1][i];
}
- printf("Found equally spaced tabulated potential from %g to %g, spacing %g\n", opt->tabMin,
- opt->tabMax, opt->tabDz);
-}
-
-//! Read the header of an PDO file (position, force const, nr of groups)
-static void read_pdo_header(FILE* file, t_UmbrellaHeader* header, t_UmbrellaOptions* opt)
-{
- char line[2048];
- char Buffer0[256], Buffer1[256], Buffer2[256], Buffer3[256], Buffer4[256];
- int i;
- std::istringstream ist;
-
- /* line 1 */
- if (fgets(line, 2048, file) == nullptr)
- {
- gmx_fatal(FARGS, "Error reading header from pdo file\n");
- }
- ist.str(line);
- ist >> Buffer0 >> Buffer1 >> Buffer2;
- if (std::strcmp(Buffer1, "UMBRELLA") != 0)
- {
- gmx_fatal(FARGS,
- "This does not appear to be a valid pdo file. Found %s, expected %s\n"
- "(Found in first line: `%s')\n",
- Buffer1, "UMBRELLA", line);
- }
- if (std::strcmp(Buffer2, "3.0") != 0)
- {
- gmx_fatal(FARGS, "This does not appear to be a version 3.0 pdo file");
- }
-
- /* line 2 */
- if (fgets(line, 2048, file) == nullptr)
- {
- gmx_fatal(FARGS, "Error reading header from pdo file\n");
- }
- ist.str(line);
- ist >> Buffer0 >> Buffer1 >> Buffer2 >> header->Dims[0] >> header->Dims[1] >> header->Dims[2];
- /* printf("%d %d %d\n", header->Dims[0],header->Dims[1],header->Dims[2]); */
-
- header->nDim = header->Dims[0] + header->Dims[1] + header->Dims[2];
- if (header->nDim != 1)
- {
- gmx_fatal(FARGS, "Currently only supports one dimension");
- }
-
- /* line3 */
- if (fgets(line, 2048, file) == nullptr)
- {
- gmx_fatal(FARGS, "Error reading header from pdo file\n");
- }
- ist.str(line);
- ist >> Buffer0 >> Buffer1 >> header->nSkip;
-
- /* line 4 */
- if (fgets(line, 2048, file) == nullptr)
- {
- gmx_fatal(FARGS, "Error reading header from pdo file\n");
- }
- ist.str(line);
- ist >> Buffer0 >> Buffer1 >> Buffer2 >> header->Reference;
-
- /* line 5 */
- if (fgets(line, 2048, file) == nullptr)
- {
- gmx_fatal(FARGS, "Error reading header from pdo file\n");
- }
- ist.str(line);
- ist >> Buffer0 >> Buffer1 >> Buffer2 >> Buffer3 >> Buffer4 >> header->nPull;
-
- if (opt->verbose)
- {
- printf("\tFound nPull=%d , nSkip=%d, ref=%s\n", header->nPull, header->nSkip, header->Reference);
- }
-
- for (i = 0; i < header->nPull; ++i)
- {
- if (fgets(line, 2048, file) == nullptr)
- {
- gmx_fatal(FARGS, "Error reading header from pdo file\n");
- }
- ist.str(line);
- ist >> Buffer0 >> Buffer1 >> Buffer2 >> header->PullName[i];
- ist >> Buffer0 >> Buffer1 >> header->UmbPos[i][0];
- ist >> Buffer0 >> Buffer1 >> header->UmbCons[i][0];
-
- if (opt->verbose)
- {
- printf("\tpullgroup %d, pullname = %s, UmbPos = %g, UmbConst = %g\n", i,
- header->PullName[i], header->UmbPos[i][0], header->UmbCons[i][0]);
- }
- }
-
- if (fgets(line, 2048, file) == nullptr)
- {
- gmx_fatal(FARGS, "Cannot read from file\n");
- }
- ist.str(line);
- ist >> Buffer3;
- if (std::strcmp(Buffer3, "#####") != 0)
- {
- gmx_fatal(FARGS, "Expected '#####', found %s. Hick.\n", Buffer3);
- }
+ printf("Found equally spaced tabulated potential from %g to %g, spacing %g\n",
+ opt->tabMin,
+ opt->tabMax,
+ opt->tabDz);
}
//! smarter fgets
return ptr;
}
-/*! \brief Read the data columns of and PDO file.
- *
- * TO DO: Get rid of the scanf function to avoid the clang warning.
- * At the moment, this warning is avoided by hiding the format string
- * the variable fmtlf.
- */
-static void read_pdo_data(FILE* file,
- t_UmbrellaHeader* header,
- int fileno,
- t_UmbrellaWindow* win,
- t_UmbrellaOptions* opt,
- gmx_bool bGetMinMax,
- real* mintmp,
- real* maxtmp)
-{
- int i, inttemp, bins, count, ntot;
- real minval, maxval, minfound = 1e20, maxfound = -1e20;
- double temp, time, time0 = 0, dt;
- char* ptr = nullptr;
- t_UmbrellaWindow* window = nullptr;
- gmx_bool timeok, dt_ok = true;
- char * tmpbuf = nullptr, fmt[256], fmtign[256], fmtlf[5] = "%lf";
- int len = STRLEN, dstep = 1;
- const int blocklen = 4096;
- int* lennow = nullptr;
-
- if (!bGetMinMax)
- {
- bins = opt->bins;
- minval = opt->min;
- maxval = opt->max;
-
- window = win + fileno;
- /* Need to alocate memory and set up structure */
- window->nPull = header->nPull;
- window->nBin = bins;
-
- snew(window->Histo, window->nPull);
- snew(window->z, window->nPull);
- snew(window->k, window->nPull);
- snew(window->pos, window->nPull);
- snew(window->N, window->nPull);
- snew(window->Ntot, window->nPull);
- snew(window->g, window->nPull);
- snew(window->bsWeight, window->nPull);
-
- window->bContrib = nullptr;
-
- if (opt->bCalcTauInt)
- {
- snew(window->ztime, window->nPull);
- }
- else
- {
- window->ztime = nullptr;
- }
- snew(lennow, window->nPull);
-
- for (i = 0; i < window->nPull; ++i)
- {
- window->z[i] = 1;
- window->bsWeight[i] = 1.;
- snew(window->Histo[i], bins);
- window->k[i] = header->UmbCons[i][0];
- window->pos[i] = header->UmbPos[i][0];
- window->N[i] = 0;
- window->Ntot[i] = 0;
- window->g[i] = 1.;
- if (opt->bCalcTauInt)
- {
- window->ztime[i] = nullptr;
- }
- }
-
- /* Done with setup */
- }
- else
- {
- minfound = 1e20;
- maxfound = -1e20;
- minval = maxval = bins = 0; /* Get rid of warnings */
- }
-
- count = 0;
- snew(tmpbuf, len);
- while ((ptr = fgets3(file, tmpbuf, &len)) != nullptr)
- {
- trim(ptr);
-
- if (ptr[0] == '#' || std::strlen(ptr) < 2)
- {
- continue;
- }
-
- /* Initiate format string */
- fmtign[0] = '\0';
- std::strcat(fmtign, "%*s");
-
- sscanf(ptr, fmtlf, &time); /* printf("Time %f\n",time); */
- /* Round time to fs */
- time = 1.0 / 1000 * (gmx::roundToInt64(time * 1000));
-
- /* get time step of pdo file */
- if (count == 0)
- {
- time0 = time;
- }
- else if (count == 1)
- {
- dt = time - time0;
- if (opt->dt > 0.0)
- {
- dstep = gmx::roundToInt(opt->dt / dt);
- if (dstep == 0)
- {
- dstep = 1;
- }
- }
- if (!bGetMinMax)
- {
- window->dt = dt * dstep;
- }
- }
- count++;
-
- dt_ok = ((count - 1) % dstep == 0);
- timeok = (dt_ok && time >= opt->tmin && time <= opt->tmax);
- /* if (opt->verbose)
- printf(" time = %f, (tmin,tmax)=(%e,%e), dt_ok=%d timeok=%d\n",
- time,opt->tmin, opt->tmax, dt_ok,timeok); */
-
- if (timeok)
- {
- for (i = 0; i < header->nPull; ++i)
- {
- std::strcpy(fmt, fmtign);
- std::strcat(fmt, "%lf"); /* Creating a format stings such as "%*s...%*s%lf" */
- std::strcat(fmtign, "%*s"); /* ignoring one more entry in the next loop */
- if (sscanf(ptr, fmt, &temp))
- {
- temp += header->UmbPos[i][0];
- if (bGetMinMax)
- {
- if (temp < minfound)
- {
- minfound = temp;
- }
- if (temp > maxfound)
- {
- maxfound = temp;
- }
- }
- else
- {
- if (opt->bCalcTauInt)
- {
- /* save time series for autocorrelation analysis */
- ntot = window->Ntot[i];
- if (ntot >= lennow[i])
- {
- lennow[i] += blocklen;
- srenew(window->ztime[i], lennow[i]);
- }
- window->ztime[i][ntot] = temp;
- }
-
- temp -= minval;
- temp /= (maxval - minval);
- temp *= bins;
- temp = std::floor(temp);
-
- inttemp = static_cast<int>(temp);
- if (opt->bCycl)
- {
- if (inttemp < 0)
- {
- inttemp += bins;
- }
- else if (inttemp >= bins)
- {
- inttemp -= bins;
- }
- }
-
- if (inttemp >= 0 && inttemp < bins)
- {
- window->Histo[i][inttemp] += 1.;
- window->N[i]++;
- }
- window->Ntot[i]++;
- }
- }
- }
- }
- if (time > opt->tmax)
- {
- if (opt->verbose)
- {
- printf("time %f larger than tmax %f, stop reading pdo file\n", time, opt->tmax);
- }
- break;
- }
- }
-
- if (bGetMinMax)
- {
- *mintmp = minfound;
- *maxtmp = maxfound;
- }
-
- sfree(lennow);
- sfree(tmpbuf);
-}
-
/*! \brief Set identical weights for all histograms
*
* Normally, the weight is given by the number data points in each
gmx_fatal(FARGS,
"Distance %f out of bounds of tabulated potential (jl=%d, ju=%d).\n"
"Provide an extended table.",
- dist, jl, ju);
+ dist,
+ jl,
+ ju);
}
pl = opt->tabY[jl];
pu = opt->tabY[ju];
}
}
/* Note: there are two contributions to bin k in the wham equations:
- i) N[j]*exp(- U/(BOLTZ*opt->Temperature) + window[i].z[j])
- ii) exp(- U/(BOLTZ*opt->Temperature))
+ i) N[j]*exp(- U/(c_boltz*opt->Temperature) + window[i].z[j])
+ ii) exp(- U/(c_boltz*opt->Temperature))
where U is the umbrella potential
If any of these number is larger wham_contrib_lim, I set contrib=TRUE
*/
{
U = tabulated_pot(distance, opt); /* Use tabulated potential */
}
- contrib1 = profile[k] * std::exp(-U / (BOLTZ * opt->Temperature));
- contrib2 = window[i].N[j] * std::exp(-U / (BOLTZ * opt->Temperature) + window[i].z[j]);
+ contrib1 = profile[k] * std::exp(-U / (gmx::c_boltz * opt->Temperature));
+ contrib2 = window[i].N[j]
+ * std::exp(-U / (gmx::c_boltz * opt->Temperature) + window[i].z[j]);
window[i].bContrib[j][k] = (contrib1 > wham_contrib_lim || contrib2 > wham_contrib_lim);
bAnyContrib = bAnyContrib || window[i].bContrib[j][k];
if (window[i].bContrib[j][k])
{
printf("Initialized rapid wham stuff (contrib tolerance %g)\n"
"Evaluating only %d of %d expressions.\n\n",
- wham_contrib_lim, nContrib, nTot);
+ wham_contrib_lim,
+ nContrib,
+ nTot);
}
if (opt->verbose)
U = tabulated_pot(distance, opt); /* Use tabulated potential */
}
denom += invg * window[j].N[k]
- * std::exp(-U / (BOLTZ * opt->Temperature) + window[j].z[k]);
+ * std::exp(-U / (gmx::c_boltz * opt->Temperature) + window[j].z[k]);
}
}
profile[i] = num / denom;
{
U = tabulated_pot(distance, opt); /* Use tabulated potential */
}
- total += profile[k] * std::exp(-U / (BOLTZ * opt->Temperature));
+ total += profile[k] * std::exp(-U / (gmx::c_boltz * opt->Temperature));
}
/* Avoid floating point exception if window is far outside min and max */
if (total != 0.0)
if (min > 0. || max < 0.)
{
- gmx_fatal(FARGS, "Cannot symmetrize profile around z=0 with min=%f and max=%f\n", opt->min,
- opt->max);
+ gmx_fatal(FARGS, "Cannot symmetrize profile around z=0 with min=%f and max=%f\n", opt->min, opt->max);
}
snew(prof2, bins);
}
else if (opt->unit == en_kJ)
{
- unit_factor = BOLTZ * opt->Temperature;
+ unit_factor = gmx::c_boltz * opt->Temperature;
}
else if (opt->unit == en_kCal)
{
- unit_factor = (BOLTZ / CAL2JOULE) * opt->Temperature;
+ unit_factor = (gmx::c_boltz / gmx::c_cal2Joule) * opt->Temperature;
}
else
{
gmx_fatal(FARGS,
"Ups, random iWin = %d, nPull = %d, nr = %d, "
"blockLength = %d, blockBase = %d\n",
- ipullRandom, nPull, nr, blockLength, blockBase);
+ ipullRandom,
+ nPull,
+ nr,
+ blockLength,
+ blockBase);
}
randomArray[ipull] = ipullRandom;
}
printf("Wrote boot strap result to %s\n", fnres);
}
-//! Return type of input file based on file extension (xvg, pdo, or tpr)
+//! Return type of input file based on file extension (xvg or tpr)
static int whaminFileType(char* fn)
{
int len;
{
return whamin_pullxf;
}
- else if (std::strcmp(fn + len - 3, "pdo") == 0 || std::strcmp(fn + len - 6, "pdo.gz") == 0)
- {
- return whamin_pdo;
- }
else
{
- gmx_fatal(FARGS, "Unknown file type of %s. Should be tpr, xvg, or pdo.\n", fn);
+ gmx_fatal(FARGS,
+ "Unknown file type of %s. Should be tpr or xvg. Use GROMACS 2021 or earlier to "
+ "read pdo files.\n",
+ fn);
}
}
-//! Read the files names in pdo-files.dat, pullf/x-files.dat, tpr-files.dat
+//! Read the files names in pullf/pullx-files.dat, tpr-files.dat
static void read_wham_in(const char* fn, char*** filenamesRet, int* nfilesRet, t_UmbrellaOptions* opt)
{
char **filename = nullptr, tmp[WHAM_MAXFILELEN + 2];
*nfilesRet = nread;
}
-//! Open a file or a pipe to a gzipped file
-static FILE* open_pdo_pipe(const char* fn, t_UmbrellaOptions* opt, gmx_bool* bPipeOpen)
-{
- char Buffer[2048], gunzip[1024], *Path = nullptr;
- FILE* pipe = nullptr;
- static gmx_bool bFirst = true;
-
- /* gzipped pdo file? */
- if ((std::strcmp(fn + std::strlen(fn) - 3, ".gz") == 0))
- {
- /* search gunzip executable */
- if (!(Path = getenv("GMX_PATH_GZIP")))
- {
- if (gmx_fexist("/bin/gunzip"))
- {
- sprintf(gunzip, "%s", "/bin/gunzip");
- }
- else if (gmx_fexist("/usr/bin/gunzip"))
- {
- sprintf(gunzip, "%s", "/usr/bin/gunzip");
- }
- else
- {
- gmx_fatal(FARGS,
- "Cannot find executable gunzip in /bin or /usr/bin.\n"
- "You may want to define the path to gunzip "
- "with the environment variable GMX_PATH_GZIP.");
- }
- }
- else
- {
- sprintf(gunzip, "%s/gunzip", Path);
- if (!gmx_fexist(gunzip))
- {
- gmx_fatal(FARGS,
- "Cannot find executable %s. Please define the path to gunzip"
- " in the environmental varialbe GMX_PATH_GZIP.",
- gunzip);
- }
- }
- if (bFirst)
- {
- printf("Using gunzip executable %s\n", gunzip);
- bFirst = false;
- }
- if (!gmx_fexist(fn))
- {
- gmx_fatal(FARGS, "File %s does not exist.\n", fn);
- }
- sprintf(Buffer, "%s -c < %s", gunzip, fn);
- if (opt->verbose)
- {
- printf("Executing command '%s'\n", Buffer);
- }
-#if HAVE_PIPES
- if ((pipe = popen(Buffer, "r")) == nullptr)
- {
- gmx_fatal(FARGS, "Unable to open pipe to `%s'\n", Buffer);
- }
-#else
- gmx_fatal(FARGS, "Cannot open a compressed file on platform without pipe support");
-#endif
- *bPipeOpen = TRUE;
- }
- else
- {
- pipe = gmx_ffopen(fn, "r");
- *bPipeOpen = FALSE;
- }
-
- return pipe;
-}
-
-//! Close file or pipe
-static void pdo_close_file(FILE* fp)
-{
-#if HAVE_PIPES
- pclose(fp);
-#else
- gmx_ffclose(fp);
-#endif
-}
-
-//! Reading all pdo files
-static void read_pdo_files(char** fn, int nfiles, t_UmbrellaHeader* header, t_UmbrellaWindow* window, t_UmbrellaOptions* opt)
-{
- FILE* file;
- real mintmp, maxtmp, done = 0.;
- int i;
- gmx_bool bPipeOpen;
- /* char Buffer0[1000]; */
-
- if (nfiles < 1)
- {
- gmx_fatal(FARGS, "No files found. Hick.");
- }
-
- /* if min and max are not given, get min and max from the input files */
- if (opt->bAuto)
- {
- printf("Automatic determination of boundaries from %d pdo files...\n", nfiles);
- opt->min = 1e20;
- opt->max = -1e20;
- for (i = 0; i < nfiles; ++i)
- {
- file = open_pdo_pipe(fn[i], opt, &bPipeOpen);
- /*fgets(Buffer0,999,file);
- fprintf(stderr,"First line '%s'\n",Buffer0); */
- done = 100.0 * (i + 1) / nfiles;
- fprintf(stdout, "\rOpening %s ... [%2.0f%%]", fn[i], done);
- fflush(stdout);
- if (opt->verbose)
- {
- printf("\n");
- }
- read_pdo_header(file, header, opt);
- /* here only determine min and max of this window */
- read_pdo_data(file, header, i, nullptr, opt, TRUE, &mintmp, &maxtmp);
- if (maxtmp > opt->max)
- {
- opt->max = maxtmp;
- }
- if (mintmp < opt->min)
- {
- opt->min = mintmp;
- }
- if (bPipeOpen)
- {
- pdo_close_file(file);
- }
- else
- {
- gmx_ffclose(file);
- }
- }
- printf("\n");
- printf("\nDetermined boundaries to %f and %f\n\n", opt->min, opt->max);
- if (opt->bBoundsOnly)
- {
- printf("Found option -boundsonly, now exiting.\n");
- exit(0);
- }
- }
- /* store stepsize in profile */
- opt->dz = (opt->max - opt->min) / opt->bins;
-
- /* Having min and max, we read in all files */
- /* Loop over all files */
- for (i = 0; i < nfiles; ++i)
- {
- done = 100.0 * (i + 1) / nfiles;
- fprintf(stdout, "\rOpening %s ... [%2.0f%%]", fn[i], done);
- fflush(stdout);
- if (opt->verbose)
- {
- printf("\n");
- }
- file = open_pdo_pipe(fn[i], opt, &bPipeOpen);
- read_pdo_header(file, header, opt);
- /* load data into window */
- read_pdo_data(file, header, i, window, opt, FALSE, nullptr, nullptr);
- if ((window + i)->Ntot[0] == 0)
- {
- fprintf(stderr, "\nWARNING, no data points read from file %s (check -b option)\n", fn[i]);
- }
- if (bPipeOpen)
- {
- pdo_close_file(file);
- }
- else
- {
- gmx_ffclose(file);
- }
- }
- printf("\n");
- for (i = 0; i < nfiles; ++i)
- {
- sfree(fn[i]);
- }
- sfree(fn);
-}
-
//! translate 0/1 to N/Y to write pull dimensions
#define int2YN(a) (((a) == 0) ? ("N") : ("Y"))
* so we need to multiply with the internal units (radians for angle)
* to user units (degrees for an angle) with the same power.
*/
- header->pcrd[i].k =
- ir->pull->coord[i].k
- / gmx::square(pull_conversion_factor_internal2userinput(&ir->pull->coord[i]));
+ header->pcrd[i].k = ir->pull->coord[i].k
+ / gmx::square(pull_conversion_factor_internal2userinput(ir->pull->coord[i]));
header->pcrd[i].init_dist = ir->pull->coord[i].init;
copy_ivec(ir->pull->coord[i].dim, header->pcrd[i].dim);
header->pcrd[i].ndim =
header->pcrd[i].dim[XX] + header->pcrd[i].dim[YY] + header->pcrd[i].dim[ZZ];
- std::strcpy(header->pcrd[i].coord_unit, pull_coordinate_units(&ir->pull->coord[i]));
+ std::strcpy(header->pcrd[i].coord_unit, pull_coordinate_units(ir->pull->coord[i]));
- if (ir->efep != efepNO && ir->pull->coord[i].k != ir->pull->coord[i].kB)
+ if (ir->efep != FreeEnergyPerturbationType::No && ir->pull->coord[i].k != ir->pull->coord[i].kB)
{
gmx_fatal(FARGS,
"Seems like you did free-energy perturbation, and you perturbed the force "
gmx_fatal(FARGS,
"Found %d pull coordinates in %s, but %d columns in the respective line\n"
"coordinate selection file (option -is)\n",
- ir->pull->ncoord, fn, coordsel->n);
+ ir->pull->ncoord,
+ fn,
+ coordsel->n);
}
}
/* Check pull coords for consistency */
- int geom = -1;
- ivec thedim = { 0, 0, 0 };
- bool geometryIsSet = false;
+ PullGroupGeometry geom = PullGroupGeometry::Count;
+ ivec thedim = { 0, 0, 0 };
+ bool geometryIsSet = false;
for (int i = 0; i < ir->pull->ncoord; i++)
{
if (coordsel == nullptr || coordsel->bUse[i])
{
- if (header->pcrd[i].pull_type != epullUMBRELLA)
+ if (header->pcrd[i].pull_type != PullingAlgorithm::Umbrella)
{
gmx_fatal(FARGS,
"%s: Pull coordinate %d is of type \"%s\", expected \"umbrella\". Only "
"umbrella coodinates can enter WHAM.\n"
"If you have umrella and non-umbrella coordinates, you can select the "
"umbrella coordinates with gmx wham -is\n",
- fn, i + 1, epull_names[header->pcrd[i].pull_type]);
+ fn,
+ i + 1,
+ enumValueToString(header->pcrd[i].pull_type));
}
if (!geometryIsSet)
{
"%s, coordinate %d: %s)\n"
"If you want to use only some pull coordinates in WHAM, please select "
"them with option gmx wham -is\n",
- fn, epullg_names[geom], i + 1, epullg_names[header->pcrd[i].geometry]);
+ fn,
+ enumValueToString(geom),
+ i + 1,
+ enumValueToString(header->pcrd[i].geometry));
}
if (thedim[XX] != header->pcrd[i].dim[XX] || thedim[YY] != header->pcrd[i].dim[YY]
|| thedim[ZZ] != header->pcrd[i].dim[ZZ])
"%s %s %s, coordinate %d: %s %s %s)\n"
"If you want to use only some pull coordinates in WHAM, please select "
"them with option gmx wham -is\n",
- fn, int2YN(thedim[XX]), int2YN(thedim[YY]), int2YN(thedim[ZZ]), i + 1,
- int2YN(header->pcrd[i].dim[XX]), int2YN(header->pcrd[i].dim[YY]),
+ fn,
+ int2YN(thedim[XX]),
+ int2YN(thedim[YY]),
+ int2YN(thedim[ZZ]),
+ i + 1,
+ int2YN(header->pcrd[i].dim[XX]),
+ int2YN(header->pcrd[i].dim[YY]),
int2YN(header->pcrd[i].dim[ZZ]));
}
- if (header->pcrd[i].geometry == epullgCYL)
+ if (header->pcrd[i].geometry == PullGroupGeometry::Cylinder)
{
if (header->pcrd[i].dim[XX] || header->pcrd[i].dim[YY] || (!header->pcrd[i].dim[ZZ]))
{
FARGS,
"With pull geometry 'cylinder', expected pulling in Z direction only.\n"
"However, found dimensions [%s %s %s]\n",
- int2YN(header->pcrd[i].dim[XX]), int2YN(header->pcrd[i].dim[YY]),
+ int2YN(header->pcrd[i].dim[XX]),
+ int2YN(header->pcrd[i].dim[YY]),
int2YN(header->pcrd[i].dim[ZZ]));
}
}
gmx_fatal(FARGS,
"%s: Pull coordinate %d has force constant of of %g.\n"
"That doesn't seem to be an Umbrella tpr.\n",
- fn, i + 1, header->pcrd[i].k);
+ fn,
+ i + 1,
+ header->pcrd[i].k);
}
}
}
int maxlen = 0;
for (int i = 0; i < ir->pull->ncoord; i++)
{
- int lentmp = strlen(epullg_names[header->pcrd[i].geometry]);
+ int lentmp = strlen(enumValueToString(header->pcrd[i].geometry));
maxlen = (lentmp > maxlen) ? lentmp : maxlen;
}
char fmt[STRLEN];
for (int i = 0; i < ir->pull->ncoord; i++)
{
bool use = (coordsel == nullptr || coordsel->bUse[i]);
- printf(fmt, epullg_names[header->pcrd[i].geometry], header->pcrd[i].k, header->pcrd[i].init_dist,
- int2YN(header->pcrd[i].dim[XX]), int2YN(header->pcrd[i].dim[YY]),
- int2YN(header->pcrd[i].dim[ZZ]), header->pcrd[i].ndim, use ? "Yes" : "No");
+ printf(fmt,
+ enumValueToString(header->pcrd[i].geometry),
+ header->pcrd[i].k,
+ header->pcrd[i].init_dist,
+ int2YN(header->pcrd[i].dim[XX]),
+ int2YN(header->pcrd[i].dim[YY]),
+ int2YN(header->pcrd[i].dim[ZZ]),
+ header->pcrd[i].ndim,
+ use ? "Yes" : "No");
printf("\tPull group coordinates of %d groups expected in pullx files.\n",
ir->pull->bPrintCOM ? header->pcrd[i].ngroup : 0);
}
printf("\t\treaction coordinate: %d\n"
"\t\tcenter-of-mass of groups: %d\n"
"\t\treference position column: %s\n",
- 1, nColCOMCrd[i], (header->bPrintRefValue ? "Yes" : "No"));
+ 1,
+ nColCOMCrd[i],
+ (header->bPrintRefValue ? "Yes" : "No"));
}
printf("\tFound %d times in %s\n", nt, fn);
bFirst = FALSE;
gmx_fatal(FARGS,
"Expected %d columns (including time column) in %s, but found %d."
" Maybe you confused options -if and -ix ?",
- nColExpect, fn, ny);
+ nColExpect,
+ fn,
+ ny);
}
if (!bGetMinMax)
gmx_fatal(FARGS,
"tpr file contains %d pull groups, but expected %d from group selection "
"file\n",
- header->npullcrds, coordsel->n);
+ header->npullcrds,
+ coordsel->n);
}
window->nPull = coordsel->nUse;
}
/* Do you want that time frame? */
t = 1.0 / 1000 * (gmx::roundToInt64((y[0][i] * 1000))); /* round time to fs */
- /* get time step of pdo file and get dstep from opt->dt */
+ /* get time step and get dstep from opt->dt */
if (i == 0)
{
time0 = t;
gmx_fatal(FARGS,
"gUsed too large (%d, nPull=%d). This error should have been "
"caught before.\n",
- gUsed, window->nPull);
+ gUsed,
+ window->nPull);
}
if (opt->bCalcTauInt && !bGetMinMax)
if (whaminFileType(fnPull[i]) != whamin_pullxf)
{
gmx_fatal(FARGS,
- "Expected the %d'th file in input file to be a xvg (pullx/pullf) file\n", i);
- }
- read_pull_xf(fnPull[i], header, nullptr, opt, TRUE, &mintmp, &maxtmp,
+ "Expected the %d'th file in input file to be a xvg (pullx/pullf) file\n",
+ i);
+ }
+ read_pull_xf(fnPull[i],
+ header,
+ nullptr,
+ opt,
+ TRUE,
+ &mintmp,
+ &maxtmp,
(opt->nCoordsel > 0) ? &opt->coordsel[i] : nullptr);
if (maxtmp > opt->max)
{
read_tpr_header(fnTprs[i], header, opt, (opt->nCoordsel > 0) ? &opt->coordsel[i] : nullptr);
if (whaminFileType(fnPull[i]) != whamin_pullxf)
{
- gmx_fatal(FARGS,
- "Expected the %d'th file in input file to be a xvg (pullx/pullf) file\n", i);
+ gmx_fatal(
+ FARGS, "Expected the %d'th file in input file to be a xvg (pullx/pullf) file\n", i);
}
- read_pull_xf(fnPull[i], header, window + i, opt, FALSE, nullptr, nullptr,
+ read_pull_xf(fnPull[i],
+ header,
+ window + i,
+ opt,
+ FALSE,
+ nullptr,
+ nullptr,
(opt->nCoordsel > 0) ? &opt->coordsel[i] : nullptr);
if (window[i].Ntot[0] == 0)
{
nlines = read_xvg(fn, &iact, &ny);
if (nlines != nwins)
{
- gmx_fatal(FARGS, "Found %d lines with integrated autocorrelation times in %s.\nExpected %d",
- nlines, fn, nwins);
+ gmx_fatal(FARGS,
+ "Found %d lines with integrated autocorrelation times in %s.\nExpected %d",
+ nlines,
+ fn,
+ nwins);
}
for (i = 0; i < nlines; i++)
{
if (opt->verbose)
{
- fpcorr = xvgropen("hist_autocorr.xvg", "Autocorrelation functions of umbrella windows",
- "time [ps]", "autocorrelation function", opt->oenv);
+ fpcorr = xvgropen("hist_autocorr.xvg",
+ "Autocorrelation functions of umbrella windows",
+ "time [ps]",
+ "autocorrelation function",
+ opt->oenv);
}
printf("\n");
for (i = 0; i < nwins; i++)
{
- fprintf(stdout, "\rEstimating integrated autocorrelation times ... [%2.0f%%] ...",
+ fprintf(stdout,
+ "\rEstimating integrated autocorrelation times ... [%2.0f%%] ...",
100. * (i + 1) / nwins);
fflush(stdout);
ntot = window[i].Ntot[0];
gmx_fatal(FARGS,
"Encountered different nr of frames in different pull groups.\n"
"That should not happen. (%d and %d)\n",
- ntot, window[i].Ntot[ig]);
+ ntot,
+ window[i].Ntot[ig]);
}
ztime = window[i].ztime[ig];
fprintf(stderr,
"\nWARNING, no data point in bin %d (z=%g) !\n"
"You may not get a reasonable profile. Check your histograms!\n",
- j, z);
+ j,
+ z);
}
/* and check for poor sampling */
else if (relcount < 0.005 && !bBoundary)
*/
for (j = 0; j < opt->bins; ++j)
{
- pot[j] = std::exp(-pot[j] / (BOLTZ * opt->Temperature));
+ pot[j] = std::exp(-pot[j] / (gmx::c_boltz * opt->Temperature));
}
calc_z(pot, window, nWindows, opt, TRUE);
printf("\nUse only these pull coordinates:\n");
for (iline = 0; iline < nTpr; iline++)
{
- printf("%s (%d of %d coordinates):", fnTpr[iline], opt->coordsel[iline].nUse,
+ printf("%s (%d of %d coordinates):",
+ fnTpr[iline],
+ opt->coordsel[iline].nUse,
opt->coordsel[iline].n);
for (i = 0; i < opt->coordsel[iline].n; i++)
{
" provides the pull force output file names ([TT]pullf.xvg[tt]) with option [TT]-if[tt].",
" From the pull force the position in the umbrella potential is",
" computed. This does not work with tabulated umbrella potentials.",
- "* With option [TT]-ip[tt], the user provides file names of (gzipped) [REF].pdo[ref] ",
- " files, i.e.",
- " the GROMACS 3.3 umbrella output files. If you have some unusual",
- " reaction coordinate you may also generate your own [REF].pdo[ref] files and",
- " feed them with the [TT]-ip[tt] option into to [THISMODULE]. The [REF].pdo[ref] file ",
- " header must be similar to the following::",
- "",
- " # UMBRELLA 3.0",
- " # Component selection: 0 0 1",
- " # nSkip 1",
- " # Ref. Group 'TestAtom'",
- " # Nr. of pull groups 2",
- " # Group 1 'GR1' Umb. Pos. 5.0 Umb. Cons. 1000.0",
- " # Group 2 'GR2' Umb. Pos. 2.0 Umb. Cons. 500.0",
- " #####",
"",
- " The number of pull groups, umbrella positions, force constants, and names ",
- " may (of course) differ. Following the header, a time column and ",
- " a data column for each pull group follows (i.e. the displacement",
- " with respect to the umbrella center). Up to four pull groups are possible ",
- " per [REF].pdo[ref] file at present.[PAR]",
"By default, all pull coordinates found in all pullx/pullf files are used in WHAM. If ",
"only ",
"some of the pull coordinates should be used, a pull coordinate selection file (option ",
"",
"Always check whether the histograms sufficiently overlap.[PAR]",
"The umbrella potential is assumed to be harmonic and the force constants are ",
- "read from the [REF].tpr[ref] or [REF].pdo[ref] files. If a non-harmonic umbrella force ",
+ "read from the [REF].tpr[ref] files. If a non-harmonic umbrella force ",
"was applied ",
"a tabulated potential can be provided with [TT]-tab[tt].",
"",
"less robust) method such as fitting to a double exponential, you can ",
"compute the IACTs with [gmx-analyze] and provide them to [THISMODULE] with the file ",
"[TT]iact-in.dat[tt] (option [TT]-iiact[tt]), which should contain one line per ",
- "input file ([REF].pdo[ref] or pullx/f file) and one column per pull coordinate in the ",
+ "input file (pullx/pullf file) and one column per pull coordinate in the ",
"respective file.",
"",
"Error analysis",
{ efDAT, "-ix", "pullx-files", ffOPTRD }, /* wham input: pullf.xvg's and tprs */
{ efDAT, "-if", "pullf-files", ffOPTRD }, /* wham input: pullf.xvg's and tprs */
{ efDAT, "-it", "tpr-files", ffOPTRD }, /* wham input: tprs */
- { efDAT, "-ip", "pdo-files", ffOPTRD }, /* wham input: pdo files (gmx3 style) */
{ efDAT, "-is", "coordsel", ffOPTRD }, /* input: select pull coords to use */
{ efXVG, "-o", "profile", ffWRITE }, /* output file for profile */
{ efXVG, "-hist", "histo", ffWRITE }, /* output file for histograms */
t_UmbrellaWindow* window = nullptr;
double * profile, maxchange = 1e20;
gmx_bool bMinSet, bMaxSet, bAutoSet, bExact = FALSE;
- char ** fninTpr, **fninPull, **fninPdo;
+ char ** fninTpr, **fninPull;
const char* fnPull;
FILE * histout, *profout;
char xlabel[STRLEN], ylabel[256], title[256];
opt.stepchange = 100;
opt.stepUpdateContrib = 100;
- if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr,
- &opt.oenv))
+ if (!parse_common_args(
+ &argc, argv, 0, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &opt.oenv))
{
return 0;
}
opt.bProf0Set = opt2parg_bSet("-zprof0", asize(pa), pa);
opt.bTab = opt2bSet("-tab", NFILE, fnm);
- opt.bPdo = opt2bSet("-ip", NFILE, fnm);
opt.bTpr = opt2bSet("-it", NFILE, fnm);
opt.bPullx = opt2bSet("-ix", NFILE, fnm);
opt.bPullf = opt2bSet("-if", NFILE, fnm);
{
gmx_fatal(FARGS,
"Force input does not work with tabulated potentials. "
- "Provide pullx.xvg or pdo files!");
+ "Provide pullx.xvg files!");
}
- if (!opt.bPdo && !WHAMBOOLXOR(opt.bPullx, opt.bPullf))
+ if (!WHAMBOOLXOR(opt.bPullx, opt.bPullf))
{
gmx_fatal(FARGS, "Give either pullx (-ix) OR pullf (-if) data. Not both.");
}
- if (!opt.bPdo && !(opt.bTpr || opt.bPullf || opt.bPullx))
- {
- gmx_fatal(FARGS,
- "gmx wham supports three input modes, pullx, pullf, or pdo file input."
- "\n\n Check gmx wham -h !");
- }
- opt.fnPdo = opt2fn("-ip", NFILE, fnm);
opt.fnTpr = opt2fn("-it", NFILE, fnm);
opt.fnPullf = opt2fn("-if", NFILE, fnm);
opt.fnPullx = opt2fn("-ix", NFILE, fnm);
}
/* Reading gmx4/gmx5 pull output and tpr files */
- if (opt.bTpr || opt.bPullf || opt.bPullx)
- {
- read_wham_in(opt.fnTpr, &fninTpr, &nfiles, &opt);
-
- fnPull = opt.bPullf ? opt.fnPullf : opt.fnPullx;
- read_wham_in(fnPull, &fninPull, &nfiles2, &opt);
- printf("Found %d tpr and %d pull %s files in %s and %s, respectively\n", nfiles, nfiles2,
- opt.bPullf ? "force" : "position", opt.fnTpr, fnPull);
- if (nfiles != nfiles2)
- {
- gmx_fatal(FARGS, "Found %d file names in %s, but %d in %s\n", nfiles, opt.fnTpr, nfiles2, fnPull);
- }
-
- /* Read file that selects the pull group to be used */
- if (opt.fnCoordSel != nullptr)
- {
- readPullCoordSelection(&opt, fninTpr, nfiles);
- }
+ read_wham_in(opt.fnTpr, &fninTpr, &nfiles, &opt);
- window = initUmbrellaWindows(nfiles);
- read_tpr_pullxf_files(fninTpr, fninPull, nfiles, &header, window, &opt);
+ fnPull = opt.bPullf ? opt.fnPullf : opt.fnPullx;
+ read_wham_in(fnPull, &fninPull, &nfiles2, &opt);
+ printf("Found %d tpr and %d pull %s files in %s and %s, respectively\n",
+ nfiles,
+ nfiles2,
+ opt.bPullf ? "force" : "position",
+ opt.fnTpr,
+ fnPull);
+ if (nfiles != nfiles2)
+ {
+ gmx_fatal(FARGS, "Found %d file names in %s, but %d in %s\n", nfiles, opt.fnTpr, nfiles2, fnPull);
}
- else
- { /* reading pdo files */
- if (opt.fnCoordSel != nullptr)
- {
- gmx_fatal(FARGS,
- "Reading a -is file is not supported with PDO input files.\n"
- "Use awk or a similar tool to pick the required pull groups from your PDO "
- "files\n");
- }
- read_wham_in(opt.fnPdo, &fninPdo, &nfiles, &opt);
- printf("Found %d pdo files in %s\n", nfiles, opt.fnPdo);
- window = initUmbrellaWindows(nfiles);
- read_pdo_files(fninPdo, nfiles, &header, window, &opt);
+
+ /* Read file that selects the pull group to be used */
+ if (opt.fnCoordSel != nullptr)
+ {
+ readPullCoordSelection(&opt, fninTpr, nfiles);
}
+ window = initUmbrellaWindows(nfiles);
+ read_tpr_pullxf_files(fninTpr, fninPull, nfiles, &header, window, &opt);
+
/* It is currently assumed that all pull coordinates have the same geometry, so they also have the same coordinate units.
We can therefore get the units for the xlabel from the first coordinate. */
sprintf(xlabel, "\\xx\\f{} (%s)", header.pcrd[0].coord_unit);
/* Bootstrap Method */
if (opt.nBootStrap)
{
- do_bootstrapping(opt2fn("-bsres", NFILE, fnm), opt2fn("-bsprof", NFILE, fnm),
- opt2fn("-hist", NFILE, fnm), xlabel, ylabel, profile, window, nwins, &opt);
+ do_bootstrapping(opt2fn("-bsres", NFILE, fnm),
+ opt2fn("-bsprof", NFILE, fnm),
+ opt2fn("-hist", NFILE, fnm),
+ xlabel,
+ ylabel,
+ profile,
+ window,
+ nwins,
+ &opt);
}
sfree(profile);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
xc = box;
yc = box;
- ps_font(&out, efontHELV, 1.5 * fontsize);
+ ps_font(&out, Fonts::Helvetica, 1.5 * fontsize);
ps_translate(&out, xc, yc);
if (title)
{
ps_ctext(&out, 0, -fontsize * 1.5 / 2.0, title, eXCenter);
}
- ps_font(&out, efontHELV, fontsize);
+ ps_font(&out, Fonts::Helvetica, fontsize);
ps_rotate(&out, rot0);
for (i = 0; (i < nres);)
{
xc = box;
yc = box;
- ps_font(&out, efontHELV, 1.5 * fontsize);
+ ps_font(&out, Fonts::Helvetica, 1.5 * fontsize);
ps_translate(&out, xc, yc);
ps_color(&out, 0, 0, 0);
if (title)
{
ps_ctext(&out, 0, -fontsize * 1.5 / 2.0, title, eXCenter);
}
- ps_font(&out, efontHELV, fontsize);
+ ps_font(&out, Fonts::Helvetica, fontsize);
ps_rotate(&out, rot0);
for (i = 0; (i < nres);)
"the number of residues and each consecutive line contains a residue name."
};
gmx_output_env_t* oenv;
- static real rot0 = 0;
- static gmx_bool bNum = TRUE;
- static char* title = nullptr;
- static int r0 = 1;
+ real rot0 = 0;
+ gmx_bool bNum = TRUE;
+ char* title = nullptr;
+ int r0 = 1;
t_pargs pa[] = { { "-r0", FALSE, etINT, { &r0 }, "The first residue number in the sequence" },
{ "-rot0",
FALSE,
done_warning(wi, FARGS);
}
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static t_rgb black = { 0, 0, 0 };
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static t_rgb white = { 1, 1, 1 };
#define BLACK (&black)
/* this must correspond to *colors[] in get_params */
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static t_rgb* linecolors[] = { nullptr, &black, &white, nullptr };
static void leg_discrete(t_psdata* ps,
/* Plot label on lowest graph only */
if (m == mat.begin())
{
- ps_ctext(ps, xx, yy00 - DDD - psr->X.majorticklen - psr->X.tickfontsize * 0.8,
- xtick[x], eXCenter);
+ ps_ctext(ps, xx, yy00 - DDD - psr->X.majorticklen - psr->X.tickfontsize * 0.8, xtick[x], eXCenter);
}
}
else if (bRmod(m->axis_x[x], psr->X.offset, psr->X.minor)
/* Major ticks */
strlength = std::max(strlength, std::strlen(ytick[y]));
ps_line(ps, xx00, yy, xx00 - psr->Y.majorticklen, yy);
- ps_ctext(ps, xx00 - psr->Y.majorticklen - DDD, yy - psr->Y.tickfontsize / 3.0,
- ytick[y], eXRight);
+ ps_ctext(ps, xx00 - psr->Y.majorticklen - DDD, yy - psr->Y.tickfontsize / 3.0, ytick[y], eXRight);
}
else if (bRmod(m->axis_y[y], psr->Y.offset, psr->Y.minor))
{
if (!mylab.empty())
{
ps_strfont(ps, psr->X.font, psr->X.fontsize);
- ps_ctext(ps, x0 + w / 2,
+ ps_ctext(ps,
+ x0 + w / 2,
y0 - DDD - psr->X.majorticklen - psr->X.tickfontsize * FUDGE - psr->X.fontsize,
- mylab, eXCenter);
+ mylab,
+ eXCenter);
}
}
{
gmx_fatal(FARGS, "Not enough symbols to merge the two colormaps\n");
}
- printf("Combining colormaps of %zu and %zu elements into one of %zu elements\n", map1.size(),
- map2.size(), map.size());
+ printf("Combining colormaps of %zu and %zu elements into one of %zu elements\n",
+ map1.size(),
+ map2.size(),
+ map.size());
gmx::index k = 0;
for (gmx::index j = 0; j < gmx::ssize(map1) && k < gmx::ssize(map); ++j, ++k)
{
if (psr->X.major <= 0)
{
tick_spacing((mat[0].flags & MAT_SPATIAL_X) ? mat[0].nx + 1 : mat[0].nx,
- mat[0].axis_x.data(), psr->X.offset, 'X', &(psr->X.major), &(psr->X.minor));
+ mat[0].axis_x.data(),
+ psr->X.offset,
+ 'X',
+ &(psr->X.major),
+ &(psr->X.minor));
}
if (psr->X.minor <= 0)
{
if (psr->Y.major <= 0)
{
tick_spacing((mat[0].flags & MAT_SPATIAL_Y) ? mat[0].ny + 1 : mat[0].ny,
- mat[0].axis_y.data(), psr->Y.offset, 'Y', &(psr->Y.major), &(psr->Y.minor));
+ mat[0].axis_y.data(),
+ psr->Y.offset,
+ 'Y',
+ &(psr->Y.major),
+ &(psr->Y.minor));
}
if (psr->Y.minor <= 0)
{
{
if (elegend != elBoth)
{
- leg_continuous(&out, x0 + w / 2, w / 2, DDD, legend, psr->legfontsize, psr->legfont,
- leg_map, mapoffset);
+ leg_continuous(
+ &out, x0 + w / 2, w / 2, DDD, legend, psr->legfontsize, psr->legfont, leg_map, mapoffset);
}
else
{
assert(!mat2.empty());
- leg_bicontinuous(&out, x0 + w / 2, w, DDD, mat[0].legend, mat2[0].legend,
- psr->legfontsize, psr->legfont, map1, map2);
+ leg_bicontinuous(
+ &out, x0 + w / 2, w, DDD, mat[0].legend, mat2[0].legend, psr->legfontsize, psr->legfont, map1, map2);
}
}
ps_comment(&out, "Done processing");
"Matrix pruning requires matrices of the same size");
for (gmx::index i = 0; i != gmx::ssize(mat); ++i)
{
- fprintf(stderr, "converting %dx%d matrix to %dx%d\n", mat[i].nx, mat[i].ny,
- (mat[i].nx + skip - 1) / skip, (mat[i].ny + skip - 1) / skip);
+ fprintf(stderr,
+ "converting %dx%d matrix to %dx%d\n",
+ mat[i].nx,
+ mat[i].ny,
+ (mat[i].nx + skip - 1) / skip,
+ (mat[i].ny + skip - 1) / skip);
/* walk through matrix */
int xs = 0;
for (int x = 0; (x < mat[i].nx); x++)
gmx_fatal(FARGS,
"Size of frame %zd in 1st (%dx%d) and 2nd matrix (%dx%d) do"
" not match.\n",
- k, mat1[k].nx, mat1[k].ny, mat2[k].nx, mat2[k].ny);
+ k,
+ mat1[k].nx,
+ mat1[k].ny,
+ mat2[k].nx,
+ mat2[k].ny);
}
printf("Combining two %dx%d matrices\n", mat1[k].nx, mat1[k].ny);
rmat1 = matrix2real(&mat1[k], nullptr);
}
else
{
- write_xpm(out, mat1[k].flags, mat1[k].title, mat1[k].legend, mat1[k].label_x,
- mat1[k].label_y, mat1[k].nx, mat1[k].ny, mat1[k].axis_x.data(),
- mat1[k].axis_y.data(), rmat1, rlo, rhi, white, black, &nlevels);
+ write_xpm(out,
+ mat1[k].flags,
+ mat1[k].title,
+ mat1[k].legend,
+ mat1[k].label_x,
+ mat1[k].label_y,
+ mat1[k].nx,
+ mat1[k].ny,
+ mat1[k].axis_x.data(),
+ mat1[k].axis_y.data(),
+ rmat1,
+ rlo,
+ rhi,
+ white,
+ black,
+ &nlevels);
}
}
gmx_ffclose(out);
gmx_fatal(FARGS,
"WAKE UP!! Size of frame %zd in 2nd matrix file (%dx%d) does not match "
"size of 1st matrix (%dx%d) or the other way around.\n",
- k, mat2[k].nx, mat2[k].ny, mat[k].nx, mat[k].ny);
+ k,
+ mat2[k].nx,
+ mat2[k].ny,
+ mat[k].nx,
+ mat[k].ny);
}
for (int j = 0; (j < mat[k].ny); j++)
{
if (epsfile != nullptr)
{
- ps_mat(epsfile, mat, mat2, bFrame, bDiag, bFirstDiag, bTitle, bTitleOnce, bYonce, elegend,
- size, boxx, boxy, m2p, m2pout, mapoffset);
+ ps_mat(epsfile, mat, mat2, bFrame, bDiag, bFirstDiag, bTitle, bTitleOnce, bYonce, elegend, size, boxx, boxy, m2p, m2pout, mapoffset);
}
if (xpmfile != nullptr)
{
{ efEPS, "-o", nullptr, ffOPTWR }, { efXPM, "-xpm", nullptr, ffOPTWR } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, NPA, pa, asize(desc), desc, 0,
- nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW, NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
fn = opt2fn("-f", NFILE, fnm);
std::vector<t_matrix> mat, mat2;
mat = read_xpm_matrix(fn);
- fprintf(stderr, "There %s %zu matri%s in %s\n", (mat.size() > 1) ? "are" : "is", mat.size(),
- (mat.size() > 1) ? "ces" : "x", fn);
+ fprintf(stderr,
+ "There %s %zu matri%s in %s\n",
+ (mat.size() > 1) ? "are" : "is",
+ mat.size(),
+ (mat.size() > 1) ? "ces" : "x",
+ fn);
fn = opt2fn_null("-f2", NFILE, fnm);
if (fn)
{
mat2 = read_xpm_matrix(fn);
- fprintf(stderr, "There %s %zu matri%s in %s\n", (mat2.size() > 1) ? "are" : "is",
- mat2.size(), (mat2.size() > 1) ? "ces" : "x", fn);
+ fprintf(stderr,
+ "There %s %zu matri%s in %s\n",
+ (mat2.size() > 1) ? "are" : "is",
+ mat2.size(),
+ (mat2.size() > 1) ? "ces" : "x",
+ fn);
if (mat.size() != mat2.size())
{
fprintf(stderr, "Different number of matrices, using the smallest number.\n");
if (ecombine && ecombine != ecHalves)
{
- write_combined_matrix(ecombine, xpmfile, mat, mat2, opt2parg_bSet("-cmin", NPA, pa) ? &cmin : nullptr,
+ write_combined_matrix(ecombine,
+ xpmfile,
+ mat,
+ mat2,
+ opt2parg_bSet("-cmin", NPA, pa) ? &cmin : nullptr,
opt2parg_bSet("-cmax", NPA, pa) ? &cmax : nullptr);
}
else
{
- do_mat(mat, mat2, bFrame, bZeroLine, bDiag, bFirstDiag, bTitle, bTitleOnce, bYonce, elegend,
- size, boxx, boxy, epsfile, xpmfile, opt2fn_null("-di", NFILE, fnm),
- opt2fn_null("-do", NFILE, fnm), skip, mapoffset);
+ do_mat(mat,
+ mat2,
+ bFrame,
+ bZeroLine,
+ bDiag,
+ bFirstDiag,
+ bTitle,
+ bTitleOnce,
+ bYonce,
+ elegend,
+ size,
+ boxx,
+ boxy,
+ epsfile,
+ xpmfile,
+ opt2fn_null("-di", NFILE, fnm),
+ opt2fn_null("-do", NFILE, fnm),
+ skip,
+ mapoffset);
}
view_all(oenv, NFILE, fnm);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/listed_forces/bonded.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/topology/index.h"
#include "gromacs/topology/topology.h"
xx = cp * x2[XX] + sp * x2[YY];
yy = -sp * x2[XX] + cp * x2[YY];
- dphi = RAD2DEG * std::atan2(yy, xx);
+ dphi = gmx::c_rad2Deg * std::atan2(yy, xx);
return dphi;
}
aj = index[i + 1];
ak = index[i + 2];
al = index[i + 3];
- phi = RAD2DEG
+ phi = gmx::c_rad2Deg
* dih_angle(x[ai], x[aj], x[ak], x[al], nullptr, r_ij, r_kj, r_kl, m, n, &t1, &t2, &t3);
phitot += phi;
}
#define NBB asize(bb_nm)
t_bb* bb;
char* grpname;
- int ai, i, i0, i1, j, k, rnr, gnx, r0, r1;
+ int gnx, r0, r1;
fprintf(stderr, "Please select a group containing the entire backbone\n");
rd_index(fn, 1, &gnx, index, &grpname);
*nall = gnx;
fprintf(stderr, "Checking group %s\n", grpname);
r0 = r1 = atom[(*index)[0]].resind;
- for (i = 1; (i < gnx); i++)
+ for (int i = 1; (i < gnx); i++)
{
r0 = std::min(r0, atom[(*index)[i]].resind);
r1 = std::max(r1, atom[(*index)[i]].resind);
}
- rnr = r1 - r0 + 1;
+ int rnr = r1 - r0 + 1;
fprintf(stderr, "There are %d residues\n", rnr);
snew(bb, rnr);
- for (i = 0; (i < rnr); i++)
+ for (int i = 0; (i < rnr); i++)
{
bb[i].N = bb[i].H = bb[i].CA = bb[i].C = bb[i].O = -1;
bb[i].resno = res0 + i;
}
- for (i = j = 0; (i < gnx); i++)
+ for (int i = 0; (i < gnx); i++)
{
- ai = (*index)[i];
+ int ai = (*index)[i];
// Create an index into the residue index for the topology.
int resindex = atom[ai].resind;
// Create an index into the residues present in the selected
bb[bbindex].H = ai;
}
}
- for (k = 0; (k < NBB); k++)
+ int k = 0;
+ for (; (k < NBB); k++)
{
if (std::strcmp(bb_nm[k], *(atomname[ai])) == 0)
{
}
}
- for (i0 = 0; (i0 < rnr); i0++)
+ int i0 = 0;
+ for (; (i0 < rnr); i0++)
{
if ((bb[i0].N != -1) && (bb[i0].H != -1) && (bb[i0].CA != -1) && (bb[i0].C != -1)
&& (bb[i0].O != -1))
break;
}
}
- for (i1 = rnr - 1; (i1 >= 0); i1--)
+ int i1 = rnr - 1;
+ for (; (i1 >= 0); i1--)
{
if ((bb[i1].N != -1) && (bb[i1].H != -1) && (bb[i1].CA != -1) && (bb[i1].C != -1)
&& (bb[i1].O != -1))
i1--;
}
- for (i = i0; (i < i1); i++)
+ for (int i = i0; (i < i1); i++)
{
bb[i].Cprev = bb[i - 1].C;
bb[i].Nnext = bb[i + 1].N;
}
rnr = std::max(0, i1 - i0 + 1);
- fprintf(stderr, "There are %d complete backbone residues (from %d to %d)\n", rnr, bb[i0].resno,
- bb[i1].resno);
+ fprintf(stderr, "There are %d complete backbone residues (from %d to %d)\n", rnr, bb[i0].resno, bb[i1].resno);
if (rnr == 0)
{
gmx_fatal(FARGS, "Zero complete backbone residues were found, cannot proceed");
}
- for (i = 0; (i < rnr); i++, i0++)
+ for (int i = 0; (i < rnr); i++, i0++)
{
bb[i] = bb[i0];
}
/* Set the labels */
- for (i = 0; (i < rnr); i++)
+ for (int i = 0; (i < rnr); i++)
{
int resindex = atom[bb[i].CA].resind;
sprintf(bb[i].label, "%s%d", *(resinfo[resindex].name), resinfo[resindex].nr);
bb[i].d5 = norm(dx);
}
- bb[i].phi = RAD2DEG
- * dih_angle(x[bb[i].Cprev], x[bb[i].N], x[bb[i].CA], x[bb[i].C], nullptr, r_ij,
- r_kj, r_kl, m, n, &t1, &t2, &t3);
- bb[i].psi = RAD2DEG
- * dih_angle(x[bb[i].N], x[bb[i].CA], x[bb[i].C], x[bb[i].Nnext], nullptr, r_ij,
- r_kj, r_kl, m, n, &t1, &t2, &t3);
+ bb[i].phi = gmx::c_rad2Deg
+ * dih_angle(x[bb[i].Cprev],
+ x[bb[i].N],
+ x[bb[i].CA],
+ x[bb[i].C],
+ nullptr,
+ r_ij,
+ r_kj,
+ r_kl,
+ m,
+ n,
+ &t1,
+ &t2,
+ &t3);
+ bb[i].psi = gmx::c_rad2Deg
+ * dih_angle(x[bb[i].N],
+ x[bb[i].CA],
+ x[bb[i].C],
+ x[bb[i].Nnext],
+ nullptr,
+ r_ij,
+ r_kj,
+ r_kl,
+ m,
+ n,
+ &t1,
+ &t2,
+ &t3);
bb[i].pprms2 = gmx::square(bb[i].phi - PHI_AHX) + gmx::square(bb[i].psi - PSI_AHX);
- bb[i].jcaha += 1.4 * std::sin((bb[i].psi + 138.0) * DEG2RAD)
- - 4.1 * std::cos(2.0 * DEG2RAD * (bb[i].psi + 138.0))
- + 2.0 * std::cos(2.0 * DEG2RAD * (bb[i].phi + 30.0));
+ bb[i].jcaha += 1.4 * std::sin((bb[i].psi + 138.0) * gmx::c_deg2Rad)
+ - 4.1 * std::cos(2.0 * gmx::c_deg2Rad * (bb[i].psi + 138.0))
+ + 2.0 * std::cos(2.0 * gmx::c_deg2Rad * (bb[i].phi + 30.0));
}
}
int i;
fprintf(fp, "\n");
- fprintf(fp, "%3s %3s %3s %3s %3s %7s %7s %7s %7s %7s %3s\n", "AA", "N", "Ca", "C", "O", "Phi",
- "Psi", "D3", "D4", "D5", "Hx?");
+ fprintf(fp,
+ "%3s %3s %3s %3s %3s %7s %7s %7s %7s %7s %3s\n",
+ "AA",
+ "N",
+ "Ca",
+ "C",
+ "O",
+ "Phi",
+ "Psi",
+ "D3",
+ "D4",
+ "D5",
+ "Hx?");
for (i = 0; (i < nres); i++)
{
- fprintf(fp, "%3d %3d %3d %3d %3d %7.2f %7.2f %7.3f %7.3f %7.3f %3s\n", bb[i].resno, bb[i].N,
- bb[i].CA, bb[i].C, bb[i].O, bb[i].phi, bb[i].psi, bb[i].d3, bb[i].d4, bb[i].d5,
+ fprintf(fp,
+ "%3d %3d %3d %3d %3d %7.2f %7.2f %7.3f %7.3f %7.3f %3s\n",
+ bb[i].resno,
+ bb[i].N,
+ bb[i].CA,
+ bb[i].C,
+ bb[i].O,
+ bb[i].phi,
+ bb[i].psi,
+ bb[i].d3,
+ bb[i].d4,
+ bb[i].d5,
bb[i].bHelix ? "Yes" : "No");
}
fprintf(fp, "\n");
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _hxprops_h
-#define _hxprops_h
+#ifndef GMX_GMXANA_HXPROPS_H
+#define GMX_GMXANA_HXPROPS_H
#include <stdio.h>
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2013,2014,2015 by the GROMACS development team.
- * Copyright (c) 2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _interf_h
-#define _interf_h
+#ifndef GMX_GMXANA_INTERF_H
+#define GMX_GMXANA_INTERF_H
#include "gromacs/utility/real.h"
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-static const char* pp_pat[] = { "C", "N", "CA", "C", "N" };
+static const char* const pp_pat[] = { "C", "N", "CA", "C", "N" };
#define NPP (sizeof(pp_pat) / sizeof(pp_pat[0]))
static bool d_comp(const t_dih& a, const t_dih& b)
for (i = 0; (i < xr->ndih); i++)
{
dd = &(xr->dih[i]);
- dd->ang = dih_angle(xr->x[dd->ai[0]], xr->x[dd->ai[1]], xr->x[dd->ai[2]], xr->x[dd->ai[3]],
- nullptr, r_ij, r_kj, r_kl, m, n, &t1, &t2, &t3);
+ dd->ang = dih_angle(xr->x[dd->ai[0]],
+ xr->x[dd->ai[1]],
+ xr->x[dd->ai[2]],
+ xr->x[dd->ai[3]],
+ nullptr,
+ r_ij,
+ r_kj,
+ r_kl,
+ m,
+ n,
+ &t1,
+ &t2,
+ &t3);
}
}
xr->pp[xr->npp].iphi = xr->ndih - 2;
xr->pp[xr->npp].ipsi = xr->ndih - 1;
xr->pp[xr->npp].bShow = FALSE;
- sprintf(buf, "%s-%d", *atoms->resinfo[atoms->atom[ff[1]].resind].name,
+ sprintf(buf,
+ "%s-%d",
+ *atoms->resinfo[atoms->atom[ff[1]].resind].name,
atoms->resinfo[atoms->atom[ff[1]].resind].nr);
xr->pp[xr->npp].label = gmx_strdup(buf);
xr->npp++;
{
if (xr->dih[i].mult == 0)
{
- fprintf(stderr, "Dihedral around %d,%d not found in topology. Using mult=%d\n",
- xr->dih[i].ai[1], xr->dih[i].ai[2], mult);
+ fprintf(stderr,
+ "Dihedral around %d,%d not found in topology. Using mult=%d\n",
+ xr->dih[i].ai[1],
+ xr->dih[i].ai[2],
+ mult);
xr->dih[i].mult = mult;
xr->dih[i].phi0 = 180;
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016, The GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx::UniformIntDistribution<int> tdist(0, isize - 1);
tid = gmx_omp_get_thread_num();
/* now starting parallel threads */
- INTEL_DIAGNOSTIC_IGNORE(593)
# pragma omp for
for (int64_t mc = 0; mc < mc_max; mc++)
{
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
}
- INTEL_DIAGNOSTIC_RESET
/* collecting data from threads */
for (i = 0; i < pr->grn; i++)
{
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2013,2014,2015 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _powerspect_h
-#define _powerspect_h
+#ifndef GMX_GMXANA_POWERSPECT_H
+#define GMX_GMXANA_POWERSPECT_H
#include <string>
#include <vector>
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/matio.h"
#include "gromacs/gmxana/gstat.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
{
snew(newdata[i], nny);
phi = i * 2 * M_PI / (nnx - 1);
- x_phi[i] = phi * RAD2DEG - 180;
+ x_phi[i] = phi * gmx::c_rad2Deg - 180;
for (j = 0; (j < nny); j++)
{
psi = j * 2 * M_PI / (nny - 1);
if (i == 0)
{
- y_psi[j] = psi * RAD2DEG - 180;
+ y_psi[j] = psi * gmx::c_rad2Deg - 180;
}
/*if (((i % nfac) == 0) && ((j % nfac) == 0))
newdata[i][j] = sd->data[i/nfac][j/nfac];
fprintf(fp, "\n *** Chemical shifts from the chemical shift index ***\n");
please_cite(fp, "Wishart98a");
- fprintf(fp, "%12s %10s %10s %10s %10s\n", "Residue", "delta Ca", "delta Ha", "delta CO",
+ fprintf(fp,
+ "%12s %10s %10s %10s %10s\n",
+ "Residue",
+ "delta Ca",
+ "delta Ha",
+ "delta CO",
"delta Cb");
for (i = 0; (i < nlist); i++)
{
co += interpolate(phi, psi, co_sd);
ha += interpolate(phi, psi, ha_sd);
}
- fprintf(fp, "%12s %10g %10g %10g %10g\n", dlist[i].name, ca / nf, ha / nf, co / nf,
- cb / nf);
+ fprintf(fp, "%12s %10g %10g %10g %10g\n", dlist[i].name, ca / nf, ha / nf, co / nf, cb / nf);
}
}
fprintf(fp, "\n");
y = inten[m][2];
z = inten[m][3];
n = x * x + y * y + z * z;
- fprintf(stderr, "%8s %8.3f %8.3f %8.3f, norm:%8.3f, d:%8.3f, e:%8.3f\n", s, x, y, z,
- std::sqrt(n), d[m], e[m]);
+ fprintf(stderr, "%8s %8.3f %8.3f %8.3f, norm:%8.3f, d:%8.3f, e:%8.3f\n", s, x, y, z, std::sqrt(n), d[m], e[m]);
}
fprintf(stderr, "\n");
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/md_enums.h"
while (get_a_line(fp.get(), line, STRLEN))
{
i = line_no;
- if (sscanf(line, "%s %d %lf %lf %lf %lf %lf %lf %lf %lf %lf", atomn, &p, &a1, &a2, &a3, &a4,
- &b1, &b2, &b3, &b4, &c)
+ if (sscanf(line, "%s %d %lf %lf %lf %lf %lf %lf %lf %lf %lf", atomn, &p, &a1, &a2, &a3, &a4, &b1, &b2, &b3, &b4, &c)
== 11)
{
gsf->atomnm[i] = gmx_strdup(atomn);
{
rearrange_atoms(red[i], &fr, index[i], isize[i], &top, FALSE, gmx_sf);
- compute_structure_factor(static_cast<structure_factor_t*>(sf), box, red[i], isize[i],
- start_q, end_q, i, sf_table);
+ compute_structure_factor(
+ static_cast<structure_factor_t*>(sf), box, red[i], isize[i], start_q, end_q, i, sf_table);
}
}
xvgrclose(fp);
}
-
extern double CMSF(gmx_structurefactors_t* gsf, int type, int nh, double lambda, double sin_theta)
/*
* return Cromer-Mann fit for the atomic scattering factor:
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
-# Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
entropy.cpp
gmx_traj.cpp
gmx_mindist.cpp
- gmx_msd.cpp
)
gmx_register_gtest_test(GmxAnaTest ${exename} INTEGRATION_TEST IGNORE_LEAKS)
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*! \internal \file
- * \brief
- * Tests for gmx msd.
- *
- * \author Kevin Boyd <kevin.boyd@uconn.edu>
- */
-
-#include "gmxpre.h"
-
-#include <cstdio>
-#include <cstdlib>
-
-#include "gromacs/gmxana/gmx_ana.h"
-#include "gromacs/gmxpreprocess/grompp.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/utility/path.h"
-#include "gromacs/utility/textreader.h"
-
-#include "testutils/cmdlinetest.h"
-#include "testutils/refdata.h"
-#include "testutils/testfilemanager.h"
-#include "testutils/textblockmatchers.h"
-#include "testutils/xvgtest.h"
-
-namespace
-{
-
-using gmx::test::CommandLine;
-using gmx::test::XvgMatch;
-
-class MsdTest : public gmx::test::CommandLineTestBase
-{
-public:
- MsdTest()
- {
- setOutputFile("-o", "msd.xvg", XvgMatch());
- setInputFile("-f", "msd_traj.xtc");
- setInputFile("-s", "msd_coords.gro");
- setInputFile("-n", "msd.ndx");
- }
-
- void runTest(const CommandLine& args)
- {
- CommandLine& cmdline = commandLine();
- cmdline.merge(args);
- ASSERT_EQ(0, gmx_msd(cmdline.argc(), cmdline.argv()));
- checkOutputFiles();
- }
-};
-
-class MsdMolTest : public gmx::test::CommandLineTestBase
-{
-public:
- MsdMolTest()
- {
- double tolerance = 1e-5;
- XvgMatch xvg;
- XvgMatch& toler = xvg.tolerance(gmx::test::relativeToleranceAsFloatingPoint(1, tolerance));
- setOutputFile("-mol", "msdmol.xvg", toler);
- }
-
- void runTest(const CommandLine& args, const char* ndxfile, const std::string& simulationName)
- {
- setInputFile("-f", simulationName + ".pdb");
- std::string tpr = fileManager().getTemporaryFilePath(".tpr");
- std::string mdp = fileManager().getTemporaryFilePath(".mdp");
- FILE* fp = fopen(mdp.c_str(), "w");
- fprintf(fp, "cutoff-scheme = verlet\n");
- fprintf(fp, "rcoulomb = 0.85\n");
- fprintf(fp, "rvdw = 0.85\n");
- fprintf(fp, "rlist = 0.85\n");
- fclose(fp);
-
- // Prepare a .tpr file
- {
- CommandLine caller;
- auto simDB = gmx::test::TestFileManager::getTestSimulationDatabaseDirectory();
- auto base = gmx::Path::join(simDB, simulationName);
- caller.append("grompp");
- caller.addOption("-maxwarn", 0);
- caller.addOption("-f", mdp.c_str());
- std::string gro = (base + ".pdb");
- caller.addOption("-c", gro.c_str());
- std::string top = (base + ".top");
- caller.addOption("-p", top.c_str());
- std::string ndx = (base + ".ndx");
- caller.addOption("-n", ndx.c_str());
- caller.addOption("-o", tpr.c_str());
- ASSERT_EQ(0, gmx_grompp(caller.argc(), caller.argv()));
- }
- // Run the MSD analysis
- {
- setInputFile("-n", ndxfile);
- CommandLine& cmdline = commandLine();
- cmdline.merge(args);
- cmdline.addOption("-s", tpr.c_str());
- ASSERT_EQ(0, gmx_msd(cmdline.argc(), cmdline.argv()));
- checkOutputFiles();
- }
- }
-};
-
-/* msd_traj.xtc contains a 10 frame (1 ps per frame) simulation
- * containing 3 atoms, with different starting positions but identical
- * displacements. The displacements are calculated to yield the following
- * diffusion coefficients when lag is calculated ONLY FROM TIME 0
- * D_x = 8 * 10 ^ -5 cm^2 /s, D_y = 4 * 10^ -5 cm^2 /s , D_z = 0
- *
- * To test for these results, -trestart is set to a larger value than the
- * total simulation length, so that only lag 0 is calculated
- */
-
-// for 3D, (8 + 4 + 0) / 3 should yield 4 cm^2 / s
-TEST_F(MsdTest, threeDimensionalDiffusion)
-{
- const char* const cmdline[] = {
- "msd", "-mw", "no", "-trestart", "200",
- };
- runTest(CommandLine(cmdline));
-}
-
-// for lateral z, (8 + 4) / 2 should yield 6 cm^2 /s
-TEST_F(MsdTest, twoDimensionalDiffusion)
-{
- const char* const cmdline[] = { "msd", "-mw", "no", "-trestart", "200", "-lateral", "z" };
- runTest(CommandLine(cmdline));
-}
-
-// for type x, should yield 8 cm^2 / s
-TEST_F(MsdTest, oneDimensionalDiffusion)
-{
- const char* const cmdline[] = { "msd", "-mw", "no", "-trestart", "200", "-type", "x" };
- runTest(CommandLine(cmdline));
-}
-
-// Test the diffusion per molecule output, mass weighted
-TEST_F(MsdMolTest, diffMolMassWeighted)
-{
- const char* const cmdline[] = { "msd", "-trestart", "200" };
- runTest(CommandLine(cmdline), "spc5.ndx", "spc5");
-}
-
-// Test the diffusion per molecule output, non-mass weighted
-TEST_F(MsdMolTest, diffMolNonMassWeighted)
-{
- const char* const cmdline[] = { "msd", "-trestart", "200", "-mw", "no" };
- runTest(CommandLine(cmdline), "spc5.ndx", "spc5");
-}
-
-// Test the diffusion per molecule output, with selection
-TEST_F(MsdMolTest, diffMolSelected)
-{
- const char* const cmdline[] = { "msd", "-trestart", "200" };
- runTest(CommandLine(cmdline), "spc5_3.ndx", "spc5");
-}
-
-} // namespace
+++ /dev/null
-<?xml version="1.0"?>
-<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
-<ReferenceData>
- <OutputFiles Name="Files">
- <File Name="-mol">
- <XvgLegend Name="Legend">
- <String Name="XvgLegend"><![CDATA[
-title "Diffusion Coefficients / Molecule"
-xaxis label "Molecule"
-yaxis label "D (1e-5 cm^2/s)"
-TYPE xy
-]]></String>
- </XvgLegend>
- <XvgData Name="Data">
- <Sequence Name="Row0">
- <Int Name="Length">2</Int>
- <Real>0</Real>
- <Real>0.747088</Real>
- </Sequence>
- <Sequence Name="Row1">
- <Int Name="Length">2</Int>
- <Real>1</Real>
- <Real>0.129497</Real>
- </Sequence>
- <Sequence Name="Row2">
- <Int Name="Length">2</Int>
- <Real>2</Real>
- <Real>1.00167</Real>
- </Sequence>
- <Sequence Name="Row3">
- <Int Name="Length">2</Int>
- <Real>3</Real>
- <Real>21.2013</Real>
- </Sequence>
- <Sequence Name="Row4">
- <Int Name="Length">2</Int>
- <Real>4</Real>
- <Real>9.28605</Real>
- </Sequence>
- </XvgData>
- </File>
- </OutputFiles>
-</ReferenceData>
+++ /dev/null
-<?xml version="1.0"?>
-<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
-<ReferenceData>
- <OutputFiles Name="Files">
- <File Name="-mol">
- <XvgLegend Name="Legend">
- <String Name="XvgLegend"><![CDATA[
-title "Diffusion Coefficients / Molecule"
-xaxis label "Molecule"
-yaxis label "D (1e-5 cm^2/s)"
-TYPE xy
-]]></String>
- </XvgLegend>
- <XvgData Name="Data">
- <Sequence Name="Row0">
- <Int Name="Length">2</Int>
- <Real>0</Real>
- <Real>0.747088</Real>
- </Sequence>
- <Sequence Name="Row1">
- <Int Name="Length">2</Int>
- <Real>1</Real>
- <Real>0.129497</Real>
- </Sequence>
- <Sequence Name="Row2">
- <Int Name="Length">2</Int>
- <Real>2</Real>
- <Real>1.00167</Real>
- </Sequence>
- <Sequence Name="Row3">
- <Int Name="Length">2</Int>
- <Real>3</Real>
- <Real>21.2013</Real>
- </Sequence>
- <Sequence Name="Row4">
- <Int Name="Length">2</Int>
- <Real>4</Real>
- <Real>9.28605</Real>
- </Sequence>
- </XvgData>
- </File>
- </OutputFiles>
-</ReferenceData>
+++ /dev/null
-<?xml version="1.0"?>
-<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
-<ReferenceData>
- <OutputFiles Name="Files">
- <File Name="-mol">
- <XvgLegend Name="Legend">
- <String Name="XvgLegend"><![CDATA[
-title "Diffusion Coefficients / Molecule"
-xaxis label "Molecule"
-yaxis label "D (1e-5 cm^2/s)"
-TYPE xy
-]]></String>
- </XvgLegend>
- <XvgData Name="Data">
- <Sequence Name="Row0">
- <Int Name="Length">2</Int>
- <Real>0</Real>
- <Real>0.747088</Real>
- </Sequence>
- <Sequence Name="Row1">
- <Int Name="Length">2</Int>
- <Real>1</Real>
- <Real>0.129497</Real>
- </Sequence>
- <Sequence Name="Row2">
- <Int Name="Length">2</Int>
- <Real>2</Real>
- <Real>21.2013</Real>
- </Sequence>
- </XvgData>
- </File>
- </OutputFiles>
-</ReferenceData>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static double eigval_to_frequency(double eigval)
{
- double factor_gmx_to_omega2 = 1.0E21 / (AVOGADRO * AMU);
+ double factor_gmx_to_omega2 = 1.0E21 / (gmx::c_avogadro * gmx::c_amu);
return std::sqrt(std::max(0.0, eigval) * factor_gmx_to_omega2);
}
double calcZeroPointEnergy(gmx::ArrayRef<const real> eigval, real scale_factor)
{
// Convert frequency (ps^-1) to energy (kJ/mol)
- double factor = PLANCK * PICO / (2.0 * M_PI);
+ double factor = gmx::c_planck * gmx::c_pico / (2.0 * M_PI);
double zpe = 0;
- for (auto& r : eigval)
+ for (const auto& r : eigval)
{
double omega = eigval_to_frequency(r);
zpe += 0.5 * factor * scale_factor * omega;
{
size_t nskip = linear ? 5 : 6;
double Evib = 0;
- double hbar = PLANCK1 / (2 * M_PI);
+ double hbar = gmx::c_planck1 / (2 * M_PI);
for (gmx::index i = nskip; i < eigval.ssize(); i++)
{
if (eigval[i] > 0)
{
double omega = scale_factor * eigval_to_frequency(eigval[i]);
- double hwkT = (hbar * omega) / (BOLTZMANN * temperature);
+ double hwkT = (hbar * omega) / (gmx::c_boltzmann * temperature);
// Prevent overflow by checking for unreasonably large numbers.
if (hwkT < 100)
{
double dEvib = hwkT * (0.5 + 1.0 / (std::expm1(hwkT)));
if (debug)
{
- fprintf(debug, "i %d eigval %g omega %g hwkT %g dEvib %g\n",
- static_cast<int>(i + 1), static_cast<double>(eigval[i]), omega, hwkT, dEvib);
+ fprintf(debug,
+ "i %d eigval %g omega %g hwkT %g dEvib %g\n",
+ static_cast<int>(i + 1),
+ static_cast<double>(eigval[i]),
+ omega,
+ hwkT,
+ dEvib);
}
Evib += dEvib;
}
}
}
- return temperature * BOLTZ * Evib;
+ return temperature * gmx::c_boltz * Evib;
}
double calcVibrationalHeatCapacity(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear, real scale_factor)
{
size_t nskip = linear ? 5 : 6;
double cv = 0;
- double hbar = PLANCK1 / (2 * M_PI);
+ double hbar = gmx::c_planck1 / (2 * M_PI);
for (gmx::index i = nskip; i < eigval.ssize(); i++)
{
if (eigval[i] > 0)
{
double omega = scale_factor * eigval_to_frequency(eigval[i]);
- double hwkT = (hbar * omega) / (BOLTZMANN * temperature);
+ double hwkT = (hbar * omega) / (gmx::c_boltzmann * temperature);
// Prevent overflow by checking for unreasonably large numbers.
if (hwkT < 100)
{
double dcv = std::exp(hwkT) * gmx::square(hwkT / std::expm1(hwkT));
if (debug)
{
- fprintf(debug, "i %d eigval %g omega %g hwkT %g dcv %g\n",
- static_cast<int>(i + 1), static_cast<double>(eigval[i]), omega, hwkT, dcv);
+ fprintf(debug,
+ "i %d eigval %g omega %g hwkT %g dcv %g\n",
+ static_cast<int>(i + 1),
+ static_cast<double>(eigval[i]),
+ omega,
+ hwkT,
+ dcv);
}
cv += dcv;
}
}
}
- return RGAS * cv;
+ return gmx::c_universalGasConstant * cv;
}
double calcTranslationalEntropy(real mass, real temperature, real pressure)
{
- double kT = BOLTZ * temperature;
+ double kT = gmx::c_boltz * temperature;
GMX_RELEASE_ASSERT(mass > 0, "Molecular mass should be larger than zero");
GMX_RELEASE_ASSERT(pressure > 0, "Pressure should be larger than zero");
GMX_RELEASE_ASSERT(temperature > 0, "Temperature should be larger than zero");
// Convert bar to Pascal
- double P = pressure * 1e5;
- double qT = (std::pow(2 * M_PI * mass * kT / gmx::square(PLANCK), 1.5) * (kT / P) * (1e30 / AVOGADRO));
- return RGAS * (std::log(qT) + 2.5);
+ double P = pressure * 1e5;
+ double qT = (std::pow(2 * M_PI * mass * kT / gmx::square(gmx::c_planck), 1.5) * (kT / P)
+ * (1e30 / gmx::c_avogadro));
+ return gmx::c_universalGasConstant * (std::log(qT) + 2.5);
}
double calcRotationalEntropy(real temperature, int natom, gmx_bool linear, const rvec theta, real sigma_r)
{
GMX_RELEASE_ASSERT(theta[0] > 0, "Theta should be larger than zero");
double qR = temperature / (sigma_r * theta[0]);
- sR = RGAS * (std::log(qR) + 1);
+ sR = gmx::c_universalGasConstant * (std::log(qR) + 1);
}
else
{
double Q = theta[XX] * theta[YY] * theta[ZZ];
GMX_RELEASE_ASSERT(Q > 0, "Q should be larger than zero");
double qR = std::sqrt(M_PI * std::pow(temperature, 3) / Q) / sigma_r;
- sR = RGAS * (std::log(qR) + 1.5);
+ sR = gmx::c_universalGasConstant * (std::log(qR) + 1.5);
}
}
return sR;
{
size_t nskip = bLinear ? 5 : 6;
double S = 0;
- double hbar = PLANCK1 / (2 * M_PI);
+ double hbar = gmx::c_planck1 / (2 * M_PI);
for (gmx::index i = nskip; (i < eigval.ssize()); i++)
{
if (eigval[i] > 0)
{
double omega = scale_factor * eigval_to_frequency(eigval[i]);
- double hwkT = (hbar * omega) / (BOLTZMANN * temperature);
+ double hwkT = (hbar * omega) / (gmx::c_boltzmann * temperature);
double dS = (hwkT / std::expm1(hwkT) - std::log1p(-std::exp(-hwkT)));
S += dS;
if (debug)
{
- fprintf(debug, "i = %5d eigval = %10g w = %10g hwkT = %10g dS = %10g\n",
- static_cast<int>(i + 1), static_cast<double>(eigval[i]), omega, hwkT, dS);
+ fprintf(debug,
+ "i = %5d eigval = %10g w = %10g hwkT = %10g dS = %10g\n",
+ static_cast<int>(i + 1),
+ static_cast<double>(eigval[i]),
+ omega,
+ hwkT,
+ dS);
}
}
else if (debug)
fprintf(debug, "eigval[%d] = %g\n", static_cast<int>(i + 1), static_cast<double>(eigval[i]));
}
}
- return S * RGAS;
+ return S * gmx::c_universalGasConstant;
}
double calcSchlitterEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool bLinear)
{
size_t nskip = bLinear ? 5 : 6;
- double hbar = PLANCK1 / (2 * M_PI); // J s
- double kt = BOLTZMANN * temperature; // J
+ double hbar = gmx::c_planck1 / (2 * M_PI); // J s
+ double kt = gmx::c_boltzmann * temperature; // J
double kteh = kt * std::exp(2.0) / (hbar * hbar); // 1/(J s^2) = 1/(kg m^2)
- double evcorr = NANO * NANO * AMU;
+ double evcorr = gmx::c_nano * gmx::c_nano * gmx::c_amu;
if (debug)
{
fprintf(debug, "n = %td, kteh = %g evcorr = %g\n", ssize(eigval), kteh, evcorr);
double dd = 1 + kteh * eigval[i] * evcorr;
deter += std::log(dd);
}
- return 0.5 * RGAS * deter;
+ return 0.5 * gmx::c_universalGasConstant * deter;
}
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2009,2010,2012,2014,2015 by the GROMACS development team.
-# Copyright (c) 2016,2020, by the GROMACS development team, led by
+# Copyright (c) 2016,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+add_library(gmxlib INTERFACE)
+
add_subdirectory(nonbonded)
# The nonbonded directory contains subdirectories that are only
set(GMXLIB_SOURCES ${GMXLIB_SOURCES} ${NONBONDED_SOURCES} PARENT_SCOPE)
-# if(BUILD_TESTING)
-# add_subdirectory(tests)
-# endif()
+# Source files have the following private module dependencies.
+target_link_libraries(gmxlib PRIVATE
+ # gmxlib
+ # math
+ # mdtypes
+ # tng_io
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(gmxlib PUBLIC
+target_include_directories(gmxlib INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(gmxlib PUBLIC
+target_link_libraries(gmxlib INTERFACE
+ legacy_api
+ )
+
+# TODO: when fileio is an OBJECT target
+#target_link_libraries(gmxlib PUBLIC legacy_api)
+#target_link_libraries(gmxlib PRIVATE common)
+
+# Module dependencies
+# fileio interfaces convey transitive dependence on these modules.
+#target_link_libraries(gmxlib PUBLIC
+target_link_libraries(gmxlib INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(gmxlib PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(gmxlib PRIVATE legacy_modules)
+
+if(BUILD_TESTING)
+ add_subdirectory(nonbonded/tests)
+endif()
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
nc->bUse = TRUE;
if (fplog)
{
- fprintf(fplog, "Using two step summing over %d groups of on average %.1f ranks\n\n", ng,
+ fprintf(fplog,
+ "Using two step summing over %d groups of on average %.1f ranks\n\n",
+ ng,
(real)n / (real)ng);
}
if (nc->rank_intra > 0)
#if !GMX_MPI
GMX_RELEASE_ASSERT(false, "Invalid call to gmx_sumd");
#else
-# if MPI_IN_PLACE_EXISTS
if (cr->nc.bUse)
{
if (cr->nc.rank_intra == 0)
{
MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mygroup);
}
-# else
- int i;
-
- if (nr > cr->mpb->dbuf_alloc)
- {
- cr->mpb->dbuf_alloc = nr;
- srenew(cr->mpb->dbuf, cr->mpb->dbuf_alloc);
- }
- if (cr->nc.bUse)
- {
- /* Use two step summing */
- MPI_Allreduce(r, cr->mpb->dbuf, nr, MPI_DOUBLE, MPI_SUM, cr->nc.comm_intra);
- if (cr->nc.rank_intra == 0)
- {
- /* Sum with the buffers reversed */
- MPI_Allreduce(cr->mpb->dbuf, r, nr, MPI_DOUBLE, MPI_SUM, cr->nc.comm_inter);
- }
- MPI_Bcast(r, nr, MPI_DOUBLE, 0, cr->nc.comm_intra);
- }
- else
- {
- MPI_Allreduce(r, cr->mpb->dbuf, nr, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mygroup);
- for (i = 0; i < nr; i++)
- {
- r[i] = cr->mpb->dbuf[i];
- }
- }
-# endif
#endif
}
#if !GMX_MPI
GMX_RELEASE_ASSERT(false, "Invalid call to gmx_sumf");
#else
-# if MPI_IN_PLACE_EXISTS
if (cr->nc.bUse)
{
/* Use two step summing. */
{
MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_FLOAT, MPI_SUM, cr->mpi_comm_mygroup);
}
-# else
- int i;
-
- if (nr > cr->mpb->fbuf_alloc)
- {
- cr->mpb->fbuf_alloc = nr;
- srenew(cr->mpb->fbuf, cr->mpb->fbuf_alloc);
- }
- if (cr->nc.bUse)
- {
- /* Use two step summing */
- MPI_Allreduce(r, cr->mpb->fbuf, nr, MPI_FLOAT, MPI_SUM, cr->nc.comm_intra);
- if (cr->nc.rank_intra == 0)
- {
- /* Sum with the buffers reversed */
- MPI_Allreduce(cr->mpb->fbuf, r, nr, MPI_FLOAT, MPI_SUM, cr->nc.comm_inter);
- }
- MPI_Bcast(r, nr, MPI_FLOAT, 0, cr->nc.comm_intra);
- }
- else
- {
- MPI_Allreduce(r, cr->mpb->fbuf, nr, MPI_FLOAT, MPI_SUM, cr->mpi_comm_mygroup);
- for (i = 0; i < nr; i++)
- {
- r[i] = cr->mpb->fbuf[i];
- }
- }
-# endif
#endif
}
#if !GMX_MPI
GMX_RELEASE_ASSERT(false, "Invalid call to gmx_sumi");
#else
-# if MPI_IN_PLACE_EXISTS
if (cr->nc.bUse)
{
/* Use two step summing */
{
MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_INT, MPI_SUM, cr->mpi_comm_mygroup);
}
-# else
- int i;
-
- if (nr > cr->mpb->ibuf_alloc)
- {
- cr->mpb->ibuf_alloc = nr;
- srenew(cr->mpb->ibuf, cr->mpb->ibuf_alloc);
- }
- if (cr->nc.bUse)
- {
- /* Use two step summing */
- MPI_Allreduce(r, cr->mpb->ibuf, nr, MPI_INT, MPI_SUM, cr->nc.comm_intra);
- if (cr->nc.rank_intra == 0)
- {
- /* Sum with the buffers reversed */
- MPI_Allreduce(cr->mpb->ibuf, r, nr, MPI_INT, MPI_SUM, cr->nc.comm_inter);
- }
- MPI_Bcast(r, nr, MPI_INT, 0, cr->nc.comm_intra);
- }
- else
- {
- MPI_Allreduce(r, cr->mpb->ibuf, nr, MPI_INT, MPI_SUM, cr->mpi_comm_mygroup);
- for (i = 0; i < nr; i++)
- {
- r[i] = cr->mpb->ibuf[i];
- }
- }
-# endif
#endif
}
#if !GMX_MPI
GMX_RELEASE_ASSERT(false, "Invalid call to gmx_sumli");
#else
-# if MPI_IN_PLACE_EXISTS
if (cr->nc.bUse)
{
/* Use two step summing */
{
MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_INT64_T, MPI_SUM, cr->mpi_comm_mygroup);
}
-# else
- int i;
-
- if (nr > cr->mpb->libuf_alloc)
- {
- cr->mpb->libuf_alloc = nr;
- srenew(cr->mpb->libuf, cr->mpb->libuf_alloc);
- }
- if (cr->nc.bUse)
- {
- /* Use two step summing */
- MPI_Allreduce(r, cr->mpb->libuf, nr, MPI_INT64_T, MPI_SUM, cr->nc.comm_intra);
- if (cr->nc.rank_intra == 0)
- {
- /* Sum with the buffers reversed */
- MPI_Allreduce(cr->mpb->libuf, r, nr, MPI_INT64_T, MPI_SUM, cr->nc.comm_inter);
- }
- MPI_Bcast(r, nr, MPI_INT64_T, 0, cr->nc.comm_intra);
- }
- else
- {
- MPI_Allreduce(r, cr->mpb->libuf, nr, MPI_INT64_T, MPI_SUM, cr->mpi_comm_mygroup);
- for (i = 0; i < nr; i++)
- {
- r[i] = cr->mpb->libuf[i];
- }
- }
-# endif
#endif
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <algorithm>
#include "gromacs/gmxlib/nrnb.h"
-#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
#include "gromacs/gmxlib/nonbonded/nonbonded.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/mdtypes/nblist.h"
#include "gromacs/simd/simd.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/arrayref.h"
//! Scalar (non-SIMD) data types.
}
template<class RealType>
-static inline RealType calculateRinv6(const RealType rinvV)
+static inline RealType calculateRinv6(const RealType rInvV)
{
- RealType rinv6 = rinvV * rinvV;
- return (rinv6 * rinv6 * rinv6);
+ RealType rInv6 = rInvV * rInvV;
+ return (rInv6 * rInv6 * rInv6);
}
template<class RealType>
-static inline RealType calculateVdw6(const RealType c6, const RealType rinv6)
+static inline RealType calculateVdw6(const RealType c6, const RealType rInv6)
{
- return (c6 * rinv6);
+ return (c6 * rInv6);
}
template<class RealType>
-static inline RealType calculateVdw12(const RealType c12, const RealType rinv6)
+static inline RealType calculateVdw12(const RealType c12, const RealType rInv6)
{
- return (c12 * rinv6 * rinv6);
+ return (c12 * rInv6 * rInv6);
}
/* reaction-field electrostatics */
template<class RealType>
static inline RealType reactionFieldScalarForce(const RealType qq,
- const RealType rinv,
+ const RealType rInv,
const RealType r,
const real krf,
const real two)
{
- return (qq * (rinv - two * krf * r * r));
+ return (qq * (rInv - two * krf * r * r));
}
template<class RealType>
static inline RealType reactionFieldPotential(const RealType qq,
- const RealType rinv,
+ const RealType rInv,
const RealType r,
const real krf,
const real potentialShift)
{
- return (qq * (rinv + krf * r * r - potentialShift));
+ return (qq * (rInv + krf * r * r - potentialShift));
}
/* Ewald electrostatics */
template<class RealType>
-static inline RealType ewaldScalarForce(const RealType coulomb, const RealType rinv)
+static inline RealType ewaldScalarForce(const RealType coulomb, const RealType rInv)
{
- return (coulomb * rinv);
+ return (coulomb * rInv);
}
template<class RealType>
-static inline RealType ewaldPotential(const RealType coulomb, const RealType rinv, const real potentialShift)
+static inline RealType ewaldPotential(const RealType coulomb, const RealType rInv, const real potentialShift)
{
- return (coulomb * (rinv - potentialShift));
+ return (coulomb * (rInv - potentialShift));
}
/* cutoff LJ */
const RealType c12,
const real repulsionShift,
const real dispersionShift,
- const real onesixth,
- const real onetwelfth)
+ const real oneSixth,
+ const real oneTwelfth)
{
- return ((v12 + c12 * repulsionShift) * onetwelfth - (v6 + c6 * dispersionShift) * onesixth);
+ return ((v12 + c12 * repulsionShift) * oneTwelfth - (v6 + c6 * dispersionShift) * oneSixth);
}
/* Ewald LJ */
-static inline real ewaldLennardJonesGridSubtract(const real c6grid, const real potentialShift, const real onesixth)
+static inline real ewaldLennardJonesGridSubtract(const real c6grid, const real potentialShift, const real oneSixth)
{
- return (c6grid * potentialShift * onesixth);
+ return (c6grid * potentialShift * oneSixth);
}
/* LJ Potential switch */
//! Templated free-energy non-bonded kernel
template<typename DataTypes, bool useSoftCore, bool scLambdasOrAlphasDiffer, bool vdwInteractionTypeIsEwald, bool elecInteractionTypeIsEwald, bool vdwModifierIsPotSwitch>
-static void nb_free_energy_kernel(const t_nblist* gmx_restrict nlist,
- rvec* gmx_restrict xx,
- gmx::ForceWithShiftForces* forceWithShiftForces,
- const t_forcerec* gmx_restrict fr,
- const t_mdatoms* gmx_restrict mdatoms,
- nb_kernel_data_t* gmx_restrict kernel_data,
+static void nb_free_energy_kernel(const t_nblist& nlist,
+ gmx::ArrayRef<const gmx::RVec> coords,
+ gmx::ForceWithShiftForces* forceWithShiftForces,
+ const int ntype,
+ const real rlist,
+ const interaction_const_t& ic,
+ gmx::ArrayRef<const gmx::RVec> shiftvec,
+ gmx::ArrayRef<const real> nbfp,
+ gmx::ArrayRef<const real> nbfp_grid,
+ gmx::ArrayRef<const real> chargeA,
+ gmx::ArrayRef<const real> chargeB,
+ gmx::ArrayRef<const int> typeA,
+ gmx::ArrayRef<const int> typeB,
+ int flags,
+ gmx::ArrayRef<const real> lambda,
+ gmx::ArrayRef<real> dvdl,
+ gmx::ArrayRef<real> energygrp_elec,
+ gmx::ArrayRef<real> energygrp_vdw,
t_nrnb* gmx_restrict nrnb)
{
#define STATE_A 0
using IntType = typename DataTypes::IntType;
/* FIXME: How should these be handled with SIMD? */
- constexpr real onetwelfth = 1.0 / 12.0;
- constexpr real onesixth = 1.0 / 6.0;
+ constexpr real oneTwelfth = 1.0 / 12.0;
+ constexpr real oneSixth = 1.0 / 6.0;
constexpr real zero = 0.0;
constexpr real half = 0.5;
constexpr real one = 1.0;
constexpr real two = 2.0;
constexpr real six = 6.0;
- /* Extract pointer to non-bonded interaction constants */
- const interaction_const_t* ic = fr->ic;
-
// Extract pair list data
- const int nri = nlist->nri;
- const int* iinr = nlist->iinr;
- const int* jindex = nlist->jindex;
- const int* jjnr = nlist->jjnr;
- const int* shift = nlist->shift;
- const int* gid = nlist->gid;
-
- const real* shiftvec = fr->shift_vec[0];
- const real* chargeA = mdatoms->chargeA;
- const real* chargeB = mdatoms->chargeB;
- real* Vc = kernel_data->energygrp_elec;
- const int* typeA = mdatoms->typeA;
- const int* typeB = mdatoms->typeB;
- const int ntype = fr->ntype;
- const real* nbfp = fr->nbfp.data();
- const real* nbfp_grid = fr->ljpme_c6grid;
- real* Vv = kernel_data->energygrp_vdw;
- const real lambda_coul = kernel_data->lambda[efptCOUL];
- const real lambda_vdw = kernel_data->lambda[efptVDW];
- real* dvdl = kernel_data->dvdl;
- const auto& scParams = *ic->softCoreParameters;
+ const int nri = nlist.nri;
+ gmx::ArrayRef<const int> iinr = nlist.iinr;
+ gmx::ArrayRef<const int> jindex = nlist.jindex;
+ gmx::ArrayRef<const int> jjnr = nlist.jjnr;
+ gmx::ArrayRef<const int> shift = nlist.shift;
+ gmx::ArrayRef<const int> gid = nlist.gid;
+
+ const real lambda_coul = lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)];
+ const real lambda_vdw = lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)];
+ const auto& scParams = *ic.softCoreParameters;
const real alpha_coul = scParams.alphaCoulomb;
const real alpha_vdw = scParams.alphaVdw;
const real lam_power = scParams.lambdaPower;
const real sigma6_def = scParams.sigma6WithInvalidSigma;
const real sigma6_min = scParams.sigma6Minimum;
- const bool doForces = ((kernel_data->flags & GMX_NONBONDED_DO_FORCE) != 0);
- const bool doShiftForces = ((kernel_data->flags & GMX_NONBONDED_DO_SHIFTFORCE) != 0);
- const bool doPotential = ((kernel_data->flags & GMX_NONBONDED_DO_POTENTIAL) != 0);
+ const bool doForces = ((flags & GMX_NONBONDED_DO_FORCE) != 0);
+ const bool doShiftForces = ((flags & GMX_NONBONDED_DO_SHIFTFORCE) != 0);
+ const bool doPotential = ((flags & GMX_NONBONDED_DO_POTENTIAL) != 0);
// Extract data from interaction_const_t
- const real facel = ic->epsfac;
- const real rcoulomb = ic->rcoulomb;
- const real krf = ic->k_rf;
- const real crf = ic->c_rf;
- const real sh_lj_ewald = ic->sh_lj_ewald;
- const real rvdw = ic->rvdw;
- const real dispersionShift = ic->dispersion_shift.cpot;
- const real repulsionShift = ic->repulsion_shift.cpot;
+ const real facel = ic.epsfac;
+ const real rCoulomb = ic.rcoulomb;
+ const real krf = ic.reactionFieldCoefficient;
+ const real crf = ic.reactionFieldShift;
+ const real shLjEwald = ic.sh_lj_ewald;
+ const real rVdw = ic.rvdw;
+ const real dispersionShift = ic.dispersion_shift.cpot;
+ const real repulsionShift = ic.repulsion_shift.cpot;
// Note that the nbnxm kernels do not support Coulomb potential switching at all
- GMX_ASSERT(ic->coulomb_modifier != eintmodPOTSWITCH,
+ GMX_ASSERT(ic.coulomb_modifier != InteractionModifiers::PotSwitch,
"Potential switching is not supported for Coulomb with FEP");
real vdw_swV3, vdw_swV4, vdw_swV5, vdw_swF2, vdw_swF3, vdw_swF4;
if (vdwModifierIsPotSwitch)
{
- const real d = ic->rvdw - ic->rvdw_switch;
+ const real d = ic.rvdw - ic.rvdw_switch;
vdw_swV3 = -10.0 / (d * d * d);
vdw_swV4 = 15.0 / (d * d * d * d);
vdw_swV5 = -6.0 / (d * d * d * d * d);
vdw_swV3 = vdw_swV4 = vdw_swV5 = vdw_swF2 = vdw_swF3 = vdw_swF4 = 0.0;
}
- int icoul;
- if (ic->eeltype == eelCUT || EEL_RF(ic->eeltype))
+ NbkernelElecType icoul;
+ if (ic.eeltype == CoulombInteractionType::Cut || EEL_RF(ic.eeltype))
{
- icoul = GMX_NBKERNEL_ELEC_REACTIONFIELD;
+ icoul = NbkernelElecType::ReactionField;
}
else
{
- icoul = GMX_NBKERNEL_ELEC_NONE;
+ icoul = NbkernelElecType::None;
}
- real rcutoff_max2 = std::max(ic->rcoulomb, ic->rvdw);
+ real rcutoff_max2 = std::max(ic.rcoulomb, ic.rvdw);
rcutoff_max2 = rcutoff_max2 * rcutoff_max2;
const real* tab_ewald_F_lj = nullptr;
real sh_ewald = 0;
if (elecInteractionTypeIsEwald || vdwInteractionTypeIsEwald)
{
- sh_ewald = ic->sh_ewald;
+ sh_ewald = ic.sh_ewald;
}
if (elecInteractionTypeIsEwald)
{
- const auto& coulombTables = *ic->coulombEwaldTables;
+ const auto& coulombTables = *ic.coulombEwaldTables;
ewtab = coulombTables.tableFDV0.data();
coulombTableScale = coulombTables.scale;
coulombTableScaleInvHalf = half / coulombTableScale;
}
if (vdwInteractionTypeIsEwald)
{
- const auto& vdwTables = *ic->vdwEwaldTables;
+ const auto& vdwTables = *ic.vdwEwaldTables;
tab_ewald_F_lj = vdwTables.tableF.data();
tab_ewald_V_lj = vdwTables.tableV.data();
vdwTableScale = vdwTables.scale;
GMX_RELEASE_ASSERT(!(vdwInteractionTypeIsEwald && vdwModifierIsPotSwitch),
"Can not apply soft-core to switched Ewald potentials");
- real dvdl_coul = 0;
- real dvdl_vdw = 0;
+ real dvdlCoul = 0;
+ real dvdlVdw = 0;
/* Lambda factor for state A, 1-lambda*/
real LFC[NSTATES], LFV[NSTATES];
DLF[STATE_A] = -1;
DLF[STATE_B] = 1;
- real lfac_coul[NSTATES], dlfac_coul[NSTATES], lfac_vdw[NSTATES], dlfac_vdw[NSTATES];
+ real lFacCoul[NSTATES], dlFacCoul[NSTATES], lFacVdw[NSTATES], dlFacVdw[NSTATES];
constexpr real sc_r_power = 6.0_real;
for (int i = 0; i < NSTATES; i++)
{
- lfac_coul[i] = (lam_power == 2 ? (1 - LFC[i]) * (1 - LFC[i]) : (1 - LFC[i]));
- dlfac_coul[i] = DLF[i] * lam_power / sc_r_power * (lam_power == 2 ? (1 - LFC[i]) : 1);
- lfac_vdw[i] = (lam_power == 2 ? (1 - LFV[i]) * (1 - LFV[i]) : (1 - LFV[i]));
- dlfac_vdw[i] = DLF[i] * lam_power / sc_r_power * (lam_power == 2 ? (1 - LFV[i]) : 1);
+ lFacCoul[i] = (lam_power == 2 ? (1 - LFC[i]) * (1 - LFC[i]) : (1 - LFC[i]));
+ dlFacCoul[i] = DLF[i] * lam_power / sc_r_power * (lam_power == 2 ? (1 - LFC[i]) : 1);
+ lFacVdw[i] = (lam_power == 2 ? (1 - LFV[i]) * (1 - LFV[i]) : (1 - LFV[i]));
+ dlFacVdw[i] = DLF[i] * lam_power / sc_r_power * (lam_power == 2 ? (1 - LFV[i]) : 1);
}
// TODO: We should get rid of using pointers to real
- const real* x = xx[0];
+ const real* x = coords[0];
real* gmx_restrict f = &(forceWithShiftForces->force()[0][0]);
real* gmx_restrict fshift = &(forceWithShiftForces->shiftForces()[0][0]);
- const real rlistSquared = gmx::square(fr->rlist);
+ const real rlistSquared = gmx::square(rlist);
int numExcludedPairsBeyondRlist = 0;
{
int npair_within_cutoff = 0;
- const int is3 = 3 * shift[n];
- const real shX = shiftvec[is3];
- const real shY = shiftvec[is3 + 1];
- const real shZ = shiftvec[is3 + 2];
+ const int is = shift[n];
+ const int is3 = DIM * is;
+ const real shX = shiftvec[is][XX];
+ const real shY = shiftvec[is][YY];
+ const real shZ = shiftvec[is][ZZ];
const int nj0 = jindex[n];
const int nj1 = jindex[n + 1];
const int ii = iinr[n];
const real iqB = facel * chargeB[ii];
const int ntiA = 2 * ntype * typeA[ii];
const int ntiB = 2 * ntype * typeB[ii];
- real vctot = 0;
- real vvtot = 0;
- real fix = 0;
- real fiy = 0;
- real fiz = 0;
+ real vCTot = 0;
+ real vVTot = 0;
+ real fIX = 0;
+ real fIY = 0;
+ real fIZ = 0;
for (int k = nj0; k < nj1; k++)
{
int tj[NSTATES];
const int jnr = jjnr[k];
const int j3 = 3 * jnr;
- RealType c6[NSTATES], c12[NSTATES], qq[NSTATES], Vcoul[NSTATES], Vvdw[NSTATES];
- RealType r, rinv, rp, rpm2;
- RealType alpha_vdw_eff, alpha_coul_eff, sigma6[NSTATES];
- const RealType dx = ix - x[j3];
- const RealType dy = iy - x[j3 + 1];
- const RealType dz = iz - x[j3 + 2];
- const RealType rsq = dx * dx + dy * dy + dz * dz;
- RealType FscalC[NSTATES], FscalV[NSTATES];
+ RealType c6[NSTATES], c12[NSTATES], qq[NSTATES], vCoul[NSTATES], vVdw[NSTATES];
+ RealType r, rInv, rp, rpm2;
+ RealType alphaVdwEff, alphaCoulEff, sigma6[NSTATES];
+ const RealType dX = ix - x[j3];
+ const RealType dY = iy - x[j3 + 1];
+ const RealType dZ = iz - x[j3 + 2];
+ const RealType rSq = dX * dX + dY * dY + dZ * dZ;
+ RealType fScalC[NSTATES], fScalV[NSTATES];
/* Check if this pair on the exlusions list.*/
- const bool bPairIncluded = nlist->excl_fep == nullptr || nlist->excl_fep[k];
+ const bool bPairIncluded = nlist.excl_fep.empty() || nlist.excl_fep[k];
- if (rsq >= rcutoff_max2 && bPairIncluded)
+ if (rSq >= rcutoff_max2 && bPairIncluded)
{
/* We save significant time by skipping all code below.
* Note that with soft-core interactions, the actual cut-off
}
npair_within_cutoff++;
- if (rsq > rlistSquared)
+ if (rSq > rlistSquared)
{
numExcludedPairsBeyondRlist++;
}
- if (rsq > 0)
+ if (rSq > 0)
{
/* Note that unlike in the nbnxn kernels, we do not need
- * to clamp the value of rsq before taking the invsqrt
+ * to clamp the value of rSq before taking the invsqrt
* to avoid NaN in the LJ calculation, since here we do
* not calculate LJ interactions when C6 and C12 are zero.
*/
- rinv = gmx::invsqrt(rsq);
- r = rsq * rinv;
+ rInv = gmx::invsqrt(rSq);
+ r = rSq * rInv;
}
else
{
* But note that the potential is in general non-zero,
* since the soft-cored r will be non-zero.
*/
- rinv = 0;
+ rInv = 0;
r = 0;
}
if (useSoftCore)
{
- rpm2 = rsq * rsq; /* r4 */
- rp = rpm2 * rsq; /* r6 */
+ rpm2 = rSq * rSq; /* r4 */
+ rp = rpm2 * rSq; /* r6 */
}
else
{
* with not using soft-core, so we use power of 0 which gives
* the simplest math and cheapest code.
*/
- rpm2 = rinv * rinv;
+ rpm2 = rInv * rInv;
rp = 1;
}
- RealType Fscal = 0;
+ RealType fScal = 0;
qq[STATE_A] = iqA * chargeA[jnr];
qq[STATE_B] = iqB * chargeB[jnr];
/* only use softcore if one of the states has a zero endstate - softcore is for avoiding infinities!*/
if ((c12[STATE_A] > 0) && (c12[STATE_B] > 0))
{
- alpha_vdw_eff = 0;
- alpha_coul_eff = 0;
+ alphaVdwEff = 0;
+ alphaCoulEff = 0;
}
else
{
- alpha_vdw_eff = alpha_vdw;
- alpha_coul_eff = alpha_coul;
+ alphaVdwEff = alpha_vdw;
+ alphaCoulEff = alpha_coul;
}
}
for (int i = 0; i < NSTATES; i++)
{
- FscalC[i] = 0;
- FscalV[i] = 0;
- Vcoul[i] = 0;
- Vvdw[i] = 0;
+ fScalC[i] = 0;
+ fScalV[i] = 0;
+ vCoul[i] = 0;
+ vVdw[i] = 0;
- RealType rinvC, rinvV, rC, rV, rpinvC, rpinvV;
+ RealType rInvC, rInvV, rC, rV, rPInvC, rPInvV;
/* Only spend time on A or B state if it is non-zero */
if ((qq[i] != 0) || (c6[i] != 0) || (c12[i] != 0))
/* this section has to be inside the loop because of the dependence on sigma6 */
if (useSoftCore)
{
- rpinvC = one / (alpha_coul_eff * lfac_coul[i] * sigma6[i] + rp);
- pthRoot(rpinvC, &rinvC, &rC);
+ rPInvC = one / (alphaCoulEff * lFacCoul[i] * sigma6[i] + rp);
+ pthRoot(rPInvC, &rInvC, &rC);
if (scLambdasOrAlphasDiffer)
{
- rpinvV = one / (alpha_vdw_eff * lfac_vdw[i] * sigma6[i] + rp);
- pthRoot(rpinvV, &rinvV, &rV);
+ rPInvV = one / (alphaVdwEff * lFacVdw[i] * sigma6[i] + rp);
+ pthRoot(rPInvV, &rInvV, &rV);
}
else
{
/* We can avoid one expensive pow and one / operation */
- rpinvV = rpinvC;
- rinvV = rinvC;
+ rPInvV = rPInvC;
+ rInvV = rInvC;
rV = rC;
}
}
else
{
- rpinvC = 1;
- rinvC = rinv;
+ rPInvC = 1;
+ rInvC = rInv;
rC = r;
- rpinvV = 1;
- rinvV = rinv;
+ rPInvV = 1;
+ rInvV = rInv;
rV = r;
}
* and if we either include all entries in the list (no cutoff
* used in the kernel), or if we are within the cutoff.
*/
- bool computeElecInteraction = (elecInteractionTypeIsEwald && r < rcoulomb)
- || (!elecInteractionTypeIsEwald && rC < rcoulomb);
+ bool computeElecInteraction = (elecInteractionTypeIsEwald && r < rCoulomb)
+ || (!elecInteractionTypeIsEwald && rC < rCoulomb);
if ((qq[i] != 0) && computeElecInteraction)
{
if (elecInteractionTypeIsEwald)
{
- Vcoul[i] = ewaldPotential(qq[i], rinvC, sh_ewald);
- FscalC[i] = ewaldScalarForce(qq[i], rinvC);
+ vCoul[i] = ewaldPotential(qq[i], rInvC, sh_ewald);
+ fScalC[i] = ewaldScalarForce(qq[i], rInvC);
}
else
{
- Vcoul[i] = reactionFieldPotential(qq[i], rinvC, rC, krf, crf);
- FscalC[i] = reactionFieldScalarForce(qq[i], rinvC, rC, krf, two);
+ vCoul[i] = reactionFieldPotential(qq[i], rInvC, rC, krf, crf);
+ fScalC[i] = reactionFieldScalarForce(qq[i], rInvC, rC, krf, two);
}
}
* include all entries in the list (no cutoff used
* in the kernel), or if we are within the cutoff.
*/
- bool computeVdwInteraction = (vdwInteractionTypeIsEwald && r < rvdw)
- || (!vdwInteractionTypeIsEwald && rV < rvdw);
+ bool computeVdwInteraction = (vdwInteractionTypeIsEwald && r < rVdw)
+ || (!vdwInteractionTypeIsEwald && rV < rVdw);
if ((c6[i] != 0 || c12[i] != 0) && computeVdwInteraction)
{
- RealType rinv6;
+ RealType rInv6;
if (useSoftCore)
{
- rinv6 = rpinvV;
+ rInv6 = rPInvV;
}
else
{
- rinv6 = calculateRinv6(rinvV);
+ rInv6 = calculateRinv6(rInvV);
}
- RealType Vvdw6 = calculateVdw6(c6[i], rinv6);
- RealType Vvdw12 = calculateVdw12(c12[i], rinv6);
+ RealType vVdw6 = calculateVdw6(c6[i], rInv6);
+ RealType vVdw12 = calculateVdw12(c12[i], rInv6);
- Vvdw[i] = lennardJonesPotential(Vvdw6, Vvdw12, c6[i], c12[i], repulsionShift,
- dispersionShift, onesixth, onetwelfth);
- FscalV[i] = lennardJonesScalarForce(Vvdw6, Vvdw12);
+ vVdw[i] = lennardJonesPotential(
+ vVdw6, vVdw12, c6[i], c12[i], repulsionShift, dispersionShift, oneSixth, oneTwelfth);
+ fScalV[i] = lennardJonesScalarForce(vVdw6, vVdw12);
if (vdwInteractionTypeIsEwald)
{
/* Subtract the grid potential at the cut-off */
- Vvdw[i] += ewaldLennardJonesGridSubtract(nbfp_grid[tj[i]],
- sh_lj_ewald, onesixth);
+ vVdw[i] += ewaldLennardJonesGridSubtract(
+ nbfp_grid[tj[i]], shLjEwald, oneSixth);
}
if (vdwModifierIsPotSwitch)
{
- RealType d = rV - ic->rvdw_switch;
+ RealType d = rV - ic.rvdw_switch;
d = (d > zero) ? d : zero;
const RealType d2 = d * d;
const RealType sw =
one + d2 * d * (vdw_swV3 + d * (vdw_swV4 + d * vdw_swV5));
const RealType dsw = d2 * (vdw_swF2 + d * (vdw_swF3 + d * vdw_swF4));
- FscalV[i] = potSwitchScalarForceMod(FscalV[i], Vvdw[i], sw, rV,
- rvdw, dsw, zero);
- Vvdw[i] = potSwitchPotentialMod(Vvdw[i], sw, rV, rvdw, zero);
+ fScalV[i] = potSwitchScalarForceMod(
+ fScalV[i], vVdw[i], sw, rV, rVdw, dsw, zero);
+ vVdw[i] = potSwitchPotentialMod(vVdw[i], sw, rV, rVdw, zero);
}
}
- /* FscalC (and FscalV) now contain: dV/drC * rC
+ /* fScalC (and fScalV) now contain: dV/drC * rC
* Now we multiply by rC^-p, so it will be: dV/drC * rC^1-p
* Further down we first multiply by r^p-2 and then by
* the vector r, which in total gives: dV/drC * (r/rC)^1-p
*/
- FscalC[i] *= rpinvC;
- FscalV[i] *= rpinvV;
+ fScalC[i] *= rPInvC;
+ fScalV[i] *= rPInvV;
}
} // end for (int i = 0; i < NSTATES; i++)
/* Assemble A and B states */
for (int i = 0; i < NSTATES; i++)
{
- vctot += LFC[i] * Vcoul[i];
- vvtot += LFV[i] * Vvdw[i];
+ vCTot += LFC[i] * vCoul[i];
+ vVTot += LFV[i] * vVdw[i];
- Fscal += LFC[i] * FscalC[i] * rpm2;
- Fscal += LFV[i] * FscalV[i] * rpm2;
+ fScal += LFC[i] * fScalC[i] * rpm2;
+ fScal += LFV[i] * fScalV[i] * rpm2;
if (useSoftCore)
{
- dvdl_coul += Vcoul[i] * DLF[i]
- + LFC[i] * alpha_coul_eff * dlfac_coul[i] * FscalC[i] * sigma6[i];
- dvdl_vdw += Vvdw[i] * DLF[i]
- + LFV[i] * alpha_vdw_eff * dlfac_vdw[i] * FscalV[i] * sigma6[i];
+ dvdlCoul += vCoul[i] * DLF[i]
+ + LFC[i] * alphaCoulEff * dlFacCoul[i] * fScalC[i] * sigma6[i];
+ dvdlVdw += vVdw[i] * DLF[i]
+ + LFV[i] * alphaVdwEff * dlFacVdw[i] * fScalV[i] * sigma6[i];
}
else
{
- dvdl_coul += Vcoul[i] * DLF[i];
- dvdl_vdw += Vvdw[i] * DLF[i];
+ dvdlCoul += vCoul[i] * DLF[i];
+ dvdlVdw += vVdw[i] * DLF[i];
}
}
} // end if (bPairIncluded)
- else if (icoul == GMX_NBKERNEL_ELEC_REACTIONFIELD)
+ else if (icoul == NbkernelElecType::ReactionField)
{
/* For excluded pairs, which are only in this pair list when
* using the Verlet scheme, we don't use soft-core.
* As there is no singularity, there is no need for soft-core.
*/
const real FF = -two * krf;
- RealType VV = krf * rsq - crf;
+ RealType VV = krf * rSq - crf;
if (ii == jnr)
{
for (int i = 0; i < NSTATES; i++)
{
- vctot += LFC[i] * qq[i] * VV;
- Fscal += LFC[i] * qq[i] * FF;
- dvdl_coul += DLF[i] * qq[i] * VV;
+ vCTot += LFC[i] * qq[i] * VV;
+ fScal += LFC[i] * qq[i] * FF;
+ dvdlCoul += DLF[i] * qq[i] * VV;
}
}
- if (elecInteractionTypeIsEwald && (r < rcoulomb || !bPairIncluded))
+ if (elecInteractionTypeIsEwald && (r < rCoulomb || !bPairIncluded))
{
/* See comment in the preamble. When using Ewald interactions
* (unless we use a switch modifier) we subtract the reciprocal-space
ewitab = 4 * ewitab;
f_lr = ewtab[ewitab] + eweps * ewtab[ewitab + 1];
v_lr = (ewtab[ewitab + 2] - coulombTableScaleInvHalf * eweps * (ewtab[ewitab] + f_lr));
- f_lr *= rinv;
+ f_lr *= rInv;
/* Note that any possible Ewald shift has already been applied in
* the normal interaction part above.
for (int i = 0; i < NSTATES; i++)
{
- vctot -= LFC[i] * qq[i] * v_lr;
- Fscal -= LFC[i] * qq[i] * f_lr;
- dvdl_coul -= (DLF[i] * qq[i]) * v_lr;
+ vCTot -= LFC[i] * qq[i] * v_lr;
+ fScal -= LFC[i] * qq[i] * f_lr;
+ dvdlCoul -= (DLF[i] * qq[i]) * v_lr;
}
}
- if (vdwInteractionTypeIsEwald && (r < rvdw || !bPairIncluded))
+ if (vdwInteractionTypeIsEwald && (r < rVdw || !bPairIncluded))
{
/* See comment in the preamble. When using LJ-Ewald interactions
* (unless we use a switch modifier) we subtract the reciprocal-space
* r close to 0 for non-interacting pairs.
*/
- const RealType rs = rsq * rinv * vdwTableScale;
+ const RealType rs = rSq * rInv * vdwTableScale;
const IntType ri = static_cast<IntType>(rs);
const RealType frac = rs - ri;
const RealType f_lr = (1 - frac) * tab_ewald_F_lj[ri] + frac * tab_ewald_F_lj[ri + 1];
/* TODO: Currently the Ewald LJ table does not contain
* the factor 1/6, we should add this.
*/
- const RealType FF = f_lr * rinv / six;
+ const RealType FF = f_lr * rInv / six;
RealType VV =
(tab_ewald_V_lj[ri] - vdwTableScaleInvHalf * frac * (tab_ewald_F_lj[ri] + f_lr))
/ six;
for (int i = 0; i < NSTATES; i++)
{
const real c6grid = nbfp_grid[tj[i]];
- vvtot += LFV[i] * c6grid * VV;
- Fscal += LFV[i] * c6grid * FF;
- dvdl_vdw += (DLF[i] * c6grid) * VV;
+ vVTot += LFV[i] * c6grid * VV;
+ fScal += LFV[i] * c6grid * FF;
+ dvdlVdw += (DLF[i] * c6grid) * VV;
}
}
if (doForces)
{
- const real tx = Fscal * dx;
- const real ty = Fscal * dy;
- const real tz = Fscal * dz;
- fix = fix + tx;
- fiy = fiy + ty;
- fiz = fiz + tz;
+ const real tX = fScal * dX;
+ const real tY = fScal * dY;
+ const real tZ = fScal * dZ;
+ fIX = fIX + tX;
+ fIY = fIY + tY;
+ fIZ = fIZ + tZ;
/* OpenMP atomics are expensive, but this kernels is also
* expensive, so we can take this hit, instead of using
* thread-local output buffers and extra reduction.
* not throw, so no need for try/catch.
*/
#pragma omp atomic
- f[j3] -= tx;
+ f[j3] -= tX;
#pragma omp atomic
- f[j3 + 1] -= ty;
+ f[j3 + 1] -= tY;
#pragma omp atomic
- f[j3 + 2] -= tz;
+ f[j3 + 2] -= tZ;
}
} // end for (int k = nj0; k < nj1; k++)
if (doForces)
{
#pragma omp atomic
- f[ii3] += fix;
+ f[ii3] += fIX;
#pragma omp atomic
- f[ii3 + 1] += fiy;
+ f[ii3 + 1] += fIY;
#pragma omp atomic
- f[ii3 + 2] += fiz;
+ f[ii3 + 2] += fIZ;
}
if (doShiftForces)
{
#pragma omp atomic
- fshift[is3] += fix;
+ fshift[is3] += fIX;
#pragma omp atomic
- fshift[is3 + 1] += fiy;
+ fshift[is3 + 1] += fIY;
#pragma omp atomic
- fshift[is3 + 2] += fiz;
+ fshift[is3 + 2] += fIZ;
}
if (doPotential)
{
int ggid = gid[n];
#pragma omp atomic
- Vc[ggid] += vctot;
+ energygrp_elec[ggid] += vCTot;
#pragma omp atomic
- Vv[ggid] += vvtot;
+ energygrp_vdw[ggid] += vVTot;
}
}
} // end for (int n = 0; n < nri; n++)
#pragma omp atomic
- dvdl[efptCOUL] += dvdl_coul;
+ dvdl[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)] += dvdlCoul;
#pragma omp atomic
- dvdl[efptVDW] += dvdl_vdw;
+ dvdl[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)] += dvdlVdw;
/* Estimate flops, average for free energy stuff:
* 12 flops per outer iteration
* 150 flops per inner iteration
*/
-#pragma omp atomic
- inc_nrnb(nrnb, eNR_NBKERNEL_FREE_ENERGY, nlist->nri * 12 + nlist->jindex[nri] * 150);
+ atomicNrnbIncrement(nrnb, eNR_NBKERNEL_FREE_ENERGY, nlist.nri * 12 + nlist.jindex[nri] * 150);
if (numExcludedPairsBeyondRlist > 0)
{
"latter is the case, you can try to increase nstlist or rlist to avoid this."
"The error is likely triggered by the use of couple-intramol=no "
"and the maximal distance in the decoupled molecule exceeding rlist.",
- numExcludedPairsBeyondRlist, fr->rlist);
+ numExcludedPairsBeyondRlist,
+ rlist);
}
}
-typedef void (*KernelFunction)(const t_nblist* gmx_restrict nlist,
- rvec* gmx_restrict xx,
- gmx::ForceWithShiftForces* forceWithShiftForces,
- const t_forcerec* gmx_restrict fr,
- const t_mdatoms* gmx_restrict mdatoms,
- nb_kernel_data_t* gmx_restrict kernel_data,
+typedef void (*KernelFunction)(const t_nblist& nlist,
+ gmx::ArrayRef<const gmx::RVec> coords,
+ gmx::ForceWithShiftForces* forceWithShiftForces,
+ const int ntype,
+ const real rlist,
+ const interaction_const_t& ic,
+ gmx::ArrayRef<const gmx::RVec> shiftvec,
+ gmx::ArrayRef<const real> nbfp,
+ gmx::ArrayRef<const real> nbfp_grid,
+ gmx::ArrayRef<const real> chargeA,
+ gmx::ArrayRef<const real> chargeB,
+ gmx::ArrayRef<const int> typeA,
+ gmx::ArrayRef<const int> typeB,
+ int flags,
+ gmx::ArrayRef<const real> lambda,
+ gmx::ArrayRef<real> dvdl,
+ gmx::ArrayRef<real> energygrp_elec,
+ gmx::ArrayRef<real> energygrp_vdw,
t_nrnb* gmx_restrict nrnb);
template<bool useSoftCore, bool scLambdasOrAlphasDiffer, bool vdwInteractionTypeIsEwald, bool elecInteractionTypeIsEwald, bool vdwModifierIsPotSwitch>
{
#if GMX_SIMD_HAVE_REAL && GMX_SIMD_HAVE_INT32_ARITHMETICS && GMX_USE_SIMD_KERNELS
/* FIXME: Here SimdDataTypes should be used to enable SIMD. So far, the code in nb_free_energy_kernel is not adapted to SIMD */
- return (nb_free_energy_kernel<ScalarDataTypes, useSoftCore, scLambdasOrAlphasDiffer, vdwInteractionTypeIsEwald,
- elecInteractionTypeIsEwald, vdwModifierIsPotSwitch>);
+ return (nb_free_energy_kernel<ScalarDataTypes, useSoftCore, scLambdasOrAlphasDiffer, vdwInteractionTypeIsEwald, elecInteractionTypeIsEwald, vdwModifierIsPotSwitch>);
#else
- return (nb_free_energy_kernel<ScalarDataTypes, useSoftCore, scLambdasOrAlphasDiffer, vdwInteractionTypeIsEwald,
- elecInteractionTypeIsEwald, vdwModifierIsPotSwitch>);
+ return (nb_free_energy_kernel<ScalarDataTypes, useSoftCore, scLambdasOrAlphasDiffer, vdwInteractionTypeIsEwald, elecInteractionTypeIsEwald, vdwModifierIsPotSwitch>);
#endif
}
else
{
- return (nb_free_energy_kernel<ScalarDataTypes, useSoftCore, scLambdasOrAlphasDiffer, vdwInteractionTypeIsEwald,
- elecInteractionTypeIsEwald, vdwModifierIsPotSwitch>);
+ return (nb_free_energy_kernel<ScalarDataTypes, useSoftCore, scLambdasOrAlphasDiffer, vdwInteractionTypeIsEwald, elecInteractionTypeIsEwald, vdwModifierIsPotSwitch>);
}
}
{
if (vdwModifierIsPotSwitch)
{
- return (dispatchKernelOnUseSimd<useSoftCore, scLambdasOrAlphasDiffer, vdwInteractionTypeIsEwald,
- elecInteractionTypeIsEwald, true>(useSimd));
+ return (dispatchKernelOnUseSimd<useSoftCore, scLambdasOrAlphasDiffer, vdwInteractionTypeIsEwald, elecInteractionTypeIsEwald, true>(
+ useSimd));
}
else
{
- return (dispatchKernelOnUseSimd<useSoftCore, scLambdasOrAlphasDiffer, vdwInteractionTypeIsEwald,
- elecInteractionTypeIsEwald, false>(useSimd));
+ return (dispatchKernelOnUseSimd<useSoftCore, scLambdasOrAlphasDiffer, vdwInteractionTypeIsEwald, elecInteractionTypeIsEwald, false>(
+ useSimd));
}
}
{
if (ic.softCoreParameters->alphaCoulomb == 0 && ic.softCoreParameters->alphaVdw == 0)
{
- return (dispatchKernelOnScLambdasOrAlphasDifference<false>(
- scLambdasOrAlphasDiffer, vdwInteractionTypeIsEwald, elecInteractionTypeIsEwald,
- vdwModifierIsPotSwitch, useSimd));
+ return (dispatchKernelOnScLambdasOrAlphasDifference<false>(scLambdasOrAlphasDiffer,
+ vdwInteractionTypeIsEwald,
+ elecInteractionTypeIsEwald,
+ vdwModifierIsPotSwitch,
+ useSimd));
}
else
{
- return (dispatchKernelOnScLambdasOrAlphasDifference<true>(
- scLambdasOrAlphasDiffer, vdwInteractionTypeIsEwald, elecInteractionTypeIsEwald,
- vdwModifierIsPotSwitch, useSimd));
+ return (dispatchKernelOnScLambdasOrAlphasDifference<true>(scLambdasOrAlphasDiffer,
+ vdwInteractionTypeIsEwald,
+ elecInteractionTypeIsEwald,
+ vdwModifierIsPotSwitch,
+ useSimd));
}
}
-void gmx_nb_free_energy_kernel(const t_nblist* nlist,
- rvec* xx,
- gmx::ForceWithShiftForces* ff,
- const t_forcerec* fr,
- const t_mdatoms* mdatoms,
- nb_kernel_data_t* kernel_data,
- t_nrnb* nrnb)
+void gmx_nb_free_energy_kernel(const t_nblist& nlist,
+ gmx::ArrayRef<const gmx::RVec> coords,
+ gmx::ForceWithShiftForces* ff,
+ const bool useSimd,
+ const int ntype,
+ const real rlist,
+ const interaction_const_t& ic,
+ gmx::ArrayRef<const gmx::RVec> shiftvec,
+ gmx::ArrayRef<const real> nbfp,
+ gmx::ArrayRef<const real> nbfp_grid,
+ gmx::ArrayRef<const real> chargeA,
+ gmx::ArrayRef<const real> chargeB,
+ gmx::ArrayRef<const int> typeA,
+ gmx::ArrayRef<const int> typeB,
+ int flags,
+ gmx::ArrayRef<const real> lambda,
+ gmx::ArrayRef<real> dvdl,
+ gmx::ArrayRef<real> energygrp_elec,
+ gmx::ArrayRef<real> energygrp_vdw,
+ t_nrnb* nrnb)
{
- const interaction_const_t& ic = *fr->ic;
- GMX_ASSERT(EEL_PME_EWALD(ic.eeltype) || ic.eeltype == eelCUT || EEL_RF(ic.eeltype),
+ GMX_ASSERT(EEL_PME_EWALD(ic.eeltype) || ic.eeltype == CoulombInteractionType::Cut || EEL_RF(ic.eeltype),
"Unsupported eeltype with free energy");
GMX_ASSERT(ic.softCoreParameters, "We need soft-core parameters");
const auto& scParams = *ic.softCoreParameters;
const bool vdwInteractionTypeIsEwald = (EVDW_PME(ic.vdwtype));
const bool elecInteractionTypeIsEwald = (EEL_PME_EWALD(ic.eeltype));
- const bool vdwModifierIsPotSwitch = (ic.vdw_modifier == eintmodPOTSWITCH);
+ const bool vdwModifierIsPotSwitch = (ic.vdw_modifier == InteractionModifiers::PotSwitch);
bool scLambdasOrAlphasDiffer = true;
- const bool useSimd = fr->use_simd_kernels;
if (scParams.alphaCoulomb == 0 && scParams.alphaVdw == 0)
{
}
else
{
- if (kernel_data->lambda[efptCOUL] == kernel_data->lambda[efptVDW]
+ if (lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)]
+ == lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)]
&& scParams.alphaCoulomb == scParams.alphaVdw)
{
scLambdasOrAlphasDiffer = false;
}
KernelFunction kernelFunc;
- kernelFunc = dispatchKernel(scLambdasOrAlphasDiffer, vdwInteractionTypeIsEwald,
- elecInteractionTypeIsEwald, vdwModifierIsPotSwitch, useSimd, ic);
- kernelFunc(nlist, xx, ff, fr, mdatoms, kernel_data, nrnb);
+ kernelFunc = dispatchKernel(scLambdasOrAlphasDiffer,
+ vdwInteractionTypeIsEwald,
+ elecInteractionTypeIsEwald,
+ vdwModifierIsPotSwitch,
+ useSimd,
+ ic);
+ kernelFunc(nlist,
+ coords,
+ ff,
+ ntype,
+ rlist,
+ ic,
+ shiftvec,
+ nbfp,
+ nbfp_grid,
+ chargeA,
+ chargeB,
+ typeA,
+ typeB,
+ flags,
+ lambda,
+ dvdl,
+ energygrp_elec,
+ energygrp_vdw,
+ nrnb);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _nb_free_energy_h_
-#define _nb_free_energy_h_
+#ifndef GMX_GMXLIB_NONBONDED_NB_FREE_ENERGY_H
+#define GMX_GMXLIB_NONBONDED_NB_FREE_ENERGY_H
-#include "gromacs/gmxlib/nrnb.h"
-#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
#include "gromacs/math/vectypes.h"
-#include "gromacs/mdtypes/nblist.h"
+#include "gromacs/utility/basedefinitions.h"
struct t_forcerec;
-struct t_mdatoms;
+struct t_nrnb;
+struct t_nblist;
+struct interaction_const_t;
namespace gmx
{
class ForceWithShiftForces;
-}
+template<typename>
+class ArrayRef;
+} // namespace gmx
-void gmx_nb_free_energy_kernel(const t_nblist* gmx_restrict nlist,
- rvec* gmx_restrict xx,
- gmx::ForceWithShiftForces* forceWithShiftForces,
- const t_forcerec* gmx_restrict fr,
- const t_mdatoms* gmx_restrict mdatoms,
- nb_kernel_data_t* gmx_restrict kernel_data,
+void gmx_nb_free_energy_kernel(const t_nblist& nlist,
+ gmx::ArrayRef<const gmx::RVec> coords,
+ gmx::ForceWithShiftForces* forceWithShiftForces,
+ bool useSimd,
+ int ntype,
+ real rlist,
+ const interaction_const_t& ic,
+ gmx::ArrayRef<const gmx::RVec> shiftvec,
+ gmx::ArrayRef<const real> nbfp,
+ gmx::ArrayRef<const real> nbfp_grid,
+ gmx::ArrayRef<const real> chargeA,
+ gmx::ArrayRef<const real> chargeB,
+ gmx::ArrayRef<const int> typeA,
+ gmx::ArrayRef<const int> typeB,
+ int flags,
+ gmx::ArrayRef<const real> lambda,
+ gmx::ArrayRef<real> dvdl,
+ gmx::ArrayRef<real> energygrp_elec,
+ gmx::ArrayRef<real> energygrp_vdw,
t_nrnb* gmx_restrict nrnb);
#endif
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2020, by the GROMACS development team, led by
+# Copyright (c) 2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-# Managing configuration for Fujitsu PrimeHPC Sparc64
-# For now this is mainly used for K computer.
-message(STATUS "Configuring for Fujitsu Sparc64 (deprecated)")
-
-set(BUILD_SHARED_LIBS OFF CACHE BOOL "Use static linking by default on Fujitsu Sparc64" FORCE)
-set(GMX_GPU OFF CACHE BOOL "Cannot do GPU acceleration on Fujitsu Sparc64" FORCE)
-
-set(GMX_SOFTWARE_INVSQRT OFF CACHE BOOL "Use native 1.0/sqrt(x) on Fujitsu Sparc64" FORCE)
-set(GMX_X11 OFF CACHE BOOL "X11 not compatible with Fujitsu Sparc64 cross-compile, disabled." FORCE)
-
+gmx_add_unit_test(GmxlibTests nonbonded-fep-test
+ CPP_SOURCE_FILES
+ nb_free_energy.cpp
+ )
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief Implements test of nonbonded fep kernel
+ *
+ * Implements the test logic from the bonded interactions also for the
+ * nonbonded fep kernel. This requires setting up some more input
+ * structures that in the bonded case.
+ *
+ * The test setup consists of an atom pair that is evaluated in an fep setting
+ * (vanishing charge and lennard-jones parameters of atom #2) with and without
+ * softcore Potentials.
+ *
+ * \author Sebastian Kehl <sebastian.kehl@mpcdf.mpg.de>
+ * \ingroup module_gmxlib_nonbonded
+ */
+#include "gmxpre.h"
+
+#include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
+#include "gromacs/gmxlib/nonbonded/nonbonded.h"
+
+#include <cmath>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/math/paddedvector.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/math/arrayrefwithpadding.h"
+#include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/mdtypes/enerdata.h"
+#include "gromacs/mdtypes/forcerec.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/interaction_const.h"
+#include "gromacs/mdtypes/nblist.h"
+#include "gromacs/mdtypes/forceoutput.h"
+#include "gromacs/mdlib/forcerec.h"
+#include "gromacs/tables/forcetable.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/forcefieldparameters.h"
+#include "gromacs/utility/enumerationhelpers.h"
+#include "gromacs/utility/strconvert.h"
+#include "gromacs/utility/stringstream.h"
+#include "gromacs/utility/textwriter.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/ewald/ewald_utils.h"
+#include "gromacs/gmxlib/nrnb.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+
+//! Number of atoms used in these tests.
+constexpr int c_numAtoms = 4;
+constexpr int c_numAtomTypes = 3;
+
+/*! \brief Output from nonbonded fep kernel
+ *
+ */
+struct OutputQuantities
+{
+ OutputQuantities() :
+ energy(static_cast<int>(NonBondedEnergyTerms::Count)),
+ dvdLambda(static_cast<int>(FreeEnergyPerturbationCouplingType::Count), 0.0),
+ fShift(1, { 0.0, 0.0, 0.0 }),
+ f(c_numAtoms, { 0.0, 0.0, 0.0 })
+ {
+ }
+
+ //! Energies of this interaction (size EgNR)
+ gmx_grppairener_t energy;
+ //! Derivative with respect to lambda (size efptNR)
+ std::vector<real> dvdLambda;
+ //! Shift force vectors (size N_IVEC but in this test only 1)
+ std::vector<RVec> fShift;
+ //! Forces (size c_numAtoms)
+ PaddedVector<RVec> f;
+};
+
+/*! \brief Utility to check the output from nonbonded test
+ *
+ * \param[in] checker Reference checker
+ * \param[in] output The output from the test to check
+ */
+void checkOutput(TestReferenceChecker* checker, const OutputQuantities& output)
+{
+ checker->checkReal(output.energy.energyGroupPairTerms[NonBondedEnergyTerms::LJSR][0], "EVdw ");
+ checker->checkReal(output.energy.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR][0],
+ "ECoul ");
+ checker->checkReal(output.dvdLambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
+ "dVdlCoul ");
+ checker->checkReal(output.dvdLambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)],
+ "dVdlVdw ");
+
+ checker->checkSequence(std::begin(output.f), std::end(output.f), "Forces");
+
+ auto shiftForcesChecker = checker->checkCompound("Shift-Forces", "Shift-forces");
+ shiftForcesChecker.checkVector(output.fShift[0], "Central");
+}
+
+class InteractionConstHelper
+{
+public:
+ InteractionConstHelper() {}
+
+ //! init data to construct interaction_const
+ void initInteractionConst(CoulombInteractionType coulType, VanDerWaalsType vdwType, InteractionModifiers vdwMod)
+ {
+ coulType_ = coulType;
+ vdwType_ = vdwType;
+ vdwMod_ = vdwMod;
+
+ // initialize correction tables
+ interaction_const_t tmp;
+ tmp.ewaldcoeff_q = calc_ewaldcoeff_q(1.0, 1.0e-5);
+ tmp.ewaldcoeff_lj = calc_ewaldcoeff_lj(1.0, 1.0e-5);
+ tmp.eeltype = coulType;
+ tmp.vdwtype = vdwType;
+ tmp.coulombEwaldTables = std::make_unique<EwaldCorrectionTables>();
+ tmp.vdwEwaldTables = std::make_unique<EwaldCorrectionTables>();
+
+ init_interaction_const_tables(nullptr, &tmp, 1.0, 0.0);
+ coulombTables_ = *tmp.coulombEwaldTables;
+ vdwTables_ = *tmp.vdwEwaldTables;
+ }
+
+ /*! \brief Setup interaction_const_t
+ *
+ * \param[in] fepVals t_lambda struct of fep values
+ * \param[out] ic interaction_const_t pointer with data
+ */
+ void getInteractionConst(const t_lambda& fepVals, interaction_const_t* ic)
+ {
+ ic->softCoreParameters = std::unique_ptr<interaction_const_t::SoftCoreParameters>(
+ new interaction_const_t::SoftCoreParameters(fepVals));
+
+ ic->coulombEwaldTables = std::unique_ptr<EwaldCorrectionTables>(new EwaldCorrectionTables);
+ *ic->coulombEwaldTables = coulombTables_;
+
+ ic->vdwEwaldTables = std::unique_ptr<EwaldCorrectionTables>(new EwaldCorrectionTables);
+ *ic->vdwEwaldTables = vdwTables_;
+
+ // set coulomb and vdw types
+ ic->eeltype = coulType_;
+ ic->vdwtype = vdwType_;
+ ic->vdw_modifier = vdwMod_;
+
+ // some non default parameters used in this testcase
+ ic->epsfac = gmx::c_one4PiEps0 * 0.25;
+ ic->reactionFieldCoefficient = 0.0; // former k_rf
+ ic->reactionFieldShift = 1.0; // former c_rf
+ ic->sh_ewald = 1.0e-5;
+ ic->sh_lj_ewald = -1.0;
+ ic->dispersion_shift.cpot = -1.0;
+ ic->repulsion_shift.cpot = -1.0;
+ }
+
+private:
+ //! correction tables
+ EwaldCorrectionTables coulombTables_;
+ EwaldCorrectionTables vdwTables_;
+
+ //! coulomb and vdw type specifiers
+ CoulombInteractionType coulType_;
+ VanDerWaalsType vdwType_;
+ InteractionModifiers vdwMod_;
+};
+
+
+/* \brief Utility class to setup forcerec
+ *
+ * This helper takes care of handling the neccessary data that are kept
+ * at various places and in various forms in the forcerec hierarchy such
+ * that this class can safely be used.
+ *
+ * Data is only initialized as necessary for the nonbonded kernel to work!
+ */
+class ForcerecHelper
+{
+public:
+ ForcerecHelper()
+ {
+ fepVals_.sc_alpha = 0.3;
+ fepVals_.sc_power = 1;
+ fepVals_.sc_r_power = 6.0;
+ fepVals_.sc_sigma = 0.3;
+ fepVals_.sc_sigma_min = 0.3;
+ fepVals_.bScCoul = true;
+ }
+
+ //! initialize data structure to construct forcerec
+ void initForcerec(const gmx_ffparams_t& idef,
+ CoulombInteractionType coulType,
+ VanDerWaalsType vdwType,
+ InteractionModifiers vdwMod)
+ {
+ icHelper_.initInteractionConst(coulType, vdwType, vdwMod);
+ nbfp_ = makeNonBondedParameterLists(idef, false);
+ t_forcerec frTmp;
+ ljPmeC6Grid_ = makeLJPmeC6GridCorrectionParameters(idef, frTmp);
+ }
+
+ void setSoftcoreAlpha(const real scAlpha) { fepVals_.sc_alpha = scAlpha; }
+ void setSoftcoreCoulomb(const real scCoulomb) { fepVals_.bScCoul = scCoulomb; }
+
+ //! get forcerec data as wanted by the nonbonded kernel
+ void getForcerec(t_forcerec* fr)
+ {
+ fr->ic = std::make_unique<interaction_const_t>();
+
+ // set data in ic
+ icHelper_.getInteractionConst(fepVals_, fr->ic.get());
+
+ // set data in fr
+ fr->ljpme_c6grid = ljPmeC6Grid_;
+ fr->nbfp = nbfp_;
+ fr->shift_vec = { { 0.0, 0.0, 0.0 } };
+ fr->rlist = rlist_;
+ fr->ntype = c_numAtomTypes;
+
+ // simd
+ fr->use_simd_kernels = GMX_USE_SIMD_KERNELS;
+ }
+
+private:
+ InteractionConstHelper icHelper_;
+ std::vector<real> ljPmeC6Grid_;
+ std::vector<real> nbfp_;
+ t_lambda fepVals_;
+ real rlist_ = 1.0;
+};
+
+/*! \brief Utility structure to hold atoms data
+ *
+ * A system having 4 interactions with the following perturbation pattern:
+ * - no perturbation
+ * - vdw- and coulomb-perturbation
+ * - coulomb-perturbation only
+ * - vdw-perturbation only
+ *
+ * This is realized by defining 3 different atom types that control
+ * the vdw-perturbation. The coulomb-perturbation is controlled by directly
+ * setting the charge of the atoms at the lambda states A/B.
+ */
+struct AtomData
+{
+ AtomData()
+ {
+ idef.atnr = c_numAtomTypes;
+ idef.iparams.resize(2 * c_numAtomTypes * c_numAtomTypes);
+
+ // set interaction parameters for different combinations of types
+ idef.iparams[0].lj = { 0.001458, 1.0062882e-6 }; // 0-0
+ idef.iparams[1].lj = { 0.0, 0.0 }; // 0-1
+ idef.iparams[2].lj = { 0.001458, 1.0062882e-6 }; // 0-2
+ idef.iparams[3].lj = { 0.0, 0.0 }; // 1-0
+ idef.iparams[4].lj = { 0.0, 0.0 }; // 1-1
+ idef.iparams[5].lj = { 0.0, 0.0 }; // 1-2
+ idef.iparams[6].lj = { 0.001458, 1.0062882e-6 }; // 2-0
+ idef.iparams[7].lj = { 0.0, 0.0 }; // 2-1
+ idef.iparams[8].lj = { 0.001458, 1.0062882e-6 }; // 2-2
+
+ GMX_ASSERT(chargeA.size() == c_numAtoms, "This test wants 4 atoms");
+ GMX_ASSERT(chargeB.size() == c_numAtoms, "This test wants 4 atoms");
+ GMX_ASSERT(typeA.size() == c_numAtoms, "This test wants 4 atoms");
+ GMX_ASSERT(typeB.size() == c_numAtoms, "This test wants 4 atoms");
+ }
+
+ // forcefield parameters
+ gmx_ffparams_t idef;
+
+ // atom data
+ std::vector<real> chargeA = { 1.0, -1.0, -1.0, 1.0 };
+ std::vector<real> chargeB = { 1.0, 0.0, 0.0, 1.0 };
+ std::vector<int> typeA = { 0, 0, 0, 0 };
+ std::vector<int> typeB = { 0, 1, 2, 1 };
+ // perturbation pattern: {no-pert, vdw- and coul-pert, coul-pert, vdw-pert}
+
+ // neighbourhood information
+ std::vector<int> iAtoms = { 0 };
+ std::vector<int> jAtoms = { 0, 1, 2, 3 };
+ std::vector<int> jIndex = { 0, 4 };
+ std::vector<int> shift = { 0 };
+ std::vector<int> gid = { 0 };
+ std::vector<int> exclFep = { 0, 1, 1, 1 };
+
+ // construct t_nblist
+ t_nblist getNbList()
+ {
+ t_nblist nbl;
+ nbl.nri = 1;
+ nbl.nrj = 4;
+ nbl.iinr = iAtoms;
+ nbl.jindex = jIndex;
+ nbl.jjnr = jAtoms;
+ nbl.shift = shift;
+ nbl.gid = gid;
+ nbl.excl_fep = exclFep;
+ return nbl;
+ }
+};
+
+/*! \brief Input structure for nonbonded fep kernel
+ */
+struct ListInput
+{
+public:
+ //! Function type
+ int fType = F_LJ;
+ //! Tolerance for float evaluation
+ float floatToler = 1e-6;
+ //! Tolerance for double evaluation
+ double doubleToler = 1e-8;
+ //! atom parameters
+ AtomData atoms;
+ //! forcerec helper
+ ForcerecHelper frHelper;
+
+ //! Constructor
+ ListInput() {}
+
+ /*! \brief Constructor with tolerance
+ *
+ * \param[in] ftol Single precision tolerance
+ * \param[in] dtol Double precision tolerance
+ */
+ ListInput(float ftol, double dtol)
+ {
+ floatToler = ftol;
+ doubleToler = dtol;
+ }
+
+ /*! \brief Set parameters for nonbonded interaction
+ *
+ * \param[in] coulType coulomb type
+ * \param[in] vdwType vdw type
+ * \param[in] vdwMod vdw potential modifier
+ */
+ ListInput setInteraction(CoulombInteractionType coulType, VanDerWaalsType vdwType, InteractionModifiers vdwMod)
+ {
+ frHelper.initForcerec(atoms.idef, coulType, vdwType, vdwMod);
+ return *this;
+ }
+};
+
+class NonbondedFepTest :
+ public ::testing::TestWithParam<std::tuple<ListInput, PaddedVector<RVec>, real, real, bool>>
+{
+protected:
+ PaddedVector<RVec> x_;
+ ListInput input_;
+ real lambda_;
+ real softcoreAlpha_;
+ bool softcoreCoulomb_;
+ TestReferenceData refData_;
+ TestReferenceChecker checker_;
+
+ NonbondedFepTest() : checker_(refData_.rootChecker())
+ {
+ input_ = std::get<0>(GetParam());
+ x_ = std::get<1>(GetParam());
+ lambda_ = std::get<2>(GetParam());
+ softcoreAlpha_ = std::get<3>(GetParam());
+ softcoreCoulomb_ = std::get<4>(GetParam());
+
+ test::FloatingPointTolerance tolerance(
+ input_.floatToler, input_.doubleToler, 1.0e-6, 1.0e-12, 10000, 100, false);
+ checker_.setDefaultTolerance(tolerance);
+ }
+
+ void testKernel()
+ {
+ input_.frHelper.setSoftcoreAlpha(softcoreAlpha_);
+ input_.frHelper.setSoftcoreCoulomb(softcoreCoulomb_);
+
+ // get forcerec and interaction_const
+ t_forcerec fr;
+ input_.frHelper.getForcerec(&fr);
+
+ // t_nblist
+ t_nblist nbl = input_.atoms.getNbList();
+
+ // output buffers
+ OutputQuantities output;
+
+ // lambda vector
+ int numFepCouplingTerms = static_cast<int>(FreeEnergyPerturbationCouplingType::Count);
+ std::vector<real> lambdas(numFepCouplingTerms, lambda_);
+
+ // fep kernel data
+ int doNBFlags = 0;
+ doNBFlags |= GMX_NONBONDED_DO_FORCE;
+ doNBFlags |= GMX_NONBONDED_DO_SHIFTFORCE;
+ doNBFlags |= GMX_NONBONDED_DO_POTENTIAL;
+
+ // force buffers
+ bool unusedBool = true; // this bool has no effect in the kernel
+ gmx::ForceWithShiftForces forces(output.f.arrayRefWithPadding(), unusedBool, output.fShift);
+
+ // dummy counter
+ t_nrnb nrnb;
+
+ // run fep kernel
+ gmx_nb_free_energy_kernel(nbl,
+ x_.arrayRefWithPadding().unpaddedArrayRef(),
+ &forces,
+ fr.use_simd_kernels,
+ fr.ntype,
+ fr.rlist,
+ *fr.ic,
+ fr.shift_vec,
+ fr.nbfp,
+ fr.ljpme_c6grid,
+ input_.atoms.chargeA,
+ input_.atoms.chargeB,
+ input_.atoms.typeA,
+ input_.atoms.typeB,
+ doNBFlags,
+ lambdas,
+ output.dvdLambda,
+ output.energy.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR],
+ output.energy.energyGroupPairTerms[NonBondedEnergyTerms::LJSR],
+ &nrnb);
+
+ checkOutput(&checker_, output);
+ }
+};
+
+TEST_P(NonbondedFepTest, testKernel)
+{
+ testKernel();
+}
+
+//! configurations to test
+std::vector<ListInput> c_interaction = {
+ { ListInput(1e-6, 1e-8).setInteraction(CoulombInteractionType::Cut, VanDerWaalsType::Cut, InteractionModifiers::None) },
+ { ListInput(1e-6, 1e-8).setInteraction(CoulombInteractionType::Cut, VanDerWaalsType::Cut, InteractionModifiers::PotSwitch) },
+ { ListInput(1e-6, 1e-8).setInteraction(CoulombInteractionType::Pme, VanDerWaalsType::Pme, InteractionModifiers::None) }
+};
+
+//! test parameters
+std::vector<real> c_fepLambdas = { 0.0, 0.5, 1.0 };
+std::vector<real> c_softcoreAlphas = { 0.0, 0.3 };
+std::vector<bool> c_softcoreCoulomb = { true, false };
+
+//! Coordinates for testing
+std::vector<PaddedVector<RVec>> c_coordinates = {
+ { { 1.0, 1.0, 1.0 }, { 1.1, 1.15, 1.2 }, { 0.9, 0.85, 0.8 }, { 1.1, 1.15, 0.8 } }
+};
+
+INSTANTIATE_TEST_CASE_P(NBInteraction,
+ NonbondedFepTest,
+ ::testing::Combine(::testing::ValuesIn(c_interaction),
+ ::testing::ValuesIn(c_coordinates),
+ ::testing::ValuesIn(c_fepLambdas),
+ ::testing::ValuesIn(c_softcoreAlphas),
+ ::testing::ValuesIn(c_softcoreCoulomb)));
+
+} // namespace
+
+} // namespace test
+
+} // namespace gmx
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="EVdw ">9.3145478052213058</Real>
+ <Real Name="ECoul ">-111.63140175473714</Real>
+ <Real Name="dVdlCoul ">188.52893909837877</Real>
+ <Real Name="dVdlVdw ">-6.2096985368142033</Real>
+ <Sequence Name="Forces">
+ <Int Name="Length">4</Int>
+ <Vector>
+ <Real Name="X">-260.95857104646757</Real>
+ <Real Name="Y">-391.43785656970101</Real>
+ <Real Name="Z">521.9171420929348</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-94.898901947422004</Real>
+ <Real Name="Y">-142.3483529211328</Real>
+ <Real Name="Z">-189.79780389484378</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">94.898901947421891</Real>
+ <Real Name="Y">142.34835292113289</Real>
+ <Real Name="Z">189.79780389484378</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">260.95857104646768</Real>
+ <Real Name="Y">391.4378565697009</Real>
+ <Real Name="Z">-521.9171420929348</Real>
+ </Vector>
+ </Sequence>
+ <Shift-Forces Name="Shift-forces">
+ <Vector Name="Central">
+ <Real Name="X">-260.95857104646757</Real>
+ <Real Name="Y">-391.43785656970101</Real>
+ <Real Name="Z">521.9171420929348</Real>
+ </Vector>
+ </Shift-Forces>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="EVdw ">9.3145478052213058</Real>
+ <Real Name="ECoul ">-111.63140175473714</Real>
+ <Real Name="dVdlCoul ">188.52893909837877</Real>
+ <Real Name="dVdlVdw ">-6.2096985368142033</Real>
+ <Sequence Name="Forces">
+ <Int Name="Length">4</Int>
+ <Vector>
+ <Real Name="X">-260.95857104646757</Real>
+ <Real Name="Y">-391.43785656970101</Real>
+ <Real Name="Z">521.9171420929348</Real>
+ </Vector>
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+ <Vector>
+ <Real Name="X">-177.92873649694485</Real>
+ <Real Name="Y">-266.89310474541691</Real>
+ <Real Name="Z">521.9171420929348</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-47.449450973711002</Real>
+ <Real Name="Y">-71.1741764605664</Real>
+ <Real Name="Z">-94.898901947421891</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">5.9345336989495747</Real>
+ <Real Name="Y">8.9018005484243652</Real>
+ <Real Name="Z">11.869067397899149</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">219.44365377170627</Real>
+ <Real Name="Y">329.16548065755893</Real>
+ <Real Name="Z">-438.88730754341202</Real>
+ </Vector>
+ </Sequence>
+ <Shift-Forces Name="Shift-forces">
+ <Vector Name="Central">
+ <Real Name="X">-177.92873649694485</Real>
+ <Real Name="Y">-266.89310474541691</Real>
+ <Real Name="Z">521.9171420929348</Real>
+ </Vector>
+ </Shift-Forces>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="EVdw ">6.2096985368142033</Real>
+ <Real Name="ECoul ">-17.366932205547741</Real>
+ <Real Name="dVdlCoul ">188.52893909837877</Real>
+ <Real Name="dVdlVdw ">-6.2096985368142033</Real>
+ <Sequence Name="Forces">
+ <Int Name="Length">4</Int>
+ <Vector>
+ <Real Name="X">-177.92873649694485</Real>
+ <Real Name="Y">-266.89310474541691</Real>
+ <Real Name="Z">521.9171420929348</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-47.449450973711002</Real>
+ <Real Name="Y">-71.1741764605664</Real>
+ <Real Name="Z">-94.898901947421891</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">5.9345336989495747</Real>
+ <Real Name="Y">8.9018005484243652</Real>
+ <Real Name="Z">11.869067397899149</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">219.44365377170627</Real>
+ <Real Name="Y">329.16548065755893</Real>
+ <Real Name="Z">-438.88730754341202</Real>
+ </Vector>
+ </Sequence>
+ <Shift-Forces Name="Shift-forces">
+ <Vector Name="Central">
+ <Real Name="X">-177.92873649694485</Real>
+ <Real Name="Y">-266.89310474541691</Real>
+ <Real Name="Z">521.9171420929348</Real>
+ </Vector>
+ </Shift-Forces>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="EVdw ">4.3172005809706242</Real>
+ <Real Name="ECoul ">-20.022624722133244</Real>
+ <Real Name="dVdlCoul ">187.81393532738895</Real>
+ <Real Name="dVdlVdw ">-4.8303990398635737</Real>
+ <Sequence Name="Forces">
+ <Int Name="Length">4</Int>
+ <Vector>
+ <Real Name="X">-106.90756741444682</Real>
+ <Real Name="Y">-160.36135112167005</Real>
+ <Real Name="Z">385.82194510152198</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-48.936236267106707</Real>
+ <Real Name="Y">-73.404354400659955</Real>
+ <Real Name="Z">-97.872472534213301</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">5.9345336989495294</Real>
+ <Real Name="Y">8.9018005484242977</Real>
+ <Real Name="Z">11.869067397899059</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">149.909269982604</Real>
+ <Real Name="Y">224.8639049739057</Real>
+ <Real Name="Z">-299.81853996520772</Real>
+ </Vector>
+ </Sequence>
+ <Shift-Forces Name="Shift-forces">
+ <Vector Name="Central">
+ <Real Name="X">-106.90756741444682</Real>
+ <Real Name="Y">-160.36135112167005</Real>
+ <Real Name="Z">385.82194510152198</Real>
+ </Vector>
+ </Shift-Forces>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="EVdw ">4.3826204154037347</Real>
+ <Real Name="ECoul ">-17.366932205547741</Real>
+ <Real Name="dVdlCoul ">188.52893909837877</Real>
+ <Real Name="dVdlVdw ">-4.9316753559057389</Real>
+ <Sequence Name="Forces">
+ <Int Name="Length">4</Int>
+ <Vector>
+ <Real Name="X">-131.09084583573497</Real>
+ <Real Name="Y">-196.63626875360214</Real>
+ <Real Name="Z">521.91714209293491</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-70.868396304315922</Real>
+ <Real Name="Y">-106.30259445647374</Real>
+ <Real Name="Z">-141.7367926086317</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">5.9345336989495294</Real>
+ <Real Name="Y">8.9018005484242977</Real>
+ <Real Name="Z">11.869067397899059</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">196.02470844110135</Real>
+ <Real Name="Y">294.03706266165159</Real>
+ <Real Name="Z">-392.04941688220231</Real>
+ </Vector>
+ </Sequence>
+ <Shift-Forces Name="Shift-forces">
+ <Vector Name="Central">
+ <Real Name="X">-131.09084583573497</Real>
+ <Real Name="Y">-196.63626875360214</Real>
+ <Real Name="Z">521.91714209293491</Real>
+ </Vector>
+ </Shift-Forces>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="EVdw ">3.1048492684071016</Real>
+ <Real Name="ECoul ">76.897537343641645</Real>
+ <Real Name="dVdlCoul ">188.52893909837877</Real>
+ <Real Name="dVdlVdw ">-6.2096985368142033</Real>
+ <Sequence Name="Forces">
+ <Int Name="Length">4</Int>
+ <Vector>
+ <Real Name="X">-94.898901947422104</Real>
+ <Real Name="Y">-142.34835292113269</Real>
+ <Real Name="Z">521.9171420929348</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-83.029834549522747</Real>
+ <Real Name="Y">-124.54475182428416</Real>
+ <Real Name="Z">-166.05966909904549</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">177.92873649694485</Real>
+ <Real Name="Y">266.89310474541685</Real>
+ <Real Name="Z">-355.8574729938893</Real>
+ </Vector>
+ </Sequence>
+ <Shift-Forces Name="Shift-forces">
+ <Vector Name="Central">
+ <Real Name="X">-94.898901947422104</Real>
+ <Real Name="Y">-142.34835292113269</Real>
+ <Real Name="Z">521.9171420929348</Real>
+ </Vector>
+ </Shift-Forces>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="EVdw ">3.1048492684071016</Real>
+ <Real Name="ECoul ">76.897537343641645</Real>
+ <Real Name="dVdlCoul ">188.52893909837877</Real>
+ <Real Name="dVdlVdw ">-6.2096985368142033</Real>
+ <Sequence Name="Forces">
+ <Int Name="Length">4</Int>
+ <Vector>
+ <Real Name="X">-94.898901947422104</Real>
+ <Real Name="Y">-142.34835292113269</Real>
+ <Real Name="Z">521.9171420929348</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-83.029834549522747</Real>
+ <Real Name="Y">-124.54475182428416</Real>
+ <Real Name="Z">-166.05966909904549</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">177.92873649694485</Real>
+ <Real Name="Y">266.89310474541685</Real>
+ <Real Name="Z">-355.8574729938893</Real>
+ </Vector>
+ </Sequence>
+ <Shift-Forces Name="Shift-forces">
+ <Vector Name="Central">
+ <Real Name="X">-94.898901947422104</Real>
+ <Real Name="Y">-142.34835292113269</Real>
+ <Real Name="Z">521.9171420929348</Real>
+ </Vector>
+ </Shift-Forces>
+</ReferenceData>
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdlib>
#include <cstring>
-#include <algorithm>
-#include <vector>
-
-#include "gromacs/mdtypes/commrec.h"
-#include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/utility/arraysize.h"
-
typedef struct
{
const char* name;
static void pr_difftime(FILE* out, double dt)
{
- int ndays, nhours, nmins, nsecs;
- gmx_bool bPrint, bPrinted;
+ int ndays, nhours, nmins, nsecs;
+ bool bPrint, bPrinted;
ndays = static_cast<int>(dt / (24 * 3600));
dt = dt - 24 * 3600 * ndays;
void clear_nrnb(t_nrnb* nrnb)
{
- int i;
-
- for (i = 0; (i < eNRNB); i++)
+ for (int i = 0; (i < eNRNB); i++)
{
nrnb->n[i] = 0.0;
}
}
-void add_nrnb(t_nrnb* dest, t_nrnb* s1, t_nrnb* s2)
-{
- int i;
-
- for (i = 0; (i < eNRNB); i++)
- {
- dest->n[i] = s1->n[i] + s2->n[i];
- }
-}
-
void print_nrnb(FILE* out, t_nrnb* nrnb)
{
- int i;
-
- for (i = 0; (i < eNRNB); i++)
+ for (int i = 0; (i < eNRNB); i++)
{
if (nrnb->n[i] > 0)
{
}
}
-void _inc_nrnb(t_nrnb* nrnb, int enr, int inc, char gmx_unused* file, int gmx_unused line)
-{
- nrnb->n[enr] += inc;
-#ifdef DEBUG_NRNB
- printf("nrnb %15s(%2d) incremented with %8d from file %s line %d\n", nbdata[enr].name, enr, inc,
- file, line);
-#endif
-}
-
/* Returns in enr is the index of a full nbnxn VdW kernel */
-static gmx_bool nrnb_is_nbnxn_vdw_kernel(int enr)
+static bool nrnb_is_nbnxn_vdw_kernel(int enr)
{
return (enr >= eNR_NBNXN_LJ_RF && enr <= eNR_NBNXN_LJ_E);
}
/* Returns in enr is the index of an nbnxn kernel addition (LJ modification) */
-static gmx_bool nrnb_is_nbnxn_kernel_addition(int enr)
+static bool nrnb_is_nbnxn_kernel_addition(int enr)
{
return (enr >= eNR_NBNXN_ADD_LJ_FSW && enr <= eNR_NBNXN_ADD_LJ_EWALD_E);
}
+void atomicNrnbIncrement(t_nrnb* nrnb, int index, int increment)
+{
+#pragma omp atomic
+ nrnb->n[index] += increment;
+}
+
void print_flop(FILE* out, t_nrnb* nrnb, double* nbfs, double* mflop)
{
- int i, j;
double mni, frac, tfrac, tflop;
const char* myline =
"-----------------------------------------------------------------------------";
*nbfs = 0.0;
- for (i = 0; (i < eNR_NBKERNEL_TOTAL_NR); i++)
+ for (int i = 0; (i < eNR_NBKERNEL_TOTAL_NR); i++)
{
if (std::strstr(nbdata[i].name, "W3-W3") != nullptr)
{
}
}
tflop = 0;
- for (i = 0; (i < eNRNB); i++)
+ for (int i = 0; (i < eNRNB); i++)
{
tflop += 1e-6 * nrnb->n[i] * nbdata[i].flop;
}
}
*mflop = 0.0;
tfrac = 0.0;
- for (i = 0; (i < eNRNB); i++)
+ for (int i = 0; (i < eNRNB); i++)
{
mni = 1e-6 * nrnb->n[i];
/* Skip empty entries and nbnxn additional flops,
if (nrnb_is_nbnxn_vdw_kernel(i))
{
/* Possibly add the cost of an LJ switch/Ewald function */
- for (j = eNR_NBNXN_ADD_LJ_FSW; j <= eNR_NBNXN_ADD_LJ_EWALD; j += 2)
+ for (int j = eNR_NBNXN_ADD_LJ_FSW; j <= eNR_NBNXN_ADD_LJ_EWALD; j += 2)
{
int e_kernel_add;
if (time_per_node > 0)
{
fprintf(out, "%12s %12s %12s %10s\n", "", "Core t (s)", "Wall t (s)", "(%)");
- fprintf(out, "%12s %12.3f %12.3f %10.1f\n", "Time:", time_per_thread, time_per_node,
- 100.0 * time_per_thread / time_per_node);
+ fprintf(out, "%12s %12.3f %12.3f %10.1f\n", "Time:", time_per_thread, time_per_node, 100.0 * time_per_thread / time_per_node);
/* only print day-hour-sec format if time_per_node is more than 30 min */
if (time_per_node > 30 * 60)
{
if (getenv("GMX_DETAILED_PERF_STATS") == nullptr)
{
fprintf(out, "%12s %12s %12s\n", "", "(ns/day)", "(hour/ns)");
- fprintf(out, "%12s %12.3f %12.3f\n", "Performance:", wallclocktime * 24 * 3.6 / time_per_node,
+ fprintf(out,
+ "%12s %12.3f %12.3f\n",
+ "Performance:",
+ wallclocktime * 24 * 3.6 / time_per_node,
1000 * time_per_node / (3600 * wallclocktime));
}
else
{
- fprintf(out, "%12s %12s %12s %12s %12s\n", "", "(Mnbf/s)",
- (mflop > 1000) ? "(GFlops)" : "(MFlops)", "(ns/day)", "(hour/ns)");
- fprintf(out, "%12s %12.3f %12.3f %12.3f %12.3f\n", "Performance:", nbfs / time_per_node,
- (mflop > 1000) ? (mflop / 1000) : mflop, wallclocktime * 24 * 3.6 / time_per_node,
+ fprintf(out,
+ "%12s %12s %12s %12s %12s\n",
+ "",
+ "(Mnbf/s)",
+ (mflop > 1000) ? "(GFlops)" : "(MFlops)",
+ "(ns/day)",
+ "(hour/ns)");
+ fprintf(out,
+ "%12s %12.3f %12.3f %12.3f %12.3f\n",
+ "Performance:",
+ nbfs / time_per_node,
+ (mflop > 1000) ? (mflop / 1000) : mflop,
+ wallclocktime * 24 * 3.6 / time_per_node,
1000 * time_per_node / (3600 * wallclocktime));
}
}
}
else
{
- fprintf(out, "%12s %12s %12s %14s\n", "", "(Mnbf/s)",
- (mflop > 1000) ? "(GFlops)" : "(MFlops)", "(steps/hour)");
- fprintf(out, "%12s %12.3f %12.3f %14.1f\n", "Performance:", nbfs / time_per_node,
- (mflop > 1000) ? (mflop / 1000) : mflop, nsteps * 3600.0 / time_per_node);
+ fprintf(out,
+ "%12s %12s %12s %14s\n",
+ "",
+ "(Mnbf/s)",
+ (mflop > 1000) ? "(GFlops)" : "(MFlops)",
+ "(steps/hour)");
+ fprintf(out,
+ "%12s %12.3f %12.3f %14.1f\n",
+ "Performance:",
+ nbfs / time_per_node,
+ (mflop > 1000) ? (mflop / 1000) : mflop,
+ nsteps * 3600.0 / time_per_node);
}
}
}
{
return nbdata[enr].name;
}
-
-static const int force_index[] = {
- eNR_BONDS, eNR_ANGLES, eNR_PROPER, eNR_IMPROPER, eNR_RB,
- eNR_DISRES, eNR_ORIRES, eNR_POSRES, eNR_FBPOSRES, eNR_NS,
-};
-#define NFORCE_INDEX asize(force_index)
-
-static const int constr_index[] = { eNR_SHAKE, eNR_SHAKE_RIJ, eNR_SETTLE, eNR_UPDATE,
- eNR_PCOUPL, eNR_CONSTR_VIR, eNR_CONSTR_V };
-#define NCONSTR_INDEX asize(constr_index)
-
-static double pr_av(FILE* log, t_commrec* cr, double fav, const double ftot[], const char* title)
-{
- int i, perc;
- double dperc, unb;
-
- unb = 0;
- if (fav > 0)
- {
- fav /= cr->nnodes - cr->npmenodes;
- fprintf(log, "\n %-26s", title);
- for (i = 0; (i < cr->nnodes); i++)
- {
- dperc = (100.0 * ftot[i]) / fav;
- unb = std::max(unb, dperc);
- perc = static_cast<int>(dperc);
- fprintf(log, "%3d ", perc);
- }
- if (unb > 0)
- {
- perc = static_cast<int>(10000.0 / unb);
- fprintf(log, "%6d%%\n\n", perc);
- }
- else
- {
- fprintf(log, "\n\n");
- }
- }
- return unb;
-}
-
-void pr_load(FILE* log, t_commrec* cr, t_nrnb nrnb[])
-{
- t_nrnb av;
-
- std::vector<double> ftot(cr->nnodes);
- std::vector<double> stot(cr->nnodes);
- for (int i = 0; (i < cr->nnodes); i++)
- {
- add_nrnb(&av, &av, &(nrnb[i]));
- /* Cost due to forces */
- for (int j = 0; (j < eNR_NBKERNEL_TOTAL_NR); j++)
- {
- ftot[i] += nrnb[i].n[j] * cost_nrnb(j);
- }
- for (int j = 0; (j < NFORCE_INDEX); j++)
- {
- ftot[i] += nrnb[i].n[force_index[j]] * cost_nrnb(force_index[j]);
- }
- /* Due to shake */
- for (int j = 0; (j < NCONSTR_INDEX); j++)
- {
- stot[i] += nrnb[i].n[constr_index[j]] * cost_nrnb(constr_index[j]);
- }
- }
- for (int j = 0; (j < eNRNB); j++)
- {
- av.n[j] = av.n[j] / static_cast<double>(cr->nnodes - cr->npmenodes);
- }
-
- fprintf(log, "\nDetailed load balancing info in percentage of average\n");
-
- fprintf(log, " Type RANK:");
- for (int i = 0; (i < cr->nnodes); i++)
- {
- fprintf(log, "%3d ", i);
- }
- fprintf(log, "Scaling\n");
- fprintf(log, "---------------------------");
- for (int i = 0; (i < cr->nnodes); i++)
- {
- fprintf(log, "----");
- }
- fprintf(log, "-------\n");
-
- for (int j = 0; (j < eNRNB); j++)
- {
- double unb = 100.0;
- if (av.n[j] > 0)
- {
- double dperc;
- int perc;
- fprintf(log, " %-26s", nrnb_str(j));
- for (int i = 0; (i < cr->nnodes); i++)
- {
- dperc = (100.0 * nrnb[i].n[j]) / av.n[j];
- unb = std::max(unb, dperc);
- perc = static_cast<int>(dperc);
- fprintf(log, "%3d ", perc);
- }
- if (unb > 0)
- {
- perc = static_cast<int>(10000.0 / unb);
- fprintf(log, "%6d%%\n", perc);
- }
- else
- {
- fprintf(log, "\n");
- }
- }
- }
- double fav = 0;
- double sav = 0;
- for (int i = 0; (i < cr->nnodes); i++)
- {
- fav += ftot[i];
- sav += stot[i];
- }
- double uf = pr_av(log, cr, fav, ftot.data(), "Total Force");
- double us = pr_av(log, cr, sav, stot.data(), "Total Constr.");
-
- double unb = (uf * fav + us * sav) / (fav + sav);
- if (unb > 0)
- {
- unb = 10000.0 / unb;
- fprintf(log, "\nTotal Scaling: %.0f%% of max performance\n\n", unb);
- }
-}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_GMXLIB_NRNB_H
#define GMX_GMXLIB_NRNB_H
-#include <stdio.h>
-
-#include "gromacs/utility/basedefinitions.h"
-
-#define eNR_NBKERNEL_NONE (-1)
+#include <array>
+#include <cstdint>
+#include <cstdio>
enum
{
struct t_nrnb
{
- double n[eNRNB] = { 0 };
+ std::array<double, eNRNB> n = { 0 };
};
-struct t_commrec;
-
void clear_nrnb(t_nrnb* nrnb);
-void add_nrnb(t_nrnb* dest, t_nrnb* s1, t_nrnb* s2);
-
void print_nrnb(FILE* out, t_nrnb* nrnb);
-void _inc_nrnb(t_nrnb* nrnb, int enr, int inc, char* file, int line);
-
-#ifdef DEBUG_NRNB
-# define inc_nrnb(nrnb, enr, inc) _inc_nrnb(nrnb, enr, inc, __FILE__, __LINE__)
-#else
-# define inc_nrnb(nrnb, enr, inc) (nrnb)->n[enr] += inc
-#endif
+/*! \brief Increment the nonbonded kernel flop counters
+ *
+ * \param nrnb The nonbonded kernel flop counters.
+ * \param index Which counter to incrememnt.
+ * \param increment How much to increment the counter by.
+ */
+static inline void inc_nrnb(t_nrnb* nrnb, int index, int increment)
+{
+ nrnb->n[index] += increment;
+}
+/*! \brief Atomic increment of nonbonded kernel flop counters
+ *
+ * \param nrnb The nonbonded kernel flop counters.
+ * \param index Which counter to incrememnt.
+ * \param increment How much to increment the counter by.
+ *
+ * Same as inc_nrnb but includes omp atomic pragma
+ */
+void atomicNrnbIncrement(t_nrnb* nrnb, int index, int increment);
void print_flop(FILE* out, t_nrnb* nrnb, double* nbfs, double* mflop);
/* Calculates the non-bonded forces and flop count.
void print_perf(FILE* out, double nodetime, double realtime, int64_t nsteps, double delta_t, double nbfs, double mflop);
/* Prints the performance, nbfs and mflop come from print_flop */
-void pr_load(FILE* log, struct t_commrec* cr, t_nrnb nrnb[]);
-/* Print detailed load balancing info */
-
int cost_nrnb(int enr);
/* Cost in i860 cycles of this component of MD */
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2011,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2011,2013,2014,2015,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(gmxpreprocess INTERFACE)
+
file(GLOB GMXPREPROCESS_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${GMXPREPROCESS_SOURCES} PARENT_SCOPE)
+# Source files have the following private module dependencies.
+target_link_libraries(gmxpreprocess PRIVATE
+ # gmxlib
+ # math
+ # mdtypes
+ # tng_io
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(gmxpreprocess PUBLIC
+target_include_directories(gmxpreprocess INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(gmxpreprocess PUBLIC
+target_link_libraries(gmxpreprocess INTERFACE
+ legacy_api
+ )
+
+# TODO: when is an OBJECT target
+#target_link_libraries(gmxpreprocess PUBLIC legacy_api)
+#target_link_libraries(gmxpreprocess PRIVATE common)
+
+# Module dependencies
+# This module convey transitive dependence on these modules.
+#target_link_libraries(gmxpreprocess PUBLIC
+target_link_libraries(gmxpreprocess INTERFACE
+ # utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(gmxpreprocess PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(gmxpreprocess PRIVATE legacy_modules)
+
if(BUILD_TESTING)
add_subdirectory(tests)
endif()
}
if (jmax == -1)
{
- gmx_fatal(FARGS, "Atom %s not found in rtp database in residue %s", searchname,
+ gmx_fatal(FARGS,
+ "Atom %s not found in rtp database in residue %s",
+ searchname,
localPpResidue.resname.c_str());
}
if (kmax != strlen(searchname))
gmx_fatal(FARGS,
"Atom %s not found in rtp database in residue %s, "
"it looks a bit like %s",
- searchname, localPpResidue.resname.c_str(), *(localPpResidue.atomname[jmax]));
+ searchname,
+ localPpResidue.resname.c_str(),
+ *(localPpResidue.atomname[jmax]));
}
return jmax;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015,2016,2019, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2016,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define alfaHpl (2 * M_PI / 3) /* 120 degrees */
#define distH 0.1
-#define alfaCOM (DEG2RAD * 117)
-#define alfaCO (DEG2RAD * 121)
-#define alfaCOA (DEG2RAD * 115)
+#define alfaCOM (gmx::c_deg2Rad * 117)
+#define alfaCO (gmx::c_deg2Rad * 121)
+#define alfaCOA (gmx::c_deg2Rad * 115)
#define distO 0.123
#define distOA 0.125
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
if (r - i > 0.01 || r - i < -0.01)
{
- gmx_fatal(FARGS, "A non-integer value (%f) was supplied for '%s' in %s", r, name,
+ gmx_fatal(FARGS,
+ "A non-integer value (%f) was supplied for '%s' in %s",
+ r,
+ name,
interaction_function[ftype].longname);
}
if (i < limit)
{
- gmx_fatal(FARGS, "Value of '%s' in %s is %d, which is smaller than the minimum of %d", name,
- interaction_function[ftype].longname, i, limit);
+ gmx_fatal(FARGS,
+ "Value of '%s' in %s is %d, which is smaller than the minimum of %d",
+ name,
+ interaction_function[ftype].longname,
+ i,
+ limit);
}
return i;
}
-static void set_ljparams(int comb, double reppow, double v, double w, real* c6, real* c12)
+static void set_ljparams(CombinationRule comb, double reppow, double v, double w, real* c6, real* c12)
{
- if (comb == eCOMB_ARITHMETIC || comb == eCOMB_GEOM_SIG_EPS)
+ if (comb == CombinationRule::Arithmetic || comb == CombinationRule::GeomSigEps)
{
if (v >= 0)
{
/* A return value of 0 means parameters were assigned successfully,
* returning -1 means this is an all-zero interaction that should not be added.
*/
-static int assign_param(t_functype ftype, t_iparams* newparam, gmx::ArrayRef<const real> old, int comb, double reppow)
+static int assign_param(t_functype ftype,
+ t_iparams* newparam,
+ gmx::ArrayRef<const real> old,
+ CombinationRule comb,
+ double reppow)
{
bool all_param_zero = true;
{
case F_G96ANGLES:
/* Post processing of input data: store cosine iso angle itself */
- newparam->harmonic.rA = cos(old[0] * DEG2RAD);
+ newparam->harmonic.rA = cos(old[0] * gmx::c_deg2Rad);
newparam->harmonic.krA = old[1];
- newparam->harmonic.rB = cos(old[2] * DEG2RAD);
+ newparam->harmonic.rB = cos(old[2] * gmx::c_deg2Rad);
newparam->harmonic.krB = old[3];
break;
case F_G96BONDS:
gmx_fatal(FARGS,
"Invalid geometry for flat-bottomed position restraint.\n"
"Expected number between 1 and %d. Found %d\n",
- efbposresNR - 1, newparam->fbposres.geom);
+ efbposresNR - 1,
+ newparam->fbposres.geom);
}
newparam->fbposres.r = old[1];
newparam->fbposres.k = old[2];
newparam->vsite.f = old[5];
break;
case F_VSITE3FAD:
- newparam->vsite.a = old[1] * cos(DEG2RAD * old[0]);
- newparam->vsite.b = old[1] * sin(DEG2RAD * old[0]);
+ newparam->vsite.a = old[1] * cos(gmx::c_deg2Rad * old[0]);
+ newparam->vsite.b = old[1] * sin(gmx::c_deg2Rad * old[0]);
newparam->vsite.c = old[2];
newparam->vsite.d = old[3];
newparam->vsite.e = old[4];
static int enter_params(gmx_ffparams_t* ffparams,
t_functype ftype,
gmx::ArrayRef<const real> forceparams,
- int comb,
+ CombinationRule comb,
real reppow,
int start,
bool bAppend)
static void enter_function(const InteractionsOfType* p,
t_functype ftype,
- int comb,
+ CombinationRule comb,
real reppow,
gmx_ffparams_t* ffparams,
InteractionList* il,
{
int start = ffparams->numTypes();
- for (auto& parm : p->interactionTypes)
+ for (const auto& parm : p->interactionTypes)
{
int type = enter_params(ffparams, ftype, parm.forceParam(), comb, reppow, start, bAppend);
/* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
gmx::ArrayRef<const InteractionsOfType> nbtypes,
gmx::ArrayRef<const MoleculeInformation> mi,
const MoleculeInformation* intermolecular_interactions,
- int comb,
+ CombinationRule comb,
double reppow,
real fudgeQQ,
gmx_mtop_t* mtop)
ffp->reppow = reppow;
enter_function(&(nbtypes[F_LJ]), static_cast<t_functype>(F_LJ), comb, reppow, ffp, nullptr, TRUE, TRUE);
- enter_function(&(nbtypes[F_BHAM]), static_cast<t_functype>(F_BHAM), comb, reppow, ffp, nullptr,
- TRUE, TRUE);
+ enter_function(
+ &(nbtypes[F_BHAM]), static_cast<t_functype>(F_BHAM), comb, reppow, ffp, nullptr, TRUE, TRUE);
for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
{
if ((i != F_LJ) && (i != F_BHAM)
&& ((flags & IF_BOND) || (flags & IF_VSITE) || (flags & IF_CONSTRAINT)))
{
- enter_function(&(interactions[i]), static_cast<t_functype>(i), comb, reppow, ffp,
- &molt->ilist[i], FALSE, (i == F_POSRES || i == F_FBPOSRES));
+ enter_function(&(interactions[i]),
+ static_cast<t_functype>(i),
+ comb,
+ reppow,
+ ffp,
+ &molt->ilist[i],
+ FALSE,
+ (i == F_POSRES || i == F_FBPOSRES));
}
}
}
}
else
{
- enter_function(&(interactions[i]), static_cast<t_functype>(i), comb, reppow,
- ffp, &(*mtop->intermolecular_ilist)[i], FALSE, FALSE);
+ enter_function(&(interactions[i]),
+ static_cast<t_functype>(i),
+ comb,
+ reppow,
+ ffp,
+ &(*mtop->intermolecular_ilist)[i],
+ FALSE,
+ FALSE);
mtop->bIntermolecularInteractions = TRUE;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct gmx_mtop_t;
struct MoleculeInformation;
struct InteractionsOfType;
+enum class CombinationRule : int;
namespace gmx
{
gmx::ArrayRef<const InteractionsOfType> nbtypes,
gmx::ArrayRef<const MoleculeInformation> mi,
const MoleculeInformation* intermolecular_interactions,
- int comb,
+ CombinationRule comb,
double reppow,
real fudgeQQ,
gmx_mtop_t* mtop);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxlib/conformation_utilities.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pbcutil/rmpbc.h"
{
if (bGetMass)
{
- aps->setAtomProperty(epropMass, std::string(*atoms->resinfo[atoms->atom[i].resind].name),
- std::string(*atoms->atomname[i]), &(atoms->atom[i].m));
+ aps->setAtomProperty(epropMass,
+ std::string(*atoms->resinfo[atoms->atom[i].resind].name),
+ std::string(*atoms->atomname[i]),
+ &(atoms->atom[i].m));
}
tmass += atoms->atom[i].m;
}
fprintf(stderr,
"Range of values for B-factors too large (min %g, max %g) "
"will scale down a factor 10\n",
- bfac_min, bfac_max);
+ bfac_min,
+ bfac_max);
for (i = 0; (i < n_bfac); i++)
{
bfac[i] /= 10;
fprintf(stderr,
"Range of values for B-factors too small (min %g, max %g) "
"will scale up a factor 10\n",
- bfac_min, bfac_max);
+ bfac_min,
+ bfac_max);
for (i = 0; (i < n_bfac); i++)
{
bfac[i] *= 10;
fprintf(stderr, "B-factors range from %g to %g\n", bfac_min, bfac_max);
for (i = 1; (i < 12); i++)
{
- fprintf(out, "%-6s%5d %-4.4s%3.3s %c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f\n", "ATOM ",
- natoms + 1 + i, "CA", "LEG", space, nres + 1, space, (xmin + (i * 0.12)) * 10,
- ymin * 10, zmin * 10, 1.0, bfac_min + ((i - 1.0) * (bfac_max - bfac_min) / 10));
+ fprintf(out,
+ "%-6s%5d %-4.4s%3.3s %c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f\n",
+ "ATOM ",
+ natoms + 1 + i,
+ "CA",
+ "LEG",
+ space,
+ nres + 1,
+ space,
+ (xmin + (i * 0.12)) * 10,
+ ymin * 10,
+ zmin * 10,
+ 1.0,
+ bfac_min + ((i - 1.0) * (bfac_max - bfac_min) / 10));
}
}
for (i = 0; i < nat; i++)
{
- gmx_fprintf_pdb_atomline(out, epdbATOM, a0 + i, "C", ' ', "BOX", 'K' + i / NCUCVERT,
- r0 + i, ' ', 10 * vert[i][XX], 10 * vert[i][YY],
- 10 * vert[i][ZZ], 1.0, 0.0, "");
+ gmx_fprintf_pdb_atomline(out,
+ PdbRecordType::Atom,
+ a0 + i,
+ "C",
+ ' ',
+ "BOX",
+ 'K' + i / NCUCVERT,
+ r0 + i,
+ ' ',
+ 10 * vert[i][XX],
+ 10 * vert[i][YY],
+ 10 * vert[i][ZZ],
+ 1.0,
+ 0.0,
+ "");
}
edge = compact_unitcell_edges();
{
for (i = 0; i < NCUCEDGE; i++)
{
- fprintf(out, "CONECT%5d%5d\n", a0 + j * NCUCVERT + edge[2 * i],
+ fprintf(out,
+ "CONECT%5d%5d\n",
+ a0 + j * NCUCVERT + edge[2 * i],
a0 + j * NCUCVERT + edge[2 * i + 1]);
}
}
{
for (x = 0; x <= 1; x++)
{
- gmx_fprintf_pdb_atomline(out, epdbATOM, a0 + i, "C", ' ', "BOX", 'K' + i / 8,
- r0 + i, ' ', x * 10 * box[XX][XX], y * 10 * box[YY][YY],
- z * 10 * box[ZZ][ZZ], 1.0, 0.0, "");
+ gmx_fprintf_pdb_atomline(out,
+ PdbRecordType::Atom,
+ a0 + i,
+ "C",
+ ' ',
+ "BOX",
+ 'K' + i / 8,
+ r0 + i,
+ ' ',
+ x * 10 * box[XX][XX],
+ y * 10 * box[YY][YY],
+ z * 10 * box[ZZ][ZZ],
+ 1.0,
+ 0.0,
+ "");
i++;
}
}
/* Determine rotation from cross product with target vector */
cprod(principal_axis, targetvec, rotvec);
unitv(rotvec, rotvec);
- printf("Aligning %g %g %g to %g %g %g : xprod %g %g %g\n", principal_axis[XX],
- principal_axis[YY], principal_axis[ZZ], targetvec[XX], targetvec[YY], targetvec[ZZ],
- rotvec[XX], rotvec[YY], rotvec[ZZ]);
+ printf("Aligning %g %g %g to %g %g %g : xprod %g %g %g\n",
+ principal_axis[XX],
+ principal_axis[YY],
+ principal_axis[ZZ],
+ targetvec[XX],
+ targetvec[YY],
+ targetvec[ZZ],
+ rotvec[XX],
+ rotvec[YY],
+ rotvec[ZZ]);
ux = rotvec[XX];
uy = rotvec[YY];
rotmatrix[2][1] = uy * uz * (1 - costheta) + ux * sintheta;
rotmatrix[2][2] = uz * uz + (1.0 - uz * uz) * costheta;
- printf("Rotation matrix: \n%g %g %g\n%g %g %g\n%g %g %g\n", rotmatrix[0][0], rotmatrix[0][1],
- rotmatrix[0][2], rotmatrix[1][0], rotmatrix[1][1], rotmatrix[1][2], rotmatrix[2][0],
- rotmatrix[2][1], rotmatrix[2][2]);
+ printf("Rotation matrix: \n%g %g %g\n%g %g %g\n%g %g %g\n",
+ rotmatrix[0][0],
+ rotmatrix[0][1],
+ rotmatrix[0][2],
+ rotmatrix[1][0],
+ rotmatrix[1][1],
+ rotmatrix[1][2],
+ rotmatrix[2][0],
+ rotmatrix[2][1],
+ rotmatrix[2][2]);
}
static void renum_resnr(t_atoms* atoms, int isize, const int* index, int resnr_start)
{ efDAT, "-bf", "bfact", ffOPTRD } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, NPA, pa, asize(desc), desc,
- asize(bugs), bugs, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW, NFILE, fnm, NPA, pa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
if (pbcType != PbcType::No)
{
real vol = det(box);
- printf("Volume: %g nm^3, corresponds to roughly %d electrons\n", vol,
+ printf("Volume: %g nm^3, corresponds to roughly %d electrons\n",
+ vol,
100 * (static_cast<int>(vol * 4.5)));
}
/* Determine the Van der Waals radius from the force field */
if (bReadVDW)
{
- if (!aps.setAtomProperty(epropVDW, *top->atoms.resinfo[top->atoms.atom[i].resind].name,
- *top->atoms.atomname[i], &vdw))
+ if (!aps.setAtomProperty(epropVDW,
+ *top->atoms.resinfo[top->atoms.atom[i].resind].name,
+ *top->atoms.atomname[i],
+ &vdw))
{
vdw = rvdw;
}
printf(" center :%7.3f%7.3f%7.3f (nm)\n", gc[XX], gc[YY], gc[ZZ]);
printf(" box vectors :%7.3f%7.3f%7.3f (nm)\n", norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
printf(" box angles :%7.2f%7.2f%7.2f (degrees)\n",
- norm2(box[ZZ]) == 0 ? 0 : RAD2DEG * gmx_angle(box[YY], box[ZZ]),
- norm2(box[ZZ]) == 0 ? 0 : RAD2DEG * gmx_angle(box[XX], box[ZZ]),
- norm2(box[YY]) == 0 ? 0 : RAD2DEG * gmx_angle(box[XX], box[YY]));
+ norm2(box[ZZ]) == 0 ? 0 : gmx::c_rad2Deg * gmx_angle(box[YY], box[ZZ]),
+ norm2(box[ZZ]) == 0 ? 0 : gmx::c_rad2Deg * gmx_angle(box[XX], box[ZZ]),
+ norm2(box[YY]) == 0 ? 0 : gmx::c_rad2Deg * gmx_angle(box[XX], box[YY]));
printf(" box volume :%7.2f (nm^3)\n", det(box));
}
real vol, dens;
vol = det(box);
- dens = (mass * AMU) / (vol * NANO * NANO * NANO);
+ dens = (mass * gmx::c_amu) / (vol * gmx::c_nano * gmx::c_nano * gmx::c_nano);
fprintf(stderr, "Volume of input %g (nm^3)\n", vol);
fprintf(stderr, "Mass of input %g (a.m.u.)\n", mass);
fprintf(stderr, "Density of input %g (g/l)\n", dens);
gmx_fatal(FARGS,
"Cannot scale density with "
"zero mass (%g) or volume (%g)\n",
- mass, vol);
+ mass,
+ vol);
}
scale[XX] = scale[YY] = scale[ZZ] = std::cbrt(dens / rho);
}
}
printf("Aligning %d atoms (out of %d) to %g %g %g, center of rotation %g %g %g\n",
- numAlignmentAtoms, natom, targetvec[XX], targetvec[YY], targetvec[ZZ],
- aligncenter[XX], aligncenter[YY], aligncenter[ZZ]);
+ numAlignmentAtoms,
+ natom,
+ targetvec[XX],
+ targetvec[YY],
+ targetvec[ZZ],
+ aligncenter[XX],
+ aligncenter[YY],
+ aligncenter[ZZ]);
/*subtract out pivot point*/
for (i = 0; i < numAlignmentAtoms; i++)
{
ssize = atoms.nr;
sindex = nullptr;
}
- printf("Translating %d atoms (out of %d) by %g %g %g nm\n", ssize, natom, translation[XX],
- translation[YY], translation[ZZ]);
+ printf("Translating %d atoms (out of %d) by %g %g %g nm\n",
+ ssize,
+ natom,
+ translation[XX],
+ translation[YY],
+ translation[ZZ]);
if (sindex)
{
for (i = 0; i < ssize; i++)
{
/* Rotate */
printf("Rotating %g, %g, %g degrees around the X, Y and Z axis respectively\n",
- rotangles[XX], rotangles[YY], rotangles[ZZ]);
+ rotangles[XX],
+ rotangles[YY],
+ rotangles[ZZ]);
for (i = 0; i < DIM; i++)
{
- rotangles[i] *= DEG2RAD;
+ rotangles[i] *= gmx::c_deg2Rad;
}
rotate_conf(natom, x, v, rotangles[XX], rotangles[YY], rotangles[ZZ]);
}
{
printf("new box vectors :%7.3f%7.3f%7.3f (nm)\n", norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
printf("new box angles :%7.2f%7.2f%7.2f (degrees)\n",
- norm2(box[ZZ]) == 0 ? 0 : RAD2DEG * gmx_angle(box[YY], box[ZZ]),
- norm2(box[ZZ]) == 0 ? 0 : RAD2DEG * gmx_angle(box[XX], box[ZZ]),
- norm2(box[YY]) == 0 ? 0 : RAD2DEG * gmx_angle(box[XX], box[YY]));
+ norm2(box[ZZ]) == 0 ? 0 : gmx::c_rad2Deg * gmx_angle(box[YY], box[ZZ]),
+ norm2(box[ZZ]) == 0 ? 0 : gmx::c_rad2Deg * gmx_angle(box[XX], box[ZZ]),
+ norm2(box[YY]) == 0 ? 0 : gmx::c_rad2Deg * gmx_angle(box[XX], box[YY]));
printf("new box volume :%7.2f (nm^3)\n", det(box));
}
}
else
{
- write_sto_conf_indexed(outfile, name, &atoms, x, bHaveV ? v : nullptr, pbcType, box,
- isize, index);
+ write_sto_conf_indexed(
+ outfile, name, &atoms, x, bHaveV ? v : nullptr, pbcType, box, isize, index);
}
sfree(grpname);
sfree(index);
{
index[i] = i;
}
- write_pdbfile_indexed(out, name, &atoms, x, pbcType, box, ' ', -1, atoms.nr, index,
- conect, outftp == efPQR);
+ write_pdbfile_indexed(
+ out, name, &atoms, x, pbcType, box, ' ', -1, atoms.nr, index, conect, outftp == efPQR);
sfree(index);
if (bLegend)
{
}
if (visbox[0] > 0)
{
- visualize_box(out, bLegend ? atoms.nr + 12 : atoms.nr,
- bLegend ? atoms.nres = 12 : atoms.nres, box, visbox);
+ visualize_box(out,
+ bLegend ? atoms.nr + 12 : atoms.nr,
+ bLegend ? atoms.nres = 12 : atoms.nres,
+ box,
+ visbox);
}
gmx_ffclose(out);
}
std::string message = gmx::formatString(
"Could not find any files ending on '%s' "
"in the force field directory '%s'",
- file_end, ffdir);
+ file_end,
+ ffdir);
GMX_THROW(gmx::InvalidInputError(message));
}
for (std::string& filename : result)
std::string message = gmx::formatString(
"No force fields found (files with name '%s' "
"in subdirectories ending on '%s')",
- filename, dirend);
+ filename,
+ dirend);
GMX_THROW(gmx::InvalidInputError(message));
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vec.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
{
// AMBER force fields with type 9 dihedrals can reach here, where we sort on
// the contents of the string that names the macro for the parameters.
- return std::lexicographical_compare(
- d1.interactionTypeName().begin(), d1.interactionTypeName().end(),
- d2.interactionTypeName().begin(), d2.interactionTypeName().end());
+ return std::lexicographical_compare(d1.interactionTypeName().begin(),
+ d1.interactionTypeName().end(),
+ d2.interactionTypeName().begin(),
+ d2.interactionTypeName().end());
}
}
int minh = 2;
int next = dihedral->second + 1;
for (int l = dihedral->second;
- (l < next && is_dihedral_on_same_bond(dihedral->first, dih[l])); l++)
+ (l < next && is_dihedral_on_same_bond(dihedral->first, dih[l]));
+ l++)
{
int nh = n_hydro(dih[l].atoms(), atoms->atomname);
if (nh < minh)
{
for (int i = 0; (i < atoms->nres); i++)
{
- BondedInteractionList* impropers = &globalPatches[i].rb[ebtsIDIHS];
+ BondedInteractionList* impropers = &globalPatches[i].rb[BondedTypes::ImproperDihedrals];
for (const auto& bondeds : impropers->b)
{
bool bStop = false;
std::vector<int> ai;
for (int k = 0; (k < 4) && !bStop; k++)
{
- const int entry = search_atom(bondeds.a[k].c_str(), start, atoms, "improper",
- bAllowMissing, cyclicBondsIndex);
+ const int entry = search_atom(
+ bondeds.a[k].c_str(), start, atoms, "improper", bAllowMissing, cyclicBondsIndex);
if (entry != -1)
{
int r = atoms->atom[a].resind;
if (a == atoms->nr - 1 || atoms->atom[a + 1].resind != r)
{
- BondedInteractionList* hbexcl = &globalPatches[r].rb[ebtsEXCLS];
+ BondedInteractionList* hbexcl = &globalPatches[r].rb[BondedTypes::Exclusions];
for (const auto& bondeds : hbexcl->b)
{
/* mark all entries as not matched yet */
for (int i = 0; i < atoms->nres; i++)
{
- for (int j = 0; j < ebtsNR; j++)
+ for (auto bondedsList : globalPatches[i].rb)
{
- for (auto& bondeds : globalPatches[i].rb[j].b)
+ for (auto& bondeds : bondedsList.b)
{
bondeds.match = false;
}
{
res += maxres - minres;
get_atomnames_min(3, anm, res, atoms, atomNumbers);
- BondedInteractionList* hbang = &globalPatches[res].rb[ebtsANGLES];
+ BondedInteractionList* hbang = &globalPatches[res].rb[BondedTypes::Angles];
for (auto& bondeds : hbang->b)
{
if (anm[1] == bondeds.aj())
{
res += maxres - minres;
get_atomnames_min(4, anm, res, atoms, atomNumbers);
- BondedInteractionList* hbdih = &globalPatches[res].rb[ebtsPDIHS];
+ BondedInteractionList* hbdih =
+ &globalPatches[res].rb[BondedTypes::ProperDihedrals];
for (auto& bondeds : hbdih->b)
{
bool bFound = false;
for (int i = 0; i < atoms->nres; i++)
{
/* Add remaining angles from hackblock */
- BondedInteractionList* hbang = &globalPatches[i].rb[ebtsANGLES];
+ BondedInteractionList* hbang = &globalPatches[i].rb[BondedTypes::Angles];
for (auto& bondeds : hbang->b)
{
if (bondeds.match)
}
/* Add remaining dihedrals from hackblock */
- BondedInteractionList* hbdih = &globalPatches[i].rb[ebtsPDIHS];
+ BondedInteractionList* hbdih = &globalPatches[i].rb[BondedTypes::ProperDihedrals];
for (auto& bondeds : hbdih->b)
{
if (bondeds.match)
if (!dih.empty())
{
fprintf(stderr, "Before cleaning: %zu dihedrals\n", dih.size());
- dih = clean_dih(dih, improper, atoms, rtpFFDB[0].bKeepAllGeneratedDihedrals,
- rtpFFDB[0].bRemoveDihedralIfWithImproper);
+ dih = clean_dih(dih, improper, atoms, rtpFFDB[0].bKeepAllGeneratedDihedrals, rtpFFDB[0].bRemoveDihedralIfWithImproper);
}
/* Now we have unique lists of angles and dihedrals
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static void low_mspeed(real tempi, gmx_mtop_t* mtop, rvec v[], gmx::ThreeFry2x64<>* rng, const gmx::MDLogger& logger)
{
int nrdf;
- real boltz;
real ekin, temp;
gmx::TabulatedNormalDistribution<real> normalDist;
- boltz = BOLTZ * tempi;
- ekin = 0.0;
- nrdf = 0;
+ ekin = 0.0;
+ nrdf = 0;
for (const AtomProxy atomP : AtomRange(*mtop))
{
const t_atom& local = atomP.atom();
if (mass > 0)
{
rng->restart(i, 0);
- real sd = std::sqrt(boltz / mass);
+ real sd = std::sqrt(gmx::c_boltz * tempi / mass);
for (int m = 0; (m < DIM); m++)
{
v[i][m] = sd * normalDist(*rng);
nrdf += DIM;
}
}
- temp = (2.0 * ekin) / (nrdf * BOLTZ);
+ temp = (2.0 * ekin) / (nrdf * gmx::c_boltz);
if (temp > 0)
{
real scal = std::sqrt(tempi / temp);
fprintf(debug,
"Velocities were taken from a Maxwell distribution\n"
"Initial generated temperature: %12.5e (scaled to: %12.5e)\n",
- temp, tempi);
+ temp,
+ tempi);
}
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstring>
#include <algorithm>
+#include <optional>
#include <string>
#include <utility>
#include <vector>
#include "gromacs/gmxpreprocess/toputil.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/topology/ifunc.h"
{
if (pline[0] == OPENDIR)
{
- strncpy(dirstr, pline + 1, STRLEN - 2);
+ strncpy(dirstr, pline + 1, STRLEN - 1);
if ((ch = strchr(dirstr, CLOSEDIR)) != nullptr)
{
(*ch) = 0;
else if (numberOfSites == 4)
{
/* angle */
- vsitetoplist->back().angle.emplace_back(s1String, s2String, s3String,
- strtod(s4, nullptr));
+ vsitetoplist->back().angle.emplace_back(
+ s1String, s2String, s3String, strtod(s4, nullptr));
/* angle */
}
else
{
gmx_fatal(FARGS,
"Need 3 or 4 values to specify bond/angle values in %s: %s\n",
- ddbname, pline);
+ ddbname,
+ pline);
}
}
break;
default:
gmx_fatal(FARGS,
- "Didnt find a case for directive %s in read_vsite_database\n", dirstr);
+ "Didnt find a case for directive %s in read_vsite_database\n",
+ dirstr);
}
}
}
});
if (foundBond == found->bond.end())
{
- gmx_fatal(FARGS, "Couldnt find bond %s-%s for residue %s in vsite database.\n",
- atom1.c_str(), atom2.c_str(), res.c_str());
+ gmx_fatal(FARGS,
+ "Couldnt find bond %s-%s for residue %s in vsite database.\n",
+ atom1.c_str(),
+ atom2.c_str(),
+ res.c_str());
}
return foundBond->value;
if (foundAngle == found->angle.end())
{
- gmx_fatal(FARGS, "Couldnt find angle %s-%s-%s for residue %s in vsite database.\n",
- atom1.c_str(), atom2.c_str(), atom3.c_str(), res.c_str());
+ gmx_fatal(FARGS,
+ "Couldnt find angle %s-%s-%s for residue %s in vsite database.\n",
+ atom1.c_str(),
+ atom2.c_str(),
+ atom3.c_str(),
+ res.c_str());
}
return foundAngle->value;
/* find heavy atom bound to this hydrogen */
heavy = NOTSET;
for (auto parm = psb->interactionTypes.begin();
- (parm != psb->interactionTypes.end()) && (heavy == NOTSET); parm++)
+ (parm != psb->interactionTypes.end()) && (heavy == NOTSET);
+ parm++)
{
if (parm->ai() == atom)
{
static int vsite_nm2type(const char* name, PreprocessingAtomTypes* atype)
{
- int tp;
-
- tp = atype->atomTypeFromName(name);
- if (tp == NOTSET)
+ auto tp = atype->atomTypeFromName(name);
+ if (!tp.has_value())
{
gmx_fatal(FARGS, "Dummy mass type (%s) not found in atom type database", name);
}
- return tp;
+ return *tp;
}
static real get_amass(int atom, t_atoms* at, gmx::ArrayRef<const PreprocessResidue> rtpFFDB, ResidueType* rt)
gmx_fatal(FARGS,
"cannot make constraint in add_vsites for %d heavy "
"atoms and %d hydrogen atoms",
- nrheavies, nrHatoms);
+ nrheavies,
+ nrHatoms);
}
my_add_param(&(plist[F_CONSTRNC]), Hatoms[i], heavies[0], NOTSET);
}
case F_VSITE3OUT:
if (nrheavies < 2)
{
- gmx_fatal(FARGS, "Not enough heavy atoms (%d) for %s (min 3)",
- nrheavies + 1, interaction_function[vsite_type[Hatoms[i]]].name);
+ gmx_fatal(FARGS,
+ "Not enough heavy atoms (%d) for %s (min 3)",
+ nrheavies + 1,
+ interaction_function[vsite_type[Hatoms[i]]].name);
}
add_vsite3_atoms(&plist[ftype], Hatoms[i], Heavy, heavies[0], heavies[1], bSwapParity);
break;
case F_VSITE4FDN:
if (nrheavies < 3)
{
- gmx_fatal(FARGS, "Not enough heavy atoms (%d) for %s (min 4)",
- nrheavies + 1, interaction_function[vsite_type[Hatoms[i]]].name);
+ gmx_fatal(FARGS,
+ "Not enough heavy atoms (%d) for %s (min 4)",
+ nrheavies + 1,
+ interaction_function[vsite_type[Hatoms[i]]].name);
}
add_vsite4_atoms(&plist[ftype], Hatoms[0], Heavy, heavies[0], heavies[1], heavies[2]);
break;
default:
- gmx_fatal(FARGS, "can't use add_vsites for interaction function %s",
+ gmx_fatal(FARGS,
+ "can't use add_vsites for interaction function %s",
interaction_function[vsite_type[Hatoms[i]]].name);
} /* switch ftype */
} /* else */
} /* for i */
}
-#define ANGLE_6RING (DEG2RAD * 120)
+#define ANGLE_6RING (gmx::c_deg2Rad * 120)
/* cosine rule: a^2 = b^2 + c^2 - 2 b c cos(alpha) */
/* get a^2 when a, b and alpha are given: */
b_CE3_HE3 = get_ddb_bond(vsitetop, "TRP", "CE3", "HE3");
b_CZ3_HZ3 = get_ddb_bond(vsitetop, "TRP", "CZ3", "HZ3");
- a_NE1_CE2_CD2 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "NE1", "CE2", "CD2");
- a_CE2_CD2_CG = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CE2", "CD2", "CG");
- a_CB_CG_CD2 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CB", "CG", "CD2");
- a_CD2_CG_CD1 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CD2", "CG", "CD1");
-
- a_CE2_CD2_CE3 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CE2", "CD2", "CE3");
- a_CD2_CE2_CZ2 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CD2", "CE2", "CZ2");
- a_CD2_CE3_CZ3 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CD2", "CE3", "CZ3");
- a_CE3_CZ3_HZ3 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CE3", "CZ3", "HZ3");
- a_CZ2_CH2_HH2 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CZ2", "CH2", "HH2");
- a_CE2_CZ2_HZ2 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CE2", "CZ2", "HZ2");
- a_CE2_CZ2_CH2 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CE2", "CZ2", "CH2");
- a_CG_CD1_HD1 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CG", "CD1", "HD1");
- a_HE1_NE1_CE2 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "HE1", "NE1", "CE2");
- a_CD2_CE3_HE3 = DEG2RAD * get_ddb_angle(vsitetop, "TRP", "CD2", "CE3", "HE3");
+ a_NE1_CE2_CD2 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, "TRP", "NE1", "CE2", "CD2");
+ a_CE2_CD2_CG = gmx::c_deg2Rad * get_ddb_angle(vsitetop, "TRP", "CE2", "CD2", "CG");
+ a_CB_CG_CD2 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, "TRP", "CB", "CG", "CD2");
+ a_CD2_CG_CD1 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, "TRP", "CD2", "CG", "CD1");
+
+ a_CE2_CD2_CE3 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, "TRP", "CE2", "CD2", "CE3");
+ a_CD2_CE2_CZ2 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, "TRP", "CD2", "CE2", "CZ2");
+ a_CD2_CE3_CZ3 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, "TRP", "CD2", "CE3", "CZ3");
+ a_CE3_CZ3_HZ3 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, "TRP", "CE3", "CZ3", "HZ3");
+ a_CZ2_CH2_HH2 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, "TRP", "CZ2", "CH2", "HH2");
+ a_CE2_CZ2_HZ2 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, "TRP", "CE2", "CZ2", "HZ2");
+ a_CE2_CZ2_CH2 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, "TRP", "CE2", "CZ2", "CH2");
+ a_CG_CD1_HD1 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, "TRP", "CG", "CD1", "HD1");
+ a_HE1_NE1_CE2 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, "TRP", "HE1", "NE1", "CE2");
+ a_CD2_CE3_HE3 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, "TRP", "CD2", "CE3", "HE3");
/* Calculate local coordinates.
* y-axis (x=0) is the bond CD2-CE2.
*/
rvec_sub(x[ats[atCB]], x[ats[atCG]], r_ij);
rvec_sub(x[ats[atCD2]], x[ats[atCG]], r_ik);
- calc_vsite3_param(xcom[0], ycom[0], xi[atCG], yi[atCG], xi[atCB], yi[atCB], xi[atCD2],
- yi[atCD2], &a, &b);
+ calc_vsite3_param(
+ xcom[0], ycom[0], xi[atCG], yi[atCG], xi[atCB], yi[atCB], xi[atCD2], yi[atCD2], &a, &b);
svmul(a, r_ij, t1);
svmul(b, r_ik, t2);
rvec_add(t1, t2, t1);
rvec_add(t1, x[ats[atCG]], (*newx)[atM[0]]);
- calc_vsite3_param(xcom[1], ycom[1], xi[atCG], yi[atCG], xi[atCB], yi[atCB], xi[atCD2],
- yi[atCD2], &a, &b);
+ calc_vsite3_param(
+ xcom[1], ycom[1], xi[atCG], yi[atCG], xi[atCB], yi[atCB], xi[atCD2], yi[atCD2], &a, &b);
svmul(a, r_ij, t1);
svmul(b, r_ik, t2);
rvec_add(t1, t2, t1);
(*newatom)[atM[j]].m = (*newatom)[atM[j]].mB = mM[j];
(*newatom)[atM[j]].q = (*newatom)[atM[j]].qB = 0.0;
(*newatom)[atM[j]].type = (*newatom)[atM[j]].typeB = tpM;
- (*newatom)[atM[j]].ptype = eptAtom;
+ (*newatom)[atM[j]].ptype = ParticleType::Atom;
(*newatom)[atM[j]].resind = at->atom[i0].resind;
(*newatom)[atM[j]].elem[0] = 'M';
(*newatom)[atM[j]].elem[1] = '\0';
{
if ((*vsite_type)[ats[i]] == F_VSITE3)
{
- calc_vsite3_param(xi[i], yi[i], xcom[0], ycom[0], xcom[1], ycom[1], xi[atCB], yi[atCB],
- &a, &b);
- add_vsite3_param(&plist[F_VSITE3], ats[i], add_shift + atM[0], add_shift + atM[1],
- ats[atCB], a, b);
+ calc_vsite3_param(
+ xi[i], yi[i], xcom[0], ycom[0], xcom[1], ycom[1], xi[atCB], yi[atCB], &a, &b);
+ add_vsite3_param(
+ &plist[F_VSITE3], ats[i], add_shift + atM[0], add_shift + atM[1], ats[atCB], a, b);
}
}
return nvsite;
bond_ch = get_ddb_bond(vsitetop, "TYR", "CD1", "HD1");
bond_co = get_ddb_bond(vsitetop, "TYR", "CZ", "OH");
bond_oh = get_ddb_bond(vsitetop, "TYR", "OH", "HH");
- angle_coh = DEG2RAD * get_ddb_angle(vsitetop, "TYR", "CZ", "OH", "HH");
+ angle_coh = gmx::c_deg2Rad * get_ddb_angle(vsitetop, "TYR", "CZ", "OH", "HH");
xi[atCG] = -bond_cc + bond_cc * std::cos(ANGLE_6RING);
xi[atCD1] = -bond_cc;
(*newatom)[atM].m = (*newatom)[atM].mB = mM;
(*newatom)[atM].q = (*newatom)[atM].qB = 0.0;
(*newatom)[atM].type = (*newatom)[atM].typeB = tpM;
- (*newatom)[atM].ptype = eptAtom;
+ (*newatom)[atM].ptype = ParticleType::Atom;
(*newatom)[atM].resind = at->atom[i0].resind;
(*newatom)[atM].elem[0] = 'M';
(*newatom)[atM].elem[1] = '\0';
b_CE1_NE2 = get_ddb_bond(vsitetop, resname, "CE1", "NE2");
b_CG_CD2 = get_ddb_bond(vsitetop, resname, "CG", "CD2");
b_CD2_NE2 = get_ddb_bond(vsitetop, resname, "CD2", "NE2");
- a_CG_ND1_CE1 = DEG2RAD * get_ddb_angle(vsitetop, resname, "CG", "ND1", "CE1");
- a_CG_CD2_NE2 = DEG2RAD * get_ddb_angle(vsitetop, resname, "CG", "CD2", "NE2");
- a_ND1_CE1_NE2 = DEG2RAD * get_ddb_angle(vsitetop, resname, "ND1", "CE1", "NE2");
- a_CE1_NE2_CD2 = DEG2RAD * get_ddb_angle(vsitetop, resname, "CE1", "NE2", "CD2");
+ a_CG_ND1_CE1 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, resname, "CG", "ND1", "CE1");
+ a_CG_CD2_NE2 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, resname, "CG", "CD2", "NE2");
+ a_ND1_CE1_NE2 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, resname, "ND1", "CE1", "NE2");
+ a_CE1_NE2_CD2 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, resname, "CE1", "NE2", "CD2");
if (ats[atHD1] != NOTSET)
{
b_ND1_HD1 = get_ddb_bond(vsitetop, resname, "ND1", "HD1");
- a_CE1_ND1_HD1 = DEG2RAD * get_ddb_angle(vsitetop, resname, "CE1", "ND1", "HD1");
+ a_CE1_ND1_HD1 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, resname, "CE1", "ND1", "HD1");
}
if (ats[atHE2] != NOTSET)
{
b_NE2_HE2 = get_ddb_bond(vsitetop, resname, "NE2", "HE2");
- a_CE1_NE2_HE2 = DEG2RAD * get_ddb_angle(vsitetop, resname, "CE1", "NE2", "HE2");
+ a_CE1_NE2_HE2 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, resname, "CE1", "NE2", "HE2");
}
if (ats[atHD2] != NOTSET)
{
b_CD2_HD2 = get_ddb_bond(vsitetop, resname, "CD2", "HD2");
- a_NE2_CD2_HD2 = DEG2RAD * get_ddb_angle(vsitetop, resname, "NE2", "CD2", "HD2");
+ a_NE2_CD2_HD2 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, resname, "NE2", "CD2", "HD2");
}
if (ats[atHE1] != NOTSET)
{
b_CE1_HE1 = get_ddb_bond(vsitetop, resname, "CE1", "HE1");
- a_NE2_CE1_HE1 = DEG2RAD * get_ddb_angle(vsitetop, resname, "NE2", "CE1", "HE1");
+ a_NE2_CE1_HE1 = gmx::c_deg2Rad * get_ddb_angle(vsitetop, resname, "NE2", "CE1", "HE1");
}
/* constraints between CG, CE1 and NE1 */
/* HE1 */
if (ats[atHE1] != NOTSET)
{
- calc_vsite3_param(x[atHE1], y[atHE1], x[atCE1], y[atCE1], x[atNE2], y[atNE2], x[atCG],
- y[atCG], &a, &b);
+ calc_vsite3_param(
+ x[atHE1], y[atHE1], x[atCE1], y[atCE1], x[atNE2], y[atNE2], x[atCG], y[atCG], &a, &b);
add_vsite3_param(&plist[F_VSITE3], ats[atHE1], ats[atCE1], ats[atNE2], ats[atCG], a, b);
}
/* HE2 */
if (ats[atHE2] != NOTSET)
{
- calc_vsite3_param(x[atHE2], y[atHE2], x[atNE2], y[atNE2], x[atCE1], y[atCE1], x[atCG],
- y[atCG], &a, &b);
+ calc_vsite3_param(
+ x[atHE2], y[atHE2], x[atNE2], y[atNE2], x[atCE1], y[atCE1], x[atCG], y[atCG], &a, &b);
add_vsite3_param(&plist[F_VSITE3], ats[atHE2], ats[atNE2], ats[atCE1], ats[atCG], a, b);
}
/* ND1 */
- calc_vsite3_param(x[atND1], y[atND1], x[atNE2], y[atNE2], x[atCE1], y[atCE1], x[atCG], y[atCG],
- &a, &b);
+ calc_vsite3_param(
+ x[atND1], y[atND1], x[atNE2], y[atNE2], x[atCE1], y[atCE1], x[atCG], y[atCG], &a, &b);
add_vsite3_param(&plist[F_VSITE3], ats[atND1], ats[atNE2], ats[atCE1], ats[atCG], a, b);
/* CD2 */
- calc_vsite3_param(x[atCD2], y[atCD2], x[atCE1], y[atCE1], x[atNE2], y[atNE2], x[atCG], y[atCG],
- &a, &b);
+ calc_vsite3_param(
+ x[atCD2], y[atCD2], x[atCE1], y[atCE1], x[atNE2], y[atNE2], x[atCG], y[atCG], &a, &b);
add_vsite3_param(&plist[F_VSITE3], ats[atCD2], ats[atCE1], ats[atNE2], ats[atCG], a, b);
/* HD1 */
if (ats[atHD1] != NOTSET)
{
- calc_vsite3_param(x[atHD1], y[atHD1], x[atNE2], y[atNE2], x[atCE1], y[atCE1], x[atCG],
- y[atCG], &a, &b);
+ calc_vsite3_param(
+ x[atHD1], y[atHD1], x[atNE2], y[atNE2], x[atCE1], y[atCE1], x[atCG], y[atCG], &a, &b);
add_vsite3_param(&plist[F_VSITE3], ats[atHD1], ats[atNE2], ats[atCE1], ats[atCG], a, b);
}
/* HD2 */
if (ats[atHD2] != NOTSET)
{
- calc_vsite3_param(x[atHD2], y[atHD2], x[atCE1], y[atCE1], x[atNE2], y[atNE2], x[atCG],
- y[atCG], &a, &b);
+ calc_vsite3_param(
+ x[atHD2], y[atHD2], x[atCE1], y[atCE1], x[atNE2], y[atNE2], x[atCG], y[atCG], &a, &b);
add_vsite3_param(&plist[F_VSITE3], ats[atHD2], ats[atCE1], ats[atNE2], ats[atCG], a, b);
}
return nvsite;
}
}
-static char atomnamesuffix[] = "1234";
+static const char atomnamesuffix[] = "1234";
void do_vsites(gmx::ArrayRef<const PreprocessResidue> rtpFFDB,
PreprocessingAtomTypes* atype,
/* the atnms for every residue MUST correspond to the enums in the
gen_vsites_* (one for each residue) routines! */
/* also the atom names in atnms MUST be in the same order as in the .rtp! */
- const char* atnms[resNR][MAXATOMSPERRESIDUE + 1] = {
- { "CG", /* PHE */
- "CD1", "HD1", "CD2", "HD2", "CE1", "HE1", "CE2", "HE2", "CZ", "HZ", nullptr },
- { "CB", /* TRP */
- "CG", "CD1", "HD1", "CD2", "NE1", "HE1", "CE2", "CE3", "HE3", "CZ2", "HZ2", "CZ3", "HZ3",
- "CH2", "HH2", nullptr },
- { "CG", /* TYR */
- "CD1", "HD1", "CD2", "HD2", "CE1", "HE1", "CE2", "HE2", "CZ", "OH", "HH", nullptr },
- { "CG", /* HIS */
- "ND1", "HD1", "CD2", "HD2", "CE1", "HE1", "NE2", "HE2", nullptr }
- };
+ const char* atnms[resNR][MAXATOMSPERRESIDUE + 1] = { { "CG", /* PHE */
+ "CD1",
+ "HD1",
+ "CD2",
+ "HD2",
+ "CE1",
+ "HE1",
+ "CE2",
+ "HE2",
+ "CZ",
+ "HZ",
+ nullptr },
+ { "CB", /* TRP */
+ "CG",
+ "CD1",
+ "HD1",
+ "CD2",
+ "NE1",
+ "HE1",
+ "CE2",
+ "CE3",
+ "HE3",
+ "CZ2",
+ "HZ2",
+ "CZ3",
+ "HZ3",
+ "CH2",
+ "HH2",
+ nullptr },
+ { "CG", /* TYR */
+ "CD1",
+ "HD1",
+ "CD2",
+ "HD2",
+ "CE1",
+ "HE1",
+ "CE2",
+ "HE2",
+ "CZ",
+ "OH",
+ "HH",
+ nullptr },
+ { "CG", /* HIS */
+ "ND1",
+ "HD1",
+ "CD2",
+ "HD2",
+ "CE1",
+ "HE1",
+ "NE2",
+ "HE2",
+ nullptr } };
if (debug)
{
"not enough atoms found (%d, need %d) in "
"residue %s %d while\n "
"generating aromatics virtual site construction",
- nrfound, needed, resnm, at->resinfo[resind].nr);
+ nrfound,
+ needed,
+ resnm,
+ at->resinfo[resind].nr);
}
/* Advance overall atom counter */
i++;
{
fprintf(stderr, "TRP at %d\n", o2n[ats[0]] + 1);
}
- nvsite += gen_vsites_trp(atype, &newx, &newatom, &newatomname, &o2n,
- &newvsite_type, &newcgnr, symtab, &nadd, *x, cgnr, at,
- vsite_type, plist, nrfound, ats, add_shift, vsitetop);
+ nvsite += gen_vsites_trp(atype,
+ &newx,
+ &newatom,
+ &newatomname,
+ &o2n,
+ &newvsite_type,
+ &newcgnr,
+ symtab,
+ &nadd,
+ *x,
+ cgnr,
+ at,
+ vsite_type,
+ plist,
+ nrfound,
+ ats,
+ add_shift,
+ vsitetop);
break;
case resTYR:
if (debug)
{
fprintf(stderr, "TYR at %d\n", o2n[ats[0]] + 1);
}
- nvsite += gen_vsites_tyr(atype, &newx, &newatom, &newatomname, &o2n,
- &newvsite_type, &newcgnr, symtab, &nadd, *x, cgnr, at,
- vsite_type, plist, nrfound, ats, add_shift, vsitetop);
+ nvsite += gen_vsites_tyr(atype,
+ &newx,
+ &newatom,
+ &newatomname,
+ &o2n,
+ &newvsite_type,
+ &newcgnr,
+ symtab,
+ &nadd,
+ *x,
+ cgnr,
+ at,
+ vsite_type,
+ plist,
+ nrfound,
+ ats,
+ add_shift,
+ vsitetop);
break;
case resHIS:
if (debug)
{
/* find heavy atom, count #bonds from it and #H atoms bound to it
and return H atom numbers (Hatoms) and heavy atom numbers (heavies) */
- count_bonds(i, &plist[F_BONDS], at->atomname, &nrbonds, &nrHatoms, Hatoms, &Heavy,
- &nrheavies, heavies);
+ count_bonds(i, &plist[F_BONDS], at->atomname, &nrbonds, &nrHatoms, Hatoms, &Heavy, &nrheavies, heavies);
/* get Heavy atom type */
tpHeavy = get_atype(Heavy, at, rtpFFDB, &rt);
- strcpy(tpname, atype->atomNameFromAtomType(tpHeavy));
+ strcpy(tpname, *atype->atomNameFromAtomType(tpHeavy));
bWARNING = FALSE;
bAddVsiteParam = TRUE;
/* get dummy mass type from first char of heavy atom type (N or C) */
strcpy(nexttpname,
- atype->atomNameFromAtomType(get_atype(heavies[0], at, rtpFFDB, &rt)));
+ *atype->atomNameFromAtomType(get_atype(heavies[0], at, rtpFFDB, &rt)));
std::string ch = get_dummymass_name(vsiteconflist, tpname, nexttpname);
std::string name;
if (ch.empty())
FARGS,
"Can't find dummy mass for type %s bonded to type %s in the "
"virtual site database (.vsd files). Add it to the database!\n",
- tpname, nexttpname);
+ tpname,
+ nexttpname);
}
else
{
gmx_fatal(FARGS,
"A dummy mass for type %s bonded to type %s is required, but "
"no virtual site database (.vsd) files where found.\n",
- tpname, nexttpname);
+ tpname,
+ nexttpname);
}
}
else
newatom[ni0 + j].m = newatom[ni0 + j].mB = mtot / NMASS;
newatom[ni0 + j].q = newatom[ni0 + j].qB = 0.0;
newatom[ni0 + j].type = newatom[ni0 + j].typeB = tpM;
- newatom[ni0 + j].ptype = eptAtom;
+ newatom[ni0 + j].ptype = ParticleType::Atom;
newatom[ni0 + j].resind = at->atom[i0].resind;
newatom[ni0 + j].elem[0] = 'M';
newatom[ni0 + j].elem[1] = '\0';
/* generate Heavy, H1, H2 and H3 from M1, M2 and heavies[0] */
/* note that vsite_type cannot be NOTSET, because we just set it */
- add_vsite3_atoms(&plist[(*vsite_type)[Heavy]], Heavy, heavies[0],
- add_shift + ni0, add_shift + ni0 + 1, FALSE);
+ add_vsite3_atoms(&plist[(*vsite_type)[Heavy]],
+ Heavy,
+ heavies[0],
+ add_shift + ni0,
+ add_shift + ni0 + 1,
+ FALSE);
for (int j = 0; j < nrHatoms; j++)
{
- add_vsite3_atoms(&plist[(*vsite_type)[Hatoms[j]]], Hatoms[j], heavies[0],
- add_shift + ni0, add_shift + ni0 + 1, Hat_SwapParity[j]);
+ add_vsite3_atoms(&plist[(*vsite_type)[Hatoms[j]]],
+ Hatoms[j],
+ heavies[0],
+ add_shift + ni0,
+ add_shift + ni0 + 1,
+ Hat_SwapParity[j]);
}
#undef NMASS
}
"Cannot convert atom %d %s (bound to a heavy atom "
"%s with \n"
" %d bonds and %d bound hydrogens atoms) to virtual site\n",
- i + 1, *(at->atomname[i]), tpname, nrbonds, nrHatoms);
+ i + 1,
+ *(at->atomname[i]),
+ tpname,
+ nrbonds,
+ nrHatoms);
}
if (bAddVsiteParam)
{
fprintf(debug, "Before inserting new atoms:\n");
for (int i = 0; i < at->nr; i++)
{
- fprintf(debug, "%4d %4d %4s %4d %4s %6d %-10s\n", i + 1, o2n[i] + 1,
- at->atomname[i] ? *(at->atomname[i]) : "(NULL)", at->resinfo[at->atom[i].resind].nr,
+ fprintf(debug,
+ "%4d %4d %4s %4d %4s %6d %-10s\n",
+ i + 1,
+ o2n[i] + 1,
+ at->atomname[i] ? *(at->atomname[i]) : "(NULL)",
+ at->resinfo[at->atom[i].resind].nr,
at->resinfo[at->atom[i].resind].name ? *(at->resinfo[at->atom[i].resind].name) : "(NULL)",
(*cgnr)[i],
((*vsite_type)[i] == NOTSET) ? "NOTSET" : interaction_function[(*vsite_type)[i]].name);
{
if (newatomname[i])
{
- fprintf(debug, "%4d %4s %4d %6d %-10s\n", i + 1,
- newatomname[i] ? *(newatomname[i]) : "(NULL)", newatom[i].resind, newcgnr[i],
+ fprintf(debug,
+ "%4d %4s %4d %6d %-10s\n",
+ i + 1,
+ newatomname[i] ? *(newatomname[i]) : "(NULL)",
+ newatom[i].resind,
+ newcgnr[i],
(newvsite_type[i] == NOTSET) ? "NOTSET"
: interaction_function[newvsite_type[i]].name);
}
gmx_fatal(FARGS,
"Added impossible amount of dummy masses "
"(%d on a total of %d atoms)\n",
- nadd, at->nr - nadd);
+ nadd,
+ at->nr - nadd);
}
if (debug)
fprintf(debug, "After inserting new atoms:\n");
for (int i = 0; i < at->nr; i++)
{
- fprintf(debug, "%4d %4s %4d %4s %6d %-10s\n", i + 1,
- at->atomname[i] ? *(at->atomname[i]) : "(NULL)", at->resinfo[at->atom[i].resind].nr,
+ fprintf(debug,
+ "%4d %4s %4d %4s %6d %-10s\n",
+ i + 1,
+ at->atomname[i] ? *(at->atomname[i]) : "(NULL)",
+ at->resinfo[at->atom[i].resind].nr,
at->resinfo[at->atom[i].resind].name ? *(at->resinfo[at->atom[i].resind].name) : "(NULL)",
(*cgnr)[i],
((*vsite_type)[i] == NOTSET) ? "NOTSET" : interaction_function[(*vsite_type)[i]].name);
/* find bonded heavy atom */
int a = NOTSET;
for (auto parm = psb->interactionTypes.begin();
- (parm != psb->interactionTypes.end()) && (a == NOTSET); parm++)
+ (parm != psb->interactionTypes.end()) && (a == NOTSET);
+ parm++)
{
/* if other atom is not a virtual site, it is the one we want */
if ((parm->ai() == i) && !is_vsite(vsite_type[parm->aj()]))
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/math/3dtransforms.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/md_enums.h"
{ "-renumber", FALSE, etBOOL, { &bRenum }, "Renumber residues" }
};
- if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa, asize(desc), desc,
- asize(bugs), bugs, &oenv))
+ if (!parse_common_args(
+ &argc, argv, 0, NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
gmx_mtop_t mtop;
bool haveTop = false;
readConfAndTopology(opt2fn("-f", NFILE, fnm), &haveTop, &mtop, &pbcType, &x, &v, box);
- t_atoms atoms = gmx_mtop_global_atoms(&mtop);
+ t_atoms atoms = gmx_mtop_global_atoms(mtop);
natoms = atoms.nr;
nres = atoms.nres; /* nr of residues in one element? */
/* make space for all the atoms */
{
/* we'll recursively add atoms to atoms */
int pos = 0;
- for (auto& singlePatch : newPatch.hack)
+ for (const auto& singlePatch : newPatch.hack)
{
/* first check if we're in the N- or C-terminus, then we should ignore
all hacks involving atoms from resp. previous or next residue
{
fprintf(debug,
"Hack '%s' %d, replacing nname '%s' with '%s' (old name '%s')\n",
- localAtomName.c_str(), pos, patch->nname.c_str(),
+ localAtomName.c_str(),
+ pos,
+ patch->nname.c_str(),
singlePatch.nname.c_str(),
patch->oname.empty() ? "" : patch->oname.c_str());
}
for (int k = 0; k < singlePatch.nr; k++)
{
expand_hackblocks_one(
- newPatch, globalPatches->at(globalPatches->size() - singlePatch.nr + k).nname,
- globalPatches, bN, bC);
+ newPatch,
+ globalPatches->at(globalPatches->size() - singlePatch.nr + k).nname,
+ globalPatches,
+ bN,
+ bC);
}
}
}
bool bFoundAll = true;
for (int m = 0; (m < patch->nctl && bFoundAll); m++)
{
- int ia = pdbasearch_atom(patch->a[m].c_str(), rnr, pdba, bCheckMissing ? "atom" : "check",
- !bCheckMissing, cyclicBondsIndex);
+ int ia = pdbasearch_atom(patch->a[m].c_str(),
+ rnr,
+ pdba,
+ bCheckMissing ? "atom" : "check",
+ !bCheckMissing,
+ cyclicBondsIndex);
if (ia < 0)
{
/* not found in original atoms, might still be in
"Atom %s not found in residue %s %d"
", rtp entry %s"
" while adding hydrogens",
- patch->a[m].c_str(), *pdba->resinfo[rnr].name,
- pdba->resinfo[rnr].nr, *pdba->resinfo[rnr].rtp);
+ patch->a[m].c_str(),
+ *pdba->resinfo[rnr].name,
+ pdba->resinfo[rnr].nr,
+ *pdba->resinfo[rnr].rtp);
}
}
}
{
if (gmx_debug_at)
{
- fprintf(debug, "Replacing %d '%s' with (old name '%s') %s\n", newi,
+ fprintf(debug,
+ "Replacing %d '%s' with (old name '%s') %s\n",
+ newi,
((*modifiedAtoms)->atomname[newi] && *(*modifiedAtoms)->atomname[newi])
? *(*modifiedAtoms)->atomname[newi]
: "",
}
if (debug)
{
- fprintf(debug, " %s %g %g", *(*modifiedAtoms)->atomname[newi],
- (*modifiedAtoms)->atom[newi].m, (*modifiedAtoms)->atom[newi].q);
+ fprintf(debug,
+ " %s %g %g",
+ *(*modifiedAtoms)->atomname[newi],
+ (*modifiedAtoms)->atom[newi].m,
+ (*modifiedAtoms)->atom[newi].q);
}
}
}
do
{
nold = nnew;
- nnew = add_h_low(initialAtoms, localAtoms, xptr, globalPatches, symtab, nterpairs, ntdb,
- ctdb, rN, rC, FALSE, cyclicBondsIndex);
+ nnew = add_h_low(
+ initialAtoms, localAtoms, xptr, globalPatches, symtab, nterpairs, ntdb, ctdb, rN, rC, FALSE, cyclicBondsIndex);
niter++;
if (niter > 100)
{
if (!bAllowMissing)
{
/* Call add_h_low once more, now only for the missing atoms check */
- add_h_low(initialAtoms, localAtoms, xptr, globalPatches, symtab, nterpairs, ntdb, ctdb, rN,
- rC, TRUE, cyclicBondsIndex);
+ add_h_low(initialAtoms, localAtoms, xptr, globalPatches, symtab, nterpairs, ntdb, ctdb, rN, rC, TRUE, cyclicBondsIndex);
}
return nnew;
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx_fatal(FARGS, "No more replaceable solvent!");
}
- fprintf(stderr, "Replacing solvent molecule %d (atom %d) with %s\n",
- solventMoleculesForReplacement->back(), solventMoleculeAtomsToBeReplaced[0], ionname);
+ fprintf(stderr,
+ "Replacing solvent molecule %d (atom %d) with %s\n",
+ solventMoleculesForReplacement->back(),
+ solventMoleculeAtomsToBeReplaced[0],
+ ionname);
/* Replace solvent molecule charges with ion charge */
notSolventGroup->push_back(solventMoleculeAtomsToBeReplaced[0]);
// charge while the rest of the solvent molecule atoms is set to 0 charge.
atoms->atom[solventMoleculeAtomsToBeReplaced.front()].q = q;
for (auto replacedMoleculeAtom = solventMoleculeAtomsToBeReplaced.begin() + 1;
- replacedMoleculeAtom != solventMoleculeAtomsToBeReplaced.end(); ++replacedMoleculeAtom)
+ replacedMoleculeAtom != solventMoleculeAtomsToBeReplaced.end();
+ ++replacedMoleculeAtom)
{
atoms->atom[*replacedMoleculeAtom].q = 0;
}
gmx_ffclose(fpout);
gmx_fatal(FARGS,
"No line with moleculetype '%s' found the [ molecules ] section of file '%s'",
- grpname, topinout);
+ grpname,
+ topinout);
}
if (nsol_last < p_num + n_num)
{
gmx_fatal(FARGS,
"The last entry for moleculetype '%s' in the [ molecules ] section of file '%s' "
"has less solvent molecules (%d) than were replaced (%d)",
- grpname, topinout, nsol_last, p_num + n_num);
+ grpname,
+ topinout,
+ nsol_last,
+ p_num + n_num);
}
/* Print all the molecule entries */
{
printf("Replacing %d solute molecules in topology file (%s) "
" by %d %s and %d %s ions.\n",
- p_num + n_num, topinout, p_num, p_name, n_num, n_name);
+ p_num + n_num,
+ topinout,
+ p_num,
+ p_name,
+ n_num,
+ n_name);
nsol_last -= p_num + n_num;
if (nsol_last > 0)
{
if (numIndicesToAdd > 0)
{
invertedGroup.resize(invertedGroup.size() + numIndicesToAdd);
- std::iota(std::end(invertedGroup) - numIndicesToAdd, std::end(invertedGroup),
- firstToAddToInvertedGroup);
+ std::iota(std::end(invertedGroup) - numIndicesToAdd, std::end(invertedGroup), firstToAddToInvertedGroup);
}
}
{ efTOP, "-p", "topol", ffOPTRW } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa, asize(desc), desc,
- asize(bugs), bugs, &oenv))
+ if (!parse_common_args(
+ &argc, argv, 0, NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
if (oenv != nullptr)
{
{
/* Compute number of ions to be added */
vol = det(box);
- nsalt = gmx::roundToInt(conc * vol * AVOGADRO / 1e24);
+ nsalt = gmx::roundToInt(conc * vol * gmx::c_avogadro / 1e24);
p_num = abs(nsalt * n_q);
n_num = abs(nsalt * p_q);
}
gmx_fatal(FARGS,
"Can't neutralize this system using -nq %d and"
" -pq %d.\n",
- n_q, p_q);
+ n_q,
+ p_q);
}
while (qdelta != 0)
gmx_fatal(FARGS,
"The solvent group %s is not continuous: "
"index[%d]=%d, index[%d]=%d",
- grpname, int(i), solventGroup[i - 1] + 1, int(i + 1), solventGroup[i] + 1);
+ grpname,
+ int(i),
+ solventGroup[i - 1] + 1,
+ int(i + 1),
+ solventGroup[i] + 1);
}
}
nsa = 1;
}
if (solventGroup.size() % nsa != 0)
{
- gmx_fatal(FARGS, "Your solvent group size (%td) is not a multiple of %d",
- gmx::ssize(solventGroup), nsa);
+ gmx_fatal(FARGS,
+ "Your solvent group size (%td) is not a multiple of %d",
+ gmx::ssize(solventGroup),
+ nsa);
}
nw = solventGroup.size() / nsa;
fprintf(stderr, "Number of (%d-atomic) solvent molecules: %d\n", nsa, nw);
// Randomly shuffle the solvent molecules that shall be replaced by ions
// then pick molecules from the back of the list as replacement candidates
gmx::DefaultRandomEngine rng(seed);
- std::shuffle(std::begin(solventMoleculesForReplacement),
- std::end(solventMoleculesForReplacement), rng);
+ std::shuffle(
+ std::begin(solventMoleculesForReplacement), std::end(solventMoleculesForReplacement), rng);
/* Now loop over the ions that have to be placed */
while (p_num-- > 0)
{
- insert_ion(nsa, &solventMoleculesForReplacement, repl, solventGroup, x, &pbc, 1, p_q,
- p_name, &atoms, rmin, ¬SolventGroup);
+ insert_ion(
+ nsa, &solventMoleculesForReplacement, repl, solventGroup, x, &pbc, 1, p_q, p_name, &atoms, rmin, ¬SolventGroup);
}
while (n_num-- > 0)
{
- insert_ion(nsa, &solventMoleculesForReplacement, repl, solventGroup, x, &pbc, -1, n_q,
- n_name, &atoms, rmin, ¬SolventGroup);
+ insert_ion(
+ nsa, &solventMoleculesForReplacement, repl, solventGroup, x, &pbc, -1, n_q, n_name, &atoms, rmin, ¬SolventGroup);
}
fprintf(stderr, "\n");
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
fprintf(stderr, "\nReading structure file\n");
readConfAndTopology(xfn, &haveTopology, &mtop, nullptr, &x, &v, box);
title = *mtop.name;
- atoms = gmx_mtop_global_atoms(&mtop);
+ atoms = gmx_mtop_global_atoms(mtop);
if (atoms.pdbinfo == nullptr)
{
snew(atoms.pdbinfo, atoms.nr);
{
fprintf(out, "; distance restraints for %s of %s\n\n", indexGroupNames, title);
fprintf(out, "[ distance_restraints ]\n");
- fprintf(out, ";%4s %5s %1s %5s %10s %10s %10s %10s %10s\n", "i", "j", "?", "label",
- "funct", "lo", "up1", "up2", "weight");
+ fprintf(out,
+ ";%4s %5s %1s %5s %10s %10s %10s %10s %10s\n",
+ "i",
+ "j",
+ "?",
+ "label",
+ "funct",
+ "lo",
+ "up1",
+ "up2",
+ "weight");
}
for (i = k = 0; i < igrp; i++)
{
}
lo = std::max(0.0_real, d - dd);
hi = d + dd;
- fprintf(out, "%5d %5d %1d %5d %10d %10g %10g %10g %10g\n", indexGroups[i] + 1,
- indexGroups[j] + 1, 1, k, 1, lo, hi, hi + disre_up2, 1.0);
+ fprintf(out,
+ "%5d %5d %1d %5d %10d %10g %10g %10g %10g\n",
+ indexGroups[i] + 1,
+ indexGroups[j] + 1,
+ 1,
+ k,
+ 1,
+ lo,
+ hi,
+ hi + disre_up2,
+ 1.0);
}
}
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
std::string inc_fn = dval.substr(i0, len);
/* Open include file and store it as a child in the handle structure */
- int status = cpp_open_file(inc_fn.c_str(), &(handle->child), nullptr, &handle->defines,
- &handle->includes);
+ int status = cpp_open_file(
+ inc_fn.c_str(), &(handle->child), nullptr, &handle->defines, &handle->includes);
if (status != eCPP_OK)
{
handle->child = nullptr;
status = eCPP_NR;
}
- sprintf(buf, "%s - File %s, line %d\nLast line read:\n'%s'", ecpp[status],
+ sprintf(buf,
+ "%s - File %s, line %d\nLast line read:\n'%s'",
+ ecpp[status],
(handle && !handle->fn.empty()) ? handle->fn.c_str() : "unknown",
- (handle) ? handle->line_nr : -1, !handle->line.empty() ? handle->line.c_str() : "");
+ (handle) ? handle->line_nr : -1,
+ !handle->line.empty() ? handle->line.c_str() : "");
return gmx_strdup(buf);
}
"The following macros were defined in the 'define' mdp field with the -D prefix, "
"but "
"were not used in the topology:\n";
- for (auto& str : handle.unmatched_defines)
+ for (const auto& str : handle.unmatched_defines)
{
warning += (" " + str + "\n");
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2011,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstring>
#include <algorithm>
+#include <optional>
#include "gromacs/gmxpreprocess/grompp_impl.h"
#include "gromacs/gmxpreprocess/notset.h"
size_t size() const { return types.size(); }
//! The actual atom type data.
std::vector<AtomTypeData> types;
+ //! Map from \c types[i].name to \c i for quick look-up in \ref atomTypeFromName. Ref #3974.
+ std::unordered_map<std::string, int> nameToAtomType;
};
bool PreprocessingAtomTypes::isSet(int nt) const
return ((nt >= 0) && (nt < gmx::ssize(*this)));
}
-int PreprocessingAtomTypes::atomTypeFromName(const std::string& str) const
+std::optional<int> PreprocessingAtomTypes::atomTypeFromName(const std::string& str) const
{
/* Atom types are always case sensitive */
- auto found = std::find_if(impl_->types.begin(), impl_->types.end(),
- [&str](const auto& type) { return str == *type.name_; });
- if (found == impl_->types.end())
+ const auto found = impl_->nameToAtomType.find(str);
+ if (found == impl_->nameToAtomType.end())
{
- return NOTSET;
+ return std::nullopt;
}
else
{
- return std::distance(impl_->types.begin(), found);
+ GMX_ASSERT(str == *impl_->types[found->second].name_,
+ "Invalid data in atomTypeFromName lookup table");
+ return std::make_optional(found->second);
}
}
return impl_->size();
}
-const char* PreprocessingAtomTypes::atomNameFromAtomType(int nt) const
+std::optional<const char*> PreprocessingAtomTypes::atomNameFromAtomType(int nt) const
{
- return isSet(nt) ? *(impl_->types[nt].name_) : nullptr;
+ return isSet(nt) ? std::make_optional(*(impl_->types[nt].name_)) : std::nullopt;
}
-real PreprocessingAtomTypes::atomMassFromAtomType(int nt) const
+std::optional<real> PreprocessingAtomTypes::atomMassFromAtomType(int nt) const
{
- return isSet(nt) ? impl_->types[nt].atom_.m : NOTSET;
+ return isSet(nt) ? std::make_optional(impl_->types[nt].atom_.m) : std::nullopt;
}
-real PreprocessingAtomTypes::atomChargeFromAtomType(int nt) const
+std::optional<real> PreprocessingAtomTypes::atomChargeFromAtomType(int nt) const
{
- return isSet(nt) ? impl_->types[nt].atom_.q : NOTSET;
+ return isSet(nt) ? std::make_optional(impl_->types[nt].atom_.q) : std::nullopt;
}
-int PreprocessingAtomTypes::atomParticleTypeFromAtomType(int nt) const
+std::optional<ParticleType> PreprocessingAtomTypes::atomParticleTypeFromAtomType(int nt) const
{
- return isSet(nt) ? impl_->types[nt].atom_.ptype : NOTSET;
+ return isSet(nt) ? std::make_optional(impl_->types[nt].atom_.ptype) : std::nullopt;
}
-int PreprocessingAtomTypes::bondAtomTypeFromAtomType(int nt) const
+std::optional<int> PreprocessingAtomTypes::bondAtomTypeFromAtomType(int nt) const
{
- return isSet(nt) ? impl_->types[nt].bondAtomType_ : NOTSET;
+ return isSet(nt) ? std::make_optional(impl_->types[nt].bondAtomType_) : std::nullopt;
}
-int PreprocessingAtomTypes::atomNumberFromAtomType(int nt) const
+std::optional<int> PreprocessingAtomTypes::atomNumberFromAtomType(int nt) const
{
- return isSet(nt) ? impl_->types[nt].atomNumber_ : NOTSET;
+ return isSet(nt) ? std::make_optional(impl_->types[nt].atomNumber_) : std::nullopt;
}
-real PreprocessingAtomTypes::atomNonBondedParamFromAtomType(int nt, int param) const
+std::optional<real> PreprocessingAtomTypes::atomNonBondedParamFromAtomType(int nt, int param) const
{
if (!isSet(nt))
{
- return NOTSET;
+ return std::nullopt;
}
gmx::ArrayRef<const real> forceParam = impl_->types[nt].nb_.forceParam();
if ((param < 0) || (param >= MAXFORCEPARAM))
{
- return NOTSET;
+ return std::nullopt;
}
- return forceParam[param];
+ return std::make_optional(forceParam[param]);
}
PreprocessingAtomTypes::PreprocessingAtomTypes() : impl_(new Impl) {}
int bondAtomType,
int atomNumber)
{
- int position = atomTypeFromName(name);
- if (position == NOTSET)
+ auto position = atomTypeFromName(name);
+ if (!position.has_value())
{
impl_->types.emplace_back(a, put_symtab(tab, name.c_str()), nb, bondAtomType, atomNumber);
- return atomTypeFromName(name);
+ const int newType = impl_->types.size() - 1;
+ impl_->nameToAtomType[name] = newType;
+ return newType;
}
else
{
- return position;
+ return *position;
}
}
-int PreprocessingAtomTypes::setType(int nt,
- t_symtab* tab,
- const t_atom& a,
- const std::string& name,
- const InteractionOfType& nb,
- int bondAtomType,
- int atomNumber)
+std::optional<int> PreprocessingAtomTypes::setType(int nt,
+ t_symtab* tab,
+ const t_atom& a,
+ const std::string& name,
+ const InteractionOfType& nb,
+ int bondAtomType,
+ int atomNumber)
{
if (!isSet(nt))
{
- return NOTSET;
+ return std::nullopt;
}
impl_->types[nt].atom_ = a;
impl_->types[nt].bondAtomType_ = bondAtomType;
impl_->types[nt].atomNumber_ = atomNumber;
- return nt;
+ return std::make_optional(nt);
}
void PreprocessingAtomTypes::printTypes(FILE* out)
{
- fprintf(out, "[ %s ]\n", dir2str(Directive::d_atomtypes));
- fprintf(out, "; %6s %8s %8s %8s %12s %12s\n", "type", "mass", "charge", "particle", "c6",
+ fprintf(out, "[ %s ]\n", enumValueToString(Directive::d_atomtypes));
+ fprintf(out,
+ "; %6s %8s %8s %8s %12s %12s\n",
+ "type",
+ "mass",
+ "charge",
+ "particle",
+ "c6",
"c12");
for (auto& entry : impl_->types)
{
- fprintf(out, "%8s %8.3f %8.3f %8s %12e %12e\n", *(entry.name_), entry.atom_.m,
- entry.atom_.q, "A", entry.nb_.c0(), entry.nb_.c1());
+ fprintf(out,
+ "%8s %8.3f %8.3f %8s %12e %12e\n",
+ *(entry.name_),
+ entry.atom_.m,
+ entry.atom_.q,
+ "A",
+ entry.nb_.c0(),
+ entry.nb_.c1());
}
fprintf(out, "\n");
/* Check atomnumber */
int tli = typelist[i];
- bFound = bFound && (ga->atomNumberFromAtomType(tli) == ga->atomNumberFromAtomType(thistype));
+ bFound = bFound
+ && (*ga->atomNumberFromAtomType(tli) == *ga->atomNumberFromAtomType(thistype));
}
if (bFound)
{
const t_atoms* atoms = &moltype.atoms;
for (int i = 0; (i < atoms->nr); i++)
{
- atoms->atom[i].type = search_atomtypes(this, &nat, typelist, atoms->atom[i].type,
- plist[ftype].interactionTypes, ftype);
- atoms->atom[i].typeB = search_atomtypes(this, &nat, typelist, atoms->atom[i].typeB,
- plist[ftype].interactionTypes, ftype);
+ atoms->atom[i].type = search_atomtypes(
+ this, &nat, typelist, atoms->atom[i].type, plist[ftype].interactionTypes, ftype);
+ atoms->atom[i].typeB = search_atomtypes(
+ this, &nat, typelist, atoms->atom[i].typeB, plist[ftype].interactionTypes, ftype);
}
}
{
if (wall_atomtype[i] >= 0)
{
- wall_atomtype[i] = search_atomtypes(this, &nat, typelist, wall_atomtype[i],
- plist[ftype].interactionTypes, ftype);
+ wall_atomtype[i] = search_atomtypes(
+ this, &nat, typelist, wall_atomtype[i], plist[ftype].interactionTypes, ftype);
}
}
/* Renumber nlist */
std::vector<InteractionOfType> nbsnew;
+ // Reset the map used for fast lookups, and refill it below
+ impl_->nameToAtomType.clear();
+
for (int i = 0; (i < nat); i++)
{
int mi = typelist[i];
{
int mj = typelist[j];
const InteractionOfType& interactionType = plist[ftype].interactionTypes[ntype * mi + mj];
- nbsnew.emplace_back(interactionType.atoms(), interactionType.forceParam(),
+ nbsnew.emplace_back(interactionType.atoms(),
+ interactionType.forceParam(),
interactionType.interactionTypeName());
}
new_types.push_back(impl_->types[mi]);
+ impl_->nameToAtomType[std::string(*impl_->types[mi].name_)] = new_types.size() - 1;
}
mtop->ffparams.atnr = nat;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2014,2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014,2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
+#include <memory>
+#include <optional>
#include <string>
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/real.h"
struct gmx_mtop_t;
class InteractionOfType;
struct InteractionsOfType;
struct t_symtab;
-
+enum class ParticleType : int;
namespace gmx
{
template<typename>
~PreprocessingAtomTypes();
/*! \brief
- * Get atom type index for atom type name if present in the database, or NOTSET.
+ * Get atom type index for atom type name if present in the database, or empty optional.
*
* \todo The code should be changed to instead use a gmx::compat version
* of std::optional to return an iterator to the element being searched,
* or an empty optional construct if the entry has not been found.
*
* \param[in] str Input string to search type for.
- * \returns Atomtype as integer.
+ * \returns Optional atomtype as integer.
*/
- int atomTypeFromName(const std::string& str) const;
+ std::optional<int> atomTypeFromName(const std::string& str) const;
//! Get number of defined atom types.
size_t size() const;
* Get name of atom from internal atom type number.
*
* \param[in] nt Internal number of atom type.
- * \returns The type name.
+ * \returns The optional type name.
*/
- const char* atomNameFromAtomType(int nt) const;
+ std::optional<const char*> atomNameFromAtomType(int nt) const;
/*! \brief
* Get normal mass of atom from internal atom type number.
*
* \param[in] nt Internal number of atom type.
- * \returns The mass for the atom or NOTSET.
+ * \returns The optional mass for the atom.
*/
- real atomMassFromAtomType(int nt) const;
+ std::optional<real> atomMassFromAtomType(int nt) const;
/*! \brief
* Get normal charge of atom from internal atom type number.
*
* \param[in] nt Internal number of atom type.
- * \returns The charge for the atom or NOTSET.
+ * \returns The optional charge for the atom.
*/
- real atomChargeFromAtomType(int nt) const;
+ std::optional<real> atomChargeFromAtomType(int nt) const;
/*! \brief
* Get particle type for atom type \p nt
*
* \param[in] nt Internal number of atom type.
- * \returns The particle type or NOTSET.
+ * \returns The optional particle type.
*/
- int atomParticleTypeFromAtomType(int nt) const;
+ std::optional<ParticleType> atomParticleTypeFromAtomType(int nt) const;
/*! \brief
* Get bond atom parameter of atom from internal atom type number.
*
* \param[in] nt Internal number of atom type.
- * \returns The bond atom parameter or NOTSET.
+ * \returns The optional bond atom parameter.
*/
- int bondAtomTypeFromAtomType(int nt) const;
+ std::optional<int> bondAtomTypeFromAtomType(int nt) const;
/*! \brief
* Get atomic number of atom from internal atom type number.
*
* \param[in] nt Internal number of atom type.
- * \returns The atomic number type or NOTSET.
+ * \returns The optional atomic number type.
*/
- int atomNumberFromAtomType(int nt) const;
+ std::optional<int> atomNumberFromAtomType(int nt) const;
/*! \brief
* Get the value of \p param of type \p nt.
*
* \param[in] param The parameter value to find.
* \param[in] nt The number of the type.
- * \returns The value of the parameter or NOTSET.
+ * \returns The optional value of the parameter.
*/
- real atomNonBondedParamFromAtomType(int nt, int param) const;
+ std::optional<real> atomNonBondedParamFromAtomType(int nt, int param) const;
/*! \brief
* If a value is within the range of the current types or not.
* \param[in] nb Nonbonded parameters.
* \param[in] bondAtomType What kind of bonded interactions are there.
* \param[in] atomNumber Atomic number of the entry.
- * \returns Number of the type set or NOTSET
+ * \returns Optional number of the type set.
*/
- int setType(int nt,
- t_symtab* tab,
- const t_atom& a,
- const std::string& name,
- const InteractionOfType& nb,
- int bondAtomType,
- int atomNumber);
+ std::optional<int> setType(int nt,
+ t_symtab* tab,
+ const t_atom& a,
+ const std::string& name,
+ const InteractionOfType& nb,
+ int bondAtomType,
+ int atomNumber);
/*! \brief
- * Add new atom type to database.
+ * Add a unique type to the database.
*
* \param[in] tab Symbol table.
* \param[in] a Atom information.
* \param[in] nb Nonbonded parameters.
* \param[in] bondAtomType What kind of bonded interactions are there.
* \param[in] atomNumber Atomic number of the entry.
- * \returns Number of entries in database.
+ * \returns Index to the type in the database. If the type shares
+ * a name with an existing type, return the index of that type.
*/
int addType(t_symtab* tab,
const t_atom& a,
private:
class Impl;
//! Pimpl that holds the data.
- gmx::PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
#endif
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2011,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstring>
#include <algorithm>
+#include <optional>
#include <vector>
#include "gromacs/gmxpreprocess/notset.h"
#include "gromacs/topology/symtab.h"
-#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
class PreprocessingBondAtomType::Impl
std::vector<char**> typeNames;
};
-int PreprocessingBondAtomType::bondAtomTypeFromName(const std::string& str) const
+std::optional<int> PreprocessingBondAtomType::bondAtomTypeFromName(const std::string& str) const
{
/* Atom types are always case sensitive */
- auto found =
- std::find_if(impl_->typeNames.begin(), impl_->typeNames.end(),
- [&str](const auto& type) { return str == const_cast<const char*>(*type); });
+ auto found = std::find_if(impl_->typeNames.begin(),
+ impl_->typeNames.end(),
+ [&str](const auto& type) { return str == std::string(*type); });
if (found == impl_->typeNames.end())
{
- return NOTSET;
+ return std::nullopt;
}
else
{
- return std::distance(impl_->typeNames.begin(), found);
+ return std::make_optional(std::distance(impl_->typeNames.begin(), found));
}
}
-const char* PreprocessingBondAtomType::atomNameFromBondAtomType(int nt) const
+std::optional<const char*> PreprocessingBondAtomType::atomNameFromBondAtomType(int nt) const
{
- return isSet(nt) ? *impl_->typeNames[nt] : nullptr;
+ return isSet(nt) ? *impl_->typeNames[nt] : std::optional<const char*>{};
}
PreprocessingBondAtomType::PreprocessingBondAtomType() : impl_(new Impl) {}
int PreprocessingBondAtomType::addBondAtomType(t_symtab* tab, const std::string& name)
{
- int position = bondAtomTypeFromName(name);
- if (position == NOTSET)
+ auto position = bondAtomTypeFromName(name);
+ if (!position.has_value())
{
impl_->typeNames.emplace_back(put_symtab(tab, name.c_str()));
- return bondAtomTypeFromName(name);
+ if (auto bondAtomType = bondAtomTypeFromName(name); bondAtomType.has_value())
+ {
+ return *bondAtomType;
+ }
+ else
+ {
+ GMX_RELEASE_ASSERT(false, "Unhandled error in adding bond atom type");
+ return 0;
+ }
}
else
{
- return position;
+ return *position;
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
+#include <memory>
+#include <optional>
#include <string>
-#include "gromacs/utility/classhelpers.h"
-
struct t_symtab;
/*! \libinternal \brief
* Get name of atom from internal bond atom type number.
*
* \param[in] nt Internal number of atom type.
- * \returns The type name.
+ * \returns The optional type name.
*/
- const char* atomNameFromBondAtomType(int nt) const;
+ std::optional<const char*> atomNameFromBondAtomType(int nt) const;
/*! \brief
* Get bond atom type index for atom type name if present in the database, or NOTSET.
* or an empty optional construct if the entry has not been found.
*
* \param[in] str Input string to search type for.
- * \returns Atomtype as integer.
+ * \returns Optional atomtype as integer.
*/
- int bondAtomTypeFromName(const std::string& str) const;
+ std::optional<int> bondAtomTypeFromName(const std::string& str) const;
/*! \brief
- * Add a complete new bond atom type.
+ * Add a unique type to the database.
*
* \param[in] tab Symbol table.
* \param[in] name Atom name.
- * \returns The number of entries in database or the type number of an already set type.
+ * \returns Index to the type in the database. If the type shares
+ * a name with an existing type, return the index of that type.
*/
int addBondAtomType(t_symtab* tab, const std::string& name);
private:
class Impl;
//! Pimpl that holds the data.
- gmx::PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
#endif
#include "grompp.h"
+#include <array>
#include <cerrno>
#include <climits>
#include <cmath>
#include "gromacs/mdlib/calc_verletbuf.h"
#include "gromacs/mdlib/compute_io.h"
#include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/md_support.h"
#include "gromacs/mdlib/perf_est.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdrun/mdmodules.h"
#include "gromacs/utility/listoflists.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/loggerbuilder.h"
-#include "gromacs/utility/mdmodulenotification.h"
+#include "gromacs/utility/mdmodulesnotifiers.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/snprintf.h"
InteractionOfType::InteractionOfType(gmx::ArrayRef<const int> atoms,
gmx::ArrayRef<const real> params,
const std::string& name) :
- atoms_(atoms.begin(), atoms.end()),
- interactionTypeName_(name)
+ atoms_(atoms.begin(), atoms.end()), interactionTypeName_(name)
{
GMX_RELEASE_ASSERT(
params.size() <= forceParam_.size(),
gmx::formatString("Cannot have more parameters than the maximum number possible (%d)", MAXFORCEPARAM)
.c_str());
- auto forceParamIt = forceParam_.begin();
+ std::array<real, MAXFORCEPARAM>::iterator forceParamIt = forceParam_.begin();
for (const auto param : params)
{
*forceParamIt++ = param;
GMX_LOG(logger.warning)
.asParagraph()
.appendTextFormatted(
- "atom name %d in %s and %s does not match (%s - %s)", i + 1,
- fn1, fn2, *(tat->atomname[j]), *(at->atomname[i]));
+ "atom name %d in %s and %s does not match (%s - %s)",
+ i + 1,
+ fn1,
+ fn2,
+ *(tat->atomname[j]),
+ *(at->atomname[i]));
}
else if (nmismatch == c_maxNumberOfMismatches)
{
"oscillational period of %.1e ps, which is less than %d times the time step of "
"%.1e ps.\n"
"%s",
- *w_moltype->name, w_a1 + 1, *w_moltype->atoms.atomname[w_a1], w_a2 + 1,
- *w_moltype->atoms.atomname[w_a2], std::sqrt(w_period2),
- bWarn ? min_steps_warn : min_steps_note, dt,
+ *w_moltype->name,
+ w_a1 + 1,
+ *w_moltype->atoms.atomname[w_a1],
+ w_a2 + 1,
+ *w_moltype->atoms.atomname[w_a2],
+ std::sqrt(w_period2),
+ bWarn ? min_steps_warn : min_steps_note,
+ dt,
bWater ? "Maybe you asked for fexible water."
: "Maybe you forgot to change the constraints mdp option.");
if (bWarn)
{
const t_atom& local = atomP.atom();
int i = atomP.globalAtomNumber();
- if (local.ptype == eptShell || local.ptype == eptBond || local.ptype == eptVSite)
+ if (local.ptype == ParticleType::Shell || local.ptype == ParticleType::Bond
+ || local.ptype == ParticleType::VSite)
{
clear_rvec(v[i]);
}
for (const AtomProxy atomP : AtomRange(*mtop))
{
const t_atom& local = atomP.atom();
- if (local.ptype == eptShell || local.ptype == eptBond)
+ if (local.ptype == ParticleType::Shell || local.ptype == ParticleType::Bond)
{
nshells++;
}
std::vector<MoleculeInformation>* mi,
std::unique_ptr<MoleculeInformation>* intermolecular_interactions,
gmx::ArrayRef<InteractionsOfType> interactions,
- int* comb,
+ CombinationRule* comb,
double* reppow,
real* fudgeQQ,
gmx_bool bMorse,
bool ffParametrizedWithHBondConstraints;
/* TOPOLOGY processing */
- sys->name = do_top(bVerbose, topfile, topppfile, opts, bZero, &(sys->symtab), interactions,
- comb, reppow, fudgeQQ, atypes, mi, intermolecular_interactions, ir,
- &molblock, &ffParametrizedWithHBondConstraints, wi, logger);
+ sys->name = do_top(bVerbose,
+ topfile,
+ topppfile,
+ opts,
+ bZero,
+ &(sys->symtab),
+ interactions,
+ comb,
+ reppow,
+ fudgeQQ,
+ atypes,
+ mi,
+ intermolecular_interactions,
+ ir,
+ &molblock,
+ &ffParametrizedWithHBondConstraints,
+ wi,
+ logger);
sys->molblock.clear();
convert_harmonics(*mi, atypes);
}
- if (ir->eDisre == edrNone)
+ if (ir->eDisre == DistanceRestraintRefinement::None)
{
i = rm_interactions(F_DISRES, *mi);
if (i > 0)
* constraints only. Do not print note with large timesteps or vsites.
*/
if (opts->nshake == eshALLBONDS && ffParametrizedWithHBondConstraints && ir->delta_t < 0.0026
- && gmx_mtop_ftype_count(sys, F_VSITE3FD) == 0)
+ && gmx_mtop_ftype_count(*sys, F_VSITE3FD) == 0)
{
set_warning_line(wi, "unknown", -1);
warning_note(wi,
gmx_fatal(FARGS,
"number of coordinates in coordinate file (%s, %d)\n"
" does not match topology (%s, %d)",
- confin, state->natoms, topfile, sys->natoms);
+ confin,
+ state->natoms,
+ topfile,
+ sys->natoms);
}
/* It would be nice to get rid of the copies below, but we don't know
* a priori if the number of atoms in confin matches what we expect.
*/
- state->flags |= (1 << estX);
+ state->flags |= enumValueToBitMask(StateEntry::X);
if (v != nullptr)
{
- state->flags |= (1 << estV);
+ state->flags |= enumValueToBitMask(StateEntry::V);
}
state_change_natoms(state, state->natoms);
std::copy(x, x + state->natoms, state->x.data());
"%d non-matching atom name%s\n"
"atom names from %s will be used\n"
"atom names from %s will be ignored\n",
- nmismatch, (nmismatch == 1) ? "" : "s", topfile, confin);
+ nmismatch,
+ (nmismatch == 1) ? "" : "s",
+ topfile,
+ confin);
warning(wi, warningMessage.c_str());
}
opts->seed = static_cast<int>(gmx::makeRandomSeed());
GMX_LOG(logger.info).asParagraph().appendTextFormatted("Setting gen_seed to %d", opts->seed);
}
- state->flags |= (1 << estV);
+ state->flags |= enumValueToBitMask(StateEntry::V);
maxwell_speed(opts->tempi, opts->seed, sys, state->v.rvec_array(), logger);
stop_cm(logger, state->natoms, mass, state->x.rvec_array(), state->v.rvec_array());
GMX_LOG(logger.info).asParagraph().appendTextFormatted("Using frame at t = %g ps", use_time);
GMX_LOG(logger.info).asParagraph().appendTextFormatted("Starting time for run is %g ps", ir->init_t);
- if ((ir->epc != epcNO || ir->etc == etcNOSEHOOVER) && ener)
+ if ((ir->epc != PressureCoupling::No || ir->etc == TemperatureCoupling::NoseHoover) && ener)
{
get_enx_state(ener, use_time, sys->groups, ir, state);
preserve_box_shape(ir, state->box_rel, state->boxv);
gmx::ArrayRef<const MoleculeInformation> molinfo,
gmx_bool bTopB,
const char* fn,
- int rc_scaling,
+ RefCoordScaling rc_scaling,
PbcType pbcType,
rvec com,
warninp* wi,
std::string warningMessage = gmx::formatString(
"The number of atoms in %s (%d) does not match the number of atoms in the topology "
"(%d). Will assume that the first %d atoms in the topology and %s match.",
- fn, natoms, mtop->natoms, std::min(mtop->natoms, natoms), fn);
+ fn,
+ natoms,
+ mtop->natoms,
+ std::min(mtop->natoms, natoms),
+ fn);
warning(wi, warningMessage.c_str());
}
npbcdim = numPbcDimensions(pbcType);
GMX_RELEASE_ASSERT(npbcdim <= DIM, "Invalid npbcdim");
clear_rvec(com);
- if (rc_scaling != erscNO)
+ if (rc_scaling != RefCoordScaling::No)
{
copy_mat(box, invbox);
for (int j = npbcdim; j < DIM; j++)
gmx_fatal(FARGS,
"Position restraint atom index (%d) in moltype '%s' is larger than "
"number of atoms in %s (%d).\n",
- ai + 1, *molinfo[molb.type].name, fn, natoms);
+ ai + 1,
+ *molinfo[molb.type].name,
+ fn,
+ natoms);
}
hadAtom[ai] = TRUE;
- if (rc_scaling == erscCOM)
+ if (rc_scaling == RefCoordScaling::Com)
{
/* Determine the center of mass of the posres reference coordinates */
for (int j = 0; j < npbcdim; j++)
gmx_fatal(FARGS,
"Position restraint atom index (%d) in moltype '%s' is larger than "
"number of atoms in %s (%d).\n",
- ai + 1, *molinfo[molb.type].name, fn, natoms);
+ ai + 1,
+ *molinfo[molb.type].name,
+ fn,
+ natoms);
}
- if (rc_scaling == erscCOM && !hadAtom[ai])
+ if (rc_scaling == RefCoordScaling::Com && !hadAtom[ai])
{
/* Determine the center of mass of the posres reference coordinates */
for (int j = 0; j < npbcdim; j++)
}
a += nat_molb;
}
- if (rc_scaling == erscCOM)
+ if (rc_scaling == RefCoordScaling::Com)
{
if (totmass == 0)
{
.asParagraph()
.appendTextFormatted(
"The center of mass of the position restraint coord's is %6.3f %6.3f %6.3f",
- com[XX], com[YY], com[ZZ]);
+ com[XX],
+ com[YY],
+ com[ZZ]);
}
- if (rc_scaling != erscNO)
+ if (rc_scaling != RefCoordScaling::No)
{
GMX_ASSERT(npbcdim <= DIM, "Only DIM dimensions can have PBC");
{
for (int j = 0; j < npbcdim; j++)
{
- if (rc_scaling == erscALL)
+ if (rc_scaling == RefCoordScaling::All)
{
/* Convert from Cartesian to crystal coordinates */
xp[i][j] *= invbox[j][j];
xp[i][j] += invbox[k][j] * xp[i][k];
}
}
- else if (rc_scaling == erscCOM)
+ else if (rc_scaling == RefCoordScaling::Com)
{
/* Subtract the center of mass */
xp[i][j] -= com[j];
}
}
- if (rc_scaling == erscCOM)
+ if (rc_scaling == RefCoordScaling::Com)
{
/* Convert the COM from Cartesian to crystal coordinates */
for (int j = 0; j < npbcdim; j++)
gmx::ArrayRef<const MoleculeInformation> mi,
const char* fnA,
const char* fnB,
- int rc_scaling,
+ RefCoordScaling rc_scaling,
PbcType pbcType,
rvec com,
rvec comB,
}
for (i = 0; i < ir->nwall; i++)
{
- ir->wall_atomtype[i] = at->atomTypeFromName(opts->wall_atomtype[i]);
- if (ir->wall_atomtype[i] == NOTSET)
+ auto atomType = at->atomTypeFromName(opts->wall_atomtype[i]);
+ if (!atomType.has_value())
{
std::string warningMessage = gmx::formatString(
"Specified wall atom type %s is not defined", opts->wall_atomtype[i]);
warning_error(wi, warningMessage.c_str());
}
+ else
+ {
+ ir->wall_atomtype[i] = *atomType;
+ }
}
}
for (i = 0; i < atoms->nr; i++)
{
/* Vsite ptype might not be set here yet, so also check the mass */
- if ((atoms->atom[i].ptype == eptAtom || atoms->atom[i].ptype == eptNucleus) && atoms->atom[i].m > 0)
+ if ((atoms->atom[i].ptype == ParticleType::Atom || atoms->atom[i].ptype == ParticleType::Nucleus)
+ && atoms->atom[i].m > 0)
{
nmass++;
}
for (i = 0; i < 2 * grid_spacing; i++)
{
- spline1d(dx, &(tmp_grid[2 * grid_spacing * i]), 2 * grid_spacing, tmp_u.data(),
+ spline1d(dx,
+ &(tmp_grid[2 * grid_spacing * i]),
+ 2 * grid_spacing,
+ tmp_u.data(),
&(tmp_t2[2 * grid_spacing * i]));
}
for (k = 0; k < 2 * grid_spacing; k++)
{
- interpolate1d(xmin, dx, &(tmp_grid[2 * grid_spacing * k]),
- &(tmp_t2[2 * grid_spacing * k]), psi, &tmp_yy[k], &tmp_y1[k]);
+ interpolate1d(xmin,
+ dx,
+ &(tmp_grid[2 * grid_spacing * k]),
+ &(tmp_t2[2 * grid_spacing * k]),
+ psi,
+ &tmp_yy[k],
+ &tmp_y1[k]);
}
spline1d(dx, tmp_yy.data(), 2 * grid_spacing, tmp_u.data(), tmp_u2.data());
"Molecule type '%s' has %d constraints.\n"
"For stability and efficiency there should not be more constraints than "
"internal number of degrees of freedom: %d.\n",
- *mi[molb.type].name, count_mol, nrdf_internal(&mi[molb.type].atoms));
+ *mi[molb.type].name,
+ count_mol,
+ nrdf_internal(&mi[molb.type].atoms));
warning(wi, warningMessage.c_str());
}
count += molb.nmol * count_mol;
nrdf += ir->opts.nrdf[g];
}
- return sum_mv2 / (nrdf * BOLTZ);
+ return sum_mv2 / (nrdf * gmx::c_boltz);
}
static real get_max_reference_temp(const t_inputrec* ir, warninp* wi)
int numDanglingAtoms = 0;
for (int a = 0; a < atoms->nr; a++)
{
- if (atoms->atom[a].ptype != eptVSite && count[a] == 0)
+ if (atoms->atom[a].ptype != ParticleType::VSite && count[a] == 0)
{
if (bVerbose)
{
.appendTextFormatted(
"Atom %d '%s' in moleculetype '%s' is not bound by a potential or "
"constraint to any other atom in the same moleculetype.",
- a + 1, *atoms->atomname[a], *molt->name);
+ a + 1,
+ *atoms->atomname[a],
+ *molt->name);
}
numDanglingAtoms++;
}
"issues in a simulation, this often means that the user forgot to add a "
"bond/potential/constraint or put multiple molecules in the same moleculetype "
"definition by mistake. Run with -v to get information for each atom.",
- *molt->name, numDanglingAtoms);
+ *molt->name,
+ numDanglingAtoms);
warning_note(wi, warningMessage.c_str());
}
}
const int lincsOrderThreshold = 4;
const real shakeToleranceThreshold = 0.005 * ir->delta_t;
- bool lincsWithSufficientTolerance = (ir->eConstrAlg == econtLINCS && ir->nLincsIter >= lincsIterationThreshold
- && ir->nProjOrder >= lincsOrderThreshold);
- bool shakeWithSufficientTolerance =
- (ir->eConstrAlg == econtSHAKE && ir->shake_tol <= 1.1 * shakeToleranceThreshold);
- if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol <= 1.1 * bufferToleranceThreshold
+ bool lincsWithSufficientTolerance =
+ (ir->eConstrAlg == ConstraintAlgorithm::Lincs
+ && ir->nLincsIter >= lincsIterationThreshold && ir->nProjOrder >= lincsOrderThreshold);
+ bool shakeWithSufficientTolerance = (ir->eConstrAlg == ConstraintAlgorithm::Shake
+ && ir->shake_tol <= 1.1 * shakeToleranceThreshold);
+ if (ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol <= 1.1 * bufferToleranceThreshold
&& (lincsWithSufficientTolerance || shakeWithSufficientTolerance))
{
return;
"and with masses that differ by more than a factor of %g. This means "
"that there are likely dynamic modes that are only very weakly coupled.",
massFactorThreshold);
- if (ir->cutoff_scheme == ecutsVERLET)
+ if (ir->cutoff_scheme == CutoffScheme::Verlet)
{
message += gmx::formatString(
" To ensure good equipartitioning, you need to either not use "
"hydrogens) or use integrator = %s or decrease one or more tolerances: "
"verlet-buffer-tolerance <= %g, LINCS iterations >= %d, LINCS order "
">= %d or SHAKE tolerance <= %g",
- ei_names[eiSD1], bufferToleranceThreshold, lincsIterationThreshold,
- lincsOrderThreshold, shakeToleranceThreshold);
+ enumValueToString(IntegrationAlgorithm::SD1),
+ bufferToleranceThreshold,
+ lincsIterationThreshold,
+ lincsOrderThreshold,
+ shakeToleranceThreshold);
}
else
{
" To ensure good equipartitioning, we suggest to switch to the %s "
"cutoff-scheme, since that allows for better control over the Verlet "
"buffer size and thus over the energy drift.",
- ecutscheme_names[ecutsVERLET]);
+ enumValueToString(CutoffScheme::Verlet));
}
warning(wi, message);
}
.asParagraph()
.appendTextFormatted(
"Determining Verlet buffer for a tolerance of %g kJ/mol/ps at %g K",
- ir->verletbuf_tol, buffer_temp);
+ ir->verletbuf_tol,
+ buffer_temp);
/* Calculate the buffer size for simple atom vs atoms list */
VerletbufListSetup listSetup1x1;
listSetup1x1.cluster_size_i = 1;
listSetup1x1.cluster_size_j = 1;
- const real rlist_1x1 = calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1,
- buffer_temp, listSetup1x1);
+ const real rlist_1x1 = calcVerletBufferSize(
+ *mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, buffer_temp, listSetup1x1);
/* Set the pair-list buffer size in ir */
VerletbufListSetup listSetup4x4 = verletbufGetSafeListSetup(ListSetupType::CpuNoSimd);
- ir->rlist = calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1,
- buffer_temp, listSetup4x4);
+ ir->rlist = calcVerletBufferSize(
+ *mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, buffer_temp, listSetup4x4);
const int n_nonlin_vsite = gmx::countNonlinearVsites(*mtop);
if (n_nonlin_vsite > 0)
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted(
- "Calculated rlist for %dx%d atom pair-list as %.3f nm, buffer size %.3f nm", 1,
- 1, rlist_1x1, rlist_1x1 - std::max(ir->rvdw, ir->rcoulomb));
+ "Calculated rlist for %dx%d atom pair-list as %.3f nm, buffer size %.3f nm",
+ 1,
+ 1,
+ rlist_1x1,
+ rlist_1x1 - std::max(ir->rvdw, ir->rcoulomb));
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted(
"Set rlist, assuming %dx%d atom pair-list, to %.3f nm, buffer size %.3f nm",
- listSetup4x4.cluster_size_i, listSetup4x4.cluster_size_j, ir->rlist,
+ listSetup4x4.cluster_size_i,
+ listSetup4x4.cluster_size_j,
+ ir->rlist,
ir->rlist - std::max(ir->rvdw, ir->rcoulomb));
GMX_LOG(logger.info)
"The pair-list cut-off (%g nm) is longer than half the shortest box vector or "
"longer than the smallest box diagonal element (%g nm). Increase the box size or "
"decrease nstlist or increase verlet-buffer-tolerance.",
- ir->rlist, std::sqrt(max_cutoff2(ir->pbcType, box)));
+ ir->rlist,
+ std::sqrt(max_cutoff2(ir->pbcType, box)));
}
}
"Then a coordinate file is read and velocities can be generated",
"from a Maxwellian distribution if requested.",
"[THISMODULE] also reads parameters for [gmx-mdrun] ",
- "(eg. number of MD steps, time step, cut-off), and others such as",
- "NEMD parameters, which are corrected so that the net acceleration",
- "is zero.",
+ "(eg. number of MD steps, time step, cut-off).",
"Eventually a binary file is produced that can serve as the sole input",
"file for the MD program.[PAR]",
};
std::vector<MoleculeInformation> mi;
std::unique_ptr<MoleculeInformation> intermolecular_interactions;
- int nvsite, comb;
+ int nvsite;
+ CombinationRule comb;
real fudgeQQ;
double reppow;
const char* mdparin;
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
- // Now that the MdModules have their options assigned from get_ir, subscribe
+ // Now that the MDModules have their options assigned from get_ir, subscribe
// to eventual notifications during pre-processing their data
mdModules.subscribeToPreProcessingNotifications();
.asParagraph()
.appendTextFormatted("checking input for internal consistency...");
}
- check_ir(mdparin, mdModules.notifier(), ir, opts, wi);
+ check_ir(mdparin, mdModules.notifiers(), ir, opts, wi);
if (ir->ld_seed == -1)
{
}
t_state state;
- new_status(fn, opt2fn_null("-pp", NFILE, fnm), opt2fn("-c", NFILE, fnm), opts, ir, bZero,
- bGenVel, bVerbose, &state, &atypes, &sys, &mi, &intermolecular_interactions,
- interactions, &comb, &reppow, &fudgeQQ, opts->bMorse, wi, logger);
+ new_status(fn,
+ opt2fn_null("-pp", NFILE, fnm),
+ opt2fn("-c", NFILE, fnm),
+ opts,
+ ir,
+ bZero,
+ bGenVel,
+ bVerbose,
+ &state,
+ &atypes,
+ &sys,
+ &mi,
+ &intermolecular_interactions,
+ interactions,
+ &comb,
+ &reppow,
+ &fudgeQQ,
+ opts->bMorse,
+ wi,
+ logger);
if (debug)
{
}
}
- if ((count_constraints(&sys, mi, wi) != 0) && (ir->eConstrAlg == econtSHAKE))
+ if ((count_constraints(&sys, mi, wi) != 0) && (ir->eConstrAlg == ConstraintAlgorithm::Shake))
{
- if (ir->eI == eiCG || ir->eI == eiLBFGS)
+ if (ir->eI == IntegrationAlgorithm::CG || ir->eI == IntegrationAlgorithm::LBFGS)
{
std::string warningMessage =
- gmx::formatString("Can not do %s with %s, use %s", EI(ir->eI),
- econstr_names[econtSHAKE], econstr_names[econtLINCS]);
+ gmx::formatString("Can not do %s with %s, use %s",
+ enumValueToString(ir->eI),
+ enumValueToString(ConstraintAlgorithm::Shake),
+ enumValueToString(ConstraintAlgorithm::Lincs));
warning_error(wi, warningMessage);
}
if (ir->bPeriodicMols)
{
std::string warningMessage =
gmx::formatString("Can not do periodic molecules with %s, use %s",
- econstr_names[econtSHAKE], econstr_names[econtLINCS]);
+ enumValueToString(ConstraintAlgorithm::Shake),
+ enumValueToString(ConstraintAlgorithm::Lincs));
warning_error(wi, warningMessage);
}
}
- if (EI_SD(ir->eI) && ir->etc != etcNO)
+ if (EI_SD(ir->eI) && ir->etc != TemperatureCoupling::No)
{
warning_note(wi, "Temperature coupling is ignored with SD integrators.");
}
if (nint_ftype(&sys, mi, F_POSRES) > 0 || nint_ftype(&sys, mi, F_FBPOSRES) > 0)
{
- if (ir->epc == epcPARRINELLORAHMAN || ir->epc == epcMTTK)
+ if (ir->epc == PressureCoupling::ParrinelloRahman || ir->epc == PressureCoupling::Mttk)
{
std::string warningMessage = gmx::formatString(
"You are combining position restraints with %s pressure coupling, which can "
"lead to instabilities. If you really want to combine position restraints with "
"pressure coupling, we suggest to use %s pressure coupling instead.",
- EPCOUPLTYPE(ir->epc), EPCOUPLTYPE(epcBERENDSEN));
+ enumValueToString(ir->epc),
+ enumValueToString(PressureCoupling::Berendsen));
warning_note(wi, warningMessage);
}
}
GMX_LOG(logger.info).asParagraph().appendText(message);
}
- gen_posres(&sys, mi, fn, fnB, ir->refcoord_scaling, ir->pbcType, ir->posres_com,
- ir->posres_comB, wi, logger);
+ gen_posres(&sys, mi, fn, fnB, ir->refcoord_scaling, ir->pbcType, ir->posres_com, ir->posres_comB, wi, logger);
}
/* If we are using CMAP, setup the pre-interpolation grid */
if (interactions[F_CMAP].ncmap() > 0)
{
- init_cmap_grid(&sys.ffparams.cmap_grid, interactions[F_CMAP].cmapAngles,
+ init_cmap_grid(&sys.ffparams.cmap_grid,
+ interactions[F_CMAP].cmapAngles,
interactions[F_CMAP].cmakeGridSpacing);
- setup_cmap(interactions[F_CMAP].cmakeGridSpacing, interactions[F_CMAP].cmapAngles,
- interactions[F_CMAP].cmap, &sys.ffparams.cmap_grid);
+ setup_cmap(interactions[F_CMAP].cmakeGridSpacing,
+ interactions[F_CMAP].cmapAngles,
+ interactions[F_CMAP].cmap,
+ &sys.ffparams.cmap_grid);
}
set_wall_atomtype(&atypes, opts, ir, wi, logger);
}
const int ntype = atypes.size();
- convertInteractionsOfType(ntype, interactions, mi, intermolecular_interactions.get(), comb,
- reppow, fudgeQQ, &sys);
+ convertInteractionsOfType(
+ ntype, interactions, mi, intermolecular_interactions.get(), comb, reppow, fudgeQQ, &sys);
if (debug)
{
checkForUnboundAtoms(&sys, bVerbose, wi, logger);
- if (EI_DYNAMICS(ir->eI) && ir->eI != eiBD)
+ if (EI_DYNAMICS(ir->eI) && ir->eI != IntegrationAlgorithm::BD)
{
check_bonds_timestep(&sys, ir->delta_t, wi);
}
{
GMX_LOG(logger.info).asParagraph().appendTextFormatted("initialising group options...");
}
- do_index(mdparin, ftp2fn_null(efNDX, NFILE, fnm), &sys, bVerbose, mdModules.notifier(), ir, wi);
+ do_index(mdparin, ftp2fn_null(efNDX, NFILE, fnm), &sys, bVerbose, mdModules.notifiers(), ir, wi);
- if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0)
+ if (ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0)
{
if (EI_DYNAMICS(ir->eI) && inputrec2nboundeddim(ir) == 3)
{
real buffer_temp;
- if (EI_MD(ir->eI) && ir->etc == etcNO)
+ if (EI_MD(ir->eI) && ir->etc == TemperatureCoupling::No)
{
if (bGenVel)
{
buffer_temp = get_max_reference_temp(ir, wi);
}
- if (EI_MD(ir->eI) && ir->etc == etcNO && buffer_temp == 0)
+ if (EI_MD(ir->eI) && ir->etc == TemperatureCoupling::No && buffer_temp == 0)
{
/* NVE with initial T=0: we add a fixed ratio to rlist.
* Since we don't actually use verletbuf_tol, we set it to -1
* Note that we can't warn when nsteps=0, since we don't
* know how many steps the user intends to run.
*/
- if (EI_MD(ir->eI) && ir->etc == etcNO && ir->nstlist > 1 && ir->nsteps > 0)
+ if (EI_MD(ir->eI) && ir->etc == TemperatureCoupling::No && ir->nstlist > 1 && ir->nsteps > 0)
{
const real driftTolerance = 0.01;
/* We use 2 DOF per atom = 2kT pot+kin energy,
* to be on the safe side with constraints.
*/
const real totalEnergyDriftPerAtomPerPicosecond =
- 2 * BOLTZ * buffer_temp / (ir->nsteps * ir->delta_t);
+ 2 * gmx::c_boltz * buffer_temp / (ir->nsteps * ir->delta_t);
if (ir->verletbuf_tol > 1.1 * driftTolerance * totalEnergyDriftPerAtomPerPicosecond)
{
"NVE simulation of length %g ps, which can give a final drift of "
"%d%%. For conserving energy to %d%% when using constraints, you "
"might need to set verlet-buffer-tolerance to %.1e.",
- ir->verletbuf_tol, ir->nsteps * ir->delta_t,
+ ir->verletbuf_tol,
+ ir->nsteps * ir->delta_t,
gmx::roundToInt(ir->verletbuf_tol / totalEnergyDriftPerAtomPerPicosecond * 100),
gmx::roundToInt(100 * driftTolerance),
driftTolerance * totalEnergyDriftPerAtomPerPicosecond);
pr_symtab(debug, 0, "After close", &sys.symtab);
}
- if (ir->eI == eiMimic)
+ if (ir->eI == IntegrationAlgorithm::Mimic)
{
generate_qmexcl(&sys, ir, logger);
}
.asParagraph()
.appendTextFormatted("getting data from old trajectory ...");
}
- cont_status(ftp2fn(efTRN, NFILE, fnm), ftp2fn_null(efEDR, NFILE, fnm), bNeedVel, bGenVel,
- fr_time, ir, &state, &sys, oenv, logger);
+ cont_status(ftp2fn(efTRN, NFILE, fnm),
+ ftp2fn_null(efEDR, NFILE, fnm),
+ bNeedVel,
+ bGenVel,
+ fr_time,
+ ir,
+ &state,
+ &sys,
+ oenv,
+ logger);
}
if (ir->pbcType == PbcType::XY && ir->nwall != 2)
wi, "Some of the Fourier grid sizes are set, but all of them need to be set.");
}
const int minGridSize = minimalPmeGridSize(ir->pme_order);
- calcFftGrid(stdout, scaledBox, ir->fourier_spacing, minGridSize, &(ir->nkx), &(ir->nky),
- &(ir->nkz));
+ calcFftGrid(stdout, scaledBox, ir->fourier_spacing, minGridSize, &(ir->nkx), &(ir->nky), &(ir->nkz));
if (ir->nkx < minGridSize || ir->nky < minGridSize || ir->nkz < minGridSize)
{
warning_error(wi,
/* MRS: eventually figure out better logic for initializing the fep
values that makes declaring the lambda and declaring the state not
potentially conflict if not handled correctly. */
- if (ir->efep != efepNO)
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
state.fep_state = ir->fepvals->init_fep_state;
- for (i = 0; i < efptNR; i++)
+ for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
{
/* init_lambda trumps state definitions*/
if (ir->fepvals->init_lambda >= 0)
}
else
{
- if (ir->fepvals->all_lambda[i] == nullptr)
+ if (ir->fepvals->all_lambda[i].empty())
{
gmx_fatal(FARGS, "Values of lambda not set for a free energy calculation!");
}
if (ir->bPull)
{
- pull = set_pull_init(ir, &sys, state.x.rvec_array(), state.box, state.lambda[efptMASS], wi);
+ pull = set_pull_init(
+ ir, sys, state.x, state.box, state.lambda[FreeEnergyPerturbationCouplingType::Mass], wi);
}
/* Modules that supply external potential for pull coordinates
if (ir->bDoAwh)
{
tensor compressibility = { { 0 } };
- if (ir->epc != epcNO)
+ if (ir->epc != PressureCoupling::No)
{
copy_mat(ir->compress, compressibility);
}
setStateDependentAwhParams(
- ir->awhParams, *ir->pull, pull, state.box, ir->pbcType, compressibility, &ir->opts,
- ir->efep != efepNO ? ir->fepvals->all_lambda[efptFEP][ir->fepvals->init_fep_state] : 0,
- sys, wi);
+ ir->awhParams.get(),
+ *ir->pull,
+ pull,
+ state.box,
+ ir->pbcType,
+ compressibility,
+ &ir->opts,
+ ir->efep != FreeEnergyPerturbationType::No ? ir->fepvals->all_lambda[static_cast<int>(
+ FreeEnergyPerturbationCouplingType::Fep)][ir->fepvals->init_fep_state]
+ : 0,
+ sys,
+ wi);
}
if (ir->bPull)
if (ir->bRot)
{
- set_reference_positions(ir->rot, state.x.rvec_array(), state.box,
- opt2fn("-ref", NFILE, fnm), opt2bSet("-ref", NFILE, fnm), wi);
+ set_reference_positions(ir->rot,
+ state.x.rvec_array(),
+ state.box,
+ opt2fn("-ref", NFILE, fnm),
+ opt2bSet("-ref", NFILE, fnm),
+ wi);
}
/* reset_multinr(sys); */
* charges. This will double the cost, but the optimal performance will
* then probably be at a slightly larger cut-off and grid spacing.
*/
- if ((ir->efep == efepNO && ratio > 1.0 / 2.0) || (ir->efep != efepNO && ratio > 2.0 / 3.0))
+ if ((ir->efep == FreeEnergyPerturbationType::No && ratio > 1.0 / 2.0)
+ || (ir->efep != FreeEnergyPerturbationType::No && ratio > 2.0 / 3.0))
{
warning_note(
wi,
"The optimal PME mesh load for parallel simulations is below 0.5\n"
"and for highly parallel simulations between 0.25 and 0.33,\n"
"for higher performance, increase the cut-off and the PME grid spacing.\n");
- if (ir->efep != efepNO)
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
warning_note(wi,
"For free energy simulations, the optimal load limit increases from "
{
gmx::KeyValueTreeBuilder internalParameterBuilder;
- mdModules.notifier().preProcessingNotifications_.notify(internalParameterBuilder.rootObject());
+ mdModules.notifiers().preProcessingNotifier_.notify(internalParameterBuilder.rootObject());
ir->internalParameters =
std::make_unique<gmx::KeyValueTreeObject>(internalParameterBuilder.build());
}
+ if (ir->comm_mode != ComRemovalAlgorithm::No)
+ {
+ const int nstglobalcomm = computeGlobalCommunicationPeriod(ir);
+ if (ir->nstcomm % nstglobalcomm != 0)
+ {
+ warning_note(
+ wi,
+ gmx::formatString(
+ "COM removal frequency is set to (%d).\n"
+ "Other settings require a global communication frequency of %d.\n"
+ "Note that this will require additional global communication steps,\n"
+ "which will reduce performance when using multiple ranks.\n"
+ "Consider setting nstcomm to a multiple of %d.",
+ ir->nstcomm,
+ nstglobalcomm,
+ nstglobalcomm));
+ }
+ }
+
if (bVerbose)
{
GMX_LOG(logger.info).asParagraph().appendTextFormatted("writing run input file...");
}
done_warning(wi, FARGS);
- write_tpx_state(ftp2fn(efTPR, NFILE, fnm), ir, &state, &sys);
+ write_tpx_state(ftp2fn(efTPR, NFILE, fnm), ir, &state, sys);
/* Output IMD group, if bIMD is TRUE */
- gmx::write_IMDgroup_to_file(ir->bIMD, ir, &state, &sys, NFILE, fnm);
+ gmx::write_IMDgroup_to_file(ir->bIMD, ir, &state, sys, NFILE, fnm);
sfree(opts->define);
sfree(opts->wall_atomtype[0]);
sfree(opts->wall_atomtype[1]);
sfree(opts->include);
+ sfree(opts->couple_moltype);
+
for (auto& mol : mi)
{
// Some of the contents of molinfo have been stolen, so
hack->tp = tp;
if ((tp < 1) || (tp >= maxcontrol))
{
- gmx_fatal(FARGS, "Error in hdb file %s:\nH-type should be in 1-%d. Offending line:\n%s", fn,
- maxcontrol - 1, line);
+ gmx_fatal(FARGS,
+ "Error in hdb file %s:\nH-type should be in 1-%d. Offending line:\n%s",
+ fn,
+ maxcontrol - 1,
+ line);
}
hack->nctl = ns - 3;
gmx_fatal(FARGS,
"Error in hdb file %s:\nWrong number of control atoms (%d instead of %d) on "
"line:\n%s\n",
- fn, hack->nctl, ncontrol[hack->tp], line);
+ fn,
+ hack->nctl,
+ ncontrol[hack->tp],
+ line);
}
for (int i = 0; (i < hack->nctl); i++)
{
gmx_fatal(FARGS,
"Expected %d lines of hydrogens, found only %d "
"while reading Hydrogen Database %s residue %s",
- nab, i - 1, block->name.c_str(), hfn);
+ nab,
+ i - 1,
+ block->name.c_str(),
+ hfn);
}
if (nullptr == fgets(buf, STRLEN, in))
{
if (!globalPatches->empty())
{
/* Sort the list for searching later */
- std::sort(globalPatches->begin(), globalPatches->end(),
+ std::sort(globalPatches->begin(),
+ globalPatches->end(),
[](const MoleculePatchDatabase& a1, const MoleculePatchDatabase& a2) {
- return std::lexicographical_compare(
- a1.name.begin(), a1.name.end(), a2.name.begin(), a2.name.end(),
- [](const char& c1, const char& c2) {
- return std::toupper(c1) < std::toupper(c2);
- });
+ return std::lexicographical_compare(a1.name.begin(),
+ a1.name.end(),
+ a2.name.begin(),
+ a2.name.end(),
+ [](const char& c1, const char& c2) {
+ return std::toupper(c1) < std::toupper(c2);
+ });
});
}
}
gmx::ArrayRef<const MoleculePatchDatabase>::iterator
search_h_db(gmx::ArrayRef<const MoleculePatchDatabase> globalPatches, const char* key)
{
- return std::find_if(
- globalPatches.begin(), globalPatches.end(),
- [&key](const MoleculePatchDatabase& a) { return gmx::equalCaseInsensitive(key, a.name); });
+ return std::find_if(globalPatches.begin(), globalPatches.end(), [&key](const MoleculePatchDatabase& a) {
+ return gmx::equalCaseInsensitive(key, a.name);
+ });
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2011,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/topology/symtab.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringcompare.h"
-/* these MUST correspond to the enum in hackblock.h */
-const char* btsNames[ebtsNR] = { "bonds", "angles", "dihedrals", "impropers", "exclusions", "cmap" };
-const int btsNiatoms[ebtsNR] = { 2, 3, 4, 4, 2, 5 };
+const char* enumValueToString(BondedTypes enumValue)
+{
+ /* these MUST correspond to the enum in hackblock.h */
+ constexpr gmx::EnumerationArray<BondedTypes, const char*> bondedTypeNames = {
+ "bonds", "angles", "dihedrals", "impropers", "exclusions", "cmap"
+ };
+ return bondedTypeNames[enumValue];
+}
+
+int enumValueToNumIAtoms(BondedTypes enumValue)
+{
+ constexpr gmx::EnumerationArray<BondedTypes, int> bondedTypeIAtoms = { 2, 3, 4, 4, 2, 5 };
+ return bondedTypeIAtoms[enumValue];
+}
MoleculePatchType MoleculePatch::type() const
{
{
globalPatches->name.clear();
globalPatches->hack.clear();
- for (int i = 0; i < ebtsNR; i++)
+ for (auto bondedsList : globalPatches->rb)
{
- globalPatches->rb[i].b.clear();
+ bondedsList.b.clear();
}
}
bool bPlus)
{
bool bBondsRemoved = false;
- for (int i = 0; i < ebtsNR; i++)
+ for (auto i : gmx::EnumerationWrapper<BondedTypes>{})
{
- if (!s[i].b.empty())
+ int value = static_cast<int>(i);
+ if (!s[value].b.empty())
{
/* Record how many bonds we have in the destination when we start.
*
* it is a hackblock entry meant to override the main rtp, and then
* we don't add the main rtp one.
*/
- int nbHackblockStart = d[i].b.size();
+ int nbHackblockStart = d[value].b.size();
- for (const auto& b : s[i].b)
+ for (const auto& b : s[value].b)
{
/* Check if this bonded string already exists before adding.
* We are merging from the main RTP to the hackblocks, so this
* will mean the hackblocks overwrite the man RTP, as intended.
*/
- int index = rbonded_find_atoms_in_list(b, d[i].b, btsNiatoms[i]);
+ int index = rbonded_find_atoms_in_list(b, d[value].b, enumValueToNumIAtoms(i));
/* - If we did not find this interaction at all, the index will be -1,
* and then we should definitely add it to the merged hackblock and rtp.
*
{
if (!(bMin && contains_char(b, '-')) && !(bPlus && contains_char(b, '+')))
{
- d[i].b.push_back(b);
+ d[value].b.push_back(b);
}
- else if (i == ebtsBONDS)
+ else if (i == BondedTypes::Bonds)
{
bBondsRemoved = true;
}
{
d->cgnr.push_back(c);
}
- for (int i = 0; i < ebtsNR; i++)
+ for (auto i : gmx::EnumerationWrapper<BondedTypes>{})
{
d->rb[i].type = s.rb[i].type;
d->rb[i].b.clear();
*d = s;
d->name = s.name;
d->hack.clear();
- for (int i = 0; i < ebtsNR; i++)
+ for (auto bondedList : d->rb)
{
- d->rb[i].b.clear();
+ bondedList.b.clear();
}
mergeAtomAndBondModifications(s, d);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxpreprocess/notset.h"
#include "gromacs/topology/ifunc.h"
+#include "gromacs/utility/enumerationhelpers.h"
struct t_atom;
struct t_symtab;
/*! \brief
* Used for reading .rtp/.tdb
- * ebtsBONDS must be the first, new types can be added to the end
+ * BondedTypes::Bonds must be the first, new types can be added to the end
* these *MUST* correspond to the arrays in hackblock.cpp
*/
-enum
+enum class BondedTypes : int
{
- ebtsBONDS,
- ebtsANGLES,
- ebtsPDIHS,
- ebtsIDIHS,
- ebtsEXCLS,
- ebtsCMAP,
- ebtsNR
+ Bonds,
+ Angles,
+ ProperDihedrals,
+ ImproperDihedrals,
+ Exclusions,
+ Cmap,
+ Count
};
//! Names for interaction type entries
-extern const char* btsNames[ebtsNR];
+const char* enumValueToString(BondedTypes enumValue);
//! Numbers for atoms in the interactions.
-extern const int btsNiatoms[ebtsNR];
+int enumValueToNumIAtoms(BondedTypes enumValue);
/* if changing any of these structs, make sure that all of the
free/clear/copy/merge_t_* functions stay updated */
//! Delete dihedrals also defined by impropers.
bool bRemoveDihedralIfWithImproper = false;
//! List of bonded interactions to potentially add.
- std::array<BondedInteractionList, ebtsNR> rb;
+ gmx::EnumerationArray<BondedTypes, BondedInteractionList> rb;
//! Get number of atoms in residue.
int natom() const { return atom.size(); }
};
//! List of changes to atoms.
std::vector<MoleculePatch> hack;
//! List of bonded interactions to potentially add.
- std::array<BondedInteractionList, ebtsNR> rb;
+ gmx::EnumerationArray<BondedTypes, BondedInteractionList> rb;
//! Number of atoms to modify
int nhack() const { return hack.size(); }
};
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxpreprocess/toputil.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/topology/block.h"
#include "gromacs/topology/symtab.h"
d2 = distance2(x[i], x[j]);
rvec_sub(x[i], xh, nh);
rvec_sub(x[aj], xh, oh);
- a = RAD2DEG * acos(cos_angle(nh, oh));
+ a = gmx::c_rad2Deg * acos(cos_angle(nh, oh));
if ((d2 < dist2) && (a > angle))
{
hbond[i] = TRUE;
"NZ", "OG", "OG1", "OH", "NE1", "OW" };
#define NPD asize(prot_don)
- bool * donor, *acceptor;
- bool* hbond;
- bool bHDd, bHEd;
- rvec xh1, xh2;
- int natom;
- int i, j, nd, na, hisind, type = -1;
- int nd1, ne2, cg, cd2, ce1;
- t_blocka* hb;
- char* atomnm;
+ bool * donor, *acceptor;
+ bool* hbond;
+ bool bHDd, bHEd;
+ rvec xh1, xh2;
+ int natom;
+ int i, j, nd, na, hisind;
+ HistidineStates type = HistidineStates::Count;
+ int nd1, ne2, cg, cd2, ce1;
+ t_blocka* hb;
+ char* atomnm;
natom = pdba->nr;
{
if (bHEd)
{
- type = ehisH;
+ type = HistidineStates::H;
}
else
{
- type = ehisA;
+ type = HistidineStates::A;
}
}
else
{
- type = ehisB;
+ type = HistidineStates::B;
}
- fprintf(stderr, "Will use %s for residue %d\n", hh[type], pdba->resinfo[hisind].nr);
+ fprintf(stderr,
+ "Will use %s for residue %d\n",
+ enumValueToString(type),
+ pdba->resinfo[hisind].nr);
}
else
{
gmx_fatal(FARGS, "Incomplete ring in HIS%d", pdba->resinfo[hisind].nr);
}
- pdba->resinfo[hisind].rtp = put_symtab(symtab, hh[type]);
+ pdba->resinfo[hisind].rtp = put_symtab(symtab, enumValueToString(type));
}
}
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxlib/conformation_utilities.h"
#include "gromacs/gmxpreprocess/makeexclusiondistances.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/options/basicoptions.h"
None,
Count
};
-static const gmx::EnumerationArray<RotationType, const char*> c_rotationTypeNames = { { "xyz", "z",
- "none" } };
+static const gmx::EnumerationArray<RotationType, const char*> c_rotationTypeNames = {
+ { "xyz", "z", "none" }
+};
static void center_molecule(gmx::ArrayRef<RVec> x)
{
// Skip a position if ntry trials were not successful.
if (trial >= firstTrial + ntry)
{
- fprintf(stderr, " skipped position (%.3f, %.3f, %.3f)\n", rpos[XX][mol],
- rpos[YY][mol], rpos[ZZ][mol]);
+ fprintf(stderr,
+ " skipped position (%.3f, %.3f, %.3f)\n",
+ rpos[XX][mol],
+ rpos[YY][mol],
+ rpos[ZZ][mol]);
++mol;
++failed;
firstTrial = trial;
generate_trial_conf(x_insrt, offset_x, enum_rot, &rng, &x_n);
gmx::AnalysisNeighborhoodPositions pos(*x);
gmx::AnalysisNeighborhoodSearch search = nb.initSearch(&pbc, pos);
- if (isInsertionAllowed(&search, exclusionDistances, x_n, exclusionDistances_insrt, *atoms,
- removableAtoms, &remover))
+ if (isInsertionAllowed(
+ &search, exclusionDistances, x_n, exclusionDistances_insrt, *atoms, removableAtoms, &remover))
{
x->insert(x->end(), x_n.begin(), x_n.end());
- exclusionDistances.insert(exclusionDistances.end(), exclusionDistances_insrt.begin(),
+ exclusionDistances.insert(exclusionDistances.end(),
+ exclusionDistances_insrt.begin(),
exclusionDistances_insrt.end());
builder.mergeAtoms(atoms_insrt);
++mol;
remover.removeMarkedAtoms(atoms);
if (atoms->nr < originalAtomCount)
{
- fprintf(stderr, "Replaced %d residues (%d atoms)\n", originalResidueCount - atoms->nres,
+ fprintf(stderr,
+ "Replaced %d residues (%d atoms)\n",
+ originalResidueCount - atoms->nres,
originalAtomCount - atoms->nr);
}
.defaultBasename("insert")
.description("Configuration to insert"));
options->addOption(FileNameOption("ip")
- .filetype(eftGenericData)
+ .filetype(OptionFileType::GenericData)
.inputFile()
.store(&positionFile_)
.defaultBasename("positions")
bool bTprFileWasRead;
rvec* temporaryX = nullptr;
fprintf(stderr, "Reading solute configuration\n");
- readConfAndTopology(inputConfFile_.c_str(), &bTprFileWasRead, &top_, &pbcType_, &temporaryX,
- nullptr, box_);
+ readConfAndTopology(
+ inputConfFile_.c_str(), &bTprFileWasRead, &top_, &pbcType_, &temporaryX, nullptr, box_);
x_.assign(temporaryX, temporaryX + top_.natoms);
sfree(temporaryX);
if (top_.natoms == 0)
PbcType pbcType_dummy;
matrix box_dummy;
rvec* temporaryX;
- readConfAndTopology(insertConfFile_.c_str(), &bTprFileWasRead, &topInserted, &pbcType_dummy,
- &temporaryX, nullptr, box_dummy);
+ readConfAndTopology(
+ insertConfFile_.c_str(), &bTprFileWasRead, &topInserted, &pbcType_dummy, &temporaryX, nullptr, box_dummy);
xInserted.assign(temporaryX, temporaryX + topInserted.natoms);
sfree(temporaryX);
- atomsInserted = gmx_mtop_global_atoms(&topInserted);
+ atomsInserted = gmx_mtop_global_atoms(topInserted);
if (atomsInserted.nr == 0)
{
gmx_fatal(FARGS, "No molecule in %s, please check your input", insertConfFile_.c_str());
}
}
- t_atoms atoms = gmx_mtop_global_atoms(&top_);
+ t_atoms atoms = gmx_mtop_global_atoms(top_);
/* add nmol_ins molecules of atoms_ins
in random orientation at random place */
- insert_mols(nmolIns_, nmolTry_, seed_, defaultDistance_, scaleFactor_, &atoms, &top_.symtab,
- &x_, removableAtoms, atomsInserted, xInserted, pbcTypeForOutput, box_,
- positionFile_, deltaR_, enumRot_);
+ insert_mols(nmolIns_,
+ nmolTry_,
+ seed_,
+ defaultDistance_,
+ scaleFactor_,
+ &atoms,
+ &top_.symtab,
+ &x_,
+ removableAtoms,
+ atomsInserted,
+ xInserted,
+ pbcTypeForOutput,
+ box_,
+ positionFile_,
+ deltaR_,
+ enumRot_);
/* write new configuration to file confout */
fprintf(stderr, "Writing generated configuration to %s\n", outputConfFile_.c_str());
- write_sto_conf(outputConfFile_.c_str(), *top_.name, &atoms, as_rvec_array(x_.data()), nullptr,
- pbcTypeForOutput, box_);
+ write_sto_conf(
+ outputConfFile_.c_str(), *top_.name, &atoms, as_rvec_array(x_.data()), nullptr, pbcTypeForOutput, box_);
/* print size of generated configuration */
fprintf(stderr, "\nOutput configuration contains %d atoms in %d residues\n", atoms.nr, atoms.nres);
for (int i = 0; i < a->nr; ++i)
{
real value;
- if (!aps->setAtomProperty(epropVDW, std::string(*(a->resinfo[a->atom[i].resind].name)),
- std::string(*(a->atomname[i])), &value))
+ if (!aps->setAtomProperty(epropVDW,
+ std::string(*(a->resinfo[a->atom[i].resind].name)),
+ std::string(*(a->atomname[i])),
+ &value))
{
value = defaultDistance;
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
fprintf(fp, "; nm2type database\n");
for (i = 0; (i < nnm); i++)
{
- fprintf(fp, "%-8s %-8s %8.4f %8.4f %-4d", nm2t[i].elem, nm2t[i].type, nm2t[i].q, nm2t[i].m,
- nm2t[i].nbonds);
+ fprintf(fp, "%-8s %-8s %8.4f %8.4f %-4d", nm2t[i].elem, nm2t[i].type, nm2t[i].q, nm2t[i].m, nm2t[i].nbonds);
for (j = 0; (j < nm2t[i].nbonds); j++)
{
fprintf(fp, " %-5s %6.4f", nm2t[i].bond[j], nm2t[i].blen[j]);
double mm = nm2t[best].m;
const char* type = nm2t[best].type;
- int k;
- if ((k = atype->atomTypeFromName(type)) == NOTSET)
+ auto atomType = atype->atomTypeFromName(type);
+ int k;
+ if (!atomType.has_value())
{
atoms->atom[i].qB = alpha;
atoms->atom[i].m = atoms->atom[i].mB = mm;
- k = atype->addType(tab, atoms->atom[i], type, InteractionOfType({}, {}),
- atoms->atom[i].type, atomnr);
+ k = atype->addType(
+ tab, atoms->atom[i], type, InteractionOfType({}, {}), atoms->atom[i].type, atomnr);
+ }
+ else
+ {
+ k = *atomType;
}
atoms->atom[i].type = k;
atoms->atom[i].typeB = k;
}
else
{
- fprintf(stderr, "Can not find forcefield for atom %s-%d with %d bonds\n",
- *atoms->atomname[i], i + 1, nb);
+ fprintf(stderr,
+ "Can not find forcefield for atom %s-%d with %d bonds\n",
+ *atoms->atomname[i],
+ i + 1,
+ nb);
}
}
sfree(bbb);
*/
#include "gmxpre.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "pdb2gmx.h"
#include <cctype>
struct RtpRename
{
RtpRename(const char* newGmx, const char* newMain, const char* newNter, const char* newCter, const char* newBter) :
- gmx(newGmx),
- main(newMain),
- nter(newNter),
- cter(newCter),
- bter(newBter)
+ gmx(newGmx), main(newMain), nter(newNter), cter(newCter), bter(newBter)
{
}
std::string gmx;
return found != rr.end() ? found->main.c_str() : name.c_str();
}
-const char* select_res(int nr,
- int resnr,
- const char* name[],
- const char* expl[],
- const char* title,
- gmx::ArrayRef<const RtpRename> rr)
+const char* enumValueToLongString(HistidineStates enumValue)
+{
+ constexpr gmx::EnumerationArray<HistidineStates, const char*> histidineStatesLongNames = {
+ "H on ND1 only", "H on NE2 only", "H on ND1 and NE2", "Coupled to Heme"
+ };
+ return histidineStatesLongNames[enumValue];
+}
+
+enum class AspartateStates : int
+{
+ Deprot,
+ Prot,
+ Count
+};
+
+const char* enumValueToString(AspartateStates enumValue)
+{
+ constexpr gmx::EnumerationArray<AspartateStates, const char*> aspartateStateNames = { "ASP",
+ "ASPH" };
+ return aspartateStateNames[enumValue];
+}
+
+const char* enumValueToLongString(AspartateStates enumValue)
+{
+ constexpr gmx::EnumerationArray<AspartateStates, const char*> aspartateStateLongNames = {
+ "Not protonated (charge -1)", "Protonated (charge 0)"
+ };
+ return aspartateStateLongNames[enumValue];
+}
+
+enum class GlutamateStates : int
+{
+ Deprot,
+ Prot,
+ Count
+};
+
+const char* enumValueToString(GlutamateStates enumValue)
+{
+ constexpr gmx::EnumerationArray<GlutamateStates, const char*> glutamateStateNames = { "GLU",
+ "GLUH" };
+ return glutamateStateNames[enumValue];
+}
+
+const char* enumValueToLongString(GlutamateStates enumValue)
+{
+ constexpr gmx::EnumerationArray<GlutamateStates, const char*> glutamateStateLongNames = {
+ "Not protonated (charge -1)", "Protonated (charge 0)"
+ };
+ return glutamateStateLongNames[enumValue];
+}
+
+enum class GlutamineStates : int
+{
+ Deprot,
+ Prot,
+ Count
+};
+
+const char* enumValueToString(GlutamineStates enumValue)
+{
+ constexpr gmx::EnumerationArray<GlutamineStates, const char*> glutamineStateNames = { "GLN",
+ "QLN" };
+ return glutamineStateNames[enumValue];
+}
+
+const char* enumValueToLongString(GlutamineStates enumValue)
+{
+ constexpr gmx::EnumerationArray<GlutamineStates, const char*> glutamineStateLongNames = {
+ "Not protonated (charge 0)", "Protonated (charge +1)"
+ };
+ return glutamineStateLongNames[enumValue];
+}
+
+enum class LysineStates : int
+{
+ Deprot,
+ Prot,
+ Count
+};
+
+const char* enumValueToString(LysineStates enumValue)
+{
+ constexpr gmx::EnumerationArray<LysineStates, const char*> lysineStateNames = { "LYSN", "LYS" };
+ return lysineStateNames[enumValue];
+}
+
+const char* enumValueToLongString(LysineStates enumValue)
+{
+ constexpr gmx::EnumerationArray<LysineStates, const char*> lysineStateLongNames = {
+ "Not protonated (charge 0)", "Protonated (charge +1)"
+ };
+ return lysineStateLongNames[enumValue];
+}
+
+enum class ArginineStates : int
+{
+ Deprot,
+ Prot,
+ Count
+};
+
+const char* enumValueToString(ArginineStates enumValue)
+{
+ constexpr gmx::EnumerationArray<ArginineStates, const char*> arginineStatesNames = { "ARGN",
+ "ARG" };
+ return arginineStatesNames[enumValue];
+}
+
+const char* enumValueToLongString(ArginineStates enumValue)
+{
+ constexpr gmx::EnumerationArray<ArginineStates, const char*> arginineStatesLongNames = {
+ "Not protonated (charge 0)", "Protonated (charge +1)"
+ };
+ return arginineStatesLongNames[enumValue];
+}
+
+template<typename EnumType>
+const char* select_res(int resnr, const char* title, gmx::ArrayRef<const RtpRename> rr)
{
printf("Which %s type do you want for residue %d\n", title, resnr + 1);
- for (int sel = 0; (sel < nr); sel++)
+ for (auto sel : gmx::EnumerationWrapper<EnumType>{})
{
- printf("%d. %s (%s)\n", sel, expl[sel], res2bb_notermini(name[sel], rr));
+ printf("%d. %s (%s)\n",
+ static_cast<int>(sel),
+ enumValueToString(sel),
+ res2bb_notermini(enumValueToString(sel), rr));
}
printf("\nType a number:");
fflush(stdout);
gmx_fatal(FARGS, "Answer me for res %s %d!", title, resnr + 1);
}
- return name[userSelection];
+ return enumValueToLongString(static_cast<EnumType>(userSelection));
}
const char* get_asptp(int resnr, gmx::ArrayRef<const RtpRename> rr)
{
- enum
- {
- easp,
- easpH,
- easpNR
- };
- const char* lh[easpNR] = { "ASP", "ASPH" };
- const char* expl[easpNR] = { "Not protonated (charge -1)", "Protonated (charge 0)" };
-
- return select_res(easpNR, resnr, lh, expl, "ASPARTIC ACID", rr);
+ return select_res<AspartateStates>(resnr, "ASPARTIC ACID", rr);
}
const char* get_glutp(int resnr, gmx::ArrayRef<const RtpRename> rr)
{
- enum
- {
- eglu,
- egluH,
- egluNR
- };
- const char* lh[egluNR] = { "GLU", "GLUH" };
- const char* expl[egluNR] = { "Not protonated (charge -1)", "Protonated (charge 0)" };
-
- return select_res(egluNR, resnr, lh, expl, "GLUTAMIC ACID", rr);
+ return select_res<GlutamateStates>(resnr, "GLUTAMIC ACID", rr);
}
const char* get_glntp(int resnr, gmx::ArrayRef<const RtpRename> rr)
{
- enum
- {
- egln,
- eglnH,
- eglnNR
- };
- const char* lh[eglnNR] = { "GLN", "QLN" };
- const char* expl[eglnNR] = { "Not protonated (charge 0)", "Protonated (charge +1)" };
-
- return select_res(eglnNR, resnr, lh, expl, "GLUTAMINE", rr);
+ return select_res<GlutamineStates>(resnr, "GLUTAMINE", rr);
}
const char* get_lystp(int resnr, gmx::ArrayRef<const RtpRename> rr)
{
- enum
- {
- elys,
- elysH,
- elysNR
- };
- const char* lh[elysNR] = { "LYSN", "LYS" };
- const char* expl[elysNR] = { "Not protonated (charge 0)", "Protonated (charge +1)" };
-
- return select_res(elysNR, resnr, lh, expl, "LYSINE", rr);
+ return select_res<LysineStates>(resnr, "LYSINE", rr);
}
const char* get_argtp(int resnr, gmx::ArrayRef<const RtpRename> rr)
{
- enum
- {
- earg,
- eargH,
- eargNR
- };
- const char* lh[eargNR] = { "ARGN", "ARG" };
- const char* expl[eargNR] = { "Not protonated (charge 0)", "Protonated (charge +1)" };
-
- return select_res(eargNR, resnr, lh, expl, "ARGININE", rr);
+ return select_res<ArginineStates>(resnr, "ARGININE", rr);
}
const char* get_histp(int resnr, gmx::ArrayRef<const RtpRename> rr)
{
- const char* expl[ehisNR] = { "H on ND1 only", "H on NE2 only", "H on ND1 and NE2",
- "Coupled to Heme" };
-
- return select_res(ehisNR, resnr, hh, expl, "HISTIDINE", rr);
+ return select_res<HistidineStates>(resnr, "HISTIDINE", rr);
}
void read_rtprename(const char* fname, FILE* fp, std::vector<RtpRename>* rtprename)
{
if (nc != 2 && nc != 5)
{
- gmx_fatal(FARGS, "Residue renaming database '%s' has %d columns instead of %d or %d",
- fname, ncol, 2, 5);
+ gmx_fatal(FARGS,
+ "Residue renaming database '%s' has %d columns instead of %d or %d",
+ fname,
+ ncol,
+ 2,
+ 5);
}
ncol = nc;
}
gmx_fatal(FARGS,
"A line in residue renaming database '%s' has %d columns, while previous "
"lines have %d columns",
- fname, nc, ncol);
+ fname,
+ nc,
+ ncol);
}
if (nc == 2)
if (newName[0] == '-')
{
- gmx_fatal(FARGS, "In the chosen force field there is no residue type for '%s'%s", name,
+ gmx_fatal(FARGS,
+ "In the chosen force field there is no residue type for '%s'%s",
+ name,
bStart ? (bEnd ? " as a standalone (starting & ending) residue" : " as a starting terminus")
: (bEnd ? " as an ending terminus" : ""));
}
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted("Changing rtp entry of residue %d %s to '%s'",
- pdba->resinfo[r].nr, *pdba->resinfo[r].name,
+ pdba->resinfo[r].nr,
+ *pdba->resinfo[r].name,
newName.c_str());
}
pdba->resinfo[r].rtp = put_symtab(symtab, newName.c_str());
.appendTextFormatted(
"Replaced %d residue%s named %s to the default %s. Use interactive "
"selection of protonated residues if that is what you need.",
- numMatchesFound, numMatchesFound > 1 ? "s" : "", oldnm, newnm);
+ numMatchesFound,
+ numMatchesFound > 1 ? "s" : "",
+ oldnm,
+ newnm);
}
}
.appendTextFormatted("Occupancy for atom %s%d-%s is %f rather than 1",
*atoms->resinfo[atoms->atom[i].resind].name,
atoms->resinfo[atoms->atom[i].resind].nr,
- *atoms->atomname[i], atoms->pdbinfo[i].occup);
+ *atoms->atomname[i],
+ atoms->pdbinfo[i].occup);
}
if (atoms->pdbinfo[i].occup == 0)
{
"there were %d atoms with zero occupancy and %d atoms with "
" occupancy unequal to one (out of %d atoms). Check your pdb "
"file.",
- nzero, nnotone, atoms->nr);
+ nzero,
+ nnotone,
+ atoms->nr);
}
else
{
"\n"
"[ position_restraints ]\n"
"; %4s%6s%8s%8s%8s\n",
- "atom", "type", "fx", "fy", "fz");
+ "atom",
+ "type",
+ "fx",
+ "fy",
+ "fz");
for (i = 0; (i < pdba->nr); i++)
{
if (!is_hydrogen(*pdba->atomname[i]) && !is_dummymass(*pdba->atomname[i]))
atomnm = *pdba->atomname[i];
const PreprocessResidue* localPpResidue = &restp_chain[pdba->atom[i].resind];
auto found =
- std::find_if(localPpResidue->atomname.begin(), localPpResidue->atomname.end(),
+ std::find_if(localPpResidue->atomname.begin(),
+ localPpResidue->atomname.end(),
[&atomnm](char** it) { return gmx::equalCaseInsensitive(atomnm, *it); });
if (found == localPpResidue->atomname.end())
{
std::string buf = gmx::formatString(
"Atom %s in residue %s %d was not found in rtp entry %s with %d atoms\n"
"while sorting atoms.\n%s",
- atomnm, *pdba->resinfo[pdba->atom[i].resind].name,
- pdba->resinfo[pdba->atom[i].resind].nr, localPpResidue->resname.c_str(),
+ atomnm,
+ *pdba->resinfo[pdba->atom[i].resind].name,
+ pdba->resinfo[pdba->atom[i].resind].nr,
+ localPpResidue->resname.c_str(),
localPpResidue->natom(),
is_hydrogen(atomnm)
? "\nFor a hydrogen, this can be a different protonation state, or it\n"
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted("deleting duplicate atom %4s %s%4d%c",
- *pdba->atomname[i], *ri->name, ri->nr, ri->ic);
+ *pdba->atomname[i],
+ *ri->name,
+ ri->nr,
+ ri->ic);
if (ri->chainid && (ri->chainid != ' '))
{
printf(" ch %c", ri->chainid);
gmx_fatal(FARGS,
"The chain covering the range %s--%s does not have a consistent chain ID. "
"The first residue has ID '%c', while residue %s has ID '%c'.",
- startResidueString.c_str(), endResidueString.c_str(), chainID0,
- residueString.c_str(), chainID);
+ startResidueString.c_str(),
+ endResidueString.c_str(),
+ chainID0,
+ residueString.c_str(),
+ chainID);
}
// At this point all residues have the same ID. If they are also non-blank
"file in the GROMACS library directory. If there are other molecules "
"such as ligands, they should not have the same chain ID as the "
"adjacent protein chain since it's a separate molecule.",
- startResidueString.c_str(), endResidueString.c_str(), restype0.c_str(),
- residueString.c_str(), restype.c_str());
+ startResidueString.c_str(),
+ endResidueString.c_str(),
+ restype0.c_str(),
+ residueString.c_str(),
+ restype.c_str());
}
}
}
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted("Identified residue %s%d as a starting terminus.",
- *pdba->resinfo[i].name, pdba->resinfo[i].nr);
+ *pdba->resinfo[i].name,
+ pdba->resinfo[i].nr);
*r_start = i;
}
else if (gmx::equalCaseInsensitive(*startrestype, "Ion"))
.appendTextFormatted(
"Residue %s%d has type 'Ion', assuming it is not linked into a "
"chain.",
- *pdba->resinfo[i].name, pdba->resinfo[i].nr);
+ *pdba->resinfo[i].name,
+ pdba->resinfo[i].nr);
}
if (ionNotes == 4)
{
"be catastrophic if they should in fact be linked. Please "
"check your structure, "
"and add %s to residuetypes.dat if this was not correct.",
- *pdba->resinfo[i].name, pdba->resinfo[i].nr, *pdba->resinfo[i].name);
+ *pdba->resinfo[i].name,
+ pdba->resinfo[i].nr,
+ *pdba->resinfo[i].name);
}
else
{
"and add all "
"necessary residue names to residuetypes.dat if this was not "
"correct.",
- *pdba->resinfo[i].name, pdba->resinfo[i].nr);
+ *pdba->resinfo[i].name,
+ pdba->resinfo[i].nr);
}
}
if (startWarnings == 4)
.appendTextFormatted(
"Residue %s%d has type 'Ion', assuming it is not linked into a "
"chain.",
- *pdba->resinfo[i].name, pdba->resinfo[i].nr);
+ *pdba->resinfo[i].name,
+ pdba->resinfo[i].nr);
}
if (ionNotes == 4)
{
"linked. Please check your structure, and add %s to "
"residuetypes.dat "
"if this was not correct.",
- *pdba->resinfo[i].name, pdba->resinfo[i].nr, restype->c_str(),
- *pdba->resinfo[*r_start].name, pdba->resinfo[*r_start].nr,
- startrestype->c_str(), *pdba->resinfo[i].name);
+ *pdba->resinfo[i].name,
+ pdba->resinfo[i].nr,
+ restype->c_str(),
+ *pdba->resinfo[*r_start].name,
+ pdba->resinfo[*r_start].nr,
+ startrestype->c_str(),
+ *pdba->resinfo[i].name);
}
if (endWarnings == 4)
{
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted("Identified residue %s%d as a ending terminus.",
- *pdba->resinfo[*r_end].name, pdba->resinfo[*r_end].nr);
+ *pdba->resinfo[*r_end].name,
+ pdba->resinfo[*r_end].nr);
}
}
"Split the chain (and introduce termini) between residue %s%d (chain id '%c', atom %d %s)\
"
"and residue %s%d (chain id '%c', atom %d %s) ? [n/y]",
- prev_resname, prev_resnum, prev_chainid, prev_atomnum,
- prev_atomname, this_resname, this_resnum, this_chainid,
- this_atomnum, this_atomname);
+ prev_resname,
+ prev_resnum,
+ prev_chainid,
+ prev_atomnum,
+ prev_atomname,
+ this_resname,
+ this_resnum,
+ this_chainid,
+ this_atomnum,
+ this_atomname);
if (nullptr == fgets(select, STRLEN - 1, stdin))
{
auto res = getDatabaseEntry(newName, rtpFFDB);
const char *name_ai, *name_aj;
- for (const auto& patch : res->rb[ebtsBONDS].b)
+ for (const auto& patch : res->rb[BondedTypes::Bonds].b)
{ /* Search backward bond for n/5' terminus */
name_ai = patch.ai().c_str();
name_aj = patch.aj().c_str();
newName = rtpname;
}
res = getDatabaseEntry(newName, rtpFFDB);
- for (const auto& patch : res->rb[ebtsBONDS].b)
+ for (const auto& patch : res->rb[BondedTypes::Bonds].b)
{
/* Seach forward bond for c/3' terminus */
name_ai = patch.ai().c_str();
struct t_pdbchain
{
char chainid = ' ';
- char chainnum = ' ';
+ int chainnum = ' '; // char, but stored as int to make clang-tidy happy
int start = -1;
int natom = -1;
bool bAllWat = false;
Aromatics,
Count
};
-const gmx::EnumerationArray<VSitesType, const char*> c_vsitesTypeNames = { { "none", "hydrogens",
- "aromatics" } };
+const gmx::EnumerationArray<VSitesType, const char*> c_vsitesTypeNames = {
+ { "none", "hydrogens", "aromatics" }
+};
enum class WaterType : int
{
Interactive,
Count
};
-const gmx::EnumerationArray<MergeType, const char*> c_mergeTypeNames = { { "no", "all",
- "interactive" } };
+const gmx::EnumerationArray<MergeType, const char*> c_mergeTypeNames = {
+ { "no", "all", "interactive" }
+};
} // namespace
}
/* Force field selection, interactive or direct */
- choose_ff(strcmp(ff_.c_str(), "select") == 0 ? nullptr : ff_.c_str(), forcefield_,
- sizeof(forcefield_), ffdir_, sizeof(ffdir_), loggerOwner_->logger());
+ choose_ff(strcmp(ff_.c_str(), "select") == 0 ? nullptr : ff_.c_str(),
+ forcefield_,
+ sizeof(forcefield_),
+ ffdir_,
+ sizeof(ffdir_),
+ loggerOwner_->logger());
if (strlen(forcefield_) > 0)
{
PbcType pbcType;
t_atoms pdba_all;
rvec* pdbx;
- int natom = read_pdball(inputConfFile_.c_str(), bOutputSet_, outFile_.c_str(), &title, &pdba_all,
- &pdbx, &pbcType, box, bRemoveH_, &symtab, &rt, watres, &aps, bVerbose_);
+ int natom = read_pdball(inputConfFile_.c_str(),
+ bOutputSet_,
+ outFile_.c_str(),
+ &title,
+ &pdba_all,
+ &pdbx,
+ &pbcType,
+ box,
+ bRemoveH_,
+ &symtab,
+ &rt,
+ watres,
+ &aps,
+ bVerbose_);
if (natom == 0)
{
"%s) and chain starting with "
"residue %s%d (chain id '%c', atom %d %s) into a single "
"moleculetype (keeping termini)? [n/y]",
- prev_resname, prev_resnum, prev_chainid, prev_atomnum,
- prev_atomname, this_resname, this_resnum, this_chainid,
- this_atomnum, this_atomname);
+ prev_resname,
+ prev_resnum,
+ prev_chainid,
+ prev_atomnum,
+ prev_atomname,
+ this_resname,
+ this_resnum,
+ this_chainid,
+ this_atomnum,
+ this_atomname);
if (nullptr == fgets(select, STRLEN - 1, stdin))
{
.appendTextFormatted(
"There are %d chains and %d blocks of water and "
"%d residues with %d atoms",
- numChains - nwaterchain, nwaterchain, pdba_all.nres, natom);
+ numChains - nwaterchain,
+ nwaterchain,
+ pdba_all.nres,
+ natom);
GMX_LOG(logger.info)
.asParagraph()
{
GMX_LOG(logger.info)
.asParagraph()
- .appendTextFormatted(" %d '%c' %5d %6d %s\n", i + 1,
- chains[i].chainid ? chains[i].chainid : '-', chains[i].pdba->nres,
- chains[i].pdba->nr, chains[i].bAllWat ? "(only water)" : "");
+ .appendTextFormatted(" %d '%c' %5d %6d %s\n",
+ i + 1,
+ chains[i].chainid ? chains[i].chainid : '-',
+ chains[i].pdba->nres,
+ chains[i].pdba->nr,
+ chains[i].bAllWat ? "(only water)" : "");
}
check_occupancy(&pdba_all, inputConfFile_.c_str(), bVerbose_, logger);
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted("Processing chain %d '%c' (%d atoms, %d residues)",
- chain + 1, cc->chainid, natom, nres);
+ chain + 1,
+ cc->chainid,
+ natom,
+ nres);
}
else
{
GMX_LOG(logger.info)
.asParagraph()
- .appendTextFormatted("Processing chain %d (%d atoms, %d residues)", chain + 1,
- natom, nres);
- }
-
- process_chain(logger, pdba, x, bUnA_, bUnA_, bUnA_, bLysMan_, bAspMan_, bGluMan_, bHisMan_,
- bArgMan_, bGlnMan_, angle_, distance_, &symtab, rtprename);
+ .appendTextFormatted(
+ "Processing chain %d (%d atoms, %d residues)", chain + 1, natom, nres);
+ }
+
+ process_chain(logger,
+ pdba,
+ x,
+ bUnA_,
+ bUnA_,
+ bUnA_,
+ bLysMan_,
+ bAspMan_,
+ bGluMan_,
+ bHisMan_,
+ bArgMan_,
+ bGlnMan_,
+ angle_,
+ distance_,
+ &symtab,
+ rtprename);
cc->chainstart[cc->nterpairs] = pdba->nres;
j = 0;
for (int i = 0; i < cc->nterpairs; i++)
{
- find_nc_ter(pdba, cc->chainstart[i], cc->chainstart[i + 1], &(cc->r_start[j]),
- &(cc->r_end[j]), &rt, logger);
+ find_nc_ter(
+ pdba, cc->chainstart[i], cc->chainstart[i + 1], &(cc->r_start[j]), &(cc->r_end[j]), &rt, logger);
if (cc->r_start[j] >= 0 && cc->r_end[j] >= 0)
{
- if (checkChainCyclicity(pdba, pdbx, cc->r_start[j], cc->r_end[j], rtpFFDB,
- rtprename, long_bond_dist_, short_bond_dist_))
+ if (checkChainCyclicity(
+ pdba, pdbx, cc->r_start[j], cc->r_end[j], rtpFFDB, rtprename, long_bond_dist_, short_bond_dist_))
{
cc->cyclicBondsIndex.push_back(cc->r_start[j]);
cc->cyclicBondsIndex.push_back(cc->r_end[j]);
{
if (bTerMan_ && !tdblist.empty())
{
- sprintf(select, "Select start terminus type for %s-%d",
- *pdba->resinfo[cc->r_start[i]].name, pdba->resinfo[cc->r_start[i]].nr);
+ sprintf(select,
+ "Select start terminus type for %s-%d",
+ *pdba->resinfo[cc->r_start[i]].name,
+ pdba->resinfo[cc->r_start[i]].nr);
cc->ntdb.push_back(choose_ter(tdblist, select));
}
else
cc->ntdb.push_back(tdblist[0]);
}
- printf("Start terminus %s-%d: %s\n", *pdba->resinfo[cc->r_start[i]].name,
- pdba->resinfo[cc->r_start[i]].nr, (cc->ntdb[i])->name.c_str());
+ printf("Start terminus %s-%d: %s\n",
+ *pdba->resinfo[cc->r_start[i]].name,
+ pdba->resinfo[cc->r_start[i]].nr,
+ (cc->ntdb[i])->name.c_str());
tdblist.clear();
}
}
{
if (bTerMan_ && !tdblist.empty())
{
- sprintf(select, "Select end terminus type for %s-%d",
- *pdba->resinfo[cc->r_end[i]].name, pdba->resinfo[cc->r_end[i]].nr);
+ sprintf(select,
+ "Select end terminus type for %s-%d",
+ *pdba->resinfo[cc->r_end[i]].name,
+ pdba->resinfo[cc->r_end[i]].nr);
cc->ctdb.push_back(choose_ter(tdblist, select));
}
else
{
cc->ctdb.push_back(tdblist[0]);
}
- printf("End terminus %s-%d: %s\n", *pdba->resinfo[cc->r_end[i]].name,
- pdba->resinfo[cc->r_end[i]].nr, (cc->ctdb[i])->name.c_str());
+ printf("End terminus %s-%d: %s\n",
+ *pdba->resinfo[cc->r_end[i]].name,
+ pdba->resinfo[cc->r_end[i]].nr,
+ (cc->ctdb[i])->name.c_str());
tdblist.clear();
}
}
std::vector<MoleculePatchDatabase> hb_chain;
/* lookup hackblocks and rtp for all residues */
std::vector<PreprocessResidue> restp_chain;
- get_hackblocks_rtp(&hb_chain, &restp_chain, rtpFFDB, pdba->nres, pdba->resinfo, cc->nterpairs,
- &symtab, cc->ntdb, cc->ctdb, cc->r_start, cc->r_end, bAllowMissing_, logger);
+ get_hackblocks_rtp(&hb_chain,
+ &restp_chain,
+ rtpFFDB,
+ pdba->nres,
+ pdba->resinfo,
+ cc->nterpairs,
+ &symtab,
+ cc->ntdb,
+ cc->ctdb,
+ cc->r_start,
+ cc->r_end,
+ bAllowMissing_,
+ logger);
/* ideally, now we would not need the rtp itself anymore, but do
everything using the hb and restp arrays. Unfortunately, that
requires some re-thinking of code in gen_vsite.c, which I won't
.asParagraph()
.appendTextFormatted(
"Generating any missing hydrogen atoms and/or adding termini.");
- add_h(&pdba, &localAtoms[chain], &x, ah, &symtab, cc->nterpairs, cc->ntdb, cc->ctdb,
- cc->r_start, cc->r_end, bAllowMissing_, cc->cyclicBondsIndex);
+ add_h(&pdba,
+ &localAtoms[chain],
+ &x,
+ ah,
+ &symtab,
+ cc->nterpairs,
+ cc->ntdb,
+ cc->ctdb,
+ cc->r_start,
+ cc->r_end,
+ bAllowMissing_,
+ cc->cyclicBondsIndex);
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted("Now there are %d residues with %d atoms", pdba->nres, pdba->nr);
top_file2 = top_file;
}
- pdb2top(top_file2, posre_fn.c_str(), molname.c_str(), pdba, &x, &atype, &symtab, rtpFFDB,
- restp_chain, hb_chain, bAllowMissing_, bVsites_, bVsiteAromatics_, ffdir_, mHmult_,
- ssbonds, long_bond_dist_, short_bond_dist_, bDeuterate_, bChargeGroups_, bCmap_,
- bRenumRes_, bRTPresname_, cc->cyclicBondsIndex, logger);
+ pdb2top(top_file2,
+ posre_fn.c_str(),
+ molname.c_str(),
+ pdba,
+ &x,
+ &atype,
+ &symtab,
+ rtpFFDB,
+ restp_chain,
+ hb_chain,
+ bAllowMissing_,
+ bVsites_,
+ bVsiteAromatics_,
+ ffdir_,
+ mHmult_,
+ ssbonds,
+ long_bond_dist_,
+ short_bond_dist_,
+ bDeuterate_,
+ bChargeGroups_,
+ bCmap_,
+ bRenumRes_,
+ bRTPresname_,
+ cc->cyclicBondsIndex,
+ logger);
if (!cc->bAllWat)
{
"The topology file '%s' for the selected water "
"model '%s' can not be found in the force field "
"directory. Select a different water model.",
- waterFile.c_str(), watermodel_);
+ waterFile.c_str(),
+ watermodel_);
GMX_THROW(InconsistentInputError(message));
}
}
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted("Including chain %d in system: %d atoms %d residues",
- i + 1, chains[i].pdba->nr, chains[i].pdba->nres);
+ i + 1,
+ chains[i].pdba->nr,
+ chains[i].pdba->nres);
}
for (int j = 0; (j < chains[i].pdba->nr); j++)
{
{
make_new_box(atoms->nr, gmx::as_rvec_array(x.data()), box, box_space, false);
}
- write_sto_conf(outputConfFile_.c_str(), title, atoms, gmx::as_rvec_array(x.data()), nullptr,
- pbcType, box);
+ write_sto_conf(
+ outputConfFile_.c_str(), title, atoms, gmx::as_rvec_array(x.data()), nullptr, pbcType, box);
done_symtab(&symtab);
done_atom(&pdba_all);
{
GMX_LOG(logger.info)
.asParagraph()
- .appendTextFormatted("The %s force field and the %s water model are used.", ffname_,
- watermodel_);
+ .appendTextFormatted(
+ "The %s force field and the %s water model are used.", ffname_, watermodel_);
sfree(watermodel_);
}
else
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/binaryinformation.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/dir_separator.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "hackblock.h"
#include "resall.h"
-/* this must correspond to enum in pdb2top.h */
-const char* hh[ehisNR] = { "HISD", "HISE", "HISH", "HIS1" };
+const char* enumValueToString(HistidineStates enumValue)
+{
+ constexpr gmx::EnumerationArray<HistidineStates, const char*> histidineStateNames = {
+ "HISD", "HISE", "HISH", "HIS1"
+ };
+ return histidineStateNames[enumValue];
+}
static int missing_atoms(const PreprocessResidue* rp, int resind, t_atoms* at, int i0, int i, const gmx::MDLogger& logger)
{
GMX_LOG(logger.warning)
.asParagraph()
.appendTextFormatted("atom %s is missing in residue %s %d in the pdb file",
- name, *(at->resinfo[resind].name), at->resinfo[resind].nr);
+ name,
+ *(at->resinfo[resind].name),
+ at->resinfo[resind].nr);
if (name[0] == 'H' || name[0] == 'h')
{
GMX_LOG(logger.warning)
"You might need to add atom %s to the hydrogen database of "
"building block %s "
"in the file %s.hdb (see the manual)",
- name, *(at->resinfo[resind].rtp), rp->filebase.c_str());
+ name,
+ *(at->resinfo[resind].rtp),
+ rp->filebase.c_str());
}
}
}
"Force field '%s' occurs in %d places. pdb2gmx is using the one in "
"the current directory. Use interactive selection "
"(not the -ff option) if you would prefer a different one.",
- ffsel, nfound);
+ ffsel,
+ nfound);
}
else
{
"the current directory.\n"
"Run without the -ff switch and select the force "
"field interactively.",
- ffsel, nfound);
+ ffsel,
+ nfound);
GMX_THROW(gmx::InconsistentInputError(message));
}
}
"to point to the desired force field first, and/or "
"rename or move the force field directory present "
"in the current working directory.",
- ffs[sel].c_str(), fflib_forcefield_dir_ext());
+ ffs[sel].c_str(),
+ fflib_forcefield_dir_ext());
GMX_THROW(gmx::NotImplementedError(message));
}
}
if (ffs[sel].length() >= static_cast<size_t>(ff_maxlen))
{
std::string message = gmx::formatString("Length of force field name (%d) >= maxlen (%d)",
- static_cast<int>(ffs[sel].length()), ff_maxlen);
+ static_cast<int>(ffs[sel].length()),
+ ff_maxlen);
GMX_THROW(gmx::InvalidInputError(message));
}
strcpy(forcefield, ffs[sel].c_str());
if (ffpath.length() >= static_cast<size_t>(ffdir_maxlen))
{
std::string message = gmx::formatString("Length of force field dir (%d) >= maxlen (%d)",
- static_cast<int>(ffpath.length()), ffdir_maxlen);
+ static_cast<int>(ffpath.length()),
+ ffdir_maxlen);
GMX_THROW(gmx::InvalidInputError(message));
}
strcpy(ffdir, ffpath.c_str());
static void print_top_system(FILE* out, const char* title)
{
- fprintf(out, "[ %s ]\n", dir2str(Directive::d_system));
+ fprintf(out, "[ %s ]\n", enumValueToString(Directive::d_system));
fprintf(out, "; Name\n");
fprintf(out, "%s\n\n", title[0] ? title : "Protein");
}
if (!mols.empty())
{
- fprintf(out, "[ %s ]\n", dir2str(Directive::d_molecules));
+ fprintf(out, "[ %s ]\n", enumValueToString(Directive::d_molecules));
fprintf(out, "; %-15s %5s\n", "Compound", "#mols");
for (const auto& mol : mols)
{
const char* molname,
t_atoms* at,
bool bRTPresname,
- int bts[],
+ gmx::ArrayRef<const int> bts,
gmx::ArrayRef<const InteractionsOfType> plist,
t_excls excls[],
PreprocessingAtomTypes* atype,
{
if (at && atype && cgnr)
{
- fprintf(out, "[ %s ]\n", dir2str(Directive::d_moleculetype));
+ fprintf(out, "[ %s ]\n", enumValueToString(Directive::d_moleculetype));
fprintf(out, "; %-15s %5s\n", "Name", "nrexcl");
fprintf(out, "%-15s %5d\n\n", molname ? molname : "Protein", nrexcl);
print_atoms(out, atype, at, cgnr, bRTPresname);
- print_bondeds(out, at->nr, Directive::d_bonds, F_BONDS, bts[ebtsBONDS], plist);
+ print_bondeds(
+ out, at->nr, Directive::d_bonds, F_BONDS, bts[static_cast<int>(BondedTypes::Bonds)], plist);
print_bondeds(out, at->nr, Directive::d_constraints, F_CONSTR, 0, plist);
print_bondeds(out, at->nr, Directive::d_constraints, F_CONSTRNC, 0, plist);
print_bondeds(out, at->nr, Directive::d_pairs, F_LJ14, 0, plist);
print_excl(out, at->nr, excls);
- print_bondeds(out, at->nr, Directive::d_angles, F_ANGLES, bts[ebtsANGLES], plist);
- print_bondeds(out, at->nr, Directive::d_dihedrals, F_PDIHS, bts[ebtsPDIHS], plist);
- print_bondeds(out, at->nr, Directive::d_dihedrals, F_IDIHS, bts[ebtsIDIHS], plist);
- print_bondeds(out, at->nr, Directive::d_cmap, F_CMAP, bts[ebtsCMAP], plist);
+ print_bondeds(
+ out, at->nr, Directive::d_angles, F_ANGLES, bts[static_cast<int>(BondedTypes::Angles)], plist);
+ print_bondeds(out,
+ at->nr,
+ Directive::d_dihedrals,
+ F_PDIHS,
+ bts[static_cast<int>(BondedTypes::ProperDihedrals)],
+ plist);
+ print_bondeds(out,
+ at->nr,
+ Directive::d_dihedrals,
+ F_IDIHS,
+ bts[static_cast<int>(BondedTypes::ImproperDihedrals)],
+ plist);
+ print_bondeds(out, at->nr, Directive::d_cmap, F_CMAP, bts[static_cast<int>(BondedTypes::Cmap)], plist);
print_bondeds(out, at->nr, Directive::d_polarization, F_POLARIZATION, 0, plist);
print_bondeds(out, at->nr, Directive::d_thole_polarization, F_THOLE_POL, 0, plist);
print_bondeds(out, at->nr, Directive::d_vsites2, F_VSITE2, 0, plist);
int aj = search_res_atom(bond.secondAtom.c_str(), rj, atoms, "special bond", bAllowMissing);
if ((ai == -1) || (aj == -1))
{
- gmx_fatal(FARGS, "Trying to make impossible special bond (%s-%s)!",
- bond.firstAtom.c_str(), bond.secondAtom.c_str());
+ gmx_fatal(FARGS,
+ "Trying to make impossible special bond (%s-%s)!",
+ bond.firstAtom.c_str(),
+ bond.secondAtom.c_str());
}
add_param(ps, ai, aj, {}, nullptr);
}
for (int resind = 0; (resind < atoms->nres) && (i < atoms->nr); resind++)
{
/* add bonds from list of bonded interactions */
- for (const auto& patch : globalPatches[resind].rb[ebtsBONDS].b)
+ for (const auto& patch : globalPatches[resind].rb[BondedTypes::Bonds].b)
{
/* Unfortunately we can not issue errors or warnings
* for missing atoms in bonds, as the hydrogens and terminal atoms
{
GMX_LOG(logger.warning)
.asParagraph()
- .appendTextFormatted("Long Bond (%d-%d = %g nm)", ai + 1, aj + 1,
- std::sqrt(dist2));
+ .appendTextFormatted(
+ "Long Bond (%d-%d = %g nm)", ai + 1, aj + 1, std::sqrt(dist2));
}
else if (dist2 < short_bond_dist2)
{
GMX_LOG(logger.warning)
.asParagraph()
- .appendTextFormatted("Short Bond (%d-%d = %g nm)", ai + 1, aj + 1,
- std::sqrt(dist2));
+ .appendTextFormatted(
+ "Short Bond (%d-%d = %g nm)", ai + 1, aj + 1, std::sqrt(dist2));
}
add_param(psb, ai, aj, {}, patch.s.c_str());
}
static void check_restp_types(const PreprocessResidue& r0, const PreprocessResidue& r1)
{
- check_restp_type("all dihedrals", static_cast<int>(r0.bKeepAllGeneratedDihedrals),
+ check_restp_type("all dihedrals",
+ static_cast<int>(r0.bKeepAllGeneratedDihedrals),
static_cast<int>(r1.bKeepAllGeneratedDihedrals));
check_restp_type("nrexcl", r0.nrexcl, r1.nrexcl);
- check_restp_type("HH14", static_cast<int>(r0.bGenerateHH14Interactions),
+ check_restp_type("HH14",
+ static_cast<int>(r0.bGenerateHH14Interactions),
static_cast<int>(r1.bGenerateHH14Interactions));
- check_restp_type("remove dihedrals", static_cast<int>(r0.bRemoveDihedralIfWithImproper),
+ check_restp_type("remove dihedrals",
+ static_cast<int>(r0.bRemoveDihedralIfWithImproper),
static_cast<int>(r1.bRemoveDihedralIfWithImproper));
- for (int i = 0; i < ebtsNR; i++)
+ for (auto i : gmx::EnumerationWrapper<BondedTypes>{})
{
- check_restp_type(btsNames[i], r0.rb[i].type, r1.rb[i].type);
+ check_restp_type(enumValueToString(i), r0.rb[i].type, r1.rb[i].type);
}
}
if (patch->nr != 0)
{
/* find atom in restp */
- auto found = std::find_if(posres->atomname.begin(), posres->atomname.end(),
- [&patch](char** name) {
- return (patch->oname.empty() && patch->a[0] == *name)
- || (patch->oname == *name);
- });
+ auto found = std::find_if(
+ posres->atomname.begin(), posres->atomname.end(), [&patch](char** name) {
+ return (patch->oname.empty() && patch->a[0] == *name)
+ || (patch->oname == *name);
+ });
if (found == posres->atomname.end())
{
"atom %s not found in buiding block %d%s "
"while combining tdb and rtp",
patch->oname.empty() ? patch->a[0].c_str() : patch->oname.c_str(),
- pos + 1, *resinfo[pos].rtp);
+ pos + 1,
+ *resinfo[pos].rtp);
}
}
else
/* This atom still has the old name, rename it */
std::string newnm = patch->nname;
auto found = std::find_if(
- localPpResidue->atomname.begin(), localPpResidue->atomname.end(),
+ localPpResidue->atomname.begin(),
+ localPpResidue->atomname.end(),
[&newnm](char** name) { return gmx::equalCaseInsensitive(newnm, *name); });
if (found == localPpResidue->atomname.end())
{
*/
bool bFoundInAdd = false;
for (auto rtpModification = singlePatch.hack.begin();
- rtpModification != singlePatch.hack.end(); rtpModification++)
+ rtpModification != singlePatch.hack.end();
+ rtpModification++)
{
int k = std::distance(localPpResidue->atomname.begin(), found);
std::string start_at;
}
else
{
- start_at = gmx::formatString("%s%d", singlePatch.hack[k].nname.c_str(),
- anmnr - 1);
+ start_at = gmx::formatString(
+ "%s%d", singlePatch.hack[k].nname.c_str(), anmnr - 1);
}
- auto found2 =
- std::find_if(localPpResidue->atomname.begin(),
- localPpResidue->atomname.end(), [&start_at](char** name) {
- return gmx::equalCaseInsensitive(start_at, *name);
- });
+ auto found2 = std::find_if(localPpResidue->atomname.begin(),
+ localPpResidue->atomname.end(),
+ [&start_at](char** name) {
+ return gmx::equalCaseInsensitive(start_at, *name);
+ });
if (found2 == localPpResidue->atomname.end())
{
gmx_fatal(FARGS,
"Could not find atom '%s' in residue building block '%s' to "
"add atom '%s' to",
- start_at.c_str(), localPpResidue->resname.c_str(), newnm.c_str());
+ start_at.c_str(),
+ localPpResidue->resname.c_str(),
+ newnm.c_str());
}
/* We can add the atom after atom start_nr */
- add_atom_to_restp(localPpResidue, symtab,
+ add_atom_to_restp(localPpResidue,
+ symtab,
std::distance(localPpResidue->atomname.begin(), found2),
&(*patch));
"Could not find an 'add' entry for atom named '%s' corresponding to "
"the 'replace' entry from atom name '%s' to '%s' for tdb or hdb "
"database of residue type '%s'",
- newnm.c_str(), patch->oname.c_str(), patch->nname.c_str(),
+ newnm.c_str(),
+ patch->oname.c_str(),
+ patch->nname.c_str(),
localPpResidue->resname.c_str());
}
}
{
GMX_LOG(logger.info)
.asParagraph()
- .appendTextFormatted("Renaming atom '%s' in residue '%s' %d to '%s'", oldnm,
- localPpResidue->resname.c_str(), resnr, newnm.c_str());
+ .appendTextFormatted("Renaming atom '%s' in residue '%s' %d to '%s'",
+ oldnm,
+ localPpResidue->resname.c_str(),
+ resnr,
+ newnm.c_str());
}
/* Rename the atom in pdba */
pdba->atomname[atind] = put_symtab(symtab, newnm.c_str());
* in the rtp entry of this residue.
*/
auto found3 = std::find_if(
- localPpResidue->atomname.begin(), localPpResidue->atomname.end(),
+ localPpResidue->atomname.begin(),
+ localPpResidue->atomname.end(),
[&oldnm](char** name) { return gmx::equalCaseInsensitive(oldnm, *name); });
if (found3 == localPpResidue->atomname.end())
{
{
GMX_LOG(logger.info)
.asParagraph()
- .appendTextFormatted("Deleting atom '%s' in residue '%s' %d", oldnm,
- localPpResidue->resname.c_str(), resnr);
+ .appendTextFormatted("Deleting atom '%s' in residue '%s' %d",
+ oldnm,
+ localPpResidue->resname.c_str(),
+ resnr);
}
/* We should free the atom name,
* but it might be used multiple times in the symtab.
const char* oldnm = *pdba->atomname[i];
PreprocessResidue* localPpResidue = &usedPpResidues[pdba->atom[i].resind];
auto found = std::find_if(
- localPpResidue->atomname.begin(), localPpResidue->atomname.end(),
- [&oldnm](char** name) { return gmx::equalCaseInsensitive(oldnm, *name); });
+ localPpResidue->atomname.begin(), localPpResidue->atomname.end(), [&oldnm](char** name) {
+ return gmx::equalCaseInsensitive(oldnm, *name);
+ });
if (found == localPpResidue->atomname.end())
{
/* Not found yet, check if we have to rename this atom */
- if (match_atomnames_with_rtp_atom(pdba, x, symtab, i, localPpResidue,
- globalPatches[pdba->atom[i].resind], bVerbose, logger))
+ if (match_atomnames_with_rtp_atom(
+ pdba, x, symtab, i, localPpResidue, globalPatches[pdba->atom[i].resind], bVerbose, logger))
{
/* We deleted this atom, decrease the atom counter by 1. */
i--;
for (residx = 0; residx < nres; residx++)
{
/* Add CMAP terms from the list of CMAP interactions */
- for (const auto& b : usedPpResidues[residx].rb[ebtsCMAP].b)
+ for (const auto& b : usedPpResidues[residx].rb[BondedTypes::Cmap].b)
{
bool bAddCMAP = true;
/* Loop over atoms in a candidate CMAP interaction and
if (bAddCMAP)
{
- add_cmap_param(psb, cmap_atomid[0], cmap_atomid[1], cmap_atomid[2], cmap_atomid[3],
- cmap_atomid[4], b.s.c_str());
+ add_cmap_param(psb,
+ cmap_atomid[0],
+ cmap_atomid[1],
+ cmap_atomid[2],
+ cmap_atomid[3],
+ cmap_atomid[4],
+ b.s.c_str());
}
}
gmx::ArrayRef<const int> cyclicBondsIndex,
const gmx::MDLogger& logger)
{
- std::array<InteractionsOfType, F_NRE> plist;
- t_excls* excls;
- int* cgnr;
- int* vsite_type;
- int i, nmissat;
- int bts[ebtsNR];
+ std::array<InteractionsOfType, F_NRE> plist;
+ t_excls* excls;
+ int* cgnr;
+ int* vsite_type;
+ int i, nmissat;
+ gmx::EnumerationArray<BondedTypes, int> bts;
ResidueType rt;
/* Make bonds */
- at2bonds(&(plist[F_BONDS]), globalPatches, atoms, *x, long_bond_dist, short_bond_dist,
- cyclicBondsIndex, logger);
+ at2bonds(&(plist[F_BONDS]), globalPatches, atoms, *x, long_bond_dist, short_bond_dist, cyclicBondsIndex, logger);
/* specbonds: disulphide bonds & heme-his */
do_ssbonds(&(plist[F_BONDS]), atoms, ssbonds, bAllowMissing);
gmx_fatal(FARGS,
"There were %d missing atoms in molecule %s, if you want to use this "
"incomplete topology anyhow, use the option -missing",
- nmissat, molname);
+ nmissat,
+ molname);
}
}
.appendTextFormatted(
"There are %4zu dihedrals, %4zu impropers, %4zu angles\n"
" %4zu pairs, %4zu bonds and %4zu virtual sites",
- plist[F_PDIHS].size(), plist[F_IDIHS].size(), plist[F_ANGLES].size(),
- plist[F_LJ14].size(), plist[F_BONDS].size(),
+ plist[F_PDIHS].size(),
+ plist[F_IDIHS].size(),
+ plist[F_ANGLES].size(),
+ plist[F_LJ14].size(),
+ plist[F_BONDS].size(),
plist[F_VSITE2].size() + plist[F_VSITE3].size() + plist[F_VSITE3FD].size()
+ plist[F_VSITE3FAD].size() + plist[F_VSITE3OUT].size()
+ plist[F_VSITE4FD].size() + plist[F_VSITE4FDN].size());
/* We can copy the bonded types from the first restp,
* since the types have to be identical for all residues in one molecule.
*/
- for (i = 0; i < ebtsNR; i++)
+ for (auto i : gmx::EnumerationWrapper<BondedTypes>{})
{
bts[i] = usedPpResidues[0].rb[i].type;
}
- write_top(top_file, posre_fn, molname, atoms, bRTPresname, bts, plist, excls, atype, cgnr,
+ write_top(top_file,
+ posre_fn,
+ molname,
+ atoms,
+ bRTPresname,
+ bts,
+ plist,
+ excls,
+ atype,
+ cgnr,
usedPpResidues[0].nrexcl);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/enumerationhelpers.h"
class PreprocessingAtomTypes;
struct DisulfideBond;
struct t_symtab;
-/* this *MUST* correspond to array in pdb2top.c */
-enum
+/* this *MUST* correspond to array in pdb2top.cpp */
+enum class HistidineStates : int
{
- ehisA,
- ehisB,
- ehisH,
- ehis1,
- ehisNR
+ A,
+ B,
+ H,
+ One,
+ Count
};
-extern const char* hh[ehisNR];
+const char* enumValueToString(HistidineStates enumValue);
void choose_ff(const char* ffsel,
char* forcefield,
const char* molname,
t_atoms* at,
bool bRTPresname,
- int bts[],
+ gmx::ArrayRef<const int> bts,
gmx::ArrayRef<const InteractionsOfType> plist,
t_excls excls[],
PreprocessingAtomTypes* atype,
{
if (0 != strcmp(bondtype, "atom"))
{
- snprintf(message_buffer, 1024,
+ snprintf(message_buffer,
+ 1024,
"Residue %d named %s of a molecule in the input file was mapped\n"
"to an entry in the topology database, but the atom %s used in\n"
"an interaction of type %s in that entry is not found in the\n"
"input file. Perhaps your atom and/or residue naming needs to be\n"
"fixed.\n",
- resind + 1, resname, atomname, bondtype);
+ resind + 1,
+ resname,
+ atomname,
+ bondtype);
}
else
{
- snprintf(message_buffer, 1024,
+ snprintf(message_buffer,
+ 1024,
"Residue %d named %s of a molecule in the input file was mapped\n"
"to an entry in the topology database, but the atom %s used in\n"
"that entry is not found in the input file. Perhaps your atom\n"
"and/or residue naming needs to be fixed.\n",
- resind + 1, resname, atomname);
+ resind + 1,
+ resname,
+ atomname);
}
if (bAllowMissing)
{
}
if (!(bNext && at[start].resind == at[natoms - 1].resind))
{
- atom_not_found(FARGS, type, at[start].resind, *atoms->resinfo[resind].name, bondtype,
- bAllowMissing);
+ atom_not_found(FARGS, type, at[start].resind, *atoms->resinfo[resind].name, bondtype, bAllowMissing);
}
}
else
}
if (start > 0)
{
- atom_not_found(FARGS, type, at[start].resind, *atoms->resinfo[resind].name, bondtype,
- bAllowMissing);
+ atom_not_found(FARGS, type, at[start].resind, *atoms->resinfo[resind].name, bondtype, bAllowMissing);
}
}
return -1;
#include <algorithm>
#include <memory>
+#include <numeric>
#include <string>
#include "gromacs/applied_forces/awh/read_params.h"
#include "gromacs/gmxpreprocess/toputil.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/calc_verletbuf.h"
#include "gromacs/mdrun/mdmodules.h"
+#include "gromacs/mdtypes/awh_params.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/multipletimestepping.h"
#include "gromacs/utility/keyvaluetreebuilder.h"
#include "gromacs/utility/keyvaluetreemdpwriter.h"
#include "gromacs/utility/keyvaluetreetransform.h"
-#include "gromacs/utility/mdmodulenotification.h"
+#include "gromacs/utility/mdmodulesnotifiers.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strconvert.h"
#include "gromacs/utility/stringcompare.h"
struct gmx_inputrec_strings
{
- char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN], acc[STRLEN], accgrps[STRLEN], freeze[STRLEN],
- frdim[STRLEN], energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN],
- x_compressed_groups[STRLEN], couple_moltype[STRLEN], orirefitgrp[STRLEN],
- egptable[STRLEN], egpexcl[STRLEN], wall_atomtype[STRLEN], wall_density[STRLEN],
- deform[STRLEN], QMMM[STRLEN], imd_grp[STRLEN];
- char fep_lambda[efptNR][STRLEN];
- char lambda_weights[STRLEN];
- std::vector<std::string> pullGroupNames;
- std::vector<std::string> rotateGroupNames;
+ char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN], freeze[STRLEN], frdim[STRLEN],
+ energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
+ couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
+ wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN], imd_grp[STRLEN];
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::string> fep_lambda;
+ char lambda_weights[STRLEN];
+ std::vector<std::string> pullGroupNames;
+ std::vector<std::string> rotateGroupNames;
char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
};
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static gmx_inputrec_strings* inputrecStrings = nullptr;
void init_inputrec_strings()
* make a rest group for the remaining particles. */
};
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static const char* constraints[eshNR + 1] = { "none", "h-bonds", "all-bonds",
"h-angles", "all-angles", nullptr };
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static const char* couple_lam[ecouplamNR + 1] = { "vdw-q", "vdw", "q", "none", nullptr };
-static void GetSimTemps(int ntemps, t_simtemp* simtemp, double* temperature_lambdas)
+static void getSimTemps(int ntemps, t_simtemp* simtemp, gmx::ArrayRef<double> temperature_lambdas)
{
int i;
for (i = 0; i < ntemps; i++)
{
/* simple linear scaling -- allows more control */
- if (simtemp->eSimTempScale == esimtempLINEAR)
+ if (simtemp->eSimTempScale == SimulatedTempering::Linear)
{
simtemp->temperatures[i] =
simtemp->simtemp_low
+ (simtemp->simtemp_high - simtemp->simtemp_low) * temperature_lambdas[i];
}
else if (simtemp->eSimTempScale
- == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
+ == SimulatedTempering::Geometric) /* should give roughly equal acceptance for constant heat capacity . . . */
{
simtemp->temperatures[i] = simtemp->simtemp_low
* std::pow(simtemp->simtemp_high / simtemp->simtemp_low,
static_cast<real>((1.0 * i) / (ntemps - 1)));
}
- else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
+ else if (simtemp->eSimTempScale == SimulatedTempering::Exponential)
{
simtemp->temperatures[i] = simtemp->simtemp_low
+ (simtemp->simtemp_high - simtemp->simtemp_low)
else
{
char errorstr[128];
- sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
+ sprintf(errorstr, "eSimTempScale=%s not defined", enumValueToString(simtemp->eSimTempScale));
gmx_fatal(FARGS, "%s", errorstr);
}
}
}
}
-static int lcd(int n1, int n2)
-{
- int d, i;
-
- d = 1;
- for (i = 2; (i <= n1 && i <= n2); i++)
- {
- if (n1 % i == 0 && n2 % i == 0)
- {
- d = i;
- }
- }
-
- return d;
-}
-
//! Convert legacy mdp entries to modern ones.
-static void process_interaction_modifier(int* eintmod)
-{
- if (*eintmod == eintmodPOTSHIFT_VERLET_UNSUPPORTED)
- {
- *eintmod = eintmodPOTSHIFT;
- }
-}
-
-static void checkMtsRequirement(const t_inputrec& ir, const char* param, const int nstValue, warninp_t wi)
+static void process_interaction_modifier(InteractionModifiers* eintmod)
{
- GMX_RELEASE_ASSERT(ir.mtsLevels.size() >= 2, "Need at least two levels for MTS");
- const int mtsFactor = ir.mtsLevels.back().stepFactor;
- if (nstValue % mtsFactor != 0)
+ if (*eintmod == InteractionModifiers::PotShiftVerletUnsupported)
{
- auto message = gmx::formatString(
- "With MTS, %s = %d should be a multiple of mts-factor = %d", param, nstValue, mtsFactor);
- warning_error(wi, message.c_str());
+ *eintmod = InteractionModifiers::PotShift;
}
}
-static void setupMtsLevels(gmx::ArrayRef<gmx::MtsLevel> mtsLevels,
- const t_inputrec& ir,
- const t_gromppopts& opts,
- warninp_t wi)
-{
- /* MD-VV has no MTS support yet.
- * SD1 needs different scaling coefficients for the different MTS forces
- * and the different forces are currently not available in ForceBuffers.
- */
- if (ir.eI != eiMD)
- {
- auto message = gmx::formatString(
- "Multiple time stepping is only supported with integrator %s", ei_names[eiMD]);
- warning_error(wi, message.c_str());
- }
- if (opts.numMtsLevels != 2)
- {
- warning_error(wi, "Only mts-levels = 2 is supported");
- }
- else
- {
- const std::vector<std::string> inputForceGroups = gmx::splitString(opts.mtsLevel2Forces);
- auto& forceGroups = mtsLevels[1].forceGroups;
- for (const auto& inputForceGroup : inputForceGroups)
- {
- bool found = false;
- int nameIndex = 0;
- for (const auto& forceGroupName : gmx::mtsForceGroupNames)
- {
- if (gmx::equalCaseInsensitive(inputForceGroup, forceGroupName))
- {
- forceGroups.set(nameIndex);
- found = true;
- }
- nameIndex++;
- }
- if (!found)
- {
- auto message =
- gmx::formatString("Unknown MTS force group '%s'", inputForceGroup.c_str());
- warning_error(wi, message.c_str());
- }
- }
-
- if (mtsLevels[1].stepFactor <= 1)
- {
- gmx_fatal(FARGS, "mts-factor should be larger than 1");
- }
-
- // Make the level 0 use the complement of the force groups of group 1
- mtsLevels[0].forceGroups = ~mtsLevels[1].forceGroups;
- mtsLevels[0].stepFactor = 1;
-
- if ((EEL_FULL(ir.coulombtype) || EVDW_PME(ir.vdwtype))
- && !mtsLevels[1].forceGroups[static_cast<int>(gmx::MtsForceGroups::LongrangeNonbonded)])
- {
- warning_error(wi,
- "With long-range electrostatics and/or LJ treatment, the long-range part "
- "has to be part of the mts-level2-forces");
- }
-
- if (ir.nstcalcenergy > 0)
- {
- checkMtsRequirement(ir, "nstcalcenergy", ir.nstcalcenergy, wi);
- }
- checkMtsRequirement(ir, "nstenergy", ir.nstenergy, wi);
- checkMtsRequirement(ir, "nstlog", ir.nstlog, wi);
- if (ir.efep != efepNO)
- {
- checkMtsRequirement(ir, "nstdhdl", ir.fepvals->nstdhdl, wi);
- }
-
- if (ir.bPull)
- {
- const int pullMtsLevel = gmx::forceGroupMtsLevel(ir.mtsLevels, gmx::MtsForceGroups::Pull);
- if (ir.pull->nstxout % ir.mtsLevels[pullMtsLevel].stepFactor != 0)
- {
- warning_error(wi, "pull-nstxout should be a multiple of mts-factor");
- }
- if (ir.pull->nstfout % ir.mtsLevels[pullMtsLevel].stepFactor != 0)
- {
- warning_error(wi, "pull-nstfout should be a multiple of mts-factor");
- }
- }
- }
-}
-
-void check_ir(const char* mdparin,
- const gmx::MdModulesNotifier& mdModulesNotifier,
- t_inputrec* ir,
- t_gromppopts* opts,
- warninp_t wi)
+void check_ir(const char* mdparin,
+ const gmx::MDModulesNotifiers& mdModulesNotifiers,
+ t_inputrec* ir,
+ t_gromppopts* opts,
+ warninp_t wi)
/* Check internal consistency.
* NOTE: index groups are not set here yet, don't check things
* like temperature coupling group options here, but in triple_check
char err_buf[256], warn_buf[STRLEN];
int i, j;
real dt_pcoupl;
- t_lambda* fep = ir->fepvals;
- t_expanded* expand = ir->expandedvals;
+ t_lambda* fep = ir->fepvals.get();
+ t_expanded* expand = ir->expandedvals.get();
set_warning_line(wi, mdparin, -1);
- if (ir->coulombtype == eelRF_NEC_UNSUPPORTED)
+ /* We cannot check MTS requirements with an invalid MTS setup
+ * and we will already have generated errors with an invalid MTS setup.
+ */
+ if (gmx::haveValidMtsSetup(*ir))
{
- sprintf(warn_buf, "%s electrostatics is no longer supported", eel_names[eelRF_NEC_UNSUPPORTED]);
- warning_error(wi, warn_buf);
+ std::vector<std::string> errorMessages = gmx::checkMtsRequirements(*ir);
+
+ for (const auto& errorMessage : errorMessages)
+ {
+ warning_error(wi, errorMessage.c_str());
+ }
+ }
+
+ if (ir->coulombtype == CoulombInteractionType::RFNecUnsupported)
+ {
+ std::string message =
+ gmx::formatString("%s electrostatics is no longer supported",
+ enumValueToString(CoulombInteractionType::RFNecUnsupported));
+ warning_error(wi, message);
}
/* BASIC CUT-OFF STUFF */
{
warning_error(wi, "rvdw should be >= 0");
}
- if (ir->rlist < 0 && !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
+ if (ir->rlist < 0 && !(ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0))
{
warning_error(wi, "rlist should be >= 0");
}
process_interaction_modifier(&ir->coulomb_modifier);
process_interaction_modifier(&ir->vdw_modifier);
- if (ir->cutoff_scheme == ecutsGROUP)
+ if (ir->cutoff_scheme == CutoffScheme::Group)
{
gmx_fatal(FARGS,
"The group cutoff scheme has been removed since GROMACS 2020. "
"Please use the Verlet cutoff scheme.");
}
- if (ir->cutoff_scheme == ecutsVERLET)
+ if (ir->cutoff_scheme == CutoffScheme::Verlet)
{
real rc_max;
{
// Since we have PME coulomb + LJ cut-off kernels with rcoulomb>rvdw
// for PME load balancing, we can support this exception.
- bool bUsesPmeTwinRangeKernel = (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == evdwCUT
- && ir->rcoulomb > ir->rvdw);
+ bool bUsesPmeTwinRangeKernel =
+ (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == VanDerWaalsType::Cut
+ && ir->rcoulomb > ir->rvdw);
if (!bUsesPmeTwinRangeKernel)
{
warning_error(wi,
}
}
- if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
+ if (ir->vdwtype == VanDerWaalsType::Shift || ir->vdwtype == VanDerWaalsType::Switch)
{
- if (ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT)
+ if (ir->vdw_modifier == InteractionModifiers::None
+ || ir->vdw_modifier == InteractionModifiers::PotShift)
{
- ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
+ ir->vdw_modifier =
+ (ir->vdwtype == VanDerWaalsType::Shift ? InteractionModifiers::ForceSwitch
+ : InteractionModifiers::PotSwitch);
sprintf(warn_buf,
"Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and "
"vdw_modifier=%s",
- evdw_names[ir->vdwtype], evdw_names[evdwCUT], eintmod_names[ir->vdw_modifier]);
+ enumValueToString(ir->vdwtype),
+ enumValueToString(VanDerWaalsType::Cut),
+ enumValueToString(ir->vdw_modifier));
warning_note(wi, warn_buf);
- ir->vdwtype = evdwCUT;
+ ir->vdwtype = VanDerWaalsType::Cut;
}
else
{
- sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s",
- evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
+ sprintf(warn_buf,
+ "Unsupported combination of vdwtype=%s and vdw_modifier=%s",
+ enumValueToString(ir->vdwtype),
+ enumValueToString(ir->vdw_modifier));
warning_error(wi, warn_buf);
}
}
- if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
+ if (!(ir->vdwtype == VanDerWaalsType::Cut || ir->vdwtype == VanDerWaalsType::Pme))
{
warning_error(wi,
"With Verlet lists only cut-off and PME LJ interactions are supported");
}
- if (!(ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype) || EEL_PME(ir->coulombtype)
- || ir->coulombtype == eelEWALD))
+ if (!(ir->coulombtype == CoulombInteractionType::Cut || EEL_RF(ir->coulombtype)
+ || EEL_PME(ir->coulombtype) || ir->coulombtype == CoulombInteractionType::Ewald))
{
warning_error(wi,
"With Verlet lists only cut-off, reaction-field, PME and Ewald "
"electrostatics are supported");
}
- if (!(ir->coulomb_modifier == eintmodNONE || ir->coulomb_modifier == eintmodPOTSHIFT))
+ if (!(ir->coulomb_modifier == InteractionModifiers::None
+ || ir->coulomb_modifier == InteractionModifiers::PotShift))
{
- sprintf(warn_buf, "coulomb_modifier=%s is not supported", eintmod_names[ir->coulomb_modifier]);
+ sprintf(warn_buf, "coulomb_modifier=%s is not supported", enumValueToString(ir->coulomb_modifier));
warning_error(wi, warn_buf);
}
if (EEL_USER(ir->coulombtype))
{
- sprintf(warn_buf, "Coulomb type %s is not supported with the verlet scheme",
- eel_names[ir->coulombtype]);
+ sprintf(warn_buf,
+ "Coulomb type %s is not supported with the verlet scheme",
+ enumValueToString(ir->coulombtype));
warning_error(wi, warn_buf);
}
/* GENERAL INTEGRATOR STUFF */
if (!EI_MD(ir->eI))
{
- if (ir->etc != etcNO)
+ if (ir->etc != TemperatureCoupling::No)
{
if (EI_RANDOM(ir->eI))
{
"Setting tcoupl from '%s' to 'no'. %s handles temperature coupling "
"implicitly. See the documentation for more information on which "
"parameters affect temperature for %s.",
- etcoupl_names[ir->etc], ei_names[ir->eI], ei_names[ir->eI]);
+ enumValueToString(ir->etc),
+ enumValueToString(ir->eI),
+ enumValueToString(ir->eI));
}
else
{
sprintf(warn_buf,
"Setting tcoupl from '%s' to 'no'. Temperature coupling does not apply to "
"%s.",
- etcoupl_names[ir->etc], ei_names[ir->eI]);
+ enumValueToString(ir->etc),
+ enumValueToString(ir->eI));
}
warning_note(wi, warn_buf);
}
- ir->etc = etcNO;
+ ir->etc = TemperatureCoupling::No;
}
- if (ir->eI == eiVVAK)
+ if (ir->eI == IntegrationAlgorithm::VVAK)
{
sprintf(warn_buf,
"Integrator method %s is implemented primarily for validation purposes; for "
"molecular dynamics, you should probably be using %s or %s",
- ei_names[eiVVAK], ei_names[eiMD], ei_names[eiVV]);
+ enumValueToString(IntegrationAlgorithm::VVAK),
+ enumValueToString(IntegrationAlgorithm::MD),
+ enumValueToString(IntegrationAlgorithm::VV));
warning_note(wi, warn_buf);
}
if (!EI_DYNAMICS(ir->eI))
{
- if (ir->epc != epcNO)
+ if (ir->epc != PressureCoupling::No)
{
sprintf(warn_buf,
"Setting pcoupl from '%s' to 'no'. Pressure coupling does not apply to %s.",
- epcoupl_names[ir->epc], ei_names[ir->eI]);
+ enumValueToString(ir->epc),
+ enumValueToString(ir->eI));
warning_note(wi, warn_buf);
}
- ir->epc = epcNO;
+ ir->epc = PressureCoupling::No;
}
if (EI_DYNAMICS(ir->eI))
{
*/
if (ir->nstlist > 0)
{
- ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
+ ir->nstcalcenergy = std::gcd(ir->nstenergy, ir->nstlist);
}
else
{
}
}
else if ((ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy)
- || (ir->efep != efepNO && ir->fepvals->nstdhdl > 0
+ || (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl > 0
&& (ir->nstcalcenergy > ir->fepvals->nstdhdl)))
{
int min_nst = ir->nstenergy;
/* find the smallest of ( nstenergy, nstdhdl ) */
- if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0
+ if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl > 0
&& (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
{
min_nst = ir->fepvals->nstdhdl;
min_name = nstdh;
}
/* If the user sets nstenergy small, we should respect that */
- sprintf(warn_buf, "Setting nstcalcenergy (%d) equal to %s (%d)", ir->nstcalcenergy,
- min_name, min_nst);
+ sprintf(warn_buf, "Setting nstcalcenergy (%d) equal to %s (%d)", ir->nstcalcenergy, min_name, min_nst);
warning_note(wi, warn_buf);
ir->nstcalcenergy = min_nst;
}
- if (ir->epc != epcNO)
+ if (ir->epc != PressureCoupling::No)
{
if (ir->nstpcouple < 0)
{
if (ir->nstcalcenergy > 0)
{
- if (ir->efep != efepNO)
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
/* nstdhdl should be a multiple of nstcalcenergy */
check_nst("nstcalcenergy", ir->nstcalcenergy, "nstdhdl", &ir->fepvals->nstdhdl, wi);
if (ir->bExpanded)
{
/* nstexpanded should be a multiple of nstcalcenergy */
- check_nst("nstcalcenergy", ir->nstcalcenergy, "nstexpanded",
- &ir->expandedvals->nstexpanded, wi);
+ check_nst("nstcalcenergy", ir->nstcalcenergy, "nstexpanded", &ir->expandedvals->nstexpanded, wi);
}
/* for storing exact averages nstenergy should be
* a multiple of nstcalcenergy
check_nst("nstcalcenergy", ir->nstcalcenergy, "nstenergy", &ir->nstenergy, wi);
}
- // Inquire all MdModules, if their parameters match with the energy
+ // Inquire all MDModules, if their parameters match with the energy
// calculation frequency
gmx::EnergyCalculationFrequencyErrors energyCalculationFrequencyErrors(ir->nstcalcenergy);
- mdModulesNotifier.preProcessingNotifications_.notify(&energyCalculationFrequencyErrors);
+ mdModulesNotifiers.preProcessingNotifier_.notify(&energyCalculationFrequencyErrors);
// Emit all errors from the energy calculation frequency checks
for (const std::string& energyFrequencyErrorMessage :
}
/* LD STUFF */
- if ((EI_SD(ir->eI) || ir->eI == eiBD) && ir->bContinuation && ir->ld_seed != -1)
+ if ((EI_SD(ir->eI) || ir->eI == IntegrationAlgorithm::BD) && ir->bContinuation && ir->ld_seed != -1)
{
warning_note(wi,
"You are doing a continuation with SD or BD, make sure that ld_seed is "
warning(wi, warn_buf);
}
- if ((EI_SD(ir->eI) || ir->eI == eiBD) && ir->bContinuation && ir->ld_seed != -1)
+ if ((EI_SD(ir->eI) || ir->eI == IntegrationAlgorithm::BD) && ir->bContinuation && ir->ld_seed != -1)
{
warning_note(wi,
"You are doing a continuation with SD or BD, make sure that ld_seed is "
bool bAllTempZero = TRUE;
for (i = 0; i < fep->n_lambda; i++)
{
- sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i,
- efpt_names[efptTEMPERATURE], fep->all_lambda[efptTEMPERATURE][i]);
- CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
- if (fep->all_lambda[efptTEMPERATURE][i] > 0)
+ sprintf(err_buf,
+ "Entry %d for %s must be between 0 and 1, instead is %g",
+ i,
+ enumValueToString(FreeEnergyPerturbationCouplingType::Temperature),
+ fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i]);
+ CHECK((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i] < 0)
+ || (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i]
+ > 1));
+ if (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i] > 0)
{
bAllTempZero = FALSE;
}
CHECK(bAllTempZero == TRUE);
sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
- CHECK(ir->eI != eiVV);
+ CHECK(ir->eI != IntegrationAlgorithm::VV);
/* check compatability of the temperature coupling with simulated tempering */
- if (ir->etc == etcNOSEHOOVER)
+ if (ir->etc == TemperatureCoupling::NoseHoover)
{
sprintf(warn_buf,
"Nose-Hoover based temperature control such as [%s] my not be "
"entirelyconsistent with simulated tempering",
- etcoupl_names[ir->etc]);
+ enumValueToString(ir->etc));
warning_note(wi, warn_buf);
}
sprintf(err_buf,
"Higher simulated tempering temperature (%g) must be >= than the simulated "
"tempering lower temperature (%g)",
- ir->simtempvals->simtemp_high, ir->simtempvals->simtemp_low);
+ ir->simtempvals->simtemp_high,
+ ir->simtempvals->simtemp_low);
CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
- sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero",
+ sprintf(err_buf,
+ "Higher simulated tempering temperature (%g) must be >= zero",
ir->simtempvals->simtemp_high);
CHECK(ir->simtempvals->simtemp_high <= 0);
- sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero",
+ sprintf(err_buf,
+ "Lower simulated tempering temperature (%g) must be >= zero",
ir->simtempvals->simtemp_low);
CHECK(ir->simtempvals->simtemp_low <= 0);
}
/* verify free energy options */
- if (ir->efep != efepNO)
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
- fep = ir->fepvals;
+ fep = ir->fepvals.get();
sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2", fep->sc_power);
CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
fep->delta_lambda);
CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
- sprintf(err_buf, "Can't use positive delta-lambda (%g) with expanded ensemble simulations",
+ sprintf(err_buf,
+ "Can't use positive delta-lambda (%g) with expanded ensemble simulations",
fep->delta_lambda);
- CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
+ CHECK(fep->delta_lambda > 0 && (ir->efep == FreeEnergyPerturbationType::Expanded));
sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
- CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
+ CHECK(!(EI_VV(ir->eI)) && (ir->efep == FreeEnergyPerturbationType::Expanded));
sprintf(err_buf, "Free-energy not implemented for Ewald");
- CHECK(ir->coulombtype == eelEWALD);
+ CHECK(ir->coulombtype == CoulombInteractionType::Ewald);
/* check validty of lambda inputs */
if (fep->n_lambda == 0)
{
/* Clear output in case of no states:*/
- sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.",
- fep->init_fep_state);
+ sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
}
else
{
- sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d",
- fep->init_fep_state, fep->n_lambda - 1);
+ sprintf(err_buf,
+ "initial thermodynamic state %d does not exist, only goes to %d",
+ fep->init_fep_state,
+ fep->n_lambda - 1);
CHECK((fep->init_fep_state >= fep->n_lambda));
}
sprintf(err_buf,
"init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with "
"init-lambda-state or with init-lambda, but not both",
- fep->init_lambda, fep->init_fep_state);
+ fep->init_lambda,
+ fep->init_fep_state);
CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
{
int n_lambda_terms;
n_lambda_terms = 0;
- for (i = 0; i < efptNR; i++)
+ for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
{
if (fep->separate_dvdl[i])
{
}
}
- for (j = 0; j < efptNR; j++)
+ for (j = 0; j < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); j++)
{
for (i = 0; i < fep->n_lambda; i++)
{
- sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i,
- efpt_names[j], fep->all_lambda[j][i]);
+ auto enumValue = static_cast<FreeEnergyPerturbationCouplingType>(j);
+ sprintf(err_buf,
+ "Entry %d for %s must be between 0 and 1, instead is %g",
+ i,
+ enumValueToString(enumValue),
+ fep->all_lambda[j][i]);
CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
}
}
"For state %d, vdw-lambdas (%f) is changing with vdw softcore, while "
"coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to "
"crashes, and is not supported.",
- i, fep->all_lambda[efptVDW][i], fep->all_lambda[efptCOUL][i]);
+ i,
+ fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i],
+ fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i]);
CHECK((fep->sc_alpha > 0)
- && (((fep->all_lambda[efptCOUL][i] > 0.0) && (fep->all_lambda[efptCOUL][i] < 1.0))
- && ((fep->all_lambda[efptVDW][i] > 0.0) && (fep->all_lambda[efptVDW][i] < 1.0))));
+ && (((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i] > 0.0)
+ && (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i] < 1.0))
+ && ((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i] > 0.0)
+ && (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i]
+ < 1.0))));
}
}
"energy conservation, but usually other effects dominate. With a common sigma "
"value of %g nm the fraction of the particle-particle potential at the cut-off "
"at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
- fep->sc_r_power, sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
+ fep->sc_r_power,
+ sigma,
+ lambda,
+ r_sc - 1.0,
+ ir->ewald_rtol);
warning_note(wi, warn_buf);
}
/* Free Energy Checks -- In an ideal world, slow growth and FEP would
be treated differently, but that's the next step */
- for (i = 0; i < efptNR; i++)
+ for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
{
+ auto enumValue = static_cast<FreeEnergyPerturbationCouplingType>(i);
for (j = 0; j < fep->n_lambda; j++)
{
- sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
+ sprintf(err_buf, "%s[%d] must be between 0 and 1", enumValueToString(enumValue), j);
CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
}
}
}
- if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
+ if ((ir->bSimTemp) || (ir->efep == FreeEnergyPerturbationType::Expanded))
{
- fep = ir->fepvals;
+ fep = ir->fepvals.get();
/* checking equilibration of weights inputs for validity */
sprintf(err_buf,
"weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal "
"to %s",
- expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
- CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
+ expand->equil_n_at_lam,
+ enumValueToString(LambdaWeightWillReachEquilibrium::NumAtLambda));
+ CHECK((expand->equil_n_at_lam > 0)
+ && (expand->elmceq != LambdaWeightWillReachEquilibrium::NumAtLambda));
sprintf(err_buf,
"weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to "
"%s",
- expand->equil_samples, elmceq_names[elmceqSAMPLES]);
- CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
+ expand->equil_samples,
+ enumValueToString(LambdaWeightWillReachEquilibrium::Samples));
+ CHECK((expand->equil_samples > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Samples));
sprintf(err_buf,
"weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
- expand->equil_steps, elmceq_names[elmceqSTEPS]);
- CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
+ expand->equil_steps,
+ enumValueToString(LambdaWeightWillReachEquilibrium::Steps));
+ CHECK((expand->equil_steps > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Steps));
sprintf(err_buf,
"weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
- expand->equil_samples, elmceq_names[elmceqWLDELTA]);
- CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
+ expand->equil_samples,
+ enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta));
+ CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::WLDelta));
sprintf(err_buf,
"weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
- expand->equil_ratio, elmceq_names[elmceqRATIO]);
- CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
+ expand->equil_ratio,
+ enumValueToString(LambdaWeightWillReachEquilibrium::Ratio));
+ CHECK((expand->equil_ratio > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Ratio));
sprintf(err_buf,
"weight-equil-number-all-lambda (%d) must be a positive integer if "
"lmc-weights-equil=%s",
- expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
- CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
+ expand->equil_n_at_lam,
+ enumValueToString(LambdaWeightWillReachEquilibrium::NumAtLambda));
+ CHECK((expand->equil_n_at_lam <= 0)
+ && (expand->elmceq == LambdaWeightWillReachEquilibrium::NumAtLambda));
sprintf(err_buf,
"weight-equil-number-samples (%d) must be a positive integer if "
"lmc-weights-equil=%s",
- expand->equil_samples, elmceq_names[elmceqSAMPLES]);
- CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
+ expand->equil_samples,
+ enumValueToString(LambdaWeightWillReachEquilibrium::Samples));
+ CHECK((expand->equil_samples <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Samples));
sprintf(err_buf,
"weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
- expand->equil_steps, elmceq_names[elmceqSTEPS]);
- CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
+ expand->equil_steps,
+ enumValueToString(LambdaWeightWillReachEquilibrium::Steps));
+ CHECK((expand->equil_steps <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Steps));
- sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
- expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
- CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
+ sprintf(err_buf,
+ "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
+ expand->equil_wl_delta,
+ enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta));
+ CHECK((expand->equil_wl_delta <= 0)
+ && (expand->elmceq == LambdaWeightWillReachEquilibrium::WLDelta));
- sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
- expand->equil_ratio, elmceq_names[elmceqRATIO]);
- CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
+ sprintf(err_buf,
+ "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
+ expand->equil_ratio,
+ enumValueToString(LambdaWeightWillReachEquilibrium::Ratio));
+ CHECK((expand->equil_ratio <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Ratio));
- sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
- elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
- CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
+ sprintf(err_buf,
+ "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
+ enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta),
+ enumValueToString(LambdaWeightCalculation::WL),
+ enumValueToString(LambdaWeightCalculation::WWL));
+ CHECK((expand->elmceq == LambdaWeightWillReachEquilibrium::WLDelta) && (!EWL(expand->elamstats)));
sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
CHECK((expand->lmc_repeats <= 0));
sprintf(err_buf,
"init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != "
"'no'",
- fep->init_fep_state, expand->lmc_forced_nstart);
+ fep->init_fep_state,
+ expand->lmc_forced_nstart);
CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0)
- && (expand->elmcmove != elmcmoveNO));
+ && (expand->elmcmove != LambdaMoveCalculation::No));
sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
CHECK((expand->lmc_forced_nstart < 0));
- sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)",
+ sprintf(err_buf,
+ "init-lambda-state (%d) must be in the interval [0,number of lambdas)",
fep->init_fep_state);
CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
/* if there is no temperature control, we need to specify an MC temperature */
- if (!integratorHasReferenceTemperature(ir) && (expand->elmcmove != elmcmoveNO)
- && (expand->mc_temp <= 0.0))
+ if (!integratorHasReferenceTemperature(ir)
+ && (expand->elmcmove != LambdaMoveCalculation::No) && (expand->mc_temp <= 0.0))
{
sprintf(err_buf,
"If there is no temperature control, and lmc-mcmove!='no', mc_temp must be set "
{
sprintf(err_buf,
"nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
- expand->nstTij, ir->nstlog);
+ expand->nstTij,
+ ir->nstlog);
CHECK((expand->nstTij % ir->nstlog) != 0);
}
}
{
if (ir->pbcType == PbcType::No)
{
- if (ir->epc != epcNO)
+ if (ir->epc != PressureCoupling::No)
{
warning(wi, "Turning off pressure coupling for vacuum system");
- ir->epc = epcNO;
+ ir->epc = PressureCoupling::No;
}
}
else
{
- sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
+ sprintf(err_buf,
+ "Can not have pressure coupling with pbc=%s",
c_pbcTypeNames[ir->pbcType].c_str());
- CHECK(ir->epc != epcNO);
+ CHECK(ir->epc != PressureCoupling::No);
}
sprintf(err_buf, "Can not have Ewald with pbc=%s", c_pbcTypeNames[ir->pbcType].c_str());
CHECK(EEL_FULL(ir->coulombtype));
- sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
+ sprintf(err_buf,
+ "Can not have dispersion correction with pbc=%s",
c_pbcTypeNames[ir->pbcType].c_str());
- CHECK(ir->eDispCorr != edispcNO);
+ CHECK(ir->eDispCorr != DispersionCorrectionType::No);
}
if (ir->rlist == 0.0)
"with coulombtype = %s or coulombtype = %s\n"
"without periodic boundary conditions (pbc = %s) and\n"
"rcoulomb and rvdw set to zero",
- eel_names[eelCUT], eel_names[eelUSER], c_pbcTypeNames[PbcType::No].c_str());
- CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER))
+ enumValueToString(CoulombInteractionType::Cut),
+ enumValueToString(CoulombInteractionType::User),
+ c_pbcTypeNames[PbcType::No].c_str());
+ CHECK(((ir->coulombtype != CoulombInteractionType::Cut)
+ && (ir->coulombtype != CoulombInteractionType::User))
|| (ir->pbcType != PbcType::No) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
if (ir->nstlist > 0)
{
// TODO Change this behaviour. There should be exactly one way
// to turn off an algorithm.
- ir->comm_mode = ecmNO;
+ ir->comm_mode = ComRemovalAlgorithm::No;
}
- if (ir->comm_mode != ecmNO)
+ if (ir->comm_mode != ComRemovalAlgorithm::No)
{
if (ir->nstcomm < 0)
{
ir->nstcomm = ir->nstcalcenergy;
}
- if (ir->comm_mode == ecmANGULAR)
+ if (ir->comm_mode == ComRemovalAlgorithm::Angular)
{
sprintf(err_buf,
"Can not remove the rotation around the center of mass with periodic "
}
}
- if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->pbcType == PbcType::No && ir->comm_mode != ecmANGULAR)
+ if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->pbcType == PbcType::No
+ && ir->comm_mode != ComRemovalAlgorithm::Angular)
{
sprintf(warn_buf,
"Tumbling and flying ice-cubes: We are not removing rotation around center of mass "
"in a non-periodic system. You should probably set comm_mode = ANGULAR or use "
"integrator = %s.",
- ei_names[eiSD1]);
+ enumValueToString(IntegrationAlgorithm::SD1));
warning_note(wi, warn_buf);
}
/* TEMPERATURE COUPLING */
- if (ir->etc == etcYES)
+ if (ir->etc == TemperatureCoupling::Yes)
{
- ir->etc = etcBERENDSEN;
+ ir->etc = TemperatureCoupling::Berendsen;
warning_note(wi,
"Old option for temperature coupling given: "
"changing \"yes\" to \"Berendsen\"\n");
}
- if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
+ if ((ir->etc == TemperatureCoupling::NoseHoover) || (ir->epc == PressureCoupling::Mttk))
{
if (ir->opts.nhchainlength < 1)
{
warning(wi, warn_buf);
}
- if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
+ if (ir->etc == TemperatureCoupling::NoseHoover && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
{
warning_note(
wi,
ir->opts.nhchainlength = 0;
}
- if (ir->eI == eiVVAK)
+ if (ir->eI == IntegrationAlgorithm::VVAK)
{
sprintf(err_buf,
"%s implemented primarily for validation, and requires nsttcouple = 1 and "
"nstpcouple = 1.",
- ei_names[eiVVAK]);
+ enumValueToString(IntegrationAlgorithm::VVAK));
CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
}
if (ETC_ANDERSEN(ir->etc))
{
- sprintf(err_buf, "%s temperature control not supported for integrator %s.",
- etcoupl_names[ir->etc], ei_names[ir->eI]);
+ sprintf(err_buf,
+ "%s temperature control not supported for integrator %s.",
+ enumValueToString(ir->etc),
+ enumValueToString(ir->eI));
CHECK(!(EI_VV(ir->eI)));
- if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
+ if (ir->nstcomm > 0 && (ir->etc == TemperatureCoupling::Andersen))
{
sprintf(warn_buf,
"Center of mass removal not necessary for %s. All velocities of coupled "
"groups are rerandomized periodically, so flying ice cube errors will not "
"occur.",
- etcoupl_names[ir->etc]);
+ enumValueToString(ir->etc));
warning_note(wi, warn_buf);
}
sprintf(err_buf,
"nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are "
"randomized every time step",
- ir->nstcomm, etcoupl_names[ir->etc]);
- CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
+ ir->nstcomm,
+ enumValueToString(ir->etc));
+ CHECK(ir->nstcomm > 1 && (ir->etc == TemperatureCoupling::Andersen));
}
- if (ir->etc == etcBERENDSEN)
+ if (ir->etc == TemperatureCoupling::Berendsen)
{
sprintf(warn_buf,
"The %s thermostat does not generate the correct kinetic energy distribution. You "
"might want to consider using the %s thermostat.",
- ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
+ enumValueToString(ir->etc),
+ enumValueToString(TemperatureCoupling::VRescale));
warning_note(wi, warn_buf);
}
- if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc)) && ir->epc == epcBERENDSEN)
+ if ((ir->etc == TemperatureCoupling::NoseHoover || ETC_ANDERSEN(ir->etc))
+ && ir->epc == PressureCoupling::Berendsen)
{
sprintf(warn_buf,
"Using Berendsen pressure coupling invalidates the "
}
/* PRESSURE COUPLING */
- if (ir->epc == epcISOTROPIC)
+ if (ir->epc == PressureCoupling::Isotropic)
{
- ir->epc = epcBERENDSEN;
+ ir->epc = PressureCoupling::Berendsen;
warning_note(wi,
"Old option for pressure coupling given: "
"changing \"Isotropic\" to \"Berendsen\"\n");
}
- if (ir->epc != epcNO)
+ if (ir->epc != PressureCoupling::No)
{
dt_pcoupl = ir->nstpcouple * ir->delta_t;
sprintf(warn_buf,
"For proper integration of the %s barostat, tau-p (%g) should be at least %d "
"times larger than nstpcouple*dt (%g)",
- EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
+ enumValueToString(ir->epc),
+ ir->tau_p,
+ pcouple_min_integration_steps(ir->epc),
+ dt_pcoupl);
warning(wi, warn_buf);
}
sprintf(err_buf,
"compressibility must be > 0 when using pressure"
" coupling %s\n",
- EPCOUPLTYPE(ir->epc));
+ enumValueToString(ir->epc));
CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 || ir->compress[ZZ][ZZ] < 0
|| (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 && ir->compress[ZZ][XX] <= 0
&& ir->compress[ZZ][YY] <= 0));
- if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
+ if (PressureCoupling::ParrinelloRahman == ir->epc && opts->bGenVel)
{
sprintf(warn_buf,
"You are generating velocities so I am assuming you "
"equilibrating first with Berendsen pressure coupling. If "
"you are not equilibrating the system, you can probably "
"ignore this warning.",
- epcoupl_names[ir->epc]);
+ enumValueToString(ir->epc));
warning(wi, warn_buf);
}
}
if (!EI_VV(ir->eI))
{
- if (ir->epc == epcMTTK)
+ if (ir->epc == PressureCoupling::Mttk)
{
warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
}
/* ELECTROSTATICS */
/* More checks are in triple check (grompp.c) */
- if (ir->coulombtype == eelSWITCH)
+ if (ir->coulombtype == CoulombInteractionType::Switch)
{
sprintf(warn_buf,
"coulombtype = %s is only for testing purposes and can lead to serious "
"artifacts, advice: use coulombtype = %s",
- eel_names[ir->coulombtype], eel_names[eelRF_ZERO]);
+ enumValueToString(ir->coulombtype),
+ enumValueToString(CoulombInteractionType::RFZero));
warning(wi, warn_buf);
}
{
/* reaction field (at the cut-off) */
- if (ir->coulombtype == eelRF_ZERO && ir->epsilon_rf != 0)
+ if (ir->coulombtype == CoulombInteractionType::RFZero && ir->epsilon_rf != 0)
{
sprintf(warn_buf,
"With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
- eel_names[ir->coulombtype]);
+ enumValueToString(ir->coulombtype));
warning(wi, warn_buf);
ir->epsilon_rf = 0.0;
}
CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) || (ir->epsilon_r == 0));
if (ir->epsilon_rf == ir->epsilon_r)
{
- sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
- eel_names[ir->coulombtype]);
+ sprintf(warn_buf,
+ "Using epsilon-rf = epsilon-r with %s does not make sense",
+ enumValueToString(ir->coulombtype));
warning(wi, warn_buf);
}
}
sprintf(err_buf,
"With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the "
"potential modifier options!",
- eel_names[ir->coulombtype]);
+ enumValueToString(ir->coulombtype));
CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
}
}
- if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
+ if (ir->coulombtype == CoulombInteractionType::Switch || ir->coulombtype == CoulombInteractionType::Shift)
{
sprintf(err_buf,
"Explicit switch/shift coulomb interactions cannot be used in combination with a "
"secondary coulomb-modifier.");
- CHECK(ir->coulomb_modifier != eintmodNONE);
+ CHECK(ir->coulomb_modifier != InteractionModifiers::None);
}
- if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
+ if (ir->vdwtype == VanDerWaalsType::Switch || ir->vdwtype == VanDerWaalsType::Shift)
{
sprintf(err_buf,
"Explicit switch/shift vdw interactions cannot be used in combination with a "
"secondary vdw-modifier.");
- CHECK(ir->vdw_modifier != eintmodNONE);
+ CHECK(ir->vdw_modifier != InteractionModifiers::None);
}
- if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT || ir->vdwtype == evdwSWITCH
- || ir->vdwtype == evdwSHIFT)
+ if (ir->coulombtype == CoulombInteractionType::Switch || ir->coulombtype == CoulombInteractionType::Shift
+ || ir->vdwtype == VanDerWaalsType::Switch || ir->vdwtype == VanDerWaalsType::Shift)
{
sprintf(warn_buf,
"The switch/shift interaction settings are just for compatibility; you will get "
warning_note(wi, warn_buf);
}
- if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
+ if (ir->coulombtype == CoulombInteractionType::PmeSwitch
+ || ir->coulomb_modifier == InteractionModifiers::PotSwitch)
{
if (ir->rcoulomb_switch / ir->rcoulomb < 0.9499)
{
"The switching range should be 5%% or less (currently %.2f%% using a switching "
"range of %4f-%4f) for accurate electrostatic energies, energy conservation "
"will be good regardless, since ewald_rtol = %g.",
- percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
+ percentage,
+ ir->rcoulomb_switch,
+ ir->rcoulomb,
+ ir->ewald_rtol);
warning(wi, warn_buf);
}
}
- if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
+ if (ir->vdwtype == VanDerWaalsType::Switch || ir->vdw_modifier == InteractionModifiers::PotSwitch)
{
if (ir->rvdw_switch == 0)
{
if (EEL_FULL(ir->coulombtype))
{
- if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER
- || ir->coulombtype == eelPMEUSERSWITCH)
+ if (ir->coulombtype == CoulombInteractionType::PmeSwitch
+ || ir->coulombtype == CoulombInteractionType::PmeUser
+ || ir->coulombtype == CoulombInteractionType::PmeUserSwitch)
{
- sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
- eel_names[ir->coulombtype]);
+ sprintf(err_buf,
+ "With coulombtype = %s, rcoulomb must be <= rlist",
+ enumValueToString(ir->coulombtype));
CHECK(ir->rcoulomb > ir->rlist);
}
}
{
// TODO: Move these checks into the ewald module with the options class
int orderMin = 3;
- int orderMax = (ir->coulombtype == eelP3M_AD ? 8 : 12);
+ int orderMax = (ir->coulombtype == CoulombInteractionType::P3mAD ? 8 : 12);
if (ir->pme_order < orderMin || ir->pme_order > orderMax)
{
- sprintf(warn_buf, "With coulombtype = %s, you should have %d <= pme-order <= %d",
- eel_names[ir->coulombtype], orderMin, orderMax);
+ sprintf(warn_buf,
+ "With coulombtype = %s, you should have %d <= pme-order <= %d",
+ enumValueToString(ir->coulombtype),
+ orderMin,
+ orderMax);
warning_error(wi, warn_buf);
}
}
if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
{
- if (ir->ewald_geometry == eewg3D)
+ if (ir->ewald_geometry == EwaldGeometry::ThreeD)
{
- sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
- c_pbcTypeNames[ir->pbcType].c_str(), eewg_names[eewg3DC]);
+ sprintf(warn_buf,
+ "With pbc=%s you should use ewald-geometry=%s",
+ c_pbcTypeNames[ir->pbcType].c_str(),
+ enumValueToString(EwaldGeometry::ThreeDC));
warning(wi, warn_buf);
}
/* This check avoids extra pbc coding for exclusion corrections */
sprintf(err_buf, "wall-ewald-zfac should be >= 2");
CHECK(ir->wall_ewald_zfac < 2);
}
- if ((ir->ewald_geometry == eewg3DC) && (ir->pbcType != PbcType::XY) && EEL_FULL(ir->coulombtype))
+ if ((ir->ewald_geometry == EwaldGeometry::ThreeDC) && (ir->pbcType != PbcType::XY)
+ && EEL_FULL(ir->coulombtype))
{
- sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
- eel_names[ir->coulombtype], eewg_names[eewg3DC], c_pbcTypeNames[PbcType::XY].c_str());
+ sprintf(warn_buf,
+ "With %s and ewald_geometry = %s you should use pbc = %s",
+ enumValueToString(ir->coulombtype),
+ enumValueToString(EwaldGeometry::ThreeDC),
+ c_pbcTypeNames[PbcType::XY].c_str());
warning(wi, warn_buf);
}
if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
"You are applying a switch function to vdw forces or potentials from %g to %g "
"nm, which is more than half the interaction range, whereas switch functions "
"are intended to act only close to the cut-off.",
- ir->rvdw_switch, ir->rvdw);
+ ir->rvdw_switch,
+ ir->rvdw);
warning_note(wi, warn_buf);
}
}
- if (ir->vdwtype == evdwPME)
+ if (ir->vdwtype == VanDerWaalsType::Pme)
{
- if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
+ if (!(ir->vdw_modifier == InteractionModifiers::None
+ || ir->vdw_modifier == InteractionModifiers::PotShift))
{
- sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s and %s",
- evdw_names[ir->vdwtype], eintmod_names[eintmodPOTSHIFT], eintmod_names[eintmodNONE]);
+ sprintf(err_buf,
+ "With vdwtype = %s, the only supported modifiers are %s and %s",
+ enumValueToString(ir->vdwtype),
+ enumValueToString(InteractionModifiers::PotShift),
+ enumValueToString(InteractionModifiers::None));
warning_error(wi, err_buf);
}
}
- if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
+ if (ir->vdwtype == VanDerWaalsType::User && ir->eDispCorr != DispersionCorrectionType::No)
{
warning_note(wi,
"You have selected user tables with dispersion correction, the dispersion "
"really want dispersion correction to -C6/r^6.");
}
- if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT) && ir->rvdw != 0)
+ if (ir->eI == IntegrationAlgorithm::LBFGS
+ && (ir->coulombtype == CoulombInteractionType::Cut || ir->vdwtype == VanDerWaalsType::Cut)
+ && ir->rvdw != 0)
{
warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
}
- if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
+ if (ir->eI == IntegrationAlgorithm::LBFGS && ir->nbfgscorr <= 0)
{
warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
}
/* IMPLICIT SOLVENT */
- if (ir->coulombtype == eelGB_NOTUSED)
+ if (ir->coulombtype == CoulombInteractionType::GBNotused)
{
- sprintf(warn_buf, "Invalid option %s for coulombtype", eel_names[ir->coulombtype]);
+ sprintf(warn_buf, "Invalid option %s for coulombtype", enumValueToString(ir->coulombtype));
warning_error(wi, warn_buf);
}
}
// cosine acceleration is only supported in leap-frog
- if (ir->cos_accel != 0.0 && ir->eI != eiMD)
+ if (ir->cos_accel != 0.0 && ir->eI != IntegrationAlgorithm::MD)
{
warning_error(wi, "cos-acceleration is only supported by integrator = md");
}
str = the input string
n = the (pre-allocated) number of doubles read
r = the output array of doubles. */
-static void parse_n_real(char* str, int* n, real** r, warninp_t wi)
+static std::vector<real> parse_n_real(const std::string& str, int* n, warninp_t wi)
{
auto values = gmx::splitString(str);
*n = values.size();
- snew(*r, *n);
+ std::vector<real> r;
for (int i = 0; i < *n; i++)
{
try
{
- (*r)[i] = gmx::fromString<real>(values[i]);
+ r.emplace_back(gmx::fromString<real>(values[i]));
}
catch (gmx::GromacsException&)
{
- warning_error(wi, "Invalid value " + values[i]
- + " in string in mdp file. Expected a real number.");
+ warning_error(wi,
+ "Invalid value " + values[i]
+ + " in string in mdp file. Expected a real number.");
}
}
+ return r;
}
-static void do_fep_params(t_inputrec* ir, char fep_lambda[][STRLEN], char weights[STRLEN], warninp_t wi)
+static void do_fep_params(t_inputrec* ir, gmx::ArrayRef<std::string> fep_lambda, char weights[STRLEN], warninp_t wi)
{
- int i, j, max_n_lambda, nweights, nfep[efptNR];
- t_lambda* fep = ir->fepvals;
- t_expanded* expand = ir->expandedvals;
- real** count_fep_lambdas;
- bool bOneLambda = TRUE;
-
- snew(count_fep_lambdas, efptNR);
+ int i, j, max_n_lambda, nweights;
+ t_lambda* fep = ir->fepvals.get();
+ t_expanded* expand = ir->expandedvals.get();
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::vector<real>> count_fep_lambdas;
+ bool bOneLambda = TRUE;
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, int> nfep;
/* FEP input processing */
/* first, identify the number of lambda values for each type.
All that are nonzero must have the same number */
- for (i = 0; i < efptNR; i++)
+ for (auto i : keysOf(nfep))
{
- parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]), wi);
+ count_fep_lambdas[i] = parse_n_real(fep_lambda[static_cast<int>(i)], &(nfep[i]), wi);
}
/* now, determine the number of components. All must be either zero, or equal. */
max_n_lambda = 0;
- for (i = 0; i < efptNR; i++)
+ for (auto i : keysOf(nfep))
{
if (nfep[i] > max_n_lambda)
{
}
}
- for (i = 0; i < efptNR; i++)
+ for (auto i : keysOf(nfep))
{
if (nfep[i] == 0)
{
}
else if (nfep[i] == max_n_lambda)
{
- if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute
+ if (i != FreeEnergyPerturbationCouplingType::Temperature) /* we treat this differently -- not really a reason to compute
the derivative with respect to the temperature currently */
{
ir->fepvals->separate_dvdl[i] = TRUE;
gmx_fatal(FARGS,
"Number of lambdas (%d) for FEP type %s not equal to number of other types "
"(%d)",
- nfep[i], efpt_names[i], max_n_lambda);
+ nfep[i],
+ enumValueToString(i),
+ max_n_lambda);
}
}
/* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
- ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
+ ir->fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Temperature] = FALSE;
/* the number of lambdas is the number we've read in, which is either zero
or the same for all */
fep->n_lambda = max_n_lambda;
- /* allocate space for the array of lambda values */
- snew(fep->all_lambda, efptNR);
/* if init_lambda is defined, we need to set lambda */
if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
{
- ir->fepvals->separate_dvdl[efptFEP] = TRUE;
+ ir->fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
}
/* otherwise allocate the space for all of the lambdas, and transfer the data */
- for (i = 0; i < efptNR; i++)
+ for (auto i : keysOf(nfep))
{
- snew(fep->all_lambda[i], fep->n_lambda);
+ fep->all_lambda[i].resize(fep->n_lambda);
if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
are zero */
{
{
fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
}
- sfree(count_fep_lambdas[i]);
}
}
- sfree(count_fep_lambdas);
/* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
internal bookkeeping -- for now, init_lambda */
- if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
+ if ((nfep[FreeEnergyPerturbationCouplingType::Fep] == 0) && (fep->init_lambda >= 0))
{
for (i = 0; i < fep->n_lambda; i++)
{
- fep->all_lambda[efptFEP][i] = fep->init_lambda;
+ fep->all_lambda[FreeEnergyPerturbationCouplingType::Fep][i] = fep->init_lambda;
}
}
}
else
{
- for (i = 0; i < efptNR; i++)
+ for (auto i : keysOf(nfep))
{
- if ((nfep[i] != 0) && (i != efptFEP))
+ if ((nfep[i] != 0) && (i != FreeEnergyPerturbationCouplingType::Fep))
{
bOneLambda = FALSE;
}
specified (i.e. nfep[i] == 0). This means if fep is not defined,
they are all zero. */
- for (i = 0; i < efptNR; i++)
+ for (auto i : keysOf(nfep))
{
- if ((nfep[i] == 0) && (i != efptFEP))
+ if ((nfep[i] == 0) && (i != FreeEnergyPerturbationCouplingType::Fep))
{
for (j = 0; j < fep->n_lambda; j++)
{
- fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
+ fep->all_lambda[i][j] = fep->all_lambda[FreeEnergyPerturbationCouplingType::Fep][j];
}
}
}
/* now read in the weights */
- parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
+ expand->init_lambda_weights = parse_n_real(weights, &nweights, wi);
if (nweights == 0)
{
- snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
+ expand->init_lambda_weights.resize(fep->n_lambda); /* initialize to zero */
}
else if (nweights != fep->n_lambda)
{
- gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
- nweights, fep->n_lambda);
+ gmx_fatal(FARGS,
+ "Number of weights (%d) is not equal to number of lambda values (%d)",
+ nweights,
+ fep->n_lambda);
}
- if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
+ if ((expand->nstexpanded < 0) && (ir->efep != FreeEnergyPerturbationType::No))
{
expand->nstexpanded = fep->nstdhdl;
/* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
static void do_simtemp_params(t_inputrec* ir)
{
-
- snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
- GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
+ ir->simtempvals->temperatures.resize(ir->fepvals->n_lambda);
+ getSimTemps(ir->fepvals->n_lambda,
+ ir->simtempvals.get(),
+ ir->fepvals->all_lambda[FreeEnergyPerturbationCouplingType::Temperature]);
}
template<typename T>
auto message = gmx::formatString(
"Invalid value for mdp option %s. %s should only consist of integers separated "
"by spaces.",
- name, name);
+ name,
+ name);
warning_error(wi, message);
}
++i;
auto message = gmx::formatString(
"Invalid value for mdp option %s. %s should only consist of real numbers "
"separated by spaces.",
- name, name);
+ name,
+ name);
warning_error(wi, message);
}
++i;
}
}
-static void convertRvecs(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, rvec* outputs)
-{
- int i = 0, d = 0;
- for (const auto& input : inputs)
- {
- try
- {
- outputs[i][d] = gmx::fromString<real>(input);
- }
- catch (gmx::GromacsException&)
- {
- auto message = gmx::formatString(
- "Invalid value for mdp option %s. %s should only consist of real numbers "
- "separated by spaces.",
- name, name);
- warning_error(wi, message);
- }
- ++d;
- if (d == DIM)
- {
- d = 0;
- ++i;
- }
- }
-}
-
static void do_wall_params(t_inputrec* ir, char* wall_atomtype, char* wall_density, t_gromppopts* opts, warninp_t wi)
{
opts->wall_atomtype[0] = nullptr;
auto wallAtomTypes = gmx::splitString(wall_atomtype);
if (wallAtomTypes.size() != size_t(ir->nwall))
{
- gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %zu", ir->nwall,
+ gmx_fatal(FARGS,
+ "Expected %d elements for wall_atomtype, found %zu",
+ ir->nwall,
wallAtomTypes.size());
}
GMX_RELEASE_ASSERT(ir->nwall < 3, "Invalid number of walls");
opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
}
- if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
+ if (ir->wall_type == WallType::NineThree || ir->wall_type == WallType::TenFour)
{
auto wallDensity = gmx::splitString(wall_density);
if (wallDensity.size() != size_t(ir->nwall))
{
- gmx_fatal(FARGS, "Expected %d elements for wall-density, found %zu", ir->nwall,
+ gmx_fatal(FARGS,
+ "Expected %d elements for wall-density, found %zu",
+ ir->nwall,
wallDensity.size());
}
convertReals(wi, wallDensity, "wall-density", ir->wall_density);
{
/* read expanded ensemble parameters */
printStringNewline(inp, "expanded ensemble variables");
- expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
- expand->elamstats = get_eeenum(inp, "lmc-stats", elamstats_names, wi);
- expand->elmcmove = get_eeenum(inp, "lmc-move", elmcmove_names, wi);
- expand->elmceq = get_eeenum(inp, "lmc-weights-equil", elmceq_names, wi);
+ expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
+ expand->elamstats = getEnum<LambdaWeightCalculation>(inp, "lmc-stats", wi);
+ expand->elmcmove = getEnum<LambdaMoveCalculation>(inp, "lmc-move", wi);
+ expand->elmceq = getEnum<LambdaWeightWillReachEquilibrium>(inp, "lmc-weights-equil", wi);
expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
expand->bSymmetrizedTMatrix =
- (get_eeenum(inp, "symmetrized-transition-matrix", yesno_names, wi) != 0);
+ (getEnum<Boolean>(inp, "symmetrized-transition-matrix", wi) != Boolean::No);
expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
- expand->bWLoneovert = (get_eeenum(inp, "wl-oneovert", yesno_names, wi) != 0);
+ expand->bWLoneovert = (getEnum<Boolean>(inp, "wl-oneovert", wi) != Boolean::No);
}
/*! \brief Return whether an end state with the given coupling-lambda
double dumdub[2][6];
int i, j, m;
char warn_buf[STRLEN];
- t_lambda* fep = ir->fepvals;
- t_expanded* expand = ir->expandedvals;
+ t_lambda* fep = ir->fepvals.get();
+ t_expanded* expand = ir->expandedvals.get();
const char* no_names[] = { "no", nullptr };
setStringEntry(&inp, "define", opts->define, nullptr);
printStringNewline(&inp, "RUN CONTROL PARAMETERS");
- ir->eI = get_eeenum(&inp, "integrator", ei_names, wi);
+ ir->eI = getEnum<IntegrationAlgorithm>(&inp, "integrator", wi);
printStringNoNewline(&inp, "Start time and timestep in ps");
ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
&inp, "Part index is updated automatically on checkpointing (keeps files separate)");
ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
printStringNoNewline(&inp, "Multiple time-stepping");
- ir->useMts = (get_eeenum(&inp, "mts", yesno_names, wi) != 0);
+ ir->useMts = (getEnum<Boolean>(&inp, "mts", wi) != Boolean::No);
if (ir->useMts)
{
- opts->numMtsLevels = get_eint(&inp, "mts-levels", 2, wi);
- ir->mtsLevels.resize(2);
- gmx::MtsLevel& mtsLevel = ir->mtsLevels[1];
- opts->mtsLevel2Forces = setStringEntry(&inp, "mts-level2-forces", "longrange-nonbonded");
- mtsLevel.stepFactor = get_eint(&inp, "mts-level2-factor", 2, wi);
+ gmx::GromppMtsOpts& mtsOpts = opts->mtsOpts;
+ mtsOpts.numLevels = get_eint(&inp, "mts-levels", 2, wi);
+ mtsOpts.level2Forces = setStringEntry(&inp, "mts-level2-forces", "longrange-nonbonded");
+ mtsOpts.level2Factor = get_eint(&inp, "mts-level2-factor", 2, wi);
// We clear after reading without dynamics to not force the user to remove MTS mdp options
if (!EI_DYNAMICS(ir->eI))
{
ir->useMts = false;
- ir->mtsLevels.clear();
}
}
printStringNoNewline(&inp, "mode for center of mass motion removal");
- ir->comm_mode = get_eeenum(&inp, "comm-mode", ecm_names, wi);
+ ir->comm_mode = getEnum<ComRemovalAlgorithm>(&inp, "comm-mode", wi);
printStringNoNewline(&inp, "number of steps for center of mass motion removal");
ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
printStringNoNewline(&inp, "group(s) for center of mass motion removal");
/* Neighbor searching */
printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs)");
- ir->cutoff_scheme = get_eeenum(&inp, "cutoff-scheme", ecutscheme_names, wi);
+ ir->cutoff_scheme = getEnum<CutoffScheme>(&inp, "cutoff-scheme", wi);
printStringNoNewline(&inp, "nblist update frequency");
ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
pbcTypesNamesChar.push_back(pbcTypeName.c_str());
}
ir->pbcType = static_cast<PbcType>(get_eeenum(&inp, "pbc", pbcTypesNamesChar.data(), wi));
- ir->bPeriodicMols = get_eeenum(&inp, "periodic-molecules", yesno_names, wi) != 0;
+ ir->bPeriodicMols = getEnum<Boolean>(&inp, "periodic-molecules", wi) != Boolean::No;
printStringNoNewline(&inp,
"Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
printStringNoNewline(&inp, "a value of -1 means: use rlist");
/* Electrostatics */
printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
printStringNoNewline(&inp, "Method for doing electrostatics");
- ir->coulombtype = get_eeenum(&inp, "coulombtype", eel_names, wi);
- ir->coulomb_modifier = get_eeenum(&inp, "coulomb-modifier", eintmod_names, wi);
+ ir->coulombtype = getEnum<CoulombInteractionType>(&inp, "coulombtype", wi);
+ ir->coulomb_modifier = getEnum<InteractionModifiers>(&inp, "coulomb-modifier", wi);
printStringNoNewline(&inp, "cut-off lengths");
ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
- printStringNoNewline(&inp,
- "Relative dielectric constant for the medium and the reaction field");
+ printStringNoNewline(&inp, "Relative dielectric constant for the medium and the reaction field");
ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
printStringNoNewline(&inp, "Method for doing Van der Waals");
- ir->vdwtype = get_eeenum(&inp, "vdw-type", evdw_names, wi);
- ir->vdw_modifier = get_eeenum(&inp, "vdw-modifier", eintmod_names, wi);
+ ir->vdwtype = getEnum<VanDerWaalsType>(&inp, "vdw-type", wi);
+ ir->vdw_modifier = getEnum<InteractionModifiers>(&inp, "vdw-modifier", wi);
printStringNoNewline(&inp, "cut-off lengths");
ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
- ir->eDispCorr = get_eeenum(&inp, "DispCorr", edispc_names, wi);
+ ir->eDispCorr = getEnum<DispersionCorrectionType>(&inp, "DispCorr", wi);
printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
printStringNoNewline(&inp, "Separate tables between energy group pairs");
ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
- ir->ljpme_combination_rule = get_eeenum(&inp, "lj-pme-comb-rule", eljpme_names, wi);
- ir->ewald_geometry = get_eeenum(&inp, "ewald-geometry", eewg_names, wi);
+ ir->ljpme_combination_rule = getEnum<LongRangeVdW>(&inp, "lj-pme-comb-rule", wi);
+ ir->ewald_geometry = getEnum<EwaldGeometry>(&inp, "ewald-geometry", wi);
ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
/* Implicit solvation is no longer supported, but we need grompp
/* Coupling stuff */
printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
printStringNoNewline(&inp, "Temperature coupling");
- ir->etc = get_eeenum(&inp, "tcoupl", etcoupl_names, wi);
+ ir->etc = getEnum<TemperatureCoupling>(&inp, "tcoupl", wi);
ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
- ir->bPrintNHChains = (get_eeenum(&inp, "print-nose-hoover-chain-variables", yesno_names, wi) != 0);
+ ir->bPrintNHChains = (getEnum<Boolean>(&inp, "print-nose-hoover-chain-variables", wi) != Boolean::No);
printStringNoNewline(&inp, "Groups to couple separately");
setStringEntry(&inp, "tc-grps", inputrecStrings->tcgrps, nullptr);
printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
setStringEntry(&inp, "tau-t", inputrecStrings->tau_t, nullptr);
setStringEntry(&inp, "ref-t", inputrecStrings->ref_t, nullptr);
printStringNoNewline(&inp, "pressure coupling");
- ir->epc = get_eeenum(&inp, "pcoupl", epcoupl_names, wi);
- ir->epct = get_eeenum(&inp, "pcoupltype", epcoupltype_names, wi);
+ ir->epc = getEnum<PressureCoupling>(&inp, "pcoupl", wi);
+ ir->epct = getEnum<PressureCouplingType>(&inp, "pcoupltype", wi);
ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
- ir->refcoord_scaling = get_eeenum(&inp, "refcoord-scaling", erefscaling_names, wi);
+ ir->refcoord_scaling = getEnum<RefCoordScaling>(&inp, "refcoord-scaling", wi);
/* QMMM */
printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
- ir->bQMMM = (get_eeenum(&inp, "QMMM", yesno_names, wi) != 0);
+ ir->bQMMM = (getEnum<Boolean>(&inp, "QMMM", wi) != Boolean::No);
printStringNoNewline(&inp, "Groups treated with MiMiC");
setStringEntry(&inp, "QMMM-grps", inputrecStrings->QMMM, nullptr);
/* Startup run */
printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
- opts->bGenVel = (get_eeenum(&inp, "gen-vel", yesno_names, wi) != 0);
+ opts->bGenVel = (getEnum<Boolean>(&inp, "gen-vel", wi) != Boolean::No);
opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
opts->seed = get_eint(&inp, "gen-seed", -1, wi);
printStringNewline(&inp, "OPTIONS FOR BONDS");
opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
printStringNoNewline(&inp, "Type of constraint algorithm");
- ir->eConstrAlg = get_eeenum(&inp, "constraint-algorithm", econstr_names, wi);
+ ir->eConstrAlg = getEnum<ConstraintAlgorithm>(&inp, "constraint-algorithm", wi);
printStringNoNewline(&inp, "Do not constrain the start configuration");
- ir->bContinuation = (get_eeenum(&inp, "continuation", yesno_names, wi) != 0);
+ ir->bContinuation = (getEnum<Boolean>(&inp, "continuation", wi) != Boolean::No);
printStringNoNewline(&inp,
"Use successive overrelaxation to reduce the number of shake iterations");
- ir->bShakeSOR = (get_eeenum(&inp, "Shake-SOR", yesno_names, wi) != 0);
+ ir->bShakeSOR = (getEnum<Boolean>(&inp, "Shake-SOR", wi) != Boolean::No);
printStringNoNewline(&inp, "Relative tolerance of shake");
ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
printStringNoNewline(&inp, "rotates over more degrees than");
ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
- opts->bMorse = (get_eeenum(&inp, "morse", yesno_names, wi) != 0);
+ opts->bMorse = (getEnum<Boolean>(&inp, "morse", wi) != Boolean::No);
/* Energy group exclusions */
printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
printStringNoNewline(
&inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
ir->nwall = get_eint(&inp, "nwall", 0, wi);
- ir->wall_type = get_eeenum(&inp, "wall-type", ewt_names, wi);
+ ir->wall_type = getEnum<WallType>(&inp, "wall-type", wi);
ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
setStringEntry(&inp, "wall-atomtype", inputrecStrings->wall_atomtype, nullptr);
setStringEntry(&inp, "wall-density", inputrecStrings->wall_density, nullptr);
/* COM pulling */
printStringNewline(&inp, "COM PULLING");
- ir->bPull = (get_eeenum(&inp, "pull", yesno_names, wi) != 0);
+ ir->bPull = (getEnum<Boolean>(&inp, "pull", wi) != Boolean::No);
if (ir->bPull)
{
ir->pull = std::make_unique<pull_params_t>();
{
for (int c = 0; c < ir->pull->ncoord; c++)
{
- if (ir->pull->coord[c].eType == epullCONSTRAINT)
+ if (ir->pull->coord[c].eType == PullingAlgorithm::Constraint)
{
warning_error(wi,
"Constraint COM pulling is not supported in combination with "
/* AWH biasing
NOTE: needs COM pulling or free energy input */
printStringNewline(&inp, "AWH biasing");
- ir->bDoAwh = (get_eeenum(&inp, "awh", yesno_names, wi) != 0);
+ ir->bDoAwh = (getEnum<Boolean>(&inp, "awh", wi) != Boolean::No);
if (ir->bDoAwh)
{
- ir->awhParams = gmx::readAwhParams(&inp, wi);
+ ir->awhParams = std::make_unique<gmx::AwhParams>(&inp, wi);
}
/* Enforced rotation */
printStringNewline(&inp, "ENFORCED ROTATION");
printStringNoNewline(&inp, "Enforced rotation: No or Yes");
- ir->bRot = (get_eeenum(&inp, "rotation", yesno_names, wi) != 0);
+ ir->bRot = (getEnum<Boolean>(&inp, "rotation", wi) != Boolean::No);
if (ir->bRot)
{
snew(ir->rot, 1);
/* Refinement */
printStringNewline(&inp, "NMR refinement stuff");
printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
- ir->eDisre = get_eeenum(&inp, "disre", edisre_names, wi);
+ ir->eDisre = getEnum<DistanceRestraintRefinement>(&inp, "disre", wi);
printStringNoNewline(
&inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
- ir->eDisreWeighting = get_eeenum(&inp, "disre-weighting", edisreweighting_names, wi);
+ ir->eDisreWeighting = getEnum<DistanceRestraintWeighting>(&inp, "disre-weighting", wi);
printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
- ir->bDisreMixed = (get_eeenum(&inp, "disre-mixed", yesno_names, wi) != 0);
+ ir->bDisreMixed = (getEnum<Boolean>(&inp, "disre-mixed", wi) != Boolean::No);
ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
printStringNoNewline(&inp, "Orientation restraints: No or Yes");
- opts->bOrire = (get_eeenum(&inp, "orire", yesno_names, wi) != 0);
+ opts->bOrire = (getEnum<Boolean>(&inp, "orire", wi) != Boolean::No);
printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
/* free energy variables */
printStringNewline(&inp, "Free energy variables");
- ir->efep = get_eeenum(&inp, "free-energy", efep_names, wi);
+ ir->efep = getEnum<FreeEnergyPerturbationType>(&inp, "free-energy", wi);
setStringEntry(&inp, "couple-moltype", inputrecStrings->couple_moltype, nullptr);
opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
- opts->bCoupleIntra = (get_eeenum(&inp, "couple-intramol", yesno_names, wi) != 0);
+ opts->bCoupleIntra = (getEnum<Boolean>(&inp, "couple-intramol", wi) != Boolean::No);
fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
we can recognize if
fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
- setStringEntry(&inp, "fep-lambdas", inputrecStrings->fep_lambda[efptFEP], nullptr);
- setStringEntry(&inp, "mass-lambdas", inputrecStrings->fep_lambda[efptMASS], nullptr);
- setStringEntry(&inp, "coul-lambdas", inputrecStrings->fep_lambda[efptCOUL], nullptr);
- setStringEntry(&inp, "vdw-lambdas", inputrecStrings->fep_lambda[efptVDW], nullptr);
- setStringEntry(&inp, "bonded-lambdas", inputrecStrings->fep_lambda[efptBONDED], nullptr);
- setStringEntry(&inp, "restraint-lambdas", inputrecStrings->fep_lambda[efptRESTRAINT], nullptr);
- setStringEntry(&inp, "temperature-lambdas", inputrecStrings->fep_lambda[efptTEMPERATURE], nullptr);
+ inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Fep] =
+ setStringEntry(&inp, "fep-lambdas", "");
+ inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Mass] =
+ setStringEntry(&inp, "mass-lambdas", "");
+ inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Coul] =
+ setStringEntry(&inp, "coul-lambdas", "");
+ inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Vdw] =
+ setStringEntry(&inp, "vdw-lambdas", "");
+ inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Bonded] =
+ setStringEntry(&inp, "bonded-lambdas", "");
+ inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Restraint] =
+ setStringEntry(&inp, "restraint-lambdas", "");
+ inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Temperature] =
+ setStringEntry(&inp, "temperature-lambdas", "");
fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
setStringEntry(&inp, "init-lambda-weights", inputrecStrings->lambda_weights, nullptr);
- fep->edHdLPrintEnergy = get_eeenum(&inp, "dhdl-print-energy", edHdLPrintEnergy_names, wi);
+ fep->edHdLPrintEnergy = getEnum<FreeEnergyPrintEnergy>(&inp, "dhdl-print-energy", wi);
fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
- fep->bScCoul = (get_eeenum(&inp, "sc-coul", yesno_names, wi) != 0);
+ fep->bScCoul = (getEnum<Boolean>(&inp, "sc-coul", wi) != Boolean::No);
fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
- fep->separate_dhdl_file = get_eeenum(&inp, "separate-dhdl-file", separate_dhdl_file_names, wi);
- fep->dhdl_derivatives = get_eeenum(&inp, "dhdl-derivatives", dhdl_derivatives_names, wi);
+ fep->separate_dhdl_file = getEnum<SeparateDhdlFile>(&inp, "separate-dhdl-file", wi);
+ fep->dhdl_derivatives = getEnum<DhDlDerivativeCalculation>(&inp, "dhdl-derivatives", wi);
fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
/* Non-equilibrium MD stuff */
printStringNewline(&inp, "Non-equilibrium MD stuff");
- setStringEntry(&inp, "acc-grps", inputrecStrings->accgrps, nullptr);
- setStringEntry(&inp, "accelerate", inputrecStrings->acc, nullptr);
setStringEntry(&inp, "freezegrps", inputrecStrings->freeze, nullptr);
setStringEntry(&inp, "freezedim", inputrecStrings->frdim, nullptr);
ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
/* simulated tempering variables */
printStringNewline(&inp, "simulated tempering variables");
- ir->bSimTemp = (get_eeenum(&inp, "simulated-tempering", yesno_names, wi) != 0);
- ir->simtempvals->eSimTempScale = get_eeenum(&inp, "simulated-tempering-scaling", esimtemp_names, wi);
+ ir->bSimTemp = (getEnum<Boolean>(&inp, "simulated-tempering", wi) != Boolean::No);
+ ir->simtempvals->eSimTempScale = getEnum<SimulatedTempering>(&inp, "simulated-tempering-scaling", wi);
ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
/* expanded ensemble variables */
- if (ir->efep == efepEXPANDED || ir->bSimTemp)
+ if (ir->efep == FreeEnergyPerturbationType::Expanded || ir->bSimTemp)
{
read_expandedparams(&inp, expand, wi);
}
printStringNewline(&inp,
"Ion/water position swapping for computational electrophysiology setups");
printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
- ir->eSwapCoords = get_eeenum(&inp, "swapcoords", eSwapTypes_names, wi);
- if (ir->eSwapCoords != eswapNO)
+ ir->eSwapCoords = getEnum<SwapType>(&inp, "swapcoords", wi);
+ if (ir->eSwapCoords != SwapType::No)
{
char buf[STRLEN];
int nIonTypes;
{
warning_error(wi, "You need to provide at least one ion type for position exchanges.");
}
- ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
+ ir->swap->ngrp = nIonTypes + static_cast<int>(SwapGroupSplittingType::Count);
snew(ir->swap->grp, ir->swap->ngrp);
for (i = 0; i < ir->swap->ngrp; i++)
{
}
printStringNoNewline(&inp,
"Two index groups that contain the compartment-partitioning atoms");
- setStringEntry(&inp, "split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
- setStringEntry(&inp, "split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
+ setStringEntry(&inp,
+ "split-group0",
+ ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname,
+ nullptr);
+ setStringEntry(&inp,
+ "split-group1",
+ ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname,
+ nullptr);
printStringNoNewline(&inp,
"Use center of mass of split groups (yes/no), otherwise center of "
"geometry is used");
- ir->swap->massw_split[0] = (get_eeenum(&inp, "massw-split0", yesno_names, wi) != 0);
- ir->swap->massw_split[1] = (get_eeenum(&inp, "massw-split1", yesno_names, wi) != 0);
+ ir->swap->massw_split[0] = (getEnum<Boolean>(&inp, "massw-split0", wi) != Boolean::No);
+ ir->swap->massw_split[1] = (getEnum<Boolean>(&inp, "massw-split1", wi) != Boolean::No);
printStringNoNewline(&inp, "Name of solvent molecules");
- setStringEntry(&inp, "solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
+ setStringEntry(&inp,
+ "solvent-group",
+ ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].molname,
+ nullptr);
printStringNoNewline(&inp,
"Split cylinder: radius, upper and lower extension (nm) (this will "
printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
for (i = 0; i < nIonTypes; i++)
{
- int ig = eSwapFixedGrpNR + i;
+ int ig = static_cast<int>(SwapGroupSplittingType::Count) + i;
sprintf(buf, "iontype%d-name", i);
setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
{
dumdub[m][i] = 0.0;
}
- if (ir->epc)
+ if (ir->epc != PressureCoupling::No)
{
switch (ir->epct)
{
- case epctISOTROPIC:
+ case PressureCouplingType::Isotropic:
if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
{
warning_error(
}
dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
break;
- case epctSEMIISOTROPIC:
- case epctSURFACETENSION:
+ case PressureCouplingType::SemiIsotropic:
+ case PressureCouplingType::SurfaceTension:
if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
{
warning_error(
}
dumdub[m][YY] = dumdub[m][XX];
break;
- case epctANISOTROPIC:
- if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf", &(dumdub[m][XX]), &(dumdub[m][YY]),
- &(dumdub[m][ZZ]), &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5]))
+ case PressureCouplingType::Anisotropic:
+ if (sscanf(dumstr[m],
+ "%lf%lf%lf%lf%lf%lf",
+ &(dumdub[m][XX]),
+ &(dumdub[m][YY]),
+ &(dumdub[m][ZZ]),
+ &(dumdub[m][3]),
+ &(dumdub[m][4]),
+ &(dumdub[m][5]))
!= 6)
{
warning_error(
}
break;
default:
- gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
- epcoupltype_names[ir->epct]);
+ gmx_fatal(FARGS,
+ "Pressure coupling type %s not implemented yet",
+ enumValueToString(ir->epct));
}
}
}
ir->ref_p[i][i] = dumdub[1][i];
ir->compress[i][i] = dumdub[0][i];
}
- if (ir->epct == epctANISOTROPIC)
+ if (ir->epct == PressureCouplingType::Anisotropic)
{
ir->ref_p[XX][YY] = dumdub[1][3];
ir->ref_p[XX][ZZ] = dumdub[1][4];
}
}
- if (ir->comm_mode == ecmNO)
+ if (ir->comm_mode == ComRemovalAlgorithm::No)
{
ir->nstcomm = 0;
}
opts->couple_moltype = nullptr;
if (strlen(inputrecStrings->couple_moltype) > 0)
{
- if (ir->efep != efepNO)
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
opts->couple_moltype = gmx_strdup(inputrecStrings->couple_moltype);
if (opts->couple_lam0 == opts->couple_lam1)
{
warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
}
- if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
+ if (ir->eI == IntegrationAlgorithm::MD
+ && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
{
warning_note(
wi,
}
}
/* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
- if (ir->efep != efepNO)
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
if (fep->delta_lambda != 0)
{
- ir->efep = efepSLOWGROWTH;
+ ir->efep = FreeEnergyPerturbationType::SlowGrowth;
}
}
- if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
+ if (fep->edHdLPrintEnergy == FreeEnergyPrintEnergy::Yes)
{
- fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
+ fep->edHdLPrintEnergy = FreeEnergyPrintEnergy::Total;
warning_note(wi,
"Old option for dhdl-print-energy given: "
"changing \"yes\" to \"total\"\n");
}
- if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
+ if (ir->bSimTemp && (fep->edHdLPrintEnergy == FreeEnergyPrintEnergy::No))
{
/* always print out the energy to dhdl if we are doing
expanded ensemble, since we need the total energy for
we will allow that if the appropriate mdp setting has
been enabled. Otherwise, total it is:
*/
- fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
+ fep->edHdLPrintEnergy = FreeEnergyPrintEnergy::Total;
}
- if ((ir->efep != efepNO) || ir->bSimTemp)
+ if ((ir->efep != FreeEnergyPerturbationType::No) || ir->bSimTemp)
{
ir->bExpanded = FALSE;
- if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
+ if ((ir->efep == FreeEnergyPerturbationType::Expanded) || ir->bSimTemp)
{
ir->bExpanded = TRUE;
}
* If the (advanced) user does FEP through manual topology changes,
* this check will not be triggered.
*/
- if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 && ir->fepvals->sc_alpha != 0
+ if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->n_lambda == 0
+ && ir->fepvals->sc_alpha != 0
&& (couple_lambda_has_vdw_on(opts->couple_lam0) && couple_lambda_has_vdw_on(opts->couple_lam1)))
{
warning(wi,
}
double gmx_unused canary;
- int ndeform = sscanf(inputrecStrings->deform, "%lf %lf %lf %lf %lf %lf %lf", &(dumdub[0][0]),
- &(dumdub[0][1]), &(dumdub[0][2]), &(dumdub[0][3]), &(dumdub[0][4]),
- &(dumdub[0][5]), &canary);
+ int ndeform = sscanf(inputrecStrings->deform,
+ "%lf %lf %lf %lf %lf %lf %lf",
+ &(dumdub[0][0]),
+ &(dumdub[0][1]),
+ &(dumdub[0][2]),
+ &(dumdub[0][3]),
+ &(dumdub[0][4]),
+ &(dumdub[0][5]),
+ &canary);
if (strlen(inputrecStrings->deform) > 0 && ndeform != 6)
{
ir->deform[YY][XX] = dumdub[0][3];
ir->deform[ZZ][XX] = dumdub[0][4];
ir->deform[ZZ][YY] = dumdub[0][5];
- if (ir->epc != epcNO)
+ if (ir->epc != PressureCoupling::No)
{
for (i = 0; i < 3; i++)
{
}
/* Ion/water position swapping checks */
- if (ir->eSwapCoords != eswapNO)
+ if (ir->eSwapCoords != SwapType::No)
{
if (ir->swap->nstswap < 1)
{
/* Set up MTS levels, this needs to happen before checking AWH parameters */
if (ir->useMts)
{
- setupMtsLevels(ir->mtsLevels, *ir, *opts, wi);
+ std::vector<std::string> errorMessages;
+ ir->mtsLevels = gmx::setupMtsLevels(opts->mtsOpts, &errorMessages);
+
+ for (const auto& errorMessage : errorMessages)
+ {
+ warning_error(wi, errorMessage.c_str());
+ }
}
if (ir->bDoAwh)
{
- gmx::checkAwhParams(ir->awhParams, ir, wi);
+ gmx::checkAwhParams(*ir->awhParams, *ir, wi);
}
sfree(dumstr[0]);
const int ognr = cbuf[aj];
if (ognr != NOGID)
{
- gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title,
- ognr + 1, i + 1);
+ gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title, ognr + 1, i + 1);
}
else
{
{
if (bVerbose)
{
- fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title,
- natoms - ntot);
+ fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title, natoms - ntot);
}
/* Add group name "rest" */
grps->emplace_back(restnm);
nrdf_tc[i] = 0;
}
for (gmx::index i = 0;
- i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; i++)
+ i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
+ i++)
{
nrdf_vcm[i] = 0;
clear_ivec(dof_vcm[i]);
const t_atom& local = atomP.atom();
int i = atomP.globalAtomNumber();
nrdf2[i] = 0;
- if (local.ptype == eptAtom || local.ptype == eptNucleus)
+ if (local.ptype == ParticleType::Atom || local.ptype == ParticleType::Nucleus)
{
int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
for (int d = 0; d < DIM; d++)
*/
int ai = as + ia[i + 1];
int aj = as + ia[i + 2];
- if (((atom[ia[i + 1]].ptype == eptNucleus) || (atom[ia[i + 1]].ptype == eptAtom))
- && ((atom[ia[i + 2]].ptype == eptNucleus) || (atom[ia[i + 2]].ptype == eptAtom)))
+ if (((atom[ia[i + 1]].ptype == ParticleType::Nucleus)
+ || (atom[ia[i + 1]].ptype == ParticleType::Atom))
+ && ((atom[ia[i + 2]].ptype == ParticleType::Nucleus)
+ || (atom[ia[i + 2]].ptype == ParticleType::Atom)))
{
if (nrdf2[ai] > 0)
{
for (int i = 0; i < pull->ncoord; i++)
{
- if (pull->coord[i].eType != epullCONSTRAINT)
+ if (pull->coord[i].eType != PullingAlgorithm::Constraint)
{
continue;
}
* Note that we do not and should not include the rest group here.
*/
for (gmx::index j = 0;
- j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]); j++)
+ j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]);
+ j++)
{
switch (ir->comm_mode)
{
- case ecmLINEAR:
- case ecmLINEAR_ACCELERATION_CORRECTION:
+ case ComRemovalAlgorithm::Linear:
+ case ComRemovalAlgorithm::LinearAccelerationCorrection:
nrdf_vcm_sub[j] = 0;
for (int d = 0; d < ndim_rm_vcm; d++)
{
}
}
break;
- case ecmANGULAR: nrdf_vcm_sub[j] = 6; break;
+ case ComRemovalAlgorithm::Angular: nrdf_vcm_sub[j] = 6; break;
default: gmx_incons("Checking comm_mode");
}
}
for (gmx::index i = 0;
- i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
+ i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]);
+ i++)
{
/* Count the number of atoms of TC group i for every VCM group */
for (gmx::index j = 0;
- j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
+ j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
+ j++)
{
na_vcm[j] = 0;
}
nrdf_uc = nrdf_tc[i];
nrdf_tc[i] = 0;
for (gmx::index j = 0;
- j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
+ j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
+ j++)
{
if (nrdf_vcm[j] > nrdf_vcm_sub[j])
{
{
opts->nrdf[i] = 0;
}
- fprintf(stderr, "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
- gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]], opts->nrdf[i]);
+ fprintf(stderr,
+ "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
+ gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]],
+ opts->nrdf[i]);
}
sfree(nrdf2);
j = 0;
while ((j < nr)
&& gmx_strcasecmp(
- names[2 * i].c_str(),
- *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
+ names[2 * i].c_str(),
+ *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
{
j++;
}
k = 0;
while ((k < nr)
&& gmx_strcasecmp(
- names[2 * i + 1].c_str(),
- *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
+ names[2 * i + 1].c_str(),
+ *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
{
k++;
}
/* Just a quick check here, more thorough checks are in mdrun */
- if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
+ if (strcmp(swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname,
+ swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname)
+ == 0)
{
- gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
+ gmx_fatal(FARGS,
+ "The split groups can not both be '%s'.",
+ swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname);
}
/* Get the index atoms of the split0, split1, solvent, and swap groups */
if (swapg->nat > 0)
{
- fprintf(stderr, "%s group '%s' contains %d atoms.\n",
- ig < 3 ? eSwapFixedGrp_names[ig] : "Swap", swap->grp[ig].molname, swapg->nat);
+ fprintf(stderr,
+ "%s group '%s' contains %d atoms.\n",
+ ig < 3 ? enumValueToString(static_cast<SwapGroupSplittingType>(ig)) : "Swap",
+ swap->grp[ig].molname,
+ swapg->nat);
snew(swapg->ind, swapg->nat);
for (i = 0; i < swapg->nat; i++)
{
fprintf(stderr,
"Group '%s' with %d atoms can be activated for interactive molecular dynamics "
"(IMD).\n",
- IMDgname, IMDgroup->nat);
+ IMDgname,
+ IMDgroup->nat);
snew(IMDgroup->ind, IMDgroup->nat);
for (i = 0; i < IMDgroup->nat; i++)
{
"removal group(s), due to limitations in the code these still contribute to the "
"mass of the COM along frozen dimensions and therefore the COMM correction will be "
"too small.",
- numPartiallyFrozenVcmAtoms, DIM);
+ numPartiallyFrozenVcmAtoms,
+ DIM);
warning(wi, warningText.c_str());
}
if (numNonVcmAtoms > 0)
}
}
-void do_index(const char* mdparin,
- const char* ndx,
- gmx_mtop_t* mtop,
- bool bVerbose,
- const gmx::MdModulesNotifier& notifier,
- t_inputrec* ir,
- warninp_t wi)
+void do_index(const char* mdparin,
+ const char* ndx,
+ gmx_mtop_t* mtop,
+ bool bVerbose,
+ const gmx::MDModulesNotifiers& mdModulesNotifiers,
+ t_inputrec* ir,
+ warninp_t wi)
{
t_blocka* defaultIndexGroups;
int natoms;
snew(defaultIndexGroups, 1);
snew(defaultIndexGroups->index, 1);
snew(gnames, 1);
- atoms_all = gmx_mtop_global_atoms(mtop);
+ atoms_all = gmx_mtop_global_atoms(*mtop);
analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
done_atom(&atoms_all);
}
gmx_fatal(FARGS,
"Invalid T coupling input: %zu groups, %zu ref-t values and "
"%zu tau-t values",
- temperatureCouplingGroupNames.size(), temperatureCouplingReferenceValues.size(),
+ temperatureCouplingGroupNames.size(),
+ temperatureCouplingReferenceValues.size(),
temperatureCouplingTauValues.size());
}
const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
- do_numbering(natoms, groups, temperatureCouplingGroupNames, defaultIndexGroups, gnames,
- SimulationAtomGroupType::TemperatureCoupling, restnm,
- useReferenceTemperature ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
+ do_numbering(natoms,
+ groups,
+ temperatureCouplingGroupNames,
+ defaultIndexGroups,
+ gnames,
+ SimulationAtomGroupType::TemperatureCoupling,
+ restnm,
+ useReferenceTemperature ? egrptpALL : egrptpALL_GENREST,
+ bVerbose,
+ wi);
nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
ir->opts.ngtc = nr;
snew(ir->opts.nrdf, nr);
snew(ir->opts.tau_t, nr);
snew(ir->opts.ref_t, nr);
- if (ir->eI == eiBD && ir->bd_fric == 0)
+ if (ir->eI == IntegrationAlgorithm::BD && ir->bd_fric == 0)
{
fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
}
convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
for (i = 0; (i < nr); i++)
{
- if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
+ if ((ir->eI == IntegrationAlgorithm::BD) && ir->opts.tau_t[i] <= 0)
{
- sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
+ sprintf(warn_buf,
+ "With integrator %s tau-t should be larger than 0",
+ enumValueToString(ir->eI));
warning_error(wi, warn_buf);
}
- if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
+ if (ir->etc != TemperatureCoupling::VRescale && ir->opts.tau_t[i] == 0)
{
warning_note(
wi,
tau_min = std::min(tau_min, ir->opts.tau_t[i]);
}
}
- if (ir->etc != etcNO && ir->nsttcouple == -1)
+ if (ir->etc != TemperatureCoupling::No && ir->nsttcouple == -1)
{
ir->nsttcouple = ir_optimal_nsttcouple(ir);
}
if (EI_VV(ir->eI))
{
- if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
+ if ((ir->etc == TemperatureCoupling::NoseHoover) && (ir->epc == PressureCoupling::Berendsen))
{
gmx_fatal(FARGS,
"Cannot do Nose-Hoover temperature with Berendsen pressure control with "
"md-vv; use either vrescale temperature with berendsen pressure or "
"Nose-Hoover temperature with MTTK pressure");
}
- if (ir->epc == epcMTTK)
+ if (ir->epc == PressureCoupling::Mttk)
{
- if (ir->etc != etcNOSEHOOVER)
+ if (ir->etc != TemperatureCoupling::NoseHoover)
{
gmx_fatal(FARGS,
"Cannot do MTTK pressure coupling without Nose-Hoover temperature "
sprintf(warn_buf,
"For proper integration of the %s thermostat, tau-t (%g) should be at "
"least %d times larger than nsttcouple*dt (%g)",
- ETCOUPLTYPE(ir->etc), tau_min, nstcmin, ir->nsttcouple * ir->delta_t);
+ enumValueToString(ir->etc),
+ tau_min,
+ nstcmin,
+ ir->nsttcouple * ir->delta_t);
warning(wi, warn_buf);
}
}
}
if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
{
- gmx_fatal(FARGS, "Wrong number of annealing values: %zu (for %d groups)\n",
- simulatedAnnealingGroupNames.size(), nr);
+ gmx_fatal(FARGS,
+ "Wrong number of annealing values: %zu (for %d groups)\n",
+ simulatedAnnealingGroupNames.size(),
+ nr);
}
else
{
snew(ir->opts.anneal_temp, nr);
for (i = 0; i < nr; i++)
{
- ir->opts.annealing[i] = eannNO;
+ ir->opts.annealing[i] = SimulatedAnnealing::No;
ir->opts.anneal_npoints[i] = 0;
ir->opts.anneal_time[i] = nullptr;
ir->opts.anneal_temp[i] = nullptr;
{
if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
{
- ir->opts.annealing[i] = eannNO;
+ ir->opts.annealing[i] = SimulatedAnnealing::No;
}
else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
{
- ir->opts.annealing[i] = eannSINGLE;
+ ir->opts.annealing[i] = SimulatedAnnealing::Single;
bAnneal = TRUE;
}
else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
{
- ir->opts.annealing[i] = eannPERIODIC;
+ ir->opts.annealing[i] = SimulatedAnnealing::Periodic;
bAnneal = TRUE;
}
}
auto simulatedAnnealingPoints = gmx::splitString(inputrecStrings->anneal_npoints);
if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
{
- gmx_fatal(FARGS, "Found %zu annealing-npoints values for %zu groups\n",
- simulatedAnnealingPoints.size(), simulatedAnnealingGroupNames.size());
+ gmx_fatal(FARGS,
+ "Found %zu annealing-npoints values for %zu groups\n",
+ simulatedAnnealingPoints.size(),
+ simulatedAnnealingGroupNames.size());
}
convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
size_t numSimulatedAnnealingFields = 0;
if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
{
- gmx_fatal(FARGS, "Found %zu annealing-time values, wanted %zu\n",
- simulatedAnnealingTimes.size(), numSimulatedAnnealingFields);
+ gmx_fatal(FARGS,
+ "Found %zu annealing-time values, wanted %zu\n",
+ simulatedAnnealingTimes.size(),
+ numSimulatedAnnealingFields);
}
auto simulatedAnnealingTemperatures = gmx::splitString(inputrecStrings->anneal_temp);
if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
{
- gmx_fatal(FARGS, "Found %zu annealing-temp values, wanted %zu\n",
- simulatedAnnealingTemperatures.size(), numSimulatedAnnealingFields);
+ gmx_fatal(FARGS,
+ "Found %zu annealing-temp values, wanted %zu\n",
+ simulatedAnnealingTemperatures.size(),
+ numSimulatedAnnealingFields);
}
std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
- convertReals(wi, simulatedAnnealingTimes, "anneal-time",
- allSimulatedAnnealingTimes.data());
- convertReals(wi, simulatedAnnealingTemperatures, "anneal-temp",
+ convertReals(wi, simulatedAnnealingTimes, "anneal-time", allSimulatedAnnealingTimes.data());
+ convertReals(wi,
+ simulatedAnnealingTemperatures,
+ "anneal-temp",
allSimulatedAnnealingTemperatures.data());
for (i = 0, k = 0; i < nr; i++)
{
gmx_fatal(FARGS,
"Annealing timepoints out of order: t=%f comes after "
"t=%f\n",
- ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j - 1]);
+ ir->opts.anneal_time[i][j],
+ ir->opts.anneal_time[i][j - 1]);
}
}
if (ir->opts.anneal_temp[i][j] < 0)
{
- gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n",
+ gmx_fatal(FARGS,
+ "Found negative temperature in annealing: %f\n",
ir->opts.anneal_temp[i][j]);
}
k++;
/* Print out some summary information, to make sure we got it right */
for (i = 0; i < nr; i++)
{
- if (ir->opts.annealing[i] != eannNO)
+ if (ir->opts.annealing[i] != SimulatedAnnealing::No)
{
j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
- fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
- *(groups->groupNames[j]), eann_names[ir->opts.annealing[i]],
+ fprintf(stderr,
+ "Simulated annealing for group %s: %s, %d timepoints\n",
+ *(groups->groupNames[j]),
+ enumValueToString(ir->opts.annealing[i]),
ir->opts.anneal_npoints[i]);
fprintf(stderr, "Time (ps) Temperature (K)\n");
/* All terms except the last one */
for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
{
- fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
+ fprintf(stderr,
+ "%9.1f %5.1f\n",
+ ir->opts.anneal_time[i][j],
ir->opts.anneal_temp[i][j]);
}
/* Finally the last one */
j = ir->opts.anneal_npoints[i] - 1;
- if (ir->opts.annealing[i] == eannSINGLE)
+ if (ir->opts.annealing[i] == SimulatedAnnealing::Single)
{
- fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j],
+ fprintf(stderr,
+ "%9.1f- %5.1f\n",
+ ir->opts.anneal_time[i][j],
ir->opts.anneal_temp[i][j]);
}
else
{
- fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
+ fprintf(stderr,
+ "%9.1f %5.1f\n",
+ ir->opts.anneal_time[i][j],
ir->opts.anneal_temp[i][j]);
if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
{
{
for (int i = 1; i < ir->pull->ngroup; i++)
{
- const int gid = search_string(inputrecStrings->pullGroupNames[i].c_str(),
- defaultIndexGroups->nr, gnames);
+ const int gid = search_string(
+ inputrecStrings->pullGroupNames[i].c_str(), defaultIndexGroups->nr, gnames);
GMX_ASSERT(defaultIndexGroups, "Must have initialized default index groups");
atomGroupRangeValidation(natoms, gid, *defaultIndexGroups);
}
make_rotation_groups(ir->rot, inputrecStrings->rotateGroupNames, defaultIndexGroups, gnames);
}
- if (ir->eSwapCoords != eswapNO)
+ if (ir->eSwapCoords != SwapType::No)
{
make_swap_groups(ir->swap, defaultIndexGroups, gnames);
}
gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
*defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
- notifier.preProcessingNotifications_.notify(defaultIndexGroupsAndNames);
-
- auto accelerations = gmx::splitString(inputrecStrings->acc);
- auto accelerationGroupNames = gmx::splitString(inputrecStrings->accgrps);
- if (accelerationGroupNames.size() * DIM != accelerations.size())
- {
- gmx_fatal(FARGS, "Invalid Acceleration input: %zu groups and %zu acc. values",
- accelerationGroupNames.size(), accelerations.size());
- }
- do_numbering(natoms, groups, accelerationGroupNames, defaultIndexGroups, gnames,
- SimulationAtomGroupType::Acceleration, restnm, egrptpALL_GENREST, bVerbose, wi);
- nr = groups->groups[SimulationAtomGroupType::Acceleration].size();
- snew(ir->opts.acc, nr);
- ir->opts.ngacc = nr;
-
- convertRvecs(wi, accelerations, "anneal-time", ir->opts.acc);
+ mdModulesNotifiers.preProcessingNotifier_.notify(defaultIndexGroupsAndNames);
auto freezeDims = gmx::splitString(inputrecStrings->frdim);
auto freezeGroupNames = gmx::splitString(inputrecStrings->freeze);
if (freezeDims.size() != DIM * freezeGroupNames.size())
{
- gmx_fatal(FARGS, "Invalid Freezing input: %zu groups and %zu freeze values",
- freezeGroupNames.size(), freezeDims.size());
- }
- do_numbering(natoms, groups, freezeGroupNames, defaultIndexGroups, gnames,
- SimulationAtomGroupType::Freeze, restnm, egrptpALL_GENREST, bVerbose, wi);
+ gmx_fatal(FARGS,
+ "Invalid Freezing input: %zu groups and %zu freeze values",
+ freezeGroupNames.size(),
+ freezeDims.size());
+ }
+ do_numbering(natoms,
+ groups,
+ freezeGroupNames,
+ defaultIndexGroups,
+ gnames,
+ SimulationAtomGroupType::Freeze,
+ restnm,
+ egrptpALL_GENREST,
+ bVerbose,
+ wi);
nr = groups->groups[SimulationAtomGroupType::Freeze].size();
ir->opts.ngfrz = nr;
snew(ir->opts.nFreeze, nr);
}
auto energyGroupNames = gmx::splitString(inputrecStrings->energy);
- do_numbering(natoms, groups, energyGroupNames, defaultIndexGroups, gnames,
- SimulationAtomGroupType::EnergyOutput, restnm, egrptpALL_GENREST, bVerbose, wi);
+ do_numbering(natoms,
+ groups,
+ energyGroupNames,
+ defaultIndexGroups,
+ gnames,
+ SimulationAtomGroupType::EnergyOutput,
+ restnm,
+ egrptpALL_GENREST,
+ bVerbose,
+ wi);
add_wall_energrps(groups, ir->nwall, symtab);
ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
auto vcmGroupNames = gmx::splitString(inputrecStrings->vcm);
- do_numbering(natoms, groups, vcmGroupNames, defaultIndexGroups, gnames,
- SimulationAtomGroupType::MassCenterVelocityRemoval, restnm,
- vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
-
- if (ir->comm_mode != ecmNO)
+ do_numbering(natoms,
+ groups,
+ vcmGroupNames,
+ defaultIndexGroups,
+ gnames,
+ SimulationAtomGroupType::MassCenterVelocityRemoval,
+ restnm,
+ vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART,
+ bVerbose,
+ wi);
+
+ if (ir->comm_mode != ComRemovalAlgorithm::No)
{
checkAndUpdateVcmFreezeGroupConsistency(groups, natoms, ir->opts, wi);
}
calc_nrdf(mtop, ir, gnames);
auto user1GroupNames = gmx::splitString(inputrecStrings->user1);
- do_numbering(natoms, groups, user1GroupNames, defaultIndexGroups, gnames,
- SimulationAtomGroupType::User1, restnm, egrptpALL_GENREST, bVerbose, wi);
+ do_numbering(natoms,
+ groups,
+ user1GroupNames,
+ defaultIndexGroups,
+ gnames,
+ SimulationAtomGroupType::User1,
+ restnm,
+ egrptpALL_GENREST,
+ bVerbose,
+ wi);
auto user2GroupNames = gmx::splitString(inputrecStrings->user2);
- do_numbering(natoms, groups, user2GroupNames, defaultIndexGroups, gnames,
- SimulationAtomGroupType::User2, restnm, egrptpALL_GENREST, bVerbose, wi);
+ do_numbering(natoms,
+ groups,
+ user2GroupNames,
+ defaultIndexGroups,
+ gnames,
+ SimulationAtomGroupType::User2,
+ restnm,
+ egrptpALL_GENREST,
+ bVerbose,
+ wi);
auto compressedXGroupNames = gmx::splitString(inputrecStrings->x_compressed_groups);
- do_numbering(natoms, groups, compressedXGroupNames, defaultIndexGroups, gnames,
- SimulationAtomGroupType::CompressedPositionOutput, restnm, egrptpONE, bVerbose, wi);
+ do_numbering(natoms,
+ groups,
+ compressedXGroupNames,
+ defaultIndexGroups,
+ gnames,
+ SimulationAtomGroupType::CompressedPositionOutput,
+ restnm,
+ egrptpONE,
+ bVerbose,
+ wi);
auto orirefFitGroupNames = gmx::splitString(inputrecStrings->orirefitgrp);
- do_numbering(natoms, groups, orirefFitGroupNames, defaultIndexGroups, gnames,
- SimulationAtomGroupType::OrientationRestraintsFit, restnm, egrptpALL_GENREST,
- bVerbose, wi);
+ do_numbering(natoms,
+ groups,
+ orirefFitGroupNames,
+ defaultIndexGroups,
+ gnames,
+ SimulationAtomGroupType::OrientationRestraintsFit,
+ restnm,
+ egrptpALL_GENREST,
+ bVerbose,
+ wi);
/* MiMiC QMMM input processing */
auto qmGroupNames = gmx::splitString(inputrecStrings->QMMM);
gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
}
/* group rest, if any, is always MM! */
- do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
- SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
+ do_numbering(natoms,
+ groups,
+ qmGroupNames,
+ defaultIndexGroups,
+ gnames,
+ SimulationAtomGroupType::QuantumMechanics,
+ restnm,
+ egrptpALL_GENREST,
+ bVerbose,
+ wi);
ir->opts.ngQM = qmGroupNames.size();
/* end of MiMiC QMMM input */
snew(ir->opts.egp_flags, nr * nr);
bExcl = do_egp_flag(ir, groups, "energygrp-excl", inputrecStrings->egpexcl, EGP_EXCL);
- if (bExcl && ir->cutoff_scheme == ecutsVERLET)
+ if (bExcl && ir->cutoff_scheme == CutoffScheme::Verlet)
{
warning_error(wi, "Energy group exclusions are currently not supported");
}
}
bTable = do_egp_flag(ir, groups, "energygrp-table", inputrecStrings->egptable, EGP_TABLE);
- if (bTable && !(ir->vdwtype == evdwUSER) && !(ir->coulombtype == eelUSER)
- && !(ir->coulombtype == eelPMEUSER) && !(ir->coulombtype == eelPMEUSERSWITCH))
+ if (bTable && !(ir->vdwtype == VanDerWaalsType::User)
+ && !(ir->coulombtype == CoulombInteractionType::User)
+ && !(ir->coulombtype == CoulombInteractionType::PmeUser)
+ && !(ir->coulombtype == CoulombInteractionType::PmeUserSwitch))
{
gmx_fatal(FARGS,
"Can only have energy group pair tables in combination with user tables for VdW "
if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
{
ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
- warning(wi, gmx::formatString(
- "the value for nstexpanded was not specified for "
- " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
- "by default, but it is recommended to set it to an explicit value!",
- ir->expandedvals->nstexpanded));
+ warning(wi,
+ gmx::formatString(
+ "the value for nstexpanded was not specified for "
+ " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
+ "by default, but it is recommended to set it to an explicit value!",
+ ir->expandedvals->nstexpanded));
}
for (i = 0; (i < defaultIndexGroups->nr); i++)
{
}
-static void check_disre(const gmx_mtop_t* mtop)
+static void check_disre(const gmx_mtop_t& mtop)
{
if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
{
- const gmx_ffparams_t& ffparams = mtop->ffparams;
+ const gmx_ffparams_t& ffparams = mtop.ffparams;
int ndouble = 0;
int old_label = -1;
for (int i = 0; i < ffparams.numTypes(); i++)
{
BasicVector<bool> havePosres = { false, false, false };
- gmx_mtop_ilistloop_t iloop = gmx_mtop_ilistloop_init(&sys);
- int nmol;
- while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
+ for (const auto ilists : IListRange(sys))
{
- if (nmol > 0 && (!havePosres[XX] || !havePosres[YY] || !havePosres[ZZ]))
+ const auto& posResList = ilists.list()[F_POSRES];
+ const auto& fbPosResList = ilists.list()[F_FBPOSRES];
+ if (ilists.nmol() > 0 && (!havePosres[XX] || !havePosres[YY] || !havePosres[ZZ]))
{
- for (int i = 0; i < (*ilist)[F_POSRES].size(); i += 2)
+ for (int i = 0; i < posResList.size(); i += 2)
{
- const t_iparams& pr = sys.ffparams.iparams[(*ilist)[F_POSRES].iatoms[i]];
+ const t_iparams& pr = sys.ffparams.iparams[posResList.iatoms[i]];
for (int d = 0; d < DIM; d++)
{
if (pr.posres.fcA[d] != 0)
}
}
}
- for (int i = 0; i < (*ilist)[F_FBPOSRES].size(); i += 2)
+ for (int i = 0; i < fbPosResList.size(); i += 2)
{
/* Check for flat-bottom posres */
- const t_iparams& pr = sys.ffparams.iparams[(*ilist)[F_FBPOSRES].iatoms[i]];
+ const t_iparams& pr = sys.ffparams.iparams[fbPosResList.iatoms[i]];
if (pr.fbposres.k != 0)
{
switch (pr.fbposres.geom)
gmx_fatal(FARGS,
"Invalid geometry for flat-bottom position restraint.\n"
"Expected nr between 1 and %d. Found %d\n",
- efbposresNR - 1, pr.fbposres.geom);
+ efbposresNR - 1,
+ pr.fbposres.geom);
}
}
}
return havePosres;
}
-static void check_combination_rule_differences(const gmx_mtop_t* mtop,
+static void check_combination_rule_differences(const gmx_mtop_t& mtop,
int state,
bool* bC6ParametersWorkWithGeometricRules,
bool* bC6ParametersWorkWithLBRules,
ptr = getenv("GMX_LJCOMB_TOL");
if (ptr != nullptr)
{
- double dbl;
+ double dbl;
double gmx_unused canary;
if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
{
- gmx_fatal(FARGS,
- "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
+ gmx_fatal(
+ FARGS, "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
}
tol = dbl;
}
*bC6ParametersWorkWithLBRules = TRUE;
*bC6ParametersWorkWithGeometricRules = TRUE;
bCanDoLBRules = TRUE;
- ntypes = mtop->ffparams.atnr;
+ ntypes = mtop.ffparams.atnr;
snew(typecount, ntypes);
gmx_mtop_count_atomtypes(mtop, state, typecount);
*bLBRulesPossible = TRUE;
for (tpi = 0; tpi < ntypes; ++tpi)
{
- c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
- c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
+ c6i = mtop.ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
+ c12i = mtop.ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
for (tpj = tpi; tpj < ntypes; ++tpj)
{
- c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
- c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
- c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
+ c6j = mtop.ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
+ c12j = mtop.ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
+ c6 = mtop.ffparams.iparams[ntypes * tpi + tpj].lj.c6;
c6_geometric = std::sqrt(c6i * c6j);
if (!gmx_numzero(c6_geometric))
{
sfree(typecount);
}
-static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t* mtop, warninp_t wi)
+static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t& mtop, warninp_t wi)
{
bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
- check_combination_rule_differences(mtop, 0, &bC6ParametersWorkWithGeometricRules,
- &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
- if (ir->ljpme_combination_rule == eljpmeLB)
+ check_combination_rule_differences(
+ mtop, 0, &bC6ParametersWorkWithGeometricRules, &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
+ if (ir->ljpme_combination_rule == LongRangeVdW::LB)
{
if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
{
{
if (!bC6ParametersWorkWithGeometricRules)
{
- if (ir->eDispCorr != edispcNO)
+ if (ir->eDispCorr != DispersionCorrectionType::No)
{
warning_note(wi,
"You are using geometric combination rules in "
void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
{
// Not meeting MTS requirements should have resulted in a fatal error, so we can assert here
- gmx::assertMtsRequirements(*ir);
+ GMX_ASSERT(gmx::checkMtsRequirements(*ir).empty(), "All MTS requirements should be met here");
char err_buf[STRLEN];
int i, m, c, nmol;
- bool bCharge, bAcc;
- real * mgrp, mt;
- rvec acc;
+ bool bCharge;
gmx_mtop_atomloop_block_t aloopb;
char warn_buf[STRLEN];
"macro-molecule, the artifacts are usually negligible.");
}
- if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 && ir->nstlist > 1
- && ((EI_MD(ir->eI) || EI_SD(ir->eI)) && (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
+ if (ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0 && ir->nstlist > 1
+ && ((EI_MD(ir->eI) || EI_SD(ir->eI))
+ && (ir->etc == TemperatureCoupling::VRescale || ir->etc == TemperatureCoupling::Berendsen)))
{
/* Check if a too small Verlet buffer might potentially
* cause more drift than the thermostat can couple off.
* of errors. The factor 0.5 is because energy distributes
* equally over Ekin and Epot.
*/
- max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * BOLTZ * T);
+ max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * gmx::c_boltz * T);
if (max_T_error > T_error_warn)
{
sprintf(warn_buf,
"of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
"To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
"%.0e or decrease tau_t.",
- ir->verletbuf_tol, T, tau, 100 * max_T_error, 100 * T_error_suggest,
+ ir->verletbuf_tol,
+ T,
+ tau,
+ 100 * max_T_error,
+ 100 * T_error_suggest,
ir->verletbuf_tol * T_error_suggest / max_T_error);
warning(wi, warn_buf);
}
sprintf(err_buf,
"all tau_t must be positive using Andersen temperature control, "
"tau_t[%d]=%10.6f",
- i, ir->opts.tau_t[i]);
+ i,
+ ir->opts.tau_t[i]);
CHECK(ir->opts.tau_t[i] < 0);
}
- if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
+ if (ir->etc == TemperatureCoupling::AndersenMassive && ir->comm_mode != ComRemovalAlgorithm::No)
{
for (i = 0; i < ir->opts.ngtc; i++)
{
"multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
"randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
"randomization",
- i, etcoupl_names[ir->etc], ir->nstcomm, ir->opts.tau_t[i], nsteps);
+ i,
+ enumValueToString(ir->etc),
+ ir->nstcomm,
+ ir->opts.tau_t[i],
+ nsteps);
CHECK(nsteps % ir->nstcomm != 0);
}
}
}
- if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD && ir->comm_mode == ecmNO
+ if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != IntegrationAlgorithm::BD
+ && ir->comm_mode == ComRemovalAlgorithm::No
&& !(allTrue(haveAbsoluteReference(*ir)) || allTrue(havePositionRestraints(*sys)) || ir->nsteps <= 10)
&& !ETC_ANDERSEN(ir->etc))
{
"rounding errors can lead to build up of kinetic energy of the center of mass");
}
- if (ir->epc == epcPARRINELLORAHMAN && ir->etc == etcNOSEHOOVER)
+ if (ir->epc == PressureCoupling::ParrinelloRahman && ir->etc == TemperatureCoupling::NoseHoover)
{
real tau_t_max = 0;
for (int g = 0; g < ir->opts.ngtc; g++)
std::string message = gmx::formatString(
"With %s T-coupling and %s p-coupling, "
"%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
- etcoupl_names[ir->etc], epcoupl_names[ir->epc], "tau-p", ir->tau_p, "tau-t",
+ enumValueToString(ir->etc),
+ enumValueToString(ir->epc),
+ "tau-p",
+ ir->tau_p,
+ "tau-t",
tau_t_max);
warning(wi, message.c_str());
}
}
/* Check for pressure coupling with absolute position restraints */
- if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
+ if (ir->epc != PressureCoupling::No && ir->refcoord_scaling == RefCoordScaling::No)
{
const BasicVector<bool> havePosres = havePositionRestraints(*sys);
{
}
bCharge = FALSE;
- aloopb = gmx_mtop_atomloop_block_init(sys);
+ aloopb = gmx_mtop_atomloop_block_init(*sys);
const t_atom* atom;
while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
{
"You are using full electrostatics treatment %s for a system without charges.\n"
"This costs a lot of performance for just processing zeros, consider using %s "
"instead.\n",
- EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
+ enumValueToString(ir->coulombtype),
+ enumValueToString(CoulombInteractionType::Cut));
warning(wi, err_buf);
}
}
else
{
- if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
+ if (ir->coulombtype == CoulombInteractionType::Cut && ir->rcoulomb > 0)
{
sprintf(err_buf,
"You are using a plain Coulomb cut-off, which might produce artifacts.\n"
"You might want to consider using %s electrostatics.\n",
- EELTYPE(eelPME));
+ enumValueToString(CoulombInteractionType::Pme));
warning_note(wi, err_buf);
}
}
/* Check if combination rules used in LJ-PME are the same as in the force field */
if (EVDW_PME(ir->vdwtype))
{
- check_combination_rules(ir, sys, wi);
+ check_combination_rules(ir, *sys, wi);
}
/* Generalized reaction field */
- if (ir->coulombtype == eelGRF_NOTUSED)
+ if (ir->coulombtype == CoulombInteractionType::GRFNotused)
{
warning_error(wi,
"Generalized reaction-field electrostatics is no longer supported. "
"constant by hand.");
}
- bAcc = FALSE;
- for (int i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
- {
- for (m = 0; (m < DIM); m++)
- {
- if (fabs(ir->opts.acc[i][m]) > 1e-6)
- {
- bAcc = TRUE;
- }
- }
- }
- if (bAcc)
- {
- clear_rvec(acc);
- snew(mgrp, sys->groups.groups[SimulationAtomGroupType::Acceleration].size());
- for (const AtomProxy atomP : AtomRange(*sys))
- {
- const t_atom& local = atomP.atom();
- int i = atomP.globalAtomNumber();
- mgrp[getGroupType(sys->groups, SimulationAtomGroupType::Acceleration, i)] += local.m;
- }
- mt = 0.0;
- for (i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
- {
- for (m = 0; (m < DIM); m++)
- {
- acc[m] += ir->opts.acc[i][m] * mgrp[i];
- }
- mt += mgrp[i];
- }
- for (m = 0; (m < DIM); m++)
- {
- if (fabs(acc[m]) > 1e-6)
- {
- const char* dim[DIM] = { "X", "Y", "Z" };
- fprintf(stderr, "Net Acceleration in %s direction, will %s be corrected\n", dim[m],
- ir->nstcomm != 0 ? "" : "not");
- if (ir->nstcomm != 0 && m < ndof_com(ir))
- {
- acc[m] /= mt;
- for (i = 0;
- (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
- {
- ir->opts.acc[i][m] -= acc[m];
- }
- }
- }
- }
- sfree(mgrp);
- }
-
- if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0
+ if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->sc_alpha != 0
&& !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
{
gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
{
for (m = 0; m <= i; m++)
{
- if ((ir->epc != epcNO && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
+ if ((ir->epc != PressureCoupling::No && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
{
for (c = 0; c < ir->pull->ncoord; c++)
{
- if (ir->pull->coord[c].eGeom == epullgDIRPBC && ir->pull->coord[c].vec[m] != 0)
+ if (ir->pull->coord[c].eGeom == PullGroupGeometry::DirectionPBC
+ && ir->pull->coord[c].vec[m] != 0)
{
gmx_fatal(FARGS,
"Can not have dynamic box while using pull geometry '%s' "
"(dim %c)",
- EPULLGEOM(ir->pull->coord[c].eGeom), 'x' + m);
+ enumValueToString(ir->pull->coord[c].eGeom),
+ 'x' + m);
}
}
}
}
}
- check_disre(sys);
+ check_disre(*sys);
}
void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
warning_error(wi, ptr);
}
- if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
+ if (bHasNormalConstraints && ir->eConstrAlg == ConstraintAlgorithm::Shake)
{
if (ir->shake_tol <= 0.0)
{
}
}
- if ((ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
+ if ((ir->eConstrAlg == ConstraintAlgorithm::Lincs) && bHasNormalConstraints)
{
/* If we have Lincs constraints: */
- if (ir->eI == eiMD && ir->etc == etcNO && ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
+ if (ir->eI == IntegrationAlgorithm::MD && ir->etc == TemperatureCoupling::No
+ && ir->eConstrAlg == ConstraintAlgorithm::Lincs && ir->nLincsIter == 1)
{
sprintf(warn_buf,
"For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
warning_note(wi, warn_buf);
}
- if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
+ if ((ir->eI == IntegrationAlgorithm::CG || ir->eI == IntegrationAlgorithm::LBFGS)
+ && (ir->nProjOrder < 8))
{
sprintf(warn_buf,
"For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
- ei_names[ir->eI]);
+ enumValueToString(ir->eI));
warning_note(wi, warn_buf);
}
- if (ir->epc == epcMTTK)
+ if (ir->epc == PressureCoupling::Mttk)
{
warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
}
}
- if (bHasAnyConstraints && ir->epc == epcMTTK)
+ if (bHasAnyConstraints && ir->epc == PressureCoupling::Mttk)
{
warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/readinp.h"
#include "gromacs/math/vectypes.h"
+#include "gromacs/mdtypes/multipletimestepping.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/real.h"
namespace gmx
{
class MDModules;
-struct MdModulesNotifier;
+struct MDModulesNotifiers;
} // namespace gmx
struct gmx_mtop_t;
struct t_gromppopts
{
- int warnings = 0;
- int nshake = 0;
- char* include = nullptr;
- char* define = nullptr;
- bool bGenVel = false;
- bool bGenPairs = false;
- real tempi = 0;
- int seed = 0;
- int numMtsLevels = 0;
- std::string mtsLevel2Forces;
- bool bOrire = false;
- bool bMorse = false;
- char* wall_atomtype[2] = { nullptr, nullptr };
- char* couple_moltype = nullptr;
- int couple_lam0 = 0;
- int couple_lam1 = 0;
- bool bCoupleIntra = false;
+ int warnings = 0;
+ int nshake = 0;
+ char* include = nullptr;
+ char* define = nullptr;
+ bool bGenVel = false;
+ bool bGenPairs = false;
+ real tempi = 0;
+ int seed = 0;
+ gmx::GromppMtsOpts mtsOpts;
+ bool bOrire = false;
+ bool bMorse = false;
+ char* wall_atomtype[2] = { nullptr, nullptr };
+ char* couple_moltype = nullptr;
+ int couple_lam0 = 0;
+ int couple_lam1 = 0;
+ bool bCoupleIntra = false;
};
/*! \brief Initialise object to hold strings parsed from an .mdp file */
/*! \brief Clean up object that holds strings parsed from an .mdp file */
void done_inputrec_strings();
-void check_ir(const char* mdparin,
- const gmx::MdModulesNotifier& mdModulesNotifier,
- t_inputrec* ir,
- t_gromppopts* opts,
- warninp_t wi);
+void check_ir(const char* mdparin,
+ const gmx::MDModulesNotifiers& mdModulesNotifiers,
+ t_inputrec* ir,
+ t_gromppopts* opts,
+ warninp_t wi);
/* Validate inputrec data.
* Fatal errors will be added to nerror.
*/
* function is called. Also prints the input file back to mdparout.
*/
-void do_index(const char* mdparin,
- const char* ndx,
- gmx_mtop_t* mtop,
- bool bVerbose,
- const gmx::MdModulesNotifier& notifier,
- t_inputrec* ir,
- warninp_t wi);
+void do_index(const char* mdparin,
+ const char* ndx,
+ gmx_mtop_t* mtop,
+ bool bVerbose,
+ const gmx::MDModulesNotifiers& mdModulesNotifiers,
+ t_inputrec* ir,
+ warninp_t wi);
/* Read the index file and assign grp numbers to atoms.
*/
gmx::ArrayRef<const t_pull_coord> pullCoords);
/* Process the pull coordinates after reading the pull groups */
-pull_t* set_pull_init(t_inputrec* ir, const gmx_mtop_t* mtop, rvec* x, matrix box, real lambda, warninp_t wi);
+pull_t* set_pull_init(t_inputrec* ir,
+ const gmx_mtop_t& mtop,
+ gmx::ArrayRef<const gmx::RVec> x,
+ matrix box,
+ real lambda,
+ warninp_t wi);
/* Prints the initial pull group distances in x.
* If requested, adds the current distance to the initial reference location.
* Returns the pull_t pull work struct. This should be passed to finish_pull()
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
gmx_fatal(FARGS, "All entries in pull dim are N");
}
- if ((pcrd->eGeom == epullgDIHEDRAL) && (ndim < 3))
+ if ((pcrd->eGeom == PullGroupGeometry::Dihedral) && (ndim < 3))
{
gmx_fatal(FARGS, "Pull geometry dihedral is only useful with pull-dim = Y Y Y");
}
- if ((pcrd->eGeom == epullgANGLE || pcrd->eGeom == epullgANGLEAXIS) && (ndim < 2))
+ if ((pcrd->eGeom == PullGroupGeometry::Angle || pcrd->eGeom == PullGroupGeometry::AngleAxis)
+ && (ndim < 2))
{
gmx_fatal(FARGS,
"Pull geometry %s is only useful with pull-dim = Y for at least 2 dimensions",
- EPULLGEOM(pcrd->eGeom));
+ enumValueToString(pcrd->eGeom));
}
}
dvec origin, vec;
char buf[STRLEN];
- if (pcrd->eType == epullCONSTRAINT
- && (pcrd->eGeom == epullgCYL || pcrd->eGeom == epullgDIRRELATIVE || pcrd->eGeom == epullgANGLE
- || pcrd->eGeom == epullgANGLEAXIS || pcrd->eGeom == epullgDIHEDRAL))
+ if (pcrd->eType == PullingAlgorithm::Constraint
+ && (pcrd->eGeom == PullGroupGeometry::Cylinder || pcrd->eGeom == PullGroupGeometry::DirectionRelative
+ || pcrd->eGeom == PullGroupGeometry::Angle || pcrd->eGeom == PullGroupGeometry::AngleAxis
+ || pcrd->eGeom == PullGroupGeometry::Dihedral))
{
gmx_fatal(FARGS,
"Pulling of type %s can not be combined with geometry %s. Consider using pull "
"type %s.",
- epull_names[pcrd->eType], epullg_names[pcrd->eGeom], epull_names[epullUMBRELLA]);
+ enumValueToString(pcrd->eType),
+ enumValueToString(pcrd->eGeom),
+ enumValueToString(PullingAlgorithm::Umbrella));
}
- if (pcrd->eType == epullEXTERNAL)
+ if (pcrd->eType == PullingAlgorithm::External)
{
if (pcrd->externalPotentialProvider[0] == '\0')
{
sprintf(buf,
"The use of pull type '%s' for pull coordinate %d requires that the name of "
"the module providing the potential external is set with the option %s%d%s",
- epull_names[pcrd->eType], coord_index_for_output, "pull-coord",
- coord_index_for_output, "-potential-provider");
+ enumValueToString(pcrd->eType),
+ coord_index_for_output,
+ "pull-coord",
+ coord_index_for_output,
+ "-potential-provider");
warning_error(wi, buf);
}
sprintf(buf,
"The use of pull type '%s' for pull coordinate %d requires that the pull rate "
"is zero",
- epull_names[pcrd->eType], coord_index_for_output);
+ enumValueToString(pcrd->eType),
+ coord_index_for_output);
warning_error(wi, buf);
}
- if (pcrd->eGeom == epullgCYL)
+ if (pcrd->eGeom == PullGroupGeometry::Cylinder)
{
/* Warn the user of a PBC restriction, caused by the fact that
* there is no reference value with an external pull potential.
"With pull type '%s' and geometry '%s', the distance component along the "
"cylinder axis between atoms in the cylinder group and the COM of the pull "
"group should be smaller than half the box length",
- epull_names[pcrd->eType], epullg_names[pcrd->eGeom]);
+ enumValueToString(pcrd->eType),
+ enumValueToString(pcrd->eGeom));
warning_note(wi, buf);
}
}
}
/* Check the given initial reference value and warn for dangerous values */
- if (pcrd->eGeom == epullgDIST)
+ if (pcrd->eGeom == PullGroupGeometry::Distance)
{
if (pcrd->bStart && pcrd->init < 0)
{
"This may work, since you have set pull-coord-start to 'yes' which modifies "
"this value, but only for certain starting distances. "
"If this is a mistake you may want to use geometry %s instead.",
- pcrd->init, EPULLGEOM(pcrd->eGeom), EPULLGEOM(epullgDIR));
+ pcrd->init,
+ enumValueToString(pcrd->eGeom),
+ enumValueToString(PullGroupGeometry::Direction));
warning(wi, buf);
}
}
- else if (pcrd->eGeom == epullgANGLE || pcrd->eGeom == epullgANGLEAXIS)
+ else if (pcrd->eGeom == PullGroupGeometry::Angle || pcrd->eGeom == PullGroupGeometry::AngleAxis)
{
if (pcrd->bStart && (pcrd->init < 0 || pcrd->init > 180))
{
"allowed range [0, 180] degrees for geometry (%s). "
"This may work, since you have set pull-coord-start to 'yes' which modifies "
"this value, but only for certain starting angles.",
- pcrd->init, EPULLGEOM(pcrd->eGeom));
+ pcrd->init,
+ enumValueToString(pcrd->eGeom));
warning(wi, buf);
}
}
- else if (pcrd->eGeom == epullgDIHEDRAL)
+ else if (pcrd->eGeom == PullGroupGeometry::Dihedral)
{
if (pcrd->bStart && (pcrd->init < -180 || pcrd->init > 180))
{
"allowed range [-180, 180] degrees for geometry (%s). "
"This may work, since you have set pull-coord-start to 'yes' which modifies "
"this value, but only for certain starting angles.",
- pcrd->init, EPULLGEOM(pcrd->eGeom));
+ pcrd->init,
+ enumValueToString(pcrd->eGeom));
warning(wi, buf);
}
}
clear_dvec(vec);
string2dvec(vec_buf, vec);
- if (pcrd->eGeom == epullgDIR || pcrd->eGeom == epullgCYL || pcrd->eGeom == epullgDIRPBC
- || pcrd->eGeom == epullgANGLEAXIS)
+ if (pcrd->eGeom == PullGroupGeometry::Direction || pcrd->eGeom == PullGroupGeometry::Cylinder
+ || pcrd->eGeom == PullGroupGeometry::DirectionPBC || pcrd->eGeom == PullGroupGeometry::AngleAxis)
{
if (dnorm2(vec) == 0)
{
- gmx_fatal(FARGS, "With pull geometry %s the pull vector can not be 0,0,0",
- epullg_names[pcrd->eGeom]);
+ gmx_fatal(FARGS,
+ "With pull geometry %s the pull vector can not be 0,0,0",
+ enumValueToString(pcrd->eGeom));
}
for (int d = 0; d < DIM; d++)
{
gmx_fatal(FARGS,
"pull-coord-vec has non-zero %c-component while pull_dim for the "
"%c-dimension is set to N",
- 'x' + d, 'x' + d);
+ 'x' + d,
+ 'x' + d);
}
}
"A pull vector is given (%g %g %g) but will not be used with geometry %s. If "
"you really want to use this "
"vector, consider using geometry %s instead.",
- vec[0], vec[1], vec[2], EPULLGEOM(pcrd->eGeom),
- pcrd->eGeom == epullgANGLE ? EPULLGEOM(epullgANGLEAXIS) : EPULLGEOM(epullgDIR));
+ vec[0],
+ vec[1],
+ vec[2],
+ enumValueToString(pcrd->eGeom),
+ pcrd->eGeom == PullGroupGeometry::Angle
+ ? enumValueToString(PullGroupGeometry::AngleAxis)
+ : enumValueToString(PullGroupGeometry::Direction));
warning(wi, buf);
}
}
printStringNoNewline(inp, "Cylinder radius for dynamic reaction force groups (nm)");
pull->cylinder_r = get_ereal(inp, "pull-cylinder-r", 1.5, wi);
pull->constr_tol = get_ereal(inp, "pull-constr-tol", 1E-6, wi);
- pull->bPrintCOM = (get_eeenum(inp, "pull-print-com", yesno_names, wi) != 0);
- pull->bPrintRefValue = (get_eeenum(inp, "pull-print-ref-value", yesno_names, wi) != 0);
- pull->bPrintComp = (get_eeenum(inp, "pull-print-components", yesno_names, wi) != 0);
+ pull->bPrintCOM = (getEnum<Boolean>(inp, "pull-print-com", wi) != Boolean::No);
+ pull->bPrintRefValue = (getEnum<Boolean>(inp, "pull-print-ref-value", wi) != Boolean::No);
+ pull->bPrintComp = (getEnum<Boolean>(inp, "pull-print-components", wi) != Boolean::No);
pull->nstxout = get_eint(inp, "pull-nstxout", 50, wi);
pull->nstfout = get_eint(inp, "pull-nstfout", 50, wi);
- pull->bSetPbcRefToPrevStepCOM = (get_eeenum(inp, "pull-pbc-ref-prev-step-com", yesno_names, wi) != 0);
- pull->bXOutAverage = (get_eeenum(inp, "pull-xout-average", yesno_names, wi) != 0);
- pull->bFOutAverage = (get_eeenum(inp, "pull-fout-average", yesno_names, wi) != 0);
+ pull->bSetPbcRefToPrevStepCOM =
+ (getEnum<Boolean>(inp, "pull-pbc-ref-prev-step-com", wi) != Boolean::No);
+ pull->bXOutAverage = (getEnum<Boolean>(inp, "pull-xout-average", wi) != Boolean::No);
+ pull->bFOutAverage = (getEnum<Boolean>(inp, "pull-fout-average", wi) != Boolean::No);
printStringNoNewline(inp, "Number of pull groups");
pull->ngroup = get_eint(inp, "pull-ngroups", 1, wi);
printStringNoNewline(inp, "Number of pull coordinates");
pull->group.emplace_back(t_pull_group());
for (int groupNum = 1; groupNum < pull->ngroup; groupNum++)
{
- t_pull_group pullGroup; //= &pull->group[groupNum];
+ t_pull_group pullGroup;
sprintf(buf, "pull-group%d-name", groupNum);
setStringEntry(inp, buf, readBuffer, "");
pullGroups[groupNum] = readBuffer;
sprintf(buf, "pull-group%d-weights", groupNum);
setStringEntry(inp, buf, wbuf, "");
sprintf(buf, "pull-group%d-pbcatom", groupNum);
- pullGroup.pbcatom = get_eint(inp, buf, 0, wi);
+ pullGroup.pbcatom = get_eint(inp, buf, 0, wi);
+ pullGroup.pbcatom_input = pullGroup.pbcatom;
/* Initialize the pull group */
pullGroup.weight = setupPullGroupWeights(wbuf);
{
t_pull_coord pullCoord; // = &pull->coord[coordNum - 1];
sprintf(buf, "pull-coord%d-type", coordNum);
- pullCoord.eType = get_eeenum(inp, buf, epull_names, wi);
+ pullCoord.eType = getEnum<PullingAlgorithm>(inp, buf, wi);
sprintf(buf, "pull-coord%d-potential-provider", coordNum);
setStringEntry(inp, buf, provider, "");
- pullCoord.externalPotentialProvider = gmx_strdup(provider);
+ pullCoord.externalPotentialProvider = provider;
sprintf(buf, "pull-coord%d-geometry", coordNum);
- pullCoord.eGeom = get_eeenum(inp, buf, epullg_names, wi);
+ pullCoord.eGeom = getEnum<PullGroupGeometry>(inp, buf, wi);
sprintf(buf, "pull-coord%d-groups", coordNum);
setStringEntry(inp, buf, groups, "");
switch (pullCoord.eGeom)
{
- case epullgDIHEDRAL: pullCoord.ngroup = 6; break;
- case epullgDIRRELATIVE:
- case epullgANGLE: pullCoord.ngroup = 4; break;
+ case PullGroupGeometry::Dihedral: pullCoord.ngroup = 6; break;
+ case PullGroupGeometry::DirectionRelative:
+ case PullGroupGeometry::Angle: pullCoord.ngroup = 4; break;
default: pullCoord.ngroup = 2; break;
}
- nscan = sscanf(groups, "%d %d %d %d %d %d %d", &pullCoord.group[0], &pullCoord.group[1],
- &pullCoord.group[2], &pullCoord.group[3], &pullCoord.group[4],
- &pullCoord.group[5], &idum);
+ nscan = sscanf(groups,
+ "%d %d %d %d %d %d %d",
+ &pullCoord.group[0],
+ &pullCoord.group[1],
+ &pullCoord.group[2],
+ &pullCoord.group[3],
+ &pullCoord.group[4],
+ &pullCoord.group[5],
+ &idum);
if (nscan != pullCoord.ngroup)
{
auto message =
gmx::formatString("%s should contain %d pull group indices with geometry %s",
- buf, pullCoord.ngroup, epullg_names[pullCoord.eGeom]);
+ buf,
+ pullCoord.ngroup,
+ enumValueToString(pullCoord.eGeom));
set_warning_line(wi, nullptr, -1);
warning_error(wi, message);
}
/* Quit with a fatal error to avoid invalid memory access */
gmx_fatal(FARGS,
"%s contains an invalid pull group %d, you should have %d <= group <= %d",
- buf, pullCoord.group[g], 0, pull->ngroup - 1);
+ buf,
+ pullCoord.group[g],
+ 0,
+ pull->ngroup - 1);
}
}
sprintf(buf, "pull-coord%d-vec", coordNum);
setStringEntry(inp, buf, vec_buf, "0.0 0.0 0.0");
sprintf(buf, "pull-coord%d-start", coordNum);
- pullCoord.bStart = (get_eeenum(inp, buf, yesno_names, wi) != 0);
+ pullCoord.bStart = (getEnum<Boolean>(inp, buf, wi) != Boolean::No);
sprintf(buf, "pull-coord%d-init", coordNum);
pullCoord.init = get_ereal(inp, buf, 0.0, wi);
sprintf(buf, "pull-coord%d-rate", coordNum);
/* Initialize the pull coordinate */
init_pull_coord(&pullCoord, coordNum, dim_buf, origin_buf, vec_buf, wi);
+
+ pullCoord.coordIndex = coordNum - 1;
pull->coord.emplace_back(pullCoord);
}
gmx_fatal(FARGS,
"Number of weights (%ld) for pull group %d '%s' does not match the number of "
"atoms (%ld)",
- gmx::ssize(pullGroup.weight), g, pullGroupNames[g].c_str(),
+ gmx::ssize(pullGroup.weight),
+ g,
+ pullGroupNames[g].c_str(),
gmx::ssize(pullGroup.ind));
}
{
for (int c = 0; c < int(pullCoords.size()); c++)
{
- t_pull_coord pcrd = pullCoords[c];
+ const t_pull_coord& pcrd = pullCoords[c];
+
+ GMX_RELEASE_ASSERT(pcrd.coordIndex == c, "coordIndex should match the index in the vector");
if (pcrd.group[0] < 0 || pcrd.group[0] >= int(pullGroups.size()) || pcrd.group[1] < 0
|| pcrd.group[1] >= int(pullGroups.size()))
gmx_fatal(FARGS,
"Pull group index in pull-coord%d-groups out of range, should be between %d "
"and %d",
- c + 1, 0, int(pullGroups.size()) + 1);
+ pcrd.coordIndex + 1,
+ 0,
+ int(pullGroups.size()) + 1);
}
if (pcrd.group[0] == pcrd.group[1])
{
- gmx_fatal(FARGS, "Identical pull group indices in pull-coord%d-groups", c + 1);
+ gmx_fatal(FARGS, "Identical pull group indices in pull-coord%d-groups", pcrd.coordIndex + 1);
}
- if (pcrd.eGeom == epullgCYL)
+ if (pcrd.eGeom == PullGroupGeometry::Cylinder)
{
if (!pullGroups[pcrd.group[0]].weight.empty())
{
}
}
-pull_t* set_pull_init(t_inputrec* ir, const gmx_mtop_t* mtop, rvec* x, matrix box, real lambda, warninp_t wi)
+pull_t* set_pull_init(t_inputrec* ir,
+ const gmx_mtop_t& mtop,
+ gmx::ArrayRef<const gmx::RVec> x,
+ matrix box,
+ real lambda,
+ warninp_t wi)
{
pull_t* pull_work;
t_pbc pbc;
pull_params_t* pull = ir->pull.get();
gmx::LocalAtomSetManager atomSets;
- pull_work = init_pull(nullptr, pull, ir, mtop, nullptr, &atomSets, lambda);
- auto mdAtoms = gmx::makeMDAtoms(nullptr, *mtop, *ir, false);
- auto md = mdAtoms->mdatoms();
- atoms2md(mtop, ir, -1, {}, mtop->natoms, mdAtoms.get());
- if (ir->efep)
+ pull_work = init_pull(nullptr, pull, ir, mtop, nullptr, &atomSets, lambda);
+ auto mdAtoms = gmx::makeMDAtoms(nullptr, mtop, *ir, false);
+ auto* md = mdAtoms->mdatoms();
+ atoms2md(mtop, *ir, -1, {}, mtop.natoms, mdAtoms.get());
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
update_mdatoms(md, lambda);
}
if (pull->bSetPbcRefToPrevStepCOM)
{
- initPullComFromPrevStep(nullptr, pull_work, md->massT, &pbc, x);
+ initPullComFromPrevStep(nullptr, pull_work, gmx::arrayRefFromArray(md->massT, md->nr), &pbc, x);
}
- pull_calc_coms(nullptr, pull_work, md->massT, &pbc, t_start, x, nullptr);
+ pull_calc_coms(nullptr, pull_work, gmx::arrayRefFromArray(md->massT, md->nr), &pbc, t_start, x, {});
for (int g = 0; g < pull->ngroup; g++)
{
- bool groupObeysPbc = pullCheckPbcWithinGroup(
- *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
- pbc, g, c_pullGroupSmallGroupThreshold);
+ bool groupObeysPbc =
+ pullCheckPbcWithinGroup(*pull_work, x, pbc, g, c_pullGroupSmallGroupThreshold);
if (!groupObeysPbc)
{
char buf[STRLEN];
"atom should be chosen as pbcatom. Pull group %d is larger than that and "
"does not have "
"a specific atom selected as reference atom.",
- c_pullGroupSmallGroupThreshold, g);
+ c_pullGroupSmallGroupThreshold,
+ g);
warning_error(wi, buf);
}
else if (!pull->bSetPbcRefToPrevStepCOM)
"other "
"atoms in the group is larger than %g times half the box size. "
"Set the pull-pbc-ref-prev-step-com option to yes.",
- pull->group[g].pbcatom + 1, g, c_pullGroupSmallGroupThreshold);
+ pull->group[g].pbcatom + 1,
+ g,
+ c_pullGroupSmallGroupThreshold);
warning_error(wi, buf);
}
}
if (groupObeysPbc)
{
- groupObeysPbc = pullCheckPbcWithinGroup(
- *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
- pbc, g, c_pullGroupPbcMargin);
+ groupObeysPbc = pullCheckPbcWithinGroup(*pull_work, x, pbc, g, c_pullGroupPbcMargin);
if (!groupObeysPbc)
{
char buf[STRLEN];
"size from the PBC atom (%d). "
"If atoms are or will more beyond half the box size from the PBC atom, the "
"COM will be ill defined.",
- g, c_pullGroupPbcMargin, pull->group[g].pbcatom + 1);
+ g,
+ c_pullGroupPbcMargin,
+ pull->group[g].pbcatom + 1);
set_warning_line(wi, nullptr, -1);
warning(wi, buf);
}
value = get_pull_coord_value(pull_work, c, &pbc);
- value *= pull_conversion_factor_internal2userinput(pcrd);
- fprintf(stderr, " %10.3f %s", value, pull_coordinate_units(pcrd));
+ value *= pull_conversion_factor_internal2userinput(*pcrd);
+ fprintf(stderr, " %10.3f %s", value, pull_coordinate_units(*pcrd));
if (pcrd->bStart)
{
pcrd->init = value + init;
}
- if (pcrd->eGeom == epullgDIST)
+ if (pcrd->eGeom == PullGroupGeometry::Distance)
{
if (pcrd->init < 0)
{
gmx_fatal(FARGS,
"The initial pull distance (%g) needs to be non-negative with geometry "
"%s. If you want a signed distance, use geometry %s instead.",
- pcrd->init, EPULLGEOM(pcrd->eGeom), EPULLGEOM(epullgDIR));
+ pcrd->init,
+ enumValueToString(pcrd->eGeom),
+ enumValueToString(PullGroupGeometry::Direction));
}
/* TODO: With a positive init but a negative rate things could still
* generalization of the pull code makes pull dim available here.
*/
}
- else if (pcrd->eGeom == epullgANGLE || pcrd->eGeom == epullgANGLEAXIS)
+ else if (pcrd->eGeom == PullGroupGeometry::Angle || pcrd->eGeom == PullGroupGeometry::AngleAxis)
{
if (pcrd->init < 0 || pcrd->init > 180)
{
pcrd->init);
}
}
- else if (pcrd->eGeom == epullgDIHEDRAL)
+ else if (pcrd->eGeom == PullGroupGeometry::Dihedral)
{
if (pcrd->init < -180 || pcrd->init > 180)
{
}
- fprintf(stderr, " %10.3f %s\n", pcrd->init, pull_coordinate_units(pcrd));
+ fprintf(stderr, " %10.3f %s\n", pcrd->init, pull_coordinate_units(*pcrd));
}
return pull_work;
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
-static const char* RotStr = "Enforced rotation:";
-
-
-static char s_vec[STRLEN];
-
+static const std::string RotStr = "Enforced rotation:";
static void string2dvec(char buf[], dvec nums)
{
/* Read the rotation groups */
std::vector<std::string> rotateGroups(rot->ngrp);
char readBuffer[STRLEN];
+ char s_vec[STRLEN];
for (g = 0; g < rot->ngrp; g++)
{
rotg = &rot->grp[g];
"Rotation potential. Can be iso, iso-pf, pm, pm-pf, rm, rm-pf, rm2, "
"rm2-pf, flex, flex-t, flex2, flex2-t");
sprintf(buf, "rot-type%d", g);
- rotg->eType = get_eenum(inp, buf, erotg_names);
+ rotg->eType = getEnum<EnforcedRotationGroupType>(inp, buf, wi);
printStringNoNewline(inp, "Use mass-weighting of the rotation group positions");
sprintf(buf, "rot-massw%d", g);
- rotg->bMassW = get_eenum(inp, buf, yesno_names);
+ rotg->bMassW = getEnum<Boolean>(inp, buf, wi) != Boolean::No;
printStringNoNewline(inp, "Rotation vector, will get normalized");
sprintf(buf, "rot-vec%d", g);
sprintf(warn_buf, "rot-vec%d = 0", g);
warning_error(wi, warn_buf);
}
- fprintf(stderr, "%s Group %d (%s) normalized rot. vector: %f %f %f\n", RotStr, g,
- erotg_names[rotg->eType], vec[0], vec[1], vec[2]);
+ fprintf(stderr,
+ "%s Group %d (%s) normalized rot. vector: %f %f %f\n",
+ RotStr.c_str(),
+ g,
+ enumValueToString(rotg->eType),
+ vec[0],
+ vec[1],
+ vec[2]);
for (m = 0; m < DIM; m++)
{
rotg->inputVec[m] = vec[m];
sprintf(buf, "rot-pivot%d", g);
setStringEntry(inp, buf, s_vec, "0.0 0.0 0.0");
clear_dvec(vec);
- if ((rotg->eType == erotgISO) || (rotg->eType == erotgPM) || (rotg->eType == erotgRM)
- || (rotg->eType == erotgRM2))
+ if ((rotg->eType == EnforcedRotationGroupType::Iso)
+ || (rotg->eType == EnforcedRotationGroupType::Pm)
+ || (rotg->eType == EnforcedRotationGroupType::Rm)
+ || (rotg->eType == EnforcedRotationGroupType::Rm2))
{
string2dvec(s_vec, vec);
}
inp, "Value of additive constant epsilon' (nm^2) for rm2* and flex2* potentials");
sprintf(buf, "rot-eps%d", g);
rotg->eps = get_ereal(inp, buf, 1e-4, wi);
- if ((rotg->eps <= 0.0) && (rotg->eType == erotgRM2 || rotg->eType == erotgFLEX2))
+ if ((rotg->eps <= 0.0)
+ && (rotg->eType == EnforcedRotationGroupType::Rm2
+ || rotg->eType == EnforcedRotationGroupType::Flex2))
{
sprintf(warn_buf, "rot-eps%d <= 0", g);
warning_error(wi, warn_buf);
inp,
"Fitting method to determine angle of rotation group (rmsd, norm, or potential)");
sprintf(buf, "rot-fit-method%d", g);
- rotg->eFittype = get_eenum(inp, buf, erotg_fitnames);
+ rotg->eFittype = getEnum<RotationGroupFitting>(inp, buf, wi);
printStringNoNewline(inp,
"For fit type 'potential', nr. of angles around the reference for "
"which the pot. is evaluated");
sprintf(buf, "rot-potfit-nsteps%d", g);
rotg->PotAngle_nstep = get_eint(inp, buf, 21, wi);
- if ((rotg->eFittype == erotgFitPOT) && (rotg->PotAngle_nstep < 1))
+ if ((rotg->eFittype == RotationGroupFitting::Pot) && (rotg->PotAngle_nstep < 1))
{
sprintf(warn_buf, "rot-potfit-nsteps%d < 1", g);
warning_error(wi, warn_buf);
}
printStringNoNewline(
- inp,
- "For fit type 'potential', distance in degrees between two consecutive angles");
+ inp, "For fit type 'potential', distance in degrees between two consecutive angles");
sprintf(buf, "rot-potfit-step%d", g);
rotg->PotAngle_step = get_ereal(inp, buf, 0.25, wi);
}
}
if (!bSame)
{
- sprintf(warn_buf, "%s Box size in reference file %s differs from actual box size!", RotStr, fn);
+ sprintf(warn_buf, "%s Box size in reference file %s differs from actual box size!", RotStr.c_str(), fn);
warning(wi, warn_buf);
pr_rvecs(stderr, 0, "Your box is:", box, 3);
pr_rvecs(stderr, 0, "Box in file:", f_box, 3);
for (g = 0; g < rot->ngrp; g++)
{
rotg = &rot->grp[g];
- fprintf(stderr, "%s group %d has %d reference positions.\n", RotStr, g, rotg->nat);
+ fprintf(stderr, "%s group %d has %d reference positions.\n", RotStr.c_str(), g, rotg->nat);
snew(rotg->x_ref, rotg->nat);
/* Construct the name for the file containing the reference positions for this group: */
gmx_fatal(FARGS,
"%s The file containing the reference positions was not found.\n"
"Expected the file '%s' for group %d.\n",
- RotStr, reffile, g);
+ RotStr.c_str(),
+ reffile,
+ g);
}
if (gmx_fexist(reffile))
gmx_fatal(FARGS,
"Number of atoms in file %s (%d) does not match the number of atoms in "
"rotation group (%d)!\n",
- reffile, header.natoms, rotg->nat);
+ reffile,
+ header.natoms,
+ rotg->nat);
}
- gmx_trr_read_single_frame(reffile, &header.step, &header.t, &header.lambda, f_box,
- &header.natoms, rotg->x_ref, nullptr, nullptr);
+ gmx_trr_read_single_frame(
+ reffile, &header.step, &header.t, &header.lambda, f_box, &header.natoms, rotg->x_ref, nullptr, nullptr);
/* Check whether the box is unchanged and output a warning if not: */
check_box_unchanged(f_box, box, reffile, wi);
if (rotg->nat > 0)
{
- fprintf(stderr, "Rotation group %d '%s' has %d atoms\n", g, rotateGroupNames[g].c_str(),
- rotg->nat);
+ fprintf(stderr, "Rotation group %d '%s' has %d atoms\n", g, rotateGroupNames[g].c_str(), rotg->nat);
snew(rotg->ind, rotg->nat);
for (i = 0; i < rotg->nat; i++)
{
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstring>
#include <algorithm>
+#include <optional>
#include <string>
#include <vector>
#include "gromacs/topology/atoms.h"
#include "gromacs/topology/symtab.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strdb.h"
+#include "gromacs/utility/stringtoenumvalueconverter.h"
#include "hackblock.h"
for (int j = 0; (j < rtpDBEntry.natom()); j++)
{
- int tp = rtpDBEntry.atom[j].type;
- const char* tpnm = atype.atomNameFromAtomType(tp);
- if (tpnm == nullptr)
+ int tp = rtpDBEntry.atom[j].type;
+ auto tpnm = atype.atomNameFromAtomType(tp);
+ if (!tpnm.has_value())
{
gmx_fatal(FARGS, "Incorrect atomtype (%d)", tp);
}
- fprintf(out, "%6s %6s %8.3f %6d\n", *(rtpDBEntry.atomname[j]), tpnm,
- rtpDBEntry.atom[j].q, rtpDBEntry.cgnr[j]);
+ fprintf(out,
+ "%6s %6s %8.3f %6d\n",
+ *(rtpDBEntry.atomname[j]),
+ *tpnm,
+ rtpDBEntry.atom[j].q,
+ rtpDBEntry.cgnr[j]);
}
}
r0->atom.emplace_back();
r0->atom.back().q = q;
r0->cgnr.push_back(cg);
- int j = atype->atomTypeFromName(buf1);
- if (j == NOTSET)
+ auto j = atype->atomTypeFromName(buf1);
+ if (!j.has_value())
{
gmx_fatal(FARGS,
"Atom type %s (residue %s) not found in atomtype "
"database",
- buf1, r0->resname.c_str());
+ buf1,
+ r0->resname.c_str());
}
- r0->atom.back().type = j;
- r0->atom.back().m = atype->atomMassFromAtomType(j);
+ r0->atom.back().type = *j;
+ r0->atom.back().m = *atype->atomMassFromAtomType(*j);
}
return TRUE;
}
-static bool read_bondeds(int bt, FILE* in, char* line, PreprocessResidue* rtpDBEntry)
+static bool read_bondeds(BondedTypes bt, FILE* in, char* line, PreprocessResidue* rtpDBEntry)
{
char str[STRLEN];
int ni;
rtpDBEntry->rb[bt].b.emplace_back();
BondedInteraction* newBond = &rtpDBEntry->rb[bt].b.back();
- for (int j = 0; j < btsNiatoms[bt]; j++)
+ for (int j = 0; j < enumValueToNumIAtoms(bt); j++)
{
if (sscanf(line + n, "%s%n", str, &ni) == 1)
{
return TRUE;
}
-static void print_resbondeds(FILE* out, int bt, const PreprocessResidue& rtpDBEntry)
+static void print_resbondeds(FILE* out, BondedTypes bt, const PreprocessResidue& rtpDBEntry)
{
if (!rtpDBEntry.rb[bt].b.empty())
{
- fprintf(out, " [ %s ]\n", btsNames[bt]);
+ fprintf(out, " [ %s ]\n", enumValueToString(bt));
for (const auto& b : rtpDBEntry.rb[bt].b)
{
- for (int j = 0; j < btsNiatoms[bt]; j++)
+ for (int j = 0; j < enumValueToNumIAtoms(bt); j++)
{
fprintf(out, "%6s ", b.a[j].c_str());
}
}
}
-static int get_bt(char* header)
+static std::optional<BondedTypes> get_bt(char* header)
{
- int i;
-
- for (i = 0; i < ebtsNR; i++)
- {
- if (gmx_strcasecmp(btsNames[i], header) == 0)
- {
- return i;
- }
- }
- return NOTSET;
+ gmx::StringToEnumValueConverter<BondedTypes, enumValueToString> converter;
+ return converter.valueFrom(header);
}
-/* print all the ebtsNR type numbers */
+/* print all the BondedTypes type numbers */
static void print_resall_header(FILE* out, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry)
{
fprintf(out, "[ bondedtypes ]\n");
fprintf(out,
"; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 "
"remove_dih\n");
- fprintf(out, " %5d %6d %9d %9d %14d %14d %14d %14d\n\n", rtpDBEntry[0].rb[0].type,
- rtpDBEntry[0].rb[1].type, rtpDBEntry[0].rb[2].type, rtpDBEntry[0].rb[3].type,
- static_cast<int>(rtpDBEntry[0].bKeepAllGeneratedDihedrals), rtpDBEntry[0].nrexcl,
+ fprintf(out,
+ " %5d %6d %9d %9d %14d %14d %14d %14d\n\n",
+ rtpDBEntry[0].rb[0].type,
+ rtpDBEntry[0].rb[1].type,
+ rtpDBEntry[0].rb[2].type,
+ rtpDBEntry[0].rb[3].type,
+ static_cast<int>(rtpDBEntry[0].bKeepAllGeneratedDihedrals),
+ rtpDBEntry[0].nrexcl,
static_cast<int>(rtpDBEntry[0].bGenerateHH14Interactions),
static_cast<int>(rtpDBEntry[0].bRemoveDihedralIfWithImproper));
}
"remove_dih");
GMX_LOG(logger.info)
.asParagraph()
- .appendTextFormatted(
- " %5d %6d %9d %9d %14d %14d %14d %14d", rtpDBEntry[0].rb[0].type,
- rtpDBEntry[0].rb[1].type, rtpDBEntry[0].rb[2].type, rtpDBEntry[0].rb[3].type,
- static_cast<int>(rtpDBEntry[0].bKeepAllGeneratedDihedrals),
- rtpDBEntry[0].nrexcl, static_cast<int>(rtpDBEntry[0].bGenerateHH14Interactions),
- static_cast<int>(rtpDBEntry[0].bRemoveDihedralIfWithImproper));
+ .appendTextFormatted(" %5d %6d %9d %9d %14d %14d %14d %14d",
+ rtpDBEntry[0].rb[0].type,
+ rtpDBEntry[0].rb[1].type,
+ rtpDBEntry[0].rb[2].type,
+ rtpDBEntry[0].rb[3].type,
+ static_cast<int>(rtpDBEntry[0].bKeepAllGeneratedDihedrals),
+ rtpDBEntry[0].nrexcl,
+ static_cast<int>(rtpDBEntry[0].bGenerateHH14Interactions),
+ static_cast<int>(rtpDBEntry[0].bRemoveDihedralIfWithImproper));
}
if (r.natom() > 0)
{
print_resatoms(out, atype, r);
- for (int bt = 0; bt < ebtsNR; bt++)
+ for (auto bt : gmx::EnumerationWrapper<BondedTypes>{})
{
print_resbondeds(out, bt, r);
}
{
FILE* in;
char filebase[STRLEN], line[STRLEN], header[STRLEN];
- int bt, nparam;
+ int nparam;
int dum1, dum2, dum3;
bool bNextResidue, bError;
/* these bonded parameters will overwritten be when *
* there is a [ bondedtypes ] entry in the .rtp file */
- header_settings.rb[ebtsBONDS].type = 1; /* normal bonds */
- header_settings.rb[ebtsANGLES].type = 1; /* normal angles */
- header_settings.rb[ebtsPDIHS].type = 1; /* normal dihedrals */
- header_settings.rb[ebtsIDIHS].type = 2; /* normal impropers */
- header_settings.rb[ebtsEXCLS].type = 1; /* normal exclusions */
- header_settings.rb[ebtsCMAP].type = 1; /* normal cmap torsions */
+ header_settings.rb[BondedTypes::Bonds].type = 1; /* normal bonds */
+ header_settings.rb[BondedTypes::Angles].type = 1; /* normal angles */
+ header_settings.rb[BondedTypes::ProperDihedrals].type = 1; /* normal dihedrals */
+ header_settings.rb[BondedTypes::ImproperDihedrals].type = 2; /* normal impropers */
+ header_settings.rb[BondedTypes::Exclusions].type = 1; /* normal exclusions */
+ header_settings.rb[BondedTypes::Cmap].type = 1; /* normal cmap torsions */
header_settings.bKeepAllGeneratedDihedrals = FALSE;
header_settings.nrexcl = 3;
if (gmx::equalCaseInsensitive("bondedtypes", header, 5))
{
get_a_line(in, line, STRLEN);
- if ((nparam = sscanf(line, "%d %d %d %d %d %d %d %d", &header_settings.rb[ebtsBONDS].type,
- &header_settings.rb[ebtsANGLES].type,
- &header_settings.rb[ebtsPDIHS].type, &header_settings.rb[ebtsIDIHS].type,
- &dum1, &header_settings.nrexcl, &dum2, &dum3))
+ if ((nparam = sscanf(line,
+ "%d %d %d %d %d %d %d %d",
+ &header_settings.rb[BondedTypes::Bonds].type,
+ &header_settings.rb[BondedTypes::Angles].type,
+ &header_settings.rb[BondedTypes::ProperDihedrals].type,
+ &header_settings.rb[BondedTypes::ImproperDihedrals].type,
+ &dum1,
+ &header_settings.nrexcl,
+ &dum2,
+ &dum3))
< 4)
{
- gmx_fatal(FARGS, "need 4 to 8 parameters in the header of .rtp file %s at line:\n%s\n",
- rrdb.c_str(), line);
+ gmx_fatal(FARGS,
+ "need 4 to 8 parameters in the header of .rtp file %s at line:\n%s\n",
+ rrdb.c_str(),
+ line);
}
header_settings.bKeepAllGeneratedDihedrals = (dum1 != 0);
header_settings.bGenerateHH14Interactions = (dum2 != 0);
}
else
{
- bt = get_bt(header);
- if (bt != NOTSET)
+ auto bt = get_bt(header);
+ if (bt.has_value())
{
/* header is an bonded directive */
- bError = !read_bondeds(bt, in, line, res);
+ bError = !read_bondeds(*bt, in, line, res);
}
else if (gmx::equalCaseInsensitive("atoms", header, 5))
{
gmx_fatal(FARGS, "No atoms found in .rtp file in residue %s\n", res->resname.c_str());
}
- auto found = std::find_if(rtpDBEntry->begin(), rtpDBEntry->end() - 1,
- [&res](const PreprocessResidue& entry) {
- return gmx::equalCaseInsensitive(entry.resname, res->resname);
- });
+ auto found = std::find_if(
+ rtpDBEntry->begin(), rtpDBEntry->end() - 1, [&res](const PreprocessResidue& entry) {
+ return gmx::equalCaseInsensitive(entry.resname, res->resname);
+ });
if (found != rtpDBEntry->end() - 1)
{
if (found >= oldArrayEnd)
{
- gmx_fatal(FARGS, "Found a second entry for '%s' in '%s'", res->resname.c_str(),
- rrdb.c_str());
+ gmx_fatal(FARGS, "Found a second entry for '%s' in '%s'", res->resname.c_str(), rrdb.c_str());
}
if (bAllowOverrideRTP)
{
.appendTextFormatted(
"Found another rtp entry for '%s' in '%s',"
" ignoring this entry and keeping the one from '%s.rtp'",
- res->resname.c_str(), rrdb.c_str(), found->filebase.c_str());
+ res->resname.c_str(),
+ rrdb.c_str(),
+ found->filebase.c_str());
/* We should free all the data for this entry.
* The current code gives a lot of dangling pointers.
*/
gmx_fatal(FARGS,
"Found rtp entries for '%s' in both '%s' and '%s'. If you want the first "
"definition to override the second one, set the -rtpo option of pdb2gmx.",
- res->resname.c_str(), found->filebase.c_str(), rrdb.c_str());
+ res->resname.c_str(),
+ found->filebase.c_str(),
+ rrdb.c_str());
}
}
}
std::sort(rtpDBEntry->begin(), rtpDBEntry->end(), [](const PreprocessResidue& a, const PreprocessResidue& b) {
return std::lexicographical_compare(
- a.resname.begin(), a.resname.end(), b.resname.begin(), b.resname.end(),
+ a.resname.begin(),
+ a.resname.end(),
+ b.resname.begin(),
+ b.resname.end(),
[](const char& c1, const char& c2) { return std::toupper(c1) < std::toupper(c2); });
});
}
if (nbest > 1)
{
- gmx_fatal(FARGS, "Residue '%s' not found in residue topology database, looks a bit like %s",
- key.c_str(), bestbuf.c_str());
+ gmx_fatal(FARGS,
+ "Residue '%s' not found in residue topology database, looks a bit like %s",
+ key.c_str(),
+ bestbuf.c_str());
}
else if (besti == -1)
{
.appendTextFormatted(
"'%s' not found in residue topology database, "
"trying to use '%s'",
- key.c_str(), rtpDBEntry[besti].resname.c_str());
+ key.c_str(),
+ rtpDBEntry[besti].resname.c_str());
}
return rtpDBEntry[besti].resname;
gmx::ArrayRef<const PreprocessResidue>::const_iterator
getDatabaseEntry(const std::string& rtpname, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry)
{
- auto found = std::find_if(rtpDBEntry.begin(), rtpDBEntry.end(),
- [&rtpname](const PreprocessResidue& entry) {
- return gmx::equalCaseInsensitive(rtpname, entry.resname);
- });
+ auto found = std::find_if(
+ rtpDBEntry.begin(), rtpDBEntry.end(), [&rtpname](const PreprocessResidue& entry) {
+ return gmx::equalCaseInsensitive(rtpname, entry.resname);
+ });
if (found == rtpDBEntry.end())
{
/* This should never happen, since searchResidueDatabase should have been called
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
numAtomsInMolType++;
}
- molTypes.emplace_back(MoleculeType{ *atoms->resinfo[atoms->atom[i].resind].name,
- numAtomsInMolType, 1 });
+ molTypes.emplace_back(MoleculeType{
+ *atoms->resinfo[atoms->atom[i].resind].name, numAtomsInMolType, 1 });
}
else
{
}
}
- fprintf(stderr, "Found %zu%s molecule type%s:\n", molTypes.size(),
- molTypes.size() == 1 ? "" : " different", molTypes.size() == 1 ? "" : "s");
+ fprintf(stderr,
+ "Found %zu%s molecule type%s:\n",
+ molTypes.size(),
+ molTypes.size() == 1 ? "" : " different",
+ molTypes.size() == 1 ? "" : "s");
for (const auto& molType : molTypes)
{
- fprintf(stderr, "%7s (%4d atoms): %5d residues\n", molType.name.c_str(), molType.numAtoms,
- molType.numMolecules);
+ fprintf(stderr, "%7s (%4d atoms): %5d residues\n", molType.name.c_str(), molType.numAtoms, molType.numMolecules);
}
/* if we have only 1 moleculetype, we don't have to sort */
}
nmol *= n_box[i];
}
- fprintf(stderr, "Will generate new solvent configuration of %dx%dx%d boxes\n", n_box[XX],
- n_box[YY], n_box[ZZ]);
+ fprintf(stderr, "Will generate new solvent configuration of %dx%dx%d boxes\n", n_box[XX], n_box[YY], n_box[ZZ]);
// Create arrays for storing the generated system (cannot be done in-place
// in case the target box is smaller than the original in one dimension,
remover.removeMarkedElements(r);
const int originalAtomCount = atoms->nr;
remover.removeMarkedAtoms(atoms);
- fprintf(stderr, "Removed %d solvent atoms due to solvent-solvent overlap\n",
- originalAtomCount - atoms->nr);
+ fprintf(stderr, "Removed %d solvent atoms due to solvent-solvent overlap\n", originalAtomCount - atoms->nr);
}
/*! \brief
remover.removeMarkedElements(r);
const int originalAtomCount = atoms->nr;
remover.removeMarkedAtoms(atoms);
- fprintf(stderr, "Removed %d solvent atoms more than %f nm from solute.\n",
- originalAtomCount - atoms->nr, rshell);
+ fprintf(stderr,
+ "Removed %d solvent atoms more than %f nm from solute.\n",
+ originalAtomCount - atoms->nr,
+ rshell);
}
/*! \brief
remover.removeMarkedElements(r);
const int originalAtomCount = atoms->nr;
remover.removeMarkedAtoms(atoms);
- fprintf(stderr, "Removed %d solvent atoms due to solute-solvent overlap\n",
- originalAtomCount - atoms->nr);
+ fprintf(stderr, "Removed %d solvent atoms due to solute-solvent overlap\n", originalAtomCount - atoms->nr);
}
/*! \brief
fprintf(stderr, "Reading solvent configuration\n");
bool bTprFileWasRead;
rvec *temporaryX = nullptr, *temporaryV = nullptr;
- readConfAndTopology(gmx::findLibraryFile(filename).c_str(), &bTprFileWasRead, &topSolvent,
- &pbcTypeSolvent, &temporaryX, &temporaryV, boxSolvent);
+ readConfAndTopology(gmx::findLibraryFile(filename).c_str(),
+ &bTprFileWasRead,
+ &topSolvent,
+ &pbcTypeSolvent,
+ &temporaryX,
+ &temporaryV,
+ boxSolvent);
t_atoms* atomsSolvent;
snew(atomsSolvent, 1);
- *atomsSolvent = gmx_mtop_global_atoms(&topSolvent);
+ *atomsSolvent = gmx_mtop_global_atoms(topSolvent);
xSolvent.assign(temporaryX, temporaryX + topSolvent.natoms);
sfree(temporaryX);
vSolvent.assign(temporaryV, temporaryV + topSolvent.natoms);
{
if (rshell > 0.0)
{
- removeSolventOutsideShell(atomsSolvent, &xSolvent, &vSolvent, &exclusionDistances_solvt,
- pbc, *x, rshell);
+ removeSolventOutsideShell(
+ atomsSolvent, &xSolvent, &vSolvent, &exclusionDistances_solvt, pbc, *x, rshell);
}
- removeSolventOverlappingWithSolute(atomsSolvent, &xSolvent, &vSolvent,
- &exclusionDistances_solvt, pbc, *x, exclusionDistances);
+ removeSolventOverlappingWithSolute(
+ atomsSolvent, &xSolvent, &vSolvent, &exclusionDistances_solvt, pbc, *x, exclusionDistances);
}
if (max_sol > 0 && atomsSolvent->nres > max_sol)
gmx::AtomsBuilder builder(atoms, symtab);
builder.mergeAtoms(*sortedAtomsSolvent);
}
- fprintf(stderr, "Generated solvent containing %d atoms in %d residues\n", atomsSolvent->nr,
+ fprintf(stderr,
+ "Generated solvent containing %d atoms in %d residues\n",
+ atomsSolvent->nr,
atomsSolvent->nres);
if (newatoms)
mtot = 0;
for (i = 0; (i < atoms->nr); i++)
{
- aps->setAtomProperty(epropMass, std::string(*atoms->resinfo[atoms->atom[i].resind].name),
- std::string(*atoms->atomname[i]), &mm);
+ aps->setAtomProperty(epropMass,
+ std::string(*atoms->resinfo[atoms->atom[i].resind].name),
+ std::string(*atoms->atomname[i]),
+ &mm);
mtot += mm;
}
vol = det(box);
fprintf(stderr, "Volume : %10g (nm^3)\n", vol);
- fprintf(stderr, "Density : %10g (g/l)\n", (mtot * 1e24) / (AVOGADRO * vol));
+ fprintf(stderr, "Density : %10g (g/l)\n", (mtot * 1e24) / (gmx::c_avogadro * vol));
fprintf(stderr, "Number of solvent molecules: %5d \n\n", nsol);
/* open topology file and append sol molecules */
fprintf(stdout,
"Adding line for %d solvent molecules with resname (%s) to "
"topology file (%s)\n",
- resCount, currRes.c_str(), topinout);
+ resCount,
+ currRes.c_str(),
+ topinout);
fprintf(fpout, "%-15s %5d\n", currRes.c_str(), resCount);
currRes = *atoms->resinfo[i].name;
resCount = 1;
fprintf(stdout,
"Adding line for %d solvent molecules with resname (%s) to "
"topology file (%s)\n",
- resCount, currRes.c_str(), topinout);
+ resCount,
+ currRes.c_str(),
+ topinout);
fprintf(fpout, "%-15s %5d\n", currRes.c_str(), resCount);
}
gmx_ffclose(fpout);
{ "-vel", FALSE, etBOOL, { &bReadV }, "Keep velocities from input solute and solvent" },
};
- if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa, asize(desc), desc,
- asize(bugs), bugs, &oenv))
+ if (!parse_common_args(
+ &argc, argv, 0, NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
fprintf(stderr, "Reading solute configuration%s\n", bReadV ? " and velocities" : "");
bool bTprFileWasRead;
rvec *temporaryX = nullptr, *temporaryV = nullptr;
- readConfAndTopology(conf_prot, &bTprFileWasRead, &top, &pbcType, &temporaryX,
- bReadV ? &temporaryV : nullptr, box);
- *atoms = gmx_mtop_global_atoms(&top);
+ readConfAndTopology(
+ conf_prot, &bTprFileWasRead, &top, &pbcType, &temporaryX, bReadV ? &temporaryV : nullptr, box);
+ *atoms = gmx_mtop_global_atoms(top);
x.assign(temporaryX, temporaryX + top.natoms);
sfree(temporaryX);
if (temporaryV)
"or give explicit -box command line option");
}
- add_solv(solventFileName, atoms, &top.symtab, &x, &v, pbcTypeForOutput, box, &aps,
- defaultDistance, scaleFactor, r_shell, max_sol);
+ add_solv(solventFileName, atoms, &top.symtab, &x, &v, pbcTypeForOutput, box, &aps, defaultDistance, scaleFactor, r_shell, max_sol);
/* write new configuration 1 to file confout */
confout = ftp2fn(efSTO, NFILE, fnm);
fprintf(stderr, "Writing generated configuration to %s\n", confout);
const char* outputTitle = (bProt ? *top.name : "Generated by gmx solvate");
- write_sto_conf(confout, outputTitle, atoms, as_rvec_array(x.data()),
- !v.empty() ? as_rvec_array(v.data()) : nullptr, pbcTypeForOutput, box);
+ write_sto_conf(confout,
+ outputTitle,
+ atoms,
+ as_rvec_array(x.data()),
+ !v.empty() ? as_rvec_array(v.data()) : nullptr,
+ pbcTypeForOutput,
+ box);
/* print size of generated configuration */
fprintf(stderr, "\nOutput configuration contains %d atoms in %d residues\n", atoms->nr, atoms->nres);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int nlines = get_lines(sbfile, &lines);
for (int i = 0; (i < nlines); i++)
{
- if (sscanf(lines[i], "%s%s%d%s%s%d%lf%s%s", r1buf, a1buf, &nb1, r2buf, a2buf, &nb2, &length,
- nr1buf, nr2buf)
+ if (sscanf(lines[i], "%s%s%d%s%s%d%lf%s%s", r1buf, a1buf, &nb1, r2buf, a2buf, &nb2, &length, nr1buf, nr2buf)
!= 9)
{
fprintf(stderr, "Invalid line '%s' in %s\n", lines[i], sbfile);
{
sfree(lines);
}
- fprintf(stderr, "%zu out of %d lines of %s converted successfully\n", specialBonds.size(),
- nlines, sbfile);
+ fprintf(stderr, "%zu out of %d lines of %s converted successfully\n", specialBonds.size(), nlines, sbfile);
return specialBonds;
}
static bool is_special(gmx::ArrayRef<const SpecialBond> sb, const char* res, const char* atom)
{
- for (const auto& bond : sb)
- {
- if (((strncmp(bond.firstResidue.c_str(), res, 3) == 0)
- && (gmx::equalCaseInsensitive(bond.firstAtomName, atom)))
- || ((strncmp(bond.secondResidue.c_str(), res, 3) == 0)
- && (gmx::equalCaseInsensitive(bond.secondAtomName, atom))))
- {
- return TRUE;
- }
- }
- return FALSE;
+ return std::any_of(sb.begin(), sb.end(), [res, atom](const auto& bond) {
+ return (((strncmp(bond.firstResidue.c_str(), res, 3) == 0)
+ && (gmx::equalCaseInsensitive(bond.firstAtomName, atom)))
+ || ((strncmp(bond.secondResidue.c_str(), res, 3) == 0)
+ && (gmx::equalCaseInsensitive(bond.secondAtomName, atom))));
+ });
}
static bool is_bond(gmx::ArrayRef<const SpecialBond> sb, t_atoms* pdba, int a1, int a2, real d, int* index_sb, bool* bSwap)
{
if (bVerbose)
{
- printf("Using rtp entry %s for %s %d\n", newres, *pdba->resinfo[resind].name,
+ printf("Using rtp entry %s for %s %d\n",
+ newres,
+ *pdba->resinfo[resind].name,
pdba->resinfo[resind].nr);
}
/* this used to free *resname, which messes up the symtab! */
int e = std::min(b + MAXCOL, nspec - 1);
for (int i = b; (i < e); i++)
{
- sprintf(buf, "%s%d", *pdba->resinfo[pdba->atom[specialBondAtomIdxs[i]].resind].name,
+ sprintf(buf,
+ "%s%d",
+ *pdba->resinfo[pdba->atom[specialBondAtomIdxs[i]].resind].name,
pdba->resinfo[specialBondResIdxs[i]].nr);
fprintf(stderr, "%8s", buf);
}
e = std::min(b + MAXCOL, nspec - 1);
for (int i = b; (i < e); i++)
{
- std::string buf = gmx::formatString("%s%d", *pdba->atomname[specialBondAtomIdxs[i]],
- specialBondAtomIdxs[i] + 1);
+ std::string buf = gmx::formatString(
+ "%s%d", *pdba->atomname[specialBondAtomIdxs[i]], specialBondAtomIdxs[i] + 1);
fprintf(stderr, "%8s", buf.c_str());
}
fprintf(stderr, "\n");
for (int i = b + 1; (i < nspec); i++)
{
std::string buf = gmx::formatString(
- "%s%d", *pdba->resinfo[pdba->atom[specialBondAtomIdxs[i]].resind].name,
+ "%s%d",
+ *pdba->resinfo[pdba->atom[specialBondAtomIdxs[i]].resind].name,
pdba->resinfo[specialBondResIdxs[i]].nr);
fprintf(stderr, "%8s", buf.c_str());
- buf = gmx::formatString("%s%d", *pdba->atomname[specialBondAtomIdxs[i]],
- specialBondAtomIdxs[i] + 1);
+ buf = gmx::formatString(
+ "%s%d", *pdba->atomname[specialBondAtomIdxs[i]], specialBondAtomIdxs[i] + 1);
fprintf(stderr, "%8s", buf.c_str());
int e2 = std::min(i, e);
for (int j = b; (j < e2); j++)
if (bonds.size() < specialBondAtomIdxs.size()
&& is_bond(specialBonds, pdba, ai, aj, d[i][j], &index_sb, &bSwap))
{
- fprintf(stderr, "%s %s-%d %s-%d and %s-%d %s-%d%s", bInteractive ? "Link" : "Linking",
+ fprintf(stderr,
+ "%s %s-%d %s-%d and %s-%d %s-%d%s",
+ bInteractive ? "Link" : "Linking",
*pdba->resinfo[pdba->atom[ai].resind].name,
- pdba->resinfo[specialBondResIdxs[i]].nr, *pdba->atomname[ai], ai + 1,
+ pdba->resinfo[specialBondResIdxs[i]].nr,
+ *pdba->atomname[ai],
+ ai + 1,
*pdba->resinfo[pdba->atom[aj].resind].name,
- pdba->resinfo[specialBondResIdxs[j]].nr, *pdba->atomname[aj], aj + 1,
+ pdba->resinfo[specialBondResIdxs[j]].nr,
+ *pdba->atomname[aj],
+ aj + 1,
bInteractive ? " (y/n) ?" : "...\n");
bool bDoit = bInteractive ? yesno() : true;
/* rename residues */
if (bSwap)
{
- rename_1res(pdba, specialBondResIdxs[i],
- specialBonds[index_sb].newSecondResidue.c_str(), bVerbose);
- rename_1res(pdba, specialBondResIdxs[j],
- specialBonds[index_sb].newFirstResidue.c_str(), bVerbose);
+ rename_1res(pdba,
+ specialBondResIdxs[i],
+ specialBonds[index_sb].newSecondResidue.c_str(),
+ bVerbose);
+ rename_1res(pdba,
+ specialBondResIdxs[j],
+ specialBonds[index_sb].newFirstResidue.c_str(),
+ bVerbose);
}
else
{
- rename_1res(pdba, specialBondResIdxs[i],
- specialBonds[index_sb].newFirstResidue.c_str(), bVerbose);
- rename_1res(pdba, specialBondResIdxs[j],
- specialBonds[index_sb].newSecondResidue.c_str(), bVerbose);
+ rename_1res(pdba,
+ specialBondResIdxs[i],
+ specialBonds[index_sb].newFirstResidue.c_str(),
+ bVerbose);
+ rename_1res(pdba,
+ specialBondResIdxs[j],
+ specialBonds[index_sb].newSecondResidue.c_str(),
+ bVerbose);
}
}
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "ter_db.h"
+#include <array>
#include <cctype>
#include <cstring>
#include <algorithm>
+#include <optional>
#include <string>
#include <vector>
#include "gromacs/gmxpreprocess/notset.h"
#include "gromacs/gmxpreprocess/toputil.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strdb.h"
+#include "gromacs/utility/stringtoenumvalueconverter.h"
#include "hackblock.h"
#include "resall.h"
/* use bonded types definitions in hackblock.h */
-#define ekwRepl (ebtsNR + 1)
-#define ekwAdd (ebtsNR + 2)
-#define ekwDel (ebtsNR + 3)
-#define ekwNR 3
-static const char* kw_names[ekwNR] = { "replace", "add", "delete" };
-
-static int find_kw(char* keyw)
+enum class ReplaceType : int
{
- int i;
+ Repl,
+ Add,
+ Del,
+ Count
+};
- for (i = 0; i < ebtsNR; i++)
- {
- if (gmx_strcasecmp(btsNames[i], keyw) == 0)
- {
- return i;
- }
- }
- for (i = 0; i < ekwNR; i++)
- {
- if (gmx_strcasecmp(kw_names[i], keyw) == 0)
- {
- return ebtsNR + 1 + i;
- }
- }
+static const char* enumValueToString(ReplaceType enumValue)
+{
+ constexpr gmx::EnumerationArray<ReplaceType, const char*> replaceTypeNames = { "replace",
+ "add",
+ "delete" };
+ return replaceTypeNames[enumValue];
+}
- return NOTSET;
+template<typename EnumType>
+static std::optional<EnumType> findTypeFromKeyword(char* keyw)
+{
+ gmx::StringToEnumValueConverter<EnumType, enumValueToString, gmx::StringCompareType::CaseInsensitive, gmx::StripStrings::Yes> converter;
+ return converter.valueFrom(keyw);
}
#define FATAL() gmx_fatal(FARGS, "Reading Termini Database: not enough items on line\n%s", line)
gmx_fatal(FARGS,
"Reading Termini Database: expected %d or %d items of atom data in stead of %d "
"on line\n%s",
- 3, 4, nr, line);
+ 3,
+ 4,
+ nr,
+ line);
}
i = 0;
if (!bAdd)
*nname = "";
}
}
- a->type = atype->atomTypeFromName(buf[i++]);
+ a->type = *atype->atomTypeFromName(buf[i++]);
sscanf(buf[i++], "%lf", &m);
a->m = m;
sscanf(buf[i++], "%lf", &q);
static void print_atom(FILE* out, const t_atom& a, PreprocessingAtomTypes* atype)
{
- fprintf(out, "\t%s\t%g\t%g\n", atype->atomNameFromAtomType(a.type), a.m, a.q);
+ fprintf(out, "\t%s\t%g\t%g\n", *atype->atomNameFromAtomType(a.type), a.m, a.q);
}
static void print_ter_db(const char* ff,
{
fprintf(out, "[ %s ]\n", modification.name.c_str());
- if (std::any_of(modification.hack.begin(), modification.hack.end(),
- [](const auto& mod) { return mod.type() == MoleculePatchType::Replace; }))
+ if (std::any_of(modification.hack.begin(), modification.hack.end(), [](const auto& mod) {
+ return mod.type() == MoleculePatchType::Replace;
+ }))
{
- fprintf(out, "[ %s ]\n", kw_names[ekwRepl - ebtsNR - 1]);
+ fprintf(out, "[ %s ]\n", enumValueToString(ReplaceType::Repl));
for (const auto& hack : modification.hack)
{
if (hack.type() == MoleculePatchType::Replace)
}
}
}
- if (std::any_of(modification.hack.begin(), modification.hack.end(),
- [](const auto& mod) { return mod.type() == MoleculePatchType::Add; }))
+ if (std::any_of(modification.hack.begin(), modification.hack.end(), [](const auto& mod) {
+ return mod.type() == MoleculePatchType::Add;
+ }))
{
- fprintf(out, "[ %s ]\n", kw_names[ekwAdd - ebtsNR - 1]);
+ fprintf(out, "[ %s ]\n", enumValueToString(ReplaceType::Add));
for (const auto& hack : modification.hack)
{
if (hack.type() == MoleculePatchType::Add)
}
}
}
- if (std::any_of(modification.hack.begin(), modification.hack.end(),
- [](const auto& mod) { return mod.type() == MoleculePatchType::Delete; }))
+ if (std::any_of(modification.hack.begin(), modification.hack.end(), [](const auto& mod) {
+ return mod.type() == MoleculePatchType::Delete;
+ }))
{
- fprintf(out, "[ %s ]\n", kw_names[ekwDel - ebtsNR - 1]);
+ fprintf(out, "[ %s ]\n", enumValueToString(ReplaceType::Del));
for (const auto& hack : modification.hack)
{
if (hack.type() == MoleculePatchType::Delete)
}
}
}
- for (int bt = 0; bt < ebtsNR; bt++)
+ for (auto bt : gmx::EnumerationWrapper<BondedTypes>{})
{
if (!modification.rb[bt].b.empty())
{
- fprintf(out, "[ %s ]\n", btsNames[bt]);
+ fprintf(out, "[ %s ]\n", enumValueToString(bt));
for (const auto& b : modification.rb[bt].b)
{
- for (int k = 0; k < btsNiatoms[bt]; k++)
+ for (int k = 0; k < enumValueToNumIAtoms(bt); k++)
{
fprintf(out, "%s%s", k ? "\t" : "", b.a[k].c_str());
}
FILE* in = fflib_open(fn);
- int kwnr = NOTSET;
+ std::optional<BondedTypes> btkw;
+ std::optional<ReplaceType> rtkw;
get_a_line(in, line, STRLEN);
MoleculePatchDatabase* block = nullptr;
while (!feof(in))
if (get_header(line, header))
{
/* this is a new block, or a new keyword */
- kwnr = find_kw(header);
+ btkw = findTypeFromKeyword<BondedTypes>(header);
+ rtkw = findTypeFromKeyword<ReplaceType>(header);
- if (kwnr == NOTSET)
+ if (!btkw.has_value() && !rtkw.has_value())
{
tbptr->emplace_back(MoleculePatchDatabase());
block = &tbptr->back();
line);
}
/* this is not a header, so it must be data */
- if (kwnr >= ebtsNR)
+ if (!btkw.has_value())
{
/* this is a hack: add/rename/delete atoms */
/* make space for hacks */
/* get data */
int n = 0;
- if (kwnr == ekwRepl || kwnr == ekwDel)
+ if (*rtkw == ReplaceType::Repl || *rtkw == ReplaceType::Del)
{
if (sscanf(line, "%s%n", buf, &n) != 1)
{
gmx_fatal(FARGS,
"Reading Termini Database '%s': "
"expected atom name on line\n%s",
- fn, line);
+ fn,
+ line);
}
hack->oname = buf;
/* we only replace or delete one atom at a time */
hack->nr = 1;
}
- else if (kwnr == ekwAdd)
+ else if (*rtkw == ReplaceType::Add)
{
read_ab(line, fn, hack);
get_a_line(in, line, STRLEN);
}
else
{
- gmx_fatal(FARGS, "unimplemented keyword number %d (%s:%d)", kwnr, __FILE__, __LINE__);
+ gmx_fatal(FARGS,
+ "unimplemented keyword number %d (%s:%d)",
+ static_cast<int>(*rtkw),
+ __FILE__,
+ __LINE__);
}
- if (kwnr == ekwRepl || kwnr == ekwAdd)
+ if (*rtkw == ReplaceType::Repl || *rtkw == ReplaceType::Add)
{
hack->atom.emplace_back();
- read_atom(line + n, kwnr == ekwAdd, &hack->nname, &hack->atom.back(), atype,
- &hack->cgnr);
+ read_atom(line + n, *rtkw == ReplaceType::Add, &hack->nname, &hack->atom.back(), atype, &hack->cgnr);
if (hack->nname.empty())
{
if (!hack->oname.empty())
gmx_fatal(FARGS,
"Reading Termini Database '%s': don't know which name the "
"new atom should have on line\n%s",
- fn, line);
+ fn,
+ line);
}
}
}
}
- else if (kwnr >= 0 && kwnr < ebtsNR)
+ else if (*btkw >= BondedTypes::Bonds && *btkw < BondedTypes::Count)
{
/* this is bonded data: bonds, angles, dihedrals or impropers */
int n = 0;
- block->rb[kwnr].b.emplace_back();
- BondedInteraction* newBond = &block->rb[kwnr].b.back();
- for (int j = 0; j < btsNiatoms[kwnr]; j++)
+ block->rb[*btkw].b.emplace_back();
+ BondedInteraction* newBond = &block->rb[*btkw].b.back();
+ for (int j = 0; j < enumValueToNumIAtoms(*btkw); j++)
{
int ni;
if (sscanf(line + n, "%s%n", buf, &ni) == 1)
gmx_fatal(FARGS,
"Reading Termini Database '%s': expected %d atom names (found "
"%d) on line\n%s",
- fn, btsNiatoms[kwnr], j - 1, line);
+ fn,
+ enumValueToNumIAtoms(*btkw),
+ j - 1,
+ line);
}
n += ni;
}
for (const auto& modification : tb)
{
bool bIsZwitterion = (0 == gmx_wcmatch("*ZWITTERION*", modification->name.c_str()));
- printf("%2d: %s%s\n", i, modification->name.c_str(),
+ printf("%2d: %s%s\n",
+ i,
+ modification->name.c_str(),
bIsZwitterion ? " (only use with zwitterions containing exactly one residue)" : "");
i++;
}
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -cppcoreguidelines-init-variables
+# These shall be fixed eventually, but clang-tidy's automatic fix of
+# initializing them with zeroes does not usually improve the code in
+# a meaningful way, and fixing them all manually is cumbersome.
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
+++ /dev/null
-TITLE Protein
-REMARK THIS IS A SIMULATION BOX
-CRYST1 114.390 114.390 114.390 90.00 90.00 90.00 P 1 1
-MODEL 1
-ATOM 1 P DA A 1 88.580 48.340 55.060 1.00 0.00
-ATOM 2 O1P DA A 1 89.240 47.170 54.420 1.00 0.00
-ATOM 3 O2P DA A 1 87.630 48.030 56.150 1.00 0.00
-ATOM 4 O5' DA A 1 89.820 49.230 55.720 1.00 0.00
-ATOM 5 C5' DA A 1 91.170 49.170 55.220 1.00 0.00
-ATOM 6 1H5' DA A 1 91.100 49.410 54.160 1.00 0.00
-ATOM 7 2H5' DA A 1 91.500 48.130 55.280 1.00 0.00
-ATOM 8 C4' DA A 1 92.340 50.070 55.780 1.00 0.00
-ATOM 9 H4' DA A 1 93.180 49.900 55.120 1.00 0.00
-ATOM 10 O4' DA A 1 91.950 51.410 55.600 1.00 0.00
-ATOM 11 C1' DA A 1 91.800 52.010 56.880 1.00 0.00
-ATOM 12 H1' DA A 1 92.610 52.730 57.020 1.00 0.00
-ATOM 13 N9 DA A 1 90.520 52.730 56.940 1.00 0.00
-ATOM 14 C8 DA A 1 89.230 52.250 56.980 1.00 0.00
-ATOM 15 H8 DA A 1 89.000 51.190 56.940 1.00 0.00
-ATOM 16 N7 DA A 1 88.320 53.170 57.090 1.00 0.00
-ATOM 17 C5 DA A 1 89.080 54.360 57.070 1.00 0.00
-ATOM 18 C6 DA A 1 88.790 55.740 57.110 1.00 0.00
-ATOM 19 N6 DA A 1 87.590 56.260 57.160 1.00 0.00
-ATOM 20 H61 DA A 1 87.480 57.270 57.170 1.00 0.00
-ATOM 21 H62 DA A 1 86.780 55.660 57.160 1.00 0.00
-ATOM 22 N1 DA A 1 89.780 56.640 57.080 1.00 0.00
-ATOM 23 C2 DA A 1 91.030 56.220 57.010 1.00 0.00
-ATOM 24 H2 DA A 1 91.790 56.990 57.000 1.00 0.00
-ATOM 25 N3 DA A 1 91.460 54.970 56.980 1.00 0.00
-ATOM 26 C4 DA A 1 90.420 54.090 56.990 1.00 0.00
-ATOM 27 C3' DA A 1 92.920 49.980 57.240 1.00 0.00
-ATOM 28 H3' DA A 1 92.840 48.970 57.630 1.00 0.00
-ATOM 29 C2' DA A 1 91.930 50.910 57.930 1.00 0.00
-ATOM 30 1H2' DA A 1 90.980 50.400 58.080 1.00 0.00
-ATOM 31 2H2' DA A 1 92.320 51.290 58.870 1.00 0.00
-ATOM 32 O3' DA A 1 94.290 50.480 57.330 1.00 0.00
-ATOM 33 P DA A 2 95.280 50.440 58.660 1.00 0.00
-ATOM 34 O1P DA A 2 96.640 50.120 58.160 1.00 0.00
-ATOM 35 O2P DA A 2 94.690 49.470 59.610 1.00 0.00
-ATOM 36 O5' DA A 2 95.410 51.910 59.450 1.00 0.00
-ATOM 37 C5' DA A 2 96.480 52.850 59.170 1.00 0.00
-ATOM 38 1H5' DA A 2 96.470 53.000 58.090 1.00 0.00
-ATOM 39 2H5' DA A 2 97.420 52.370 59.410 1.00 0.00
-ATOM 40 C4' DA A 2 96.520 54.310 59.780 1.00 0.00
-ATOM 41 H4' DA A 2 97.290 54.840 59.220 1.00 0.00
-ATOM 42 O4' DA A 2 95.300 54.930 59.450 1.00 0.00
-ATOM 43 C1' DA A 2 94.640 55.290 60.650 1.00 0.00
-ATOM 44 H1' DA A 2 94.670 56.380 60.760 1.00 0.00
-ATOM 45 N9 DA A 2 93.240 54.860 60.570 1.00 0.00
-ATOM 46 C8 DA A 2 92.710 53.600 60.430 1.00 0.00
-ATOM 47 H8 DA A 2 93.330 52.720 60.340 1.00 0.00
-ATOM 48 N7 DA A 2 91.400 53.560 60.400 1.00 0.00
-ATOM 49 C5 DA A 2 91.060 54.930 60.520 1.00 0.00
-ATOM 50 C6 DA A 2 89.860 55.670 60.530 1.00 0.00
-ATOM 51 N6 DA A 2 88.660 55.160 60.390 1.00 0.00
-ATOM 52 H61 DA A 2 87.870 55.800 60.350 1.00 0.00
-ATOM 53 H62 DA A 2 88.550 54.190 60.200 1.00 0.00
-ATOM 54 N1 DA A 2 89.880 56.990 60.660 1.00 0.00
-ATOM 55 C2 DA A 2 91.050 57.620 60.760 1.00 0.00
-ATOM 56 H2 DA A 2 91.010 58.690 60.850 1.00 0.00
-ATOM 57 N3 DA A 2 92.250 57.070 60.760 1.00 0.00
-ATOM 58 C4 DA A 2 92.170 55.710 60.630 1.00 0.00
-ATOM 59 C3' DA A 2 96.800 54.670 61.290 1.00 0.00
-ATOM 60 H3' DA A 2 97.410 53.920 61.770 1.00 0.00
-ATOM 61 C2' DA A 2 95.380 54.640 61.820 1.00 0.00
-ATOM 62 1H2' DA A 2 95.050 53.610 61.960 1.00 0.00
-ATOM 63 2H2' DA A 2 95.260 55.220 62.730 1.00 0.00
-ATOM 64 O3' DA A 2 97.390 56.000 61.450 1.00 0.00
-ATOM 65 P DG A 3 97.900 56.690 62.870 1.00 0.00
-ATOM 66 O1P DG A 3 99.190 57.370 62.570 1.00 0.00
-ATOM 67 O2P DG A 3 97.960 55.600 63.880 1.00 0.00
-ATOM 68 O5' DG A 3 96.870 57.870 63.450 1.00 0.00
-ATOM 69 C5' DG A 3 97.000 59.270 63.090 1.00 0.00
-ATOM 70 1H5' DG A 3 97.020 59.280 62.000 1.00 0.00
-ATOM 71 2H5' DG A 3 97.960 59.630 63.430 1.00 0.00
-ATOM 72 C4' DG A 3 95.910 60.350 63.480 1.00 0.00
-ATOM 73 H4' DG A 3 96.080 61.200 62.820 1.00 0.00
-ATOM 74 O4' DG A 3 94.670 59.820 63.110 1.00 0.00
-ATOM 75 C1' DG A 3 93.830 59.770 64.250 1.00 0.00
-ATOM 76 H1' DG A 3 93.080 60.570 64.180 1.00 0.00
-ATOM 77 N9 DG A 3 93.140 58.470 64.290 1.00 0.00
-ATOM 78 C8 DG A 3 93.640 57.200 64.400 1.00 0.00
-ATOM 79 H8 DG A 3 94.700 57.000 64.450 1.00 0.00
-ATOM 80 N7 DG A 3 92.730 56.270 64.430 1.00 0.00
-ATOM 81 C5 DG A 3 91.520 56.990 64.280 1.00 0.00
-ATOM 82 C6 DG A 3 90.140 56.590 64.190 1.00 0.00
-ATOM 83 O6 DG A 3 89.670 55.450 64.200 1.00 0.00
-ATOM 84 N1 DG A 3 89.270 57.660 64.060 1.00 0.00
-ATOM 85 H1 DG A 3 88.290 57.450 63.960 1.00 0.00
-ATOM 86 C2 DG A 3 89.660 58.960 63.990 1.00 0.00
-ATOM 87 N2 DG A 3 88.760 59.880 63.880 1.00 0.00
-ATOM 88 H21 DG A 3 87.770 59.640 63.850 1.00 0.00
-ATOM 89 H22 DG A 3 89.060 60.830 63.780 1.00 0.00
-ATOM 90 N3 DG A 3 90.910 59.370 64.090 1.00 0.00
-ATOM 91 C4 DG A 3 91.790 58.340 64.220 1.00 0.00
-ATOM 92 C3' DG A 3 95.720 60.970 64.910 1.00 0.00
-ATOM 93 H3' DG A 3 96.650 60.940 65.480 1.00 0.00
-ATOM 94 C2' DG A 3 94.700 60.010 65.480 1.00 0.00
-ATOM 95 1H2' DG A 3 95.190 59.090 65.800 1.00 0.00
-ATOM 96 2H2' DG A 3 94.120 60.450 66.300 1.00 0.00
-ATOM 97 O3' DG A 3 95.210 62.340 64.850 1.00 0.00
-ATOM 98 P DA A 4 94.880 63.320 66.140 1.00 0.00
-ATOM 99 O1P DA A 4 95.380 64.680 65.790 1.00 0.00
-ATOM 100 O2P DA A 4 95.490 62.690 67.330 1.00 0.00
-ATOM 101 O5' DA A 4 93.240 63.470 66.420 1.00 0.00
-ATOM 102 C5' DA A 4 92.390 64.390 65.680 1.00 0.00
-ATOM 103 1H5' DA A 4 92.590 64.200 64.630 1.00 0.00
-ATOM 104 2H5' DA A 4 92.720 65.410 65.890 1.00 0.00
-ATOM 105 C4' DA A 4 90.820 64.350 65.810 1.00 0.00
-ATOM 106 H4' DA A 4 90.430 64.880 64.940 1.00 0.00
-ATOM 107 O4' DA A 4 90.420 63.010 65.660 1.00 0.00
-ATOM 108 C1' DA A 4 89.600 62.630 66.750 1.00 0.00
-ATOM 109 H1' DA A 4 88.540 62.600 66.450 1.00 0.00
-ATOM 110 N9 DA A 4 90.030 61.290 67.190 1.00 0.00
-ATOM 111 C8 DA A 4 91.300 60.860 67.510 1.00 0.00
-ATOM 112 H8 DA A 4 92.140 61.540 67.510 1.00 0.00
-ATOM 113 N7 DA A 4 91.390 59.590 67.770 1.00 0.00
-ATOM 114 C5 DA A 4 90.070 59.150 67.560 1.00 0.00
-ATOM 115 C6 DA A 4 89.410 57.900 67.550 1.00 0.00
-ATOM 116 N6 DA A 4 90.020 56.750 67.720 1.00 0.00
-ATOM 117 H61 DA A 4 89.460 55.910 67.580 1.00 0.00
-ATOM 118 H62 DA A 4 91.010 56.740 67.770 1.00 0.00
-ATOM 119 N1 DA A 4 88.120 57.800 67.270 1.00 0.00
-ATOM 120 C2 DA A 4 87.430 58.910 67.020 1.00 0.00
-ATOM 121 H2 DA A 4 86.370 58.780 66.800 1.00 0.00
-ATOM 122 N3 DA A 4 87.900 60.150 67.010 1.00 0.00
-ATOM 123 C4 DA A 4 89.230 60.190 67.250 1.00 0.00
-ATOM 124 C3' DA A 4 90.030 64.920 67.030 1.00 0.00
-ATOM 125 H3' DA A 4 90.620 65.640 67.590 1.00 0.00
-ATOM 126 C2' DA A 4 89.800 63.660 67.850 1.00 0.00
-ATOM 127 1H2' DA A 4 90.690 63.440 68.440 1.00 0.00
-ATOM 128 2H2' DA A 4 88.920 63.730 68.490 1.00 0.00
-ATOM 129 O3' DA A 4 88.760 65.520 66.650 1.00 0.00
-ATOM 130 P DT A 5 87.640 66.150 67.690 1.00 0.00
-ATOM 131 O1P DT A 5 87.130 67.400 67.070 1.00 0.00
-ATOM 132 O2P DT A 5 88.340 66.310 68.990 1.00 0.00
-ATOM 133 O5' DT A 5 86.380 65.100 67.890 1.00 0.00
-ATOM 134 C5' DT A 5 85.310 64.910 66.910 1.00 0.00
-ATOM 135 1H5' DT A 5 85.810 64.770 65.950 1.00 0.00
-ATOM 136 2H5' DT A 5 84.740 65.830 66.840 1.00 0.00
-ATOM 137 C4' DT A 5 84.300 63.710 67.040 1.00 0.00
-ATOM 138 H4' DT A 5 83.870 63.540 66.050 1.00 0.00
-ATOM 139 O4' DT A 5 85.070 62.560 67.360 1.00 0.00
-ATOM 140 C1' DT A 5 84.450 61.860 68.420 1.00 0.00
-ATOM 141 H1' DT A 5 83.780 61.080 68.020 1.00 0.00
-ATOM 142 N1 DT A 5 85.510 61.280 69.270 1.00 0.00
-ATOM 143 C6 DT A 5 86.510 62.090 69.780 1.00 0.00
-ATOM 144 H6 DT A 5 86.460 63.150 69.550 1.00 0.00
-ATOM 145 C5 DT A 5 87.540 61.570 70.490 1.00 0.00
-ATOM 146 C7 DT A 5 88.610 62.490 71.040 1.00 0.00
-ATOM 147 H71 DT A 5 88.340 63.540 70.860 1.00 0.00
-ATOM 148 H72 DT A 5 88.700 62.310 72.110 1.00 0.00
-ATOM 149 H73 DT A 5 89.550 62.260 70.550 1.00 0.00
-ATOM 150 C4 DT A 5 87.630 60.130 70.710 1.00 0.00
-ATOM 151 O4 DT A 5 88.560 59.560 71.290 1.00 0.00
-ATOM 152 N3 DT A 5 86.580 59.400 70.200 1.00 0.00
-ATOM 153 H3 DT A 5 86.600 58.390 70.270 1.00 0.00
-ATOM 154 C2 DT A 5 85.520 59.900 69.480 1.00 0.00
-ATOM 155 O2 DT A 5 84.680 59.130 69.060 1.00 0.00
-ATOM 156 C3' DT A 5 83.080 63.720 68.020 1.00 0.00
-ATOM 157 H3' DT A 5 82.820 64.730 68.330 1.00 0.00
-ATOM 158 C2' DT A 5 83.620 62.900 69.180 1.00 0.00
-ATOM 159 1H2' DT A 5 84.240 63.540 69.810 1.00 0.00
-ATOM 160 2H2' DT A 5 82.840 62.430 69.770 1.00 0.00
-ATOM 161 O3' DT A 5 81.910 63.060 67.470 1.00 0.00
-ATOM 162 P DG A 6 80.460 62.930 68.240 1.00 0.00
-ATOM 163 O1P DG A 6 79.410 63.350 67.290 1.00 0.00
-ATOM 164 O2P DG A 6 80.590 63.740 69.480 1.00 0.00
-ATOM 165 O5' DG A 6 80.170 61.360 68.680 1.00 0.00
-ATOM 166 C5' DG A 6 79.700 60.350 67.750 1.00 0.00
-ATOM 167 1H5' DG A 6 80.380 60.420 66.900 1.00 0.00
-ATOM 168 2H5' DG A 6 78.710 60.630 67.390 1.00 0.00
-ATOM 169 C4' DG A 6 79.680 58.820 68.140 1.00 0.00
-ATOM 170 H4' DG A 6 79.610 58.260 67.220 1.00 0.00
-ATOM 171 O4' DG A 6 80.950 58.560 68.710 1.00 0.00
-ATOM 172 C1' DG A 6 80.740 58.160 70.050 1.00 0.00
-ATOM 173 H1' DG A 6 80.840 57.070 70.110 1.00 0.00
-ATOM 174 N9 DG A 6 81.750 58.790 70.910 1.00 0.00
-ATOM 175 C8 DG A 6 82.020 60.120 71.130 1.00 0.00
-ATOM 176 H8 DG A 6 81.420 60.900 70.680 1.00 0.00
-ATOM 177 N7 DG A 6 83.080 60.340 71.870 1.00 0.00
-ATOM 178 C5 DG A 6 83.510 59.030 72.180 1.00 0.00
-ATOM 179 C6 DG A 6 84.640 58.540 72.930 1.00 0.00
-ATOM 180 O6 DG A 6 85.540 59.170 73.480 1.00 0.00
-ATOM 181 N1 DG A 6 84.690 57.160 73.000 1.00 0.00
-ATOM 182 H1 DG A 6 85.470 56.750 73.480 1.00 0.00
-ATOM 183 C2 DG A 6 83.790 56.340 72.410 1.00 0.00
-ATOM 184 N2 DG A 6 83.920 55.050 72.580 1.00 0.00
-ATOM 185 H21 DG A 6 84.700 54.650 73.070 1.00 0.00
-ATOM 186 H22 DG A 6 83.210 54.500 72.120 1.00 0.00
-ATOM 187 N3 DG A 6 82.770 56.730 71.700 1.00 0.00
-ATOM 188 C4 DG A 6 82.680 58.090 71.620 1.00 0.00
-ATOM 189 C3' DG A 6 78.650 58.150 69.110 1.00 0.00
-ATOM 190 H3' DG A 6 77.660 58.590 69.020 1.00 0.00
-ATOM 191 C2' DG A 6 79.310 58.520 70.430 1.00 0.00
-ATOM 192 1H2' DG A 6 79.200 59.580 70.630 1.00 0.00
-ATOM 193 2H2' DG A 6 78.940 57.910 71.260 1.00 0.00
-ATOM 194 O3' DG A 6 78.590 56.700 68.950 1.00 0.00
-ATOM 195 P DG A 7 77.600 55.670 69.770 1.00 0.00
-ATOM 196 O1P DG A 7 76.890 54.820 68.790 1.00 0.00
-ATOM 197 O2P DG A 7 76.780 56.500 70.690 1.00 0.00
-ATOM 198 O5' DG A 7 78.450 54.630 70.740 1.00 0.00
-ATOM 199 C5' DG A 7 78.970 53.370 70.300 1.00 0.00
-ATOM 200 1H5' DG A 7 79.680 53.610 69.500 1.00 0.00
-ATOM 201 2H5' DG A 7 78.170 52.790 69.840 1.00 0.00
-ATOM 202 C4' DG A 7 79.730 52.440 71.320 1.00 0.00
-ATOM 203 H4' DG A 7 80.280 51.710 70.730 1.00 0.00
-ATOM 204 O4' DG A 7 80.670 53.240 72.010 1.00 0.00
-ATOM 205 C1' DG A 7 80.180 53.420 73.330 1.00 0.00
-ATOM 206 H1' DG A 7 80.830 52.850 73.980 1.00 0.00
-ATOM 207 N9 DG A 7 80.270 54.840 73.720 1.00 0.00
-ATOM 208 C8 DG A 7 79.560 55.950 73.330 1.00 0.00
-ATOM 209 H8 DG A 7 78.710 55.910 72.660 1.00 0.00
-ATOM 210 N7 DG A 7 80.010 57.070 73.830 1.00 0.00
-ATOM 211 C5 DG A 7 81.110 56.670 74.600 1.00 0.00
-ATOM 212 C6 DG A 7 82.100 57.400 75.340 1.00 0.00
-ATOM 213 O6 DG A 7 82.270 58.610 75.470 1.00 0.00
-ATOM 214 N1 DG A 7 83.020 56.580 75.970 1.00 0.00
-ATOM 215 H1 DG A 7 83.770 57.050 76.450 1.00 0.00
-ATOM 216 C2 DG A 7 83.010 55.240 75.920 1.00 0.00
-ATOM 217 N2 DG A 7 83.920 54.570 76.560 1.00 0.00
-ATOM 218 H21 DG A 7 84.670 55.070 77.030 1.00 0.00
-ATOM 219 H22 DG A 7 83.870 53.580 76.470 1.00 0.00
-ATOM 220 N3 DG A 7 82.130 54.510 75.250 1.00 0.00
-ATOM 221 C4 DG A 7 81.230 55.290 74.580 1.00 0.00
-ATOM 222 C3' DG A 7 79.000 51.650 72.460 1.00 0.00
-ATOM 223 H3' DG A 7 78.040 51.250 72.110 1.00 0.00
-ATOM 224 C2' DG A 7 78.790 52.800 73.420 1.00 0.00
-ATOM 225 1H2' DG A 7 78.020 53.480 73.060 1.00 0.00
-ATOM 226 2H2' DG A 7 78.560 52.450 74.420 1.00 0.00
-ATOM 227 O3' DG A 7 79.830 50.590 73.050 1.00 0.00
-ATOM 228 P DC A 8 79.390 49.550 74.260 1.00 0.00
-ATOM 229 O1P DC A 8 79.890 48.200 73.910 1.00 0.00
-ATOM 230 O2P DC A 8 77.940 49.690 74.490 1.00 0.00
-ATOM 231 O5' DC A 8 80.130 49.920 75.700 1.00 0.00
-ATOM 232 C5' DC A 8 81.390 49.350 76.090 1.00 0.00
-ATOM 233 1H5' DC A 8 82.090 49.610 75.300 1.00 0.00
-ATOM 234 2H5' DC A 8 81.290 48.260 76.070 1.00 0.00
-ATOM 235 C4' DC A 8 82.070 49.750 77.450 1.00 0.00
-ATOM 236 H4' DC A 8 83.090 49.370 77.400 1.00 0.00
-ATOM 237 O4' DC A 8 82.160 51.160 77.470 1.00 0.00
-ATOM 238 C1' DC A 8 81.340 51.640 78.520 1.00 0.00
-ATOM 239 H1' DC A 8 82.010 51.910 79.340 1.00 0.00
-ATOM 240 N1 DC A 8 80.590 52.850 78.080 1.00 0.00
-ATOM 241 C6 DC A 8 79.540 52.810 77.190 1.00 0.00
-ATOM 242 H6 DC A 8 79.230 51.860 76.770 1.00 0.00
-ATOM 243 C5 DC A 8 78.940 53.960 76.810 1.00 0.00
-ATOM 244 H5 DC A 8 78.120 53.950 76.100 1.00 0.00
-ATOM 245 C4 DC A 8 79.450 55.180 77.330 1.00 0.00
-ATOM 246 N4 DC A 8 78.950 56.320 76.960 1.00 0.00
-ATOM 247 H41 DC A 8 79.330 57.170 77.360 1.00 0.00
-ATOM 248 H42 DC A 8 78.270 56.380 76.240 1.00 0.00
-ATOM 249 N3 DC A 8 80.440 55.230 78.200 1.00 0.00
-ATOM 250 C2 DC A 8 81.020 54.080 78.580 1.00 0.00
-ATOM 251 O2 DC A 8 81.930 54.140 79.410 1.00 0.00
-ATOM 252 C3' DC A 8 81.520 49.340 78.860 1.00 0.00
-ATOM 253 H3' DC A 8 81.020 48.370 78.810 1.00 0.00
-ATOM 254 C2' DC A 8 80.510 50.470 79.030 1.00 0.00
-ATOM 255 1H2' DC A 8 79.640 50.290 78.400 1.00 0.00
-ATOM 256 2H2' DC A 8 80.210 50.590 80.070 1.00 0.00
-ATOM 257 O3' DC A 8 82.560 49.350 79.890 1.00 0.00
-ATOM 258 P DA A 9 82.440 48.820 81.460 1.00 0.00
-ATOM 259 O1P DA A 9 83.660 48.020 81.750 1.00 0.00
-ATOM 260 O2P DA A 9 81.150 48.100 81.600 1.00 0.00
-ATOM 261 O5' DA A 9 82.440 50.060 82.570 1.00 0.00
-ATOM 262 C5' DA A 9 83.650 50.520 83.210 1.00 0.00
-ATOM 263 1H5' DA A 9 84.350 50.720 82.390 1.00 0.00
-ATOM 264 2H5' DA A 9 84.070 49.690 83.780 1.00 0.00
-ATOM 265 C4' DA A 9 83.700 51.810 84.120 1.00 0.00
-ATOM 266 H4' DA A 9 84.750 51.990 84.300 1.00 0.00
-ATOM 267 O4' DA A 9 83.240 52.890 83.340 1.00 0.00
-ATOM 268 C1' DA A 9 82.050 53.390 83.920 1.00 0.00
-ATOM 269 H1' DA A 9 82.250 54.390 84.330 1.00 0.00
-ATOM 270 N9 DA A 9 80.990 53.510 82.900 1.00 0.00
-ATOM 271 C8 DA A 9 80.370 52.550 82.150 1.00 0.00
-ATOM 272 H8 DA A 9 80.620 51.500 82.200 1.00 0.00
-ATOM 273 N7 DA A 9 79.430 53.000 81.360 1.00 0.00
-ATOM 274 C5 DA A 9 79.470 54.390 81.610 1.00 0.00
-ATOM 275 C6 DA A 9 78.790 55.530 81.110 1.00 0.00
-ATOM 276 N6 DA A 9 77.870 55.510 80.180 1.00 0.00
-ATOM 277 H61 DA A 9 77.520 56.400 79.820 1.00 0.00
-ATOM 278 H62 DA A 9 77.630 54.650 79.730 1.00 0.00
-ATOM 279 N1 DA A 9 79.080 56.730 81.590 1.00 0.00
-ATOM 280 C2 DA A 9 80.000 56.870 82.530 1.00 0.00
-ATOM 281 H2 DA A 9 80.190 57.880 82.870 1.00 0.00
-ATOM 282 N3 DA A 9 80.720 55.910 83.090 1.00 0.00
-ATOM 283 C4 DA A 9 80.410 54.690 82.560 1.00 0.00
-ATOM 284 C3' DA A 9 83.000 51.950 85.520 1.00 0.00
-ATOM 285 H3' DA A 9 82.910 50.990 86.010 1.00 0.00
-ATOM 286 C2' DA A 9 81.650 52.460 85.070 1.00 0.00
-ATOM 287 1H2' DA A 9 81.040 51.630 84.700 1.00 0.00
-ATOM 288 2H2' DA A 9 81.130 53.010 85.850 1.00 0.00
-ATOM 289 O3' DA A 9 83.670 52.920 86.390 1.00 0.00
-ATOM 290 P DT A 10 83.250 53.280 87.960 1.00 0.00
-ATOM 291 O1P DT A 10 84.520 53.540 88.690 1.00 0.00
-ATOM 292 O2P DT A 10 82.430 52.150 88.460 1.00 0.00
-ATOM 293 O5' DT A 10 82.330 54.660 88.100 1.00 0.00
-ATOM 294 C5' DT A 10 82.920 55.980 88.350 1.00 0.00
-ATOM 295 1H5' DT A 10 83.720 56.080 87.620 1.00 0.00
-ATOM 296 2H5' DT A 10 83.380 55.960 89.330 1.00 0.00
-ATOM 297 C4' DT A 10 82.060 57.300 88.220 1.00 0.00
-ATOM 298 H4' DT A 10 82.770 58.100 88.010 1.00 0.00
-ATOM 299 O4' DT A 10 81.290 57.140 87.050 1.00 0.00
-ATOM 300 C1' DT A 10 79.960 57.510 87.310 1.00 0.00
-ATOM 301 H1' DT A 10 79.800 58.550 87.000 1.00 0.00
-ATOM 302 N1 DT A 10 79.050 56.600 86.570 1.00 0.00
-ATOM 303 C6 DT A 10 79.090 55.230 86.740 1.00 0.00
-ATOM 304 H6 DT A 10 79.790 54.820 87.450 1.00 0.00
-ATOM 305 C5 DT A 10 78.290 54.420 86.000 1.00 0.00
-ATOM 306 C7 DT A 10 78.280 52.930 86.270 1.00 0.00
-ATOM 307 H71 DT A 10 78.730 52.700 87.230 1.00 0.00
-ATOM 308 H72 DT A 10 77.240 52.590 86.260 1.00 0.00
-ATOM 309 H73 DT A 10 78.800 52.420 85.460 1.00 0.00
-ATOM 310 C4 DT A 10 77.420 54.980 84.970 1.00 0.00
-ATOM 311 O4 DT A 10 76.710 54.330 84.210 1.00 0.00
-ATOM 312 N3 DT A 10 77.410 56.350 84.910 1.00 0.00
-ATOM 313 H3 DT A 10 76.820 56.780 84.210 1.00 0.00
-ATOM 314 C2 DT A 10 78.140 57.200 85.700 1.00 0.00
-ATOM 315 O2 DT A 10 77.950 58.410 85.670 1.00 0.00
-ATOM 316 C3' DT A 10 81.120 57.870 89.340 1.00 0.00
-ATOM 317 H3' DT A 10 81.330 57.420 90.300 1.00 0.00
-ATOM 318 C2' DT A 10 79.760 57.420 88.820 1.00 0.00
-ATOM 319 1H2' DT A 10 79.570 56.400 89.140 1.00 0.00
-ATOM 320 2H2' DT A 10 78.960 58.090 89.140 1.00 0.00
-ATOM 321 O3' DT A 10 81.150 59.330 89.450 1.00 0.00
-ATOM 322 P DT A 11 80.300 60.230 90.560 1.00 0.00
-ATOM 323 O1P DT A 11 81.200 61.340 90.980 1.00 0.00
-ATOM 324 O2P DT A 11 79.890 59.300 91.630 1.00 0.00
-ATOM 325 O5' DT A 11 78.920 60.920 89.930 1.00 0.00
-ATOM 326 C5' DT A 11 78.910 62.220 89.270 1.00 0.00
-ATOM 327 1H5' DT A 11 79.740 62.220 88.570 1.00 0.00
-ATOM 328 2H5' DT A 11 79.120 62.990 90.010 1.00 0.00
-ATOM 329 C4' DT A 11 77.660 62.690 88.420 1.00 0.00
-ATOM 330 H4' DT A 11 78.040 63.390 87.680 1.00 0.00
-ATOM 331 O4' DT A 11 77.240 61.550 87.700 1.00 0.00
-ATOM 332 C1' DT A 11 75.830 61.440 87.760 1.00 0.00
-ATOM 333 H1' DT A 11 75.390 61.890 86.860 1.00 0.00
-ATOM 334 N1 DT A 11 75.500 60.000 87.860 1.00 0.00
-ATOM 335 C6 DT A 11 75.990 59.220 88.890 1.00 0.00
-ATOM 336 H6 DT A 11 76.590 59.690 89.650 1.00 0.00
-ATOM 337 C5 DT A 11 75.750 57.890 88.920 1.00 0.00
-ATOM 338 C7 DT A 11 76.210 57.090 90.120 1.00 0.00
-ATOM 339 H71 DT A 11 75.840 57.560 91.030 1.00 0.00
-ATOM 340 H72 DT A 11 75.800 56.080 90.060 1.00 0.00
-ATOM 341 H73 DT A 11 77.290 57.020 90.140 1.00 0.00
-ATOM 342 C4 DT A 11 75.030 57.240 87.820 1.00 0.00
-ATOM 343 O4 DT A 11 74.860 56.030 87.700 1.00 0.00
-ATOM 344 N3 DT A 11 74.540 58.100 86.870 1.00 0.00
-ATOM 345 H3 DT A 11 74.000 57.720 86.110 1.00 0.00
-ATOM 346 C2 DT A 11 74.680 59.460 86.870 1.00 0.00
-ATOM 347 O2 DT A 11 74.060 60.150 86.070 1.00 0.00
-ATOM 348 C3' DT A 11 76.380 63.380 89.010 1.00 0.00
-ATOM 349 H3' DT A 11 76.550 63.720 90.030 1.00 0.00
-ATOM 350 C2' DT A 11 75.380 62.230 88.990 1.00 0.00
-ATOM 351 1H2' DT A 11 75.480 61.650 89.900 1.00 0.00
-ATOM 352 2H2' DT A 11 74.350 62.580 88.860 1.00 0.00
-ATOM 353 O3' DT A 11 75.900 64.490 88.200 1.00 0.00
-ATOM 354 P DT A 12 74.550 65.400 88.520 1.00 0.00
-ATOM 355 O1P DT A 12 74.890 66.800 88.190 1.00 0.00
-ATOM 356 O2P DT A 12 74.200 65.130 89.940 1.00 0.00
-ATOM 357 O5' DT A 12 73.270 64.940 87.570 1.00 0.00
-ATOM 358 C5' DT A 12 73.100 65.340 86.180 1.00 0.00
-ATOM 359 1H5' DT A 12 74.070 65.190 85.700 1.00 0.00
-ATOM 360 2H5' DT A 12 72.900 66.410 86.140 1.00 0.00
-ATOM 361 C4' DT A 12 72.070 64.600 85.250 1.00 0.00
-ATOM 362 H4' DT A 12 72.420 64.730 84.220 1.00 0.00
-ATOM 363 O4' DT A 12 72.190 63.230 85.550 1.00 0.00
-ATOM 364 C1' DT A 12 70.900 62.650 85.640 1.00 0.00
-ATOM 365 H1' DT A 12 70.600 62.230 84.670 1.00 0.00
-ATOM 366 N1 DT A 12 70.980 61.600 86.690 1.00 0.00
-ATOM 367 C6 DT A 12 71.450 61.910 87.950 1.00 0.00
-ATOM 368 H6 DT A 12 71.690 62.940 88.160 1.00 0.00
-ATOM 369 C5 DT A 12 71.670 60.930 88.860 1.00 0.00
-ATOM 370 C7 DT A 12 72.160 61.300 90.250 1.00 0.00
-ATOM 371 H71 DT A 12 72.200 62.380 90.370 1.00 0.00
-ATOM 372 H72 DT A 12 71.480 60.860 90.980 1.00 0.00
-ATOM 373 H73 DT A 12 73.150 60.860 90.390 1.00 0.00
-ATOM 374 C4 DT A 12 71.450 59.530 88.510 1.00 0.00
-ATOM 375 O4 DT A 12 71.720 58.580 89.250 1.00 0.00
-ATOM 376 N3 DT A 12 70.920 59.330 87.260 1.00 0.00
-ATOM 377 H3 DT A 12 70.690 58.390 86.970 1.00 0.00
-ATOM 378 C2 DT A 12 70.630 60.300 86.340 1.00 0.00
-ATOM 379 O2 DT A 12 70.070 60.000 85.300 1.00 0.00
-ATOM 380 C3' DT A 12 70.540 64.930 85.200 1.00 0.00
-ATOM 381 H3' DT A 12 70.330 65.890 85.670 1.00 0.00
-ATOM 382 C2' DT A 12 69.960 63.790 86.020 1.00 0.00
-ATOM 383 1H2' DT A 12 70.010 64.030 87.080 1.00 0.00
-ATOM 384 2H2' DT A 12 68.930 63.550 85.740 1.00 0.00
-ATOM 385 O3' DT A 12 70.000 64.900 83.860 1.00 0.00
-ATOM 386 P DC A 13 68.420 65.200 83.480 1.00 0.00
-ATOM 387 O1P DC A 13 68.420 66.140 82.330 1.00 0.00
-ATOM 388 O2P DC A 13 67.790 65.680 84.730 1.00 0.00
-ATOM 389 O5' DC A 13 67.660 63.800 83.020 1.00 0.00
-ATOM 390 C5' DC A 13 67.850 63.130 81.740 1.00 0.00
-ATOM 391 1H5' DC A 13 68.920 63.080 81.580 1.00 0.00
-ATOM 392 2H5' DC A 13 67.440 63.760 80.950 1.00 0.00
-ATOM 393 C4' DC A 13 67.330 61.650 81.530 1.00 0.00
-ATOM 394 H4' DC A 13 67.840 61.250 80.660 1.00 0.00
-ATOM 395 O4' DC A 13 67.780 60.930 82.670 1.00 0.00
-ATOM 396 C1' DC A 13 66.670 60.270 83.250 1.00 0.00
-ATOM 397 H1' DC A 13 66.650 59.230 82.900 1.00 0.00
-ATOM 398 N1 DC A 13 66.800 60.340 84.730 1.00 0.00
-ATOM 399 C6 DC A 13 66.910 61.560 85.360 1.00 0.00
-ATOM 400 H6 DC A 13 66.870 62.450 84.760 1.00 0.00
-ATOM 401 C5 DC A 13 67.110 61.620 86.700 1.00 0.00
-ATOM 402 H5 DC A 13 67.200 62.570 87.180 1.00 0.00
-ATOM 403 C4 DC A 13 67.200 60.380 87.370 1.00 0.00
-ATOM 404 N4 DC A 13 67.480 60.330 88.640 1.00 0.00
-ATOM 405 H41 DC A 13 67.570 59.380 89.000 1.00 0.00
-ATOM 406 H42 DC A 13 67.580 61.150 89.170 1.00 0.00
-ATOM 407 N3 DC A 13 67.080 59.210 86.800 1.00 0.00
-ATOM 408 C2 DC A 13 66.850 59.160 85.470 1.00 0.00
-ATOM 409 O2 DC A 13 66.660 58.060 84.970 1.00 0.00
-ATOM 410 C3' DC A 13 65.830 61.270 81.320 1.00 0.00
-ATOM 411 H3' DC A 13 65.260 62.090 80.890 1.00 0.00
-ATOM 412 C2' DC A 13 65.430 60.990 82.750 1.00 0.00
-ATOM 413 1H2' DC A 13 65.250 61.930 83.270 1.00 0.00
-ATOM 414 2H2' DC A 13 64.570 60.340 82.810 1.00 0.00
-ATOM 415 O3' DC A 13 65.620 60.050 80.550 1.00 0.00
-ATOM 416 P DT A 14 64.130 59.420 80.190 1.00 0.00
-ATOM 417 O1P DT A 14 64.110 59.100 78.740 1.00 0.00
-ATOM 418 O2P DT A 14 63.130 60.400 80.690 1.00 0.00
-ATOM 419 O5' DT A 14 63.860 58.000 81.000 1.00 0.00
-ATOM 420 C5' DT A 14 64.360 56.720 80.560 1.00 0.00
-ATOM 421 1H5' DT A 14 65.440 56.850 80.460 1.00 0.00
-ATOM 422 2H5' DT A 14 63.980 56.530 79.550 1.00 0.00
-ATOM 423 C4' DT A 14 64.140 55.430 81.440 1.00 0.00
-ATOM 424 H4' DT A 14 64.900 54.710 81.120 1.00 0.00
-ATOM 425 O4' DT A 14 64.420 55.790 82.780 1.00 0.00
-ATOM 426 C1' DT A 14 63.220 55.680 83.520 1.00 0.00
-ATOM 427 H1' DT A 14 63.270 54.750 84.090 1.00 0.00
-ATOM 428 N1 DT A 14 63.130 56.830 84.460 1.00 0.00
-ATOM 429 C6 DT A 14 62.830 58.120 84.050 1.00 0.00
-ATOM 430 H6 DT A 14 62.560 58.300 83.020 1.00 0.00
-ATOM 431 C5 DT A 14 62.920 59.160 84.920 1.00 0.00
-ATOM 432 C7 DT A 14 62.540 60.560 84.480 1.00 0.00
-ATOM 433 H71 DT A 14 62.280 60.580 83.420 1.00 0.00
-ATOM 434 H72 DT A 14 61.680 60.890 85.070 1.00 0.00
-ATOM 435 H73 DT A 14 63.360 61.240 84.670 1.00 0.00
-ATOM 436 C4 DT A 14 63.410 58.950 86.280 1.00 0.00
-ATOM 437 O4 DT A 14 63.630 59.820 87.120 1.00 0.00
-ATOM 438 N3 DT A 14 63.620 57.630 86.610 1.00 0.00
-ATOM 439 H3 DT A 14 63.880 57.420 87.550 1.00 0.00
-ATOM 440 C2 DT A 14 63.430 56.550 85.790 1.00 0.00
-ATOM 441 O2 DT A 14 63.500 55.430 86.280 1.00 0.00
-ATOM 442 C3' DT A 14 62.790 54.650 81.500 1.00 0.00
-ATOM 443 H3' DT A 14 62.280 54.660 80.540 1.00 0.00
-ATOM 444 C2' DT A 14 62.070 55.520 82.520 1.00 0.00
-ATOM 445 1H2' DT A 14 61.790 56.470 82.070 1.00 0.00
-ATOM 446 2H2' DT A 14 61.210 55.030 82.950 1.00 0.00
-ATOM 447 O3' DT A 14 62.950 53.280 81.990 1.00 0.00
-ATOM 448 P DA A 15 61.750 52.150 82.120 1.00 0.00
-ATOM 449 O1P DA A 15 62.210 50.900 81.440 1.00 0.00
-ATOM 450 O2P DA A 15 60.490 52.750 81.650 1.00 0.00
-ATOM 451 O5' DA A 15 61.490 51.720 83.690 1.00 0.00
-ATOM 452 C5' DA A 15 62.190 50.650 84.340 1.00 0.00
-ATOM 453 1H5' DA A 15 63.250 50.910 84.280 1.00 0.00
-ATOM 454 2H5' DA A 15 62.050 49.740 83.760 1.00 0.00
-ATOM 455 C4' DA A 15 61.890 50.330 85.850 1.00 0.00
-ATOM 456 H4' DA A 15 62.670 49.650 86.180 1.00 0.00
-ATOM 457 O4' DA A 15 62.030 51.530 86.580 1.00 0.00
-ATOM 458 C1' DA A 15 60.740 51.960 86.980 1.00 0.00
-ATOM 459 H1' DA A 15 60.690 51.860 88.070 1.00 0.00
-ATOM 460 N9 DA A 15 60.540 53.380 86.640 1.00 0.00
-ATOM 461 C8 DA A 15 60.290 54.000 85.440 1.00 0.00
-ATOM 462 H8 DA A 15 60.210 53.470 84.500 1.00 0.00
-ATOM 463 N7 DA A 15 60.170 55.300 85.520 1.00 0.00
-ATOM 464 C5 DA A 15 60.380 55.550 86.880 1.00 0.00
-ATOM 465 C6 DA A 15 60.450 56.700 87.690 1.00 0.00
-ATOM 466 N6 DA A 15 60.350 57.940 87.240 1.00 0.00
-ATOM 467 H61 DA A 15 60.410 58.710 87.890 1.00 0.00
-ATOM 468 H62 DA A 15 60.080 58.060 86.280 1.00 0.00
-ATOM 469 N1 DA A 15 60.640 56.600 89.000 1.00 0.00
-ATOM 470 C2 DA A 15 60.760 55.390 89.540 1.00 0.00
-ATOM 471 H2 DA A 15 60.900 55.360 90.610 1.00 0.00
-ATOM 472 N3 DA A 15 60.730 54.220 88.920 1.00 0.00
-ATOM 473 C4 DA A 15 60.570 54.380 87.570 1.00 0.00
-ATOM 474 C3' DA A 15 60.530 49.720 86.330 1.00 0.00
-ATOM 475 H3' DA A 15 60.120 49.030 85.580 1.00 0.00
-ATOM 476 C2' DA A 15 59.710 51.000 86.370 1.00 0.00
-ATOM 477 1H2' DA A 15 59.440 51.320 85.360 1.00 0.00
-ATOM 478 2H2' DA A 15 58.830 50.890 86.990 1.00 0.00
-ATOM 479 O3' DA A 15 60.620 49.090 87.640 1.00 0.00
-ATOM 480 P DC A 16 59.410 48.300 88.450 1.00 0.00
-ATOM 481 O1P DC A 16 60.010 47.110 89.110 1.00 0.00
-ATOM 482 O2P DC A 16 58.320 48.020 87.480 1.00 0.00
-ATOM 483 O5' DC A 16 58.760 49.210 89.670 1.00 0.00
-ATOM 484 C5' DC A 16 59.320 49.230 91.000 1.00 0.00
-ATOM 485 1H5' DC A 16 60.360 49.510 90.880 1.00 0.00
-ATOM 486 2H5' DC A 16 59.300 48.220 91.380 1.00 0.00
-ATOM 487 C4' DC A 16 58.740 50.190 92.100 1.00 0.00
-ATOM 488 H4' DC A 16 59.430 50.140 92.940 1.00 0.00
-ATOM 489 O4' DC A 16 58.820 51.490 91.580 1.00 0.00
-ATOM 490 C1' DC A 16 57.530 52.060 91.560 1.00 0.00
-ATOM 491 H1' DC A 16 57.440 52.710 92.430 1.00 0.00
-ATOM 492 N1 DC A 16 57.360 52.860 90.310 1.00 0.00
-ATOM 493 C6 DC A 16 57.430 52.300 89.060 1.00 0.00
-ATOM 494 H6 DC A 16 57.610 51.240 88.960 1.00 0.00
-ATOM 495 C5 DC A 16 57.330 53.100 87.960 1.00 0.00
-ATOM 496 H5 DC A 16 57.400 52.680 86.970 1.00 0.00
-ATOM 497 C4 DC A 16 57.190 54.500 88.170 1.00 0.00
-ATOM 498 N4 DC A 16 57.180 55.310 87.160 1.00 0.00
-ATOM 499 H41 DC A 16 57.070 56.310 87.350 1.00 0.00
-ATOM 500 H42 DC A 16 57.340 55.000 86.230 1.00 0.00
-ATOM 501 N3 DC A 16 57.100 55.030 89.370 1.00 0.00
-ATOM 502 C2 DC A 16 57.170 54.240 90.450 1.00 0.00
-ATOM 503 O2 DC A 16 57.040 54.740 91.560 1.00 0.00
-ATOM 504 C3' DC A 16 57.300 50.040 92.720 1.00 0.00
-ATOM 505 H3' DC A 16 56.960 49.010 92.670 1.00 0.00
-ATOM 506 C2' DC A 16 56.540 50.910 91.730 1.00 0.00
-ATOM 507 1H2' DC A 16 56.380 50.370 90.800 1.00 0.00
-ATOM 508 2H2' DC A 16 55.600 51.250 92.160 1.00 0.00
-ATOM 509 O3' DC A 16 57.200 50.560 94.080 1.00 0.00
-ATOM 510 P DC A 17 55.880 50.460 95.080 1.00 0.00
-ATOM 511 O1P DC A 17 56.400 50.120 96.440 1.00 0.00
-ATOM 512 O2P DC A 17 54.950 49.480 94.480 1.00 0.00
-ATOM 513 O5' DC A 17 55.070 51.900 95.250 1.00 0.00
-ATOM 514 C5' DC A 17 55.360 52.870 96.290 1.00 0.00
-ATOM 515 1H5' DC A 17 56.440 53.020 96.250 1.00 0.00
-ATOM 516 2H5' DC A 17 55.140 52.410 97.250 1.00 0.00
-ATOM 517 C4' DC A 17 54.730 54.310 96.280 1.00 0.00
-ATOM 518 H4' DC A 17 55.340 54.910 96.960 1.00 0.00
-ATOM 519 O4' DC A 17 54.950 54.830 94.990 1.00 0.00
-ATOM 520 C1' DC A 17 53.710 55.200 94.420 1.00 0.00
-ATOM 521 H1' DC A 17 53.610 56.290 94.520 1.00 0.00
-ATOM 522 N1 DC A 17 53.690 54.820 92.990 1.00 0.00
-ATOM 523 C6 DC A 17 53.830 53.520 92.570 1.00 0.00
-ATOM 524 H6 DC A 17 53.960 52.740 93.310 1.00 0.00
-ATOM 525 C5 DC A 17 53.840 53.220 91.250 1.00 0.00
-ATOM 526 H5 DC A 17 53.960 52.210 90.900 1.00 0.00
-ATOM 527 C4 DC A 17 53.730 54.320 90.340 1.00 0.00
-ATOM 528 N4 DC A 17 53.840 54.120 89.070 1.00 0.00
-ATOM 529 H41 DC A 17 53.850 54.970 88.490 1.00 0.00
-ATOM 530 H42 DC A 17 54.080 53.240 88.680 1.00 0.00
-ATOM 531 N3 DC A 17 53.580 55.560 90.740 1.00 0.00
-ATOM 532 C2 DC A 17 53.550 55.840 92.050 1.00 0.00
-ATOM 533 O2 DC A 17 53.400 57.000 92.410 1.00 0.00
-ATOM 534 C3' DC A 17 53.240 54.670 96.640 1.00 0.00
-ATOM 535 H3' DC A 17 52.810 53.930 97.320 1.00 0.00
-ATOM 536 C2' DC A 17 52.610 54.560 95.260 1.00 0.00
-ATOM 537 1H2' DC A 17 52.470 53.510 94.990 1.00 0.00
-ATOM 538 2H2' DC A 17 51.680 55.110 95.180 1.00 0.00
-ATOM 539 O3' DC A 17 53.090 56.010 97.190 1.00 0.00
-ATOM 540 P DG A 18 51.690 56.700 97.770 1.00 0.00
-ATOM 541 O1P DG A 18 52.040 57.350 99.060 1.00 0.00
-ATOM 542 O2P DG A 18 50.680 55.620 97.840 1.00 0.00
-ATOM 543 O5' DG A 18 51.080 57.900 96.790 1.00 0.00
-ATOM 544 C5' DG A 18 51.460 59.300 96.920 1.00 0.00
-ATOM 545 1H5' DG A 18 52.550 59.300 96.930 1.00 0.00
-ATOM 546 2H5' DG A 18 51.140 59.650 97.900 1.00 0.00
-ATOM 547 C4' DG A 18 51.050 60.380 95.850 1.00 0.00
-ATOM 548 H4' DG A 18 51.710 61.230 96.010 1.00 0.00
-ATOM 549 O4' DG A 18 51.390 59.850 94.600 1.00 0.00
-ATOM 550 C1' DG A 18 50.220 59.780 93.800 1.00 0.00
-ATOM 551 H1' DG A 18 50.270 60.570 93.040 1.00 0.00
-ATOM 552 N9 DG A 18 50.160 58.470 93.130 1.00 0.00
-ATOM 553 C8 DG A 18 50.100 57.200 93.650 1.00 0.00
-ATOM 554 H8 DG A 18 50.120 57.020 94.710 1.00 0.00
-ATOM 555 N7 DG A 18 50.040 56.260 92.750 1.00 0.00
-ATOM 556 C5 DG A 18 50.100 56.970 91.530 1.00 0.00
-ATOM 557 C6 DG A 18 50.130 56.550 90.150 1.00 0.00
-ATOM 558 O6 DG A 18 50.100 55.410 89.700 1.00 0.00
-ATOM 559 N1 DG A 18 50.200 57.620 89.260 1.00 0.00
-ATOM 560 H1 DG A 18 50.300 57.400 88.280 1.00 0.00
-ATOM 561 C2 DG A 18 50.240 58.920 89.630 1.00 0.00
-ATOM 562 N2 DG A 18 50.330 59.840 88.730 1.00 0.00
-ATOM 563 H21 DG A 18 50.430 59.580 87.740 1.00 0.00
-ATOM 564 H22 DG A 18 50.470 60.790 89.010 1.00 0.00
-ATOM 565 N3 DG A 18 50.170 59.350 90.890 1.00 0.00
-ATOM 566 C4 DG A 18 50.140 58.320 91.780 1.00 0.00
-ATOM 567 C3' DG A 18 49.610 61.000 95.700 1.00 0.00
-ATOM 568 H3' DG A 18 49.070 60.970 96.640 1.00 0.00
-ATOM 569 C2' DG A 18 49.020 60.030 94.700 1.00 0.00
-ATOM 570 1H2' DG A 18 48.710 59.110 95.200 1.00 0.00
-ATOM 571 2H2' DG A 18 48.190 60.460 94.140 1.00 0.00
-ATOM 572 O3' DG A 18 49.630 62.360 95.160 1.00 0.00
-ATOM 573 P DT A 19 48.300 63.300 94.840 1.00 0.00
-ATOM 574 O1P DT A 19 48.620 64.670 95.300 1.00 0.00
-ATOM 575 O2P DT A 19 47.150 62.650 95.500 1.00 0.00
-ATOM 576 O5' DT A 19 47.970 63.390 93.210 1.00 0.00
-ATOM 577 C5' DT A 19 48.630 64.320 92.310 1.00 0.00
-ATOM 578 1H5' DT A 19 49.700 64.220 92.500 1.00 0.00
-ATOM 579 2H5' DT A 19 48.360 65.340 92.590 1.00 0.00
-ATOM 580 C4' DT A 19 48.470 64.190 90.740 1.00 0.00
-ATOM 581 H4' DT A 19 49.360 64.660 90.310 1.00 0.00
-ATOM 582 O4' DT A 19 48.560 62.820 90.430 1.00 0.00
-ATOM 583 C1' DT A 19 47.540 62.470 89.520 1.00 0.00
-ATOM 584 H1' DT A 19 47.930 62.480 88.490 1.00 0.00
-ATOM 585 N1 DT A 19 47.050 61.120 89.880 1.00 0.00
-ATOM 586 C6 DT A 19 46.630 60.850 91.170 1.00 0.00
-ATOM 587 H6 DT A 19 46.650 61.650 91.890 1.00 0.00
-ATOM 588 C5 DT A 19 46.260 59.590 91.520 1.00 0.00
-ATOM 589 C7 DT A 19 45.760 59.330 92.930 1.00 0.00
-ATOM 590 H71 DT A 19 45.500 60.270 93.420 1.00 0.00
-ATOM 591 H72 DT A 19 44.880 58.690 92.870 1.00 0.00
-ATOM 592 H73 DT A 19 46.540 58.810 93.490 1.00 0.00
-ATOM 593 C4 DT A 19 46.330 58.490 90.560 1.00 0.00
-ATOM 594 O4 DT A 19 46.060 57.320 90.810 1.00 0.00
-ATOM 595 N3 DT A 19 46.710 58.870 89.300 1.00 0.00
-ATOM 596 H3 DT A 19 46.820 58.150 88.590 1.00 0.00
-ATOM 597 C2 DT A 19 47.050 60.130 88.890 1.00 0.00
-ATOM 598 O2 DT A 19 47.310 60.360 87.720 1.00 0.00
-ATOM 599 C3' DT A 19 47.270 64.780 89.930 1.00 0.00
-ATOM 600 H3' DT A 19 46.700 65.490 90.520 1.00 0.00
-ATOM 601 C2' DT A 19 46.450 63.530 89.660 1.00 0.00
-ATOM 602 1H2' DT A 19 45.800 63.320 90.520 1.00 0.00
-ATOM 603 2H2' DT A 19 45.850 63.600 88.760 1.00 0.00
-ATOM 604 O3' DT A 19 47.680 65.390 88.680 1.00 0.00
-ATOM 605 P DA A 20 46.670 66.080 87.570 1.00 0.00
-ATOM 606 O1P DA A 20 47.300 67.350 87.130 1.00 0.00
-ATOM 607 O2P DA A 20 45.350 66.220 88.250 1.00 0.00
-ATOM 608 O5' DA A 20 46.480 65.090 86.250 1.00 0.00
-ATOM 609 C5' DA A 20 47.470 64.970 85.190 1.00 0.00
-ATOM 610 1H5' DA A 20 48.440 64.840 85.680 1.00 0.00
-ATOM 611 2H5' DA A 20 47.520 65.910 84.640 1.00 0.00
-ATOM 612 C4' DA A 20 47.400 63.790 84.140 1.00 0.00
-ATOM 613 H4' DA A 20 48.390 63.680 83.700 1.00 0.00
-ATOM 614 O4' DA A 20 47.140 62.630 84.890 1.00 0.00
-ATOM 615 C1' DA A 20 46.030 61.960 84.340 1.00 0.00
-ATOM 616 H1' DA A 20 46.370 61.140 83.670 1.00 0.00
-ATOM 617 N9 DA A 20 45.230 61.430 85.440 1.00 0.00
-ATOM 618 C8 DA A 20 44.710 62.110 86.520 1.00 0.00
-ATOM 619 H8 DA A 20 44.840 63.180 86.620 1.00 0.00
-ATOM 620 N7 DA A 20 44.080 61.360 87.390 1.00 0.00
-ATOM 621 C5 DA A 20 44.240 60.080 86.830 1.00 0.00
-ATOM 622 C6 DA A 20 43.910 58.770 87.220 1.00 0.00
-ATOM 623 N6 DA A 20 43.310 58.470 88.350 1.00 0.00
-ATOM 624 H61 DA A 20 43.150 57.490 88.550 1.00 0.00
-ATOM 625 H62 DA A 20 43.040 59.230 88.940 1.00 0.00
-ATOM 626 N1 DA A 20 44.220 57.710 86.480 1.00 0.00
-ATOM 627 C2 DA A 20 44.840 57.910 85.320 1.00 0.00
-ATOM 628 H2 DA A 20 45.070 57.040 84.730 1.00 0.00
-ATOM 629 N3 DA A 20 45.230 59.080 84.830 1.00 0.00
-ATOM 630 C4 DA A 20 44.910 60.120 85.640 1.00 0.00
-ATOM 631 C3' DA A 20 46.400 63.770 82.930 1.00 0.00
-ATOM 632 H3' DA A 20 46.100 64.770 82.640 1.00 0.00
-ATOM 633 C2' DA A 20 45.250 62.990 83.530 1.00 0.00
-ATOM 634 1H2' DA A 20 44.660 63.640 84.180 1.00 0.00
-ATOM 635 2H2' DA A 20 44.610 62.510 82.790 1.00 0.00
-ATOM 636 O3' DA A 20 46.930 63.050 81.780 1.00 0.00
-ATOM 637 P DA A 21 46.130 62.860 80.350 1.00 0.00
-ATOM 638 O1P DA A 21 47.050 63.280 79.270 1.00 0.00
-ATOM 639 O2P DA A 21 44.870 63.620 80.480 1.00 0.00
-ATOM 640 O5' DA A 21 45.730 61.260 80.100 1.00 0.00
-ATOM 641 C5' DA A 21 46.670 60.260 79.610 1.00 0.00
-ATOM 642 1H5' DA A 21 47.550 60.340 80.250 1.00 0.00
-ATOM 643 2H5' DA A 21 46.980 60.530 78.610 1.00 0.00
-ATOM 644 C4' DA A 21 46.270 58.730 79.620 1.00 0.00
-ATOM 645 H4' DA A 21 47.200 58.160 79.580 1.00 0.00
-ATOM 646 O4' DA A 21 45.670 58.480 80.880 1.00 0.00
-ATOM 647 C1' DA A 21 44.330 58.070 80.650 1.00 0.00
-ATOM 648 H1' DA A 21 44.270 56.990 80.770 1.00 0.00
-ATOM 649 N9 DA A 21 43.460 58.740 81.620 1.00 0.00
-ATOM 650 C8 DA A 21 43.190 60.080 81.780 1.00 0.00
-ATOM 651 H8 DA A 21 43.610 60.830 81.130 1.00 0.00
-ATOM 652 N7 DA A 21 42.400 60.360 82.800 1.00 0.00
-ATOM 653 C5 DA A 21 42.180 59.080 83.330 1.00 0.00
-ATOM 654 C6 DA A 21 41.500 58.580 84.460 1.00 0.00
-ATOM 655 N6 DA A 21 40.880 59.350 85.330 1.00 0.00
-ATOM 656 H61 DA A 21 40.450 58.920 86.140 1.00 0.00
-ATOM 657 H62 DA A 21 40.880 60.330 85.140 1.00 0.00
-ATOM 658 N1 DA A 21 41.450 57.280 84.750 1.00 0.00
-ATOM 659 C2 DA A 21 42.070 56.440 83.920 1.00 0.00
-ATOM 660 H2 DA A 21 42.010 55.390 84.160 1.00 0.00
-ATOM 661 N3 DA A 21 42.760 56.750 82.840 1.00 0.00
-ATOM 662 C4 DA A 21 42.790 58.090 82.610 1.00 0.00
-ATOM 663 C3' DA A 21 45.320 58.060 78.570 1.00 0.00
-ATOM 664 H3' DA A 21 45.440 58.500 77.580 1.00 0.00
-ATOM 665 C2' DA A 21 43.990 58.420 79.200 1.00 0.00
-ATOM 666 1H2' DA A 21 43.790 59.480 79.070 1.00 0.00
-ATOM 667 2H2' DA A 21 43.170 57.810 78.820 1.00 0.00
-ATOM 668 O3' DA A 21 45.470 56.600 78.510 1.00 0.00
-ATOM 669 P DA A 22 44.650 55.600 77.480 1.00 0.00
-ATOM 670 O1P DA A 22 45.630 54.730 76.800 1.00 0.00
-ATOM 671 O2P DA A 22 43.800 56.470 76.630 1.00 0.00
-ATOM 672 O5' DA A 22 43.620 54.590 78.290 1.00 0.00
-ATOM 673 C5' DA A 22 44.000 53.290 78.790 1.00 0.00
-ATOM 674 1H5' DA A 22 44.820 53.470 79.490 1.00 0.00
-ATOM 675 2H5' DA A 22 44.410 52.710 77.960 1.00 0.00
-ATOM 676 C4' DA A 22 42.950 52.400 79.550 1.00 0.00
-ATOM 677 H4' DA A 22 43.530 51.630 80.070 1.00 0.00
-ATOM 678 O4' DA A 22 42.340 53.210 80.530 1.00 0.00
-ATOM 679 C1' DA A 22 41.000 53.450 80.120 1.00 0.00
-ATOM 680 H1' DA A 22 40.350 52.900 80.810 1.00 0.00
-ATOM 681 N9 DA A 22 40.690 54.880 80.240 1.00 0.00
-ATOM 682 C8 DA A 22 41.080 55.960 79.470 1.00 0.00
-ATOM 683 H8 DA A 22 41.700 55.870 78.590 1.00 0.00
-ATOM 684 N7 DA A 22 40.650 57.120 79.910 1.00 0.00
-ATOM 685 C5 DA A 22 39.910 56.750 81.040 1.00 0.00
-ATOM 686 C6 DA A 22 39.180 57.450 82.030 1.00 0.00
-ATOM 687 N6 DA A 22 39.080 58.760 82.080 1.00 0.00
-ATOM 688 H61 DA A 22 38.560 59.190 82.820 1.00 0.00
-ATOM 689 H62 DA A 22 39.570 59.270 81.370 1.00 0.00
-ATOM 690 N1 DA A 22 38.570 56.810 83.020 1.00 0.00
-ATOM 691 C2 DA A 22 38.660 55.490 83.060 1.00 0.00
-ATOM 692 H2 DA A 22 38.140 55.000 83.880 1.00 0.00
-ATOM 693 N3 DA A 22 39.290 54.690 82.230 1.00 0.00
-ATOM 694 C4 DA A 22 39.920 55.400 81.240 1.00 0.00
-ATOM 695 C3' DA A 22 41.760 51.660 78.850 1.00 0.00
-ATOM 696 H3' DA A 22 42.050 51.290 77.870 1.00 0.00
-ATOM 697 C2' DA A 22 40.820 52.850 78.730 1.00 0.00
-ATOM 698 1H2' DA A 22 41.160 53.540 77.960 1.00 0.00
-ATOM 699 2H2' DA A 22 39.790 52.550 78.550 1.00 0.00
-ATOM 700 O3' DA A 22 41.190 50.590 79.670 1.00 0.00
-ATOM 701 P DG A 23 39.990 49.540 79.240 1.00 0.00
-ATOM 702 O1P DG A 23 40.380 48.180 79.720 1.00 0.00
-ATOM 703 O2P DG A 23 39.740 49.680 77.790 1.00 0.00
-ATOM 704 O5' DG A 23 38.550 49.850 80.010 1.00 0.00
-ATOM 705 C5' DG A 23 38.220 49.260 81.280 1.00 0.00
-ATOM 706 1H5' DG A 23 39.000 49.590 81.970 1.00 0.00
-ATOM 707 2H5' DG A 23 38.310 48.180 81.180 1.00 0.00
-ATOM 708 C4' DG A 23 36.850 49.560 82.000 1.00 0.00
-ATOM 709 H4' DG A 23 36.930 49.090 82.980 1.00 0.00
-ATOM 710 O4' DG A 23 36.790 50.950 82.230 1.00 0.00
-ATOM 711 C1' DG A 23 35.790 51.480 81.380 1.00 0.00
-ATOM 712 H1' DG A 23 34.960 51.800 82.020 1.00 0.00
-ATOM 713 N9 DG A 23 36.290 52.670 80.670 1.00 0.00
-ATOM 714 C8 DG A 23 37.150 52.810 79.610 1.00 0.00
-ATOM 715 H8 DG A 23 37.630 51.970 79.130 1.00 0.00
-ATOM 716 N7 DG A 23 37.350 54.050 79.250 1.00 0.00
-ATOM 717 C5 DG A 23 36.580 54.790 80.160 1.00 0.00
-ATOM 718 C6 DG A 23 36.380 56.200 80.360 1.00 0.00
-ATOM 719 O6 DG A 23 36.860 57.170 79.780 1.00 0.00
-ATOM 720 N1 DG A 23 35.490 56.490 81.370 1.00 0.00
-ATOM 721 H1 DG A 23 35.330 57.460 81.550 1.00 0.00
-ATOM 722 C2 DG A 23 34.880 55.560 82.130 1.00 0.00
-ATOM 723 N2 DG A 23 34.020 55.940 83.030 1.00 0.00
-ATOM 724 H21 DG A 23 33.880 56.940 83.190 1.00 0.00
-ATOM 725 H22 DG A 23 33.590 55.220 83.560 1.00 0.00
-ATOM 726 N3 DG A 23 35.030 54.250 82.010 1.00 0.00
-ATOM 727 C4 DG A 23 35.910 53.940 81.010 1.00 0.00
-ATOM 728 C3' DG A 23 35.440 49.180 81.440 1.00 0.00
-ATOM 729 H3' DG A 23 35.480 48.240 80.890 1.00 0.00
-ATOM 730 C2' DG A 23 35.270 50.360 80.490 1.00 0.00
-ATOM 731 1H2' DG A 23 35.910 50.240 79.610 1.00 0.00
-ATOM 732 2H2' DG A 23 34.240 50.510 80.190 1.00 0.00
-ATOM 733 O3' DG A 23 34.410 49.150 82.490 1.00 0.00
-ATOM 734 P DA A 24 32.830 48.700 82.350 1.00 0.00
-ATOM 735 O1P DA A 24 32.490 47.910 83.570 1.00 0.00
-ATOM 736 O2P DA A 24 32.660 47.990 81.060 1.00 0.00
-ATOM 737 O5' DA A 24 31.760 49.980 82.350 1.00 0.00
-ATOM 738 C5' DA A 24 31.160 50.490 83.560 1.00 0.00
-ATOM 739 1H5' DA A 24 31.990 50.700 84.230 1.00 0.00
-ATOM 740 2H5' DA A 24 30.590 49.680 84.010 1.00 0.00
-ATOM 741 C4' DA A 24 30.250 51.780 83.590 1.00 0.00
-ATOM 742 H4' DA A 24 30.070 51.980 84.650 1.00 0.00
-ATOM 743 O4' DA A 24 31.030 52.860 83.120 1.00 0.00
-ATOM 744 C1' DA A 24 30.440 53.360 81.940 1.00 0.00
-ATOM 745 H1' DA A 24 30.030 54.360 82.140 1.00 0.00
-ATOM 746 N9 DA A 24 31.460 53.480 80.880 1.00 0.00
-ATOM 747 C8 DA A 24 32.230 52.520 80.290 1.00 0.00
-ATOM 748 H8 DA A 24 32.180 51.470 80.550 1.00 0.00
-ATOM 749 N7 DA A 24 33.050 52.970 79.370 1.00 0.00
-ATOM 750 C5 DA A 24 32.800 54.350 79.390 1.00 0.00
-ATOM 751 C6 DA A 24 33.320 55.490 78.740 1.00 0.00
-ATOM 752 N6 DA A 24 34.340 55.490 77.910 1.00 0.00
-ATOM 753 H61 DA A 24 34.690 56.370 77.550 1.00 0.00
-ATOM 754 H62 DA A 24 34.860 54.640 77.740 1.00 0.00
-ATOM 755 N1 DA A 24 32.830 56.700 79.010 1.00 0.00
-ATOM 756 C2 DA A 24 31.850 56.830 79.880 1.00 0.00
-ATOM 757 H2 DA A 24 31.490 57.840 80.050 1.00 0.00
-ATOM 758 N3 DA A 24 31.260 55.870 80.580 1.00 0.00
-ATOM 759 C4 DA A 24 31.810 54.660 80.290 1.00 0.00
-ATOM 760 C3' DA A 24 28.850 51.920 82.900 1.00 0.00
-ATOM 761 H3' DA A 24 28.360 50.950 82.810 1.00 0.00
-ATOM 762 C2' DA A 24 29.300 52.430 81.540 1.00 0.00
-ATOM 763 1H2' DA A 24 29.670 51.600 80.940 1.00 0.00
-ATOM 764 2H2' DA A 24 28.510 52.970 81.020 1.00 0.00
-ATOM 765 O3' DA A 24 27.970 52.890 83.560 1.00 0.00
-ATOM 766 P DT A 25 26.400 53.240 83.140 1.00 0.00
-ATOM 767 O1P DT A 25 25.690 53.520 84.410 1.00 0.00
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-ATOM 769 O5' DT A 25 26.250 54.610 82.200 1.00 0.00
-ATOM 770 C5' DT A 25 25.990 55.930 82.760 1.00 0.00
-ATOM 771 1H5' DT A 25 26.730 56.050 83.560 1.00 0.00
-ATOM 772 2H5' DT A 25 25.010 55.910 83.240 1.00 0.00
-ATOM 773 C4' DT A 25 26.090 57.240 81.890 1.00 0.00
-ATOM 774 H4' DT A 25 26.280 58.050 82.600 1.00 0.00
-ATOM 775 O4' DT A 25 27.260 57.120 81.120 1.00 0.00
-ATOM 776 C1' DT A 25 26.970 57.450 79.770 1.00 0.00
-ATOM 777 H1' DT A 25 27.240 58.490 79.600 1.00 0.00
-ATOM 778 N1 DT A 25 27.770 56.550 78.910 1.00 0.00
-ATOM 779 C6 DT A 25 27.590 55.180 78.920 1.00 0.00
-ATOM 780 H6 DT A 25 26.840 54.760 79.560 1.00 0.00
-ATOM 781 C5 DT A 25 28.390 54.380 78.170 1.00 0.00
-ATOM 782 C7 DT A 25 28.150 52.880 78.150 1.00 0.00
-ATOM 783 H71 DT A 25 27.190 52.630 78.610 1.00 0.00
-ATOM 784 H72 DT A 25 28.150 52.550 77.110 1.00 0.00
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-ATOM 786 C4 DT A 25 29.480 54.940 77.370 1.00 0.00
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-ATOM 790 C2 DT A 25 28.760 57.150 78.120 1.00 0.00
-ATOM 791 O2 DT A 25 28.920 58.370 78.060 1.00 0.00
-ATOM 792 C3' DT A 25 24.960 57.790 80.950 1.00 0.00
-ATOM 793 H3' DT A 25 24.000 57.350 81.190 1.00 0.00
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-ATOM 795 1H2' DT A 25 25.170 56.260 79.450 1.00 0.00
-ATOM 796 2H2' DT A 25 25.100 57.910 78.770 1.00 0.00
-ATOM 797 O3' DT A 25 24.870 59.250 80.970 1.00 0.00
-ATOM 798 P DG A 26 23.750 60.170 80.170 1.00 0.00
-ATOM 799 O1P DG A 26 23.350 61.260 81.100 1.00 0.00
-ATOM 800 O2P DG A 26 22.670 59.260 79.750 1.00 0.00
-ATOM 801 O5' DG A 26 24.370 60.910 78.810 1.00 0.00
-ATOM 802 C5' DG A 26 25.040 62.200 78.840 1.00 0.00
-ATOM 803 1H5' DG A 26 25.770 62.130 79.650 1.00 0.00
-ATOM 804 2H5' DG A 26 24.320 62.950 79.140 1.00 0.00
-ATOM 805 C4' DG A 26 25.870 62.760 77.620 1.00 0.00
-ATOM 806 H4' DG A 26 26.520 63.530 78.030 1.00 0.00
-ATOM 807 O4' DG A 26 26.710 61.720 77.190 1.00 0.00
-ATOM 808 C1' DG A 26 26.540 61.520 75.800 1.00 0.00
-ATOM 809 H1' DG A 26 27.390 61.950 75.260 1.00 0.00
-ATOM 810 N9 DG A 26 26.510 60.070 75.570 1.00 0.00
-ATOM 811 C8 DG A 26 25.700 59.110 76.120 1.00 0.00
-ATOM 812 H8 DG A 26 24.920 59.360 76.820 1.00 0.00
-ATOM 813 N7 DG A 26 25.980 57.890 75.750 1.00 0.00
-ATOM 814 C5 DG A 26 27.080 58.070 74.890 1.00 0.00
-ATOM 815 C6 DG A 26 27.930 57.140 74.190 1.00 0.00
-ATOM 816 O6 DG A 26 27.860 55.900 74.180 1.00 0.00
-ATOM 817 N1 DG A 26 28.930 57.760 73.450 1.00 0.00
-ATOM 818 H1 DG A 26 29.600 57.170 72.980 1.00 0.00
-ATOM 819 C2 DG A 26 29.130 59.100 73.420 1.00 0.00
-ATOM 820 N2 DG A 26 30.130 59.570 72.740 1.00 0.00
-ATOM 821 H21 DG A 26 30.770 58.940 72.250 1.00 0.00
-ATOM 822 H22 DG A 26 30.300 60.560 72.760 1.00 0.00
-ATOM 823 N3 DG A 26 28.380 59.990 74.050 1.00 0.00
-ATOM 824 C4 DG A 26 27.390 59.400 74.770 1.00 0.00
-ATOM 825 C3' DG A 26 25.260 63.410 76.330 1.00 0.00
-ATOM 826 H3' DG A 26 24.250 63.770 76.500 1.00 0.00
-ATOM 827 C2' DG A 26 25.250 62.210 75.390 1.00 0.00
-ATOM 828 1H2' DG A 26 24.390 61.580 75.590 1.00 0.00
-ATOM 829 2H2' DG A 26 25.280 62.500 74.330 1.00 0.00
-ATOM 830 O3' DG A 26 26.100 64.480 75.820 1.00 0.00
-ATOM 831 P DG A 27 25.830 65.380 74.470 1.00 0.00
-ATOM 832 O1P DG A 27 26.180 66.780 74.810 1.00 0.00
-ATOM 833 O2P DG A 27 24.410 65.150 74.090 1.00 0.00
-ATOM 834 O5' DG A 27 26.800 64.910 73.200 1.00 0.00
-ATOM 835 C5' DG A 27 28.200 65.280 73.090 1.00 0.00
-ATOM 836 1H5' DG A 27 28.650 65.050 74.060 1.00 0.00
-ATOM 837 2H5' DG A 27 28.270 66.360 72.960 1.00 0.00
-ATOM 838 C4' DG A 27 29.150 64.610 72.030 1.00 0.00
-ATOM 839 H4' DG A 27 30.180 64.770 72.370 1.00 0.00
-ATOM 840 O4' DG A 27 28.910 63.220 72.090 1.00 0.00
-ATOM 841 C1' DG A 27 28.710 62.730 70.780 1.00 0.00
-ATOM 842 H1' DG A 27 29.640 62.320 70.370 1.00 0.00
-ATOM 843 N9 DG A 27 27.680 61.680 70.840 1.00 0.00
-ATOM 844 C8 DG A 27 26.430 61.740 71.400 1.00 0.00
-ATOM 845 H8 DG A 27 26.050 62.660 71.820 1.00 0.00
-ATOM 846 N7 DG A 27 25.790 60.610 71.400 1.00 0.00
-ATOM 847 C5 DG A 27 26.720 59.720 70.840 1.00 0.00
-ATOM 848 C6 DG A 27 26.710 58.290 70.670 1.00 0.00
-ATOM 849 O6 DG A 27 25.830 57.490 70.990 1.00 0.00
-ATOM 850 N1 DG A 27 27.880 57.790 70.110 1.00 0.00
-ATOM 851 H1 DG A 27 27.990 56.790 70.050 1.00 0.00
-ATOM 852 C2 DG A 27 28.930 58.560 69.730 1.00 0.00
-ATOM 853 N2 DG A 27 29.980 57.970 69.240 1.00 0.00
-ATOM 854 H21 DG A 27 30.050 56.960 69.190 1.00 0.00
-ATOM 855 H22 DG A 27 30.780 58.540 69.020 1.00 0.00
-ATOM 856 N3 DG A 27 28.970 59.880 69.850 1.00 0.00
-ATOM 857 C4 DG A 27 27.850 60.390 70.440 1.00 0.00
-ATOM 858 C3' DG A 27 29.170 64.980 70.510 1.00 0.00
-ATOM 859 H3' DG A 27 28.770 65.980 70.330 1.00 0.00
-ATOM 860 C2' DG A 27 28.260 63.910 69.940 1.00 0.00
-ATOM 861 1H2' DG A 27 27.220 64.160 70.140 1.00 0.00
-ATOM 862 2H2' DG A 27 28.430 63.730 68.880 1.00 0.00
-ATOM 863 O3' DG A 27 30.490 64.870 69.930 1.00 0.00
-ATOM 864 P DC A 28 30.870 65.150 68.350 1.00 0.00
-ATOM 865 O1P DC A 28 32.060 66.030 68.330 1.00 0.00
-ATOM 866 O2P DC A 28 29.630 65.700 67.730 1.00 0.00
-ATOM 867 O5' DC A 28 31.250 63.730 67.580 1.00 0.00
-ATOM 868 C5' DC A 28 32.510 63.020 67.720 1.00 0.00
-ATOM 869 1H5' DC A 28 32.700 62.940 68.790 1.00 0.00
-ATOM 870 2H5' DC A 28 33.310 63.640 67.310 1.00 0.00
-ATOM 871 C4' DC A 28 32.690 61.550 67.160 1.00 0.00
-ATOM 872 H4' DC A 28 33.530 61.110 67.690 1.00 0.00
-ATOM 873 O4' DC A 28 31.530 60.810 67.530 1.00 0.00
-ATOM 874 C1' DC A 28 30.960 60.250 66.350 1.00 0.00
-ATOM 875 H1' DC A 28 31.280 59.210 66.250 1.00 0.00
-ATOM 876 N1 DC A 28 29.480 60.350 66.470 1.00 0.00
-ATOM 877 C6 DC A 28 28.880 61.560 66.710 1.00 0.00
-ATOM 878 H6 DC A 28 29.500 62.450 66.710 1.00 0.00
-ATOM 879 C5 DC A 28 27.560 61.630 66.990 1.00 0.00
-ATOM 880 H5 DC A 28 27.100 62.570 67.210 1.00 0.00
-ATOM 881 C4 DC A 28 26.870 60.390 67.030 1.00 0.00
-ATOM 882 N4 DC A 28 25.630 60.340 67.430 1.00 0.00
-ATOM 883 H41 DC A 28 25.270 59.390 67.500 1.00 0.00
-ATOM 884 H42 DC A 28 25.200 61.130 67.840 1.00 0.00
-ATOM 885 N3 DC A 28 27.410 59.230 66.780 1.00 0.00
-ATOM 886 C2 DC A 28 28.720 59.180 66.490 1.00 0.00
-ATOM 887 O2 DC A 28 29.200 58.070 66.270 1.00 0.00
-ATOM 888 C3' DC A 28 32.940 61.220 65.650 1.00 0.00
-ATOM 889 H3' DC A 28 33.450 62.030 65.140 1.00 0.00
-ATOM 890 C2' DC A 28 31.510 61.040 65.170 1.00 0.00
-ATOM 891 1H2' DC A 28 31.040 62.020 65.070 1.00 0.00
-ATOM 892 2H2' DC A 28 31.450 60.480 64.250 1.00 0.00
-ATOM 893 O3' DC A 28 33.670 59.970 65.480 1.00 0.00
-ATOM 894 P DA A 29 34.170 59.360 64.030 1.00 0.00
-ATOM 895 O1P DA A 29 35.640 59.160 64.100 1.00 0.00
-ATOM 896 O2P DA A 29 33.650 60.270 62.990 1.00 0.00
-ATOM 897 O5' DA A 29 33.490 57.880 63.770 1.00 0.00
-ATOM 898 C5' DA A 29 33.970 56.660 64.380 1.00 0.00
-ATOM 899 1H5' DA A 29 34.010 56.870 65.440 1.00 0.00
-ATOM 900 2H5' DA A 29 34.990 56.490 64.050 1.00 0.00
-ATOM 901 C4' DA A 29 33.140 55.330 64.230 1.00 0.00
-ATOM 902 H4' DA A 29 33.530 54.640 64.970 1.00 0.00
-ATOM 903 O4' DA A 29 31.800 55.630 64.550 1.00 0.00
-ATOM 904 C1' DA A 29 31.040 55.530 63.360 1.00 0.00
-ATOM 905 H1' DA A 29 30.430 54.630 63.440 1.00 0.00
-ATOM 906 N9 DA A 29 30.150 56.700 63.210 1.00 0.00
-ATOM 907 C8 DA A 29 30.440 58.030 63.030 1.00 0.00
-ATOM 908 H8 DA A 29 31.450 58.400 62.870 1.00 0.00
-ATOM 909 N7 DA A 29 29.400 58.830 63.080 1.00 0.00
-ATOM 910 C5 DA A 29 28.360 57.920 63.300 1.00 0.00
-ATOM 911 C6 DA A 29 26.970 58.040 63.520 1.00 0.00
-ATOM 912 N6 DA A 29 26.340 59.190 63.590 1.00 0.00
-ATOM 913 H61 DA A 29 25.360 59.210 63.820 1.00 0.00
-ATOM 914 H62 DA A 29 26.910 60.010 63.470 1.00 0.00
-ATOM 915 N1 DA A 29 26.200 56.970 63.700 1.00 0.00
-ATOM 916 C2 DA A 29 26.770 55.770 63.660 1.00 0.00
-ATOM 917 H2 DA A 29 26.120 54.920 63.800 1.00 0.00
-ATOM 918 N3 DA A 29 28.050 55.490 63.480 1.00 0.00
-ATOM 919 C4 DA A 29 28.800 56.630 63.330 1.00 0.00
-ATOM 920 C3' DA A 29 33.060 54.510 62.900 1.00 0.00
-ATOM 921 H3' DA A 29 34.010 54.530 62.350 1.00 0.00
-ATOM 922 C2' DA A 29 32.000 55.330 62.200 1.00 0.00
-ATOM 923 1H2' DA A 29 32.420 56.280 61.860 1.00 0.00
-ATOM 924 2H2' DA A 29 31.540 54.770 61.400 1.00 0.00
-ATOM 925 O3' DA A 29 32.590 53.140 63.080 1.00 0.00
-ATOM 926 P DT A 30 32.360 52.030 61.870 1.00 0.00
-ATOM 927 O1P DT A 30 32.920 50.730 62.320 1.00 0.00
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-ATOM 930 C5' DT A 30 30.030 50.700 62.300 1.00 0.00
-ATOM 931 1H5' DT A 30 30.110 50.930 63.370 1.00 0.00
-ATOM 932 2H5' DT A 30 30.540 49.760 62.140 1.00 0.00
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-ATOM 941 C5 DT A 30 29.030 55.380 59.860 1.00 0.00
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-ATOM 1031 O4' DC A 33 19.860 59.670 51.220 1.00 0.00
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-ATOM 1034 N1 DC A 33 21.360 58.390 49.930 1.00 0.00
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-ATOM 1043 N3 DC A 33 23.400 57.190 49.740 1.00 0.00
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-ATOM 1045 O2 DC A 33 23.370 59.410 49.580 1.00 0.00
-ATOM 1046 C3' DC A 33 18.760 60.960 49.530 1.00 0.00
-ATOM 1047 H3' DC A 33 17.810 60.930 48.990 1.00 0.00
-ATOM 1048 C2' DC A 33 19.770 60.020 48.890 1.00 0.00
-ATOM 1049 1H2' DC A 33 19.270 59.130 48.520 1.00 0.00
-ATOM 1050 2H2' DC A 33 20.330 60.510 48.090 1.00 0.00
-ATOM 1051 O3' DC A 33 19.270 62.320 49.560 1.00 0.00
-ATOM 1052 P DT A 34 19.550 63.290 48.250 1.00 0.00
-ATOM 1053 O1P DT A 34 19.070 64.650 48.600 1.00 0.00
-ATOM 1054 O2P DT A 34 18.880 62.650 47.090 1.00 0.00
-ATOM 1055 O5' DT A 34 21.160 63.420 47.890 1.00 0.00
-ATOM 1056 C5' DT A 34 22.060 64.340 48.560 1.00 0.00
-ATOM 1057 1H5' DT A 34 21.870 64.220 49.630 1.00 0.00
-ATOM 1058 2H5' DT A 34 21.780 65.360 48.310 1.00 0.00
-ATOM 1059 C4' DT A 34 23.630 64.210 48.400 1.00 0.00
-ATOM 1060 H4' DT A 34 24.060 64.680 49.290 1.00 0.00
-ATOM 1061 O4' DT A 34 23.930 62.840 48.480 1.00 0.00
-ATOM 1062 C1' DT A 34 24.840 62.490 47.450 1.00 0.00
-ATOM 1063 H1' DT A 34 25.870 62.510 47.840 1.00 0.00
-ATOM 1064 N1 DT A 34 24.470 61.140 46.970 1.00 0.00
-ATOM 1065 C6 DT A 34 23.190 60.880 46.530 1.00 0.00
-ATOM 1066 H6 DT A 34 22.480 61.690 46.520 1.00 0.00
-ATOM 1067 C5 DT A 34 22.820 59.610 46.200 1.00 0.00
-ATOM 1068 C7 DT A 34 21.420 59.360 45.680 1.00 0.00
-ATOM 1069 H71 DT A 34 20.910 60.290 45.460 1.00 0.00
-ATOM 1070 H72 DT A 34 21.490 58.750 44.780 1.00 0.00
-ATOM 1071 H73 DT A 34 20.860 58.790 46.430 1.00 0.00
-ATOM 1072 C4 DT A 34 23.760 58.500 46.330 1.00 0.00
-ATOM 1073 O4 DT A 34 23.480 57.320 46.130 1.00 0.00
-ATOM 1074 N3 DT A 34 25.030 58.870 46.710 1.00 0.00
-ATOM 1075 H3 DT A 34 25.720 58.150 46.850 1.00 0.00
-ATOM 1076 C2 DT A 34 25.440 60.140 47.020 1.00 0.00
-ATOM 1077 O2 DT A 34 26.620 60.360 47.280 1.00 0.00
-ATOM 1078 C3' DT A 34 24.430 64.810 47.200 1.00 0.00
-ATOM 1079 H3' DT A 34 23.840 65.530 46.640 1.00 0.00
-ATOM 1080 C2' DT A 34 24.700 63.560 46.370 1.00 0.00
-ATOM 1081 1H2' DT A 34 23.840 63.360 45.720 1.00 0.00
-ATOM 1082 2H2' DT A 34 25.600 63.630 45.770 1.00 0.00
-ATOM 1083 O3' DT A 34 25.680 65.420 47.620 1.00 0.00
-ATOM 1084 P DA A 35 26.790 66.110 46.610 1.00 0.00
-ATOM 1085 O1P DA A 35 27.240 67.370 47.250 1.00 0.00
-ATOM 1086 O2P DA A 35 26.140 66.240 45.290 1.00 0.00
-ATOM 1087 O5' DA A 35 28.110 65.110 46.450 1.00 0.00
-ATOM 1088 C5' DA A 35 29.150 64.980 47.460 1.00 0.00
-ATOM 1089 1H5' DA A 35 28.630 64.850 48.410 1.00 0.00
-ATOM 1090 2H5' DA A 35 29.700 65.920 47.530 1.00 0.00
-ATOM 1091 C4' DA A 35 30.190 63.800 47.390 1.00 0.00
-ATOM 1092 H4' DA A 35 30.620 63.680 48.390 1.00 0.00
-ATOM 1093 O4' DA A 35 29.440 62.640 47.120 1.00 0.00
-ATOM 1094 C1' DA A 35 30.010 61.970 46.020 1.00 0.00
-ATOM 1095 H1' DA A 35 30.670 61.160 46.360 1.00 0.00
-ATOM 1096 N9 DA A 35 28.920 61.440 45.190 1.00 0.00
-ATOM 1097 C8 DA A 35 27.820 62.110 44.710 1.00 0.00
-ATOM 1098 H8 DA A 35 27.690 63.170 44.880 1.00 0.00
-ATOM 1099 N7 DA A 35 26.970 61.360 44.050 1.00 0.00
-ATOM 1100 C5 DA A 35 27.570 60.090 44.150 1.00 0.00
-ATOM 1101 C6 DA A 35 27.210 58.780 43.780 1.00 0.00
-ATOM 1102 N6 DA A 35 26.060 58.480 43.200 1.00 0.00
-ATOM 1103 H61 DA A 35 25.870 57.500 43.030 1.00 0.00
-ATOM 1104 H62 DA A 35 25.460 59.230 42.950 1.00 0.00
-ATOM 1105 N1 DA A 35 27.980 57.730 44.030 1.00 0.00
-ATOM 1106 C2 DA A 35 29.140 57.940 44.650 1.00 0.00
-ATOM 1107 H2 DA A 35 29.760 57.070 44.840 1.00 0.00
-ATOM 1108 N3 DA A 35 29.610 59.100 45.070 1.00 0.00
-ATOM 1109 C4 DA A 35 28.760 60.130 44.820 1.00 0.00
-ATOM 1110 C3' DA A 35 31.410 63.790 46.410 1.00 0.00
-ATOM 1111 H3' DA A 35 31.690 64.790 46.110 1.00 0.00
-ATOM 1112 C2' DA A 35 30.810 63.010 45.250 1.00 0.00
-ATOM 1113 1H2' DA A 35 30.160 63.660 44.660 1.00 0.00
-ATOM 1114 2H2' DA A 35 31.570 62.540 44.620 1.00 0.00
-ATOM 1115 O3' DA A 35 32.560 63.080 46.930 1.00 0.00
-ATOM 1116 P DC A 36 33.990 62.890 46.140 1.00 0.00
-ATOM 1117 O1P DC A 36 35.070 63.320 47.060 1.00 0.00
-ATOM 1118 O2P DC A 36 33.860 63.650 44.870 1.00 0.00
-ATOM 1119 O5' DC A 36 34.240 61.310 45.740 1.00 0.00
-ATOM 1120 C5' DC A 36 34.600 60.260 46.680 1.00 0.00
-ATOM 1121 1H5' DC A 36 33.890 60.340 47.510 1.00 0.00
-ATOM 1122 2H5' DC A 36 35.590 60.480 47.080 1.00 0.00
-ATOM 1123 C4' DC A 36 34.550 58.750 46.220 1.00 0.00
-ATOM 1124 H4' DC A 36 34.510 58.140 47.120 1.00 0.00
-ATOM 1125 O4' DC A 36 33.330 58.580 45.530 1.00 0.00
-ATOM 1126 C1' DC A 36 33.610 58.120 44.220 1.00 0.00
-ATOM 1127 H1' DC A 36 33.490 57.030 44.210 1.00 0.00
-ATOM 1128 N1 DC A 36 32.670 58.770 43.280 1.00 0.00
-ATOM 1129 C6 DC A 36 32.620 60.140 43.160 1.00 0.00
-ATOM 1130 H6 DC A 36 33.340 60.740 43.710 1.00 0.00
-ATOM 1131 C5 DC A 36 31.640 60.730 42.420 1.00 0.00
-ATOM 1132 H5 DC A 36 31.590 61.800 42.370 1.00 0.00
-ATOM 1133 C4 DC A 36 30.700 59.860 41.810 1.00 0.00
-ATOM 1134 N4 DC A 36 29.670 60.340 41.190 1.00 0.00
-ATOM 1135 H41 DC A 36 29.040 59.630 40.820 1.00 0.00
-ATOM 1136 H42 DC A 36 29.510 61.310 41.160 1.00 0.00
-ATOM 1137 N3 DC A 36 30.760 58.560 41.870 1.00 0.00
-ATOM 1138 C2 DC A 36 31.750 57.980 42.600 1.00 0.00
-ATOM 1139 O2 DC A 36 31.780 56.760 42.620 1.00 0.00
-ATOM 1140 C3' DC A 36 35.650 58.080 45.320 1.00 0.00
-ATOM 1141 H3' DC A 36 36.630 58.530 45.480 1.00 0.00
-ATOM 1142 C2' DC A 36 35.080 58.440 43.960 1.00 0.00
-ATOM 1143 1H2' DC A 36 35.250 59.490 43.750 1.00 0.00
-ATOM 1144 2H2' DC A 36 35.500 57.810 43.180 1.00 0.00
-ATOM 1145 O3' DC A 36 35.710 56.630 45.460 1.00 0.00
-ATOM 1146 P DC A 37 36.760 55.640 44.650 1.00 0.00
-ATOM 1147 O1P DC A 37 37.440 54.760 45.630 1.00 0.00
-ATOM 1148 O2P DC A 37 37.610 56.510 43.810 1.00 0.00
-ATOM 1149 O5' DC A 37 35.960 54.640 43.610 1.00 0.00
-ATOM 1150 C5' DC A 37 35.400 53.370 43.990 1.00 0.00
-ATOM 1151 1H5' DC A 37 34.690 53.580 44.790 1.00 0.00
-ATOM 1152 2H5' DC A 37 36.200 52.760 44.420 1.00 0.00
-ATOM 1153 C4' DC A 37 34.640 52.520 42.900 1.00 0.00
-ATOM 1154 H4' DC A 37 34.030 51.800 43.450 1.00 0.00
-ATOM 1155 O4' DC A 37 33.760 53.400 42.220 1.00 0.00
-ATOM 1156 C1' DC A 37 34.250 53.570 40.910 1.00 0.00
-ATOM 1157 H1' DC A 37 33.590 52.990 40.250 1.00 0.00
-ATOM 1158 N1 DC A 37 34.160 55.010 40.520 1.00 0.00
-ATOM 1159 C6 DC A 37 35.060 55.970 40.930 1.00 0.00
-ATOM 1160 H6 DC A 37 35.910 55.690 41.530 1.00 0.00
-ATOM 1161 C5 DC A 37 34.850 57.270 40.600 1.00 0.00
-ATOM 1162 H5 DC A 37 35.550 58.020 40.930 1.00 0.00
-ATOM 1163 C4 DC A 37 33.690 57.570 39.840 1.00 0.00
-ATOM 1164 N4 DC A 37 33.370 58.810 39.580 1.00 0.00
-ATOM 1165 H41 DC A 37 32.510 58.950 39.070 1.00 0.00
-ATOM 1166 H42 DC A 37 33.950 59.540 39.920 1.00 0.00
-ATOM 1167 N3 DC A 37 32.830 56.670 39.420 1.00 0.00
-ATOM 1168 C2 DC A 37 33.070 55.380 39.740 1.00 0.00
-ATOM 1169 O2 DC A 37 32.290 54.540 39.290 1.00 0.00
-ATOM 1170 C3' DC A 37 35.370 51.730 41.760 1.00 0.00
-ATOM 1171 H3' DC A 37 36.310 51.300 42.120 1.00 0.00
-ATOM 1172 C2' DC A 37 35.620 52.900 40.820 1.00 0.00
-ATOM 1173 1H2' DC A 37 36.410 53.540 41.210 1.00 0.00
-ATOM 1174 2H2' DC A 37 35.860 52.570 39.810 1.00 0.00
-ATOM 1175 O3' DC A 37 34.520 50.700 41.150 1.00 0.00
-ATOM 1176 P DG A 38 34.960 49.590 40.010 1.00 0.00
-ATOM 1177 O1P DG A 38 34.500 48.250 40.460 1.00 0.00
-ATOM 1178 O2P DG A 38 36.400 49.740 39.740 1.00 0.00
-ATOM 1179 O5' DG A 38 34.180 49.850 38.570 1.00 0.00
-ATOM 1180 C5' DG A 38 32.900 49.260 38.270 1.00 0.00
-ATOM 1181 1H5' DG A 38 32.230 49.610 39.060 1.00 0.00
-ATOM 1182 2H5' DG A 38 32.990 48.190 38.380 1.00 0.00
-ATOM 1183 C4' DG A 38 32.180 49.560 36.900 1.00 0.00
-ATOM 1184 H4' DG A 38 31.190 49.120 36.980 1.00 0.00
-ATOM 1185 O4' DG A 38 32.000 50.960 36.830 1.00 0.00
-ATOM 1186 C1' DG A 38 32.870 51.450 35.840 1.00 0.00
-ATOM 1187 H1' DG A 38 32.250 51.790 35.010 1.00 0.00
-ATOM 1188 N9 DG A 38 33.640 52.610 36.320 1.00 0.00
-ATOM 1189 C8 DG A 38 34.670 52.730 37.230 1.00 0.00
-ATOM 1190 H8 DG A 38 35.090 51.880 37.750 1.00 0.00
-ATOM 1191 N7 DG A 38 35.080 53.950 37.410 1.00 0.00
-ATOM 1192 C5 DG A 38 34.250 54.710 36.570 1.00 0.00
-ATOM 1193 C6 DG A 38 34.150 56.130 36.320 1.00 0.00
-ATOM 1194 O6 DG A 38 34.760 57.070 36.800 1.00 0.00
-ATOM 1195 N1 DG A 38 33.180 56.430 35.380 1.00 0.00
-ATOM 1196 H1 DG A 38 33.030 57.410 35.200 1.00 0.00
-ATOM 1197 C2 DG A 38 32.410 55.520 34.750 1.00 0.00
-ATOM 1198 N2 DG A 38 31.520 55.920 33.890 1.00 0.00
-ATOM 1199 H21 DG A 38 31.360 56.910 33.770 1.00 0.00
-ATOM 1200 H22 DG A 38 30.940 55.210 33.500 1.00 0.00
-ATOM 1201 N3 DG A 38 32.480 54.210 34.930 1.00 0.00
-ATOM 1202 C4 DG A 38 33.410 53.880 35.880 1.00 0.00
-ATOM 1203 C3' DG A 38 32.760 49.150 35.510 1.00 0.00
-ATOM 1204 H3' DG A 38 33.290 48.200 35.570 1.00 0.00
-ATOM 1205 C2' DG A 38 33.720 50.300 35.320 1.00 0.00
-ATOM 1206 1H2' DG A 38 34.610 50.160 35.930 1.00 0.00
-ATOM 1207 2H2' DG A 38 33.980 50.430 34.270 1.00 0.00
-ATOM 1208 O3' DG A 38 31.750 49.110 34.440 1.00 0.00
-ATOM 1209 P DT A 39 31.980 48.700 32.850 1.00 0.00
-ATOM 1210 O1P DT A 39 30.770 47.950 32.420 1.00 0.00
-ATOM 1211 O2P DT A 39 33.260 47.960 32.760 1.00 0.00
-ATOM 1212 O5' DT A 39 32.090 50.000 31.820 1.00 0.00
-ATOM 1213 C5' DT A 39 30.940 50.520 31.110 1.00 0.00
-ATOM 1214 1H5' DT A 39 30.180 50.710 31.870 1.00 0.00
-ATOM 1215 2H5' DT A 39 30.560 49.730 30.470 1.00 0.00
-ATOM 1216 C4' DT A 39 31.010 51.850 30.250 1.00 0.00
-ATOM 1217 H4' DT A 39 29.970 52.150 30.100 1.00 0.00
-ATOM 1218 O4' DT A 39 31.580 52.830 31.080 1.00 0.00
-ATOM 1219 C1' DT A 39 32.710 53.380 30.420 1.00 0.00
-ATOM 1220 H1' DT A 39 32.400 54.330 29.970 1.00 0.00
-ATOM 1221 N1 DT A 39 33.790 53.620 31.410 1.00 0.00
-ATOM 1222 C6 DT A 39 34.460 52.590 32.040 1.00 0.00
-ATOM 1223 H6 DT A 39 34.170 51.570 31.850 1.00 0.00
-ATOM 1224 C5 DT A 39 35.450 52.850 32.930 1.00 0.00
-ATOM 1225 C7 DT A 39 36.240 51.720 33.560 1.00 0.00
-ATOM 1226 H71 DT A 39 35.940 50.750 33.170 1.00 0.00
-ATOM 1227 H72 DT A 39 37.300 51.880 33.370 1.00 0.00
-ATOM 1228 H73 DT A 39 36.110 51.760 34.650 1.00 0.00
-ATOM 1229 C4 DT A 39 35.790 54.230 33.280 1.00 0.00
-ATOM 1230 O4 DT A 39 36.630 54.590 34.090 1.00 0.00
-ATOM 1231 N3 DT A 39 35.080 55.180 32.600 1.00 0.00
-ATOM 1232 H3 DT A 39 35.310 56.140 32.810 1.00 0.00
-ATOM 1233 C2 DT A 39 34.120 54.960 31.660 1.00 0.00
-ATOM 1234 O2 DT A 39 33.610 55.900 31.050 1.00 0.00
-ATOM 1235 C3' DT A 39 31.690 51.990 28.850 1.00 0.00
-ATOM 1236 H3' DT A 39 31.730 51.020 28.340 1.00 0.00
-ATOM 1237 C2' DT A 39 33.070 52.430 29.290 1.00 0.00
-ATOM 1238 1H2' DT A 39 33.640 51.580 29.650 1.00 0.00
-ATOM 1239 2H2' DT A 39 33.620 52.950 28.490 1.00 0.00
-ATOM 1240 O3' DT A 39 31.050 52.990 27.990 1.00 0.00
-ATOM 1241 P DA A 40 31.400 53.310 26.400 1.00 0.00
-ATOM 1242 O1P DA A 40 30.090 53.510 25.710 1.00 0.00
-ATOM 1243 O2P DA A 40 32.220 52.190 25.900 1.00 0.00
-ATOM 1244 O5' DA A 40 32.260 54.720 26.160 1.00 0.00
-ATOM 1245 C5' DA A 40 31.630 56.000 25.870 1.00 0.00
-ATOM 1246 1H5' DA A 40 30.850 56.110 26.630 1.00 0.00
-ATOM 1247 2H5' DA A 40 31.120 55.910 24.910 1.00 0.00
-ATOM 1248 C4' DA A 40 32.410 57.370 25.870 1.00 0.00
-ATOM 1249 H4' DA A 40 31.640 58.140 25.930 1.00 0.00
-ATOM 1250 O4' DA A 40 33.110 57.450 27.090 1.00 0.00
-ATOM 1251 C1' DA A 40 34.490 57.590 26.830 1.00 0.00
-ATOM 1252 H1' DA A 40 34.810 58.600 27.100 1.00 0.00
-ATOM 1253 N9 DA A 40 35.220 56.620 27.660 1.00 0.00
-ATOM 1254 C8 DA A 40 35.160 55.250 27.670 1.00 0.00
-ATOM 1255 H8 DA A 40 34.500 54.690 27.020 1.00 0.00
-ATOM 1256 N7 DA A 40 35.950 54.670 28.540 1.00 0.00
-ATOM 1257 C5 DA A 40 36.560 55.780 29.160 1.00 0.00
-ATOM 1258 C6 DA A 40 37.490 55.980 30.200 1.00 0.00
-ATOM 1259 N6 DA A 40 38.040 55.010 30.900 1.00 0.00
-ATOM 1260 H61 DA A 40 38.670 55.280 31.670 1.00 0.00
-ATOM 1261 H62 DA A 40 37.840 54.060 30.700 1.00 0.00
-ATOM 1262 N1 DA A 40 37.870 57.200 30.550 1.00 0.00
-ATOM 1263 C2 DA A 40 37.370 58.250 29.920 1.00 0.00
-ATOM 1264 H2 DA A 40 37.720 59.220 30.250 1.00 0.00
-ATOM 1265 N3 DA A 40 36.500 58.230 28.930 1.00 0.00
-ATOM 1266 C4 DA A 40 36.130 56.960 28.610 1.00 0.00
-ATOM 1267 C3' DA A 40 33.400 57.880 24.770 1.00 0.00
-ATOM 1268 H3' DA A 40 33.190 57.430 23.800 1.00 0.00
-ATOM 1269 C2' DA A 40 34.710 57.360 25.330 1.00 0.00
-ATOM 1270 1H2' DA A 40 34.820 56.300 25.110 1.00 0.00
-ATOM 1271 2H2' DA A 40 35.580 57.920 24.970 1.00 0.00
-ATOM 1272 O3' DA A 40 33.410 59.340 24.660 1.00 0.00
-ATOM 1273 P DA A 41 34.300 60.240 23.580 1.00 0.00
-ATOM 1274 O1P DA A 41 33.410 61.350 23.140 1.00 0.00
-ATOM 1275 O2P DA A 41 34.740 59.310 22.520 1.00 0.00
-ATOM 1276 O5' DA A 41 35.640 60.950 24.260 1.00 0.00
-ATOM 1277 C5' DA A 41 35.620 62.250 24.910 1.00 0.00
-ATOM 1278 1H5' DA A 41 34.780 62.210 25.610 1.00 0.00
-ATOM 1279 2H5' DA A 41 35.370 63.000 24.170 1.00 0.00
-ATOM 1280 C4' DA A 41 36.830 62.800 25.770 1.00 0.00
-ATOM 1281 H4' DA A 41 36.410 63.560 26.420 1.00 0.00
-ATOM 1282 O4' DA A 41 37.240 61.750 26.620 1.00 0.00
-ATOM 1283 C1' DA A 41 38.630 61.560 26.500 1.00 0.00
-ATOM 1284 H1' DA A 41 39.150 61.990 27.370 1.00 0.00
-ATOM 1285 N9 DA A 41 38.860 60.110 26.440 1.00 0.00
-ATOM 1286 C8 DA A 41 38.330 59.190 25.570 1.00 0.00
-ATOM 1287 H8 DA A 41 37.660 59.480 24.780 1.00 0.00
-ATOM 1288 N7 DA A 41 38.690 57.950 25.810 1.00 0.00
-ATOM 1289 C5 DA A 41 39.490 58.100 26.960 1.00 0.00
-ATOM 1290 C6 DA A 41 40.150 57.230 27.850 1.00 0.00
-ATOM 1291 N6 DA A 41 40.150 55.910 27.740 1.00 0.00
-ATOM 1292 H61 DA A 41 40.620 55.390 28.480 1.00 0.00
-ATOM 1293 H62 DA A 41 39.650 55.490 27.000 1.00 0.00
-ATOM 1294 N1 DA A 41 40.820 57.680 28.900 1.00 0.00
-ATOM 1295 C2 DA A 41 40.870 58.990 29.120 1.00 0.00
-ATOM 1296 H2 DA A 41 41.430 59.320 29.980 1.00 0.00
-ATOM 1297 N3 DA A 41 40.300 59.930 28.380 1.00 0.00
-ATOM 1298 C4 DA A 41 39.610 59.410 27.330 1.00 0.00
-ATOM 1299 C3' DA A 41 38.130 63.450 25.180 1.00 0.00
-ATOM 1300 H3' DA A 41 37.990 63.790 24.160 1.00 0.00
-ATOM 1301 C2' DA A 41 39.090 62.270 25.230 1.00 0.00
-ATOM 1302 1H2' DA A 41 38.940 61.640 24.350 1.00 0.00
-ATOM 1303 2H2' DA A 41 40.140 62.570 25.300 1.00 0.00
-ATOM 1304 O3' DA A 41 38.610 64.540 26.010 1.00 0.00
-ATOM 1305 P DA A 42 39.970 65.450 25.730 1.00 0.00
-ATOM 1306 O1P DA A 42 39.620 66.850 26.080 1.00 0.00
-ATOM 1307 O2P DA A 42 40.330 65.220 24.310 1.00 0.00
-ATOM 1308 O5' DA A 42 41.240 64.980 26.690 1.00 0.00
-ATOM 1309 C5' DA A 42 41.400 65.390 28.080 1.00 0.00
-ATOM 1310 1H5' DA A 42 40.430 65.230 28.550 1.00 0.00
-ATOM 1311 2H5' DA A 42 41.590 66.460 28.100 1.00 0.00
-ATOM 1312 C4' DA A 42 42.430 64.690 29.040 1.00 0.00
-ATOM 1313 H4' DA A 42 42.100 64.890 30.060 1.00 0.00
-ATOM 1314 O4' DA A 42 42.290 63.310 28.830 1.00 0.00
-ATOM 1315 C1' DA A 42 43.570 62.720 28.680 1.00 0.00
-ATOM 1316 H1' DA A 42 43.920 62.290 29.630 1.00 0.00
-ATOM 1317 N9 DA A 42 43.440 61.680 27.660 1.00 0.00
-ATOM 1318 C8 DA A 42 42.910 61.780 26.400 1.00 0.00
-ATOM 1319 H8 DA A 42 42.540 62.730 26.020 1.00 0.00
-ATOM 1320 N7 DA A 42 42.850 60.660 25.730 1.00 0.00
-ATOM 1321 C5 DA A 42 43.390 59.750 26.660 1.00 0.00
-ATOM 1322 C6 DA A 42 43.590 58.350 26.700 1.00 0.00
-ATOM 1323 N6 DA A 42 43.250 57.540 25.720 1.00 0.00
-ATOM 1324 H61 DA A 42 43.370 56.540 25.880 1.00 0.00
-ATOM 1325 H62 DA A 42 42.840 57.940 24.910 1.00 0.00
-ATOM 1326 N1 DA A 42 44.080 57.730 27.770 1.00 0.00
-ATOM 1327 C2 DA A 42 44.410 58.470 28.830 1.00 0.00
-ATOM 1328 H2 DA A 42 44.820 57.960 29.680 1.00 0.00
-ATOM 1329 N3 DA A 42 44.280 59.790 28.940 1.00 0.00
-ATOM 1330 C4 DA A 42 43.760 60.360 27.830 1.00 0.00
-ATOM 1331 C3' DA A 42 43.970 65.000 29.050 1.00 0.00
-ATOM 1332 H3' DA A 42 44.200 65.950 28.580 1.00 0.00
-ATOM 1333 C2' DA A 42 44.510 63.830 28.230 1.00 0.00
-ATOM 1334 1H2' DA A 42 44.390 64.050 27.170 1.00 0.00
-ATOM 1335 2H2' DA A 42 45.550 63.600 28.460 1.00 0.00
-ATOM 1336 O3' DA A 42 44.520 64.970 30.390 1.00 0.00
-ATOM 1337 P DG A 43 46.110 65.230 30.780 1.00 0.00
-ATOM 1338 O1P DG A 43 46.120 66.130 31.950 1.00 0.00
-ATOM 1339 O2P DG A 43 46.740 65.750 29.540 1.00 0.00
-ATOM 1340 O5' DG A 43 46.860 63.800 31.190 1.00 0.00
-ATOM 1341 C5' DG A 43 46.720 63.170 32.500 1.00 0.00
-ATOM 1342 1H5' DG A 43 45.650 63.130 32.710 1.00 0.00
-ATOM 1343 2H5' DG A 43 47.160 63.820 33.260 1.00 0.00
-ATOM 1344 C4' DG A 43 47.250 61.700 32.740 1.00 0.00
-ATOM 1345 H4' DG A 43 46.740 61.310 33.630 1.00 0.00
-ATOM 1346 O4' DG A 43 46.810 60.950 31.630 1.00 0.00
-ATOM 1347 C1' DG A 43 47.940 60.350 31.030 1.00 0.00
-ATOM 1348 H1' DG A 43 48.030 59.320 31.390 1.00 0.00
-ATOM 1349 N9 DG A 43 47.770 60.360 29.580 1.00 0.00
-ATOM 1350 C8 DG A 43 47.590 61.420 28.730 1.00 0.00
-ATOM 1351 H8 DG A 43 47.590 62.440 29.100 1.00 0.00
-ATOM 1352 N7 DG A 43 47.400 61.090 27.470 1.00 0.00
-ATOM 1353 C5 DG A 43 47.440 59.680 27.520 1.00 0.00
-ATOM 1354 C6 DG A 43 47.240 58.670 26.510 1.00 0.00
-ATOM 1355 O6 DG A 43 46.960 58.810 25.320 1.00 0.00
-ATOM 1356 N1 DG A 43 47.380 57.380 26.990 1.00 0.00
-ATOM 1357 H1 DG A 43 47.230 56.620 26.350 1.00 0.00
-ATOM 1358 C2 DG A 43 47.640 57.070 28.280 1.00 0.00
-ATOM 1359 N2 DG A 43 47.790 55.820 28.610 1.00 0.00
-ATOM 1360 H21 DG A 43 47.700 55.070 27.930 1.00 0.00
-ATOM 1361 H22 DG A 43 47.990 55.650 29.580 1.00 0.00
-ATOM 1362 N3 DG A 43 47.810 57.960 29.240 1.00 0.00
-ATOM 1363 C4 DG A 43 47.690 59.240 28.800 1.00 0.00
-ATOM 1364 C3' DG A 43 48.760 61.330 32.940 1.00 0.00
-ATOM 1365 H3' DG A 43 49.320 62.140 33.410 1.00 0.00
-ATOM 1366 C2' DG A 43 49.160 61.140 31.490 1.00 0.00
-ATOM 1367 1H2' DG A 43 49.230 62.100 30.980 1.00 0.00
-ATOM 1368 2H2' DG A 43 50.080 60.560 31.380 1.00 0.00
-ATOM 1369 O3' DG A 43 48.950 60.090 33.670 1.00 0.00
-ATOM 1370 P DA A 44 50.420 59.460 34.110 1.00 0.00
-ATOM 1371 O1P DA A 44 50.400 59.250 35.570 1.00 0.00
-ATOM 1372 O2P DA A 44 51.440 60.370 33.560 1.00 0.00
-ATOM 1373 O5' DA A 44 50.670 57.980 33.410 1.00 0.00
-ATOM 1374 C5' DA A 44 50.050 56.760 33.870 1.00 0.00
-ATOM 1375 1H5' DA A 44 48.990 56.970 33.870 1.00 0.00
-ATOM 1376 2H5' DA A 44 50.340 56.590 34.910 1.00 0.00
-ATOM 1377 C4' DA A 44 50.230 55.410 33.070 1.00 0.00
-ATOM 1378 H4' DA A 44 49.490 54.720 33.470 1.00 0.00
-ATOM 1379 O4' DA A 44 49.890 55.680 31.720 1.00 0.00
-ATOM 1380 C1' DA A 44 51.070 55.570 30.950 1.00 0.00
-ATOM 1381 H1' DA A 44 51.000 54.660 30.350 1.00 0.00
-ATOM 1382 N9 DA A 44 51.190 56.740 30.060 1.00 0.00
-ATOM 1383 C8 DA A 44 51.340 58.080 30.350 1.00 0.00
-ATOM 1384 H8 DA A 44 51.490 58.450 31.350 1.00 0.00
-ATOM 1385 N7 DA A 44 51.260 58.870 29.300 1.00 0.00
-ATOM 1386 C5 DA A 44 51.050 57.950 28.260 1.00 0.00
-ATOM 1387 C6 DA A 44 50.790 58.070 26.890 1.00 0.00
-ATOM 1388 N6 DA A 44 50.630 59.220 26.270 1.00 0.00
-ATOM 1389 H61 DA A 44 50.380 59.240 25.290 1.00 0.00
-ATOM 1390 H62 DA A 44 50.670 60.040 26.850 1.00 0.00
-ATOM 1391 N1 DA A 44 50.620 56.990 26.120 1.00 0.00
-ATOM 1392 C2 DA A 44 50.710 55.800 26.680 1.00 0.00
-ATOM 1393 H2 DA A 44 50.590 54.940 26.030 1.00 0.00
-ATOM 1394 N3 DA A 44 50.920 55.530 27.960 1.00 0.00
-ATOM 1395 C4 DA A 44 51.060 56.660 28.700 1.00 0.00
-ATOM 1396 C3' DA A 44 51.570 54.600 32.990 1.00 0.00
-ATOM 1397 H3' DA A 44 52.120 54.650 33.930 1.00 0.00
-ATOM 1398 C2' DA A 44 52.240 55.410 31.910 1.00 0.00
-ATOM 1399 1H2' DA A 44 52.580 56.370 32.300 1.00 0.00
-ATOM 1400 2H2' DA A 44 53.050 54.840 31.450 1.00 0.00
-ATOM 1401 O3' DA A 44 51.400 53.220 32.560 1.00 0.00
-ATOM 1402 P DT A 45 52.610 52.120 32.340 1.00 0.00
-ATOM 1403 O1P DT A 45 52.160 50.810 32.880 1.00 0.00
-ATOM 1404 O2P DT A 45 53.850 52.700 32.900 1.00 0.00
-ATOM 1405 O5' DT A 45 52.920 51.840 30.730 1.00 0.00
-ATOM 1406 C5' DT A 45 52.280 50.780 30.000 1.00 0.00
-ATOM 1407 1H5' DT A 45 51.210 50.960 30.070 1.00 0.00
-ATOM 1408 2H5' DT A 45 52.470 49.840 30.520 1.00 0.00
-ATOM 1409 C4' DT A 45 52.610 50.560 28.480 1.00 0.00
-ATOM 1410 H4' DT A 45 51.820 49.930 28.080 1.00 0.00
-ATOM 1411 O4' DT A 45 52.510 51.820 27.840 1.00 0.00
-ATOM 1412 C1' DT A 45 53.790 52.190 27.380 1.00 0.00
-ATOM 1413 H1' DT A 45 53.810 52.010 26.300 1.00 0.00
-ATOM 1414 N1 DT A 45 54.030 53.640 27.620 1.00 0.00
-ATOM 1415 C6 DT A 45 54.410 54.160 28.850 1.00 0.00
-ATOM 1416 H6 DT A 45 54.540 53.500 29.700 1.00 0.00
-ATOM 1417 C5 DT A 45 54.610 55.500 29.010 1.00 0.00
-ATOM 1418 C7 DT A 45 55.100 56.070 30.330 1.00 0.00
-ATOM 1419 H71 DT A 45 55.250 55.280 31.070 1.00 0.00
-ATOM 1420 H72 DT A 45 56.040 56.590 30.160 1.00 0.00
-ATOM 1421 H73 DT A 45 54.370 56.800 30.690 1.00 0.00
-ATOM 1422 C4 DT A 45 54.360 56.420 27.900 1.00 0.00
-ATOM 1423 O4 DT A 45 54.420 57.650 27.930 1.00 0.00
-ATOM 1424 N3 DT A 45 54.000 55.820 26.730 1.00 0.00
-ATOM 1425 H3 DT A 45 53.840 56.420 25.940 1.00 0.00
-ATOM 1426 C2 DT A 45 53.850 54.480 26.520 1.00 0.00
-ATOM 1427 O2 DT A 45 53.580 54.090 25.380 1.00 0.00
-ATOM 1428 C3' DT A 45 53.960 49.940 27.980 1.00 0.00
-ATOM 1429 H3' DT A 45 54.340 49.210 28.700 1.00 0.00
-ATOM 1430 C2' DT A 45 54.800 51.210 28.000 1.00 0.00
-ATOM 1431 1H2' DT A 45 55.050 51.480 29.020 1.00 0.00
-ATOM 1432 2H2' DT A 45 55.700 51.110 27.400 1.00 0.00
-ATOM 1433 O3' DT A 45 53.850 49.350 26.650 1.00 0.00
-ATOM 1434 P DG A 46 54.990 48.440 25.860 1.00 0.00
-ATOM 1435 O1P DG A 46 54.280 47.300 25.230 1.00 0.00
-ATOM 1436 O2P DG A 46 56.060 48.100 26.820 1.00 0.00
-ATOM 1437 O5' DG A 46 55.700 49.260 24.600 1.00 0.00
-ATOM 1438 C5' DG A 46 55.170 49.210 23.260 1.00 0.00
-ATOM 1439 1H5' DG A 46 54.130 49.520 23.340 1.00 0.00
-ATOM 1440 2H5' DG A 46 55.170 48.170 22.940 1.00 0.00
-ATOM 1441 C4' DG A 46 55.770 50.070 22.080 1.00 0.00
-ATOM 1442 H4' DG A 46 55.110 49.900 21.230 1.00 0.00
-ATOM 1443 O4' DG A 46 55.620 51.420 22.440 1.00 0.00
-ATOM 1444 C1' DG A 46 56.910 51.970 22.630 1.00 0.00
-ATOM 1445 H1' DG A 46 57.100 52.670 21.810 1.00 0.00
-ATOM 1446 N9 DG A 46 56.970 52.710 23.890 1.00 0.00
-ATOM 1447 C8 DG A 46 56.930 52.290 25.200 1.00 0.00
-ATOM 1448 H8 DG A 46 56.820 51.250 25.470 1.00 0.00
-ATOM 1449 N7 DG A 46 57.000 53.260 26.070 1.00 0.00
-ATOM 1450 C5 DG A 46 57.110 54.410 25.280 1.00 0.00
-ATOM 1451 C6 DG A 46 57.210 55.820 25.590 1.00 0.00
-ATOM 1452 O6 DG A 46 57.210 56.390 26.670 1.00 0.00
-ATOM 1453 N1 DG A 46 57.280 56.620 24.470 1.00 0.00
-ATOM 1454 H1 DG A 46 57.330 57.610 24.630 1.00 0.00
-ATOM 1455 C2 DG A 46 57.260 56.150 23.200 1.00 0.00
-ATOM 1456 N2 DG A 46 57.350 56.990 22.210 1.00 0.00
-ATOM 1457 H21 DG A 46 57.390 57.990 22.400 1.00 0.00
-ATOM 1458 H22 DG A 46 57.330 56.600 21.290 1.00 0.00
-ATOM 1459 N3 DG A 46 57.180 54.880 22.850 1.00 0.00
-ATOM 1460 C4 DG A 46 57.100 54.070 23.940 1.00 0.00
-ATOM 1461 C3' DG A 46 57.230 49.950 21.510 1.00 0.00
-ATOM 1462 H3' DG A 46 57.590 48.930 21.570 1.00 0.00
-ATOM 1463 C2' DG A 46 57.940 50.840 22.520 1.00 0.00
-ATOM 1464 1H2' DG A 46 58.050 50.330 23.480 1.00 0.00
-ATOM 1465 2H2' DG A 46 58.900 51.200 22.160 1.00 0.00
-ATOM 1466 O3' DG A 46 57.330 50.470 20.140 1.00 0.00
-ATOM 1467 P DG A 47 58.660 50.440 19.160 1.00 0.00
-ATOM 1468 O1P DG A 47 58.160 50.080 17.800 1.00 0.00
-ATOM 1469 O2P DG A 47 59.630 49.490 19.750 1.00 0.00
-ATOM 1470 O5' DG A 47 59.420 51.910 18.990 1.00 0.00
-ATOM 1471 C5' DG A 47 59.080 52.850 17.930 1.00 0.00
-ATOM 1472 1H5' DG A 47 58.000 53.000 18.010 1.00 0.00
-ATOM 1473 2H5' DG A 47 59.260 52.360 16.980 1.00 0.00
-ATOM 1474 C4' DG A 47 59.690 54.310 17.850 1.00 0.00
-ATOM 1475 H4' DG A 47 59.090 54.840 17.120 1.00 0.00
-ATOM 1476 O4' DG A 47 59.430 54.920 19.090 1.00 0.00
-ATOM 1477 C1' DG A 47 60.670 55.230 19.690 1.00 0.00
-ATOM 1478 H1' DG A 47 60.820 56.320 19.640 1.00 0.00
-ATOM 1479 N9 DG A 47 60.670 54.830 21.110 1.00 0.00
-ATOM 1480 C8 DG A 47 60.560 53.590 21.680 1.00 0.00
-ATOM 1481 H8 DG A 47 60.440 52.690 21.100 1.00 0.00
-ATOM 1482 N7 DG A 47 60.610 53.610 22.980 1.00 0.00
-ATOM 1483 C5 DG A 47 60.700 54.980 23.290 1.00 0.00
-ATOM 1484 C6 DG A 47 60.710 55.710 24.530 1.00 0.00
-ATOM 1485 O6 DG A 47 60.620 55.290 25.680 1.00 0.00
-ATOM 1486 N1 DG A 47 60.830 57.080 24.360 1.00 0.00
-ATOM 1487 H1 DG A 47 60.760 57.640 25.190 1.00 0.00
-ATOM 1488 C2 DG A 47 60.910 57.690 23.160 1.00 0.00
-ATOM 1489 N2 DG A 47 61.000 58.980 23.110 1.00 0.00
-ATOM 1490 H21 DG A 47 60.900 59.520 23.970 1.00 0.00
-ATOM 1491 H22 DG A 47 60.960 59.420 22.210 1.00 0.00
-ATOM 1492 N3 DG A 47 60.910 57.070 21.990 1.00 0.00
-ATOM 1493 C4 DG A 47 60.780 55.720 22.130 1.00 0.00
-ATOM 1494 C3' DG A 47 61.180 54.650 17.510 1.00 0.00
-ATOM 1495 H3' DG A 47 61.620 53.910 16.840 1.00 0.00
-ATOM 1496 C2' DG A 47 61.780 54.550 18.900 1.00 0.00
-ATOM 1497 1H2' DG A 47 61.880 53.500 19.190 1.00 0.00
-ATOM 1498 2H2' DG A 47 62.720 55.080 18.980 1.00 0.00
-ATOM 1499 O3' DG A 47 61.350 56.000 16.970 1.00 0.00
-ATOM 1500 P DC A 48 62.780 56.690 16.460 1.00 0.00
-ATOM 1501 O1P DC A 48 62.480 57.390 15.190 1.00 0.00
-ATOM 1502 O2P DC A 48 63.770 55.590 16.390 1.00 0.00
-ATOM 1503 O5' DC A 48 63.380 57.840 17.510 1.00 0.00
-ATOM 1504 C5' DC A 48 63.040 59.250 17.440 1.00 0.00
-ATOM 1505 1H5' DC A 48 61.950 59.290 17.400 1.00 0.00
-ATOM 1506 2H5' DC A 48 63.400 59.640 16.490 1.00 0.00
-ATOM 1507 C4' DC A 48 63.470 60.260 18.580 1.00 0.00
-ATOM 1508 H4' DC A 48 62.790 61.110 18.480 1.00 0.00
-ATOM 1509 O4' DC A 48 63.160 59.660 19.820 1.00 0.00
-ATOM 1510 C1' DC A 48 64.310 59.670 20.650 1.00 0.00
-ATOM 1511 H1' DC A 48 64.210 60.480 21.390 1.00 0.00
-ATOM 1512 N1 DC A 48 64.410 58.360 21.330 1.00 0.00
-ATOM 1513 C6 DC A 48 64.340 57.180 20.630 1.00 0.00
-ATOM 1514 H6 DC A 48 64.260 57.220 19.560 1.00 0.00
-ATOM 1515 C5 DC A 48 64.310 55.990 21.280 1.00 0.00
-ATOM 1516 H5 DC A 48 64.230 55.060 20.750 1.00 0.00
-ATOM 1517 C4 DC A 48 64.360 56.040 22.700 1.00 0.00
-ATOM 1518 N4 DC A 48 64.240 54.960 23.400 1.00 0.00
-ATOM 1519 H41 DC A 48 64.220 55.100 24.410 1.00 0.00
-ATOM 1520 H42 DC A 48 63.860 54.130 23.010 1.00 0.00
-ATOM 1521 N3 DC A 48 64.490 57.160 23.380 1.00 0.00
-ATOM 1522 C2 DC A 48 64.500 58.340 22.720 1.00 0.00
-ATOM 1523 O2 DC A 48 64.590 59.370 23.370 1.00 0.00
-ATOM 1524 C3' DC A 48 64.890 60.910 18.730 1.00 0.00
-ATOM 1525 H3' DC A 48 65.440 60.880 17.800 1.00 0.00
-ATOM 1526 C2' DC A 48 65.510 59.970 19.750 1.00 0.00
-ATOM 1527 1H2' DC A 48 65.860 59.060 19.260 1.00 0.00
-ATOM 1528 2H2' DC A 48 66.320 60.430 20.320 1.00 0.00
-ATOM 1529 O3' DC A 48 64.820 62.270 19.240 1.00 0.00
-ATOM 1530 P DA A 49 66.110 63.280 19.520 1.00 0.00
-ATOM 1531 O1P DA A 49 65.730 64.620 18.990 1.00 0.00
-ATOM 1532 O2P DA A 49 67.300 62.650 18.890 1.00 0.00
-ATOM 1533 O5' DA A 49 66.420 63.460 21.140 1.00 0.00
-ATOM 1534 C5' DA A 49 65.700 64.400 21.980 1.00 0.00
-ATOM 1535 1H5' DA A 49 64.640 64.240 21.770 1.00 0.00
-ATOM 1536 2H5' DA A 49 65.930 65.410 21.660 1.00 0.00
-ATOM 1537 C4' DA A 49 65.820 64.350 23.550 1.00 0.00
-ATOM 1538 H4' DA A 49 64.940 64.870 23.940 1.00 0.00
-ATOM 1539 O4' DA A 49 65.680 63.000 23.940 1.00 0.00
-ATOM 1540 C1' DA A 49 66.770 62.620 24.760 1.00 0.00
-ATOM 1541 H1' DA A 49 66.460 62.590 25.810 1.00 0.00
-ATOM 1542 N9 DA A 49 67.230 61.290 24.330 1.00 0.00
-ATOM 1543 C8 DA A 49 67.560 60.870 23.060 1.00 0.00
-ATOM 1544 H8 DA A 49 67.560 61.540 22.220 1.00 0.00
-ATOM 1545 N7 DA A 49 67.860 59.600 22.970 1.00 0.00
-ATOM 1546 C5 DA A 49 67.650 59.160 24.300 1.00 0.00
-ATOM 1547 C6 DA A 49 67.660 57.920 24.960 1.00 0.00
-ATOM 1548 N6 DA A 49 67.880 56.760 24.370 1.00 0.00
-ATOM 1549 H61 DA A 49 67.740 55.930 24.940 1.00 0.00
-ATOM 1550 H62 DA A 49 67.910 56.740 23.380 1.00 0.00
-ATOM 1551 N1 DA A 49 67.400 57.820 26.260 1.00 0.00
-ATOM 1552 C2 DA A 49 67.120 58.920 26.950 1.00 0.00
-ATOM 1553 H2 DA A 49 66.910 58.800 28.000 1.00 0.00
-ATOM 1554 N3 DA A 49 67.070 60.160 26.460 1.00 0.00
-ATOM 1555 C4 DA A 49 67.310 60.200 25.130 1.00 0.00
-ATOM 1556 C3' DA A 49 67.030 64.930 24.360 1.00 0.00
-ATOM 1557 H3' DA A 49 67.580 65.660 23.770 1.00 0.00
-ATOM 1558 C2' DA A 49 67.860 63.670 24.570 1.00 0.00
-ATOM 1559 1H2' DA A 49 68.460 63.470 23.690 1.00 0.00
-ATOM 1560 2H2' DA A 49 68.490 63.740 25.460 1.00 0.00
-ATOM 1561 O3' DA A 49 66.620 65.510 25.620 1.00 0.00
-ATOM 1562 P DT A 50 67.640 66.150 26.750 1.00 0.00
-ATOM 1563 O1P DT A 50 67.020 67.400 27.240 1.00 0.00
-ATOM 1564 O2P DT A 50 68.960 66.280 26.090 1.00 0.00
-ATOM 1565 O5' DT A 50 67.800 65.100 28.030 1.00 0.00
-ATOM 1566 C5' DT A 50 66.770 64.920 29.050 1.00 0.00
-ATOM 1567 1H5' DT A 50 65.830 64.780 28.520 1.00 0.00
-ATOM 1568 2H5' DT A 50 66.680 65.830 29.630 1.00 0.00
-ATOM 1569 C4' DT A 50 66.870 63.710 30.060 1.00 0.00
-ATOM 1570 H4' DT A 50 65.870 63.530 30.460 1.00 0.00
-ATOM 1571 O4' DT A 50 67.220 62.580 29.280 1.00 0.00
-ATOM 1572 C1' DT A 50 68.270 61.880 29.910 1.00 0.00
-ATOM 1573 H1' DT A 50 67.870 61.100 30.560 1.00 0.00
-ATOM 1574 N1 DT A 50 69.170 61.320 28.880 1.00 0.00
-ATOM 1575 C6 DT A 50 69.690 62.140 27.890 1.00 0.00
-ATOM 1576 H6 DT A 50 69.420 63.180 27.910 1.00 0.00
-ATOM 1577 C5 DT A 50 70.460 61.620 26.900 1.00 0.00
-ATOM 1578 C7 DT A 50 71.030 62.540 25.840 1.00 0.00
-ATOM 1579 H71 DT A 50 70.830 63.580 26.090 1.00 0.00
-ATOM 1580 H72 DT A 50 72.100 62.380 25.780 1.00 0.00
-ATOM 1581 H73 DT A 50 70.580 62.290 24.880 1.00 0.00
-ATOM 1582 C4 DT A 50 70.740 60.190 26.850 1.00 0.00
-ATOM 1583 O4 DT A 50 71.370 59.620 25.950 1.00 0.00
-ATOM 1584 N3 DT A 50 70.240 59.460 27.900 1.00 0.00
-ATOM 1585 H3 DT A 50 70.360 58.460 27.920 1.00 0.00
-ATOM 1586 C2 DT A 50 69.490 59.970 28.940 1.00 0.00
-ATOM 1587 O2 DT A 50 69.170 59.230 29.850 1.00 0.00
-ATOM 1588 C3' DT A 50 67.820 63.710 31.310 1.00 0.00
-ATOM 1589 H3' DT A 50 68.110 64.720 31.580 1.00 0.00
-ATOM 1590 C2' DT A 50 68.990 62.920 30.770 1.00 0.00
-ATOM 1591 1H2' DT A 50 69.630 63.570 30.170 1.00 0.00
-ATOM 1592 2H2' DT A 50 69.560 62.430 31.550 1.00 0.00
-ATOM 1593 O3' DT A 50 67.280 63.020 32.460 1.00 0.00
-ATOM 1594 P DT A 51 68.070 62.870 33.910 1.00 0.00
-ATOM 1595 O1P DT A 51 67.130 63.260 34.980 1.00 0.00
-ATOM 1596 O2P DT A 51 69.310 63.670 33.780 1.00 0.00
-ATOM 1597 O5' DT A 51 68.520 61.290 34.160 1.00 0.00
-ATOM 1598 C5' DT A 51 67.600 60.250 34.590 1.00 0.00
-ATOM 1599 1H5' DT A 51 66.750 60.330 33.910 1.00 0.00
-ATOM 1600 2H5' DT A 51 67.220 60.490 35.590 1.00 0.00
-ATOM 1601 C4' DT A 51 68.030 58.730 34.560 1.00 0.00
-ATOM 1602 H4' DT A 51 67.110 58.150 34.580 1.00 0.00
-ATOM 1603 O4' DT A 51 68.640 58.540 33.300 1.00 0.00
-ATOM 1604 C1' DT A 51 69.950 58.060 33.510 1.00 0.00
-ATOM 1605 H1' DT A 51 69.940 56.970 33.380 1.00 0.00
-ATOM 1606 N1 DT A 51 70.880 58.690 32.550 1.00 0.00
-ATOM 1607 C6 DT A 51 71.130 60.050 32.570 1.00 0.00
-ATOM 1608 H6 DT A 51 70.650 60.650 33.330 1.00 0.00
-ATOM 1609 C5 DT A 51 71.930 60.630 31.640 1.00 0.00
-ATOM 1610 C7 DT A 51 72.230 62.110 31.720 1.00 0.00
-ATOM 1611 H71 DT A 51 71.720 62.570 32.570 1.00 0.00
-ATOM 1612 H72 DT A 51 73.300 62.250 31.820 1.00 0.00
-ATOM 1613 H73 DT A 51 71.900 62.590 30.800 1.00 0.00
-ATOM 1614 C4 DT A 51 72.500 59.830 30.570 1.00 0.00
-ATOM 1615 O4 DT A 51 73.160 60.270 29.620 1.00 0.00
-ATOM 1616 N3 DT A 51 72.240 58.490 30.640 1.00 0.00
-ATOM 1617 H3 DT A 51 72.660 57.870 29.980 1.00 0.00
-ATOM 1618 C2 DT A 51 71.500 57.870 31.610 1.00 0.00
-ATOM 1619 O2 DT A 51 71.470 56.640 31.620 1.00 0.00
-ATOM 1620 C3' DT A 51 68.970 58.060 35.620 1.00 0.00
-ATOM 1621 H3' DT A 51 68.880 58.540 36.590 1.00 0.00
-ATOM 1622 C2' DT A 51 70.290 58.360 34.960 1.00 0.00
-ATOM 1623 1H2' DT A 51 70.550 59.400 35.130 1.00 0.00
-ATOM 1624 2H2' DT A 51 71.070 57.690 35.320 1.00 0.00
-ATOM 1625 O3' DT A 51 68.820 56.620 35.740 1.00 0.00
-ATOM 1626 P DT A 52 69.720 55.650 36.750 1.00 0.00
-ATOM 1627 O1P DT A 52 68.800 54.760 37.480 1.00 0.00
-ATOM 1628 O2P DT A 52 70.600 56.550 37.540 1.00 0.00
-ATOM 1629 O5' DT A 52 70.740 54.670 35.900 1.00 0.00
-ATOM 1630 C5' DT A 52 70.350 53.370 35.400 1.00 0.00
-ATOM 1631 1H5' DT A 52 69.510 53.540 34.730 1.00 0.00
-ATOM 1632 2H5' DT A 52 69.980 52.770 36.230 1.00 0.00
-ATOM 1633 C4' DT A 52 71.400 52.510 34.600 1.00 0.00
-ATOM 1634 H4' DT A 52 70.830 51.780 34.030 1.00 0.00
-ATOM 1635 O4' DT A 52 72.040 53.380 33.690 1.00 0.00
-ATOM 1636 C1' DT A 52 73.380 53.550 34.100 1.00 0.00
-ATOM 1637 H1' DT A 52 73.990 52.940 33.410 1.00 0.00
-ATOM 1638 N1 DT A 52 73.770 54.980 33.950 1.00 0.00
-ATOM 1639 C6 DT A 52 73.480 55.960 34.890 1.00 0.00
-ATOM 1640 H6 DT A 52 72.950 55.690 35.800 1.00 0.00
-ATOM 1641 C5 DT A 52 73.800 57.260 34.670 1.00 0.00
-ATOM 1642 C7 DT A 52 73.560 58.320 35.730 1.00 0.00
-ATOM 1643 H71 DT A 52 73.030 57.900 36.590 1.00 0.00
-ATOM 1644 H72 DT A 52 74.510 58.740 36.040 1.00 0.00
-ATOM 1645 H73 DT A 52 72.970 59.130 35.300 1.00 0.00
-ATOM 1646 C4 DT A 52 74.390 57.670 33.390 1.00 0.00
-ATOM 1647 O4 DT A 52 74.630 58.810 33.030 1.00 0.00
-ATOM 1648 N3 DT A 52 74.680 56.630 32.540 1.00 0.00
-ATOM 1649 H3 DT A 52 75.180 56.850 31.700 1.00 0.00
-ATOM 1650 C2 DT A 52 74.470 55.300 32.790 1.00 0.00
-ATOM 1651 O2 DT A 52 74.950 54.480 32.010 1.00 0.00
-ATOM 1652 C3' DT A 52 72.560 51.740 35.310 1.00 0.00
-ATOM 1653 H3' DT A 52 72.240 51.350 36.280 1.00 0.00
-ATOM 1654 C2' DT A 52 73.520 52.900 35.480 1.00 0.00
-ATOM 1655 1H2' DT A 52 73.170 53.560 36.280 1.00 0.00
-ATOM 1656 2H2' DT A 52 74.520 52.540 35.670 1.00 0.00
-ATOM 1657 O3' DT A 52 73.150 50.680 34.490 1.00 0.00
-ATOM 1658 P DC A 53 74.330 49.610 34.960 1.00 0.00
-ATOM 1659 O1P DC A 53 73.920 48.250 34.540 1.00 0.00
-ATOM 1660 O2P DC A 53 74.600 49.830 36.390 1.00 0.00
-ATOM 1661 O5' DC A 53 75.760 49.890 34.180 1.00 0.00
-ATOM 1662 C5' DC A 53 76.080 49.320 32.890 1.00 0.00
-ATOM 1663 1H5' DC A 53 75.280 49.630 32.220 1.00 0.00
-ATOM 1664 2H5' DC A 53 76.010 48.240 32.980 1.00 0.00
-ATOM 1665 C4' DC A 53 77.440 49.680 32.190 1.00 0.00
-ATOM 1666 H4' DC A 53 77.360 49.300 31.170 1.00 0.00
-ATOM 1667 O4' DC A 53 77.460 51.090 32.100 1.00 0.00
-ATOM 1668 C1' DC A 53 78.520 51.570 32.910 1.00 0.00
-ATOM 1669 H1' DC A 53 79.320 51.850 32.230 1.00 0.00
-ATOM 1670 N1 DC A 53 78.080 52.770 33.680 1.00 0.00
-ATOM 1671 C6 DC A 53 77.230 52.730 34.760 1.00 0.00
-ATOM 1672 H6 DC A 53 76.840 51.780 35.110 1.00 0.00
-ATOM 1673 C5 DC A 53 76.850 53.880 35.370 1.00 0.00
-ATOM 1674 H5 DC A 53 76.180 53.860 36.220 1.00 0.00
-ATOM 1675 C4 DC A 53 77.330 55.100 34.830 1.00 0.00
-ATOM 1676 N4 DC A 53 76.930 56.240 35.310 1.00 0.00
-ATOM 1677 H41 DC A 53 77.300 57.090 34.900 1.00 0.00
-ATOM 1678 H42 DC A 53 76.250 56.260 36.050 1.00 0.00
-ATOM 1679 N3 DC A 53 78.180 55.160 33.830 1.00 0.00
-ATOM 1680 C2 DC A 53 78.580 54.000 33.260 1.00 0.00
-ATOM 1681 O2 DC A 53 79.450 54.060 32.390 1.00 0.00
-ATOM 1682 C3' DC A 53 78.840 49.260 32.740 1.00 0.00
-ATOM 1683 H3' DC A 53 78.770 48.300 33.260 1.00 0.00
-ATOM 1684 C2' DC A 53 79.050 50.390 33.730 1.00 0.00
-ATOM 1685 1H2' DC A 53 78.450 50.230 34.630 1.00 0.00
-ATOM 1686 2H2' DC A 53 80.100 50.520 33.960 1.00 0.00
-ATOM 1687 O3' DC A 53 79.900 49.230 31.730 1.00 0.00
-ATOM 1688 P DT A 54 81.480 48.760 31.950 1.00 0.00
-ATOM 1689 O1P DT A 54 81.880 48.000 30.730 1.00 0.00
-ATOM 1690 O2P DT A 54 81.560 48.020 33.230 1.00 0.00
-ATOM 1691 O5' DT A 54 82.540 50.040 32.050 1.00 0.00
-ATOM 1692 C5' DT A 54 83.250 50.540 30.890 1.00 0.00
-ATOM 1693 1H5' DT A 54 82.480 50.740 30.140 1.00 0.00
-ATOM 1694 2H5' DT A 54 83.870 49.740 30.500 1.00 0.00
-ATOM 1695 C4' DT A 54 84.130 51.850 30.940 1.00 0.00
-ATOM 1696 H4' DT A 54 84.290 52.140 29.910 1.00 0.00
-ATOM 1697 O4' DT A 54 83.320 52.850 31.510 1.00 0.00
-ATOM 1698 C1' DT A 54 83.970 53.370 32.660 1.00 0.00
-ATOM 1699 H1' DT A 54 84.430 54.320 32.380 1.00 0.00
-ATOM 1700 N1 DT A 54 82.960 53.600 33.730 1.00 0.00
-ATOM 1701 C6 DT A 54 82.370 52.560 34.430 1.00 0.00
-ATOM 1702 H6 DT A 54 82.630 51.540 34.200 1.00 0.00
-ATOM 1703 C5 DT A 54 81.440 52.820 35.400 1.00 0.00
-ATOM 1704 C7 DT A 54 80.860 51.700 36.230 1.00 0.00
-ATOM 1705 H71 DT A 54 81.270 50.730 35.950 1.00 0.00
-ATOM 1706 H72 DT A 54 81.080 51.890 37.290 1.00 0.00
-ATOM 1707 H73 DT A 54 79.770 51.710 36.130 1.00 0.00
-ATOM 1708 C4 DT A 54 81.000 54.190 35.650 1.00 0.00
-ATOM 1709 O4 DT A 54 80.130 54.540 36.430 1.00 0.00
-ATOM 1710 N3 DT A 54 81.640 55.140 34.900 1.00 0.00
-ATOM 1711 H3 DT A 54 81.380 56.100 35.080 1.00 0.00
-ATOM 1712 C2 DT A 54 82.630 54.930 33.990 1.00 0.00
-ATOM 1713 O2 DT A 54 83.210 55.880 33.460 1.00 0.00
-ATOM 1714 C3' DT A 54 85.540 51.970 31.620 1.00 0.00
-ATOM 1715 H3' DT A 54 86.040 51.000 31.660 1.00 0.00
-ATOM 1716 C2' DT A 54 85.100 52.400 33.020 1.00 0.00
-ATOM 1717 1H2' DT A 54 84.740 51.540 33.570 1.00 0.00
-ATOM 1718 2H2' DT A 54 85.900 52.900 33.560 1.00 0.00
-ATOM 1719 O3' DT A 54 86.400 52.970 30.980 1.00 0.00
-ATOM 1720 P DA A 55 87.990 53.280 31.320 1.00 0.00
-ATOM 1721 O1P DA A 55 88.680 53.460 30.010 1.00 0.00
-ATOM 1722 O2P DA A 55 88.490 52.160 32.160 1.00 0.00
-ATOM 1723 O5' DA A 55 88.240 54.690 32.170 1.00 0.00
-ATOM 1724 C5' DA A 55 88.490 55.970 31.520 1.00 0.00
-ATOM 1725 1H5' DA A 55 87.710 56.070 30.760 1.00 0.00
-ATOM 1726 2H5' DA A 55 89.440 55.890 30.990 1.00 0.00
-ATOM 1727 C4' DA A 55 88.480 57.340 32.300 1.00 0.00
-ATOM 1728 H4' DA A 55 88.410 58.110 31.540 1.00 0.00
-ATOM 1729 O4' DA A 55 87.280 57.390 33.020 1.00 0.00
-ATOM 1730 C1' DA A 55 87.560 57.540 34.400 1.00 0.00
-ATOM 1731 H1' DA A 55 87.300 58.560 34.720 1.00 0.00
-ATOM 1732 N9 DA A 55 86.760 56.580 35.160 1.00 0.00
-ATOM 1733 C8 DA A 55 86.700 55.210 35.060 1.00 0.00
-ATOM 1734 H8 DA A 55 87.310 54.660 34.370 1.00 0.00
-ATOM 1735 N7 DA A 55 85.850 54.640 35.870 1.00 0.00
-ATOM 1736 C5 DA A 55 85.280 55.750 36.530 1.00 0.00
-ATOM 1737 C6 DA A 55 84.250 55.950 37.470 1.00 0.00
-ATOM 1738 N6 DA A 55 83.500 55.000 37.980 1.00 0.00
-ATOM 1739 H61 DA A 55 82.740 55.260 38.610 1.00 0.00
-ATOM 1740 H62 DA A 55 83.690 54.040 37.780 1.00 0.00
-ATOM 1741 N1 DA A 55 83.940 57.170 37.890 1.00 0.00
-ATOM 1742 C2 DA A 55 84.600 58.220 37.410 1.00 0.00
-ATOM 1743 H2 DA A 55 84.310 59.190 37.790 1.00 0.00
-ATOM 1744 N3 DA A 55 85.590 58.200 36.530 1.00 0.00
-ATOM 1745 C4 DA A 55 85.850 56.930 36.110 1.00 0.00
-ATOM 1746 C3' DA A 55 89.600 57.850 33.280 1.00 0.00
-ATOM 1747 H3' DA A 55 90.560 57.400 33.050 1.00 0.00
-ATOM 1748 C2' DA A 55 89.060 57.320 34.600 1.00 0.00
-ATOM 1749 1H2' DA A 55 89.280 56.260 34.690 1.00 0.00
-ATOM 1750 2H2' DA A 55 89.440 57.880 35.450 1.00 0.00
-ATOM 1751 O3' DA A 55 89.710 59.300 33.300 1.00 0.00
-ATOM 1752 P DC A 56 90.780 60.190 34.190 1.00 0.00
-ATOM 1753 O1P DC A 56 91.240 61.300 33.310 1.00 0.00
-ATOM 1754 O2P DC A 56 91.830 59.250 34.640 1.00 0.00
-ATOM 1755 O5' DC A 56 90.100 60.880 35.540 1.00 0.00
-ATOM 1756 C5' DC A 56 89.370 62.140 35.510 1.00 0.00
-ATOM 1757 1H5' DC A 56 88.650 62.060 34.700 1.00 0.00
-ATOM 1758 2H5' DC A 56 90.060 62.940 35.240 1.00 0.00
-ATOM 1759 C4' DC A 56 88.520 62.640 36.750 1.00 0.00
-ATOM 1760 H4' DC A 56 87.820 63.370 36.360 1.00 0.00
-ATOM 1761 O4' DC A 56 87.740 61.550 37.180 1.00 0.00
-ATOM 1762 C1' DC A 56 87.830 61.400 38.590 1.00 0.00
-ATOM 1763 H1' DC A 56 86.960 61.860 39.070 1.00 0.00
-ATOM 1764 N1 DC A 56 87.900 59.950 38.880 1.00 0.00
-ATOM 1765 C6 DC A 56 88.740 59.130 38.170 1.00 0.00
-ATOM 1766 H6 DC A 56 89.370 59.580 37.420 1.00 0.00
-ATOM 1767 C5 DC A 56 88.730 57.790 38.370 1.00 0.00
-ATOM 1768 H5 DC A 56 89.360 57.140 37.800 1.00 0.00
-ATOM 1769 C4 DC A 56 87.800 57.300 39.330 1.00 0.00
-ATOM 1770 N4 DC A 56 87.660 56.030 39.510 1.00 0.00
-ATOM 1771 H41 DC A 56 86.900 55.780 40.140 1.00 0.00
-ATOM 1772 H42 DC A 56 88.030 55.370 38.870 1.00 0.00
-ATOM 1773 N3 DC A 56 87.030 58.080 40.050 1.00 0.00
-ATOM 1774 C2 DC A 56 87.040 59.410 39.850 1.00 0.00
-ATOM 1775 O2 DC A 56 86.320 60.130 40.520 1.00 0.00
-ATOM 1776 C3' DC A 56 89.120 63.310 38.030 1.00 0.00
-ATOM 1777 H3' DC A 56 90.140 63.650 37.870 1.00 0.00
-ATOM 1778 C2' DC A 56 89.100 62.140 39.020 1.00 0.00
-ATOM 1779 1H2' DC A 56 89.980 61.520 38.870 1.00 0.00
-ATOM 1780 2H2' DC A 56 89.030 62.470 40.050 1.00 0.00
-ATOM 1781 O3' DC A 56 88.300 64.410 38.510 1.00 0.00
-ATOM 1782 P DC A 57 88.600 65.330 39.850 1.00 0.00
-ATOM 1783 O1P DC A 57 88.260 66.730 39.490 1.00 0.00
-ATOM 1784 O2P DC A 57 90.010 65.070 40.210 1.00 0.00
-ATOM 1785 O5' DC A 57 87.640 64.870 41.120 1.00 0.00
-ATOM 1786 C5' DC A 57 86.230 65.240 41.250 1.00 0.00
-ATOM 1787 1H5' DC A 57 85.780 65.020 40.280 1.00 0.00
-ATOM 1788 2H5' DC A 57 86.160 66.310 41.400 1.00 0.00
-ATOM 1789 C4' DC A 57 85.300 64.530 42.300 1.00 0.00
-ATOM 1790 H4' DC A 57 84.270 64.690 41.960 1.00 0.00
-ATOM 1791 O4' DC A 57 85.540 63.140 42.220 1.00 0.00
-ATOM 1792 C1' DC A 57 85.730 62.610 43.520 1.00 0.00
-ATOM 1793 H1' DC A 57 84.790 62.170 43.880 1.00 0.00
-ATOM 1794 N1 DC A 57 86.800 61.590 43.430 1.00 0.00
-ATOM 1795 C6 DC A 57 87.990 61.890 42.820 1.00 0.00
-ATOM 1796 H6 DC A 57 88.130 62.900 42.450 1.00 0.00
-ATOM 1797 C5 DC A 57 88.930 60.940 42.630 1.00 0.00
-ATOM 1798 H5 DC A 57 89.850 61.160 42.120 1.00 0.00
-ATOM 1799 C4 DC A 57 88.600 59.640 43.100 1.00 0.00
-ATOM 1800 N4 DC A 57 89.390 58.640 42.850 1.00 0.00
-ATOM 1801 H41 DC A 57 88.980 57.730 43.110 1.00 0.00
-ATOM 1802 H42 DC A 57 90.130 58.720 42.210 1.00 0.00
-ATOM 1803 N3 DC A 57 87.490 59.330 43.700 1.00 0.00
-ATOM 1804 C2 DC A 57 86.550 60.290 43.880 1.00 0.00
-ATOM 1805 O2 DC A 57 85.500 59.980 44.430 1.00 0.00
-ATOM 1806 C3' DC A 57 85.270 64.900 43.820 1.00 0.00
-ATOM 1807 H3' DC A 57 85.710 65.870 44.010 1.00 0.00
-ATOM 1808 C2' DC A 57 86.120 63.780 44.410 1.00 0.00
-ATOM 1809 1H2' DC A 57 87.170 64.030 44.310 1.00 0.00
-ATOM 1810 2H2' DC A 57 85.880 63.580 45.460 1.00 0.00
-ATOM 1811 O3' DC A 57 83.920 64.860 44.360 1.00 0.00
-ATOM 1812 P DG A 58 83.520 65.170 45.920 1.00 0.00
-ATOM 1813 O1P DG A 58 82.350 66.090 45.900 1.00 0.00
-ATOM 1814 O2P DG A 58 84.750 65.700 46.570 1.00 0.00
-ATOM 1815 O5' DG A 58 83.080 63.770 46.690 1.00 0.00
-ATOM 1816 C5' DG A 58 81.780 63.130 46.510 1.00 0.00
-ATOM 1817 1H5' DG A 58 81.620 63.070 45.430 1.00 0.00
-ATOM 1818 2H5' DG A 58 81.000 63.780 46.900 1.00 0.00
-ATOM 1819 C4' DG A 58 81.540 61.670 47.050 1.00 0.00
-ATOM 1820 H4' DG A 58 80.660 61.270 46.550 1.00 0.00
-ATOM 1821 O4' DG A 58 82.660 60.920 46.640 1.00 0.00
-ATOM 1822 C1' DG A 58 83.270 60.390 47.800 1.00 0.00
-ATOM 1823 H1' DG A 58 82.950 59.350 47.930 1.00 0.00
-ATOM 1824 N9 DG A 58 84.730 60.440 47.680 1.00 0.00
-ATOM 1825 C8 DG A 58 85.550 61.510 47.430 1.00 0.00
-ATOM 1826 H8 DG A 58 85.150 62.510 47.350 1.00 0.00
-ATOM 1827 N7 DG A 58 86.810 61.200 47.260 1.00 0.00
-ATOM 1828 C5 DG A 58 86.810 59.790 47.410 1.00 0.00
-ATOM 1829 C6 DG A 58 87.840 58.800 47.280 1.00 0.00
-ATOM 1830 O6 DG A 58 89.030 58.960 46.990 1.00 0.00
-ATOM 1831 N1 DG A 58 87.390 57.510 47.500 1.00 0.00
-ATOM 1832 H1 DG A 58 88.040 56.750 47.370 1.00 0.00
-ATOM 1833 C2 DG A 58 86.120 57.190 47.850 1.00 0.00
-ATOM 1834 N2 DG A 58 85.810 55.940 48.010 1.00 0.00
-ATOM 1835 H21 DG A 58 86.470 55.190 47.840 1.00 0.00
-ATOM 1836 H22 DG A 58 84.850 55.740 48.240 1.00 0.00
-ATOM 1837 N3 DG A 58 85.150 58.070 48.010 1.00 0.00
-ATOM 1838 C4 DG A 58 85.550 59.350 47.740 1.00 0.00
-ATOM 1839 C3' DG A 58 81.330 61.350 48.570 1.00 0.00
-ATOM 1840 H3' DG A 58 80.840 62.170 49.090 1.00 0.00
-ATOM 1841 C2' DG A 58 82.780 61.200 48.980 1.00 0.00
-ATOM 1842 1H2' DG A 58 83.260 62.170 49.040 1.00 0.00
-ATOM 1843 2H2' DG A 58 82.870 60.640 49.900 1.00 0.00
-ATOM 1844 O3' DG A 58 80.630 60.100 48.820 1.00 0.00
-ATOM 1845 P DT A 59 80.280 59.490 50.320 1.00 0.00
-ATOM 1846 O1P DT A 59 78.840 59.180 50.350 1.00 0.00
-ATOM 1847 O2P DT A 59 80.780 60.480 51.300 1.00 0.00
-ATOM 1848 O5' DT A 59 81.100 58.080 50.610 1.00 0.00
-ATOM 1849 C5' DT A 59 80.680 56.800 50.080 1.00 0.00
-ATOM 1850 1H5' DT A 59 80.640 56.940 49.000 1.00 0.00
-ATOM 1851 2H5' DT A 59 79.660 56.600 50.410 1.00 0.00
-ATOM 1852 C4' DT A 59 81.550 55.500 50.310 1.00 0.00
-ATOM 1853 H4' DT A 59 81.230 54.780 49.550 1.00 0.00
-ATOM 1854 O4' DT A 59 82.900 55.840 50.030 1.00 0.00
-ATOM 1855 C1' DT A 59 83.640 55.700 51.220 1.00 0.00
-ATOM 1856 H1' DT A 59 84.190 54.760 51.160 1.00 0.00
-ATOM 1857 N1 DT A 59 84.590 56.830 51.350 1.00 0.00
-ATOM 1858 C6 DT A 59 84.170 58.120 51.610 1.00 0.00
-ATOM 1859 H6 DT A 59 83.120 58.310 51.800 1.00 0.00
-ATOM 1860 C5 DT A 59 85.050 59.160 51.570 1.00 0.00
-ATOM 1861 C7 DT A 59 84.590 60.570 51.890 1.00 0.00
-ATOM 1862 H71 DT A 59 83.520 60.590 52.120 1.00 0.00
-ATOM 1863 H72 DT A 59 85.150 60.940 52.750 1.00 0.00
-ATOM 1864 H73 DT A 59 84.800 61.220 51.040 1.00 0.00
-ATOM 1865 C4 DT A 59 86.440 58.940 51.200 1.00 0.00
-ATOM 1866 O4 DT A 59 87.310 59.800 51.050 1.00 0.00
-ATOM 1867 N3 DT A 59 86.780 57.620 51.030 1.00 0.00
-ATOM 1868 H3 DT A 59 87.730 57.400 50.810 1.00 0.00
-ATOM 1869 C2 DT A 59 85.930 56.550 51.110 1.00 0.00
-ATOM 1870 O2 DT A 59 86.410 55.420 51.000 1.00 0.00
-ATOM 1871 C3' DT A 59 81.600 54.710 51.660 1.00 0.00
-ATOM 1872 H3' DT A 59 80.640 54.740 52.170 1.00 0.00
-ATOM 1873 C2' DT A 59 82.640 55.550 52.370 1.00 0.00
-ATOM 1874 1H2' DT A 59 82.210 56.500 52.670 1.00 0.00
-ATOM 1875 2H2' DT A 59 83.070 55.030 53.230 1.00 0.00
-ATOM 1876 O3' DT A 59 82.070 53.330 51.490 1.00 0.00
-ATOM 1877 P DA A 60 82.200 52.200 52.690 1.00 0.00
-ATOM 1878 O1P DA A 60 81.540 50.950 52.220 1.00 0.00
-ATOM 1879 O2P DA A 60 81.700 52.800 53.930 1.00 0.00
-ATOM 1880 O5' DA A 60 83.780 51.790 52.970 1.00 0.00
-ATOM 1881 C5' DA A 60 84.430 50.690 52.310 1.00 0.00
-ATOM 1882 1H5' DA A 60 84.370 50.900 51.240 1.00 0.00
-ATOM 1883 2H5' DA A 60 83.840 49.790 52.480 1.00 0.00
-ATOM 1884 C4' DA A 60 85.940 50.360 52.610 1.00 0.00
-ATOM 1885 H4' DA A 60 86.260 49.680 51.830 1.00 0.00
-ATOM 1886 O4' DA A 60 86.670 51.560 52.450 1.00 0.00
-ATOM 1887 C1' DA A 60 87.080 52.000 53.730 1.00 0.00
-ATOM 1888 H1' DA A 60 88.170 51.900 53.780 1.00 0.00
-ATOM 1889 N9 DA A 60 86.750 53.420 53.920 1.00 0.00
-ATOM 1890 C8 DA A 60 85.560 54.040 54.240 1.00 0.00
-ATOM 1891 H8 DA A 60 84.630 53.500 54.380 1.00 0.00
-ATOM 1892 N7 DA A 60 85.650 55.340 54.370 1.00 0.00
-ATOM 1893 C5 DA A 60 87.000 55.580 54.070 1.00 0.00
-ATOM 1894 C6 DA A 60 87.800 56.730 53.970 1.00 0.00
-ATOM 1895 N6 DA A 60 87.370 57.960 54.170 1.00 0.00
-ATOM 1896 H61 DA A 60 88.010 58.740 54.080 1.00 0.00
-ATOM 1897 H62 DA A 60 86.430 58.080 54.490 1.00 0.00
-ATOM 1898 N1 DA A 60 89.090 56.650 53.660 1.00 0.00
-ATOM 1899 C2 DA A 60 89.620 55.440 53.470 1.00 0.00
-ATOM 1900 H2 DA A 60 90.670 55.410 53.250 1.00 0.00
-ATOM 1901 N3 DA A 60 89.010 54.270 53.540 1.00 0.00
-ATOM 1902 C4 DA A 60 87.680 54.420 53.820 1.00 0.00
-ATOM 1903 C3' DA A 60 86.440 49.770 53.970 1.00 0.00
-ATOM 1904 H3' DA A 60 85.710 49.070 54.390 1.00 0.00
-ATOM 1905 C2' DA A 60 86.470 51.060 54.770 1.00 0.00
-ATOM 1906 1H2' DA A 60 85.460 51.370 55.040 1.00 0.00
-ATOM 1907 2H2' DA A 60 87.090 50.980 55.660 1.00 0.00
-ATOM 1908 O3' DA A 60 87.760 49.150 53.870 1.00 0.00
-ATOM 1909 P DT B 1 95.150 63.890 55.830 1.00 0.00
-ATOM 1910 O1P DT B 1 96.530 64.220 56.280 1.00 0.00
-ATOM 1911 O2P DT B 1 94.520 64.870 54.910 1.00 0.00
-ATOM 1912 O5' DT B 1 95.270 62.440 55.000 1.00 0.00
-ATOM 1913 C5' DT B 1 96.380 61.510 55.190 1.00 0.00
-ATOM 1914 1H5' DT B 1 96.450 61.370 56.260 1.00 0.00
-ATOM 1915 2H5' DT B 1 97.290 62.010 54.870 1.00 0.00
-ATOM 1916 C4' DT B 1 96.370 60.060 54.570 1.00 0.00
-ATOM 1917 H4' DT B 1 97.080 59.480 55.160 1.00 0.00
-ATOM 1918 O4' DT B 1 95.100 59.520 54.840 1.00 0.00
-ATOM 1919 C1' DT B 1 94.500 59.120 53.630 1.00 0.00
-ATOM 1920 H1' DT B 1 94.600 58.030 53.550 1.00 0.00
-ATOM 1921 N1 DT B 1 93.060 59.480 53.670 1.00 0.00
-ATOM 1922 C6 DT B 1 92.630 60.800 53.600 1.00 0.00
-ATOM 1923 H6 DT B 1 93.360 61.590 53.500 1.00 0.00
-ATOM 1924 C5 DT B 1 91.310 61.100 53.670 1.00 0.00
-ATOM 1925 C7 DT B 1 90.840 62.540 53.490 1.00 0.00
-ATOM 1926 H71 DT B 1 91.680 63.220 53.370 1.00 0.00
-ATOM 1927 H72 DT B 1 90.200 62.580 52.610 1.00 0.00
-ATOM 1928 H73 DT B 1 90.240 62.820 54.360 1.00 0.00
-ATOM 1929 C4 DT B 1 90.320 60.060 53.920 1.00 0.00
-ATOM 1930 O4 DT B 1 89.120 60.230 54.070 1.00 0.00
-ATOM 1931 N3 DT B 1 90.840 58.790 53.990 1.00 0.00
-ATOM 1932 H3 DT B 1 90.180 58.030 54.090 1.00 0.00
-ATOM 1933 C2 DT B 1 92.150 58.430 53.820 1.00 0.00
-ATOM 1934 O2 DT B 1 92.470 57.250 53.770 1.00 0.00
-ATOM 1935 C3' DT B 1 96.690 59.700 53.070 1.00 0.00
-ATOM 1936 H3' DT B 1 97.330 60.460 52.620 1.00 0.00
-ATOM 1937 C2' DT B 1 95.290 59.750 52.480 1.00 0.00
-ATOM 1938 1H2' DT B 1 95.000 60.780 52.310 1.00 0.00
-ATOM 1939 2H2' DT B 1 95.210 59.160 51.570 1.00 0.00
-ATOM 1940 O3' DT B 1 97.280 58.370 52.910 1.00 0.00
-ATOM 1941 P DA B 2 97.840 57.710 51.490 1.00 0.00
-ATOM 1942 O1P DA B 2 99.150 57.070 51.800 1.00 0.00
-ATOM 1943 O2P DA B 2 97.880 58.810 50.490 1.00 0.00
-ATOM 1944 O5' DA B 2 96.860 56.520 50.880 1.00 0.00
-ATOM 1945 C5' DA B 2 97.020 55.110 51.210 1.00 0.00
-ATOM 1946 1H5' DA B 2 97.070 55.070 52.300 1.00 0.00
-ATOM 1947 2H5' DA B 2 97.980 54.770 50.840 1.00 0.00
-ATOM 1948 C4' DA B 2 95.930 54.030 50.810 1.00 0.00
-ATOM 1949 H4' DA B 2 96.110 53.170 51.460 1.00 0.00
-ATOM 1950 O4' DA B 2 94.680 54.550 51.180 1.00 0.00
-ATOM 1951 C1' DA B 2 93.840 54.610 50.050 1.00 0.00
-ATOM 1952 H1' DA B 2 93.070 53.820 50.120 1.00 0.00
-ATOM 1953 N9 DA B 2 93.190 55.920 50.020 1.00 0.00
-ATOM 1954 C8 DA B 2 93.760 57.170 50.010 1.00 0.00
-ATOM 1955 H8 DA B 2 94.830 57.320 50.030 1.00 0.00
-ATOM 1956 N7 DA B 2 92.910 58.160 49.990 1.00 0.00
-ATOM 1957 C5 DA B 2 91.670 57.480 50.030 1.00 0.00
-ATOM 1958 C6 DA B 2 90.310 57.860 50.110 1.00 0.00
-ATOM 1959 N6 DA B 2 89.890 59.100 50.210 1.00 0.00
-ATOM 1960 H61 DA B 2 88.890 59.250 50.340 1.00 0.00
-ATOM 1961 H62 DA B 2 90.550 59.850 50.220 1.00 0.00
-ATOM 1962 N1 DA B 2 89.350 56.950 50.110 1.00 0.00
-ATOM 1963 C2 DA B 2 89.670 55.660 50.070 1.00 0.00
-ATOM 1964 H2 DA B 2 88.850 54.950 50.080 1.00 0.00
-ATOM 1965 N3 DA B 2 90.890 55.150 50.000 1.00 0.00
-ATOM 1966 C4 DA B 2 91.840 56.120 50.020 1.00 0.00
-ATOM 1967 C3' DA B 2 95.750 53.430 49.370 1.00 0.00
-ATOM 1968 H3' DA B 2 96.670 53.490 48.800 1.00 0.00
-ATOM 1969 C2' DA B 2 94.700 54.370 48.810 1.00 0.00
-ATOM 1970 1H2' DA B 2 95.170 55.290 48.490 1.00 0.00
-ATOM 1971 2H2' DA B 2 94.120 53.920 48.000 1.00 0.00
-ATOM 1972 O3' DA B 2 95.260 52.050 49.400 1.00 0.00
-ATOM 1973 P DC B 3 94.930 51.110 48.080 1.00 0.00
-ATOM 1974 O1P DC B 3 95.420 49.740 48.390 1.00 0.00
-ATOM 1975 O2P DC B 3 95.570 51.780 46.920 1.00 0.00
-ATOM 1976 O5' DC B 3 93.300 51.000 47.780 1.00 0.00
-ATOM 1977 C5' DC B 3 92.410 50.120 48.530 1.00 0.00
-ATOM 1978 1H5' DC B 3 92.610 50.320 49.580 1.00 0.00
-ATOM 1979 2H5' DC B 3 92.700 49.090 48.340 1.00 0.00
-ATOM 1980 C4' DC B 3 90.840 50.230 48.370 1.00 0.00
-ATOM 1981 H4' DC B 3 90.420 49.730 49.250 1.00 0.00
-ATOM 1982 O4' DC B 3 90.500 51.590 48.490 1.00 0.00
-ATOM 1983 C1' DC B 3 89.590 51.960 47.470 1.00 0.00
-ATOM 1984 H1' DC B 3 88.560 51.950 47.850 1.00 0.00
-ATOM 1985 N1 DC B 3 89.980 53.320 47.010 1.00 0.00
-ATOM 1986 C6 DC B 3 91.300 53.600 46.740 1.00 0.00
-ATOM 1987 H6 DC B 3 92.020 52.800 46.830 1.00 0.00
-ATOM 1988 C5 DC B 3 91.690 54.870 46.450 1.00 0.00
-ATOM 1989 H5 DC B 3 92.720 55.100 46.280 1.00 0.00
-ATOM 1990 C4 DC B 3 90.660 55.850 46.430 1.00 0.00
-ATOM 1991 N4 DC B 3 90.960 57.100 46.280 1.00 0.00
-ATOM 1992 H41 DC B 3 90.160 57.720 46.430 1.00 0.00
-ATOM 1993 H42 DC B 3 91.890 57.410 46.440 1.00 0.00
-ATOM 1994 N3 DC B 3 89.400 55.600 46.660 1.00 0.00
-ATOM 1995 C2 DC B 3 89.020 54.340 46.970 1.00 0.00
-ATOM 1996 O2 DC B 3 87.850 54.130 47.230 1.00 0.00
-ATOM 1997 C3' DC B 3 90.040 49.650 47.160 1.00 0.00
-ATOM 1998 H3' DC B 3 90.640 48.960 46.580 1.00 0.00
-ATOM 1999 C2' DC B 3 89.740 50.910 46.370 1.00 0.00
-ATOM 2000 1H2' DC B 3 90.580 51.140 45.720 1.00 0.00
-ATOM 2001 2H2' DC B 3 88.830 50.830 45.780 1.00 0.00
-ATOM 2002 O3' DC B 3 88.820 48.990 47.590 1.00 0.00
-ATOM 2003 P DG B 4 87.700 48.300 46.600 1.00 0.00
-ATOM 2004 O1P DG B 4 87.250 47.050 47.250 1.00 0.00
-ATOM 2005 O2P DG B 4 88.350 48.150 45.270 1.00 0.00
-ATOM 2006 O5' DG B 4 86.380 49.300 46.430 1.00 0.00
-ATOM 2007 C5' DG B 4 85.370 49.470 47.460 1.00 0.00
-ATOM 2008 1H5' DG B 4 85.920 49.640 48.390 1.00 0.00
-ATOM 2009 2H5' DG B 4 84.830 48.530 47.580 1.00 0.00
-ATOM 2010 C4' DG B 4 84.320 50.640 47.380 1.00 0.00
-ATOM 2011 H4' DG B 4 83.910 50.780 48.380 1.00 0.00
-ATOM 2012 O4' DG B 4 85.070 51.800 47.060 1.00 0.00
-ATOM 2013 C1' DG B 4 84.480 52.410 45.930 1.00 0.00
-ATOM 2014 H1' DG B 4 83.800 53.210 46.250 1.00 0.00
-ATOM 2015 N9 DG B 4 85.550 52.970 45.090 1.00 0.00
-ATOM 2016 C8 DG B 4 86.650 52.350 44.570 1.00 0.00
-ATOM 2017 H8 DG B 4 86.800 51.280 44.700 1.00 0.00
-ATOM 2018 N7 DG B 4 87.480 53.140 43.940 1.00 0.00
-ATOM 2019 C5 DG B 4 86.860 54.400 44.090 1.00 0.00
-ATOM 2020 C6 DG B 4 87.270 55.730 43.710 1.00 0.00
-ATOM 2021 O6 DG B 4 88.290 56.080 43.110 1.00 0.00
-ATOM 2022 N1 DG B 4 86.360 56.710 44.080 1.00 0.00
-ATOM 2023 H1 DG B 4 86.600 57.680 43.900 1.00 0.00
-ATOM 2024 C2 DG B 4 85.200 56.470 44.730 1.00 0.00
-ATOM 2025 N2 DG B 4 84.430 57.470 45.040 1.00 0.00
-ATOM 2026 H21 DG B 4 84.680 58.430 44.820 1.00 0.00
-ATOM 2027 H22 DG B 4 83.580 57.250 45.530 1.00 0.00
-ATOM 2028 N3 DG B 4 84.790 55.270 45.090 1.00 0.00
-ATOM 2029 C4 DG B 4 85.670 54.290 44.760 1.00 0.00
-ATOM 2030 C3' DG B 4 83.090 50.630 46.420 1.00 0.00
-ATOM 2031 H3' DG B 4 82.780 49.620 46.170 1.00 0.00
-ATOM 2032 C2' DG B 4 83.680 51.340 45.210 1.00 0.00
-ATOM 2033 1H2' DG B 4 84.340 50.660 44.660 1.00 0.00
-ATOM 2034 2H2' DG B 4 82.930 51.770 44.560 1.00 0.00
-ATOM 2035 O3' DG B 4 81.970 51.390 46.950 1.00 0.00
-ATOM 2036 P DG B 5 80.510 51.570 46.210 1.00 0.00
-ATOM 2037 O1P DG B 5 79.470 51.160 47.180 1.00 0.00
-ATOM 2038 O2P DG B 5 80.590 50.790 44.940 1.00 0.00
-ATOM 2039 O5' DG B 5 80.260 53.160 45.820 1.00 0.00
-ATOM 2040 C5' DG B 5 79.840 54.160 46.780 1.00 0.00
-ATOM 2041 1H5' DG B 5 80.540 54.090 47.610 1.00 0.00
-ATOM 2042 2H5' DG B 5 78.860 53.900 47.160 1.00 0.00
-ATOM 2043 C4' DG B 5 79.820 55.690 46.370 1.00 0.00
-ATOM 2044 H4' DG B 5 79.810 56.270 47.290 1.00 0.00
-ATOM 2045 O4' DG B 5 81.050 55.940 45.710 1.00 0.00
-ATOM 2046 C1' DG B 5 80.740 56.290 44.370 1.00 0.00
-ATOM 2047 H1' DG B 5 80.830 57.380 44.280 1.00 0.00
-ATOM 2048 N9 DG B 5 81.650 55.640 43.430 1.00 0.00
-ATOM 2049 C8 DG B 5 81.900 54.310 43.200 1.00 0.00
-ATOM 2050 H8 DG B 5 81.340 53.530 43.700 1.00 0.00
-ATOM 2051 N7 DG B 5 82.890 54.090 42.370 1.00 0.00
-ATOM 2052 C5 DG B 5 83.320 55.380 42.040 1.00 0.00
-ATOM 2053 C6 DG B 5 84.430 55.860 41.270 1.00 0.00
-ATOM 2054 O6 DG B 5 85.310 55.220 40.680 1.00 0.00
-ATOM 2055 N1 DG B 5 84.530 57.240 41.230 1.00 0.00
-ATOM 2056 H1 DG B 5 85.320 57.640 40.770 1.00 0.00
-ATOM 2057 C2 DG B 5 83.660 58.080 41.840 1.00 0.00
-ATOM 2058 N2 DG B 5 83.850 59.360 41.760 1.00 0.00
-ATOM 2059 H21 DG B 5 84.660 59.750 41.280 1.00 0.00
-ATOM 2060 H22 DG B 5 83.170 59.940 42.230 1.00 0.00
-ATOM 2061 N3 DG B 5 82.610 57.690 42.540 1.00 0.00
-ATOM 2062 C4 DG B 5 82.520 56.330 42.630 1.00 0.00
-ATOM 2063 C3' DG B 5 78.720 56.330 45.470 1.00 0.00
-ATOM 2064 H3' DG B 5 77.740 55.890 45.640 1.00 0.00
-ATOM 2065 C2' DG B 5 79.280 55.930 44.130 1.00 0.00
-ATOM 2066 1H2' DG B 5 79.150 54.860 43.950 1.00 0.00
-ATOM 2067 2H2' DG B 5 78.860 56.530 43.330 1.00 0.00
-ATOM 2068 O3' DG B 5 78.650 57.790 45.540 1.00 0.00
-ATOM 2069 P DT B 6 77.630 58.750 44.670 1.00 0.00
-ATOM 2070 O1P DT B 6 76.960 59.690 45.600 1.00 0.00
-ATOM 2071 O2P DT B 6 76.780 57.860 43.850 1.00 0.00
-ATOM 2072 O5' DT B 6 78.450 59.700 43.580 1.00 0.00
-ATOM 2073 C5' DT B 6 79.000 60.990 43.920 1.00 0.00
-ATOM 2074 1H5' DT B 6 79.710 60.800 44.720 1.00 0.00
-ATOM 2075 2H5' DT B 6 78.200 61.600 44.350 1.00 0.00
-ATOM 2076 C4' DT B 6 79.760 61.840 42.830 1.00 0.00
-ATOM 2077 H4' DT B 6 80.350 62.570 43.380 1.00 0.00
-ATOM 2078 O4' DT B 6 80.650 60.970 42.160 1.00 0.00
-ATOM 2079 C1' DT B 6 80.200 60.820 40.830 1.00 0.00
-ATOM 2080 H1' DT B 6 80.850 61.430 40.200 1.00 0.00
-ATOM 2081 N1 DT B 6 80.310 59.400 40.410 1.00 0.00
-ATOM 2082 C6 DT B 6 79.400 58.420 40.790 1.00 0.00
-ATOM 2083 H6 DT B 6 78.550 58.680 41.410 1.00 0.00
-ATOM 2084 C5 DT B 6 79.600 57.120 40.440 1.00 0.00
-ATOM 2085 C7 DT B 6 78.580 56.050 40.800 1.00 0.00
-ATOM 2086 H71 DT B 6 77.740 56.480 41.350 1.00 0.00
-ATOM 2087 H72 DT B 6 78.210 55.590 39.880 1.00 0.00
-ATOM 2088 H73 DT B 6 79.070 55.280 41.390 1.00 0.00
-ATOM 2089 C4 DT B 6 80.800 56.720 39.700 1.00 0.00
-ATOM 2090 O4 DT B 6 81.140 55.590 39.390 1.00 0.00
-ATOM 2091 N3 DT B 6 81.590 57.770 39.320 1.00 0.00
-ATOM 2092 H3 DT B 6 82.410 57.550 38.780 1.00 0.00
-ATOM 2093 C2 DT B 6 81.400 59.090 39.600 1.00 0.00
-ATOM 2094 O2 DT B 6 82.180 59.910 39.120 1.00 0.00
-ATOM 2095 C3' DT B 6 79.010 62.620 41.690 1.00 0.00
-ATOM 2096 H3' DT B 6 78.060 63.020 42.050 1.00 0.00
-ATOM 2097 C2' DT B 6 78.810 61.460 40.740 1.00 0.00
-ATOM 2098 1H2' DT B 6 78.030 60.790 41.120 1.00 0.00
-ATOM 2099 2H2' DT B 6 78.570 61.790 39.730 1.00 0.00
-ATOM 2100 O3' DT B 6 79.840 63.670 41.100 1.00 0.00
-ATOM 2101 P DA B 7 79.360 64.770 39.950 1.00 0.00
-ATOM 2102 O1P DA B 7 79.840 66.120 40.380 1.00 0.00
-ATOM 2103 O2P DA B 7 77.910 64.620 39.740 1.00 0.00
-ATOM 2104 O5' DA B 7 80.090 64.510 38.490 1.00 0.00
-ATOM 2105 C5' DA B 7 81.320 65.150 38.110 1.00 0.00
-ATOM 2106 1H5' DA B 7 82.040 64.900 38.900 1.00 0.00
-ATOM 2107 2H5' DA B 7 81.160 66.230 38.160 1.00 0.00
-ATOM 2108 C4' DA B 7 82.040 64.830 36.750 1.00 0.00
-ATOM 2109 H4' DA B 7 83.010 65.320 36.810 1.00 0.00
-ATOM 2110 O4' DA B 7 82.280 63.440 36.710 1.00 0.00
-ATOM 2111 C1' DA B 7 81.450 62.870 35.720 1.00 0.00
-ATOM 2112 H1' DA B 7 82.090 62.520 34.910 1.00 0.00
-ATOM 2113 N9 DA B 7 80.720 61.710 36.260 1.00 0.00
-ATOM 2114 C8 DA B 7 79.650 61.640 37.130 1.00 0.00
-ATOM 2115 H8 DA B 7 79.200 62.510 37.590 1.00 0.00
-ATOM 2116 N7 DA B 7 79.230 60.420 37.350 1.00 0.00
-ATOM 2117 C5 DA B 7 80.100 59.650 36.570 1.00 0.00
-ATOM 2118 C6 DA B 7 80.260 58.270 36.330 1.00 0.00
-ATOM 2119 N6 DA B 7 79.520 57.320 36.870 1.00 0.00
-ATOM 2120 H61 DA B 7 79.740 56.350 36.680 1.00 0.00
-ATOM 2121 H62 DA B 7 78.770 57.600 37.460 1.00 0.00
-ATOM 2122 N1 DA B 7 81.230 57.830 35.530 1.00 0.00
-ATOM 2123 C2 DA B 7 82.030 58.710 34.950 1.00 0.00
-ATOM 2124 H2 DA B 7 82.790 58.310 34.300 1.00 0.00
-ATOM 2125 N3 DA B 7 82.000 60.020 35.060 1.00 0.00
-ATOM 2126 C4 DA B 7 81.010 60.420 35.910 1.00 0.00
-ATOM 2127 C3' DA B 7 81.450 65.180 35.340 1.00 0.00
-ATOM 2128 H3' DA B 7 80.880 66.100 35.370 1.00 0.00
-ATOM 2129 C2' DA B 7 80.540 63.970 35.170 1.00 0.00
-ATOM 2130 1H2' DA B 7 79.650 64.090 35.790 1.00 0.00
-ATOM 2131 2H2' DA B 7 80.280 63.800 34.130 1.00 0.00
-ATOM 2132 O3' DA B 7 82.500 65.240 34.310 1.00 0.00
-ATOM 2133 P DG B 8 82.320 65.700 32.720 1.00 0.00
-ATOM 2134 O1P DG B 8 83.540 66.480 32.370 1.00 0.00
-ATOM 2135 O2P DG B 8 81.030 66.420 32.590 1.00 0.00
-ATOM 2136 O5' DG B 8 82.290 64.420 31.660 1.00 0.00
-ATOM 2137 C5' DG B 8 83.500 63.900 31.040 1.00 0.00
-ATOM 2138 1H5' DG B 8 84.170 63.660 31.880 1.00 0.00
-ATOM 2139 2H5' DG B 8 83.970 64.720 30.500 1.00 0.00
-ATOM 2140 C4' DG B 8 83.520 62.630 30.120 1.00 0.00
-ATOM 2141 H4' DG B 8 84.580 62.420 29.930 1.00 0.00
-ATOM 2142 O4' DG B 8 83.050 61.550 30.890 1.00 0.00
-ATOM 2143 C1' DG B 8 81.850 61.080 30.310 1.00 0.00
-ATOM 2144 H1' DG B 8 82.050 60.110 29.860 1.00 0.00
-ATOM 2145 N9 DG B 8 80.830 60.900 31.350 1.00 0.00
-ATOM 2146 C8 DG B 8 80.140 61.820 32.100 1.00 0.00
-ATOM 2147 H8 DG B 8 80.310 62.880 32.040 1.00 0.00
-ATOM 2148 N7 DG B 8 79.260 61.280 32.910 1.00 0.00
-ATOM 2149 C5 DG B 8 79.400 59.900 32.690 1.00 0.00
-ATOM 2150 C6 DG B 8 78.770 58.730 33.250 1.00 0.00
-ATOM 2151 O6 DG B 8 77.900 58.650 34.120 1.00 0.00
-ATOM 2152 N1 DG B 8 79.230 57.550 32.710 1.00 0.00
-ATOM 2153 H1 DG B 8 78.810 56.700 33.060 1.00 0.00
-ATOM 2154 C2 DG B 8 80.170 57.470 31.750 1.00 0.00
-ATOM 2155 N2 DG B 8 80.500 56.310 31.280 1.00 0.00
-ATOM 2156 H21 DG B 8 80.060 55.470 31.650 1.00 0.00
-ATOM 2157 H22 DG B 8 81.210 56.280 30.570 1.00 0.00
-ATOM 2158 N3 DG B 8 80.780 58.500 31.190 1.00 0.00
-ATOM 2159 C4 DG B 8 80.360 59.680 31.720 1.00 0.00
-ATOM 2160 C3' DG B 8 82.820 62.490 28.720 1.00 0.00
-ATOM 2161 H3' DG B 8 82.760 63.450 28.210 1.00 0.00
-ATOM 2162 C2' DG B 8 81.440 62.040 29.200 1.00 0.00
-ATOM 2163 1H2' DG B 8 80.890 62.890 29.600 1.00 0.00
-ATOM 2164 2H2' DG B 8 80.870 61.540 28.420 1.00 0.00
-ATOM 2165 O3' DG B 8 83.460 61.480 27.870 1.00 0.00
-ATOM 2166 P DA B 9 83.080 61.100 26.300 1.00 0.00
-ATOM 2167 O1P DA B 9 84.370 60.870 25.600 1.00 0.00
-ATOM 2168 O2P DA B 9 82.250 62.220 25.770 1.00 0.00
-ATOM 2169 O5' DA B 9 82.200 59.690 26.120 1.00 0.00
-ATOM 2170 C5' DA B 9 82.830 58.400 25.870 1.00 0.00
-ATOM 2171 1H5' DA B 9 83.590 58.300 26.650 1.00 0.00
-ATOM 2172 2H5' DA B 9 83.360 58.460 24.920 1.00 0.00
-ATOM 2173 C4' DA B 9 82.040 57.030 25.890 1.00 0.00
-ATOM 2174 H4' DA B 9 82.810 56.260 25.960 1.00 0.00
-ATOM 2175 O4' DA B 9 81.330 56.960 27.110 1.00 0.00
-ATOM 2176 C1' DA B 9 79.950 56.820 26.830 1.00 0.00
-ATOM 2177 H1' DA B 9 79.620 55.810 27.090 1.00 0.00
-ATOM 2178 N9 DA B 9 79.210 57.790 27.640 1.00 0.00
-ATOM 2179 C8 DA B 9 79.280 59.160 27.660 1.00 0.00
-ATOM 2180 H8 DA B 9 79.930 59.720 27.010 1.00 0.00
-ATOM 2181 N7 DA B 9 78.490 59.730 28.520 1.00 0.00
-ATOM 2182 C5 DA B 9 77.880 58.620 29.150 1.00 0.00
-ATOM 2183 C6 DA B 9 76.980 58.430 30.220 1.00 0.00
-ATOM 2184 N6 DA B 9 76.460 59.390 30.960 1.00 0.00
-ATOM 2185 H61 DA B 9 75.860 59.120 31.730 1.00 0.00
-ATOM 2186 H62 DA B 9 76.740 60.340 30.830 1.00 0.00
-ATOM 2187 N1 DA B 9 76.610 57.210 30.580 1.00 0.00
-ATOM 2188 C2 DA B 9 77.090 56.160 29.940 1.00 0.00
-ATOM 2189 H2 DA B 9 76.750 55.190 30.270 1.00 0.00
-ATOM 2190 N3 DA B 9 77.940 56.180 28.920 1.00 0.00
-ATOM 2191 C4 DA B 9 78.300 57.450 28.600 1.00 0.00
-ATOM 2192 C3' DA B 9 81.060 56.510 24.780 1.00 0.00
-ATOM 2193 H3' DA B 9 81.280 56.950 23.820 1.00 0.00
-ATOM 2194 C2' DA B 9 79.740 57.040 25.330 1.00 0.00
-ATOM 2195 1H2' DA B 9 79.640 58.100 25.100 1.00 0.00
-ATOM 2196 2H2' DA B 9 78.880 56.480 24.960 1.00 0.00
-ATOM 2197 O3' DA B 9 81.050 55.050 24.690 1.00 0.00
-ATOM 2198 P DA B 10 80.170 54.140 23.610 1.00 0.00
-ATOM 2199 O1P DA B 10 81.070 53.030 23.180 1.00 0.00
-ATOM 2200 O2P DA B 10 79.730 55.070 22.540 1.00 0.00
-ATOM 2201 O5' DA B 10 78.820 53.440 24.290 1.00 0.00
-ATOM 2202 C5' DA B 10 78.840 52.140 24.940 1.00 0.00
-ATOM 2203 1H5' DA B 10 79.680 52.180 25.640 1.00 0.00
-ATOM 2204 2H5' DA B 10 79.080 51.390 24.200 1.00 0.00
-ATOM 2205 C4' DA B 10 77.630 51.600 25.810 1.00 0.00
-ATOM 2206 H4' DA B 10 78.060 50.850 26.470 1.00 0.00
-ATOM 2207 O4' DA B 10 77.220 52.660 26.640 1.00 0.00
-ATOM 2208 C1' DA B 10 75.820 52.840 26.530 1.00 0.00
-ATOM 2209 H1' DA B 10 75.310 52.420 27.400 1.00 0.00
-ATOM 2210 N9 DA B 10 75.590 54.290 26.460 1.00 0.00
-ATOM 2211 C8 DA B 10 76.120 55.210 25.600 1.00 0.00
-ATOM 2212 H8 DA B 10 76.790 54.920 24.800 1.00 0.00
-ATOM 2213 N7 DA B 10 75.770 56.450 25.830 1.00 0.00
-ATOM 2214 C5 DA B 10 74.970 56.300 26.990 1.00 0.00
-ATOM 2215 C6 DA B 10 74.310 57.180 27.870 1.00 0.00
-ATOM 2216 N6 DA B 10 74.330 58.490 27.770 1.00 0.00
-ATOM 2217 H61 DA B 10 73.860 59.020 28.500 1.00 0.00
-ATOM 2218 H62 DA B 10 74.840 58.920 27.030 1.00 0.00
-ATOM 2219 N1 DA B 10 73.630 56.730 28.920 1.00 0.00
-ATOM 2220 C2 DA B 10 73.580 55.420 29.140 1.00 0.00
-ATOM 2221 H2 DA B 10 73.010 55.090 30.000 1.00 0.00
-ATOM 2222 N3 DA B 10 74.150 54.470 28.400 1.00 0.00
-ATOM 2223 C4 DA B 10 74.840 54.990 27.350 1.00 0.00
-ATOM 2224 C3' DA B 10 76.330 50.940 25.230 1.00 0.00
-ATOM 2225 H3' DA B 10 76.480 50.590 24.210 1.00 0.00
-ATOM 2226 C2' DA B 10 75.370 52.120 25.260 1.00 0.00
-ATOM 2227 1H2' DA B 10 75.530 52.750 24.380 1.00 0.00
-ATOM 2228 2H2' DA B 10 74.330 51.820 25.330 1.00 0.00
-ATOM 2229 O3' DA B 10 75.860 49.850 26.070 1.00 0.00
-ATOM 2230 P DA B 11 74.510 48.940 25.810 1.00 0.00
-ATOM 2231 O1P DA B 11 74.870 47.540 26.160 1.00 0.00
-ATOM 2232 O2P DA B 11 74.120 49.170 24.400 1.00 0.00
-ATOM 2233 O5' DA B 11 73.260 49.400 26.800 1.00 0.00
-ATOM 2234 C5' DA B 11 73.150 49.010 28.200 1.00 0.00
-ATOM 2235 1H5' DA B 11 74.120 49.200 28.640 1.00 0.00
-ATOM 2236 2H5' DA B 11 72.990 47.930 28.240 1.00 0.00
-ATOM 2237 C4' DA B 11 72.110 49.700 29.160 1.00 0.00
-ATOM 2238 H4' DA B 11 72.450 49.510 30.180 1.00 0.00
-ATOM 2239 O4' DA B 11 72.230 51.090 28.940 1.00 0.00
-ATOM 2240 C1' DA B 11 70.950 51.650 28.770 1.00 0.00
-ATOM 2241 H1' DA B 11 70.580 52.090 29.710 1.00 0.00
-ATOM 2242 N9 DA B 11 71.050 52.670 27.720 1.00 0.00
-ATOM 2243 C8 DA B 11 71.610 52.550 26.470 1.00 0.00
-ATOM 2244 H8 DA B 11 71.990 51.610 26.120 1.00 0.00
-ATOM 2245 N7 DA B 11 71.660 53.670 25.780 1.00 0.00
-ATOM 2246 C5 DA B 11 71.100 54.590 26.700 1.00 0.00
-ATOM 2247 C6 DA B 11 70.890 55.980 26.720 1.00 0.00
-ATOM 2248 N6 DA B 11 71.260 56.790 25.750 1.00 0.00
-ATOM 2249 H61 DA B 11 71.150 57.780 25.910 1.00 0.00
-ATOM 2250 H62 DA B 11 71.720 56.400 24.960 1.00 0.00
-ATOM 2251 N1 DA B 11 70.360 56.600 27.760 1.00 0.00
-ATOM 2252 C2 DA B 11 70.000 55.870 28.820 1.00 0.00
-ATOM 2253 H2 DA B 11 69.560 56.400 29.650 1.00 0.00
-ATOM 2254 N3 DA B 11 70.120 54.560 28.940 1.00 0.00
-ATOM 2255 C4 DA B 11 70.700 53.980 27.860 1.00 0.00
-ATOM 2256 C3' DA B 11 70.580 49.370 29.180 1.00 0.00
-ATOM 2257 H3' DA B 11 70.370 48.410 28.720 1.00 0.00
-ATOM 2258 C2' DA B 11 70.030 50.510 28.340 1.00 0.00
-ATOM 2259 1H2' DA B 11 70.150 50.280 27.280 1.00 0.00
-ATOM 2260 2H2' DA B 11 68.990 50.740 28.570 1.00 0.00
-ATOM 2261 O3' DA B 11 70.000 49.420 30.510 1.00 0.00
-ATOM 2262 P DT B 12 68.400 49.160 30.850 1.00 0.00
-ATOM 2263 O1P DT B 12 68.350 48.290 32.050 1.00 0.00
-ATOM 2264 O2P DT B 12 67.810 48.610 29.600 1.00 0.00
-ATOM 2265 O5' DT B 12 67.630 50.600 31.200 1.00 0.00
-ATOM 2266 C5' DT B 12 67.710 51.270 32.480 1.00 0.00
-ATOM 2267 1H5' DT B 12 68.780 51.320 32.730 1.00 0.00
-ATOM 2268 2H5' DT B 12 67.250 50.650 33.240 1.00 0.00
-ATOM 2269 C4' DT B 12 67.170 52.750 32.650 1.00 0.00
-ATOM 2270 H4' DT B 12 67.690 53.180 33.520 1.00 0.00
-ATOM 2271 O4' DT B 12 67.600 53.470 31.510 1.00 0.00
-ATOM 2272 C1' DT B 12 66.470 54.120 30.940 1.00 0.00
-ATOM 2273 H1' DT B 12 66.420 55.150 31.330 1.00 0.00
-ATOM 2274 N1 DT B 12 66.630 54.110 29.470 1.00 0.00
-ATOM 2275 C6 DT B 12 66.740 52.910 28.800 1.00 0.00
-ATOM 2276 H6 DT B 12 66.670 51.990 29.370 1.00 0.00
-ATOM 2277 C5 DT B 12 66.970 52.880 27.460 1.00 0.00
-ATOM 2278 C7 DT B 12 67.070 51.550 26.740 1.00 0.00
-ATOM 2279 H71 DT B 12 66.880 50.730 27.430 1.00 0.00
-ATOM 2280 H72 DT B 12 66.330 51.540 25.940 1.00 0.00
-ATOM 2281 H73 DT B 12 68.060 51.460 26.310 1.00 0.00
-ATOM 2282 C4 DT B 12 67.150 54.130 26.710 1.00 0.00
-ATOM 2283 O4 DT B 12 67.440 54.220 25.520 1.00 0.00
-ATOM 2284 N3 DT B 12 66.990 55.270 27.460 1.00 0.00
-ATOM 2285 H3 DT B 12 67.090 56.170 27.020 1.00 0.00
-ATOM 2286 C2 DT B 12 66.730 55.330 28.810 1.00 0.00
-ATOM 2287 O2 DT B 12 66.620 56.430 29.330 1.00 0.00
-ATOM 2288 C3' DT B 12 65.660 53.100 32.860 1.00 0.00
-ATOM 2289 H3' DT B 12 65.110 52.280 33.310 1.00 0.00
-ATOM 2290 C2' DT B 12 65.250 53.350 31.430 1.00 0.00
-ATOM 2291 1H2' DT B 12 65.120 52.400 30.910 1.00 0.00
-ATOM 2292 2H2' DT B 12 64.340 53.950 31.350 1.00 0.00
-ATOM 2293 O3' DT B 12 65.460 54.320 33.640 1.00 0.00
-ATOM 2294 P DG B 13 63.990 54.910 34.100 1.00 0.00
-ATOM 2295 O1P DG B 13 64.010 55.100 35.560 1.00 0.00
-ATOM 2296 O2P DG B 13 62.980 53.980 33.550 1.00 0.00
-ATOM 2297 O5' DG B 13 63.700 56.390 33.410 1.00 0.00
-ATOM 2298 C5' DG B 13 64.290 57.610 33.900 1.00 0.00
-ATOM 2299 1H5' DG B 13 65.360 57.410 33.910 1.00 0.00
-ATOM 2300 2H5' DG B 13 63.990 57.760 34.940 1.00 0.00
-ATOM 2301 C4' DG B 13 64.110 58.960 33.110 1.00 0.00
-ATOM 2302 H4' DG B 13 64.820 59.670 33.530 1.00 0.00
-ATOM 2303 O4' DG B 13 64.490 58.700 31.780 1.00 0.00
-ATOM 2304 C1' DG B 13 63.320 58.790 30.980 1.00 0.00
-ATOM 2305 H1' DG B 13 63.390 59.710 30.400 1.00 0.00
-ATOM 2306 N9 DG B 13 63.280 57.650 30.050 1.00 0.00
-ATOM 2307 C8 DG B 13 63.180 56.300 30.280 1.00 0.00
-ATOM 2308 H8 DG B 13 63.030 55.880 31.270 1.00 0.00
-ATOM 2309 N7 DG B 13 63.320 55.560 29.210 1.00 0.00
-ATOM 2310 C5 DG B 13 63.520 56.510 28.190 1.00 0.00
-ATOM 2311 C6 DG B 13 63.790 56.380 26.790 1.00 0.00
-ATOM 2312 O6 DG B 13 63.980 55.370 26.120 1.00 0.00
-ATOM 2313 N1 DG B 13 63.870 57.590 26.130 1.00 0.00
-ATOM 2314 H1 DG B 13 64.090 57.570 25.150 1.00 0.00
-ATOM 2315 C2 DG B 13 63.730 58.790 26.740 1.00 0.00
-ATOM 2316 N2 DG B 13 63.810 59.880 26.020 1.00 0.00
-ATOM 2317 H21 DG B 13 64.040 59.820 25.030 1.00 0.00
-ATOM 2318 H22 DG B 13 63.720 60.740 26.530 1.00 0.00
-ATOM 2319 N3 DG B 13 63.520 58.970 28.030 1.00 0.00
-ATOM 2320 C4 DG B 13 63.430 57.790 28.700 1.00 0.00
-ATOM 2321 C3' DG B 13 62.760 59.740 33.000 1.00 0.00
-ATOM 2322 H3' DG B 13 62.190 59.700 33.930 1.00 0.00
-ATOM 2323 C2' DG B 13 62.120 58.900 31.910 1.00 0.00
-ATOM 2324 1H2' DG B 13 61.810 57.930 32.300 1.00 0.00
-ATOM 2325 2H2' DG B 13 61.290 59.430 31.450 1.00 0.00
-ATOM 2326 O3' DG B 13 62.940 61.130 32.550 1.00 0.00
-ATOM 2327 P DC B 14 61.740 62.240 32.290 1.00 0.00
-ATOM 2328 O1P DC B 14 62.150 63.530 32.900 1.00 0.00
-ATOM 2329 O2P DC B 14 60.470 61.640 32.740 1.00 0.00
-ATOM 2330 O5' DC B 14 61.540 62.560 30.680 1.00 0.00
-ATOM 2331 C5' DC B 14 62.270 63.590 29.980 1.00 0.00
-ATOM 2332 1H5' DC B 14 63.320 63.320 30.050 1.00 0.00
-ATOM 2333 2H5' DC B 14 62.140 64.530 30.520 1.00 0.00
-ATOM 2334 C4' DC B 14 61.950 63.830 28.460 1.00 0.00
-ATOM 2335 H4' DC B 14 62.760 64.440 28.070 1.00 0.00
-ATOM 2336 O4' DC B 14 62.000 62.580 27.810 1.00 0.00
-ATOM 2337 C1' DC B 14 60.690 62.240 27.380 1.00 0.00
-ATOM 2338 H1' DC B 14 60.660 62.420 26.310 1.00 0.00
-ATOM 2339 N1 DC B 14 60.420 60.800 27.650 1.00 0.00
-ATOM 2340 C6 DC B 14 60.180 60.290 28.910 1.00 0.00
-ATOM 2341 H6 DC B 14 60.140 60.950 29.770 1.00 0.00
-ATOM 2342 C5 DC B 14 60.020 58.950 29.070 1.00 0.00
-ATOM 2343 H5 DC B 14 59.850 58.540 30.050 1.00 0.00
-ATOM 2344 C4 DC B 14 60.170 58.130 27.930 1.00 0.00
-ATOM 2345 N4 DC B 14 60.160 56.830 28.040 1.00 0.00
-ATOM 2346 H41 DC B 14 60.250 56.280 27.200 1.00 0.00
-ATOM 2347 H42 DC B 14 60.090 56.400 28.940 1.00 0.00
-ATOM 2348 N3 DC B 14 60.350 58.600 26.710 1.00 0.00
-ATOM 2349 C2 DC B 14 60.450 59.940 26.560 1.00 0.00
-ATOM 2350 O2 DC B 14 60.540 60.370 25.410 1.00 0.00
-ATOM 2351 C3' DC B 14 60.610 64.490 27.980 1.00 0.00
-ATOM 2352 H3' DC B 14 60.260 65.230 28.700 1.00 0.00
-ATOM 2353 C2' DC B 14 59.730 63.260 28.000 1.00 0.00
-ATOM 2354 1H2' DC B 14 59.470 62.990 29.030 1.00 0.00
-ATOM 2355 2H2' DC B 14 58.840 63.400 27.400 1.00 0.00
-ATOM 2356 O3' DC B 14 60.710 65.080 26.640 1.00 0.00
-ATOM 2357 P DC B 15 59.530 65.940 25.850 1.00 0.00
-ATOM 2358 O1P DC B 15 60.200 67.100 25.200 1.00 0.00
-ATOM 2359 O2P DC B 15 58.470 66.260 26.820 1.00 0.00
-ATOM 2360 O5' DC B 15 58.830 65.080 24.620 1.00 0.00
-ATOM 2361 C5' DC B 15 59.330 65.130 23.270 1.00 0.00
-ATOM 2362 1H5' DC B 15 60.390 64.880 23.330 1.00 0.00
-ATOM 2363 2H5' DC B 15 59.270 66.150 22.920 1.00 0.00
-ATOM 2364 C4' DC B 15 58.730 64.190 22.150 1.00 0.00
-ATOM 2365 H4' DC B 15 59.420 64.250 21.310 1.00 0.00
-ATOM 2366 O4' DC B 15 58.820 62.880 22.650 1.00 0.00
-ATOM 2367 C1' DC B 15 57.510 62.350 22.750 1.00 0.00
-ATOM 2368 H1' DC B 15 57.360 61.690 21.900 1.00 0.00
-ATOM 2369 N1 DC B 15 57.370 61.580 24.020 1.00 0.00
-ATOM 2370 C6 DC B 15 57.330 62.160 25.260 1.00 0.00
-ATOM 2371 H6 DC B 15 57.420 63.240 25.350 1.00 0.00
-ATOM 2372 C5 DC B 15 57.200 61.390 26.370 1.00 0.00
-ATOM 2373 H5 DC B 15 57.160 61.830 27.350 1.00 0.00
-ATOM 2374 C4 DC B 15 57.150 59.980 26.180 1.00 0.00
-ATOM 2375 N4 DC B 15 57.060 59.180 27.200 1.00 0.00
-ATOM 2376 H41 DC B 15 57.040 58.180 27.010 1.00 0.00
-ATOM 2377 H42 DC B 15 56.990 59.520 28.130 1.00 0.00
-ATOM 2378 N3 DC B 15 57.190 59.410 25.000 1.00 0.00
-ATOM 2379 C2 DC B 15 57.310 60.190 23.900 1.00 0.00
-ATOM 2380 O2 DC B 15 57.330 59.650 22.800 1.00 0.00
-ATOM 2381 C3' DC B 15 57.290 64.340 21.540 1.00 0.00
-ATOM 2382 H3' DC B 15 56.970 65.380 21.550 1.00 0.00
-ATOM 2383 C2' DC B 15 56.530 63.510 22.570 1.00 0.00
-ATOM 2384 1H2' DC B 15 56.410 64.080 23.490 1.00 0.00
-ATOM 2385 2H2' DC B 15 55.570 63.180 22.190 1.00 0.00
-ATOM 2386 O3' DC B 15 57.200 63.770 20.190 1.00 0.00
-ATOM 2387 P DA B 16 55.910 63.880 19.160 1.00 0.00
-ATOM 2388 O1P DA B 16 56.460 64.240 17.820 1.00 0.00
-ATOM 2389 O2P DA B 16 54.940 64.840 19.740 1.00 0.00
-ATOM 2390 O5' DA B 16 55.110 62.430 18.950 1.00 0.00
-ATOM 2391 C5' DA B 16 55.400 61.510 17.870 1.00 0.00
-ATOM 2392 1H5' DA B 16 56.480 61.380 17.880 1.00 0.00
-ATOM 2393 2H5' DA B 16 55.160 62.010 16.930 1.00 0.00
-ATOM 2394 C4' DA B 16 54.800 60.050 17.810 1.00 0.00
-ATOM 2395 H4' DA B 16 55.360 59.530 17.040 1.00 0.00
-ATOM 2396 O4' DA B 16 55.130 59.430 19.030 1.00 0.00
-ATOM 2397 C1' DA B 16 53.940 59.080 19.700 1.00 0.00
-ATOM 2398 H1' DA B 16 53.830 57.980 19.680 1.00 0.00
-ATOM 2399 N9 DA B 16 53.990 59.520 21.100 1.00 0.00
-ATOM 2400 C8 DA B 16 54.130 60.790 21.620 1.00 0.00
-ATOM 2401 H8 DA B 16 54.260 61.660 21.000 1.00 0.00
-ATOM 2402 N7 DA B 16 54.100 60.850 22.920 1.00 0.00
-ATOM 2403 C5 DA B 16 53.930 59.490 23.270 1.00 0.00
-ATOM 2404 C6 DA B 16 53.840 58.770 24.480 1.00 0.00
-ATOM 2405 N6 DA B 16 53.930 59.290 25.680 1.00 0.00
-ATOM 2406 H61 DA B 16 53.980 58.660 26.480 1.00 0.00
-ATOM 2407 H62 DA B 16 54.110 60.270 25.790 1.00 0.00
-ATOM 2408 N1 DA B 16 53.670 57.450 24.470 1.00 0.00
-ATOM 2409 C2 DA B 16 53.580 56.810 23.310 1.00 0.00
-ATOM 2410 H2 DA B 16 53.440 55.740 23.360 1.00 0.00
-ATOM 2411 N3 DA B 16 53.630 57.350 22.100 1.00 0.00
-ATOM 2412 C4 DA B 16 53.840 58.690 22.170 1.00 0.00
-ATOM 2413 C3' DA B 16 53.290 59.700 17.530 1.00 0.00
-ATOM 2414 H3' DA B 16 52.810 60.470 16.930 1.00 0.00
-ATOM 2415 C2' DA B 16 52.770 59.700 18.950 1.00 0.00
-ATOM 2416 1H2' DA B 16 52.590 60.730 19.280 1.00 0.00
-ATOM 2417 2H2' DA B 16 51.870 59.090 19.060 1.00 0.00
-ATOM 2418 O3' DA B 16 53.100 58.380 16.920 1.00 0.00
-ATOM 2419 P DT B 17 51.650 57.730 16.460 1.00 0.00
-ATOM 2420 O1P DT B 17 51.890 57.020 15.170 1.00 0.00
-ATOM 2421 O2P DT B 17 50.670 58.840 16.410 1.00 0.00
-ATOM 2422 O5' DT B 17 51.050 56.590 17.520 1.00 0.00
-ATOM 2423 C5' DT B 17 51.340 55.170 17.410 1.00 0.00
-ATOM 2424 1H5' DT B 17 52.420 55.090 17.300 1.00 0.00
-ATOM 2425 2H5' DT B 17 50.910 54.800 16.480 1.00 0.00
-ATOM 2426 C4' DT B 17 50.960 54.170 18.570 1.00 0.00
-ATOM 2427 H4' DT B 17 51.660 53.340 18.500 1.00 0.00
-ATOM 2428 O4' DT B 17 51.250 54.840 19.780 1.00 0.00
-ATOM 2429 C1' DT B 17 50.140 54.750 20.650 1.00 0.00
-ATOM 2430 H1' DT B 17 50.300 53.930 21.350 1.00 0.00
-ATOM 2431 N1 DT B 17 50.000 56.040 21.360 1.00 0.00
-ATOM 2432 C6 DT B 17 49.840 57.220 20.680 1.00 0.00
-ATOM 2433 H6 DT B 17 49.820 57.210 19.600 1.00 0.00
-ATOM 2434 C5 DT B 17 49.720 58.400 21.350 1.00 0.00
-ATOM 2435 C7 DT B 17 49.460 59.680 20.580 1.00 0.00
-ATOM 2436 H71 DT B 17 48.400 59.930 20.680 1.00 0.00
-ATOM 2437 H72 DT B 17 50.040 60.490 21.030 1.00 0.00
-ATOM 2438 H73 DT B 17 49.720 59.570 19.530 1.00 0.00
-ATOM 2439 C4 DT B 17 49.860 58.440 22.800 1.00 0.00
-ATOM 2440 O4 DT B 17 49.870 59.450 23.490 1.00 0.00
-ATOM 2441 N3 DT B 17 49.970 57.210 23.400 1.00 0.00
-ATOM 2442 H3 DT B 17 50.110 57.170 24.400 1.00 0.00
-ATOM 2443 C2 DT B 17 49.990 56.000 22.760 1.00 0.00
-ATOM 2444 O2 DT B 17 49.930 54.950 23.390 1.00 0.00
-ATOM 2445 C3' DT B 17 49.550 53.510 18.730 1.00 0.00
-ATOM 2446 H3' DT B 17 48.980 53.540 17.800 1.00 0.00
-ATOM 2447 C2' DT B 17 48.920 54.420 19.780 1.00 0.00
-ATOM 2448 1H2' DT B 17 48.530 55.310 19.290 1.00 0.00
-ATOM 2449 2H2' DT B 17 48.150 53.920 20.360 1.00 0.00
-ATOM 2450 O3' DT B 17 49.610 52.130 19.220 1.00 0.00
-ATOM 2451 P DC B 18 48.320 51.140 19.500 1.00 0.00
-ATOM 2452 O1P DC B 18 48.670 49.800 18.950 1.00 0.00
-ATOM 2453 O2P DC B 18 47.140 51.800 18.890 1.00 0.00
-ATOM 2454 O5' DC B 18 48.010 50.950 21.110 1.00 0.00
-ATOM 2455 C5' DC B 18 48.770 50.070 21.990 1.00 0.00
-ATOM 2456 1H5' DC B 18 49.820 50.280 21.780 1.00 0.00
-ATOM 2457 2H5' DC B 18 48.590 49.040 21.690 1.00 0.00
-ATOM 2458 C4' DC B 18 48.630 50.170 23.550 1.00 0.00
-ATOM 2459 H4' DC B 18 49.520 49.700 23.980 1.00 0.00
-ATOM 2460 O4' DC B 18 48.720 51.540 23.880 1.00 0.00
-ATOM 2461 C1' DC B 18 47.670 51.900 24.760 1.00 0.00
-ATOM 2462 H1' DC B 18 48.050 51.920 25.800 1.00 0.00
-ATOM 2463 N1 DC B 18 47.170 53.240 24.360 1.00 0.00
-ATOM 2464 C6 DC B 18 46.900 53.510 23.040 1.00 0.00
-ATOM 2465 H6 DC B 18 47.040 52.720 22.320 1.00 0.00
-ATOM 2466 C5 DC B 18 46.540 54.760 22.650 1.00 0.00
-ATOM 2467 H5 DC B 18 46.360 54.980 21.620 1.00 0.00
-ATOM 2468 C4 DC B 18 46.460 55.740 23.680 1.00 0.00
-ATOM 2469 N4 DC B 18 46.240 56.980 23.380 1.00 0.00
-ATOM 2470 H41 DC B 18 46.370 57.610 24.170 1.00 0.00
-ATOM 2471 H42 DC B 18 46.350 57.300 22.450 1.00 0.00
-ATOM 2472 N3 DC B 18 46.650 55.480 24.940 1.00 0.00
-ATOM 2473 C2 DC B 18 47.020 54.240 25.320 1.00 0.00
-ATOM 2474 O2 DC B 18 47.160 54.010 26.510 1.00 0.00
-ATOM 2475 C3' DC B 18 47.430 49.580 24.370 1.00 0.00
-ATOM 2476 H3' DC B 18 46.870 48.860 23.770 1.00 0.00
-ATOM 2477 C2' DC B 18 46.600 50.830 24.630 1.00 0.00
-ATOM 2478 1H2' DC B 18 45.960 51.020 23.770 1.00 0.00
-ATOM 2479 2H2' DC B 18 46.020 50.750 25.540 1.00 0.00
-ATOM 2480 O3' DC B 18 47.840 48.960 25.610 1.00 0.00
-ATOM 2481 P DT B 19 46.830 48.310 26.740 1.00 0.00
-ATOM 2482 O1P DT B 19 47.450 47.040 27.200 1.00 0.00
-ATOM 2483 O2P DT B 19 45.500 48.180 26.080 1.00 0.00
-ATOM 2484 O5' DT B 19 46.670 49.320 28.040 1.00 0.00
-ATOM 2485 C5' DT B 19 47.700 49.510 29.060 1.00 0.00
-ATOM 2486 1H5' DT B 19 48.630 49.670 28.520 1.00 0.00
-ATOM 2487 2H5' DT B 19 47.810 48.580 29.620 1.00 0.00
-ATOM 2488 C4' DT B 19 47.590 50.700 30.080 1.00 0.00
-ATOM 2489 H4' DT B 19 48.590 50.880 30.490 1.00 0.00
-ATOM 2490 O4' DT B 19 47.230 51.840 29.320 1.00 0.00
-ATOM 2491 C1' DT B 19 46.130 52.480 29.930 1.00 0.00
-ATOM 2492 H1' DT B 19 46.490 53.270 30.600 1.00 0.00
-ATOM 2493 N1 DT B 19 45.240 53.030 28.880 1.00 0.00
-ATOM 2494 C6 DT B 19 44.750 52.210 27.880 1.00 0.00
-ATOM 2495 H6 DT B 19 45.030 51.170 27.900 1.00 0.00
-ATOM 2496 C5 DT B 19 43.990 52.720 26.880 1.00 0.00
-ATOM 2497 C7 DT B 19 43.440 51.800 25.820 1.00 0.00
-ATOM 2498 H71 DT B 19 43.660 50.760 26.060 1.00 0.00
-ATOM 2499 H72 DT B 19 42.360 51.940 25.760 1.00 0.00
-ATOM 2500 H73 DT B 19 43.880 52.070 24.860 1.00 0.00
-ATOM 2501 C4 DT B 19 43.700 54.150 26.830 1.00 0.00
-ATOM 2502 O4 DT B 19 43.080 54.710 25.920 1.00 0.00
-ATOM 2503 N3 DT B 19 44.180 54.880 27.890 1.00 0.00
-ATOM 2504 H3 DT B 19 44.040 55.880 27.910 1.00 0.00
-ATOM 2505 C2 DT B 19 44.890 54.380 28.950 1.00 0.00
-ATOM 2506 O2 DT B 19 45.150 55.100 29.900 1.00 0.00
-ATOM 2507 C3' DT B 19 46.630 50.670 31.320 1.00 0.00
-ATOM 2508 H3' DT B 19 46.370 49.650 31.600 1.00 0.00
-ATOM 2509 C2' DT B 19 45.430 51.410 30.750 1.00 0.00
-ATOM 2510 1H2' DT B 19 44.840 50.730 30.140 1.00 0.00
-ATOM 2511 2H2' DT B 19 44.830 51.870 31.530 1.00 0.00
-ATOM 2512 O3' DT B 19 47.120 51.380 32.480 1.00 0.00
-ATOM 2513 P DT B 20 46.310 51.520 33.910 1.00 0.00
-ATOM 2514 O1P DT B 20 47.240 51.110 34.990 1.00 0.00
-ATOM 2515 O2P DT B 20 45.070 50.720 33.760 1.00 0.00
-ATOM 2516 O5' DT B 20 45.860 53.090 34.180 1.00 0.00
-ATOM 2517 C5' DT B 20 46.780 54.120 34.630 1.00 0.00
-ATOM 2518 1H5' DT B 20 47.630 54.040 33.960 1.00 0.00
-ATOM 2519 2H5' DT B 20 47.140 53.880 35.620 1.00 0.00
-ATOM 2520 C4' DT B 20 46.360 55.640 34.590 1.00 0.00
-ATOM 2521 H4' DT B 20 47.280 56.220 34.620 1.00 0.00
-ATOM 2522 O4' DT B 20 45.770 55.850 33.320 1.00 0.00
-ATOM 2523 C1' DT B 20 44.460 56.340 33.530 1.00 0.00
-ATOM 2524 H1' DT B 20 44.480 57.430 33.400 1.00 0.00
-ATOM 2525 N1 DT B 20 43.530 55.710 32.560 1.00 0.00
-ATOM 2526 C6 DT B 20 43.280 54.350 32.590 1.00 0.00
-ATOM 2527 H6 DT B 20 43.750 53.750 33.350 1.00 0.00
-ATOM 2528 C5 DT B 20 42.470 53.770 31.660 1.00 0.00
-ATOM 2529 C7 DT B 20 42.190 52.280 31.730 1.00 0.00
-ATOM 2530 H71 DT B 20 42.700 51.830 32.580 1.00 0.00
-ATOM 2531 H72 DT B 20 41.110 52.140 31.830 1.00 0.00
-ATOM 2532 H73 DT B 20 42.520 51.820 30.800 1.00 0.00
-ATOM 2533 C4 DT B 20 41.900 54.570 30.580 1.00 0.00
-ATOM 2534 O4 DT B 20 41.230 54.130 29.640 1.00 0.00
-ATOM 2535 N3 DT B 20 42.160 55.910 30.660 1.00 0.00
-ATOM 2536 H3 DT B 20 41.750 56.540 29.990 1.00 0.00
-ATOM 2537 C2 DT B 20 42.910 56.530 31.620 1.00 0.00
-ATOM 2538 O2 DT B 20 42.950 57.760 31.630 1.00 0.00
-ATOM 2539 C3' DT B 20 45.420 56.330 35.640 1.00 0.00
-ATOM 2540 H3' DT B 20 45.500 55.860 36.620 1.00 0.00
-ATOM 2541 C2' DT B 20 44.100 56.050 34.980 1.00 0.00
-ATOM 2542 1H2' DT B 20 43.820 55.010 35.150 1.00 0.00
-ATOM 2543 2H2' DT B 20 43.330 56.730 35.330 1.00 0.00
-ATOM 2544 O3' DT B 20 45.580 57.770 35.760 1.00 0.00
-ATOM 2545 P DT B 21 44.700 58.750 36.770 1.00 0.00
-ATOM 2546 O1P DT B 21 45.630 59.650 37.470 1.00 0.00
-ATOM 2547 O2P DT B 21 43.860 57.850 37.590 1.00 0.00
-ATOM 2548 O5' DT B 21 43.650 59.720 35.940 1.00 0.00
-ATOM 2549 C5' DT B 21 44.000 61.030 35.450 1.00 0.00
-ATOM 2550 1H5' DT B 21 44.840 60.880 34.760 1.00 0.00
-ATOM 2551 2H5' DT B 21 44.380 61.620 36.280 1.00 0.00
-ATOM 2552 C4' DT B 21 42.930 61.890 34.680 1.00 0.00
-ATOM 2553 H4' DT B 21 43.490 62.650 34.120 1.00 0.00
-ATOM 2554 O4' DT B 21 42.310 61.040 33.740 1.00 0.00
-ATOM 2555 C1' DT B 21 40.970 60.830 34.160 1.00 0.00
-ATOM 2556 H1' DT B 21 40.340 61.430 33.490 1.00 0.00
-ATOM 2557 N1 DT B 21 40.620 59.390 33.990 1.00 0.00
-ATOM 2558 C6 DT B 21 40.900 58.410 34.920 1.00 0.00
-ATOM 2559 H6 DT B 21 41.400 58.680 35.850 1.00 0.00
-ATOM 2560 C5 DT B 21 40.600 57.110 34.680 1.00 0.00
-ATOM 2561 C7 DT B 21 40.840 56.050 35.750 1.00 0.00
-ATOM 2562 H71 DT B 21 41.350 56.470 36.610 1.00 0.00
-ATOM 2563 H72 DT B 21 39.880 55.630 36.050 1.00 0.00
-ATOM 2564 H73 DT B 21 41.430 55.240 35.320 1.00 0.00
-ATOM 2565 C4 DT B 21 40.050 56.700 33.390 1.00 0.00
-ATOM 2566 O4 DT B 21 39.810 55.550 33.020 1.00 0.00
-ATOM 2567 N3 DT B 21 39.780 57.740 32.540 1.00 0.00
-ATOM 2568 H3 DT B 21 39.300 57.520 31.680 1.00 0.00
-ATOM 2569 C2 DT B 21 39.970 59.070 32.790 1.00 0.00
-ATOM 2570 O2 DT B 21 39.510 59.880 32.000 1.00 0.00
-ATOM 2571 C3' DT B 21 41.750 62.630 35.400 1.00 0.00
-ATOM 2572 H3' DT B 21 42.070 63.010 36.370 1.00 0.00
-ATOM 2573 C2' DT B 21 40.820 61.440 35.550 1.00 0.00
-ATOM 2574 1H2' DT B 21 41.190 60.770 36.330 1.00 0.00
-ATOM 2575 2H2' DT B 21 39.800 61.750 35.770 1.00 0.00
-ATOM 2576 O3' DT B 21 41.160 63.700 34.590 1.00 0.00
-ATOM 2577 P DA B 22 39.990 64.770 35.070 1.00 0.00
-ATOM 2578 O1P DA B 22 40.430 66.140 34.670 1.00 0.00
-ATOM 2579 O2P DA B 22 39.720 64.560 36.500 1.00 0.00
-ATOM 2580 O5' DA B 22 38.550 64.540 34.290 1.00 0.00
-ATOM 2581 C5' DA B 22 38.240 65.160 33.030 1.00 0.00
-ATOM 2582 1H5' DA B 22 39.040 64.860 32.340 1.00 0.00
-ATOM 2583 2H5' DA B 22 38.330 66.240 33.160 1.00 0.00
-ATOM 2584 C4' DA B 22 36.880 64.860 32.300 1.00 0.00
-ATOM 2585 H4' DA B 22 36.960 65.340 31.320 1.00 0.00
-ATOM 2586 O4' DA B 22 36.830 63.470 32.060 1.00 0.00
-ATOM 2587 C1' DA B 22 35.820 62.910 32.890 1.00 0.00
-ATOM 2588 H1' DA B 22 35.020 62.560 32.240 1.00 0.00
-ATOM 2589 N9 DA B 22 36.360 61.750 33.630 1.00 0.00
-ATOM 2590 C8 DA B 22 37.250 61.680 34.670 1.00 0.00
-ATOM 2591 H8 DA B 22 37.710 62.550 35.120 1.00 0.00
-ATOM 2592 N7 DA B 22 37.480 60.470 35.090 1.00 0.00
-ATOM 2593 C5 DA B 22 36.710 59.680 34.220 1.00 0.00
-ATOM 2594 C6 DA B 22 36.500 58.300 34.050 1.00 0.00
-ATOM 2595 N6 DA B 22 37.100 57.350 34.740 1.00 0.00
-ATOM 2596 H61 DA B 22 36.880 56.380 34.550 1.00 0.00
-ATOM 2597 H62 DA B 22 37.700 57.610 35.500 1.00 0.00
-ATOM 2598 N1 DA B 22 35.630 57.860 33.130 1.00 0.00
-ATOM 2599 C2 DA B 22 34.990 58.750 32.390 1.00 0.00
-ATOM 2600 H2 DA B 22 34.290 58.340 31.660 1.00 0.00
-ATOM 2601 N3 DA B 22 35.090 60.060 32.410 1.00 0.00
-ATOM 2602 C4 DA B 22 36.000 60.460 33.350 1.00 0.00
-ATOM 2603 C3' DA B 22 35.480 65.230 32.870 1.00 0.00
-ATOM 2604 H3' DA B 22 35.530 66.150 33.450 1.00 0.00
-ATOM 2605 C2' DA B 22 35.280 64.030 33.780 1.00 0.00
-ATOM 2606 1H2' DA B 22 35.880 64.140 34.680 1.00 0.00
-ATOM 2607 2H2' DA B 22 34.230 63.890 34.020 1.00 0.00
-ATOM 2608 O3' DA B 22 34.450 65.320 31.840 1.00 0.00
-ATOM 2609 P DC B 23 32.860 65.760 32.050 1.00 0.00
-ATOM 2610 O1P DC B 23 32.470 66.540 30.840 1.00 0.00
-ATOM 2611 O2P DC B 23 32.760 66.480 33.330 1.00 0.00
-ATOM 2612 O5' DC B 23 31.820 64.470 32.110 1.00 0.00
-ATOM 2613 C5' DC B 23 31.210 63.900 30.930 1.00 0.00
-ATOM 2614 1H5' DC B 23 32.040 63.680 30.250 1.00 0.00
-ATOM 2615 2H5' DC B 23 30.620 64.680 30.450 1.00 0.00
-ATOM 2616 C4' DC B 23 30.340 62.590 30.980 1.00 0.00
-ATOM 2617 H4' DC B 23 30.200 62.290 29.940 1.00 0.00
-ATOM 2618 O4' DC B 23 31.150 61.600 31.570 1.00 0.00
-ATOM 2619 C1' DC B 23 30.480 61.070 32.690 1.00 0.00
-ATOM 2620 H1' DC B 23 30.020 60.120 32.390 1.00 0.00
-ATOM 2621 N1 DC B 23 31.460 60.830 33.780 1.00 0.00
-ATOM 2622 C6 DC B 23 32.230 61.840 34.310 1.00 0.00
-ATOM 2623 H6 DC B 23 32.090 62.850 33.960 1.00 0.00
-ATOM 2624 C5 DC B 23 33.180 61.550 35.240 1.00 0.00
-ATOM 2625 H5 DC B 23 33.800 62.320 35.660 1.00 0.00
-ATOM 2626 C4 DC B 23 33.330 60.180 35.610 1.00 0.00
-ATOM 2627 N4 DC B 23 34.290 59.820 36.410 1.00 0.00
-ATOM 2628 H41 DC B 23 34.390 58.830 36.620 1.00 0.00
-ATOM 2629 H42 DC B 23 35.000 60.460 36.700 1.00 0.00
-ATOM 2630 N3 DC B 23 32.610 59.210 35.110 1.00 0.00
-ATOM 2631 C2 DC B 23 31.660 59.510 34.200 1.00 0.00
-ATOM 2632 O2 DC B 23 30.980 58.600 33.730 1.00 0.00
-ATOM 2633 C3' DC B 23 28.920 62.470 31.650 1.00 0.00
-ATOM 2634 H3' DC B 23 28.420 63.440 31.680 1.00 0.00
-ATOM 2635 C2' DC B 23 29.350 62.030 33.040 1.00 0.00
-ATOM 2636 1H2' DC B 23 29.720 62.880 33.610 1.00 0.00
-ATOM 2637 2H2' DC B 23 28.540 61.530 33.580 1.00 0.00
-ATOM 2638 O3' DC B 23 28.080 61.470 30.990 1.00 0.00
-ATOM 2639 P DG B 24 26.480 61.140 31.300 1.00 0.00
-ATOM 2640 O1P DG B 24 25.830 60.950 29.980 1.00 0.00
-ATOM 2641 O2P DG B 24 25.950 62.260 32.110 1.00 0.00
-ATOM 2642 O5' DG B 24 26.240 59.730 32.150 1.00 0.00
-ATOM 2643 C5' DG B 24 26.020 58.450 31.500 1.00 0.00
-ATOM 2644 1H5' DG B 24 26.830 58.360 30.770 1.00 0.00
-ATOM 2645 2H5' DG B 24 25.090 58.520 30.930 1.00 0.00
-ATOM 2646 C4' DG B 24 26.010 57.070 32.270 1.00 0.00
-ATOM 2647 H4' DG B 24 26.090 56.310 31.500 1.00 0.00
-ATOM 2648 O4' DG B 24 27.210 57.010 33.000 1.00 0.00
-ATOM 2649 C1' DG B 24 26.900 56.900 34.370 1.00 0.00
-ATOM 2650 H1' DG B 24 27.140 55.880 34.700 1.00 0.00
-ATOM 2651 N9 DG B 24 27.720 57.840 35.140 1.00 0.00
-ATOM 2652 C8 DG B 24 27.780 59.210 35.110 1.00 0.00
-ATOM 2653 H8 DG B 24 27.170 59.800 34.450 1.00 0.00
-ATOM 2654 N7 DG B 24 28.640 59.730 35.950 1.00 0.00
-ATOM 2655 C5 DG B 24 29.220 58.590 36.560 1.00 0.00
-ATOM 2656 C6 DG B 24 30.260 58.430 37.540 1.00 0.00
-ATOM 2657 O6 DG B 24 30.930 59.290 38.110 1.00 0.00
-ATOM 2658 N1 DG B 24 30.510 57.100 37.850 1.00 0.00
-ATOM 2659 H1 DG B 24 31.260 56.910 38.500 1.00 0.00
-ATOM 2660 C2 DG B 24 29.860 56.050 37.280 1.00 0.00
-ATOM 2661 N2 DG B 24 30.180 54.840 37.620 1.00 0.00
-ATOM 2662 H21 DG B 24 30.930 54.690 38.290 1.00 0.00
-ATOM 2663 H22 DG B 24 29.710 54.080 37.180 1.00 0.00
-ATOM 2664 N3 DG B 24 28.900 56.150 36.380 1.00 0.00
-ATOM 2665 C4 DG B 24 28.640 57.450 36.060 1.00 0.00
-ATOM 2666 C3' DG B 24 24.890 56.560 33.240 1.00 0.00
-ATOM 2667 H3' DG B 24 23.920 56.980 32.990 1.00 0.00
-ATOM 2668 C2' DG B 24 25.400 57.120 34.550 1.00 0.00
-ATOM 2669 1H2' DG B 24 25.180 58.190 34.620 1.00 0.00
-ATOM 2670 2H2' DG B 24 25.020 56.590 35.420 1.00 0.00
-ATOM 2671 O3' DG B 24 24.820 55.100 33.260 1.00 0.00
-ATOM 2672 P DG B 25 23.750 54.170 34.130 1.00 0.00
-ATOM 2673 O1P DG B 25 23.330 53.070 33.220 1.00 0.00
-ATOM 2674 O2P DG B 25 22.670 55.070 34.580 1.00 0.00
-ATOM 2675 O5' DG B 25 24.430 53.450 35.470 1.00 0.00
-ATOM 2676 C5' DG B 25 25.150 52.180 35.420 1.00 0.00
-ATOM 2677 1H5' DG B 25 25.870 52.290 34.610 1.00 0.00
-ATOM 2678 2H5' DG B 25 24.450 51.410 35.110 1.00 0.00
-ATOM 2679 C4' DG B 25 25.980 51.630 36.640 1.00 0.00
-ATOM 2680 H4' DG B 25 26.660 50.890 36.220 1.00 0.00
-ATOM 2681 O4' DG B 25 26.790 52.690 37.090 1.00 0.00
-ATOM 2682 C1' DG B 25 26.600 52.850 38.490 1.00 0.00
-ATOM 2683 H1' DG B 25 27.440 52.400 39.030 1.00 0.00
-ATOM 2684 N9 DG B 25 26.520 54.280 38.780 1.00 0.00
-ATOM 2685 C8 DG B 25 25.690 55.240 38.270 1.00 0.00
-ATOM 2686 H8 DG B 25 24.930 55.000 37.540 1.00 0.00
-ATOM 2687 N7 DG B 25 25.920 56.450 38.710 1.00 0.00
-ATOM 2688 C5 DG B 25 27.030 56.270 39.560 1.00 0.00
-ATOM 2689 C6 DG B 25 27.850 57.190 40.300 1.00 0.00
-ATOM 2690 O6 DG B 25 27.740 58.420 40.360 1.00 0.00
-ATOM 2691 N1 DG B 25 28.890 56.580 40.980 1.00 0.00
-ATOM 2692 H1 DG B 25 29.550 57.170 41.470 1.00 0.00
-ATOM 2693 C2 DG B 25 29.130 55.240 40.970 1.00 0.00
-ATOM 2694 N2 DG B 25 30.160 54.780 41.620 1.00 0.00
-ATOM 2695 H21 DG B 25 30.790 55.420 42.100 1.00 0.00
-ATOM 2696 H22 DG B 25 30.390 53.810 41.540 1.00 0.00
-ATOM 2697 N3 DG B 25 28.370 54.350 40.330 1.00 0.00
-ATOM 2698 C4 DG B 25 27.370 54.940 39.630 1.00 0.00
-ATOM 2699 C3' DG B 25 25.370 50.950 37.910 1.00 0.00
-ATOM 2700 H3' DG B 25 24.370 50.560 37.710 1.00 0.00
-ATOM 2701 C2' DG B 25 25.310 52.130 38.860 1.00 0.00
-ATOM 2702 1H2' DG B 25 24.440 52.740 38.640 1.00 0.00
-ATOM 2703 2H2' DG B 25 25.320 51.820 39.910 1.00 0.00
-ATOM 2704 O3' DG B 25 26.210 49.890 38.440 1.00 0.00
-ATOM 2705 P DT B 26 25.910 49.010 39.810 1.00 0.00
-ATOM 2706 O1P DT B 26 26.290 47.600 39.500 1.00 0.00
-ATOM 2707 O2P DT B 26 24.490 49.240 40.150 1.00 0.00
-ATOM 2708 O5' DT B 26 26.840 49.520 41.090 1.00 0.00
-ATOM 2709 C5' DT B 26 28.230 49.130 41.290 1.00 0.00
-ATOM 2710 1H5' DT B 26 28.730 49.290 40.330 1.00 0.00
-ATOM 2711 2H5' DT B 26 28.280 48.060 41.480 1.00 0.00
-ATOM 2712 C4' DT B 26 29.150 49.850 42.350 1.00 0.00
-ATOM 2713 H4' DT B 26 30.180 49.710 42.020 1.00 0.00
-ATOM 2714 O4' DT B 26 28.890 51.240 42.260 1.00 0.00
-ATOM 2715 C1' DT B 26 28.740 51.780 43.570 1.00 0.00
-ATOM 2716 H1' DT B 26 29.690 52.200 43.920 1.00 0.00
-ATOM 2717 N1 DT B 26 27.690 52.820 43.500 1.00 0.00
-ATOM 2718 C6 DT B 26 26.460 52.520 42.950 1.00 0.00
-ATOM 2719 H6 DT B 26 26.280 51.510 42.610 1.00 0.00
-ATOM 2720 C5 DT B 26 25.520 53.490 42.780 1.00 0.00
-ATOM 2721 C7 DT B 26 24.170 53.130 42.190 1.00 0.00
-ATOM 2722 H71 DT B 26 24.070 52.050 42.090 1.00 0.00
-ATOM 2723 H72 DT B 26 23.400 53.520 42.850 1.00 0.00
-ATOM 2724 H73 DT B 26 24.080 53.620 41.220 1.00 0.00
-ATOM 2725 C4 DT B 26 25.810 54.870 43.160 1.00 0.00
-ATOM 2726 O4 DT B 26 25.050 55.820 42.970 1.00 0.00
-ATOM 2727 N3 DT B 26 27.040 55.070 43.750 1.00 0.00
-ATOM 2728 H3 DT B 26 27.320 56.000 44.000 1.00 0.00
-ATOM 2729 C2 DT B 26 27.990 54.100 43.950 1.00 0.00
-ATOM 2730 O2 DT B 26 29.040 54.400 44.510 1.00 0.00
-ATOM 2731 C3' DT B 26 29.170 49.490 43.880 1.00 0.00
-ATOM 2732 H3' DT B 26 28.710 48.520 44.060 1.00 0.00
-ATOM 2733 C2' DT B 26 28.330 50.620 44.470 1.00 0.00
-ATOM 2734 1H2' DT B 26 27.280 50.380 44.370 1.00 0.00
-ATOM 2735 2H2' DT B 26 28.580 50.820 45.510 1.00 0.00
-ATOM 2736 O3' DT B 26 30.500 49.510 44.430 1.00 0.00
-ATOM 2737 P DA B 27 30.880 49.200 46.010 1.00 0.00
-ATOM 2738 O1P DA B 27 32.040 48.280 46.010 1.00 0.00
-ATOM 2739 O2P DA B 27 29.630 48.660 46.620 1.00 0.00
-ATOM 2740 O5' DA B 27 31.290 50.600 46.800 1.00 0.00
-ATOM 2741 C5' DA B 27 32.610 51.220 46.700 1.00 0.00
-ATOM 2742 1H5' DA B 27 32.850 51.250 45.640 1.00 0.00
-ATOM 2743 2H5' DA B 27 33.340 50.570 47.170 1.00 0.00
-ATOM 2744 C4' DA B 27 32.840 52.690 47.230 1.00 0.00
-ATOM 2745 H4' DA B 27 33.740 53.070 46.740 1.00 0.00
-ATOM 2746 O4' DA B 27 31.750 53.450 46.760 1.00 0.00
-ATOM 2747 C1' DA B 27 31.120 54.060 47.880 1.00 0.00
-ATOM 2748 H1' DA B 27 31.450 55.100 47.970 1.00 0.00
-ATOM 2749 N9 DA B 27 29.670 53.990 47.690 1.00 0.00
-ATOM 2750 C8 DA B 27 28.870 52.890 47.500 1.00 0.00
-ATOM 2751 H8 DA B 27 29.290 51.900 47.490 1.00 0.00
-ATOM 2752 N7 DA B 27 27.600 53.160 47.300 1.00 0.00
-ATOM 2753 C5 DA B 27 27.600 54.560 47.380 1.00 0.00
-ATOM 2754 C6 DA B 27 26.630 55.570 47.210 1.00 0.00
-ATOM 2755 N6 DA B 27 25.370 55.320 46.920 1.00 0.00
-ATOM 2756 H61 DA B 27 24.750 56.100 46.780 1.00 0.00
-ATOM 2757 H62 DA B 27 25.100 54.360 46.860 1.00 0.00
-ATOM 2758 N1 DA B 27 26.910 56.860 47.310 1.00 0.00
-ATOM 2759 C2 DA B 27 28.170 57.200 47.580 1.00 0.00
-ATOM 2760 H2 DA B 27 28.380 58.260 47.670 1.00 0.00
-ATOM 2761 N3 DA B 27 29.190 56.380 47.750 1.00 0.00
-ATOM 2762 C4 DA B 27 28.840 55.080 47.620 1.00 0.00
-ATOM 2763 C3' DA B 27 33.010 53.060 48.740 1.00 0.00
-ATOM 2764 H3' DA B 27 33.460 52.250 49.310 1.00 0.00
-ATOM 2765 C2' DA B 27 31.560 53.280 49.120 1.00 0.00
-ATOM 2766 1H2' DA B 27 31.040 52.330 49.200 1.00 0.00
-ATOM 2767 2H2' DA B 27 31.440 53.880 50.020 1.00 0.00
-ATOM 2768 O3' DA B 27 33.760 54.290 48.950 1.00 0.00
-ATOM 2769 P DG B 28 34.150 54.930 50.420 1.00 0.00
-ATOM 2770 O1P DG B 28 35.610 55.170 50.430 1.00 0.00
-ATOM 2771 O2P DG B 28 33.610 53.990 51.430 1.00 0.00
-ATOM 2772 O5' DG B 28 33.410 56.390 50.660 1.00 0.00
-ATOM 2773 C5' DG B 28 33.920 57.640 50.130 1.00 0.00
-ATOM 2774 1H5' DG B 28 34.020 57.480 49.060 1.00 0.00
-ATOM 2775 2H5' DG B 28 34.930 57.790 50.520 1.00 0.00
-ATOM 2776 C4' DG B 28 33.100 58.970 50.300 1.00 0.00
-ATOM 2777 H4' DG B 28 33.500 59.680 49.580 1.00 0.00
-ATOM 2778 O4' DG B 28 31.770 58.670 49.930 1.00 0.00
-ATOM 2779 C1' DG B 28 30.980 58.750 51.100 1.00 0.00
-ATOM 2780 H1' DG B 28 30.390 59.670 51.030 1.00 0.00
-ATOM 2781 N9 DG B 28 30.050 57.610 51.160 1.00 0.00
-ATOM 2782 C8 DG B 28 30.270 56.270 51.350 1.00 0.00
-ATOM 2783 H8 DG B 28 31.260 55.860 51.540 1.00 0.00
-ATOM 2784 N7 DG B 28 29.190 55.530 51.240 1.00 0.00
-ATOM 2785 C5 DG B 28 28.190 56.460 50.960 1.00 0.00
-ATOM 2786 C6 DG B 28 26.790 56.330 50.680 1.00 0.00
-ATOM 2787 O6 DG B 28 26.090 55.310 50.600 1.00 0.00
-ATOM 2788 N1 DG B 28 26.150 57.530 50.460 1.00 0.00
-ATOM 2789 H1 DG B 28 25.170 57.510 50.240 1.00 0.00
-ATOM 2790 C2 DG B 28 26.770 58.740 50.500 1.00 0.00
-ATOM 2791 N2 DG B 28 26.060 59.810 50.340 1.00 0.00
-ATOM 2792 H21 DG B 28 25.070 59.770 50.140 1.00 0.00
-ATOM 2793 H22 DG B 28 26.580 60.670 50.410 1.00 0.00
-ATOM 2794 N3 DG B 28 28.050 58.910 50.730 1.00 0.00
-ATOM 2795 C4 DG B 28 28.710 57.740 50.940 1.00 0.00
-ATOM 2796 C3' DG B 28 32.960 59.760 51.650 1.00 0.00
-ATOM 2797 H3' DG B 28 33.900 59.740 52.220 1.00 0.00
-ATOM 2798 C2' DG B 28 31.900 58.890 52.300 1.00 0.00
-ATOM 2799 1H2' DG B 28 32.320 57.930 52.600 1.00 0.00
-ATOM 2800 2H2' DG B 28 31.420 59.390 53.140 1.00 0.00
-ATOM 2801 O3' DG B 28 32.480 61.130 51.470 1.00 0.00
-ATOM 2802 P DA B 29 32.270 62.270 52.650 1.00 0.00
-ATOM 2803 O1P DA B 29 32.880 63.540 52.180 1.00 0.00
-ATOM 2804 O2P DA B 29 32.780 61.700 53.910 1.00 0.00
-ATOM 2805 O5' DA B 29 30.670 62.620 52.920 1.00 0.00
-ATOM 2806 C5' DA B 29 29.990 63.700 52.250 1.00 0.00
-ATOM 2807 1H5' DA B 29 30.050 63.490 51.180 1.00 0.00
-ATOM 2808 2H5' DA B 29 30.560 64.610 52.420 1.00 0.00
-ATOM 2809 C4' DA B 29 28.480 64.010 52.570 1.00 0.00
-ATOM 2810 H4' DA B 29 28.140 64.690 51.790 1.00 0.00
-ATOM 2811 O4' DA B 29 27.740 62.810 52.430 1.00 0.00
-ATOM 2812 C1' DA B 29 27.350 62.380 53.720 1.00 0.00
-ATOM 2813 H1' DA B 29 26.270 62.480 53.790 1.00 0.00
-ATOM 2814 N9 DA B 29 27.690 60.960 53.910 1.00 0.00
-ATOM 2815 C8 DA B 29 28.900 60.340 54.170 1.00 0.00
-ATOM 2816 H8 DA B 29 29.830 60.880 54.280 1.00 0.00
-ATOM 2817 N7 DA B 29 28.820 59.040 54.260 1.00 0.00
-ATOM 2818 C5 DA B 29 27.470 58.790 54.010 1.00 0.00
-ATOM 2819 C6 DA B 29 26.660 57.640 53.900 1.00 0.00
-ATOM 2820 N6 DA B 29 27.110 56.410 54.000 1.00 0.00
-ATOM 2821 H61 DA B 29 26.480 55.620 53.900 1.00 0.00
-ATOM 2822 H62 DA B 29 28.100 56.270 54.150 1.00 0.00
-ATOM 2823 N1 DA B 29 25.350 57.730 53.670 1.00 0.00
-ATOM 2824 C2 DA B 29 24.820 58.940 53.560 1.00 0.00
-ATOM 2825 H2 DA B 29 23.750 58.970 53.380 1.00 0.00
-ATOM 2826 N3 DA B 29 25.430 60.110 53.630 1.00 0.00
-ATOM 2827 C4 DA B 29 26.770 59.960 53.840 1.00 0.00
-ATOM 2828 C3' DA B 29 27.990 64.610 53.930 1.00 0.00
-ATOM 2829 H3' DA B 29 28.710 65.320 54.330 1.00 0.00
-ATOM 2830 C2' DA B 29 27.970 63.330 54.750 1.00 0.00
-ATOM 2831 1H2' DA B 29 28.990 63.030 55.000 1.00 0.00
-ATOM 2832 2H2' DA B 29 27.370 63.420 55.640 1.00 0.00
-ATOM 2833 O3' DA B 29 26.660 65.220 53.830 1.00 0.00
-ATOM 2834 P DA B 30 25.840 66.040 55.010 1.00 0.00
-ATOM 2835 O1P DA B 30 25.170 67.200 54.350 1.00 0.00
-ATOM 2836 O2P DA B 30 26.790 66.370 56.090 1.00 0.00
-ATOM 2837 O5' DA B 30 24.610 65.150 55.680 1.00 0.00
-ATOM 2838 C5' DA B 30 23.250 65.220 55.180 1.00 0.00
-ATOM 2839 1H5' DA B 30 23.330 64.970 54.120 1.00 0.00
-ATOM 2840 2H5' DA B 30 22.930 66.250 55.240 1.00 0.00
-ATOM 2841 C4' DA B 30 22.090 64.310 55.750 1.00 0.00
-ATOM 2842 H4' DA B 30 21.250 64.460 55.070 1.00 0.00
-ATOM 2843 O4' DA B 30 22.490 62.970 55.590 1.00 0.00
-ATOM 2844 C1' DA B 30 22.640 62.390 56.870 1.00 0.00
-ATOM 2845 H1' DA B 30 21.830 61.660 57.020 1.00 0.00
-ATOM 2846 N9 DA B 30 23.920 61.670 56.940 1.00 0.00
-ATOM 2847 C8 DA B 30 25.210 62.160 56.990 1.00 0.00
-ATOM 2848 H8 DA B 30 25.440 63.210 56.940 1.00 0.00
-ATOM 2849 N7 DA B 30 26.120 61.230 57.080 1.00 0.00
-ATOM 2850 C5 DA B 30 25.370 60.040 57.060 1.00 0.00
-ATOM 2851 C6 DA B 30 25.660 58.660 57.070 1.00 0.00
-ATOM 2852 N6 DA B 30 26.860 58.140 57.100 1.00 0.00
-ATOM 2853 H61 DA B 30 26.970 57.130 57.090 1.00 0.00
-ATOM 2854 H62 DA B 30 27.670 58.740 57.120 1.00 0.00
-ATOM 2855 N1 DA B 30 24.670 57.760 57.040 1.00 0.00
-ATOM 2856 C2 DA B 30 23.420 58.180 56.990 1.00 0.00
-ATOM 2857 H2 DA B 30 22.660 57.410 56.970 1.00 0.00
-ATOM 2858 N3 DA B 30 22.990 59.430 56.970 1.00 0.00
-ATOM 2859 C4 DA B 30 24.030 60.310 56.990 1.00 0.00
-ATOM 2860 C3' DA B 30 21.510 64.410 57.190 1.00 0.00
-ATOM 2861 H3' DA B 30 21.570 65.430 57.570 1.00 0.00
-ATOM 2862 C2' DA B 30 22.500 63.500 57.900 1.00 0.00
-ATOM 2863 1H2' DA B 30 23.450 64.020 58.050 1.00 0.00
-ATOM 2864 2H2' DA B 30 22.110 63.130 58.850 1.00 0.00
-ATOM 2865 O3' DA B 30 20.140 63.900 57.280 1.00 0.00
-ATOM 2866 P DA B 31 19.140 63.940 58.600 1.00 0.00
-ATOM 2867 O1P DA B 31 17.780 64.290 58.090 1.00 0.00
-ATOM 2868 O2P DA B 31 19.730 64.890 59.570 1.00 0.00
-ATOM 2869 O5' DA B 31 18.980 62.470 59.360 1.00 0.00
-ATOM 2870 C5' DA B 31 17.920 61.520 59.050 1.00 0.00
-ATOM 2871 1H5' DA B 31 17.960 61.400 57.960 1.00 0.00
-ATOM 2872 2H5' DA B 31 16.970 62.000 59.270 1.00 0.00
-ATOM 2873 C4' DA B 31 17.880 60.060 59.630 1.00 0.00
-ATOM 2874 H4' DA B 31 17.110 59.540 59.050 1.00 0.00
-ATOM 2875 O4' DA B 31 19.100 59.450 59.310 1.00 0.00
-ATOM 2876 C1' DA B 31 19.760 59.070 60.500 1.00 0.00
-ATOM 2877 H1' DA B 31 19.740 57.970 60.580 1.00 0.00
-ATOM 2878 N9 DA B 31 21.160 59.520 60.460 1.00 0.00
-ATOM 2879 C8 DA B 31 21.670 60.780 60.320 1.00 0.00
-ATOM 2880 H8 DA B 31 21.040 61.650 60.200 1.00 0.00
-ATOM 2881 N7 DA B 31 22.970 60.840 60.320 1.00 0.00
-ATOM 2882 C5 DA B 31 23.340 59.490 60.460 1.00 0.00
-ATOM 2883 C6 DA B 31 24.550 58.760 60.490 1.00 0.00
-ATOM 2884 N6 DA B 31 25.750 59.270 60.330 1.00 0.00
-ATOM 2885 H61 DA B 31 26.540 58.630 60.290 1.00 0.00
-ATOM 2886 H62 DA B 31 25.850 60.240 60.100 1.00 0.00
-ATOM 2887 N1 DA B 31 24.530 57.440 60.660 1.00 0.00
-ATOM 2888 C2 DA B 31 23.380 56.810 60.790 1.00 0.00
-ATOM 2889 H2 DA B 31 23.430 55.730 60.920 1.00 0.00
-ATOM 2890 N3 DA B 31 22.170 57.340 60.780 1.00 0.00
-ATOM 2891 C4 DA B 31 22.230 58.690 60.590 1.00 0.00
-ATOM 2892 C3' DA B 31 17.580 59.690 61.130 1.00 0.00
-ATOM 2893 H3' DA B 31 16.990 60.460 61.620 1.00 0.00
-ATOM 2894 C2' DA B 31 19.000 59.670 61.670 1.00 0.00
-ATOM 2895 1H2' DA B 31 19.330 60.690 61.870 1.00 0.00
-ATOM 2896 2H2' DA B 31 19.090 59.050 62.560 1.00 0.00
-ATOM 2897 O3' DA B 31 16.960 58.370 61.310 1.00 0.00
-ATOM 2898 P DT B 32 16.490 57.710 62.750 1.00 0.00
-ATOM 2899 O1P DT B 32 15.220 56.970 62.480 1.00 0.00
-ATOM 2900 O2P DT B 32 16.390 58.820 63.720 1.00 0.00
-ATOM 2901 O5' DT B 32 17.560 56.600 63.370 1.00 0.00
-ATOM 2902 C5' DT B 32 17.480 55.170 63.090 1.00 0.00
-ATOM 2903 1H5' DT B 32 17.390 55.080 62.010 1.00 0.00
-ATOM 2904 2H5' DT B 32 16.540 54.790 63.510 1.00 0.00
-ATOM 2905 C4' DT B 32 18.640 54.180 63.500 1.00 0.00
-ATOM 2906 H4' DT B 32 18.570 53.340 62.810 1.00 0.00
-ATOM 2907 O4' DT B 32 19.850 54.840 63.200 1.00 0.00
-ATOM 2908 C1' DT B 32 20.720 54.760 64.310 1.00 0.00
-ATOM 2909 H1' DT B 32 21.420 53.930 64.150 1.00 0.00
-ATOM 2910 N1 DT B 32 21.450 56.050 64.420 1.00 0.00
-ATOM 2911 C6 DT B 32 20.780 57.240 64.640 1.00 0.00
-ATOM 2912 H6 DT B 32 19.710 57.220 64.750 1.00 0.00
-ATOM 2913 C5 DT B 32 21.450 58.420 64.670 1.00 0.00
-ATOM 2914 C7 DT B 32 20.710 59.690 65.010 1.00 0.00
-ATOM 2915 H71 DT B 32 19.880 59.480 65.680 1.00 0.00
-ATOM 2916 H72 DT B 32 21.400 60.380 65.500 1.00 0.00
-ATOM 2917 H73 DT B 32 20.360 60.170 64.090 1.00 0.00
-ATOM 2918 C4 DT B 32 22.890 58.450 64.420 1.00 0.00
-ATOM 2919 O4 DT B 32 23.580 59.470 64.360 1.00 0.00
-ATOM 2920 N3 DT B 32 23.470 57.220 64.250 1.00 0.00
-ATOM 2921 H3 DT B 32 24.460 57.190 64.070 1.00 0.00
-ATOM 2922 C2 DT B 32 22.830 56.010 64.270 1.00 0.00
-ATOM 2923 O2 DT B 32 23.470 54.970 64.180 1.00 0.00
-ATOM 2924 C3' DT B 32 18.800 53.530 64.920 1.00 0.00
-ATOM 2925 H3' DT B 32 17.880 53.580 65.490 1.00 0.00
-ATOM 2926 C2' DT B 32 19.860 54.440 65.530 1.00 0.00
-ATOM 2927 1H2' DT B 32 19.380 55.330 65.930 1.00 0.00
-ATOM 2928 2H2' DT B 32 20.440 53.940 66.310 1.00 0.00
-ATOM 2929 O3' DT B 32 19.270 52.150 64.860 1.00 0.00
-ATOM 2930 P DG B 33 19.550 51.160 66.150 1.00 0.00
-ATOM 2931 O1P DG B 33 19.020 49.820 65.790 1.00 0.00
-ATOM 2932 O2P DG B 33 18.920 51.800 67.330 1.00 0.00
-ATOM 2933 O5' DG B 33 21.160 50.970 66.470 1.00 0.00
-ATOM 2934 C5' DG B 33 22.010 50.050 65.730 1.00 0.00
-ATOM 2935 1H5' DG B 33 21.810 50.240 64.670 1.00 0.00
-ATOM 2936 2H5' DG B 33 21.680 49.030 65.930 1.00 0.00
-ATOM 2937 C4' DG B 33 23.580 50.090 65.860 1.00 0.00
-ATOM 2938 H4' DG B 33 23.980 49.570 64.990 1.00 0.00
-ATOM 2939 O4' DG B 33 23.940 51.440 65.720 1.00 0.00
-ATOM 2940 C1' DG B 33 24.790 51.820 66.790 1.00 0.00
-ATOM 2941 H1' DG B 33 25.840 51.800 66.460 1.00 0.00
-ATOM 2942 N9 DG B 33 24.420 53.180 67.200 1.00 0.00
-ATOM 2943 C8 DG B 33 23.190 53.660 67.550 1.00 0.00
-ATOM 2944 H8 DG B 33 22.310 53.030 67.580 1.00 0.00
-ATOM 2945 N7 DG B 33 23.170 54.940 67.820 1.00 0.00
-ATOM 2946 C5 DG B 33 24.500 55.330 67.570 1.00 0.00
-ATOM 2947 C6 DG B 33 25.160 56.610 67.570 1.00 0.00
-ATOM 2948 O6 DG B 33 24.660 57.720 67.790 1.00 0.00
-ATOM 2949 N1 DG B 33 26.510 56.540 67.250 1.00 0.00
-ATOM 2950 H1 DG B 33 27.010 57.410 67.130 1.00 0.00
-ATOM 2951 C2 DG B 33 27.160 55.390 66.960 1.00 0.00
-ATOM 2952 N2 DG B 33 28.420 55.450 66.650 1.00 0.00
-ATOM 2953 H21 DG B 33 28.890 56.350 66.540 1.00 0.00
-ATOM 2954 H22 DG B 33 28.870 54.610 66.320 1.00 0.00
-ATOM 2955 N3 DG B 33 26.600 54.190 66.950 1.00 0.00
-ATOM 2956 C4 DG B 33 25.270 54.240 67.230 1.00 0.00
-ATOM 2957 C3' DG B 33 24.380 49.530 67.080 1.00 0.00
-ATOM 2958 H3' DG B 33 23.800 48.790 67.630 1.00 0.00
-ATOM 2959 C2' DG B 33 24.570 50.800 67.900 1.00 0.00
-ATOM 2960 1H2' DG B 33 23.660 51.020 68.460 1.00 0.00
-ATOM 2961 2H2' DG B 33 25.430 50.740 68.560 1.00 0.00
-ATOM 2962 O3' DG B 33 25.660 48.970 66.680 1.00 0.00
-ATOM 2963 P DC B 34 26.790 48.340 67.700 1.00 0.00
-ATOM 2964 O1P DC B 34 27.270 47.080 67.090 1.00 0.00
-ATOM 2965 O2P DC B 34 26.130 48.220 69.020 1.00 0.00
-ATOM 2966 O5' DC B 34 28.080 49.370 67.860 1.00 0.00
-ATOM 2967 C5' DC B 34 29.080 49.600 66.830 1.00 0.00
-ATOM 2968 1H5' DC B 34 28.540 49.800 65.900 1.00 0.00
-ATOM 2969 2H5' DC B 34 29.640 48.670 66.670 1.00 0.00
-ATOM 2970 C4' DC B 34 30.130 50.780 66.960 1.00 0.00
-ATOM 2971 H4' DC B 34 30.560 50.930 65.960 1.00 0.00
-ATOM 2972 O4' DC B 34 29.400 51.950 67.280 1.00 0.00
-ATOM 2973 C1' DC B 34 29.980 52.560 68.430 1.00 0.00
-ATOM 2974 H1' DC B 34 30.660 53.370 68.120 1.00 0.00
-ATOM 2975 N1 DC B 34 28.880 53.070 69.280 1.00 0.00
-ATOM 2976 C6 DC B 34 27.820 52.260 69.600 1.00 0.00
-ATOM 2977 H6 DC B 34 27.850 51.230 69.260 1.00 0.00
-ATOM 2978 C5 DC B 34 26.750 52.750 70.260 1.00 0.00
-ATOM 2979 H5 DC B 34 25.910 52.120 70.480 1.00 0.00
-ATOM 2980 C4 DC B 34 26.800 54.130 70.590 1.00 0.00
-ATOM 2981 N4 DC B 34 25.750 54.710 71.090 1.00 0.00
-ATOM 2982 H41 DC B 34 25.870 55.720 71.160 1.00 0.00
-ATOM 2983 H42 DC B 34 24.870 54.280 71.010 1.00 0.00
-ATOM 2984 N3 DC B 34 27.810 54.920 70.330 1.00 0.00
-ATOM 2985 C2 DC B 34 28.880 54.410 69.680 1.00 0.00
-ATOM 2986 O2 DC B 34 29.820 55.160 69.460 1.00 0.00
-ATOM 2987 C3' DC B 34 31.350 50.740 67.930 1.00 0.00
-ATOM 2988 H3' DC B 34 31.630 49.710 68.180 1.00 0.00
-ATOM 2989 C2' DC B 34 30.780 51.470 69.130 1.00 0.00
-ATOM 2990 1H2' DC B 34 30.140 50.800 69.700 1.00 0.00
-ATOM 2991 2H2' DC B 34 31.550 51.900 69.760 1.00 0.00
-ATOM 2992 O3' DC B 34 32.500 51.460 67.430 1.00 0.00
-ATOM 2993 P DC B 35 33.950 51.570 68.200 1.00 0.00
-ATOM 2994 O1P DC B 35 35.000 51.160 67.250 1.00 0.00
-ATOM 2995 O2P DC B 35 33.810 50.770 69.440 1.00 0.00
-ATOM 2996 O5' DC B 35 34.230 53.140 68.660 1.00 0.00
-ATOM 2997 C5' DC B 35 34.620 54.190 67.740 1.00 0.00
-ATOM 2998 1H5' DC B 35 33.920 54.120 66.910 1.00 0.00
-ATOM 2999 2H5' DC B 35 35.610 53.970 67.340 1.00 0.00
-ATOM 3000 C4' DC B 35 34.590 55.700 68.200 1.00 0.00
-ATOM 3001 H4' DC B 35 34.560 56.300 67.290 1.00 0.00
-ATOM 3002 O4' DC B 35 33.370 55.900 68.880 1.00 0.00
-ATOM 3003 C1' DC B 35 33.660 56.300 70.200 1.00 0.00
-ATOM 3004 H1' DC B 35 33.540 57.390 70.260 1.00 0.00
-ATOM 3005 N1 DC B 35 32.710 55.620 71.120 1.00 0.00
-ATOM 3006 C6 DC B 35 32.710 54.260 71.260 1.00 0.00
-ATOM 3007 H6 DC B 35 33.470 53.680 70.760 1.00 0.00
-ATOM 3008 C5 DC B 35 31.730 53.650 71.980 1.00 0.00
-ATOM 3009 H5 DC B 35 31.720 52.580 72.070 1.00 0.00
-ATOM 3010 C4 DC B 35 30.750 54.500 72.550 1.00 0.00
-ATOM 3011 N4 DC B 35 29.740 54.000 73.200 1.00 0.00
-ATOM 3012 H41 DC B 35 29.080 54.690 73.550 1.00 0.00
-ATOM 3013 H42 DC B 35 29.670 53.020 73.340 1.00 0.00
-ATOM 3014 N3 DC B 35 30.750 55.800 72.460 1.00 0.00
-ATOM 3015 C2 DC B 35 31.740 56.390 71.750 1.00 0.00
-ATOM 3016 O2 DC B 35 31.730 57.620 71.700 1.00 0.00
-ATOM 3017 C3' DC B 35 35.680 56.390 69.090 1.00 0.00
-ATOM 3018 H3' DC B 35 36.670 55.970 68.910 1.00 0.00
-ATOM 3019 C2' DC B 35 35.130 55.990 70.450 1.00 0.00
-ATOM 3020 1H2' DC B 35 35.310 54.940 70.640 1.00 0.00
-ATOM 3021 2H2' DC B 35 35.560 56.600 71.250 1.00 0.00
-ATOM 3022 O3' DC B 35 35.690 57.840 68.940 1.00 0.00
-ATOM 3023 P DA B 36 36.750 58.870 69.680 1.00 0.00
-ATOM 3024 O1P DA B 36 37.410 59.690 68.640 1.00 0.00
-ATOM 3025 O2P DA B 36 37.610 58.050 70.560 1.00 0.00
-ATOM 3026 O5' DA B 36 35.960 59.930 70.670 1.00 0.00
-ATOM 3027 C5' DA B 36 35.410 61.180 70.220 1.00 0.00
-ATOM 3028 1H5' DA B 36 34.710 60.930 69.430 1.00 0.00
-ATOM 3029 2H5' DA B 36 36.210 61.770 69.770 1.00 0.00
-ATOM 3030 C4' DA B 36 34.640 62.090 71.250 1.00 0.00
-ATOM 3031 H4' DA B 36 34.100 62.830 70.670 1.00 0.00
-ATOM 3032 O4' DA B 36 33.690 61.270 71.910 1.00 0.00
-ATOM 3033 C1' DA B 36 34.140 61.060 73.230 1.00 0.00
-ATOM 3034 H1' DA B 36 33.450 61.600 73.890 1.00 0.00
-ATOM 3035 N9 DA B 36 34.080 59.630 73.600 1.00 0.00
-ATOM 3036 C8 DA B 36 34.830 58.550 73.180 1.00 0.00
-ATOM 3037 H8 DA B 36 35.680 58.640 72.510 1.00 0.00
-ATOM 3038 N7 DA B 36 34.420 57.400 73.640 1.00 0.00
-ATOM 3039 C5 DA B 36 33.340 57.760 74.440 1.00 0.00
-ATOM 3040 C6 DA B 36 32.410 57.060 75.220 1.00 0.00
-ATOM 3041 N6 DA B 36 32.370 55.750 75.320 1.00 0.00
-ATOM 3042 H61 DA B 36 31.640 55.300 75.850 1.00 0.00
-ATOM 3043 H62 DA B 36 33.080 55.240 74.820 1.00 0.00
-ATOM 3044 N1 DA B 36 31.470 57.700 75.920 1.00 0.00
-ATOM 3045 C2 DA B 36 31.440 59.030 75.870 1.00 0.00
-ATOM 3046 H2 DA B 36 30.670 59.510 76.450 1.00 0.00
-ATOM 3047 N3 DA B 36 32.240 59.830 75.190 1.00 0.00
-ATOM 3048 C4 DA B 36 33.160 59.120 74.470 1.00 0.00
-ATOM 3049 C3' DA B 36 35.370 62.850 72.410 1.00 0.00
-ATOM 3050 H3' DA B 36 36.340 63.220 72.080 1.00 0.00
-ATOM 3051 C2' DA B 36 35.510 61.700 73.380 1.00 0.00
-ATOM 3052 1H2' DA B 36 36.300 61.020 73.050 1.00 0.00
-ATOM 3053 2H2' DA B 36 35.680 62.060 74.390 1.00 0.00
-ATOM 3054 O3' DA B 36 34.570 63.930 73.000 1.00 0.00
-ATOM 3055 P DT B 37 35.040 64.930 74.240 1.00 0.00
-ATOM 3056 O1P DT B 37 34.560 66.300 73.930 1.00 0.00
-ATOM 3057 O2P DT B 37 36.490 64.760 74.450 1.00 0.00
-ATOM 3058 O5' DT B 37 34.320 64.520 75.670 1.00 0.00
-ATOM 3059 C5' DT B 37 33.050 65.100 76.070 1.00 0.00
-ATOM 3060 1H5' DT B 37 32.350 64.860 75.270 1.00 0.00
-ATOM 3061 2H5' DT B 37 33.160 66.180 76.090 1.00 0.00
-ATOM 3062 C4' DT B 37 32.370 64.660 77.420 1.00 0.00
-ATOM 3063 H4' DT B 37 31.350 65.010 77.360 1.00 0.00
-ATOM 3064 O4' DT B 37 32.320 63.250 77.410 1.00 0.00
-ATOM 3065 C1' DT B 37 33.060 62.760 78.510 1.00 0.00
-ATOM 3066 H1' DT B 37 32.340 62.510 79.290 1.00 0.00
-ATOM 3067 N1 DT B 37 33.810 61.530 78.130 1.00 0.00
-ATOM 3068 C6 DT B 37 34.930 61.550 77.310 1.00 0.00
-ATOM 3069 H6 DT B 37 35.310 62.480 76.930 1.00 0.00
-ATOM 3070 C5 DT B 37 35.540 60.380 76.950 1.00 0.00
-ATOM 3071 C7 DT B 37 36.820 60.390 76.130 1.00 0.00
-ATOM 3072 H71 DT B 37 37.170 61.400 75.940 1.00 0.00
-ATOM 3073 H72 DT B 37 37.590 59.830 76.670 1.00 0.00
-ATOM 3074 H73 DT B 37 36.650 59.860 75.200 1.00 0.00
-ATOM 3075 C4 DT B 37 34.970 59.100 77.350 1.00 0.00
-ATOM 3076 O4 DT B 37 35.360 57.980 77.020 1.00 0.00
-ATOM 3077 N3 DT B 37 33.890 59.180 78.180 1.00 0.00
-ATOM 3078 H3 DT B 37 33.500 58.310 78.480 1.00 0.00
-ATOM 3079 C2 DT B 37 33.310 60.330 78.640 1.00 0.00
-ATOM 3080 O2 DT B 37 32.420 60.260 79.490 1.00 0.00
-ATOM 3081 C3' DT B 37 32.920 65.080 78.820 1.00 0.00
-ATOM 3082 H3' DT B 37 33.440 66.030 78.770 1.00 0.00
-ATOM 3083 C2' DT B 37 33.900 63.930 79.040 1.00 0.00
-ATOM 3084 1H2' DT B 37 34.790 64.080 78.430 1.00 0.00
-ATOM 3085 2H2' DT B 37 34.150 63.820 80.090 1.00 0.00
-ATOM 3086 O3' DT B 37 31.880 65.110 79.860 1.00 0.00
-ATOM 3087 P DC B 38 32.050 65.630 81.420 1.00 0.00
-ATOM 3088 O1P DC B 38 30.850 66.450 81.750 1.00 0.00
-ATOM 3089 O2P DC B 38 33.350 66.320 81.540 1.00 0.00
-ATOM 3090 O5' DC B 38 32.050 64.390 82.520 1.00 0.00
-ATOM 3091 C5' DC B 38 30.840 63.860 83.100 1.00 0.00
-ATOM 3092 1H5' DC B 38 30.180 63.640 82.260 1.00 0.00
-ATOM 3093 2H5' DC B 38 30.370 64.650 83.680 1.00 0.00
-ATOM 3094 C4' DC B 38 30.860 62.550 83.980 1.00 0.00
-ATOM 3095 H4' DC B 38 29.820 62.250 84.090 1.00 0.00
-ATOM 3096 O4' DC B 38 31.480 61.560 83.180 1.00 0.00
-ATOM 3097 C1' DC B 38 32.590 61.050 83.870 1.00 0.00
-ATOM 3098 H1' DC B 38 32.290 60.090 84.310 1.00 0.00
-ATOM 3099 N1 DC B 38 33.730 60.840 82.930 1.00 0.00
-ATOM 3100 C6 DC B 38 34.280 61.870 82.200 1.00 0.00
-ATOM 3101 H6 DC B 38 33.890 62.870 82.310 1.00 0.00
-ATOM 3102 C5 DC B 38 35.280 61.610 81.320 1.00 0.00
-ATOM 3103 H5 DC B 38 35.720 62.390 80.730 1.00 0.00
-ATOM 3104 C4 DC B 38 35.690 60.250 81.170 1.00 0.00
-ATOM 3105 N4 DC B 38 36.550 59.920 80.260 1.00 0.00
-ATOM 3106 H41 DC B 38 36.750 58.920 80.150 1.00 0.00
-ATOM 3107 H42 DC B 38 36.940 60.590 79.630 1.00 0.00
-ATOM 3108 N3 DC B 38 35.190 59.280 81.900 1.00 0.00
-ATOM 3109 C2 DC B 38 34.230 59.550 82.800 1.00 0.00
-ATOM 3110 O2 DC B 38 33.830 58.650 83.540 1.00 0.00
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-ATOM 3247 O2P DC B 43 51.400 53.960 80.720 1.00 0.00
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-ATOM 3251 2H5' DC B 43 50.440 57.830 79.520 1.00 0.00
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-ATOM 3273 2H2' DC B 43 53.190 59.380 82.970 1.00 0.00
-ATOM 3274 O3' DC B 43 51.450 61.080 81.970 1.00 0.00
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-ATOM 3282 C4' DG B 44 52.560 64.010 85.870 1.00 0.00
-ATOM 3283 H4' DG B 44 51.770 64.680 86.200 1.00 0.00
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-ATOM 3287 N9 DG B 44 53.920 60.960 86.650 1.00 0.00
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-ATOM 3292 C6 DG B 44 54.040 57.610 87.800 1.00 0.00
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-ATOM 3294 N1 DG B 44 53.890 57.890 89.150 1.00 0.00
-ATOM 3295 H1 DG B 44 53.850 57.100 89.770 1.00 0.00
-ATOM 3296 C2 DG B 44 53.770 59.140 89.660 1.00 0.00
-ATOM 3297 N2 DG B 44 53.680 59.300 90.940 1.00 0.00
-ATOM 3298 H21 DG B 44 53.620 58.490 91.550 1.00 0.00
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-ATOM 3300 N3 DG B 44 53.770 60.250 88.960 1.00 0.00
-ATOM 3301 C4 DG B 44 53.910 60.000 87.620 1.00 0.00
-ATOM 3302 C3' DG B 44 53.920 64.620 86.350 1.00 0.00
-ATOM 3303 H3' DG B 44 54.300 65.350 85.630 1.00 0.00
-ATOM 3304 C2' DG B 44 54.740 63.340 86.330 1.00 0.00
-ATOM 3305 1H2' DG B 44 54.980 63.050 85.300 1.00 0.00
-ATOM 3306 2H2' DG B 44 55.650 63.430 86.920 1.00 0.00
-ATOM 3307 O3' DG B 44 53.800 65.200 87.690 1.00 0.00
-ATOM 3308 P DG B 45 54.960 66.040 88.530 1.00 0.00
-ATOM 3309 O1P DG B 45 54.280 67.200 89.170 1.00 0.00
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-ATOM 3311 O5' DG B 45 55.600 65.160 89.800 1.00 0.00
-ATOM 3312 C5' DG B 45 55.010 65.180 91.120 1.00 0.00
-ATOM 3313 1H5' DG B 45 53.970 64.870 90.990 1.00 0.00
-ATOM 3314 2H5' DG B 45 54.980 66.220 91.450 1.00 0.00
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-ATOM 3316 H4' DG B 45 54.890 64.440 93.130 1.00 0.00
-ATOM 3317 O4' DG B 45 55.480 62.970 91.900 1.00 0.00
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-ATOM 3320 N9 DG B 45 56.940 61.730 90.490 1.00 0.00
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-ATOM 3323 N7 DG B 45 57.080 61.220 88.310 1.00 0.00
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-ATOM 3325 C6 DG B 45 57.280 58.650 88.770 1.00 0.00
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-ATOM 3329 C2 DG B 45 57.290 58.280 91.150 1.00 0.00
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-ATOM 3333 N3 DG B 45 57.210 59.550 91.510 1.00 0.00
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-ATOM 3338 1H2' DG B 45 57.910 64.140 90.970 1.00 0.00
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-ATOM 3379 2H5' DA B 47 63.550 54.800 97.910 1.00 0.00
-ATOM 3380 C4' DA B 47 63.560 54.040 95.870 1.00 0.00
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-ATOM 3382 O4' DA B 47 63.160 54.530 94.610 1.00 0.00
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-ATOM 3385 N9 DA B 47 64.290 55.940 93.120 1.00 0.00
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-ATOM 3388 N7 DA B 47 64.310 58.180 92.830 1.00 0.00
-ATOM 3389 C5 DA B 47 64.260 57.490 91.600 1.00 0.00
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-ATOM 3391 N6 DA B 47 64.140 59.100 89.800 1.00 0.00
-ATOM 3392 H61 DA B 47 64.010 59.240 88.800 1.00 0.00
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-ATOM 3394 N1 DA B 47 64.170 56.940 89.280 1.00 0.00
-ATOM 3395 C2 DA B 47 64.170 55.660 89.600 1.00 0.00
-ATOM 3396 H2 DA B 47 64.140 54.950 88.790 1.00 0.00
-ATOM 3397 N3 DA B 47 64.230 55.150 90.830 1.00 0.00
-ATOM 3398 C4 DA B 47 64.260 56.130 91.770 1.00 0.00
-ATOM 3399 C3' DA B 47 65.000 53.440 95.670 1.00 0.00
-ATOM 3400 H3' DA B 47 65.590 53.510 96.580 1.00 0.00
-ATOM 3401 C2' DA B 47 65.540 54.390 94.610 1.00 0.00
-ATOM 3402 1H2' DA B 47 65.870 55.320 95.080 1.00 0.00
-ATOM 3403 2H2' DA B 47 66.350 53.950 94.020 1.00 0.00
-ATOM 3404 O3' DA B 47 64.970 52.070 95.190 1.00 0.00
-ATOM 3405 P DG B 48 66.280 51.100 94.870 1.00 0.00
-ATOM 3406 O1P DG B 48 65.940 49.750 95.370 1.00 0.00
-ATOM 3407 O2P DG B 48 67.450 51.760 95.500 1.00 0.00
-ATOM 3408 O5' DG B 48 66.580 50.960 93.240 1.00 0.00
-ATOM 3409 C5' DG B 48 65.860 50.040 92.380 1.00 0.00
-ATOM 3410 1H5' DG B 48 64.800 50.200 92.590 1.00 0.00
-ATOM 3411 2H5' DG B 48 66.080 49.020 92.690 1.00 0.00
-ATOM 3412 C4' DG B 48 65.980 50.110 90.810 1.00 0.00
-ATOM 3413 H4' DG B 48 65.100 49.600 90.410 1.00 0.00
-ATOM 3414 O4' DG B 48 65.830 51.470 90.470 1.00 0.00
-ATOM 3415 C1' DG B 48 66.870 51.840 89.600 1.00 0.00
-ATOM 3416 H1' DG B 48 66.510 51.830 88.560 1.00 0.00
-ATOM 3417 N9 DG B 48 67.290 53.200 89.960 1.00 0.00
-ATOM 3418 C8 DG B 48 67.740 53.690 91.160 1.00 0.00
-ATOM 3419 H8 DG B 48 67.830 53.050 92.020 1.00 0.00
-ATOM 3420 N7 DG B 48 68.020 54.960 91.160 1.00 0.00
-ATOM 3421 C5 DG B 48 67.680 55.360 89.850 1.00 0.00
-ATOM 3422 C6 DG B 48 67.680 56.640 89.190 1.00 0.00
-ATOM 3423 O6 DG B 48 68.000 57.740 89.650 1.00 0.00
-ATOM 3424 N1 DG B 48 67.250 56.570 87.870 1.00 0.00
-ATOM 3425 H1 DG B 48 67.210 57.430 87.340 1.00 0.00
-ATOM 3426 C2 DG B 48 66.850 55.430 87.250 1.00 0.00
-ATOM 3427 N2 DG B 48 66.490 55.500 86.000 1.00 0.00
-ATOM 3428 H21 DG B 48 66.540 56.370 85.480 1.00 0.00
-ATOM 3429 H22 DG B 48 66.150 54.660 85.570 1.00 0.00
-ATOM 3430 N3 DG B 48 66.840 54.240 87.820 1.00 0.00
-ATOM 3431 C4 DG B 48 67.250 54.270 89.120 1.00 0.00
-ATOM 3432 C3' DG B 48 67.190 49.560 89.980 1.00 0.00
-ATOM 3433 H3' DG B 48 67.760 48.830 90.550 1.00 0.00
-ATOM 3434 C2' DG B 48 67.990 50.830 89.770 1.00 0.00
-ATOM 3435 1H2' DG B 48 68.580 51.050 90.660 1.00 0.00
-ATOM 3436 2H2' DG B 48 68.630 50.790 88.890 1.00 0.00
-ATOM 3437 O3' DG B 48 66.780 48.980 88.710 1.00 0.00
-ATOM 3438 P DA B 49 67.780 48.340 87.570 1.00 0.00
-ATOM 3439 O1P DA B 49 67.150 47.090 87.090 1.00 0.00
-ATOM 3440 O2P DA B 49 69.110 48.190 88.220 1.00 0.00
-ATOM 3441 O5' DA B 49 67.950 49.360 86.270 1.00 0.00
-ATOM 3442 C5' DA B 49 66.950 49.510 85.220 1.00 0.00
-ATOM 3443 1H5' DA B 49 66.000 49.660 85.730 1.00 0.00
-ATOM 3444 2H5' DA B 49 66.870 48.560 84.680 1.00 0.00
-ATOM 3445 C4' DA B 49 67.040 50.670 84.150 1.00 0.00
-ATOM 3446 H4' DA B 49 66.040 50.790 83.730 1.00 0.00
-ATOM 3447 O4' DA B 49 67.320 51.850 84.870 1.00 0.00
-ATOM 3448 C1' DA B 49 68.470 52.460 84.300 1.00 0.00
-ATOM 3449 H1' DA B 49 68.180 53.270 83.620 1.00 0.00
-ATOM 3450 N9 DA B 49 69.290 52.970 85.400 1.00 0.00
-ATOM 3451 C8 DA B 49 69.770 52.300 86.490 1.00 0.00
-ATOM 3452 H8 DA B 49 69.630 51.230 86.600 1.00 0.00
-ATOM 3453 N7 DA B 49 70.370 53.050 87.380 1.00 0.00
-ATOM 3454 C5 DA B 49 70.220 54.330 86.810 1.00 0.00
-ATOM 3455 C6 DA B 49 70.510 55.640 87.220 1.00 0.00
-ATOM 3456 N6 DA B 49 71.030 55.950 88.390 1.00 0.00
-ATOM 3457 H61 DA B 49 71.140 56.930 88.620 1.00 0.00
-ATOM 3458 H62 DA B 49 71.180 55.200 89.040 1.00 0.00
-ATOM 3459 N1 DA B 49 70.210 56.700 86.480 1.00 0.00
-ATOM 3460 C2 DA B 49 69.630 56.490 85.290 1.00 0.00
-ATOM 3461 H2 DA B 49 69.400 57.370 84.700 1.00 0.00
-ATOM 3462 N3 DA B 49 69.320 55.320 84.770 1.00 0.00
-ATOM 3463 C4 DA B 49 69.610 54.280 85.590 1.00 0.00
-ATOM 3464 C3' DA B 49 68.010 50.660 82.920 1.00 0.00
-ATOM 3465 H3' DA B 49 68.260 49.640 82.620 1.00 0.00
-ATOM 3466 C2' DA B 49 69.200 51.380 83.520 1.00 0.00
-ATOM 3467 1H2' DA B 49 69.760 50.710 84.170 1.00 0.00
-ATOM 3468 2H2' DA B 49 69.860 51.810 82.760 1.00 0.00
-ATOM 3469 O3' DA B 49 67.490 51.400 81.790 1.00 0.00
-ATOM 3470 P DA B 50 68.260 51.590 80.350 1.00 0.00
-ATOM 3471 O1P DA B 50 67.310 51.190 79.290 1.00 0.00
-ATOM 3472 O2P DA B 50 69.510 50.790 80.450 1.00 0.00
-ATOM 3473 O5' DA B 50 68.680 53.180 80.100 1.00 0.00
-ATOM 3474 C5' DA B 50 67.770 54.190 79.600 1.00 0.00
-ATOM 3475 1H5' DA B 50 66.870 54.110 80.210 1.00 0.00
-ATOM 3476 2H5' DA B 50 67.480 53.920 78.580 1.00 0.00
-ATOM 3477 C4' DA B 50 68.170 55.720 79.620 1.00 0.00
-ATOM 3478 H4' DA B 50 67.240 56.290 79.580 1.00 0.00
-ATOM 3479 O4' DA B 50 68.770 55.950 80.870 1.00 0.00
-ATOM 3480 C1' DA B 50 70.110 56.350 80.640 1.00 0.00
-ATOM 3481 H1' DA B 50 70.180 57.430 80.770 1.00 0.00
-ATOM 3482 N9 DA B 50 70.980 55.680 81.610 1.00 0.00
-ATOM 3483 C8 DA B 50 71.250 54.340 81.760 1.00 0.00
-ATOM 3484 H8 DA B 50 70.830 53.590 81.110 1.00 0.00
-ATOM 3485 N7 DA B 50 72.040 54.050 82.770 1.00 0.00
-ATOM 3486 C5 DA B 50 72.260 55.330 83.330 1.00 0.00
-ATOM 3487 C6 DA B 50 72.940 55.820 84.460 1.00 0.00
-ATOM 3488 N6 DA B 50 73.570 55.040 85.330 1.00 0.00
-ATOM 3489 H61 DA B 50 74.000 55.470 86.130 1.00 0.00
-ATOM 3490 H62 DA B 50 73.570 54.060 85.120 1.00 0.00
-ATOM 3491 N1 DA B 50 72.990 57.110 84.760 1.00 0.00
-ATOM 3492 C2 DA B 50 72.360 57.960 83.940 1.00 0.00
-ATOM 3493 H2 DA B 50 72.410 59.010 84.190 1.00 0.00
-ATOM 3494 N3 DA B 50 71.670 57.660 82.860 1.00 0.00
-ATOM 3495 C4 DA B 50 71.650 56.320 82.610 1.00 0.00
-ATOM 3496 C3' DA B 50 69.120 56.390 78.570 1.00 0.00
-ATOM 3497 H3' DA B 50 69.000 55.960 77.580 1.00 0.00
-ATOM 3498 C2' DA B 50 70.450 56.010 79.190 1.00 0.00
-ATOM 3499 1H2' DA B 50 70.640 54.950 79.060 1.00 0.00
-ATOM 3500 2H2' DA B 50 71.270 56.610 78.810 1.00 0.00
-ATOM 3501 O3' DA B 50 68.980 57.840 78.530 1.00 0.00
-ATOM 3502 P DA B 51 69.780 58.850 77.490 1.00 0.00
-ATOM 3503 O1P DA B 51 68.780 59.690 76.790 1.00 0.00
-ATOM 3504 O2P DA B 51 70.670 58.010 76.670 1.00 0.00
-ATOM 3505 O5' DA B 51 70.770 59.910 78.290 1.00 0.00
-ATOM 3506 C5' DA B 51 70.310 61.130 78.890 1.00 0.00
-ATOM 3507 1H5' DA B 51 69.560 60.830 79.620 1.00 0.00
-ATOM 3508 2H5' DA B 51 69.800 61.730 78.130 1.00 0.00
-ATOM 3509 C4' DA B 51 71.330 62.060 79.660 1.00 0.00
-ATOM 3510 H4' DA B 51 70.730 62.800 80.180 1.00 0.00
-ATOM 3511 O4' DA B 51 71.960 61.260 80.640 1.00 0.00
-ATOM 3512 C1' DA B 51 73.300 61.050 80.230 1.00 0.00
-ATOM 3513 H1' DA B 51 73.930 61.590 80.940 1.00 0.00
-ATOM 3514 N9 DA B 51 73.650 59.620 80.300 1.00 0.00
-ATOM 3515 C8 DA B 51 73.250 58.540 79.540 1.00 0.00
-ATOM 3516 H8 DA B 51 72.610 58.630 78.670 1.00 0.00
-ATOM 3517 N7 DA B 51 73.700 57.380 79.950 1.00 0.00
-ATOM 3518 C5 DA B 51 74.470 57.750 81.070 1.00 0.00
-ATOM 3519 C6 DA B 51 75.210 57.040 82.030 1.00 0.00
-ATOM 3520 N6 DA B 51 75.290 55.720 82.080 1.00 0.00
-ATOM 3521 H61 DA B 51 75.810 55.280 82.820 1.00 0.00
-ATOM 3522 H62 DA B 51 74.750 55.210 81.400 1.00 0.00
-ATOM 3523 N1 DA B 51 75.880 57.670 82.990 1.00 0.00
-ATOM 3524 C2 DA B 51 75.810 59.000 83.030 1.00 0.00
-ATOM 3525 H2 DA B 51 76.360 59.480 83.820 1.00 0.00
-ATOM 3526 N3 DA B 51 75.150 59.800 82.220 1.00 0.00
-ATOM 3527 C4 DA B 51 74.470 59.100 81.260 1.00 0.00
-ATOM 3528 C3' DA B 51 72.500 62.830 78.960 1.00 0.00
-ATOM 3529 H3' DA B 51 72.200 63.190 77.980 1.00 0.00
-ATOM 3530 C2' DA B 51 73.480 61.690 78.860 1.00 0.00
-ATOM 3531 1H2' DA B 51 73.190 61.000 78.060 1.00 0.00
-ATOM 3532 2H2' DA B 51 74.490 62.050 78.720 1.00 0.00
-ATOM 3533 O3' DA B 51 73.060 63.920 79.770 1.00 0.00
-ATOM 3534 P DT B 52 74.290 64.940 79.330 1.00 0.00
-ATOM 3535 O1P DT B 52 73.980 66.290 79.870 1.00 0.00
-ATOM 3536 O2P DT B 52 74.470 64.840 77.860 1.00 0.00
-ATOM 3537 O5' DT B 52 75.740 64.520 80.010 1.00 0.00
-ATOM 3538 C5' DT B 52 76.180 65.090 81.270 1.00 0.00
-ATOM 3539 1H5' DT B 52 75.400 64.850 81.990 1.00 0.00
-ATOM 3540 2H5' DT B 52 76.190 66.170 81.160 1.00 0.00
-ATOM 3541 C4' DT B 52 77.540 64.660 81.930 1.00 0.00
-ATOM 3542 H4' DT B 52 77.510 65.040 82.940 1.00 0.00
-ATOM 3543 O4' DT B 52 77.530 63.250 82.030 1.00 0.00
-ATOM 3544 C1' DT B 52 78.590 62.730 81.260 1.00 0.00
-ATOM 3545 H1' DT B 52 79.390 62.470 81.950 1.00 0.00
-ATOM 3546 N1 DT B 52 78.150 61.500 80.550 1.00 0.00
-ATOM 3547 C6 DT B 52 77.370 61.510 79.400 1.00 0.00
-ATOM 3548 H6 DT B 52 77.030 62.460 78.990 1.00 0.00
-ATOM 3549 C5 DT B 52 77.000 60.350 78.800 1.00 0.00
-ATOM 3550 C7 DT B 52 76.210 60.360 77.500 1.00 0.00
-ATOM 3551 H71 DT B 52 76.020 61.380 77.160 1.00 0.00
-ATOM 3552 H72 DT B 52 76.780 59.830 76.740 1.00 0.00
-ATOM 3553 H73 DT B 52 75.270 59.830 77.640 1.00 0.00
-ATOM 3554 C4 DT B 52 77.360 59.060 79.380 1.00 0.00
-ATOM 3555 O4 DT B 52 77.040 57.950 78.990 1.00 0.00
-ATOM 3556 N3 DT B 52 78.120 59.150 80.510 1.00 0.00
-ATOM 3557 H3 DT B 52 78.400 58.280 80.920 1.00 0.00
-ATOM 3558 C2 DT B 52 78.580 60.290 81.100 1.00 0.00
-ATOM 3559 O2 DT B 52 79.360 60.200 82.060 1.00 0.00
-ATOM 3560 C3' DT B 52 78.950 65.040 81.360 1.00 0.00
-ATOM 3561 H3' DT B 52 78.900 65.990 80.830 1.00 0.00
-ATOM 3562 C2' DT B 52 79.120 63.880 80.390 1.00 0.00
-ATOM 3563 1H2' DT B 52 78.490 64.030 79.510 1.00 0.00
-ATOM 3564 2H2' DT B 52 80.150 63.730 80.100 1.00 0.00
-ATOM 3565 O3' DT B 52 79.980 65.070 82.400 1.00 0.00
-ATOM 3566 P DG B 53 81.540 65.610 82.260 1.00 0.00
-ATOM 3567 O1P DG B 53 81.840 66.420 83.470 1.00 0.00
-ATOM 3568 O2P DG B 53 81.680 66.310 80.960 1.00 0.00
-ATOM 3569 O5' DG B 53 82.660 64.380 82.270 1.00 0.00
-ATOM 3570 C5' DG B 53 83.250 63.880 83.500 1.00 0.00
-ATOM 3571 1H5' DG B 53 82.400 63.620 84.140 1.00 0.00
-ATOM 3572 2H5' DG B 53 83.760 64.710 83.970 1.00 0.00
-ATOM 3573 C4' DG B 53 84.210 62.630 83.540 1.00 0.00
-ATOM 3574 H4' DG B 53 84.380 62.430 84.590 1.00 0.00
-ATOM 3575 O4' DG B 53 83.480 61.540 83.050 1.00 0.00
-ATOM 3576 C1' DG B 53 84.080 61.110 81.840 1.00 0.00
-ATOM 3577 H1' DG B 53 84.550 60.130 82.020 1.00 0.00
-ATOM 3578 N9 DG B 53 83.060 60.930 80.800 1.00 0.00
-ATOM 3579 C8 DG B 53 82.240 61.840 80.180 1.00 0.00
-ATOM 3580 H8 DG B 53 82.270 62.900 80.400 1.00 0.00
-ATOM 3581 N7 DG B 53 81.420 61.320 79.320 1.00 0.00
-ATOM 3582 C5 DG B 53 81.700 59.940 79.390 1.00 0.00
-ATOM 3583 C6 DG B 53 81.110 58.780 78.760 1.00 0.00
-ATOM 3584 O6 DG B 53 80.160 58.710 78.000 1.00 0.00
-ATOM 3585 N1 DG B 53 81.730 57.600 79.120 1.00 0.00
-ATOM 3586 H1 DG B 53 81.320 56.760 78.750 1.00 0.00
-ATOM 3587 C2 DG B 53 82.760 57.520 79.990 1.00 0.00
-ATOM 3588 N2 DG B 53 83.260 56.350 80.280 1.00 0.00
-ATOM 3589 H21 DG B 53 82.800 55.520 79.900 1.00 0.00
-ATOM 3590 H22 DG B 53 83.950 56.310 80.990 1.00 0.00
-ATOM 3591 N3 DG B 53 83.330 58.540 80.610 1.00 0.00
-ATOM 3592 C4 DG B 53 82.730 59.720 80.270 1.00 0.00
-ATOM 3593 C3' DG B 53 85.620 62.540 82.850 1.00 0.00
-ATOM 3594 H3' DG B 53 86.100 63.510 82.820 1.00 0.00
-ATOM 3595 C2' DG B 53 85.170 62.110 81.470 1.00 0.00
-ATOM 3596 1H2' DG B 53 84.750 62.950 80.920 1.00 0.00
-ATOM 3597 2H2' DG B 53 85.980 61.640 80.910 1.00 0.00
-ATOM 3598 O3' DG B 53 86.480 61.540 83.480 1.00 0.00
-ATOM 3599 P DC B 54 88.050 61.180 83.080 1.00 0.00
-ATOM 3600 O1P DC B 54 88.770 60.960 84.360 1.00 0.00
-ATOM 3601 O2P DC B 54 88.540 62.290 82.240 1.00 0.00
-ATOM 3602 O5' DC B 54 88.200 59.770 82.200 1.00 0.00
-ATOM 3603 C5' DC B 54 88.380 58.470 82.810 1.00 0.00
-ATOM 3604 1H5' DC B 54 87.580 58.380 83.550 1.00 0.00
-ATOM 3605 2H5' DC B 54 89.320 58.470 83.360 1.00 0.00
-ATOM 3606 C4' DC B 54 88.310 57.130 81.970 1.00 0.00
-ATOM 3607 H4' DC B 54 88.150 56.330 82.700 1.00 0.00
-ATOM 3608 O4' DC B 54 87.130 57.190 81.200 1.00 0.00
-ATOM 3609 C1' DC B 54 87.440 56.950 79.840 1.00 0.00
-ATOM 3610 H1' DC B 54 87.200 55.910 79.600 1.00 0.00
-ATOM 3611 N1 DC B 54 86.650 57.870 78.990 1.00 0.00
-ATOM 3612 C6 DC B 54 86.620 59.220 79.240 1.00 0.00
-ATOM 3613 H6 DC B 54 87.210 59.620 80.050 1.00 0.00
-ATOM 3614 C5 DC B 54 85.810 60.030 78.500 1.00 0.00
-ATOM 3615 H5 DC B 54 85.750 61.080 78.700 1.00 0.00
-ATOM 3616 C4 DC B 54 85.010 59.400 77.510 1.00 0.00
-ATOM 3617 N4 DC B 54 84.140 60.100 76.850 1.00 0.00
-ATOM 3618 H41 DC B 54 83.540 59.570 76.200 1.00 0.00
-ATOM 3619 H42 DC B 54 83.870 61.020 77.110 1.00 0.00
-ATOM 3620 N3 DC B 54 85.080 58.120 77.240 1.00 0.00
-ATOM 3621 C2 DC B 54 85.890 57.330 77.960 1.00 0.00
-ATOM 3622 O2 DC B 54 85.970 56.130 77.680 1.00 0.00
-ATOM 3623 C3' DC B 54 89.440 56.590 81.030 1.00 0.00
-ATOM 3624 H3' DC B 54 90.410 57.020 81.290 1.00 0.00
-ATOM 3625 C2' DC B 54 88.950 57.140 79.690 1.00 0.00
-ATOM 3626 1H2' DC B 54 89.210 58.190 79.610 1.00 0.00
-ATOM 3627 2H2' DC B 54 89.340 56.570 78.850 1.00 0.00
-ATOM 3628 O3' DC B 54 89.510 55.130 81.010 1.00 0.00
-ATOM 3629 P DC B 55 90.620 54.220 80.180 1.00 0.00
-ATOM 3630 O1P DC B 55 91.050 53.130 81.100 1.00 0.00
-ATOM 3631 O2P DC B 55 91.690 55.150 79.740 1.00 0.00
-ATOM 3632 O5' DC B 55 89.990 53.500 78.820 1.00 0.00
-ATOM 3633 C5' DC B 55 89.300 52.220 78.840 1.00 0.00
-ATOM 3634 1H5' DC B 55 88.580 52.270 79.660 1.00 0.00
-ATOM 3635 2H5' DC B 55 90.020 51.440 79.090 1.00 0.00
-ATOM 3636 C4' DC B 55 88.460 51.710 77.600 1.00 0.00
-ATOM 3637 H4' DC B 55 87.750 50.990 78.000 1.00 0.00
-ATOM 3638 O4' DC B 55 87.680 52.800 77.150 1.00 0.00
-ATOM 3639 C1' DC B 55 87.830 52.950 75.750 1.00 0.00
-ATOM 3640 H1' DC B 55 86.960 52.520 75.240 1.00 0.00
-ATOM 3641 N1 DC B 55 87.930 54.400 75.460 1.00 0.00
-ATOM 3642 C6 DC B 55 88.820 55.190 76.140 1.00 0.00
-ATOM 3643 H6 DC B 55 89.470 54.730 76.870 1.00 0.00
-ATOM 3644 C5 DC B 55 88.850 56.540 75.940 1.00 0.00
-ATOM 3645 H5 DC B 55 89.520 57.160 76.480 1.00 0.00
-ATOM 3646 C4 DC B 55 87.910 57.050 75.000 1.00 0.00
-ATOM 3647 N4 DC B 55 87.810 58.320 74.810 1.00 0.00
-ATOM 3648 H41 DC B 55 87.030 58.590 74.200 1.00 0.00
-ATOM 3649 H42 DC B 55 88.240 58.980 75.410 1.00 0.00
-ATOM 3650 N3 DC B 55 87.090 56.300 74.310 1.00 0.00
-ATOM 3651 C2 DC B 55 87.060 54.970 74.530 1.00 0.00
-ATOM 3652 O2 DC B 55 86.260 54.280 73.910 1.00 0.00
-ATOM 3653 C3' DC B 55 89.050 51.020 76.320 1.00 0.00
-ATOM 3654 H3' DC B 55 90.060 50.640 76.510 1.00 0.00
-ATOM 3655 C2' DC B 55 89.080 52.180 75.340 1.00 0.00
-ATOM 3656 1H2' DC B 55 89.980 52.780 75.500 1.00 0.00
-ATOM 3657 2H2' DC B 55 89.020 51.860 74.300 1.00 0.00
-ATOM 3658 O3' DC B 55 88.200 49.940 75.850 1.00 0.00
-ATOM 3659 P DA B 56 88.490 48.990 74.530 1.00 0.00
-ATOM 3660 O1P DA B 56 88.130 47.600 74.910 1.00 0.00
-ATOM 3661 O2P DA B 56 89.900 49.220 74.150 1.00 0.00
-ATOM 3662 O5' DA B 56 87.520 49.430 73.250 1.00 0.00
-ATOM 3663 C5' DA B 56 86.130 49.030 73.120 1.00 0.00
-ATOM 3664 1H5' DA B 56 85.670 49.230 74.090 1.00 0.00
-ATOM 3665 2H5' DA B 56 86.090 47.950 72.960 1.00 0.00
-ATOM 3666 C4' DA B 56 85.170 49.710 72.060 1.00 0.00
-ATOM 3667 H4' DA B 56 84.150 49.530 72.400 1.00 0.00
-ATOM 3668 O4' DA B 56 85.390 51.100 72.160 1.00 0.00
-ATOM 3669 C1' DA B 56 85.630 51.630 70.870 1.00 0.00
-ATOM 3670 H1' DA B 56 84.710 52.090 70.470 1.00 0.00
-ATOM 3671 N9 DA B 56 86.690 52.640 70.990 1.00 0.00
-ATOM 3672 C8 DA B 56 87.910 52.510 71.600 1.00 0.00
-ATOM 3673 H8 DA B 56 88.230 51.570 72.030 1.00 0.00
-ATOM 3674 N7 DA B 56 88.620 53.610 71.660 1.00 0.00
-ATOM 3675 C5 DA B 56 87.750 54.530 71.030 1.00 0.00
-ATOM 3676 C6 DA B 56 87.760 55.920 70.790 1.00 0.00
-ATOM 3677 N6 DA B 56 88.720 56.730 71.190 1.00 0.00
-ATOM 3678 H61 DA B 56 88.560 57.720 71.070 1.00 0.00
-ATOM 3679 H62 DA B 56 89.450 56.340 71.740 1.00 0.00
-ATOM 3680 N1 DA B 56 86.750 56.540 70.190 1.00 0.00
-ATOM 3681 C2 DA B 56 85.720 55.820 69.780 1.00 0.00
-ATOM 3682 H2 DA B 56 84.910 56.350 69.280 1.00 0.00
-ATOM 3683 N3 DA B 56 85.570 54.510 69.910 1.00 0.00
-ATOM 3684 C4 DA B 56 86.610 53.940 70.580 1.00 0.00
-ATOM 3685 C3' DA B 56 85.180 49.360 70.540 1.00 0.00
-ATOM 3686 H3' DA B 56 85.620 48.380 70.360 1.00 0.00
-ATOM 3687 C2' DA B 56 86.050 50.470 69.990 1.00 0.00
-ATOM 3688 1H2' DA B 56 87.100 50.220 70.140 1.00 0.00
-ATOM 3689 2H2' DA B 56 85.850 50.680 68.950 1.00 0.00
-ATOM 3690 O3' DA B 56 83.860 49.420 69.940 1.00 0.00
-ATOM 3691 P DT B 57 83.530 49.160 68.350 1.00 0.00
-ATOM 3692 O1P DT B 57 82.340 48.270 68.290 1.00 0.00
-ATOM 3693 O2P DT B 57 84.780 48.630 67.750 1.00 0.00
-ATOM 3694 O5' DT B 57 83.150 50.590 67.600 1.00 0.00
-ATOM 3695 C5' DT B 57 81.870 51.260 67.710 1.00 0.00
-ATOM 3696 1H5' DT B 57 81.640 51.290 68.780 1.00 0.00
-ATOM 3697 2H5' DT B 57 81.100 50.650 67.250 1.00 0.00
-ATOM 3698 C4' DT B 57 81.700 52.750 67.200 1.00 0.00
-ATOM 3699 H4' DT B 57 80.860 53.180 67.750 1.00 0.00
-ATOM 3700 O4' DT B 57 82.870 53.440 67.590 1.00 0.00
-ATOM 3701 C1' DT B 57 83.400 54.110 66.460 1.00 0.00
-ATOM 3702 H1' DT B 57 83.010 55.130 66.430 1.00 0.00
-ATOM 3703 N1 DT B 57 84.870 54.090 66.550 1.00 0.00
-ATOM 3704 C6 DT B 57 85.550 52.890 66.680 1.00 0.00
-ATOM 3705 H6 DT B 57 84.980 51.980 66.670 1.00 0.00
-ATOM 3706 C5 DT B 57 86.890 52.880 66.900 1.00 0.00
-ATOM 3707 C7 DT B 57 87.620 51.550 67.030 1.00 0.00
-ATOM 3708 H71 DT B 57 86.930 50.720 66.850 1.00 0.00
-ATOM 3709 H72 DT B 57 88.430 51.530 66.300 1.00 0.00
-ATOM 3710 H73 DT B 57 88.040 51.490 68.030 1.00 0.00
-ATOM 3711 C4 DT B 57 87.640 54.130 67.030 1.00 0.00
-ATOM 3712 O4 DT B 57 88.820 54.220 67.340 1.00 0.00
-ATOM 3713 N3 DT B 57 86.900 55.260 66.790 1.00 0.00
-ATOM 3714 H3 DT B 57 87.340 56.160 66.860 1.00 0.00
-ATOM 3715 C2 DT B 57 85.550 55.310 66.550 1.00 0.00
-ATOM 3716 O2 DT B 57 85.020 56.390 66.350 1.00 0.00
-ATOM 3717 C3' DT B 57 81.450 53.110 65.700 1.00 0.00
-ATOM 3718 H3' DT B 57 80.980 52.300 65.160 1.00 0.00
-ATOM 3719 C2' DT B 57 82.880 53.350 65.250 1.00 0.00
-ATOM 3720 1H2' DT B 57 83.380 52.390 65.110 1.00 0.00
-ATOM 3721 2H2' DT B 57 82.930 53.950 64.350 1.00 0.00
-ATOM 3722 O3' DT B 57 80.690 54.340 65.530 1.00 0.00
-ATOM 3723 P DC B 58 80.230 54.970 64.070 1.00 0.00
-ATOM 3724 O1P DC B 58 78.760 55.150 64.090 1.00 0.00
-ATOM 3725 O2P DC B 58 80.790 54.060 63.040 1.00 0.00
-ATOM 3726 O5' DC B 58 80.920 56.450 63.820 1.00 0.00
-ATOM 3727 C5' DC B 58 80.480 57.670 64.450 1.00 0.00
-ATOM 3728 1H5' DC B 58 80.460 57.440 65.520 1.00 0.00
-ATOM 3729 2H5' DC B 58 79.450 57.870 64.150 1.00 0.00
-ATOM 3730 C4' DC B 58 81.340 58.980 64.300 1.00 0.00
-ATOM 3731 H4' DC B 58 81.000 59.670 65.060 1.00 0.00
-ATOM 3732 O4' DC B 58 82.670 58.600 64.600 1.00 0.00
-ATOM 3733 C1' DC B 58 83.460 58.770 63.450 1.00 0.00
-ATOM 3734 H1' DC B 58 84.030 59.700 63.590 1.00 0.00
-ATOM 3735 N1 DC B 58 84.390 57.620 63.290 1.00 0.00
-ATOM 3736 C6 DC B 58 83.950 56.360 62.950 1.00 0.00
-ATOM 3737 H6 DC B 58 82.900 56.190 62.740 1.00 0.00
-ATOM 3738 C5 DC B 58 84.820 55.320 62.910 1.00 0.00
-ATOM 3739 H5 DC B 58 84.470 54.340 62.670 1.00 0.00
-ATOM 3740 C4 DC B 58 86.170 55.610 63.240 1.00 0.00
-ATOM 3741 N4 DC B 58 87.050 54.660 63.330 1.00 0.00
-ATOM 3742 H41 DC B 58 87.990 54.950 63.580 1.00 0.00
-ATOM 3743 H42 DC B 58 86.780 53.720 63.130 1.00 0.00
-ATOM 3744 N3 DC B 58 86.620 56.810 63.510 1.00 0.00
-ATOM 3745 C2 DC B 58 85.740 57.830 63.530 1.00 0.00
-ATOM 3746 O2 DC B 58 86.200 58.960 63.700 1.00 0.00
-ATOM 3747 C3' DC B 58 81.430 59.810 62.970 1.00 0.00
-ATOM 3748 H3' DC B 58 80.490 59.780 62.420 1.00 0.00
-ATOM 3749 C2' DC B 58 82.510 59.000 62.280 1.00 0.00
-ATOM 3750 1H2' DC B 58 82.090 58.080 61.890 1.00 0.00
-ATOM 3751 2H2' DC B 58 82.980 59.590 61.500 1.00 0.00
-ATOM 3752 O3' DC B 58 81.890 61.190 63.140 1.00 0.00
-ATOM 3753 P DT B 59 82.110 62.290 61.920 1.00 0.00
-ATOM 3754 O1P DT B 59 81.510 63.590 62.340 1.00 0.00
-ATOM 3755 O2P DT B 59 81.620 61.690 60.670 1.00 0.00
-ATOM 3756 O5' DT B 59 83.710 62.610 61.670 1.00 0.00
-ATOM 3757 C5' DT B 59 84.420 63.660 62.360 1.00 0.00
-ATOM 3758 1H5' DT B 59 84.340 63.430 63.430 1.00 0.00
-ATOM 3759 2H5' DT B 59 83.880 64.590 62.200 1.00 0.00
-ATOM 3760 C4' DT B 59 85.940 63.900 62.050 1.00 0.00
-ATOM 3761 H4' DT B 59 86.320 64.510 62.870 1.00 0.00
-ATOM 3762 O4' DT B 59 86.580 62.640 62.120 1.00 0.00
-ATOM 3763 C1' DT B 59 87.020 62.300 60.820 1.00 0.00
-ATOM 3764 H1' DT B 59 88.100 62.480 60.810 1.00 0.00
-ATOM 3765 N1 DT B 59 86.770 60.860 60.530 1.00 0.00
-ATOM 3766 C6 DT B 59 85.530 60.360 60.150 1.00 0.00
-ATOM 3767 H6 DT B 59 84.680 61.020 60.060 1.00 0.00
-ATOM 3768 C5 DT B 59 85.370 59.030 59.910 1.00 0.00
-ATOM 3769 C7 DT B 59 84.050 58.480 59.390 1.00 0.00
-ATOM 3770 H71 DT B 59 83.310 59.270 59.270 1.00 0.00
-ATOM 3771 H72 DT B 59 84.220 58.000 58.430 1.00 0.00
-ATOM 3772 H73 DT B 59 83.680 57.720 60.080 1.00 0.00
-ATOM 3773 C4 DT B 59 86.460 58.090 60.130 1.00 0.00
-ATOM 3774 O4 DT B 59 86.420 56.870 60.040 1.00 0.00
-ATOM 3775 N3 DT B 59 87.650 58.680 60.470 1.00 0.00
-ATOM 3776 H3 DT B 59 88.440 58.080 60.590 1.00 0.00
-ATOM 3777 C2 DT B 59 87.880 60.020 60.600 1.00 0.00
-ATOM 3778 O2 DT B 59 89.040 60.420 60.720 1.00 0.00
-ATOM 3779 C3' DT B 59 86.420 64.560 60.720 1.00 0.00
-ATOM 3780 H3' DT B 59 85.690 65.290 60.360 1.00 0.00
-ATOM 3781 C2' DT B 59 86.420 63.320 59.850 1.00 0.00
-ATOM 3782 1H2' DT B 59 85.400 63.060 59.570 1.00 0.00
-ATOM 3783 2H2' DT B 59 87.050 63.450 58.980 1.00 0.00
-ATOM 3784 O3' DT B 59 87.760 65.150 60.790 1.00 0.00
-ATOM 3785 P DT B 60 88.540 65.970 59.580 1.00 0.00
-ATOM 3786 O1P DT B 60 89.210 67.150 60.200 1.00 0.00
-ATOM 3787 O2P DT B 60 87.560 66.260 58.510 1.00 0.00
-ATOM 3788 O5' DT B 60 89.760 65.090 58.880 1.00 0.00
-ATOM 3789 C5' DT B 60 91.130 65.150 59.350 1.00 0.00
-ATOM 3790 1H5' DT B 60 91.080 64.940 60.420 1.00 0.00
-ATOM 3791 2H5' DT B 60 91.470 66.180 59.250 1.00 0.00
-ATOM 3792 C4' DT B 60 92.240 64.200 58.770 1.00 0.00
-ATOM 3793 H4' DT B 60 93.080 64.270 59.460 1.00 0.00
-ATOM 3794 O4' DT B 60 91.720 62.890 58.880 1.00 0.00
-ATOM 3795 C1' DT B 60 91.670 62.320 57.600 1.00 0.00
-ATOM 3796 H1' DT B 60 92.530 61.650 57.510 1.00 0.00
-ATOM 3797 N1 DT B 60 90.420 61.530 57.440 1.00 0.00
-ATOM 3798 C6 DT B 60 89.180 62.120 57.260 1.00 0.00
-ATOM 3799 H6 DT B 60 89.080 63.190 57.270 1.00 0.00
-ATOM 3800 C5 DT B 60 88.060 61.350 57.080 1.00 0.00
-ATOM 3801 C7 DT B 60 86.720 61.990 56.780 1.00 0.00
-ATOM 3802 H71 DT B 60 86.790 63.070 56.730 1.00 0.00
-ATOM 3803 H72 DT B 60 86.360 61.600 55.830 1.00 0.00
-ATOM 3804 H73 DT B 60 86.000 61.690 57.550 1.00 0.00
-ATOM 3805 C4 DT B 60 88.150 59.890 57.160 1.00 0.00
-ATOM 3806 O4 DT B 60 87.210 59.110 57.090 1.00 0.00
-ATOM 3807 N3 DT B 60 89.410 59.410 57.360 1.00 0.00
-ATOM 3808 H3 DT B 60 89.510 58.400 57.370 1.00 0.00
-ATOM 3809 C2 DT B 60 90.560 60.140 57.420 1.00 0.00
-ATOM 3810 O2 DT B 60 91.650 59.570 57.410 1.00 0.00
-ATOM 3811 C3' DT B 60 92.840 64.330 57.330 1.00 0.00
-ATOM 3812 H3' DT B 60 92.780 65.360 56.980 1.00 0.00
-ATOM 3813 C2' DT B 60 91.870 63.450 56.590 1.00 0.00
-ATOM 3814 1H2' DT B 60 90.940 63.990 56.400 1.00 0.00
-ATOM 3815 2H2' DT B 60 92.300 63.070 55.660 1.00 0.00
-ATOM 3816 O3' DT B 60 94.210 63.820 57.200 1.00 0.00
-TER
-ENDMDL
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
ASSERT_EQ(0, gmx_editconf(cmdline.argc(), cmdline.argv()));
// Check the output
- auto extension = ftp2ext(std::get<1>(GetParam()));
+ const auto* extension = ftp2ext(std::get<1>(GetParam()));
TestReferenceChecker rootChecker(this->rootChecker());
rootChecker.checkString(extension, testName);
checkOutputFiles();
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
TEST_F(PreprocessingAtomTypesTest, WrongNameNotFound)
{
EXPECT_EQ(addType("Foo", 1, 2), 0);
- EXPECT_EQ(atypes_.atomTypeFromName("Bar"), NOTSET);
+ EXPECT_FALSE(atypes_.atomTypeFromName("Bar").has_value());
}
TEST_F(PreprocessingAtomTypesTest, CorrectNameFromTypeNumber)
{
EXPECT_EQ(addType("Foo", 1, 2), 0);
EXPECT_EQ(addType("Bar", 3, 4), 1);
- EXPECT_STREQ(atypes_.atomNameFromAtomType(0), "Foo");
- EXPECT_STREQ(atypes_.atomNameFromAtomType(1), "Bar");
+ EXPECT_STREQ(*atypes_.atomNameFromAtomType(0), "Foo");
+ EXPECT_STREQ(*atypes_.atomNameFromAtomType(1), "Bar");
}
TEST_F(PreprocessingAtomTypesTest, NoNameFromIncorrectTypeNumber)
{
- EXPECT_EQ(atypes_.atomNameFromAtomType(-1), nullptr);
+ EXPECT_FALSE(atypes_.atomNameFromAtomType(-1).has_value());
}
} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
TEST_F(PreprocessingBondAtomTypeTest, WrongNameNotFound)
{
EXPECT_EQ(addType("Foo"), 0);
- EXPECT_EQ(bat_.bondAtomTypeFromName("Bar"), NOTSET);
+ EXPECT_FALSE(bat_.bondAtomTypeFromName("Bar").has_value());
}
TEST_F(PreprocessingBondAtomTypeTest, CorrectNameFromTypeNumber)
{
EXPECT_EQ(addType("Foo"), 0);
EXPECT_EQ(addType("Bar"), 1);
- EXPECT_STREQ(bat_.atomNameFromBondAtomType(0), "Foo");
- EXPECT_STREQ(bat_.atomNameFromBondAtomType(1), "Bar");
+ EXPECT_STREQ(*bat_.atomNameFromBondAtomType(0), "Foo");
+ EXPECT_STREQ(*bat_.atomNameFromBondAtomType(1), "Bar");
}
TEST_F(PreprocessingBondAtomTypeTest, NoNameFromIncorrectTypeNumber)
{
- EXPECT_EQ(bat_.atomNameFromBondAtomType(-1), nullptr);
+ EXPECT_FALSE(bat_.atomNameFromBondAtomType(-1).has_value());
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx::test::TestReferenceChecker rootChecker(this->rootChecker());
rootChecker.checkString(args.toString(), "CommandLine");
- ASSERT_EQ(0, gmx::test::CommandLineTestHelper::runModuleFactory(
- &gmx::InsertMoleculesInfo::create, &cmdline));
+ ASSERT_EQ(0,
+ gmx::test::CommandLineTestHelper::runModuleFactory(
+ &gmx::InsertMoleculesInfo::create, &cmdline));
checkOutputFiles();
}
TEST_F(InsertMoleculesTest, InsertsMoleculesIntoFixedPositions)
{
const char* const cmdline[] = { "insert-molecules", "-box", "4", "-seed", "1997" };
- const char* const positions[] = { "0.0 0.0 0.0", "1.0 2.0 3.0", "0.99 2.01 3.0",
- "2.0 1.0 2.0" };
+ const char* const positions[] = {
+ "0.0 0.0 0.0", "1.0 2.0 3.0", "0.99 2.01 3.0", "2.0 1.0 2.0"
+ };
setInputFile("-ci", "x0.gro");
setInputFileContents("-ip", "dat", positions);
runTest(CommandLine(cmdline));
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
TextWriter::writeFileFromString(inputMdpFilename, inputMdpFileContents);
- get_ir(inputMdpFilename.c_str(), outputMdpFilename.c_str(), &mdModules_, &ir_, &opts_,
- WriteMdpHeader::no, wi_);
+ get_ir(inputMdpFilename.c_str(), outputMdpFilename.c_str(), &mdModules_, &ir_, &opts_, WriteMdpHeader::no, wi_);
- check_ir(inputMdpFilename.c_str(), mdModules_.notifier(), &ir_, &opts_, wi_);
+ check_ir(inputMdpFilename.c_str(), mdModules_.notifiers(), &ir_, &opts_, wi_);
// Now check
bool failure = warning_errors_exist(wi_);
TestReferenceData data;
dh_hist_spacing = 0.1
; Non-equilibrium MD stuff
-acc-grps =
-accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
dh_hist_spacing = 0.1
; Non-equilibrium MD stuff
-acc-grps =
-accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
dh_hist_spacing = 0.1
; Non-equilibrium MD stuff
-acc-grps =
-accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
dh_hist_spacing = 0.1
; Non-equilibrium MD stuff
-acc-grps =
-accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
dh_hist_spacing = 0.1
; Non-equilibrium MD stuff
-acc-grps =
-accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
dh_hist_spacing = 0.1
; Non-equilibrium MD stuff
-acc-grps =
-accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
dh_hist_spacing = 0.1
; Non-equilibrium MD stuff
-acc-grps =
-accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
dh_hist_spacing = 0.1
; Non-equilibrium MD stuff
-acc-grps =
-accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
dh_hist_spacing = 0.1
; Non-equilibrium MD stuff
-acc-grps =
-accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
// If the enumeration is extended, but there is no matching
// name, then at least one element will be value initialized,
// ie. to nullptr, which this test will catch.
- auto name = dir2str(d);
+ const auto* name = enumValueToString(d);
EXPECT_NE(name, nullptr);
}
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
int ni = harmonic->ai();
int nj = harmonic->aj();
- real edis = search_e_diss(n2m, t2m,
- atype->atomNameFromAtomType(mol.atoms.atom[ni].type),
- atype->atomNameFromAtomType(mol.atoms.atom[nj].type));
+ real edis = search_e_diss(n2m,
+ t2m,
+ *atype->atomNameFromAtomType(mol.atoms.atom[ni].type),
+ *atype->atomNameFromAtomType(mol.atoms.atom[nj].type));
if (edis != 0)
{
real b0 = harmonic->c0();
}
int newHarmonics = mol.interactions[bb].size();
- fprintf(stderr, "Converted %d out of %d %s to morse bonds for mol %d\n",
- nrharm - newHarmonics, nrharm, interaction_function[bb].name, i);
+ fprintf(stderr,
+ "Converted %d out of %d %s to morse bonds for mol %d\n",
+ nrharm - newHarmonics,
+ nrharm,
+ interaction_function[bb].name,
+ i);
}
}
i++;
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringtoenumvalueconverter.h"
-/* Must correspond to the Directive enum in grompp_impl.h */
-static gmx::EnumerationArray<Directive, const char*> directive_names = {
- { "defaults", "atomtypes", "bondtypes", "constrainttypes", "pairtypes", "angletypes",
- "dihedraltypes", "nonbond_params", "implicit_genborn_params", "implicit_surface_params",
- "cmaptypes",
- /* All the directives above can not appear after moleculetype */
- "moleculetype", "atoms", "virtual_sites1", "virtual_sites2", "virtual_sites3",
- "virtual_sites4", "virtual_sitesn", "bonds", "exclusions", "pairs", "pairs_nb", "angles",
- "dihedrals", "constraints", "settles", "polarization", "water_polarization",
- "thole_polarization", "system", "molecules", "position_restraints", "angle_restraints",
- "angle_restraints_z", "distance_restraints", "orientation_restraints", "dihedral_restraints",
- "cmap", "intermolecular_interactions", "maxdirs", "invalid", "none" }
-};
+const char* enumValueToString(Directive d)
+{
+ /* Must correspond to the Directive enum in topdirs.h */
+ static constexpr gmx::EnumerationArray<Directive, const char*> directiveNames = {
+ "defaults",
+ "atomtypes",
+ "bondtypes",
+ "constrainttypes",
+ "pairtypes",
+ "angletypes",
+ "dihedraltypes",
+ "nonbond_params",
+ "implicit_genborn_params",
+ "implicit_surface_params",
+ "cmaptypes",
+ /* All the directives above can not appear after moleculetype */
+ "moleculetype",
+ "atoms",
+ "virtual_sites1",
+ "virtual_sites2",
+ "virtual_sites3",
+ "virtual_sites4",
+ "virtual_sitesn",
+ "bonds",
+ "exclusions",
+ "pairs",
+ "pairs_nb",
+ "angles",
+ "dihedrals",
+ "constraints",
+ "settles",
+ "polarization",
+ "water_polarization",
+ "thole_polarization",
+ "system",
+ "molecules",
+ "position_restraints",
+ "angle_restraints",
+ "angle_restraints_z",
+ "distance_restraints",
+ "orientation_restraints",
+ "dihedral_restraints",
+ "cmap",
+ "intermolecular_interactions",
+ "maxdirs",
+ "invalid",
+ "none"
+ };
+ return directiveNames[d];
+}
int ifunc_index(Directive d, int type)
{
case Directive::d_orientation_restraints: return F_ORIRES;
case Directive::d_dihedral_restraints: return F_DIHRES;
default:
- gmx_fatal(FARGS, "invalid directive %s in ifunc_index (%s:%d)", dir2str(d), __FILE__, __LINE__);
+ gmx_fatal(FARGS, "invalid directive %s in ifunc_index (%s:%d)", enumValueToString(d), __FILE__, __LINE__);
}
}
-const char* dir2str(Directive d)
+enum class DeprecatedDirectives : int
+{
+ d_dummies1,
+ d_dummies2,
+ d_dummies3,
+ d_dummies4,
+ d_dummiesn,
+ Count
+};
+
+static const char* enumValueToString(DeprecatedDirectives d)
{
- int index = static_cast<int>(d);
- return directive_names[index];
+ static constexpr gmx::EnumerationArray<DeprecatedDirectives, const char*> directiveNames = {
+ "dummies1", "dummies2", "dummies3", "dummies4", "dummiesn"
+ };
+ return directiveNames[d];
}
Directive str2dir(char* dstr)
{
- char buf[STRLEN], *ptr;
+ static const gmx::StringToEnumValueConverter<Directive, enumValueToString, gmx::StringCompareType::CaseAndDashInsensitive> s_converter;
- /* Hack to be able to read old topologies */
- if (gmx_strncasecmp_min(dstr, "dummies", 7) == 0)
+ if (std::optional<Directive> d = s_converter.valueFrom(dstr); d.has_value())
{
- sprintf(buf, "virtual_sites%s", dstr + 7);
- ptr = buf;
- }
- else
- {
- ptr = dstr;
+ return d.value();
}
+ // Also handle deprecated directives that have modern replacements, like
+ // "dummies*" -> "virtual_sites*"
+
+ static const gmx::StringToEnumValueConverter<DeprecatedDirectives, enumValueToString, gmx::StringCompareType::CaseAndDashInsensitive>
+ s_converterForDeprecated;
- for (auto d : gmx::EnumerationWrapper<Directive>())
+ if (std::optional<DeprecatedDirectives> d = s_converterForDeprecated.valueFrom(dstr); d.has_value())
{
- if (gmx_strcasecmp_min(ptr, dir2str(static_cast<Directive>(d))) == 0)
- {
- return static_cast<Directive>(d);
- }
+ static constexpr gmx::EnumerationArray<DeprecatedDirectives, Directive> s_deprecatedDirectiveToDirective = {
+ Directive::d_vsites1, Directive::d_vsites2, Directive::d_vsites3,
+ Directive::d_vsites4, Directive::d_vsitesn,
+ };
+ return s_deprecatedDirectiveToDirective[d.value()];
}
-
return Directive::d_invalid;
}
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static gmx::EnumerationArray<Directive, Directive*> necessary = { { nullptr } };
static void set_nec(Directive** n, ...)
// be in the same place that was valid in old versions (ie. child
// directive of [atomtypes]) but any relevant case will
// satisfy that.
- set_nec(&(necessary[Directive::d_implicit_genborn_params]), Directive::d_atomtypes,
- Directive::d_none);
- set_nec(&(necessary[Directive::d_implicit_surface_params]), Directive::d_atomtypes,
- Directive::d_none);
+ set_nec(&(necessary[Directive::d_implicit_genborn_params]), Directive::d_atomtypes, Directive::d_none);
+ set_nec(&(necessary[Directive::d_implicit_surface_params]), Directive::d_atomtypes, Directive::d_none);
set_nec(&(necessary[Directive::d_cmaptypes]), Directive::d_atomtypes, Directive::d_none);
set_nec(&(necessary[Directive::d_moleculetype]), Directive::d_atomtypes, Directive::d_none);
set_nec(&(necessary[Directive::d_atoms]), Directive::d_moleculetype, Directive::d_none);
set_nec(&(necessary[Directive::d_vsites4]), Directive::d_atoms, Directive::d_none);
set_nec(&(necessary[Directive::d_vsitesn]), Directive::d_atoms, Directive::d_none);
set_nec(&(necessary[Directive::d_bonds]), Directive::d_atoms, Directive::d_none);
- set_nec(&(necessary[Directive::d_exclusions]), Directive::d_bonds, Directive::d_constraints,
- Directive::d_settles, Directive::d_none);
+ set_nec(&(necessary[Directive::d_exclusions]),
+ Directive::d_bonds,
+ Directive::d_constraints,
+ Directive::d_settles,
+ Directive::d_none);
set_nec(&(necessary[Directive::d_pairs]), Directive::d_atoms, Directive::d_none);
set_nec(&(necessary[Directive::d_pairs_nb]), Directive::d_atoms, Directive::d_none);
set_nec(&(necessary[Directive::d_angles]), Directive::d_atoms, Directive::d_none);
set_nec(&(necessary[Directive::d_orientation_restraints]), Directive::d_atoms, Directive::d_none);
set_nec(&(necessary[Directive::d_dihedral_restraints]), Directive::d_atoms, Directive::d_none);
set_nec(&(necessary[Directive::d_cmap]), Directive::d_atoms, Directive::d_none);
- set_nec(&(necessary[Directive::d_intermolecular_interactions]), Directive::d_molecules,
+ set_nec(&(necessary[Directive::d_intermolecular_interactions]),
+ Directive::d_molecules,
Directive::d_none);
}
*DS = nullptr;
Count
};
+const char* enumValueToString(Directive d);
+
struct DirStack
{
Directive d;
int ifunc_index(Directive d, int type);
-const char* dir2str(Directive d);
-
Directive str2dir(char* dstr);
void DS_Init(DirStack** DS);
*/
#include "gmxpre.h"
+#include "gromacs/utility/enumerationhelpers.h"
+#include "gromacs/utility/stringutil.h"
#include "topio.h"
#include <cassert>
#define OPENDIR '[' /* starting sign for directive */
#define CLOSEDIR ']' /* ending sign for directive */
-static void gen_pairs(const InteractionsOfType& nbs, InteractionsOfType* pairs, real fudge, int comb)
+static void gen_pairs(const InteractionsOfType& nbs, InteractionsOfType* pairs, real fudge, CombinationRule comb)
{
real scaling;
int ntp = nbs.size();
* should be scaled, but not sigma.
* The sigma values have even indices 0,2, etc.
*/
- if ((comb == eCOMB_ARITHMETIC || comb == eCOMB_GEOM_SIG_EPS) && (j % 2 == 0))
+ if ((comb == CombinationRule::Arithmetic || comb == CombinationRule::GeomSigEps)
+ && (j % 2 == 0))
{
scaling = 1.0;
}
double check_mol(const gmx_mtop_t* mtop, warninp* wi)
{
char buf[256];
- int i, ri, pt;
+ int i, ri;
double q;
real m, mB;
for (i = 0; (i < atoms->nr); i++)
{
q += molb.nmol * atoms->atom[i].q;
- m = atoms->atom[i].m;
- mB = atoms->atom[i].mB;
- pt = atoms->atom[i].ptype;
+ m = atoms->atom[i].m;
+ mB = atoms->atom[i].mB;
+ ParticleType pt = atoms->atom[i].ptype;
/* If the particle is an atom or a nucleus it must have a mass,
* else, if it is a shell, a vsite or a bondshell it can have mass zero
*/
- if (((m <= 0.0) || (mB <= 0.0)) && ((pt == eptAtom) || (pt == eptNucleus)))
+ if (((m <= 0.0) || (mB <= 0.0)) && ((pt == ParticleType::Atom) || (pt == ParticleType::Nucleus)))
{
ri = atoms->atom[i].resind;
- sprintf(buf, "atom %s (Res %s-%d) has mass %g (state A) / %g (state B)\n",
- *(atoms->atomname[i]), *(atoms->resinfo[ri].name), atoms->resinfo[ri].nr, m, mB);
+ sprintf(buf,
+ "atom %s (Res %s-%d) has mass %g (state A) / %g (state B)\n",
+ *(atoms->atomname[i]),
+ *(atoms->resinfo[ri].name),
+ atoms->resinfo[ri].nr,
+ m,
+ mB);
warning_error(wi, buf);
}
- else if (((m != 0) || (mB != 0)) && (pt == eptVSite))
+ else if (((m != 0) || (mB != 0)) && (pt == ParticleType::VSite))
{
ri = atoms->atom[i].resind;
sprintf(buf,
"virtual site %s (Res %s-%d) has non-zero mass %g (state A) / %g (state "
"B)\n"
" Check your topology.\n",
- *(atoms->atomname[i]), *(atoms->resinfo[ri].name), atoms->resinfo[ri].nr, m, mB);
+ *(atoms->atomname[i]),
+ *(atoms->resinfo[ri].name),
+ atoms->resinfo[ri].nr,
+ m,
+ mB);
warning_error(wi, buf);
/* The following statements make LINCS break! */
/* atoms->atom[i].m=0; */
*qTotB += numMols * roundedMoleculeCharge(qmolB, sumAbsQB);
}
-static void get_nbparm(char* nb_str, char* comb_str, int* nb, int* comb, warninp* wi)
+static void get_nbparm(char* nb_str, char* comb_str, VanDerWaalsPotential* nb, CombinationRule* comb, warninp* wi)
{
- int i;
- char warn_buf[STRLEN];
-
- *nb = -1;
- for (i = 1; (i < eNBF_NR); i++)
+ *nb = VanDerWaalsPotential::Count;
+ for (auto i : gmx::EnumerationArray<VanDerWaalsPotential, bool>::keys())
{
- if (gmx_strcasecmp(nb_str, enbf_names[i]) == 0)
+ if (gmx_strcasecmp(nb_str, enumValueToString(i)) == 0)
{
*nb = i;
}
}
- if (*nb == -1)
+ if (*nb == VanDerWaalsPotential::Count)
{
- *nb = strtol(nb_str, nullptr, 10);
- }
- if ((*nb < 1) || (*nb >= eNBF_NR))
- {
- sprintf(warn_buf, "Invalid nonbond function selector '%s' using %s", nb_str, enbf_names[1]);
- warning_error(wi, warn_buf);
- *nb = 1;
+ int integerValue = strtol(nb_str, nullptr, 10);
+ if ((integerValue < 1) || (integerValue >= static_cast<int>(VanDerWaalsPotential::Count)))
+ {
+ std::string message =
+ gmx::formatString("Invalid nonbond function selector '%s' using %s",
+ nb_str,
+ enumValueToString(VanDerWaalsPotential::LJ));
+ warning_error(wi, message);
+ *nb = VanDerWaalsPotential::LJ;
+ }
+ else
+ {
+ *nb = static_cast<VanDerWaalsPotential>(integerValue);
+ }
}
- *comb = -1;
- for (i = 1; (i < eCOMB_NR); i++)
+ *comb = CombinationRule::Count;
+ for (auto i : gmx::EnumerationArray<CombinationRule, bool>::keys())
{
- if (gmx_strcasecmp(comb_str, ecomb_names[i]) == 0)
+ if (gmx_strcasecmp(comb_str, enumValueToString(i)) == 0)
{
*comb = i;
}
}
- if (*comb == -1)
- {
- *comb = strtol(comb_str, nullptr, 10);
- }
- if ((*comb < 1) || (*comb >= eCOMB_NR))
+ if (*comb == CombinationRule::Count)
{
- sprintf(warn_buf, "Invalid combination rule selector '%s' using %s", comb_str, ecomb_names[1]);
- warning_error(wi, warn_buf);
- *comb = 1;
+ int integerValue = strtol(comb_str, nullptr, 10);
+ if ((integerValue < 1) || (integerValue >= static_cast<int>(CombinationRule::Count)))
+ {
+ std::string message =
+ gmx::formatString("Invalid combination rule selector '%s' using %s",
+ comb_str,
+ enumValueToString(CombinationRule::Geometric));
+ warning_error(wi, message);
+ *comb = CombinationRule::Geometric;
+ }
+ else
+ {
+ *comb = static_cast<CombinationRule>(integerValue);
+ }
}
}
-static char** cpp_opts(const char* define, const char* include, warninp* wi)
+/*! \brief Parses define and include flags.
+ *
+ * Returns a vector of parsed include/define flags, with an extra nullptr entry at the back
+ * for consumers that expect null-terminated char** structures.
+ */
+static std::vector<char*> cpp_opts(const char* define, const char* include, warninp* wi)
{
int n, len;
- int ncppopts = 0;
const char* cppadds[2];
- char** cppopts = nullptr;
const char* option[2] = { "-D", "-I" };
const char* nopt[2] = { "define", "include" };
const char* ptr;
cppadds[0] = define;
cppadds[1] = include;
+ std::vector<char*> cppOptions;
for (n = 0; (n < 2); n++)
{
if (cppadds[n])
}
else
{
- srenew(cppopts, ++ncppopts);
- cppopts[ncppopts - 1] = gmx_strdup(buf);
+ cppOptions.emplace_back(gmx_strdup(buf));
}
sfree(buf);
ptr = rptr;
}
}
}
- srenew(cppopts, ++ncppopts);
- cppopts[ncppopts - 1] = nullptr;
-
- return cppopts;
+ // Users of cppOptions expect a null last element.
+ cppOptions.emplace_back(nullptr);
+ return cppOptions;
}
std::vector<MoleculeInformation>* molinfo,
std::unique_ptr<MoleculeInformation>* intermolecular_interactions,
gmx::ArrayRef<InteractionsOfType> interactions,
- int* combination_rule,
+ CombinationRule* combination_rule,
double* reppow,
t_gromppopts* opts,
real* fudgeQQ,
const gmx::MDLogger& logger)
{
FILE* out;
- int sl, nb_funct;
+ int sl;
char * pline = nullptr, **title = nullptr;
char line[STRLEN], errbuf[256], comb_str[256], nb_str[256];
char genpairs[32];
/* open input file */
auto cpp_opts_return = cpp_opts(define, include, wi);
- status = cpp_open_file(infile, &handle, cpp_opts_return);
+ status = cpp_open_file(infile, &handle, cpp_opts_return.data());
if (status != 0)
{
gmx_fatal(FARGS, "%s", cpp_error(&handle, status));
nbparam = nullptr; /* The temporary non-bonded matrix */
pair = nullptr; /* The temporary pair interaction matrix */
std::vector<std::vector<gmx::ExclusionBlock>> exclusionBlocks;
- nb_funct = F_LJ;
+ VanDerWaalsPotential nb_funct = VanDerWaalsPotential::LJ;
*reppow = 12.0; /* Default value for repulsion power */
{
/* we should print here which directives should have
been present, and which actually are */
- gmx_fatal(FARGS, "%s\nInvalid order for directive %s",
- cpp_error(&handle, eCPP_SYNTAX), dir2str(newd));
+ gmx_fatal(FARGS,
+ "%s\nInvalid order for directive %s",
+ cpp_error(&handle, eCPP_SYNTAX),
+ enumValueToString(newd));
/* d = Directive::d_invalid; */
}
case Directive::d_defaults:
if (bReadDefaults)
{
- gmx_fatal(FARGS, "%s\nFound a second defaults directive.\n",
+ gmx_fatal(FARGS,
+ "%s\nFound a second defaults directive.\n",
cpp_error(&handle, eCPP_SYNTAX));
}
bReadDefaults = TRUE;
- nscan = sscanf(pline, "%s%s%s%lf%lf%lf", nb_str, comb_str, genpairs,
- &fLJ, &fQQ, &fPOW);
+ nscan = sscanf(
+ pline, "%s%s%s%lf%lf%lf", nb_str, comb_str, genpairs, &fLJ, &fQQ, &fPOW);
if (nscan < 2)
{
too_few(wi);
if (nscan >= 3)
{
bGenPairs = (gmx::equalCaseInsensitive(genpairs, "Y", 1));
- if (nb_funct != eNBF_LJ && bGenPairs)
+ if (nb_funct != VanDerWaalsPotential::LJ && bGenPairs)
{
gmx_fatal(FARGS,
"Generating pair parameters is only supported "
*reppow = fPOW;
}
}
- nb_funct = ifunc_index(Directive::d_nonbond_params, nb_funct);
+ nb_funct = static_cast<VanDerWaalsPotential>(ifunc_index(
+ Directive::d_nonbond_params, static_cast<int>(nb_funct)));
break;
case Directive::d_atomtypes:
- push_at(symtab, atypes, &bondAtomType, pline, nb_funct, &nbparam,
- bGenPairs ? &pair : nullptr, wi);
+ push_at(symtab,
+ atypes,
+ &bondAtomType,
+ pline,
+ static_cast<int>(nb_funct),
+ &nbparam,
+ bGenPairs ? &pair : nullptr,
+ wi);
break;
case Directive::d_bondtypes: // Intended to fall through
break;
case Directive::d_nonbond_params:
- push_nbt(d, nbparam, atypes, pline, nb_funct, wi);
+ push_nbt(d, nbparam, atypes, pline, static_cast<int>(nb_funct), wi);
break;
case Directive::d_implicit_genborn_params: // NOLINT bugprone-branch-clone
|| opts->couple_lam1 == ecouplamNONE
|| opts->couple_lam1 == ecouplamQ))
{
- dcatt = add_atomtype_decoupled(symtab, atypes, &nbparam,
- bGenPairs ? &pair : nullptr);
+ dcatt = add_atomtype_decoupled(
+ symtab, atypes, &nbparam, bGenPairs ? &pair : nullptr);
}
ntype = atypes->size();
ncombs = (ntype * (ntype + 1)) / 2;
- generate_nbparams(*combination_rule, nb_funct,
- &(interactions[nb_funct]), atypes, wi);
- ncopy = copy_nbparams(nbparam, nb_funct, &(interactions[nb_funct]), ntype);
+ generate_nbparams(*combination_rule,
+ static_cast<int>(nb_funct),
+ &(interactions[static_cast<int>(nb_funct)]),
+ atypes,
+ wi);
+ ncopy = copy_nbparams(nbparam,
+ static_cast<int>(nb_funct),
+ &(interactions[static_cast<int>(nb_funct)]),
+ ntype);
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted(
"Generated %d of the %d non-bonded parameter "
"combinations",
- ncombs - ncopy, ncombs);
+ ncombs - ncopy,
+ ncombs);
free_nbparam(nbparam, ntype);
if (bGenPairs)
{
- gen_pairs((interactions[nb_funct]), &(interactions[F_LJ14]),
- fudgeLJ, *combination_rule);
- ncopy = copy_nbparams(pair, nb_funct, &(interactions[F_LJ14]), ntype);
+ gen_pairs((interactions[static_cast<int>(nb_funct)]),
+ &(interactions[F_LJ14]),
+ fudgeLJ,
+ *combination_rule);
+ ncopy = copy_nbparams(
+ pair, static_cast<int>(nb_funct), &(interactions[F_LJ14]), ntype);
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted(
"Generated %d of the %d 1-4 parameter "
"combinations",
- ncombs - ncopy, ncombs);
+ ncombs - ncopy,
+ ncombs);
free_nbparam(pair, ntype);
}
/* Copy GBSA parameters to atomtype array? */
GMX_RELEASE_ASSERT(
mi0,
"Need to have a valid MoleculeInformation object to work on");
- push_bond(d, interactions, mi0->interactions, &(mi0->atoms), atypes,
- pline, FALSE, bGenPairs, *fudgeQQ, bZero, &bWarn_copy_A_B, wi);
+ push_bond(d,
+ interactions,
+ mi0->interactions,
+ &(mi0->atoms),
+ atypes,
+ pline,
+ FALSE,
+ bGenPairs,
+ *fudgeQQ,
+ bZero,
+ &bWarn_copy_A_B,
+ wi);
break;
case Directive::d_pairs_nb:
GMX_RELEASE_ASSERT(
mi0,
"Need to have a valid MoleculeInformation object to work on");
- push_bond(d, interactions, mi0->interactions, &(mi0->atoms), atypes,
- pline, FALSE, FALSE, 1.0, bZero, &bWarn_copy_A_B, wi);
+ push_bond(d,
+ interactions,
+ mi0->interactions,
+ &(mi0->atoms),
+ atypes,
+ pline,
+ FALSE,
+ FALSE,
+ 1.0,
+ bZero,
+ &bWarn_copy_A_B,
+ wi);
break;
case Directive::d_vsites1:
GMX_RELEASE_ASSERT(
mi0,
"Need to have a valid MoleculeInformation object to work on");
- push_bond(d, interactions, mi0->interactions, &(mi0->atoms), atypes,
- pline, TRUE, bGenPairs, *fudgeQQ, bZero, &bWarn_copy_A_B, wi);
+ push_bond(d,
+ interactions,
+ mi0->interactions,
+ &(mi0->atoms),
+ atypes,
+ pline,
+ TRUE,
+ bGenPairs,
+ *fudgeQQ,
+ bZero,
+ &bWarn_copy_A_B,
+ wi);
break;
case Directive::d_cmap:
GMX_RELEASE_ASSERT(
.asParagraph()
.appendTextFormatted(
"Excluding %d bonded neighbours molecule type '%s'",
- mi0->nrexcl, *mi0->name);
+ mi0->nrexcl,
+ *mi0->name);
sum_q(&mi0->atoms, nrcopies, &qt, &qBt);
if (!mi0->bProcessed)
{
if (bCouple)
{
- convert_moltype_couple(mi0, dcatt, *fudgeQQ, opts->couple_lam0,
- opts->couple_lam1, opts->bCoupleIntra,
- nb_funct, &(interactions[nb_funct]), wi);
+ convert_moltype_couple(mi0,
+ dcatt,
+ *fudgeQQ,
+ opts->couple_lam0,
+ opts->couple_lam1,
+ opts->bCoupleIntra,
+ static_cast<int>(nb_funct),
+ &(interactions[static_cast<int>(nb_funct)]),
+ wi);
}
stupid_fill_block(&mi0->mols, mi0->atoms.nr, TRUE);
mi0->bProcessed = TRUE;
warning(wi, unusedDefineWarning);
}
- sfree(cpp_opts_return);
+ for (char* element : cpp_opts_return)
+ {
+ sfree(element);
+ }
if (out)
{
}
GMX_LOG(logger.info)
.asParagraph()
- .appendTextFormatted("Coupling %d copies of molecule type '%s'", nmol_couple,
- opts->couple_moltype);
+ .appendTextFormatted(
+ "Coupling %d copies of molecule type '%s'", nmol_couple, opts->couple_moltype);
}
/* this is not very clean, but fixes core dump on empty system name */
}
if (fabs(qBt) > 1e-4 && !gmx_within_tol(qBt, qt, 1e-6))
{
- sprintf(warn_buf, "State B has non-zero total charge: %.6f\n%s\n", qBt,
- floating_point_arithmetic_tip);
+ sprintf(warn_buf, "State B has non-zero total charge: %.6f\n%s\n", qBt, floating_point_arithmetic_tip);
warning_note(wi, warn_buf);
}
if (usingFullRangeElectrostatics && (fabs(qt) > 1e-4 || fabs(qBt) > 1e-4))
bool bZero,
t_symtab* symtab,
gmx::ArrayRef<InteractionsOfType> interactions,
- int* combination_rule,
+ CombinationRule* combination_rule,
double* repulsion_power,
real* fudgeQQ,
PreprocessingAtomTypes* atypes,
{
GMX_LOG(logger.info).asParagraph().appendTextFormatted("processing topology...");
}
- title = read_topol(topfile, tmpfile, opts->define, opts->include, symtab, atypes, molinfo,
- intermolecular_interactions, interactions, combination_rule, repulsion_power,
- opts, fudgeQQ, molblock, ffParametrizedWithHBondConstraints,
- ir->efep != efepNO, bZero, EEL_FULL(ir->coulombtype), wi, logger);
-
- if ((*combination_rule != eCOMB_GEOMETRIC) && (ir->vdwtype == evdwUSER))
+ title = read_topol(topfile,
+ tmpfile,
+ opts->define,
+ opts->include,
+ symtab,
+ atypes,
+ molinfo,
+ intermolecular_interactions,
+ interactions,
+ combination_rule,
+ repulsion_power,
+ opts,
+ fudgeQQ,
+ molblock,
+ ffParametrizedWithHBondConstraints,
+ ir->efep != FreeEnergyPerturbationType::No,
+ bZero,
+ EEL_FULL(ir->coulombtype),
+ wi,
+ logger);
+
+ if ((*combination_rule != CombinationRule::Geometric) && (ir->vdwtype == VanDerWaalsType::User))
{
warning(wi,
"Using sigma/epsilon based combination rules with"
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2012,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct t_symtab;
struct warninp;
typedef warninp* warninp_t;
+enum class CombinationRule : int;
namespace gmx
{
bool bZero,
t_symtab* symtab,
gmx::ArrayRef<InteractionsOfType> plist,
- int* combination_rule,
+ CombinationRule* combination_rule,
double* repulsion_power,
real* fudgeQQ,
PreprocessingAtomTypes* atype,
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/topology/symtab.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringtoenumvalueconverter.h"
#include "gromacs/utility/stringutil.h"
-void generate_nbparams(int comb,
+void generate_nbparams(CombinationRule comb,
int ftype,
InteractionsOfType* interactions,
PreprocessingAtomTypes* atypes,
case F_LJ:
switch (comb)
{
- case eCOMB_GEOMETRIC:
+ case CombinationRule::Geometric:
/* Gromos rules */
for (int i = 0; (i < nr); i++)
{
{
for (int nf = 0; (nf < nrfp); nf++)
{
- ci = atypes->atomNonBondedParamFromAtomType(i, nf);
- cj = atypes->atomNonBondedParamFromAtomType(j, nf);
+ ci = *atypes->atomNonBondedParamFromAtomType(i, nf);
+ cj = *atypes->atomNonBondedParamFromAtomType(j, nf);
c = std::sqrt(ci * cj);
forceParam[nf] = c;
}
}
break;
- case eCOMB_ARITHMETIC:
+ case CombinationRule::Arithmetic:
/* c0 and c1 are sigma and epsilon */
for (int i = 0; (i < nr); i++)
{
for (int j = 0; (j < nr); j++)
{
- ci0 = atypes->atomNonBondedParamFromAtomType(i, 0);
- cj0 = atypes->atomNonBondedParamFromAtomType(j, 0);
- ci1 = atypes->atomNonBondedParamFromAtomType(i, 1);
- cj1 = atypes->atomNonBondedParamFromAtomType(j, 1);
+ ci0 = *atypes->atomNonBondedParamFromAtomType(i, 0);
+ cj0 = *atypes->atomNonBondedParamFromAtomType(j, 0);
+ ci1 = *atypes->atomNonBondedParamFromAtomType(i, 1);
+ cj1 = *atypes->atomNonBondedParamFromAtomType(j, 1);
forceParam[0] = (fabs(ci0) + fabs(cj0)) * 0.5;
/* Negative sigma signals that c6 should be set to zero later,
* so we need to propagate that through the combination rules.
}
break;
- case eCOMB_GEOM_SIG_EPS:
+ case CombinationRule::GeomSigEps:
/* c0 and c1 are sigma and epsilon */
for (int i = 0; (i < nr); i++)
{
for (int j = 0; (j < nr); j++)
{
- ci0 = atypes->atomNonBondedParamFromAtomType(i, 0);
- cj0 = atypes->atomNonBondedParamFromAtomType(j, 0);
- ci1 = atypes->atomNonBondedParamFromAtomType(i, 1);
- cj1 = atypes->atomNonBondedParamFromAtomType(j, 1);
+ ci0 = *atypes->atomNonBondedParamFromAtomType(i, 0);
+ cj0 = *atypes->atomNonBondedParamFromAtomType(j, 0);
+ ci1 = *atypes->atomNonBondedParamFromAtomType(i, 1);
+ cj1 = *atypes->atomNonBondedParamFromAtomType(j, 1);
forceParam[0] = std::sqrt(std::fabs(ci0 * cj0));
/* Negative sigma signals that c6 should be set to zero later,
* so we need to propagate that through the combination rules.
break;
default:
- auto message = gmx::formatString("No such combination rule %d", comb);
+ auto message =
+ gmx::formatString("No such combination rule %s", enumValueToString(comb));
warning_error_and_exit(wi, message, FARGS);
}
break;
{
for (int j = 0; (j < nr); j++)
{
- ci0 = atypes->atomNonBondedParamFromAtomType(i, 0);
- cj0 = atypes->atomNonBondedParamFromAtomType(j, 0);
- ci2 = atypes->atomNonBondedParamFromAtomType(i, 2);
- cj2 = atypes->atomNonBondedParamFromAtomType(j, 2);
- bi = atypes->atomNonBondedParamFromAtomType(i, 1);
- bj = atypes->atomNonBondedParamFromAtomType(j, 1);
+ ci0 = *atypes->atomNonBondedParamFromAtomType(i, 0);
+ cj0 = *atypes->atomNonBondedParamFromAtomType(j, 0);
+ ci2 = *atypes->atomNonBondedParamFromAtomType(i, 2);
+ cj2 = *atypes->atomNonBondedParamFromAtomType(j, 2);
+ bi = *atypes->atomNonBondedParamFromAtomType(i, 1);
+ bj = *atypes->atomNonBondedParamFromAtomType(j, 1);
forceParam[0] = std::sqrt(ci0 * cj0);
if ((bi == 0) || (bj == 0))
{
}
}
+//! Local definition that supersedes the central one, as we only want the leading letter
+static const char* enumValueToLetterAsString(ParticleType enumValue)
+{
+ static constexpr gmx::EnumerationArray<ParticleType, const char*> particleTypeLetters = {
+ "A", "N", "S", "B", "V"
+ };
+ return particleTypeLetters[enumValue];
+}
+
void push_at(t_symtab* symtab,
PreprocessingAtomTypes* at,
PreprocessingBondAtomType* bondAtomType,
t_nbparam*** pair,
warninp* wi)
{
- typedef struct
- {
- const char* entry;
- int ptype;
- } t_xlate;
- t_xlate xl[eptNR] = {
- { "A", eptAtom }, { "N", eptNucleus }, { "S", eptShell },
- { "B", eptBond }, { "V", eptVSite },
- };
-
- int nr, nfields, j, pt, nfp0 = -1;
- int batype_nr, nread;
+ int nfields, nfp0 = -1;
+ int nread;
char type[STRLEN], btype[STRLEN], ptype[STRLEN];
double m, q;
double c[MAXFORCEPARAM];
snew(atom, 1);
/* First assign input line to temporary array */
- nfields = sscanf(line, "%s%s%s%s%s%s%s%s%s%s%s%s", tmpfield[0], tmpfield[1], tmpfield[2],
- tmpfield[3], tmpfield[4], tmpfield[5], tmpfield[6], tmpfield[7], tmpfield[8],
- tmpfield[9], tmpfield[10], tmpfield[11]);
+ nfields = sscanf(line,
+ "%s%s%s%s%s%s%s%s%s%s%s%s",
+ tmpfield[0],
+ tmpfield[1],
+ tmpfield[2],
+ tmpfield[3],
+ tmpfield[4],
+ tmpfield[5],
+ tmpfield[6],
+ tmpfield[7],
+ tmpfield[8],
+ tmpfield[9],
+ tmpfield[10],
+ tmpfield[11]);
/* Comments on optional fields in the atomtypes section:
*
{
if (have_bonded_type)
{
- nread = sscanf(line, "%s%s%d%lf%lf%s%lf%lf", type, btype, &atomnr, &m, &q,
- ptype, &c[0], &c[1]);
+ nread = sscanf(
+ line, "%s%s%d%lf%lf%s%lf%lf", type, btype, &atomnr, &m, &q, ptype, &c[0], &c[1]);
if (nread < 8)
{
too_few(wi);
{
if (have_bonded_type)
{
- nread = sscanf(line, "%s%s%d%lf%lf%s%lf%lf%lf", type, btype, &atomnr, &m, &q,
- ptype, &c[0], &c[1], &c[2]);
+ nread = sscanf(
+ line, "%s%s%d%lf%lf%s%lf%lf%lf", type, btype, &atomnr, &m, &q, ptype, &c[0], &c[1], &c[2]);
if (nread < 9)
{
too_few(wi);
else
{
/* have_atomic_number && !have_bonded_type */
- nread = sscanf(line, "%s%d%lf%lf%s%lf%lf%lf", type, &atomnr, &m, &q, ptype,
- &c[0], &c[1], &c[2]);
+ nread = sscanf(
+ line, "%s%d%lf%lf%s%lf%lf%lf", type, &atomnr, &m, &q, ptype, &c[0], &c[1], &c[2]);
if (nread < 8)
{
too_few(wi);
if (have_bonded_type)
{
/* !have_atomic_number && have_bonded_type */
- nread = sscanf(line, "%s%s%lf%lf%s%lf%lf%lf", type, btype, &m, &q, ptype, &c[0],
- &c[1], &c[2]);
+ nread = sscanf(
+ line, "%s%s%lf%lf%s%lf%lf%lf", type, btype, &m, &q, ptype, &c[0], &c[1], &c[2]);
if (nread < 8)
{
too_few(wi);
{
sprintf(ptype, "V");
}
- for (j = 0; (j < eptNR); j++)
- {
- if (gmx_strcasecmp(ptype, xl[j].entry) == 0)
- {
- break;
- }
- }
- if (j == eptNR)
+ static const gmx::StringToEnumValueConverter<ParticleType, enumValueToLetterAsString, gmx::StringCompareType::CaseInsensitive, gmx::StripStrings::No>
+ s_stringToParticleType;
+ std::optional<ParticleType> pt = s_stringToParticleType.valueFrom(ptype);
+ if (!pt)
{
auto message = gmx::formatString("Invalid particle type %s", ptype);
warning_error_and_exit(wi, message, FARGS);
}
- pt = xl[j].ptype;
atom->q = q;
atom->m = m;
- atom->ptype = pt;
+ atom->ptype = pt.value();
for (int i = 0; i < MAXFORCEPARAM; i++)
{
forceParam[i] = c[i];
InteractionOfType interactionType({}, forceParam, "");
- batype_nr = bondAtomType->addBondAtomType(symtab, btype);
+ auto batype_nr = bondAtomType->addBondAtomType(symtab, btype);
- if ((nr = at->atomTypeFromName(type)) != NOTSET)
+ auto atomType = at->atomTypeFromName(type);
+ if (atomType.has_value())
{
auto message = gmx::formatString(
"Atomtype %s was defined previously (e.g. in the forcefield files), "
"to suppress this warning with -maxwarn.",
type);
warning(wi, message);
- if ((nr = at->setType(nr, symtab, *atom, type, interactionType, batype_nr, atomnr)) == NOTSET)
+ auto newAtomType = at->setType(*atomType, symtab, *atom, type, interactionType, batype_nr, atomnr);
+ if (!newAtomType.has_value())
{
auto message = gmx::formatString("Replacing atomtype %s failed", type);
warning_error_and_exit(wi, message, FARGS);
}
}
- else if ((at->addType(symtab, *atom, type, interactionType, batype_nr, atomnr)) == NOTSET)
- {
- auto message = gmx::formatString("Adding atomtype %s failed", type);
- warning_error_and_exit(wi, message, FARGS);
- }
else
{
+ at->addType(symtab, *atom, type, interactionType, batype_nr, atomnr);
/* Add space in the non-bonded parameters matrix */
realloc_nb_params(at, nbparam, pair);
}
GMX_ASSERT(nrfp <= MAXFORCEPARAM,
"This is ensured in other places, but we need this assert to keep the clang "
"analyzer happy");
- const bool identicalParameters = std::equal(
- bt->interactionTypes[i].forceParam().begin(),
- bt->interactionTypes[i].forceParam().begin() + nrfp, b.forceParam().begin());
+ const bool identicalParameters = std::equal(bt->interactionTypes[i].forceParam().begin(),
+ bt->interactionTypes[i].forceParam().begin() + nrfp,
+ b.forceParam().begin());
if (!bAllowRepeat || identicalParameters)
{
{
if (atomTypes != nullptr)
{
- int atomType = atomTypes->atomTypeFromName(name);
- if (atomType == NOTSET)
+ auto atomType = atomTypes->atomTypeFromName(name);
+ if (!atomType.has_value())
{
auto message = gmx::formatString("Unknown atomtype %s\n", name);
warning_error_and_exit(wi, message, FARGS);
}
- atomTypesFromAtomNames.emplace_back(atomType);
+ atomTypesFromAtomNames.emplace_back(*atomType);
}
else if (bondAtomTypes != nullptr)
{
- int atomType = bondAtomTypes->bondAtomTypeFromName(name);
- if (atomType == NOTSET)
+ auto bondAtomType = bondAtomTypes->bondAtomTypeFromName(name);
+ if (!bondAtomType.has_value())
{
auto message = gmx::formatString("Unknown bond_atomtype %s\n", name);
warning_error_and_exit(wi, message, FARGS);
}
- atomTypesFromAtomNames.emplace_back(atomType);
+ atomTypesFromAtomNames.emplace_back(*bondAtomType);
}
}
return atomTypesFromAtomNames;
nrfpA = interaction_function[ftype].nrfpA;
strcpy(f1, formnl[nral]);
strcat(f1, formlf);
- if ((nn = sscanf(line, f1, &c[0], &c[1], &c[2], &c[3], &c[4], &c[5], &c[6], &c[7], &c[8], &c[9],
- &c[10], &c[11], &c[12]))
+ if ((nn = sscanf(
+ line, f1, &c[0], &c[1], &c[2], &c[3], &c[4], &c[5], &c[6], &c[7], &c[8], &c[9], &c[10], &c[11], &c[12]))
!= nrfp)
{
if (nn == nrfpA)
strcat(f1, formlf[nrfp - 1]);
/* Check number of parameters given */
- if ((nn = sscanf(line, f1, &c[0], &c[1], &c[2], &c[3], &c[4], &c[5], &c[6], &c[7], &c[8], &c[9],
- &c[10], &c[11]))
+ if ((nn = sscanf(
+ line, f1, &c[0], &c[1], &c[2], &c[3], &c[4], &c[5], &c[6], &c[7], &c[8], &c[9], &c[10], &c[11]))
!= nrfp)
{
if (nn == nrfpA)
}
else
{
- int atomNumber;
- if ((atomNumber = bondAtomType->bondAtomTypeFromName(alc[i])) == NOTSET)
+ auto atomNumber = bondAtomType->bondAtomTypeFromName(alc[i]);
+ if (!atomNumber.has_value())
{
auto message = gmx::formatString("Unknown bond_atomtype %s", alc[i]);
warning_error_and_exit(wi, message, FARGS);
}
- atoms.emplace_back(atomNumber);
+ atoms.emplace_back(*atomNumber);
}
}
for (int i = 0; (i < nrfp); i++)
int i, f, n, ftype, nrfp;
double c[4], dum;
real cr[4];
- int ai, aj;
t_nbparam* nbp;
bool bId;
}
/* Put the parameters in the matrix */
- if ((ai = atypes->atomTypeFromName(a0)) == NOTSET)
+ auto ai = atypes->atomTypeFromName(a0);
+ if (!ai.has_value())
{
auto message = gmx::formatString("Atomtype %s not found", a0);
warning_error_and_exit(wi, message, FARGS);
}
- if ((aj = atypes->atomTypeFromName(a1)) == NOTSET)
+ auto aj = atypes->atomTypeFromName(a1);
+ if (!aj.has_value())
{
auto message = gmx::formatString("Atomtype %s not found", a1);
warning_error_and_exit(wi, message, FARGS);
}
- nbp = &(nbt[std::max(ai, aj)][std::min(ai, aj)]);
+ nbp = &(nbt[std::max(*ai, *aj)][std::min(*ai, *aj)]);
if (nbp->bSet)
{
{
auto message =
gmx::formatString("Error in reading cmap parameter for angle %s %s %s %s %s",
- alc[0], alc[1], alc[2], alc[3], alc[4]);
+ alc[0],
+ alc[1],
+ alc[2],
+ alc[3],
+ alc[4]);
warning_error(wi, message);
}
}
{
/* Assign a grid number to each cmap_type */
GMX_RELEASE_ASSERT(bondAtomType != nullptr, "Need valid PreprocessingBondAtomType object");
- bt[F_CMAP].cmapAtomTypes.emplace_back(bondAtomType->bondAtomTypeFromName(alc[i]));
+ bt[F_CMAP].cmapAtomTypes.emplace_back(*bondAtomType->bondAtomTypeFromName(alc[i]));
}
/* Assign a type number to this cmap */
/* Check for the correct number of atoms (again) */
if (bt[F_CMAP].nct() != nct)
{
- auto message = gmx::formatString("Incorrect number of atom types (%d) in cmap type %d\n",
- nct, bt[F_CMAP].cmapAngles);
+ auto message = gmx::formatString(
+ "Incorrect number of atom types (%d) in cmap type %d\n", nct, bt[F_CMAP].cmapAngles);
warning_error(wi, message);
}
std::vector<int> atomTypes =
}
-static void push_atom_now(t_symtab* symtab,
- t_atoms* at,
- int atomnr,
- int atomicnumber,
- int type,
- char* ctype,
- int ptype,
- char* resnumberic,
- char* resname,
- char* name,
- real m0,
- real q0,
- int typeB,
- char* ctypeB,
- real mB,
- real qB,
- warninp* wi)
+static void push_atom_now(t_symtab* symtab,
+ t_atoms* at,
+ int atomnr,
+ int atomicnumber,
+ int type,
+ char* ctype,
+ ParticleType ptype,
+ char* resnumberic,
+ char* resname,
+ char* name,
+ real m0,
+ real q0,
+ int typeB,
+ char* ctypeB,
+ real mB,
+ real qB,
+ warninp* wi)
{
int j, resind = 0, resnr;
unsigned char ric;
auto message = gmx::formatString(
"Atoms in the .top are not numbered consecutively from 1 (rather, "
"atomnr = %d, while at->nr = %d)",
- atomnr, at->nr);
+ atomnr,
+ at->nr);
warning_error_and_exit(wi, message, FARGS);
}
void push_atom(t_symtab* symtab, t_atoms* at, PreprocessingAtomTypes* atypes, char* line, warninp* wi)
{
- int ptype;
- int cgnumber, atomnr, type, typeB, nscan;
+ int cgnumber, atomnr, nscan;
char id[STRLEN], ctype[STRLEN], ctypeB[STRLEN], resnumberic[STRLEN], resname[STRLEN],
name[STRLEN], check[STRLEN];
double m, q, mb, qb;
return;
}
sscanf(id, "%d", &atomnr);
- if ((type = atypes->atomTypeFromName(ctype)) == NOTSET)
+ auto type = atypes->atomTypeFromName(ctype);
+ if (!type.has_value())
{
auto message = gmx::formatString("Atomtype %s not found", ctype);
warning_error_and_exit(wi, message, FARGS);
}
- ptype = atypes->atomParticleTypeFromAtomType(type);
+ ParticleType ptype = *atypes->atomParticleTypeFromAtomType(*type);
/* Set default from type */
- q0 = atypes->atomChargeFromAtomType(type);
- m0 = atypes->atomMassFromAtomType(type);
- typeB = type;
- qB = q0;
- mB = m0;
+ q0 = *atypes->atomChargeFromAtomType(*type);
+ m0 = *atypes->atomMassFromAtomType(*type);
+ auto typeB = type;
+ qB = q0;
+ mB = m0;
/* Optional parameters */
nscan = sscanf(line, "%*s%*s%*s%*s%*s%*s%lf%lf%s%lf%lf%s", &q, &m, ctypeB, &qb, &mb, check);
m0 = mB = m;
if (nscan > 2)
{
- if ((typeB = atypes->atomTypeFromName(ctypeB)) == NOTSET)
+ typeB = atypes->atomTypeFromName(ctypeB);
+ if (!typeB.has_value())
{
auto message = gmx::formatString("Atomtype %s not found", ctypeB);
warning_error_and_exit(wi, message, FARGS);
}
- qB = atypes->atomChargeFromAtomType(typeB);
- mB = atypes->atomMassFromAtomType(typeB);
+ qB = *atypes->atomChargeFromAtomType(*typeB);
+ mB = *atypes->atomMassFromAtomType(*typeB);
if (nscan > 3)
{
qB = qb;
}
}
- push_atom_now(symtab, at, atomnr, atypes->atomNumberFromAtomType(type), type, ctype, ptype,
- resnumberic, resname, name, m0, q0, typeB, typeB == type ? ctype : ctypeB, mB, qB, wi);
+ push_atom_now(symtab,
+ at,
+ atomnr,
+ *atypes->atomNumberFromAtomType(*type),
+ *type,
+ ctype,
+ ptype,
+ resnumberic,
+ resname,
+ name,
+ m0,
+ q0,
+ *typeB,
+ typeB == type ? ctype : ctypeB,
+ mB,
+ qB,
+ wi);
}
void push_molt(t_symtab* symtab, std::vector<MoleculeInformation>* mol, char* line, warninp* wi)
}
/* Test if this moleculetype overwrites another */
- const auto found = std::find_if(mol->begin(), mol->end(),
- [&type](const auto& m) { return strcmp(*(m.name), type) == 0; });
+ const auto found = std::find_if(
+ mol->begin(), mol->end(), [&type](const auto& m) { return strcmp(*(m.name), type) == 0; });
if (found != mol->end())
{
auto message = gmx::formatString("moleculetype %s is redefined", type);
if (!bFound)
{
auto foundParameter =
- std::find_if(bt[ftype].interactionTypes.begin(), bt[ftype].interactionTypes.end(),
+ std::find_if(bt[ftype].interactionTypes.begin(),
+ bt[ftype].interactionTypes.end(),
[¶mAtoms, &at, &bB](const auto& param) {
return findIfAllNBAtomsMatch(param.atoms(), paramAtoms, at, bB);
});
/* If we did not find a matching type for this cmap torsion */
if (!bFound)
{
- auto message = gmx::formatString("Unknown cmap torsion between atoms %d %d %d %d %d", p->ai() + 1,
- p->aj() + 1, p->ak() + 1, p->al() + 1, p->am() + 1);
+ auto message = gmx::formatString("Unknown cmap torsion between atoms %d %d %d %d %d",
+ p->ai() + 1,
+ p->aj() + 1,
+ p->ak() + 1,
+ p->al() + 1,
+ p->am() + 1);
warning_error_and_exit(wi, message, FARGS);
}
{
if (bB)
{
- return natom_match(currentParamFromParameterArray, at->atom[parameterToAdd.ai()].typeB,
- at->atom[parameterToAdd.aj()].typeB, at->atom[parameterToAdd.ak()].typeB,
- at->atom[parameterToAdd.al()].typeB, atypes);
+ return natom_match(currentParamFromParameterArray,
+ at->atom[parameterToAdd.ai()].typeB,
+ at->atom[parameterToAdd.aj()].typeB,
+ at->atom[parameterToAdd.ak()].typeB,
+ at->atom[parameterToAdd.al()].typeB,
+ atypes);
}
else
{
- return natom_match(currentParamFromParameterArray, at->atom[parameterToAdd.ai()].type,
- at->atom[parameterToAdd.aj()].type, at->atom[parameterToAdd.ak()].type,
- at->atom[parameterToAdd.al()].type, atypes);
+ return natom_match(currentParamFromParameterArray,
+ at->atom[parameterToAdd.ai()].type,
+ at->atom[parameterToAdd.aj()].type,
+ at->atom[parameterToAdd.ak()].type,
+ at->atom[parameterToAdd.al()].type,
+ atypes);
}
}
auto pos = bt[ftype].interactionTypes.begin();
while (pos != bt[ftype].interactionTypes.end() && nmatch_max < 4)
{
- pos = std::find_if(bt[ftype].interactionTypes.begin(), bt[ftype].interactionTypes.end(),
+ pos = std::find_if(bt[ftype].interactionTypes.begin(),
+ bt[ftype].interactionTypes.end(),
[&p, &at, &atypes, &bB, &nmatch_max](const auto& param) {
return (findNumberOfDihedralAtomMatches(param, p, at, atypes, bB)
> nmatch_max);
else /* Not a dihedral */
{
gmx::ArrayRef<const int> atomParam = p.atoms();
- auto found = std::find_if(
- bt[ftype].interactionTypes.begin(), bt[ftype].interactionTypes.end(),
- [&atomParam, &at, &atypes, &bB](const auto& param) {
- return findIfAllParameterAtomsMatch(param.atoms(), atomParam, at, atypes, bB);
- });
+ auto found = std::find_if(bt[ftype].interactionTypes.begin(),
+ bt[ftype].interactionTypes.end(),
+ [&atomParam, &at, &atypes, &bB](const auto& param) {
+ return findIfAllParameterAtomsMatch(
+ param.atoms(), atomParam, at, atypes, bB);
+ });
if (found != bt[ftype].interactionTypes.end())
{
nparam_found = 1;
"This probably means that you have inserted topology section \"%s\"\n"
"in a part belonging to a different molecule than you intended to.\n"
"In that case move the \"%s\" section to the right molecule.",
- aa[i], dir2str(d), at->nr, dir2str(d), dir2str(d));
+ aa[i],
+ enumValueToString(d),
+ at->nr,
+ enumValueToString(d),
+ enumValueToString(d));
warning_error_and_exit(wi, message, FARGS);
}
for (int j = i + 1; (j < nral); j++)
"Values from nral=NRAL() will satisfy this, we assert to keep gcc 4 happy");
if (aa[i] == aa[j])
{
- auto message = gmx::formatString("Duplicate atom index (%d) in %s", aa[i], dir2str(d));
+ auto message = gmx::formatString(
+ "Duplicate atom index (%d) in %s", aa[i], enumValueToString(d));
if (ftype == F_ANGRES)
{
/* Since the angle restraints uses 2 pairs of atoms to
strcpy(format, asformat[nral_fmt - 1]);
strcat(format, ccformat);
- nread = sscanf(line, format, &cc[0], &cc[1], &cc[2], &cc[3], &cc[4], &cc[5], &cc[6], &cc[7],
- &cc[8], &cc[9], &cc[10], &cc[11], &cc[12]);
+ nread = sscanf(line,
+ format,
+ &cc[0],
+ &cc[1],
+ &cc[2],
+ &cc[3],
+ &cc[4],
+ &cc[5],
+ &cc[6],
+ &cc[7],
+ &cc[8],
+ &cc[9],
+ &cc[10],
+ &cc[11],
+ &cc[12]);
if ((nread == NRFPA(ftype)) && (NRFPB(ftype) != 0))
{
auto message = gmx::formatString(
"Incorrect number of parameters - found %d, expected %d "
"or %d for %s (after the function type).",
- nread, NRFPA(ftype), NRFP(ftype), interaction_function[ftype].longname);
+ nread,
+ NRFPA(ftype),
+ NRFP(ftype),
+ interaction_function[ftype].longname);
warning_error_and_exit(wi, message, FARGS);
}
{
if (bZero)
{
- fprintf(stderr, "NOTE: No default %s types, using zeroes\n",
+ fprintf(stderr,
+ "NOTE: No default %s types, using zeroes\n",
interaction_function[ftype].longname);
}
else
if ((ftype == F_PDIHS || ftype == F_ANGRES || ftype == F_ANGRESZ) && paramValue[5] != paramValue[2])
{
auto message = gmx::formatString("%s multiplicity can not be perturbed %f!=%f",
- interaction_function[ftype].longname, paramValue[2],
+ interaction_function[ftype].longname,
+ paramValue[2],
paramValue[5]);
warning_error_and_exit(wi, message, FARGS);
}
{
auto message = gmx::formatString("%s table number can not be perturbed %d!=%d",
interaction_function[ftype].longname,
- gmx::roundToInt(param.c0()), gmx::roundToInt(param.c0()));
+ gmx::roundToInt(param.c0()),
+ gmx::roundToInt(param.c0()));
warning_error_and_exit(wi, message, FARGS);
}
"This probably means that you have inserted topology section \"%s\"\n"
"in a part belonging to a different molecule than you intended to.\n"
"In that case move the \"%s\" section to the right molecule.",
- aa[i], dir2str(d), at->nr, dir2str(d), dir2str(d));
+ aa[i],
+ enumValueToString(d),
+ at->nr,
+ enumValueToString(d),
+ enumValueToString(d));
warning_error_and_exit(wi, message, FARGS);
}
{
if (aa[i] == aa[j])
{
- auto message = gmx::formatString("Duplicate atom index (%d) in %s", aa[i], dir2str(d));
+ auto message = gmx::formatString(
+ "Duplicate atom index (%d) in %s", aa[i], enumValueToString(d));
warning_error(wi, message);
}
}
else
{
/* This is essentially the same check as in default_cmap_params() done one more time */
- auto message = gmx::formatString(
- "Unable to assign a cmap type to torsion %d %d %d %d and %d\n", param.ai() + 1,
- param.aj() + 1, param.ak() + 1, param.al() + 1, param.am() + 1);
+ auto message =
+ gmx::formatString("Unable to assign a cmap type to torsion %d %d %d %d and %d\n",
+ param.ai() + 1,
+ param.aj() + 1,
+ param.ak() + 1,
+ param.al() + 1,
+ param.am() + 1);
warning_error_and_exit(wi, message, FARGS);
}
}
ptr += n;
if (ret == 0)
{
- auto message = gmx::formatString("Expected an atom index in section \"%s\"", dir2str(d));
+ auto message =
+ gmx::formatString("Expected an atom index in section \"%s\"", enumValueToString(d));
warning_error_and_exit(wi, message, FARGS);
}
auto message = gmx::formatString(
"No weight or negative weight found for vsiten "
"constructing atom %d (atom index %d)",
- nj + 1, atc[nj] + 1);
+ nj + 1,
+ atc[nj] + 1);
warning_error_and_exit(wi, message, FARGS);
}
break;
if (nj == 0)
{
- auto message =
- gmx::formatString("Expected more than one atom index in section \"%s\"", dir2str(d));
+ auto message = gmx::formatString("Expected more than one atom index in section \"%s\"",
+ enumValueToString(d));
warning_error_and_exit(wi, message, FARGS);
}
"For moleculetype '%s' in [ system ] %d case insensitive "
"matches, but %d case sensitive matches were found. Check "
"the case of the characters in the moleculetypes.",
- type, nrci, nrcs);
+ type,
+ nrci,
+ nrcs);
warning_error_and_exit(wi, message, FARGS);
}
if (nrci == 1)
/* Type for decoupled atoms could be anything,
* this should be changed automatically later when required.
*/
- atom.ptype = eptAtom;
+ atom.ptype = ParticleType::Atom;
std::array<real, MAXFORCEPARAM> forceParam = { 0.0 };
nr = at->addType(symtab, atom, "decoupled", InteractionOfType({}, forceParam, ""), -1, 0);
for (const auto& param : paramp1)
{
- std::vector<real> forceParam = { fudgeQQ, atoms->atom[param.ai()].q,
- atoms->atom[param.aj()].q, param.c0(), param.c1() };
+ std::vector<real> forceParam = {
+ fudgeQQ, atoms->atom[param.ai()].q, atoms->atom[param.aj()].q, param.c0(), param.c1()
+ };
paramnew.emplace_back(InteractionOfType(param.atoms(), forceParam, ""));
}
}
std::vector<int> atoms = { i, j };
std::vector<real> forceParam = {
- atom[i].q, atom[j].q, nbp->interactionTypes[ntype * atom[i].type + atom[j].type].c0(),
+ atom[i].q,
+ atom[j].q,
+ nbp->interactionTypes[ntype * atom[i].type + atom[j].type].c0(),
nbp->interactionTypes[ntype * atom[i].type + atom[j].type].c1()
};
add_param_to_list(&mol->interactions[F_LJC_PAIRS_NB], InteractionOfType(atoms, forceParam));
"charges and/or atom types set in the topology file as well "
"as through the mdp option '%s'. You can not use both "
"these methods simultaneously.",
- i + 1, mol_name, "couple-moltype");
+ i + 1,
+ mol_name,
+ "couple-moltype");
warning_error_and_exit(wi, message, FARGS);
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct InteractionsOfType;
struct PreprocessResidue;
struct warninp;
-
+enum class CombinationRule : int;
namespace gmx
{
template<typename>
struct ExclusionBlock;
} // namespace gmx
-void generate_nbparams(int comb, int funct, InteractionsOfType* plist, PreprocessingAtomTypes* atype, warninp* wi);
+void generate_nbparams(CombinationRule comb,
+ int funct,
+ InteractionsOfType* plist,
+ PreprocessingAtomTypes* atype,
+ warninp* wi);
void push_at(struct t_symtab* symtab,
PreprocessingAtomTypes* at,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxpreprocess/toppush.h"
#include "gromacs/gmxpreprocess/toputil.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/logger.h"
#ifdef DEBUG
GMX_LOG(logger.info)
.asParagraph()
- .appendTextFormatted("Angle: %d-%d-%d", ang->ai(),
- ang->aj(), ang->ak());
+ .appendTextFormatted(
+ "Angle: %d-%d-%d", ang->ai(), ang->aj(), ang->ak());
#endif
int numhydrogens = count_hydrogens(info, 3, ang->atoms());
if ((nshake == eshALLANGLES) || (numhydrogens > 1)
}
if (bFound)
{
- real param = std::sqrt(b_ij * b_ij + b_jk * b_jk
- - 2.0 * b_ij * b_jk
- * cos(DEG2RAD * ang->c0()));
+ real param = std::sqrt(
+ b_ij * b_ij + b_jk * b_jk
+ - 2.0 * b_ij * b_jk * cos(gmx::c_deg2Rad * ang->c0()));
std::vector<real> forceParm = { param, param };
if (ftype == F_CONNBONDS || ftype_a == F_CONNBONDS)
{
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted("p: %d, q: %d, dist: %12.5e",
- atomNumbers[0], atomNumbers[1],
+ atomNumbers[0],
+ atomNumbers[1],
forceParm[0]);
#endif
add_param_to_list(&(plist[F_CONSTR]),
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2012,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "gromacs/utility/strconvert.h"
#include "toputil.h"
#include <climits>
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
/* UTILITIES */
nrfp = NRFP(ftype);
/* header */
- fprintf(out, "[ %s ]\n", dir2str(d));
+ fprintf(out, "[ %s ]\n", enumValueToString(d));
fprintf(out, "; ");
if (!bDih)
{
{
for (int j = 0; (j < nral); j++)
{
- fprintf(out, "%5s ", at->atomNameFromAtomType(atoms[j]));
+ fprintf(out, "%5s ", *at->atomNameFromAtomType(atoms[j]));
}
}
else
{
for (int j = 0; (j < 2); j++)
{
- fprintf(out, "%5s ", at->atomNameFromAtomType(atoms[dihp[f][j]]));
+ fprintf(out, "%5s ", *at->atomNameFromAtomType(atoms[dihp[f][j]]));
}
}
fprintf(out, "%5d ", bSwapParity ? -f - 1 : f + 1);
if (have_excl)
{
- fprintf(out, "[ %s ]\n", dir2str(Directive::d_exclusions));
+ fprintf(out, "[ %s ]\n", enumValueToString(Directive::d_exclusions));
fprintf(out, "; %4s %s\n", "i", "excluded from i");
for (i = 0; i < natoms; i++)
{
int i, ri;
int tpA, tpB;
const char* as;
- const char *tpnmA, *tpnmB;
double qres, qtot;
- as = dir2str(Directive::d_atoms);
+ as = enumValueToString(Directive::d_atoms);
fprintf(out, "[ %s ]\n", as);
- fprintf(out, "; %4s %10s %6s %7s%6s %6s %10s %10s %6s %10s %10s\n", "nr", "type", "resnr",
- "residue", "atom", "cgnr", "charge", "mass", "typeB", "chargeB", "massB");
+ fprintf(out,
+ "; %4s %10s %6s %7s%6s %6s %10s %10s %6s %10s %10s\n",
+ "nr",
+ "type",
+ "resnr",
+ "residue",
+ "atom",
+ "cgnr",
+ "charge",
+ "mass",
+ "typeB",
+ "chargeB",
+ "massB");
qtot = 0;
if ((i == 0 || ri != at->atom[i - 1].resind) && at->resinfo[ri].rtp != nullptr)
{
qres = get_residue_charge(at, i);
- fprintf(out, "; residue %3d %-3s rtp %-4s q ", at->resinfo[ri].nr,
- *at->resinfo[ri].name, *at->resinfo[ri].rtp);
+ fprintf(out,
+ "; residue %3d %-3s rtp %-4s q ",
+ at->resinfo[ri].nr,
+ *at->resinfo[ri].name,
+ *at->resinfo[ri].rtp);
if (fabs(qres) < 0.001)
{
fprintf(out, " %s", "0.0");
}
fprintf(out, "\n");
}
- tpA = at->atom[i].type;
- if ((tpnmA = atype->atomNameFromAtomType(tpA)) == nullptr)
+ tpA = at->atom[i].type;
+ auto tpnmA = atype->atomNameFromAtomType(tpA);
+ if (!tpnmA.has_value())
{
gmx_fatal(FARGS, "tpA = %d, i= %d in print_atoms", tpA, i);
}
/* This is true by construction, but static analysers don't know */
GMX_ASSERT(!bRTPresname || at->resinfo[at->atom[i].resind].rtp,
"-rtpres did not have residue name available");
- fprintf(out, "%6d %10s %6d%c %5s %6s %6d %10g %10g", i + 1, tpnmA, at->resinfo[ri].nr,
+ fprintf(out,
+ "%6d %10s %6d%c %5s %6s %6d %10g %10g",
+ i + 1,
+ *tpnmA,
+ at->resinfo[ri].nr,
at->resinfo[ri].ic,
bRTPresname ? *(at->resinfo[at->atom[i].resind].rtp)
: *(at->resinfo[at->atom[i].resind].name),
- *(at->atomname[i]), cgnr[i], at->atom[i].q, at->atom[i].m);
+ *(at->atomname[i]),
+ cgnr[i],
+ at->atom[i].q,
+ at->atom[i].m);
if (PERTURBED(at->atom[i]))
{
- tpB = at->atom[i].typeB;
- if ((tpnmB = atype->atomNameFromAtomType(tpB)) == nullptr)
+ tpB = at->atom[i].typeB;
+ auto tpnmB = atype->atomNameFromAtomType(tpB);
+ if (!tpnmB.has_value())
{
gmx_fatal(FARGS, "tpB = %d, i= %d in print_atoms", tpB, i);
}
- fprintf(out, " %6s %10g %10g", tpnmB, at->atom[i].qB, at->atom[i].mB);
+ fprintf(out, " %6s %10g %10g", *tpnmB, at->atom[i].qB, at->atom[i].mB);
}
// Accumulate the total charge to help troubleshoot issues.
qtot += static_cast<double>(at->atom[i].q);
open_symtab(&stab);
for (int i = 0; (i < natoms); i++)
{
- char buf[12];
- sprintf(buf, "%4d", (i + 1));
- atype.addType(&stab, *a, buf, InteractionOfType({}, {}), 0, 0);
+ std::string name = gmx::toString(i + 1);
+ atype.addType(&stab, *a, name, InteractionOfType({}, {}), 0, 0);
}
print_bt(out, d, &atype, ftype, fsubtype, plist, TRUE);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "vsite_parm.h"
+#include <array>
#include <cmath>
#include <cstdio>
#include <cstring>
#include "gromacs/gmxpreprocess/toputil.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/topology/ifunc.h"
{
GMX_RELEASE_ASSERT(atomIndex.size() <= atomIndex_.size(),
"Cannot add more atom indices than maximum number");
- auto atomIndexIt = atomIndex_.begin();
+ std::array<int, 4>::iterator atomIndexIt = atomIndex_.begin();
for (const auto index : atomIndex)
{
*atomIndexIt++ = index;
AllVsiteBondedInteractions allVsiteBondeds;
for (int k = 0; k < nrat; k++)
{
- for (auto& vsite : at2vb[atoms[k]].vSiteBondedParameters)
+ for (const auto& vsite : at2vb[atoms[k]].vSiteBondedParameters)
{
int ftype = vsite.ftype_;
const InteractionOfType& type = vsite.vsiteInteraction_;
fprintf(fp, "angles:");
for (const auto& angle : angles)
{
- fprintf(fp, " %d-%d-%d (%g)", angle.ai() + 1, angle.aj() + 1, angle.ak() + 1,
- angle.parameterValue());
+ fprintf(fp, " %d-%d-%d (%g)", angle.ai() + 1, angle.aj() + 1, angle.ak() + 1, angle.parameterValue());
}
fprintf(fp, "\n");
}
fprintf(fp, "idihs:");
for (const auto& idih : idihs)
{
- fprintf(fp, " %d-%d-%d-%d (%g)", idih.ai() + 1, idih.aj() + 1, idih.ak() + 1,
- idih.al() + 1, idih.parameterValue());
+ fprintf(fp,
+ " %d-%d-%d-%d (%g)",
+ idih.ai() + 1,
+ idih.aj() + 1,
+ idih.ak() + 1,
+ idih.al() + 1,
+ idih.parameterValue());
}
fprintf(fp, "\n");
}
if (((ai == ang.ai()) && (aj == ang.aj()) && (ak == ang.ak()))
|| ((ai == ang.ak()) && (aj == ang.aj()) && (ak == ang.ai())))
{
- angle = DEG2RAD * ang.parameterValue();
+ angle = gmx::c_deg2Rad * ang.parameterValue();
break;
}
}
static const char* get_atomtype_name_AB(t_atom* atom, PreprocessingAtomTypes* atypes)
{
- const char* name = atypes->atomNameFromAtomType(atom->type);
+ const char* name = *atypes->atomNameFromAtomType(atom->type);
/* When using the decoupling option, atom types are changed
* to decoupled for the non-bonded interactions, but the virtual
*/
if (strcmp(name, "decoupled") == 0)
{
- name = atypes->atomNameFromAtomType(atom->typeB);
+ name = *atypes->atomNameFromAtomType(atom->typeB);
}
return name;
/* check if this is part of a NH3 , NH2-umbrella or CH3 group,
* i.e. if atom k and l are dummy masses (MNH* or MCH3*) */
bXH3 = ((gmx::equalCaseInsensitive(get_atomtype_name_AB(&at->atom[vsite->ak()], atypes), "MNH", 3))
- && (gmx::equalCaseInsensitive(get_atomtype_name_AB(&at->atom[vsite->al()], atypes),
- "MNH", 3)))
- || ((gmx::equalCaseInsensitive(get_atomtype_name_AB(&at->atom[vsite->ak()], atypes),
- "MCH3", 4))
- && (gmx::equalCaseInsensitive(get_atomtype_name_AB(&at->atom[vsite->al()], atypes),
- "MCH3", 4)));
+ && (gmx::equalCaseInsensitive(
+ get_atomtype_name_AB(&at->atom[vsite->al()], atypes), "MNH", 3)))
+ || ((gmx::equalCaseInsensitive(
+ get_atomtype_name_AB(&at->atom[vsite->ak()], atypes), "MCH3", 4))
+ && (gmx::equalCaseInsensitive(
+ get_atomtype_name_AB(&at->atom[vsite->al()], atypes), "MCH3", 4)));
bjk = get_bond_length(bonds, vsite->aj(), vsite->ak());
bjl = get_bond_length(bonds, vsite->aj(), vsite->al());
bError = (bij == NOTSET) || (aijk == NOTSET);
vsite->setForceParameter(1, bij);
- vsite->setForceParameter(0, RAD2DEG * aijk);
+ vsite->setForceParameter(0, gmx::c_rad2Deg * aijk);
if (bSwapParity)
{
/* check if this is part of a NH2-umbrella, NH3 or CH3 group,
* i.e. if atom k and l are dummy masses (MNH* or MCH3*) */
bXH3 = ((gmx::equalCaseInsensitive(get_atomtype_name_AB(&at->atom[vsite->ak()], atypes), "MNH", 3))
- && (gmx::equalCaseInsensitive(get_atomtype_name_AB(&at->atom[vsite->al()], atypes),
- "MNH", 3)))
- || ((gmx::equalCaseInsensitive(get_atomtype_name_AB(&at->atom[vsite->ak()], atypes),
- "MCH3", 4))
- && (gmx::equalCaseInsensitive(get_atomtype_name_AB(&at->atom[vsite->al()], atypes),
- "MCH3", 4)));
+ && (gmx::equalCaseInsensitive(
+ get_atomtype_name_AB(&at->atom[vsite->al()], atypes), "MNH", 3)))
+ || ((gmx::equalCaseInsensitive(
+ get_atomtype_name_AB(&at->atom[vsite->ak()], atypes), "MCH3", 4))
+ && (gmx::equalCaseInsensitive(
+ get_atomtype_name_AB(&at->atom[vsite->al()], atypes), "MCH3", 4)));
/* check if construction parity must be swapped */
bSwapParity = (vsite->c1() == -1);
dH = bCN - bNH * std::cos(aCNH);
rH = bNH * std::sin(aCNH);
/* we assume the H's are symmetrically distributed */
- rHx = rH * std::cos(DEG2RAD * 30);
- rHy = rH * std::sin(DEG2RAD * 30);
+ rHx = rH * std::cos(gmx::c_deg2Rad * 30);
+ rHy = rH * std::sin(gmx::c_deg2Rad * 30);
rM = 0.5 * bMM;
dM = std::sqrt(gmx::square(bCM) - gmx::square(rM));
a = 0.5 * ((dH / dM) - (rHy / rM));
.asParagraph()
.appendTextFormatted(
"virtual site %d: angle ijk = %f, angle ijl = %f, angle ijm = %f",
- vsite->ai() + 1, RAD2DEG * aijk, RAD2DEG * aijl, RAD2DEG * aijm);
+ vsite->ai() + 1,
+ gmx::c_rad2Deg * aijk,
+ gmx::c_rad2Deg * aijl,
+ gmx::c_rad2Deg * aijm);
gmx_fatal(FARGS,
"invalid construction in calc_vsite4fd for atom %d: "
"cosakl=%f, cosakm=%f\n",
- vsite->ai() + 1, cosakl, cosakm);
+ vsite->ai() + 1,
+ cosakl,
+ cosakm);
}
sinakl = std::sqrt(1 - gmx::square(cosakl));
sinakm = std::sqrt(1 - gmx::square(cosakm));
.asParagraph()
.appendTextFormatted(
"virtual site %d: angle ijk = %f, angle ijl = %f, angle ijm = %f",
- vsite->ai() + 1, RAD2DEG * aijk, RAD2DEG * aijl, RAD2DEG * aijm);
+ vsite->ai() + 1,
+ gmx::c_rad2Deg * aijk,
+ gmx::c_rad2Deg * aijl,
+ gmx::c_rad2Deg * aijm);
gmx_fatal(FARGS,
"invalid construction in calc_vsite4fdn for atom %d: "
"pl=%f, pm=%f\n",
- vsite->ai() + 1, pl, pm);
+ vsite->ai() + 1,
+ pl,
+ pm);
}
a = pk / pl;
fprintf(debug,
"Found %zu bonds, %zu angles and %zu idihs "
"for virtual site %d (%s)\n",
- allVsiteBondeds.bonds.size(), allVsiteBondeds.angles.size(),
- allVsiteBondeds.dihedrals.size(), param.ai() + 1,
+ allVsiteBondeds.bonds.size(),
+ allVsiteBondeds.angles.size(),
+ allVsiteBondeds.dihedrals.size(),
+ param.ai() + 1,
interaction_function[ftype].longname);
- print_bad(debug, allVsiteBondeds.bonds, allVsiteBondeds.angles,
+ print_bad(debug,
+ allVsiteBondeds.bonds,
+ allVsiteBondeds.angles,
allVsiteBondeds.dihedrals);
} /* debug */
switch (ftype)
{
case F_VSITE3:
- bERROR = calc_vsite3_param(atypes, ¶m, atoms, allVsiteBondeds.bonds,
- allVsiteBondeds.angles);
+ bERROR = calc_vsite3_param(
+ atypes, ¶m, atoms, allVsiteBondeds.bonds, allVsiteBondeds.angles);
break;
case F_VSITE3FD:
- bERROR = calc_vsite3fd_param(¶m, allVsiteBondeds.bonds,
- allVsiteBondeds.angles);
+ bERROR = calc_vsite3fd_param(
+ ¶m, allVsiteBondeds.bonds, allVsiteBondeds.angles);
break;
case F_VSITE3FAD:
- bERROR = calc_vsite3fad_param(¶m, allVsiteBondeds.bonds,
- allVsiteBondeds.angles);
+ bERROR = calc_vsite3fad_param(
+ ¶m, allVsiteBondeds.bonds, allVsiteBondeds.angles);
break;
case F_VSITE3OUT:
- bERROR = calc_vsite3out_param(atypes, ¶m, atoms, allVsiteBondeds.bonds,
- allVsiteBondeds.angles);
+ bERROR = calc_vsite3out_param(
+ atypes, ¶m, atoms, allVsiteBondeds.bonds, allVsiteBondeds.angles);
break;
case F_VSITE4FD:
- bERROR = calc_vsite4fd_param(¶m, allVsiteBondeds.bonds,
- allVsiteBondeds.angles, logger);
+ bERROR = calc_vsite4fd_param(
+ ¶m, allVsiteBondeds.bonds, allVsiteBondeds.angles, logger);
break;
case F_VSITE4FDN:
- bERROR = calc_vsite4fdn_param(¶m, allVsiteBondeds.bonds,
- allVsiteBondeds.angles, logger);
+ bERROR = calc_vsite4fdn_param(
+ ¶m, allVsiteBondeds.bonds, allVsiteBondeds.angles, logger);
break;
default:
gmx_fatal(FARGS,
"Automatic parameter generation not supported "
"for %s atom %d",
- interaction_function[ftype].longname, param.ai() + 1);
+ interaction_function[ftype].longname,
+ param.ai() + 1);
bERROR = TRUE;
} /* switch */
if (bERROR)
gmx_fatal(FARGS,
"Automatic parameter generation not supported "
"for %s atom %d for this bonding configuration",
- interaction_function[ftype].longname, param.ai() + 1);
+ interaction_function[ftype].longname,
+ param.ai() + 1);
}
} /* if bSet */
i++;
{
GMX_LOG(logger.info)
.asParagraph()
- .appendTextFormatted("doing %d %s virtual sites", (nrd / (nra + 1)),
+ .appendTextFormatted("doing %d %s virtual sites",
+ (nrd / (nra + 1)),
interaction_function[ftype].longname);
}
{
/* The virtual site */
int avsite = ia[i + 1];
- molt->atoms.atom[avsite].ptype = eptVSite;
+ molt->atoms.atom[avsite].ptype = ParticleType::VSite;
i += nra + 1;
}
.asParagraph()
.appendTextFormatted(
"ERROR: Cannot have constraint (%d-%d) with virtual site (%d)",
- param.ai() + 1, param.aj() + 1, atom + 1);
+ param.ai() + 1,
+ param.aj() + 1,
+ atom + 1);
n++;
}
}
if (interaction_function[ftype].flags & IF_CONSTRAINT)
{
for (auto entry = plist[ftype].interactionTypes.begin();
- (entry != plist[ftype].interactionTypes.end()) && !bPresent; entry++)
+ (entry != plist[ftype].interactionTypes.end()) && !bPresent;
+ entry++)
{
/* all constraints until one matches */
bPresent = (((entry->ai() == at1) && (entry->aj() == at2))
{
GMX_LOG(logger.info)
.asParagraph()
- .appendTextFormatted("Removed %4d %15ss with virtual sites, %zu left", nremoved,
- interaction_function[cftype].longname, ps->size());
+ .appendTextFormatted("Removed %4d %15ss with virtual sites, %zu left",
+ nremoved,
+ interaction_function[cftype].longname,
+ ps->size());
}
if (nconverted)
{
.asParagraph()
.appendTextFormatted(
"Converted %4d %15ss with virtual sites to connections, %zu left",
- nconverted, interaction_function[cftype].longname, ps->size());
+ nconverted,
+ interaction_function[cftype].longname,
+ ps->size());
}
if (nOut)
{
"bond-length\n"
" If the constructions were generated by pdb2gmx ignore "
"this warning",
- nOut, interaction_function[cftype].longname,
+ nOut,
+ interaction_function[cftype].longname,
interaction_function[F_VSITE3OUT].longname);
}
}
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted("Removed %4zu %15ss with virtual sites, %zu left",
- oldSize - ps->size(), interaction_function[cftype].longname,
+ oldSize - ps->size(),
+ interaction_function[cftype].longname,
ps->size());
}
}
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted("Removed %4zu %15ss with virtual sites, %zu left",
- oldSize - ps->size(), interaction_function[cftype].longname,
+ oldSize - ps->size(),
+ interaction_function[cftype].longname,
ps->size());
}
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int ai = angle.ai();
int aj = angle.aj();
int ak = angle.ak();
- real th = RAD2DEG
+ real th = gmx::c_rad2Deg
* bond_angle(x[ai], x[aj], x[ak], bPBC ? &pbc : nullptr, r_ij, r_kj, &costh, &t1, &t2);
angle.setForceParameter(0, th);
}
int aj = dihedral.aj();
int ak = dihedral.ak();
int al = dihedral.al();
- real ph = RAD2DEG
- * dih_angle(x[ai], x[aj], x[ak], x[al], bPBC ? &pbc : nullptr, r_ij, r_kj, r_kl,
- m, n, &t1, &t2, &t3);
+ real ph =
+ gmx::c_rad2Deg
+ * dih_angle(x[ai], x[aj], x[ak], x[al], bPBC ? &pbc : nullptr, r_ij, r_kj, r_kl, m, n, &t1, &t2, &t3);
dihedral.setForceParameter(0, ph);
}
}
PreprocessingAtomTypes* atypes,
int cgnr[])
{
- FILE* fp;
- int i, tp;
- const char* tpnm;
+ FILE* fp;
+ int i, tp;
fp = gmx_fio_fopen(filenm, "w");
fprintf(fp, "; %s\n", title);
fprintf(fp, "[ atoms ]\n");
for (i = 0; (i < atoms->nr); i++)
{
- tp = atoms->atom[i].type;
- if ((tpnm = atypes->atomNameFromAtomType(tp)) == nullptr)
+ tp = atoms->atom[i].type;
+ auto tpnm = atypes->atomNameFromAtomType(tp);
+ if (!tpnm.has_value())
{
gmx_fatal(FARGS, "tp = %d, i = %d in print_rtp", tp, i);
}
- fprintf(fp, "%-8s %12s %8.4f %5d\n", *atoms->atomname[i], tpnm, atoms->atom[i].q, cgnr[i]);
+ fprintf(fp, "%-8s %12s %8.4f %5d\n", *atoms->atomname[i], *tpnm, atoms->atom[i].q, cgnr[i]);
}
print_pl(fp, plist, F_BONDS, "bonds", atoms->atomname);
print_pl(fp, plist, F_ANGLES, "angles", atoms->atomname);
};
const char* bugs[] = {
"The atom type selection is primitive. Virtually no chemical knowledge is used",
- "Periodic boundary conditions screw up the bonding", "No improper dihedrals are generated",
+ "Periodic boundary conditions screw up the bonding",
+ "No improper dihedrals are generated",
"The atoms to atomtype translation table is incomplete ([TT]atomname2type.n2t[tt] file in",
"the data directory). Please extend it and send the results back to the GROMACS crew."
};
{ "-kp", FALSE, etREAL, { &kp }, "Dihedral angle force constant (kJ/mol/rad^2)" }
};
- if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa, asize(desc), desc,
- asize(bugs), bugs, &oenv))
+ if (!parse_common_args(
+ &argc, argv, 0, NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
/* Force field selection, interactive or direct */
- choose_ff(strcmp(ff, "select") == 0 ? nullptr : ff, forcefield, sizeof(forcefield), ffdir,
- sizeof(ffdir), logger);
+ choose_ff(strcmp(ff, "select") == 0 ? nullptr : ff, forcefield, sizeof(forcefield), ffdir, sizeof(ffdir), logger);
bOPLS = (strcmp(forcefield, "oplsaa") == 0);
.appendTextFormatted(
"There are %4zu %s dihedrals, %4zu impropers, %4zu angles\n"
" %4zu pairs, %4zu bonds and %4d atoms\n",
- plist[F_PDIHS].size(), bOPLS ? "Ryckaert-Bellemans" : "proper", plist[F_IDIHS].size(),
- plist[F_ANGLES].size(), plist[F_LJ14].size(), plist[F_BONDS].size(), atoms->nr);
+ plist[F_PDIHS].size(),
+ bOPLS ? "Ryckaert-Bellemans" : "proper",
+ plist[F_IDIHS].size(),
+ plist[F_ANGLES].size(),
+ plist[F_LJ14].size(),
+ plist[F_BONDS].size(),
+ atoms->nr);
calc_angles_dihs(&plist[F_ANGLES], &plist[F_PDIHS], x, bPBC, box);
fp = ftp2FILE(efTOP, NFILE, fnm, "w");
print_top_header(fp, ftp2fn(efTOP, NFILE, fnm), TRUE, ffdir, 1.0);
- write_top(fp, nullptr, mymol.name.c_str(), atoms, FALSE, bts, plist, excls, &atypes, cgnr,
+ write_top(fp,
+ nullptr,
+ mymol.name.c_str(),
+ atoms,
+ FALSE,
+ bts,
+ plist,
+ excls,
+ &atypes,
+ cgnr,
rtp_header_settings.nrexcl);
print_top_mols(fp, mymol.name.c_str(), ffdir, nullptr, {}, gmx::arrayRefFromArray(&mymol, 1));
}
if (na != 3)
{
- gmx_fatal(FARGS, "Expected a residue name and two atom names in file '%s', not '%s'",
- filename.c_str(), line);
+ gmx_fatal(FARGS,
+ "Expected a residue name and two atom names in file '%s', not '%s'",
+ filename.c_str(),
+ line);
}
srenew(xl, n + 1);
const char* ptr0 = xlatom[i].replace;
if (bVerbose)
{
- printf("Renaming atom '%s' in residue %d %s to '%s'\n", *atoms->atomname[a],
- atoms->resinfo[resind].nr, *atoms->resinfo[resind].name, ptr0);
+ printf("Renaming atom '%s' in residue %d %s to '%s'\n",
+ *atoms->atomname[a],
+ atoms->resinfo[resind].nr,
+ *atoms->resinfo[resind].name,
+ ptr0);
}
atoms->atomname[a] = put_symtab(symtab, ptr0);
bRenamed = TRUE;
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team.
+# Copyright (c) 2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# the incidence of textual clashes when adding/moving files that
# otherwise make the end of the list a hotspot.
+add_library(gpu_utils INTERFACE)
+
gmx_add_libgromacs_sources(
clfftinitializer.cpp
device_stream_manager.cpp
gmx_add_libgromacs_sources(
device_context_ocl.cpp
device_stream_ocl.cpp
+ pmalloc_ocl.cpp
ocl_compiler.cpp
ocl_caching.cpp
oclutils.cpp
device_stream.cu
gpu_utils.cu
pinning.cu
- pmalloc_cuda.cu
+ pmalloc.cu
)
_gmx_add_files_to_property(CUDA_SOURCES
device_stream_manager.cpp
- )
+ )
elseif(GMX_GPU_SYCL)
gmx_add_libgromacs_sources(
devicebuffer_sycl.cpp
device_context_sycl.cpp
device_stream_sycl.cpp
+ pmalloc_sycl.cpp
)
_gmx_add_files_to_property(SYCL_SOURCES
devicebuffer_sycl.cpp
device_context_sycl.cpp
device_stream_manager.cpp
device_stream_sycl.cpp
+ pmalloc_sycl.cpp
)
else()
gmx_add_libgromacs_sources(
)
endif()
+# Source files have the following private module dependencies.
+target_link_libraries(gpu_utils PRIVATE
+# gmxlib
+# math
+# mdtypes
+# tng_io
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(gpu_utils PUBLIC
+target_include_directories(gpu_utils INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(gpu_utils PUBLIC
+target_link_libraries(gpu_utils INTERFACE
+ legacy_api
+ )
+
+# TODO: when gpu_utils is an OBJECT target
+#target_link_libraries(gpu_utils PUBLIC legacy_api)
+#target_link_libraries(gpu_utils PRIVATE common)
+
+# Module dependencies
+# gpu_utils interfaces convey transitive dependence on these modules.
+#target_link_libraries(gpu_utils PUBLIC
+target_link_libraries(gpu_utils INTERFACE
+# utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(gpu_utils PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(gpu_utils PRIVATE legacy_modules)
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "config.h"
+#include <mutex>
+
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/exceptions.h"
-#include "gromacs/utility/mutex.h"
#include "gromacs/utility/stringutil.h"
#if GMX_GPU_OPENCL
* initialize it more than once. */
//! @{
bool g_clfftInitialized = false;
-gmx::Mutex g_clfftMutex;
+std::mutex g_clfftMutex;
//! @}
#endif
ClfftInitializer::ClfftInitializer()
{
#if GMX_GPU_OPENCL
- gmx::lock_guard<gmx::Mutex> guard(g_clfftMutex);
+ std::lock_guard<std::mutex> guard(g_clfftMutex);
clfftSetupData fftSetup;
int initErrorCode = clfftInitSetupData(&fftSetup);
if (initErrorCode != 0)
ClfftInitializer::~ClfftInitializer()
{
#if GMX_GPU_OPENCL
- gmx::lock_guard<gmx::Mutex> guard(g_clfftMutex);
+ std::lock_guard<std::mutex> guard(g_clfftMutex);
if (g_clfftInitialized)
{
clfftTeardown();
*/
static inline std::string getDeviceErrorString(const cudaError_t deviceError)
{
- return formatString("CUDA error #%d (%s): %s.", deviceError, cudaGetErrorName(deviceError),
+ return formatString("CUDA error #%d (%s): %s.",
+ deviceError,
+ cudaGetErrorName(deviceError),
cudaGetErrorString(deviceError));
}
{
dim3 blockSize(config.blockSize[0], config.blockSize[1], config.blockSize[2]);
dim3 gridSize(config.gridSize[0], config.gridSize[1], config.gridSize[2]);
- cudaLaunchKernel((void*)kernel, gridSize, blockSize, const_cast<void**>(kernelArgs.data()),
- config.sharedMemorySize, deviceStream.stream());
+ cudaLaunchKernel((void*)kernel,
+ gridSize,
+ blockSize,
+ const_cast<void**>(kernelArgs.data()),
+ config.sharedMemorySize,
+ deviceStream.stream());
gmx::ensureNoPendingDeviceError("GPU kernel (" + std::string(kernelName)
+ ") failed to launch.");
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "config.h"
+#include <memory>
+
#if GMX_GPU_OPENCL
# include "gromacs/gpu_utils/gmxopencl.h"
#endif
#if GMX_GPU_SYCL
# include "gromacs/gpu_utils/gmxsycl.h"
#endif
+
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/hardware/device_management.h"
#include "gromacs/utility/classhelpers.h"
//! Constructor.
DeviceContext(const DeviceInformation& deviceInfo);
//! Destructor
+ // NOLINTNEXTLINE(performance-trivially-destructible)
~DeviceContext();
//! Get the associated device information
{
GMX_THROW(gmx::InternalError(gmx::formatString(
"Failed to create OpenCL context on device %s (OpenCL error ID %d).",
- deviceInfo.device_name, clError)));
+ deviceInfo.device_name,
+ clError)));
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "config.h"
+#include <memory>
+
#if GMX_GPU_CUDA
# include <cuda_runtime.h>
#elif GMX_GPU_SYCL
# include "gromacs/gpu_utils/gmxsycl.h"
#endif
+
#include "gromacs/utility/classhelpers.h"
struct DeviceInformation;
DeviceStream(const DeviceContext& deviceContext, DeviceStreamPriority priority, bool useTiming);
//! Destructor
+ // NOLINTNEXTLINE(performance-trivially-destructible)
~DeviceStream();
/*! \brief Check if the underlying stream is valid.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_GPU_UTILS_GPUSTREAMMANAGER_H
#define GMX_GPU_UTILS_GPUSTREAMMANAGER_H
+#include <memory>
#include <string>
-#include "gromacs/utility/classhelpers.h"
-
class DeviceContext;
struct DeviceInformation;
class DeviceStream;
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
{
GMX_THROW(gmx::InternalError(gmx::formatString(
"Failed to create OpenCL command queue on GPU %s (OpenCL error ID %d).",
- deviceInfo.device_name, clError)));
+ deviceInfo.device_name,
+ clError)));
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const bool deviceSupportsTiming = device.get_info<cl::sycl::info::device::queue_profiling>();
if (deviceSupportsTiming)
{
+#if (!GMX_SYCL_HIPSYCL)
+ /* Support for profiling and even the `::enable_profile` property is added in
+ * https://github.com/illuhad/hipSYCL/pull/428, which is not merged at the
+ * time of writing */
propertyList = cl::sycl::property::queue::enable_profiling();
+#endif
}
}
stream_ = cl::sycl::queue(deviceContext.context(), device, propertyList);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
switch (transferKind)
{
case GpuApiCallBehavior::Async:
- GMX_ASSERT(isHostMemoryPinned(hostBuffer),
- "Source host buffer was not pinned for CUDA");
- stat = cudaMemcpyAsync(*((ValueType**)buffer) + startingOffset, hostBuffer, bytes,
- cudaMemcpyHostToDevice, deviceStream.stream());
+ GMX_ASSERT(isHostMemoryPinned(hostBuffer), "Source host buffer was not pinned for CUDA");
+ stat = cudaMemcpyAsync(*((ValueType**)buffer) + startingOffset,
+ hostBuffer,
+ bytes,
+ cudaMemcpyHostToDevice,
+ deviceStream.stream());
GMX_RELEASE_ASSERT(
stat == cudaSuccess,
("Asynchronous H2D copy failed. " + gmx::getDeviceErrorString(stat)).c_str());
break;
case GpuApiCallBehavior::Sync:
- stat = cudaMemcpy(*((ValueType**)buffer) + startingOffset, hostBuffer, bytes,
- cudaMemcpyHostToDevice);
+ stat = cudaMemcpy(
+ *((ValueType**)buffer) + startingOffset, hostBuffer, bytes, cudaMemcpyHostToDevice);
GMX_RELEASE_ASSERT(
stat == cudaSuccess,
("Synchronous H2D copy failed. " + gmx::getDeviceErrorString(stat)).c_str());
case GpuApiCallBehavior::Async:
GMX_ASSERT(isHostMemoryPinned(hostBuffer),
"Destination host buffer was not pinned for CUDA");
- stat = cudaMemcpyAsync(hostBuffer, *((ValueType**)buffer) + startingOffset, bytes,
- cudaMemcpyDeviceToHost, deviceStream.stream());
+ stat = cudaMemcpyAsync(hostBuffer,
+ *((ValueType**)buffer) + startingOffset,
+ bytes,
+ cudaMemcpyDeviceToHost,
+ deviceStream.stream());
GMX_RELEASE_ASSERT(
stat == cudaSuccess,
("Asynchronous D2H copy failed. " + gmx::getDeviceErrorString(stat)).c_str());
break;
case GpuApiCallBehavior::Sync:
- stat = cudaMemcpy(hostBuffer, *((ValueType**)buffer) + startingOffset, bytes,
- cudaMemcpyDeviceToHost);
+ stat = cudaMemcpy(
+ hostBuffer, *((ValueType**)buffer) + startingOffset, bytes, cudaMemcpyDeviceToHost);
GMX_RELEASE_ASSERT(
stat == cudaSuccess,
("Synchronous D2H copy failed. " + gmx::getDeviceErrorString(stat)).c_str());
}
}
+/*! \brief
+ * Performs the device-to-device data copy, synchronous or asynchronously on request.
+ *
+ * \tparam ValueType Raw value type of the \p buffer.
+ * \param[in,out] destinationDeviceBuffer Device-side buffer to copy to
+ * \param[in] sourceDeviceBuffer Device-side buffer to copy from
+ * \param[in] numValues Number of values to copy.
+ * \param[in] deviceStream GPU stream to perform asynchronous copy in.
+ * \param[in] transferKind Copy type: synchronous or asynchronous.
+ * \param[out] timingEvent A dummy pointer to the D2D copy timing event to be filled
+ * in. Not used in CUDA implementation.
+ */
+template<typename ValueType>
+void copyBetweenDeviceBuffers(DeviceBuffer<ValueType>* destinationDeviceBuffer,
+ DeviceBuffer<ValueType>* sourceDeviceBuffer,
+ size_t numValues,
+ const DeviceStream& deviceStream,
+ GpuApiCallBehavior transferKind,
+ CommandEvent* /*timingEvent*/)
+{
+ if (numValues == 0)
+ {
+ return;
+ }
+ GMX_ASSERT(destinationDeviceBuffer, "needs a destination buffer pointer");
+ GMX_ASSERT(sourceDeviceBuffer, "needs a source buffer pointer");
+
+ cudaError_t stat;
+ const size_t bytes = numValues * sizeof(ValueType);
+ switch (transferKind)
+ {
+ case GpuApiCallBehavior::Async:
+ stat = cudaMemcpyAsync(*destinationDeviceBuffer,
+ *sourceDeviceBuffer,
+ bytes,
+ cudaMemcpyDeviceToDevice,
+ deviceStream.stream());
+ GMX_RELEASE_ASSERT(
+ stat == cudaSuccess,
+ ("Asynchronous D2D copy failed. " + gmx::getDeviceErrorString(stat)).c_str());
+ break;
+
+ case GpuApiCallBehavior::Sync:
+ stat = cudaMemcpy(*destinationDeviceBuffer, *sourceDeviceBuffer, bytes, cudaMemcpyDeviceToDevice);
+ GMX_RELEASE_ASSERT(
+ stat == cudaSuccess,
+ ("Synchronous D2D copy failed. " + gmx::getDeviceErrorString(stat)).c_str());
+ break;
+
+ default: throw;
+ }
+}
+
/*! \brief
* Clears the device buffer asynchronously.
*
size_t numValues,
const DeviceStream& deviceStream)
{
+ if (numValues == 0)
+ {
+ return;
+ }
GMX_ASSERT(buffer, "needs a buffer pointer");
const size_t bytes = numValues * sizeof(ValueType);
const char pattern = 0;
- cudaError_t stat = cudaMemsetAsync(*((ValueType**)buffer) + startingOffset, pattern, bytes,
- deviceStream.stream());
+ cudaError_t stat = cudaMemsetAsync(
+ *((ValueType**)buffer) + startingOffset, pattern, bytes, deviceStream.stream());
GMX_RELEASE_ASSERT(stat == cudaSuccess,
("Couldn't clear the device buffer. " + gmx::getDeviceErrorString(stat)).c_str());
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_GPU_UTILS_DEVICEBUFFER_H
/*! \libinternal \file
- * \brief Implements the logic for handling of DeviceBuffer types in OpenCL/CUDA.
+ * \brief Implements the logic for handling of DeviceBuffer types in OpenCL, CUDA and SYCL.
+ *
* Can only be included on GPU build paths.
*
+ * Note that most of the buffer operations have an early return, if the requested operation
+ * size is zero. This allows for calling these functions with zero operation size even when
+ * the underlying buffers were not properly intialized.
+ *
* \author Aleksei Iupinov <a.yupinov@gmail.com>
*
* \inlibraryapi
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
GMX_ASSERT(buffer, "needs a buffer pointer");
void* hostPtr = nullptr;
cl_int clError;
- *buffer = clCreateBuffer(deviceContext.context(), CL_MEM_READ_WRITE,
- numValues * sizeof(ValueType), hostPtr, &clError);
+ *buffer = clCreateBuffer(
+ deviceContext.context(), CL_MEM_READ_WRITE, numValues * sizeof(ValueType), hostPtr, &clError);
GMX_RELEASE_ASSERT(clError == CL_SUCCESS,
- gmx::formatString("clCreateBuffer failure (OpenCL error %d: %s)", clError,
+ gmx::formatString("clCreateBuffer failure (OpenCL error %d: %s)",
+ clError,
ocl_get_error_string(clError).c_str())
.c_str());
}
cl_int clError = clReleaseMemObject(*buffer);
GMX_RELEASE_ASSERT(clError == CL_SUCCESS,
gmx::formatString("clReleaseMemObject failed (OpenCL error %d: %s)",
- clError, ocl_get_error_string(clError).c_str())
+ clError,
+ ocl_get_error_string(clError).c_str())
.c_str());
}
}
switch (transferKind)
{
case GpuApiCallBehavior::Async:
- clError = clEnqueueWriteBuffer(deviceStream.stream(), *buffer, CL_FALSE, offset, bytes,
- hostBuffer, 0, nullptr, timingEvent);
+ clError = clEnqueueWriteBuffer(
+ deviceStream.stream(), *buffer, CL_FALSE, offset, bytes, hostBuffer, 0, nullptr, timingEvent);
GMX_RELEASE_ASSERT(
clError == CL_SUCCESS,
- gmx::formatString("Asynchronous H2D copy failed (OpenCL error %d: %s)", clError,
+ gmx::formatString("Asynchronous H2D copy failed (OpenCL error %d: %s)",
+ clError,
ocl_get_error_string(clError).c_str())
.c_str());
break;
case GpuApiCallBehavior::Sync:
- clError = clEnqueueWriteBuffer(deviceStream.stream(), *buffer, CL_TRUE, offset, bytes,
- hostBuffer, 0, nullptr, timingEvent);
+ clError = clEnqueueWriteBuffer(
+ deviceStream.stream(), *buffer, CL_TRUE, offset, bytes, hostBuffer, 0, nullptr, timingEvent);
GMX_RELEASE_ASSERT(
clError == CL_SUCCESS,
- gmx::formatString("Synchronous H2D copy failed (OpenCL error %d: %s)", clError,
+ gmx::formatString("Synchronous H2D copy failed (OpenCL error %d: %s)",
+ clError,
ocl_get_error_string(clError).c_str())
.c_str());
break;
switch (transferKind)
{
case GpuApiCallBehavior::Async:
- clError = clEnqueueReadBuffer(deviceStream.stream(), *buffer, CL_FALSE, offset, bytes,
- hostBuffer, 0, nullptr, timingEvent);
+ clError = clEnqueueReadBuffer(
+ deviceStream.stream(), *buffer, CL_FALSE, offset, bytes, hostBuffer, 0, nullptr, timingEvent);
GMX_RELEASE_ASSERT(
clError == CL_SUCCESS,
- gmx::formatString("Asynchronous D2H copy failed (OpenCL error %d: %s)", clError,
+ gmx::formatString("Asynchronous D2H copy failed (OpenCL error %d: %s)",
+ clError,
ocl_get_error_string(clError).c_str())
.c_str());
break;
case GpuApiCallBehavior::Sync:
- clError = clEnqueueReadBuffer(deviceStream.stream(), *buffer, CL_TRUE, offset, bytes,
- hostBuffer, 0, nullptr, timingEvent);
+ clError = clEnqueueReadBuffer(
+ deviceStream.stream(), *buffer, CL_TRUE, offset, bytes, hostBuffer, 0, nullptr, timingEvent);
GMX_RELEASE_ASSERT(
clError == CL_SUCCESS,
- gmx::formatString("Synchronous D2H copy failed (OpenCL error %d: %s)", clError,
+ gmx::formatString("Synchronous D2H copy failed (OpenCL error %d: %s)",
+ clError,
ocl_get_error_string(clError).c_str())
.c_str());
break;
}
}
+/*! \brief
+ * Performs the device-to-device data copy, synchronous or asynchronously on request.
+ *
+ * \tparam ValueType Raw value type of the \p buffer.
+ */
+template<typename ValueType>
+void copyBetweenDeviceBuffers(DeviceBuffer<ValueType>* /* destinationDeviceBuffer */,
+ DeviceBuffer<ValueType>* /* sourceDeviceBuffer */,
+ size_t /* numValues */,
+ const DeviceStream& /* deviceStream */,
+ GpuApiCallBehavior /* transferKind */,
+ CommandEvent* /*timingEvent*/)
+{
+ // OpenCL-TODO
+ gmx_fatal(FARGS, "D2D copy stub was called. Not yet implemented in OpenCL.");
+}
+
/*! \brief
* Clears the device buffer asynchronously.
*
size_t numValues,
const DeviceStream& deviceStream)
{
+ if (numValues == 0)
+ {
+ return;
+ }
GMX_ASSERT(buffer, "needs a buffer pointer");
const size_t offset = startingOffset * sizeof(ValueType);
const size_t bytes = numValues * sizeof(ValueType);
const cl_uint numWaitEvents = 0;
const cl_event* waitEvents = nullptr;
cl_event commandEvent;
- cl_int clError = clEnqueueFillBuffer(deviceStream.stream(), *buffer, &pattern, sizeof(pattern),
- offset, bytes, numWaitEvents, waitEvents, &commandEvent);
+ cl_int clError = clEnqueueFillBuffer(
+ deviceStream.stream(), *buffer, &pattern, sizeof(pattern), offset, bytes, numWaitEvents, waitEvents, &commandEvent);
GMX_RELEASE_ASSERT(clError == CL_SUCCESS,
gmx::formatString("Couldn't clear the device buffer (OpenCL error %d: %s)",
- clError, ocl_get_error_string(clError).c_str())
+ clError,
+ ocl_get_error_string(clError).c_str())
.c_str());
}
cl_int clError;
*deviceBuffer = clCreateBuffer(deviceContext.context(),
CL_MEM_READ_ONLY | CL_MEM_HOST_WRITE_ONLY | CL_MEM_COPY_HOST_PTR,
- bytes, const_cast<ValueType*>(hostBuffer), &clError);
+ bytes,
+ const_cast<ValueType*>(hostBuffer),
+ &clError);
GMX_RELEASE_ASSERT(clError == CL_SUCCESS,
gmx::formatString("Constant memory allocation failed (OpenCL error %d: %s)",
- clError, ocl_get_error_string(clError).c_str())
+ clError,
+ ocl_get_error_string(clError).c_str())
.c_str());
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \inlibraryapi
*/
+#include <utility>
+
#include "gromacs/gpu_utils/device_context.h"
#include "gromacs/gpu_utils/device_stream.h"
#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/gpu_utils/gmxsycl.h"
#include "gromacs/gpu_utils/gpu_utils.h" //only for GpuApiCallBehavior
#include "gromacs/gpu_utils/gputraits_sycl.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/stringutil.h"
namespace gmx::internal
{
//! Shorthand alias to create a placeholder SYCL accessor with chosen data type and access mode.
-template<class T, enum cl::sycl::access::mode mode>
+template<class T, cl::sycl::access::mode mode>
using PlaceholderAccessor =
cl::sycl::accessor<T, 1, mode, cl::sycl::access::target::global_buffer, cl::sycl::access::placeholder::true_t>;
} // namespace gmx::internal
* \tparam T Type of buffer content.
* \tparam mode Access mode.
*/
-template<class T, enum cl::sycl::access::mode mode>
+template<class T, cl::sycl::access::mode mode>
class DeviceAccessor : public gmx::internal::PlaceholderAccessor<T, mode>
{
public:
gmx::internal::PlaceholderAccessor<T, mode>(getSyclBuffer(buffer))
{
}
+ //! Construct read-only Accessor from a const DeviceBuffer (must be initialized)
+ DeviceAccessor(const DeviceBuffer<T>& buffer) :
+ gmx::internal::PlaceholderAccessor<T, mode>(getSyclBuffer(const_cast<DeviceBuffer<T>&>(buffer)))
+ {
+ /* There were some discussions about making it possible to create read-only sycl::accessor
+ * from a const sycl::buffer (https://github.com/KhronosGroup/SYCL-Docs/issues/10), but
+ * it did not make it into the SYCL2020 standard. So, we have to use const_cast above */
+ /* Using static_assert to ensure that only mode::read accessors can be created from a
+ * const DeviceBuffer. static_assert provides better error messages than std::enable_if. */
+ static_assert(mode == cl::sycl::access::mode::read,
+ "Can not create non-read-only accessor from a const DeviceBuffer");
+ }
private:
//! Helper function to get sycl:buffer object from DeviceBuffer wrapper, with a sanity check.
* \tparam mode Access mode of the accessor
* \tparam enabled Compile-time flag indicating whether we want to actually create an accessor.
*/
-template<class T, enum cl::sycl::access::mode mode, bool enabled>
+template<class T, cl::sycl::access::mode mode, bool enabled>
using OptionalAccessor =
std::conditional_t<enabled, DeviceAccessor<T, mode>, gmx::internal::EmptyClassThatIgnoresConstructorArguments>;
}
}
+/*! \brief
+ * Performs the device-to-device data copy, synchronous or asynchronously on request.
+ *
+ * \tparam ValueType Raw value type of the \p buffer.
+ */
+template<typename ValueType>
+void copyBetweenDeviceBuffers(DeviceBuffer<ValueType>* /* destinationDeviceBuffer */,
+ DeviceBuffer<ValueType>* /* sourceDeviceBuffer */,
+ size_t /* numValues */,
+ const DeviceStream& /* deviceStream */,
+ GpuApiCallBehavior /* transferKind */,
+ CommandEvent* /*timingEvent*/)
+{
+ // SYCL-TODO
+ gmx_fatal(FARGS, "D2D copy stub was called. Not yet implemented in SYCL.");
+}
+
+
+namespace gmx::internal
+{
+/*! \brief Helper function to clear device buffer.
+ *
+ * Not applicable to GROMACS's float3 (a.k.a. gmx::RVec) and other custom types.
+ * From SYCL specs: "T must be a scalar value or a SYCL vector type."
+ */
+template<typename ValueType>
+cl::sycl::event fillSyclBufferWithNull(cl::sycl::buffer<ValueType, 1>& buffer,
+ size_t startingOffset,
+ size_t numValues,
+ cl::sycl::queue queue)
+{
+ using cl::sycl::access::mode;
+ const cl::sycl::range<1> range(numValues);
+ const cl::sycl::id<1> offset(startingOffset);
+ const ValueType pattern = ValueType(0); // SYCL vectors support initialization by scalar
+
+ return queue.submit([&](cl::sycl::handler& cgh) {
+ auto d_bufferAccessor =
+ cl::sycl::accessor<ValueType, 1, mode::discard_write>{ buffer, cgh, range, offset };
+ cgh.fill(d_bufferAccessor, pattern);
+ });
+}
+
+//! \brief Helper function to clear device buffer of type float3.
+template<>
+inline cl::sycl::event fillSyclBufferWithNull(cl::sycl::buffer<Float3, 1>& buffer,
+ size_t startingOffset,
+ size_t numValues,
+ cl::sycl::queue queue)
+{
+ cl::sycl::buffer<float, 1> bufferAsFloat = buffer.reinterpret<float, 1>(buffer.get_count() * DIM);
+ return fillSyclBufferWithNull<float>(
+ bufferAsFloat, startingOffset * DIM, numValues * DIM, std::move(queue));
+}
+} // namespace gmx::internal
+
/*! \brief
* Clears the device buffer asynchronously.
*
GMX_ASSERT(checkDeviceBuffer(*buffer, startingOffset + numValues),
"buffer too small or not initialized");
- const ValueType pattern{};
cl::sycl::buffer<ValueType>& syclBuffer = *(buffer->buffer_);
- cl::sycl::event ev = deviceStream.stream().submit([&](cl::sycl::handler& cgh) {
- auto d_bufferAccessor = cl::sycl::accessor<ValueType, 1, cl::sycl::access::mode::discard_write>{
- syclBuffer, cgh, cl::sycl::range(numValues), cl::sycl::id(startingOffset)
- };
- cgh.fill(d_bufferAccessor, pattern);
- });
+ gmx::internal::fillSyclBufferWithNull<ValueType>(
+ syclBuffer, startingOffset, numValues, deviceStream.stream());
}
/*! \brief Create a texture object for an array of type ValueType.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \brief
* Wraps the complexity of including SYCL in GROMACS.
*
- * SYCL headers use symbol DIM as a template parameter, which gets broken by macro DIM defined
+ * The __SYCL_COMPILER_VERSION macro is used to identify Intel DPCPP compiler.
+ * See https://github.com/intel/llvm/pull/2998 for better proposal.
+ *
+ * Intel SYCL headers use symbol DIM as a template parameter, which gets broken by macro DIM defined
* in gromacs/math/vectypes.h. Here, we include the SYCL header while temporary undefining this macro.
+ * See https://github.com/intel/llvm/issues/2981.
+ *
+ * Different compilers, at the time of writing, have different names for some of the proposed features
+ * of the SYCL2020 standard. For uniformity, they are all aliased in our custom sycl_2020 namespace.
*
* \inlibraryapi
*/
#ifndef GMX_GPU_UTILS_GMXSYCL_H
#define GMX_GPU_UTILS_GMXSYCL_H
+#include "config.h"
+
+/* Some versions of Intel ICPX compiler (at least 2021.1.1 and 2021.1.2) fail to unroll a loop
+ * in sycl::accessor::__init, and emit -Wpass-failed=transform-warning. This is a useful
+ * warning, but mostly noise right now. Probably related to using shared memory accessors.
+ * The unroll directive was introduced in https://github.com/intel/llvm/pull/2449. */
+#if GMX_SYCL_DPCPP
+# include <CL/sycl/version.hpp>
+# define DISABLE_UNROLL_WARNINGS \
+ ((__SYCL_COMPILER_VERSION >= 20201113) && (__SYCL_COMPILER_VERSION <= 20201214))
+#else
+# define DISABLE_UNROLL_WARNINGS 0
+#endif
+
+#if DISABLE_UNROLL_WARNINGS
+# pragma clang diagnostic push
+# pragma clang diagnostic ignored "-Wpass-failed"
+#endif
+
+// For hipSYCL, we need to activate floating-point atomics
+#if GMX_SYCL_HIPSYCL
+# define HIPSYCL_EXT_FP_ATOMICS
+# pragma clang diagnostic push
+# pragma clang diagnostic ignored "-Wunused-variable"
+# pragma clang diagnostic ignored "-Wunused-parameter"
+# pragma clang diagnostic ignored "-Wmissing-noreturn"
+# pragma clang diagnostic ignored "-Wshadow-field"
+# pragma clang diagnostic ignored "-Wctad-maybe-unsupported"
+# pragma clang diagnostic ignored "-Wdeprecated-copy-dtor"
+# pragma clang diagnostic ignored "-Winconsistent-missing-destructor-override"
+# pragma clang diagnostic ignored "-Wunused-template"
+# pragma clang diagnostic ignored "-Wsign-compare"
+# pragma clang diagnostic ignored "-Wundefined-reinterpret-cast"
+# pragma clang diagnostic ignored "-Wdeprecated-copy"
+# pragma clang diagnostic ignored "-Wnewline-eof"
+# pragma clang diagnostic ignored "-Wextra-semi"
+# pragma clang diagnostic ignored "-Wsuggest-override"
+# pragma clang diagnostic ignored "-Wsuggest-destructor-override"
+# pragma clang diagnostic ignored "-Wgcc-compat"
+#endif
+
#ifdef DIM
# if DIM != 3
# include <CL/sycl.hpp>
#endif
+#if DISABLE_UNROLL_WARNINGS
+# pragma clang diagnostic pop
+#endif
+
+#if GMX_SYCL_HIPSYCL
+# pragma clang diagnostic pop
+#endif
+
+#undef DISABLE_UNROLL_WARNINGS
+
+/* Exposing Intel-specific extensions in a manner compatible with SYCL2020 provisional spec.
+ * Despite ICPX (up to 2021.1.2 at the least) having SYCL_LANGUAGE_VERSION=202001,
+ * some parts of the spec are still in custom sycl::ONEAPI namespace (sycl::intel in beta versions),
+ * and some functions have different names. To make things easier to upgrade
+ * in the future, this thin layer is added.
+ * */
+namespace sycl_2020
+{
+namespace detail
+{
+#if GMX_SYCL_DPCPP
+// Confirmed to work for 2021.1-beta10 (20201005), 2021.1.1 (20201113), 2021.1.2 (20201214).
+namespace origin = cl::sycl::ONEAPI;
+#elif GMX_SYCL_HIPSYCL
+namespace origin = cl::sycl;
+#else
+# error "Unsupported version of SYCL compiler"
+#endif
+} // namespace detail
+
+using detail::origin::memory_order;
+using detail::origin::memory_scope;
+using detail::origin::plus;
+using detail::origin::sub_group;
+
+#if GMX_SYCL_DPCPP
+using detail::origin::atomic_ref;
+template<typename... Args>
+bool group_any_of(Args&&... args)
+{
+ return detail::origin::any_of(std::forward<Args>(args)...);
+}
+template<typename... Args>
+auto group_reduce(Args&&... args) -> decltype(detail::origin::reduce(std::forward<Args>(args)...))
+{
+ return detail::origin::reduce(std::forward<Args>(args)...);
+}
+#elif GMX_SYCL_HIPSYCL
+// No atomic_ref in hipSYCL yet (2021-02-22)
+using detail::origin::group_any_of;
+using detail::origin::group_reduce;
+#else
+# error "Unsupported SYCL compiler"
+#endif
+
+} // namespace sycl_2020
+
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018,2019, by the GROMACS development team.
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
# define OPENCL_FUNC_ARGUMENT REAL_FUNC_ARGUMENT
# define OPENCL_FUNC_TERM REAL_FUNC_TERM
# define OPENCL_FUNC_TERM_WITH_RETURN(arg) REAL_FUNC_TERM_WITH_RETURN(arg)
+# define SYCL_FUNC_QUALIFIER REAL_FUNC_QUALIFIER
+# define SYCL_FUNC_ARGUMENT REAL_FUNC_ARGUMENT
+# define SYCL_FUNC_TERM REAL_FUNC_TERM
+# define SYCL_FUNC_TERM_WITH_RETURN(arg) REAL_FUNC_TERM_WITH_RETURN(arg)
#else // Not DOXYGEN
/* GPU support is enabled, so these functions will have real code defined somewhere */
-# if GMX_GPU && !GMX_GPU_SYCL
+# if GMX_GPU
# define GPU_FUNC_QUALIFIER REAL_FUNC_QUALIFIER
# define GPU_FUNC_ARGUMENT REAL_FUNC_ARGUMENT
# define GPU_FUNC_TERM REAL_FUNC_TERM
# define GPU_FUNC_ARGUMENT NULL_FUNC_ARGUMENT
# define GPU_FUNC_TERM NULL_FUNC_TERM
# define GPU_FUNC_TERM_WITH_RETURN(arg) NULL_FUNC_TERM_WITH_RETURN(arg)
-#
# endif
/* Enable and disable platform-specific function implementations */
# define CUDA_FUNC_TERM_WITH_RETURN(arg) NULL_FUNC_TERM_WITH_RETURN(arg)
# endif
+# if GMX_GPU_SYCL
+# define SYCL_FUNC_QUALIFIER REAL_FUNC_QUALIFIER
+# define SYCL_FUNC_ARGUMENT REAL_FUNC_ARGUMENT
+# define SYCL_FUNC_TERM REAL_FUNC_TERM
+# define SYCL_FUNC_TERM_WITH_RETURN(arg) REAL_FUNC_TERM_WITH_RETURN(arg)
+# else
+# define SYCL_FUNC_QUALIFIER NULL_FUNC_QUALIFIER
+# define SYCL_FUNC_ARGUMENT NULL_FUNC_ARGUMENT
+# define SYCL_FUNC_TERM NULL_FUNC_TERM
+# define SYCL_FUNC_TERM_WITH_RETURN(arg) NULL_FUNC_TERM_WITH_RETURN(arg)
+# endif
+
#endif // ifdef DOXYGEN
#endif // GMX_GPU_UTILS_MACROS_H
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018,2019, by the GROMACS development team.
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "config.h"
-#include <cassert>
-
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/stringutil.h"
#ifdef _MSC_VER
# pragma warning(disable : 6237)
#endif
+const char* enumValueToString(GpuApiCallBehavior enumValue)
+{
+ static constexpr gmx::EnumerationArray<GpuApiCallBehavior, const char*> s_gpuApiCallBehaviorNames = {
+ "Synchronous", "Asynchronous"
+ };
+ return s_gpuApiCallBehaviorNames[enumValue];
+}
+
/*! \brief Help build a descriptive message in \c error if there are
* \c errorReasons why nonbondeds on a GPU are not supported.
*
{
errorReasons.emplace_back("non-GPU build of GROMACS");
}
- if (GMX_GPU_SYCL)
- {
- errorReasons.emplace_back("SYCL build of GROMACS");
- }
return addMessageIfNotSupported(errorReasons, error);
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2013,2014,2015,2016, The GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gpu_utils/cudautils.cuh"
#include "gromacs/gpu_utils/device_context.h"
#include "gromacs/gpu_utils/device_stream.h"
-#include "gromacs/gpu_utils/pmalloc_cuda.h"
#include "gromacs/hardware/device_information.h"
#include "gromacs/hardware/device_management.h"
#include "gromacs/utility/basedefinitions.h"
}
}
-/*! \brief Check status returned from peer access CUDA call, and error out or warn appropriately
+/*! \brief Check and act on status returned from peer access CUDA call
+ *
+ * If status is "cudaSuccess", we continue. If
+ * "cudaErrorPeerAccessAlreadyEnabled", then peer access has already
+ * been enabled so we ignore. If "cudaErrorInvalidDevice" then the
+ * run is trying to access an invalid GPU, so we throw an error. If
+ * "cudaErrorInvalidValue" then there is a problem with the arguments
+ * to the CUDA call, and we throw an error. These cover all expected
+ * statuses, but if any other is returned we issue a warning and
+ * continue.
+ *
* \param[in] stat CUDA call return status
* \param[in] gpuA ID for GPU initiating peer access call
* \param[in] gpuB ID for remote GPU
const gmx::MDLogger& mdlog,
const char* cudaCallName)
{
+
+ if (stat == cudaErrorPeerAccessAlreadyEnabled)
+ {
+ // Since peer access has already been enabled, this error can safely be ignored.
+ // Now clear the error internally within CUDA:
+ cudaGetLastError();
+ return;
+ }
if ((stat == cudaErrorInvalidDevice) || (stat == cudaErrorInvalidValue))
{
std::string errorString =
.appendTextFormatted(
"GPU peer access not enabled between GPUs %d and %d due to unexpected "
"return value from %s. %s",
- gpuA, gpuB, cudaCallName, gmx::getDeviceErrorString(stat).c_str());
+ gpuA,
+ gpuB,
+ cudaCallName,
+ gmx::getDeviceErrorString(stat).c_str());
+ // Clear the error internally within CUDA
+ cudaGetLastError();
}
}
.appendTextFormatted(
"GPU peer access not enabled due to unexpected return value from "
"cudaSetDevice(%d). %s",
- gpuA, gmx::getDeviceErrorString(stat).c_str());
+ gpuA,
+ gmx::getDeviceErrorString(stat).c_str());
return;
}
for (unsigned int j = 0; j < gpuIdsToUse.size(); j++)
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2010, The GROMACS development team.
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
//! Enum which is only used to describe transfer calls at the moment
-enum class GpuApiCallBehavior
+enum class GpuApiCallBehavior : int
{
+ //! Synchronous
Sync,
- Async
+ //! Asynchronous
+ Async,
+ //! Size of the enumeration
+ Count
};
+//! String corresponding to GPU API call behavior
+const char* enumValueToString(GpuApiCallBehavior enumValue);
+
//! Types of actions associated to waiting or checking the completion of GPU tasks
enum class GpuTaskCompletion
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
GMX_ASSERT(stat == cudaSuccess,
("cudaEventSynchronize failed. " + gmx::getDeviceErrorString(stat)).c_str());
}
+ /*! \brief Checks the completion of the underlying event and resets the object if it was. */
+ inline bool isReady()
+ {
+ cudaError_t gmx_used_in_debug stat = cudaEventQuery(event_);
+ GMX_ASSERT((stat == cudaSuccess) || (stat == cudaErrorNotReady),
+ ("cudaEventQuery failed. " + gmx::getDeviceErrorString(stat)).c_str());
+ return (stat == cudaSuccess);
+ }
/*! \brief Enqueues a wait for the recorded event in stream \p stream */
inline void enqueueWaitEvent(const DeviceStream& deviceStream)
{
GMX_ASSERT(stat == cudaSuccess,
("cudaStreamWaitEvent failed. " + gmx::getDeviceErrorString(stat)).c_str());
}
+ //! Reset the event (not needed in CUDA)
+ inline void reset() {}
private:
cudaEvent_t event_;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
+ ocl_get_error_string(clError)));
}
- releaseEvent();
+ reset();
+ }
+ /*! \brief Checks the completion of the underlying event and resets the object if it was. */
+ inline bool isReady()
+ {
+ cl_int result;
+ cl_int clError = clGetEventInfo(
+ event_, CL_EVENT_COMMAND_EXECUTION_STATUS, sizeof(cl_int), &result, nullptr);
+ if (CL_SUCCESS != clError)
+ {
+ GMX_THROW(gmx::InternalError("Failed to retrieve event info: " + ocl_get_error_string(clError)));
+ }
+ bool hasTriggered = (result == CL_COMPLETE);
+ if (hasTriggered)
+ {
+ reset();
+ }
+ return hasTriggered;
}
/*! \brief Enqueues a wait for the recorded event in stream \p stream
*
+ ocl_get_error_string(clError)));
}
- releaseEvent();
+ reset();
}
-private:
- inline void releaseEvent()
+ //! Reset (release) the event to unmarked state.
+ inline void reset()
{
cl_int clError = clReleaseEvent(event_);
if (CL_SUCCESS != clError)
event_ = nullptr;
}
+private:
cl_event event_;
};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
public:
//! A constructor.
- GpuEventSynchronizer() = default;
+ GpuEventSynchronizer()
+ {
+ doNotSynchronizeBetweenStreams_ = (std::getenv("GMX_GPU_SYCL_NO_SYNCHRONIZE") != nullptr);
+ }
//! A constructor from an existing event.
GpuEventSynchronizer(const cl::sycl::event& event) : event_(event) {}
//! A destructor.
*/
inline void markEvent(const DeviceStream& deviceStream)
{
+# if GMX_SYCL_HIPSYCL
+ deviceStream.stream().wait_and_throw(); // SYCL-TODO: Use CUDA/HIP-specific solutions
+# else
GMX_ASSERT(!event_.has_value(), "Do not call markEvent more than once!");
// Relies on SYCL_INTEL_enqueue_barrier
event_ = deviceStream.stream().submit_barrier();
+# endif
}
/*! \brief Synchronizes the host thread on the marked event.
* As in the OpenCL implementation, the event is released.
*/
inline void waitForEvent()
{
+# if (!GMX_SYCL_HIPSYCL)
event_->wait_and_throw();
+# endif
event_.reset();
}
+ /*! \brief Checks the completion of the underlying event and resets the object if it was. */
+ inline bool isReady()
+ {
+ auto info = event_->get_info<cl::sycl::info::event::command_execution_status>();
+ bool hasTriggered = (info == cl::sycl::info::event_command_status::complete);
+ if (hasTriggered)
+ {
+ event_.reset();
+ }
+ return hasTriggered;
+ }
/*! \brief Enqueues a wait for the recorded event in stream \p deviceStream.
* As in the OpenCL implementation, the event is released.
*/
inline void enqueueWaitEvent(const DeviceStream& deviceStream)
{
+ if (doNotSynchronizeBetweenStreams_)
+ {
+ event_.reset();
+ return;
+ }
+# if GMX_SYCL_HIPSYCL
+ deviceStream.stream().wait_and_throw(); // SYCL-TODO: Use CUDA/HIP-specific solutions
+# else
// Relies on SYCL_INTEL_enqueue_barrier
const std::vector<cl::sycl::event> waitlist{ event_.value() };
deviceStream.stream().submit_barrier(waitlist);
event_.reset();
+# endif
}
+ //! Reset the event to unmarked state.
+ inline void reset() { event_.reset(); }
+ //! Check if the event is marked. Needed for some workarounds for #3988
+ inline bool isMarked() const { return event_.has_value(); }
private:
std::optional<cl::sycl::event> event_ = std::nullopt;
+ /*! \brief Dev. setting to no-op enqueueWaitEvent
+ *
+ * In SYCL, dependencies between the GPU tasks are managed by the runtime, so manual
+ * synchronization between GPU streams should be redundant, but we keep it on by default.
+ *
+ * Setting this to \c true via \c GMX_GPU_SYCL_NO_SYNCHRONIZE environment variable will
+ * immediately return from \ref enqueueWaitEvent, without placing a barrier into the stream.
+ */
+ bool doNotSynchronizeBetweenStreams_;
};
#endif // !defined DOXYGEN
cl_ulong start_ns, end_ns;
cl_int gmx_unused cl_error;
- cl_error = clGetEventProfilingInfo(events_[i], CL_PROFILING_COMMAND_START,
- sizeof(cl_ulong), &start_ns, nullptr);
+ cl_error = clGetEventProfilingInfo(
+ events_[i], CL_PROFILING_COMMAND_START, sizeof(cl_ulong), &start_ns, nullptr);
GMX_ASSERT(CL_SUCCESS == cl_error,
gmx::formatString("GPU timing update failure (OpenCL error %d: %s).",
- cl_error, ocl_get_error_string(cl_error).c_str())
+ cl_error,
+ ocl_get_error_string(cl_error).c_str())
.c_str());
- cl_error = clGetEventProfilingInfo(events_[i], CL_PROFILING_COMMAND_END,
- sizeof(cl_ulong), &end_ns, nullptr);
+ cl_error = clGetEventProfilingInfo(
+ events_[i], CL_PROFILING_COMMAND_END, sizeof(cl_ulong), &end_ns, nullptr);
GMX_ASSERT(CL_SUCCESS == cl_error,
gmx::formatString("GPU timing update failure (OpenCL error %d: %s).",
- cl_error, ocl_get_error_string(cl_error).c_str())
+ cl_error,
+ ocl_get_error_string(cl_error).c_str())
.c_str());
milliseconds += (end_ns - start_ns) / 1000000.0;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \ingroup module_gpu_utils
*/
#include <cuda_runtime.h>
+#include "gromacs/math/vectypes.h"
//! Device texture for fast read-only data fetching
using DeviceTexture = cudaTextureObject_t;
//! \brief Single GPU call timing event - meaningless in CUDA
using CommandEvent = void;
+//! Convenience alias for 2-wide float
+using Float2 = float2;
+
+//! Convenience alias for 3-wide float
+using Float3 = gmx::RVec;
+
+//! Convenience alias for 4-wide float.
+using Float4 = float4;
+
/*! \internal \brief
* GPU kernels scheduling description. This is same in OpenCL/CUDA.
* Provides reasonable defaults, one typically only needs to set the GPU stream
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! \brief Single GPU call timing event
using CommandEvent = void*;
+// Stubs for CPU-only build. Might be changed in #3312.
+struct Float2
+{
+};
+struct Float3
+{
+};
+struct Float4
+{
+};
+
#endif // GMX_GPU
+namespace gmx
+{
+template<typename T>
+static inline Float3* asGenericFloat3Pointer(T* in)
+{
+ static_assert(sizeof(T) == sizeof(Float3),
+ "Size of the host-side data-type is different from the size of the generic "
+ "device-side counterpart.");
+ return reinterpret_cast<Float3*>(in);
+}
+
+template<typename T>
+static inline const Float3* asGenericFloat3Pointer(const T* in)
+{
+ static_assert(sizeof(T) == sizeof(Float3),
+ "Size of the host-side data-type is different from the size of the generic "
+ "device-side counterpart.");
+ return reinterpret_cast<const Float3*>(in);
+}
+
+template<typename C>
+static inline Float3* asGenericFloat3Pointer(C& in)
+{
+ static_assert(sizeof(*in.data()) == sizeof(Float3),
+ "Size of the host-side data-type is different from the size of the device-side "
+ "counterpart.");
+ return reinterpret_cast<Float3*>(in.data());
+}
+
+template<typename C>
+static inline const Float3* asGenericFloat3Pointer(const C& in)
+{
+ static_assert(sizeof(*in.data()) == sizeof(Float3),
+ "Size of the host-side data-type is different from the size of the device-side "
+ "counterpart.");
+ return reinterpret_cast<const Float3*>(in.data());
+}
+} // namespace gmx
+
#endif // GMX_GPU_UTILS_GPUTRAITS_H
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gromacs/gpu_utils/gmxopencl.h"
+#include "gromacs/math/vectypes.h"
using DeviceTexture = void*;
//! \brief Single GPU call timing event
using CommandEvent = cl_event;
+//! Convenience alias for 2-wide float
+using Float2 = cl_float2;
+
+//! Convenience alias for 3-wide float. Not using cl_float3 due to alignment issues.
+using Float3 = gmx::RVec;
+
+//! Convenience alias for 4-wide float.
+using Float4 = cl_float4;
+
/*! \internal \brief
* GPU kernels scheduling description. This is same in OpenCL/CUDA.
* Provides reasonable defaults, one typically only needs to set the GPU stream
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstddef>
#include "gromacs/gpu_utils/gmxsycl.h"
+#include "gromacs/math/vectypes.h"
using DeviceTexture = void*;
//! \brief Single GPU call timing event, not used with SYCL
using CommandEvent = void*;
+// TODO: Issue #3312
//! Convenience alias.
-using float4 = cl::sycl::float4;
-
+using Float4 = cl::sycl::float4;
//! Convenience alias. Not using cl::sycl::float3 due to alignment issues.
-using float3 = gmx::RVec;
-
+using Float3 = gmx::RVec;
//! Convenience alias for cl::sycl::float2
-using float2 = cl::sycl::float2;
+using Float2 = cl::sycl::float2;
/*! \internal \brief
* GPU kernels scheduling description. This is same in OpenCL/CUDA.
// assume that sizeof(char) is one byte.
std::array<char, 1024> deviceName;
size_t deviceNameLength;
- cl_int cl_error = clGetDeviceInfo(deviceId, CL_DEVICE_NAME, deviceName.size(),
- deviceName.data(), &deviceNameLength);
+ cl_int cl_error = clGetDeviceInfo(
+ deviceId, CL_DEVICE_NAME, deviceName.size(), deviceName.data(), &deviceNameLength);
if (cl_error != CL_SUCCESS)
{
GMX_THROW(InternalError(formatString("Could not get OpenCL device name, error was %s",
(symbols), by permitting only alphanumeric characters from the
current locale. We assume these work well enough in a
filename. */
- std::copy_if(deviceName.begin(), deviceName.begin() + deviceNameLength,
- std::back_inserter(cacheFilename), isalnum);
+ std::copy_if(deviceName.begin(),
+ deviceName.begin() + deviceNameLength,
+ std::back_inserter(cacheFilename),
+ isalnum);
cacheFilename += ".bin";
return cacheFilename;
/* Create program from pre-built binary */
cl_int cl_error;
- cl_program program = clCreateProgramWithBinary(context, 1, &deviceId, &fileSize,
- const_cast<const unsigned char**>(&binary),
- nullptr, &cl_error);
+ cl_program program = clCreateProgramWithBinary(
+ context, 1, &deviceId, &fileSize, const_cast<const unsigned char**>(&binary), nullptr, &cl_error);
if (cl_error != CL_SUCCESS)
{
GMX_THROW(InternalError("Could not create OpenCL program from the cache file " + filename
buildLogGuard.reset(buildLog);
/* Get the actual compilation log */
- cl_error = clGetProgramBuildInfo(program, deviceId, CL_PROGRAM_BUILD_LOG, buildLogSize,
- buildLog, nullptr);
+ cl_error = clGetProgramBuildInfo(
+ program, deviceId, CL_PROGRAM_BUILD_LOG, buildLogSize, buildLog, nullptr);
if (cl_error != CL_SUCCESS)
{
GMX_THROW(InternalError("Could not get OpenCL program build log, error was "
size_t getKernelWarpSize(cl_kernel kernel, cl_device_id deviceId)
{
size_t warpSize = 0;
- cl_int cl_error =
- clGetKernelWorkGroupInfo(kernel, deviceId, CL_KERNEL_PREFERRED_WORK_GROUP_SIZE_MULTIPLE,
- sizeof(warpSize), &warpSize, nullptr);
+ cl_int cl_error = clGetKernelWorkGroupInfo(
+ kernel, deviceId, CL_KERNEL_PREFERRED_WORK_GROUP_SIZE_MULTIPLE, sizeof(warpSize), &warpSize, nullptr);
if (cl_error != CL_SUCCESS)
{
GMX_THROW(InternalError("Could not query OpenCL preferred workgroup size, error was "
// Failing to read from the cache is not a critical error
formatExceptionMessageToFile(fplog, e);
}
- fprintf(fplog, "OpenCL binary cache file %s is present, will load kernels.\n",
+ fprintf(fplog,
+ "OpenCL binary cache file %s is present, will load kernels.\n",
cacheFilename.c_str());
}
else
/* Write log first, and then throw exception that the user know what is
the issue even if the build fails. */
- writeOclBuildLog(fplog, program, deviceId, kernelFilename, preprocessorOptions,
- buildStatus != CL_SUCCESS);
+ writeOclBuildLog(fplog, program, deviceId, kernelFilename, preprocessorOptions, buildStatus != CL_SUCCESS);
if (buildStatus != CL_SUCCESS)
{
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
#include "gromacs/gpu_utils/gpu_utils.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-/*! \brief \brief Allocates nbytes of host memory. Use ocl_free to free memory allocated with this function.
- *
- * \todo
- * This function should allocate page-locked memory to help reduce D2H and H2D
- * transfer times, similar with pmalloc from pmalloc_cuda.cu.
- *
- * \param[in,out] h_ptr Pointer where to store the address of the newly allocated buffer.
- * \param[in] nbytes Size in bytes of the buffer to be allocated.
- */
-void pmalloc(void** h_ptr, size_t nbytes)
-{
- /* Need a temporary type whose size is 1 byte, so that the
- * implementation of snew_aligned can cope without issuing
- * warnings. */
- char** temporary = reinterpret_cast<char**>(h_ptr);
-
- /* 16-byte alignment is required by the neighbour-searching code,
- * because it uses four-wide SIMD for bounding-box calculation.
- * However, when we organize using page-locked memory for
- * device-host transfers, it will probably need to be aligned to a
- * 4kb page, like CUDA does. */
- snew_aligned(*temporary, nbytes, 16);
-}
-
-/*! \brief Frees memory allocated with pmalloc.
- *
- * \param[in] h_ptr Buffer allocated with pmalloc that needs to be freed.
- */
-void pfree(void* h_ptr)
-{
-
- if (h_ptr)
- {
- sfree_aligned(h_ptr);
- }
-}
/*! \brief Convert error code to diagnostic string */
std::string ocl_get_error_string(cl_int error)
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
cl_program program;
};
-/*! \brief Allocate host memory in malloc style */
-void pmalloc(void** h_ptr, size_t nbytes);
-
-/*! \brief Free host memory in malloc style */
-void pfree(void* h_ptr);
-
/*! \brief Convert error code to diagnostic string */
std::string ocl_get_error_string(cl_int error);
{
globalWorkSize[i] = config.gridSize[i] * config.blockSize[i];
}
- cl_int clError = clEnqueueNDRangeKernel(deviceStream.stream(), kernel, workDimensions,
- globalWorkOffset, globalWorkSize, config.blockSize,
- waitListSize, waitList, timingEvent);
+ cl_int clError = clEnqueueNDRangeKernel(deviceStream.stream(),
+ kernel,
+ workDimensions,
+ globalWorkOffset,
+ globalWorkSize,
+ config.blockSize,
+ waitListSize,
+ waitList,
+ timingEvent);
if (CL_SUCCESS != clError)
{
const std::string errorMessage = "GPU kernel (" + std::string(kernelName)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gmxpre.h"
-#include "pmalloc_cuda.h"
+#include "pmalloc.h"
#include <stdlib.h>
CU_RET_ERR(stat, strbuf);
}
-/*! Allocates nbytes of page-locked memory with write-combining.
- * This memory should always be freed using pfree (or with the page-locked
- * free functions provied by the CUDA library).
- */
-void pmalloc_wc(void** h_ptr, size_t nbytes)
-{
- cudaError_t stat;
- char strbuf[STRLEN];
- int flag = cudaHostAllocDefault | cudaHostAllocWriteCombined;
-
- if (nbytes == 0)
- {
- *h_ptr = nullptr;
- return;
- }
-
- gmx::ensureNoPendingDeviceError("Could not allocate page-locked memory with write-combining.");
-
- stat = cudaMallocHost(h_ptr, nbytes, flag);
- sprintf(strbuf, "cudaMallocHost of size %d bytes failed", (int)nbytes);
- CU_RET_ERR(stat, strbuf);
-}
-
/*! Frees page locked memory allocated with pmalloc.
* This function can safely be called also with a pointer to a page-locked
* memory allocated directly with CUDA API calls.
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
/*! \libinternal \file
- * \brief Declare functions for host-side memory handling when using CUDA devices.
+ * \brief Declare functions for host-side memory handling.
*
* \author Szilard Pall <pall.szilard@gmail.com>
* \inlibraryapi
*/
-#ifndef GMX_GPU_UTILS_PMALLOC_CUDA_H
-#define GMX_GPU_UTILS_PMALLOC_CUDA_H
+#ifndef GMX_GPU_UTILS_PMALLOC_H
+#define GMX_GPU_UTILS_PMALLOC_H
#include <stdlib.h>
/*! \brief Allocates nbytes of page-locked memory. */
void pmalloc(void** h_ptr, size_t nbytes);
-/*! \brief Allocates nbytes of page-locked memory with write-combining. */
-void pmalloc_wc(void** h_ptr, size_t nbytes);
-
/*! \brief Frees page locked memory allocated with pmalloc. */
void pfree(void* h_ptr);
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2012,2014,2015,2018,2019,2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief Define functions for host-side memory handling when using OpenCL devices.
+ *
+ * \author Anca Hamuraru <anca@streamcomputing.eu>
+ */
+
+#include "gmxpre.h"
+
+#include "pmalloc.h"
+
+#include "gromacs/utility/smalloc.h"
+
+/*! \brief \brief Allocates nbytes of host memory. Use pfree to free memory allocated with this function.
+ *
+ * \todo
+ * This function should allocate page-locked memory to help reduce D2H and H2D
+ * transfer times, similar with pmalloc from pmalloc.cu.
+ *
+ * \param[in,out] h_ptr Pointer where to store the address of the newly allocated buffer.
+ * \param[in] nbytes Size in bytes of the buffer to be allocated.
+ */
+void pmalloc(void** h_ptr, size_t nbytes)
+{
+ /* Need a temporary type whose size is 1 byte, so that the
+ * implementation of snew_aligned can cope without issuing
+ * warnings. */
+ char** temporary = reinterpret_cast<char**>(h_ptr);
+
+ /* 16-byte alignment is required by the neighbour-searching code,
+ * because it uses four-wide SIMD for bounding-box calculation.
+ * However, when we organize using page-locked memory for
+ * device-host transfers, it will probably need to be aligned to a
+ * 4kb page, like CUDA does. */
+ snew_aligned(*temporary, nbytes, 16);
+}
+
+/*! \brief Frees memory allocated with pmalloc.
+ *
+ * \param[in] h_ptr Buffer allocated with pmalloc that needs to be freed.
+ */
+void pfree(void* h_ptr)
+{
+
+ if (h_ptr)
+ {
+ sfree_aligned(h_ptr);
+ }
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2012,2014,2015,2018,2019,2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief Define utility routines for SYCL
+ *
+ * \author Andrey Alekseenko <al42and@gmail.com>
+ */
+#include "gmxpre.h"
+
+#include "pmalloc.h"
+
+#include "gromacs/utility/smalloc.h"
+
+/*! \brief Allocates \p nbytes of host memory. Use \c pfree to free memory allocated with this function.
+ *
+ * \todo
+ * This function was copied from OpenCL implementation, not tuned for SYCL at all.
+ * Once SYCL2020 is out, might be worthwhile to look into USM and sycl::malloc_host / sycl::aligned_alloc_host.
+ * Overall, it is better to directly use sycl::buffer instead of pinned arrays. But this function
+ * is needed to compile some PME code with SYCL enabled, even if it is never used.
+ *
+ * \param[in,out] h_ptr Pointer where to store the address of the newly allocated buffer.
+ * \param[in] nbytes Size in bytes of the buffer to be allocated.
+ */
+void pmalloc(void** h_ptr, size_t nbytes)
+{
+ /* Need a temporary type whose size is 1 byte, so that the
+ * implementation of snew_aligned can cope without issuing
+ * warnings. */
+ auto** temporary = reinterpret_cast<std::byte**>(h_ptr);
+
+ /* 16-byte alignment inherited from OpenCL and does not sound unreasonable */
+ snew_aligned(*temporary, nbytes, 16);
+}
+
+/*! \brief Frees memory allocated with pmalloc.
+ *
+ * \param[in] h_ptr Buffer allocated with pmalloc that needs to be freed.
+ */
+void pfree(void* h_ptr)
+{
+ if (h_ptr)
+ {
+ sfree_aligned(h_ptr);
+ }
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef GMX_GPU_UTILS_SYCL_KERNEL_UTILS_H
+#define GMX_GPU_UTILS_SYCL_KERNEL_UTILS_H
+
+#include "gmxsycl.h"
+
+/*! \file
+ * \brief SYCL kernel helper functions.
+ *
+ * \author Andrey Alekseenko <al42and@gmail.com>
+ */
+
+/*! \brief Access mode to use for atomic accessors.
+ *
+ * Intel DPCPP compiler has \c sycl::atomic_ref, but has no \c sycl::atomic_fetch_add for floats.
+ * However, \c atomic_ref can not be constructed from \c sycl::atomic, so we can not use
+ * atomic accessors. Thus, we use \c mode::read_write accessors and \c atomic_ref.
+ *
+ * hipSYCL does not have \c sycl::atomic_ref, but has \c sycl::atomic_fetch_add for floats, which
+ * requires using atomic accessors. Thus, we use \c mode::atomic accessors.
+ *
+ * The \ref atomicFetchAdd function could be used for doing operations on such accessors.
+ */
+static constexpr auto mode_atomic = GMX_SYCL_DPCPP ? cl::sycl::access::mode::read_write :
+ /* GMX_SYCL_HIPSYCL */ cl::sycl::access::mode::atomic;
+
+/*! \brief Convenience wrapper to do atomic addition to a global buffer.
+ *
+ * The implementation differences between DPCPP and hipSYCL are explained in \ref mode_atomic.
+ */
+template<class IndexType>
+static inline void atomicFetchAdd(DeviceAccessor<float, mode_atomic> acc, const IndexType idx, const float val)
+{
+#if GMX_SYCL_DPCPP
+ sycl_2020::atomic_ref<float, sycl_2020::memory_order::relaxed, sycl_2020::memory_scope::device, cl::sycl::access::address_space::global_space>
+ fout_atomic(acc[idx]);
+ fout_atomic.fetch_add(val);
+#elif GMX_SYCL_HIPSYCL
+# ifdef SYCL_DEVICE_ONLY
+ /* While there is support for float atomics on device, the host implementation uses
+ * Clang's __atomic_fetch_add intrinsic, that, at least in Clang 11, does not support
+ * floats. Luckily, we don't want to run on host. */
+ acc[idx].fetch_add(val);
+# else
+ GMX_ASSERT(false, "hipSYCL host codepath not supported");
+ GMX_UNUSED_VALUE(val);
+ GMX_UNUSED_VALUE(acc);
+ GMX_UNUSED_VALUE(idx);
+# endif
+#endif
+}
+
+namespace sycl_2020
+{
+#if GMX_SYCL_HIPSYCL
+__device__ static inline float shift_left(sycl_2020::sub_group, float var, sycl_2020::sub_group::linear_id_type delta)
+{
+ // No sycl::sub_group::shift_left / shuffle_down in hipSYCL yet
+# ifdef SYCL_DEVICE_ONLY
+# if defined(HIPSYCL_PLATFORM_CUDA) && defined(__HIPSYCL_ENABLE_CUDA_TARGET__)
+ static const unsigned int sc_cudaFullWarpMask = 0xffffffff;
+ return __shfl_down_sync(sc_cudaFullWarpMask, var, delta);
+# elif defined(HIPSYCL_PLATFORM_ROCM) && defined(__HIPSYCL_ENABLE_HIP_TARGET__)
+ // Do we need more ifdefs? https://github.com/ROCm-Developer-Tools/HIP/issues/1491
+ return __shfl_down(var, delta);
+# else
+# error "Unsupported hipSYCL target"
+# endif
+# else
+ // Should never be called
+ GMX_UNUSED_VALUE(var);
+ GMX_UNUSED_VALUE(delta);
+ assert(false);
+ return NAN;
+# endif
+}
+__host__ static inline float shift_left(sycl_2020::sub_group, float, sycl_2020::sub_group::linear_id_type)
+{
+ // Should never be called
+ assert(false);
+ return NAN;
+}
+#elif GMX_SYCL_DPCPP
+static inline float shift_left(sycl_2020::sub_group sg, float var, sycl_2020::sub_group::linear_id_type delta)
+{
+ return sg.shuffle_down(var, delta);
+}
+#endif
+
+#if GMX_SYCL_HIPSYCL
+__device__ static inline float shift_right(sycl_2020::sub_group,
+ float var,
+ sycl_2020::sub_group::linear_id_type delta)
+{
+ // No sycl::sub_group::shift_right / shuffle_up in hipSYCL yet
+# ifdef SYCL_DEVICE_ONLY
+# if defined(HIPSYCL_PLATFORM_CUDA) && defined(__HIPSYCL_ENABLE_CUDA_TARGET__)
+ static const unsigned int sc_cudaFullWarpMask = 0xffffffff;
+ return __shfl_up_sync(sc_cudaFullWarpMask, var, delta);
+# elif defined(HIPSYCL_PLATFORM_ROCM) && defined(__HIPSYCL_ENABLE_HIP_TARGET__)
+ // Do we need more ifdefs? https://github.com/ROCm-Developer-Tools/HIP/issues/1491
+ return __shfl_up(var, delta);
+# else
+# error "Unsupported hipSYCL target"
+# endif
+# else
+ // Should never be called
+ assert(false);
+ GMX_UNUSED_VALUE(var);
+ GMX_UNUSED_VALUE(delta);
+ return NAN;
+# endif
+}
+__host__ static inline float shift_right(sycl_2020::sub_group, float, sycl_2020::sub_group::linear_id_type)
+{
+ // Should never be called
+ assert(false);
+ return NAN;
+}
+#elif GMX_SYCL_DPCPP
+static inline float shift_right(sycl_2020::sub_group sg, float var, sycl_2020::sub_group::linear_id_type delta)
+{
+ return sg.shuffle_up(var, delta);
+}
+#endif
+} // namespace sycl_2020
+
+#endif /* GMX_GPU_UTILS_SYCL_KERNEL_UTILS_H */
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief Declare utility routines for SYCL
+ *
+ * \author Andrey Alekseenko <al42and@gmail.com>
+ * \inlibraryapi
+ */
+#ifndef GMX_GPU_UTILS_SYCLUTILS_H
+#define GMX_GPU_UTILS_SYCLUTILS_H
+
+#include <string>
+
+#include "gromacs/gpu_utils/gmxsycl.h"
+#include "gromacs/gpu_utils/gputraits.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/stringutil.h"
+
+class DeviceStream;
+enum class GpuApiCallBehavior;
+
+/*! \internal
+ * \brief SYCL GPU runtime data
+ *
+ * The device runtime data is meant to hold objects associated with a GROMACS rank's
+ * (thread or process) use of a single device (multiple devices per rank is not
+ * implemented). These objects should be constructed at the point where a device
+ * gets assigned to a rank and released at when this assignment is no longer valid
+ * (i.e. at cleanup in the current implementation).
+ */
+struct gmx_device_runtime_data_t
+{
+};
+
+#ifndef DOXYGEN
+
+/* To properly mark function as [[noreturn]], we must do it everywhere it is declared, which
+ * will pollute common headers.*/
+# pragma clang diagnostic push
+# pragma clang diagnostic ignored "-Wmissing-noreturn"
+
+/*! \brief
+ * A wrapper function for setting up all the SYCL kernel arguments.
+ * Calls the recursive functions above.
+ *
+ * \tparam Args Types of all the kernel arguments
+ * \param[in] kernel Kernel function handle
+ * \param[in] config Kernel configuration for launching
+ * \param[in] argsPtrs Pointers to all the kernel arguments
+ * \returns A handle for the prepared parameter pack to be used with launchGpuKernel() as the last argument.
+ */
+template<typename... Args>
+void* prepareGpuKernelArguments(void* /*kernel*/, const KernelLaunchConfig& /*config*/, const Args*... /*argsPtrs*/)
+{
+ GMX_THROW(gmx::NotImplementedError("Not implemented on SYCL yet"));
+}
+
+/*! \brief Launches the SYCL kernel and handles the errors.
+ *
+ * \param[in] kernel Kernel function handle
+ * \param[in] config Kernel configuration for launching
+ * \param[in] deviceStream GPU stream to launch kernel in
+ * \param[in] timingEvent Timing event, fetched from GpuRegionTimer
+ * \param[in] kernelName Human readable kernel description, for error handling only
+ * \throws gmx::InternalError on kernel launch failure
+ */
+inline void launchGpuKernel(void* /*kernel*/,
+ const KernelLaunchConfig& /*config*/,
+ const DeviceStream& /*deviceStream*/,
+ CommandEvent* /*timingEvent*/,
+ const char* /*kernelName*/,
+ const void* /*kernelArgs*/)
+{
+ GMX_THROW(gmx::NotImplementedError("Not implemented on SYCL yet"));
+}
+
+/*! \brief Pretend to check a SYCL stream for unfinished work (dummy implementation).
+ *
+ * \returns Not implemented in SYCL.
+ */
+static inline bool haveStreamTasksCompleted(const DeviceStream& /* deviceStream */)
+{
+ GMX_THROW(gmx::NotImplementedError("Not implemented on SYCL yet"));
+}
+
+# pragma clang diagnostic pop
+
+#endif // !DOXYGEN
+
+#endif
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
# include "gromacs/gpu_utils/device_context.h"
# include "gromacs/gpu_utils/device_stream.h"
# include "gromacs/gpu_utils/devicebuffer.h"
+# include "gromacs/gpu_utils/hostallocator.h"
# include "testutils/test_hardware_environment.h"
# include "testutils/testasserts.h"
TYPED_TEST(DeviceBufferTest, CanCopyToAndFromDevice)
{
- for (const auto& testDevice : getTestHardwareEnvironment()->getTestDeviceList())
+ for (auto transferKind : { GpuApiCallBehavior::Sync, GpuApiCallBehavior::Async })
{
- const DeviceContext& deviceContext = testDevice->deviceContext();
- const DeviceStream& deviceStream = testDevice->deviceStream();
- setActiveDevice(testDevice->deviceInfo());
-
- DeviceBuffer<TypeParam> buffer;
- int numValues = 123;
- allocateDeviceBuffer(&buffer, numValues, deviceContext);
- std::vector<TypeParam> valuesIn(numValues);
- std::vector<TypeParam> valuesOut(numValues);
-
- std::iota(valuesIn.begin(), valuesIn.end(), c_initialValue<TypeParam>);
-
- copyToDeviceBuffer(&buffer, valuesIn.data(), 0, numValues, deviceStream,
- GpuApiCallBehavior::Sync, nullptr);
- copyFromDeviceBuffer(valuesOut.data(), &buffer, 0, numValues, deviceStream,
- GpuApiCallBehavior::Sync, nullptr);
- EXPECT_THAT(valuesOut, Pointwise(Eq(), valuesIn)) << "Changed after H2D and D2H copy.";
- freeDeviceBuffer(&buffer);
+ PinningPolicy pinningPolicy = (transferKind == GpuApiCallBehavior::Async)
+ ? PinningPolicy::PinnedIfSupported
+ : PinningPolicy::CannotBePinned;
+ for (const auto& testDevice : getTestHardwareEnvironment()->getTestDeviceList())
+ {
+ const DeviceContext& deviceContext = testDevice->deviceContext();
+ const DeviceStream& deviceStream = testDevice->deviceStream();
+ setActiveDevice(testDevice->deviceInfo());
+
+ DeviceBuffer<TypeParam> buffer;
+ int numValues = 123;
+ allocateDeviceBuffer(&buffer, numValues, deviceContext);
+ HostVector<TypeParam> valuesIn(numValues, { pinningPolicy });
+ HostVector<TypeParam> valuesOut(numValues, { pinningPolicy });
+
+ std::iota(valuesIn.begin(), valuesIn.end(), c_initialValue<TypeParam>);
+
+ copyToDeviceBuffer(&buffer, valuesIn.data(), 0, numValues, deviceStream, transferKind, nullptr);
+ copyFromDeviceBuffer(
+ valuesOut.data(), &buffer, 0, numValues, deviceStream, transferKind, nullptr);
+ if (transferKind == GpuApiCallBehavior::Async)
+ {
+ deviceStream.synchronize();
+ }
+ EXPECT_THAT(valuesOut, Pointwise(Eq(), valuesIn))
+ << "Changed after H2D and D2H " << enumValueToString(transferKind) << " copy.";
+ freeDeviceBuffer(&buffer);
+ }
}
}
TYPED_TEST(DeviceBufferTest, CanCopyToAndFromDeviceWithOffset)
{
- for (const auto& testDevice : getTestHardwareEnvironment()->getTestDeviceList())
+ for (auto transferKind : { GpuApiCallBehavior::Sync, GpuApiCallBehavior::Async })
{
- const DeviceContext& deviceContext = testDevice->deviceContext();
- const DeviceStream& deviceStream = testDevice->deviceStream();
- setActiveDevice(testDevice->deviceInfo());
+ PinningPolicy pinningPolicy = (transferKind == GpuApiCallBehavior::Async)
+ ? PinningPolicy::PinnedIfSupported
+ : PinningPolicy::CannotBePinned;
+ for (const auto& testDevice : getTestHardwareEnvironment()->getTestDeviceList())
+ {
+ const DeviceContext& deviceContext = testDevice->deviceContext();
+ const DeviceStream& deviceStream = testDevice->deviceStream();
+ setActiveDevice(testDevice->deviceInfo());
+
+ DeviceBuffer<TypeParam> buffer;
+ int numValues = 123;
+ allocateDeviceBuffer(&buffer, 2 * numValues, deviceContext);
+ HostVector<TypeParam> valuesIn(numValues, { pinningPolicy });
+ HostVector<TypeParam> valuesOut(2 * numValues, { pinningPolicy });
+
+ std::iota(valuesIn.begin(), valuesIn.end(), c_initialValue<TypeParam>);
+
+ // Fill the buffer with two copies of valuesIn, one after the other.
+ copyToDeviceBuffer(&buffer, valuesIn.data(), 0, numValues, deviceStream, transferKind, nullptr);
+ copyToDeviceBuffer(
+ &buffer, valuesIn.data(), numValues, numValues, deviceStream, transferKind, nullptr);
+ // Wait until GPU is done andd o the same copying on the CPU, so we can test it works correctly.
+ if (transferKind == GpuApiCallBehavior::Async)
+ {
+ deviceStream.synchronize();
+ }
+ valuesIn.insert(valuesIn.end(), valuesIn.begin(), valuesIn.end());
+
+ copyFromDeviceBuffer(
+ valuesOut.data(), &buffer, 0, 2 * numValues, deviceStream, transferKind, nullptr);
+ if (transferKind == GpuApiCallBehavior::Async)
+ {
+ deviceStream.synchronize();
+ }
+ EXPECT_THAT(valuesOut, Pointwise(Eq(), valuesIn))
+ << "Changed after H2D and D2H " << enumValueToString(transferKind) << " copy.";
+
+ SCOPED_TRACE("Checking the copy respects the output range");
+
+ // Remove the first element, and push another copy of the last
+ // element, so we can check that a copy of all of the data
+ // skipping the first element correctly over-writes exactly
+ // all but one of the old values.
+ valuesIn.erase(valuesIn.begin());
+ valuesIn.push_back(valuesIn.back());
+ copyFromDeviceBuffer(
+ valuesOut.data(), &buffer, 1, 2 * numValues - 1, deviceStream, transferKind, nullptr);
+ if (transferKind == GpuApiCallBehavior::Async)
+ {
+ deviceStream.synchronize();
+ }
+ EXPECT_THAT(valuesOut, Pointwise(Eq(), valuesIn))
+ << "Changed after H2D and D2H " << enumValueToString(transferKind) << " copy.";
+ }
+ }
+}
- DeviceBuffer<TypeParam> buffer;
- int numValues = 123;
- allocateDeviceBuffer(&buffer, 2 * numValues, deviceContext);
- std::vector<TypeParam> valuesIn(numValues);
- std::vector<TypeParam> valuesOut(2 * numValues);
-
- std::iota(valuesIn.begin(), valuesIn.end(), c_initialValue<TypeParam>);
-
- // Fill the buffer with two copies of valuesIn, one after the other.
- copyToDeviceBuffer(&buffer, valuesIn.data(), 0, numValues, deviceStream,
- GpuApiCallBehavior::Sync, nullptr);
- copyToDeviceBuffer(&buffer, valuesIn.data(), numValues, numValues, deviceStream,
- GpuApiCallBehavior::Sync, nullptr);
- // Do the same copying on the CPU, so we can test it works
- // correctly.
- valuesIn.insert(valuesIn.end(), valuesIn.begin(), valuesIn.end());
-
- copyFromDeviceBuffer(valuesOut.data(), &buffer, 0, 2 * numValues, deviceStream,
- GpuApiCallBehavior::Sync, nullptr);
- EXPECT_THAT(valuesOut, Pointwise(Eq(), valuesIn)) << "Changed after H2D and D2H copy.";
-
- SCOPED_TRACE("Checking the copy respects the output range");
-
- // Remove the first element, and push another copy of the last
- // element, so we can check that a copy of all of the data
- // skipping the first element correctly over-writes exactly
- // all but one of the old values.
- valuesIn.erase(valuesIn.begin());
- valuesIn.push_back(valuesIn.back());
- copyFromDeviceBuffer(valuesOut.data(), &buffer, 1, 2 * numValues - 1, deviceStream,
- GpuApiCallBehavior::Sync, nullptr);
- EXPECT_THAT(valuesOut, Pointwise(Eq(), valuesIn)) << "Changed after H2D and D2H copy.";
+# if GMX_GPU_CUDA
+
+TYPED_TEST(DeviceBufferTest, CanCopyBetweenDeviceBuffers)
+{
+ for (auto transferKind : { GpuApiCallBehavior::Sync, GpuApiCallBehavior::Async })
+ {
+ PinningPolicy pinningPolicy = (transferKind == GpuApiCallBehavior::Async)
+ ? PinningPolicy::PinnedIfSupported
+ : PinningPolicy::CannotBePinned;
+ for (const auto& testDeviceIn : getTestHardwareEnvironment()->getTestDeviceList())
+ {
+ for (const auto& testDeviceOut : getTestHardwareEnvironment()->getTestDeviceList())
+ {
+ int numValues = 321;
+ HostVector<TypeParam> valuesIn(numValues, { pinningPolicy });
+ HostVector<TypeParam> valuesOut(numValues, { pinningPolicy });
+
+ std::iota(valuesIn.begin(), valuesIn.end(), c_initialValue<TypeParam>);
+
+ const DeviceContext& deviceContextIn = testDeviceIn->deviceContext();
+ const DeviceStream& deviceStreamIn = testDeviceIn->deviceStream();
+ setActiveDevice(testDeviceIn->deviceInfo());
+ DeviceBuffer<TypeParam> bufferIn;
+ allocateDeviceBuffer(&bufferIn, numValues, deviceContextIn);
+
+ const DeviceContext& deviceContextOut = testDeviceOut->deviceContext();
+ const DeviceStream& deviceStreamOut = testDeviceOut->deviceStream();
+ setActiveDevice(testDeviceOut->deviceInfo());
+ DeviceBuffer<TypeParam> bufferOut;
+ allocateDeviceBuffer(&bufferOut, numValues, deviceContextOut);
+
+ copyToDeviceBuffer(
+ &bufferIn, valuesIn.data(), 0, numValues, deviceStreamIn, transferKind, nullptr);
+ copyBetweenDeviceBuffers(
+ &bufferOut, &bufferIn, numValues, deviceStreamIn, transferKind, nullptr);
+ if (transferKind == GpuApiCallBehavior::Async)
+ {
+ deviceStreamIn.synchronize();
+ }
+ copyFromDeviceBuffer(
+ valuesOut.data(), &bufferOut, 0, numValues, deviceStreamOut, transferKind, nullptr);
+ if (transferKind == GpuApiCallBehavior::Async)
+ {
+ deviceStreamOut.synchronize();
+ }
+ EXPECT_THAT(valuesOut, Pointwise(Eq(), valuesIn))
+ << "Changed after H2D, D2D and D2H " << enumValueToString(transferKind)
+ << " copy.";
+ freeDeviceBuffer(&bufferIn);
+ freeDeviceBuffer(&bufferOut);
+ }
+ }
}
}
+# endif // GMX_GPU_CUDA
+
} // namespace
} // namespace test
DeviceStreamManager manager(deviceInfo, havePpDomainDecomposition, simulationWork, useTiming);
expectValidStreams(&manager, { DeviceStreamType::NonBondedLocal });
- expectInvalidStreams(&manager, { DeviceStreamType::NonBondedNonLocal,
- DeviceStreamType::Pme, DeviceStreamType::PmePpTransfer,
- DeviceStreamType::UpdateAndConstraints });
+ expectInvalidStreams(&manager,
+ { DeviceStreamType::NonBondedNonLocal,
+ DeviceStreamType::Pme,
+ DeviceStreamType::PmePpTransfer,
+ DeviceStreamType::UpdateAndConstraints });
}
{
bool havePpDomainDecomposition = true;
DeviceStreamManager manager(deviceInfo, havePpDomainDecomposition, simulationWork, useTiming);
- expectValidStreams(&manager, { DeviceStreamType::NonBondedLocal,
- DeviceStreamType::NonBondedNonLocal });
- expectInvalidStreams(&manager, { DeviceStreamType::Pme, DeviceStreamType::PmePpTransfer,
- DeviceStreamType::UpdateAndConstraints });
+ expectValidStreams(
+ &manager, { DeviceStreamType::NonBondedLocal, DeviceStreamType::NonBondedNonLocal });
+ expectInvalidStreams(&manager,
+ { DeviceStreamType::Pme,
+ DeviceStreamType::PmePpTransfer,
+ DeviceStreamType::UpdateAndConstraints });
}
{
bool havePpDomainDecomposition = false;
DeviceStreamManager manager(deviceInfo, havePpDomainDecomposition, simulationWork, useTiming);
- expectValidStreams(&manager, { DeviceStreamType::Pme, DeviceStreamType::NonBondedLocal,
- DeviceStreamType::PmePpTransfer,
- DeviceStreamType::UpdateAndConstraints });
+ expectValidStreams(&manager,
+ { DeviceStreamType::Pme,
+ DeviceStreamType::NonBondedLocal,
+ DeviceStreamType::PmePpTransfer,
+ DeviceStreamType::UpdateAndConstraints });
expectInvalidStreams(&manager, { DeviceStreamType::NonBondedNonLocal });
}
bool havePpDomainDecomposition = true;
DeviceStreamManager manager(deviceInfo, havePpDomainDecomposition, simulationWork, useTiming);
- expectValidStreams(&manager, { DeviceStreamType::Pme, DeviceStreamType::NonBondedLocal,
- DeviceStreamType::NonBondedNonLocal, DeviceStreamType::PmePpTransfer,
- DeviceStreamType::UpdateAndConstraints });
+ expectValidStreams(&manager,
+ { DeviceStreamType::Pme,
+ DeviceStreamType::NonBondedLocal,
+ DeviceStreamType::NonBondedNonLocal,
+ DeviceStreamType::PmePpTransfer,
+ DeviceStreamType::UpdateAndConstraints });
}
{
bool havePpDomainDecomposition = false;
DeviceStreamManager manager(deviceInfo, havePpDomainDecomposition, simulationWork, useTiming);
- expectValidStreams(&manager, { DeviceStreamType::NonBondedLocal,
- DeviceStreamType::UpdateAndConstraints });
- expectInvalidStreams(&manager, { DeviceStreamType::NonBondedNonLocal,
- DeviceStreamType::Pme, DeviceStreamType::PmePpTransfer });
+ expectValidStreams(
+ &manager, { DeviceStreamType::NonBondedLocal, DeviceStreamType::UpdateAndConstraints });
+ expectInvalidStreams(&manager,
+ { DeviceStreamType::NonBondedNonLocal,
+ DeviceStreamType::Pme,
+ DeviceStreamType::PmePpTransfer });
}
{
bool havePpDomainDecomposition = true;
DeviceStreamManager manager(deviceInfo, havePpDomainDecomposition, simulationWork, useTiming);
- expectValidStreams(&manager, { DeviceStreamType::NonBondedLocal, DeviceStreamType::NonBondedNonLocal,
- DeviceStreamType::UpdateAndConstraints });
+ expectValidStreams(&manager,
+ { DeviceStreamType::NonBondedLocal,
+ DeviceStreamType::NonBondedNonLocal,
+ DeviceStreamType::UpdateAndConstraints });
expectInvalidStreams(&manager, { DeviceStreamType::Pme, DeviceStreamType::PmePpTransfer });
}
bool havePpDomainDecomposition = false;
DeviceStreamManager manager(deviceInfo, havePpDomainDecomposition, simulationWork, useTiming);
- expectValidStreams(&manager, { DeviceStreamType::Pme, DeviceStreamType::NonBondedLocal,
- DeviceStreamType::PmePpTransfer,
- DeviceStreamType::UpdateAndConstraints });
+ expectValidStreams(&manager,
+ { DeviceStreamType::Pme,
+ DeviceStreamType::NonBondedLocal,
+ DeviceStreamType::PmePpTransfer,
+ DeviceStreamType::UpdateAndConstraints });
expectInvalidStreams(&manager, { DeviceStreamType::NonBondedNonLocal });
}
bool havePpDomainDecomposition = true;
DeviceStreamManager manager(deviceInfo, havePpDomainDecomposition, simulationWork, useTiming);
- expectValidStreams(&manager, { DeviceStreamType::Pme, DeviceStreamType::NonBondedLocal,
- DeviceStreamType::NonBondedNonLocal, DeviceStreamType::PmePpTransfer,
- DeviceStreamType::UpdateAndConstraints });
+ expectValidStreams(&manager,
+ { DeviceStreamType::Pme,
+ DeviceStreamType::NonBondedLocal,
+ DeviceStreamType::NonBondedNonLocal,
+ DeviceStreamType::PmePpTransfer,
+ DeviceStreamType::UpdateAndConstraints });
}
}
}
{
if (status != CL_SUCCESS)
{
- GMX_THROW(InternalError(formatString("Failure while %s, error was %s", message,
- ocl_get_error_string(status).c_str())));
+ GMX_THROW(InternalError(formatString(
+ "Failure while %s, error was %s", message, ocl_get_error_string(status).c_str())));
}
}
auto devicePointer = clCreateBuffer(context, CL_MEM_READ_WRITE, input.size(), nullptr, &status);
throwUponFailure(status, "creating buffer");
- status = clEnqueueWriteBuffer(commandQueue, devicePointer, CL_TRUE, 0, input.size(),
- input.data(), 0, nullptr, nullptr);
+ status = clEnqueueWriteBuffer(
+ commandQueue, devicePointer, CL_TRUE, 0, input.size(), input.data(), 0, nullptr, nullptr);
throwUponFailure(status, "transferring host to device");
- status = clEnqueueReadBuffer(commandQueue, devicePointer, CL_TRUE, 0, output.size(),
- output.data(), 0, nullptr, nullptr);
+ status = clEnqueueReadBuffer(
+ commandQueue, devicePointer, CL_TRUE, 0, output.size(), output.data(), 0, nullptr, nullptr);
throwUponFailure(status, "transferring device to host");
status = clReleaseMemObject(devicePointer);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
# include "gromacs/gpu_utils/gpu_utils.h"
# include "gromacs/gpu_utils/hostallocator.h"
-# include "gromacs/gpu_utils/pmalloc_cuda.h"
+# include "gromacs/gpu_utils/pmalloc.h"
# include "gromacs/utility/real.h"
# include "gromacs/utility/smalloc.h"
DeviceBuffer<RVec> d_rVecInput;
allocateDeviceBuffer(&d_rVecInput, numElements, deviceContext);
- copyToDeviceBuffer(&d_rVecInput, h_rVecInput.data(), 0, numElements, deviceStream,
- GpuApiCallBehavior::Sync, nullptr);
+ copyToDeviceBuffer(
+ &d_rVecInput, h_rVecInput.data(), 0, numElements, deviceStream, GpuApiCallBehavior::Sync, nullptr);
DeviceBuffer<float3> d_float3Output;
allocateDeviceBuffer(&d_float3Output, numElements * DIM, deviceContext);
kernelLaunchConfig.sharedMemorySize = 0;
auto kernelPtr = convertRVecToFloat3OnDevice_kernel;
- const auto kernelArgs = prepareGpuKernelArguments(kernelPtr, kernelLaunchConfig,
- &d_float3Output, &d_rVecInput, &numElements);
- launchGpuKernel(kernelPtr, kernelLaunchConfig, deviceStream, nullptr,
- "convertRVecToFloat3OnDevice_kernel", kernelArgs);
-
- copyFromDeviceBuffer(h_float3Output.data(), &d_float3Output, 0, numElements, deviceStream,
- GpuApiCallBehavior::Sync, nullptr);
+ const auto kernelArgs = prepareGpuKernelArguments(
+ kernelPtr, kernelLaunchConfig, &d_float3Output, &d_rVecInput, &numElements);
+ launchGpuKernel(kernelPtr,
+ kernelLaunchConfig,
+ deviceStream,
+ nullptr,
+ "convertRVecToFloat3OnDevice_kernel",
+ kernelArgs);
+
+ copyFromDeviceBuffer(
+ h_float3Output.data(), &d_float3Output, 0, numElements, deviceStream, GpuApiCallBehavior::Sync, nullptr);
saveFloat3InRVecFormat(h_rVecOutput, h_float3Output.data(), numElements);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return reinterpret_cast<float3*>(in);
}
+/*! \brief Cast pointer RVec buffer to a pointer to float3 buffer.
+ *
+ * \param[in] in The Pointer to RVec buffer to cast.
+ *
+ * \returns Buffer pointer, casted to float3*.
+ */
+static inline __host__ __device__ float3** asFloat3Pointer(gmx::RVec** in)
+{
+ static_assert(sizeof((*in)[0]) == sizeof(float3),
+ "Size of the host-side data-type is different from the size of the device-side "
+ "counterpart.");
+ return reinterpret_cast<float3**>(in);
+}
+static inline __host__ __device__ const float3* const* asFloat3Pointer(const gmx::RVec* const* in)
+{
+ static_assert(sizeof((*in)[0]) == sizeof(float3),
+ "Size of the host-side data-type is different from the size of the device-side "
+ "counterpart.");
+ return reinterpret_cast<const float3* const*>(in);
+}
+
#endif // GMX_GPU_UTILS_TYPECASTS_CUH
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+add_library(hardware INTERFACE)
gmx_add_libgromacs_sources(
cpuinfo.cpp
detecthardware.cpp
)
endif()
+# Source files have the following private module dependencies.
+target_link_libraries(hardware PRIVATE
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(hardware PUBLIC
+target_include_directories(hardware INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(hardware PUBLIC
+target_link_libraries(hardware INTERFACE
+ legacy_api
+ )
+
+# TODO: when hardware is an OBJECT target
+#target_link_libraries(hardware PUBLIC legacy_api)
+#target_link_libraries(hardware PRIVATE common)
+
+# Module dependencies
+# hardware interfaces convey transitive dependence on these modules.
+#target_link_libraries(hardware PUBLIC
+target_link_libraries(hardware INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(hardware PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(hardware PRIVATE legacy_modules)
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
for (std::size_t i = 0; i < uniqueSortedV.size(); i++)
{
unsigned int val = uniqueSortedV[i];
- std::replace_if(v->begin(), v->end(), [val](unsigned int& c) -> bool { return c == val; },
+ std::replace_if(v->begin(),
+ v->end(),
+ [val](unsigned int& c) -> bool { return c == val; },
static_cast<unsigned int>(i));
}
}
// For each label in /proc/cpuinfo, compare the value to the name in the
// testNames map above, and if it's a match return the vendor.
- for (auto& l : { "vendor_id", "vendor", "manufacture", "model", "processor", "cpu" })
+ for (const auto& l : { "vendor_id", "vendor", "manufacture", "model", "processor", "cpu" })
{
if (cpuInfo.count(l) != 0U)
{
// there was a line with this left-hand side in /proc/cpuinfo
const std::string& s1 = cpuInfo.at(l);
- for (auto& t : testVendors)
+ for (const auto& t : testVendors)
{
const std::string& s2 = t.first;
features->insert(CpuInfo::Feature::Ibm_Qpx);
}
- for (auto& l : { "model name", "model", "Processor", "cpu" })
+ for (const auto& l : { "model name", "model", "Processor", "cpu" })
{
if (cpuInfo.count(l) != 0U)
{
{
result.features_.insert(CpuInfo::Feature::X86_Hygon);
}
- detectX86Features(&result.brandString_, &result.family_, &result.model_, &result.stepping_,
- &result.features_);
+ detectX86Features(
+ &result.brandString_, &result.family_, &result.model_, &result.stepping_, &result.features_);
result.logicalProcessors_ = detectX86LogicalProcessors();
}
else
// On Linux we might be able to find information in /proc/cpuinfo. If vendor or brand
// is set to a known value this routine will not overwrite it.
- detectProcCpuInfo(&result.vendor_, &result.brandString_, &result.family_, &result.model_,
- &result.stepping_, &result.features_);
+ detectProcCpuInfo(&result.vendor_,
+ &result.brandString_,
+ &result.family_,
+ &result.model_,
+ &result.stepping_,
+ &result.features_);
}
if (!result.logicalProcessors_.empty())
bool cpuIsX86Nehalem(const CpuInfo& cpuInfo)
{
- return (cpuInfo.vendor() == gmx::CpuInfo::Vendor::Intel && cpuInfo.family() == 6
+ return (cpuInfo.vendor() == CpuInfo::Vendor::Intel && cpuInfo.family() == 6
&& (cpuInfo.model() == 0x2E || cpuInfo.model() == 0x1A || cpuInfo.model() == 0x1E
|| cpuInfo.model() == 0x2F || cpuInfo.model() == 0x2C || cpuInfo.model() == 0x25));
}
+bool cpuIsAmdZen1(const CpuInfo& cpuInfo)
+{
+ /* Both Zen/Zen+/Zen2 have family==23
+ * Model numbers for Zen:
+ * 1) Naples, Whitehaven, Summit Ridge, and Snowy Owl;
+ * 17) Raven Ridge.
+ * Model numbers for Zen+:
+ * 8) Pinnacle Ridge;
+ * 24) Picasso.
+ * Hygon got license for Zen1, but not Zen2 (https://www.tomshardware.com/news/amd-zen-china-x86-ip-license,39573.html)
+ */
+ return (cpuInfo.vendor() == CpuInfo::Vendor::Amd && cpuInfo.family() == 23
+ && (cpuInfo.model() == 1 || cpuInfo.model() == 17 || cpuInfo.model() == 8
+ || cpuInfo.model() == 24))
+ || (cpuInfo.vendor() == CpuInfo::Vendor::Hygon);
+}
+
} // namespace gmx
#ifdef GMX_CPUINFO_STANDALONE
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int hwThreadRankInCore; //!< Relative rank of logical processor in its core
};
-public:
/*! \brief Perform detection and construct a CpuInfo class from the results.
*
* \note The detection should generally be performed again in different
*/
bool cpuIsX86Nehalem(const CpuInfo& cpuInfo);
+/*! \brief Return true if the CPU is a first generation AMD Zen (produced by AMD or Hygon)
+ *
+ * \param cpuInfo Object with cpu information
+ *
+ * \returns True if running on a first generation AMD Zen
+ */
+bool cpuIsAmdZen1(const CpuInfo& cpuInfo);
+
} // namespace gmx
#endif // GMX_HARDWARE_CPUINFO_H
* - family=23 with the below listed models;
* - Hygon as vendor.
*/
- const bool cpuIsAmdZen1 = ((cpuInfo.vendor() == CpuInfo::Vendor::Amd && cpuInfo.family() == 23
- && (cpuInfo.model() == 1 || cpuInfo.model() == 17
- || cpuInfo.model() == 8 || cpuInfo.model() == 24))
- || cpuInfo.vendor() == CpuInfo::Vendor::Hygon);
+ const bool cpuIsAmdZen1 = gmx::cpuIsAmdZen1(cpuInfo);
int numCompatibleDevices = getCompatibleDevices(hardwareInfo->deviceInfoList).size();
#if GMX_LIB_MPI
countsLocal[3] = numCompatibleDevices;
}
- MPI_Allreduce(countsLocal.data(), countsReduced.data(), countsLocal.size(), MPI_INT,
- MPI_SUM, MPI_COMM_WORLD);
+ MPI_Allreduce(countsLocal.data(), countsReduced.data(), countsLocal.size(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
}
constexpr int numElementsMax = 11;
maxMinLocal[9] = -maxMinLocal[4];
maxMinLocal[10] = (cpuIsAmdZen1 ? 1 : 0);
- MPI_Allreduce(maxMinLocal.data(), maxMinReduced.data(), maxMinLocal.size(), MPI_INT,
- MPI_MAX, MPI_COMM_WORLD);
+ MPI_Allreduce(maxMinLocal.data(), maxMinReduced.data(), maxMinLocal.size(), MPI_INT, MPI_MAX, MPI_COMM_WORLD);
}
hardwareInfo->nphysicalnode = countsReduced[0];
GMX_LOG(mdlog.info)
.appendTextFormatted(
"Note: %d CPUs configured, but only %d were detected to be online.\n",
- countConfigured, countFromDetection);
+ countConfigured,
+ countFromDetection);
if (c_architecture == Architecture::X86 && countConfigured == 2 * countFromDetection)
{
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
Incompatible = 2,
//! OpenCL device has incompatible cluster size for non-bonded kernels.
IncompatibleClusterSize = 3,
- //! There are known issues with NVIDIA Volta and newer.
+ //! There are known issues with OpenCL on NVIDIA Volta and newer.
IncompatibleNvidiaVolta = 4,
+ /* \brief The device originates from non-recommended SYCL backend.
+ * The device might work by itself, but to simplify device allocation, it is marked as incompatible.
+ * */
+ NotPreferredBackend = 5,
/*! \brief An error occurred during the functionality checks.
* That indicates malfunctioning of the device, driver, or incompatible driver/runtime.
*/
- NonFunctional = 5,
+ NonFunctional = 6,
/*! \brief CUDA devices are busy or unavailable.
* typically due to use of \p cudaComputeModeExclusive, \p cudaComputeModeProhibited modes.
*/
- Unavailable = 6,
+ Unavailable = 7,
//! Enumeration size
- Count = 7
+ Count = 8
};
/*! \brief Names of the GPU detection/check results
* missing, so that is suppressed.
*/
static const gmx::EnumerationArray<DeviceStatus, const char*> c_deviceStateString = {
- "compatible", "nonexistent", "incompatible",
+ "compatible",
+ "nonexistent",
+ "incompatible",
// clang-format off
// NOLINTNEXTLINE(bugprone-suspicious-missing-comma)
- "incompatible (please recompile with correct GMX" "_OPENCL_NB_CLUSTER_SIZE of 4)",
+ "incompatible (please recompile with correct GMX" "_GPU_NB_CLUSTER_SIZE of 4)",
// clang-format on
- "incompatible (please use CUDA build for NVIDIA Volta GPUs or newer)", "non-functional",
+ "incompatible (please use CUDA build for NVIDIA Volta GPUs or newer)",
+ "not recommended (please use SYCL_DEVICE_FILTER to limit visibility to a single backend)",
+ "non-functional",
"unavailable"
};
"might be rare, or some architectures were disabled in the build. \n"
"Consult the install guide for how to use the GMX_CUDA_TARGET_SM and "
"GMX_CUDA_TARGET_COMPUTE CMake variables to add this architecture. \n",
- gmx::getProgramContext().displayName(), deviceId, deviceProp.major, deviceProp.minor);
+ gmx::getProgramContext().displayName(),
+ deviceId,
+ deviceProp.major,
+ deviceProp.minor);
}
return stat;
cu_err = cudaSetDevice(deviceInfo.id);
if (cu_err != cudaSuccess)
{
- fprintf(stderr, "Error while switching to device #%d. %s\n", deviceInfo.id,
+ fprintf(stderr,
+ "Error while switching to device #%d. %s\n",
+ deviceInfo.id,
gmx::getDeviceErrorString(cu_err).c_str());
return DeviceStatus::NonFunctional;
}
// launchGpuKernel error is not fatal and should continue with marking the device bad
fprintf(stderr,
"Error occurred while running dummy kernel sanity check on device #%d:\n %s\n",
- deviceInfo.id, formatExceptionMessageToString(ex).c_str());
+ deviceInfo.id,
+ formatExceptionMessageToString(ex).c_str());
return DeviceStatus::NonFunctional;
}
if (!gpuExists)
{
- return gmx::formatString("#%d: %s, stat: %s", deviceInfo.id, "N/A",
- c_deviceStateString[deviceInfo.status]);
+ return gmx::formatString(
+ "#%d: %s, stat: %s", deviceInfo.id, "N/A", c_deviceStateString[deviceInfo.status]);
}
else
{
return gmx::formatString("#%d: NVIDIA %s, compute cap.: %d.%d, ECC: %3s, stat: %s",
- deviceInfo.id, deviceInfo.prop.name, deviceInfo.prop.major,
- deviceInfo.prop.minor, deviceInfo.prop.ECCEnabled ? "yes" : " no",
+ deviceInfo.id,
+ deviceInfo.prop.name,
+ deviceInfo.prop.major,
+ deviceInfo.prop.minor,
+ deviceInfo.prop.ECCEnabled ? "yes" : " no",
c_deviceStateString[deviceInfo.status]);
}
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
#include <vector>
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/iserializer.h"
*
* \return Vector of compatible GPU ids.
*/
-std::vector<int> getCompatibleDeviceIds(const std::vector<std::unique_ptr<DeviceInformation>>& deviceInfoList);
+std::vector<int> getCompatibleDeviceIds(gmx::ArrayRef<const std::unique_ptr<DeviceInformation>> deviceInfoList);
/*! \brief Return whether \p deviceId is found in \p deviceInfoList and is compatible
*
*
* \return Whether \c deviceId is compatible.
*/
-bool deviceIdIsCompatible(const std::vector<std::unique_ptr<DeviceInformation>>& deviceInfoList,
- int deviceId);
+bool deviceIdIsCompatible(gmx::ArrayRef<const std::unique_ptr<DeviceInformation>> deviceInfoList,
+ int deviceId);
/*! \brief Set the active GPU.
*
* \param[in] deviceId An index of the device to check
* \returns A string describing the compatibility status, useful for error messages.
*/
-std::string getDeviceCompatibilityDescription(const std::vector<std::unique_ptr<DeviceInformation>>& deviceInfoList,
+std::string getDeviceCompatibilityDescription(gmx::ArrayRef<const std::unique_ptr<DeviceInformation>> deviceInfoList,
int deviceId);
/*! \brief Serialization of information on devices for MPI broadcasting.
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return compatibleDeviceInfoList;
}
-std::vector<int> getCompatibleDeviceIds(const std::vector<std::unique_ptr<DeviceInformation>>& deviceInfoList)
+std::vector<int> getCompatibleDeviceIds(gmx::ArrayRef<const std::unique_ptr<DeviceInformation>> deviceInfoList)
{
// Possible minor over-allocation here, but not important for anything
std::vector<int> compatibleDeviceIds;
return compatibleDeviceIds;
}
-bool deviceIdIsCompatible(const std::vector<std::unique_ptr<DeviceInformation>>& deviceInfoList,
- const int deviceId)
+bool deviceIdIsCompatible(gmx::ArrayRef<const std::unique_ptr<DeviceInformation>> deviceInfoList,
+ const int deviceId)
{
- auto foundIt = std::find_if(deviceInfoList.begin(), deviceInfoList.end(),
+ auto foundIt = std::find_if(deviceInfoList.begin(),
+ deviceInfoList.end(),
[deviceId](auto& deviceInfo) { return deviceInfo->id == deviceId; });
if (foundIt == deviceInfoList.end())
{
GMX_THROW(gmx::RangeError(gmx::formatString(
- "Device ID %d did not correspond to any of the %zu detected device(s)", deviceId,
+ "Device ID %d did not correspond to any of the %zu detected device(s)",
+ deviceId,
deviceInfoList.size())));
}
return (*foundIt)->status == DeviceStatus::Compatible;
}
-std::string getDeviceCompatibilityDescription(const std::vector<std::unique_ptr<DeviceInformation>>& deviceInfoList,
+std::string getDeviceCompatibilityDescription(const gmx::ArrayRef<const std::unique_ptr<DeviceInformation>> deviceInfoList,
int deviceId)
{
return (deviceId >= static_cast<int>(deviceInfoList.size())
"DeviceInformation for OpenCL/SYCL can not be serialized");
int numDevices = deviceInfoList.size();
serializer->doInt(&numDevices);
- for (auto& deviceInfo : deviceInfoList)
+ for (const auto& deviceInfo : deviceInfoList)
{
serializer->doOpaque(reinterpret_cast<char*>(deviceInfo.get()), sizeof(DeviceInformation));
}
static const unsigned int ccMajorBad = 7; // Volta and Turing
unsigned int ccMajor;
cl_device_id devId = deviceInfo.oclDeviceId;
- const cl_int err = clGetDeviceInfo(devId, CL_DEVICE_COMPUTE_CAPABILITY_MAJOR_NV,
- sizeof(ccMajor), &ccMajor, nullptr);
+ const cl_int err = clGetDeviceInfo(
+ devId, CL_DEVICE_COMPUTE_CAPABILITY_MAJOR_NV, sizeof(ccMajor), &ccMajor, nullptr);
if (err != CL_SUCCESS)
{
return true; // Err on a side of trusting the user to know what they are doing.
// the device which has the following format:
// OpenCL<space><major_version.minor_version><space><vendor-specific information>
unsigned int deviceVersionMinor, deviceVersionMajor;
- const int valuesScanned = std::sscanf(deviceInfo.device_version, "OpenCL %u.%u",
- &deviceVersionMajor, &deviceVersionMinor);
- const bool versionLargeEnough =
+ const int valuesScanned = std::sscanf(
+ deviceInfo.device_version, "OpenCL %u.%u", &deviceVersionMajor, &deviceVersionMinor);
+ const bool versionLargeEnough =
((valuesScanned == 2)
&& ((deviceVersionMajor > minVersionMajor)
|| (deviceVersionMajor == minVersionMajor && deviceVersionMinor >= minVersionMinor)));
case DeviceVendor::Amd:
return runningOnCompatibleOSForAmd() ? DeviceStatus::Compatible : DeviceStatus::Incompatible;
case DeviceVendor::Intel:
- return GMX_OPENCL_NB_CLUSTER_SIZE == 4 ? DeviceStatus::Compatible
- : DeviceStatus::IncompatibleClusterSize;
+ return GMX_GPU_NB_CLUSTER_SIZE == 4 ? DeviceStatus::Compatible
+ : DeviceStatus::IncompatibleClusterSize;
default: return DeviceStatus::Incompatible;
}
}
{
if (message != nullptr)
{
- return gmx::formatString("%s did %ssucceed %d: %s", message,
- ((status != CL_SUCCESS) ? "not " : ""), status,
+ return gmx::formatString("%s did %ssucceed %d: %s",
+ message,
+ ((status != CL_SUCCESS) ? "not " : ""),
+ status,
ocl_get_error_string(status).c_str());
}
else
{
return gmx::formatString("%sOpenCL error encountered %d: %s",
- ((status != CL_SUCCESS) ? "" : "No "), status,
+ ((status != CL_SUCCESS) ? "" : "No "),
+ status,
ocl_get_error_string(status).c_str());
}
}
clSetKernelArg(kernel, 0, sizeof(void*), nullptr);
const size_t localWorkSize = 1, globalWorkSize = 1;
- if ((status = clEnqueueNDRangeKernel(commandQueue, kernel, 1, nullptr, &globalWorkSize,
- &localWorkSize, 0, nullptr, nullptr))
+ if ((status = clEnqueueNDRangeKernel(
+ commandQueue, kernel, 1, nullptr, &globalWorkSize, &localWorkSize, 0, nullptr, nullptr))
!= CL_SUCCESS)
{
errorMessage->assign(makeOpenClInternalErrorString("clEnqueueNDRangeKernel", status));
GMX_RELEASE_ASSERT(
status == CL_SUCCESS,
gmx::formatString("An unexpected value was returned from clGetPlatformIDs %d: %s",
- status, ocl_get_error_string(status).c_str())
+ status,
+ ocl_get_error_string(status).c_str())
.c_str());
bool foundPlatform = (numPlatforms > 0);
if (!foundPlatform && errorMessage != nullptr)
/* If requesting req_dev_type devices fails, just go to the next platform */
if (CL_SUCCESS
- != clGetDeviceIDs(ocl_platform_ids[i], req_dev_type, numDevices, ocl_device_ids,
- &ocl_device_count))
+ != clGetDeviceIDs(ocl_platform_ids[i], req_dev_type, numDevices, ocl_device_ids, &ocl_device_count))
{
continue;
}
deviceInfoList[device_index]->oclDeviceId = ocl_device_ids[j];
deviceInfoList[device_index]->device_name[0] = 0;
- clGetDeviceInfo(ocl_device_ids[j], CL_DEVICE_NAME,
+ clGetDeviceInfo(ocl_device_ids[j],
+ CL_DEVICE_NAME,
sizeof(deviceInfoList[device_index]->device_name),
- deviceInfoList[device_index]->device_name, nullptr);
+ deviceInfoList[device_index]->device_name,
+ nullptr);
deviceInfoList[device_index]->device_version[0] = 0;
- clGetDeviceInfo(ocl_device_ids[j], CL_DEVICE_VERSION,
+ clGetDeviceInfo(ocl_device_ids[j],
+ CL_DEVICE_VERSION,
sizeof(deviceInfoList[device_index]->device_version),
- deviceInfoList[device_index]->device_version, nullptr);
+ deviceInfoList[device_index]->device_version,
+ nullptr);
deviceInfoList[device_index]->vendorName[0] = 0;
- clGetDeviceInfo(ocl_device_ids[j], CL_DEVICE_VENDOR,
+ clGetDeviceInfo(ocl_device_ids[j],
+ CL_DEVICE_VENDOR,
sizeof(deviceInfoList[device_index]->vendorName),
- deviceInfoList[device_index]->vendorName, nullptr);
+ deviceInfoList[device_index]->vendorName,
+ nullptr);
deviceInfoList[device_index]->compute_units = 0;
- clGetDeviceInfo(ocl_device_ids[j], CL_DEVICE_MAX_COMPUTE_UNITS,
+ clGetDeviceInfo(ocl_device_ids[j],
+ CL_DEVICE_MAX_COMPUTE_UNITS,
sizeof(deviceInfoList[device_index]->compute_units),
- &(deviceInfoList[device_index]->compute_units), nullptr);
+ &(deviceInfoList[device_index]->compute_units),
+ nullptr);
deviceInfoList[device_index]->adress_bits = 0;
- clGetDeviceInfo(ocl_device_ids[j], CL_DEVICE_ADDRESS_BITS,
+ clGetDeviceInfo(ocl_device_ids[j],
+ CL_DEVICE_ADDRESS_BITS,
sizeof(deviceInfoList[device_index]->adress_bits),
- &(deviceInfoList[device_index]->adress_bits), nullptr);
+ &(deviceInfoList[device_index]->adress_bits),
+ nullptr);
deviceInfoList[device_index]->deviceVendor =
getDeviceVendor(deviceInfoList[device_index]->vendorName);
- clGetDeviceInfo(ocl_device_ids[j], CL_DEVICE_MAX_WORK_ITEM_SIZES, 3 * sizeof(size_t),
- &deviceInfoList[device_index]->maxWorkItemSizes, nullptr);
+ clGetDeviceInfo(ocl_device_ids[j],
+ CL_DEVICE_MAX_WORK_ITEM_SIZES,
+ 3 * sizeof(size_t),
+ &deviceInfoList[device_index]->maxWorkItemSizes,
+ nullptr);
- clGetDeviceInfo(ocl_device_ids[j], CL_DEVICE_MAX_WORK_GROUP_SIZE, sizeof(size_t),
- &deviceInfoList[device_index]->maxWorkGroupSize, nullptr);
+ clGetDeviceInfo(ocl_device_ids[j],
+ CL_DEVICE_MAX_WORK_GROUP_SIZE,
+ sizeof(size_t),
+ &deviceInfoList[device_index]->maxWorkGroupSize,
+ nullptr);
deviceInfoList[device_index]->status =
gmx::checkGpu(device_index, *deviceInfoList[device_index]);
if (!gpuExists)
{
- return gmx::formatString("#%d: %s, status: %s", deviceInfo.id, "N/A",
- c_deviceStateString[deviceInfo.status]);
+ return gmx::formatString(
+ "#%d: %s, status: %s", deviceInfo.id, "N/A", c_deviceStateString[deviceInfo.status]);
}
else
{
return gmx::formatString("#%d: name: %s, vendor: %s, device version: %s, status: %s",
- deviceInfo.id, deviceInfo.device_name, deviceInfo.vendorName,
- deviceInfo.device_version, c_deviceStateString[deviceInfo.status]);
+ deviceInfo.id,
+ deviceInfo.device_name,
+ deviceInfo.vendorName,
+ deviceInfo.device_version,
+ c_deviceStateString[deviceInfo.status]);
}
}
*/
#include "gmxpre.h"
+#include <map>
+
#include "gromacs/gpu_utils/gmxsycl.h"
#include "gromacs/hardware/device_management.h"
#include "gromacs/utility/fatalerror.h"
return DeviceStatus::Compatible;
}
- if (syclDevice.is_accelerator()) // FPGAs and FPGA emulators
+ if (syclDevice.get_info<cl::sycl::info::device::local_mem_type>() == cl::sycl::info::local_mem_type::none)
{
+ // While some kernels (leapfrog) can run without shared/local memory, this is a bad sign
return DeviceStatus::Incompatible;
}
- else
+
+ if (syclDevice.is_host())
+ {
+ // Host device does not support subgroups or even querying for sub_group_sizes
+ return DeviceStatus::Incompatible;
+ }
+
+#if GMX_SYCL_HIPSYCL
+ /* At the time of writing:
+ * 1. SYCL NB kernels currently don't support sub_group size of 32 or 64, which are the only
+ * ones available on NVIDIA and AMD hardware, respectively. That's not a fundamental limitation,
+ * but requires porting more OpenCL code, see #3934.
+ * 2. hipSYCL does not support cl::sycl::info::device::sub_group_sizes,
+ * see https://github.com/illuhad/hipSYCL/pull/449
+ */
+ const std::vector<size_t> supportedSubGroupSizes{ warpSize };
+#else
+ const std::vector<size_t> supportedSubGroupSizes =
+ syclDevice.get_info<cl::sycl::info::device::sub_group_sizes>();
+#endif
+ const size_t requiredSubGroupSizeForNBNXM = 8;
+ if (std::find(supportedSubGroupSizes.begin(), supportedSubGroupSizes.end(), requiredSubGroupSizeForNBNXM)
+ == supportedSubGroupSizes.end())
+ {
+ return DeviceStatus::IncompatibleClusterSize;
+ }
+
+ /* Host device can not be used, because NBNXM requires sub-groups, which are not supported.
+ * Accelerators (FPGAs and their emulators) are not supported.
+ * So, the only viable options are CPUs and GPUs. */
+ const bool forceCpu = (getenv("GMX_SYCL_FORCE_CPU") != nullptr);
+
+ if (forceCpu && syclDevice.is_cpu())
{
return DeviceStatus::Compatible;
}
+ else if (!forceCpu && syclDevice.is_gpu())
+ {
+ return DeviceStatus::Compatible;
+ }
+ else
+ {
+ return DeviceStatus::Incompatible;
+ }
}
{
if (errorMessage != nullptr)
{
- errorMessage->assign(gmx::formatString(
- "Unable to run dummy kernel on device %s: %s",
- syclDevice.get_info<cl::sycl::info::device::name>().c_str(), e.what()));
+ errorMessage->assign(
+ gmx::formatString("Unable to run dummy kernel on device %s: %s",
+ syclDevice.get_info<cl::sycl::info::device::name>().c_str(),
+ e.what()));
}
return false;
}
return DeviceStatus::Compatible;
}
+/* In DPCPP, the same physical device can appear as different virtual devices provided
+ * by different backends (e.g., the same GPU can be accessible via both OpenCL and L0).
+ * Thus, using devices from two backends is more likely to be a user error than the
+ * desired behavior. In this function, we choose the backend with the most compatible
+ * devices. In case of a tie, we choose OpenCL (if present), or some arbitrary backend
+ * among those with the most devices.
+ *
+ * In hipSYCL, this problem is unlikely to manifest. It has (as of 2021-03-03) another
+ * issues: D2D copy between different backends is not allowed. We don't use D2D in
+ * SYCL yet. Additionally, hipSYCL does not implement the `sycl::platform::get_backend()`
+ * function.
+ * Thus, we only do the backend filtering with DPCPP.
+ * */
+#if GMX_SYCL_DPCPP
+static std::optional<cl::sycl::backend>
+chooseBestBackend(const std::vector<std::unique_ptr<DeviceInformation>>& deviceInfos)
+{
+ // Count the number of compatible devices per backend
+ std::map<cl::sycl::backend, int> countDevicesByBackend; // Default initialized with zeros
+ for (const auto& deviceInfo : deviceInfos)
+ {
+ if (deviceInfo->status == DeviceStatus::Compatible)
+ {
+ const cl::sycl::backend backend = deviceInfo->syclDevice.get_platform().get_backend();
+ ++countDevicesByBackend[backend];
+ }
+ }
+ // If we have devices from more than one backend...
+ if (countDevicesByBackend.size() > 1)
+ {
+ // Find backend with most devices
+ const auto backendWithMostDevices = std::max_element(
+ countDevicesByBackend.cbegin(),
+ countDevicesByBackend.cend(),
+ [](const auto& kv1, const auto& kv2) { return kv1.second < kv2.second; });
+ // Count devices provided by OpenCL. Will be zero if no OpenCL devices found.
+ const int devicesInOpenCL = countDevicesByBackend[cl::sycl::backend::opencl];
+ if (devicesInOpenCL == backendWithMostDevices->second)
+ {
+ // Prefer OpenCL backend as more stable, if it has as many devices as others
+ return cl::sycl::backend::opencl;
+ }
+ else
+ {
+ // Otherwise, just return max
+ return backendWithMostDevices->first;
+ }
+ }
+ else if (countDevicesByBackend.size() == 1)
+ {
+ return countDevicesByBackend.cbegin()->first;
+ }
+ else // No devices found
+ {
+ return std::nullopt;
+ }
+}
+#endif
+
std::vector<std::unique_ptr<DeviceInformation>> findDevices()
{
std::vector<std::unique_ptr<DeviceInformation>> deviceInfos(0);
deviceInfos[i]->deviceVendor =
getDeviceVendor(syclDevice.get_info<cl::sycl::info::device::vendor>().c_str());
}
+#if GMX_SYCL_DPCPP
+ // Now, filter by the backend if we did not disable compatibility check
+ if (getenv("GMX_GPU_DISABLE_COMPATIBILITY_CHECK") == nullptr)
+ {
+ std::optional<cl::sycl::backend> preferredBackend = chooseBestBackend(deviceInfos);
+ if (preferredBackend.has_value())
+ {
+ for (auto& deviceInfo : deviceInfos)
+ {
+ if (deviceInfo->syclDevice.get_platform().get_backend() != *preferredBackend)
+ {
+ deviceInfo->status = DeviceStatus::NotPreferredBackend;
+ }
+ }
+ }
+ }
+#endif
return deviceInfos;
}
if (!deviceExists)
{
- return gmx::formatString("#%d: %s, status: %s", deviceInfo.id, "N/A",
- c_deviceStateString[deviceInfo.status]);
+ return gmx::formatString(
+ "#%d: %s, status: %s", deviceInfo.id, "N/A", c_deviceStateString[deviceInfo.status]);
}
else
{
return gmx::formatString(
- "#%d: name: %s, vendor: %s, device version: %s, status: %s", deviceInfo.id,
+ "#%d: name: %s, vendor: %s, device version: %s, status: %s",
+ deviceInfo.id,
deviceInfo.syclDevice.get_info<cl::sycl::info::device::name>().c_str(),
deviceInfo.syclDevice.get_info<cl::sycl::info::device::vendor>().c_str(),
deviceInfo.syclDevice.get_info<cl::sycl::info::device::version>().c_str(),
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int nHwThreads = 0;
// Copy the logical processor information from cpuinfo
- for (auto& l : cpuInfo.logicalProcessors())
+ for (const auto& l : cpuInfo.logicalProcessors())
{
machine->logicalProcessors.push_back(
{ l.socketRankInMachine, l.coreRankInSocket, l.hwThreadRankInCore, -1 });
// Go through children; if this object has no children obj->arity is 0,
// and we'll return an empty vector.
hwloc_obj_t tempNode = nullptr;
- while ((tempNode = hwloc_get_next_child(const_cast<hwloc_topology_t>(topo),
- const_cast<hwloc_obj_t>(obj), tempNode))
+ while ((tempNode = hwloc_get_next_child(
+ const_cast<hwloc_topology_t>(topo), const_cast<hwloc_obj_t>(obj), tempNode))
!= nullptr)
{
std::vector<const hwloc_obj*> v2 = getHwLocDescendantsByType(topo, tempNode, type);
return !machine->caches.empty();
}
-
/*! \brief Read numa information from hwloc topology
*
* \param topo hwloc topology handle that has been initialized and loaded
// assign stuff
for (auto& v : machine->numa.relativeLatency)
{
- std::transform(v.begin(), v.end(), v.begin(),
- std::bind(std::multiplies<float>(), std::placeholders::_1, 1.0 / minLatency));
+ // Rescale the latencies to a relative float-point value
+ for (float& value : v)
+ {
+ value /= minLatency;
+ }
}
machine->numa.baseLatency = 1.0; // latencies still do not have any units in hwloc-2.x
machine->numa.maxRelativeLatency = maxLatency / minLatency;
GMX_RELEASE_ASSERT(p->attr, "Attributes should not be NULL for hwloc PCI object");
- machine->devices.push_back({ p->attr->pcidev.vendor_id, p->attr->pcidev.device_id,
- p->attr->pcidev.class_id, p->attr->pcidev.domain,
- p->attr->pcidev.bus, p->attr->pcidev.dev, p->attr->pcidev.func,
+ machine->devices.push_back({ p->attr->pcidev.vendor_id,
+ p->attr->pcidev.device_id,
+ p->attr->pcidev.class_id,
+ p->attr->pcidev.domain,
+ p->attr->pcidev.bus,
+ p->attr->pcidev.dev,
+ p->attr->pcidev.func,
numaId });
}
return !pcidevs.empty();
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
std::vector<Device> devices; //!< Devices on PCI bus
};
-public:
/*! \brief Detects the hardware topology. */
static HardwareTopology detect();
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! Logical core pinning offset.
int core_pinning_offset = 0;
//! Empty, or a string provided by the user declaring (unique) GPU IDs available for mdrun to use.
- std::string gpuIdsAvailable = "";
+ std::string devicesSelectedByUser;
//! Empty, or a string provided by the user mapping GPU tasks to devices.
- std::string userGpuTaskAssignment = "";
+ std::string userGpuTaskAssignment;
//! Tells whether mdrun is free to choose the total number of threads (by choosing the number of OpenMP and/or thread-MPI threads).
bool totNumThreadsIsAuto;
};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"\tmovq %%rdx, %0\n"
: "=r"(cycles)
: "r"(loopCount)
- : "rax", "rbx", "rcx", "rdx", "zmm0", "zmm1", "zmm2", "zmm3", "zmm4", "zmm5", "zmm6",
- "zmm7", "zmm8", "zmm9", "zmm10", "zmm11", "zmm12", "zmm13", "zmm14", "zmm15", "zmm16",
- "zmm17", "zmm18", "zmm19", "zmm20", "zmm21", "zmm22", "zmm23", "zmm30");
+ : "rax",
+ "rbx",
+ "rcx",
+ "rdx",
+ "zmm0",
+ "zmm1",
+ "zmm2",
+ "zmm3",
+ "zmm4",
+ "zmm5",
+ "zmm6",
+ "zmm7",
+ "zmm8",
+ "zmm9",
+ "zmm10",
+ "zmm11",
+ "zmm12",
+ "zmm13",
+ "zmm14",
+ "zmm15",
+ "zmm16",
+ "zmm17",
+ "zmm18",
+ "zmm19",
+ "zmm20",
+ "zmm21",
+ "zmm22",
+ "zmm23",
+ "zmm30");
return cycles;
}
"\tmovq %%rdx, %0\n"
: "=r"(cycles)
: "r"(loopCount)
- : "rax", "rbx", "rcx", "rdx", "zmm0", "zmm1", "zmm2", "zmm3", "zmm4", "zmm5", "zmm6",
- "zmm7", "zmm8", "zmm9", "zmm10", "zmm11");
+ : "rax",
+ "rbx",
+ "rcx",
+ "rdx",
+ "zmm0",
+ "zmm1",
+ "zmm2",
+ "zmm3",
+ "zmm4",
+ "zmm5",
+ "zmm6",
+ "zmm7",
+ "zmm8",
+ "zmm9",
+ "zmm10",
+ "zmm11");
return cycles;
}
* We only execute the test once, and return the saved result
* on subsequent calls.
*/
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
std::mutex initMutex;
} // namespace
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* (using sysconf), and the spins doing dummy compute operations for up to
* 2 seconds, or until all cores have come online. This can be used prior to
* hardware detection for platforms that take unused processors offline.
- *
- * This routine will not throw exceptions. In principle it should be
- * declared noexcept, but at least icc 19.1 and 21-beta08 with the
- * libstdc++-7.5 has difficulty implementing a std::vector of
- * std::thread started with this function when declared noexcept. It
- * is a known compiler bug that should be fixed after 19.1.
- * Fortunately, this function is not performance sensitive,
- * and only runs on platforms other than x86 and POWER (ie ARM),
- * so the possible overhead introduced by omitting noexcept is not
- * important.
*/
-static void spinUpCore()
+static void spinUpCore() noexcept
{
#if defined(HAVE_SYSCONF) && defined(_SC_NPROCESSORS_CONF) && defined(_SC_NPROCESSORS_ONLN)
float dummy = 0.1;
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016, The GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"speed as accurate timings are needed for load-balancing.\n"
"Please consider rebuilding %s with the GMX_USE_RDTSCP=ON CMake "
"option.",
- programName, programName);
+ programName,
+ programName);
}
}
}
const gmx::HardwareTopology& hwTop = *hwinfo->hardwareTopology;
s = gmx::formatString("\n");
- s += gmx::formatString("Running on %d node%s with total", hwinfo->nphysicalnode,
+ s += gmx::formatString("Running on %d node%s with total",
+ hwinfo->nphysicalnode,
hwinfo->nphysicalnode == 1 ? "" : "s");
if (hwinfo->ncore_tot > 0)
{
s += gmx::formatString(" %d logical cores", hwinfo->nhwthread_tot);
if (canPerformDeviceDetection(nullptr))
{
- s += gmx::formatString(", %d compatible GPU%s", hwinfo->ngpu_compatible_tot,
+ s += gmx::formatString(", %d compatible GPU%s",
+ hwinfo->ngpu_compatible_tot,
hwinfo->ngpu_compatible_tot == 1 ? "" : "s");
}
else if (bGPUBinary)
if (bFullCpuInfo)
{
- s += gmx::formatString(" Family: %d Model: %d Stepping: %d\n", cpuInfo.family(),
- cpuInfo.model(), cpuInfo.stepping());
+ s += gmx::formatString(" Family: %d Model: %d Stepping: %d\n",
+ cpuInfo.family(),
+ cpuInfo.model(),
+ cpuInfo.stepping());
s += gmx::formatString(" Features:");
- for (auto& f : cpuInfo.featureSet())
+ for (const auto& f : cpuInfo.featureSet())
{
s += gmx::formatString(" %s", gmx::CpuInfo::featureString(f).c_str());
}
{
s += gmx::formatString(" Sockets, cores, and logical processors:\n");
- for (auto& socket : hwTop.machine().sockets)
+ for (const auto& socket : hwTop.machine().sockets)
{
s += gmx::formatString(" Socket %2d:", socket.id);
- for (auto& c : socket.cores)
+ for (const auto& c : socket.cores)
{
s += gmx::formatString(" [");
- for (auto& t : c.hwThreads)
+ for (const auto& t : c.hwThreads)
{
s += gmx::formatString(" %3d", t.logicalProcessorId);
}
if (hwTop.supportLevel() >= gmx::HardwareTopology::SupportLevel::Full)
{
s += gmx::formatString(" Numa nodes:\n");
- for (auto& n : hwTop.machine().numa.nodes)
+ for (const auto& n : hwTop.machine().numa.nodes)
{
s += gmx::formatString(" Node %2d (%zu bytes mem):", n.id, n.memory);
- for (auto& l : n.logicalProcessorId)
+ for (const auto& l : n.logicalProcessorId)
{
s += gmx::formatString(" %3d", l);
}
s += gmx::formatString(" Caches:\n");
- for (auto& c : hwTop.machine().caches)
+ for (const auto& c : hwTop.machine().caches)
{
s += gmx::formatString(
" L%d: %zu bytes, linesize %d bytes, assoc. %d, shared %d ways\n",
- c.level, c.size, c.linesize, c.associativity, c.shared);
+ c.level,
+ c.size,
+ c.linesize,
+ c.associativity,
+ c.shared);
}
}
if (hwTop.supportLevel() >= gmx::HardwareTopology::SupportLevel::FullWithDevices)
{
s += gmx::formatString(" PCI devices:\n");
- for (auto& d : hwTop.machine().devices)
+ for (const auto& d : hwTop.machine().devices)
{
s += gmx::formatString(
- " %04x:%02x:%02x.%1x Id: %04x:%04x Class: 0x%04x Numa: %d\n", d.domain,
- d.bus, d.dev, d.func, d.vendorId, d.deviceId, d.classId, d.numaNodeId);
+ " %04x:%02x:%02x.%1x Id: %04x:%04x Class: 0x%04x Numa: %d\n",
+ d.domain,
+ d.bus,
+ d.dev,
+ d.func,
+ d.vendorId,
+ d.deviceId,
+ d.classId,
+ d.numaNodeId);
}
}
}
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
if (c.supportLevel() >= gmx::CpuInfo::SupportLevel::LogicalProcessorInfo)
{
// Make sure assigned numbers are reasonable if we have them
- for (auto& l : c.logicalProcessors())
+ for (const auto& l : c.logicalProcessors())
{
EXPECT_GE(l.socketRankInMachine, 0)
<< "Impossible socket index for logical processor. " << commonMsg << std::endl;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
auto logicalProcessors = hwTop.machine().logicalProcessors;
for (auto logicalProcessorIt = logicalProcessors.begin();
- logicalProcessorIt != logicalProcessors.end(); ++logicalProcessorIt)
+ logicalProcessorIt != logicalProcessors.end();
+ ++logicalProcessorIt)
{
// Check that logical processor information contains
// reasonable values.
// for each logical processor.
for (auto remainingLogicalProcessorIt = logicalProcessorIt + 1;
- remainingLogicalProcessorIt != logicalProcessors.end(); ++remainingLogicalProcessorIt)
+ remainingLogicalProcessorIt != logicalProcessors.end();
+ ++remainingLogicalProcessorIt)
{
SCOPED_TRACE(gmx::formatString("Other socket rank in machine: %d",
remainingLogicalProcessorIt->socketRankInMachine));
// Check that the sum of numa domains is the total processor count
int processorsinNumaNudes = 0;
- for (auto& n : hwTop.machine().numa.nodes)
+ for (const auto& n : hwTop.machine().numa.nodes)
{
processorsinNumaNudes += n.logicalProcessorId.size();
}
{
elem = 0;
}
- for (auto& n : hwTop.machine().numa.nodes)
+ for (const auto& n : hwTop.machine().numa.nodes)
{
- for (auto& idx : n.logicalProcessorId)
+ for (const auto& idx : n.logicalProcessorId)
{
v[idx] = 1;
}
EXPECT_EQ(uniqueProcessorsinNumaNudes, hwTop.machine().logicalProcessorCount);
// We must have some memory in a numa node
- for (auto& n : hwTop.machine().numa.nodes)
+ for (const auto& n : hwTop.machine().numa.nodes)
{
EXPECT_GT(n.memory, 0);
}
EXPECT_GT(hwTop.machine().numa.maxRelativeLatency, 0);
// Check number of rows matches # numa nodes
EXPECT_EQ(hwTop.machine().numa.relativeLatency.size(), hwTop.machine().numa.nodes.size());
- for (auto& v2 : hwTop.machine().numa.relativeLatency)
+ for (const auto& v2 : hwTop.machine().numa.relativeLatency)
{
// Check that size of each row matches # numa nodes
EXPECT_EQ(v2.size(), hwTop.machine().numa.nodes.size());
- for (auto& latency : v2)
+ for (const auto& latency : v2)
{
// Latency values should be positive
EXPECT_GT(latency, 0);
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+add_library(imd INTERFACE)
file(GLOB IMD_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${IMD_SOURCES} PARENT_SCOPE)
+
+# Source files have the following private module dependencies.
+target_link_libraries(imd PRIVATE
+# gmxlib
+# math
+# mdtypes
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(imd PUBLIC
+target_include_directories(imd INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(imd PUBLIC
+target_link_libraries(imd INTERFACE
+ legacy_api
+ )
+
+# TODO: when imd is an OBJECT target
+#target_link_libraries(imd PUBLIC legacy_api)
+#target_link_libraries(imd PRIVATE common)
+
+# Module dependencies
+# imd interfaces convey transitive dependence on these modules.
+#target_link_libraries(imd PUBLIC
+target_link_libraries(imd INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(imd PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(imd PRIVATE legacy_modules)
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "imd.h"
#include "config.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/smalloc.h"
/*! \brief IMD Protocol Version. */
constexpr int c_protocolVersion = 2;
+enum class IMDMessageType : int;
+
/*! \internal
* \brief
* IMD (interactive molecular dynamics) energy record.
* Do conversion from Cal->Joule and from
* Angstrom -> nm and from a pointer array to arrays to 3*N array.
*/
- void copyToMDForces();
+ void copyToMDForces() const;
/*! \brief Return true if any of the forces or indices changed. */
bool bForcesChanged() const;
/*! \brief Update the old_f_ind and old_forces arrays to contain the current values. */
*/
void openOutputFile(const char* fn, int nat_total, const gmx_output_env_t* oenv, StartingBehavior startingBehavior);
/*! \brief Creates the molecule start-end position array of molecules in the IMD group. */
- void prepareMoleculesInImdGroup(const gmx_mtop_t* top_global);
+ void prepareMoleculesInImdGroup(const gmx_mtop_t& top_global);
/*! \brief Removes shifts of molecules diffused outside of the box. */
- void removeMolecularShifts(const matrix box);
+ void removeMolecularShifts(const matrix box) const;
/*! \brief Initialize arrays used to assemble the positions from the other nodes. */
- void prepareForPositionAssembly(const t_commrec* cr, const rvec x[]);
+ void prepareForPositionAssembly(const t_commrec* cr, gmx::ArrayRef<const gmx::RVec> coords);
/*! \brief Interact with any connected VMD session */
- bool run(int64_t step, bool bNS, const matrix box, const rvec x[], double t);
+ bool run(int64_t step, bool bNS, const matrix box, gmx::ArrayRef<const gmx::RVec> coords, double t);
// TODO rename all the data members to have underscore suffixes
IMdpOptionProvider* mdpOptionProvider() override { return nullptr; }
IMDOutputProvider* outputProvider() override { return nullptr; }
void initForceProviders(ForceProviders* /* forceProviders */) override {}
- void subscribeToSimulationSetupNotifications(MdModulesNotifier* /* notifier */) override {}
- void subscribeToPreProcessingNotifications(MdModulesNotifier* /* notifier */) override {}
+ void subscribeToSimulationSetupNotifications(MDModulesNotifiers* /* notifiers */) override {}
+ void subscribeToPreProcessingNotifications(MDModulesNotifiers* /* notifiers */) override {}
};
std::unique_ptr<IMDModule> createInteractiveMolecularDynamicsModule()
*
* We use the same records as the NAMD/VMD IMD implementation.
*/
-typedef enum IMDType_t
+enum class IMDMessageType : int
{
- IMD_DISCONNECT, /**< client disconnect */
- IMD_ENERGIES, /**< energy data */
- IMD_FCOORDS, /**< atomic coordinates */
- IMD_GO, /**< start command for the simulation */
- IMD_HANDSHAKE, /**< handshake to determine little/big endianness */
- IMD_KILL, /**< terminates the simulation */
- IMD_MDCOMM, /**< force data */
- IMD_PAUSE, /**< pauses the simulation */
- IMD_TRATE, /**< sets the IMD transmission and processing rate */
- IMD_IOERROR, /**< I/O error */
- IMD_NR /**< number of entries */
-} IMDMessageType;
+ Disconnect, /**< client disconnect */
+ Energies, /**< energy data */
+ FCoords, /**< atomic coordinates */
+ Go, /**< start command for the simulation */
+ Handshake, /**< handshake to determine little/big endianness */
+ Kill, /**< terminates the simulation */
+ Mdcomm, /**< force data */
+ Pause, /**< pauses the simulation */
+ TRate, /**< sets the IMD transmission and processing rate */
+ IOerror, /**< I/O error */
+ Count /**< number of entries */
+};
/*! \brief Names of the IMDType for error messages.
*/
-static const char* eIMDType_names[IMD_NR + 1] = { "IMD_DISCONNECT", "IMD_ENERGIES", "IMD_FCOORDS",
- "IMD_GO", "IMD_HANDSHAKE", "IMD_KILL",
- "IMD_MDCOMM", "IMD_PAUSE", "IMD_TRATE",
- "IMD_IOERROR", nullptr };
+static const char* enumValueToString(IMDMessageType enumValue)
+{
+ constexpr gmx::EnumerationArray<IMDMessageType, const char*> imdMessageTypeNames = {
+ "IMD_DISCONNECT", "IMD_ENERGIES", "IMD_FCOORDS", "IMD_GO", "IMD_HANDSHAKE",
+ "IMD_KILL", "IMD_MDCOMM", "IMD_PAUSE", "IMD_TRATE", "IMD_IOERROR"
+ };
+ return imdMessageTypeNames[enumValue];
+}
/*! \brief Fills the header with message and the length argument. */
static void fill_header(IMDHeader* header, IMDMessageType type, int32_t length)
{
/* We (ab-)use htonl network function for the correct endianness */
- header->type = imd_htonl(static_cast<int32_t>(type));
+ header->type = imd_htonl(static_cast<int>(type));
header->length = imd_htonl(length);
}
static void swap_header(IMDHeader* header)
{
/* and vice versa... */
- header->type = imd_ntohl(header->type);
+ header->type = imd_ntohl(static_cast<int>(header->type));
header->length = imd_ntohl(header->length);
}
IMDHeader header;
- fill_header(&header, IMD_HANDSHAKE, 1);
+ fill_header(&header, IMDMessageType::Handshake, 1);
header.length = c_protocolVersion; /* client wants unswapped version */
return static_cast<int>(imd_write_multiple(socket, reinterpret_cast<char*>(&header), c_headerSize)
recsize = c_headerSize + sizeof(IMDEnergyBlock);
- fill_header(reinterpret_cast<IMDHeader*>(buffer), IMD_ENERGIES, 1);
+ fill_header(reinterpret_cast<IMDHeader*>(buffer), IMDMessageType::Energies, 1);
memcpy(buffer + c_headerSize, energies, sizeof(IMDEnergyBlock));
return static_cast<int>(imd_write_multiple(socket, buffer, recsize) != recsize);
if (imd_read_multiple(socket, reinterpret_cast<char*>(&header), c_headerSize) != c_headerSize)
{
- return IMD_IOERROR;
+ return IMDMessageType::IOerror;
}
swap_header(&header);
*length = header.length;
void write_IMDgroup_to_file(bool bIMD,
t_inputrec* ir,
const t_state* state,
- const gmx_mtop_t* sys,
+ const gmx_mtop_t& sys,
int nfile,
const t_filenm fnm[])
{
if (bIMD)
{
IMDatoms = gmx_mtop_global_atoms(sys);
- write_sto_conf_indexed(opt2fn("-imd", nfile, fnm), "IMDgroup", &IMDatoms,
- state->x.rvec_array(), state->v.rvec_array(), ir->pbcType,
- state->box, ir->imd->nat, ir->imd->ind);
+ write_sto_conf_indexed(opt2fn("-imd", nfile, fnm),
+ "IMDgroup",
+ &IMDatoms,
+ state->x.rvec_array(),
+ state->v.rvec_array(),
+ ir->pbcType,
+ state->box,
+ ir->imd->nat,
+ ir->imd->ind);
}
}
return;
}
- dd_make_local_group_indices(dd->ga2la, impl_->nat, impl_->ind, &impl_->nat_loc, &impl_->ind_loc,
- &impl_->nalloc_loc, impl_->xa_ind);
+ dd_make_local_group_indices(
+ dd->ga2la, impl_->nat, impl_->ind, &impl_->nat_loc, &impl_->ind_loc, &impl_->nalloc_loc, impl_->xa_ind);
}
size = c_headerSize + 3 * sizeof(float) * nat;
/* Prepare header */
- fill_header(reinterpret_cast<IMDHeader*>(buffer), IMD_FCOORDS, static_cast<int32_t>(nat));
+ fill_header(reinterpret_cast<IMDHeader*>(buffer), IMDMessageType::FCoords, static_cast<int32_t>(nat));
for (i = 0; i < nat; i++)
{
- sendx[0] = static_cast<float>(x[i][0]) * NM2A;
- sendx[1] = static_cast<float>(x[i][1]) * NM2A;
- sendx[2] = static_cast<float>(x[i][2]) * NM2A;
+ sendx[0] = static_cast<float>(x[i][0]) * gmx::c_nm2A;
+ sendx[1] = static_cast<float>(x[i][1]) * gmx::c_nm2A;
+ sendx[2] = static_cast<float>(x[i][2]) * gmx::c_nm2A;
memcpy(buffer + c_headerSize + i * tuplesize, sendx, tuplesize);
}
/* Check if we get the proper "GO" command from client. */
if (imdsock_tryread(clientsocket, c_connectWait, 0) != 1
- || imd_recv_header(clientsocket, &(length)) != IMD_GO)
+ || imd_recv_header(clientsocket, &(length)) != IMDMessageType::Go)
{
issueFatalError("No IMD_GO order received. IMD connection failed.");
}
void ImdSession::Impl::blockConnect()
{
/* do not wait for connection, when e.g. ctrl+c is pressed and we will terminate anyways. */
- if (!(static_cast<int>(gmx_get_stop_condition()) == gmx_stop_cond_none))
+ if (!(gmx_get_stop_condition() == StopCondition::None))
{
return;
}
.appendTextFormatted("%s Will wait until I have a connection and IMD_GO orders.", IMDstr);
/* while we have no clientsocket... 2nd part: we should still react on ctrl+c */
- while ((!clientsocket) && (static_cast<int>(gmx_get_stop_condition()) == gmx_stop_cond_none))
+ while ((!clientsocket) && (gmx_get_stop_condition() == StopCondition::None))
{
tryConnect();
imd_sleep(c_loopWait);
}
-void ImdSession::Impl::copyToMDForces()
+void ImdSession::Impl::copyToMDForces() const
{
int i;
- real conversion = CAL2JOULE * NM2A;
+ real conversion = gmx::c_cal2Joule * gmx::c_nm2A;
for (i = 0; i < nforces; i++)
switch (itype)
{
/* IMD asks us to terminate the simulation, check if the user allowed this */
- case IMD_KILL:
+ case IMDMessageType::Kill:
if (bTerminatable)
{
GMX_LOG(mdlog.warning)
IMDstr);
bTerminated = true;
bWConnect = false;
- gmx_set_stop_condition(gmx_stop_cond_next);
+ gmx_set_stop_condition(StopCondition::Next);
}
else
{
break;
/* the client doen't want to talk to us anymore */
- case IMD_DISCONNECT:
+ case IMDMessageType::Disconnect:
GMX_LOG(mdlog.warning).appendTextFormatted(" %s Disconnecting client.", IMDstr);
disconnectClient();
break;
/* we got new forces, read them and set bNewForces flag */
- case IMD_MDCOMM:
+ case IMDMessageType::Mdcomm:
readVmdForces();
bNewForces = true;
break;
/* the client asks us to (un)pause the simulation. So we toggle the IMDpaused state */
- case IMD_PAUSE:
+ case IMDMessageType::Pause:
if (IMDpaused)
{
GMX_LOG(mdlog.warning).appendTextFormatted(" %s Un-pause command received.", IMDstr);
/* the client sets a new transfer rate, if we get 0, we reset the rate
* to the default. VMD filters 0 however */
- case IMD_TRATE:
+ case IMDMessageType::TRate:
nstimd_new = (length > 0) ? length : defaultNstImd;
GMX_LOG(mdlog.warning)
.appendTextFormatted(" %s Update frequency will be set to %d.", IMDstr, nstimd_new);
/* Catch all rule for the remaining IMD types which we don't expect */
default:
GMX_LOG(mdlog.warning)
- .appendTextFormatted(" %s Received unexpected %s.", IMDstr,
- enum_name(static_cast<int>(itype), IMD_NR, eIMDType_names));
+ .appendTextFormatted(
+ " %s Received unexpected %s.", IMDstr, enumValueToString(itype));
issueFatalError("Terminating connection");
break;
} /* end switch */
"%s For a log of the IMD pull forces explicitly specify '-if' on the command "
"line.\n"
"%s (Not possible with energy minimization.)\n",
- IMDstr, IMDstr);
+ IMDstr,
+ IMDstr);
return;
}
"the atoms suffices.\n");
}
- xvgr_header(outf, "IMD Pull Forces", "Time (ps)",
- "# of Forces / Atom IDs / Forces (kJ/mol)", exvggtNONE, oenv);
+ xvgr_header(outf, "IMD Pull Forces", "Time (ps)", "# of Forces / Atom IDs / Forces (kJ/mol)", exvggtNONE, oenv);
fprintf(outf, "# Can display and manipulate %d (of a total of %d) atoms via IMD.\n", nat, nat_total);
fprintf(outf, "# column 1 : time (ps)\n");
}
-void ImdSession::Impl::prepareMoleculesInImdGroup(const gmx_mtop_t* top_global)
+void ImdSession::Impl::prepareMoleculesInImdGroup(const gmx_mtop_t& top_global)
{
/* check whether index is sorted */
for (int i = 0; i < nat - 1; i++)
}
}
- RangePartitioning gmols = gmx_mtop_molecules(*top_global);
+ RangePartitioning gmols = gmx_mtop_molecules(top_global);
t_block lmols;
lmols.nr = 0;
snew(lmols.index, gmols.numBlocks() + 1);
}
-void ImdSession::Impl::removeMolecularShifts(const matrix box)
+void ImdSession::Impl::removeMolecularShifts(const matrix box) const
{
/* for each molecule also present in IMD group */
for (int i = 0; i < mols.nr; i++)
}
-void ImdSession::Impl::prepareForPositionAssembly(const t_commrec* cr, const rvec x[])
+void ImdSession::Impl::prepareForPositionAssembly(const t_commrec* cr, gmx::ArrayRef<const gmx::RVec> coords)
{
snew(xa, nat);
snew(xa_ind, nat);
for (int i = 0; i < nat; i++)
{
int ii = ind[i];
- copy_rvec(x[ii], xa_old[i]);
+ copy_rvec(coords[ii], xa_old[i]);
}
}
{
if (PAR(cr))
{
- if (((ir->eI) == eiSteep) || ((ir->eI) == eiCG) || ((ir->eI) == eiLBFGS) || ((ir->eI) == eiNM))
+ if (((ir->eI) == IntegrationAlgorithm::Steep) || ((ir->eI) == IntegrationAlgorithm::CG)
+ || ((ir->eI) == IntegrationAlgorithm::LBFGS) || ((ir->eI) == IntegrationAlgorithm::NM))
{
gmx_fatal(FARGS,
"%s Energy minimization via steep, CG, lbfgs and nm in parallel is currently "
}
}
-std::unique_ptr<ImdSession> makeImdSession(const t_inputrec* ir,
- const t_commrec* cr,
- gmx_wallcycle* wcycle,
- gmx_enerdata_t* enerd,
- const gmx_multisim_t* ms,
- const gmx_mtop_t* top_global,
- const MDLogger& mdlog,
- const rvec x[],
- int nfile,
- const t_filenm fnm[],
- const gmx_output_env_t* oenv,
- const ImdOptions& options,
- const gmx::StartingBehavior startingBehavior)
+std::unique_ptr<ImdSession> makeImdSession(const t_inputrec* ir,
+ const t_commrec* cr,
+ gmx_wallcycle* wcycle,
+ gmx_enerdata_t* enerd,
+ const gmx_multisim_t* ms,
+ const gmx_mtop_t& top_global,
+ const MDLogger& mdlog,
+ gmx::ArrayRef<const gmx::RVec> coords,
+ int nfile,
+ const t_filenm fnm[],
+ const gmx_output_env_t* oenv,
+ const ImdOptions& options,
+ const gmx::StartingBehavior startingBehavior)
{
std::unique_ptr<ImdSession> session(new ImdSession(mdlog));
- auto impl = session->impl_.get();
+ auto* impl = session->impl_.get();
/* We will allow IMD sessions only if supported by the binary and
explicitly enabled in the .tpr file */
.appendTextFormatted(
"%s Integrator '%s' is not supported for Interactive Molecular Dynamics, "
"running normally instead",
- IMDstr, ei_names[ir->eI]);
+ IMDstr,
+ enumValueToString(ir->eI));
return session;
}
if (isMultiSim(ms))
.appendTextFormatted(
"%s None of the -imd switches was used.\n"
"%s This run will not accept incoming IMD connections",
- IMDstr, IMDstr);
+ IMDstr,
+ IMDstr);
}
} /* end master only */
*****************************************************
*/
- int nat_total = top_global->natoms;
+ int nat_total = top_global.natoms;
/* Initialize IMD session. If we read in a pre-IMD .tpr file, ir->imd->nat
* will be zero. For those cases we transfer _all_ atomic positions */
impl->syncNodes(cr, 0);
/* Initialize arrays used to assemble the positions from the other nodes */
- impl->prepareForPositionAssembly(cr, x);
+ impl->prepareForPositionAssembly(cr, coords);
/* Initialize molecule blocks to make them whole later...*/
if (MASTER(cr))
}
-bool ImdSession::Impl::run(int64_t step, bool bNS, const matrix box, const rvec x[], double t)
+bool ImdSession::Impl::run(int64_t step, bool bNS, const matrix box, gmx::ArrayRef<const gmx::RVec> coords, double t)
{
/* IMD at all? */
if (!sessionPossible)
return false;
}
- wallcycle_start(wcycle, ewcIMD);
+ wallcycle_start(wcycle, WallCycleCounter::Imd);
/* read command from client and check if new incoming connection */
if (MASTER(cr))
{
/* Transfer the IMD positions to the master node. Every node contributes
* its local positions x and stores them in the assembled xa array. */
- communicate_group_positions(cr, xa, xa_shifts, xa_eshifts, true, x, nat, nat_loc, ind_loc,
- xa_ind, xa_old, box);
+ communicate_group_positions(
+ cr, xa, xa_shifts, xa_eshifts, true, as_rvec_array(coords.data()), nat, nat_loc, ind_loc, xa_ind, xa_old, box);
/* If connected and master -> remove shifts */
if ((imdstep && bConnected) && MASTER(cr))
}
}
- wallcycle_stop(wcycle, ewcIMD);
+ wallcycle_stop(wcycle, WallCycleCounter::Imd);
return imdstep;
}
-bool ImdSession::run(int64_t step, bool bNS, const matrix box, const rvec x[], double t)
+bool ImdSession::run(int64_t step, bool bNS, const matrix box, gmx::ArrayRef<const gmx::RVec> coords, double t)
{
- return impl_->run(step, bNS, box, x, t);
+ return impl_->run(step, bNS, box, coords, t);
}
void ImdSession::fillEnergyRecord(int64_t step, bool bHaveNewEnergies)
return;
}
- wallcycle_start(impl_->wcycle, ewcIMD);
+ wallcycle_start(impl_->wcycle, WallCycleCounter::Imd);
/* Update time step for IMD and prepare IMD energy record if we have new energies. */
fillEnergyRecord(step, bHaveNewEnergies);
sendPositionsAndEnergies();
}
- wallcycle_stop(impl_->wcycle, ewcIMD);
+ wallcycle_stop(impl_->wcycle, WallCycleCounter::Imd);
}
-void ImdSession::applyForces(rvec* f)
+void ImdSession::applyForces(gmx::ArrayRef<gmx::RVec> force)
{
if (!impl_->sessionPossible || !impl_->bForceActivated)
{
return;
}
- wallcycle_start(impl_->wcycle, ewcIMD);
+ wallcycle_start(impl_->wcycle, WallCycleCounter::Imd);
for (int i = 0; i < impl_->nforces; i++)
{
j = *locndx;
}
- rvec_inc(f[j], impl_->f[i]);
+ rvec_inc(force[j], impl_->f[i]);
}
- wallcycle_stop(impl_->wcycle, ewcIMD);
+ wallcycle_stop(impl_->wcycle, WallCycleCounter::Imd);
}
ImdSession::ImdSession(const MDLogger& mdlog) : impl_(new Impl(mdlog)) {}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <memory>
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/classhelpers.h"
struct gmx_domdec_t;
struct gmx_enerdata_t;
class MDLogger;
struct ImdOptions;
struct MdrunOptions;
+template<typename>
+class ArrayRef;
/*! \brief
* Creates a module for interactive molecular dynamics.
void write_IMDgroup_to_file(bool bIMD,
t_inputrec* ir,
const t_state* state,
- const gmx_mtop_t* sys,
+ const gmx_mtop_t& sys,
int nfile,
const t_filenm fnm[]);
* \param ms Handler for multi-simulations.
* \param top_global The topology of the whole system.
* \param mdlog Logger
- * \param x The starting positions of the atoms.
+ * \param coords The starting positions of the atoms.
* \param nfile Number of files.
* \param fnm Struct containing file names etc.
* \param oenv Output options.
* \param options Options for interactive MD.
* \param startingBehavior Describes whether this is a restart appending to output files
*/
-std::unique_ptr<ImdSession> makeImdSession(const t_inputrec* ir,
- const t_commrec* cr,
- gmx_wallcycle* wcycle,
- gmx_enerdata_t* enerd,
- const gmx_multisim_t* ms,
- const gmx_mtop_t* top_global,
- const MDLogger& mdlog,
- const rvec x[],
- int nfile,
- const t_filenm fnm[],
- const gmx_output_env_t* oenv,
- const ImdOptions& options,
- StartingBehavior startingBehavior);
+std::unique_ptr<ImdSession> makeImdSession(const t_inputrec* ir,
+ const t_commrec* cr,
+ gmx_wallcycle* wcycle,
+ gmx_enerdata_t* enerd,
+ const gmx_multisim_t* ms,
+ const gmx_mtop_t& top_global,
+ const MDLogger& mdlog,
+ gmx::ArrayRef<const gmx::RVec> coords,
+ int nfile,
+ const t_filenm fnm[],
+ const gmx_output_env_t* oenv,
+ const ImdOptions& options,
+ StartingBehavior startingBehavior);
class ImdSession
{
* \param step The time step.
* \param bNS Is this a neighbor searching step?
* \param box The simulation box.
- * \param x The local atomic positions on this node.
+ * \param coords The local atomic positions on this node.
* \param t The time.
*
* \returns Whether or not we have to do IMD communication at this step.
*/
- bool run(int64_t step, bool bNS, const matrix box, const rvec x[], double t);
+ bool run(int64_t step, bool bNS, const matrix box, gmx::ArrayRef<const gmx::RVec> coords, double t);
/*! \brief Add external forces from a running interactive molecular dynamics session.
*
- * \param f The forces.
+ * \param force The forces.
*/
- void applyForces(rvec* f);
+ void applyForces(gmx::ArrayRef<gmx::RVec> force);
/*! \brief Copy energies and convert to float from enerdata to the IMD energy record.
*
//! Implementation type.
class Impl;
//! Implementation object.
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
public:
// Befriend the factory function.
- friend std::unique_ptr<ImdSession> makeImdSession(const t_inputrec* ir,
- const t_commrec* cr,
- gmx_wallcycle* wcycle,
- gmx_enerdata_t* enerd,
- const gmx_multisim_t* ms,
- const gmx_mtop_t* top_global,
- const MDLogger& mdlog,
- const rvec x[],
- int nfile,
- const t_filenm fnm[],
- const gmx_output_env_t* oenv,
- const ImdOptions& options,
- StartingBehavior startingBehavior);
+ friend std::unique_ptr<ImdSession> makeImdSession(const t_inputrec* ir,
+ const t_commrec* cr,
+ gmx_wallcycle* wcycle,
+ gmx_enerdata_t* enerd,
+ const gmx_multisim_t* ms,
+ const gmx_mtop_t& top_global,
+ const MDLogger& mdlog,
+ gmx::ArrayRef<const gmx::RVec> coords,
+ int nfile,
+ const t_filenm fnm[],
+ const gmx_output_env_t* oenv,
+ const ImdOptions& options,
+ StartingBehavior startingBehavior);
};
} // namespace gmx
${LINEARALGEBRA_SOURCES} ${BLAS_SOURCES} ${LAPACK_SOURCES})
add_library(linearalgebra OBJECT ${LINEARALGEBRA_SOURCES})
+# TODO: Only expose the module's public headers.
+target_include_directories(linearalgebra INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+target_include_directories(linearalgebra PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
+
gmx_target_compile_options(linearalgebra)
target_compile_definitions(linearalgebra PRIVATE HAVE_CONFIG_H)
# The linearalgebra code is all considered external, and we will
# not expect null termination of C strings.
gmx_target_warning_suppression(linearalgebra -Wno-stringop-truncation HAS_NO_STRINGOP_TRUNCATION)
endif()
+target_link_libraries(linearalgebra PRIVATE legacy_api)
+target_link_libraries(linearalgebra PRIVATE common)
+# TODO: Link specific modules.
+target_link_libraries(linearalgebra PRIVATE legacy_modules)
list(APPEND libgromacs_object_library_dependencies linearalgebra)
set(libgromacs_object_library_dependencies ${libgromacs_object_library_dependencies} PARENT_SCOPE)
*/
#if GMX_DOUBLE
F77_FUNC(dsyevr, DSYEVR)
- (jobz, "I", "L", &n, a, &n, &vl, &vu, &index_lower, &index_upper, &abstol, &m, eigenvalues,
- eigenvectors, &n, isuppz, &w0, &lwork, &iw0, &liwork, &info);
+ (jobz,
+ "I",
+ "L",
+ &n,
+ a,
+ &n,
+ &vl,
+ &vu,
+ &index_lower,
+ &index_upper,
+ &abstol,
+ &m,
+ eigenvalues,
+ eigenvectors,
+ &n,
+ isuppz,
+ &w0,
+ &lwork,
+ &iw0,
+ &liwork,
+ &info);
#else
F77_FUNC(ssyevr, SSYEVR)
- (jobz, "I", "L", &n, a, &n, &vl, &vu, &index_lower, &index_upper, &abstol, &m, eigenvalues,
- eigenvectors, &n, isuppz, &w0, &lwork, &iw0, &liwork, &info);
+ (jobz,
+ "I",
+ "L",
+ &n,
+ a,
+ &n,
+ &vl,
+ &vu,
+ &index_lower,
+ &index_upper,
+ &abstol,
+ &m,
+ eigenvalues,
+ eigenvectors,
+ &n,
+ isuppz,
+ &w0,
+ &lwork,
+ &iw0,
+ &liwork,
+ &info);
#endif
if (info != 0)
#if GMX_DOUBLE
F77_FUNC(dsyevr, DSYEVR)
- (jobz, "I", "L", &n, a, &n, &vl, &vu, &index_lower, &index_upper, &abstol, &m, eigenvalues,
- eigenvectors, &n, isuppz, work, &lwork, iwork, &liwork, &info);
+ (jobz,
+ "I",
+ "L",
+ &n,
+ a,
+ &n,
+ &vl,
+ &vu,
+ &index_lower,
+ &index_upper,
+ &abstol,
+ &m,
+ eigenvalues,
+ eigenvectors,
+ &n,
+ isuppz,
+ work,
+ &lwork,
+ iwork,
+ &liwork,
+ &info);
#else
F77_FUNC(ssyevr, SSYEVR)
- (jobz, "I", "L", &n, a, &n, &vl, &vu, &index_lower, &index_upper, &abstol, &m, eigenvalues,
- eigenvectors, &n, isuppz, work, &lwork, iwork, &liwork, &info);
+ (jobz,
+ "I",
+ "L",
+ &n,
+ a,
+ &n,
+ &vl,
+ &vu,
+ &index_lower,
+ &index_upper,
+ &abstol,
+ &m,
+ eigenvalues,
+ eigenvectors,
+ &n,
+ isuppz,
+ work,
+ &lwork,
+ iwork,
+ &liwork,
+ &info);
#endif
sfree(isuppz);
{
# if GMX_DOUBLE
F77_FUNC(pdsaupd, PDSAUPD)
- (&ido, "I", &n, "SA", &neig, &abstol, resid, &ncv, v, &n, iparam, ipntr, workd, iwork,
- workl, &lworkl, &info);
+ (&ido, "I", &n, "SA", &neig, &abstol, resid, &ncv, v, &n, iparam, ipntr, workd, iwork, workl, &lworkl, &info);
# else
F77_FUNC(pssaupd, PSSAUPD)
- (&ido, "I", &n, "SA", &neig, &abstol, resid, &ncv, v, &n, iparam, ipntr, workd, iwork,
- workl, &lworkl, &info);
+ (&ido, "I", &n, "SA", &neig, &abstol, resid, &ncv, v, &n, iparam, ipntr, workd, iwork, workl, &lworkl, &info);
# endif
if (ido == -1 || ido == 1)
{
gmx_fatal(FARGS,
"Maximum number of iterations (%d) reached in Arnoldi\n"
"diagonalization, but only %d of %d eigenvectors converged.\n",
- maxiter, iparam[4], neig);
+ maxiter,
+ iparam[4],
+ neig);
}
else if (info != 0)
{
# if GMX_DOUBLE
F77_FUNC(pdseupd, PDSEUPD)
- (&dovec, "A", select, eigenvalues, eigenvectors, &n, NULL, "I", &n, "SA", &neig, &abstol, resid,
- &ncv, v, &n, iparam, ipntr, workd, workl, &lworkl, &info);
+ (&dovec,
+ "A",
+ select,
+ eigenvalues,
+ eigenvectors,
+ &n,
+ NULL,
+ "I",
+ &n,
+ "SA",
+ &neig,
+ &abstol,
+ resid,
+ &ncv,
+ v,
+ &n,
+ iparam,
+ ipntr,
+ workd,
+ workl,
+ &lworkl,
+ &info);
# else
F77_FUNC(psseupd, PSSEUPD)
- (&dovec, "A", select, eigenvalues, eigenvectors, &n, NULL, "I", &n, "SA", &neig, &abstol, resid,
- &ncv, v, &n, iparam, ipntr, workd, workl, &lworkl, &info);
+ (&dovec,
+ "A",
+ select,
+ eigenvalues,
+ eigenvectors,
+ &n,
+ NULL,
+ "I",
+ &n,
+ "SA",
+ &neig,
+ &abstol,
+ resid,
+ &ncv,
+ v,
+ &n,
+ iparam,
+ ipntr,
+ workd,
+ workl,
+ &lworkl,
+ &info);
# endif
sfree(v);
{
#if GMX_DOUBLE
F77_FUNC(dsaupd, DSAUPD)
- (&ido, "I", &n, "SA", &neig, &abstol, resid, &ncv, v, &n, iparam, ipntr, workd, iwork,
- workl, &lworkl, &info);
+ (&ido, "I", &n, "SA", &neig, &abstol, resid, &ncv, v, &n, iparam, ipntr, workd, iwork, workl, &lworkl, &info);
#else
F77_FUNC(ssaupd, SSAUPD)
- (&ido, "I", &n, "SA", &neig, &abstol, resid, &ncv, v, &n, iparam, ipntr, workd, iwork,
- workl, &lworkl, &info);
+ (&ido, "I", &n, "SA", &neig, &abstol, resid, &ncv, v, &n, iparam, ipntr, workd, iwork, workl, &lworkl, &info);
#endif
if (ido == -1 || ido == 1)
{
gmx_fatal(FARGS,
"Maximum number of iterations (%d) reached in Arnoldi\n"
"diagonalization, but only %d of %d eigenvectors converged.\n",
- maxiter, iparam[4], neig);
+ maxiter,
+ iparam[4],
+ neig);
}
else if (info != 0)
{
#if GMX_DOUBLE
F77_FUNC(dseupd, DSEUPD)
- (&dovec, "A", select, eigenvalues, eigenvectors, &n, nullptr, "I", &n, "SA", &neig, &abstol,
- resid, &ncv, v, &n, iparam, ipntr, workd, workl, &lworkl, &info);
+ (&dovec,
+ "A",
+ select,
+ eigenvalues,
+ eigenvectors,
+ &n,
+ nullptr,
+ "I",
+ &n,
+ "SA",
+ &neig,
+ &abstol,
+ resid,
+ &ncv,
+ v,
+ &n,
+ iparam,
+ ipntr,
+ workd,
+ workl,
+ &lworkl,
+ &info);
#else
F77_FUNC(sseupd, SSEUPD)
- (&dovec, "A", select, eigenvalues, eigenvectors, &n, nullptr, "I", &n, "SA", &neig, &abstol,
- resid, &ncv, v, &n, iparam, ipntr, workd, workl, &lworkl, &info);
+ (&dovec,
+ "A",
+ select,
+ eigenvalues,
+ eigenvectors,
+ &n,
+ nullptr,
+ "I",
+ &n,
+ "SA",
+ &neig,
+ &abstol,
+ resid,
+ &ncv,
+ v,
+ &n,
+ iparam,
+ ipntr,
+ workd,
+ workl,
+ &lworkl,
+ &info);
#endif
sfree(v);
if (h__[*kev + 1 + h_dim1] > 0.)
{
F77_FUNC(dgemv, DGEMV)
- ("N", n, &kplusp, &c_b5, &v[v_offset], ldv, &q[(*kev + 1) * q_dim1 + 1], &c__1, &c_b4,
- &workd[*n + 1], &c__1);
+ ("N", n, &kplusp, &c_b5, &v[v_offset], ldv, &q[(*kev + 1) * q_dim1 + 1], &c__1, &c_b4, &workd[*n + 1], &c__1);
}
i__1 = *kev;
{
i__2 = kplusp - i__ + 1;
F77_FUNC(dgemv, DGEMV)
- ("N", n, &i__2, &c_b5, &v[v_offset], ldv, &q[(*kev - i__ + 1) * q_dim1 + 1], &c__1, &c_b4,
- &workd[1], &c__1);
+ ("N", n, &i__2, &c_b5, &v[v_offset], ldv, &q[(*kev - i__ + 1) * q_dim1 + 1], &c__1, &c_b4, &workd[1], &c__1);
F77_FUNC(dcopy, DCOPY)(n, &workd[1], &c__1, &v[(kplusp - i__ + 1) * v_dim1 + 1], &c__1);
}
L30:
F77_FUNC(dgetv0, DGETV0)
- (ido, bmat, &iwork[11], &c__0, n, &iwork[12], &v[v_offset], ldv, &resid[1], rnorm, &ipntr[1],
- &workd[1], &iwork[21], &iwork[7]);
+ (ido,
+ bmat,
+ &iwork[11],
+ &c__0,
+ n,
+ &iwork[12],
+ &v[v_offset],
+ ldv,
+ &resid[1],
+ rnorm,
+ &ipntr[1],
+ &workd[1],
+ &iwork[21],
+ &iwork[7]);
if (*ido != 99)
{
goto L9000;
if (*mode != 2)
{
F77_FUNC(dgemv, DGEMV)
- ("T", n, &iwork[12], &c_b18, &v[v_offset], ldv, &workd[iwork[8]], &c__1, &c_b42,
- &workd[iwork[9]], &c__1);
+ ("T", n, &iwork[12], &c_b18, &v[v_offset], ldv, &workd[iwork[8]], &c__1, &c_b42, &workd[iwork[9]], &c__1);
}
else
{
F77_FUNC(dgemv, DGEMV)
- ("T", n, &iwork[12], &c_b18, &v[v_offset], ldv, &workd[iwork[10]], &c__1, &c_b42,
- &workd[iwork[9]], &c__1);
+ ("T", n, &iwork[12], &c_b18, &v[v_offset], ldv, &workd[iwork[10]], &c__1, &c_b42, &workd[iwork[9]], &c__1);
}
F77_FUNC(dgemv, DGEMV)
L80:
F77_FUNC(dgemv, DGEMV)
- ("T", n, &iwork[12], &c_b18, &v[v_offset], ldv, &workd[iwork[8]], &c__1, &c_b42,
- &workd[iwork[9]], &c__1);
+ ("T", n, &iwork[12], &c_b18, &v[v_offset], ldv, &workd[iwork[8]], &c__1, &c_b42, &workd[iwork[9]], &c__1);
F77_FUNC(dgemv, DGEMV)
("N", n, &iwork[12], &c_b50, &v[v_offset], ldv, &workd[iwork[9]], &c__1, &c_b18, &resid[1], &c__1);
if (iwork[2] == 1)
{
F77_FUNC(dgetv0, DGETV0)
- (ido, bmat, &c__1, &iwork[3], n, &c__1, &v[v_offset], ldv, &resid[1], &workd[*n * 3 + 1],
- &ipntr[1], &workd[1], &iwork[41], info);
+ (ido,
+ bmat,
+ &c__1,
+ &iwork[3],
+ n,
+ &c__1,
+ &v[v_offset],
+ ldv,
+ &resid[1],
+ &workd[*n * 3 + 1],
+ &ipntr[1],
+ &workd[1],
+ &iwork[41],
+ info);
if (*ido != 99)
{
}
F77_FUNC(dsaitr, DSAITR)
- (ido, bmat, n, &c__0, &iwork[9], mode, &resid[1], &workd[*n * 3 + 1], &v[v_offset], ldv,
- &h__[h_offset], ldh, &ipntr[1], &workd[1], &iwork[21], info);
+ (ido,
+ bmat,
+ n,
+ &c__0,
+ &iwork[9],
+ mode,
+ &resid[1],
+ &workd[*n * 3 + 1],
+ &v[v_offset],
+ ldv,
+ &h__[h_offset],
+ ldh,
+ &ipntr[1],
+ &workd[1],
+ &iwork[21],
+ info);
if (*ido != 99)
{
iwork[4] = 1;
F77_FUNC(dsaitr, DSAITR)
- (ido, bmat, n, nev, np, mode, &resid[1], &workd[*n * 3 + 1], &v[v_offset], ldv, &h__[h_offset],
- ldh, &ipntr[1], &workd[1], &iwork[21], info);
+ (ido,
+ bmat,
+ n,
+ nev,
+ np,
+ mode,
+ &resid[1],
+ &workd[*n * 3 + 1],
+ &v[v_offset],
+ ldv,
+ &h__[h_offset],
+ ldh,
+ &ipntr[1],
+ &workd[1],
+ &iwork[21],
+ info);
if (*ido != 99)
{
}
F77_FUNC(dsapps, DSAPPS)
- (n, nev, np, &ritz[1], &v[v_offset], ldv, &h__[h_offset], ldh, &resid[1], &q[q_offset], ldq,
- &workd[1]);
+ (n, nev, np, &ritz[1], &v[v_offset], ldv, &h__[h_offset], ldh, &resid[1], &q[q_offset], ldq, &workd[1]);
iwork[1] = 1;
if (*bmat == 'G')
}
F77_FUNC(dsaup2, DSAUP2)
- (ido, bmat, n, which, &iwork[13], &iwork[15], tol, &resid[1], &iwork[11], &iwork[6], &iwork[5],
- &iwork[10], &v[v_offset], ldv, &workl[iwork[3]], &iwork[8], &workl[iwork[16]], &workl[iwork[1]],
- &workl[iwork[4]], &iwork[9], &workl[iwork[7]], &ipntr[1], &workd[1], &iwork[21], info);
+ (ido,
+ bmat,
+ n,
+ which,
+ &iwork[13],
+ &iwork[15],
+ tol,
+ &resid[1],
+ &iwork[11],
+ &iwork[6],
+ &iwork[5],
+ &iwork[10],
+ &v[v_offset],
+ ldv,
+ &workl[iwork[3]],
+ &iwork[8],
+ &workl[iwork[16]],
+ &workl[iwork[1]],
+ &workl[iwork[4]],
+ &iwork[9],
+ &workl[iwork[7]],
+ &ipntr[1],
+ &workd[1],
+ &iwork[21],
+ info);
if (*ido == 3)
{
(ncv, &nconv, &workl[iq], &ldq, &workl[iw + *ncv], &workl[ihb], &ierr);
F77_FUNC(dorm2r, DORM2R)
- ("Right", "Notranspose", n, ncv, &nconv, &workl[iq], &ldq, &workl[iw + *ncv], &v[v_offset],
- ldv, &workd[*n + 1], &ierr);
+ ("Right",
+ "Notranspose",
+ n,
+ ncv,
+ &nconv,
+ &workl[iq],
+ &ldq,
+ &workl[iw + *ncv],
+ &v[v_offset],
+ ldv,
+ &workd[*n + 1],
+ &ierr);
F77_FUNC(dlacpy, DLACPY)("All", n, &nconv, &v[v_offset], ldv, &z__[z_offset], ldz);
i__1 = *ncv - 1;
}
workl[ihb + *ncv - 1] = 1.;
F77_FUNC(dorm2r, DORM2R)
- ("Left", "Transpose", ncv, &c__1, &nconv, &workl[iq], &ldq, &workl[iw + *ncv], &workl[ihb],
- ncv, &temp, &ierr);
+ ("Left", "Transpose", ncv, &c__1, &nconv, &workl[iq], &ldq, &workl[iw + *ncv], &workl[ihb], ncv, &temp, &ierr);
}
else if (*rvec && *howmny == 'S')
{
if (h__[*kev + 1 + h_dim1] > 0.)
{
F77_FUNC(sgemv, SGEMV)
- ("N", n, &kplusp, &c_b5, &v[v_offset], ldv, &q[(*kev + 1) * q_dim1 + 1], &c__1, &c_b4,
- &workd[*n + 1], &c__1);
+ ("N", n, &kplusp, &c_b5, &v[v_offset], ldv, &q[(*kev + 1) * q_dim1 + 1], &c__1, &c_b4, &workd[*n + 1], &c__1);
}
i__1 = *kev;
{
i__2 = kplusp - i__ + 1;
F77_FUNC(sgemv, SGEMV)
- ("N", n, &i__2, &c_b5, &v[v_offset], ldv, &q[(*kev - i__ + 1) * q_dim1 + 1], &c__1, &c_b4,
- &workd[1], &c__1);
+ ("N", n, &i__2, &c_b5, &v[v_offset], ldv, &q[(*kev - i__ + 1) * q_dim1 + 1], &c__1, &c_b4, &workd[1], &c__1);
F77_FUNC(scopy, SCOPY)(n, &workd[1], &c__1, &v[(kplusp - i__ + 1) * v_dim1 + 1], &c__1);
}
L30:
F77_FUNC(sgetv0, sgetv0)
- (ido, bmat, &iwork[11], &c__0, n, &iwork[12], &v[v_offset], ldv, &resid[1], rnorm, &ipntr[1],
- &workd[1], &iwork[21], &iwork[7]);
+ (ido,
+ bmat,
+ &iwork[11],
+ &c__0,
+ n,
+ &iwork[12],
+ &v[v_offset],
+ ldv,
+ &resid[1],
+ rnorm,
+ &ipntr[1],
+ &workd[1],
+ &iwork[21],
+ &iwork[7]);
if (*ido != 99)
{
goto L9000;
if (*mode != 2)
{
F77_FUNC(sgemv, SGEMV)
- ("T", n, &iwork[12], &c_b18, &v[v_offset], ldv, &workd[iwork[8]], &c__1, &c_b42,
- &workd[iwork[9]], &c__1);
+ ("T", n, &iwork[12], &c_b18, &v[v_offset], ldv, &workd[iwork[8]], &c__1, &c_b42, &workd[iwork[9]], &c__1);
}
else
{
F77_FUNC(sgemv, SGEMV)
- ("T", n, &iwork[12], &c_b18, &v[v_offset], ldv, &workd[iwork[10]], &c__1, &c_b42,
- &workd[iwork[9]], &c__1);
+ ("T", n, &iwork[12], &c_b18, &v[v_offset], ldv, &workd[iwork[10]], &c__1, &c_b42, &workd[iwork[9]], &c__1);
}
F77_FUNC(sgemv, SGEMV)
L80:
F77_FUNC(sgemv, SGEMV)
- ("T", n, &iwork[12], &c_b18, &v[v_offset], ldv, &workd[iwork[8]], &c__1, &c_b42,
- &workd[iwork[9]], &c__1);
+ ("T", n, &iwork[12], &c_b18, &v[v_offset], ldv, &workd[iwork[8]], &c__1, &c_b42, &workd[iwork[9]], &c__1);
F77_FUNC(sgemv, SGEMV)
("N", n, &iwork[12], &c_b50, &v[v_offset], ldv, &workd[iwork[9]], &c__1, &c_b18, &resid[1], &c__1);
if (iwork[2] == 1)
{
F77_FUNC(sgetv0, SGETV0)
- (ido, bmat, &c__1, &iwork[3], n, &c__1, &v[v_offset], ldv, &resid[1], &workd[*n * 3 + 1],
- &ipntr[1], &workd[1], &iwork[41], info);
+ (ido,
+ bmat,
+ &c__1,
+ &iwork[3],
+ n,
+ &c__1,
+ &v[v_offset],
+ ldv,
+ &resid[1],
+ &workd[*n * 3 + 1],
+ &ipntr[1],
+ &workd[1],
+ &iwork[41],
+ info);
if (*ido != 99)
{
}
F77_FUNC(ssaitr, SSAITR)
- (ido, bmat, n, &c__0, &iwork[9], mode, &resid[1], &workd[*n * 3 + 1], &v[v_offset], ldv,
- &h__[h_offset], ldh, &ipntr[1], &workd[1], &iwork[21], info);
+ (ido,
+ bmat,
+ n,
+ &c__0,
+ &iwork[9],
+ mode,
+ &resid[1],
+ &workd[*n * 3 + 1],
+ &v[v_offset],
+ ldv,
+ &h__[h_offset],
+ ldh,
+ &ipntr[1],
+ &workd[1],
+ &iwork[21],
+ info);
if (*ido != 99)
{
iwork[4] = 1;
F77_FUNC(ssaitr, SSAITR)
- (ido, bmat, n, nev, np, mode, &resid[1], &workd[*n * 3 + 1], &v[v_offset], ldv, &h__[h_offset],
- ldh, &ipntr[1], &workd[1], &iwork[21], info);
+ (ido,
+ bmat,
+ n,
+ nev,
+ np,
+ mode,
+ &resid[1],
+ &workd[*n * 3 + 1],
+ &v[v_offset],
+ ldv,
+ &h__[h_offset],
+ ldh,
+ &ipntr[1],
+ &workd[1],
+ &iwork[21],
+ info);
if (*ido != 99)
{
}
F77_FUNC(ssapps, SSAPPS)
- (n, nev, np, &ritz[1], &v[v_offset], ldv, &h__[h_offset], ldh, &resid[1], &q[q_offset], ldq,
- &workd[1]);
+ (n, nev, np, &ritz[1], &v[v_offset], ldv, &h__[h_offset], ldh, &resid[1], &q[q_offset], ldq, &workd[1]);
iwork[1] = 1;
if (*bmat == 'G')
}
F77_FUNC(ssaup2, SSAUP2)
- (ido, bmat, n, which, &iwork[13], &iwork[15], tol, &resid[1], &iwork[11], &iwork[6], &iwork[5],
- &iwork[10], &v[v_offset], ldv, &workl[iwork[3]], &iwork[8], &workl[iwork[16]], &workl[iwork[1]],
- &workl[iwork[4]], &iwork[9], &workl[iwork[7]], &ipntr[1], &workd[1], &iwork[21], info);
+ (ido,
+ bmat,
+ n,
+ which,
+ &iwork[13],
+ &iwork[15],
+ tol,
+ &resid[1],
+ &iwork[11],
+ &iwork[6],
+ &iwork[5],
+ &iwork[10],
+ &v[v_offset],
+ ldv,
+ &workl[iwork[3]],
+ &iwork[8],
+ &workl[iwork[16]],
+ &workl[iwork[1]],
+ &workl[iwork[4]],
+ &iwork[9],
+ &workl[iwork[7]],
+ &ipntr[1],
+ &workd[1],
+ &iwork[21],
+ info);
if (*ido == 3)
{
(ncv, &nconv, &workl[iq], &ldq, &workl[iw + *ncv], &workl[ihb], &ierr);
F77_FUNC(sorm2r, SORM2R)
- ("Right", "Notranspose", n, ncv, &nconv, &workl[iq], &ldq, &workl[iw + *ncv], &v[v_offset],
- ldv, &workd[*n + 1], &ierr);
+ ("Right",
+ "Notranspose",
+ n,
+ ncv,
+ &nconv,
+ &workl[iq],
+ &ldq,
+ &workl[iw + *ncv],
+ &v[v_offset],
+ ldv,
+ &workd[*n + 1],
+ &ierr);
F77_FUNC(slacpy, SLACPY)("All", n, &nconv, &v[v_offset], ldv, &z__[z_offset], ldz);
i__1 = *ncv - 1;
}
workl[ihb + *ncv - 1] = 1.;
F77_FUNC(sorm2r, SORM2R)
- ("Left", "Transpose", ncv, &c__1, &nconv, &workl[iq], &ldq, &workl[iw + *ncv], &workl[ihb],
- ncv, &temp, &ierr);
+ ("Left", "Transpose", ncv, &c__1, &nconv, &workl[iq], &ldq, &workl[iw + *ncv], &workl[ihb], ncv, &temp, &ierr);
}
else if (*rvec && *howmny == 'S')
{
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2012,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cmath>
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
-static inline void do_rotate(double** a, int i, int j, int k, int l, double tau, double s)
+template<typename MatrixType>
+static inline void do_rotate(MatrixType a, int i, int j, int k, int l, double tau, double s)
{
double g, h;
g = a[i][j];
a[k][l] = h + s * (g - h * tau);
}
-void jacobi(double** a, int n, double d[], double** v, int* nrot)
+template<typename MatrixType>
+static int jacobi(MatrixType a, const int n, double d[], MatrixType v)
{
int j, i;
int iq, ip;
b[ip] = d[ip] = a[ip][ip];
z[ip] = 0.0;
}
- *nrot = 0;
+ int nrot = 0;
for (i = 1; i <= 50; i++)
{
sm = 0.0;
{
sfree(z);
sfree(b);
- return;
+ return nrot;
}
if (i < 4)
{
{
do_rotate(v, j, ip, j, iq, tau, s);
}
- ++(*nrot);
+ ++nrot;
}
}
}
}
}
gmx_fatal(FARGS, "Error: Too many iterations in routine JACOBI\n");
+
+ return nrot;
+}
+
+void jacobi(double** a, const int numDimensions, double* eigenvalues, double** eigenvectors, int* numRotations)
+{
+ int numRot = jacobi(a, numDimensions, eigenvalues, eigenvectors);
+
+ if (numRotations)
+ {
+ *numRotations = numRot;
+ }
+}
+
+int jacobi(gmx::ArrayRef<gmx::DVec> a, gmx::ArrayRef<double> eigenvalues, gmx::ArrayRef<gmx::DVec> eigenvectors)
+{
+ GMX_RELEASE_ASSERT(gmx::ssize(a) == DIM, "Size should be 3");
+ GMX_RELEASE_ASSERT(gmx::ssize(eigenvalues) == DIM, "Size should be 3");
+ GMX_RELEASE_ASSERT(gmx::ssize(eigenvectors) == DIM, "Size should be 3");
+
+ return jacobi(a, DIM, eigenvalues.data(), eigenvectors);
}
int m_inv_gen(real* m, int n, real* minv)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2017,2018,2019 by the GROMACS development team.
+ * Copyright (c) 2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_LINEARALGEBRA_NRJAC_H
#define GMX_LINEARALGEBRA_NRJAC_H
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/real.h"
-void jacobi(double** a, int n, double d[], double** v, int* nrot);
-/*
- * real **omega = input matrix a[0..n-1][0..n-1] must be symmetric
- * int natoms = number of rows and columns
- * real NULL = d[0]..d[n-1] are the eigenvalues of a[][]
- * real **v = v[0..n-1][0..n-1] the eigenvectors:
- * v[i][j] is component i of vector j
- * int *irot = number of jacobi rotations
+/* Diagonalizes a symmetric matrix
+ *
+ * \param[in,out] a Input matrix a[0..n-1][0..n-1] must be symmetric, gets modified
+ * \param[in] numDimensions Number of rows and columns
+ * \param[out] eigenvalues eigenvalues[0]..eigenvalues[n-1] are the eigenvalues of a
+ * \param[out] eigenvectors v[0..n-1][0..n-1] the eigenvectors: v[i][j] is component i of vector j
+ * \param[out] numRotations The number of jacobi rotations, can be nullptr
+ */
+void jacobi(double** a, int numDimensions, double* eigenvalues, double** eigenvectors, int* numRotations);
+
+/* Like jacobi above, but specialized for n=3
+ *
+ * \param[in,out] a The symmetric matrix to diagonalize, size 3, note that the contents gets modified
+ * \param[out] eigenvalues The eigenvalues, size 3
+ * \param[out] eigenvectors The eigenvectors, size 3
+
+ * Returns the number of jacobi rotations.
*/
+int jacobi(gmx::ArrayRef<gmx::DVec> a, gmx::ArrayRef<double> eigenvalues, gmx::ArrayRef<gmx::DVec> eigenvectors);
int m_inv_gen(real* m, int n, real* minv);
/* Produces minv, a generalized inverse of m, both stored as linear arrays.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+add_library(listed_forces INTERFACE)
gmx_add_libgromacs_sources(
bonded.cpp
disre.cpp
)
endif()
+# Source files have the following private module dependencies.
+target_link_libraries(listed_forces PRIVATE
+# gmxlib
+# math
+# mdtypes
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(listed_forces PUBLIC
+target_include_directories(listed_forces INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(listed_forces PUBLIC
+target_link_libraries(listed_forces INTERFACE
+ legacy_api
+ )
+
+# TODO: when listed_forces is an OBJECT target
+#target_link_libraries(listed_forces PUBLIC legacy_api)
+#target_link_libraries(listed_forces PRIVATE common)
+
+# Module dependencies
+# listed_forces interfaces convey transitive dependence on these modules.
+#target_link_libraries(listed_forces PUBLIC
+target_link_libraries(listed_forces INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(listed_forces PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(listed_forces PRIVATE legacy_modules)
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/simd/simd.h"
#include "gromacs/simd/simd_math.h"
#include "gromacs/simd/vector_operations.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
using namespace gmx; // TODO: Remove when this file is moved into gmx namespace
const EnumerationArray<BondedKernelFlavor, std::string> c_bondedKernelFlavorStrings = {
- "forces, using SIMD when available", "forces, not using SIMD",
- "forces, virial, and energy (ie. not using SIMD)", "forces and energy (ie. not using SIMD)"
+ "forces, using SIMD when available",
+ "forces, not using SIMD",
+ "forces, virial, and energy (ie. not using SIMD)",
+ "forces and energy (ie. not using SIMD)"
};
namespace
{
//! Type of CPU function to compute a bonded interaction.
-using BondedFunction = real (*)(int nbonds,
- const t_iatom iatoms[],
- const t_iparams iparams[],
- const rvec x[],
- rvec4 f[],
- rvec fshift[],
- const t_pbc* pbc,
- real lambda,
- real* dvdlambda,
- const t_mdatoms* md,
- t_fcdata* fcd,
- int* ddgatindex);
+using BondedFunction = real (*)(int nbonds,
+ const t_iatom iatoms[],
+ const t_iparams iparams[],
+ const rvec x[],
+ rvec4 f[],
+ rvec fshift[],
+ const t_pbc* pbc,
+ real lambda,
+ real* dvdlambda,
+ gmx::ArrayRef<const real> charge,
+ t_fcdata* fcd,
+ t_disresdata* disresdata,
+ t_oriresdata* oriresdata,
+ int* ddgatindex);
/*! \brief Mysterious CMAP coefficient matrix */
const int cmap_coeff_matrix[] = {
else
{
rvec_sub(xi, xj, dx);
- return CENTRAL;
+ return c_centralShiftIndex;
}
}
if (computeVirial(flavor))
{
fshift[shiftIndex][m] += fij;
- fshift[CENTRAL][m] -= fij;
+ fshift[c_centralShiftIndex][m] -= fij;
}
}
}
const t_pbc* pbc,
real lambda,
real* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
const real one = 1.0;
const t_pbc* pbc,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
const real three = 3.0;
const t_pbc* pbc,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
- int* global_atom_index)
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
+ int* global_atom_index)
{
const real half = 0.5;
const real one = 1.0;
if (dr2 >= bm2)
{
- gmx_fatal(FARGS, "r^2 (%f) >= bm^2 (%f) in FENE bond between atoms %d and %d", dr2, bm2,
- glatnr(global_atom_index, ai), glatnr(global_atom_index, aj));
+ gmx_fatal(FARGS,
+ "r^2 (%f) >= bm^2 (%f) in FENE bond between atoms %d and %d",
+ dr2,
+ bm2,
+ glatnr(global_atom_index, ai),
+ glatnr(global_atom_index, aj));
}
omdr2obm2 = one - dr2 / bm2;
const t_pbc* pbc,
real lambda,
real* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int i, ki, ai, aj, type;
dr2 = iprod(dx, dx); /* 5 */
dr = std::sqrt(dr2); /* 10 */
- *dvdlambda += harmonic(forceparams[type].harmonic.krA, forceparams[type].harmonic.krB,
- forceparams[type].harmonic.rA, forceparams[type].harmonic.rB, dr,
- lambda, &vbond, &fbond); /* 19 */
+ *dvdlambda += harmonic(forceparams[type].harmonic.krA,
+ forceparams[type].harmonic.krB,
+ forceparams[type].harmonic.rA,
+ forceparams[type].harmonic.rB,
+ dr,
+ lambda,
+ &vbond,
+ &fbond); /* 19 */
if (dr2 == 0.0)
{
const t_pbc* pbc,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
constexpr int nfa1 = 3;
const t_pbc* pbc,
real lambda,
real* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int i, ki, ai, aj, type;
}
template<BondedKernelFlavor flavor>
-real polarize(int nbonds,
- const t_iatom forceatoms[],
- const t_iparams forceparams[],
- const rvec x[],
- rvec4 f[],
- rvec fshift[],
- const t_pbc* pbc,
- real lambda,
- real* dvdlambda,
- const t_mdatoms* md,
+real polarize(int nbonds,
+ const t_iatom forceatoms[],
+ const t_iparams forceparams[],
+ const rvec x[],
+ rvec4 f[],
+ rvec fshift[],
+ const t_pbc* pbc,
+ real lambda,
+ real* dvdlambda,
+ gmx::ArrayRef<const real> charge,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int i, ki, ai, aj, type;
type = forceatoms[i++];
ai = forceatoms[i++];
aj = forceatoms[i++];
- ksh = gmx::square(md->chargeA[aj]) * ONE_4PI_EPS0 / forceparams[type].polarize.alpha;
+ ksh = gmx::square(charge[aj]) * gmx::c_one4PiEps0 / forceparams[type].polarize.alpha;
ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
dr2 = iprod(dx, dx); /* 5 */
}
template<BondedKernelFlavor flavor>
-real anharm_polarize(int nbonds,
- const t_iatom forceatoms[],
- const t_iparams forceparams[],
- const rvec x[],
- rvec4 f[],
- rvec fshift[],
- const t_pbc* pbc,
- real lambda,
- real* dvdlambda,
- const t_mdatoms* md,
+real anharm_polarize(int nbonds,
+ const t_iatom forceatoms[],
+ const t_iparams forceparams[],
+ const rvec x[],
+ rvec4 f[],
+ rvec fshift[],
+ const t_pbc* pbc,
+ real lambda,
+ real* dvdlambda,
+ gmx::ArrayRef<const real> charge,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int i, ki, ai, aj, type;
type = forceatoms[i++];
ai = forceatoms[i++];
aj = forceatoms[i++];
- ksh = gmx::square(md->chargeA[aj]) * ONE_4PI_EPS0 / forceparams[type].anharm_polarize.alpha; /* 7*/
+ ksh = gmx::square(charge[aj]) * gmx::c_one4PiEps0 / forceparams[type].anharm_polarize.alpha; /* 7*/
khyp = forceparams[type].anharm_polarize.khyp;
drcut = forceparams[type].anharm_polarize.drcut;
rvec gmx_unused fshift[],
const t_pbc gmx_unused* pbc,
real gmx_unused lambda,
- real gmx_unused* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ real gmx_unused* dvdlambda,
+ gmx::ArrayRef<const real> charge,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
/* This routine implements anisotropic polarizibility for water, through
{
type0 = forceatoms[0];
aS = forceatoms[5];
- qS = md->chargeA[aS];
- kk[XX] = gmx::square(qS) * ONE_4PI_EPS0 / forceparams[type0].wpol.al_x;
- kk[YY] = gmx::square(qS) * ONE_4PI_EPS0 / forceparams[type0].wpol.al_y;
- kk[ZZ] = gmx::square(qS) * ONE_4PI_EPS0 / forceparams[type0].wpol.al_z;
+ qS = charge[aS];
+ kk[XX] = gmx::square(qS) * gmx::c_one4PiEps0 / forceparams[type0].wpol.al_x;
+ kk[YY] = gmx::square(qS) * gmx::c_one4PiEps0 / forceparams[type0].wpol.al_y;
+ kk[ZZ] = gmx::square(qS) * gmx::c_one4PiEps0 / forceparams[type0].wpol.al_z;
r_HH = 1.0 / forceparams[type0].wpol.rHH;
for (i = 0; (i < nbonds); i += 6)
{
type = forceatoms[i];
if (type != type0)
{
- gmx_fatal(FARGS, "Sorry, type = %d, type0 = %d, file = %s, line = %d", type, type0,
- __FILE__, __LINE__);
+ gmx_fatal(FARGS, "Sorry, type = %d, type0 = %d, file = %s, line = %d", type, type0, __FILE__, __LINE__);
}
aO = forceatoms[i + 1];
aH1 = forceatoms[i + 2];
if (computeVirial(flavor))
{
fshift[ki][m] += fij;
- fshift[CENTRAL][m] -= fij;
+ fshift[c_centralShiftIndex][m] -= fij;
}
}
}
r12sq = iprod(r12, r12); /* 5 */
r12_1 = gmx::invsqrt(r12sq); /* 5 */
r12bar = afac / r12_1; /* 5 */
- v0 = qq * ONE_4PI_EPS0 * r12_1; /* 2 */
+ v0 = qq * gmx::c_one4PiEps0 * r12_1; /* 2 */
ebar = std::exp(-r12bar); /* 5 */
v1 = (1 - (1 + 0.5 * r12bar) * ebar); /* 4 */
fscal = ((v0 * r12_1) * v1 - v0 * 0.5 * afac * ebar * (r12bar + 1)) * r12_1; /* 9 */
if (computeVirial(flavor))
{
fshift[t][m] += fff;
- fshift[CENTRAL][m] -= fff;
+ fshift[c_centralShiftIndex][m] -= fff;
}
} /* 15 */
rvec fshift[],
const t_pbc* pbc,
real gmx_unused lambda,
- real gmx_unused* dvdlambda,
- const t_mdatoms* md,
+ real gmx_unused* dvdlambda,
+ gmx::ArrayRef<const real> charge,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
/* Interaction between two pairs of particles with opposite charge */
da1 = forceatoms[i++];
a2 = forceatoms[i++];
da2 = forceatoms[i++];
- q1 = md->chargeA[da1];
- q2 = md->chargeA[da2];
+ q1 = charge[da1];
+ q2 = charge[da2];
a = forceparams[type].thole.a;
al1 = forceparams[type].thole.alpha1;
al2 = forceparams[type].thole.alpha2;
const t_pbc* pbc,
real lambda,
real* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int i, ai, aj, ak, t1, t2, type;
theta = bond_angle(x[ai], x[aj], x[ak], pbc, r_ij, r_kj, &cos_theta, &t1, &t2); /* 41 */
- *dvdlambda += harmonic(forceparams[type].harmonic.krA, forceparams[type].harmonic.krB,
- forceparams[type].harmonic.rA * DEG2RAD,
- forceparams[type].harmonic.rB * DEG2RAD, theta, lambda, &va, &dVdt); /* 21 */
+ *dvdlambda += harmonic(forceparams[type].harmonic.krA,
+ forceparams[type].harmonic.krB,
+ forceparams[type].harmonic.rA * gmx::c_deg2Rad,
+ forceparams[type].harmonic.rB * gmx::c_deg2Rad,
+ theta,
+ lambda,
+ &va,
+ &dVdt); /* 21 */
vtot += va;
cos_theta2 = gmx::square(cos_theta);
if (computeVirial(flavor))
{
rvec_inc(fshift[t1], f_i);
- rvec_inc(fshift[CENTRAL], f_j);
+ rvec_inc(fshift[c_centralShiftIndex], f_j);
rvec_inc(fshift[t2], f_k);
}
} /* 161 TOTAL */
const t_pbc* pbc,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
const int nfa1 = 4;
alignas(GMX_SIMD_ALIGNMENT) std::int32_t aj[GMX_SIMD_REAL_WIDTH];
alignas(GMX_SIMD_ALIGNMENT) std::int32_t ak[GMX_SIMD_REAL_WIDTH];
alignas(GMX_SIMD_ALIGNMENT) real coeff[2 * GMX_SIMD_REAL_WIDTH];
- SimdReal deg2rad_S(DEG2RAD);
+ SimdReal deg2rad_S(gmx::c_deg2Rad);
SimdReal xi_S, yi_S, zi_S;
SimdReal xj_S, yj_S, zj_S;
SimdReal xk_S, yk_S, zk_S;
f_kz_S = fnma(cik_S, rijz_S, f_kz_S);
transposeScatterIncrU<4>(reinterpret_cast<real*>(f), ai, f_ix_S, f_iy_S, f_iz_S);
- transposeScatterDecrU<4>(reinterpret_cast<real*>(f), aj, f_ix_S + f_kx_S, f_iy_S + f_ky_S,
- f_iz_S + f_kz_S);
+ transposeScatterDecrU<4>(
+ reinterpret_cast<real*>(f), aj, f_ix_S + f_kx_S, f_iy_S + f_ky_S, f_iz_S + f_kz_S);
transposeScatterIncrU<4>(reinterpret_cast<real*>(f), ak, f_kx_S, f_ky_S, f_kz_S);
}
const t_pbc* pbc,
real lambda,
real* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int i, m, ai, aj, ak, t1, t2, type;
if (computeVirial(flavor))
{
rvec_inc(fshift[t1], f_i);
- rvec_inc(fshift[CENTRAL], f_j);
+ rvec_inc(fshift[c_centralShiftIndex], f_j);
rvec_inc(fshift[t2], f_k);
}
} /* 57 TOTAL */
const t_pbc* pbc,
real lambda,
real* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int i, m, ai, aj, ak, t1, t2, type, ki;
ai = forceatoms[i++];
aj = forceatoms[i++];
ak = forceatoms[i++];
- th0A = forceparams[type].u_b.thetaA * DEG2RAD;
+ th0A = forceparams[type].u_b.thetaA * gmx::c_deg2Rad;
kthA = forceparams[type].u_b.kthetaA;
r13A = forceparams[type].u_b.r13A;
kUBA = forceparams[type].u_b.kUBA;
- th0B = forceparams[type].u_b.thetaB * DEG2RAD;
+ th0B = forceparams[type].u_b.thetaB * gmx::c_deg2Rad;
kthB = forceparams[type].u_b.kthetaB;
r13B = forceparams[type].u_b.r13B;
kUBB = forceparams[type].u_b.kUBB;
if (computeVirial(flavor))
{
rvec_inc(fshift[t1], f_i);
- rvec_inc(fshift[CENTRAL], f_j);
+ rvec_inc(fshift[c_centralShiftIndex], f_j);
rvec_inc(fshift[t2], f_k);
}
} /* 161 TOTAL */
if (computeVirial(flavor))
{
fshift[ki][m] += fik;
- fshift[CENTRAL][m] -= fik;
+ fshift[c_centralShiftIndex][m] -= fik;
}
}
}
const t_pbc* pbc,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
constexpr int nfa1 = 4;
SimdReal rikz_S = zi_S - zk_S;
const SimdReal ktheta_S = load<SimdReal>(coeff);
- const SimdReal theta0_S = load<SimdReal>(coeff + GMX_SIMD_REAL_WIDTH) * DEG2RAD;
+ const SimdReal theta0_S = load<SimdReal>(coeff + GMX_SIMD_REAL_WIDTH) * gmx::c_deg2Rad;
const SimdReal kUB_S = load<SimdReal>(coeff + 2 * GMX_SIMD_REAL_WIDTH);
const SimdReal r13_S = load<SimdReal>(coeff + 3 * GMX_SIMD_REAL_WIDTH);
const SimdReal f_kz_S = fnma(cik_S, rijz_S, ckk_S * rkjz_S) - f_ikz_S;
transposeScatterIncrU<4>(reinterpret_cast<real*>(f), ai, f_ix_S, f_iy_S, f_iz_S);
- transposeScatterDecrU<4>(reinterpret_cast<real*>(f), aj, f_ix_S + f_kx_S, f_iy_S + f_ky_S,
- f_iz_S + f_kz_S);
+ transposeScatterDecrU<4>(
+ reinterpret_cast<real*>(f), aj, f_ix_S + f_kx_S, f_iy_S + f_ky_S, f_iz_S + f_kz_S);
transposeScatterIncrU<4>(reinterpret_cast<real*>(f), ak, f_kx_S, f_ky_S, f_kz_S);
}
const t_pbc* pbc,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int i, j, ai, aj, ak, t1, t2, type;
theta = bond_angle(x[ai], x[aj], x[ak], pbc, r_ij, r_kj, &cos_theta, &t1, &t2); /* 41 */
- dt = theta - forceparams[type].qangle.theta * DEG2RAD; /* 2 */
+ dt = theta - forceparams[type].qangle.theta * gmx::c_deg2Rad; /* 2 */
dVdt = 0;
va = forceparams[type].qangle.c[0];
if (computeVirial(flavor))
{
rvec_inc(fshift[t1], f_i);
- rvec_inc(fshift[CENTRAL], f_j);
+ rvec_inc(fshift[c_centralShiftIndex], f_j);
rvec_inc(fshift[t2], f_k);
}
} /* 153 TOTAL */
}
else
{
- t3 = CENTRAL;
+ t3 = c_centralShiftIndex;
}
rvec_inc(fshift[t1], f_i);
- rvec_dec(fshift[CENTRAL], f_j);
+ rvec_dec(fshift[c_centralShiftIndex], f_j);
rvec_dec(fshift[t2], f_k);
rvec_inc(fshift[t3], f_l);
}
real dopdihs(real cpA, real cpB, real phiA, real phiB, int mult, real phi, real lambda, real* V, real* dvdlambda)
{
const real L1 = 1.0 - lambda;
- const real ph0 = (L1 * phiA + lambda * phiB) * DEG2RAD;
- const real dph0 = (phiB - phiA) * DEG2RAD;
+ const real ph0 = (L1 * phiA + lambda * phiB) * gmx::c_deg2Rad;
+ const real dph0 = (phiB - phiA) * gmx::c_deg2Rad;
const real cp = L1 * cpA + lambda * cpB;
const real mdphi = mult * phi - ph0;
{
real v, dvdlambda, mdphi, v1, sdphi, ddphi;
real L1 = 1.0 - lambda;
- real ph0 = (L1 * phiA + lambda * phiB) * DEG2RAD;
- real dph0 = (phiB - phiA) * DEG2RAD;
+ real ph0 = (L1 * phiA + lambda * phiB) * gmx::c_deg2Rad;
+ real dph0 = (phiB - phiA) * gmx::c_deg2Rad;
real cp = L1 * cpA + lambda * cpB;
mdphi = mult * (phi - ph0);
const t_pbc* pbc,
real lambda,
real* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int t1, t2, t3;
const int ak = forceatoms[i + 3];
const int al = forceatoms[i + 4];
- const real phi = dih_angle(x[ai], x[aj], x[ak], x[al], pbc, r_ij, r_kj, r_kl, m, n, &t1,
- &t2, &t3); /* 84 */
+ const real phi =
+ dih_angle(x[ai], x[aj], x[ak], x[al], pbc, r_ij, r_kj, r_kl, m, n, &t1, &t2, &t3); /* 84 */
/* Loop over dihedrals working on the same atoms,
* so we avoid recalculating angles and distributing forces.
do
{
const int type = forceatoms[i];
- ddphi_tot += dopdihs<flavor>(forceparams[type].pdihs.cpA, forceparams[type].pdihs.cpB,
- forceparams[type].pdihs.phiA, forceparams[type].pdihs.phiB,
- forceparams[type].pdihs.mult, phi, lambda, &vtot, dvdlambda);
+ ddphi_tot += dopdihs<flavor>(forceparams[type].pdihs.cpA,
+ forceparams[type].pdihs.cpB,
+ forceparams[type].pdihs.phiA,
+ forceparams[type].pdihs.phiB,
+ forceparams[type].pdihs.mult,
+ phi,
+ lambda,
+ &vtot,
+ dvdlambda);
i += 5;
} while (i < nbonds && forceatoms[i + 1] == ai && forceatoms[i + 2] == aj
&& forceatoms[i + 3] == ak && forceatoms[i + 4] == al);
- do_dih_fup<flavor>(ai, aj, ak, al, ddphi_tot, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, x, t1,
- t2, t3); /* 112 */
- } /* 223 TOTAL */
+ do_dih_fup<flavor>(
+ ai, aj, ak, al, ddphi_tot, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, x, t1, t2, t3); /* 112 */
+ } /* 223 TOTAL */
return vtot;
}
const t_pbc* pbc,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
const int nfa1 = 5;
alignas(GMX_SIMD_ALIGNMENT) std::int32_t al[GMX_SIMD_REAL_WIDTH];
alignas(GMX_SIMD_ALIGNMENT) real buf[3 * GMX_SIMD_REAL_WIDTH];
real * cp, *phi0, *mult;
- SimdReal deg2rad_S(DEG2RAD);
+ SimdReal deg2rad_S(gmx::c_deg2Rad);
SimdReal p_S, q_S;
SimdReal phi0_S, phi_S;
SimdReal mx_S, my_S, mz_S;
}
/* Calculate GMX_SIMD_REAL_WIDTH dihedral angles at once */
- dih_angle_simd(x, ai, aj, ak, al, pbc_simd, &phi_S, &mx_S, &my_S, &mz_S, &nx_S, &ny_S,
- &nz_S, &nrkj_m2_S, &nrkj_n2_S, &p_S, &q_S);
+ dih_angle_simd(
+ x, ai, aj, ak, al, pbc_simd, &phi_S, &mx_S, &my_S, &mz_S, &nx_S, &ny_S, &nz_S, &nrkj_m2_S, &nrkj_n2_S, &p_S, &q_S);
cp_S = load<SimdReal>(cp);
phi0_S = load<SimdReal>(phi0) * deg2rad_S;
const t_pbc* pbc,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
const int nfa1 = 5;
}
/* Calculate GMX_SIMD_REAL_WIDTH dihedral angles at once */
- dih_angle_simd(x, ai, aj, ak, al, pbc_simd, &phi_S, &mx_S, &my_S, &mz_S, &nx_S, &ny_S,
- &nz_S, &nrkj_m2_S, &nrkj_n2_S, &p_S, &q_S);
+ dih_angle_simd(
+ x, ai, aj, ak, al, pbc_simd, &phi_S, &mx_S, &my_S, &mz_S, &nx_S, &ny_S, &nz_S, &nrkj_m2_S, &nrkj_n2_S, &p_S, &q_S);
/* Change to polymer convention */
phi_S = phi_S - pi_S;
const t_pbc* pbc,
real lambda,
real* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int i, type, ai, aj, ak, al;
pB = forceparams[type].harmonic.rB;
kk = L1 * kA + lambda * kB;
- phi0 = (L1 * pA + lambda * pB) * DEG2RAD;
- dphi0 = (pB - pA) * DEG2RAD;
+ phi0 = (L1 * pA + lambda * pB) * gmx::c_deg2Rad;
+ dphi0 = (pB - pA) * gmx::c_deg2Rad;
dp = phi - phi0;
dvdl_term += 0.5 * (kB - kA) * dp2 - kk * dphi0 * dp;
- do_dih_fup<flavor>(ai, aj, ak, al, -ddphi, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, x, t1,
- t2, t3); /* 112 */
+ do_dih_fup<flavor>(ai, aj, ak, al, -ddphi, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, x, t1, t2, t3); /* 112 */
/* 218 TOTAL */
}
cos_phi = cos_angle(r_ij, r_kl); /* 25 */
phi = std::acos(cos_phi); /* 10 */
- *dvdlambda += dopdihs_min(forceparams[type].pdihs.cpA, forceparams[type].pdihs.cpB,
- forceparams[type].pdihs.phiA, forceparams[type].pdihs.phiB,
- forceparams[type].pdihs.mult, phi, lambda, &vid, &dVdphi); /* 40 */
+ *dvdlambda += dopdihs_min(forceparams[type].pdihs.cpA,
+ forceparams[type].pdihs.cpB,
+ forceparams[type].pdihs.phiA,
+ forceparams[type].pdihs.phiB,
+ forceparams[type].pdihs.mult,
+ phi,
+ lambda,
+ &vid,
+ &dVdphi); /* 40 */
vtot += vid;
if (computeVirial(flavor))
{
rvec_inc(fshift[t1], f_i);
- rvec_dec(fshift[CENTRAL], f_i);
+ rvec_dec(fshift[c_centralShiftIndex], f_i);
if (!bZAxis)
{
rvec_inc(fshift[t2], f_k);
- rvec_dec(fshift[CENTRAL], f_k);
+ rvec_dec(fshift[c_centralShiftIndex], f_k);
}
}
}
const t_pbc* pbc,
real lambda,
real* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
return low_angres<flavor>(nbonds, forceatoms, forceparams, x, f, fshift, pbc, lambda, dvdlambda, FALSE);
const t_pbc* pbc,
real lambda,
real* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
return low_angres<flavor>(nbonds, forceatoms, forceparams, x, f, fshift, pbc, lambda, dvdlambda, TRUE);
const t_pbc* pbc,
real lambda,
real* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
real vtot = 0;
L1 = 1.0 - lambda;
- d2r = DEG2RAD;
+ d2r = gmx::c_deg2Rad;
for (i = 0; (i < nbonds);)
{
{
*dvdlambda += kfac * ddp * ((dphiB - dphiA) - (phi0B - phi0A));
}
- do_dih_fup<flavor>(ai, aj, ak, al, ddphi, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, x, t1,
- t2, t3); /* 112 */
+ do_dih_fup<flavor>(
+ ai, aj, ak, al, ddphi, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, x, t1, t2, t3); /* 112 */
}
}
return vtot;
const t_pbc gmx_unused* pbc,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
gmx_impl("*** you are using a not implemented function");
const t_pbc* pbc,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int i, d, ai, aj, ak, type, m;
* {\sin^2\theta_i}\f] ({eq:ReB} and ref \cite{MonicaGoga2013} from the manual).
* For more explanations see comments file "restcbt.h". */
- compute_factors_restangles(type, forceparams, delta_ante, delta_post, &prefactor,
- &ratio_ante, &ratio_post, &v);
+ compute_factors_restangles(
+ type, forceparams, delta_ante, delta_post, &prefactor, &ratio_ante, &ratio_post, &v);
/* Forces are computed per component */
for (d = 0; d < DIM; d++)
if (computeVirial(flavor))
{
rvec_inc(fshift[t1], f_i);
- rvec_inc(fshift[CENTRAL], f_j);
+ rvec_inc(fshift[c_centralShiftIndex], f_j);
rvec_inc(fshift[t2], f_k);
}
}
const t_pbc* pbc,
real gmx_unused lambda,
real gmx_unused* dvlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int i, d, type, ai, aj, ak, al;
* ({eq:ReB} and ref \cite{MonicaGoga2013} from the manual).
* For more explanations see comments file "restcbt.h" */
- compute_factors_restrdihs(
- type, forceparams, delta_ante, delta_crnt, delta_post, &factor_phi_ai_ante,
- &factor_phi_ai_crnt, &factor_phi_ai_post, &factor_phi_aj_ante, &factor_phi_aj_crnt,
- &factor_phi_aj_post, &factor_phi_ak_ante, &factor_phi_ak_crnt, &factor_phi_ak_post,
- &factor_phi_al_ante, &factor_phi_al_crnt, &factor_phi_al_post, &prefactor_phi, &v);
+ compute_factors_restrdihs(type,
+ forceparams,
+ delta_ante,
+ delta_crnt,
+ delta_post,
+ &factor_phi_ai_ante,
+ &factor_phi_ai_crnt,
+ &factor_phi_ai_post,
+ &factor_phi_aj_ante,
+ &factor_phi_aj_crnt,
+ &factor_phi_aj_post,
+ &factor_phi_ak_ante,
+ &factor_phi_ak_crnt,
+ &factor_phi_ak_post,
+ &factor_phi_al_ante,
+ &factor_phi_al_crnt,
+ &factor_phi_al_post,
+ &prefactor_phi,
+ &v);
/* Computation of forces per component */
}
else
{
- t3 = CENTRAL;
+ t3 = c_centralShiftIndex;
}
rvec_inc(fshift[t1], f_i);
- rvec_inc(fshift[CENTRAL], f_j);
+ rvec_inc(fshift[c_centralShiftIndex], f_j);
rvec_inc(fshift[t2], f_k);
rvec_inc(fshift[t3], f_l);
}
const t_pbc* pbc,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int type, ai, aj, ak, al, i, d;
* --- the adjacent bending angles.
* For more explanations see comments file "restcbt.h". */
- compute_factors_cbtdihs(type, forceparams, delta_ante, delta_crnt, delta_post, f_phi_ai,
- f_phi_aj, f_phi_ak, f_phi_al, f_theta_ante_ai, f_theta_ante_aj,
- f_theta_ante_ak, f_theta_post_aj, f_theta_post_ak, f_theta_post_al, &v);
+ compute_factors_cbtdihs(type,
+ forceparams,
+ delta_ante,
+ delta_crnt,
+ delta_post,
+ f_phi_ai,
+ f_phi_aj,
+ f_phi_ak,
+ f_phi_al,
+ f_theta_ante_ai,
+ f_theta_ante_aj,
+ f_theta_ante_ak,
+ f_theta_post_aj,
+ f_theta_post_ak,
+ f_theta_post_al,
+ &v);
/* Acumulate the resuts per beads */
}
else
{
- t3 = CENTRAL;
+ t3 = c_centralShiftIndex;
}
rvec_inc(fshift[t1], f_i);
- rvec_inc(fshift[CENTRAL], f_j);
+ rvec_inc(fshift[c_centralShiftIndex], f_j);
rvec_inc(fshift[t2], f_k);
rvec_inc(fshift[t3], f_l);
}
const t_pbc* pbc,
real lambda,
real* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
const real c0 = 0.0, c1 = 1.0, c2 = 2.0, c3 = 3.0, c4 = 4.0, c5 = 5.0;
ddphi = -ddphi * sin_phi; /* 11 */
- do_dih_fup<flavor>(ai, aj, ak, al, ddphi, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, x, t1, t2,
- t3); /* 112 */
+ do_dih_fup<flavor>(ai, aj, ak, al, ddphi, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, x, t1, t2, t3); /* 112 */
vtot += v;
}
*dvdlambda += dvdl_term;
const struct t_pbc* pbc,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int i, n;
a1k = ak;
a1l = al;
- phi1 = dih_angle(x[a1i], x[a1j], x[a1k], x[a1l], pbc, r1_ij, r1_kj, r1_kl, m1, n1, &t11,
- &t21, &t31); /* 84 */
+ phi1 = dih_angle(
+ x[a1i], x[a1j], x[a1k], x[a1l], pbc, r1_ij, r1_kj, r1_kl, m1, n1, &t11, &t21, &t31); /* 84 */
cos_phi1 = std::cos(phi1);
a2k = al;
a2l = am;
- phi2 = dih_angle(x[a2i], x[a2j], x[a2k], x[a2l], pbc, r2_ij, r2_kj, r2_kl, m2, n2, &t12,
- &t22, &t32); /* 84 */
+ phi2 = dih_angle(
+ x[a2i], x[a2j], x[a2k], x[a2l], pbc, r2_ij, r2_kj, r2_kl, m2, n2, &t12, &t22, &t32); /* 84 */
cos_phi2 = std::cos(phi2);
/* Switch to degrees */
dx = 360.0 / cmap_grid->grid_spacing;
- xphi1 = xphi1 * RAD2DEG;
- xphi2 = xphi2 * RAD2DEG;
+ xphi1 = xphi1 * gmx::c_rad2Deg;
+ xphi2 = xphi2 * gmx::c_rad2Deg;
for (i = 0; i < 4; i++) /* 16 */
{
df2 = tt * df2 + (3.0 * tc[i * 4 + 3] * tu + 2.0 * tc[i * 4 + 2]) * tu + tc[i * 4 + 1];
}
- fac = RAD2DEG / dx;
+ fac = gmx::c_rad2Deg / dx;
df1 = df1 * fac;
df2 = df2 * fac;
}
else
{
- t31 = CENTRAL;
- t32 = CENTRAL;
+ t31 = c_centralShiftIndex;
+ t32 = c_centralShiftIndex;
}
rvec_inc(fshift[t11], f1_i);
- rvec_inc(fshift[CENTRAL], f1_j);
+ rvec_inc(fshift[c_centralShiftIndex], f1_j);
rvec_inc(fshift[t21], f1_k);
rvec_inc(fshift[t31], f1_l);
rvec_inc(fshift[t12], f2_i);
- rvec_inc(fshift[CENTRAL], f2_j);
+ rvec_inc(fshift[c_centralShiftIndex], f2_j);
rvec_inc(fshift[t22], f2_k);
rvec_inc(fshift[t32], f2_l);
}
const t_pbc* pbc,
real lambda,
real* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int i, ki, ai, aj, type;
ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
dr2 = iprod(dx, dx); /* 5 */
- *dvdlambda += g96harmonic(forceparams[type].harmonic.krA, forceparams[type].harmonic.krB,
- forceparams[type].harmonic.rA, forceparams[type].harmonic.rB, dr2,
- lambda, &vbond, &fbond);
+ *dvdlambda += g96harmonic(forceparams[type].harmonic.krA,
+ forceparams[type].harmonic.krB,
+ forceparams[type].harmonic.rA,
+ forceparams[type].harmonic.rB,
+ dr2,
+ lambda,
+ &vbond,
+ &fbond);
vtot += 0.5 * vbond; /* 1*/
const t_pbc* pbc,
real lambda,
real* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int i, ai, aj, ak, type, m, t1, t2;
cos_theta = g96bond_angle(x[ai], x[aj], x[ak], pbc, r_ij, r_kj, &t1, &t2);
- *dvdlambda += g96harmonic(forceparams[type].harmonic.krA, forceparams[type].harmonic.krB,
- forceparams[type].harmonic.rA, forceparams[type].harmonic.rB,
- cos_theta, lambda, &va, &dVdt);
+ *dvdlambda += g96harmonic(forceparams[type].harmonic.krA,
+ forceparams[type].harmonic.krB,
+ forceparams[type].harmonic.rA,
+ forceparams[type].harmonic.rB,
+ cos_theta,
+ lambda,
+ &va,
+ &dVdt);
vtot += va;
rij_1 = gmx::invsqrt(iprod(r_ij, r_ij));
if (computeVirial(flavor))
{
rvec_inc(fshift[t1], f_i);
- rvec_inc(fshift[CENTRAL], f_j);
+ rvec_inc(fshift[c_centralShiftIndex], f_j);
rvec_inc(fshift[t2], f_k); /* 9 */
}
/* 163 TOTAL */
const t_pbc* pbc,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
/* Potential from Lawrence and Skimmer, Chem. Phys. Lett. 372 (2003)
if (computeVirial(flavor))
{
rvec_inc(fshift[t1], f_i);
- rvec_inc(fshift[CENTRAL], f_j);
+ rvec_inc(fshift[c_centralShiftIndex], f_j);
rvec_inc(fshift[t2], f_k); /* 9 */
}
/* 163 TOTAL */
const t_pbc* pbc,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
/* Potential from Lawrence and Skimmer, Chem. Phys. Lett. 372 (2003)
if (computeVirial(flavor))
{
rvec_inc(fshift[t1], f_i);
- rvec_inc(fshift[CENTRAL], f_j);
+ rvec_inc(fshift[c_centralShiftIndex], f_j);
rvec_inc(fshift[t2], f_k); /* 9 */
}
/* 163 TOTAL */
gmx_fatal(FARGS,
"A tabulated %s interaction table number %d is out of the table range: r %f, "
"between table indices %d and %d, table length %d",
- type, table_nr, r, n0, n0 + 1, table->n);
+ type,
+ table_nr,
+ r,
+ n0,
+ n0 + 1,
+ table->n);
}
eps = rt - n0;
eps2 = eps * eps;
const t_pbc* pbc,
real lambda,
real* dvdlambda,
- const t_mdatoms gmx_unused* md,
- t_fcdata* fcd,
+ gmx::ArrayRef<const real> /*charge*/,
+ t_fcdata* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int i, ki, ai, aj, type, table;
table = forceparams[type].tab.table;
- *dvdlambda += bonded_tab("bond", table, &fcd->bondtab[table], forceparams[type].tab.kA,
- forceparams[type].tab.kB, dr, lambda, &vbond, &fbond); /* 22 */
+ *dvdlambda += bonded_tab("bond",
+ table,
+ &fcd->bondtab[table],
+ forceparams[type].tab.kA,
+ forceparams[type].tab.kB,
+ dr,
+ lambda,
+ &vbond,
+ &fbond); /* 22 */
if (dr2 == 0.0)
{
const t_pbc* pbc,
real lambda,
real* dvdlambda,
- const t_mdatoms gmx_unused* md,
- t_fcdata* fcd,
+ gmx::ArrayRef<const real> /*charge*/,
+ t_fcdata* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int i, ai, aj, ak, t1, t2, type, table;
table = forceparams[type].tab.table;
- *dvdlambda += bonded_tab("angle", table, &fcd->angletab[table], forceparams[type].tab.kA,
- forceparams[type].tab.kB, theta, lambda, &va, &dVdt); /* 22 */
+ *dvdlambda += bonded_tab("angle",
+ table,
+ &fcd->angletab[table],
+ forceparams[type].tab.kA,
+ forceparams[type].tab.kB,
+ theta,
+ lambda,
+ &va,
+ &dVdt); /* 22 */
vtot += va;
cos_theta2 = gmx::square(cos_theta); /* 1 */
if (computeVirial(flavor))
{
rvec_inc(fshift[t1], f_i);
- rvec_inc(fshift[CENTRAL], f_j);
+ rvec_inc(fshift[c_centralShiftIndex], f_j);
rvec_inc(fshift[t2], f_k);
}
} /* 169 TOTAL */
const t_pbc* pbc,
real lambda,
real* dvdlambda,
- const t_mdatoms gmx_unused* md,
- t_fcdata* fcd,
+ gmx::ArrayRef<const real> /*charge*/,
+ t_fcdata* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
int i, type, ai, aj, ak, al, table;
table = forceparams[type].tab.table;
/* Hopefully phi+M_PI never results in values < 0 */
- *dvdlambda += bonded_tab("dihedral", table, &fcd->dihtab[table], forceparams[type].tab.kA,
- forceparams[type].tab.kB, phi + M_PI, lambda, &vpd, &ddphi);
+ *dvdlambda += bonded_tab("dihedral",
+ table,
+ &fcd->dihtab[table],
+ forceparams[type].tab.kA,
+ forceparams[type].tab.kB,
+ phi + M_PI,
+ lambda,
+ &vpd,
+ &ddphi);
vtot += vpd;
- do_dih_fup<flavor>(ai, aj, ak, al, -ddphi, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, x, t1,
- t2, t3); /* 112 */
+ do_dih_fup<flavor>(ai, aj, ak, al, -ddphi, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, x, t1, t2, t3); /* 112 */
} /* 227 TOTAL */
} // namespace
-real calculateSimpleBond(const int ftype,
- const int numForceatoms,
- const t_iatom forceatoms[],
- const t_iparams forceparams[],
- const rvec x[],
- rvec4 f[],
- rvec fshift[],
- const struct t_pbc* pbc,
- const real lambda,
- real* dvdlambda,
- const t_mdatoms* md,
- t_fcdata* fcd,
+real calculateSimpleBond(const int ftype,
+ const int numForceatoms,
+ const t_iatom forceatoms[],
+ const t_iparams forceparams[],
+ const rvec x[],
+ rvec4 f[],
+ rvec fshift[],
+ const struct t_pbc* pbc,
+ const real lambda,
+ real* dvdlambda,
+ gmx::ArrayRef<const real> charge,
+ t_fcdata* fcd,
+ t_disresdata* disresdata,
+ t_oriresdata* oriresdata,
int gmx_unused* global_atom_index,
const BondedKernelFlavor bondedKernelFlavor)
{
const BondedInteractions& bonded = c_bondedInteractionFunctionsPerFlavor[bondedKernelFlavor][ftype];
- real v = bonded.function(numForceatoms, forceatoms, forceparams, x, f, fshift, pbc, lambda,
- dvdlambda, md, fcd, global_atom_index);
+ real v = bonded.function(
+ numForceatoms, forceatoms, forceparams, x, f, fshift, pbc, lambda, dvdlambda, charge, fcd, disresdata, oriresdata, global_atom_index);
return v;
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct gmx_cmap_t;
struct t_fcdata;
-struct t_mdatom;
struct t_nrnb;
struct t_pbc;
+struct t_disresdata;
+struct t_oriresdata;
namespace gmx
{
template<typename EnumType, typename DataType, EnumType ArraySize>
struct EnumerationArray;
+template<typename>
+class ArrayRef;
} // namespace gmx
/*! \brief Calculate bond-angle. No PBC is taken into account (use mol-shift) */
const struct t_pbc* pbc,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
- const t_mdatoms gmx_unused* md,
+ gmx::ArrayRef<const real> /*charge*/,
t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index);
/*! \brief For selecting which flavor of bonded kernel is used for simple bonded types */
* All pointers should be non-null, except for pbc and g which can be nullptr.
* \returns the energy or 0 when \p bondedKernelFlavor did not request the energy.
*/
-real calculateSimpleBond(int ftype,
- int numForceatoms,
- const t_iatom forceatoms[],
- const t_iparams forceparams[],
- const rvec x[],
- rvec4 f[],
- rvec fshift[],
- const struct t_pbc* pbc,
- real lambda,
- real* dvdlambda,
- const t_mdatoms* md,
- t_fcdata* fcd,
+real calculateSimpleBond(int ftype,
+ int numForceatoms,
+ const t_iatom forceatoms[],
+ const t_iparams forceparams[],
+ const rvec x[],
+ rvec4 f[],
+ rvec fshift[],
+ const struct t_pbc* pbc,
+ real lambda,
+ real* dvdlambda,
+ gmx::ArrayRef<const real> charge,
+ t_fcdata* fcd,
+ t_disresdata* disresdata,
+ t_oriresdata* oriresdata,
int gmx_unused* global_atom_index,
BondedKernelFlavor bondedKernelFlavor);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/fcdata.h"
#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
void init_disres(FILE* fplog,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
t_inputrec* ir,
DisResRunMode disResRunMode,
DDRole ddRole,
t_state* state,
gmx_bool bIsREMD)
{
- int fa, nmol, npair, np;
- history_t* hist;
- gmx_mtop_ilistloop_t iloop;
- char* ptr;
- int type_min, type_max;
+ history_t* hist;
+ char* ptr;
+ int type_min, type_max;
if (gmx_mtop_ftype_count(mtop, F_DISRES) == 0)
{
dd->npair = 0;
type_min = INT_MAX;
type_max = 0;
- iloop = gmx_mtop_ilistloop_init(mtop);
- while (const InteractionLists* il = gmx_mtop_ilistloop_next(iloop, &nmol))
+ for (const auto il : IListRange(mtop))
{
- if (nmol > 1 && !(*il)[F_DISRES].empty() && ir->eDisre != edrEnsemble)
+ if (il.nmol() > 1 && !il.list()[F_DISRES].empty()
+ && ir->eDisre != DistanceRestraintRefinement::Ensemble)
{
gmx_fatal(FARGS,
"NMR distance restraints with multiple copies of the same molecule are "
"a restraint potential (bonds type 10) instead.");
}
- np = 0;
- for (fa = 0; fa < (*il)[F_DISRES].size(); fa += 3)
+ int np = 0;
+ for (int fa = 0; fa < il.list()[F_DISRES].size(); fa += 3)
{
- int type;
-
- type = (*il)[F_DISRES].iatoms[fa];
+ int type = il.list()[F_DISRES].iatoms[fa];
np++;
- npair = mtop->ffparams.iparams[type].disres.npair;
+ int npair = mtop.ffparams.iparams[type].disres.npair;
if (np == npair)
{
- dd->nres += (ir->eDisre == edrEnsemble ? 1 : nmol);
- dd->npair += nmol * npair;
+ dd->nres += (ir->eDisre == DistanceRestraintRefinement::Ensemble ? 1 : il.nmol());
+ dd->npair += il.nmol() * npair;
np = 0;
type_min = std::min(type_min, type);
hist = &state->hist;
/* Set the "history lack" factor to 1 */
- state->flags |= (1 << estDISRE_INITF);
+ state->flags |= enumValueToBitMask(StateEntry::DisreInitF);
hist->disre_initf = 1.0;
/* Allocate space for the r^-3 time averages */
- state->flags |= (1 << estDISRE_RM3TAV);
- hist->ndisrepairs = dd->npair;
- snew(hist->disre_rm3tav, hist->ndisrepairs);
+ state->flags |= enumValueToBitMask(StateEntry::DisreRm3Tav);
+ hist->disre_rm3tav.resize(dd->npair);
}
/* Allocate space for a copy of rm3tav,
* so we can call do_force without modifying the state.
gmx_fatal(FARGS,
"GMX_DISRE_ENSEMBLE_SIZE (%d) is not equal to 1 or the number of systems "
"(option -multidir) %d",
- dd->nsystems, ms->numSimulations_);
+ dd->nsystems,
+ ms->numSimulations_);
}
if (fplog)
{
{
if (fplog)
{
- fprintf(fplog, "There are %d distance restraints involving %d atom pairs\n", dd->nres,
- dd->npair);
+ fprintf(fplog, "There are %d distance restraints involving %d atom pairs\n", dd->nres, dd->npair);
}
/* Have to avoid g_disre de-referencing cr blindly, mdrun not
* doing consistency checks for ensemble-averaged distance
const rvec x[],
const t_pbc* pbc,
t_disresdata* dd,
- history_t* hist)
+ const history_t* hist)
{
rvec dx;
real * rt, *rm3tav, *Rtl_6, *Rt_6, *Rtav_6;
dd->sumviol = 0;
}
-real ta_disres(int nfa,
- const t_iatom forceatoms[],
- const t_iparams ip[],
- const rvec x[],
- rvec4 f[],
- rvec fshift[],
- const t_pbc* pbc,
+real ta_disres(int nfa,
+ const t_iatom* forceatoms,
+ const t_iparams* ip,
+ const rvec* x,
+ rvec4* f,
+ rvec* fshift,
+ const t_pbc* pbc,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
- const t_mdatoms gmx_unused* md,
- t_fcdata* fcd,
+ gmx::ArrayRef<const real> /*charge*/,
+ t_fcdata gmx_unused* fcd,
+ t_disresdata* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
int gmx_unused* global_atom_index)
{
const real seven_three = 7.0 / 3.0;
- rvec dx;
- real weight_rt_1;
- real smooth_fc, Rt, Rtav, rt2, *Rtl_6, *Rt_6, *Rtav_6;
- real k0, f_scal = 0, fmax_scal, fk_scal, fij;
- real tav_viol, instant_viol, mixed_viol, violtot, vtot;
- real tav_viol_Rtav7, instant_viol_Rtav7;
- real up1, up2, low;
- gmx_bool bConservative, bMixed, bViolation;
- t_disresdata* dd;
- int dr_weighting;
- gmx_bool dr_bMixed;
-
- dd = fcd->disres;
- dr_weighting = dd->dr_weighting;
- dr_bMixed = dd->dr_bMixed;
- Rtl_6 = dd->Rtl_6;
- Rt_6 = dd->Rt_6;
- Rtav_6 = dd->Rtav_6;
+ rvec dx;
+ real weight_rt_1;
+ real smooth_fc, Rt, Rtav, rt2, *Rtl_6, *Rt_6, *Rtav_6;
+ real k0, f_scal = 0, fmax_scal, fk_scal, fij;
+ real tav_viol, instant_viol, mixed_viol, violtot, vtot;
+ real tav_viol_Rtav7, instant_viol_Rtav7;
+ real up1, up2, low;
+ gmx_bool bConservative, bMixed, bViolation;
+ gmx_bool dr_bMixed;
+
+ DistanceRestraintWeighting dr_weighting = disresdata->dr_weighting;
+ dr_bMixed = disresdata->dr_bMixed;
+ Rtl_6 = disresdata->Rtl_6;
+ Rt_6 = disresdata->Rt_6;
+ Rtav_6 = disresdata->Rtav_6;
tav_viol = instant_viol = mixed_viol = tav_viol_Rtav7 = instant_viol_Rtav7 = 0;
- smooth_fc = dd->dr_fc;
- if (dd->dr_tau != 0)
+ smooth_fc = disresdata->dr_fc;
+ if (disresdata->dr_tau != 0)
{
/* scaling factor to smoothly turn on the restraint forces *
* when using time averaging */
- smooth_fc *= (1.0 - dd->exp_min_t_tau);
+ smooth_fc *= (1.0 - disresdata->exp_min_t_tau);
}
violtot = 0;
/* 'loop' over all atom pairs (pair_nr=fa/3) involved in restraints, *
* the total number of atoms pairs is nfa/3 */
- int faOffset = static_cast<int>(forceatoms - dd->forceatomsStart);
+ int faOffset = static_cast<int>(forceatoms - disresdata->forceatomsStart);
for (int fa = 0; fa < nfa; fa += 3)
{
int type = forceatoms[fa];
low = ip[type].disres.low;
k0 = smooth_fc * ip[type].disres.kfac;
- int res = type - dd->type_min;
+ int res = type - disresdata->type_min;
/* save some flops when there is only one pair */
if (ip[type].disres.type != 2)
{
- bConservative = (dr_weighting == edrwConservative) && (npair > 1);
+ bConservative = (dr_weighting == DistanceRestraintWeighting::Conservative) && (npair > 1);
bMixed = dr_bMixed;
Rt = gmx::invsixthroot(Rt_6[res]);
Rtav = gmx::invsixthroot(Rtav_6[res]);
int pair = (faOffset + fa) / 3;
int ai = forceatoms[fa + 1];
int aj = forceatoms[fa + 2];
- int ki = CENTRAL;
+ int ki = gmx::c_centralShiftIndex;
if (pbc)
{
ki = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
{
if (!dr_bMixed)
{
- weight_rt_1 *= std::pow(dd->rm3tav[pair], seven_three);
+ weight_rt_1 *= std::pow(disresdata->rm3tav[pair], seven_three);
}
else
{
- weight_rt_1 *= tav_viol_Rtav7 * std::pow(dd->rm3tav[pair], seven_three)
- + instant_viol_Rtav7 / (dd->rt[pair] * gmx::power6(dd->rt[pair]));
+ weight_rt_1 *=
+ tav_viol_Rtav7 * std::pow(disresdata->rm3tav[pair], seven_three)
+ + instant_viol_Rtav7
+ / (disresdata->rt[pair] * gmx::power6(disresdata->rt[pair]));
}
}
if (fshift)
{
fshift[ki][m] += fij;
- fshift[CENTRAL][m] -= fij;
+ fshift[gmx::c_centralShiftIndex][m] -= fij;
}
}
}
}
#pragma omp atomic
- dd->sumviol += violtot;
+ disresdata->sumviol += violtot;
/* Return energy */
return vtot;
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
class history_t;
struct t_commrec;
struct t_disresdata;
+struct t_oriresdata;
struct t_fcdata;
struct t_inputrec;
struct t_pbc;
enum class DDRole;
enum class NumRanks;
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+} // namespace gmx
+
//! Whether distance restraints are called from mdrun or from an analysis tool
enum class DisResRunMode
{
* must differ according to whether REMD is active.
*/
void init_disres(FILE* fplog,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
t_inputrec* ir,
DisResRunMode disResRunMode,
DDRole ddRole,
const rvec* x,
const t_pbc* pbc,
t_disresdata* disresdata,
- history_t* hist);
+ const history_t* hist);
//! Calculates the distance restraint forces, return the potential.
-real ta_disres(int nfa,
- const t_iatom forceatoms[],
- const t_iparams ip[],
- const rvec x[],
- rvec4 f[],
- rvec fshift[],
- const t_pbc* pbc,
- real lambda,
- real* dvdlambda,
- const t_mdatoms* md,
- t_fcdata* fcdata,
- int* global_atom_index);
+real ta_disres(int nfa,
+ const t_iatom* forceatoms,
+ const t_iparams* ip,
+ const rvec* x,
+ rvec4* f,
+ rvec* fshift,
+ const t_pbc* pbc,
+ real lambda,
+ real* dvdlambda,
+ gmx::ArrayRef<const real> charge,
+ t_fcdata gmx_unused* fcd,
+ t_disresdata* disresdata,
+ t_oriresdata gmx_unused* oriresdata,
+ int* global_atom_index);
//! Copies the new time averages that have been calculated in calc_disres_R_6.
void update_disres_history(const t_disresdata& disresdata, history_t* hist);
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_LISTED_FORCES_GPUBONDED_H
#define GMX_LISTED_FORCES_GPUBONDED_H
+#include <memory>
+
#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/idef.h"
-#include "gromacs/utility/classhelpers.h"
class DeviceContext;
class DeviceStream;
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "config.h"
+#include <algorithm>
#include <string>
#include "gromacs/listed_forces/gpubonded.h"
//! Returns whether there are any interactions in ilists suitable for a GPU.
static bool someInteractionsCanRunOnGpu(const InteractionLists& ilists)
{
- for (int fType : fTypesOnGpu)
- {
- if (!ilists[fType].iatoms.empty())
- {
- // Perturbation is not implemented in the GPU bonded
- // kernels. If all the interactions were actually
- // perturbed, then that will be detected later on each
- // domain, and work will never run on the GPU. This is
- // very unlikely to occur, and has little run-time cost,
- // so we don't complicate the code by catering for it
- // here.
- return true;
- }
- }
- return false;
+ // Perturbation is not implemented in the GPU bonded
+ // kernels. If all the interactions were actually
+ // perturbed, then that will be detected later on each
+ // domain, and work will never run on the GPU. This is
+ // very unlikely to occur, and has little run-time cost,
+ // so we don't complicate the code by catering for it
+ // here.
+ return std::any_of(fTypesOnGpu.begin(), fTypesOnGpu.end(), [ilists](int fType) {
+ return !ilists[fType].iatoms.empty();
+ });
}
//! Returns whether there are any bonded interactions in the global topology suitable for a GPU.
{
errorReasons.emplace_back("not supported with OpenCL build of GROMACS");
}
+ if (GMX_GPU_SYCL)
+ {
+ errorReasons.emplace_back("not supported with SYCL build of GROMACS");
+ }
else if (!GMX_GPU)
{
errorReasons.emplace_back("not supported with CPU-only build of GROMACS");
GMX_RELEASE_ASSERT(deviceStream.isValid(),
"Can't run GPU version of bonded forces in stream that is not valid.");
- static_assert(c_threadsPerBlock >= SHIFTS,
- "Threads per block in GPU bonded must be >= SHIFTS for the virial kernel "
- "(calcVir=true)");
+ static_assert(
+ c_threadsPerBlock >= c_numShiftVectors,
+ "Threads per block in GPU bonded must be >= c_numShiftVectors for the virial kernel "
+ "(calcVir=true)");
wcycle_ = wcycle;
// This could be an async transfer (if the source is pinned), so
// long as it uses the same stream as the kernels and we are happy
// to consume additional pinned pages.
- copyToDeviceBuffer(&d_forceParams_, ffparams.iparams.data(), 0, ffparams.numTypes(),
- deviceStream_, GpuApiCallBehavior::Sync, nullptr);
+ copyToDeviceBuffer(&d_forceParams_,
+ ffparams.iparams.data(),
+ 0,
+ ffparams.numTypes(),
+ deviceStream_,
+ GpuApiCallBehavior::Sync,
+ nullptr);
vTot_.resize(F_NRE);
allocateDeviceBuffer(&d_vTot_, F_NRE, deviceContext_);
clearDeviceBufferAsync(&d_vTot_, 0, F_NRE, deviceStream_);
kernelLaunchConfig_.gridSize[1] = 1;
kernelLaunchConfig_.gridSize[2] = 1;
kernelLaunchConfig_.sharedMemorySize =
- SHIFTS * sizeof(float3) + (c_threadsPerBlock / warp_size) * 3 * sizeof(float);
+ c_numShiftVectors * sizeof(float3) + (c_threadsPerBlock / warp_size) * 3 * sizeof(float);
}
GpuBonded::Impl::~Impl()
{
t_ilist& d_iList = d_iLists_[fType];
- reallocateDeviceBuffer(&d_iList.iatoms, iList.size(), &d_iList.nr, &d_iList.nalloc,
- deviceContext_);
+ reallocateDeviceBuffer(
+ &d_iList.iatoms, iList.size(), &d_iList.nr, &d_iList.nalloc, deviceContext_);
- copyToDeviceBuffer(&d_iList.iatoms, iList.iatoms.data(), 0, iList.size(), deviceStream_,
- GpuApiCallBehavior::Async, nullptr);
+ copyToDeviceBuffer(&d_iList.iatoms,
+ iList.iatoms.data(),
+ 0,
+ iList.size(),
+ deviceStream_,
+ GpuApiCallBehavior::Async,
+ nullptr);
}
kernelParams_.fTypesOnGpu[fTypesCounter] = fType;
kernelParams_.numFTypeIAtoms[fTypesCounter] = iList.size();
GMX_ASSERT(haveInteractions_,
"No GPU bonded interactions, so no energies will be computed, so transfer should "
"not be called");
- wallcycle_sub_start_nocount(wcycle_, ewcsLAUNCH_GPU_BONDED);
+ wallcycle_sub_start_nocount(wcycle_, WallCycleSubCounter::LaunchGpuBonded);
// TODO add conditional on whether there has been any compute (and make sure host buffer doesn't contain garbage)
float* h_vTot = vTot_.data();
copyFromDeviceBuffer(h_vTot, &d_vTot_, 0, F_NRE, deviceStream_, GpuApiCallBehavior::Async, nullptr);
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_GPU_BONDED);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchGpuBonded);
}
void GpuBonded::Impl::waitAccumulateEnergyTerms(gmx_enerdata_t* enerd)
"No GPU bonded interactions, so no energies will be computed or transferred, so "
"accumulation should not occur");
- wallcycle_start(wcycle_, ewcWAIT_GPU_BONDED);
+ wallcycle_start(wcycle_, WallCycleCounter::WaitGpuBonded);
cudaError_t stat = cudaStreamSynchronize(deviceStream_.stream());
CU_RET_ERR(stat, "D2H transfer of bonded energies failed");
- wallcycle_stop(wcycle_, ewcWAIT_GPU_BONDED);
+ wallcycle_stop(wcycle_, WallCycleCounter::WaitGpuBonded);
for (int fType : fTypesOnGpu)
{
// Note: We do not support energy groups here
gmx_grppairener_t* grppener = &enerd->grpp;
GMX_RELEASE_ASSERT(grppener->nener == 1, "No energy group support for bondeds on the GPU");
- grppener->ener[egLJ14][0] += vTot_[F_LJ14];
- grppener->ener[egCOUL14][0] += vTot_[F_COUL14];
+ grppener->energyGroupPairTerms[NonBondedEnergyTerms::LJ14][0] += vTot_[F_LJ14];
+ grppener->energyGroupPairTerms[NonBondedEnergyTerms::Coulomb14][0] += vTot_[F_COUL14];
}
void GpuBonded::Impl::clearEnergies()
{
- wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU);
- wallcycle_sub_start_nocount(wcycle_, ewcsLAUNCH_GPU_BONDED);
+ wallcycle_start_nocount(wcycle_, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start_nocount(wcycle_, WallCycleSubCounter::LaunchGpuBonded);
clearDeviceBufferAsync(&d_vTot_, 0, F_NRE, deviceStream_);
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_GPU_BONDED);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchGpuBonded);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
}
// ---- GpuBonded
float3 fij = fbond * dx;
atomicAdd(&gm_f[ai], fij);
atomicAdd(&gm_f[aj], -fij);
- if (calcVir && ki != CENTRAL)
+ if (calcVir && ki != gmx::c_centralShiftIndex)
{
atomicAdd(&sm_fShiftLoc[ki], fij);
- atomicAdd(&sm_fShiftLoc[CENTRAL], -fij);
+ atomicAdd(&sm_fShiftLoc[gmx::c_centralShiftIndex], -fij);
}
}
}
float cos_theta;
int t1;
int t2;
- float theta = bond_angle_gpu<calcVir>(gm_xq[ai], gm_xq[aj], gm_xq[ak], pbcAiuc, &r_ij,
- &r_kj, &cos_theta, &t1, &t2);
+ float theta = bond_angle_gpu<calcVir>(
+ gm_xq[ai], gm_xq[aj], gm_xq[ak], pbcAiuc, &r_ij, &r_kj, &cos_theta, &t1, &t2);
float va;
float dVdt;
harmonic_gpu(d_forceparams[type].harmonic.krA,
- d_forceparams[type].harmonic.rA * CUDA_DEG2RAD_F, theta, &va, &dVdt);
+ d_forceparams[type].harmonic.rA * CUDA_DEG2RAD_F,
+ theta,
+ &va,
+ &dVdt);
if (calcEner)
{
if (calcVir)
{
atomicAdd(&sm_fShiftLoc[t1], f_i);
- atomicAdd(&sm_fShiftLoc[CENTRAL], f_j);
+ atomicAdd(&sm_fShiftLoc[gmx::c_centralShiftIndex], f_j);
atomicAdd(&sm_fShiftLoc[t2], f_k);
}
}
float cos_theta;
int t1;
int t2;
- float theta = bond_angle_gpu<calcVir>(gm_xq[ai], gm_xq[aj], gm_xq[ak], pbcAiuc, &r_ij,
- &r_kj, &cos_theta, &t1, &t2);
+ float theta = bond_angle_gpu<calcVir>(
+ gm_xq[ai], gm_xq[aj], gm_xq[ak], pbcAiuc, &r_ij, &r_kj, &cos_theta, &t1, &t2);
float va;
float dVdt;
if (calcVir)
{
atomicAdd(&sm_fShiftLoc[t1], f_i);
- atomicAdd(&sm_fShiftLoc[CENTRAL], f_j);
+ atomicAdd(&sm_fShiftLoc[gmx::c_centralShiftIndex], f_j);
atomicAdd(&sm_fShiftLoc[t2], f_k);
}
}
atomicAdd(&gm_f[ai], fik);
atomicAdd(&gm_f[ak], -fik);
- if (calcVir && ki != CENTRAL)
+ if (calcVir && ki != gmx::c_centralShiftIndex)
{
atomicAdd(&sm_fShiftLoc[ki], fik);
- atomicAdd(&sm_fShiftLoc[CENTRAL], -fik);
+ atomicAdd(&sm_fShiftLoc[gmx::c_centralShiftIndex], -fik);
}
}
}
int t3 = pbcDxAiuc<calcVir>(pbcAiuc, gm_xq[l], gm_xq[j], dx_jl);
atomicAdd(&sm_fShiftLoc[t1], f_i);
- atomicAdd(&sm_fShiftLoc[CENTRAL], -f_j);
+ atomicAdd(&sm_fShiftLoc[gmx::c_centralShiftIndex], -f_j);
atomicAdd(&sm_fShiftLoc[t2], -f_k);
atomicAdd(&sm_fShiftLoc[t3], f_l);
}
int t1;
int t2;
int t3;
- float phi = dih_angle_gpu<calcVir>(gm_xq[ai], gm_xq[aj], gm_xq[ak], gm_xq[al], pbcAiuc,
- &r_ij, &r_kj, &r_kl, &m, &n, &t1, &t2, &t3);
+ float phi = dih_angle_gpu<calcVir>(
+ gm_xq[ai], gm_xq[aj], gm_xq[ak], gm_xq[al], pbcAiuc, &r_ij, &r_kj, &r_kl, &m, &n, &t1, &t2, &t3);
float vpd;
float ddphi;
- dopdihs_gpu(d_forceparams[type].pdihs.cpA, d_forceparams[type].pdihs.phiA,
- d_forceparams[type].pdihs.mult, phi, &vpd, &ddphi);
+ dopdihs_gpu(d_forceparams[type].pdihs.cpA,
+ d_forceparams[type].pdihs.phiA,
+ d_forceparams[type].pdihs.mult,
+ phi,
+ &vpd,
+ &ddphi);
if (calcEner)
{
*vtot_loc += vpd;
}
- do_dih_fup_gpu<calcVir>(ai, aj, ak, al, ddphi, r_ij, r_kj, r_kl, m, n, gm_f, sm_fShiftLoc,
- pbcAiuc, gm_xq, t1, t2, t3);
+ do_dih_fup_gpu<calcVir>(
+ ai, aj, ak, al, ddphi, r_ij, r_kj, r_kl, m, n, gm_f, sm_fShiftLoc, pbcAiuc, gm_xq, t1, t2, t3);
}
}
int t1;
int t2;
int t3;
- float phi = dih_angle_gpu<calcVir>(gm_xq[ai], gm_xq[aj], gm_xq[ak], gm_xq[al], pbcAiuc,
- &r_ij, &r_kj, &r_kl, &m, &n, &t1, &t2, &t3);
+ float phi = dih_angle_gpu<calcVir>(
+ gm_xq[ai], gm_xq[aj], gm_xq[ak], gm_xq[al], pbcAiuc, &r_ij, &r_kj, &r_kl, &m, &n, &t1, &t2, &t3);
/* Change to polymer convention */
if (phi < c0)
ddphi = -ddphi * sin_phi;
- do_dih_fup_gpu<calcVir>(ai, aj, ak, al, ddphi, r_ij, r_kj, r_kl, m, n, gm_f, sm_fShiftLoc,
- pbcAiuc, gm_xq, t1, t2, t3);
+ do_dih_fup_gpu<calcVir>(
+ ai, aj, ak, al, ddphi, r_ij, r_kj, r_kl, m, n, gm_f, sm_fShiftLoc, pbcAiuc, gm_xq, t1, t2, t3);
if (calcEner)
{
*vtot_loc += v;
int t1;
int t2;
int t3;
- float phi = dih_angle_gpu<calcVir>(gm_xq[ai], gm_xq[aj], gm_xq[ak], gm_xq[al], pbcAiuc,
- &r_ij, &r_kj, &r_kl, &m, &n, &t1, &t2, &t3);
+ float phi = dih_angle_gpu<calcVir>(
+ gm_xq[ai], gm_xq[aj], gm_xq[ak], gm_xq[al], pbcAiuc, &r_ij, &r_kj, &r_kl, &m, &n, &t1, &t2, &t3);
/* phi can jump if phi0 is close to Pi/-Pi, which will cause huge
* force changes if we just apply a normal harmonic.
float ddphi = -kA * dp;
- do_dih_fup_gpu<calcVir>(ai, aj, ak, al, -ddphi, r_ij, r_kj, r_kl, m, n, gm_f, sm_fShiftLoc,
- pbcAiuc, gm_xq, t1, t2, t3);
+ do_dih_fup_gpu<calcVir>(
+ ai, aj, ak, al, -ddphi, r_ij, r_kj, r_kl, m, n, gm_f, sm_fShiftLoc, pbcAiuc, gm_xq, t1, t2, t3);
if (calcEner)
{
/* Add the forces */
atomicAdd(&gm_f[ai], f);
atomicAdd(&gm_f[aj], -f);
- if (calcVir && fshift_index != CENTRAL)
+ if (calcVir && fshift_index != gmx::c_centralShiftIndex)
{
atomicAdd(&sm_fShiftLoc[fshift_index], f);
- atomicAdd(&sm_fShiftLoc[CENTRAL], -f);
+ atomicAdd(&sm_fShiftLoc[gmx::c_centralShiftIndex], -f);
}
if (calcEner)
extern __shared__ char sm_dynamicShmem[];
char* sm_nextSlotPtr = sm_dynamicShmem;
float3* sm_fShiftLoc = (float3*)sm_nextSlotPtr;
- sm_nextSlotPtr += SHIFTS * sizeof(float3);
+ sm_nextSlotPtr += c_numShiftVectors * sizeof(float3);
if (calcVir)
{
- if (threadIdx.x < SHIFTS)
+ if (threadIdx.x < c_numShiftVectors)
{
sm_fShiftLoc[threadIdx.x] = make_float3(0.0f, 0.0f, 0.0f);
}
switch (fType)
{
case F_BONDS:
- bonds_gpu<calcVir, calcEner>(fTypeTid, &vtot_loc, numBonds, iatoms,
- kernelParams.d_forceParams, kernelParams.d_xq,
- kernelParams.d_f, sm_fShiftLoc, kernelParams.pbcAiuc);
+ bonds_gpu<calcVir, calcEner>(fTypeTid,
+ &vtot_loc,
+ numBonds,
+ iatoms,
+ kernelParams.d_forceParams,
+ kernelParams.d_xq,
+ kernelParams.d_f,
+ sm_fShiftLoc,
+ kernelParams.pbcAiuc);
break;
case F_ANGLES:
- angles_gpu<calcVir, calcEner>(
- fTypeTid, &vtot_loc, numBonds, iatoms, kernelParams.d_forceParams,
- kernelParams.d_xq, kernelParams.d_f, sm_fShiftLoc, kernelParams.pbcAiuc);
+ angles_gpu<calcVir, calcEner>(fTypeTid,
+ &vtot_loc,
+ numBonds,
+ iatoms,
+ kernelParams.d_forceParams,
+ kernelParams.d_xq,
+ kernelParams.d_f,
+ sm_fShiftLoc,
+ kernelParams.pbcAiuc);
break;
case F_UREY_BRADLEY:
- urey_bradley_gpu<calcVir, calcEner>(
- fTypeTid, &vtot_loc, numBonds, iatoms, kernelParams.d_forceParams,
- kernelParams.d_xq, kernelParams.d_f, sm_fShiftLoc, kernelParams.pbcAiuc);
+ urey_bradley_gpu<calcVir, calcEner>(fTypeTid,
+ &vtot_loc,
+ numBonds,
+ iatoms,
+ kernelParams.d_forceParams,
+ kernelParams.d_xq,
+ kernelParams.d_f,
+ sm_fShiftLoc,
+ kernelParams.pbcAiuc);
break;
case F_PDIHS:
case F_PIDIHS:
- pdihs_gpu<calcVir, calcEner>(fTypeTid, &vtot_loc, numBonds, iatoms,
- kernelParams.d_forceParams, kernelParams.d_xq,
- kernelParams.d_f, sm_fShiftLoc, kernelParams.pbcAiuc);
+ pdihs_gpu<calcVir, calcEner>(fTypeTid,
+ &vtot_loc,
+ numBonds,
+ iatoms,
+ kernelParams.d_forceParams,
+ kernelParams.d_xq,
+ kernelParams.d_f,
+ sm_fShiftLoc,
+ kernelParams.pbcAiuc);
break;
case F_RBDIHS:
- rbdihs_gpu<calcVir, calcEner>(
- fTypeTid, &vtot_loc, numBonds, iatoms, kernelParams.d_forceParams,
- kernelParams.d_xq, kernelParams.d_f, sm_fShiftLoc, kernelParams.pbcAiuc);
+ rbdihs_gpu<calcVir, calcEner>(fTypeTid,
+ &vtot_loc,
+ numBonds,
+ iatoms,
+ kernelParams.d_forceParams,
+ kernelParams.d_xq,
+ kernelParams.d_f,
+ sm_fShiftLoc,
+ kernelParams.pbcAiuc);
break;
case F_IDIHS:
- idihs_gpu<calcVir, calcEner>(fTypeTid, &vtot_loc, numBonds, iatoms,
- kernelParams.d_forceParams, kernelParams.d_xq,
- kernelParams.d_f, sm_fShiftLoc, kernelParams.pbcAiuc);
+ idihs_gpu<calcVir, calcEner>(fTypeTid,
+ &vtot_loc,
+ numBonds,
+ iatoms,
+ kernelParams.d_forceParams,
+ kernelParams.d_xq,
+ kernelParams.d_f,
+ sm_fShiftLoc,
+ kernelParams.pbcAiuc);
break;
case F_LJ14:
- pairs_gpu<calcVir, calcEner>(
- fTypeTid, numBonds, iatoms, kernelParams.d_forceParams,
- kernelParams.d_xq, kernelParams.d_f, sm_fShiftLoc, kernelParams.pbcAiuc,
- kernelParams.electrostaticsScaleFactor, &vtotVdw_loc, &vtotElec_loc);
+ pairs_gpu<calcVir, calcEner>(fTypeTid,
+ numBonds,
+ iatoms,
+ kernelParams.d_forceParams,
+ kernelParams.d_xq,
+ kernelParams.d_f,
+ sm_fShiftLoc,
+ kernelParams.pbcAiuc,
+ kernelParams.electrostaticsScaleFactor,
+ &vtotVdw_loc,
+ &vtotElec_loc);
break;
}
break;
atomicAdd(vtotElec, sm_vTotElec[warpId]);
}
}
- /* Accumulate shift vectors from shared memory to global memory on the first SHIFTS threads of the block. */
+ /* Accumulate shift vectors from shared memory to global memory on the first c_numShiftVectors threads of the block. */
if (calcVir)
{
__syncthreads();
- if (threadIdx.x < SHIFTS)
+ if (threadIdx.x < c_numShiftVectors)
{
atomicAdd(kernelParams.d_fShift[threadIdx.x], sm_fShiftLoc[threadIdx.x]);
}
GMX_ASSERT(haveInteractions_,
"Cannot launch bonded GPU kernels unless bonded GPU work was scheduled");
- wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU);
- wallcycle_sub_start(wcycle_, ewcsLAUNCH_GPU_BONDED);
+ wallcycle_start_nocount(wcycle_, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::LaunchGpuBonded);
int fTypeRangeEnd = kernelParams_.fTypeRangeEnd[numFTypesOnGpu - 1];
const auto kernelArgs = prepareGpuKernelArguments(kernelPtr, kernelLaunchConfig_, &kernelParams_);
- launchGpuKernel(kernelPtr, kernelLaunchConfig_, deviceStream_, nullptr,
- "exec_kernel_gpu<calcVir, calcEner>", kernelArgs);
+ launchGpuKernel(kernelPtr,
+ kernelLaunchConfig_,
+ deviceStream_,
+ nullptr,
+ "exec_kernel_gpu<calcVir, calcEner>",
+ kernelArgs);
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_GPU_BONDED);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchGpuBonded);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
}
void GpuBonded::launchKernel(const gmx::StepWorkload& stepWork)
*/
#include "gmxpre.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "listed_forces.h"
#include <cassert>
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/mdtypes/fcdata.h"
#include "gromacs/mdtypes/forceoutput.h"
#include "gromacs/mdtypes/forcerec.h"
if (idef_->ilsort == ilsortFE_SORTED)
{
forceBufferLambda_.resize(numAtomsForce * sizeof(rvec4) / sizeof(real));
- shiftForceBufferLambda_.resize(SHIFTS);
+ shiftForceBufferLambda_.resize(gmx::c_numShiftVectors);
}
}
}
}
- for (int i = 0; i < SHIFTS; i++)
+ for (int i = 0; i < gmx::c_numShiftVectors; i++)
{
clear_rvec(f_t->fshift[i]);
}
{
f_t->ener[i] = 0;
}
- for (int i = 0; i < egNR; i++)
+ for (int i = 0; i < static_cast<int>(NonBondedEnergyTerms::Count); i++)
{
for (int j = 0; j < f_t->grpp.nener; j++)
{
- f_t->grpp.ener[i][j] = 0;
+ f_t->grpp.energyGroupPairTerms[i][j] = 0;
}
}
- for (int i = 0; i < efptNR; i++)
+ for (auto i : keysOf(f_t->dvdl))
{
f_t->dvdl[i] = 0;
}
void reduce_thread_output(gmx::ForceWithShiftForces* forceWithShiftForces,
real* ener,
gmx_grppairener_t* grpp,
- real* dvdl,
+ gmx::ArrayRef<real> dvdl,
const bonded_threading_t* bt,
const gmx::StepWorkload& stepWork)
{
if (stepWork.computeVirial)
{
- for (int i = 0; i < SHIFTS; i++)
+ for (int i = 0; i < gmx::c_numShiftVectors; i++)
{
for (int t = 1; t < bt->nthreads; t++)
{
ener[i] += f_t[t]->ener[i];
}
}
- for (int i = 0; i < egNR; i++)
+ for (int i = 0; i < static_cast<int>(NonBondedEnergyTerms::Count); i++)
{
for (int j = 0; j < f_t[1]->grpp.nener; j++)
{
for (int t = 1; t < bt->nthreads; t++)
{
- grpp->ener[i][j] += f_t[t]->grpp.ener[i][j];
+ grpp->energyGroupPairTerms[i][j] += f_t[t]->grpp.energyGroupPairTerms[i][j];
}
}
}
}
if (stepWork.computeDhdl)
{
- for (int i = 0; i < efptNR; i++)
+ for (auto i : keysOf(f_t[1]->dvdl))
{
for (int t = 1; t < bt->nthreads; t++)
{
- dvdl[i] += f_t[t]->dvdl[i];
+ dvdl[static_cast<int>(i)] += f_t[t]->dvdl[i];
}
}
}
const t_pbc* pbc,
gmx_grppairener_t* grpp,
t_nrnb* nrnb,
- const real* lambda,
- real* dvdl,
+ gmx::ArrayRef<const real> lambda,
+ gmx::ArrayRef<real> dvdl,
const t_mdatoms* md,
t_fcdata* fcd,
const gmx::StepWorkload& stepWork,
(idef.ilsort == ilsortFE_SORTED && numNonperturbedInteractions < iatoms.ssize());
BondedKernelFlavor flavor =
selectBondedKernelFlavor(stepWork, fr->use_simd_kernels, havePerturbedInteractions);
- int efptFTYPE;
+ FreeEnergyPerturbationCouplingType efptFTYPE;
if (IS_RESTRAINT_TYPE(ftype))
{
- efptFTYPE = efptRESTRAINT;
+ efptFTYPE = FreeEnergyPerturbationCouplingType::Restraint;
}
else
{
- efptFTYPE = efptBONDED;
+ efptFTYPE = FreeEnergyPerturbationCouplingType::Bonded;
}
const int nat1 = interaction_function[ftype].nratoms + 1;
nice to account to its own subtimer, but first
wallcycle needs to be extended to support calling from
multiple threads. */
- v = cmap_dihs(nbn, iatoms.data() + nb0, iparams.data(), &idef.cmap_grid, x, f, fshift,
- pbc, lambda[efptFTYPE], &(dvdl[efptFTYPE]), md, fcd, global_atom_index);
+ v = cmap_dihs(nbn,
+ iatoms.data() + nb0,
+ iparams.data(),
+ &idef.cmap_grid,
+ x,
+ f,
+ fshift,
+ pbc,
+ lambda[static_cast<int>(efptFTYPE)],
+ &(dvdl[static_cast<int>(efptFTYPE)]),
+ gmx::arrayRefFromArray(md->chargeA, md->nr),
+ fcd,
+ nullptr,
+ nullptr,
+ global_atom_index);
}
else
{
- v = calculateSimpleBond(ftype, nbn, iatoms.data() + nb0, iparams.data(), x, f, fshift,
- pbc, lambda[efptFTYPE], &(dvdl[efptFTYPE]), md, fcd,
- global_atom_index, flavor);
+ v = calculateSimpleBond(ftype,
+ nbn,
+ iatoms.data() + nb0,
+ iparams.data(),
+ x,
+ f,
+ fshift,
+ pbc,
+ lambda[static_cast<int>(efptFTYPE)],
+ &(dvdl[static_cast<int>(efptFTYPE)]),
+ gmx::arrayRefFromArray(md->chargeA, md->nr),
+ fcd,
+ fcd->disres,
+ fcd->orires.get(),
+ global_atom_index,
+ flavor);
}
}
else
/* TODO The execution time for pairs might be nice to account
to its own subtimer, but first wallcycle needs to be
extended to support calling from multiple threads. */
- do_pairs(ftype, nbn, iatoms.data() + nb0, iparams.data(), x, f, fshift, pbc, lambda, dvdl,
- md, fr, havePerturbedInteractions, stepWork, grpp, global_atom_index);
+ do_pairs(ftype,
+ nbn,
+ iatoms.data() + nb0,
+ iparams.data(),
+ x,
+ f,
+ fshift,
+ pbc,
+ lambda.data(),
+ dvdl.data(),
+ md->chargeA ? gmx::arrayRefFromArray(md->chargeA, md->nr) : gmx::ArrayRef<real>{},
+ md->chargeB ? gmx::arrayRefFromArray(md->chargeB, md->nr) : gmx::ArrayRef<real>{},
+ md->bPerturbed ? gmx::arrayRefFromArray(md->bPerturbed, md->nr) : gmx::ArrayRef<bool>(),
+ gmx::arrayRefFromArray(md->cENER, md->nr),
+ md->nPerturbed,
+ fr,
+ havePerturbedInteractions,
+ stepWork,
+ grpp,
+ global_atom_index);
}
if (thread == 0)
rvec* fshiftMasterBuffer,
gmx_enerdata_t* enerd,
t_nrnb* nrnb,
- const real* lambda,
- real* dvdl,
+ gmx::ArrayRef<const real> lambda,
+ gmx::ArrayRef<real> dvdl,
const t_mdatoms* md,
t_fcdata* fcd,
const gmx::StepWorkload& stepWork,
{
f_thread_t& threadBuffers = *bt->f_t[thread];
int ftype;
- real * epot, v;
+ real v;
/* thread stuff */
- rvec* fshift;
- real* dvdlt;
- gmx_grppairener_t* grpp;
+ rvec* fshift;
+ gmx::ArrayRef<real> dvdlt;
+ gmx::ArrayRef<real> epot;
+ gmx_grppairener_t* grpp;
zero_thread_output(&threadBuffers);
if (!ilist.empty() && ftype_is_bonded_potential(ftype))
{
ArrayRef<const int> iatoms = gmx::makeConstArrayRef(ilist.iatoms);
- v = calc_one_bond(thread, ftype, idef, iatoms, idef.numNonperturbedInteractions[ftype],
- bt->workDivision, x, ft, fshift, fr, pbc_null, grpp, nrnb,
- lambda, dvdlt, md, fcd, stepWork, global_atom_index);
+ v = calc_one_bond(thread,
+ ftype,
+ idef,
+ iatoms,
+ idef.numNonperturbedInteractions[ftype],
+ bt->workDivision,
+ x,
+ ft,
+ fshift,
+ fr,
+ pbc_null,
+ grpp,
+ nrnb,
+ lambda,
+ dvdlt,
+ md,
+ fcd,
+ stepWork,
+ global_atom_index);
epot[ftype] += v;
}
}
bool ListedForces::haveRestraints(const t_fcdata& fcdata) const
{
- GMX_ASSERT(fcdata.orires && fcdata.disres, "NMR restraints objects should be set up");
+ GMX_ASSERT(fcdata.disres, "NMR distance restraint object should be set up");
- return (!idef_->il[F_POSRES].empty() || !idef_->il[F_FBPOSRES].empty() || fcdata.orires->nr > 0
+ return (!idef_->il[F_POSRES].empty() || !idef_->il[F_FBPOSRES].empty() || fcdata.orires
|| fcdata.disres->nres > 0);
}
const t_pbc* pbc,
gmx_enerdata_t* enerd,
t_nrnb* nrnb,
- const real* lambda,
+ gmx::ArrayRef<const real> lambda,
const t_mdatoms* md,
t_fcdata* fcd,
int* global_atom_index,
{
gmx::ForceWithShiftForces& forceWithShiftForces = forceOutputs->forceWithShiftForces();
- wallcycle_sub_start(wcycle, ewcsLISTED);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::Listed);
/* The dummy array is to have a place to store the dhdl at other values
of lambda, which will be thrown away in the end */
- real dvdl[efptNR] = { 0 };
- calcBondedForces(idef, bt, x, fr, fr->bMolPBC ? pbc : nullptr,
- as_rvec_array(forceWithShiftForces.shiftForces().data()), enerd, nrnb,
- lambda, dvdl, md, fcd, stepWork, global_atom_index);
- wallcycle_sub_stop(wcycle, ewcsLISTED);
-
- wallcycle_sub_start(wcycle, ewcsLISTED_BUF_OPS);
- reduce_thread_output(&forceWithShiftForces, enerd->term, &enerd->grpp, dvdl, bt, stepWork);
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real> dvdl = { 0 };
+ calcBondedForces(idef,
+ bt,
+ x,
+ fr,
+ fr->bMolPBC ? pbc : nullptr,
+ as_rvec_array(forceWithShiftForces.shiftForces().data()),
+ enerd,
+ nrnb,
+ lambda,
+ dvdl,
+ md,
+ fcd,
+ stepWork,
+ global_atom_index);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::Listed);
+
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::ListedBufOps);
+ reduce_thread_output(&forceWithShiftForces, enerd->term.data(), &enerd->grpp, dvdl, bt, stepWork);
if (stepWork.computeDhdl)
{
- for (int i = 0; i < efptNR; i++)
+ for (auto i : keysOf(enerd->dvdl_lin))
{
enerd->dvdl_nonlin[i] += dvdl[i];
}
}
- wallcycle_sub_stop(wcycle, ewcsLISTED_BUF_OPS);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::ListedBufOps);
}
/* Copy the sum of violations for the distance restraints from fcd */
real* epot,
gmx::ArrayRef<real> dvdl,
t_nrnb* nrnb,
- const real* lambda,
+ gmx::ArrayRef<const real> lambda,
const t_mdatoms* md,
t_fcdata* fcd,
int* global_atom_index)
/* We already have the forces, so we use temp buffers here */
std::fill(forceBufferLambda.begin(), forceBufferLambda.end(), 0.0_real);
- std::fill(shiftForceBufferLambda.begin(), shiftForceBufferLambda.end(),
+ std::fill(shiftForceBufferLambda.begin(),
+ shiftForceBufferLambda.end(),
gmx::RVec{ 0.0_real, 0.0_real, 0.0_real });
rvec4* f = reinterpret_cast<rvec4*>(forceBufferLambda.data());
rvec* fshift = as_rvec_array(shiftForceBufferLambda.data());
gmx::StepWorkload tempFlags;
tempFlags.computeEnergy = true;
- real v = calc_one_bond(0, ftype, idef, iatomsPerturbed, iatomsPerturbed.ssize(),
- workDivision, x, f, fshift, fr, pbc_null, grpp, nrnb, lambda,
- dvdl.data(), md, fcd, tempFlags, global_atom_index);
+ real v = calc_one_bond(0,
+ ftype,
+ idef,
+ iatomsPerturbed,
+ iatomsPerturbed.ssize(),
+ workDivision,
+ x,
+ f,
+ fshift,
+ fr,
+ pbc_null,
+ grpp,
+ nrnb,
+ lambda,
+ dvdl,
+ md,
+ fcd,
+ tempFlags,
+ global_atom_index);
epot[ftype] += v;
}
}
gmx::ArrayRefWithPadding<const gmx::RVec> coordinates,
gmx::ArrayRef<const gmx::RVec> xWholeMolecules,
t_fcdata* fcdata,
- history_t* hist,
+ const history_t* hist,
gmx::ForceOutputs* forceOutputs,
const t_forcerec* fr,
const struct t_pbc* pbc,
gmx_enerdata_t* enerd,
t_nrnb* nrnb,
- const real* lambda,
+ gmx::ArrayRef<const real> lambda,
const t_mdatoms* md,
int* global_atom_index,
const gmx::StepWorkload& stepWork)
awkward to account to this subtimer properly in the present
code. We don't test / care much about performance with
restraints, anyway. */
- wallcycle_sub_start(wcycle, ewcsRESTRAINTS);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::Restraints);
if (!idef.il[F_POSRES].empty())
{
}
/* Do pre force calculation stuff which might require communication */
- if (fcdata->orires->nr > 0)
+ if (fcdata->orires)
{
GMX_ASSERT(!xWholeMolecules.empty(), "Need whole molecules for orienation restraints");
- enerd->term[F_ORIRESDEV] = calc_orires_dev(
- ms, idef.il[F_ORIRES].size(), idef.il[F_ORIRES].iatoms.data(), idef.iparams.data(),
- md, xWholeMolecules, x, fr->bMolPBC ? pbc : nullptr, fcdata->orires, hist);
+ enerd->term[F_ORIRESDEV] = calc_orires_dev(ms,
+ idef.il[F_ORIRES].size(),
+ idef.il[F_ORIRES].iatoms.data(),
+ idef.iparams.data(),
+ md,
+ xWholeMolecules,
+ x,
+ fr->bMolPBC ? pbc : nullptr,
+ fcdata->orires.get(),
+ hist);
}
if (fcdata->disres->nres > 0)
{
- calc_disres_R_6(cr, ms, idef.il[F_DISRES].size(), idef.il[F_DISRES].iatoms.data(), x,
- fr->bMolPBC ? pbc : nullptr, fcdata->disres, hist);
+ calc_disres_R_6(cr,
+ ms,
+ idef.il[F_DISRES].size(),
+ idef.il[F_DISRES].iatoms.data(),
+ x,
+ fr->bMolPBC ? pbc : nullptr,
+ fcdata->disres,
+ hist);
}
- wallcycle_sub_stop(wcycle, ewcsRESTRAINTS);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::Restraints);
}
- calc_listed(wcycle, idef, threading_.get(), x, forceOutputs, fr, pbc, enerd, nrnb, lambda, md,
- fcdata, global_atom_index, stepWork);
+ calc_listed(wcycle, idef, threading_.get(), x, forceOutputs, fr, pbc, enerd, nrnb, lambda, md, fcdata, global_atom_index, stepWork);
/* Check if we have to determine energy differences
* at foreign lambda's.
*/
if (fepvals->n_lambda > 0 && stepWork.computeDhdl)
{
- real dvdl[efptNR] = { 0 };
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real> dvdl = { 0 };
if (!idef.il[F_POSRES].empty())
{
posres_wrapper_lambda(wcycle, fepvals, idef, &pbc_full, x, enerd, lambda, fr);
}
if (idef.ilsort != ilsortNO_FE)
{
- wallcycle_sub_start(wcycle, ewcsLISTED_FEP);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::ListedFep);
if (idef.ilsort != ilsortFE_SORTED)
{
gmx_incons("The bonded interactions are not sorted for free energy");
}
for (int i = 0; i < 1 + enerd->foreignLambdaTerms.numLambdas(); i++)
{
- real lam_i[efptNR];
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real> lam_i;
reset_foreign_enerdata(enerd);
- for (int j = 0; j < efptNR; j++)
+ for (auto j : keysOf(lam_i))
{
- lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i - 1]);
+ lam_i[j] = (i == 0 ? lambda[static_cast<int>(j)] : fepvals->all_lambda[j][i - 1]);
}
- calc_listed_lambda(idef, threading_.get(), x, fr, pbc, forceBufferLambda_,
- shiftForceBufferLambda_, &(enerd->foreign_grpp), enerd->foreign_term,
- dvdl, nrnb, lam_i, md, fcdata, global_atom_index);
- sum_epot(enerd->foreign_grpp, enerd->foreign_term);
+ calc_listed_lambda(idef,
+ threading_.get(),
+ x,
+ fr,
+ pbc,
+ forceBufferLambda_,
+ shiftForceBufferLambda_,
+ &(enerd->foreign_grpp),
+ enerd->foreign_term.data(),
+ dvdl,
+ nrnb,
+ lam_i,
+ md,
+ fcdata,
+ global_atom_index);
+ sum_epot(enerd->foreign_grpp, enerd->foreign_term.data());
const double dvdlSum = std::accumulate(std::begin(dvdl), std::end(dvdl), 0.);
std::fill(std::begin(dvdl), std::end(dvdl), 0.0);
enerd->foreignLambdaTerms.accumulate(i, enerd->foreign_term[F_EPOT], dvdlSum);
}
- wallcycle_sub_stop(wcycle, ewcsLISTED_FEP);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::ListedFep);
}
}
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/idef.h"
#include "gromacs/topology/ifunc.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/classhelpers.h"
struct bonded_threading_t;
struct t_mdatoms;
struct t_nrnb;
class t_state;
+struct t_disresdata;
+struct t_oriresdata;
namespace gmx
{
} // namespace gmx
//! Type of CPU function to compute a bonded interaction.
-using BondedFunction = real (*)(int nbonds,
- const t_iatom iatoms[],
- const t_iparams iparams[],
- const rvec x[],
- rvec4 f[],
- rvec fshift[],
- const t_pbc* pbc,
- real lambda,
- real* dvdlambda,
- const t_mdatoms* md,
- t_fcdata* fcd,
- int* ddgatindex);
+using BondedFunction = real (*)(int nbonds,
+ const t_iatom iatoms[],
+ const t_iparams iparams[],
+ const rvec x[],
+ rvec4 f[],
+ rvec fshift[],
+ const t_pbc* pbc,
+ real lambda,
+ gmx::ArrayRef<real> dvdlambda,
+ const t_mdatoms* md,
+ t_fcdata* fcd,
+ t_disresdata* disresdata,
+ t_oriresdata* oriresdata,
+ int* ddgatindex);
//! Getter for finding a callable CPU function to compute an \c ftype interaction.
BondedFunction bondedFunction(int ftype);
gmx::ArrayRefWithPadding<const gmx::RVec> coordinates,
gmx::ArrayRef<const gmx::RVec> xWholeMolecules,
t_fcdata* fcdata,
- history_t* hist,
+ const history_t* hist,
gmx::ForceOutputs* forceOutputs,
const t_forcerec* fr,
const struct t_pbc* pbc,
gmx_enerdata_t* enerd,
t_nrnb* nrnb,
- const real* lambda,
+ gmx::ArrayRef<const real> lambda,
const t_mdatoms* md,
int* global_atom_index,
const gmx::StepWorkload& stepWork);
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/alignedallocator.h"
#include "gromacs/utility/bitmask.h"
#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/enumerationhelpers.h"
/* We reduce the force array in blocks of 32 atoms. This is large enough
* to not cause overhead and 32*sizeof(rvec) is a multiple of the cache-line
//! Index to touched blocks
std::vector<int> block_index;
- //! Shift force array, size SHIFTS
+ //! Shift force array, size c_numShiftVectors
std::vector<gmx::RVec> fshift;
//! Energy array
real ener[F_NRE];
//! Group pair energy data for pairs
gmx_grppairener_t grpp;
//! Free-energy dV/dl output
- real dvdl[efptNR];
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real> dvdl;
GMX_DISALLOW_COPY_MOVE_AND_ASSIGN(f_thread_t);
};
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
fprintf(debug, "%16s", interaction_function[f].name);
for (t = 0; t < numThreads; t++)
{
- fprintf(debug, " %4d",
+ fprintf(debug,
+ " %4d",
(bt->workDivision.bound(f, t + 1) - bt->workDivision.bound(f, t))
/ (1 + NRAL(f)));
}
"You are using %d OpenMP threads, which is larger than GMX_OPENMP_MAX_THREADS "
"(%d). Decrease the number of OpenMP threads or rebuild GROMACS with a larger "
"value for GMX_OPENMP_MAX_THREADS passed to CMake.",
- bondedThreading.nthreads, GMX_OPENMP_MAX_THREADS);
+ bondedThreading.nthreads,
+ GMX_OPENMP_MAX_THREADS);
}
GMX_ASSERT(bondedThreading.nthreads <= BITMASK_SIZE,
"We need at least nthreads bits in the mask");
if (debug)
{
fprintf(debug, "Number of %d atom blocks to reduce: %d\n", reduction_block_size, bt->nblock_used);
- fprintf(debug, "Reduction density %.2f for touched blocks only %.2f\n",
+ fprintf(debug,
+ "Reduction density %.2f for touched blocks only %.2f\n",
ctot * reduction_block_size / static_cast<double>(numAtomsForce),
ctot / static_cast<double>(bt->nblock_used));
}
}
-f_thread_t::f_thread_t(int numEnergyGroups) : fshift(SHIFTS), grpp(numEnergyGroups) {}
+f_thread_t::f_thread_t(int numEnergyGroups) : fshift(gmx::c_numShiftVectors), grpp(numEnergyGroups)
+{
+}
bonded_threading_t::bonded_threading_t(const int numThreads, const int numEnergyGroups, FILE* fplog) :
nthreads(numThreads),
sscanf(ptr, "%d", &max_nthread_uniform);
if (fplog != nullptr)
{
- fprintf(fplog, "\nMax threads for uniform bonded distribution set to %d by env.var.\n",
+ fprintf(fplog,
+ "\nMax threads for uniform bonded distribution set to %d by env.var.\n",
max_nthread_uniform);
}
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/smalloc.h"
// TODO This implementation of ensemble orientation restraints is nasty because
// a user can't just do multi-sim with single-sim orientation restraints.
-void init_orires(FILE* fplog,
- const gmx_mtop_t* mtop,
- const t_inputrec* ir,
- const t_commrec* cr,
- const gmx_multisim_t* ms,
- t_state* globalState,
- t_oriresdata* od)
+t_oriresdata::t_oriresdata(FILE* fplog,
+ const gmx_mtop_t& mtop,
+ const t_inputrec& ir,
+ const t_commrec* cr,
+ const gmx_multisim_t* ms,
+ t_state* globalState) :
+ numRestraints(gmx_mtop_ftype_count(mtop, F_ORIRES))
{
- od->nr = gmx_mtop_ftype_count(mtop, F_ORIRES);
- if (0 == od->nr)
- {
- /* Not doing orientation restraints */
- return;
- }
+ GMX_RELEASE_ASSERT(numRestraints > 0,
+ "orires() should only be called with orientation restraints present");
const int numFitParams = 5;
- if (od->nr <= numFitParams)
+ if (numRestraints <= numFitParams)
{
- gmx_fatal(FARGS,
- "The system has %d orientation restraints, but at least %d are required, since "
- "there are %d fitting parameters.",
- od->nr, numFitParams + 1, numFitParams);
+ const std::string mesg = gmx::formatString(
+ "The system has %d orientation restraints, but at least %d are required, since "
+ "there are %d fitting parameters.",
+ numRestraints,
+ numFitParams + 1,
+ numFitParams);
+ GMX_THROW(gmx::InvalidInputError(mesg));
}
- if (ir->bPeriodicMols)
+ if (ir.bPeriodicMols)
{
/* Since we apply fitting, we need to make molecules whole and this
* can not be done when periodic molecules are present.
*/
- gmx_fatal(FARGS,
- "Orientation restraints can not be applied when periodic molecules are present "
- "in the system");
+ GMX_THROW(gmx::InvalidInputError(
+ "Orientation restraints can not be applied when periodic molecules are present "
+ "in the system"));
}
- if (PAR(cr))
+ if (cr && PAR(cr))
{
- gmx_fatal(FARGS,
- "Orientation restraints do not work with MPI parallelization. Choose 1 MPI rank, "
- "if possible.");
+ GMX_THROW(gmx::InvalidInputError(
+ "Orientation restraints do not work with MPI parallelization. Choose 1 MPI rank, "
+ "if possible."));
}
- GMX_RELEASE_ASSERT(globalState != nullptr, "We need a valid global state in init_orires");
+ GMX_RELEASE_ASSERT(globalState != nullptr, "We need a valid global state in t_oriresdata()");
- od->fc = ir->orires_fc;
- od->nex = 0;
- od->S = nullptr;
- od->M = nullptr;
- od->eig = nullptr;
- od->v = nullptr;
+ fc = ir.orires_fc;
+ numExperiments = 0;
- int* nr_ex = nullptr;
- int typeMin = INT_MAX;
- int typeMax = 0;
- gmx_mtop_ilistloop_t iloop = gmx_mtop_ilistloop_init(mtop);
- int nmol;
- while (const InteractionLists* il = gmx_mtop_ilistloop_next(iloop, &nmol))
+ std::vector<int> nr_ex;
+ typeMin = INT_MAX;
+ int typeMax = 0;
+ for (const auto il : IListRange(mtop))
{
- const int numOrires = (*il)[F_ORIRES].size();
- if (nmol > 1 && numOrires > 0)
+ const int numOrires = il.list()[F_ORIRES].size();
+ if (il.nmol() > 1 && numOrires > 0)
{
- gmx_fatal(FARGS,
- "Found %d copies of a molecule with orientation restrains while the current "
- "code only supports a single copy. If you want to ensemble average, run "
- "multiple copies of the system using the multi-sim feature of mdrun.",
- nmol);
+ const std::string mesg = gmx::formatString(
+ "Found %d copies of a molecule with orientation restrains while the current "
+ "code only supports a single copy. If you want to ensemble average, run "
+ "multiple copies of the system using the multi-sim feature of mdrun.",
+ il.nmol());
+ GMX_THROW(gmx::InvalidInputError(mesg));
}
for (int i = 0; i < numOrires; i += 3)
{
- int type = (*il)[F_ORIRES].iatoms[i];
- int ex = mtop->ffparams.iparams[type].orires.ex;
- if (ex >= od->nex)
+ int type = il.list()[F_ORIRES].iatoms[i];
+ int ex = mtop.ffparams.iparams[type].orires.ex;
+ if (ex >= numExperiments)
{
- srenew(nr_ex, ex + 1);
- for (int j = od->nex; j < ex + 1; j++)
- {
- nr_ex[j] = 0;
- }
- od->nex = ex + 1;
+ nr_ex.resize(ex + 1, 0);
+ numExperiments = ex + 1;
}
- GMX_ASSERT(nr_ex, "Check for allocated nr_ex to keep the static analyzer happy");
nr_ex[ex]++;
typeMin = std::min(typeMin, type);
}
/* With domain decomposition we use the type index for indexing in global arrays */
GMX_RELEASE_ASSERT(
- typeMax - typeMin + 1 == od->nr,
+ typeMax - typeMin + 1 == numRestraints,
"All orientation restraint parameter entries in the topology should be consecutive");
- /* Store typeMin so we can index array with the type offset */
- od->typeMin = typeMin;
- snew(od->S, od->nex);
+ snew(orderTensors, numExperiments);
/* When not doing time averaging, the instaneous and time averaged data
* are indentical and the pointers can point to the same memory.
*/
- snew(od->Dinsl, od->nr);
+ snew(DTensors, numRestraints);
if (ms)
{
- snew(od->Dins, od->nr);
+ snew(DTensorsEnsembleAv, numRestraints);
}
else
{
- od->Dins = od->Dinsl;
+ DTensorsEnsembleAv = DTensors;
}
- if (ir->orires_tau == 0)
+ if (ir.orires_tau == 0)
{
- od->Dtav = od->Dins;
- od->edt = 0.0;
- od->edt_1 = 1.0;
+ DTensorsTimeAndEnsembleAv = DTensorsEnsembleAv;
+ edt = 0.0;
+ edt_1 = 1.0;
}
else
{
- snew(od->Dtav, od->nr);
- od->edt = std::exp(-ir->delta_t / ir->orires_tau);
- od->edt_1 = 1.0 - od->edt;
+ snew(DTensorsTimeAndEnsembleAv, numRestraints);
+ edt = std::exp(-ir.delta_t / ir.orires_tau);
+ edt_1 = 1.0 - edt;
/* Extend the state with the orires history */
- globalState->flags |= (1 << estORIRE_INITF);
+ globalState->flags |= enumValueToBitMask(StateEntry::OrireInitF);
globalState->hist.orire_initf = 1;
- globalState->flags |= (1 << estORIRE_DTAV);
- globalState->hist.norire_Dtav = od->nr * 5;
- snew(globalState->hist.orire_Dtav, globalState->hist.norire_Dtav);
+ globalState->flags |= enumValueToBitMask(StateEntry::OrireDtav);
+ globalState->hist.orire_Dtav.resize(numRestraints * 5);
}
- snew(od->oinsl, od->nr);
+ orientations.resize(numRestraints);
if (ms)
{
- snew(od->oins, od->nr);
+ orientationsEnsembleAvBuffer.resize(numRestraints);
+ orientationsEnsembleAv = orientationsEnsembleAvBuffer;
}
else
{
- od->oins = od->oinsl;
+ orientationsEnsembleAv = orientations;
}
- if (ir->orires_tau == 0)
+ if (ir.orires_tau == 0)
{
- od->otav = od->oins;
+ orientationsTimeAndEnsembleAv = orientationsEnsembleAv;
}
else
{
- snew(od->otav, od->nr);
+ orientationsTimeAndEnsembleAvBuffer.resize(numRestraints);
+ orientationsTimeAndEnsembleAv = orientationsTimeAndEnsembleAvBuffer;
}
- snew(od->tmpEq, od->nex);
+ tmpEq.resize(numExperiments);
- od->nref = 0;
- for (int i = 0; i < mtop->natoms; i++)
+ numReferenceAtoms = 0;
+ for (int i = 0; i < mtop.natoms; i++)
{
- if (getGroupType(mtop->groups, SimulationAtomGroupType::OrientationRestraintsFit, i) == 0)
+ if (getGroupType(mtop.groups, SimulationAtomGroupType::OrientationRestraintsFit, i) == 0)
{
- od->nref++;
+ numReferenceAtoms++;
}
}
- snew(od->mref, od->nref);
- snew(od->xref, od->nref);
- snew(od->xtmp, od->nref);
+ mref.resize(numReferenceAtoms);
+ xref.resize(numReferenceAtoms);
+ xtmp.resize(numReferenceAtoms);
- snew(od->eig, od->nex * 12);
+ eigenOutput.resize(numExperiments * c_numEigenRealsPerExperiment);
/* Determine the reference structure on the master node.
* Copy it to the other nodes after checking multi compatibility,
rvec com = { 0, 0, 0 };
double mtot = 0.0;
int j = 0;
- for (const AtomProxy atomP : AtomRange(*mtop))
+ for (const AtomProxy atomP : AtomRange(mtop))
{
const t_atom& local = atomP.atom();
int i = atomP.globalAtomNumber();
- if (mtop->groups.groupNumbers[SimulationAtomGroupType::OrientationRestraintsFit].empty()
- || mtop->groups.groupNumbers[SimulationAtomGroupType::OrientationRestraintsFit][i] == 0)
+ if (mtop.groups.groupNumbers[SimulationAtomGroupType::OrientationRestraintsFit].empty()
+ || mtop.groups.groupNumbers[SimulationAtomGroupType::OrientationRestraintsFit][i] == 0)
{
/* Not correct for free-energy with changing masses */
- od->mref[j] = local.m;
+ mref[j] = local.m;
// Note that only one rank per sim is supported.
if (isMasterSim(ms))
{
- copy_rvec(x[i], od->xref[j]);
+ copy_rvec(x[i], xref[j]);
for (int d = 0; d < DIM; d++)
{
- com[d] += od->mref[j] * x[i][d];
+ com[d] += mref[j] * x[i][d];
}
}
- mtot += od->mref[j];
+ mtot += mref[j];
j++;
}
}
svmul(1.0 / mtot, com, com);
if (isMasterSim(ms))
{
- for (int j = 0; j < od->nref; j++)
+ for (int j = 0; j < numReferenceAtoms; j++)
{
- rvec_dec(od->xref[j], com);
+ rvec_dec(xref[j], com);
}
}
- fprintf(fplog, "Found %d orientation experiments\n", od->nex);
- for (int i = 0; i < od->nex; i++)
+ if (fplog)
{
- fprintf(fplog, " experiment %d has %d restraints\n", i + 1, nr_ex[i]);
- }
-
- sfree(nr_ex);
+ fprintf(fplog, "Found %d orientation experiments\n", numExperiments);
+ for (int i = 0; i < numExperiments; i++)
+ {
+ fprintf(fplog, " experiment %d has %d restraints\n", i + 1, nr_ex[i]);
+ }
- fprintf(fplog, " the fit group consists of %d atoms and has total mass %g\n", od->nref, mtot);
+ fprintf(fplog, " the fit group consists of %d atoms and has total mass %g\n", numReferenceAtoms, mtot);
+ }
if (ms)
{
- fprintf(fplog, " the orientation restraints are ensemble averaged over %d systems\n",
- ms->numSimulations_);
+ if (fplog)
+ {
+ fprintf(fplog,
+ " the orientation restraints are ensemble averaged over %d systems\n",
+ ms->numSimulations_);
+ }
- check_multi_int(fplog, ms, od->nr, "the number of orientation restraints", FALSE);
- check_multi_int(fplog, ms, od->nref, "the number of fit atoms for orientation restraining", FALSE);
- check_multi_int(fplog, ms, ir->nsteps, "nsteps", FALSE);
+ check_multi_int(fplog, ms, numRestraints, "the number of orientation restraints", FALSE);
+ check_multi_int(
+ fplog, ms, numReferenceAtoms, "the number of fit atoms for orientation restraining", FALSE);
+ check_multi_int(fplog, ms, ir.nsteps, "nsteps", FALSE);
/* Copy the reference coordinates from the master to the other nodes */
- gmx_sum_sim(DIM * od->nref, od->xref[0], ms);
+ gmx_sum_sim(DIM * numReferenceAtoms, xref[0], ms);
}
please_cite(fplog, "Hess2003");
}
-void diagonalize_orires_tensors(t_oriresdata* od)
+t_oriresdata::~t_oriresdata()
{
- if (od->M == nullptr)
+ sfree(orderTensors);
+ if (DTensorsTimeAndEnsembleAv != DTensorsEnsembleAv)
{
- snew(od->M, DIM);
- for (int i = 0; i < DIM; i++)
- {
- snew(od->M[i], DIM);
- }
- snew(od->eig_diag, DIM);
- snew(od->v, DIM);
- for (int i = 0; i < DIM; i++)
- {
- snew(od->v[i], DIM);
- }
+ sfree(DTensorsTimeAndEnsembleAv);
}
+ if (DTensorsEnsembleAv != DTensors)
+ {
+ sfree(DTensorsEnsembleAv);
+ }
+ sfree(DTensors);
+}
- for (int ex = 0; ex < od->nex; ex++)
+void diagonalize_orires_tensors(t_oriresdata* od)
+{
+ for (int ex = 0; ex < od->numExperiments; ex++)
{
/* Rotate the S tensor back to the reference frame */
matrix S, TMP;
- mmul(od->R, od->S[ex], TMP);
- mtmul(TMP, od->R, S);
+ mmul(od->rotationMatrix, od->orderTensors[ex], TMP);
+ mtmul(TMP, od->rotationMatrix, S);
for (int i = 0; i < DIM; i++)
{
for (int j = 0; j < DIM; j++)
}
}
- int nrot;
- jacobi(od->M, DIM, od->eig_diag, od->v, &nrot);
+ jacobi(od->M, od->eig_diag, od->v);
int ord[DIM];
for (int i = 0; i < DIM; i++)
for (int i = 0; i < DIM; i++)
{
- od->eig[ex * 12 + i] = od->eig_diag[ord[i]];
+ od->eigenOutput[ex * t_oriresdata::c_numEigenRealsPerExperiment + i] = od->eig_diag[ord[i]];
}
for (int i = 0; i < DIM; i++)
{
for (int j = 0; j < DIM; j++)
{
- od->eig[ex * 12 + 3 + 3 * i + j] = od->v[j][ord[i]];
+ od->eigenOutput[ex * t_oriresdata::c_numEigenRealsPerExperiment + 3 + 3 * i + j] =
+ od->v[j][ord[i]];
}
}
}
void print_orires_log(FILE* log, t_oriresdata* od)
{
- real* eig;
-
diagonalize_orires_tensors(od);
- for (int ex = 0; ex < od->nex; ex++)
+ for (int ex = 0; ex < od->numExperiments; ex++)
{
- eig = od->eig + ex * 12;
+ const real* eig = od->eigenOutput.data() + ex * t_oriresdata::c_numEigenRealsPerExperiment;
fprintf(log, " Orientation experiment %d:\n", ex + 1);
fprintf(log, " order parameter: %g\n", eig[0]);
for (int i = 0; i < DIM; i++)
{
- fprintf(log, " eig: %6.3f %6.3f %6.3f %6.3f\n", (eig[0] != 0) ? eig[i] / eig[0] : eig[i],
- eig[DIM + i * DIM + XX], eig[DIM + i * DIM + YY], eig[DIM + i * DIM + ZZ]);
+ fprintf(log,
+ " eig: %6.3f %6.3f %6.3f %6.3f\n",
+ (eig[0] != 0) ? eig[i] / eig[0] : eig[i],
+ eig[DIM + i * DIM + XX],
+ eig[DIM + i * DIM + YY],
+ eig[DIM + i * DIM + ZZ]);
}
fprintf(log, "\n");
}
const rvec x[],
const t_pbc* pbc,
t_oriresdata* od,
- history_t* hist)
+ const history_t* hist)
{
- int nref;
- real edt, edt_1, invn, pfac, r2, invr, corrfac, wsv2, sw, dev;
- OriresMatEq* matEq;
- real* mref;
- double mtot;
- rvec * xref, *xtmp, com, r_unrot, r;
- gmx_bool bTAV;
- const real two_thr = 2.0 / 3.0;
-
- if (od->nr == 0)
- {
- /* This means that this is not the master node */
- gmx_fatal(FARGS,
- "Orientation restraints are only supported on the master rank, use fewer ranks");
- }
-
- bTAV = (od->edt != 0);
- edt = od->edt;
- edt_1 = od->edt_1;
- matEq = od->tmpEq;
- nref = od->nref;
- mref = od->mref;
- xref = od->xref;
- xtmp = od->xtmp;
+ real invn, pfac, r2, invr, corrfac, wsv2, sw, dev;
+ double mtot;
+ rvec com, r_unrot, r;
+ const real two_thr = 2.0 / 3.0;
+
+ const bool bTAV = (od->edt != 0);
+ const real edt = od->edt;
+ const real edt_1 = od->edt_1;
+ gmx::ArrayRef<OriresMatEq> matEq = od->tmpEq;
+ const int nref = od->numReferenceAtoms;
+ gmx::ArrayRef<real> mref = od->mref;
+ gmx::ArrayRef<const gmx::RVec> xref = od->xref;
+ gmx::ArrayRef<gmx::RVec> xtmp = od->xtmp;
if (bTAV)
{
}
clear_rvec(com);
- mtot = 0;
- int j = 0;
+ mtot = 0;
+ int j = 0;
+ auto* massT = md->massT;
+ auto* cORF = md->cORF;
for (int i = 0; i < md->nr; i++)
{
- if (md->cORF[i] == 0)
+ if (cORF[i] == 0)
{
copy_rvec(xWholeMolecules[i], xtmp[j]);
- mref[j] = md->massT[i];
+ mref[j] = massT[i];
for (int d = 0; d < DIM; d++)
{
com[d] += mref[j] * xtmp[j][d];
rvec_dec(xtmp[j], com);
}
/* Calculate the rotation matrix to rotate x to the reference orientation */
- calc_fit_R(DIM, nref, mref, xref, xtmp, od->R);
+ calc_fit_R(DIM, nref, mref.data(), as_rvec_array(xref.data()), as_rvec_array(xtmp.data()), od->rotationMatrix);
for (int fa = 0; fa < nfa; fa += 3)
{
{
rvec_sub(x[forceatoms[fa + 1]], x[forceatoms[fa + 2]], r_unrot);
}
- mvmul(od->R, r_unrot, r);
+ mvmul(od->rotationMatrix, r_unrot, r);
r2 = norm2(r);
invr = gmx::invsqrt(r2);
/* Calculate the prefactor for the D tensor, this includes the factor 3! */
{
pfac *= invr;
}
- rvec5& Dinsl = od->Dinsl[restraintIndex];
+ rvec5& Dinsl = od->DTensors[restraintIndex];
Dinsl[0] = pfac * (2 * r[0] * r[0] + r[1] * r[1] - r2);
Dinsl[1] = pfac * (2 * r[0] * r[1]);
Dinsl[2] = pfac * (2 * r[0] * r[2]);
{
for (int i = 0; i < 5; i++)
{
- od->Dins[restraintIndex][i] = Dinsl[i] * invn;
+ od->DTensorsEnsembleAv[restraintIndex][i] = Dinsl[i] * invn;
}
}
}
if (ms)
{
- gmx_sum_sim(5 * od->nr, od->Dins[0], ms);
+ gmx_sum_sim(5 * od->numRestraints, od->DTensorsEnsembleAv[0], ms);
}
/* Calculate the order tensor S for each experiment via optimization */
- for (int ex = 0; ex < od->nex; ex++)
+ for (int ex = 0; ex < od->numExperiments; ex++)
{
for (int i = 0; i < 5; i++)
{
{
const int type = forceatoms[fa];
const int restraintIndex = type - od->typeMin;
- rvec5& Dtav = od->Dtav[restraintIndex];
+ rvec5& Dtav = od->DTensorsTimeAndEnsembleAv[restraintIndex];
if (bTAV)
{
- /* Here we update Dtav in t_fcdata using the data in history_t.
+ /* Here we update DTensorsTimeAndEnsembleAv in t_fcdata using the data in history_t.
* Thus the results stay correct when this routine
* is called multiple times.
*/
for (int i = 0; i < 5; i++)
{
Dtav[i] = edt * hist->orire_Dtav[restraintIndex * 5 + i]
- + edt_1 * od->Dins[restraintIndex][i];
+ + edt_1 * od->DTensorsEnsembleAv[restraintIndex][i];
}
}
}
}
/* Now we have all the data we can calculate S */
- for (int ex = 0; ex < od->nex; ex++)
+ for (int ex = 0; ex < od->numExperiments; ex++)
{
OriresMatEq& eq = matEq[ex];
/* Correct corrfac and copy one half of T to the other half */
}
m_inv_gen(&eq.mat[0][0], 5, &eq.mat[0][0]);
/* Calculate the orientation tensor S for this experiment */
- matrix& S = od->S[ex];
+ matrix& S = od->orderTensors[ex];
S[0][0] = 0;
S[0][1] = 0;
S[0][2] = 0;
S[2][2] = -S[0][0] - S[1][1];
}
- const matrix* S = od->S;
+ const matrix* S = od->orderTensors;
wsv2 = 0;
sw = 0;
const int restraintIndex = type - od->typeMin;
const int ex = ip[type].orires.ex;
- const rvec5& Dtav = od->Dtav[restraintIndex];
- od->otav[restraintIndex] =
+ const rvec5& Dtav = od->DTensorsTimeAndEnsembleAv[restraintIndex];
+ od->orientationsTimeAndEnsembleAv[restraintIndex] =
two_thr * corrfac
* (S[ex][0][0] * Dtav[0] + S[ex][0][1] * Dtav[1] + S[ex][0][2] * Dtav[2]
+ S[ex][1][1] * Dtav[3] + S[ex][1][2] * Dtav[4]);
if (bTAV)
{
- const rvec5& Dins = od->Dins[restraintIndex];
- od->oins[restraintIndex] =
+ const rvec5& Dins = od->DTensorsEnsembleAv[restraintIndex];
+ od->orientationsEnsembleAv[restraintIndex] =
two_thr
* (S[ex][0][0] * Dins[0] + S[ex][0][1] * Dins[1] + S[ex][0][2] * Dins[2]
+ S[ex][1][1] * Dins[3] + S[ex][1][2] * Dins[4]);
/* When ensemble averaging is used recalculate the local orientation
* for output to the energy file.
*/
- const rvec5& Dinsl = od->Dinsl[restraintIndex];
- od->oinsl[restraintIndex] =
+ const rvec5& Dinsl = od->DTensors[restraintIndex];
+ od->orientations[restraintIndex] =
two_thr
* (S[ex][0][0] * Dinsl[0] + S[ex][0][1] * Dinsl[1] + S[ex][0][2] * Dinsl[2]
+ S[ex][1][1] * Dinsl[3] + S[ex][1][2] * Dinsl[4]);
}
- dev = od->otav[restraintIndex] - ip[type].orires.obs;
+ dev = od->orientationsTimeAndEnsembleAv[restraintIndex] - ip[type].orires.obs;
wsv2 += ip[type].orires.kfac * gmx::square(dev);
sw += ip[type].orires.kfac;
od->rmsdev = std::sqrt(wsv2 / sw);
/* Rotate the S matrices back, so we get the correct grad(tr(S D)) */
- for (int ex = 0; ex < od->nex; ex++)
+ for (int ex = 0; ex < od->numExperiments; ex++)
{
matrix RS;
- tmmul(od->R, od->S[ex], RS);
- mmul(RS, od->R, od->S[ex]);
+ tmmul(od->rotationMatrix, od->orderTensors[ex], RS);
+ mmul(RS, od->rotationMatrix, od->orderTensors[ex]);
}
return od->rmsdev;
const t_pbc* pbc,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
- const t_mdatoms gmx_unused* md,
- t_fcdata* fcd,
+ gmx::ArrayRef<const real> /*charge*/,
+ t_fcdata gmx_unused* fcd,
+ t_disresdata gmx_unused* disresdata,
+ t_oriresdata* oriresdata,
int gmx_unused* global_atom_index)
{
- int ex, power, ki = CENTRAL;
- real r2, invr, invr2, fc, smooth_fc, dev, devins, pfac;
- rvec r, Sr, fij;
- real vtot;
- const t_oriresdata* od;
- gmx_bool bTAV;
+ int ex, power, ki = gmx::c_centralShiftIndex;
+ real r2, invr, invr2, fc, smooth_fc, dev, devins, pfac;
+ rvec r, Sr, fij;
+ real vtot;
+ gmx_bool bTAV;
vtot = 0;
- od = fcd->orires;
- if (od->fc != 0)
+ if (oriresdata->fc != 0)
{
- bTAV = (od->edt != 0);
+ bTAV = (oriresdata->edt != 0);
- smooth_fc = od->fc;
+ smooth_fc = oriresdata->fc;
if (bTAV)
{
/* Smoothly switch on the restraining when time averaging is used */
- smooth_fc *= (1.0 - od->exp_min_t_tau);
+ smooth_fc *= (1.0 - oriresdata->exp_min_t_tau);
}
for (int fa = 0; fa < nfa; fa += 3)
const int type = forceatoms[fa];
const int ai = forceatoms[fa + 1];
const int aj = forceatoms[fa + 2];
- const int restraintIndex = type - od->typeMin;
+ const int restraintIndex = type - oriresdata->typeMin;
if (pbc)
{
ki = pbc_dx_aiuc(pbc, x[ai], x[aj], r);
ex = ip[type].orires.ex;
power = ip[type].orires.power;
fc = smooth_fc * ip[type].orires.kfac;
- dev = od->otav[restraintIndex] - ip[type].orires.obs;
+ dev = oriresdata->orientationsTimeAndEnsembleAv[restraintIndex] - ip[type].orires.obs;
/* NOTE:
* there is no real potential when time averaging is applied
if (bTAV)
{
/* Calculate the force as the sqrt of tav times instantaneous */
- devins = od->oins[restraintIndex] - ip[type].orires.obs;
+ devins = oriresdata->orientationsEnsembleAv[restraintIndex] - ip[type].orires.obs;
if (dev * devins <= 0)
{
dev = 0;
{
pfac *= invr;
}
- mvmul(od->S[ex], r, Sr);
+ mvmul(oriresdata->orderTensors[ex], r, Sr);
for (int i = 0; i < DIM; i++)
{
fij[i] = -pfac * dev * (4 * Sr[i] - 2 * (2 + power) * invr2 * iprod(Sr, r) * r[i]);
if (fshift)
{
fshift[ki][i] += fij[i];
- fshift[CENTRAL][i] -= fij[i];
+ fshift[gmx::c_centralShiftIndex][i] -= fij[i];
}
}
}
* in calc_orires_dev.
*/
hist->orire_initf = od.exp_min_t_tau;
- for (int pair = 0; pair < od.nr; pair++)
+ for (int pair = 0; pair < od.numRestraints; pair++)
{
for (int i = 0; i < 5; i++)
{
- hist->orire_Dtav[pair * 5 + i] = od.Dtav[pair][i];
+ hist->orire_Dtav[pair * 5 + i] = od.DTensorsTimeAndEnsembleAv[pair][i];
}
}
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2010,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct t_pbc;
struct t_commrec;
struct t_oriresdata;
+struct t_disresdata;
+struct t_fcdata;
class t_state;
+struct t_mdatoms;
namespace gmx
{
class ArrayRef;
} // namespace gmx
-/*! \brief
- * Decides whether orientation restraints can work, and initializes
- * all the orientation restraint stuff in *od (and assumes *od is
- * already allocated.
- * If orientation restraint are used, globalState is read and modified
- * on the master rank (which is the only rank, since orientation
- * restraints can not run in parallel).
- */
-void init_orires(FILE* fplog,
- const gmx_mtop_t* mtop,
- const t_inputrec* ir,
- const t_commrec* cr,
- const gmx_multisim_t* ms,
- t_state* globalState,
- t_oriresdata* od);
-
/*! \brief
* Calculates the time averaged D matrices, the S matrix for each experiment.
*
const rvec x[],
const t_pbc* pbc,
t_oriresdata* oriresdata,
- history_t* hist);
+ const history_t* hist);
/*! \brief
* Diagonalizes the order tensor(s) of the orienation restraints.
void print_orires_log(FILE* log, t_oriresdata* od);
//! Calculates the orientation restraint forces.
-real orires(int nfa,
- const t_iatom forceatoms[],
- const t_iparams ip[],
- const rvec x[],
- rvec4 f[],
- rvec fshift[],
- const t_pbc* pbc,
- real lambda,
- real* dvdlambda,
- const t_mdatoms* md,
- t_fcdata* fcd,
- int* global_atom_index);
+real orires(int nfa,
+ const t_iatom forceatoms[],
+ const t_iparams ip[],
+ const rvec x[],
+ rvec4 f[],
+ rvec fshift[],
+ const t_pbc* pbc,
+ real lambda,
+ real* dvdlambda,
+ gmx::ArrayRef<const real> charge,
+ t_fcdata* fcd,
+ t_disresdata* disresdata,
+ t_oriresdata* oriresdata,
+ int* global_atom_index);
//! Copies the new time averages that have been calculated in calc_orires_dev.
void update_orires_history(const t_oriresdata& oriresdata, history_t* hist);
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/group.h"
#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/mdtypes/nblist.h"
#include "gromacs/mdtypes/simulation_workload.h"
#include "gromacs/pbcutil/ishift.h"
"IMPORTANT: This should not happen in a stable simulation, so there is\n"
"probably something wrong with your system. Only change the table-extension\n"
"distance in the mdp file if you are really sure that is the reason.\n",
- glatnr(global_atom_index, ai), glatnr(global_atom_index, aj), r, rlimit);
+ glatnr(global_atom_index, ai),
+ glatnr(global_atom_index, aj),
+ r,
+ rlimit);
if (debug)
{
fprintf(debug,
"%8f %8f %8f\n%8f %8f %8f\n1-4 (%d,%d) interaction not within cut-off! r=%g. "
"Ignored\n",
- x[ai][XX], x[ai][YY], x[ai][ZZ], x[aj][XX], x[aj][YY], x[aj][ZZ],
- glatnr(global_atom_index, ai), glatnr(global_atom_index, aj), r);
+ x[ai][XX],
+ x[ai][YY],
+ x[ai][ZZ],
+ x[aj][XX],
+ x[aj][YY],
+ x[aj][ZZ],
+ glatnr(global_atom_index, ai),
+ glatnr(global_atom_index, aj),
+ r);
}
}
+ LFV[i] * alpha_vdw_eff * dlfac_vdw[i] * fscal_vdw[i] * sigma_pow[i];
}
- dvdl[efptCOUL] += dvdl_coul;
- dvdl[efptVDW] += dvdl_vdw;
+ dvdl[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)] += dvdl_coul;
+ dvdl[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)] += dvdl_vdw;
*velectot = velecsum;
*vvdwtot = vvdwsum;
/*! \brief Calculate pair interactions, supports all types and conditions. */
template<BondedKernelFlavor flavor>
-static real do_pairs_general(int ftype,
- int nbonds,
- const t_iatom iatoms[],
- const t_iparams iparams[],
- const rvec x[],
- rvec4 f[],
- rvec fshift[],
- const struct t_pbc* pbc,
- const real* lambda,
- real* dvdl,
- const t_mdatoms* md,
- const t_forcerec* fr,
- gmx_grppairener_t* grppener,
- int* global_atom_index)
+static real do_pairs_general(int ftype,
+ int nbonds,
+ const t_iatom iatoms[],
+ const t_iparams iparams[],
+ const rvec x[],
+ rvec4 f[],
+ rvec fshift[],
+ const struct t_pbc* pbc,
+ const real* lambda,
+ real* dvdl,
+ gmx::ArrayRef<real> chargeA,
+ gmx::ArrayRef<real> chargeB,
+ gmx::ArrayRef<bool> atomIsPerturbed,
+ gmx::ArrayRef<unsigned short> cENER,
+ int numEnergyGroups,
+ const t_forcerec* fr,
+ gmx_grppairener_t* grppener,
+ int* global_atom_index)
{
real qq, c6, c12;
rvec dx;
{
case F_LJ14:
case F_LJC14_Q:
- energygrp_elec = grppener->ener[egCOUL14].data();
- energygrp_vdw = grppener->ener[egLJ14].data();
+ energygrp_elec = grppener->energyGroupPairTerms[NonBondedEnergyTerms::Coulomb14].data();
+ energygrp_vdw = grppener->energyGroupPairTerms[NonBondedEnergyTerms::LJ14].data();
break;
case F_LJC_PAIRS_NB:
- energygrp_elec = grppener->ener[egCOULSR].data();
- energygrp_vdw = grppener->ener[egLJSR].data();
+ energygrp_elec = grppener->energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR].data();
+ energygrp_vdw = grppener->energyGroupPairTerms[NonBondedEnergyTerms::LJSR].data();
break;
default:
energygrp_elec = nullptr; /* Keep compiler happy */
gmx_fatal(FARGS, "Unknown function type %d in do_nonbonded14", ftype);
}
- if (fr->efep != efepNO)
+ if (fr->efep != FreeEnergyPerturbationType::No)
{
/* Lambda factor for state A=1-lambda and B=lambda */
- LFC[0] = 1.0 - lambda[efptCOUL];
- LFV[0] = 1.0 - lambda[efptVDW];
- LFC[1] = lambda[efptCOUL];
- LFV[1] = lambda[efptVDW];
+ LFC[0] = 1.0 - lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)];
+ LFV[0] = 1.0 - lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)];
+ LFC[1] = lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)];
+ LFV[1] = lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)];
/*derivative of the lambda factor for state A and B */
DLF[0] = -1;
itype = iatoms[i++];
ai = iatoms[i++];
aj = iatoms[i++];
- gid = GID(md->cENER[ai], md->cENER[aj], md->nenergrp);
+ gid = GID(cENER[ai], cENER[aj], numEnergyGroups);
/* Get parameters */
switch (ftype)
{
case F_LJ14:
- bFreeEnergy = (fr->efep != efepNO
- && (((md->nPerturbed != 0) && (md->bPerturbed[ai] || md->bPerturbed[aj]))
- || iparams[itype].lj14.c6A != iparams[itype].lj14.c6B
- || iparams[itype].lj14.c12A != iparams[itype].lj14.c12B));
- qq = md->chargeA[ai] * md->chargeA[aj] * epsfac * fr->fudgeQQ;
- c6 = iparams[itype].lj14.c6A;
- c12 = iparams[itype].lj14.c12A;
+ bFreeEnergy =
+ (fr->efep != FreeEnergyPerturbationType::No
+ && ((!atomIsPerturbed.empty() && (atomIsPerturbed[ai] || atomIsPerturbed[aj]))
+ || iparams[itype].lj14.c6A != iparams[itype].lj14.c6B
+ || iparams[itype].lj14.c12A != iparams[itype].lj14.c12B));
+ qq = chargeA[ai] * chargeA[aj] * epsfac * fr->fudgeQQ;
+ c6 = iparams[itype].lj14.c6A;
+ c12 = iparams[itype].lj14.c12A;
break;
case F_LJC14_Q:
qq = iparams[itype].ljc14.qi * iparams[itype].ljc14.qj * epsfac
}
else
{
- fshift_index = CENTRAL;
+ fshift_index = c_centralShiftIndex;
rvec_sub(x[ai], x[aj], dx);
}
r2 = norm2(dx);
if (bFreeEnergy)
{
/* Currently free energy is only supported for F_LJ14, so no need to check for that if we got here */
- qqB = md->chargeB[ai] * md->chargeB[aj] * epsfac * fr->fudgeQQ;
+ qqB = chargeB[ai] * chargeB[aj] * epsfac * fr->fudgeQQ;
c6B = iparams[itype].lj14.c6B * 6.0;
c12B = iparams[itype].lj14.c12B * 12.0;
- fscal = free_energy_evaluate_single(
- r2, *fr->ic->softCoreParameters, fr->pairsTable->scale,
- fr->pairsTable->data.data(), fr->pairsTable->stride, qq, c6, c12, qqB, c6B, c12B,
- LFC, LFV, DLF, lfac_coul, lfac_vdw, dlfac_coul, dlfac_vdw, &velec, &vvdw, dvdl);
+ fscal = free_energy_evaluate_single(r2,
+ *fr->ic->softCoreParameters,
+ fr->pairsTable->scale,
+ fr->pairsTable->data.data(),
+ fr->pairsTable->stride,
+ qq,
+ c6,
+ c12,
+ qqB,
+ c6B,
+ c12B,
+ LFC,
+ LFV,
+ DLF,
+ lfac_coul,
+ lfac_vdw,
+ dlfac_coul,
+ dlfac_vdw,
+ &velec,
+ &vvdw,
+ dvdl);
}
else
{
/* Evaluate tabulated interaction without free energy */
- fscal = evaluate_single(r2, fr->pairsTable->scale, fr->pairsTable->data.data(),
- fr->pairsTable->stride, qq, c6, c12, &velec, &vvdw);
+ fscal = evaluate_single(r2,
+ fr->pairsTable->scale,
+ fr->pairsTable->data.data(),
+ fr->pairsTable->stride,
+ qq,
+ c6,
+ c12,
+ &velec,
+ &vvdw);
}
energygrp_elec[gid] += velec;
if (computeVirial(flavor))
{
- if (fshift_index != CENTRAL)
+ if (fshift_index != c_centralShiftIndex)
{
rvec_inc(fshift[fshift_index], dx);
- rvec_dec(fshift[CENTRAL], dx);
+ rvec_dec(fshift[c_centralShiftIndex], dx);
}
}
}
* This function is templated for real/SimdReal and for optimization.
*/
template<typename T, int pack_size, typename pbc_type>
-static void do_pairs_simple(int nbonds,
- const t_iatom iatoms[],
- const t_iparams iparams[],
- const rvec x[],
- rvec4 f[],
- const pbc_type pbc,
- const t_mdatoms* md,
- const real scale_factor)
+static void do_pairs_simple(int nbonds,
+ const t_iatom iatoms[],
+ const t_iparams iparams[],
+ const rvec x[],
+ rvec4 f[],
+ const pbc_type pbc,
+ gmx::ArrayRef<real> charge,
+ const real scale_factor)
{
const int nfa1 = 1 + 2;
{
coeff[0 * pack_size + s] = iparams[itype].lj14.c6A;
coeff[1 * pack_size + s] = iparams[itype].lj14.c12A;
- coeff[2 * pack_size + s] = md->chargeA[ai[s]] * md->chargeA[aj[s]];
+ coeff[2 * pack_size + s] = charge[ai[s]] * charge[aj[s]];
/* Avoid indexing the iatoms array out of bounds.
* We pad the coordinate indices with the last atom pair.
}
/*! \brief Calculate all listed pair interactions */
-void do_pairs(int ftype,
- int nbonds,
- const t_iatom iatoms[],
- const t_iparams iparams[],
- const rvec x[],
- rvec4 f[],
- rvec fshift[],
- const struct t_pbc* pbc,
- const real* lambda,
- real* dvdl,
- const t_mdatoms* md,
- const t_forcerec* fr,
- const bool havePerturbedInteractions,
- const gmx::StepWorkload& stepWork,
- gmx_grppairener_t* grppener,
- int* global_atom_index)
+void do_pairs(int ftype,
+ int nbonds,
+ const t_iatom iatoms[],
+ const t_iparams iparams[],
+ const rvec x[],
+ rvec4 f[],
+ rvec fshift[],
+ const struct t_pbc* pbc,
+ const real* lambda,
+ real* dvdl,
+ gmx::ArrayRef<real> chargeA,
+ gmx::ArrayRef<real> chargeB,
+ gmx::ArrayRef<bool> atomIsPerturbed,
+ gmx::ArrayRef<unsigned short> cENER,
+ const int numEnergyGroups,
+ const t_forcerec* fr,
+ const bool havePerturbedInteractions,
+ const gmx::StepWorkload& stepWork,
+ gmx_grppairener_t* grppener,
+ int* global_atom_index)
{
- if (ftype == F_LJ14 && fr->ic->vdwtype != evdwUSER && !EEL_USER(fr->ic->eeltype)
+ if (ftype == F_LJ14 && fr->ic->vdwtype != VanDerWaalsType::User && !EEL_USER(fr->ic->eeltype)
&& !havePerturbedInteractions && (!stepWork.computeVirial && !stepWork.computeEnergy))
{
/* We use a fast code-path for plain LJ 1-4 without FEP.
set_pbc_simd(pbc, pbc_simd);
do_pairs_simple<SimdReal, GMX_SIMD_REAL_WIDTH, const real*>(
- nbonds, iatoms, iparams, x, f, pbc_simd, md, fr->ic->epsfac * fr->fudgeQQ);
+ nbonds, iatoms, iparams, x, f, pbc_simd, chargeA, fr->ic->epsfac * fr->fudgeQQ);
}
else
#endif
pbc_nonnull = &pbc_no;
}
- do_pairs_simple<real, 1, const t_pbc*>(nbonds, iatoms, iparams, x, f, pbc_nonnull, md,
- fr->ic->epsfac * fr->fudgeQQ);
+ do_pairs_simple<real, 1, const t_pbc*>(
+ nbonds, iatoms, iparams, x, f, pbc_nonnull, chargeA, fr->ic->epsfac * fr->fudgeQQ);
}
}
else if (stepWork.computeVirial)
{
- do_pairs_general<BondedKernelFlavor::ForcesAndVirialAndEnergy>(
- ftype, nbonds, iatoms, iparams, x, f, fshift, pbc, lambda, dvdl, md, fr, grppener,
- global_atom_index);
+ do_pairs_general<BondedKernelFlavor::ForcesAndVirialAndEnergy>(ftype,
+ nbonds,
+ iatoms,
+ iparams,
+ x,
+ f,
+ fshift,
+ pbc,
+ lambda,
+ dvdl,
+ chargeA,
+ chargeB,
+ atomIsPerturbed,
+ cENER,
+ numEnergyGroups,
+ fr,
+ grppener,
+ global_atom_index);
}
else
{
- do_pairs_general<BondedKernelFlavor::ForcesAndEnergy>(ftype, nbonds, iatoms, iparams, x, f,
- fshift, pbc, lambda, dvdl, md, fr,
- grppener, global_atom_index);
+ do_pairs_general<BondedKernelFlavor::ForcesAndEnergy>(ftype,
+ nbonds,
+ iatoms,
+ iparams,
+ x,
+ f,
+ fshift,
+ pbc,
+ lambda,
+ dvdl,
+ chargeA,
+ chargeB,
+ atomIsPerturbed,
+ cENER,
+ numEnergyGroups,
+ fr,
+ grppener,
+ global_atom_index);
}
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vec.h"
#include "gromacs/topology/ifunc.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
struct gmx_grppairener_t;
namespace gmx
{
class StepWorkload;
-}
+template<typename>
+class ArrayRef;
+} // namespace gmx
/*! \brief Calculate VdW/charge listed pair interactions (usually 1-4
* interactions).
*
* global_atom_index is only passed for printing error messages.
*/
-void do_pairs(int ftype,
- int nbonds,
- const t_iatom iatoms[],
- const t_iparams iparams[],
- const rvec x[],
- rvec4 f[],
- rvec fshift[],
- const struct t_pbc* pbc,
- const real* lambda,
- real* dvdl,
- const t_mdatoms* md,
- const t_forcerec* fr,
- bool havePerturbedPairs,
- const gmx::StepWorkload& stepWork,
- gmx_grppairener_t* grppener,
- int* global_atom_index);
+void do_pairs(int ftype,
+ int nbonds,
+ const t_iatom iatoms[],
+ const t_iparams iparams[],
+ const rvec x[],
+ rvec4 f[],
+ rvec fshift[],
+ const struct t_pbc* pbc,
+ const real* lambda,
+ real* dvdl,
+ gmx::ArrayRef<real> chargeA,
+ gmx::ArrayRef<real> chargeB,
+ gmx::ArrayRef<bool> atomIsPerturbed,
+ gmx::ArrayRef<unsigned short> cENER,
+ int numEnergyGroups,
+ const t_forcerec* fr,
+ bool havePerturbedPairs,
+ const gmx::StepWorkload& stepWork,
+ gmx_grppairener_t* grppener,
+ int* global_atom_index);
#endif
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gmxpre.h"
+#include "gromacs/utility/arrayref.h"
#include "position_restraints.h"
#include <cassert>
/*! \brief returns dx, rdist, and dpdl for functions posres() and fbposres()
*/
-void posres_dx(const rvec x,
- const rvec pos0A,
- const rvec pos0B,
- const rvec comA_sc,
- const rvec comB_sc,
- real lambda,
- const t_pbc* pbc,
- int refcoord_scaling,
- int npbcdim,
- rvec dx,
- rvec rdist,
- rvec dpdl)
+void posres_dx(const rvec x,
+ const rvec pos0A,
+ const rvec pos0B,
+ const rvec comA_sc,
+ const rvec comB_sc,
+ real lambda,
+ const t_pbc* pbc,
+ RefCoordScaling refcoord_scaling,
+ int npbcdim,
+ rvec dx,
+ rvec rdist,
+ rvec dpdl)
{
int m, d;
real posA, posB, L1, ref = 0.;
{
switch (refcoord_scaling)
{
- case erscNO:
+ case RefCoordScaling::No:
ref = 0;
rdist[m] = L1 * posA + lambda * posB;
dpdl[m] = posB - posA;
break;
- case erscALL:
+ case RefCoordScaling::All:
/* Box relative coordinates are stored for dimensions with pbc */
posA *= pbc->box[m][m];
posB *= pbc->box[m][m];
rdist[m] = 0;
dpdl[m] = posB - posA;
break;
- case erscCOM:
+ case RefCoordScaling::Com:
ref = L1 * comA_sc[m] + lambda * comB_sc[m];
rdist[m] = L1 * posA + lambda * posB;
dpdl[m] = comB_sc[m] - comA_sc[m] + posB - posA;
const rvec x[],
gmx::ForceWithVirial* forceWithVirial,
const t_pbc* pbc,
- int refcoord_scaling,
+ RefCoordScaling refcoord_scaling,
PbcType pbcType,
const rvec com)
/* compute flat-bottomed positions restraints */
npbcdim = numPbcDimensions(pbcType);
GMX_ASSERT((pbcType == PbcType::No) == (npbcdim == 0), "");
- if (refcoord_scaling == erscCOM)
+ if (refcoord_scaling == RefCoordScaling::Com)
{
clear_rvec(com_sc);
for (m = 0; m < npbcdim; m++)
pr = &forceparams[type];
/* same calculation as for normal posres, but with identical A and B states, and lambda==0 */
- posres_dx(x[ai], forceparams[type].fbposres.pos0, forceparams[type].fbposres.pos0, com_sc,
- com_sc, 0.0, pbc, refcoord_scaling, npbcdim, dx, rdist, dpdl);
+ posres_dx(x[ai],
+ forceparams[type].fbposres.pos0,
+ forceparams[type].fbposres.pos0,
+ com_sc,
+ com_sc,
+ 0.0,
+ pbc,
+ refcoord_scaling,
+ npbcdim,
+ dx,
+ rdist,
+ dpdl);
clear_rvec(fm);
v = 0.0;
const struct t_pbc* pbc,
real lambda,
real* dvdlambda,
- int refcoord_scaling,
+ RefCoordScaling refcoord_scaling,
PbcType pbcType,
const rvec comA,
const rvec comB)
npbcdim = numPbcDimensions(pbcType);
GMX_ASSERT((pbcType == PbcType::No) == (npbcdim == 0), "");
- if (refcoord_scaling == erscCOM)
+ if (refcoord_scaling == RefCoordScaling::Com)
{
clear_rvec(comA_sc);
clear_rvec(comB_sc);
pr = &forceparams[type];
/* return dx, rdist, and dpdl */
- posres_dx(x[ai], forceparams[type].posres.pos0A, forceparams[type].posres.pos0B, comA_sc,
- comB_sc, lambda, pbc, refcoord_scaling, npbcdim, dx, rdist, dpdl);
+ posres_dx(x[ai],
+ forceparams[type].posres.pos0A,
+ forceparams[type].posres.pos0B,
+ comA_sc,
+ comB_sc,
+ lambda,
+ pbc,
+ refcoord_scaling,
+ npbcdim,
+ dx,
+ rdist,
+ dpdl);
for (m = 0; (m < DIM); m++)
{
const struct t_pbc* pbc,
const rvec* x,
gmx_enerdata_t* enerd,
- const real* lambda,
+ gmx::ArrayRef<const real> lambda,
const t_forcerec* fr,
gmx::ForceWithVirial* forceWithVirial)
{
real v, dvdl;
dvdl = 0;
- v = posres<true>(idef.il[F_POSRES].size(), idef.il[F_POSRES].iatoms.data(),
- idef.iparams_posres.data(), x, forceWithVirial,
- fr->pbcType == PbcType::No ? nullptr : pbc, lambda[efptRESTRAINT], &dvdl,
- fr->rc_scaling, fr->pbcType, fr->posres_com, fr->posres_comB);
+ v = posres<true>(idef.il[F_POSRES].size(),
+ idef.il[F_POSRES].iatoms.data(),
+ idef.iparams_posres.data(),
+ x,
+ forceWithVirial,
+ fr->pbcType == PbcType::No ? nullptr : pbc,
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Restraint)],
+ &dvdl,
+ fr->rc_scaling,
+ fr->pbcType,
+ fr->posres_com,
+ fr->posres_comB);
enerd->term[F_POSRES] += v;
/* If just the force constant changes, the FEP term is linear,
* but if k changes, it is not.
*/
- enerd->dvdl_nonlin[efptRESTRAINT] += dvdl;
+ enerd->dvdl_nonlin[FreeEnergyPerturbationCouplingType::Restraint] += dvdl;
inc_nrnb(nrnb, eNR_POSRES, gmx::exactDiv(idef.il[F_POSRES].size(), 2));
}
const struct t_pbc* pbc,
const rvec x[],
gmx_enerdata_t* enerd,
- const real* lambda,
+ gmx::ArrayRef<const real> lambda,
const t_forcerec* fr)
{
- wallcycle_sub_start_nocount(wcycle, ewcsRESTRAINTS);
+ wallcycle_sub_start_nocount(wcycle, WallCycleSubCounter::Restraints);
auto& foreignTerms = enerd->foreignLambdaTerms;
for (int i = 0; i < 1 + foreignTerms.numLambdas(); i++)
real dvdl = 0;
const real lambda_dum =
- (i == 0 ? lambda[efptRESTRAINT] : fepvals->all_lambda[efptRESTRAINT][i - 1]);
- const real v = posres<false>(idef.il[F_POSRES].size(), idef.il[F_POSRES].iatoms.data(),
- idef.iparams_posres.data(), x, nullptr,
- fr->pbcType == PbcType::No ? nullptr : pbc, lambda_dum, &dvdl,
- fr->rc_scaling, fr->pbcType, fr->posres_com, fr->posres_comB);
+ (i == 0 ? lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Restraint)]
+ : fepvals->all_lambda[FreeEnergyPerturbationCouplingType::Restraint][i - 1]);
+ const real v = posres<false>(idef.il[F_POSRES].size(),
+ idef.il[F_POSRES].iatoms.data(),
+ idef.iparams_posres.data(),
+ x,
+ nullptr,
+ fr->pbcType == PbcType::No ? nullptr : pbc,
+ lambda_dum,
+ &dvdl,
+ fr->rc_scaling,
+ fr->pbcType,
+ fr->posres_com,
+ fr->posres_comB);
foreignTerms.accumulate(i, v, dvdl);
}
- wallcycle_sub_stop(wcycle, ewcsRESTRAINTS);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::Restraints);
}
/*! \brief Helper function that wraps calls to fbposres for
{
real v;
- v = fbposres(idef.il[F_FBPOSRES].size(), idef.il[F_FBPOSRES].iatoms.data(),
- idef.iparams_fbposres.data(), x, forceWithVirial,
- fr->pbcType == PbcType::No ? nullptr : pbc, fr->rc_scaling, fr->pbcType, fr->posres_com);
+ v = fbposres(idef.il[F_FBPOSRES].size(),
+ idef.il[F_FBPOSRES].iatoms.data(),
+ idef.iparams_fbposres.data(),
+ x,
+ forceWithVirial,
+ fr->pbcType == PbcType::No ? nullptr : pbc,
+ fr->rc_scaling,
+ fr->pbcType,
+ fr->posres_com);
enerd->term[F_FBPOSRES] += v;
inc_nrnb(nrnb, eNR_FBPOSRES, gmx::exactDiv(idef.il[F_FBPOSRES].size(), 2));
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <stdio.h>
#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/real.h"
struct gmx_enerdata_t;
const struct t_pbc* pbc,
const rvec* x,
gmx_enerdata_t* enerd,
- const real* lambda,
+ gmx::ArrayRef<const real> lambda,
const t_forcerec* fr,
gmx::ForceWithVirial* forceWithVirial);
const struct t_pbc* pbc,
const rvec x[],
gmx_enerdata_t* enerd,
- const real* lambda,
+ gmx::ArrayRef<const real> lambda,
const t_forcerec* fr);
/*! \brief Helper function that wraps calls to fbposres for
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
double term_theta_theta_equil;
k_bending = forceparams[type].harmonic.krA;
- theta_equil = forceparams[type].harmonic.rA * DEG2RAD;
+ theta_equil = forceparams[type].harmonic.rA * gmx::c_deg2Rad;
theta_equil = M_PI - theta_equil;
cosine_theta_equil = cos(theta_equil);
real norm_phi;
/* Read parameters phi0 and k_torsion */
- phi0 = forceparams[type].pdihs.phiA * DEG2RAD;
+ phi0 = forceparams[type].pdihs.phiA * gmx::c_deg2Rad;
cosine_phi0 = cos(phi0);
k_torsion = forceparams[type].pdihs.cpA;
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2016,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2016,2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
gmx_add_unit_test(ListedForcesTest listed_forces-test
CPP_SOURCE_FILES
bonded.cpp
+ pairs.cpp
+ position_restraints.cpp
)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! Derivative with respect to lambda
real dvdlambda = 0;
//! Shift vectors
- rvec fshift[N_IVEC] = { { 0 } };
+ rvec fshift[c_numShiftVectors] = { { 0 } };
//! Forces
alignas(GMX_REAL_MAX_SIMD_WIDTH * sizeof(real)) rvec4 f[c_numAtoms] = { { 0 } };
};
// have an implementation for uint64_t(!) but this is likely to
// work because that type is likely to be a typedef for one of
// the other numerical types that happens to be 64-bits wide.
- shiftForcesTolerance_ = FloatingPointTolerance(singleShiftForcesAbsoluteTolerance, 1e-8, 1e-6,
- 1e-12, std::numeric_limits<uint64_t>::max(),
- std::numeric_limits<uint64_t>::max(), false);
+ shiftForcesTolerance_ = FloatingPointTolerance(singleShiftForcesAbsoluteTolerance,
+ 1e-8,
+ 1e-6,
+ 1e-12,
+ std::numeric_limits<uint64_t>::max(),
+ std::numeric_limits<uint64_t>::max(),
+ false);
}
void testOneIfunc(TestReferenceChecker* checker, const std::vector<t_iatom>& iatoms, const real lambda)
{
SCOPED_TRACE(std::string("Testing PBC type: ") + c_pbcTypeNames[pbcType_]);
std::vector<int> ddgatindex = { 0, 1, 2, 3 };
- std::vector<real> chargeA = { 1.5, -2.0, 1.5, -1.0 };
- t_mdatoms mdatoms = { 0 };
- mdatoms.chargeA = chargeA.data();
+ std::vector<real> charge = { 1.5, -2.0, 1.5, -1.0 };
/* Here we run both the standard, plain-C force+shift-forces+energy+free-energy
* kernel flavor and the potentially optimized, with SIMD and less output,
* force only kernels. Note that we also run the optimized kernel for free-energy
{
SCOPED_TRACE("Testing bonded kernel flavor: " + c_bondedKernelFlavorStrings[flavor]);
OutputQuantities output;
- output.energy =
- calculateSimpleBond(input_.ftype, iatoms.size(), iatoms.data(), &input_.iparams,
- as_rvec_array(x_.data()), output.f, output.fshift, &pbc_,
- lambda, &output.dvdlambda, &mdatoms,
- /* struct t_fcdata * */ nullptr, ddgatindex.data(), flavor);
+ output.energy = calculateSimpleBond(input_.ftype,
+ iatoms.size(),
+ iatoms.data(),
+ &input_.iparams,
+ as_rvec_array(x_.data()),
+ output.f,
+ output.fshift,
+ &pbc_,
+ lambda,
+ &output.dvdlambda,
+ charge,
+ /* struct t_fcdata * */ nullptr,
+ nullptr,
+ nullptr,
+ ddgatindex.data(),
+ flavor);
// Internal consistency test of both test input
// and bonded functions.
EXPECT_TRUE((input_.fep || (output.dvdlambda == 0.0))) << "dvdlambda was " << output.dvdlambda;
if (computeVirial(flavor))
{
shiftForcesChecker.setDefaultTolerance(shiftForcesTolerance_);
- shiftForcesChecker.checkVector(output.fshift[CENTRAL], "Central");
+ shiftForcesChecker.checkVector(output.fshift[c_centralShiftIndex], "Central");
}
else
{
//! PBC values for testing
std::vector<PbcType> c_pbcForTests = { PbcType::No, PbcType::XY, PbcType::Xyz };
-// Those tests give errors with the intel compiler and nothing else, so we disable them only there.
-#ifndef __INTEL_COMPILER
INSTANTIATE_TEST_CASE_P(Bond,
ListedForcesTest,
::testing::Combine(::testing::ValuesIn(c_InputBonds),
::testing::Combine(::testing::ValuesIn(c_InputAnglesZeroAngle),
::testing::ValuesIn(c_coordinatesForTestsZeroAngle),
::testing::ValuesIn(c_pbcForTests)));
-#endif
} // namespace
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief Implements test of 1-4 interactions
+ *
+ * This test is copied from the bonded interactions test and slightly
+ * modified since 'do_pairs' takes a different set of arguments than
+ * 'calculateSimpleBond'. To keep the test setup uncluttered this test is
+ * therefore not merged into the bonded test but implemented standalone.
+ *
+ * The test setup consists of 2 atom pairs that are tested in an fep setting
+ * (vanishing charge and lennard-jones parameters of one atom) and without
+ * fep. Placement of the atoms in the box is such that shift-forces and pbc
+ * paths in do_pairs are covered.
+ *
+ * \author Sebastian Kehl <sebastian.kehl@mpcdf.mpg.de>
+ * \ingroup module_listed_forces
+ */
+#include "gmxpre.h"
+
+#include "gromacs/listed_forces/bonded.h"
+
+#include <cmath>
+
+#include <memory>
+#include <unordered_map>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/listed_forces/listed_forces.h"
+#include "gromacs/listed_forces/pairs.h"
+#include "gromacs/math/paddedvector.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/mdtypes/simulation_workload.h"
+#include "gromacs/mdtypes/enerdata.h"
+#include "gromacs/mdtypes/forcerec.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/interaction_const.h"
+#include "gromacs/mdtypes/nblist.h"
+#include "gromacs/tables/forcetable.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/utility/enumerationhelpers.h"
+#include "gromacs/utility/strconvert.h"
+#include "gromacs/utility/stringstream.h"
+#include "gromacs/utility/textwriter.h"
+#include "gromacs/utility/fatalerror.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+
+//! Number of atoms used in these tests.
+constexpr int c_numAtoms = 3;
+
+/*! \brief Output from pairs kernels
+ *
+ */
+struct OutputQuantities
+{
+ OutputQuantities(int energyGroup) :
+ energy(energyGroup),
+ dvdLambda(static_cast<int>(FreeEnergyPerturbationCouplingType::Count), 0.0)
+ {
+ }
+
+ //! Energy of this interaction
+ gmx_grppairener_t energy;
+ //! Derivative with respect to lambda
+ std::vector<real> dvdLambda;
+ //! Shift vectors
+ rvec fShift[gmx::detail::c_numIvecs] = { { 0 } };
+ //! Forces
+ alignas(GMX_REAL_MAX_SIMD_WIDTH * sizeof(real)) rvec4 f[c_numAtoms] = { { 0 } };
+};
+
+/*! \brief Utility to check the output from pairs tests
+ *
+ * \param[in] checker Reference checker
+ * \param[in] output The output from the test to check
+ * \param[in] bondedKernelFlavor Flavor for determining what output to check
+ * \param[in] functionType type of the interaction
+ */
+void checkOutput(TestReferenceChecker* checker,
+ const OutputQuantities& output,
+ const BondedKernelFlavor bondedKernelFlavor,
+ const int functionType)
+{
+ if (computeEnergy(bondedKernelFlavor))
+ {
+ switch (functionType)
+ {
+ case F_LJ14:
+ case F_LJC14_Q:
+ checker->checkReal(output.energy.energyGroupPairTerms[NonBondedEnergyTerms::Coulomb14][0],
+ "Epot Coulomb14");
+ checker->checkReal(output.energy.energyGroupPairTerms[NonBondedEnergyTerms::LJ14][0],
+ "Epot LJ14");
+ break;
+ case F_LJC_PAIRS_NB:
+ checker->checkReal(output.energy.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR][0],
+ "Epot Coulomb14");
+ checker->checkReal(output.energy.energyGroupPairTerms[NonBondedEnergyTerms::LJSR][0],
+ "Epot LJ14");
+ break;
+ default: gmx_fatal(FARGS, "Unknown function type %d in do_nonbonded14", functionType);
+ }
+ checker->checkReal(output.dvdLambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
+ "dVdlCoul ");
+ checker->checkReal(output.dvdLambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)],
+ "dVdlVdw ");
+ }
+ checker->checkSequence(std::begin(output.f), std::end(output.f), "Forces");
+}
+
+/* \brief Utility class to setup forcerec and interaction parameters
+ *
+ * Data is only initialized as necessary for the 1-4 interactions to work!
+ */
+class ForcerecHelper
+{
+public:
+ ForcerecHelper()
+ {
+ fepVals_.sc_alpha = 0.3;
+ fepVals_.sc_power = 1;
+ fepVals_.sc_r_power = 6.0;
+ fepVals_.sc_sigma = 0.3;
+ fepVals_.sc_sigma_min = 0.3;
+ fepVals_.bScCoul = true;
+
+ fr_.ic = std::make_unique<interaction_const_t>();
+ // set data in ic
+ fr_.ic->softCoreParameters = std::make_unique<interaction_const_t::SoftCoreParameters>(fepVals_);
+
+ // set data in fr
+ real tableRange = 2.9;
+ fr_.pairsTable = make_tables(nullptr, fr_.ic.get(), nullptr, tableRange, GMX_MAKETABLES_14ONLY);
+ fr_.efep = haveFep_;
+ fr_.fudgeQQ = 0.5;
+ fr_.use_simd_kernels = useSimd_;
+ fr_.bMolPBC = haveMolPBC_;
+ }
+
+ t_forcerec* get() { return &fr_; }
+
+private:
+ FreeEnergyPerturbationType haveFep_ = FreeEnergyPerturbationType::No;
+ bool useSimd_ = false;
+ bool haveMolPBC_ = false;
+
+ t_lambda fepVals_;
+ t_forcerec fr_;
+};
+
+ForcerecHelper frHelper;
+
+
+/*! \brief Input structure for listed forces tests
+ */
+struct ListInput
+{
+public:
+ //! Function type
+ int fType = -1;
+ //! do fep
+ bool fep = false;
+ //! Tolerance for float evaluation
+ float floatToler = 1e-6;
+ //! Tolerance for double evaluation
+ double doubleToler = 1e-8;
+ //! Interaction parameters
+ t_iparams iparams = { { 0 } };
+
+ //! Constructor
+ ListInput() {}
+
+ /*! \brief Constructor with tolerance
+ *
+ * \param[in] ftol Single precision tolerance
+ * \param[in] dtol Double precision tolerance
+ */
+ ListInput(float ftol, double dtol)
+ {
+ floatToler = ftol;
+ doubleToler = dtol;
+ }
+
+ /*! \brief Set parameters for lj14 interaction
+ *
+ * Fep is used if either c6A != c6B or c12A != c12B.
+ *
+ * \param[in] c6A lj-c6 of state A
+ * \param[in] c12A lj-c12 of state A
+ * \param[in] c6B lj-c6 of state B
+ * \param[in] c12B lj-c12 of state B
+ */
+ ListInput setLj14Interaction(real c6A, real c12A, real c6B, real c12B)
+ {
+ fType = F_LJ14;
+ fep = (c6A != c6B || c12A != c12B);
+ iparams.lj14.c6A = c6A;
+ iparams.lj14.c12A = c12A;
+ iparams.lj14.c6B = c6B;
+ iparams.lj14.c12B = c12B;
+
+ return *this;
+ }
+
+ /*! \brief Set parameters for ljc14 interaction
+ *
+ * \param[in] qi charge i
+ * \param[in] qj charge j
+ * \param[in] c6 lj-c6
+ * \param[in] c12 lj-c12
+ * \param[in] fudgeQ fudge factor
+ */
+ ListInput setLjc14Interaction(real qi, real qj, real c6, real c12, real fudgeQ)
+ {
+ fType = F_LJC14_Q;
+ iparams.ljc14.qi = qi;
+ iparams.ljc14.qj = qj;
+ iparams.ljc14.c6 = c6;
+ iparams.ljc14.c12 = c12;
+ iparams.ljc14.fqq = fudgeQ;
+
+ return *this;
+ }
+
+ /*! \brief Set parameters for ljcnb interaction
+ *
+ * \param[in] qi charge i
+ * \param[in] qj charge j
+ * \param[in] c6 lj-c6
+ * \param[in] c12 lj-c12
+ */
+ ListInput setLjcnbInteraction(real qi, real qj, real c6, real c12)
+ {
+ fType = F_LJC_PAIRS_NB;
+ iparams.ljcnb.qi = qi;
+ iparams.ljcnb.qj = qj;
+ iparams.ljcnb.c6 = c6;
+ iparams.ljcnb.c12 = c12;
+
+ return *this;
+ }
+};
+
+class ListedForcesPairsTest :
+ public ::testing::TestWithParam<std::tuple<ListInput, PaddedVector<RVec>, PbcType>>
+{
+protected:
+ matrix box_;
+ t_pbc pbc_;
+ PaddedVector<RVec> x_;
+ PbcType pbcType_;
+ ListInput input_;
+ TestReferenceData refData_;
+ TestReferenceChecker checker_;
+
+ ListedForcesPairsTest() : checker_(refData_.rootChecker())
+ {
+ input_ = std::get<0>(GetParam());
+ x_ = std::get<1>(GetParam());
+ pbcType_ = std::get<2>(GetParam());
+ clear_mat(box_);
+ box_[0][0] = box_[1][1] = box_[2][2] = 1.0;
+ set_pbc(&pbc_, pbcType_, box_);
+
+ FloatingPointTolerance tolerance = relativeToleranceAsPrecisionDependentFloatingPoint(
+ 1.0, input_.floatToler, input_.doubleToler);
+
+ checker_.setDefaultTolerance(tolerance);
+ }
+
+ void testOneIfunc(TestReferenceChecker* checker, const real lambda)
+ {
+ SCOPED_TRACE(std::string("Testing PBC type: ") + c_pbcTypeNames[pbcType_]);
+
+ // 'definition of pairs' is a concatenation of #npairs (here 2)
+ // 'nAtomsPerPair+1'-tuples (fType a_0 a_i ... a_nAtomsPerPair)
+ std::vector<t_iatom> iatoms = { 0, 1, 2, 0, 0, 2 };
+
+ std::vector<int> ddgatindex = { 0, 1, 2 };
+ std::vector<real> chargeA = { 1.0, -0.5, -0.5 };
+ std::vector<real> chargeB = { 0.0, 0.0, 0.0 };
+ std::vector<unsigned short> egrp = { 0, 0, 0 };
+ t_mdatoms mdatoms = { 0 };
+
+ mdatoms.chargeA = chargeA.data();
+ mdatoms.chargeB = chargeB.data();
+ mdatoms.cENER = egrp.data();
+ // nPerturbed is not decisive for fep to be used; it is overruled by
+ // other conditions in do_pairs_general; just here to not segfault
+ // upon query
+ mdatoms.nPerturbed = 0;
+
+ t_forcerec* fr = frHelper.get();
+ fr->efep = input_.fep ? FreeEnergyPerturbationType::Yes : FreeEnergyPerturbationType::No;
+ if (pbcType_ != PbcType::No)
+ {
+ fr->bMolPBC = true;
+ }
+
+ std::vector<BondedKernelFlavor> flavors = { BondedKernelFlavor::ForcesAndVirialAndEnergy };
+
+ if (!input_.fep || lambda == 0)
+ {
+ fr->use_simd_kernels = true;
+ flavors.push_back(BondedKernelFlavor::ForcesSimdWhenAvailable);
+ }
+
+ for (const auto flavor : flavors)
+ {
+ SCOPED_TRACE("Testing bonded kernel flavor: " + c_bondedKernelFlavorStrings[flavor]);
+
+ StepWorkload stepWork;
+ stepWork.computeVirial = computeVirial(flavor);
+ stepWork.computeEnergy = computeEnergy(flavor);
+
+ bool havePerturbedInteractions = input_.fep;
+ if (flavor == BondedKernelFlavor::ForcesSimdWhenAvailable)
+ {
+ havePerturbedInteractions = false;
+ }
+
+ int numEnergyTerms = static_cast<int>(NonBondedEnergyTerms::Count);
+ int numFepCouplingTerms = static_cast<int>(FreeEnergyPerturbationCouplingType::Count);
+ OutputQuantities output(numEnergyTerms);
+ std::vector<real> lambdas(numFepCouplingTerms, lambda);
+
+ do_pairs(input_.fType,
+ iatoms.size(),
+ iatoms.data(),
+ &input_.iparams,
+ as_rvec_array(x_.data()),
+ output.f,
+ output.fShift,
+ &pbc_,
+ lambdas.data(),
+ output.dvdLambda.data(),
+ gmx::arrayRefFromArray(mdatoms.chargeA, mdatoms.nr),
+ gmx::arrayRefFromArray(mdatoms.chargeB, mdatoms.nr),
+ gmx::arrayRefFromArray(mdatoms.bPerturbed, mdatoms.nr),
+ gmx::arrayRefFromArray(mdatoms.cENER, mdatoms.nr),
+ mdatoms.nPerturbed,
+ fr,
+ havePerturbedInteractions,
+ stepWork,
+ &output.energy,
+ ddgatindex.data());
+
+ checkOutput(checker, output, flavor, input_.fType);
+ auto shiftForcesChecker = checker->checkCompound("Shift-Forces", "Shift-forces");
+
+ if (computeVirial(flavor))
+ {
+ shiftForcesChecker.checkVector(output.fShift[gmx::c_centralShiftIndex], "Central");
+ }
+ else
+ {
+ // Permit omitting to compare shift forces with
+ // reference data when that is useless.
+ shiftForcesChecker.disableUnusedEntriesCheck();
+ }
+ }
+ }
+
+ void testIfunc()
+ {
+ TestReferenceChecker thisChecker =
+ checker_.checkCompound("FunctionType", interaction_function[input_.fType].name)
+ .checkCompound("FEP", (input_.fep ? "Yes" : "No"));
+
+ if (input_.fep)
+ {
+ const int numLambdas = 3;
+ for (int i = 0; i < numLambdas; ++i)
+ {
+ const real lambda = i / (numLambdas - 1.0);
+ auto lambdaChecker = thisChecker.checkCompound("Lambda", toString(lambda));
+ testOneIfunc(&lambdaChecker, lambda);
+ }
+ }
+ else
+ {
+ testOneIfunc(&thisChecker, 0.0);
+ }
+ }
+};
+
+TEST_P(ListedForcesPairsTest, Ifunc)
+{
+ testIfunc();
+}
+
+//! Function types for testing 1-4 interaction. Add new terms at the end.
+std::vector<ListInput> c_14Interaction = {
+ { ListInput(1e-5, 1e-7).setLj14Interaction(0.001458, 1.0062882e-6, 0.0, 0.0) },
+ { ListInput(1e-5, 1e-7).setLj14Interaction(0.001458, 1.0062882e-6, 0.001458, 1.0062882e-6) },
+ { ListInput(1e-5, 1e-7).setLjc14Interaction(1.0, -1.0, 0.001458, 1.0062882e-6, 0.5) },
+ { ListInput(1e-5, 1e-7).setLjcnbInteraction(1.0, -1.0, 0.001458, 1.0062882e-6) }
+};
+
+//! PBC values for testing
+std::vector<PbcType> c_pbcForTests = { PbcType::No, PbcType::XY, PbcType::Xyz };
+
+/*! \brief Coordinates for testing 1-4 interaction
+ *
+ * Define coordinates for 3 atoms here, which will be used in 2 interactions.
+ */
+std::vector<PaddedVector<RVec>> c_coordinatesFor14Interaction = {
+ { { 0.0, 0.0, 0.0 }, { 1.0, 1.0, 1.0 }, { 1.1, 1.2, 1.3 } }
+};
+
+INSTANTIATE_TEST_CASE_P(14Interaction,
+ ListedForcesPairsTest,
+ ::testing::Combine(::testing::ValuesIn(c_14Interaction),
+ ::testing::ValuesIn(c_coordinatesFor14Interaction),
+ ::testing::ValuesIn(c_pbcForTests)));
+
+} // namespace
+
+} // namespace test
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief Implements position restraint tests.
+ *
+ * \author Kevin Boyd <kevin44boyd@gmail.com>
+ * \ingroup module_listed_forces
+ */
+#include "gmxpre.h"
+
+#include "gromacs/listed_forces/position_restraints.h"
+
+#include <cmath>
+
+#include <memory>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/gmxlib/nrnb.h"
+#include "gromacs/listed_forces/listed_forces.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/mdtypes/enerdata.h"
+#include "gromacs/mdtypes/forcerec.h"
+#include "gromacs/mdtypes/forceoutput.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/interaction_const.h"
+#include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/mdtypes/nblist.h"
+#include "gromacs/mdtypes/simulation_workload.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/tables/forcetable.h"
+#include "gromacs/topology/forcefieldparameters.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/stringstream.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+
+//! Tolerance for float evaluation
+constexpr float c_precisionTolerance = 1e-6;
+
+
+class PositionRestraintsTest : public ::testing::TestWithParam<std::tuple<RefCoordScaling, PbcType>>
+{
+protected:
+ std::vector<RVec> x_;
+ std::vector<RVec> f_;
+
+ matrix box_;
+ t_pbc pbc_;
+ PbcType pbcType_;
+
+ t_nrnb nrnb_;
+ t_forcerec fr_;
+ InteractionDefinitions idef_;
+ gmx_enerdata_t enerd_;
+ std::unique_ptr<ForceWithVirial> forceWithVirial_;
+ RefCoordScaling refCoordScaling_;
+
+ TestReferenceData refData_;
+ TestReferenceChecker checker_;
+
+ PositionRestraintsTest() : idef_({}), enerd_(1, 0), checker_(refData_.rootChecker())
+ {
+ refCoordScaling_ = std::get<0>(GetParam());
+ pbcType_ = std::get<1>(GetParam());
+
+ clear_mat(box_);
+ box_[0][0] = 0.9;
+ box_[1][1] = 1.0;
+ box_[2][2] = 1.1;
+ set_pbc(&pbc_, pbcType_, box_);
+
+ FloatingPointTolerance tolerance = relativeToleranceAsFloatingPoint(1.0, c_precisionTolerance);
+ checker_.setDefaultTolerance(tolerance);
+
+ fr_.rc_scaling = refCoordScaling_;
+ fr_.pbcType = pbcType_;
+ fr_.posres_com[1] = 0.5;
+ }
+
+ //! Prepares the test with the coordinate and force constant input.
+ void setValues(gmx::ArrayRef<const RVec> positions,
+ gmx::ArrayRef<const RVec> referencePositions,
+ gmx::ArrayRef<const RVec> forceConstants)
+ {
+ x_.resize(positions.size());
+ std::copy(positions.begin(), positions.end(), x_.begin());
+
+ for (size_t i = 0; i < positions.size(); i++)
+ {
+ // First item is "type" - each atom will have a different forceparam type
+ // Second item is index - we'll just go from 0.
+ idef_.il[F_POSRES].iatoms.push_back(i);
+ idef_.il[F_POSRES].iatoms.push_back(i);
+
+ auto& entry = idef_.iparams_posres.emplace_back();
+ copy_rvec(referencePositions[i], entry.posres.pos0A);
+ copy_rvec(forceConstants[i], entry.posres.fcA);
+ clear_rvec(entry.posres.pos0B);
+ clear_rvec(entry.posres.fcB);
+ }
+ f_.resize(x_.size(), { 0, 0, 0 });
+ forceWithVirial_ = std::make_unique<ForceWithVirial>(f_, /*computeVirial=*/true);
+ }
+};
+
+std::array<real, static_cast<size_t>(FreeEnergyPerturbationCouplingType::Count)> c_emptyLambdas = { { 0 } };
+
+TEST_P(PositionRestraintsTest, BasicPosResNoFreeEnergy)
+{
+ SCOPED_TRACE(formatString("Testing PBC type: %s, refcoord type: %s",
+ c_pbcTypeNames[pbcType_].c_str(),
+ enumValueToString(refCoordScaling_)));
+ const std::vector<RVec> positions = { { 0.0, 0.0, 0.0 }, { 0.4, 0.5, 0.6 } };
+ const std::vector<RVec> referencePositions = { { 0.0, 0.0, 0.0 }, { 0.5, 0.6, 0.0 } };
+ const std::vector<RVec> forceConstants = { { 1000, 500, 250 }, { 0, 200, 400 } };
+ setValues(positions, referencePositions, forceConstants);
+ posres_wrapper(&nrnb_,
+ idef_,
+ &pbc_,
+ as_rvec_array(x_.data()),
+ &enerd_,
+ c_emptyLambdas,
+ &fr_,
+ forceWithVirial_.get());
+ checker_.checkSequence(
+ std::begin(forceWithVirial_->force_), std::end(forceWithVirial_->force_), "Forces");
+ checker_.checkSequenceArray(3, forceWithVirial_->getVirial(), "Virial contribution");
+ checker_.checkReal(enerd_.term[F_POSRES], "Potential energy");
+}
+
+//! PBC values for testing
+std::vector<PbcType> c_pbcForTests = { PbcType::No, PbcType::XY, PbcType::Xyz };
+//! Reference Coordinate Scaling values for testing
+std::vector<RefCoordScaling> c_refCoordScalingForTests = { RefCoordScaling::No,
+ RefCoordScaling::Com,
+ RefCoordScaling::All };
+
+INSTANTIATE_TEST_CASE_P(PosResBasicTest,
+ PositionRestraintsTest,
+ ::testing::Combine(::testing::ValuesIn(c_refCoordScalingForTests),
+ ::testing::ValuesIn(c_pbcForTests)));
+
+} // namespace
+
+} // namespace test
+
+} // namespace gmx
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <FunctionType Name="LJ14">
+ <FEP Name="Yes">
+ <Lambda Name="0">
+ <Real Name="Epot Coulomb14">0.21407271220614837</Real>
+ <Real Name="Epot LJ14">-0.39771349695163671</Real>
+ <Real Name="dVdlCoul ">-0.21851037383566912</Real>
+ <Real Name="dVdlVdw ">0.41875860652489377</Real>
+ <Sequence Name="Forces">
+ <Int Name="Length">3</Int>
+ <Vector>
+ <Real Name="X">0.030442842705220918</Real>
+ <Real Name="Y">0.033210373860240998</Real>
+ <Real Name="Z">0.035977905015261082</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.89301764058624677</Real>
+ <Real Name="Y">1.7860352811724916</Real>
+ <Real Name="Z">2.6790529217587382</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.92346048329146768</Real>
+ <Real Name="Y">-1.8192456550327325</Real>
+ <Real Name="Z">-2.7150308267739991</Real>
+ </Vector>
+ </Sequence>
+ <Shift-Forces Name="Shift-forces">
+ <Vector Name="Central">
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Shift-Forces>
+ </Lambda>
+ <Lambda Name="0.5">
+ <Real Name="Epot Coulomb14">0.10595201107466379</Real>
+ <Real Name="Epot LJ14">-0.19369895958475428</Real>
+ <Real Name="dVdlCoul ">-0.21402396676422034</Real>
+ <Real Name="dVdlVdw ">0.39750692921973912</Real>
+ <Sequence Name="Forces">
+ <Int Name="Length">3</Int>
+ <Vector>
+ <Real Name="X">0.015221397582715825</Real>
+ <Real Name="Y">0.016605160999326352</Real>
+ <Real Name="Z">0.017988924415936882</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.42958890996342458</Real>
+ <Real Name="Y">0.85917781992684816</Real>
+ <Real Name="Z">1.2887667298902727</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.44481030754614043</Real>
+ <Real Name="Y">-0.87578298092617457</Real>
+ <Real Name="Z">-1.3067556543062095</Real>
+ </Vector>
+ </Sequence>
+ <Shift-Forces Name="Shift-forces">
+ <Vector Name="Central">
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Shift-Forces>
+ </Lambda>
+ <Lambda Name="1">
+ <Real Name="Epot Coulomb14">0</Real>
+ <Real Name="Epot LJ14">0</Real>
+ <Real Name="dVdlCoul ">-0.20983019696952224</Real>
+ <Real Name="dVdlVdw ">0.37749364747323017</Real>
+ <Sequence Name="Forces">
+ <Int Name="Length">3</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+ <Shift-Forces Name="Shift-forces">
+ <Vector Name="Central">
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Shift-Forces>
+ </Lambda>
+ </FEP>
+ </FunctionType>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <FunctionType Name="LJ14">
+ <FEP Name="Yes">
+ <Lambda Name="0">
+ <Real Name="Epot Coulomb14">0.1445520414957524</Real>
+ <Real Name="Epot LJ14">-0.3979723893321509</Real>
+ <Real Name="dVdlCoul ">-0.14898844529427274</Real>
+ <Real Name="dVdlVdw ">0.41901751034443802</Real>
+ <Sequence Name="Forces">
+ <Int Name="Length">3</Int>
+ <Vector>
+ <Real Name="X">0.010987624164811038</Real>
+ <Real Name="Y">0.021975248329622051</Real>
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+ <Vector>
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+ <Real Name="Y">-1.8080105295021136</Real>
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+ </Vector>
+ </Sequence>
+ <Shift-Forces Name="Shift-forces">
+ <Vector Name="Central">
+ <Real Name="X">-0.010987624164811038</Real>
+ <Real Name="Y">-0.021975248329622051</Real>
+ <Real Name="Z">-0.14283911414254338</Real>
+ </Vector>
+ </Shift-Forces>
+ </Lambda>
+ <Lambda Name="0.5">
+ <Real Name="Epot Coulomb14">0.071191990173256878</Real>
+ <Real Name="Epot LJ14">-0.19382840291531345</Real>
+ <Real Name="dVdlCoul ">-0.14450329606174245</Real>
+ <Real Name="dVdlVdw ">0.39776582160013413</Real>
+ <Sequence Name="Forces">
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+ <Vector>
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+ </Vector>
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+ <Real Name="Y">0.85917781992684816</Real>
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+ <Vector>
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+ <Real Name="Y">-0.010987356435234625</Real>
+ <Real Name="Z">-0.07141781682902508</Real>
+ </Vector>
+ </Shift-Forces>
+ </Lambda>
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+ <Real Name="Epot Coulomb14">0</Real>
+ <Real Name="Epot LJ14">0</Real>
+ <Real Name="dVdlCoul ">-0.14031078405845462</Real>
+ <Real Name="dVdlVdw ">0.37775252841519097</Real>
+ <Sequence Name="Forces">
+ <Int Name="Length">3</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
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+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+ <Shift-Forces Name="Shift-forces">
+ <Vector Name="Central">
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Shift-Forces>
+ </Lambda>
+ </FEP>
+ </FunctionType>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <FunctionType Name="LJC_NB">
+ <FEP Name="No">
+ <Real Name="Epot Coulomb14">-3.4307104627027285</Real>
+ <Real Name="Epot LJ14">-0.3979723893321509</Real>
+ <Real Name="dVdlCoul ">0</Real>
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+ <Vector>
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+ </Vector>
+ </Shift-Forces>
+ </FEP>
+ </FunctionType>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <FunctionType Name="LJC_NB">
+ <FEP Name="No">
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+ <Shift-Forces Name="Shift-forces">
+ <Vector Name="Central">
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+ <Real Name="Y">-6.0813052420083142</Real>
+ <Real Name="Z">-9.1219578630124758</Real>
+ </Vector>
+ </Shift-Forces>
+ </FEP>
+ </FunctionType>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
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+ <Lambda Name="0">
+ <Real Name="Epot Coulomb14">-0.33407655239047818</Real>
+ <Real Name="Epot LJ14">-0.79539132295421022</Real>
+ <Real Name="dVdlCoul ">0.3385142675285866</Real>
+ <Real Name="dVdlVdw ">0.83748154200529312</Real>
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+ <Shift-Forces Name="Shift-forces">
+ <Vector Name="Central">
+ <Real Name="X">-1.6088959673922179</Real>
+ <Real Name="Y">-3.2177919347844322</Real>
+ <Real Name="Z">-4.8266879021766504</Real>
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+ </Shift-Forces>
+ </Lambda>
+ <Lambda Name="0.5">
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+ <Real Name="Epot LJ14">-0.38738008371883476</Real>
+ <Real Name="dVdlCoul ">0.33402780694852929</Real>
+ <Real Name="dVdlVdw ">0.79497818749041516</Real>
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+ <Vector>
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--- /dev/null
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--- /dev/null
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--- /dev/null
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--- /dev/null
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--- /dev/null
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--- /dev/null
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--- /dev/null
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+ </FunctionType>
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--- /dev/null
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--- /dev/null
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--- /dev/null
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--- /dev/null
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--- /dev/null
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--- /dev/null
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--- /dev/null
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--- /dev/null
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--- /dev/null
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# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(math INTERFACE)
+
file(GLOB MATH_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${MATH_SOURCES} PARENT_SCOPE)
-# TODO: (https://gitlab.com/gromacs/gromacs/-/issues/988) Find a new convention for defining public API.
-install(FILES
- do_fit.h
- functions.h
- units.h
- utilities.h
- vec.h
- vectypes.h
- DESTINATION include/gromacs/math)
-
-if(GMX_INSTALL_LEGACY_API)
- install(FILES
- do_fit.h
- units.h
- utilities.h
- DESTINATION include/gromacs/math)
-endif()
+# Source files have the following private module dependencies.
+target_link_libraries(math PRIVATE
+ # gmxlib
+ # math
+ # mdtypes
+ # tng_io
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(math PUBLIC
+target_include_directories(math INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(math PUBLIC
+target_link_libraries(math INTERFACE
+ legacy_api
+ )
+
+# TODO: when fileio is an OBJECT target
+#target_link_libraries(math PUBLIC legacy_api)
+#target_link_libraries(math PRIVATE common)
+
+# Module dependencies
+# fileio interfaces convey transitive dependence on these modules.
+#target_link_libraries(math PUBLIC
+target_link_libraries(math INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(math PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(math PRIVATE legacy_modules)
if (BUILD_TESTING)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MATH_COORDINATETRANSFORMATION_H
#define GMX_MATH_COORDINATETRANSFORMATION_H
+#include <memory>
+
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/classhelpers.h"
#include "matrix.h"
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
/*! \libinternal \brief Transform coordinates in three dimensions by first
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
/*! \libinternal
const auto numVoxels = gradient_.asConstView().mapping().required_span_size();
/* the gradient for the inner product measure of fit is constant and does not
* depend on the compared density, so it is pre-computed here */
- std::transform(begin(referenceDensity_), end(referenceDensity_), begin(gradient_),
- [numVoxels](float x) { return x / numVoxels; });
+ std::transform(begin(referenceDensity_), end(referenceDensity_), begin(gradient_), [numVoxels](float x) {
+ return x / numVoxels;
+ });
}
real DensitySimilarityInnerProduct::similarity(density comparedDensity)
{
GMX_THROW(RangeError("Reference density and compared density need to have same extents."));
}
- return std::inner_product(begin(referenceDensity_), end(referenceDensity_),
- begin(comparedDensity), 0., std::plus<>(), relativeEntropyAtVoxel);
+ return std::inner_product(begin(referenceDensity_),
+ end(referenceDensity_),
+ begin(comparedDensity),
+ 0.,
+ std::plus<>(),
+ relativeEntropyAtVoxel);
}
DensitySimilarityMeasure::density DensitySimilarityRelativeEntropy::gradient(density comparedDensity)
{
GMX_THROW(RangeError("Reference density and compared density need to have same extents."));
}
- std::transform(begin(referenceDensity_), end(referenceDensity_), begin(comparedDensity),
- begin(gradient_), relativeEntropyGradientAtVoxel);
+ std::transform(begin(referenceDensity_),
+ end(referenceDensity_),
+ begin(comparedDensity),
+ begin(gradient_),
+ relativeEntropyGradientAtVoxel);
return gradient_.asConstView();
}
index i = 0;
- auto referenceIterator = begin(reference);
+ const auto* referenceIterator = begin(reference);
for (const real comp : compared)
{
const real refHelper = *referenceIterator - helperValues.meanReference;
{
}
//! Evaluate the cross correlation gradient at a voxel
- real operator()(real reference, real comparison)
+ real operator()(real reference, real comparison) const
{
return prefactor_
* (reference - meanReference_ - comparisonPrefactor_ * (comparison - meanComparison_));
CrossCorrelationEvaluationHelperValues helperValues =
evaluateHelperValues(referenceDensity_, comparedDensity);
- std::transform(begin(referenceDensity_), end(referenceDensity_), begin(comparedDensity),
- begin(gradient_), CrossCorrelationGradientAtVoxel(helperValues));
+ std::transform(begin(referenceDensity_),
+ end(referenceDensity_),
+ begin(comparedDensity),
+ begin(gradient_),
+ CrossCorrelationGradientAtVoxel(helperValues));
return gradient_.asConstView();
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MATH_DENSITYFIT_H
#define GMX_MATH_DENSITYFIT_H
+#include <memory>
+
#include "gromacs/mdspan/extensions.h"
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/real.h"
namespace gmx
{
// multiply with amplitude so that Gauss3D = (amplitude * Gauss_x) * Gauss_y * Gauss_z
const float gauss1DAmplitude = dimension > XX ? 1.0 : localParameters.amplitude_;
- gauss1d_[dimension].spread(gauss1DAmplitude, localParameters.coordinate_[dimension]
- - closestLatticePoint[dimension]);
+ gauss1d_[dimension].spread(
+ gauss1DAmplitude, localParameters.coordinate_[dimension] - closestLatticePoint[dimension]);
}
const auto spreadZY = outerProductZY_(gauss1d_[ZZ].view(), gauss1d_[YY].view());
latticeSpreadRange_[YY] - closestLatticePoint[YY],
latticeSpreadRange_[ZZ] - closestLatticePoint[ZZ]);
- const DVec differenceVectorScale = { 1. / (square(sigma_[XX])), 1. / (square(sigma_[YY])),
+ const DVec differenceVectorScale = { 1. / (square(sigma_[XX])),
+ 1. / (square(sigma_[YY])),
1. / (square(sigma_[ZZ])) };
const DVec differenceVectorOffset = scaleByVector(
spreadRange.begin().toDVec() - localParameters.coordinate_.toDVec(), differenceVectorScale);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \ingroup module_math
*/
+#include <memory>
+
#include "gromacs/math/gausstransform.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdspan/extensions.h"
#include "gromacs/mdspan/mdspan.h"
-#include "gromacs/utility/classhelpers.h"
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2012,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "do_fit.h"
+#include "gromacs/math/do_fit.h"
#include <cmath>
#include <cstdio>
#include "gromacs/linearalgebra/nrjac.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/utility/fatalerror.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gmxpre.h"
-#include "functions.h"
+#include "gromacs/math/functions.h"
#include "config.h"
# include <intrin.h> // _BitScanReverse, _BitScanReverse64
#endif
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/utility/gmxassert.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/functions.h"
#include "gromacs/math/multidimarray.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
+#include "gromacs/utility/basedefinitions.h"
namespace gmx
{
std::min(maxEvaluatedSpreadDistance_,
static_cast<int>(std::floor(sigma * sqrt(-2.0 * c_logMinFloat))) - 1);
- std::generate_n(std::back_inserter(e3_), maxEvaluatedSpreadDistance_ + 1,
- [sigma, latticeIndex = 0]() mutable {
- return std::exp(-0.5 * square(latticeIndex++ / sigma));
- });
+ std::generate_n(
+ std::back_inserter(e3_), maxEvaluatedSpreadDistance_ + 1, [sigma, latticeIndex = 0]() mutable {
+ return std::exp(-0.5 * square(latticeIndex++ / sigma));
+ });
std::fill(std::begin(spreadingResult_), std::end(spreadingResult_), 0.);
};
*/
IVec rangeEndWithinLattice(const IVec& index, const dynamicExtents3D& extents, const IVec& range)
{
- IVec extentAsIvec(static_cast<int>(extents.extent(ZZ)), static_cast<int>(extents.extent(YY)),
+ IVec extentAsIvec(static_cast<int>(extents.extent(ZZ)),
+ static_cast<int>(extents.extent(YY)),
static_cast<int>(extents.extent(XX)));
return elementWiseMin(extentAsIvec, index + range);
}
for (gmx::index xIndex = 0; xIndex < ssize(x); ++xIndex)
{
const auto xValue = x[xIndex];
- std::transform(std::begin(y), std::end(y), begin(data_.asView()[xIndex]),
- [xValue](float yValue) { return xValue * yValue; });
+ std::transform(std::begin(y), std::end(y), begin(data_.asView()[xIndex]), [xValue](float yValue) {
+ return xValue * yValue;
+ });
}
return data_.asConstView();
}
{
// multiply with amplitude so that Gauss3D = (amplitude * Gauss_x) * Gauss_y * Gauss_z
const float gauss1DAmplitude = dimension > XX ? 1.0 : localParameters.amplitude_;
- gauss1d_[dimension].spread(gauss1DAmplitude, localParameters.coordinate_[dimension]
- - closestLatticePoint[dimension]);
+ gauss1d_[dimension].spread(
+ gauss1DAmplitude, localParameters.coordinate_[dimension] - closestLatticePoint[dimension]);
}
const auto spreadZY = outerProductZY_(gauss1d_[ZZ].view(), gauss1d_[YY].view());
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MATH_GAUSSTRANSFORM_H
#define GMX_MATH_GAUSSTRANSFORM_H
+#include <memory>
#include <vector>
#include "gromacs/math/multidimarray.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdspan/extensions.h"
#include "gromacs/mdspan/mdspan.h"
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/real.h"
namespace gmx
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
/*! \libinternal \brief Parameters for density spreading kernels.
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
/*! \internal \brief A 3-orthotope over integer intervals.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2017,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
real re, im;
};
-typedef t_complex cvec[DIM];
-
static t_complex rcmul(real r, t_complex c)
{
t_complex d;
Matrix3x3 transpose(Matrix3x3ConstSpan matrixView)
{
- return Matrix3x3({ matrixView(0, 0), matrixView(1, 0), matrixView(2, 0), matrixView(0, 1),
- matrixView(1, 1), matrixView(2, 1), matrixView(0, 2), matrixView(1, 2),
+ return Matrix3x3({ matrixView(0, 0),
+ matrixView(1, 0),
+ matrixView(2, 0),
+ matrixView(0, 1),
+ matrixView(1, 1),
+ matrixView(2, 1),
+ matrixView(0, 2),
+ matrixView(1, 2),
matrixView(2, 2) });
}
GMX_ASSERT(a.size() == b.size(),
"Input vectors have to have the same size to evaluate their linear combination.");
std::vector<real> result(a.size());
- std::transform(std::begin(a), std::end(a), std::begin(b), std::begin(result),
- [alpha, beta](auto a, auto b) { return alpha * a + beta * b; });
+ std::transform(
+ std::begin(a), std::end(a), std::begin(b), std::begin(result), [alpha, beta](auto a, auto b) {
+ return alpha * a + beta * b;
+ });
return result;
};
NelderMeadSimplex::evaluateExpansionPoint(const std::function<real(ArrayRef<const real>)>& f) const
{
const std::vector<real> expansionPointCoordinate =
- linearCombination(1 - defaultNelderMeadParameters.gamma_, centroidWithoutWorstPoint_,
- defaultNelderMeadParameters.gamma_, reflectionPointCoordinates_);
+ linearCombination(1 - defaultNelderMeadParameters.gamma_,
+ centroidWithoutWorstPoint_,
+ defaultNelderMeadParameters.gamma_,
+ reflectionPointCoordinates_);
return { expansionPointCoordinate, f(expansionPointCoordinate) };
}
RealFunctionvalueAtCoordinate
NelderMeadSimplex::evaluateContractionPoint(const std::function<real(ArrayRef<const real>)>& f) const
{
- std::vector<real> contractionPoint =
- linearCombination(1 - defaultNelderMeadParameters.rho_, centroidWithoutWorstPoint_,
- defaultNelderMeadParameters.rho_, worstVertex().coordinate_);
+ std::vector<real> contractionPoint = linearCombination(1 - defaultNelderMeadParameters.rho_,
+ centroidWithoutWorstPoint_,
+ defaultNelderMeadParameters.rho_,
+ worstVertex().coordinate_);
return { contractionPoint, f(contractionPoint) };
}
// find the point to insert the new vertex, so that the simplex vertices
// keep being sorted according to function value
const auto insertionPoint = std::lower_bound(
- std::begin(simplex_), std::end(simplex_), newVertex.value_,
+ std::begin(simplex_),
+ std::end(simplex_),
+ newVertex.value_,
[](const RealFunctionvalueAtCoordinate& lhs, real value) { return lhs.value_ < value; });
simplex_.insert(insertionPoint, newVertex);
// now that the simplex has changed, it has a new centroid and reflection point
std::vector<real> bestPointCoordinate = simplex_.front().coordinate_;
// skipping over the first simplex vertex, pull points closer to the best
// vertex
- std::transform(std::next(std::begin(simplex_)), std::end(simplex_), std::next(std::begin(simplex_)),
+ std::transform(std::next(std::begin(simplex_)),
+ std::end(simplex_),
+ std::next(std::begin(simplex_)),
[bestPointCoordinate, f](const RealFunctionvalueAtCoordinate& d) -> RealFunctionvalueAtCoordinate {
- const std::vector<real> shrinkPoint = linearCombination(
- defaultNelderMeadParameters.sigma_, d.coordinate_,
- 1 - defaultNelderMeadParameters.sigma_, bestPointCoordinate);
+ const std::vector<real> shrinkPoint =
+ linearCombination(defaultNelderMeadParameters.sigma_,
+ d.coordinate_,
+ 1 - defaultNelderMeadParameters.sigma_,
+ bestPointCoordinate);
return { shrinkPoint, f(shrinkPoint) };
});
{
const std::vector<real> differenceVector =
linearCombination(1, firstSimplexVertexCoordinate, -1, simplexVertex.coordinate_);
- const real thisLength =
- std::accumulate(std::begin(differenceVector), std::end(differenceVector), 0.,
- [](real sum, real value) { return sum + value * value; });
+ const real thisLength = std::accumulate(
+ std::begin(differenceVector), std::end(differenceVector), 0., [](real sum, real value) {
+ return sum + value * value;
+ });
result = std::max(result, thisLength);
}
return sqrt(result);
{
// intialize with first vertex, then add up all other vertex coordinates
// expect last one
- centroidWithoutWorstPoint_ = std::accumulate(
- std::next(std::begin(simplex_)), std::prev(std::end(simplex_)), simplex_.front().coordinate_,
- [](std::vector<real> sum, const RealFunctionvalueAtCoordinate& x) {
- std::transform(std::begin(sum), std::end(sum), std::begin(x.coordinate_),
- std::begin(sum), std::plus<>());
- return sum;
- });
+ centroidWithoutWorstPoint_ =
+ std::accumulate(std::next(std::begin(simplex_)),
+ std::prev(std::end(simplex_)),
+ simplex_.front().coordinate_,
+ [](std::vector<real> sum, const RealFunctionvalueAtCoordinate& x) {
+ std::transform(std::begin(sum),
+ std::end(sum),
+ std::begin(x.coordinate_),
+ std::begin(sum),
+ std::plus<>());
+ return sum;
+ });
// divide the summed up coordinates by N (the simplex has N+1 vertices)
- std::transform(std::begin(centroidWithoutWorstPoint_), std::end(centroidWithoutWorstPoint_),
+ std::transform(std::begin(centroidWithoutWorstPoint_),
+ std::end(centroidWithoutWorstPoint_),
std::begin(centroidWithoutWorstPoint_),
[n = simplex_.size() - 1](const auto& x) { return x / n; });
// now, that we have evaluated the centroid, update the reflection points
- reflectionPointCoordinates_ =
- linearCombination(defaultNelderMeadParameters.alpha_ + 1, centroidWithoutWorstPoint_,
- -1, worstVertex().coordinate_);
+ reflectionPointCoordinates_ = linearCombination(
+ defaultNelderMeadParameters.alpha_ + 1, centroidWithoutWorstPoint_, -1, worstVertex().coordinate_);
}
} // namespace gmx
// the oriented simplex length is smaller or equal a given number.
const real minimumSimplexLength = minimumRelativeSimplexLength * nelderMeadSimplex.orientedLength();
for (int currentStep = 0;
- nelderMeadSimplex.orientedLength() > minimumSimplexLength && currentStep < maxSteps; ++currentStep)
+ nelderMeadSimplex.orientedLength() > minimumSimplexLength && currentStep < maxSteps;
+ ++currentStep)
{
// see if simplex can by improved by reflecing the worst vertex at the centroid
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2018,2019, The GROMACS development team.
+# Copyright (c) 2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
TYPED_TEST(ArrayRefWithPaddingTest, ConstructFromPointersWorks)
{
- typename TestFixture::ArrayRefType arrayRef(this->v.data(), this->v.data() + this->v.size(),
- this->v.data() + this->v.paddedSize());
+ typename TestFixture::ArrayRefType arrayRef(
+ this->v.data(), this->v.data() + this->v.size(), this->v.data() + this->v.paddedSize());
this->runTests(arrayRef);
}
RVec vectorTransformed = vector;
affineTransformation(&vectorTransformed);
// need relaxed tolerance here, due to the number of operations involved
- EXPECT_REAL_EQ_TOL((*expected)[XX], vectorTransformed[XX],
+ EXPECT_REAL_EQ_TOL((*expected)[XX],
+ vectorTransformed[XX],
relativeToleranceAsFloatingPoint((*expected)[XX], 1e-5));
- EXPECT_REAL_EQ_TOL((*expected)[YY], vectorTransformed[YY],
+ EXPECT_REAL_EQ_TOL((*expected)[YY],
+ vectorTransformed[YY],
relativeToleranceAsFloatingPoint((*expected)[YY], 1e-5));
- EXPECT_REAL_EQ_TOL((*expected)[ZZ], vectorTransformed[ZZ],
+ EXPECT_REAL_EQ_TOL((*expected)[ZZ],
+ vectorTransformed[ZZ],
relativeToleranceAsFloatingPoint((*expected)[ZZ], 1e-5));
++expected;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
std::iota(begin(comparedDensity), end(comparedDensity), -18);
std::vector<float> expectedSimilarityGradient;
- std::copy(begin(referenceDensity), end(referenceDensity),
- std::back_inserter(expectedSimilarityGradient));
+ std::copy(begin(referenceDensity), end(referenceDensity), std::back_inserter(expectedSimilarityGradient));
for (auto& x : expectedSimilarityGradient)
{
x /= comparedDensity.asConstView().mapping().required_span_size();
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/multidimarray.h"
#include "gromacs/math/utilities.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdspan/extensions.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
TEST_F(StructureSimilarityTest, YieldsCorrectRMSDWithIndex)
{
- EXPECT_REAL_EQ_TOL(sqrt(2.0), rmsdev_ind(index_.size(), index_.data(), m_, x1_, x2_),
- defaultRealTolerance());
+ EXPECT_REAL_EQ_TOL(
+ sqrt(2.0), rmsdev_ind(index_.size(), index_.data(), m_, x1_, x2_), defaultRealTolerance());
}
TEST_F(StructureSimilarityTest, YieldsCorrectRhoWidthIndex)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019 by the GROMACS development team.
+ * Copyright (c) 2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
}
+template<typename T>
+class FunctionTestIntegerTypes : public ::testing::Test
+{
+};
+
+typedef ::testing::Types<char, unsigned char, int, unsigned int, long, unsigned long> IntegerTypes;
+TYPED_TEST_CASE(FunctionTestIntegerTypes, IntegerTypes);
+
+TYPED_TEST(FunctionTestIntegerTypes, IsPowerOfTwo)
+{
+ if (std::is_signed_v<TypeParam>)
+ {
+ EXPECT_EQ(false, gmx::isPowerOfTwo<TypeParam>(std::numeric_limits<TypeParam>::min()));
+ EXPECT_EQ(false, gmx::isPowerOfTwo<TypeParam>(-16));
+ EXPECT_EQ(false, gmx::isPowerOfTwo<TypeParam>(-3));
+ EXPECT_EQ(false, gmx::isPowerOfTwo<TypeParam>(-2));
+ EXPECT_EQ(false, gmx::isPowerOfTwo<TypeParam>(-1));
+ }
+ EXPECT_EQ(false, gmx::isPowerOfTwo<TypeParam>(0));
+ EXPECT_EQ(true, gmx::isPowerOfTwo<TypeParam>(1));
+ EXPECT_EQ(true, gmx::isPowerOfTwo<TypeParam>(2));
+ EXPECT_EQ(false, gmx::isPowerOfTwo<TypeParam>(3));
+ EXPECT_EQ(true, gmx::isPowerOfTwo<TypeParam>(4));
+ EXPECT_EQ(false, gmx::isPowerOfTwo<TypeParam>(5));
+ EXPECT_EQ(false, gmx::isPowerOfTwo<TypeParam>(6));
+ EXPECT_EQ(false, gmx::isPowerOfTwo<TypeParam>(24));
+ EXPECT_EQ(false, gmx::isPowerOfTwo<TypeParam>(63));
+ EXPECT_EQ(true, gmx::isPowerOfTwo<TypeParam>(64));
+ EXPECT_EQ(false, gmx::isPowerOfTwo<TypeParam>(66));
+ // Max for any type is always 2^x - 1
+ EXPECT_EQ(false, gmx::isPowerOfTwo<TypeParam>(std::numeric_limits<TypeParam>::max()));
+}
+
} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
FloatingPointTolerance tolerance(defaultFloatTolerance());
const real amplitude = 1.0;
gauss1d.spread(amplitude, shift);
- std::array<float, 2 * spreadWidth + 1> expected = {
- 0.0047816522419452667236328125, 0.2613909542560577392578125, 0.65811407566070556640625,
- 0.07631497085094451904296875, 0.000407583254855126142501831054688
- };
+ std::array<float, 2 * spreadWidth + 1> expected = { 0.0047816522419452667236328125,
+ 0.2613909542560577392578125,
+ 0.65811407566070556640625,
+ 0.07631497085094451904296875,
+ 0.000407583254855126142501831054688 };
EXPECT_THAT(expected, Pointwise(FloatEq(tolerance), viewOnResult));
}
gauss1d.spread(amplitude, shift);
std::vector<float> sumOfComplementaryGaussians;
// keep a copy of the first Gaussian
- std::copy(std::begin(viewOnResult), std::end(viewOnResult),
- std::back_inserter(sumOfComplementaryGaussians));
+ std::copy(std::begin(viewOnResult), std::end(viewOnResult), std::back_inserter(sumOfComplementaryGaussians));
gauss1d.spread(-amplitude, shift);
// add the two spread Gaussians
- std::transform(std::begin(viewOnResult), std::end(viewOnResult),
- std::begin(sumOfComplementaryGaussians), std::begin(sumOfComplementaryGaussians),
+ std::transform(std::begin(viewOnResult),
+ std::end(viewOnResult),
+ std::begin(sumOfComplementaryGaussians),
+ std::begin(sumOfComplementaryGaussians),
std::plus<>());
// Expect all zeros
std::array<float, 2 * spreadWidth + 1> expected = {};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
TEST_F(MultiDimArrayTest, viewEnd)
{
static_array_type::view_type view = staticArray_.asView();
- auto x = end(view);
+ auto* x = end(view);
--x;
view(2, 2) = testNumber_;
EXPECT_EQ(*x, testNumber_);
TEST_F(MultiDimArrayTest, constViewConstEnd)
{
staticArray_(2, 2) = testNumber_;
- const auto view = staticArray_.asConstView();
- auto x = end(view);
+ const auto view = staticArray_.asConstView();
+ const auto* x = end(view);
--x;
EXPECT_EQ(*x, testNumber_);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
EXPECT_EQ(4, r[1][ZZ]);
}
+TEST(RVecTest, ComparesEqual)
+{
+ RVec a(1, 2, 3);
+ RVec b(1, 2, 3);
+ RVec c(1, 2, 2);
+ EXPECT_EQ(a == b, true);
+ EXPECT_EQ(a == c, false);
+}
+
+TEST(RVecTest, ComparesUnequal)
+{
+ RVec a(1, 2, 3);
+ RVec b(1, 2, 3);
+ RVec c(1, 2, 2);
+ EXPECT_EQ(a != b, false);
+ EXPECT_EQ(a != c, true);
+}
+
/*! \brief
* Test overloaded math operations
*/
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2010,2011,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "gmxpre.h"
-
-#include "units.h"
-
-#include <cstdio>
-
-#include "gromacs/utility/cstringutil.h"
-
-double convert2gmx(double x, int unit)
-{
- switch (unit)
- {
- case eg2cAngstrom: return x * A2NM;
- case eg2cNm: return x;
- case eg2cBohr: return x * BOHR2NM;
- case eg2cKcal_Mole: return x / CAL2JOULE;
- case eg2cHartree: return x * ONE_4PI_EPS0 / BOHR2NM; // NOLINT bugprone-branch-clone
- case eg2cHartree_e: return x * ONE_4PI_EPS0 / BOHR2NM;
- case eg2cAngstrom3: return x * A2NM * A2NM * A2NM;
- case eg2cCoulomb: return x / E_CHARGE;
- case eg2cDebye: return x * DEBYE2ENM;
- case eg2cElectron: return x;
- case eg2cBuckingham: return x * A2NM * DEBYE2ENM;
- default: fprintf(stderr, "Unknown unit %d, not converting.\n", unit);
- }
- return x;
-}
-
-double gmx2convert(double x, int unit)
-{
- switch (unit)
- {
- case eg2cAngstrom: return x / A2NM;
- case eg2cNm: return x;
- case eg2cBohr: return x / BOHR2NM;
- case eg2cKcal_Mole: return x * CAL2JOULE;
- case eg2cHartree: return x / (ONE_4PI_EPS0 / BOHR2NM); // NOLINT bugprone-branch-clone
- case eg2cHartree_e: return x / (ONE_4PI_EPS0 / BOHR2NM);
- case eg2cAngstrom3: return x / (A2NM * A2NM * A2NM);
- case eg2cCoulomb: return x * E_CHARGE;
- case eg2cDebye: return x / DEBYE2ENM;
- case eg2cElectron: return x;
- case eg2cBuckingham: return x / (A2NM * DEBYE2ENM);
- default: fprintf(stderr, "Unknown unit %d, not converting.\n", unit);
- }
- return x;
-}
-
-/* This has to have the same order as the enums. */
-static const char* eg2c_names[eg2cNR] = { "Angstrom", "Nm", "Bohr", "Kcal_Mole",
- "Hartree", "Hartree_e", "Angstrom3", "Coulomb",
- "Debye", "Electron", "Buckingham" };
-
-int string2unit(char* string)
-{
- int i;
-
- for (i = 0; (i < eg2cNR); i++)
- {
- if (gmx_strcasecmp(string, eg2c_names[i]) == 0)
- {
- return i;
- }
- }
- return -1;
-}
-
-const char* unit2string(int unit)
-{
- if ((unit >= 0) && (unit < eg2cNR))
- {
- return eg2c_names[unit];
- }
-
- return nullptr;
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2018,2019, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifndef GMX_MATH_UNITS_H
-#define GMX_MATH_UNITS_H
-
-/*
- * Physical constants to be used in Gromacs.
- * No constants (apart from 0, 1 or 2) should
- * be anywhere else in the code.
- */
-
-#include "gromacs/math/utilities.h"
-
-#define ANGSTROM (1e-10) /* Old... */
-#define KILO (1e3) /* Thousand */
-#define NANO (1e-9) /* A Number */
-#define PICO (1e-12) /* A Number */
-#define A2NM (ANGSTROM / NANO) /* NANO */
-#define NM2A (NANO / ANGSTROM) /* 10.0 */
-#define RAD2DEG (180.0 / M_PI) /* Conversion */
-#define DEG2RAD (M_PI / 180.0) /* id */
-#define CAL2JOULE (4.184) /* Exact definition of the calorie */
-#define E_CHARGE (1.602176634e-19) /* Exact definition, Coulomb NIST 2018 CODATA */
-
-#define AMU (1.66053906660e-27) /* kg, NIST 2018 CODATA */
-#define BOLTZMANN (1.380649e-23) /* (J/K, Exact definition, NIST 2018 CODATA */
-#define AVOGADRO (6.02214076e23) /* 1/mol, Exact definition, NIST 2018 CODATA */
-#define RGAS (BOLTZMANN * AVOGADRO) /* (J/(mol K)) */
-#define BOLTZ (RGAS / KILO) /* (kJ/(mol K)) */
-#define FARADAY (E_CHARGE * AVOGADRO) /* (C/mol) */
-#define ELECTRONVOLT (E_CHARGE * AVOGADRO / KILO) /* (kJ/mol) */
-#define PLANCK1 (6.62607015e-34) /* J/Hz, Exact definition, NIST 2018 CODATA */
-#define PLANCK (PLANCK1 * AVOGADRO / (PICO * KILO)) /* (kJ/mol) ps */
-
-#define EPSILON0_SI (8.8541878128e-12) /* F/m, NIST 2018 CODATA */
-/* Epsilon in our MD units: (e^2 / Na (kJ nm)) == (e^2 mol/(kJ nm)) */
-#define EPSILON0 ((EPSILON0_SI * NANO * KILO) / (E_CHARGE * E_CHARGE * AVOGADRO))
-
-#define SPEED_OF_LIGHT (2.99792458e05) /* units of nm/ps, Exact definition, NIST 2018 CODATA */
-#define ATOMICMASS_keV (931494.10242) /* Atomic mass in keV, NIST 2018 CODATA */
-#define ELECTRONMASS_keV (510.99895000) /* Electron mas in keV, NIST 2018 CODATA */
-
-#define RYDBERG (1.0973731568160e-02) /* nm^-1, NIST 2018 CODATA */
-
-#define ONE_4PI_EPS0 (1.0 / (4.0 * M_PI * EPSILON0))
-#define FACEL (10.0 * ONE_4PI_EPS0)
-
-/* Pressure in MD units is:
- * 1 bar = 1e5 Pa = 1e5 kg m^-1 s^-2 = 1e-28 kg nm^-1 ps^-2 = 1e-28 / AMU amu nm^1 ps ^2
- */
-#define BAR_MDUNITS (1e5 * NANO * PICO * PICO / AMU)
-#define PRESFAC (1.0 / BAR_MDUNITS)
-
-/* DEBYE2ENM should be (1e-21*PICO)/(SPEED_OF_LIGHT*E_CHARGE*NANO*NANO),
- * but we need to factor out some of the exponents to avoid single-precision overflows.
- */
-#define DEBYE2ENM (1e-15 / (SPEED_OF_LIGHT * E_CHARGE))
-#define ENM2DEBYE (1.0 / DEBYE2ENM)
-
-/* to convert from a acceleration in (e V)/(amu nm) */
-/* FIELDFAC is also Faraday's constant and E_CHARGE/(1e6 AMU) */
-#define FIELDFAC (FARADAY / KILO)
-
-/* to convert AU to MD units: */
-#define HARTREE2KJ ((2.0 * RYDBERG * PLANCK * SPEED_OF_LIGHT) / AVOGADRO)
-#define BOHR2NM (0.0529177210903) /* nm^-1, NIST 2018 CODATA */
-#define HARTREE_BOHR2MD (HARTREE2KJ * AVOGADRO / BOHR2NM)
-
-
-/* The four basic units */
-#define unit_length "nm"
-#define unit_time "ps"
-#define unit_mass "u"
-#define unit_energy "kJ/mol"
-
-/* Temperature unit, T in this unit times BOLTZ give energy in unit_energy */
-#define unit_temp_K "K"
-
-/* Charge unit, electron charge, involves ONE_4PI_EPS0 */
-#define unit_charge_e "e"
-
-/* Pressure unit, pressure in basic units times PRESFAC gives this unit */
-#define unit_pres_bar "bar"
-
-/* Dipole unit, debye, conversion from the unit_charge_e involves ENM2DEBYE */
-#define unit_dipole_D "D"
-
-/* Derived units from basic units only */
-#define unit_vel unit_length "/" unit_time
-#define unit_volume unit_length "^3"
-#define unit_invtime "1/" unit_time
-
-/* Other derived units */
-#define unit_surft_bar unit_pres_bar " " unit_length
-
-/* SI units, conversion from basic units involves NANO, PICO and AMU */
-#define unit_length_SI "m"
-#define unit_time_SI "s"
-#define unit_mass_SI "kg"
-
-#define unit_density_SI unit_mass_SI "/" unit_length_SI "^3"
-#define unit_invvisc_SI unit_length_SI " " unit_time_SI "/" unit_mass_SI
-
-/* The routines below can be used for converting units from or to GROMACS
- internal units. */
-enum
-{
- eg2cAngstrom,
- eg2cNm,
- eg2cBohr,
- eg2cKcal_Mole,
- eg2cHartree,
- eg2cHartree_e,
- eg2cAngstrom3,
- eg2cCoulomb,
- eg2cDebye,
- eg2cElectron,
- eg2cBuckingham,
- eg2cNR
-};
-
-/* Convert value x to GROMACS units. Energy -> Energy, Length -> Length etc.
- The type of x is deduced from unit,
- which should be taken from the enum above. */
-extern double convert2gmx(double x, int unit);
-
-/* Convert value x from GROMACS units to the desired one.
- The type of return value is deduced from unit, see above */
-extern double gmx2convert(double x, int unit);
-
-/* Convert the string to one of the units supported. Returns -1 if not found. */
-extern int string2unit(char* string);
-
-/* Convert the unit to a string. Return NULL when unit is out of range. */
-extern const char* unit2string(int unit);
-
-#endif
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "utilities.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/utility/real.h"
#include "config.h"
-#include <cassert>
-#include <climits>
+#include <cstdint>
#include <cmath>
-#include <algorithm>
#include <cfenv>
//! Floating point exception set that we use and care about
}
-gmx_bool check_int_multiply_for_overflow(int64_t a, int64_t b, int64_t* result)
+bool check_int_multiply_for_overflow(int64_t a, int64_t b, int64_t* result)
{
int64_t sign = 1;
if ((0 == a) || (0 == b))
{
*result = 0;
- return TRUE;
+ return true;
}
if (a < 0)
{
if (INT64_MAX / b < a)
{
*result = (sign > 0) ? INT64_MAX : INT64_MIN;
- return FALSE;
+ return false;
}
*result = sign * a * b;
- return TRUE;
+ return true;
}
int gmx_feenableexcept()
return -1;
#endif
}
+
+bool gmxShouldEnableFPExceptions()
+{
+#if defined(NDEBUG)
+ return false; // Release build
+#elif ((defined __clang__ || (defined(__GNUC__) && __GNUC__ == 7)) && defined __OPTIMIZE__)
+ return false; // Buggy compiler
+#elif GMX_GPU_SYCL
+ return false; // avoid spurious FPE during SYCL JIT
+#else
+ return true;
+#endif
+}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
if (index != -1)
{
- fprintf(fp, "%s[%5d] (%12.5e %12.5e %12.5e) - (%12.5e %12.5e %12.5e)\n", s, index,
- i1[XX], i1[YY], i1[ZZ], i2[XX], i2[YY], i2[ZZ]);
+ fprintf(fp,
+ "%s[%5d] (%12.5e %12.5e %12.5e) - (%12.5e %12.5e %12.5e)\n",
+ s,
+ index,
+ i1[XX],
+ i1[YY],
+ i1[ZZ],
+ i2[XX],
+ i2[YY],
+ i2[ZZ]);
}
else
{
- fprintf(fp, "%s (%12.5e %12.5e %12.5e) - (%12.5e %12.5e %12.5e)\n", s, i1[XX], i1[YY],
- i1[ZZ], i2[XX], i2[YY], i2[ZZ]);
+ fprintf(fp,
+ "%s (%12.5e %12.5e %12.5e) - (%12.5e %12.5e %12.5e)\n",
+ s,
+ i1[XX],
+ i1[YY],
+ i1[ZZ],
+ i2[XX],
+ i2[YY],
+ i2[ZZ]);
}
}
}
{
if (index != -1)
{
- fprintf(fp, "%s[%5d] (%8d,%8d,%8d - %8d,%8d,%8d)\n", s, index, i1[XX], i1[YY], i1[ZZ],
- i2[XX], i2[YY], i2[ZZ]);
+ fprintf(fp,
+ "%s[%5d] (%8d,%8d,%8d - %8d,%8d,%8d)\n",
+ s,
+ index,
+ i1[XX],
+ i1[YY],
+ i1[ZZ],
+ i2[XX],
+ i2[YY],
+ i2[ZZ]);
}
else
{
- fprintf(fp, "%s (%8d,%8d,%8d - %8d,%8d,%8d)\n", s, i1[XX], i1[YY], i1[ZZ], i2[XX],
- i2[YY], i2[ZZ]);
+ fprintf(fp, "%s (%8d,%8d,%8d - %8d,%8d,%8d)\n", s, i1[XX], i1[YY], i1[ZZ], i2[XX], i2[YY], i2[ZZ]);
}
}
}
else
{
pr_indent(fp, indent);
- fprintf(fp, "%s[%d,...,%d] = {%d,...,%d}\n", title, bShowNumbers ? i : -1,
- bShowNumbers ? j - 1 : -1, vec[i], vec[j - 1]);
+ fprintf(fp,
+ "%s[%d,...,%d] = {%d,...,%d}\n",
+ title,
+ bShowNumbers ? i : -1,
+ bShowNumbers ? j - 1 : -1,
+ vec[i],
+ vec[j - 1]);
i = j;
}
}
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2010,2012,2013,2014,2015 by the GROMACS development team.
-# Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+add_library(mdlib INTERFACE)
+
file(GLOB MDLIB_SOURCES *.cpp)
-# To avoid listing all the necessary files manually, we will remove SYCL-specfific one here:
-list(REMOVE_ITEM MDLIB_SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/leapfrog_gpu_sycl.cpp)
+# To avoid listing all the necessary files manually, we will remove SYCL-specific files here:
+list(REMOVE_ITEM MDLIB_SOURCES
+ ${CMAKE_CURRENT_SOURCE_DIR}/gpuforcereduction_impl.cpp
+ ${CMAKE_CURRENT_SOURCE_DIR}/leapfrog_gpu_sycl.cpp
+ ${CMAKE_CURRENT_SOURCE_DIR}/lincs_gpu.cpp
+ ${CMAKE_CURRENT_SOURCE_DIR}/lincs_gpu_internal_sycl.cpp
+ ${CMAKE_CURRENT_SOURCE_DIR}/settle_gpu.cpp
+ ${CMAKE_CURRENT_SOURCE_DIR}/settle_gpu_internal_sycl.cpp)
set(MDLIB_SOURCES ${MDLIB_SOURCES} PARENT_SCOPE)
-if (BUILD_TESTING)
- add_subdirectory(tests)
-endif()
if(GMX_GPU_CUDA)
gmx_add_libgromacs_sources(
leapfrog_gpu.cu
- lincs_gpu.cu
- settle_gpu.cu
+ gpuforcereduction_impl.cpp
+ gpuforcereduction_impl_internal.cu
+ lincs_gpu.cpp
+ lincs_gpu_internal.cu
+ settle_gpu.cpp
+ settle_gpu_internal.cu
update_constrain_gpu_impl.cu
- gpuforcereduction_impl.cu
+ )
+ _gmx_add_files_to_property(CUDA_SOURCES
+ gpuforcereduction_impl.cpp
+ lincs_gpu.cpp
+ settle_gpu.cpp
)
endif()
+
if(GMX_GPU_SYCL)
gmx_add_libgromacs_sources(
leapfrog_gpu_sycl.cpp
+ lincs_gpu.cpp
+ lincs_gpu_internal_sycl.cpp
+ settle_gpu.cpp
+ settle_gpu_internal_sycl.cpp
)
+
_gmx_add_files_to_property(SYCL_SOURCES
leapfrog_gpu_sycl.cpp
+ lincs_gpu.cpp
+ lincs_gpu_internal_sycl.cpp
+ settle_gpu.cpp
+ settle_gpu_internal_sycl.cpp
)
endif()
+
+# Source files have the following private module dependencies.
+target_link_libraries(mdlib PRIVATE
+# gmxlib
+# math
+# mdtypes
+# tng_io
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(mdlib PUBLIC
+target_include_directories(mdlib INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(mdlib PUBLIC
+target_link_libraries(mdlib INTERFACE
+ legacy_api
+ )
+
+# TODO: when mdlib is an OBJECT target
+#target_link_libraries(mdlib PUBLIC legacy_api)
+#target_link_libraries(mdlib PRIVATE common)
+
+# Module dependencies
+# mdlib interfaces convey transitive dependence on these modules.
+#target_link_libraries(mdlib PUBLIC
+target_link_libraries(mdlib INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(mdlib PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(mdlib PRIVATE legacy_modules)
+
+if (BUILD_TESTING)
+ add_subdirectory(tests)
+endif()
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/tpxio.h"
#include "gromacs/mdtypes/state.h"
+#include "gromacs/utility/enumerationhelpers.h"
template<typename AllocatorType>
static void bcastPaddedRVecVector(MPI_Comm communicator,
block_bc(communicator, state->natoms);
block_bc(communicator, state->flags);
- for (int i = 0; i < estNR; i++)
+ for (auto i : gmx::EnumerationArray<StateEntry, bool>::keys())
{
- if (state->flags & (1 << i))
+ if (state->flags & enumValueToBitMask(i))
{
switch (i)
{
- case estLAMBDA: nblock_bc(communicator, efptNR, state->lambda.data()); break;
- case estFEPSTATE: block_bc(communicator, state->fep_state); break;
- case estBOX: block_bc(communicator, state->box); break;
- case estX: bcastPaddedRVecVector(communicator, &state->x, state->natoms); break;
+ case StateEntry::Lambda:
+ nblock_bc(communicator,
+ static_cast<int>(FreeEnergyPerturbationCouplingType::Count),
+ state->lambda.data());
+ break;
+ case StateEntry::FepState: block_bc(communicator, state->fep_state); break;
+ case StateEntry::Box: block_bc(communicator, state->box); break;
+ case StateEntry::X:
+ bcastPaddedRVecVector(communicator, &state->x, state->natoms);
+ break;
default:
GMX_RELEASE_ASSERT(false,
"The state has a dynamic entry, while no dynamic entries "
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int aj = ilist.iatoms[i + j + 2];
real coeff = ffparams.iparams[ilist.iatoms[i + j]].vsiten.a;
real m_aj;
- if (moltype.atoms.atom[aj].ptype == eptVSite)
+ if (moltype.atoms.atom[aj].ptype == ParticleType::VSite)
{
m_aj = vsite_m[aj];
}
}
if (gmx_debug_at)
{
- fprintf(debug, "atom %4d %-20s mass %6.3f\n", a1,
- interaction_function[ilist.functionType].longname, vsite_m[a1]);
+ fprintf(debug,
+ "atom %4d %-20s mass %6.3f\n",
+ a1,
+ interaction_function[ilist.functionType].longname,
+ vsite_m[a1]);
}
}
}
for (a = 0; a < atoms->nr; a++)
{
- if (atoms->atom[a].ptype == eptVSite)
+ if (atoms->atom[a].ptype == ParticleType::VSite)
{
prop[a].mass = vsite_m[a];
}
{
for (size_t a = 0; a < att.size(); a++)
{
- fprintf(debug, "type %zu: m %5.2f t %d q %6.3f con %s con_m %5.3f con_l %5.3f n %d\n",
- a, att[a].prop.mass, att[a].prop.type, att[a].prop.q,
- gmx::boolToString(att[a].prop.bConstr), att[a].prop.con_mass,
- att[a].prop.con_len, att[a].n);
+ fprintf(debug,
+ "type %zu: m %5.2f t %d q %6.3f con %s con_m %5.3f con_l %5.3f n %d\n",
+ a,
+ att[a].prop.mass,
+ att[a].prop.type,
+ att[a].prop.q,
+ gmx::boolToString(att[a].prop.bConstr),
+ att[a].prop.con_mass,
+ att[a].prop.con_len,
+ att[a].n);
}
}
lj.d2 = c6 * ljDisp->d2 + c12 * ljRep->d2;
lj.md3 = c6 * ljDisp->md3 + c12 * ljRep->md3;
- real pot_lj = energyDriftAtomPair(prop_i->bConstr, prop_j->bConstr, s2, s2i_2d, s2j_2d,
- rlist - rlj, &lj);
+ real pot_lj = energyDriftAtomPair(
+ prop_i->bConstr, prop_j->bConstr, s2, s2i_2d, s2j_2d, rlist - rlj, &lj);
// Set -V' and V'' at the cut-off for Coulomb
pot_derivatives_t elec_qq;
elec_qq.d2 = elec->d2 * prop_i->q * prop_j->q;
elec_qq.md3 = 0;
- real pot_q = energyDriftAtomPair(prop_i->bConstr, prop_j->bConstr, s2, s2i_2d, s2j_2d,
- rlist - rcoulomb, &elec_qq);
+ real pot_q = energyDriftAtomPair(
+ prop_i->bConstr, prop_j->bConstr, s2, s2i_2d, s2j_2d, rlist - rcoulomb, &elec_qq);
// Note that attractive and repulsive potentials for individual
// pairs can partially cancel.
{
real kT_fac;
- if (ir.eI == eiBD)
+ if (ir.eI == IntegrationAlgorithm::BD)
{
/* Get the displacement distribution from the random component only.
* With accurate integration the systematic (force) displacement
* should be negligible (unless nstlist is extremely large, which
* you wouldn't do anyhow).
*/
- kT_fac = 2 * BOLTZ * temperature * timePeriod;
+ kT_fac = 2 * gmx::c_boltz * temperature * timePeriod;
if (ir.bd_fric > 0)
{
/* This is directly sigma^2 of the displacement */
}
else
{
- kT_fac = BOLTZ * temperature * gmx::square(timePeriod);
+ kT_fac = gmx::c_boltz * temperature * gmx::square(timePeriod);
}
return kT_fac;
/* TODO: Obtain masses through (future) integrator functionality
* to avoid scattering the code with (or forgetting) checks.
*/
- const bool setMassesToOne = (ir.eI == eiBD && ir.bd_fric > 0);
+ const bool setMassesToOne = (ir.eI == IntegrationAlgorithm::BD && ir.bd_fric > 0);
const auto att = getVerletBufferAtomtypes(mtop, setMassesToOne);
GMX_ASSERT(!att.empty(), "We expect at least one type");
pot_derivatives_t ljRep = { 0, 0, 0 };
real repPow = mtop.ffparams.reppow;
- if (ir.vdwtype == evdwCUT)
+ if (ir.vdwtype == VanDerWaalsType::Cut)
{
real sw_range, md3_pswf;
switch (ir.vdw_modifier)
{
- case eintmodNONE:
- case eintmodPOTSHIFT:
+ case InteractionModifiers::None:
+ case InteractionModifiers::PotShift:
/* -dV/dr of -r^-6 and r^-reppow */
ljDisp.md1 = -6 * std::pow(ir.rvdw, -7.0);
ljRep.md1 = repPow * std::pow(ir.rvdw, -(repPow + 1));
/* The contribution of the higher derivatives is negligible */
break;
- case eintmodFORCESWITCH:
+ case InteractionModifiers::ForceSwitch:
/* At the cut-off: V=V'=V''=0, so we use only V''' */
ljDisp.md3 = -md3_force_switch(6.0, ir.rvdw_switch, ir.rvdw);
ljRep.md3 = md3_force_switch(repPow, ir.rvdw_switch, ir.rvdw);
break;
- case eintmodPOTSWITCH:
+ case InteractionModifiers::PotSwitch:
/* At the cut-off: V=V'=V''=0.
* V''' is given by the original potential times
* the third derivative of the switch function.
"interactions");
}
- elfac = ONE_4PI_EPS0 / ir.epsilon_r;
+ elfac = gmx::c_one4PiEps0 / ir.epsilon_r;
// Determine the 1st and 2nd derivative for the electostatics
pot_derivatives_t elec = { 0, 0, 0 };
- if (ir.coulombtype == eelCUT || EEL_RF(ir.coulombtype))
+ if (ir.coulombtype == CoulombInteractionType::Cut || EEL_RF(ir.coulombtype))
{
real eps_rf, k_rf;
- if (ir.coulombtype == eelCUT)
+ if (ir.coulombtype == CoulombInteractionType::Cut)
{
eps_rf = 1;
k_rf = 0;
}
else
{
- /* epsilon_rf = infinity */
+ /* reactionFieldPermitivity = infinity */
k_rf = 0.5 / gmx::power3(ir.rcoulomb);
}
}
}
elec.d2 = elfac * (2.0 / gmx::power3(ir.rcoulomb) + 2 * k_rf);
}
- else if (EEL_PME(ir.coulombtype) || ir.coulombtype == eelEWALD)
+ else if (EEL_PME(ir.coulombtype) || ir.coulombtype == CoulombInteractionType::Ewald)
{
real b, rc, br;
/* Calculate the average energy drift at the last step
* of the nstlist steps at which the pair-list is used.
*/
- drift = energyDrift(att, &mtop.ffparams, kT_fac, &ljDisp, &ljRep, &elec, ir.rvdw,
- ir.rcoulomb, rl, boxVolume);
+ drift = energyDrift(
+ att, &mtop.ffparams, kT_fac, &ljDisp, &ljRep, &elec, ir.rvdw, ir.rcoulomb, rl, boxVolume);
/* Correct for the fact that we are using a Ni x Nj particle pair list
* and not a 1 x 1 particle pair list. This reduces the drift.
if (debug)
{
- fprintf(debug, "ib %3d %3d %3d rb %.3f %dx%d fac %.3f drift %.1e\n", ib0, ib, ib1, rb,
- listSetup.cluster_size_i, listSetup.cluster_size_j,
- nb_clust_frac_pairs_not_in_list_at_cutoff, drift);
+ fprintf(debug,
+ "ib %3d %3d %3d rb %.3f %dx%d fac %.3f drift %.1e\n",
+ ib0,
+ ib,
+ ib1,
+ rb,
+ listSetup.cluster_size_i,
+ listSetup.cluster_size_j,
+ nb_clust_frac_pairs_not_in_list_at_cutoff,
+ drift);
}
if (std::abs(drift) > ir.verletbuf_tol)
real s2_3d;
get_atom_sigma2(kT_fac, &propAtom, &s2_2d, &s2_3d);
- real chancePerAtom = energyDriftAtomPair(propAtom.bConstr, false, s2_2d + s2_3d, s2_2d, 0,
- cellSize, &boundaryInteraction);
+ real chancePerAtom = energyDriftAtomPair(
+ propAtom.bConstr, false, s2_2d + s2_3d, s2_2d, 0, cellSize, &boundaryInteraction);
if (propAtom.bConstr)
{
}
}
real s2_3d = kT_fac / massSum;
- chance += energyDriftAtomPair(false, false, s2_3d, 0, 0, cellSize - 2 * maxComCogDistance,
- &boundaryInteraction);
+ chance += energyDriftAtomPair(
+ false, false, s2_3d, 0, 0, cellSize - 2 * maxComCogDistance, &boundaryInteraction);
}
return chance;
{
const gmx_moltype_t& moltype = mtop.moltype[molblock.type];
chance += molblock.nmol
- * chanceOfUpdateGroupCrossingCell(moltype, mtop.ffparams,
- updateGrouping[molblock.type], kT_fac, cellSize);
+ * chanceOfUpdateGroupCrossingCell(
+ moltype, mtop.ffparams, updateGrouping[molblock.type], kT_fac, cellSize);
}
return chance;
PartitioningPerMoltype updateGrouping,
real chanceRequested)
{
- if (!EI_DYNAMICS(ir.eI) || (EI_MD(ir.eI) && ir.etc == etcNO))
+ if (!EI_DYNAMICS(ir.eI) || (EI_MD(ir.eI) && ir.etc == TemperatureCoupling::No))
{
return minCellSizeFromPairlistBuffer(ir);
}
*/
const real temperature = maxReferenceTemperature(ir);
- const bool setMassesToOne = (ir.eI == eiBD && ir.bd_fric > 0);
+ const bool setMassesToOne = (ir.eI == IntegrationAlgorithm::BD && ir.bd_fric > 0);
const auto atomtypes = getVerletBufferAtomtypes(mtop, setMassesToOne);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2012,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void calc_mu(int start,
int homenr,
gmx::ArrayRef<const gmx::RVec> x,
- const real q[],
- const real qB[],
- int nChargePerturbed,
+ gmx::ArrayRef<const real> q,
+ gmx::ArrayRef<const real> qB,
+ bool havePerturbedCharges,
dvec mu,
dvec mu_B)
{
mu_x = mu_y = mu_z = 0.0;
#pragma omp parallel for reduction(+: mu_x, mu_y, mu_z) schedule(static) \
- num_threads(gmx_omp_nthreads_get(emntDefault))
+ num_threads(gmx_omp_nthreads_get(ModuleMultiThread::Default))
for (int i = start; i < end; i++)
{
// Trivial OpenMP region that cannot throw
for (m = 0; (m < DIM); m++)
{
- mu[m] *= ENM2DEBYE;
+ mu[m] *= gmx::c_enm2Debye;
}
- if (nChargePerturbed)
+ if (havePerturbedCharges)
{
mu_x = mu_y = mu_z = 0.0;
#pragma omp parallel for reduction(+: mu_x, mu_y, mu_z) schedule(static) \
- num_threads(gmx_omp_nthreads_get(emntDefault))
+ num_threads(gmx_omp_nthreads_get(ModuleMultiThread::Default))
for (int i = start; i < end; i++)
{
// Trivial OpenMP region that cannot throw
mu_y += qB[i] * x[i][YY];
mu_z += qB[i] * x[i][ZZ];
}
- mu_B[XX] = mu_x * ENM2DEBYE;
- mu_B[YY] = mu_y * ENM2DEBYE;
- mu_B[ZZ] = mu_z * ENM2DEBYE;
+ mu_B[XX] = mu_x * gmx::c_enm2Debye;
+ mu_B[YY] = mu_y * gmx::c_enm2Debye;
+ mu_B[ZZ] = mu_z * gmx::c_enm2Debye;
}
else
{
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2010,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void calc_mu(int start,
int homenr,
gmx::ArrayRef<const gmx::RVec> x,
- const real q[],
- const real qB[],
- int nChargePerturbed,
+ gmx::ArrayRef<const real> q,
+ gmx::ArrayRef<const real> qB,
+ bool havePerturbedCharges,
dvec mu,
dvec mu_B);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
if (bScrewPBC)
{
- int isx = IS2X(i);
+ int isx = gmx::shiftIndexToXDim(i);
/* We should correct all odd x-shifts, but the range of isx is -2 to 2 */
if (isx == 1 || isx == -1)
{
{
matrix x_times_f;
- int nthreads = gmx_omp_nthreads_get_simple_rvec_task(emntDefault, nxf * 9);
+ int nthreads = gmx_omp_nthreads_get_simple_rvec_task(ModuleMultiThread::Default, nxf * 9);
GMX_ASSERT(nthreads >= 1, "Avoids uninitialized x_times_f (warning)");
int start = (nxf * thread) / nthreads;
int end = std::min(nxf * (thread + 1) / nthreads, nxf);
- calc_x_times_f(end - start, x + start, f + start, bScrewPBC, box,
+ calc_x_times_f(end - start,
+ x + start,
+ f + start,
+ bScrewPBC,
+ box,
thread == 0 ? x_times_f : xf_buf[thread * 3]);
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2012,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
double compute_io(const t_inputrec* ir, int natoms, const SimulationGroups& groups, int nrener, int nrepl)
{
- int nsteps = ir->nsteps;
- int i, nxtcatoms = 0;
+ int nsteps = ir->nsteps;
+ int nxtcatoms = 0;
int nstx, nstv, nstf, nste, nstlog, nstxtc;
double cio;
/* t_energy contains doubles, but real is written to edr */
cio += (1.0 * nste) * nrener * 3 * sizeof(real);
- if ((ir->efep != efepNO || ir->bSimTemp) && (ir->fepvals->nstdhdl > 0))
+ if ((ir->efep != FreeEnergyPerturbationType::No || ir->bSimTemp) && (ir->fepvals->nstdhdl > 0))
{
int ndh = ir->fepvals->n_lambda;
int ndhdl = 0;
int nchars = 0;
- for (i = 0; i < efptNR; i++)
+ for (auto i : keysOf(ir->fepvals->separate_dvdl))
{
if (ir->fepvals->separate_dvdl[i])
{
}
}
- if (ir->fepvals->separate_dhdl_file == esepdhdlfileYES)
+ if (ir->fepvals->separate_dhdl_file == SeparateDhdlFile::Yes)
{
nchars = 8 + ndhdl * 8 + ndh * 10; /* time data ~8 chars/entry, dH data ~10 chars/entry */
- if (ir->expandedvals->elmcmove > elmcmoveNO)
+ if (ir->expandedvals->elmcmove > LambdaMoveCalculation::No)
{
nchars += 5; /* alchemical state */
}
- if (ir->fepvals->edHdLPrintEnergy != edHdLPrintEnergyNO)
+ if (ir->fepvals->edHdLPrintEnergy != FreeEnergyPrintEnergy::No)
{
nchars += 12; /* energy for dhdl */
}
if (ir->fepvals->dh_hist_size <= 0)
{
int ndh_tot = ndh + ndhdl;
- if (ir->expandedvals->elmcmove > elmcmoveNO)
+ if (ir->expandedvals->elmcmove > LambdaMoveCalculation::No)
{
ndh_tot += 1;
}
- if (ir->fepvals->edHdLPrintEnergy != edHdLPrintEnergyNO)
+ if (ir->fepvals->edHdLPrintEnergy != FreeEnergyPrintEnergy::No)
{
ndh_tot += 1;
}
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/gmxlib/nrnb.h"
+#include "gromacs/math/arrayrefwithpadding.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
pull_t* pull_work,
FILE* log_p,
const t_commrec* cr_p,
+ bool useUpdateGroups,
const gmx_multisim_t* ms,
t_nrnb* nrnb,
gmx_wallcycle* wcycle_p,
int numConstraints,
int numSettles);
~Impl();
- void setConstraints(gmx_localtop_t* top,
- int numAtoms,
- int numHomeAtoms,
- real* masses,
- real* inverseMasses,
- bool hasMassPerturbedAtoms,
- real lambda,
- unsigned short* cFREEZE);
+ void setConstraints(gmx_localtop_t* top,
+ int numAtoms,
+ int numHomeAtoms,
+ gmx::ArrayRef<const real> masses,
+ gmx::ArrayRef<const real> inverseMasses,
+ bool hasMassPerturbedAtoms,
+ real lambda,
+ gmx::ArrayRef<const unsigned short> cFREEZE);
bool apply(bool bLog,
bool bEner,
int64_t step,
//! Number of local atoms.
int numHomeAtoms_ = 0;
//! Atoms masses.
- real* masses_;
+ gmx::ArrayRef<const real> masses_;
//! Inverse masses.
- real* inverseMasses_;
+ gmx::ArrayRef<const real> inverseMasses_;
//! If there are atoms with perturbed mass (for FEP).
bool hasMassPerturbedAtoms_;
//! FEP lambda value.
real lambda_;
//! Freeze groups data
- unsigned short* cFREEZE_;
+ gmx::ArrayRef<const unsigned short> cFREEZE_;
//! Whether we need to do pbc for handling bonds.
bool pbcHandlingRequired_ = false;
}
//! Clears constraint quantities for atoms in nonlocal region.
-static void clear_constraint_quantity_nonlocal(gmx_domdec_t* dd, ArrayRef<RVec> q)
+static void clear_constraint_quantity_nonlocal(const gmx_domdec_t& dd, ArrayRef<RVec> q)
{
- int nonlocal_at_start, nonlocal_at_end, at;
+ int nonlocal_at_start, nonlocal_at_end;
dd_get_constraint_range(dd, &nonlocal_at_start, &nonlocal_at_end);
- for (at = nonlocal_at_start; at < nonlocal_at_end; at++)
+ for (int at = nonlocal_at_start; at < nonlocal_at_end; at++)
{
clear_rvec(q[at]);
}
}
-void too_many_constraint_warnings(int eConstrAlg, int warncount)
+void too_many_constraint_warnings(ConstraintAlgorithm eConstrAlg, int warncount)
{
- gmx_fatal(
- FARGS,
- "Too many %s warnings (%d)\n"
- "If you know what you are doing you can %s"
- "set the environment variable GMX_MAXCONSTRWARN to -1,\n"
- "but normally it is better to fix the problem",
- (eConstrAlg == econtLINCS) ? "LINCS" : "SETTLE", warncount,
- (eConstrAlg == econtLINCS) ? "adjust the lincs warning threshold in your mdp file\nor " : "\n");
+ gmx_fatal(FARGS,
+ "Too many %s warnings (%d)\n"
+ "If you know what you are doing you can %s"
+ "set the environment variable GMX_MAXCONSTRWARN to -1,\n"
+ "but normally it is better to fix the problem",
+ (eConstrAlg == ConstraintAlgorithm::Lincs) ? "LINCS" : "SETTLE",
+ warncount,
+ (eConstrAlg == ConstraintAlgorithm::Lincs)
+ ? "adjust the lincs warning threshold in your mdp file\nor "
+ : "\n");
}
//! Writes out coordinates.
if (DOMAINDECOMP(cr))
{
dd = cr->dd;
- dd_get_constraint_range(dd, &dd_ac0, &dd_ac1);
+ dd_get_constraint_range(*dd, &dd_ac0, &dd_ac1);
start = 0;
homenr = dd_ac1;
}
ii = i;
}
mtopGetAtomAndResidueName(mtop, ii, &molb, &anm, &resnr, &resnm, nullptr);
- gmx_fprintf_pdb_atomline(out, epdbATOM, ii + 1, anm, ' ', resnm, ' ', resnr, ' ',
- 10 * x[i][XX], 10 * x[i][YY], 10 * x[i][ZZ], 1.0, 0.0, "");
+ gmx_fprintf_pdb_atomline(out,
+ PdbRecordType::Atom,
+ ii + 1,
+ anm,
+ ' ',
+ resnm,
+ ' ',
+ resnr,
+ ' ',
+ 10 * x[i][XX],
+ 10 * x[i][YY],
+ 10 * x[i][ZZ],
+ 1.0,
+ 0.0,
+ "");
}
fprintf(out, "TER\n");
tensor constraintsVirial,
ConstraintVariable econq)
{
- return impl_->apply(bLog, bEner, step, delta_step, step_scaling, std::move(x),
- std::move(xprime), min_proj, box, lambda, dvdlambda, std::move(v),
- computeVirial, constraintsVirial, econq);
+ return impl_->apply(bLog,
+ bEner,
+ step,
+ delta_step,
+ step_scaling,
+ std::move(x),
+ std::move(xprime),
+ min_proj,
+ box,
+ lambda,
+ dvdlambda,
+ std::move(v),
+ computeVirial,
+ constraintsVirial,
+ econq);
}
bool Constraints::Impl::apply(bool bLog,
char buf[22];
int nth;
- wallcycle_start(wcycle, ewcCONSTR);
+ wallcycle_start(wcycle, WallCycleCounter::Constr);
if (econq == ConstraintVariable::ForceDispl && !EI_ENERGY_MINIMIZATION(ir.eI))
{
invdt = 1.0 / scaled_delta_t;
}
- if (ir.efep != efepNO && EI_DYNAMICS(ir.eI))
+ if (ir.efep != FreeEnergyPerturbationType::No && EI_DYNAMICS(ir.eI))
{
/* Set the constraint lengths for the step at which this configuration
* is meant to be. The invmasses should not be changed.
if (nsettle > 0)
{
- nth = gmx_omp_nthreads_get(emntSETTLE);
+ nth = gmx_omp_nthreads_get(ModuleMultiThread::Settle);
}
else
{
*/
if (cr->dd)
{
- dd_move_x_constraints(cr->dd, box, x.unpaddedArrayRef(), xprime.unpaddedArrayRef(),
+ dd_move_x_constraints(cr->dd,
+ box,
+ x.unpaddedArrayRef(),
+ xprime.unpaddedArrayRef(),
econq == ConstraintVariable::Positions);
if (!v.empty())
* We never actually use these values, but we do increment them,
* so we should avoid uninitialized variables and overflows.
*/
- clear_constraint_quantity_nonlocal(cr->dd, v.unpaddedArrayRef());
+ clear_constraint_quantity_nonlocal(*cr->dd, v.unpaddedArrayRef());
}
}
if (lincsd != nullptr)
{
- bOK = constrain_lincs(bLog || bEner, ir, step, lincsd, inverseMasses_, cr, ms, x, xprime,
- min_proj, box, pbc_null, hasMassPerturbedAtoms_, lambda, dvdlambda,
- invdt, v.unpaddedArrayRef(), computeVirial, constraintsVirial, econq,
- nrnb, maxwarn, &warncount_lincs);
+ bOK = constrain_lincs(bLog || bEner,
+ ir,
+ step,
+ lincsd,
+ inverseMasses_,
+ cr,
+ ms,
+ x,
+ xprime,
+ min_proj,
+ box,
+ pbc_null,
+ hasMassPerturbedAtoms_,
+ lambda,
+ dvdlambda,
+ invdt,
+ v.unpaddedArrayRef(),
+ computeVirial,
+ constraintsVirial,
+ econq,
+ nrnb,
+ maxwarn,
+ &warncount_lincs);
if (!bOK && maxwarn < INT_MAX)
{
if (log != nullptr)
{
- fprintf(log, "Constraint error in algorithm %s at step %s\n",
- econstr_names[econtLINCS], gmx_step_str(step, buf));
+ fprintf(log,
+ "Constraint error in algorithm %s at step %s\n",
+ enumValueToString(ConstraintAlgorithm::Lincs),
+ gmx_step_str(step, buf));
}
bDump = TRUE;
}
if (shaked != nullptr)
{
- bOK = constrain_shake(log, shaked.get(), inverseMasses_, *idef, ir, x.unpaddedArrayRef(),
- xprime.unpaddedArrayRef(), min_proj, pbc_null, nrnb, lambda,
- dvdlambda, invdt, v.unpaddedArrayRef(), computeVirial,
- constraintsVirial, maxwarn < INT_MAX, econq);
+ bOK = constrain_shake(log,
+ shaked.get(),
+ inverseMasses_,
+ *idef,
+ ir,
+ x.unpaddedArrayRef(),
+ xprime.unpaddedArrayRef(),
+ min_proj,
+ pbc_null,
+ nrnb,
+ lambda,
+ dvdlambda,
+ invdt,
+ v.unpaddedArrayRef(),
+ computeVirial,
+ constraintsVirial,
+ maxwarn < INT_MAX,
+ econq);
if (!bOK && maxwarn < INT_MAX)
{
if (log != nullptr)
{
- fprintf(log, "Constraint error in algorithm %s at step %s\n",
- econstr_names[econtSHAKE], gmx_step_str(step, buf));
+ fprintf(log,
+ "Constraint error in algorithm %s at step %s\n",
+ enumValueToString(ConstraintAlgorithm::Shake),
+ gmx_step_str(step, buf));
}
bDump = TRUE;
}
clear_mat(threadConstraintsVirial[th]);
}
- csettle(*settled, nth, th, pbc_null, x, xprime, invdt, v, computeVirial,
+ csettle(*settled,
+ nth,
+ th,
+ pbc_null,
+ x,
+ xprime,
+ invdt,
+ v,
+ computeVirial,
th == 0 ? constraintsVirial : threadConstraintsVirial[th],
th == 0 ? &bSettleErrorHasOccurred0 : &bSettleErrorHasOccurred[th]);
}
if (start_th >= 0 && end_th - start_th > 0)
{
- settle_proj(*settled, econq, end_th - start_th,
+ settle_proj(*settled,
+ econq,
+ end_th - start_th,
settle.iatoms.data() + start_th * (1 + NRAL(F_SETTLE)),
- pbc_null, x.unpaddedArrayRef(), xprime.unpaddedArrayRef(),
- min_proj, calcvir_atom_end,
+ pbc_null,
+ x.unpaddedArrayRef(),
+ xprime.unpaddedArrayRef(),
+ min_proj,
+ calcvir_atom_end,
th == 0 ? constraintsVirial : threadConstraintsVirial[th]);
}
}
warncount_settle++;
if (warncount_settle > maxwarn)
{
- too_many_constraint_warnings(-1, warncount_settle);
+ too_many_constraint_warnings(ConstraintAlgorithm::Count, warncount_settle);
}
bDump = TRUE;
if (bDump)
{
- dump_confs(log, step, mtop, start, numHomeAtoms_, cr, x.unpaddedArrayRef(),
- xprime.unpaddedArrayRef(), box);
+ dump_confs(log, step, mtop, start, numHomeAtoms_, cr, x.unpaddedArrayRef(), xprime.unpaddedArrayRef(), box);
}
if (econq == ConstraintVariable::Positions)
t = ir.init_t;
}
set_pbc(&pbc, ir.pbcType, box);
- pull_constraint(pull_work, masses_, &pbc, cr, ir.delta_t, t,
- as_rvec_array(x.unpaddedArrayRef().data()),
- as_rvec_array(xprime.unpaddedArrayRef().data()),
- as_rvec_array(v.unpaddedArrayRef().data()), constraintsVirial);
+ pull_constraint(pull_work,
+ masses_,
+ &pbc,
+ cr,
+ ir.delta_t,
+ t,
+ x.unpaddedArrayRef(),
+ xprime.unpaddedArrayRef(),
+ v.unpaddedArrayRef(),
+ constraintsVirial);
}
if (ed && delta_step > 0)
{
/* apply the essential dynamics constraints here */
- do_edsam(&ir, step, cr, as_rvec_array(xprime.unpaddedArrayRef().data()),
- as_rvec_array(v.unpaddedArrayRef().data()), box, ed);
+ do_edsam(&ir, step, cr, xprime.unpaddedArrayRef(), v.unpaddedArrayRef(), box, ed);
}
}
- wallcycle_stop(wcycle, ewcCONSTR);
+ wallcycle_stop(wcycle, WallCycleCounter::Constr);
const bool haveVelocities = (!v.empty() || econq == ConstraintVariable::Velocities);
- if (haveVelocities && cFREEZE_)
+ if (haveVelocities && !cFREEZE_.empty())
{
/* Set the velocities of frozen dimensions to zero */
ArrayRef<RVec> vRef;
vRef = v.unpaddedArrayRef();
}
- int gmx_unused numThreads = gmx_omp_nthreads_get(emntUpdate);
+ int gmx_unused numThreads = gmx_omp_nthreads_get(ModuleMultiThread::Update);
#pragma omp parallel for num_threads(numThreads) schedule(static)
for (int i = 0; i < numHomeAtoms_; i++)
gmx::ArrayRef<const t_iparams> iparams,
FlexibleConstraintTreatment flexibleConstraintTreatment)
{
- return makeAtomsToConstraintsList(moltype.atoms.nr, makeConstArrayRef(moltype.ilist), iparams,
- flexibleConstraintTreatment);
+ return makeAtomsToConstraintsList(
+ moltype.atoms.nr, makeConstArrayRef(moltype.ilist), iparams, flexibleConstraintTreatment);
}
//! Return the number of flexible constraints in the \c ilist and \c iparams.
return at2s;
}
-void Constraints::Impl::setConstraints(gmx_localtop_t* top,
- int numAtoms,
- int numHomeAtoms,
- real* masses,
- real* inverseMasses,
- const bool hasMassPerturbedAtoms,
- const real lambda,
- unsigned short* cFREEZE)
+void Constraints::Impl::setConstraints(gmx_localtop_t* top,
+ int numAtoms,
+ int numHomeAtoms,
+ gmx::ArrayRef<const real> masses,
+ gmx::ArrayRef<const real> inverseMasses,
+ const bool hasMassPerturbedAtoms,
+ const real lambda,
+ gmx::ArrayRef<const unsigned short> cFREEZE)
{
numAtoms_ = numAtoms;
numHomeAtoms_ = numHomeAtoms;
/* With DD we might also need to call LINCS on a domain no constraints for
* communicating coordinates to other nodes that do have constraints.
*/
- if (ir.eConstrAlg == econtLINCS)
+ if (ir.eConstrAlg == ConstraintAlgorithm::Lincs)
{
set_lincs(*idef, numAtoms_, inverseMasses_, lambda_, EI_DYNAMICS(ir.eI), cr, lincsd);
}
- if (ir.eConstrAlg == econtSHAKE)
+ if (ir.eConstrAlg == ConstraintAlgorithm::Shake)
{
if (cr->dd)
{
}
}
-void Constraints::setConstraints(gmx_localtop_t* top,
- const int numAtoms,
- const int numHomeAtoms,
- real* masses,
- real* inverseMasses,
- const bool hasMassPerturbedAtoms,
- const real lambda,
- unsigned short* cFREEZE)
+void Constraints::setConstraints(gmx_localtop_t* top,
+ const int numAtoms,
+ const int numHomeAtoms,
+ gmx::ArrayRef<const real> masses,
+ gmx::ArrayRef<const real> inverseMasses,
+ const bool hasMassPerturbedAtoms,
+ const real lambda,
+ gmx::ArrayRef<const unsigned short> cFREEZE)
{
- impl_->setConstraints(top, numAtoms, numHomeAtoms, masses, inverseMasses, hasMassPerturbedAtoms,
- lambda, cFREEZE);
+ impl_->setConstraints(
+ top, numAtoms, numHomeAtoms, masses, inverseMasses, hasMassPerturbedAtoms, lambda, cFREEZE);
}
/*! \brief Makes a per-moleculetype container of mappings from atom
pull_t* pull_work,
FILE* log,
const t_commrec* cr,
+ const bool useUpdateGroups,
const gmx_multisim_t* ms,
t_nrnb* nrnb,
gmx_wallcycle* wcycle,
bool pbcHandlingRequired,
int numConstraints,
int numSettles) :
- impl_(new Impl(mtop, ir, pull_work, log, cr, ms, nrnb, wcycle, pbcHandlingRequired, numConstraints, numSettles))
+ impl_(new Impl(mtop, ir, pull_work, log, cr, useUpdateGroups, ms, nrnb, wcycle, pbcHandlingRequired, numConstraints, numSettles))
{
}
pull_t* pull_work,
FILE* log_p,
const t_commrec* cr_p,
+ const bool mayHaveSplitConstraints,
const gmx_multisim_t* ms_p,
t_nrnb* nrnb_p,
gmx_wallcycle* wcycle_p,
nrnb(nrnb_p),
wcycle(wcycle_p)
{
- if (numConstraints + numSettles > 0 && ir.epc == epcMTTK)
+ if (numConstraints + numSettles > 0 && ir.epc == PressureCoupling::Mttk)
{
gmx_fatal(FARGS, "Constraints are not implemented with MTTK pressure control.");
}
}
}
- if (ir.eConstrAlg == econtLINCS)
+ // When there are multiple PP domains and update groups are not in use,
+ // the constraints might be split across them.
+ if (ir.eConstrAlg == ConstraintAlgorithm::Lincs)
{
- lincsd = init_lincs(log, mtop, nflexcon, at2con_mt,
- DOMAINDECOMP(cr) && ddHaveSplitConstraints(*cr->dd), ir.nLincsIter,
- ir.nProjOrder);
+ lincsd = init_lincs(
+ log, mtop, nflexcon, at2con_mt, mayHaveSplitConstraints, ir.nLincsIter, ir.nProjOrder);
}
- if (ir.eConstrAlg == econtSHAKE)
+ if (ir.eConstrAlg == ConstraintAlgorithm::Shake)
{
- if (DOMAINDECOMP(cr) && ddHaveSplitConstraints(*cr->dd))
+ if (mayHaveSplitConstraints)
{
gmx_fatal(FARGS,
- "SHAKE is not supported with domain decomposition and constraint that "
+ "SHAKE is not supported with domain decomposition and constraints that "
"cross domain boundaries, use LINCS");
}
if (nflexcon)
}
/* Allocate thread-local work arrays */
- int nthreads = gmx_omp_nthreads_get(emntSETTLE);
+ int nthreads = gmx_omp_nthreads_get(ModuleMultiThread::Settle);
if (nthreads > 1 && threadConstraintsVirial == nullptr)
{
snew(threadConstraintsVirial, nthreads);
bool computeEnergy = false;
bool computeVirial = false;
/* constrain the current position */
- constr->apply(needsLogging, computeEnergy, step, 0, 1.0, x, x, {}, box, lambda, &dvdl_dum, {},
- computeVirial, nullptr, gmx::ConstraintVariable::Positions);
+ constr->apply(needsLogging,
+ computeEnergy,
+ step,
+ 0,
+ 1.0,
+ x,
+ x,
+ {},
+ box,
+ lambda,
+ &dvdl_dum,
+ {},
+ computeVirial,
+ nullptr,
+ gmx::ConstraintVariable::Positions);
if (EI_VV(ir->eI))
{
/* constrain the inital velocity, and save it */
/* also may be useful if we need the ekin from the halfstep for velocity verlet */
- constr->apply(needsLogging, computeEnergy, step, 0, 1.0, x, v, v.unpaddedArrayRef(), box, lambda,
- &dvdl_dum, {}, computeVirial, nullptr, gmx::ConstraintVariable::Velocities);
+ constr->apply(needsLogging,
+ computeEnergy,
+ step,
+ 0,
+ 1.0,
+ x,
+ v,
+ v.unpaddedArrayRef(),
+ box,
+ lambda,
+ &dvdl_dum,
+ {},
+ computeVirial,
+ nullptr,
+ gmx::ConstraintVariable::Velocities);
}
/* constrain the inital velocities at t-dt/2 */
- if (EI_STATE_VELOCITY(ir->eI) && ir->eI != eiVV)
+ if (EI_STATE_VELOCITY(ir->eI) && ir->eI != IntegrationAlgorithm::VV)
{
auto subX = x.paddedArrayRef().subArray(start, end);
auto subV = v.paddedArrayRef().subArray(start, end);
fprintf(fplog, "\nConstraining the coordinates at t0-dt (step %s)\n", gmx_step_str(step, buf));
}
dvdl_dum = 0;
- constr->apply(needsLogging, computeEnergy, step, -1, 1.0, x, savex.arrayRefWithPadding(),
- {}, box, lambda, &dvdl_dum, v, computeVirial, nullptr,
+ constr->apply(needsLogging,
+ computeEnergy,
+ step,
+ -1,
+ 1.0,
+ x,
+ savex.arrayRefWithPadding(),
+ {},
+ box,
+ lambda,
+ &dvdl_dum,
+ v,
+ computeVirial,
+ nullptr,
gmx::ConstraintVariable::Positions);
for (i = start; i < end; i++)
{
if (constr != nullptr)
{
- constr->apply(do_log, do_ene, step, 1, 1.0, state->x.arrayRefWithPadding(),
- state->v.arrayRefWithPadding(), state->v.arrayRefWithPadding().unpaddedArrayRef(),
- state->box, state->lambda[efptBONDED], dvdlambda, ArrayRefWithPadding<RVec>(),
- computeVirial, constraintsVirial, ConstraintVariable::Velocities);
+ constr->apply(do_log,
+ do_ene,
+ step,
+ 1,
+ 1.0,
+ state->x.arrayRefWithPadding(),
+ state->v.arrayRefWithPadding(),
+ state->v.arrayRefWithPadding().unpaddedArrayRef(),
+ state->box,
+ state->lambda[FreeEnergyPerturbationCouplingType::Bonded],
+ dvdlambda,
+ ArrayRefWithPadding<RVec>(),
+ computeVirial,
+ constraintsVirial,
+ ConstraintVariable::Velocities);
}
}
{
if (constr != nullptr)
{
- constr->apply(do_log, do_ene, step, 1, 1.0, state->x.arrayRefWithPadding(), std::move(xp),
- ArrayRef<RVec>(), state->box, state->lambda[efptBONDED], dvdlambda,
- state->v.arrayRefWithPadding(), computeVirial, constraintsVirial,
+ constr->apply(do_log,
+ do_ene,
+ step,
+ 1,
+ 1.0,
+ state->x.arrayRefWithPadding(),
+ std::move(xp),
+ ArrayRef<RVec>(),
+ state->box,
+ state->lambda[FreeEnergyPerturbationCouplingType::Bonded],
+ dvdlambda,
+ state->v.arrayRefWithPadding(),
+ computeVirial,
+ constraintsVirial,
ConstraintVariable::Positions);
}
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
+#include <memory>
+
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/idef.h"
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/real.h"
struct t_nrnb;
struct t_pbc;
class t_state;
-
+enum class ConstraintAlgorithm : int;
namespace gmx
{
template<typename T>
pull_t* pull_work,
FILE* log,
const t_commrec* cr,
+ bool haveHaveSplitConstraints,
const gmx_multisim_t* ms,
t_nrnb* nrnb,
gmx_wallcycle* wcycle,
*
* \todo Make this a callback that is called automatically
* once a new domain has been made. */
- void setConstraints(gmx_localtop_t* top,
- int numAtoms,
- int numHomeAtoms,
- real* masses,
- real* inverseMasses,
- bool hasMassPerturbedAtoms,
- real lambda,
- unsigned short* cFREEZE);
+ void setConstraints(gmx_localtop_t* top,
+ int numAtoms,
+ int numHomeAtoms,
+ gmx::ArrayRef<const real> masses,
+ gmx::ArrayRef<const real> inverseMasses,
+ bool hasMassPerturbedAtoms,
+ real lambda,
+ gmx::ArrayRef<const unsigned short> cFREEZE);
/*! \brief Applies constraints to coordinates.
*
//! Implementation type.
class Impl;
//! Implementation object.
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
/*! \brief Generate a fatal error because of too many LINCS/SETTLE warnings. */
-[[noreturn]] void too_many_constraint_warnings(int eConstrAlg, int warncount);
+[[noreturn]] void too_many_constraint_warnings(ConstraintAlgorithm eConstrAlg, int warncount);
/*! \brief Returns whether constraint with parameter \p iparamsIndex is a flexible constraint */
static inline bool isConstraintFlexible(ArrayRef<const t_iparams> iparams, int iparamsIndex)
int64_t step,
t_state* state,
real* dvdlambda,
- gmx_bool computeVirial,
+ bool computeVirial,
tensor constraintsVirial);
/*! \brief Constraint coordinates.
t_state* state,
ArrayRefWithPadding<RVec> xp,
real* dvdlambda,
- gmx_bool computeVirial,
+ bool computeVirial,
tensor constraintsVirial);
} // namespace gmx
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
if (debug)
{
fprintf(debug,
- "Found longer constraint distance: r0 %5.3f r1 %5.3f rmax %5.3f\n", rn0,
- rn1, sqrt(*r2max));
+ "Found longer constraint distance: r0 %5.3f r1 %5.3f rmax %5.3f\n",
+ rn0,
+ rn1,
+ sqrt(*r2max));
for (int a1 = 0; a1 < depth; a1++)
{
- fprintf(debug, " %d %5.3f", path[a1],
+ fprintf(debug,
+ " %d %5.3f",
+ path[a1],
iparams[constr_iatomptr(ia1, ia2, con)[0]].constr.dA);
}
fprintf(debug, " %d %5.3f\n", con, len);
r1 = 0;
count = 0;
- constr_recur(at2con, molt->ilist, iparams, FALSE, at, 0, 1 + ir->nProjOrder, path, r0, r1,
- &r2maxA, &count);
+ constr_recur(
+ at2con, molt->ilist, iparams, FALSE, at, 0, 1 + ir->nProjOrder, path, r0, r1, &r2maxA, &count);
}
- if (ir->efep == efepNO)
+ if (ir->efep == FreeEnergyPerturbationType::No)
{
rmax = sqrt(r2maxA);
}
r0 = 0;
r1 = 0;
count = 0;
- constr_recur(at2con, molt->ilist, iparams, TRUE, at, 0, 1 + ir->nProjOrder, path, r0,
- r1, &r2maxB, &count);
+ constr_recur(
+ at2con, molt->ilist, iparams, TRUE, at, 0, 1 + ir->nProjOrder, path, r0, r1, &r2maxB, &count);
}
lam0 = ir->fepvals->init_lambda;
if (EI_DYNAMICS(ir->eI))
GMX_LOG(mdlog.info)
.appendTextFormatted(
"Maximum distance for %d constraints, at 120 deg. angles, all-trans: %.3f nm",
- 1 + ir->nProjOrder, rmax);
+ 1 + ir->nProjOrder,
+ rmax);
return rmax;
}
#include "gromacs/mdtypes/group.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/boxutilities.h"
#include "gromacs/pbcutil/pbc.h"
static const double sy_const_1[] = { 1. };
static const double sy_const_3[] = { 0.828981543588751, -0.657963087177502, 0.828981543588751 };
-static const double sy_const_5[] = { 0.2967324292201065, 0.2967324292201065, -0.186929716880426,
- 0.2967324292201065, 0.2967324292201065 };
+static const double sy_const_5[] = { 0.2967324292201065,
+ 0.2967324292201065,
+ -0.186929716880426,
+ 0.2967324292201065,
+ 0.2967324292201065 };
-static const double* sy_const[] = { nullptr, sy_const_1, nullptr, sy_const_3, nullptr, sy_const_5 };
+static constexpr std::array<const double*, 6> sy_const = { nullptr, sy_const_1, nullptr,
+ sy_const_3, nullptr, sy_const_5 };
-void update_tcouple(int64_t step,
- const t_inputrec* inputrec,
- t_state* state,
- gmx_ekindata_t* ekind,
- const t_extmass* MassQ,
- const t_mdatoms* md)
+void update_tcouple(int64_t step,
+ const t_inputrec* inputrec,
+ t_state* state,
+ gmx_ekindata_t* ekind,
+ const t_extmass* MassQ,
+ int homenr,
+ gmx::ArrayRef<const unsigned short> cTC)
{
// This condition was explicitly checked in previous version, but should have never been satisfied
// For VV temperature coupling parameters are updated on the current
// step, for the others - one step before.
- if (inputrec->etc == etcNO)
+ if (inputrec->etc == TemperatureCoupling::No)
{
doTemperatureCoupling = false;
}
// subroutines
switch (inputrec->etc)
{
- case etcNO: break;
- case etcBERENDSEN:
+ case TemperatureCoupling::No:
+ case TemperatureCoupling::Andersen:
+ case TemperatureCoupling::AndersenMassive: break;
+ case TemperatureCoupling::Berendsen:
berendsen_tcoupl(inputrec, ekind, dttc, state->therm_integral);
break;
- case etcNOSEHOOVER:
- nosehoover_tcoupl(&(inputrec->opts), ekind, dttc, state->nosehoover_xi.data(),
- state->nosehoover_vxi.data(), MassQ);
+ case TemperatureCoupling::NoseHoover:
+ nosehoover_tcoupl(
+ &(inputrec->opts), ekind, dttc, state->nosehoover_xi, state->nosehoover_vxi, MassQ);
break;
- case etcVRESCALE:
- vrescale_tcoupl(inputrec, step, ekind, dttc, state->therm_integral.data());
+ case TemperatureCoupling::VRescale:
+ vrescale_tcoupl(inputrec, step, ekind, dttc, state->therm_integral);
break;
+ default: gmx_fatal(FARGS, "Unknown temperature coupling algorithm");
}
/* rescale in place here */
if (EI_VV(inputrec->eI))
{
- rescale_velocities(ekind, md, 0, md->homenr, state->v.rvec_array());
+ rescale_velocities(ekind, cTC, 0, homenr, state->v);
}
}
else
t_state* state,
matrix parrinellorahmanMu,
matrix M,
- gmx_bool bInitStep)
+ bool bInitStep)
{
/* Berendsen P-coupling is completely handled after the coordinate update.
* Trotter P-coupling is handled by separate calls to trotter_update().
*/
- if (inputrec->epc == epcPARRINELLORAHMAN
+ if (inputrec->epc == PressureCoupling::ParrinelloRahman
&& do_per_step(step + inputrec->nstpcouple - 1, inputrec->nstpcouple))
{
real dtpc = inputrec->nstpcouple * inputrec->delta_t;
- parrinellorahman_pcoupl(fplog, step, inputrec, dtpc, state->pres_prev, state->box,
- state->box_rel, state->boxv, M, parrinellorahmanMu, bInitStep);
+ parrinellorahman_pcoupl(
+ fplog, step, inputrec, dtpc, state->pres_prev, state->box, state->box_rel, state->boxv, M, parrinellorahmanMu, bInitStep);
}
}
-void update_pcouple_after_coordinates(FILE* fplog,
- int64_t step,
- const t_inputrec* inputrec,
- const t_mdatoms* md,
- const matrix pressure,
- const matrix forceVirial,
- const matrix constraintVirial,
- matrix pressureCouplingMu,
- t_state* state,
- t_nrnb* nrnb,
- gmx::BoxDeformation* boxDeformation,
- const bool scaleCoordinates)
+void update_pcouple_after_coordinates(FILE* fplog,
+ int64_t step,
+ const t_inputrec* inputrec,
+ const int homenr,
+ gmx::ArrayRef<const unsigned short> cFREEZE,
+ const matrix pressure,
+ const matrix forceVirial,
+ const matrix constraintVirial,
+ matrix pressureCouplingMu,
+ t_state* state,
+ t_nrnb* nrnb,
+ gmx::BoxDeformation* boxDeformation,
+ const bool scaleCoordinates)
{
- int start = 0;
- int homenr = md->homenr;
+ int start = 0;
/* Cast to real for faster code, no loss in precision (see comment above) */
real dt = inputrec->delta_t;
/* now update boxes */
switch (inputrec->epc)
{
- case (epcNO): break;
- case (epcBERENDSEN):
+ case (PressureCoupling::No): break;
+ case (PressureCoupling::Berendsen):
if (do_per_step(step, inputrec->nstpcouple))
{
real dtpc = inputrec->nstpcouple * dt;
- berendsen_pcoupl(fplog, step, inputrec, dtpc, pressure, state->box, forceVirial,
- constraintVirial, pressureCouplingMu, &state->baros_integral);
- berendsen_pscale(inputrec, pressureCouplingMu, state->box, state->box_rel, start,
- homenr, state->x.rvec_array(), md->cFREEZE, nrnb, scaleCoordinates);
+ pressureCouplingCalculateScalingMatrix<PressureCoupling::Berendsen>(fplog,
+ step,
+ inputrec,
+ dtpc,
+ pressure,
+ state->box,
+ forceVirial,
+ constraintVirial,
+ pressureCouplingMu,
+ &state->baros_integral);
+ pressureCouplingScaleBoxAndCoordinates<PressureCoupling::Berendsen>(
+ inputrec,
+ pressureCouplingMu,
+ state->box,
+ state->box_rel,
+ start,
+ homenr,
+ state->x,
+ gmx::ArrayRef<gmx::RVec>(),
+ cFREEZE,
+ nrnb,
+ scaleCoordinates);
}
break;
- case (epcCRESCALE):
+ case (PressureCoupling::CRescale):
if (do_per_step(step, inputrec->nstpcouple))
{
real dtpc = inputrec->nstpcouple * dt;
- crescale_pcoupl(fplog, step, inputrec, dtpc, pressure, state->box, forceVirial,
- constraintVirial, pressureCouplingMu, &state->baros_integral);
- crescale_pscale(inputrec, pressureCouplingMu, state->box, state->box_rel, start,
- homenr, state->x.rvec_array(), state->v.rvec_array(), md->cFREEZE,
- nrnb, scaleCoordinates);
+ pressureCouplingCalculateScalingMatrix<PressureCoupling::CRescale>(fplog,
+ step,
+ inputrec,
+ dtpc,
+ pressure,
+ state->box,
+ forceVirial,
+ constraintVirial,
+ pressureCouplingMu,
+ &state->baros_integral);
+ pressureCouplingScaleBoxAndCoordinates<PressureCoupling::CRescale>(inputrec,
+ pressureCouplingMu,
+ state->box,
+ state->box_rel,
+ start,
+ homenr,
+ state->x,
+ state->v,
+ cFREEZE,
+ nrnb,
+ scaleCoordinates);
}
break;
- case (epcPARRINELLORAHMAN):
+ case (PressureCoupling::ParrinelloRahman):
if (do_per_step(step + inputrec->nstpcouple - 1, inputrec->nstpcouple))
{
/* The box velocities were updated in do_pr_pcoupl,
/* Scale the coordinates */
if (scaleCoordinates)
{
- auto x = state->x.rvec_array();
+ auto* x = state->x.rvec_array();
for (int n = start; n < start + homenr; n++)
{
tmvmul_ur0(pressureCouplingMu, x[n], x[n]);
}
}
break;
- case (epcMTTK):
+ case (PressureCoupling::Mttk):
switch (inputrec->epct)
{
- case (epctISOTROPIC):
+ case (PressureCouplingType::Isotropic):
/* DIM * eta = ln V. so DIM*eta_new = DIM*eta_old + DIM*dt*veta =>
ln V_new = ln V_old + 3*dt*veta => V_new = V_old*exp(3*dt*veta) =>
Side length scales as exp(veta*dt) */
}
}
-extern gmx_bool update_randomize_velocities(const t_inputrec* ir,
- int64_t step,
- const t_commrec* cr,
- const t_mdatoms* md,
- gmx::ArrayRef<gmx::RVec> v,
- const gmx::Update* upd,
- const gmx::Constraints* constr)
+extern bool update_randomize_velocities(const t_inputrec* ir,
+ int64_t step,
+ const t_commrec* cr,
+ int homenr,
+ gmx::ArrayRef<const unsigned short> cTC,
+ gmx::ArrayRef<const real> invMass,
+ gmx::ArrayRef<gmx::RVec> v,
+ const gmx::Update* upd,
+ const gmx::Constraints* constr)
{
real rate = (ir->delta_t) / ir->opts.tau_t[0];
- if (ir->etc == etcANDERSEN && constr != nullptr)
+ if (ir->etc == TemperatureCoupling::Andersen && constr != nullptr)
{
/* Currently, Andersen thermostat does not support constrained
systems. Functionality exists in the andersen_tcoupl
/* proceed with andersen if 1) it's fixed probability per
particle andersen or 2) it's massive andersen and it's tau_t/dt */
- if ((ir->etc == etcANDERSEN) || do_per_step(step, gmx::roundToInt(1.0 / rate)))
+ if ((ir->etc == TemperatureCoupling::Andersen) || do_per_step(step, gmx::roundToInt(1.0 / rate)))
{
- andersen_tcoupl(ir, step, cr, md, v, rate, upd->getAndersenRandomizeGroup(),
- upd->getBoltzmanFactor());
+ andersen_tcoupl(
+ ir, step, cr, homenr, cTC, invMass, v, rate, upd->getAndersenRandomizeGroup(), upd->getBoltzmanFactor());
return TRUE;
}
return FALSE;
}
-/*
- static const double sy_const[MAX_SUZUKI_YOSHIDA_NUM+1][MAX_SUZUKI_YOSHIDA_NUM+1] = {
- {},
- {1},
- {},
- {0.828981543588751,-0.657963087177502,0.828981543588751},
- {},
- {0.2967324292201065,0.2967324292201065,-0.186929716880426,0.2967324292201065,0.2967324292201065}
- };*/
-
/* these integration routines are only referenced inside this file */
static void NHC_trotter(const t_grpopts* opts,
int nvar,
double scalefac[],
real* veta,
const t_extmass* MassQ,
- gmx_bool bEkinAveVel)
+ bool bEkinAveVel)
{
/* general routine for both barostat and thermostat nose hoover chains */
- int i, j, mi, mj;
- double Ekin, Efac, reft, kT, nd;
- double dt;
- double * ivxi, *ixi;
- double* GQ;
- gmx_bool bBarostat;
- int mstepsi, mstepsj;
- int ns = SUZUKI_YOSHIDA_NUM; /* set the degree of integration in the types/state.h file */
- int nh = opts->nhchainlength;
+ int i, j, mi, mj;
+ double Ekin, Efac, reft, kT, nd;
+ double dt;
+ double *ivxi, *ixi;
+ double* GQ;
+ bool bBarostat;
+ int mstepsi, mstepsj;
+ int ns = SUZUKI_YOSHIDA_NUM; /* set the degree of integration in the types/state.h file */
+ int nh = opts->nhchainlength;
snew(GQ, nh);
mstepsi = mstepsj = ns;
Ekin = 2 * trace(tcstat->ekinh) * tcstat->ekinscaleh_nhc;
}
}
- kT = BOLTZ * reft;
+ kT = gmx::c_boltz * reft;
for (mi = 0; mi < mstepsi; mi++)
{
2006 Tuckerman et al paper., the order is iL_{T_baro} iL {T_part}
*/
- if (ir->epct == epctSEMIISOTROPIC)
+ if (ir->epct == PressureCouplingType::SemiIsotropic)
{
nwall = 2;
}
pscal = calc_pres(ir->pbcType, nwall, box, ekinmod, vir, localpres) + pcorr;
vol = det(box);
- GW = (vol * (MassQ->Winv / PRESFAC)) * (DIM * pscal - trace(ir->ref_p)); /* W is in ps^2 * bar * nm^3 */
+ GW = (vol * (MassQ->Winv / gmx::c_presfac))
+ * (DIM * pscal - trace(ir->ref_p)); /* W is in ps^2 * bar * nm^3 */
*veta += 0.5 * dt * GW;
}
* het systeem...
*/
- fac = PRESFAC * 2.0 / det(box);
+ fac = gmx::c_presfac * 2.0 / det(box);
for (n = 0; (n < DIM); n++)
{
for (m = 0; (m < DIM); m++)
{
if (nrdf > 0)
{
- return (2.0 * ekin) / (nrdf * BOLTZ);
+ return (2.0 * ekin) / (nrdf * gmx::c_boltz);
}
else
{
}
}
-/*! \brief Sets 1/mass for Parrinello-Rahman in wInv; NOTE: PRESFAC is not included, so not in GROMACS units! */
+/*! \brief Sets 1/mass for Parrinello-Rahman in wInv; NOTE: c_presfac is not included, so not in GROMACS units! */
static void calcParrinelloRahmanInvMass(const t_inputrec* ir, const matrix box, tensor wInv)
{
real maxBoxLength;
tensor boxv,
tensor M,
matrix mu,
- gmx_bool bFirstStep)
+ bool bFirstStep)
{
/* This doesn't do any coordinate updating. It just
* integrates the box vector equations from the calculated
if (!bFirstStep)
{
- /* Note that PRESFAC does not occur here.
+ /* Note that c_presfac does not occur here.
* The pressure and compressibility always occur as a product,
* therefore the pressure unit drops out.
*/
m_sub(pres, ir->ref_p, pdiff);
- if (ir->epct == epctSURFACETENSION)
+ if (ir->epct == PressureCouplingType::SurfaceTension)
{
/* Unlike Berendsen coupling it might not be trivial to include a z
* pressure correction here? On the other hand we don't scale the
switch (ir->epct)
{
- case epctANISOTROPIC:
+ case PressureCouplingType::Anisotropic:
for (int d = 0; d < DIM; d++)
{
for (int n = 0; n <= d; n++)
}
}
break;
- case epctISOTROPIC:
+ case PressureCouplingType::Isotropic:
/* calculate total volume acceleration */
atot = box[XX][XX] * box[YY][YY] * t1[ZZ][ZZ] + box[XX][XX] * t1[YY][YY] * box[ZZ][ZZ]
+ t1[XX][XX] * box[YY][YY] * box[ZZ][ZZ];
}
}
break;
- case epctSEMIISOTROPIC:
- case epctSURFACETENSION:
+ case PressureCouplingType::SemiIsotropic:
+ case PressureCouplingType::SurfaceTension:
/* Note the correction to pdiff above for surftens. coupling */
/* calculate total XY volume acceleration */
gmx_fatal(FARGS,
"Parrinello-Rahman pressure coupling type %s "
"not supported yet\n",
- EPCOUPLTYPETYPE(ir->epct));
+ enumValueToString(ir->epct));
}
real maxchange = 0;
mmul_ur0(invbox, t1, mu);
}
-void berendsen_pcoupl(FILE* fplog,
- int64_t step,
- const t_inputrec* ir,
- real dt,
- const tensor pres,
- const matrix box,
- const matrix force_vir,
- const matrix constraint_vir,
- matrix mu,
- double* baros_integral)
+//! Return compressibility factor for entry (i,j) of Berendsen / C-rescale scaling matrix
+static inline real compressibilityFactor(int i, int j, const t_inputrec* ir, real dt)
{
- real scalar_pressure, xy_pressure, p_corr_z;
- char buf[STRLEN];
+ return ir->compress[i][j] * dt / ir->tau_p;
+}
- /*
- * Calculate the scaling matrix mu
- */
- scalar_pressure = 0;
- xy_pressure = 0;
+//! Details of Berendsen / C-rescale scaling matrix calculation
+template<PressureCoupling pressureCouplingType>
+static void calculateScalingMatrixImplDetail(const t_inputrec* ir,
+ matrix mu,
+ real dt,
+ const matrix pres,
+ const matrix box,
+ real scalar_pressure,
+ real xy_pressure,
+ int64_t step);
+
+//! Calculate Berendsen / C-rescale scaling matrix
+template<PressureCoupling pressureCouplingType>
+static void calculateScalingMatrixImpl(const t_inputrec* ir,
+ matrix mu,
+ real dt,
+ const matrix pres,
+ const matrix box,
+ int64_t step)
+{
+ real scalar_pressure = 0;
+ real xy_pressure = 0;
for (int d = 0; d < DIM; d++)
{
scalar_pressure += pres[d][d] / DIM;
xy_pressure += pres[d][d] / (DIM - 1);
}
}
- /* Pressure is now in bar, everywhere. */
-#define factor(d, m) (ir->compress[d][m] * dt / ir->tau_p)
-
- /* mu has been changed from pow(1+...,1/3) to 1+.../3, since this is
- * necessary for triclinic scaling
- */
clear_mat(mu);
+ calculateScalingMatrixImplDetail<pressureCouplingType>(
+ ir, mu, dt, pres, box, scalar_pressure, xy_pressure, step);
+}
+
+template<>
+void calculateScalingMatrixImplDetail<PressureCoupling::Berendsen>(const t_inputrec* ir,
+ matrix mu,
+ real dt,
+ const matrix pres,
+ const matrix box,
+ real scalar_pressure,
+ real xy_pressure,
+ int64_t gmx_unused step)
+{
+ real p_corr_z = 0;
switch (ir->epct)
{
- case epctISOTROPIC:
+ case PressureCouplingType::Isotropic:
for (int d = 0; d < DIM; d++)
{
- mu[d][d] = 1.0 - factor(d, d) * (ir->ref_p[d][d] - scalar_pressure) / DIM;
+ mu[d][d] = 1.0 - compressibilityFactor(d, d, ir, dt) * (ir->ref_p[d][d] - scalar_pressure) / DIM;
}
break;
- case epctSEMIISOTROPIC:
+ case PressureCouplingType::SemiIsotropic:
for (int d = 0; d < ZZ; d++)
{
- mu[d][d] = 1.0 - factor(d, d) * (ir->ref_p[d][d] - xy_pressure) / DIM;
+ mu[d][d] = 1.0 - compressibilityFactor(d, d, ir, dt) * (ir->ref_p[d][d] - xy_pressure) / DIM;
}
- mu[ZZ][ZZ] = 1.0 - factor(ZZ, ZZ) * (ir->ref_p[ZZ][ZZ] - pres[ZZ][ZZ]) / DIM;
+ mu[ZZ][ZZ] =
+ 1.0 - compressibilityFactor(ZZ, ZZ, ir, dt) * (ir->ref_p[ZZ][ZZ] - pres[ZZ][ZZ]) / DIM;
break;
- case epctANISOTROPIC:
+ case PressureCouplingType::Anisotropic:
for (int d = 0; d < DIM; d++)
{
for (int n = 0; n < DIM; n++)
{
- mu[d][n] = (d == n ? 1.0 : 0.0) - factor(d, n) * (ir->ref_p[d][n] - pres[d][n]) / DIM;
+ mu[d][n] = (d == n ? 1.0 : 0.0)
+ - compressibilityFactor(d, n, ir, dt) * (ir->ref_p[d][n] - pres[d][n]) / DIM;
}
}
break;
- case epctSURFACETENSION:
+ case PressureCouplingType::SurfaceTension:
/* ir->ref_p[0/1] is the reference surface-tension times *
* the number of surfaces */
if (ir->compress[ZZ][ZZ] != 0.0F)
for (int d = 0; d < DIM - 1; d++)
{
mu[d][d] = 1.0
- + factor(d, d)
+ + compressibilityFactor(d, d, ir, dt)
* (ir->ref_p[d][d] / (mu[ZZ][ZZ] * box[ZZ][ZZ])
- (pres[ZZ][ZZ] + p_corr_z - xy_pressure))
/ (DIM - 1);
}
break;
default:
- gmx_fatal(FARGS, "Berendsen pressure coupling type %s not supported yet\n",
- EPCOUPLTYPETYPE(ir->epct));
- }
- /* To fullfill the orientation restrictions on triclinic boxes
- * we will set mu_yx, mu_zx and mu_zy to 0 and correct
- * the other elements of mu to first order.
- */
- mu[YY][XX] += mu[XX][YY];
- mu[ZZ][XX] += mu[XX][ZZ];
- mu[ZZ][YY] += mu[YY][ZZ];
- mu[XX][YY] = 0;
- mu[XX][ZZ] = 0;
- mu[YY][ZZ] = 0;
-
- /* Keep track of the work the barostat applies on the system.
- * Without constraints force_vir tells us how Epot changes when scaling.
- * With constraints constraint_vir gives us the constraint contribution
- * to both Epot and Ekin. Although we are not scaling velocities, scaling
- * the coordinates leads to scaling of distances involved in constraints.
- * This in turn changes the angular momentum (even if the constrained
- * distances are corrected at the next step). The kinetic component
- * of the constraint virial captures the angular momentum change.
- */
- for (int d = 0; d < DIM; d++)
- {
- for (int n = 0; n <= d; n++)
- {
- *baros_integral -=
- 2 * (mu[d][n] - (n == d ? 1 : 0)) * (force_vir[d][n] + constraint_vir[d][n]);
- }
- }
-
- if (debug)
- {
- pr_rvecs(debug, 0, "PC: pres ", pres, 3);
- pr_rvecs(debug, 0, "PC: mu ", mu, 3);
- }
-
- if (mu[XX][XX] < 0.99 || mu[XX][XX] > 1.01 || mu[YY][YY] < 0.99 || mu[YY][YY] > 1.01
- || mu[ZZ][ZZ] < 0.99 || mu[ZZ][ZZ] > 1.01)
- {
- char buf2[22];
- sprintf(buf,
- "\nStep %s Warning: pressure scaling more than 1%%, "
- "mu: %g %g %g\n",
- gmx_step_str(step, buf2), mu[XX][XX], mu[YY][YY], mu[ZZ][ZZ]);
- if (fplog)
- {
- fprintf(fplog, "%s", buf);
- }
- fprintf(stderr, "%s", buf);
+ gmx_fatal(FARGS,
+ "Berendsen pressure coupling type %s not supported yet\n",
+ enumValueToString(ir->epct));
}
}
-void crescale_pcoupl(FILE* fplog,
- int64_t step,
- const t_inputrec* ir,
- real dt,
- const tensor pres,
- const matrix box,
- const matrix force_vir,
- const matrix constraint_vir,
- matrix mu,
- double* baros_integral)
+template<>
+void calculateScalingMatrixImplDetail<PressureCoupling::CRescale>(const t_inputrec* ir,
+ matrix mu,
+ real dt,
+ const matrix pres,
+ const matrix box,
+ real scalar_pressure,
+ real xy_pressure,
+ int64_t step)
{
- /*
- * Calculate the scaling matrix mu
- */
- real scalar_pressure = 0;
- real xy_pressure = 0;
- for (int d = 0; d < DIM; d++)
- {
- scalar_pressure += pres[d][d] / DIM;
- if (d != ZZ)
- {
- xy_pressure += pres[d][d] / (DIM - 1);
- }
- }
- clear_mat(mu);
-
gmx::ThreeFry2x64<64> rng(ir->ld_seed, gmx::RandomDomain::Barostat);
gmx::NormalDistribution<real> normalDist;
rng.restart(step, 0);
{
vol *= box[d][d];
}
- real gauss;
- real gauss2;
- real kt = ir->opts.ref_t[0] * BOLTZ;
+ real gauss = 0;
+ real gauss2 = 0;
+ real kt = ir->opts.ref_t[0] * gmx::c_boltz;
if (kt < 0.0)
{
kt = 0.0;
switch (ir->epct)
{
- case epctISOTROPIC:
+ case PressureCouplingType::Isotropic:
gauss = normalDist(rng);
for (int d = 0; d < DIM; d++)
{
- const real compressibilityFactor = ir->compress[d][d] * dt / ir->tau_p;
- mu[d][d] = std::exp(-compressibilityFactor * (ir->ref_p[d][d] - scalar_pressure) / DIM
- + std::sqrt(2.0 * kt * compressibilityFactor * PRESFAC / vol)
- * gauss / DIM);
+ const real factor = compressibilityFactor(d, d, ir, dt);
+ mu[d][d] = std::exp(-factor * (ir->ref_p[d][d] - scalar_pressure) / DIM
+ + std::sqrt(2.0 * kt * factor * gmx::c_presfac / vol) * gauss / DIM);
}
break;
- case epctSEMIISOTROPIC:
+ case PressureCouplingType::SemiIsotropic:
gauss = normalDist(rng);
gauss2 = normalDist(rng);
for (int d = 0; d < ZZ; d++)
{
- const real compressibilityFactor = ir->compress[d][d] * dt / ir->tau_p;
- mu[d][d] = std::exp(
- -compressibilityFactor * (ir->ref_p[d][d] - xy_pressure) / DIM
- + std::sqrt((DIM - 1) * 2.0 * kt * compressibilityFactor * PRESFAC / vol / DIM)
- / (DIM - 1) * gauss);
+ const real factor = compressibilityFactor(d, d, ir, dt);
+ mu[d][d] = std::exp(-factor * (ir->ref_p[d][d] - xy_pressure) / DIM
+ + std::sqrt((DIM - 1) * 2.0 * kt * factor * gmx::c_presfac / vol / DIM)
+ / (DIM - 1) * gauss);
}
{
- const real compressibilityFactor = ir->compress[ZZ][ZZ] * dt / ir->tau_p;
- mu[ZZ][ZZ] = std::exp(
- -compressibilityFactor * (ir->ref_p[ZZ][ZZ] - pres[ZZ][ZZ]) / DIM
- + std::sqrt(2.0 * kt * compressibilityFactor * PRESFAC / vol / DIM) * gauss2);
+ const real factor = compressibilityFactor(ZZ, ZZ, ir, dt);
+ mu[ZZ][ZZ] = std::exp(-factor * (ir->ref_p[ZZ][ZZ] - pres[ZZ][ZZ]) / DIM
+ + std::sqrt(2.0 * kt * factor * gmx::c_presfac / vol / DIM) * gauss2);
}
break;
- case epctSURFACETENSION:
+ case PressureCouplingType::SurfaceTension:
gauss = normalDist(rng);
gauss2 = normalDist(rng);
for (int d = 0; d < ZZ; d++)
{
- const real compressibilityFactor = ir->compress[d][d] * dt / ir->tau_p;
+ const real factor = compressibilityFactor(d, d, ir, dt);
/* Notice: we here use ref_p[ZZ][ZZ] as isotropic pressure and ir->ref_p[d][d] as surface tension */
mu[d][d] = std::exp(
- -compressibilityFactor
- * (ir->ref_p[ZZ][ZZ] - ir->ref_p[d][d] / box[ZZ][ZZ] - xy_pressure) / DIM
- + std::sqrt(4.0 / 3.0 * kt * compressibilityFactor * PRESFAC / vol)
- / (DIM - 1) * gauss);
+ -factor * (ir->ref_p[ZZ][ZZ] - ir->ref_p[d][d] / box[ZZ][ZZ] - xy_pressure) / DIM
+ + std::sqrt(4.0 / 3.0 * kt * factor * gmx::c_presfac / vol) / (DIM - 1) * gauss);
}
{
- const real compressibilityFactor = ir->compress[ZZ][ZZ] * dt / ir->tau_p;
- mu[ZZ][ZZ] = std::exp(
- -compressibilityFactor * (ir->ref_p[ZZ][ZZ] - pres[ZZ][ZZ]) / DIM
- + std::sqrt(2.0 / 3.0 * kt * compressibilityFactor * PRESFAC / vol) * gauss2);
+ const real factor = compressibilityFactor(ZZ, ZZ, ir, dt);
+ mu[ZZ][ZZ] = std::exp(-factor * (ir->ref_p[ZZ][ZZ] - pres[ZZ][ZZ]) / DIM
+ + std::sqrt(2.0 / 3.0 * kt * factor * gmx::c_presfac / vol) * gauss2);
}
break;
default:
- gmx_fatal(FARGS, "C-rescale pressure coupling type %s not supported yet\n",
- EPCOUPLTYPETYPE(ir->epct));
+ gmx_fatal(FARGS,
+ "C-rescale pressure coupling type %s not supported yet\n",
+ enumValueToString(ir->epct));
}
- /* To fullfill the orientation restrictions on triclinic boxes
+}
+
+template<PressureCoupling pressureCouplingType>
+void pressureCouplingCalculateScalingMatrix(FILE* fplog,
+ int64_t step,
+ const t_inputrec* ir,
+ real dt,
+ const tensor pres,
+ const matrix box,
+ const matrix force_vir,
+ const matrix constraint_vir,
+ matrix mu,
+ double* baros_integral)
+{
+ static_assert(pressureCouplingType == PressureCoupling::Berendsen
+ || pressureCouplingType == PressureCoupling::CRescale,
+ "pressureCouplingCalculateScalingMatrix is only implemented for Berendsen and "
+ "C-rescale pressure coupling");
+
+ calculateScalingMatrixImpl<pressureCouplingType>(ir, mu, dt, pres, box, step);
+
+ /* To fulfill the orientation restrictions on triclinic boxes
* we will set mu_yx, mu_zx and mu_zy to 0 and correct
* the other elements of mu to first order.
*/
sprintf(buf,
"\nStep %s Warning: pressure scaling more than 1%%, "
"mu: %g %g %g\n",
- gmx_step_str(step, buf2), mu[XX][XX], mu[YY][YY], mu[ZZ][ZZ]);
+ gmx_step_str(step, buf2),
+ mu[XX][XX],
+ mu[YY][YY],
+ mu[ZZ][ZZ]);
if (fplog)
{
fprintf(fplog, "%s", buf);
}
}
-void crescale_pscale(const t_inputrec* ir,
- const matrix mu,
- matrix box,
- matrix box_rel,
- int start,
- int nr_atoms,
- rvec x[],
- rvec v[],
- const unsigned short cFREEZE[],
- t_nrnb* nrnb,
- const bool scaleCoordinates)
+template<PressureCoupling pressureCouplingType>
+void pressureCouplingScaleBoxAndCoordinates(const t_inputrec* ir,
+ const matrix mu,
+ matrix box,
+ matrix box_rel,
+ int start,
+ int nr_atoms,
+ gmx::ArrayRef<gmx::RVec> x,
+ gmx::ArrayRef<gmx::RVec> v,
+ gmx::ArrayRef<const unsigned short> cFREEZE,
+ t_nrnb* nrnb,
+ const bool scaleCoordinates)
{
- ivec* nFreeze = ir->opts.nFreeze;
- int nthreads gmx_unused;
- matrix inv_mu;
-
-#ifndef __clang_analyzer__
- nthreads = gmx_omp_nthreads_get(emntUpdate);
-#endif
-
- gmx::invertBoxMatrix(mu, inv_mu);
-
- /* Scale the positions and the velocities */
- if (scaleCoordinates)
- {
-#pragma omp parallel for num_threads(nthreads) schedule(static)
- for (int n = start; n < start + nr_atoms; n++)
- {
- // Trivial OpenMP region that does not throw
- int g;
+ static_assert(pressureCouplingType == PressureCoupling::Berendsen
+ || pressureCouplingType == PressureCoupling::CRescale,
+ "pressureCouplingScaleBoxAndCoordinates is only implemented for Berendsen and "
+ "C-rescale pressure coupling");
- if (cFREEZE == nullptr)
- {
- g = 0;
- }
- else
- {
- g = cFREEZE[n];
- }
-
- if (!nFreeze[g][XX])
- {
- x[n][XX] = mu[XX][XX] * x[n][XX] + mu[YY][XX] * x[n][YY] + mu[ZZ][XX] * x[n][ZZ];
- v[n][XX] = inv_mu[XX][XX] * v[n][XX] + inv_mu[YY][XX] * v[n][YY]
- + inv_mu[ZZ][XX] * v[n][ZZ];
- }
- if (!nFreeze[g][YY])
- {
- x[n][YY] = mu[YY][YY] * x[n][YY] + mu[ZZ][YY] * x[n][ZZ];
- v[n][YY] = inv_mu[YY][YY] * v[n][YY] + inv_mu[ZZ][YY] * v[n][ZZ];
- }
- if (!nFreeze[g][ZZ])
- {
- x[n][ZZ] = mu[ZZ][ZZ] * x[n][ZZ];
- v[n][ZZ] = inv_mu[ZZ][ZZ] * v[n][ZZ];
- }
- }
- }
- /* compute final boxlengths */
- for (int d = 0; d < DIM; d++)
+ ivec* nFreeze = ir->opts.nFreeze;
+ matrix inv_mu;
+ if (pressureCouplingType == PressureCoupling::CRescale)
{
- box[d][XX] = mu[XX][XX] * box[d][XX] + mu[YY][XX] * box[d][YY] + mu[ZZ][XX] * box[d][ZZ];
- box[d][YY] = mu[YY][YY] * box[d][YY] + mu[ZZ][YY] * box[d][ZZ];
- box[d][ZZ] = mu[ZZ][ZZ] * box[d][ZZ];
+ gmx::invertBoxMatrix(mu, inv_mu);
}
- preserve_box_shape(ir, box_rel, box);
-
- /* (un)shifting should NOT be done after this,
- * since the box vectors might have changed
- */
- inc_nrnb(nrnb, eNR_PCOUPL, nr_atoms);
-}
-
-void berendsen_pscale(const t_inputrec* ir,
- const matrix mu,
- matrix box,
- matrix box_rel,
- int start,
- int nr_atoms,
- rvec x[],
- const unsigned short cFREEZE[],
- t_nrnb* nrnb,
- const bool scaleCoordinates)
-{
- ivec* nFreeze = ir->opts.nFreeze;
- int d;
- int nthreads gmx_unused;
-
-#ifndef __clang_analyzer__
- nthreads = gmx_omp_nthreads_get(emntUpdate);
-#endif
-
- /* Scale the positions */
+ /* Scale the positions and the velocities */
if (scaleCoordinates)
{
-#pragma omp parallel for num_threads(nthreads) schedule(static)
+ const int gmx_unused numThreads = gmx_omp_nthreads_get(ModuleMultiThread::Update);
+#pragma omp parallel for num_threads(numThreads) schedule(static)
for (int n = start; n < start + nr_atoms; n++)
{
// Trivial OpenMP region that does not throw
- int g;
-
- if (cFREEZE == nullptr)
- {
- g = 0;
- }
- else
+ int g = 0;
+ if (!cFREEZE.empty())
{
g = cFREEZE[n];
}
if (!nFreeze[g][XX])
{
x[n][XX] = mu[XX][XX] * x[n][XX] + mu[YY][XX] * x[n][YY] + mu[ZZ][XX] * x[n][ZZ];
+ if (pressureCouplingType == PressureCoupling::CRescale)
+ {
+ v[n][XX] = inv_mu[XX][XX] * v[n][XX] + inv_mu[YY][XX] * v[n][YY]
+ + inv_mu[ZZ][XX] * v[n][ZZ];
+ }
}
if (!nFreeze[g][YY])
{
x[n][YY] = mu[YY][YY] * x[n][YY] + mu[ZZ][YY] * x[n][ZZ];
+ if (pressureCouplingType == PressureCoupling::CRescale)
+ {
+ v[n][YY] = inv_mu[YY][YY] * v[n][YY] + inv_mu[ZZ][YY] * v[n][ZZ];
+ }
}
if (!nFreeze[g][ZZ])
{
x[n][ZZ] = mu[ZZ][ZZ] * x[n][ZZ];
+ if (pressureCouplingType == PressureCoupling::CRescale)
+ {
+ v[n][ZZ] = inv_mu[ZZ][ZZ] * v[n][ZZ];
+ }
}
}
}
/* compute final boxlengths */
- for (d = 0; d < DIM; d++)
+ for (int d = 0; d < DIM; d++)
{
box[d][XX] = mu[XX][XX] * box[d][XX] + mu[YY][XX] * box[d][YY] + mu[ZZ][XX] * box[d][ZZ];
box[d][YY] = mu[YY][YY] * box[d][YY] + mu[ZZ][YY] * box[d][ZZ];
{
real Ek, T;
- if (ir->eI == eiVV)
+ if (ir->eI == IntegrationAlgorithm::VV)
{
Ek = trace(ekind->tcstat[i].ekinf);
T = ekind->tcstat[i].T;
}
}
-void andersen_tcoupl(const t_inputrec* ir,
- int64_t step,
- const t_commrec* cr,
- const t_mdatoms* md,
- gmx::ArrayRef<gmx::RVec> v,
- real rate,
- const std::vector<bool>& randomize,
- gmx::ArrayRef<const real> boltzfac)
+void andersen_tcoupl(const t_inputrec* ir,
+ int64_t step,
+ const t_commrec* cr,
+ const int homenr,
+ gmx::ArrayRef<const unsigned short> cTC,
+ gmx::ArrayRef<const real> invMass,
+ gmx::ArrayRef<gmx::RVec> v,
+ real rate,
+ const std::vector<bool>& randomize,
+ gmx::ArrayRef<const real> boltzfac)
{
const int* gatindex = (DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr);
int i;
/* randomize the velocities of the selected particles */
- for (i = 0; i < md->homenr; i++) /* now loop over the list of atoms */
+ for (i = 0; i < homenr; i++) /* now loop over the list of atoms */
{
- int ng = gatindex ? gatindex[i] : i;
- gmx_bool bRandomize;
+ int ng = gatindex ? gatindex[i] : i;
+ bool bRandomize;
rng.restart(step, ng);
- if (md->cTC)
+ if (!cTC.empty())
{
- gc = md->cTC[i]; /* assign the atom to a temperature group if there are more than one */
+ gc = cTC[i]; /* assign the atom to a temperature group if there are more than one */
}
if (randomize[gc])
{
- if (ir->etc == etcANDERSENMASSIVE)
+ if (ir->etc == TemperatureCoupling::AndersenMassive)
{
/* Randomize particle always */
bRandomize = TRUE;
real scal;
int d;
- scal = std::sqrt(boltzfac[gc] * md->invmass[i]);
+ scal = std::sqrt(boltzfac[gc] * invMass[i]);
normalDist.reset();
void nosehoover_tcoupl(const t_grpopts* opts,
const gmx_ekindata_t* ekind,
real dt,
- double xi[],
- double vxi[],
+ gmx::ArrayRef<double> xi,
+ gmx::ArrayRef<double> vxi,
const t_extmass* MassQ)
{
int i;
}
}
-void trotter_update(const t_inputrec* ir,
- int64_t step,
- gmx_ekindata_t* ekind,
- const gmx_enerdata_t* enerd,
- t_state* state,
- const tensor vir,
- const t_mdatoms* md,
- const t_extmass* MassQ,
- gmx::ArrayRef<std::vector<int>> trotter_seqlist,
- int trotter_seqno)
+void trotter_update(const t_inputrec* ir,
+ int64_t step,
+ gmx_ekindata_t* ekind,
+ const gmx_enerdata_t* enerd,
+ t_state* state,
+ const tensor vir,
+ int homenr,
+ gmx::ArrayRef<const unsigned short> cTC,
+ gmx::ArrayRef<const real> invMass,
+ const t_extmass* MassQ,
+ gmx::ArrayRef<std::vector<int>> trotter_seqlist,
+ int trotter_seqno)
{
int n, i, d, ngtc, gc = 0, t;
real dt;
double * scalefac, dtc;
rvec sumv = { 0, 0, 0 };
- gmx_bool bCouple;
+ bool bCouple;
if (trotter_seqno <= ettTSEQ2)
{
{
case etrtBAROV:
case etrtBAROV2:
- boxv_trotter(ir, &(state->veta), dt, state->box, ekind, vir,
- enerd->term[F_PDISPCORR], MassQ);
+ boxv_trotter(ir, &(state->veta), dt, state->box, ekind, vir, enerd->term[F_PDISPCORR], MassQ);
break;
case etrtBARONHC:
case etrtBARONHC2:
- NHC_trotter(opts, state->nnhpres, ekind, dt, state->nhpres_xi.data(),
- state->nhpres_vxi.data(), nullptr, &(state->veta), MassQ, FALSE);
+ NHC_trotter(opts,
+ state->nnhpres,
+ ekind,
+ dt,
+ state->nhpres_xi.data(),
+ state->nhpres_vxi.data(),
+ nullptr,
+ &(state->veta),
+ MassQ,
+ FALSE);
break;
case etrtNHC:
case etrtNHC2:
- NHC_trotter(opts, opts->ngtc, ekind, dt, state->nosehoover_xi.data(),
- state->nosehoover_vxi.data(), scalefac, nullptr, MassQ, (ir->eI == eiVV));
+ NHC_trotter(opts,
+ opts->ngtc,
+ ekind,
+ dt,
+ state->nosehoover_xi.data(),
+ state->nosehoover_vxi.data(),
+ scalefac,
+ nullptr,
+ MassQ,
+ (ir->eI == IntegrationAlgorithm::VV));
/* need to rescale the kinetic energies and velocities here. Could
scale the velocities later, but we need them scaled in order to
produce the correct outputs, so we'll scale them here. */
/* but do we actually need the total? */
/* modify the velocities as well */
- for (n = 0; n < md->homenr; n++)
+ for (n = 0; n < homenr; n++)
{
- if (md->cTC) /* does this conditional need to be here? is this always true?*/
+ if (!cTC.empty()) /* does this conditional need to be here? is this always true?*/
{
- gc = md->cTC[n];
+ gc = cTC[n];
}
for (d = 0; d < DIM; d++)
{
{
for (d = 0; d < DIM; d++)
{
- sumv[d] += (v[n][d]) / md->invmass[n];
+ sumv[d] += (v[n][d]) / invMass[n];
}
}
}
}
-extern void init_npt_masses(const t_inputrec* ir, t_state* state, t_extmass* MassQ, gmx_bool bInit)
+extern void init_npt_masses(const t_inputrec* ir, t_state* state, t_extmass* MassQ, bool bInit)
{
int n, i, j, d, ngtc, nh;
const t_grpopts* opts;
ngtc = ir->opts.ngtc;
nh = state->nhchainlength;
- if (ir->eI == eiMD)
+ if (ir->eI == IntegrationAlgorithm::MD)
{
if (bInit)
{
/* units are nm^3 * ns^2 / (nm^3 * bar / kJ/mol) = kJ/mol */
/* Consider evaluating eventually if this the right mass to use. All are correct, some might be more stable */
- MassQ->Winv = (PRESFAC * trace(ir->compress) * BOLTZ * opts->ref_t[0])
+ MassQ->Winv = (gmx::c_presfac * trace(ir->compress) * gmx::c_boltz * opts->ref_t[0])
/ (DIM * state->vol0 * gmx::square(ir->tau_p / M_2PI));
/* An alternate mass definition, from Tuckerman et al. */
- /* MassQ->Winv = 1.0/(gmx::square(ir->tau_p/M_2PI)*(opts->nrdf[0]+DIM)*BOLTZ*opts->ref_t[0]); */
+ /* MassQ->Winv = 1.0/(gmx::square(ir->tau_p/M_2PI)*(opts->nrdf[0]+DIM)*c_boltz*opts->ref_t[0]); */
for (d = 0; d < DIM; d++)
{
for (n = 0; n < DIM; n++)
{
- MassQ->Winvm[d][n] =
- PRESFAC * ir->compress[d][n] / (state->vol0 * gmx::square(ir->tau_p / M_2PI));
+ MassQ->Winvm[d][n] = gmx::c_presfac * ir->compress[d][n]
+ / (state->vol0 * gmx::square(ir->tau_p / M_2PI));
/* not clear this is correct yet for the anisotropic case. Will need to reevaluate
before using MTTK for anisotropic states.*/
}
{
reft = std::max<real>(0, opts->ref_t[i]);
nd = opts->nrdf[i];
- kT = BOLTZ * reft;
+ kT = gmx::c_boltz * reft;
for (j = 0; j < nh; j++)
{
if (j == 0)
}
std::array<std::vector<int>, ettTSEQMAX>
-init_npt_vars(const t_inputrec* ir, t_state* state, t_extmass* MassQ, gmx_bool bTrotter)
+init_npt_vars(const t_inputrec* ir, t_state* state, t_extmass* MassQ, bool bTrotter)
{
int i, j, nnhpres, nh;
const t_grpopts* opts;
nnhpres = state->nnhpres;
nh = state->nhchainlength;
- if (EI_VV(ir->eI) && (ir->epc == epcMTTK) && (ir->etc != etcNOSEHOOVER))
+ if (EI_VV(ir->eI) && (ir->epc == PressureCoupling::Mttk) && (ir->etc != TemperatureCoupling::NoseHoover))
{
- gmx_fatal(FARGS,
- "Cannot do MTTK pressure coupling without Nose-Hoover temperature control");
+ gmx_fatal(FARGS, "Cannot do MTTK pressure coupling without Nose-Hoover temperature control");
}
init_npt_masses(ir, state, MassQ, TRUE);
/* compute the kinetic energy by using the half step velocities or
* the kinetic energies, depending on the order of the trotter calls */
- if (ir->eI == eiVV)
+ if (ir->eI == IntegrationAlgorithm::VV)
{
if (inputrecNptTrotter(ir))
{
/* trotter_seq[4] is etrtNHC for second 1/2 step velocities - leave zero */
}
}
- else if (ir->eI == eiVVAK)
+ else if (ir->eI == IntegrationAlgorithm::VVAK)
{
if (inputrecNptTrotter(ir))
{
switch (ir->epct)
{
- case epctISOTROPIC:
+ case PressureCouplingType::Isotropic:
default: bmass = DIM * DIM; /* recommended mass parameters for isotropic barostat */
}
if ((ir->tau_p > 0) && (opts->ref_t[0] > 0))
{
reft = std::max<real>(0, opts->ref_t[0]);
- kT = BOLTZ * reft;
+ kT = gmx::c_boltz * reft;
for (i = 0; i < nnhpres; i++)
{
for (j = 0; j < nh; j++)
real nd = ir->opts.nrdf[i];
real reft = std::max<real>(ir->opts.ref_t[i], 0);
- real kT = BOLTZ * reft;
+ real kT = gmx::c_boltz * reft;
if (nd > 0.0)
{
}
else /* Other non Trotter temperature NH control -- no chains yet. */
{
- energy += 0.5 * BOLTZ * nd * gmx::square(ivxi[0]) / iQinv[0];
+ energy += 0.5 * gmx::c_boltz * nd * gmx::square(ivxi[0]) / iQinv[0];
energy += nd * ixi[0] * kT;
}
}
{
/* note -- assumes only one degree of freedom that is thermostatted in barostat */
real reft = std::max<real>(ir->opts.ref_t[0], 0.0); /* using 'System' temperature */
- real kT = BOLTZ * reft;
+ real kT = gmx::c_boltz * reft;
for (int j = 0; j < nh; j++)
{
}
if (debug)
{
- fprintf(debug, "P-T-group: %10d Chain %4d ThermV: %15.8f ThermX: %15.8f", i, j,
- state->nhpres_vxi[i * nh + j], state->nhpres_xi[i * nh + j]);
+ fprintf(debug,
+ "P-T-group: %10d Chain %4d ThermV: %15.8f ThermX: %15.8f",
+ i,
+ j,
+ state->nhpres_vxi[i * nh + j],
+ state->nhpres_xi[i * nh + j]);
}
}
}
{
real energyNPT = 0;
- if (ir->epc != epcNO)
+ if (ir->epc != PressureCoupling::No)
{
/* Compute the contribution of the pressure to the conserved quantity*/
switch (ir->epc)
{
- case epcPARRINELLORAHMAN:
+ case PressureCoupling::ParrinelloRahman:
{
/* contribution from the pressure momenta */
tensor invMass;
{
if (invMass[d][n] > 0)
{
- energyNPT += 0.5 * gmx::square(state->boxv[d][n]) / (invMass[d][n] * PRESFAC);
+ energyNPT += 0.5 * gmx::square(state->boxv[d][n])
+ / (invMass[d][n] * gmx::c_presfac);
}
}
}
* track of unwrapped box diagonal elements. This case is
* excluded in integratorHasConservedEnergyQuantity().
*/
- energyNPT += vol * trace(ir->ref_p) / (DIM * PRESFAC);
+ energyNPT += vol * trace(ir->ref_p) / (DIM * gmx::c_presfac);
break;
}
- case epcMTTK:
+ case PressureCoupling::Mttk:
/* contribution from the pressure momenta */
energyNPT += 0.5 * gmx::square(state->veta) / MassQ->Winv;
/* contribution from the PV term */
- energyNPT += vol * trace(ir->ref_p) / (DIM * PRESFAC);
+ energyNPT += vol * trace(ir->ref_p) / (DIM * gmx::c_presfac);
- if (ir->epc == epcMTTK)
+ if (ir->epc == PressureCoupling::Mttk)
{
/* contribution from the MTTK chain */
energyNPT += energyPressureMTTK(ir, state, MassQ);
}
break;
- case epcBERENDSEN:
- case epcCRESCALE: energyNPT += state->baros_integral; break;
+ case PressureCoupling::Berendsen:
+ case PressureCoupling::CRescale: energyNPT += state->baros_integral; break;
default:
GMX_RELEASE_ASSERT(
false,
switch (ir->etc)
{
- case etcNO: break;
- case etcVRESCALE:
- case etcBERENDSEN: energyNPT += energyVrescale(ir, state); break;
- case etcNOSEHOOVER: energyNPT += energyNoseHoover(ir, state, MassQ); break;
- case etcANDERSEN:
- case etcANDERSENMASSIVE:
+ case TemperatureCoupling::No: break;
+ case TemperatureCoupling::VRescale:
+ case TemperatureCoupling::Berendsen: energyNPT += energyVrescale(ir, state); break;
+ case TemperatureCoupling::NoseHoover:
+ energyNPT += energyNoseHoover(ir, state, MassQ);
+ break;
+ case TemperatureCoupling::Andersen:
+ case TemperatureCoupling::AndersenMassive:
// Not supported, excluded in integratorHasConservedEnergyQuantity()
break;
default:
return ekin_new;
}
-void vrescale_tcoupl(const t_inputrec* ir, int64_t step, gmx_ekindata_t* ekind, real dt, double therm_integral[])
+void vrescale_tcoupl(const t_inputrec* ir, int64_t step, gmx_ekindata_t* ekind, real dt, gmx::ArrayRef<double> therm_integral)
{
const t_grpopts* opts;
int i;
for (i = 0; (i < opts->ngtc); i++)
{
- if (ir->eI == eiVV)
+ if (ir->eI == IntegrationAlgorithm::VV)
{
Ek = trace(ekind->tcstat[i].ekinf);
}
if (opts->tau_t[i] >= 0 && opts->nrdf[i] > 0 && Ek > 0)
{
- Ek_ref1 = 0.5 * opts->ref_t[i] * BOLTZ;
+ Ek_ref1 = 0.5 * opts->ref_t[i] * gmx::c_boltz;
Ek_ref = Ek_ref1 * opts->nrdf[i];
Ek_new = vrescale_resamplekin(Ek, Ek_ref, opts->nrdf[i], opts->tau_t[i] / dt, step, ir->ld_seed);
if (debug)
{
- fprintf(debug, "TC: group %d: Ekr %g, Ek %g, Ek_new %g, Lambda: %g\n", i, Ek_ref,
- Ek, Ek_new, ekind->tcstat[i].lambda);
+ fprintf(debug,
+ "TC: group %d: Ekr %g, Ek %g, Ek_new %g, Lambda: %g\n",
+ i,
+ Ek_ref,
+ Ek,
+ Ek_new,
+ ekind->tcstat[i].lambda);
}
}
else
}
}
-void rescale_velocities(const gmx_ekindata_t* ekind, const t_mdatoms* mdatoms, int start, int end, rvec v[])
+void rescale_velocities(const gmx_ekindata_t* ekind,
+ gmx::ArrayRef<const unsigned short> cTC,
+ int start,
+ int end,
+ gmx::ArrayRef<gmx::RVec> v)
{
- unsigned short *cACC, *cTC;
- int ga, gt, n, d;
- real lg;
- rvec vrel;
-
- cTC = mdatoms->cTC;
-
gmx::ArrayRef<const t_grp_tcstat> tcstat = ekind->tcstat;
- if (ekind->bNEMD)
+ for (int n = start; n < end; n++)
{
- gmx::ArrayRef<const t_grp_acc> gstat = ekind->grpstat;
- cACC = mdatoms->cACC;
-
- ga = 0;
- gt = 0;
- for (n = start; n < end; n++)
+ int gt = 0;
+ if (!cTC.empty())
{
- if (cACC)
- {
- ga = cACC[n];
- }
- if (cTC)
- {
- gt = cTC[n];
- }
- /* Only scale the velocity component relative to the COM velocity */
- rvec_sub(v[n], gstat[ga].u, vrel);
- lg = tcstat[gt].lambda;
- for (d = 0; d < DIM; d++)
- {
- v[n][d] = gstat[ga].u[d] + lg * vrel[d];
- }
+ gt = cTC[n];
}
- }
- else
- {
- gt = 0;
- for (n = start; n < end; n++)
+ const real lg = tcstat[gt].lambda;
+ for (int d = 0; d < DIM; d++)
{
- if (cTC)
- {
- gt = cTC[n];
- }
- lg = tcstat[gt].lambda;
- for (d = 0; d < DIM; d++)
- {
- v[n][d] *= lg;
- }
+ v[n][d] *= lg;
}
}
}
for (int i = 0; i < ir->opts.ngtc; i++)
{
/* set bSimAnn if any group is being annealed */
- if (ir->opts.annealing[i] != eannNO)
+ if (ir->opts.annealing[i] != SimulatedAnnealing::No)
{
return true;
}
npoints = ir->opts.anneal_npoints[i];
switch (ir->opts.annealing[i])
{
- case eannNO: continue;
- case eannPERIODIC:
+ case SimulatedAnnealing::No: continue;
+ case SimulatedAnnealing::Periodic:
/* calculate time modulo the period */
pert = ir->opts.anneal_time[i][npoints - 1];
n = static_cast<int>(t / pert);
thist = 0;
}
break;
- case eannSINGLE: thist = t; break;
+ case SimulatedAnnealing::Single: thist = t; break;
default:
- gmx_fatal(FARGS, "Death horror in update_annealing_target_temp (i=%d/%d npoints=%d)",
- i, ir->opts.ngtc, npoints);
+ gmx_fatal(FARGS,
+ "Death horror in update_annealing_target_temp (i=%d/%d npoints=%d)",
+ i,
+ ir->opts.ngtc,
+ npoints);
}
/* We are doing annealing for this group if we got here,
* and we have the (relative) time as thist.
{
if (EI_DYNAMICS(ir.eI))
{
- if (ir.etc == etcBERENDSEN)
+ if (ir.etc == TemperatureCoupling::Berendsen)
{
please_cite(fplog, "Berendsen84a");
}
- if (ir.etc == etcVRESCALE)
+ if (ir.etc == TemperatureCoupling::VRescale)
{
please_cite(fplog, "Bussi2007a");
}
- if (ir.epc == epcCRESCALE)
+ if (ir.epc == PressureCoupling::CRescale)
{
please_cite(fplog, "Bernetti2020");
}
// TODO this is actually an integrator, not a coupling algorithm
- if (ir.eI == eiSD1)
+ if (ir.eI == IntegrationAlgorithm::SD1)
{
please_cite(fplog, "Goga2012");
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MDLIB_COUPLING_H
#define GMX_MDLIB_COUPLING_H
-#include "gromacs/math/paddedvector.h"
+#include <cstdio>
+
+#include <array>
+#include <vector>
+
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
struct gmx_enerdata_t;
struct t_commrec;
struct t_extmass;
struct t_grpopts;
struct t_inputrec;
-struct t_mdatoms;
struct t_nrnb;
class t_state;
class BoxDeformation;
class Constraints;
class Update;
+template<typename>
+class ArrayRef;
}; // namespace gmx
/* Update the size of per-atom arrays (e.g. after DD re-partitioning,
which might increase the number of home atoms). */
-void update_tcouple(int64_t step,
- const t_inputrec* inputrec,
- t_state* state,
- gmx_ekindata_t* ekind,
- const t_extmass* MassQ,
- const t_mdatoms* md);
+void update_tcouple(int64_t step,
+ const t_inputrec* inputrec,
+ t_state* state,
+ gmx_ekindata_t* ekind,
+ const t_extmass* MassQ,
+ int homenr,
+ gmx::ArrayRef<const unsigned short> cTC);
/* Update Parrinello-Rahman, to be called before the coordinate update */
void update_pcouple_before_coordinates(FILE* fplog,
t_state* state,
matrix parrinellorahmanMu,
matrix M,
- gmx_bool bInitStep);
+ bool bInitStep);
/* Update the box, to be called after the coordinate update.
* For Berendsen P-coupling, also calculates the scaling factor
* and scales the coordinates.
* When the deform option is used, scales coordinates and box here.
*/
-void update_pcouple_after_coordinates(FILE* fplog,
- int64_t step,
- const t_inputrec* inputrec,
- const t_mdatoms* md,
- const matrix pressure,
- const matrix forceVirial,
- const matrix constraintVirial,
- matrix pressureCouplingMu,
- t_state* state,
- t_nrnb* nrnb,
- gmx::BoxDeformation* boxDeformation,
- bool scaleCoordinates);
+void update_pcouple_after_coordinates(FILE* fplog,
+ int64_t step,
+ const t_inputrec* inputrec,
+ int homenr,
+ gmx::ArrayRef<const unsigned short> cFREEZE,
+ const matrix pressure,
+ const matrix forceVirial,
+ const matrix constraintVirial,
+ matrix pressureCouplingMu,
+ t_state* state,
+ t_nrnb* nrnb,
+ gmx::BoxDeformation* boxDeformation,
+ bool scaleCoordinates);
/* Return TRUE if OK, FALSE in case of Shake Error */
-extern gmx_bool update_randomize_velocities(const t_inputrec* ir,
- int64_t step,
- const t_commrec* cr,
- const t_mdatoms* md,
- gmx::ArrayRef<gmx::RVec> v,
- const gmx::Update* upd,
- const gmx::Constraints* constr);
+extern bool update_randomize_velocities(const t_inputrec* ir,
+ int64_t step,
+ const t_commrec* cr,
+ int homenr,
+ gmx::ArrayRef<const unsigned short> cTC,
+ gmx::ArrayRef<const real> invMass,
+ gmx::ArrayRef<gmx::RVec> v,
+ const gmx::Update* upd,
+ const gmx::Constraints* constr);
void berendsen_tcoupl(const t_inputrec* ir,
gmx_ekindata_t* ekind,
real dt,
std::vector<double>& therm_integral); //NOLINT(google-runtime-references)
-void andersen_tcoupl(const t_inputrec* ir,
- int64_t step,
- const t_commrec* cr,
- const t_mdatoms* md,
- gmx::ArrayRef<gmx::RVec> v,
- real rate,
- const std::vector<bool>& randomize,
- gmx::ArrayRef<const real> boltzfac);
+void andersen_tcoupl(const t_inputrec* ir,
+ int64_t step,
+ const t_commrec* cr,
+ int homenr,
+ gmx::ArrayRef<const unsigned short> cTC,
+ gmx::ArrayRef<const real> invMass,
+ gmx::ArrayRef<gmx::RVec> v,
+ real rate,
+ const std::vector<bool>& randomize,
+ gmx::ArrayRef<const real> boltzfac);
void nosehoover_tcoupl(const t_grpopts* opts,
const gmx_ekindata_t* ekind,
real dt,
- double xi[],
- double vxi[],
+ gmx::ArrayRef<double> xi,
+ gmx::ArrayRef<double> vxi,
const t_extmass* MassQ);
-void trotter_update(const t_inputrec* ir,
- int64_t step,
- gmx_ekindata_t* ekind,
- const gmx_enerdata_t* enerd,
- t_state* state,
- const tensor vir,
- const t_mdatoms* md,
- const t_extmass* MassQ,
- gmx::ArrayRef<std::vector<int>> trotter_seqlist,
- int trotter_seqno);
+void trotter_update(const t_inputrec* ir,
+ int64_t step,
+ gmx_ekindata_t* ekind,
+ const gmx_enerdata_t* enerd,
+ t_state* state,
+ const tensor vir,
+ int homenr,
+ gmx::ArrayRef<const unsigned short> cTC,
+ gmx::ArrayRef<const real> invMass,
+ const t_extmass* MassQ,
+ gmx::ArrayRef<std::vector<int>> trotter_seqlist,
+ int trotter_seqno);
std::array<std::vector<int>, ettTSEQMAX>
-init_npt_vars(const t_inputrec* ir, t_state* state, t_extmass* Mass, gmx_bool bTrotter);
+init_npt_vars(const t_inputrec* ir, t_state* state, t_extmass* Mass, bool bTrotter);
real NPT_energy(const t_inputrec* ir, const t_state* state, const t_extmass* MassQ);
/* computes all the pressure/tempertature control energy terms to get a conserved energy */
-void vrescale_tcoupl(const t_inputrec* ir, int64_t step, gmx_ekindata_t* ekind, real dt, double therm_integral[]);
+void vrescale_tcoupl(const t_inputrec* ir,
+ int64_t step,
+ gmx_ekindata_t* ekind,
+ real dt,
+ gmx::ArrayRef<double> therm_integral);
/* Compute temperature scaling. For V-rescale it is done in update. */
-void rescale_velocities(const gmx_ekindata_t* ekind, const t_mdatoms* mdatoms, int start, int end, rvec v[]);
+void rescale_velocities(const gmx_ekindata_t* ekind,
+ gmx::ArrayRef<const unsigned short> cTC,
+ int start,
+ int end,
+ gmx::ArrayRef<gmx::RVec> v);
/* Rescale the velocities with the scaling factor in ekind */
//! Check whether we do simulated annealing.
tensor boxv,
tensor M,
matrix mu,
- gmx_bool bFirstStep);
-
-void berendsen_pcoupl(FILE* fplog,
- int64_t step,
- const t_inputrec* ir,
- real dt,
- const tensor pres,
- const matrix box,
- const matrix force_vir,
- const matrix constraint_vir,
- matrix mu,
- double* baros_integral);
-
-void berendsen_pscale(const t_inputrec* ir,
- const matrix mu,
- matrix box,
- matrix box_rel,
- int start,
- int nr_atoms,
- rvec x[],
- const unsigned short cFREEZE[],
- t_nrnb* nrnb,
- bool scaleCoordinates);
-void crescale_pcoupl(FILE* fplog,
- int64_t step,
- const t_inputrec* ir,
- real dt,
- const tensor pres,
- const matrix box,
- const matrix force_vir,
- const matrix constraint_vir,
- matrix mu,
- double* baros_integral);
-
-void crescale_pscale(const t_inputrec* ir,
- const matrix mu,
- matrix box,
- matrix box_rel,
- int start,
- int nr_atoms,
- rvec x[],
- rvec v[],
- const unsigned short cFREEZE[],
- t_nrnb* nrnb,
- bool scaleCoordinates);
+ bool bFirstStep);
+
+/*! \brief Calculate the pressure coupling scaling matrix
+ *
+ * Used by Berendsen and C-Rescale pressure coupling, this function
+ * computes the current value of the scaling matrix. The template
+ * parameter determines the pressure coupling algorithm.
+ */
+template<PressureCoupling pressureCouplingType>
+void pressureCouplingCalculateScalingMatrix(FILE* fplog,
+ int64_t step,
+ const t_inputrec* ir,
+ real dt,
+ const tensor pres,
+ const matrix box,
+ const matrix force_vir,
+ const matrix constraint_vir,
+ matrix mu,
+ double* baros_integral);
+
+/*! \brief Scale the box and coordinates
+ *
+ * Used by Berendsen and C-Rescale pressure coupling, this function scales
+ * the box, the positions, and the velocities (C-Rescale only) according to
+ * the scaling matrix mu. The template parameter determines the pressure
+ * coupling algorithm.
+ */
+template<PressureCoupling pressureCouplingType>
+void pressureCouplingScaleBoxAndCoordinates(const t_inputrec* ir,
+ const matrix mu,
+ matrix box,
+ matrix box_rel,
+ int start,
+ int nr_atoms,
+ gmx::ArrayRef<gmx::RVec> x,
+ gmx::ArrayRef<gmx::RVec> v,
+ gmx::ArrayRef<const unsigned short> cFREEZE,
+ t_nrnb* nrnb,
+ bool scaleCoordinates);
void pleaseCiteCouplingAlgorithms(FILE* fplog, const t_inputrec& ir);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
DispersionCorrection::InteractionParams::~InteractionParams() = default;
/* Returns a matrix, as flat list, of combination rule combined LJ parameters */
-static std::vector<real> mk_nbfp_combination_rule(const gmx_ffparams_t& ffparams, const int comb_rule)
+static std::vector<real> mk_nbfp_combination_rule(const gmx_ffparams_t& ffparams,
+ const CombinationRule comb_rule)
{
const int atnr = ffparams.atnr;
const real c12j = ffparams.iparams[j * (atnr + 1)].lj.c12;
real c6 = std::sqrt(c6i * c6j);
real c12 = std::sqrt(c12i * c12j);
- if (comb_rule == eCOMB_ARITHMETIC && !gmx_numzero(c6) && !gmx_numzero(c12))
+ if (comb_rule == CombinationRule::Arithmetic && !gmx_numzero(c6) && !gmx_numzero(c12))
{
const real sigmai = gmx::sixthroot(c12i / c6i);
const real sigmaj = gmx::sixthroot(c12j / c6j);
* combination rules. */
if (EVDW_PME(inputrec.vdwtype))
{
- nbfp_comb = mk_nbfp_combination_rule(
- mtop.ffparams,
- (inputrec.ljpme_combination_rule == eljpmeLB) ? eCOMB_ARITHMETIC : eCOMB_GEOMETRIC);
+ nbfp_comb = mk_nbfp_combination_rule(mtop.ffparams,
+ (inputrec.ljpme_combination_rule == LongRangeVdW::LB)
+ ? CombinationRule::Arithmetic
+ : CombinationRule::Geometric);
for (int tpi = 0; tpi < ntp; ++tpi)
{
for (int tpj = 0; tpj < ntp; ++tpj)
nbfp = nbfp_comb;
}
- for (int q = 0; q < (inputrec.efep == efepNO ? 1 : 2); q++)
+ for (int q = 0; q < (inputrec.efep == FreeEnergyPerturbationType::No ? 1 : 2); q++)
{
double csix = 0;
double ctwelve = 0;
/* Count the types so we avoid natoms^2 operations */
std::vector<int> typecount(ntp);
- gmx_mtop_count_atomtypes(&mtop, q, typecount.data());
+ gmx_mtop_count_atomtypes(mtop, q, typecount.data());
for (int tpi = 0; tpi < ntp; tpi++)
{
InteractionCorrection energy;
InteractionCorrection virial;
- if ((ic.vdw_modifier == eintmodPOTSHIFT) || (ic.vdw_modifier == eintmodPOTSWITCH)
- || (ic.vdw_modifier == eintmodFORCESWITCH) || (ic.vdwtype == evdwSHIFT)
- || (ic.vdwtype == evdwSWITCH))
+ if ((ic.vdw_modifier == InteractionModifiers::PotShift)
+ || (ic.vdw_modifier == InteractionModifiers::PotSwitch)
+ || (ic.vdw_modifier == InteractionModifiers::ForceSwitch)
+ || (ic.vdwtype == VanDerWaalsType::Shift) || (ic.vdwtype == VanDerWaalsType::Switch))
{
- if (((ic.vdw_modifier == eintmodPOTSWITCH) || (ic.vdw_modifier == eintmodFORCESWITCH)
- || (ic.vdwtype == evdwSWITCH))
+ if (((ic.vdw_modifier == InteractionModifiers::PotSwitch)
+ || (ic.vdw_modifier == InteractionModifiers::ForceSwitch)
+ || (ic.vdwtype == VanDerWaalsType::Switch))
&& ic.rvdw_switch == 0)
{
gmx_fatal(FARGS,
"With dispersion correction rvdw-switch can not be zero "
"for vdw-type = %s",
- evdw_names[ic.vdwtype]);
+ enumValueToString(ic.vdwtype));
}
GMX_ASSERT(iParams->dispersionCorrectionTable_, "We need an initialized table");
* we need to calculate the constant shift up to the point where we
* start modifying the potential.
*/
- ri0 = (ic.vdw_modifier == eintmodPOTSHIFT) ? ri1 : ri0;
+ ri0 = (ic.vdw_modifier == InteractionModifiers::PotShift) ? ri1 : ri0;
const double r0 = ri0 / scale;
const double rc3 = r0 * r0 * r0;
const double rc9 = rc3 * rc3 * rc3;
- if ((ic.vdw_modifier == eintmodFORCESWITCH) || (ic.vdwtype == evdwSHIFT))
+ if ((ic.vdw_modifier == InteractionModifiers::ForceSwitch) || (ic.vdwtype == VanDerWaalsType::Shift))
{
/* Determine the constant energy shift below rvdw_switch.
* Table has a scale factor since we have scaled it down to compensate
iParams->enershiftsix_ = static_cast<real>(-1.0 / (rc3 * rc3)) - 6.0 * vdwtab[8 * ri0];
iParams->enershifttwelve_ = static_cast<real>(1.0 / (rc9 * rc3)) - 12.0 * vdwtab[8 * ri0 + 4];
}
- else if (ic.vdw_modifier == eintmodPOTSHIFT)
+ else if (ic.vdw_modifier == InteractionModifiers::PotShift)
{
iParams->enershiftsix_ = static_cast<real>(-1.0 / (rc3 * rc3));
iParams->enershifttwelve_ = static_cast<real>(1.0 / (rc9 * rc3));
*/
addCorrectionBeyondCutoff(&energy, &virial, r0);
}
- else if (ic.vdwtype == evdwCUT || EVDW_PME(ic.vdwtype) || ic.vdwtype == evdwUSER)
+ else if (ic.vdwtype == VanDerWaalsType::Cut || EVDW_PME(ic.vdwtype)
+ || ic.vdwtype == VanDerWaalsType::User)
{
/* Note that with LJ-PME, the dispersion correction is multiplied
* by the difference between the actual C6 and the value of C6
const double rc3 = ic.rvdw * ic.rvdw * ic.rvdw;
const double rc9 = rc3 * rc3 * rc3;
- if (ic.vdw_modifier == eintmodPOTSHIFT)
+ if (ic.vdw_modifier == InteractionModifiers::PotShift)
{
/* Contribution within the cut-off */
energy.dispersion += -4.0 * M_PI / (3.0 * rc3);
}
else
{
- gmx_fatal(FARGS, "Dispersion correction is not implemented for vdw-type = %s",
- evdw_names[ic.vdwtype]);
+ gmx_fatal(FARGS,
+ "Dispersion correction is not implemented for vdw-type = %s",
+ enumValueToString(ic.vdwtype));
}
iParams->enerdiffsix_ = energy.dispersion;
eFep_(inputrec.efep),
topParams_(mtop, inputrec, useBuckingham, numAtomTypes, nonbondedForceParameters)
{
- if (eDispCorr_ != edispcNO)
+ if (eDispCorr_ != DispersionCorrectionType::No)
{
GMX_RELEASE_ASSERT(tableFileName, "Need a table file name");
bool DispersionCorrection::correctFullInteraction() const
{
- return (eDispCorr_ == edispcAllEner || eDispCorr_ == edispcAllEnerPres);
+ return (eDispCorr_ == DispersionCorrectionType::AllEner
+ || eDispCorr_ == DispersionCorrectionType::AllEnerPres);
}
void DispersionCorrection::print(const gmx::MDLogger& mdlog) const
.asParagraph()
.appendText("WARNING: There are no atom pairs for dispersion correction");
}
- else if (vdwType_ == evdwUSER)
+ else if (vdwType_ == VanDerWaalsType::User)
{
GMX_LOG(mdlog.warning)
.asParagraph()
void DispersionCorrection::setParameters(const interaction_const_t& ic)
{
- if (eDispCorr_ != edispcNO)
+ if (eDispCorr_ != DispersionCorrectionType::No)
{
setInteractionParameters(&iParams_, ic, nullptr);
}
{
Correction corr;
- if (eDispCorr_ == edispcNO)
+ if (eDispCorr_ == DispersionCorrectionType::No)
{
return corr;
}
const bool bCorrAll = correctFullInteraction();
- const bool bCorrPres = (eDispCorr_ == edispcEnerPres || eDispCorr_ == edispcAllEnerPres);
+ const bool bCorrPres = (eDispCorr_ == DispersionCorrectionType::EnerPres
+ || eDispCorr_ == DispersionCorrectionType::AllEnerPres);
const real invvol = 1 / det(box);
const real density = topParams_.numAtomsForDensity_ * invvol;
real avcsix;
real avctwelve;
- if (eFep_ == efepNO)
+ if (eFep_ == FreeEnergyPerturbationType::No)
{
avcsix = topParams_.avcsix_[0];
avctwelve = topParams_.avctwelve_[0];
const real enerdiff = numCorr * (density * iParams_.enerdiffsix_ - iParams_.enershiftsix_);
corr.energy += avcsix * enerdiff;
real dvdlambda = 0;
- if (eFep_ != efepNO)
+ if (eFep_ != FreeEnergyPerturbationType::No)
{
dvdlambda += (topParams_.avcsix_[1] - topParams_.avcsix_[0]) * enerdiff;
}
{
const real enerdiff = numCorr * (density * iParams_.enerdifftwelve_ - iParams_.enershifttwelve_);
corr.energy += avctwelve * enerdiff;
- if (eFep_ != efepNO)
+ if (eFep_ != FreeEnergyPerturbationType::No)
{
dvdlambda += (topParams_.avctwelve_[1] - topParams_.avctwelve_[0]) * enerdiff;
}
if (bCorrPres)
{
corr.virial = numCorr * density * avcsix * iParams_.virdiffsix_ / 3.0;
- if (eDispCorr_ == edispcAllEnerPres)
+ if (eDispCorr_ == DispersionCorrectionType::AllEnerPres)
{
corr.virial += numCorr * density * avctwelve * iParams_.virdifftwelve_ / 3.0;
}
/* The factor 2 is because of the Gromacs virial definition */
- corr.pressure = -2.0 * invvol * corr.virial * PRESFAC;
+ corr.pressure = -2.0 * invvol * corr.virial * gmx::c_presfac;
}
- if (eFep_ != efepNO)
+ if (eFep_ != FreeEnergyPerturbationType::No)
{
corr.dvdl += dvdlambda;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct t_forcerec;
struct t_forcetable;
struct t_inputrec;
-
+enum class DispersionCorrectionType : int;
+enum class VanDerWaalsType : int;
+enum class FreeEnergyPerturbationType : int;
namespace gmx
{
template<typename>
bool correctFullInteraction() const;
//! Type of dispersion correction
- int eDispCorr_;
+ DispersionCorrectionType eDispCorr_;
//! Type of Van der Waals interaction
- int vdwType_;
+ VanDerWaalsType vdwType_;
//! Free-energy perturbation
- int eFep_;
+ FreeEnergyPerturbationType eFep_;
//! Topology parameters
TopologyParams topParams_;
//! Interaction parameters
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2012,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return index;
}
-// ICC 19 -O3 -msse2 generates wrong code. Lower optimization levels
-// and other SIMD levels seem fine, however.
-#if defined __ICC
-# pragma intel optimization_level 2
-#endif
void add_ebin(t_ebin* eb, int entryIndex, int nener, const real ener[], gmx_bool bSum)
{
int i, m;
if ((entryIndex + nener > eb->nener) || (entryIndex < 0))
{
- gmx_fatal(FARGS, "%s-%d: Energies out of range: entryIndex=%d nener=%d maxener=%d",
- __FILE__, __LINE__, entryIndex, nener, eb->nener);
+ gmx_fatal(FARGS,
+ "%s-%d: Energies out of range: entryIndex=%d nener=%d maxener=%d",
+ __FILE__,
+ __LINE__,
+ entryIndex,
+ nener,
+ eb->nener);
}
eg = &(eb->e[entryIndex]);
GMX_ASSERT(shouldUse.size() == ener.size(), "View sizes must match");
GMX_ASSERT(entryIndex + std::count(shouldUse.begin(), shouldUse.end(), true) <= eb->nener,
- gmx::formatString("Energies out of range: entryIndex=%d nener=%td maxener=%d", entryIndex,
- std::count(shouldUse.begin(), shouldUse.end(), true), eb->nener)
+ gmx::formatString("Energies out of range: entryIndex=%d nener=%td maxener=%d",
+ entryIndex,
+ std::count(shouldUse.begin(), shouldUse.end(), true),
+ eb->nener)
.c_str());
GMX_ASSERT(entryIndex >= 0, "Must have non-negative entry");
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
ForeignLambdaTerms::ForeignLambdaTerms(int numLambdas) :
- numLambdas_(numLambdas),
- energies_(1 + numLambdas),
- dhdl_(1 + numLambdas)
+ numLambdas_(numLambdas), energies_(1 + numLambdas), dhdl_(1 + numLambdas)
{
}
}
gmx_enerdata_t::gmx_enerdata_t(int numEnergyGroups, int numFepLambdas) :
- grpp(numEnergyGroups),
- foreignLambdaTerms(numFepLambdas),
- foreign_grpp(numEnergyGroups)
+ grpp(numEnergyGroups), foreignLambdaTerms(numFepLambdas), foreign_grpp(numEnergyGroups)
{
}
int i;
/* Accumulate energies */
- epot[F_COUL_SR] = sum_v(grpp.nener, grpp.ener[egCOULSR]);
- epot[F_LJ] = sum_v(grpp.nener, grpp.ener[egLJSR]);
- epot[F_LJ14] = sum_v(grpp.nener, grpp.ener[egLJ14]);
- epot[F_COUL14] = sum_v(grpp.nener, grpp.ener[egCOUL14]);
+ epot[F_COUL_SR] = sum_v(grpp.nener, grpp.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR]);
+ epot[F_LJ] = sum_v(grpp.nener, grpp.energyGroupPairTerms[NonBondedEnergyTerms::LJSR]);
+ epot[F_LJ14] = sum_v(grpp.nener, grpp.energyGroupPairTerms[NonBondedEnergyTerms::LJ14]);
+ epot[F_COUL14] = sum_v(grpp.nener, grpp.energyGroupPairTerms[NonBondedEnergyTerms::Coulomb14]);
/* lattice part of LR doesnt belong to any group
* and has been added earlier
*/
- epot[F_BHAM] = sum_v(grpp.nener, grpp.ener[egBHAMSR]);
+ epot[F_BHAM] = sum_v(grpp.nener, grpp.energyGroupPairTerms[NonBondedEnergyTerms::BuckinghamSR]);
epot[F_EPOT] = 0;
for (i = 0; (i < F_EPOT); i++)
}
// Adds computed dH/dlambda contribution i to the requested output
-static void set_dhdl_output(gmx_enerdata_t* enerd, int i, const t_lambda& fepvals)
+static void set_dhdl_output(gmx_enerdata_t* enerd, FreeEnergyPerturbationCouplingType i, const t_lambda& fepvals)
{
if (fepvals.separate_dvdl[i])
{
int index;
switch (i)
{
- case (efptMASS): index = F_DKDL; break;
- case (efptCOUL): index = F_DVDL_COUL; break;
- case (efptVDW): index = F_DVDL_VDW; break;
- case (efptBONDED): index = F_DVDL_BONDED; break;
- case (efptRESTRAINT): index = F_DVDL_RESTRAINT; break;
+ case (FreeEnergyPerturbationCouplingType::Mass): index = F_DKDL; break;
+ case (FreeEnergyPerturbationCouplingType::Coul): index = F_DVDL_COUL; break;
+ case (FreeEnergyPerturbationCouplingType::Vdw): index = F_DVDL_VDW; break;
+ case (FreeEnergyPerturbationCouplingType::Bonded): index = F_DVDL_BONDED; break;
+ case (FreeEnergyPerturbationCouplingType::Restraint): index = F_DVDL_RESTRAINT; break;
default: index = F_DVDL; break;
}
enerd->term[index] = enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i];
if (debug)
{
- fprintf(debug, "dvdl-%s[%2d]: %f: non-linear %f + linear %f\n", efpt_names[i], i,
- enerd->term[index], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]);
+ fprintf(debug,
+ "dvdl-%s[%2d]: %f: non-linear %f + linear %f\n",
+ enumValueToString(i),
+ static_cast<int>(i),
+ enerd->term[index],
+ enerd->dvdl_nonlin[i],
+ enerd->dvdl_lin[i]);
}
}
else
enerd->term[F_DVDL] += enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i];
if (debug)
{
- fprintf(debug, "dvd-%sl[%2d]: %f: non-linear %f + linear %f\n", efpt_names[0], i,
- enerd->term[F_DVDL], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]);
+ fprintf(debug,
+ "dvd-%sl[%2d]: %f: non-linear %f + linear %f\n",
+ enumValueToString(FreeEnergyPerturbationCouplingType::Fep),
+ static_cast<int>(i),
+ enerd->term[F_DVDL],
+ enerd->dvdl_nonlin[i],
+ enerd->dvdl_lin[i]);
}
}
}
}
double dvdl_lin = 0;
- for (int i = 0; i < efptNR; i++)
+ for (int i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
{
dvdl_lin += dvdlLinear[i];
}
void accumulatePotentialEnergies(gmx_enerdata_t* enerd, gmx::ArrayRef<const real> lambda, const t_lambda* fepvals)
{
- sum_epot(enerd->grpp, enerd->term);
+ sum_epot(enerd->grpp, enerd->term.data());
if (fepvals)
{
enerd->term[F_DVDL] = 0.0;
- for (int i = 0; i < efptNR; i++)
+ for (auto i : gmx::EnumerationWrapper<FreeEnergyPerturbationCouplingType>{})
{
// Skip kinetic terms here, as those are not available here yet
- if (i != efptMASS)
+ if (i != FreeEnergyPerturbationCouplingType::Mass)
{
set_dhdl_output(enerd, i, *fepvals);
}
// Treat current lambda, the deltaH contribution is 0 as delta-lambda=0 for the current lambda
accumulateKinetic(0, 0.0, energyTerms[F_DVDL_CONSTR]);
- if (!fepvals.separate_dvdl[efptMASS])
+ if (!fepvals.separate_dvdl[FreeEnergyPerturbationCouplingType::Mass])
{
accumulateKinetic(0, 0.0, energyTerms[F_DKDL]);
}
* a linear extrapolation. This is an approximation, but usually
* quite accurate since constraints change little between lambdas.
*/
- const int lambdaIndex = (fepvals.separate_dvdl[efptBONDED] ? efptBONDED : efptFEP);
- const double dlam = fepvals.all_lambda[lambdaIndex][i] - lambda[lambdaIndex];
+ const FreeEnergyPerturbationCouplingType lambdaIndex =
+ (fepvals.separate_dvdl[FreeEnergyPerturbationCouplingType::Bonded]
+ ? FreeEnergyPerturbationCouplingType::Bonded
+ : FreeEnergyPerturbationCouplingType::Fep);
+ const double dlam = fepvals.all_lambda[lambdaIndex][i] - lambda[static_cast<int>(lambdaIndex)];
accumulateKinetic(1 + i, dlam * energyTerms[F_DVDL_CONSTR], energyTerms[F_DVDL_CONSTR]);
- if (!fepvals.separate_dvdl[efptMASS])
+ if (!fepvals.separate_dvdl[FreeEnergyPerturbationCouplingType::Mass])
{
- const double dlam = fepvals.all_lambda[efptMASS][i] - lambda[efptMASS];
+ const double dlam = fepvals.all_lambda[FreeEnergyPerturbationCouplingType::Mass][i]
+ - lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Mass)];
accumulateKinetic(1 + i, dlam * energyTerms[F_DKDL], energyTerms[F_DKDL]);
}
}
gmx::ArrayRef<const real> lambda,
const t_lambda& fepvals)
{
- if (fepvals.separate_dvdl[efptBONDED])
+ if (fepvals.separate_dvdl[FreeEnergyPerturbationCouplingType::Bonded])
{
enerd->term[F_DVDL_BONDED] += enerd->term[F_DVDL_CONSTR];
}
}
// Add computed mass dH/dlambda contribution to the requested output
- set_dhdl_output(enerd, efptMASS, fepvals);
+ set_dhdl_output(enerd, FreeEnergyPerturbationCouplingType::Mass, fepvals);
- enerd->foreignLambdaTerms.finalizeKineticContributions(enerd->term, enerd->dvdl_lin[efptMASS],
- lambda, fepvals);
+ enerd->foreignLambdaTerms.finalizeKineticContributions(
+ enerd->term, enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Mass], lambda, fepvals);
/* The constrain contribution is now included in other terms, so clear it */
enerd->term[F_DVDL_CONSTR] = 0;
/* First reset all foreign energy components. Foreign energies always called on
neighbor search steps */
- for (i = 0; (i < egNR); i++)
+ for (i = 0; (i < static_cast<int>(NonBondedEnergyTerms::Count)); i++)
{
for (j = 0; (j < enerd->grpp.nener); j++)
{
- enerd->foreign_grpp.ener[i][j] = 0.0;
+ enerd->foreign_grpp.energyGroupPairTerms[i][j] = 0.0;
}
}
void reset_dvdl_enerdata(gmx_enerdata_t* enerd)
{
- for (int i = 0; i < efptNR; i++)
+ for (auto i : keysOf(enerd->dvdl_lin))
{
enerd->dvdl_lin[i] = 0.0;
enerd->dvdl_nonlin[i] = 0.0;
int i, j;
/* First reset all energy components. */
- for (i = 0; (i < egNR); i++)
+ for (i = 0; (i < static_cast<int>(NonBondedEnergyTerms::Count)); i++)
{
for (j = 0; (j < enerd->grpp.nener); j++)
{
- enerd->grpp.ener[i][j] = 0.0_real;
+ enerd->grpp.energyGroupPairTerms[i][j] = 0.0_real;
}
}
if (timeInterval() > 0)
{
mesg = formatString("Energy conservation over %s of length %g ns, time %g to %g ns\n",
- partName.c_str(), timeInterval(), firstTime_, lastTime_);
+ partName.c_str(),
+ timeInterval(),
+ firstTime_,
+ lastTime_);
mesg += formatString(" Conserved energy drift: %.2e kJ/mol/ps per atom\n", energyDrift());
}
else
{
mesg = formatString(
"Time interval for measuring conserved energy has length 0, time %g to %g\n",
- firstTime_, lastTime_);
+ firstTime_,
+ lastTime_);
}
return mesg;
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/topology/mtop_util.h"
#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/arraysize.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/mdmodulenotification.h"
+#include "gromacs/utility/mdmodulesnotifiers.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
//! Labels for energy file quantities
//! \{
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static const char* conrmsd_nm[] = { "Constr. rmsd", "Constr.2 rmsd" };
-static std::array<const char*, 3> boxs_nm = { "Box-X", "Box-Y", "Box-Z" };
+static constexpr std::array<const char*, 3> boxs_nm = { "Box-X", "Box-Y", "Box-Z" };
-static std::array<const char*, 6> tricl_boxs_nm = { "Box-XX", "Box-YY", "Box-ZZ",
- "Box-YX", "Box-ZX", "Box-ZY" };
+static constexpr std::array<const char*, 6> tricl_boxs_nm = { "Box-XX", "Box-YY", "Box-ZZ",
+ "Box-YX", "Box-ZX", "Box-ZY" };
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static const char* vol_nm[] = { "Volume" };
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static const char* dens_nm[] = { "Density" };
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static const char* pv_nm[] = { "pV" };
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static const char* enthalpy_nm[] = { "Enthalpy" };
-static std::array<const char*, 6> boxvel_nm = { "Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
- "Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY" };
+static constexpr std::array<const char*, 6> boxvel_nm = { "Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
+ "Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY" };
+
+const char* enumValueToString(NonBondedEnergyTerms enumValue)
+{
+ static constexpr gmx::EnumerationArray<NonBondedEnergyTerms, const char*> nonBondedEnergyTermTypeNames = {
+ "Coul-SR", "LJ-SR", "Buck-SR", "Coul-14", "LJ-14"
+ };
+ return nonBondedEnergyTermTypeNames[enumValue];
+}
-const char* egrp_nm[egNR + 1] = { "Coul-SR", "LJ-SR", "Buck-SR", "Coul-14", "LJ-14", nullptr };
//! \}
namespace gmx
* \todo Remove GMX_CONSTRAINTVIR
* \todo Write free-energy output also to energy file (after adding more tests)
*/
-EnergyOutput::EnergyOutput(ener_file* fp_ene,
- const gmx_mtop_t* mtop,
- const t_inputrec* ir,
- const pull_t* pull_work,
- FILE* fp_dhdl,
- bool isRerun,
- const StartingBehavior startingBehavior,
- const bool simulationsShareState,
- const MdModulesNotifier& mdModulesNotifier)
+EnergyOutput::EnergyOutput(ener_file* fp_ene,
+ const gmx_mtop_t& mtop,
+ const t_inputrec& inputrec,
+ const pull_t* pull_work,
+ FILE* fp_dhdl,
+ bool isRerun,
+ const StartingBehavior startingBehavior,
+ const bool simulationsShareState,
+ const MDModulesNotifiers& mdModulesNotifiers)
{
const char* ener_nm[F_NRE];
static const char* vir_nm[] = { "Vir-XX", "Vir-XY", "Vir-XZ", "Vir-YX", "Vir-YY",
char** gnm;
char buf[256];
const char* bufi;
- int i, j, ni, nj, n, k, kk, ncon, nset;
+ int i, j, ni, nj, n, ncon, nset;
bool bBHAM, b14;
- if (EI_DYNAMICS(ir->eI))
+ if (EI_DYNAMICS(inputrec.eI))
{
- delta_t_ = ir->delta_t;
+ delta_t_ = inputrec.delta_t;
}
else
{
delta_t_ = 0;
}
- groups = &mtop->groups;
+ groups = &mtop.groups;
- bBHAM = (mtop->ffparams.numTypes() > 0) && (mtop->ffparams.functype[0] == F_BHAM);
+ bBHAM = (mtop.ffparams.numTypes() > 0) && (mtop.ffparams.functype[0] == F_BHAM);
b14 = (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 || gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0);
ncon = gmx_mtop_ftype_count(mtop, F_CONSTR);
nCrmsd_ = 0;
if (bConstr)
{
- if (ncon > 0 && ir->eConstrAlg == econtLINCS)
+ if (ncon > 0 && inputrec.eConstrAlg == ConstraintAlgorithm::Lincs)
{
nCrmsd_ = 1;
}
}
/* Energy monitoring */
- for (i = 0; i < egNR; i++)
+ for (auto& term : bEInd_)
{
- bEInd_[i] = false;
+ term = false;
}
// Setting true only to those energy terms, that have active interactions and
if (!isRerun)
{
- bEner_[F_EKIN] = EI_DYNAMICS(ir->eI);
- bEner_[F_ETOT] = EI_DYNAMICS(ir->eI);
- bEner_[F_TEMP] = EI_DYNAMICS(ir->eI);
+ bEner_[F_EKIN] = EI_DYNAMICS(inputrec.eI);
+ bEner_[F_ETOT] = EI_DYNAMICS(inputrec.eI);
+ bEner_[F_TEMP] = EI_DYNAMICS(inputrec.eI);
- bEner_[F_ECONSERVED] = integratorHasConservedEnergyQuantity(ir);
- bEner_[F_PDISPCORR] = (ir->eDispCorr != edispcNO);
+ bEner_[F_ECONSERVED] = integratorHasConservedEnergyQuantity(&inputrec);
+ bEner_[F_PDISPCORR] = (inputrec.eDispCorr != DispersionCorrectionType::No);
bEner_[F_PRES] = true;
}
- bEner_[F_LJ] = !bBHAM;
- bEner_[F_BHAM] = bBHAM;
- bEner_[F_EQM] = ir->bQMMM;
- bEner_[F_RF_EXCL] = (EEL_RF(ir->coulombtype) && ir->cutoff_scheme == ecutsGROUP);
- bEner_[F_COUL_RECIP] = EEL_FULL(ir->coulombtype);
- bEner_[F_LJ_RECIP] = EVDW_PME(ir->vdwtype);
+ bEner_[F_LJ] = !bBHAM;
+ bEner_[F_BHAM] = bBHAM;
+ bEner_[F_EQM] = inputrec.bQMMM;
+ bEner_[F_RF_EXCL] = (EEL_RF(inputrec.coulombtype) && inputrec.cutoff_scheme == CutoffScheme::Group);
+ bEner_[F_COUL_RECIP] = EEL_FULL(inputrec.coulombtype);
+ bEner_[F_LJ_RECIP] = EVDW_PME(inputrec.vdwtype);
bEner_[F_LJ14] = b14;
bEner_[F_COUL14] = b14;
bEner_[F_LJC14_Q] = false;
bEner_[F_LJC_PAIRS_NB] = false;
- bEner_[F_DVDL_COUL] = (ir->efep != efepNO) && ir->fepvals->separate_dvdl[efptCOUL];
- bEner_[F_DVDL_VDW] = (ir->efep != efepNO) && ir->fepvals->separate_dvdl[efptVDW];
- bEner_[F_DVDL_BONDED] = (ir->efep != efepNO) && ir->fepvals->separate_dvdl[efptBONDED];
- bEner_[F_DVDL_RESTRAINT] = (ir->efep != efepNO) && ir->fepvals->separate_dvdl[efptRESTRAINT];
- bEner_[F_DKDL] = (ir->efep != efepNO) && ir->fepvals->separate_dvdl[efptMASS];
- bEner_[F_DVDL] = (ir->efep != efepNO) && ir->fepvals->separate_dvdl[efptFEP];
+ bEner_[F_DVDL_COUL] = (inputrec.efep != FreeEnergyPerturbationType::No)
+ && inputrec.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Coul];
+ bEner_[F_DVDL_VDW] = (inputrec.efep != FreeEnergyPerturbationType::No)
+ && inputrec.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Vdw];
+ bEner_[F_DVDL_BONDED] = (inputrec.efep != FreeEnergyPerturbationType::No)
+ && inputrec.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Bonded];
+ bEner_[F_DVDL_RESTRAINT] =
+ (inputrec.efep != FreeEnergyPerturbationType::No)
+ && inputrec.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Restraint];
+ bEner_[F_DKDL] = (inputrec.efep != FreeEnergyPerturbationType::No)
+ && inputrec.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Mass];
+ bEner_[F_DVDL] = (inputrec.efep != FreeEnergyPerturbationType::No)
+ && inputrec.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep];
bEner_[F_CONSTR] = false;
bEner_[F_CONSTRNC] = false;
bEner_[F_COUL_SR] = true;
bEner_[F_EPOT] = true;
- bEner_[F_DISPCORR] = (ir->eDispCorr != edispcNO);
+ bEner_[F_DISPCORR] = (inputrec.eDispCorr != DispersionCorrectionType::No);
bEner_[F_DISRESVIOL] = (gmx_mtop_ftype_count(mtop, F_DISRES) > 0);
bEner_[F_ORIRESDEV] = (gmx_mtop_ftype_count(mtop, F_ORIRES) > 0);
- bEner_[F_COM_PULL] = ((ir->bPull && pull_have_potential(*pull_work)) || ir->bRot);
+ bEner_[F_COM_PULL] = ((inputrec.bPull && pull_have_potential(*pull_work)) || inputrec.bRot);
- MdModulesEnergyOutputToDensityFittingRequestChecker mdModulesAddOutputToDensityFittingFieldRequest;
- mdModulesNotifier.simulationSetupNotifications_.notify(&mdModulesAddOutputToDensityFittingFieldRequest);
+ MDModulesEnergyOutputToDensityFittingRequestChecker mdModulesAddOutputToDensityFittingFieldRequest;
+ mdModulesNotifiers.simulationSetupNotifier_.notify(&mdModulesAddOutputToDensityFittingFieldRequest);
bEner_[F_DENSITYFITTING] = mdModulesAddOutputToDensityFittingFieldRequest.energyOutputToDensityFitting_;
}
}
- epc_ = isRerun ? epcNO : ir->epc;
- bDiagPres_ = !TRICLINIC(ir->ref_p) && !isRerun;
- ref_p_ = (ir->ref_p[XX][XX] + ir->ref_p[YY][YY] + ir->ref_p[ZZ][ZZ]) / DIM;
- bTricl_ = TRICLINIC(ir->compress) || TRICLINIC(ir->deform);
- bDynBox_ = inputrecDynamicBox(ir);
- etc_ = isRerun ? etcNO : ir->etc;
- bNHC_trotter_ = inputrecNvtTrotter(ir) && !isRerun;
- bPrintNHChains_ = ir->bPrintNHChains && !isRerun;
- bMTTK_ = (inputrecNptTrotter(ir) || inputrecNphTrotter(ir)) && !isRerun;
- bMu_ = inputrecNeedMutot(ir);
+ epc_ = isRerun ? PressureCoupling::No : inputrec.epc;
+ bDiagPres_ = !TRICLINIC(inputrec.ref_p) && !isRerun;
+ ref_p_ = (inputrec.ref_p[XX][XX] + inputrec.ref_p[YY][YY] + inputrec.ref_p[ZZ][ZZ]) / DIM;
+ bTricl_ = TRICLINIC(inputrec.compress) || TRICLINIC(inputrec.deform);
+ bDynBox_ = inputrecDynamicBox(&inputrec);
+ etc_ = isRerun ? TemperatureCoupling::No : inputrec.etc;
+ bNHC_trotter_ = inputrecNvtTrotter(&inputrec) && !isRerun;
+ bPrintNHChains_ = inputrec.bPrintNHChains && !isRerun;
+ bMTTK_ = (inputrecNptTrotter(&inputrec) || inputrecNphTrotter(&inputrec)) && !isRerun;
+ bMu_ = inputrecNeedMutot(&inputrec);
bPres_ = !isRerun;
ebin_ = mk_ebin();
}
if (bDynBox_)
{
- ib_ = get_ebin_space(ebin_, bTricl_ ? tricl_boxs_nm.size() : boxs_nm.size(),
- bTricl_ ? tricl_boxs_nm.data() : boxs_nm.data(), unit_length);
+ ib_ = get_ebin_space(ebin_,
+ bTricl_ ? tricl_boxs_nm.size() : boxs_nm.size(),
+ bTricl_ ? tricl_boxs_nm.data() : boxs_nm.data(),
+ unit_length);
ivol_ = get_ebin_space(ebin_, 1, vol_nm, unit_volume);
idens_ = get_ebin_space(ebin_, 1, dens_nm, unit_density_SI);
if (bDiagPres_)
ipres_ = get_ebin_space(ebin_, asize(pres_nm), pres_nm, unit_pres_bar);
isurft_ = get_ebin_space(ebin_, asize(surft_nm), surft_nm, unit_surft_bar);
}
- if (epc_ == epcPARRINELLORAHMAN || epc_ == epcMTTK)
+ if (epc_ == PressureCoupling::ParrinelloRahman || epc_ == PressureCoupling::Mttk)
{
ipc_ = get_ebin_space(ebin_, bTricl_ ? boxvel_nm.size() : DIM, boxvel_nm.data(), unit_vel);
}
{
imu_ = get_ebin_space(ebin_, asize(mu_nm), mu_nm, unit_dipole_D);
}
- if (ir->cos_accel != 0)
+ if (inputrec.cos_accel != 0)
{
ivcos_ = get_ebin_space(ebin_, asize(vcos_nm), vcos_nm, unit_vel);
ivisc_ = get_ebin_space(ebin_, asize(visc_nm), visc_nm, unit_invvisc_SI);
}
/* Energy monitoring */
- for (i = 0; i < egNR; i++)
+ for (auto& term : bEInd_)
{
- bEInd_[i] = false;
+ term = false;
}
- bEInd_[egCOULSR] = true;
- bEInd_[egLJSR] = true;
+ bEInd_[NonBondedEnergyTerms::CoulombSR] = true;
+ bEInd_[NonBondedEnergyTerms::LJSR] = true;
if (bBHAM)
{
- bEInd_[egLJSR] = false;
- bEInd_[egBHAMSR] = true;
+ bEInd_[NonBondedEnergyTerms::LJSR] = false;
+ bEInd_[NonBondedEnergyTerms::BuckinghamSR] = true;
}
if (b14)
{
- bEInd_[egLJ14] = true;
- bEInd_[egCOUL14] = true;
+ bEInd_[NonBondedEnergyTerms::LJ14] = true;
+ bEInd_[NonBondedEnergyTerms::Coulomb14] = true;
}
nEc_ = 0;
- for (i = 0; (i < egNR); i++)
+ for (auto term : bEInd_)
{
- if (bEInd_[i])
+ if (term)
{
nEc_++;
}
nEg_ = n;
nE_ = (n * (n + 1)) / 2;
- snew(igrp_, nE_);
+ igrp_.resize(nE_);
if (nE_ > 1)
{
n = 0;
snew(gnm, nEc_);
- for (k = 0; (k < nEc_); k++)
+ for (int k = 0; (k < nEc_); k++)
{
snew(gnm[k], STRLEN);
}
ni = groups->groups[SimulationAtomGroupType::EnergyOutput][i];
for (j = i; (j < gmx::ssize(groups->groups[SimulationAtomGroupType::EnergyOutput])); j++)
{
- nj = groups->groups[SimulationAtomGroupType::EnergyOutput][j];
- for (k = kk = 0; (k < egNR); k++)
+ nj = groups->groups[SimulationAtomGroupType::EnergyOutput][j];
+ int k = 0;
+ for (auto key : keysOf(bEInd_))
{
- if (bEInd_[k])
+ if (bEInd_[key])
{
- sprintf(gnm[kk], "%s:%s-%s", egrp_nm[k], *(groups->groupNames[ni]),
+ sprintf(gnm[k],
+ "%s:%s-%s",
+ enumValueToString(key),
+ *(groups->groupNames[ni]),
*(groups->groupNames[nj]));
- kk++;
+ k++;
}
}
igrp_[n] = get_ebin_space(ebin_, nEc_, gnm, unit_energy);
n++;
}
}
- for (k = 0; (k < nEc_); k++)
+ for (int k = 0; (k < nEc_); k++)
{
sfree(gnm[k]);
}
}
nTC_ = isRerun ? 0 : groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
- nNHC_ = ir->opts.nhchainlength; /* shorthand for number of NH chains */
+ nNHC_ = inputrec.opts.nhchainlength; /* shorthand for number of NH chains */
if (bMTTK_)
{
nTCP_ = 1; /* assume only one possible coupling system for barostat
{
nTCP_ = 0;
}
- if (etc_ == etcNOSEHOOVER)
+ if (etc_ == TemperatureCoupling::NoseHoover)
{
if (bNHC_trotter_)
{
{
mde_n_ = 2 * nTC_;
}
- if (epc_ == epcMTTK)
+ if (epc_ == PressureCoupling::Mttk)
{
mdeb_n_ = 2 * nNHC_ * nTCP_;
}
mdeb_n_ = 0;
}
- snew(tmp_r_, mde_n_);
+ tmp_r_.resize(mde_n_);
// TODO redo the group name memory management to make it more clear
char** grpnms;
snew(grpnms, std::max(mde_n_, mdeb_n_)); // Just in case mdeb_n_ > mde_n_
}
int allocated = 0;
- if (etc_ == etcNOSEHOOVER)
+ if (etc_ == TemperatureCoupling::NoseHoover)
{
if (bPrintNHChains_)
{
}
}
}
- else if (etc_ == etcBERENDSEN || etc_ == etcYES || etc_ == etcVRESCALE)
+ else if (etc_ == TemperatureCoupling::Berendsen || etc_ == TemperatureCoupling::Yes
+ || etc_ == TemperatureCoupling::VRescale)
{
for (i = 0; (i < nTC_); i++)
{
}
sfree(grpnms);
- nU_ = groups->groups[SimulationAtomGroupType::Acceleration].size();
- snew(tmp_v_, nU_);
- if (nU_ > 1)
- {
- snew(grpnms, 3 * nU_);
- for (i = 0; (i < nU_); i++)
- {
- ni = groups->groups[SimulationAtomGroupType::Acceleration][i];
- sprintf(buf, "Ux-%s", *(groups->groupNames[ni]));
- grpnms[3 * i + XX] = gmx_strdup(buf);
- sprintf(buf, "Uy-%s", *(groups->groupNames[ni]));
- grpnms[3 * i + YY] = gmx_strdup(buf);
- sprintf(buf, "Uz-%s", *(groups->groupNames[ni]));
- grpnms[3 * i + ZZ] = gmx_strdup(buf);
- }
- iu_ = get_ebin_space(ebin_, 3 * nU_, grpnms, unit_vel);
- for (i = 0; i < 3 * nU_; i++)
- {
- sfree(grpnms[i]);
- }
- sfree(grpnms);
- }
-
/* Note that fp_ene should be valid on the master rank and null otherwise */
if (fp_ene != nullptr && startingBehavior != StartingBehavior::RestartWithAppending)
{
/* check whether we're going to write dh histograms */
dhc_ = nullptr;
- if (ir->fepvals->separate_dhdl_file == esepdhdlfileNO)
+ if (inputrec.fepvals->separate_dhdl_file == SeparateDhdlFile::No)
{
/* Currently dh histograms are only written with dynamics */
- if (EI_DYNAMICS(ir->eI))
+ if (EI_DYNAMICS(inputrec.eI))
{
- snew(dhc_, 1);
-
- mde_delta_h_coll_init(dhc_, ir);
+ dhc_ = std::make_unique<t_mde_delta_h_coll>(inputrec);
}
fp_dhdl_ = nullptr;
- snew(dE_, ir->fepvals->n_lambda);
+ dE_.resize(inputrec.fepvals->n_lambda);
}
else
{
fp_dhdl_ = fp_dhdl;
- snew(dE_, ir->fepvals->n_lambda);
+ dE_.resize(inputrec.fepvals->n_lambda);
}
- if (ir->bSimTemp)
+ if (inputrec.bSimTemp)
{
- int i;
- snew(temperatures_, ir->fepvals->n_lambda);
- numTemperatures_ = ir->fepvals->n_lambda;
- for (i = 0; i < ir->fepvals->n_lambda; i++)
- {
- temperatures_[i] = ir->simtempvals->temperatures[i];
- }
- }
- else
- {
- numTemperatures_ = 0;
+ temperatures_ = inputrec.simtempvals->temperatures;
}
- if (EI_MD(ir->eI) && !simulationsShareState)
+ if (EI_MD(inputrec.eI) && !simulationsShareState)
{
- conservedEnergyTracker_ = std::make_unique<EnergyDriftTracker>(mtop->natoms);
+ conservedEnergyTracker_ = std::make_unique<EnergyDriftTracker>(mtop.natoms);
}
}
EnergyOutput::~EnergyOutput()
{
- sfree(igrp_);
- sfree(tmp_r_);
- sfree(tmp_v_);
done_ebin(ebin_);
- done_mde_delta_h_coll(dhc_);
- sfree(dE_);
- if (numTemperatures_ > 0)
- {
- sfree(temperatures_);
- }
}
} // namespace gmx
*/
static void print_lambda_vector(t_lambda* fep, int i, bool get_native_lambda, bool get_names, char* str)
{
- int j, k = 0;
+ int k = 0;
int Nsep = 0;
- for (j = 0; j < efptNR; j++)
+ for (auto j : keysOf(fep->separate_dvdl))
{
if (fep->separate_dvdl[j])
{
{
str += sprintf(str, "("); /* set the opening parenthesis*/
}
- for (j = 0; j < efptNR; j++)
+ for (auto j : keysOf(fep->separate_dvdl))
{
if (fep->separate_dvdl[j])
{
}
else
{
- str += sprintf(str, "%s", efpt_singular_names[j]);
+ str += sprintf(str, "%s", enumValueToStringSingular(j));
}
/* print comma for the next item */
if (k < Nsep - 1)
*lambdastate = "\\lambda state";
int i, nsets, nsets_de, nsetsbegin;
int n_lambda_terms = 0;
- t_lambda* fep = ir->fepvals; /* for simplicity */
- t_expanded* expand = ir->expandedvals;
+ t_lambda* fep = ir->fepvals.get(); /* for simplicity */
+ t_expanded* expand = ir->expandedvals.get();
char lambda_vec_str[STRLEN], lambda_name_str[STRLEN];
int nsets_dhdl = 0;
bool write_pV = false;
/* count the number of different lambda terms */
- for (i = 0; i < efptNR; i++)
+ for (auto i : keysOf(fep->separate_dvdl))
{
if (fep->separate_dvdl[i])
{
{
title = gmx::formatString("%s and %s", dhdl, deltag);
label_x = gmx::formatString("Time (ps)");
- label_y = gmx::formatString("%s and %s (%s %s)", dhdl, deltag, unit_energy,
- "[\\8l\\4]\\S-1\\N");
+ label_y = gmx::formatString(
+ "%s and %s (%s %s)", dhdl, deltag, unit_energy, "[\\8l\\4]\\S-1\\N");
}
fp = gmx_fio_fopen(filename, "w+");
xvgr_header(fp, title.c_str(), label_x, label_y, exvggtXNY, oenv);
{
buf = gmx::formatString("T = %g (K) ", ir->opts.ref_t[0]);
}
- if ((ir->efep != efepSLOWGROWTH) && (ir->efep != efepEXPANDED))
+ if ((ir->efep != FreeEnergyPerturbationType::SlowGrowth)
+ && (ir->efep != FreeEnergyPerturbationType::Expanded))
{
if ((fep->init_lambda >= 0) && (n_lambda_terms == 1))
{
{
print_lambda_vector(fep, fep->init_fep_state, true, false, lambda_vec_str);
print_lambda_vector(fep, fep->init_fep_state, true, true, lambda_name_str);
- buf += gmx::formatString("%s %d: %s = %s", lambdastate, fep->init_fep_state,
- lambda_name_str, lambda_vec_str);
+ buf += gmx::formatString(
+ "%s %d: %s = %s", lambdastate, fep->init_fep_state, lambda_name_str, lambda_vec_str);
}
}
xvgr_subtitle(fp, buf.c_str(), oenv);
nsets_dhdl = 0;
- if (fep->dhdl_derivatives == edhdlderivativesYES)
+ if (fep->dhdl_derivatives == DhDlDerivativeCalculation::Yes)
{
nsets_dhdl = n_lambda_terms;
}
nsets = nsets_dhdl + nsets_de; /* dhdl + fep differences */
- if (fep->n_lambda > 0 && (expand->elmcmove > elmcmoveNO))
+ if (fep->n_lambda > 0 && (expand->elmcmove > LambdaMoveCalculation::No))
{
nsets += 1; /*add fep state for expanded ensemble */
}
- if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
+ if (fep->edHdLPrintEnergy != FreeEnergyPrintEnergy::No)
{
nsets += 1; /* add energy to the dhdl as well */
}
nsetsextend = nsets;
- if ((ir->epc != epcNO) && (fep->n_lambda > 0) && (fep->init_lambda < 0))
+ if ((ir->epc != PressureCoupling::No) && (fep->n_lambda > 0) && (fep->init_lambda < 0))
{
nsetsextend += 1; /* for PV term, other terms possible if required for
the reduced potential (only needed with foreign
}
std::vector<std::string> setname(nsetsextend);
- if (expand->elmcmove > elmcmoveNO)
+ if (expand->elmcmove > LambdaMoveCalculation::No)
{
/* state for the fep_vals, if we have alchemical sampling */
setname[s++] = "Thermodynamic state";
}
- if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
+ if (fep->edHdLPrintEnergy != FreeEnergyPrintEnergy::No)
{
std::string energy;
switch (fep->edHdLPrintEnergy)
{
- case edHdLPrintEnergyPOTENTIAL:
+ case FreeEnergyPrintEnergy::Potential:
energy = gmx::formatString("%s (%s)", "Potential Energy", unit_energy);
break;
- case edHdLPrintEnergyTOTAL:
- case edHdLPrintEnergyYES:
+ case FreeEnergyPrintEnergy::Total:
+ case FreeEnergyPrintEnergy::Yes:
default: energy = gmx::formatString("%s (%s)", "Total Energy", unit_energy);
}
setname[s++] = energy;
}
- if (fep->dhdl_derivatives == edhdlderivativesYES)
+ if (fep->dhdl_derivatives == DhDlDerivativeCalculation::Yes)
{
- for (i = 0; i < efptNR; i++)
+ for (auto i : keysOf(fep->separate_dvdl))
{
if (fep->separate_dvdl[i])
{
{
lam = fep->all_lambda[i][fep->init_fep_state];
}
- derivative = gmx::formatString("%s %s = %.4f", dhdl, efpt_singular_names[i], lam);
+ derivative = gmx::formatString("%s %s = %.4f", dhdl, enumValueToStringSingular(i), lam);
}
setname[s++] = derivative;
}
* from this xvg legend.
*/
- if (expand->elmcmove > elmcmoveNO)
+ if (expand->elmcmove > LambdaMoveCalculation::No)
{
nsetsbegin = 1; /* for including the expanded ensemble */
}
nsetsbegin = 0;
}
- if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
+ if (fep->edHdLPrintEnergy != FreeEnergyPrintEnergy::No)
{
nsetsbegin += 1;
}
const rvec mu_tot,
const gmx::Constraints* constr)
{
- int j, k, kk, n, gid;
- real crmsd[2], tmp6[6];
- real bs[tricl_boxs_nm.size()], vol, dens, pv, enthalpy;
- real eee[egNR];
- double store_dhdl[efptNR];
- real store_energy = 0;
- real tmp;
+ int j, k, kk, n, gid;
+ real crmsd[2], tmp6[6];
+ real bs[tricl_boxs_nm.size()], vol, dens, enthalpy;
+ real eee[static_cast<int>(NonBondedEnergyTerms::Count)];
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, double> store_dhdl;
+ real store_energy = 0;
+ real tmp;
+ real pv = 0.0; // static analyzer warns about uninitialized variable warnings here.
/* Do NOT use the box in the state variable, but the separate box provided
* as an argument. This is because we sometimes need to write the box from
nboxs = boxs_nm.size();
}
vol = box[XX][XX] * box[YY][YY] * box[ZZ][ZZ];
- dens = (tmass * AMU) / (vol * NANO * NANO * NANO);
+ dens = (tmass * gmx::c_amu) / (vol * gmx::c_nano * gmx::c_nano * gmx::c_nano);
add_ebin(ebin_, ib_, nboxs, bs, bSum);
add_ebin(ebin_, ivol_, 1, &vol, bSum);
add_ebin(ebin_, idens_, 1, &dens, bSum);
{
/* This is pV (in kJ/mol). The pressure is the reference pressure,
not the instantaneous pressure */
- pv = vol * ref_p_ / PRESFAC;
+ pv = vol * ref_p_ / gmx::c_presfac;
add_ebin(ebin_, ipv_, 1, &pv, bSum);
enthalpy = pv + enerd->term[F_ETOT];
tmp = (pres[ZZ][ZZ] - (pres[XX][XX] + pres[YY][YY]) * 0.5) * box[ZZ][ZZ];
add_ebin(ebin_, isurft_, 1, &tmp, bSum);
}
- if (epc_ == epcPARRINELLORAHMAN || epc_ == epcMTTK)
+ if (epc_ == PressureCoupling::ParrinelloRahman || epc_ == PressureCoupling::Mttk)
{
tmp6[0] = ptCouplingArrays.boxv[XX][XX];
tmp6[1] = ptCouplingArrays.boxv[YY][YY];
if (ekind && ekind->cosacc.cos_accel != 0)
{
vol = box[XX][XX] * box[YY][YY] * box[ZZ][ZZ];
- dens = (tmass * AMU) / (vol * NANO * NANO * NANO);
+ dens = (tmass * gmx::c_amu) / (vol * gmx::c_nano * gmx::c_nano * gmx::c_nano);
add_ebin(ebin_, ivcos_, 1, &(ekind->cosacc.vcos), bSum);
/* 1/viscosity, unit 1/(kg m^-1 s^-1) */
tmp = 1
- / (ekind->cosacc.cos_accel / (ekind->cosacc.vcos * PICO) * dens
- * gmx::square(box[ZZ][ZZ] * NANO / (2 * M_PI)));
+ / (ekind->cosacc.cos_accel / (ekind->cosacc.vcos * gmx::c_pico) * dens
+ * gmx::square(box[ZZ][ZZ] * gmx::c_nano / (2 * M_PI)));
add_ebin(ebin_, ivisc_, 1, &tmp, bSum);
}
if (nE_ > 1)
for (j = i; (j < nEg_); j++)
{
gid = GID(i, j, nEg_);
- for (k = kk = 0; (k < egNR); k++)
+ for (k = kk = 0; (k < static_cast<int>(NonBondedEnergyTerms::Count)); k++)
{
if (bEInd_[k])
{
- eee[kk++] = enerd->grpp.ener[k][gid];
+ eee[kk++] = enerd->grpp.energyGroupPairTerms[k][gid];
}
}
add_ebin(ebin_, igrp_[n], nEc_, eee, bSum);
{
tmp_r_[i] = ekind->tcstat[i].T;
}
- add_ebin(ebin_, itemp_, nTC_, tmp_r_, bSum);
+ add_ebin(ebin_, itemp_, nTC_, tmp_r_.data(), bSum);
- if (etc_ == etcNOSEHOOVER)
+ if (etc_ == TemperatureCoupling::NoseHoover)
{
/* whether to print Nose-Hoover chains: */
if (bPrintNHChains_)
tmp_r_[2 * k + 1] = ptCouplingArrays.nosehoover_vxi[k];
}
}
- add_ebin(ebin_, itc_, mde_n_, tmp_r_, bSum);
+ add_ebin(ebin_, itc_, mde_n_, tmp_r_.data(), bSum);
if (bMTTK_)
{
tmp_r_[2 * k + 1] = ptCouplingArrays.nhpres_vxi[k];
}
}
- add_ebin(ebin_, itcb_, mdeb_n_, tmp_r_, bSum);
+ add_ebin(ebin_, itcb_, mdeb_n_, tmp_r_.data(), bSum);
}
}
else
tmp_r_[2 * i] = ptCouplingArrays.nosehoover_xi[i];
tmp_r_[2 * i + 1] = ptCouplingArrays.nosehoover_vxi[i];
}
- add_ebin(ebin_, itc_, mde_n_, tmp_r_, bSum);
+ add_ebin(ebin_, itc_, mde_n_, tmp_r_.data(), bSum);
}
}
}
- else if (etc_ == etcBERENDSEN || etc_ == etcYES || etc_ == etcVRESCALE)
+ else if (etc_ == TemperatureCoupling::Berendsen || etc_ == TemperatureCoupling::Yes
+ || etc_ == TemperatureCoupling::VRescale)
{
for (int i = 0; (i < nTC_); i++)
{
tmp_r_[i] = ekind->tcstat[i].lambda;
}
- add_ebin(ebin_, itc_, nTC_, tmp_r_, bSum);
- }
- }
-
- if (ekind && nU_ > 1)
- {
- for (int i = 0; (i < nU_); i++)
- {
- copy_rvec(ekind->grpstat[i].u, tmp_v_[i]);
+ add_ebin(ebin_, itc_, nTC_, tmp_r_.data(), bSum);
}
- add_ebin(ebin_, iu_, 3 * nU_, tmp_v_[0], bSum);
}
ebin_increase_count(1, ebin_, bSum);
{
/* zero for simulated tempering */
dE_[i] = foreignTerms.deltaH(i);
- if (numTemperatures_ > 0)
+ if (!temperatures_.empty())
{
- GMX_RELEASE_ASSERT(numTemperatures_ > fep_state,
+ GMX_RELEASE_ASSERT(gmx::ssize(temperatures_) > fep_state,
"Number of lambdas in state is bigger then in input record");
GMX_RELEASE_ASSERT(
- numTemperatures_ >= foreignTerms.numLambdas(),
+ gmx::ssize(temperatures_) >= foreignTerms.numLambdas(),
"Number of lambdas in energy data is bigger then in input record");
/* MRS: is this right, given the way we have defined the exchange probabilities? */
/* is this even useful to have at all? */
/* the current free energy state */
/* print the current state if we are doing expanded ensemble */
- if (expand->elmcmove > elmcmoveNO)
+ if (expand->elmcmove > LambdaMoveCalculation::No)
{
fprintf(fp_dhdl_, " %4d", fep_state);
}
/* total energy (for if the temperature changes */
- if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
+ if (fep->edHdLPrintEnergy != FreeEnergyPrintEnergy::No)
{
switch (fep->edHdLPrintEnergy)
{
- case edHdLPrintEnergyPOTENTIAL: store_energy = enerd->term[F_EPOT]; break;
- case edHdLPrintEnergyTOTAL:
- case edHdLPrintEnergyYES:
+ case FreeEnergyPrintEnergy::Potential:
+ store_energy = enerd->term[F_EPOT];
+ break;
+ case FreeEnergyPrintEnergy::Total:
+ case FreeEnergyPrintEnergy::Yes:
default: store_energy = enerd->term[F_ETOT];
}
fprintf(fp_dhdl_, " %#.8g", store_energy);
}
- if (fep->dhdl_derivatives == edhdlderivativesYES)
+ if (fep->dhdl_derivatives == DhDlDerivativeCalculation::Yes)
{
- for (int i = 0; i < efptNR; i++)
+ for (auto i : keysOf(fep->separate_dvdl))
{
if (fep->separate_dvdl[i])
{
/* assumes F_DVDL is first */
- fprintf(fp_dhdl_, " %#.8g", enerd->term[F_DVDL + i]);
+ fprintf(fp_dhdl_, " %#.8g", enerd->term[F_DVDL + static_cast<int>(i)]);
}
}
}
{
fprintf(fp_dhdl_, " %#.8g", dE_[i]);
}
- if (bDynBox_ && bDiagPres_ && (epc_ != epcNO) && foreignTerms.numLambdas() > 0
- && (fep->init_lambda < 0))
+ if (bDynBox_ && bDiagPres_ && (epc_ != PressureCoupling::No)
+ && foreignTerms.numLambdas() > 0 && (fep->init_lambda < 0))
{
fprintf(fp_dhdl_, " %#.8g", pv); /* PV term only needed when
there are alternate state
if (dhc_ && bDoDHDL)
{
int idhdl = 0;
- for (int i = 0; i < efptNR; i++)
+ for (auto i : keysOf(fep->separate_dvdl))
{
if (fep->separate_dvdl[i])
{
/* assumes F_DVDL is first */
- store_dhdl[idhdl] = enerd->term[F_DVDL + i];
+ store_dhdl[idhdl] = enerd->term[F_DVDL + static_cast<int>(i)];
idhdl += 1;
}
}
store_energy = enerd->term[F_ETOT];
/* store_dh is dE */
- mde_delta_h_coll_add_dh(dhc_, static_cast<double>(fep_state), store_energy, pv,
- store_dhdl, dE_ + fep->lambda_start_n, time);
+ mde_delta_h_coll_add_dh(dhc_.get(),
+ static_cast<double>(fep_state),
+ store_energy,
+ pv,
+ store_dhdl,
+ dE_.data() + fep->lambda_start_n,
+ time);
}
}
fprintf(log,
" %12s %12s\n"
" %12s %12.5f\n\n",
- "Step", "Time", gmx_step_str(steps, buf), time);
+ "Step",
+ "Time",
+ gmx_step_str(steps, buf),
+ time);
}
void EnergyOutput::printStepToEnergyFile(ener_file* fp_ene,
nr[i] = 0;
}
- if (bOR && fcd->orires->nr > 0)
+ if (bOR && fcd->orires)
{
t_oriresdata& orires = *fcd->orires;
diagonalize_orires_tensors(&orires);
- nr[enxOR] = orires.nr;
- block[enxOR] = orires.otav;
- id[enxOR] = enxOR;
- nr[enxORI] = (orires.oinsl != orires.otav) ? orires.nr : 0;
- block[enxORI] = orires.oinsl;
+ nr[enxOR] = orires.numRestraints;
+ block[enxOR] = orires.orientationsTimeAndEnsembleAv.data();
+ id[enxOR] = enxOR;
+ nr[enxORI] = (orires.orientations.data() != orires.orientationsTimeAndEnsembleAv.data())
+ ? orires.numRestraints
+ : 0;
+ block[enxORI] = orires.orientations.data();
id[enxORI] = enxORI;
- nr[enxORT] = orires.nex * 12;
- block[enxORT] = orires.eig;
+ nr[enxORT] = ssize(orires.eigenOutput);
+ block[enxORT] = orires.eigenOutput.data();
id[enxORT] = enxORT;
}
fr.block[b].id = id[b];
fr.block[b].sub[0].nr = nr[b];
#if !GMX_DOUBLE
- fr.block[b].sub[0].type = xdr_datatype_float;
+ fr.block[b].sub[0].type = XdrDataType::Float;
fr.block[b].sub[0].fval = block[b];
#else
- fr.block[b].sub[0].type = xdr_datatype_double;
+ fr.block[b].sub[0].type = XdrDataType::Double;
fr.block[b].sub[0].dval = block[b];
#endif
}
fr.block[db].sub[0].nr = ndisre;
fr.block[db].sub[1].nr = ndisre;
#if !GMX_DOUBLE
- fr.block[db].sub[0].type = xdr_datatype_float;
- fr.block[db].sub[1].type = xdr_datatype_float;
+ fr.block[db].sub[0].type = XdrDataType::Float;
+ fr.block[db].sub[1].type = XdrDataType::Float;
fr.block[db].sub[0].fval = disres.rt;
fr.block[db].sub[1].fval = disres.rm3tav;
#else
- fr.block[db].sub[0].type = xdr_datatype_double;
- fr.block[db].sub[1].type = xdr_datatype_double;
+ fr.block[db].sub[0].type = XdrDataType::Double;
+ fr.block[db].sub[1].type = XdrDataType::Double;
fr.block[db].sub[0].dval = disres.rt;
fr.block[db].sub[1].dval = disres.rm3tav;
#endif
/* Free energy perturbation blocks */
if (dhc_)
{
- mde_delta_h_coll_handle_block(dhc_, &fr, fr.nblock);
+ mde_delta_h_coll_handle_block(dhc_.get(), &fr, fr.nblock);
}
/* we can now free & reset the data in the blocks */
if (dhc_)
{
- mde_delta_h_coll_reset(dhc_);
+ mde_delta_h_coll_reset(dhc_.get());
}
/* AWH bias blocks. */
free_enxframe(&fr);
if (log)
{
- if (bOR && fcd->orires->nr > 0)
+ if (bOR && fcd->orires)
{
- print_orires_log(log, fcd->orires);
+ print_orires_log(log, fcd->orires.get());
}
fprintf(log, " Energies (%s)\n", unit_energy);
}
}
-void EnergyOutput::printAnnealingTemperatures(FILE* log, const SimulationGroups* groups, t_grpopts* opts)
+void EnergyOutput::printAnnealingTemperatures(FILE* log, const SimulationGroups* groups, const t_grpopts* opts)
{
if (log)
{
{
for (int i = 0; i < opts->ngtc; i++)
{
- if (opts->annealing[i] != eannNO)
+ if (opts->annealing[i] != SimulatedAnnealing::No)
{
- fprintf(log, "Current ref_t for group %s: %8.1f\n",
+ fprintf(log,
+ "Current ref_t for group %s: %8.1f\n",
*(groups->groupNames[groups->groups[SimulationAtomGroupType::TemperatureCoupling][i]]),
opts->ref_t[i]);
}
fprintf(log, "\t<==== A V E R A G E S ====>\n");
fprintf(log, "\t<== ############### ======>\n\n");
- fprintf(log, "\tStatistics over %s steps using %s frames\n",
- gmx_step_str(ebin_->nsteps_sim, buf1), gmx_step_str(ebin_->nsum_sim, buf2));
+ fprintf(log,
+ "\tStatistics over %s steps using %s frames\n",
+ gmx_step_str(ebin_->nsteps_sim, buf1),
+ gmx_step_str(ebin_->nsum_sim, buf2));
fprintf(log, "\n");
fprintf(log, " Energies (%s)\n", unit_energy);
{
int padding = 8 - strlen(unit_energy);
fprintf(log, "%*sEpot (%s) ", padding, "", unit_energy);
- for (int i = 0; (i < egNR); i++)
+ for (auto key : keysOf(bEInd_))
{
- if (bEInd_[i])
+ if (bEInd_[key])
{
- fprintf(log, "%12s ", egrp_nm[i]);
+ fprintf(log, "%12s ", enumValueToString(key));
}
}
fprintf(log, "\n");
int nj = groups->groups[SimulationAtomGroupType::EnergyOutput][j];
int padding =
14 - (strlen(*(groups->groupNames[ni])) + strlen(*(groups->groupNames[nj])));
- fprintf(log, "%*s%s-%s", padding, "", *(groups->groupNames[ni]),
- *(groups->groupNames[nj]));
+ fprintf(log, "%*s%s-%s", padding, "", *(groups->groupNames[ni]), *(groups->groupNames[nj]));
pr_ebin(log, ebin_, igrp_[n], nEc_, nEc_, eprAVER, false);
n++;
}
pr_ebin(log, ebin_, itemp_, nTC_, 4, eprAVER, true);
fprintf(log, "\n");
}
- if (nU_ > 1)
- {
- fprintf(log, "%15s %12s %12s %12s\n", "Group", "Ux", "Uy", "Uz");
- for (int i = 0; (i < nU_); i++)
- {
- int ni = groups->groups[SimulationAtomGroupType::Acceleration][i];
- fprintf(log, "%15s", *groups->groupNames[ni]);
- pr_ebin(log, ebin_, iu_ + 3 * i, 3, 3, eprAVER, false);
- }
- fprintf(log, "\n");
- }
}
}
}
if (dhc_)
{
- mde_delta_h_coll_update_energyhistory(dhc_, enerhist);
+ mde_delta_h_coll_update_energyhistory(dhc_.get(), enerhist);
}
}
gmx_fatal(FARGS,
"Mismatch between number of energies in run input (%u) and checkpoint file (%zu "
"or %zu).",
- nener, enerhist.ener_sum.size(), enerhist.ener_sum_sim.size());
+ nener,
+ enerhist.ener_sum.size(),
+ enerhist.ener_sum_sim.size());
}
ebin_->nsteps = enerhist.nsteps;
}
if (dhc_)
{
- mde_delta_h_coll_restore_energyhistory(dhc_, enerhist.deltaHForeignLambdas.get());
+ mde_delta_h_coll_restore_energyhistory(dhc_.get(), enerhist.deltaHForeignLambdas.get());
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
class energyhistory_t;
struct ener_file;
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
struct gmx_enerdata_t;
struct SimulationGroups;
struct gmx_mtop_t;
{
class Awh;
class Constraints;
-struct MdModulesNotifier;
+struct MDModulesNotifiers;
enum class StartingBehavior;
} // namespace gmx
//! \brief Printed names for intergroup energies
-extern const char* egrp_nm[egNR + 1];
+const char* enumValueToString(NonBondedEnergyTerms enumValue);
/* \brief delta_h block type enum: the kinds of energies written out. */
enum
*
* \param[in] fp_ene Energy output file.
* \param[in] mtop Topology.
- * \param[in] ir Input parameters.
+ * \param[in] inputrec Input parameters.
* \param[in] pull_work Pulling simulations data
* \param[in] fp_dhdl FEP file.
* \param[in] isRerun Is this is a rerun instead of the simulations.
* \param[in] startingBehavior Run starting behavior.
* \param[in] simulationsShareState Tells whether the physical state is shared over simulations
- * \param[in] mdModulesNotifier Notifications to MD modules.
+ * \param[in] mdModulesNotifiers Notifications to MD modules.
*/
- EnergyOutput(ener_file* fp_ene,
- const gmx_mtop_t* mtop,
- const t_inputrec* ir,
- const pull_t* pull_work,
- FILE* fp_dhdl,
- bool isRerun,
- StartingBehavior startingBehavior,
- bool simulationsShareState,
- const MdModulesNotifier& mdModulesNotifier);
+ EnergyOutput(ener_file* fp_ene,
+ const gmx_mtop_t& mtop,
+ const t_inputrec& inputrec,
+ const pull_t* pull_work,
+ FILE* fp_dhdl,
+ bool isRerun,
+ StartingBehavior startingBehavior,
+ bool simulationsShareState,
+ const MDModulesNotifiers& mdModulesNotifiers);
~EnergyOutput();
* \param[in] opts Atom temperature coupling groups options
* (annealing is done by groups).
*/
- static void printAnnealingTemperatures(FILE* log, const SimulationGroups* groups, t_grpopts* opts);
+ static void printAnnealingTemperatures(FILE* log, const SimulationGroups* groups, const t_grpopts* opts);
/*! \brief Prints average values to log file.
*
bool bMTTK_ = false;
//! Temperature control scheme
- int etc_ = 0;
+ TemperatureCoupling etc_ = TemperatureCoupling::No;
//! Which of the main energy terms should be printed
bool bEner_[F_NRE] = { false };
int isurft_ = 0;
//! Pressure control scheme
- int epc_ = 0;
+ PressureCoupling epc_ = PressureCoupling::No;
//! Index for velocity of the box borders
int ipc_ = 0;
//! Index for viscocity
int ivisc_ = 0;
- //! Which energy terms from egNR list should be printed in group-to-group block
- bool bEInd_[egNR] = { false };
+ //! Which energy terms from NonBondedEnergyTerms list should be printed in group-to-group block
+ gmx::EnumerationArray<NonBondedEnergyTerms, bool> bEInd_;
//! Number of energy terms to be printed (these, for which bEInd[] == true)
int nEc_ = 0;
//! Number of energy output groups
//! Number of intergroup energy sets to be printed for each energy term (nE = (nEg*(nEg+1))/2)
int nE_ = 0;
//! Indexes for integroup energy sets (each set with nEc energies)
- int* igrp_ = nullptr;
+ std::vector<int> igrp_;
//! Number of temperature coupling groups
int nTC_ = 0;
//! Index for scalling factor of MTTK
int itcb_ = 0;
- //! Number of acceleration groups
- int nU_ = 0;
- //! Index for group velocities
- int iu_ = 0;
-
- //! Array to accumulate values during update
- real* tmp_r_ = nullptr;
//! Array to accumulate values during update
- rvec* tmp_v_ = nullptr;
+ std::vector<real> tmp_r_;
//! The dhdl.xvg output file
FILE* fp_dhdl_ = nullptr;
//! Energy components for dhdl.xvg output
- double* dE_ = nullptr;
+ std::vector<double> dE_;
//! The delta U components (raw data + histogram)
- t_mde_delta_h_coll* dhc_ = nullptr;
+ std::unique_ptr<t_mde_delta_h_coll> dhc_;
//! Temperatures for simulated tempering groups
- real* temperatures_ = nullptr;
- //! Number of temperatures actually saved
- int numTemperatures_ = 0;
+ std::vector<real> temperatures_;
//! For tracking the conserved or total energy
std::unique_ptr<EnergyDriftTracker> conservedEnergyTracker_;
#include <cmath>
#include <cstdio>
-#include <algorithm>
-
-#include "gromacs/domdec/domdec.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/xtcio.h"
-#include "gromacs/gmxlib/network.h"
-#include "gromacs/gmxlib/nrnb.h"
-#include "gromacs/listed_forces/disre.h"
-#include "gromacs/listed_forces/orires.h"
-#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/mdlib/calcmu.h"
-#include "gromacs/mdlib/constr.h"
-#include "gromacs/mdlib/force.h"
-#include "gromacs/mdlib/update.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/random/threefry.h"
#include "gromacs/random/uniformrealdistribution.h"
-#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/smalloc.h"
#include "expanded_internal.h"
{
if (!bStateFromCP)
{
- init_df_history_weights(dfhist, ir->expandedvals, ir->fepvals->n_lambda);
+ init_df_history_weights(dfhist, ir->expandedvals.get(), ir->fepvals->n_lambda);
}
}
/* calculate the total number of samples */
switch (expand->elmceq)
{
- case elmceqNO:
+ case LambdaWeightWillReachEquilibrium::No:
/* We have not equilibrated, and won't, ever. */
bDoneEquilibrating = FALSE;
break;
- case elmceqYES:
+ case LambdaWeightWillReachEquilibrium::Yes:
/* we have equilibrated -- we're done */
bDoneEquilibrating = TRUE;
break;
- case elmceqSTEPS:
+ case LambdaWeightWillReachEquilibrium::Steps:
/* first, check if we are equilibrating by steps, if we're still under */
if (step < expand->equil_steps)
{
bDoneEquilibrating = FALSE;
}
break;
- case elmceqSAMPLES:
+ case LambdaWeightWillReachEquilibrium::Samples:
totalsamples = 0;
for (i = 0; i < nlim; i++)
{
bDoneEquilibrating = FALSE;
}
break;
- case elmceqNUMATLAM:
+ case LambdaWeightWillReachEquilibrium::NumAtLambda:
for (i = 0; i < nlim; i++)
{
if (dfhist->n_at_lam[i]
}
}
break;
- case elmceqWLDELTA:
+ case LambdaWeightWillReachEquilibrium::WLDelta:
if (EWL(expand->elamstats)) /* This check is in readir as well, but
just to be sure */
{
}
}
break;
- case elmceqRATIO:
+ case LambdaWeightWillReachEquilibrium::Ratio:
/* we can use the flatness as a judge of good weights, as long as
we're not doing minvar, or Wang-Landau.
But turn off for now until we figure out exactly how we do this.
*/
- if (!(EWL(expand->elamstats) || expand->elamstats == elamstatsMINVAR))
+ if (!(EWL(expand->elamstats) || expand->elamstats == LambdaWeightCalculation::Minvar))
{
/* we want to use flatness -avoiding- the forced-through samples. Plus, we need
to convert to floats for this histogram function. */
if (EWL(expand->elamstats))
{
- if (expand->elamstats == elamstatsWL) /* Using standard Wang-Landau for weight updates */
+ if (expand->elamstats
+ == LambdaWeightCalculation::WL) /* Using standard Wang-Landau for weight updates */
{
dfhist->sum_weights[fep_state] -= dfhist->wl_delta;
dfhist->wl_histo[fep_state] += 1.0;
}
- else if (expand->elamstats == elamstatsWWL)
+ else if (expand->elamstats == LambdaWeightCalculation::WWL)
/* Using weighted Wang-Landau for weight updates.
* Very closly equivalent to accelerated weight histogram approach
* applied to expanded ensemble. */
/* then increment weights (uses count) */
pks = 0.0;
- GenerateWeightedGibbsProbabilities(weighted_lamee, p_k, &pks, nlim, dfhist->wl_histo,
- dfhist->wl_delta);
+ GenerateWeightedGibbsProbabilities(
+ weighted_lamee, p_k, &pks, nlim, dfhist->wl_histo, dfhist->wl_delta);
for (i = 0; i < nlim; i++)
{
}
}
- if (expand->elamstats == elamstatsBARKER || expand->elamstats == elamstatsMETROPOLIS
- || expand->elamstats == elamstatsMINVAR)
+ if (expand->elamstats == LambdaWeightCalculation::Barker
+ || expand->elamstats == LambdaWeightCalculation::Metropolis
+ || expand->elamstats == LambdaWeightCalculation::Minvar)
{
maxc = 2 * expand->c_range + 1;
lam_variance[fep_state] = clam_varp;
}
- if (expand->elamstats == elamstatsMINVAR)
+ if (expand->elamstats == LambdaWeightCalculation::Minvar)
{
bSufficientSamples = TRUE;
/* make sure the number of samples in each state are all
accept[ifep] = 0;
}
- if ((expand->elmcmove == elmcmoveGIBBS) || (expand->elmcmove == elmcmoveMETGIBBS))
+ if ((expand->elmcmove == LambdaMoveCalculation::Gibbs)
+ || (expand->elmcmove == LambdaMoveCalculation::MetropolisGibbs))
{
/* use the Gibbs sampler, with restricted range */
if (expand->gibbsdeltalam < 0)
GenerateGibbsProbabilities(weighted_lamee, p_k, &pks, minfep, maxfep);
- if (expand->elmcmove == elmcmoveGIBBS)
+ if (expand->elmcmove == LambdaMoveCalculation::Gibbs)
{
for (ifep = minfep; ifep <= maxfep; ifep++)
{
r1 -= p_k[lamnew];
}
}
- else if (expand->elmcmove == elmcmoveMETGIBBS)
+ else if (expand->elmcmove == LambdaMoveCalculation::MetropolisGibbs)
{
/* Metropolized Gibbs sampling */
"Something wrong in choosing new lambda state with a Gibbs move -- "
"probably underflow in weight determination.\nDenominator is: "
"%3d%17.10e\n i dE numerator weights\n",
- 0, pks);
+ 0,
+ pks);
for (ifep = minfep; ifep <= maxfep; ifep++)
{
- loc += sprintf(&errorstr[loc], "%3d %17.10e%17.10e%17.10e\n", ifep,
- weighted_lamee[ifep], p_k[ifep], dfhist->sum_weights[ifep]);
+ loc += sprintf(&errorstr[loc],
+ "%3d %17.10e%17.10e%17.10e\n",
+ ifep,
+ weighted_lamee[ifep],
+ p_k[ifep],
+ dfhist->sum_weights[ifep]);
}
gmx_fatal(FARGS, "%s", errorstr);
}
}
}
- else if ((expand->elmcmove == elmcmoveMETROPOLIS) || (expand->elmcmove == elmcmoveBARKER))
+ else if ((expand->elmcmove == LambdaMoveCalculation::Metropolis)
+ || (expand->elmcmove == LambdaMoveCalculation::Barker))
{
/* use the metropolis sampler with trial +/- 1 */
r1 = dist(rng);
}
de = weighted_lamee[lamtrial] - weighted_lamee[fep_state];
- if (expand->elmcmove == elmcmoveMETROPOLIS)
+ if (expand->elmcmove == LambdaMoveCalculation::Metropolis)
{
tprob = 1.0;
if (de < 0)
1.0; /* doesn't actually matter, never proposed unless fep_state = ntrial, in which case it's 1.0 anyway */
accept[lamtrial] = tprob;
}
- else if (expand->elmcmove == elmcmoveBARKER)
+ else if (expand->elmcmove == LambdaMoveCalculation::Barker)
{
if (de > 0) /* Numerically stable version */
{
int frequency,
int64_t step)
{
- int nlim, i, ifep, jfep;
- real dw, dg, dv, Tprint;
- const char* print_names[efptNR] = { " FEPL", "MassL", "CoulL", " VdwL",
- "BondL", "RestT", "Temp.(K)" };
- gmx_bool bSimTemp = FALSE;
+ int nlim, ifep, jfep;
+ real dw, dg, dv, Tprint;
+ gmx_bool bSimTemp = FALSE;
nlim = fep->n_lambda;
if (simtemp != nullptr)
fprintf(outfile, " Wang-Landau incrementor is: %11.5g\n", dfhist->wl_delta);
}
fprintf(outfile, " N");
- for (i = 0; i < efptNR; i++)
+ for (auto i : keysOf(fep->separate_dvdl))
{
if (fep->separate_dvdl[i])
{
- fprintf(outfile, "%7s", print_names[i]);
+ fprintf(outfile, "%7s", enumValueToString(i));
}
- else if ((i == efptTEMPERATURE) && bSimTemp)
+ else if ((i == FreeEnergyPerturbationCouplingType::Temperature) && bSimTemp)
{
- fprintf(outfile, "%10s", print_names[i]); /* more space for temperature formats */
+ fprintf(outfile, "%10s", enumValueToString(i)); /* more space for temperature formats */
}
}
fprintf(outfile, " Count ");
- if (expand->elamstats == elamstatsMINVAR)
+ if (expand->elamstats == LambdaWeightCalculation::Minvar)
{
fprintf(outfile, "W(in kT) G(in kT) dG(in kT) dV(in kT)\n");
}
- gmx::square(dfhist->sum_variance[ifep]));
}
fprintf(outfile, "%3d", (ifep + 1));
- for (i = 0; i < efptNR; i++)
+ for (auto i : keysOf(fep->separate_dvdl))
{
if (fep->separate_dvdl[i])
{
fprintf(outfile, "%7.3f", fep->all_lambda[i][ifep]);
}
- else if (i == efptTEMPERATURE && bSimTemp)
+ else if (i == FreeEnergyPerturbationCouplingType::Temperature && bSimTemp)
{
fprintf(outfile, "%9.3f", simtemp->temperatures[ifep]);
}
if (EWL(expand->elamstats)
&& (!(dfhist->bEquil))) /* if performing WL and still haven't equilibrated */
{
- if (expand->elamstats == elamstatsWL)
+ if (expand->elamstats == LambdaWeightCalculation::WL)
{
fprintf(outfile, " %8d", static_cast<int>(dfhist->wl_histo[ifep]));
}
{
fprintf(outfile, " %8d", dfhist->n_at_lam[ifep]);
}
- if (expand->elamstats == elamstatsMINVAR)
+ if (expand->elamstats == LambdaWeightCalculation::Minvar)
{
- fprintf(outfile, " %10.5f %10.5f %10.5f %10.5f", dfhist->sum_weights[ifep],
- dfhist->sum_dg[ifep], dg, dv);
+ fprintf(outfile,
+ " %10.5f %10.5f %10.5f %10.5f",
+ dfhist->sum_weights[ifep],
+ dfhist->sum_dg[ifep],
+ dg,
+ dv);
}
else
{
}
}
-int ExpandedEnsembleDynamics(FILE* log,
- const t_inputrec* ir,
- const gmx_enerdata_t* enerd,
- t_state* state,
- t_extmass* MassQ,
- int fep_state,
- df_history_t* dfhist,
- int64_t step,
- rvec* v,
- const t_mdatoms* mdatoms)
+int ExpandedEnsembleDynamics(FILE* log,
+ t_inputrec* ir,
+ const gmx_enerdata_t* enerd,
+ t_state* state,
+ t_extmass* MassQ,
+ int fep_state,
+ df_history_t* dfhist,
+ int64_t step,
+ rvec* v,
+ const int homenr,
+ gmx::ArrayRef<const unsigned short> cTC)
/* Note that the state variable is only needed for simulated tempering, not
Hamiltonian expanded ensemble. May be able to remove it after integrator refactoring. */
{
t_simtemp* simtemp;
gmx_bool bIfReset, bSwitchtoOneOverT, bDoneEquilibrating = FALSE;
- expand = ir->expandedvals;
- simtemp = ir->simtempvals;
+ expand = ir->expandedvals.get();
+ simtemp = ir->simtempvals.get();
nlim = ir->fepvals->n_lambda;
snew(scaled_lamee, nlim);
/* we don't need to include the pressure term, since the volume is the same between the two.
is there some term we are neglecting, however? */
- if (ir->efep != efepNO)
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
for (i = 0; i < nlim; i++)
{
if (ir->bSimTemp)
{
/* Note -- this assumes no mass changes, since kinetic energy is not added . . . */
- scaled_lamee[i] = enerd->foreignLambdaTerms.deltaH(i) / (simtemp->temperatures[i] * BOLTZ)
- + enerd->term[F_EPOT]
- * (1.0 / (simtemp->temperatures[i])
- - 1.0 / (simtemp->temperatures[fep_state]))
- / BOLTZ;
+ scaled_lamee[i] =
+ enerd->foreignLambdaTerms.deltaH(i) / (simtemp->temperatures[i] * gmx::c_boltz)
+ + enerd->term[F_EPOT]
+ * (1.0 / (simtemp->temperatures[i])
+ - 1.0 / (simtemp->temperatures[fep_state]))
+ / gmx::c_boltz;
}
else
{
- scaled_lamee[i] = enerd->foreignLambdaTerms.deltaH(i) / (expand->mc_temp * BOLTZ);
+ scaled_lamee[i] = enerd->foreignLambdaTerms.deltaH(i) / (expand->mc_temp * gmx::c_boltz);
/* mc_temp is currently set to the system reft unless otherwise defined */
}
{
scaled_lamee[i] =
enerd->term[F_EPOT]
- * (1.0 / simtemp->temperatures[i] - 1.0 / simtemp->temperatures[fep_state]) / BOLTZ;
+ * (1.0 / simtemp->temperatures[i] - 1.0 / simtemp->temperatures[fep_state])
+ / gmx::c_boltz;
}
}
}
{
if (log)
{
- fprintf(log, "\nStep %" PRId64 ": Weights have equilibrated, using criteria: %s\n",
- step, elmceq_names[expand->elmceq]);
+ fprintf(log,
+ "\nStep %" PRId64 ": Weights have equilibrated, using criteria: %s\n",
+ step,
+ enumValueToString(expand->elmceq));
}
}
- lamnew = ChooseNewLambda(nlim, expand, dfhist, fep_state, weighted_lamee, p_k,
- ir->expandedvals->lmc_seed, step);
+ lamnew = ChooseNewLambda(
+ nlim, expand, dfhist, fep_state, weighted_lamee, p_k, ir->expandedvals->lmc_seed, step);
/* if using simulated tempering, we need to adjust the temperatures */
if (ir->bSimTemp && (lamnew != fep_state)) /* only need to change the temperatures if we change the state */
{
/* we don't need to manipulate the ekind information, as it isn't due to be reset until the next step anyway */
nstart = 0;
- nend = mdatoms->homenr;
+ nend = homenr;
for (n = nstart; n < nend; n++)
{
gt = 0;
- if (mdatoms->cTC)
+ if (!cTC.empty())
{
- gt = mdatoms->cTC[n];
+ gt = cTC[n];
}
for (d = 0; d < DIM; d++)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <stdio.h>
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/basedefinitions.h"
struct df_history_t;
struct gmx_enerdata_t;
struct t_extmass;
struct t_inputrec;
struct t_lambda;
-struct t_mdatoms;
struct t_simtemp;
class t_state;
-void init_npt_masses(const t_inputrec* ir, t_state* state, t_extmass* MassQ, gmx_bool bInit);
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
-void init_expanded_ensemble(gmx_bool bStateFromCP, const t_inputrec* ir, df_history_t* dfhist);
+void init_npt_masses(const t_inputrec* ir, t_state* state, t_extmass* MassQ, bool bInit);
-int ExpandedEnsembleDynamics(FILE* log,
- const t_inputrec* ir,
- const gmx_enerdata_t* enerd,
- t_state* state,
- t_extmass* MassQ,
- int fep_state,
- df_history_t* dfhist,
- int64_t step,
- rvec* v,
- const t_mdatoms* mdatoms);
+void init_expanded_ensemble(bool bStateFromCP, const t_inputrec* ir, df_history_t* dfhist);
+
+int ExpandedEnsembleDynamics(FILE* log,
+ t_inputrec* ir,
+ const gmx_enerdata_t* enerd,
+ t_state* state,
+ t_extmass* MassQ,
+ int fep_state,
+ df_history_t* dfhist,
+ int64_t step,
+ rvec* v,
+ int homenr,
+ gmx::ArrayRef<const unsigned short> cTC);
void PrintFreeEnergyInfoToFile(FILE* outfile,
const t_lambda* fep,
namespace gmx
{
-real calculateAcceptanceWeight(int calculationMode, real lambdaEnergyDifference)
+real calculateAcceptanceWeight(LambdaWeightCalculation calculationMode, real lambdaEnergyDifference)
{
- if (calculationMode == elamstatsBARKER || calculationMode == elamstatsMINVAR)
+ if (calculationMode == LambdaWeightCalculation::Barker
+ || calculationMode == LambdaWeightCalculation::Minvar)
{
/* Barker acceptance rule forumula is used for accumulation of probability for
* both the Barker variant of the weight accumulation algorithm and the
return std::exp(-lambdaEnergyDifference) / (1.0 + std::exp(-lambdaEnergyDifference));
}
}
- else if (calculationMode == elamstatsMETROPOLIS)
+ else if (calculationMode == LambdaWeightCalculation::Metropolis)
{
/* Metropolis acceptance rule for a jump from state i -> j is defined as
* 1 (if dE_ij < 0)
#include "gromacs/utility/real.h"
+enum class LambdaWeightCalculation : int;
+
namespace gmx
{
/*! \brief Calculates the acceptance weight for a lambda state transition
* \param[in] lambdaEnergyDifference The difference in energy between the two states
* \return The acceptance weight
*/
-real calculateAcceptanceWeight(int calculationMode, real lambdaEnergyDifference);
+real calculateAcceptanceWeight(LambdaWeightCalculation calculationMode, real lambdaEnergyDifference);
} // namespace gmx
#endif // GMX_MDLIB_EXPANDEDINTERNAL_H
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static void clearEwaldThreadOutput(ewald_corr_thread_t* ewc_t)
{
- ewc_t->Vcorr_q = 0;
- ewc_t->Vcorr_lj = 0;
- ewc_t->dvdl[efptCOUL] = 0;
- ewc_t->dvdl[efptVDW] = 0;
+ ewc_t->Vcorr_q = 0;
+ ewc_t->Vcorr_lj = 0;
+ ewc_t->dvdl[FreeEnergyPerturbationCouplingType::Coul] = 0;
+ ewc_t->dvdl[FreeEnergyPerturbationCouplingType::Vdw] = 0;
clear_mat(ewc_t->vir_q);
clear_mat(ewc_t->vir_lj);
}
-static void reduceEwaldThreadOuput(int nthreads, ewald_corr_thread_t* ewc_t)
+static void reduceEwaldThreadOuput(int nthreads, gmx::ArrayRef<ewald_corr_thread_t> ewc_t)
{
ewald_corr_thread_t& dest = ewc_t[0];
{
dest.Vcorr_q += ewc_t[t].Vcorr_q;
dest.Vcorr_lj += ewc_t[t].Vcorr_lj;
- dest.dvdl[efptCOUL] += ewc_t[t].dvdl[efptCOUL];
- dest.dvdl[efptVDW] += ewc_t[t].dvdl[efptVDW];
+ dest.dvdl[FreeEnergyPerturbationCouplingType::Coul] +=
+ ewc_t[t].dvdl[FreeEnergyPerturbationCouplingType::Coul];
+ dest.dvdl[FreeEnergyPerturbationCouplingType::Vdw] +=
+ ewc_t[t].dvdl[FreeEnergyPerturbationCouplingType::Vdw];
m_add(dest.vir_q, ewc_t[t].vir_q, dest.vir_q);
m_add(dest.vir_lj, ewc_t[t].vir_lj, dest.vir_lj);
}
}
-void calculateLongRangeNonbondeds(t_forcerec* fr,
- const t_inputrec* ir,
- const t_commrec* cr,
- t_nrnb* nrnb,
- gmx_wallcycle_t wcycle,
- const t_mdatoms* md,
- gmx::ArrayRef<const RVec> coordinates,
- gmx::ForceWithVirial* forceWithVirial,
- gmx_enerdata_t* enerd,
- const matrix box,
- const real* lambda,
- const rvec* mu_tot,
- const gmx::StepWorkload& stepWork,
- const DDBalanceRegionHandler& ddBalanceRegionHandler)
+void calculateLongRangeNonbondeds(t_forcerec* fr,
+ const t_inputrec& ir,
+ const t_commrec* cr,
+ t_nrnb* nrnb,
+ gmx_wallcycle* wcycle,
+ const t_mdatoms* md,
+ gmx::ArrayRef<const RVec> coordinates,
+ gmx::ForceWithVirial* forceWithVirial,
+ gmx_enerdata_t* enerd,
+ const matrix box,
+ gmx::ArrayRef<const real> lambda,
+ gmx::ArrayRef<const gmx::RVec> mu_tot,
+ const gmx::StepWorkload& stepWork,
+ const DDBalanceRegionHandler& ddBalanceRegionHandler)
{
const bool computePmeOnCpu = (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
&& thisRankHasDuty(cr, DUTY_PME)
&& (pme_run_mode(fr->pmedata) == PmeRunMode::CPU);
- const bool haveEwaldSurfaceTerm = haveEwaldSurfaceContribution(*ir);
+ const bool haveEwaldSurfaceTerm = haveEwaldSurfaceContribution(ir);
/* Do long-range electrostatics and/or LJ-PME
* and compute PME surface terms when necessary.
*/
- if ((computePmeOnCpu || fr->ic->eeltype == eelEWALD || haveEwaldSurfaceTerm)
+ if ((computePmeOnCpu || fr->ic->eeltype == CoulombInteractionType::Ewald || haveEwaldSurfaceTerm)
&& stepWork.computeNonbondedForces)
{
int status = 0;
/* Calculate the Ewald surface force and energy contributions, when necessary */
if (haveEwaldSurfaceTerm)
{
- wallcycle_sub_start(wcycle, ewcsEWALD_CORRECTION);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::EwaldCorrection);
int nthreads = fr->nthread_ewc;
#pragma omp parallel for num_threads(nthreads) schedule(static)
* exclusion forces) are calculated, so we can store
* the forces in the normal, single forceWithVirial->force_ array.
*/
- const rvec* x = as_rvec_array(coordinates.data());
- ewald_LRcorrection(md->homenr, cr, nthreads, t, *fr, *ir, md->chargeA,
- md->chargeB, (md->nChargePerturbed != 0), x, box, mu_tot,
- as_rvec_array(forceWithVirial->force_.data()),
- &ewc_t.Vcorr_q, lambda[efptCOUL], &ewc_t.dvdl[efptCOUL]);
+ ewald_LRcorrection(
+ md->homenr,
+ cr,
+ nthreads,
+ t,
+ *fr,
+ ir,
+ md->chargeA ? gmx::constArrayRefFromArray(md->chargeA, md->nr)
+ : gmx::ArrayRef<const real>{},
+ md->chargeB ? gmx::constArrayRefFromArray(md->chargeB, md->nr)
+ : gmx::ArrayRef<const real>{},
+ (md->nChargePerturbed != 0),
+ coordinates,
+ box,
+ mu_tot,
+ forceWithVirial->force_,
+ &ewc_t.Vcorr_q,
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
+ &ewc_t.dvdl[FreeEnergyPerturbationCouplingType::Coul]);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
{
reduceEwaldThreadOuput(nthreads, fr->ewc_t);
}
- wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::EwaldCorrection);
}
if (EEL_PME_EWALD(fr->ic->eeltype) && fr->n_tpi == 0)
/* This is not in a subcounter because it takes a
negligible and constant-sized amount of time */
ewaldOutput.Vcorr_q += ewald_charge_correction(
- cr, fr, lambda[efptCOUL], box, &ewaldOutput.dvdl[efptCOUL], ewaldOutput.vir_q);
+ cr,
+ fr,
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
+ box,
+ &ewaldOutput.dvdl[FreeEnergyPerturbationCouplingType::Coul],
+ ewaldOutput.vir_q);
}
if (computePmeOnCpu)
*/
ddBalanceRegionHandler.closeAfterForceComputationCpu();
- wallcycle_start(wcycle, ewcPMEMESH);
+ wallcycle_start(wcycle, WallCycleCounter::PmeMesh);
status = gmx_pme_do(
fr->pmedata,
gmx::constArrayRefFromArray(coordinates.data(), md->homenr - fr->n_tpi),
- forceWithVirial->force_, md->chargeA, md->chargeB, md->sqrt_c6A,
- md->sqrt_c6B, md->sigmaA, md->sigmaB, box, cr,
- DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
- DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0, nrnb, wcycle,
- ewaldOutput.vir_q, ewaldOutput.vir_lj, &Vlr_q, &Vlr_lj,
- lambda[efptCOUL], lambda[efptVDW], &ewaldOutput.dvdl[efptCOUL],
- &ewaldOutput.dvdl[efptVDW], stepWork);
- wallcycle_stop(wcycle, ewcPMEMESH);
+ forceWithVirial->force_,
+ md->chargeA ? gmx::constArrayRefFromArray(md->chargeA, md->nr)
+ : gmx::ArrayRef<const real>{},
+ md->chargeB ? gmx::constArrayRefFromArray(md->chargeB, md->nr)
+ : gmx::ArrayRef<const real>{},
+ md->sqrt_c6A ? gmx::constArrayRefFromArray(md->sqrt_c6A, md->nr)
+ : gmx::ArrayRef<const real>{},
+ md->sqrt_c6B ? gmx::constArrayRefFromArray(md->sqrt_c6B, md->nr)
+ : gmx::ArrayRef<const real>{},
+ md->sigmaA ? gmx::constArrayRefFromArray(md->sigmaA, md->nr)
+ : gmx::ArrayRef<const real>{},
+ md->sigmaB ? gmx::constArrayRefFromArray(md->sigmaB, md->nr)
+ : gmx::ArrayRef<const real>{},
+ box,
+ cr,
+ DOMAINDECOMP(cr) ? dd_pme_maxshift_x(*cr->dd) : 0,
+ DOMAINDECOMP(cr) ? dd_pme_maxshift_y(*cr->dd) : 0,
+ nrnb,
+ wcycle,
+ ewaldOutput.vir_q,
+ ewaldOutput.vir_lj,
+ &Vlr_q,
+ &Vlr_lj,
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)],
+ &ewaldOutput.dvdl[FreeEnergyPerturbationCouplingType::Coul],
+ &ewaldOutput.dvdl[FreeEnergyPerturbationCouplingType::Vdw],
+ stepWork);
+ wallcycle_stop(wcycle, WallCycleCounter::PmeMesh);
if (status != 0)
{
gmx_fatal(FARGS, "Error %d in reciprocal PME routine", status);
/* Determine the PME grid energy of the test molecule
* with the PME grid potential of the other charges.
*/
- gmx_pme_calc_energy(
- fr->pmedata, coordinates.subArray(md->homenr - fr->n_tpi, fr->n_tpi),
- gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
- &Vlr_q);
+ Vlr_q = gmx_pme_calc_energy(
+ fr->pmedata,
+ coordinates.subArray(md->homenr - fr->n_tpi, fr->n_tpi),
+ gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi));
}
}
}
- if (fr->ic->eeltype == eelEWALD)
+ if (fr->ic->eeltype == CoulombInteractionType::Ewald)
{
- const rvec* x = as_rvec_array(coordinates.data());
- Vlr_q = do_ewald(ir, x, as_rvec_array(forceWithVirial->force_.data()), md->chargeA,
- md->chargeB, box, cr, md->homenr, ewaldOutput.vir_q, fr->ic->ewaldcoeff_q,
- lambda[efptCOUL], &ewaldOutput.dvdl[efptCOUL], fr->ewald_table);
+ Vlr_q = do_ewald(ir,
+ coordinates,
+ forceWithVirial->force_,
+ gmx::arrayRefFromArray(md->chargeA, md->nr),
+ gmx::arrayRefFromArray(md->chargeB, md->nr),
+ box,
+ cr,
+ md->homenr,
+ ewaldOutput.vir_q,
+ fr->ic->ewaldcoeff_q,
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
+ &ewaldOutput.dvdl[FreeEnergyPerturbationCouplingType::Coul],
+ fr->ewald_table.get());
}
/* Note that with separate PME nodes we get the real energies later */
// long-range virial contribution.
forceWithVirial->addVirialContribution(ewaldOutput.vir_q);
forceWithVirial->addVirialContribution(ewaldOutput.vir_lj);
- enerd->dvdl_lin[efptCOUL] += ewaldOutput.dvdl[efptCOUL];
- enerd->dvdl_lin[efptVDW] += ewaldOutput.dvdl[efptVDW];
+ enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Coul] +=
+ ewaldOutput.dvdl[FreeEnergyPerturbationCouplingType::Coul];
+ enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Vdw] +=
+ ewaldOutput.dvdl[FreeEnergyPerturbationCouplingType::Vdw];
enerd->term[F_COUL_RECIP] = Vlr_q + ewaldOutput.Vcorr_q;
enerd->term[F_LJ_RECIP] = Vlr_lj + ewaldOutput.Vcorr_lj;
if (debug)
{
- fprintf(debug, "Vlr_q = %g, Vcorr_q = %g, Vlr_corr_q = %g\n", Vlr_q,
- ewaldOutput.Vcorr_q, enerd->term[F_COUL_RECIP]);
+ fprintf(debug,
+ "Vlr_q = %g, Vcorr_q = %g, Vlr_corr_q = %g\n",
+ Vlr_q,
+ ewaldOutput.Vcorr_q,
+ enerd->term[F_COUL_RECIP]);
pr_rvecs(debug, 0, "vir_el_recip after corr", ewaldOutput.vir_q, DIM);
- fprintf(debug, "Vlr_lj: %g, Vcorr_lj = %g, Vlr_corr_lj = %g\n", Vlr_lj,
- ewaldOutput.Vcorr_lj, enerd->term[F_LJ_RECIP]);
+ fprintf(debug,
+ "Vlr_lj: %g, Vcorr_lj = %g, Vlr_corr_lj = %g\n",
+ Vlr_lj,
+ ewaldOutput.Vcorr_lj,
+ enerd->term[F_LJ_RECIP]);
pr_rvecs(debug, 0, "vir_lj_recip after corr", ewaldOutput.vir_lj, DIM);
}
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void do_force(FILE* log,
const t_commrec* cr,
const gmx_multisim_t* ms,
- const t_inputrec* inputrec,
+ const t_inputrec& inputrec,
gmx::Awh* awh,
gmx_enfrot* enforcedRotation,
gmx::ImdSession* imdSession,
const gmx_localtop_t* top,
const matrix box,
gmx::ArrayRefWithPadding<gmx::RVec> coordinates,
- history_t* hist,
+ const history_t* hist,
gmx::ForceBuffersView* force,
tensor vir_force,
const t_mdatoms* mdatoms,
* on whether the PME-mesh contribution is computed on a separate PME rank or on a GPU.
*/
void calculateLongRangeNonbondeds(t_forcerec* fr,
- const t_inputrec* ir,
+ const t_inputrec& ir,
const t_commrec* cr,
t_nrnb* nrnb,
gmx_wallcycle* wcycle,
gmx::ForceWithVirial* forceWithVirial,
gmx_enerdata_t* enerd,
const matrix box,
- const real* lambda,
- const rvec* mu_tot,
+ gmx::ArrayRef<const real> lambda,
+ gmx::ArrayRef<const gmx::RVec> mu_tot,
const gmx::StepWorkload& stepWork,
const DDBalanceRegionHandler& ddBalanceRegionHandler);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013-2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013-2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "config.h"
-#include <cassert>
#include <cmath>
#include <cstdlib>
#include <cstring>
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/ewald/ewald.h"
-#include "gromacs/ewald/ewald_utils.h"
#include "gromacs/ewald/pme_pp_comm_gpu.h"
#include "gromacs/fileio/filetypes.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/listed_forces/listed_forces.h"
#include "gromacs/listed_forces/pairs.h"
#include "gromacs/math/functions.h"
-#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/dispersioncorrection.h"
#include "gromacs/mdlib/forcerec_threading.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdlib/md_support.h"
-#include "gromacs/mdlib/rf_util.h"
#include "gromacs/mdlib/wall.h"
#include "gromacs/mdlib/wholemoleculetransform.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/multipletimestepping.h"
+#include "gromacs/mdtypes/nblist.h"
#include "gromacs/nbnxm/nbnxm.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/pbc.h"
ForceHelperBuffers::ForceHelperBuffers(bool haveDirectVirialContributions) :
haveDirectVirialContributions_(haveDirectVirialContributions)
{
- shiftForces_.resize(SHIFTS);
+ shiftForces_.resize(gmx::c_numShiftVectors);
}
void ForceHelperBuffers::resize(int numAtoms)
}
}
-static std::vector<real> mk_nbfp(const gmx_ffparams_t* idef, gmx_bool bBHAM)
+std::vector<real> makeNonBondedParameterLists(const gmx_ffparams_t& forceFieldParams, bool useBuckinghamPotential)
{
std::vector<real> nbfp;
int atnr;
- atnr = idef->atnr;
- if (bBHAM)
+ atnr = forceFieldParams.atnr;
+ if (useBuckinghamPotential)
{
nbfp.resize(3 * atnr * atnr);
int k = 0;
{
for (int j = 0; (j < atnr); j++, k++)
{
- BHAMA(nbfp, atnr, i, j) = idef->iparams[k].bham.a;
- BHAMB(nbfp, atnr, i, j) = idef->iparams[k].bham.b;
+ BHAMA(nbfp, atnr, i, j) = forceFieldParams.iparams[k].bham.a;
+ BHAMB(nbfp, atnr, i, j) = forceFieldParams.iparams[k].bham.b;
/* nbfp now includes the 6.0 derivative prefactor */
- BHAMC(nbfp, atnr, i, j) = idef->iparams[k].bham.c * 6.0;
+ BHAMC(nbfp, atnr, i, j) = forceFieldParams.iparams[k].bham.c * 6.0;
}
}
}
for (int j = 0; (j < atnr); j++, k++)
{
/* nbfp now includes the 6.0/12.0 derivative prefactors */
- C6(nbfp, atnr, i, j) = idef->iparams[k].lj.c6 * 6.0;
- C12(nbfp, atnr, i, j) = idef->iparams[k].lj.c12 * 12.0;
+ C6(nbfp, atnr, i, j) = forceFieldParams.iparams[k].lj.c6 * 6.0;
+ C12(nbfp, atnr, i, j) = forceFieldParams.iparams[k].lj.c12 * 12.0;
}
}
}
return nbfp;
}
-static real* make_ljpme_c6grid(const gmx_ffparams_t* idef, t_forcerec* fr)
+std::vector<real> makeLJPmeC6GridCorrectionParameters(const gmx_ffparams_t& forceFieldParams,
+ const t_forcerec& forceRec)
{
- int i, j, k, atnr;
- real c6, c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
- real* grid;
+ int i, j, k, atnr;
+ real c6, c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
/* For LJ-PME simulations, we correct the energies with the reciprocal space
* inside of the cut-off. To do this the non-bonded kernels needs to have
* access to the C6-values used on the reciprocal grid in pme.c
*/
- atnr = idef->atnr;
- snew(grid, 2 * atnr * atnr);
+ atnr = forceFieldParams.atnr;
+ std::vector<real> grid(2 * atnr * atnr, 0.0);
for (i = k = 0; (i < atnr); i++)
{
for (j = 0; (j < atnr); j++, k++)
{
- c6i = idef->iparams[i * (atnr + 1)].lj.c6;
- c12i = idef->iparams[i * (atnr + 1)].lj.c12;
- c6j = idef->iparams[j * (atnr + 1)].lj.c6;
- c12j = idef->iparams[j * (atnr + 1)].lj.c12;
+ c6i = forceFieldParams.iparams[i * (atnr + 1)].lj.c6;
+ c12i = forceFieldParams.iparams[i * (atnr + 1)].lj.c12;
+ c6j = forceFieldParams.iparams[j * (atnr + 1)].lj.c6;
+ c12j = forceFieldParams.iparams[j * (atnr + 1)].lj.c12;
c6 = std::sqrt(c6i * c6j);
- if (fr->ljpme_combination_rule == eljpmeLB && !gmx_numzero(c6) && !gmx_numzero(c12i)
- && !gmx_numzero(c12j))
+ if (forceRec.ljpme_combination_rule == LongRangeVdW::LB && !gmx_numzero(c6)
+ && !gmx_numzero(c12i) && !gmx_numzero(c12j))
{
sigmai = gmx::sixthroot(c12i / c6i);
sigmaj = gmx::sixthroot(c12j / c6j);
acSETTLE
};
-static std::vector<cginfo_mb_t> init_cginfo_mb(const gmx_mtop_t* mtop, const t_forcerec* fr)
+static std::vector<cginfo_mb_t> init_cginfo_mb(const gmx_mtop_t& mtop, const t_forcerec* fr)
{
gmx_bool* type_VDW;
int* a_con;
type_VDW[ai] = FALSE;
for (int j = 0; j < fr->ntype; j++)
{
- type_VDW[ai] = type_VDW[ai] || fr->bBHAM || C6(fr->nbfp, fr->ntype, ai, j) != 0
+ type_VDW[ai] = type_VDW[ai] || fr->haveBuckingham || C6(fr->nbfp, fr->ntype, ai, j) != 0
|| C12(fr->nbfp, fr->ntype, ai, j) != 0;
}
}
std::vector<cginfo_mb_t> cginfoPerMolblock;
int a_offset = 0;
- for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
+ for (size_t mb = 0; mb < mtop.molblock.size(); mb++)
{
- const gmx_molblock_t& molb = mtop->molblock[mb];
- const gmx_moltype_t& molt = mtop->moltype[molb.type];
+ const gmx_molblock_t& molb = mtop.molblock[mb];
+ const gmx_moltype_t& molt = mtop.moltype[molb.type];
const auto& excl = molt.excls;
/* Check if the cginfo is identical for all molecules in this block.
const int am = m * molt.atoms.nr;
for (int a = 0; a < molt.atoms.nr; a++)
{
- if (getGroupType(mtop->groups, SimulationAtomGroupType::QuantumMechanics, a_offset + am + a)
- != getGroupType(mtop->groups, SimulationAtomGroupType::QuantumMechanics, a_offset + a))
+ if (getGroupType(mtop.groups, SimulationAtomGroupType::QuantumMechanics, a_offset + am + a)
+ != getGroupType(mtop.groups, SimulationAtomGroupType::QuantumMechanics, a_offset + a))
{
bId = FALSE;
}
- if (!mtop->groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics].empty())
+ if (!mtop.groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics].empty())
{
- if (mtop->groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics][a_offset + am + a]
- != mtop->groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics][a_offset + a])
+ if (mtop.groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics][a_offset + am + a]
+ != mtop.groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics][a_offset + a])
{
bId = FALSE;
}
int& atomInfo = cginfo[molculeOffsetInBlock + a];
/* Store the energy group in cginfo */
- int gid = getGroupType(mtop->groups, SimulationAtomGroupType::EnergyOutput,
+ int gid = getGroupType(mtop.groups,
+ SimulationAtomGroupType::EnergyOutput,
a_offset + molculeOffsetInBlock + a);
SET_CGINFO_GID(atomInfo, gid);
{
SET_CGINFO_HAS_Q(atomInfo);
}
- if (fr->efep != efepNO && PERTURBED(atom))
+ if (fr->efep != FreeEnergyPerturbationType::No && PERTURBED(atom))
{
SET_CGINFO_FEP(atomInfo);
}
/* Sets the sum of charges (squared) and C6 in the system in fr.
* Returns whether the system has a net charge.
*/
-static bool set_chargesum(FILE* log, t_forcerec* fr, const gmx_mtop_t* mtop)
+static bool set_chargesum(FILE* log, t_forcerec* fr, const gmx_mtop_t& mtop)
{
/*This now calculates sum for q and c6*/
double qsum, q2sum, q, c6sum, c6;
qsum = 0;
q2sum = 0;
c6sum = 0;
- for (const gmx_molblock_t& molb : mtop->molblock)
+ for (const gmx_molblock_t& molb : mtop.molblock)
{
int nmol = molb.nmol;
- const t_atoms* atoms = &mtop->moltype[molb.type].atoms;
+ const t_atoms* atoms = &mtop.moltype[molb.type].atoms;
for (int i = 0; i < atoms->nr; i++)
{
q = atoms->atom[i].q;
qsum += nmol * q;
q2sum += nmol * q * q;
- c6 = mtop->ffparams.iparams[atoms->atom[i].type * (mtop->ffparams.atnr + 1)].lj.c6;
+ c6 = mtop.ffparams.iparams[atoms->atom[i].type * (mtop.ffparams.atnr + 1)].lj.c6;
c6sum += nmol * c6;
}
}
fr->q2sum[0] = q2sum;
fr->c6sum[0] = c6sum;
- if (fr->efep != efepNO)
+ if (fr->efep != FreeEnergyPerturbationType::No)
{
qsum = 0;
q2sum = 0;
c6sum = 0;
- for (const gmx_molblock_t& molb : mtop->molblock)
+ for (const gmx_molblock_t& molb : mtop.molblock)
{
int nmol = molb.nmol;
- const t_atoms* atoms = &mtop->moltype[molb.type].atoms;
+ const t_atoms* atoms = &mtop.moltype[molb.type].atoms;
for (int i = 0; i < atoms->nr; i++)
{
q = atoms->atom[i].qB;
qsum += nmol * q;
q2sum += nmol * q * q;
- c6 = mtop->ffparams.iparams[atoms->atom[i].typeB * (mtop->ffparams.atnr + 1)].lj.c6;
+ c6 = mtop.ffparams.iparams[atoms->atom[i].typeB * (mtop.ffparams.atnr + 1)].lj.c6;
c6sum += nmol * c6;
}
fr->qsum[1] = qsum;
}
if (log)
{
- if (fr->efep == efepNO)
+ if (fr->efep == FreeEnergyPerturbationType::No)
{
fprintf(log, "System total charge: %.3f\n", fr->qsum[0]);
}
return (std::abs(fr->qsum[0]) > 1e-4 || std::abs(fr->qsum[1]) > 1e-4);
}
-static real calcBuckinghamBMax(FILE* fplog, const gmx_mtop_t* mtop)
-{
- const t_atoms *at1, *at2;
- int i, j, tpi, tpj, ntypes;
- real b, bmin;
-
- if (fplog)
- {
- fprintf(fplog, "Determining largest Buckingham b parameter for table\n");
- }
- ntypes = mtop->ffparams.atnr;
-
- bmin = -1;
- real bham_b_max = 0;
- for (size_t mt1 = 0; mt1 < mtop->moltype.size(); mt1++)
- {
- at1 = &mtop->moltype[mt1].atoms;
- for (i = 0; (i < at1->nr); i++)
- {
- tpi = at1->atom[i].type;
- if (tpi >= ntypes)
- {
- gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", i, tpi, ntypes);
- }
-
- for (size_t mt2 = mt1; mt2 < mtop->moltype.size(); mt2++)
- {
- at2 = &mtop->moltype[mt2].atoms;
- for (j = 0; (j < at2->nr); j++)
- {
- tpj = at2->atom[j].type;
- if (tpj >= ntypes)
- {
- gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", j, tpj, ntypes);
- }
- b = mtop->ffparams.iparams[tpi * ntypes + tpj].bham.b;
- if (b > bham_b_max)
- {
- bham_b_max = b;
- }
- if ((b < bmin) || (bmin == -1))
- {
- bmin = b;
- }
- }
- }
- }
- }
- if (fplog)
- {
- fprintf(fplog, "Buckingham b parameters, min: %g, max: %g\n", bmin, bham_b_max);
- }
-
- return bham_b_max;
-}
-
/*!\brief If there's bonded interactions of type \c ftype1 or \c
* ftype2 present in the topology, build an array of the number of
* interactions present for each bonded interaction index found in the
* \c ncount. It will contain zero for every bonded interaction index
* for which no interactions are present in the topology.
*/
-static void count_tables(int ftype1, int ftype2, const gmx_mtop_t* mtop, int* ncount, int** count)
+static void count_tables(int ftype1, int ftype2, const gmx_mtop_t& mtop, int* ncount, int** count)
{
int ftype, i, j, tabnr;
// Loop over all moleculetypes
- for (const gmx_moltype_t& molt : mtop->moltype)
+ for (const gmx_moltype_t& molt : mtop.moltype)
{
// Loop over all interaction types
for (ftype = 0; ftype < F_NRE; ftype++)
for (i = 0; i < il.size(); i += stride)
{
// Find out which table index the user wanted
- tabnr = mtop->ffparams.iparams[il.iatoms[i]].tab.table;
+ tabnr = mtop.ffparams.iparams[il.iatoms[i]].tab.table;
if (tabnr < 0)
{
gmx_fatal(FARGS, "A bonded table number is smaller than 0: %d\n", tabnr);
static std::vector<bondedtable_t> make_bonded_tables(FILE* fplog,
int ftype1,
int ftype2,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
gmx::ArrayRef<const std::string> tabbfnm,
const char* tabext)
{
"Tabulated interaction of type '%s%s%s' with index %d cannot be used "
"because no table file whose name matched '%s' was passed via the "
"gmx mdrun -tableb command-line option.",
- interaction_function[ftype1].longname, isPlural ? "' or '" : "",
- isPlural ? interaction_function[ftype2].longname : "", i,
+ interaction_function[ftype1].longname,
+ isPlural ? "' or '" : "",
+ isPlural ? interaction_function[ftype2].longname : "",
+ i,
patternToFind.c_str());
}
}
}
}
-static real cutoff_inf(real cutoff)
-{
- if (cutoff == 0)
- {
- cutoff = GMX_CUTOFF_INF;
- }
-
- return cutoff;
-}
-
-/*! \brief Print Coulomb Ewald citations and set ewald coefficients */
-static void initCoulombEwaldParameters(FILE* fp,
- const t_inputrec* ir,
- bool systemHasNetCharge,
- interaction_const_t* ic)
-{
- if (!EEL_PME_EWALD(ir->coulombtype))
- {
- return;
- }
-
- if (fp)
- {
- fprintf(fp, "Will do PME sum in reciprocal space for electrostatic interactions.\n");
-
- if (ir->coulombtype == eelP3M_AD)
- {
- please_cite(fp, "Hockney1988");
- please_cite(fp, "Ballenegger2012");
- }
- else
- {
- please_cite(fp, "Essmann95a");
- }
-
- if (ir->ewald_geometry == eewg3DC)
- {
- if (fp)
- {
- fprintf(fp, "Using the Ewald3DC correction for systems with a slab geometry%s.\n",
- systemHasNetCharge ? " and net charge" : "");
- }
- please_cite(fp, "In-Chul99a");
- if (systemHasNetCharge)
- {
- please_cite(fp, "Ballenegger2009");
- }
- }
- }
-
- ic->ewaldcoeff_q = calc_ewaldcoeff_q(ir->rcoulomb, ir->ewald_rtol);
- if (fp)
- {
- fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for Ewald\n", 1 / ic->ewaldcoeff_q);
- }
-
- if (ic->coulomb_modifier == eintmodPOTSHIFT)
- {
- GMX_RELEASE_ASSERT(ic->rcoulomb != 0, "Cutoff radius cannot be zero");
- ic->sh_ewald = std::erfc(ic->ewaldcoeff_q * ic->rcoulomb) / ic->rcoulomb;
- }
- else
- {
- ic->sh_ewald = 0;
- }
-}
-
-/*! \brief Print Van der Waals Ewald citations and set ewald coefficients */
-static void initVdwEwaldParameters(FILE* fp, const t_inputrec* ir, interaction_const_t* ic)
-{
- if (!EVDW_PME(ir->vdwtype))
- {
- return;
- }
-
- if (fp)
- {
- fprintf(fp, "Will do PME sum in reciprocal space for LJ dispersion interactions.\n");
- please_cite(fp, "Essmann95a");
- }
- ic->ewaldcoeff_lj = calc_ewaldcoeff_lj(ir->rvdw, ir->ewald_rtol_lj);
- if (fp)
- {
- fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for LJ Ewald\n", 1 / ic->ewaldcoeff_lj);
- }
-
- if (ic->vdw_modifier == eintmodPOTSHIFT)
- {
- real crc2 = gmx::square(ic->ewaldcoeff_lj * ic->rvdw);
- ic->sh_lj_ewald = (std::exp(-crc2) * (1 + crc2 + 0.5 * crc2 * crc2) - 1) / gmx::power6(ic->rvdw);
- }
- else
- {
- ic->sh_lj_ewald = 0;
- }
-}
-
/* Generate Coulomb and/or Van der Waals Ewald long-range correction tables
*
* Tables are generated for one or both, depending on if the pointers
{
if (EEL_PME_EWALD(ic->eeltype) || EVDW_PME(ic->vdwtype))
{
- init_ewald_f_table(*ic, rlist, tableExtensionLength, ic->coulombEwaldTables.get(),
- ic->vdwEwaldTables.get());
+ init_ewald_f_table(
+ *ic, rlist, tableExtensionLength, ic->coulombEwaldTables.get(), ic->vdwEwaldTables.get());
if (fp != nullptr)
{
- fprintf(fp, "Initialized non-bonded Ewald tables, spacing: %.2e size: %zu\n\n",
- 1 / ic->coulombEwaldTables->scale, ic->coulombEwaldTables->tableF.size());
+ fprintf(fp,
+ "Initialized non-bonded Ewald tables, spacing: %.2e size: %zu\n\n",
+ 1 / ic->coulombEwaldTables->scale,
+ ic->coulombEwaldTables->tableF.size());
}
}
}
-static void clear_force_switch_constants(shift_consts_t* sc)
-{
- sc->c2 = 0;
- sc->c3 = 0;
- sc->cpot = 0;
-}
-
-static void force_switch_constants(real p, real rsw, real rc, shift_consts_t* sc)
-{
- /* Here we determine the coefficient for shifting the force to zero
- * between distance rsw and the cut-off rc.
- * For a potential of r^-p, we have force p*r^-(p+1).
- * But to save flops we absorb p in the coefficient.
- * Thus we get:
- * force/p = r^-(p+1) + c2*r^2 + c3*r^3
- * potential = r^-p + c2/3*r^3 + c3/4*r^4 + cpot
- */
- sc->c2 = ((p + 1) * rsw - (p + 4) * rc) / (pow(rc, p + 2) * gmx::square(rc - rsw));
- sc->c3 = -((p + 1) * rsw - (p + 3) * rc) / (pow(rc, p + 2) * gmx::power3(rc - rsw));
- sc->cpot = -pow(rc, -p) + p * sc->c2 / 3 * gmx::power3(rc - rsw)
- + p * sc->c3 / 4 * gmx::power4(rc - rsw);
-}
-
-static void potential_switch_constants(real rsw, real rc, switch_consts_t* sc)
-{
- /* The switch function is 1 at rsw and 0 at rc.
- * The derivative and second derivate are zero at both ends.
- * rsw = max(r - r_switch, 0)
- * sw = 1 + c3*rsw^3 + c4*rsw^4 + c5*rsw^5
- * dsw = 3*c3*rsw^2 + 4*c4*rsw^3 + 5*c5*rsw^4
- * force = force*dsw - potential*sw
- * potential *= sw
- */
- sc->c3 = -10 / gmx::power3(rc - rsw);
- sc->c4 = 15 / gmx::power4(rc - rsw);
- sc->c5 = -6 / gmx::power5(rc - rsw);
-}
-
-/*! \brief Construct interaction constants
- *
- * This data is used (particularly) by search and force code for
- * short-range interactions. Many of these are constant for the whole
- * simulation; some are constant only after PME tuning completes.
- */
-static void init_interaction_const(FILE* fp,
- interaction_const_t** interaction_const,
- const t_inputrec* ir,
- const gmx_mtop_t* mtop,
- bool systemHasNetCharge)
+real cutoff_inf(real cutoff)
{
- interaction_const_t* ic = new interaction_const_t;
-
- ic->coulombEwaldTables = std::make_unique<EwaldCorrectionTables>();
- ic->vdwEwaldTables = std::make_unique<EwaldCorrectionTables>();
-
- /* Lennard-Jones */
- ic->vdwtype = ir->vdwtype;
- ic->vdw_modifier = ir->vdw_modifier;
- ic->reppow = mtop->ffparams.reppow;
- ic->rvdw = cutoff_inf(ir->rvdw);
- ic->rvdw_switch = ir->rvdw_switch;
- ic->ljpme_comb_rule = ir->ljpme_combination_rule;
- ic->useBuckingham = (mtop->ffparams.functype[0] == F_BHAM);
- if (ic->useBuckingham)
- {
- ic->buckinghamBMax = calcBuckinghamBMax(fp, mtop);
- }
-
- initVdwEwaldParameters(fp, ir, ic);
-
- clear_force_switch_constants(&ic->dispersion_shift);
- clear_force_switch_constants(&ic->repulsion_shift);
-
- switch (ic->vdw_modifier)
- {
- case eintmodPOTSHIFT:
- /* Only shift the potential, don't touch the force */
- ic->dispersion_shift.cpot = -1.0 / gmx::power6(ic->rvdw);
- ic->repulsion_shift.cpot = -1.0 / gmx::power12(ic->rvdw);
- break;
- case eintmodFORCESWITCH:
- /* Switch the force, switch and shift the potential */
- force_switch_constants(6.0, ic->rvdw_switch, ic->rvdw, &ic->dispersion_shift);
- force_switch_constants(12.0, ic->rvdw_switch, ic->rvdw, &ic->repulsion_shift);
- break;
- case eintmodPOTSWITCH:
- /* Switch the potential and force */
- potential_switch_constants(ic->rvdw_switch, ic->rvdw, &ic->vdw_switch);
- break;
- case eintmodNONE:
- case eintmodEXACTCUTOFF:
- /* Nothing to do here */
- break;
- default: gmx_incons("unimplemented potential modifier");
- }
-
- /* Electrostatics */
- ic->eeltype = ir->coulombtype;
- ic->coulomb_modifier = ir->coulomb_modifier;
- ic->rcoulomb = cutoff_inf(ir->rcoulomb);
- ic->rcoulomb_switch = ir->rcoulomb_switch;
- ic->epsilon_r = ir->epsilon_r;
-
- /* Set the Coulomb energy conversion factor */
- if (ic->epsilon_r != 0)
- {
- ic->epsfac = ONE_4PI_EPS0 / ic->epsilon_r;
- }
- else
- {
- /* eps = 0 is infinite dieletric: no Coulomb interactions */
- ic->epsfac = 0;
- }
-
- /* Reaction-field */
- if (EEL_RF(ic->eeltype))
- {
- GMX_RELEASE_ASSERT(ic->eeltype != eelGRF_NOTUSED, "GRF is no longer supported");
- ic->epsilon_rf = ir->epsilon_rf;
-
- calc_rffac(fp, ic->epsilon_r, ic->epsilon_rf, ic->rcoulomb, &ic->k_rf, &ic->c_rf);
- }
- else
- {
- /* For plain cut-off we might use the reaction-field kernels */
- ic->epsilon_rf = ic->epsilon_r;
- ic->k_rf = 0;
- if (ir->coulomb_modifier == eintmodPOTSHIFT)
- {
- ic->c_rf = 1 / ic->rcoulomb;
- }
- else
- {
- ic->c_rf = 0;
- }
- }
-
- initCoulombEwaldParameters(fp, ir, systemHasNetCharge, ic);
-
- if (fp != nullptr)
- {
- real dispersion_shift;
-
- dispersion_shift = ic->dispersion_shift.cpot;
- if (EVDW_PME(ic->vdwtype))
- {
- dispersion_shift -= ic->sh_lj_ewald;
- }
- fprintf(fp, "Potential shift: LJ r^-12: %.3e r^-6: %.3e", ic->repulsion_shift.cpot, dispersion_shift);
-
- if (ic->eeltype == eelCUT)
- {
- fprintf(fp, ", Coulomb %.e", -ic->c_rf);
- }
- else if (EEL_PME(ic->eeltype))
- {
- fprintf(fp, ", Ewald %.3e", -ic->sh_ewald);
- }
- fprintf(fp, "\n");
- }
-
- if (ir->efep != efepNO)
+ if (cutoff == 0)
{
- GMX_RELEASE_ASSERT(ir->fepvals, "ir->fepvals should be set wth free-energy");
- ic->softCoreParameters = std::make_unique<interaction_const_t::SoftCoreParameters>(*ir->fepvals);
+ cutoff = GMX_CUTOFF_INF;
}
- *interaction_const = ic;
+ return cutoff;
}
-void init_forcerec(FILE* fp,
+void init_forcerec(FILE* fplog,
const gmx::MDLogger& mdlog,
- t_forcerec* fr,
- const t_inputrec* ir,
- const gmx_mtop_t* mtop,
- const t_commrec* cr,
+ t_forcerec* forcerec,
+ const t_inputrec& inputrec,
+ const gmx_mtop_t& mtop,
+ const t_commrec* commrec,
matrix box,
const char* tabfn,
const char* tabpfn,
real print_force)
{
/* The CMake default turns SIMD kernels on, but it might be turned off further down... */
- fr->use_simd_kernels = GMX_USE_SIMD_KERNELS;
+ forcerec->use_simd_kernels = GMX_USE_SIMD_KERNELS;
- if (check_box(ir->pbcType, box))
+ if (check_box(inputrec.pbcType, box))
{
- gmx_fatal(FARGS, "%s", check_box(ir->pbcType, box));
+ gmx_fatal(FARGS, "%s", check_box(inputrec.pbcType, box));
}
/* Test particle insertion ? */
- if (EI_TPI(ir->eI))
+ if (EI_TPI(inputrec.eI))
{
/* Set to the size of the molecule to be inserted (the last one) */
- gmx::RangePartitioning molecules = gmx_mtop_molecules(*mtop);
- fr->n_tpi = molecules.block(molecules.numBlocks() - 1).size();
+ gmx::RangePartitioning molecules = gmx_mtop_molecules(mtop);
+ forcerec->n_tpi = molecules.block(molecules.numBlocks() - 1).size();
}
else
{
- fr->n_tpi = 0;
+ forcerec->n_tpi = 0;
}
- if (ir->coulombtype == eelRF_NEC_UNSUPPORTED || ir->coulombtype == eelGRF_NOTUSED)
+ if (inputrec.coulombtype == CoulombInteractionType::RFNecUnsupported
+ || inputrec.coulombtype == CoulombInteractionType::GRFNotused)
{
- gmx_fatal(FARGS, "%s electrostatics is no longer supported", eel_names[ir->coulombtype]);
+ gmx_fatal(FARGS, "%s electrostatics is no longer supported", enumValueToString(inputrec.coulombtype));
}
- if (ir->bAdress)
+ if (inputrec.bAdress)
{
gmx_fatal(FARGS, "AdResS simulations are no longer supported");
}
- if (ir->useTwinRange)
+ if (inputrec.useTwinRange)
{
gmx_fatal(FARGS, "Twin-range simulations are no longer supported");
}
/* Copy the user determined parameters */
- fr->userint1 = ir->userint1;
- fr->userint2 = ir->userint2;
- fr->userint3 = ir->userint3;
- fr->userint4 = ir->userint4;
- fr->userreal1 = ir->userreal1;
- fr->userreal2 = ir->userreal2;
- fr->userreal3 = ir->userreal3;
- fr->userreal4 = ir->userreal4;
+ forcerec->userint1 = inputrec.userint1;
+ forcerec->userint2 = inputrec.userint2;
+ forcerec->userint3 = inputrec.userint3;
+ forcerec->userint4 = inputrec.userint4;
+ forcerec->userreal1 = inputrec.userreal1;
+ forcerec->userreal2 = inputrec.userreal2;
+ forcerec->userreal3 = inputrec.userreal3;
+ forcerec->userreal4 = inputrec.userreal4;
/* Shell stuff */
- fr->fc_stepsize = ir->fc_stepsize;
+ forcerec->fc_stepsize = inputrec.fc_stepsize;
/* Free energy */
- fr->efep = ir->efep;
+ forcerec->efep = inputrec.efep;
if ((getenv("GMX_DISABLE_SIMD_KERNELS") != nullptr) || (getenv("GMX_NOOPTIMIZEDKERNELS") != nullptr))
{
- fr->use_simd_kernels = FALSE;
- if (fp != nullptr)
+ forcerec->use_simd_kernels = FALSE;
+ if (fplog != nullptr)
{
- fprintf(fp,
+ fprintf(fplog,
"\nFound environment variable GMX_DISABLE_SIMD_KERNELS.\n"
"Disabling the usage of any SIMD-specific non-bonded & bonded kernel routines\n"
"(e.g. SSE2/SSE4.1/AVX).\n\n");
}
}
- fr->bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
+ forcerec->haveBuckingham = (mtop.ffparams.functype[0] == F_BHAM);
/* Neighbour searching stuff */
- fr->pbcType = ir->pbcType;
+ forcerec->pbcType = inputrec.pbcType;
/* Determine if we will do PBC for distances in bonded interactions */
- if (fr->pbcType == PbcType::No)
+ if (forcerec->pbcType == PbcType::No)
{
- fr->bMolPBC = FALSE;
+ forcerec->bMolPBC = FALSE;
}
else
{
const bool useEwaldSurfaceCorrection =
- (EEL_PME_EWALD(ir->coulombtype) && ir->epsilon_surface != 0);
+ (EEL_PME_EWALD(inputrec.coulombtype) && inputrec.epsilon_surface != 0);
const bool haveOrientationRestraints = (gmx_mtop_ftype_count(mtop, F_ORIRES) > 0);
- if (!DOMAINDECOMP(cr))
+ if (!DOMAINDECOMP(commrec))
{
- fr->bMolPBC = true;
+ forcerec->bMolPBC = true;
if (useEwaldSurfaceCorrection || haveOrientationRestraints)
{
- fr->wholeMoleculeTransform =
- std::make_unique<gmx::WholeMoleculeTransform>(*mtop, ir->pbcType);
+ forcerec->wholeMoleculeTransform =
+ std::make_unique<gmx::WholeMoleculeTransform>(mtop, inputrec.pbcType);
}
}
else
{
- fr->bMolPBC = dd_bonded_molpbc(cr->dd, fr->pbcType);
+ forcerec->bMolPBC = dd_bonded_molpbc(*commrec->dd, forcerec->pbcType);
/* With Ewald surface correction it is useful to support e.g. running water
* in parallel with update groups.
* With orientation restraints there is no sensible use case supported with DD.
*/
- if ((useEwaldSurfaceCorrection && !dd_moleculesAreAlwaysWhole(*cr->dd)) || haveOrientationRestraints)
+ if ((useEwaldSurfaceCorrection && !dd_moleculesAreAlwaysWhole(*commrec->dd))
+ || haveOrientationRestraints)
{
gmx_fatal(FARGS,
"You requested Ewald surface correction or orientation restraints, "
if (useEwaldSurfaceCorrection)
{
- GMX_RELEASE_ASSERT(!DOMAINDECOMP(cr) || dd_moleculesAreAlwaysWhole(*cr->dd),
+ GMX_RELEASE_ASSERT(!DOMAINDECOMP(commrec) || dd_moleculesAreAlwaysWhole(*commrec->dd),
"Molecules can not be broken by PBC with epsilon_surface > 0");
}
}
- fr->rc_scaling = ir->refcoord_scaling;
- copy_rvec(ir->posres_com, fr->posres_com);
- copy_rvec(ir->posres_comB, fr->posres_comB);
- fr->rlist = cutoff_inf(ir->rlist);
- fr->ljpme_combination_rule = ir->ljpme_combination_rule;
+ forcerec->rc_scaling = inputrec.refcoord_scaling;
+ copy_rvec(inputrec.posres_com, forcerec->posres_com);
+ copy_rvec(inputrec.posres_comB, forcerec->posres_comB);
+ forcerec->rlist = cutoff_inf(inputrec.rlist);
+ forcerec->ljpme_combination_rule = inputrec.ljpme_combination_rule;
/* This now calculates sum for q and c6*/
- bool systemHasNetCharge = set_chargesum(fp, fr, mtop);
+ bool systemHasNetCharge = set_chargesum(fplog, forcerec, mtop);
- /* fr->ic is used both by verlet and group kernels (to some extent) now */
- init_interaction_const(fp, &fr->ic, ir, mtop, systemHasNetCharge);
- init_interaction_const_tables(fp, fr->ic, fr->rlist, ir->tabext);
+ /* Make data structure used by kernels */
+ forcerec->ic = std::make_unique<interaction_const_t>(
+ init_interaction_const(fplog, inputrec, mtop, systemHasNetCharge));
+ init_interaction_const_tables(fplog, forcerec->ic.get(), forcerec->rlist, inputrec.tabext);
- const interaction_const_t* ic = fr->ic;
+ const interaction_const_t* interactionConst = forcerec->ic.get();
/* TODO: Replace this Ewald table or move it into interaction_const_t */
- if (ir->coulombtype == eelEWALD)
+ if (inputrec.coulombtype == CoulombInteractionType::Ewald)
{
- init_ewald_tab(&(fr->ewald_table), ir, fp);
+ forcerec->ewald_table = std::make_unique<gmx_ewald_tab_t>(inputrec, fplog);
}
/* Electrostatics: Translate from interaction-setting-in-mdp-file to kernel interaction format */
- switch (ic->eeltype)
+ switch (interactionConst->eeltype)
{
- case eelCUT: fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_COULOMB; break;
-
- case eelRF:
- case eelRF_ZERO: fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD; break;
-
- case eelSWITCH:
- case eelSHIFT:
- case eelUSER:
- case eelPMESWITCH:
- case eelPMEUSER:
- case eelPMEUSERSWITCH:
- fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
+ case CoulombInteractionType::Cut:
+ forcerec->nbkernel_elec_interaction = NbkernelElecType::Coulomb;
break;
- case eelPME:
- case eelP3M_AD:
- case eelEWALD: fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_EWALD; break;
+ case CoulombInteractionType::RF:
+ case CoulombInteractionType::RFZero:
+ forcerec->nbkernel_elec_interaction = NbkernelElecType::ReactionField;
+ break;
+
+ case CoulombInteractionType::Switch:
+ case CoulombInteractionType::Shift:
+ case CoulombInteractionType::User:
+ case CoulombInteractionType::PmeSwitch:
+ case CoulombInteractionType::PmeUser:
+ case CoulombInteractionType::PmeUserSwitch:
+ forcerec->nbkernel_elec_interaction = NbkernelElecType::CubicSplineTable;
+ break;
+
+ case CoulombInteractionType::Pme:
+ case CoulombInteractionType::P3mAD:
+ case CoulombInteractionType::Ewald:
+ forcerec->nbkernel_elec_interaction = NbkernelElecType::Ewald;
+ break;
default:
- gmx_fatal(FARGS, "Unsupported electrostatic interaction: %s", eel_names[ic->eeltype]);
+ gmx_fatal(FARGS,
+ "Unsupported electrostatic interaction: %s",
+ enumValueToString(interactionConst->eeltype));
}
- fr->nbkernel_elec_modifier = ic->coulomb_modifier;
+ forcerec->nbkernel_elec_modifier = interactionConst->coulomb_modifier;
/* Vdw: Translate from mdp settings to kernel format */
- switch (ic->vdwtype)
+ switch (interactionConst->vdwtype)
{
- case evdwCUT:
- if (fr->bBHAM)
+ case VanDerWaalsType::Cut:
+ if (forcerec->haveBuckingham)
{
- fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_BUCKINGHAM;
+ forcerec->nbkernel_vdw_interaction = NbkernelVdwType::Buckingham;
}
else
{
- fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LENNARDJONES;
+ forcerec->nbkernel_vdw_interaction = NbkernelVdwType::LennardJones;
}
break;
- case evdwPME: fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LJEWALD; break;
+ case VanDerWaalsType::Pme:
+ forcerec->nbkernel_vdw_interaction = NbkernelVdwType::LJEwald;
+ break;
- case evdwSWITCH:
- case evdwSHIFT:
- case evdwUSER: fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE; break;
+ case VanDerWaalsType::Switch:
+ case VanDerWaalsType::Shift:
+ case VanDerWaalsType::User:
+ forcerec->nbkernel_vdw_interaction = NbkernelVdwType::CubicSplineTable;
+ break;
- default: gmx_fatal(FARGS, "Unsupported vdw interaction: %s", evdw_names[ic->vdwtype]);
+ default:
+ gmx_fatal(FARGS, "Unsupported vdw interaction: %s", enumValueToString(interactionConst->vdwtype));
}
- fr->nbkernel_vdw_modifier = ic->vdw_modifier;
+ forcerec->nbkernel_vdw_modifier = interactionConst->vdw_modifier;
- if (!gmx_within_tol(ic->reppow, 12.0, 10 * GMX_DOUBLE_EPS))
+ if (!gmx_within_tol(interactionConst->reppow, 12.0, 10 * GMX_DOUBLE_EPS))
{
gmx_fatal(FARGS, "Only LJ repulsion power 12 is supported");
}
/* Older tpr files can contain Coulomb user tables with the Verlet cutoff-scheme,
* while mdrun does not (and never did) support this.
*/
- if (EEL_USER(fr->ic->eeltype))
+ if (EEL_USER(forcerec->ic->eeltype))
{
- gmx_fatal(FARGS, "Electrostatics type %s is currently not supported", eel_names[ir->coulombtype]);
+ gmx_fatal(FARGS,
+ "Electrostatics type %s is currently not supported",
+ enumValueToString(inputrec.coulombtype));
}
- fr->bvdwtab = FALSE;
- fr->bcoultab = FALSE;
-
/* 1-4 interaction electrostatics */
- fr->fudgeQQ = mtop->ffparams.fudgeQQ;
+ forcerec->fudgeQQ = mtop.ffparams.fudgeQQ;
// Multiple time stepping
- fr->useMts = ir->useMts;
+ forcerec->useMts = inputrec.useMts;
- if (fr->useMts)
+ if (forcerec->useMts)
{
- gmx::assertMtsRequirements(*ir);
+ GMX_ASSERT(gmx::checkMtsRequirements(inputrec).empty(),
+ "All MTS requirements should be met here");
}
const bool haveDirectVirialContributionsFast =
- fr->forceProviders->hasForceProvider() || gmx_mtop_ftype_count(mtop, F_POSRES) > 0
- || gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0 || ir->nwall > 0 || ir->bPull || ir->bRot
- || ir->bIMD;
- const bool haveDirectVirialContributionsSlow = EEL_FULL(ic->eeltype) || EVDW_PME(ic->vdwtype);
- for (int i = 0; i < (fr->useMts ? 2 : 1); i++)
+ forcerec->forceProviders->hasForceProvider() || gmx_mtop_ftype_count(mtop, F_POSRES) > 0
+ || gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0 || inputrec.nwall > 0 || inputrec.bPull
+ || inputrec.bRot || inputrec.bIMD;
+ const bool haveDirectVirialContributionsSlow =
+ EEL_FULL(interactionConst->eeltype) || EVDW_PME(interactionConst->vdwtype);
+ for (int i = 0; i < (forcerec->useMts ? 2 : 1); i++)
{
bool haveDirectVirialContributions =
- (((!fr->useMts || i == 0) && haveDirectVirialContributionsFast)
- || ((!fr->useMts || i == 1) && haveDirectVirialContributionsSlow));
- fr->forceHelperBuffers.emplace_back(haveDirectVirialContributions);
+ (((!forcerec->useMts || i == 0) && haveDirectVirialContributionsFast)
+ || ((!forcerec->useMts || i == 1) && haveDirectVirialContributionsSlow));
+ forcerec->forceHelperBuffers.emplace_back(haveDirectVirialContributions);
}
- if (fr->shift_vec == nullptr)
+ if (forcerec->shift_vec.empty())
{
- snew(fr->shift_vec, SHIFTS);
+ forcerec->shift_vec.resize(gmx::c_numShiftVectors);
}
- if (fr->nbfp.empty())
+ if (forcerec->nbfp.empty())
{
- fr->ntype = mtop->ffparams.atnr;
- fr->nbfp = mk_nbfp(&mtop->ffparams, fr->bBHAM);
- if (EVDW_PME(ic->vdwtype))
+ forcerec->ntype = mtop.ffparams.atnr;
+ forcerec->nbfp = makeNonBondedParameterLists(mtop.ffparams, forcerec->haveBuckingham);
+ if (EVDW_PME(interactionConst->vdwtype))
{
- fr->ljpme_c6grid = make_ljpme_c6grid(&mtop->ffparams, fr);
+ forcerec->ljpme_c6grid = makeLJPmeC6GridCorrectionParameters(mtop.ffparams, *forcerec);
}
}
/* Copy the energy group exclusions */
- fr->egp_flags = ir->opts.egp_flags;
+ forcerec->egp_flags = inputrec.opts.egp_flags;
/* Van der Waals stuff */
- if ((ic->vdwtype != evdwCUT) && (ic->vdwtype != evdwUSER) && !fr->bBHAM)
+ if ((interactionConst->vdwtype != VanDerWaalsType::Cut)
+ && (interactionConst->vdwtype != VanDerWaalsType::User) && !forcerec->haveBuckingham)
{
- if (ic->rvdw_switch >= ic->rvdw)
+ if (interactionConst->rvdw_switch >= interactionConst->rvdw)
{
- gmx_fatal(FARGS, "rvdw_switch (%f) must be < rvdw (%f)", ic->rvdw_switch, ic->rvdw);
+ gmx_fatal(FARGS,
+ "rvdw_switch (%f) must be < rvdw (%f)",
+ interactionConst->rvdw_switch,
+ interactionConst->rvdw);
}
- if (fp)
+ if (fplog)
{
- fprintf(fp, "Using %s Lennard-Jones, switch between %g and %g nm\n",
- (ic->eeltype == eelSWITCH) ? "switched" : "shifted", ic->rvdw_switch, ic->rvdw);
+ fprintf(fplog,
+ "Using %s Lennard-Jones, switch between %g and %g nm\n",
+ (interactionConst->eeltype == CoulombInteractionType::Switch) ? "switched" : "shifted",
+ interactionConst->rvdw_switch,
+ interactionConst->rvdw);
}
}
- if (fr->bBHAM && EVDW_PME(ic->vdwtype))
+ if (forcerec->haveBuckingham && EVDW_PME(interactionConst->vdwtype))
{
gmx_fatal(FARGS, "LJ PME not supported with Buckingham");
}
- if (fr->bBHAM && (ic->vdwtype == evdwSHIFT || ic->vdwtype == evdwSWITCH))
+ if (forcerec->haveBuckingham
+ && (interactionConst->vdwtype == VanDerWaalsType::Shift
+ || interactionConst->vdwtype == VanDerWaalsType::Switch))
{
gmx_fatal(FARGS, "Switch/shift interaction not supported with Buckingham");
}
- if (fr->bBHAM)
+ if (forcerec->haveBuckingham)
{
gmx_fatal(FARGS, "The Verlet cutoff-scheme does not (yet) support Buckingham");
}
- if (ir->implicit_solvent)
+ if (inputrec.implicit_solvent)
{
gmx_fatal(FARGS, "Implict solvation is no longer supported.");
}
* in that case grompp should already have checked that we do not need
* normal tables and we only generate tables for 1-4 interactions.
*/
- real rtab = ir->rlist + ir->tabext;
+ real rtab = inputrec.rlist + inputrec.tabext;
/* We want to use unmodified tables for 1-4 coulombic
* interactions, so we must in general have an extra set of
if (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 || gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0
|| gmx_mtop_ftype_count(mtop, F_LJC_PAIRS_NB) > 0)
{
- fr->pairsTable = make_tables(fp, ic, tabpfn, rtab, GMX_MAKETABLES_14ONLY);
+ forcerec->pairsTable = make_tables(fplog, interactionConst, tabpfn, rtab, GMX_MAKETABLES_14ONLY);
}
/* Wall stuff */
- fr->nwall = ir->nwall;
- if (ir->nwall && ir->wall_type == ewtTABLE)
+ forcerec->nwall = inputrec.nwall;
+ if (inputrec.nwall && inputrec.wall_type == WallType::Table)
{
- make_wall_tables(fp, ir, tabfn, &mtop->groups, fr);
+ make_wall_tables(fplog, inputrec, tabfn, &mtop.groups, forcerec);
}
- fr->fcdata = std::make_unique<t_fcdata>();
+ forcerec->fcdata = std::make_unique<t_fcdata>();
if (!tabbfnm.empty())
{
- t_fcdata& fcdata = *fr->fcdata;
+ t_fcdata& fcdata = *forcerec->fcdata;
// Need to catch std::bad_alloc
// TODO Don't need to catch this here, when merging with master branch
try
{
// TODO move these tables into a separate struct and store reference in ListedForces
- fcdata.bondtab = make_bonded_tables(fp, F_TABBONDS, F_TABBONDSNC, mtop, tabbfnm, "b");
- fcdata.angletab = make_bonded_tables(fp, F_TABANGLES, -1, mtop, tabbfnm, "a");
- fcdata.dihtab = make_bonded_tables(fp, F_TABDIHS, -1, mtop, tabbfnm, "d");
+ fcdata.bondtab = make_bonded_tables(fplog, F_TABBONDS, F_TABBONDSNC, mtop, tabbfnm, "b");
+ fcdata.angletab = make_bonded_tables(fplog, F_TABANGLES, -1, mtop, tabbfnm, "a");
+ fcdata.dihtab = make_bonded_tables(fplog, F_TABDIHS, -1, mtop, tabbfnm, "d");
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
}
/* Initialize the thread working data for bonded interactions */
- if (fr->useMts)
+ if (forcerec->useMts)
{
// Add one ListedForces object for each MTS level
bool isFirstLevel = true;
- for (const auto& mtsLevel : ir->mtsLevels)
+ for (const auto& mtsLevel : inputrec.mtsLevels)
{
ListedForces::InteractionSelection interactionSelection;
const auto& forceGroups = mtsLevel.forceGroups;
interactionSelection.set(static_cast<int>(ListedForces::InteractionGroup::Rest));
isFirstLevel = false;
}
- fr->listedForces.emplace_back(
- mtop->ffparams, mtop->groups.groups[SimulationAtomGroupType::EnergyOutput].size(),
- gmx_omp_nthreads_get(emntBonded), interactionSelection, fp);
+ forcerec->listedForces.emplace_back(
+ mtop.ffparams,
+ mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size(),
+ gmx_omp_nthreads_get(ModuleMultiThread::Bonded),
+ interactionSelection,
+ fplog);
}
}
else
{
// Add one ListedForces object with all listed interactions
- fr->listedForces.emplace_back(
- mtop->ffparams, mtop->groups.groups[SimulationAtomGroupType::EnergyOutput].size(),
- gmx_omp_nthreads_get(emntBonded), ListedForces::interactionSelectionAll(), fp);
+ forcerec->listedForces.emplace_back(
+ mtop.ffparams,
+ mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size(),
+ gmx_omp_nthreads_get(ModuleMultiThread::Bonded),
+ ListedForces::interactionSelectionAll(),
+ fplog);
}
// QM/MM initialization if requested
- if (ir->bQMMM)
+ if (inputrec.bQMMM)
{
gmx_incons("QM/MM was requested, but is no longer available in GROMACS");
}
/* Set all the static charge group info */
- fr->cginfo_mb = init_cginfo_mb(mtop, fr);
- if (!DOMAINDECOMP(cr))
+ forcerec->cginfo_mb = init_cginfo_mb(mtop, forcerec);
+ if (!DOMAINDECOMP(commrec))
{
- fr->cginfo = cginfo_expand(mtop->molblock.size(), fr->cginfo_mb);
+ forcerec->cginfo = cginfo_expand(mtop.molblock.size(), forcerec->cginfo_mb);
}
- if (!DOMAINDECOMP(cr))
+ if (!DOMAINDECOMP(commrec))
{
- forcerec_set_ranges(fr, mtop->natoms, mtop->natoms, mtop->natoms);
+ forcerec_set_ranges(forcerec, mtop.natoms, mtop.natoms, mtop.natoms);
}
- fr->print_force = print_force;
+ forcerec->print_force = print_force;
- fr->nthread_ewc = gmx_omp_nthreads_get(emntBonded);
- snew(fr->ewc_t, fr->nthread_ewc);
+ forcerec->nthread_ewc = gmx_omp_nthreads_get(ModuleMultiThread::Bonded);
+ forcerec->ewc_t.resize(forcerec->nthread_ewc);
- if (ir->eDispCorr != edispcNO)
+ if (inputrec.eDispCorr != DispersionCorrectionType::No)
{
- fr->dispersionCorrection = std::make_unique<DispersionCorrection>(
- *mtop, *ir, fr->bBHAM, fr->ntype, fr->nbfp, *fr->ic, tabfn);
- fr->dispersionCorrection->print(mdlog);
+ forcerec->dispersionCorrection = std::make_unique<DispersionCorrection>(
+ mtop, inputrec, forcerec->haveBuckingham, forcerec->ntype, forcerec->nbfp, *forcerec->ic, tabfn);
+ forcerec->dispersionCorrection->print(mdlog);
}
- if (fp != nullptr)
+ if (fplog != nullptr)
{
/* Here we switch from using mdlog, which prints the newline before
* the paragraph, to our old fprintf logging, which prints the newline
* after the paragraph, so we should add a newline here.
*/
- fprintf(fp, "\n");
+ fprintf(fplog, "\n");
}
}
t_forcerec::t_forcerec() = default;
-t_forcerec::~t_forcerec()
-{
- /* Note: This code will disappear when types are converted to C++ */
- sfree(shift_vec);
- sfree(ewc_t);
-}
+t_forcerec::~t_forcerec() = default;
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct gmx_mtop_t;
struct gmx_wallcycle;
struct interaction_const_t;
+struct gmx_ffparams_t;
namespace gmx
{
class PhysicalNodeCommunicator;
} // namespace gmx
-/*! \brief Print the contents of the forcerec to a file
+/*! \brief Create nonbonded parameter lists
*
- * \param[in] fplog The log file to print to
- * \param[in] fr The forcerec structure
+ * \param[in] forceFieldParams The forcefield parameters
+ * \param[in] useBuckinghamPotential Use Buckingham potential
*/
-void pr_forcerec(FILE* fplog, t_forcerec* fr);
+std::vector<real> makeNonBondedParameterLists(const gmx_ffparams_t& forceFieldParams,
+ bool useBuckinghamPotential);
+
+/*! \brief Calculate c6 parameters for grid correction
+ *
+ * \param[in] forceFieldParams The forcefield parameters
+ * \param[in] forceRec The forcerec
+ */
+std::vector<real> makeLJPmeC6GridCorrectionParameters(const gmx_ffparams_t& forceFieldParams,
+ const t_forcerec& forceRec);
/*! \brief Set the number of charge groups and atoms.
*
*
* \param[in] fplog File for printing
* \param[in] mdlog File for printing
- * \param[out] fr The forcerec
- * \param[in] ir Inputrec structure
+ * \param[out] forcerec The forcerec
+ * \param[in] inputrec Inputrec structure
* \param[in] mtop Molecular topology
- * \param[in] cr Communication structures
+ * \param[in] commrec Communication structures
* \param[in] box Simulation box
* \param[in] tabfn Table potential file for non-bonded interactions
* \param[in] tabpfn Table potential file for pair interactions
*/
void init_forcerec(FILE* fplog,
const gmx::MDLogger& mdlog,
- t_forcerec* fr,
- const t_inputrec* ir,
- const gmx_mtop_t* mtop,
- const t_commrec* cr,
+ t_forcerec* forcerec,
+ const t_inputrec& inputrec,
+ const gmx_mtop_t& mtop,
+ const t_commrec* commrec,
matrix box,
const char* tabfn,
const char* tabpfn,
gmx::ArrayRef<const std::string> tabbfnm,
real print_force);
-/*! \brief Check whether molecules are ever distributed over PBC boundaries
- *
- * Note: This covers only the non-DD case. For DD runs, domdec.h offers an
- * equivalent dd_bonded_molpbc(...) function.
- *
- * \param[in] ir Inputrec structure
- * \param[in] mtop Molecular topology
- * \param[in] mdlog File for printing
- */
-bool areMoleculesDistributedOverPbc(const t_inputrec& ir, const gmx_mtop_t& mtop, const gmx::MDLogger& mdlog);
-
-/*! \brief Divide exclusions over threads
- *
- * Set the exclusion load for the local exclusions and possibly threads
- * \param[out] fr The force record
- * \param[in] top The topology
- */
-void forcerec_set_excl_load(t_forcerec* fr, const gmx_localtop_t* top);
-
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/utility/enumerationhelpers.h"
struct ewald_corr_thread_t
{
- real Vcorr_q;
- real Vcorr_lj;
- real dvdl[efptNR];
- tensor vir_q;
- tensor vir_lj;
+ real Vcorr_q;
+ real Vcorr_lj;
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real> dvdl;
+ tensor vir_q;
+ tensor vir_lj;
};
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Christian Blau <blau@kth.se>
*/
+#include <vector>
#include "gmxpre.h"
#include "freeenergyparameters.h"
#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/enumerationhelpers.h"
namespace gmx
{
namespace
{
-std::array<real, efptNR> lambdasAtState(const int stateIndex, double** const lambdaArray, const int lambdaArrayExtent)
+gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real>
+lambdasAtState(const int stateIndex, gmx::ArrayRef<const std::vector<double>> lambdaArray, const int lambdaArrayExtent)
{
- std::array<real, efptNR> lambda;
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real> lambda;
// set lambda from an fep state index from stateIndex, if stateIndex was defined (> -1)
if (stateIndex >= 0 && stateIndex < lambdaArrayExtent)
{
- for (int i = 0; i < efptNR; i++)
+ for (int i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
{
lambda[i] = lambdaArray[i][stateIndex];
}
* \param[in] lambdaArray array of lambda values
* \param[in] lambdaArrayExtent number of lambda values
*/
-std::array<real, efptNR> interpolatedLambdas(const double currentGlobalLambda,
- double** const lambdaArray,
- const int lambdaArrayExtent)
+gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real>
+interpolatedLambdas(const double currentGlobalLambda,
+ gmx::ArrayRef<const std::vector<double>> lambdaArray,
+ const int lambdaArrayExtent)
{
- std::array<real, efptNR> lambda;
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real> lambda;
// when there is no lambda value array, set all lambdas to steps * deltaLambdaPerStep
if (lambdaArrayExtent <= 0)
{
// if we run over the boundary of the lambda array, return the boundary array values
if (currentGlobalLambda <= 0)
{
- for (int i = 0; i < efptNR; i++)
+ for (int i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
{
lambda[i] = lambdaArray[i][0];
}
}
if (currentGlobalLambda >= 1)
{
- for (int i = 0; i < efptNR; i++)
+ for (int i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
{
lambda[i] = lambdaArray[i][lambdaArrayExtent - 1];
}
const int fepStateRight = fepStateLeft + 1;
// interpolate between this state and the next
const double fracBetween = currentGlobalLambda * (lambdaArrayExtent - 1) - fepStateLeft;
- for (int i = 0; i < efptNR; i++)
+ for (int i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
{
lambda[i] = lambdaArray[i][fepStateLeft]
+ fracBetween * (lambdaArray[i][fepStateRight] - lambdaArray[i][fepStateLeft]);
} // namespace
-std::array<real, efptNR> currentLambdas(const int64_t step, const t_lambda& fepvals, const int currentLambdaState)
+gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real>
+currentLambdas(const int64_t step, const t_lambda& fepvals, const int currentLambdaState)
{
if (fepvals.delta_lambda == 0)
{
return lambdasAtState(fepvals.init_fep_state, fepvals.all_lambda, fepvals.n_lambda);
}
- std::array<real, efptNR> lambdas;
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real> lambdas;
std::fill(std::begin(lambdas), std::end(lambdas), fepvals.init_lambda);
return lambdas;
}
- const double globalLambda = currentGlobalLambda(step, fepvals.delta_lambda, fepvals.init_fep_state,
- fepvals.init_lambda, fepvals.n_lambda);
+ const double globalLambda = currentGlobalLambda(
+ step, fepvals.delta_lambda, fepvals.init_fep_state, fepvals.init_lambda, fepvals.n_lambda);
return interpolatedLambdas(globalLambda, fepvals.all_lambda, fepvals.n_lambda);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <array>
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/real.h"
struct t_lambda;
* \param[in] currentLambdaState the lambda state to use to set the lambdas, -1 if not set
* \returns the current lambda-value array
*/
-std::array<real, efptNR> currentLambdas(int64_t step, const t_lambda& fepvals, int currentLambdaState);
+gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real> currentLambdas(int64_t step,
+ const t_lambda& fepvals,
+ int currentLambdaState);
} // namespace gmx
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxlib/network.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/gmxomp.h"
int gnth; /**< Global num. of threads per PP or PP+PME process/tMPI thread. */
int gnth_pme; /**< Global num. of threads per PME only process/tMPI thread. */
- int nth[emntNR]; /**< Number of threads for each module, indexed with module_nth_t */
- gmx_bool initialized; /**< TRUE if the module as been initialized. */
+ gmx::EnumerationArray<ModuleMultiThread, int> nth; /**< Number of threads for each module, indexed with module_nth_t */
+ bool initialized; /**< TRUE if the module as been initialized. */
} omp_module_nthreads_t;
/** Names of environment variables to set the per module number of threads.
*
* Indexed with the values of module_nth_t.
* */
-static const char* modth_env_var[emntNR] = { "GMX_DEFAULT_NUM_THREADS should never be set",
- "GMX_DOMDEC_NUM_THREADS",
- "GMX_PAIRSEARCH_NUM_THREADS",
- "GMX_NONBONDED_NUM_THREADS",
- "GMX_LISTED_FORCES_NUM_THREADS",
- "GMX_PME_NUM_THREADS",
- "GMX_UPDATE_NUM_THREADS",
- "GMX_VSITE_NUM_THREADS",
- "GMX_LINCS_NUM_THREADS",
- "GMX_SETTLE_NUM_THREADS" };
+static const char* enumValueToEnvVariableString(ModuleMultiThread enumValue)
+{
+ constexpr gmx::EnumerationArray<ModuleMultiThread, const char*> moduleMultiThreadEnvVariableNames = {
+ "GMX_DEFAULT_NUM_THREADS should never be set",
+ "GMX_DOMDEC_NUM_THREADS",
+ "GMX_PAIRSEARCH_NUM_THREADS",
+ "GMX_NONBONDED_NUM_THREADS",
+ "GMX_LISTED_FORCES_NUM_THREADS",
+ "GMX_PME_NUM_THREADS",
+ "GMX_UPDATE_NUM_THREADS",
+ "GMX_VSITE_NUM_THREADS",
+ "GMX_LINCS_NUM_THREADS",
+ "GMX_SETTLE_NUM_THREADS"
+ };
+ return moduleMultiThreadEnvVariableNames[enumValue];
+}
/** Names of the modules. */
-static const char* mod_name[emntNR] = { "default", "domain decomposition",
- "pair search", "non-bonded",
- "bonded", "PME",
- "update", "LINCS",
- "SETTLE" };
+static const char* enumValueToString(ModuleMultiThread enumValue)
+{
+ constexpr gmx::EnumerationArray<ModuleMultiThread, const char*> moduleMultiThreadNames = {
+ "default", "domain decomposition",
+ "pair search", "non-bonded",
+ "bonded", "PME",
+ "update", "LINCS",
+ "SETTLE"
+ };
+ return moduleMultiThreadNames[enumValue];
+}
/** Number of threads for each algorithmic module.
*
* All fields are initialized to 0 which should result in errors if
* the init call is omitted.
* */
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static omp_module_nthreads_t modth = { 0, 0, { 0, 0, 0, 0, 0, 0, 0, 0, 0 }, FALSE };
* GMX_*_NUM_THERADS env var is set, case in which its value overrides
* the default.
*/
-static void pick_module_nthreads(const gmx::MDLogger& mdlog, int m, gmx_bool bSepPME)
+static void pick_module_nthreads(const gmx::MDLogger& mdlog, ModuleMultiThread m, gmx_bool bSepPME)
{
char* env;
int nth;
/* The default should never be set through a GMX_*_NUM_THREADS env var
* as it's always equal with gnth. */
- if (m == emntDefault)
+ if (m == ModuleMultiThread::Default)
{
return;
}
/* check the environment variable */
- if ((env = getenv(modth_env_var[m])) != nullptr)
+ if ((env = getenv(enumValueToEnvVariableString(m))) != nullptr)
{
sscanf(env, "%d", &nth);
if (!bOMP)
{
- gmx_warning("%s=%d is set, but %s is compiled without OpenMP!", modth_env_var[m], nth,
+ gmx_warning("%s=%d is set, but %s is compiled without OpenMP!",
+ enumValueToEnvVariableString(m),
+ nth,
gmx::getProgramContext().displayName());
}
gmx_warning(
"%s=%d is set, the default number of threads also "
"needs to be set with OMP_NUM_THREADS!",
- modth_env_var[m], nth);
+ enumValueToEnvVariableString(m),
+ nth);
}
/* only babble if we are really overriding with a different value */
- if ((bSepPME && m == emntPME && nth != modth.gnth_pme) || (nth != modth.gnth))
+ if ((bSepPME && m == ModuleMultiThread::Pme && nth != modth.gnth_pme) || (nth != modth.gnth))
{
GMX_LOG(mdlog.warning)
.asParagraph()
.appendTextFormatted("%s=%d set, overriding the default number of %s threads",
- modth_env_var[m], nth, mod_name[m]);
+ enumValueToString(m),
+ nth,
+ enumValueToEnvVariableString(m));
}
}
else
{
/* pick the global PME node nthreads if we are setting the number
* of threads in separate PME nodes */
- nth = (bSepPME && m == emntPME) ? modth.gnth_pme : modth.gnth;
+ nth = (bSepPME && m == ModuleMultiThread::Pme) ? modth.gnth_pme : modth.gnth;
}
gmx_omp_nthreads_set(m, nth);
"Environment variable OMP_NUM_THREADS (%d) and the number of threads "
"requested on the command line (%d) have different values. Either omit one, "
"or set them both to the same value.",
- nt_omp, *nthreads_omp);
+ nt_omp,
+ *nthreads_omp);
}
/* Setting the number of OpenMP threads. */
}
/* now set the per-module values */
- modth.nth[emntDefault] = modth.gnth;
- pick_module_nthreads(mdlog, emntDomdec, bSepPME);
- pick_module_nthreads(mdlog, emntPairsearch, bSepPME);
- pick_module_nthreads(mdlog, emntNonbonded, bSepPME);
- pick_module_nthreads(mdlog, emntBonded, bSepPME);
- pick_module_nthreads(mdlog, emntPME, bSepPME);
- pick_module_nthreads(mdlog, emntUpdate, bSepPME);
- pick_module_nthreads(mdlog, emntVSITE, bSepPME);
- pick_module_nthreads(mdlog, emntLINCS, bSepPME);
- pick_module_nthreads(mdlog, emntSETTLE, bSepPME);
+ modth.nth[ModuleMultiThread::Default] = modth.gnth;
+ pick_module_nthreads(mdlog, ModuleMultiThread::Domdec, bSepPME);
+ pick_module_nthreads(mdlog, ModuleMultiThread::Pairsearch, bSepPME);
+ pick_module_nthreads(mdlog, ModuleMultiThread::Nonbonded, bSepPME);
+ pick_module_nthreads(mdlog, ModuleMultiThread::Bonded, bSepPME);
+ pick_module_nthreads(mdlog, ModuleMultiThread::Pme, bSepPME);
+ pick_module_nthreads(mdlog, ModuleMultiThread::Update, bSepPME);
+ pick_module_nthreads(mdlog, ModuleMultiThread::VirtualSite, bSepPME);
+ pick_module_nthreads(mdlog, ModuleMultiThread::Lincs, bSepPME);
+ pick_module_nthreads(mdlog, ModuleMultiThread::Settle, bSepPME);
/* set the number of threads globally */
if (bOMP)
if (nth_max == nth_min)
{
GMX_LOG(mdlog.warning)
- .appendTextFormatted("Using %d OpenMP thread%s %s", nth_min, nth_min > 1 ? "s" : "",
+ .appendTextFormatted("Using %d OpenMP thread%s %s",
+ nth_min,
+ nth_min > 1 ? "s" : "",
cr->nnodes > 1 ? mpi_str : "");
}
else
if (nth_pme_max == nth_pme_min)
{
GMX_LOG(mdlog.warning)
- .appendTextFormatted("Using %d OpenMP thread%s %s for PME", nth_pme_min,
- nth_pme_min > 1 ? "s" : "", cr->nnodes > 1 ? mpi_str : "");
+ .appendTextFormatted("Using %d OpenMP thread%s %s for PME",
+ nth_pme_min,
+ nth_pme_min > 1 ? "s" : "",
+ cr->nnodes > 1 ? mpi_str : "");
}
else
{
GMX_LOG(mdlog.warning)
- .appendTextFormatted("Using %d - %d OpenMP threads %s for PME", nth_pme_min,
- nth_pme_max, mpi_str);
+ .appendTextFormatted(
+ "Using %d - %d OpenMP threads %s for PME", nth_pme_min, nth_pme_max, mpi_str);
}
}
GMX_LOG(mdlog.warning);
bSepPME = (thisRankHasDuty(cr, DUTY_PP) != thisRankHasDuty(cr, DUTY_PME));
- manage_number_of_openmp_threads(mdlog, cr, bOMP, nthreads_hw_avail, omp_nthreads_req,
- omp_nthreads_pme_req, bThisNodePMEOnly, numRanksOnThisNode, bSepPME);
+ manage_number_of_openmp_threads(mdlog,
+ cr,
+ bOMP,
+ nthreads_hw_avail,
+ omp_nthreads_req,
+ omp_nthreads_pme_req,
+ bThisNodePMEOnly,
+ numRanksOnThisNode,
+ bSepPME);
#if GMX_THREAD_MPI
/* Non-master threads have to wait for the OpenMP management to be
* done, so that code elsewhere that uses OpenMP can be certain
reportOpenmpSettings(mdlog, cr, bOMP, bSepPME);
}
-int gmx_omp_nthreads_get(int mod)
+int gmx_omp_nthreads_get(ModuleMultiThread mod)
{
- if (mod < 0 || mod >= emntNR)
+ if (mod < ModuleMultiThread::Default || mod >= ModuleMultiThread::Count)
{
/* invalid module queried */
return -1;
}
}
-void gmx_omp_nthreads_set(int mod, int nthreads)
+void gmx_omp_nthreads_set(ModuleMultiThread mod, int nthreads)
{
/* Catch an attempt to set the number of threads on an invalid
* OpenMP module. */
- GMX_RELEASE_ASSERT(mod >= 0 && mod < emntNR, "Trying to set nthreads on invalid OpenMP module");
+ GMX_RELEASE_ASSERT(mod >= ModuleMultiThread::Default && mod < ModuleMultiThread::Count,
+ "Trying to set nthreads on invalid OpenMP module");
modth.nth[mod] = nthreads;
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
/** Enum values corresponding to multithreaded algorithmic modules. */
-typedef enum module_nth
+enum class ModuleMultiThread : int
{
/* Default is meant to be used in OMP regions outside the named
* algorithmic modules listed below. */
- emntDefault,
- emntDomdec,
- emntPairsearch,
- emntNonbonded,
- emntBonded,
- emntPME,
- emntUpdate,
- emntVSITE,
- emntLINCS,
- emntSETTLE,
- emntNR
-} module_nth_t;
+ Default,
+ Domdec,
+ Pairsearch,
+ Nonbonded,
+ Bonded,
+ Pme,
+ Update,
+ VirtualSite,
+ Lincs,
+ Settle,
+ Count
+};
/*! \brief
* Initializes the per-module thread count.
/*! \brief
* Returns the number of threads to be used in the given module \p mod. */
-int gmx_omp_nthreads_get(int mod);
+int gmx_omp_nthreads_get(ModuleMultiThread mod);
/*! \brief
* Returns the number of threads to be used in the given module \p mod for simple rvec operations.
* the reduction in computional cost due to parallelization. This routine
* returns 1 when the overhead is expected to be higher than the gain.
*/
-static inline int gmx_omp_nthreads_get_simple_rvec_task(int mod, int nrvec)
+static inline int gmx_omp_nthreads_get_simple_rvec_task(ModuleMultiThread mod, int nrvec)
{
/* There can be a relatively large overhead to an OpenMP parallel for loop.
* This overhead increases, slowly, with the numbe of threads used.
/*! \brief Sets the number of threads to be used in module.
*
* Intended for use in testing. */
-void gmx_omp_nthreads_set(int mod, int nthreads);
+void gmx_omp_nthreads_set(ModuleMultiThread mod, int nthreads);
/*! \brief
* Read the OMP_NUM_THREADS env. var. and check against the value set on the
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MDLIB_GPUFORCEREDUCTION_H
#define GMX_MDLIB_GPUFORCEREDUCTION_H
+#include <memory>
+
+#include "config.h"
+
#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/fixedcapacityvector.h"
class GpuEventSynchronizer;
namespace gmx
{
+#define HAVE_GPU_FORCE_REDUCTION (GMX_GPU_CUDA)
+
/*! \internal
* \brief Manages the force reduction directly in GPU memory
*
*
* \param [in] forcePtr Pointer to force to be reduced
*/
- void registerNbnxmForce(void* forcePtr);
+ void registerNbnxmForce(DeviceBuffer<RVec> forcePtr);
/*! \brief Register a rvec-format force to be reduced
*
* \param [in] forcePtr Pointer to force to be reduced
*/
- void registerRvecForce(void* forcePtr);
+ void registerRvecForce(DeviceBuffer<RVec> forcePtr);
/*! \brief Add a dependency for this force reduction
*
private:
class Impl;
- gmx::PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
/*! \internal \file
*
- * \brief May be used to implement force reduction interfaces for non-GPU builds.
+ * \brief Implements backend-agnostic GPU Force Reduction functions
*
* \author Alan Gray <alang@nvidia.com>
*
#include "gmxpre.h"
-#include "config.h"
+#include "gpuforcereduction_impl.h"
-#include "gpuforcereduction.h"
-
-#if !GMX_GPU_CUDA
+#include "gromacs/gpu_utils/device_stream.h"
+#include "gromacs/gpu_utils/devicebuffer.h"
+#if GMX_GPU_CUDA
+# include "gromacs/gpu_utils/gpueventsynchronizer.cuh"
+#elif GMX_GPU_SYCL
+# include "gromacs/gpu_utils/gpueventsynchronizer_sycl.h"
+#endif
+#include "gromacs/mdlib/gpuforcereduction_impl_internal.h"
+#include "gromacs/utility/gmxassert.h"
namespace gmx
{
-class GpuForceReduction::Impl
+GpuForceReduction::Impl::Impl(const DeviceContext& deviceContext,
+ const DeviceStream& deviceStream,
+ gmx_wallcycle* wcycle) :
+ baseForce_(),
+ deviceContext_(deviceContext),
+ deviceStream_(deviceStream),
+ nbnxmForceToAdd_(),
+ rvecForceToAdd_(),
+ wcycle_(wcycle)
+{
+}
+
+void GpuForceReduction::Impl::reinit(DeviceBuffer<Float3> baseForcePtr,
+ const int numAtoms,
+ ArrayRef<const int> cell,
+ const int atomStart,
+ const bool accumulate,
+ GpuEventSynchronizer* completionMarker)
+{
+ GMX_ASSERT((baseForcePtr != nullptr), "Input base force for reduction has no data");
+ baseForce_ = baseForcePtr;
+ numAtoms_ = numAtoms;
+ atomStart_ = atomStart;
+ accumulate_ = static_cast<int>(accumulate);
+ completionMarker_ = completionMarker;
+ cellInfo_.cell = cell.data();
+
+ wallcycle_start_nocount(wcycle_, WallCycleCounter::LaunchGpu);
+ reallocateDeviceBuffer(
+ &cellInfo_.d_cell, numAtoms_, &cellInfo_.cellSize, &cellInfo_.cellSizeAlloc, deviceContext_);
+ copyToDeviceBuffer(&cellInfo_.d_cell,
+ &(cellInfo_.cell[atomStart]),
+ 0,
+ numAtoms_,
+ deviceStream_,
+ GpuApiCallBehavior::Async,
+ nullptr);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
+
+ dependencyList_.clear();
+};
+
+void GpuForceReduction::Impl::registerNbnxmForce(DeviceBuffer<RVec> forcePtr)
{
+ GMX_ASSERT(forcePtr, "Input force for reduction has no data");
+ nbnxmForceToAdd_ = forcePtr;
};
-GpuForceReduction::GpuForceReduction(const DeviceContext& /* deviceContext */,
- const DeviceStream& /* deviceStream */,
- gmx_wallcycle* /*wcycle*/) :
- impl_(nullptr)
+void GpuForceReduction::Impl::registerRvecForce(DeviceBuffer<RVec> forcePtr)
+{
+ GMX_ASSERT(forcePtr, "Input force for reduction has no data");
+ rvecForceToAdd_ = forcePtr;
+};
+
+void GpuForceReduction::Impl::addDependency(GpuEventSynchronizer* const dependency)
+{
+ dependencyList_.push_back(dependency);
+}
+
+void GpuForceReduction::Impl::execute()
{
- GMX_ASSERT(false, "A CPU stub has been called instead of the correct implementation.");
+ wallcycle_start_nocount(wcycle_, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::LaunchGpuNBFBufOps);
+
+ if (numAtoms_ == 0)
+ {
+ return;
+ }
+
+ GMX_ASSERT(nbnxmForceToAdd_, "Nbnxm force for reduction has no data");
+
+ // Enqueue wait on all dependencies passed
+ for (auto* synchronizer : dependencyList_)
+ {
+ synchronizer->enqueueWaitEvent(deviceStream_);
+ }
+
+ const bool addRvecForce = static_cast<bool>(rvecForceToAdd_); // True iff initialized
+
+ launchForceReductionKernel(numAtoms_,
+ atomStart_,
+ addRvecForce,
+ accumulate_,
+ nbnxmForceToAdd_,
+ rvecForceToAdd_,
+ baseForce_,
+ cellInfo_.d_cell,
+ deviceStream_);
+
+ // Mark that kernel has been launched
+ if (completionMarker_ != nullptr)
+ {
+ completionMarker_->markEvent(deviceStream_);
+ }
+
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchGpuNBFBufOps);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
}
-// NOLINTNEXTLINE readability-convert-member-functions-to-static
-void GpuForceReduction::reinit(DeviceBuffer<RVec> /*baseForcePtr*/,
- const int /*numAtoms*/,
- ArrayRef<const int> /*cell*/,
- const int /*atomStart*/,
- const bool /*accumulate*/,
- GpuEventSynchronizer* /*completionMarker*/)
+GpuForceReduction::Impl::~Impl() = default;
+
+GpuForceReduction::GpuForceReduction(const DeviceContext& deviceContext,
+ const DeviceStream& deviceStream,
+ gmx_wallcycle* wcycle) :
+ impl_(new Impl(deviceContext, deviceStream, wcycle))
{
- GMX_ASSERT(false, "A CPU stub has been called instead of the correct implementation.");
}
-// NOLINTNEXTLINE readability-convert-member-functions-to-static
-void GpuForceReduction::registerNbnxmForce(void* /* forcePtr */)
+void GpuForceReduction::registerNbnxmForce(DeviceBuffer<RVec> forcePtr)
{
- GMX_ASSERT(false, "A CPU stub has been called instead of the correct implementation.");
+ impl_->registerNbnxmForce(forcePtr);
}
-// NOLINTNEXTLINE readability-convert-member-functions-to-static
-void GpuForceReduction::registerRvecForce(void* /* forcePtr */)
+void GpuForceReduction::registerRvecForce(DeviceBuffer<RVec> forcePtr)
{
- GMX_ASSERT(false, "A CPU stub has been called instead of the correct implementation.");
+ impl_->registerRvecForce(forcePtr);
}
-// NOLINTNEXTLINE readability-convert-member-functions-to-static
-void GpuForceReduction::addDependency(GpuEventSynchronizer* const /* dependency */)
+void GpuForceReduction::addDependency(GpuEventSynchronizer* const dependency)
{
- GMX_ASSERT(false, "A CPU stub has been called instead of the correct implementation.");
+ impl_->addDependency(dependency);
}
-// NOLINTNEXTLINE readability-convert-member-functions-to-static
+void GpuForceReduction::reinit(DeviceBuffer<RVec> baseForcePtr,
+ const int numAtoms,
+ ArrayRef<const int> cell,
+ const int atomStart,
+ const bool accumulate,
+ GpuEventSynchronizer* completionMarker)
+{
+ impl_->reinit(baseForcePtr, numAtoms, cell, atomStart, accumulate, completionMarker);
+}
void GpuForceReduction::execute()
{
- GMX_ASSERT(false, "A CPU stub has been called instead of the correct implementation.");
+ impl_->execute();
}
GpuForceReduction::~GpuForceReduction() = default;
} // namespace gmx
-
-#endif
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2020, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*! \internal \file
- *
- * \brief Implements GPU Force Reduction using CUDA
- *
- * \author Alan Gray <alang@nvidia.com>
- *
- * \ingroup module_mdlib
- */
-
-#include "gmxpre.h"
-
-#include "gpuforcereduction_impl.cuh"
-
-#include <stdio.h>
-
-#include "gromacs/gpu_utils/cudautils.cuh"
-#include "gromacs/gpu_utils/device_context.h"
-#include "gromacs/gpu_utils/devicebuffer.h"
-#include "gromacs/gpu_utils/gpu_utils.h"
-#include "gromacs/gpu_utils/gpueventsynchronizer.cuh"
-#include "gromacs/gpu_utils/typecasts.cuh"
-#include "gromacs/gpu_utils/vectype_ops.cuh"
-#include "gromacs/utility/gmxassert.h"
-
-#include "gpuforcereduction.h"
-
-namespace gmx
-{
-
-constexpr static int c_threadsPerBlock = 128;
-
-typedef struct rvecDeviceForceData rvecDeviceForceData_t;
-
-
-template<bool addRvecForce, bool accumulateForce>
-static __global__ void reduceKernel(const float3* __restrict__ gm_nbnxmForce,
- const float3* __restrict__ rvecForceToAdd,
- float3* gm_fTotal,
- const int* gm_cell,
- const int numAtoms)
-{
-
- // map particle-level parallelism to 1D CUDA thread and block index
- const int threadIndex = blockIdx.x * blockDim.x + threadIdx.x;
-
- // perform addition for each particle
- if (threadIndex < numAtoms)
- {
-
- float3* gm_fDest = &gm_fTotal[threadIndex];
- float3 temp;
-
- // Accumulate or set nbnxm force
- if (accumulateForce)
- {
- temp = *gm_fDest;
- temp += gm_nbnxmForce[gm_cell[threadIndex]];
- }
- else
- {
- temp = gm_nbnxmForce[gm_cell[threadIndex]];
- }
-
- if (addRvecForce)
- {
- temp += rvecForceToAdd[threadIndex];
- }
-
- *gm_fDest = temp;
- }
- return;
-}
-
-GpuForceReduction::Impl::Impl(const DeviceContext& deviceContext,
- const DeviceStream& deviceStream,
- gmx_wallcycle* wcycle) :
- deviceContext_(deviceContext),
- deviceStream_(deviceStream),
- wcycle_(wcycle){};
-
-void GpuForceReduction::Impl::reinit(float3* baseForcePtr,
- const int numAtoms,
- ArrayRef<const int> cell,
- const int atomStart,
- const bool accumulate,
- GpuEventSynchronizer* completionMarker)
-{
- GMX_ASSERT((baseForcePtr != nullptr), "Input base force for reduction has no data");
- baseForce_ = &(baseForcePtr[atomStart]);
- numAtoms_ = numAtoms;
- atomStart_ = atomStart;
- accumulate_ = accumulate;
- completionMarker_ = completionMarker;
- cellInfo_.cell = cell.data();
-
- wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU);
- reallocateDeviceBuffer(&cellInfo_.d_cell, numAtoms_, &cellInfo_.cellSize,
- &cellInfo_.cellSizeAlloc, deviceContext_);
- copyToDeviceBuffer(&cellInfo_.d_cell, &(cellInfo_.cell[atomStart]), 0, numAtoms_, deviceStream_,
- GpuApiCallBehavior::Async, nullptr);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
-
- dependencyList_.clear();
-};
-
-void GpuForceReduction::Impl::registerNbnxmForce(DeviceBuffer<RVec> forcePtr)
-{
- GMX_ASSERT((forcePtr != nullptr), "Input force for reduction has no data");
- nbnxmForceToAdd_ = forcePtr;
-};
-
-void GpuForceReduction::Impl::registerRvecForce(DeviceBuffer<RVec> forcePtr)
-{
- GMX_ASSERT((forcePtr != nullptr), "Input force for reduction has no data");
- rvecForceToAdd_ = forcePtr;
-};
-
-void GpuForceReduction::Impl::addDependency(GpuEventSynchronizer* const dependency)
-{
- dependencyList_.push_back(dependency);
-}
-
-void GpuForceReduction::Impl::execute()
-{
- wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU);
- wallcycle_sub_start(wcycle_, ewcsLAUNCH_GPU_NB_F_BUF_OPS);
-
- if (numAtoms_ == 0)
- {
- return;
- }
-
- GMX_ASSERT((nbnxmForceToAdd_ != nullptr), "Nbnxm force for reduction has no data");
-
- // Enqueue wait on all dependencies passed
- for (auto const synchronizer : dependencyList_)
- {
- synchronizer->enqueueWaitEvent(deviceStream_);
- }
-
- float3* d_nbnxmForce = asFloat3(nbnxmForceToAdd_);
- float3* d_rvecForceToAdd = &(asFloat3(rvecForceToAdd_)[atomStart_]);
-
- // Configure and launch kernel
- KernelLaunchConfig config;
- config.blockSize[0] = c_threadsPerBlock;
- config.blockSize[1] = 1;
- config.blockSize[2] = 1;
- config.gridSize[0] = ((numAtoms_ + 1) + c_threadsPerBlock - 1) / c_threadsPerBlock;
- config.gridSize[1] = 1;
- config.gridSize[2] = 1;
- config.sharedMemorySize = 0;
-
- auto kernelFn = (rvecForceToAdd_ != nullptr)
- ? (accumulate_ ? reduceKernel<true, true> : reduceKernel<true, false>)
- : (accumulate_ ? reduceKernel<false, true> : reduceKernel<false, false>);
-
- const auto kernelArgs = prepareGpuKernelArguments(kernelFn, config, &d_nbnxmForce, &d_rvecForceToAdd,
- &baseForce_, &cellInfo_.d_cell, &numAtoms_);
-
- launchGpuKernel(kernelFn, config, deviceStream_, nullptr, "Force Reduction", kernelArgs);
-
- // Mark that kernel has been launched
- if (completionMarker_ != nullptr)
- {
- completionMarker_->markEvent(deviceStream_);
- }
-
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_GPU_NB_F_BUF_OPS);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
-}
-
-GpuForceReduction::Impl::~Impl(){};
-
-GpuForceReduction::GpuForceReduction(const DeviceContext& deviceContext,
- const DeviceStream& deviceStream,
- gmx_wallcycle* wcycle) :
- impl_(new Impl(deviceContext, deviceStream, wcycle))
-{
-}
-
-void GpuForceReduction::registerNbnxmForce(void* forcePtr)
-{
- impl_->registerNbnxmForce(reinterpret_cast<DeviceBuffer<RVec>>(forcePtr));
-}
-
-void GpuForceReduction::registerRvecForce(void* forcePtr)
-{
- impl_->registerRvecForce(reinterpret_cast<DeviceBuffer<RVec>>(forcePtr));
-}
-
-void GpuForceReduction::addDependency(GpuEventSynchronizer* const dependency)
-{
- impl_->addDependency(dependency);
-}
-
-void GpuForceReduction::reinit(DeviceBuffer<RVec> baseForcePtr,
- const int numAtoms,
- ArrayRef<const int> cell,
- const int atomStart,
- const bool accumulate,
- GpuEventSynchronizer* completionMarker)
-{
- impl_->reinit(asFloat3(baseForcePtr), numAtoms, cell, atomStart, accumulate, completionMarker);
-}
-void GpuForceReduction::execute()
-{
- impl_->execute();
-}
-
-GpuForceReduction::~GpuForceReduction() = default;
-
-} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gpu_utils/device_stream.h"
#include "gromacs/gpu_utils/devicebuffer_datatype.h"
+#include "gromacs/gpu_utils/gputraits.h"
#include "gromacs/math/vectypes.h"
#include "gpuforcereduction.h"
namespace gmx
{
-//! structure to hold cell information for any nbat-format forces
+//! \internal
+//! \brief structure to hold cell information for any nbat-format forces
struct cellInfo
{
//! cell index mapping for any nbat-format forces
const int* cell = nullptr;
//! device copy of cell index mapping for any nbat-format forces
- int* d_cell = nullptr;
+ DeviceBuffer<int> d_cell;
//! number of atoms in cell array
int cellSize = -1;
//! number of atoms allocated in cell array
* \param [in] deviceContext GPU device context
* \param [in] wcycle The wallclock counter
*/
- Impl(const DeviceContext& deviceContext, const DeviceStream& deviceStreami, gmx_wallcycle* wcycle);
+ Impl(const DeviceContext& deviceContext, const DeviceStream& deviceStream, gmx_wallcycle* wcycle);
~Impl();
/*! \brief Register a nbnxm-format force to be reduced
*
* \param [in] forcePtr Pointer to force to be reduced
*/
- void registerNbnxmForce(DeviceBuffer<RVec> forcePtr);
+ void registerNbnxmForce(DeviceBuffer<Float3> forcePtr);
/*! \brief Register a rvec-format force to be reduced
*
* \param [in] forcePtr Pointer to force to be reduced
*/
- void registerRvecForce(DeviceBuffer<RVec> forcePtr);
+ void registerRvecForce(DeviceBuffer<Float3> forcePtr);
/*! \brief Add a dependency for this force reduction
*
* \param [in] accumulate Whether reduction should be accumulated
* \param [in] completionMarker Event to be marked when launch of reduction is complete
*/
- void reinit(float3* baseForcePtr,
+ void reinit(DeviceBuffer<Float3> baseForcePtr,
const int numAtoms,
ArrayRef<const int> cell,
const int atomStart,
private:
//! force to be used as a base for this reduction
- float3* baseForce_ = nullptr;
+ DeviceBuffer<Float3> baseForce_;
//! starting atom
int atomStart_ = 0;
//! number of atoms
//! stream to be used for this reduction
const DeviceStream& deviceStream_;
//! Nbnxm force to be added in this reduction
- DeviceBuffer<RVec> nbnxmForceToAdd_ = nullptr;
+ DeviceBuffer<RVec> nbnxmForceToAdd_;
//! Rvec-format force to be added in this reduction
- DeviceBuffer<RVec> rvecForceToAdd_ = nullptr;
- //! event to be marked when redcution launch has been completed
+ DeviceBuffer<RVec> rvecForceToAdd_;
+ //! event to be marked when reduction launch has been completed
GpuEventSynchronizer* completionMarker_ = nullptr;
//! The wallclock counter
gmx_wallcycle* wcycle_ = nullptr;
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief Implements GPU Force Reduction using CUDA
+ *
+ * \author Alan Gray <alang@nvidia.com>
+ *
+ * \ingroup module_mdlib
+ */
+
+#include "gmxpre.h"
+
+#include "gpuforcereduction_impl_internal.h"
+
+#include "gromacs/gpu_utils/cudautils.cuh"
+#include "gromacs/gpu_utils/devicebuffer.h"
+#include "gromacs/gpu_utils/typecasts.cuh"
+#include "gromacs/gpu_utils/vectype_ops.cuh"
+
+namespace gmx
+{
+
+constexpr static int c_threadsPerBlock = 128;
+
+template<bool addRvecForce, bool accumulateForce>
+static __global__ void reduceKernel(const float3* __restrict__ gm_nbnxmForce,
+ const float3* __restrict__ rvecForceToAdd,
+ float3* gm_fTotal,
+ const int* gm_cell,
+ const int numAtoms)
+{
+
+ // map particle-level parallelism to 1D CUDA thread and block index
+ const int threadIndex = blockIdx.x * blockDim.x + threadIdx.x;
+
+ // perform addition for each particle
+ if (threadIndex < numAtoms)
+ {
+
+ float3* gm_fDest = &gm_fTotal[threadIndex];
+ float3 temp;
+
+ // Accumulate or set nbnxm force
+ if (accumulateForce)
+ {
+ temp = *gm_fDest;
+ temp += gm_nbnxmForce[gm_cell[threadIndex]];
+ }
+ else
+ {
+ temp = gm_nbnxmForce[gm_cell[threadIndex]];
+ }
+
+ if (addRvecForce)
+ {
+ temp += rvecForceToAdd[threadIndex];
+ }
+
+ *gm_fDest = temp;
+ }
+ return;
+}
+
+void launchForceReductionKernel(int numAtoms,
+ int atomStart,
+ bool addRvecForce,
+ bool accumulate,
+ const DeviceBuffer<Float3> d_nbnxmForceToAdd,
+ const DeviceBuffer<Float3> d_rvecForceToAdd,
+ DeviceBuffer<Float3> d_baseForce,
+ DeviceBuffer<int> d_cell,
+ const DeviceStream& deviceStream)
+{
+ float3* d_baseForcePtr = &(asFloat3(d_baseForce)[atomStart]);
+ float3* d_nbnxmForcePtr = asFloat3(d_nbnxmForceToAdd);
+ float3* d_rvecForceToAddPtr = &(asFloat3(d_rvecForceToAdd)[atomStart]);
+
+ // Configure and launch kernel
+ KernelLaunchConfig config;
+ config.blockSize[0] = c_threadsPerBlock;
+ config.blockSize[1] = 1;
+ config.blockSize[2] = 1;
+ config.gridSize[0] = ((numAtoms + 1) + c_threadsPerBlock - 1) / c_threadsPerBlock;
+ config.gridSize[1] = 1;
+ config.gridSize[2] = 1;
+ config.sharedMemorySize = 0;
+
+ auto kernelFn = addRvecForce
+ ? (accumulate ? reduceKernel<true, true> : reduceKernel<true, false>)
+ : (accumulate ? reduceKernel<false, true> : reduceKernel<false, false>);
+
+ const auto kernelArgs = prepareGpuKernelArguments(
+ kernelFn, config, &d_nbnxmForcePtr, &d_rvecForceToAddPtr, &d_baseForcePtr, &d_cell, &numAtoms);
+
+ launchGpuKernel(kernelFn, config, deviceStream, nullptr, "Force Reduction", kernelArgs);
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief Declares vendor-specific function to launch force reduction kernel
+ *
+ * \author Andrey Alekseenko <al42and@gmail.com>
+ *
+ * \ingroup module_mdlib
+ */
+
+#include "gromacs/gpu_utils/devicebuffer_datatype.h"
+#include "gromacs/gpu_utils/gputraits.h"
+
+class DeviceStream;
+
+namespace gmx
+{
+
+/*! \brief Backend-specific function to launch GPU Force Reduction kernel.
+ *
+ * In pseudocode:
+ *
+ * \code{.cpp}
+ * for (int i = 0; i < numAtoms; i++) {
+ * totalForce = d_nbnxmForceToAdd[d_cell[i]]
+ * if (accumulate)
+ * totalForce += d_baseForce[atomStart + i]
+ * if (addRvecForce)
+ * totalForce += d_rvecForceToAdd[atomStart + i]
+ * d_baseForce[atomStart + i] = totalForce[i]
+ * }
+ * \endcode
+ *
+ * \param numAtoms Number of atoms subject to reduction.
+ * \param atomStart First atom index (for \p d_rvecForceToAdd and \p d_baseForce).
+ * \param addRvecForce When \c false, \p d_rvecForceToAdd is ignored.
+ * \param accumulate When \c false, the previous values of \p d_baseForce are discarded.
+ * \param d_nbnxmForceToAdd Buffer containing Nbnxm forces in Nbnxm layout.
+ * \param d_rvecForceToAdd Optional buffer containing arbitrary forces in linear layout.
+ * \param d_baseForce Destination buffer for forces in linear layout.
+ * \param d_cell Atom index to Nbnxm cell index.
+ * \param deviceStream Device stream for kernel submission.
+ */
+void launchForceReductionKernel(int numAtoms,
+ int atomStart,
+ bool addRvecForce,
+ bool accumulate,
+ DeviceBuffer<Float3> d_nbnxmForceToAdd,
+ DeviceBuffer<Float3> d_rvecForceToAdd,
+ DeviceBuffer<Float3> d_baseForce,
+ DeviceBuffer<int> d_cell,
+ const DeviceStream& deviceStream);
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief May be used to implement force reduction interfaces for non-GPU builds.
+ *
+ * \author Alan Gray <alang@nvidia.com>
+ *
+ * \ingroup module_mdlib
+ */
+
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include "gpuforcereduction.h"
+
+#if !HAVE_GPU_FORCE_REDUCTION
+
+namespace gmx
+{
+
+class GpuForceReduction::Impl
+{
+};
+
+GpuForceReduction::GpuForceReduction(const DeviceContext& /* deviceContext */,
+ const DeviceStream& /* deviceStream */,
+ gmx_wallcycle* /*wcycle*/) :
+ impl_(nullptr)
+{
+ GMX_RELEASE_ASSERT(false, "A CPU stub has been called instead of the correct implementation.");
+}
+
+// NOLINTNEXTLINE readability-convert-member-functions-to-static
+void GpuForceReduction::reinit(DeviceBuffer<RVec> /*baseForcePtr*/,
+ const int /*numAtoms*/,
+ ArrayRef<const int> /*cell*/,
+ const int /*atomStart*/,
+ const bool /*accumulate*/,
+ GpuEventSynchronizer* /*completionMarker*/)
+{
+ GMX_RELEASE_ASSERT(false, "A CPU stub has been called instead of the correct implementation.");
+}
+
+// NOLINTNEXTLINE readability-convert-member-functions-to-static
+void GpuForceReduction::registerNbnxmForce(DeviceBuffer<RVec> /* forcePtr */)
+{
+ GMX_RELEASE_ASSERT(false, "A CPU stub has been called instead of the correct implementation.");
+}
+
+// NOLINTNEXTLINE readability-convert-member-functions-to-static
+void GpuForceReduction::registerRvecForce(DeviceBuffer<gmx::RVec> /* forcePtr */)
+{
+ GMX_RELEASE_ASSERT(false, "A CPU stub has been called instead of the correct implementation.");
+}
+
+// NOLINTNEXTLINE readability-convert-member-functions-to-static
+void GpuForceReduction::addDependency(GpuEventSynchronizer* const /* dependency */)
+{
+ GMX_RELEASE_ASSERT(false, "A CPU stub has been called instead of the correct implementation.");
+}
+
+// NOLINTNEXTLINE readability-convert-member-functions-to-static
+void GpuForceReduction::execute()
+{
+ GMX_RELEASE_ASSERT(false, "A CPU stub has been called instead of the correct implementation.");
+}
+
+GpuForceReduction::~GpuForceReduction() = default;
+
+} // namespace gmx
+
+#endif /* !HAVE_GPU_FORCE_REDUCTION */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gpu_utils/cudautils.cuh"
#include "gromacs/gpu_utils/devicebuffer.h"
+#include "gromacs/gpu_utils/typecasts.cuh"
#include "gromacs/gpu_utils/vectype_ops.cuh"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/group.h"
return kernelPtr;
}
-void LeapFrogGpu::integrate(const DeviceBuffer<float3> d_x,
- DeviceBuffer<float3> d_xp,
- DeviceBuffer<float3> d_v,
- const DeviceBuffer<float3> d_f,
+void LeapFrogGpu::integrate(DeviceBuffer<Float3> d_x,
+ DeviceBuffer<Float3> d_xp,
+ DeviceBuffer<Float3> d_v,
+ const DeviceBuffer<Float3> d_f,
const real dt,
const bool doTemperatureScaling,
gmx::ArrayRef<const t_grp_tcstat> tcstat,
{
h_lambdas_[i] = tcstat[i].lambda;
}
- copyToDeviceBuffer(&d_lambdas_, h_lambdas_.data(), 0, numTempScaleValues_,
- deviceStream_, GpuApiCallBehavior::Async, nullptr);
+ copyToDeviceBuffer(&d_lambdas_,
+ h_lambdas_.data(),
+ 0,
+ numTempScaleValues_,
+ deviceStream_,
+ GpuApiCallBehavior::Async,
+ nullptr);
}
VelocityScalingType prVelocityScalingType = VelocityScalingType::None;
if (doParrinelloRahman)
"Fully anisotropic Parrinello-Rahman pressure coupling is not yet supported "
"in GPU version of Leap-Frog integrator.");
prVelocityScalingMatrixDiagonal_ =
- make_float3(dtPressureCouple * prVelocityScalingMatrix[XX][XX],
- dtPressureCouple * prVelocityScalingMatrix[YY][YY],
- dtPressureCouple * prVelocityScalingMatrix[ZZ][ZZ]);
+ Float3{ dtPressureCouple * prVelocityScalingMatrix[XX][XX],
+ dtPressureCouple * prVelocityScalingMatrix[YY][YY],
+ dtPressureCouple * prVelocityScalingMatrix[ZZ][ZZ] };
}
kernelPtr = selectLeapFrogKernelPtr(doTemperatureScaling, numTempScaleValues_, prVelocityScalingType);
}
- const auto kernelArgs = prepareGpuKernelArguments(
- kernelPtr, kernelLaunchConfig_, &numAtoms_, &d_x, &d_xp, &d_v, &d_f, &d_inverseMasses_,
- &dt, &d_lambdas_, &d_tempScaleGroups_, &prVelocityScalingMatrixDiagonal_);
+ // Checking the buffer types against the kernel argument types
+ static_assert(sizeof(*d_inverseMasses_) == sizeof(float), "Incompatible types");
+ const auto kernelArgs = prepareGpuKernelArguments(kernelPtr,
+ kernelLaunchConfig_,
+ &numAtoms_,
+ asFloat3Pointer(&d_x),
+ asFloat3Pointer(&d_xp),
+ asFloat3Pointer(&d_v),
+ asFloat3Pointer(&d_f),
+ &d_inverseMasses_,
+ &dt,
+ &d_lambdas_,
+ &d_tempScaleGroups_,
+ &prVelocityScalingMatrixDiagonal_);
launchGpuKernel(kernelPtr, kernelLaunchConfig_, deviceStream_, nullptr, "leapfrog_kernel", kernelArgs);
return;
}
-LeapFrogGpu::LeapFrogGpu(const DeviceContext& deviceContext, const DeviceStream& deviceStream) :
+LeapFrogGpu::LeapFrogGpu(const DeviceContext& deviceContext,
+ const DeviceStream& deviceStream,
+ const int numTempScaleValues) :
deviceContext_(deviceContext),
- deviceStream_(deviceStream)
+ deviceStream_(deviceStream),
+ numTempScaleValues_(numTempScaleValues)
{
numAtoms_ = 0;
kernelLaunchConfig_.blockSize[1] = 1;
kernelLaunchConfig_.blockSize[2] = 1;
kernelLaunchConfig_.sharedMemorySize = 0;
+
+ // If the temperature coupling is enabled, we need to make space for scaling factors
+ if (numTempScaleValues_ > 0)
+ {
+ h_lambdas_.resize(numTempScaleValues_);
+ reallocateDeviceBuffer(
+ &d_lambdas_, numTempScaleValues_, &numLambdas_, &numLambdasAlloc_, deviceContext_);
+ }
}
LeapFrogGpu::~LeapFrogGpu()
freeDeviceBuffer(&d_inverseMasses_);
}
-void LeapFrogGpu::set(const int numAtoms,
- const real* inverseMasses,
- const int numTempScaleValues,
- const unsigned short* tempScaleGroups)
+void LeapFrogGpu::set(const int numAtoms, const real* inverseMasses, const unsigned short* tempScaleGroups)
{
numAtoms_ = numAtoms;
kernelLaunchConfig_.gridSize[0] = (numAtoms_ + c_threadsPerBlock - 1) / c_threadsPerBlock;
- numTempScaleValues_ = numTempScaleValues;
-
- reallocateDeviceBuffer(&d_inverseMasses_, numAtoms_, &numInverseMasses_,
- &numInverseMassesAlloc_, deviceContext_);
- copyToDeviceBuffer(&d_inverseMasses_, (float*)inverseMasses, 0, numAtoms_, deviceStream_,
- GpuApiCallBehavior::Sync, nullptr);
+ reallocateDeviceBuffer(
+ &d_inverseMasses_, numAtoms_, &numInverseMasses_, &numInverseMassesAlloc_, deviceContext_);
+ copyToDeviceBuffer(
+ &d_inverseMasses_, inverseMasses, 0, numAtoms_, deviceStream_, GpuApiCallBehavior::Sync, nullptr);
// Temperature scale group map only used if there are more then one group
- if (numTempScaleValues > 1)
- {
- reallocateDeviceBuffer(&d_tempScaleGroups_, numAtoms_, &numTempScaleGroups_,
- &numTempScaleGroupsAlloc_, deviceContext_);
- copyToDeviceBuffer(&d_tempScaleGroups_, tempScaleGroups, 0, numAtoms_, deviceStream_,
- GpuApiCallBehavior::Sync, nullptr);
- }
-
- // If the temperature coupling is enabled, we need to make space for scaling factors
- if (numTempScaleValues_ > 0)
+ if (numTempScaleValues_ > 1)
{
- h_lambdas_.resize(numTempScaleValues);
- reallocateDeviceBuffer(&d_lambdas_, numTempScaleValues_, &numLambdas_, &numLambdasAlloc_,
- deviceContext_);
+ reallocateDeviceBuffer(
+ &d_tempScaleGroups_, numAtoms_, &numTempScaleGroups_, &numTempScaleGroupsAlloc_, deviceContext_);
+ copyToDeviceBuffer(
+ &d_tempScaleGroups_, tempScaleGroups, 0, numAtoms_, deviceStream_, GpuApiCallBehavior::Sync, nullptr);
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "config.h"
#if GMX_GPU_CUDA
-# include "gromacs/gpu_utils/devicebuffer.cuh"
# include "gromacs/gpu_utils/gputraits.cuh"
#endif
#if GMX_GPU_SYCL
-# include "gromacs/gpu_utils/devicebuffer_sycl.h"
# include "gromacs/gpu_utils/gputraits_sycl.h"
#endif
+#include <memory>
+
+#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/gpu_utils/hostallocator.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/pbcutil/pbc_aiuc.h"
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/classhelpers.h"
class DeviceContext;
class DeviceStream;
public:
/*! \brief Constructor.
*
- * \param[in] deviceContext Device context (dummy in CUDA).
- * \param[in] deviceStream Device stream to use.
+ * \param[in] deviceContext Device context (dummy in CUDA).
+ * \param[in] deviceStream Device stream to use.
+ * \param[in] numTempScaleValues Number of temperature scale groups.
*/
- LeapFrogGpu(const DeviceContext& deviceContext, const DeviceStream& deviceStream);
+ LeapFrogGpu(const DeviceContext& deviceContext, const DeviceStream& deviceStream, int numTempScaleValues);
~LeapFrogGpu();
/*! \brief Integrate
* \param[in] dtPressureCouple Period between pressure coupling steps
* \param[in] prVelocityScalingMatrix Parrinello-Rahman velocity scaling matrix
*/
- void integrate(const DeviceBuffer<float3> d_x,
- DeviceBuffer<float3> d_xp,
- DeviceBuffer<float3> d_v,
- const DeviceBuffer<float3> d_f,
+ void integrate(DeviceBuffer<Float3> d_x,
+ DeviceBuffer<Float3> d_xp,
+ DeviceBuffer<Float3> d_v,
+ const DeviceBuffer<Float3> d_f,
const real dt,
const bool doTemperatureScaling,
gmx::ArrayRef<const t_grp_tcstat> tcstat,
* and temperature coupling groups. Copies inverse masses and temperature coupling groups
* to the GPU.
*
- * \param[in] numAtoms Number of atoms in the system.
- * \param[in] inverseMasses Inverse masses of atoms.
- * \param[in] numTempScaleValues Number of temperature scale groups.
- * \param[in] tempScaleGroups Maps the atom index to temperature scale value.
+ * \param[in] numAtoms Number of atoms in the system.
+ * \param[in] inverseMasses Inverse masses of atoms.
+ * \param[in] tempScaleGroups Maps the atom index to temperature scale value.
*/
- void set(const int numAtoms,
- const real* inverseMasses,
- int numTempScaleValues,
- const unsigned short* tempScaleGroups);
+ void set(const int numAtoms, const real* inverseMasses, const unsigned short* tempScaleGroups);
/*! \brief Class with hardware-specific interfaces and implementations.*/
class Impl;
int numTempScaleValues_ = 0;
/*! \brief Array with temperature scaling factors.
* This is temporary solution to remap data from t_grp_tcstat into plain array.
- * Not used in SYCL.
* \todo Replace with better solution.
*/
gmx::HostVector<float> h_lambdas_;
int numTempScaleGroupsAlloc_ = -1;
//! Vector with diagonal elements of the Parrinello-Rahman pressure coupling velocity rescale factors
- float3 prVelocityScalingMatrixDiagonal_;
+ Float3 prVelocityScalingMatrixDiagonal_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
template<NumTempScaleValues numTempScaleValues, VelocityScalingType velocityScaling>
auto leapFrogKernel(
cl::sycl::handler& cgh,
- DeviceAccessor<float3, mode::read_write> a_x,
- DeviceAccessor<float3, mode::discard_write> a_xp,
- DeviceAccessor<float3, mode::read_write> a_v,
- DeviceAccessor<float3, mode::read> a_f,
+ DeviceAccessor<Float3, mode::read_write> a_x,
+ DeviceAccessor<Float3, mode::discard_write> a_xp,
+ DeviceAccessor<Float3, mode::read_write> a_v,
+ DeviceAccessor<Float3, mode::read> a_f,
DeviceAccessor<float, mode::read> a_inverseMasses,
float dt,
OptionalAccessor<float, mode::read, numTempScaleValues != NumTempScaleValues::None> a_lambdas,
OptionalAccessor<unsigned short, mode::read, numTempScaleValues == NumTempScaleValues::Multiple> a_tempScaleGroups,
- float3 prVelocityScalingMatrixDiagonal)
+ Float3 prVelocityScalingMatrixDiagonal)
{
cgh.require(a_x);
cgh.require(a_xp);
}
return [=](cl::sycl::id<1> itemIdx) {
- const float3 x = a_x[itemIdx];
- const float3 v = a_v[itemIdx];
- const float3 f = a_f[itemIdx];
+ const Float3 x = a_x[itemIdx];
+ const Float3 v = a_v[itemIdx];
+ const Float3 f = a_f[itemIdx];
const float im = a_inverseMasses[itemIdx];
const float imdt = im * dt;
}
}();
- const float3 prVelocityDelta = [=]() {
+ const Float3 prVelocityDelta = [=]() {
if constexpr (velocityScaling == VelocityScalingType::Diagonal)
{
- return float3{ prVelocityScalingMatrixDiagonal[0] * v[0],
+ return Float3{ prVelocityScalingMatrixDiagonal[0] * v[0],
prVelocityScalingMatrixDiagonal[1] * v[1],
prVelocityScalingMatrixDiagonal[2] * v[2] };
}
else if constexpr (velocityScaling == VelocityScalingType::None)
{
- return float3{ 0, 0, 0 };
+ return Float3{ 0, 0, 0 };
}
}();
- const float3 v_new = v * lambda - prVelocityDelta + f * imdt;
+ const Float3 v_new = v * lambda - prVelocityDelta + f * imdt;
a_v[itemIdx] = v_new;
a_x[itemIdx] = x + v_new * dt;
};
[&](auto tempScalingType_, auto prScalingType_) {
return launchLeapFrogKernel<tempScalingType_, prScalingType_>(std::forward<Args>(args)...);
},
- tempScalingType, prVelocityScalingType);
+ tempScalingType,
+ prVelocityScalingType);
}
-void LeapFrogGpu::integrate(DeviceBuffer<float3> d_x,
- DeviceBuffer<float3> d_xp,
- DeviceBuffer<float3> d_v,
- DeviceBuffer<float3> d_f,
+void LeapFrogGpu::integrate(DeviceBuffer<Float3> d_x,
+ DeviceBuffer<Float3> d_xp,
+ DeviceBuffer<Float3> d_v,
+ DeviceBuffer<Float3> d_f,
const real dt,
const bool doTemperatureScaling,
gmx::ArrayRef<const t_grp_tcstat> tcstat,
GMX_ASSERT(checkDeviceBuffer(d_lambdas_, numTempScaleValues_),
"Number of temperature scaling factors changed since it was set for the "
"last time.");
- { // Explicitly limiting the scope of host accessor. Not strictly necessary here.
- auto ha_lambdas_ = d_lambdas_.buffer_->get_access<mode::discard_write>();
- for (int i = 0; i < numTempScaleValues_; i++)
- {
- ha_lambdas_[i] = tcstat[i].lambda;
- }
+ GMX_RELEASE_ASSERT(gmx::ssize(h_lambdas_) == numTempScaleValues_,
+ "Number of temperature scaling factors changed since it was set for the "
+ "last time.");
+ /* We could use host accessors here, without h_lambdas_.
+ * According to a quick test, host accessor is slightly faster when using DPC++ and
+ * LevelZero compared to using h_lambdas_ + cgh.copy. But with DPC++ and OpenCL, the host
+ * accessor waits for fReadyOnDevice in UpdateConstrainGpu::Impl::integrate. See #4023. */
+
+ for (int i = 0; i < numTempScaleValues_; i++)
+ {
+ h_lambdas_[i] = tcstat[i].lambda;
}
+ copyToDeviceBuffer(&d_lambdas_,
+ h_lambdas_.data(),
+ 0,
+ numTempScaleValues_,
+ deviceStream_,
+ GpuApiCallBehavior::Async,
+ nullptr);
}
NumTempScaleValues tempVelocityScalingType =
getTempScalingType(doTemperatureScaling, numTempScaleValues_);
&& prVelocityScalingMatrix[XX][ZZ] == 0 && prVelocityScalingMatrix[YY][ZZ] == 0,
"Fully anisotropic Parrinello-Rahman pressure coupling is not yet supported "
"in GPU version of Leap-Frog integrator.");
- prVelocityScalingMatrixDiagonal_ =
- dtPressureCouple
- * float3{ prVelocityScalingMatrix[XX][XX], prVelocityScalingMatrix[YY][YY],
- prVelocityScalingMatrix[ZZ][ZZ] };
+ prVelocityScalingMatrixDiagonal_ = dtPressureCouple
+ * Float3{ prVelocityScalingMatrix[XX][XX],
+ prVelocityScalingMatrix[YY][YY],
+ prVelocityScalingMatrix[ZZ][ZZ] };
}
- launchLeapFrogKernel(tempVelocityScalingType, prVelocityScalingType, deviceStream_, numAtoms_,
- d_x, d_xp, d_v, d_f, d_inverseMasses_, dt, d_lambdas_, d_tempScaleGroups_,
+ launchLeapFrogKernel(tempVelocityScalingType,
+ prVelocityScalingType,
+ deviceStream_,
+ numAtoms_,
+ d_x,
+ d_xp,
+ d_v,
+ d_f,
+ d_inverseMasses_,
+ dt,
+ d_lambdas_,
+ d_tempScaleGroups_,
prVelocityScalingMatrixDiagonal_);
}
-LeapFrogGpu::LeapFrogGpu(const DeviceContext& deviceContext, const DeviceStream& deviceStream) :
+LeapFrogGpu::LeapFrogGpu(const DeviceContext& deviceContext,
+ const DeviceStream& deviceStream,
+ const int numTempScaleValues) :
deviceContext_(deviceContext),
deviceStream_(deviceStream),
- numAtoms_(0)
+ numAtoms_(0),
+ numTempScaleValues_(numTempScaleValues)
{
+ // If the temperature coupling is enabled, we need to make space for scaling factors
+ if (numTempScaleValues_ > 0)
+ {
+ h_lambdas_.resize(numTempScaleValues_);
+ reallocateDeviceBuffer(
+ &d_lambdas_, numTempScaleValues_, &numLambdas_, &numLambdasAlloc_, deviceContext_);
+ }
}
LeapFrogGpu::~LeapFrogGpu()
freeDeviceBuffer(&d_inverseMasses_);
}
-void LeapFrogGpu::set(const int numAtoms,
- const real* inverseMasses,
- const int numTempScaleValues,
- const unsigned short* tempScaleGroups)
+void LeapFrogGpu::set(const int numAtoms, const real* inverseMasses, const unsigned short* tempScaleGroups)
{
- numAtoms_ = numAtoms;
- numTempScaleValues_ = numTempScaleValues;
+ numAtoms_ = numAtoms;
- reallocateDeviceBuffer(&d_inverseMasses_, numAtoms_, &numInverseMasses_,
- &numInverseMassesAlloc_, deviceContext_);
- copyToDeviceBuffer(&d_inverseMasses_, inverseMasses, 0, numAtoms_, deviceStream_,
- GpuApiCallBehavior::Sync, nullptr);
+ reallocateDeviceBuffer(
+ &d_inverseMasses_, numAtoms_, &numInverseMasses_, &numInverseMassesAlloc_, deviceContext_);
+ copyToDeviceBuffer(
+ &d_inverseMasses_, inverseMasses, 0, numAtoms_, deviceStream_, GpuApiCallBehavior::Sync, nullptr);
// Temperature scale group map only used if there are more then one group
if (numTempScaleValues_ > 1)
{
- reallocateDeviceBuffer(&d_tempScaleGroups_, numAtoms_, &numTempScaleGroups_,
- &numTempScaleGroupsAlloc_, deviceContext_);
- copyToDeviceBuffer(&d_tempScaleGroups_, tempScaleGroups, 0, numAtoms_, deviceStream_,
- GpuApiCallBehavior::Sync, nullptr);
- }
-
- // If the temperature coupling is enabled, we need to make space for scaling factors
- if (numTempScaleValues_ > 0)
- {
- reallocateDeviceBuffer(&d_lambdas_, numTempScaleValues_, &numLambdas_, &numLambdasAlloc_,
- deviceContext_);
+ reallocateDeviceBuffer(
+ &d_tempScaleGroups_, numAtoms_, &numTempScaleGroups_, &numTempScaleGroupsAlloc_, deviceContext_);
+ copyToDeviceBuffer(
+ &d_tempScaleGroups_, tempScaleGroups, 0, numAtoms_, deviceStream_, GpuApiCallBehavior::Sync, nullptr);
}
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
real preFactor,
gmx::ArrayRef<const real> fac,
gmx::ArrayRef<const gmx::RVec> r,
- const real* invmass,
+ gmx::ArrayRef<const real> invmass,
rvec* x)
{
- if (invmass != nullptr)
+ if (!invmass.empty())
{
for (int b = 0; b < ncons; b++)
{
real preFactor,
gmx::ArrayRef<const real> fac,
gmx::ArrayRef<const gmx::RVec> r,
- const real* invmass,
+ gmx::ArrayRef<const real> invmass,
rvec* x)
{
- if (invmass != nullptr)
+ if (!invmass.empty())
{
for (int b : ind)
{
real preFactor,
gmx::ArrayRef<const real> fac,
gmx::ArrayRef<const gmx::RVec> r,
- const real* invmass,
+ gmx::ArrayRef<const real> invmass,
rvec* x)
{
if (li->ntask == 1)
t_pbc* pbc,
Lincs* lincsd,
int th,
- const real* invmass,
+ ArrayRef<const real> invmass,
ConstraintVariable econq,
bool bCalcDHDL,
bool bCalcVir,
/* Compute normalized x i-j vectors, store in r.
* Compute the inner product of r and xp i-j and store in rhs1.
*/
- calc_dr_x_f_simd(b0, b1, atoms, x, f, blc.data(), pbc_simd, as_rvec_array(r.data()),
- rhs1.data(), sol.data());
+ calc_dr_x_f_simd(
+ b0, b1, atoms, x, f, blc.data(), pbc_simd, as_rvec_array(r.data()), rhs1.data(), sol.data());
#else // GMX_SIMD_HAVE_REAL
/* When constraining forces, we should not use mass weighting,
* so we pass invmass=NULL, which results in the use of 1 for all atoms.
*/
- lincs_update_atoms(lincsd, th, 1.0, sol, r, (econq != ConstraintVariable::Force) ? invmass : nullptr,
+ lincs_update_atoms(lincsd,
+ th,
+ 1.0,
+ sol,
+ r,
+ (econq != ConstraintVariable::Force) ? invmass : gmx::ArrayRef<real>(),
as_rvec_array(fp.data()));
if (bCalcDHDL)
t_pbc* pbc,
Lincs* lincsd,
int th,
- const real* invmass,
+ ArrayRef<const real> invmass,
const t_commrec* cr,
bool bCalcDHDL,
real wangle,
/* Compute normalized x i-j vectors, store in r.
* Compute the inner product of r and xp i-j and store in rhs1.
*/
- calc_dr_x_xp_simd(b0, b1, atoms, x, xp, bllen.data(), blc.data(), pbc_simd,
- as_rvec_array(r.data()), rhs1.data(), sol.data());
+ calc_dr_x_xp_simd(
+ b0, b1, atoms, x, xp, bllen.data(), blc.data(), pbc_simd, as_rvec_array(r.data()), rhs1.data(), sol.data());
#else // GMX_SIMD_HAVE_REAL
real wfac;
- wfac = std::cos(DEG2RAD * wangle);
+ wfac = std::cos(gmx::c_deg2Rad * wangle);
wfac = wfac * wfac;
for (int iter = 0; iter < lincsd->nIter; iter++)
}
#if GMX_SIMD_HAVE_REAL
- calc_dist_iter_simd(b0, b1, atoms, xp, bllen.data(), blc.data(), pbc_simd, wfac,
- rhs1.data(), sol.data(), bWarn);
+ calc_dist_iter_simd(
+ b0, b1, atoms, xp, bllen.data(), blc.data(), pbc_simd, wfac, rhs1.data(), sol.data(), bWarn);
#else
- calc_dist_iter(b0, b1, atoms, xp, bllen.data(), blc.data(), pbc, wfac, rhs1.data(),
- sol.data(), bWarn);
+ calc_dist_iter(b0, b1, atoms, xp, bllen.data(), blc.data(), pbc, wfac, rhs1.data(), sol.data(), bWarn);
/* 20*ncons flops */
#endif // GMX_SIMD_HAVE_REAL
}
/*! \brief Sets the elements in the LINCS matrix for task task. */
-static void set_lincs_matrix_task(Lincs* li, Task* li_task, const real* invmass, int* ncc_triangle, int* nCrossTaskTriangles)
+static void set_lincs_matrix_task(Lincs* li,
+ Task* li_task,
+ ArrayRef<const real> invmass,
+ int* ncc_triangle,
+ int* nCrossTaskTriangles)
{
/* Construct the coupling coefficient matrix blmf */
li_task->ntriangle = 0;
}
/*! \brief Sets the elements in the LINCS matrix. */
-static void set_lincs_matrix(Lincs* li, const real* invmass, real lambda)
+static void set_lincs_matrix(Lincs* li, ArrayRef<const real> invmass, real lambda)
{
const real invsqrt2 = 0.7071067811865475244;
if (debug)
{
fprintf(debug, "The %d constraints participate in %d triangles\n", li->nc, li->ntriangle);
- fprintf(debug, "There are %d constraint couplings, of which %d in triangles\n", li->ncc,
- li->ncc_triangle);
+ fprintf(debug, "There are %d constraint couplings, of which %d in triangles\n", li->ncc, li->ncc_triangle);
if (li->ntriangle > 0 && li->ntask > 1)
{
fprintf(debug,
* The current constraint to task assignment code can create independent
* tasks only when not more than two constraints are connected sequentially.
*/
- li->ntask = gmx_omp_nthreads_get(emntLINCS);
+ li->ntask = gmx_omp_nthreads_get(ModuleMultiThread::Lincs);
li->bTaskDep = (li->ntask > 1 && bMoreThanTwoSeq);
if (debug)
{
- fprintf(debug, "LINCS: using %d threads, tasks are %sdependent\n", li->ntask,
- li->bTaskDep ? "" : "in");
+ fprintf(debug, "LINCS: using %d threads, tasks are %sdependent\n", li->ntask, li->bTaskDep ? "" : "in");
}
if (li->ntask == 1)
{
"%d constraints are involved in constraint triangles,\n"
"will apply an additional matrix expansion of order %d for couplings\n"
"between constraints inside triangles\n",
- li->ncg_triangle, li->nOrder);
+ li->ncg_triangle,
+ li->nOrder);
}
}
void set_lincs(const InteractionDefinitions& idef,
const int numAtoms,
- const real* invmass,
+ ArrayRef<const real> invmass,
const real lambda,
bool bDynamics,
const t_commrec* cr,
{
int start;
- dd_get_constraint_range(cr->dd, &start, &natoms);
+ dd_get_constraint_range(*cr->dd, &start, &natoms);
}
else
{
if (debug)
{
- fprintf(debug, "Number of constraints is %d, padded %d, couplings %d\n", li->nc_real,
- li->nc, li->ncc);
+ fprintf(debug, "Number of constraints is %d, padded %d, couplings %d\n", li->nc_real, li->nc, li->ncc);
}
if (li->ntask > 1)
int maxwarn,
int* warncount)
{
- real wfac = std::cos(DEG2RAD * wangle);
+ real wfac = std::cos(gmx::c_deg2Rad * wangle);
fprintf(stderr,
"bonds that rotated more than %g degrees:\n"
real cosine = ::iprod(v0, v1) / (d0 * d1);
if (cosine < wfac)
{
- fprintf(stderr, " %6d %6d %5.1f %8.4f %8.4f %8.4f\n", ddglatnr(dd, i),
- ddglatnr(dd, j), RAD2DEG * std::acos(cosine), d0, d1, bllen[b]);
+ fprintf(stderr,
+ " %6d %6d %5.1f %8.4f %8.4f %8.4f\n",
+ ddglatnr(dd, i),
+ ddglatnr(dd, j),
+ gmx::c_rad2Deg * std::acos(cosine),
+ d0,
+ d1,
+ bllen[b]);
if (!std::isfinite(d1))
{
gmx_fatal(FARGS, "Bond length not finite.");
}
if (*warncount > maxwarn)
{
- too_many_constraint_warnings(econtLINCS, *warncount);
+ too_many_constraint_warnings(ConstraintAlgorithm::Lincs, *warncount);
}
}
const t_inputrec& ir,
int64_t step,
Lincs* lincsd,
- const real* invmass,
+ ArrayRef<const real> invmass,
const t_commrec* cr,
const gmx_multisim_t* ms,
ArrayRefWithPadding<const RVec> xPadded,
* We can also easily check if any constraint length is changed,
* if not dH/dlambda=0 and we can also set the boolean to FALSE.
*/
- bool bCalcDHDL = (ir.efep != efepNO && dvdlambda != nullptr);
+ bool bCalcDHDL = (ir.efep != FreeEnergyPerturbationType::No && dvdlambda != nullptr);
if (lincsd->nc == 0 && cr->dd == nullptr)
{
/* We can't use bCalcDHDL here, since NULL can be passed for dvdlambda
* also with efep!=fepNO.
*/
- if (ir.efep != efepNO)
+ if (ir.efep != FreeEnergyPerturbationType::No)
{
if (hasMassPerturbed && lincsd->matlam != lambda)
{
{
LincsDeviations deviations = makeLincsDeviations(*lincsd, xprime, pbc);
fprintf(debug, " Rel. Constraint Deviation: RMS MAX between atoms\n");
- fprintf(debug, " Before LINCS %.6f %.6f %6d %6d\n",
+ fprintf(debug,
+ " Before LINCS %.6f %.6f %6d %6d\n",
std::sqrt(deviations.sumSquaredDeviation / deviations.numConstraints),
deviations.maxDeviation,
ddglatnr(cr->dd, lincsd->atoms[deviations.indexOfMaxDeviation].index1),
clear_mat(lincsd->task[th].vir_r_m_dr);
- do_lincs(xPadded, xprimePadded, box, pbc, lincsd, th, invmass, cr, bCalcDHDL,
- ir.LincsWarnAngle, &bWarn, invdt, v, bCalcVir,
+ do_lincs(xPadded,
+ xprimePadded,
+ box,
+ pbc,
+ lincsd,
+ th,
+ invmass,
+ cr,
+ bCalcDHDL,
+ ir.LincsWarnAngle,
+ &bWarn,
+ invdt,
+ v,
+ bCalcVir,
th == 0 ? vir_r_m_dr : lincsd->task[th].vir_r_m_dr);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
if (printDebugOutput)
{
- fprintf(debug, " After LINCS %.6f %.6f %6d %6d\n\n",
+ fprintf(debug,
+ " After LINCS %.6f %.6f %6d %6d\n\n",
std::sqrt(deviations.sumSquaredDeviation / deviations.numConstraints),
deviations.maxDeviation,
ddglatnr(cr->dd, lincsd->atoms[deviations.indexOfMaxDeviation].index1),
", time %g (ps) LINCS WARNING%s\n"
"relative constraint deviation after LINCS:\n"
"rms %.6f, max %.6f (between atoms %d and %d)\n",
- step, ir.init_t + step * ir.delta_t, simMesg.c_str(),
+ step,
+ ir.init_t + step * ir.delta_t,
+ simMesg.c_str(),
std::sqrt(deviations.sumSquaredDeviation / deviations.numConstraints),
deviations.maxDeviation,
ddglatnr(cr->dd, lincsd->atoms[deviations.indexOfMaxDeviation].index1),
ddglatnr(cr->dd, lincsd->atoms[deviations.indexOfMaxDeviation].index2));
- lincs_warning(cr->dd, x, xprime, pbc, lincsd->nc, lincsd->atoms, lincsd->bllen,
- ir.LincsWarnAngle, maxwarn, warncount);
+ lincs_warning(
+ cr->dd, x, xprime, pbc, lincsd->nc, lincsd->atoms, lincsd->bllen, ir.LincsWarnAngle, maxwarn, warncount);
}
bOK = (deviations.maxDeviation < 0.5);
}
{
int th = gmx_omp_get_thread_num();
- do_lincsp(xPadded, xprimePadded, min_proj, pbc, lincsd, th, invmass, econq,
- bCalcDHDL, bCalcVir, th == 0 ? vir_r_m_dr : lincsd->task[th].vir_r_m_dr);
+ do_lincsp(xPadded,
+ xprimePadded,
+ min_proj,
+ pbc,
+ lincsd,
+ th,
+ invmass,
+ econq,
+ bCalcDHDL,
+ bCalcVir,
+ th == 0 ? vir_r_m_dr : lincsd->task[th].vir_r_m_dr);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
namespace gmx
{
-
template<typename>
class ArrayRefWithPadding;
+template<typename>
+class ArrayRef;
enum class ConstraintVariable : int;
class Lincs;
template<typename>
/*! \brief Initialize lincs stuff */
void set_lincs(const InteractionDefinitions& idef,
int numAtoms,
- const real* invmass,
+ ArrayRef<const real> invmass,
real lambda,
bool bDynamics,
const t_commrec* cr,
const t_inputrec& ir,
int64_t step,
Lincs* lincsd,
- const real* invmass,
+ ArrayRef<const real> invmass,
const t_commrec* cr,
const gmx_multisim_t* ms,
ArrayRefWithPadding<const RVec> x,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
/*! \internal \file
*
- * \brief Implements LINCS using CUDA
+ * \brief Implementations of LINCS GPU class
*
- * This file contains implementation of LINCS constraints algorithm
- * using CUDA, including class initialization, data-structures management
- * and GPU kernel.
+ * This file contains back-end agnostic implementation of LINCS GPU class.
*
* \author Artem Zhmurov <zhmurov@gmail.com>
* \author Alan Gray <alang@nvidia.com>
*/
#include "gmxpre.h"
-#include "lincs_gpu.cuh"
+#include "lincs_gpu.h"
#include <assert.h>
#include <stdio.h>
#include <algorithm>
-#include "gromacs/gpu_utils/cuda_arch_utils.cuh"
-#include "gromacs/gpu_utils/cudautils.cuh"
-#include "gromacs/gpu_utils/devicebuffer.cuh"
-#include "gromacs/gpu_utils/gputraits.cuh"
-#include "gromacs/gpu_utils/vectype_ops.cuh"
+#include "gromacs/gpu_utils/devicebuffer.h"
+#include "gromacs/gpu_utils/gputraits.h"
+#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/lincs_gpu_internal.h"
#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/pbcutil/pbc_aiuc_cuda.cuh"
-#include "gromacs/topology/forcefieldparameters.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/topology.h"
namespace gmx
{
-//! Number of CUDA threads in a block
-constexpr static int c_threadsPerBlock = 256;
-//! Maximum number of threads in a block (for __launch_bounds__)
-constexpr static int c_maxThreadsPerBlock = c_threadsPerBlock;
-
-/*! \brief Main kernel for LINCS constraints.
- *
- * See Hess et al., J. Comput. Chem. 18: 1463-1472 (1997) for the description of the algorithm.
- *
- * In CUDA version, one thread is responsible for all computations for one constraint. The blocks are
- * filled in a way that no constraint is coupled to the constraint from the next block. This is achieved
- * by moving active threads to the next block, if the correspondent group of coupled constraints is to big
- * to fit the current thread block. This may leave some 'dummy' threads in the end of the thread block, i.e.
- * threads that are not required to do actual work. Since constraints from different blocks are not coupled,
- * there is no need to synchronize across the device. However, extensive communication in a thread block
- * are still needed.
- *
- * \todo Reduce synchronization overhead. Some ideas are:
- * 1. Consider going to warp-level synchronization for the coupled constraints.
- * 2. Move more data to local/shared memory and try to get rid of atomic operations (at least on
- * the device level).
- * 3. Use analytical solution for matrix A inversion.
- * 4. Introduce mapping of thread id to both single constraint and single atom, thus designating
- * Nth threads to deal with Nat <= Nth coupled atoms and Nc <= Nth coupled constraints.
- * See Issue #2885 for details (https://gitlab.com/gromacs/gromacs/-/issues/2885)
- * \todo The use of __restrict__ for gm_xp and gm_v causes failure, probably because of the atomic
- operations. Investigate this issue further.
- *
- * \param[in,out] kernelParams All parameters and pointers for the kernel condensed in single struct.
- * \param[in] invdt Inverse timestep (needed to update velocities).
- */
-template<bool updateVelocities, bool computeVirial>
-__launch_bounds__(c_maxThreadsPerBlock) __global__
- void lincs_kernel(LincsGpuKernelParameters kernelParams,
- const float3* __restrict__ gm_x,
- float3* gm_xp,
- float3* gm_v,
- const float invdt)
-{
- const PbcAiuc pbcAiuc = kernelParams.pbcAiuc;
- const int numConstraintsThreads = kernelParams.numConstraintsThreads;
- const int numIterations = kernelParams.numIterations;
- const int expansionOrder = kernelParams.expansionOrder;
- const int2* __restrict__ gm_constraints = kernelParams.d_constraints;
- const float* __restrict__ gm_constraintsTargetLengths = kernelParams.d_constraintsTargetLengths;
- const int* __restrict__ gm_coupledConstraintsCounts = kernelParams.d_coupledConstraintsCounts;
- const int* __restrict__ gm_coupledConstraintsIdxes = kernelParams.d_coupledConstraintsIndices;
- const float* __restrict__ gm_massFactors = kernelParams.d_massFactors;
- float* __restrict__ gm_matrixA = kernelParams.d_matrixA;
- const float* __restrict__ gm_inverseMasses = kernelParams.d_inverseMasses;
- float* __restrict__ gm_virialScaled = kernelParams.d_virialScaled;
-
- int threadIndex = blockIdx.x * blockDim.x + threadIdx.x;
-
- // numConstraintsThreads should be a integer multiple of blockSize (numConstraintsThreads = numBlocks*blockSize).
- // This is to ensure proper synchronizations and reduction. All array are padded to the required size.
- assert(threadIndex < numConstraintsThreads);
-
- // Vectors connecting constrained atoms before algorithm was applied.
- // Needed to construct constrain matrix A
- extern __shared__ float3 sm_r[];
-
- int2 pair = gm_constraints[threadIndex];
- int i = pair.x;
- int j = pair.y;
-
- // Mass-scaled Lagrange multiplier
- float lagrangeScaled = 0.0f;
-
- float targetLength;
- float inverseMassi;
- float inverseMassj;
- float sqrtReducedMass;
-
- float3 xi;
- float3 xj;
- float3 rc;
-
- // i == -1 indicates dummy constraint at the end of the thread block.
- bool isDummyThread = (i == -1);
-
- // Everything computed for these dummies will be equal to zero
- if (isDummyThread)
- {
- targetLength = 0.0f;
- inverseMassi = 0.0f;
- inverseMassj = 0.0f;
- sqrtReducedMass = 0.0f;
-
- xi = make_float3(0.0f, 0.0f, 0.0f);
- xj = make_float3(0.0f, 0.0f, 0.0f);
- rc = make_float3(0.0f, 0.0f, 0.0f);
- }
- else
- {
- // Collecting data
- targetLength = gm_constraintsTargetLengths[threadIndex];
- inverseMassi = gm_inverseMasses[i];
- inverseMassj = gm_inverseMasses[j];
- sqrtReducedMass = rsqrt(inverseMassi + inverseMassj);
-
- xi = gm_x[i];
- xj = gm_x[j];
-
- float3 dx = pbcDxAiuc(pbcAiuc, xi, xj);
-
- float rlen = rsqrtf(dx.x * dx.x + dx.y * dx.y + dx.z * dx.z);
- rc = rlen * dx;
- }
-
- sm_r[threadIdx.x] = rc;
- // Make sure that all r's are saved into shared memory
- // before they are accessed in the loop below
- __syncthreads();
-
- /*
- * Constructing LINCS matrix (A)
- */
-
- // Only non-zero values are saved (for coupled constraints)
- int coupledConstraintsCount = gm_coupledConstraintsCounts[threadIndex];
- for (int n = 0; n < coupledConstraintsCount; n++)
- {
- int index = n * numConstraintsThreads + threadIndex;
- int c1 = gm_coupledConstraintsIdxes[index];
-
- float3 rc1 = sm_r[c1 - blockIdx.x * blockDim.x];
- gm_matrixA[index] = gm_massFactors[index] * (rc.x * rc1.x + rc.y * rc1.y + rc.z * rc1.z);
- }
-
- // Skipping in dummy threads
- if (!isDummyThread)
- {
- xi = gm_xp[i];
- xj = gm_xp[j];
- }
-
- float3 dx = pbcDxAiuc(pbcAiuc, xi, xj);
-
- float sol = sqrtReducedMass * ((rc.x * dx.x + rc.y * dx.y + rc.z * dx.z) - targetLength);
-
- /*
- * Inverse matrix using a set of expansionOrder matrix multiplications
- */
-
- // This will use the same memory space as sm_r, which is no longer needed.
- extern __shared__ float sm_rhs[];
- // Save current right-hand-side vector in the shared memory
- sm_rhs[threadIdx.x] = sol;
-
- for (int rec = 0; rec < expansionOrder; rec++)
- {
- // Making sure that all sm_rhs are saved before they are accessed in a loop below
- __syncthreads();
- float mvb = 0.0f;
-
- for (int n = 0; n < coupledConstraintsCount; n++)
- {
- int index = n * numConstraintsThreads + threadIndex;
- int c1 = gm_coupledConstraintsIdxes[index];
- // Convolute current right-hand-side with A
- // Different, non overlapping parts of sm_rhs[..] are read during odd and even iterations
- mvb = mvb + gm_matrixA[index] * sm_rhs[c1 - blockIdx.x * blockDim.x + blockDim.x * (rec % 2)];
- }
- // 'Switch' rhs vectors, save current result
- // These values will be accessed in the loop above during the next iteration.
- sm_rhs[threadIdx.x + blockDim.x * ((rec + 1) % 2)] = mvb;
- sol = sol + mvb;
- }
-
- // Current mass-scaled Lagrange multipliers
- lagrangeScaled = sqrtReducedMass * sol;
-
- // Save updated coordinates before correction for the rotational lengthening
- float3 tmp = rc * lagrangeScaled;
-
- // Writing for all but dummy constraints
- if (!isDummyThread)
- {
- atomicAdd(&gm_xp[i], -tmp * inverseMassi);
- atomicAdd(&gm_xp[j], tmp * inverseMassj);
- }
-
- /*
- * Correction for centripetal effects
- */
- for (int iter = 0; iter < numIterations; iter++)
- {
- // Make sure that all xp's are saved: atomic operation calls before are
- // communicating current xp[..] values across thread block.
- __syncthreads();
-
- if (!isDummyThread)
- {
- xi = gm_xp[i];
- xj = gm_xp[j];
- }
-
- float3 dx = pbcDxAiuc(pbcAiuc, xi, xj);
-
- float len2 = targetLength * targetLength;
- float dlen2 = 2.0f * len2 - norm2(dx);
-
- // TODO A little bit more effective but slightly less readable version of the below would be:
- // float proj = sqrtReducedMass*(targetLength - (dlen2 > 0.0f ? 1.0f : 0.0f)*dlen2*rsqrt(dlen2));
- float proj;
- if (dlen2 > 0.0f)
- {
- proj = sqrtReducedMass * (targetLength - dlen2 * rsqrt(dlen2));
- }
- else
- {
- proj = sqrtReducedMass * targetLength;
- }
-
- sm_rhs[threadIdx.x] = proj;
- float sol = proj;
-
- /*
- * Same matrix inversion as above is used for updated data
- */
- for (int rec = 0; rec < expansionOrder; rec++)
- {
- // Make sure that all elements of rhs are saved into shared memory
- __syncthreads();
- float mvb = 0;
-
- for (int n = 0; n < coupledConstraintsCount; n++)
- {
- int index = n * numConstraintsThreads + threadIndex;
- int c1 = gm_coupledConstraintsIdxes[index];
-
- mvb = mvb + gm_matrixA[index] * sm_rhs[c1 - blockIdx.x * blockDim.x + blockDim.x * (rec % 2)];
- }
- sm_rhs[threadIdx.x + blockDim.x * ((rec + 1) % 2)] = mvb;
- sol = sol + mvb;
- }
-
- // Add corrections to Lagrange multipliers
- float sqrtmu_sol = sqrtReducedMass * sol;
- lagrangeScaled += sqrtmu_sol;
-
- // Save updated coordinates for the next iteration
- // Dummy constraints are skipped
- if (!isDummyThread)
- {
- float3 tmp = rc * sqrtmu_sol;
- atomicAdd(&gm_xp[i], -tmp * inverseMassi);
- atomicAdd(&gm_xp[j], tmp * inverseMassj);
- }
- }
-
- // Updating particle velocities for all but dummy threads
- if (updateVelocities && !isDummyThread)
- {
- float3 tmp = rc * invdt * lagrangeScaled;
- atomicAdd(&gm_v[i], -tmp * inverseMassi);
- atomicAdd(&gm_v[j], tmp * inverseMassj);
- }
-
-
- if (computeVirial)
- {
- // Virial is computed from Lagrange multiplier (lagrangeScaled), target constrain length
- // (targetLength) and the normalized vector connecting constrained atoms before
- // the algorithm was applied (rc). The evaluation of virial in each thread is
- // followed by basic reduction for the values inside single thread block.
- // Then, the values are reduced across grid by atomicAdd(...).
- //
- // TODO Shuffle reduction.
- // TODO Should be unified and/or done once when virial is actually needed.
- // TODO Recursive version that removes atomicAdd(...)'s entirely is needed. Ideally,
- // one that works for any datatype.
-
- // Save virial for each thread into the shared memory. Tensor is symmetrical, hence only
- // 6 values are saved. Dummy threads will have zeroes in their virial: targetLength,
- // lagrangeScaled and rc are all set to zero for them in the beginning of the kernel.
- // The sm_threadVirial[..] will overlap with the sm_r[..] and sm_rhs[..], but the latter
- // two are no longer in use.
- extern __shared__ float sm_threadVirial[];
- float mult = targetLength * lagrangeScaled;
- sm_threadVirial[0 * blockDim.x + threadIdx.x] = mult * rc.x * rc.x;
- sm_threadVirial[1 * blockDim.x + threadIdx.x] = mult * rc.x * rc.y;
- sm_threadVirial[2 * blockDim.x + threadIdx.x] = mult * rc.x * rc.z;
- sm_threadVirial[3 * blockDim.x + threadIdx.x] = mult * rc.y * rc.y;
- sm_threadVirial[4 * blockDim.x + threadIdx.x] = mult * rc.y * rc.z;
- sm_threadVirial[5 * blockDim.x + threadIdx.x] = mult * rc.z * rc.z;
-
- __syncthreads();
-
- // Reduce up to one virial per thread block. All blocks are divided by half, the first
- // half of threads sums two virials. Then the first half is divided by two and the first
- // half of it sums two values. This procedure is repeated until only one thread is left.
- // Only works if the threads per blocks is a power of two (hence static_assert
- // in the beginning of the kernel).
- for (int divideBy = 2; divideBy <= static_cast<int>(blockDim.x); divideBy *= 2)
- {
- int dividedAt = blockDim.x / divideBy;
- if (static_cast<int>(threadIdx.x) < dividedAt)
- {
- for (int d = 0; d < 6; d++)
- {
- sm_threadVirial[d * blockDim.x + threadIdx.x] +=
- sm_threadVirial[d * blockDim.x + (threadIdx.x + dividedAt)];
- }
- }
- // Syncronize if not within one warp
- if (dividedAt > warpSize / 2)
- {
- __syncthreads();
- }
- }
- // First 6 threads in the block add the results of 6 tensor components to the global memory address.
- if (threadIdx.x < 6)
- {
- atomicAdd(&(gm_virialScaled[threadIdx.x]), sm_threadVirial[threadIdx.x * blockDim.x]);
- }
- }
-
- return;
-}
-
-/*! \brief Select templated kernel.
- *
- * Returns pointer to a CUDA kernel based on provided booleans.
- *
- * \param[in] updateVelocities If the velocities should be constrained.
- * \param[in] computeVirial If virial should be updated.
- *
- * \return Pointer to CUDA kernel
- */
-inline auto getLincsKernelPtr(const bool updateVelocities, const bool computeVirial)
+void LincsGpu::apply(const DeviceBuffer<Float3> d_x,
+ DeviceBuffer<Float3> d_xp,
+ const bool updateVelocities,
+ DeviceBuffer<Float3> d_v,
+ const real invdt,
+ const bool computeVirial,
+ tensor virialScaled,
+ const PbcAiuc pbcAiuc)
{
-
- auto kernelPtr = lincs_kernel<true, true>;
- if (updateVelocities && computeVirial)
- {
- kernelPtr = lincs_kernel<true, true>;
- }
- else if (updateVelocities && !computeVirial)
- {
- kernelPtr = lincs_kernel<true, false>;
- }
- else if (!updateVelocities && computeVirial)
- {
- kernelPtr = lincs_kernel<false, true>;
- }
- else if (!updateVelocities && !computeVirial)
- {
- kernelPtr = lincs_kernel<false, false>;
- }
- return kernelPtr;
-}
-
-void LincsGpu::apply(const float3* d_x,
- float3* d_xp,
- const bool updateVelocities,
- float3* d_v,
- const real invdt,
- const bool computeVirial,
- tensor virialScaled,
- const PbcAiuc pbcAiuc)
-{
- ensureNoPendingDeviceError("In CUDA version of LINCS");
+ GMX_ASSERT(GMX_GPU_CUDA, "LINCS GPU is only implemented in CUDA.");
// Early exit if no constraints
if (kernelParams_.numConstraintsThreads == 0)
clearDeviceBufferAsync(&kernelParams_.d_virialScaled, 0, 6, deviceStream_);
}
- auto kernelPtr = getLincsKernelPtr(updateVelocities, computeVirial);
-
- KernelLaunchConfig config;
- config.blockSize[0] = c_threadsPerBlock;
- config.blockSize[1] = 1;
- config.blockSize[2] = 1;
- config.gridSize[0] = (kernelParams_.numConstraintsThreads + c_threadsPerBlock - 1) / c_threadsPerBlock;
- config.gridSize[1] = 1;
- config.gridSize[2] = 1;
-
- // Shared memory is used to store:
- // -- Current coordinates (3 floats per thread)
- // -- Right-hand-sides for matrix inversion (2 floats per thread)
- // -- Virial tensor components (6 floats per thread)
- // Since none of these three are needed simultaneously, they can be saved at the same shared memory address
- // (i.e. correspondent arrays are intentionally overlapped in address space). Consequently, only
- // max{3, 2, 6} = 6 floats per thread are needed in case virial is computed, or max{3, 2} = 3 if not.
- if (computeVirial)
- {
- config.sharedMemorySize = c_threadsPerBlock * 6 * sizeof(float);
- }
- else
- {
- config.sharedMemorySize = c_threadsPerBlock * 3 * sizeof(float);
- }
-
kernelParams_.pbcAiuc = pbcAiuc;
- const auto kernelArgs =
- prepareGpuKernelArguments(kernelPtr, config, &kernelParams_, &d_x, &d_xp, &d_v, &invdt);
-
- launchGpuKernel(kernelPtr, config, deviceStream_, nullptr,
- "lincs_kernel<updateVelocities, computeVirial>", kernelArgs);
+ launchLincsGpuKernel(
+ kernelParams_, d_x, d_xp, updateVelocities, d_v, invdt, computeVirial, deviceStream_);
if (computeVirial)
{
// Copy LINCS virial data and add it to the common virial
- copyFromDeviceBuffer(h_virialScaled_.data(), &kernelParams_.d_virialScaled, 0, 6,
- deviceStream_, GpuApiCallBehavior::Sync, nullptr);
+ copyFromDeviceBuffer(h_virialScaled_.data(),
+ &kernelParams_.d_virialScaled,
+ 0,
+ 6,
+ deviceStream_,
+ GpuApiCallBehavior::Sync,
+ nullptr);
// Mapping [XX, XY, XZ, YY, YZ, ZZ] internal format to a tensor object
virialScaled[XX][XX] += h_virialScaled_[0];
deviceContext_(deviceContext),
deviceStream_(deviceStream)
{
+ GMX_RELEASE_ASSERT(GMX_GPU_CUDA, "LINCS GPU is only implemented in CUDA.");
kernelParams_.numIterations = numIterations;
kernelParams_.expansionOrder = expansionOrder;
static_assert(sizeof(real) == sizeof(float),
"Real numbers should be in single precision in GPU code.");
static_assert(
- c_threadsPerBlock > 0 && ((c_threadsPerBlock & (c_threadsPerBlock - 1)) == 0),
+ gmx::isPowerOfTwo(c_threadsPerBlock),
"Number of threads per block should be a power of two in order for reduction to work.");
allocateDeviceBuffer(&kernelParams_.d_virialScaled, 6, deviceContext_);
numCoupledConstraints[c2] = 0; // To indicate we've been here
counted += 1
+ countCoupled(adjacentAtom.indexOfSecondConstrainedAtom_,
- numCoupledConstraints, atomsAdjacencyList);
+ numCoupledConstraints,
+ atomsAdjacencyList);
}
}
return counted;
* \param[in] iatoms The list of constraints.
* \param[in] stride Number of elements per constraint in \p iatoms.
* \param[in] atomsAdjacencyList Information about connections between atoms.
- * \param[our] splitMap Map of sequential constraint indexes to indexes to be on the device
+ * \param[out] splitMap Map of sequential constraint indexes to indexes to be on the device
* \param[in] c Sequential index for constraint to consider adding.
* \param[in,out] currentMapIndex The rolling index for the constraints mapping.
*/
void LincsGpu::set(const InteractionDefinitions& idef, const int numAtoms, const real* invmass)
{
+ GMX_RELEASE_ASSERT(GMX_GPU_CUDA, "LINCS GPU is only implemented in CUDA.");
// List of constrained atoms (CPU memory)
- std::vector<int2> constraintsHost;
+ std::vector<AtomPair> constraintsHost;
// Equilibrium distances for the constraints (CPU)
std::vector<float> constraintsTargetLengthsHost;
// Number of constraints, coupled with the current one (CPU)
"LINCS with constraints on all-bonds, which is not supported for large "
"molecules. When compatible with the force field and integration settings, "
"using constraints on H-bonds only.",
- numCoupledConstraints.at(c), c_threadsPerBlock);
+ numCoupledConstraints.at(c),
+ c_threadsPerBlock);
}
if (currentMapIndex / c_threadsPerBlock
!= (currentMapIndex + numCoupledConstraints.at(c)) / c_threadsPerBlock)
"Number of threads should be a multiple of the block size");
// Initialize constraints and their target indexes taking into account the splits in the data arrays.
- int2 pair;
- pair.x = -1;
- pair.y = -1;
+ AtomPair pair;
+ pair.i = -1;
+ pair.j = -1;
constraintsHost.resize(kernelParams_.numConstraintsThreads, pair);
std::fill(constraintsHost.begin(), constraintsHost.end(), pair);
constraintsTargetLengthsHost.resize(kernelParams_.numConstraintsThreads, 0.0);
int a2 = iatoms[stride * c + 2];
int type = iatoms[stride * c];
- int2 pair;
- pair.x = a1;
- pair.y = a2;
+ AtomPair pair;
+ pair.i = a1;
+ pair.j = a2;
constraintsHost.at(splitMap.at(c)) = pair;
constraintsTargetLengthsHost.at(splitMap.at(c)) = idef.iparams[type].constr.dA;
}
numConstraintsThreadsAlloc_ = kernelParams_.numConstraintsThreads;
- allocateDeviceBuffer(&kernelParams_.d_constraints, kernelParams_.numConstraintsThreads,
- deviceContext_);
+ allocateDeviceBuffer(
+ &kernelParams_.d_constraints, kernelParams_.numConstraintsThreads, deviceContext_);
allocateDeviceBuffer(&kernelParams_.d_constraintsTargetLengths,
- kernelParams_.numConstraintsThreads, deviceContext_);
+ kernelParams_.numConstraintsThreads,
+ deviceContext_);
allocateDeviceBuffer(&kernelParams_.d_coupledConstraintsCounts,
- kernelParams_.numConstraintsThreads, deviceContext_);
+ kernelParams_.numConstraintsThreads,
+ deviceContext_);
allocateDeviceBuffer(&kernelParams_.d_coupledConstraintsIndices,
- maxCoupledConstraints * kernelParams_.numConstraintsThreads, deviceContext_);
+ maxCoupledConstraints * kernelParams_.numConstraintsThreads,
+ deviceContext_);
allocateDeviceBuffer(&kernelParams_.d_massFactors,
- maxCoupledConstraints * kernelParams_.numConstraintsThreads, deviceContext_);
+ maxCoupledConstraints * kernelParams_.numConstraintsThreads,
+ deviceContext_);
allocateDeviceBuffer(&kernelParams_.d_matrixA,
- maxCoupledConstraints * kernelParams_.numConstraintsThreads, deviceContext_);
+ maxCoupledConstraints * kernelParams_.numConstraintsThreads,
+ deviceContext_);
}
// (Re)allocate the memory, if the number of atoms has increased.
}
// Copy data to GPU.
- copyToDeviceBuffer(&kernelParams_.d_constraints, constraintsHost.data(), 0,
- kernelParams_.numConstraintsThreads, deviceStream_, GpuApiCallBehavior::Sync,
+ copyToDeviceBuffer(&kernelParams_.d_constraints,
+ constraintsHost.data(),
+ 0,
+ kernelParams_.numConstraintsThreads,
+ deviceStream_,
+ GpuApiCallBehavior::Sync,
nullptr);
copyToDeviceBuffer(&kernelParams_.d_constraintsTargetLengths,
- constraintsTargetLengthsHost.data(), 0, kernelParams_.numConstraintsThreads,
- deviceStream_, GpuApiCallBehavior::Sync, nullptr);
+ constraintsTargetLengthsHost.data(),
+ 0,
+ kernelParams_.numConstraintsThreads,
+ deviceStream_,
+ GpuApiCallBehavior::Sync,
+ nullptr);
copyToDeviceBuffer(&kernelParams_.d_coupledConstraintsCounts,
- coupledConstraintsCountsHost.data(), 0, kernelParams_.numConstraintsThreads,
- deviceStream_, GpuApiCallBehavior::Sync, nullptr);
- copyToDeviceBuffer(&kernelParams_.d_coupledConstraintsIndices, coupledConstraintsIndicesHost.data(),
- 0, maxCoupledConstraints * kernelParams_.numConstraintsThreads,
- deviceStream_, GpuApiCallBehavior::Sync, nullptr);
- copyToDeviceBuffer(&kernelParams_.d_massFactors, massFactorsHost.data(), 0,
- maxCoupledConstraints * kernelParams_.numConstraintsThreads, deviceStream_,
- GpuApiCallBehavior::Sync, nullptr);
+ coupledConstraintsCountsHost.data(),
+ 0,
+ kernelParams_.numConstraintsThreads,
+ deviceStream_,
+ GpuApiCallBehavior::Sync,
+ nullptr);
+ copyToDeviceBuffer(&kernelParams_.d_coupledConstraintsIndices,
+ coupledConstraintsIndicesHost.data(),
+ 0,
+ maxCoupledConstraints * kernelParams_.numConstraintsThreads,
+ deviceStream_,
+ GpuApiCallBehavior::Sync,
+ nullptr);
+ copyToDeviceBuffer(&kernelParams_.d_massFactors,
+ massFactorsHost.data(),
+ 0,
+ maxCoupledConstraints * kernelParams_.numConstraintsThreads,
+ deviceStream_,
+ GpuApiCallBehavior::Sync,
+ nullptr);
GMX_RELEASE_ASSERT(invmass != nullptr, "Masses of atoms should be specified.\n");
- copyToDeviceBuffer(&kernelParams_.d_inverseMasses, invmass, 0, numAtoms, deviceStream_,
- GpuApiCallBehavior::Sync, nullptr);
+ copyToDeviceBuffer(
+ &kernelParams_.d_inverseMasses, invmass, 0, numAtoms, deviceStream_, GpuApiCallBehavior::Sync, nullptr);
}
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MDLIB_LINCS_GPU_CUH
#define GMX_MDLIB_LINCS_GPU_CUH
+#include <memory>
+
+#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/gpu_utils/device_context.h"
#include "gromacs/gpu_utils/device_stream.h"
-#include "gromacs/gpu_utils/gputraits.cuh"
+#include "gromacs/gpu_utils/gputraits.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/pbcutil/pbc_aiuc.h"
-#include "gromacs/utility/classhelpers.h"
class InteractionDefinitions;
namespace gmx
{
+//! A pair of atoms indexes
+struct AtomPair
+{
+ //! First atom
+ int i;
+ //! Second atom
+ int j;
+};
+
/* \brief LINCS parameters and GPU pointers
*
* This is used to accumulate all the parameters and pointers so they can be passed
//! Number of iterations used to correct the projection
int numIterations;
//! 1/mass for all atoms (GPU)
- float* d_inverseMasses;
+ DeviceBuffer<float> d_inverseMasses;
//! Scaled virial tensor (6 floats: [XX, XY, XZ, YY, YZ, ZZ], GPU)
- float* d_virialScaled;
+ DeviceBuffer<float> d_virialScaled;
/*! \brief Total number of threads.
*
* This covers all constraints and gaps in the ends of the thread blocks
*/
int numConstraintsThreads;
//! List of constrained atoms (GPU memory)
- int2* d_constraints;
+ DeviceBuffer<AtomPair> d_constraints;
//! Equilibrium distances for the constraints (GPU)
- float* d_constraintsTargetLengths;
+ DeviceBuffer<float> d_constraintsTargetLengths;
//! Number of constraints, coupled with the current one (GPU)
- int* d_coupledConstraintsCounts;
+ DeviceBuffer<int> d_coupledConstraintsCounts;
//! List of coupled with the current one (GPU)
- int* d_coupledConstraintsIndices;
+ DeviceBuffer<int> d_coupledConstraintsIndices;
//! Elements of the coupling matrix.
- float* d_matrixA;
+ DeviceBuffer<float> d_matrixA;
//! Mass factors (GPU)
- float* d_massFactors;
+ DeviceBuffer<float> d_massFactors;
};
/*! \internal \brief Class with interfaces and data for GPU version of LINCS. */
* \param[in,out] virialScaled Scaled virial tensor to be updated.
* \param[in] pbcAiuc PBC data.
*/
- void apply(const float3* d_x,
- float3* d_xp,
- const bool updateVelocities,
- float3* d_v,
- const real invdt,
- const bool computeVirial,
- tensor virialScaled,
- const PbcAiuc pbcAiuc);
+ void apply(const DeviceBuffer<Float3> d_x,
+ DeviceBuffer<Float3> d_xp,
+ const bool updateVelocities,
+ DeviceBuffer<Float3> d_v,
+ const real invdt,
+ const bool computeVirial,
+ tensor virialScaled,
+ const PbcAiuc pbcAiuc);
/*! \brief
* Update data-structures (e.g. after NB search step).
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief Implements LINCS kernels using CUDA
+ *
+ * This file contains CUDA kernels of LINCS constraints algorithm.
+ *
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ * \author Alan Gray <alang@nvidia.com>
+ *
+ * \ingroup module_mdlib
+ */
+#include "gromacs/gpu_utils/cuda_arch_utils.cuh"
+#include "gromacs/gpu_utils/cudautils.cuh"
+#include "gromacs/gpu_utils/devicebuffer.cuh"
+#include "gromacs/gpu_utils/gputraits.h"
+#include "gromacs/gpu_utils/typecasts.cuh"
+#include "gromacs/gpu_utils/vectype_ops.cuh"
+#include "gromacs/mdlib/lincs_gpu.h"
+#include "gromacs/pbcutil/pbc_aiuc_cuda.cuh"
+
+#include "lincs_gpu_internal.h"
+
+namespace gmx
+{
+
+//! Maximum number of threads in a block (for __launch_bounds__)
+constexpr static int c_maxThreadsPerBlock = c_threadsPerBlock;
+
+/*! \brief Main kernel for LINCS constraints.
+ *
+ * See Hess et al., J. Comput. Chem. 18: 1463-1472 (1997) for the description of the algorithm.
+ *
+ * In CUDA version, one thread is responsible for all computations for one constraint. The blocks are
+ * filled in a way that no constraint is coupled to the constraint from the next block. This is achieved
+ * by moving active threads to the next block, if the correspondent group of coupled constraints is to big
+ * to fit the current thread block. This may leave some 'dummy' threads in the end of the thread block, i.e.
+ * threads that are not required to do actual work. Since constraints from different blocks are not coupled,
+ * there is no need to synchronize across the device. However, extensive communication in a thread block
+ * are still needed.
+ *
+ * \todo Reduce synchronization overhead. Some ideas are:
+ * 1. Consider going to warp-level synchronization for the coupled constraints.
+ * 2. Move more data to local/shared memory and try to get rid of atomic operations (at least on
+ * the device level).
+ * 3. Use analytical solution for matrix A inversion.
+ * 4. Introduce mapping of thread id to both single constraint and single atom, thus designating
+ * Nth threads to deal with Nat <= Nth coupled atoms and Nc <= Nth coupled constraints.
+ * See Issue #2885 for details (https://gitlab.com/gromacs/gromacs/-/issues/2885)
+ * \todo The use of __restrict__ for gm_xp and gm_v causes failure, probably because of the atomic
+ operations. Investigate this issue further.
+ *
+ * \param[in,out] kernelParams All parameters and pointers for the kernel condensed in single struct.
+ * \param[in] invdt Inverse timestep (needed to update velocities).
+ */
+template<bool updateVelocities, bool computeVirial>
+__launch_bounds__(c_maxThreadsPerBlock) __global__
+ void lincs_kernel(LincsGpuKernelParameters kernelParams,
+ const float3* __restrict__ gm_x,
+ float3* gm_xp,
+ float3* gm_v,
+ const float invdt)
+{
+ const PbcAiuc pbcAiuc = kernelParams.pbcAiuc;
+ const int numConstraintsThreads = kernelParams.numConstraintsThreads;
+ const int numIterations = kernelParams.numIterations;
+ const int expansionOrder = kernelParams.expansionOrder;
+ const AtomPair* __restrict__ gm_constraints = kernelParams.d_constraints;
+ const float* __restrict__ gm_constraintsTargetLengths = kernelParams.d_constraintsTargetLengths;
+ const int* __restrict__ gm_coupledConstraintsCounts = kernelParams.d_coupledConstraintsCounts;
+ const int* __restrict__ gm_coupledConstraintsIdxes = kernelParams.d_coupledConstraintsIndices;
+ const float* __restrict__ gm_massFactors = kernelParams.d_massFactors;
+ float* __restrict__ gm_matrixA = kernelParams.d_matrixA;
+ const float* __restrict__ gm_inverseMasses = kernelParams.d_inverseMasses;
+ float* __restrict__ gm_virialScaled = kernelParams.d_virialScaled;
+
+ int threadIndex = blockIdx.x * blockDim.x + threadIdx.x;
+
+ // numConstraintsThreads should be a integer multiple of blockSize (numConstraintsThreads = numBlocks*blockSize).
+ // This is to ensure proper synchronizations and reduction. All array are padded to the required size.
+ assert(threadIndex < numConstraintsThreads);
+
+ // Vectors connecting constrained atoms before algorithm was applied.
+ // Needed to construct constrain matrix A
+ extern __shared__ float3 sm_r[];
+
+ AtomPair pair = gm_constraints[threadIndex];
+ int i = pair.i;
+ int j = pair.j;
+
+ // Mass-scaled Lagrange multiplier
+ float lagrangeScaled = 0.0f;
+
+ float targetLength;
+ float inverseMassi;
+ float inverseMassj;
+ float sqrtReducedMass;
+
+ float3 xi;
+ float3 xj;
+ float3 rc;
+
+ // i == -1 indicates dummy constraint at the end of the thread block.
+ bool isDummyThread = (i == -1);
+
+ // Everything computed for these dummies will be equal to zero
+ if (isDummyThread)
+ {
+ targetLength = 0.0f;
+ inverseMassi = 0.0f;
+ inverseMassj = 0.0f;
+ sqrtReducedMass = 0.0f;
+
+ xi = make_float3(0.0f, 0.0f, 0.0f);
+ xj = make_float3(0.0f, 0.0f, 0.0f);
+ rc = make_float3(0.0f, 0.0f, 0.0f);
+ }
+ else
+ {
+ // Collecting data
+ targetLength = gm_constraintsTargetLengths[threadIndex];
+ inverseMassi = gm_inverseMasses[i];
+ inverseMassj = gm_inverseMasses[j];
+ sqrtReducedMass = rsqrt(inverseMassi + inverseMassj);
+
+ xi = gm_x[i];
+ xj = gm_x[j];
+
+ float3 dx = pbcDxAiuc(pbcAiuc, xi, xj);
+
+ float rlen = rsqrtf(dx.x * dx.x + dx.y * dx.y + dx.z * dx.z);
+ rc = rlen * dx;
+ }
+
+ sm_r[threadIdx.x] = rc;
+ // Make sure that all r's are saved into shared memory
+ // before they are accessed in the loop below
+ __syncthreads();
+
+ /*
+ * Constructing LINCS matrix (A)
+ */
+
+ // Only non-zero values are saved (for coupled constraints)
+ int coupledConstraintsCount = gm_coupledConstraintsCounts[threadIndex];
+ for (int n = 0; n < coupledConstraintsCount; n++)
+ {
+ int index = n * numConstraintsThreads + threadIndex;
+ int c1 = gm_coupledConstraintsIdxes[index];
+
+ float3 rc1 = sm_r[c1 - blockIdx.x * blockDim.x];
+ gm_matrixA[index] = gm_massFactors[index] * (rc.x * rc1.x + rc.y * rc1.y + rc.z * rc1.z);
+ }
+
+ // Skipping in dummy threads
+ if (!isDummyThread)
+ {
+ xi = gm_xp[i];
+ xj = gm_xp[j];
+ }
+
+ float3 dx = pbcDxAiuc(pbcAiuc, xi, xj);
+
+ float sol = sqrtReducedMass * ((rc.x * dx.x + rc.y * dx.y + rc.z * dx.z) - targetLength);
+
+ /*
+ * Inverse matrix using a set of expansionOrder matrix multiplications
+ */
+
+ // This will use the same memory space as sm_r, which is no longer needed.
+ extern __shared__ float sm_rhs[];
+ // Save current right-hand-side vector in the shared memory
+ sm_rhs[threadIdx.x] = sol;
+
+ for (int rec = 0; rec < expansionOrder; rec++)
+ {
+ // Making sure that all sm_rhs are saved before they are accessed in a loop below
+ __syncthreads();
+ float mvb = 0.0f;
+
+ for (int n = 0; n < coupledConstraintsCount; n++)
+ {
+ int index = n * numConstraintsThreads + threadIndex;
+ int c1 = gm_coupledConstraintsIdxes[index];
+ // Convolute current right-hand-side with A
+ // Different, non overlapping parts of sm_rhs[..] are read during odd and even iterations
+ mvb = mvb + gm_matrixA[index] * sm_rhs[c1 - blockIdx.x * blockDim.x + blockDim.x * (rec % 2)];
+ }
+ // 'Switch' rhs vectors, save current result
+ // These values will be accessed in the loop above during the next iteration.
+ sm_rhs[threadIdx.x + blockDim.x * ((rec + 1) % 2)] = mvb;
+ sol = sol + mvb;
+ }
+
+ // Current mass-scaled Lagrange multipliers
+ lagrangeScaled = sqrtReducedMass * sol;
+
+ // Save updated coordinates before correction for the rotational lengthening
+ float3 tmp = rc * lagrangeScaled;
+
+ // Writing for all but dummy constraints
+ if (!isDummyThread)
+ {
+ atomicAdd(&gm_xp[i], -tmp * inverseMassi);
+ atomicAdd(&gm_xp[j], tmp * inverseMassj);
+ }
+
+ /*
+ * Correction for centripetal effects
+ */
+ for (int iter = 0; iter < numIterations; iter++)
+ {
+ // Make sure that all xp's are saved: atomic operation calls before are
+ // communicating current xp[..] values across thread block.
+ __syncthreads();
+
+ if (!isDummyThread)
+ {
+ xi = gm_xp[i];
+ xj = gm_xp[j];
+ }
+
+ float3 dx = pbcDxAiuc(pbcAiuc, xi, xj);
+
+ float len2 = targetLength * targetLength;
+ float dlen2 = 2.0f * len2 - norm2(dx);
+
+ // TODO A little bit more effective but slightly less readable version of the below would be:
+ // float proj = sqrtReducedMass*(targetLength - (dlen2 > 0.0f ? 1.0f : 0.0f)*dlen2*rsqrt(dlen2));
+ float proj;
+ if (dlen2 > 0.0f)
+ {
+ proj = sqrtReducedMass * (targetLength - dlen2 * rsqrt(dlen2));
+ }
+ else
+ {
+ proj = sqrtReducedMass * targetLength;
+ }
+
+ sm_rhs[threadIdx.x] = proj;
+ float sol = proj;
+
+ /*
+ * Same matrix inversion as above is used for updated data
+ */
+ for (int rec = 0; rec < expansionOrder; rec++)
+ {
+ // Make sure that all elements of rhs are saved into shared memory
+ __syncthreads();
+ float mvb = 0;
+
+ for (int n = 0; n < coupledConstraintsCount; n++)
+ {
+ int index = n * numConstraintsThreads + threadIndex;
+ int c1 = gm_coupledConstraintsIdxes[index];
+
+ mvb = mvb + gm_matrixA[index] * sm_rhs[c1 - blockIdx.x * blockDim.x + blockDim.x * (rec % 2)];
+ }
+ sm_rhs[threadIdx.x + blockDim.x * ((rec + 1) % 2)] = mvb;
+ sol = sol + mvb;
+ }
+
+ // Add corrections to Lagrange multipliers
+ float sqrtmu_sol = sqrtReducedMass * sol;
+ lagrangeScaled += sqrtmu_sol;
+
+ // Save updated coordinates for the next iteration
+ // Dummy constraints are skipped
+ if (!isDummyThread)
+ {
+ float3 tmp = rc * sqrtmu_sol;
+ atomicAdd(&gm_xp[i], -tmp * inverseMassi);
+ atomicAdd(&gm_xp[j], tmp * inverseMassj);
+ }
+ }
+
+ // Updating particle velocities for all but dummy threads
+ if (updateVelocities && !isDummyThread)
+ {
+ float3 tmp = rc * invdt * lagrangeScaled;
+ atomicAdd(&gm_v[i], -tmp * inverseMassi);
+ atomicAdd(&gm_v[j], tmp * inverseMassj);
+ }
+
+
+ if (computeVirial)
+ {
+ // Virial is computed from Lagrange multiplier (lagrangeScaled), target constrain length
+ // (targetLength) and the normalized vector connecting constrained atoms before
+ // the algorithm was applied (rc). The evaluation of virial in each thread is
+ // followed by basic reduction for the values inside single thread block.
+ // Then, the values are reduced across grid by atomicAdd(...).
+ //
+ // TODO Shuffle reduction.
+ // TODO Should be unified and/or done once when virial is actually needed.
+ // TODO Recursive version that removes atomicAdd(...)'s entirely is needed. Ideally,
+ // one that works for any datatype.
+
+ // Save virial for each thread into the shared memory. Tensor is symmetrical, hence only
+ // 6 values are saved. Dummy threads will have zeroes in their virial: targetLength,
+ // lagrangeScaled and rc are all set to zero for them in the beginning of the kernel.
+ // The sm_threadVirial[..] will overlap with the sm_r[..] and sm_rhs[..], but the latter
+ // two are no longer in use.
+ extern __shared__ float sm_threadVirial[];
+ float mult = targetLength * lagrangeScaled;
+ sm_threadVirial[0 * blockDim.x + threadIdx.x] = mult * rc.x * rc.x;
+ sm_threadVirial[1 * blockDim.x + threadIdx.x] = mult * rc.x * rc.y;
+ sm_threadVirial[2 * blockDim.x + threadIdx.x] = mult * rc.x * rc.z;
+ sm_threadVirial[3 * blockDim.x + threadIdx.x] = mult * rc.y * rc.y;
+ sm_threadVirial[4 * blockDim.x + threadIdx.x] = mult * rc.y * rc.z;
+ sm_threadVirial[5 * blockDim.x + threadIdx.x] = mult * rc.z * rc.z;
+
+ __syncthreads();
+
+ // Reduce up to one virial per thread block. All blocks are divided by half, the first
+ // half of threads sums two virials. Then the first half is divided by two and the first
+ // half of it sums two values. This procedure is repeated until only one thread is left.
+ // Only works if the threads per blocks is a power of two (hence static_assert
+ // in the beginning of the kernel).
+ for (int divideBy = 2; divideBy <= static_cast<int>(blockDim.x); divideBy *= 2)
+ {
+ int dividedAt = blockDim.x / divideBy;
+ if (static_cast<int>(threadIdx.x) < dividedAt)
+ {
+ for (int d = 0; d < 6; d++)
+ {
+ sm_threadVirial[d * blockDim.x + threadIdx.x] +=
+ sm_threadVirial[d * blockDim.x + (threadIdx.x + dividedAt)];
+ }
+ }
+ // Syncronize if not within one warp
+ if (dividedAt > warpSize / 2)
+ {
+ __syncthreads();
+ }
+ }
+ // First 6 threads in the block add the results of 6 tensor components to the global memory address.
+ if (threadIdx.x < 6)
+ {
+ atomicAdd(&(gm_virialScaled[threadIdx.x]), sm_threadVirial[threadIdx.x * blockDim.x]);
+ }
+ }
+
+ return;
+}
+
+/*! \brief Select templated kernel.
+ *
+ * Returns pointer to a CUDA kernel based on provided booleans.
+ *
+ * \param[in] updateVelocities If the velocities should be constrained.
+ * \param[in] computeVirial If virial should be updated.
+ *
+ * \return Pointer to CUDA kernel
+ */
+inline auto getLincsKernelPtr(const bool updateVelocities, const bool computeVirial)
+{
+
+ auto kernelPtr = lincs_kernel<true, true>;
+ if (updateVelocities && computeVirial)
+ {
+ kernelPtr = lincs_kernel<true, true>;
+ }
+ else if (updateVelocities && !computeVirial)
+ {
+ kernelPtr = lincs_kernel<true, false>;
+ }
+ else if (!updateVelocities && computeVirial)
+ {
+ kernelPtr = lincs_kernel<false, true>;
+ }
+ else if (!updateVelocities && !computeVirial)
+ {
+ kernelPtr = lincs_kernel<false, false>;
+ }
+ return kernelPtr;
+}
+
+void launchLincsGpuKernel(LincsGpuKernelParameters& kernelParams,
+ const DeviceBuffer<Float3> d_x,
+ DeviceBuffer<Float3> d_xp,
+ const bool updateVelocities,
+ DeviceBuffer<Float3> d_v,
+ const real invdt,
+ const bool computeVirial,
+ const DeviceStream& deviceStream)
+{
+
+ auto kernelPtr = getLincsKernelPtr(updateVelocities, computeVirial);
+
+ KernelLaunchConfig config;
+ config.blockSize[0] = c_threadsPerBlock;
+ config.blockSize[1] = 1;
+ config.blockSize[2] = 1;
+ config.gridSize[0] = (kernelParams.numConstraintsThreads + c_threadsPerBlock - 1) / c_threadsPerBlock;
+ config.gridSize[1] = 1;
+ config.gridSize[2] = 1;
+
+ // Shared memory is used to store:
+ // -- Current coordinates (3 floats per thread)
+ // -- Right-hand-sides for matrix inversion (2 floats per thread)
+ // -- Virial tensor components (6 floats per thread)
+ // Since none of these three are needed simultaneously, they can be saved at the same shared memory address
+ // (i.e. correspondent arrays are intentionally overlapped in address space). Consequently, only
+ // max{3, 2, 6} = 6 floats per thread are needed in case virial is computed, or max{3, 2} = 3 if not.
+ if (computeVirial)
+ {
+ config.sharedMemorySize = c_threadsPerBlock * 6 * sizeof(float);
+ }
+ else
+ {
+ config.sharedMemorySize = c_threadsPerBlock * 3 * sizeof(float);
+ }
+
+ const auto kernelArgs = prepareGpuKernelArguments(kernelPtr,
+ config,
+ &kernelParams,
+ asFloat3Pointer(&d_x),
+ asFloat3Pointer(&d_xp),
+ asFloat3Pointer(&d_v),
+ &invdt);
+
+ launchGpuKernel(kernelPtr,
+ config,
+ deviceStream,
+ nullptr,
+ "lincs_kernel<updateVelocities, computeVirial>",
+ kernelArgs);
+
+ return;
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief Declare backend-specific LINCS GPU functions
+ *
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ * \author Alan Gray <alang@nvidia.com>
+ *
+ * \ingroup module_mdlib
+ */
+#ifndef GMX_MDLIB_LINCS_GPU_INTERNAL_H
+#define GMX_MDLIB_LINCS_GPU_INTERNAL_H
+
+#include "gromacs/gpu_utils/devicebuffer_datatype.h"
+#include "gromacs/gpu_utils/gputraits.h"
+
+class DeviceStream;
+
+namespace gmx
+{
+
+struct LincsGpuKernelParameters;
+
+//! Number of threads in a GPU block
+constexpr static int c_threadsPerBlock = 256;
+
+void launchLincsGpuKernel(LincsGpuKernelParameters& kernelParams,
+ const DeviceBuffer<Float3> d_x,
+ DeviceBuffer<Float3> d_xp,
+ const bool updateVelocities,
+ DeviceBuffer<Float3> d_v,
+ const real invdt,
+ const bool computeVirial,
+ const DeviceStream& deviceStream);
+
+} // namespace gmx
+
+#endif // GMX_MDLIB_LINCS_GPU_INTERNAL_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief Implements LINCS kernels using SYCL
+ *
+ * This file contains SYCL kernels of LINCS constraints algorithm.
+ *
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ *
+ * \ingroup module_mdlib
+ */
+#include "lincs_gpu_internal.h"
+
+#include "gromacs/utility/gmxassert.h"
+
+namespace gmx
+{
+
+void launchLincsGpuKernel(LincsGpuKernelParameters& /* kernelParams */,
+ const DeviceBuffer<Float3> /* d_x */,
+ DeviceBuffer<Float3> /* d_xp */,
+ const bool /* updateVelocities */,
+ DeviceBuffer<Float3> /* d_v */,
+ const real /* invdt */,
+ const bool /* computeVirial */,
+ const DeviceStream& /* deviceStream */)
+{
+
+ // SYCL_TODO
+ GMX_RELEASE_ASSERT(false, "LINCS is not yet implemented in SYCL.");
+
+ return;
+}
+
+} // namespace gmx
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/domdec/domdec.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/coupling.h"
gmx_bool bEkinAveVel)
{
int g;
- gmx::ArrayRef<t_grp_tcstat> tcstat = ekind->tcstat;
- gmx::ArrayRef<t_grp_acc> grpstat = ekind->grpstat;
+ gmx::ArrayRef<t_grp_tcstat> tcstat = ekind->tcstat;
/* three main: VV with AveVel, vv with AveEkin, leap with AveEkin. Leap with AveVel is also
an option, but not supported now.
bEkinAveVel: If TRUE, we sum into ekin, if FALSE, into ekinh.
*/
- /* group velocities are calculated in update_ekindata and
- * accumulated in acumulate_groups.
- * Now the partial global and groups ekin.
- */
+ // Now accumulate the partial global and groups ekin.
for (g = 0; (g < opts->ngtc); g++)
{
copy_mat(tcstat[g].ekinh, tcstat[g].ekinh_old);
}
}
ekind->dekindl_old = ekind->dekindl;
- int nthread = gmx_omp_nthreads_get(emntUpdate);
+ int nthread = gmx_omp_nthreads_get(ModuleMultiThread::Update);
#pragma omp parallel for num_threads(nthread) schedule(static)
for (int thread = 0; thread < nthread; thread++)
// or memory allocation. It should not be able to throw, so for now
// we do not need a try/catch wrapper.
int start_t, end_t, n;
- int ga, gt;
- rvec v_corrt;
+ int gt;
real hm;
int d, m;
matrix* ekin_sum;
}
*dekindl_sum = 0.0;
- ga = 0;
gt = 0;
for (n = start_t; n < end_t; n++)
{
- if (md->cACC)
- {
- ga = md->cACC[n];
- }
if (md->cTC)
{
gt = md->cTC[n];
}
hm = 0.5 * md->massT[n];
- for (d = 0; (d < DIM); d++)
- {
- v_corrt[d] = v[n][d] - grpstat[ga].u[d];
- }
for (d = 0; (d < DIM); d++)
{
for (m = 0; (m < DIM); m++)
{
- /* if we're computing a full step velocity, v_corrt[d] has v(t). Otherwise, v(t+dt/2) */
- ekin_sum[gt][m][d] += hm * v_corrt[m] * v_corrt[d];
+ /* if we're computing a full step velocity, v[d] has v(t). Otherwise, v(t+dt/2) */
+ ekin_sum[gt][m][d] += hm * v[n][m] * v[n][d];
}
}
if (md->nMassPerturbed && md->bPerturbed[n])
{
- *dekindl_sum += 0.5 * (md->massB[n] - md->massA[n]) * iprod(v_corrt, v_corrt);
+ *dekindl_sum += 0.5 * (md->massB[n] - md->massA[n]) * iprod(v[n], v[n]);
}
}
}
const t_mdatoms* mdatoms,
t_nrnb* nrnb,
t_vcm* vcm,
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle* wcycle,
gmx_enerdata_t* enerd,
tensor force_vir,
tensor shake_vir,
tensor total_vir,
tensor pres,
- gmx::Constraints* constr,
+ gmx::ArrayRef<real> constraintsRmsdData,
gmx::SimulationSignaller* signalCoordinator,
const matrix lastbox,
- int* totalNumberOfBondedInteractions,
gmx_bool* bSumEkinhOld,
const int flags)
{
/* we calculate a full state kinetic energy either with full-step velocity verlet
or half step where we need the pressure */
- bEkinAveVel = (ir->eI == eiVV || (ir->eI == eiVVAK && bPres) || bReadEkin);
+ bEkinAveVel = (ir->eI == IntegrationAlgorithm::VV
+ || (ir->eI == IntegrationAlgorithm::VVAK && bPres) || bReadEkin);
/* in initalization, it sums the shake virial in vv, and to
sums ekinh_old in leapfrog (or if we are calculating ekinh_old) for other reasons */
if (bTemp)
{
- /* Non-equilibrium MD: this is parallellized, but only does communication
- * when there really is NEMD.
- */
-
- if (PAR(cr) && (ekind->bNEMD))
- {
- accumulate_u(cr, &(ir->opts), ekind);
- }
if (!bReadEkin)
{
calc_ke_part(x, v, box, &(ir->opts), mdatoms, ekind, nrnb, bEkinAveVel);
gmx::ArrayRef<real> signalBuffer = signalCoordinator->getCommunicationBuffer();
if (PAR(cr))
{
- wallcycle_start(wcycle, ewcMoveE);
- global_stat(gstat, cr, enerd, force_vir, shake_vir, ir, ekind, constr,
- bStopCM ? vcm : nullptr, signalBuffer.size(), signalBuffer.data(),
- totalNumberOfBondedInteractions, *bSumEkinhOld, flags);
- wallcycle_stop(wcycle, ewcMoveE);
+ wallcycle_start(wcycle, WallCycleCounter::MoveE);
+ global_stat(*gstat,
+ cr,
+ enerd,
+ force_vir,
+ shake_vir,
+ *ir,
+ ekind,
+ constraintsRmsdData,
+ bStopCM ? vcm : nullptr,
+ signalBuffer,
+ *bSumEkinhOld,
+ flags);
+ wallcycle_stop(wcycle, WallCycleCounter::MoveE);
}
signalCoordinator->finalizeSignals();
*bSumEkinhOld = FALSE;
If FALSE, we average ekinh_old and ekinh*ekinscale_nhc to get an averaged half step kinetic energy.
*/
enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, &dvdl_ekin, bEkinAveVel, bScaleEkin);
- enerd->dvdl_lin[efptMASS] = static_cast<double>(dvdl_ekin);
+ enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Mass] = static_cast<double>(dvdl_ekin);
enerd->term[F_EKIN] = trace(ekind->ekin);
}
return nst;
}
-int computeGlobalCommunicationPeriod(const gmx::MDLogger& mdlog, t_inputrec* ir, const t_commrec* cr)
+int computeGlobalCommunicationPeriod(const t_inputrec* ir)
{
- int nstglobalcomm;
+ int nstglobalcomm = 10;
{
// Set up the default behaviour
- if (!(ir->nstcalcenergy > 0 || ir->nstlist > 0 || ir->etc != etcNO || ir->epc != epcNO))
+ if (!(ir->nstcalcenergy > 0 || ir->nstlist > 0 || ir->etc != TemperatureCoupling::No
+ || ir->epc != PressureCoupling::No))
{
/* The user didn't choose the period for anything
important, so we just make sure we can send signals and
write output suitably. */
- nstglobalcomm = 10;
if (ir->nstenergy > 0 && ir->nstenergy < nstglobalcomm)
{
nstglobalcomm = ir->nstenergy;
* here a leftover of the twin-range scheme? Can we remove
* nstlist when we remove the group scheme?
*/
- nstglobalcomm = lcd4(ir->nstcalcenergy, ir->nstlist, ir->etc != etcNO ? ir->nsttcouple : 0,
- ir->epc != epcNO ? ir->nstpcouple : 0);
+ nstglobalcomm = lcd4(ir->nstcalcenergy,
+ ir->nstlist,
+ ir->etc != TemperatureCoupling::No ? ir->nsttcouple : 0,
+ ir->epc != PressureCoupling::No ? ir->nstpcouple : 0);
}
}
+ return nstglobalcomm;
+}
- // TODO change this behaviour. Instead grompp should print
- // a (performance) note and mdrun should not change ir.
- if (ir->comm_mode != ecmNO && ir->nstcomm < nstglobalcomm)
- {
- GMX_LOG(mdlog.warning)
- .asParagraph()
- .appendTextFormatted("WARNING: Changing nstcomm from %d to %d", ir->nstcomm, nstglobalcomm);
- ir->nstcomm = nstglobalcomm;
- }
+int computeGlobalCommunicationPeriod(const gmx::MDLogger& mdlog, const t_inputrec* ir, const t_commrec* cr)
+{
+ const int nstglobalcomm = computeGlobalCommunicationPeriod(ir);
if (cr->nnodes > 1)
{
* with what is needed, so we correct this here.
*/
state->flags = 0;
- if (ir->efep != efepNO || ir->bExpanded)
+ if (ir->efep != FreeEnergyPerturbationType::No || ir->bExpanded)
{
- state->flags |= (1 << estLAMBDA);
- state->flags |= (1 << estFEPSTATE);
+ state->flags |= enumValueToBitMask(StateEntry::Lambda);
+ state->flags |= enumValueToBitMask(StateEntry::FepState);
}
- state->flags |= (1 << estX);
+ state->flags |= enumValueToBitMask(StateEntry::X);
GMX_RELEASE_ASSERT(state->x.size() == state->natoms,
"We should start a run with an initialized state->x");
if (EI_DYNAMICS(ir->eI))
{
- state->flags |= (1 << estV);
+ state->flags |= enumValueToBitMask(StateEntry::V);
}
state->nnhpres = 0;
if (ir->pbcType != PbcType::No)
{
- state->flags |= (1 << estBOX);
+ state->flags |= enumValueToBitMask(StateEntry::Box);
if (inputrecPreserveShape(ir))
{
- state->flags |= (1 << estBOX_REL);
+ state->flags |= enumValueToBitMask(StateEntry::BoxRel);
}
- if ((ir->epc == epcPARRINELLORAHMAN) || (ir->epc == epcMTTK))
+ if ((ir->epc == PressureCoupling::ParrinelloRahman) || (ir->epc == PressureCoupling::Mttk))
{
- state->flags |= (1 << estBOXV);
+ state->flags |= enumValueToBitMask(StateEntry::BoxV);
if (!useModularSimulator)
{
- state->flags |= (1 << estPRES_PREV);
+ state->flags |= enumValueToBitMask(StateEntry::PressurePrevious);
}
}
if (inputrecNptTrotter(ir) || (inputrecNphTrotter(ir)))
{
state->nnhpres = 1;
- state->flags |= (1 << estNHPRES_XI);
- state->flags |= (1 << estNHPRES_VXI);
- state->flags |= (1 << estSVIR_PREV);
- state->flags |= (1 << estFVIR_PREV);
- state->flags |= (1 << estVETA);
- state->flags |= (1 << estVOL0);
+ state->flags |= enumValueToBitMask(StateEntry::Nhpresxi);
+ state->flags |= enumValueToBitMask(StateEntry::Nhpresvxi);
+ state->flags |= enumValueToBitMask(StateEntry::SVirPrev);
+ state->flags |= enumValueToBitMask(StateEntry::FVirPrev);
+ state->flags |= enumValueToBitMask(StateEntry::Veta);
+ state->flags |= enumValueToBitMask(StateEntry::Vol0);
}
- if (ir->epc == epcBERENDSEN || ir->epc == epcCRESCALE)
+ if (ir->epc == PressureCoupling::Berendsen || ir->epc == PressureCoupling::CRescale)
{
- state->flags |= (1 << estBAROS_INT);
+ state->flags |= enumValueToBitMask(StateEntry::BarosInt);
}
}
- if (ir->etc == etcNOSEHOOVER)
+ if (ir->etc == TemperatureCoupling::NoseHoover)
{
- state->flags |= (1 << estNH_XI);
- state->flags |= (1 << estNH_VXI);
+ state->flags |= enumValueToBitMask(StateEntry::Nhxi);
+ state->flags |= enumValueToBitMask(StateEntry::Nhvxi);
}
- if (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)
+ if (ir->etc == TemperatureCoupling::VRescale || ir->etc == TemperatureCoupling::Berendsen)
{
- state->flags |= (1 << estTHERM_INT);
+ state->flags |= enumValueToBitMask(StateEntry::ThermInt);
}
- init_gtc_state(state, state->ngtc, state->nnhpres,
- ir->opts.nhchainlength); /* allocate the space for nose-hoover chains */
+ init_gtc_state(state, state->ngtc, state->nnhpres, ir->opts.nhchainlength); /* allocate the space for nose-hoover chains */
init_ekinstate(&state->ekinstate, ir);
if (ir->bExpanded)
if (ir->pull && ir->pull->bSetPbcRefToPrevStepCOM)
{
- state->flags |= (1 << estPULLCOMPREVSTEP);
+ state->flags |= enumValueToBitMask(StateEntry::PullComPrevStep);
}
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/timing/wallcycle.h"
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
struct gmx_enerdata_t;
struct gmx_global_stat;
struct gmx_signalling_t;
* will be computed, to check none are missing. */
#define CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS (1u << 12u)
-
/*! \brief Return the number of steps that will take place between
* intra-simulation communications, given the constraints of the
* inputrec. */
-int computeGlobalCommunicationPeriod(const gmx::MDLogger& mdlog, t_inputrec* ir, const t_commrec* cr);
+int computeGlobalCommunicationPeriod(const t_inputrec* ir);
+
+/*! \brief Return the number of steps that will take place between
+ * intra-simulation communications, given the constraints of the
+ * inputrec, and write information to log.
+ * Calls computeGlobalCommunicationPeriod(ir) internally. */
+int computeGlobalCommunicationPeriod(const gmx::MDLogger& mdlog, const t_inputrec* ir, const t_commrec* cr);
void rerun_parallel_comm(t_commrec* cr, t_trxframe* fr, gmx_bool* bLastStep);
const t_mdatoms* mdatoms,
t_nrnb* nrnb,
t_vcm* vcm,
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle* wcycle,
gmx_enerdata_t* enerd,
tensor force_vir,
tensor shake_vir,
tensor total_vir,
tensor pres,
- gmx::Constraints* constr,
+ gmx::ArrayRef<real> constraintsRmsdData,
gmx::SimulationSignaller* signalCoordinator,
const matrix lastbox,
- int* totalNumberOfBondedInteractions,
gmx_bool* bSumEkinhOld,
int flags);
sfree(mdatoms_->ptype);
sfree(mdatoms_->cTC);
sfree(mdatoms_->cENER);
- sfree(mdatoms_->cACC);
sfree(mdatoms_->cFREEZE);
sfree(mdatoms_->cVCM);
sfree(mdatoms_->cORF);
double totalMassB = 0.0;
md->haveVsites = FALSE;
- gmx_mtop_atomloop_block_t aloop = gmx_mtop_atomloop_block_init(&mtop);
+ gmx_mtop_atomloop_block_t aloop = gmx_mtop_atomloop_block_init(mtop);
const t_atom* atom;
int nmol;
while (gmx_mtop_atomloop_block_next(aloop, &atom, &nmol))
totalMassA += nmol * atom->m;
totalMassB += nmol * atom->mB;
- if (atom->ptype == eptVSite)
+ if (atom->ptype == ParticleType::VSite)
{
md->haveVsites = TRUE;
}
- if (ir.efep != efepNO && PERTURBED(*atom))
+ if (ir.efep != FreeEnergyPerturbationType::No && PERTURBED(*atom))
{
md->nPerturbed++;
if (atom->mB != atom->m)
md->tmassA = totalMassA;
md->tmassB = totalMassB;
- if (ir.efep != efepNO && fp)
+ if (ir.efep != FreeEnergyPerturbationType::No && fp)
{
- fprintf(fp, "There are %d atoms and %d charges for free energy perturbation\n",
- md->nPerturbed, md->nChargePerturbed);
+ fprintf(fp,
+ "There are %d atoms and %d charges for free energy perturbation\n",
+ md->nPerturbed,
+ md->nChargePerturbed);
}
md->havePartiallyFrozenAtoms = FALSE;
}
}
- md->bOrires = (gmx_mtop_ftype_count(&mtop, F_ORIRES) != 0);
+ md->bOrires = (gmx_mtop_ftype_count(mtop, F_ORIRES) != 0);
return mdAtoms;
}
} // namespace gmx
-void atoms2md(const gmx_mtop_t* mtop,
- const t_inputrec* ir,
+void atoms2md(const gmx_mtop_t& mtop,
+ const t_inputrec& inputrec,
int nindex,
gmx::ArrayRef<int> index,
int homenr,
const t_grpopts* opts;
int nthreads gmx_unused;
- bLJPME = EVDW_PME(ir->vdwtype);
+ bLJPME = EVDW_PME(inputrec.vdwtype);
- opts = &ir->opts;
+ opts = &inputrec.opts;
- const SimulationGroups& groups = mtop->groups;
+ const SimulationGroups& groups = mtop.groups;
- auto md = mdAtoms->mdatoms();
+ auto* md = mdAtoms->mdatoms();
/* nindex>=0 indicates DD where we use an index */
if (nindex >= 0)
{
}
else
{
- md->nr = mtop->natoms;
+ md->nr = mtop.natoms;
}
if (md->nr > md->nalloc)
/* We always copy cTC with domain decomposition */
}
srenew(md->cENER, md->nalloc);
- if (opts->ngacc > 1)
- {
- srenew(md->cACC, md->nalloc);
- }
- if (inputrecFrozenAtoms(ir))
+ if (inputrecFrozenAtoms(&inputrec))
{
srenew(md->cFREEZE, md->nalloc);
}
* Therefore, when adding code, the user should use something like:
* gprnrU1 = (md->cU1==NULL ? 0 : md->cU1[localatindex])
*/
- if (!mtop->groups.groupNumbers[SimulationAtomGroupType::User1].empty())
+ if (!mtop.groups.groupNumbers[SimulationAtomGroupType::User1].empty())
{
srenew(md->cU1, md->nalloc);
}
- if (!mtop->groups.groupNumbers[SimulationAtomGroupType::User2].empty())
+ if (!mtop.groups.groupNumbers[SimulationAtomGroupType::User2].empty())
{
srenew(md->cU2, md->nalloc);
}
int molb = 0;
- nthreads = gmx_omp_nthreads_get(emntDefault);
+ nthreads = gmx_omp_nthreads_get(ModuleMultiThread::Default);
#pragma omp parallel for num_threads(nthreads) schedule(static) firstprivate(molb)
for (int i = 0; i < md->nr; i++)
{
{
md->cFREEZE[i] = getGroupType(groups, SimulationAtomGroupType::Freeze, ag);
}
- if (EI_ENERGY_MINIMIZATION(ir->eI))
+ if (EI_ENERGY_MINIMIZATION(inputrec.eI))
{
/* Displacement is proportional to F, masses used for constraints */
mA = 1.0;
mB = 1.0;
}
- else if (ir->eI == eiBD)
+ else if (inputrec.eI == IntegrationAlgorithm::BD)
{
/* With BD the physical masses are irrelevant.
* To keep the code simple we use most of the normal MD code path
* Thus with BD v*dt will give the displacement and the reported
* temperature can signal bad integration (too large time step).
*/
- if (ir->bd_fric > 0)
+ if (inputrec.bd_fric > 0)
{
- mA = 0.5 * ir->bd_fric * ir->delta_t;
- mB = 0.5 * ir->bd_fric * ir->delta_t;
+ mA = 0.5 * inputrec.bd_fric * inputrec.delta_t;
+ mB = 0.5 * inputrec.bd_fric * inputrec.delta_t;
}
else
{
/* The friction coefficient is mass/tau_t */
- fac = ir->delta_t
+ fac = inputrec.delta_t
/ opts->tau_t[md->cTC ? groups.groupNumbers[SimulationAtomGroupType::TemperatureCoupling][ag] : 0];
mA = 0.5 * atom.m * fac;
mB = 0.5 * atom.mB * fac;
else if (md->cFREEZE)
{
g = md->cFREEZE[i];
- GMX_ASSERT(opts->nFreeze != nullptr,
- "Must have freeze groups to initialize masses");
+ GMX_ASSERT(opts->nFreeze != nullptr, "Must have freeze groups to initialize masses");
if (opts->nFreeze[g][XX] && opts->nFreeze[g][YY] && opts->nFreeze[g][ZZ])
{
/* Set the mass of completely frozen particles to ALMOST_ZERO
md->typeA[i] = atom.type;
if (bLJPME)
{
- c6 = mtop->ffparams.iparams[atom.type * (mtop->ffparams.atnr + 1)].lj.c6;
- c12 = mtop->ffparams.iparams[atom.type * (mtop->ffparams.atnr + 1)].lj.c12;
- md->sqrt_c6A[i] = sqrt(c6);
+ c6 = mtop.ffparams.iparams[atom.type * (mtop.ffparams.atnr + 1)].lj.c6;
+ c12 = mtop.ffparams.iparams[atom.type * (mtop.ffparams.atnr + 1)].lj.c12;
+ md->sqrt_c6A[i] = std::sqrt(c6);
if (c6 == 0.0 || c12 == 0)
{
md->sigmaA[i] = 1.0;
md->typeB[i] = atom.typeB;
if (bLJPME)
{
- c6 = mtop->ffparams.iparams[atom.typeB * (mtop->ffparams.atnr + 1)].lj.c6;
- c12 = mtop->ffparams.iparams[atom.typeB * (mtop->ffparams.atnr + 1)].lj.c12;
- md->sqrt_c6B[i] = sqrt(c6);
+ c6 = mtop.ffparams.iparams[atom.typeB * (mtop.ffparams.atnr + 1)].lj.c6;
+ c12 = mtop.ffparams.iparams[atom.typeB * (mtop.ffparams.atnr + 1)].lj.c12;
+ md->sqrt_c6B[i] = std::sqrt(c6);
if (c6 == 0.0 || c12 == 0)
{
md->sigmaB[i] = 1.0;
md->cTC[i] = groups.groupNumbers[SimulationAtomGroupType::TemperatureCoupling][ag];
}
md->cENER[i] = getGroupType(groups, SimulationAtomGroupType::EnergyOutput, ag);
- if (md->cACC)
- {
- md->cACC[i] = groups.groupNumbers[SimulationAtomGroupType::Acceleration][ag];
- }
if (md->cVCM)
{
md->cVCM[i] = groups.groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][ag];
real L1 = 1 - lambda;
/* Update masses of perturbed atoms for the change in lambda */
- int gmx_unused nthreads = gmx_omp_nthreads_get(emntDefault);
+ int gmx_unused nthreads = gmx_omp_nthreads_get(ModuleMultiThread::Default);
#pragma omp parallel for num_threads(nthreads) schedule(static)
for (int i = 0; i < md->nr; i++)
{
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2010,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
#include "gromacs/gpu_utils/hostallocator.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/unique_cptr.h"
} // namespace gmx
-void atoms2md(const gmx_mtop_t* mtop,
- const t_inputrec* ir,
- int nindex,
- gmx::ArrayRef<int> index,
- int homenr,
- gmx::MDAtoms* mdAtoms);
-/* This routine copies the atoms->atom struct into md.
+/*! \brief This routine copies the atoms->atom struct into md.
+ *
+ * \param[in] mtop The molecular topology.
+ * \param[in] inputrec The input record.
+ * \param[in] nindex If nindex>=0 we are doing DD.
+ * \param[in] index Lookup table for global atom index.
+ * \param[in] homenr Number of atoms on this processor.
+ * \param[inout] mdAtoms Data set up by this routine.
+ *
* If index!=NULL only the indexed atoms are copied.
* For the masses the A-state (lambda=0) mass is used.
* Sets md->lambda = 0.
* In free-energy runs, update_mdatoms() should be called after atoms2md()
* to set the masses corresponding to the value of lambda at each step.
*/
+void atoms2md(const gmx_mtop_t& mtop,
+ const t_inputrec& inputrec,
+ int nindex,
+ gmx::ArrayRef<int> index,
+ int homenr,
+ gmx::MDAtoms* mdAtoms);
void update_mdatoms(t_mdatoms* md, real lambda);
/* When necessary, sets all the mass parameters to values corresponding
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "gromacs/utility/arrayref.h"
#include "mdebin_bar.h"
#include <cassert>
dh->derivative = derivative;
dh->nlambda = nlambda;
- snew(dh->lambda, nlambda);
+ dh->lambda.resize(nlambda);
for (i = 0; i < nlambda; i++)
{
assert(lambda);
}
- snew(dh->subblock_meta_d, dh->nlambda + 1);
+ dh->subblock_meta_d.resize(dh->nlambda + 1);
dh->ndhmax = ndhmax + 2;
- for (i = 0; i < 2; i++)
- {
- dh->bin[i] = nullptr;
- }
- snew(dh->dh, dh->ndhmax);
- snew(dh->dhf, dh->ndhmax);
+ dh->dh.resize(dh->ndhmax);
+ dh->dhf.resize(dh->ndhmax);
if (nbins <= 0 || dx < GMX_REAL_EPS * 10)
{
dh->nbins = nbins;
for (i = 0; i < dh->nhist; i++)
{
- snew(dh->bin[i], dh->nbins);
+ dh->bin[i].resize(dh->nbins);
}
}
mde_delta_h_reset(dh);
}
-static void done_mde_delta_h(t_mde_delta_h* dh)
-{
- sfree(dh->lambda);
- sfree(dh->subblock_meta_d);
- sfree(dh->dh);
- sfree(dh->dhf);
- for (int i = 0; i < dh->nhist; i++)
- {
- sfree(dh->bin[i]);
- }
-}
-
/* Add a value to the delta_h list */
static void mde_delta_h_add_dh(t_mde_delta_h* dh, double delta_h)
{
starting from first coord in
the main delta_h_coll) */
blk->sub[0].nr = 2;
- blk->sub[0].type = xdr_datatype_int;
- blk->sub[0].ival = dh->subblock_meta_i;
+ blk->sub[0].type = XdrDataType::Int;
+ blk->sub[0].ival = dh->subblock_meta_i.data();
/* subblock 2 */
for (i = 0; i < dh->nlambda; i++)
dh->subblock_meta_d[i] = dh->lambda[i];
}
blk->sub[1].nr = dh->nlambda;
- blk->sub[1].type = xdr_datatype_double;
- blk->sub[1].dval = dh->subblock_meta_d;
+ blk->sub[1].type = XdrDataType::Double;
+ blk->sub[1].dval = dh->subblock_meta_d.data();
/* subblock 3 */
/* check if there's actual data to be written. */
blk->sub[2].nr = dh->ndh;
/* Michael commented in 2012 that this use of explicit
- xdr_datatype_float was good for F@H for now.
+ XdrDataType::Float was good for F@H for now.
Apparently it's still good enough. */
- blk->sub[2].type = xdr_datatype_float;
+ blk->sub[2].type = XdrDataType::Float;
for (i = 0; i < dh->ndh; i++)
{
dh->dhf[i] = static_cast<float>(dh->dh[i]);
}
- blk->sub[2].fval = dh->dhf;
+ blk->sub[2].fval = dh->dhf.data();
dh->written = TRUE;
}
else
{
blk->sub[2].nr = 0;
- blk->sub[2].type = xdr_datatype_float;
+ blk->sub[2].type = XdrDataType::Float;
blk->sub[2].fval = nullptr;
}
}
}
dh->subblock_meta_d[1] = dh->dx;
blk->sub[0].nr = 2 + ((dh->nlambda > 1) ? dh->nlambda : 0);
- blk->sub[0].type = xdr_datatype_double;
- blk->sub[0].dval = dh->subblock_meta_d;
+ blk->sub[0].type = XdrDataType::Double;
+ blk->sub[0].dval = dh->subblock_meta_d.data();
/* subblock 2: the starting point(s) as a long integer */
dh->subblock_meta_l[0] = nhist_written;
dh->subblock_meta_l[k++] = dh->derivative;
blk->sub[1].nr = nhist_written + 3;
- blk->sub[1].type = xdr_datatype_int64;
- blk->sub[1].lval = dh->subblock_meta_l;
+ blk->sub[1].type = XdrDataType::Int64;
+ blk->sub[1].lval = dh->subblock_meta_l.data();
/* subblock 3 + 4 : the histogram data */
for (i = 0; i < nhist_written; i++)
{
blk->sub[i + 2].nr = dh->maxbin[i] + 1; /* it's +1 because size=index+1
in C */
- blk->sub[i + 2].type = xdr_datatype_int;
- blk->sub[i + 2].ival = dh->bin[i];
+ blk->sub[i + 2].type = XdrDataType::Int;
+ blk->sub[i + 2].ival = dh->bin[i].data();
}
}
}
/* initialize the collection*/
-void mde_delta_h_coll_init(t_mde_delta_h_coll* dhc, const t_inputrec* ir)
+t_mde_delta_h_coll::t_mde_delta_h_coll(const t_inputrec& inputrec)
{
int i, j, n;
double* lambda_vec;
- int ndhmax = ir->nstenergy / ir->nstcalcenergy;
- t_lambda* fep = ir->fepvals;
+ int ndhmax = inputrec.nstenergy / inputrec.nstcalcenergy;
+ t_lambda* fep = inputrec.fepvals.get();
- dhc->temperature = ir->opts.ref_t[0]; /* only store system temperature */
- dhc->start_time = 0.;
- dhc->delta_time = ir->delta_t * ir->fepvals->nstdhdl;
- dhc->start_time_set = FALSE;
+ temperature = inputrec.opts.ref_t[0]; /* only store system temperature */
+ start_time = 0.;
+ delta_time = inputrec.delta_t * inputrec.fepvals->nstdhdl;
+ start_time_set = FALSE;
/* this is the compatibility lambda value. If it is >=0, it is valid,
and there is either an old-style lambda or a slow growth simulation. */
- dhc->start_lambda = ir->fepvals->init_lambda;
+ start_lambda = inputrec.fepvals->init_lambda;
/* for continuous change of lambda values */
- dhc->delta_lambda = ir->fepvals->delta_lambda * ir->fepvals->nstdhdl;
+ delta_lambda = inputrec.fepvals->delta_lambda * inputrec.fepvals->nstdhdl;
- if (dhc->start_lambda < 0)
+ if (start_lambda < 0)
{
/* create the native lambda vectors */
- dhc->lambda_index = fep->init_fep_state;
- dhc->n_lambda_vec = 0;
- for (i = 0; i < efptNR; i++)
+ lambda_index = fep->init_fep_state;
+ n_lambda_vec = 0;
+ for (auto i : keysOf(fep->separate_dvdl))
{
if (fep->separate_dvdl[i])
{
- dhc->n_lambda_vec++;
+ n_lambda_vec++;
}
}
- snew(dhc->native_lambda_vec, dhc->n_lambda_vec);
- snew(dhc->native_lambda_components, dhc->n_lambda_vec);
+ native_lambda_vec.resize(n_lambda_vec);
+ native_lambda_components.resize(n_lambda_vec);
j = 0;
- for (i = 0; i < efptNR; i++)
+ for (auto i : keysOf(fep->separate_dvdl))
{
if (fep->separate_dvdl[i])
{
- dhc->native_lambda_components[j] = i;
+ native_lambda_components[j] = static_cast<int>(i);
if (fep->init_fep_state >= 0 && fep->init_fep_state < fep->n_lambda)
{
- dhc->native_lambda_vec[j] = fep->all_lambda[i][fep->init_fep_state];
+ native_lambda_vec[j] = fep->all_lambda[i][fep->init_fep_state];
}
else
{
- dhc->native_lambda_vec[j] = -1;
+ native_lambda_vec[j] = -1;
}
j++;
}
else
{
/* don't allocate the meta-data subblocks for lambda vectors */
- dhc->native_lambda_vec = nullptr;
- dhc->n_lambda_vec = 0;
- dhc->native_lambda_components = nullptr;
- dhc->lambda_index = -1;
+ n_lambda_vec = 0;
+ lambda_index = -1;
}
/* allocate metadata subblocks */
- snew(dhc->subblock_d, c_subblockDNumPreEntries + dhc->n_lambda_vec);
- snew(dhc->subblock_i, c_subblockINumPreEntries + dhc->n_lambda_vec);
+ subblock_d.resize(c_subblockDNumPreEntries + n_lambda_vec);
+ subblock_i.resize(c_subblockINumPreEntries + n_lambda_vec);
/* now decide which data to write out */
- dhc->nlambda = 0;
- dhc->ndhdl = 0;
- dhc->dh_expanded = nullptr;
- dhc->dh_energy = nullptr;
- dhc->dh_pv = nullptr;
+ nlambda = 0;
+ ndhdl = 0;
+ dh_expanded_index = -1;
+ dh_energy_index = -1;
+ dh_pv_index = -1;
/* total number of raw data point collections in the sample */
- dhc->ndh = 0;
+ ndh = 0;
{
gmx_bool bExpanded = FALSE;
/* first count the number of states */
/* add the dhdl's */
- if (fep->dhdl_derivatives == edhdlderivativesYES)
+ if (fep->dhdl_derivatives == DhDlDerivativeCalculation::Yes)
{
- for (i = 0; i < efptNR; i++)
+ for (auto i : keysOf(fep->separate_dvdl))
{
- if (ir->fepvals->separate_dvdl[i])
+ if (inputrec.fepvals->separate_dvdl[i])
{
- dhc->ndh += 1;
- dhc->ndhdl += 1;
+ ndh += 1;
+ ndhdl += 1;
}
}
}
/* add the lambdas */
- dhc->nlambda = ir->fepvals->lambda_stop_n - ir->fepvals->lambda_start_n;
- dhc->ndh += dhc->nlambda;
+ nlambda = inputrec.fepvals->lambda_stop_n - inputrec.fepvals->lambda_start_n;
+ ndh += nlambda;
/* another compatibility check */
- if (dhc->start_lambda < 0)
+ if (start_lambda < 0)
{
/* include one more for the specification of the state, by lambda or
fep_state*/
- if (ir->expandedvals->elmcmove > elmcmoveNO)
+ if (inputrec.expandedvals->elmcmove > LambdaMoveCalculation::No)
{
- dhc->ndh += 1;
+ ndh += 1;
bExpanded = TRUE;
}
/* whether to print energies */
- if (ir->fepvals->edHdLPrintEnergy != edHdLPrintEnergyNO)
+ if (inputrec.fepvals->edHdLPrintEnergy != FreeEnergyPrintEnergy::No)
{
- dhc->ndh += 1;
+ ndh += 1;
bEnergy = TRUE;
}
- if (ir->epc > epcNO)
+ if (inputrec.epc > PressureCoupling::No)
{
- dhc->ndh += 1; /* include pressure-volume work */
+ ndh += 1; /* include pressure-volume work */
bPV = TRUE;
}
}
/* allocate them */
- snew(dhc->dh, dhc->ndh);
+ dh.resize(ndh);
/* now initialize them */
/* the order, for now, must match that of the dhdl.xvg file because of
n = 0;
if (bExpanded)
{
- dhc->dh_expanded = dhc->dh + n;
- mde_delta_h_init(dhc->dh + n, ir->fepvals->dh_hist_size, ir->fepvals->dh_hist_spacing,
- ndhmax, dhbtEXPANDED, 0, 0, nullptr);
+ dh_expanded_index = n;
+ mde_delta_h_init(&dh[n],
+ inputrec.fepvals->dh_hist_size,
+ inputrec.fepvals->dh_hist_spacing,
+ ndhmax,
+ dhbtEXPANDED,
+ 0,
+ 0,
+ nullptr);
n++;
}
if (bEnergy)
{
- dhc->dh_energy = dhc->dh + n;
- mde_delta_h_init(dhc->dh + n, ir->fepvals->dh_hist_size, ir->fepvals->dh_hist_spacing,
- ndhmax, dhbtEN, 0, 0, nullptr);
+ dh_energy_index = n;
+ mde_delta_h_init(&dh[n],
+ inputrec.fepvals->dh_hist_size,
+ inputrec.fepvals->dh_hist_spacing,
+ ndhmax,
+ dhbtEN,
+ 0,
+ 0,
+ nullptr);
n++;
}
/* add the dhdl's */
n_lambda_components = 0;
- if (fep->dhdl_derivatives == edhdlderivativesYES)
+ if (fep->dhdl_derivatives == DhDlDerivativeCalculation::Yes)
{
- dhc->dh_dhdl = dhc->dh + n;
- for (i = 0; i < efptNR; i++)
+ dh_dhdl_index = n;
+ for (auto i : keysOf(fep->separate_dvdl))
{
- if (ir->fepvals->separate_dvdl[i])
+ if (inputrec.fepvals->separate_dvdl[i])
{
/* we give it init_lambda for compatibility */
- mde_delta_h_init(dhc->dh + n, ir->fepvals->dh_hist_size, ir->fepvals->dh_hist_spacing,
- ndhmax, dhbtDHDL, n_lambda_components, 1, &(fep->init_lambda));
+ mde_delta_h_init(&dh[n],
+ inputrec.fepvals->dh_hist_size,
+ inputrec.fepvals->dh_hist_spacing,
+ ndhmax,
+ dhbtDHDL,
+ n_lambda_components,
+ 1,
+ &(fep->init_lambda));
n++;
n_lambda_components++;
}
}
else
{
- for (i = 0; i < efptNR; i++)
+ for (auto i : keysOf(fep->separate_dvdl))
{
- if (ir->fepvals->separate_dvdl[i])
+ if (fep->separate_dvdl[i])
{
n_lambda_components++; /* count the components */
}
}
}
/* add the lambdas */
- dhc->dh_du = dhc->dh + n;
+ dh_du_index = n;
snew(lambda_vec, n_lambda_components);
- for (i = ir->fepvals->lambda_start_n; i < ir->fepvals->lambda_stop_n; i++)
+ for (i = inputrec.fepvals->lambda_start_n; i < inputrec.fepvals->lambda_stop_n; i++)
{
int k = 0;
- for (j = 0; j < efptNR; j++)
+ for (auto j : keysOf(fep->separate_dvdl))
{
- if (ir->fepvals->separate_dvdl[j])
+ if (fep->separate_dvdl[j])
{
lambda_vec[k++] = fep->all_lambda[j][i];
}
}
- mde_delta_h_init(dhc->dh + n, ir->fepvals->dh_hist_size, ir->fepvals->dh_hist_spacing,
- ndhmax, dhbtDH, 0, n_lambda_components, lambda_vec);
+ mde_delta_h_init(&dh[n],
+ inputrec.fepvals->dh_hist_size,
+ inputrec.fepvals->dh_hist_spacing,
+ ndhmax,
+ dhbtDH,
+ 0,
+ n_lambda_components,
+ lambda_vec);
n++;
}
sfree(lambda_vec);
if (bPV)
{
- dhc->dh_pv = dhc->dh + n;
- mde_delta_h_init(dhc->dh + n, ir->fepvals->dh_hist_size, ir->fepvals->dh_hist_spacing,
- ndhmax, dhbtPV, 0, 0, nullptr);
+ dh_pv_index = n;
+ mde_delta_h_init(&dh[n],
+ inputrec.fepvals->dh_hist_size,
+ inputrec.fepvals->dh_hist_spacing,
+ ndhmax,
+ dhbtPV,
+ 0,
+ 0,
+ nullptr);
n++;
}
}
}
-void done_mde_delta_h_coll(t_mde_delta_h_coll* dhc)
-{
- if (dhc == nullptr)
- {
- return;
- }
- sfree(dhc->native_lambda_vec);
- sfree(dhc->native_lambda_components);
- sfree(dhc->subblock_d);
- sfree(dhc->subblock_i);
- for (int i = 0; i < dhc->ndh; ++i)
- {
- done_mde_delta_h(&dhc->dh[i]);
- }
- sfree(dhc->dh);
- sfree(dhc);
-}
-
/* add a bunch of samples - note fep_state is double to allow for better data storage */
-void mde_delta_h_coll_add_dh(t_mde_delta_h_coll* dhc,
- double fep_state,
- double energy,
- double pV,
- double* dhdl,
- double* foreign_dU,
- double time)
+void mde_delta_h_coll_add_dh(t_mde_delta_h_coll* dhc,
+ double fep_state,
+ double energy,
+ double pV,
+ gmx::ArrayRef<double> dhdl,
+ double* foreign_dU,
+ double time)
{
int i;
for (i = 0; i < dhc->ndhdl; i++)
{
- mde_delta_h_add_dh(dhc->dh_dhdl + i, dhdl[i]);
+ mde_delta_h_add_dh(&dhc->dh[dhc->dh_dhdl_index + i], dhdl[i]);
}
for (i = 0; i < dhc->nlambda; i++)
{
- mde_delta_h_add_dh(dhc->dh_du + i, foreign_dU[i]);
+ mde_delta_h_add_dh(&dhc->dh[dhc->dh_du_index + i], foreign_dU[i]);
}
- if (dhc->dh_pv != nullptr)
+ if (dhc->dh_pv_index >= 0)
{
- mde_delta_h_add_dh(dhc->dh_pv, pV);
+ mde_delta_h_add_dh(&dhc->dh[dhc->dh_pv_index], pV);
}
- if (dhc->dh_energy != nullptr)
+ if (dhc->dh_energy_index >= 0)
{
- mde_delta_h_add_dh(dhc->dh_energy, energy);
+ mde_delta_h_add_dh(&dhc->dh[dhc->dh_energy_index], energy);
}
- if (dhc->dh_expanded != nullptr)
+ if (dhc->dh_expanded_index >= 0)
{
- mde_delta_h_add_dh(dhc->dh_expanded, fep_state);
+ mde_delta_h_add_dh(&dhc->dh[dhc->dh_expanded_index], fep_state);
}
}
/* only allocate lambda vector component blocks if they must be written out
for backward compatibility */
- if (dhc->native_lambda_components != nullptr)
+ if (!dhc->native_lambda_components.empty())
{
add_subblocks_enxblock(blk, 2);
}
dhc->subblock_d[3] = dhc->start_lambda; /* old-style lambda at starttime */
dhc->subblock_d[4] = dhc->delta_lambda; /* lambda diff. between samples */
/* set the lambda vector components if they exist */
- if (dhc->native_lambda_components != nullptr)
+ if (!dhc->native_lambda_components.empty())
{
for (i = 0; i < dhc->n_lambda_vec; i++)
{
}
blk->id = enxDHCOLL;
blk->sub[0].nr = c_subblockDNumPreEntries + dhc->n_lambda_vec;
- blk->sub[0].type = xdr_datatype_double;
- blk->sub[0].dval = dhc->subblock_d;
+ blk->sub[0].type = XdrDataType::Double;
+ blk->sub[0].dval = dhc->subblock_d.data();
- if (dhc->native_lambda_components != nullptr)
+ if (!dhc->native_lambda_components.empty())
{
dhc->subblock_i[0] = dhc->lambda_index;
/* set the lambda vector component IDs if they exist */
dhc->subblock_i[c_subblockINumPreEntries + i] = dhc->native_lambda_components[i];
}
blk->sub[1].nr = c_subblockINumPreEntries + dhc->n_lambda_vec;
- blk->sub[1].type = xdr_datatype_int;
- blk->sub[1].ival = dhc->subblock_i;
+ blk->sub[1].type = XdrDataType::Int;
+ blk->sub[1].ival = dhc->subblock_i.data();
}
for (i = 0; i < dhc->ndh; i++)
add_blocks_enxframe(fr, nblock);
blk = fr->block + (nblock - 1);
- mde_delta_h_handle_block(dhc->dh + i, blk);
+ mde_delta_h_handle_block(&dhc->dh[i], blk);
}
}
if (dhc->dh[i].written)
{
/* we can now throw away the data */
- mde_delta_h_reset(dhc->dh + i);
+ mde_delta_h_reset(&dhc->dh[i]);
}
}
dhc->start_time_set = FALSE;
for (int i = 0; i < dhc->ndh; i++)
{
std::vector<real>& dh = deltaH->dh[i];
- dh.resize(dhc->dh[i].ndh);
- std::copy(dhc->dh[i].dh, dhc->dh[i].dh + dhc->dh[i].ndh, dh.begin());
+ for (unsigned int j = 0; j < dhc->dh[i].ndh; j++)
+ {
+ dh.emplace_back(dhc->dh[i].dh[j]);
+ }
}
deltaH->start_time = dhc->start_time;
deltaH->start_lambda = dhc->start_lambda;
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _mdebin_bar_h
-#define _mdebin_bar_h
+#ifndef GMX_MDLIB_MDEBIN_BAR_H
+#define GMX_MDLIB_MDEBIN_BAR_H
-#include "gromacs/mdlib/energyoutput.h"
+#include "gromacs/utility/real.h"
/* The functions & data structures here describe writing
energy differences (or their histogram )for use with g_bar */
class delta_h_history_t;
struct t_enxframe;
+class energyhistory_t;
+struct t_inputrec;
+
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
/* Data for one foreign lambda, or derivative. */
typedef struct
{
- real* dh; /* the raw energy data. */
- float* dhf; /* raw difference data -- in floats, for storage. */
- unsigned int ndh; /* number of data points */
- unsigned int ndhmax; /* the maximum number of points */
-
- int nhist; /* the number of histograms. There can either be
- 0 (for no histograms)
- 1 (for 'foreign lambda' histograms)
- 2 (for derivative histograms: there's
- a 'forward' and 'backward' histogram
- containing the minimum and maximum
- values, respectively). */
- int* bin[2]; /* the histogram(s) */
- double dx; /* the histogram spacing in kJ/mol. This is the
- same for the two histograms? */
- unsigned int nbins; /* the number of bins in the histograms*/
- int64_t x0[2]; /* the starting point in units of spacing
- of the histogram */
- unsigned int maxbin[2]; /* highest bin number with data */
-
- int type; /* the block type according to dhbtDH, etc. */
- int derivative; /* The derivative direction (as an index in the lambda
- vector) if this delta_h contains derivatives */
- double* lambda; /* lambda vector (or NULL if not applicable) */
- int nlambda; /* length of the lambda vector */
- gmx_bool written; /* whether this data has already been written out */
-
- int64_t subblock_meta_l[5]; /* metadata for an mdebin subblock for
+ std::vector<real> dh; /* the raw energy data. */
+ std::vector<float> dhf; /* raw difference data -- in floats, for storage. */
+ unsigned int ndh; /* number of data points */
+ unsigned int ndhmax; /* the maximum number of points */
+
+ int nhist; /* the number of histograms. There can either be
+ 0 (for no histograms)
+ 1 (for 'foreign lambda' histograms)
+ 2 (for derivative histograms: there's
+ a 'forward' and 'backward' histogram
+ containing the minimum and maximum
+ values, respectively). */
+ std::array<std::vector<int>, 2> bin; /* the histogram(s) */
+ double dx; /* the histogram spacing in kJ/mol. This is the
+ same for the two histograms? */
+ unsigned int nbins; /* the number of bins in the histograms*/
+ std::array<int64_t, 2> x0; /* the starting point in units of spacing
+ of the histogram */
+ std::array<unsigned int, 2> maxbin; /* highest bin number with data */
+
+ int type; /* the block type according to dhbtDH, etc. */
+ int derivative; /* The derivative direction (as an index in the lambda
+ vector) if this delta_h contains derivatives */
+ std::vector<double> lambda; /* lambda vector (or NULL if not applicable) */
+ int nlambda; /* length of the lambda vector */
+ bool written; /* whether this data has already been written out */
+
+ std::array<int64_t, 5> subblock_meta_l; /* metadata for an mdebin subblock for
I/O: for histogram counts, etc.*/
- double* subblock_meta_d; /* metadata subblock for I/O, used for
+ std::vector<double> subblock_meta_d; /* metadata subblock for I/O, used for
communicating doubles (i.e. the lambda
vector) */
- int subblock_meta_i[4]; /* metadata subblock for I/O, used for
+ std::array<int, 4> subblock_meta_i; /* metadata subblock for I/O, used for
communicating ints (i.e. derivative indices,
etc.) */
} t_mde_delta_h;
/* the type definition is in mdebin_bar.h */
struct t_mde_delta_h_coll
{
- t_mde_delta_h* dh; /* the delta h data */
- int ndh; /* the number of delta_h structures */
+ t_mde_delta_h_coll(const t_inputrec& inputrec);
+
+ std::vector<t_mde_delta_h> dh; /* the delta h data */
+ int ndh; /* the number of delta_h structures */
- int nlambda; /* number of bar dU delta_h structures */
- t_mde_delta_h* dh_du; /* the delta h data (pointer into dh) */
+ int nlambda; /* number of bar dU delta_h structures */
+ int dh_du_index; /* the delta h data (index into dh) */
- int ndhdl; /* number of bar dU delta_h structures */
- t_mde_delta_h* dh_dhdl; /* the dhdl data (pointer into dh) */
+ int ndhdl; /* number of bar dU delta_h structures */
+ int dh_dhdl_index; /* the dhdl data (index into dh) */
- t_mde_delta_h* dh_energy; /* energy output block (pointer into dh) */
- t_mde_delta_h* dh_pv; /* pV output block (pointer into dh) */
- t_mde_delta_h* dh_expanded; /* expanded ensemble output block (pointer
- into dh) */
+ int dh_energy_index; /* energy output block (index into dh) */
+ int dh_pv_index; /* pV output block (index into dh) */
+ int dh_expanded_index; /* expanded ensemble output block (index into dh) */
- double start_time; /* start time of the current dh collection */
- double delta_time; /* time difference between samples */
- gmx_bool start_time_set; /* whether the start time has been set */
- double start_lambda; /* starting lambda for continuous motion of state*/
- double delta_lambda; /* delta lambda, for continuous motion of state */
- double temperature; /* the temperature of the samples*/
+ double start_time; /* start time of the current dh collection */
+ double delta_time; /* time difference between samples */
+ bool start_time_set; /* whether the start time has been set */
+ double start_lambda; /* starting lambda for continuous motion of state*/
+ double delta_lambda; /* delta lambda, for continuous motion of state */
+ double temperature; /* the temperature of the samples*/
- double* native_lambda_vec; /* The lambda vector describing the current
+ std::vector<double> native_lambda_vec; /* The lambda vector describing the current
lambda state if it is set (NULL otherwise) */
- int n_lambda_vec; /* the size of the native lambda vector */
- int* native_lambda_components; /* the native lambda (and by extension,
+ int n_lambda_vec; /* the size of the native lambda vector */
+ std::vector<int> native_lambda_components; /* the native lambda (and by extension,
foreign lambda) components in terms
of efptFEP, efptMASS, etc. */
- int lambda_index; /* the lambda_fep_state */
+ int lambda_index; /* the lambda_fep_state */
- double* subblock_d; /* for writing a metadata mdebin subblock for I/O */
- int* subblock_i; /* for writing a metadata mdebin subblock for I/O */
-
- double* lambda_vec_subblock; /* native lambda vector data subblock for
- I/O */
- int* lambda_index_subblock; /* lambda vector index data subblock for I/O */
+ std::vector<double> subblock_d; /* for writing a metadata mdebin subblock for I/O */
+ std::vector<int> subblock_i; /* for writing a metadata mdebin subblock for I/O */
};
-
-/* initialize a collection of delta h histograms/sets
- dhc = the collection
- ir = the input record */
-
-void mde_delta_h_coll_init(t_mde_delta_h_coll* dhc, const t_inputrec* ir);
-
-void done_mde_delta_h_coll(t_mde_delta_h_coll* dhc);
-
/* add a bunch of samples to the delta_h collection
dhc = the collection
dhdl = the hamiltonian derivatives
*/
/* add a bunch of samples - note fep_state is double to allow for better data storage */
-void mde_delta_h_coll_add_dh(t_mde_delta_h_coll* dhc,
- double fep_state,
- double energy,
- double pV,
- double* dhdl,
- double* foreign_dU,
- double time);
+void mde_delta_h_coll_add_dh(t_mde_delta_h_coll* dhc,
+ double fep_state,
+ double energy,
+ double pV,
+ gmx::ArrayRef<double> dhdl,
+ double* foreign_dU,
+ double time);
/* write the data associated with the du blocks collection as a collection
of mdebin blocks.
/* restore the variables from an energyhistory */
void mde_delta_h_coll_restore_energyhistory(t_mde_delta_h_coll* dhc, const delta_h_history_t* deltaH);
-#endif /* _mdebin_bar_h */
+#endif /* GMX_MDLIB_MDEBIN_BAR_H */
struct gmx_mdoutf
{
- t_fileio* fp_trn;
- t_fileio* fp_xtc;
- gmx_tng_trajectory_t tng;
- gmx_tng_trajectory_t tng_low_prec;
- int x_compression_precision; /* only used by XTC output */
- ener_file_t fp_ene;
- const char* fn_cpt;
- gmx_bool bKeepAndNumCPT;
- int eIntegrator;
- gmx_bool bExpanded;
- int elamstats;
- int simulation_part;
- FILE* fp_dhdl;
- int natoms_global;
- int natoms_x_compressed;
- const SimulationGroups* groups; /* for compressed position writing */
- gmx_wallcycle_t wcycle;
- rvec* f_global;
- gmx::IMDOutputProvider* outputProvider;
- const gmx::MdModulesNotifier* mdModulesNotifier;
- bool simulationsShareState;
- MPI_Comm mastersComm;
+ t_fileio* fp_trn;
+ t_fileio* fp_xtc;
+ gmx_tng_trajectory_t tng;
+ gmx_tng_trajectory_t tng_low_prec;
+ int x_compression_precision; /* only used by XTC output */
+ ener_file_t fp_ene;
+ const char* fn_cpt;
+ gmx_bool bKeepAndNumCPT;
+ IntegrationAlgorithm eIntegrator;
+ gmx_bool bExpanded;
+ LambdaWeightCalculation elamstats;
+ int simulation_part;
+ FILE* fp_dhdl;
+ int natoms_global;
+ int natoms_x_compressed;
+ const SimulationGroups* groups; /* for compressed position writing */
+ gmx_wallcycle* wcycle;
+ rvec* f_global;
+ gmx::IMDOutputProvider* outputProvider;
+ const gmx::MDModulesNotifiers* mdModulesNotifiers;
+ bool simulationsShareState;
+ MPI_Comm mastersComm;
};
-gmx_mdoutf_t init_mdoutf(FILE* fplog,
- int nfile,
- const t_filenm fnm[],
- const gmx::MdrunOptions& mdrunOptions,
- const t_commrec* cr,
- gmx::IMDOutputProvider* outputProvider,
- const gmx::MdModulesNotifier& mdModulesNotifier,
- const t_inputrec* ir,
- const gmx_mtop_t* top_global,
- const gmx_output_env_t* oenv,
- gmx_wallcycle_t wcycle,
- const gmx::StartingBehavior startingBehavior,
- bool simulationsShareState,
- const gmx_multisim_t* ms)
+gmx_mdoutf_t init_mdoutf(FILE* fplog,
+ int nfile,
+ const t_filenm fnm[],
+ const gmx::MdrunOptions& mdrunOptions,
+ const t_commrec* cr,
+ gmx::IMDOutputProvider* outputProvider,
+ const gmx::MDModulesNotifiers& mdModulesNotifiers,
+ const t_inputrec* ir,
+ const gmx_mtop_t& top_global,
+ const gmx_output_env_t* oenv,
+ gmx_wallcycle* wcycle,
+ const gmx::StartingBehavior startingBehavior,
+ bool simulationsShareState,
+ const gmx_multisim_t* ms)
{
gmx_mdoutf_t of;
const char * appendMode = "a+", *writeMode = "w+", *filemode;
gmx_tng_open(filename, filemode[0], &of->tng_low_prec);
if (filemode[0] == 'w')
{
- gmx_tng_prepare_low_prec_writing(of->tng_low_prec, top_global, ir);
+ gmx_tng_prepare_low_prec_writing(of->tng_low_prec, &top_global, ir);
}
bCiteTng = TRUE;
break;
gmx_tng_open(filename, filemode[0], &of->tng);
if (filemode[0] == 'w')
{
- gmx_tng_prepare_md_writing(of->tng, top_global, ir);
+ gmx_tng_prepare_md_writing(of->tng, &top_global, ir);
}
bCiteTng = TRUE;
break;
}
of->fn_cpt = opt2fn("-cpo", nfile, fnm);
- if ((ir->efep != efepNO || ir->bSimTemp) && ir->fepvals->nstdhdl > 0
- && (ir->fepvals->separate_dhdl_file == esepdhdlfileYES) && EI_DYNAMICS(ir->eI))
+ if ((ir->efep != FreeEnergyPerturbationType::No || ir->bSimTemp) && ir->fepvals->nstdhdl > 0
+ && (ir->fepvals->separate_dhdl_file == SeparateDhdlFile::Yes) && EI_DYNAMICS(ir->eI))
{
if (restartWithAppending)
{
}
outputProvider->initOutput(fplog, nfile, fnm, restartWithAppending, oenv);
- of->mdModulesNotifier = &mdModulesNotifier;
+ of->mdModulesNotifiers = &mdModulesNotifiers;
/* Set up atom counts so they can be passed to actual
trajectory-writing routines later. Also, XTC writing needs
to know what (and how many) atoms might be in the XTC
groups, and how to look up later which ones they are. */
- of->natoms_global = top_global->natoms;
- of->groups = &top_global->groups;
+ of->natoms_global = top_global.natoms;
+ of->groups = &top_global.groups;
of->natoms_x_compressed = 0;
- for (i = 0; (i < top_global->natoms); i++)
+ for (i = 0; (i < top_global.natoms); i++)
{
if (getGroupType(*of->groups, SimulationAtomGroupType::CompressedPositionOutput, i) == 0)
{
if (ir->nstfout && DOMAINDECOMP(cr))
{
- snew(of->f_global, top_global->natoms);
+ snew(of->f_global, top_global.natoms);
}
}
return of->fp_dhdl;
}
-gmx_wallcycle_t mdoutf_get_wcycle(gmx_mdoutf_t of)
+gmx_wallcycle* mdoutf_get_wcycle(gmx_mdoutf_t of)
{
return of->wcycle;
}
const t_commrec* cr,
ivec domdecCells,
int nppnodes,
- int eIntegrator,
+ IntegrationAlgorithm eIntegrator,
int simulation_part,
gmx_bool bExpanded,
- int elamstats,
+ LambdaWeightCalculation elamstats,
int64_t step,
double t,
t_state* state,
ObservablesHistory* observablesHistory,
- const gmx::MdModulesNotifier& mdModulesNotifier,
+ const gmx::MDModulesNotifiers& mdModulesNotifiers,
gmx::WriteCheckpointDataHolder* modularSimulatorCheckpointData,
bool applyMpiBarrierBeforeRename,
MPI_Comm mpiBarrierCommunicator)
int nED = (edsamhist ? edsamhist->nED : 0);
swaphistory_t* swaphist = observablesHistory->swapHistory.get();
- int eSwapCoords = (swaphist ? swaphist->eSwapCoords : eswapNO);
+ SwapType eSwapCoords = (swaphist ? swaphist->eSwapCoords : SwapType::No);
CheckpointHeaderContents headerContents = { 0,
{ 0 },
copy_ivec(domdecCells, headerContents.dd_nc);
}
- write_checkpoint_data(fp, headerContents, bExpanded, elamstats, state, observablesHistory,
- mdModulesNotifier, &outputfiles, modularSimulatorCheckpointData);
+ write_checkpoint_data(fp,
+ headerContents,
+ bExpanded,
+ elamstats,
+ state,
+ observablesHistory,
+ mdModulesNotifiers,
+ &outputfiles,
+ modularSimulatorCheckpointData);
/* we really, REALLY, want to make sure to physically write the checkpoint,
and all the files it depends on, out to disk. Because we've
#if !GMX_NO_RENAME
if (!bNumberAndKeep && !ret)
{
+ // Add a barrier before renaming to reduce chance to get out of sync (#2440)
+ // Note: Checkpoint might only exist on some ranks, so put barrier before if clause (#3919)
+ mpiBarrierBeforeRename(applyMpiBarrierBeforeRename, mpiBarrierCommunicator);
if (gmx_fexist(fn))
{
/* Rename the previous checkpoint file */
- mpiBarrierBeforeRename(applyMpiBarrierBeforeRename, mpiBarrierCommunicator);
-
std::strcpy(buf, fn);
buf[std::strlen(fn) - std::strlen(ftp2ext(fn2ftp(fn))) - 1] = '\0';
std::strcat(buf, "_prev");
* checkpoint files getting out of sync.
*/
ivec one_ivec = { 1, 1, 1 };
- write_checkpoint(of->fn_cpt, of->bKeepAndNumCPT, fplog, cr,
+ write_checkpoint(of->fn_cpt,
+ of->bKeepAndNumCPT,
+ fplog,
+ cr,
DOMAINDECOMP(cr) ? cr->dd->numCells : one_ivec,
- DOMAINDECOMP(cr) ? cr->dd->nnodes : cr->nnodes, of->eIntegrator,
- of->simulation_part, of->bExpanded, of->elamstats, step, t, state_global,
- observablesHistory, *(of->mdModulesNotifier), modularSimulatorCheckpointData,
- of->simulationsShareState, of->mastersComm);
+ DOMAINDECOMP(cr) ? cr->dd->nnodes : cr->nnodes,
+ of->eIntegrator,
+ of->simulation_part,
+ of->bExpanded,
+ of->elamstats,
+ step,
+ t,
+ state_global,
+ observablesHistory,
+ *(of->mdModulesNotifiers),
+ modularSimulatorCheckpointData,
+ of->simulationsShareState,
+ of->mastersComm);
}
void mdoutf_write_to_trajectory_files(FILE* fplog,
if (mdof_flags & (MDOF_X | MDOF_X_COMPRESSED))
{
auto globalXRef = MASTER(cr) ? state_global->x : gmx::ArrayRef<gmx::RVec>();
- dd_collect_vec(cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl,
- state_local->cg_gl, state_local->x, globalXRef);
+ dd_collect_vec(cr->dd,
+ state_local->ddp_count,
+ state_local->ddp_count_cg_gl,
+ state_local->cg_gl,
+ state_local->x,
+ globalXRef);
}
if (mdof_flags & MDOF_V)
{
auto globalVRef = MASTER(cr) ? state_global->v : gmx::ArrayRef<gmx::RVec>();
- dd_collect_vec(cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl,
- state_local->cg_gl, state_local->v, globalVRef);
+ dd_collect_vec(cr->dd,
+ state_local->ddp_count,
+ state_local->ddp_count_cg_gl,
+ state_local->cg_gl,
+ state_local->v,
+ globalVRef);
}
}
f_global = of->f_global;
if (mdof_flags & MDOF_F)
{
- dd_collect_vec(
- cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl, f_local,
- gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(of->f_global), f_local.size()));
+ auto globalFRef = MASTER(cr) ? gmx::arrayRefFromArray(
+ reinterpret_cast<gmx::RVec*>(of->f_global), of->natoms_global)
+ : gmx::ArrayRef<gmx::RVec>();
+ dd_collect_vec(cr->dd,
+ state_local->ddp_count,
+ state_local->ddp_count_cg_gl,
+ state_local->cg_gl,
+ f_local,
+ globalFRef);
}
}
else
{
if (mdof_flags & MDOF_CPT)
{
- mdoutf_write_checkpoint(of, fplog, cr, step, t, state_global, observablesHistory,
- modularSimulatorCheckpointData);
+ mdoutf_write_checkpoint(
+ of, fplog, cr, step, t, state_global, observablesHistory, modularSimulatorCheckpointData);
}
if (mdof_flags & (MDOF_X | MDOF_V | MDOF_F))
if (of->fp_trn)
{
- gmx_trr_write_frame(of->fp_trn, step, t, state_local->lambda[efptFEP],
- state_local->box, natoms, x, v, f);
+ gmx_trr_write_frame(of->fp_trn,
+ step,
+ t,
+ state_local->lambda[FreeEnergyPerturbationCouplingType::Fep],
+ state_local->box,
+ natoms,
+ x,
+ v,
+ f);
if (gmx_fio_flush(of->fp_trn) != 0)
{
gmx_file("Cannot write trajectory; maybe you are out of disk space?");
velocities and forces to it. */
else if (of->tng)
{
- gmx_fwrite_tng(of->tng, FALSE, step, t, state_local->lambda[efptFEP],
- state_local->box, natoms, x, v, f);
+ gmx_fwrite_tng(of->tng,
+ FALSE,
+ step,
+ t,
+ state_local->lambda[FreeEnergyPerturbationCouplingType::Fep],
+ state_local->box,
+ natoms,
+ x,
+ v,
+ f);
}
/* If only a TNG file is open for compressed coordinate output (no uncompressed
coordinate output) also write forces and velocities to it. */
else if (of->tng_low_prec)
{
- gmx_fwrite_tng(of->tng_low_prec, FALSE, step, t, state_local->lambda[efptFEP],
- state_local->box, natoms, x, v, f);
+ gmx_fwrite_tng(of->tng_low_prec,
+ FALSE,
+ step,
+ t,
+ state_local->lambda[FreeEnergyPerturbationCouplingType::Fep],
+ state_local->box,
+ natoms,
+ x,
+ v,
+ f);
}
}
if (mdof_flags & MDOF_X_COMPRESSED)
}
}
}
- if (write_xtc(of->fp_xtc, of->natoms_x_compressed, step, t, state_local->box, xxtc,
- of->x_compression_precision)
+ if (write_xtc(of->fp_xtc, of->natoms_x_compressed, step, t, state_local->box, xxtc, of->x_compression_precision)
== 0)
{
gmx_fatal(FARGS,
"simulation with major instabilities resulting in coordinates "
"that are NaN or too large to be represented in the XTC format.\n");
}
- gmx_fwrite_tng(of->tng_low_prec, TRUE, step, t, state_local->lambda[efptFEP],
- state_local->box, of->natoms_x_compressed, xxtc, nullptr, nullptr);
+ gmx_fwrite_tng(of->tng_low_prec,
+ TRUE,
+ step,
+ t,
+ state_local->lambda[FreeEnergyPerturbationCouplingType::Fep],
+ state_local->box,
+ of->natoms_x_compressed,
+ xxtc,
+ nullptr,
+ nullptr);
if (of->natoms_x_compressed != of->natoms_global)
{
sfree(xxtc);
}
if (mdof_flags & MDOF_LAMBDA)
{
- lambda = state_local->lambda[efptFEP];
+ lambda = state_local->lambda[FreeEnergyPerturbationCouplingType::Fep];
}
gmx_fwrite_tng(of->tng, FALSE, step, t, lambda, box, natoms, nullptr, nullptr, nullptr);
}
}
if (mdof_flags & MDOF_LAMBDA_COMPRESSED)
{
- lambda = state_local->lambda[efptFEP];
+ lambda = state_local->lambda[FreeEnergyPerturbationCouplingType::Fep];
}
- gmx_fwrite_tng(of->tng_low_prec, FALSE, step, t, lambda, box, natoms, nullptr,
- nullptr, nullptr);
+ gmx_fwrite_tng(of->tng_low_prec, FALSE, step, t, lambda, box, natoms, nullptr, nullptr, nullptr);
}
}
{
if (of->tng || of->tng_low_prec)
{
- wallcycle_start(of->wcycle, ewcTRAJ);
+ wallcycle_start(of->wcycle, WallCycleCounter::Traj);
gmx_tng_close(&of->tng);
gmx_tng_close(&of->tng_low_prec);
- wallcycle_stop(of->wcycle, ewcTRAJ);
+ wallcycle_stop(of->wcycle, WallCycleCounter::Traj);
}
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
enum class StartingBehavior;
class IMDOutputProvider;
-struct MdModulesNotifier;
+struct MDModulesNotifiers;
struct MdrunOptions;
class WriteCheckpointDataHolder;
} // namespace gmx
* Returns a pointer to a data structure with all output file pointers
* and names required by mdrun.
*/
-gmx_mdoutf_t init_mdoutf(FILE* fplog,
- int nfile,
- const t_filenm fnm[],
- const gmx::MdrunOptions& mdrunOptions,
- const t_commrec* cr,
- gmx::IMDOutputProvider* outputProvider,
- const gmx::MdModulesNotifier& mdModulesNotifier,
- const t_inputrec* ir,
- const gmx_mtop_t* mtop,
- const gmx_output_env_t* oenv,
- gmx_wallcycle_t wcycle,
- gmx::StartingBehavior startingBehavior,
- bool simulationsShareState,
- const gmx_multisim_t* ms);
+gmx_mdoutf_t init_mdoutf(FILE* fplog,
+ int nfile,
+ const t_filenm fnm[],
+ const gmx::MdrunOptions& mdrunOptions,
+ const t_commrec* cr,
+ gmx::IMDOutputProvider* outputProvider,
+ const gmx::MDModulesNotifiers& mdModulesNotifiers,
+ const t_inputrec* ir,
+ const gmx_mtop_t& mtop,
+ const gmx_output_env_t* oenv,
+ gmx_wallcycle* wcycle,
+ gmx::StartingBehavior startingBehavior,
+ bool simulationsShareState,
+ const gmx_multisim_t* ms);
/*! \brief Getter for file pointer */
ener_file_t mdoutf_get_fp_ene(gmx_mdoutf_t of);
FILE* mdoutf_get_fp_dhdl(gmx_mdoutf_t of);
/*! \brief Getter for wallcycle timer */
-gmx_wallcycle_t mdoutf_get_wcycle(gmx_mdoutf_t of);
+gmx_wallcycle* mdoutf_get_wcycle(gmx_mdoutf_t of);
/*! \brief Close TNG files if they are open.
*
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* Get the global molecule id, and the corresponding molecule type and id of the *
* molblock from the global atom nr. */
-static int get_mol_id(int at, gmx_mtop_t* mtop, int* type, int* block)
+static int get_mol_id(int at, const gmx_mtop_t& mtop, int* type, int* block)
{
int mol_id = 0;
int i;
mtopGetMolblockIndex(mtop, at, block, &mol_id, &atnr_mol);
for (i = 0; i < *block; i++)
{
- mol_id += mtop->molblock[i].nmol;
+ mol_id += mtop.molblock[i].nmol;
}
- *type = mtop->molblock[*block].type;
+ *type = mtop.molblock[*block].type;
return mol_id;
}
* level, if the same molecule type is found in another part of the system, these *
* would also be affected. Therefore we have to check if the embedded and rest group *
* share common molecule types. If so, membed will stop with an error. */
-static int get_mtype_list(t_block* at, gmx_mtop_t* mtop, t_block* tlist)
+static int get_mtype_list(t_block* at, const gmx_mtop_t& mtop, t_block* tlist)
{
int i, j, nr;
int type = 0, block = 0;
}
/* Do the actual check of the molecule types between embedded and rest group */
-static void check_types(t_block* ins_at, t_block* rest_at, gmx_mtop_t* mtop)
+static void check_types(t_block* ins_at, t_block* rest_at, const gmx_mtop_t& mtop)
{
t_block *ins_mtype, *rest_mtype;
int i, j;
"moleculetype of the molecules %s in the inserted group. Do not forget to "
"provide\n"
"an appropriate *.itp file",
- *(mtop->moltype[rest_mtype->index[j]].name),
- *(mtop->moltype[rest_mtype->index[j]].name),
- *(mtop->moltype[rest_mtype->index[j]].name));
+ *(mtop.moltype[rest_mtype->index[j]].name),
+ *(mtop.moltype[rest_mtype->index[j]].name),
+ *(mtop.moltype[rest_mtype->index[j]].name));
}
}
}
return area;
}
-static int init_mem_at(mem_t* mem_p, gmx_mtop_t* mtop, rvec* r, matrix box, pos_ins_t* pos_ins)
+static int init_mem_at(mem_t* mem_p, const gmx_mtop_t& mtop, rvec* r, matrix box, pos_ins_t* pos_ins)
{
int i, j, at, mol, nmol, nmolbox, count;
t_block* mem_a;
"so that one membrane is distributed over two periodic box images. Another "
"possibility is that\n"
"your water layer is not thick enough.\n",
- zmax, zmin);
+ zmax,
+ zmin);
}
mem_p->zmin = zmin;
mem_p->zmax = zmax;
mem_p->zmed = (zmax - zmin) / 2 + zmin;
/*number of membrane molecules in protein box*/
- nmolbox = count / mtop->moltype[mtop->molblock[block].type].atoms.nr;
+ nmolbox = count / mtop.moltype[mtop.molblock[block].type].atoms.nr;
/*membrane area within the box defined by the min and max coordinates of the embedded molecule*/
mem_area = (pos_ins->xmax[XX] - pos_ins->xmin[XX]) * (pos_ins->xmax[YY] - pos_ins->xmin[YY]);
/*rough estimate of area per lipid, assuming there is only one type of lipid in the membrane*/
pos_ins->geom_cent[i][ZZ] = mem_p->zmed;
}
- fprintf(stderr, "Embedding piece %d with center of geometry: %f %f %f\n", i,
- pos_ins->geom_cent[i][XX], pos_ins->geom_cent[i][YY], pos_ins->geom_cent[i][ZZ]);
+ fprintf(stderr,
+ "Embedding piece %d with center of geometry: %f %f %f\n",
+ i,
+ pos_ins->geom_cent[i][XX],
+ pos_ins->geom_cent[i][YY],
+ pos_ins->geom_cent[i][ZZ]);
}
fprintf(stderr, "\n");
}
/* generate the list of membrane molecules that overlap with the molecule to be embedded. *
* The molecule to be embedded is already reduced in size. */
-static int gen_rm_list(rm_t* rm_p,
- t_block* ins_at,
- t_block* rest_at,
- t_pbc* pbc,
- gmx_mtop_t* mtop,
- rvec* r,
- mem_t* mem_p,
- pos_ins_t* pos_ins,
- real probe_rad,
- int low_up_rm,
- gmx_bool bALLOW_ASYMMETRY)
+static int gen_rm_list(rm_t* rm_p,
+ t_block* ins_at,
+ t_block* rest_at,
+ t_pbc* pbc,
+ const gmx_mtop_t& mtop,
+ rvec* r,
+ mem_t* mem_p,
+ pos_ins_t* pos_ins,
+ real probe_rad,
+ int low_up_rm,
+ gmx_bool bALLOW_ASYMMETRY)
{
int i, j, k, l, at, at2, mol_id;
int type = 0, block = 0;
int* order;
r_min_rad = probe_rad * probe_rad;
- gmx::RangePartitioning molecules = gmx_mtop_molecules(*mtop);
+ gmx::RangePartitioning molecules = gmx_mtop_molecules(mtop);
snew(rm_p->block, molecules.numBlocks());
snew(rm_p->mol, molecules.numBlocks());
nrm = nupper = 0;
while (nupper != nlower)
{
mol_id = mem_p->mol_id[order[i]];
- block = get_molblock(mol_id, mtop->molblock);
+ block = get_molblock(mol_id, mtop.molblock);
bRM = TRUE;
for (l = 0; l < nrm; l++)
{
/* get input data out membed file */
try
{
- get_input(opt2fn("-membed", nfile, fnm), &xy_fac, &xy_max, &z_fac, &z_max, &it_xy,
- &it_z, &probe_rad, &low_up_rm, &maxwarn, &pieces, &bALLOW_ASYMMETRY);
+ get_input(opt2fn("-membed", nfile, fnm),
+ &xy_fac,
+ &xy_max,
+ &z_fac,
+ &z_max,
+ &it_xy,
+ &it_z,
+ &probe_rad,
+ &low_up_rm,
+ &maxwarn,
+ &pieces,
+ &bALLOW_ASYMMETRY);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
gnames.emplace_back(*groupName);
}
- atoms = gmx_mtop_global_atoms(mtop);
+ atoms = gmx_mtop_global_atoms(*mtop);
snew(mem_p, 1);
fprintf(stderr, "\nSelect a group to embed in the membrane:\n");
get_index(&atoms, opt2fn_null("-mn", nfile, fnm), 1, &(ins_at->nr), &(ins_at->index), &ins);
ins_grp_id = std::distance(gnames.begin(), found);
}
fprintf(stderr, "\nSelect a group to embed %s into (e.g. the membrane):\n", ins);
- get_index(&atoms, opt2fn_null("-mn", nfile, fnm), 1, &(mem_p->mem_at.nr),
- &(mem_p->mem_at.index), &(mem_p->name));
+ get_index(&atoms,
+ opt2fn_null("-mn", nfile, fnm),
+ 1,
+ &(mem_p->mem_at.nr),
+ &(mem_p->mem_at.index),
+ &(mem_p->name));
pos_ins->pieces = pieces;
snew(pos_ins->nidx, pieces);
if (pieces > 1)
{
fprintf(stderr, "\nSelect pieces to embed:\n");
- get_index(&atoms, opt2fn_null("-mn", nfile, fnm), pieces, pos_ins->nidx,
- pos_ins->subindex, piecename);
+ get_index(&atoms, opt2fn_null("-mn", nfile, fnm), pieces, pos_ins->nidx, pos_ins->subindex, piecename);
}
else
{
fprintf(stderr,
"\nWarning %d;\nThe number of steps used to grow the xy-coordinates of %s (%d)"
" is probably too small.\nIncrease -nxy or.\n\n",
- warn, ins, it_xy);
+ warn,
+ ins,
+ it_xy);
}
if ((it_z < min_it_z) && (z_fac < 0.99999999 || z_fac > 1.0000001))
"\nWarning %d;\nThe number of steps used to grow the z-coordinate of %s (%d)"
" is probably too small.\nIncrease -nz or the maxwarn setting in the membed "
"input file.\n\n",
- warn, ins, it_z);
+ warn,
+ ins,
+ it_z);
}
if (it_xy + it_z > inputrec->nsteps)
snew(rest_at, 1);
init_ins_at(ins_at, rest_at, state, pos_ins, groups, ins_grp_id, xy_max);
/* Check that moleculetypes in insertion group are not part of the rest of the system */
- check_types(ins_at, rest_at, mtop);
+ check_types(ins_at, rest_at, *mtop);
- init_mem_at(mem_p, mtop, state->x.rvec_array(), state->box, pos_ins);
+ init_mem_at(mem_p, *mtop, state->x.rvec_array(), state->box, pos_ins);
prot_area = est_prot_area(pos_ins, state->x.rvec_array(), ins_at, mem_p);
if ((prot_area > prot_vs_box)
printf("The estimated area of the protein in the membrane is %.3f nm^2\n", prot_area);
printf("\nThere are %d lipids in the membrane part that overlaps the protein.\n"
"The area per lipid is %.4f nm^2.\n",
- mem_p->nmol, mem_p->lip_area);
+ mem_p->nmol,
+ mem_p->lip_area);
/* Maximum number of lipids to be removed*/
max_lip_rm = static_cast<int>(2 * prot_area / mem_p->lip_area);
"This resizing will be done with respect to the geometrical center of all protein "
"atoms\n"
"that span the membrane region, i.e. z between %.3f and %.3f\n\n",
- xy_fac, z_fac, mem_p->zmin, mem_p->zmax);
+ xy_fac,
+ z_fac,
+ mem_p->zmin,
+ mem_p->zmax);
/* resize the protein by xy and by z if necessary*/
snew(r_ins, ins_at->nr);
set_pbc(pbc, inputrec->pbcType, state->box);
snew(rm_p, 1);
- lip_rm = gen_rm_list(rm_p, ins_at, rest_at, pbc, mtop, state->x.rvec_array(), mem_p,
- pos_ins, probe_rad, low_up_rm, bALLOW_ASYMMETRY);
+ lip_rm = gen_rm_list(
+ rm_p, ins_at, rest_at, pbc, *mtop, state->x.rvec_array(), mem_p, pos_ins, probe_rad, low_up_rm, bALLOW_ASYMMETRY);
lip_rm -= low_up_rm;
if (fplog)
"while %d atoms are embedded. Make sure that the atoms to be embedded are not "
"in the same"
"molecule type as atoms that are not to be embedded.\n",
- rm_bonded_at, ins_at->nr);
+ rm_bonded_at,
+ ins_at->nr);
}
if (warn > maxwarn)
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _gmx_membed_h
-#define _gmx_membed_h
+#ifndef GMX_MDLIB_MEMBED_H
+#define GMX_MDLIB_MEMBED_H
#include <cstdio>
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/* This file is completely threadsafe - keep it that way! */
-#include "gmxpre.h"
-
-#include "nsgrid.h"
-
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-
-#include <algorithm>
-
-#include "gromacs/domdec/dlb.h"
-#include "gromacs/domdec/domdec.h"
-#include "gromacs/domdec/domdec_struct.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/gmxlib/network.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/mdtypes/forcerec.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/utility/smalloc.h"
-
-/***********************************
- * Grid Routines
- ***********************************/
-
-static const char* range_warn =
- "Explanation: During neighborsearching, we assign each particle to a grid\n"
- "based on its coordinates. If your system contains collisions or parameter\n"
- "errors that give particles very high velocities you might end up with some\n"
- "coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot\n"
- "put these on a grid, so this is usually where we detect those errors.\n"
- "Make sure your system is properly energy-minimized and that the potential\n"
- "energy seems reasonable before trying again.";
-
-static void calc_x_av_stddev(int n, rvec* x, rvec av, rvec stddev)
-{
- dvec s1, s2;
- int i, d;
-
- clear_dvec(s1);
- clear_dvec(s2);
-
- for (i = 0; i < n; i++)
- {
- for (d = 0; d < DIM; d++)
- {
- s1[d] += x[i][d];
- s2[d] += x[i][d] * x[i][d];
- }
- }
-
- dsvmul(1.0 / n, s1, s1);
- dsvmul(1.0 / n, s2, s2);
-
- for (d = 0; d < DIM; d++)
- {
- av[d] = s1[d];
- stddev[d] = std::sqrt(s2[d] - s1[d] * s1[d]);
- }
-}
-
-static void get_nsgrid_boundaries_vac(real av, real stddev, real* bound0, real* bound1, real* bdens0, real* bdens1)
-{
- /* Set the grid to 2 times the standard deviation of
- * the charge group centers in both directions.
- * For a uniform bounded distribution the width is sqrt(3)*stddev,
- * so all charge groups fall within the width.
- * For a sphere stddev is r/sqrt(5): 99.2% falls within the width.
- * For a Gaussian distribution 98% fall within the width.
- */
- *bound0 = av - NSGRID_STDDEV_FAC * stddev;
- *bound1 = av + NSGRID_STDDEV_FAC * stddev;
-
- *bdens0 = av - GRID_STDDEV_FAC * stddev;
- *bdens1 = av + GRID_STDDEV_FAC * stddev;
-}
-
-static void dd_box_bounds_to_ns_bounds(real box0, real box_size, real* gr0, real* gr1)
-{
- real av, stddev;
-
- /* Redetermine av and stddev from the DD box boundaries */
- av = box0 + 0.5 * box_size;
- stddev = 0.5 * box_size / GRID_STDDEV_FAC;
-
- *gr0 = av - NSGRID_STDDEV_FAC * stddev;
- *gr1 = av + NSGRID_STDDEV_FAC * stddev;
-}
-
-void get_nsgrid_boundaries(int nboundeddim,
- matrix box,
- gmx_domdec_t* dd,
- gmx_ddbox_t* ddbox,
- rvec* gr0,
- rvec* gr1,
- int ncg,
- rvec* cgcm,
- rvec grid_x0,
- rvec grid_x1,
- real* grid_density)
-{
- rvec av, stddev;
- real vol, bdens0, bdens1;
- int d;
-
- if (nboundeddim < DIM)
- {
- calc_x_av_stddev(ncg, cgcm, av, stddev);
- }
-
- vol = 1;
- for (d = 0; d < DIM; d++)
- {
- if (d < nboundeddim)
- {
- grid_x0[d] = (gr0 != nullptr ? (*gr0)[d] : 0);
- grid_x1[d] = (gr1 != nullptr ? (*gr1)[d] : box[d][d]);
- vol *= (grid_x1[d] - grid_x0[d]);
- }
- else
- {
- if (ddbox == nullptr)
- {
- get_nsgrid_boundaries_vac(av[d], stddev[d], &grid_x0[d], &grid_x1[d], &bdens0, &bdens1);
- }
- else
- {
- /* Temporary fix which uses global ddbox boundaries
- * for unbounded dimensions.
- * Should be replaced by local boundaries, which makes
- * the ns grid smaller and does not require global comm.
- */
- dd_box_bounds_to_ns_bounds(ddbox->box0[d], ddbox->box_size[d], &grid_x0[d], &grid_x1[d]);
- bdens0 = grid_x0[d];
- bdens1 = grid_x1[d];
- }
- /* Check for a DD cell not at a lower edge */
- if (dd != nullptr && gr0 != nullptr && dd->ci[d] > 0)
- {
- grid_x0[d] = (*gr0)[d];
- bdens0 = (*gr0)[d];
- }
- /* Check for a DD cell not at a higher edge */
- if (dd != nullptr && gr1 != nullptr && dd->ci[d] < dd->numCells[d] - 1)
- {
- grid_x1[d] = (*gr1)[d];
- bdens1 = (*gr1)[d];
- }
- vol *= (bdens1 - bdens0);
- }
-
- if (debug)
- {
- fprintf(debug, "Set grid boundaries dim %d: %f %f\n", d, grid_x0[d], grid_x1[d]);
- }
- }
-
- *grid_density = ncg / vol;
-}
-
-static void set_grid_sizes(matrix box,
- rvec izones_x0,
- rvec izones_x1,
- real rlist,
- const gmx_domdec_t* dd,
- const gmx_ddbox_t* ddbox,
- t_grid* grid,
- real grid_density)
-{
- int i, j;
- gmx_bool bDD, bDDRect;
- rvec izones_size;
- real inv_r_ideal, size, add_tric, radd;
-
- for (i = 0; (i < DIM); i++)
- {
- if (debug)
- {
- fprintf(debug, "set_grid_sizes, i-zone bounds for dim %d: %6.3f %6.3f\n", i,
- izones_x0[i], izones_x1[i]);
- }
- izones_size[i] = izones_x1[i] - izones_x0[i];
- }
-
- /* Use the ideal number of cg's per cell to set the ideal cell size */
- inv_r_ideal = std::cbrt(grid_density / grid->ncg_ideal);
- if (rlist > 0 && inv_r_ideal * rlist < 1)
- {
- inv_r_ideal = 1 / rlist;
- }
- if (debug)
- {
- fprintf(debug, "CG density %f ideal ns cell size %f\n", grid_density, 1 / inv_r_ideal);
- }
-
- clear_rvec(grid->cell_offset);
- for (i = 0; (i < DIM); i++)
- {
- /* Initial settings, for DD might change below */
- grid->cell_offset[i] = izones_x0[i];
- size = izones_size[i];
-
- bDD = (dd != nullptr) && (dd->numCells[i] > 1);
- if (!bDD)
- {
- bDDRect = FALSE;
- }
- else
- {
- /* With DD grid cell jumps only the first decomposition
- * direction has uniform DD cell boundaries.
- */
- bDDRect = !((ddbox->tric_dir[i] != 0) || (dd_dlb_is_on(dd) && i != dd->dim[0]));
-
- radd = rlist;
- if (i >= ddbox->npbcdim
- && (rlist == 0 || izones_x1[i] + radd > ddbox->box0[i] + ddbox->box_size[i]))
- {
- radd = ddbox->box0[i] + ddbox->box_size[i] - izones_x1[i];
- if (radd < 0)
- {
- radd = 0;
- }
- }
-
- /* With DD we only need a grid of one DD cell size + rlist */
- if (bDDRect)
- {
- size += radd;
- }
- else
- {
- size += radd / ddbox->skew_fac[i];
- }
-
- /* Check if the cell boundary in this direction is
- * perpendicular to the Cartesian axis.
- * Since grid->npbcdim isan integer that in principle can take
- * any value, we help the compiler avoid warnings and potentially
- * optimize by ensuring that j < DIM here.
- */
- for (j = i + 1; j < grid->npbcdim && j < DIM; j++)
- {
- if (box[j][i] != 0)
- {
- /* Correct the offset for the home cell location */
- grid->cell_offset[i] += izones_x0[j] * box[j][i] / box[j][j];
-
- /* Correct the offset and size for the off-diagonal
- * displacement of opposing DD cell corners.
- */
- /* Without rouding we would need to add:
- * box[j][i]*rlist/(dd->skew_fac[i]*box[j][j])
- */
- /* Determine the shift for the corners of the triclinic box */
- add_tric = izones_size[j] * box[j][i] / box[j][j];
- if (dd->ndim == 1 && j == ZZ)
- {
- /* With 1D domain decomposition the cg's are not in
- * the triclinic box, but trilinic x-y and rectangular y-z.
- * Therefore we need to add the shift from the trilinic
- * corner to the corner at y=0.
- */
- add_tric += -box[YY][XX] * box[ZZ][YY] / box[YY][YY];
- }
- if (box[j][i] < 0)
- {
- grid->cell_offset[i] += add_tric;
- size -= add_tric;
- }
- else
- {
- size += add_tric;
- }
- }
- }
- }
- if (!bDDRect)
- {
- /* No DD or the box is triclinic is this direction:
- * we will use the normal grid ns that checks all cells
- * that are within cut-off distance of the i-particle.
- */
- grid->n[i] = gmx::roundToInt(size * inv_r_ideal);
- if (grid->n[i] < 2)
- {
- grid->n[i] = 2;
- }
- grid->cell_size[i] = size / grid->n[i];
- grid->ncpddc[i] = 0;
- }
- else
- {
- /* We use grid->ncpddc[i] such that all particles
- * in one ns cell belong to a single DD cell only.
- * We can then beforehand exclude certain ns grid cells
- * for non-home i-particles.
- */
- grid->ncpddc[i] = gmx::roundToInt(izones_size[i] * inv_r_ideal);
- if (grid->ncpddc[i] < 2)
- {
- grid->ncpddc[i] = 2;
- }
- grid->cell_size[i] = izones_size[i] / grid->ncpddc[i];
- grid->n[i] = grid->ncpddc[i] + static_cast<int>(radd / grid->cell_size[i]) + 1;
- }
- if (debug)
- {
- fprintf(debug, "grid dim %d size %d x %f: %f - %f\n", i, grid->n[i], grid->cell_size[i],
- grid->cell_offset[i], grid->cell_offset[i] + grid->n[i] * grid->cell_size[i]);
- }
- }
-
- if (debug)
- {
- fprintf(debug, "CG ncg ideal %d, actual density %.1f\n", grid->ncg_ideal,
- grid_density * grid->cell_size[XX] * grid->cell_size[YY] * grid->cell_size[ZZ]);
- }
-}
-
-t_grid* init_grid(FILE* fplog, t_forcerec* fr)
-{
- char* ptr;
- t_grid* grid;
-
- snew(grid, 1);
-
- grid->npbcdim = numPbcDimensions(fr->pbcType);
-
- if (fr->pbcType == PbcType::XY && fr->nwall == 2)
- {
- grid->nboundeddim = 3;
- }
- else
- {
- grid->nboundeddim = grid->npbcdim;
- }
-
- if (debug)
- {
- fprintf(debug, "The coordinates are bounded in %d dimensions\n", grid->nboundeddim);
- }
-
- /* The ideal number of cg's per ns grid cell seems to be 10 */
- grid->ncg_ideal = 10;
- ptr = getenv("GMX_NSCELL_NCG");
- if (ptr)
- {
- sscanf(ptr, "%d", &grid->ncg_ideal);
- if (fplog)
- {
- fprintf(fplog, "Set ncg_ideal to %d\n", grid->ncg_ideal);
- }
- if (grid->ncg_ideal <= 0)
- {
- gmx_fatal(FARGS, "The number of cg's per cell should be > 0");
- }
- }
- if (debug)
- {
- fprintf(debug, "Set ncg_ideal to %d\n", grid->ncg_ideal);
- }
-
- return grid;
-}
-
-void done_grid(t_grid* grid)
-{
- if (grid == nullptr)
- {
- return;
- }
- grid->nr = 0;
- clear_ivec(grid->n);
- grid->ncells = 0;
- sfree(grid->cell_index);
- sfree(grid->a);
- sfree(grid->index);
- sfree(grid->nra);
- grid->cells_nalloc = 0;
- sfree(grid->dcx2);
- sfree(grid->dcy2);
- sfree(grid->dcz2);
- grid->dc_nalloc = 0;
-
- if (debug)
- {
- fprintf(debug, "Successfully freed memory for grid pointers.");
- }
- sfree(grid);
-}
-
-int xyz2ci_(int nry, int nrz, int x, int y, int z)
-/* Return the cell index */
-{
- return (nry * nrz * x + nrz * y + z);
-}
-
-void ci2xyz(t_grid* grid, int i, int* x, int* y, int* z)
-/* Return x,y and z from the cell index */
-{
- int ci;
-
- range_check_mesg(i, 0, grid->nr, range_warn);
-
- ci = grid->cell_index[i];
- *x = ci / (grid->n[YY] * grid->n[ZZ]);
- ci -= (*x) * grid->n[YY] * grid->n[ZZ];
- *y = ci / grid->n[ZZ];
- ci -= (*y) * grid->n[ZZ];
- *z = ci;
-}
-
-static int ci_not_used(const ivec n)
-{
- /* Return an improbable value */
- return xyz2ci(n[YY], n[ZZ], 3 * n[XX], 3 * n[YY], 3 * n[ZZ]);
-}
-
-static void set_grid_ncg(t_grid* grid, int ncg)
-{
- int nr_old, i;
-
- grid->nr = ncg;
- if (grid->nr + 1 > grid->nr_alloc)
- {
- nr_old = grid->nr_alloc;
- grid->nr_alloc = over_alloc_dd(grid->nr) + 1;
- srenew(grid->cell_index, grid->nr_alloc);
- for (i = nr_old; i < grid->nr_alloc; i++)
- {
- grid->cell_index[i] = 0;
- }
- srenew(grid->a, grid->nr_alloc);
- }
-}
-
-void grid_first(FILE* fplog,
- t_grid* grid,
- gmx_domdec_t* dd,
- const gmx_ddbox_t* ddbox,
- matrix box,
- rvec izones_x0,
- rvec izones_x1,
- real rlist,
- real grid_density)
-{
- int i, m;
-
- set_grid_sizes(box, izones_x0, izones_x1, rlist, dd, ddbox, grid, grid_density);
-
- grid->ncells = grid->n[XX] * grid->n[YY] * grid->n[ZZ];
-
- if (grid->ncells + 1 > grid->cells_nalloc)
- {
- /* Allocate double the size so we have some headroom */
- grid->cells_nalloc = 2 * grid->ncells;
- srenew(grid->nra, grid->cells_nalloc + 1);
- srenew(grid->index, grid->cells_nalloc + 1);
-
- if (fplog)
- {
- fprintf(fplog, "Grid: %d x %d x %d cells\n", grid->n[XX], grid->n[YY], grid->n[ZZ]);
- }
- }
-
- m = std::max(grid->n[XX], std::max(grid->n[YY], grid->n[ZZ]));
- if (m > grid->dc_nalloc)
- {
- /* Allocate with double the initial size for box scaling */
- grid->dc_nalloc = 2 * m;
- srenew(grid->dcx2, grid->dc_nalloc);
- srenew(grid->dcy2, grid->dc_nalloc);
- srenew(grid->dcz2, grid->dc_nalloc);
- }
-
- grid->nr = 0;
- for (i = 0; (i < grid->ncells); i++)
- {
- grid->nra[i] = 0;
- }
-}
-
-static void calc_bor(int cg0, int cg1, int ncg, int CG0[2], int CG1[2])
-{
- if (cg1 > ncg)
- {
- CG0[0] = cg0;
- CG1[0] = ncg;
- CG0[1] = 0;
- CG1[1] = cg1 - ncg;
- }
- else
- {
- CG0[0] = cg0;
- CG1[0] = cg1;
- CG0[1] = 0;
- CG1[1] = 0;
- }
- if (debug)
- {
- int m;
-
- fprintf(debug, "calc_bor: cg0=%d, cg1=%d, ncg=%d\n", cg0, cg1, ncg);
- for (m = 0; (m < 2); m++)
- {
- fprintf(debug, "CG0[%d]=%d, CG1[%d]=%d\n", m, CG0[m], m, CG1[m]);
- }
- }
-}
-
-void calc_elemnr(t_grid* grid, int cg0, int cg1, int ncg)
-{
- int CG0[2], CG1[2];
- int* cell_index = grid->cell_index;
- int* nra = grid->nra;
- int i, m, ncells;
- int ci, not_used;
-
- ncells = grid->ncells;
- if (ncells <= 0)
- {
- gmx_fatal(FARGS, "Number of grid cells is zero. Probably the system and box collapsed.\n");
- }
-
- not_used = ci_not_used(grid->n);
-
- calc_bor(cg0, cg1, ncg, CG0, CG1);
- for (m = 0; (m < 2); m++)
- {
- for (i = CG0[m]; (i < CG1[m]); i++)
- {
- ci = cell_index[i];
- if (ci != not_used)
- {
- range_check_mesg(ci, 0, ncells, range_warn);
- nra[ci]++;
- }
- }
- }
-}
-
-void calc_ptrs(t_grid* grid)
-{
- int* index = grid->index;
- int* nra = grid->nra;
- int ix, iy, iz, ci, nr;
- int nnra, ncells;
-
- ncells = grid->ncells;
- if (ncells <= 0)
- {
- gmx_fatal(FARGS, "Number of grid cells is zero. Probably the system and box collapsed.\n");
- }
-
- ci = nr = 0;
- for (ix = 0; (ix < grid->n[XX]); ix++)
- {
- for (iy = 0; (iy < grid->n[YY]); iy++)
- {
- for (iz = 0; (iz < grid->n[ZZ]); iz++, ci++)
- {
- range_check_mesg(ci, 0, ncells, range_warn);
- index[ci] = nr;
- nnra = nra[ci];
- nr += nnra;
- nra[ci] = 0;
- }
- }
- }
-}
-
-void grid_last(t_grid* grid, int cg0, int cg1, int ncg)
-{
- int CG0[2], CG1[2];
- int i, m;
- int ci, not_used, ind, ncells;
- int* cell_index = grid->cell_index;
- int* nra = grid->nra;
- int* index = grid->index;
- int* a = grid->a;
-
- ncells = grid->ncells;
- if (ncells <= 0)
- {
- gmx_fatal(FARGS, "Number of grid cells is zero. Probably the system and box collapsed.\n");
- }
-
- not_used = ci_not_used(grid->n);
-
- calc_bor(cg0, cg1, ncg, CG0, CG1);
- for (m = 0; (m < 2); m++)
- {
- for (i = CG0[m]; (i < CG1[m]); i++)
- {
- ci = cell_index[i];
- if (ci != not_used)
- {
- range_check_mesg(ci, 0, ncells, range_warn);
- ind = index[ci] + nra[ci]++;
- range_check_mesg(ind, 0, grid->nr, range_warn);
- a[ind] = i;
- }
- }
- }
-}
-
-void fill_grid(gmx_domdec_zones_t* dd_zones, t_grid* grid, int ncg_tot, int cg0, int cg1, rvec cg_cm[])
-{
- int* cell_index;
- int nry, nrz;
- rvec n_box, offset;
- int zone, ccg0, ccg1, cg, d, not_used;
- ivec shift0, useall, b0, b1, ind;
- gmx_bool bUse;
-
- if (cg0 == -1)
- {
- /* We have already filled the grid up to grid->ncg,
- * continue from there.
- */
- cg0 = grid->nr;
- }
-
- set_grid_ncg(grid, ncg_tot);
-
- cell_index = grid->cell_index;
-
- /* Initiate cell borders */
- nry = grid->n[YY];
- nrz = grid->n[ZZ];
- for (d = 0; d < DIM; d++)
- {
- if (grid->cell_size[d] > 0)
- {
- n_box[d] = 1 / grid->cell_size[d];
- }
- else
- {
- n_box[d] = 0;
- }
- }
- copy_rvec(grid->cell_offset, offset);
-
- if (debug)
- {
- fprintf(debug, "Filling grid from %d to %d\n", cg0, cg1);
- }
-
- if (dd_zones == nullptr)
- {
- for (cg = cg0; cg < cg1; cg++)
- {
- for (d = 0; d < DIM; d++)
- {
- ind[d] = static_cast<int>((cg_cm[cg][d] - offset[d]) * n_box[d]);
- /* With pbc we should be done here.
- * Without pbc cg's outside the grid
- * should be assigned to the closest grid cell.
- */
- if (ind[d] < 0)
- {
- ind[d] = 0;
- }
- else if (ind[d] >= grid->n[d])
- {
- ind[d] = grid->n[d] - 1;
- }
- }
- cell_index[cg] = xyz2ci(nry, nrz, ind[XX], ind[YY], ind[ZZ]);
- }
- }
- else
- {
- for (zone = 0; zone < dd_zones->n; zone++)
- {
- ccg0 = dd_zones->cg_range[zone];
- ccg1 = dd_zones->cg_range[zone + 1];
- if (ccg1 <= cg0 || ccg0 >= cg1)
- {
- continue;
- }
-
- /* Determine the ns grid cell limits for this DD zone */
- for (d = 0; d < DIM; d++)
- {
- shift0[d] = dd_zones->shift[zone][d];
- useall[d] = static_cast<int>(shift0[d] == 0 || d >= grid->npbcdim);
- /* Check if we need to do normal or optimized grid assignments.
- * Normal is required for dims without DD or triclinic dims.
- * DD edge cell on dims without pbc will be automatically
- * be correct, since the shift=0 zones with have b0 and b1
- * set to the grid boundaries and there are no shift=1 zones.
- */
- if (grid->ncpddc[d] == 0)
- {
- b0[d] = 0;
- b1[d] = grid->n[d];
- }
- else
- {
- if (shift0[d] == 0)
- {
- b0[d] = 0;
- b1[d] = grid->ncpddc[d];
- }
- else
- {
- /* shift = 1 */
- b0[d] = grid->ncpddc[d];
- b1[d] = grid->n[d];
- }
- }
- }
-
- not_used = ci_not_used(grid->n);
-
- /* Put all the charge groups of this DD zone on the grid */
- for (cg = ccg0; cg < ccg1; cg++)
- {
- if (cell_index[cg] == -1)
- {
- /* This cg has moved to another node */
- cell_index[cg] = NSGRID_SIGNAL_MOVED_FAC * grid->ncells;
- continue;
- }
-
- bUse = TRUE;
- for (d = 0; d < DIM; d++)
- {
- ind[d] = static_cast<int>((cg_cm[cg][d] - offset[d]) * n_box[d]);
- /* Here we have to correct for rounding problems,
- * as this cg_cm to cell index operation is not necessarily
- * binary identical to the operation for the DD zone assignment
- * and therefore a cg could end up in an unused grid cell.
- * For dimensions without pbc we need to check
- * for cells on the edge if charge groups are beyond
- * the grid and if so, store them in the closest cell.
- */
- if (ind[d] < b0[d])
- {
- ind[d] = b0[d];
- }
- else if (ind[d] >= b1[d])
- {
- if (useall[d])
- {
- ind[d] = b1[d] - 1;
- }
- else
- {
- /* Charge groups in this DD zone further away than the cut-off
- * in direction do not participate in non-bonded interactions.
- */
- bUse = FALSE;
- }
- }
- }
- if (cg > grid->nr_alloc)
- {
- fprintf(stderr, "WARNING: nra_alloc %d cg0 %d cg1 %d cg %d\n", grid->nr_alloc,
- cg0, cg1, cg);
- }
- if (bUse)
- {
- cell_index[cg] = xyz2ci(nry, nrz, ind[XX], ind[YY], ind[ZZ]);
- }
- else
- {
- cell_index[cg] = not_used;
- }
- }
- }
- }
-}
-
-void check_grid(t_grid* grid)
-{
- int ix, iy, iz, ci, cci, nra;
-
- if (grid->ncells <= 0)
- {
- gmx_fatal(FARGS, "Number of grid cells is zero. Probably the system and box collapsed.\n");
- }
-
- ci = 0;
- cci = 0;
- for (ix = 0; (ix < grid->n[XX]); ix++)
- {
- for (iy = 0; (iy < grid->n[YY]); iy++)
- {
- for (iz = 0; (iz < grid->n[ZZ]); iz++, ci++)
- {
- if (ci > 0)
- {
- nra = grid->index[ci] - grid->index[cci];
- if (nra != grid->nra[cci])
- {
- gmx_fatal(FARGS, "nra=%d, grid->nra=%d, cci=%d", nra, grid->nra[cci], cci);
- }
- }
- cci = xyz2ci(grid->n[YY], grid->n[ZZ], ix, iy, iz);
- range_check_mesg(cci, 0, grid->ncells, range_warn);
-
- if (cci != ci)
- {
- gmx_fatal(FARGS, "ci = %d, cci = %d", ci, cci);
- }
- }
- }
- }
-}
-
-void print_grid(FILE* log, t_grid* grid)
-{
- int i, nra, index;
- int ix, iy, iz, ci;
-
- fprintf(log, "nr: %d\n", grid->nr);
- fprintf(log, "nrx: %d\n", grid->n[XX]);
- fprintf(log, "nry: %d\n", grid->n[YY]);
- fprintf(log, "nrz: %d\n", grid->n[ZZ]);
- fprintf(log, "ncg_ideal: %d\n", grid->ncg_ideal);
- fprintf(log, " i cell_index\n");
- for (i = 0; (i < grid->nr); i++)
- {
- fprintf(log, "%5d %5d\n", i, grid->cell_index[i]);
- }
- fprintf(log, "cells\n");
- fprintf(log, " ix iy iz nr index cgs...\n");
- ci = 0;
- for (ix = 0; (ix < grid->n[XX]); ix++)
- {
- for (iy = 0; (iy < grid->n[YY]); iy++)
- {
- for (iz = 0; (iz < grid->n[ZZ]); iz++, ci++)
- {
- index = grid->index[ci];
- nra = grid->nra[ci];
- fprintf(log, "%3d%3d%3d%5d%5d", ix, iy, iz, nra, index);
- for (i = 0; (i < nra); i++)
- {
- fprintf(log, "%5d", grid->a[index + i]);
- }
- fprintf(log, "\n");
- }
- }
- }
- fflush(log);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2019, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifndef GMX_MDLIB_NSGRID_H
-#define GMX_MDLIB_NSGRID_H
-
-#include <cstdio>
-
-#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/real.h"
-
-struct gmx_domdec_t;
-struct gmx_domdec_zones_t;
-struct gmx_ddbox_t;
-struct t_forcerec;
-struct t_grid;
-
-typedef struct t_grid
-{
- int nr; // Total number of charge groups
- int nboundeddim; // The number of bounded dimensions
- int npbcdim; // The number of dimensions with pbc
- int ncg_ideal; // The ideal number of cg's per cell
- ivec n; // The dimension of the grid
- int ncells; // Total number of cells
- int cells_nalloc; // Allocation size of index and nra
- ivec ncpddc; // The number of cells per DD cell
- rvec cell_size; // The size of the cells
- rvec cell_offset; // The offset of the cell (0,0,0)
- int* cell_index; // The cell number of each cg
- int* index; // The index into a for each cell
- // The location of the cell in the index
- // array can be found by calling xyz2ci
- int* nra; // The number of entries in a cell
- int icg0; // The start of the i-cg range
- int icg1; // The end of the i-cg range
- rvec* os0;
- rvec* os1;
- int* a; // The grid of cgs
- int nr_alloc; // Allocation size of cell_index and a
- real* dcx2; // Squared distance from atom to j-cell
- real* dcy2; // Squared distance from atom to j-cell
- real* dcz2; // Squared distance from atom to j-cell
- int dc_nalloc; // Allocation size of dcx2, dyc2, dcz2
-} t_grid;
-
-/*! \brief Used when estimating the interaction density.
- *
- * GRID_STDDEV_FAC * stddev estimates the interaction density. The
- * value sqrt(3) == 1.73205080757 gives a uniform load for a
- * rectangular 3D block of charge groups. For a sphere, it is not a
- * bad approximation for 4x1x1 up to 4x2x2.
- *
- * \todo It would be nicer to use sqrt(3) here, when all code that
- * includes this file is in C++, which will let us cope with the
- * std::sqrt<T> on Windows. */
-static const real GRID_STDDEV_FAC = 1.73205080757;
-
-/*! \brief The extent of the neighborsearch grid is a bit larger than sqrt(3)
- * to account for less dense regions at the edges of the system.
- */
-static const real NSGRID_STDDEV_FAC = 2.0;
-
-#define NSGRID_SIGNAL_MOVED_FAC 4
-/* A cell index of NSGRID_SIGNAL_MOVED_FAC*ncells signals
- * that a charge group moved to another DD domain.
- */
-
-t_grid* init_grid(FILE* fplog, t_forcerec* fr);
-
-void done_grid(t_grid* grid);
-
-void get_nsgrid_boundaries(int nboundeddim,
- matrix box,
- struct gmx_domdec_t* dd,
- gmx_ddbox_t* ddbox,
- rvec* gr0,
- rvec* gr1,
- int ncg,
- rvec* cgcm,
- rvec grid_x0,
- rvec grid_x1,
- real* grid_density);
-/* Return the ns grid boundaries grid_x0 and grid_x1
- * and the estimate for the grid density.
- * For non-bounded dimensions the boundaries are determined
- * from the average and std.dev. of cgcm.
- * The are determined from box, unless gr0!=NULL or gr1!=NULL,
- * then they are taken from gr0 or gr1.
- * With dd and unbounded dimensions, the proper grid borders for cells
- * on the edges are determined from cgcm.
- */
-
-void grid_first(FILE* log,
- t_grid* grid,
- struct gmx_domdec_t* dd,
- const gmx_ddbox_t* ddbox,
- matrix box,
- rvec izones_x0,
- rvec izones_x1,
- real rlong,
- real grid_density);
-
-void fill_grid(struct gmx_domdec_zones_t* dd_zones, t_grid* grid, int ncg_tot, int cg0, int cg1, rvec cg_cm[]);
-/* Allocates space on the grid for ncg_tot cg's.
- * Fills the grid with cg's from cg0 to cg1.
- * When cg0 is -1, contiues filling from grid->nr to cg1.
- */
-
-void calc_elemnr(t_grid* grid, int cg0, int cg1, int ncg);
-
-void calc_ptrs(t_grid* grid);
-
-void grid_last(t_grid* grid, int cg0, int cg1, int ncg);
-
-int xyz2ci_(int nry, int nrz, int x, int y, int z);
-#define xyz2ci(nry, nrz, x, y, z) ((nry) * (nrz) * (x) + (nrz) * (y) + (z))
-/* Return the cell index */
-
-void ci2xyz(t_grid* grid, int i, int* x, int* y, int* z);
-
-void check_grid(t_grid* grid);
-
-void print_grid(FILE* log, t_grid* grid);
-
-#endif
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
* Copyright (c) 2012,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cmath>
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/commrec.h"
gmx_bool bSimdBondeds = FALSE;
#endif
- bExcl = (ir.cutoff_scheme == ecutsGROUP && inputrecExclForces(&ir) && !EEL_FULL(ir.coulombtype));
+ bExcl = (ir.cutoff_scheme == CutoffScheme::Group && inputrecExclForces(&ir)
+ && !EEL_FULL(ir.coulombtype));
if (bSimdBondeds)
{
{
nonsimd_step_frac = 0;
}
- if (ir.epc != epcNO && 1.0 / ir.nstpcouple > nonsimd_step_frac)
+ if (ir.epc != PressureCoupling::No && 1.0 / ir.nstpcouple > nonsimd_step_frac)
{
nonsimd_step_frac = 1.0 / ir.nstpcouple;
}
const real nbnxn_refkernel_fac = 8.0;
#endif
- bQRF = (EEL_RF(ir.coulombtype) || ir.coulombtype == eelCUT);
+ bQRF = (EEL_RF(ir.coulombtype) || ir.coulombtype == CoulombInteractionType::Cut);
gmx::ArrayRef<const t_iparams> iparams = mtop.ffparams.iparams;
atnr = mtop.ffparams.atnr;
if (debug)
{
- fprintf(debug, "nqlj %d nq %d nlj %d rlist %.3f r_eff %.3f pairs per atom %.1f\n", nqlj, nq,
- nlj, ir.rlist, r_eff, nppa);
+ fprintf(debug,
+ "nqlj %d nq %d nlj %d rlist %.3f r_eff %.3f pairs per atom %.1f\n",
+ nqlj,
+ nq,
+ nlj,
+ ir.rlist,
+ r_eff,
+ nppa);
}
/* Determine the cost per pair interaction */
c_qlj = (bQRF ? c_nbnxn_qrf_lj : c_nbnxn_qexp_lj);
c_q = (bQRF ? c_nbnxn_qrf : c_nbnxn_qexp);
c_lj = c_nbnxn_lj;
- if (ir.vdw_modifier == eintmodPOTSWITCH || EVDW_PME(ir.vdwtype))
+ if (ir.vdw_modifier == InteractionModifiers::PotSwitch || EVDW_PME(ir.vdwtype))
{
c_qlj += c_nbnxn_ljexp_add;
c_lj += c_nbnxn_ljexp_add;
}
- if (EVDW_PME(ir.vdwtype) && ir.ljpme_combination_rule == eljpmeLB)
+ if (EVDW_PME(ir.vdwtype) && ir.ljpme_combination_rule == LongRangeVdW::LB)
{
/* We don't have LJ-PME LB comb. rule kernels, we use slow kernels */
c_qlj *= nbnxn_refkernel_fac;
{
double grid = ir.nkx * ir.nky * gridNkzFactor;
- int f = ((ir.efep != efepNO && bChargePerturbed) ? 2 : 1);
+ int f = ((ir.efep != FreeEnergyPerturbationType::No && bChargePerturbed) ? 2 : 1);
cost_redist += c_pme_redist * nq_tot;
cost_spread += f * c_pme_spread * nq_tot * gmx::power3(ir.pme_order);
cost_fft += f * c_pme_fft * grid * std::log(grid) / std::log(2.0);
{
double grid = ir.nkx * ir.nky * gridNkzFactor;
- int f = ((ir.efep != efepNO && bTypePerturbed) ? 2 : 1);
- if (ir.ljpme_combination_rule == eljpmeLB)
+ int f = ((ir.efep != FreeEnergyPerturbationType::No && bTypePerturbed) ? 2 : 1);
+ if (ir.ljpme_combination_rule == LongRangeVdW::LB)
{
/* LB combination rule: we have 7 mesh terms */
f *= 7;
"cost_spread %f\n"
"cost_fft %f\n"
"cost_solve %f\n",
- cost_bond, cost_pp, cost_redist, cost_spread, cost_fft, cost_solve);
+ cost_bond,
+ cost_pp,
+ cost_redist,
+ cost_spread,
+ cost_fft,
+ cost_solve);
fprintf(debug, "Estimate for relative PME load: %.3f\n", ratio);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* Copy pointer */
rbuf = b->rbuf + b->nreal;
-#if (defined __ICC && __ICC >= 1500 || defined __ICL && __ICL >= 1500) && defined __MIC__
-# pragma novector /* Work-around for incorrect vectorization */
-#endif
for (i = 0; (i < nr); i++)
{
rbuf[i] = r[i];
return index;
}
+int add_bind(t_bin* b, gmx::ArrayRef<const double> r)
+{
+ return add_bind(b, r.size(), r.data());
+}
+
void sum_bin(t_bin* b, const t_commrec* cr)
{
int i;
r[i] = rbuf[i];
}
}
+
+void extract_bind(t_bin* b, int index, gmx::ArrayRef<double> r)
+{
+ extract_bind(b, index, r.size(), r.data());
+}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int add_binr(t_bin* b, int nr, const real r[]);
int add_binr(t_bin* b, gmx::ArrayRef<const real> r);
int add_bind(t_bin* b, int nr, const double r[]);
+int add_bind(t_bin* b, gmx::ArrayRef<const double> r);
/* Add reals to the bin. Returns index */
void sum_bin(t_bin* b, const t_commrec* cr);
void extract_binr(t_bin* b, int index, int nr, real r[]);
void extract_binr(t_bin* b, int index, gmx::ArrayRef<real> r);
void extract_bind(t_bin* b, int index, int nr, double r[]);
+void extract_bind(t_bin* b, int index, gmx::ArrayRef<double> r);
/* Extract values from the bin, starting from index (see add_bin) */
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
bool resetHalfway,
real maximumHoursToRun,
const MDLogger& mdlog,
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle* wcycle,
gmx_walltime_accounting_t walltime_accounting) :
signal_(*signal),
rankCanSetSignal_(false),
t_nrnb* nrnb,
const gmx_pme_t* pme,
const pme_load_balancing_t* pme_loadbal,
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle* wcycle,
gmx_walltime_accounting_t walltime_accounting)
{
/* Reset either if signal has been passed, or if reset step has been reached */
resetGpuProfiler();
}
- wallcycle_stop(wcycle, ewcRUN);
+ wallcycle_stop(wcycle, WallCycleCounter::Run);
wallcycle_reset_all(wcycle);
if (DOMAINDECOMP(cr))
{
reset_dd_statistics_counters(cr->dd);
}
clear_nrnb(nrnb);
- wallcycle_start(wcycle, ewcRUN);
+ wallcycle_start(wcycle, WallCycleCounter::Run);
walltime_accounting_reset_time(walltime_accounting, step);
print_date_and_time(fplog, cr->nodeid, "Restarted time", gmx_gettime());
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
if (simulationNeedsReset_)
{
- if (resetCountersImpl(step, step_rel, mdlog, fplog, cr, nbv, nrnb, pme, pme_loadbal,
- wcycle, walltime_accounting))
+ if (resetCountersImpl(step, step_rel, mdlog, fplog, cr, nbv, nrnb, pme, pme_loadbal, wcycle, walltime_accounting))
{
// need to reset the counters only once
simulationNeedsReset_ = false;
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
fprintf(fplog,
"%s:\n"
"epsRF = %g, rc = %g, krf = %g, crf = %g, epsfac = %g\n",
- eel_names[eelRF], eps_rf, Rc, *krf, *crf, ONE_4PI_EPS0 / eps_r);
+ enumValueToString(CoulombInteractionType::RF),
+ eps_rf,
+ Rc,
+ *krf,
+ *crf,
+ gmx::c_one4PiEps0 / eps_r);
// Make sure we don't lose resolution in pow() by casting real arg to double
real rmin = gmx::invcbrt(static_cast<double>(*krf * 2.0));
fprintf(fplog, "The electrostatics potential has its minimum at r = %g\n", rmin);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/invertmatrix.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/constr.h"
-#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pbcutil/pbc_simd.h"
#include "gromacs/topology/idef.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
if (debug)
{
fprintf(debug, "wh =%g, rc = %g, ra = %g\n", params.wh, params.rc, params.ra);
- fprintf(debug, "rb = %g, irc2 = %g, dHH = %g, dOH = %g\n", params.rb, params.irc2,
- params.dHH, params.dOH);
+ fprintf(debug, "rb = %g, irc2 = %g, dHH = %g, dOH = %g\n", params.rb, params.irc2, params.dHH, params.dOH);
}
return params;
useSimd_(getenv("GMX_DISABLE_SIMD_KERNELS") == nullptr)
{
/* Check that we have only one settle type */
- int settle_type = -1;
- gmx_mtop_ilistloop_t iloop = gmx_mtop_ilistloop_init(mtop);
- int nmol;
- const int nral1 = 1 + NRAL(F_SETTLE);
- while (const InteractionLists* ilists = gmx_mtop_ilistloop_next(iloop, &nmol))
+ int settle_type = -1;
+ const int nral1 = 1 + NRAL(F_SETTLE);
+ for (const auto ilists : IListRange(mtop))
{
- const InteractionList& ilist = (*ilists)[F_SETTLE];
+ const InteractionList& ilist = ilists.list()[F_SETTLE];
for (int i = 0; i < ilist.size(); i += nral1)
{
if (settle_type == -1)
parametersAllMasses1_ = settleParameters(1.0, 1.0, 1.0, 1.0, dOH, dHH);
}
-void SettleData::setConstraints(const InteractionList& il_settle,
- const int numHomeAtoms,
- const real* masses,
- const real* inverseMasses)
+void SettleData::setConstraints(const InteractionList& il_settle,
+ const int numHomeAtoms,
+ gmx::ArrayRef<const real> masses,
+ gmx::ArrayRef<const real> inverseMasses)
{
#if GMX_SIMD_HAVE_REAL
const int pack_size = GMX_SIMD_REAL_WIDTH;
{
int firstO = iatoms[1];
int firstH = iatoms[2];
- parametersMassWeighted_ = settleParameters(
- masses[firstO], masses[firstH], inverseMasses[firstO], inverseMasses[firstH],
- parametersAllMasses1_.dOH, parametersAllMasses1_.dHH);
+ parametersMassWeighted_ = settleParameters(masses[firstO],
+ masses[firstH],
+ inverseMasses[firstO],
+ inverseMasses[firstH],
+ parametersAllMasses1_.dOH,
+ parametersAllMasses1_.dHH);
}
const int paddedSize = ((nsettle + pack_size - 1) / pack_size) * pack_size;
set_pbc_simd(pbc, pbcSimd);
settleTemplateWrapper<SimdReal, SimdBool, GMX_SIMD_REAL_WIDTH, const real*>(
- settled, nthread, thread, pbcSimd, xPtr, xprimePtr, invdt, vPtr, bCalcVirial,
- vir_r_m_dr, bErrorHasOccurred);
+ settled, nthread, thread, pbcSimd, xPtr, xprimePtr, invdt, vPtr, bCalcVirial, vir_r_m_dr, bErrorHasOccurred);
}
else
#endif
pbcNonNull = &pbcNo;
}
- settleTemplateWrapper<real, bool, 1, const t_pbc*>(settled, nthread, thread, pbcNonNull,
- &xPtr[0], &xprimePtr[0], invdt, &vPtr[0],
- bCalcVirial, vir_r_m_dr, bErrorHasOccurred);
+ settleTemplateWrapper<real, bool, 1, const t_pbc*>(
+ settled, nthread, thread, pbcNonNull, &xPtr[0], &xprimePtr[0], invdt, &vPtr[0], bCalcVirial, vir_r_m_dr, bErrorHasOccurred);
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
SettleData(const gmx_mtop_t& mtop);
//! Sets the constraints from the interaction list and the masses
- void setConstraints(const InteractionList& il_settle,
- int numHomeAtoms,
- const real* masses,
- const real* inverseMasses);
+ void setConstraints(const InteractionList& il_settle,
+ int numHomeAtoms,
+ gmx::ArrayRef<const real> masses,
+ gmx::ArrayRef<const real> inverseMasses);
//! Returns settle parameters for constraining coordinates and forces
const SettleParameters& parametersMassWeighted() const { return parametersMassWeighted_; }
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief Implements SETTLE using GPU
+ *
+ * This file contains implementation for the data management of GPU version of SETTLE constraints algorithm.
+ *
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ *
+ * \ingroup module_mdlib
+ */
+#include "gmxpre.h"
+
+#include "settle_gpu.h"
+
+#include <assert.h>
+#include <stdio.h>
+
+#include <cmath>
+
+#include <algorithm>
+
+#include "gromacs/gpu_utils/devicebuffer.h"
+#include "gromacs/gpu_utils/gputraits.h"
+#include "gromacs/math/functions.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/settle_gpu_internal.h"
+#include "gromacs/pbcutil/pbc.h"
+
+namespace gmx
+{
+
+void SettleGpu::apply(const DeviceBuffer<Float3> d_x,
+ DeviceBuffer<Float3> d_xp,
+ const bool updateVelocities,
+ DeviceBuffer<Float3> d_v,
+ const real invdt,
+ const bool computeVirial,
+ tensor virialScaled,
+ const PbcAiuc pbcAiuc)
+{
+
+ // Early exit if no settles
+ if (numSettles_ == 0)
+ {
+ return;
+ }
+
+ if (computeVirial)
+ {
+ // Fill with zeros so the values can be reduced to it
+ // Only 6 values are needed because virial is symmetrical
+ clearDeviceBufferAsync(&d_virialScaled_, 0, 6, deviceStream_);
+ }
+
+ launchSettleGpuKernel(numSettles_,
+ d_atomIds_,
+ settleParameters_,
+ d_x,
+ d_xp,
+ updateVelocities,
+ d_v,
+ invdt,
+ computeVirial,
+ d_virialScaled_,
+ pbcAiuc,
+ deviceStream_);
+
+
+ if (computeVirial)
+ {
+ copyFromDeviceBuffer(
+ h_virialScaled_.data(), &d_virialScaled_, 0, 6, deviceStream_, GpuApiCallBehavior::Sync, nullptr);
+
+ // Mapping [XX, XY, XZ, YY, YZ, ZZ] internal format to a tensor object
+ virialScaled[XX][XX] += h_virialScaled_[0];
+ virialScaled[XX][YY] += h_virialScaled_[1];
+ virialScaled[XX][ZZ] += h_virialScaled_[2];
+
+ virialScaled[YY][XX] += h_virialScaled_[1];
+ virialScaled[YY][YY] += h_virialScaled_[3];
+ virialScaled[YY][ZZ] += h_virialScaled_[4];
+
+ virialScaled[ZZ][XX] += h_virialScaled_[2];
+ virialScaled[ZZ][YY] += h_virialScaled_[4];
+ virialScaled[ZZ][ZZ] += h_virialScaled_[5];
+ }
+
+ return;
+}
+
+SettleGpu::SettleGpu(const gmx_mtop_t& mtop, const DeviceContext& deviceContext, const DeviceStream& deviceStream) :
+ deviceContext_(deviceContext),
+ deviceStream_(deviceStream)
+{
+ static_assert(sizeof(real) == sizeof(float),
+ "Real numbers should be in single precision in GPU code.");
+
+ // This is to prevent the assertion failure for the systems without water
+ int totalSettles = 0;
+ for (unsigned mt = 0; mt < mtop.moltype.size(); mt++)
+ {
+ const int nral1 = 1 + NRAL(F_SETTLE);
+ InteractionList interactionList = mtop.moltype[mt].ilist[F_SETTLE];
+ std::vector<int> iatoms = interactionList.iatoms;
+ totalSettles += iatoms.size() / nral1;
+ }
+ if (totalSettles == 0)
+ {
+ return;
+ }
+
+ // TODO This should be lifted to a separate subroutine that gets the values of Oxygen and
+ // Hydrogen masses, checks if they are consistent across the topology and if there is no more
+ // than two values for each mass if the free energy perturbation is enabled. In later case,
+ // masses may need to be updated on a regular basis (i.e. in set(...) method).
+ // TODO Do the checks for FEP
+ real mO = -1.0;
+ real mH = -1.0;
+
+ for (unsigned mt = 0; mt < mtop.moltype.size(); mt++)
+ {
+ const int nral1 = 1 + NRAL(F_SETTLE);
+ InteractionList interactionList = mtop.moltype[mt].ilist[F_SETTLE];
+ std::vector<int> iatoms = interactionList.iatoms;
+ for (unsigned i = 0; i < iatoms.size() / nral1; i++)
+ {
+ WaterMolecule settler;
+ settler.ow1 = iatoms[i * nral1 + 1]; // Oxygen index
+ settler.hw2 = iatoms[i * nral1 + 2]; // First hydrogen index
+ settler.hw3 = iatoms[i * nral1 + 3]; // Second hydrogen index
+ t_atom ow1 = mtop.moltype[mt].atoms.atom[settler.ow1];
+ t_atom hw2 = mtop.moltype[mt].atoms.atom[settler.hw2];
+ t_atom hw3 = mtop.moltype[mt].atoms.atom[settler.hw3];
+
+ if (mO < 0)
+ {
+ mO = ow1.m;
+ }
+ if (mH < 0)
+ {
+ mH = hw2.m;
+ }
+ GMX_RELEASE_ASSERT(mO == ow1.m,
+ "Topology has different values for oxygen mass. Should be identical "
+ "in order to use SETTLE.");
+ GMX_RELEASE_ASSERT(hw2.m == hw3.m && hw2.m == mH,
+ "Topology has different values for hydrogen mass. Should be "
+ "identical in order to use SETTLE.");
+ }
+ }
+
+ GMX_RELEASE_ASSERT(mO > 0, "Could not find oxygen mass in the topology. Needed in SETTLE.");
+ GMX_RELEASE_ASSERT(mH > 0, "Could not find hydrogen mass in the topology. Needed in SETTLE.");
+
+ // TODO Very similar to SETTLE initialization on CPU. Should be lifted to a separate method
+ // (one that gets dOH and dHH values and checks them for consistency)
+ int settle_type = -1;
+ for (unsigned mt = 0; mt < mtop.moltype.size(); mt++)
+ {
+ const int nral1 = 1 + NRAL(F_SETTLE);
+ InteractionList interactionList = mtop.moltype[mt].ilist[F_SETTLE];
+ for (int i = 0; i < interactionList.size(); i += nral1)
+ {
+ if (settle_type == -1)
+ {
+ settle_type = interactionList.iatoms[i];
+ }
+ else if (interactionList.iatoms[i] != settle_type)
+ {
+ gmx_fatal(FARGS,
+ "The [molecules] section of your topology specifies more than one block "
+ "of\n"
+ "a [moleculetype] with a [settles] block. Only one such is allowed.\n"
+ "If you are trying to partition your solvent into different *groups*\n"
+ "(e.g. for freezing, T-coupling, etc.), you are using the wrong "
+ "approach. Index\n"
+ "files specify groups. Otherwise, you may wish to change the least-used\n"
+ "block of molecules with SETTLE constraints into 3 normal constraints.");
+ }
+ }
+ }
+
+ GMX_RELEASE_ASSERT(settle_type >= 0, "settle_init called without settles");
+
+ real dOH = mtop.ffparams.iparams[settle_type].settle.doh;
+ real dHH = mtop.ffparams.iparams[settle_type].settle.dhh;
+
+ settleParameters_ = settleParameters(mO, mH, 1.0 / mO, 1.0 / mH, dOH, dHH);
+
+ allocateDeviceBuffer(&d_virialScaled_, 6, deviceContext_);
+ h_virialScaled_.resize(6);
+}
+
+SettleGpu::~SettleGpu()
+{
+ // Early exit if there is no settles
+ if (numSettles_ == 0)
+ {
+ return;
+ }
+ freeDeviceBuffer(&d_virialScaled_);
+ if (numAtomIdsAlloc_ > 0)
+ {
+ freeDeviceBuffer(&d_atomIds_);
+ }
+}
+
+void SettleGpu::set(const InteractionDefinitions& idef)
+{
+ const int nral1 = 1 + NRAL(F_SETTLE);
+ const InteractionList& il_settle = idef.il[F_SETTLE];
+ ArrayRef<const int> iatoms = il_settle.iatoms;
+ numSettles_ = il_settle.size() / nral1;
+
+ reallocateDeviceBuffer(&d_atomIds_, numSettles_, &numAtomIds_, &numAtomIdsAlloc_, deviceContext_);
+ h_atomIds_.resize(numSettles_);
+ for (int i = 0; i < numSettles_; i++)
+ {
+ WaterMolecule settler;
+ settler.ow1 = iatoms[i * nral1 + 1]; // Oxygen index
+ settler.hw2 = iatoms[i * nral1 + 2]; // First hydrogen index
+ settler.hw3 = iatoms[i * nral1 + 3]; // Second hydrogen index
+ h_atomIds_[i] = settler;
+ }
+ copyToDeviceBuffer(
+ &d_atomIds_, h_atomIds_.data(), 0, numSettles_, deviceStream_, GpuApiCallBehavior::Sync, nullptr);
+}
+
+} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* \ingroup module_mdlib
*/
-#ifndef GMX_MDLIB_SETTLE_GPU_CUH
-#define GMX_MDLIB_SETTLE_GPU_CUH
+#ifndef GMX_MDLIB_SETTLE_GPU_H
+#define GMX_MDLIB_SETTLE_GPU_H
#include "gmxpre.h"
+#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/gpu_utils/device_context.h"
#include "gromacs/gpu_utils/device_stream.h"
-#include "gromacs/gpu_utils/gputraits.cuh"
+#include "gromacs/gpu_utils/gputraits.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/invertmatrix.h"
#include "gromacs/math/vec.h"
namespace gmx
{
+//! Indices of atoms in a water molecule
+struct WaterMolecule
+{
+ //! Oxygen atom
+ int ow1;
+ //! First hydrogen atom
+ int hw2;
+ //! Second hydrogen atom
+ int hw3;
+};
+
+
/*! \internal \brief Class with interfaces and data for GPU version of SETTLE. */
class SettleGpu
{
* \param[in,out] virialScaled Scaled virial tensor to be updated.
* \param[in] pbcAiuc PBC data.
*/
- void apply(const float3* d_x,
- float3* d_xp,
- const bool updateVelocities,
- float3* d_v,
- const real invdt,
- const bool computeVirial,
- tensor virialScaled,
- const PbcAiuc pbcAiuc);
+ void apply(const DeviceBuffer<Float3> d_x,
+ DeviceBuffer<Float3> d_xp,
+ const bool updateVelocities,
+ DeviceBuffer<Float3> d_v,
+ const real invdt,
+ const bool computeVirial,
+ tensor virialScaled,
+ const PbcAiuc pbcAiuc);
/*! \brief
* Update data-structures (e.g. after NB search step).
//! Scaled virial tensor (9 reals, GPU)
std::vector<float> h_virialScaled_;
//! Scaled virial tensor (9 reals, GPU)
- float* d_virialScaled_;
+ DeviceBuffer<float> d_virialScaled_;
//! Number of settles
int numSettles_ = 0;
- //! Indexes of atoms (.x for oxygen, .y and.z for hydrogens, CPU)
- std::vector<int3> h_atomIds_;
- //! Indexes of atoms (.x for oxygen, .y and.z for hydrogens, GPU)
- int3* d_atomIds_;
+ //! Indexes of atoms (.i for oxygen, .j and.k for hydrogens, CPU)
+ std::vector<WaterMolecule> h_atomIds_;
+ //! Indexes of atoms (.i for oxygen, .j and.k for hydrogens, GPU)
+ DeviceBuffer<WaterMolecule> d_atomIds_;
//! Current size of the array of atom IDs
int numAtomIds_ = -1;
//! Allocated size for the array of atom IDs
} // namespace gmx
-#endif // GMX_MDLIB_SETTLE_GPU_CUH
+#endif // GMX_MDLIB_SETTLE_GPU_H
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
/*! \internal \file
*
- * \brief Implements SETTLE using CUDA
- *
- * This file contains implementation of SETTLE constraints algorithm
- * using CUDA, including class initialization, data-structures management
- * and GPU kernel.
+ * \brief CUDA-specific routines for the GPU implementation of SETTLE constraints algorithm.
*
*
* \author Artem Zhmurov <zhmurov@gmail.com>
*/
#include "gmxpre.h"
-#include "settle_gpu.cuh"
+#include "settle_gpu_internal.h"
#include <assert.h>
#include <stdio.h>
#include "gromacs/gpu_utils/cuda_arch_utils.cuh"
#include "gromacs/gpu_utils/cudautils.cuh"
#include "gromacs/gpu_utils/devicebuffer.h"
-#include "gromacs/gpu_utils/gputraits.cuh"
+#include "gromacs/gpu_utils/gputraits.h"
+#include "gromacs/gpu_utils/typecasts.cuh"
#include "gromacs/gpu_utils/vectype_ops.cuh"
+#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pbcutil/pbc_aiuc_cuda.cuh"
{
//! Number of CUDA threads in a block
-constexpr static int c_threadsPerBlock = 256;
+constexpr static int sc_threadsPerBlock = 256;
+
//! Maximum number of threads in a block (for __launch_bounds__)
-constexpr static int c_maxThreadsPerBlock = c_threadsPerBlock;
+constexpr static int sc_maxThreadsPerBlock = sc_threadsPerBlock;
/*! \brief SETTLE constraints kernel
*
* \param [in] pbcAiuc Periodic boundary conditions data.
*/
template<bool updateVelocities, bool computeVirial>
-__launch_bounds__(c_maxThreadsPerBlock) __global__
+__launch_bounds__(sc_maxThreadsPerBlock) __global__
void settle_kernel(const int numSettles,
- const int3* __restrict__ gm_settles,
+ const WaterMolecule* __restrict__ gm_settles,
const SettleParameters pars,
const float3* __restrict__ gm_x,
float3* __restrict__ gm_xprime,
{
// These are the indexes of three atoms in a single 'water' molecule.
// TODO Can be reduced to one integer if atoms are consecutive in memory.
- int3 indices = gm_settles[tid];
+ WaterMolecule indices = gm_settles[tid];
- float3 x_ow1 = gm_x[indices.x];
- float3 x_hw2 = gm_x[indices.y];
- float3 x_hw3 = gm_x[indices.z];
+ float3 x_ow1 = gm_x[indices.ow1];
+ float3 x_hw2 = gm_x[indices.hw2];
+ float3 x_hw3 = gm_x[indices.hw3];
- float3 xprime_ow1 = gm_xprime[indices.x];
- float3 xprime_hw2 = gm_xprime[indices.y];
- float3 xprime_hw3 = gm_xprime[indices.z];
+ float3 xprime_ow1 = gm_xprime[indices.ow1];
+ float3 xprime_hw2 = gm_xprime[indices.hw2];
+ float3 xprime_hw3 = gm_xprime[indices.hw3];
float3 dist21 = pbcDxAiuc(pbcAiuc, x_hw2, x_ow1);
float3 dist31 = pbcDxAiuc(pbcAiuc, x_hw3, x_ow1);
const float3 dxHw2 = b3 - b1;
const float3 dxHw3 = c3 - c1;
- gm_xprime[indices.x] = xprime_ow1 + dxOw1;
- gm_xprime[indices.y] = xprime_hw2 + dxHw2;
- gm_xprime[indices.z] = xprime_hw3 + dxHw3;
+ gm_xprime[indices.ow1] = xprime_ow1 + dxOw1;
+ gm_xprime[indices.hw2] = xprime_hw2 + dxHw2;
+ gm_xprime[indices.hw3] = xprime_hw3 + dxHw3;
if (updateVelocities)
{
- float3 v_ow1 = gm_v[indices.x];
- float3 v_hw2 = gm_v[indices.y];
- float3 v_hw3 = gm_v[indices.z];
+ float3 v_ow1 = gm_v[indices.ow1];
+ float3 v_hw2 = gm_v[indices.hw2];
+ float3 v_hw3 = gm_v[indices.hw3];
/* Add the position correction divided by dt to the velocity */
v_ow1 = dxOw1 * invdt + v_ow1;
v_hw2 = dxHw2 * invdt + v_hw2;
v_hw3 = dxHw3 * invdt + v_hw3;
- gm_v[indices.x] = v_ow1;
- gm_v[indices.y] = v_hw2;
- gm_v[indices.z] = v_hw3;
+ gm_v[indices.ow1] = v_ow1;
+ gm_v[indices.hw2] = v_hw2;
+ gm_v[indices.hw3] = v_hw3;
}
if (computeVirial)
return kernelPtr;
}
-void SettleGpu::apply(const float3* d_x,
- float3* d_xp,
- const bool updateVelocities,
- float3* d_v,
- const real invdt,
- const bool computeVirial,
- tensor virialScaled,
- const PbcAiuc pbcAiuc)
+void launchSettleGpuKernel(const int numSettles,
+ const DeviceBuffer<WaterMolecule> d_atomIds,
+ const SettleParameters settleParameters,
+ const DeviceBuffer<Float3> d_x,
+ DeviceBuffer<Float3> d_xp,
+ const bool updateVelocities,
+ DeviceBuffer<Float3> d_v,
+ const real invdt,
+ const bool computeVirial,
+ DeviceBuffer<float> virialScaled,
+ const PbcAiuc pbcAiuc,
+ const DeviceStream& deviceStream)
{
-
- ensureNoPendingDeviceError("In CUDA version SETTLE");
-
- // Early exit if no settles
- if (numSettles_ == 0)
- {
- return;
- }
-
- if (computeVirial)
- {
- // Fill with zeros so the values can be reduced to it
- // Only 6 values are needed because virial is symmetrical
- clearDeviceBufferAsync(&d_virialScaled_, 0, 6, deviceStream_);
- }
+ static_assert(
+ gmx::isPowerOfTwo(sc_threadsPerBlock),
+ "Number of threads per block should be a power of two in order for reduction to work.");
auto kernelPtr = getSettleKernelPtr(updateVelocities, computeVirial);
KernelLaunchConfig config;
- config.blockSize[0] = c_threadsPerBlock;
+ config.blockSize[0] = sc_threadsPerBlock;
config.blockSize[1] = 1;
config.blockSize[2] = 1;
- config.gridSize[0] = (numSettles_ + c_threadsPerBlock - 1) / c_threadsPerBlock;
+ config.gridSize[0] = (numSettles + sc_threadsPerBlock - 1) / sc_threadsPerBlock;
config.gridSize[1] = 1;
config.gridSize[2] = 1;
+
// Shared memory is only used for virial reduction
if (computeVirial)
{
- config.sharedMemorySize = c_threadsPerBlock * 6 * sizeof(float);
+ config.sharedMemorySize = sc_threadsPerBlock * 6 * sizeof(float);
}
else
{
config.sharedMemorySize = 0;
}
- const auto kernelArgs = prepareGpuKernelArguments(kernelPtr, config, &numSettles_, &d_atomIds_,
- &settleParameters_, &d_x, &d_xp, &invdt, &d_v,
- &d_virialScaled_, &pbcAiuc);
-
- launchGpuKernel(kernelPtr, config, deviceStream_, nullptr,
- "settle_kernel<updateVelocities, computeVirial>", kernelArgs);
-
- if (computeVirial)
- {
- copyFromDeviceBuffer(h_virialScaled_.data(), &d_virialScaled_, 0, 6, deviceStream_,
- GpuApiCallBehavior::Sync, nullptr);
-
- // Mapping [XX, XY, XZ, YY, YZ, ZZ] internal format to a tensor object
- virialScaled[XX][XX] += h_virialScaled_[0];
- virialScaled[XX][YY] += h_virialScaled_[1];
- virialScaled[XX][ZZ] += h_virialScaled_[2];
-
- virialScaled[YY][XX] += h_virialScaled_[1];
- virialScaled[YY][YY] += h_virialScaled_[3];
- virialScaled[YY][ZZ] += h_virialScaled_[4];
-
- virialScaled[ZZ][XX] += h_virialScaled_[2];
- virialScaled[ZZ][YY] += h_virialScaled_[4];
- virialScaled[ZZ][ZZ] += h_virialScaled_[5];
- }
+ const auto kernelArgs = prepareGpuKernelArguments(kernelPtr,
+ config,
+ &numSettles,
+ &d_atomIds,
+ &settleParameters,
+ asFloat3Pointer(&d_x),
+ asFloat3Pointer(&d_xp),
+ &invdt,
+ asFloat3Pointer(&d_v),
+ &virialScaled,
+ &pbcAiuc);
+
+ launchGpuKernel(kernelPtr,
+ config,
+ deviceStream,
+ nullptr,
+ "settle_kernel<updateVelocities, computeVirial>",
+ kernelArgs);
return;
}
-SettleGpu::SettleGpu(const gmx_mtop_t& mtop, const DeviceContext& deviceContext, const DeviceStream& deviceStream) :
- deviceContext_(deviceContext),
- deviceStream_(deviceStream)
-{
- static_assert(sizeof(real) == sizeof(float),
- "Real numbers should be in single precision in GPU code.");
- static_assert(
- c_threadsPerBlock > 0 && ((c_threadsPerBlock & (c_threadsPerBlock - 1)) == 0),
- "Number of threads per block should be a power of two in order for reduction to work.");
-
- // This is to prevent the assertion failure for the systems without water
- int totalSettles = 0;
- for (unsigned mt = 0; mt < mtop.moltype.size(); mt++)
- {
- const int nral1 = 1 + NRAL(F_SETTLE);
- InteractionList interactionList = mtop.moltype.at(mt).ilist[F_SETTLE];
- std::vector<int> iatoms = interactionList.iatoms;
- totalSettles += iatoms.size() / nral1;
- }
- if (totalSettles == 0)
- {
- return;
- }
-
- // TODO This should be lifted to a separate subroutine that gets the values of Oxygen and
- // Hydrogen masses, checks if they are consistent across the topology and if there is no more
- // than two values for each mass if the free energy perturbation is enabled. In later case,
- // masses may need to be updated on a regular basis (i.e. in set(...) method).
- // TODO Do the checks for FEP
- real mO = -1.0;
- real mH = -1.0;
-
- for (unsigned mt = 0; mt < mtop.moltype.size(); mt++)
- {
- const int nral1 = 1 + NRAL(F_SETTLE);
- InteractionList interactionList = mtop.moltype.at(mt).ilist[F_SETTLE];
- std::vector<int> iatoms = interactionList.iatoms;
- for (unsigned i = 0; i < iatoms.size() / nral1; i++)
- {
- int3 settler;
- settler.x = iatoms[i * nral1 + 1]; // Oxygen index
- settler.y = iatoms[i * nral1 + 2]; // First hydrogen index
- settler.z = iatoms[i * nral1 + 3]; // Second hydrogen index
- t_atom ow1 = mtop.moltype.at(mt).atoms.atom[settler.x];
- t_atom hw2 = mtop.moltype.at(mt).atoms.atom[settler.y];
- t_atom hw3 = mtop.moltype.at(mt).atoms.atom[settler.z];
-
- if (mO < 0)
- {
- mO = ow1.m;
- }
- if (mH < 0)
- {
- mH = hw2.m;
- }
- GMX_RELEASE_ASSERT(mO == ow1.m,
- "Topology has different values for oxygen mass. Should be identical "
- "in order to use SETTLE.");
- GMX_RELEASE_ASSERT(hw2.m == hw3.m && hw2.m == mH,
- "Topology has different values for hydrogen mass. Should be "
- "identical in order to use SETTLE.");
- }
- }
-
- GMX_RELEASE_ASSERT(mO > 0, "Could not find oxygen mass in the topology. Needed in SETTLE.");
- GMX_RELEASE_ASSERT(mH > 0, "Could not find hydrogen mass in the topology. Needed in SETTLE.");
-
- // TODO Very similar to SETTLE initialization on CPU. Should be lifted to a separate method
- // (one that gets dOH and dHH values and checks them for consistency)
- int settle_type = -1;
- for (unsigned mt = 0; mt < mtop.moltype.size(); mt++)
- {
- const int nral1 = 1 + NRAL(F_SETTLE);
- InteractionList interactionList = mtop.moltype.at(mt).ilist[F_SETTLE];
- for (int i = 0; i < interactionList.size(); i += nral1)
- {
- if (settle_type == -1)
- {
- settle_type = interactionList.iatoms[i];
- }
- else if (interactionList.iatoms[i] != settle_type)
- {
- gmx_fatal(FARGS,
- "The [molecules] section of your topology specifies more than one block "
- "of\n"
- "a [moleculetype] with a [settles] block. Only one such is allowed.\n"
- "If you are trying to partition your solvent into different *groups*\n"
- "(e.g. for freezing, T-coupling, etc.), you are using the wrong "
- "approach. Index\n"
- "files specify groups. Otherwise, you may wish to change the least-used\n"
- "block of molecules with SETTLE constraints into 3 normal constraints.");
- }
- }
- }
-
- GMX_RELEASE_ASSERT(settle_type >= 0, "settle_init called without settles");
-
- real dOH = mtop.ffparams.iparams[settle_type].settle.doh;
- real dHH = mtop.ffparams.iparams[settle_type].settle.dhh;
-
- settleParameters_ = settleParameters(mO, mH, 1.0 / mO, 1.0 / mH, dOH, dHH);
-
- allocateDeviceBuffer(&d_virialScaled_, 6, deviceContext_);
- h_virialScaled_.resize(6);
-}
-
-SettleGpu::~SettleGpu()
-{
- // Early exit if there is no settles
- if (numSettles_ == 0)
- {
- return;
- }
- freeDeviceBuffer(&d_virialScaled_);
- if (numAtomIdsAlloc_ > 0)
- {
- freeDeviceBuffer(&d_atomIds_);
- }
-}
-
-void SettleGpu::set(const InteractionDefinitions& idef)
-{
- const int nral1 = 1 + NRAL(F_SETTLE);
- const InteractionList& il_settle = idef.il[F_SETTLE];
- ArrayRef<const int> iatoms = il_settle.iatoms;
- numSettles_ = il_settle.size() / nral1;
-
- reallocateDeviceBuffer(&d_atomIds_, numSettles_, &numAtomIds_, &numAtomIdsAlloc_, deviceContext_);
- h_atomIds_.resize(numSettles_);
- for (int i = 0; i < numSettles_; i++)
- {
- int3 settler;
- settler.x = iatoms[i * nral1 + 1]; // Oxygen index
- settler.y = iatoms[i * nral1 + 2]; // First hydrogen index
- settler.z = iatoms[i * nral1 + 3]; // Second hydrogen index
- h_atomIds_.at(i) = settler;
- }
- copyToDeviceBuffer(&d_atomIds_, h_atomIds_.data(), 0, numSettles_, deviceStream_,
- GpuApiCallBehavior::Sync, nullptr);
-}
-
} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief Declares backend-specific functions for GPU implementation of SETTLE.
+ *
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ *
+ * \ingroup module_mdlib
+ */
+#ifndef GMX_MDLIB_SETTLE_GPU_INTERNAL_H
+#define GMX_MDLIB_SETTLE_GPU_INTERNAL_H
+
+#include "gromacs/gpu_utils/devicebuffer_datatype.h"
+#include "gromacs/gpu_utils/gputraits.h"
+#include "gromacs/mdlib/settle_gpu.h"
+
+namespace gmx
+{
+
+/*! \brief Apply SETTLE.
+ *
+ * Applies SETTLE to coordinates and velocities, stored on GPU. Data at pointers d_xp and
+ * d_v change in the GPU memory. The results are not automatically copied back to the CPU
+ * memory. Method uses this class data structures which should be updated when needed using
+ * update method.
+ *
+ * \param[in] numSettles Number of SETTLE constraints.
+ * \param[in] d_atomIds Device buffer with indices of atoms to be SETTLEd.
+ * \param[in] settleParameters Parameters for SETTLE constraints.
+ * \param[in] d_x Coordinates before timestep (in GPU memory)
+ * \param[in,out] d_xp Coordinates after timestep (in GPU memory). The
+ * resulting constrained coordinates will be saved here.
+ * \param[in] updateVelocities If the velocities should be updated.
+ * \param[in,out] d_v Velocities to update (in GPU memory, can be nullptr
+ * if not updated)
+ * \param[in] invdt Reciprocal timestep (to scale Lagrange
+ * multipliers when velocities are updated)
+ * \param[in] computeVirial If virial should be updated.
+ * \param[in,out] virialScaled Scaled virial tensor to be updated.
+ * \param[in] pbcAiuc PBC data.
+ * \param[in] deviceStream Device stream to launch kernel in.
+ */
+void launchSettleGpuKernel(int numSettles,
+ const DeviceBuffer<WaterMolecule> d_atomIds,
+ const SettleParameters settleParameters,
+ const DeviceBuffer<Float3> d_x,
+ DeviceBuffer<Float3> d_xp,
+ const bool updateVelocities,
+ DeviceBuffer<Float3> d_v,
+ const real invdt,
+ const bool computeVirial,
+ DeviceBuffer<float> virialScaled,
+ const PbcAiuc pbcAiuc,
+ const DeviceStream& deviceStream);
+
+} // namespace gmx
+
+#endif // GMX_MDLIB_SETTLE_GPU_INTERNAL_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief SYCL-specific routines for the GPU implementation of SETTLE constraints algorithm.
+ *
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ *
+ * \ingroup module_mdlib
+ */
+
+#include "settle_gpu_internal.h"
+
+#include "gromacs/utility/gmxassert.h"
+
+namespace gmx
+{
+
+void launchSettleGpuKernel(const int /* numSettles */,
+ const DeviceBuffer<WaterMolecule> /* d_atomIds */,
+ const SettleParameters /* settleParameters */,
+ const DeviceBuffer<Float3> /* d_x */,
+ DeviceBuffer<Float3> /* d_xp */,
+ const bool /* updateVelocities */,
+ DeviceBuffer<Float3> /* d_v */,
+ const real /* invdt */,
+ const bool /* computeVirial */,
+ DeviceBuffer<float> /* virialScaled */,
+ const PbcAiuc /* pbcAiuc */,
+ const DeviceStream& /* deviceStream */)
+{
+ // SYCL_TODO
+ GMX_RELEASE_ASSERT(false, "SETTLE is not yet implemented in SYCL.");
+
+ return;
+}
+
+} // namespace gmx
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/invblock.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
fprintf(fp, "%s\n", title);
for (i = 0; (i < nsb); i++)
{
- fprintf(fp, "i: %5d, iatom: (%5d %5d %5d), blocknr: %5d\n", i, sb[i].iatom[0],
- sb[i].iatom[1], sb[i].iatom[2], sb[i].blocknr);
+ fprintf(fp,
+ "i: %5d, iatom: (%5d %5d %5d), blocknr: %5d\n",
+ i,
+ sb[i].iatom[0],
+ sb[i].iatom[1],
+ sb[i].iatom[2],
+ sb[i].blocknr);
}
}
ArrayRef<const RVec> initial_displacements,
ArrayRef<const real> half_of_reduced_mass,
real omega,
- const real invmass[],
+ ArrayRef<const real> invmass,
ArrayRef<const real> distance_squared_tolerance,
ArrayRef<real> scaled_lagrange_multiplier,
int* nerror)
ArrayRef<const RVec> rij,
ArrayRef<const real> m2,
real omega,
- const real invmass[],
+ ArrayRef<const real> invmass,
ArrayRef<const real> distance_squared_tolerance,
ArrayRef<real> scaled_lagrange_multiplier,
int* nerror,
//! Applies SHAKE
static int vec_shakef(FILE* fplog,
shakedata* shaked,
- const real invmass[],
+ ArrayRef<const real> invmass,
int ncon,
ArrayRef<const t_iparams> ip,
const int* iatom,
switch (econq)
{
case ConstraintVariable::Positions:
- cshake(iatom, ncon, &nit, maxnit, constraint_distance_squared, prime, pbc, rij,
- half_of_reduced_mass, omega, invmass, distance_squared_tolerance,
- scaled_lagrange_multiplier, &error);
+ cshake(iatom,
+ ncon,
+ &nit,
+ maxnit,
+ constraint_distance_squared,
+ prime,
+ pbc,
+ rij,
+ half_of_reduced_mass,
+ omega,
+ invmass,
+ distance_squared_tolerance,
+ scaled_lagrange_multiplier,
+ &error);
break;
case ConstraintVariable::Velocities:
- crattle(iatom, ncon, &nit, maxnit, constraint_distance_squared, prime, rij,
- half_of_reduced_mass, omega, invmass, distance_squared_tolerance,
- scaled_lagrange_multiplier, &error, invdt);
+ crattle(iatom,
+ ncon,
+ &nit,
+ maxnit,
+ constraint_distance_squared,
+ prime,
+ rij,
+ half_of_reduced_mass,
+ omega,
+ invmass,
+ distance_squared_tolerance,
+ scaled_lagrange_multiplier,
+ &error,
+ invdt);
break;
default: gmx_incons("Unknown constraint quantity for SHAKE");
}
fprintf(fplog,
"Inner product between old and new vector <= 0.0!\n"
"constraint #%d atoms %d and %d\n",
- error - 1, iatom[3 * (error - 1) + 1] + 1, iatom[3 * (error - 1) + 2] + 1);
+ error - 1,
+ iatom[3 * (error - 1) + 1] + 1,
+ iatom[3 * (error - 1) + 2] + 1);
}
fprintf(stderr,
"Inner product between old and new vector <= 0.0!\n"
"constraint #%d atoms %d and %d\n",
- error - 1, iatom[3 * (error - 1) + 1] + 1, iatom[3 * (error - 1) + 2] + 1);
+ error - 1,
+ iatom[3 * (error - 1) + 1] + 1,
+ iatom[3 * (error - 1) + 2] + 1);
nit = 0;
}
const t_pbc* pbc,
ArrayRef<const t_iparams> ip,
const int* iatom,
- const real invmass[],
+ ArrayRef<const real> invmass,
ConstraintVariable econq)
{
int ai, aj;
rvec_sub(prime[ai], prime[aj], dx);
}
dp = norm(dx);
- fprintf(log, "%5d %5.2f %5d %5.2f %10.5f %10.5f %10.5f\n", ai + 1,
- 1.0 / invmass[ai], aj + 1, 1.0 / invmass[aj], d, dp, ip[ia[0]].constr.dA);
+ fprintf(log,
+ "%5d %5.2f %5d %5.2f %10.5f %10.5f %10.5f\n",
+ ai + 1,
+ 1.0 / invmass[ai],
+ aj + 1,
+ 1.0 / invmass[aj],
+ d,
+ dp,
+ ip[ia[0]].constr.dA);
break;
case ConstraintVariable::Velocities:
rvec_sub(v[ai], v[aj], dv);
d = iprod(dx, dv);
rvec_sub(prime[ai], prime[aj], dv);
dp = iprod(dx, dv);
- fprintf(log, "%5d %5.2f %5d %5.2f %10.5f %10.5f %10.5f\n", ai + 1,
- 1.0 / invmass[ai], aj + 1, 1.0 / invmass[aj], d, dp, 0.);
+ fprintf(log,
+ "%5d %5.2f %5d %5.2f %10.5f %10.5f %10.5f\n",
+ ai + 1,
+ 1.0 / invmass[ai],
+ aj + 1,
+ 1.0 / invmass[aj],
+ d,
+ dp,
+ 0.);
break;
default: gmx_incons("Unknown constraint quantity for SHAKE");
}
//! Applies SHAKE.
static bool bshakef(FILE* log,
shakedata* shaked,
- const real invmass[],
+ ArrayRef<const real> invmass,
const InteractionDefinitions& idef,
const t_inputrec& ir,
ArrayRef<const RVec> x_s,
{
blen = (shaked->sblock[i + 1] - shaked->sblock[i]);
blen /= 3;
- n0 = vec_shakef(log, shaked, invmass, blen, idef.iparams, iatoms, ir.shake_tol, x_s, prime,
- pbc, shaked->omega, ir.efep != efepNO, lambda, lam, invdt, v, bCalcVir,
- vir_r_m_dr, econq);
+ n0 = vec_shakef(log,
+ shaked,
+ invmass,
+ blen,
+ idef.iparams,
+ iatoms,
+ ir.shake_tol,
+ x_s,
+ prime,
+ pbc,
+ shaked->omega,
+ ir.efep != FreeEnergyPerturbationType::No,
+ lambda,
+ lam,
+ invdt,
+ v,
+ bCalcVir,
+ vir_r_m_dr,
+ econq);
if (n0 == 0)
{
/* only for position part? */
if (econq == ConstraintVariable::Positions)
{
- if (ir.efep != efepNO)
+ if (ir.efep != FreeEnergyPerturbationType::No)
{
ArrayRef<const t_iparams> iparams = idef.iparams;
bool constrain_shake(FILE* log,
shakedata* shaked,
- const real invmass[],
+ ArrayRef<const real> invmass,
const InteractionDefinitions& idef,
const t_inputrec& ir,
ArrayRef<const RVec> x_s,
switch (econq)
{
case (ConstraintVariable::Positions):
- bOK = bshakef(log, shaked, invmass, idef, ir, x_s, xprime, pbc, nrnb, lambda, dvdlambda,
- invdt, v, bCalcVir, vir_r_m_dr, bDumpOnError, econq);
+ bOK = bshakef(
+ log, shaked, invmass, idef, ir, x_s, xprime, pbc, nrnb, lambda, dvdlambda, invdt, v, bCalcVir, vir_r_m_dr, bDumpOnError, econq);
break;
case (ConstraintVariable::Velocities):
- bOK = bshakef(log, shaked, invmass, idef, ir, x_s, vprime, pbc, nrnb, lambda, dvdlambda,
- invdt, {}, bCalcVir, vir_r_m_dr, bDumpOnError, econq);
+ bOK = bshakef(log,
+ shaked,
+ invmass,
+ idef,
+ ir,
+ x_s,
+ vprime,
+ pbc,
+ nrnb,
+ lambda,
+ dvdlambda,
+ invdt,
+ {},
+ bCalcVir,
+ vir_r_m_dr,
+ bDumpOnError,
+ econq);
break;
default:
gmx_fatal(FARGS,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* sblock[n] to sblock[n+1]. Array sblock should be large enough.
* Return TRUE when OK, FALSE when shake-error
*/
-bool constrain_shake(FILE* log, /* Log file */
- shakedata* shaked, /* Total number of atoms */
- const real invmass[], /* Atomic masses */
- const InteractionDefinitions& idef, /* The interaction def */
- const t_inputrec& ir, /* Input record */
- ArrayRef<const RVec> x_s, /* Coords before update */
- ArrayRef<RVec> xprime, /* Output coords when constraining x */
- ArrayRef<RVec> vprime, /* Output coords when constraining v */
- const t_pbc* pbc, /* PBC information */
- t_nrnb* nrnb, /* Performance measure */
- real lambda, /* FEP lambda */
+bool constrain_shake(FILE* log, /* Log file */
+ shakedata* shaked, /* Total number of atoms */
+ gmx::ArrayRef<const real> invmass, /* Atomic masses */
+ const InteractionDefinitions& idef, /* The interaction def */
+ const t_inputrec& ir, /* Input record */
+ ArrayRef<const RVec> x_s, /* Coords before update */
+ ArrayRef<RVec> xprime, /* Output coords when constraining x */
+ ArrayRef<RVec> vprime, /* Output coords when constraining v */
+ const t_pbc* pbc, /* PBC information */
+ t_nrnb* nrnb, /* Performance measure */
+ real lambda, /* FEP lambda */
real* dvdlambda, /* FEP force */
real invdt, /* 1/delta_t */
ArrayRef<RVec> v, /* Also constrain v if not empty */
ArrayRef<const RVec> rij,
ArrayRef<const real> half_of_reduced_mass,
real omega,
- const real invmass[],
+ ArrayRef<const real> invmass,
ArrayRef<const real> distance_squared_tolerance,
ArrayRef<real> scaled_lagrange_multiplier,
int* nerror);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2012,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <csignal>
#include <cstdlib>
+#include "gromacs/utility/enumerationhelpers.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
-const char* gmx_stop_cond_name[] = { "None", "Stop at the next neighbor search step",
- "Stop at the next step", "Abort" };
+const char* enumValueToString(StopCondition enumValue)
+{
+ constexpr gmx::EnumerationArray<StopCondition, const char*> stopConditionNames = {
+ "None", "Stop at the next neighbor search step", "Stop at the next step", "Abort"
+ };
+ return stopConditionNames[enumValue];
+}
/* these do not neccesarily match the stop condition, but are
referred to in the signal handler. */
-static const char* gmx_signal_name[] = {
+static const char* const gmx_signal_name[] = {
"None", "INT", "TERM", "second INT/TERM", "remote INT/TERM", "remote second INT/TERM",
"USR1", "Abort"
};
-static volatile sig_atomic_t stop_condition = gmx_stop_cond_none;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static volatile StopCondition stop_condition = StopCondition::None;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static volatile sig_atomic_t last_signal_name = 0;
-
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static volatile sig_atomic_t usr_condition = 0;
void gmx_reset_stop_condition()
{
- stop_condition = gmx_stop_cond_none;
+ stop_condition = StopCondition::None;
// last_signal_name and usr_condition are left untouched by reset.
}
case SIGTERM:
case SIGINT:
/* we explicitly set things up to allow this: */
- stop_condition++;
+ switch (stop_condition)
+ {
+ case StopCondition::None: stop_condition = StopCondition::NextNS; break;
+ case StopCondition::NextNS: stop_condition = StopCondition::Next; break;
+ case StopCondition::Next: stop_condition = StopCondition::Abort; break;
+ default: GMX_THROW(gmx::InternalError("Stop condition increased beyond abort"));
+ }
if (n == SIGINT)
{
last_signal_name = 1;
{
last_signal_name = 2;
}
- if (stop_condition == gmx_stop_cond_next)
+ if (stop_condition == StopCondition::Next)
{
last_signal_name = 3;
}
- if (stop_condition >= gmx_stop_cond_abort)
+ if (stop_condition >= StopCondition::Abort)
{
abort();
}
#endif
}
-gmx_stop_cond_t gmx_get_stop_condition()
+StopCondition gmx_get_stop_condition()
{
- return static_cast<gmx_stop_cond_t>(stop_condition);
+ return stop_condition;
}
-void gmx_set_stop_condition(gmx_stop_cond_t recvd_stop_cond)
+void gmx_set_stop_condition(StopCondition recvd_stop_cond)
{
if (recvd_stop_cond > stop_condition)
{
stop_condition = recvd_stop_cond;
- if (stop_condition == gmx_stop_cond_next_ns)
+ if (stop_condition == StopCondition::NextNS)
{
last_signal_name = 4;
}
- if (stop_condition == gmx_stop_cond_next)
+ if (stop_condition == StopCondition::Next)
{
last_signal_name = 5;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/basedefinitions.h"
+#include <csignal>
+
/* NOTE: the terminology is:
incoming signals (provided by the operating system, or transmitted from
other nodes) lead to stop conditions. These stop conditions should be
/* the stop conditions. They are explicitly allowed to be compared against
each other. */
-typedef enum
+enum class StopCondition : sig_atomic_t
{
- gmx_stop_cond_none = 0,
- gmx_stop_cond_next_ns, /* stop a the next neighbour searching step */
- gmx_stop_cond_next, /* stop a the next step */
- gmx_stop_cond_abort /* stop now. (this should never be seen) */
-} gmx_stop_cond_t;
+ None = 0,
+ NextNS, /* stop a the next neighbour searching step */
+ Next, /* stop a the next step */
+ Abort, /* stop now. (this should never be seen) */
+ Count
+};
/* Our names for the stop conditions.
These must match the number given in gmx_stop_cond_t.*/
-extern const char* gmx_stop_cond_name[];
+const char* enumValueToString(StopCondition enumValue);
/* the externally visible functions: */
void signal_handler_install();
/* get the current stop condition */
-gmx_stop_cond_t gmx_get_stop_condition();
+StopCondition gmx_get_stop_condition();
/* set the stop condition upon receiving a remote one */
-void gmx_set_stop_condition(gmx_stop_cond_t recvd_stop_cond);
+void gmx_set_stop_condition(StopCondition recvd_stop_cond);
/*!
* \brief Reinitializes the global stop condition.
#include "gromacs/ewald/pme_pp_comm_gpu.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
-#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
#include "gromacs/gmxlib/nonbonded/nonbonded.h"
+#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/imd/imd.h"
#include "gromacs/listed_forces/disre.h"
GMX_ASSERT(f.size() >= forceToAdd.size(), "Accumulation buffer should be sufficiently large");
const int end = forceToAdd.size();
- int gmx_unused nt = gmx_omp_nthreads_get(emntDefault);
+ int gmx_unused nt = gmx_omp_nthreads_get(ModuleMultiThread::Default);
#pragma omp parallel for num_threads(nt) schedule(static)
for (int i = 0; i < end; i++)
{
PbcType pbcType)
{
/* The short-range virial from surrounding boxes */
- const rvec* fshift = as_rvec_array(forceWithShiftForces.shiftForces().data());
- calc_vir(SHIFTS, fr->shift_vec, fshift, vir_part, pbcType == PbcType::Screw, box);
- inc_nrnb(nrnb, eNR_VIRIAL, SHIFTS);
+ const rvec* fshift = as_rvec_array(forceWithShiftForces.shiftForces().data());
+ const rvec* shiftVecPointer = as_rvec_array(fr->shift_vec.data());
+ calc_vir(gmx::c_numShiftVectors, shiftVecPointer, fshift, vir_part, pbcType == PbcType::Screw, box);
+ inc_nrnb(nrnb, eNR_VIRIAL, gmx::c_numShiftVectors);
/* Calculate partial virial, for local atoms only, based on short range.
* Total virial is computed in global_stat, called from do_md
}
static void pull_potential_wrapper(const t_commrec* cr,
- const t_inputrec* ir,
+ const t_inputrec& ir,
const matrix box,
gmx::ArrayRef<const gmx::RVec> x,
gmx::ForceWithVirial* force,
pull_t* pull_work,
const real* lambda,
double t,
- gmx_wallcycle_t wcycle)
+ gmx_wallcycle* wcycle)
{
t_pbc pbc;
real dvdl;
/* Calculate the center of mass forces, this requires communication,
* which is why pull_potential is called close to other communication.
*/
- wallcycle_start(wcycle, ewcPULLPOT);
- set_pbc(&pbc, ir->pbcType, box);
+ wallcycle_start(wcycle, WallCycleCounter::PullPot);
+ set_pbc(&pbc, ir.pbcType, box);
dvdl = 0;
enerd->term[F_COM_PULL] +=
- pull_potential(pull_work, mdatoms->massT, &pbc, cr, t, lambda[efptRESTRAINT],
- as_rvec_array(x.data()), force, &dvdl);
- enerd->dvdl_lin[efptRESTRAINT] += dvdl;
- wallcycle_stop(wcycle, ewcPULLPOT);
+ pull_potential(pull_work,
+ gmx::arrayRefFromArray(mdatoms->massT, mdatoms->nr),
+ &pbc,
+ cr,
+ t,
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Restraint)],
+ x,
+ force,
+ &dvdl);
+ enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Restraint] += dvdl;
+ wallcycle_stop(wcycle, WallCycleCounter::PullPot);
}
static void pme_receive_force_ener(t_forcerec* fr,
gmx_enerdata_t* enerd,
bool useGpuPmePpComms,
bool receivePmeForceToGpu,
- gmx_wallcycle_t wcycle)
+ gmx_wallcycle* wcycle)
{
real e_q, e_lj, dvdl_q, dvdl_lj;
float cycles_ppdpme, cycles_seppme;
- cycles_ppdpme = wallcycle_stop(wcycle, ewcPPDURINGPME);
+ cycles_ppdpme = wallcycle_stop(wcycle, WallCycleCounter::PpDuringPme);
dd_cycles_add(cr->dd, cycles_ppdpme, ddCyclPPduringPME);
/* In case of node-splitting, the PP nodes receive the long-range
* forces, virial and energy from the PME nodes here.
*/
- wallcycle_start(wcycle, ewcPP_PMEWAITRECVF);
+ wallcycle_start(wcycle, WallCycleCounter::PpPmeWaitRecvF);
dvdl_q = 0;
dvdl_lj = 0;
- gmx_pme_receive_f(fr->pmePpCommGpu.get(), cr, forceWithVirial, &e_q, &e_lj, &dvdl_q, &dvdl_lj,
- useGpuPmePpComms, receivePmeForceToGpu, &cycles_seppme);
+ gmx_pme_receive_f(fr->pmePpCommGpu.get(),
+ cr,
+ forceWithVirial,
+ &e_q,
+ &e_lj,
+ &dvdl_q,
+ &dvdl_lj,
+ useGpuPmePpComms,
+ receivePmeForceToGpu,
+ &cycles_seppme);
enerd->term[F_COUL_RECIP] += e_q;
enerd->term[F_LJ_RECIP] += e_lj;
- enerd->dvdl_lin[efptCOUL] += dvdl_q;
- enerd->dvdl_lin[efptVDW] += dvdl_lj;
+ enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Coul] += dvdl_q;
+ enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Vdw] += dvdl_lj;
if (wcycle)
{
dd_cycles_add(cr->dd, cycles_seppme, ddCyclPME);
}
- wallcycle_stop(wcycle, ewcPP_PMEWAITRECVF);
+ wallcycle_stop(wcycle, WallCycleCounter::PpPmeWaitRecvF);
}
static void print_large_forces(FILE* fp,
bool nonFinite = !std::isfinite(force2);
if (force2 >= force2Tolerance || nonFinite)
{
- fprintf(fp, "step %" PRId64 " atom %6d x %8.3f %8.3f %8.3f force %12.5e\n", step,
- ddglatnr(cr->dd, i), x[i][XX], x[i][YY], x[i][ZZ], std::sqrt(force2));
+ fprintf(fp,
+ "step %" PRId64 " atom %6d x %8.3f %8.3f %8.3f force %12.5e\n",
+ step,
+ ddglatnr(cr->dd, i),
+ x[i][XX],
+ x[i][YY],
+ x[i][ZZ],
+ std::sqrt(force2));
}
if (nonFinite)
{
//! When necessary, spreads forces on vsites and computes the virial for \p forceOutputs->forceWithShiftForces()
static void postProcessForceWithShiftForces(t_nrnb* nrnb,
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle* wcycle,
const matrix box,
ArrayRef<const RVec> x,
ForceOutputs* forceOutputs,
if (stepWork.computeVirial)
{
/* Calculation of the virial must be done after vsites! */
- calc_virial(0, mdatoms.homenr, as_rvec_array(x.data()), forceWithShiftForces, vir_force,
- box, nrnb, &fr, fr.pbcType);
+ calc_virial(
+ 0, mdatoms.homenr, as_rvec_array(x.data()), forceWithShiftForces, vir_force, box, nrnb, &fr, fr.pbcType);
}
}
static void postProcessForces(const t_commrec* cr,
int64_t step,
t_nrnb* nrnb,
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle* wcycle,
const matrix box,
ArrayRef<const RVec> x,
ForceOutputs* forceOutputs,
const int clearF,
const int64_t step,
t_nrnb* nrnb,
- gmx_wallcycle_t wcycle)
+ gmx_wallcycle* wcycle)
{
if (!stepWork.computeNonbondedForces)
{
/* Prune the pair-list beyond fr->ic->rlistPrune using
* the current coordinates of the atoms.
*/
- wallcycle_sub_start(wcycle, ewcsNONBONDED_PRUNING);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::NonbondedPruning);
nbv->dispatchPruneKernelCpu(ilocality, fr->shift_vec);
- wallcycle_sub_stop(wcycle, ewcsNONBONDED_PRUNING);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::NonbondedPruning);
}
}
- nbv->dispatchNonbondedKernel(ilocality, *ic, stepWork, clearF, *fr, enerd, nrnb);
+ nbv->dispatchNonbondedKernel(
+ ilocality,
+ *ic,
+ stepWork,
+ clearF,
+ fr->shift_vec,
+ enerd->grpp.energyGroupPairTerms[fr->haveBuckingham ? NonBondedEnergyTerms::BuckinghamSR
+ : NonBondedEnergyTerms::LJSR],
+ enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR],
+ nrnb);
}
static inline void clearRVecs(ArrayRef<RVec> v, const bool useOpenmpThreading)
{
- int nth = gmx_omp_nthreads_get_simple_rvec_task(emntDefault, v.ssize());
+ int nth = gmx_omp_nthreads_get_simple_rvec_task(ModuleMultiThread::Default, v.ssize());
/* Note that we would like to avoid this conditional by putting it
* into the omp pragma instead, but then we still take the full
if (groupOptions.tau_t[g] >= 0)
{
nrdfCoupled += groupOptions.nrdf[g];
- kineticEnergy += groupOptions.nrdf[g] * 0.5 * groupOptions.ref_t[g] * BOLTZ;
+ kineticEnergy += groupOptions.nrdf[g] * 0.5 * groupOptions.ref_t[g] * gmx::c_boltz;
}
else
{
"can be caused by overlapping interactions in bonded interactions or very large%s "
"coordinate values. Usually this is caused by a badly- or non-equilibrated initial "
"configuration, incorrect interactions or parameters in the topology.",
- step, enerd.term[F_EPOT], energyIsNotFinite ? "not finite" : "extremely high",
- enerd.term[F_LJ], enerd.term[F_COUL_SR],
- energyIsNotFinite ? "non-finite" : "very high", energyIsNotFinite ? " or Nan" : "");
+ step,
+ enerd.term[F_EPOT],
+ energyIsNotFinite ? "not finite" : "extremely high",
+ enerd.term[F_LJ],
+ enerd.term[F_COUL_SR],
+ energyIsNotFinite ? "non-finite" : "very high",
+ energyIsNotFinite ? " or Nan" : "");
}
}
*/
static void computeSpecialForces(FILE* fplog,
const t_commrec* cr,
- const t_inputrec* inputrec,
+ const t_inputrec& inputrec,
gmx::Awh* awh,
gmx_enfrot* enforcedRotation,
gmx::ImdSession* imdSession,
pull_t* pull_work,
int64_t step,
double t,
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle* wcycle,
gmx::ForceProviders* forceProviders,
const matrix box,
gmx::ArrayRef<const gmx::RVec> x,
*/
if (stepWork.computeForces)
{
- gmx::ForceProviderInput forceProviderInput(x, *mdatoms, t, box, *cr);
+ gmx::ForceProviderInput forceProviderInput(
+ x,
+ mdatoms->homenr,
+ gmx::arrayRefFromArray(mdatoms->chargeA, mdatoms->homenr),
+ gmx::arrayRefFromArray(mdatoms->massT, mdatoms->homenr),
+ t,
+ box,
+ *cr);
gmx::ForceProviderOutput forceProviderOutput(forceWithVirialMtsLevel0, enerd);
/* Collect forces from modules */
forceProviders->calculateForces(forceProviderInput, &forceProviderOutput);
}
- if (inputrec->bPull && pull_have_potential(*pull_work))
+ if (inputrec.bPull && pull_have_potential(*pull_work))
{
- const int mtsLevel = forceGroupMtsLevel(inputrec->mtsLevels, gmx::MtsForceGroups::Pull);
+ const int mtsLevel = forceGroupMtsLevel(inputrec.mtsLevels, gmx::MtsForceGroups::Pull);
if (mtsLevel == 0 || stepWork.computeSlowForces)
{
auto& forceWithVirial = (mtsLevel == 0) ? forceWithVirialMtsLevel0 : forceWithVirialMtsLevel1;
- pull_potential_wrapper(cr, inputrec, box, x, forceWithVirial, mdatoms, enerd, pull_work,
- lambda.data(), t, wcycle);
+ pull_potential_wrapper(
+ cr, inputrec, box, x, forceWithVirial, mdatoms, enerd, pull_work, lambda.data(), t, wcycle);
}
}
if (awh)
{
- const int mtsLevel = forceGroupMtsLevel(inputrec->mtsLevels, gmx::MtsForceGroups::Pull);
+ const int mtsLevel = forceGroupMtsLevel(inputrec.mtsLevels, gmx::MtsForceGroups::Pull);
if (mtsLevel == 0 || stepWork.computeSlowForces)
{
const bool needForeignEnergyDifferences = awh->needForeignEnergyDifferences(step);
std::vector<double> foreignLambdaDeltaH, foreignLambdaDhDl;
if (needForeignEnergyDifferences)
{
- enerd->foreignLambdaTerms.finalizePotentialContributions(enerd->dvdl_lin, lambda,
- *inputrec->fepvals);
+ enerd->foreignLambdaTerms.finalizePotentialContributions(
+ enerd->dvdl_lin, lambda, *inputrec.fepvals);
std::tie(foreignLambdaDeltaH, foreignLambdaDhDl) = enerd->foreignLambdaTerms.getTerms(cr);
}
auto& forceWithVirial = (mtsLevel == 0) ? forceWithVirialMtsLevel0 : forceWithVirialMtsLevel1;
enerd->term[F_COM_PULL] += awh->applyBiasForcesAndUpdateBias(
- inputrec->pbcType, mdatoms->massT, foreignLambdaDeltaH, foreignLambdaDhDl, box,
- forceWithVirial, t, step, wcycle, fplog);
+ inputrec.pbcType,
+ gmx::arrayRefFromArray(mdatoms->massT, mdatoms->nr),
+ foreignLambdaDeltaH,
+ foreignLambdaDhDl,
+ box,
+ forceWithVirial,
+ t,
+ step,
+ wcycle,
+ fplog);
}
}
-
- rvec* f = as_rvec_array(forceWithVirialMtsLevel0->force_.data());
-
/* Add the forces from enforced rotation potentials (if any) */
- if (inputrec->bRot)
+ if (inputrec.bRot)
{
- wallcycle_start(wcycle, ewcROTadd);
- enerd->term[F_COM_PULL] += add_rot_forces(enforcedRotation, f, cr, step, t);
- wallcycle_stop(wcycle, ewcROTadd);
+ wallcycle_start(wcycle, WallCycleCounter::RotAdd);
+ enerd->term[F_COM_PULL] +=
+ add_rot_forces(enforcedRotation, forceWithVirialMtsLevel0->force_, cr, step, t);
+ wallcycle_stop(wcycle, WallCycleCounter::RotAdd);
}
if (ed)
* Thus if no other algorithm (e.g. PME) requires it, the forces
* here will contribute to the virial.
*/
- do_flood(cr, inputrec, as_rvec_array(x.data()), f, ed, box, step, didNeighborSearch);
+ do_flood(cr, inputrec, x, forceWithVirialMtsLevel0->force_, ed, box, step, didNeighborSearch);
}
/* Add forces from interactive molecular dynamics (IMD), if any */
- if (inputrec->bIMD && stepWork.computeForces)
+ if (inputrec.bIMD && stepWork.computeForces)
{
- imdSession->applyForces(f);
+ imdSession->applyForces(forceWithVirialMtsLevel0->force_);
}
}
const StepWorkload& stepWork,
GpuEventSynchronizer* xReadyOnDevice,
const real lambdaQ,
- gmx_wallcycle_t wcycle)
+ gmx_wallcycle* wcycle)
{
pme_gpu_prepare_computation(pmedata, box, wcycle, stepWork);
pme_gpu_launch_spread(pmedata, xReadyOnDevice, wcycle, lambdaQ);
*/
static void launchPmeGpuFftAndGather(gmx_pme_t* pmedata,
const real lambdaQ,
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle* wcycle,
const gmx::StepWorkload& stepWork)
{
pme_gpu_launch_complex_transforms(pmedata, wcycle, stepWork);
gmx_enerdata_t* enerd,
const real lambdaQ,
const StepWorkload& stepWork,
- gmx_wallcycle_t wcycle)
+ gmx_wallcycle* wcycle)
{
bool isPmeGpuDone = false;
bool isNbGpuDone = false;
{
GpuTaskCompletion completionType =
(isNbGpuDone) ? GpuTaskCompletion::Wait : GpuTaskCompletion::Check;
- isPmeGpuDone = pme_gpu_try_finish_task(pmedata, stepWork, wcycle,
- &forceOutputsPme->forceWithVirial(), enerd,
- lambdaQ, completionType);
+ isPmeGpuDone = pme_gpu_try_finish_task(
+ pmedata, stepWork, wcycle, &forceOutputsPme->forceWithVirial(), enerd, lambdaQ, completionType);
}
if (!isNbGpuDone)
GpuTaskCompletion completionType =
(isPmeGpuDone) ? GpuTaskCompletion::Wait : GpuTaskCompletion::Check;
isNbGpuDone = Nbnxm::gpu_try_finish_task(
- nbv->gpu_nbv, stepWork, AtomLocality::Local, enerd->grpp.ener[egLJSR].data(),
- enerd->grpp.ener[egCOULSR].data(), forceBuffersNonbonded.shiftForces(),
- completionType, wcycle);
+ nbv->gpu_nbv,
+ stepWork,
+ AtomLocality::Local,
+ enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::LJSR].data(),
+ enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR].data(),
+ forceBuffersNonbonded.shiftForces(),
+ completionType,
+ wcycle);
if (isNbGpuDone)
{
/*! \brief Set up the different force buffers; also does clearing.
*
- * \param[in] forceHelperBuffers Helper force buffers
- * \param[in] force force array
- * \param[in] stepWork Step schedule flags
- * \param[out] wcycle wallcycle recording structure
+ * \param[in] forceHelperBuffers Helper force buffers
+ * \param[in] force force array
+ * \param[in] domainWork Domain lifetime workload flags
+ * \param[in] stepWork Step schedule flags
+ * \param[in] havePpDomainDecomposition Whether we have a PP domain decomposition
+ * \param[out] wcycle wallcycle recording structure
*
- * \returns Cleared force output structure
+ * \returns Cleared force output structure
*/
static ForceOutputs setupForceOutputs(ForceHelperBuffers* forceHelperBuffers,
gmx::ArrayRefWithPadding<gmx::RVec> force,
+ const DomainLifetimeWorkload& domainWork,
const StepWorkload& stepWork,
- gmx_wallcycle_t wcycle)
+ const bool havePpDomainDecomposition,
+ gmx_wallcycle* wcycle)
{
- wallcycle_sub_start(wcycle, ewcsCLEAR_FORCE_BUFFER);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::ClearForceBuffer);
/* NOTE: We assume fr->shiftForces is all zeros here */
- gmx::ForceWithShiftForces forceWithShiftForces(force, stepWork.computeVirial,
- forceHelperBuffers->shiftForces());
+ gmx::ForceWithShiftForces forceWithShiftForces(
+ force, stepWork.computeVirial, forceHelperBuffers->shiftForces());
- if (stepWork.computeForces)
+ if (stepWork.computeForces
+ && (domainWork.haveCpuLocalForceWork || !stepWork.useGpuFBufferOps
+ || (havePpDomainDecomposition && !stepWork.useGpuFHalo)))
{
/* Clear the short- and long-range forces */
clearRVecs(forceWithShiftForces.force(), true);
clearRVecs(forceWithVirial.force_, true);
}
- wallcycle_sub_stop(wcycle, ewcsCLEAR_FORCE_BUFFER);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::ClearForceBuffer);
- return ForceOutputs(forceWithShiftForces, forceHelperBuffers->haveDirectVirialContributions(),
- forceWithVirial);
+ return ForceOutputs(
+ forceWithShiftForces, forceHelperBuffers->haveDirectVirialContributions(), forceWithVirial);
}
}
domainWork.haveGpuBondedWork = ((fr.gpuBonded != nullptr) && fr.gpuBonded->haveInteractions());
// Note that haveFreeEnergyWork is constant over the whole run
- domainWork.haveFreeEnergyWork = (fr.efep != efepNO && mdatoms.nPerturbed != 0);
+ domainWork.haveFreeEnergyWork =
+ (fr.efep != FreeEnergyPerturbationType::No && mdatoms.nPerturbed != 0);
// We assume we have local force work if there are CPU
// force tasks including PME or nonbondeds.
domainWork.haveCpuLocalForceWork =
const gmx::MdrunScheduleWorkload& runScheduleWork,
bool useGpuPmeOnThisRank,
int64_t step,
- gmx_wallcycle_t wcycle)
+ gmx_wallcycle* wcycle)
{
if (runScheduleWork.simulationWork.useGpuNonbonded && runScheduleWork.stepWork.computeNonbondedForces)
{
}
/* now clear the GPU outputs while we finish the step on the CPU */
- wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
- wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start_nocount(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
Nbnxm::gpu_clear_outputs(nbv->gpu_nbv, runScheduleWork.stepWork.computeVirial);
- wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
- wallcycle_stop(wcycle, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+ wallcycle_stop(wcycle, WallCycleCounter::LaunchGpu);
}
if (useGpuPmeOnThisRank)
{
for (int j = 0; j < DIM; j++)
{
- muTotal[j] = (1.0 - lambda[efptCOUL]) * dipoleData->muStateAB[0][j]
- + lambda[efptCOUL] * dipoleData->muStateAB[1][j];
+ muTotal[j] = (1.0 - lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)])
+ * dipoleData->muStateAB[0][j]
+ + lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)]
+ * dipoleData->muStateAB[1][j];
}
}
}
ArrayRef<RVec> forceMts,
const real mtsFactor)
{
- const int gmx_unused numThreads = gmx_omp_nthreads_get(emntDefault);
+ const int gmx_unused numThreads = gmx_omp_nthreads_get(ModuleMultiThread::Default);
#pragma omp parallel for num_threads(numThreads) schedule(static)
for (int i = 0; i < numAtoms; i++)
{
const bool accumulate =
runScheduleWork->domainWork.haveCpuLocalForceWork || havePPDomainDecomposition(cr);
const int atomStart = 0;
- fr->gpuForceReduction[gmx::AtomLocality::Local]->reinit(
- stateGpu->getForces(), nbv->getNumAtoms(AtomLocality::Local), nbv->getGridIndices(),
- atomStart, accumulate, stateGpu->fReducedOnDevice());
+ fr->gpuForceReduction[gmx::AtomLocality::Local]->reinit(stateGpu->getForces(),
+ nbv->getNumAtoms(AtomLocality::Local),
+ nbv->getGridIndices(),
+ atomStart,
+ accumulate,
+ stateGpu->fReducedOnDevice());
// register forces and add dependencies
fr->gpuForceReduction[gmx::AtomLocality::Local]->registerNbnxmForce(nbv->getGpuForces());
if (runScheduleWork->simulationWork.useGpuPme
&& (thisRankHasDuty(cr, DUTY_PME) || runScheduleWork->simulationWork.useGpuPmePpCommunication))
{
- void* forcePtr = thisRankHasDuty(cr, DUTY_PME) ? pme_gpu_get_device_f(fr->pmedata)
- : // PME force buffer on same GPU
- fr->pmePpCommGpu->getGpuForceStagingPtr(); // buffer received from other GPU
+ DeviceBuffer<gmx::RVec> forcePtr =
+ thisRankHasDuty(cr, DUTY_PME) ? pme_gpu_get_device_f(fr->pmedata)
+ : // PME force buffer on same GPU
+ fr->pmePpCommGpu->getGpuForceStagingPtr(); // buffer received from other GPU
fr->gpuForceReduction[gmx::AtomLocality::Local]->registerRvecForce(forcePtr);
GpuEventSynchronizer* const pmeSynchronizer =
(thisRankHasDuty(cr, DUTY_PME) ? pme_gpu_get_f_ready_synchronizer(fr->pmedata)
: // PME force buffer on same GPU
fr->pmePpCommGpu->getForcesReadySynchronizer()); // buffer received from other GPU
- fr->gpuForceReduction[gmx::AtomLocality::Local]->addDependency(pmeSynchronizer);
+
+ if (GMX_THREAD_MPI)
+ {
+ GMX_ASSERT(pmeSynchronizer != nullptr, "PME force ready cuda event should not be NULL");
+ fr->gpuForceReduction[gmx::AtomLocality::Local]->addDependency(pmeSynchronizer);
+ }
}
if ((runScheduleWork->domainWork.haveCpuLocalForceWork || havePPDomainDecomposition(cr))
const bool accumulate = runScheduleWork->domainWork.haveCpuBondedWork
|| runScheduleWork->domainWork.haveFreeEnergyWork;
const int atomStart = dd_numHomeAtoms(*cr->dd);
- fr->gpuForceReduction[gmx::AtomLocality::NonLocal]->reinit(
- stateGpu->getForces(), nbv->getNumAtoms(AtomLocality::NonLocal),
- nbv->getGridIndices(), atomStart, accumulate);
+ fr->gpuForceReduction[gmx::AtomLocality::NonLocal]->reinit(stateGpu->getForces(),
+ nbv->getNumAtoms(AtomLocality::NonLocal),
+ nbv->getGridIndices(),
+ atomStart,
+ accumulate);
// register forces and add dependencies
fr->gpuForceReduction[gmx::AtomLocality::NonLocal]->registerNbnxmForce(nbv->getGpuForces());
void do_force(FILE* fplog,
const t_commrec* cr,
const gmx_multisim_t* ms,
- const t_inputrec* inputrec,
+ const t_inputrec& inputrec,
gmx::Awh* awh,
gmx_enfrot* enforcedRotation,
gmx::ImdSession* imdSession,
pull_t* pull_work,
int64_t step,
t_nrnb* nrnb,
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle* wcycle,
const gmx_localtop_t* top,
const matrix box,
gmx::ArrayRefWithPadding<gmx::RVec> x,
- history_t* hist,
+ const history_t* hist,
gmx::ForceBuffersView* forceView,
tensor vir_force,
const t_mdatoms* mdatoms,
"forces for");
nonbonded_verlet_t* nbv = fr->nbv.get();
- interaction_const_t* ic = fr->ic;
+ interaction_const_t* ic = fr->ic.get();
gmx::StatePropagatorDataGpu* stateGpu = fr->stateGpu;
const SimulationWorkload& simulationWork = runScheduleWork->simulationWork;
- runScheduleWork->stepWork = setupStepWorkload(legacyFlags, inputrec->mtsLevels, step,
- simulationWork, thisRankHasDuty(cr, DUTY_PME));
+ runScheduleWork->stepWork = setupStepWorkload(
+ legacyFlags, inputrec.mtsLevels, step, simulationWork, thisRankHasDuty(cr, DUTY_PME));
const StepWorkload& stepWork = runScheduleWork->stepWork;
const bool useGpuPmeOnThisRank =
const bool calcCGCM = (fillGrid && !DOMAINDECOMP(cr));
if (calcCGCM)
{
- put_atoms_in_box_omp(fr->pbcType, box, x.unpaddedArrayRef().subArray(0, mdatoms->homenr),
- gmx_omp_nthreads_get(emntDefault));
+ put_atoms_in_box_omp(fr->pbcType,
+ box,
+ x.unpaddedArrayRef().subArray(0, mdatoms->homenr),
+ gmx_omp_nthreads_get(ModuleMultiThread::Default));
inc_nrnb(nrnb, eNR_SHIFTX, mdatoms->homenr);
}
}
const bool reinitGpuPmePpComms =
GMX_MPI && simulationWork.useGpuPmePpCommunication && (stepWork.doNeighborSearch);
- const auto localXReadyOnDevice = (useGpuPmeOnThisRank || simulationWork.useGpuBufferOps)
- ? stateGpu->getCoordinatesReadyOnDeviceEvent(
- AtomLocality::Local, simulationWork, stepWork)
- : nullptr;
+ auto* localXReadyOnDevice = (useGpuPmeOnThisRank || simulationWork.useGpuBufferOps)
+ ? stateGpu->getCoordinatesReadyOnDeviceEvent(
+ AtomLocality::Local, simulationWork, stepWork)
+ : nullptr;
// Copy coordinate from the GPU if update is on the GPU and there
// are forces to be computed on the CPU, or for the computation of
haveCopiedXFromGpu = true;
}
- // If coordinates are to be sent to PME task from CPU memory, perform that send here.
- // Otherwise the send will occur after H2D coordinate transfer.
- if (GMX_MPI && !thisRankHasDuty(cr, DUTY_PME) && !pmeSendCoordinatesFromGpu && stepWork.computeSlowForces)
- {
- /* Send particle coordinates to the pme nodes */
- if (!stepWork.doNeighborSearch && simulationWork.useGpuUpdate)
- {
- stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
- }
-
- gmx_pme_send_coordinates(fr, cr, box, as_rvec_array(x.unpaddedArrayRef().data()), lambda[efptCOUL],
- lambda[efptVDW], (stepWork.computeVirial || stepWork.computeEnergy),
- step, simulationWork.useGpuPmePpCommunication, reinitGpuPmePpComms,
- pmeSendCoordinatesFromGpu, localXReadyOnDevice, wcycle);
- }
-
// Coordinates on the device are needed if PME or BufferOps are offloaded.
// The local coordinates can be copied right away.
// NOTE: Consider moving this copy to right after they are updated and constrained,
}
}
- // If coordinates are to be sent to PME task from GPU memory, perform that send here.
- // Otherwise the send will occur before the H2D coordinate transfer.
- if (!thisRankHasDuty(cr, DUTY_PME) && pmeSendCoordinatesFromGpu)
+ if (GMX_MPI && !thisRankHasDuty(cr, DUTY_PME) && stepWork.computeSlowForces)
{
/* Send particle coordinates to the pme nodes */
- gmx_pme_send_coordinates(fr, cr, box, as_rvec_array(x.unpaddedArrayRef().data()), lambda[efptCOUL],
- lambda[efptVDW], (stepWork.computeVirial || stepWork.computeEnergy),
- step, simulationWork.useGpuPmePpCommunication, reinitGpuPmePpComms,
- pmeSendCoordinatesFromGpu, localXReadyOnDevice, wcycle);
+ if (!pmeSendCoordinatesFromGpu && !stepWork.doNeighborSearch && simulationWork.useGpuUpdate)
+ {
+ GMX_ASSERT(haveCopiedXFromGpu,
+ "a wait should only be triggered if copy has been scheduled");
+ stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
+ }
+
+ gmx_pme_send_coordinates(fr,
+ cr,
+ box,
+ as_rvec_array(x.unpaddedArrayRef().data()),
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)],
+ (stepWork.computeVirial || stepWork.computeEnergy),
+ step,
+ simulationWork.useGpuPmePpCommunication,
+ reinitGpuPmePpComms,
+ pmeSendCoordinatesFromGpu,
+ localXReadyOnDevice,
+ wcycle);
}
if (useGpuPmeOnThisRank)
{
- launchPmeGpuSpread(fr->pmedata, box, stepWork, localXReadyOnDevice, lambda[efptCOUL], wcycle);
+ launchPmeGpuSpread(fr->pmedata,
+ box,
+ stepWork,
+ localXReadyOnDevice,
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
+ wcycle);
}
const gmx::DomainLifetimeWorkload& domainWork = runScheduleWork->domainWork;
fr->wholeMoleculeTransform->updateForAtomPbcJumps(x.unpaddedArrayRef(), box);
}
- // TODO
- // - vzero is constant, do we need to pass it?
- // - box_diag should be passed directly to nbnxn_put_on_grid
- //
- rvec vzero;
- clear_rvec(vzero);
-
- rvec box_diag;
- box_diag[XX] = box[XX][XX];
- box_diag[YY] = box[YY][YY];
- box_diag[ZZ] = box[ZZ][ZZ];
-
- wallcycle_start(wcycle, ewcNS);
+ wallcycle_start(wcycle, WallCycleCounter::NS);
if (!DOMAINDECOMP(cr))
{
- wallcycle_sub_start(wcycle, ewcsNBS_GRID_LOCAL);
- nbnxn_put_on_grid(nbv, box, 0, vzero, box_diag, nullptr, { 0, mdatoms->homenr }, -1,
- fr->cginfo, x.unpaddedArrayRef(), 0, nullptr);
- wallcycle_sub_stop(wcycle, ewcsNBS_GRID_LOCAL);
+ const rvec vzero = { 0.0_real, 0.0_real, 0.0_real };
+ const rvec boxDiagonal = { box[XX][XX], box[YY][YY], box[ZZ][ZZ] };
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::NBSGridLocal);
+ nbnxn_put_on_grid(nbv,
+ box,
+ 0,
+ vzero,
+ boxDiagonal,
+ nullptr,
+ { 0, mdatoms->homenr },
+ -1,
+ fr->cginfo,
+ x.unpaddedArrayRef(),
+ 0,
+ nullptr);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::NBSGridLocal);
}
else
{
- wallcycle_sub_start(wcycle, ewcsNBS_GRID_NONLOCAL);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::NBSGridNonLocal);
nbnxn_put_on_grid_nonlocal(nbv, domdec_zones(cr->dd), fr->cginfo, x.unpaddedArrayRef());
- wallcycle_sub_stop(wcycle, ewcsNBS_GRID_NONLOCAL);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::NBSGridNonLocal);
}
nbv->setAtomProperties(gmx::constArrayRefFromArray(mdatoms->typeA, mdatoms->nr),
- gmx::constArrayRefFromArray(mdatoms->chargeA, mdatoms->nr), fr->cginfo);
+ gmx::constArrayRefFromArray(mdatoms->chargeA, mdatoms->nr),
+ fr->cginfo);
- wallcycle_stop(wcycle, ewcNS);
+ wallcycle_stop(wcycle, WallCycleCounter::NS);
/* initialize the GPU nbnxm atom data and bonded data structures */
if (simulationWork.useGpuNonbonded)
{
// Note: cycle counting only nononbondeds, gpuBonded counts internally
- wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
- wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start_nocount(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
Nbnxm::gpu_init_atomdata(nbv->gpu_nbv, nbv->nbat.get());
- wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
- wallcycle_stop(wcycle, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+ wallcycle_stop(wcycle, WallCycleCounter::LaunchGpu);
if (fr->gpuBonded)
{
// TODO the xq, f, and fshift buffers are now shared
// resources, so they should be maintained by a
// higher-level object than the nb module.
- fr->gpuBonded->updateInteractionListsAndDeviceBuffers(
- nbv->getGridIndices(), top->idef, Nbnxm::gpu_get_xq(nbv->gpu_nbv),
- Nbnxm::gpu_get_f(nbv->gpu_nbv), Nbnxm::gpu_get_fshift(nbv->gpu_nbv));
+ fr->gpuBonded->updateInteractionListsAndDeviceBuffers(nbv->getGridIndices(),
+ top->idef,
+ Nbnxm::gpu_get_xq(nbv->gpu_nbv),
+ Nbnxm::gpu_get_f(nbv->gpu_nbv),
+ Nbnxm::gpu_get_fshift(nbv->gpu_nbv));
}
}
// Need to run after the GPU-offload bonded interaction lists
// are set up to be able to determine whether there is bonded work.
runScheduleWork->domainWork = setupDomainLifetimeWorkload(
- *inputrec, *fr, pull_work, ed, *mdatoms, simulationWork, stepWork);
+ inputrec, *fr, pull_work, ed, *mdatoms, simulationWork, stepWork);
- wallcycle_start_nocount(wcycle, ewcNS);
- wallcycle_sub_start(wcycle, ewcsNBS_SEARCH_LOCAL);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::NS);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::NBSSearchLocal);
/* Note that with a GPU the launch overhead of the list transfer is not timed separately */
nbv->constructPairlist(InteractionLocality::Local, top->excls, step, nrnb);
nbv->setupGpuShortRangeWork(fr->gpuBonded, InteractionLocality::Local);
- wallcycle_sub_stop(wcycle, ewcsNBS_SEARCH_LOCAL);
- wallcycle_stop(wcycle, ewcNS);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::NBSSearchLocal);
+ wallcycle_stop(wcycle, WallCycleCounter::NS);
if (stepWork.useGpuXBufferOps)
{
setupGpuForceReductions(runScheduleWork, cr, fr);
}
}
- else if (!EI_TPI(inputrec->eI) && stepWork.computeNonbondedForces)
+ else if (!EI_TPI(inputrec.eI) && stepWork.computeNonbondedForces)
{
if (stepWork.useGpuXBufferOps)
{
GMX_ASSERT(stateGpu, "stateGpu should be valid when buffer ops are offloaded");
- nbv->convertCoordinatesGpu(AtomLocality::Local, false, stateGpu->getCoordinates(),
- localXReadyOnDevice);
+ nbv->convertCoordinatesGpu(AtomLocality::Local, stateGpu->getCoordinates(), localXReadyOnDevice);
}
else
{
"a wait should only be triggered if copy has been scheduled");
stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
}
- nbv->convertCoordinates(AtomLocality::Local, false, x.unpaddedArrayRef());
+ nbv->convertCoordinates(AtomLocality::Local, x.unpaddedArrayRef());
}
}
{
ddBalanceRegionHandler.openBeforeForceComputationGpu();
- wallcycle_start(wcycle, ewcLAUNCH_GPU);
- wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_NONBONDED);
+ wallcycle_start(wcycle, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
Nbnxm::gpu_upload_shiftvec(nbv->gpu_nbv, nbv->nbat.get());
if (stepWork.doNeighborSearch || !stepWork.useGpuXBufferOps)
{
Nbnxm::gpu_copy_xq_to_gpu(nbv->gpu_nbv, nbv->nbat.get(), AtomLocality::Local);
}
- wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
- wallcycle_stop(wcycle, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+ wallcycle_stop(wcycle, WallCycleCounter::LaunchGpu);
// with X buffer ops offloaded to the GPU on all but the search steps
// bonded work not split into separate local and non-local, so with DD
}
/* launch local nonbonded work on GPU */
- wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
- wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start_nocount(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::Local, enbvClearFNo, step, nrnb, wcycle);
- wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
- wallcycle_stop(wcycle, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+ wallcycle_stop(wcycle, WallCycleCounter::LaunchGpu);
}
if (useGpuPmeOnThisRank)
// X copy/transform to allow overlap as well as after the GPU NB
// launch to avoid FFT launch overhead hijacking the CPU and delaying
// the nonbonded kernel.
- launchPmeGpuFftAndGather(fr->pmedata, lambda[efptCOUL], wcycle, stepWork);
+ launchPmeGpuFftAndGather(fr->pmedata,
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
+ wcycle,
+ stepWork);
}
/* Communicate coordinates and sum dipole if necessary +
if (stepWork.doNeighborSearch)
{
// TODO: fuse this branch with the above large stepWork.doNeighborSearch block
- wallcycle_start_nocount(wcycle, ewcNS);
- wallcycle_sub_start(wcycle, ewcsNBS_SEARCH_NONLOCAL);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::NS);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::NBSSearchNonLocal);
/* Note that with a GPU the launch overhead of the list transfer is not timed separately */
nbv->constructPairlist(InteractionLocality::NonLocal, top->excls, step, nrnb);
nbv->setupGpuShortRangeWork(fr->gpuBonded, InteractionLocality::NonLocal);
- wallcycle_sub_stop(wcycle, ewcsNBS_SEARCH_NONLOCAL);
- wallcycle_stop(wcycle, ewcNS);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::NBSSearchNonLocal);
+ wallcycle_stop(wcycle, WallCycleCounter::NS);
// TODO refactor this GPU halo exchange re-initialisation
// to location in do_md where GPU halo exchange is
// constructed at partitioning, after above stateGpu
{
stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
}
- nbv->convertCoordinatesGpu(AtomLocality::NonLocal, false, stateGpu->getCoordinates(),
+ nbv->convertCoordinatesGpu(AtomLocality::NonLocal,
+ stateGpu->getCoordinates(),
stateGpu->getCoordinatesReadyOnDeviceEvent(
AtomLocality::NonLocal, simulationWork, stepWork));
}
else
{
- nbv->convertCoordinates(AtomLocality::NonLocal, false, x.unpaddedArrayRef());
+ nbv->convertCoordinates(AtomLocality::NonLocal, x.unpaddedArrayRef());
}
}
if (stepWork.doNeighborSearch || !stepWork.useGpuXBufferOps)
{
- wallcycle_start(wcycle, ewcLAUNCH_GPU);
- wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_NONBONDED);
+ wallcycle_start(wcycle, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
Nbnxm::gpu_copy_xq_to_gpu(nbv->gpu_nbv, nbv->nbat.get(), AtomLocality::NonLocal);
- wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
- wallcycle_stop(wcycle, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+ wallcycle_stop(wcycle, WallCycleCounter::LaunchGpu);
}
if (domainWork.haveGpuBondedWork)
}
/* launch non-local nonbonded tasks on GPU */
- wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
- wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_NONBONDED);
- do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::NonLocal, enbvClearFNo, step,
- nrnb, wcycle);
- wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
- wallcycle_stop(wcycle, ewcLAUNCH_GPU);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+ do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::NonLocal, enbvClearFNo, step, nrnb, wcycle);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+ wallcycle_stop(wcycle, WallCycleCounter::LaunchGpu);
}
}
if (simulationWork.useGpuNonbonded && stepWork.computeNonbondedForces)
{
/* launch D2H copy-back F */
- wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
- wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start_nocount(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
if (havePPDomainDecomposition(cr))
{
Nbnxm::gpu_launch_cpyback(nbv->gpu_nbv, nbv->nbat.get(), stepWork, AtomLocality::NonLocal);
}
Nbnxm::gpu_launch_cpyback(nbv->gpu_nbv, nbv->nbat.get(), stepWork, AtomLocality::Local);
- wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
if (domainWork.haveGpuBondedWork && stepWork.computeEnergy)
{
fr->gpuBonded->launchEnergyTransfer();
}
- wallcycle_stop(wcycle, ewcLAUNCH_GPU);
+ wallcycle_stop(wcycle, WallCycleCounter::LaunchGpu);
}
gmx::ArrayRef<const gmx::RVec> xWholeMolecules;
*/
gmx::ArrayRef<const gmx::RVec> xRef =
(xWholeMolecules.empty() ? x.unpaddedArrayRef() : xWholeMolecules);
- calc_mu(start, mdatoms->homenr, xRef, mdatoms->chargeA, mdatoms->chargeB,
- mdatoms->nChargePerturbed, dipoleData.muStaging[0], dipoleData.muStaging[1]);
+ calc_mu(start,
+ mdatoms->homenr,
+ xRef,
+ mdatoms->chargeA ? gmx::arrayRefFromArray(mdatoms->chargeA, mdatoms->nr)
+ : gmx::ArrayRef<real>{},
+ mdatoms->chargeB ? gmx::arrayRefFromArray(mdatoms->chargeB, mdatoms->nr)
+ : gmx::ArrayRef<real>{},
+ mdatoms->nChargePerturbed != 0,
+ dipoleData.muStaging[0],
+ dipoleData.muStaging[1]);
- reduceAndUpdateMuTot(&dipoleData, cr, (fr->efep != efepNO), lambda, muTotal, ddBalanceRegionHandler);
+ reduceAndUpdateMuTot(
+ &dipoleData, cr, (fr->efep != FreeEnergyPerturbationType::No), lambda, muTotal, ddBalanceRegionHandler);
}
/* Reset energies */
if (DOMAINDECOMP(cr) && !thisRankHasDuty(cr, DUTY_PME))
{
- wallcycle_start(wcycle, ewcPPDURINGPME);
+ wallcycle_start(wcycle, WallCycleCounter::PpDuringPme);
dd_force_flop_start(cr->dd, nrnb);
}
// For the rest of the CPU tasks that depend on GPU-update produced coordinates,
// this wait ensures that the D2H transfer is complete.
- if ((simulationWork.useGpuUpdate)
+ if (simulationWork.useGpuUpdate && !stepWork.doNeighborSearch
&& (runScheduleWork->domainWork.haveCpuLocalForceWork || stepWork.computeVirial))
{
+ GMX_ASSERT(haveCopiedXFromGpu, "a wait should only be triggered if copy has been scheduled");
stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
}
- if (inputrec->bRot)
+ if (inputrec.bRot)
{
- wallcycle_start(wcycle, ewcROT);
- do_rotation(cr, enforcedRotation, box, as_rvec_array(x.unpaddedArrayRef().data()), t, step,
- stepWork.doNeighborSearch);
- wallcycle_stop(wcycle, ewcROT);
+ wallcycle_start(wcycle, WallCycleCounter::Rot);
+ do_rotation(cr, enforcedRotation, box, x.unpaddedConstArrayRef(), t, step, stepWork.doNeighborSearch);
+ wallcycle_stop(wcycle, WallCycleCounter::Rot);
}
/* Start the force cycle counter.
* Note that a different counter is used for dynamic load balancing.
*/
- wallcycle_start(wcycle, ewcFORCE);
+ wallcycle_start(wcycle, WallCycleCounter::Force);
/* Set up and clear force outputs:
* forceOutMtsLevel0: everything except what is in the other two outputs
* Without multiple time stepping all point to the same object.
* With multiple time-stepping the use is different for MTS fast (level0 only) and slow steps.
*/
- ForceOutputs forceOutMtsLevel0 =
- setupForceOutputs(&fr->forceHelperBuffers[0], force, stepWork, wcycle);
+ ForceOutputs forceOutMtsLevel0 = setupForceOutputs(
+ &fr->forceHelperBuffers[0], force, domainWork, stepWork, havePPDomainDecomposition(cr), wcycle);
// Force output for MTS combined forces, only set at level1 MTS steps
std::optional<ForceOutputs> forceOutMts =
(fr->useMts && stepWork.computeSlowForces)
? std::optional(setupForceOutputs(&fr->forceHelperBuffers[1],
forceView->forceMtsCombinedWithPadding(),
- stepWork, wcycle))
+ domainWork,
+ stepWork,
+ havePPDomainDecomposition(cr),
+ wcycle))
: std::nullopt;
ForceOutputs* forceOutMtsLevel1 =
ForceOutputs* forceOutNonbonded = nonbondedAtMtsLevel1 ? forceOutMtsLevel1 : &forceOutMtsLevel0;
- if (inputrec->bPull && pull_have_constraint(*pull_work))
+ if (inputrec.bPull && pull_have_constraint(*pull_work))
{
clear_pull_forces(pull_work);
}
do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::Local, enbvClearFYes, step, nrnb, wcycle);
}
- if (fr->efep != efepNO && stepWork.computeNonbondedForces)
+ if (fr->efep != FreeEnergyPerturbationType::No && stepWork.computeNonbondedForces)
{
/* Calculate the local and non-local free energy interactions here.
* Happens here on the CPU both with and without GPU.
*/
- nbv->dispatchFreeEnergyKernel(InteractionLocality::Local, fr,
- as_rvec_array(x.unpaddedArrayRef().data()),
- &forceOutNonbonded->forceWithShiftForces(), *mdatoms,
- inputrec->fepvals, lambda, enerd, stepWork, nrnb);
+ nbv->dispatchFreeEnergyKernel(
+ InteractionLocality::Local,
+ *fr,
+ x.unpaddedArrayRef(),
+ &forceOutNonbonded->forceWithShiftForces(),
+ mdatoms->chargeA ? gmx::arrayRefFromArray(mdatoms->chargeA, mdatoms->nr)
+ : gmx::ArrayRef<real>{},
+ mdatoms->chargeB ? gmx::arrayRefFromArray(mdatoms->chargeB, mdatoms->nr)
+ : gmx::ArrayRef<real>{},
+ mdatoms->typeA ? gmx::arrayRefFromArray(mdatoms->typeA, mdatoms->nr)
+ : gmx::ArrayRef<int>{},
+ mdatoms->typeB ? gmx::arrayRefFromArray(mdatoms->typeB, mdatoms->nr)
+ : gmx::ArrayRef<int>{},
+ inputrec.fepvals.get(),
+ lambda,
+ enerd,
+ stepWork,
+ nrnb);
if (havePPDomainDecomposition(cr))
{
- nbv->dispatchFreeEnergyKernel(InteractionLocality::NonLocal, fr,
- as_rvec_array(x.unpaddedArrayRef().data()),
- &forceOutNonbonded->forceWithShiftForces(), *mdatoms,
- inputrec->fepvals, lambda, enerd, stepWork, nrnb);
+ nbv->dispatchFreeEnergyKernel(
+ InteractionLocality::NonLocal,
+ *fr,
+ x.unpaddedArrayRef(),
+ &forceOutNonbonded->forceWithShiftForces(),
+ mdatoms->chargeA ? gmx::arrayRefFromArray(mdatoms->chargeA, mdatoms->nr)
+ : gmx::ArrayRef<real>{},
+ mdatoms->chargeB ? gmx::arrayRefFromArray(mdatoms->chargeB, mdatoms->nr)
+ : gmx::ArrayRef<real>{},
+ mdatoms->typeA ? gmx::arrayRefFromArray(mdatoms->typeA, mdatoms->nr)
+ : gmx::ArrayRef<int>{},
+ mdatoms->typeB ? gmx::arrayRefFromArray(mdatoms->typeB, mdatoms->nr)
+ : gmx::ArrayRef<int>{},
+ inputrec.fepvals.get(),
+ lambda,
+ enerd,
+ stepWork,
+ nrnb);
}
}
{
if (havePPDomainDecomposition(cr))
{
- do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::NonLocal, enbvClearFNo, step,
- nrnb, wcycle);
+ do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::NonLocal, enbvClearFNo, step, nrnb, wcycle);
}
if (stepWork.computeForces)
* This can be split into a local and a non-local part when overlapping
* communication with calculation with domain decomposition.
*/
- wallcycle_stop(wcycle, ewcFORCE);
+ wallcycle_stop(wcycle, WallCycleCounter::Force);
nbv->atomdata_add_nbat_f_to_f(AtomLocality::All,
forceOutNonbonded->forceWithShiftForces().force());
- wallcycle_start_nocount(wcycle, ewcFORCE);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::Force);
}
/* If there are multiple fshift output buffers we need to reduce them */
// TODO Force flags should include haveFreeEnergyWork for this domain
if (stepWork.useGpuXHalo && (domainWork.haveCpuBondedWork || domainWork.haveFreeEnergyWork))
{
- wallcycle_stop(wcycle, ewcFORCE);
+ wallcycle_stop(wcycle, WallCycleCounter::Force);
/* Wait for non-local coordinate data to be copied from device */
stateGpu->waitCoordinatesReadyOnHost(AtomLocality::NonLocal);
- wallcycle_start_nocount(wcycle, ewcFORCE);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::Force);
}
// Compute wall interactions, when present.
// Note: should be moved to special forces.
- if (inputrec->nwall && stepWork.computeNonbondedForces)
+ if (inputrec.nwall && stepWork.computeNonbondedForces)
{
/* foreign lambda component for walls */
- real dvdl_walls = do_walls(*inputrec, *fr, box, *mdatoms, x.unpaddedConstArrayRef(),
- &forceOutMtsLevel0.forceWithVirial(), lambda[efptVDW],
- enerd->grpp.ener[egLJSR].data(), nrnb);
- enerd->dvdl_lin[efptVDW] += dvdl_walls;
+ real dvdl_walls = do_walls(inputrec,
+ *fr,
+ box,
+ mdatoms->typeA ? gmx::arrayRefFromArray(mdatoms->typeA, mdatoms->nr)
+ : gmx::ArrayRef<int>{},
+ mdatoms->typeB ? gmx::arrayRefFromArray(mdatoms->typeB, mdatoms->nr)
+ : gmx::ArrayRef<int>{},
+ mdatoms->cENER ? gmx::arrayRefFromArray(mdatoms->cENER, mdatoms->nr)
+ : gmx::ArrayRef<unsigned short>{},
+ mdatoms->homenr,
+ mdatoms->nPerturbed,
+ x.unpaddedConstArrayRef(),
+ &forceOutMtsLevel0.forceWithVirial(),
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)],
+ enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::LJSR],
+ nrnb);
+ enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Vdw] += dvdl_walls;
}
if (stepWork.computeListedForces)
{
ListedForces& listedForces = fr->listedForces[mtsIndex];
ForceOutputs& forceOut = (mtsIndex == 0 ? forceOutMtsLevel0 : *forceOutMtsLevel1);
- listedForces.calculate(
- wcycle, box, inputrec->fepvals, cr, ms, x, xWholeMolecules, fr->fcdata.get(),
- hist, &forceOut, fr, &pbc, enerd, nrnb, lambda.data(), mdatoms,
- DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr, stepWork);
+ listedForces.calculate(wcycle,
+ box,
+ inputrec.fepvals.get(),
+ cr,
+ ms,
+ x,
+ xWholeMolecules,
+ fr->fcdata.get(),
+ hist,
+ &forceOut,
+ fr,
+ &pbc,
+ enerd,
+ nrnb,
+ lambda,
+ mdatoms,
+ DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr,
+ stepWork);
}
}
if (stepWork.computeSlowForces)
{
- calculateLongRangeNonbondeds(fr, inputrec, cr, nrnb, wcycle, mdatoms,
- x.unpaddedConstArrayRef(), &forceOutMtsLevel1->forceWithVirial(),
- enerd, box, lambda.data(), as_rvec_array(dipoleData.muStateAB),
- stepWork, ddBalanceRegionHandler);
+ calculateLongRangeNonbondeds(fr,
+ inputrec,
+ cr,
+ nrnb,
+ wcycle,
+ mdatoms,
+ x.unpaddedConstArrayRef(),
+ &forceOutMtsLevel1->forceWithVirial(),
+ enerd,
+ box,
+ lambda,
+ dipoleData.muStateAB,
+ stepWork,
+ ddBalanceRegionHandler);
}
- wallcycle_stop(wcycle, ewcFORCE);
+ wallcycle_stop(wcycle, WallCycleCounter::Force);
// VdW dispersion correction, only computed on master rank to avoid double counting
if ((stepWork.computeEnergy || stepWork.computeVirial) && fr->dispersionCorrection && MASTER(cr))
{
// Calculate long range corrections to pressure and energy
- const DispersionCorrection::Correction correction =
- fr->dispersionCorrection->calculate(box, lambda[efptVDW]);
+ const DispersionCorrection::Correction correction = fr->dispersionCorrection->calculate(
+ box, lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)]);
if (stepWork.computeEnergy)
{
enerd->term[F_DISPCORR] = correction.energy;
enerd->term[F_DVDL_VDW] += correction.dvdl;
- enerd->dvdl_lin[efptVDW] += correction.dvdl;
+ enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Vdw] += correction.dvdl;
}
if (stepWork.computeVirial)
{
}
}
- computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation, imdSession, pull_work, step, t,
- wcycle, fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda,
- stepWork, &forceOutMtsLevel0.forceWithVirial(),
- forceOutMtsLevel1 ? &forceOutMtsLevel1->forceWithVirial() : nullptr, enerd,
- ed, stepWork.doNeighborSearch);
+ computeSpecialForces(fplog,
+ cr,
+ inputrec,
+ awh,
+ enforcedRotation,
+ imdSession,
+ pull_work,
+ step,
+ t,
+ wcycle,
+ fr->forceProviders,
+ box,
+ x.unpaddedArrayRef(),
+ mdatoms,
+ lambda,
+ stepWork,
+ &forceOutMtsLevel0.forceWithVirial(),
+ forceOutMtsLevel1 ? &forceOutMtsLevel1->forceWithVirial() : nullptr,
+ enerd,
+ ed,
+ stepWork.doNeighborSearch);
+
+ if (havePPDomainDecomposition(cr) && stepWork.computeForces && stepWork.useGpuFHalo
+ && domainWork.haveCpuLocalForceWork)
+ {
+ stateGpu->copyForcesToGpu(forceOutMtsLevel0.forceWithShiftForces().force(), AtomLocality::Local);
+ }
GMX_ASSERT(!(nonbondedAtMtsLevel1 && stepWork.useGpuFBufferOps),
"The schedule below does not allow for nonbonded MTS with GPU buffer ops");
if (simulationWork.useGpuNonbonded)
{
cycles_wait_gpu += Nbnxm::gpu_wait_finish_task(
- nbv->gpu_nbv, stepWork, AtomLocality::NonLocal, enerd->grpp.ener[egLJSR].data(),
- enerd->grpp.ener[egCOULSR].data(), forceWithShiftForces.shiftForces(), wcycle);
+ nbv->gpu_nbv,
+ stepWork,
+ AtomLocality::NonLocal,
+ enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::LJSR].data(),
+ enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR].data(),
+ forceWithShiftForces.shiftForces(),
+ wcycle);
}
else
{
- wallcycle_start_nocount(wcycle, ewcFORCE);
- do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::NonLocal, enbvClearFYes,
- step, nrnb, wcycle);
- wallcycle_stop(wcycle, ewcFORCE);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::Force);
+ do_nb_verlet(
+ fr, ic, enerd, stepWork, InteractionLocality::NonLocal, enbvClearFYes, step, nrnb, wcycle);
+ wallcycle_stop(wcycle, WallCycleCounter::Force);
}
if (stepWork.useGpuFBufferOps)
if (combineMtsForcesBeforeHaloExchange)
{
const int numAtoms = havePPDomainDecomposition(cr) ? dd_numAtomsZones(*cr->dd) : mdatoms->homenr;
- combineMtsForces(numAtoms, force.unpaddedArrayRef(), forceView->forceMtsCombined(),
- inputrec->mtsLevels[1].stepFactor);
+ combineMtsForces(numAtoms,
+ force.unpaddedArrayRef(),
+ forceView->forceMtsCombined(),
+ inputrec.mtsLevels[1].stepFactor);
}
if (havePPDomainDecomposition(cr))
if (stepWork.useGpuFHalo)
{
- if (domainWork.haveCpuLocalForceWork)
+ // If there exist CPU forces, data from halo exchange should accumulate into these
+ bool accumulateForces = domainWork.haveCpuLocalForceWork;
+ if (!accumulateForces)
{
- stateGpu->copyForcesToGpu(forceOutMtsLevel0.forceWithShiftForces().force(),
- AtomLocality::Local);
+ // Force halo exchange will set a subset of local atoms with remote non-local data
+ // First clear local portion of force array, so that untouched atoms are zero
+ stateGpu->clearForcesOnGpu(AtomLocality::Local);
}
- communicateGpuHaloForces(*cr, domainWork.haveCpuLocalForceWork);
+ communicateGpuHaloForces(*cr, accumulateForces);
}
else
{
&& !DOMAINDECOMP(cr) && !stepWork.useGpuFBufferOps);
if (alternateGpuWait)
{
- alternatePmeNbGpuWaitReduce(fr->nbv.get(), fr->pmedata, forceOutNonbonded,
- forceOutMtsLevel1, enerd, lambda[efptCOUL], stepWork, wcycle);
+ alternatePmeNbGpuWaitReduce(fr->nbv.get(),
+ fr->pmedata,
+ forceOutNonbonded,
+ forceOutMtsLevel1,
+ enerd,
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
+ stepWork,
+ wcycle);
}
if (!alternateGpuWait && useGpuPmeOnThisRank)
{
- pme_gpu_wait_and_reduce(fr->pmedata, stepWork, wcycle,
- &forceOutMtsLevel1->forceWithVirial(), enerd, lambda[efptCOUL]);
+ pme_gpu_wait_and_reduce(fr->pmedata,
+ stepWork,
+ wcycle,
+ &forceOutMtsLevel1->forceWithVirial(),
+ enerd,
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)]);
}
/* Wait for local GPU NB outputs on the non-alternating wait path */
*/
const float gpuWaitApiOverheadMargin = 2e6F; /* cycles */
const float waitCycles = Nbnxm::gpu_wait_finish_task(
- nbv->gpu_nbv, stepWork, AtomLocality::Local, enerd->grpp.ener[egLJSR].data(),
- enerd->grpp.ener[egCOULSR].data(),
- forceOutNonbonded->forceWithShiftForces().shiftForces(), wcycle);
+ nbv->gpu_nbv,
+ stepWork,
+ AtomLocality::Local,
+ enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::LJSR].data(),
+ enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR].data(),
+ forceOutNonbonded->forceWithShiftForces().shiftForces(),
+ wcycle);
if (ddBalanceRegionHandler.useBalancingRegion())
{
{
// NOTE: emulation kernel is not included in the balancing region,
// but emulation mode does not target performance anyway
- wallcycle_start_nocount(wcycle, ewcFORCE);
- do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::Local,
- DOMAINDECOMP(cr) ? enbvClearFNo : enbvClearFYes, step, nrnb, wcycle);
- wallcycle_stop(wcycle, ewcFORCE);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::Force);
+ do_nb_verlet(fr,
+ ic,
+ enerd,
+ stepWork,
+ InteractionLocality::Local,
+ DOMAINDECOMP(cr) ? enbvClearFNo : enbvClearFYes,
+ step,
+ nrnb,
+ wcycle);
+ wallcycle_stop(wcycle, WallCycleCounter::Force);
}
// If on GPU PME-PP comms path, receive forces from PME before GPU buffer ops
/* In case of node-splitting, the PP nodes receive the long-range
* forces, virial and energy from the PME nodes here.
*/
- pme_receive_force_ener(fr, cr, &forceOutMtsLevel1->forceWithVirial(), enerd,
+ pme_receive_force_ener(fr,
+ cr,
+ &forceOutMtsLevel1->forceWithVirial(),
+ enerd,
simulationWork.useGpuPmePpCommunication,
- stepWork.useGpuPmeFReduction, wcycle);
+ stepWork.useGpuPmeFReduction,
+ wcycle);
}
}
}
- launchGpuEndOfStepTasks(nbv, fr->gpuBonded, fr->pmedata, enerd, *runScheduleWork,
- useGpuPmeOnThisRank, step, wcycle);
+ launchGpuEndOfStepTasks(
+ nbv, fr->gpuBonded, fr->pmedata, enerd, *runScheduleWork, useGpuPmeOnThisRank, step, wcycle);
if (DOMAINDECOMP(cr))
{
&& combineMtsForcesBeforeHaloExchange);
if (stepWork.computeForces)
{
- postProcessForceWithShiftForces(nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutMtsLevel0,
- vir_force, *mdatoms, *fr, vsite, stepWork);
+ postProcessForceWithShiftForces(
+ nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutMtsLevel0, vir_force, *mdatoms, *fr, vsite, stepWork);
if (fr->useMts && stepWork.computeSlowForces && !haveCombinedMtsForces)
{
- postProcessForceWithShiftForces(nrnb, wcycle, box, x.unpaddedArrayRef(), forceOutMtsLevel1,
- vir_force, *mdatoms, *fr, vsite, stepWork);
+ postProcessForceWithShiftForces(
+ nrnb, wcycle, box, x.unpaddedArrayRef(), forceOutMtsLevel1, vir_force, *mdatoms, *fr, vsite, stepWork);
}
}
/* In case of node-splitting, the PP nodes receive the long-range
* forces, virial and energy from the PME nodes here.
*/
- pme_receive_force_ener(fr, cr, &forceOutMtsLevel1->forceWithVirial(), enerd,
- simulationWork.useGpuPmePpCommunication, false, wcycle);
+ pme_receive_force_ener(fr,
+ cr,
+ &forceOutMtsLevel1->forceWithVirial(),
+ enerd,
+ simulationWork.useGpuPmePpCommunication,
+ false,
+ wcycle);
}
if (stepWork.computeForces)
* otherwise we have to post-process two outputs and then combine them.
*/
ForceOutputs& forceOutCombined = (haveCombinedMtsForces ? forceOutMts.value() : forceOutMtsLevel0);
- postProcessForces(cr, step, nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutCombined,
- vir_force, mdatoms, fr, vsite, stepWork);
+ postProcessForces(
+ cr, step, nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutCombined, vir_force, mdatoms, fr, vsite, stepWork);
if (fr->useMts && stepWork.computeSlowForces && !haveCombinedMtsForces)
{
- postProcessForces(cr, step, nrnb, wcycle, box, x.unpaddedArrayRef(), forceOutMtsLevel1,
- vir_force, mdatoms, fr, vsite, stepWork);
+ postProcessForces(
+ cr, step, nrnb, wcycle, box, x.unpaddedArrayRef(), forceOutMtsLevel1, vir_force, mdatoms, fr, vsite, stepWork);
- combineMtsForces(mdatoms->homenr, force.unpaddedArrayRef(),
- forceView->forceMtsCombined(), inputrec->mtsLevels[1].stepFactor);
+ combineMtsForces(mdatoms->homenr,
+ force.unpaddedArrayRef(),
+ forceView->forceMtsCombined(),
+ inputrec.mtsLevels[1].stepFactor);
}
}
if (stepWork.computeEnergy)
{
/* Compute the final potential energy terms */
- accumulatePotentialEnergies(enerd, lambda, inputrec->fepvals);
+ accumulatePotentialEnergies(enerd, lambda, inputrec.fepvals.get());
- if (!EI_TPI(inputrec->eI))
+ if (!EI_TPI(inputrec.eI))
{
- checkPotentialEnergyValidity(step, *enerd, *inputrec);
+ checkPotentialEnergyValidity(step, *enerd, inputrec);
}
}
{
if (doIntraSim_)
{
- std::transform(std::begin(*signals_), std::end(*signals_), std::begin(mpiBuffer_),
+ std::transform(std::begin(*signals_),
+ std::end(*signals_),
+ std::begin(mpiBuffer_),
[](const SimulationSignals::value_type& s) { return s.sig; });
return mpiBuffer_;
range_check(ai + g0, 0, maxsid);
if (sid[aj + g0].sid != -1)
{
- gmx_fatal(FARGS, "sid[%d]=%d, sid[%d]=%d, file %s, line %d", ai, sid[ai + g0].sid,
- aj, sid[aj + g0].sid, __FILE__, __LINE__);
+ gmx_fatal(FARGS,
+ "sid[%d]=%d, sid[%d]=%d, file %s, line %d",
+ ai,
+ sid[ai + g0].sid,
+ aj,
+ sid[aj + g0].sid,
+ __FILE__,
+ __LINE__);
}
else
{
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
-#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/md_support.h"
#include "gromacs/mdlib/rbin.h"
#include "gromacs/mdlib/tgroup.h"
return to;
}
-void global_stat(const gmx_global_stat* gs,
- const t_commrec* cr,
- gmx_enerdata_t* enerd,
- tensor fvir,
- tensor svir,
- const t_inputrec* inputrec,
- gmx_ekindata_t* ekind,
- const gmx::Constraints* constr,
- t_vcm* vcm,
- int nsig,
- real* sig,
- int* totalNumberOfBondedInteractions,
- bool bSumEkinhOld,
- int flags)
+void global_stat(const gmx_global_stat& gs,
+ const t_commrec* cr,
+ gmx_enerdata_t* enerd,
+ tensor fvir,
+ tensor svir,
+ const t_inputrec& inputrec,
+ gmx_ekindata_t* ekind,
+ gmx::ArrayRef<real> constraintsRmsdData,
+ t_vcm* vcm,
+ gmx::ArrayRef<real> sig,
+ bool bSumEkinhOld,
+ int flags)
/* instead of current system, gmx_booleans for summing virial, kinetic energy, and other terms */
{
- t_bin* rb;
- int * itc0, *itc1;
- int ie = 0, ifv = 0, isv = 0, irmsd = 0;
+ int ie = 0, ifv = 0, isv = 0, irmsd = 0;
int idedl = 0, idedlo = 0, idvdll = 0, idvdlnl = 0, iepl = 0, icm = 0, imass = 0, ica = 0, inb = 0;
- int isig = -1;
- int icj = -1, ici = -1, icx = -1;
- int inn[egNR];
- real copyenerd[F_NRE];
- int nener, j;
- double nb;
- gmx_bool bVV, bTemp, bEner, bPres, bConstrVir, bEkinAveVel, bReadEkin;
- bool checkNumberOfBondedInteractions = (flags & CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS) != 0;
+ int isig = -1;
+ int icj = -1, ici = -1, icx = -1;
- bVV = EI_VV(inputrec->eI);
- bTemp = ((flags & CGLO_TEMPERATURE) != 0);
- bEner = ((flags & CGLO_ENERGY) != 0);
- bPres = ((flags & CGLO_PRESSURE) != 0);
- bConstrVir = ((flags & CGLO_CONSTRAINT) != 0);
- bEkinAveVel = (inputrec->eI == eiVV || (inputrec->eI == eiVVAK && bPres));
- bReadEkin = ((flags & CGLO_READEKIN) != 0);
+ bool checkNumberOfBondedInteractions = (flags & CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS) != 0;
+ bool bVV = EI_VV(inputrec.eI);
+ bool bTemp = ((flags & CGLO_TEMPERATURE) != 0);
+ bool bEner = ((flags & CGLO_ENERGY) != 0);
+ bool bPres = ((flags & CGLO_PRESSURE) != 0);
+ bool bConstrVir = ((flags & CGLO_CONSTRAINT) != 0);
+ bool bEkinAveVel = (inputrec.eI == IntegrationAlgorithm::VV
+ || (inputrec.eI == IntegrationAlgorithm::VVAK && bPres));
+ bool bReadEkin = ((flags & CGLO_READEKIN) != 0);
- rb = gs->rb;
- itc0 = gs->itc0;
- itc1 = gs->itc1;
+ t_bin* rb = gs.rb;
+ int* itc0 = gs.itc0;
+ int* itc1 = gs.itc1;
reset_bin(rb);
communicated and summed when they need to be, to avoid repeating
the sums and overcounting. */
- nener = filter_enerdterm(enerd->term, TRUE, copyenerd, bTemp, bPres, bEner);
+ std::array<real, F_NRE> copyenerd;
+ int nener = filter_enerdterm(enerd->term.data(), TRUE, copyenerd.data(), bTemp, bPres, bEner);
/* First, the data that needs to be communicated with velocity verlet every time
This is just the constraint virial.*/
{
if (ekind)
{
- for (j = 0; (j < inputrec->opts.ngtc); j++)
+ for (int j = 0; (j < inputrec.opts.ngtc); j++)
{
if (bSumEkinhOld)
{
ifv = add_binr(rb, DIM * DIM, fvir[0]);
}
- gmx::ArrayRef<real> rmsdData;
+ gmx::EnumerationArray<NonBondedEnergyTerms, int> inn;
if (bEner)
{
- ie = add_binr(rb, nener, copyenerd);
- if (constr)
+ ie = add_binr(rb, nener, copyenerd.data());
+ if (!constraintsRmsdData.empty())
{
- rmsdData = constr->rmsdData();
- if (!rmsdData.empty())
- {
- irmsd = add_binr(rb, 2, rmsdData.data());
- }
+ irmsd = add_binr(rb, 2, constraintsRmsdData.data());
}
-
- for (j = 0; (j < egNR); j++)
+ for (auto key : gmx::keysOf(inn))
{
- inn[j] = add_binr(rb, enerd->grpp.nener, enerd->grpp.ener[j].data());
+ inn[key] = add_binr(rb, enerd->grpp.nener, enerd->grpp.energyGroupPairTerms[key].data());
}
- if (inputrec->efep != efepNO)
+ if (inputrec.efep != FreeEnergyPerturbationType::No)
{
- idvdll = add_bind(rb, efptNR, enerd->dvdl_lin);
- idvdlnl = add_bind(rb, efptNR, enerd->dvdl_nonlin);
+ idvdll = add_bind(rb, enerd->dvdl_lin);
+ idvdlnl = add_bind(rb, enerd->dvdl_nonlin);
if (enerd->foreignLambdaTerms.numLambdas() > 0)
{
- iepl = add_bind(rb, enerd->foreignLambdaTerms.energies().size(),
+ iepl = add_bind(rb,
+ enerd->foreignLambdaTerms.energies().size(),
enerd->foreignLambdaTerms.energies().data());
}
}
{
icm = add_binr(rb, DIM * vcm->nr, vcm->group_p[0]);
imass = add_binr(rb, vcm->nr, vcm->group_mass.data());
- if (vcm->mode == ecmANGULAR)
+ if (vcm->mode == ComRemovalAlgorithm::Angular)
{
icj = add_binr(rb, DIM * vcm->nr, vcm->group_j[0]);
icx = add_binr(rb, DIM * vcm->nr, vcm->group_x[0]);
}
}
+ double nb;
if (checkNumberOfBondedInteractions)
{
- nb = cr->dd->nbonded_local;
+ GMX_RELEASE_ASSERT(DOMAINDECOMP(cr),
+ "No need to check number of bonded interactions when not using domain "
+ "decomposition");
+ nb = numBondedInteractions(*cr->dd);
inb = add_bind(rb, 1, &nb);
}
- if (nsig > 0)
+ if (!sig.empty())
{
- isig = add_binr(rb, nsig, sig);
+ isig = add_binr(rb, sig);
}
- /* Global sum it all */
- if (debug)
- {
- fprintf(debug, "Summing %d energies\n", rb->maxreal);
- }
sum_bin(rb, cr);
/* Extract all the data locally */
{
if (ekind)
{
- for (j = 0; (j < inputrec->opts.ngtc); j++)
+ for (int j = 0; (j < inputrec.opts.ngtc); j++)
{
if (bSumEkinhOld)
{
if (bEner)
{
- extract_binr(rb, ie, nener, copyenerd);
- if (!rmsdData.empty())
+ extract_binr(rb, ie, nener, copyenerd.data());
+ if (!constraintsRmsdData.empty())
{
- extract_binr(rb, irmsd, rmsdData);
+ extract_binr(rb, irmsd, constraintsRmsdData);
}
-
- for (j = 0; (j < egNR); j++)
+ for (auto key : gmx::keysOf(inn))
{
- extract_binr(rb, inn[j], enerd->grpp.nener, enerd->grpp.ener[j].data());
+ extract_binr(rb, inn[key], enerd->grpp.nener, enerd->grpp.energyGroupPairTerms[key].data());
}
- if (inputrec->efep != efepNO)
+ if (inputrec.efep != FreeEnergyPerturbationType::No)
{
- extract_bind(rb, idvdll, efptNR, enerd->dvdl_lin);
- extract_bind(rb, idvdlnl, efptNR, enerd->dvdl_nonlin);
+ extract_bind(rb, idvdll, enerd->dvdl_lin);
+ extract_bind(rb, idvdlnl, enerd->dvdl_nonlin);
if (enerd->foreignLambdaTerms.numLambdas() > 0)
{
- extract_bind(rb, iepl, enerd->foreignLambdaTerms.energies().size(),
+ extract_bind(rb,
+ iepl,
+ enerd->foreignLambdaTerms.energies().size(),
enerd->foreignLambdaTerms.energies().data());
}
}
- filter_enerdterm(copyenerd, FALSE, enerd->term, bTemp, bPres, bEner);
+ filter_enerdterm(copyenerd.data(), FALSE, enerd->term.data(), bTemp, bPres, bEner);
}
if (vcm)
{
extract_binr(rb, icm, DIM * vcm->nr, vcm->group_p[0]);
extract_binr(rb, imass, vcm->nr, vcm->group_mass.data());
- if (vcm->mode == ecmANGULAR)
+ if (vcm->mode == ComRemovalAlgorithm::Angular)
{
extract_binr(rb, icj, DIM * vcm->nr, vcm->group_j[0]);
extract_binr(rb, icx, DIM * vcm->nr, vcm->group_x[0]);
if (checkNumberOfBondedInteractions)
{
extract_bind(rb, inb, 1, &nb);
- *totalNumberOfBondedInteractions = gmx::roundToInt(nb);
+ GMX_RELEASE_ASSERT(DOMAINDECOMP(cr),
+ "No need to check number of bonded interactions when not using domain "
+ "decomposition");
+ setNumberOfBondedInteractionsOverAllDomains(*cr->dd, gmx::roundToInt(nb));
}
- if (nsig > 0)
+ if (!sig.empty())
{
- extract_binr(rb, isig, nsig, sig);
+ extract_binr(rb, isig, sig);
}
}
#include "gromacs/math/vectypes.h"
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
struct gmx_enerdata_t;
struct t_vcm;
struct t_inputrec;
namespace gmx
{
+template<typename T>
+class ArrayRef;
class Constraints;
-}
+} // namespace gmx
typedef struct gmx_global_stat* gmx_global_stat_t;
void global_stat_destroy(gmx_global_stat_t gs);
/*! \brief All-reduce energy-like quantities over cr->mpi_comm_mysim */
-void global_stat(const gmx_global_stat* gs,
- const t_commrec* cr,
- gmx_enerdata_t* enerd,
- tensor fvir,
- tensor svir,
- const t_inputrec* inputrec,
- gmx_ekindata_t* ekind,
- const gmx::Constraints* constr,
- t_vcm* vcm,
- int nsig,
- real* sig,
- int* totalNumberOfBondedInteractions,
- bool bSumEkinhOld,
- int flags);
+void global_stat(const gmx_global_stat& gs,
+ const t_commrec* cr,
+ gmx_enerdata_t* enerd,
+ tensor fvir,
+ tensor svir,
+ const t_inputrec& inputrec,
+ gmx_ekindata_t* ekind,
+ gmx::ArrayRef<real> constraintsRmsdData,
+ t_vcm* vcm,
+ gmx::ArrayRef<real> sig,
+ bool bSumEkinhOld,
+ int flags);
/*! \brief Returns TRUE if io should be done */
inline bool do_per_step(int64_t step, int64_t nstep)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
StopConditionSignal::StopConditionSignal(int nstList, bool makeBinaryReproducibleSimulation, int nstSignalComm) :
- handledStopCondition_(gmx_stop_cond_none),
+ handledStopCondition_(StopCondition::None),
makeBinaryReproducibleSimulation_(makeBinaryReproducibleSimulation),
nstSignalComm_(nstSignalComm),
nstList_(nstList)
StopSignal signal = StopSignal::noSignal;
/* Check whether everything is still alright */
- if (static_cast<int>(gmx_get_stop_condition()) > handledStopCondition_)
+ if (gmx_get_stop_condition() > handledStopCondition_)
{
int nsteps_stop = -1;
/* this just makes signals[].sig compatible with the hack
of sending signals around by MPI_Reduce together with
other floats */
- if ((gmx_get_stop_condition() == gmx_stop_cond_next_ns)
- || (makeBinaryReproducibleSimulation_ && gmx_get_stop_condition() == gmx_stop_cond_next))
+ if ((gmx_get_stop_condition() == StopCondition::NextNS)
+ || (makeBinaryReproducibleSimulation_ && gmx_get_stop_condition() == StopCondition::Next))
{
/* We need at least two global communication steps to pass
* around the signal. We stop at a pair-list creation step
signal = StopSignal::stopAtNextNSStep;
nsteps_stop = std::max(nstList_, 2 * nstSignalComm_);
}
- else if (gmx_get_stop_condition() == gmx_stop_cond_next)
+ else if (gmx_get_stop_condition() == StopCondition::Next)
{
/* Stop directly after the next global communication step.
* This breaks exact continuation.
}
if (fplog)
{
- fprintf(fplog, "\n\nReceived the %s signal, stopping within %d steps\n\n",
- gmx_get_signal_name(), nsteps_stop);
+ fprintf(fplog,
+ "\n\nReceived the %s signal, stopping within %d steps\n\n",
+ gmx_get_signal_name(),
+ nsteps_stop);
fflush(fplog);
}
- fprintf(stderr, "\n\nReceived the %s signal, stopping within %d steps\n\n",
- gmx_get_signal_name(), nsteps_stop);
+ fprintf(stderr,
+ "\n\nReceived the %s signal, stopping within %d steps\n\n",
+ gmx_get_signal_name(),
+ nsteps_stop);
fflush(stderr);
- handledStopCondition_ = static_cast<int>(gmx_get_stop_condition());
+ handledStopCondition_ = gmx_get_stop_condition();
}
return signal;
fprintf(fplog,
"\nStep %s: Run time exceeded %.3f hours, "
"will terminate the run within %d steps\n",
- gmx_step_str(step, sbuf), maximumHoursToRun_ * 0.99, nsteps_stop);
+ gmx_step_str(step, sbuf),
+ maximumHoursToRun_ * 0.99,
+ nsteps_stop);
}
fprintf(stderr,
"\nStep %s: Run time exceeded %.3f hours, "
"will terminate the run within %d steps\n",
- gmx_step_str(step, sbuf), maximumHoursToRun_ * 0.99, nsteps_stop);
+ gmx_step_str(step, sbuf),
+ maximumHoursToRun_ * 0.99,
+ nsteps_stop);
signalSent_ = true;
return StopSignal::stopAtNextNSStep;
}
});
}
- return std::make_unique<StopHandler>(signal, simulationShareState, stopConditions_,
- neverUpdateNeighborList);
+ return std::make_unique<StopHandler>(
+ signal, simulationShareState, stopConditions_, neverUpdateNeighborList);
}
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* * stop at the next neighbor-searching step
* * stop as soon as signal is received
*/
-enum class StopSignal
+enum class StopSignal : int
{
noSignal = 0,
stopAtNextNSStep = 1,
*/
void setSignal() const
{
- for (auto& condition : stopConditions_)
+ for (const auto& condition : stopConditions_)
{
const StopSignal sig = condition();
if (sig != StopSignal::noSignal)
StopSignal getSignal(FILE* fplog);
private:
- int handledStopCondition_;
- const bool makeBinaryReproducibleSimulation_;
- const int nstSignalComm_;
- const int nstList_;
+ StopCondition handledStopCondition_;
+ const bool makeBinaryReproducibleSimulation_;
+ const int nstSignalComm_;
+ const int nstList_;
};
/*! \libinternal
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
gmx_add_unit_test(MdlibUnitTest mdlib-test HARDWARE_DETECTION
CPP_SOURCE_FILES
calc_verletbuf.cpp
+ calcvir.cpp
constr.cpp
constrtestdata.cpp
constrtestrunners.cpp
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief Tests for virial calculation.
+ *
+ * \author Joe Jordan <ejjordan@kth.se>
+ */
+#include "gmxpre.h"
+
+#include "gromacs/mdlib/calcvir.h"
+
+#include <gtest/gtest.h>
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+
+
+class CalcvirTest : public ::testing::Test
+{
+public:
+ TestReferenceData refData_;
+ TestReferenceChecker checker_;
+ std::vector<gmx::RVec> coordinates_;
+ std::vector<gmx::RVec> forces_;
+ int numVirialAtoms_;
+ tensor virial_{ { 0 } };
+ FloatingPointTolerance tolerances =
+ FloatingPointTolerance(1e-16, 1.0e-16, 1e-16, 1.0e-7, 1000, 100, false);
+
+ CalcvirTest() :
+ checker_(refData_.rootChecker()),
+ coordinates_{ { 1, 2, 3 },
+ {
+ 4,
+ 5,
+ 6,
+ },
+ { 7, 8, 9 },
+ { 1, 5, 9 } },
+ forces_{ { 0.9, 0.1, 0.3 }, { 0.4, 0.7, 0.2 }, { 0.5, 1, 0.6 }, { 0.9, 0.7, 0.6 } },
+ numVirialAtoms_(coordinates_.size())
+ {
+ checker_.setDefaultTolerance(tolerances);
+ }
+
+private:
+};
+
+TEST_F(CalcvirTest, CanCalculateVirialAllAtomsInBox)
+{
+ calc_vir(numVirialAtoms_, as_rvec_array(coordinates_.data()), as_rvec_array(forces_.data()), virial_, false, nullptr);
+
+ checker_.checkVector(virial_[0], "Virial x");
+ checker_.checkVector(virial_[1], "Virial y");
+ checker_.checkVector(virial_[2], "Virial z");
+}
+
+TEST_F(CalcvirTest, CanCalculateVirialAllAtomsInBoxScrew)
+{
+
+ const matrix box = { { 10, 0, 0 }, { 0, 12, 0 }, { 0, 0, 14 } };
+ calc_vir(numVirialAtoms_, as_rvec_array(coordinates_.data()), as_rvec_array(forces_.data()), virial_, true, box);
+
+ checker_.checkVector(virial_[0], "Virial x");
+ checker_.checkVector(virial_[1], "Virial y");
+ checker_.checkVector(virial_[2], "Virial z");
+}
+
+TEST_F(CalcvirTest, CanCalculateVirialAtomsOutOfBoxScrewX)
+{
+
+ const matrix box = { { 5, 0, 0 }, { 0, 10, 0 }, { 0, 0, 12 } };
+ calc_vir(numVirialAtoms_, as_rvec_array(coordinates_.data()), as_rvec_array(forces_.data()), virial_, true, box);
+
+ checker_.checkVector(virial_[0], "Virial x");
+ checker_.checkVector(virial_[1], "Virial y");
+ checker_.checkVector(virial_[2], "Virial z");
+}
+
+TEST_F(CalcvirTest, CanCalculateVirialAtomsOutOfBoxScrewY)
+{
+
+ const matrix box = { { 10, 0, 0 }, { 0, 5, 0 }, { 0, 0, 12 } };
+ calc_vir(numVirialAtoms_, as_rvec_array(coordinates_.data()), as_rvec_array(forces_.data()), virial_, true, box);
+
+ checker_.checkVector(virial_[0], "Virial x");
+ checker_.checkVector(virial_[1], "Virial y");
+ checker_.checkVector(virial_[2], "Virial z");
+}
+
+TEST_F(CalcvirTest, CanCalculateVirialAtomsOutOfBoxScrewZ)
+{
+
+ const matrix box = { { 10, 0, 0 }, { 0, 12, 0 }, { 0, 0, 5 } };
+ calc_vir(numVirialAtoms_, as_rvec_array(coordinates_.data()), as_rvec_array(forces_.data()), virial_, true, box);
+
+ checker_.checkVector(virial_[0], "Virial x");
+ checker_.checkVector(virial_[1], "Virial y");
+ checker_.checkVector(virial_[2], "Virial z");
+}
+
+TEST_F(CalcvirTest, CanCalculateVirialAtomsOutOfBoxScrewXYZ)
+{
+
+ const matrix box = { { 4, 0, 0 }, { 0, 5, 0 }, { 0, 0, 6 } };
+ calc_vir(numVirialAtoms_, as_rvec_array(coordinates_.data()), as_rvec_array(forces_.data()), virial_, true, box);
+
+ checker_.checkVector(virial_[0], "Virial x");
+ checker_.checkVector(virial_[1], "Virial y");
+ checker_.checkVector(virial_[2], "Virial z");
+}
+
+} // namespace
+} // namespace test
+} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
namespace
{
+// Define the set of PBCs to run the test for
+const std::vector<t_pbc> c_pbcs = [] {
+ std::vector<t_pbc> pbcs;
+ t_pbc pbc;
+
+ // Infinitely small box
+ matrix boxNone = { { 0, 0, 0 }, { 0, 0, 0 }, { 0, 0, 0 } };
+ set_pbc(&pbc, PbcType::No, boxNone);
+ pbcs.emplace_back(pbc);
+
+ // Rectangular box
+ matrix boxXyz = { { 10.0, 0.0, 0.0 }, { 0.0, 20.0, 0.0 }, { 0.0, 0.0, 15.0 } };
+ set_pbc(&pbc, PbcType::Xyz, boxXyz);
+ pbcs.emplace_back(pbc);
+
+ return pbcs;
+}();
+
+
+struct ConstraintsTestSystem
+{
+ //! Human-friendly name of the system.
+ std::string title;
+ //! Number of atoms in the system.
+ int numAtoms;
+ //! Atom masses. Size of this vector should be equal to numAtoms.
+ std::vector<real> masses;
+ /*! \brief List of constraints, organized in triples of integers.
+ *
+ * First integer is the index of type for a constraint, second
+ * and third are the indices of constrained atoms. The types
+ * of constraints should be sequential but not necessarily
+ * start from zero (which is the way they normally are in
+ * GROMACS).
+ */
+ std::vector<int> constraints;
+ /*! \brief Target values for bond lengths for bonds of each type.
+ *
+ * The size of this vector should be equal to the total number of
+ * unique types in constraints vector.
+ */
+ std::vector<real> constraintsR0;
+ //! Coordinates before integration step.
+ std::vector<RVec> x;
+ //! Coordinates after integration step, but before constraining.
+ std::vector<RVec> xPrime;
+ //! Velocities before constraining.
+ std::vector<RVec> v;
+
+ //! Reference values for scaled virial tensor.
+ tensor virialScaledRef;
+
+ //! Target tolerance for SHAKE.
+ real shakeTolerance = 0.0001;
+ /*! \brief Use successive over-relaxation method for SHAKE iterations.
+ *
+ * The general formula is:
+ * x_n+1 = (1-omega)*x_n + omega*f(x_n),
+ * where omega = 1 if SOR is off and may be < 1 if SOR is on.
+ */
+ bool shakeUseSOR = false;
+
+ //! Number of iterations used to compute the inverse matrix.
+ int lincsNIter = 1;
+ //! The order for algorithm that adjusts the direction of the bond after constraints are applied.
+ int lincslincsExpansionOrder = 4;
+ //! The threshold value for the change in bond angle. When exceeded the program will issue a warning
+ real lincsWarnAngle = 30.0;
+
+ FloatingPointTolerance lengthTolerance = absoluteTolerance(0.0002);
+ FloatingPointTolerance comTolerance = absoluteTolerance(0.0001);
+ FloatingPointTolerance virialTolerance = absoluteTolerance(0.0001);
+};
+
+const std::vector<ConstraintsTestSystem> c_constraintsTestSystemList = [] {
+ std::vector<ConstraintsTestSystem> constraintsTestSystemList;
+ {
+ ConstraintsTestSystem constraintsTestSystem;
+
+ constraintsTestSystem.title = "one constraint (e.g. OH)";
+ constraintsTestSystem.numAtoms = 2;
+
+ constraintsTestSystem.masses = { 1.0, 12.0 };
+ constraintsTestSystem.constraints = { 0, 0, 1 };
+ constraintsTestSystem.constraintsR0 = { 0.1 };
+
+ real oneTenthOverSqrtTwo = 0.1_real / std::sqrt(2.0_real);
+
+ constraintsTestSystem.x = { { 0.0, oneTenthOverSqrtTwo, 0.0 }, { oneTenthOverSqrtTwo, 0.0, 0.0 } };
+ constraintsTestSystem.xPrime = { { 0.01, 0.08, 0.01 }, { 0.06, 0.01, -0.01 } };
+ constraintsTestSystem.v = { { 1.0, 2.0, 3.0 }, { 3.0, 2.0, 1.0 } };
+
+ tensor virialScaledRef = { { -5.58e-04, 5.58e-04, 0.00e+00 },
+ { 5.58e-04, -5.58e-04, 0.00e+00 },
+ { 0.00e+00, 0.00e+00, 0.00e+00 } };
+
+ memcpy(constraintsTestSystem.virialScaledRef, virialScaledRef, DIM * DIM * sizeof(real));
+
+ constraintsTestSystemList.emplace_back(constraintsTestSystem);
+ }
+ {
+ ConstraintsTestSystem constraintsTestSystem;
+
+ constraintsTestSystem.title = "two disjoint constraints";
+ constraintsTestSystem.numAtoms = 4;
+ constraintsTestSystem.masses = { 0.5, 1.0 / 3.0, 0.25, 1.0 };
+ constraintsTestSystem.constraints = { 0, 0, 1, 1, 2, 3 };
+ constraintsTestSystem.constraintsR0 = { 2.0, 1.0 };
+
+
+ constraintsTestSystem.x = { { 2.50, -3.10, 15.70 },
+ { 0.51, -3.02, 15.55 },
+ { -0.50, -3.00, 15.20 },
+ { -1.51, -2.95, 15.05 } };
+
+ constraintsTestSystem.xPrime = { { 2.50, -3.10, 15.70 },
+ { 0.51, -3.02, 15.55 },
+ { -0.50, -3.00, 15.20 },
+ { -1.51, -2.95, 15.05 } };
+
+ constraintsTestSystem.v = { { 0.0, 1.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 0.0, 0.0, 1.0 }, { 0.0, 0.0, 0.0 } };
+
+ tensor virialScaledRef = { { 3.3e-03, -1.7e-04, 5.6e-04 },
+ { -1.7e-04, 8.9e-06, -2.8e-05 },
+ { 5.6e-04, -2.8e-05, 8.9e-05 } };
+
+ memcpy(constraintsTestSystem.virialScaledRef, virialScaledRef, DIM * DIM * sizeof(real));
+
+ constraintsTestSystemList.emplace_back(constraintsTestSystem);
+ }
+ {
+ ConstraintsTestSystem constraintsTestSystem;
+
+ constraintsTestSystem.title = "three atoms, connected longitudinally (e.g. CH2)";
+ constraintsTestSystem.numAtoms = 3;
+ constraintsTestSystem.masses = { 1.0, 12.0, 16.0 };
+ constraintsTestSystem.constraints = { 0, 0, 1, 1, 1, 2 };
+ constraintsTestSystem.constraintsR0 = { 0.1, 0.2 };
+
+ real oneTenthOverSqrtTwo = 0.1_real / std::sqrt(2.0_real);
+ real twoTenthsOverSqrtThree = 0.2_real / std::sqrt(3.0_real);
+
+ constraintsTestSystem.x = { { oneTenthOverSqrtTwo, oneTenthOverSqrtTwo, 0.0 },
+ { 0.0, 0.0, 0.0 },
+ { twoTenthsOverSqrtThree, twoTenthsOverSqrtThree, twoTenthsOverSqrtThree } };
+
+ constraintsTestSystem.xPrime = { { 0.08, 0.07, 0.01 }, { -0.02, 0.01, -0.02 }, { 0.10, 0.12, 0.11 } };
+
+ constraintsTestSystem.v = { { 1.0, 0.0, 0.0 }, { 0.0, 1.0, 0.0 }, { 0.0, 0.0, 1.0 } };
+
+ tensor virialScaledRef = { { 4.14e-03, 4.14e-03, 3.31e-03 },
+ { 4.14e-03, 4.14e-03, 3.31e-03 },
+ { 3.31e-03, 3.31e-03, 3.31e-03 } };
+
+ memcpy(constraintsTestSystem.virialScaledRef, virialScaledRef, DIM * DIM * sizeof(real));
+
+ constraintsTestSystemList.emplace_back(constraintsTestSystem);
+ }
+ {
+ ConstraintsTestSystem constraintsTestSystem;
+
+ constraintsTestSystem.title = "four atoms, connected longitudinally";
+ constraintsTestSystem.numAtoms = 4;
+ constraintsTestSystem.masses = { 0.5, 1.0 / 3.0, 0.25, 1.0 };
+ constraintsTestSystem.constraints = { 0, 0, 1, 1, 1, 2, 2, 2, 3 };
+ constraintsTestSystem.constraintsR0 = { 2.0, 1.0, 1.0 };
+
+
+ constraintsTestSystem.x = { { 2.50, -3.10, 15.70 },
+ { 0.51, -3.02, 15.55 },
+ { -0.50, -3.00, 15.20 },
+ { -1.51, -2.95, 15.05 } };
+
+ constraintsTestSystem.xPrime = { { 2.50, -3.10, 15.70 },
+ { 0.51, -3.02, 15.55 },
+ { -0.50, -3.00, 15.20 },
+ { -1.51, -2.95, 15.05 } };
+
+ constraintsTestSystem.v = {
+ { 0.0, 0.0, 2.0 }, { 0.0, 0.0, 3.0 }, { 0.0, 0.0, -4.0 }, { 0.0, 0.0, -1.0 }
+ };
+
+ tensor virialScaledRef = { { 1.15e-01, -4.20e-03, 2.12e-02 },
+ { -4.20e-03, 1.70e-04, -6.41e-04 },
+ { 2.12e-02, -6.41e-04, 5.45e-03 } };
+
+ memcpy(constraintsTestSystem.virialScaledRef, virialScaledRef, DIM * DIM * sizeof(real));
+
+
+ // Overriding default values since LINCS converges slowly for this system.
+ constraintsTestSystem.lincsNIter = 4;
+ constraintsTestSystem.lincslincsExpansionOrder = 8;
+ constraintsTestSystem.virialTolerance = absoluteTolerance(0.01);
+
+ constraintsTestSystemList.emplace_back(constraintsTestSystem);
+ }
+ {
+ ConstraintsTestSystem constraintsTestSystem;
+
+ constraintsTestSystem.title = "three atoms, connected to the central atom (e.g. CH3)";
+ constraintsTestSystem.numAtoms = 4;
+ constraintsTestSystem.masses = { 12.0, 1.0, 1.0, 1.0 };
+ constraintsTestSystem.constraints = { 0, 0, 1, 0, 0, 2, 0, 0, 3 };
+ constraintsTestSystem.constraintsR0 = { 0.1 };
+
+
+ constraintsTestSystem.x = {
+ { 0.00, 0.00, 0.00 }, { 0.10, 0.00, 0.00 }, { 0.00, -0.10, 0.00 }, { 0.00, 0.00, 0.10 }
+ };
+
+ constraintsTestSystem.xPrime = { { 0.004, 0.009, -0.010 },
+ { 0.110, -0.006, 0.003 },
+ { -0.007, -0.102, -0.007 },
+ { -0.005, 0.011, 0.102 } };
+
+ constraintsTestSystem.v = { { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 } };
+
+ tensor virialScaledRef = { { 7.14e-04, 0.00e+00, 0.00e+00 },
+ { 0.00e+00, 1.08e-03, 0.00e+00 },
+ { 0.00e+00, 0.00e+00, 1.15e-03 } };
+
+ memcpy(constraintsTestSystem.virialScaledRef, virialScaledRef, DIM * DIM * sizeof(real));
+
+ constraintsTestSystemList.emplace_back(constraintsTestSystem);
+ }
+ {
+ ConstraintsTestSystem constraintsTestSystem;
+
+ constraintsTestSystem.title = "basic triangle (three atoms, connected to each other)";
+ constraintsTestSystem.numAtoms = 3;
+ constraintsTestSystem.masses = { 1.0, 1.0, 1.0 };
+ constraintsTestSystem.constraints = { 0, 0, 1, 2, 0, 2, 1, 1, 2 };
+ constraintsTestSystem.constraintsR0 = { 0.1, 0.1, 0.1 };
+
+ real oneTenthOverSqrtTwo = 0.1_real / std::sqrt(2.0_real);
+
+ constraintsTestSystem.x = { { oneTenthOverSqrtTwo, 0.0, 0.0 },
+ { 0.0, oneTenthOverSqrtTwo, 0.0 },
+ { 0.0, 0.0, oneTenthOverSqrtTwo } };
+
+ constraintsTestSystem.xPrime = { { 0.09, -0.02, 0.01 }, { -0.02, 0.10, -0.02 }, { 0.03, -0.01, 0.07 } };
+
+ constraintsTestSystem.v = { { 1.0, 1.0, 1.0 }, { -2.0, -2.0, -2.0 }, { 1.0, 1.0, 1.0 } };
+
+ tensor virialScaledRef = { { 6.00e-04, -1.61e-03, 1.01e-03 },
+ { -1.61e-03, 2.53e-03, -9.25e-04 },
+ { 1.01e-03, -9.25e-04, -8.05e-05 } };
+
+ memcpy(constraintsTestSystem.virialScaledRef, virialScaledRef, DIM * DIM * sizeof(real));
+
+ constraintsTestSystemList.emplace_back(constraintsTestSystem);
+ }
+
+ return constraintsTestSystemList;
+}();
+
+
/*! \brief Test fixture for constraints.
*
* The fixture uses following test systems:
* For some systems, the value for scaled virial tensor is checked against
* pre-computed data.
*/
-class ConstraintsTest : public ::testing::TestWithParam<std::string>
+class ConstraintsTest : public ::testing::TestWithParam<std::tuple<ConstraintsTestSystem, t_pbc>>
{
public:
- //! PBC setups
- std::unordered_map<std::string, t_pbc> pbcs_;
-
- /*! \brief Test setup function.
- *
- * Setting up the pbcs and algorithms. Note, that corresponding string keywords
- * have to be explicitly added at the end of this file when the tests are called.
- *
- */
- void SetUp() override
- {
-
- //
- // PBC initialization
- //
- t_pbc pbc;
-
- // Infinitely small box
- matrix boxNone = { { 0, 0, 0 }, { 0, 0, 0 }, { 0, 0, 0 } };
- set_pbc(&pbc, PbcType::No, boxNone);
- pbcs_["PBCNone"] = pbc;
-
- // Rectangular box
- matrix boxXyz = { { 10.0, 0.0, 0.0 }, { 0.0, 20.0, 0.0 }, { 0.0, 0.0, 15.0 } };
- set_pbc(&pbc, PbcType::Xyz, boxXyz);
- pbcs_["PBCXYZ"] = pbc;
- }
-
/*! \brief
* The test on the final length of constrained bonds.
*
"rij = %f, which is not equal to r0 = %f for constraint #%zd, between atoms %d "
"and %d"
" (before constraining rij was %f).",
- d1, r0, c, i, j, d0);
+ d1,
+ r0,
+ c,
+ i,
+ j,
+ d0);
}
}
<< gmx::formatString(
"Values in virial tensor at [%d][%d] are not within the "
"tolerance from reference value.",
- i, j);
+ i,
+ j);
}
}
}
}
};
-TEST_P(ConstraintsTest, SingleConstraint)
+TEST_P(ConstraintsTest, ConstraintsTest)
{
- std::string title = "one constraint (e.g. OH)";
- int numAtoms = 2;
-
- std::vector<real> masses = { 1.0, 12.0 };
- std::vector<int> constraints = { 0, 0, 1 };
- std::vector<real> constraintsR0 = { 0.1 };
-
- real oneTenthOverSqrtTwo = 0.1_real / std::sqrt(2.0_real);
-
- std::vector<RVec> x = { { 0.0, oneTenthOverSqrtTwo, 0.0 }, { oneTenthOverSqrtTwo, 0.0, 0.0 } };
- std::vector<RVec> xPrime = { { 0.01, 0.08, 0.01 }, { 0.06, 0.01, -0.01 } };
- std::vector<RVec> v = { { 1.0, 2.0, 3.0 }, { 3.0, 2.0, 1.0 } };
-
- tensor virialScaledRef = { { -5.58e-04, 5.58e-04, 0.00e+00 },
- { 5.58e-04, -5.58e-04, 0.00e+00 },
- { 0.00e+00, 0.00e+00, 0.00e+00 } };
-
- real shakeTolerance = 0.0001;
- gmx_bool shakeUseSOR = false;
-
- int lincsNIter = 1;
- int lincslincsExpansionOrder = 4;
- real lincsWarnAngle = 30.0;
-
- std::unique_ptr<ConstraintsTestData> testData = std::make_unique<ConstraintsTestData>(
- title, numAtoms, masses, constraints, constraintsR0, true, virialScaledRef, false, 0,
- real(0.0), real(0.001), x, xPrime, v, shakeTolerance, shakeUseSOR, lincsNIter,
- lincslincsExpansionOrder, lincsWarnAngle);
-
- std::string pbcName = GetParam();
- t_pbc pbc = pbcs_.at(pbcName);
+ auto params = GetParam();
+ ConstraintsTestSystem constraintsTestSystem = std::get<0>(params);
+ t_pbc pbc = std::get<1>(params);
+
+ ConstraintsTestData testData(constraintsTestSystem.title,
+ constraintsTestSystem.numAtoms,
+ constraintsTestSystem.masses,
+ constraintsTestSystem.constraints,
+ constraintsTestSystem.constraintsR0,
+ true,
+ constraintsTestSystem.virialScaledRef,
+ false,
+ 0,
+ real(0.0),
+ real(0.001),
+ constraintsTestSystem.x,
+ constraintsTestSystem.xPrime,
+ constraintsTestSystem.v,
+ constraintsTestSystem.shakeTolerance,
+ constraintsTestSystem.shakeUseSOR,
+ constraintsTestSystem.lincsNIter,
+ constraintsTestSystem.lincslincsExpansionOrder,
+ constraintsTestSystem.lincsWarnAngle);
// Cycle through all available runners
for (const auto& runner : getRunners())
{
- SCOPED_TRACE(formatString("Testing %s with %s using %s.", testData->title_.c_str(),
- pbcName.c_str(), runner->name().c_str()));
+ SCOPED_TRACE(formatString("Testing %s with %s PBC using %s.",
+ testData.title_.c_str(),
+ c_pbcTypeNames[pbc.pbcType].c_str(),
+ runner->name().c_str()));
- testData->reset();
+ testData.reset();
// Apply constraints
- runner->applyConstraints(testData.get(), pbc);
+ runner->applyConstraints(&testData, pbc);
- checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
- checkConstrainsDirection(*testData, pbc);
- checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
- checkCOMVelocity(absoluteTolerance(0.0001), *testData);
-
- checkVirialTensor(absoluteTolerance(0.0001), *testData);
+ checkConstrainsLength(constraintsTestSystem.lengthTolerance, testData, pbc);
+ checkConstrainsDirection(testData, pbc);
+ checkCOMCoordinates(constraintsTestSystem.comTolerance, testData);
+ checkCOMVelocity(constraintsTestSystem.comTolerance, testData);
+ checkVirialTensor(constraintsTestSystem.virialTolerance, testData);
}
}
-TEST_P(ConstraintsTest, TwoDisjointConstraints)
-{
-
- std::string title = "two disjoint constraints";
- int numAtoms = 4;
- std::vector<real> masses = { 0.5, 1.0 / 3.0, 0.25, 1.0 };
- std::vector<int> constraints = { 0, 0, 1, 1, 2, 3 };
- std::vector<real> constraintsR0 = { 2.0, 1.0 };
-
-
- std::vector<RVec> x = {
- { 2.50, -3.10, 15.70 }, { 0.51, -3.02, 15.55 }, { -0.50, -3.00, 15.20 }, { -1.51, -2.95, 15.05 }
- };
-
- std::vector<RVec> xPrime = {
- { 2.50, -3.10, 15.70 }, { 0.51, -3.02, 15.55 }, { -0.50, -3.00, 15.20 }, { -1.51, -2.95, 15.05 }
- };
-
- std::vector<RVec> v = { { 0.0, 1.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 0.0, 0.0, 1.0 }, { 0.0, 0.0, 0.0 } };
-
- tensor virialScaledRef = { { 3.3e-03, -1.7e-04, 5.6e-04 },
- { -1.7e-04, 8.9e-06, -2.8e-05 },
- { 5.6e-04, -2.8e-05, 8.9e-05 } };
-
- real shakeTolerance = 0.0001;
- gmx_bool shakeUseSOR = false;
-
- int lincsNIter = 1;
- int lincslincsExpansionOrder = 4;
- real lincsWarnAngle = 30.0;
-
- std::unique_ptr<ConstraintsTestData> testData = std::make_unique<ConstraintsTestData>(
- title, numAtoms, masses, constraints, constraintsR0, true, virialScaledRef, false, 0,
- real(0.0), real(0.001), x, xPrime, v, shakeTolerance, shakeUseSOR, lincsNIter,
- lincslincsExpansionOrder, lincsWarnAngle);
-
- std::string pbcName = GetParam();
- t_pbc pbc = pbcs_.at(pbcName);
-
- // Cycle through all available runners
- for (const auto& runner : getRunners())
- {
- SCOPED_TRACE(formatString("Testing %s with %s using %s.", testData->title_.c_str(),
- pbcName.c_str(), runner->name().c_str()));
-
- testData->reset();
-
- // Apply constraints
- runner->applyConstraints(testData.get(), pbc);
-
- checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
- checkConstrainsDirection(*testData, pbc);
- checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
- checkCOMVelocity(absoluteTolerance(0.0001), *testData);
-
- checkVirialTensor(absoluteTolerance(0.0001), *testData);
- }
-}
-
-TEST_P(ConstraintsTest, ThreeSequentialConstraints)
-{
-
- std::string title = "three atoms, connected longitudinally (e.g. CH2)";
- int numAtoms = 3;
- std::vector<real> masses = { 1.0, 12.0, 16.0 };
- std::vector<int> constraints = { 0, 0, 1, 1, 1, 2 };
- std::vector<real> constraintsR0 = { 0.1, 0.2 };
-
- real oneTenthOverSqrtTwo = 0.1_real / std::sqrt(2.0_real);
- real twoTenthsOverSqrtThree = 0.2_real / std::sqrt(3.0_real);
-
- std::vector<RVec> x = { { oneTenthOverSqrtTwo, oneTenthOverSqrtTwo, 0.0 },
- { 0.0, 0.0, 0.0 },
- { twoTenthsOverSqrtThree, twoTenthsOverSqrtThree, twoTenthsOverSqrtThree } };
-
- std::vector<RVec> xPrime = { { 0.08, 0.07, 0.01 }, { -0.02, 0.01, -0.02 }, { 0.10, 0.12, 0.11 } };
-
- std::vector<RVec> v = { { 1.0, 0.0, 0.0 }, { 0.0, 1.0, 0.0 }, { 0.0, 0.0, 1.0 } };
-
- tensor virialScaledRef = { { 4.14e-03, 4.14e-03, 3.31e-03 },
- { 4.14e-03, 4.14e-03, 3.31e-03 },
- { 3.31e-03, 3.31e-03, 3.31e-03 } };
-
- real shakeTolerance = 0.0001;
- gmx_bool shakeUseSOR = false;
-
- int lincsNIter = 1;
- int lincslincsExpansionOrder = 4;
- real lincsWarnAngle = 30.0;
-
- std::unique_ptr<ConstraintsTestData> testData = std::make_unique<ConstraintsTestData>(
- title, numAtoms, masses, constraints, constraintsR0, true, virialScaledRef, false, 0,
- real(0.0), real(0.001), x, xPrime, v, shakeTolerance, shakeUseSOR, lincsNIter,
- lincslincsExpansionOrder, lincsWarnAngle);
-
- std::string pbcName = GetParam();
- t_pbc pbc = pbcs_.at(pbcName);
-
- // Cycle through all available runners
- for (const auto& runner : getRunners())
- {
- SCOPED_TRACE(formatString("Testing %s with %s using %s.", testData->title_.c_str(),
- pbcName.c_str(), runner->name().c_str()));
-
- testData->reset();
-
- // Apply constraints
- runner->applyConstraints(testData.get(), pbc);
-
- checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
- checkConstrainsDirection(*testData, pbc);
- checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
- checkCOMVelocity(absoluteTolerance(0.0001), *testData);
-
- checkVirialTensor(absoluteTolerance(0.0001), *testData);
- }
-}
-
-TEST_P(ConstraintsTest, ThreeConstraintsWithCentralAtom)
-{
-
- std::string title = "three atoms, connected to the central atom (e.g. CH3)";
- int numAtoms = 4;
- std::vector<real> masses = { 12.0, 1.0, 1.0, 1.0 };
- std::vector<int> constraints = { 0, 0, 1, 0, 0, 2, 0, 0, 3 };
- std::vector<real> constraintsR0 = { 0.1 };
-
-
- std::vector<RVec> x = {
- { 0.00, 0.00, 0.00 }, { 0.10, 0.00, 0.00 }, { 0.00, -0.10, 0.00 }, { 0.00, 0.00, 0.10 }
- };
-
- std::vector<RVec> xPrime = { { 0.004, 0.009, -0.010 },
- { 0.110, -0.006, 0.003 },
- { -0.007, -0.102, -0.007 },
- { -0.005, 0.011, 0.102 } };
-
- std::vector<RVec> v = { { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 } };
-
- tensor virialScaledRef = { { 7.14e-04, 0.00e+00, 0.00e+00 },
- { 0.00e+00, 1.08e-03, 0.00e+00 },
- { 0.00e+00, 0.00e+00, 1.15e-03 } };
-
- real shakeTolerance = 0.0001;
- gmx_bool shakeUseSOR = false;
-
- int lincsNIter = 1;
- int lincslincsExpansionOrder = 4;
- real lincsWarnAngle = 30.0;
-
- std::unique_ptr<ConstraintsTestData> testData = std::make_unique<ConstraintsTestData>(
- title, numAtoms, masses, constraints, constraintsR0, true, virialScaledRef, false, 0,
- real(0.0), real(0.001), x, xPrime, v, shakeTolerance, shakeUseSOR, lincsNIter,
- lincslincsExpansionOrder, lincsWarnAngle);
-
- std::string pbcName = GetParam();
- t_pbc pbc = pbcs_.at(pbcName);
-
- // Cycle through all available runners
- for (const auto& runner : getRunners())
- {
- SCOPED_TRACE(formatString("Testing %s with %s using %s.", testData->title_.c_str(),
- pbcName.c_str(), runner->name().c_str()));
-
- testData->reset();
-
- // Apply constraints
- runner->applyConstraints(testData.get(), pbc);
-
- checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
- checkConstrainsDirection(*testData, pbc);
- checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
- checkCOMVelocity(absoluteTolerance(0.0001), *testData);
-
- checkVirialTensor(absoluteTolerance(0.0001), *testData);
- }
-}
-
-TEST_P(ConstraintsTest, FourSequentialConstraints)
-{
-
- std::string title = "four atoms, connected longitudinally";
- int numAtoms = 4;
- std::vector<real> masses = { 0.5, 1.0 / 3.0, 0.25, 1.0 };
- std::vector<int> constraints = { 0, 0, 1, 1, 1, 2, 2, 2, 3 };
- std::vector<real> constraintsR0 = { 2.0, 1.0, 1.0 };
-
-
- std::vector<RVec> x = {
- { 2.50, -3.10, 15.70 }, { 0.51, -3.02, 15.55 }, { -0.50, -3.00, 15.20 }, { -1.51, -2.95, 15.05 }
- };
-
- std::vector<RVec> xPrime = {
- { 2.50, -3.10, 15.70 }, { 0.51, -3.02, 15.55 }, { -0.50, -3.00, 15.20 }, { -1.51, -2.95, 15.05 }
- };
-
- std::vector<RVec> v = { { 0.0, 0.0, 2.0 }, { 0.0, 0.0, 3.0 }, { 0.0, 0.0, -4.0 }, { 0.0, 0.0, -1.0 } };
-
- tensor virialScaledRef = { { 1.15e-01, -4.20e-03, 2.12e-02 },
- { -4.20e-03, 1.70e-04, -6.41e-04 },
- { 2.12e-02, -6.41e-04, 5.45e-03 } };
-
- real shakeTolerance = 0.0001;
- gmx_bool shakeUseSOR = false;
-
- int lincsNIter = 4;
- int lincslincsExpansionOrder = 8;
- real lincsWarnAngle = 30.0;
-
- std::unique_ptr<ConstraintsTestData> testData = std::make_unique<ConstraintsTestData>(
- title, numAtoms, masses, constraints, constraintsR0, true, virialScaledRef, false, 0,
- real(0.0), real(0.001), x, xPrime, v, shakeTolerance, shakeUseSOR, lincsNIter,
- lincslincsExpansionOrder, lincsWarnAngle);
-
- std::string pbcName = GetParam();
- t_pbc pbc = pbcs_.at(pbcName);
-
- // Cycle through all available runners
- for (const auto& runner : getRunners())
- {
- SCOPED_TRACE(formatString("Testing %s with %s using %s.", testData->title_.c_str(),
- pbcName.c_str(), runner->name().c_str()));
-
- testData->reset();
-
- // Apply constraints
- runner->applyConstraints(testData.get(), pbc);
-
- checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
- checkConstrainsDirection(*testData, pbc);
- checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
- checkCOMVelocity(absoluteTolerance(0.0001), *testData);
-
- checkVirialTensor(absoluteTolerance(0.01), *testData);
- }
-}
-
-TEST_P(ConstraintsTest, TriangleOfConstraints)
-{
-
- std::string title = "basic triangle (tree atoms, connected to each other)";
- int numAtoms = 3;
- std::vector<real> masses = { 1.0, 1.0, 1.0 };
- std::vector<int> constraints = { 0, 0, 1, 2, 0, 2, 1, 1, 2 };
- std::vector<real> constraintsR0 = { 0.1, 0.1, 0.1 };
-
- real oneTenthOverSqrtTwo = 0.1_real / std::sqrt(2.0_real);
-
- std::vector<RVec> x = { { oneTenthOverSqrtTwo, 0.0, 0.0 },
- { 0.0, oneTenthOverSqrtTwo, 0.0 },
- { 0.0, 0.0, oneTenthOverSqrtTwo } };
-
- std::vector<RVec> xPrime = { { 0.09, -0.02, 0.01 }, { -0.02, 0.10, -0.02 }, { 0.03, -0.01, 0.07 } };
-
- std::vector<RVec> v = { { 1.0, 1.0, 1.0 }, { -2.0, -2.0, -2.0 }, { 1.0, 1.0, 1.0 } };
-
- tensor virialScaledRef = { { 6.00e-04, -1.61e-03, 1.01e-03 },
- { -1.61e-03, 2.53e-03, -9.25e-04 },
- { 1.01e-03, -9.25e-04, -8.05e-05 } };
-
- real shakeTolerance = 0.0001;
- gmx_bool shakeUseSOR = false;
-
- int lincsNIter = 1;
- int lincslincsExpansionOrder = 4;
- real lincsWarnAngle = 30.0;
-
- std::unique_ptr<ConstraintsTestData> testData = std::make_unique<ConstraintsTestData>(
- title, numAtoms, masses, constraints, constraintsR0, true, virialScaledRef, false, 0,
- real(0.0), real(0.001), x, xPrime, v, shakeTolerance, shakeUseSOR, lincsNIter,
- lincslincsExpansionOrder, lincsWarnAngle);
-
- std::string pbcName = GetParam();
- t_pbc pbc = pbcs_.at(pbcName);
-
- // Cycle through all available runners
- for (const auto& runner : getRunners())
- {
- SCOPED_TRACE(formatString("Testing %s with %s using %s.", testData->title_.c_str(),
- pbcName.c_str(), runner->name().c_str()));
-
- testData->reset();
-
- // Apply constraints
- runner->applyConstraints(testData.get(), pbc);
-
- checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
- checkConstrainsDirection(*testData, pbc);
- checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
- checkCOMVelocity(absoluteTolerance(0.0001), *testData);
-
- checkVirialTensor(absoluteTolerance(0.00001), *testData);
- }
-}
-
-
-INSTANTIATE_TEST_CASE_P(WithParameters, ConstraintsTest, ::testing::Values("PBCNone", "PBCXYZ"));
+INSTANTIATE_TEST_CASE_P(WithParameters,
+ ConstraintsTest,
+ ::testing::Combine(::testing::ValuesIn(c_constraintsTestSystemList),
+ ::testing::ValuesIn(c_pbcs)));
} // namespace
} // namespace test
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
invdt_ = 1.0 / timestep; // Inverse timestep
// Input record - data that usually comes from configuration file (.mdp)
- ir_.efep = 0;
+ ir_.efep = FreeEnergyPerturbationType::No;
ir_.init_t = initialTime;
ir_.delta_t = timestep;
- ir_.eI = 0;
+ ir_.eI = IntegrationAlgorithm::MD;
// Virial evaluation
computeVirial_ = computeVirial;
dHdLambda_ = 0;
if (compute_dHdLambda_)
{
- ir_.efep = efepYES;
+ ir_.efep = FreeEnergyPerturbationType::Yes;
dHdLambdaRef_ = dHdLambdaRef;
}
else
{
- ir_.efep = efepNO;
+ ir_.efep = FreeEnergyPerturbationType::No;
dHdLambdaRef_ = 0;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
shakedata shaked;
make_shake_sblock_serial(&shaked, testData->idef_.get(), testData->numAtoms_);
- bool success = constrain_shake(
- nullptr, &shaked, testData->invmass_.data(), *testData->idef_, testData->ir_, testData->x_,
- testData->xPrime_, testData->xPrime2_, nullptr, &testData->nrnb_, testData->lambda_,
- &testData->dHdLambda_, testData->invdt_, testData->v_, testData->computeVirial_,
- testData->virialScaled_, false, gmx::ConstraintVariable::Positions);
+ bool success = constrain_shake(nullptr,
+ &shaked,
+ testData->invmass_,
+ *testData->idef_,
+ testData->ir_,
+ testData->x_,
+ testData->xPrime_,
+ testData->xPrime2_,
+ nullptr,
+ &testData->nrnb_,
+ testData->lambda_,
+ &testData->dHdLambda_,
+ testData->invdt_,
+ testData->v_,
+ testData->computeVirial_,
+ testData->virialScaled_,
+ false,
+ gmx::ConstraintVariable::Positions);
EXPECT_TRUE(success) << "Test failed with a false return value in SHAKE.";
}
Lincs* lincsd;
int maxwarn = 100;
int warncount_lincs = 0;
- gmx_omp_nthreads_set(emntLINCS, 1);
+ gmx_omp_nthreads_set(ModuleMultiThread::Lincs, 1);
// Communication record
t_commrec cr;
for (const gmx_moltype_t& moltype : testData->mtop_.moltype)
{
// This function is in constr.cpp
- at2con_mt.push_back(make_at2con(moltype, testData->mtop_.ffparams.iparams,
+ at2con_mt.push_back(make_at2con(moltype,
+ testData->mtop_.ffparams.iparams,
flexibleConstraintTreatment(EI_DYNAMICS(testData->ir_.eI))));
}
// Initialize LINCS
- lincsd = init_lincs(nullptr, testData->mtop_, testData->nflexcon_, at2con_mt, false,
- testData->ir_.nLincsIter, testData->ir_.nProjOrder);
- set_lincs(*testData->idef_, testData->numAtoms_, testData->invmass_.data(), testData->lambda_,
- EI_DYNAMICS(testData->ir_.eI), &cr, lincsd);
+ lincsd = init_lincs(nullptr,
+ testData->mtop_,
+ testData->nflexcon_,
+ at2con_mt,
+ false,
+ testData->ir_.nLincsIter,
+ testData->ir_.nProjOrder);
+ set_lincs(*testData->idef_,
+ testData->numAtoms_,
+ testData->invmass_,
+ testData->lambda_,
+ EI_DYNAMICS(testData->ir_.eI),
+ &cr,
+ lincsd);
// Evaluate constraints
- bool success = constrain_lincs(
- false, testData->ir_, 0, lincsd, testData->invmass_.data(), &cr, &ms,
- testData->x_.arrayRefWithPadding(), testData->xPrime_.arrayRefWithPadding(),
- testData->xPrime2_.arrayRefWithPadding().unpaddedArrayRef(), pbc.box, &pbc,
- testData->hasMassPerturbed_, testData->lambda_, &testData->dHdLambda_, testData->invdt_,
- testData->v_.arrayRefWithPadding().unpaddedArrayRef(), testData->computeVirial_,
- testData->virialScaled_, gmx::ConstraintVariable::Positions, &testData->nrnb_, maxwarn,
- &warncount_lincs);
+ bool success = constrain_lincs(false,
+ testData->ir_,
+ 0,
+ lincsd,
+ testData->invmass_,
+ &cr,
+ &ms,
+ testData->x_.arrayRefWithPadding(),
+ testData->xPrime_.arrayRefWithPadding(),
+ testData->xPrime2_.arrayRefWithPadding().unpaddedArrayRef(),
+ pbc.box,
+ &pbc,
+ testData->hasMassPerturbed_,
+ testData->lambda_,
+ &testData->dHdLambda_,
+ testData->invdt_,
+ testData->v_.arrayRefWithPadding().unpaddedArrayRef(),
+ testData->computeVirial_,
+ testData->virialScaled_,
+ gmx::ConstraintVariable::Positions,
+ &testData->nrnb_,
+ maxwarn,
+ &warncount_lincs);
EXPECT_TRUE(success) << "Test failed with a false return value in LINCS.";
EXPECT_EQ(warncount_lincs, 0) << "There were warnings in LINCS.";
done_lincs(lincsd);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
#include "gromacs/gpu_utils/devicebuffer.cuh"
+#include "gromacs/gpu_utils/gputraits.h"
#include "gromacs/hardware/device_information.h"
-#include "gromacs/mdlib/lincs_gpu.cuh"
+#include "gromacs/mdlib/lincs_gpu.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/utility/unique_cptr.h"
const DeviceStream& deviceStream = testDevice_.deviceStream();
setActiveDevice(testDevice_.deviceInfo());
- auto lincsGpu = std::make_unique<LincsGpu>(testData->ir_.nLincsIter, testData->ir_.nProjOrder,
- deviceContext, deviceStream);
+ auto lincsGpu = std::make_unique<LincsGpu>(
+ testData->ir_.nLincsIter, testData->ir_.nProjOrder, deviceContext, deviceStream);
- bool updateVelocities = true;
- int numAtoms = testData->numAtoms_;
- float3 *d_x, *d_xp, *d_v;
+ bool updateVelocities = true;
+ int numAtoms = testData->numAtoms_;
+
+ Float3* h_x = gmx::asGenericFloat3Pointer(testData->x_);
+ Float3* h_xp = gmx::asGenericFloat3Pointer(testData->xPrime_);
+ Float3* h_v = gmx::asGenericFloat3Pointer(testData->v_);
+
+ DeviceBuffer<Float3> d_x, d_xp, d_v;
lincsGpu->set(*testData->idef_, testData->numAtoms_, testData->invmass_.data());
PbcAiuc pbcAiuc;
allocateDeviceBuffer(&d_xp, numAtoms, deviceContext);
allocateDeviceBuffer(&d_v, numAtoms, deviceContext);
- copyToDeviceBuffer(&d_x, (float3*)(testData->x_.data()), 0, numAtoms, deviceStream,
- GpuApiCallBehavior::Sync, nullptr);
- copyToDeviceBuffer(&d_xp, (float3*)(testData->xPrime_.data()), 0, numAtoms, deviceStream,
- GpuApiCallBehavior::Sync, nullptr);
+ copyToDeviceBuffer(&d_x, h_x, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr);
+ copyToDeviceBuffer(&d_xp, h_xp, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr);
if (updateVelocities)
{
- copyToDeviceBuffer(&d_v, (float3*)(testData->v_.data()), 0, numAtoms, deviceStream,
- GpuApiCallBehavior::Sync, nullptr);
+ copyToDeviceBuffer(&d_v, h_v, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr);
}
- lincsGpu->apply(d_x, d_xp, updateVelocities, d_v, testData->invdt_, testData->computeVirial_,
- testData->virialScaled_, pbcAiuc);
+ lincsGpu->apply(
+ d_x, d_xp, updateVelocities, d_v, testData->invdt_, testData->computeVirial_, testData->virialScaled_, pbcAiuc);
- copyFromDeviceBuffer((float3*)(testData->xPrime_.data()), &d_xp, 0, numAtoms, deviceStream,
- GpuApiCallBehavior::Sync, nullptr);
+ copyFromDeviceBuffer(h_xp, &d_xp, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr);
if (updateVelocities)
{
- copyFromDeviceBuffer((float3*)(testData->v_.data()), &d_v, 0, numAtoms, deviceStream,
- GpuApiCallBehavior::Sync, nullptr);
+ copyFromDeviceBuffer(h_v, &d_v, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr);
}
freeDeviceBuffer(&d_x);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/state.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/mdmodulenotification.h"
+#include "gromacs/utility/mdmodulesnotifiers.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/textreader.h"
#include "gromacs/utility/unique_cptr.h"
struct EnergyOutputTestParameters
{
//! Thermostat (enum)
- int temperatureCouplingScheme;
+ TemperatureCoupling temperatureCouplingScheme;
//! Barostat (enum)
- int pressureCouplingScheme;
+ PressureCoupling pressureCouplingScheme;
//! Integrator
- int integrator;
+ IntegrationAlgorithm integrator;
//! Number of saved energy frames (to test averages output).
int numFrames;
//! If output should be initialized as a rerun.
* Only several combinations of the parameters are used. Using all possible combinations will
* require ~10 MB of test data and ~2 sec to run the tests.
*/
-const EnergyOutputTestParameters parametersSets[] = { { etcNO, epcNO, eiMD, 1, false, false },
- { etcNO, epcNO, eiMD, 1, true, false },
- { etcNO, epcNO, eiMD, 1, false, true },
- { etcNO, epcNO, eiMD, 0, false, false },
- { etcNO, epcNO, eiMD, 10, false, false },
- { etcVRESCALE, epcNO, eiMD, 1, false, false },
- { etcNOSEHOOVER, epcNO, eiMD, 1, false, false },
- { etcNO, epcPARRINELLORAHMAN, eiMD, 1, false, false },
- { etcNO, epcMTTK, eiMD, 1, false, false },
- { etcNO, epcNO, eiVV, 1, false, false },
- { etcNO, epcMTTK, eiVV, 1, false, false } };
+const EnergyOutputTestParameters parametersSets[] = {
+ { TemperatureCoupling::No, PressureCoupling::No, IntegrationAlgorithm::MD, 1, false, false },
+ { TemperatureCoupling::No, PressureCoupling::No, IntegrationAlgorithm::MD, 1, true, false },
+ { TemperatureCoupling::No, PressureCoupling::No, IntegrationAlgorithm::MD, 1, false, true },
+ { TemperatureCoupling::No, PressureCoupling::No, IntegrationAlgorithm::MD, 0, false, false },
+ { TemperatureCoupling::No, PressureCoupling::No, IntegrationAlgorithm::MD, 10, false, false },
+ { TemperatureCoupling::VRescale, PressureCoupling::No, IntegrationAlgorithm::MD, 1, false, false },
+ { TemperatureCoupling::NoseHoover, PressureCoupling::No, IntegrationAlgorithm::MD, 1, false, false },
+ { TemperatureCoupling::No, PressureCoupling::ParrinelloRahman, IntegrationAlgorithm::MD, 1, false, false },
+ { TemperatureCoupling::No, PressureCoupling::Mttk, IntegrationAlgorithm::MD, 1, false, false },
+ { TemperatureCoupling::No, PressureCoupling::No, IntegrationAlgorithm::VV, 1, false, false },
+ { TemperatureCoupling::No, PressureCoupling::Mttk, IntegrationAlgorithm::VV, 1, false, false }
+};
/*! \brief Test fixture to test energy output.
*
*/
class EnergyOutputTest : public ::testing::TestWithParam<EnergyOutputTestParameters>
{
+ int numTempCouplingGroups_ = 3;
+ real cosAccel_ = 1.0;
+
public:
//! File manager
TestFileManager fileManager_;
TestReferenceChecker checker_;
EnergyOutputTest() :
+ ekindata_(numTempCouplingGroups_, cosAccel_, 1),
logFilename_(fileManager_.getTemporaryFilePath(".log")),
edrFilename_(fileManager_.getTemporaryFilePath(".edr")),
log_(std::fopen(logFilename_.c_str(), "w")),
// F_EQM
inputrec_.bQMMM = true;
// F_RF_EXCL will not be tested - group scheme is not supported any more
- inputrec_.cutoff_scheme = ecutsVERLET;
+ inputrec_.cutoff_scheme = CutoffScheme::Verlet;
// F_COUL_RECIP
- inputrec_.coulombtype = eelPME;
+ inputrec_.coulombtype = CoulombInteractionType::Pme;
// F_LJ_RECIP
- inputrec_.vdwtype = evdwPME;
+ inputrec_.vdwtype = VanDerWaalsType::Pme;
// F_DVDL_COUL, F_DVDL_VDW, F_DVDL_BONDED, F_DVDL_RESTRAINT, F_DKDL and F_DVDL
- inputrec_.efep = efepYES;
- inputrec_.fepvals->separate_dvdl[efptCOUL] = true;
- inputrec_.fepvals->separate_dvdl[efptVDW] = true;
- inputrec_.fepvals->separate_dvdl[efptBONDED] = true;
- inputrec_.fepvals->separate_dvdl[efptRESTRAINT] = true;
- inputrec_.fepvals->separate_dvdl[efptMASS] = true;
- inputrec_.fepvals->separate_dvdl[efptCOUL] = true;
- inputrec_.fepvals->separate_dvdl[efptFEP] = true;
+ inputrec_.efep = FreeEnergyPerturbationType::Yes;
+ inputrec_.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Coul] = true;
+ inputrec_.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Vdw] = true;
+ inputrec_.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Bonded] = true;
+ inputrec_.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Restraint] = true;
+ inputrec_.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Mass] = true;
+ inputrec_.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Coul] = true;
+ inputrec_.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = true;
// F_DISPCORR and F_PDISPCORR
- inputrec_.eDispCorr = edispcEner;
+ inputrec_.eDispCorr = DispersionCorrectionType::Ener;
inputrec_.bRot = true;
// F_ECONSERVED
inputrec_.ref_p[ZZ][YY] = 0.0;
// Dipole (mu)
- inputrec_.ewald_geometry = eewg3DC;
+ inputrec_.ewald_geometry = EwaldGeometry::ThreeDC;
// GMX_CONSTRAINTVIR environment variable should also be
// set to print constraints and force virials separately.
gmxSetenv("GMX_CONSTRAINTVIR", "true", 1);
// To print constrain RMSD, constraints algorithm should be set to LINCS.
- inputrec_.eConstrAlg = econtLINCS;
+ inputrec_.eConstrAlg = ConstraintAlgorithm::Lincs;
mtop_.bIntermolecularInteractions = false;
mtop_.groups.groupNames.emplace_back(&handle);
}
- mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].resize(3);
+ mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].resize(numTempCouplingGroups_);
mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput][0] = 0;
mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput][1] = 1;
mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput][2] = 2;
- mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].resize(3);
+ mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].resize(numTempCouplingGroups_);
mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling][0] = 0;
mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling][1] = 1;
mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling][2] = 2;
- mtop_.groups.groups[SimulationAtomGroupType::Acceleration].resize(2);
- mtop_.groups.groups[SimulationAtomGroupType::Acceleration][0] = 0;
- mtop_.groups.groups[SimulationAtomGroupType::Acceleration][1] = 2;
-
// Nose-Hoover chains
inputrec_.bPrintNHChains = true;
inputrec_.opts.nhchainlength = 2;
// Kinetic energy and related data
ekindata_.tcstat.resize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].size());
- ekindata_.grpstat.resize(mtop_.groups.groups[SimulationAtomGroupType::Acceleration].size());
// This is needed so that the ebin space will be allocated
- inputrec_.cos_accel = 1.0;
- // This is to keep the destructor happy (otherwise sfree() segfaults)
- ekindata_.nthreads = 0;
- snew(ekindata_.ekin_work_alloc, 1);
- snew(ekindata_.ekin_work, 1);
- snew(ekindata_.dekindl_work, 1);
+ inputrec_.cos_accel = cosAccel_;
// Group options for annealing output
- inputrec_.opts.ngtc = 3;
+ inputrec_.opts.ngtc = numTempCouplingGroups_;
snew(inputrec_.opts.ref_t, inputrec_.opts.ngtc);
snew(inputrec_.opts.annealing, inputrec_.opts.ngtc);
- inputrec_.opts.annealing[0] = eannNO;
- inputrec_.opts.annealing[1] = eannSINGLE;
- inputrec_.opts.annealing[2] = eannPERIODIC;
+ inputrec_.opts.annealing[0] = SimulatedAnnealing::No;
+ inputrec_.opts.annealing[1] = SimulatedAnnealing::Single;
+ inputrec_.opts.annealing[2] = SimulatedAnnealing::Periodic;
// This is to keep done_inputrec happy (otherwise sfree() segfaults)
snew(inputrec_.opts.anneal_time, inputrec_.opts.ngtc);
// TODO EnergyOutput should not take Constraints object
// TODO This object will always return zero as RMSD value.
// It is more relevant to have non-zero value for testing.
- constraints_ = makeConstraints(mtop_, inputrec_, nullptr, false, nullptr, &cr_, nullptr,
- nullptr, nullptr, false);
+ constraints_ = makeConstraints(
+ mtop_, inputrec_, nullptr, false, nullptr, &cr_, false, nullptr, nullptr, nullptr, false);
}
/*! \brief Helper function to generate synthetic data to output
// Group pairs
for (int i = 0; i < enerdata_->grpp.nener; i++)
{
- for (int k = 0; k < egNR; k++)
+ for (int k = 0; k < static_cast<int>(NonBondedEnergyTerms::Count); k++)
{
- enerdata_->grpp.ener[k][i] = (*testValue += 0.1);
+ enerdata_->grpp.energyGroupPairTerms[k][i] = (*testValue += 0.1);
}
}
tcstat.T = (*testValue += 0.1);
tcstat.lambda = (*testValue += 0.1);
}
- for (auto& grpstat : ekindata_.grpstat)
- {
- grpstat.u[XX] = (*testValue += 0.1);
- grpstat.u[YY] = (*testValue += 0.1);
- grpstat.u[ZZ] = (*testValue += 0.1);
- }
+ // Removing constant acceleration removed a total increment of 0.6
+ // To avoid unnecessary changes in reference data, we keep the increment
+ (*testValue += 0.6);
// This conditional is to check whether the ebin was allocated.
// Otherwise it will print cosacc data into the first bin.
inputrec_.ref_p[YY][XX] = 1.0;
}
- MdModulesNotifier mdModulesNotifier;
- std::unique_ptr<EnergyOutput> energyOutput = std::make_unique<EnergyOutput>(
- energyFile_, &mtop_, &inputrec_, nullptr, nullptr, parameters.isRerun,
- StartingBehavior::NewSimulation, false, mdModulesNotifier);
+ MDModulesNotifiers mdModulesNotifiers;
+ std::unique_ptr<EnergyOutput> energyOutput =
+ std::make_unique<EnergyOutput>(energyFile_,
+ mtop_,
+ inputrec_,
+ nullptr,
+ nullptr,
+ parameters.isRerun,
+ StartingBehavior::NewSimulation,
+ false,
+ mdModulesNotifiers);
// Add synthetic data for a single step
double testValue = 10.0;
for (int frame = 0; frame < parameters.numFrames; frame++)
{
setStepData(&testValue);
- energyOutput->addDataAtEnergyStep(
- false, true, time_, tmass_, enerdata_.get(), nullptr, nullptr, box_,
- PTCouplingArrays({ state_.boxv, state_.nosehoover_xi, state_.nosehoover_vxi,
- state_.nhpres_xi, state_.nhpres_vxi }),
- state_.fep_state, constraintsVirial_, forceVirial_, totalVirial_, pressure_,
- &ekindata_, muTotal_, constraints_.get());
+ energyOutput->addDataAtEnergyStep(false,
+ true,
+ time_,
+ tmass_,
+ enerdata_.get(),
+ nullptr,
+ nullptr,
+ box_,
+ PTCouplingArrays({ state_.boxv,
+ state_.nosehoover_xi,
+ state_.nosehoover_vxi,
+ state_.nhpres_xi,
+ state_.nhpres_vxi }),
+ state_.fep_state,
+ constraintsVirial_,
+ forceVirial_,
+ totalVirial_,
+ pressure_,
+ &ekindata_,
+ muTotal_,
+ constraints_.get());
energyOutput->printAnnealingTemperatures(log_, &mtop_.groups, &inputrec_.opts);
- energyOutput->printStepToEnergyFile(energyFile_, true, false, false, log_, 100 * frame,
- time_, nullptr, nullptr);
+ energyOutput->printStepToEnergyFile(
+ energyFile_, true, false, false, log_, 100 * frame, time_, nullptr, nullptr);
time_ += 1.0;
}
#include "gromacs/mdlib/expanded_internal.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "testutils/testasserts.h"
namespace gmx
// Check that unimplemented calculation modes throw
TEST_P(CalculateAcceptanceWeightSimple, UnknownCalculationModeThrows)
{
- for (auto calculationMode = 0; calculationMode < elamstatsNR; ++calculationMode)
+ for (auto calculationMode : gmx::EnumerationArray<LambdaWeightCalculation, bool>::keys())
{
- if (calculationMode != elamstatsBARKER && calculationMode != elamstatsMINVAR
- && calculationMode != elamstatsMETROPOLIS)
+ if (calculationMode != LambdaWeightCalculation::Barker
+ && calculationMode != LambdaWeightCalculation::Minvar
+ && calculationMode != LambdaWeightCalculation::Metropolis)
{
EXPECT_THROW_GMX(calculateAcceptanceWeight(calculationMode, GetParam()), NotImplementedError);
}
// Check that implemented calculation modes don't throw
TEST_P(CalculateAcceptanceWeightSimple, KnownCalculationModeDoesNotThrow)
{
- EXPECT_NO_THROW(calculateAcceptanceWeight(elamstatsMETROPOLIS, GetParam()));
- EXPECT_NO_THROW(calculateAcceptanceWeight(elamstatsBARKER, GetParam()));
- EXPECT_NO_THROW(calculateAcceptanceWeight(elamstatsMINVAR, GetParam()));
+ EXPECT_NO_THROW(calculateAcceptanceWeight(LambdaWeightCalculation::Metropolis, GetParam()));
+ EXPECT_NO_THROW(calculateAcceptanceWeight(LambdaWeightCalculation::Barker, GetParam()));
+ EXPECT_NO_THROW(calculateAcceptanceWeight(LambdaWeightCalculation::Minvar, GetParam()));
}
// Barker and MinVar are expected to be equal
TEST_P(CalculateAcceptanceWeightSimple, BarkerAndMinVarAreIdentical)
{
- EXPECT_EQ(calculateAcceptanceWeight(elamstatsBARKER, GetParam()),
- calculateAcceptanceWeight(elamstatsMINVAR, GetParam()));
+ EXPECT_EQ(calculateAcceptanceWeight(LambdaWeightCalculation::Barker, GetParam()),
+ calculateAcceptanceWeight(LambdaWeightCalculation::Minvar, GetParam()));
}
/*! \brief Test fixture accepting a calculation mode and an input value for
* calculateAcceptanceWeight as well as the expected output value
*/
-using RegressionTuple = std::tuple<int, real, real>;
+using RegressionTuple = std::tuple<LambdaWeightCalculation, real, real>;
class CalculateAcceptanceWeightRangeRegression :
public ::testing::Test,
public ::testing::WithParamInterface<RegressionTuple>
INSTANTIATE_TEST_CASE_P(
RegressionTests,
CalculateAcceptanceWeightRangeRegression,
- ::testing::Values(RegressionTuple{ elamstatsMETROPOLIS, 0.0, 1.0 },
- RegressionTuple{ elamstatsMETROPOLIS, GMX_REAL_NEGZERO, 1.0 },
- RegressionTuple{ elamstatsMETROPOLIS, GMX_REAL_EPS, 1.0 },
- RegressionTuple{ elamstatsMETROPOLIS, -1.0, 1.0 },
- RegressionTuple{ elamstatsMETROPOLIS, -GMX_REAL_MAX, 1.0 },
- RegressionTuple{ elamstatsMETROPOLIS, 1.0, std::exp(-1.0) },
- RegressionTuple{ elamstatsMETROPOLIS, GMX_REAL_MAX, 0.0 },
- RegressionTuple{ elamstatsBARKER, 0.0, 0.5 },
- RegressionTuple{ elamstatsBARKER, GMX_REAL_NEGZERO, 0.5 },
- RegressionTuple{ elamstatsBARKER, GMX_REAL_EPS, 0.5 },
- RegressionTuple{ elamstatsBARKER, -1.0, 1.0 / (1.0 + std::exp(-1.0)) },
- RegressionTuple{ elamstatsBARKER, -GMX_REAL_MAX, 1.0 },
- RegressionTuple{ elamstatsBARKER, 1.0, 1.0 / (1.0 + std::exp(1.0)) },
- RegressionTuple{ elamstatsBARKER, GMX_REAL_MAX, 0.0 }));
+ ::testing::Values(
+ RegressionTuple{ LambdaWeightCalculation::Metropolis, 0.0, 1.0 },
+ RegressionTuple{ LambdaWeightCalculation::Metropolis, GMX_REAL_NEGZERO, 1.0 },
+ RegressionTuple{ LambdaWeightCalculation::Metropolis, GMX_REAL_EPS, 1.0 },
+ RegressionTuple{ LambdaWeightCalculation::Metropolis, -1.0, 1.0 },
+ RegressionTuple{ LambdaWeightCalculation::Metropolis, -GMX_REAL_MAX, 1.0 },
+ RegressionTuple{ LambdaWeightCalculation::Metropolis, 1.0, std::exp(-1.0) },
+ RegressionTuple{ LambdaWeightCalculation::Metropolis, GMX_REAL_MAX, 0.0 },
+ RegressionTuple{ LambdaWeightCalculation::Barker, 0.0, 0.5 },
+ RegressionTuple{ LambdaWeightCalculation::Barker, GMX_REAL_NEGZERO, 0.5 },
+ RegressionTuple{ LambdaWeightCalculation::Barker, GMX_REAL_EPS, 0.5 },
+ RegressionTuple{ LambdaWeightCalculation::Barker, -1.0, 1.0 / (1.0 + std::exp(-1.0)) },
+ RegressionTuple{ LambdaWeightCalculation::Barker, -GMX_REAL_MAX, 1.0 },
+ RegressionTuple{ LambdaWeightCalculation::Barker, 1.0, 1.0 / (1.0 + std::exp(1.0)) },
+ RegressionTuple{ LambdaWeightCalculation::Barker, GMX_REAL_MAX, 0.0 }));
} // namespace
} // namespace test
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "testutils/testasserts.h"
#include "testutils/testmatchers.h"
//! the current simulation step
int64_t step = 0;
//! the expected lambda at the current simulation step
- std::array<real, efptNR> expectedLambdas = { -1, -1, -1, -1, -1, -1, -1 };
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real> expectedLambdas = { -1, -1, -1,
+ -1, -1, -1,
+ -1 };
};
fepvals.init_fep_state = GetParam().initFepState;
fepvals.init_lambda = GetParam().initLambda;
fepvals.delta_lambda = GetParam().deltaLambda;
- fepvals.all_lambda = getLambdaMatrix(GetParam().nLambda);
- fepvals.n_lambda = GetParam().nLambda;
+ std::fill(fepvals.all_lambda.begin(),
+ fepvals.all_lambda.end(),
+ defaultLambdaArrayForTest_[GetParam().nLambda]);
+ fepvals.n_lambda = GetParam().nLambda;
return fepvals;
}
- /*! \brief construct a lambda matrix
- *
- * \param[in] nLambda
- * \returns nLambda * eftpNR matrix with pre-defined values
- */
- double** getLambdaMatrix(int nLambda)
- {
- for (int i = 0; i < efptNR; ++i)
- {
- allLambda_[i] = defaultLambdaArrayForTest_[nLambda].data();
- }
- return allLambda_.data();
- }
-
private:
- //! Construction aide for double ** matrix without snew
- std::array<double*, efptNR> allLambda_;
//! a set of default lambda arrays for different lengths
std::vector<std::vector<double>> defaultLambdaArrayForTest_ = { {}, { 0.8 }, { 0.2, 0.8 }, { 0.2, 0.8, 0.8 } };
};
"groups and "
"%s pressure coupling (dt = %f, v0=(%f, %f, %f), f0=(%f, %f, %f), nstpcouple = "
"%d)",
- runner->hardwareDescription().c_str(), parameters.numAtoms, parameters.numSteps,
- parameters.numTCoupleGroups, parameters.nstpcouple == 0 ? "without" : "with",
- parameters.timestep, parameters.v[XX], parameters.v[YY], parameters.v[ZZ],
- parameters.f[XX], parameters.f[YY], parameters.f[ZZ], parameters.nstpcouple);
+ runner->hardwareDescription().c_str(),
+ parameters.numAtoms,
+ parameters.numSteps,
+ parameters.numTCoupleGroups,
+ parameters.nstpcouple == 0 ? "without" : "with",
+ parameters.timestep,
+ parameters.v[XX],
+ parameters.v[YY],
+ parameters.v[ZZ],
+ parameters.f[XX],
+ parameters.f[YY],
+ parameters.f[ZZ],
+ parameters.nstpcouple);
SCOPED_TRACE(testDescription);
- std::unique_ptr<LeapFrogTestData> testData = std::make_unique<LeapFrogTestData>(
- parameters.numAtoms, parameters.timestep, parameters.v, parameters.f,
- parameters.numTCoupleGroups, parameters.nstpcouple);
+ std::unique_ptr<LeapFrogTestData> testData =
+ std::make_unique<LeapFrogTestData>(parameters.numAtoms,
+ parameters.timestep,
+ parameters.v,
+ parameters.f,
+ parameters.numTCoupleGroups,
+ parameters.nstpcouple);
runner->integrate(testData.get(), parameters.numSteps);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
f_(numAtoms),
inverseMasses_(numAtoms),
inverseMassesPerDim_(numAtoms),
+ kineticEnergyData_(numTCoupleGroups == 0 ? 1 : numTCoupleGroups, 0.0, 1),
numTCoupleGroups_(numTCoupleGroups)
{
mdAtoms_.nr = numAtoms_;
if (numTCoupleGroups_ == 0)
{
- inputRecord_.etc = etcNO;
+ inputRecord_.etc = TemperatureCoupling::No;
for (int i = 0; i < numAtoms_; i++)
{
mdAtoms_.cTC[i] = 0;
}
- kineticEnergyData_.ngtc = 1;
t_grp_tcstat temperatureCouplingGroupData;
temperatureCouplingGroupData.lambda = 1.0;
- kineticEnergyData_.tcstat.emplace_back(temperatureCouplingGroupData);
+ kineticEnergyData_.tcstat[0] = temperatureCouplingGroupData;
}
else
{
- inputRecord_.etc = etcYES;
+ inputRecord_.etc = TemperatureCoupling::Yes;
for (int i = 0; i < numAtoms_; i++)
{
mdAtoms_.cTC[i] = i % numTCoupleGroups_;
}
- kineticEnergyData_.ngtc = numTCoupleGroups_;
- for (int i = 0; i < numTCoupleGroups; i++)
+ for (int i = 0; i < numTCoupleGroups_; i++)
{
real tCoupleLambda = 1.0 - (i + 1.0) / 10.0;
t_grp_tcstat temperatureCouplingGroupData;
temperatureCouplingGroupData.lambda = tCoupleLambda;
- kineticEnergyData_.tcstat.emplace_back(temperatureCouplingGroupData);
+ kineticEnergyData_.tcstat[i] = temperatureCouplingGroupData;
}
}
- inputRecord_.eI = eiMD;
+ inputRecord_.eI = IntegrationAlgorithm::MD;
inputRecord_.delta_t = timestep_;
state_.flags = 0;
state_.box[ZZ][YY] = 0.0;
state_.box[ZZ][ZZ] = 10.0;
- kineticEnergyData_.bNEMD = false;
- kineticEnergyData_.cosacc.cos_accel = 0.0;
-
- kineticEnergyData_.nthreads = 1;
- snew(kineticEnergyData_.ekin_work_alloc, kineticEnergyData_.nthreads);
- snew(kineticEnergyData_.ekin_work, kineticEnergyData_.nthreads);
- snew(kineticEnergyData_.dekindl_work, kineticEnergyData_.nthreads);
-
mdAtoms_.homenr = numAtoms_;
mdAtoms_.haveVsites = false;
mdAtoms_.havePartiallyFrozenAtoms = false;
mdAtoms_.cFREEZE = nullptr;
update_ = std::make_unique<Update>(inputRecord_, nullptr);
- update_->setNumAtoms(numAtoms);
+ update_->updateAfterPartition(numAtoms,
+ gmx::ArrayRef<const unsigned short>(),
+ gmx::arrayRefFromArray(mdAtoms_.cTC, mdAtoms_.nr));
doPressureCouple_ = (nstpcouple != 0);
if (doPressureCouple_)
{
- inputRecord_.epc = epcPARRINELLORAHMAN;
+ inputRecord_.epc = PressureCoupling::ParrinelloRahman;
inputRecord_.nstpcouple = nstpcouple;
dtPressureCouple_ = inputRecord_.nstpcouple * inputRecord_.delta_t;
}
else
{
- inputRecord_.epc = epcNO;
+ inputRecord_.epc = PressureCoupling::No;
velocityScalingMatrix_[XX][XX] = 1.0;
velocityScalingMatrix_[XX][YY] = 0.0;
velocityScalingMatrix_[XX][ZZ] = 0.0;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
testData->state_.v[i] = testData->v_[i];
}
- gmx_omp_nthreads_set(emntUpdate, 1);
+ gmx_omp_nthreads_set(ModuleMultiThread::Update, 1);
for (int step = 0; step < numSteps; step++)
{
testData->update_->update_coords(
- testData->inputRecord_, step, &testData->mdAtoms_, &testData->state_, testData->f_,
- testData->forceCalculationData_, &testData->kineticEnergyData_,
- testData->velocityScalingMatrix_, etrtNONE, nullptr, false);
- testData->update_->finish_update(testData->inputRecord_, &testData->mdAtoms_,
- &testData->state_, nullptr, false);
+ testData->inputRecord_,
+ step,
+ testData->mdAtoms_.homenr,
+ testData->mdAtoms_.havePartiallyFrozenAtoms,
+ testData->mdAtoms_.ptype
+ ? gmx::arrayRefFromArray(testData->mdAtoms_.ptype, testData->mdAtoms_.nr)
+ : gmx::ArrayRef<ParticleType>{},
+ testData->mdAtoms_.invmass
+ ? gmx::arrayRefFromArray(testData->mdAtoms_.invmass, testData->mdAtoms_.nr)
+ : gmx::ArrayRef<real>{},
+ testData->mdAtoms_.invMassPerDim ? gmx::arrayRefFromArray(testData->mdAtoms_.invMassPerDim,
+ testData->mdAtoms_.nr)
+ : gmx::ArrayRef<rvec>{},
+ &testData->state_,
+ testData->f_,
+ testData->forceCalculationData_,
+ &testData->kineticEnergyData_,
+ testData->velocityScalingMatrix_,
+ etrtNONE,
+ nullptr,
+ false);
+ testData->update_->finish_update(testData->inputRecord_,
+ testData->mdAtoms_.havePartiallyFrozenAtoms,
+ testData->mdAtoms_.homenr,
+ &testData->state_,
+ nullptr,
+ false);
}
const auto xp = makeArrayRef(*testData->update_->xp()).subArray(0, testData->numAtoms_);
for (int i = 0; i < testData->numAtoms_; i++)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "leapfrogtestdata.h"
+/*
+ * LeapFrog is available with CUDA and SYCL.
+ */
#define HAVE_GPU_LEAPFROG (GMX_GPU_CUDA || GMX_GPU_SYCL)
namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
# include "gromacs/mdlib/leapfrog_gpu.h"
#endif
+#include "gromacs/gpu_utils/gputraits.h"
#include "gromacs/hardware/device_information.h"
#include "gromacs/mdlib/stat.h"
int numAtoms = testData->numAtoms_;
- static_assert(sizeof(float3) == sizeof(*testData->x_.data()), "Incompatible types");
+ Float3* h_x = gmx::asGenericFloat3Pointer(testData->x_);
+ Float3* h_xp = gmx::asGenericFloat3Pointer(testData->xPrime_);
+ Float3* h_v = gmx::asGenericFloat3Pointer(testData->v_);
+ Float3* h_f = gmx::asGenericFloat3Pointer(testData->f_);
- float3* h_x = reinterpret_cast<float3*>(testData->x_.data());
- float3* h_xp = reinterpret_cast<float3*>(testData->xPrime_.data());
- float3* h_v = reinterpret_cast<float3*>(testData->v_.data());
- float3* h_f = reinterpret_cast<float3*>(testData->f_.data());
-
- DeviceBuffer<float3> d_x, d_xp, d_v, d_f;
+ DeviceBuffer<Float3> d_x, d_xp, d_v, d_f;
allocateDeviceBuffer(&d_x, numAtoms, deviceContext);
allocateDeviceBuffer(&d_xp, numAtoms, deviceContext);
copyToDeviceBuffer(&d_v, h_v, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr);
copyToDeviceBuffer(&d_f, h_f, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr);
- auto integrator = std::make_unique<LeapFrogGpu>(deviceContext, deviceStream);
+ auto integrator =
+ std::make_unique<LeapFrogGpu>(deviceContext, deviceStream, testData->numTCoupleGroups_);
- integrator->set(testData->numAtoms_, testData->inverseMasses_.data(),
- testData->numTCoupleGroups_, testData->mdAtoms_.cTC);
+ integrator->set(testData->numAtoms_, testData->inverseMasses_.data(), testData->mdAtoms_.cTC);
bool doTempCouple = testData->numTCoupleGroups_ > 0;
for (int step = 0; step < numSteps; step++)
bool doPressureCouple = testData->doPressureCouple_
&& do_per_step(step + testData->inputRecord_.nstpcouple - 1,
testData->inputRecord_.nstpcouple);
- integrator->integrate(d_x, d_xp, d_v, d_f, testData->timestep_, doTempCouple,
- testData->kineticEnergyData_.tcstat, doPressureCouple,
- testData->dtPressureCouple_, testData->velocityScalingMatrix_);
+ integrator->integrate(d_x,
+ d_xp,
+ d_v,
+ d_f,
+ testData->timestep_,
+ doTempCouple,
+ testData->kineticEnergyData_.tcstat,
+ doPressureCouple,
+ testData->dtPressureCouple_,
+ testData->velocityScalingMatrix_);
}
copyFromDeviceBuffer(h_xp, &d_x, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr);
--- /dev/null
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+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
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+ <Vector Name="Virial z">
+ <Real Name="X">-8.8500000000000014</Real>
+ <Real Name="Y">-9.9000000000000004</Real>
+ <Real Name="Z">-6.4500000000000002</Real>
+ </Vector>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
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+ <Real Name="X">-17.949999999999999</Real>
+ <Real Name="Y">-19.699999999999999</Real>
+ <Real Name="Z">-12.050000000000001</Real>
+ </Vector>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
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+ <Real Name="Z">-11.25</Real>
+ </Vector>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
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+<ReferenceData>
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+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
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--- /dev/null
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+ <Real Name="Y">-13.4</Real>
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+ </Vector>
+</ReferenceData>
<ReferenceData>
<File Name="EnergyFile">
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- <Int Name="Length">97</Int>
+ <Int Name="Length">91</Int>
<EnergyTerm>
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Current ref_t for group Lipid: 25.8
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-
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- <Int Name="Length">51</Int>
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Current ref_t for group Lipid: 25.8
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- Group Ux Uy Uz
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Current ref_t for group Lipid: 0.0
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Current ref_t for group Lipid: 25.8
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Current ref_t for group Lipid: 25.8
T-Protein T-Water T-Lipid
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Current ref_t for group Lipid: 25.8
T-Protein T-Water T-Lipid
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- Group Ux Uy Uz
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- <String Name="Name">Ux-Lipid</String>
- <String Name="Units">nm/ps</String>
- </EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Uy-Lipid</String>
- <String Name="Units">nm/ps</String>
- </EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Uz-Lipid</String>
- <String Name="Units">nm/ps</String>
- </EnergyTerm>
</Sequence>
<Sequence Name="Frames">
<Int Name="Length">1</Int>
<String Name="Step">0</String>
<String Name="NumSteps">0</String>
<Sequence Name="EnergyTerms">
- <Int Name="Length">108</Int>
+ <Int Name="Length">102</Int>
<EnergyTerm>
<String Name="Name">LJ-14</String>
<Real Name="Value">11.499999999999995</Real>
<String Name="Name">T-Lipid</String>
<Real Name="Value">18.000000000000007</Real>
</EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Ux-Protein</String>
- <Real Name="Value">18.20000000000001</Real>
- </EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Uy-Protein</String>
- <Real Name="Value">18.300000000000011</Real>
- </EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Uz-Protein</String>
- <Real Name="Value">18.400000000000013</Real>
- </EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Ux-Lipid</String>
- <Real Name="Value">18.500000000000014</Real>
- </EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Uy-Lipid</String>
- <Real Name="Value">18.600000000000016</Real>
- </EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Uz-Lipid</String>
- <Real Name="Value">18.700000000000017</Real>
- </EnergyTerm>
</Sequence>
</Frame>
</Sequence>
</File>
- <Int Name="Number of Energy Terms">108</Int>
+ <Int Name="Number of Energy Terms">102</Int>
<String Name="log">Current ref_t for group Water: 25.7
Current ref_t for group Lipid: 25.8
T-Protein T-Water T-Lipid
1.76000e+01 1.78000e+01 1.80000e+01
- Group Ux Uy Uz
- Protein 1.82000e+01 1.83000e+01 1.84000e+01
- Lipid 1.85000e+01 1.86000e+01 1.87000e+01
-
</String>
</ReferenceData>
<ReferenceData>
<File Name="EnergyFile">
<Sequence Name="EnergyTerms">
- <Int Name="Length">97</Int>
+ <Int Name="Length">91</Int>
<EnergyTerm>
<String Name="Name">LJ-14</String>
<String Name="Units">kJ/mol</String>
<String Name="Name">T-Lipid</String>
<String Name="Units">K</String>
</EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Ux-Protein</String>
- <String Name="Units">nm/ps</String>
- </EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Uy-Protein</String>
- <String Name="Units">nm/ps</String>
- </EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Uz-Protein</String>
- <String Name="Units">nm/ps</String>
- </EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Ux-Lipid</String>
- <String Name="Units">nm/ps</String>
- </EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Uy-Lipid</String>
- <String Name="Units">nm/ps</String>
- </EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Uz-Lipid</String>
- <String Name="Units">nm/ps</String>
- </EnergyTerm>
</Sequence>
<Sequence Name="Frames">
<Int Name="Length">1</Int>
<String Name="Step">0</String>
<String Name="NumSteps">0</String>
<Sequence Name="EnergyTerms">
- <Int Name="Length">97</Int>
+ <Int Name="Length">91</Int>
<EnergyTerm>
<String Name="Name">LJ-14</String>
<Real Name="Value">11.499999999999995</Real>
<String Name="Name">T-Lipid</String>
<Real Name="Value">18.000000000000007</Real>
</EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Ux-Protein</String>
- <Real Name="Value">18.20000000000001</Real>
- </EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Uy-Protein</String>
- <Real Name="Value">18.300000000000011</Real>
- </EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Uz-Protein</String>
- <Real Name="Value">18.400000000000013</Real>
- </EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Ux-Lipid</String>
- <Real Name="Value">18.500000000000014</Real>
- </EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Uy-Lipid</String>
- <Real Name="Value">18.600000000000016</Real>
- </EnergyTerm>
- <EnergyTerm>
- <String Name="Name">Uz-Lipid</String>
- <Real Name="Value">18.700000000000017</Real>
- </EnergyTerm>
</Sequence>
</Frame>
</Sequence>
</File>
- <Int Name="Number of Energy Terms">97</Int>
+ <Int Name="Number of Energy Terms">91</Int>
<String Name="log">Current ref_t for group Water: 25.7
Current ref_t for group Lipid: 25.8
T-Protein T-Water T-Lipid
1.76000e+01 1.78000e+01 1.80000e+01
- Group Ux Uy Uz
- Protein 1.82000e+01 1.83000e+01 1.84000e+01
- Lipid 1.85000e+01 1.86000e+01 1.87000e+01
-
</String>
</ReferenceData>
// being tested, to help make failing tests comprehensible.
std::string testDescription = formatString(
"Testing %s with %d SETTLEs, %s, %svelocities and %scalculating the virial.",
- runner->hardwareDescription().c_str(), numSettles, pbcName.c_str(),
- updateVelocities ? "with " : "without ", calcVirial ? "" : "not ");
+ runner->hardwareDescription().c_str(),
+ numSettles,
+ pbcName.c_str(),
+ updateVelocities ? "with " : "without ",
+ calcVirial ? "" : "not ");
SCOPED_TRACE(testDescription);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
SettleData settled(testData->mtop_);
- settled.setConstraints(testData->idef_->il[F_SETTLE], testData->numAtoms_,
- testData->masses_.data(), testData->inverseMasses_.data());
+ settled.setConstraints(
+ testData->idef_->il[F_SETTLE], testData->numAtoms_, testData->masses_, testData->inverseMasses_);
bool errorOccured;
int numThreads = 1;
int threadIndex = 0;
- csettle(settled, numThreads, threadIndex, &pbc, testData->x_.arrayRefWithPadding(),
- testData->xPrime_.arrayRefWithPadding(), testData->reciprocalTimeStep_,
+ csettle(settled,
+ numThreads,
+ threadIndex,
+ &pbc,
+ testData->x_.arrayRefWithPadding(),
+ testData->xPrime_.arrayRefWithPadding(),
+ testData->reciprocalTimeStep_,
updateVelocities ? testData->v_.arrayRefWithPadding() : ArrayRefWithPadding<RVec>(),
- calcVirial, testData->virial_, &errorOccured);
+ calcVirial,
+ testData->virial_,
+ &errorOccured);
EXPECT_FALSE(errorOccured) << testDescription;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
#include "gromacs/gpu_utils/devicebuffer.cuh"
+#include "gromacs/gpu_utils/gputraits.h"
#include "gromacs/hardware/device_information.h"
-#include "gromacs/mdlib/settle_gpu.cuh"
+#include "gromacs/mdlib/settle_gpu.h"
#include "gromacs/utility/unique_cptr.h"
#include "testutils/test_device.h"
int numAtoms = testData->numAtoms_;
- float3 *d_x, *d_xp, *d_v;
+ DeviceBuffer<Float3> d_x, d_xp, d_v;
- float3* h_x = (float3*)(as_rvec_array(testData->x_.data()));
- float3* h_xp = (float3*)(as_rvec_array(testData->xPrime_.data()));
- float3* h_v = (float3*)(as_rvec_array(testData->v_.data()));
+ Float3* h_x = gmx::asGenericFloat3Pointer(testData->x_);
+ Float3* h_xp = gmx::asGenericFloat3Pointer(testData->xPrime_);
+ Float3* h_v = gmx::asGenericFloat3Pointer(testData->v_);
allocateDeviceBuffer(&d_x, numAtoms, deviceContext);
allocateDeviceBuffer(&d_xp, numAtoms, deviceContext);
allocateDeviceBuffer(&d_v, numAtoms, deviceContext);
- copyToDeviceBuffer(&d_x, (float3*)h_x, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr);
- copyToDeviceBuffer(&d_xp, (float3*)h_xp, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr);
+ copyToDeviceBuffer(&d_x, h_x, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr);
+ copyToDeviceBuffer(&d_xp, h_xp, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr);
if (updateVelocities)
{
- copyToDeviceBuffer(&d_v, (float3*)h_v, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr);
+ copyToDeviceBuffer(&d_v, h_v, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr);
}
- settleGpu->apply(d_x, d_xp, updateVelocities, d_v, testData->reciprocalTimeStep_, calcVirial,
- testData->virial_, pbcAiuc);
+ settleGpu->apply(
+ d_x, d_xp, updateVelocities, d_v, testData->reciprocalTimeStep_, calcVirial, testData->virial_, pbcAiuc);
- copyFromDeviceBuffer((float3*)h_xp, &d_xp, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr);
+ copyFromDeviceBuffer(h_xp, &d_xp, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr);
if (updateVelocities)
{
- copyFromDeviceBuffer((float3*)h_v, &d_v, 0, numAtoms, deviceStream,
- GpuApiCallBehavior::Sync, nullptr);
+ copyFromDeviceBuffer(h_v, &d_v, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr);
}
freeDeviceBuffer(&d_x);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int numIterations = 0;
int numErrors = 0;
- cshake(iatom.data(), numConstraints, &numIterations, ShakeTest::maxNumIterations_,
- constrainedDistancesSquared, finalPositions, nullptr, initialDisplacements,
- halfOfReducedMasses, omega_, inverseMasses.data(), distanceSquaredTolerances,
- lagrangianValues, &numErrors);
+ cshake(iatom.data(),
+ numConstraints,
+ &numIterations,
+ ShakeTest::maxNumIterations_,
+ constrainedDistancesSquared,
+ finalPositions,
+ nullptr,
+ initialDisplacements,
+ halfOfReducedMasses,
+ omega_,
+ inverseMasses,
+ distanceSquaredTolerances,
+ lagrangianValues,
+ &numErrors);
std::vector<RVec> finalDisplacements = computeDisplacements(iatom, finalPositions);
std::vector<real> finalDistancesSquared = computeDistancesSquared(finalDisplacements);
+ coordMax * GMX_REAL_EPS);
// Assert that the constrained distances are within the required tolerance
EXPECT_FLOAT_EQ_TOL(std::sqrt(constrainedDistancesSquared[i]),
- std::sqrt(finalDistancesSquared[i]), constraintTolerance);
+ std::sqrt(finalDistancesSquared[i]),
+ constraintTolerance);
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return moltype;
}
-TEST(UpdateGroups, ethaneUA)
+//! Test fixture class
+class UpdateGroupsTest : public ::testing::Test
{
- gmx_mtop_t mtop;
-
- mtop.moltype.emplace_back(ethaneUA());
- t_iparams iparams;
- iparams.constr = { 0.3, 0.3 };
- mtop.ffparams.iparams.push_back(iparams);
+public:
+ //! Global toplogy to use in tests
+ gmx_mtop_t mtop_;
+ //! Default temperature for tests
+ real temperature_ = 298;
+};
+
+TEST_F(UpdateGroupsTest, WithEthaneUA)
+{
+ mtop_.moltype.emplace_back(ethaneUA());
+ {
+ t_iparams iparams;
+ iparams.constr = { 0.3, 0.3 };
+ mtop_.ffparams.iparams.push_back(iparams);
+ }
- auto updateGroups = gmx::makeUpdateGroups(mtop);
+ auto updateGroupingsPerMoleculeType = gmx::makeUpdateGroupingsPerMoleculeType(mtop_);
- ASSERT_EQ(updateGroups.size(), 1);
- EXPECT_EQ(updateGroups[0].numBlocks(), 1);
+ ASSERT_EQ(updateGroupingsPerMoleculeType.size(), 1);
+ EXPECT_EQ(updateGroupingsPerMoleculeType[0].numBlocks(), 1);
- real temperature = 298;
- real maxRadius = computeMaxUpdateGroupRadius(mtop, updateGroups, temperature);
+ real maxRadius = computeMaxUpdateGroupRadius(mtop_, updateGroupingsPerMoleculeType, temperature_);
EXPECT_FLOAT_EQ(maxRadius, 0.3 / 2);
}
-TEST(UpdateGroups, methane)
+TEST_F(UpdateGroupsTest, WithMethane)
{
- gmx_mtop_t mtop;
-
- mtop.moltype.emplace_back(methane());
- t_iparams iparams;
- iparams.constr = { 0.1, 0.1 };
- mtop.ffparams.iparams.push_back(iparams);
+ mtop_.moltype.emplace_back(methane());
+ {
+ t_iparams iparams;
+ iparams.constr = { 0.1, 0.1 };
+ mtop_.ffparams.iparams.push_back(iparams);
+ }
- auto updateGroups = gmx::makeUpdateGroups(mtop);
+ auto updateGroupingsPerMoleculeType = gmx::makeUpdateGroupingsPerMoleculeType(mtop_);
- ASSERT_EQ(updateGroups.size(), 1);
- EXPECT_EQ(updateGroups[0].numBlocks(), 1);
+ ASSERT_EQ(updateGroupingsPerMoleculeType.size(), 1);
+ EXPECT_EQ(updateGroupingsPerMoleculeType[0].numBlocks(), 1);
- real temperature = 298;
- real maxRadius = computeMaxUpdateGroupRadius(mtop, updateGroups, temperature);
+ real maxRadius = computeMaxUpdateGroupRadius(mtop_, updateGroupingsPerMoleculeType, temperature_);
EXPECT_FLOAT_EQ(maxRadius, 0.14);
}
-TEST(UpdateGroups, ethane)
+TEST_F(UpdateGroupsTest, WithEthane)
{
- gmx_mtop_t mtop;
+ mtop_.moltype.emplace_back(ethane());
+ {
+ t_iparams iparams;
+ iparams.constr = { 0.1, 0.1 };
+ mtop_.ffparams.iparams.push_back(iparams);
+ iparams.harmonic = { 107.800, 276.144, 107.800, 276.144 };
+ mtop_.ffparams.iparams.push_back(iparams);
+ }
+
+ auto updateGroupingsPerMoleculeType = gmx::makeUpdateGroupingsPerMoleculeType(mtop_);
+
+ ASSERT_EQ(updateGroupingsPerMoleculeType.size(), 1);
+ EXPECT_EQ(updateGroupingsPerMoleculeType[0].numBlocks(), 2);
- mtop.moltype.emplace_back(ethane());
- t_iparams iparams;
- iparams.constr = { 0.1, 0.1 };
- mtop.ffparams.iparams.push_back(iparams);
- iparams.harmonic = { 107.800, 276.144, 107.800, 276.144 };
- mtop.ffparams.iparams.push_back(iparams);
+ real maxRadius = computeMaxUpdateGroupRadius(mtop_, updateGroupingsPerMoleculeType, temperature_);
+ EXPECT_FLOAT_EQ(maxRadius, 0.094746813);
+}
- auto updateGroups = gmx::makeUpdateGroups(mtop);
+TEST_F(UpdateGroupsTest, CheckRadiusCalculationAtDifferentTemperaturesWithEthane)
+{
+ mtop_.moltype.emplace_back(ethane());
+ {
+ t_iparams iparams;
+ iparams.constr = { 0.1, 0.1 };
+ mtop_.ffparams.iparams.push_back(iparams);
+ iparams.harmonic = { 107.800, 276.144, 107.800, 276.144 };
+ mtop_.ffparams.iparams.push_back(iparams);
+ }
- ASSERT_EQ(updateGroups.size(), 1);
- EXPECT_EQ(updateGroups[0].numBlocks(), 2);
+ auto updateGroupingsPerMoleculeType = gmx::makeUpdateGroupingsPerMoleculeType(mtop_);
- real temperature = 298;
- real maxRadius = computeMaxUpdateGroupRadius(mtop, updateGroups, temperature);
+ ASSERT_EQ(updateGroupingsPerMoleculeType.size(), 1);
+ EXPECT_EQ(updateGroupingsPerMoleculeType[0].numBlocks(), 2);
+
+ real maxRadius = computeMaxUpdateGroupRadius(mtop_, updateGroupingsPerMoleculeType, temperature_);
EXPECT_FLOAT_EQ(maxRadius, 0.094746813);
- temperature = 0;
- maxRadius = computeMaxUpdateGroupRadius(mtop, updateGroups, temperature);
+ // Observe that the temperature affects the radius only when valid
+ temperature_ = 0;
+ maxRadius = computeMaxUpdateGroupRadius(mtop_, updateGroupingsPerMoleculeType, temperature_);
EXPECT_FLOAT_EQ(maxRadius, 0.10310466);
- temperature = -1;
- maxRadius = computeMaxUpdateGroupRadius(mtop, updateGroups, temperature);
+ temperature_ = -1;
+ maxRadius = computeMaxUpdateGroupRadius(mtop_, updateGroupingsPerMoleculeType, temperature_);
EXPECT_FLOAT_EQ(maxRadius, 0.125);
}
-TEST(UpdateGroups, butaneUA)
+TEST_F(UpdateGroupsTest, WithButaneUA)
{
- gmx_mtop_t mtop;
-
- mtop.moltype.emplace_back(butaneUA());
- t_iparams iparams;
- iparams.constr = { 0.3, 0.3 };
- mtop.ffparams.iparams.push_back(iparams);
+ mtop_.moltype.emplace_back(butaneUA());
+ {
+ t_iparams iparams;
+ iparams.constr = { 0.3, 0.3 };
+ mtop_.ffparams.iparams.push_back(iparams);
+ }
- auto updateGroups = gmx::makeUpdateGroups(mtop);
+ auto updateGroupingsPerMoleculeType = gmx::makeUpdateGroupingsPerMoleculeType(mtop_);
- EXPECT_EQ(updateGroups.size(), 0);
+ EXPECT_EQ(updateGroupingsPerMoleculeType.size(), 0);
}
-TEST(UpdateGroups, waterThreeSite)
+TEST_F(UpdateGroupsTest, WithWaterThreeSite)
{
- gmx_mtop_t mtop;
+ mtop_.moltype.emplace_back(waterThreeSite());
+ {
+ t_iparams iparams;
+ iparams.settle = { 0.1, 0.1633 };
+ mtop_.ffparams.iparams.push_back(iparams);
+ }
- mtop.moltype.emplace_back(waterThreeSite());
- t_iparams iparams;
- iparams.settle = { 0.1, 0.1633 };
- mtop.ffparams.iparams.push_back(iparams);
+ auto updateGroupingsPerMoleculeType = gmx::makeUpdateGroupingsPerMoleculeType(mtop_);
- auto updateGroups = gmx::makeUpdateGroups(mtop);
+ ASSERT_EQ(updateGroupingsPerMoleculeType.size(), 1);
+ EXPECT_EQ(updateGroupingsPerMoleculeType[0].numBlocks(), 1);
- ASSERT_EQ(updateGroups.size(), 1);
- EXPECT_EQ(updateGroups[0].numBlocks(), 1);
-
- real temperature = 298;
- real maxRadius = computeMaxUpdateGroupRadius(mtop, updateGroups, temperature);
+ real maxRadius = computeMaxUpdateGroupRadius(mtop_, updateGroupingsPerMoleculeType, temperature_);
EXPECT_FLOAT_EQ(maxRadius, 0.083887339);
}
// Tests update group with virtual site
-TEST(UpdateGroups, waterFourSite)
+TEST_F(UpdateGroupsTest, WithWaterFourSite)
{
- gmx_mtop_t mtop;
+ mtop_.moltype.emplace_back(waterFourSite());
+ {
+ t_iparams iparams[2];
+ iparams[0].settle = { 0.1, 0.1633 };
+ iparams[1].vsite = { 0.128, 0.128 };
+ mtop_.ffparams.iparams.push_back(iparams[0]);
+ mtop_.ffparams.iparams.push_back(iparams[1]);
+ }
+
+ auto updateGroupingsPerMoleculeType = gmx::makeUpdateGroupingsPerMoleculeType(mtop_);
+
+ ASSERT_EQ(updateGroupingsPerMoleculeType.size(), 1);
+ EXPECT_EQ(updateGroupingsPerMoleculeType[0].numBlocks(), 1);
+}
- mtop.moltype.emplace_back(waterFourSite());
- t_iparams iparams[2];
- iparams[0].settle = { 0.1, 0.1633 };
- iparams[1].vsite = { 0.128, 0.128 };
- mtop.ffparams.iparams.push_back(iparams[0]);
- mtop.ffparams.iparams.push_back(iparams[1]);
+TEST_F(UpdateGroupsTest, WithFourAtomsWithSettle)
+{
+ mtop_.moltype.emplace_back(waterThreeSite());
+ mtop_.moltype.back().atoms.nr = 4;
- auto updateGroups = gmx::makeUpdateGroups(mtop);
+ auto updateGroupingsPerMoleculeType = gmx::makeUpdateGroupingsPerMoleculeType(mtop_);
- ASSERT_EQ(updateGroups.size(), 1);
- EXPECT_EQ(updateGroups[0].numBlocks(), 1);
+ ASSERT_EQ(updateGroupingsPerMoleculeType.size(), 1);
+ EXPECT_EQ(updateGroupingsPerMoleculeType[0].numBlocks(), 2);
}
-TEST(UpdateGroups, fourAtomsWithSettle)
+// Tests groups with two constraints and an angle potential
+TEST_F(UpdateGroupsTest, WithWaterFlexAngle)
{
- gmx_mtop_t mtop;
+ mtop_.moltype.emplace_back(waterFlexAngle());
+ {
+ t_iparams iparams;
+ iparams.constr = { 0.1, 0.1 };
+ mtop_.ffparams.iparams.push_back(iparams);
+ iparams.harmonic = { 109.47, 383.0, 109.47, 383.0 };
+ mtop_.ffparams.iparams.push_back(iparams);
+ }
- mtop.moltype.emplace_back(waterThreeSite());
- mtop.moltype.back().atoms.nr = 4;
+ auto updateGroupingsPerMoleculeType = gmx::makeUpdateGroupingsPerMoleculeType(mtop_);
- auto updateGroups = gmx::makeUpdateGroups(mtop);
+ ASSERT_EQ(updateGroupingsPerMoleculeType.size(), 1);
+ EXPECT_EQ(updateGroupingsPerMoleculeType[0].numBlocks(), 1);
- ASSERT_EQ(updateGroups.size(), 1);
- EXPECT_EQ(updateGroups[0].numBlocks(), 2);
+ real maxRadius = computeMaxUpdateGroupRadius(mtop_, updateGroupingsPerMoleculeType, temperature_);
+ EXPECT_FLOAT_EQ(maxRadius, 0.090824135);
}
-// Tests groups with two constraints and an angle potential
-TEST(UpdateGroups, waterFlexAngle)
+TEST_F(UpdateGroupsTest, CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle)
{
- gmx_mtop_t mtop;
-
- mtop.moltype.emplace_back(waterFlexAngle());
- t_iparams iparams;
- iparams.constr = { 0.1, 0.1 };
- mtop.ffparams.iparams.push_back(iparams);
- iparams.harmonic = { 109.47, 383.0, 109.47, 383.0 };
- mtop.ffparams.iparams.push_back(iparams);
+ mtop_.moltype.emplace_back(waterFlexAngle());
+ {
+ t_iparams iparams;
+ iparams.constr = { 0.1, 0.1 };
+ mtop_.ffparams.iparams.push_back(iparams);
+ iparams.harmonic = { 109.47, 383.0, 109.47, 383.0 };
+ mtop_.ffparams.iparams.push_back(iparams);
+ }
- auto updateGroups = gmx::makeUpdateGroups(mtop);
+ auto updateGroupingsPerMoleculeType = gmx::makeUpdateGroupingsPerMoleculeType(mtop_);
- ASSERT_EQ(updateGroups.size(), 1);
- EXPECT_EQ(updateGroups[0].numBlocks(), 1);
+ ASSERT_EQ(updateGroupingsPerMoleculeType.size(), 1);
+ EXPECT_EQ(updateGroupingsPerMoleculeType[0].numBlocks(), 1);
- real temperature = 298;
- real maxRadius = computeMaxUpdateGroupRadius(mtop, updateGroups, temperature);
+ real maxRadius = computeMaxUpdateGroupRadius(mtop_, updateGroupingsPerMoleculeType, temperature_);
EXPECT_FLOAT_EQ(maxRadius, 0.090824135);
- temperature = 0;
- maxRadius = computeMaxUpdateGroupRadius(mtop, updateGroups, temperature);
+ // Observe that the temperature affects the radius only when valid
+ temperature_ = 0;
+ maxRadius = computeMaxUpdateGroupRadius(mtop_, updateGroupingsPerMoleculeType, temperature_);
EXPECT_FLOAT_EQ(maxRadius, 0.1);
- temperature = -1;
- maxRadius = computeMaxUpdateGroupRadius(mtop, updateGroups, temperature);
+ temperature_ = -1;
+ maxRadius = computeMaxUpdateGroupRadius(mtop_, updateGroupingsPerMoleculeType, temperature_);
EXPECT_FLOAT_EQ(maxRadius, 0.1);
}
-TEST(UpdateGroups, twoMoltypes)
+TEST_F(UpdateGroupsTest, WithTwoMoltypes)
{
- gmx_mtop_t mtop;
-
- mtop.moltype.emplace_back(methane());
- t_iparams iparams;
- iparams.constr = { 0.1, 0.1 };
- mtop.ffparams.iparams.push_back(iparams);
-
- mtop.moltype.emplace_back(waterThreeSite());
+ mtop_.moltype.emplace_back(methane());
+ {
+ t_iparams iparams;
+ iparams.constr = { 0.1, 0.1 };
+ mtop_.ffparams.iparams.push_back(iparams);
+ }
+
+ mtop_.moltype.emplace_back(waterThreeSite());
// Note: iparams not accessed for SETTLE when not computing radius
- auto updateGroups = gmx::makeUpdateGroups(mtop);
+ auto updateGroupingsPerMoleculeType = gmx::makeUpdateGroupingsPerMoleculeType(mtop_);
- ASSERT_EQ(updateGroups.size(), 2);
- EXPECT_EQ(updateGroups[0].numBlocks(), 1);
- EXPECT_EQ(updateGroups[1].numBlocks(), 1);
+ ASSERT_EQ(updateGroupingsPerMoleculeType.size(), 2);
+ EXPECT_EQ(updateGroupingsPerMoleculeType[0].numBlocks(), 1);
+ EXPECT_EQ(updateGroupingsPerMoleculeType[1].numBlocks(), 1);
}
} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
mtop.ffparams.iparams.push_back(iparams);
// Run the test
- auto updateGroups = makeUpdateGroups(mtop);
- real temperature = 300;
+ auto updateGroupingsPerMoleculeType = makeUpdateGroupingsPerMoleculeType(mtop);
+ real temperature = 300;
- UpdateGroupsCog updateGroupsCog(mtop, updateGroups, temperature, numAtoms);
+ UpdateGroupsCog updateGroupsCog(mtop, updateGroupingsPerMoleculeType, temperature, numAtoms);
EXPECT_FLOAT_EQ(updateGroupsCog.maxUpdateGroupRadius(), 0.083887339);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "tgroup.h"
-#include <cmath>
-
-#include "gromacs/gmxlib/network.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/coupling.h"
-#include "gromacs/mdlib/gmx_omp_nthreads.h"
-#include "gromacs/mdlib/rbin.h"
#include "gromacs/mdtypes/group.h"
#include "gromacs/mdtypes/inputrec.h"
-#include "gromacs/mdtypes/mdatom.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/topology/topology.h"
-#include "gromacs/utility/exceptions.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/utility/smalloc.h"
-
-static void init_grpstat(const gmx_mtop_t* mtop, int ngacc, t_grp_acc gstat[])
-{
- if (ngacc > 0)
- {
- const SimulationGroups& groups = mtop->groups;
- for (const AtomProxy atomP : AtomRange(*mtop))
- {
- const t_atom& local = atomP.atom();
- int i = atomP.globalAtomNumber();
- int grp = getGroupType(groups, SimulationAtomGroupType::Acceleration, i);
- if ((grp < 0) && (grp >= ngacc))
- {
- gmx_incons("Input for acceleration groups wrong");
- }
- gstat[grp].nat++;
- /* This will not work for integrator BD */
- gstat[grp].mA += local.m;
- gstat[grp].mB += local.mB;
- }
- }
-}
-
-void init_ekindata(FILE gmx_unused* log,
- const gmx_mtop_t* mtop,
- const t_grpopts* opts,
- gmx_ekindata_t* ekind,
- real cos_accel)
-{
- int i;
-
- /* bNEMD tells if we should remove remove the COM velocity
- * from the velocities during velocity scaling in T-coupling.
- * Turn this on when we have multiple acceleration groups
- * or one accelerated group.
- */
- ekind->bNEMD = (opts->ngacc > 1 || norm2(opts->acc[0]) > 0);
-
- ekind->ngtc = opts->ngtc;
- ekind->tcstat.resize(opts->ngtc);
- /* Set Berendsen tcoupl lambda's to 1,
- * so runs without Berendsen coupling are not affected.
- */
- for (i = 0; i < opts->ngtc; i++)
- {
- ekind->tcstat[i].lambda = 1.0;
- ekind->tcstat[i].vscale_nhc = 1.0;
- ekind->tcstat[i].ekinscaleh_nhc = 1.0;
- ekind->tcstat[i].ekinscalef_nhc = 1.0;
- }
-
- int nthread = gmx_omp_nthreads_get(emntUpdate);
- ekind->nthreads = nthread;
- snew(ekind->ekin_work_alloc, nthread);
- snew(ekind->ekin_work, nthread);
- snew(ekind->dekindl_work, nthread);
-#pragma omp parallel for num_threads(nthread) schedule(static)
- for (int thread = 0; thread < nthread; thread++)
- {
- try
- {
-#define EKIN_WORK_BUFFER_SIZE 2
- /* Allocate 2 extra elements on both sides, so in single
- * precision we have
- * EKIN_WORK_BUFFER_SIZE*DIM*DIM*sizeof(real) = 72/144 bytes
- * buffer on both sides to avoid cache pollution.
- */
- snew(ekind->ekin_work_alloc[thread], ekind->ngtc + 2 * EKIN_WORK_BUFFER_SIZE);
- ekind->ekin_work[thread] = ekind->ekin_work_alloc[thread] + EKIN_WORK_BUFFER_SIZE;
- /* Nasty hack so we can have the per-thread accumulation
- * variable for dekindl in the same thread-local cache lines
- * as the per-thread accumulation tensors for ekin[fh],
- * because they are accumulated in the same loop. */
- ekind->dekindl_work[thread] = &(ekind->ekin_work[thread][ekind->ngtc][0][0]);
-#undef EKIN_WORK_BUFFER_SIZE
- }
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
- }
-
- ekind->ngacc = opts->ngacc;
- ekind->grpstat.resize(opts->ngacc);
- init_grpstat(mtop, opts->ngacc, ekind->grpstat.data());
-
- ekind->cosacc.cos_accel = cos_accel;
-}
-
-void accumulate_u(const t_commrec* cr, const t_grpopts* opts, gmx_ekindata_t* ekind)
-{
- /* This routine will only be called when it's necessary */
- t_bin* rb;
- int g;
-
- rb = mk_bin();
-
- for (g = 0; (g < opts->ngacc); g++)
- {
- add_binr(rb, DIM, ekind->grpstat[g].u);
- }
- sum_bin(rb, cr);
-
- for (g = 0; (g < opts->ngacc); g++)
- {
- extract_binr(rb, DIM * g, DIM, ekind->grpstat[g].u);
- }
- destroy_bin(rb);
-}
-
-void update_ekindata(int start,
- int homenr,
- gmx_ekindata_t* ekind,
- const t_grpopts* opts,
- const rvec v[],
- const t_mdatoms* md,
- real lambda)
-{
- int d, g, n;
- real mv;
-
- /* calculate mean velocities at whole timestep */
- for (g = 0; (g < opts->ngtc); g++)
- {
- ekind->tcstat[g].T = 0;
- }
-
- if (ekind->bNEMD)
- {
- for (g = 0; (g < opts->ngacc); g++)
- {
- clear_rvec(ekind->grpstat[g].u);
- }
-
- g = 0;
- for (n = start; (n < start + homenr); n++)
- {
- if (md->cACC)
- {
- g = md->cACC[n];
- }
- for (d = 0; (d < DIM); d++)
- {
- mv = md->massT[n] * v[n][d];
- ekind->grpstat[g].u[d] += mv;
- }
- }
- for (g = 0; (g < opts->ngacc); g++)
- {
- for (d = 0; (d < DIM); d++)
- {
- ekind->grpstat[g].u[d] /=
- (1 - lambda) * ekind->grpstat[g].mA + lambda * ekind->grpstat[g].mB;
- }
- }
- }
-}
-real sum_ekin(const t_grpopts* opts, gmx_ekindata_t* ekind, real* dekindlambda, gmx_bool bEkinAveVel, gmx_bool bScaleEkin)
+real sum_ekin(const t_grpopts* opts, gmx_ekindata_t* ekind, real* dekindlambda, bool bEkinAveVel, bool bScaleEkin)
{
int i, j, m, ngtc;
real T;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MDLIB_TGROUP_H
#define GMX_MDLIB_TGROUP_H
-#include <cstdio>
-
-#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
-struct gmx_ekindata_t;
-struct gmx_mtop_t;
-struct t_commrec;
+class gmx_ekindata_t;
struct t_grpopts;
-struct t_mdatoms;
-
-void init_ekindata(FILE* log, const gmx_mtop_t* mtop, const t_grpopts* opts, gmx_ekindata_t* ekind, real cos_accel);
-/* Allocate memory and set the grpnr array. */
-
-void done_ekindata(gmx_ekindata_t* ekind);
-/* Free the memory */
-
-void accumulate_u(const t_commrec* cr, const t_grpopts* opts, gmx_ekindata_t* ekind);
-/* Communicate subsystem - group velocities and subsystem ekin respectively
- * and sum them up. Return them in grps.
- */
-
-real sum_ekin(const t_grpopts* opts, gmx_ekindata_t* ekind, real* dekindlambda, gmx_bool bEkinFullStep, gmx_bool bScaleEkin);
+real sum_ekin(const t_grpopts* opts, gmx_ekindata_t* ekind, real* dekindlambda, bool bEkinFullStep, bool bScaleEkin);
/* Sum the group ekins into total ekin and calc temp per group,
* return total temperature.
*/
-void update_ekindata(int start,
- int homenr,
- gmx_ekindata_t* ekind,
- const t_grpopts* opts,
- const rvec v[],
- const t_mdatoms* md,
- real lambda);
-/* Do the update of group velocities (if bNEMD) and
- * (partial) group ekin.
- */
-
#endif
int64_t step,
int64_t step_rel,
double t,
- t_inputrec* ir,
+ const t_inputrec* ir,
t_state* state,
t_state* state_global,
ObservablesHistory* observablesHistory,
- const gmx_mtop_t* top_global,
+ const gmx_mtop_t& top_global,
t_forcerec* fr,
gmx_mdoutf_t outf,
const gmx::EnergyOutput& energyOutput,
if (mdof_flags != 0)
{
- wallcycle_start(mdoutf_get_wcycle(outf), ewcTRAJ);
+ wallcycle_start(mdoutf_get_wcycle(outf), WallCycleCounter::Traj);
if (bCPT)
{
if (MASTER(cr))
// Note that part of the following code is duplicated in StatePropagatorData::trajectoryWriterTeardown.
// This duplication is needed while both legacy and modular code paths are in use.
// TODO: Remove duplication asap, make sure to keep in sync in the meantime.
- mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step, t, state,
- state_global, observablesHistory, f, &checkpointDataHolder);
+ mdoutf_write_to_trajectory_files(
+ fplog, cr, outf, mdof_flags, top_global.natoms, step, t, state, state_global, observablesHistory, f, &checkpointDataHolder);
if (bLastStep && step_rel == ir->nsteps && bDoConfOut && MASTER(cr) && !bRerunMD)
{
if (fr->bMolPBC && state == state_global)
if (fr->bMolPBC && !ir->bPeriodicMols)
{
/* Make molecules whole only for confout writing */
- do_pbc_mtop(ir->pbcType, state->box, top_global, x_for_confout);
+ do_pbc_mtop(ir->pbcType, state->box, &top_global, x_for_confout);
}
- write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm), *top_global->name, top_global,
- x_for_confout, state_global->v.rvec_array(), ir->pbcType, state->box);
+ write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
+ *top_global.name,
+ top_global,
+ x_for_confout,
+ state_global->v.rvec_array(),
+ ir->pbcType,
+ state->box);
if (fr->bMolPBC && state == state_global)
{
sfree(x_for_confout);
}
}
- wallcycle_stop(mdoutf_get_wcycle(outf), ewcTRAJ);
+ wallcycle_stop(mdoutf_get_wcycle(outf), WallCycleCounter::Traj);
}
#if GMX_FAHCORE
if (MASTER(cr))
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdlib/mdoutf.h"
#include "gromacs/timing/wallcycle.h"
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
struct gmx_mtop_t;
struct ObservablesHistory;
struct t_commrec;
int64_t step,
int64_t step_rel,
double t,
- t_inputrec* ir,
+ const t_inputrec* ir,
t_state* state,
t_state* state_global,
ObservablesHistory* observablesHistory,
- const gmx_mtop_t* top_global,
+ const gmx_mtop_t& top_global,
t_forcerec* fr,
gmx_mdoutf_t outf,
const gmx::EnergyOutput& energyOutput,
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <memory>
#include "gromacs/domdec/domdec_struct.h"
-#include "gromacs/fileio/confio.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/listed_forces/disre.h"
#include "gromacs/listed_forces/orires.h"
#include "gromacs/math/functions.h"
-#include "gromacs/math/invertmatrix.h"
#include "gromacs/math/paddedvector.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
-#include "gromacs/math/vecdump.h"
#include "gromacs/mdlib/boxdeformation.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
-#include "gromacs/mdlib/mdatoms.h"
#include "gromacs/mdlib/stat.h"
#include "gromacs/mdlib/tgroup.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/group.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/mdtypes/state.h"
-#include "gromacs/pbcutil/boxutilities.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/random/tabulatednormaldistribution.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
-#include "gromacs/utility/gmxomp.h"
#include "gromacs/utility/smalloc.h"
using namespace gmx; // TODO: Remove when this file is moved into gmx namespace
void update_coords(const t_inputrec& inputRecord,
int64_t step,
- const t_mdatoms* md,
+ int homenr,
+ bool havePartiallyFrozenAtoms,
+ gmx::ArrayRef<const ParticleType> ptype,
+ gmx::ArrayRef<const real> invMass,
+ gmx::ArrayRef<const rvec> invMassPerDim,
t_state* state,
const gmx::ArrayRefWithPadding<const gmx::RVec>& f,
const t_fcdata& fcdata,
const t_commrec* cr,
bool haveConstraints);
- void finish_update(const t_inputrec& inputRecord,
- const t_mdatoms* md,
- t_state* state,
- gmx_wallcycle_t wcycle,
- bool haveConstraints);
-
- void update_sd_second_half(const t_inputrec& inputRecord,
- int64_t step,
- real* dvdlambda,
- const t_mdatoms* md,
- t_state* state,
- const t_commrec* cr,
- t_nrnb* nrnb,
- gmx_wallcycle_t wcycle,
- gmx::Constraints* constr,
- bool do_log,
- bool do_ene);
-
- void update_for_constraint_virial(const t_inputrec& inputRecord,
- const t_mdatoms& md,
- const t_state& state,
+ void finish_update(const t_inputrec& inputRecord,
+ bool havePartiallyFrozenAtoms,
+ int homenr,
+ gmx::ArrayRef<const unsigned short> cFREEZE,
+ t_state* state,
+ gmx_wallcycle* wcycle,
+ bool haveConstraints);
+
+ void update_sd_second_half(const t_inputrec& inputRecord,
+ int64_t step,
+ real* dvdlambda,
+ int homenr,
+ gmx::ArrayRef<const ParticleType> ptype,
+ gmx::ArrayRef<const real> invMass,
+ t_state* state,
+ const t_commrec* cr,
+ t_nrnb* nrnb,
+ gmx_wallcycle* wcycle,
+ gmx::Constraints* constr,
+ bool do_log,
+ bool do_ene);
+
+ void update_for_constraint_virial(const t_inputrec& inputRecord,
+ int homenr,
+ bool havePartiallyFrozenAtoms,
+ gmx::ArrayRef<const real> invmass,
+ gmx::ArrayRef<const rvec> invMassPerDim,
+ const t_state& state,
const gmx::ArrayRefWithPadding<const gmx::RVec>& f,
const gmx_ekindata_t& ekind);
BoxDeformation* deform() const { return deform_; }
+ //! Group index for freezing
+ gmx::ArrayRef<const unsigned short> cFREEZE_;
+ //! Group index for temperature coupling
+ gmx::ArrayRef<const unsigned short> cTC_;
+
private:
//! stochastic dynamics struct
gmx_stochd_t sd_;
return impl_->deform();
}
-void Update::update_coords(const t_inputrec& inputRecord,
- int64_t step,
- const t_mdatoms* md,
- t_state* state,
+void Update::update_coords(const t_inputrec& inputRecord,
+ int64_t step,
+ const int homenr,
+ const bool havePartiallyFrozenAtoms,
+ gmx::ArrayRef<const ParticleType> ptype,
+ gmx::ArrayRef<const real> invMass,
+ gmx::ArrayRef<const rvec> invMassPerDim,
+ t_state* state,
const gmx::ArrayRefWithPadding<const gmx::RVec>& f,
const t_fcdata& fcdata,
const gmx_ekindata_t* ekind,
const t_commrec* cr,
const bool haveConstraints)
{
- return impl_->update_coords(inputRecord, step, md, state, f, fcdata, ekind, M, updatePart, cr,
+ return impl_->update_coords(inputRecord,
+ step,
+ homenr,
+ havePartiallyFrozenAtoms,
+ ptype,
+ invMass,
+ invMassPerDim,
+ state,
+ f,
+ fcdata,
+ ekind,
+ M,
+ updatePart,
+ cr,
haveConstraints);
}
void Update::finish_update(const t_inputrec& inputRecord,
- const t_mdatoms* md,
+ const bool havePartiallyFrozenAtoms,
+ const int homenr,
t_state* state,
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle* wcycle,
const bool haveConstraints)
{
- return impl_->finish_update(inputRecord, md, state, wcycle, haveConstraints);
+ return impl_->finish_update(
+ inputRecord, havePartiallyFrozenAtoms, homenr, impl_->cFREEZE_, state, wcycle, haveConstraints);
}
-void Update::update_sd_second_half(const t_inputrec& inputRecord,
- int64_t step,
- real* dvdlambda,
- const t_mdatoms* md,
- t_state* state,
- const t_commrec* cr,
- t_nrnb* nrnb,
- gmx_wallcycle_t wcycle,
- gmx::Constraints* constr,
- bool do_log,
- bool do_ene)
+void Update::update_sd_second_half(const t_inputrec& inputRecord,
+ int64_t step,
+ real* dvdlambda,
+ const int homenr,
+ gmx::ArrayRef<const ParticleType> ptype,
+ gmx::ArrayRef<const real> invMass,
+ t_state* state,
+ const t_commrec* cr,
+ t_nrnb* nrnb,
+ gmx_wallcycle* wcycle,
+ gmx::Constraints* constr,
+ bool do_log,
+ bool do_ene)
{
- return impl_->update_sd_second_half(inputRecord, step, dvdlambda, md, state, cr, nrnb, wcycle,
- constr, do_log, do_ene);
+ return impl_->update_sd_second_half(
+ inputRecord, step, dvdlambda, homenr, ptype, invMass, state, cr, nrnb, wcycle, constr, do_log, do_ene);
}
-void Update::update_for_constraint_virial(const t_inputrec& inputRecord,
- const t_mdatoms& md,
- const t_state& state,
+void Update::update_for_constraint_virial(const t_inputrec& inputRecord,
+ const int homenr,
+ const bool havePartiallyFrozenAtoms,
+ gmx::ArrayRef<const real> invmass,
+ gmx::ArrayRef<const rvec> invMassPerDim,
+ const t_state& state,
const gmx::ArrayRefWithPadding<const gmx::RVec>& f,
const gmx_ekindata_t& ekind)
{
- return impl_->update_for_constraint_virial(inputRecord, md, state, f, ekind);
+ return impl_->update_for_constraint_virial(
+ inputRecord, homenr, havePartiallyFrozenAtoms, invmass, invMassPerDim, state, f, ekind);
}
void Update::update_temperature_constants(const t_inputrec& inputRecord)
return impl_->update_temperature_constants(inputRecord);
}
-/*! \brief Sets the velocities of virtual sites to zero */
-static void clearVsiteVelocities(int start, int nrend, const unsigned short* particleType, rvec* gmx_restrict v)
-{
- for (int a = start; a < nrend; a++)
- {
- if (particleType[a] == eptVSite)
- {
- clear_rvec(v[a]);
- }
- }
-}
-
/*! \brief Sets whether we store the updated velocities */
enum class StoreUpdatedVelocities
{
* \param[in] pRVScaleMatrixDiagonal Parrinello-Rahman v-scale matrix diagonal
* \param[in] x Input coordinates
* \param[out] xprime Updated coordinates
- * \param[inout] v Velocities
+ * \param[inout] v Velocities, type either rvec* or const rvec*
* \param[in] f Forces
*
* We expect this template to get good SIMD acceleration by most compilers,
* Note that we might get even better SIMD acceleration when we introduce
* aligned (and padded) memory, possibly with some hints for the compilers.
*/
-template<StoreUpdatedVelocities storeUpdatedVelocities, NumTempScaleValues numTempScaleValues, ApplyParrinelloRahmanVScaling applyPRVScaling>
-static void updateMDLeapfrogSimple(int start,
- int nrend,
- real dt,
- real dtPressureCouple,
- const rvec* gmx_restrict invMassPerDim,
- gmx::ArrayRef<const t_grp_tcstat> tcstat,
- const unsigned short* cTC,
- const rvec pRVScaleMatrixDiagonal,
- const rvec* gmx_restrict x,
- rvec* gmx_restrict xprime,
- rvec* gmx_restrict v,
- const rvec* gmx_restrict f)
+template<StoreUpdatedVelocities storeUpdatedVelocities, NumTempScaleValues numTempScaleValues, ApplyParrinelloRahmanVScaling applyPRVScaling, typename VelocityType>
+static std::enable_if_t<std::is_same<VelocityType, rvec>::value || std::is_same<VelocityType, const rvec>::value, void>
+updateMDLeapfrogSimple(int start,
+ int nrend,
+ real dt,
+ real dtPressureCouple,
+ gmx::ArrayRef<const rvec> invMassPerDim,
+ gmx::ArrayRef<const t_grp_tcstat> tcstat,
+ gmx::ArrayRef<const unsigned short> cTC,
+ const rvec pRVScaleMatrixDiagonal,
+ const rvec* gmx_restrict x,
+ rvec* gmx_restrict xprime,
+ VelocityType* gmx_restrict v,
+ const rvec* gmx_restrict f)
{
real lambdaGroup;
{
vNew -= dtPressureCouple * pRVScaleMatrixDiagonal[d] * v[a][d];
}
- if (storeUpdatedVelocities == StoreUpdatedVelocities::yes)
+ // TODO: Remove NOLINTs once clang-tidy is updated to v11, it should be able to handle constexpr.
+ if constexpr (storeUpdatedVelocities == StoreUpdatedVelocities::yes) // NOLINT // NOLINTNEXTLINE
{
v[a][d] = vNew;
}
- xprime[a][d] = x[a][d] + vNew * dt;
+ xprime[a][d] = x[a][d] + vNew * dt; // NOLINT(readability-misleading-indentation)
}
}
}
* \param[in] tcstat Temperature coupling information
* \param[in] x Input coordinates
* \param[out] xprime Updated coordinates
- * \param[inout] v Velocities
+ * \param[inout] v Velocities, type either rvec* or const rvec*
* \param[in] f Forces
*/
-template<StoreUpdatedVelocities storeUpdatedVelocities>
-static void updateMDLeapfrogSimpleSimd(int start,
- int nrend,
- real dt,
- const real* gmx_restrict invMass,
- gmx::ArrayRef<const t_grp_tcstat> tcstat,
- const rvec* gmx_restrict x,
- rvec* gmx_restrict xprime,
- rvec* gmx_restrict v,
- const rvec* gmx_restrict f)
+template<StoreUpdatedVelocities storeUpdatedVelocities, typename VelocityType>
+static std::enable_if_t<std::is_same<VelocityType, rvec>::value || std::is_same<VelocityType, const rvec>::value, void>
+updateMDLeapfrogSimpleSimd(int start,
+ int nrend,
+ real dt,
+ gmx::ArrayRef<const real> invMass,
+ gmx::ArrayRef<const t_grp_tcstat> tcstat,
+ const rvec* gmx_restrict x,
+ rvec* gmx_restrict xprime,
+ VelocityType* gmx_restrict v,
+ const rvec* gmx_restrict f)
{
SimdReal timestep(dt);
SimdReal lambdaSystem(tcstat[0].lambda);
/* We declare variables here, since code is often slower when declaring them inside the loop */
/* Note: We should implement a proper PaddedVector, so we don't need this check */
- GMX_ASSERT(isSimdAligned(invMass), "invMass should be aligned");
+ GMX_ASSERT(isSimdAligned(invMass.data()), "invMass should be aligned");
for (int a = start; a < nrend; a += GMX_SIMD_REAL_WIDTH)
{
SimdReal invMass0, invMass1, invMass2;
- expandScalarsToTriplets(simdLoad(invMass + a), &invMass0, &invMass1, &invMass2);
+ expandScalarsToTriplets(simdLoad(invMass.data() + a), &invMass0, &invMass1, &invMass2);
SimdReal v0, v1, v2;
SimdReal f0, f1, f2;
v1 = fma(f1 * invMass1, timestep, lambdaSystem * v1);
v2 = fma(f2 * invMass2, timestep, lambdaSystem * v2);
- if (storeUpdatedVelocities == StoreUpdatedVelocities::yes)
+ // TODO: Remove NOLINTs once clang-tidy is updated to v11, it should be able to handle constexpr.
+ if constexpr (storeUpdatedVelocities == StoreUpdatedVelocities::yes) // NOLINT // NOLINTNEXTLINE
{
simdStoreRvecs(v, a, v0, v1, v2);
}
- SimdReal x0, x1, x2;
+ SimdReal x0, x1, x2; // NOLINT(readability-misleading-indentation)
simdLoadRvecs(x, a, &x0, &x1, &x2);
SimdReal xprime0 = fma(v0, timestep, x0);
enum class AccelerationType
{
none,
- group,
cosine
};
* \param[in] dt The time step.
* \param[in] dtPressureCouple Time step for pressure coupling, is 0 when no pressure
* coupling should be applied at this step.
- * \param[in] accel Acceleration per group.
- * \param[in] md Atom properties.
+ * \param[in] cTC Temperature coupling group indices
+ * \param[in] invMassPerDim Inverse mass per dimension
* \param[in] ekind Kinetic energy data.
* \param[in] box The box dimensions.
* \param[in] x Input coordinates.
* \param[in] M Parrinello-Rahman scaling matrix.
*/
template<AccelerationType accelerationType>
-static void updateMDLeapfrogGeneral(int start,
- int nrend,
- bool doNoseHoover,
- real dt,
- real dtPressureCouple,
- const rvec* accel,
- const t_mdatoms* md,
- const gmx_ekindata_t* ekind,
- const matrix box,
+static void updateMDLeapfrogGeneral(int start,
+ int nrend,
+ bool doNoseHoover,
+ real dt,
+ real dtPressureCouple,
+ gmx::ArrayRef<const unsigned short> cTC,
+ gmx::ArrayRef<const rvec> invMassPerDim,
+ const gmx_ekindata_t* ekind,
+ const matrix box,
const rvec* gmx_restrict x,
rvec* gmx_restrict xprime,
rvec* gmx_restrict v,
* Holian et al. Phys Rev E 52(3) : 2338, 1995
*/
- gmx::ArrayRef<const t_grp_tcstat> tcstat = ekind->tcstat;
- gmx::ArrayRef<const t_grp_acc> grpstat = ekind->grpstat;
- const unsigned short* cTC = md->cTC;
- const unsigned short* cACC = md->cACC;
-
- const rvec* gmx_restrict invMassPerDim = md->invMassPerDim;
+ gmx::ArrayRef<const t_grp_tcstat> tcstat = ekind->tcstat;
/* Initialize group values, changed later when multiple groups are used */
- int ga = 0;
int gt = 0;
real omega_Z = 2 * static_cast<real>(M_PI) / box[ZZ][ZZ];
for (int n = start; n < nrend; n++)
{
- if (cTC)
+ if (!cTC.empty())
{
gt = cTC[n];
}
rvec vRel;
real cosineZ, vCosine;
-#ifdef __INTEL_COMPILER
-# pragma warning(disable : 280)
-#endif
switch (accelerationType)
{
case AccelerationType::none: copy_rvec(v[n], vRel); break;
- case AccelerationType::group:
- if (cACC)
- {
- ga = cACC[n];
- }
- /* Avoid scaling the group velocity */
- rvec_sub(v[n], grpstat[ga].u, vRel);
- break;
case AccelerationType::cosine:
cosineZ = std::cos(x[n][ZZ] * omega_Z);
vCosine = cosineZ * ekind->cosacc.vcos;
switch (accelerationType)
{
case AccelerationType::none: break;
- case AccelerationType::group:
- /* Add back the mean velocity and apply acceleration */
- vNew += grpstat[ga].u[d] + accel[ga][d] * dt;
- break;
case AccelerationType::cosine:
if (d == XX)
{
const rvec* gmx_restrict x,
rvec* gmx_restrict xprime,
rvec* gmx_restrict v,
- const rvec* gmx_restrict f,
- const rvec* gmx_restrict accel,
- const int etc,
- const int epc,
- const int nsttcouple,
- const int nstpcouple,
- const t_mdatoms* md,
- const gmx_ekindata_t* ekind,
- const matrix box,
+ const rvec* gmx_restrict f,
+ const TemperatureCoupling etc,
+ const PressureCoupling epc,
+ const int nsttcouple,
+ const int nstpcouple,
+ gmx::ArrayRef<const unsigned short> cTC,
+ gmx::ArrayRef<const real> gmx_unused invmass,
+ gmx::ArrayRef<const rvec> invMassPerDim,
+ const gmx_ekindata_t* ekind,
+ const matrix box,
const double* gmx_restrict nh_vxi,
- const matrix M)
+ const matrix M,
+ bool gmx_unused havePartiallyFrozenAtoms)
{
GMX_ASSERT(nrend == start || xprime != x,
"For SIMD optimization certain compilers need to have xprime != x");
/* Note: Berendsen pressure scaling is handled after do_update_md() */
- bool doTempCouple = (etc != etcNO && do_per_step(step + nsttcouple - 1, nsttcouple));
- bool doNoseHoover = (etc == etcNOSEHOOVER && doTempCouple);
- bool doParrinelloRahman =
- (epc == epcPARRINELLORAHMAN && do_per_step(step + nstpcouple - 1, nstpcouple));
+ bool doTempCouple =
+ (etc != TemperatureCoupling::No && do_per_step(step + nsttcouple - 1, nsttcouple));
+ bool doNoseHoover = (etc == TemperatureCoupling::NoseHoover && doTempCouple);
+ bool doParrinelloRahman = (epc == PressureCoupling::ParrinelloRahman
+ && do_per_step(step + nstpcouple - 1, nstpcouple));
bool doPROffDiagonal = (doParrinelloRahman && (M[YY][XX] != 0 || M[ZZ][XX] != 0 || M[ZZ][YY] != 0));
real dtPressureCouple = (doParrinelloRahman ? nstpcouple * dt : 0);
- /* NEMD (also cosine) acceleration is applied in updateMDLeapFrogGeneral */
- bool doAcceleration = (ekind->bNEMD || ekind->cosacc.cos_accel != 0);
+ /* NEMD cosine acceleration is applied in updateMDLeapFrogGeneral */
+ bool doAcceleration = (ekind->cosacc.cos_accel != 0);
if (doNoseHoover || doPROffDiagonal || doAcceleration)
{
if (!doAcceleration)
{
- updateMDLeapfrogGeneral<AccelerationType::none>(start, nrend, doNoseHoover, dt,
- dtPressureCouple, accel, md, ekind, box, x,
- xprime, v, f, nh_vxi, nsttcouple, stepM);
- }
- else if (ekind->bNEMD)
- {
- updateMDLeapfrogGeneral<AccelerationType::group>(
- start, nrend, doNoseHoover, dt, dtPressureCouple, accel, md, ekind, box, x,
- xprime, v, f, nh_vxi, nsttcouple, stepM);
+ updateMDLeapfrogGeneral<AccelerationType::none>(start,
+ nrend,
+ doNoseHoover,
+ dt,
+ dtPressureCouple,
+ cTC,
+ invMassPerDim,
+ ekind,
+ box,
+ x,
+ xprime,
+ v,
+ f,
+ nh_vxi,
+ nsttcouple,
+ stepM);
}
else
{
- updateMDLeapfrogGeneral<AccelerationType::cosine>(
- start, nrend, doNoseHoover, dt, dtPressureCouple, accel, md, ekind, box, x,
- xprime, v, f, nh_vxi, nsttcouple, stepM);
+ updateMDLeapfrogGeneral<AccelerationType::cosine>(start,
+ nrend,
+ doNoseHoover,
+ dt,
+ dtPressureCouple,
+ cTC,
+ invMassPerDim,
+ ekind,
+ box,
+ x,
+ xprime,
+ v,
+ f,
+ nh_vxi,
+ nsttcouple,
+ stepM);
}
}
else
{
- /* Use a simple and thus more efficient integration loop. */
- /* The simple loop does not check for particle type (so it can
- * be vectorized), which means we need to clear the velocities
- * of virtual sites in advance, when present. Note that vsite
- * velocities are computed after update and constraints from
- * their displacement.
- */
- if (md->haveVsites)
- {
- /* Note: The overhead of this loop is completely neligible */
- clearVsiteVelocities(start, nrend, md->ptype, v);
- }
-
/* We determine if we have a single T-coupling lambda value for all
* atoms. That allows for better SIMD acceleration in the template.
* If we do not do temperature coupling (in the run or this step),
bool haveSingleTempScaleValue = (!doTempCouple || ekind->ngtc == 1);
/* Extract some pointers needed by all cases */
- const unsigned short* cTC = md->cTC;
- gmx::ArrayRef<const t_grp_tcstat> tcstat = ekind->tcstat;
- const rvec* invMassPerDim = md->invMassPerDim;
+ gmx::ArrayRef<const t_grp_tcstat> tcstat = ekind->tcstat;
if (doParrinelloRahman)
{
if (haveSingleTempScaleValue)
{
- updateMDLeapfrogSimple<StoreUpdatedVelocities::yes, NumTempScaleValues::single,
- ApplyParrinelloRahmanVScaling::diagonal>(
- start, nrend, dt, dtPressureCouple, invMassPerDim, tcstat, cTC, diagM, x,
- xprime, v, f);
+ updateMDLeapfrogSimple<StoreUpdatedVelocities::yes, NumTempScaleValues::single, ApplyParrinelloRahmanVScaling::diagonal>(
+ start, nrend, dt, dtPressureCouple, invMassPerDim, tcstat, cTC, diagM, x, xprime, v, f);
}
else
{
- updateMDLeapfrogSimple<StoreUpdatedVelocities::yes, NumTempScaleValues::multiple,
- ApplyParrinelloRahmanVScaling::diagonal>(
- start, nrend, dt, dtPressureCouple, invMassPerDim, tcstat, cTC, diagM, x,
- xprime, v, f);
+ updateMDLeapfrogSimple<StoreUpdatedVelocities::yes, NumTempScaleValues::multiple, ApplyParrinelloRahmanVScaling::diagonal>(
+ start, nrend, dt, dtPressureCouple, invMassPerDim, tcstat, cTC, diagM, x, xprime, v, f);
}
}
else
*/
#if GMX_HAVE_SIMD_UPDATE
/* Check if we can use invmass instead of invMassPerDim */
- if (!md->havePartiallyFrozenAtoms)
+ if (!havePartiallyFrozenAtoms)
{
updateMDLeapfrogSimpleSimd<StoreUpdatedVelocities::yes>(
- start, nrend, dt, md->invmass, tcstat, x, xprime, v, f);
+ start, nrend, dt, invmass, tcstat, x, xprime, v, f);
}
else
#endif
{
- updateMDLeapfrogSimple<StoreUpdatedVelocities::yes, NumTempScaleValues::single,
- ApplyParrinelloRahmanVScaling::no>(
- start, nrend, dt, dtPressureCouple, invMassPerDim, tcstat, cTC, nullptr,
- x, xprime, v, f);
+ updateMDLeapfrogSimple<StoreUpdatedVelocities::yes, NumTempScaleValues::single, ApplyParrinelloRahmanVScaling::no>(
+ start, nrend, dt, dtPressureCouple, invMassPerDim, tcstat, cTC, nullptr, x, xprime, v, f);
}
}
else
{
- updateMDLeapfrogSimple<StoreUpdatedVelocities::yes, NumTempScaleValues::multiple,
- ApplyParrinelloRahmanVScaling::no>(
- start, nrend, dt, dtPressureCouple, invMassPerDim, tcstat, cTC, nullptr, x,
- xprime, v, f);
+ updateMDLeapfrogSimple<StoreUpdatedVelocities::yes, NumTempScaleValues::multiple, ApplyParrinelloRahmanVScaling::no>(
+ start, nrend, dt, dtPressureCouple, invMassPerDim, tcstat, cTC, nullptr, x, xprime, v, f);
}
}
}
real dt,
const rvec* gmx_restrict x,
rvec* gmx_restrict xprime,
- rvec* gmx_restrict v,
+ const rvec* gmx_restrict v,
const rvec* gmx_restrict f,
- const t_mdatoms& md,
- const gmx_ekindata_t& ekind)
+ bool gmx_unused havePartiallyFrozenAtoms,
+ gmx::ArrayRef<const real> gmx_unused invmass,
+ gmx::ArrayRef<const rvec> invMassPerDim,
+ const gmx_ekindata_t& ekind)
{
GMX_ASSERT(nrend == start || xprime != x,
"For SIMD optimization certain compilers need to have xprime != x");
/* Check if we can use invmass instead of invMassPerDim */
#if GMX_HAVE_SIMD_UPDATE
- if (!md.havePartiallyFrozenAtoms)
+ if (!havePartiallyFrozenAtoms)
{
- updateMDLeapfrogSimpleSimd<StoreUpdatedVelocities::no>(start, nrend, dt, md.invmass, tcstat,
- x, xprime, v, f);
+ updateMDLeapfrogSimpleSimd<StoreUpdatedVelocities::no>(
+ start, nrend, dt, invmass, tcstat, x, xprime, v, f);
}
else
#endif
{
updateMDLeapfrogSimple<StoreUpdatedVelocities::no, NumTempScaleValues::single, ApplyParrinelloRahmanVScaling::no>(
- start, nrend, dt, dt, md.invMassPerDim, tcstat, nullptr, nullptr, x, xprime, v, f);
+ start, nrend, dt, dt, invMassPerDim, tcstat, gmx::ArrayRef<const unsigned short>(), nullptr, x, xprime, v, f);
}
}
-static void do_update_vv_vel(int start,
- int nrend,
- real dt,
- const rvec accel[],
- const ivec nFreeze[],
- const real invmass[],
- const unsigned short ptype[],
- const unsigned short cFREEZE[],
- const unsigned short cACC[],
- rvec v[],
- const rvec f[],
- gmx_bool bExtended,
- real veta,
- real alpha)
+static void do_update_vv_vel(int start,
+ int nrend,
+ real dt,
+ gmx::ArrayRef<const ivec> nFreeze,
+ gmx::ArrayRef<const real> invmass,
+ gmx::ArrayRef<const ParticleType> ptype,
+ gmx::ArrayRef<const unsigned short> cFREEZE,
+ rvec v[],
+ const rvec f[],
+ gmx_bool bExtended,
+ real veta,
+ real alpha)
{
- int gf = 0, ga = 0;
+ int gf = 0;
int n, d;
real g, mv1, mv2;
for (n = start; n < nrend; n++)
{
real w_dt = invmass[n] * dt;
- if (cFREEZE)
+ if (!cFREEZE.empty())
{
gf = cFREEZE[n];
}
- if (cACC)
- {
- ga = cACC[n];
- }
for (d = 0; d < DIM; d++)
{
- if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
+ if ((ptype[n] != ParticleType::Shell) && !nFreeze[gf][d])
{
- v[n][d] = mv1 * (mv1 * v[n][d] + 0.5 * (w_dt * mv2 * f[n][d])) + 0.5 * accel[ga][d] * dt;
+ v[n][d] = mv1 * (mv1 * v[n][d] + 0.5 * (w_dt * mv2 * f[n][d]));
}
else
{
}
} /* do_update_vv_vel */
-static void do_update_vv_pos(int start,
- int nrend,
- real dt,
- const ivec nFreeze[],
- const unsigned short ptype[],
- const unsigned short cFREEZE[],
- const rvec x[],
- rvec xprime[],
- const rvec v[],
- gmx_bool bExtended,
- real veta)
+static void do_update_vv_pos(int start,
+ int nrend,
+ real dt,
+ gmx::ArrayRef<const ivec> nFreeze,
+ gmx::ArrayRef<const ParticleType> ptype,
+ gmx::ArrayRef<const unsigned short> cFREEZE,
+ const rvec x[],
+ rvec xprime[],
+ const rvec v[],
+ gmx_bool bExtended,
+ real veta)
{
int gf = 0;
int n, d;
for (n = start; n < nrend; n++)
{
- if (cFREEZE)
+ if (!cFREEZE.empty())
{
gf = cFREEZE[n];
}
for (d = 0; d < DIM; d++)
{
- if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
+ if ((ptype[n] != ParticleType::Shell) && !nFreeze[gf][d])
{
xprime[n][d] = mr1 * (mr1 * x[n][d] + mr2 * dt * v[n][d]);
}
const t_grpopts* opts = &inputRecord.opts;
const int ngtc = opts->ngtc;
- if (inputRecord.eI == eiBD)
+ if (inputRecord.eI == IntegrationAlgorithm::BD)
{
bd_rf.resize(ngtc);
}
&& (reft > 0)) /* tau_t or ref_t = 0 means that no randomization is done */
{
randomize_group[gt] = true;
- boltzfac[gt] = BOLTZ * opts->ref_t[gt];
+ boltzfac[gt] = gmx::c_boltz * opts->ref_t[gt];
}
else
{
void Update::Impl::update_temperature_constants(const t_inputrec& inputRecord)
{
- if (inputRecord.eI == eiBD)
+ if (inputRecord.eI == IntegrationAlgorithm::BD)
{
if (inputRecord.bd_fric != 0)
{
for (int gt = 0; gt < inputRecord.opts.ngtc; gt++)
{
- sd_.bd_rf[gt] = std::sqrt(2.0 * BOLTZ * inputRecord.opts.ref_t[gt]
+ sd_.bd_rf[gt] = std::sqrt(2.0 * gmx::c_boltz * inputRecord.opts.ref_t[gt]
/ (inputRecord.bd_fric * inputRecord.delta_t));
}
}
{
for (int gt = 0; gt < inputRecord.opts.ngtc; gt++)
{
- sd_.bd_rf[gt] = std::sqrt(2.0 * BOLTZ * inputRecord.opts.ref_t[gt]);
+ sd_.bd_rf[gt] = std::sqrt(2.0 * gmx::c_boltz * inputRecord.opts.ref_t[gt]);
}
}
}
- if (inputRecord.eI == eiSD1)
+ if (inputRecord.eI == IntegrationAlgorithm::SD1)
{
for (int gt = 0; gt < inputRecord.opts.ngtc; gt++)
{
- real kT = BOLTZ * inputRecord.opts.ref_t[gt];
+ real kT = gmx::c_boltz * inputRecord.opts.ref_t[gt];
/* The mass is accounted for later, since this differs per atom */
sd_.sdsig[gt].V = std::sqrt(kT * (1 - sd_.sdc[gt].em * sd_.sdc[gt].em));
}
xp_.resizeWithPadding(0);
}
-void Update::setNumAtoms(int numAtoms)
+void Update::updateAfterPartition(int numAtoms,
+ gmx::ArrayRef<const unsigned short> cFREEZE,
+ gmx::ArrayRef<const unsigned short> cTC)
{
impl_->xp()->resizeWithPadding(numAtoms);
+ impl_->cFREEZE_ = cFREEZE;
+ impl_->cTC_ = cTC;
}
/*! \brief Sets the SD update type */
* Thus three instantiations of this templated function will be made,
* two with only one contribution, and one with both contributions. */
template<SDUpdate updateType>
-static void doSDUpdateGeneral(const gmx_stochd_t& sd,
- int start,
- int nrend,
- real dt,
- const rvec accel[],
- const ivec nFreeze[],
- const real invmass[],
- const unsigned short ptype[],
- const unsigned short cFREEZE[],
- const unsigned short cACC[],
- const unsigned short cTC[],
- const rvec x[],
- rvec xprime[],
- rvec v[],
- const rvec f[],
- int64_t step,
- int seed,
- const int* gatindex)
+static void doSDUpdateGeneral(const gmx_stochd_t& sd,
+ int start,
+ int nrend,
+ real dt,
+ gmx::ArrayRef<const ivec> nFreeze,
+ gmx::ArrayRef<const real> invmass,
+ gmx::ArrayRef<const ParticleType> ptype,
+ gmx::ArrayRef<const unsigned short> cFREEZE,
+ gmx::ArrayRef<const unsigned short> cTC,
+ const rvec x[],
+ rvec xprime[],
+ rvec v[],
+ const rvec f[],
+ int64_t step,
+ int seed,
+ const int* gatindex)
{
- // cTC, cACC and cFREEZE can be nullptr any time, but various
+ // cTC and cFREEZE can be nullptr any time, but various
// instantiations do not make sense with particular pointer
// values.
if (updateType == SDUpdate::ForcesOnly)
{
GMX_ASSERT(f != nullptr, "SD update with only forces requires forces");
- GMX_ASSERT(cTC == nullptr, "SD update with only forces cannot handle temperature groups");
+ GMX_ASSERT(cTC.empty(), "SD update with only forces cannot handle temperature groups");
}
if (updateType == SDUpdate::FrictionAndNoiseOnly)
{
GMX_ASSERT(f == nullptr, "SD update with only noise cannot handle forces");
- GMX_ASSERT(cACC == nullptr, "SD update with only noise cannot handle acceleration groups");
}
if (updateType == SDUpdate::Combined)
{
real inverseMass = invmass[n];
real invsqrtMass = std::sqrt(inverseMass);
- int freezeGroup = cFREEZE ? cFREEZE[n] : 0;
- int accelerationGroup = cACC ? cACC[n] : 0;
- int temperatureGroup = cTC ? cTC[n] : 0;
+ int freezeGroup = !cFREEZE.empty() ? cFREEZE[n] : 0;
+ int temperatureGroup = !cTC.empty() ? cTC[n] : 0;
for (int d = 0; d < DIM; d++)
{
- if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[freezeGroup][d])
+ if ((ptype[n] != ParticleType::Shell) && !nFreeze[freezeGroup][d])
{
if (updateType == SDUpdate::ForcesOnly)
{
- real vn = v[n][d] + (inverseMass * f[n][d] + accel[accelerationGroup][d]) * dt;
+ real vn = v[n][d] + inverseMass * f[n][d] * dt;
v[n][d] = vn;
// Simple position update.
xprime[n][d] = x[n][d] + v[n][d] * dt;
}
else
{
- real vn = v[n][d] + (inverseMass * f[n][d] + accel[accelerationGroup][d]) * dt;
+ real vn = v[n][d] + inverseMass * f[n][d] * dt;
v[n][d] = (vn * sd.sdc[temperatureGroup].em
+ invsqrtMass * sd.sdsig[temperatureGroup].V * dist(rng));
// Here we include half of the friction+noise
const rvec* gmx_restrict x,
rvec* gmx_restrict xprime,
rvec* gmx_restrict v,
- const rvec* gmx_restrict f,
- const rvec accel[],
- const ivec nFreeze[],
- const real invmass[],
- const unsigned short ptype[],
- const unsigned short cFREEZE[],
- const unsigned short cACC[],
- const unsigned short cTC[],
- int seed,
- const t_commrec* cr,
- const gmx_stochd_t& sd,
- bool haveConstraints)
+ const rvec* gmx_restrict f,
+ gmx::ArrayRef<const ivec> nFreeze,
+ gmx::ArrayRef<const real> invmass,
+ gmx::ArrayRef<const ParticleType> ptype,
+ gmx::ArrayRef<const unsigned short> cFREEZE,
+ gmx::ArrayRef<const unsigned short> cTC,
+ int seed,
+ const t_commrec* cr,
+ const gmx_stochd_t& sd,
+ bool haveConstraints)
{
if (haveConstraints)
{
// With constraints, the SD update is done in 2 parts
- doSDUpdateGeneral<SDUpdate::ForcesOnly>(sd, start, nrend, dt, accel, nFreeze, invmass,
- ptype, cFREEZE, cACC, nullptr, x, xprime, v, f,
- step, seed, nullptr);
+ doSDUpdateGeneral<SDUpdate::ForcesOnly>(sd,
+ start,
+ nrend,
+ dt,
+ nFreeze,
+ invmass,
+ ptype,
+ cFREEZE,
+ gmx::ArrayRef<const unsigned short>(),
+ x,
+ xprime,
+ v,
+ f,
+ step,
+ seed,
+ nullptr);
}
else
{
- doSDUpdateGeneral<SDUpdate::Combined>(
- sd, start, nrend, dt, accel, nFreeze, invmass, ptype, cFREEZE, cACC, cTC, x, xprime,
- v, f, step, seed, DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr);
+ doSDUpdateGeneral<SDUpdate::Combined>(sd,
+ start,
+ nrend,
+ dt,
+ nFreeze,
+ invmass,
+ ptype,
+ cFREEZE,
+ cTC,
+ x,
+ xprime,
+ v,
+ f,
+ step,
+ seed,
+ DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr);
}
}
const rvec* gmx_restrict x,
rvec* gmx_restrict xprime,
rvec* gmx_restrict v,
- const rvec* gmx_restrict f,
- const ivec nFreeze[],
- const real invmass[],
- const unsigned short ptype[],
- const unsigned short cFREEZE[],
- const unsigned short cTC[],
- real friction_coefficient,
- const real* rf,
- int seed,
- const int* gatindex)
+ const rvec* gmx_restrict f,
+ gmx::ArrayRef<const ivec> nFreeze,
+ gmx::ArrayRef<const real> invmass,
+ gmx::ArrayRef<const ParticleType> ptype,
+ gmx::ArrayRef<const unsigned short> cFREEZE,
+ gmx::ArrayRef<const unsigned short> cTC,
+ real friction_coefficient,
+ const real* rf,
+ int seed,
+ const int* gatindex)
{
/* note -- these appear to be full step velocities . . . */
int gf = 0, gt = 0;
rng.restart(step, ng);
dist.reset();
- if (cFREEZE)
+ if (!cFREEZE.empty())
{
gf = cFREEZE[n];
}
- if (cTC)
+ if (!cTC.empty())
{
gt = cTC[n];
}
for (d = 0; (d < DIM); d++)
{
- if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
+ if ((ptype[n] != ParticleType::Shell) && !nFreeze[gf][d])
{
if (friction_coefficient != 0)
{
gmx_bcast(sizeof(n), &n, cr->mpi_comm_mygroup);
for (i = 0; i < n; i++)
{
- gmx_bcast(DIM * DIM * sizeof(ekind->tcstat[i].ekinh[0][0]), ekind->tcstat[i].ekinh[0],
+ gmx_bcast(DIM * DIM * sizeof(ekind->tcstat[i].ekinh[0][0]),
+ ekind->tcstat[i].ekinh[0],
cr->mpi_comm_mygroup);
- gmx_bcast(DIM * DIM * sizeof(ekind->tcstat[i].ekinf[0][0]), ekind->tcstat[i].ekinf[0],
+ gmx_bcast(DIM * DIM * sizeof(ekind->tcstat[i].ekinf[0][0]),
+ ekind->tcstat[i].ekinf[0],
cr->mpi_comm_mygroup);
gmx_bcast(DIM * DIM * sizeof(ekind->tcstat[i].ekinh_old[0][0]),
- ekind->tcstat[i].ekinh_old[0], cr->mpi_comm_mygroup);
-
- gmx_bcast(sizeof(ekind->tcstat[i].ekinscalef_nhc), &(ekind->tcstat[i].ekinscalef_nhc),
+ ekind->tcstat[i].ekinh_old[0],
cr->mpi_comm_mygroup);
- gmx_bcast(sizeof(ekind->tcstat[i].ekinscaleh_nhc), &(ekind->tcstat[i].ekinscaleh_nhc),
+
+ gmx_bcast(sizeof(ekind->tcstat[i].ekinscalef_nhc),
+ &(ekind->tcstat[i].ekinscalef_nhc),
cr->mpi_comm_mygroup);
- gmx_bcast(sizeof(ekind->tcstat[i].vscale_nhc), &(ekind->tcstat[i].vscale_nhc),
+ gmx_bcast(sizeof(ekind->tcstat[i].ekinscaleh_nhc),
+ &(ekind->tcstat[i].ekinscaleh_nhc),
cr->mpi_comm_mygroup);
+ gmx_bcast(sizeof(ekind->tcstat[i].vscale_nhc), &(ekind->tcstat[i].vscale_nhc), cr->mpi_comm_mygroup);
}
gmx_bcast(DIM * DIM * sizeof(ekind->ekin[0][0]), ekind->ekin[0], cr->mpi_comm_mygroup);
}
}
-void Update::Impl::update_sd_second_half(const t_inputrec& inputRecord,
- int64_t step,
- real* dvdlambda,
- const t_mdatoms* md,
- t_state* state,
- const t_commrec* cr,
- t_nrnb* nrnb,
- gmx_wallcycle_t wcycle,
- gmx::Constraints* constr,
- bool do_log,
- bool do_ene)
+void Update::Impl::update_sd_second_half(const t_inputrec& inputRecord,
+ int64_t step,
+ real* dvdlambda,
+ int homenr,
+ gmx::ArrayRef<const ParticleType> ptype,
+ gmx::ArrayRef<const real> invMass,
+ t_state* state,
+ const t_commrec* cr,
+ t_nrnb* nrnb,
+ gmx_wallcycle* wcycle,
+ gmx::Constraints* constr,
+ bool do_log,
+ bool do_ene)
{
if (!constr)
{
return;
}
- if (inputRecord.eI == eiSD1)
+ if (inputRecord.eI == IntegrationAlgorithm::SD1)
{
- int homenr = md->homenr;
/* Cast delta_t from double to real to make the integrators faster.
* The only reason for having delta_t double is to get accurate values
*/
real dt = inputRecord.delta_t;
- wallcycle_start(wcycle, ewcUPDATE);
+ wallcycle_start(wcycle, WallCycleCounter::Update);
- int nth = gmx_omp_nthreads_get(emntUpdate);
+ int nth = gmx_omp_nthreads_get(ModuleMultiThread::Update);
#pragma omp parallel for num_threads(nth) schedule(static)
for (int th = 0; th < nth; th++)
getThreadAtomRange(nth, th, homenr, &start_th, &end_th);
doSDUpdateGeneral<SDUpdate::FrictionAndNoiseOnly>(
- sd_, start_th, end_th, dt, inputRecord.opts.acc, inputRecord.opts.nFreeze,
- md->invmass, md->ptype, md->cFREEZE, nullptr, md->cTC, state->x.rvec_array(),
- xp_.rvec_array(), state->v.rvec_array(), nullptr, step, inputRecord.ld_seed,
+ sd_,
+ start_th,
+ end_th,
+ dt,
+ gmx::arrayRefFromArray(inputRecord.opts.nFreeze, inputRecord.opts.ngfrz),
+ invMass,
+ ptype,
+ cFREEZE_,
+ cTC_,
+ state->x.rvec_array(),
+ xp_.rvec_array(),
+ state->v.rvec_array(),
+ nullptr,
+ step,
+ inputRecord.ld_seed,
DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
inc_nrnb(nrnb, eNR_UPDATE, homenr);
- wallcycle_stop(wcycle, ewcUPDATE);
+ wallcycle_stop(wcycle, WallCycleCounter::Update);
/* Constrain the coordinates upd->xp for half a time step */
bool computeVirial = false;
- constr->apply(do_log, do_ene, step, 1, 0.5, state->x.arrayRefWithPadding(),
- xp_.arrayRefWithPadding(), ArrayRef<RVec>(), state->box,
- state->lambda[efptBONDED], dvdlambda, state->v.arrayRefWithPadding(),
- computeVirial, nullptr, ConstraintVariable::Positions);
+ constr->apply(do_log,
+ do_ene,
+ step,
+ 1,
+ 0.5,
+ state->x.arrayRefWithPadding(),
+ xp_.arrayRefWithPadding(),
+ ArrayRef<RVec>(),
+ state->box,
+ state->lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Bonded)],
+ dvdlambda,
+ state->v.arrayRefWithPadding(),
+ computeVirial,
+ nullptr,
+ ConstraintVariable::Positions);
}
}
-void Update::Impl::finish_update(const t_inputrec& inputRecord,
- const t_mdatoms* md,
- t_state* state,
- gmx_wallcycle_t wcycle,
- const bool haveConstraints)
+void Update::Impl::finish_update(const t_inputrec& inputRecord,
+ const bool havePartiallyFrozenAtoms,
+ const int homenr,
+ gmx::ArrayRef<const unsigned short> cFREEZE,
+ t_state* state,
+ gmx_wallcycle* wcycle,
+ const bool haveConstraints)
{
/* NOTE: Currently we always integrate to a temporary buffer and
* then copy the results back here.
*/
- wallcycle_start_nocount(wcycle, ewcUPDATE);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::Update);
- const int homenr = md->homenr;
- auto xp = makeConstArrayRef(xp_).subArray(0, homenr);
- auto x = makeArrayRef(state->x).subArray(0, homenr);
+ auto xp = makeConstArrayRef(xp_).subArray(0, homenr);
+ auto x = makeArrayRef(state->x).subArray(0, homenr);
- if (md->havePartiallyFrozenAtoms && haveConstraints)
+ if (havePartiallyFrozenAtoms && haveConstraints)
{
/* We have atoms that are frozen along some, but not all dimensions,
* then constraints will have moved them also along the frozen dimensions.
for (int i = 0; i < homenr; i++)
{
- const int g = md->cFREEZE[i];
+ const int g = cFREEZE[i];
for (int d = 0; d < DIM; d++)
{
/* We have no frozen atoms or fully frozen atoms which have not
* been moved by the update, so we can simply copy all coordinates.
*/
- int gmx_unused nth = gmx_omp_nthreads_get(emntUpdate);
+ int gmx_unused nth = gmx_omp_nthreads_get(ModuleMultiThread::Update);
#pragma omp parallel for num_threads(nth) schedule(static)
for (int i = 0; i < homenr; i++)
{
}
}
- wallcycle_stop(wcycle, ewcUPDATE);
+ wallcycle_stop(wcycle, WallCycleCounter::Update);
}
-void Update::Impl::update_coords(const t_inputrec& inputRecord,
- int64_t step,
- const t_mdatoms* md,
- t_state* state,
+void Update::Impl::update_coords(const t_inputrec& inputRecord,
+ int64_t step,
+ int homenr,
+ bool havePartiallyFrozenAtoms,
+ gmx::ArrayRef<const ParticleType> ptype,
+ gmx::ArrayRef<const real> invMass,
+ gmx::ArrayRef<const rvec> invMassPerDim,
+ t_state* state,
const gmx::ArrayRefWithPadding<const gmx::RVec>& f,
const t_fcdata& fcdata,
const gmx_ekindata_t* ekind,
gmx_incons("update_coords called for velocity without VV integrator");
}
- int homenr = md->homenr;
-
/* Cast to real for faster code, no loss in precision (see comment above) */
real dt = inputRecord.delta_t;
/* We need to update the NMR restraint history when time averaging is used */
- if (state->flags & (1 << estDISRE_RM3TAV))
+ if (state->flags & enumValueToBitMask(StateEntry::DisreRm3Tav))
{
update_disres_history(*fcdata.disres, &state->hist);
}
- if (state->flags & (1 << estORIRE_DTAV))
+ if (state->flags & enumValueToBitMask(StateEntry::OrireDtav))
{
update_orires_history(*fcdata.orires, &state->hist);
}
/* ############# START The update of velocities and positions ######### */
- int nth = gmx_omp_nthreads_get(emntUpdate);
+ int nth = gmx_omp_nthreads_get(ModuleMultiThread::Update);
#pragma omp parallel for num_threads(nth) schedule(static)
for (int th = 0; th < nth; th++)
switch (inputRecord.eI)
{
- case (eiMD):
- do_update_md(start_th, end_th, dt, step, x_rvec, xp_rvec, v_rvec, f_rvec,
- inputRecord.opts.acc, inputRecord.etc, inputRecord.epc,
- inputRecord.nsttcouple, inputRecord.nstpcouple, md, ekind,
- state->box, state->nosehoover_vxi.data(), M);
+ case (IntegrationAlgorithm::MD):
+ do_update_md(start_th,
+ end_th,
+ dt,
+ step,
+ x_rvec,
+ xp_rvec,
+ v_rvec,
+ f_rvec,
+ inputRecord.etc,
+ inputRecord.epc,
+ inputRecord.nsttcouple,
+ inputRecord.nstpcouple,
+ cTC_,
+ invMass,
+ invMassPerDim,
+ ekind,
+ state->box,
+ state->nosehoover_vxi.data(),
+ M,
+ havePartiallyFrozenAtoms);
break;
- case (eiSD1):
- do_update_sd(start_th, end_th, dt, step, x_rvec, xp_rvec, v_rvec, f_rvec,
- inputRecord.opts.acc, inputRecord.opts.nFreeze, md->invmass,
- md->ptype, md->cFREEZE, md->cACC, md->cTC, inputRecord.ld_seed, cr,
- sd_, haveConstraints);
+ case (IntegrationAlgorithm::SD1):
+ do_update_sd(start_th,
+ end_th,
+ dt,
+ step,
+ x_rvec,
+ xp_rvec,
+ v_rvec,
+ f_rvec,
+ gmx::arrayRefFromArray(inputRecord.opts.nFreeze, inputRecord.opts.ngfrz),
+ invMass,
+ ptype,
+ cFREEZE_,
+ cTC_,
+ inputRecord.ld_seed,
+ cr,
+ sd_,
+ haveConstraints);
break;
- case (eiBD):
- do_update_bd(start_th, end_th, dt, step, x_rvec, xp_rvec, v_rvec, f_rvec,
- inputRecord.opts.nFreeze, md->invmass, md->ptype, md->cFREEZE,
- md->cTC, inputRecord.bd_fric, sd_.bd_rf.data(), inputRecord.ld_seed,
+ case (IntegrationAlgorithm::BD):
+ do_update_bd(start_th,
+ end_th,
+ dt,
+ step,
+ x_rvec,
+ xp_rvec,
+ v_rvec,
+ f_rvec,
+ gmx::arrayRefFromArray(inputRecord.opts.nFreeze, inputRecord.opts.ngfrz),
+ invMass,
+ ptype,
+ cFREEZE_,
+ cTC_,
+ inputRecord.bd_fric,
+ sd_.bd_rf.data(),
+ inputRecord.ld_seed,
DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr);
break;
- case (eiVV):
- case (eiVVAK):
+ case (IntegrationAlgorithm::VV):
+ case (IntegrationAlgorithm::VVAK):
{
- gmx_bool bExtended = (inputRecord.etc == etcNOSEHOOVER || inputRecord.epc == epcPARRINELLORAHMAN
- || inputRecord.epc == epcMTTK);
+ gmx_bool bExtended = (inputRecord.etc == TemperatureCoupling::NoseHoover
+ || inputRecord.epc == PressureCoupling::ParrinelloRahman
+ || inputRecord.epc == PressureCoupling::Mttk);
/* assuming barostat coupled to group 0 */
real alpha = 1.0 + DIM / static_cast<real>(inputRecord.opts.nrdf[0]);
{
case etrtVELOCITY1:
case etrtVELOCITY2:
- do_update_vv_vel(start_th, end_th, dt, inputRecord.opts.acc,
- inputRecord.opts.nFreeze, md->invmass, md->ptype, md->cFREEZE,
- md->cACC, v_rvec, f_rvec, bExtended, state->veta, alpha);
+ do_update_vv_vel(start_th,
+ end_th,
+ dt,
+ gmx::arrayRefFromArray(inputRecord.opts.nFreeze,
+ inputRecord.opts.ngfrz),
+ invMass,
+ ptype,
+ cFREEZE_,
+ v_rvec,
+ f_rvec,
+ bExtended,
+ state->veta,
+ alpha);
break;
case etrtPOSITION:
- do_update_vv_pos(start_th, end_th, dt, inputRecord.opts.nFreeze,
- md->ptype, md->cFREEZE, x_rvec, xp_rvec, v_rvec,
- bExtended, state->veta);
+ do_update_vv_pos(start_th,
+ end_th,
+ dt,
+ gmx::arrayRefFromArray(inputRecord.opts.nFreeze,
+ inputRecord.opts.ngfrz),
+ ptype,
+ cFREEZE_,
+ x_rvec,
+ xp_rvec,
+ v_rvec,
+ bExtended,
+ state->veta);
break;
}
break;
}
}
-void Update::Impl::update_for_constraint_virial(const t_inputrec& inputRecord,
- const t_mdatoms& md,
- const t_state& state,
+void Update::Impl::update_for_constraint_virial(const t_inputrec& inputRecord,
+ int homenr,
+ bool havePartiallyFrozenAtoms,
+ gmx::ArrayRef<const real> invmass,
+ gmx::ArrayRef<const rvec> invMassPerDim,
+ const t_state& state,
const gmx::ArrayRefWithPadding<const gmx::RVec>& f,
const gmx_ekindata_t& ekind)
{
- GMX_ASSERT(inputRecord.eI == eiMD || inputRecord.eI == eiSD1,
+ GMX_ASSERT(inputRecord.eI == IntegrationAlgorithm::MD || inputRecord.eI == IntegrationAlgorithm::SD1,
"Only leap-frog is supported here");
// Cast to real for faster code, no loss in precision
const real dt = inputRecord.delta_t;
- const int nth = gmx_omp_nthreads_get(emntUpdate);
+ const int nth = gmx_omp_nthreads_get(ModuleMultiThread::Update);
#pragma omp parallel for num_threads(nth) schedule(static)
for (int th = 0; th < nth; th++)
try
{
int start_th, end_th;
- getThreadAtomRange(nth, th, md.homenr, &start_th, &end_th);
+ getThreadAtomRange(nth, th, homenr, &start_th, &end_th);
const rvec* x_rvec = state.x.rvec_array();
rvec* xp_rvec = xp_.rvec_array();
- rvec* v_rvec = const_cast<rvec*>(state.v.rvec_array());
+ const rvec* v_rvec = state.v.rvec_array();
const rvec* f_rvec = as_rvec_array(f.unpaddedConstArrayRef().data());
- doUpdateMDDoNotUpdateVelocities(start_th, end_th, dt, x_rvec, xp_rvec, v_rvec, f_rvec,
- md, ekind);
+ doUpdateMDDoNotUpdateVelocities(
+ start_th, end_th, dt, x_rvec, xp_rvec, v_rvec, f_rvec, havePartiallyFrozenAtoms, invmass, invMassPerDim, ekind);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MDLIB_UPDATE_H
#define GMX_MDLIB_UPDATE_H
+#include <memory>
+
#include "gromacs/math/paddedvector.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/real.h"
class ekinstate_t;
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
struct gmx_enerdata_t;
enum class PbcType;
struct t_fcdata;
struct t_graph;
struct t_grpopts;
struct t_inputrec;
-struct t_mdatoms;
struct t_nrnb;
class t_state;
+enum class ParticleType;
namespace gmx
{
* \returns handle to box deformation class
*/
BoxDeformation* deform() const;
- /*! \brief Resizes buffer that stores intermediate coordinates.
+ /*! \brief Sets data that changes only at domain decomposition time.
*
* \param[in] numAtoms Updated number of atoms.
+ * \param[in] cFREEZE Group index for freezing
+ * \param[in] cTC Group index for center of mass motion removal
*/
- void setNumAtoms(int numAtoms);
+ void updateAfterPartition(int numAtoms,
+ gmx::ArrayRef<const unsigned short> cFREEZE,
+ gmx::ArrayRef<const unsigned short> cTC);
/*! \brief Perform numerical integration step.
*
* Selects the appropriate integrator, based on the input record and performs a numerical integration step.
*
- * \param[in] inputRecord Input record.
- * \param[in] step Current timestep.
- * \param[in] md MD atoms data.
- * \param[in] state System state object.
- * \param[in] f Buffer with atomic forces for home particles.
- * \param[in] fcdata Force calculation data to update distance and orientation restraints.
- * \param[in] ekind Kinetic energy data (for temperature coupling, energy groups, etc.).
- * \param[in] M Parrinello-Rahman velocity scaling matrix.
- * \param[in] updatePart What should be updated, coordinates or velocities. This enum only used in VV integrator.
- * \param[in] cr Comunication record (Old comment: these shouldn't be here -- need to think about it).
- * \param[in] haveConstraints If the system has constraints.
+ * \param[in] inputRecord Input record.
+ * \param[in] step Current timestep.
+ * \param[in] homenr The number of atoms on this processor.
+ * \param[in] havePartiallyFrozenAtoms Whether atoms are frozen along 1 or 2 (not 3) dimensions?
+ * \param[in] ptype The list of particle types.
+ * \param[in] invMass Inverse atomic mass per atom, 0 for vsites and shells.
+ * \param[in] invMassPerDim Inverse atomic mass per atom and dimension, 0 for vsites, shells and frozen dimensions
+ * \param[in] state System state object.
+ * \param[in] f Buffer with atomic forces for home particles.
+ * \param[in] fcdata Force calculation data to update distance and orientation restraints.
+ * \param[in] ekind Kinetic energy data (for temperature coupling, energy groups, etc.).
+ * \param[in] M Parrinello-Rahman velocity scaling matrix.
+ * \param[in] updatePart What should be updated, coordinates or velocities. This enum only used in VV integrator.
+ * \param[in] cr Comunication record (Old comment: these shouldn't be here -- need to think about it).
+ * \param[in] haveConstraints If the system has constraints.
*/
void update_coords(const t_inputrec& inputRecord,
int64_t step,
- const t_mdatoms* md,
+ int homenr,
+ bool havePartiallyFrozenAtoms,
+ gmx::ArrayRef<const ParticleType> ptype,
+ gmx::ArrayRef<const real> invMass,
+ gmx::ArrayRef<const rvec> invMassPerDim,
t_state* state,
const gmx::ArrayRefWithPadding<const gmx::RVec>& f,
const t_fcdata& fcdata,
* Copy the updated coordinates to the main coordinates buffer for the atoms that are not frozen.
*
* \param[in] inputRecord Input record.
- * \param[in] md MD atoms data.
+ * \param[in] havePartiallyFrozenAtoms Whether atoms are frozen along 1 or 2 (not 3) dimensions?
+ * \param[in] homenr The number of atoms on this processor.
* \param[in] state System state object.
* \param[in] wcycle Wall-clock cycle counter.
* \param[in] haveConstraints If the system has constraints.
*/
void finish_update(const t_inputrec& inputRecord,
- const t_mdatoms* md,
+ bool havePartiallyFrozenAtoms,
+ int homenr,
t_state* state,
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle* wcycle,
bool haveConstraints);
/*! \brief Secong part of the SD integrator.
* \param[in] step Current timestep.
* \param[in] dvdlambda Free energy derivative. Contribution to be added to
* the bonded interactions.
- * \param[in] md MD atoms data.
+ * \param[in] homenr The number of atoms on this processor.
+ * \param[in] ptype The list of particle types.
+ * \param[in] invMass Inverse atomic mass per atom, 0 for vsites and shells.
* \param[in] state System state object.
* \param[in] cr Comunication record.
* \param[in] nrnb Cycle counters.
* \param[in] do_log If this is logging step.
* \param[in] do_ene If this is an energy evaluation step.
*/
- void update_sd_second_half(const t_inputrec& inputRecord,
- int64_t step,
- real* dvdlambda,
- const t_mdatoms* md,
- t_state* state,
- const t_commrec* cr,
- t_nrnb* nrnb,
- gmx_wallcycle_t wcycle,
- gmx::Constraints* constr,
- bool do_log,
- bool do_ene);
+ void update_sd_second_half(const t_inputrec& inputRecord,
+ int64_t step,
+ real* dvdlambda,
+ int homenr,
+ gmx::ArrayRef<const ParticleType> ptype,
+ gmx::ArrayRef<const real> invMass,
+ t_state* state,
+ const t_commrec* cr,
+ t_nrnb* nrnb,
+ gmx_wallcycle* wcycle,
+ gmx::Constraints* constr,
+ bool do_log,
+ bool do_ene);
/*! \brief Performs a leap-frog update without updating \p state so the constrain virial
* can be computed.
*/
- void update_for_constraint_virial(const t_inputrec& inputRecord,
- const t_mdatoms& md,
- const t_state& state,
+ void update_for_constraint_virial(const t_inputrec& inputRecord,
+ int homenr,
+ bool havePartiallyFrozenAtoms,
+ gmx::ArrayRef<const real> invmass,
+ gmx::ArrayRef<const rvec> invMassPerDim,
+ const t_state& state,
const gmx::ArrayRefWithPadding<const gmx::RVec>& f,
const gmx_ekindata_t& ekind);
//! Implementation type.
class Impl;
//! Implementation object.
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
}; // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MDLIB_UPDATE_CONSTRAIN_GPU_H
#define GMX_MDLIB_UPDATE_CONSTRAIN_GPU_H
+#include <memory>
+
#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/mdtypes/group.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/classhelpers.h"
class DeviceContext;
class DeviceStream;
* any) consumers of the updated coordinates. The \p xUpdatedOnDevice also can not be a nullptr
* because the markEvent(...) method is called unconditionally.
*
- * \param[in] ir Input record data: LINCS takes number of iterations and order of
- * projection from it.
- * \param[in] mtop Topology of the system: SETTLE gets the masses for O and H atoms
- * and target O-H and H-H distances from this object.
- * \param[in] deviceContext GPU device context.
- * \param[in] deviceStream GPU stream to use.
- * \param[in] xUpdatedOnDevice The event synchronizer to use to mark that update is done
- * on the GPU.
- * \param[in] wcycle The wallclock counter
+ * \param[in] ir Input record data: LINCS takes number of iterations and order of
+ * projection from it.
+ * \param[in] mtop Topology of the system: SETTLE gets the masses for O and H atoms
+ * and target O-H and H-H distances from this object.
+ * \param[in] numTempScaleValues Number of temperature scaling groups. Zero for no temperature scaling.
+ * \param[in] deviceContext GPU device context.
+ * \param[in] deviceStream GPU stream to use.
+ * \param[in] xUpdatedOnDevice The event synchronizer to use to mark that update is done
+ * on the GPU.
+ * \param[in] wcycle The wallclock counter
*/
UpdateConstrainGpu(const t_inputrec& ir,
const gmx_mtop_t& mtop,
+ int numTempScaleValues,
const DeviceContext& deviceContext,
const DeviceStream& deviceStream,
GpuEventSynchronizer* xUpdatedOnDevice,
* \param[in] d_f Device buffer with forces.
* \param[in] idef System topology
* \param[in] md Atoms data.
- * \param[in] numTempScaleValues Number of temperature scaling groups. Zero for no temperature scaling.
*/
void set(DeviceBuffer<RVec> d_x,
DeviceBuffer<RVec> d_v,
DeviceBuffer<RVec> d_f,
const InteractionDefinitions& idef,
- const t_mdatoms& md,
- int numTempScaleValues);
+ const t_mdatoms& md);
/*! \brief
* Update PBC data.
private:
class Impl;
- gmx::PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
UpdateConstrainGpu::UpdateConstrainGpu(const t_inputrec& /* ir */,
const gmx_mtop_t& /* mtop */,
+ const int /* numTempScaleValues */,
const DeviceContext& /* deviceContext */,
const DeviceStream& /* deviceStream */,
GpuEventSynchronizer* /* xUpdatedOnDevice */,
DeviceBuffer<RVec> /* d_v */,
const DeviceBuffer<RVec> /* d_f */,
const InteractionDefinitions& /* idef */,
- const t_mdatoms& /* md */,
- const int /* numTempScaleValues */)
+ const t_mdatoms& /* md */)
{
GMX_ASSERT(!impl_,
"A CPU stub for UpdateConstrain was called instead of the correct implementation.");
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gpu_utils/device_context.h"
#include "gromacs/gpu_utils/device_stream.h"
#include "gromacs/gpu_utils/devicebuffer.h"
+#include "gromacs/gpu_utils/gpueventsynchronizer.cuh"
#include "gromacs/gpu_utils/gputraits.cuh"
#include "gromacs/gpu_utils/vectype_ops.cuh"
#include "gromacs/mdlib/leapfrog_gpu.h"
-#include "gromacs/mdlib/lincs_gpu.cuh"
-#include "gromacs/mdlib/settle_gpu.cuh"
#include "gromacs/mdlib/update_constrain_gpu.h"
#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/timing/wallcycle.h"
//! Maximum number of threads in a block (for __launch_bounds__)
constexpr static int c_maxThreadsPerBlock = c_threadsPerBlock;
-/*! \brief Scaling matrix struct.
- *
- * \todo Should be generalized.
- */
-struct ScalingMatrix
-{
- float xx, yy, zz, yx, zx, zy;
-};
-
__launch_bounds__(c_maxThreadsPerBlock) __global__
static void scaleCoordinates_kernel(const int numAtoms,
float3* __restrict__ gm_x,
const float dtPressureCouple,
const matrix prVelocityScalingMatrix)
{
- wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU);
- wallcycle_sub_start(wcycle_, ewcsLAUNCH_GPU_UPDATE_CONSTRAIN);
+ wallcycle_start_nocount(wcycle_, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::LaunchGpuUpdateConstrain);
// Clearing virial matrix
// TODO There is no point in having separate virial matrix for constraints
// The integrate should save a copy of the current coordinates in d_xp_ and write updated
// once into d_x_. The d_xp_ is only needed by constraints.
- integrator_->integrate(d_x_, d_xp_, d_v_, d_f_, dt, doTemperatureScaling, tcstat,
- doParrinelloRahman, dtPressureCouple, prVelocityScalingMatrix);
+ integrator_->integrate(
+ d_x_, d_xp_, d_v_, d_f_, dt, doTemperatureScaling, tcstat, doParrinelloRahman, dtPressureCouple, prVelocityScalingMatrix);
// Constraints need both coordinates before (d_x_) and after (d_xp_) update. However, after constraints
// are applied, the d_x_ can be discarded. So we intentionally swap the d_x_ and d_xp_ here to avoid the
// d_xp_ -> d_x_ copy after constraints. Note that the integrate saves them in the wrong order as well.
coordinatesReady_->markEvent(deviceStream_);
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_GPU_UPDATE_CONSTRAIN);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchGpuUpdateConstrain);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
return;
}
void UpdateConstrainGpu::Impl::scaleCoordinates(const matrix scalingMatrix)
{
- wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU);
- wallcycle_sub_start(wcycle_, ewcsLAUNCH_GPU_UPDATE_CONSTRAIN);
+ wallcycle_start_nocount(wcycle_, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::LaunchGpuUpdateConstrain);
- ScalingMatrix mu;
- mu.xx = scalingMatrix[XX][XX];
- mu.yy = scalingMatrix[YY][YY];
- mu.zz = scalingMatrix[ZZ][ZZ];
- mu.yx = scalingMatrix[YY][XX];
- mu.zx = scalingMatrix[ZZ][XX];
- mu.zy = scalingMatrix[ZZ][YY];
+ ScalingMatrix mu(scalingMatrix);
const auto kernelArgs = prepareGpuKernelArguments(
scaleCoordinates_kernel, coordinateScalingKernelLaunchConfig_, &numAtoms_, &d_x_, &mu);
- launchGpuKernel(scaleCoordinates_kernel, coordinateScalingKernelLaunchConfig_, deviceStream_,
- nullptr, "scaleCoordinates_kernel", kernelArgs);
+ launchGpuKernel(scaleCoordinates_kernel,
+ coordinateScalingKernelLaunchConfig_,
+ deviceStream_,
+ nullptr,
+ "scaleCoordinates_kernel",
+ kernelArgs);
// TODO: Although this only happens on the pressure coupling steps, this synchronization
// can affect the performance if nstpcouple is small.
deviceStream_.synchronize();
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_GPU_UPDATE_CONSTRAIN);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchGpuUpdateConstrain);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
}
void UpdateConstrainGpu::Impl::scaleVelocities(const matrix scalingMatrix)
{
- wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU);
- wallcycle_sub_start(wcycle_, ewcsLAUNCH_GPU_UPDATE_CONSTRAIN);
+ wallcycle_start_nocount(wcycle_, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::LaunchGpuUpdateConstrain);
- ScalingMatrix mu;
- mu.xx = scalingMatrix[XX][XX];
- mu.yy = scalingMatrix[YY][YY];
- mu.zz = scalingMatrix[ZZ][ZZ];
- mu.yx = scalingMatrix[YY][XX];
- mu.zx = scalingMatrix[ZZ][XX];
- mu.zy = scalingMatrix[ZZ][YY];
+ ScalingMatrix mu(scalingMatrix);
const auto kernelArgs = prepareGpuKernelArguments(
scaleCoordinates_kernel, coordinateScalingKernelLaunchConfig_, &numAtoms_, &d_v_, &mu);
- launchGpuKernel(scaleCoordinates_kernel, coordinateScalingKernelLaunchConfig_, deviceStream_,
- nullptr, "scaleCoordinates_kernel", kernelArgs);
+ launchGpuKernel(scaleCoordinates_kernel,
+ coordinateScalingKernelLaunchConfig_,
+ deviceStream_,
+ nullptr,
+ "scaleCoordinates_kernel",
+ kernelArgs);
// TODO: Although this only happens on the pressure coupling steps, this synchronization
// can affect the performance if nstpcouple is small.
deviceStream_.synchronize();
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_GPU_UPDATE_CONSTRAIN);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchGpuUpdateConstrain);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
}
UpdateConstrainGpu::Impl::Impl(const t_inputrec& ir,
const gmx_mtop_t& mtop,
+ const int numTempScaleValues,
const DeviceContext& deviceContext,
const DeviceStream& deviceStream,
GpuEventSynchronizer* xUpdatedOnDevice,
GMX_ASSERT(xUpdatedOnDevice != nullptr, "The event synchronizer can not be nullptr.");
- integrator_ = std::make_unique<LeapFrogGpu>(deviceContext_, deviceStream_);
+ integrator_ = std::make_unique<LeapFrogGpu>(deviceContext_, deviceStream_, numTempScaleValues);
lincsGpu_ = std::make_unique<LincsGpu>(ir.nLincsIter, ir.nProjOrder, deviceContext_, deviceStream_);
settleGpu_ = std::make_unique<SettleGpu>(mtop, deviceContext_, deviceStream_);
UpdateConstrainGpu::Impl::~Impl() {}
-void UpdateConstrainGpu::Impl::set(DeviceBuffer<RVec> d_x,
- DeviceBuffer<RVec> d_v,
- const DeviceBuffer<RVec> d_f,
+void UpdateConstrainGpu::Impl::set(DeviceBuffer<Float3> d_x,
+ DeviceBuffer<Float3> d_v,
+ const DeviceBuffer<Float3> d_f,
const InteractionDefinitions& idef,
- const t_mdatoms& md,
- const int numTempScaleValues)
+ const t_mdatoms& md)
{
// TODO wallcycle
- wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU);
- wallcycle_sub_start(wcycle_, ewcsLAUNCH_GPU_UPDATE_CONSTRAIN);
+ wallcycle_start_nocount(wcycle_, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::LaunchGpuUpdateConstrain);
GMX_ASSERT(d_x != nullptr, "Coordinates device buffer should not be null.");
GMX_ASSERT(d_v != nullptr, "Velocities device buffer should not be null.");
GMX_ASSERT(d_f != nullptr, "Forces device buffer should not be null.");
- d_x_ = reinterpret_cast<float3*>(d_x);
- d_v_ = reinterpret_cast<float3*>(d_v);
- d_f_ = reinterpret_cast<float3*>(d_f);
+ d_x_ = d_x;
+ d_v_ = d_v;
+ d_f_ = d_f;
numAtoms_ = md.nr;
reallocateDeviceBuffer(&d_xp_, numAtoms_, &numXp_, &numXpAlloc_, deviceContext_);
- reallocateDeviceBuffer(&d_inverseMasses_, numAtoms_, &numInverseMasses_,
- &numInverseMassesAlloc_, deviceContext_);
+ reallocateDeviceBuffer(
+ &d_inverseMasses_, numAtoms_, &numInverseMasses_, &numInverseMassesAlloc_, deviceContext_);
// Integrator should also update something, but it does not even have a method yet
- integrator_->set(numAtoms_, md.invmass, numTempScaleValues, md.cTC);
+ integrator_->set(numAtoms_, md.invmass, md.cTC);
lincsGpu_->set(idef, numAtoms_, md.invmass);
settleGpu_->set(idef);
coordinateScalingKernelLaunchConfig_.gridSize[0] =
(numAtoms_ + c_threadsPerBlock - 1) / c_threadsPerBlock;
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_GPU_UPDATE_CONSTRAIN);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchGpuUpdateConstrain);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
}
void UpdateConstrainGpu::Impl::setPbc(const PbcType pbcType, const matrix box)
UpdateConstrainGpu::UpdateConstrainGpu(const t_inputrec& ir,
const gmx_mtop_t& mtop,
+ const int numTempScaleValues,
const DeviceContext& deviceContext,
const DeviceStream& deviceStream,
GpuEventSynchronizer* xUpdatedOnDevice,
gmx_wallcycle* wcycle) :
- impl_(new Impl(ir, mtop, deviceContext, deviceStream, xUpdatedOnDevice, wcycle))
+ impl_(new Impl(ir, mtop, numTempScaleValues, deviceContext, deviceStream, xUpdatedOnDevice, wcycle))
{
}
const float dtPressureCouple,
const matrix prVelocityScalingMatrix)
{
- impl_->integrate(fReadyOnDevice, dt, updateVelocities, computeVirial, virialScaled, doTemperatureScaling,
- tcstat, doParrinelloRahman, dtPressureCouple, prVelocityScalingMatrix);
+ impl_->integrate(fReadyOnDevice,
+ dt,
+ updateVelocities,
+ computeVirial,
+ virialScaled,
+ doTemperatureScaling,
+ tcstat,
+ doParrinelloRahman,
+ dtPressureCouple,
+ prVelocityScalingMatrix);
}
void UpdateConstrainGpu::scaleCoordinates(const matrix scalingMatrix)
impl_->scaleVelocities(scalingMatrix);
}
-void UpdateConstrainGpu::set(DeviceBuffer<RVec> d_x,
- DeviceBuffer<RVec> d_v,
- const DeviceBuffer<RVec> d_f,
+void UpdateConstrainGpu::set(DeviceBuffer<Float3> d_x,
+ DeviceBuffer<Float3> d_v,
+ const DeviceBuffer<Float3> d_f,
const InteractionDefinitions& idef,
- const t_mdatoms& md,
- const int numTempScaleValues)
+ const t_mdatoms& md)
{
- impl_->set(d_x, d_v, d_f, idef, md, numTempScaleValues);
+ impl_->set(d_x, d_v, d_f, idef, md);
}
void UpdateConstrainGpu::setPbc(const PbcType pbcType, const matrix box)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gmxpre.h"
-#include "gromacs/gpu_utils/gpueventsynchronizer.cuh"
#include "gromacs/mdlib/leapfrog_gpu.h"
-#include "gromacs/mdlib/lincs_gpu.cuh"
-#include "gromacs/mdlib/settle_gpu.cuh"
+#include "gromacs/mdlib/lincs_gpu.h"
+#include "gromacs/mdlib/settle_gpu.h"
#include "gromacs/mdlib/update_constrain_gpu.h"
#include "gromacs/mdtypes/inputrec.h"
+class GpuEventSynchronizer;
+
namespace gmx
{
* any) consumers of the updated coordinates. The \p xUpdatedOnDevice also can not be a nullptr
* because the markEvent(...) method is called unconditionally.
*
- * \param[in] ir Input record data: LINCS takes number of iterations and order of
- * projection from it.
- * \param[in] mtop Topology of the system: SETTLE gets the masses for O and H atoms
- * and target O-H and H-H distances from this object.
- * \param[in] deviceContext GPU device context.
- * \param[in] deviceStream GPU stream to use.
- * \param[in] xUpdatedOnDevice The event synchronizer to use to mark that
- * update is done on the GPU.
- * \param[in] wcycle The wallclock counter
+ * \param[in] ir Input record data: LINCS takes number of iterations and order of
+ * projection from it.
+ * \param[in] mtop Topology of the system: SETTLE gets the masses for O and H atoms
+ * and target O-H and H-H distances from this object.
+ * \param[in] numTempScaleValues Number of temperature scaling groups. Set zero for no temperature coupling.
+ * \param[in] deviceContext GPU device context.
+ * \param[in] deviceStream GPU stream to use.
+ * \param[in] xUpdatedOnDevice The event synchronizer to use to mark that
+ * update is done on the GPU.
+ * \param[in] wcycle The wallclock counter
*/
Impl(const t_inputrec& ir,
const gmx_mtop_t& mtop,
+ int numTempScaleValues,
const DeviceContext& deviceContext,
const DeviceStream& deviceStream,
GpuEventSynchronizer* xUpdatedOnDevice,
* \param[in] d_f Device buffer with forces.
* \param[in] idef System topology
* \param[in] md Atoms data.
- * \param[in] numTempScaleValues Number of temperature scaling groups. Set zero for no temperature coupling.
*/
- void set(DeviceBuffer<RVec> d_x,
- DeviceBuffer<RVec> d_v,
- const DeviceBuffer<RVec> d_f,
+ void set(DeviceBuffer<Float3> d_x,
+ DeviceBuffer<Float3> d_v,
+ const DeviceBuffer<Float3> d_f,
const InteractionDefinitions& idef,
- const t_mdatoms& md,
- const int numTempScaleValues);
+ const t_mdatoms& md);
/*! \brief
* Update PBC data.
int numAtoms_;
//! Local copy of the pointer to the device positions buffer
- float3* d_x_;
+ DeviceBuffer<Float3> d_x_;
//! Local copy of the pointer to the device velocities buffer
- float3* d_v_;
+ DeviceBuffer<Float3> d_v_;
//! Local copy of the pointer to the device forces buffer
- float3* d_f_;
+ DeviceBuffer<Float3> d_f_;
//! Device buffer for intermediate positions (maintained internally)
- float3* d_xp_;
+ DeviceBuffer<Float3> d_xp_;
//! Number of elements in shifted coordinates buffer
int numXp_ = -1;
//! Allocation size for the shifted coordinates buffer
//! 1/mass for all atoms (GPU)
- real* d_inverseMasses_;
+ DeviceBuffer<real> d_inverseMasses_;
//! Number of elements in reciprocal masses buffer
int numInverseMasses_ = -1;
//! Allocation size for the reciprocal masses buffer
gmx_wallcycle* wcycle_ = nullptr;
};
+/*! \brief Scaling matrix struct.
+ *
+ * \todo Should be generalized.
+ */
+struct ScalingMatrix
+{
+ ScalingMatrix(const matrix m) :
+ xx(m[XX][XX]),
+ yy(m[YY][YY]),
+ zz(m[ZZ][ZZ]),
+ yx(m[YY][XX]),
+ zx(m[ZZ][XX]),
+ zy(m[ZZ][YY])
+ {
+ }
+ float xx, yy, zz, yx, zx, zy;
+};
+
} // namespace gmx
#endif // GMX_MDLIB_UPDATE_CONSTRAIN_GPU_IMPL_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "update_vv.h"
+
+#include <cmath>
+#include <cstdio>
+
+#include <algorithm>
+#include <memory>
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/gmxlib/nrnb.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/coupling.h"
+#include "gromacs/mdlib/enerdata_utils.h"
+#include "gromacs/mdlib/mdatoms.h"
+#include "gromacs/mdlib/md_support.h"
+#include "gromacs/mdlib/stat.h"
+#include "gromacs/mdlib/tgroup.h"
+#include "gromacs/mdlib/update.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/enerdata.h"
+#include "gromacs/mdtypes/fcdata.h"
+#include "gromacs/mdtypes/forcebuffers.h"
+#include "gromacs/mdtypes/forcerec.h"
+#include "gromacs/mdtypes/group.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/mdtypes/state.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/topology.h"
+
+void integrateVVFirstStep(int64_t step,
+ bool bFirstStep,
+ bool bInitStep,
+ gmx::StartingBehavior startingBehavior,
+ int nstglobalcomm,
+ const t_inputrec* ir,
+ t_forcerec* fr,
+ t_commrec* cr,
+ t_state* state,
+ t_mdatoms* mdatoms,
+ const t_fcdata& fcdata,
+ t_extmass* MassQ,
+ t_vcm* vcm,
+ const gmx_mtop_t& top_global,
+ const gmx_localtop_t& top,
+ gmx_enerdata_t* enerd,
+ gmx_ekindata_t* ekind,
+ gmx_global_stat* gstat,
+ real* last_ekin,
+ bool bCalcVir,
+ tensor total_vir,
+ tensor shake_vir,
+ tensor force_vir,
+ tensor pres,
+ matrix M,
+ bool do_log,
+ bool do_ene,
+ bool bCalcEner,
+ bool bGStat,
+ bool bStopCM,
+ bool bTrotter,
+ bool bExchanged,
+ bool* bSumEkinhOld,
+ real* saved_conserved_quantity,
+ gmx::ForceBuffers* f,
+ gmx::Update* upd,
+ gmx::Constraints* constr,
+ gmx::SimulationSignaller* nullSignaller,
+ std::array<std::vector<int>, ettTSEQMAX> trotter_seq,
+ t_nrnb* nrnb,
+ const gmx::MDLogger& mdlog,
+ FILE* fplog,
+ gmx_wallcycle* wcycle)
+{
+ if (!bFirstStep || startingBehavior == gmx::StartingBehavior::NewSimulation)
+ {
+ /* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
+ rvec* vbuf = nullptr;
+
+ wallcycle_start(wcycle, WallCycleCounter::Update);
+ if (ir->eI == IntegrationAlgorithm::VV && bInitStep)
+ {
+ /* if using velocity verlet with full time step Ekin,
+ * take the first half step only to compute the
+ * virial for the first step. From there,
+ * revert back to the initial coordinates
+ * so that the input is actually the initial step.
+ */
+ snew(vbuf, state->natoms);
+ copy_rvecn(state->v.rvec_array(), vbuf, 0, state->natoms); /* should make this better for parallelizing? */
+ }
+ else
+ {
+ /* this is for NHC in the Ekin(t+dt/2) version of vv */
+ trotter_update(ir,
+ step,
+ ekind,
+ enerd,
+ state,
+ total_vir,
+ mdatoms->homenr,
+ mdatoms->cTC ? gmx::arrayRefFromArray(mdatoms->cTC, mdatoms->nr)
+ : gmx::ArrayRef<const unsigned short>(),
+ gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
+ MassQ,
+ trotter_seq,
+ ettTSEQ1);
+ }
+
+ upd->update_coords(*ir,
+ step,
+ mdatoms->homenr,
+ mdatoms->havePartiallyFrozenAtoms,
+ gmx::arrayRefFromArray(mdatoms->ptype, mdatoms->nr),
+ gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
+ gmx::arrayRefFromArray(mdatoms->invMassPerDim, mdatoms->nr),
+ state,
+ f->view().forceWithPadding(),
+ fcdata,
+ ekind,
+ M,
+ etrtVELOCITY1,
+ cr,
+ constr != nullptr);
+
+ wallcycle_stop(wcycle, WallCycleCounter::Update);
+ constrain_velocities(constr, do_log, do_ene, step, state, nullptr, bCalcVir, shake_vir);
+ wallcycle_start(wcycle, WallCycleCounter::Update);
+ /* if VV, compute the pressure and constraints */
+ /* For VV2, we strictly only need this if using pressure
+ * control, but we really would like to have accurate pressures
+ * printed out.
+ * Think about ways around this in the future?
+ * For now, keep this choice in comments.
+ */
+ /*bPres = (ir->eI==IntegrationAlgorithm::VV || inputrecNptTrotter(ir)); */
+ /*bTemp = ((ir->eI==IntegrationAlgorithm::VV &&(!bInitStep)) || (ir->eI==IntegrationAlgorithm::VVAK && inputrecNptTrotter(ir)));*/
+ bool bPres = TRUE;
+ bool bTemp = ((ir->eI == IntegrationAlgorithm::VV && (!bInitStep))
+ || (ir->eI == IntegrationAlgorithm::VVAK));
+ if (bCalcEner && ir->eI == IntegrationAlgorithm::VVAK)
+ {
+ *bSumEkinhOld = TRUE;
+ }
+ /* for vv, the first half of the integration actually corresponds to the previous step.
+ So we need information from the last step in the first half of the integration */
+ if (bGStat || do_per_step(step - 1, nstglobalcomm))
+ {
+ wallcycle_stop(wcycle, WallCycleCounter::Update);
+ int cglo_flags =
+ ((bGStat ? CGLO_GSTAT : 0) | (bCalcEner ? CGLO_ENERGY : 0)
+ | (bTemp ? CGLO_TEMPERATURE : 0) | (bPres ? CGLO_PRESSURE : 0)
+ | (bPres ? CGLO_CONSTRAINT : 0) | (bStopCM ? CGLO_STOPCM : 0) | CGLO_SCALEEKIN);
+ if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
+ {
+ cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
+ }
+ compute_globals(gstat,
+ cr,
+ ir,
+ fr,
+ ekind,
+ makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v),
+ state->box,
+ mdatoms,
+ nrnb,
+ vcm,
+ wcycle,
+ enerd,
+ force_vir,
+ shake_vir,
+ total_vir,
+ pres,
+ (bCalcEner && constr != nullptr) ? constr->rmsdData() : gmx::ArrayRef<real>{},
+ nullSignaller,
+ state->box,
+ bSumEkinhOld,
+ cglo_flags);
+ /* explanation of above:
+ a) We compute Ekin at the full time step
+ if 1) we are using the AveVel Ekin, and it's not the
+ initial step, or 2) if we are using AveEkin, but need the full
+ time step kinetic energy for the pressure (always true now, since we want accurate statistics).
+ b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
+ EkinAveVel because it's needed for the pressure */
+ if (DOMAINDECOMP(cr))
+ {
+ checkNumberOfBondedInteractions(
+ mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
+ }
+ if (bStopCM)
+ {
+ process_and_stopcm_grp(
+ fplog, vcm, *mdatoms, makeArrayRef(state->x), makeArrayRef(state->v));
+ inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
+ }
+ wallcycle_start(wcycle, WallCycleCounter::Update);
+ }
+ /* temperature scaling and pressure scaling to produce the extended variables at t+dt */
+ if (!bInitStep)
+ {
+ if (bTrotter)
+ {
+ m_add(force_vir, shake_vir, total_vir); /* we need the un-dispersion corrected total vir here */
+ trotter_update(ir,
+ step,
+ ekind,
+ enerd,
+ state,
+ total_vir,
+ mdatoms->homenr,
+ mdatoms->cTC ? gmx::arrayRefFromArray(mdatoms->cTC, mdatoms->nr)
+ : gmx::ArrayRef<const unsigned short>(),
+ gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
+ MassQ,
+ trotter_seq,
+ ettTSEQ2);
+
+ /* TODO This is only needed when we're about to write
+ * a checkpoint, because we use it after the restart
+ * (in a kludge?). But what should we be doing if
+ * the startingBehavior is NewSimulation or bInitStep are true? */
+ if (inputrecNptTrotter(ir) || inputrecNphTrotter(ir))
+ {
+ copy_mat(shake_vir, state->svir_prev);
+ copy_mat(force_vir, state->fvir_prev);
+ }
+ if ((inputrecNptTrotter(ir) || inputrecNvtTrotter(ir)) && ir->eI == IntegrationAlgorithm::VV)
+ {
+ /* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
+ enerd->term[F_TEMP] = sum_ekin(
+ &(ir->opts), ekind, nullptr, (ir->eI == IntegrationAlgorithm::VV), FALSE);
+ enerd->term[F_EKIN] = trace(ekind->ekin);
+ }
+ }
+ else if (bExchanged)
+ {
+ wallcycle_stop(wcycle, WallCycleCounter::Update);
+ /* We need the kinetic energy at minus the half step for determining
+ * the full step kinetic energy and possibly for T-coupling.*/
+ /* This may not be quite working correctly yet . . . . */
+ compute_globals(gstat,
+ cr,
+ ir,
+ fr,
+ ekind,
+ makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v),
+ state->box,
+ mdatoms,
+ nrnb,
+ vcm,
+ wcycle,
+ enerd,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ gmx::ArrayRef<real>{},
+ nullSignaller,
+ state->box,
+ bSumEkinhOld,
+ CGLO_GSTAT | CGLO_TEMPERATURE);
+ wallcycle_start(wcycle, WallCycleCounter::Update);
+ }
+ }
+ /* if it's the initial step, we performed this first step just to get the constraint virial */
+ if (ir->eI == IntegrationAlgorithm::VV && bInitStep)
+ {
+ copy_rvecn(vbuf, state->v.rvec_array(), 0, state->natoms);
+ sfree(vbuf);
+ }
+ wallcycle_stop(wcycle, WallCycleCounter::Update);
+ }
+
+ /* compute the conserved quantity */
+ *saved_conserved_quantity = NPT_energy(ir, state, MassQ);
+ if (ir->eI == IntegrationAlgorithm::VV)
+ {
+ *last_ekin = enerd->term[F_EKIN];
+ }
+ if ((ir->eDispCorr != DispersionCorrectionType::EnerPres)
+ && (ir->eDispCorr != DispersionCorrectionType::AllEnerPres))
+ {
+ *saved_conserved_quantity -= enerd->term[F_DISPCORR];
+ }
+ /* sum up the foreign kinetic energy and dK/dl terms for vv. currently done every step so that dhdl is correct in the .edr */
+ if (ir->efep != FreeEnergyPerturbationType::No)
+ {
+ accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
+ }
+}
+
+void integrateVVSecondStep(int64_t step,
+ const t_inputrec* ir,
+ t_forcerec* fr,
+ t_commrec* cr,
+ t_state* state,
+ t_mdatoms* mdatoms,
+ const t_fcdata& fcdata,
+ t_extmass* MassQ,
+ t_vcm* vcm,
+ pull_t* pull_work,
+ gmx_enerdata_t* enerd,
+ gmx_ekindata_t* ekind,
+ gmx_global_stat* gstat,
+ real* dvdl_constr,
+ bool bCalcVir,
+ tensor total_vir,
+ tensor shake_vir,
+ tensor force_vir,
+ tensor pres,
+ matrix M,
+ matrix lastbox,
+ bool do_log,
+ bool do_ene,
+ bool bGStat,
+ bool* bSumEkinhOld,
+ gmx::ForceBuffers* f,
+ std::vector<gmx::RVec>* cbuf,
+ gmx::Update* upd,
+ gmx::Constraints* constr,
+ gmx::SimulationSignaller* nullSignaller,
+ std::array<std::vector<int>, ettTSEQMAX> trotter_seq,
+ t_nrnb* nrnb,
+ gmx_wallcycle* wcycle)
+{
+ /* velocity half-step update */
+ upd->update_coords(*ir,
+ step,
+ mdatoms->homenr,
+ mdatoms->havePartiallyFrozenAtoms,
+ gmx::arrayRefFromArray(mdatoms->ptype, mdatoms->nr),
+ gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
+ gmx::arrayRefFromArray(mdatoms->invMassPerDim, mdatoms->nr),
+ state,
+ f->view().forceWithPadding(),
+ fcdata,
+ ekind,
+ M,
+ etrtVELOCITY2,
+ cr,
+ constr != nullptr);
+
+
+ /* Above, initialize just copies ekinh into ekin,
+ * it doesn't copy position (for VV),
+ * and entire integrator for MD.
+ */
+
+ if (ir->eI == IntegrationAlgorithm::VVAK)
+ {
+ cbuf->resize(state->x.size());
+ std::copy(state->x.begin(), state->x.end(), cbuf->begin());
+ }
+
+ if (ir->bPull && ir->pull->bSetPbcRefToPrevStepCOM)
+ {
+ updatePrevStepPullCom(pull_work, state);
+ }
+
+ upd->update_coords(*ir,
+ step,
+ mdatoms->homenr,
+ mdatoms->havePartiallyFrozenAtoms,
+ gmx::arrayRefFromArray(mdatoms->ptype, mdatoms->nr),
+ gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
+ gmx::arrayRefFromArray(mdatoms->invMassPerDim, mdatoms->nr),
+ state,
+ f->view().forceWithPadding(),
+ fcdata,
+ ekind,
+ M,
+ etrtPOSITION,
+ cr,
+ constr != nullptr);
+
+ wallcycle_stop(wcycle, WallCycleCounter::Update);
+
+ constrain_coordinates(
+ constr, do_log, do_ene, step, state, upd->xp()->arrayRefWithPadding(), dvdl_constr, bCalcVir, shake_vir);
+
+ upd->update_sd_second_half(*ir,
+ step,
+ dvdl_constr,
+ mdatoms->homenr,
+ gmx::arrayRefFromArray(mdatoms->ptype, mdatoms->nr),
+ gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
+ state,
+ cr,
+ nrnb,
+ wcycle,
+ constr,
+ do_log,
+ do_ene);
+ upd->finish_update(
+ *ir, mdatoms->havePartiallyFrozenAtoms, mdatoms->homenr, state, wcycle, constr != nullptr);
+
+ if (ir->eI == IntegrationAlgorithm::VVAK)
+ {
+ /* erase F_EKIN and F_TEMP here? */
+ /* just compute the kinetic energy at the half step to perform a trotter step */
+ compute_globals(gstat,
+ cr,
+ ir,
+ fr,
+ ekind,
+ makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v),
+ state->box,
+ mdatoms,
+ nrnb,
+ vcm,
+ wcycle,
+ enerd,
+ force_vir,
+ shake_vir,
+ total_vir,
+ pres,
+ gmx::ArrayRef<real>{},
+ nullSignaller,
+ lastbox,
+ bSumEkinhOld,
+ (bGStat ? CGLO_GSTAT : 0) | CGLO_TEMPERATURE);
+ wallcycle_start(wcycle, WallCycleCounter::Update);
+ trotter_update(ir,
+ step,
+ ekind,
+ enerd,
+ state,
+ total_vir,
+ mdatoms->homenr,
+ mdatoms->cTC ? gmx::arrayRefFromArray(mdatoms->cTC, mdatoms->nr)
+ : gmx::ArrayRef<const unsigned short>(),
+ gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
+ MassQ,
+ trotter_seq,
+ ettTSEQ4);
+ /* now we know the scaling, we can compute the positions again */
+ std::copy(cbuf->begin(), cbuf->end(), state->x.begin());
+
+ upd->update_coords(*ir,
+ step,
+ mdatoms->homenr,
+ mdatoms->havePartiallyFrozenAtoms,
+ gmx::arrayRefFromArray(mdatoms->ptype, mdatoms->nr),
+ gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
+ gmx::arrayRefFromArray(mdatoms->invMassPerDim, mdatoms->nr),
+ state,
+ f->view().forceWithPadding(),
+ fcdata,
+ ekind,
+ M,
+ etrtPOSITION,
+ cr,
+ constr != nullptr);
+ wallcycle_stop(wcycle, WallCycleCounter::Update);
+
+ /* do we need an extra constraint here? just need to copy out of as_rvec_array(state->v.data()) to upd->xp? */
+ /* are the small terms in the shake_vir here due
+ * to numerical errors, or are they important
+ * physically? I'm thinking they are just errors, but not completely sure.
+ * For now, will call without actually constraining, constr=NULL*/
+ upd->finish_update(*ir, mdatoms->havePartiallyFrozenAtoms, mdatoms->homenr, state, wcycle, false);
+ }
+ /* this factor or 2 correction is necessary
+ because half of the constraint force is removed
+ in the vv step, so we have to double it. See
+ the Issue #1255. It is not yet clear
+ if the factor of 2 is exact, or just a very
+ good approximation, and this will be
+ investigated. The next step is to see if this
+ can be done adding a dhdl contribution from the
+ rattle step, but this is somewhat more
+ complicated with the current code. Will be
+ investigated, hopefully for 4.6.3. However,
+ this current solution is much better than
+ having it completely wrong.
+ */
+ enerd->term[F_DVDL_CONSTR] += 2 * *dvdl_constr;
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_MDLIB_UPDATE_VV_H
+#define GMX_MDLIB_UPDATE_VV_H
+
+#include <vector>
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/mdrunutility/handlerestart.h"
+#include "gromacs/mdtypes/md_enums.h"
+
+class gmx_ekindata_t;
+struct gmx_enerdata_t;
+struct gmx_global_stat;
+struct gmx_localtop_t;
+struct gmx_mtop_t;
+struct gmx_wallcycle;
+struct pull_t;
+struct t_commrec;
+struct t_extmass;
+struct t_fcdata;
+struct t_forcerec;
+struct t_inputrec;
+struct t_mdatoms;
+struct t_nrnb;
+class t_state;
+struct t_vcm;
+
+namespace gmx
+{
+class Constraints;
+class ForceBuffers;
+class MDLogger;
+class SimulationSignaller;
+class Update;
+} // namespace gmx
+
+/*! \brief Make the first step of Velocity Verlet integration
+ *
+ * \param[in] step Current timestep.
+ * \param[in] bFirstStep Is it a first step.
+ * \param[in] bInitStep Is it an initialization step.
+ * \param[in] startingBehavior Describes whether this is a restart appending to output files.
+ * \param[in] nstglobalcomm Will globals be computed on this step.
+ * \param[in] ir Input record.
+ * \param[in] fr Force record.
+ * \param[in] cr Comunication record.
+ * \param[in] state Simulation state.
+ * \param[in] mdatoms MD atoms data.
+ * \param[in] fcdata Force calculation data.
+ * \param[in] MassQ Mass/pressure data.
+ * \param[in] vcm Center of mass motion removal.
+ * \param[in] top_global Global topology.
+ * \param[in] top Local topology.
+ * \param[in] enerd Energy data.
+ * \param[in] ekind Kinetic energy data.
+ * \param[in] gstat Storage of thermodynamic parameters data.
+ * \param[out] last_ekin Kinetic energies of the last step.
+ * \param[in] bCalcVir If the virial is computed on this step.
+ * \param[in] total_vir Total virial tensor.
+ * \param[in] shake_vir Constraints virial.
+ * \param[in] force_vir Force virial.
+ * \param[in] pres Pressure tensor.
+ * \param[in] M Parrinello-Rahman velocity scaling matrix.
+ * \param[in] do_log Do logging on this step.
+ * \param[in] do_ene Print energies on this step.
+ * \param[in] bCalcEner Compute energies on this step.
+ * \param[in] bGStat Collect globals this step.
+ * \param[in] bStopCM Stop the center of mass motion on this step.
+ * \param[in] bTrotter Do trotter routines this step.
+ * \param[in] bExchanged If this is a replica exchange step.
+ * \param[out] bSumEkinhOld Old kinetic energies will need to be summed up.
+ * \param[out] saved_conserved_quantity Place to store the conserved energy.
+ * \param[in] f Force buffers.
+ * \param[in] upd Update object.
+ * \param[in] constr Constraints object.
+ * \param[in] nullSignaller Simulation signaller.
+ * \param[in] trotter_seq NPT variables.
+ * \param[in] nrnb Cycle counters.
+ * \param[in] mdlog Logger.
+ * \param[in] fplog Another logger.
+ * \param[in] wcycle Wall-clock cycle counter.
+ */
+void integrateVVFirstStep(int64_t step,
+ bool bFirstStep,
+ bool bInitStep,
+ gmx::StartingBehavior startingBehavior,
+ int nstglobalcomm,
+ const t_inputrec* ir,
+ t_forcerec* fr,
+ t_commrec* cr,
+ t_state* state,
+ t_mdatoms* mdatoms,
+ const t_fcdata& fcdata,
+ t_extmass* MassQ,
+ t_vcm* vcm,
+ const gmx_mtop_t& top_global,
+ const gmx_localtop_t& top,
+ gmx_enerdata_t* enerd,
+ gmx_ekindata_t* ekind,
+ gmx_global_stat* gstat,
+ real* last_ekin,
+ bool bCalcVir,
+ tensor total_vir,
+ tensor shake_vir,
+ tensor force_vir,
+ tensor pres,
+ matrix M,
+ bool do_log,
+ bool do_ene,
+ bool bCalcEner,
+ bool bGStat,
+ bool bStopCM,
+ bool bTrotter,
+ bool bExchanged,
+ bool* bSumEkinhOld,
+ real* saved_conserved_quantity,
+ gmx::ForceBuffers* f,
+ gmx::Update* upd,
+ gmx::Constraints* constr,
+ gmx::SimulationSignaller* nullSignaller,
+ std::array<std::vector<int>, ettTSEQMAX> trotter_seq,
+ t_nrnb* nrnb,
+ const gmx::MDLogger& mdlog,
+ FILE* fplog,
+ gmx_wallcycle* wcycle);
+
+
+/*! \brief Make the second step of Velocity Verlet integration
+ *
+ * \param[in] step Current timestep.
+ * \param[in] ir Input record.
+ * \param[in] fr Force record.
+ * \param[in] cr Comunication record.
+ * \param[in] state Simulation state.
+ * \param[in] mdatoms MD atoms data.
+ * \param[in] fcdata Force calculation data.
+ * \param[in] MassQ Mass/pressure data.
+ * \param[in] vcm Center of mass motion removal.
+ * \param[in] pull_work Pulling data.
+ * \param[in] enerd Energy data.
+ * \param[in] ekind Kinetic energy data.
+ * \param[in] gstat Storage of thermodynamic parameters data.
+ * \param[out] dvdl_constr FEP data for constraints.
+ * \param[in] bCalcVir If the virial is computed on this step.
+ * \param[in] total_vir Total virial tensor.
+ * \param[in] shake_vir Constraints virial.
+ * \param[in] force_vir Force virial.
+ * \param[in] pres Pressure tensor.
+ * \param[in] M Parrinello-Rahman velocity scaling matrix.
+ * \param[in] lastbox Last recorded PBC box.
+ * \param[in] do_log Do logging on this step.
+ * \param[in] do_ene Print energies on this step.
+ * \param[in] bGStat Collect globals this step.
+ * \param[out] bSumEkinhOld Old kinetic energies need to be summed up.
+ * \param[in] f Force buffers.
+ * \param[in] cbuf Buffer to store intermediate coordinates
+ * \param[in] upd Update object.
+ * \param[in] constr Constraints object.
+ * \param[in] nullSignaller Simulation signaller.
+ * \param[in] trotter_seq NPT variables.
+ * \param[in] nrnb Cycle counters.
+ * \param[in] wcycle Wall-clock cycle counter.
+ */
+void integrateVVSecondStep(int64_t step,
+ const t_inputrec* ir,
+ t_forcerec* fr,
+ t_commrec* cr,
+ t_state* state,
+ t_mdatoms* mdatoms,
+ const t_fcdata& fcdata,
+ t_extmass* MassQ,
+ t_vcm* vcm,
+ pull_t* pull_work,
+ gmx_enerdata_t* enerd,
+ gmx_ekindata_t* ekind,
+ gmx_global_stat* gstat,
+ real* dvdl_constr,
+ bool bCalcVir,
+ tensor total_vir,
+ tensor shake_vir,
+ tensor force_vir,
+ tensor pres,
+ matrix M,
+ matrix lastbox,
+ bool do_log,
+ bool do_ene,
+ bool bGStat,
+ bool* bSumEkinhOld,
+ gmx::ForceBuffers* f,
+ std::vector<gmx::RVec>* cbuf,
+ gmx::Update* upd,
+ gmx::Constraints* constr,
+ gmx::SimulationSignaller* nullSignaller,
+ std::array<std::vector<int>, ettTSEQMAX> trotter_seq,
+ t_nrnb* nrnb,
+ gmx_wallcycle* wcycle);
+
+
+#endif // GMX_MDLIB_UPDATE_VV_H
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/topology/idef.h"
}
/*! \brief Returns a list of update groups for \p moltype */
-static RangePartitioning makeUpdateGroups(const gmx_moltype_t& moltype, gmx::ArrayRef<const t_iparams> iparams)
+static RangePartitioning makeUpdateGroupingsPerMoleculeType(const gmx_moltype_t& moltype,
+ gmx::ArrayRef<const t_iparams> iparams)
{
RangePartitioning groups;
std::array<InteractionList, F_NRE> ilistsCombined;
ilistsCombined[F_CONSTR] = jointConstraintList(moltype);
/* We "include" flexible constraints, but none are present (checked above) */
- const ListOfLists<int> at2con = make_at2con(moltype.atoms.nr, ilistsCombined, iparams,
- FlexibleConstraintTreatment::Include);
+ const ListOfLists<int> at2con = make_at2con(
+ moltype.atoms.nr, ilistsCombined, iparams, FlexibleConstraintTreatment::Include);
bool satisfiesCriteria = true;
return groups;
}
-std::vector<RangePartitioning> makeUpdateGroups(const gmx_mtop_t& mtop)
+std::vector<RangePartitioning> makeUpdateGroupingsPerMoleculeType(const gmx_mtop_t& mtop)
{
- std::vector<RangePartitioning> updateGroups;
+ std::vector<RangePartitioning> updateGroupingsPerMoleculeType;
bool systemSatisfiesCriteria = true;
for (const gmx_moltype_t& moltype : mtop.moltype)
{
- updateGroups.push_back(makeUpdateGroups(moltype, mtop.ffparams.iparams));
+ updateGroupingsPerMoleculeType.push_back(
+ makeUpdateGroupingsPerMoleculeType(moltype, mtop.ffparams.iparams));
- if (updateGroups.back().numBlocks() == 0)
+ if (updateGroupingsPerMoleculeType.back().numBlocks() == 0)
{
systemSatisfiesCriteria = false;
}
if (!systemSatisfiesCriteria)
{
- updateGroups.clear();
+ updateGroupingsPerMoleculeType.clear();
}
- return updateGroups;
+ return updateGroupingsPerMoleculeType;
}
/*! \brief Returns a map of angles ilist.iatoms indices with the middle atom as key */
/* Set number of stddevs such that change of exceeding < 10^-9 */
constexpr real c_numSigma = 6.0;
/* Compute the maximally stretched angle */
- const real eqAngle = angleParams.harmonic.rA * DEG2RAD;
+ const real eqAngle = angleParams.harmonic.rA * gmx::c_deg2Rad;
const real fc = angleParams.harmonic.krA;
- const real maxAngle = eqAngle + c_numSigma * BOLTZ * temperature / ((numPartnerAtoms - 1) * fc);
+ const real maxAngle =
+ eqAngle + c_numSigma * gmx::c_boltz * temperature / ((numPartnerAtoms - 1) * fc);
if (maxAngle >= M_PI)
{
return -1;
/*! \brief Returns the maximum update group radius for \p moltype */
static real computeMaxUpdateGroupRadius(const gmx_moltype_t& moltype,
gmx::ArrayRef<const t_iparams> iparams,
- const RangePartitioning& updateGroups,
+ const RangePartitioning& updateGrouping,
real temperature)
{
GMX_RELEASE_ASSERT(!hasFlexibleConstraints(moltype, iparams),
const auto angleIndices = getAngleIndices(moltype);
real maxRadius = 0;
- for (int group = 0; group < updateGroups.numBlocks(); group++)
+ for (int group = 0; group < updateGrouping.numBlocks(); group++)
{
- if (updateGroups.block(group).size() == 1)
+ if (updateGrouping.block(group).size() == 1)
{
/* Single atom group, radius is zero */
continue;
/* Find the atom maxAtom with the maximum number of constraints */
int maxNumConstraints = 0;
int maxAtom = -1;
- for (int a : updateGroups.block(group))
+ for (int a : updateGrouping.block(group))
{
const int numConstraints = at2con[a].ssize();
if (numConstraints > maxNumConstraints)
*/
if (numConstraints == 2 && allTypesAreEqual && temperature > 0)
{
- radius = constraintGroupRadius<2>(moltype, iparams, maxAtom, at2con, angleIndices,
- maxConstraintLength, temperature);
+ radius = constraintGroupRadius<2>(
+ moltype, iparams, maxAtom, at2con, angleIndices, maxConstraintLength, temperature);
}
/* With 3 constraints the maximum possible radius is 1.4 times
* the constraint length, so it is worth computing a smaller
*/
if (numConstraints == 3 && allTypesAreEqual && temperature >= 0)
{
- radius = constraintGroupRadius<3>(moltype, iparams, maxAtom, at2con, angleIndices,
- maxConstraintLength, temperature);
+ radius = constraintGroupRadius<3>(
+ moltype, iparams, maxAtom, at2con, angleIndices, maxConstraintLength, temperature);
if (temperature == 0 && radius >= 0)
{
/* Add a 10% margin for deviation at 0 K */
}
real computeMaxUpdateGroupRadius(const gmx_mtop_t& mtop,
- gmx::ArrayRef<const RangePartitioning> updateGroups,
+ gmx::ArrayRef<const RangePartitioning> updateGroupingsPerMoleculeType,
real temperature)
{
- if (updateGroups.empty())
+ if (updateGroupingsPerMoleculeType.empty())
{
return 0;
}
- GMX_RELEASE_ASSERT(updateGroups.size() == mtop.moltype.size(),
+ GMX_RELEASE_ASSERT(updateGroupingsPerMoleculeType.size() == mtop.moltype.size(),
"We need one update group entry per moleculetype");
real maxRadius = 0;
for (size_t moltype = 0; moltype < mtop.moltype.size(); moltype++)
{
- maxRadius = std::max(
- maxRadius, computeMaxUpdateGroupRadius(mtop.moltype[moltype], mtop.ffparams.iparams,
- updateGroups[moltype], temperature));
+ const real radiusOfThisMoleculeType = computeMaxUpdateGroupRadius(
+ mtop.moltype[moltype], mtop.ffparams.iparams, updateGroupingsPerMoleculeType[moltype], temperature);
+ maxRadius = std::max(maxRadius, radiusOfThisMoleculeType);
}
return maxRadius;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* \param[in] mtop The system topology
*/
-std::vector<RangePartitioning> makeUpdateGroups(const gmx_mtop_t& mtop);
+std::vector<RangePartitioning> makeUpdateGroupingsPerMoleculeType(const gmx_mtop_t& mtop);
/*! \brief Returns the maximum update group radius
*
- * \note When \p updateGroups is empty, 0 is returned.
+ * \note When \p updateGroupingsPerMoleculeType is empty, 0 is returned.
*
* \param[in] mtop The system topology
- * \param[in] updateGroups List of update group, size should match the number of moltypes in \p mtop or be 0
+ * \param[in] updateGroupingsPerMoleculeType List of update group, size should match the number of moltypes in \p mtop or be 0
* \param[in] temperature The maximum reference temperature, pass -1 when unknown or not applicable
*/
real computeMaxUpdateGroupRadius(const gmx_mtop_t& mtop,
- gmx::ArrayRef<const RangePartitioning> updateGroups,
+ gmx::ArrayRef<const RangePartitioning> updateGroupingsPerMoleculeType,
real temperature);
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
UpdateGroupsCog::UpdateGroupsCog(const gmx_mtop_t& mtop,
- gmx::ArrayRef<const gmx::RangePartitioning> updateGroupsPerMoleculetype,
+ gmx::ArrayRef<const gmx::RangePartitioning> updateGroupingsPerMoleculeType,
real temperature,
int numHomeAtoms) :
globalToLocalMap_(numHomeAtoms),
int firstUpdateGroupInMolecule = 0;
for (const auto& molblock : mtop.molblock)
{
- const auto& updateGroups = updateGroupsPerMoleculetype[molblock.type];
- indicesPerMoleculeblock_.push_back({ firstUpdateGroupInMolecule, updateGroups.numBlocks(), {} });
+ const auto& updateGrouping = updateGroupingsPerMoleculeType[molblock.type];
+ indicesPerMoleculeblock_.push_back({ firstUpdateGroupInMolecule, updateGrouping.numBlocks(), {} });
auto& groupIndex = indicesPerMoleculeblock_.back().groupIndex_;
- for (int block = 0; block < updateGroups.numBlocks(); block++)
+ for (int block = 0; block < updateGrouping.numBlocks(); block++)
{
- groupIndex.insert(groupIndex.end(), updateGroups.block(block).size(), block);
+ groupIndex.insert(groupIndex.end(), updateGrouping.block(block).size(), block);
}
- firstUpdateGroupInMolecule += molblock.nmol * updateGroups.numBlocks();
+ firstUpdateGroupInMolecule += molblock.nmol * updateGrouping.numBlocks();
}
- maxUpdateGroupRadius_ = computeMaxUpdateGroupRadius(mtop, updateGroupsPerMoleculetype, temperature);
+ maxUpdateGroupRadius_ = computeMaxUpdateGroupRadius(mtop, updateGroupingsPerMoleculeType, temperature);
}
void UpdateGroupsCog::addCogs(gmx::ArrayRef<const int> globalAtomIndices,
const int globalAtom = globalAtomIndices[localAtom];
int moleculeIndex;
int atomIndexInMolecule;
- mtopGetMolblockIndex(&mtop_, globalAtom, &moleculeBlock, &moleculeIndex, &atomIndexInMolecule);
+ mtopGetMolblockIndex(mtop_, globalAtom, &moleculeBlock, &moleculeIndex, &atomIndexInMolecule);
const auto& indicesForBlock = indicesPerMoleculeblock_[moleculeBlock];
int globalUpdateGroupIndex = indicesForBlock.groupStart_
+ moleculeIndex * indicesForBlock.numGroupsPerMolecule_
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \note \p numHomeAtoms only affects the performance up till the first
* call to clear().
*
- * \param[in] mtop The global topology
- * \param[in] updateGroupsPerMoleculetype List of update groups for each molecule type in \p mtop
- * \param[in] temperature The maximum reference temperature, pass -1 when unknown or not applicable
- * \param[in] numHomeAtoms Estimate of the number of home atoms per DD cell
+ * \param[in] mtop The global topology
+ * \param[in] updateGroupingsPerMoleculeType List of update groups for each molecule type in \p mtop
+ * \param[in] temperature The maximum reference temperature, pass -1 when unknown or not applicable
+ * \param[in] numHomeAtoms Estimate of the number of home atoms per DD cell
*/
UpdateGroupsCog(const gmx_mtop_t& mtop,
- gmx::ArrayRef<const gmx::RangePartitioning> updateGroupsPerMoleculetype,
+ gmx::ArrayRef<const gmx::RangePartitioning> updateGroupingsPerMoleculeType,
real temperature,
int numHomeAtoms);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
t_vcm::t_vcm(const SimulationGroups& groups, const t_inputrec& ir) :
integratorConservesMomentum(!EI_RANDOM(ir.eI))
{
- mode = (ir.nstcomm > 0) ? ir.comm_mode : ecmNO;
+ mode = (ir.nstcomm > 0) ? ir.comm_mode : ComRemovalAlgorithm::No;
ndim = ndof_com(&ir);
timeStep = ir.nstcomm * ir.delta_t;
- if (mode == ecmANGULAR && ndim < 3)
+ if (mode == ComRemovalAlgorithm::Angular && ndim < 3)
{
- gmx_fatal(FARGS, "Can not have angular comm removal with pbc=%s",
- c_pbcTypeNames[ir.pbcType].c_str());
+ gmx_fatal(FARGS, "Can not have angular comm removal with pbc=%s", c_pbcTypeNames[ir.pbcType].c_str());
}
- if (mode != ecmNO)
+ if (mode != ComRemovalAlgorithm::No)
{
nr = groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size();
/* Allocate one extra for a possible rest group */
* invalidation we add 2 elements to get a 152 byte separation.
*/
stride = nr + 3;
- if (mode == ecmANGULAR)
+ if (mode == ComRemovalAlgorithm::Angular)
{
snew(group_i, size);
*groups.groupNames[groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval][g]];
}
- thread_vcm.resize(gmx_omp_nthreads_get(emntDefault) * stride);
+ thread_vcm.resize(gmx_omp_nthreads_get(ModuleMultiThread::Default) * stride);
}
nFreeze = ir.opts.nFreeze;
t_vcm::~t_vcm()
{
- if (mode == ecmANGULAR)
+ if (mode == ComRemovalAlgorithm::Angular)
{
sfree(group_i);
}
{
/* Copy pointer to group names and print it. */
- if (fp && vcm.mode != ecmNO)
+ if (fp && vcm.mode != ComRemovalAlgorithm::No)
{
- fprintf(fp, "Center of mass motion removal mode is %s\n", ECOM(vcm.mode));
+ fprintf(fp, "Center of mass motion removal mode is %s\n", enumValueToString(vcm.mode));
fprintf(fp,
"We have the following groups for center of"
" mass motion removal:\n");
gmx::ArrayRef<const gmx::RVec> v,
t_vcm* vcm)
{
- if (vcm->mode == ecmNO)
+ if (vcm->mode == ComRemovalAlgorithm::No)
{
return;
}
- int nthreads = gmx_omp_nthreads_get(emntDefault);
+ int nthreads = gmx_omp_nthreads_get(ModuleMultiThread::Default);
{
#pragma omp parallel num_threads(nthreads) default(none) shared(x, v, vcm, md)
t_vcm_thread* vcm_t = &vcm->thread_vcm[t * vcm->stride + g];
vcm_t->mass = 0;
clear_rvec(vcm_t->p);
- if (vcm->mode == ecmANGULAR)
+ if (vcm->mode == ComRemovalAlgorithm::Angular)
{
/* Reset angular momentum */
clear_rvec(vcm_t->j);
vcm_t->p[m] += m0 * v[i][m];
}
- if (vcm->mode == ecmANGULAR)
+ if (vcm->mode == ComRemovalAlgorithm::Angular)
{
/* Calculate angular momentum */
rvec j0;
/* Reset linear momentum */
vcm->group_mass[g] = 0;
clear_rvec(vcm->group_p[g]);
- if (vcm->mode == ecmANGULAR)
+ if (vcm->mode == ComRemovalAlgorithm::Angular)
{
/* Reset angular momentum */
clear_rvec(vcm->group_j[g]);
t_vcm_thread* vcm_t = &vcm->thread_vcm[t * vcm->stride + g];
vcm->group_mass[g] += vcm_t->mass;
rvec_inc(vcm->group_p[g], vcm_t->p);
- if (vcm->mode == ecmANGULAR)
+ if (vcm->mode == ComRemovalAlgorithm::Angular)
{
rvec_inc(vcm->group_j[g], vcm_t->j);
rvec_inc(vcm->group_x[g], vcm_t->x);
gmx::ArrayRef<gmx::RVec> v,
const t_vcm& vcm)
{
- if (vcm.mode == ecmNO)
+ if (vcm.mode == ComRemovalAlgorithm::No)
{
return;
}
const int homenr = mdatoms.homenr;
const unsigned short* group_id = mdatoms.cVCM;
- int gmx_unused nth = gmx_omp_nthreads_get(emntDefault);
+ int gmx_unused nth = gmx_omp_nthreads_get(ModuleMultiThread::Default);
// homenr could be shared, but gcc-8 & gcc-9 don't agree how to write that...
// https://www.gnu.org/software/gcc/gcc-9/porting_to.html -> OpenMP data sharing
#pragma omp parallel num_threads(nth) default(none) shared(x, v, vcm, group_id, mdatoms) \
firstprivate(homenr)
{
- if (vcm.mode == ecmLINEAR || vcm.mode == ecmANGULAR
- || (vcm.mode == ecmLINEAR_ACCELERATION_CORRECTION && x.empty()))
+ if (vcm.mode == ComRemovalAlgorithm::Linear || vcm.mode == ComRemovalAlgorithm::Angular
+ || (vcm.mode == ComRemovalAlgorithm::LinearAccelerationCorrection && x.empty()))
{
/* Subtract linear momentum for v */
switch (vcm.ndim)
}
else
{
- GMX_ASSERT(vcm.mode == ecmLINEAR_ACCELERATION_CORRECTION,
+ GMX_ASSERT(vcm.mode == ComRemovalAlgorithm::LinearAccelerationCorrection,
"When the mode is not linear or angular, it should be acceleration "
"correction");
/* Subtract linear momentum for v and x*/
break;
}
}
- if (vcm.mode == ecmANGULAR)
+ if (vcm.mode == ComRemovalAlgorithm::Angular)
{
/* Subtract angular momentum */
GMX_ASSERT(!x.empty(), "Need x to compute angular momentum correction");
tensor Icm;
/* First analyse the total results */
- if (vcm->mode != ecmNO)
+ if (vcm->mode != ComRemovalAlgorithm::No)
{
for (g = 0; (g < vcm->nr); g++)
{
}
/* Else it's zero anyway! */
}
- if (vcm->mode == ecmANGULAR)
+ if (vcm->mode == ComRemovalAlgorithm::Angular)
{
for (g = 0; (g < vcm->nr); g++)
{
if ((Temp_cm > Temp_Max) && fp)
{
- fprintf(fp, "Large VCM(group %s): %12.5f, %12.5f, %12.5f, Temp-cm: %12.5e\n",
- vcm->group_name[g], vcm->group_v[g][XX], vcm->group_v[g][YY],
- vcm->group_v[g][ZZ], Temp_cm);
+ fprintf(fp,
+ "Large VCM(group %s): %12.5f, %12.5f, %12.5f, Temp-cm: %12.5e\n",
+ vcm->group_name[g],
+ vcm->group_v[g][XX],
+ vcm->group_v[g][YY],
+ vcm->group_v[g][ZZ],
+ Temp_cm);
}
- if (vcm->mode == ecmANGULAR)
+ if (vcm->mode == ComRemovalAlgorithm::Angular)
{
ekrot = 0.5 * iprod(vcm->group_j[g], vcm->group_w[g]);
// TODO: Change absolute energy comparison to relative
{
/* if we have an integrator that may not conserve momenta, skip */
tm = vcm->group_mass[g];
- fprintf(fp, "Group %s with mass %12.5e, Ekrot %12.5e Det(I) = %12.5e\n",
- vcm->group_name[g], tm, ekrot, det(vcm->group_i[g]));
- fprintf(fp, " COM: %12.5f %12.5f %12.5f\n", vcm->group_x[g][XX],
- vcm->group_x[g][YY], vcm->group_x[g][ZZ]);
- fprintf(fp, " P: %12.5f %12.5f %12.5f\n", vcm->group_p[g][XX],
- vcm->group_p[g][YY], vcm->group_p[g][ZZ]);
- fprintf(fp, " V: %12.5f %12.5f %12.5f\n", vcm->group_v[g][XX],
- vcm->group_v[g][YY], vcm->group_v[g][ZZ]);
- fprintf(fp, " J: %12.5f %12.5f %12.5f\n", vcm->group_j[g][XX],
- vcm->group_j[g][YY], vcm->group_j[g][ZZ]);
- fprintf(fp, " w: %12.5f %12.5f %12.5f\n", vcm->group_w[g][XX],
- vcm->group_w[g][YY], vcm->group_w[g][ZZ]);
+ fprintf(fp,
+ "Group %s with mass %12.5e, Ekrot %12.5e Det(I) = %12.5e\n",
+ vcm->group_name[g],
+ tm,
+ ekrot,
+ det(vcm->group_i[g]));
+ fprintf(fp,
+ " COM: %12.5f %12.5f %12.5f\n",
+ vcm->group_x[g][XX],
+ vcm->group_x[g][YY],
+ vcm->group_x[g][ZZ]);
+ fprintf(fp,
+ " P: %12.5f %12.5f %12.5f\n",
+ vcm->group_p[g][XX],
+ vcm->group_p[g][YY],
+ vcm->group_p[g][ZZ]);
+ fprintf(fp,
+ " V: %12.5f %12.5f %12.5f\n",
+ vcm->group_v[g][XX],
+ vcm->group_v[g][YY],
+ vcm->group_v[g][ZZ]);
+ fprintf(fp,
+ " J: %12.5f %12.5f %12.5f\n",
+ vcm->group_j[g][XX],
+ vcm->group_j[g][YY],
+ vcm->group_j[g][ZZ]);
+ fprintf(fp,
+ " w: %12.5f %12.5f %12.5f\n",
+ vcm->group_w[g][XX],
+ vcm->group_w[g][YY],
+ vcm->group_w[g][ZZ]);
pr_rvecs(fp, 0, "Inertia tensor", vcm->group_i[g], DIM);
}
}
gmx::ArrayRef<gmx::RVec> x,
gmx::ArrayRef<gmx::RVec> v)
{
- if (vcm->mode != ecmNO)
+ if (vcm->mode != ComRemovalAlgorithm::No)
{
// TODO: Replace fixed temperature of 1 by a system value
process_and_check_cm_grp(fplog, vcm, 1);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
#include "gromacs/math/vectypes.h"
+#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
//! Stride for thread data
int stride = 0;
//! One of the enums above
- int mode = 0;
+ ComRemovalAlgorithm mode = ComRemovalAlgorithm::Linear;
//! The number of dimensions for corr.
int ndim = 0;
//! The time step for COMM removal
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdtypes/commrec.h"
-#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
//! The interaction lists, only vsite entries are used
std::array<InteractionList, F_NRE> ilist;
//! Local fshift accumulation buffer
- std::array<RVec, SHIFTS> fshift;
+ std::array<RVec, c_numShiftVectors> fshift;
//! Local virial dx*df accumulation buffer
matrix dxdf;
//! Tells if interdependent task idTask should be used (in addition to the rest of this task), this bool has the same value on all threads
//! Set VSites and distribute VSite work over threads, should be called after DD partitioning
void setVirtualSites(ArrayRef<const InteractionList> ilist,
ArrayRef<const t_iparams> iparams,
- const t_mdatoms& mdatoms,
+ int numAtoms,
+ int homenr,
+ ArrayRef<const ParticleType> ptype,
bool useDomdec);
private:
{
public:
//! Constructor, domdec should be nullptr without DD
- Impl(const gmx_mtop_t& mtop, gmx_domdec_t* domdec, PbcType pbcType);
+ Impl(const gmx_mtop_t& mtop,
+ gmx_domdec_t* domdec,
+ PbcType pbcType,
+ ArrayRef<const RangePartitioning> updateGroupingPerMoleculeType);
//! Returns the number of virtual sites acting over multiple update groups
int numInterUpdategroupVirtualSites() const { return numInterUpdategroupVirtualSites_; }
//! Set VSites and distribute VSite work over threads, should be called after DD partitioning
- void setVirtualSites(ArrayRef<const InteractionList> ilist, const t_mdatoms& mdatoms);
+ void setVirtualSites(ArrayRef<const InteractionList> ilist,
+ int numAtoms,
+ int homenr,
+ ArrayRef<const ParticleType> ptype);
/*! \brief Create positions of vsite atoms based for the local system
*
- * \param[in,out] x The coordinates
- * \param[in] dt The time step
- * \param[in,out] v When != nullptr, velocities for vsites are set as displacement/dt
- * \param[in] box The box
+ * \param[in,out] x The coordinates
+ * \param[in,out] v The velocities, needed if operation requires it
+ * \param[in] box The box
+ * \param[in] operation Whether we calculate positions, velocities, or both
*/
- void construct(ArrayRef<RVec> x, real dt, ArrayRef<RVec> v, const matrix box) const;
+ void construct(ArrayRef<RVec> x, ArrayRef<RVec> v, const matrix box, VSiteOperation operation) const;
/*! \brief Spread the force operating on the vsite atoms on the surrounding atoms.
*
else
{
rvec_sub(xi, xj, dx);
- return CENTRAL;
+ return c_centralShiftIndex;
}
}
return gmx::invsqrt(iprod(x, x));
}
+//! Whether we're calculating the virtual site position
+enum class VSiteCalculatePosition
+{
+ Yes,
+ No
+};
+//! Whether we're calculating the virtual site velocity
+enum class VSiteCalculateVelocity
+{
+ Yes,
+ No
+};
+
#ifndef DOXYGEN
/* Vsite construction routines */
-static void constr_vsite1(const rvec xi, rvec x)
-{
- copy_rvec(xi, x);
+// GCC 8 falsely flags unused variables if constexpr prunes a code path, fixed in GCC 9
+// https://gcc.gnu.org/bugzilla/show_bug.cgi?id=85827
+// clang-format off
+GCC_DIAGNOSTIC_IGNORE(-Wunused-but-set-parameter)
+// clang-format on
- /* TOTAL: 0 flops */
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static void constr_vsite1(const rvec xi, rvec x, const rvec vi, rvec v)
+{
+ if (calculatePosition == VSiteCalculatePosition::Yes)
+ {
+ copy_rvec(xi, x);
+ /* TOTAL: 0 flops */
+ }
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ copy_rvec(vi, v);
+ }
}
-static void constr_vsite2(const rvec xi, const rvec xj, rvec x, real a, const t_pbc* pbc)
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static void
+constr_vsite2(const rvec xi, const rvec xj, rvec x, real a, const t_pbc* pbc, const rvec vi, const rvec vj, rvec v)
{
- real b = 1 - a;
+ const real b = 1 - a;
/* 1 flop */
- if (pbc)
+ if (calculatePosition == VSiteCalculatePosition::Yes)
{
- rvec dx;
- pbc_dx_aiuc(pbc, xj, xi, dx);
- x[XX] = xi[XX] + a * dx[XX];
- x[YY] = xi[YY] + a * dx[YY];
- x[ZZ] = xi[ZZ] + a * dx[ZZ];
+ if (pbc)
+ {
+ rvec dx;
+ pbc_dx_aiuc(pbc, xj, xi, dx);
+ x[XX] = xi[XX] + a * dx[XX];
+ x[YY] = xi[YY] + a * dx[YY];
+ x[ZZ] = xi[ZZ] + a * dx[ZZ];
+ }
+ else
+ {
+ x[XX] = b * xi[XX] + a * xj[XX];
+ x[YY] = b * xi[YY] + a * xj[YY];
+ x[ZZ] = b * xi[ZZ] + a * xj[ZZ];
+ /* 9 Flops */
+ }
+ /* TOTAL: 10 flops */
}
- else
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
{
- x[XX] = b * xi[XX] + a * xj[XX];
- x[YY] = b * xi[YY] + a * xj[YY];
- x[ZZ] = b * xi[ZZ] + a * xj[ZZ];
- /* 9 Flops */
+ v[XX] = b * vi[XX] + a * vj[XX];
+ v[YY] = b * vi[YY] + a * vj[YY];
+ v[ZZ] = b * vi[ZZ] + a * vj[ZZ];
}
-
- /* TOTAL: 10 flops */
}
-static void constr_vsite2FD(const rvec xi, const rvec xj, rvec x, real a, const t_pbc* pbc)
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static void
+constr_vsite2FD(const rvec xi, const rvec xj, rvec x, real a, const t_pbc* pbc, const rvec vi, const rvec vj, rvec v)
{
- rvec xij;
+ rvec xij = { 0 };
pbc_rvec_sub(pbc, xj, xi, xij);
/* 3 flops */
- const real b = a * inverseNorm(xij);
+ const real invNormXij = inverseNorm(xij);
+ const real b = a * invNormXij;
/* 6 + 10 flops */
- x[XX] = xi[XX] + b * xij[XX];
- x[YY] = xi[YY] + b * xij[YY];
- x[ZZ] = xi[ZZ] + b * xij[ZZ];
- /* 6 Flops */
+ if (calculatePosition == VSiteCalculatePosition::Yes)
+ {
+ x[XX] = xi[XX] + b * xij[XX];
+ x[YY] = xi[YY] + b * xij[YY];
+ x[ZZ] = xi[ZZ] + b * xij[ZZ];
+ /* 6 Flops */
+ /* TOTAL: 25 flops */
+ }
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ rvec vij = { 0 };
+ rvec_sub(vj, vi, vij);
+ const real vijDotXij = iprod(vij, xij);
- /* TOTAL: 25 flops */
+ v[XX] = vi[XX] + b * (vij[XX] - xij[XX] * vijDotXij * invNormXij * invNormXij);
+ v[YY] = vi[YY] + b * (vij[YY] - xij[YY] * vijDotXij * invNormXij * invNormXij);
+ v[ZZ] = vi[ZZ] + b * (vij[ZZ] - xij[ZZ] * vijDotXij * invNormXij * invNormXij);
+ }
}
-static void constr_vsite3(const rvec xi, const rvec xj, const rvec xk, rvec x, real a, real b, const t_pbc* pbc)
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static void constr_vsite3(const rvec xi,
+ const rvec xj,
+ const rvec xk,
+ rvec x,
+ real a,
+ real b,
+ const t_pbc* pbc,
+ const rvec vi,
+ const rvec vj,
+ const rvec vk,
+ rvec v)
{
- real c = 1 - a - b;
+ const real c = 1 - a - b;
/* 2 flops */
- if (pbc)
+ if (calculatePosition == VSiteCalculatePosition::Yes)
{
- rvec dxj, dxk;
+ if (pbc)
+ {
+ rvec dxj, dxk;
- pbc_dx_aiuc(pbc, xj, xi, dxj);
- pbc_dx_aiuc(pbc, xk, xi, dxk);
- x[XX] = xi[XX] + a * dxj[XX] + b * dxk[XX];
- x[YY] = xi[YY] + a * dxj[YY] + b * dxk[YY];
- x[ZZ] = xi[ZZ] + a * dxj[ZZ] + b * dxk[ZZ];
+ pbc_dx_aiuc(pbc, xj, xi, dxj);
+ pbc_dx_aiuc(pbc, xk, xi, dxk);
+ x[XX] = xi[XX] + a * dxj[XX] + b * dxk[XX];
+ x[YY] = xi[YY] + a * dxj[YY] + b * dxk[YY];
+ x[ZZ] = xi[ZZ] + a * dxj[ZZ] + b * dxk[ZZ];
+ }
+ else
+ {
+ x[XX] = c * xi[XX] + a * xj[XX] + b * xk[XX];
+ x[YY] = c * xi[YY] + a * xj[YY] + b * xk[YY];
+ x[ZZ] = c * xi[ZZ] + a * xj[ZZ] + b * xk[ZZ];
+ /* 15 Flops */
+ }
+ /* TOTAL: 17 flops */
}
- else
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
{
- x[XX] = c * xi[XX] + a * xj[XX] + b * xk[XX];
- x[YY] = c * xi[YY] + a * xj[YY] + b * xk[YY];
- x[ZZ] = c * xi[ZZ] + a * xj[ZZ] + b * xk[ZZ];
- /* 15 Flops */
+ v[XX] = c * vi[XX] + a * vj[XX] + b * vk[XX];
+ v[YY] = c * vi[YY] + a * vj[YY] + b * vk[YY];
+ v[ZZ] = c * vi[ZZ] + a * vj[ZZ] + b * vk[ZZ];
}
-
- /* TOTAL: 17 flops */
}
-static void constr_vsite3FD(const rvec xi, const rvec xj, const rvec xk, rvec x, real a, real b, const t_pbc* pbc)
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static void constr_vsite3FD(const rvec xi,
+ const rvec xj,
+ const rvec xk,
+ rvec x,
+ real a,
+ real b,
+ const t_pbc* pbc,
+ const rvec vi,
+ const rvec vj,
+ const rvec vk,
+ rvec v)
{
rvec xij, xjk, temp;
- real c;
pbc_rvec_sub(pbc, xj, xi, xij);
pbc_rvec_sub(pbc, xk, xj, xjk);
temp[ZZ] = xij[ZZ] + a * xjk[ZZ];
/* 6 flops */
- c = b * inverseNorm(temp);
+ const real invNormTemp = inverseNorm(temp);
+ const real c = b * invNormTemp;
/* 6 + 10 flops */
- x[XX] = xi[XX] + c * temp[XX];
- x[YY] = xi[YY] + c * temp[YY];
- x[ZZ] = xi[ZZ] + c * temp[ZZ];
- /* 6 Flops */
+ if (calculatePosition == VSiteCalculatePosition::Yes)
+ {
+ x[XX] = xi[XX] + c * temp[XX];
+ x[YY] = xi[YY] + c * temp[YY];
+ x[ZZ] = xi[ZZ] + c * temp[ZZ];
+ /* 6 Flops */
+ /* TOTAL: 34 flops */
+ }
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ rvec vij = { 0 };
+ rvec vjk = { 0 };
+ rvec_sub(vj, vi, vij);
+ rvec_sub(vk, vj, vjk);
+ const rvec tempV = { vij[XX] + a * vjk[XX], vij[YY] + a * vjk[YY], vij[ZZ] + a * vjk[ZZ] };
+ const real tempDotTempV = iprod(temp, tempV);
- /* TOTAL: 34 flops */
+ v[XX] = vi[XX] + c * (tempV[XX] - temp[XX] * tempDotTempV * invNormTemp * invNormTemp);
+ v[YY] = vi[YY] + c * (tempV[YY] - temp[YY] * tempDotTempV * invNormTemp * invNormTemp);
+ v[ZZ] = vi[ZZ] + c * (tempV[ZZ] - temp[ZZ] * tempDotTempV * invNormTemp * invNormTemp);
+ }
}
-static void constr_vsite3FAD(const rvec xi, const rvec xj, const rvec xk, rvec x, real a, real b, const t_pbc* pbc)
-{
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static void constr_vsite3FAD(const rvec xi,
+ const rvec xj,
+ const rvec xk,
+ rvec x,
+ real a,
+ real b,
+ const t_pbc* pbc,
+ const rvec vi,
+ const rvec vj,
+ const rvec vk,
+ rvec v)
+{ // Note: a = d * cos(theta)
+ // b = d * sin(theta)
rvec xij, xjk, xp;
- real a1, b1, c1, invdij;
pbc_rvec_sub(pbc, xj, xi, xij);
pbc_rvec_sub(pbc, xk, xj, xjk);
/* 6 flops */
- invdij = inverseNorm(xij);
- c1 = invdij * invdij * iprod(xij, xjk);
- xp[XX] = xjk[XX] - c1 * xij[XX];
- xp[YY] = xjk[YY] - c1 * xij[YY];
- xp[ZZ] = xjk[ZZ] - c1 * xij[ZZ];
- a1 = a * invdij;
- b1 = b * inverseNorm(xp);
+ const real invdij = inverseNorm(xij);
+ const real xijDotXjk = iprod(xij, xjk);
+ const real c1 = invdij * invdij * xijDotXjk;
+ xp[XX] = xjk[XX] - c1 * xij[XX];
+ xp[YY] = xjk[YY] - c1 * xij[YY];
+ xp[ZZ] = xjk[ZZ] - c1 * xij[ZZ];
+ const real a1 = a * invdij;
+ const real invNormXp = inverseNorm(xp);
+ const real b1 = b * invNormXp;
/* 45 */
- x[XX] = xi[XX] + a1 * xij[XX] + b1 * xp[XX];
- x[YY] = xi[YY] + a1 * xij[YY] + b1 * xp[YY];
- x[ZZ] = xi[ZZ] + a1 * xij[ZZ] + b1 * xp[ZZ];
- /* 12 Flops */
-
- /* TOTAL: 63 flops */
+ if (calculatePosition == VSiteCalculatePosition::Yes)
+ {
+ x[XX] = xi[XX] + a1 * xij[XX] + b1 * xp[XX];
+ x[YY] = xi[YY] + a1 * xij[YY] + b1 * xp[YY];
+ x[ZZ] = xi[ZZ] + a1 * xij[ZZ] + b1 * xp[ZZ];
+ /* 12 Flops */
+ /* TOTAL: 63 flops */
+ }
+
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ rvec vij = { 0 };
+ rvec vjk = { 0 };
+ rvec_sub(vj, vi, vij);
+ rvec_sub(vk, vj, vjk);
+
+ const real vijDotXjkPlusXijDotVjk = iprod(vij, xjk) + iprod(xij, vjk);
+ const real xijDotVij = iprod(xij, vij);
+ const real invNormXij2 = invdij * invdij;
+
+ rvec vp = { 0 };
+ vp[XX] = vjk[XX]
+ - xij[XX] * invNormXij2
+ * (vijDotXjkPlusXijDotVjk - invNormXij2 * xijDotXjk * xijDotVij * 2)
+ - vij[XX] * xijDotXjk * invNormXij2;
+ vp[YY] = vjk[YY]
+ - xij[YY] * invNormXij2
+ * (vijDotXjkPlusXijDotVjk - invNormXij2 * xijDotXjk * xijDotVij * 2)
+ - vij[YY] * xijDotXjk * invNormXij2;
+ vp[ZZ] = vjk[ZZ]
+ - xij[ZZ] * invNormXij2
+ * (vijDotXjkPlusXijDotVjk - invNormXij2 * xijDotXjk * xijDotVij * 2)
+ - vij[ZZ] * xijDotXjk * invNormXij2;
+
+ const real xpDotVp = iprod(xp, vp);
+
+ v[XX] = vi[XX] + a1 * (vij[XX] - xij[XX] * xijDotVij * invdij * invdij)
+ + b1 * (vp[XX] - xp[XX] * xpDotVp * invNormXp * invNormXp);
+ v[YY] = vi[YY] + a1 * (vij[YY] - xij[YY] * xijDotVij * invdij * invdij)
+ + b1 * (vp[YY] - xp[YY] * xpDotVp * invNormXp * invNormXp);
+ v[ZZ] = vi[ZZ] + a1 * (vij[ZZ] - xij[ZZ] * xijDotVij * invdij * invdij)
+ + b1 * (vp[ZZ] - xp[ZZ] * xpDotVp * invNormXp * invNormXp);
+ }
}
-static void
-constr_vsite3OUT(const rvec xi, const rvec xj, const rvec xk, rvec x, real a, real b, real c, const t_pbc* pbc)
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static void constr_vsite3OUT(const rvec xi,
+ const rvec xj,
+ const rvec xk,
+ rvec x,
+ real a,
+ real b,
+ real c,
+ const t_pbc* pbc,
+ const rvec vi,
+ const rvec vj,
+ const rvec vk,
+ rvec v)
{
rvec xij, xik, temp;
cprod(xij, xik, temp);
/* 15 Flops */
- x[XX] = xi[XX] + a * xij[XX] + b * xik[XX] + c * temp[XX];
- x[YY] = xi[YY] + a * xij[YY] + b * xik[YY] + c * temp[YY];
- x[ZZ] = xi[ZZ] + a * xij[ZZ] + b * xik[ZZ] + c * temp[ZZ];
- /* 18 Flops */
+ if (calculatePosition == VSiteCalculatePosition::Yes)
+ {
+ x[XX] = xi[XX] + a * xij[XX] + b * xik[XX] + c * temp[XX];
+ x[YY] = xi[YY] + a * xij[YY] + b * xik[YY] + c * temp[YY];
+ x[ZZ] = xi[ZZ] + a * xij[ZZ] + b * xik[ZZ] + c * temp[ZZ];
+ /* 18 Flops */
+ /* TOTAL: 33 flops */
+ }
+
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ rvec vij = { 0 };
+ rvec vik = { 0 };
+ rvec_sub(vj, vi, vij);
+ rvec_sub(vk, vi, vik);
+
+ rvec temp1 = { 0 };
+ rvec temp2 = { 0 };
+ cprod(vij, xik, temp1);
+ cprod(xij, vik, temp2);
- /* TOTAL: 33 flops */
+ v[XX] = vi[XX] + a * vij[XX] + b * vik[XX] + c * (temp1[XX] + temp2[XX]);
+ v[YY] = vi[YY] + a * vij[YY] + b * vik[YY] + c * (temp1[YY] + temp2[YY]);
+ v[ZZ] = vi[ZZ] + a * vij[ZZ] + b * vik[ZZ] + c * (temp1[ZZ] + temp2[ZZ]);
+ }
}
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
static void constr_vsite4FD(const rvec xi,
const rvec xj,
const rvec xk,
real a,
real b,
real c,
- const t_pbc* pbc)
+ const t_pbc* pbc,
+ const rvec vi,
+ const rvec vj,
+ const rvec vk,
+ const rvec vl,
+ rvec v)
{
rvec xij, xjk, xjl, temp;
real d;
temp[ZZ] = xij[ZZ] + a * xjk[ZZ] + b * xjl[ZZ];
/* 12 flops */
- d = c * inverseNorm(temp);
+ const real invRm = inverseNorm(temp);
+ d = c * invRm;
/* 6 + 10 flops */
- x[XX] = xi[XX] + d * temp[XX];
- x[YY] = xi[YY] + d * temp[YY];
- x[ZZ] = xi[ZZ] + d * temp[ZZ];
- /* 6 Flops */
+ if (calculatePosition == VSiteCalculatePosition::Yes)
+ {
+ x[XX] = xi[XX] + d * temp[XX];
+ x[YY] = xi[YY] + d * temp[YY];
+ x[ZZ] = xi[ZZ] + d * temp[ZZ];
+ /* 6 Flops */
+ /* TOTAL: 43 flops */
+ }
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ rvec vij = { 0 };
+ rvec vjk = { 0 };
+ rvec vjl = { 0 };
+
+ rvec_sub(vj, vi, vij);
+ rvec_sub(vk, vj, vjk);
+ rvec_sub(vl, vj, vjl);
- /* TOTAL: 43 flops */
+ rvec vm = { 0 };
+ vm[XX] = vij[XX] + a * vjk[XX] + b * vjl[XX];
+ vm[YY] = vij[YY] + a * vjk[YY] + b * vjl[YY];
+ vm[ZZ] = vij[ZZ] + a * vjk[ZZ] + b * vjl[ZZ];
+
+ const real vmDotRm = iprod(vm, temp);
+ v[XX] = vi[XX] + d * (vm[XX] - temp[XX] * vmDotRm * invRm * invRm);
+ v[YY] = vi[YY] + d * (vm[YY] - temp[YY] * vmDotRm * invRm * invRm);
+ v[ZZ] = vi[ZZ] + d * (vm[ZZ] - temp[ZZ] * vmDotRm * invRm * invRm);
+ }
}
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
static void constr_vsite4FDN(const rvec xi,
const rvec xj,
const rvec xk,
real a,
real b,
real c,
- const t_pbc* pbc)
+ const t_pbc* pbc,
+ const rvec vi,
+ const rvec vj,
+ const rvec vk,
+ const rvec vl,
+ rvec v)
{
rvec xij, xik, xil, ra, rb, rja, rjb, rm;
real d;
cprod(rja, rjb, rm);
/* 9 flops */
- d = c * inverseNorm(rm);
+ const real invNormRm = inverseNorm(rm);
+ d = c * invNormRm;
/* 5+5+1 flops */
- x[XX] = xi[XX] + d * rm[XX];
- x[YY] = xi[YY] + d * rm[YY];
- x[ZZ] = xi[ZZ] + d * rm[ZZ];
- /* 6 Flops */
+ if (calculatePosition == VSiteCalculatePosition::Yes)
+ {
+ x[XX] = xi[XX] + d * rm[XX];
+ x[YY] = xi[YY] + d * rm[YY];
+ x[ZZ] = xi[ZZ] + d * rm[ZZ];
+ /* 6 Flops */
+ /* TOTAL: 47 flops */
+ }
+
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ rvec vij = { 0 };
+ rvec vik = { 0 };
+ rvec vil = { 0 };
+ rvec_sub(vj, vi, vij);
+ rvec_sub(vk, vi, vik);
+ rvec_sub(vl, vi, vil);
+
+ rvec vja = { 0 };
+ rvec vjb = { 0 };
+
+ vja[XX] = a * vik[XX] - vij[XX];
+ vja[YY] = a * vik[YY] - vij[YY];
+ vja[ZZ] = a * vik[ZZ] - vij[ZZ];
+ vjb[XX] = b * vil[XX] - vij[XX];
+ vjb[YY] = b * vil[YY] - vij[YY];
+ vjb[ZZ] = b * vil[ZZ] - vij[ZZ];
+
+ rvec temp1 = { 0 };
+ rvec temp2 = { 0 };
+ cprod(vja, rjb, temp1);
+ cprod(rja, vjb, temp2);
- /* TOTAL: 47 flops */
+ rvec vm = { 0 };
+ vm[XX] = temp1[XX] + temp2[XX];
+ vm[YY] = temp1[YY] + temp2[YY];
+ vm[ZZ] = temp1[ZZ] + temp2[ZZ];
+
+ const real rmDotVm = iprod(rm, vm);
+ v[XX] = vi[XX] + d * (vm[XX] - rm[XX] * rmDotVm * invNormRm * invNormRm);
+ v[YY] = vi[YY] + d * (vm[YY] - rm[YY] * rmDotVm * invNormRm * invNormRm);
+ v[ZZ] = vi[ZZ] + d * (vm[ZZ] - rm[ZZ] * rmDotVm * invNormRm * invNormRm);
+ }
}
-static int constr_vsiten(const t_iatom* ia, ArrayRef<const t_iparams> ip, ArrayRef<RVec> x, const t_pbc* pbc)
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static int constr_vsiten(const t_iatom* ia,
+ ArrayRef<const t_iparams> ip,
+ ArrayRef<RVec> x,
+ const t_pbc* pbc,
+ ArrayRef<RVec> v)
{
rvec x1, dx;
dvec dsum;
- int n3, av, ai;
real a;
+ dvec dvsum = { 0 };
+ rvec v1 = { 0 };
- n3 = 3 * ip[ia[0]].vsiten.n;
- av = ia[1];
- ai = ia[2];
+ const int n3 = 3 * ip[ia[0]].vsiten.n;
+ const int av = ia[1];
+ int ai = ia[2];
copy_rvec(x[ai], x1);
+ copy_rvec(v[ai], v1);
clear_dvec(dsum);
for (int i = 3; i < n3; i += 3)
{
ai = ia[i + 2];
a = ip[ia[i]].vsiten.a;
- if (pbc)
+ if (calculatePosition == VSiteCalculatePosition::Yes)
{
- pbc_dx_aiuc(pbc, x[ai], x1, dx);
+ if (pbc)
+ {
+ pbc_dx_aiuc(pbc, x[ai], x1, dx);
+ }
+ else
+ {
+ rvec_sub(x[ai], x1, dx);
+ }
+ dsum[XX] += a * dx[XX];
+ dsum[YY] += a * dx[YY];
+ dsum[ZZ] += a * dx[ZZ];
+ /* 9 Flops */
}
- else
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
{
- rvec_sub(x[ai], x1, dx);
+ rvec_sub(v[ai], v1, dx);
+ dvsum[XX] += a * dx[XX];
+ dvsum[YY] += a * dx[YY];
+ dvsum[ZZ] += a * dx[ZZ];
+ /* 9 Flops */
}
- dsum[XX] += a * dx[XX];
- dsum[YY] += a * dx[YY];
- dsum[ZZ] += a * dx[ZZ];
- /* 9 Flops */
}
- x[av][XX] = x1[XX] + dsum[XX];
- x[av][YY] = x1[YY] + dsum[YY];
- x[av][ZZ] = x1[ZZ] + dsum[ZZ];
+ if (calculatePosition == VSiteCalculatePosition::Yes)
+ {
+ x[av][XX] = x1[XX] + dsum[XX];
+ x[av][YY] = x1[YY] + dsum[YY];
+ x[av][ZZ] = x1[ZZ] + dsum[ZZ];
+ }
+
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ v[av][XX] = v1[XX] + dvsum[XX];
+ v[av][YY] = v1[YY] + dvsum[YY];
+ v[av][ZZ] = v1[ZZ] + dvsum[ZZ];
+ }
return n3;
}
+// End GCC 8 bug
+GCC_DIAGNOSTIC_RESET
#endif // DOXYGEN
/*! \brief Executes the vsite construction task for a single thread
*
+ * \tparam operation Whether we are calculating positions, velocities, or both
* \param[in,out] x Coordinates to construct vsites for
- * \param[in] dt Time step, needed when v is not empty
- * \param[in,out] v When not empty, velocities are generated for virtual sites
+ * \param[in,out] v Velocities are generated for virtual sites if `operation` requires it
* \param[in] ip Interaction parameters for all interaction, only vsite parameters are used
* \param[in] ilist The interaction lists, only vsites are usesd
* \param[in] pbc_null PBC struct, used for PBC distance calculations when !=nullptr
*/
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
static void construct_vsites_thread(ArrayRef<RVec> x,
- const real dt,
ArrayRef<RVec> v,
ArrayRef<const t_iparams> ip,
ArrayRef<const InteractionList> ilist,
const t_pbc* pbc_null)
{
- real inv_dt;
- if (!v.empty())
- {
- inv_dt = 1.0 / dt;
- }
- else
- {
- inv_dt = 1.0;
- }
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ GMX_RELEASE_ASSERT(!v.empty(),
+ "Can't calculate velocities without access to velocity vector.");
+ }
+
+ // Work around clang bug (unfixed as of Feb 2021)
+ // https://bugs.llvm.org/show_bug.cgi?id=35450
+ // clang-format off
+ CLANG_DIAGNOSTIC_IGNORE(-Wunused-lambda-capture)
+ // clang-format on
+ // GCC 8 falsely flags unused variables if constexpr prunes a code path, fixed in GCC 9
+ // https://gcc.gnu.org/bugzilla/show_bug.cgi?id=85827
+ // clang-format off
+ GCC_DIAGNOSTIC_IGNORE(-Wunused-but-set-parameter)
+ // clang-format on
+ // getVOrNull returns a velocity rvec if we need it, nullptr otherwise.
+ auto getVOrNull = [v](int idx) -> real* {
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ return v[idx].as_vec();
+ }
+ else
+ {
+ return nullptr;
+ }
+ };
+ GCC_DIAGNOSTIC_RESET
+ CLANG_DIAGNOSTIC_RESET
const PbcMode pbcMode = getPbcMode(pbc_null);
/* We need another pbc pointer, as with charge groups we switch per vsite */
real b1, c1;
switch (ftype)
{
- case F_VSITE1: constr_vsite1(x[ai], x[avsite]); break;
+ case F_VSITE1:
+ constr_vsite1<calculatePosition, calculateVelocity>(
+ x[ai], x[avsite], getVOrNull(ai), getVOrNull(avsite));
+ break;
case F_VSITE2:
aj = ia[3];
- constr_vsite2(x[ai], x[aj], x[avsite], a1, pbc_null2);
+ constr_vsite2<calculatePosition, calculateVelocity>(x[ai],
+ x[aj],
+ x[avsite],
+ a1,
+ pbc_null2,
+ getVOrNull(ai),
+ getVOrNull(aj),
+ getVOrNull(avsite));
break;
case F_VSITE2FD:
aj = ia[3];
- constr_vsite2FD(x[ai], x[aj], x[avsite], a1, pbc_null2);
+ constr_vsite2FD<calculatePosition, calculateVelocity>(x[ai],
+ x[aj],
+ x[avsite],
+ a1,
+ pbc_null2,
+ getVOrNull(ai),
+ getVOrNull(aj),
+ getVOrNull(avsite));
break;
case F_VSITE3:
aj = ia[3];
ak = ia[4];
b1 = ip[tp].vsite.b;
- constr_vsite3(x[ai], x[aj], x[ak], x[avsite], a1, b1, pbc_null2);
+ constr_vsite3<calculatePosition, calculateVelocity>(x[ai],
+ x[aj],
+ x[ak],
+ x[avsite],
+ a1,
+ b1,
+ pbc_null2,
+ getVOrNull(ai),
+ getVOrNull(aj),
+ getVOrNull(ak),
+ getVOrNull(avsite));
break;
case F_VSITE3FD:
aj = ia[3];
ak = ia[4];
b1 = ip[tp].vsite.b;
- constr_vsite3FD(x[ai], x[aj], x[ak], x[avsite], a1, b1, pbc_null2);
+ constr_vsite3FD<calculatePosition, calculateVelocity>(x[ai],
+ x[aj],
+ x[ak],
+ x[avsite],
+ a1,
+ b1,
+ pbc_null2,
+ getVOrNull(ai),
+ getVOrNull(aj),
+ getVOrNull(ak),
+ getVOrNull(avsite));
break;
case F_VSITE3FAD:
aj = ia[3];
ak = ia[4];
b1 = ip[tp].vsite.b;
- constr_vsite3FAD(x[ai], x[aj], x[ak], x[avsite], a1, b1, pbc_null2);
+ constr_vsite3FAD<calculatePosition, calculateVelocity>(x[ai],
+ x[aj],
+ x[ak],
+ x[avsite],
+ a1,
+ b1,
+ pbc_null2,
+ getVOrNull(ai),
+ getVOrNull(aj),
+ getVOrNull(ak),
+ getVOrNull(avsite));
break;
case F_VSITE3OUT:
aj = ia[3];
ak = ia[4];
b1 = ip[tp].vsite.b;
c1 = ip[tp].vsite.c;
- constr_vsite3OUT(x[ai], x[aj], x[ak], x[avsite], a1, b1, c1, pbc_null2);
+ constr_vsite3OUT<calculatePosition, calculateVelocity>(x[ai],
+ x[aj],
+ x[ak],
+ x[avsite],
+ a1,
+ b1,
+ c1,
+ pbc_null2,
+ getVOrNull(ai),
+ getVOrNull(aj),
+ getVOrNull(ak),
+ getVOrNull(avsite));
break;
case F_VSITE4FD:
aj = ia[3];
al = ia[5];
b1 = ip[tp].vsite.b;
c1 = ip[tp].vsite.c;
- constr_vsite4FD(x[ai], x[aj], x[ak], x[al], x[avsite], a1, b1, c1, pbc_null2);
+ constr_vsite4FD<calculatePosition, calculateVelocity>(x[ai],
+ x[aj],
+ x[ak],
+ x[al],
+ x[avsite],
+ a1,
+ b1,
+ c1,
+ pbc_null2,
+ getVOrNull(ai),
+ getVOrNull(aj),
+ getVOrNull(ak),
+ getVOrNull(al),
+ getVOrNull(avsite));
break;
case F_VSITE4FDN:
aj = ia[3];
al = ia[5];
b1 = ip[tp].vsite.b;
c1 = ip[tp].vsite.c;
- constr_vsite4FDN(x[ai], x[aj], x[ak], x[al], x[avsite], a1, b1, c1, pbc_null2);
+ constr_vsite4FDN<calculatePosition, calculateVelocity>(x[ai],
+ x[aj],
+ x[ak],
+ x[al],
+ x[avsite],
+ a1,
+ b1,
+ c1,
+ pbc_null2,
+ getVOrNull(ai),
+ getVOrNull(aj),
+ getVOrNull(ak),
+ getVOrNull(al),
+ getVOrNull(avsite));
+ break;
+ case F_VSITEN:
+ inc = constr_vsiten<calculatePosition, calculateVelocity>(ia, ip, x, pbc_null2, v);
break;
- case F_VSITEN: inc = constr_vsiten(ia, ip, x, pbc_null2); break;
default:
gmx_fatal(FARGS, "No such vsite type %d in %s, line %d", ftype, __FILE__, __LINE__);
}
/* Keep the vsite in the same periodic image as before */
rvec dx;
int ishift = pbc_dx_aiuc(pbc_null, x[avsite], xv, dx);
- if (ishift != CENTRAL)
+ if (ishift != c_centralShiftIndex)
{
rvec_add(xv, dx, x[avsite]);
}
}
- if (!v.empty())
- {
- /* Calculate velocity of vsite... */
- rvec vv;
- rvec_sub(x[avsite], xv, vv);
- svmul(inv_dt, vv, v[avsite]);
- }
/* Increment loop variables */
i += inc;
*
* \param[in] threadingInfo Used to divide work over threads when != nullptr
* \param[in,out] x Coordinates to construct vsites for
- * \param[in] dt Time step, needed when v is not empty
* \param[in,out] v When not empty, velocities are generated for virtual sites
* \param[in] ip Interaction parameters for all interaction, only vsite parameters are used
* \param[in] ilist The interaction lists, only vsites are usesd
* \param[in] domainInfo Information about PBC and DD
* \param[in] box Used for PBC when PBC is set in domainInfo
*/
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
static void construct_vsites(const ThreadingInfo* threadingInfo,
ArrayRef<RVec> x,
- real dt,
ArrayRef<RVec> v,
ArrayRef<const t_iparams> ip,
ArrayRef<const InteractionList> ilist,
*/
ivec null_ivec;
clear_ivec(null_ivec);
- pbc_null = set_pbc_dd(&pbc, domainInfo.pbcType_,
- useDomdec ? domainInfo.domdec_->numCells : null_ivec, FALSE, box);
+ pbc_null = set_pbc_dd(
+ &pbc, domainInfo.pbcType_, useDomdec ? domainInfo.domdec_->numCells : null_ivec, FALSE, box);
}
else
{
if (useDomdec)
{
- dd_move_x_vsites(*domainInfo.domdec_, box, as_rvec_array(x.data()));
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ dd_move_x_and_v_vsites(
+ *domainInfo.domdec_, box, as_rvec_array(x.data()), as_rvec_array(v.data()));
+ }
+ else
+ {
+ dd_move_x_vsites(*domainInfo.domdec_, box, as_rvec_array(x.data()));
+ }
}
if (threadingInfo == nullptr || threadingInfo->numThreads() == 1)
{
- construct_vsites_thread(x, dt, v, ip, ilist, pbc_null);
+ construct_vsites_thread<calculatePosition, calculateVelocity>(x, v, ip, ilist, pbc_null);
}
else
{
GMX_ASSERT(tData.rangeStart >= 0,
"The thread data should be initialized before calling construct_vsites");
- construct_vsites_thread(x, dt, v, ip, tData.ilist, pbc_null);
+ construct_vsites_thread<calculatePosition, calculateVelocity>(
+ x, v, ip, tData.ilist, pbc_null);
if (tData.useInterdependentTask)
{
/* Here we don't need a barrier (unlike the spreading),
* since both tasks only construct vsites from particles,
* or local vsites, not from non-local vsites.
*/
- construct_vsites_thread(x, dt, v, ip, tData.idTask.ilist, pbc_null);
+ construct_vsites_thread<calculatePosition, calculateVelocity>(
+ x, v, ip, tData.idTask.ilist, pbc_null);
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
/* Now we can construct the vsites that might depend on other vsites */
- construct_vsites_thread(x, dt, v, ip, threadingInfo->threadDataNonLocalDependent().ilist, pbc_null);
+ construct_vsites_thread<calculatePosition, calculateVelocity>(
+ x, v, ip, threadingInfo->threadDataNonLocalDependent().ilist, pbc_null);
}
}
-void VirtualSitesHandler::Impl::construct(ArrayRef<RVec> x, real dt, ArrayRef<RVec> v, const matrix box) const
+void VirtualSitesHandler::Impl::construct(ArrayRef<RVec> x,
+ ArrayRef<RVec> v,
+ const matrix box,
+ VSiteOperation operation) const
{
- construct_vsites(&threadingInfo_, x, dt, v, iparams_, ilists_, domainInfo_, box);
+ switch (operation)
+ {
+ case VSiteOperation::Positions:
+ construct_vsites<VSiteCalculatePosition::Yes, VSiteCalculateVelocity::No>(
+ &threadingInfo_, x, v, iparams_, ilists_, domainInfo_, box);
+ break;
+ case VSiteOperation::Velocities:
+ construct_vsites<VSiteCalculatePosition::No, VSiteCalculateVelocity::Yes>(
+ &threadingInfo_, x, v, iparams_, ilists_, domainInfo_, box);
+ break;
+ case VSiteOperation::PositionsAndVelocities:
+ construct_vsites<VSiteCalculatePosition::Yes, VSiteCalculateVelocity::Yes>(
+ &threadingInfo_, x, v, iparams_, ilists_, domainInfo_, box);
+ break;
+ default: gmx_fatal(FARGS, "Unknown virtual site operation");
+ }
}
-void VirtualSitesHandler::construct(ArrayRef<RVec> x, real dt, ArrayRef<RVec> v, const matrix box) const
+void VirtualSitesHandler::construct(ArrayRef<RVec> x, ArrayRef<RVec> v, const matrix box, VSiteOperation operation) const
{
- impl_->construct(x, dt, v, box);
+ impl_->construct(x, v, box, operation);
}
void constructVirtualSites(ArrayRef<RVec> x, ArrayRef<const t_iparams> ip, ArrayRef<const InteractionList> ilist)
{
// No PBC, no DD
const DomainInfo domainInfo;
- construct_vsites(nullptr, x, 0, {}, ip, ilist, domainInfo, nullptr);
+ construct_vsites<VSiteCalculatePosition::Yes, VSiteCalculateVelocity::No>(
+ nullptr, x, {}, ip, ilist, domainInfo, nullptr);
}
#ifndef DOXYGEN
}
else
{
- siv = CENTRAL;
- sij = CENTRAL;
+ siv = c_centralShiftIndex;
+ sij = c_centralShiftIndex;
}
- if (siv != CENTRAL || sij != CENTRAL)
+ if (siv != c_centralShiftIndex || sij != c_centralShiftIndex)
{
rvec_inc(fshift[siv], f[av]);
- rvec_dec(fshift[CENTRAL], fi);
+ rvec_dec(fshift[c_centralShiftIndex], fi);
rvec_dec(fshift[sij], fj);
}
}
int atomOffset = mtop.moleculeBlockIndices[mb].globalAtomStart;
for (int mol = 0; mol < molb.nmol; mol++)
{
- constructVirtualSites(x.subArray(atomOffset, molt.atoms.nr), mtop.ffparams.iparams,
- molt.ilist);
+ constructVirtualSites(
+ x.subArray(atomOffset, molt.atoms.nr), mtop.ffparams.iparams, molt.ilist);
atomOffset += molt.atoms.nr;
}
}
}
else
{
- svi = CENTRAL;
+ svi = c_centralShiftIndex;
}
- if (svi != CENTRAL || sji != CENTRAL)
+ if (svi != c_centralShiftIndex || sji != c_centralShiftIndex)
{
rvec_dec(fshift[svi], fv);
- fshift[CENTRAL][XX] += fv[XX] - fj[XX];
- fshift[CENTRAL][YY] += fv[YY] - fj[YY];
- fshift[CENTRAL][ZZ] += fv[ZZ] - fj[ZZ];
+ fshift[c_centralShiftIndex][XX] += fv[XX] - fj[XX];
+ fshift[c_centralShiftIndex][YY] += fv[YY] - fj[YY];
+ fshift[c_centralShiftIndex][ZZ] += fv[ZZ] - fj[ZZ];
fshift[sji][XX] += fj[XX];
fshift[sji][YY] += fj[YY];
fshift[sji][ZZ] += fj[ZZ];
}
else
{
- siv = CENTRAL;
- sij = CENTRAL;
- sik = CENTRAL;
+ siv = c_centralShiftIndex;
+ sij = c_centralShiftIndex;
+ sik = c_centralShiftIndex;
}
- if (siv != CENTRAL || sij != CENTRAL || sik != CENTRAL)
+ if (siv != c_centralShiftIndex || sij != c_centralShiftIndex || sik != c_centralShiftIndex)
{
rvec_inc(fshift[siv], f[av]);
- rvec_dec(fshift[CENTRAL], fi);
+ rvec_dec(fshift[c_centralShiftIndex], fi);
rvec_dec(fshift[sij], fj);
rvec_dec(fshift[sik], fk);
}
}
else
{
- svi = CENTRAL;
+ svi = c_centralShiftIndex;
}
- if (svi != CENTRAL || sji != CENTRAL || skj != CENTRAL)
+ if (svi != c_centralShiftIndex || sji != c_centralShiftIndex || skj != c_centralShiftIndex)
{
rvec_dec(fshift[svi], fv);
- fshift[CENTRAL][XX] += fv[XX] - (1 + a) * temp[XX];
- fshift[CENTRAL][YY] += fv[YY] - (1 + a) * temp[YY];
- fshift[CENTRAL][ZZ] += fv[ZZ] - (1 + a) * temp[ZZ];
+ fshift[c_centralShiftIndex][XX] += fv[XX] - (1 + a) * temp[XX];
+ fshift[c_centralShiftIndex][YY] += fv[YY] - (1 + a) * temp[YY];
+ fshift[c_centralShiftIndex][ZZ] += fv[ZZ] - (1 + a) * temp[ZZ];
fshift[sji][XX] += temp[XX];
fshift[sji][YY] += temp[YY];
fshift[sji][ZZ] += temp[ZZ];
}
else
{
- svi = CENTRAL;
+ svi = c_centralShiftIndex;
}
- if (svi != CENTRAL || sji != CENTRAL || skj != CENTRAL)
+ if (svi != c_centralShiftIndex || sji != c_centralShiftIndex || skj != c_centralShiftIndex)
{
rvec_dec(fshift[svi], fv);
- fshift[CENTRAL][XX] += fv[XX] - f1[XX] - (1 - c1) * f2[XX] + f3[XX];
- fshift[CENTRAL][YY] += fv[YY] - f1[YY] - (1 - c1) * f2[YY] + f3[YY];
- fshift[CENTRAL][ZZ] += fv[ZZ] - f1[ZZ] - (1 - c1) * f2[ZZ] + f3[ZZ];
+ fshift[c_centralShiftIndex][XX] += fv[XX] - f1[XX] - (1 - c1) * f2[XX] + f3[XX];
+ fshift[c_centralShiftIndex][YY] += fv[YY] - f1[YY] - (1 - c1) * f2[YY] + f3[YY];
+ fshift[c_centralShiftIndex][ZZ] += fv[ZZ] - f1[ZZ] - (1 - c1) * f2[ZZ] + f3[ZZ];
fshift[sji][XX] += f1[XX] - c1 * f2[XX] - f3[XX];
fshift[sji][YY] += f1[YY] - c1 * f2[YY] - f3[YY];
fshift[sji][ZZ] += f1[ZZ] - c1 * f2[ZZ] - f3[ZZ];
}
else
{
- svi = CENTRAL;
+ svi = c_centralShiftIndex;
}
- if (svi != CENTRAL || sji != CENTRAL || ski != CENTRAL)
+ if (svi != c_centralShiftIndex || sji != c_centralShiftIndex || ski != c_centralShiftIndex)
{
rvec_dec(fshift[svi], fv);
- fshift[CENTRAL][XX] += fv[XX] - fj[XX] - fk[XX];
- fshift[CENTRAL][YY] += fv[YY] - fj[YY] - fk[YY];
- fshift[CENTRAL][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ];
+ fshift[c_centralShiftIndex][XX] += fv[XX] - fj[XX] - fk[XX];
+ fshift[c_centralShiftIndex][YY] += fv[YY] - fj[YY] - fk[YY];
+ fshift[c_centralShiftIndex][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ];
rvec_inc(fshift[sji], fj);
rvec_inc(fshift[ski], fk);
}
}
else
{
- svi = CENTRAL;
+ svi = c_centralShiftIndex;
}
- if (svi != CENTRAL || sji != CENTRAL || skj != CENTRAL || slj != CENTRAL)
+ if (svi != c_centralShiftIndex || sji != c_centralShiftIndex || skj != c_centralShiftIndex
+ || slj != c_centralShiftIndex)
{
rvec_dec(fshift[svi], fv);
for (m = 0; m < DIM; m++)
{
- fshift[CENTRAL][m] += fv[m] - (1 + a + b) * temp[m];
+ fshift[c_centralShiftIndex][m] += fv[m] - (1 + a + b) * temp[m];
fshift[sji][m] += temp[m];
fshift[skj][m] += a * temp[m];
fshift[slj][m] += b * temp[m];
}
else
{
- svi = CENTRAL;
+ svi = c_centralShiftIndex;
}
- if (svi != CENTRAL || sij != CENTRAL || sik != CENTRAL || sil != CENTRAL)
+ if (svi != c_centralShiftIndex || sij != c_centralShiftIndex || sik != c_centralShiftIndex
+ || sil != c_centralShiftIndex)
{
rvec_dec(fshift[svi], fv);
- fshift[CENTRAL][XX] += fv[XX] - fj[XX] - fk[XX] - fl[XX];
- fshift[CENTRAL][YY] += fv[YY] - fj[YY] - fk[YY] - fl[YY];
- fshift[CENTRAL][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ] - fl[ZZ];
+ fshift[c_centralShiftIndex][XX] += fv[XX] - fj[XX] - fk[XX] - fl[XX];
+ fshift[c_centralShiftIndex][YY] += fv[YY] - fj[YY] - fk[YY] - fl[YY];
+ fshift[c_centralShiftIndex][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ] - fl[ZZ];
rvec_inc(fshift[sij], fj);
rvec_inc(fshift[sik], fk);
rvec_inc(fshift[sil], fl);
}
else
{
- siv = CENTRAL;
+ siv = c_centralShiftIndex;
}
a = ip[ia[i]].vsiten.a;
svmul(a, f[av], fi);
rvec_inc(f[ai], fi);
- if (virialHandling == VirialHandling::Pbc && siv != CENTRAL)
+ if (virialHandling == VirialHandling::Pbc && siv != c_centralShiftIndex)
{
rvec_inc(fshift[siv], fi);
- rvec_dec(fshift[CENTRAL], fi);
+ rvec_dec(fshift[c_centralShiftIndex], fi);
}
/* 6 Flops */
}
const matrix box,
gmx_wallcycle* wcycle)
{
- wallcycle_start(wcycle, ewcVSITESPREAD);
+ wallcycle_start(wcycle, WallCycleCounter::VsiteSpread);
const bool useDomdec = domainInfo_.useDomdec();
/* This is wasting some CPU time as we now do this multiple times
* per MD step.
*/
- pbc_null = set_pbc_dd(&pbc, domainInfo_.pbcType_,
- useDomdec ? domainInfo_.domdec_->numCells : nullptr, FALSE, box);
+ pbc_null = set_pbc_dd(
+ &pbc, domainInfo_.pbcType_, useDomdec ? domainInfo_.domdec_->numCells : nullptr, FALSE, box);
}
else
{
{
/* First spread the vsites that might depend on non-local vsites */
auto& nlDependentVSites = threadingInfo_.threadDataNonLocalDependent();
- spreadForceWrapper(x, f, virialHandling, fshift, nlDependentVSites.dxdf, true, iparams_,
- nlDependentVSites.ilist, pbc_null);
+ spreadForceWrapper(x,
+ f,
+ virialHandling,
+ fshift,
+ nlDependentVSites.dxdf,
+ true,
+ iparams_,
+ nlDependentVSites.ilist,
+ pbc_null);
#pragma omp parallel num_threads(numThreads)
{
{
fshift_t = tData.fshift;
- for (int i = 0; i < SHIFTS; i++)
+ for (int i = 0; i < c_numShiftVectors; i++)
{
clear_rvec(fshift_t[i]);
}
{
copy_rvec(f[idTask->vsite[i]], idTask->force[idTask->vsite[i]]);
}
- spreadForceWrapper(x, idTask->force, virialHandling, fshift_t, tData.dxdf, true,
- iparams_, tData.idTask.ilist, pbc_null);
+ spreadForceWrapper(x,
+ idTask->force,
+ virialHandling,
+ fshift_t,
+ tData.dxdf,
+ true,
+ iparams_,
+ tData.idTask.ilist,
+ pbc_null);
/* We need a barrier before reducing forces below
* that have been produced by a different thread above.
}
/* Spread the vsites that spread locally only */
- spreadForceWrapper(x, f, virialHandling, fshift_t, tData.dxdf, false, iparams_,
- tData.ilist, pbc_null);
+ spreadForceWrapper(
+ x, f, virialHandling, fshift_t, tData.dxdf, false, iparams_, tData.ilist, pbc_null);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
{
for (int th = 1; th < numThreads; th++)
{
- for (int i = 0; i < SHIFTS; i++)
+ for (int i = 0; i < c_numShiftVectors; i++)
{
rvec_inc(fshift[i], threadingInfo_.threadData(th).fshift[i]);
}
inc_nrnb(nrnb, eNR_VSITE4FDN, vsite_count(ilists_, F_VSITE4FDN));
inc_nrnb(nrnb, eNR_VSITEN, vsite_count(ilists_, F_VSITEN));
- wallcycle_stop(wcycle, ewcVSITESPREAD);
+ wallcycle_stop(wcycle, WallCycleCounter::VsiteSpread);
}
/*! \brief Returns the an array with group indices for each atom
}
int countInterUpdategroupVsites(const gmx_mtop_t& mtop,
- gmx::ArrayRef<const gmx::RangePartitioning> updateGroupingPerMoleculetype)
+ gmx::ArrayRef<const gmx::RangePartitioning> updateGroupingsPerMoleculeType)
{
int n_intercg_vsite = 0;
for (const gmx_molblock_t& molb : mtop.molblock)
const gmx_moltype_t& molt = mtop.moltype[molb.type];
std::vector<int> atomToGroup;
- if (!updateGroupingPerMoleculetype.empty())
+ if (!updateGroupingsPerMoleculeType.empty())
{
- atomToGroup = makeAtomToGroupMapping(updateGroupingPerMoleculetype[molb.type]);
+ atomToGroup = makeAtomToGroupMapping(updateGroupingsPerMoleculeType[molb.type]);
}
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
{
std::unique_ptr<VirtualSitesHandler> makeVirtualSitesHandler(const gmx_mtop_t& mtop,
const t_commrec* cr,
- PbcType pbcType)
+ PbcType pbcType,
+ ArrayRef<const RangePartitioning> updateGroupingPerMoleculeType)
{
GMX_RELEASE_ASSERT(cr != nullptr, "We need a valid commrec");
GMX_ASSERT(ftype >= c_ftypeVsiteStart && ftype < c_ftypeVsiteEnd,
"c_ftypeVsiteStart and/or c_ftypeVsiteEnd do not have correct values");
- nvsite += gmx_mtop_ftype_count(&mtop, ftype);
+ nvsite += gmx_mtop_ftype_count(mtop, ftype);
}
else
{
return vsite;
}
- return std::make_unique<VirtualSitesHandler>(mtop, cr->dd, pbcType);
+ return std::make_unique<VirtualSitesHandler>(mtop, cr->dd, pbcType, updateGroupingPerMoleculeType);
}
-ThreadingInfo::ThreadingInfo() : numThreads_(gmx_omp_nthreads_get(emntVSITE))
+ThreadingInfo::ThreadingInfo() : numThreads_(gmx_omp_nthreads_get(ModuleMultiThread::VirtualSite))
{
if (numThreads_ > 1)
{
}
}
-//! Returns the number of inter update-group vsites
-static int getNumInterUpdategroupVsites(const gmx_mtop_t& mtop, const gmx_domdec_t* domdec)
-{
- gmx::ArrayRef<const gmx::RangePartitioning> updateGroupingPerMoleculetype;
- if (domdec)
- {
- updateGroupingPerMoleculetype = getUpdateGroupingPerMoleculetype(*domdec);
- }
-
- return countInterUpdategroupVsites(mtop, updateGroupingPerMoleculetype);
-}
-
-VirtualSitesHandler::Impl::Impl(const gmx_mtop_t& mtop, gmx_domdec_t* domdec, const PbcType pbcType) :
- numInterUpdategroupVirtualSites_(getNumInterUpdategroupVsites(mtop, domdec)),
+VirtualSitesHandler::Impl::Impl(const gmx_mtop_t& mtop,
+ gmx_domdec_t* domdec,
+ const PbcType pbcType,
+ const ArrayRef<const RangePartitioning> updateGroupingPerMoleculeType) :
+ numInterUpdategroupVirtualSites_(countInterUpdategroupVsites(mtop, updateGroupingPerMoleculeType)),
domainInfo_({ pbcType, pbcType != PbcType::No && numInterUpdategroupVirtualSites_ > 0, domdec }),
iparams_(mtop.ffparams.iparams)
{
}
-VirtualSitesHandler::VirtualSitesHandler(const gmx_mtop_t& mtop, gmx_domdec_t* domdec, const PbcType pbcType) :
- impl_(new Impl(mtop, domdec, pbcType))
+VirtualSitesHandler::VirtualSitesHandler(const gmx_mtop_t& mtop,
+ gmx_domdec_t* domdec,
+ const PbcType pbcType,
+ const ArrayRef<const RangePartitioning> updateGroupingPerMoleculeType) :
+ impl_(new Impl(mtop, domdec, pbcType, updateGroupingPerMoleculeType))
{
}
gmx::ArrayRef<int> taskIndex,
ArrayRef<const InteractionList> ilist,
ArrayRef<const t_iparams> ip,
- const unsigned short* ptype)
+ ArrayRef<const ParticleType> ptype)
{
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
{
/* Do a range check to avoid a harmless race on taskIndex */
if (iat[j] < tData->rangeStart || iat[j] >= tData->rangeEnd || taskIndex[iat[j]] != thread)
{
- if (!tData->useInterdependentTask || ptype[iat[j]] == eptVSite)
+ if (!tData->useInterdependentTask || ptype[iat[j]] == ParticleType::VSite)
{
/* At least one constructing atom is a vsite
* that is not assigned to the same thread.
/* Do a range check to avoid a harmless race on taskIndex */
if (iat[j] < tData->rangeStart || iat[j] >= tData->rangeEnd || taskIndex[iat[j]] != thread)
{
- GMX_ASSERT(ptype[iat[j]] != eptVSite,
+ GMX_ASSERT(ptype[iat[j]] != ParticleType::VSite,
"A vsite to be assigned in assignVsitesToThread has a vsite as "
"a constructing atom that does not belong to our task, such "
"vsites should be assigned to the single 'master' task");
void ThreadingInfo::setVirtualSites(ArrayRef<const InteractionList> ilists,
ArrayRef<const t_iparams> iparams,
- const t_mdatoms& mdatoms,
+ const int numAtoms,
+ const int homenr,
+ ArrayRef<const ParticleType> ptype,
const bool useDomdec)
{
if (numThreads_ <= 1)
* When assigning vsites to threads, we should take care that the last
* threads also covers the non-local range.
*/
- vsite_atom_range = mdatoms.nr;
- natperthread = (mdatoms.homenr + numThreads_ - 1) / numThreads_;
+ vsite_atom_range = numAtoms;
+ natperthread = (homenr + numThreads_ - 1) / numThreads_;
}
if (debug)
{
- fprintf(debug, "virtual site thread dist: natoms %d, range %d, natperthread %d\n",
- mdatoms.nr, vsite_atom_range, natperthread);
+ fprintf(debug,
+ "virtual site thread dist: natoms %d, range %d, natperthread %d\n",
+ numAtoms,
+ vsite_atom_range,
+ natperthread);
}
/* To simplify the vsite assignment, we make an index which tells us
* to which task particles, both non-vsites and vsites, are assigned.
*/
- taskIndex_.resize(mdatoms.nr);
+ taskIndex_.resize(numAtoms);
/* Initialize the task index array. Here we assign the non-vsite
* particles to task=thread, so we easily figure out if vsites
*/
{
int thread = 0;
- for (int i = 0; i < mdatoms.nr; i++)
+ for (int i = 0; i < numAtoms; i++)
{
- if (mdatoms.ptype[i] == eptVSite)
+ if (ptype[i] == ParticleType::VSite)
{
/* vsites are not assigned to a task yet */
taskIndex_[i] = -1;
else
{
/* The last thread should cover up to the end of the range */
- tData.rangeEnd = mdatoms.nr;
+ tData.rangeEnd = numAtoms;
}
- assignVsitesToThread(&tData, thread, numThreads_, natperthread, taskIndex_, ilists,
- iparams, mdatoms.ptype);
+ assignVsitesToThread(
+ &tData, thread, numThreads_, natperthread, taskIndex_, ilists, iparams, ptype);
if (tData.useInterdependentTask)
{
if (debug && numThreads_ > 1)
{
- fprintf(debug, "virtual site useInterdependentTask %d, nuse:\n",
+ fprintf(debug,
+ "virtual site useInterdependentTask %d, nuse:\n",
static_cast<int>(tData_[0]->useInterdependentTask));
for (int th = 0; th < numThreads_ + 1; th++)
{
fprintf(debug, "%-20s thread dist:", interaction_function[ftype].longname);
for (int th = 0; th < numThreads_ + 1; th++)
{
- fprintf(debug, " %4d %4d ", tData_[th]->ilist[ftype].size(),
+ fprintf(debug,
+ " %4d %4d ",
+ tData_[th]->ilist[ftype].size(),
tData_[th]->idTask.ilist[ftype].size());
}
fprintf(debug, "\n");
}
void VirtualSitesHandler::Impl::setVirtualSites(ArrayRef<const InteractionList> ilists,
- const t_mdatoms& mdatoms)
+ const int numAtoms,
+ const int homenr,
+ ArrayRef<const ParticleType> ptype)
{
ilists_ = ilists;
- threadingInfo_.setVirtualSites(ilists, iparams_, mdatoms, domainInfo_.useDomdec());
+ threadingInfo_.setVirtualSites(ilists, iparams_, numAtoms, homenr, ptype, domainInfo_.useDomdec());
}
-void VirtualSitesHandler::setVirtualSites(ArrayRef<const InteractionList> ilists, const t_mdatoms& mdatoms)
+void VirtualSitesHandler::setVirtualSites(ArrayRef<const InteractionList> ilists,
+ const int numAtoms,
+ const int homenr,
+ ArrayRef<const ParticleType> ptype)
{
- impl_->setVirtualSites(ilists, mdatoms);
+ impl_->setVirtualSites(ilists, numAtoms, homenr, ptype);
}
} // namespace gmx
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/idef.h"
-#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/real.h"
struct gmx_domdec_t;
struct gmx_mtop_t;
struct t_commrec;
struct InteractionList;
-struct t_mdatoms;
struct t_nrnb;
struct gmx_wallcycle;
enum class PbcType : int;
+enum class ParticleType : int;
namespace gmx
{
class RangePartitioning;
+template<typename T>
+class ArrayRef;
/*! \brief The start value of the vsite indices in the ftype enum
*
//! Type for storing PBC atom information for all vsite types in the system
typedef std::array<std::vector<int>, c_ftypeVsiteEnd - c_ftypeVsiteStart> VsitePbc;
+//! Whether we calculate vsite positions, velocities, or both
+enum class VSiteOperation
+{
+ Positions, //!< Calculate only positions
+ Velocities, //!< Calculate only velocities
+ PositionsAndVelocities, //!< Calculate both positions and velocities
+ Count //!< The number of entries
+};
+
/*! \libinternal
* \brief Class that handles construction of vsites and spreading of vsite forces
*/
{
public:
//! Constructor, used only be the makeVirtualSitesHandler() factory function
- VirtualSitesHandler(const gmx_mtop_t& mtop, gmx_domdec_t* domdec, PbcType pbcType);
+ VirtualSitesHandler(const gmx_mtop_t& mtop,
+ gmx_domdec_t* domdec,
+ PbcType pbcType,
+ ArrayRef<const RangePartitioning> updateGroupingPerMoleculeType);
~VirtualSitesHandler();
int numInterUpdategroupVirtualSites() const;
//! Set VSites and distribute VSite work over threads, should be called after each DD partitioning
- void setVirtualSites(ArrayRef<const InteractionList> ilist, const t_mdatoms& mdatoms);
+ void setVirtualSites(ArrayRef<const InteractionList> ilist,
+ int numAtoms,
+ int homenr,
+ ArrayRef<const ParticleType> ptype);
/*! \brief Create positions of vsite atoms based for the local system
*
- * \param[in,out] x The coordinates
- * \param[in] dt The time step
- * \param[in,out] v When not empty, velocities for vsites are set as displacement/dt
- * \param[in] box The box
+ * \param[in,out] x The coordinates
+ * \param[in,out] v The velocities, needed if operation requires it
+ * \param[in] box The box
+ * \param[in] operation Whether we calculate positions, velocities, or both
*/
- void construct(ArrayRef<RVec> x, real dt, ArrayRef<RVec> v, const matrix box) const;
+ void construct(ArrayRef<RVec> x, ArrayRef<RVec> v, const matrix box, VSiteOperation operation) const;
//! Tells how to handle virial contributions due to virtual sites
enum class VirialHandling : int
//! Implementation type.
class Impl;
//! Implementation object.
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
/*! \brief Create positions of vsite atoms based for the local system
/*! \brief Return the number of virtual sites that cross update groups
*
* \param[in] mtop The global topology
- * \param[in] updateGroupingPerMoleculetype Update grouping per molecule type, pass empty when not using update groups
+ * \param[in] updateGroupingsPerMoleculeType Update grouping per molecule type, pass empty when not using update groups
*/
int countInterUpdategroupVsites(const gmx_mtop_t& mtop,
- ArrayRef<const RangePartitioning> updateGroupingPerMoleculetype);
+ ArrayRef<const RangePartitioning> updateGroupingsPerMoleculeType);
/*! \brief Create the virtual site handler
*
- * \param[in] mtop The global topology
- * \param[in] cr The communication record
- * \param[in] pbcType The type of PBC
+ * \param[in] mtop The global topology
+ * \param[in] cr The communication record
+ * \param[in] pbcType The type of PBC
+ * \param[in] updateGroupingPerMoleculeType Update grouping per molecule type, pass
+ * empty when not using update groups
* \returns A valid vsite handler object or nullptr when there are no virtual sites
*/
-std::unique_ptr<VirtualSitesHandler> makeVirtualSitesHandler(const gmx_mtop_t& mtop,
- const t_commrec* cr,
- PbcType pbcType);
+std::unique_ptr<VirtualSitesHandler>
+makeVirtualSitesHandler(const gmx_mtop_t& mtop,
+ const t_commrec* cr,
+ PbcType pbcType,
+ ArrayRef<const RangePartitioning> updateGroupingPerMoleculeType);
} // namespace gmx
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/filetypes.h"
#include "gromacs/gmxlib/nrnb.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/forceoutput.h"
#include "gromacs/utility/smalloc.h"
void make_wall_tables(FILE* fplog,
- const t_inputrec* ir,
+ const t_inputrec& ir,
const char* tabfn,
const SimulationGroups* groups,
t_forcerec* fr)
int negp_pp;
char buf[STRLEN];
- negp_pp = ir->opts.ngener - ir->nwall;
+ negp_pp = ir.opts.ngener - ir.nwall;
gmx::ArrayRef<const int> nm_ind = groups->groups[SimulationAtomGroupType::EnergyOutput];
if (fplog)
{
- fprintf(fplog, "Reading user tables for %d energy groups with %d walls\n", negp_pp, ir->nwall);
+ fprintf(fplog, "Reading user tables for %d energy groups with %d walls\n", negp_pp, ir.nwall);
}
- snew(fr->wall_tab, ir->nwall);
- for (int w = 0; w < ir->nwall; w++)
+ fr->wall_tab.resize(ir.nwall);
+ for (int w = 0; w < ir.nwall; w++)
{
- snew(fr->wall_tab[w], negp_pp);
+ fr->wall_tab[w].resize(negp_pp);
for (int egp = 0; egp < negp_pp; egp++)
{
/* If the energy group pair is excluded, we don't need a table */
- if (!(fr->egp_flags[egp * ir->opts.ngener + negp_pp + w] & EGP_EXCL))
+ if (!(fr->egp_flags[egp * ir.opts.ngener + negp_pp + w] & EGP_EXCL))
{
sprintf(buf, "%s", tabfn);
- sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
- *groups->groupNames[nm_ind[egp]], *groups->groupNames[nm_ind[negp_pp + w]],
+ sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1,
+ "_%s_%s.%s",
+ *groups->groupNames[nm_ind[egp]],
+ *groups->groupNames[nm_ind[negp_pp + w]],
ftp2ext(efXVG));
- fr->wall_tab[w][egp] = make_tables(fplog, fr->ic, buf, 0, GMX_MAKETABLES_FORCEUSER);
+ fr->wall_tab[w][egp] = make_tables(fplog, fr->ic.get(), buf, 0, GMX_MAKETABLES_FORCEUSER);
/* Since wall have no charge, we can compress the table */
for (int i = 0; i <= fr->wall_tab[w][egp]->n; i++)
gmx_fatal(FARGS,
"An atom is beyond the wall: coordinates %f %f %f, distance %f\n"
"You might want to use the mdp option wall_r_linpot",
- x[a][XX], x[a][YY], x[a][ZZ], r);
+ x[a][XX],
+ x[a][YY],
+ x[a][ZZ],
+ r);
}
static void tableForce(real r, const t_forcetable& tab, real Cd, real Cr, real* V, real* F)
}
}
-real do_walls(const t_inputrec& ir,
- const t_forcerec& fr,
- const matrix box,
- const t_mdatoms& md,
- gmx::ArrayRef<const gmx::RVec> x,
- gmx::ForceWithVirial* forceWithVirial,
- real lambda,
- real Vlj[],
- t_nrnb* nrnb)
+real do_walls(const t_inputrec& ir,
+ const t_forcerec& fr,
+ const matrix box,
+ gmx::ArrayRef<const int> typeA,
+ gmx::ArrayRef<const int> typeB,
+ gmx::ArrayRef<const unsigned short> cENER,
+ const int homenr,
+ const int numPerturbedAtoms,
+ gmx::ArrayRef<const gmx::RVec> x,
+ gmx::ForceWithVirial* forceWithVirial,
+ real lambda,
+ gmx::ArrayRef<real> Vlj,
+ t_nrnb* nrnb)
{
constexpr real sixth = 1.0 / 6.0;
constexpr real twelfth = 1.0 / 12.0;
- int ntw[2];
- real fac_d[2], fac_r[2];
- const unsigned short* gid = md.cENER;
+ int ntw[2];
+ real fac_d[2], fac_r[2];
const int nwall = ir.nwall;
const int ngid = ir.opts.ngener;
ntw[w] = 2 * ntype * ir.wall_atomtype[w];
switch (ir.wall_type)
{
- case ewt93:
+ case WallType::NineThree:
fac_d[w] = ir.wall_density[w] * M_PI / 6;
fac_r[w] = ir.wall_density[w] * M_PI / 45;
break;
- case ewt104:
+ case WallType::TenFour:
fac_d[w] = ir.wall_density[w] * M_PI / 2;
fac_r[w] = ir.wall_density[w] * M_PI / 5;
break;
real dvdlambda = 0;
double sumRF = 0;
- for (int lam = 0; lam < (md.nPerturbed ? 2 : 1); lam++)
+ for (int lam = 0; lam < (numPerturbedAtoms ? 2 : 1); lam++)
{
- real lamfac;
- const int* type;
- if (md.nPerturbed)
+ real lamfac;
+ gmx::ArrayRef<const int> type;
+ if (numPerturbedAtoms != 0)
{
if (lam == 0)
{
lamfac = 1 - lambda;
- type = md.typeA;
+ type = typeA;
}
else
{
lamfac = lambda;
- type = md.typeB;
+ type = typeB;
}
}
else
{
lamfac = 1;
- type = md.typeA;
+ type = typeA;
}
real Vlambda = 0;
- for (int i = 0; i < md.homenr; i++)
+ for (int i = 0; i < homenr; i++)
{
for (int w = 0; w < std::min(nwall, 2); w++)
{
/* The wall energy groups are always at the end of the list */
- const int ggid = gid[i] * ngid + ngid - nwall + w;
+ const int ggid = cENER[i] * ngid + ngid - nwall + w;
const int at = type[i];
/* nbfp now includes the 6/12 derivative prefactors */
const real Cd = nbfp[ntw[w] + 2 * at] * sixth;
real r1, r2, r4, Vd, Vr;
switch (ir.wall_type)
{
- case ewtTABLE:
- tableForce(r, *fr.wall_tab[w][gid[i]], Cd, Cr, &V, &F);
+ case WallType::Table:
+ tableForce(r, *fr.wall_tab[w][cENER[i]], Cd, Cr, &V, &F);
F *= lamfac;
break;
- case ewt93:
+ case WallType::NineThree:
r1 = 1 / r;
r2 = r1 * r1;
r4 = r2 * r2;
V = Vr - Vd;
F = lamfac * (9 * Vr - 3 * Vd) * r1;
break;
- case ewt104:
+ case WallType::TenFour:
r1 = 1 / r;
r2 = r1 * r1;
r4 = r2 * r2;
V = Vr - Vd;
F = lamfac * (10 * Vr - 4 * Vd) * r1;
break;
- case ewt126:
+ case WallType::TwelveSix:
r1 = 1 / r;
r2 = r1 * r1;
r4 = r2 * r2;
}
}
}
- if (md.nPerturbed)
+ if (numPerturbedAtoms != 0)
{
dvdlambda += (lam == 0 ? -1 : 1) * Vlambda;
}
- inc_nrnb(nrnb, eNR_WALLS, md.homenr);
+ inc_nrnb(nrnb, eNR_WALLS, homenr);
}
if (forceWithVirial->computeVirial_)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
} // namespace gmx
void make_wall_tables(FILE* fplog,
- const t_inputrec* ir,
+ const t_inputrec& ir,
const char* tabfn,
const SimulationGroups* groups,
t_forcerec* fr);
-real do_walls(const t_inputrec& ir,
- const t_forcerec& fr,
- const matrix box,
- const t_mdatoms& md,
- gmx::ArrayRef<const gmx::RVec> x,
- gmx::ForceWithVirial* forceWithVirial,
- real lambda,
- real Vlj[],
- t_nrnb* nrnb);
+real do_walls(const t_inputrec& ir,
+ const t_forcerec& fr,
+ const matrix box,
+ gmx::ArrayRef<const int> typeA,
+ gmx::ArrayRef<const int> typeB,
+ gmx::ArrayRef<const unsigned short> cENER,
+ int homenr,
+ int numPerturbedAtoms,
+ gmx::ArrayRef<const gmx::RVec> x,
+ gmx::ForceWithVirial* forceWithVirial,
+ real lambda,
+ gmx::ArrayRef<real> Vlj,
+ t_nrnb* nrnb);
#endif
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+add_library(mdrun INTERFACE)
gmx_add_libgromacs_sources(
legacymdrunoptions.cpp
legacysimulator.cpp
tpi.cpp
)
+# Source files have the following private module dependencies.
+target_link_libraries(mdrun PRIVATE
+# gmxlib
+# math
+# mdtypes
+# tng_io
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(mdrun PUBLIC
+target_include_directories(mdrun INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(mdrun PUBLIC
+target_link_libraries(mdrun INTERFACE
+ legacy_api
+ )
+
+# TODO: when mdrun is an OBJECT target
+#target_link_libraries(mdrun PUBLIC legacy_api)
+#target_link_libraries(mdrun PRIVATE common)
+
+# Module dependencies
+# mdrun interfaces convey transitive dependence on these modules.
+#target_link_libraries(mdrun PUBLIC
+target_link_libraries(mdrun INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(mdrun PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(mdrun PRIVATE legacy_modules)
+
# TODO: Find a home for this header and a scheme for installation.
# This header straddles the installed libraries and is a transitive interface
# from libgromacs to libgmxapi to libgmxapi clients. Near term efforts are
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdlib/stophandler.h"
class energyhistory_t;
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
struct gmx_enerdata_t;
struct gmx_enfrot;
struct gmx_mtop_t;
class Constraints;
class MdrunScheduleWorkload;
class IMDOutputProvider;
-struct MdModulesNotifier;
+struct MDModulesNotifiers;
class ImdSession;
class MDLogger;
class MDAtoms;
gmx_enfrot* enforcedRotation,
BoxDeformation* deform,
IMDOutputProvider* outputProvider,
- const MdModulesNotifier& mdModulesNotifier,
+ const MDModulesNotifiers& mdModulesNotifiers,
t_inputrec* inputrec,
ImdSession* imdSession,
pull_t* pull_work,
t_swap* swap,
- gmx_mtop_t* top_global,
+ const gmx_mtop_t& top_global,
t_state* state_global,
ObservablesHistory* observablesHistory,
MDAtoms* mdAtoms,
enforcedRotation(enforcedRotation),
deform(deform),
outputProvider(outputProvider),
- mdModulesNotifier(mdModulesNotifier),
+ mdModulesNotifiers(mdModulesNotifiers),
inputrec(inputrec),
imdSession(imdSession),
pull_work(pull_work),
BoxDeformation* deform;
//! Handles writing output files.
IMDOutputProvider* outputProvider;
- //! Handles notifications to MdModules for checkpoint writing
- const MdModulesNotifier& mdModulesNotifier;
- //! Contains user input mdp options.
- t_inputrec* inputrec;
+ //! Handles notifications to MDModules for checkpoint writing
+ const MDModulesNotifiers& mdModulesNotifiers;
+ //! Contains user input mdp options. Note: The const-ness is casted away in a few instances, see #3854.
+ const t_inputrec* inputrec;
//! The Interactive Molecular Dynamics session.
ImdSession* imdSession;
//! The pull work object.
//! The coordinate-swapping session.
t_swap* swap;
//! Full system topology.
- const gmx_mtop_t* top_global;
+ const gmx_mtop_t& top_global;
//! Full simulation state (only non-nullptr on master rank).
t_state* state_global;
//! History of simulation observables.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011-2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2011-2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
PCA_Flags |= PCA_DISABLE_INPUT_FILE_CHECKING;
}
- if (!parse_common_args(&argc, argv, PCA_Flags, ssize(filenames), filenames.data(), asize(pa),
- pa, ssize(desc), desc.data(), 0, nullptr, &oenv))
+ if (!parse_common_args(&argc,
+ argv,
+ PCA_Flags,
+ ssize(filenames),
+ filenames.data(),
+ asize(pa),
+ pa,
+ ssize(desc),
+ desc.data(),
+ 0,
+ nullptr,
+ &oenv))
{
return 0;
}
// fix that by changing the parsing, once more of the roles of
// handling, validating and implementing defaults for user
// command-line options have been seperated.
- hw_opt.gpuIdsAvailable = gpuIdsAvailable;
+ hw_opt.devicesSelectedByUser = devicesSelectedByUser;
hw_opt.userGpuTaskAssignment = userGpuTaskAssignment;
const char* env = getenv("GMX_GPU_ID");
if (env != nullptr)
{
- if (!hw_opt.gpuIdsAvailable.empty())
+ if (!hw_opt.devicesSelectedByUser.empty())
{
gmx_fatal(FARGS, "GMX_GPU_ID and -gpu_id can not be used at the same time");
}
- hw_opt.gpuIdsAvailable = env;
+ hw_opt.devicesSelectedByUser = env;
}
env = getenv("GMX_GPUTASKS");
hw_opt.userGpuTaskAssignment = env;
}
- if (!hw_opt.gpuIdsAvailable.empty() && !hw_opt.userGpuTaskAssignment.empty())
+ if (!hw_opt.devicesSelectedByUser.empty() && !hw_opt.userGpuTaskAssignment.empty())
{
gmx_fatal(FARGS, "-gpu_id and -gputasks cannot be used at the same time");
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011-2020, by the GROMACS development team, led by
+ * Copyright (c) 2011-2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*! \brief Command line options, defaults, docs and storage for them to fill. */
/*! \{ */
- rvec realddxyz = { 0, 0, 0 };
- const char* ddrank_opt_choices[static_cast<int>(DdRankOrder::Count) + 1] = {
- nullptr, "interleave", "pp_pme", "cartesian", nullptr
- };
- const char* dddlb_opt_choices[static_cast<int>(DlbOption::Count) + 1] = { nullptr, "auto", "no",
- "yes", nullptr };
- const char* thread_aff_opt_choices[static_cast<int>(ThreadAffinity::Count) + 1] = {
- nullptr, "auto", "on", "off", nullptr
- };
+ rvec realddxyz = { 0, 0, 0 };
+ const char* ddrank_opt_choices[static_cast<int>(DdRankOrder::Count) + 1] = { nullptr,
+ "interleave",
+ "pp_pme",
+ "cartesian",
+ nullptr };
+ const char* dddlb_opt_choices[static_cast<int>(DlbOption::Count) + 1] = { nullptr,
+ "auto",
+ "no",
+ "yes",
+ nullptr };
+ const char* thread_aff_opt_choices[static_cast<int>(ThreadAffinity::Count) + 1] = { nullptr,
+ "auto",
+ "on",
+ "off",
+ nullptr };
const char* nbpu_opt_choices[5] = { nullptr, "auto", "cpu", "gpu", nullptr };
const char* pme_opt_choices[5] = { nullptr, "auto", "cpu", "gpu", nullptr };
const char* pme_fft_opt_choices[5] = { nullptr, "auto", "cpu", "gpu", nullptr };
const char* bonded_opt_choices[5] = { nullptr, "auto", "cpu", "gpu", nullptr };
const char* update_opt_choices[5] = { nullptr, "auto", "cpu", "gpu", nullptr };
- const char* gpuIdsAvailable = "";
+ const char* devicesSelectedByUser = "";
const char* userGpuTaskAssignment = "";
{ "-gpu_id",
FALSE,
etSTR,
- { &gpuIdsAvailable },
+ { &devicesSelectedByUser },
"List of unique GPU device IDs available to use" },
{ "-gputasks",
FALSE,
{ "-ddcheck",
FALSE,
etBOOL,
- { &domdecOptions.checkBondedInteractions },
+ { &domdecOptions.ddBondedChecking },
"Check for all bonded interactions with DD" },
{ "-ddbondcomm",
FALSE,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
switch (inputrec->eI)
{
- case eiMD:
- case eiBD:
- case eiSD1:
- case eiVV:
- case eiVVAK:
+ case IntegrationAlgorithm::MD:
+ case IntegrationAlgorithm::BD:
+ case IntegrationAlgorithm::SD1:
+ case IntegrationAlgorithm::VV:
+ case IntegrationAlgorithm::VVAK:
if (!EI_DYNAMICS(inputrec->eI))
{
GMX_THROW(APIError(
do_md();
}
break;
- case eiMimic:
+ case IntegrationAlgorithm::Mimic:
if (doRerun)
{
do_rerun();
do_mimic();
}
break;
- case eiSteep: do_steep(); break;
- case eiCG: do_cg(); break;
- case eiNM: do_nm(); break;
- case eiLBFGS: do_lbfgs(); break;
- case eiTPI:
- case eiTPIC:
+ case IntegrationAlgorithm::Steep: do_steep(); break;
+ case IntegrationAlgorithm::CG: do_cg(); break;
+ case IntegrationAlgorithm::NM: do_nm(); break;
+ case IntegrationAlgorithm::LBFGS: do_lbfgs(); break;
+ case IntegrationAlgorithm::TPI:
+ case IntegrationAlgorithm::TPIC:
if (!EI_TPI(inputrec->eI))
{
GMX_THROW(APIError("do_tpi integrator would be called for a non-TPI integrator"));
}
do_tpi();
break;
- case eiSD2_REMOVED: GMX_THROW(NotImplementedError("SD2 integrator has been removed"));
+ case IntegrationAlgorithm::SD2Removed:
+ GMX_THROW(NotImplementedError("SD2 integrator has been removed"));
default: GMX_THROW(APIError("Non existing integrator selected"));
}
}
#include <numeric>
#include "gromacs/applied_forces/awh/awh.h"
+#include "gromacs/applied_forces/awh/read_params.h"
#include "gromacs/commandline/filenm.h"
#include "gromacs/domdec/collect.h"
#include "gromacs/domdec/dlbtiming.h"
#include "gromacs/mdlib/trajectory_writing.h"
#include "gromacs/mdlib/update.h"
#include "gromacs/mdlib/update_constrain_gpu.h"
+#include "gromacs/mdlib/update_vv.h"
#include "gromacs/mdlib/vcm.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdrunutility/handlerestart.h"
// alias to avoid a large ripple of nearly useless changes.
// t_inputrec is being replaced by IMdpOptionsProvider, so this
// will go away eventually.
- t_inputrec* ir = inputrec;
+ const t_inputrec* ir = inputrec;
+
int64_t step, step_rel;
double t, t0 = ir->init_t;
gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEnerStep, bCalcEner;
gmx_global_stat_t gstat;
gmx_shellfc_t* shellfc;
gmx_bool bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
- gmx_bool bTemp, bPres, bTrotter;
+ gmx_bool bTrotter;
real dvdl_constr;
std::vector<RVec> cbuf;
matrix lastbox;
bool bInteractiveMDstep = false;
- /* Domain decomposition could incorrectly miss a bonded
- interaction, but checking for that requires a global
- communication stage, which does not otherwise happen in DD
- code. So we do that alongside the first global energy reduction
- after a new DD is made. These variables handle whether the
- check happens, and the result it returns. */
- bool shouldCheckNumberOfBondedInteractions = false;
- int totalNumberOfBondedInteractions = -1;
-
SimulationSignals signals;
// Most global communnication stages don't propagate mdrun
// signals, and will use this object to achieve that.
int nstglobalcomm = computeGlobalCommunicationPeriod(mdlog, ir, cr);
bGStatEveryStep = (nstglobalcomm == 1);
- const SimulationGroups* groups = &top_global->groups;
+ const SimulationGroups* groups = &top_global.groups;
std::unique_ptr<EssentialDynamics> ed = nullptr;
if (opt2bSet("-ei", nfile, fnm))
{
/* Initialize essential dynamics sampling */
- ed = init_edsam(mdlog, opt2fn_null("-ei", nfile, fnm), opt2fn("-eo", nfile, fnm), top_global,
- ir, cr, constr, state_global, observablesHistory, oenv, startingBehavior);
+ ed = init_edsam(mdlog,
+ opt2fn_null("-ei", nfile, fnm),
+ opt2fn("-eo", nfile, fnm),
+ top_global,
+ *ir,
+ cr,
+ constr,
+ state_global,
+ observablesHistory,
+ oenv,
+ startingBehavior);
}
else if (observablesHistory->edsamHistory)
{
int* fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
gmx::ArrayRef<real> lambda = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
- initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
- Update upd(*ir, deform);
- const bool doSimulatedAnnealing = initSimulatedAnnealing(ir, &upd);
- const bool useReplicaExchange = (replExParams.exchangeInterval > 0);
+ initialize_lambdas(fplog,
+ ir->efep,
+ ir->bSimTemp,
+ *ir->fepvals,
+ ir->simtempvals->temperatures,
+ gmx::arrayRefFromArray(ir->opts.ref_t, ir->opts.ngtc),
+ MASTER(cr),
+ fep_state,
+ lambda);
+ Update upd(*ir, deform);
+ bool doSimulatedAnnealing = false;
+ {
+ // TODO: Avoid changing inputrec (#3854)
+ // Simulated annealing updates the reference temperature.
+ auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
+ doSimulatedAnnealing = initSimulatedAnnealing(nonConstInputrec, &upd);
+ }
+ const bool useReplicaExchange = (replExParams.exchangeInterval > 0);
const t_fcdata& fcdata = *fr->fcdata;
{
// TODO This implementation of ensemble orientation restraints is nasty because
// a user can't just do multi-sim with single-sim orientation restraints.
- bool usingEnsembleRestraints =
- (fcdata.disres->nsystems > 1) || ((ms != nullptr) && (fcdata.orires->nr != 0));
- bool awhUsesMultiSim = (ir->bDoAwh && ir->awhParams->shareBiasMultisim && (ms != nullptr));
+ bool usingEnsembleRestraints = (fcdata.disres->nsystems > 1) || ((ms != nullptr) && fcdata.orires);
+ bool awhUsesMultiSim = (ir->bDoAwh && ir->awhParams->shareBiasMultisim() && (ms != nullptr));
// Replica exchange, ensemble restraints and AWH need all
// simulations to remain synchronized, so they need
{
pleaseCiteCouplingAlgorithms(fplog, *ir);
}
- gmx_mdoutf* outf =
- init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, mdModulesNotifier, ir,
- top_global, oenv, wcycle, startingBehavior, simulationsShareState, ms);
- gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work,
- mdoutf_get_fp_dhdl(outf), false, startingBehavior,
- simulationsShareState, mdModulesNotifier);
+ gmx_mdoutf* outf = init_mdoutf(fplog,
+ nfile,
+ fnm,
+ mdrunOptions,
+ cr,
+ outputProvider,
+ mdModulesNotifiers,
+ ir,
+ top_global,
+ oenv,
+ wcycle,
+ startingBehavior,
+ simulationsShareState,
+ ms);
+ gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
+ top_global,
+ *ir,
+ pull_work,
+ mdoutf_get_fp_dhdl(outf),
+ false,
+ startingBehavior,
+ simulationsShareState,
+ mdModulesNotifiers);
gstat = global_stat_init(ir);
const bool useGpuForUpdate = simulationWork.useGpuUpdate;
/* Check for polarizable models and flexible constraints */
- shellfc = init_shell_flexcon(fplog, top_global, constr ? constr->numFlexibleConstraints() : 0,
- ir->nstcalcenergy, DOMAINDECOMP(cr), useGpuForPme);
+ shellfc = init_shell_flexcon(fplog,
+ top_global,
+ constr ? constr->numFlexibleConstraints() : 0,
+ ir->nstcalcenergy,
+ DOMAINDECOMP(cr),
+ useGpuForPme);
{
- double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
+ double io = compute_io(ir, top_global.natoms, *groups, energyOutput.numEnergyTerms(), 1);
if ((io > 2000) && MASTER(cr))
{
fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
std::unique_ptr<t_state> stateInstance;
t_state* state;
- gmx_localtop_t top(top_global->ffparams);
+ gmx_localtop_t top(top_global.ffparams);
- auto mdatoms = mdAtoms->mdatoms();
-
- ForceBuffers f(fr->useMts, ((useGpuForNonbonded && useGpuForBufferOps) || useGpuForUpdate)
- ? PinningPolicy::PinnedIfSupported
- : PinningPolicy::CannotBePinned);
+ ForceBuffers f(fr->useMts,
+ ((useGpuForNonbonded && useGpuForBufferOps) || useGpuForUpdate)
+ ? PinningPolicy::PinnedIfSupported
+ : PinningPolicy::CannotBePinned);
+ const t_mdatoms* md = mdAtoms->mdatoms();
if (DOMAINDECOMP(cr))
{
stateInstance = std::make_unique<t_state>();
state = stateInstance.get();
- dd_init_local_state(cr->dd, state_global, state);
+ dd_init_local_state(*cr->dd, state_global, state);
/* Distribute the charge groups over the nodes from the master node */
- dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1, state_global, *top_global, ir,
- imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
- nrnb, nullptr, FALSE);
- shouldCheckNumberOfBondedInteractions = true;
- upd.setNumAtoms(state->natoms);
+ dd_partition_system(fplog,
+ mdlog,
+ ir->init_step,
+ cr,
+ TRUE,
+ 1,
+ state_global,
+ top_global,
+ *ir,
+ imdSession,
+ pull_work,
+ state,
+ &f,
+ mdAtoms,
+ &top,
+ fr,
+ vsite,
+ constr,
+ nrnb,
+ nullptr,
+ FALSE);
+ upd.updateAfterPartition(state->natoms,
+ md->cFREEZE ? gmx::arrayRefFromArray(md->cFREEZE, md->nr)
+ : gmx::ArrayRef<const unsigned short>(),
+ md->cTC ? gmx::arrayRefFromArray(md->cTC, md->nr)
+ : gmx::ArrayRef<const unsigned short>());
}
else
{
state = state_global;
/* Generate and initialize new topology */
- mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
+ mdAlgorithmsSetupAtomData(cr, *ir, top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
- upd.setNumAtoms(state->natoms);
+ upd.updateAfterPartition(state->natoms,
+ md->cFREEZE ? gmx::arrayRefFromArray(md->cFREEZE, md->nr)
+ : gmx::ArrayRef<const unsigned short>(),
+ md->cTC ? gmx::arrayRefFromArray(md->cTC, md->nr)
+ : gmx::ArrayRef<const unsigned short>());
}
std::unique_ptr<UpdateConstrainGpu> integrator;
|| constr->numConstraintsTotal() == 0,
"Constraints in domain decomposition are only supported with update "
"groups if using GPU update.\n");
- GMX_RELEASE_ASSERT(ir->eConstrAlg != econtSHAKE || constr == nullptr
+ GMX_RELEASE_ASSERT(ir->eConstrAlg != ConstraintAlgorithm::Shake || constr == nullptr
|| constr->numConstraintsTotal() == 0,
"SHAKE is not supported with GPU update.");
GMX_RELEASE_ASSERT(useGpuForPme || (useGpuForNonbonded && simulationWork.useGpuBufferOps),
"Either PME or short-ranged non-bonded interaction tasks must run on "
"the GPU to use GPU update.\n");
- GMX_RELEASE_ASSERT(ir->eI == eiMD,
+ GMX_RELEASE_ASSERT(ir->eI == IntegrationAlgorithm::MD,
"Only the md integrator is supported with the GPU update.\n");
GMX_RELEASE_ASSERT(
- ir->etc != etcNOSEHOOVER,
+ ir->etc != TemperatureCoupling::NoseHoover,
"Nose-Hoover temperature coupling is not supported with the GPU update.\n");
GMX_RELEASE_ASSERT(
- ir->epc == epcNO || ir->epc == epcPARRINELLORAHMAN || ir->epc == epcBERENDSEN
- || ir->epc == epcCRESCALE,
+ ir->epc == PressureCoupling::No || ir->epc == PressureCoupling::ParrinelloRahman
+ || ir->epc == PressureCoupling::Berendsen || ir->epc == PressureCoupling::CRescale,
"Only Parrinello-Rahman, Berendsen, and C-rescale pressure coupling are supported "
"with the GPU update.\n");
- GMX_RELEASE_ASSERT(!mdatoms->haveVsites,
+ GMX_RELEASE_ASSERT(!md->haveVsites,
"Virtual sites are not supported with the GPU update.\n");
GMX_RELEASE_ASSERT(ed == nullptr,
"Essential dynamics is not supported with the GPU update.\n");
GMX_RELEASE_ASSERT(!ir->bPull || !pull_have_constraint(*ir->pull),
"Constraints pulling is not supported with the GPU update.\n");
- GMX_RELEASE_ASSERT(fcdata.orires->nr == 0,
+ GMX_RELEASE_ASSERT(fcdata.orires == nullptr,
"Orientation restraints are not supported with the GPU update.\n");
GMX_RELEASE_ASSERT(
- ir->efep == efepNO
- || (!haveFepPerturbedMasses(*top_global) && !havePerturbedConstraints(*top_global)),
+ ir->efep == FreeEnergyPerturbationType::No
+ || (!haveFepPerturbedMasses(top_global) && !havePerturbedConstraints(top_global)),
"Free energy perturbation of masses and constraints are not supported with the GPU "
"update.");
"Update stream should be initialized in order to use GPU "
"update-constraints.");
integrator = std::make_unique<UpdateConstrainGpu>(
- *ir, *top_global, fr->deviceStreamManager->context(),
+ *ir,
+ top_global,
+ ekind->ngtc,
+ fr->deviceStreamManager->context(),
fr->deviceStreamManager->stream(gmx::DeviceStreamType::UpdateAndConstraints),
- stateGpu->xUpdatedOnDevice(), wcycle);
+ stateGpu->xUpdatedOnDevice(),
+ wcycle);
integrator->setPbc(PbcType::Xyz, state->box);
}
// the global state to file and potentially for replica exchange.
// (Global topology should persist.)
- update_mdatoms(mdatoms, state->lambda[efptMASS]);
+ update_mdatoms(mdAtoms->mdatoms(), state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
if (ir->bExpanded)
{
EnergyData::initializeEnergyHistory(startingBehavior, observablesHistory, &energyOutput);
}
- preparePrevStepPullCom(ir, pull_work, mdatoms->massT, state, state_global, cr,
+ preparePrevStepPullCom(ir,
+ pull_work,
+ gmx::arrayRefFromArray(md->massT, md->nr),
+ state,
+ state_global,
+ cr,
startingBehavior != StartingBehavior::NewSimulation);
// TODO: Remove this by converting AWH into a ForceProvider
- auto awh = prepareAwhModule(fplog, *ir, state_global, cr, ms,
+ auto awh = prepareAwhModule(fplog,
+ *ir,
+ state_global,
+ cr,
+ ms,
startingBehavior != StartingBehavior::NewSimulation,
- shellfc != nullptr, opt2fn("-awh", nfile, fnm), pull_work);
+ shellfc != nullptr,
+ opt2fn("-awh", nfile, fnm),
+ pull_work);
if (useReplicaExchange && MASTER(cr))
{
- repl_ex = init_replica_exchange(fplog, ms, top_global->natoms, ir, replExParams);
+ repl_ex = init_replica_exchange(fplog, ms, top_global.natoms, ir, replExParams);
}
/* PME tuning is only supported in the Verlet scheme, with PME for
* Coulomb. It is not supported with only LJ PME. */
bPMETune = (mdrunOptions.tunePme && EEL_PME(fr->ic->eeltype) && !mdrunOptions.reproducible
- && ir->cutoff_scheme != ecutsGROUP);
+ && ir->cutoff_scheme != CutoffScheme::Group);
pme_load_balancing_t* pme_loadbal = nullptr;
if (bPMETune)
{
- pme_loadbal_init(&pme_loadbal, cr, mdlog, *ir, state->box, *fr->ic, *fr->nbv, fr->pmedata,
- fr->nbv->useGpu());
+ pme_loadbal_init(
+ &pme_loadbal, cr, mdlog, *ir, state->box, *fr->ic, *fr->nbv, fr->pmedata, fr->nbv->useGpu());
}
if (!ir->bContinuation)
{
- if (state->flags & (1U << estV))
+ if (state->flags & enumValueToBitMask(StateEntry::V))
{
auto v = makeArrayRef(state->v);
/* Set the velocities of vsites, shells and frozen atoms to zero */
- for (i = 0; i < mdatoms->homenr; i++)
+ for (i = 0; i < md->homenr; i++)
{
- if (mdatoms->ptype[i] == eptVSite || mdatoms->ptype[i] == eptShell)
+ if (md->ptype[i] == ParticleType::Shell)
{
clear_rvec(v[i]);
}
- else if (mdatoms->cFREEZE)
+ else if (md->cFREEZE)
{
for (m = 0; m < DIM; m++)
{
- if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
+ if (ir->opts.nFreeze[md->cFREEZE[i]][m])
{
v[i][m] = 0;
}
if (constr)
{
/* Constrain the initial coordinates and velocities */
- do_constrain_first(fplog, constr, ir, mdatoms->nr, mdatoms->homenr,
- state->x.arrayRefWithPadding(), state->v.arrayRefWithPadding(),
- state->box, state->lambda[efptBONDED]);
- }
- if (vsite)
- {
- /* Construct the virtual sites for the initial configuration */
- vsite->construct(state->x, ir->delta_t, {}, state->box);
+ do_constrain_first(fplog,
+ constr,
+ ir,
+ md->nr,
+ md->homenr,
+ state->x.arrayRefWithPadding(),
+ state->v.arrayRefWithPadding(),
+ state->box,
+ state->lambda[FreeEnergyPerturbationCouplingType::Bonded]);
}
}
- if (ir->efep != efepNO)
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
/* Set free energy calculation frequency as the greatest common
* denominator of nstdhdl and repl_ex_nst. */
}
if (ir->bDoAwh)
{
- nstfep = std::gcd(ir->awhParams->nstSampleCoord, nstfep);
+ nstfep = std::gcd(ir->awhParams->nstSampleCoord(), nstfep);
}
}
* this is the first step, since we might be restarting from a checkpoint,
* and in that case we should not do any modifications to the state.
*/
- bStopCM = (ir->comm_mode != ecmNO && !ir->bContinuation);
+ bStopCM = (ir->comm_mode != ComRemovalAlgorithm::No && !ir->bContinuation);
// When restarting from a checkpoint, it can be appropriate to
// initialize ekind from quantities in the checkpoint. Otherwise,
bSumEkinhOld = FALSE;
- t_vcm vcm(top_global->groups, *ir);
+ t_vcm vcm(top_global.groups, *ir);
reportComRemovalInfo(fplog, vcm);
/* To minimize communication, compute_globals computes the COM velocity
cglo_flags_iteration |= CGLO_STOPCM;
cglo_flags_iteration &= ~CGLO_TEMPERATURE;
}
- compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
- makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, nullptr,
- enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
- state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
- cglo_flags_iteration
- | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
- : 0));
+ if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd) && cgloIteration == 0)
+ {
+ cglo_flags_iteration |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
+ }
+ compute_globals(gstat,
+ cr,
+ ir,
+ fr,
+ ekind,
+ makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v),
+ state->box,
+ md,
+ nrnb,
+ &vcm,
+ nullptr,
+ enerd,
+ force_vir,
+ shake_vir,
+ total_vir,
+ pres,
+ gmx::ArrayRef<real>{},
+ &nullSignaller,
+ state->box,
+ &bSumEkinhOld,
+ cglo_flags_iteration);
if (cglo_flags_iteration & CGLO_STOPCM)
{
/* At initialization, do not pass x with acceleration-correction mode
* to avoid (incorrect) correction of the initial coordinates.
*/
- auto x = (vcm.mode == ecmLINEAR_ACCELERATION_CORRECTION) ? ArrayRef<RVec>()
- : makeArrayRef(state->x);
- process_and_stopcm_grp(fplog, &vcm, *mdatoms, x, makeArrayRef(state->v));
- inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
+ auto x = (vcm.mode == ComRemovalAlgorithm::LinearAccelerationCorrection)
+ ? ArrayRef<RVec>()
+ : makeArrayRef(state->x);
+ process_and_stopcm_grp(fplog, &vcm, *md, x, makeArrayRef(state->v));
+ inc_nrnb(nrnb, eNR_STOPCM, md->homenr);
}
}
- checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
- makeConstArrayRef(state->x), state->box,
- &shouldCheckNumberOfBondedInteractions);
- if (ir->eI == eiVVAK)
+ if (DOMAINDECOMP(cr))
+ {
+ checkNumberOfBondedInteractions(
+ mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
+ }
+ if (ir->eI == IntegrationAlgorithm::VVAK)
{
/* a second call to get the half step temperature initialized as well */
/* we do the same call as above, but turn the pressure off -- internally to
kinetic energy calculation. This minimized excess variables, but
perhaps loses some logic?*/
- compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
- makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, nullptr,
- enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
- state->box, nullptr, &bSumEkinhOld, cglo_flags & ~CGLO_PRESSURE);
+ compute_globals(gstat,
+ cr,
+ ir,
+ fr,
+ ekind,
+ makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v),
+ state->box,
+ md,
+ nrnb,
+ &vcm,
+ nullptr,
+ enerd,
+ force_vir,
+ shake_vir,
+ total_vir,
+ pres,
+ gmx::ArrayRef<real>{},
+ &nullSignaller,
+ state->box,
+ &bSumEkinhOld,
+ cglo_flags & ~CGLO_PRESSURE);
}
/* Calculate the initial half step temperature, and save the ekinh_old */
{
if (!ir->bContinuation)
{
- if (constr && ir->eConstrAlg == econtLINCS)
+ if (constr && ir->eConstrAlg == ConstraintAlgorithm::Lincs)
{
- fprintf(fplog, "RMS relative constraint deviation after constraining: %.2e\n",
+ fprintf(fplog,
+ "RMS relative constraint deviation after constraining: %.2e\n",
constr->rmsd());
}
if (EI_STATE_VELOCITY(ir->eI))
{
real temp = enerd->term[F_TEMP];
- if (ir->eI != eiVV)
+ if (ir->eI != IntegrationAlgorithm::VV)
{
/* Result of Ekin averaged over velocities of -half
* and +half step, while we only have -half step here.
}
char tbuf[20];
- fprintf(stderr, "starting mdrun '%s'\n", *(top_global->name));
+ fprintf(stderr, "starting mdrun '%s'\n", *(top_global.name));
if (ir->nsteps >= 0)
{
sprintf(tbuf, "%8.1f", (ir->init_step + ir->nsteps) * ir->delta_t);
}
if (ir->init_step > 0)
{
- fprintf(stderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
- gmx_step_str(ir->init_step + ir->nsteps, sbuf), tbuf,
- gmx_step_str(ir->init_step, sbuf2), ir->init_step * ir->delta_t);
+ fprintf(stderr,
+ "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
+ gmx_step_str(ir->init_step + ir->nsteps, sbuf),
+ tbuf,
+ gmx_step_str(ir->init_step, sbuf2),
+ ir->init_step * ir->delta_t);
}
else
{
}
walltime_accounting_start_time(walltime_accounting);
- wallcycle_start(wcycle, ewcRUN);
+ wallcycle_start(wcycle, WallCycleCounter::Run);
print_start(fplog, cr, walltime_accounting, "mdrun");
/***********************************************************
step_rel = 0;
auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
- compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), simulationsShareState,
- MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstSignalComm,
- mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
+ compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
+ simulationsShareState,
+ MASTER(cr),
+ ir->nstlist,
+ mdrunOptions.reproducible,
+ nstSignalComm,
+ mdrunOptions.maximumHoursToRun,
+ ir->nstlist == 0,
+ fplog,
+ step,
+ bNS,
+ walltime_accounting);
auto checkpointHandler = std::make_unique<CheckpointHandler>(
- compat::make_not_null<SimulationSignal*>(&signals[eglsCHKPT]), simulationsShareState,
- ir->nstlist == 0, MASTER(cr), mdrunOptions.writeConfout,
+ compat::make_not_null<SimulationSignal*>(&signals[eglsCHKPT]),
+ simulationsShareState,
+ ir->nstlist == 0,
+ MASTER(cr),
+ mdrunOptions.writeConfout,
mdrunOptions.checkpointOptions.period);
const bool resetCountersIsLocal = true;
auto resetHandler = std::make_unique<ResetHandler>(
compat::make_not_null<SimulationSignal*>(&signals[eglsRESETCOUNTERS]),
- !resetCountersIsLocal, ir->nsteps, MASTER(cr), mdrunOptions.timingOptions.resetHalfway,
- mdrunOptions.maximumHoursToRun, mdlog, wcycle, walltime_accounting);
+ !resetCountersIsLocal,
+ ir->nsteps,
+ MASTER(cr),
+ mdrunOptions.timingOptions.resetHalfway,
+ mdrunOptions.maximumHoursToRun,
+ mdlog,
+ wcycle,
+ walltime_accounting);
const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
}
/* PME grid + cut-off optimization with GPUs or PME nodes */
- pme_loadbal_do(pme_loadbal, cr, (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
- fplog, mdlog, *ir, fr, state->box, state->x, wcycle, step, step_rel,
- &bPMETunePrinting, simulationWork.useGpuPmePpCommunication);
- }
-
- wallcycle_start(wcycle, ewcSTEP);
+ pme_loadbal_do(pme_loadbal,
+ cr,
+ (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
+ fplog,
+ mdlog,
+ *ir,
+ fr,
+ state->box,
+ state->x,
+ wcycle,
+ step,
+ step_rel,
+ &bPMETunePrinting,
+ simulationWork.useGpuPmePpCommunication);
+ }
+
+ wallcycle_start(wcycle, WallCycleCounter::Step);
bLastStep = (step_rel == ir->nsteps);
t = t0 + step * ir->delta_t;
// TODO Refactor this, so that nstfep does not need a default value of zero
- if (ir->efep != efepNO || ir->bSimTemp)
+ if (ir->efep != FreeEnergyPerturbationType::No || ir->bSimTemp)
{
/* find and set the current lambdas */
state->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
- bDoDHDL = do_per_step(step, ir->fepvals->nstdhdl);
- bDoFEP = ((ir->efep != efepNO) && do_per_step(step, nstfep));
+ bDoDHDL = do_per_step(step, ir->fepvals->nstdhdl);
+ bDoFEP = ((ir->efep != FreeEnergyPerturbationType::No) && do_per_step(step, nstfep));
bDoExpanded = (do_per_step(step, ir->expandedvals->nstexpanded) && (ir->bExpanded)
&& (!bFirstStep));
}
if (doSimulatedAnnealing)
{
- update_annealing_target_temp(ir, t, &upd);
+ // TODO: Avoid changing inputrec (#3854)
+ // Simulated annealing updates the reference temperature.
+ auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
+ update_annealing_target_temp(nonConstInputrec, t, &upd);
}
/* Stop Center of Mass motion */
- bStopCM = (ir->comm_mode != ecmNO && do_per_step(step, ir->nstcomm));
+ bStopCM = (ir->comm_mode != ComRemovalAlgorithm::No && do_per_step(step, ir->nstcomm));
/* Determine whether or not to do Neighbour Searching */
bNS = (bFirstStep || bNStList || bExchanged || bNeedRepartition);
stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
}
+ // We only need to calculate virtual velocities if we are writing them in the current step
+ const bool needVirtualVelocitiesThisStep =
+ (vsite != nullptr)
+ && (do_per_step(step, ir->nstvout) || checkpointHandler->isCheckpointingStep());
+
+ if (vsite != nullptr)
+ {
+ // Virtual sites need to be updated before domain decomposition and forces are calculated
+ wallcycle_start(wcycle, WallCycleCounter::VsiteConstr);
+ // md-vv calculates virtual velocities once it has full-step real velocities
+ vsite->construct(state->x,
+ state->v,
+ state->box,
+ (!EI_VV(inputrec->eI) && needVirtualVelocitiesThisStep)
+ ? VSiteOperation::PositionsAndVelocities
+ : VSiteOperation::Positions);
+ wallcycle_stop(wcycle, WallCycleCounter::VsiteConstr);
+ }
+
if (bNS && !(bFirstStep && ir->bContinuation))
{
bMasterState = FALSE;
if (DOMAINDECOMP(cr))
{
/* Repartition the domain decomposition */
- dd_partition_system(fplog, mdlog, step, cr, bMasterState, nstglobalcomm, state_global,
- *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top,
- fr, vsite, constr, nrnb, wcycle, do_verbose && !bPMETunePrinting);
- shouldCheckNumberOfBondedInteractions = true;
- upd.setNumAtoms(state->natoms);
+ dd_partition_system(fplog,
+ mdlog,
+ step,
+ cr,
+ bMasterState,
+ nstglobalcomm,
+ state_global,
+ top_global,
+ *ir,
+ imdSession,
+ pull_work,
+ state,
+ &f,
+ mdAtoms,
+ &top,
+ fr,
+ vsite,
+ constr,
+ nrnb,
+ wcycle,
+ do_verbose && !bPMETunePrinting);
+ upd.updateAfterPartition(state->natoms,
+ md->cFREEZE ? gmx::arrayRefFromArray(md->cFREEZE, md->nr)
+ : gmx::ArrayRef<const unsigned short>(),
+ md->cTC ? gmx::arrayRefFromArray(md->cTC, md->nr)
+ : gmx::ArrayRef<const unsigned short>());
}
}
if (MASTER(cr) && do_log)
{
- gmx::EnergyOutput::printHeader(fplog, step,
- t); /* can we improve the information printed here? */
+ gmx::EnergyOutput::printHeader(
+ fplog, step, t); /* can we improve the information printed here? */
}
- if (ir->efep != efepNO)
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
- update_mdatoms(mdatoms, state->lambda[efptMASS]);
+ update_mdatoms(mdAtoms->mdatoms(), state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
}
if (bExchanged)
{
-
/* We need the kinetic energy at minus the half step for determining
* the full step kinetic energy and possibly for T-coupling.*/
/* This may not be quite working correctly yet . . . . */
- compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
- makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
- enerd, nullptr, nullptr, nullptr, nullptr, constr, &nullSignaller,
- state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
- CGLO_GSTAT | CGLO_TEMPERATURE | CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS);
- checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
- &top, makeConstArrayRef(state->x), state->box,
- &shouldCheckNumberOfBondedInteractions);
+ int cglo_flags = CGLO_GSTAT | CGLO_TEMPERATURE;
+ if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
+ {
+ cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
+ }
+ compute_globals(gstat,
+ cr,
+ ir,
+ fr,
+ ekind,
+ makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v),
+ state->box,
+ md,
+ nrnb,
+ &vcm,
+ wcycle,
+ enerd,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ gmx::ArrayRef<real>{},
+ &nullSignaller,
+ state->box,
+ &bSumEkinhOld,
+ cglo_flags);
+ if (DOMAINDECOMP(cr))
+ {
+ checkNumberOfBondedInteractions(
+ mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
+ }
}
clear_mat(force_vir);
{
bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
bCalcVir = bCalcEnerStep
- || (ir->epc != epcNO
+ || (ir->epc != PressureCoupling::No
&& (do_per_step(step, ir->nstpcouple) || do_per_step(step - 1, ir->nstpcouple)));
}
else
{
bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
- bCalcVir = bCalcEnerStep || (ir->epc != epcNO && do_per_step(step, ir->nstpcouple));
+ bCalcVir = bCalcEnerStep
+ || (ir->epc != PressureCoupling::No && do_per_step(step, ir->nstpcouple));
}
bCalcEner = bCalcEnerStep;
if (shellfc)
{
/* Now is the time to relax the shells */
- relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
- imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
- state->natoms, state->x.arrayRefWithPadding(),
- state->v.arrayRefWithPadding(), state->box, state->lambda,
- &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
- fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
+ relax_shell_flexcon(fplog,
+ cr,
+ ms,
+ mdrunOptions.verbose,
+ enforcedRotation,
+ step,
+ ir,
+ imdSession,
+ pull_work,
+ bNS,
+ force_flags,
+ &top,
+ constr,
+ enerd,
+ state->natoms,
+ state->x.arrayRefWithPadding(),
+ state->v.arrayRefWithPadding(),
+ state->box,
+ state->lambda,
+ &state->hist,
+ &f.view(),
+ force_vir,
+ *md,
+ nrnb,
+ wcycle,
+ shellfc,
+ fr,
+ runScheduleWork,
+ t,
+ mu_tot,
+ vsite,
+ ddBalanceRegionHandler);
}
else
{
* This is parallellized as well, and does communication too.
* Check comments in sim_util.c
*/
- do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step,
- nrnb, wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
- &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
- vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
- (bNS ? GMX_FORCE_NS : 0) | force_flags, ddBalanceRegionHandler);
+ do_force(fplog,
+ cr,
+ ms,
+ *ir,
+ awh.get(),
+ enforcedRotation,
+ imdSession,
+ pull_work,
+ step,
+ nrnb,
+ wcycle,
+ &top,
+ state->box,
+ state->x.arrayRefWithPadding(),
+ &state->hist,
+ &f.view(),
+ force_vir,
+ md,
+ enerd,
+ state->lambda,
+ fr,
+ runScheduleWork,
+ vsite,
+ mu_tot,
+ t,
+ ed ? ed->getLegacyED() : nullptr,
+ (bNS ? GMX_FORCE_NS : 0) | force_flags,
+ ddBalanceRegionHandler);
}
// VV integrators do not need the following velocity half step
// if it is the first step after starting from a checkpoint.
// That is, the half step is needed on all other steps, and
// also the first step when starting from a .tpr file.
- if (EI_VV(ir->eI) && (!bFirstStep || startingBehavior == StartingBehavior::NewSimulation))
- /* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
- {
- rvec* vbuf = nullptr;
-
- wallcycle_start(wcycle, ewcUPDATE);
- if (ir->eI == eiVV && bInitStep)
- {
- /* if using velocity verlet with full time step Ekin,
- * take the first half step only to compute the
- * virial for the first step. From there,
- * revert back to the initial coordinates
- * so that the input is actually the initial step.
- */
- snew(vbuf, state->natoms);
- copy_rvecn(state->v.rvec_array(), vbuf, 0,
- state->natoms); /* should make this better for parallelizing? */
- }
- else
- {
- /* this is for NHC in the Ekin(t+dt/2) version of vv */
- trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ,
- trotter_seq, ettTSEQ1);
- }
-
- upd.update_coords(*ir, step, mdatoms, state, f.view().forceWithPadding(), fcdata, ekind,
- M, etrtVELOCITY1, cr, constr != nullptr);
-
- wallcycle_stop(wcycle, ewcUPDATE);
- constrain_velocities(constr, do_log, do_ene, step, state, nullptr, bCalcVir, shake_vir);
- wallcycle_start(wcycle, ewcUPDATE);
- /* if VV, compute the pressure and constraints */
- /* For VV2, we strictly only need this if using pressure
- * control, but we really would like to have accurate pressures
- * printed out.
- * Think about ways around this in the future?
- * For now, keep this choice in comments.
- */
- /*bPres = (ir->eI==eiVV || inputrecNptTrotter(ir)); */
- /*bTemp = ((ir->eI==eiVV &&(!bInitStep)) || (ir->eI==eiVVAK && inputrecNptTrotter(ir)));*/
- bPres = TRUE;
- bTemp = ((ir->eI == eiVV && (!bInitStep)) || (ir->eI == eiVVAK));
- if (bCalcEner && ir->eI == eiVVAK)
- {
- bSumEkinhOld = TRUE;
- }
- /* for vv, the first half of the integration actually corresponds to the previous step.
- So we need information from the last step in the first half of the integration */
- if (bGStat || do_per_step(step - 1, nstglobalcomm))
- {
- wallcycle_stop(wcycle, ewcUPDATE);
- compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
- makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
- enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
- state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
- (bGStat ? CGLO_GSTAT : 0) | (bCalcEner ? CGLO_ENERGY : 0)
- | (bTemp ? CGLO_TEMPERATURE : 0) | (bPres ? CGLO_PRESSURE : 0)
- | (bPres ? CGLO_CONSTRAINT : 0) | (bStopCM ? CGLO_STOPCM : 0)
- | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
- : 0)
- | CGLO_SCALEEKIN);
- /* explanation of above:
- a) We compute Ekin at the full time step
- if 1) we are using the AveVel Ekin, and it's not the
- initial step, or 2) if we are using AveEkin, but need the full
- time step kinetic energy for the pressure (always true now, since we want accurate statistics).
- b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
- EkinAveVel because it's needed for the pressure */
- checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
- top_global, &top, makeConstArrayRef(state->x),
- state->box, &shouldCheckNumberOfBondedInteractions);
- if (bStopCM)
- {
- process_and_stopcm_grp(fplog, &vcm, *mdatoms, makeArrayRef(state->x),
- makeArrayRef(state->v));
- inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
- }
- wallcycle_start(wcycle, ewcUPDATE);
- }
- /* temperature scaling and pressure scaling to produce the extended variables at t+dt */
- if (!bInitStep)
- {
- if (bTrotter)
- {
- m_add(force_vir, shake_vir,
- total_vir); /* we need the un-dispersion corrected total vir here */
- trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ,
- trotter_seq, ettTSEQ2);
-
- /* TODO This is only needed when we're about to write
- * a checkpoint, because we use it after the restart
- * (in a kludge?). But what should we be doing if
- * the startingBehavior is NewSimulation or bInitStep are true? */
- if (inputrecNptTrotter(ir) || inputrecNphTrotter(ir))
- {
- copy_mat(shake_vir, state->svir_prev);
- copy_mat(force_vir, state->fvir_prev);
- }
- if ((inputrecNptTrotter(ir) || inputrecNvtTrotter(ir)) && ir->eI == eiVV)
- {
- /* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
- enerd->term[F_TEMP] =
- sum_ekin(&(ir->opts), ekind, nullptr, (ir->eI == eiVV), FALSE);
- enerd->term[F_EKIN] = trace(ekind->ekin);
- }
- }
- else if (bExchanged)
- {
- wallcycle_stop(wcycle, ewcUPDATE);
- /* We need the kinetic energy at minus the half step for determining
- * the full step kinetic energy and possibly for T-coupling.*/
- /* This may not be quite working correctly yet . . . . */
- compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
- makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
- enerd, nullptr, nullptr, nullptr, nullptr, constr, &nullSignaller,
- state->box, nullptr, &bSumEkinhOld, CGLO_GSTAT | CGLO_TEMPERATURE);
- wallcycle_start(wcycle, ewcUPDATE);
- }
- }
- /* if it's the initial step, we performed this first step just to get the constraint virial */
- if (ir->eI == eiVV && bInitStep)
- {
- copy_rvecn(vbuf, state->v.rvec_array(), 0, state->natoms);
- sfree(vbuf);
- }
- wallcycle_stop(wcycle, ewcUPDATE);
- }
-
- /* compute the conserved quantity */
if (EI_VV(ir->eI))
{
- saved_conserved_quantity = NPT_energy(ir, state, &MassQ);
- if (ir->eI == eiVV)
+ integrateVVFirstStep(step,
+ bFirstStep,
+ bInitStep,
+ startingBehavior,
+ nstglobalcomm,
+ ir,
+ fr,
+ cr,
+ state,
+ mdAtoms->mdatoms(),
+ fcdata,
+ &MassQ,
+ &vcm,
+ top_global,
+ top,
+ enerd,
+ ekind,
+ gstat,
+ &last_ekin,
+ bCalcVir,
+ total_vir,
+ shake_vir,
+ force_vir,
+ pres,
+ M,
+ do_log,
+ do_ene,
+ bCalcEner,
+ bGStat,
+ bStopCM,
+ bTrotter,
+ bExchanged,
+ &bSumEkinhOld,
+ &saved_conserved_quantity,
+ &f,
+ &upd,
+ constr,
+ &nullSignaller,
+ trotter_seq,
+ nrnb,
+ mdlog,
+ fplog,
+ wcycle);
+ if (vsite != nullptr && needVirtualVelocitiesThisStep)
{
- last_ekin = enerd->term[F_EKIN];
- }
- if ((ir->eDispCorr != edispcEnerPres) && (ir->eDispCorr != edispcAllEnerPres))
- {
- saved_conserved_quantity -= enerd->term[F_DISPCORR];
- }
- /* sum up the foreign kinetic energy and dK/dl terms for vv. currently done every step so that dhdl is correct in the .edr */
- if (ir->efep != efepNO)
- {
- accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
+ // Positions were calculated earlier
+ wallcycle_start(wcycle, WallCycleCounter::VsiteConstr);
+ vsite->construct(state->x, state->v, state->box, VSiteOperation::Velocities);
+ wallcycle_stop(wcycle, WallCycleCounter::VsiteConstr);
}
}
actually move to the new state before outputting
statistics, but if performing simulated tempering, we
do update the velocities and the tau_t. */
-
- lamnew = ExpandedEnsembleDynamics(fplog, ir, enerd, state, &MassQ, state->fep_state,
- state->dfhist, step, state->v.rvec_array(), mdatoms);
+ // TODO: Avoid changing inputrec (#3854)
+ // Simulated tempering updates the reference temperature.
+ // Expanded ensemble without simulated tempering does not change the inputrec.
+ auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
+ lamnew = ExpandedEnsembleDynamics(fplog,
+ nonConstInputrec,
+ enerd,
+ state,
+ &MassQ,
+ state->fep_state,
+ state->dfhist,
+ step,
+ state->v.rvec_array(),
+ md->homenr,
+ md->cTC ? gmx::arrayRefFromArray(md->cTC, md->nr)
+ : gmx::ArrayRef<const unsigned short>());
/* history is maintained in state->dfhist, but state_global is what is sent to trajectory and log output */
if (MASTER(cr))
{
* coordinates at time t. We must output all of this before
* the update.
*/
- do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state, state_global,
- observablesHistory, top_global, fr, outf, energyOutput, ekind,
- f.view().force(), checkpointHandler->isCheckpointingStep(),
- bRerunMD, bLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
+ do_md_trajectory_writing(fplog,
+ cr,
+ nfile,
+ fnm,
+ step,
+ step_rel,
+ t,
+ ir,
+ state,
+ state_global,
+ observablesHistory,
+ top_global,
+ fr,
+ outf,
+ energyOutput,
+ ekind,
+ f.view().force(),
+ checkpointHandler->isCheckpointingStep(),
+ bRerunMD,
+ bLastStep,
+ mdrunOptions.writeConfout,
+ bSumEkinhOld);
/* Check if IMD step and do IMD communication, if bIMD is TRUE. */
- bInteractiveMDstep = imdSession->run(step, bNS, state->box, state->x.rvec_array(), t);
+ bInteractiveMDstep = imdSession->run(step, bNS, state->box, state->x, t);
/* kludge -- virial is lost with restart for MTTK NPT control. Must reload (saved earlier). */
if (startingBehavior != StartingBehavior::NewSimulation && bFirstStep
if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
{
gmx_bool bIfRandomize;
- bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, &upd, constr);
+ bIfRandomize = update_randomize_velocities(ir,
+ step,
+ cr,
+ md->homenr,
+ md->cTC ? gmx::arrayRefFromArray(md->cTC, md->nr)
+ : gmx::ArrayRef<const unsigned short>(),
+ gmx::arrayRefFromArray(md->invmass, md->nr),
+ state->v,
+ &upd,
+ constr);
/* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
if (constr && bIfRandomize)
{
if (!useGpuForUpdate)
{
- wallcycle_start(wcycle, ewcUPDATE);
+ wallcycle_start(wcycle, WallCycleCounter::Update);
}
/* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
if (bTrotter)
{
- trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ3);
+ trotter_update(ir,
+ step,
+ ekind,
+ enerd,
+ state,
+ total_vir,
+ md->homenr,
+ md->cTC ? gmx::arrayRefFromArray(md->cTC, md->nr)
+ : gmx::ArrayRef<const unsigned short>(),
+ gmx::arrayRefFromArray(md->invmass, md->nr),
+ &MassQ,
+ trotter_seq,
+ ettTSEQ3);
/* We can only do Berendsen coupling after we have summed
* the kinetic energy or virial. Since the happens
* in global_state after update, we should only do it at
}
else
{
- update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
+ update_tcouple(step,
+ ir,
+ state,
+ ekind,
+ &MassQ,
+ md->homenr,
+ md->cTC ? gmx::arrayRefFromArray(md->cTC, md->nr)
+ : gmx::ArrayRef<const unsigned short>());
update_pcouple_before_coordinates(fplog, step, ir, state, pressureCouplingMu, M, bInitStep);
}
- if (EI_VV(ir->eI))
- {
- /* velocity half-step update */
- upd.update_coords(*ir, step, mdatoms, state, f.view().forceWithPadding(), fcdata, ekind,
- M, etrtVELOCITY2, cr, constr != nullptr);
- }
-
- /* Above, initialize just copies ekinh into ekin,
- * it doesn't copy position (for VV),
- * and entire integrator for MD.
- */
-
- if (ir->eI == eiVVAK)
- {
- cbuf.resize(state->x.size());
- std::copy(state->x.begin(), state->x.end(), cbuf.begin());
- }
-
/* With leap-frog type integrators we compute the kinetic energy
* at a whole time step as the average of the half-time step kinetic
* energies of two subsequent steps. Therefore we need to compute the
// Parrinello-Rahman requires the pressure to be availible before the update to compute
// the velocity scaling matrix. Hence, it runs one step after the nstpcouple step.
- const bool doParrinelloRahman = (ir->epc == epcPARRINELLORAHMAN
+ const bool doParrinelloRahman = (ir->epc == PressureCoupling::ParrinelloRahman
&& do_per_step(step + ir->nstpcouple - 1, ir->nstpcouple));
- if (useGpuForUpdate)
+ if (EI_VV(ir->eI))
{
- if (bNS && (bFirstStep || DOMAINDECOMP(cr)))
+ GMX_ASSERT(!useGpuForUpdate, "GPU update is not supported with VVAK integrator.");
+
+ integrateVVSecondStep(step,
+ ir,
+ fr,
+ cr,
+ state,
+ mdAtoms->mdatoms(),
+ fcdata,
+ &MassQ,
+ &vcm,
+ pull_work,
+ enerd,
+ ekind,
+ gstat,
+ &dvdl_constr,
+ bCalcVir,
+ total_vir,
+ shake_vir,
+ force_vir,
+ pres,
+ M,
+ lastbox,
+ do_log,
+ do_ene,
+ bGStat,
+ &bSumEkinhOld,
+ &f,
+ &cbuf,
+ &upd,
+ constr,
+ &nullSignaller,
+ trotter_seq,
+ nrnb,
+ wcycle);
+ }
+ else
+ {
+ if (useGpuForUpdate)
{
- integrator->set(stateGpu->getCoordinates(), stateGpu->getVelocities(),
- stateGpu->getForces(), top.idef, *mdatoms, ekind->ngtc);
+ if (bNS && (bFirstStep || DOMAINDECOMP(cr)))
+ {
+ integrator->set(stateGpu->getCoordinates(),
+ stateGpu->getVelocities(),
+ stateGpu->getForces(),
+ top.idef,
+ *md);
+
+ // Copy data to the GPU after buffers might have being reinitialized
+ stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
+ stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
+ }
- // Copy data to the GPU after buffers might have being reinitialized
- stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
- stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
- }
+ if (simulationWork.useGpuPme && !runScheduleWork->simulationWork.useGpuPmePpCommunication
+ && !thisRankHasDuty(cr, DUTY_PME))
+ {
+ // The PME forces were recieved to the host, so have to be copied
+ stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::All);
+ }
+ else if (!runScheduleWork->stepWork.useGpuFBufferOps)
+ {
+ // The buffer ops were not offloaded this step, so the forces are on the
+ // host and have to be copied
+ stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::Local);
+ }
- if (simulationWork.useGpuPme && !runScheduleWork->simulationWork.useGpuPmePpCommunication
- && !thisRankHasDuty(cr, DUTY_PME))
- {
- // The PME forces were recieved to the host, so have to be copied
- stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::All);
+ const bool doTemperatureScaling =
+ (ir->etc != TemperatureCoupling::No
+ && do_per_step(step + ir->nsttcouple - 1, ir->nsttcouple));
+
+ // This applies Leap-Frog, LINCS and SETTLE in succession
+ integrator->integrate(
+ stateGpu->getForcesReadyOnDeviceEvent(
+ AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
+ ir->delta_t,
+ true,
+ bCalcVir,
+ shake_vir,
+ doTemperatureScaling,
+ ekind->tcstat,
+ doParrinelloRahman,
+ ir->nstpcouple * ir->delta_t,
+ M);
+
+ // Copy velocities D2H after update if:
+ // - Globals are computed this step (includes the energy output steps).
+ // - Temperature is needed for the next step.
+ if (bGStat || needHalfStepKineticEnergy)
+ {
+ stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
+ stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
+ }
}
- else if (!runScheduleWork->stepWork.useGpuFBufferOps)
+ else
{
- // The buffer ops were not offloaded this step, so the forces are on the
- // host and have to be copied
- stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::Local);
- }
-
- const bool doTemperatureScaling =
- (ir->etc != etcNO && do_per_step(step + ir->nsttcouple - 1, ir->nsttcouple));
-
- // This applies Leap-Frog, LINCS and SETTLE in succession
- integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
- AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
- ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
- ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
+ /* With multiple time stepping we need to do an additional normal
+ * update step to obtain the virial, as the actual MTS integration
+ * using an acceleration where the slow forces are multiplied by mtsFactor.
+ * Using that acceleration would result in a virial with the slow
+ * force contribution would be a factor mtsFactor too large.
+ */
+ if (fr->useMts && bCalcVir && constr != nullptr)
+ {
+ upd.update_for_constraint_virial(*ir,
+ md->homenr,
+ md->havePartiallyFrozenAtoms,
+ gmx::arrayRefFromArray(md->invmass, md->nr),
+ gmx::arrayRefFromArray(md->invMassPerDim, md->nr),
+ *state,
+ f.view().forceWithPadding(),
+ *ekind);
+
+ constrain_coordinates(constr,
+ do_log,
+ do_ene,
+ step,
+ state,
+ upd.xp()->arrayRefWithPadding(),
+ &dvdl_constr,
+ bCalcVir,
+ shake_vir);
+ }
- // Copy velocities D2H after update if:
- // - Globals are computed this step (includes the energy output steps).
- // - Temperature is needed for the next step.
- if (bGStat || needHalfStepKineticEnergy)
- {
- stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
- stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
+ ArrayRefWithPadding<const RVec> forceCombined =
+ (fr->useMts && step % ir->mtsLevels[1].stepFactor == 0)
+ ? f.view().forceMtsCombinedWithPadding()
+ : f.view().forceWithPadding();
+ upd.update_coords(*ir,
+ step,
+ md->homenr,
+ md->havePartiallyFrozenAtoms,
+ gmx::arrayRefFromArray(md->ptype, md->nr),
+ gmx::arrayRefFromArray(md->invmass, md->nr),
+ gmx::arrayRefFromArray(md->invMassPerDim, md->nr),
+ state,
+ forceCombined,
+ fcdata,
+ ekind,
+ M,
+ etrtPOSITION,
+ cr,
+ constr != nullptr);
+
+ wallcycle_stop(wcycle, WallCycleCounter::Update);
+
+ constrain_coordinates(constr,
+ do_log,
+ do_ene,
+ step,
+ state,
+ upd.xp()->arrayRefWithPadding(),
+ &dvdl_constr,
+ bCalcVir && !fr->useMts,
+ shake_vir);
+
+ upd.update_sd_second_half(*ir,
+ step,
+ &dvdl_constr,
+ md->homenr,
+ gmx::arrayRefFromArray(md->ptype, md->nr),
+ gmx::arrayRefFromArray(md->invmass, md->nr),
+ state,
+ cr,
+ nrnb,
+ wcycle,
+ constr,
+ do_log,
+ do_ene);
+ upd.finish_update(
+ *ir, md->havePartiallyFrozenAtoms, md->homenr, state, wcycle, constr != nullptr);
}
- }
- else
- {
- /* With multiple time stepping we need to do an additional normal
- * update step to obtain the virial, as the actual MTS integration
- * using an acceleration where the slow forces are multiplied by mtsFactor.
- * Using that acceleration would result in a virial with the slow
- * force contribution would be a factor mtsFactor too large.
- */
- if (fr->useMts && bCalcVir && constr != nullptr)
- {
- upd.update_for_constraint_virial(*ir, *mdatoms, *state, f.view().forceWithPadding(), *ekind);
- constrain_coordinates(constr, do_log, do_ene, step, state,
- upd.xp()->arrayRefWithPadding(), &dvdl_constr, bCalcVir, shake_vir);
+ if (ir->bPull && ir->pull->bSetPbcRefToPrevStepCOM)
+ {
+ updatePrevStepPullCom(pull_work, state);
}
- ArrayRefWithPadding<const RVec> forceCombined =
- (fr->useMts && step % ir->mtsLevels[1].stepFactor == 0)
- ? f.view().forceMtsCombinedWithPadding()
- : f.view().forceWithPadding();
- upd.update_coords(*ir, step, mdatoms, state, forceCombined, fcdata, ekind, M,
- etrtPOSITION, cr, constr != nullptr);
-
- wallcycle_stop(wcycle, ewcUPDATE);
-
- constrain_coordinates(constr, do_log, do_ene, step, state, upd.xp()->arrayRefWithPadding(),
- &dvdl_constr, bCalcVir && !fr->useMts, shake_vir);
-
- upd.update_sd_second_half(*ir, step, &dvdl_constr, mdatoms, state, cr, nrnb, wcycle,
- constr, do_log, do_ene);
- upd.finish_update(*ir, mdatoms, state, wcycle, constr != nullptr);
- }
-
- if (ir->bPull && ir->pull->bSetPbcRefToPrevStepCOM)
- {
- updatePrevStepPullCom(pull_work, state);
- }
-
- if (ir->eI == eiVVAK)
- {
- /* erase F_EKIN and F_TEMP here? */
- /* just compute the kinetic energy at the half step to perform a trotter step */
- compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
- makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle, enerd,
- force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, lastbox,
- nullptr, &bSumEkinhOld, (bGStat ? CGLO_GSTAT : 0) | CGLO_TEMPERATURE);
- wallcycle_start(wcycle, ewcUPDATE);
- trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ4);
- /* now we know the scaling, we can compute the positions again */
- std::copy(cbuf.begin(), cbuf.end(), state->x.begin());
-
- upd.update_coords(*ir, step, mdatoms, state, f.view().forceWithPadding(), fcdata, ekind,
- M, etrtPOSITION, cr, constr != nullptr);
- wallcycle_stop(wcycle, ewcUPDATE);
-
- /* do we need an extra constraint here? just need to copy out of as_rvec_array(state->v.data()) to upd->xp? */
- /* are the small terms in the shake_vir here due
- * to numerical errors, or are they important
- * physically? I'm thinking they are just errors, but not completely sure.
- * For now, will call without actually constraining, constr=NULL*/
- upd.finish_update(*ir, mdatoms, state, wcycle, false);
- }
- if (EI_VV(ir->eI))
- {
- /* this factor or 2 correction is necessary
- because half of the constraint force is removed
- in the vv step, so we have to double it. See
- the Issue #1255. It is not yet clear
- if the factor of 2 is exact, or just a very
- good approximation, and this will be
- investigated. The next step is to see if this
- can be done adding a dhdl contribution from the
- rattle step, but this is somewhat more
- complicated with the current code. Will be
- investigated, hopefully for 4.6.3. However,
- this current solution is much better than
- having it completely wrong.
- */
- enerd->term[F_DVDL_CONSTR] += 2 * dvdl_constr;
- }
- else
- {
enerd->term[F_DVDL_CONSTR] += dvdl_constr;
}
- if (vsite != nullptr)
- {
- wallcycle_start(wcycle, ewcVSITECONSTR);
- vsite->construct(state->x, ir->delta_t, state->v, state->box);
- wallcycle_stop(wcycle, ewcVSITECONSTR);
- }
-
/* ############## IF NOT VV, Calculate globals HERE ############ */
/* With Leap-Frog we can skip compute_globals at
* non-communication steps, but we need to calculate
bool doIntraSimSignal = true;
SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
- compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
- makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm,
- wcycle, enerd, force_vir, shake_vir, total_vir, pres, constr,
- &signaller, lastbox, &totalNumberOfBondedInteractions, &bSumEkinhOld,
- (bGStat ? CGLO_GSTAT : 0) | (!EI_VV(ir->eI) && bCalcEner ? CGLO_ENERGY : 0)
- | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
- | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
- | (!EI_VV(ir->eI) ? CGLO_PRESSURE : 0) | CGLO_CONSTRAINT
- | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
- : 0));
- checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
- top_global, &top, makeConstArrayRef(state->x),
- state->box, &shouldCheckNumberOfBondedInteractions);
+ compute_globals(
+ gstat,
+ cr,
+ ir,
+ fr,
+ ekind,
+ makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v),
+ state->box,
+ md,
+ nrnb,
+ &vcm,
+ wcycle,
+ enerd,
+ force_vir,
+ shake_vir,
+ total_vir,
+ pres,
+ (!EI_VV(ir->eI) && bCalcEner && constr != nullptr) ? constr->rmsdData()
+ : gmx::ArrayRef<real>{},
+ &signaller,
+ lastbox,
+ &bSumEkinhOld,
+ (bGStat ? CGLO_GSTAT : 0) | (!EI_VV(ir->eI) && bCalcEner ? CGLO_ENERGY : 0)
+ | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
+ | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
+ | (!EI_VV(ir->eI) ? CGLO_PRESSURE : 0) | CGLO_CONSTRAINT
+ | (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd)
+ ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
+ : 0));
+ if (DOMAINDECOMP(cr))
+ {
+ checkNumberOfBondedInteractions(
+ mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
+ }
if (!EI_VV(ir->eI) && bStopCM)
{
- process_and_stopcm_grp(fplog, &vcm, *mdatoms, makeArrayRef(state->x),
- makeArrayRef(state->v));
- inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
+ process_and_stopcm_grp(
+ fplog, &vcm, *md, makeArrayRef(state->x), makeArrayRef(state->v));
+ inc_nrnb(nrnb, eNR_STOPCM, md->homenr);
// TODO: The special case of removing CM motion should be dealt more gracefully
if (useGpuForUpdate)
// (not because of a race on state->x being modified on the CPU while H2D is in progress).
stateGpu->waitCoordinatesCopiedToDevice(AtomLocality::Local);
// If the COM removal changed the velocities on the CPU, this has to be accounted for.
- if (vcm.mode != ecmNO)
+ if (vcm.mode != ComRemovalAlgorithm::No)
{
stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
}
but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
- if (ir->efep != efepNO && !EI_VV(ir->eI))
+ if (ir->efep != FreeEnergyPerturbationType::No && !EI_VV(ir->eI))
{
/* Sum up the foreign energy and dK/dl terms for md and sd.
Currently done every step so that dH/dl is correct in the .edr */
accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
}
- update_pcouple_after_coordinates(fplog, step, ir, mdatoms, pres, force_vir, shake_vir,
- pressureCouplingMu, state, nrnb, upd.deform(), !useGpuForUpdate);
-
- const bool doBerendsenPressureCoupling =
- (inputrec->epc == epcBERENDSEN && do_per_step(step, inputrec->nstpcouple));
- const bool doCRescalePressureCoupling =
- (inputrec->epc == epcCRESCALE && do_per_step(step, inputrec->nstpcouple));
+ update_pcouple_after_coordinates(fplog,
+ step,
+ ir,
+ md->homenr,
+ md->cFREEZE ? gmx::arrayRefFromArray(md->cFREEZE, md->nr)
+ : gmx::ArrayRef<const unsigned short>(),
+ pres,
+ force_vir,
+ shake_vir,
+ pressureCouplingMu,
+ state,
+ nrnb,
+ upd.deform(),
+ !useGpuForUpdate);
+
+ const bool doBerendsenPressureCoupling = (inputrec->epc == PressureCoupling::Berendsen
+ && do_per_step(step, inputrec->nstpcouple));
+ const bool doCRescalePressureCoupling = (inputrec->epc == PressureCoupling::CRescale
+ && do_per_step(step, inputrec->nstpcouple));
if (useGpuForUpdate
&& (doBerendsenPressureCoupling || doCRescalePressureCoupling || doParrinelloRahman))
{
/* ######### BEGIN PREPARING EDR OUTPUT ########### */
/* use the directly determined last velocity, not actually the averaged half steps */
- if (bTrotter && ir->eI == eiVV)
+ if (bTrotter && ir->eI == IntegrationAlgorithm::VV)
{
enerd->term[F_EKIN] = last_ekin;
}
if (fplog && do_log && bDoExpanded)
{
/* only needed if doing expanded ensemble */
- PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals,
- ir->bSimTemp ? ir->simtempvals : nullptr,
- state_global->dfhist, state->fep_state, ir->nstlog, step);
+ PrintFreeEnergyInfoToFile(fplog,
+ ir->fepvals.get(),
+ ir->expandedvals.get(),
+ ir->bSimTemp ? ir->simtempvals.get() : nullptr,
+ state_global->dfhist,
+ state->fep_state,
+ ir->nstlog,
+ step);
}
if (bCalcEner)
{
- energyOutput.addDataAtEnergyStep(
- bDoDHDL, bCalcEnerStep, t, mdatoms->tmass, enerd, ir->fepvals,
- ir->expandedvals, lastbox,
- PTCouplingArrays{ state->boxv, state->nosehoover_xi, state->nosehoover_vxi,
- state->nhpres_xi, state->nhpres_vxi },
- state->fep_state, shake_vir, force_vir, total_vir, pres, ekind, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(bDoDHDL,
+ bCalcEnerStep,
+ t,
+ md->tmass,
+ enerd,
+ ir->fepvals.get(),
+ ir->expandedvals.get(),
+ lastbox,
+ PTCouplingArrays{ state->boxv,
+ state->nosehoover_xi,
+ state->nosehoover_vxi,
+ state->nhpres_xi,
+ state->nhpres_vxi },
+ state->fep_state,
+ shake_vir,
+ force_vir,
+ total_vir,
+ pres,
+ ekind,
+ mu_tot,
+ constr);
}
else
{
if (doSimulatedAnnealing)
{
- gmx::EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups,
- &(ir->opts));
+ gmx::EnergyOutput::printAnnealingTemperatures(
+ do_log ? fplog : nullptr, groups, &(ir->opts));
}
if (do_log || do_ene || do_dr || do_or)
{
- energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
- do_log ? fplog : nullptr, step, t,
- fr->fcdata.get(), awh.get());
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
+ do_ene,
+ do_dr,
+ do_or,
+ do_log ? fplog : nullptr,
+ step,
+ t,
+ fr->fcdata.get(),
+ awh.get());
}
if (do_log && ir->bDoAwh && awh->hasFepLambdaDimension())
{
* Not done in last step since trajectory writing happens before this call
* in the MD loop and exchanges would be lost anyway. */
bNeedRepartition = FALSE;
- if ((ir->eSwapCoords != eswapNO) && (step > 0) && !bLastStep && do_per_step(step, ir->swap->nstswap))
- {
- bNeedRepartition =
- do_swapcoords(cr, step, t, ir, swap, wcycle, as_rvec_array(state->x.data()),
- state->box, MASTER(cr) && mdrunOptions.verbose, bRerunMD);
+ if ((ir->eSwapCoords != SwapType::No) && (step > 0) && !bLastStep
+ && do_per_step(step, ir->swap->nstswap))
+ {
+ bNeedRepartition = do_swapcoords(cr,
+ step,
+ t,
+ ir,
+ swap,
+ wcycle,
+ as_rvec_array(state->x.data()),
+ state->box,
+ MASTER(cr) && mdrunOptions.verbose,
+ bRerunMD);
if (bNeedRepartition && DOMAINDECOMP(cr))
{
if ((bExchanged || bNeedRepartition) && DOMAINDECOMP(cr))
{
- dd_partition_system(fplog, mdlog, step, cr, TRUE, 1, state_global, *top_global, ir,
- imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
- nrnb, wcycle, FALSE);
- shouldCheckNumberOfBondedInteractions = true;
- upd.setNumAtoms(state->natoms);
+ dd_partition_system(fplog,
+ mdlog,
+ step,
+ cr,
+ TRUE,
+ 1,
+ state_global,
+ top_global,
+ *ir,
+ imdSession,
+ pull_work,
+ state,
+ &f,
+ mdAtoms,
+ &top,
+ fr,
+ vsite,
+ constr,
+ nrnb,
+ wcycle,
+ FALSE);
+ upd.updateAfterPartition(state->natoms,
+ md->cFREEZE ? gmx::arrayRefFromArray(md->cFREEZE, md->nr)
+ : gmx::ArrayRef<const unsigned short>(),
+ md->cTC ? gmx::arrayRefFromArray(md->cTC, md->nr)
+ : gmx::ArrayRef<const unsigned short>());
}
bFirstStep = FALSE;
/* With all integrators, except VV, we need to retain the pressure
* at the current step for coupling at the next step.
*/
- if ((state->flags & (1U << estPRES_PREV))
+ if ((state->flags & enumValueToBitMask(StateEntry::PressurePrevious))
&& (bGStatEveryStep || (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
{
/* Store the pressure in t_state for pressure coupling
rescale_membed(step_rel, membed, as_rvec_array(state_global->x.data()));
}
- cycles = wallcycle_stop(wcycle, ewcSTEP);
+ cycles = wallcycle_stop(wcycle, WallCycleCounter::Step);
if (DOMAINDECOMP(cr) && wcycle)
{
dd_cycles_add(cr->dd, cycles, ddCyclStep);
}
#endif
- resetHandler->resetCounters(step, step_rel, mdlog, fplog, cr, fr->nbv.get(), nrnb,
- fr->pmedata, pme_loadbal, wcycle, walltime_accounting);
+ resetHandler->resetCounters(
+ step, step_rel, mdlog, fplog, cr, fr->nbv.get(), nrnb, fr->pmedata, pme_loadbal, wcycle, walltime_accounting);
/* If bIMD is TRUE, the master updates the IMD energy record and sends positions to VMD client */
imdSession->updateEnergyRecordAndSendPositionsAndEnergies(bInteractiveMDstep, step, bCalcEner);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/keyvaluetree.h"
#include "gromacs/utility/keyvaluetreebuilder.h"
#include "gromacs/utility/keyvaluetreetransform.h"
-#include "gromacs/utility/mdmodulenotification.h"
+#include "gromacs/utility/mdmodulesnotifiers.h"
#include "gromacs/utility/smalloc.h"
namespace gmx
{
}
- void makeModuleOptions(Options* options)
+ void makeModuleOptions(Options* options) const
{
// Create a section for applied-forces modules
auto appliedForcesOptions = options->addSection(OptionSection("applied-forces"));
* \note The notifier must be constructed before the modules and shall
* not be destructed before the modules are destructed.
*/
- MdModulesNotifier notifier_;
+ MDModulesNotifiers notifiers_;
std::unique_ptr<IMDModule> densityFitting_;
std::unique_ptr<IMDModule> field_;
void MDModules::subscribeToPreProcessingNotifications()
{
- impl_->densityFitting_->subscribeToPreProcessingNotifications(&impl_->notifier_);
+ impl_->densityFitting_->subscribeToPreProcessingNotifications(&impl_->notifiers_);
}
void MDModules::subscribeToSimulationSetupNotifications()
{
- impl_->densityFitting_->subscribeToSimulationSetupNotifications(&impl_->notifier_);
+ impl_->densityFitting_->subscribeToSimulationSetupNotifications(&impl_->notifiers_);
}
void MDModules::add(std::shared_ptr<gmx::IMDModule> module)
impl_->modules_.emplace_back(std::move(module));
}
-const MdModulesNotifier& MDModules::notifier()
+const MDModulesNotifiers& MDModules::notifiers()
{
- return impl_->notifier_;
+ return impl_->notifiers_;
}
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MDRUN_MDMODULES_H
#define GMX_MDRUN_MDMODULES_H
-#include "gromacs/utility/classhelpers.h"
+#include <memory>
struct t_inputrec;
class IKeyValueTreeTransformRules;
class IMDModule;
class IMDOutputProvider;
-struct MdModulesNotifier;
+struct MDModulesNotifiers;
/*! \libinternal \brief
* Manages the collection of all modules used for mdrun.
*/
ForceProviders* initForceProviders();
- /*! \brief Subscribe MdModules to simulation setup notifications.
+ /*! \brief Subscribe MDModules to simulation setup notifications.
*
- * Allows MdModules to subscribe to notifications that are called back
+ * Allows MDModules to subscribe to notifications that are called back
* during the set up of an MD simulation, after the options were
* assigned to the modules.
*/
void subscribeToSimulationSetupNotifications();
- /*! \brief Subscribe MdModules to notifications during pre-processing.
+ /*! \brief Subscribe MDModules to notifications during pre-processing.
*
- * Allows MdModules to subscribe to notifications that are called back
+ * Allows MDModules to subscribe to notifications that are called back
* during pre processing an MD simulation, after the options were
* assigned to the modules.
*/
*/
void add(std::shared_ptr<IMDModule> module);
- /*! \brief Return a handle to the callbacks.
+ /*! \brief Return a handle to the notifiers used for callbacks between modules.
*/
- const MdModulesNotifier& notifier();
+ const MDModulesNotifiers& notifiers();
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
void gmx::LegacySimulator::do_mimic()
{
- t_inputrec* ir = inputrec;
+ const t_inputrec* ir = inputrec;
int64_t step, step_rel;
double t;
bool isLastStep = false;
double cycles;
- /* Domain decomposition could incorrectly miss a bonded
- interaction, but checking for that requires a global
- communication stage, which does not otherwise happen in DD
- code. So we do that alongside the first global energy reduction
- after a new DD is made. These variables handle whether the
- check happens, and the result it returns. */
- bool shouldCheckNumberOfBondedInteractions = false;
- int totalNumberOfBondedInteractions = -1;
-
SimulationSignals signals;
// Most global communnication stages don't propagate mdrun
// signals, and will use this object to achieve that.
{
gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
}
- if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
- [](int i) { return i != eannNO; }))
+ if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc, [](SimulatedAnnealing i) {
+ return i != SimulatedAnnealing::No;
+ }))
{
gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
}
/* Settings for rerun */
- ir->nstlist = 1;
- ir->nstcalcenergy = 1;
+ {
+ // TODO: Avoid changing inputrec (#3854)
+ auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
+ nonConstInputrec->nstlist = 1;
+ nonConstInputrec->nstcalcenergy = 1;
+ nonConstInputrec->nstxout_compressed = 0;
+ }
int nstglobalcomm = 1;
const bool bNS = true;
if (MASTER(cr))
{
MimicCommunicator::init();
- auto nonConstGlobalTopology = const_cast<gmx_mtop_t*>(top_global);
+ auto* nonConstGlobalTopology = const_cast<gmx_mtop_t*>(&top_global);
MimicCommunicator::sendInitData(nonConstGlobalTopology, state_global->x);
- ir->nsteps = MimicCommunicator::getStepNumber();
+ // TODO: Avoid changing inputrec (#3854)
+ auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
+ nonConstInputrec->nsteps = MimicCommunicator::getStepNumber();
+ }
+ if (DOMAINDECOMP(cr))
+ {
+ // TODO: Avoid changing inputrec (#3854)
+ auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
+ gmx_bcast(sizeof(ir->nsteps), &nonConstInputrec->nsteps, cr->mpi_comm_mygroup);
}
- ir->nstxout_compressed = 0;
- const SimulationGroups* groups = &top_global->groups;
+ const SimulationGroups* groups = &top_global.groups;
{
- auto nonConstGlobalTopology = const_cast<gmx_mtop_t*>(top_global);
- nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(*top_global);
+ auto* nonConstGlobalTopology = const_cast<gmx_mtop_t*>(&top_global);
+ nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(top_global);
}
- initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda);
+ initialize_lambdas(fplog,
+ ir->efep,
+ ir->bSimTemp,
+ *ir->fepvals,
+ ir->simtempvals->temperatures,
+ gmx::arrayRefFromArray(ir->opts.ref_t, ir->opts.ngtc),
+ MASTER(cr),
+ &state_global->fep_state,
+ state_global->lambda);
const bool simulationsShareState = false;
- gmx_mdoutf* outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider,
- mdModulesNotifier, ir, top_global, oenv, wcycle,
- StartingBehavior::NewSimulation, simulationsShareState, ms);
- gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work,
- mdoutf_get_fp_dhdl(outf), true, StartingBehavior::NewSimulation,
- simulationsShareState, mdModulesNotifier);
+ gmx_mdoutf* outf = init_mdoutf(fplog,
+ nfile,
+ fnm,
+ mdrunOptions,
+ cr,
+ outputProvider,
+ mdModulesNotifiers,
+ ir,
+ top_global,
+ oenv,
+ wcycle,
+ StartingBehavior::NewSimulation,
+ simulationsShareState,
+ ms);
+ gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
+ top_global,
+ *ir,
+ pull_work,
+ mdoutf_get_fp_dhdl(outf),
+ true,
+ StartingBehavior::NewSimulation,
+ simulationsShareState,
+ mdModulesNotifiers);
gstat = global_stat_init(ir);
/* Check for polarizable models and flexible constraints */
- shellfc = init_shell_flexcon(fplog, top_global, constr ? constr->numFlexibleConstraints() : 0,
- ir->nstcalcenergy, DOMAINDECOMP(cr),
+ shellfc = init_shell_flexcon(fplog,
+ top_global,
+ constr ? constr->numFlexibleConstraints() : 0,
+ ir->nstcalcenergy,
+ DOMAINDECOMP(cr),
runScheduleWork->simulationWork.useGpuPme);
{
- double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
+ double io = compute_io(ir, top_global.natoms, *groups, energyOutput.numEnergyTerms(), 1);
if ((io > 2000) && MASTER(cr))
{
fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
std::unique_ptr<t_state> stateInstance;
t_state* state;
- gmx_localtop_t top(top_global->ffparams);
+ gmx_localtop_t top(top_global.ffparams);
if (DOMAINDECOMP(cr))
{
stateInstance = std::make_unique<t_state>();
state = stateInstance.get();
- dd_init_local_state(cr->dd, state_global, state);
+ dd_init_local_state(*cr->dd, state_global, state);
/* Distribute the charge groups over the nodes from the master node */
- dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1, state_global, *top_global, ir,
- imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
- nrnb, nullptr, FALSE);
- shouldCheckNumberOfBondedInteractions = true;
- gmx_bcast(sizeof(ir->nsteps), &ir->nsteps, cr->mpi_comm_mygroup);
+ dd_partition_system(fplog,
+ mdlog,
+ ir->init_step,
+ cr,
+ TRUE,
+ 1,
+ state_global,
+ top_global,
+ *ir,
+ imdSession,
+ pull_work,
+ state,
+ &f,
+ mdAtoms,
+ &top,
+ fr,
+ vsite,
+ constr,
+ nrnb,
+ nullptr,
+ FALSE);
}
else
{
/* Copy the pointer to the global state */
state = state_global;
- mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
+ mdAlgorithmsSetupAtomData(cr, *ir, top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
}
- auto mdatoms = mdAtoms->mdatoms();
+ auto* mdatoms = mdAtoms->mdatoms();
// NOTE: The global state is no longer used at this point.
// But state_global is still used as temporary storage space for writing
// the global state to file and potentially for replica exchange.
// (Global topology should persist.)
- update_mdatoms(mdatoms, state->lambda[efptMASS]);
+ update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
- if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
+ if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
{
doFreeEnergyPerturbation = true;
}
{
- int cglo_flags =
- (CGLO_GSTAT
- | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
+ int cglo_flags = CGLO_GSTAT;
+ if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
+ {
+ cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
+ }
bool bSumEkinhOld = false;
t_vcm* vcm = nullptr;
- compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
- makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, nullptr, enerd,
- force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, state->box,
- &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
+ compute_globals(gstat,
+ cr,
+ ir,
+ fr,
+ ekind,
+ makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v),
+ state->box,
+ mdatoms,
+ nrnb,
+ vcm,
+ nullptr,
+ enerd,
+ force_vir,
+ shake_vir,
+ total_vir,
+ pres,
+ gmx::ArrayRef<real>{},
+ &nullSignaller,
+ state->box,
+ &bSumEkinhOld,
+ cglo_flags);
+ if (DOMAINDECOMP(cr))
+ {
+ checkNumberOfBondedInteractions(
+ mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
+ }
}
- checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
- makeConstArrayRef(state->x), state->box,
- &shouldCheckNumberOfBondedInteractions);
if (MASTER(cr))
{
- fprintf(stderr, "starting MiMiC MD run '%s'\n\n", *(top_global->name));
+ fprintf(stderr, "starting MiMiC MD run '%s'\n\n", *(top_global.name));
if (mdrunOptions.verbose)
{
fprintf(stderr,
}
walltime_accounting_start_time(walltime_accounting);
- wallcycle_start(wcycle, ewcRUN);
+ wallcycle_start(wcycle, WallCycleCounter::Run);
print_start(fplog, cr, walltime_accounting, "mdrun");
/***********************************************************
step_rel = 0;
auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
- compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false, MASTER(cr),
- ir->nstlist, mdrunOptions.reproducible, nstglobalcomm, mdrunOptions.maximumHoursToRun,
- ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
+ compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
+ false,
+ MASTER(cr),
+ ir->nstlist,
+ mdrunOptions.reproducible,
+ nstglobalcomm,
+ mdrunOptions.maximumHoursToRun,
+ ir->nstlist == 0,
+ fplog,
+ step,
+ bNS,
+ walltime_accounting);
// we don't do counter resetting in rerun - finish will always be valid
walltime_accounting_set_valid_finish(walltime_accounting);
while (!isLastStep)
{
isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
- wallcycle_start(wcycle, ewcSTEP);
+ wallcycle_start(wcycle, WallCycleCounter::Step);
t = step;
MimicCommunicator::getCoords(&state_global->x, state_global->natoms);
}
- if (ir->efep != efepNO)
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
state->lambda = currentLambdas(step, *(ir->fepvals), state_global->fep_state);
}
}
if (constructVsites)
{
- wallcycle_start(wcycle, ewcVSITECONSTR);
- vsite->construct(state->x, ir->delta_t, state->v, state->box);
- wallcycle_stop(wcycle, ewcVSITECONSTR);
+ wallcycle_start(wcycle, WallCycleCounter::VsiteConstr);
+ vsite->construct(state->x, state->v, state->box, VSiteOperation::PositionsAndVelocities);
+ wallcycle_stop(wcycle, WallCycleCounter::VsiteConstr);
}
}
{
/* Repartition the domain decomposition */
const bool bMasterState = true;
- dd_partition_system(fplog, mdlog, step, cr, bMasterState, nstglobalcomm, state_global,
- *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top,
- fr, vsite, constr, nrnb, wcycle, mdrunOptions.verbose);
- shouldCheckNumberOfBondedInteractions = true;
+ dd_partition_system(fplog,
+ mdlog,
+ step,
+ cr,
+ bMasterState,
+ nstglobalcomm,
+ state_global,
+ top_global,
+ *ir,
+ imdSession,
+ pull_work,
+ state,
+ &f,
+ mdAtoms,
+ &top,
+ fr,
+ vsite,
+ constr,
+ nrnb,
+ wcycle,
+ mdrunOptions.verbose);
}
if (MASTER(cr))
EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
}
- if (ir->efep != efepNO)
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
- update_mdatoms(mdatoms, state->lambda[efptMASS]);
+ update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
}
force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
if (shellfc)
{
/* Now is the time to relax the shells */
- relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
- imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
- state->natoms, state->x.arrayRefWithPadding(),
- state->v.arrayRefWithPadding(), state->box, state->lambda,
- &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
- fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
+ relax_shell_flexcon(fplog,
+ cr,
+ ms,
+ mdrunOptions.verbose,
+ enforcedRotation,
+ step,
+ ir,
+ imdSession,
+ pull_work,
+ bNS,
+ force_flags,
+ &top,
+ constr,
+ enerd,
+ state->natoms,
+ state->x.arrayRefWithPadding(),
+ state->v.arrayRefWithPadding(),
+ state->box,
+ state->lambda,
+ &state->hist,
+ &f.view(),
+ force_vir,
+ *mdatoms,
+ nrnb,
+ wcycle,
+ shellfc,
+ fr,
+ runScheduleWork,
+ t,
+ mu_tot,
+ vsite,
+ ddBalanceRegionHandler);
}
else
{
*/
Awh* awh = nullptr;
gmx_edsam* ed = nullptr;
- do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
- wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
- &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
- vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags, ddBalanceRegionHandler);
+ do_force(fplog,
+ cr,
+ ms,
+ *ir,
+ awh,
+ enforcedRotation,
+ imdSession,
+ pull_work,
+ step,
+ nrnb,
+ wcycle,
+ &top,
+ state->box,
+ state->x.arrayRefWithPadding(),
+ &state->hist,
+ &f.view(),
+ force_vir,
+ mdatoms,
+ enerd,
+ state->lambda,
+ fr,
+ runScheduleWork,
+ vsite,
+ mu_tot,
+ t,
+ ed,
+ GMX_FORCE_NS | force_flags,
+ ddBalanceRegionHandler);
}
/* Now we have the energies and forces corresponding to the
const bool isCheckpointingStep = false;
const bool doRerun = false;
const bool bSumEkinhOld = false;
- do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
- state_global, observablesHistory, top_global, fr, outf,
- energyOutput, ekind, f.view().force(), isCheckpointingStep,
- doRerun, isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
+ do_md_trajectory_writing(fplog,
+ cr,
+ nfile,
+ fnm,
+ step,
+ step_rel,
+ t,
+ ir,
+ state,
+ state_global,
+ observablesHistory,
+ top_global,
+ fr,
+ outf,
+ energyOutput,
+ ekind,
+ f.view().force(),
+ isCheckpointingStep,
+ doRerun,
+ isLastStep,
+ mdrunOptions.writeConfout,
+ bSumEkinhOld);
}
stopHandler->setSignal();
t_vcm* vcm = nullptr;
SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
- compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
- makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, wcycle,
- enerd, nullptr, nullptr, nullptr, nullptr, constr, &signaller,
- state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
- CGLO_GSTAT | CGLO_ENERGY
- | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
- : 0));
- checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
- &top, makeConstArrayRef(state->x), state->box,
- &shouldCheckNumberOfBondedInteractions);
+ int cglo_flags = CGLO_GSTAT | CGLO_ENERGY;
+ if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
+ {
+ cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
+ }
+ compute_globals(gstat,
+ cr,
+ ir,
+ fr,
+ ekind,
+ makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v),
+ state->box,
+ mdatoms,
+ nrnb,
+ vcm,
+ wcycle,
+ enerd,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ constr != nullptr ? constr->rmsdData() : gmx::ArrayRef<real>{},
+ &signaller,
+ state->box,
+ &bSumEkinhOld,
+ cglo_flags);
+ if (DOMAINDECOMP(cr))
+ {
+ checkNumberOfBondedInteractions(
+ mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
+ }
}
{
- gmx::HostVector<gmx::RVec> fglobal(top_global->natoms);
+ gmx::HostVector<gmx::RVec> fglobal(top_global.natoms);
gmx::ArrayRef<gmx::RVec> ftemp;
gmx::ArrayRef<const gmx::RVec> flocal = f.view().force();
if (DOMAINDECOMP(cr))
{
ftemp = gmx::makeArrayRef(fglobal);
- dd_collect_vec(cr->dd, state->ddp_count, state->ddp_count_cg_gl, state->cg_gl,
- flocal, ftemp);
+ dd_collect_vec(cr->dd, state->ddp_count, state->ddp_count_cg_gl, state->cg_gl, flocal, ftemp);
}
else
{
but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
- if (ir->efep != efepNO)
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
/* Sum up the foreign energy and dhdl terms for md and sd.
Currently done every step so that dhdl is correct in the .edr */
if (MASTER(cr))
{
const bool bCalcEnerStep = true;
- energyOutput.addDataAtEnergyStep(
- doFreeEnergyPerturbation, bCalcEnerStep, t, mdatoms->tmass, enerd, ir->fepvals,
- ir->expandedvals, state->box,
- PTCouplingArrays({ state->boxv, state->nosehoover_xi, state->nosehoover_vxi,
- state->nhpres_xi, state->nhpres_vxi }),
- state->fep_state, shake_vir, force_vir, total_vir, pres, ekind, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
+ bCalcEnerStep,
+ t,
+ mdatoms->tmass,
+ enerd,
+ ir->fepvals.get(),
+ ir->expandedvals.get(),
+ state->box,
+ PTCouplingArrays({ state->boxv,
+ state->nosehoover_xi,
+ state->nosehoover_vxi,
+ state->nhpres_xi,
+ state->nhpres_vxi }),
+ state->fep_state,
+ shake_vir,
+ force_vir,
+ total_vir,
+ pres,
+ ekind,
+ mu_tot,
+ constr);
const bool do_ene = true;
const bool do_log = true;
const bool do_or = ir->nstorireout != 0;
EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
- energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
- do_log ? fplog : nullptr, step, t, fr->fcdata.get(), awh);
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
+ do_ene,
+ do_dr,
+ do_or,
+ do_log ? fplog : nullptr,
+ step,
+ t,
+ fr->fcdata.get(),
+ awh);
if (do_per_step(step, ir->nstlog))
{
print_time(stderr, walltime_accounting, step, ir, cr);
}
- cycles = wallcycle_stop(wcycle, ewcSTEP);
+ cycles = wallcycle_stop(wcycle, WallCycleCounter::Step);
if (DOMAINDECOMP(cr) && wcycle)
{
dd_cycles_add(cr->dd, cycles, ddCyclStep);
static void print_em_start(FILE* fplog,
const t_commrec* cr,
gmx_walltime_accounting_t walltime_accounting,
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle* wcycle,
const char* name)
{
walltime_accounting_start_time(walltime_accounting);
- wallcycle_start(wcycle, ewcRUN);
+ wallcycle_start(wcycle, WallCycleCounter::Run);
print_start(fplog, cr, walltime_accounting, name);
}
//! Stop counting time for EM
-static void em_time_end(gmx_walltime_accounting_t walltime_accounting, gmx_wallcycle_t wcycle)
+static void em_time_end(gmx_walltime_accounting_t walltime_accounting, gmx_wallcycle* wcycle)
{
- wallcycle_stop(wcycle, ewcRUN);
+ wallcycle_stop(wcycle, WallCycleCounter::Run);
walltime_accounting_end_time(walltime_accounting);
}
fprintf(fp,
"\n%s converged to machine precision in %s steps,\n"
"but did not reach the requested Fmax < %g.\n",
- alg, gmx_step_str(count, buf), ftol);
+ alg,
+ gmx_step_str(count, buf),
+ ftol);
}
else
{
- fprintf(fp, "\n%s did not converge to Fmax < %g in %s steps.\n", alg, ftol,
- gmx_step_str(count, buf));
+ fprintf(fp, "\n%s did not converge to Fmax < %g in %s steps.\n", alg, ftol, gmx_step_str(count, buf));
}
#if GMX_DOUBLE
//! Compute the norm and max of the force array in parallel
static void get_f_norm_max(const t_commrec* cr,
- t_grpopts* opts,
+ const t_grpopts* opts,
t_mdatoms* mdatoms,
gmx::ArrayRef<const gmx::RVec> f,
real* fnorm,
}
//! Compute the norm of the force
-static void get_state_f_norm_max(const t_commrec* cr, t_grpopts* opts, t_mdatoms* mdatoms, em_state_t* ems)
+static void get_state_f_norm_max(const t_commrec* cr, const t_grpopts* opts, t_mdatoms* mdatoms, em_state_t* ems)
{
get_f_norm_max(cr, opts, mdatoms, ems->f.view().force(), &ems->fnorm, &ems->fmax, &ems->a_fmax);
}
const gmx::MDLogger& mdlog,
const char* title,
const t_commrec* cr,
- t_inputrec* ir,
+ const t_inputrec* ir,
gmx::ImdSession* imdSession,
pull_t* pull_work,
t_state* state_global,
- const gmx_mtop_t* top_global,
+ const gmx_mtop_t& top_global,
em_state_t* ems,
gmx_localtop_t* top,
t_nrnb* nrnb,
}
int* fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
gmx::ArrayRef<real> lambda = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
- initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
-
- if (ir->eI == eiNM)
+ initialize_lambdas(fplog,
+ ir->efep,
+ ir->bSimTemp,
+ *ir->fepvals,
+ ir->simtempvals->temperatures,
+ gmx::arrayRefFromArray(ir->opts.ref_t, ir->opts.ngtc),
+ MASTER(cr),
+ fep_state,
+ lambda);
+
+ if (ir->eI == IntegrationAlgorithm::NM)
{
GMX_ASSERT(shellfc != nullptr, "With NM we always support shells");
- *shellfc =
- init_shell_flexcon(stdout, top_global, constr ? constr->numFlexibleConstraints() : 0,
- ir->nstcalcenergy, DOMAINDECOMP(cr), thisRankHasDuty(cr, DUTY_PME));
+ *shellfc = init_shell_flexcon(stdout,
+ top_global,
+ constr ? constr->numFlexibleConstraints() : 0,
+ ir->nstcalcenergy,
+ DOMAINDECOMP(cr),
+ thisRankHasDuty(cr, DUTY_PME));
}
else
{
if (DOMAINDECOMP(cr))
{
- dd_init_local_state(cr->dd, state_global, &ems->s);
+ dd_init_local_state(*cr->dd, state_global, &ems->s);
/* Distribute the charge groups over the nodes from the master node */
- dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1, state_global, *top_global, ir,
- imdSession, pull_work, &ems->s, &ems->f, mdAtoms, top, fr, vsite,
- constr, nrnb, nullptr, FALSE);
- dd_store_state(cr->dd, &ems->s);
+ dd_partition_system(fplog,
+ mdlog,
+ ir->init_step,
+ cr,
+ TRUE,
+ 1,
+ state_global,
+ top_global,
+ *ir,
+ imdSession,
+ pull_work,
+ &ems->s,
+ &ems->f,
+ mdAtoms,
+ top,
+ fr,
+ vsite,
+ constr,
+ nrnb,
+ nullptr,
+ FALSE);
+ dd_store_state(*cr->dd, &ems->s);
}
else
{
ems->s = *state_global;
state_change_natoms(&ems->s, ems->s.natoms);
- mdAlgorithmsSetupAtomData(cr, ir, *top_global, top, fr, &ems->f, mdAtoms, constr, vsite,
- shellfc ? *shellfc : nullptr);
+ mdAlgorithmsSetupAtomData(
+ cr, *ir, top_global, top, fr, &ems->f, mdAtoms, constr, vsite, shellfc ? *shellfc : nullptr);
}
- update_mdatoms(mdAtoms->mdatoms(), ems->s.lambda[efptMASS]);
+ update_mdatoms(mdAtoms->mdatoms(), ems->s.lambda[FreeEnergyPerturbationCouplingType::Mass]);
if (constr)
{
// TODO how should this cross-module support dependency be managed?
- if (ir->eConstrAlg == econtSHAKE && gmx_mtop_ftype_count(top_global, F_CONSTR) > 0)
+ if (ir->eConstrAlg == ConstraintAlgorithm::Shake && gmx_mtop_ftype_count(top_global, F_CONSTR) > 0)
{
- gmx_fatal(FARGS, "Can not do energy minimization with %s, use %s\n",
- econstr_names[econtSHAKE], econstr_names[econtLINCS]);
+ gmx_fatal(FARGS,
+ "Can not do energy minimization with %s, use %s\n",
+ enumValueToString(ConstraintAlgorithm::Shake),
+ enumValueToString(ConstraintAlgorithm::Lincs));
}
if (!ir->bContinuation)
bool computeEnergy = true;
bool computeVirial = false;
dvdl_constr = 0;
- constr->apply(needsLogging, computeEnergy, -1, 0, 1.0, ems->s.x.arrayRefWithPadding(),
- ems->s.x.arrayRefWithPadding(), ArrayRef<RVec>(), ems->s.box,
- ems->s.lambda[efptFEP], &dvdl_constr, gmx::ArrayRefWithPadding<RVec>(),
- computeVirial, nullptr, gmx::ConstraintVariable::Positions);
+ constr->apply(needsLogging,
+ computeEnergy,
+ -1,
+ 0,
+ 1.0,
+ ems->s.x.arrayRefWithPadding(),
+ ems->s.x.arrayRefWithPadding(),
+ ArrayRef<RVec>(),
+ ems->s.box,
+ ems->s.lambda[FreeEnergyPerturbationCouplingType::Fep],
+ &dvdl_constr,
+ gmx::ArrayRefWithPadding<RVec>(),
+ computeVirial,
+ nullptr,
+ gmx::ConstraintVariable::Positions);
}
}
static void finish_em(const t_commrec* cr,
gmx_mdoutf_t outf,
gmx_walltime_accounting_t walltime_accounting,
- gmx_wallcycle_t wcycle)
+ gmx_wallcycle* wcycle)
{
if (!thisRankHasDuty(cr, DUTY_PME))
{
gmx_bool bX,
gmx_bool bF,
const char* confout,
- const gmx_mtop_t* top_global,
- t_inputrec* ir,
+ const gmx_mtop_t& top_global,
+ const t_inputrec* ir,
int64_t step,
em_state_t* state,
t_state* state_global,
}
gmx::WriteCheckpointDataHolder checkpointDataHolder;
- mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
- static_cast<double>(step), &state->s, state_global,
- observablesHistory, state->f.view().force(), &checkpointDataHolder);
+ mdoutf_write_to_trajectory_files(fplog,
+ cr,
+ outf,
+ mdof_flags,
+ top_global.natoms,
+ step,
+ static_cast<double>(step),
+ &state->s,
+ state_global,
+ observablesHistory,
+ state->f.view().force(),
+ &checkpointDataHolder);
if (confout != nullptr)
{
if (!bX)
{
auto globalXRef = MASTER(cr) ? state_global->x : gmx::ArrayRef<gmx::RVec>();
- dd_collect_vec(cr->dd, state->s.ddp_count, state->s.ddp_count_cg_gl, state->s.cg_gl,
- state->s.x, globalXRef);
+ dd_collect_vec(
+ cr->dd, state->s.ddp_count, state->s.ddp_count_cg_gl, state->s.cg_gl, state->s.x, globalXRef);
}
}
else
if (ir->pbcType != PbcType::No && !ir->bPeriodicMols && DOMAINDECOMP(cr))
{
/* Make molecules whole only for confout writing */
- do_pbc_mtop(ir->pbcType, state->s.box, top_global, state_global->x.rvec_array());
+ do_pbc_mtop(ir->pbcType, state->s.box, &top_global, state_global->x.rvec_array());
}
- write_sto_conf_mtop(confout, *top_global->name, top_global,
- state_global->x.rvec_array(), nullptr, ir->pbcType, state->s.box);
+ write_sto_conf_mtop(confout,
+ *top_global.name,
+ top_global,
+ state_global->x.rvec_array(),
+ nullptr,
+ ir->pbcType,
+ state->s.box);
}
}
}
//
// \returns true when the step succeeded, false when a constraint error occurred
static bool do_em_step(const t_commrec* cr,
- t_inputrec* ir,
+ const t_inputrec* ir,
t_mdatoms* md,
em_state_t* ems1,
real a,
int64_t count)
{
- t_state *s1, *s2;
- int start, end;
- real dvdl_constr;
+ t_state * s1, *s2;
+ int start, end;
+ real dvdl_constr;
int nthreads gmx_unused;
bool validStep = true;
start = 0;
end = md->homenr;
- nthreads = gmx_omp_nthreads_get(emntUpdate);
+ nthreads = gmx_omp_nthreads_get(ModuleMultiThread::Update);
#pragma omp parallel num_threads(nthreads)
{
const rvec* x1 = s1->x.rvec_array();
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- if (s2->flags & (1 << estCGP))
+ if (s2->flags & enumValueToBitMask(StateEntry::Cgp))
{
/* Copy the CG p vector */
const rvec* p1 = s1->cg_p.rvec_array();
if (constr)
{
dvdl_constr = 0;
- validStep = constr->apply(
- TRUE, TRUE, count, 0, 1.0, s1->x.arrayRefWithPadding(), s2->x.arrayRefWithPadding(),
- ArrayRef<RVec>(), s2->box, s2->lambda[efptBONDED], &dvdl_constr,
- gmx::ArrayRefWithPadding<RVec>(), false, nullptr, gmx::ConstraintVariable::Positions);
+ validStep = constr->apply(TRUE,
+ TRUE,
+ count,
+ 0,
+ 1.0,
+ s1->x.arrayRefWithPadding(),
+ s2->x.arrayRefWithPadding(),
+ ArrayRef<RVec>(),
+ s2->box,
+ s2->lambda[FreeEnergyPerturbationCouplingType::Bonded],
+ &dvdl_constr,
+ gmx::ArrayRefWithPadding<RVec>(),
+ false,
+ nullptr,
+ gmx::ConstraintVariable::Positions);
if (cr->nnodes > 1)
{
}
// We should move this check to the different minimizers
- if (!validStep && ir->eI != eiSteep)
+ if (!validStep && ir->eI != IntegrationAlgorithm::Steep)
{
gmx_fatal(FARGS,
"The coordinates could not be constrained. Minimizer '%s' can not handle "
"constraint failures, use minimizer '%s' before using '%s'.",
- EI(ir->eI), EI(eiSteep), EI(ir->eI));
+ enumValueToString(ir->eI),
+ enumValueToString(IntegrationAlgorithm::Steep),
+ enumValueToString(ir->eI));
}
}
const gmx::MDLogger& mdlog,
int step,
const t_commrec* cr,
- const gmx_mtop_t* top_global,
- t_inputrec* ir,
+ const gmx_mtop_t& top_global,
+ const t_inputrec* ir,
gmx::ImdSession* imdSession,
pull_t* pull_work,
em_state_t* ems,
VirtualSitesHandler* vsite,
gmx::Constraints* constr,
t_nrnb* nrnb,
- gmx_wallcycle_t wcycle)
+ gmx_wallcycle* wcycle)
{
/* Repartition the domain decomposition */
- dd_partition_system(fplog, mdlog, step, cr, FALSE, 1, nullptr, *top_global, ir, imdSession, pull_work,
- &ems->s, &ems->f, mdAtoms, top, fr, vsite, constr, nrnb, wcycle, FALSE);
- dd_store_state(cr->dd, &ems->s);
+ dd_partition_system(fplog,
+ mdlog,
+ step,
+ cr,
+ FALSE,
+ 1,
+ nullptr,
+ top_global,
+ *ir,
+ imdSession,
+ pull_work,
+ &ems->s,
+ &ems->f,
+ mdAtoms,
+ top,
+ fr,
+ vsite,
+ constr,
+ nrnb,
+ wcycle,
+ FALSE);
+ dd_store_state(*cr->dd, &ems->s);
}
namespace
{
+//! Copy coordinates, OpenMP parallelized, from \p refCoords to coords
+void setCoordinates(std::vector<RVec>* coords, ArrayRef<const RVec> refCoords)
+{
+ coords->resize(refCoords.size());
+
+ const int gmx_unused nthreads = gmx_omp_nthreads_get(ModuleMultiThread::Update);
+#pragma omp parallel for num_threads(nthreads) schedule(static)
+ for (int i = 0; i < ssize(refCoords); i++)
+ {
+ (*coords)[i] = refCoords[i];
+ }
+}
+
+//! Returns the maximum difference an atom moved between two coordinate sets, over all ranks
+real maxCoordinateDifference(ArrayRef<const RVec> coords1, ArrayRef<const RVec> coords2, MPI_Comm mpiCommMyGroup)
+{
+ GMX_RELEASE_ASSERT(coords1.size() == coords2.size(), "Coordinate counts should match");
+
+ real maxDiffSquared = 0;
+
+ const int gmx_unused nthreads = gmx_omp_nthreads_get(ModuleMultiThread::Update);
+#pragma omp parallel for reduction(max : maxDiffSquared) num_threads(nthreads) schedule(static)
+ for (int i = 0; i < ssize(coords1); i++)
+ {
+ maxDiffSquared = std::max(maxDiffSquared, gmx::norm2(coords1[i] - coords2[i]));
+ }
+
+#if GMX_MPI
+ int numRanks = 1;
+ if (mpiCommMyGroup != MPI_COMM_NULL)
+ {
+ MPI_Comm_size(mpiCommMyGroup, &numRanks);
+ }
+ if (numRanks > 1)
+ {
+ real maxDiffSquaredReduced;
+ MPI_Allreduce(
+ &maxDiffSquared, &maxDiffSquaredReduced, 1, GMX_DOUBLE ? MPI_DOUBLE : MPI_FLOAT, MPI_MAX, mpiCommMyGroup);
+ maxDiffSquared = maxDiffSquaredReduced;
+ }
+#else
+ GMX_UNUSED_VALUE(mpiCommMyGroup);
+#endif
+
+ return std::sqrt(maxDiffSquared);
+}
+
/*! \brief Class to handle the work of setting and doing an energy evaluation.
*
* This class is a mere aggregate of parameters to pass to evaluate an
//! Coordinates multi-simulations.
const gmx_multisim_t* ms;
//! Holds the simulation topology.
- const gmx_mtop_t* top_global;
+ const gmx_mtop_t& top_global;
//! Holds the domain topology.
gmx_localtop_t* top;
//! User input options.
- t_inputrec* inputrec;
+ const t_inputrec* inputrec;
//! The Interactive Molecular Dynamics session.
gmx::ImdSession* imdSession;
//! The pull work object.
//! Manages flop accounting.
t_nrnb* nrnb;
//! Manages wall cycle accounting.
- gmx_wallcycle_t wcycle;
+ gmx_wallcycle* wcycle;
//! Coordinates global reduction.
gmx_global_stat_t gstat;
//! Handles virtual sites.
MdrunScheduleWorkload* runScheduleWork;
//! Stores the computed energies.
gmx_enerdata_t* enerd;
+ //! The DD partitioning count at which the pair list was generated
+ int ddpCountPairSearch;
+ //! The local coordinates that were used for pair searching, stored for computing displacements
+ std::vector<RVec> pairSearchCoordinates;
};
void EnergyEvaluator::run(em_state_t* ems, rvec mu_tot, tensor vir, tensor pres, int64_t count, gmx_bool bFirst)
/* Set the time to the initial time, the time does not change during EM */
t = inputrec->init_t;
- if (bFirst || (DOMAINDECOMP(cr) && ems->s.ddp_count < cr->dd->ddp_count))
+ if (vsite)
+ {
+ vsite->construct(ems->s.x, {}, ems->s.box, gmx::VSiteOperation::Positions);
+ }
+
+ // Compute the buffer size of the pair list
+ const real bufferSize = inputrec->rlist - std::max(inputrec->rcoulomb, inputrec->rvdw);
+
+ if (bFirst || bufferSize <= 0 || (DOMAINDECOMP(cr) && ems->s.ddp_count != ddpCountPairSearch))
{
/* This is the first state or an old state used before the last ns */
bNS = TRUE;
}
else
{
- bNS = FALSE;
- if (inputrec->nstlist > 0)
- {
- bNS = TRUE;
- }
+ // We need to generate a new pairlist when one atom moved more than half the buffer size
+ ArrayRef<const RVec> localCoordinates =
+ ArrayRef<const RVec>(ems->s.x).subArray(0, mdAtoms->mdatoms()->homenr);
+ bNS = 2 * maxCoordinateDifference(pairSearchCoordinates, localCoordinates, cr->mpi_comm_mygroup)
+ > bufferSize;
}
- if (vsite)
+ if (DOMAINDECOMP(cr) && bNS)
{
- vsite->construct(ems->s.x, 1, {}, ems->s.box);
+ /* Repartition the domain decomposition */
+ em_dd_partition_system(
+ fplog, mdlog, count, cr, top_global, inputrec, imdSession, pull_work, ems, top, mdAtoms, fr, vsite, constr, nrnb, wcycle);
+ ddpCountPairSearch = cr->dd->ddp_count;
}
- if (DOMAINDECOMP(cr) && bNS)
+ /* Store the local coordinates that will be used in the pair search, after we re-partitioned */
+ if (bufferSize > 0 && bNS)
{
- /* Repartition the domain decomposition */
- em_dd_partition_system(fplog, mdlog, count, cr, top_global, inputrec, imdSession, pull_work,
- ems, top, mdAtoms, fr, vsite, constr, nrnb, wcycle);
+ ArrayRef<const RVec> localCoordinates =
+ constArrayRefFromArray(ems->s.x.data(), mdAtoms->mdatoms()->homenr);
+ setCoordinates(&pairSearchCoordinates, localCoordinates);
}
/* Calc force & energy on new trial position */
/* do_force always puts the charge groups in the box and shifts again
* We do not unshift, so molecules are always whole in congrad.c
*/
- do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, count, nrnb, wcycle,
- top, ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist, &ems->f.view(), force_vir,
- mdAtoms->mdatoms(), enerd, ems->s.lambda, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
+ do_force(fplog,
+ cr,
+ ms,
+ *inputrec,
+ nullptr,
+ nullptr,
+ imdSession,
+ pull_work,
+ count,
+ nrnb,
+ wcycle,
+ top,
+ ems->s.box,
+ ems->s.x.arrayRefWithPadding(),
+ &ems->s.hist,
+ &ems->f.view(),
+ force_vir,
+ mdAtoms->mdatoms(),
+ enerd,
+ ems->s.lambda,
+ fr,
+ runScheduleWork,
+ vsite,
+ mu_tot,
+ t,
+ nullptr,
GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES | GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY
| (bNS ? GMX_FORCE_NS : 0),
DDBalanceRegionHandler(cr));
clear_mat(pres);
/* Communicate stuff when parallel */
- if (PAR(cr) && inputrec->eI != eiNM)
+ if (PAR(cr) && inputrec->eI != IntegrationAlgorithm::NM)
{
- wallcycle_start(wcycle, ewcMoveE);
+ wallcycle_start(wcycle, WallCycleCounter::MoveE);
- global_stat(gstat, cr, enerd, force_vir, shake_vir, inputrec, nullptr, nullptr, nullptr, 1,
- &terminate, nullptr, FALSE, CGLO_ENERGY | CGLO_PRESSURE | CGLO_CONSTRAINT);
+ global_stat(*gstat,
+ cr,
+ enerd,
+ force_vir,
+ shake_vir,
+ *inputrec,
+ nullptr,
+ gmx::ArrayRef<real>{},
+ nullptr,
+ std::vector<real>(1, terminate),
+ FALSE,
+ CGLO_ENERGY | CGLO_PRESSURE | CGLO_CONSTRAINT);
- wallcycle_stop(wcycle, ewcMoveE);
+ wallcycle_stop(wcycle, WallCycleCounter::MoveE);
}
if (fr->dispersionCorrection)
{
/* Calculate long range corrections to pressure and energy */
- const DispersionCorrection::Correction correction =
- fr->dispersionCorrection->calculate(ems->s.box, ems->s.lambda[efptVDW]);
+ const DispersionCorrection::Correction correction = fr->dispersionCorrection->calculate(
+ ems->s.box, ems->s.lambda[FreeEnergyPerturbationCouplingType::Vdw]);
enerd->term[F_DISPCORR] = correction.energy;
enerd->term[F_EPOT] += correction.energy;
bool computeVirial = true;
dvdl_constr = 0;
auto f = ems->f.view().forceWithPadding();
- constr->apply(needsLogging, computeEnergy, count, 0, 1.0, ems->s.x.arrayRefWithPadding(), f,
- f.unpaddedArrayRef(), ems->s.box, ems->s.lambda[efptBONDED], &dvdl_constr,
- gmx::ArrayRefWithPadding<RVec>(), computeVirial, shake_vir,
+ constr->apply(needsLogging,
+ computeEnergy,
+ count,
+ 0,
+ 1.0,
+ ems->s.x.arrayRefWithPadding(),
+ f,
+ f.unpaddedArrayRef(),
+ ems->s.box,
+ ems->s.lambda[FreeEnergyPerturbationCouplingType::Bonded],
+ &dvdl_constr,
+ gmx::ArrayRefWithPadding<RVec>(),
+ computeVirial,
+ shake_vir,
gmx::ConstraintVariable::ForceDispl);
enerd->term[F_DVDL_CONSTR] += dvdl_constr;
m_add(force_vir, shake_vir, vir);
clear_mat(ekin);
enerd->term[F_PRES] = calc_pres(fr->pbcType, inputrec->nwall, ems->s.box, ekin, vir, pres);
- if (inputrec->efep != efepNO)
+ if (inputrec->efep != FreeEnergyPerturbationType::No)
{
accumulateKineticLambdaComponents(enerd, ems->s.lambda, *inputrec->fepvals);
}
//! Parallel utility summing energies and forces
static double reorder_partsum(const t_commrec* cr,
- t_grpopts* opts,
- const gmx_mtop_t* top_global,
+ const t_grpopts* opts,
+ const gmx_mtop_t& top_global,
const em_state_t* s_min,
const em_state_t* s_b)
{
* This conflicts with the spirit of domain decomposition,
* but to fully optimize this a much more complicated algorithm is required.
*/
- const int natoms = top_global->natoms;
+ const int natoms = top_global.natoms;
rvec* fmg;
snew(fmg, natoms);
copy_rvec(fm[i], fmg[a]);
i++;
}
- gmx_sum(top_global->natoms * 3, fmg[0], cr);
+ gmx_sum(top_global.natoms * 3, fmg[0], cr);
/* Now we will determine the part of the sum for the cgs in state s_b */
gmx::ArrayRef<const int> indicesB = s_b->s.cg_gl;
i = 0;
int gf = 0;
gmx::ArrayRef<const unsigned char> grpnrFREEZE =
- top_global->groups.groupNumbers[SimulationAtomGroupType::Freeze];
+ top_global.groups.groupNumbers[SimulationAtomGroupType::Freeze];
for (int a : indicesB)
{
if (!grpnrFREEZE.empty())
//! Print some stuff, like beta, whatever that means.
static real pr_beta(const t_commrec* cr,
- t_grpopts* opts,
+ const t_grpopts* opts,
t_mdatoms* mdatoms,
- const gmx_mtop_t* top_global,
+ const gmx_mtop_t& top_global,
const em_state_t* s_min,
const em_state_t* s_b)
{
{
const char* CG = "Polak-Ribiere Conjugate Gradients";
- gmx_localtop_t top(top_global->ffparams);
+ gmx_localtop_t top(top_global.ffparams);
gmx_global_stat_t gstat;
double tmp, minstep;
real stepsize;
tensor vir, pres;
int number_steps, neval = 0, nstcg = inputrec->nstcgsteep;
int m, step, nminstep;
- auto mdatoms = mdAtoms->mdatoms();
+ auto* mdatoms = mdAtoms->mdatoms();
GMX_LOG(mdlog.info)
.asParagraph()
if (MASTER(cr))
{
// In CG, the state is extended with a search direction
- state_global->flags |= (1 << estCGP);
+ state_global->flags |= enumValueToBitMask(StateEntry::Cgp);
// Ensure the extra per-atom state array gets allocated
state_change_natoms(state_global, state_global->natoms);
em_state_t* s_c = &s3;
/* Init em and store the local state in s_min */
- init_em(fplog, mdlog, CG, cr, inputrec, imdSession, pull_work, state_global, top_global, s_min,
- &top, nrnb, fr, mdAtoms, &gstat, vsite, constr, nullptr);
+ init_em(fplog,
+ mdlog,
+ CG,
+ cr,
+ inputrec,
+ imdSession,
+ pull_work,
+ state_global,
+ top_global,
+ s_min,
+ &top,
+ nrnb,
+ fr,
+ mdAtoms,
+ &gstat,
+ vsite,
+ constr,
+ nullptr);
const bool simulationsShareState = false;
- gmx_mdoutf* outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider,
- mdModulesNotifier, inputrec, top_global, nullptr, wcycle,
- StartingBehavior::NewSimulation, simulationsShareState, ms);
- gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, inputrec, pull_work,
- nullptr, false, StartingBehavior::NewSimulation,
- simulationsShareState, mdModulesNotifier);
+ gmx_mdoutf* outf = init_mdoutf(fplog,
+ nfile,
+ fnm,
+ mdrunOptions,
+ cr,
+ outputProvider,
+ mdModulesNotifiers,
+ inputrec,
+ top_global,
+ nullptr,
+ wcycle,
+ StartingBehavior::NewSimulation,
+ simulationsShareState,
+ ms);
+ gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
+ top_global,
+ *inputrec,
+ pull_work,
+ nullptr,
+ false,
+ StartingBehavior::NewSimulation,
+ simulationsShareState,
+ mdModulesNotifiers);
/* Print to log file */
print_em_start(fplog, cr, walltime_accounting, wcycle, CG);
sp_header(fplog, CG, inputrec->em_tol, number_steps);
}
- EnergyEvaluator energyEvaluator{ fplog, mdlog, cr, ms, top_global, &top,
- inputrec, imdSession, pull_work, nrnb, wcycle, gstat,
- vsite, constr, mdAtoms, fr, runScheduleWork, enerd };
+ EnergyEvaluator energyEvaluator{ fplog, mdlog, cr, ms, top_global,
+ &top, inputrec, imdSession, pull_work, nrnb,
+ wcycle, gstat, vsite, constr, mdAtoms,
+ fr, runScheduleWork, enerd, -1, {} };
/* Call the force routine and some auxiliary (neighboursearching etc.) */
/* do_force always puts the charge groups in the box and shifts again
* We do not unshift, so molecules are always whole in congrad.c
{
/* Copy stuff to the energy bin for easy printing etc. */
matrix nullBox = {};
- energyOutput.addDataAtEnergyStep(false, false, static_cast<double>(step), mdatoms->tmass,
- enerd, nullptr, nullptr, nullBox, PTCouplingArrays(), 0,
- nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(false,
+ false,
+ static_cast<double>(step),
+ mdatoms->tmass,
+ enerd,
+ nullptr,
+ nullptr,
+ nullBox,
+ PTCouplingArrays(),
+ 0,
+ nullptr,
+ nullptr,
+ vir,
+ pres,
+ nullptr,
+ mu_tot,
+ constr);
EnergyOutput::printHeader(fplog, step, step);
- energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step,
- step, fr->fcdata.get(), nullptr);
+ energyOutput.printStepToEnergyFile(
+ mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, fr->fcdata.get(), nullptr);
}
/* Estimate/guess the initial stepsize */
gmx_sumd(1, &minstep, cr);
}
- minstep = GMX_REAL_EPS / sqrt(minstep / (3 * top_global->natoms));
+ minstep = GMX_REAL_EPS / sqrt(minstep / (3 * top_global.natoms));
if (stepsize < minstep)
{
do_x = do_per_step(step, inputrec->nstxout);
do_f = do_per_step(step, inputrec->nstfout);
- write_em_traj(fplog, cr, outf, do_x, do_f, nullptr, top_global, inputrec, step, s_min,
- state_global, observablesHistory);
+ write_em_traj(
+ fplog, cr, outf, do_x, do_f, nullptr, top_global, inputrec, step, s_min, state_global, observablesHistory);
/* Take a step downhill.
* In theory, we should minimize the function along this direction.
if (DOMAINDECOMP(cr) && s_min->s.ddp_count < cr->dd->ddp_count)
{
- em_dd_partition_system(fplog, mdlog, step, cr, top_global, inputrec, imdSession,
- pull_work, s_min, &top, mdAtoms, fr, vsite, constr, nrnb, wcycle);
+ em_dd_partition_system(fplog,
+ mdlog,
+ step,
+ cr,
+ top_global,
+ inputrec,
+ imdSession,
+ pull_work,
+ s_min,
+ &top,
+ mdAtoms,
+ fr,
+ vsite,
+ constr,
+ nrnb,
+ wcycle);
}
/* Take a trial step (new coords in s_c) */
- do_em_step(cr, inputrec, mdatoms, s_min, c, s_min->s.cg_p.constArrayRefWithPadding(), s_c,
- constr, -1);
+ do_em_step(cr, inputrec, mdatoms, s_min, c, s_min->s.cg_p.constArrayRefWithPadding(), s_c, constr, -1);
neval++;
/* Calculate energy for the trial step */
if (DOMAINDECOMP(cr) && s_min->s.ddp_count != cr->dd->ddp_count)
{
/* Reload the old state */
- em_dd_partition_system(fplog, mdlog, -1, cr, top_global, inputrec, imdSession, pull_work,
- s_min, &top, mdAtoms, fr, vsite, constr, nrnb, wcycle);
+ em_dd_partition_system(fplog,
+ mdlog,
+ -1,
+ cr,
+ top_global,
+ inputrec,
+ imdSession,
+ pull_work,
+ s_min,
+ &top,
+ mdAtoms,
+ fr,
+ vsite,
+ constr,
+ nrnb,
+ wcycle);
}
/* Take a trial step to this new point - new coords in s_b */
- do_em_step(cr, inputrec, mdatoms, s_min, b,
- s_min->s.cg_p.constArrayRefWithPadding(), s_b, constr, -1);
+ do_em_step(cr, inputrec, mdatoms, s_min, b, s_min->s.cg_p.constArrayRefWithPadding(), s_b, constr, -1);
neval++;
/* Calculate energy for the trial step */
if (debug)
{
- fprintf(debug, "CGE: EpotA %f EpotB %f EpotC %f gpb %f\n", s_a->epot, s_b->epot,
- s_c->epot, gpb);
+ fprintf(debug, "CGE: EpotA %f EpotB %f EpotC %f gpb %f\n", s_a->epot, s_b->epot, s_c->epot, gpb);
}
epot_repl = s_b->epot;
{
if (debug)
{
- fprintf(debug, "CGE: C (%f) is lower than A (%f), moving C to B\n", s_c->epot,
- s_a->epot);
+ fprintf(debug, "CGE: C (%f) is lower than A (%f), moving C to B\n", s_c->epot, s_a->epot);
}
swap_em_state(&s_b, &s_c);
gpb = gpc;
{
if (debug)
{
- fprintf(debug, "CGE: A (%f) is lower than C (%f), moving A to B\n", s_a->epot,
- s_c->epot);
+ fprintf(debug, "CGE: A (%f) is lower than C (%f), moving A to B\n", s_a->epot, s_c->epot);
}
swap_em_state(&s_b, &s_a);
gpb = gpa;
if (mdrunOptions.verbose)
{
double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
- fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n", step,
- s_min->epot, s_min->fnorm / sqrtNumAtoms, s_min->fmax, s_min->a_fmax + 1);
+ fprintf(stderr,
+ "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
+ step,
+ s_min->epot,
+ s_min->fnorm / sqrtNumAtoms,
+ s_min->fmax,
+ s_min->a_fmax + 1);
fflush(stderr);
}
/* Store the new (lower) energies */
matrix nullBox = {};
- energyOutput.addDataAtEnergyStep(false, false, static_cast<double>(step), mdatoms->tmass,
- enerd, nullptr, nullptr, nullBox, PTCouplingArrays(), 0,
- nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(false,
+ false,
+ static_cast<double>(step),
+ mdatoms->tmass,
+ enerd,
+ nullptr,
+ nullptr,
+ nullBox,
+ PTCouplingArrays(),
+ 0,
+ nullptr,
+ nullptr,
+ vir,
+ pres,
+ nullptr,
+ mu_tot,
+ constr);
do_log = do_per_step(step, inputrec->nstlog);
do_ene = do_per_step(step, inputrec->nstenergy);
{
EnergyOutput::printHeader(fplog, step, step);
}
- energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
- do_log ? fplog : nullptr, step, step,
- fr->fcdata.get(), nullptr);
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
+ do_ene,
+ FALSE,
+ FALSE,
+ do_log ? fplog : nullptr,
+ step,
+ step,
+ fr->fcdata.get(),
+ nullptr);
}
/* Send energies and positions to the IMD client if bIMD is TRUE. */
- if (MASTER(cr) && imdSession->run(step, TRUE, state_global->box, state_global->x.rvec_array(), 0))
+ if (MASTER(cr) && imdSession->run(step, TRUE, state_global->box, state_global->x, 0))
{
imdSession->sendPositionsAndEnergies();
}
if (!do_ene || !do_log)
{
/* Write final energy file entries */
- energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
- !do_log ? fplog : nullptr, step, step,
- fr->fcdata.get(), nullptr);
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
+ !do_ene,
+ FALSE,
+ FALSE,
+ !do_log ? fplog : nullptr,
+ step,
+ step,
+ fr->fcdata.get(),
+ nullptr);
}
}
do_x = !do_per_step(step, inputrec->nstxout);
do_f = (inputrec->nstfout > 0 && !do_per_step(step, inputrec->nstfout));
- write_em_traj(fplog, cr, outf, do_x, do_f, ftp2fn(efSTO, nfile, fnm), top_global, inputrec,
- step, s_min, state_global, observablesHistory);
+ write_em_traj(
+ fplog, cr, outf, do_x, do_f, ftp2fn(efSTO, nfile, fnm), top_global, inputrec, step, s_min, state_global, observablesHistory);
if (MASTER(cr))
{
static const char* LBFGS = "Low-Memory BFGS Minimizer";
em_state_t ems;
- gmx_localtop_t top(top_global->ffparams);
+ gmx_localtop_t top(top_global.ffparams);
gmx_global_stat_t gstat;
- int ncorr, nmaxcorr, point, cp, neval, nminstep;
- double stepsize, step_taken, gpa, gpb, gpc, tmp, minstep;
- real * rho, *alpha, *p, *s, **dx, **dg;
- real a, b, c, maxdelta, delta;
- real diag, Epot0;
- real dgdx, dgdg, sq, yr, beta;
- gmx_bool converged;
- rvec mu_tot = { 0 };
- gmx_bool do_log, do_ene, do_x, do_f, foundlower, *frozen;
- tensor vir, pres;
- int start, end, number_steps;
- int i, k, m, n, gf, step;
- int mdof_flags;
- auto mdatoms = mdAtoms->mdatoms();
+ auto* mdatoms = mdAtoms->mdatoms();
GMX_LOG(mdlog.info)
.asParagraph()
"do not use constraints, or use another minimizer (e.g. steepest descent).");
}
- n = 3 * state_global->natoms;
- nmaxcorr = inputrec->nbfgscorr;
-
- snew(frozen, n);
+ const int n = 3 * state_global->natoms;
+ const int nmaxcorr = inputrec->nbfgscorr;
- snew(p, n);
- snew(rho, nmaxcorr);
- snew(alpha, nmaxcorr);
+ std::vector<real> p(n);
+ std::vector<real> rho(nmaxcorr);
+ std::vector<real> alpha(nmaxcorr);
- snew(dx, nmaxcorr);
- for (i = 0; i < nmaxcorr; i++)
+ std::vector<std::vector<real>> dx(nmaxcorr);
+ for (auto& dxCorr : dx)
{
- snew(dx[i], n);
+ dxCorr.resize(n);
}
- snew(dg, nmaxcorr);
- for (i = 0; i < nmaxcorr; i++)
+ std::vector<std::vector<real>> dg(nmaxcorr);
+ for (auto& dgCorr : dg)
{
- snew(dg[i], n);
+ dgCorr.resize(n);
}
- step = 0;
- neval = 0;
+ int step = 0;
+ int neval = 0;
/* Init em */
- init_em(fplog, mdlog, LBFGS, cr, inputrec, imdSession, pull_work, state_global, top_global,
- &ems, &top, nrnb, fr, mdAtoms, &gstat, vsite, constr, nullptr);
+ init_em(fplog,
+ mdlog,
+ LBFGS,
+ cr,
+ inputrec,
+ imdSession,
+ pull_work,
+ state_global,
+ top_global,
+ &ems,
+ &top,
+ nrnb,
+ fr,
+ mdAtoms,
+ &gstat,
+ vsite,
+ constr,
+ nullptr);
const bool simulationsShareState = false;
- gmx_mdoutf* outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider,
- mdModulesNotifier, inputrec, top_global, nullptr, wcycle,
- StartingBehavior::NewSimulation, simulationsShareState, ms);
- gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, inputrec, pull_work,
- nullptr, false, StartingBehavior::NewSimulation,
- simulationsShareState, mdModulesNotifier);
-
- start = 0;
- end = mdatoms->homenr;
+ gmx_mdoutf* outf = init_mdoutf(fplog,
+ nfile,
+ fnm,
+ mdrunOptions,
+ cr,
+ outputProvider,
+ mdModulesNotifiers,
+ inputrec,
+ top_global,
+ nullptr,
+ wcycle,
+ StartingBehavior::NewSimulation,
+ simulationsShareState,
+ ms);
+ gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
+ top_global,
+ *inputrec,
+ pull_work,
+ nullptr,
+ false,
+ StartingBehavior::NewSimulation,
+ simulationsShareState,
+ mdModulesNotifiers);
+
+ const int start = 0;
+ const int end = mdatoms->homenr;
/* We need 4 working states */
em_state_t s0{}, s1{}, s2{}, s3{};
/* Print to log file */
print_em_start(fplog, cr, walltime_accounting, wcycle, LBFGS);
- do_log = do_ene = do_x = do_f = TRUE;
-
/* Max number of steps */
- number_steps = inputrec->nsteps;
+ const int number_steps = inputrec->nsteps;
/* Create a 3*natoms index to tell whether each degree of freedom is frozen */
- gf = 0;
- for (i = start; i < end; i++)
+ std::vector<bool> frozen(n);
+ int gf = 0;
+ for (int i = start; i < end; i++)
{
if (mdatoms->cFREEZE)
{
gf = mdatoms->cFREEZE[i];
}
- for (m = 0; m < DIM; m++)
+ for (int m = 0; m < DIM; m++)
{
frozen[3 * i + m] = (inputrec->opts.nFreeze[gf][m] != 0);
}
if (vsite)
{
- vsite->construct(state_global->x, 1, {}, state_global->box);
+ vsite->construct(state_global->x, {}, state_global->box, VSiteOperation::Positions);
}
/* Call the force routine and some auxiliary (neighboursearching etc.) */
EnergyEvaluator energyEvaluator{ fplog, mdlog, cr, ms, top_global, &top,
inputrec, imdSession, pull_work, nrnb, wcycle, gstat,
vsite, constr, mdAtoms, fr, runScheduleWork, enerd };
+ rvec mu_tot;
+ tensor vir;
+ tensor pres;
energyEvaluator.run(&ems, mu_tot, vir, pres, -1, TRUE);
if (MASTER(cr))
{
/* Copy stuff to the energy bin for easy printing etc. */
matrix nullBox = {};
- energyOutput.addDataAtEnergyStep(false, false, static_cast<double>(step), mdatoms->tmass,
- enerd, nullptr, nullptr, nullBox, PTCouplingArrays(), 0,
- nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(false,
+ false,
+ static_cast<double>(step),
+ mdatoms->tmass,
+ enerd,
+ nullptr,
+ nullptr,
+ nullBox,
+ PTCouplingArrays(),
+ 0,
+ nullptr,
+ nullptr,
+ vir,
+ pres,
+ nullptr,
+ mu_tot,
+ constr);
EnergyOutput::printHeader(fplog, step, step);
- energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step,
- step, fr->fcdata.get(), nullptr);
+ energyOutput.printStepToEnergyFile(
+ mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, fr->fcdata.get(), nullptr);
}
/* Set the initial step.
}
// Point is an index to the memory of search directions, where 0 is the first one.
- point = 0;
+ int point = 0;
// Set initial search direction to the force (-gradient), or 0 for frozen particles.
real* fInit = static_cast<real*>(ems.f.view().force().data()[0]);
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
if (!frozen[i])
{
// (the main efficiency in the algorithm comes from changing directions), but
// we still need an initial value, so estimate it as the inverse of the norm
// so we take small steps where the potential fluctuates a lot.
- stepsize = 1.0 / ems.fnorm;
+ double stepsize = 1.0 / ems.fnorm;
/* Start the loop over BFGS steps.
* Each successful step is counted, and we continue until
* we either converge or reach the max number of steps.
*/
- ncorr = 0;
+ bool do_log = true;
+ bool do_ene = true;
+
+ int ncorr = 0;
/* Set the gradient from the force */
- converged = FALSE;
- for (step = 0; (number_steps < 0 || step <= number_steps) && !converged; step++)
+ bool converged = false;
+ for (int step = 0; (number_steps < 0 || step <= number_steps) && !converged; step++)
{
/* Write coordinates if necessary */
- do_x = do_per_step(step, inputrec->nstxout);
- do_f = do_per_step(step, inputrec->nstfout);
+ const bool do_x = do_per_step(step, inputrec->nstxout);
+ const bool do_f = do_per_step(step, inputrec->nstfout);
- mdof_flags = 0;
+ int mdof_flags = 0;
if (do_x)
{
mdof_flags |= MDOF_X;
}
gmx::WriteCheckpointDataHolder checkpointDataHolder;
- mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
- static_cast<real>(step), &ems.s, state_global, observablesHistory,
- ems.f.view().force(), &checkpointDataHolder);
+ mdoutf_write_to_trajectory_files(fplog,
+ cr,
+ outf,
+ mdof_flags,
+ top_global.natoms,
+ step,
+ static_cast<real>(step),
+ &ems.s,
+ state_global,
+ observablesHistory,
+ ems.f.view().force(),
+ &checkpointDataHolder);
/* Do the linesearching in the direction dx[point][0..(n-1)] */
/* make s a pointer to current search direction - point=0 first time we get here */
- s = dx[point];
+ gmx::ArrayRef<const real> s = dx[point];
- real* xx = static_cast<real*>(ems.s.x.rvec_array()[0]);
- real* ff = static_cast<real*>(ems.f.view().force().data()[0]);
+ const real* xx = static_cast<real*>(ems.s.x.rvec_array()[0]);
+ const real* ff = static_cast<real*>(ems.f.view().force().data()[0]);
// calculate line gradient in position A
- for (gpa = 0, i = 0; i < n; i++)
+ double gpa = 0;
+ for (int i = 0; i < n; i++)
{
gpa -= s[i] * ff[i];
}
/* Calculate minimum allowed stepsize along the line, before the average (norm)
* relative change in coordinate is smaller than precision
*/
- for (minstep = 0, i = 0; i < n; i++)
+ double minstep = 0;
+ for (int i = 0; i < n; i++)
{
- tmp = fabs(xx[i]);
+ double tmp = fabs(xx[i]);
if (tmp < 1.0)
{
tmp = 1.0;
if (stepsize < minstep)
{
- converged = TRUE;
+ converged = true;
break;
}
// Before taking any steps along the line, store the old position
- *last = ems;
- real* lastx = static_cast<real*>(last->s.x.data()[0]);
- real* lastf = static_cast<real*>(last->f.view().force().data()[0]);
- Epot0 = ems.epot;
+ *last = ems;
+ real* lastx = static_cast<real*>(last->s.x.data()[0]);
+ real* lastf = static_cast<real*>(last->f.view().force().data()[0]);
+ const real Epot0 = ems.epot;
*sa = ems;
// State "A" is the first position along the line.
// reference position along line is initially zero
- a = 0.0;
+ real a = 0;
// Check stepsize first. We do not allow displacements
// larger than emstep.
//
+ real c;
+ real maxdelta;
do
{
// Pick a new position C by adding stepsize to A.
// Calculate what the largest change in any individual coordinate
// would be (translation along line * gradient along line)
maxdelta = 0;
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
- delta = c * s[i];
+ real delta = c * s[i];
if (delta > maxdelta)
{
maxdelta = delta;
// Take a trial step and move the coordinate array xc[] to position C
real* xc = static_cast<real*>(sc->s.x.rvec_array()[0]);
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
xc[i] = lastx[i] + c * s[i];
}
energyEvaluator.run(sc, mu_tot, vir, pres, step, FALSE);
// Calc line gradient in position C
- real* fc = static_cast<real*>(sc->f.view().force()[0]);
- for (gpc = 0, i = 0; i < n; i++)
+ real* fc = static_cast<real*>(sc->f.view().force()[0]);
+ double gpc = 0;
+ for (int i = 0; i < n; i++)
{
gpc -= s[i] * fc[i]; /* f is negative gradient, thus the sign */
}
// This is the max amount of increase in energy we tolerate.
// By allowing VERY small changes (close to numerical precision) we
// frequently find even better (lower) final energies.
- tmp = std::sqrt(GMX_REAL_EPS) * fabs(sa->epot);
+ double tmp = std::sqrt(GMX_REAL_EPS) * fabs(sa->epot);
// Accept the step if the energy is lower in the new position C (compared to A),
// or if it is not significantly higher and the line derivative is still negative.
- foundlower = sc->epot < sa->epot || (gpc < 0 && sc->epot < (sa->epot + tmp));
+ bool foundlower = sc->epot < sa->epot || (gpc < 0 && sc->epot < (sa->epot + tmp));
// If true, great, we found a better energy. We no longer try to alter the
// stepsize, but simply accept this new better position. The we select a new
// search direction instead, which will be much more efficient than continuing
// than with the stepsize, so no need to modify it. For the next search direction
// it will be reset to 1/fnorm anyway.
+ double step_taken;
if (!foundlower)
{
// OK, if we didn't find a lower value we will have to locate one now - there must
// I also have a safeguard for potentially really pathological functions so we never
// take more than 20 steps before we give up.
// If we already found a lower value we just skip this step and continue to the update.
- real fnorm = 0;
- nminstep = 0;
+ real fnorm = 0;
+ int nminstep = 0;
do
{
// Select a new trial point B in the interval [A,C].
// If the derivatives at points a & c have different sign we interpolate to zero,
// otherwise just do a bisection since there might be multiple minima/maxima
// inside the interval.
+ real b;
if (gpa < 0 && gpc > 0)
{
b = a + gpa * (a - c) / (gpc - gpa);
// Take a trial step to point B
real* xb = static_cast<real*>(sb->s.x.rvec_array()[0]);
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
xb[i] = lastx[i] + b * s[i];
}
fnorm = sb->fnorm;
// Calculate gradient in point B
- real* fb = static_cast<real*>(sb->f.view().force()[0]);
- for (gpb = 0, i = 0; i < n; i++)
+ real* fb = static_cast<real*>(sb->f.view().force()[0]);
+ double gpb = 0;
+ for (int i = 0; i < n; i++)
{
gpb -= s[i] * fb[i]; /* f is negative gradient, thus the sign */
}
if (ncorr == 0)
{
/* Converged */
- converged = TRUE;
+ converged = true;
break;
}
else
/* Reset memory */
ncorr = 0;
/* Search in gradient direction */
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
dx[point][i] = ff[i];
}
ncorr++;
}
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
dg[point][i] = lastf[i] - ff[i];
dx[point][i] *= step_taken;
}
- dgdg = 0;
- dgdx = 0;
- for (i = 0; i < n; i++)
+ real dgdg = 0;
+ real dgdx = 0;
+ for (int i = 0; i < n; i++)
{
dgdg += dg[point][i] * dg[point][i];
dgdx += dg[point][i] * dx[point][i];
}
- diag = dgdx / dgdg;
+ const real diag = dgdx / dgdg;
rho[point] = 1.0 / dgdx;
point++;
}
/* Update */
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
p[i] = ff[i];
}
- cp = point;
+ int cp = point;
/* Recursive update. First go back over the memory points */
- for (k = 0; k < ncorr; k++)
+ for (int k = 0; k < ncorr; k++)
{
cp--;
if (cp < 0)
cp = ncorr - 1;
}
- sq = 0;
- for (i = 0; i < n; i++)
+ real sq = 0;
+ for (int i = 0; i < n; i++)
{
sq += dx[cp][i] * p[i];
}
alpha[cp] = rho[cp] * sq;
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
p[i] -= alpha[cp] * dg[cp][i];
}
}
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
p[i] *= diag;
}
/* And then go forward again */
- for (k = 0; k < ncorr; k++)
+ for (int k = 0; k < ncorr; k++)
{
- yr = 0;
- for (i = 0; i < n; i++)
+ real yr = 0;
+ for (int i = 0; i < n; i++)
{
yr += p[i] * dg[cp][i];
}
- beta = rho[cp] * yr;
- beta = alpha[cp] - beta;
+ real beta = rho[cp] * yr;
+ beta = alpha[cp] - beta;
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
p[i] += beta * dx[cp][i];
}
}
}
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
if (!frozen[i])
{
if (mdrunOptions.verbose)
{
double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
- fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n", step,
- ems.epot, ems.fnorm / sqrtNumAtoms, ems.fmax, ems.a_fmax + 1);
+ fprintf(stderr,
+ "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
+ step,
+ ems.epot,
+ ems.fnorm / sqrtNumAtoms,
+ ems.fmax,
+ ems.a_fmax + 1);
fflush(stderr);
}
/* Store the new (lower) energies */
matrix nullBox = {};
- energyOutput.addDataAtEnergyStep(false, false, static_cast<double>(step), mdatoms->tmass,
- enerd, nullptr, nullptr, nullBox, PTCouplingArrays(), 0,
- nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(false,
+ false,
+ static_cast<double>(step),
+ mdatoms->tmass,
+ enerd,
+ nullptr,
+ nullptr,
+ nullBox,
+ PTCouplingArrays(),
+ 0,
+ nullptr,
+ nullptr,
+ vir,
+ pres,
+ nullptr,
+ mu_tot,
+ constr);
do_log = do_per_step(step, inputrec->nstlog);
do_ene = do_per_step(step, inputrec->nstenergy);
{
EnergyOutput::printHeader(fplog, step, step);
}
- energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
- do_log ? fplog : nullptr, step, step,
- fr->fcdata.get(), nullptr);
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
+ do_ene,
+ FALSE,
+ FALSE,
+ do_log ? fplog : nullptr,
+ step,
+ step,
+ fr->fcdata.get(),
+ nullptr);
}
/* Send x and E to IMD client, if bIMD is TRUE. */
- if (imdSession->run(step, TRUE, state_global->box, state_global->x.rvec_array(), 0) && MASTER(cr))
+ if (imdSession->run(step, TRUE, state_global->box, state_global->x, 0) && MASTER(cr))
{
imdSession->sendPositionsAndEnergies();
}
}
if (!do_ene || !do_log) /* Write final energy file entries */
{
- energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
- !do_log ? fplog : nullptr, step, step, fr->fcdata.get(),
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
+ !do_ene,
+ FALSE,
+ FALSE,
+ !do_log ? fplog : nullptr,
+ step,
+ step,
+ fr->fcdata.get(),
nullptr);
}
* However, we should only do it if we did NOT already write this step
* above (which we did if do_x or do_f was true).
*/
- do_x = !do_per_step(step, inputrec->nstxout);
- do_f = !do_per_step(step, inputrec->nstfout);
- write_em_traj(fplog, cr, outf, do_x, do_f, ftp2fn(efSTO, nfile, fnm), top_global, inputrec,
- step, &ems, state_global, observablesHistory);
+ const bool do_x = !do_per_step(step, inputrec->nstxout);
+ const bool do_f = !do_per_step(step, inputrec->nstfout);
+ write_em_traj(
+ fplog, cr, outf, do_x, do_f, ftp2fn(efSTO, nfile, fnm), top_global, inputrec, step, &ems, state_global, observablesHistory);
if (MASTER(cr))
{
void LegacySimulator::do_steep()
{
const char* SD = "Steepest Descents";
- gmx_localtop_t top(top_global->ffparams);
+ gmx_localtop_t top(top_global.ffparams);
gmx_global_stat_t gstat;
real stepsize;
real ustep;
int nsteps;
int count = 0;
int steps_accepted = 0;
- auto mdatoms = mdAtoms->mdatoms();
+ auto* mdatoms = mdAtoms->mdatoms();
GMX_LOG(mdlog.info)
.asParagraph()
em_state_t* s_try = &s1;
/* Init em and store the local state in s_try */
- init_em(fplog, mdlog, SD, cr, inputrec, imdSession, pull_work, state_global, top_global, s_try,
- &top, nrnb, fr, mdAtoms, &gstat, vsite, constr, nullptr);
+ init_em(fplog,
+ mdlog,
+ SD,
+ cr,
+ inputrec,
+ imdSession,
+ pull_work,
+ state_global,
+ top_global,
+ s_try,
+ &top,
+ nrnb,
+ fr,
+ mdAtoms,
+ &gstat,
+ vsite,
+ constr,
+ nullptr);
const bool simulationsShareState = false;
- gmx_mdoutf* outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider,
- mdModulesNotifier, inputrec, top_global, nullptr, wcycle,
- StartingBehavior::NewSimulation, simulationsShareState, ms);
- gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, inputrec, pull_work,
- nullptr, false, StartingBehavior::NewSimulation,
- simulationsShareState, mdModulesNotifier);
+ gmx_mdoutf* outf = init_mdoutf(fplog,
+ nfile,
+ fnm,
+ mdrunOptions,
+ cr,
+ outputProvider,
+ mdModulesNotifiers,
+ inputrec,
+ top_global,
+ nullptr,
+ wcycle,
+ StartingBehavior::NewSimulation,
+ simulationsShareState,
+ ms);
+ gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
+ top_global,
+ *inputrec,
+ pull_work,
+ nullptr,
+ false,
+ StartingBehavior::NewSimulation,
+ simulationsShareState,
+ mdModulesNotifiers);
/* Print to log file */
print_em_start(fplog, cr, walltime_accounting, wcycle, SD);
bool validStep = true;
if (count > 0)
{
- validStep = do_em_step(cr, inputrec, mdatoms, s_min, stepsize,
- s_min->f.view().forceWithPadding(), s_try, constr, count);
+ validStep = do_em_step(
+ cr, inputrec, mdatoms, s_min, stepsize, s_min->f.view().forceWithPadding(), s_try, constr, count);
}
if (validStep)
{
if (mdrunOptions.verbose)
{
- fprintf(stderr, "Step=%5d, Dmax= %6.1e nm, Epot= %12.5e Fmax= %11.5e, atom= %d%c",
- count, ustep, s_try->epot, s_try->fmax, s_try->a_fmax + 1,
+ fprintf(stderr,
+ "Step=%5d, Dmax= %6.1e nm, Epot= %12.5e Fmax= %11.5e, atom= %d%c",
+ count,
+ ustep,
+ s_try->epot,
+ s_try->fmax,
+ s_try->a_fmax + 1,
((count == 0) || (s_try->epot < s_min->epot)) ? '\n' : '\r');
fflush(stderr);
}
{
/* Store the new (lower) energies */
matrix nullBox = {};
- energyOutput.addDataAtEnergyStep(false, false, static_cast<double>(count),
- mdatoms->tmass, enerd, nullptr, nullptr, nullBox,
- PTCouplingArrays(), 0, nullptr, nullptr, vir, pres,
- nullptr, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(false,
+ false,
+ static_cast<double>(count),
+ mdatoms->tmass,
+ enerd,
+ nullptr,
+ nullptr,
+ nullBox,
+ PTCouplingArrays(),
+ 0,
+ nullptr,
+ nullptr,
+ vir,
+ pres,
+ nullptr,
+ mu_tot,
+ constr);
imdSession->fillEnergyRecord(count, TRUE);
const bool do_dr = do_per_step(steps_accepted, inputrec->nstdisreout);
const bool do_or = do_per_step(steps_accepted, inputrec->nstorireout);
- energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), TRUE, do_dr, do_or,
- fplog, count, count, fr->fcdata.get(), nullptr);
+ energyOutput.printStepToEnergyFile(
+ mdoutf_get_fp_ene(outf), TRUE, do_dr, do_or, fplog, count, count, fr->fcdata.get(), nullptr);
fflush(fplog);
}
}
/* Write to trn, if necessary */
do_x = do_per_step(steps_accepted, inputrec->nstxout);
do_f = do_per_step(steps_accepted, inputrec->nstfout);
- write_em_traj(fplog, cr, outf, do_x, do_f, nullptr, top_global, inputrec, count, s_min,
- state_global, observablesHistory);
+ write_em_traj(
+ fplog, cr, outf, do_x, do_f, nullptr, top_global, inputrec, count, s_min, state_global, observablesHistory);
}
else
{
if (DOMAINDECOMP(cr) && s_min->s.ddp_count != cr->dd->ddp_count)
{
/* Reload the old state */
- em_dd_partition_system(fplog, mdlog, count, cr, top_global, inputrec, imdSession,
- pull_work, s_min, &top, mdAtoms, fr, vsite, constr, nrnb, wcycle);
+ em_dd_partition_system(fplog,
+ mdlog,
+ count,
+ cr,
+ top_global,
+ inputrec,
+ imdSession,
+ pull_work,
+ s_min,
+ &top,
+ mdAtoms,
+ fr,
+ vsite,
+ constr,
+ nrnb,
+ wcycle);
}
}
}
/* Send IMD energies and positions, if bIMD is TRUE. */
- if (imdSession->run(count, TRUE, MASTER(cr) ? state_global->box : nullptr,
- MASTER(cr) ? state_global->x.rvec_array() : nullptr, 0)
+ if (imdSession->run(count,
+ TRUE,
+ MASTER(cr) ? state_global->box : nullptr,
+ MASTER(cr) ? state_global->x : gmx::ArrayRef<gmx::RVec>(),
+ 0)
&& MASTER(cr))
{
imdSession->sendPositionsAndEnergies();
{
fprintf(stderr, "\nwriting lowest energy coordinates.\n");
}
- write_em_traj(fplog, cr, outf, TRUE, inputrec->nstfout != 0, ftp2fn(efSTO, nfile, fnm),
- top_global, inputrec, count, s_min, state_global, observablesHistory);
+ write_em_traj(fplog,
+ cr,
+ outf,
+ TRUE,
+ inputrec->nstfout != 0,
+ ftp2fn(efSTO, nfile, fnm),
+ top_global,
+ inputrec,
+ count,
+ s_min,
+ state_global,
+ observablesHistory);
if (MASTER(cr))
{
finish_em(cr, outf, walltime_accounting, wcycle);
/* To print the actual number of steps we needed somewhere */
- inputrec->nsteps = count;
+ {
+ // TODO: Avoid changing inputrec (#3854)
+ auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
+ nonConstInputrec->nsteps = count;
+ }
walltime_accounting_set_nsteps_done(walltime_accounting, count);
}
{
const char* NM = "Normal Mode Analysis";
int nnodes;
- gmx_localtop_t top(top_global->ffparams);
+ gmx_localtop_t top(top_global.ffparams);
gmx_global_stat_t gstat;
tensor vir, pres;
rvec mu_tot = { 0 };
real* full_matrix = nullptr;
/* added with respect to mdrun */
- int row, col;
- real der_range = 10.0 * std::sqrt(GMX_REAL_EPS);
- real x_min;
- bool bIsMaster = MASTER(cr);
- auto mdatoms = mdAtoms->mdatoms();
+ int row, col;
+ real der_range = 10.0 * std::sqrt(GMX_REAL_EPS);
+ real x_min;
+ bool bIsMaster = MASTER(cr);
+ auto* mdatoms = mdAtoms->mdatoms();
GMX_LOG(mdlog.info)
.asParagraph()
em_state_t state_work{};
/* Init em and store the local state in state_minimum */
- init_em(fplog, mdlog, NM, cr, inputrec, imdSession, pull_work, state_global, top_global,
- &state_work, &top, nrnb, fr, mdAtoms, &gstat, vsite, constr, &shellfc);
+ init_em(fplog,
+ mdlog,
+ NM,
+ cr,
+ inputrec,
+ imdSession,
+ pull_work,
+ state_global,
+ top_global,
+ &state_work,
+ &top,
+ nrnb,
+ fr,
+ mdAtoms,
+ &gstat,
+ vsite,
+ constr,
+ &shellfc);
const bool simulationsShareState = false;
- gmx_mdoutf* outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider,
- mdModulesNotifier, inputrec, top_global, nullptr, wcycle,
- StartingBehavior::NewSimulation, simulationsShareState, ms);
+ gmx_mdoutf* outf = init_mdoutf(fplog,
+ nfile,
+ fnm,
+ mdrunOptions,
+ cr,
+ outputProvider,
+ mdModulesNotifiers,
+ inputrec,
+ top_global,
+ nullptr,
+ wcycle,
+ StartingBehavior::NewSimulation,
+ simulationsShareState,
+ ms);
std::vector<int> atom_index = get_atom_index(top_global);
std::vector<gmx::RVec> fneg(atom_index.size(), { 0, 0, 0 });
print_em_start(fplog, cr, walltime_accounting, wcycle, NM);
/* fudge nr of steps to nr of atoms */
- inputrec->nsteps = atom_index.size() * 2;
+ {
+ // TODO: Avoid changing inputrec (#3854)
+ auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
+ nonConstInputrec->nsteps = atom_index.size() * 2;
+ }
if (bIsMaster)
{
- fprintf(stderr, "starting normal mode calculation '%s'\n%" PRId64 " steps.\n\n",
- *(top_global->name), inputrec->nsteps);
+ fprintf(stderr,
+ "starting normal mode calculation '%s'\n%" PRId64 " steps.\n\n",
+ *(top_global.name),
+ inputrec->nsteps);
}
nnodes = cr->nnodes;
if (shellfc)
{
/* Now is the time to relax the shells */
- relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, nullptr, step, inputrec,
- imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
- state_work.s.natoms, state_work.s.x.arrayRefWithPadding(),
- state_work.s.v.arrayRefWithPadding(), state_work.s.box,
- state_work.s.lambda, &state_work.s.hist, &state_work.f.view(),
- vir, mdatoms, nrnb, wcycle, shellfc, fr, runScheduleWork, t,
- mu_tot, vsite, DDBalanceRegionHandler(nullptr));
+ relax_shell_flexcon(fplog,
+ cr,
+ ms,
+ mdrunOptions.verbose,
+ nullptr,
+ step,
+ inputrec,
+ imdSession,
+ pull_work,
+ bNS,
+ force_flags,
+ &top,
+ constr,
+ enerd,
+ state_work.s.natoms,
+ state_work.s.x.arrayRefWithPadding(),
+ state_work.s.v.arrayRefWithPadding(),
+ state_work.s.box,
+ state_work.s.lambda,
+ &state_work.s.hist,
+ &state_work.f.view(),
+ vir,
+ *mdatoms,
+ nrnb,
+ wcycle,
+ shellfc,
+ fr,
+ runScheduleWork,
+ t,
+ mu_tot,
+ vsite,
+ DDBalanceRegionHandler(nullptr));
bNS = false;
step++;
}
if (dx == 0)
{
- std::copy(state_work_f.begin(), state_work_f.begin() + atom_index.size(),
- fneg.begin());
+ std::copy(state_work_f.begin(), state_work_f.begin() + atom_index.size(), fneg.begin());
}
}
{
#if GMX_MPI
# define mpi_type GMX_MPI_REAL
- MPI_Send(dfdx[0], atom_index.size() * DIM, mpi_type, MASTER(cr), cr->nodeid,
- cr->mpi_comm_mygroup);
+ MPI_Send(dfdx[0], atom_index.size() * DIM, mpi_type, MASTER(cr), cr->nodeid, cr->mpi_comm_mygroup);
#endif
}
else
{
#if GMX_MPI
MPI_Status stat;
- MPI_Recv(dfdx[0], atom_index.size() * DIM, mpi_type, node, node,
- cr->mpi_comm_mygroup, &stat);
+ MPI_Recv(dfdx[0], atom_index.size() * DIM, mpi_type, node, node, cr->mpi_comm_mygroup, &stat);
# undef mpi_type
#endif
}
/* write progress */
if (bIsMaster && mdrunOptions.verbose)
{
- fprintf(stderr, "\rFinished step %d out of %td",
- std::min<int>(atom + nnodes, atom_index.size()), ssize(atom_index));
+ fprintf(stderr,
+ "\rFinished step %d out of %td",
+ std::min<int>(atom + nnodes, atom_index.size()),
+ ssize(atom_index));
fflush(stderr);
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011-2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2011-2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "replicaexchange.h"
#include "config.h"
#include "gromacs/random/threefry.h"
#include "gromacs/random/uniformintdistribution.h"
#include "gromacs/random/uniformrealdistribution.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/smalloc.h"
#define MSRANK(ms, nodeid) (nodeid)
//! Enum for replica exchange flavours
-enum
+enum class ReplicaExchangeType : int
{
- ereTEMP,
- ereLAMBDA,
- ereENDSINGLE,
- ereTL,
- ereNR
+ Temperature,
+ Lambda,
+ EndSingle,
+ TemperatureLambda,
+ Count
};
/*! \brief Strings describing replica exchange flavours.
*
* 'lambda_and_pressure', 'temperature_lambda_pressure'?; Let's wait
* until we feel better about the pressure control methods giving
* exact ensembles. Right now, we assume constant pressure */
-static const char* erename[ereNR] = { "temperature", "lambda", "end_single_marker",
- "temperature and lambda" };
+static const char* enumValueToString(ReplicaExchangeType enumValue)
+{
+ constexpr gmx::EnumerationArray<ReplicaExchangeType, const char*> replicateExchangeTypeNames = {
+ "temperature", "lambda", "end_single_marker", "temperature and lambda"
+ };
+ return replicateExchangeTypeNames[enumValue];
+}
//! Working data for replica exchange.
struct gmx_repl_ex
int nrepl;
//! Temperature
real temp;
- //! Replica exchange type from ere enum
- int type;
+ //! Replica exchange type from ReplicaExchangeType enum
+ ReplicaExchangeType type;
//! Quantity, e.g. temperature or lambda; first index is ere, second index is replica ID
- real** q;
+ gmx::EnumerationArray<ReplicaExchangeType, real*> q;
//! Use constant pressure and temperature
gmx_bool bNPT;
//! Replica pressures
// TODO We should add Doxygen here some time.
//! \cond
-static gmx_bool repl_quantity(const gmx_multisim_t* ms, struct gmx_repl_ex* re, int ere, real q)
+static gmx_bool repl_quantity(const gmx_multisim_t* ms, struct gmx_repl_ex* re, ReplicaExchangeType ere, real q)
{
real* qall;
gmx_bool bDiff;
re->repl = ms->simulationIndex_;
re->nrepl = ms->numSimulations_;
- snew(re->q, ereENDSINGLE);
fprintf(fplog, "Repl There are %d replicas:\n", re->nrepl);
* but it does guarantee that we can perform replica exchange.
*/
check_multi_int(fplog, ms, numAtomsInSystem, "the number of atoms", FALSE);
- check_multi_int(fplog, ms, ir->eI, "the integrator", FALSE);
+ check_multi_int(fplog, ms, static_cast<int>(ir->eI), "the integrator", FALSE);
check_multi_int64(fplog, ms, ir->init_step + ir->nsteps, "init_step+nsteps", FALSE);
const int nst = replExParams.exchangeInterval;
- check_multi_int64(fplog, ms, (ir->init_step + nst - 1) / nst,
- "first exchange step: init_step/-replex", FALSE);
- check_multi_int(fplog, ms, ir->etc, "the temperature coupling", FALSE);
+ check_multi_int64(
+ fplog, ms, (ir->init_step + nst - 1) / nst, "first exchange step: init_step/-replex", FALSE);
+ check_multi_int(fplog, ms, static_cast<int>(ir->etc), "the temperature coupling", FALSE);
check_multi_int(fplog, ms, ir->opts.ngtc, "the number of temperature coupling groups", FALSE);
- check_multi_int(fplog, ms, ir->epc, "the pressure coupling", FALSE);
- check_multi_int(fplog, ms, ir->efep, "free energy", FALSE);
+ check_multi_int(fplog, ms, static_cast<int>(ir->epc), "the pressure coupling", FALSE);
+ check_multi_int(fplog, ms, static_cast<int>(ir->efep), "free energy", FALSE);
check_multi_int(fplog, ms, ir->fepvals->n_lambda, "number of lambda states", FALSE);
re->temp = ir->opts.ref_t[0];
}
}
- re->type = -1;
- bTemp = repl_quantity(ms, re, ereTEMP, re->temp);
- if (ir->efep != efepNO)
+ re->type = ReplicaExchangeType::Count;
+ bTemp = repl_quantity(ms, re, ReplicaExchangeType::Temperature, re->temp);
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
- bLambda = repl_quantity(ms, re, ereLAMBDA, static_cast<real>(ir->fepvals->init_fep_state));
+ bLambda = repl_quantity(
+ ms, re, ReplicaExchangeType::Lambda, static_cast<real>(ir->fepvals->init_fep_state));
}
- if (re->type == -1) /* nothing was assigned */
+ if (re->type == ReplicaExchangeType::Count) /* nothing was assigned */
{
gmx_fatal(FARGS,
"The properties of the %d systems are all the same, there is nothing to exchange",
}
if (bLambda && bTemp)
{
- re->type = ereTL;
+ re->type = ReplicaExchangeType::TemperatureLambda;
}
if (bTemp)
{
please_cite(fplog, "Sugita1999a");
- if (ir->epc != epcNO)
+ if (ir->epc != PressureCoupling::No)
{
re->bNPT = TRUE;
fprintf(fplog, "Repl Using Constant Pressure REMD.\n");
please_cite(fplog, "Okabe2001a");
}
- if (ir->etc == etcBERENDSEN)
+ if (ir->etc == TemperatureCoupling::Berendsen)
{
gmx_fatal(FARGS,
"REMD with the %s thermostat does not produce correct potential energy "
"distributions, consider using the %s thermostat instead",
- ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
+ enumValueToString(ir->etc),
+ enumValueToString(TemperatureCoupling::VRescale));
}
}
if (bLambda)
if (re->bNPT)
{
snew(re->pres, re->nrepl);
- if (ir->epct == epctSURFACETENSION)
+ if (ir->epct == PressureCouplingType::SurfaceTension)
{
pres = ir->ref_p[ZZ][ZZ];
}
re->ind[i] = i;
}
- if (re->type < ereENDSINGLE)
+ if (re->type < ReplicaExchangeType::EndSingle)
{
for (i = 0; i < re->nrepl; i++)
gmx_fatal(FARGS,
"Replicas with indices %d < %d have %ss %g > %g, please order your "
"replicas on increasing %s",
- i, j, erename[re->type], re->q[re->type][i], re->q[re->type][j],
- erename[re->type]);
+ i,
+ j,
+ enumValueToString(re->type),
+ re->q[re->type][i],
+ re->q[re->type][j],
+ enumValueToString(re->type));
}
else if (re->q[re->type][re->ind[j]] == re->q[re->type][re->ind[i]])
{
- gmx_fatal(FARGS, "Two replicas have identical %ss", erename[re->type]);
+ gmx_fatal(FARGS, "Two replicas have identical %ss", enumValueToString(re->type));
}
}
}
switch (re->type)
{
- case ereTEMP:
+ case ReplicaExchangeType::Temperature:
fprintf(fplog, "\nReplica exchange in temperature\n");
for (i = 0; i < re->nrepl; i++)
{
}
fprintf(fplog, "\n");
break;
- case ereLAMBDA:
+ case ReplicaExchangeType::Lambda:
fprintf(fplog, "\nReplica exchange in lambda\n");
for (i = 0; i < re->nrepl; i++)
{
}
fprintf(fplog, "\n");
break;
- case ereTL:
+ case ReplicaExchangeType::TemperatureLambda:
fprintf(fplog, "\nReplica exchange in temperature and lambda state\n");
for (i = 0; i < re->nrepl; i++)
{
- fprintf(fplog, " %5.1f", re->q[ereTEMP][re->ind[i]]);
+ fprintf(fplog, " %5.1f", re->q[ReplicaExchangeType::Temperature][re->ind[i]]);
}
fprintf(fplog, "\n");
for (i = 0; i < re->nrepl; i++)
{
- fprintf(fplog, " %5d", static_cast<int>(re->q[ereLAMBDA][re->ind[i]]));
+ fprintf(fplog, " %5d", static_cast<int>(re->q[ReplicaExchangeType::Lambda][re->ind[i]]));
}
fprintf(fplog, "\n");
break;
MPI_Request mpi_req;
MPI_Isend(v, n * sizeof(double), MPI_BYTE, MSRANK(ms, b), 0, ms->mastersComm_, &mpi_req);
- MPI_Recv(buf, n * sizeof(double), MPI_BYTE, MSRANK(ms, b), 0, ms->mastersComm_,
- MPI_STATUS_IGNORE);
+ MPI_Recv(buf, n * sizeof(double), MPI_BYTE, MSRANK(ms, b), 0, ms->mastersComm_, MPI_STATUS_IGNORE);
MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
}
#endif
MPI_Request mpi_req;
MPI_Isend(v[0], n * sizeof(rvec), MPI_BYTE, MSRANK(ms, b), 0, ms->mastersComm_, &mpi_req);
- MPI_Recv(buf[0], n * sizeof(rvec), MPI_BYTE, MSRANK(ms, b), 0, ms->mastersComm_,
- MPI_STATUS_IGNORE);
+ MPI_Recv(buf[0], n * sizeof(rvec), MPI_BYTE, MSRANK(ms, b), 0, ms->mastersComm_, MPI_STATUS_IGNORE);
MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
}
#endif
switch (re->type)
{
- case ereTEMP:
+ case ReplicaExchangeType::Temperature:
/*
* Okabe et. al. Chem. Phys. Lett. 335 (2001) 435-439
*/
ediff = Epot[b] - Epot[a];
delta = -(beta[bp] - beta[ap]) * ediff;
break;
- case ereLAMBDA:
+ case ReplicaExchangeType::Lambda:
/* two cases: when we are permuted, and not. */
/* non-permuted:
ediff = E_new - E_old
ediff = (de[bp][a] - de[ap][a]) + (de[ap][b] - de[bp][b]);
delta = ediff * beta[a]; /* assume all same temperature in this case */
break;
- case ereTL:
+ case ReplicaExchangeType::TemperatureLambda:
/* not permuted: */
/* delta = reduced E_new - reduced E_old
= [beta_b H_b(x_a) + beta_a H_a(x_b)] - [beta_b H_b(x_b) + beta_a H_a(x_a)]
if (re->bNPT)
{
/* revist the calculation for 5.0. Might be some improvements. */
- dpV = (beta[ap] * re->pres[ap] - beta[bp] * re->pres[bp]) * (Vol[b] - Vol[a]) / PRESFAC;
+ dpV = (beta[ap] * re->pres[ap] - beta[bp] * re->pres[bp]) * (Vol[b] - Vol[a]) / gmx::c_presfac;
if (bPrint)
{
fprintf(fplog, " dpV = %10.3e d = %10.3e\n", dpV, delta + dpV);
bVol = TRUE;
re->Vol[re->repl] = vol;
}
- if ((re->type == ereTEMP || re->type == ereTL))
+ if ((re->type == ReplicaExchangeType::Temperature || re->type == ReplicaExchangeType::TemperatureLambda))
{
for (i = 0; i < re->nrepl; i++)
{
/* temperatures of different states*/
for (i = 0; i < re->nrepl; i++)
{
- re->beta[i] = 1.0 / (re->q[ereTEMP][i] * BOLTZ);
+ re->beta[i] = 1.0 / (re->q[ReplicaExchangeType::Temperature][i] * gmx::c_boltz);
}
}
else
{
for (i = 0; i < re->nrepl; i++)
{
- re->beta[i] = 1.0 / (re->temp * BOLTZ); /* we have a single temperature */
+ re->beta[i] = 1.0 / (re->temp * gmx::c_boltz); /* we have a single temperature */
}
}
- if (re->type == ereLAMBDA || re->type == ereTL)
+ if (re->type == ReplicaExchangeType::Lambda || re->type == ReplicaExchangeType::TemperatureLambda)
{
bDLambda = TRUE;
/* lambda differences. */
}
for (i = 0; i < re->nrepl; i++)
{
- re->de[i][re->repl] = enerd->foreignLambdaTerms.deltaH(re->q[ereLAMBDA][i]);
+ re->de[i][re->repl] =
+ enerd->foreignLambdaTerms.deltaH(re->q[ReplicaExchangeType::Lambda][i]);
}
}
}
/* For temperature-type replica exchange, we need to scale
* the velocities. */
- if (re->type == ereTEMP || re->type == ereTL)
+ if (re->type == ReplicaExchangeType::Temperature || re->type == ReplicaExchangeType::TemperatureLambda)
{
- scale_velocities(state->v, std::sqrt(re->q[ereTEMP][replica_id]
- / re->q[ereTEMP][re->destinations[replica_id]]));
+ scale_velocities(
+ state->v,
+ std::sqrt(re->q[ReplicaExchangeType::Temperature][replica_id]
+ / re->q[ReplicaExchangeType::Temperature][re->destinations[replica_id]]));
}
}
if (re->nex == 0)
{
- fprintf(fplog, "Repl %d attempts, %d odd, %d even\n", re->nattempt[0] + re->nattempt[1],
- re->nattempt[1], re->nattempt[0]);
+ fprintf(fplog,
+ "Repl %d attempts, %d odd, %d even\n",
+ re->nattempt[0] + re->nattempt[1],
+ re->nattempt[1],
+ re->nattempt[0]);
fprintf(fplog, "Repl average probabilities:\n");
for (i = 1; i < re->nrepl; i++)
* \param[in,out] globalState The global state container
* \param[in] constructVsites When true, vsite coordinates are constructed
* \param[in] vsite Vsite setup, can be nullptr when \p constructVsites = false
- * \param[in] timeStep Time step, used for constructing vsites
*/
static void prepareRerunState(const t_trxframe& rerunFrame,
t_state* globalState,
bool constructVsites,
- const VirtualSitesHandler* vsite,
- double timeStep)
+ const VirtualSitesHandler* vsite)
{
auto x = makeArrayRef(globalState->x);
auto rerunX = arrayRefFromArray(reinterpret_cast<gmx::RVec*>(rerunFrame.x), globalState->natoms);
{
GMX_ASSERT(vsite, "Need valid vsite for constructing vsites");
- vsite->construct(globalState->x, timeStep, globalState->v, globalState->box);
+ vsite->construct(globalState->x, globalState->v, globalState->box, gmx::VSiteOperation::PositionsAndVelocities);
}
}
// alias to avoid a large ripple of nearly useless changes.
// t_inputrec is being replaced by IMdpOptionsProvider, so this
// will go away eventually.
- t_inputrec* ir = inputrec;
+ const t_inputrec* ir = inputrec;
int64_t step, step_rel;
double t;
bool isLastStep = false;
t_trxstatus* status = nullptr;
rvec mu_tot;
t_trxframe rerun_fr;
- gmx_localtop_t top(top_global->ffparams);
+ gmx_localtop_t top(top_global.ffparams);
ForceBuffers f;
gmx_global_stat_t gstat;
gmx_shellfc_t* shellfc;
double cycles;
- /* Domain decomposition could incorrectly miss a bonded
- interaction, but checking for that requires a global
- communication stage, which does not otherwise happen in DD
- code. So we do that alongside the first global energy reduction
- after a new DD is made. These variables handle whether the
- check happens, and the result it returns. */
- bool shouldCheckNumberOfBondedInteractions = false;
- int totalNumberOfBondedInteractions = -1;
-
SimulationSignals signals;
// Most global communnication stages don't propagate mdrun
// signals, and will use this object to achieve that.
"be available in a different form in a future version of GROMACS, "
"e.g. gmx rerun -f.");
- if (ir->efep != efepNO
+ if (ir->efep != FreeEnergyPerturbationType::No
&& (mdAtoms->mdatoms()->nMassPerturbed > 0 || (constr && constr->havePerturbedConstraints())))
{
gmx_fatal(FARGS,
{
gmx_fatal(FARGS, "Multiple simulations not supported by rerun.");
}
- if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
- [](int i) { return i != eannNO; }))
+ if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc, [](SimulatedAnnealing i) {
+ return i != SimulatedAnnealing::No;
+ }))
{
gmx_fatal(FARGS, "Simulated annealing not supported by rerun.");
}
}
/* Settings for rerun */
- ir->nstlist = 1;
- ir->nstcalcenergy = 1;
+ {
+ // TODO: Avoid changing inputrec (#3854)
+ auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
+ nonConstInputrec->nstlist = 1;
+ nonConstInputrec->nstcalcenergy = 1;
+ nonConstInputrec->nstxout_compressed = 0;
+ }
int nstglobalcomm = 1;
const bool bNS = true;
- ir->nstxout_compressed = 0;
- const SimulationGroups* groups = &top_global->groups;
- if (ir->eI == eiMimic)
+ const SimulationGroups* groups = &top_global.groups;
+ if (ir->eI == IntegrationAlgorithm::Mimic)
{
- auto nonConstGlobalTopology = const_cast<gmx_mtop_t*>(top_global);
- nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(*top_global);
+ auto* nonConstGlobalTopology = const_cast<gmx_mtop_t*>(&top_global);
+ nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(top_global);
}
int* fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
gmx::ArrayRef<real> lambda = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
- initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
+ initialize_lambdas(fplog,
+ ir->efep,
+ ir->bSimTemp,
+ *ir->fepvals,
+ ir->simtempvals->temperatures,
+ gmx::arrayRefFromArray(ir->opts.ref_t, ir->opts.ngtc),
+ MASTER(cr),
+ fep_state,
+ lambda);
const bool simulationsShareState = false;
- gmx_mdoutf* outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider,
- mdModulesNotifier, ir, top_global, oenv, wcycle,
- StartingBehavior::NewSimulation, simulationsShareState, ms);
- gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work,
- mdoutf_get_fp_dhdl(outf), true, StartingBehavior::NewSimulation,
- simulationsShareState, mdModulesNotifier);
+ gmx_mdoutf* outf = init_mdoutf(fplog,
+ nfile,
+ fnm,
+ mdrunOptions,
+ cr,
+ outputProvider,
+ mdModulesNotifiers,
+ ir,
+ top_global,
+ oenv,
+ wcycle,
+ StartingBehavior::NewSimulation,
+ simulationsShareState,
+ ms);
+ gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
+ top_global,
+ *ir,
+ pull_work,
+ mdoutf_get_fp_dhdl(outf),
+ true,
+ StartingBehavior::NewSimulation,
+ simulationsShareState,
+ mdModulesNotifiers);
gstat = global_stat_init(ir);
/* Check for polarizable models and flexible constraints */
- shellfc = init_shell_flexcon(fplog, top_global, constr ? constr->numFlexibleConstraints() : 0,
- ir->nstcalcenergy, DOMAINDECOMP(cr),
+ shellfc = init_shell_flexcon(fplog,
+ top_global,
+ constr ? constr->numFlexibleConstraints() : 0,
+ ir->nstcalcenergy,
+ DOMAINDECOMP(cr),
runScheduleWork->simulationWork.useGpuPme);
{
- double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
+ double io = compute_io(ir, top_global.natoms, *groups, energyOutput.numEnergyTerms(), 1);
if ((io > 2000) && MASTER(cr))
{
fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
{
stateInstance = std::make_unique<t_state>();
state = stateInstance.get();
- dd_init_local_state(cr->dd, state_global, state);
+ dd_init_local_state(*cr->dd, state_global, state);
/* Distribute the charge groups over the nodes from the master node */
- dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1, state_global, *top_global, ir,
- imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
- nrnb, nullptr, FALSE);
- shouldCheckNumberOfBondedInteractions = true;
+ dd_partition_system(fplog,
+ mdlog,
+ ir->init_step,
+ cr,
+ TRUE,
+ 1,
+ state_global,
+ top_global,
+ *ir,
+ imdSession,
+ pull_work,
+ state,
+ &f,
+ mdAtoms,
+ &top,
+ fr,
+ vsite,
+ constr,
+ nrnb,
+ nullptr,
+ FALSE);
}
else
{
/* Copy the pointer to the global state */
state = state_global;
- mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
+ mdAlgorithmsSetupAtomData(cr, *ir, top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
}
- auto mdatoms = mdAtoms->mdatoms();
+ auto* mdatoms = mdAtoms->mdatoms();
// NOTE: The global state is no longer used at this point.
// But state_global is still used as temporary storage space for writing
// the global state to file and potentially for replica exchange.
// (Global topology should persist.)
- update_mdatoms(mdatoms, state->lambda[efptMASS]);
+ update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
- if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
+ if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
{
doFreeEnergyPerturbation = true;
}
{
- int cglo_flags =
- (CGLO_GSTAT
- | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
+ int cglo_flags = CGLO_GSTAT;
+ if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
+ {
+ cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
+ }
bool bSumEkinhOld = false;
t_vcm* vcm = nullptr;
- compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
- makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, nullptr, enerd,
- force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, state->box,
- &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
+ compute_globals(gstat,
+ cr,
+ ir,
+ fr,
+ ekind,
+ makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v),
+ state->box,
+ mdatoms,
+ nrnb,
+ vcm,
+ nullptr,
+ enerd,
+ force_vir,
+ shake_vir,
+ total_vir,
+ pres,
+ gmx::ArrayRef<real>{},
+ &nullSignaller,
+ state->box,
+ &bSumEkinhOld,
+ cglo_flags);
+ if (DOMAINDECOMP(cr))
+ {
+ checkNumberOfBondedInteractions(
+ mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
+ }
}
- checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
- makeConstArrayRef(state->x), state->box,
- &shouldCheckNumberOfBondedInteractions);
if (MASTER(cr))
{
fprintf(stderr,
"starting md rerun '%s', reading coordinates from"
" input trajectory '%s'\n\n",
- *(top_global->name), opt2fn("-rerun", nfile, fnm));
+ *(top_global.name),
+ opt2fn("-rerun", nfile, fnm));
if (mdrunOptions.verbose)
{
fprintf(stderr,
}
walltime_accounting_start_time(walltime_accounting);
- wallcycle_start(wcycle, ewcRUN);
+ wallcycle_start(wcycle, WallCycleCounter::Run);
print_start(fplog, cr, walltime_accounting, "mdrun");
/***********************************************************
if (MASTER(cr))
{
isLastStep = !read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm), &rerun_fr, TRX_NEED_X);
- if (rerun_fr.natoms != top_global->natoms)
+ if (rerun_fr.natoms != top_global.natoms)
{
gmx_fatal(FARGS,
"Number of atoms in trajectory (%d) does not match the "
"run input file (%d)\n",
- rerun_fr.natoms, top_global->natoms);
+ rerun_fr.natoms,
+ top_global.natoms);
}
if (ir->pbcType != PbcType::No)
"Rerun trajectory frame step %" PRId64
" time %f "
"does not contain a box, while pbc is used",
- rerun_fr.step, rerun_fr.time);
+ rerun_fr.step,
+ rerun_fr.time);
}
if (max_cutoff2(ir->pbcType, rerun_fr.box) < gmx::square(fr->rlist))
{
"Rerun trajectory frame step %" PRId64
" time %f "
"has too small box dimensions",
- rerun_fr.step, rerun_fr.time);
+ rerun_fr.step,
+ rerun_fr.time);
}
}
}
step_rel = 0;
auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
- compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false, MASTER(cr),
- ir->nstlist, mdrunOptions.reproducible, nstglobalcomm, mdrunOptions.maximumHoursToRun,
- ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
+ compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
+ false,
+ MASTER(cr),
+ ir->nstlist,
+ mdrunOptions.reproducible,
+ nstglobalcomm,
+ mdrunOptions.maximumHoursToRun,
+ ir->nstlist == 0,
+ fplog,
+ step,
+ bNS,
+ walltime_accounting);
// we don't do counter resetting in rerun - finish will always be valid
walltime_accounting_set_valid_finish(walltime_accounting);
isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
while (!isLastStep)
{
- wallcycle_start(wcycle, ewcSTEP);
+ wallcycle_start(wcycle, WallCycleCounter::Step);
if (rerun_fr.bStep)
{
t = step;
}
- if (ir->efep != efepNO && MASTER(cr))
+ if (ir->efep != FreeEnergyPerturbationType::No && MASTER(cr))
{
if (rerun_fr.bLambda)
{
"decomposition, "
"use a single rank");
}
- prepareRerunState(rerun_fr, state_global, constructVsites, vsite, ir->delta_t);
+ prepareRerunState(rerun_fr, state_global, constructVsites, vsite);
}
isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
{
/* Repartition the domain decomposition */
const bool bMasterState = true;
- dd_partition_system(fplog, mdlog, step, cr, bMasterState, nstglobalcomm, state_global,
- *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top,
- fr, vsite, constr, nrnb, wcycle, mdrunOptions.verbose);
- shouldCheckNumberOfBondedInteractions = true;
+ dd_partition_system(fplog,
+ mdlog,
+ step,
+ cr,
+ bMasterState,
+ nstglobalcomm,
+ state_global,
+ top_global,
+ *ir,
+ imdSession,
+ pull_work,
+ state,
+ &f,
+ mdAtoms,
+ &top,
+ fr,
+ vsite,
+ constr,
+ nrnb,
+ wcycle,
+ mdrunOptions.verbose);
}
if (MASTER(cr))
EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
}
- if (ir->efep != efepNO)
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
- update_mdatoms(mdatoms, state->lambda[efptMASS]);
+ update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
}
force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
if (shellfc)
{
/* Now is the time to relax the shells */
- relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
- imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
- state->natoms, state->x.arrayRefWithPadding(),
- state->v.arrayRefWithPadding(), state->box, state->lambda,
- &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
- fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
+ relax_shell_flexcon(fplog,
+ cr,
+ ms,
+ mdrunOptions.verbose,
+ enforcedRotation,
+ step,
+ ir,
+ imdSession,
+ pull_work,
+ bNS,
+ force_flags,
+ &top,
+ constr,
+ enerd,
+ state->natoms,
+ state->x.arrayRefWithPadding(),
+ state->v.arrayRefWithPadding(),
+ state->box,
+ state->lambda,
+ &state->hist,
+ &f.view(),
+ force_vir,
+ *mdatoms,
+ nrnb,
+ wcycle,
+ shellfc,
+ fr,
+ runScheduleWork,
+ t,
+ mu_tot,
+ vsite,
+ ddBalanceRegionHandler);
}
else
{
*/
Awh* awh = nullptr;
gmx_edsam* ed = nullptr;
- do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
- wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
- &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
- vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags, ddBalanceRegionHandler);
+ do_force(fplog,
+ cr,
+ ms,
+ *ir,
+ awh,
+ enforcedRotation,
+ imdSession,
+ pull_work,
+ step,
+ nrnb,
+ wcycle,
+ &top,
+ state->box,
+ state->x.arrayRefWithPadding(),
+ &state->hist,
+ &f.view(),
+ force_vir,
+ mdatoms,
+ enerd,
+ state->lambda,
+ fr,
+ runScheduleWork,
+ vsite,
+ mu_tot,
+ t,
+ ed,
+ GMX_FORCE_NS | force_flags,
+ ddBalanceRegionHandler);
}
/* Now we have the energies and forces corresponding to the
const bool isCheckpointingStep = false;
const bool doRerun = true;
const bool bSumEkinhOld = false;
- do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
- state_global, observablesHistory, top_global, fr, outf,
- energyOutput, ekind, f.view().force(), isCheckpointingStep,
- doRerun, isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
+ do_md_trajectory_writing(fplog,
+ cr,
+ nfile,
+ fnm,
+ step,
+ step_rel,
+ t,
+ ir,
+ state,
+ state_global,
+ observablesHistory,
+ top_global,
+ fr,
+ outf,
+ energyOutput,
+ ekind,
+ f.view().force(),
+ isCheckpointingStep,
+ doRerun,
+ isLastStep,
+ mdrunOptions.writeConfout,
+ bSumEkinhOld);
}
stopHandler->setSignal();
- if (vsite != nullptr)
- {
- wallcycle_start(wcycle, ewcVSITECONSTR);
- vsite->construct(state->x, ir->delta_t, state->v, state->box);
- wallcycle_stop(wcycle, ewcVSITECONSTR);
- }
-
{
const bool doInterSimSignal = false;
const bool doIntraSimSignal = true;
t_vcm* vcm = nullptr;
SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
- compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
- makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, wcycle,
- enerd, force_vir, shake_vir, total_vir, pres, constr, &signaller,
- state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
- CGLO_GSTAT | CGLO_ENERGY
- | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
- : 0));
- checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
- &top, makeConstArrayRef(state->x), state->box,
- &shouldCheckNumberOfBondedInteractions);
+ int cglo_flags = CGLO_GSTAT | CGLO_ENERGY;
+ if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
+ {
+ cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
+ }
+ compute_globals(gstat,
+ cr,
+ ir,
+ fr,
+ ekind,
+ makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v),
+ state->box,
+ mdatoms,
+ nrnb,
+ vcm,
+ wcycle,
+ enerd,
+ force_vir,
+ shake_vir,
+ total_vir,
+ pres,
+ constr != nullptr ? constr->rmsdData() : gmx::ArrayRef<real>{},
+ &signaller,
+ state->box,
+ &bSumEkinhOld,
+ cglo_flags);
+ if (DOMAINDECOMP(cr))
+ {
+ checkNumberOfBondedInteractions(
+ mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
+ }
}
/* Note: this is OK, but there are some numerical precision issues with using the convergence of
if (MASTER(cr))
{
const bool bCalcEnerStep = true;
- energyOutput.addDataAtEnergyStep(
- doFreeEnergyPerturbation, bCalcEnerStep, t, mdatoms->tmass, enerd, ir->fepvals,
- ir->expandedvals, state->box,
- PTCouplingArrays({ state->boxv, state->nosehoover_xi, state->nosehoover_vxi,
- state->nhpres_xi, state->nhpres_vxi }),
- state->fep_state, shake_vir, force_vir, total_vir, pres, ekind, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
+ bCalcEnerStep,
+ t,
+ mdatoms->tmass,
+ enerd,
+ ir->fepvals.get(),
+ ir->expandedvals.get(),
+ state->box,
+ PTCouplingArrays({ state->boxv,
+ state->nosehoover_xi,
+ state->nosehoover_vxi,
+ state->nhpres_xi,
+ state->nhpres_vxi }),
+ state->fep_state,
+ shake_vir,
+ force_vir,
+ total_vir,
+ pres,
+ ekind,
+ mu_tot,
+ constr);
const bool do_ene = true;
const bool do_log = true;
const bool do_or = ir->nstorireout != 0;
EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
- energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
- do_log ? fplog : nullptr, step, t, fr->fcdata.get(), awh);
+ energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
+ do_ene,
+ do_dr,
+ do_or,
+ do_log ? fplog : nullptr,
+ step,
+ t,
+ fr->fcdata.get(),
+ awh);
if (ir->bPull)
{
/* Ion/water position swapping.
* Not done in last step since trajectory writing happens before this call
* in the MD loop and exchanges would be lost anyway. */
- if ((ir->eSwapCoords != eswapNO) && (step > 0) && !isLastStep && do_per_step(step, ir->swap->nstswap))
+ if ((ir->eSwapCoords != SwapType::No) && (step > 0) && !isLastStep
+ && do_per_step(step, ir->swap->nstswap))
{
const bool doRerun = true;
- do_swapcoords(cr, step, t, ir, swap, wcycle, rerun_fr.x, rerun_fr.box,
- MASTER(cr) && mdrunOptions.verbose, doRerun);
+ do_swapcoords(cr,
+ step,
+ t,
+ ir,
+ swap,
+ wcycle,
+ rerun_fr.x,
+ rerun_fr.box,
+ MASTER(cr) && mdrunOptions.verbose,
+ doRerun);
}
if (MASTER(cr))
rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
}
- cycles = wallcycle_stop(wcycle, ewcSTEP);
+ cycles = wallcycle_stop(wcycle, WallCycleCounter::Step);
if (DOMAINDECOMP(cr) && wcycle)
{
dd_cycles_add(cr->dd, cycles, ddCyclStep);
#include "gromacs/domdec/localatomsetmanager.h"
#include "gromacs/domdec/partition.h"
#include "gromacs/ewald/ewald_utils.h"
+#include "gromacs/ewald/pme.h"
#include "gromacs/ewald/pme_gpu_program.h"
#include "gromacs/ewald/pme_only.h"
#include "gromacs/ewald/pme_pp_comm_gpu.h"
#include "gromacs/utility/keyvaluetree.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/loggerbuilder.h"
-#include "gromacs/utility/mdmodulenotification.h"
+#include "gromacs/utility/mdmodulesnotifiers.h"
#include "gromacs/utility/physicalnodecommunicator.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/mpiinfo.h"
#include "isimulator.h"
#include "membedholder.h"
devFlags.enableGpuBufferOps =
GMX_GPU_CUDA && useGpuForNonbonded && (getenv("GMX_USE_GPU_BUFFER_OPS") != nullptr);
- devFlags.enableGpuHaloExchange = GMX_GPU_CUDA && GMX_THREAD_MPI && getenv("GMX_GPU_DD_COMMS") != nullptr;
+ devFlags.enableGpuHaloExchange = GMX_GPU_CUDA && getenv("GMX_GPU_DD_COMMS") != nullptr;
devFlags.forceGpuUpdateDefault = (getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") != nullptr) || GMX_FAHCORE;
- devFlags.enableGpuPmePPComm =
- GMX_GPU_CUDA && GMX_THREAD_MPI && getenv("GMX_GPU_PME_PP_COMMS") != nullptr;
+ devFlags.enableGpuPmePPComm = GMX_GPU_CUDA && getenv("GMX_GPU_PME_PP_COMMS") != nullptr;
#pragma GCC diagnostic pop
+ // Direct GPU comm path is being used with CUDA_AWARE_MPI
+ // make sure underlying MPI implementation is CUDA-aware
+ if (!GMX_THREAD_MPI && (devFlags.enableGpuPmePPComm || devFlags.enableGpuHaloExchange))
+ {
+ const bool haveDetectedCudaAwareMpi =
+ (checkMpiCudaAwareSupport() == CudaAwareMpiStatus::Supported);
+ const bool forceCudaAwareMpi = (getenv("GMX_FORCE_CUDA_AWARE_MPI") != nullptr);
+
+ if (!haveDetectedCudaAwareMpi && forceCudaAwareMpi)
+ {
+ // CUDA-aware support not detected in MPI library but, user has forced it's use
+ GMX_LOG(mdlog.warning)
+ .asParagraph()
+ .appendTextFormatted(
+ "This run has forced use of 'CUDA-aware MPI'. "
+ "But, GROMACS cannot determine if underlying MPI "
+ "is CUDA-aware. GROMACS recommends use of latest openMPI version "
+ "for CUDA-aware support. "
+ "If you observe failures at runtime, try unsetting "
+ "GMX_FORCE_CUDA_AWARE_MPI environment variable.");
+ }
+
+ if (haveDetectedCudaAwareMpi || forceCudaAwareMpi)
+ {
+ devFlags.usingCudaAwareMpi = true;
+ GMX_LOG(mdlog.warning)
+ .asParagraph()
+ .appendTextFormatted(
+ "Using CUDA-aware MPI for 'GPU halo exchange' or 'GPU PME-PP "
+ "communications' feature.");
+ }
+ else
+ {
+ if (devFlags.enableGpuHaloExchange)
+ {
+ GMX_LOG(mdlog.warning)
+ .asParagraph()
+ .appendTextFormatted(
+ "GMX_GPU_DD_COMMS environment variable detected, but the 'GPU "
+ "halo exchange' feature will not be enabled as GROMACS couldn't "
+ "detect CUDA_aware support in underlying MPI implementation.");
+ devFlags.enableGpuHaloExchange = false;
+ }
+ if (devFlags.enableGpuPmePPComm)
+ {
+ GMX_LOG(mdlog.warning)
+ .asParagraph()
+ .appendText(
+ "GMX_GPU_PME_PP_COMMS environment variable detected, but the "
+ "'GPU PME-PP communications' feature will not be enabled as "
+ "GROMACS couldn't "
+ "detect CUDA_aware support in underlying MPI implementation.");
+ devFlags.enableGpuPmePPComm = false;
+ }
+
+ GMX_LOG(mdlog.warning)
+ .asParagraph()
+ .appendTextFormatted(
+ "GROMACS recommends use of latest OpenMPI version for CUDA-aware "
+ "support. "
+ "If you are certain about CUDA-aware support in your MPI library, "
+ "you can force it's use by setting environment variable "
+ " GMX_FORCE_CUDA_AWARE_MPI.");
+ }
+ }
+
if (devFlags.enableGpuBufferOps)
{
GMX_LOG(mdlog.warning)
{
try
{
- auto masterMdrunner = reinterpret_cast<const gmx::Mdrunner*>(arg);
+ const auto* masterMdrunner = reinterpret_cast<const gmx::Mdrunner*>(arg);
/* copy the arg list to make sure that it's thread-local. This
doesn't copy pointed-to items, of course; fnm, cr and fplog
are reset in the call below, all others should be const. */
#if GMX_THREAD_MPI
/* now spawn new threads that start mdrunner_start_fn(), while
the main thread returns. Thread affinity is handled later. */
- if (tMPI_Init_fn(TRUE, numThreadsToLaunch, TMPI_AFFINITY_NONE, mdrunner_start_fn,
- static_cast<const void*>(this))
+ if (tMPI_Init_fn(TRUE, numThreadsToLaunch, TMPI_AFFINITY_NONE, mdrunner_start_fn, static_cast<const void*>(this))
!= TMPI_SUCCESS)
{
GMX_THROW(gmx::InternalError("Failed to spawn thread-MPI threads"));
t_commrec* cr,
t_inputrec* ir,
int nstlist_cmdline,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const matrix box,
bool makeGpuPairList,
const gmx::CpuInfo& cpuinfo)
{
// We checked the cut-offs in grompp, but double-check here.
// We have PME+LJcutoff kernels for rcoulomb>rvdw.
- if (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == eelCUT)
+ if (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == VanDerWaalsType::Cut)
{
GMX_RELEASE_ASSERT(ir->rcoulomb >= ir->rvdw,
"With Verlet lists and PME we should have rcoulomb>=rvdw");
"With Verlet lists and no PME rcoulomb and rvdw should be identical");
}
/* For NVE simulations, we will retain the initial list buffer */
- if (EI_DYNAMICS(ir->eI) && ir->verletbuf_tol > 0 && !(EI_MD(ir->eI) && ir->etc == etcNO))
+ if (EI_DYNAMICS(ir->eI) && ir->verletbuf_tol > 0
+ && !(EI_MD(ir->eI) && ir->etc == TemperatureCoupling::No))
{
/* Update the Verlet buffer size for the current run setup */
VerletbufListSetup listSetup = verletbufGetSafeListSetup(listType);
const real rlist_new =
- calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, -1, listSetup);
+ calcVerletBufferSize(mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, -1, listSetup);
if (rlist_new != ir->rlist)
{
{
fprintf(fplog,
"\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
- ir->rlist, rlist_new, listSetup.cluster_size_i, listSetup.cluster_size_j);
+ ir->rlist,
+ rlist_new,
+ listSetup.cluster_size_i,
+ listSetup.cluster_size_j);
}
ir->rlist = rlist_new;
}
if (nstlist_cmdline > 0 && (!EI_DYNAMICS(ir->eI) || ir->verletbuf_tol <= 0))
{
- gmx_fatal(FARGS, "Can not set nstlist without %s",
+ gmx_fatal(FARGS,
+ "Can not set nstlist without %s",
!EI_DYNAMICS(ir->eI) ? "dynamics" : "verlet-buffer-tolerance");
}
if (EI_DYNAMICS(ir->eI))
{
/* Set or try nstlist values */
- increaseNstlist(fplog, cr, ir, nstlist_cmdline, mtop, box, makeGpuPairList, cpuinfo);
+ increaseNstlist(fplog, cr, ir, nstlist_cmdline, &mtop, box, makeGpuPairList, cpuinfo);
}
}
{
sprintf(sbuf_msg,
"Overriding nsteps with value passed on the command line: %s steps, %.3g ps",
- gmx_step_str(nsteps_cmdline, sbuf_steps), fabs(nsteps_cmdline * ir->delta_t));
+ gmx_step_str(nsteps_cmdline, sbuf_steps),
+ fabs(nsteps_cmdline * ir->delta_t));
}
else
{
- sprintf(sbuf_msg, "Overriding nsteps with value passed on the command line: %s steps",
+ sprintf(sbuf_msg,
+ "Overriding nsteps with value passed on the command line: %s steps",
gmx_step_str(nsteps_cmdline, sbuf_steps));
}
static void finish_run(FILE* fplog,
const gmx::MDLogger& mdlog,
const t_commrec* cr,
- const t_inputrec* inputrec,
+ const t_inputrec& inputrec,
t_nrnb nrnb[],
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle* wcycle,
gmx_walltime_accounting_t walltime_accounting,
nonbonded_verlet_t* nbv,
const gmx_pme_t* pme,
Further, we only report performance for dynamical integrators,
because those are the only ones for which we plan to
consider doing any optimizations. */
- bool printReport = EI_DYNAMICS(inputrec->eI) && SIMMASTER(cr);
+ bool printReport = EI_DYNAMICS(inputrec.eI) && SIMMASTER(cr);
if (printReport && !walltime_accounting_get_valid_finish(walltime_accounting))
{
nrnbTotalStorage = std::make_unique<t_nrnb>();
nrnb_tot = nrnbTotalStorage.get();
#if GMX_MPI
- MPI_Allreduce(nrnb->n, nrnb_tot->n, eNRNB, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
+ MPI_Allreduce(nrnb->n.data(), nrnb_tot->n.data(), eNRNB, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
#endif
}
else
{
#if GMX_MPI
/* reduce elapsed_time over all MPI ranks in the current simulation */
- MPI_Allreduce(&elapsed_time, &elapsed_time_over_all_ranks, 1, MPI_DOUBLE, MPI_SUM,
- cr->mpi_comm_mysim);
+ MPI_Allreduce(&elapsed_time, &elapsed_time_over_all_ranks, 1, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
elapsed_time_over_all_ranks /= cr->nnodes;
/* Reduce elapsed_time_over_all_threads over all MPI ranks in the
* current simulation. */
- MPI_Allreduce(&elapsed_time_over_all_threads, &elapsed_time_over_all_threads_over_all_ranks,
- 1, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
+ MPI_Allreduce(&elapsed_time_over_all_threads,
+ &elapsed_time_over_all_threads_over_all_ranks,
+ 1,
+ MPI_DOUBLE,
+ MPI_SUM,
+ cr->mpi_comm_mysim);
#endif
}
else
* to the code that handled the thread region, so that there's a
* mechanism to keep cycle counting working during the transition
* to task parallelism. */
- int nthreads_pp = gmx_omp_nthreads_get(emntNonbonded);
- int nthreads_pme = gmx_omp_nthreads_get(emntPME);
- wallcycle_scale_by_num_threads(wcycle, thisRankHasDuty(cr, DUTY_PME) && !thisRankHasDuty(cr, DUTY_PP),
- nthreads_pp, nthreads_pme);
+ int nthreads_pp = gmx_omp_nthreads_get(ModuleMultiThread::Nonbonded);
+ int nthreads_pme = gmx_omp_nthreads_get(ModuleMultiThread::Pme);
+ wallcycle_scale_by_num_threads(
+ wcycle, thisRankHasDuty(cr, DUTY_PME) && !thisRankHasDuty(cr, DUTY_PP), nthreads_pp, nthreads_pme);
auto cycle_sum(wallcycle_sum(cr, wcycle));
if (printReport)
{
- auto nbnxn_gpu_timings =
+ auto* nbnxn_gpu_timings =
(nbv != nullptr && nbv->useGpu()) ? Nbnxm::gpu_get_timings(nbv->gpu_nbv) : nullptr;
gmx_wallclock_gpu_pme_t pme_gpu_timings = {};
{
pme_gpu_get_timings(pme, &pme_gpu_timings);
}
- wallcycle_print(fplog, mdlog, cr->nnodes, cr->npmenodes, nthreads_pp, nthreads_pme,
- elapsed_time_over_all_ranks, wcycle, cycle_sum, nbnxn_gpu_timings,
+ wallcycle_print(fplog,
+ mdlog,
+ cr->nnodes,
+ cr->npmenodes,
+ nthreads_pp,
+ nthreads_pme,
+ elapsed_time_over_all_ranks,
+ wcycle,
+ cycle_sum,
+ nbnxn_gpu_timings,
&pme_gpu_timings);
- if (EI_DYNAMICS(inputrec->eI))
+ if (EI_DYNAMICS(inputrec.eI))
{
- delta_t = inputrec->delta_t;
+ delta_t = inputrec.delta_t;
}
if (fplog)
{
- print_perf(fplog, elapsed_time_over_all_threads_over_all_ranks, elapsed_time_over_all_ranks,
+ print_perf(fplog,
+ elapsed_time_over_all_threads_over_all_ranks,
+ elapsed_time_over_all_ranks,
walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
- delta_t, nbfs, mflop);
+ delta_t,
+ nbfs,
+ mflop);
}
if (bWriteStat)
{
- print_perf(stderr, elapsed_time_over_all_threads_over_all_ranks, elapsed_time_over_all_ranks,
+ print_perf(stderr,
+ elapsed_time_over_all_threads_over_all_ranks,
+ elapsed_time_over_all_ranks,
walltime_accounting_get_nsteps_done_since_reset(walltime_accounting),
- delta_t, nbfs, mflop);
+ delta_t,
+ nbfs,
+ mflop);
}
}
}
int Mdrunner::mdrunner()
{
- matrix box;
- t_forcerec* fr = nullptr;
- real ewaldcoeff_q = 0;
- real ewaldcoeff_lj = 0;
- int nChargePerturbed = -1, nTypePerturbed = 0;
- gmx_wallcycle_t wcycle;
- gmx_walltime_accounting_t walltime_accounting = nullptr;
- MembedHolder membedHolder(filenames.size(), filenames.data());
+ matrix box;
+ std::unique_ptr<t_forcerec> fr;
+ real ewaldcoeff_q = 0;
+ real ewaldcoeff_lj = 0;
+ int nChargePerturbed = -1, nTypePerturbed = 0;
+ gmx_walltime_accounting_t walltime_accounting = nullptr;
+ MembedHolder membedHolder(filenames.size(), filenames.data());
/* CAUTION: threads may be started later on in this function, so
cr doesn't reflect the final parallel state right now */
gmx_print_detected_hardware(fplog, isSimulationMasterRank && isMasterSim(ms), mdlog, hwinfo_);
- std::vector<int> gpuIdsToUse = makeGpuIdsToUse(hwinfo_->deviceInfoList, hw_opt.gpuIdsAvailable);
- const int numDevicesToUse = gmx::ssize(gpuIdsToUse);
+ std::vector<int> availableDevices =
+ makeListOfAvailableDevices(hwinfo_->deviceInfoList, hw_opt.devicesSelectedByUser);
+ const int numAvailableDevices = gmx::ssize(availableDevices);
// Print citation requests after all software/hardware printing
pleaseCiteGromacs(fplog);
/* Read (nearly) all data required for the simulation
* and keep the partly serialized tpr contents to send to other ranks later
*/
- applyGlobalSimulationState(*inputHolder_.get(), partialDeserializedTpr.get(),
- globalState.get(), inputrec.get(), &mtop);
+ applyGlobalSimulationState(
+ *inputHolder_.get(), partialDeserializedTpr.get(), globalState.get(), inputrec.get(), &mtop);
}
/* Check and update the hardware options for internal consistency */
- checkAndUpdateHardwareOptions(mdlog, &hw_opt, isSimulationMasterRank, domdecOptions.numPmeRanks,
- inputrec.get());
+ checkAndUpdateHardwareOptions(
+ mdlog, &hw_opt, isSimulationMasterRank, domdecOptions.numPmeRanks, inputrec.get());
if (GMX_THREAD_MPI && isSimulationMasterRank)
{
// the number of GPUs to choose the number of ranks.
auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
useGpuForNonbonded = decideWhetherToUseGpusForNonbondedWithThreadMpi(
- nonbondedTarget, numDevicesToUse, userGpuTaskAssignment, emulateGpuNonbonded,
+ nonbondedTarget,
+ numAvailableDevices > 0,
+ userGpuTaskAssignment,
+ emulateGpuNonbonded,
canUseGpuForNonbonded,
gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, GMX_THREAD_MPI),
hw_opt.nthreads_tmpi);
- useGpuForPme = decideWhetherToUseGpusForPmeWithThreadMpi(
- useGpuForNonbonded, pmeTarget, numDevicesToUse, userGpuTaskAssignment, *hwinfo_,
- *inputrec, hw_opt.nthreads_tmpi, domdecOptions.numPmeRanks);
+ useGpuForPme = decideWhetherToUseGpusForPmeWithThreadMpi(useGpuForNonbonded,
+ pmeTarget,
+ numAvailableDevices,
+ userGpuTaskAssignment,
+ *hwinfo_,
+ *inputrec,
+ hw_opt.nthreads_tmpi,
+ domdecOptions.numPmeRanks);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
* TODO Over-writing the user-supplied value here does
* prevent any possible subsequent checks from working
* correctly. */
- hw_opt.nthreads_tmpi =
- get_nthreads_mpi(hwinfo_, &hw_opt, numDevicesToUse, useGpuForNonbonded, useGpuForPme,
- inputrec.get(), &mtop, mdlog, membedHolder.doMembed());
+ hw_opt.nthreads_tmpi = get_nthreads_mpi(hwinfo_,
+ &hw_opt,
+ numAvailableDevices,
+ useGpuForNonbonded,
+ useGpuForPme,
+ inputrec.get(),
+ mtop,
+ mdlog,
+ membedHolder.doMembed());
// Now start the threads for thread MPI.
spawnThreads(hw_opt.nthreads_tmpi);
// On non-master ranks, allocate the object that will receive data in the following call.
inputrec = std::make_unique<t_inputrec>();
}
- init_parallel(cr->mpiDefaultCommunicator, MASTER(cr), inputrec.get(), &mtop,
+ init_parallel(cr->mpiDefaultCommunicator,
+ MASTER(cr),
+ inputrec.get(),
+ &mtop,
partialDeserializedTpr.get());
}
GMX_RELEASE_ASSERT(inputrec != nullptr, "All ranks should have a valid inputrec now");
partialDeserializedTpr.reset(nullptr);
+ GMX_RELEASE_ASSERT(
+ !inputrec->useConstantAcceleration,
+ "Linear acceleration has been removed in GROMACS 2022, and was broken for many years "
+ "before that. Use GROMACS 4.5 or earlier if you need this feature.");
+
// Now the number of ranks is known to all ranks, and each knows
// the inputrec read by the master rank. The ranks can now all run
// the task-deciding functions and will agree on the result
// without needing to communicate.
- const bool useDomainDecomposition = (PAR(cr) && !(EI_TPI(inputrec->eI) || inputrec->eI == eiNM));
+ const bool useDomainDecomposition =
+ (PAR(cr) && !(EI_TPI(inputrec->eI) || inputrec->eI == IntegrationAlgorithm::NM));
// Note that these variables describe only their own node.
//
// assignment.
auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
useGpuForNonbonded = decideWhetherToUseGpusForNonbonded(
- nonbondedTarget, userGpuTaskAssignment, emulateGpuNonbonded, canUseGpuForNonbonded,
- gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, !GMX_THREAD_MPI), gpusWereDetected);
- useGpuForPme = decideWhetherToUseGpusForPme(
- useGpuForNonbonded, pmeTarget, userGpuTaskAssignment, *hwinfo_, *inputrec,
- cr->sizeOfDefaultCommunicator, domdecOptions.numPmeRanks, gpusWereDetected);
- useGpuForBonded = decideWhetherToUseGpusForBonded(useGpuForNonbonded, useGpuForPme,
- bondedTarget, *inputrec, mtop,
- domdecOptions.numPmeRanks, gpusWereDetected);
+ nonbondedTarget,
+ userGpuTaskAssignment,
+ emulateGpuNonbonded,
+ canUseGpuForNonbonded,
+ gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, !GMX_THREAD_MPI),
+ gpusWereDetected);
+ useGpuForPme = decideWhetherToUseGpusForPme(useGpuForNonbonded,
+ pmeTarget,
+ userGpuTaskAssignment,
+ *hwinfo_,
+ *inputrec,
+ cr->sizeOfDefaultCommunicator,
+ domdecOptions.numPmeRanks,
+ gpusWereDetected);
+ useGpuForBonded = decideWhetherToUseGpusForBonded(
+ useGpuForNonbonded, useGpuForPme, bondedTarget, *inputrec, mtop, domdecOptions.numPmeRanks, gpusWereDetected);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
const DevelopmentFeatureFlags devFlags =
manageDevelopmentFeatures(mdlog, useGpuForNonbonded, pmeRunMode);
- const bool useModularSimulator =
- checkUseModularSimulator(false, inputrec.get(), doRerun, mtop, ms, replExParams,
- nullptr, doEssentialDynamics, membedHolder.doMembed());
+ const bool useModularSimulator = checkUseModularSimulator(false,
+ inputrec.get(),
+ doRerun,
+ mtop,
+ ms,
+ replExParams,
+ nullptr,
+ doEssentialDynamics,
+ membedHolder.doMembed());
// Build restraints.
// TODO: hide restraint implementation details from Mdrunner.
// TODO: Error handling
mdModules_->assignOptionsToModules(*inputrec->params, nullptr);
- // now that the MdModules know their options, they know which callbacks to sign up to
+ // now that the MDModules know their options, they know which callbacks to sign up to
mdModules_->subscribeToSimulationSetupNotifications();
- const auto& mdModulesNotifier = mdModules_->notifier().simulationSetupNotifications_;
+ const auto& setupNotifier = mdModules_->notifiers().simulationSetupNotifier_;
if (inputrec->internalParameters != nullptr)
{
- mdModulesNotifier.notify(*inputrec->internalParameters);
+ setupNotifier.notify(*inputrec->internalParameters);
}
if (fplog != nullptr)
if (SIMMASTER(cr))
{
/* In rerun, set velocities to zero if present */
- if (doRerun && ((globalState->flags & (1 << estV)) != 0))
+ if (doRerun && ((globalState->flags & enumValueToBitMask(StateEntry::V)) != 0))
{
// rerun does not use velocities
GMX_LOG(mdlog.info)
{
clear_rvec(globalState->v[i]);
}
- globalState->flags &= ~(1 << estV);
+ globalState->flags &= ~enumValueToBitMask(StateEntry::V);
}
/* now make sure the state is initialized and propagated */
/* NM and TPI parallelize over force/energy calculations, not atoms,
* so we need to initialize and broadcast the global state.
*/
- if (inputrec->eI == eiNM || inputrec->eI == eiTPI)
+ if (inputrec->eI == IntegrationAlgorithm::NM || inputrec->eI == IntegrationAlgorithm::TPI)
{
if (!MASTER(cr))
{
globalState = std::make_unique<t_state>();
}
- broadcastStateWithoutDynamics(cr->mpiDefaultCommunicator, DOMAINDECOMP(cr), PAR(cr),
- globalState.get());
+ broadcastStateWithoutDynamics(
+ cr->mpiDefaultCommunicator, DOMAINDECOMP(cr), PAR(cr), globalState.get());
}
/* A parallel command line option consistency check that we can
#endif
}
- if (doRerun && (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
+ if (doRerun && (EI_ENERGY_MINIMIZATION(inputrec->eI) || IntegrationAlgorithm::NM == inputrec->eI))
{
gmx_fatal(FARGS,
"The .mdp file specified an energy mininization or normal mode algorithm, and "
"these are not compatible with mdrun -rerun");
}
+ /* Object for collecting reasons for not using PME-only ranks */
+ SeparatePmeRanksPermitted separatePmeRanksPermitted;
+
+ /* Permit MDModules to notify whether they want to use PME-only ranks */
+ setupNotifier.notify(&separatePmeRanksPermitted);
+
+ /* If simulation is not using PME then disable PME-only ranks */
if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
{
- if (domdecOptions.numPmeRanks > 0)
- {
- gmx_fatal_collective(FARGS, cr->mpiDefaultCommunicator, MASTER(cr),
- "PME-only ranks are requested, but the system does not use PME "
- "for electrostatics or LJ");
- }
-
- domdecOptions.numPmeRanks = 0;
+ separatePmeRanksPermitted.disablePmeRanks(
+ "PME-only ranks are requested, but the system does not use PME "
+ "for electrostatics or LJ");
}
+ /* With NB GPUs we don't automatically use PME-only CPU ranks. PME ranks can
+ * improve performance with many threads per GPU, since our OpenMP
+ * scaling is bad, but it's difficult to automate the setup.
+ */
if (useGpuForNonbonded && domdecOptions.numPmeRanks < 0)
{
- /* With NB GPUs we don't automatically use PME-only CPU ranks. PME ranks can
- * improve performance with many threads per GPU, since our OpenMP
- * scaling is bad, but it's difficult to automate the setup.
- */
+ separatePmeRanksPermitted.disablePmeRanks(
+ "PME-only CPU ranks are not automatically used when "
+ "non-bonded interactions are computed on GPUs");
+ }
+
+ /* If GPU is used for PME then only 1 PME rank is permitted */
+ if (useGpuForPme && (domdecOptions.numPmeRanks < 0 || domdecOptions.numPmeRanks > 1))
+ {
+ separatePmeRanksPermitted.disablePmeRanks(
+ "PME GPU decomposition is not supported. Only one separate PME-only GPU rank "
+ "can be used.");
+ }
+
+ /* Disable PME-only ranks if some parts of the code requested so and it's up to GROMACS to decide */
+ if (!separatePmeRanksPermitted.permitSeparatePmeRanks() && domdecOptions.numPmeRanks < 0)
+ {
domdecOptions.numPmeRanks = 0;
+ GMX_LOG(mdlog.info)
+ .asParagraph()
+ .appendText("Simulation will not use PME-only ranks because: "
+ + separatePmeRanksPermitted.reasonsWhyDisabled());
}
- if (useGpuForPme)
+
+ /* If some parts of the code could not use PME-only ranks and
+ * user explicitly used mdrun -npme option then throw an error */
+ if (!separatePmeRanksPermitted.permitSeparatePmeRanks() && domdecOptions.numPmeRanks > 0)
{
- if (domdecOptions.numPmeRanks < 0)
- {
- domdecOptions.numPmeRanks = 0;
- // TODO possibly print a note that one can opt-in for a separate PME GPU rank?
- }
- else
- {
- GMX_RELEASE_ASSERT(domdecOptions.numPmeRanks <= 1,
- "PME GPU decomposition is not supported");
- }
+ gmx_fatal_collective(FARGS,
+ cr->mpiDefaultCommunicator,
+ MASTER(cr),
+ "Requested -npme %d option is not viable because: %s",
+ domdecOptions.numPmeRanks,
+ separatePmeRanksPermitted.reasonsWhyDisabled().c_str());
}
/* NMR restraints must be initialized before load_checkpoint,
/* This needs to be called before read_checkpoint to extend the state */
t_disresdata* disresdata;
snew(disresdata, 1);
- init_disres(fplog, &mtop, inputrec.get(), DisResRunMode::MDRun,
+ init_disres(fplog,
+ mtop,
+ inputrec.get(),
+ DisResRunMode::MDRun,
MASTER(cr) ? DDRole::Master : DDRole::Agent,
- PAR(cr) ? NumRanks::Multiple : NumRanks::Single, cr->mpi_comm_mysim, ms, disresdata,
- globalState.get(), replExParams.exchangeInterval > 0);
+ PAR(cr) ? NumRanks::Multiple : NumRanks::Single,
+ cr->mpi_comm_mysim,
+ ms,
+ disresdata,
+ globalState.get(),
+ replExParams.exchangeInterval > 0);
- t_oriresdata* oriresdata;
- snew(oriresdata, 1);
- init_orires(fplog, &mtop, inputrec.get(), cr, ms, globalState.get(), oriresdata);
+ std::unique_ptr<t_oriresdata> oriresData;
+ if (gmx_mtop_ftype_count(mtop, F_ORIRES) > 0)
+ {
+ oriresData = std::make_unique<t_oriresdata>(fplog, mtop, *inputrec, cr, ms, globalState.get());
+ }
- auto deform = prepareBoxDeformation(
- globalState != nullptr ? globalState->box : box, MASTER(cr) ? DDRole::Master : DDRole::Agent,
- PAR(cr) ? NumRanks::Multiple : NumRanks::Single, cr->mpi_comm_mygroup, *inputrec);
+ auto deform = prepareBoxDeformation(globalState != nullptr ? globalState->box : box,
+ MASTER(cr) ? DDRole::Master : DDRole::Agent,
+ PAR(cr) ? NumRanks::Multiple : NumRanks::Single,
+ cr->mpi_comm_mygroup,
+ *inputrec);
#if GMX_FAHCORE
/* We have to remember the generation's first step before reading checkpoint.
// Finish applying initial simulation state information from external sources on all ranks.
// Reconcile checkpoint file data with Mdrunner state established up to this point.
- applyLocalState(*inputHolder_.get(), logFileHandle, cr, domdecOptions.numCells,
- inputrec.get(), globalState.get(), &observablesHistory,
- mdrunOptions.reproducible, mdModules_->notifier(),
- modularSimulatorCheckpointData.get(), useModularSimulator);
+ applyLocalState(*inputHolder_.get(),
+ logFileHandle,
+ cr,
+ domdecOptions.numCells,
+ inputrec.get(),
+ globalState.get(),
+ &observablesHistory,
+ mdrunOptions.reproducible,
+ mdModules_->notifiers(),
+ modularSimulatorCheckpointData.get(),
+ useModularSimulator);
// TODO: (#3652) Synchronize filesystem state, SimulationInput contents, and program
// invariants
// on all code paths.
gmx_bcast(sizeof(box), box, cr->mpiDefaultCommunicator);
}
- if (inputrec->cutoff_scheme != ecutsVERLET)
+ if (inputrec->cutoff_scheme != CutoffScheme::Verlet)
{
gmx_fatal(FARGS,
"This group-scheme .tpr file can no longer be run by mdrun. Please update to the "
* increase rlist) tries to check if the newly chosen value fits with the DD scheme. As this is
* run before any DD scheme is set up, this check is never executed. See #3334 for more details.
*/
- prepare_verlet_scheme(fplog, cr, inputrec.get(), nstlist_cmdline, &mtop, box,
+ prepare_verlet_scheme(fplog,
+ cr,
+ inputrec.get(),
+ nstlist_cmdline,
+ mtop,
+ box,
useGpuForNonbonded || (emulateGpuNonbonded == EmulateGpuNonbonded::Yes),
*hwinfo_->cpuInfo);
if (useDomainDecomposition)
{
ddBuilder = std::make_unique<DomainDecompositionBuilder>(
- mdlog, cr, domdecOptions, mdrunOptions, mtop, *inputrec, box,
+ mdlog,
+ cr,
+ domdecOptions,
+ mdrunOptions,
+ mtop,
+ *inputrec,
+ box,
positionsFromStatePointer(globalState.get()));
}
else
// Produce the task assignment for this rank - done after DD is constructed
GpuTaskAssignments gpuTaskAssignments = GpuTaskAssignmentsBuilder::build(
- gpuIdsToUse, userGpuTaskAssignment, *hwinfo_, simulationCommunicator, physicalNodeComm,
- nonbondedTarget, pmeTarget, bondedTarget, updateTarget, useGpuForNonbonded,
- useGpuForPme, thisRankHasDuty(cr, DUTY_PP),
+ availableDevices,
+ userGpuTaskAssignment,
+ *hwinfo_,
+ simulationCommunicator,
+ physicalNodeComm,
+ nonbondedTarget,
+ pmeTarget,
+ bondedTarget,
+ updateTarget,
+ useGpuForNonbonded,
+ useGpuForPme,
+ thisRankHasDuty(cr, DUTY_PP),
// TODO cr->duty & DUTY_PME should imply that a PME
// algorithm is active, but currently does not.
EEL_PME(inputrec->coulombtype) && thisRankHasDuty(cr, DUTY_PME));
const bool useUpdateGroups = cr->dd ? ddUsesUpdateGroups(*cr->dd) : false;
const bool haveFrozenAtoms = inputrecFrozenAtoms(inputrec.get());
- useGpuForUpdate = decideWhetherToUseGpuForUpdate(
- useDomainDecomposition, useUpdateGroups, pmeRunMode, domdecOptions.numPmeRanks > 0,
- useGpuForNonbonded, updateTarget, gpusWereDetected, *inputrec, mtop,
- doEssentialDynamics, gmx_mtop_ftype_count(mtop, F_ORIRES) > 0,
- replExParams.exchangeInterval > 0, haveFrozenAtoms, doRerun, devFlags, mdlog);
+ useGpuForUpdate = decideWhetherToUseGpuForUpdate(useDomainDecomposition,
+ useUpdateGroups,
+ pmeRunMode,
+ domdecOptions.numPmeRanks > 0,
+ useGpuForNonbonded,
+ updateTarget,
+ gpusWereDetected,
+ *inputrec,
+ mtop,
+ doEssentialDynamics,
+ gmx_mtop_ftype_count(mtop, F_ORIRES) > 0,
+ replExParams.exchangeInterval > 0,
+ haveFrozenAtoms,
+ doRerun,
+ devFlags,
+ mdlog);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
MdrunScheduleWorkload runScheduleWork;
- bool useGpuDirectHalo = decideWhetherToUseGpuForHalo(
- devFlags, havePPDomainDecomposition(cr), useGpuForNonbonded, useModularSimulator,
- doRerun, EI_ENERGY_MINIMIZATION(inputrec->eI));
+ bool useGpuDirectHalo = decideWhetherToUseGpuForHalo(devFlags,
+ havePPDomainDecomposition(cr),
+ useGpuForNonbonded,
+ useModularSimulator,
+ doRerun,
+ EI_ENERGY_MINIMIZATION(inputrec->eI));
// Also populates the simulation constant workload description.
- runScheduleWork.simulationWork = createSimulationWorkload(
- *inputrec, disableNonbondedCalculation, devFlags, useGpuForNonbonded, pmeRunMode,
- useGpuForBonded, useGpuForUpdate, useGpuDirectHalo);
+ runScheduleWork.simulationWork = createSimulationWorkload(*inputrec,
+ disableNonbondedCalculation,
+ devFlags,
+ useGpuForNonbonded,
+ pmeRunMode,
+ useGpuForBonded,
+ useGpuForUpdate,
+ useGpuDirectHalo);
std::unique_ptr<DeviceStreamManager> deviceStreamManager = nullptr;
// where appropriate.
if (!userGpuTaskAssignment.empty())
{
- gpuTaskAssignments.logPerformanceHints(mdlog, numDevicesToUse);
+ gpuTaskAssignments.logPerformanceHints(mdlog, numAvailableDevices);
}
if (PAR(cr))
.appendTextFormatted(
"This is simulation %d out of %d running as a composite GROMACS\n"
"multi-simulation job. Setup for this simulation:\n",
- ms->simulationIndex_, ms->numSimulations_);
+ ms->simulationIndex_,
+ ms->numSimulations_);
}
GMX_LOG(mdlog.warning)
- .appendTextFormatted("Using %d MPI %s\n", cr->nnodes,
+ .appendTextFormatted("Using %d MPI %s\n",
+ cr->nnodes,
# if GMX_THREAD_MPI
cr->nnodes == 1 ? "thread" : "threads"
# else
// the OpenMP support.
gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo_->nthreads_hw_avail, FALSE);
/* Check and update the number of OpenMP threads requested */
- checkAndUpdateRequestedNumOpenmpThreads(&hw_opt, *hwinfo_, cr, ms, physicalNodeComm.size_,
- pmeRunMode, mtop, *inputrec);
-
- gmx_omp_nthreads_init(mdlog, cr, hwinfo_->nthreads_hw_avail, physicalNodeComm.size_,
- hw_opt.nthreads_omp, hw_opt.nthreads_omp_pme, !thisRankHasDuty(cr, DUTY_PP));
-
- // Enable FP exception detection, but not in
- // Release mode and not for compilers with known buggy FP
- // exception support (clang with any optimization) or suspected
- // buggy FP exception support (gcc 7.* with optimization).
-#if !defined NDEBUG \
- && !((defined __clang__ || (defined(__GNUC__) && !defined(__ICC) && __GNUC__ == 7)) \
- && defined __OPTIMIZE__)
- const bool bEnableFPE = true;
-#else
- const bool bEnableFPE = false;
-#endif
+ checkAndUpdateRequestedNumOpenmpThreads(
+ &hw_opt, *hwinfo_, cr, ms, physicalNodeComm.size_, pmeRunMode, mtop, *inputrec);
+
+ gmx_omp_nthreads_init(mdlog,
+ cr,
+ hwinfo_->nthreads_hw_avail,
+ physicalNodeComm.size_,
+ hw_opt.nthreads_omp,
+ hw_opt.nthreads_omp_pme,
+ !thisRankHasDuty(cr, DUTY_PP));
+
+ const bool bEnableFPE = gmxShouldEnableFPExceptions();
// FIXME - reconcile with gmx_feenableexcept() call from CommandLineModuleManager::run()
if (bEnableFPE)
{
}
/* Now that we know the setup is consistent, check for efficiency */
- check_resource_division_efficiency(hwinfo_, gpuTaskAssignments.thisRankHasAnyGpuTask(),
- mdrunOptions.ntompOptionIsSet, cr, mdlog);
+ check_resource_division_efficiency(
+ hwinfo_, gpuTaskAssignments.thisRankHasAnyGpuTask(), mdrunOptions.ntompOptionIsSet, cr, mdlog);
/* getting number of PP/PME threads on this MPI / tMPI rank.
PME: env variable should be read only on one node to make sure it is
identical everywhere;
*/
- const int numThreadsOnThisRank = thisRankHasDuty(cr, DUTY_PP) ? gmx_omp_nthreads_get(emntNonbonded)
- : gmx_omp_nthreads_get(emntPME);
- checkHardwareOversubscription(numThreadsOnThisRank, cr->nodeid, *hwinfo_->hardwareTopology,
- physicalNodeComm, mdlog);
+ const int numThreadsOnThisRank = thisRankHasDuty(cr, DUTY_PP)
+ ? gmx_omp_nthreads_get(ModuleMultiThread::Nonbonded)
+ : gmx_omp_nthreads_get(ModuleMultiThread::Pme);
+ checkHardwareOversubscription(
+ numThreadsOnThisRank, cr->nodeid, *hwinfo_->hardwareTopology, physicalNodeComm, mdlog);
// Enable Peer access between GPUs where available
// Only for DD, only master PP rank needs to perform setup, and only if thread MPI plus
&& (runScheduleWork.simulationWork.useGpuHaloExchange
|| runScheduleWork.simulationWork.useGpuPmePpCommunication))
{
- setupGpuDevicePeerAccess(gpuIdsToUse, mdlog);
+ setupGpuDevicePeerAccess(gpuTaskAssignments.deviceIdsAssigned(), mdlog);
}
if (hw_opt.threadAffinity != ThreadAffinity::Off)
gmx_check_thread_affinity_set(mdlog, &hw_opt, hwinfo_->nthreads_hw_avail, TRUE);
int numThreadsOnThisNode, intraNodeThreadOffset;
- analyzeThreadsOnThisNode(physicalNodeComm, numThreadsOnThisRank, &numThreadsOnThisNode,
- &intraNodeThreadOffset);
+ analyzeThreadsOnThisNode(
+ physicalNodeComm, numThreadsOnThisRank, &numThreadsOnThisNode, &intraNodeThreadOffset);
/* Set the CPU affinity */
- gmx_set_thread_affinity(mdlog, cr, &hw_opt, *hwinfo_->hardwareTopology, numThreadsOnThisRank,
- numThreadsOnThisNode, intraNodeThreadOffset, nullptr);
+ gmx_set_thread_affinity(mdlog,
+ cr,
+ &hw_opt,
+ *hwinfo_->hardwareTopology,
+ numThreadsOnThisRank,
+ numThreadsOnThisNode,
+ intraNodeThreadOffset,
+ nullptr);
}
if (mdrunOptions.timingOptions.resetStep > -1)
"The -resetstep functionality is deprecated, and may be removed in a "
"future version.");
}
- wcycle = wallcycle_init(fplog, mdrunOptions.timingOptions.resetStep, cr);
+ std::unique_ptr<gmx_wallcycle> wcycle =
+ wallcycle_init(fplog, mdrunOptions.timingOptions.resetStep, cr);
if (PAR(cr))
{
/* Master synchronizes its value of reset_counters with all nodes
* including PME only nodes */
- int64_t reset_counters = wcycle_get_reset_counters(wcycle);
+ int64_t reset_counters = wcycle_get_reset_counters(wcycle.get());
gmx_bcast(sizeof(reset_counters), &reset_counters, cr->mpi_comm_mysim);
- wcycle_set_reset_counters(wcycle, reset_counters);
+ wcycle_set_reset_counters(wcycle.get(), reset_counters);
}
// Membrane embedding must be initialized before we call init_forcerec()
- membedHolder.initializeMembed(fplog, filenames.size(), filenames.data(), &mtop, inputrec.get(),
- globalState.get(), cr, &mdrunOptions.checkpointOptions.period);
+ membedHolder.initializeMembed(fplog,
+ filenames.size(),
+ filenames.data(),
+ &mtop,
+ inputrec.get(),
+ globalState.get(),
+ cr,
+ &mdrunOptions.checkpointOptions.period);
const bool thisRankHasPmeGpuTask = gpuTaskAssignments.thisRankHasPmeGpuTask();
std::unique_ptr<MDAtoms> mdAtoms;
t_nrnb nrnb;
if (thisRankHasDuty(cr, DUTY_PP))
{
- mdModulesNotifier.notify(*cr);
- mdModulesNotifier.notify(&atomSets);
- mdModulesNotifier.notify(inputrec->pbcType);
- mdModulesNotifier.notify(SimulationTimeStep{ inputrec->delta_t });
+ setupNotifier.notify(*cr);
+ setupNotifier.notify(&atomSets);
+ setupNotifier.notify(mtop);
+ setupNotifier.notify(inputrec->pbcType);
+ setupNotifier.notify(SimulationTimeStep{ inputrec->delta_t });
/* Initiate forcerecord */
- fr = new t_forcerec;
+ fr = std::make_unique<t_forcerec>();
fr->forceProviders = mdModules_->initForceProviders();
- init_forcerec(fplog, mdlog, fr, inputrec.get(), &mtop, cr, box,
+ init_forcerec(fplog,
+ mdlog,
+ fr.get(),
+ *inputrec,
+ mtop,
+ cr,
+ box,
opt2fn("-table", filenames.size(), filenames.data()),
opt2fn("-tablep", filenames.size(), filenames.data()),
- opt2fns("-tableb", filenames.size(), filenames.data()), pforce);
+ opt2fns("-tableb", filenames.size(), filenames.data()),
+ pforce);
// Dirty hack, for fixing disres and orires should be made mdmodules
fr->fcdata->disres = disresdata;
- fr->fcdata->orires = oriresdata;
+ fr->fcdata->orires.swap(oriresData);
// Save a handle to device stream manager to use elsewhere in the code
// TODO: Forcerec is not a correct place to store it.
"GPU PP-PME stream should be valid in order to use GPU PME-PP direct "
"communications.");
fr->pmePpCommGpu = std::make_unique<gmx::PmePpCommGpu>(
- cr->mpi_comm_mysim, cr->dd->pme_nodeid, deviceStreamManager->context(),
+ cr->mpi_comm_mysim,
+ cr->dd->pme_nodeid,
+ deviceStreamManager->context(),
deviceStreamManager->stream(DeviceStreamType::PmePpTransfer));
}
- fr->nbv = Nbnxm::init_nb_verlet(mdlog, inputrec.get(), fr, cr, *hwinfo_,
+ fr->nbv = Nbnxm::init_nb_verlet(mdlog,
+ *inputrec,
+ *fr,
+ cr,
+ *hwinfo_,
runScheduleWork.simulationWork.useGpuNonbonded,
- deviceStreamManager.get(), &mtop, box, wcycle);
+ deviceStreamManager.get(),
+ mtop,
+ box,
+ wcycle.get());
// TODO: Move the logic below to a GPU bonded builder
if (runScheduleWork.simulationWork.useGpuBonded)
{
"GPU device stream manager should be valid in order to use GPU "
"version of bonded forces.");
gpuBonded = std::make_unique<GpuBonded>(
- mtop.ffparams, fr->ic->epsfac * fr->fudgeQQ, deviceStreamManager->context(),
- deviceStreamManager->bondedStream(havePPDomainDecomposition(cr)), wcycle);
+ mtop.ffparams,
+ fr->ic->epsfac * fr->fudgeQQ,
+ deviceStreamManager->context(),
+ deviceStreamManager->bondedStream(havePPDomainDecomposition(cr)),
+ wcycle.get());
fr->gpuBonded = gpuBonded.get();
}
}
/* Initialize the virtual site communication */
- vsite = makeVirtualSitesHandler(mtop, cr, fr->pbcType);
+ gmx::ArrayRef<const gmx::RangePartitioning> updateGroupingsPerMoleculeType;
+ if (DOMAINDECOMP(cr))
+ {
+ updateGroupingsPerMoleculeType = getUpdateGroupingsPerMoleculeType(*cr->dd);
+ }
+ vsite = makeVirtualSitesHandler(mtop, cr, fr->pbcType, updateGroupingsPerMoleculeType);
calc_shifts(box, fr->shift_vec);
constructVirtualSitesGlobal(mtop, globalState->x);
}
}
+ // Make the DD reverse topology, now that any vsites that are present are available
+ if (DOMAINDECOMP(cr))
+ {
+ dd_make_reverse_top(fplog, cr->dd, mtop, vsite.get(), *inputrec, domdecOptions.ddBondedChecking);
+ }
if (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
{
? &deviceStreamManager->stream(DeviceStreamType::Pme)
: nullptr;
- pmedata = gmx_pme_init(cr, getNumPmeDomains(cr->dd), inputrec.get(),
- nChargePerturbed != 0, nTypePerturbed != 0,
- mdrunOptions.reproducible, ewaldcoeff_q, ewaldcoeff_lj,
- gmx_omp_nthreads_get(emntPME), pmeRunMode, nullptr,
- deviceContext, pmeStream, pmeGpuProgram.get(), mdlog);
+ pmedata = gmx_pme_init(cr,
+ getNumPmeDomains(cr->dd),
+ inputrec.get(),
+ nChargePerturbed != 0,
+ nTypePerturbed != 0,
+ mdrunOptions.reproducible,
+ ewaldcoeff_q,
+ ewaldcoeff_lj,
+ gmx_omp_nthreads_get(ModuleMultiThread::Pme),
+ pmeRunMode,
+ nullptr,
+ deviceContext,
+ pmeStream,
+ pmeGpuProgram.get(),
+ mdlog);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
if (thisRankHasDuty(cr, DUTY_PP))
{
/* Assumes uniform use of the number of OpenMP threads */
- walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));
+ walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(ModuleMultiThread::Default));
if (inputrec->bPull)
{
/* Initialize pull code */
- pull_work = init_pull(fplog, inputrec->pull.get(), inputrec.get(), &mtop, cr, &atomSets,
+ pull_work = init_pull(fplog,
+ inputrec->pull.get(),
+ inputrec.get(),
+ mtop,
+ cr,
+ &atomSets,
inputrec->fepvals->init_lambda);
if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage)
{
if (inputrec->bRot)
{
/* Initialize enforced rotation code */
- enforcedRotation = init_rot(fplog, inputrec.get(), filenames.size(), filenames.data(),
- cr, &atomSets, globalState.get(), &mtop, oenv, mdrunOptions,
+ enforcedRotation = init_rot(fplog,
+ inputrec.get(),
+ filenames.size(),
+ filenames.data(),
+ cr,
+ &atomSets,
+ globalState.get(),
+ mtop,
+ oenv,
+ mdrunOptions,
startingBehavior);
}
t_swap* swap = nullptr;
- if (inputrec->eSwapCoords != eswapNO)
+ if (inputrec->eSwapCoords != SwapType::No)
{
/* Initialize ion swapping code */
- swap = init_swapcoords(fplog, inputrec.get(),
+ swap = init_swapcoords(fplog,
+ inputrec.get(),
opt2fn_master("-swap", filenames.size(), filenames.data(), cr),
- &mtop, globalState.get(), &observablesHistory, cr, &atomSets,
- oenv, mdrunOptions, startingBehavior);
+ mtop,
+ globalState.get(),
+ &observablesHistory,
+ cr,
+ &atomSets,
+ oenv,
+ mdrunOptions,
+ startingBehavior);
}
/* Let makeConstraints know whether we have essential dynamics constraints. */
- auto constr = makeConstraints(mtop, *inputrec, pull_work, doEssentialDynamics, fplog, cr,
- ms, &nrnb, wcycle, fr->bMolPBC);
+ auto constr = makeConstraints(mtop,
+ *inputrec,
+ pull_work,
+ doEssentialDynamics,
+ fplog,
+ cr,
+ DOMAINDECOMP(cr) && ddMayHaveSplitConstraints(*cr->dd),
+ ms,
+ &nrnb,
+ wcycle.get(),
+ fr->bMolPBC);
/* Energy terms and groups */
gmx_enerdata_t enerd(mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size(),
// cos acceleration is only supported by md, but older tpr
// files might still combine it with other integrators
- GMX_RELEASE_ASSERT(inputrec->cos_accel == 0.0 || inputrec->eI == eiMD,
+ GMX_RELEASE_ASSERT(inputrec->cos_accel == 0.0 || inputrec->eI == IntegrationAlgorithm::MD,
"cos_acceleration is only supported by integrator=md");
/* Kinetic energy data */
- gmx_ekindata_t ekind;
- init_ekindata(fplog, &mtop, &(inputrec->opts), &ekind, inputrec->cos_accel);
+ gmx_ekindata_t ekind(inputrec->opts.ngtc,
+ inputrec->cos_accel,
+ gmx_omp_nthreads_get(ModuleMultiThread::Update));
/* Set up interactive MD (IMD) */
- auto imdSession =
- makeImdSession(inputrec.get(), cr, wcycle, &enerd, ms, &mtop, mdlog,
- MASTER(cr) ? globalState->x.rvec_array() : nullptr, filenames.size(),
- filenames.data(), oenv, mdrunOptions.imdOptions, startingBehavior);
+ auto imdSession = makeImdSession(inputrec.get(),
+ cr,
+ wcycle.get(),
+ &enerd,
+ ms,
+ mtop,
+ mdlog,
+ MASTER(cr) ? globalState->x : gmx::ArrayRef<gmx::RVec>(),
+ filenames.size(),
+ filenames.data(),
+ oenv,
+ mdrunOptions.imdOptions,
+ startingBehavior);
if (DOMAINDECOMP(cr))
{
GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
- /* This call is not included in init_domain_decomposition mainly
+ /* This call is not included in init_domain_decomposition
* because fr->cginfo_mb is set later.
*/
- dd_init_bondeds(fplog, cr->dd, mtop, vsite.get(), inputrec.get(),
- domdecOptions.checkBondedInteractions, fr->cginfo_mb);
+ makeBondedLinks(cr->dd, mtop, fr->cginfo_mb);
}
if (runScheduleWork.simulationWork.useGpuBufferOps)
{
fr->gpuForceReduction[gmx::AtomLocality::Local] = std::make_unique<gmx::GpuForceReduction>(
deviceStreamManager->context(),
- deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedLocal), wcycle);
+ deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedLocal),
+ wcycle.get());
fr->gpuForceReduction[gmx::AtomLocality::NonLocal] = std::make_unique<gmx::GpuForceReduction>(
deviceStreamManager->context(),
- deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedNonLocal), wcycle);
+ deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedNonLocal),
+ wcycle.get());
}
std::unique_ptr<gmx::StatePropagatorDataGpu> stateGpu;
&& ((runScheduleWork.simulationWork.useGpuPme && thisRankHasDuty(cr, DUTY_PME))
|| runScheduleWork.simulationWork.useGpuBufferOps))
{
- GpuApiCallBehavior transferKind = (inputrec->eI == eiMD && !doRerun && !useModularSimulator)
- ? GpuApiCallBehavior::Async
- : GpuApiCallBehavior::Sync;
+ GpuApiCallBehavior transferKind =
+ (inputrec->eI == IntegrationAlgorithm::MD && !doRerun && !useModularSimulator)
+ ? GpuApiCallBehavior::Async
+ : GpuApiCallBehavior::Sync;
GMX_RELEASE_ASSERT(deviceStreamManager != nullptr,
"GPU device stream manager should be initialized to use GPU.");
stateGpu = std::make_unique<gmx::StatePropagatorDataGpu>(
- *deviceStreamManager, transferKind, pme_gpu_get_block_size(fr->pmedata), wcycle);
+ *deviceStreamManager, transferKind, pme_gpu_get_block_size(fr->pmedata), wcycle.get());
fr->stateGpu = stateGpu.get();
}
simulatorBuilder.add(SimulatorEnv(fplog, cr, ms, mdlog, oenv));
- simulatorBuilder.add(Profiling(&nrnb, walltime_accounting, wcycle));
+ simulatorBuilder.add(Profiling(&nrnb, walltime_accounting, wcycle.get()));
simulatorBuilder.add(ConstraintsParam(
- constr.get(), enforcedRotation ? enforcedRotation->getLegacyEnfrot() : nullptr,
- vsite.get()));
+ constr.get(), enforcedRotation ? enforcedRotation->getLegacyEnfrot() : nullptr, vsite.get()));
// TODO: Separate `fr` to a separate add, and make the `build` handle the coupling sensibly.
- simulatorBuilder.add(LegacyInput(static_cast<int>(filenames.size()), filenames.data(),
- inputrec.get(), fr));
+ simulatorBuilder.add(LegacyInput(
+ static_cast<int>(filenames.size()), filenames.data(), inputrec.get(), fr.get()));
simulatorBuilder.add(ReplicaExchangeParameters(replExParams));
simulatorBuilder.add(InteractiveMD(imdSession.get()));
- simulatorBuilder.add(SimulatorModules(mdModules_->outputProvider(), mdModules_->notifier()));
+ simulatorBuilder.add(SimulatorModules(mdModules_->outputProvider(), mdModules_->notifiers()));
simulatorBuilder.add(CenterOfMassPulling(pull_work));
// Todo move to an MDModule
simulatorBuilder.add(IonSwapping(swap));
- simulatorBuilder.add(TopologyData(&mtop, mdAtoms.get()));
+ simulatorBuilder.add(TopologyData(mtop, mdAtoms.get()));
simulatorBuilder.add(BoxDeformationHandle(deform.get()));
simulatorBuilder.add(std::move(modularSimulatorCheckpointData));
{
GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
/* do PME only */
- walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
- gmx_pmeonly(pmedata, cr, &nrnb, wcycle, walltime_accounting, inputrec.get(), pmeRunMode,
+ walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(ModuleMultiThread::Pme));
+ gmx_pmeonly(pmedata,
+ cr,
+ &nrnb,
+ wcycle.get(),
+ walltime_accounting,
+ inputrec.get(),
+ pmeRunMode,
+ runScheduleWork.simulationWork.useGpuPmePpCommunication,
deviceStreamManager.get());
}
- wallcycle_stop(wcycle, ewcRUN);
+ wallcycle_stop(wcycle.get(), WallCycleCounter::Run);
/* Finish up, write some stuff
* if rerunMD, don't write last frame again
*/
- finish_run(fplog, mdlog, cr, inputrec.get(), &nrnb, wcycle, walltime_accounting,
- fr ? fr->nbv.get() : nullptr, pmedata, EI_DYNAMICS(inputrec->eI) && !isMultiSim(ms));
+ finish_run(fplog,
+ mdlog,
+ cr,
+ *inputrec,
+ &nrnb,
+ wcycle.get(),
+ walltime_accounting,
+ fr ? fr->nbv.get() : nullptr,
+ pmedata,
+ EI_DYNAMICS(inputrec->eI) && !isMultiSim(ms));
- // clean up cycle counter
- wallcycle_destroy(wcycle);
deviceStreamManager.reset(nullptr);
// Free PME data
globalState.reset(nullptr);
mdModules_.reset(nullptr); // destruct force providers here as they might also use the GPU
gpuBonded.reset(nullptr);
- /* Free pinned buffers in *fr */
- delete fr;
- fr = nullptr;
+ fr.reset(nullptr); // destruct forcerec before gpu
// TODO convert to C++ so we can get rid of these frees
sfree(disresdata);
- sfree(oriresdata);
if (!hwinfo_->deviceInfoList.empty())
{
{
physicalNodeComm.barrier();
}
- releaseDevice(deviceInfo);
+
+ if (!devFlags.usingCudaAwareMpi)
+ {
+ // Don't reset GPU in case of CUDA-AWARE MPI
+ // UCX creates CUDA buffers which are cleaned-up as part of MPI_Finalize()
+ // resetting the device before MPI_Finalize() results in crashes inside UCX
+ releaseDevice(deviceInfo);
+ }
/* Does what it says */
print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vecdump.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/force_flags.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
-#include "gromacs/mdlib/mdatoms.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/enerdata.h"
* started, but even when called, the prediction was always
* over-written by a subsequent call in the MD loop, so has been
* removed. */
-static void predict_shells(FILE* fplog,
- ArrayRef<RVec> x,
- ArrayRef<RVec> v,
- real dt,
- ArrayRef<const t_shell> shells,
- const real mass[],
- gmx_mtop_t* mtop,
- gmx_bool bInit)
+static void predict_shells(FILE* fplog,
+ ArrayRef<RVec> x,
+ ArrayRef<RVec> v,
+ real dt,
+ ArrayRef<const t_shell> shells,
+ gmx::ArrayRef<const real> mass,
+ gmx_bool bInit)
{
int m, n1, n2, n3;
real dt_1, fudge, tm, m1, m2, m3;
- GMX_RELEASE_ASSERT(mass || mtop, "Must have masses or a way to look them up");
-
/* We introduce a fudge factor for performance reasons: with this choice
* the initial force on the shells is about a factor of two lower than
* without
dt_1 = fudge * dt;
}
- int molb = 0;
for (const t_shell& shell : shells)
{
const int s1 = shell.shellIndex;
case 2:
n1 = shell.nucl1;
n2 = shell.nucl2;
- if (mass)
- {
- m1 = mass[n1];
- m2 = mass[n2];
- }
- else
- {
- /* Not the correct masses with FE, but it is just a prediction... */
- m1 = mtopGetAtomMass(mtop, n1, &molb);
- m2 = mtopGetAtomMass(mtop, n2, &molb);
- }
+ m1 = mass[n1];
+ m2 = mass[n2];
tm = dt_1 / (m1 + m2);
for (m = 0; (m < DIM); m++)
{
n1 = shell.nucl1;
n2 = shell.nucl2;
n3 = shell.nucl3;
- if (mass)
- {
- m1 = mass[n1];
- m2 = mass[n2];
- m3 = mass[n3];
- }
- else
- {
- /* Not the correct masses with FE, but it is just a prediction... */
- m1 = mtopGetAtomMass(mtop, n1, &molb);
- m2 = mtopGetAtomMass(mtop, n2, &molb);
- m3 = mtopGetAtomMass(mtop, n3, &molb);
- }
+ m1 = mass[n1];
+ m2 = mass[n2];
+ m3 = mass[n3];
tm = dt_1 / (m1 + m2 + m3);
for (m = 0; (m < DIM); m++)
{
}
gmx_shellfc_t* init_shell_flexcon(FILE* fplog,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
int nflexcon,
int nstcalcenergy,
bool usingDomainDecomposition,
#define NBT asize(bondtypes)
const gmx_ffparams_t* ffparams;
- const std::array<int, eptNR> numParticles = gmx_mtop_particletype_count(*mtop);
+ const gmx::EnumerationArray<ParticleType, int> numParticles = gmx_mtop_particletype_count(mtop);
if (fplog)
{
/* Print the number of each particle type */
- int pType = 0;
- for (const auto& n : numParticles)
+ for (const auto entry : gmx::keysOf(numParticles))
{
- if (n != 0)
+ const int number = numParticles[entry];
+ if (number != 0)
{
- fprintf(fplog, "There are: %d %ss\n", n, ptype_str[pType]);
+ fprintf(fplog, "There are: %d %ss\n", number, enumValueToString(entry));
}
- pType++;
}
}
- nshell = numParticles[eptShell];
+ nshell = numParticles[ParticleType::Shell];
if (nshell == 0 && nflexcon == 0)
{
/* We have shells: fill the shell data structure */
/* Global system sized array, this should be avoided */
- std::vector<int> shell_index(mtop->natoms);
+ std::vector<int> shell_index(mtop.natoms);
nshell = 0;
- for (const AtomProxy atomP : AtomRange(*mtop))
+ for (const AtomProxy atomP : AtomRange(mtop))
{
const t_atom& local = atomP.atom();
int i = atomP.globalAtomNumber();
- if (local.ptype == eptShell)
+ if (local.ptype == ParticleType::Shell)
{
shell_index[i] = nshell++;
}
std::vector<t_shell> shell(nshell);
- ffparams = &mtop->ffparams;
+ ffparams = &mtop.ffparams;
/* Now fill the structures */
/* TODO: See if we can use update groups that cover shell constructions */
shfc->bInterCG = FALSE;
ns = 0;
a_offset = 0;
- for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
+ for (size_t mb = 0; mb < mtop.molblock.size(); mb++)
{
- const gmx_molblock_t* molb = &mtop->molblock[mb];
- const gmx_moltype_t* molt = &mtop->moltype[molb->type];
+ const gmx_molblock_t& molb = mtop.molblock[mb];
+ const gmx_moltype_t& molt = mtop.moltype[molb.type];
- const t_atom* atom = molt->atoms.atom;
- for (mol = 0; mol < molb->nmol; mol++)
+ const t_atom* atom = molt.atoms.atom;
+ for (mol = 0; mol < molb.nmol; mol++)
{
for (j = 0; (j < NBT); j++)
{
- const int* ia = molt->ilist[bondtypes[j]].iatoms.data();
- for (i = 0; (i < molt->ilist[bondtypes[j]].size());)
+ const int* ia = molt.ilist[bondtypes[j]].iatoms.data();
+ for (i = 0; (i < molt.ilist[bondtypes[j]].size());)
{
type = ia[0];
ftype = ffparams->functype[type];
case F_CUBICBONDS:
case F_POLARIZATION:
case F_ANHARM_POL:
- if (atom[ia[1]].ptype == eptShell)
+ if (atom[ia[1]].ptype == ParticleType::Shell)
{
aS = ia[1];
aN = ia[2];
}
- else if (atom[ia[2]].ptype == eptShell)
+ else if (atom[ia[2]].ptype == ParticleType::Shell)
{
aS = ia[2];
aN = ia[1];
gmx_fatal(FARGS,
"polarize can not be used with qA(%e) != qB(%e) for "
"atom %d of molecule block %zu",
- qS, atom[aS].qB, aS + 1, mb + 1);
+ qS,
+ atom[aS].qB,
+ aS + 1,
+ mb + 1);
}
- shell[nsi].k += gmx::square(qS) * ONE_4PI_EPS0
+ shell[nsi].k += gmx::square(qS) * gmx::c_one4PiEps0
/ ffparams->iparams[type].polarize.alpha;
break;
case F_WATER_POL:
gmx_fatal(FARGS,
"water_pol can not be used with qA(%e) != qB(%e) for "
"atom %d of molecule block %zu",
- qS, atom[aS].qB, aS + 1, mb + 1);
+ qS,
+ atom[aS].qB,
+ aS + 1,
+ mb + 1);
}
alpha = (ffparams->iparams[type].wpol.al_x
+ ffparams->iparams[type].wpol.al_y
+ ffparams->iparams[type].wpol.al_z)
/ 3.0;
- shell[nsi].k += gmx::square(qS) * ONE_4PI_EPS0 / alpha;
+ shell[nsi].k += gmx::square(qS) * gmx::c_one4PiEps0 / alpha;
break;
default: gmx_fatal(FARGS, "Death Horror: %s, %d", __FILE__, __LINE__);
}
i += nra + 1;
}
}
- a_offset += molt->atoms.nr;
+ a_offset += molt.atoms.nr;
}
/* Done with this molecule type */
}
return shfc;
}
-void gmx::make_local_shells(const t_commrec* cr, const t_mdatoms* md, gmx_shellfc_t* shfc)
+void gmx::make_local_shells(const t_commrec* cr, const t_mdatoms& md, gmx_shellfc_t* shfc)
{
int a0, a1;
gmx_domdec_t* dd = nullptr;
std::vector<t_shell>& shells = shfc->shells;
shells.clear();
+ auto* ptype = md.ptype;
for (int i = a0; i < a1; i++)
{
- if (md->ptype[i] == eptShell)
+ if (ptype[i] == ParticleType::Shell)
{
if (dd)
{
ff2 = iprod(f[ind], f[ind]);
if (ff2 > ft2)
{
- fprintf(fp, "SHELL %5d, force %10.5f %10.5f %10.5f, |f| %10.5f\n", ind, f[ind][XX],
- f[ind][YY], f[ind][ZZ], std::sqrt(ff2));
+ fprintf(fp,
+ "SHELL %5d, force %10.5f %10.5f %10.5f, |f| %10.5f\n",
+ ind,
+ f[ind][XX],
+ f[ind][YY],
+ f[ind][ZZ],
+ std::sqrt(ff2));
}
}
}
const t_commrec* cr,
int dd_ac1,
int64_t step,
- const t_mdatoms* md,
+ const t_mdatoms& md,
int end,
ArrayRefWithPadding<RVec> xOld,
ArrayRef<RVec> x_init,
ArrayRef<const real> lambda,
real* dvdlambda)
{
- double dt, w_dt;
- int n, d;
- unsigned short* ptype;
+ double dt, w_dt;
+ int n, d;
if (DOMAINDECOMP(cr))
{
rvec* x_old = as_rvec_array(xOld.paddedArrayRef().data());
rvec* x = as_rvec_array(xCurrent.paddedArrayRef().data());
- ptype = md->ptype;
-
- dt = ir->delta_t;
+ auto* ptype = md.ptype;
+ auto invmass = gmx::arrayRefFromArray(md.invmass, md.nr);
+ dt = ir->delta_t;
- /* Does NOT work with freeze or acceleration groups (yet) */
+ /* Does NOT work with freeze groups (yet) */
for (n = 0; n < end; n++)
{
- w_dt = md->invmass[n] * dt;
+ w_dt = invmass[n] * dt;
for (d = 0; d < DIM; d++)
{
- if ((ptype[n] != eptVSite) && (ptype[n] != eptShell))
+ if ((ptype[n] != ParticleType::VSite) && (ptype[n] != ParticleType::Shell))
{
xnold[n][d] = x[n][d] - (x_init[n][d] - x_old[n][d]);
xnew[n][d] = 2 * x[n][d] - x_old[n][d] + f[n][d] * w_dt * dt;
bool needsLogging = false;
bool computeEnergy = false;
bool computeVirial = false;
- constr->apply(needsLogging, computeEnergy, step, 0, 1.0, xCurrent,
- shfc->adir_xnold.arrayRefWithPadding(), {}, box, lambda[efptBONDED],
- &(dvdlambda[efptBONDED]), {}, computeVirial, nullptr,
+ constr->apply(needsLogging,
+ computeEnergy,
+ step,
+ 0,
+ 1.0,
+ xCurrent,
+ shfc->adir_xnold.arrayRefWithPadding(),
+ {},
+ box,
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Bonded)],
+ &(dvdlambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Bonded)]),
+ {},
+ computeVirial,
+ nullptr,
gmx::ConstraintVariable::Positions);
- constr->apply(needsLogging, computeEnergy, step, 0, 1.0, xCurrent,
- shfc->adir_xnew.arrayRefWithPadding(), {}, box, lambda[efptBONDED],
- &(dvdlambda[efptBONDED]), {}, computeVirial, nullptr,
+ constr->apply(needsLogging,
+ computeEnergy,
+ step,
+ 0,
+ 1.0,
+ xCurrent,
+ shfc->adir_xnew.arrayRefWithPadding(),
+ {},
+ box,
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Bonded)],
+ &(dvdlambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Bonded)]),
+ {},
+ computeVirial,
+ nullptr,
gmx::ConstraintVariable::Positions);
for (n = 0; n < end; n++)
for (d = 0; d < DIM; d++)
{
xnew[n][d] = -(2 * x[n][d] - xnold[n][d] - xnew[n][d]) / gmx::square(dt)
- - f[n][d] * md->invmass[n];
+ - f[n][d] * invmass[n];
}
clear_rvec(acc_dir[n]);
}
/* Project the acceleration on the old bond directions */
- constr->apply(needsLogging, computeEnergy, step, 0, 1.0, xOld, shfc->adir_xnew.arrayRefWithPadding(),
- acc_dir, box, lambda[efptBONDED], &(dvdlambda[efptBONDED]), {}, computeVirial,
- nullptr, gmx::ConstraintVariable::Deriv_FlexCon);
+ constr->apply(needsLogging,
+ computeEnergy,
+ step,
+ 0,
+ 1.0,
+ xOld,
+ shfc->adir_xnew.arrayRefWithPadding(),
+ acc_dir,
+ box,
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Bonded)],
+ &(dvdlambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Bonded)]),
+ {},
+ computeVirial,
+ nullptr,
+ gmx::ConstraintVariable::Deriv_FlexCon);
}
void relax_shell_flexcon(FILE* fplog,
ArrayRefWithPadding<RVec> vPadded,
const matrix box,
ArrayRef<real> lambda,
- history_t* hist,
+ const history_t* hist,
gmx::ForceBuffersView* f,
tensor force_vir,
- const t_mdatoms* md,
+ const t_mdatoms& md,
t_nrnb* nrnb,
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle* wcycle,
gmx_shellfc_t* shfc,
t_forcerec* fr,
gmx::MdrunScheduleWorkload* runScheduleWork,
real dum = 0;
char sbuf[22];
int nat, dd_ac0, dd_ac1 = 0, i;
- int homenr = md->homenr, end = homenr;
+ int homenr = md.homenr, end = homenr;
int d, Min = 0, count = 0;
#define Try (1 - Min) /* At start Try = 1 */
if (DOMAINDECOMP(cr))
{
- nat = dd_natoms_vsite(cr->dd);
+ nat = dd_natoms_vsite(*cr->dd);
if (nflexcon > 0)
{
- dd_get_constraint_range(cr->dd, &dd_ac0, &dd_ac1);
+ dd_get_constraint_range(*cr->dd, &dd_ac0, &dd_ac1);
nat = std::max(nat, dd_ac1);
}
}
* before do_force is called, which normally puts all
* charge groups in the box.
*/
- put_atoms_in_box_omp(fr->pbcType, box, x.subArray(0, md->homenr),
- gmx_omp_nthreads_get(emntDefault));
+ put_atoms_in_box_omp(
+ fr->pbcType, box, x.subArray(0, md.homenr), gmx_omp_nthreads_get(ModuleMultiThread::Default));
}
if (nflexcon)
}
}
+ auto massT = gmx::arrayRefFromArray(md.massT, md.nr);
/* Do a prediction of the shell positions, when appropriate.
* Without velocities (EM, NM, BD) we only do initial prediction.
*/
if (shfc->predictShells && !bCont && (EI_STATE_VELOCITY(inputrec->eI) || bInit))
{
- predict_shells(fplog, x, v, inputrec->delta_t, shells, md->massT, nullptr, bInit);
+ predict_shells(fplog, x, v, inputrec->delta_t, shells, massT, bInit);
}
/* Calculate the forces first time around */
}
int shellfc_flags = force_flags | (bVerbose ? GMX_FORCE_ENERGY : 0);
gmx::ForceBuffersView forceViewInit = gmx::ForceBuffersView(forceWithPadding[Min], {}, false);
- do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, mdstep,
- nrnb, wcycle, top, box, xPadded, hist, &forceViewInit, force_vir, md, enerd, lambda,
- fr, runScheduleWork, vsite, mu_tot, t, nullptr,
- (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags, ddBalanceRegionHandler);
+ do_force(fplog,
+ cr,
+ ms,
+ *inputrec,
+ nullptr,
+ enforcedRotation,
+ imdSession,
+ pull_work,
+ mdstep,
+ nrnb,
+ wcycle,
+ top,
+ box,
+ xPadded,
+ hist,
+ &forceViewInit,
+ force_vir,
+ &md,
+ enerd,
+ lambda,
+ fr,
+ runScheduleWork,
+ vsite,
+ mu_tot,
+ t,
+ nullptr,
+ (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags,
+ ddBalanceRegionHandler);
sf_dir = 0;
if (nflexcon)
{
- init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end, shfc->x_old.arrayRefWithPadding(),
- x, xPadded, force[Min], shfc->acc_dir, box, lambda, &dum);
+ init_adir(shfc,
+ constr,
+ inputrec,
+ cr,
+ dd_ac1,
+ mdstep,
+ md,
+ end,
+ shfc->x_old.arrayRefWithPadding(),
+ x,
+ xPadded,
+ force[Min],
+ shfc->acc_dir,
+ box,
+ lambda,
+ &dum);
for (i = 0; i < end; i++)
{
- sf_dir += md->massT[i] * norm2(shfc->acc_dir[i]);
+ sf_dir += massT[i] * norm2(shfc->acc_dir[i]);
}
}
- accumulatePotentialEnergies(enerd, lambda, inputrec->fepvals);
+ accumulatePotentialEnergies(enerd, lambda, inputrec->fepvals.get());
Epot[Min] = enerd->term[F_EPOT];
df[Min] = rms_force(cr, forceWithPadding[Min].paddedArrayRef(), shells, nflexcon, &sf_dir, &Epot[Min]);
if (gmx_debug_at)
{
- pr_rvecs(debug, 0, "force0", as_rvec_array(force[Min].data()), md->nr);
+ pr_rvecs(debug, 0, "force0", as_rvec_array(force[Min].data()), md.nr);
}
if (!shells.empty() || nflexcon > 0)
* shell positions are updated, therefore the other particles must
* be set here, in advance.
*/
- std::copy(xPadded.paddedArrayRef().begin(), xPadded.paddedArrayRef().end(),
+ std::copy(xPadded.paddedArrayRef().begin(),
+ xPadded.paddedArrayRef().end(),
posWithPadding[Min].paddedArrayRef().begin());
- std::copy(xPadded.paddedArrayRef().begin(), xPadded.paddedArrayRef().end(),
+ std::copy(xPadded.paddedArrayRef().begin(),
+ xPadded.paddedArrayRef().end(),
posWithPadding[Try].paddedArrayRef().begin());
}
{
if (vsite)
{
- vsite->construct(pos[Min], inputrec->delta_t, v, box);
+ vsite->construct(pos[Min], v, box, gmx::VSiteOperation::PositionsAndVelocities);
}
if (nflexcon)
{
- init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end,
- shfc->x_old.arrayRefWithPadding(), x, posWithPadding[Min], force[Min],
- shfc->acc_dir, box, lambda, &dum);
+ init_adir(shfc,
+ constr,
+ inputrec,
+ cr,
+ dd_ac1,
+ mdstep,
+ md,
+ end,
+ shfc->x_old.arrayRefWithPadding(),
+ x,
+ posWithPadding[Min],
+ force[Min],
+ shfc->acc_dir,
+ box,
+ lambda,
+ &dum);
directional_sd(pos[Min], pos[Try], shfc->acc_dir, end, fr->fc_stepsize);
}
}
/* Try the new positions */
gmx::ForceBuffersView forceViewTry = gmx::ForceBuffersView(forceWithPadding[Try], {}, false);
- do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, 1, nrnb, wcycle,
- top, box, posWithPadding[Try], hist, &forceViewTry, force_vir, md, enerd, lambda, fr,
- runScheduleWork, vsite, mu_tot, t, nullptr, shellfc_flags, ddBalanceRegionHandler);
- accumulatePotentialEnergies(enerd, lambda, inputrec->fepvals);
+ do_force(fplog,
+ cr,
+ ms,
+ *inputrec,
+ nullptr,
+ enforcedRotation,
+ imdSession,
+ pull_work,
+ 1,
+ nrnb,
+ wcycle,
+ top,
+ box,
+ posWithPadding[Try],
+ hist,
+ &forceViewTry,
+ force_vir,
+ &md,
+ enerd,
+ lambda,
+ fr,
+ runScheduleWork,
+ vsite,
+ mu_tot,
+ t,
+ nullptr,
+ shellfc_flags,
+ ddBalanceRegionHandler);
+ accumulatePotentialEnergies(enerd, lambda, inputrec->fepvals.get());
if (gmx_debug_at)
{
pr_rvecs(debug, 0, "RELAX: force[Min]", as_rvec_array(force[Min].data()), homenr);
sf_dir = 0;
if (nflexcon)
{
- init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end,
- shfc->x_old.arrayRefWithPadding(), x, posWithPadding[Try], force[Try],
- shfc->acc_dir, box, lambda, &dum);
+ init_adir(shfc,
+ constr,
+ inputrec,
+ cr,
+ dd_ac1,
+ mdstep,
+ md,
+ end,
+ shfc->x_old.arrayRefWithPadding(),
+ x,
+ posWithPadding[Try],
+ force[Try],
+ shfc->acc_dir,
+ box,
+ lambda,
+ &dum);
ArrayRef<const RVec> acc_dir = shfc->acc_dir;
for (i = 0; i < end; i++)
{
- sf_dir += md->massT[i] * norm2(acc_dir[i]);
+ sf_dir += massT[i] * norm2(acc_dir[i]);
}
}
/* Note that the energies and virial are incorrect when not converged */
if (fplog)
{
- fprintf(fplog, "step %s: EM did not converge in %d iterations, RMS force %6.2e\n",
- gmx_step_str(mdstep, sbuf), number_steps, df[Min]);
+ fprintf(fplog,
+ "step %s: EM did not converge in %d iterations, RMS force %6.2e\n",
+ gmx_step_str(mdstep, sbuf),
+ number_steps,
+ df[Min]);
}
- fprintf(stderr, "step %s: EM did not converge in %d iterations, RMS force %6.2e\n",
- gmx_step_str(mdstep, sbuf), number_steps, df[Min]);
+ fprintf(stderr,
+ "step %s: EM did not converge in %d iterations, RMS force %6.2e\n",
+ gmx_step_str(mdstep, sbuf),
+ number_steps,
+ df[Min]);
}
/* Copy back the coordinates and the forces */
if (shfc && fplog && numSteps > 0)
{
double numStepsAsDouble = static_cast<double>(numSteps);
- fprintf(fplog, "Fraction of iterations that converged: %.2f %%\n",
+ fprintf(fplog,
+ "Fraction of iterations that converged: %.2f %%\n",
(shfc->numConvergedIterations * 100.0) / numStepsAsDouble);
- fprintf(fplog, "Average number of force evaluations per MD step: %.2f\n\n",
+ fprintf(fplog,
+ "Average number of force evaluations per MD step: %.2f\n\n",
shfc->numForceEvaluations / numStepsAsDouble);
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vectypes.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/topology/atoms.h"
+#include "gromacs/utility/enumerationhelpers.h"
class DDBalanceRegionHandler;
struct gmx_enerdata_t;
* \returns a pointer to an initialized \c shellfc object.
*/
gmx_shellfc_t* init_shell_flexcon(FILE* fplog,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
int nflexcon,
int nstcalcenergy,
bool usingDomainDecomposition,
gmx::ArrayRefWithPadding<gmx::RVec> v,
const matrix box,
gmx::ArrayRef<real> lambda,
- history_t* hist,
+ const history_t* hist,
gmx::ForceBuffersView* f,
tensor force_vir,
- const t_mdatoms* md,
+ const t_mdatoms& md,
t_nrnb* nrnb,
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle* wcycle,
gmx_shellfc_t* shfc,
t_forcerec* fr,
gmx::MdrunScheduleWorkload* runScheduleWork,
* \param[in] mtop Molecular topology.
* \returns Array holding the number of particles of a type
*/
-std::array<int, eptNR> countPtypes(FILE* fplog, const gmx_mtop_t* mtop);
+gmx::EnumerationArray<ParticleType, int> countPtypes(FILE* fplog, const gmx_mtop_t& mtop);
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
t_inputrec* inputRecord,
gmx_mtop_t* molecularTopology)
{
- *partialDeserializedTpr = read_tpx_state(simulationInput.tprFilename_.c_str(), inputRecord,
- globalState, molecularTopology);
+ *partialDeserializedTpr = read_tpx_state(
+ simulationInput.tprFilename_.c_str(), inputRecord, globalState, molecularTopology);
}
void applyLocalState(const SimulationInput& simulationInput,
t_state* state,
ObservablesHistory* observablesHistory,
bool reproducibilityRequested,
- const MdModulesNotifier& mdModulesNotifier,
+ const MDModulesNotifiers& mdModulesNotifiers,
gmx::ReadCheckpointDataHolder* modularSimulatorCheckpointData,
const bool useModularSimulator)
{
- load_checkpoint(simulationInput.cpiFilename_.c_str(), logfio, cr, dd_nc, inputRecord, state,
- observablesHistory, reproducibilityRequested, mdModulesNotifier,
- modularSimulatorCheckpointData, useModularSimulator);
+ load_checkpoint(simulationInput.cpiFilename_.c_str(),
+ logfio,
+ cr,
+ dd_nc,
+ inputRecord,
+ state,
+ observablesHistory,
+ reproducibilityRequested,
+ mdModulesNotifiers,
+ modularSimulatorCheckpointData,
+ useModularSimulator);
}
} // end namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdrun/simulationinputhandle.h"
#include "gromacs/mdtypes/checkpointdata.h"
-#include "gromacs/utility/mdmodulenotification.h"
+#include "gromacs/utility/mdmodulesnotifiers.h"
// Forward declarations for types from other modules that are opaque to the public API.
// TODO: Document the sources of these symbols or import a (self-documenting) fwd header.
* SimulationInput implementation.
*
* \todo Consider refactoring to decouple the checkpoint facility from its consumers
- * (state, observablesHistory, mdModulesNotifier, and parts of ir).
+ * (state, observablesHistory, mdModulesNotifiers, and parts of ir).
*
* \warning It is the caller’s responsibility to make sure that
* preconditions are satisfied for the parameter objects.
t_state* state,
ObservablesHistory* observablesHistory,
bool reproducibilityRequested,
- const MdModulesNotifier& notifier,
+ const MDModulesNotifiers& notifiers,
gmx::ReadCheckpointDataHolder* modularSimulatorCheckpointData,
bool useModularSimulator);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019-2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/state.h"
#include "gromacs/modularsimulator/modularsimulator.h"
#include "gromacs/topology/topology.h"
-#include "gromacs/utility/mdmodulenotification.h"
+#include "gromacs/utility/mdmodulesnotifiers.h"
#include "legacysimulator.h"
#include "membedholder.h"
{
// NOLINTNEXTLINE(modernize-make-unique): make_unique does not work with private constructor
return std::unique_ptr<ModularSimulator>(new ModularSimulator(
- std::make_unique<LegacySimulatorData>(
- simulatorEnv_->fplog_, simulatorEnv_->commRec_, simulatorEnv_->multisimCommRec_,
- simulatorEnv_->logger_, legacyInput_->numFile, legacyInput_->filenames,
- simulatorEnv_->outputEnv_, simulatorConfig_->mdrunOptions_,
- simulatorConfig_->startingBehavior_, constraintsParam_->vsite,
- constraintsParam_->constr, constraintsParam_->enforcedRotation,
- boxDeformation_->deform, simulatorModules_->outputProvider,
- simulatorModules_->mdModulesNotifier, legacyInput_->inputrec,
- interactiveMD_->imdSession, centerOfMassPulling_->pull_work, ionSwapping_->ionSwap,
- topologyData_->top_global, simulatorStateData_->globalState_p,
- simulatorStateData_->observablesHistory_p, topologyData_->mdAtoms,
- profiling_->nrnb, profiling_->wallCycle, legacyInput_->forceRec,
- simulatorStateData_->enerdata_p, simulatorStateData_->ekindata_p,
- simulatorConfig_->runScheduleWork_, *replicaExchangeParameters_,
- membedHolder_->membed(), profiling_->walltimeAccounting,
- std::move(stopHandlerBuilder_), simulatorConfig_->mdrunOptions_.rerun),
+ std::make_unique<LegacySimulatorData>(simulatorEnv_->fplog_,
+ simulatorEnv_->commRec_,
+ simulatorEnv_->multisimCommRec_,
+ simulatorEnv_->logger_,
+ legacyInput_->numFile,
+ legacyInput_->filenames,
+ simulatorEnv_->outputEnv_,
+ simulatorConfig_->mdrunOptions_,
+ simulatorConfig_->startingBehavior_,
+ constraintsParam_->vsite,
+ constraintsParam_->constr,
+ constraintsParam_->enforcedRotation,
+ boxDeformation_->deform,
+ simulatorModules_->outputProvider,
+ simulatorModules_->mdModulesNotifiers,
+ legacyInput_->inputrec,
+ interactiveMD_->imdSession,
+ centerOfMassPulling_->pull_work,
+ ionSwapping_->ionSwap,
+ topologyData_->top_global,
+ simulatorStateData_->globalState_p,
+ simulatorStateData_->observablesHistory_p,
+ topologyData_->mdAtoms,
+ profiling_->nrnb,
+ profiling_->wallCycle,
+ legacyInput_->forceRec,
+ simulatorStateData_->enerdata_p,
+ simulatorStateData_->ekindata_p,
+ simulatorConfig_->runScheduleWork_,
+ *replicaExchangeParameters_,
+ membedHolder_->membed(),
+ profiling_->walltimeAccounting,
+ std::move(stopHandlerBuilder_),
+ simulatorConfig_->mdrunOptions_.rerun),
std::move(modularSimulatorCheckpointData_)));
}
// NOLINTNEXTLINE(modernize-make-unique): make_unique does not work with private constructor
- return std::unique_ptr<LegacySimulator>(new LegacySimulator(
- simulatorEnv_->fplog_, simulatorEnv_->commRec_, simulatorEnv_->multisimCommRec_,
- simulatorEnv_->logger_, legacyInput_->numFile, legacyInput_->filenames,
- simulatorEnv_->outputEnv_, simulatorConfig_->mdrunOptions_,
- simulatorConfig_->startingBehavior_, constraintsParam_->vsite,
- constraintsParam_->constr, constraintsParam_->enforcedRotation, boxDeformation_->deform,
- simulatorModules_->outputProvider, simulatorModules_->mdModulesNotifier,
- legacyInput_->inputrec, interactiveMD_->imdSession, centerOfMassPulling_->pull_work,
- ionSwapping_->ionSwap, topologyData_->top_global, simulatorStateData_->globalState_p,
- simulatorStateData_->observablesHistory_p, topologyData_->mdAtoms, profiling_->nrnb,
- profiling_->wallCycle, legacyInput_->forceRec, simulatorStateData_->enerdata_p,
- simulatorStateData_->ekindata_p, simulatorConfig_->runScheduleWork_,
- *replicaExchangeParameters_, membedHolder_->membed(), profiling_->walltimeAccounting,
- std::move(stopHandlerBuilder_), simulatorConfig_->mdrunOptions_.rerun));
+ return std::unique_ptr<LegacySimulator>(new LegacySimulator(simulatorEnv_->fplog_,
+ simulatorEnv_->commRec_,
+ simulatorEnv_->multisimCommRec_,
+ simulatorEnv_->logger_,
+ legacyInput_->numFile,
+ legacyInput_->filenames,
+ simulatorEnv_->outputEnv_,
+ simulatorConfig_->mdrunOptions_,
+ simulatorConfig_->startingBehavior_,
+ constraintsParam_->vsite,
+ constraintsParam_->constr,
+ constraintsParam_->enforcedRotation,
+ boxDeformation_->deform,
+ simulatorModules_->outputProvider,
+ simulatorModules_->mdModulesNotifiers,
+ legacyInput_->inputrec,
+ interactiveMD_->imdSession,
+ centerOfMassPulling_->pull_work,
+ ionSwapping_->ionSwap,
+ topologyData_->top_global,
+ simulatorStateData_->globalState_p,
+ simulatorStateData_->observablesHistory_p,
+ topologyData_->mdAtoms,
+ profiling_->nrnb,
+ profiling_->wallCycle,
+ legacyInput_->forceRec,
+ simulatorStateData_->enerdata_p,
+ simulatorStateData_->ekindata_p,
+ simulatorConfig_->runScheduleWork_,
+ *replicaExchangeParameters_,
+ membedHolder_->membed(),
+ profiling_->walltimeAccounting,
+ std::move(stopHandlerBuilder_),
+ simulatorConfig_->mdrunOptions_.rerun));
}
void SimulatorBuilder::add(MembedHolder&& membedHolder)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019-2020, by the GROMACS development team, led by
+ * Copyright (c) 2019-2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
class energyhistory_t;
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
struct gmx_enerdata_t;
struct gmx_enfrot;
struct gmx_mtop_t;
class MembedHolder;
class MDAtoms;
class MDLogger;
-struct MdModulesNotifier;
+struct MDModulesNotifiers;
struct MdrunOptions;
class ReadCheckpointDataHolder;
enum class StartingBehavior;
class SimulatorModules
{
public:
- SimulatorModules(IMDOutputProvider* mdOutputProvider, const MdModulesNotifier& notifier) :
+ SimulatorModules(IMDOutputProvider* mdOutputProvider, const MDModulesNotifiers& notifiers) :
outputProvider(mdOutputProvider),
- mdModulesNotifier(notifier)
+ mdModulesNotifiers(notifiers)
{
}
- IMDOutputProvider* outputProvider;
- const MdModulesNotifier& mdModulesNotifier;
+ IMDOutputProvider* outputProvider;
+ const MDModulesNotifiers& mdModulesNotifiers;
};
class CenterOfMassPulling
{
public:
//! Build collection from simulation data.
- TopologyData(gmx_mtop_t* globalTopology, MDAtoms* mdAtoms) :
+ TopologyData(const gmx_mtop_t& globalTopology, MDAtoms* mdAtoms) :
top_global(globalTopology),
mdAtoms(mdAtoms)
{
}
//! Handle to global simulation topology.
- gmx_mtop_t* top_global;
+ const gmx_mtop_t& top_global;
//! Handle to information about MDAtoms.
MDAtoms* mdAtoms;
};
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
for (int i = beginAtom; i < mdatoms.homenr; i++)
{
const real qi = mdatoms.chargeA[i];
- energy -= 0.5 * qi * qi * ic.c_rf;
+ energy -= 0.5 * qi * qi * ic.reactionFieldShift;
for (int j = i + 1; j < mdatoms.homenr; j++)
{
const real qj = mdatoms.chargeA[j];
const real rsq = distance2(x[i], x[j]);
- energy += qi * qj * (ic.k_rf * rsq - ic.c_rf);
+ energy += qi * qj * (ic.reactionFieldCoefficient * rsq - ic.reactionFieldShift);
}
}
// TODO: Convert to use the nbnxm kernels by putting the system and the teset molecule on two separate search grids
void LegacySimulator::do_tpi()
{
- GMX_RELEASE_ASSERT(gmx_omp_nthreads_get(emntDefault) == 1, "TPI does not support OpenMP");
+ GMX_RELEASE_ASSERT(gmx_omp_nthreads_get(ModuleMultiThread::Default) == 1,
+ "TPI does not support OpenMP");
- gmx_localtop_t top(top_global->ffparams);
+ gmx_localtop_t top(top_global.ffparams);
gmx::ForceBuffers f;
real lambda, t, temp, beta, drmax, epot;
double embU, sum_embU, *sum_UgembU, V, V_all, VembU_all;
double invbinw, *bin, refvolshift, logV, bUlogV;
gmx_bool bEnergyOutOfBounds;
const char* tpid_leg[2] = { "direct", "reweighted" };
- auto mdatoms = mdAtoms->mdatoms();
+ auto* mdatoms = mdAtoms->mdatoms();
GMX_UNUSED_VALUE(outputProvider);
nnodes = cr->nnodes;
- gmx_mtop_generate_local_top(*top_global, &top, inputrec->efep != efepNO);
+ gmx_mtop_generate_local_top(top_global, &top, inputrec->efep != FreeEnergyPerturbationType::No);
- const SimulationGroups* groups = &top_global->groups;
+ const SimulationGroups* groups = &top_global.groups;
- bCavity = (inputrec->eI == eiTPIC);
+ bCavity = (inputrec->eI == IntegrationAlgorithm::TPIC);
if (bCavity)
{
ptr = getenv("GMX_TPIC_MASSES");
}
fprintf(fplog, "\n The temperature for test particle insertion is %.3f K\n\n", temp);
}
- beta = 1.0 / (BOLTZ * temp);
+ beta = 1.0 / (gmx::c_boltz * temp);
/* Number of insertions per frame */
nsteps = inputrec->nsteps;
sscanf(dump_pdb, "%20lf", &dump_ener);
}
- atoms2md(top_global, inputrec, -1, {}, top_global->natoms, mdAtoms);
+ atoms2md(top_global, *inputrec, -1, {}, top_global.natoms, mdAtoms);
update_mdatoms(mdatoms, inputrec->fepvals->init_lambda);
- f.resize(top_global->natoms);
+ f.resize(top_global.natoms);
/* Print to log file */
walltime_accounting_start_time(walltime_accounting);
- wallcycle_start(wcycle, ewcRUN);
+ wallcycle_start(wcycle, WallCycleCounter::Run);
print_start(fplog, cr, walltime_accounting, "Test Particle Insertion");
/* The last charge group is the group to be inserted */
- const t_atoms& atomsToInsert = top_global->moltype[top_global->molblock.back().type].atoms;
- a_tp0 = top_global->natoms - atomsToInsert.nr;
- a_tp1 = top_global->natoms;
+ const t_atoms& atomsToInsert = top_global.moltype[top_global.molblock.back().type].atoms;
+ a_tp0 = top_global.natoms - atomsToInsert.nr;
+ a_tp1 = top_global.natoms;
if (debug)
{
fprintf(debug, "TPI atoms %d-%d\n", a_tp0, a_tp1);
if (EEL_PME(fr->ic->eeltype))
{
- gmx_pme_reinit_atoms(fr->pmedata, a_tp0, nullptr, nullptr);
+ gmx_pme_reinit_atoms(fr->pmedata, a_tp0, {}, {});
}
/* With reacion-field we have distance dependent potentials
snew(x_mol, a_tp1 - a_tp0);
- bDispCorr = (inputrec->eDispCorr != edispcNO);
+ bDispCorr = (inputrec->eDispCorr != DispersionCorrectionType::No);
bCharge = FALSE;
for (i = a_tp0; i < a_tp1; i++)
{
if (fplog)
{
- fprintf(fplog, "\nWill insert %d atoms %s partial charges\n", a_tp1 - a_tp0,
- bCharge ? "with" : "without");
+ fprintf(fplog, "\nWill insert %d atoms %s partial charges\n", a_tp1 - a_tp0, bCharge ? "with" : "without");
- fprintf(fplog, "\nWill insert %" PRId64 " times in each frame of %s\n", nsteps,
+ fprintf(fplog,
+ "\nWill insert %" PRId64 " times in each frame of %s\n",
+ nsteps,
opt2fn("-rerun", nfile, fnm));
}
gmx_fatal(FARGS,
"Re-using the neighborlist %d times for insertions of a single atom in a "
"sphere of radius %f does not make sense",
- inputrec->nstlist, drmax);
+ inputrec->nstlist,
+ drmax);
}
if (fplog)
{
fprintf(fplog,
"Will use the same neighborlist for %d insertions in a sphere of radius "
"%f\n",
- inputrec->nstlist, drmax);
+ inputrec->nstlist,
+ drmax);
}
}
}
* inserted atoms located in the center of the sphere, so we need
* a buffer of size of the sphere and molecule radius.
*/
- inputrec->rlist = maxCutoff + 2 * inputrec->rtpi + 2 * molRadius;
- fr->rlist = inputrec->rlist;
+ {
+ // TODO: Avoid changing inputrec (#3854)
+ auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
+ nonConstInputrec->rlist = maxCutoff + 2 * inputrec->rtpi + 2 * molRadius;
+ }
+ fr->rlist = inputrec->rlist;
fr->nbv->changePairlistRadii(inputrec->rlist, inputrec->rlist);
ngid = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
if (MASTER(cr))
{
- fp_tpi = xvgropen(opt2fn("-tpi", nfile, fnm), "TPI energies", "Time (ps)",
- "(kJ mol\\S-1\\N) / (nm\\S3\\N)", oenv);
+ fp_tpi = xvgropen(opt2fn("-tpi", nfile, fnm),
+ "TPI energies",
+ "Time (ps)",
+ "(kJ mol\\S-1\\N) / (nm\\S3\\N)",
+ oenv);
xvgr_subtitle(fp_tpi, "f. are averages over one frame", oenv);
snew(leg, 4 + nener);
e = 0;
leg[e++] = gmx_strdup(str);
for (i = 0; i < ngid; i++)
{
- sprintf(str, "f. <U\\sVdW %s\\Ne\\S-\\betaU\\N>",
+ sprintf(str,
+ "f. <U\\sVdW %s\\Ne\\S-\\betaU\\N>",
*(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][i]]));
leg[e++] = gmx_strdup(str);
}
{
for (i = 0; i < ngid; i++)
{
- sprintf(str, "f. <U\\sCoul %s\\Ne\\S-\\betaU\\N>",
+ sprintf(str,
+ "f. <U\\sCoul %s\\Ne\\S-\\betaU\\N>",
*(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][i]]));
leg[e++] = gmx_strdup(str);
}
"Number of atoms in trajectory (%d)%s "
"is not equal the number in the run input file (%d) "
"minus the number of atoms to insert (%d)\n",
- rerun_fr.natoms, bCavity ? " minus one" : "", mdatoms->nr, a_tp1 - a_tp0);
+ rerun_fr.natoms,
+ bCavity ? " minus one" : "",
+ mdatoms->nr,
+ a_tp1 - a_tp0);
}
refvolshift = log(det(rerun_fr.box));
switch (inputrec->eI)
{
- case eiTPI: stepblocksize = inputrec->nstlist; break;
- case eiTPIC: stepblocksize = 1; break;
- default: gmx_fatal(FARGS, "Unknown integrator %s", ei_names[inputrec->eI]);
+ case IntegrationAlgorithm::TPI: stepblocksize = inputrec->nstlist; break;
+ case IntegrationAlgorithm::TPIC: stepblocksize = 1; break;
+ default: gmx_fatal(FARGS, "Unknown integrator %s", enumValueToString(inputrec->eI));
}
while (bNotLastFrame)
/* Put all atoms except for the inserted ones on the grid */
rvec vzero = { 0, 0, 0 };
rvec boxDiagonal = { box[XX][XX], box[YY][YY], box[ZZ][ZZ] };
- nbnxn_put_on_grid(fr->nbv.get(), box, 0, vzero, boxDiagonal, nullptr, { 0, a_tp0 }, -1,
- fr->cginfo, x, 0, nullptr);
+ nbnxn_put_on_grid(
+ fr->nbv.get(), box, 0, vzero, boxDiagonal, nullptr, { 0, a_tp0 }, -1, fr->cginfo, x, 0, nullptr);
step = cr->nodeid * stepblocksize;
while (step < nsteps)
}
/* Put the inserted molecule on it's own search grid */
- nbnxn_put_on_grid(fr->nbv.get(), box, 1, x_init, x_init, nullptr, { a_tp0, a_tp1 },
- -1, fr->cginfo, x, 0, nullptr);
+ nbnxn_put_on_grid(
+ fr->nbv.get(), box, 1, x_init, x_init, nullptr, { a_tp0, a_tp1 }, -1, fr->cginfo, x, 0, nullptr);
/* TODO: Avoid updating all atoms at every bNS step */
fr->nbv->setAtomProperties(gmx::constArrayRefFromArray(mdatoms->typeA, mdatoms->nr),
real angleX = 2 * M_PI * dist(rng);
real angleY = 2 * M_PI * dist(rng);
real angleZ = 2 * M_PI * dist(rng);
- rotate_conf(a_tp1 - a_tp0, state_global->x.rvec_array() + a_tp0, nullptr, angleX,
- angleY, angleZ);
+ rotate_conf(a_tp1 - a_tp0, state_global->x.rvec_array() + a_tp0, nullptr, angleX, angleY, angleZ);
/* Shift to the insertion location */
for (i = a_tp0; i < a_tp1; i++)
{
}
/* Note: NonLocal refers to the inserted molecule */
- fr->nbv->convertCoordinates(AtomLocality::NonLocal, false, x);
+ fr->nbv->convertCoordinates(AtomLocality::NonLocal, x);
/* Clear some matrix variables */
clear_mat(force_vir);
// might raise, then restore the old behaviour.
std::fenv_t floatingPointEnvironment;
std::feholdexcept(&floatingPointEnvironment);
- do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, step, nrnb,
- wcycle, &top, state_global->box, state_global->x.arrayRefWithPadding(),
- &state_global->hist, &f.view(), force_vir, mdatoms, enerd,
- state_global->lambda, fr, runScheduleWork, nullptr, mu_tot, t, nullptr,
+ do_force(fplog,
+ cr,
+ ms,
+ *inputrec,
+ nullptr,
+ nullptr,
+ imdSession,
+ pull_work,
+ step,
+ nrnb,
+ wcycle,
+ &top,
+ state_global->box,
+ state_global->x.arrayRefWithPadding(),
+ &state_global->hist,
+ &f.view(),
+ force_vir,
+ mdatoms,
+ enerd,
+ state_global->lambda,
+ fr,
+ runScheduleWork,
+ nullptr,
+ mu_tot,
+ t,
+ nullptr,
GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY | (bStateChanged ? GMX_FORCE_STATECHANGED : 0),
DDBalanceRegionHandler(nullptr));
std::feclearexcept(FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW);
if (debug)
{
fprintf(debug,
- "\n time %.3f, step %d: non-finite energy %f, using exp(-bU)=0\n", t,
- static_cast<int>(step), epot);
+ "\n time %.3f, step %d: non-finite energy %f, using exp(-bU)=0\n",
+ t,
+ static_cast<int>(step),
+ epot);
}
embU = 0;
}
/* Determine the weighted energy contributions of each energy group */
e = 0;
sum_UgembU[e++] += epot * embU;
- if (fr->bBHAM)
+ if (fr->haveBuckingham)
{
for (i = 0; i < ngid; i++)
{
- sum_UgembU[e++] += enerd->grpp.ener[egBHAMSR][GID(i, gid_tp, ngid)] * embU;
+ sum_UgembU[e++] +=
+ enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::BuckinghamSR][GID(i, gid_tp, ngid)]
+ * embU;
}
}
else
{
for (i = 0; i < ngid; i++)
{
- sum_UgembU[e++] += enerd->grpp.ener[egLJSR][GID(i, gid_tp, ngid)] * embU;
+ sum_UgembU[e++] +=
+ enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::LJSR][GID(i, gid_tp, ngid)]
+ * embU;
}
}
if (bDispCorr)
{
for (i = 0; i < ngid; i++)
{
- sum_UgembU[e++] += enerd->grpp.ener[egCOULSR][GID(i, gid_tp, ngid)] * embU;
+ sum_UgembU[e++] +=
+ enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR][GID(i, gid_tp, ngid)]
+ * embU;
}
if (bRFExcl)
{
if (debug)
{
- fprintf(debug, "TPI %7d %12.5e %12.5f %12.5f %12.5f\n", static_cast<int>(step),
- epot, x_tp[XX], x_tp[YY], x_tp[ZZ]);
+ fprintf(debug,
+ "TPI %7d %12.5e %12.5f %12.5f %12.5f\n",
+ static_cast<int>(step),
+ epot,
+ x_tp[XX],
+ x_tp[YY],
+ x_tp[ZZ]);
}
if (dump_pdb && epot <= dump_ener)
{
sprintf(str, "t%g_step%d.pdb", t, static_cast<int>(step));
sprintf(str2, "t: %f step %d ener: %f", t, static_cast<int>(step), epot);
- write_sto_conf_mtop(str, str2, top_global, state_global->x.rvec_array(),
- state_global->v.rvec_array(), inputrec->pbcType, state_global->box);
+ write_sto_conf_mtop(str,
+ str2,
+ top_global,
+ state_global->x.rvec_array(),
+ state_global->v.rvec_array(),
+ inputrec->pbcType,
+ state_global->box);
}
step++;
{
if (mdrunOptions.verbose || frame % 10 == 0 || frame < 10)
{
- fprintf(stderr, "mu %10.3e <mu> %10.3e\n", -log(sum_embU / nsteps) / beta,
+ fprintf(stderr,
+ "mu %10.3e <mu> %10.3e\n",
+ -log(sum_embU / nsteps) / beta,
-log(VembU_all / V_all) / beta);
}
- fprintf(fp_tpi, "%10.3f %12.5e %12.5e %12.5e %12.5e", t,
+ fprintf(fp_tpi,
+ "%10.3f %12.5e %12.5e %12.5e %12.5e",
+ t,
VembU_all == 0 ? 20 / beta : -log(VembU_all / V_all) / beta,
- sum_embU == 0 ? 20 / beta : -log(sum_embU / nsteps) / beta, sum_embU / nsteps, V);
+ sum_embU == 0 ? 20 / beta : -log(sum_embU / nsteps) / beta,
+ sum_embU / nsteps,
+ V);
for (e = 0; e < nener; e++)
{
fprintf(fp_tpi, " %12.5e", sum_UgembU[e] / nsteps);
}
if (MASTER(cr))
{
- fp_tpi = xvgropen(opt2fn("-tpid", nfile, fnm), "TPI energy distribution",
- "\\betaU - log(V/<V>)", "count", oenv);
+ fp_tpi = xvgropen(opt2fn("-tpid", nfile, fnm),
+ "TPI energy distribution",
+ "\\betaU - log(V/<V>)",
+ "count",
+ oenv);
sprintf(str, "number \\betaU > %g: %9.3e", bU_bin_limit, bin[0]);
xvgr_subtitle(fp_tpi, str, oenv);
xvgr_legend(fp_tpi, 2, tpid_leg, oenv);
for (i = nbin - 1; i > 0; i--)
{
bUlogV = -i / invbinw + bU_logV_bin_limit - refvolshift + log(V_all / frame);
- fprintf(fp_tpi, "%6.2f %10d %12.5e\n", bUlogV, roundToInt(bin[i]),
- bin[i] * exp(-bUlogV) * V_all / VembU_all);
+ fprintf(fp_tpi, "%6.2f %10d %12.5e\n", bUlogV, roundToInt(bin[i]), bin[i] * exp(-bUlogV) * V_all / VembU_all);
}
xvgrclose(fp_tpi);
}
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015,2016,2019, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,2019,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+add_library(mdrunutility INTERFACE)
gmx_add_libgromacs_sources(
handlerestart.cpp
logging.cpp
threadaffinity.cpp
)
+# Source files have the following private module dependencies.
+target_link_libraries(mdrunutility PRIVATE
+# gmxlib
+# math
+# mdtypes
+# tng_io
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(mdrunutility PUBLIC
+target_include_directories(mdrunutility INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(mdrunutility PUBLIC
+target_link_libraries(mdrunutility INTERFACE
+ legacy_api
+ )
+
+# TODO: when mdrunutility is an OBJECT target
+#target_link_libraries(mdrunutility PUBLIC legacy_api)
+#target_link_libraries(mdrunutility PRIVATE common)
+
+# Module dependencies
+# mdrunutility interfaces convey transitive dependence on these modules.
+#target_link_libraries(mdrunutility PUBLIC
+target_link_libraries(mdrunutility INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(mdrunutility PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(mdrunutility PRIVATE legacy_modules)
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
"part), or instruct mdrun to write new output files with mdrun -noappend. In "
"the last case, you will not be able to use appending in future for this "
"simulation.",
- numFilesMissing, outputfiles.size());
+ numFilesMissing,
+ outputfiles.size());
GMX_THROW(InconsistentInputError(stream.toString()));
}
GMX_RELEASE_ASSERT(Path::extensionMatches(logFilename, ftp2ext(efLOG)),
formatString("The checkpoint file or its reading is broken, the first "
"output file '%s' must be a log file with extension '%s'",
- logFilename, ftp2ext(efLOG))
+ logFilename,
+ ftp2ext(efLOG))
.c_str());
if (appendingBehavior != AppendingBehavior::NoAppending)
"Cannot restart with appending because the previous simulation part used "
"%s precision which does not match the %s precision used by this build "
"of GROMACS. Either use matching precision or use mdrun -noappend.",
- precisionToString(headerContents.double_prec), precisionToString(GMX_DOUBLE))));
+ precisionToString(headerContents.double_prec),
+ precisionToString(GMX_DOUBLE))));
}
}
// If the previous log filename had a part number, then we
"Can't read %d bytes of '%s' to compute checksum. The file "
"has been replaced or its contents have been modified. Cannot "
"do appending because of this condition.",
- outputfile.checksumSize, outputfile.filename);
+ outputfile.checksumSize,
+ outputfile.filename);
GMX_THROW(InconsistentInputError(message));
}
}
auto startingBehaviors = gatherIntFromMultiSimulation(ms, static_cast<int>(startingBehavior));
bool identicalStartingBehaviors =
- (std::adjacent_find(std::begin(startingBehaviors), std::end(startingBehaviors),
- std::not_equal_to<>())
+ (std::adjacent_find(
+ std::begin(startingBehaviors), std::end(startingBehaviors), std::not_equal_to<>())
== std::end(startingBehaviors));
const EnumerationArray<StartingBehavior, std::string> behaviorStrings = {
for (index simIndex = 0; simIndex != ssize(startingBehaviors); ++simIndex)
{
auto behavior = static_cast<StartingBehavior>(startingBehaviors[simIndex]);
- message += formatString(" Simulation %6zd: %s\n", simIndex,
- behaviorStrings[behavior].c_str());
+ message += formatString(
+ " Simulation %6zd: %s\n", simIndex, behaviorStrings[behavior].c_str());
}
GMX_THROW(InconsistentInputError(message));
}
// describes the same simulation part. If those don't match, then
// the simulation cannot proceed.
auto simulationParts = gatherIntFromMultiSimulation(ms, headerContents->simulation_part);
- bool identicalSimulationParts = (std::adjacent_find(std::begin(simulationParts),
- std::end(simulationParts), std::not_equal_to<>())
- == std::end(simulationParts));
+ bool identicalSimulationParts =
+ (std::adjacent_find(
+ std::begin(simulationParts), std::end(simulationParts), std::not_equal_to<>())
+ == std::end(simulationParts));
if (!identicalSimulationParts)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
auto message = gmx::formatString(
"The number of ranks (%d) is not a multiple of the number of simulations (%td)",
- numRanks, multidirs.ssize());
+ numRanks,
+ multidirs.ssize());
GMX_THROW(gmx::InconsistentInputError(message));
}
if (debug)
{
- fprintf(debug, "We have %td simulations, %d ranks per simulation, local simulation is %d\n",
- multidirs.ssize(), numRanksPerSimulation, rankWithinWorldComm / numRanksPerSimulation);
+ fprintf(debug,
+ "We have %td simulations, %d ranks per simulation, local simulation is %d\n",
+ multidirs.ssize(),
+ numRanksPerSimulation,
+ rankWithinWorldComm / numRanksPerSimulation);
}
int numSimulations = multidirs.size();
#if GMX_MPI
static void gmx_sumd_comm(int nr, double r[], MPI_Comm mpi_comm)
{
-# if MPI_IN_PLACE_EXISTS
MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_DOUBLE, MPI_SUM, mpi_comm);
-# else
- /* this function is only used in code that is not performance critical,
- (during setup, when comm_rec is not the appropriate communication
- structure), so this isn't as bad as it looks. */
- double* buf;
- int i;
-
- snew(buf, nr);
- MPI_Allreduce(r, buf, nr, MPI_DOUBLE, MPI_SUM, mpi_comm);
- for (i = 0; i < nr; i++)
- {
- r[i] = buf[i];
- }
- sfree(buf);
-# endif
}
#endif
#if GMX_MPI
static void gmx_sumf_comm(int nr, float r[], MPI_Comm mpi_comm)
{
-# if MPI_IN_PLACE_EXISTS
MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_FLOAT, MPI_SUM, mpi_comm);
-# else
- /* this function is only used in code that is not performance critical,
- (during setup, when comm_rec is not the appropriate communication
- structure), so this isn't as bad as it looks. */
- float* buf;
- int i;
-
- snew(buf, nr);
- MPI_Allreduce(r, buf, nr, MPI_FLOAT, MPI_SUM, mpi_comm);
- for (i = 0; i < nr; i++)
- {
- r[i] = buf[i];
- }
- sfree(buf);
-# endif
}
#endif
#if !GMX_MPI
GMX_RELEASE_ASSERT(false, "Invalid call to gmx_sumi_sim");
#else
-# if MPI_IN_PLACE_EXISTS
MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_INT, MPI_SUM, ms->mastersComm_);
-# else
- /* this is thread-unsafe, but it will do for now: */
- ms->intBuffer.resize(nr);
- MPI_Allreduce(r, ms->intBuffer.data(), ms->intBuffer.size(), MPI_INT, MPI_SUM, ms->mastersComm_);
- std::copy(std::begin(ms->intBuffer), std::end(ms->intBuffer), r);
-# endif
#endif
}
#if !GMX_MPI
GMX_RELEASE_ASSERT(false, "Invalid call to gmx_sumli_sim");
#else
-# if MPI_IN_PLACE_EXISTS
MPI_Allreduce(MPI_IN_PLACE, r, nr, MPI_INT64_T, MPI_SUM, ms->mastersComm_);
-# else
- /* this is thread-unsafe, but it will do for now: */
- ms->int64Buffer.resize(nr);
- MPI_Allreduce(r, ms->int64Buffer.data(), ms->int64Buffer.size(), MPI_INT64_T, MPI_SUM, ms->mastersComm_);
- std::copy(std::begin(ms->int64Buffer), std::end(ms->int64Buffer), r);
-# endif
#endif
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
MPI_Comm mastersComm_ = MPI_COMM_NULL;
//! The MPI communicator between ranks of this simulation.
MPI_Comm simulationComm_ = MPI_COMM_NULL;
- /*! \brief Communication buffers needed if MPI_IN_PLACE isn't supported
- *
- * Other types could be added as needed.
- *
- * These vectors are unused when MPI_IN_PLACE is available
- * and could be removed with preprocessing (or perhaps
- * templating) or simply requiring MPI 2.0 (the standard
- * introduced in 1997). However, the additional cache pressure
- * introduced by the extra size of this type is not of great
- * concern, since we have at most one per MPI rank.
- * See issue #3591. */
- //! \{
- std::vector<int> intBuffer_;
- std::vector<int64_t> int64Buffer_;
- //! \}
};
//! Calculate the sum over the simulations of an array of ints
char buf[STRLEN];
sprintf(buf, "Started %s", name);
- print_date_and_time(fplog, cr->nodeid, buf,
- walltime_accounting_get_start_time_stamp(walltime_accounting));
+ print_date_and_time(
+ fplog, cr->nodeid, buf, walltime_accounting_get_start_time_stamp(walltime_accounting));
}
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
gmx_add_unit_test_library(mdrunutility-test-shared
threadaffinitytest.cpp)
+target_link_libraries(mdrunutility-test-shared PRIVATE common)
+target_link_libraries(mdrunutility-test-shared PUBLIC legacy_api)
gmx_add_unit_test(MdrunUtilityUnitTests mdrunutility-test
CPP_SOURCE_FILES
}
void expectPinningMessage(bool userSpecifiedStride, int stride)
{
- std::string pattern = formatString("Pinning threads .* %s.* stride of %d",
- userSpecifiedStride ? "user" : "auto", stride);
+ std::string pattern = formatString(
+ "Pinning threads .* %s.* stride of %d", userSpecifiedStride ? "user" : "auto", stride);
expectInfoMatchingRegex(pattern.c_str());
}
void expectLogMessageMatchingRegexIf(MDLogger::LogLevel level, const char* re, bool condition)
}
gmx::PhysicalNodeCommunicator comm(MPI_COMM_WORLD, physicalNodeId_);
int numThreadsOnThisNode, indexWithinNodeOfFirstThreadOnThisRank;
- analyzeThreadsOnThisNode(comm, numThreadsOnThisRank, &numThreadsOnThisNode,
- &indexWithinNodeOfFirstThreadOnThisRank);
- gmx_set_thread_affinity(logHelper_.logger(), cr_, &hwOpt_, *hwTop_, numThreadsOnThisRank,
- numThreadsOnThisNode, indexWithinNodeOfFirstThreadOnThisRank,
+ analyzeThreadsOnThisNode(
+ comm, numThreadsOnThisRank, &numThreadsOnThisNode, &indexWithinNodeOfFirstThreadOnThisRank);
+ gmx_set_thread_affinity(logHelper_.logger(),
+ cr_,
+ &hwOpt_,
+ *hwTop_,
+ numThreadsOnThisRank,
+ numThreadsOnThisNode,
+ indexWithinNodeOfFirstThreadOnThisRank,
&affinityAccess_);
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
//! Global instance of DefaultThreadAffinityAccess
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
DefaultThreadAffinityAccess g_defaultAffinityAccess;
} // namespace
hwThreadsPerCore = hwTop.machine().sockets[0].cores[0].hwThreads.size();
snew(*localityOrder, hwThreads);
int i = 0;
- for (auto& s : hwTop.machine().sockets)
+ for (const auto& s : hwTop.machine().sockets)
{
- for (auto& c : s.cores)
+ for (const auto& c : s.cores)
{
- for (auto& t : c.hwThreads)
+ for (const auto& t : c.hwThreads)
{
(*localityOrder)[i++] = t.logicalProcessorId;
}
{
GMX_LOG(mdlog.info)
.appendTextFormatted("Pinning threads with a%s logical core stride of %d",
- bPickPinStride ? "n auto-selected" : " user-specified", *pin_stride);
+ bPickPinStride ? "n auto-selected" : " user-specified",
+ *pin_stride);
}
*issuedWarning = alreadyWarned;
fprintf(debug,
"On rank %2d, thread %2d, index %2d, core %2d the affinity setting "
"returned %d\n",
- cr->nodeid, gmx_omp_get_thread_num(), index, core, ret ? 1 : 0);
+ cr->nodeid,
+ gmx_omp_get_thread_num(),
+ index,
+ core,
+ ret ? 1 : 0);
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
sprintf(msg,
"Looks like we have set affinity for more threads than "
"we have (%d > %d)!\n",
- nth_affinity_set, nthread_local);
+ nth_affinity_set,
+ nthread_local);
gmx_incons(msg);
}
if (nthread_local > 1)
{
- sprintf(sbuf2, "for %d/%d thread%s ", nthread_local - nth_affinity_set, nthread_local,
+ sprintf(sbuf2,
+ "for %d/%d thread%s ",
+ nthread_local - nth_affinity_set,
+ nthread_local,
nthread_local > 1 ? "s" : "");
}
/* MPI_Scan is inclusive, but here we need exclusive */
*intraNodeThreadOffset -= numThreadsOnThisRank;
/* Get the total number of threads on this physical node */
- MPI_Allreduce(&numThreadsOnThisRank, numThreadsOnThisNode, 1, MPI_INT, MPI_SUM,
- physicalNodeComm.comm_);
+ MPI_Allreduce(
+ &numThreadsOnThisRank, numThreadsOnThisNode, 1, MPI_INT, MPI_SUM, physicalNodeComm.comm_);
}
#else
GMX_UNUSED_VALUE(physicalNodeComm);
bool affinityIsAutoAndNumThreadsIsNotAuto =
(hw_opt->threadAffinity == ThreadAffinity::Auto && !hw_opt->totNumThreadsIsAuto);
- bool issuedWarning;
- bool validLayout = get_thread_affinity_layout(
- mdlog, cr, hwTop, numThreadsOnThisNode, affinityIsAutoAndNumThreadsIsNotAuto, offset,
- &core_pinning_stride, &localityOrder, &issuedWarning);
+ bool issuedWarning;
+ bool validLayout = get_thread_affinity_layout(mdlog,
+ cr,
+ hwTop,
+ numThreadsOnThisNode,
+ affinityIsAutoAndNumThreadsIsNotAuto,
+ offset,
+ &core_pinning_stride,
+ &localityOrder,
+ &issuedWarning);
const gmx::sfree_guard localityOrderGuard(localityOrder);
bool allAffinitiesSet;
if (validLayout)
{
- allAffinitiesSet = set_affinity(cr, numThreadsOnThisRank, intraNodeThreadOffset, offset,
- core_pinning_stride, localityOrder, affinityAccess);
+ allAffinitiesSet = set_affinity(
+ cr, numThreadsOnThisRank, intraNodeThreadOffset, offset, core_pinning_stride, localityOrder, affinityAccess);
}
else
{
{
if (debug)
{
- fprintf(debug, "%d hardware threads detected, but %d was returned by CPU_COUNT",
- nthreads_hw_avail, CPU_COUNT(&mask_current));
+ fprintf(debug,
+ "%d hardware threads detected, but %d was returned by CPU_COUNT",
+ nthreads_hw_avail,
+ CPU_COUNT(&mask_current));
}
detectedDefaultAffinityMask = false;
}
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2018, by the GROMACS development team, led by
+# Copyright (c) 2018,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(mdspan INTERFACE)
+
+# Public interface for modules, including dependencies and interfaces
+target_include_directories(mdspan INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
constexpr BasicMdspan addElementwise(const BasicMdspan& span1, const BasicMdspan& span2)
{
BasicMdspan result(span1);
- std::transform(begin(span1), end(span1), begin(span2), begin(result),
+ std::transform(begin(span1),
+ end(span1),
+ begin(span2),
+ begin(result),
std::plus<typename BasicMdspan::element_type>());
return result;
}
constexpr BasicMdspan subtractElementwise(const BasicMdspan& span1, const BasicMdspan& span2)
{
BasicMdspan result(span1);
- std::transform(begin(span1), end(span1), begin(span2), begin(result),
+ std::transform(begin(span1),
+ end(span1),
+ begin(span2),
+ begin(result),
std::minus<typename BasicMdspan::element_type>());
return result;
}
constexpr BasicMdspan multiplyElementwise(const BasicMdspan& span1, const BasicMdspan& span2)
{
BasicMdspan result(span1);
- std::transform(begin(span1), end(span1), begin(span2), begin(result),
+ std::transform(begin(span1),
+ end(span1),
+ begin(span2),
+ begin(result),
std::multiplies<typename BasicMdspan::element_type>());
return result;
}
constexpr BasicMdspan divideElementwise(const BasicMdspan& span1, const BasicMdspan& span2)
{
BasicMdspan result(span1);
- std::transform(begin(span1), end(span1), begin(span2), begin(result),
+ std::transform(begin(span1),
+ end(span1),
+ begin(span2),
+ begin(result),
std::divides<typename BasicMdspan::element_type>());
return result;
}
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
layouts.cpp
mdspan.cpp
)
+target_link_libraries(mdspan-test PRIVATE mdspan)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
bool contiguous,
bool strided)
{
- check_properties_internal(my_mdspan_mapping, always_unique, always_contiguous,
- always_strided, unique, contiguous, strided);
- check_properties_internal(my_mdspan_map_acc, always_unique, always_contiguous,
- always_strided, unique, contiguous, strided);
- check_properties_internal(my_mdspan_extents, always_unique, always_contiguous,
- always_strided, unique, contiguous, strided);
- check_properties_internal(my_mdspan_copy, always_unique, always_contiguous, always_strided,
- unique, contiguous, strided);
+ check_properties_internal(
+ my_mdspan_mapping, always_unique, always_contiguous, always_strided, unique, contiguous, strided);
+ check_properties_internal(
+ my_mdspan_map_acc, always_unique, always_contiguous, always_strided, unique, contiguous, strided);
+ check_properties_internal(
+ my_mdspan_extents, always_unique, always_contiguous, always_strided, unique, contiguous, strided);
+ check_properties_internal(
+ my_mdspan_copy, always_unique, always_contiguous, always_strided, unique, contiguous, strided);
}
void check_operator()
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(mdtypes INTERFACE)
+
file(GLOB MDTYPES_SOURCES
checkpointdata.cpp
df_history.cpp
)
endif()
+# Source files have the following private module dependencies.
+target_link_libraries(mdtypes PRIVATE
+ # gmxlib
+ # math
+ # mdtypes
+ # tng_io
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(mdtypes PUBLIC
+target_include_directories(mdtypes INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(mdtypes PUBLIC
+target_link_libraries(mdtypes INTERFACE
+ legacy_api
+ )
+
+# TODO: when fileio is an OBJECT target
+#target_link_libraries(mdtypes PUBLIC legacy_api)
+#target_link_libraries(mdtypes PRIVATE common)
+
+# Module dependencies
+# fileio interfaces convey transitive dependence on these modules.
+#target_link_libraries(mdtypes PUBLIC
+target_link_libraries(mdtypes INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(mdtypes PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(mdtypes PRIVATE legacy_modules)
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
#include "gromacs/mdtypes/awh_correlation_history.h"
-#include "gromacs/utility/basedefinitions.h"
namespace gmx
{
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MDTYPES_AWH_PARAMS_H
#define GMX_MDTYPES_AWH_PARAMS_H
+#include <vector>
+
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/classhelpers.h"
+
+struct t_inpfile;
+struct t_inputrec;
+struct pull_params_t;
+using warninp_t = struct warninp*;
namespace gmx
{
+class ISerializer;
//! Target distribution enum.
-enum
+enum class AwhTargetType : int
{
- eawhtargetCONSTANT,
- eawhtargetCUTOFF,
- eawhtargetBOLTZMANN,
- eawhtargetLOCALBOLTZMANN,
- eawhtargetNR
+ Constant,
+ Cutoff,
+ Boltzmann,
+ LocalBoltzmann,
+ Count,
+ Default = Constant
};
//! String for target distribution.
-extern const char* eawhtarget_names[eawhtargetNR + 1];
-//! Macro for target distribution string.
-#define EAWHTARGET(e) enum_name(e, gmx::eawhtargetNR, gmx::eawhtarget_names)
+const char* enumValueToString(AwhTargetType enumValue);
//! Weight histogram growth enum.
-enum
+enum class AwhHistogramGrowthType : int
{
- eawhgrowthEXP_LINEAR,
- eawhgrowthLINEAR,
- eawhgrowthNR
+ ExponentialLinear,
+ Linear,
+ Count,
+ Default = ExponentialLinear
};
//! String for weight histogram growth
-extern const char* eawhgrowth_names[eawhgrowthNR + 1];
-//! Macro for weight histogram growth string.
-#define EAWHGROWTH(e) enum_name(e, gmx::eawhgrowthNR, gmx::eawhgrowth_names)
+const char* enumValueToString(AwhHistogramGrowthType enumValue);
//! AWH potential type enum.
-enum
+enum class AwhPotentialType : int
{
- eawhpotentialCONVOLVED,
- eawhpotentialUMBRELLA,
- eawhpotentialNR
+ Convolved,
+ Umbrella,
+ Count,
+ Default = Convolved
};
//! String for AWH potential type
-extern const char* eawhpotential_names[eawhpotentialNR + 1];
-//! Macro for AWH potential type string.
-#define EAWHPOTENTIAL(e) enum_name(e, gmx::eawhpotentialNR, gmx::eawhpotential_names)
+const char* enumValueToString(AwhPotentialType enumValue);
//! AWH bias reaction coordinate provider
-enum
+enum class AwhCoordinateProviderType : int
{
- eawhcoordproviderPULL,
- eawhcoordproviderFREE_ENERGY_LAMBDA,
- eawhcoordproviderNR
+ Pull,
+ FreeEnergyLambda,
+ Count,
+ Default = Pull
};
//! String for AWH bias reaction coordinate provider.
-extern const char* eawhcoordprovider_names[eawhcoordproviderNR + 1];
-//! Macro for AWH bias reaction coordinate provider.
-#define EAWHCOORDPROVIDER(e) enum_name(e, gmx::eawhcoordproviderNR, gmx::eawhcoordprovider_names)
+const char* enumValueToString(AwhCoordinateProviderType enumValue);
-/*! \cond INTERNAL */
-
-//! Parameters for an AWH coordinate dimension.
-struct AwhDimParams
+class AwhDimParams
{
- int eCoordProvider; /**< The module providing the reaction coordinate. */
- int coordIndex; /**< Index of reaction coordinate in the provider. */
- double origin; /**< Start value of the interval. */
- double end; /**< End value of the interval. */
- double period; /**< The period of this dimension (= 0 if not periodic). */
- double forceConstant; /**< The force constant in kJ/mol/nm^2, kJ/mol/rad^2 */
- double diffusion; /**< Estimated diffusion constant in units of nm^2/ps, rad^2/ps or ps^-1. */
- double coordValueInit; /**< The initial coordinate value. */
- double coverDiameter; /**< The diameter that needs to be sampled around a point before it is considered covered. */
-};
+public:
+ //! Constructor from input file.
+ AwhDimParams(std::vector<t_inpfile>* inp, const std::string& prefix, warninp_t wi, bool bComment);
+ //! Constructor to generate from file reading.
+ explicit AwhDimParams(ISerializer* serializer);
-//! Parameters for an AWH bias.
-struct AwhBiasParams
-{
- // TODO: Turn dimParams into a std::vector when moved into AWH module
- int ndim; /**< Dimension of the coordinate space. */
- AwhDimParams* dimParams; /**< AWH parameters per dimension. */
- int eTarget; /**< Type of target distribution. */
- double targetBetaScaling; /**< Beta scaling value for Boltzmann type target distributions. */
- double targetCutoff; /**< Free energy cutoff value for cutoff type target distribution in kJ/mol.*/
- int eGrowth; /**< How the biasing histogram grows. */
- int bUserData; /**< Is there a user-defined initial PMF estimate and target estimate? */
- double errorInitial; /**< Estimated initial free energy error in kJ/mol. */
- int shareGroup; /**< When >0, the bias is shared with biases of the same group and across multiple simulations when shareBiasMultisim=true */
- gmx_bool equilibrateHistogram; /**< True if the simulation starts out by equilibrating the histogram. */
+ //! Move constructor.
+ AwhDimParams(AwhDimParams&&) = default;
+ //! Move assignment operator.
+ AwhDimParams& operator=(AwhDimParams&&) = default;
+ //! Delete copy constructor.
+ AwhDimParams(const AwhDimParams&) = delete;
+ //! Delete copy assignment.
+ AwhDimParams& operator=(const AwhDimParams&) = delete;
+
+ //! Which module is providing the reaction coordinate.
+ AwhCoordinateProviderType coordinateProvider() const { return eCoordProvider_; }
+ //! Index for reaction coordinate in provider.
+ int coordinateIndex() const { return coordIndex_; }
+ //! Start value for interval.
+ double origin() const { return origin_; }
+ //! End value for interval.
+ double end() const { return end_; }
+ //! Period for the dimension.
+ double period() const { return period_; }
+ //! Set period value dependent on state.
+ void setPeriod(double period) { period_ = period; }
+ //! Force constant for this dimension.
+ double forceConstant() const { return forceConstant_; }
+ //! Estimated diffusion constant.
+ double diffusion() const { return diffusion_; }
+ //! Initial value for coordinate.
+ double initialCoordinate() const { return coordValueInit_; }
+ //! Set initial coordinate value dependent on state.
+ void setInitialCoordinate(double initialCoordinate) { coordValueInit_ = initialCoordinate; }
+ //! Diameter needed to be sampled.
+ double coverDiameter() const { return coverDiameter_; }
+ //! Write datastructure.
+ void serialize(ISerializer* serializer);
+
+private:
+ //! The module providing the reaction coordinate.
+ AwhCoordinateProviderType eCoordProvider_;
+ //! Index of reaction coordinate in the provider.
+ int coordIndex_ = 0;
+ //! Start value of the interval.
+ double origin_ = 0.0;
+ //! End value of the interval.
+ double end_ = 0.0;
+ //! The period of this dimension (= 0 if not periodic).
+ double period_ = 0.0;
+ //! The force constant in kJ/mol/nm^2, kJ/mol/rad^2
+ double forceConstant_ = 0.0;
+ //! Estimated diffusion constant in units of nm^2/ps or rad^2/ps or ps^-1.
+ double diffusion_ = 0.0;
+ //! The initial coordinate value.
+ double coordValueInit_ = 0.0;
+ //! The diameter that needs to be sampled around a point before it is considered covered.
+ double coverDiameter_ = 0.0;
};
-//! Parameters for AWH.
-struct AwhParams
+class AwhBiasParams
{
- // TODO: Turn awhBiasParams into a std::vector when moved into AWH module
- int numBias; /**< The number of AWH biases.*/
- AwhBiasParams* awhBiasParams; /**< AWH bias parameters.*/
- int64_t seed; /**< Random seed.*/
- int nstOut; /**< Output step interval.*/
- int nstSampleCoord; /**< Number of samples per coordinate sample (also used for PMF) */
- int numSamplesUpdateFreeEnergy; /**< Number of samples per free energy update. */
- int ePotential; /**< Type of potential. */
- gmx_bool shareBiasMultisim; /**< When true, share biases with shareGroup>0 between multi-simulations */
+public:
+ //! Constructor from input file.
+ AwhBiasParams(std::vector<t_inpfile>* inp, const std::string& prefix, warninp_t wi, bool bComment);
+ //! Constructor to generate from file reading.
+ explicit AwhBiasParams(ISerializer* serializer);
+
+ //! Move constructor.
+ AwhBiasParams(AwhBiasParams&&) = default;
+ //! Move assignment operator.
+ AwhBiasParams& operator=(AwhBiasParams&&) = default;
+ //! Delete copy constructor.
+ AwhBiasParams(const AwhBiasParams&) = delete;
+ //! Delete copy assignment.
+ AwhBiasParams& operator=(const AwhBiasParams&) = delete;
+
+ //! Which target distribution is searched.
+ AwhTargetType targetDistribution() const { return eTarget_; }
+ //! Beta scaling to reach target distribution.
+ double targetBetaScaling() const { return targetBetaScaling_; }
+ //! Cutoff for target.
+ double targetCutoff() const { return targetCutoff_; }
+ //! Which kind of growth to use.
+ AwhHistogramGrowthType growthType() const { return eGrowth_; }
+ //! User provided PMF estimate.
+ bool userPMFEstimate() const { return bUserData_; }
+ //! Estimated initial free energy error in kJ/mol.
+ double initialErrorEstimate() const { return errorInitial_; }
+ //! Dimensions of coordinate space.
+ int ndim() const { return dimParams_.size(); }
+ //! Number of groups to share this bias with.
+ int shareGroup() const { return shareGroup_; }
+ //! If the simulation starts with equilibrating histogram.
+ bool equilibrateHistogram() const { return equilibrateHistogram_; }
+ //! Access to dimension parameters.
+ ArrayRef<AwhDimParams> dimParams() { return dimParams_; }
+ //! Const access to dimension parameters.
+ ArrayRef<const AwhDimParams> dimParams() const { return dimParams_; }
+ //! Write datastructure.
+ void serialize(ISerializer* serializer);
+
+private:
+ //! AWH parameters per dimension.
+ std::vector<AwhDimParams> dimParams_;
+ //! Type of target distribution.
+ AwhTargetType eTarget_;
+ //! Beta scaling value for Boltzmann type target distributions.
+ double targetBetaScaling_;
+ //! Free energy cutoff value for cutoff type target distribution in kJ/mol.
+ double targetCutoff_;
+ //! How the biasing histogram grows.
+ AwhHistogramGrowthType eGrowth_;
+ //! Is there a user-defined initial PMF estimate and target estimate?
+ bool bUserData_;
+ //! Estimated initial free energy error in kJ/mol.
+ double errorInitial_;
+ //! When >0, the bias is shared with biases of the same group and across multiple simulations when shareBiasMultisim=true
+ int shareGroup_;
+ //! True if the simulation starts out by equilibrating the histogram.
+ bool equilibrateHistogram_;
};
+/*! \internal
+ * \brief Structure holding parameter information for AWH.
+ */
+class AwhParams
+{
+public:
+ //! Constructor from input file.
+ AwhParams(std::vector<t_inpfile>* inp, warninp_t wi);
+ //! Constructor used to generate awh parameter from file reading.
+ explicit AwhParams(ISerializer* serializer);
-/*! \endcond */
+ //! Move constructor.
+ AwhParams(AwhParams&&) = default;
+ //! Move assignment operator.
+ AwhParams& operator=(AwhParams&&) = default;
+ //! Delete copy constructor.
+ AwhParams(const AwhParams&) = delete;
+ //! Delete copy assignment.
+ AwhParams& operator=(const AwhParams&) = delete;
+
+ //! Get number of biases.
+ int numBias() const { return awhBiasParams_.size(); }
+ //! Get access to bias parameters.
+ ArrayRef<AwhBiasParams> awhBiasParams() { return awhBiasParams_; }
+ //! Const access to bias parameters.
+ ArrayRef<const AwhBiasParams> awhBiasParams() const { return awhBiasParams_; }
+ //! What king of potential is being used. \todo should use actual enum class.
+ AwhPotentialType potential() const { return potentialEnum_; }
+ //! Seed used for starting AWH.
+ int64_t seed() const { return seed_; }
+ //! Output step interval.
+ int nstout() const { return nstOut_; }
+ //! Number of samples per coordinate sample.
+ int nstSampleCoord() const { return nstSampleCoord_; }
+ //! Number of samples per free energy update.
+ int numSamplesUpdateFreeEnergy() const { return numSamplesUpdateFreeEnergy_; }
+ //! If biases are shared in multisim.
+ bool shareBiasMultisim() const { return shareBiasMultisim_; }
+ //! Serialize awh parameters.
+ void serialize(ISerializer* serializer);
+
+private:
+ //! AWH bias parameters.
+ std::vector<AwhBiasParams> awhBiasParams_;
+ //! Random seed.
+ int64_t seed_;
+ //! Output step interval.
+ int nstOut_;
+ //! Number of samples per coordinate sample (also used for PMF)
+ int nstSampleCoord_;
+ //! Number of samples per free energy update.
+ int numSamplesUpdateFreeEnergy_;
+ //! Type of potential.
+ AwhPotentialType potentialEnum_;
+ //! Whether to share biases with shareGroup>0 between multi-simulations.
+ bool shareBiasMultisim_;
+};
} // namespace gmx
for (; outputIt != outputEnd && inputIt != inputEnd; outputIt++, inputIt++)
{
auto storedRVec = inputIt->asObject()["RVec"].asArray().values();
- *outputIt = { storedRVec[XX].cast<real>(), storedRVec[YY].cast<real>(),
- storedRVec[ZZ].cast<real>() };
+ *outputIt = { storedRVec[XX].cast<real>(), storedRVec[YY].cast<real>(), storedRVec[ZZ].cast<real>() };
}
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <stddef.h>
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/gmxmpi.h"
-struct mpi_in_place_buf_t;
struct gmx_domdec_t;
#define DUTY_PP (1U << 0U)
* This should be read through thisRankHasDuty() or getThisRankDuties().
*/
int duty;
-
- /* these buffers are used as destination buffers if MPI_IN_PLACE isn't
- supported.*/
- mpi_in_place_buf_t* mpb;
};
/*! \brief
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/topology/idef.h"
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/real.h"
struct t_lambda;
// The non-bonded energy terms accumulated for energy group pairs
-enum
+enum class NonBondedEnergyTerms : int
{
- egCOULSR,
- egLJSR,
- egBHAMSR,
- egCOUL14,
- egLJ14,
- egNR
+ CoulombSR,
+ LJSR,
+ BuckinghamSR,
+ Coulomb14,
+ LJ14,
+ Count
};
// Struct for accumulating non-bonded energies between energy group pairs
{
gmx_grppairener_t(int numEnergyGroups) : nener(numEnergyGroups * numEnergyGroups)
{
- for (auto& elem : ener)
+ for (auto& term : energyGroupPairTerms)
{
- elem.resize(nener);
+ term.resize(nener);
}
}
- int nener; /* The number of energy group pairs */
- std::array<std::vector<real>, egNR> ener; /* Energy terms for each pair of groups */
+ int nener; /* The number of energy group pairs */
+ gmx::EnumerationArray<NonBondedEnergyTerms, std::vector<real>> energyGroupPairTerms; /* Energy terms for each pair of groups */
};
//! Accumulates free-energy foreign lambda energies and dH/dlamba
gmx_enerdata_t(int numEnergyGroups, int numFepLambdas);
//! The energies for all different interaction types
- real term[F_NRE] = { 0 };
+ std::array<real, F_NRE> term = { 0 };
//! Energy group pair non-bonded energies
struct gmx_grppairener_t grpp;
//! Contributions to dV/dlambda with linear dependence on lambda
- double dvdl_lin[efptNR] = { 0 };
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, double> dvdl_lin = { 0 };
//! Contributions to dV/dlambda with non-linear dependence on lambda
- double dvdl_nonlin[efptNR] = { 0 };
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, double> dvdl_nonlin = { 0 };
/* The idea is that dvdl terms with linear lambda dependence will be added
* automatically to enerpart_lambda. Terms with non-linear lambda dependence
* should explicitly determine the energies at foreign lambda points
ForeignLambdaTerms foreignLambdaTerms;
//! Alternate, temporary array for storing foreign lambda energies
- real foreign_term[F_NRE] = { 0 };
+ std::array<real, F_NRE> foreign_term = { 0 };
//! Alternate, temporary array for storing foreign lambda group pair energies
struct gmx_grppairener_t foreign_grpp;
};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <memory>
#include <vector>
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
//! \cond INTERNAL
//! Lambda at start time
double start_lambda;
//! Whether the lambda value is set. Here for backward-compatibility.
- gmx_bool start_lambda_set;
+ bool start_lambda_set;
//! Read / write data from / to checkpoint object
template<gmx::CheckpointDataOperation operation>
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2012,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MDTYPES_FCDATA_H
#define GMX_MDTYPES_FCDATA_H
+#include <memory>
#include <vector>
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/idef.h"
-#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/real.h"
+enum class DistanceRestraintWeighting : int;
+struct gmx_mtop_t;
+struct gmx_multisim_t;
+struct t_commrec;
+struct t_inputrec;
+class t_state;
+
typedef real rvec5[5];
/* Distance restraining stuff */
typedef struct t_disresdata
{
- int dr_weighting; /* Weighting of pairs in one restraint */
- gmx_bool dr_bMixed; /* Use sqrt of the instantaneous times *
- * the time averaged violation */
- real dr_fc; /* Force constant for disres, *
- * which is multiplied by a (possibly) *
- * different factor for each restraint */
- real dr_tau; /* Time constant for disres */
- real ETerm; /* multiplication factor for time averaging */
- real ETerm1; /* 1 - ETerm1 */
- real exp_min_t_tau; /* Factor for slowly switching on the force */
- int nres; /* The number of distance restraints */
- int npair; /* The number of distance restraint pairs */
- int type_min; /* The minimum iparam type index for restraints */
- real sumviol; /* The sum of violations */
- real* rt; /* The instantaneous distance (npair) */
- real* rm3tav; /* The time averaged distance (npair) */
- real* Rtl_6; /* The instantaneous r^-6 (nres) */
- real* Rt_6; /* The instantaneous ensemble averaged r^-6 (nres) */
- real* Rtav_6; /* The time and ensemble averaged r^-6 (nres) */
- int nsystems; /* The number of systems for ensemble averaging */
+ DistanceRestraintWeighting dr_weighting; /* Weighting of pairs in one restraint */
+ bool dr_bMixed; /* Use sqrt of the instantaneous times *
+ * the time averaged violation */
+ real dr_fc; /* Force constant for disres, *
+ * which is multiplied by a (possibly) *
+ * different factor for each restraint */
+ real dr_tau; /* Time constant for disres */
+ real ETerm; /* multiplication factor for time averaging */
+ real ETerm1; /* 1 - ETerm1 */
+ real exp_min_t_tau; /* Factor for slowly switching on the force */
+ int nres; /* The number of distance restraints */
+ int npair; /* The number of distance restraint pairs */
+ int type_min; /* The minimum iparam type index for restraints */
+ real sumviol; /* The sum of violations */
+ real* rt; /* The instantaneous distance (npair) */
+ real* rm3tav; /* The time averaged distance (npair) */
+ real* Rtl_6; /* The instantaneous r^-6 (nres) */
+ real* Rt_6; /* The instantaneous ensemble averaged r^-6 (nres) */
+ real* Rtav_6; /* The time and ensemble averaged r^-6 (nres) */
+ int nsystems; /* The number of systems for ensemble averaging */
/* TODO: Implement a proper solution for parallel disre indexing */
const t_iatom* forceatomsStart; /* Pointer to the start of the disre forceatoms */
};
/* Orientation restraining stuff */
-typedef struct t_oriresdata
+struct t_oriresdata
{
- real fc; /* Force constant for the restraints */
- real edt; /* Multiplication factor for time averaging */
- real edt_1; /* 1 - edt */
- real exp_min_t_tau; /* Factor for slowly switching on the force */
- int nr; /* The number of orientation restraints */
- int nex; /* The number of experiments */
- int typeMin; /* The minimum iparam type index for restraints */
- int nref; /* The number of atoms for the fit */
- real* mref; /* The masses of the reference atoms */
- rvec* xref; /* The reference coordinates for the fit (nref) */
- rvec* xtmp; /* Temporary array for fitting (nref) */
- matrix R; /* Rotation matrix to rotate to the reference coor. */
- tensor* S; /* Array of order tensors for each experiment (nexp) */
- rvec5* Dinsl; /* The order matrix D for all restraints (nr x 5) */
- rvec5* Dins; /* The ensemble averaged D (nr x 5) */
- rvec5* Dtav; /* The time and ensemble averaged D (nr x 5) */
- real* oinsl; /* The calculated instantaneous orientations */
- real* oins; /* The calculated emsemble averaged orientations */
- real* otav; /* The calculated time and ensemble averaged orient. */
- real rmsdev; /* The weighted (using kfac) RMS deviation */
- OriresMatEq* tmpEq; /* An temporary array of matrix + rhs */
- real* eig; /* Eigenvalues/vectors, for output only (nex x 12) */
-
- /* variables for diagonalization with diagonalize_orires_tensors()*/
- double** M;
- double* eig_diag;
- double** v;
-} t_oriresdata;
+ /*! Constructor
+ *
+ * \param[in] fplog Log file, can be nullptr
+ * \param[in] mtop The global topology
+ * \param[in] ir The input record
+ * \param[in] cr The commrec, can be nullptr when not running in parallel
+ * \param[in] ms The multisim communicator, pass nullptr to avoid ensemble averaging
+ * \param[in,out] globalState The global state, orientation restraint entires are added
+ *
+ * \throws InvalidInputError when there is domain decomposition, fewer than 5 restraints,
+ * periodic molecules or more than 1 molecule for a moleculetype with restraints.
+ */
+ t_oriresdata(FILE* fplog,
+ const gmx_mtop_t& mtop,
+ const t_inputrec& ir,
+ const t_commrec* cr,
+ const gmx_multisim_t* ms,
+ t_state* globalState);
+
+ //! Destructor
+ ~t_oriresdata();
+
+ //! Force constant for the restraints
+ real fc;
+ //! Multiplication factor for time averaging
+ real edt;
+ //! 1 - edt
+ real edt_1;
+ //! Factor for slowly switching on the force
+ real exp_min_t_tau;
+ //! The number of orientation restraints
+ const int numRestraints;
+ //! The number of experiments
+ int numExperiments;
+ //! The minimum iparam type index for restraints
+ int typeMin;
+ //! The number of atoms for the fit
+ int numReferenceAtoms;
+ //! The masses of the reference atoms
+ std::vector<real> mref;
+ //! The reference coordinates for the fit
+ std::vector<gmx::RVec> xref;
+ //! Temporary array for fitting
+ std::vector<gmx::RVec> xtmp;
+ //! Rotation matrix to rotate to the reference coordinates
+ matrix rotationMatrix;
+ //! Array of order tensors, one for each experiment
+ tensor* orderTensors = nullptr;
+ //! The order tensor D for all restraints
+ rvec5* DTensors = nullptr;
+ //! The ensemble averaged D for all restraints
+ rvec5* DTensorsEnsembleAv = nullptr;
+ //! The time and ensemble averaged D restraints
+ rvec5* DTensorsTimeAndEnsembleAv = nullptr;
+ //! The calculated instantaneous orientations
+ std::vector<real> orientations;
+ //! The calculated emsemble averaged orientations
+ gmx::ArrayRef<real> orientationsEnsembleAv;
+ //! Buffer for the calculated emsemble averaged orientations, only used with ensemble averaging
+ std::vector<real> orientationsEnsembleAvBuffer;
+ //! The calculated time and ensemble averaged orientations
+ gmx::ArrayRef<real> orientationsTimeAndEnsembleAv;
+ //! The weighted (using kfac) RMS deviation
+ std::vector<real> orientationsTimeAndEnsembleAvBuffer;
+ //! Buffer for the weighted (using kfac) RMS deviation, only used with time averaging
+ real rmsdev;
+ //! An temporary array of matrix + rhs
+ std::vector<OriresMatEq> tmpEq;
+ //! The number of eigenvalues + eigenvectors per experiment
+ static constexpr int c_numEigenRealsPerExperiment = 12;
+ //! Eigenvalues/vectors, for output only (numExperiments x 12)
+ std::vector<real> eigenOutput;
+
+ // variables for diagonalization with diagonalize_orires_tensors()
+ //! Tensor to diagonalize
+ std::array<gmx::DVec, DIM> M;
+ //! Eigenvalues
+ std::array<double, DIM> eig_diag;
+ //! Eigenvectors
+ std::array<gmx::DVec, DIM> v;
+
+ // Default copy and assign would be incorrect and manual versions are not yet implemented.
+ GMX_DISALLOW_COPY_AND_ASSIGN(t_oriresdata);
+};
/* Cubic spline table for tabulated bonded interactions */
struct bondedtable_t
std::vector<bondedtable_t> dihtab;
// TODO: Convert to C++ and unique_ptr (currently this data is not freed)
- t_disresdata* disres = nullptr;
- t_oriresdata* orires = nullptr;
+ t_disresdata* disres = nullptr;
+ std::unique_ptr<t_oriresdata> orires;
};
#endif
{
forceMtsCombined_.resizeWithPadding(numAtoms);
}
- view_ = ForceBuffersView(force_.arrayRefWithPadding(), forceMtsCombined_.arrayRefWithPadding(),
- useForceMtsCombined_);
+ view_ = ForceBuffersView(
+ force_.arrayRefWithPadding(), forceMtsCombined_.arrayRefWithPadding(), useForceMtsCombined_);
}
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MDTYPES_FORCEBUFFERS_H
#define GMX_MDTYPES_FORCEBUFFERS_H
+#include <memory>
+
#include "gromacs/gpu_utils/hostallocator.h"
-#include "gromacs/math/arrayrefwithpadding.h"
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/classhelpers.h"
namespace gmx
{
+template<typename T>
+class ArrayRef;
+template<typename T>
+class ArrayRefWithPadding;
enum class PinningPolicy : int;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* \param[in] force A force buffer that will be used for storing forces
* \param[in] computeVirial True when algorithms are required to provide their virial contribution (for the current force evaluation)
- * \param[in] shiftForces A shift forces buffer of size SHIFTS, only used with \p computeVirial = true
+ * \param[in] shiftForces A shift forces buffer of size c_numShiftVectors, only used with \p computeVirial = true
*/
ForceWithShiftForces(const gmx::ArrayRefWithPadding<gmx::RVec>& force,
const bool computeVirial,
gmx::ArrayRefWithPadding<gmx::RVec> force_;
//! True when virial computation is requested
bool computeVirial_;
- //! A buffer for storing the shift forces, size SHIFTS
+ //! A buffer for storing the shift forces, size c_numShiftVectors
gmx::ArrayRef<gmx::RVec> shiftForces_;
//! Tells whether we have spread the vsite forces
bool haveSpreadVsiteForces_ = false;
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
#include "locality.h"
class ListedForces;
struct t_fcdata;
struct t_forcetable;
-struct t_QMMMrec;
+struct interaction_const_t;
namespace gmx
{
* this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
*/
#define GMX_CUTOFF_INF 1E+18
-
-/* enums for the neighborlist type */
-enum
-{
- enbvdwNONE,
- enbvdwLJ,
- enbvdwBHAM,
- enbvdwTAB,
- enbvdwNR
-};
+//! Check the cuttoff
+real cutoff_inf(real cutoff);
struct cginfo_mb_t
{
return forceBufferForDirectVirialContributions_;
}
- //! Returns the buffer for shift forces, size SHIFTS
+ //! Returns the buffer for shift forces, size c_numShiftVectors
gmx::ArrayRef<gmx::RVec> shiftForces() { return shiftForces_; }
//! Resizes the direct virial contribution buffer, when present
bool haveDirectVirialContributions_ = false;
//! Force buffer for force computation with direct virial contributions
std::vector<gmx::RVec> forceBufferForDirectVirialContributions_;
- //! Shift force array for computing the virial, size SHIFTS
+ //! Shift force array for computing the virial, size c_numShiftVectors
std::vector<gmx::RVec> shiftForces_;
};
-
+// NOLINTNEXTLINE (clang-analyzer-optin.performance.Padding)
struct t_forcerec
-{ // NOLINT (clang-analyzer-optin.performance.Padding)
+{
// Declare an explicit constructor and destructor, so they can be
// implemented in a single source file, so that not every source
// file that includes this one needs to understand how to find the
t_forcerec();
~t_forcerec();
- struct interaction_const_t* ic = nullptr;
+ std::unique_ptr<interaction_const_t> ic;
/* PBC stuff */
PbcType pbcType = PbcType::Xyz;
//! Tells whether atoms inside a molecule can be in different periodic images,
// i.e. whether we need to take into account PBC when computing distances inside molecules.
// This determines whether PBC must be considered for e.g. bonded interactions.
- gmx_bool bMolPBC = FALSE;
- int rc_scaling = 0;
- rvec posres_com = { 0 };
- rvec posres_comB = { 0 };
+ bool bMolPBC = false;
+ RefCoordScaling rc_scaling = RefCoordScaling::No;
+ gmx::RVec posres_com = { 0, 0, 0 };
+ gmx::RVec posres_comB = { 0, 0, 0 };
- gmx_bool use_simd_kernels = FALSE;
+ bool use_simd_kernels = false;
/* Interaction for calculated in kernels. In many cases this is similar to
* the electrostatics settings in the inputrecord, but the difference is that
* tabulated we already included the inputrec modification there, so the kernel
* modification setting will say 'none' in that case.
*/
- int nbkernel_elec_interaction = 0;
- int nbkernel_vdw_interaction = 0;
- int nbkernel_elec_modifier = 0;
- int nbkernel_vdw_modifier = 0;
+ NbkernelElecType nbkernel_elec_interaction = NbkernelElecType::None;
+ NbkernelVdwType nbkernel_vdw_interaction = NbkernelVdwType::None;
+ InteractionModifiers nbkernel_elec_modifier = InteractionModifiers::None;
+ InteractionModifiers nbkernel_vdw_modifier = InteractionModifiers::None;
/* Cut-Off stuff.
* Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
real rlist = 0;
/* Charge sum for topology A/B ([0]/[1]) for Ewald corrections */
- double qsum[2] = { 0 };
- double q2sum[2] = { 0 };
- double c6sum[2] = { 0 };
+ std::array<double, 2> qsum = { 0 };
+ std::array<double, 2> q2sum = { 0 };
+ std::array<double, 2> c6sum = { 0 };
/* Dispersion correction stuff */
std::unique_ptr<DispersionCorrection> dispersionCorrection;
/* Fudge factors */
real fudgeQQ = 0;
- /* Table stuff */
- gmx_bool bcoultab = FALSE;
- gmx_bool bvdwtab = FALSE;
-
- t_forcetable* pairsTable = nullptr; /* for 1-4 interactions, [pairs] and [pairs_nb] */
+ std::unique_ptr<t_forcetable> pairsTable; /* for 1-4 interactions, [pairs] and [pairs_nb] */
/* Free energy */
- int efep = 0;
+ FreeEnergyPerturbationType efep = FreeEnergyPerturbationType::No;
/* Information about atom properties for the molecule blocks in the system */
std::vector<cginfo_mb_t> cginfo_mb;
/* Information about atom properties for local and non-local atoms */
std::vector<int> cginfo;
- rvec* shift_vec = nullptr;
+ std::vector<gmx::RVec> shift_vec;
std::unique_ptr<gmx::WholeMoleculeTransform> wholeMoleculeTransform;
std::unique_ptr<nonbonded_verlet_t> nbv;
/* The wall tables (if used) */
- int nwall = 0;
- t_forcetable*** wall_tab = nullptr;
+ int nwall = 0;
+ std::vector<std::vector<std::unique_ptr<t_forcetable>>> wall_tab;
/* The number of atoms participating in do_force_lowlevel */
int natoms_force = 0;
std::vector<ForceHelperBuffers> forceHelperBuffers;
/* Data for PPPM/PME/Ewald */
- struct gmx_pme_t* pmedata = nullptr;
- int ljpme_combination_rule = 0;
+ gmx_pme_t* pmedata = nullptr;
+ LongRangeVdW ljpme_combination_rule = LongRangeVdW::Geom;
/* PME/Ewald stuff */
- struct gmx_ewald_tab_t* ewald_table = nullptr;
+ std::unique_ptr<gmx_ewald_tab_t> ewald_table;
/* Non bonded Parameter lists */
- int ntype = 0; /* Number of atom types */
- gmx_bool bBHAM = FALSE;
+ int ntype = 0; /* Number of atom types */
+ bool haveBuckingham = false;
std::vector<real> nbfp;
- real* ljpme_c6grid = nullptr; /* C6-values used on grid in LJPME */
+ std::vector<real> ljpme_c6grid; /* C6-values used on grid in LJPME */
/* Energy group pair flags */
int* egp_flags = nullptr;
gmx::GpuBonded* gpuBonded = nullptr;
/* Ewald correction thread local virial and energy data */
- int nthread_ewc = 0;
- struct ewald_corr_thread_t* ewc_t = nullptr;
+ int nthread_ewc = 0;
+ std::vector<ewald_corr_thread_t> ewc_t;
gmx::ForceProviders* forceProviders = nullptr;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "group.h"
+#include "gromacs/utility/exceptions.h"
+
+gmx_ekindata_t::gmx_ekindata_t(int numTempCoupleGroups, real cos_accel, int numThreads) :
+ ngtc(numTempCoupleGroups),
+ nthreads_(numThreads)
+{
+ tcstat.resize(ngtc);
+ /* Set Berendsen tcoupl lambda's to 1,
+ * so runs without Berendsen coupling are not affected.
+ */
+ for (int i = 0; i < ngtc; i++)
+ {
+ tcstat[i].lambda = 1.0;
+ tcstat[i].vscale_nhc = 1.0;
+ tcstat[i].ekinscaleh_nhc = 1.0;
+ tcstat[i].ekinscalef_nhc = 1.0;
+ }
+
+ snew(ekin_work_alloc, nthreads_);
+ snew(ekin_work, nthreads_);
+ snew(dekindl_work, nthreads_);
+
+#pragma omp parallel for num_threads(nthreads_) schedule(static)
+ for (int thread = 0; thread < nthreads_; thread++)
+ {
+ try
+ {
+ constexpr int EKIN_WORK_BUFFER_SIZE = 2;
+ /* Allocate 2 extra elements on both sides, so in single
+ * precision we have
+ * EKIN_WORK_BUFFER_SIZE*DIM*DIM*sizeof(real) = 72/144 bytes
+ * buffer on both sides to avoid cache pollution.
+ */
+ snew(ekin_work_alloc[thread], ngtc + 2 * EKIN_WORK_BUFFER_SIZE);
+ ekin_work[thread] = ekin_work_alloc[thread] + EKIN_WORK_BUFFER_SIZE;
+ /* Nasty hack so we can have the per-thread accumulation
+ * variable for dekindl in the same thread-local cache lines
+ * as the per-thread accumulation tensors for ekin[fh],
+ * because they are accumulated in the same loop. */
+ dekindl_work[thread] = &(ekin_work[thread][ngtc][0][0]);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
+ }
+
+ cosacc.cos_accel = cos_accel;
+}
+
gmx_ekindata_t::~gmx_ekindata_t()
{
- for (int i = 0; i < nthreads; i++)
+ for (int i = 0; i < nthreads_; i++)
{
sfree(ekin_work_alloc[i]);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
double vscale_nhc = 0;
};
-struct t_grp_acc
-{
- //! Number of atoms in this group
- int nat = 0;
- //! Mean velocities of home particles
- rvec u = { 0 };
- //! Previous mean velocities of home particles
- rvec uold = { 0 };
- //! Mass for topology A
- double mA = 0;
- //! Mass for topology B
- double mB = 0;
-};
-
struct t_cos_acc
{
//! The acceleration for the cosine profile
real vcos = 0;
};
-struct gmx_ekindata_t
+class gmx_ekindata_t
{
- //! Whether non-equilibrium MD is active (ie. constant or cosine acceleration)
- gmx_bool bNEMD;
+public:
+ gmx_ekindata_t(int numTempCoupleGroups, real cos_accel, int numThreads);
//! The number of T-coupling groups
- int ngtc = 0;
- //! For size of ekin_work
- int nthreads = 0;
+ int ngtc;
//! T-coupling data
std::vector<t_grp_tcstat> tcstat;
//! Allocated locations for *_work members
tensor** ekin_work = nullptr;
//! Work location for dekindl per thread
real** dekindl_work = nullptr;
- //! The number of acceleration groups
- int ngacc = 0;
- //! Acceleration data
- std::vector<t_grp_acc> grpstat;
//! overall kinetic energy
tensor ekin = { { 0 } };
//! overall 1/2 step kinetic energy
t_cos_acc cosacc;
~gmx_ekindata_t();
+
+private:
+ //! For size of ekin_work
+ int nthreads_ = 0;
};
#define GID(igid, jgid, gnr) \
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void ForceProviders::calculateForces(const ForceProviderInput& forceProviderInput,
ForceProviderOutput* forceProviderOutput) const
{
- for (auto provider : impl_->providers_)
+ for (auto* provider : impl_->providers_)
{
provider->calculateForces(forceProviderInput, forceProviderOutput);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MDTYPES_IFORCEPROVIDER_H
#define GMX_MDTYPES_IFORCEPROVIDER_H
+#include <memory>
+
#include "gromacs/math/vec.h"
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/gmxassert.h"
struct gmx_enerdata_t;
struct t_commrec;
struct t_forcerec;
-struct t_mdatoms;
namespace gmx
{
public:
/*! \brief Constructor assembles all necessary force provider input data
*
- * \param[in] x Atomic positions
- * \param[in] cr Communication record structure
- * \param[in] box The simulation box
- * \param[in] time The current time in the simulation
- * \param[in] mdatoms The atomic data
+ * \param[in] x Atomic positions.
+ * \param[in] homenr Number of atoms on the domain.
+ * \param[in] chargeA Atomic charges for atoms on the domain.
+ * \param[in] massT Atomic masses for atoms on the domain.
+ * \param[in] time The current time in the simulation.
+ * \param[in] box The simulation box.
+ * \param[in] cr Communication record structure.
*/
ForceProviderInput(ArrayRef<const RVec> x,
- const t_mdatoms& mdatoms,
+ int homenr,
+ ArrayRef<const real> chargeA,
+ ArrayRef<const real> massT,
double time,
const matrix box,
const t_commrec& cr) :
x_(x),
- mdatoms_(mdatoms),
+ homenr_(homenr),
+ chargeA_(chargeA),
+ massT_(massT),
t_(time),
cr_(cr)
{
copy_mat(box, box_);
}
- ArrayRef<const RVec> x_; //!< The atomic positions
- const t_mdatoms& mdatoms_; //!< Atomic data
- double t_; //!< The current time in the simulation
+ ArrayRef<const RVec> x_; //!< The atomic positions
+ int homenr_;
+ ArrayRef<const real> chargeA_;
+ ArrayRef<const real> massT_;
+ double t_; //!< The current time in the simulation
matrix box_ = { { 0, 0, 0 }, { 0, 0, 0 }, { 0, 0, 0 } }; //!< The simulation box
const t_commrec& cr_; //!< Communication record structure
};
private:
class Impl;
- gmx::PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
class ForceProviders;
class IMDOutputProvider;
class IMdpOptionProvider;
-struct MdModulesNotifier;
+struct MDModulesNotifiers;
/*! \libinternal \brief
* Extension module for \Gromacs simulations.
//! Initializes force providers from this module.
virtual void initForceProviders(ForceProviders* forceProviders) = 0;
//! Subscribe to simulation setup notifications
- virtual void subscribeToSimulationSetupNotifications(MdModulesNotifier* notifier) = 0;
+ virtual void subscribeToSimulationSetupNotifications(MDModulesNotifiers* notifiers) = 0;
//! Subscribe to pre processing notifications
- virtual void subscribeToPreProcessingNotifications(MdModulesNotifier* notifier) = 0;
+ virtual void subscribeToPreProcessingNotifications(MDModulesNotifiers* notifiers) = 0;
};
} // namespace gmx
*/
#include "gmxpre.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "inputrec.h"
#include <cstdio>
#include <cstring>
#include <algorithm>
+#include <memory>
#include <numeric>
+#include "gromacs/applied_forces/awh/read_params.h"
#include "gromacs/math/veccompare.h"
#include "gromacs/math/vecdump.h"
#include "gromacs/mdtypes/awh_params.h"
// TODO When this memset is removed, remove the suppression of
// gcc -Wno-class-memaccess in a CMakeLists.txt file.
std::memset(this, 0, sizeof(*this)); // NOLINT(bugprone-undefined-memory-manipulation)
- snew(fepvals, 1);
- snew(expandedvals, 1);
- snew(simtempvals, 1);
+ fepvals = std::make_unique<t_lambda>();
+ expandedvals = std::make_unique<t_expanded>();
+ simtempvals = std::make_unique<t_simtemp>();
}
t_inputrec::~t_inputrec()
return nst;
}
-int tcouple_min_integration_steps(int etc)
+int tcouple_min_integration_steps(TemperatureCoupling etc)
{
int n;
switch (etc)
{
- case etcNO: n = 0; break;
- case etcBERENDSEN:
- case etcYES: n = nstmin_berendsen_tcouple; break;
- case etcVRESCALE:
+ case TemperatureCoupling::No: n = 0; break;
+ case TemperatureCoupling::Berendsen:
+ case TemperatureCoupling::Yes: n = nstmin_berendsen_tcouple; break;
+ case TemperatureCoupling::VRescale:
/* V-rescale supports instantaneous rescaling */
n = 0;
break;
- case etcNOSEHOOVER: n = nstmin_harmonic; break;
- case etcANDERSEN:
- case etcANDERSENMASSIVE: n = 1; break;
+ case TemperatureCoupling::NoseHoover: n = nstmin_harmonic; break;
+ case TemperatureCoupling::Andersen:
+ case TemperatureCoupling::AndersenMassive: n = 1; break;
default: gmx_incons("Unknown etc value");
}
nwanted = c_defaultNstTCouple;
tau_min = 1e20;
- if (ir->etc != etcNO)
+ if (ir->etc != TemperatureCoupling::No)
{
for (g = 0; g < ir->opts.ngtc; g++)
{
return n;
}
-int pcouple_min_integration_steps(int epc)
+int pcouple_min_integration_steps(PressureCoupling epc)
{
int n;
switch (epc)
{
- case epcNO: n = 0; break;
- case epcBERENDSEN:
- case epcCRESCALE:
- case epcISOTROPIC: n = nstmin_berendsen_pcouple; break;
- case epcPARRINELLORAHMAN:
- case epcMTTK: n = nstmin_harmonic; break;
+ case PressureCoupling::No: n = 0; break;
+ case PressureCoupling::Berendsen:
+ case PressureCoupling::CRescale:
+ case PressureCoupling::Isotropic: n = nstmin_berendsen_pcouple; break;
+ case PressureCoupling::ParrinelloRahman:
+ case PressureCoupling::Mttk: n = nstmin_harmonic; break;
default: gmx_incons("Unknown epc value");
}
gmx_bool ir_coulomb_switched(const t_inputrec* ir)
{
- return (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT
- || ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSERSWITCH
- || ir->coulomb_modifier == eintmodPOTSWITCH || ir->coulomb_modifier == eintmodFORCESWITCH);
+ return (ir->coulombtype == CoulombInteractionType::Switch
+ || ir->coulombtype == CoulombInteractionType::Shift
+ || ir->coulombtype == CoulombInteractionType::PmeSwitch
+ || ir->coulombtype == CoulombInteractionType::PmeUserSwitch
+ || ir->coulomb_modifier == InteractionModifiers::PotSwitch
+ || ir->coulomb_modifier == InteractionModifiers::ForceSwitch);
}
gmx_bool ir_coulomb_is_zero_at_cutoff(const t_inputrec* ir)
{
- return (ir->cutoff_scheme == ecutsVERLET || ir_coulomb_switched(ir)
- || ir->coulomb_modifier != eintmodNONE || ir->coulombtype == eelRF_ZERO);
+ return (ir->cutoff_scheme == CutoffScheme::Verlet || ir_coulomb_switched(ir)
+ || ir->coulomb_modifier != InteractionModifiers::None
+ || ir->coulombtype == CoulombInteractionType::RFZero);
}
gmx_bool ir_coulomb_might_be_zero_at_cutoff(const t_inputrec* ir)
{
- return (ir_coulomb_is_zero_at_cutoff(ir) || ir->coulombtype == eelUSER || ir->coulombtype == eelPMEUSER);
+ return (ir_coulomb_is_zero_at_cutoff(ir) || ir->coulombtype == CoulombInteractionType::User
+ || ir->coulombtype == CoulombInteractionType::PmeUser);
}
gmx_bool ir_vdw_switched(const t_inputrec* ir)
{
- return (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT
- || ir->vdw_modifier == eintmodPOTSWITCH || ir->vdw_modifier == eintmodFORCESWITCH);
+ return (ir->vdwtype == VanDerWaalsType::Switch || ir->vdwtype == VanDerWaalsType::Shift
+ || ir->vdw_modifier == InteractionModifiers::PotSwitch
+ || ir->vdw_modifier == InteractionModifiers::ForceSwitch);
}
gmx_bool ir_vdw_is_zero_at_cutoff(const t_inputrec* ir)
{
- return (ir->cutoff_scheme == ecutsVERLET || ir_vdw_switched(ir) || ir->vdw_modifier != eintmodNONE);
+ return (ir->cutoff_scheme == CutoffScheme::Verlet || ir_vdw_switched(ir)
+ || ir->vdw_modifier != InteractionModifiers::None);
}
gmx_bool ir_vdw_might_be_zero_at_cutoff(const t_inputrec* ir)
{
- return (ir_vdw_is_zero_at_cutoff(ir) || ir->vdwtype == evdwUSER);
-}
-
-static void done_lambdas(t_lambda* fep)
-{
- if (fep->n_lambda > 0)
- {
- for (int i = 0; i < efptNR; i++)
- {
- sfree(fep->all_lambda[i]);
- }
- }
- sfree(fep->all_lambda);
+ return (ir_vdw_is_zero_at_cutoff(ir) || ir->vdwtype == VanDerWaalsType::User);
}
static void done_t_rot(t_rot* rot)
sfree(rot);
}
+static void done_t_swapCoords(t_swapcoords* swapCoords)
+{
+ if (swapCoords == nullptr)
+ {
+ return;
+ }
+ for (int i = 0; i < swapCoords->ngrp; i++)
+ {
+ sfree(swapCoords->grp[i].ind);
+ sfree(swapCoords->grp[i].molname);
+ }
+ sfree(swapCoords->grp);
+ sfree(swapCoords);
+}
+
void done_inputrec(t_inputrec* ir)
{
sfree(ir->opts.nrdf);
sfree(ir->opts.anneal_time);
sfree(ir->opts.anneal_temp);
sfree(ir->opts.tau_t);
- sfree(ir->opts.acc);
sfree(ir->opts.nFreeze);
sfree(ir->opts.egp_flags);
- done_lambdas(ir->fepvals);
- sfree(ir->fepvals);
- sfree(ir->expandedvals);
- sfree(ir->simtempvals);
+ done_t_swapCoords(ir->swap);
done_t_rot(ir->rot);
delete ir->params;
}
fprintf(out, "annealing%s", bMDPformat ? " = " : ":");
for (i = 0; (i < opts->ngtc); i++)
{
- fprintf(out, " %10s", EANNEAL(opts->annealing[i]));
+ fprintf(out, " %10s", enumValueToString(opts->annealing[i]));
}
fprintf(out, "\n");
}
}
- pr_indent(out, indent);
- fprintf(out, "acc:\t");
- for (i = 0; (i < opts->ngacc); i++)
- {
- for (m = 0; (m < DIM); m++)
- {
- fprintf(out, " %10g", opts->acc[i][m]);
- }
- }
- fprintf(out, "\n");
-
pr_indent(out, indent);
fprintf(out, "nfreeze:");
for (i = 0; (i < opts->ngfrz); i++)
{
if (bMDPformat)
{
- fprintf(fp, "%-10s = %g %g %g %g %g %g\n", title, m[XX][XX], m[YY][YY], m[ZZ][ZZ],
- m[XX][YY], m[XX][ZZ], m[YY][ZZ]);
+ fprintf(fp,
+ "%-10s = %g %g %g %g %g %g\n",
+ title,
+ m[XX][XX],
+ m[YY][YY],
+ m[ZZ][ZZ],
+ m[XX][YY],
+ m[XX][ZZ],
+ m[YY][ZZ]);
}
else
{
pr_indent(fp, indent);
fprintf(fp, "pull-coord %d:\n", c);
- PS("type", EPULLTYPE(pcrd->eType));
- if (pcrd->eType == epullEXTERNAL)
+ PS("type", enumValueToString(pcrd->eType));
+ if (pcrd->eType == PullingAlgorithm::External)
{
PS("potential-provider", pcrd->externalPotentialProvider.c_str());
}
- PS("geometry", EPULLGEOM(pcrd->eGeom));
+ PS("geometry", enumValueToString(pcrd->eGeom));
for (g = 0; g < pcrd->ngroup; g++)
{
char buf[STRLEN];
static void pr_simtempvals(FILE* fp, int indent, const t_simtemp* simtemp, int n_lambda)
{
- PS("simulated-tempering-scaling", ESIMTEMP(simtemp->eSimTempScale));
+ PS("simulated-tempering-scaling", enumValueToString(simtemp->eSimTempScale));
PR("sim-temp-low", simtemp->simtemp_low);
PR("sim-temp-high", simtemp->simtemp_high);
- pr_rvec(fp, indent, "simulated tempering temperatures", simtemp->temperatures, n_lambda, TRUE);
+ pr_rvec(fp, indent, "simulated tempering temperatures", simtemp->temperatures.data(), n_lambda, TRUE);
}
static void pr_expandedvals(FILE* fp, int indent, const t_expanded* expand, int n_lambda)
{
PI("nstexpanded", expand->nstexpanded);
- PS("lmc-stats", elamstats_names[expand->elamstats]);
- PS("lmc-move", elmcmove_names[expand->elmcmove]);
- PS("lmc-weights-equil", elmceq_names[expand->elmceq]);
- if (expand->elmceq == elmceqNUMATLAM)
+ PS("lmc-stats", enumValueToString(expand->elamstats));
+ PS("lmc-move", enumValueToString(expand->elmcmove));
+ PS("lmc-weights-equil", enumValueToString(expand->elmceq));
+ if (expand->elmceq == LambdaWeightWillReachEquilibrium::NumAtLambda)
{
PI("weight-equil-number-all-lambda", expand->equil_n_at_lam);
}
- if (expand->elmceq == elmceqSAMPLES)
+ if (expand->elmceq == LambdaWeightWillReachEquilibrium::Samples)
{
PI("weight-equil-number-samples", expand->equil_samples);
}
- if (expand->elmceq == elmceqSTEPS)
+ if (expand->elmceq == LambdaWeightWillReachEquilibrium::Steps)
{
PI("weight-equil-number-steps", expand->equil_steps);
}
- if (expand->elmceq == elmceqWLDELTA)
+ if (expand->elmceq == LambdaWeightWillReachEquilibrium::WLDelta)
{
PR("weight-equil-wl-delta", expand->equil_wl_delta);
}
- if (expand->elmceq == elmceqRATIO)
+ if (expand->elmceq == LambdaWeightWillReachEquilibrium::Ratio)
{
PR("weight-equil-count-ratio", expand->equil_ratio);
}
PS("wl-oneovert", EBOOL(expand->bWLoneovert));
pr_indent(fp, indent);
- pr_rvec(fp, indent, "init-lambda-weights", expand->init_lambda_weights, n_lambda, TRUE);
+ pr_rvec(fp, indent, "init-lambda-weights", expand->init_lambda_weights.data(), n_lambda, TRUE);
PS("init-weights", EBOOL(expand->bInit_weights));
}
static void pr_fepvals(FILE* fp, int indent, const t_lambda* fep, gmx_bool bMDPformat)
{
- int i, j;
+ int j;
PR("init-lambda", fep->init_lambda);
PI("init-lambda-state", fep->init_fep_state);
{
pr_indent(fp, indent);
fprintf(fp, "separate-dvdl%s\n", bMDPformat ? " = " : ":");
- for (i = 0; i < efptNR; i++)
+ for (auto i : gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, bool>::keys())
{
- fprintf(fp, "%18s = ", efpt_names[i]);
+ fprintf(fp, "%18s = ", enumValueToString(i));
if (fep->separate_dvdl[i])
{
fprintf(fp, " TRUE");
fprintf(fp, "\n");
}
fprintf(fp, "all-lambdas%s\n", bMDPformat ? " = " : ":");
- for (i = 0; i < efptNR; i++)
+ for (auto key : gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, bool>::keys())
{
- fprintf(fp, "%18s = ", efpt_names[i]);
+ fprintf(fp, "%18s = ", enumValueToString(key));
+ int i = static_cast<int>(key);
for (j = 0; j < fep->n_lambda; j++)
{
fprintf(fp, " %10g", fep->all_lambda[i][j]);
}
}
PI("calc-lambda-neighbors", fep->lambda_neighbors);
- PS("dhdl-print-energy", edHdLPrintEnergy_names[fep->edHdLPrintEnergy]);
+ PS("dhdl-print-energy", enumValueToString(fep->edHdLPrintEnergy));
PR("sc-alpha", fep->sc_alpha);
PI("sc-power", fep->sc_power);
PR("sc-r-power", fep->sc_r_power);
PS("sc-coul", EBOOL(fep->bScCoul));
PI("dh-hist-size", fep->dh_hist_size);
PD("dh-hist-spacing", fep->dh_hist_spacing);
- PS("separate-dhdl-file", SEPDHDLFILETYPE(fep->separate_dhdl_file));
- PS("dhdl-derivatives", DHDLDERIVATIVESTYPE(fep->dhdl_derivatives));
+ PS("separate-dhdl-file", enumValueToString(fep->separate_dhdl_file));
+ PS("dhdl-derivatives", enumValueToString(fep->dhdl_derivatives));
};
static void pr_pull(FILE* fp, int indent, const pull_params_t& pull)
}
}
-static void pr_awh_bias_dim(FILE* fp, int indent, gmx::AwhDimParams* awhDimParams, const char* prefix)
+static void pr_awh_bias_dim(FILE* fp, int indent, const gmx::AwhDimParams& awhDimParams, const char* prefix)
{
pr_indent(fp, indent);
indent++;
fprintf(fp, "%s:\n", prefix);
- PS("coord-provider", EAWHCOORDPROVIDER(awhDimParams->eCoordProvider));
- PI("coord-index", awhDimParams->coordIndex + 1);
- PR("start", awhDimParams->origin);
- PR("end", awhDimParams->end);
- PR("period", awhDimParams->period);
- PR("force-constant", awhDimParams->forceConstant);
- PR("diffusion", awhDimParams->diffusion);
- PR("cover-diameter", awhDimParams->coverDiameter);
+ PS("coord-provider", enumValueToString(awhDimParams.coordinateProvider()));
+ PI("coord-index", awhDimParams.coordinateIndex() + 1);
+ PR("start", awhDimParams.origin());
+ PR("end", awhDimParams.end());
+ PR("period", awhDimParams.period());
+ PR("force-constant", awhDimParams.forceConstant());
+ PR("diffusion", awhDimParams.diffusion());
+ PR("cover-diameter", awhDimParams.coverDiameter());
}
-static void pr_awh_bias(FILE* fp, int indent, gmx::AwhBiasParams* awhBiasParams, const char* prefix)
+static void pr_awh_bias(FILE* fp, int indent, const gmx::AwhBiasParams& awhBiasParams, const char* prefix)
{
char opt[STRLEN];
sprintf(opt, "%s-error-init", prefix);
- PR(opt, awhBiasParams->errorInitial);
+ PR(opt, awhBiasParams.initialErrorEstimate());
sprintf(opt, "%s-growth", prefix);
- PS(opt, EAWHGROWTH(awhBiasParams->eGrowth));
+ PS(opt, enumValueToString(awhBiasParams.growthType()));
sprintf(opt, "%s-target", prefix);
- PS(opt, EAWHTARGET(awhBiasParams->eTarget));
+ PS(opt, enumValueToString(awhBiasParams.targetDistribution()));
sprintf(opt, "%s-target-beta-scalng", prefix);
- PR(opt, awhBiasParams->targetBetaScaling);
+ PR(opt, awhBiasParams.targetBetaScaling());
sprintf(opt, "%s-target-cutoff", prefix);
- PR(opt, awhBiasParams->targetCutoff);
+ PR(opt, awhBiasParams.targetCutoff());
sprintf(opt, "%s-user-data", prefix);
- PS(opt, EBOOL(awhBiasParams->bUserData));
+ PS(opt, EBOOL(awhBiasParams.userPMFEstimate()));
sprintf(opt, "%s-share-group", prefix);
- PI(opt, awhBiasParams->shareGroup);
+ PI(opt, awhBiasParams.shareGroup());
sprintf(opt, "%s-equilibrate-histogram", prefix);
- PS(opt, EBOOL(awhBiasParams->equilibrateHistogram));
+ PS(opt, EBOOL(awhBiasParams.equilibrateHistogram()));
sprintf(opt, "%s-ndim", prefix);
- PI(opt, awhBiasParams->ndim);
+ PI(opt, awhBiasParams.ndim());
- for (int d = 0; d < awhBiasParams->ndim; d++)
+ int d = 0;
+ for (const auto& dimParam : awhBiasParams.dimParams())
{
char prefixdim[STRLEN];
sprintf(prefixdim, "%s-dim%d", prefix, d + 1);
- pr_awh_bias_dim(fp, indent, &awhBiasParams->dimParams[d], prefixdim);
+ pr_awh_bias_dim(fp, indent, dimParam, prefixdim);
+ d++;
}
}
static void pr_awh(FILE* fp, int indent, gmx::AwhParams* awhParams)
{
- PS("awh-potential", EAWHPOTENTIAL(awhParams->ePotential));
- PI("awh-seed", awhParams->seed);
- PI("awh-nstout", awhParams->nstOut);
- PI("awh-nstsample", awhParams->nstSampleCoord);
- PI("awh-nsamples-update", awhParams->numSamplesUpdateFreeEnergy);
- PS("awh-share-bias-multisim", EBOOL(awhParams->shareBiasMultisim));
- PI("awh-nbias", awhParams->numBias);
+ PS("awh-potential", enumValueToString(awhParams->potential()));
+ PI("awh-seed", awhParams->seed());
+ PI("awh-nstout", awhParams->nstout());
+ PI("awh-nstsample", awhParams->nstSampleCoord());
+ PI("awh-nsamples-update", awhParams->numSamplesUpdateFreeEnergy());
+ PS("awh-share-bias-multisim", EBOOL(awhParams->shareBiasMultisim()));
+ PI("awh-nbias", awhParams->numBias());
- for (int k = 0; k < awhParams->numBias; k++)
+ int k = 0;
+ for (const auto& awhBiasParam : awhParams->awhBiasParams())
{
auto prefix = gmx::formatString("awh%d", k + 1);
- pr_awh_bias(fp, indent, &awhParams->awhBiasParams[k], prefix.c_str());
+ pr_awh_bias(fp, indent, awhBiasParam, prefix.c_str());
+ k++;
}
}
pr_indent(fp, indent);
fprintf(fp, "rot-group %d:\n", g);
indent += 2;
- PS("rot-type", EROTGEOM(rotg->eType));
+ PS("rot-type", enumValueToString(rotg->eType));
PS("rot-massw", EBOOL(rotg->bMassW));
pr_ivec_block(fp, indent, "atom", rotg->ind, rotg->nat, TRUE);
pr_rvecs(fp, indent, "x-ref", rotg->x_ref, rotg->nat);
PR("rot-slab-dist", rotg->slab_dist);
PR("rot-min-gauss", rotg->min_gaussian);
PR("rot-eps", rotg->eps);
- PS("rot-fit-method", EROTFIT(rotg->eFittype));
+ PS("rot-fit-method", enumValueToString(rotg->eFittype));
PI("rot-potfit-nstep", rotg->PotAngle_nstep);
PR("rot-potfit-step", rotg->PotAngle_step);
}
}
/* The solvent group */
- snprintf(str, STRLEN, "solvent group %s", swap->grp[eGrpSolvent].molname);
- pr_ivec_block(fp, indent, str, swap->grp[eGrpSolvent].ind, swap->grp[eGrpSolvent].nat, TRUE);
+ snprintf(str,
+ STRLEN,
+ "solvent group %s",
+ swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].molname);
+ pr_ivec_block(fp,
+ indent,
+ str,
+ swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].ind,
+ swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].nat,
+ TRUE);
/* Now print the indices for all the ion groups: */
- for (int ig = eSwapFixedGrpNR; ig < swap->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < swap->ngrp; ig++)
{
snprintf(str, STRLEN, "ion group %s", swap->grp[ig].molname);
pr_ivec_block(fp, indent, str, swap->grp[ig].ind, swap->grp[ig].nat, TRUE);
/* Print the requested ion counts for both compartments */
for (int ic = eCompA; ic <= eCompB; ic++)
{
- for (int ig = eSwapFixedGrpNR; ig < swap->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < swap->ngrp; ig++)
{
snprintf(str, STRLEN, "%s-in-%c", swap->grp[ig].molname, 'A' + ic);
PI(str, swap->grp[ig].nmolReq[ic]);
* options are written in the default mdout.mdp, and with
* the same user-exposed names to facilitate debugging.
*/
- PS("integrator", EI(ir->eI));
+ PS("integrator", enumValueToString(ir->eI));
PR("tinit", ir->init_t);
PR("dt", ir->delta_t);
PSTEP("nsteps", ir->nsteps);
PI(factorKey.c_str(), mtsLevel.stepFactor);
}
}
- PS("comm-mode", ECOM(ir->comm_mode));
+ PS("comm-mode", enumValueToString(ir->comm_mode));
PI("nstcomm", ir->nstcomm);
/* Langevin dynamics */
PR("compressed-x-precision", ir->x_compression_precision);
/* Neighborsearching parameters */
- PS("cutoff-scheme", ECUTSCHEME(ir->cutoff_scheme));
+ PS("cutoff-scheme", enumValueToString(ir->cutoff_scheme));
PI("nstlist", ir->nstlist);
PS("pbc", c_pbcTypeNames[ir->pbcType].c_str());
PS("periodic-molecules", EBOOL(ir->bPeriodicMols));
PR("rlist", ir->rlist);
/* Options for electrostatics and VdW */
- PS("coulombtype", EELTYPE(ir->coulombtype));
- PS("coulomb-modifier", INTMODIFIER(ir->coulomb_modifier));
+ PS("coulombtype", enumValueToString(ir->coulombtype));
+ PS("coulomb-modifier", enumValueToString(ir->coulomb_modifier));
PR("rcoulomb-switch", ir->rcoulomb_switch);
PR("rcoulomb", ir->rcoulomb);
if (ir->epsilon_r != 0)
{
PS("epsilon-rf", infbuf);
}
- PS("vdw-type", EVDWTYPE(ir->vdwtype));
- PS("vdw-modifier", INTMODIFIER(ir->vdw_modifier));
+ PS("vdw-type", enumValueToString(ir->vdwtype));
+ PS("vdw-modifier", enumValueToString(ir->vdw_modifier));
PR("rvdw-switch", ir->rvdw_switch);
PR("rvdw", ir->rvdw);
- PS("DispCorr", EDISPCORR(ir->eDispCorr));
+ PS("DispCorr", enumValueToString(ir->eDispCorr));
PR("table-extension", ir->tabext);
PR("fourierspacing", ir->fourier_spacing);
PI("pme-order", ir->pme_order);
PR("ewald-rtol", ir->ewald_rtol);
PR("ewald-rtol-lj", ir->ewald_rtol_lj);
- PS("lj-pme-comb-rule", ELJPMECOMBNAMES(ir->ljpme_combination_rule));
- PR("ewald-geometry", ir->ewald_geometry);
+ PS("lj-pme-comb-rule", enumValueToString(ir->ljpme_combination_rule));
+ PS("ewald-geometry", enumValueToString(ir->ewald_geometry));
PR("epsilon-surface", ir->epsilon_surface);
/* Options for weak coupling algorithms */
- PS("tcoupl", ETCOUPLTYPE(ir->etc));
+ PS("tcoupl", enumValueToString(ir->etc));
PI("nsttcouple", ir->nsttcouple);
PI("nh-chain-length", ir->opts.nhchainlength);
PS("print-nose-hoover-chain-variables", EBOOL(ir->bPrintNHChains));
- PS("pcoupl", EPCOUPLTYPE(ir->epc));
- PS("pcoupltype", EPCOUPLTYPETYPE(ir->epct));
+ PS("pcoupl", enumValueToString(ir->epc));
+ PS("pcoupltype", enumValueToString(ir->epct));
PI("nstpcouple", ir->nstpcouple);
PR("tau-p", ir->tau_p);
pr_matrix(fp, indent, "compressibility", ir->compress, bMDPformat);
pr_matrix(fp, indent, "ref-p", ir->ref_p, bMDPformat);
- PS("refcoord-scaling", EREFSCALINGTYPE(ir->refcoord_scaling));
+ PS("refcoord-scaling", enumValueToString(ir->refcoord_scaling));
if (bMDPformat)
{
- fprintf(fp, "posres-com = %g %g %g\n", ir->posres_com[XX], ir->posres_com[YY],
- ir->posres_com[ZZ]);
- fprintf(fp, "posres-comB = %g %g %g\n", ir->posres_comB[XX], ir->posres_comB[YY],
- ir->posres_comB[ZZ]);
+ fprintf(fp, "posres-com = %g %g %g\n", ir->posres_com[XX], ir->posres_com[YY], ir->posres_com[ZZ]);
+ fprintf(fp, "posres-comB = %g %g %g\n", ir->posres_comB[XX], ir->posres_comB[YY], ir->posres_comB[ZZ]);
}
else
{
pr_int(fp, indent, "ngQM", ir->opts.ngQM);
/* CONSTRAINT OPTIONS */
- PS("constraint-algorithm", ECONSTRTYPE(ir->eConstrAlg));
+ PS("constraint-algorithm", enumValueToString(ir->eConstrAlg));
PS("continuation", EBOOL(ir->bContinuation));
PS("Shake-SOR", EBOOL(ir->bShakeSOR));
/* Walls */
PI("nwall", ir->nwall);
- PS("wall-type", EWALLTYPE(ir->wall_type));
+ PS("wall-type", enumValueToString(ir->wall_type));
PR("wall-r-linpot", ir->wall_r_linpot);
/* wall-atomtype */
PI("wall-atomtype[0]", ir->wall_atomtype[0]);
PS("awh", EBOOL(ir->bDoAwh));
if (ir->bDoAwh)
{
- pr_awh(fp, indent, ir->awhParams);
+ pr_awh(fp, indent, ir->awhParams.get());
}
/* ENFORCED ROTATION */
}
/* NMR refinement stuff */
- PS("disre", EDISRETYPE(ir->eDisre));
- PS("disre-weighting", EDISREWEIGHTING(ir->eDisreWeighting));
+ PS("disre", enumValueToString(ir->eDisre));
+ PS("disre-weighting", enumValueToString(ir->eDisreWeighting));
PS("disre-mixed", EBOOL(ir->bDisreMixed));
PR("dr-fc", ir->dr_fc);
PR("dr-tau", ir->dr_tau);
PR("nstorireout", ir->nstorireout);
/* FREE ENERGY VARIABLES */
- PS("free-energy", EFEPTYPE(ir->efep));
- if (ir->efep != efepNO || ir->bSimTemp)
+ PS("free-energy", enumValueToString(ir->efep));
+ if (ir->efep != FreeEnergyPerturbationType::No || ir->bSimTemp)
{
- pr_fepvals(fp, indent, ir->fepvals, bMDPformat);
+ pr_fepvals(fp, indent, ir->fepvals.get(), bMDPformat);
}
if (ir->bExpanded)
{
- pr_expandedvals(fp, indent, ir->expandedvals, ir->fepvals->n_lambda);
+ pr_expandedvals(fp, indent, ir->expandedvals.get(), ir->fepvals->n_lambda);
}
/* NON-equilibrium MD stuff */
PS("simulated-tempering", EBOOL(ir->bSimTemp));
if (ir->bSimTemp)
{
- pr_simtempvals(fp, indent, ir->simtempvals, ir->fepvals->n_lambda);
+ pr_simtempvals(fp, indent, ir->simtempvals.get(), ir->fepvals->n_lambda);
}
/* ION/WATER SWAPPING FOR COMPUTATIONAL ELECTROPHYSIOLOGY */
- PS("swapcoords", ESWAPTYPE(ir->eSwapCoords));
- if (ir->eSwapCoords != eswapNO)
+ PS("swapcoords", enumValueToString(ir->eSwapCoords));
+ if (ir->eSwapCoords != SwapType::No)
{
pr_swap(fp, indent, ir->swap);
}
char buf1[256], buf2[256];
cmp_int(fp, "inputrec->grpopts.ngtc", -1, opt1->ngtc, opt2->ngtc);
- cmp_int(fp, "inputrec->grpopts.ngacc", -1, opt1->ngacc, opt2->ngacc);
cmp_int(fp, "inputrec->grpopts.ngfrz", -1, opt1->ngfrz, opt2->ngfrz);
cmp_int(fp, "inputrec->grpopts.ngener", -1, opt1->ngener, opt2->ngener);
for (i = 0; (i < std::min(opt1->ngtc, opt2->ngtc)); i++)
cmp_real(fp, "inputrec->grpopts.nrdf", i, opt1->nrdf[i], opt2->nrdf[i], ftol, abstol);
cmp_real(fp, "inputrec->grpopts.ref_t", i, opt1->ref_t[i], opt2->ref_t[i], ftol, abstol);
cmp_real(fp, "inputrec->grpopts.tau_t", i, opt1->tau_t[i], opt2->tau_t[i], ftol, abstol);
- cmp_int(fp, "inputrec->grpopts.annealing", i, opt1->annealing[i], opt2->annealing[i]);
- cmp_int(fp, "inputrec->grpopts.anneal_npoints", i, opt1->anneal_npoints[i],
- opt2->anneal_npoints[i]);
+ cmpEnum(fp, "inputrec->grpopts.annealing", opt1->annealing[i], opt2->annealing[i]);
+ cmp_int(fp, "inputrec->grpopts.anneal_npoints", i, opt1->anneal_npoints[i], opt2->anneal_npoints[i]);
if (opt1->anneal_npoints[i] == opt2->anneal_npoints[i])
{
sprintf(buf1, "inputrec->grpopts.anneal_time[%d]", i);
for (j = i; j < opt1->ngener; j++)
{
sprintf(buf1, "inputrec->grpopts.egp_flags[%d]", i);
- cmp_int(fp, buf1, j, opt1->egp_flags[opt1->ngener * i + j],
- opt2->egp_flags[opt1->ngener * i + j]);
+ cmp_int(fp, buf1, j, opt1->egp_flags[opt1->ngener * i + j], opt2->egp_flags[opt1->ngener * i + j]);
}
}
}
- for (i = 0; (i < std::min(opt1->ngacc, opt2->ngacc)); i++)
- {
- cmp_rvec(fp, "inputrec->grpopts.acc", i, opt1->acc[i], opt2->acc[i], ftol, abstol);
- }
for (i = 0; (i < std::min(opt1->ngfrz, opt2->ngfrz)); i++)
{
cmp_ivec(fp, "inputrec->grpopts.nFreeze", i, opt1->nFreeze[i], opt2->nFreeze[i]);
}
static void cmp_awhDimParams(FILE* fp,
- const gmx::AwhDimParams* dimp1,
- const gmx::AwhDimParams* dimp2,
+ const gmx::AwhDimParams& dimp1,
+ const gmx::AwhDimParams& dimp2,
int dimIndex,
real ftol,
real abstol)
/* Note that we have double index here, but the compare functions only
* support one index, so here we only print the dim index and not the bias.
*/
- cmp_int(fp, "inputrec.awhParams->bias?->dim->coord_index", dimIndex, dimp1->coordIndex,
- dimp2->coordIndex);
- cmp_double(fp, "inputrec->awhParams->bias?->dim->period", dimIndex, dimp1->period,
- dimp2->period, ftol, abstol);
- cmp_double(fp, "inputrec->awhParams->bias?->dim->diffusion", dimIndex, dimp1->diffusion,
- dimp2->diffusion, ftol, abstol);
- cmp_double(fp, "inputrec->awhParams->bias?->dim->origin", dimIndex, dimp1->origin,
- dimp2->origin, ftol, abstol);
- cmp_double(fp, "inputrec->awhParams->bias?->dim->end", dimIndex, dimp1->end, dimp2->end, ftol, abstol);
- cmp_double(fp, "inputrec->awhParams->bias?->dim->coord_value_init", dimIndex,
- dimp1->coordValueInit, dimp2->coordValueInit, ftol, abstol);
- cmp_double(fp, "inputrec->awhParams->bias?->dim->coverDiameter", dimIndex, dimp1->coverDiameter,
- dimp2->coverDiameter, ftol, abstol);
+ cmp_int(fp,
+ "inputrec.awhParams->bias?->dim->coord_index",
+ dimIndex,
+ dimp1.coordinateIndex(),
+ dimp2.coordinateIndex());
+ cmp_double(fp, "inputrec->awhParams->bias?->dim->period", dimIndex, dimp1.period(), dimp2.period(), ftol, abstol);
+ cmp_double(fp,
+ "inputrec->awhParams->bias?->dim->diffusion",
+ dimIndex,
+ dimp1.diffusion(),
+ dimp2.diffusion(),
+ ftol,
+ abstol);
+ cmp_double(fp, "inputrec->awhParams->bias?->dim->origin", dimIndex, dimp1.origin(), dimp2.origin(), ftol, abstol);
+ cmp_double(fp, "inputrec->awhParams->bias?->dim->end", dimIndex, dimp1.end(), dimp2.end(), ftol, abstol);
+ cmp_double(fp,
+ "inputrec->awhParams->bias?->dim->coord_value_init",
+ dimIndex,
+ dimp1.initialCoordinate(),
+ dimp2.initialCoordinate(),
+ ftol,
+ abstol);
+ cmp_double(fp,
+ "inputrec->awhParams->bias?->dim->coverDiameter",
+ dimIndex,
+ dimp1.coverDiameter(),
+ dimp2.coverDiameter(),
+ ftol,
+ abstol);
}
static void cmp_awhBiasParams(FILE* fp,
- const gmx::AwhBiasParams* bias1,
- const gmx::AwhBiasParams* bias2,
+ const gmx::AwhBiasParams& bias1,
+ const gmx::AwhBiasParams& bias2,
int biasIndex,
real ftol,
real abstol)
{
- cmp_int(fp, "inputrec->awhParams->ndim", biasIndex, bias1->ndim, bias2->ndim);
- cmp_int(fp, "inputrec->awhParams->biaseTarget", biasIndex, bias1->eTarget, bias2->eTarget);
- cmp_double(fp, "inputrec->awhParams->biastargetBetaScaling", biasIndex,
- bias1->targetBetaScaling, bias2->targetBetaScaling, ftol, abstol);
- cmp_double(fp, "inputrec->awhParams->biastargetCutoff", biasIndex, bias1->targetCutoff,
- bias2->targetCutoff, ftol, abstol);
- cmp_int(fp, "inputrec->awhParams->biaseGrowth", biasIndex, bias1->eGrowth, bias2->eGrowth);
- cmp_bool(fp, "inputrec->awhParams->biasbUserData", biasIndex, bias1->bUserData != 0,
- bias2->bUserData != 0);
- cmp_double(fp, "inputrec->awhParams->biaserror_initial", biasIndex, bias1->errorInitial,
- bias2->errorInitial, ftol, abstol);
- cmp_int(fp, "inputrec->awhParams->biasShareGroup", biasIndex, bias1->shareGroup, bias2->shareGroup);
-
- for (int dim = 0; dim < std::min(bias1->ndim, bias2->ndim); dim++)
- {
- cmp_awhDimParams(fp, &bias1->dimParams[dim], &bias2->dimParams[dim], dim, ftol, abstol);
+ cmp_int(fp, "inputrec->awhParams->ndim", biasIndex, bias1.ndim(), bias2.ndim());
+ cmpEnum<gmx::AwhTargetType>(
+ fp, "inputrec->awhParams->biaseTarget", bias1.targetDistribution(), bias2.targetDistribution());
+ cmp_double(fp,
+ "inputrec->awhParams->biastargetBetaScaling",
+ biasIndex,
+ bias1.targetBetaScaling(),
+ bias2.targetBetaScaling(),
+ ftol,
+ abstol);
+ cmp_double(fp,
+ "inputrec->awhParams->biastargetCutoff",
+ biasIndex,
+ bias1.targetCutoff(),
+ bias2.targetCutoff(),
+ ftol,
+ abstol);
+ cmpEnum<gmx::AwhHistogramGrowthType>(
+ fp, "inputrec->awhParams->biaseGrowth", bias1.growthType(), bias2.growthType());
+ cmp_bool(fp, "inputrec->awhParams->biasbUserData", biasIndex, bias1.userPMFEstimate(), bias2.userPMFEstimate());
+ cmp_double(fp,
+ "inputrec->awhParams->biaserror_initial",
+ biasIndex,
+ bias1.initialErrorEstimate(),
+ bias2.initialErrorEstimate(),
+ ftol,
+ abstol);
+ cmp_int(fp, "inputrec->awhParams->biasShareGroup", biasIndex, bias1.shareGroup(), bias2.shareGroup());
+
+ const auto dimParams1 = bias1.dimParams();
+ const auto dimParams2 = bias2.dimParams();
+ for (int dim = 0; dim < std::min(bias1.ndim(), bias2.ndim()); dim++)
+ {
+ cmp_awhDimParams(fp, dimParams1[dim], dimParams2[dim], dim, ftol, abstol);
}
}
-static void cmp_awhParams(FILE* fp, const gmx::AwhParams* awh1, const gmx::AwhParams* awh2, real ftol, real abstol)
+static void cmp_awhParams(FILE* fp, const gmx::AwhParams& awh1, const gmx::AwhParams& awh2, real ftol, real abstol)
{
- cmp_int(fp, "inputrec->awhParams->nbias", -1, awh1->numBias, awh2->numBias);
- cmp_int64(fp, "inputrec->awhParams->seed", awh1->seed, awh2->seed);
- cmp_int(fp, "inputrec->awhParams->nstout", -1, awh1->nstOut, awh2->nstOut);
- cmp_int(fp, "inputrec->awhParams->nstsample_coord", -1, awh1->nstSampleCoord, awh2->nstSampleCoord);
- cmp_int(fp, "inputrec->awhParams->nsamples_update_free_energy", -1,
- awh1->numSamplesUpdateFreeEnergy, awh2->numSamplesUpdateFreeEnergy);
- cmp_int(fp, "inputrec->awhParams->ePotential", -1, awh1->ePotential, awh2->ePotential);
- cmp_bool(fp, "inputrec->awhParams->shareBiasMultisim", -1, awh1->shareBiasMultisim,
- awh2->shareBiasMultisim);
-
- if (awh1->numBias == awh2->numBias)
- {
- for (int bias = 0; bias < awh1->numBias; bias++)
+ cmp_int(fp, "inputrec->awhParams->nbias", -1, awh1.numBias(), awh2.numBias());
+ cmp_int64(fp, "inputrec->awhParams->seed", awh1.seed(), awh2.seed());
+ cmp_int(fp, "inputrec->awhParams->nstout", -1, awh1.nstout(), awh2.nstout());
+ cmp_int(fp, "inputrec->awhParams->nstsample_coord", -1, awh1.nstSampleCoord(), awh2.nstSampleCoord());
+ cmp_int(fp,
+ "inputrec->awhParams->nsamples_update_free_energy",
+ -1,
+ awh1.numSamplesUpdateFreeEnergy(),
+ awh2.numSamplesUpdateFreeEnergy());
+ cmpEnum<gmx::AwhPotentialType>(
+ fp, "inputrec->awhParams->ePotential", awh1.potential(), awh2.potential());
+ cmp_bool(fp, "inputrec->awhParams->shareBiasMultisim", -1, awh1.shareBiasMultisim(), awh2.shareBiasMultisim());
+
+ if (awh1.numBias() == awh2.numBias())
+ {
+ const auto awhBiasParams1 = awh1.awhBiasParams();
+ const auto awhBiasParams2 = awh2.awhBiasParams();
+ for (int bias = 0; bias < awh1.numBias(); bias++)
{
- cmp_awhBiasParams(fp, &awh1->awhBiasParams[bias], &awh2->awhBiasParams[bias], bias, ftol, abstol);
+ cmp_awhBiasParams(fp, awhBiasParams1[bias], awhBiasParams2[bias], bias, ftol, abstol);
}
}
}
real abstol)
{
int i;
- cmp_int(fp, "inputrec->simtempvals->eSimTempScale", -1, simtemp1->eSimTempScale, simtemp2->eSimTempScale);
- cmp_real(fp, "inputrec->simtempvals->simtemp_high", -1, simtemp1->simtemp_high,
- simtemp2->simtemp_high, ftol, abstol);
- cmp_real(fp, "inputrec->simtempvals->simtemp_low", -1, simtemp1->simtemp_low,
- simtemp2->simtemp_low, ftol, abstol);
+ cmpEnum(fp, "inputrec->simtempvals->eSimTempScale", simtemp1->eSimTempScale, simtemp2->eSimTempScale);
+ cmp_real(fp, "inputrec->simtempvals->simtemp_high", -1, simtemp1->simtemp_high, simtemp2->simtemp_high, ftol, abstol);
+ cmp_real(fp, "inputrec->simtempvals->simtemp_low", -1, simtemp1->simtemp_low, simtemp2->simtemp_low, ftol, abstol);
for (i = 0; i < n_lambda; i++)
{
- cmp_real(fp, "inputrec->simtempvals->temperatures", -1, simtemp1->temperatures[i],
- simtemp2->temperatures[i], ftol, abstol);
+ cmp_real(fp,
+ "inputrec->simtempvals->temperatures",
+ -1,
+ simtemp1->temperatures[i],
+ simtemp2->temperatures[i],
+ ftol,
+ abstol);
}
}
for (i = 0; i < n_lambda; i++)
{
- cmp_real(fp, "inputrec->expandedvals->init_lambda_weights", -1,
- expand1->init_lambda_weights[i], expand2->init_lambda_weights[i], ftol, abstol);
+ cmp_real(fp,
+ "inputrec->expandedvals->init_lambda_weights",
+ -1,
+ expand1->init_lambda_weights[i],
+ expand2->init_lambda_weights[i],
+ ftol,
+ abstol);
}
- cmp_int(fp, "inputrec->expandedvals->lambda-stats", -1, expand1->elamstats, expand2->elamstats);
- cmp_int(fp, "inputrec->expandedvals->lambda-mc-move", -1, expand1->elmcmove, expand2->elmcmove);
+ cmpEnum(fp, "inputrec->expandedvals->lambda-stats", expand1->elamstats, expand2->elamstats);
+ cmpEnum(fp, "inputrec->expandedvals->lambda-mc-move", expand1->elmcmove, expand2->elmcmove);
cmp_int(fp, "inputrec->expandedvals->lmc-repeats", -1, expand1->lmc_repeats, expand2->lmc_repeats);
cmp_int(fp, "inputrec->expandedvals->lmc-gibbsdelta", -1, expand1->gibbsdeltalam, expand2->gibbsdeltalam);
- cmp_int(fp, "inputrec->expandedvals->lmc-forced-nstart", -1, expand1->lmc_forced_nstart,
- expand2->lmc_forced_nstart);
- cmp_int(fp, "inputrec->expandedvals->lambda-weights-equil", -1, expand1->elmceq, expand2->elmceq);
- cmp_int(fp, "inputrec->expandedvals->,weight-equil-number-all-lambda", -1,
- expand1->equil_n_at_lam, expand2->equil_n_at_lam);
- cmp_int(fp, "inputrec->expandedvals->weight-equil-number-samples", -1, expand1->equil_samples,
- expand2->equil_samples);
- cmp_int(fp, "inputrec->expandedvals->weight-equil-number-steps", -1, expand1->equil_steps,
- expand2->equil_steps);
- cmp_real(fp, "inputrec->expandedvals->weight-equil-wl-delta", -1, expand1->equil_wl_delta,
- expand2->equil_wl_delta, ftol, abstol);
- cmp_real(fp, "inputrec->expandedvals->weight-equil-count-ratio", -1, expand1->equil_ratio,
- expand2->equil_ratio, ftol, abstol);
- cmp_bool(fp, "inputrec->expandedvals->symmetrized-transition-matrix", -1,
- expand1->bSymmetrizedTMatrix, expand2->bSymmetrizedTMatrix);
+ cmp_int(fp, "inputrec->expandedvals->lmc-forced-nstart", -1, expand1->lmc_forced_nstart, expand2->lmc_forced_nstart);
+ cmpEnum(fp, "inputrec->expandedvals->lambda-weights-equil", expand1->elmceq, expand2->elmceq);
+ cmp_int(fp,
+ "inputrec->expandedvals->,weight-equil-number-all-lambda",
+ -1,
+ expand1->equil_n_at_lam,
+ expand2->equil_n_at_lam);
+ cmp_int(fp, "inputrec->expandedvals->weight-equil-number-samples", -1, expand1->equil_samples, expand2->equil_samples);
+ cmp_int(fp, "inputrec->expandedvals->weight-equil-number-steps", -1, expand1->equil_steps, expand2->equil_steps);
+ cmp_real(fp,
+ "inputrec->expandedvals->weight-equil-wl-delta",
+ -1,
+ expand1->equil_wl_delta,
+ expand2->equil_wl_delta,
+ ftol,
+ abstol);
+ cmp_real(fp,
+ "inputrec->expandedvals->weight-equil-count-ratio",
+ -1,
+ expand1->equil_ratio,
+ expand2->equil_ratio,
+ ftol,
+ abstol);
+ cmp_bool(fp,
+ "inputrec->expandedvals->symmetrized-transition-matrix",
+ -1,
+ expand1->bSymmetrizedTMatrix,
+ expand2->bSymmetrizedTMatrix);
cmp_int(fp, "inputrec->expandedvals->nstTij", -1, expand1->nstTij, expand2->nstTij);
- cmp_int(fp, "inputrec->expandedvals->mininum-var-min", -1, expand1->minvarmin,
- expand2->minvarmin); /*default is reasonable */
+ cmp_int(fp, "inputrec->expandedvals->mininum-var-min", -1, expand1->minvarmin, expand2->minvarmin); /*default is reasonable */
cmp_int(fp, "inputrec->expandedvals->weight-c-range", -1, expand1->c_range, expand2->c_range); /* default is just C=0 */
cmp_real(fp, "inputrec->expandedvals->wl-scale", -1, expand1->wl_scale, expand2->wl_scale, ftol, abstol);
- cmp_real(fp, "inputrec->expandedvals->init-wl-delta", -1, expand1->init_wl_delta,
- expand2->init_wl_delta, ftol, abstol);
+ cmp_real(fp, "inputrec->expandedvals->init-wl-delta", -1, expand1->init_wl_delta, expand2->init_wl_delta, ftol, abstol);
cmp_real(fp, "inputrec->expandedvals->wl-ratio", -1, expand1->wl_ratio, expand2->wl_ratio, ftol, abstol);
cmp_int(fp, "inputrec->expandedvals->nstexpanded", -1, expand1->nstexpanded, expand2->nstexpanded);
cmp_int(fp, "inputrec->expandedvals->lmc-seed", -1, expand1->lmc_seed, expand2->lmc_seed);
- cmp_real(fp, "inputrec->expandedvals->mc-temperature", -1, expand1->mc_temp, expand2->mc_temp,
- ftol, abstol);
+ cmp_real(fp, "inputrec->expandedvals->mc-temperature", -1, expand1->mc_temp, expand2->mc_temp, ftol, abstol);
}
static void cmp_fepvals(FILE* fp, const t_lambda* fep1, const t_lambda* fep2, real ftol, real abstol)
{
int i, j;
cmp_int(fp, "inputrec->nstdhdl", -1, fep1->nstdhdl, fep2->nstdhdl);
- cmp_double(fp, "inputrec->fepvals->init_fep_state", -1, fep1->init_fep_state,
- fep2->init_fep_state, ftol, abstol);
- cmp_double(fp, "inputrec->fepvals->delta_lambda", -1, fep1->delta_lambda, fep2->delta_lambda,
- ftol, abstol);
+ cmp_double(fp, "inputrec->fepvals->init_fep_state", -1, fep1->init_fep_state, fep2->init_fep_state, ftol, abstol);
+ cmp_double(fp, "inputrec->fepvals->delta_lambda", -1, fep1->delta_lambda, fep2->delta_lambda, ftol, abstol);
cmp_int(fp, "inputrec->fepvals->n_lambda", -1, fep1->n_lambda, fep2->n_lambda);
- for (i = 0; i < efptNR; i++)
+ for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
{
for (j = 0; j < std::min(fep1->n_lambda, fep2->n_lambda); j++)
{
- cmp_double(fp, "inputrec->fepvals->all_lambda", -1, fep1->all_lambda[i][j],
- fep2->all_lambda[i][j], ftol, abstol);
+ cmp_double(fp,
+ "inputrec->fepvals->all_lambda",
+ -1,
+ fep1->all_lambda[i][j],
+ fep2->all_lambda[i][j],
+ ftol,
+ abstol);
}
}
cmp_int(fp, "inputrec->fepvals->lambda_neighbors", 1, fep1->lambda_neighbors, fep2->lambda_neighbors);
cmp_int(fp, "inputrec->fepvals->sc_power", -1, fep1->sc_power, fep2->sc_power);
cmp_real(fp, "inputrec->fepvals->sc_r_power", -1, fep1->sc_r_power, fep2->sc_r_power, ftol, abstol);
cmp_real(fp, "inputrec->fepvals->sc_sigma", -1, fep1->sc_sigma, fep2->sc_sigma, ftol, abstol);
- cmp_int(fp, "inputrec->fepvals->edHdLPrintEnergy", -1, fep1->edHdLPrintEnergy, fep1->edHdLPrintEnergy);
+ cmpEnum(fp, "inputrec->fepvals->edHdLPrintEnergy", fep1->edHdLPrintEnergy, fep1->edHdLPrintEnergy);
cmp_bool(fp, "inputrec->fepvals->bScCoul", -1, fep1->bScCoul, fep1->bScCoul);
- cmp_int(fp, "inputrec->separate_dhdl_file", -1, fep1->separate_dhdl_file, fep2->separate_dhdl_file);
- cmp_int(fp, "inputrec->dhdl_derivatives", -1, fep1->dhdl_derivatives, fep2->dhdl_derivatives);
+ cmpEnum(fp, "inputrec->separate_dhdl_file", fep1->separate_dhdl_file, fep2->separate_dhdl_file);
+ cmpEnum(fp, "inputrec->dhdl_derivatives", fep1->dhdl_derivatives, fep2->dhdl_derivatives);
cmp_int(fp, "inputrec->dh_hist_size", -1, fep1->dh_hist_size, fep2->dh_hist_size);
- cmp_double(fp, "inputrec->dh_hist_spacing", -1, fep1->dh_hist_spacing, fep2->dh_hist_spacing,
- ftol, abstol);
+ cmp_double(fp, "inputrec->dh_hist_spacing", -1, fep1->dh_hist_spacing, fep2->dh_hist_spacing, ftol, abstol);
}
void cmp_inputrec(FILE* fp, const t_inputrec* ir1, const t_inputrec* ir2, real ftol, real abstol)
* #define CII(s) cmp_int(fp,"inputrec->"#s,0,ir1->##s,ir2->##s)
* #define CIR(s) cmp_real(fp,"inputrec->"#s,0,ir1->##s,ir2->##s,ftol)
*/
- cmp_int(fp, "inputrec->eI", -1, ir1->eI, ir2->eI);
+ cmpEnum(fp, "inputrec->eI", ir1->eI, ir2->eI);
cmp_int64(fp, "inputrec->nsteps", ir1->nsteps, ir2->nsteps);
cmp_int64(fp, "inputrec->init_step", ir1->init_step, ir2->init_step);
cmp_int(fp, "inputrec->simulation_part", -1, ir1->simulation_part, ir2->simulation_part);
if (ir1->useMts && ir2->useMts)
{
cmp_int(fp, "inputrec->mts-levels", -1, ir1->mtsLevels.size(), ir2->mtsLevels.size());
- cmp_int(fp, "inputrec->mts-level2-forces", -1, ir1->mtsLevels[1].forceGroups.to_ulong(),
+ cmp_int(fp,
+ "inputrec->mts-level2-forces",
+ -1,
+ ir1->mtsLevels[1].forceGroups.to_ulong(),
ir2->mtsLevels[1].forceGroups.to_ulong());
- cmp_int(fp, "inputrec->mts-level2-factor", -1, ir1->mtsLevels[1].stepFactor,
+ cmp_int(fp,
+ "inputrec->mts-level2-factor",
+ -1,
+ ir1->mtsLevels[1].stepFactor,
ir2->mtsLevels[1].stepFactor);
}
cmp_int(fp, "inputrec->pbcType", -1, static_cast<int>(ir1->pbcType), static_cast<int>(ir2->pbcType));
cmp_bool(fp, "inputrec->bPeriodicMols", -1, ir1->bPeriodicMols, ir2->bPeriodicMols);
- cmp_int(fp, "inputrec->cutoff_scheme", -1, ir1->cutoff_scheme, ir2->cutoff_scheme);
+ cmpEnum(fp, "inputrec->cutoff_scheme", ir1->cutoff_scheme, ir2->cutoff_scheme);
cmp_int(fp, "inputrec->nstlist", -1, ir1->nstlist, ir2->nstlist);
cmp_int(fp, "inputrec->nstcomm", -1, ir1->nstcomm, ir2->nstcomm);
- cmp_int(fp, "inputrec->comm_mode", -1, ir1->comm_mode, ir2->comm_mode);
+ cmpEnum(fp, "inputrec->comm_mode", ir1->comm_mode, ir2->comm_mode);
cmp_int(fp, "inputrec->nstlog", -1, ir1->nstlog, ir2->nstlog);
cmp_int(fp, "inputrec->nstxout", -1, ir1->nstxout, ir2->nstxout);
cmp_int(fp, "inputrec->nstvout", -1, ir1->nstvout, ir2->nstvout);
cmp_int(fp, "inputrec->nstxout_compressed", -1, ir1->nstxout_compressed, ir2->nstxout_compressed);
cmp_double(fp, "inputrec->init_t", -1, ir1->init_t, ir2->init_t, ftol, abstol);
cmp_double(fp, "inputrec->delta_t", -1, ir1->delta_t, ir2->delta_t, ftol, abstol);
- cmp_real(fp, "inputrec->x_compression_precision", -1, ir1->x_compression_precision,
- ir2->x_compression_precision, ftol, abstol);
+ cmp_real(fp,
+ "inputrec->x_compression_precision",
+ -1,
+ ir1->x_compression_precision,
+ ir2->x_compression_precision,
+ ftol,
+ abstol);
cmp_real(fp, "inputrec->fourierspacing", -1, ir1->fourier_spacing, ir2->fourier_spacing, ftol, abstol);
cmp_int(fp, "inputrec->nkx", -1, ir1->nkx, ir2->nkx);
cmp_int(fp, "inputrec->nky", -1, ir1->nky, ir2->nky);
cmp_int(fp, "inputrec->nkz", -1, ir1->nkz, ir2->nkz);
cmp_int(fp, "inputrec->pme_order", -1, ir1->pme_order, ir2->pme_order);
cmp_real(fp, "inputrec->ewald_rtol", -1, ir1->ewald_rtol, ir2->ewald_rtol, ftol, abstol);
- cmp_int(fp, "inputrec->ewald_geometry", -1, ir1->ewald_geometry, ir2->ewald_geometry);
+ cmpEnum(fp, "inputrec->ewald_geometry", ir1->ewald_geometry, ir2->ewald_geometry);
cmp_real(fp, "inputrec->epsilon_surface", -1, ir1->epsilon_surface, ir2->epsilon_surface, ftol, abstol);
- cmp_int(fp, "inputrec->bContinuation", -1, static_cast<int>(ir1->bContinuation),
+ cmp_int(fp,
+ "inputrec->bContinuation",
+ -1,
+ static_cast<int>(ir1->bContinuation),
static_cast<int>(ir2->bContinuation));
- cmp_int(fp, "inputrec->bShakeSOR", -1, static_cast<int>(ir1->bShakeSOR),
- static_cast<int>(ir2->bShakeSOR));
- cmp_int(fp, "inputrec->etc", -1, ir1->etc, ir2->etc);
- cmp_int(fp, "inputrec->bPrintNHChains", -1, static_cast<int>(ir1->bPrintNHChains),
+ cmp_int(fp, "inputrec->bShakeSOR", -1, static_cast<int>(ir1->bShakeSOR), static_cast<int>(ir2->bShakeSOR));
+ cmpEnum(fp, "inputrec->etc", ir1->etc, ir2->etc);
+ cmp_int(fp,
+ "inputrec->bPrintNHChains",
+ -1,
+ static_cast<int>(ir1->bPrintNHChains),
static_cast<int>(ir2->bPrintNHChains));
- cmp_int(fp, "inputrec->epc", -1, ir1->epc, ir2->epc);
- cmp_int(fp, "inputrec->epct", -1, ir1->epct, ir2->epct);
+ cmpEnum(fp, "inputrec->epc", ir1->epc, ir2->epc);
+ cmpEnum(fp, "inputrec->epct", ir1->epct, ir2->epct);
cmp_real(fp, "inputrec->tau_p", -1, ir1->tau_p, ir2->tau_p, ftol, abstol);
cmp_rvec(fp, "inputrec->ref_p(x)", -1, ir1->ref_p[XX], ir2->ref_p[XX], ftol, abstol);
cmp_rvec(fp, "inputrec->ref_p(y)", -1, ir1->ref_p[YY], ir2->ref_p[YY], ftol, abstol);
cmp_rvec(fp, "inputrec->compress(x)", -1, ir1->compress[XX], ir2->compress[XX], ftol, abstol);
cmp_rvec(fp, "inputrec->compress(y)", -1, ir1->compress[YY], ir2->compress[YY], ftol, abstol);
cmp_rvec(fp, "inputrec->compress(z)", -1, ir1->compress[ZZ], ir2->compress[ZZ], ftol, abstol);
- cmp_int(fp, "refcoord_scaling", -1, ir1->refcoord_scaling, ir2->refcoord_scaling);
+ cmpEnum(fp, "refcoord_scaling", ir1->refcoord_scaling, ir2->refcoord_scaling);
cmp_rvec(fp, "inputrec->posres_com", -1, ir1->posres_com, ir2->posres_com, ftol, abstol);
cmp_rvec(fp, "inputrec->posres_comB", -1, ir1->posres_comB, ir2->posres_comB, ftol, abstol);
cmp_real(fp, "inputrec->verletbuf_tol", -1, ir1->verletbuf_tol, ir2->verletbuf_tol, ftol, abstol);
cmp_real(fp, "inputrec->rlist", -1, ir1->rlist, ir2->rlist, ftol, abstol);
cmp_real(fp, "inputrec->rtpi", -1, ir1->rtpi, ir2->rtpi, ftol, abstol);
- cmp_int(fp, "inputrec->coulombtype", -1, ir1->coulombtype, ir2->coulombtype);
- cmp_int(fp, "inputrec->coulomb_modifier", -1, ir1->coulomb_modifier, ir2->coulomb_modifier);
+ cmpEnum(fp, "inputrec->coulombtype", ir1->coulombtype, ir2->coulombtype);
+ cmpEnum(fp, "inputrec->coulomb_modifier", ir1->coulomb_modifier, ir2->coulomb_modifier);
cmp_real(fp, "inputrec->rcoulomb_switch", -1, ir1->rcoulomb_switch, ir2->rcoulomb_switch, ftol, abstol);
cmp_real(fp, "inputrec->rcoulomb", -1, ir1->rcoulomb, ir2->rcoulomb, ftol, abstol);
- cmp_int(fp, "inputrec->vdwtype", -1, ir1->vdwtype, ir2->vdwtype);
- cmp_int(fp, "inputrec->vdw_modifier", -1, ir1->vdw_modifier, ir2->vdw_modifier);
+ cmpEnum(fp, "inputrec->vdwtype", ir1->vdwtype, ir2->vdwtype);
+ cmpEnum(fp, "inputrec->vdw_modifier", ir1->vdw_modifier, ir2->vdw_modifier);
cmp_real(fp, "inputrec->rvdw_switch", -1, ir1->rvdw_switch, ir2->rvdw_switch, ftol, abstol);
cmp_real(fp, "inputrec->rvdw", -1, ir1->rvdw, ir2->rvdw, ftol, abstol);
cmp_real(fp, "inputrec->epsilon_r", -1, ir1->epsilon_r, ir2->epsilon_r, ftol, abstol);
cmp_real(fp, "inputrec->epsilon_rf", -1, ir1->epsilon_rf, ir2->epsilon_rf, ftol, abstol);
cmp_real(fp, "inputrec->tabext", -1, ir1->tabext, ir2->tabext, ftol, abstol);
- cmp_int(fp, "inputrec->eDispCorr", -1, ir1->eDispCorr, ir2->eDispCorr);
+ cmpEnum(fp, "inputrec->eDispCorr", ir1->eDispCorr, ir2->eDispCorr);
cmp_real(fp, "inputrec->shake_tol", -1, ir1->shake_tol, ir2->shake_tol, ftol, abstol);
- cmp_int(fp, "inputrec->efep", -1, ir1->efep, ir2->efep);
- cmp_fepvals(fp, ir1->fepvals, ir2->fepvals, ftol, abstol);
+ cmpEnum(fp, "inputrec->efep", ir1->efep, ir2->efep);
+ cmp_fepvals(fp, ir1->fepvals.get(), ir2->fepvals.get(), ftol, abstol);
cmp_int(fp, "inputrec->bSimTemp", -1, static_cast<int>(ir1->bSimTemp), static_cast<int>(ir2->bSimTemp));
if ((ir1->bSimTemp == ir2->bSimTemp) && (ir1->bSimTemp))
{
- cmp_simtempvals(fp, ir1->simtempvals, ir2->simtempvals,
- std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda), ftol, abstol);
+ cmp_simtempvals(fp,
+ ir1->simtempvals.get(),
+ ir2->simtempvals.get(),
+ std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda),
+ ftol,
+ abstol);
}
- cmp_int(fp, "inputrec->bExpanded", -1, static_cast<int>(ir1->bExpanded),
- static_cast<int>(ir2->bExpanded));
+ cmp_int(fp, "inputrec->bExpanded", -1, static_cast<int>(ir1->bExpanded), static_cast<int>(ir2->bExpanded));
if ((ir1->bExpanded == ir2->bExpanded) && (ir1->bExpanded))
{
- cmp_expandedvals(fp, ir1->expandedvals, ir2->expandedvals,
- std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda), ftol, abstol);
+ cmp_expandedvals(fp,
+ ir1->expandedvals.get(),
+ ir2->expandedvals.get(),
+ std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda),
+ ftol,
+ abstol);
}
cmp_int(fp, "inputrec->nwall", -1, ir1->nwall, ir2->nwall);
- cmp_int(fp, "inputrec->wall_type", -1, ir1->wall_type, ir2->wall_type);
+ cmpEnum(fp, "inputrec->wall_type", ir1->wall_type, ir2->wall_type);
cmp_int(fp, "inputrec->wall_atomtype[0]", -1, ir1->wall_atomtype[0], ir2->wall_atomtype[0]);
cmp_int(fp, "inputrec->wall_atomtype[1]", -1, ir1->wall_atomtype[1], ir2->wall_atomtype[1]);
cmp_real(fp, "inputrec->wall_density[0]", -1, ir1->wall_density[0], ir2->wall_density[0], ftol, abstol);
cmp_bool(fp, "inputrec->bDoAwh", -1, ir1->bDoAwh, ir2->bDoAwh);
if (ir1->bDoAwh && ir2->bDoAwh)
{
- cmp_awhParams(fp, ir1->awhParams, ir2->awhParams, ftol, abstol);
+ cmp_awhParams(fp, *ir1->awhParams, *ir2->awhParams, ftol, abstol);
}
- cmp_int(fp, "inputrec->eDisre", -1, ir1->eDisre, ir2->eDisre);
+ cmpEnum(fp, "inputrec->eDisre", ir1->eDisre, ir2->eDisre);
cmp_real(fp, "inputrec->dr_fc", -1, ir1->dr_fc, ir2->dr_fc, ftol, abstol);
- cmp_int(fp, "inputrec->eDisreWeighting", -1, ir1->eDisreWeighting, ir2->eDisreWeighting);
- cmp_int(fp, "inputrec->bDisreMixed", -1, static_cast<int>(ir1->bDisreMixed),
- static_cast<int>(ir2->bDisreMixed));
+ cmpEnum(fp, "inputrec->eDisreWeighting", ir1->eDisreWeighting, ir2->eDisreWeighting);
+ cmp_int(fp, "inputrec->bDisreMixed", -1, static_cast<int>(ir1->bDisreMixed), static_cast<int>(ir2->bDisreMixed));
cmp_int(fp, "inputrec->nstdisreout", -1, ir1->nstdisreout, ir2->nstdisreout);
cmp_real(fp, "inputrec->dr_tau", -1, ir1->dr_tau, ir2->dr_tau, ftol, abstol);
cmp_real(fp, "inputrec->orires_fc", -1, ir1->orires_fc, ir2->orires_fc, ftol, abstol);
cmp_real(fp, "inputrec->fc_stepsize", -1, ir1->fc_stepsize, ir2->fc_stepsize, ftol, abstol);
cmp_int(fp, "inputrec->nstcgsteep", -1, ir1->nstcgsteep, ir2->nstcgsteep);
cmp_int(fp, "inputrec->nbfgscorr", 0, ir1->nbfgscorr, ir2->nbfgscorr);
- cmp_int(fp, "inputrec->eConstrAlg", -1, ir1->eConstrAlg, ir2->eConstrAlg);
+ cmpEnum(fp, "inputrec->eConstrAlg", ir1->eConstrAlg, ir2->eConstrAlg);
cmp_int(fp, "inputrec->nProjOrder", -1, ir1->nProjOrder, ir2->nProjOrder);
cmp_real(fp, "inputrec->LincsWarnAngle", -1, ir1->LincsWarnAngle, ir2->LincsWarnAngle, ftol, abstol);
cmp_int(fp, "inputrec->nLincsIter", -1, ir1->nLincsIter, ir2->nLincsIter);
gmx_bool inputrecDynamicBox(const t_inputrec* ir)
{
- return (ir->epc != epcNO || ir->eI == eiTPI || inputrecDeform(ir));
+ return (ir->epc != PressureCoupling::No || ir->eI == IntegrationAlgorithm::TPI || inputrecDeform(ir));
}
gmx_bool inputrecPreserveShape(const t_inputrec* ir)
{
- return (ir->epc != epcNO && ir->deform[XX][XX] == 0
- && (ir->epct == epctISOTROPIC || ir->epct == epctSEMIISOTROPIC));
+ return (ir->epc != PressureCoupling::No && ir->deform[XX][XX] == 0
+ && (ir->epct == PressureCouplingType::Isotropic
+ || ir->epct == PressureCouplingType::SemiIsotropic));
}
gmx_bool inputrecNeedMutot(const t_inputrec* ir)
{
- return ((ir->coulombtype == eelEWALD || EEL_PME(ir->coulombtype))
- && (ir->ewald_geometry == eewg3DC || ir->epsilon_surface != 0));
+ return ((ir->coulombtype == CoulombInteractionType::Ewald || EEL_PME(ir->coulombtype))
+ && (ir->ewald_geometry == EwaldGeometry::ThreeDC || ir->epsilon_surface != 0));
}
gmx_bool inputrecExclForces(const t_inputrec* ir)
gmx_bool inputrecNptTrotter(const t_inputrec* ir)
{
- return (((ir->eI == eiVV) || (ir->eI == eiVVAK)) && (ir->epc == epcMTTK) && (ir->etc == etcNOSEHOOVER));
+ return (((ir->eI == IntegrationAlgorithm::VV) || (ir->eI == IntegrationAlgorithm::VVAK))
+ && (ir->epc == PressureCoupling::Mttk) && (ir->etc == TemperatureCoupling::NoseHoover));
}
gmx_bool inputrecNvtTrotter(const t_inputrec* ir)
{
- return (((ir->eI == eiVV) || (ir->eI == eiVVAK)) && (ir->epc != epcMTTK) && (ir->etc == etcNOSEHOOVER));
+ return (((ir->eI == IntegrationAlgorithm::VV) || (ir->eI == IntegrationAlgorithm::VVAK))
+ && (ir->epc != PressureCoupling::Mttk) && (ir->etc == TemperatureCoupling::NoseHoover));
}
gmx_bool inputrecNphTrotter(const t_inputrec* ir)
{
- return (((ir->eI == eiVV) || (ir->eI == eiVVAK)) && (ir->epc == epcMTTK) && (ir->etc != etcNOSEHOOVER));
+ return (((ir->eI == IntegrationAlgorithm::VV) || (ir->eI == IntegrationAlgorithm::VVAK))
+ && (ir->epc == PressureCoupling::Mttk) && (ir->etc != TemperatureCoupling::NoseHoover));
}
bool inputrecPbcXY2Walls(const t_inputrec* ir)
// Energy minimization or stochastic integrator: no conservation
return false;
}
- else if (ir->etc == etcNO && ir->epc == epcNO)
+ else if (ir->etc == TemperatureCoupling::No && ir->epc == PressureCoupling::No)
{
// The total energy is conserved, no additional conserved quanitity
return false;
{
// Shear stress with Parrinello-Rahman is not supported (tedious)
bool shearWithPR =
- ((ir->epc == epcPARRINELLORAHMAN || ir->epc == epcMTTK)
+ ((ir->epc == PressureCoupling::ParrinelloRahman || ir->epc == PressureCoupling::Mttk)
&& (ir->ref_p[YY][XX] != 0 || ir->ref_p[ZZ][XX] != 0 || ir->ref_p[ZZ][YY] != 0));
return !ETC_ANDERSEN(ir->etc) && !shearWithPR;
bool integratorHasReferenceTemperature(const t_inputrec* ir)
{
- return ((ir->etc != etcNO) || EI_SD(ir->eI) || (ir->eI == eiBD) || EI_TPI(ir->eI));
+ return ((ir->etc != TemperatureCoupling::No) || EI_SD(ir->eI)
+ || (ir->eI == IntegrationAlgorithm::BD) || EI_TPI(ir->eI));
}
int inputrec2nboundeddim(const t_inputrec* ir)
real maxReferenceTemperature(const t_inputrec& ir)
{
- if (EI_ENERGY_MINIMIZATION(ir.eI) || ir.eI == eiNM)
+ if (EI_ENERGY_MINIMIZATION(ir.eI) || ir.eI == IntegrationAlgorithm::NM)
{
return 0;
}
- if (EI_MD(ir.eI) && ir.etc == etcNO)
+ if (EI_MD(ir.eI) && ir.etc == TemperatureCoupling::No)
{
return -1;
}
bool haveEwaldSurfaceContribution(const t_inputrec& ir)
{
- return EEL_PME_EWALD(ir.coulombtype) && (ir.ewald_geometry == eewg3DC || ir.epsilon_surface != 0);
+ return EEL_PME_EWALD(ir.coulombtype)
+ && (ir.ewald_geometry == EwaldGeometry::ThreeDC || ir.epsilon_surface != 0);
}
bool haveFreeEnergyType(const t_inputrec& ir, const int fepType)
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/real.h"
#define EGP_EXCL (1 << 0)
namespace gmx
{
class Awh;
-struct AwhParams;
+class AwhParams;
class KeyValueTreeObject;
struct MtsLevel;
} // namespace gmx
int ngtc;
//! Number of of Nose-Hoover chains per group
int nhchainlength;
- //! Number of Accelerate groups
- int ngacc;
//! Number of Freeze groups
int ngfrz;
//! Number of Energy groups
//! Coupling temperature per group
real* ref_t;
//! No/simple/periodic simulated annealing for each group
- int* annealing;
+ SimulatedAnnealing* annealing;
//! Number of annealing time points per group
int* anneal_npoints;
//! For each group: Time points
real** anneal_temp;
//! Tau coupling time
real* tau_t;
- //! Acceleration per group
- rvec* acc;
//! Whether the group will be frozen in each direction
ivec* nFreeze;
//! Exclusions/tables of energy group pairs
struct t_simtemp
{
//! Simulated temperature scaling; linear or exponential
- int eSimTempScale;
+ SimulatedTempering eSimTempScale;
//! The low temperature for simulated tempering
real simtemp_low;
//! The high temperature for simulated tempering
real simtemp_high;
//! The range of temperatures used for simulated tempering
- real* temperatures;
+ std::vector<real> temperatures;
};
struct t_lambda
//! Change of lambda per time step (fraction of (0.1)
double delta_lambda;
//! Print no, total or potential energies in dhdl
- int edHdLPrintEnergy;
+ FreeEnergyPrintEnergy edHdLPrintEnergy;
//! The number of foreign lambda points
int n_lambda;
//! The array of all lambda values
- double** all_lambda;
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::vector<double>> all_lambda;
//! The number of neighboring lambda states to calculate the energy for in up and down directions (-1 for all)
int lambda_neighbors;
//! The first lambda to calculate energies for
//! Free energy soft-core sigma for ?????
real sc_sigma_min;
//! Use softcore for the coulomb portion as well (default FALSE)
- gmx_bool bScCoul;
+ bool bScCoul;
//! Whether to print the dvdl term associated with this term; if it is not specified as separate, it is lumped with the FEP term
- gmx_bool separate_dvdl[efptNR];
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, bool> separate_dvdl;
//! Whether to write a separate dhdl.xvg file note: NOT a gmx_bool, but an enum
- int separate_dhdl_file;
+ SeparateDhdlFile separate_dhdl_file;
//! Whether to calculate+write dhdl derivatives note: NOT a gmx_bool, but an enum
- int dhdl_derivatives;
+ DhDlDerivativeCalculation dhdl_derivatives;
//! The maximum table size for the dH histogram
int dh_hist_size;
//! The spacing for the dH histogram
//! The frequency of expanded ensemble state changes
int nstexpanded;
//! Which type of move updating do we use for lambda monte carlo (or no for none)
- int elamstats;
+ LambdaWeightCalculation elamstats;
//! What move set will be we using for state space moves
- int elmcmove;
+ LambdaMoveCalculation elmcmove;
//! The method we use to decide of we have equilibrated the weights
- int elmceq;
+ LambdaWeightWillReachEquilibrium elmceq;
//! The minumum number of samples at each lambda for deciding whether we have reached a minimum
int equil_n_at_lam;
//! Wang-Landau delta at which we stop equilibrating weights
//! Random number seed for lambda mc switches
int lmc_seed;
//! Whether to use minumum variance weighting
- gmx_bool minvar;
+ bool minvar;
//! The number of samples needed before kicking into minvar routine
int minvarmin;
//! The offset for the variance in MinVar
//! Range of cvalues used for BAR
int c_range;
//! Whether to print symmetrized matrices
- gmx_bool bSymmetrizedTMatrix;
+ bool bSymmetrizedTMatrix;
//! How frequently to print the transition matrices
int nstTij;
//! Number of repetitions in the MC lambda jumps MRS -- VERIFY THIS
//! Starting delta for Wang-Landau
real init_wl_delta;
//! Use one over t convergence for Wang-Landau when the delta get sufficiently small
- gmx_bool bWLoneovert;
+ bool bWLoneovert;
//! Did we initialize the weights? TODO: REMOVE FOR 5.0, no longer needed with new logic
- gmx_bool bInit_weights;
+ bool bInit_weights;
//! To override the main temperature, or define it if it's not defined
real mc_temp;
//! User-specified initial weights to start with
- real* init_lambda_weights;
+ std::vector<real> init_lambda_weights;
};
struct t_rotgrp
{
//! Rotation type for this group
- int eType;
+ EnforcedRotationGroupType eType;
//! Use mass-weighed positions?
- int bMassW;
+ bool bMassW;
//! Number of atoms in the group
int nat;
//! The global atoms numbers
//! Pivot point of rotation axis (nm)
rvec pivot;
//! Type of fit to determine actual group angle
- int eFittype;
+ RotationGroupFitting eFittype;
//! Number of angles around the reference angle for which the rotation potential is also evaluated (for fit type 'potential' only)
int PotAngle_nstep;
//! Distance between two angles in degrees (for fit type 'potential' only)
//! The global ion group atoms numbers
int* ind;
//! Requested number of molecules of this type per compartment
- int nmolReq[eCompNR];
+ gmx::EnumerationArray<Compartment, int> nmolReq;
};
struct t_swapcoords
//! Period between when a swap is attempted
int nstswap;
//! Use mass-weighted positions in split group
- gmx_bool massw_split[2];
+ bool massw_split[2];
/*! \brief Split cylinders defined by radius, upper and lower
* extension. The split cylinders define the channels and are
* each anchored in the center of the split group */
//! Ion counts may deviate from the requested values by +-threshold before a swap is done
real threshold;
//! Offset of the swap layer (='bulk') with respect to the compartment-defining layers
- real bulkOffset[eCompNR];
+ gmx::EnumerationArray<Compartment, real> bulkOffset;
//! Number of groups to be controlled
int ngrp;
//! All swap groups, including split and solvent
~t_inputrec();
//! Integration method
- int eI;
+ IntegrationAlgorithm eI;
//! Number of steps to be taken
int64_t nsteps;
//! Used in checkpointing to separate chunks
//! Frequency of energy calc. and T/P coupl. upd.
int nstcalcenergy;
//! Group or verlet cutoffs
- int cutoff_scheme;
+ CutoffScheme cutoff_scheme;
//! Number of steps before pairlist is generated
int nstlist;
//! Number of steps after which center of mass motion is removed
int nstcomm;
//! Center of mass motion removal algorithm
- int comm_mode;
+ ComRemovalAlgorithm comm_mode;
//! Number of steps after which print to logfile
int nstlog;
//! Number of steps after which X is output
//! Real space tolerance for LJ-Ewald
real ewald_rtol_lj;
//! Normal/3D ewald, or pseudo-2D LR corrections
- int ewald_geometry;
+ EwaldGeometry ewald_geometry;
//! Epsilon for PME dipole correction
real epsilon_surface;
//! Type of combination rule in LJ-PME
- int ljpme_combination_rule;
+ LongRangeVdW ljpme_combination_rule;
//! Type of periodic boundary conditions
PbcType pbcType;
//! Periodic molecules
bool bPeriodicMols;
//! Continuation run: starting state is correct (ie. constrained)
- gmx_bool bContinuation;
+ bool bContinuation;
//! Temperature coupling
- int etc;
+ TemperatureCoupling etc;
//! Interval in steps for temperature coupling
int nsttcouple;
//! Whether to print nose-hoover chains
- gmx_bool bPrintNHChains;
+ bool bPrintNHChains;
//! Pressure coupling
- int epc;
+ PressureCoupling epc;
//! Pressure coupling type
- int epct;
+ PressureCouplingType epct;
//! Interval in steps for pressure coupling
int nstpcouple;
//! Pressure coupling time (ps)
//! Compressibility ((mol nm^3)/kJ)
tensor compress;
//! How to scale absolute reference coordinates
- int refcoord_scaling;
+ RefCoordScaling refcoord_scaling;
//! The COM of the posres atoms
rvec posres_com;
//! The B-state COM of the posres atoms
//! Radius for test particle insertion
real rtpi;
//! Type of electrostatics treatment
- int coulombtype;
+ CoulombInteractionType coulombtype;
//! Modify the Coulomb interaction
- int coulomb_modifier;
+ InteractionModifiers coulomb_modifier;
//! Coulomb switch range start (nm)
real rcoulomb_switch;
//! Coulomb cutoff (nm)
//! Always false (no longer supported)
bool implicit_solvent;
//! Type of Van der Waals treatment
- int vdwtype;
+ VanDerWaalsType vdwtype;
//! Modify the Van der Waals interaction
- int vdw_modifier;
+ InteractionModifiers vdw_modifier;
//! Van der Waals switch range start (nm)
real rvdw_switch;
//! Van der Waals cutoff (nm)
real rvdw;
//! Perform Long range dispersion corrections
- int eDispCorr;
+ DispersionCorrectionType eDispCorr;
//! Extension of the table beyond the cut-off, as well as the table length for 1-4 interac.
real tabext;
//! Tolerance for shake
real shake_tol;
//! Free energy calculations
- int efep;
+ FreeEnergyPerturbationType efep;
//! Data for the FEP state
- t_lambda* fepvals;
+ std::unique_ptr<t_lambda> fepvals;
//! Whether to do simulated tempering
- gmx_bool bSimTemp;
+ bool bSimTemp;
//! Variables for simulated tempering
- t_simtemp* simtempvals;
+ std::unique_ptr<t_simtemp> simtempvals;
//! Whether expanded ensembles are used
- gmx_bool bExpanded;
+ bool bExpanded;
//! Expanded ensemble parameters
- t_expanded* expandedvals;
+ std::unique_ptr<t_expanded> expandedvals;
//! Type of distance restraining
- int eDisre;
+ DistanceRestraintRefinement eDisre;
//! Force constant for time averaged distance restraints
real dr_fc;
//! Type of weighting of pairs in one restraints
- int eDisreWeighting;
+ DistanceRestraintWeighting eDisreWeighting;
//! Use combination of time averaged and instantaneous violations
- gmx_bool bDisreMixed;
+ bool bDisreMixed;
//! Frequency of writing pair distances to enx
int nstdisreout;
//! Time constant for memory function in disres
//! Number of corrections to the Hessian to keep
int nbfgscorr;
//! Type of constraint algorithm
- int eConstrAlg;
+ ConstraintAlgorithm eConstrAlg;
//! Order of the LINCS Projection Algorithm
int nProjOrder;
//! Warn if any bond rotates more than this many degrees
//! Number of iterations in the final LINCS step
int nLincsIter;
//! Use successive overrelaxation for shake
- gmx_bool bShakeSOR;
+ bool bShakeSOR;
//! Friction coefficient for BD (amu/ps)
real bd_fric;
//! Random seed for SD and BD
//! The number of walls
int nwall;
//! The type of walls
- int wall_type;
+ WallType wall_type;
//! The potentail is linear for r<=wall_r_linpot
real wall_r_linpot;
//! The atom type for walls
/* COM pulling data */
//! Do we do COM pulling?
- gmx_bool bPull;
+ bool bPull;
//! The data for center of mass pulling
std::unique_ptr<pull_params_t> pull;
/* AWH bias data */
//! Whether to use AWH biasing for PMF calculations
- gmx_bool bDoAwh;
+ bool bDoAwh;
//! AWH biasing parameters
- gmx::AwhParams* awhParams;
+ std::unique_ptr<gmx::AwhParams> awhParams;
/* Enforced rotation data */
//! Whether to calculate enforced rotation potential(s)
- gmx_bool bRot;
+ bool bRot;
//! The data for enforced rotation potentials
t_rot* rot;
//! Whether to do ion/water position exchanges (CompEL)
- int eSwapCoords;
+ SwapType eSwapCoords;
//! Swap data structure.
t_swapcoords* swap;
//! Whether the tpr makes an interactive MD session possible.
- gmx_bool bIMD;
+ bool bIMD;
//! Interactive molecular dynamics
t_IMD* imd;
//! Group options
t_grpopts opts;
//! QM/MM calculation
- gmx_bool bQMMM;
+ bool bQMMM;
/* Fields for removed features go here (better caching) */
//! Whether AdResS is enabled - always false if a valid .tpr was read
- gmx_bool bAdress;
+ bool bAdress;
//! Whether twin-range scheme is active - always false if a valid .tpr was read
- gmx_bool useTwinRange;
+ bool useTwinRange;
+ //! Whether we have constant acceleration - removed in GROMACS 2022
+ bool useConstantAcceleration;
//! KVT object that contains input parameters converted to the new style.
gmx::KeyValueTreeObject* params;
int ir_optimal_nstcalcenergy(const t_inputrec* ir);
-int tcouple_min_integration_steps(int etc);
+int tcouple_min_integration_steps(TemperatureCoupling etc);
int ir_optimal_nsttcouple(const t_inputrec* ir);
-int pcouple_min_integration_steps(int epc);
+int pcouple_min_integration_steps(PressureCoupling epc);
int ir_optimal_nstpcouple(const t_inputrec* ir);
/* Returns if the Coulomb force or potential is switched to zero */
-gmx_bool ir_coulomb_switched(const t_inputrec* ir);
+bool ir_coulomb_switched(const t_inputrec* ir);
/* Returns if the Coulomb interactions are zero beyond the rcoulomb.
* Note: always returns TRUE for the Verlet cut-off scheme.
*/
-gmx_bool ir_coulomb_is_zero_at_cutoff(const t_inputrec* ir);
+bool ir_coulomb_is_zero_at_cutoff(const t_inputrec* ir);
/* As ir_coulomb_is_zero_at_cutoff, but also returns TRUE for user tabulated
* interactions, since these might be zero beyond rcoulomb.
*/
-gmx_bool ir_coulomb_might_be_zero_at_cutoff(const t_inputrec* ir);
+bool ir_coulomb_might_be_zero_at_cutoff(const t_inputrec* ir);
/* Returns if the Van der Waals force or potential is switched to zero */
-gmx_bool ir_vdw_switched(const t_inputrec* ir);
+bool ir_vdw_switched(const t_inputrec* ir);
/* Returns if the Van der Waals interactions are zero beyond the rvdw.
* Note: always returns TRUE for the Verlet cut-off scheme.
*/
-gmx_bool ir_vdw_is_zero_at_cutoff(const t_inputrec* ir);
+bool ir_vdw_is_zero_at_cutoff(const t_inputrec* ir);
/* As ir_vdw_is_zero_at_cutoff, but also returns TRUE for user tabulated
* interactions, since these might be zero beyond rvdw.
*/
-gmx_bool ir_vdw_might_be_zero_at_cutoff(const t_inputrec* ir);
+bool ir_vdw_might_be_zero_at_cutoff(const t_inputrec* ir);
/*! \brief Free memory from input record.
*
*/
void done_inputrec(t_inputrec* ir);
-void pr_inputrec(FILE* fp, int indent, const char* title, const t_inputrec* ir, gmx_bool bMDPformat);
+void pr_inputrec(FILE* fp, int indent, const char* title, const t_inputrec* ir, bool bMDPformat);
void cmp_inputrec(FILE* fp, const t_inputrec* ir1, const t_inputrec* ir2, real ftol, real abstol);
void comp_pull_AB(FILE* fp, const pull_params_t& pull, real ftol, real abstol);
-gmx_bool inputrecDeform(const t_inputrec* ir);
+bool inputrecDeform(const t_inputrec* ir);
-gmx_bool inputrecDynamicBox(const t_inputrec* ir);
+bool inputrecDynamicBox(const t_inputrec* ir);
-gmx_bool inputrecPreserveShape(const t_inputrec* ir);
+bool inputrecPreserveShape(const t_inputrec* ir);
-gmx_bool inputrecNeedMutot(const t_inputrec* ir);
+bool inputrecNeedMutot(const t_inputrec* ir);
-gmx_bool inputrecTwinRange(const t_inputrec* ir);
+bool inputrecTwinRange(const t_inputrec* ir);
-gmx_bool inputrecExclForces(const t_inputrec* ir);
+bool inputrecExclForces(const t_inputrec* ir);
-gmx_bool inputrecNptTrotter(const t_inputrec* ir);
+bool inputrecNptTrotter(const t_inputrec* ir);
-gmx_bool inputrecNvtTrotter(const t_inputrec* ir);
+bool inputrecNvtTrotter(const t_inputrec* ir);
-gmx_bool inputrecNphTrotter(const t_inputrec* ir);
+bool inputrecNphTrotter(const t_inputrec* ir);
/*! \brief Return true if the simulation is 2D periodic with two walls. */
bool inputrecPbcXY2Walls(const t_inputrec* ir);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
+#include "gromacs/ewald/ewald_utils.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
+#include "gromacs/mdlib/rf_util.h"
+#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/pleasecite.h"
interaction_const_t::SoftCoreParameters::SoftCoreParameters(const t_lambda& fepvals) :
alphaVdw(fepvals.sc_alpha),
// This is checked during tpr reading, so we can assert here
GMX_RELEASE_ASSERT(fepvals.sc_r_power == 6.0, "We only support soft-core r-power 6");
}
+
+/*! \brief Print Coulomb Ewald citations and set ewald coefficients */
+static void initCoulombEwaldParameters(FILE* fp,
+ const t_inputrec& ir,
+ bool systemHasNetCharge,
+ interaction_const_t* ic)
+{
+ if (!EEL_PME_EWALD(ir.coulombtype))
+ {
+ return;
+ }
+
+ if (fp)
+ {
+ fprintf(fp, "Will do PME sum in reciprocal space for electrostatic interactions.\n");
+
+ if (ir.coulombtype == CoulombInteractionType::P3mAD)
+ {
+ please_cite(fp, "Hockney1988");
+ please_cite(fp, "Ballenegger2012");
+ }
+ else
+ {
+ please_cite(fp, "Essmann95a");
+ }
+
+ if (ir.ewald_geometry == EwaldGeometry::ThreeDC)
+ {
+ if (fp)
+ {
+ fprintf(fp,
+ "Using the Ewald3DC correction for systems with a slab geometry%s.\n",
+ systemHasNetCharge ? " and net charge" : "");
+ }
+ please_cite(fp, "In-Chul99a");
+ if (systemHasNetCharge)
+ {
+ please_cite(fp, "Ballenegger2009");
+ }
+ }
+ }
+
+ ic->ewaldcoeff_q = calc_ewaldcoeff_q(ir.rcoulomb, ir.ewald_rtol);
+ if (fp)
+ {
+ fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for Ewald\n", 1 / ic->ewaldcoeff_q);
+ }
+
+ if (ic->coulomb_modifier == InteractionModifiers::PotShift)
+ {
+ GMX_RELEASE_ASSERT(ic->rcoulomb != 0, "Cutoff radius cannot be zero");
+ ic->sh_ewald = std::erfc(ic->ewaldcoeff_q * ic->rcoulomb) / ic->rcoulomb;
+ }
+ else
+ {
+ ic->sh_ewald = 0;
+ }
+}
+
+/*! \brief Print Van der Waals Ewald citations and set ewald coefficients */
+static void initVdwEwaldParameters(FILE* fp, const t_inputrec& ir, interaction_const_t* ic)
+{
+ if (!EVDW_PME(ir.vdwtype))
+ {
+ return;
+ }
+
+ if (fp)
+ {
+ fprintf(fp, "Will do PME sum in reciprocal space for LJ dispersion interactions.\n");
+ please_cite(fp, "Essmann95a");
+ }
+ ic->ewaldcoeff_lj = calc_ewaldcoeff_lj(ir.rvdw, ir.ewald_rtol_lj);
+ if (fp)
+ {
+ fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for LJ Ewald\n", 1 / ic->ewaldcoeff_lj);
+ }
+
+ if (ic->vdw_modifier == InteractionModifiers::PotShift)
+ {
+ real crc2 = gmx::square(ic->ewaldcoeff_lj * ic->rvdw);
+ ic->sh_lj_ewald = (std::exp(-crc2) * (1 + crc2 + 0.5 * crc2 * crc2) - 1) / gmx::power6(ic->rvdw);
+ }
+ else
+ {
+ ic->sh_lj_ewald = 0;
+ }
+}
+
+static real calcBuckinghamBMax(FILE* fplog, const gmx_mtop_t& mtop)
+{
+ const t_atoms *at1, *at2;
+ int i, j, tpi, tpj, ntypes;
+ real b, bmin;
+
+ if (fplog)
+ {
+ fprintf(fplog, "Determining largest Buckingham b parameter for table\n");
+ }
+ ntypes = mtop.ffparams.atnr;
+
+ bmin = -1;
+ real bham_b_max = 0;
+ for (size_t mt1 = 0; mt1 < mtop.moltype.size(); mt1++)
+ {
+ at1 = &mtop.moltype[mt1].atoms;
+ for (i = 0; (i < at1->nr); i++)
+ {
+ tpi = at1->atom[i].type;
+ if (tpi >= ntypes)
+ {
+ gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", i, tpi, ntypes);
+ }
+
+ for (size_t mt2 = mt1; mt2 < mtop.moltype.size(); mt2++)
+ {
+ at2 = &mtop.moltype[mt2].atoms;
+ for (j = 0; (j < at2->nr); j++)
+ {
+ tpj = at2->atom[j].type;
+ if (tpj >= ntypes)
+ {
+ gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", j, tpj, ntypes);
+ }
+ b = mtop.ffparams.iparams[tpi * ntypes + tpj].bham.b;
+ if (b > bham_b_max)
+ {
+ bham_b_max = b;
+ }
+ if ((b < bmin) || (bmin == -1))
+ {
+ bmin = b;
+ }
+ }
+ }
+ }
+ }
+ if (fplog)
+ {
+ fprintf(fplog, "Buckingham b parameters, min: %g, max: %g\n", bmin, bham_b_max);
+ }
+
+ return bham_b_max;
+}
+
+static void clear_force_switch_constants(shift_consts_t* sc)
+{
+ sc->c2 = 0;
+ sc->c3 = 0;
+ sc->cpot = 0;
+}
+
+static void force_switch_constants(real p, real rsw, real rc, shift_consts_t* sc)
+{
+ /* Here we determine the coefficient for shifting the force to zero
+ * between distance rsw and the cut-off rc.
+ * For a potential of r^-p, we have force p*r^-(p+1).
+ * But to save flops we absorb p in the coefficient.
+ * Thus we get:
+ * force/p = r^-(p+1) + c2*r^2 + c3*r^3
+ * potential = r^-p + c2/3*r^3 + c3/4*r^4 + cpot
+ */
+ sc->c2 = ((p + 1) * rsw - (p + 4) * rc) / (pow(rc, p + 2) * gmx::square(rc - rsw));
+ sc->c3 = -((p + 1) * rsw - (p + 3) * rc) / (pow(rc, p + 2) * gmx::power3(rc - rsw));
+ sc->cpot = -pow(rc, -p) + p * sc->c2 / 3 * gmx::power3(rc - rsw)
+ + p * sc->c3 / 4 * gmx::power4(rc - rsw);
+}
+
+static void potential_switch_constants(real rsw, real rc, switch_consts_t* sc)
+{
+ /* The switch function is 1 at rsw and 0 at rc.
+ * The derivative and second derivate are zero at both ends.
+ * rsw = max(r - r_switch, 0)
+ * sw = 1 + c3*rsw^3 + c4*rsw^4 + c5*rsw^5
+ * dsw = 3*c3*rsw^2 + 4*c4*rsw^3 + 5*c5*rsw^4
+ * force = force*dsw - potential*sw
+ * potential *= sw
+ */
+ sc->c3 = -10 / gmx::power3(rc - rsw);
+ sc->c4 = 15 / gmx::power4(rc - rsw);
+ sc->c5 = -6 / gmx::power5(rc - rsw);
+}
+
+
+interaction_const_t init_interaction_const(FILE* fp, const t_inputrec& ir, const gmx_mtop_t& mtop, bool systemHasNetCharge)
+{
+ interaction_const_t interactionConst;
+
+ interactionConst.coulombEwaldTables = std::make_unique<EwaldCorrectionTables>();
+ interactionConst.vdwEwaldTables = std::make_unique<EwaldCorrectionTables>();
+
+ /* Lennard-Jones */
+ interactionConst.vdwtype = ir.vdwtype;
+ interactionConst.vdw_modifier = ir.vdw_modifier;
+ interactionConst.reppow = mtop.ffparams.reppow;
+ interactionConst.rvdw = cutoff_inf(ir.rvdw);
+ interactionConst.rvdw_switch = ir.rvdw_switch;
+ interactionConst.ljpme_comb_rule = ir.ljpme_combination_rule;
+ interactionConst.useBuckingham = (mtop.ffparams.functype[0] == F_BHAM);
+ if (interactionConst.useBuckingham)
+ {
+ interactionConst.buckinghamBMax = calcBuckinghamBMax(fp, mtop);
+ }
+
+ initVdwEwaldParameters(fp, ir, &interactionConst);
+
+ clear_force_switch_constants(&interactionConst.dispersion_shift);
+ clear_force_switch_constants(&interactionConst.repulsion_shift);
+
+ switch (interactionConst.vdw_modifier)
+ {
+ case InteractionModifiers::PotShift:
+ /* Only shift the potential, don't touch the force */
+ interactionConst.dispersion_shift.cpot = -1.0 / gmx::power6(interactionConst.rvdw);
+ interactionConst.repulsion_shift.cpot = -1.0 / gmx::power12(interactionConst.rvdw);
+ break;
+ case InteractionModifiers::ForceSwitch:
+ /* Switch the force, switch and shift the potential */
+ force_switch_constants(
+ 6.0, interactionConst.rvdw_switch, interactionConst.rvdw, &interactionConst.dispersion_shift);
+ force_switch_constants(
+ 12.0, interactionConst.rvdw_switch, interactionConst.rvdw, &interactionConst.repulsion_shift);
+ break;
+ case InteractionModifiers::PotSwitch:
+ /* Switch the potential and force */
+ potential_switch_constants(
+ interactionConst.rvdw_switch, interactionConst.rvdw, &interactionConst.vdw_switch);
+ break;
+ case InteractionModifiers::None:
+ case InteractionModifiers::ExactCutoff:
+ /* Nothing to do here */
+ break;
+ default: gmx_incons("unimplemented potential modifier");
+ }
+
+ /* Electrostatics */
+ interactionConst.eeltype = ir.coulombtype;
+ interactionConst.coulomb_modifier = ir.coulomb_modifier;
+ interactionConst.rcoulomb = cutoff_inf(ir.rcoulomb);
+ interactionConst.rcoulomb_switch = ir.rcoulomb_switch;
+ interactionConst.epsilon_r = ir.epsilon_r;
+
+ /* Set the Coulomb energy conversion factor */
+ if (interactionConst.epsilon_r != 0)
+ {
+ interactionConst.epsfac = gmx::c_one4PiEps0 / interactionConst.epsilon_r;
+ }
+ else
+ {
+ /* eps = 0 is infinite dieletric: no Coulomb interactions */
+ interactionConst.epsfac = 0;
+ }
+
+ /* Reaction-field */
+ if (EEL_RF(interactionConst.eeltype))
+ {
+ GMX_RELEASE_ASSERT(interactionConst.eeltype != CoulombInteractionType::GRFNotused,
+ "GRF is no longer supported");
+ interactionConst.reactionFieldPermitivity = ir.epsilon_rf;
+ calc_rffac(fp,
+ interactionConst.epsilon_r,
+ interactionConst.reactionFieldPermitivity,
+ interactionConst.rcoulomb,
+ &interactionConst.reactionFieldCoefficient,
+ &interactionConst.reactionFieldShift);
+ }
+ else
+ {
+ /* For plain cut-off we might use the reaction-field kernels */
+ interactionConst.reactionFieldPermitivity = interactionConst.epsilon_r;
+ interactionConst.reactionFieldCoefficient = 0;
+ if (ir.coulomb_modifier == InteractionModifiers::PotShift)
+ {
+ interactionConst.reactionFieldShift = 1 / interactionConst.rcoulomb;
+ }
+ else
+ {
+ interactionConst.reactionFieldShift = 0;
+ }
+ }
+
+ initCoulombEwaldParameters(fp, ir, systemHasNetCharge, &interactionConst);
+
+ if (fp != nullptr)
+ {
+ real dispersion_shift;
+
+ dispersion_shift = interactionConst.dispersion_shift.cpot;
+ if (EVDW_PME(interactionConst.vdwtype))
+ {
+ dispersion_shift -= interactionConst.sh_lj_ewald;
+ }
+ fprintf(fp,
+ "Potential shift: LJ r^-12: %.3e r^-6: %.3e",
+ interactionConst.repulsion_shift.cpot,
+ dispersion_shift);
+
+ if (interactionConst.eeltype == CoulombInteractionType::Cut)
+ {
+ fprintf(fp, ", Coulomb %.e", -interactionConst.reactionFieldShift);
+ }
+ else if (EEL_PME(interactionConst.eeltype))
+ {
+ fprintf(fp, ", Ewald %.3e", -interactionConst.sh_ewald);
+ }
+ fprintf(fp, "\n");
+ }
+
+ if (ir.efep != FreeEnergyPerturbationType::No)
+ {
+ GMX_RELEASE_ASSERT(ir.fepvals, "ir.fepvals should be set wth free-energy");
+ interactionConst.softCoreParameters =
+ std::make_unique<interaction_const_t::SoftCoreParameters>(*ir.fepvals);
+ }
+
+ return interactionConst;
+}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MDTYPES_INTERACTION_CONST_H
#define GMX_MDTYPES_INTERACTION_CONST_H
+#include <cstdio>
+
#include <memory>
#include <vector>
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/alignedallocator.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
struct t_lambda;
+struct t_inputrec;
+struct gmx_mtop_t;
/* Used with force switching or a constant potential shift:
* rsw = max(r - r_switch, 0)
};
/* VdW */
- int vdwtype = evdwCUT;
- int vdw_modifier = eintmodNONE;
+ VanDerWaalsType vdwtype = VanDerWaalsType::Cut;
+ InteractionModifiers vdw_modifier = InteractionModifiers::None;
double reppow = 12;
real rvdw = 1;
real rvdw_switch = 0;
struct shift_consts_t dispersion_shift = { 0, 0, 0 };
struct shift_consts_t repulsion_shift = { 0, 0, 0 };
struct switch_consts_t vdw_switch = { 0, 0, 0 };
- gmx_bool useBuckingham = false;
+ bool useBuckingham = false;
real buckinghamBMax = 0;
/* type of electrostatics */
- int eeltype = eelCUT;
- int coulomb_modifier = eintmodNONE;
+ CoulombInteractionType eeltype = CoulombInteractionType::Cut;
+ InteractionModifiers coulomb_modifier = InteractionModifiers::None;
/* Coulomb */
real rcoulomb = 1;
real rcoulomb_switch = 0;
/* PME/Ewald */
- real ewaldcoeff_q = 0;
- real ewaldcoeff_lj = 0;
- int ljpme_comb_rule = eljpmeGEOM; /* LJ combination rule for the LJ PME mesh part */
- real sh_ewald = 0; /* -sh_ewald is added to the direct space potential */
- real sh_lj_ewald = 0; /* sh_lj_ewald is added to the correction potential */
+ real ewaldcoeff_q = 0;
+ real ewaldcoeff_lj = 0;
+ LongRangeVdW ljpme_comb_rule = LongRangeVdW::Geom; /* LJ combination rule for the LJ PME mesh part */
+ real sh_ewald = 0; /* -sh_ewald is added to the direct space potential */
+ real sh_lj_ewald = 0; /* sh_lj_ewald is added to the correction potential */
/* Dielectric constant resp. multiplication factor for charges */
real epsilon_r = 1;
real epsfac = 1;
/* Constants for reaction-field or plain cut-off */
- real epsilon_rf = 1;
- real k_rf = 0;
- real c_rf = 0;
+ //! Dielectric constant for reaction field beyond the cutoff distance
+ real reactionFieldPermitivity = 1;
+ //! Coefficient for reaction field; scales relation between epsilon_r and reactionFieldPermitivity
+ real reactionFieldCoefficient = 0;
+ //! Constant shift to reaction field Coulomb interaction to make potential an integral of force
+ real reactionFieldShift = 0;
// Coulomb Ewald correction table
std::unique_ptr<EwaldCorrectionTables> coulombEwaldTables;
std::unique_ptr<SoftCoreParameters> softCoreParameters;
};
+/*! \brief Construct interaction constants
+ *
+ * This data is used (particularly) by search and force code for
+ * short-range interactions. Many of these are constant for the whole
+ * simulation; some are constant only after PME tuning completes.
+ */
+interaction_const_t init_interaction_const(FILE* fp,
+ const t_inputrec& ir,
+ const gmx_mtop_t& mtop,
+ bool systemHasNetCharge);
+
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_MDTYPES_LOCALITY_H
#include "gromacs/utility/enumerationhelpers.h"
+#include "gromacs/utility/exceptions.h"
namespace gmx
{
{ "local", "non-local" }
};
+/*! \brief Convert atom locality to interaction locality.
+ *
+ * In the current implementation the this is straightforward conversion:
+ * local to local, non-local to non-local.
+ *
+ * \param[in] atomLocality Atom locality specifier
+ * \returns Interaction locality corresponding to the atom locality passed.
+ */
+static inline InteractionLocality atomToInteractionLocality(const AtomLocality atomLocality)
+{
+
+ /* determine interaction locality from atom locality */
+ if (atomLocality == AtomLocality::Local)
+ {
+ return InteractionLocality::Local;
+ }
+ else if (atomLocality == AtomLocality::NonLocal)
+ {
+ return InteractionLocality::NonLocal;
+ }
+ else
+ {
+ GMX_THROW(gmx::InconsistentInputError(
+ "Only Local and NonLocal atom locities can be converted to interaction locality."));
+ }
+}
+
} // namespace gmx
#endif // GMX_MDTYPES_LOCALITY_H
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "md_enums.h"
-const char* enum_name(int index, int max_index, const char* names[])
+#include "gromacs/utility/enumerationhelpers.h"
+
+const char* enum_name(int index, int max_index, const char* const names[])
{
if (index < 0 || index >= max_index)
{
}
}
-const char* yesno_names[BOOL_NR + 1] = { "no", "yes", nullptr };
-
-const char* ei_names[eiNR + 1] = { "md", "steep", "cg", "bd", "sd2 - removed",
- "nm", "l-bfgs", "tpi", "tpic", "sd",
- "md-vv", "md-vv-avek", "mimic", nullptr };
+const char* enumValueToString(IntegrationAlgorithm enumValue)
+{
+ static constexpr gmx::EnumerationArray<IntegrationAlgorithm, const char*> interationAlgorithmNames = {
+ "md", "steep", "cg", "bd", "sd2 - removed", "nm", "l-bfgs",
+ "tpi", "tpic", "sd", "md-vv", "md-vv-avek", "mimic"
+ };
+ return interationAlgorithmNames[enumValue];
+}
-const char* ecutscheme_names[ecutsNR + 1] = { "Verlet", "Group", nullptr };
+const char* enumValueToString(CoulombInteractionType enumValue)
+{
+ static constexpr gmx::EnumerationArray<CoulombInteractionType, const char*> coloumbTreatmentNames = {
+ "Cut-off",
+ "Reaction-Field",
+ "Generalized-Reaction-Field (unused)",
+ "PME",
+ "Ewald",
+ "P3M-AD",
+ "Poisson",
+ "Switch",
+ "Shift",
+ "User",
+ "Generalized-Born (unused)",
+ "Reaction-Field-nec (unsupported)",
+ "Encad-shift (unused)",
+ "PME-User",
+ "PME-Switch",
+ "PME-User-Switch",
+ "Reaction-Field-zero"
+ };
+ return coloumbTreatmentNames[enumValue];
+}
-const char* erefscaling_names[erscNR + 1] = { "No", "All", "COM", nullptr };
+const char* enumValueToString(EwaldGeometry enumValue)
+{
+ static constexpr gmx::EnumerationArray<EwaldGeometry, const char*> ewaldGeometryNames = {
+ "3d", "3dc"
+ };
+ return ewaldGeometryNames[enumValue];
+}
-const char* eel_names[eelNR + 1] = { "Cut-off",
- "Reaction-Field",
- "Generalized-Reaction-Field (unused)",
- "PME",
- "Ewald",
- "P3M-AD",
- "Poisson",
- "Switch",
- "Shift",
- "User",
- "Generalized-Born (unused)",
- "Reaction-Field-nec (unsupported)",
- "Encad-shift (unused)",
- "PME-User",
- "PME-Switch",
- "PME-User-Switch",
- "Reaction-Field-zero",
- nullptr };
+const char* enumValueToString(LongRangeVdW enumValue)
+{
+ static constexpr gmx::EnumerationArray<LongRangeVdW, const char*> longRangeVdWNames = {
+ "Geometric", "Lorentz-Berthelot"
+ };
+ return longRangeVdWNames[enumValue];
+}
-const char* eewg_names[eewgNR + 1] = { "3d", "3dc", nullptr };
+const char* enumValueToString(VanDerWaalsType enumValue)
+{
+ static constexpr gmx::EnumerationArray<VanDerWaalsType, const char*> vanDerWaalsTypeNames = {
+ "Cut-off", "Switch", "Shift", "User", "Encad-shift (unused)", "PME"
+ };
+ return vanDerWaalsTypeNames[enumValue];
+}
-const char* eljpme_names[eljpmeNR + 1] = { "Geometric", "Lorentz-Berthelot", nullptr };
+const char* enumValueToString(ConstraintAlgorithm enumValue)
+{
+ static constexpr gmx::EnumerationArray<ConstraintAlgorithm, const char*> constraintAlgorithmNames = {
+ "Lincs", "Shake"
+ };
+ return constraintAlgorithmNames[enumValue];
+}
-const char* evdw_names[evdwNR + 1] = { "Cut-off", "Switch", "Shift", "User", "Encad-shift (unused)",
- "PME", nullptr };
+const char* enumValueToString(InteractionModifiers enumValue)
+{
+ static constexpr gmx::EnumerationArray<InteractionModifiers, const char*> interactionModifierNames = {
+ "Potential-shift-Verlet", "Potential-shift", "None",
+ "Potential-switch", "Exact-cutoff", "Force-switch"
+ };
+ return interactionModifierNames[enumValue];
+}
-const char* econstr_names[econtNR + 1] = { "Lincs", "Shake", nullptr };
+const char* enumValueToString(TemperatureCoupling enumValue)
+{
+ static constexpr gmx::EnumerationArray<TemperatureCoupling, const char*> temperatureCouplingNames = {
+ "No", "Berendsen", "Nose-Hoover", "yes", "Andersen", "Andersen-massive", "V-rescale"
+ }; /* yes is alias for berendsen */
+ return temperatureCouplingNames[enumValue];
+}
-const char* eintmod_names[eintmodNR + 1] = {
- "Potential-shift-Verlet", "Potential-shift", "None", "Potential-switch",
- "Exact-cutoff", "Force-switch", nullptr
-};
+const char* enumValueToString(PressureCoupling enumValue)
+{
+ static constexpr gmx::EnumerationArray<PressureCoupling, const char*> pressureCouplingNames = {
+ "No", "Berendsen", "Parrinello-Rahman", "Isotropic", "MTTK", "C-rescale"
+ }; /* isotropic is alias for berendsen */
+ return pressureCouplingNames[enumValue];
+}
-const char* etcoupl_names[etcNR + 1] = {
- "No", "Berendsen", "Nose-Hoover", "yes", "Andersen", "Andersen-massive", "V-rescale", nullptr
-}; /* yes is alias for berendsen */
+const char* enumValueToString(Boolean enumValue)
+{
+ static constexpr gmx::EnumerationArray<Boolean, const char*> booleanNames = { "no", "yes" };
+ return booleanNames[enumValue];
+}
-const char* epcoupl_names[epcNR + 1] = { "No", "Berendsen", "Parrinello-Rahman",
- "Isotropic", "MTTK", "C-rescale",
- nullptr }; /* isotropic is alias for berendsen */
+const char* booleanValueToString(bool value)
+{
+ Boolean enumValue = value ? Boolean::Yes : Boolean::No;
+ return enumValueToString(enumValue);
+}
-const char* epcoupltype_names[epctNR + 1] = { "Isotropic", "Semiisotropic", "Anisotropic",
- "Surface-Tension", nullptr };
+const char* enumValueToString(RefCoordScaling enumValue)
+{
+ static constexpr gmx::EnumerationArray<RefCoordScaling, const char*> refCoordScalingNames = {
+ "No", "All", "COM"
+ };
+ return refCoordScalingNames[enumValue];
+}
-const char* edisre_names[edrNR + 1] = { "No", "Simple", "Ensemble", nullptr };
+const char* enumValueToString(CutoffScheme enumValue)
+{
+ static constexpr gmx::EnumerationArray<CutoffScheme, const char*> cutoffSchemeNames = {
+ "Verlet", "Group"
+ };
+ return cutoffSchemeNames[enumValue];
+}
-const char* edisreweighting_names[edrwNR + 1] = { "Conservative", "Equal", nullptr };
+const char* enumValueToString(PressureCouplingType enumValue)
+{
+ static constexpr gmx::EnumerationArray<PressureCouplingType, const char*> pressureCouplingTypeNames = {
+ "Isotropic", "Semiisotropic", "Anisotropic", "Surface-Tension"
+ };
+ return pressureCouplingTypeNames[enumValue];
+}
-const char* enbf_names[eNBF_NR + 1] = { "", "LJ", "Buckingham", nullptr };
+const char* enumValueToString(DistanceRestraintRefinement enumValue)
+{
+ static constexpr gmx::EnumerationArray<DistanceRestraintRefinement, const char*> distanceRestraintRefinementNames = {
+ "No", "Simple", "Ensemble"
+ };
+ return distanceRestraintRefinementNames[enumValue];
+}
-const char* ecomb_names[eCOMB_NR + 1] = { "", "Geometric", "Arithmetic", "GeomSigEps", nullptr };
+const char* enumValueToString(DistanceRestraintWeighting enumValue)
+{
+ static constexpr gmx::EnumerationArray<DistanceRestraintWeighting, const char*> distanceRestraintWeightingNames = {
+ "Conservative", "Equal"
+ };
+ return distanceRestraintWeightingNames[enumValue];
+}
-const char* esimtemp_names[esimtempNR + 1] = { "geometric", "exponential", "linear", nullptr };
+const char* enumValueToString(VanDerWaalsPotential enumValue)
+{
+ static constexpr gmx::EnumerationArray<VanDerWaalsPotential, const char*> vanDerWaalsPotentialNames = {
+ "None", "LJ", "Buckingham"
+ };
+ return vanDerWaalsPotentialNames[enumValue];
+}
-const char* efep_names[efepNR + 1] = { "no", "yes", "static", "slow-growth", "expanded", nullptr };
+const char* enumValueToString(CombinationRule enumValue)
+{
+ static constexpr gmx::EnumerationArray<CombinationRule, const char*> combinationRuleNames = {
+ "None", "Geometric", "Arithmetic", "GeomSigEps"
+ };
+ return combinationRuleNames[enumValue];
+}
-const char* efpt_names[efptNR + 1] = { "fep-lambdas", "mass-lambdas", "coul-lambdas",
- "vdw-lambdas", "bonded-lambdas", "restraint-lambdas",
- "temperature-lambdas", nullptr };
+const char* enumValueToString(SimulatedTempering enumValue)
+{
+ static constexpr gmx::EnumerationArray<SimulatedTempering, const char*> simulatedTemperingNames = {
+ "geometric", "exponential", "linear"
+ };
+ return simulatedTemperingNames[enumValue];
+}
-const char* efpt_singular_names[efptNR + 1] = { "fep-lambda", "mass-lambda",
- "coul-lambda", "vdw-lambda",
- "bonded-lambda", "restraint-lambda",
- "temperature-lambda", nullptr };
+const char* enumValueToString(FreeEnergyPerturbationType enumValue)
+{
+ static constexpr gmx::EnumerationArray<FreeEnergyPerturbationType, const char*> freeEnergyPerturbationTypeNames = {
+ "no", "yes", "static", "slow-growth", "expanded"
+ };
+ return freeEnergyPerturbationTypeNames[enumValue];
+}
-const char* edHdLPrintEnergy_names[edHdLPrintEnergyNR + 1] = { "no", "total", "potential", "yes", nullptr };
+const char* enumValueToString(FreeEnergyPerturbationCouplingType enumValue)
+{
+ static constexpr gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, const char*> freeEnergyPerturbationCouplingTypeNames = {
+ "fep-lambdas", "mass-lambdas", "coul-lambdas", "vdw-lambdas",
+ "bonded-lambdas", "restraint-lambdas", "temperature-lambdas"
+ };
+ return freeEnergyPerturbationCouplingTypeNames[enumValue];
+}
-const char* elamstats_names[elamstatsNR + 1] = {
- "no", "metropolis-transition", "barker-transition",
- "minvar", "wang-landau", "weighted-wang-landau",
- nullptr
-};
+const char* enumValueToStringSingular(FreeEnergyPerturbationCouplingType enumValue)
+{
+ static constexpr gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, const char*> freeEnergyPerturbationCouplingTypeNames = {
+ "fep-lambda", "mass-lambda", "coul-lambda", "vdw-lambda",
+ "bonded-lambda", "restraint-lambda", "temperature-lambda"
+ };
+ return freeEnergyPerturbationCouplingTypeNames[enumValue];
+}
-const char* elmcmove_names[elmcmoveNR + 1] = { "no", "metropolis", "barker",
- "gibbs", "metropolized-gibbs", nullptr };
+const char* enumValueToString(FreeEnergyPrintEnergy enumValue)
+{
+ static constexpr gmx::EnumerationArray<FreeEnergyPrintEnergy, const char*> freeEnergyPrintNames = {
+ "no", "total", "potential", "yes"
+ };
+ return freeEnergyPrintNames[enumValue];
+}
-const char* elmceq_names[elmceqNR + 1] = { "no", "yes",
- "wl-delta", "number-all-lambda",
- "number-steps", "number-samples",
- "count-ratio", nullptr };
+const char* enumValueToString(LambdaWeightCalculation enumValue)
+{
+ static constexpr gmx::EnumerationArray<LambdaWeightCalculation, const char*> lambdaWeightCalculationNames = {
+ "no", "metropolis-transition", "barker-transition",
+ "minvar", "wang-landau", "weighted-wang-landau"
+ };
+ return lambdaWeightCalculationNames[enumValue];
+}
-const char* separate_dhdl_file_names[esepdhdlfileNR + 1] = { "yes", "no", nullptr };
+const char* enumValueToString(LambdaMoveCalculation enumValue)
+{
+ static constexpr gmx::EnumerationArray<LambdaMoveCalculation, const char*> lambdaMoveCalculationNames = {
+ "no", "metropolis", "barker", "gibbs", "metropolized-gibbs"
+ };
+ return lambdaMoveCalculationNames[enumValue];
+}
-const char* dhdl_derivatives_names[edhdlderivativesNR + 1] = { "yes", "no", nullptr };
+const char* enumValueToString(LambdaWeightWillReachEquilibrium enumValue)
+{
+ static constexpr gmx::EnumerationArray<LambdaWeightWillReachEquilibrium, const char*> lambdaWeightEquilibriumNames = {
+ "no", "yes", "wl-delta", "number-all-lambda", "number-steps", "number-samples",
+ "count-ratio"
+ };
+ return lambdaWeightEquilibriumNames[enumValue];
+}
-const char* esol_names[esolNR + 1] = { "No", "SPC", "TIP4p", nullptr };
+const char* enumValueToString(SeparateDhdlFile enumValue)
+{
+ static constexpr gmx::EnumerationArray<SeparateDhdlFile, const char*> separateDhdlFileNames = {
+ "yes", "no"
+ };
+ return separateDhdlFileNames[enumValue];
+}
-const char* edispc_names[edispcNR + 1] = { "No", "EnerPres", "Ener",
- "AllEnerPres", "AllEner", nullptr };
+const char* enumValueToString(DhDlDerivativeCalculation enumValue)
+{
+ static constexpr gmx::EnumerationArray<DhDlDerivativeCalculation, const char*> dhdlDerivativeCalculationNames = {
+ "yes", "no"
+ };
+ return dhdlDerivativeCalculationNames[enumValue];
+}
-const char* ecm_names[ecmNR + 1] = { "Linear", "Angular", "None", "Linear-acceleration-correction", nullptr };
+const char* enumValueToString(SolventModel enumValue)
+{
+ static constexpr gmx::EnumerationArray<SolventModel, const char*> solventModelNames = {
+ "No", "SPC", "TIP4p"
+ };
+ return solventModelNames[enumValue];
+}
-const char* eann_names[eannNR + 1] = { "No", "Single", "Periodic", nullptr };
+const char* enumValueToString(DispersionCorrectionType enumValue)
+{
+ static constexpr gmx::EnumerationArray<DispersionCorrectionType, const char*> dispersionCorrectionTypeNames = {
+ "No", "EnerPres", "Ener", "AllEnerPres", "AllEner"
+ };
+ return dispersionCorrectionTypeNames[enumValue];
+}
-const char* ewt_names[ewtNR + 1] = { "9-3", "10-4", "table", "12-6", nullptr };
+const char* enumValueToString(ComRemovalAlgorithm enumValue)
+{
+ static constexpr gmx::EnumerationArray<ComRemovalAlgorithm, const char*> comRemovalAlgorithmNames = {
+ "Linear", "Angular", "None", "Linear-acceleration-correction"
+ };
+ return comRemovalAlgorithmNames[enumValue];
+}
-const char* epull_names[epullNR + 1] = { "umbrella", "constraint", "constant-force",
- "flat-bottom", "flat-bottom-high", "external-potential",
- nullptr };
+const char* enumValueToString(SimulatedAnnealing enumValue)
+{
+ static constexpr gmx::EnumerationArray<SimulatedAnnealing, const char*> simulatedAnnealingNames = {
+ "No", "Single", "Periodic"
+ };
+ return simulatedAnnealingNames[enumValue];
+}
-const char* epullg_names[epullgNR + 1] = { "distance", "direction", "cylinder",
- "direction-periodic", "direction-relative", "angle",
- "dihedral", "angle-axis", nullptr };
+const char* enumValueToString(WallType enumValue)
+{
+ static constexpr gmx::EnumerationArray<WallType, const char*> wallTypeNames = {
+ "9-3", "10-4", "table", "12-6"
+ };
+ return wallTypeNames[enumValue];
+}
-const char* erotg_names[erotgNR + 1] = { "iso", "iso-pf", "pm", "pm-pf", "rm",
- "rm-pf", "rm2", "rm2-pf", "flex", "flex-t",
- "flex2", "flex2-t", nullptr };
+const char* enumValueToString(PullingAlgorithm enumValue)
+{
+ static constexpr gmx::EnumerationArray<PullingAlgorithm, const char*> pullAlgorithmNames = {
+ "umbrella", "constraint", "constant-force",
+ "flat-bottom", "flat-bottom-high", "external-potential"
+ };
+ return pullAlgorithmNames[enumValue];
+}
-const char* erotg_fitnames[erotgFitNR + 1] = { "rmsd", "norm", "potential", nullptr };
+const char* enumValueToString(PullGroupGeometry enumValue)
+{
+ static constexpr gmx::EnumerationArray<PullGroupGeometry, const char*> pullGroupControlNames = {
+ "distance", "direction", "cylinder", "direction-periodic",
+ "direction-relative", "angle", "dihedral", "angle-axis"
+ };
+ return pullGroupControlNames[enumValue];
+}
-const char* eSwapTypes_names[eSwapTypesNR + 1] = { "no", "X", "Y", "Z", nullptr };
+const char* enumValueToString(EnforcedRotationGroupType enumValue)
+{
+ static constexpr gmx::EnumerationArray<EnforcedRotationGroupType, const char*> enforcedRotationGroupNames = {
+ "iso", "iso-pf", "pm", "pm-pf", "rm", "rm-pf",
+ "rm2", "rm2-pf", "flex", "flex-t", "flex2", "flex2-t"
+ };
+ return enforcedRotationGroupNames[enumValue];
+}
-const char* eSwapFixedGrp_names[eSwapFixedGrpNR + 1] = { "Split0", "Split1", "Solvent", nullptr };
+const char* enumValueToString(RotationGroupFitting enumValue)
+{
+ static constexpr gmx::EnumerationArray<RotationGroupFitting, const char*> rotationGroupFittingNames = {
+ "rmsd", "norm", "potential"
+ };
+ return rotationGroupFittingNames[enumValue];
+}
-const char* gmx_nblist_geometry_names[GMX_NBLIST_GEOMETRY_NR + 1] = {
- "Particle-Particle", "Water3-Particle", "Water3-Water3", "Water4-Particle",
- "Water4-Water4", "CG-CG", nullptr
-};
+const char* enumValueToString(SwapType enumValue)
+{
+ static constexpr gmx::EnumerationArray<SwapType, const char*> swapTypeNames = {
+ "no", "X", "Y", "Z"
+ };
+ return swapTypeNames[enumValue];
+}
-const char* gmx_nblist_interaction_names[GMX_NBLIST_INTERACTION_NR + 1] = { "Standard",
- "Free_Energy", nullptr };
+const char* enumValueToString(SwapGroupSplittingType enumValue)
+{
+ static constexpr gmx::EnumerationArray<SwapGroupSplittingType, const char*> swapGroupSplittingTypeNames = {
+ "Split0", "Split1", "Solvent"
+ };
+ return swapGroupSplittingTypeNames[enumValue];
+}
-const char* gmx_nbkernel_elec_names[GMX_NBKERNEL_ELEC_NR + 1] = {
- "None", "Coulomb", "Reaction-Field", "Cubic-Spline-Table", "Ewald", nullptr
-};
+const char* enumValueToString(NbkernelElecType enumValue)
+{
+ static constexpr gmx::EnumerationArray<NbkernelElecType, const char*> nbkernelElecTypeNames = {
+ "None", "Coulomb", "Reaction-Field", "Cubic-Spline-Table", "Ewald"
+ };
+ return nbkernelElecTypeNames[enumValue];
+}
-const char* gmx_nbkernel_vdw_names[GMX_NBKERNEL_VDW_NR + 1] = { "None", "Lennard-Jones",
- "Buckingham", "Cubic-Spline-Table",
- "LJEwald", nullptr };
+const char* enumValueToString(NbkernelVdwType enumValue)
+{
+ static constexpr gmx::EnumerationArray<NbkernelVdwType, const char*> nbkernelVdwTypeNames = {
+ "None", "Lennard-Jones", "Buckingham", "Cubic-Spline-Table", "LJEwald"
+ };
+ return nbkernelVdwTypeNames[enumValue];
+}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MDTYPES_MD_ENUMS_H
#define GMX_MDTYPES_MD_ENUMS_H
-#include "gromacs/utility/basedefinitions.h"
-
/*! \brief Return a string from a list of strings
*
* If index if within 0 .. max_index-1 returns the corresponding string
* \param[in] names The array
* \return the correct string or "no name defined"
*/
-const char* enum_name(int index, int max_index, const char* names[]);
+const char* enum_name(int index, int max_index, const char* const names[]);
+
+/*! \brief Enum for setting answer to yes or no
+ */
+enum class Boolean : int
+{
+ No,
+ Yes,
+ Count,
+ Default = No
+};
-//! Boolean strings no or yes
-extern const char* yesno_names[BOOL_NR + 1];
+//! Return name of boolean selection.
+const char* enumValueToString(Boolean enumValue);
+//! Return name of boolean selection for actual bool.
+const char* booleanValueToString(bool value);
//! \brief The two compartments for CompEL setups.
-enum eCompartment
+enum class Compartment : int
{
- eCompA,
- eCompB,
- eCompNR
+ A,
+ B,
+ Count
};
/*! \brief The channels that define with their COM the compartment boundaries in CompEL setups.
*
* In principle one could also use modified setups with more than two channels.
*/
-enum eChannel
+enum class Channel : int
{
- eChan0,
- eChan1,
- eChanNR
+ Zero,
+ One,
+ Count
};
/*! \brief Temperature coupling type
*
* yes is an alias for berendsen
+ *
+ * Note: Keep `Count` as the second-to-last entry, and `Default` as the last entry -
+ * this is needed to keep EnumerationWrapper, EnumerationArray and (de)serialization
+ * working.
*/
-enum
-{
- etcNO,
- etcBERENDSEN,
- etcNOSEHOOVER,
- etcYES,
- etcANDERSEN,
- etcANDERSENMASSIVE,
- etcVRESCALE,
- etcNR
-};
-//! Strings corresponding to temperatyre coupling types
-extern const char* etcoupl_names[etcNR + 1];
-//! Macro for selecting t coupling string
-#define ETCOUPLTYPE(e) enum_name(e, etcNR, etcoupl_names)
+enum class TemperatureCoupling : int
+{
+ No,
+ Berendsen,
+ NoseHoover,
+ Yes,
+ Andersen,
+ AndersenMassive,
+ VRescale,
+ Count,
+ Default = No
+};
+//! Return names of temperature coupling schemes
+const char* enumValueToString(TemperatureCoupling enumValue);
//! Return whether this is andersen coupling
-#define ETC_ANDERSEN(e) (((e) == etcANDERSENMASSIVE) || ((e) == etcANDERSEN))
+#define ETC_ANDERSEN(e) \
+ (((e) == TemperatureCoupling::AndersenMassive) || ((e) == TemperatureCoupling::Andersen))
/*! \brief Pressure coupling types
*
* isotropic is an alias for berendsen
+ *
+ * Note: Keep `Count` as the second-to-last entry, and `Default` as the last entry -
+ * this is needed to keep EnumerationWrapper, EnumerationArray and (de)serialization
+ * working.
*/
-enum
+enum class PressureCoupling : int
{
- epcNO,
- epcBERENDSEN,
- epcPARRINELLORAHMAN,
- epcISOTROPIC,
- epcMTTK,
- epcCRESCALE,
- epcNR
+ No,
+ Berendsen,
+ ParrinelloRahman,
+ Isotropic,
+ Mttk,
+ CRescale,
+ Count,
+ Default = No
};
-//! String corresponding to pressure coupling algorithm
-extern const char* epcoupl_names[epcNR + 1];
-//! Macro to return the correct pcoupling string
-#define EPCOUPLTYPE(e) enum_name(e, epcNR, epcoupl_names)
+//! Return names of pressure coupling schemes
+const char* enumValueToString(PressureCoupling enumValue);
//! Flat-bottom posres geometries
enum
};
//! Relative coordinate scaling type for position restraints.
-enum
+enum class RefCoordScaling : int
{
- erscNO,
- erscALL,
- erscCOM,
- erscNR
+ No,
+ All,
+ Com,
+ Count,
+ Default = No
};
-//! String corresponding to relativ coordinate scaling.
-extern const char* erefscaling_names[erscNR + 1];
-//! Macro to select correct coordinate scaling string.
-#define EREFSCALINGTYPE(e) enum_name(e, erscNR, erefscaling_names)
+
+//! String corresponding to relative coordinate scaling.
+const char* enumValueToString(RefCoordScaling enumValue);
//! Trotter decomposition extended variable parts.
enum
};
//! Pressure coupling type
-enum
+enum class PressureCouplingType : int
{
- epctISOTROPIC,
- epctSEMIISOTROPIC,
- epctANISOTROPIC,
- epctSURFACETENSION,
- epctNR
+ Isotropic,
+ SemiIsotropic,
+ Anisotropic,
+ SurfaceTension,
+ Count,
+ Default = Isotropic
};
//! String corresponding to pressure coupling type
-extern const char* epcoupltype_names[epctNR + 1];
-//! Macro to select the right string for pcoupl type
-#define EPCOUPLTYPETYPE(e) enum_name(e, epctNR, epcoupltype_names)
+const char* enumValueToString(PressureCouplingType enumValue);
//! \\brief Cutoff scheme
-enum
+enum class CutoffScheme : int
{
- ecutsVERLET,
- ecutsGROUP,
- ecutsNR
+ Verlet,
+ Group,
+ Count,
+ Default = Verlet
};
//! String corresponding to cutoff scheme
-extern const char* ecutscheme_names[ecutsNR + 1];
-//! Macro to select the right string for cutoff scheme
-#define ECUTSCHEME(e) enum_name(e, ecutsNR, ecutscheme_names)
+const char* enumValueToString(CutoffScheme enumValue);
/*! \brief Coulomb / VdW interaction modifiers.
*
* grompp replaces eintmodPOTSHIFT_VERLET_UNSUPPORTED by eintmodPOTSHIFT.
* Exactcutoff is only used by Reaction-field-zero, and is not user-selectable.
*/
-enum eintmod
+enum class InteractionModifiers : int
{
- eintmodPOTSHIFT_VERLET_UNSUPPORTED,
- eintmodPOTSHIFT,
- eintmodNONE,
- eintmodPOTSWITCH,
- eintmodEXACTCUTOFF,
- eintmodFORCESWITCH,
- eintmodNR
+ PotShiftVerletUnsupported,
+ PotShift,
+ None,
+ PotSwitch,
+ ExactCutoff,
+ ForceSwitch,
+ Count,
+ Default = PotShiftVerletUnsupported
};
//! String corresponding to interaction modifiers
-extern const char* eintmod_names[eintmodNR + 1];
-//! Macro to select the correct string for modifiers
-#define INTMODIFIER(e) enum_name(e, eintmodNR, eintmod_names)
+const char* enumValueToString(InteractionModifiers enumValue);
/*! \brief Cut-off treatment for Coulomb */
-enum
-{
- eelCUT,
- eelRF,
- eelGRF_NOTUSED,
- eelPME,
- eelEWALD,
- eelP3M_AD,
- eelPOISSON,
- eelSWITCH,
- eelSHIFT,
- eelUSER,
- eelGB_NOTUSED,
- eelRF_NEC_UNSUPPORTED,
- eelENCADSHIFT_NOTUSED,
- eelPMEUSER,
- eelPMESWITCH,
- eelPMEUSERSWITCH,
- eelRF_ZERO,
- eelNR
+enum class CoulombInteractionType : int
+{
+ Cut,
+ RF,
+ GRFNotused,
+ Pme,
+ Ewald,
+ P3mAD,
+ Poisson,
+ Switch,
+ Shift,
+ User,
+ GBNotused,
+ RFNecUnsupported,
+ EncadShiftNotused,
+ PmeUser,
+ PmeSwitch,
+ PmeUserSwitch,
+ RFZero,
+ Count,
+ Default = Cut
};
//! String corresponding to Coulomb treatment
-extern const char* eel_names[eelNR + 1];
-//! Macro for correct string for Coulomb treatment
-#define EELTYPE(e) enum_name(e, eelNR, eel_names)
+const char* enumValueToString(CoulombInteractionType enumValue);
//! Ewald geometry.
-enum
+enum class EwaldGeometry : int
{
- eewg3D,
- eewg3DC,
- eewgNR
+ ThreeD,
+ ThreeDC,
+ Count,
+ Default = ThreeD
};
//! String corresponding to Ewald geometry
-extern const char* eewg_names[eewgNR + 1];
+const char* enumValueToString(EwaldGeometry enumValue);
//! Macro telling us whether we use reaction field
-#define EEL_RF(e) \
- ((e) == eelRF || (e) == eelGRF_NOTUSED || (e) == eelRF_NEC_UNSUPPORTED || (e) == eelRF_ZERO)
+#define EEL_RF(e) \
+ ((e) == CoulombInteractionType::RF || (e) == CoulombInteractionType::GRFNotused \
+ || (e) == CoulombInteractionType::RFNecUnsupported || (e) == CoulombInteractionType::RFZero)
//! Macro telling us whether we use PME
-#define EEL_PME(e) \
- ((e) == eelPME || (e) == eelPMESWITCH || (e) == eelPMEUSER || (e) == eelPMEUSERSWITCH || (e) == eelP3M_AD)
+#define EEL_PME(e) \
+ ((e) == CoulombInteractionType::Pme || (e) == CoulombInteractionType::PmeSwitch \
+ || (e) == CoulombInteractionType::PmeUser || (e) == CoulombInteractionType::PmeUserSwitch \
+ || (e) == CoulombInteractionType::P3mAD)
//! Macro telling us whether we use PME or full Ewald
-#define EEL_PME_EWALD(e) (EEL_PME(e) || (e) == eelEWALD)
+#define EEL_PME_EWALD(e) (EEL_PME(e) || (e) == CoulombInteractionType::Ewald)
//! Macro telling us whether we use full electrostatics of any sort
-#define EEL_FULL(e) (EEL_PME_EWALD(e) || (e) == eelPOISSON)
+#define EEL_FULL(e) (EEL_PME_EWALD(e) || (e) == CoulombInteractionType::Poisson)
//! Macro telling us whether we use user defined electrostatics
-#define EEL_USER(e) ((e) == eelUSER || (e) == eelPMEUSER || (e) == (eelPMEUSERSWITCH))
+#define EEL_USER(e) \
+ ((e) == CoulombInteractionType::User || (e) == CoulombInteractionType::PmeUser \
+ || (e) == (CoulombInteractionType::PmeUserSwitch))
//! Van der Waals interaction treatment
-enum
+enum class VanDerWaalsType : int
{
- evdwCUT,
- evdwSWITCH,
- evdwSHIFT,
- evdwUSER,
- evdwENCADSHIFT_UNUSED,
- evdwPME,
- evdwNR
+ Cut,
+ Switch,
+ Shift,
+ User,
+ EncadShiftUnused,
+ Pme,
+ Count,
+ Default = Cut
};
//! String corresponding to Van der Waals treatment
-extern const char* evdw_names[evdwNR + 1];
-//! Macro for selecting correct string for VdW treatment
-#define EVDWTYPE(e) enum_name(e, evdwNR, evdw_names)
+const char* enumValueToString(VanDerWaalsType enumValue);
//! Type of long-range VdW treatment of combination rules
-enum
+enum class LongRangeVdW : int
{
- eljpmeGEOM,
- eljpmeLB,
- eljpmeNR
+ Geom,
+ LB,
+ Count,
+ Default = Geom
};
//! String for LJPME combination rule treatment
-extern const char* eljpme_names[eljpmeNR + 1];
-//! Macro for correct LJPME comb rule name
-#define ELJPMECOMBNAMES(e) enum_name(e, eljpmeNR, eljpme_names)
+const char* enumValueToString(LongRangeVdW enumValue);
//! Macro to tell us whether we use LJPME
-#define EVDW_PME(e) ((e) == evdwPME)
+#define EVDW_PME(e) ((e) == VanDerWaalsType::Pme)
/*! \brief Integrator algorithm
*
* eiVVAK uses 1/2*(KE(t-dt/2)+KE(t+dt/2)) as the kinetic energy,
* and the half step kinetic energy for temperature control
*/
-enum
-{
- eiMD,
- eiSteep,
- eiCG,
- eiBD,
- eiSD2_REMOVED,
- eiNM,
- eiLBFGS,
- eiTPI,
- eiTPIC,
- eiSD1,
- eiVV,
- eiVVAK,
- eiMimic,
- eiNR
+enum class IntegrationAlgorithm : int
+{
+ MD,
+ Steep,
+ CG,
+ BD,
+ SD2Removed,
+ NM,
+ LBFGS,
+ TPI,
+ TPIC,
+ SD1,
+ VV,
+ VVAK,
+ Mimic,
+ Count,
+ Default = MD
};
//! Name of the integrator algorithm
-extern const char* ei_names[eiNR + 1];
-//! Macro returning integrator string
-#define EI(e) enum_name(e, eiNR, ei_names)
+const char* enumValueToString(IntegrationAlgorithm enumValue);
//! Do we use MiMiC QM/MM?
-#define EI_MIMIC(e) ((e) == eiMimic)
+#define EI_MIMIC(e) ((e) == IntegrationAlgorithm::Mimic)
//! Do we use velocity Verlet
-#define EI_VV(e) ((e) == eiVV || (e) == eiVVAK)
+#define EI_VV(e) ((e) == IntegrationAlgorithm::VV || (e) == IntegrationAlgorithm::VVAK)
//! Do we use molecular dynamics
-#define EI_MD(e) ((e) == eiMD || EI_VV(e) || EI_MIMIC(e))
+#define EI_MD(e) ((e) == IntegrationAlgorithm::MD || EI_VV(e) || EI_MIMIC(e))
//! Do we use stochastic dynamics
-#define EI_SD(e) ((e) == eiSD1)
+#define EI_SD(e) ((e) == IntegrationAlgorithm::SD1)
//! Do we use any stochastic integrator
-#define EI_RANDOM(e) (EI_SD(e) || (e) == eiBD)
+#define EI_RANDOM(e) (EI_SD(e) || (e) == IntegrationAlgorithm::BD)
/*above integrators may not conserve momenta*/
//! Do we use any type of dynamics
#define EI_DYNAMICS(e) (EI_MD(e) || EI_RANDOM(e))
//! Or do we use minimization
-#define EI_ENERGY_MINIMIZATION(e) ((e) == eiSteep || (e) == eiCG || (e) == eiLBFGS)
+#define EI_ENERGY_MINIMIZATION(e) \
+ ((e) == IntegrationAlgorithm::Steep || (e) == IntegrationAlgorithm::CG \
+ || (e) == IntegrationAlgorithm::LBFGS)
//! Do we apply test particle insertion
-#define EI_TPI(e) ((e) == eiTPI || (e) == eiTPIC)
+#define EI_TPI(e) ((e) == IntegrationAlgorithm::TPI || (e) == IntegrationAlgorithm::TPIC)
//! Do we deal with particle velocities
#define EI_STATE_VELOCITY(e) (EI_MD(e) || EI_SD(e))
//! Constraint algorithm
-enum
+enum class ConstraintAlgorithm : int
{
- econtLINCS,
- econtSHAKE,
- econtNR
+ Lincs,
+ Shake,
+ Count,
+ Default = Lincs
};
//! String corresponding to constraint algorithm
-extern const char* econstr_names[econtNR + 1];
-//! Macro to select the correct string
-#define ECONSTRTYPE(e) enum_name(e, econtNR, econstr_names)
+const char* enumValueToString(ConstraintAlgorithm enumValue);
//! Distance restraint refinement algorithm
-enum
+enum class DistanceRestraintRefinement : int
{
- edrNone,
- edrSimple,
- edrEnsemble,
- edrNR
+ None,
+ Simple,
+ Ensemble,
+ Count,
+ Default = None
};
//! String corresponding to distance restraint algorithm
-extern const char* edisre_names[edrNR + 1];
-//! Macro to select the right disre algorithm string
-#define EDISRETYPE(e) enum_name(e, edrNR, edisre_names)
+const char* enumValueToString(DistanceRestraintRefinement enumValue);
//! Distance restraints weighting type
-enum
+enum class DistanceRestraintWeighting : int
{
- edrwConservative,
- edrwEqual,
- edrwNR
+ Conservative,
+ Equal,
+ Count,
+ Default = Conservative
};
//! String corresponding to distance restraint weighting
-extern const char* edisreweighting_names[edrwNR + 1];
-//! Macro corresponding to dr weighting
-#define EDISREWEIGHTING(e) enum_name(e, edrwNR, edisreweighting_names)
+const char* enumValueToString(DistanceRestraintWeighting enumValue);
//! Combination rule algorithm.
-enum
+enum class CombinationRule : int
{
- eCOMB_NONE,
- eCOMB_GEOMETRIC,
- eCOMB_ARITHMETIC,
- eCOMB_GEOM_SIG_EPS,
- eCOMB_NR
+ None,
+ Geometric,
+ Arithmetic,
+ GeomSigEps,
+ Count,
+ Default = Geometric
};
//! String for combination rule algorithm
-extern const char* ecomb_names[eCOMB_NR + 1];
-//! Macro to select the comb rule string
-#define ECOMBNAME(e) enum_name(e, eCOMB_NR, ecomb_names)
+const char* enumValueToString(CombinationRule enumValue);
//! Van der Waals potential.
-enum
+enum class VanDerWaalsPotential : int
{
- eNBF_NONE,
- eNBF_LJ,
- eNBF_BHAM,
- eNBF_NR
+ None,
+ LJ,
+ Buckingham,
+ Count,
+ Default = LJ
};
//! String corresponding to Van der Waals potential
-extern const char* enbf_names[eNBF_NR + 1];
-//! Macro for correct VdW potential string
-#define ENBFNAME(e) enum_name(e, eNBF_NR, enbf_names)
+const char* enumValueToString(VanDerWaalsPotential enumValue);
//! Simulated tempering methods.
-enum
+enum class SimulatedTempering : int
{
- esimtempGEOMETRIC,
- esimtempEXPONENTIAL,
- esimtempLINEAR,
- esimtempNR
+ Geometric,
+ Exponential,
+ Linear,
+ Count,
+ Default = Geometric
};
//! String corresponding to simulated tempering
-extern const char* esimtemp_names[esimtempNR + 1];
-//! Macro for correct tempering string
-#define ESIMTEMP(e) enum_name(e, esimtempNR, esimtemp_names)
+const char* enumValueToString(SimulatedTempering enumValue);
/*! \brief Free energy perturbation type
- *
- * efepNO, there are no evaluations at other states.
- * efepYES, treated equivalently to efepSTATIC.
- * efepSTATIC, then lambdas do not change during the simulation.
- * efepSLOWGROWTH, then the states change monotonically
- * throughout the simulation.
- * efepEXPANDED, then expanded ensemble simulations are occuring.
*/
-enum
-{
- efepNO,
- efepYES,
- efepSTATIC,
- efepSLOWGROWTH,
- efepEXPANDED,
- efepNR
+enum class FreeEnergyPerturbationType : int
+{
+ //! there are no evaluations at other states
+ No,
+ //! treated equivalently to Static
+ Yes,
+ //! then lambdas do not change during the simulation
+ Static,
+ //! then the states change monotonically throughout the simulation
+ SlowGrowth,
+ //! then expanded ensemble simulations are occuring
+ Expanded,
+ Count,
+ Default = No
};
//! String corresponding to FEP type.
-extern const char* efep_names[efepNR + 1];
-//! Macro corresponding to FEP string.
-#define EFEPTYPE(e) enum_name(e, efepNR, efep_names)
+const char* enumValueToString(FreeEnergyPerturbationType enumValue);
//! Free energy pertubation coupling types.
-enum
-{
- efptFEP,
- efptMASS,
- efptCOUL,
- efptVDW,
- efptBONDED,
- efptRESTRAINT,
- efptTEMPERATURE,
- efptNR
+enum class FreeEnergyPerturbationCouplingType : int
+{
+ Fep,
+ Mass,
+ Coul,
+ Vdw,
+ Bonded,
+ Restraint,
+ Temperature,
+ Count,
+ Default = Fep
};
//! String for FEP coupling type
-extern const char* efpt_names[efptNR + 1];
-//! Long names for FEP coupling type
-extern const char* efpt_singular_names[efptNR + 1];
+const char* enumValueToString(FreeEnergyPerturbationCouplingType enumValue);
+//! String for FEP coupling type, singular mention.
+const char* enumValueToStringSingular(FreeEnergyPerturbationCouplingType enumValue);
/*! \brief What to print for free energy calculations
*
* Printing the energy to the free energy dhdl file.
- * YES is an alias to TOTAL, and
+ * Yes is an alias to Total, and
* will be converted in readir, so we never have to account for it in code.
*/
-enum
+enum class FreeEnergyPrintEnergy : int
{
- edHdLPrintEnergyNO,
- edHdLPrintEnergyTOTAL,
- edHdLPrintEnergyPOTENTIAL,
- edHdLPrintEnergyYES,
- edHdLPrintEnergyNR
+ No,
+ Total,
+ Potential,
+ Yes,
+ Count,
+ Default = No
};
//! String corresponding to printing of free energy
-extern const char* edHdLPrintEnergy_names[edHdLPrintEnergyNR + 1];
+const char* enumValueToString(FreeEnergyPrintEnergy enumValue);
/*! \brief How the lambda weights are calculated
- *
- * elamstatsMETROPOLIS - using the metropolis criteria
- * elamstatsBARKER - using the Barker critera for transition weights,
- * also called unoptimized Bennett
- * elamstatsMINVAR - using Barker + minimum variance for weights
- * elamstatsWL - Wang-Landu (using visitation counts)
- * elamstatsWWL - Weighted Wang-Landau (using optimized Gibbs
- * weighted visitation counts)
*/
-enum
-{
- elamstatsNO,
- elamstatsMETROPOLIS,
- elamstatsBARKER,
- elamstatsMINVAR,
- elamstatsWL,
- elamstatsWWL,
- elamstatsNR
+enum class LambdaWeightCalculation : int
+{
+ //! don't calculate
+ No,
+ //! using the metropolis criteria
+ Metropolis,
+ //! using the Barker critera for transition weights, also called unoptimized Bennett
+ Barker,
+ //! using Barker + minimum variance for weights
+ Minvar,
+ //! Wang-Landu (using visitation counts)
+ WL,
+ //! Weighted Wang-Landau (using optimized Gibbs weighted visitation counts)
+ WWL,
+ Count,
+ Default = No
};
//! String corresponding to lambda weights
-extern const char* elamstats_names[elamstatsNR + 1];
+const char* enumValueToString(LambdaWeightCalculation enumValue);
//! Macro telling us whether we use expanded ensemble
-#define ELAMSTATS_EXPANDED(e) ((e) > elamstatsNO)
+#define ELAMSTATS_EXPANDED(e) ((e) > LambdaWeightCalculation::No)
//! Macro telling us whether we use some kind of Wang-Landau
-#define EWL(e) ((e) == elamstatsWL || (e) == elamstatsWWL)
+#define EWL(e) ((e) == LambdaWeightCalculation::WL || (e) == LambdaWeightCalculation::WWL)
/*! \brief How moves in lambda are calculated
- *
- * elmovemcMETROPOLIS - using the Metropolis criteria, and 50% up and down
- * elmovemcBARKER - using the Barker criteria, and 50% up and down
- * elmovemcGIBBS - computing the transition using the marginalized
- * probabilities of the lambdas
- * elmovemcMETGIBBS - computing the transition using the metropolized
- * version of Gibbs (Monte Carlo Strategies in
- * Scientific computing, Liu, p. 134)
*/
-enum
-{
- elmcmoveNO,
- elmcmoveMETROPOLIS,
- elmcmoveBARKER,
- elmcmoveGIBBS,
- elmcmoveMETGIBBS,
- elmcmoveNR
+enum class LambdaMoveCalculation : int
+{
+ //! don't calculate move
+ No,
+ //! using the Metropolis criteria, and 50% up and down
+ Metropolis,
+ //! using the Barker criteria, and 50% up and down
+ Barker,
+ //! computing the transition using the marginalized probabilities of the lambdas
+ Gibbs,
+ /*! \brief
+ * using the metropolized version of Gibbs
+ *
+ * Monte Carlo Strategies in Scientific computing, Liu, p. 134
+ */
+ MetropolisGibbs,
+ Count,
+ Default = No
};
//! String corresponding to lambda moves
-extern const char* elmcmove_names[elmcmoveNR + 1];
+const char* enumValueToString(LambdaMoveCalculation enumValue);
/*! \brief How we decide whether weights have reached equilibrium
- *
- * elmceqNO - never stop, weights keep going
- * elmceqYES - fix the weights from the beginning; no movement
- * elmceqWLDELTA - stop when the WL-delta falls below a certain level
- * elmceqNUMATLAM - stop when we have a certain number of samples at
- * every step
- * elmceqSTEPS - stop when we've run a certain total number of steps
- * elmceqSAMPLES - stop when we've run a certain total number of samples
- * elmceqRATIO - stop when the ratio of samples (lowest to highest)
- * is sufficiently large
*/
-enum
-{
- elmceqNO,
- elmceqYES,
- elmceqWLDELTA,
- elmceqNUMATLAM,
- elmceqSTEPS,
- elmceqSAMPLES,
- elmceqRATIO,
- elmceqNR
+enum class LambdaWeightWillReachEquilibrium : int
+{
+ //! never stop, weights keep going
+ No,
+ //! fix the weights from the beginning; no movement
+ Yes,
+ //! stop when the WL-delta falls below a certain level
+ WLDelta,
+ //! stop when we have a certain number of samples at every step
+ NumAtLambda,
+ //! stop when we've run a certain total number of steps
+ Steps,
+ //! stop when we've run a certain total number of samples
+ Samples,
+ //! stop when the ratio of samples (lowest to highest) is sufficiently large
+ Ratio,
+ Count,
+ Default = No
};
//! String corresponding to equilibrium algorithm
-extern const char* elmceq_names[elmceqNR + 1];
+const char* enumValueToString(LambdaWeightWillReachEquilibrium enumValue);
/*! \brief separate_dhdl_file selection
*
* NOTE: YES is the first one. Do NOT interpret this one as a gmx_bool
+ * Why was this done this way, just .........
*/
-enum
+enum class SeparateDhdlFile : int
{
- esepdhdlfileYES,
- esepdhdlfileNO,
- esepdhdlfileNR
+ Yes,
+ No,
+ Count,
+ Default = Yes
};
//! String corresponding to separate DHDL file selection
-extern const char* separate_dhdl_file_names[esepdhdlfileNR + 1];
-//! Monster macro for DHDL file selection
-#define SEPDHDLFILETYPE(e) enum_name(e, esepdhdlfileNR, separate_dhdl_file_names)
+const char* enumValueToString(SeparateDhdlFile enumValue);
/*! \brief dhdl_derivatives selection \
*
* NOTE: YES is the first one. Do NOT interpret this one as a gmx_bool
+ * Why was this done this way, just .........
*/
-enum
+enum class DhDlDerivativeCalculation : int
{
- edhdlderivativesYES,
- edhdlderivativesNO,
- edhdlderivativesNR
+ Yes,
+ No,
+ Count,
+ Default = Yes
};
//! String for DHDL derivatives
-extern const char* dhdl_derivatives_names[edhdlderivativesNR + 1];
-//! YAMM (Yet another monster macro)
-#define DHDLDERIVATIVESTYPE(e) enum_name(e, edhdlderivativesNR, dhdl_derivatives_names)
+const char* enumValueToString(DhDlDerivativeCalculation enumValue);
/*! \brief Solvent model
*
* Distinguishes classical water types with 3 or 4 particles
*/
-enum
+enum class SolventModel : int
{
- esolNO,
- esolSPC,
- esolTIP4P,
- esolNR
+ No,
+ Spc,
+ Tip4p,
+ Count,
+ Default = Spc
};
//! String corresponding to solvent type
-extern const char* esol_names[esolNR + 1];
-//! Macro lest we print the wrong solvent model string
-#define ESOLTYPE(e) enum_name(e, esolNR, esol_names)
+const char* enumValueToString(SolventModel enumValue);
//! Dispersion correction.
-enum
+enum class DispersionCorrectionType : int
{
- edispcNO,
- edispcEnerPres,
- edispcEner,
- edispcAllEnerPres,
- edispcAllEner,
- edispcNR
+ No,
+ EnerPres,
+ Ener,
+ AllEnerPres,
+ AllEner,
+ Count,
+ Default = No
};
//! String corresponding to dispersion corrections
-extern const char* edispc_names[edispcNR + 1];
-//! Macro for dispcorr string
-#define EDISPCORR(e) enum_name(e, edispcNR, edispc_names)
+const char* enumValueToString(DispersionCorrectionType enumValue);
//! Center of mass motion removal algorithm.
-enum
+enum class ComRemovalAlgorithm : int
{
- ecmLINEAR,
- ecmANGULAR,
- ecmNO,
- ecmLINEAR_ACCELERATION_CORRECTION,
- ecmNR
+ Linear,
+ Angular,
+ No,
+ LinearAccelerationCorrection,
+ Count,
+ Default = Linear
};
//! String corresponding to COM removal
-extern const char* ecm_names[ecmNR + 1];
-//! Macro for COM removal string
-#define ECOM(e) enum_name(e, ecmNR, ecm_names)
+const char* enumValueToString(ComRemovalAlgorithm enumValue);
//! Algorithm for simulated annealing.
-enum
+enum class SimulatedAnnealing : int
{
- eannNO,
- eannSINGLE,
- eannPERIODIC,
- eannNR
+ No,
+ Single,
+ Periodic,
+ Count,
+ Default = No
};
//! String for simulated annealing
-extern const char* eann_names[eannNR + 1];
-//! And macro for simulated annealing string
-#define EANNEAL(e) enum_name(e, eannNR, eann_names)
+const char* enumValueToString(SimulatedAnnealing enumValue);
//! Wall types.
-enum
+enum class WallType : int
{
- ewt93,
- ewt104,
- ewtTABLE,
- ewt126,
- ewtNR
+ NineThree,
+ TenFour,
+ Table,
+ TwelveSix,
+ Count,
+ Default = NineThree
};
//! String corresponding to wall type
-extern const char* ewt_names[ewtNR + 1];
-//! Macro for wall type string
-#define EWALLTYPE(e) enum_name(e, ewtNR, ewt_names)
+const char* enumValueToString(WallType enumValue);
//! Pulling algorithm.
-enum
+enum class PullingAlgorithm : int
{
- epullUMBRELLA,
- epullCONSTRAINT,
- epullCONST_F,
- epullFLATBOTTOM,
- epullFLATBOTTOMHIGH,
- epullEXTERNAL,
- epullNR
+ Umbrella,
+ Constraint,
+ ConstantForce,
+ FlatBottom,
+ FlatBottomHigh,
+ External,
+ Count,
+ Default = Umbrella
};
//! String for pulling algorithm
-extern const char* epull_names[epullNR + 1];
-//! Macro for pulling string
-#define EPULLTYPE(e) enum_name(e, epullNR, epull_names)
+const char* enumValueToString(PullingAlgorithm enumValue);
//! Control of pull groups
-enum
-{
- epullgDIST,
- epullgDIR,
- epullgCYL,
- epullgDIRPBC,
- epullgDIRRELATIVE,
- epullgANGLE,
- epullgDIHEDRAL,
- epullgANGLEAXIS,
- epullgNR
+enum class PullGroupGeometry : int
+{
+ Distance,
+ Direction,
+ Cylinder,
+ DirectionPBC,
+ DirectionRelative,
+ Angle,
+ Dihedral,
+ AngleAxis,
+ Count,
+ Default = Distance
};
//! String for pull groups
-extern const char* epullg_names[epullgNR + 1];
-//! Macro for pull group string
-#define EPULLGEOM(e) enum_name(e, epullgNR, epullg_names)
+const char* enumValueToString(PullGroupGeometry enumValue);
//! Enforced rotation groups.
-enum
-{
- erotgISO,
- erotgISOPF,
- erotgPM,
- erotgPMPF,
- erotgRM,
- erotgRMPF,
- erotgRM2,
- erotgRM2PF,
- erotgFLEX,
- erotgFLEXT,
- erotgFLEX2,
- erotgFLEX2T,
- erotgNR
+enum class EnforcedRotationGroupType : int
+{
+ Iso,
+ Isopf,
+ Pm,
+ Pmpf,
+ Rm,
+ Rmpf,
+ Rm2,
+ Rm2pf,
+ Flex,
+ Flext,
+ Flex2,
+ Flex2t,
+ Count,
+ Default = Iso
};
//! Rotation group names
-extern const char* erotg_names[erotgNR + 1];
-//! Macro for rot group names
-#define EROTGEOM(e) enum_name(e, erotgNR, erotg_names)
+const char* enumValueToString(EnforcedRotationGroupType enumValue);
//! String for rotation group origin names
-extern const char* erotg_originnames[erotgNR + 1];
-//! Macro for rot group origin names
-#define EROTORIGIN(e) enum_name(e, erotgOriginNR, erotg_originnames)
+const char* enumValueToLongString(EnforcedRotationGroupType enumValue);
//! Rotation group fitting type
-enum
+enum class RotationGroupFitting : int
{
- erotgFitRMSD,
- erotgFitNORM,
- erotgFitPOT,
- erotgFitNR
+ Rmsd,
+ Norm,
+ Pot,
+ Count,
+ Default = Rmsd
};
//! String corresponding to rotation group fitting
-extern const char* erotg_fitnames[erotgFitNR + 1];
-//! Macro for rot group fit names
-#define EROTFIT(e) enum_name(e, erotgFitNR, erotg_fitnames)
+const char* enumValueToString(RotationGroupFitting enumValue);
/*! \brief Direction along which ion/water swaps happen
*
* Part of "Computational Electrophysiology" (CompEL) setups
*/
-enum eSwaptype
+enum class SwapType : int
{
- eswapNO,
- eswapX,
- eswapY,
- eswapZ,
- eSwapTypesNR
+ No,
+ X,
+ Y,
+ Z,
+ Count,
+ Default = No
};
//! Names for swapping
-extern const char* eSwapTypes_names[eSwapTypesNR + 1];
-//! Macro for swapping string
-#define ESWAPTYPE(e) enum_name(e, eSwapTypesNR, eSwapTypes_names)
+const char* enumValueToString(SwapType enumValue);
/*! \brief Swap group splitting type
*
* These are just the fixed groups we need for any setup. In t_swap's grp
* entry after that follows the variable number of swap groups.
*/
-enum
+enum class SwapGroupSplittingType : int
{
- eGrpSplit0,
- eGrpSplit1,
- eGrpSolvent,
- eSwapFixedGrpNR
+ Split0,
+ Split1,
+ Solvent,
+ Count,
+ Default = Solvent
};
//! String for swap group splitting
-extern const char* eSwapFixedGrp_names[eSwapFixedGrpNR + 1];
-
-/*! \brief Neighborlist geometry type.
- *
- * Kernels will compute interactions between two particles,
- * 3-center water, 4-center water or coarse-grained beads.
- */
-enum gmx_nblist_kernel_geometry
-{
- GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE,
- GMX_NBLIST_GEOMETRY_WATER3_PARTICLE,
- GMX_NBLIST_GEOMETRY_WATER3_WATER3,
- GMX_NBLIST_GEOMETRY_WATER4_PARTICLE,
- GMX_NBLIST_GEOMETRY_WATER4_WATER4,
- GMX_NBLIST_GEOMETRY_CG_CG,
- GMX_NBLIST_GEOMETRY_NR
-};
-//! String corresponding to nblist geometry names
-extern const char* gmx_nblist_geometry_names[GMX_NBLIST_GEOMETRY_NR + 1];
+const char* enumValueToString(SwapGroupSplittingType enumValue);
/*! \brief Types of electrostatics calculations
*
* Note that these do NOT necessarily correspond to the user selections
* in the MDP file; many interactions for instance map to tabulated kernels.
*/
-enum gmx_nbkernel_elec
+enum class NbkernelElecType : int
{
- GMX_NBKERNEL_ELEC_NONE,
- GMX_NBKERNEL_ELEC_COULOMB,
- GMX_NBKERNEL_ELEC_REACTIONFIELD,
- GMX_NBKERNEL_ELEC_CUBICSPLINETABLE,
- GMX_NBKERNEL_ELEC_EWALD,
- GMX_NBKERNEL_ELEC_NR
+ None,
+ Coulomb,
+ ReactionField,
+ CubicSplineTable,
+ Ewald,
+ Count,
+ Default = None
};
//! String corresponding to electrostatics kernels
-extern const char* gmx_nbkernel_elec_names[GMX_NBKERNEL_ELEC_NR + 1];
+const char* enumValueToString(NbkernelElecType enumValue);
/*! \brief Types of vdw calculations available
*
* Note that these do NOT necessarily correspond to the user selections
* in the MDP file; many interactions for instance map to tabulated kernels.
*/
-enum gmx_nbkernel_vdw
+enum class NbkernelVdwType : int
{
- GMX_NBKERNEL_VDW_NONE,
- GMX_NBKERNEL_VDW_LENNARDJONES,
- GMX_NBKERNEL_VDW_BUCKINGHAM,
- GMX_NBKERNEL_VDW_CUBICSPLINETABLE,
- GMX_NBKERNEL_VDW_LJEWALD,
- GMX_NBKERNEL_VDW_NR
+ None,
+ LennardJones,
+ Buckingham,
+ CubicSplineTable,
+ LJEwald,
+ Count,
+ Default = None
};
//! String corresponding to VdW kernels
-extern const char* gmx_nbkernel_vdw_names[GMX_NBKERNEL_VDW_NR + 1];
-
-//! \brief Types of interactions inside the neighborlist
-enum gmx_nblist_interaction_type
-{
- GMX_NBLIST_INTERACTION_STANDARD,
- GMX_NBLIST_INTERACTION_FREE_ENERGY,
- GMX_NBLIST_INTERACTION_NR
-};
-//! String corresponding to interactions in neighborlist code
-extern const char* gmx_nblist_interaction_names[GMX_NBLIST_INTERACTION_NR + 1];
+const char* enumValueToString(NbkernelVdwType enumValue);
#endif /* GMX_MDTYPES_MD_ENUMS_H */
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_MDTYPES_MDATOM_H
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
+enum class ParticleType : int;
+
typedef struct t_mdatoms
{
//! Total mass in state A
//! Number of energy groups
int nenergrp;
//! Do we have multiple center of mass motion removal groups
- gmx_bool bVCMgrps;
+ bool bVCMgrps;
//! Do we have any virtual sites?
- gmx_bool haveVsites;
+ bool haveVsites;
//! Do we have atoms that are frozen along 1 or 2 (not 3) dimensions?
- gmx_bool havePartiallyFrozenAtoms;
+ bool havePartiallyFrozenAtoms;
//! Number of perturbed atoms
int nPerturbed;
//! Number of atoms for which the mass is perturbed
//! Number of atoms for which the type is perturbed
int nTypePerturbed;
//! Do we have orientation restraints
- gmx_bool bOrires;
+ bool bOrires;
//! Atomic mass in A state
real* massA;
//! Atomic mass in B state
//! Van der Waals radius sigma^3 in the B state
real* sigma3B;
//! Is this atom perturbed
- gmx_bool* bPerturbed;
+ bool* bPerturbed;
//! Type of atom in the A state
int* typeA;
//! Type of atom in the B state
int* typeB;
//! Particle type
- unsigned short* ptype;
+ ParticleType* ptype;
//! Group index for temperature coupling
unsigned short* cTC;
//! Group index for energy matrix
unsigned short* cENER;
- //! Group index for acceleration
- unsigned short* cACC;
//! Group index for freezing
unsigned short* cFREEZE;
//! Group index for center of mass motion removal
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "multipletimestepping.h"
+#include <optional>
+
#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/pull_params.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/stringutil.h"
namespace gmx
{
}
}
-void assertMtsRequirements(const t_inputrec& ir)
+std::vector<MtsLevel> setupMtsLevels(const GromppMtsOpts& mtsOpts, std::vector<std::string>* errorMessages)
+{
+ std::vector<MtsLevel> mtsLevels;
+
+ if (mtsOpts.numLevels != 2)
+ {
+ if (errorMessages)
+ {
+ errorMessages->push_back("Only mts-levels = 2 is supported");
+ }
+ }
+ else
+ {
+ mtsLevels.resize(2);
+
+ const std::vector<std::string> inputForceGroups = gmx::splitString(mtsOpts.level2Forces);
+ auto& forceGroups = mtsLevels[1].forceGroups;
+ for (const auto& inputForceGroup : inputForceGroups)
+ {
+ bool found = false;
+ int nameIndex = 0;
+ for (const auto& forceGroupName : gmx::mtsForceGroupNames)
+ {
+ if (gmx::equalCaseInsensitive(inputForceGroup, forceGroupName))
+ {
+ forceGroups.set(nameIndex);
+ found = true;
+ }
+ nameIndex++;
+ }
+ if (!found && errorMessages)
+ {
+ errorMessages->push_back(
+ gmx::formatString("Unknown MTS force group '%s'", inputForceGroup.c_str()));
+ }
+ }
+
+ // Make the level 0 use the complement of the force groups of group 1
+ mtsLevels[0].forceGroups = ~mtsLevels[1].forceGroups;
+ mtsLevels[0].stepFactor = 1;
+
+ mtsLevels[1].stepFactor = mtsOpts.level2Factor;
+
+ if (errorMessages && mtsLevels[1].stepFactor <= 1)
+ {
+ errorMessages->push_back("mts-factor should be larger than 1");
+ }
+ }
+
+ return mtsLevels;
+}
+
+bool haveValidMtsSetup(const t_inputrec& ir)
+{
+ return (ir.useMts && ir.mtsLevels.size() == 2 && ir.mtsLevels[1].stepFactor > 1);
+}
+
+namespace
+{
+
+//! Checks whether \p nstValue is a multiple of the largest MTS step, returns an error string for parameter \p param when this is not the case
+std::optional<std::string> checkMtsInterval(ArrayRef<const MtsLevel> mtsLevels, const char* param, const int nstValue)
+{
+ GMX_RELEASE_ASSERT(mtsLevels.size() >= 2, "Need at least two levels for MTS");
+
+ const int mtsFactor = mtsLevels.back().stepFactor;
+ if (nstValue % mtsFactor == 0)
+ {
+ return {};
+ }
+ else
+ {
+ return gmx::formatString(
+ "With MTS, %s = %d should be a multiple of mts-factor = %d", param, nstValue, mtsFactor);
+ }
+}
+
+} // namespace
+
+std::vector<std::string> checkMtsRequirements(const t_inputrec& ir)
{
+ std::vector<std::string> errorMessages;
+
if (!ir.useMts)
{
- return;
+ return errorMessages;
}
- GMX_RELEASE_ASSERT(ir.mtsLevels.size() >= 2, "Need at least two levels for MTS");
+ GMX_RELEASE_ASSERT(haveValidMtsSetup(ir), "MTS setup should be valid here");
+
+ ArrayRef<const MtsLevel> mtsLevels = ir.mtsLevels;
+
+ if (!(ir.eI == IntegrationAlgorithm::MD || ir.eI == IntegrationAlgorithm::SD1))
+ {
+ errorMessages.push_back(gmx::formatString(
+ "Multiple time stepping is only supported with integrators %s and %s",
+ enumValueToString(IntegrationAlgorithm::MD),
+ enumValueToString(IntegrationAlgorithm::SD1)));
+ }
- GMX_RELEASE_ASSERT(ir.mtsLevels[0].stepFactor == 1, "Base MTS step should be 1");
+ if ((EEL_FULL(ir.coulombtype) || EVDW_PME(ir.vdwtype))
+ && forceGroupMtsLevel(ir.mtsLevels, MtsForceGroups::LongrangeNonbonded) == 0)
+ {
+ errorMessages.emplace_back(
+ "With long-range electrostatics and/or LJ treatment, the long-range part "
+ "has to be part of the mts-level2-forces");
+ }
- GMX_RELEASE_ASSERT((!EEL_FULL(ir.coulombtype) && !EVDW_PME(ir.vdwtype))
- || forceGroupMtsLevel(ir.mtsLevels, MtsForceGroups::LongrangeNonbonded) > 0,
- "Long-range nonbondeds should be in the highest MTS level");
+ std::optional<std::string> mesg;
+ if (ir.nstcalcenergy > 0)
+ {
+ if ((mesg = checkMtsInterval(mtsLevels, "nstcalcenergy", ir.nstcalcenergy)))
+ {
+ errorMessages.push_back(mesg.value());
+ }
+ }
+ if ((mesg = checkMtsInterval(mtsLevels, "nstenergy", ir.nstenergy)))
+ {
+ errorMessages.push_back(mesg.value());
+ }
+ if ((mesg = checkMtsInterval(mtsLevels, "nstlog", ir.nstlog)))
+ {
+ errorMessages.push_back(mesg.value());
+ }
+ if ((mesg = checkMtsInterval(mtsLevels, "nstfout", ir.nstfout)))
+ {
+ errorMessages.push_back(mesg.value());
+ }
+ if (ir.efep != FreeEnergyPerturbationType::No)
+ {
+ if ((mesg = checkMtsInterval(mtsLevels, "nstdhdl", ir.fepvals->nstdhdl)))
+ {
+ errorMessages.push_back(mesg.value());
+ }
+ }
+ if (mtsLevels.back().forceGroups[static_cast<int>(gmx::MtsForceGroups::Nonbonded)])
+ {
+ if ((mesg = checkMtsInterval(mtsLevels, "nstlist", ir.nstlist)))
+ {
+ errorMessages.push_back(mesg.value());
+ }
+ }
- for (const auto& mtsLevel : ir.mtsLevels)
+ if (ir.bPull)
{
- const int mtsFactor = mtsLevel.stepFactor;
- GMX_RELEASE_ASSERT(ir.nstcalcenergy % mtsFactor == 0,
- "nstcalcenergy should be a multiple of mtsFactor");
- GMX_RELEASE_ASSERT(ir.nstenergy % mtsFactor == 0,
- "nstenergy should be a multiple of mtsFactor");
- GMX_RELEASE_ASSERT(ir.nstlog % mtsFactor == 0, "nstlog should be a multiple of mtsFactor");
- GMX_RELEASE_ASSERT(ir.epc == epcNO || ir.nstpcouple % mtsFactor == 0,
- "nstpcouple should be a multiple of mtsFactor");
- GMX_RELEASE_ASSERT(ir.efep == efepNO || ir.fepvals->nstdhdl % mtsFactor == 0,
- "nstdhdl should be a multiple of mtsFactor");
- if (ir.mtsLevels.back().forceGroups[static_cast<int>(gmx::MtsForceGroups::Nonbonded)])
+ const int pullMtsLevel = gmx::forceGroupMtsLevel(ir.mtsLevels, gmx::MtsForceGroups::Pull);
+ const int mtsStepFactor = ir.mtsLevels[pullMtsLevel].stepFactor;
+ if (ir.pull->nstxout % mtsStepFactor != 0)
+ {
+ errorMessages.emplace_back("pull-nstxout should be a multiple of mts-factor");
+ }
+ if (ir.pull->nstfout % mtsStepFactor != 0)
{
- GMX_RELEASE_ASSERT(ir.nstlist % ir.mtsLevels.back().stepFactor == 0,
- "With multiple time stepping for the non-bonded pair interactions, "
- "nstlist should be a "
- "multiple of mtsFactor");
+ errorMessages.emplace_back("pull-nstfout should be a multiple of mts-factor");
}
}
+
+ return errorMessages;
}
} // namespace gmx
#ifndef GMX_MULTIPLETIMESTEPPING_H
#define GMX_MULTIPLETIMESTEPPING_H
+#include <string>
+#include <vector>
+
#include <bitset>
#include "gromacs/utility/arrayref.h"
Count //!< The number of groups above
};
+//! Names for the MTS force groups
static const gmx::EnumerationArray<MtsForceGroups, std::string> mtsForceGroupNames = {
"longrange-nonbonded", "nonbonded", "pair", "dihedral", "angle", "pull", "awh"
};
*/
int nonbondedMtsFactor(const t_inputrec& ir);
-//! (Release) Asserts that all multiple time-stepping requirements on \p ir are fulfilled
-void assertMtsRequirements(const t_inputrec& ir);
+//! Struct for passing the MTS mdp options to setupMtsLevels()
+struct GromppMtsOpts
+{
+ //! The number of MTS levels
+ int numLevels = 0;
+ //! The names of the force groups assigned by the user to level 2, internal index 1
+ std::string level2Forces;
+ //! The step factor assigned by the user to level 2, internal index 1
+ int level2Factor = 0;
+};
+
+/*! \brief Sets up and returns the MTS levels and checks requirements of MTS
+ *
+ * Appends errors about allowed input values ir to errorMessages, when not nullptr.
+ *
+ * \param[in] mtsOpts Options for setting the MTS levels
+ * \param[in,out] errorMessages List of error messages, can be nullptr
+ */
+std::vector<MtsLevel> setupMtsLevels(const GromppMtsOpts& mtsOpts, std::vector<std::string>* errorMessages);
+
+/*! \brief Returns whether we use MTS and the MTS setup is internally valid
+ *
+ * Note that setupMtsLevels would have returned at least one error message
+ * when this function returns false
+ */
+bool haveValidMtsSetup(const t_inputrec& ir);
+
+/*! \brief Checks whether the MTS requirements on other algorithms and output frequencies are met
+ *
+ * Note: exits with an assertion failure when
+ * ir.useMts == true && haveValidMtsSetup(ir) == false
+ *
+ * \param[in] ir Complete input record
+ * \returns list of error messages, empty when all MTS requirements are met
+ */
+std::vector<std::string> checkMtsRequirements(const t_inputrec& ir);
} // namespace gmx
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
+#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/alignedallocator.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
-typedef unsigned long t_excl;
-
/* The interactions contained in a (possibly merged) table
* for computing electrostatic, VDW repulsion and/or VDW dispersion
* contributions.
GMX_TABLE_FORMAT_NR
};
-enum
+struct t_nblist
{
- eNL_VDWQQ,
- eNL_VDW,
- eNL_QQ,
- eNL_VDWQQ_FREE,
- eNL_VDW_FREE,
- eNL_QQ_FREE,
- eNL_VDWQQ_WATER,
- eNL_QQ_WATER,
- eNL_VDWQQ_WATERWATER,
- eNL_QQ_WATERWATER,
- eNL_NR
+ int nri = 0; /* Current number of i particles */
+ int maxnri = 0; /* Max number of i particles */
+ int nrj = 0; /* Current number of j particles */
+ int maxnrj = 0; /* ;Max number of j particles */
+ std::vector<int> iinr; /* The i-elements */
+ std::vector<int> gid; /* Index in energy arrays */
+ std::vector<int> shift; /* Shift vector index */
+ std::vector<int> jindex; /* Index in jjnr */
+ std::vector<int> jjnr; /* The j-atom list */
+ std::vector<int> excl_fep; /* Exclusions for FEP with Verlet scheme */
};
-#define MAX_CG 1024
-
-typedef struct
-{
- int ncg;
- int nj;
- int jcg[MAX_CG];
-} t_ns_buf;
-
-
-/* The maximum charge group size because of minimum size of t_excl
- * could be 32 bits.
- */
-#define MAX_CHARGEGROUP_SIZE 32
-
-/* The maximum charge group size for CG-CG nblists.
- * The excl entry in t_nblist uses blocks of this size.
- */
-#define MAX_CGCGSIZE 32
-
-typedef struct t_nblist
-{
- int igeometry; /* The type of list (atom, water, etc.) */
- int ielec; /* Coulomb loop type index for kernels */
- int ielecmod; /* Coulomb modifier (e.g. switch/shift) */
- int ivdw; /* VdW loop type index for kernels */
- int ivdwmod; /* VdW modifier (e.g. switch/shift) */
- int type; /* Type of interaction, listed in
- gmx_nblist_interaction_type */
-
- int nri, maxnri; /* Current/max number of i particles */
- int nrj, maxnrj; /* Current/max number of j particles */
- int* iinr; /* The i-elements */
- int* iinr_end; /* The end atom, only with enlistCG */
- int* gid; /* Index in energy arrays */
- int* shift; /* Shift vector index */
- int* jindex; /* Index in jjnr */
- int* jjnr; /* The j-atom list */
- int* jjnr_end; /* The end atom, only with enltypeCG */
- char* excl_fep; /* Exclusions for FEP with Verlet scheme */
- t_excl* excl; /* Exclusions, only with enltypeCG */
-
- /* We use separate pointers for kernels that compute both potential
- * and force (vf suffix), only potential (v) or only force (f)
- */
- void* kernelptr_vf;
- void* kernelptr_v;
- void* kernelptr_f;
-
- /* Pad the list of neighbors for each i atom with "-1" entries up to the
- * simd_padding_width, if it is larger than 0. This is necessary for many
- * accelerated kernels using single-instruction multiple-data operations
- * internally.
- */
- int simd_padding_width;
-
-} t_nblist;
-
-/* For atom I = nblist->iinr[N] (0 <= N < nblist->nri) there can be
- * several neighborlists (N's), for different energy groups (gid) and
- * different shifts (shift).
- * For corresponding J atoms for each list start at:
- * nblist->jjnr[JI]
- * with nblist->jindex[N] <= JI < nblist->jindex[N+1]
- *
- * enlist is of the form enlistUNIT1_UNIT2:
- * UNIT ATOM: there is one atom: iinr[N] or jjnr[JI]
- * UNIT SPC: there are 3 atoms: iinr[N],iinr[N]+1,iinr[N]+2, jjnr analog.
- * UNIT TIP4P: there are 4 atoms: iinr[N],...,iinr[N]+3, jjnr analog.
- * UNIT CG: there are N atoms: iinr[N],...,iinr_end[N]-1, jjnr analog.
- *
- * Clear?
- */
-
/* Structure describing the data in a single table */
struct t_forcetable
{
t_forcetable(enum gmx_table_interaction interaction, enum gmx_table_format format);
+ ~t_forcetable();
+
enum gmx_table_interaction interaction; /* Types of interactions stored in this table */
enum gmx_table_format format; /* Interpolation type and data format */
int stride; /* Distance to next table point (number of fp variables per table point in total) */
};
-struct gmx_ns_t
-{
- gmx_bool bCGlist;
- int* simple_aaj;
- struct t_grid* grid;
- t_excl* bexcl;
- gmx_bool* bHaveVdW;
- t_ns_buf** ns_buf;
- gmx_bool* bExcludeAlleg;
- int nra_alloc;
- int cg_alloc;
- int** nl_sr;
- int* nsr;
- int** nl_lr_ljc;
- int** nl_lr_one;
- int* nlr_ljc;
- int* nlr_one;
- /* the nblists should probably go in here */
- gmx_bool nblist_initialized; /* has the nblist been initialized? */
- int dump_nl; /* neighbour list dump level (from env. var. GMX_DUMP_NL)*/
-};
-
#endif /* GMX_MDTYPES_NBLIST_H */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
/*! Maximum number of pull groups that can be used in a pull coordinate */
-static const int c_pullCoordNgroupMax = 6;
+static constexpr int c_pullCoordNgroupMax = 6;
/*! \brief Struct that defines a pull coordinate */
struct t_pull_coord
{
//! The pull type: umbrella, constraint, ...
- int eType = 0;
+ PullingAlgorithm eType = PullingAlgorithm::Umbrella;
//! Name of the module providing the external potential, only used with eType==epullEXTERNAL
std::string externalPotentialProvider;
//! The pull geometry
- int eGeom = 0;
+ PullGroupGeometry eGeom = PullGroupGeometry::Distance;
//! The number of groups, depends on eGeom
int ngroup = 0;
/*! \brief The pull groups:
real k = 0.0;
//! Force constant for state B
real kB = 0.0;
+ //! The index of this coordinate in the list of coordinates
+ int coordIndex = -1;
};
/*! \brief Struct containing all pull parameters */
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* The source code in this file should be thread-safe.
Please keep it that way. */
-history_t::history_t() :
- disre_initf(0),
- ndisrepairs(0),
- disre_rm3tav(nullptr),
- orire_initf(0),
- norire_Dtav(0),
- orire_Dtav(nullptr)
-{
-}
+history_t::history_t() : disre_initf(0), orire_initf(0) {}
ekinstate_t::ekinstate_t() :
bUpToDate(FALSE),
/* We need padding, since we might use SIMD access, but the
* containers here all ensure that. */
- if (state->flags & (1 << estX))
+ if (state->flags & enumValueToBitMask(StateEntry::X))
{
state->x.resizeWithPadding(natoms);
}
- if (state->flags & (1 << estV))
+ if (state->flags & enumValueToBitMask(StateEntry::V))
{
state->v.resizeWithPadding(natoms);
}
- if (state->flags & (1 << estCGP))
+ if (state->flags & enumValueToBitMask(StateEntry::Cgp))
{
state->cg_p.resizeWithPadding(natoms);
}
cmp_rvecs(stdout, "box_rel", DIM, st1->box_rel, st2->box_rel, FALSE, ftol, abstol);
fprintf(stdout, "comparing boxv\n");
cmp_rvecs(stdout, "boxv", DIM, st1->boxv, st2->boxv, FALSE, ftol, abstol);
- if (st1->flags & (1 << estSVIR_PREV))
+ if (st1->flags & enumValueToBitMask(StateEntry::SVirPrev))
{
fprintf(stdout, "comparing shake vir_prev\n");
cmp_rvecs(stdout, "svir_prev", DIM, st1->svir_prev, st2->svir_prev, FALSE, ftol, abstol);
}
- if (st1->flags & (1 << estFVIR_PREV))
+ if (st1->flags & enumValueToBitMask(StateEntry::FVirPrev))
{
fprintf(stdout, "comparing force vir_prev\n");
cmp_rvecs(stdout, "fvir_prev", DIM, st1->fvir_prev, st2->fvir_prev, FALSE, ftol, abstol);
}
- if (st1->flags & (1 << estPRES_PREV))
+ if (st1->flags & enumValueToBitMask(StateEntry::PressurePrevious))
{
fprintf(stdout, "comparing prev_pres\n");
cmp_rvecs(stdout, "pres_prev", DIM, st1->pres_prev, st2->pres_prev, FALSE, ftol, abstol);
nc = i * st1->nhchainlength;
for (j = 0; j < nc; j++)
{
- cmp_real(stdout, "nosehoover_xi", i, st1->nosehoover_xi[nc + j],
- st2->nosehoover_xi[nc + j], ftol, abstol);
+ cmp_real(stdout, "nosehoover_xi", i, st1->nosehoover_xi[nc + j], st2->nosehoover_xi[nc + j], ftol, abstol);
}
}
}
nc = i * st1->nhchainlength;
for (j = 0; j < nc; j++)
{
- cmp_real(stdout, "nosehoover_xi", i, st1->nhpres_xi[nc + j], st2->nhpres_xi[nc + j],
- ftol, abstol);
+ cmp_real(stdout, "nosehoover_xi", i, st1->nhpres_xi[nc + j], st2->nhpres_xi[nc + j], ftol, abstol);
}
}
}
cmp_int(stdout, "natoms", -1, st1->natoms, st2->natoms);
if (st1->natoms == st2->natoms)
{
- if ((st1->flags & (1 << estX)) && (st2->flags & (1 << estX)))
+ if ((st1->flags & enumValueToBitMask(StateEntry::X))
+ && (st2->flags & enumValueToBitMask(StateEntry::X)))
{
fprintf(stdout, "comparing x\n");
- cmp_rvecs(stdout, "x", st1->natoms, st1->x.rvec_array(), st2->x.rvec_array(), bRMSD,
- ftol, abstol);
+ cmp_rvecs(stdout, "x", st1->natoms, st1->x.rvec_array(), st2->x.rvec_array(), bRMSD, ftol, abstol);
}
- if ((st1->flags & (1 << estV)) && (st2->flags & (1 << estV)))
+ if ((st1->flags & enumValueToBitMask(StateEntry::V))
+ && (st2->flags & enumValueToBitMask(StateEntry::V)))
{
fprintf(stdout, "comparing v\n");
- cmp_rvecs(stdout, "v", st1->natoms, st1->v.rvec_array(), st2->v.rvec_array(), bRMSD,
- ftol, abstol);
+ cmp_rvecs(stdout, "v", st1->natoms, st1->v.rvec_array(), st2->v.rvec_array(), bRMSD, ftol, abstol);
}
}
}
if (inputrecPreserveShape(ir))
{
- const int ndim = ir->epct == epctSEMIISOTROPIC ? 2 : 3;
+ const int ndim = ir->epct == PressureCouplingType::SemiIsotropic ? 2 : 3;
do_box_rel(ndim, ir->deform, state->box_rel, state->box, true);
}
}
{
if (inputrecPreserveShape(ir))
{
- const int ndim = ir->epct == epctSEMIISOTROPIC ? 2 : 3;
+ const int ndim = ir->epct == PressureCouplingType::SemiIsotropic ? 2 : 3;
do_box_rel(ndim, ir->deform, box_rel, box, false);
}
}
-void printLambdaStateToLog(FILE* fplog, const gmx::ArrayRef<real> lambda, const bool isInitialOutput)
+void printLambdaStateToLog(FILE* fplog, gmx::ArrayRef<const real> lambda, const bool isInitialOutput)
{
if (fplog != nullptr)
{
}
}
-void initialize_lambdas(FILE* fplog, const t_inputrec& ir, bool isMaster, int* fep_state, gmx::ArrayRef<real> lambda)
+void initialize_lambdas(FILE* fplog,
+ const FreeEnergyPerturbationType freeEnergyPerturbationType,
+ const bool haveSimulatedTempering,
+ const t_lambda& fep,
+ gmx::ArrayRef<const real> simulatedTemperingTemps,
+ gmx::ArrayRef<real> ref_t,
+ bool isMaster,
+ int* fep_state,
+ gmx::ArrayRef<real> lambda)
{
/* TODO: Clean up initialization of fep_state and lambda in
t_state. This function works, but could probably use a logic
rewrite to keep all the different types of efep straight. */
- if ((ir.efep == efepNO) && (!ir.bSimTemp))
+ if ((freeEnergyPerturbationType == FreeEnergyPerturbationType::No) && (!haveSimulatedTempering))
{
return;
}
- const t_lambda* fep = ir.fepvals;
if (isMaster)
{
- *fep_state = fep->init_fep_state; /* this might overwrite the checkpoint
+ *fep_state = fep.init_fep_state; /* this might overwrite the checkpoint
if checkpoint is set -- a kludge is in for now
to prevent this.*/
}
- for (int i = 0; i < efptNR; i++)
+ for (int i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
{
double thisLambda;
/* overwrite lambda state with init_lambda for now for backwards compatibility */
- if (fep->init_lambda >= 0) /* if it's -1, it was never initialized */
+ if (fep.init_lambda >= 0) /* if it's -1, it was never initialized */
{
- thisLambda = fep->init_lambda;
+ thisLambda = fep.init_lambda;
}
else
{
- thisLambda = fep->all_lambda[i][fep->init_fep_state];
+ thisLambda = fep.all_lambda[i][fep.init_fep_state];
}
if (isMaster)
{
lambda[i] = thisLambda;
}
}
- if (ir.bSimTemp)
+ if (haveSimulatedTempering)
{
/* need to rescale control temperatures to match current state */
- for (int i = 0; i < ir.opts.ngtc; i++)
+ for (int i = 0; i < ref_t.ssize(); i++)
{
- if (ir.opts.ref_t[i] > 0)
+ if (ref_t[i] > 0)
{
- ir.opts.ref_t[i] = ir.simtempvals->temperatures[fep->init_fep_state];
+ ref_t[i] = simulatedTemperingTemps[fep.init_fep_state];
}
}
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/paddedvector.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/real.h"
struct t_inputrec;
+struct t_lambda;
+enum class FreeEnergyPerturbationType;
namespace gmx
{
* The order of these enums should not be changed,
* since that affects the checkpoint (.cpt) file format.
*/
-enum
+enum class StateEntry : int
{
- estLAMBDA,
- estBOX,
- estBOX_REL,
- estBOXV,
- estPRES_PREV,
- estNH_XI,
- estTHERM_INT,
- estX,
- estV,
- estSDX_NOTSUPPORTED,
- estCGP,
- estLD_RNG_NOTSUPPORTED,
- estLD_RNGI_NOTSUPPORTED,
- estDISRE_INITF,
- estDISRE_RM3TAV,
- estORIRE_INITF,
- estORIRE_DTAV,
- estSVIR_PREV,
- estNH_VXI,
- estVETA,
- estVOL0,
- estNHPRES_XI,
- estNHPRES_VXI,
- estFVIR_PREV,
- estFEPSTATE,
- estMC_RNG_NOTSUPPORTED,
- estMC_RNGI_NOTSUPPORTED,
- estBAROS_INT,
- estPULLCOMPREVSTEP,
- estNR
+ Lambda,
+ Box,
+ BoxRel,
+ BoxV,
+ PressurePrevious,
+ Nhxi,
+ ThermInt,
+ X,
+ V,
+ SDxNotSupported,
+ Cgp,
+ LDRngNotSupported,
+ LDRngINotSupported,
+ DisreInitF,
+ DisreRm3Tav,
+ OrireInitF,
+ OrireDtav,
+ SVirPrev,
+ Nhvxi,
+ Veta,
+ Vol0,
+ Nhpresxi,
+ Nhpresvxi,
+ FVirPrev,
+ FepState,
+ MCRngNotSupported,
+ MCRngINotSupported,
+ BarosInt,
+ PullComPrevStep,
+ Count
};
-//! \brief The names of the state entries, defined in src/gmxlib/checkpoint.c
-extern const char* est_names[estNR];
+//! \brief The names of the state entries, defined in src/gromacs/fileio/checkpoint.cpp
+const char* enumValueToString(StateEntry enumValue);
+/*! \brief Convert enum to bitmask value.
+ *
+ * Used for setting flags in checkpoint header and verifying which flags are set.
+ */
+template<typename Enum>
+inline int enumValueToBitMask(Enum enumValue)
+{
+ static_assert(static_cast<int>(Enum::Count) <= std::numeric_limits<int>::digits);
+ return 1 << static_cast<int>(enumValue);
+}
/*! \libinternal \brief History information for NMR distance and orientation restraints
*
public:
history_t();
- real disre_initf; //!< The scaling factor for initializing the time av.
- int ndisrepairs; //!< The number of distance restraints
- real* disre_rm3tav; //!< The r^-3 time averaged pair distances
- real orire_initf; //!< The scaling factor for initializing the time av.
- int norire_Dtav; //!< The number of matrix element in dtav (npair*5)
- real* orire_Dtav; //!< The time averaged orientation tensors
+ real disre_initf; //!< The scaling factor for initializing the time av.
+ std::vector<real> disre_rm3tav; //!< The r^-3 time averaged pair distances
+ real orire_initf; //!< The scaling factor for initializing the time av.
+ std::vector<real> orire_Dtav; //!< The time averaged orientation tensors
};
/*! \libinternal \brief Struct used for checkpointing only
public:
ekinstate_t();
- gmx_bool bUpToDate; //!< Test if all data is up to date
+ bool bUpToDate; //!< Test if all data is up to date
int ekin_n; //!< The number of tensors
tensor* ekinh; //!< Half step Ekin, size \p ekin_n
tensor* ekinf; //!< Full step Ekin, size \p ekin_n
{
int nlambda; //!< total number of lambda states - for history
- gmx_bool bEquil; //!< Have we reached equilibration
- int* n_at_lam; //!< number of points observed at each lambda
- real* wl_histo; //!< histogram for WL flatness determination
- real wl_delta; //!< current wang-landau delta
+ bool bEquil; //!< Have we reached equilibration
+ int* n_at_lam; //!< number of points observed at each lambda
+ real* wl_histo; //!< histogram for WL flatness determination
+ real wl_delta; //!< current wang-landau delta
real* sum_weights; //!< weights of the states
real* sum_dg; //!< free energies of the states -- not actually used for weighting, but informational
int nnhpres; //!< The number of NH-chains for the MTTK barostat (always 1 or 0)
int nhchainlength; //!< The NH-chain length for temperature coupling and MTTK barostat
int flags; //!< Set of bit-flags telling which entries are present, see enum at the top of the file
- int fep_state; //!< indicates which of the alchemical states we are in
- std::array<real, efptNR> lambda; //!< Free-energy lambda vector
- matrix box; //!< Matrix of box vectors
- matrix box_rel; //!< Relative box vectors to preserve box shape
- matrix boxv; //!< Box velocities for Parrinello-Rahman P-coupling
- matrix pres_prev; //!< Pressure of the previous step for pcoupl
- matrix svir_prev; //!< Shake virial for previous step for pcoupl
- matrix fvir_prev; //!< Force virial of the previous step for pcoupl
- std::vector<double> nosehoover_xi; //!< Nose-Hoover coordinates (ngtc)
- std::vector<double> nosehoover_vxi; //!< Nose-Hoover velocities (ngtc)
- std::vector<double> nhpres_xi; //!< Pressure Nose-Hoover coordinates
- std::vector<double> nhpres_vxi; //!< Pressure Nose-Hoover velocities
- std::vector<double> therm_integral; //!< Work exterted N-H/V-rescale T-coupling (ngtc)
- double baros_integral; //!< For Berendsen P-coupling conserved quantity
- real veta; //!< Trotter based isotropic P-coupling
- real vol0; //!< Initial volume,required for computing MTTK conserved quantity
+ int fep_state; //!< indicates which of the alchemical states we are in
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real> lambda; //!< Free-energy lambda vector
+ matrix box; //!< Matrix of box vectors
+ matrix box_rel; //!< Relative box vectors to preserve box shape
+ matrix boxv; //!< Box velocities for Parrinello-Rahman P-coupling
+ matrix pres_prev; //!< Pressure of the previous step for pcoupl
+ matrix svir_prev; //!< Shake virial for previous step for pcoupl
+ matrix fvir_prev; //!< Force virial of the previous step for pcoupl
+ std::vector<double> nosehoover_xi; //!< Nose-Hoover coordinates (ngtc)
+ std::vector<double> nosehoover_vxi; //!< Nose-Hoover velocities (ngtc)
+ std::vector<double> nhpres_xi; //!< Pressure Nose-Hoover coordinates
+ std::vector<double> nhpres_vxi; //!< Pressure Nose-Hoover velocities
+ std::vector<double> therm_integral; //!< Work exterted N-H/V-rescale T-coupling (ngtc)
+ double baros_integral; //!< For Berendsen P-coupling conserved quantity
+ real veta; //!< Trotter based isotropic P-coupling
+ real vol0; //!< Initial volume,required for computing MTTK conserved quantity
PaddedHostVector<gmx::RVec> x; //!< The coordinates (natoms)
PaddedHostVector<gmx::RVec> v; //!< The velocities (natoms)
PaddedHostVector<gmx::RVec> cg_p; //!< p vector for conjugate gradient minimization
tensor Winvm; /* inverse pressure mass tensor, computed */
};
-
-typedef struct
-{
- real veta;
- double rscale;
- double vscale;
- double rvscale;
- double alpha;
- double* vscale_nhc;
-} t_vetavars;
-
#endif // DOXYGEN
//! Resizes the T- and P-coupling state variables
void init_dfhist_state(t_state* state, int dfhistNumLambda);
/*! \brief Compares two states, write the differences to stdout */
-void comp_state(const t_state* st1, const t_state* st2, gmx_bool bRMSD, real ftol, real abstol);
+void comp_state(const t_state* st1, const t_state* st2, bool bRMSD, real ftol, real abstol);
/*! \brief Allocates an rvec pointer and copy the contents of v to it */
rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n);
* \param[in] lambda The array of lambda values.
* \param[in] isInitialOutput Whether this output is the initial lambda state or not.
*/
-void printLambdaStateToLog(FILE* fplog, gmx::ArrayRef<real> lambda, bool isInitialOutput);
+void printLambdaStateToLog(FILE* fplog, gmx::ArrayRef<const real> lambda, bool isInitialOutput);
/*! \brief Fills fep_state and lambda if needed
* and lambda on master rank.
*
* Reports the initial lambda state to the log file. */
-void initialize_lambdas(FILE* fplog, const t_inputrec& ir, bool isMaster, int* fep_state, gmx::ArrayRef<real> lambda);
+void initialize_lambdas(FILE* fplog,
+ FreeEnergyPerturbationType freeEnergyPerturbationType,
+ bool haveSimulatedTempering,
+ const t_lambda& fep,
+ gmx::ArrayRef<const real> simulatedTemperingTemps,
+ gmx::ArrayRef<real> ref_t,
+ bool isMaster,
+ int* fep_state,
+ gmx::ArrayRef<real> lambda);
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MDTYPES_STATE_PROPAGATOR_DATA_GPU_H
#define GMX_MDTYPES_STATE_PROPAGATOR_DATA_GPU_H
+#include <memory>
#include <tuple>
#include "gromacs/gpu_utils/devicebuffer_datatype.h"
*/
void copyForcesToGpu(gmx::ArrayRef<const gmx::RVec> h_f, AtomLocality atomLocality);
+ /*! \brief Clear forces in the GPU memory.
+ *
+ * \param[in] atomLocality Locality of the particles to clear.
+ */
+ void clearForcesOnGpu(AtomLocality atomLocality);
+
/*! \brief Get the event synchronizer for the forces ready on device.
*
* Returns either of the event synchronizers, depending on the offload scenario
private:
class Impl;
- gmx::PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
GMX_DISALLOW_COPY_AND_ASSIGN(StatePropagatorDataGpu);
};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"GPU implementation.");
}
+void StatePropagatorDataGpu::clearForcesOnGpu(AtomLocality /* atomLocality */)
+{
+ GMX_ASSERT(!impl_,
+ "A CPU stub method from GPU state propagator data was called instead of one from "
+ "GPU implementation.");
+}
+
GpuEventSynchronizer* StatePropagatorDataGpu::getForcesReadyOnDeviceEvent(AtomLocality /* atomLocality */,
bool /* useGpuFBufferOps */)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "config.h"
+#include <memory>
+
#include "gromacs/gpu_utils/devicebuffer.h"
#if GMX_GPU_CUDA
# include "gromacs/gpu_utils/gpueventsynchronizer.cuh"
#elif GMX_GPU_SYCL
# include "gromacs/gpu_utils/gpueventsynchronizer_sycl.h"
#endif
+
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/state_propagator_data_gpu.h"
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/enumerationhelpers.h"
struct gmx_wallcycle;
*/
void copyForcesToGpu(gmx::ArrayRef<const gmx::RVec> h_f, AtomLocality atomLocality);
+ /*! \brief Clear forces in the GPU memory.
+ *
+ * \param[in] atomLocality Locality of the particles to clear.
+ */
+ void clearForcesOnGpu(AtomLocality atomLocality);
+
/*! \brief Get the event synchronizer for the forces ready on device.
*
* Returns either of the event synchronizers, depending on the offload scenario
int dataSize,
AtomLocality atomLocality,
const DeviceStream& deviceStream);
+
+ /*! \brief Performs the clearing of data in device buffer.
+ *
+ * \todo Template on locality.
+ *
+ * \param[out] d_data Device-side buffer.
+ * \param[in] dataSize Device-side data allocation size.
+ * \param[in] atomLocality If all, local or non-local ranges should be cleared.
+ * \param[in] deviceStream GPU stream to execute copy in.
+ */
+ void clearOnDevice(DeviceBuffer<RVec> d_data,
+ int dataSize,
+ AtomLocality atomLocality,
+ const DeviceStream& deviceStream);
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void StatePropagatorDataGpu::Impl::reinit(int numAtomsLocal, int numAtomsAll)
{
- wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU);
- wallcycle_sub_start_nocount(wcycle_, ewcsLAUNCH_STATE_PROPAGATOR_DATA);
+ wallcycle_start_nocount(wcycle_, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start_nocount(wcycle_, WallCycleSubCounter::LaunchStatePropagatorData);
numAtomsLocal_ = numAtomsLocal;
numAtomsAll_ = numAtomsAll;
clearDeviceBufferAsync(&d_f_, 0, d_fCapacity_, *localStream_);
}
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_STATE_PROPAGATOR_DATA);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchStatePropagatorData);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
}
std::tuple<int, int> StatePropagatorDataGpu::Impl::getAtomRangesFromAtomLocality(AtomLocality atomLocality)
GMX_ASSERT(atomsStartAt + numAtomsToCopy <= h_data.ssize(),
"The host buffer is smaller than the requested copy range.");
- copyToDeviceBuffer(&d_data, reinterpret_cast<const RVec*>(&h_data.data()[atomsStartAt]),
- atomsStartAt, numAtomsToCopy, deviceStream, transferKind_, nullptr);
+ copyToDeviceBuffer(&d_data,
+ reinterpret_cast<const RVec*>(&h_data.data()[atomsStartAt]),
+ atomsStartAt,
+ numAtomsToCopy,
+ deviceStream,
+ transferKind_,
+ nullptr);
}
}
GMX_ASSERT(atomsStartAt + numAtomsToCopy <= h_data.ssize(),
"The host buffer is smaller than the requested copy range.");
- copyFromDeviceBuffer(reinterpret_cast<RVec*>(&h_data.data()[atomsStartAt]), &d_data,
- atomsStartAt, numAtomsToCopy, deviceStream, transferKind_, nullptr);
+ copyFromDeviceBuffer(reinterpret_cast<RVec*>(&h_data.data()[atomsStartAt]),
+ &d_data,
+ atomsStartAt,
+ numAtomsToCopy,
+ deviceStream,
+ transferKind_,
+ nullptr);
+ }
+}
+
+void StatePropagatorDataGpu::Impl::clearOnDevice(DeviceBuffer<RVec> d_data,
+ int dataSize,
+ AtomLocality atomLocality,
+ const DeviceStream& deviceStream)
+{
+ GMX_UNUSED_VALUE(dataSize);
+
+ GMX_ASSERT(atomLocality < AtomLocality::Count, "Wrong atom locality.");
+
+ GMX_ASSERT(dataSize >= 0, "Trying to clear to device buffer before it was allocated.");
+
+ GMX_ASSERT(deviceStream.isValid(), "No stream is valid for clearing with given atom locality.");
+
+ int atomsStartAt, numAtomsToClear;
+ std::tie(atomsStartAt, numAtomsToClear) = getAtomRangesFromAtomLocality(atomLocality);
+
+ if (numAtomsToClear != 0)
+ {
+ GMX_ASSERT(atomsStartAt + numAtomsToClear <= dataSize,
+ "The device allocation is smaller than requested clear range.");
+
+ clearDeviceBufferAsync(&d_data, atomsStartAt, numAtomsToClear, deviceStream);
}
}
GMX_ASSERT(deviceStream != nullptr,
"No stream is valid for copying positions with given atom locality.");
- wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU);
- wallcycle_sub_start(wcycle_, ewcsLAUNCH_STATE_PROPAGATOR_DATA);
+ wallcycle_start_nocount(wcycle_, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::LaunchStatePropagatorData);
copyToDevice(d_x_, h_x, d_xSize_, atomLocality, *deviceStream);
xReadyOnDevice_[atomLocality].markEvent(*deviceStream);
}
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_STATE_PROPAGATOR_DATA);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchStatePropagatorData);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
}
GpuEventSynchronizer*
void StatePropagatorDataGpu::Impl::waitCoordinatesCopiedToDevice(AtomLocality atomLocality)
{
- wallcycle_start(wcycle_, ewcWAIT_GPU_STATE_PROPAGATOR_DATA);
+ wallcycle_start(wcycle_, WallCycleCounter::WaitGpuStatePropagatorData);
GMX_ASSERT(atomLocality < AtomLocality::Count, "Wrong atom locality.");
xReadyOnDevice_[atomLocality].waitForEvent();
- wallcycle_stop(wcycle_, ewcWAIT_GPU_STATE_PROPAGATOR_DATA);
+ wallcycle_stop(wcycle_, WallCycleCounter::WaitGpuStatePropagatorData);
}
GpuEventSynchronizer* StatePropagatorDataGpu::Impl::xUpdatedOnDevice()
GMX_ASSERT(deviceStream != nullptr,
"No stream is valid for copying positions with given atom locality.");
- wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU);
- wallcycle_sub_start(wcycle_, ewcsLAUNCH_STATE_PROPAGATOR_DATA);
+ wallcycle_start_nocount(wcycle_, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::LaunchStatePropagatorData);
copyFromDevice(h_x, d_x_, d_xSize_, atomLocality, *deviceStream);
// Note: unlike copyCoordinatesToGpu this is not used in OpenCL, and the conditional is not needed.
xReadyOnHost_[atomLocality].markEvent(*deviceStream);
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_STATE_PROPAGATOR_DATA);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchStatePropagatorData);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
}
void StatePropagatorDataGpu::Impl::waitCoordinatesReadyOnHost(AtomLocality atomLocality)
{
- wallcycle_start(wcycle_, ewcWAIT_GPU_STATE_PROPAGATOR_DATA);
+ wallcycle_start(wcycle_, WallCycleCounter::WaitGpuStatePropagatorData);
xReadyOnHost_[atomLocality].waitForEvent();
- wallcycle_stop(wcycle_, ewcWAIT_GPU_STATE_PROPAGATOR_DATA);
+ wallcycle_stop(wcycle_, WallCycleCounter::WaitGpuStatePropagatorData);
}
GMX_ASSERT(deviceStream != nullptr,
"No stream is valid for copying velocities with given atom locality.");
- wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU);
- wallcycle_sub_start(wcycle_, ewcsLAUNCH_STATE_PROPAGATOR_DATA);
+ wallcycle_start_nocount(wcycle_, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::LaunchStatePropagatorData);
copyToDevice(d_v_, h_v, d_vSize_, atomLocality, *deviceStream);
vReadyOnDevice_[atomLocality].markEvent(*deviceStream);
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_STATE_PROPAGATOR_DATA);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchStatePropagatorData);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
}
GpuEventSynchronizer* StatePropagatorDataGpu::Impl::getVelocitiesReadyOnDeviceEvent(AtomLocality atomLocality)
GMX_ASSERT(deviceStream != nullptr,
"No stream is valid for copying velocities with given atom locality.");
- wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU);
- wallcycle_sub_start(wcycle_, ewcsLAUNCH_STATE_PROPAGATOR_DATA);
+ wallcycle_start_nocount(wcycle_, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::LaunchStatePropagatorData);
copyFromDevice(h_v, d_v_, d_vSize_, atomLocality, *deviceStream);
vReadyOnHost_[atomLocality].markEvent(*deviceStream);
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_STATE_PROPAGATOR_DATA);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchStatePropagatorData);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
}
void StatePropagatorDataGpu::Impl::waitVelocitiesReadyOnHost(AtomLocality atomLocality)
{
- wallcycle_start(wcycle_, ewcWAIT_GPU_STATE_PROPAGATOR_DATA);
+ wallcycle_start(wcycle_, WallCycleCounter::WaitGpuStatePropagatorData);
vReadyOnHost_[atomLocality].waitForEvent();
- wallcycle_stop(wcycle_, ewcWAIT_GPU_STATE_PROPAGATOR_DATA);
+ wallcycle_stop(wcycle_, WallCycleCounter::WaitGpuStatePropagatorData);
}
GMX_ASSERT(deviceStream != nullptr,
"No stream is valid for copying forces with given atom locality.");
- wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU);
- wallcycle_sub_start(wcycle_, ewcsLAUNCH_STATE_PROPAGATOR_DATA);
+ wallcycle_start_nocount(wcycle_, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::LaunchStatePropagatorData);
copyToDevice(d_f_, h_f, d_fSize_, atomLocality, *deviceStream);
fReadyOnDevice_[atomLocality].markEvent(*deviceStream);
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_STATE_PROPAGATOR_DATA);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchStatePropagatorData);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
+}
+
+void StatePropagatorDataGpu::Impl::clearForcesOnGpu(AtomLocality atomLocality)
+{
+ GMX_ASSERT(atomLocality < AtomLocality::Count, "Wrong atom locality.");
+ const DeviceStream* deviceStream = fCopyStreams_[atomLocality];
+ GMX_ASSERT(deviceStream != nullptr,
+ "No stream is valid for clearing forces with given atom locality.");
+
+ wallcycle_start_nocount(wcycle_, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::LaunchStatePropagatorData);
+
+ clearOnDevice(d_f_, d_fSize_, atomLocality, *deviceStream);
+
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchStatePropagatorData);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
}
GpuEventSynchronizer* StatePropagatorDataGpu::Impl::getForcesReadyOnDeviceEvent(AtomLocality atomLocality,
GMX_ASSERT(deviceStream != nullptr,
"No stream is valid for copying forces with given atom locality.");
- wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU);
- wallcycle_sub_start(wcycle_, ewcsLAUNCH_STATE_PROPAGATOR_DATA);
+ wallcycle_start_nocount(wcycle_, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::LaunchStatePropagatorData);
copyFromDevice(h_f, d_f_, d_fSize_, atomLocality, *deviceStream);
fReadyOnHost_[atomLocality].markEvent(*deviceStream);
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_STATE_PROPAGATOR_DATA);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchStatePropagatorData);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
}
void StatePropagatorDataGpu::Impl::waitForcesReadyOnHost(AtomLocality atomLocality)
{
- wallcycle_start(wcycle_, ewcWAIT_GPU_STATE_PROPAGATOR_DATA);
+ wallcycle_start(wcycle_, WallCycleCounter::WaitGpuStatePropagatorData);
fReadyOnHost_[atomLocality].waitForEvent();
- wallcycle_stop(wcycle_, ewcWAIT_GPU_STATE_PROPAGATOR_DATA);
+ wallcycle_stop(wcycle_, WallCycleCounter::WaitGpuStatePropagatorData);
}
const DeviceStream* StatePropagatorDataGpu::Impl::getUpdateStream()
return impl_->copyForcesToGpu(h_f, atomLocality);
}
+void StatePropagatorDataGpu::clearForcesOnGpu(AtomLocality atomLocality)
+{
+ return impl_->clearForcesOnGpu(atomLocality);
+}
+
GpuEventSynchronizer* StatePropagatorDataGpu::getForcesReadyOnDeviceEvent(AtomLocality atomLocality,
bool useGpuFBufferOps)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_MDLIB_SWAPHISTORY_H
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/utility/enumerationhelpers.h"
+enum class Domain : int;
+enum class ChannelHistory : int;
/* History of an ion type used in position swapping
*/
-typedef struct swapstateIons_t
+struct swapstateIons_t
{
- int nMolReq[eCompNR]; // Requested # of molecules per compartment
- int* nMolReq_p[eCompNR]; // Pointer to this data (for checkpoint writing)
- int inflow_net[eCompNR]; // Flux determined from the # of swaps
- int* inflow_net_p[eCompNR]; // Pointer to this data
- int* nMolPast[eCompNR]; // Array with nAverage entries for history
- int* nMolPast_p[eCompNR]; // Pointer points to the first entry only
+ gmx::EnumerationArray<Compartment, int> nMolReq; // Requested # of molecules per compartment
+ gmx::EnumerationArray<Compartment, int*> nMolReq_p; // Pointer to this data (for checkpoint writing)
+ gmx::EnumerationArray<Compartment, int> inflow_net; // Flux determined from the # of swaps
+ gmx::EnumerationArray<Compartment, int*> inflow_net_p; // Pointer to this data
+ gmx::EnumerationArray<Compartment, int*> nMolPast; // Array with nAverage entries for history
+ gmx::EnumerationArray<Compartment, int*> nMolPast_p; // Pointer points to the first entry only
// Channel flux detection, this is counting only and has no influence on whether swaps are performed or not: */
- int fluxfromAtoB[eCompNR]; // Flux determined from the split cylinders
- int* fluxfromAtoB_p[eCompNR]; // Pointer to this data
- int nMol; // Number of molecules, size of the following arrays
- unsigned char* comp_from; // Ion came from which compartment?
- unsigned char* channel_label; // Through which channel did this ion pass?
-} swapstateIons_t;
+ gmx::EnumerationArray<Channel, int> fluxfromAtoB; // Flux determined from the split cylinders
+ gmx::EnumerationArray<Channel, int*> fluxfromAtoB_p; // Pointer to this data
+ int nMol; // Number of molecules, size of the following arrays
+ Domain* comp_from; // Ion came from which compartment?
+ ChannelHistory* channel_label; // Through which channel did this ion pass?
+};
/* Position swapping state
*
*/
typedef struct swaphistory_t
{
- int eSwapCoords; // Swapping along x, y, or z-direction?
- int nIonTypes; // Number of ion types, this is the size of the following arrays
+ SwapType eSwapCoords; // Swapping along x, y, or z-direction?
+ int nIonTypes; // Number of ion types, this is the size of the following arrays
int nAverage; // Use average over this many swap attempt steps when determining the ion counts
int fluxleak; // Ions not going through any channel (bad!)
- int* fluxleak_p; // Pointer to this data
- gmx_bool bFromCpt; // Did we start from a checkpoint file?
- int nat[eChanNR]; // Size of xc_old_whole, i.e. the number of atoms in each channel
- rvec* xc_old_whole[eChanNR]; // Last known whole positions of the two channels (important for multimeric ch.!)
- rvec** xc_old_whole_p[eChanNR]; // Pointer to these positions
- swapstateIons_t* ionType; // History information for one ion type
+ int* fluxleak_p; // Pointer to this data
+ bool bFromCpt; // Did we start from a checkpoint file?
+ gmx::EnumerationArray<Channel, int> nat; // Size of xc_old_whole, i.e. the number of atoms in each channel
+ gmx::EnumerationArray<Channel, rvec*> xc_old_whole; // Last known whole positions of the two channels (important for multimeric ch.!)
+ gmx::EnumerationArray<Channel, rvec**> xc_old_whole_p; // Pointer to these positions
+ swapstateIons_t* ionType; // History information for one ion type
} swaphistory_t;
#endif
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
CPP_SOURCE_FILES
checkpointdata.cpp
forcebuffers.cpp
+ multipletimestepping.cpp
)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for the MultipleTimeStepping class and stand-alone functions.
+ *
+ * \author berk Hess <hess@kth.se>
+ * \ingroup module_mdtypes
+ */
+#include "gmxpre.h"
+
+#include "gromacs/mdtypes/multipletimestepping.h"
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "testutils/testasserts.h"
+
+namespace gmx
+{
+
+namespace test
+{
+
+namespace
+{
+
+//! brief Sets up the MTS levels in \p ir and tests whether the number of errors matches \p numExpectedErrors
+void setAndCheckMtsLevels(const GromppMtsOpts& mtsOpts, t_inputrec* ir, const int numExpectedErrors)
+{
+ std::vector<std::string> errorMessages;
+ ir->useMts = true;
+ ir->mtsLevels = setupMtsLevels(mtsOpts, &errorMessages);
+
+ if (haveValidMtsSetup(*ir))
+ {
+ std::vector<std::string> errorMessagesCheck = checkMtsRequirements(*ir);
+
+ // Concatenate the two lists with error messages
+ errorMessages.insert(errorMessages.end(), errorMessagesCheck.begin(), errorMessagesCheck.end());
+ }
+
+ EXPECT_EQ(errorMessages.size(), numExpectedErrors);
+}
+
+} // namespace
+
+//! Checks that only numLevels = 2 does not produce an error
+TEST(MultipleTimeStepping, ChecksNumLevels)
+{
+ for (int numLevels = 0; numLevels <= 3; numLevels++)
+ {
+ GromppMtsOpts mtsOpts;
+ mtsOpts.numLevels = numLevels;
+ mtsOpts.level2Factor = 2;
+
+ t_inputrec ir;
+
+ setAndCheckMtsLevels(mtsOpts, &ir, numLevels != 2 ? 1 : 0);
+ }
+}
+
+//! Test that each force group works
+TEST(MultipleTimeStepping, SelectsForceGroups)
+{
+ for (int forceGroupIndex = 0; forceGroupIndex < static_cast<int>(MtsForceGroups::Count);
+ forceGroupIndex++)
+ {
+ const MtsForceGroups forceGroup = static_cast<MtsForceGroups>(forceGroupIndex);
+ SCOPED_TRACE("Testing force group " + mtsForceGroupNames[forceGroup]);
+
+ GromppMtsOpts mtsOpts;
+ mtsOpts.numLevels = 2;
+ mtsOpts.level2Forces = mtsForceGroupNames[forceGroup];
+ mtsOpts.level2Factor = 2;
+
+ t_inputrec ir;
+
+ setAndCheckMtsLevels(mtsOpts, &ir, 0);
+
+ EXPECT_EQ(ir.mtsLevels[1].forceGroups.count(), 1);
+ EXPECT_EQ(ir.mtsLevels[1].forceGroups[forceGroupIndex], true);
+ }
+}
+
+//! Checks that factor is checked
+TEST(MultipleTimeStepping, ChecksStepFactor)
+{
+ for (int stepFactor = 0; stepFactor <= 3; stepFactor++)
+ {
+ GromppMtsOpts mtsOpts;
+ mtsOpts.numLevels = 2;
+ mtsOpts.level2Factor = stepFactor;
+
+ t_inputrec ir;
+
+ setAndCheckMtsLevels(mtsOpts, &ir, stepFactor < 2 ? 1 : 0);
+ }
+}
+
+namespace
+{
+
+GromppMtsOpts simpleMtsOpts()
+{
+ GromppMtsOpts mtsOpts;
+ mtsOpts.numLevels = 2;
+ mtsOpts.level2Forces = "nonbonded";
+ mtsOpts.level2Factor = 4;
+
+ return mtsOpts;
+}
+
+} // namespace
+
+TEST(MultipleTimeStepping, ChecksPmeIsAtLastLevel)
+{
+ const GromppMtsOpts mtsOpts = simpleMtsOpts();
+
+ t_inputrec ir;
+ ir.coulombtype = CoulombInteractionType::Pme;
+
+ setAndCheckMtsLevels(mtsOpts, &ir, 1);
+}
+
+//! Test fixture base for parametrizing interval tests
+using MtsIntervalTestParams = std::tuple<std::string, int>;
+class MtsIntervalTest : public ::testing::Test, public ::testing::WithParamInterface<MtsIntervalTestParams>
+{
+public:
+ MtsIntervalTest()
+ {
+ const auto params = GetParam();
+ const auto& parameterName = std::get<0>(params);
+ const auto interval = std::get<1>(params);
+ numExpectedErrors_ = (interval == 4 ? 0 : 1);
+
+ if (parameterName == "nstcalcenergy")
+ {
+ ir_.nstcalcenergy = interval;
+ }
+ else if (parameterName == "nstenergy")
+ {
+ ir_.nstenergy = interval;
+ }
+ else if (parameterName == "nstfout")
+ {
+ ir_.nstfout = interval;
+ }
+ else if (parameterName == "nstlist")
+ {
+ ir_.nstlist = interval;
+ }
+ else if (parameterName == "nstdhdl")
+ {
+ ir_.efep = FreeEnergyPerturbationType::Yes;
+ ir_.fepvals->nstdhdl = interval;
+ }
+ else
+
+ {
+ GMX_RELEASE_ASSERT(false, "unknown parameter name");
+ }
+ }
+
+ t_inputrec ir_;
+ int numExpectedErrors_;
+};
+
+TEST_P(MtsIntervalTest, Works)
+{
+ const GromppMtsOpts mtsOpts = simpleMtsOpts();
+
+ setAndCheckMtsLevels(mtsOpts, &ir_, numExpectedErrors_);
+}
+
+INSTANTIATE_TEST_CASE_P(
+ ChecksStepInterval,
+ MtsIntervalTest,
+ ::testing::Combine(
+ ::testing::Values("nstcalcenergy", "nstenergy", "nstfout", "nstlist", "nstdhdl"),
+ ::testing::Values(3, 4, 5)));
+
+// Check that correct input does not produce errors
+TEST(MultipleTimeStepping, ChecksIntegrator)
+{
+ const GromppMtsOpts mtsOpts = simpleMtsOpts();
+
+ t_inputrec ir;
+ ir.eI = IntegrationAlgorithm::BD;
+
+ setAndCheckMtsLevels(mtsOpts, &ir, 1);
+}
+
+} // namespace test
+} // namespace gmx
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2018,2019, by the GROMACS development team, led by
+# Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-gmx_add_libgromacs_sources(
- communicator.cpp
- utilities.cpp
+# Set up the module library
+add_library(mimic INTERFACE)
+file(GLOB MIMIC_SOURCES *.cpp)
+set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${MIMIC_SOURCES} PARENT_SCOPE)
+
+# Source files have the following dependencies on library infrastructure.
+#target_link_libraries(mimic PRIVATE
+# common
+# legacy_modules
+#)
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(mimic PUBLIC
+target_include_directories(mimic INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(mimic PUBLIC
+target_link_libraries(mimic INTERFACE
+ legacy_api
)
+# TODO: when mimic is an OBJECT target
+#target_link_libraries(mimic PUBLIC legacy_api)
+#target_link_libraries(mimic PRIVATE common)
+
+# Module dependencies
+# mimic interfaces convey transitive dependence on these modules.
+#target_link_libraries(mimic PUBLIC
+target_link_libraries(mimic INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(mimic PRIVATE NOTHING)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(mimic PRIVATE legacy_modules)
+
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
bonds.push_back(offset + at1 + 1);
bonds.push_back(offset + at2 + 1);
bondLengths.push_back(static_cast<double>(mtop->ffparams.iparams[contype].constr.dA)
- / BOHR2NM);
+ / gmx::c_bohr2Nm);
}
for (int ncon = 0; ncon < nsettle; ++ncon)
bonds.push_back(offset + h1 + 1);
bonds.push_back(offset + h2 + 1);
bondLengths.push_back(static_cast<double>(mtop->ffparams.iparams[contype].constr.dA)
- / BOHR2NM);
+ / gmx::c_bohr2Nm);
bondLengths.push_back(static_cast<double>(mtop->ffparams.iparams[contype].constr.dA)
- / BOHR2NM);
+ / gmx::c_bohr2Nm);
bondLengths.push_back(static_cast<double>(mtop->ffparams.iparams[contype].constr.dB)
- / BOHR2NM);
+ / gmx::c_bohr2Nm);
}
nAtomsMol.push_back(type->atoms.nr);
std::vector<double> convertedCoords;
for (auto& coord : coords)
{
- convertedCoords.push_back(static_cast<double>(coord[0]) / BOHR2NM);
- convertedCoords.push_back(static_cast<double>(coord[1]) / BOHR2NM);
- convertedCoords.push_back(static_cast<double>(coord[2]) / BOHR2NM);
+ convertedCoords.push_back(static_cast<double>(coord[0]) / gmx::c_bohr2Nm);
+ convertedCoords.push_back(static_cast<double>(coord[1]) / gmx::c_bohr2Nm);
+ convertedCoords.push_back(static_cast<double>(coord[2]) / gmx::c_bohr2Nm);
}
// sending array of coordinates
MCL_receive(&*coords.begin(), 3 * natoms, TYPE_DOUBLE, 0);
for (int j = 0; j < natoms; ++j)
{
- (*x)[j][0] = static_cast<real>(coords[j * 3] * BOHR2NM);
- (*x)[j][1] = static_cast<real>(coords[j * 3 + 1] * BOHR2NM);
- (*x)[j][2] = static_cast<real>(coords[j * 3 + 2] * BOHR2NM);
+ (*x)[j][0] = static_cast<real>(coords[j * 3] * gmx::c_bohr2Nm);
+ (*x)[j][1] = static_cast<real>(coords[j * 3 + 1] * gmx::c_bohr2Nm);
+ (*x)[j][2] = static_cast<real>(coords[j * 3 + 2] * gmx::c_bohr2Nm);
}
}
void gmx::MimicCommunicator::sendEnergies(real energy)
{
- double convertedEnergy = energy / (HARTREE2KJ * AVOGADRO);
+ double convertedEnergy = energy / (gmx::c_hartree2Kj * gmx::c_avogadro);
MCL_send(&convertedEnergy, 1, TYPE_DOUBLE, 0);
}
std::vector<double> convertedForce;
for (int j = 0; j < natoms; ++j)
{
- convertedForce.push_back(static_cast<real>(forces[j][0]) / HARTREE_BOHR2MD);
- convertedForce.push_back(static_cast<real>(forces[j][1]) / HARTREE_BOHR2MD);
- convertedForce.push_back(static_cast<real>(forces[j][2]) / HARTREE_BOHR2MD);
+ convertedForce.push_back(static_cast<real>(forces[j][0]) / gmx::c_hartreeBohr2Md);
+ convertedForce.push_back(static_cast<real>(forces[j][1]) / gmx::c_hartreeBohr2Md);
+ convertedForce.push_back(static_cast<real>(forces[j][2]) / gmx::c_hartreeBohr2Md);
}
MCL_send(&*convertedForce.begin(), convertedForce.size(), TYPE_DOUBLE, 0);
}
file(GLOB MODULARSIMULATOR_SOURCES *.cpp)
add_library(modularsimulator OBJECT ${MODULARSIMULATOR_SOURCES})
-target_include_directories(modularsimulator SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
-gmx_target_compile_options(modularsimulator)
-target_compile_definitions(modularsimulator PRIVATE HAVE_CONFIG_H)
-# Should be possible to remove this when resolving #3290
-target_include_directories(modularsimulator SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
-if(GMX_OPENMP)
+if (GMX_OPENMP)
# Explicitly set properties for modular simulator module to compile with openmp
set_target_properties(modularsimulator PROPERTIES COMPILE_OPTIONS $<TARGET_PROPERTY:OpenMP::OpenMP_CXX,INTERFACE_COMPILE_OPTIONS>)
-endif()
+endif ()
if (WIN32)
gmx_target_warning_suppression(modularsimulator /wd4244 HAS_NO_MSVC_LOSSY_CONVERSION)
gmx_target_warning_suppression(modularsimulator /wd4996 HAS_NO_MSVC_UNSAFE_FUNCTION)
-else()
+else ()
# Several std::move uses are redundant in C++14, but clang before
# 3.9 had a bug that needed them. gcc 9 can warn about their use,
# which we need to supress. This suppression should be removed
# when GROMACS requires clang 3.9 or higher.
gmx_target_warning_suppression(modularsimulator "-Wno-redundant-move" HAS_NO_REDUNDANT_MOVE)
-endif()
+endif ()
+
+target_include_directories(modularsimulator SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
+gmx_target_compile_options(modularsimulator)
+target_compile_definitions(modularsimulator PRIVATE HAVE_CONFIG_H)
+# Should be possible to remove this when resolving #3290
+target_include_directories(modularsimulator SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
+
+# Source files have the following private external dependencies.
+target_link_libraries(modularsimulator PRIVATE tng_io)
+
+# Source files have the following private infrastructure dependencies.
+target_link_libraries(modularsimulator PRIVATE common)
+
+# Source files have the following private module dependencies.
+# TODO: Explicitly link specific modules.
+target_link_libraries(modularsimulator PRIVATE legacy_modules)
+target_link_libraries(modularsimulator PRIVATE
+ gmxlib
+ math
+ mdtypes
+ tng_io
+ )
+
+# Public interface for modules, including dependencies and interfaces
+target_include_directories(modularsimulator PUBLIC
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+target_link_libraries(modularsimulator PUBLIC
+ legacy_api
+ )
+
+# Module dependencies
+# This module convey transitive dependence on these modules.
+target_link_libraries(modularsimulator PUBLIC
+ utility
+ )
list(APPEND libgromacs_object_library_dependencies modularsimulator)
set(libgromacs_object_library_dependencies ${libgromacs_object_library_dependencies} PARENT_SCOPE)
if (MASTER(cr_))
{
- mdoutf_write_checkpoint(trajectoryElement_->outf_, fplog_, cr_, step, time, state_global_,
- observablesHistory_, &checkpointDataHolder);
+ mdoutf_write_checkpoint(
+ trajectoryElement_->outf_, fplog_, cr_, step, time, state_global_, observablesHistory_, &checkpointDataHolder);
}
}
formatString(
"CheckpointHelper client with key %s registered for checkpointing, "
"but %s does not exist in the input checkpoint file.",
- key.c_str(), key.c_str())
+ key.c_str(),
+ key.c_str())
.c_str());
}
client->restoreCheckpointState(
std::vector<std::tuple<std::string, ICheckpointHelperClient*>>&& clients = { clientsMap_.begin(),
clientsMap_.end() };
- return std::make_unique<CheckpointHelper>(std::move(clients), std::move(checkpointHandler_),
-
std::forward<Args>(args)...);
+ return std::make_unique<CheckpointHelper>(
+
std::move(clients), std::move(checkpointHandler_), std::forward<Args>(args)...);
}
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "computeglobalselement.h"
-#include "gromacs/domdec/partition.h"
+#include "gromacs/domdec/domdec.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/md_support.h"
#include "gromacs/mdlib/mdatoms.h"
#include "gromacs/mdlib/stat.h"
t_nrnb* nrnb,
gmx_wallcycle* wcycle,
t_forcerec* fr,
- const gmx_mtop_t* global_top,
+ const gmx_mtop_t& global_top,
Constraints* constr) :
energyReductionStep_(-1),
virialReductionStep_(-1),
vvSchedulingStep_(-1),
- doStopCM_(inputrec->comm_mode != ecmNO),
+ doStopCM_(inputrec->comm_mode != ComRemovalAlgorithm::No),
nstcomm_(inputrec->nstcomm),
nstglobalcomm_(nstglobalcomm),
lastStep_(inputrec->nsteps + inputrec->init_step),
initStep_(inputrec->init_step),
nullSignaller_(std::make_unique<SimulationSignaller>(nullptr, nullptr, nullptr, false, false)),
- totalNumberOfBondedInteractions_(0),
- shouldCheckNumberOfBondedInteractions_(false),
statePropagatorData_(statePropagatorData),
energyData_(energyData),
localTopology_(nullptr),
freeEnergyPerturbationData_(freeEnergyPerturbationData),
- vcm_(global_top->groups, *inputrec),
+ vcm_(global_top.groups, *inputrec),
signals_(signals),
fplog_(fplog),
mdlog_(mdlog),
auto v = statePropagatorData_->velocitiesView();
// At initialization, do not pass x with acceleration-correction mode
// to avoid (incorrect) correction of the initial coordinates.
- auto x = vcm_.mode == ecmLINEAR_ACCELERATION_CORRECTION ? ArrayRefWithPadding<RVec>()
- : statePropagatorData_->positionsView();
- process_and_stopcm_grp(fplog_, &vcm_, *mdAtoms_->mdatoms(), x.unpaddedArrayRef(),
- v.unpaddedArrayRef());
+ auto x = vcm_.mode == ComRemovalAlgorithm::LinearAccelerationCorrection
+ ? ArrayRefWithPadding<RVec>()
+ : statePropagatorData_->positionsView();
+ process_and_stopcm_grp(
+ fplog_, &vcm_, *mdAtoms_->mdatoms(), x.unpaddedArrayRef(), v.unpaddedArrayRef());
inc_nrnb(nrnb_, eNR_STOPCM, mdAtoms_->mdatoms()->homenr);
}
const bool doInterSimSignal = false;
// Make signaller to signal stop / reset / checkpointing signals
- auto signaller = std::make_shared<SimulationSignaller>(signals_, cr_, nullptr,
- doInterSimSignal, doIntraSimSignal);
+ auto signaller = std::make_shared<SimulationSignaller>(
+ signals_, cr_, nullptr, doInterSimSignal, doIntraSimSignal);
registerRunFunction([this, step, flags, signaller = std::move(signaller)]() {
compute(step, flags, signaller.get(), true);
auto lastbox = useLastBox ? statePropagatorData_->constPreviousBox()
: statePropagatorData_->constBox();
- compute_globals(
- gstat_, cr_, inputrec_, fr_, energyData_->ekindata(), x, v, box, mdAtoms_->mdatoms(),
- nrnb_, &vcm_, step != -1 ? wcycle_ : nullptr, energyData_->enerdata(),
- energyData_->forceVirial(step), energyData_->constraintVirial(step),
- energyData_->totalVirial(step), energyData_->pressure(step), constr_, signaller,
- lastbox, &totalNumberOfBondedInteractions_, energyData_->needToSumEkinhOld(),
- flags | (shouldCheckNumberOfBondedInteractions_ ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
- checkNumberOfBondedInteractions(mdlog_, cr_, totalNumberOfBondedInteractions_, top_global_,
- localTopology_, x, box, &shouldCheckNumberOfBondedInteractions_);
+ if (DOMAINDECOMP(cr_) && shouldCheckNumberOfBondedInteractions(*cr_->dd))
+ {
+ flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
+ }
+ compute_globals(gstat_,
+ cr_,
+ inputrec_,
+ fr_,
+ energyData_->ekindata(),
+ x,
+ v,
+ box,
+ mdAtoms_->mdatoms(),
+ nrnb_,
+ &vcm_,
+ step != -1 ? wcycle_ : nullptr,
+ energyData_->enerdata(),
+ energyData_->forceVirial(step),
+ energyData_->constraintVirial(step),
+ energyData_->totalVirial(step),
+ energyData_->pressure(step),
+ (((flags & CGLO_ENERGY) != 0) && constr_ != nullptr) ? constr_->rmsdData()
+ : gmx::ArrayRef<real>{},
+ signaller,
+ lastbox,
+ energyData_->needToSumEkinhOld(),
+ flags);
+ if (DOMAINDECOMP(cr_))
+ {
+ checkNumberOfBondedInteractions(mdlog_, cr_, top_global_, localTopology_, x, box);
+ }
if (flags & CGLO_STOPCM && !isInit)
{
process_and_stopcm_grp(fplog_, &vcm_, *mdAtoms_->mdatoms(), x, v);
}
}
-template<ComputeGlobalsAlgorithm algorithm>
-CheckBondedInteractionsCallback ComputeGlobalsElement<algorithm>::getCheckNumberOfBondedInteractionsCallback()
-{
- return [this]() { needToCheckNumberOfBondedInteractions(); };
-}
-
-template<ComputeGlobalsAlgorithm algorithm>
-void ComputeGlobalsElement<algorithm>::needToCheckNumberOfBondedInteractions()
-{
- shouldCheckNumberOfBondedInteractions_ = true;
-}
-
template<ComputeGlobalsAlgorithm algorithm>
void ComputeGlobalsElement<algorithm>::setTopology(const gmx_localtop_t* top)
{
{
auto* element = builderHelper->storeElement(
std::make_unique<ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>>(
- statePropagatorData, energyData, freeEnergyPerturbationData,
+ statePropagatorData,
+ energyData,
+ freeEnergyPerturbationData,
globalCommunicationHelper->simulationSignals(),
- globalCommunicationHelper->nstglobalcomm(), legacySimulatorData->fplog,
- legacySimulatorData->mdlog, legacySimulatorData->cr,
- legacySimulatorData->inputrec, legacySimulatorData->mdAtoms,
- legacySimulatorData->nrnb, legacySimulatorData->wcycle, legacySimulatorData->fr,
- legacySimulatorData->top_global, legacySimulatorData->constr));
-
- // TODO: Remove this when DD can reduce bonded interactions independently (#3421)
- auto* castedElement = static_cast<ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>*>(element);
- globalCommunicationHelper->setCheckBondedInteractionsCallback(
- castedElement->getCheckNumberOfBondedInteractionsCallback());
+ globalCommunicationHelper->nstglobalcomm(),
+ legacySimulatorData->fplog,
+ legacySimulatorData->mdlog,
+ legacySimulatorData->cr,
+ legacySimulatorData->inputrec,
+ legacySimulatorData->mdAtoms,
+ legacySimulatorData->nrnb,
+ legacySimulatorData->wcycle,
+ legacySimulatorData->fr,
+ legacySimulatorData->top_global,
+ legacySimulatorData->constr));
return element;
}
{
ISimulatorElement* vvComputeGlobalsElement = builderHelper->storeElement(
std::make_unique<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>(
- statePropagatorData, energyData, freeEnergyPerturbationData,
+ statePropagatorData,
+ energyData,
+ freeEnergyPerturbationData,
globalCommunicationHelper->simulationSignals(),
- globalCommunicationHelper->nstglobalcomm(), simulator->fplog, simulator->mdlog,
- simulator->cr, simulator->inputrec, simulator->mdAtoms, simulator->nrnb,
- simulator->wcycle, simulator->fr, simulator->top_global, simulator->constr));
-
- // TODO: Remove this when DD can reduce bonded interactions independently (#3421)
- auto* castedElement =
- static_cast<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>*>(
- vvComputeGlobalsElement);
- globalCommunicationHelper->setCheckBondedInteractionsCallback(
- castedElement->getCheckNumberOfBondedInteractionsCallback());
+ globalCommunicationHelper->nstglobalcomm(),
+ simulator->fplog,
+ simulator->mdlog,
+ simulator->cr,
+ simulator->inputrec,
+ simulator->mdAtoms,
+ simulator->nrnb,
+ simulator->wcycle,
+ simulator->fr,
+ simulator->top_global,
+ simulator->constr));
builderHelper->storeValue(key, vvComputeGlobalsElement);
return vvComputeGlobalsElement;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
t_nrnb* nrnb,
gmx_wallcycle* wcycle,
t_forcerec* fr,
- const gmx_mtop_t* global_top,
+ const gmx_mtop_t& global_top,
Constraints* constr);
//! Destructor
//! Contains user input mdp options.
const t_inputrec* inputrec_;
//! Full system topology - only needed for checkNumberOfBondedInteractions.
- const gmx_mtop_t* top_global_;
+ const gmx_mtop_t& top_global_;
//! Atom parameters for this domain.
const MDAtoms* mdAtoms_;
//! Handles constraints.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void ConstraintsElement<variable>::elementSetup()
{
if (!inputrec_->bContinuation
- && ((variable == ConstraintVariable::Positions && inputrec_->eI == eiMD)
- || (variable == ConstraintVariable::Velocities && inputrec_->eI == eiVV)))
+ && ((variable == ConstraintVariable::Positions && inputrec_->eI == IntegrationAlgorithm::MD)
+ || (variable == ConstraintVariable::Velocities && inputrec_->eI == IntegrationAlgorithm::VV)))
{
- const real lambdaBonded = freeEnergyPerturbationData_
- ? freeEnergyPerturbationData_->constLambdaView()[efptBONDED]
- : 0;
+ const real lambdaBonded =
+ freeEnergyPerturbationData_
+ ? freeEnergyPerturbationData_->constLambdaView()[static_cast<int>(
+ FreeEnergyPerturbationCouplingType::Bonded)]
+ : 0;
// Constrain the initial coordinates and velocities
- do_constrain_first(
- fplog_, constr_, inputrec_, statePropagatorData_->totalNumAtoms(),
- statePropagatorData_->localNumAtoms(), statePropagatorData_->positionsView(),
- statePropagatorData_->velocitiesView(), statePropagatorData_->box(), lambdaBonded);
+ do_constrain_first(fplog_,
+ constr_,
+ inputrec_,
+ statePropagatorData_->totalNumAtoms(),
+ statePropagatorData_->localNumAtoms(),
+ statePropagatorData_->positionsView(),
+ statePropagatorData_->velocitiesView(),
+ statePropagatorData_->box(),
+ lambdaBonded);
if (isMasterRank_)
{
- if (inputrec_->eConstrAlg == econtLINCS)
+ if (inputrec_->eConstrAlg == ConstraintAlgorithm::Lincs)
{
- fprintf(fplog_, "RMS relative constraint deviation after constraining: %.2e\n",
+ fprintf(fplog_,
+ "RMS relative constraint deviation after constraining: %.2e\n",
constr_->rmsd());
}
}
ArrayRefWithPadding<RVec> v;
const real lambdaBonded =
- freeEnergyPerturbationData_ ? freeEnergyPerturbationData_->constLambdaView()[efptBONDED] : 0;
+ freeEnergyPerturbationData_
+ ? freeEnergyPerturbationData_
+ ->constLambdaView()[static_cast<int>(FreeEnergyPerturbationCouplingType::Bonded)]
+ : 0;
real dvdlambda = 0;
switch (variable)
default: gmx_fatal(FARGS, "Constraint algorithm not implemented for modular simulator.");
}
- constr_->apply(writeLog, writeEnergy, step, 1, 1.0, x, xprime, min_proj, statePropagatorData_->box(),
- lambdaBonded, &dvdlambda, v, calculateVirial, vir_con, variable);
+ constr_->apply(writeLog,
+ writeEnergy,
+ step,
+ 1,
+ 1.0,
+ x,
+ xprime,
+ min_proj,
+ statePropagatorData_->box(),
+ lambdaBonded,
+ &dvdlambda,
+ v,
+ calculateVirial,
+ vir_con,
+ variable);
if (calculateVirial)
{
- if (inputrec_->eI == eiVV)
+ if (inputrec_->eI == IntegrationAlgorithm::VV)
{
// For some reason, the shake virial in VV is reset twice a step.
// Energy element will only do this once per step.
FreeEnergyPerturbationData* freeEnergyPerturbationData,
GlobalCommunicationHelper gmx_unused* globalCommunicationHelper)
{
- return builderHelper->storeElement(std::make_unique<ConstraintsElement<variable>>(
- legacySimulatorData->constr, statePropagatorData, energyData,
- freeEnergyPerturbationData, MASTER(legacySimulatorData->cr), legacySimulatorData->fplog,
- legacySimulatorData->inputrec, legacySimulatorData->mdAtoms->mdatoms()));
+ return builderHelper->storeElement(
+ std::make_unique<ConstraintsElement<variable>>(legacySimulatorData->constr,
+ statePropagatorData,
+ energyData,
+ freeEnergyPerturbationData,
+ MASTER(legacySimulatorData->cr),
+ legacySimulatorData->fplog,
+ legacySimulatorData->inputrec,
+ legacySimulatorData->mdAtoms->mdatoms()));
}
// Explicit template initializations
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
namespace gmx
{
-DomDecHelper::DomDecHelper(bool isVerbose,
- int verbosePrintInterval,
- StatePropagatorData* statePropagatorData,
- FreeEnergyPerturbationData* freeEnergyPerturbationData,
- TopologyHolder* topologyHolder,
- CheckBondedInteractionsCallback checkBondedInteractionsCallback,
- int nstglobalcomm,
- FILE* fplog,
- t_commrec* cr,
- const MDLogger& mdlog,
- Constraints* constr,
- t_inputrec* inputrec,
- MDAtoms* mdAtoms,
- t_nrnb* nrnb,
- gmx_wallcycle* wcycle,
- t_forcerec* fr,
- VirtualSitesHandler* vsite,
- ImdSession* imdSession,
- pull_t* pull_work) :
+DomDecHelper::DomDecHelper(bool isVerbose,
+ int verbosePrintInterval,
+ StatePropagatorData* statePropagatorData,
+ FreeEnergyPerturbationData* freeEnergyPerturbationData,
+ TopologyHolder* topologyHolder,
+ int nstglobalcomm,
+ FILE* fplog,
+ t_commrec* cr,
+ const MDLogger& mdlog,
+ Constraints* constr,
+ const t_inputrec* inputrec,
+ MDAtoms* mdAtoms,
+ t_nrnb* nrnb,
+ gmx_wallcycle* wcycle,
+ t_forcerec* fr,
+ VirtualSitesHandler* vsite,
+ ImdSession* imdSession,
+ pull_t* pull_work) :
nextNSStep_(-1),
isVerbose_(isVerbose),
verbosePrintInterval_(verbosePrintInterval),
statePropagatorData_(statePropagatorData),
freeEnergyPerturbationData_(freeEnergyPerturbationData),
topologyHolder_(topologyHolder),
- checkBondedInteractionsCallback_(std::move(checkBondedInteractionsCallback)),
fplog_(fplog),
cr_(cr),
mdlog_(mdlog),
gmx_wallcycle* wcycle = nullptr;
// Distribute the charge groups over the nodes from the master node
- partitionSystem(verbose, isMasterState, nstglobalcomm, wcycle,
- statePropagatorData_->localState(), statePropagatorData_->globalState());
+ partitionSystem(verbose,
+ isMasterState,
+ nstglobalcomm,
+ wcycle,
+ statePropagatorData_->localState(),
+ statePropagatorData_->globalState());
}
void DomDecHelper::run(Step step, Time gmx_unused time)
ForceBuffers* forcePointer = statePropagatorData_->forcePointer();
// Distribute the charge groups over the nodes from the master node
- dd_partition_system(fplog_, mdlog_, inputrec_->init_step, cr_, isMasterState, nstglobalcomm,
- globalState, topologyHolder_->globalTopology(), inputrec_, imdSession_,
- pull_work_, localState.get(), forcePointer, mdAtoms_,
- topologyHolder_->localTopology_.get(), fr_, vsite_, constr_, nrnb_, wcycle,
+ dd_partition_system(fplog_,
+ mdlog_,
+ inputrec_->init_step,
+ cr_,
+ isMasterState,
+ nstglobalcomm,
+ globalState,
+ topologyHolder_->globalTopology(),
+ *inputrec_,
+ imdSession_,
+ pull_work_,
+ localState.get(),
+ forcePointer,
+ mdAtoms_,
+ topologyHolder_->localTopology_.get(),
+ fr_,
+ vsite_,
+ constr_,
+ nrnb_,
+ wcycle,
verbose);
topologyHolder_->updateLocalTopology();
- checkBondedInteractionsCallback_();
statePropagatorData_->setLocalState(std::move(localState));
if (freeEnergyPerturbationData_)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! \addtogroup module_modularsimulator
//! \{
-//! The function type allowing to request a check of the number of bonded interactions
-typedef std::function<void()> CheckBondedInteractionsCallback;
-
/*! \internal
* \brief Infrastructure element responsible for domain decomposition
*
{
public:
//! Constructor
- DomDecHelper(bool isVerbose,
- int verbosePrintInterval,
- StatePropagatorData* statePropagatorData,
- FreeEnergyPerturbationData* freeEnergyPerturbationData,
- TopologyHolder* topologyHolder,
- CheckBondedInteractionsCallback checkBondedInteractionsCallback,
- int nstglobalcomm,
- FILE* fplog,
- t_commrec* cr,
- const MDLogger& mdlog,
- Constraints* constr,
- t_inputrec* inputrec,
- MDAtoms* mdAtoms,
- t_nrnb* nrnb,
- gmx_wallcycle* wcycle,
- t_forcerec* fr,
- VirtualSitesHandler* vsite,
- ImdSession* imdSession,
- pull_t* pull_work);
+ DomDecHelper(bool isVerbose,
+ int verbosePrintInterval,
+ StatePropagatorData* statePropagatorData,
+ FreeEnergyPerturbationData* freeEnergyPerturbationData,
+ TopologyHolder* topologyHolder,
+ int nstglobalcomm,
+ FILE* fplog,
+ t_commrec* cr,
+ const MDLogger& mdlog,
+ Constraints* constr,
+ const t_inputrec* inputrec,
+ MDAtoms* mdAtoms,
+ t_nrnb* nrnb,
+ gmx_wallcycle* wcycle,
+ t_forcerec* fr,
+ VirtualSitesHandler* vsite,
+ ImdSession* imdSession,
+ pull_t* pull_work);
/*! \brief Run domain decomposition
*
FreeEnergyPerturbationData* freeEnergyPerturbationData_;
//! Pointer to the topology
TopologyHolder* topologyHolder_;
- //! Pointer to the ComputeGlobalsHelper object - to ask for # of bonded interaction checking
- CheckBondedInteractionsCallback checkBondedInteractionsCallback_;
//! Helper function unifying the DD partitioning calls in setup() and run()
void partitionSystem(bool verbose,
//! Handles constraints.
Constraints* constr_;
//! Contains user input mdp options.
- t_inputrec* inputrec_;
+ const t_inputrec* inputrec_;
//! Atom parameters for this domain.
MDAtoms* mdAtoms_;
//! Manages flop accounting.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/compute_io.h"
-#include "gromacs/mdlib/coupling.h"
#include "gromacs/mdlib/enerdata_utils.h"
#include "gromacs/mdlib/energyoutput.h"
#include "gromacs/mdlib/mdatoms.h"
#include "gromacs/mdlib/mdoutf.h"
#include "gromacs/mdlib/stat.h"
+#include "gromacs/mdlib/tgroup.h"
#include "gromacs/mdlib/update.h"
-#include "gromacs/mdrunutility/handlerestart.h"
-#include "gromacs/mdtypes/checkpointdata.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/energyhistory.h"
+#include "gromacs/mdtypes/group.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/mdtypes/observableshistory.h"
#include "freeenergyperturbationdata.h"
#include "modularsimulator.h"
-#include "parrinellorahmanbarostat.h"
#include "simulatoralgorithm.h"
#include "statepropagatordata.h"
-#include "velocityscalingtemperaturecoupling.h"
struct pull_t;
class t_state;
EnergyData::EnergyData(StatePropagatorData* statePropagatorData,
FreeEnergyPerturbationData* freeEnergyPerturbationData,
- const gmx_mtop_t* globalTopology,
+ const gmx_mtop_t& globalTopology,
const t_inputrec* inputrec,
const MDAtoms* mdAtoms,
gmx_enerdata_t* enerd,
const Constraints* constr,
FILE* fplog,
t_fcdata* fcd,
- const MdModulesNotifier& mdModulesNotifier,
+ const MDModulesNotifiers& mdModulesNotifiers,
bool isMasterRank,
ObservablesHistory* observablesHistory,
StartingBehavior startingBehavior,
startingBehavior_(startingBehavior),
statePropagatorData_(statePropagatorData),
freeEnergyPerturbationData_(freeEnergyPerturbationData),
- velocityScalingTemperatureCoupling_(nullptr),
- parrinelloRahmanBarostat_(nullptr),
inputrec_(inputrec),
top_global_(globalTopology),
mdAtoms_(mdAtoms),
constr_(constr),
fplog_(fplog),
fcd_(fcd),
- mdModulesNotifier_(mdModulesNotifier),
- groups_(&globalTopology->groups),
+ mdModulesNotifiers_(mdModulesNotifiers),
+ groups_(&globalTopology.groups),
observablesHistory_(observablesHistory),
simulationsShareState_(simulationsShareState)
{
auto isFreeEnergyCalculationStep = freeEnergyCalculationStep_ == step;
if (isEnergyCalculationStep || writeEnergy)
{
- registerRunFunction([this, time, isEnergyCalculationStep, isFreeEnergyCalculationStep]() {
- energyData_->doStep(time, isEnergyCalculationStep, isFreeEnergyCalculationStep);
+ registerRunFunction([this, step, time, isEnergyCalculationStep, isFreeEnergyCalculationStep]() {
+ energyData_->doStep(step, time, isEnergyCalculationStep, isFreeEnergyCalculationStep);
});
}
else
void EnergyData::setup(gmx_mdoutf* outf)
{
pull_t* pull_work = nullptr;
- energyOutput_ = std::make_unique<EnergyOutput>(
- mdoutf_get_fp_ene(outf), top_global_, inputrec_, pull_work, mdoutf_get_fp_dhdl(outf),
- false, startingBehavior_, simulationsShareState_, mdModulesNotifier_);
+ energyOutput_ = std::make_unique<EnergyOutput>(mdoutf_get_fp_ene(outf),
+ top_global_,
+ *inputrec_,
+ pull_work,
+ mdoutf_get_fp_dhdl(outf),
+ false,
+ startingBehavior_,
+ simulationsShareState_,
+ mdModulesNotifiers_);
if (!isMasterRank_)
{
// TODO: This probably doesn't really belong here...
// but we have all we need in this element,
// so we'll leave it here for now!
- double io = compute_io(inputrec_, top_global_->natoms, *groups_, energyOutput_->numEnergyTerms(), 1);
+ double io = compute_io(inputrec_, top_global_.natoms, *groups_, energyOutput_->numEnergyTerms(), 1);
if ((io > 2000) && isMasterRank_)
{
fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
if (!inputrec_->bContinuation)
{
real temp = enerd_->term[F_TEMP];
- if (inputrec_->eI != eiVV)
+ if (inputrec_->eI != IntegrationAlgorithm::VV)
{
/* Result of Ekin averaged over velocities of -half
* and +half step, while we only have -half step here.
return std::nullopt;
}
-void EnergyData::doStep(Time time, bool isEnergyCalculationStep, bool isFreeEnergyCalculationStep)
+void EnergyData::doStep(Step step, Time time, bool isEnergyCalculationStep, bool isFreeEnergyCalculationStep)
{
enerd_->term[F_ETOT] = enerd_->term[F_EPOT] + enerd_->term[F_EKIN];
if (freeEnergyPerturbationData_)
{
- accumulateKineticLambdaComponents(enerd_, freeEnergyPerturbationData_->constLambdaView(),
- *inputrec_->fepvals);
+ accumulateKineticLambdaComponents(
+ enerd_, freeEnergyPerturbationData_->constLambdaView(), *inputrec_->fepvals);
}
if (integratorHasConservedEnergyQuantity(inputrec_))
{
- enerd_->term[F_ECONSERVED] =
- enerd_->term[F_ETOT]
- + (velocityScalingTemperatureCoupling_
- ? velocityScalingTemperatureCoupling_->conservedEnergyContribution()
- : 0)
- + (parrinelloRahmanBarostat_ ? parrinelloRahmanBarostat_->conservedEnergyContribution() : 0);
+ enerd_->term[F_ECONSERVED] = enerd_->term[F_ETOT];
+ for (const auto& energyContibution : conservedEnergyContributions_)
+ {
+ enerd_->term[F_ECONSERVED] += energyContibution(step, time);
+ }
}
matrix nullMatrix = {};
energyOutput_->addDataAtEnergyStep(
- isFreeEnergyCalculationStep, isEnergyCalculationStep, time, mdAtoms_->mdatoms()->tmass, enerd_,
- inputrec_->fepvals, inputrec_->expandedvals, statePropagatorData_->constPreviousBox(),
- PTCouplingArrays({ parrinelloRahmanBarostat_ ? parrinelloRahmanBarostat_->boxVelocities() : nullMatrix,
+ isFreeEnergyCalculationStep,
+ isEnergyCalculationStep,
+ time,
+ mdAtoms_->mdatoms()->tmass,
+ enerd_,
+ inputrec_->fepvals.get(),
+ inputrec_->expandedvals.get(),
+ statePropagatorData_->constPreviousBox(),
+ PTCouplingArrays({ parrinelloRahmanBoxVelocities_ ? parrinelloRahmanBoxVelocities_() : nullMatrix,
{},
{},
{},
{} }),
freeEnergyPerturbationData_ ? freeEnergyPerturbationData_->currentFEPState() : 0,
- shakeVirial_, forceVirial_, totalVirial_, pressure_, ekind_, muTot_, constr_);
+ shakeVirial_,
+ forceVirial_,
+ totalVirial_,
+ pressure_,
+ ekind_,
+ muTot_,
+ constr_);
}
void EnergyData::write(gmx_mdoutf* outf, Step step, Time time, bool writeTrajectory, bool writeLog)
// energyOutput_->printAnnealingTemperatures(writeLog ? fplog_ : nullptr, groups_, &(inputrec_->opts));
Awh* awh = nullptr;
- energyOutput_->printStepToEnergyFile(mdoutf_get_fp_ene(outf), writeTrajectory, do_dr, do_or,
- writeLog ? fplog_ : nullptr, step, time, fcd_, awh);
+ energyOutput_->printStepToEnergyFile(
+ mdoutf_get_fp_ene(outf), writeTrajectory, do_dr, do_or, writeLog ? fplog_ : nullptr, step, time, fcd_, awh);
}
void EnergyData::addToForceVirial(const tensor virial, Step step)
pressureStep_ = step;
clear_mat(pressure_);
}
- GMX_ASSERT(step >= pressureStep_ || pressureStep_ == -1,
- "Asked for pressure of previous step.");
+ GMX_ASSERT(step >= pressureStep_ || pressureStep_ == -1, "Asked for pressure of previous step.");
return pressure_;
}
energyData_->hasReadEkinFromCheckpoint_ = MASTER(cr) ? energyData_->ekinstate_.bUpToDate : false;
if (PAR(cr))
{
- gmx_bcast(sizeof(hasReadEkinFromCheckpoint_), &energyData_->hasReadEkinFromCheckpoint_,
+ gmx_bcast(sizeof(hasReadEkinFromCheckpoint_),
+ &energyData_->hasReadEkinFromCheckpoint_,
cr->mpi_comm_mygroup);
}
if (energyData_->hasReadEkinFromCheckpoint_)
energyOutput->fillEnergyHistory(observablesHistory->energyHistory.get());
}
-void EnergyData::setVelocityScalingTemperatureCoupling(const VelocityScalingTemperatureCoupling* velocityScalingTemperatureCoupling)
+void EnergyData::addConservedEnergyContribution(EnergyContribution&& energyContribution)
{
- velocityScalingTemperatureCoupling_ = velocityScalingTemperatureCoupling;
+ conservedEnergyContributions_.emplace_back(std::move(energyContribution));
}
-void EnergyData::setParrinelloRahamnBarostat(const gmx::ParrinelloRahmanBarostat* parrinelloRahmanBarostat)
+void EnergyData::setParrinelloRahmanBoxVelocities(std::function<const rvec*()>&& parrinelloRahmanBoxVelocities)
{
- parrinelloRahmanBarostat_ = parrinelloRahmanBarostat;
+ GMX_RELEASE_ASSERT(!parrinelloRahmanBoxVelocities_,
+ "Received a second callback to the Parrinello-Rahman velocities");
+ parrinelloRahmanBoxVelocities_ = parrinelloRahmanBoxVelocities;
+}
+
+void EnergyData::updateKineticEnergy()
+{
+ // The legacy sum_ekin function does not offer named types, so define variables for readability
+ // dEkin/dlambda is not handled here
+ real* dEkinDLambda = nullptr;
+ // Whether we use the full step kinetic energy (vs the average of half step KEs)
+ const bool useFullStepKineticEnergy = (inputrec_->eI == IntegrationAlgorithm::VV);
+ /* Whether we're ignoring the NHC scaling factor, only used if useFullStepKineticEnergy
+ * is true. (This parameter is confusing, as it is named `bScaleEkin`, but prompts the
+ * function to ignore scaling. There is no use case within modular simulator to ignore
+ * these, so we set this to false.) */
+ const bool ignoreScalingFactor = false;
+
+ enerd_->term[F_TEMP] = sum_ekin(
+ &(inputrec_->opts), ekind_, dEkinDLambda, useFullStepKineticEnergy, ignoreScalingFactor);
+ enerd_->term[F_EKIN] = trace(ekind_->ekin);
}
EnergyData::Element* EnergyData::element()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_ENERGYELEMENT_MICROSTATE_H
#define GMX_ENERGYELEMENT_MICROSTATE_H
-#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/state.h"
#include "modularsimulatorinterfaces.h"
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
struct gmx_enerdata_t;
struct gmx_mtop_t;
struct ObservablesHistory;
class ParrinelloRahmanBarostat;
class StatePropagatorData;
class VelocityScalingTemperatureCoupling;
-struct MdModulesNotifier;
+struct MDModulesNotifiers;
+
+//! Function type for elements contributing energy
+using EnergyContribution = std::function<real(Step, Time)>;
/*! \internal
* \ingroup module_modularsimulator
//! Constructor
EnergyData(StatePropagatorData* statePropagatorData,
FreeEnergyPerturbationData* freeEnergyPerturbationData,
- const gmx_mtop_t* globalTopology,
+ const gmx_mtop_t& globalTopology,
const t_inputrec* inputrec,
const MDAtoms* mdAtoms,
gmx_enerdata_t* enerd,
const Constraints* constr,
FILE* fplog,
t_fcdata* fcd,
- const MdModulesNotifier& mdModulesNotifier,
+ const MDModulesNotifiers& mdModulesNotifiers,
bool isMasterRank,
ObservablesHistory* observablesHistory,
StartingBehavior startingBehavior,
*/
[[nodiscard]] bool hasReadEkinFromCheckpoint() const;
- /*! \brief Set velocity scaling temperature coupling
+ /*! \brief Add conserved energy contribution
*
- * This allows to set a pointer to a velocity scaling temperature coupling
- * element used to obtain contributions to the conserved energy.
- * TODO: This should be made obsolete my a more modular energy element
+ * This allows other elements to register callbacks for contributions to
+ * the conserved energy term.
*/
- void setVelocityScalingTemperatureCoupling(const VelocityScalingTemperatureCoupling* velocityScalingTemperatureCoupling);
+ void addConservedEnergyContribution(EnergyContribution&& energyContribution);
/*! \brief set Parrinello-Rahman barostat
*
* This allows to set a pointer to the Parrinello-Rahman barostat used to
* print the box velocities.
- * TODO: This should be made obsolete my a more modular energy element
*/
- void setParrinelloRahamnBarostat(const ParrinelloRahmanBarostat* parrinelloRahmanBarostat);
+ void setParrinelloRahmanBoxVelocities(std::function<const rvec*()>&& parrinelloRahmanBoxVelocities);
/*! \brief Initialize energy history
*
ObservablesHistory* observablesHistory,
EnergyOutput* energyOutput);
+ /*! \brief Request (local) kinetic energy update
+ */
+ void updateKineticEnergy();
+
//! The element taking part in the simulator loop
class Element;
//! Get pointer to element (whose lifetime is managed by this)
/*! \brief Save data at energy steps
*
+ * \param step The current step
* \param time The current time
* \param isEnergyCalculationStep Whether the current step is an energy calculation step
* \param isFreeEnergyCalculationStep Whether the current step is a free energy calculation step
*/
- void doStep(Time time, bool isEnergyCalculationStep, bool isFreeEnergyCalculationStep);
+ void doStep(Step step, Time time, bool isEnergyCalculationStep, bool isFreeEnergyCalculationStep);
/*! \brief Write to energy trajectory
*
StatePropagatorData* statePropagatorData_;
//! Pointer to the free energy perturbation data
FreeEnergyPerturbationData* freeEnergyPerturbationData_;
- //! Pointer to the vrescale thermostat
- const VelocityScalingTemperatureCoupling* velocityScalingTemperatureCoupling_;
- //! Pointer to the Parrinello-Rahman barostat
- const ParrinelloRahmanBarostat* parrinelloRahmanBarostat_;
+
+ //! Callbacks contributing to the conserved energy term
+ std::vector<EnergyContribution> conservedEnergyContributions_;
+ //! Callback to the Parrinello-Rahman box velocities
+ std::function<const rvec*()> parrinelloRahmanBoxVelocities_;
+
//! Contains user input mdp options.
const t_inputrec* inputrec_;
//! Full system topology.
- const gmx_mtop_t* top_global_;
+ const gmx_mtop_t& top_global_;
//! Atom parameters for this domain.
const MDAtoms* mdAtoms_;
//! Energy data structure
FILE* fplog_;
//! Helper struct for force calculations.
t_fcdata* fcd_;
- //! Notification to MD modules
- const MdModulesNotifier& mdModulesNotifier_;
+ //! Notifiers to MD modules
+ const MDModulesNotifiers& mdModulesNotifiers_;
//! Global topology groups
const SimulationGroups* groups_;
//! History of simulation observables.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
ImdSession* imdSession,
pull_t* pull_work,
Constraints* constr,
- const gmx_mtop_t* globalTopology,
+ const gmx_mtop_t& globalTopology,
gmx_enfrot* enforcedRotation) :
shellfc_(init_shell_flexcon(fplog,
globalTopology,
constr_(constr),
enforcedRotation_(enforcedRotation)
{
- lambda_.fill(0);
+ std::fill(lambda_.begin(), lambda_.end(), 0);
if (doShellFC_ && !DOMAINDECOMP(cr))
{
// This was done in mdAlgorithmsSetupAtomData(), but shellfc
// won't be available outside this element.
- make_local_shells(cr, mdAtoms->mdatoms(), shellfc_);
+ make_local_shells(cr, *mdAtoms->mdatoms(), shellfc_);
}
}
{
auto v = statePropagatorData_->velocitiesView();
- relax_shell_flexcon(
- fplog_, cr_, ms, isVerbose_, enforcedRotation_, step, inputrec_, imdSession_,
- pull_work_, step == nextNSStep_, static_cast<int>(flags), localTopology_, constr_,
- energyData_->enerdata(), statePropagatorData_->localNumAtoms(), x, v, box, lambda,
- hist, &forces, force_vir, mdAtoms_->mdatoms(), nrnb_, wcycle_, shellfc_, fr_,
- runScheduleWork_, time, energyData_->muTot(), vsite_, ddBalanceRegionHandler_);
+ relax_shell_flexcon(fplog_,
+ cr_,
+ ms,
+ isVerbose_,
+ enforcedRotation_,
+ step,
+ inputrec_,
+ imdSession_,
+ pull_work_,
+ step == nextNSStep_,
+ static_cast<int>(flags),
+ localTopology_,
+ constr_,
+ energyData_->enerdata(),
+ statePropagatorData_->localNumAtoms(),
+ x,
+ v,
+ box,
+ lambda,
+ hist,
+ &forces,
+ force_vir,
+ *mdAtoms_->mdatoms(),
+ nrnb_,
+ wcycle_,
+ shellfc_,
+ fr_,
+ runScheduleWork_,
+ time,
+ energyData_->muTot(),
+ vsite_,
+ ddBalanceRegionHandler_);
nShellRelaxationSteps_++;
}
else
Awh* awh = nullptr;
gmx_edsam* ed = nullptr;
- do_force(fplog_, cr_, ms, inputrec_, awh, enforcedRotation_, imdSession_, pull_work_, step,
- nrnb_, wcycle_, localTopology_, box, x, hist, &forces, force_vir,
- mdAtoms_->mdatoms(), energyData_->enerdata(), lambda, fr_, runScheduleWork_, vsite_,
- energyData_->muTot(), time, ed, static_cast<int>(flags), ddBalanceRegionHandler_);
+ do_force(fplog_,
+ cr_,
+ ms,
+ *inputrec_,
+ awh,
+ enforcedRotation_,
+ imdSession_,
+ pull_work_,
+ step,
+ nrnb_,
+ wcycle_,
+ localTopology_,
+ box,
+ x,
+ hist,
+ &forces,
+ force_vir,
+ mdAtoms_->mdatoms(),
+ energyData_->enerdata(),
+ lambda,
+ fr_,
+ runScheduleWork_,
+ vsite_,
+ energyData_->muTot(),
+ time,
+ ed,
+ static_cast<int>(flags),
+ ddBalanceRegionHandler_);
}
energyData_->addToForceVirial(force_vir, step);
}
{
const bool isVerbose = legacySimulatorData->mdrunOptions.verbose;
const bool isDynamicBox = inputrecDynamicBox(legacySimulatorData->inputrec);
- return builderHelper->storeElement(std::make_unique<ForceElement>(
- statePropagatorData, energyData, freeEnergyPerturbationData, isVerbose, isDynamicBox,
- legacySimulatorData->fplog, legacySimulatorData->cr, legacySimulatorData->inputrec,
- legacySimulatorData->mdAtoms, legacySimulatorData->nrnb, legacySimulatorData->fr,
- legacySimulatorData->wcycle, legacySimulatorData->runScheduleWork, legacySimulatorData->vsite,
- legacySimulatorData->imdSession, legacySimulatorData->pull_work, legacySimulatorData->constr,
- legacySimulatorData->top_global, legacySimulatorData->enforcedRotation));
+ return builderHelper->storeElement(
+ std::make_unique<ForceElement>(statePropagatorData,
+ energyData,
+ freeEnergyPerturbationData,
+ isVerbose,
+ isDynamicBox,
+ legacySimulatorData->fplog,
+ legacySimulatorData->cr,
+ legacySimulatorData->inputrec,
+ legacySimulatorData->mdAtoms,
+ legacySimulatorData->nrnb,
+ legacySimulatorData->fr,
+ legacySimulatorData->wcycle,
+ legacySimulatorData->runScheduleWork,
+ legacySimulatorData->vsite,
+ legacySimulatorData->imdSession,
+ legacySimulatorData->pull_work,
+ legacySimulatorData->constr,
+ legacySimulatorData->top_global,
+ legacySimulatorData->enforcedRotation));
}
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/domdec/dlbtiming.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/real.h"
#include "modularsimulatorinterfaces.h"
ImdSession* imdSession,
pull_t* pull_work,
Constraints* constr,
- const gmx_mtop_t* globalTopology,
+ const gmx_mtop_t& globalTopology,
gmx_enfrot* enforcedRotation);
/*! \brief Register force calculation for step / time
* Used if FEP is off, since do_force
* requires lambda to be allocated anyway
*/
- std::array<real, efptNR> lambda_;
+ gmx::EnumerationArray<FreeEnergyPerturbationType, real> lambda_;
// Access to ISimulator data
//! Handles logging.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
namespace gmx
{
-FreeEnergyPerturbationData::FreeEnergyPerturbationData(FILE* fplog, const t_inputrec* inputrec, MDAtoms* mdAtoms) :
- element_(std::make_unique<Element>(this, inputrec->fepvals->delta_lambda)),
+FreeEnergyPerturbationData::FreeEnergyPerturbationData(FILE* fplog, const t_inputrec& inputrec, MDAtoms* mdAtoms) :
+ element_(std::make_unique<Element>(this, inputrec.fepvals->delta_lambda)),
lambda_(),
currentFEPState_(0),
fplog_(fplog),
inputrec_(inputrec),
mdAtoms_(mdAtoms)
{
- lambda_.fill(0);
+ std::fill(lambda_.begin(), lambda_.end(), 0);
// The legacy implementation only filled the lambda vector in state_global, which is only
// available on master. We have the lambda vector available everywhere, so we pass a `true`
// for isMaster on all ranks. See #3647.
- initialize_lambdas(fplog_, *inputrec_, true, ¤tFEPState_, lambda_);
+ initialize_lambdas(fplog_,
+ inputrec_.efep,
+ inputrec_.bSimTemp,
+ *inputrec_.fepvals,
+ inputrec_.simtempvals->temperatures,
+ gmx::arrayRefFromArray(inputrec_.opts.ref_t, inputrec_.opts.ngtc),
+ true,
+ ¤tFEPState_,
+ lambda_);
}
void FreeEnergyPerturbationData::Element::scheduleTask(Step step,
void FreeEnergyPerturbationData::updateLambdas(Step step)
{
// at beginning of step (if lambdas change...)
- lambda_ = currentLambdas(step, *(inputrec_->fepvals), currentFEPState_);
+ lambda_ = currentLambdas(step, *(inputrec_.fepvals), currentFEPState_);
updateMDAtoms();
}
void FreeEnergyPerturbationData::updateMDAtoms()
{
- update_mdatoms(mdAtoms_->mdatoms(), lambda_[efptMASS]);
+ update_mdatoms(mdAtoms_->mdatoms(), lambda_[FreeEnergyPerturbationCouplingType::Mass]);
}
namespace
if (DOMAINDECOMP(cr))
{
dd_bcast(cr->dd, sizeof(int), &freeEnergyPerturbationData_->currentFEPState_);
- dd_bcast(cr->dd, ssize(freeEnergyPerturbationData_->lambda_) * int(sizeof(real)),
+ dd_bcast(cr->dd,
+ ssize(freeEnergyPerturbationData_->lambda_) * int(sizeof(real)),
freeEnergyPerturbationData_->lambda_.data());
}
}
{
if (readCheckpointData)
{
- FreeEnergyPerturbationData freeEnergyPerturbationData;
+ FreeEnergyPerturbationData freeEnergyPerturbationData(nullptr, t_inputrec(), nullptr);
freeEnergyPerturbationData.doCheckpointData(&readCheckpointData.value());
- trxFrame->lambda = freeEnergyPerturbationData.lambda_[efptFEP];
+ trxFrame->lambda = freeEnergyPerturbationData.lambda_[FreeEnergyPerturbationCouplingType::Fep];
trxFrame->fep_state = freeEnergyPerturbationData.currentFEPState_;
}
else
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/real.h"
#include "modularsimulatorinterfaces.h"
{
public:
//! Constructor
- FreeEnergyPerturbationData(FILE* fplog, const t_inputrec* inputrec, MDAtoms* mdAtoms);
+ FreeEnergyPerturbationData(FILE* fplog, const t_inputrec& inputrec, MDAtoms* mdAtoms);
//! Get a view of the current lambda vector
ArrayRef<real> lambdaView();
static const std::string& checkpointID();
private:
- //! Default constructor - only used internally
- FreeEnergyPerturbationData() = default;
//! Update the lambda values
void updateLambdas(Step step);
//! Helper function to read from / write to CheckpointData
std::unique_ptr<Element> element_;
//! The lambda vector
- std::array<real, efptNR> lambda_;
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real> lambda_;
//! The current free energy state
int currentFEPState_;
//! Handles logging.
FILE* fplog_;
//! Contains user input mdp options.
- const t_inputrec* inputrec_;
+ const t_inputrec& inputrec_;
//! Atom parameters for this domain.
MDAtoms* mdAtoms_;
};
void ModularSimulator::addIntegrationElements(ModularSimulatorAlgorithmBuilder* builder)
{
- if (legacySimulatorData_->inputrec->eI == eiMD)
+ if (legacySimulatorData_->inputrec->eI == IntegrationAlgorithm::MD)
{
// The leap frog integration algorithm
builder->add<ForceElement>();
builder->add<StatePropagatorData::Element>();
- if (legacySimulatorData_->inputrec->etc == etcVRESCALE
- || legacySimulatorData_->inputrec->etc == etcBERENDSEN)
+ if (legacySimulatorData_->inputrec->etc == TemperatureCoupling::VRescale
+ || legacySimulatorData_->inputrec->etc == TemperatureCoupling::Berendsen
+ || legacySimulatorData_->inputrec->etc == TemperatureCoupling::NoseHoover)
{
- builder->add<VelocityScalingTemperatureCoupling>(-1, UseFullStepKE::No,
- ReportPreviousStepConservedEnergy::No);
+ builder->add<VelocityScalingTemperatureCoupling>(Offset(-1),
+ UseFullStepKE::No,
+ ReportPreviousStepConservedEnergy::No,
+ PropagatorTag("LeapFrogPropagator"));
}
- builder->add<Propagator<IntegrationStep::LeapFrog>>(legacySimulatorData_->inputrec->delta_t,
- RegisterWithThermostat::True,
- RegisterWithBarostat::True);
+ builder->add<Propagator<IntegrationStage::LeapFrog>>(
+ PropagatorTag("LeapFrogPropagator"), TimeStep(legacySimulatorData_->inputrec->delta_t));
if (legacySimulatorData_->constr)
{
builder->add<ConstraintsElement<ConstraintVariable::Positions>>();
}
builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>>();
- builder->add<EnergyData::Element>();
- if (legacySimulatorData_->inputrec->epc == epcPARRINELLORAHMAN)
+ if (legacySimulatorData_->inputrec->epc == PressureCoupling::ParrinelloRahman)
{
- builder->add<ParrinelloRahmanBarostat>(-1);
+ builder->add<ParrinelloRahmanBarostat>(Offset(-1), PropagatorTag("LeapFrogPropagator"));
}
}
- else if (legacySimulatorData_->inputrec->eI == eiVV)
+ else if (legacySimulatorData_->inputrec->eI == IntegrationAlgorithm::VV)
{
// The velocity verlet integration algorithm
builder->add<ForceElement>();
- builder->add<Propagator<IntegrationStep::VelocitiesOnly>>(
- 0.5 * legacySimulatorData_->inputrec->delta_t, RegisterWithThermostat::False,
- RegisterWithBarostat::True);
+ builder->add<Propagator<IntegrationStage::VelocitiesOnly>>(
+ PropagatorTag("VelocityHalfStep"), TimeStep(0.5 * legacySimulatorData_->inputrec->delta_t));
if (legacySimulatorData_->constr)
{
builder->add<ConstraintsElement<ConstraintVariable::Velocities>>();
}
builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
builder->add<StatePropagatorData::Element>();
- if (legacySimulatorData_->inputrec->etc == etcVRESCALE
- || legacySimulatorData_->inputrec->etc == etcBERENDSEN)
+ if (legacySimulatorData_->inputrec->etc == TemperatureCoupling::VRescale
+ || legacySimulatorData_->inputrec->etc == TemperatureCoupling::Berendsen)
{
builder->add<VelocityScalingTemperatureCoupling>(
- 0, UseFullStepKE::Yes, ReportPreviousStepConservedEnergy::Yes);
+ Offset(0),
+ UseFullStepKE::Yes,
+ ReportPreviousStepConservedEnergy::Yes,
+ PropagatorTag("VelocityHalfAndPositionFullStep"));
}
- builder->add<Propagator<IntegrationStep::VelocityVerletPositionsAndVelocities>>(
- legacySimulatorData_->inputrec->delta_t, RegisterWithThermostat::True,
- RegisterWithBarostat::False);
+ builder->add<Propagator<IntegrationStage::VelocityVerletPositionsAndVelocities>>(
+ PropagatorTag("VelocityHalfAndPositionFullStep"),
+ TimeStep(legacySimulatorData_->inputrec->delta_t));
if (legacySimulatorData_->constr)
{
builder->add<ConstraintsElement<ConstraintVariable::Positions>>();
}
builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
- builder->add<EnergyData::Element>();
- if (legacySimulatorData_->inputrec->epc == epcPARRINELLORAHMAN)
+ if (legacySimulatorData_->inputrec->epc == PressureCoupling::ParrinelloRahman)
{
- builder->add<ParrinelloRahmanBarostat>(-1);
+ builder->add<ParrinelloRahmanBarostat>(Offset(-1), PropagatorTag("VelocityHalfStep"));
}
}
else
{
gmx_fatal(FARGS, "Integrator not implemented for the modular simulator.");
}
+ builder->add<EnergyData::Element>();
}
bool ModularSimulator::isInputCompatible(bool exitOnFailure,
"or unset both to recover default behavior.");
GMX_RELEASE_ASSERT(
- !(modularSimulatorExplicitlyTurnedOff && inputrec->eI == eiVV
- && inputrec->epc == epcPARRINELLORAHMAN),
+ !(modularSimulatorExplicitlyTurnedOff && inputrec->eI == IntegrationAlgorithm::VV
+ && inputrec->epc == PressureCoupling::ParrinelloRahman),
"Cannot use a Parrinello-Rahman barostat with md-vv and "
"GMX_DISABLE_MODULAR_SIMULATOR=ON, "
"as the Parrinello-Rahman barostat is not implemented in the legacy simulator. Unset "
"GMX_DISABLE_MODULAR_SIMULATOR or use a different pressure control algorithm.");
bool isInputCompatible = conditionalAssert(
- inputrec->eI == eiMD || inputrec->eI == eiVV,
+ inputrec->eI == IntegrationAlgorithm::MD || inputrec->eI == IntegrationAlgorithm::VV,
"Only integrators md and md-vv are supported by the modular simulator.");
isInputCompatible = isInputCompatible
- && conditionalAssert(inputrec->eI != eiMD || modularSimulatorExplicitlyTurnedOn,
+ && conditionalAssert(inputrec->eI != IntegrationAlgorithm::MD
+ || modularSimulatorExplicitlyTurnedOn,
"Set GMX_USE_MODULAR_SIMULATOR=ON to use the modular "
"simulator with integrator md.");
isInputCompatible =
isInputCompatible
&& conditionalAssert(
- !inputrec->useMts,
- "Multiple time stepping is not supported by the modular simulator.");
+ !inputrec->useMts,
+ "Multiple time stepping is not supported by the modular simulator.");
isInputCompatible =
isInputCompatible
&& conditionalAssert(!doRerun, "Rerun is not supported by the modular simulator.");
isInputCompatible = isInputCompatible
- && conditionalAssert(inputrec->etc == etcNO || inputrec->etc == etcVRESCALE
- || inputrec->etc == etcBERENDSEN,
- "Only v-rescale and Berendsen thermostat are "
- "supported by the modular simulator.");
+ && conditionalAssert(inputrec->etc == TemperatureCoupling::No
+ || inputrec->etc == TemperatureCoupling::VRescale
+ || inputrec->etc == TemperatureCoupling::Berendsen
+ || (inputrec->etc == TemperatureCoupling::NoseHoover
+ && inputrec->eI == IntegrationAlgorithm::MD),
+ "Only v-rescale, Berendsen and Nose-Hoover "
+ "thermostats are supported by the modular simulator.");
isInputCompatible =
isInputCompatible
&& conditionalAssert(
- inputrec->epc == epcNO || inputrec->epc == epcPARRINELLORAHMAN,
- "Only Parrinello-Rahman barostat is supported by the modular simulator.");
+ inputrec->epc == PressureCoupling::No || inputrec->epc == PressureCoupling::ParrinelloRahman,
+ "Only Parrinello-Rahman barostat is supported by the modular simulator.");
isInputCompatible =
isInputCompatible
&& conditionalAssert(
- !(inputrecNptTrotter(inputrec) || inputrecNphTrotter(inputrec)
- || inputrecNvtTrotter(inputrec)),
- "Legacy Trotter decomposition is not supported by the modular simulator.");
- isInputCompatible = isInputCompatible
- && conditionalAssert(inputrec->efep == efepNO || inputrec->efep == efepYES
- || inputrec->efep == efepSLOWGROWTH,
- "Expanded ensemble free energy calculation is not "
- "supported by the modular simulator.");
+ !(inputrecNptTrotter(inputrec) || inputrecNphTrotter(inputrec)
+ || inputrecNvtTrotter(inputrec)),
+ "Legacy Trotter decomposition is not supported by the modular simulator.");
+ isInputCompatible =
+ isInputCompatible
+ && conditionalAssert(inputrec->efep == FreeEnergyPerturbationType::No
+ || inputrec->efep == FreeEnergyPerturbationType::Yes
+ || inputrec->efep == FreeEnergyPerturbationType::SlowGrowth,
+ "Expanded ensemble free energy calculation is not "
+ "supported by the modular simulator.");
isInputCompatible = isInputCompatible
&& conditionalAssert(!inputrec->bPull,
"Pulling is not supported by the modular simulator.");
isInputCompatible =
isInputCompatible
- && conditionalAssert(inputrec->opts.ngacc == 1 && inputrec->opts.acc[0][XX] == 0.0
- && inputrec->opts.acc[0][YY] == 0.0
- && inputrec->opts.acc[0][ZZ] == 0.0 && inputrec->cos_accel == 0.0,
+ && conditionalAssert(inputrec->cos_accel == 0.0,
"Acceleration is not supported by the modular simulator.");
isInputCompatible =
isInputCompatible
isInputCompatible =
isInputCompatible
&& conditionalAssert(
- inputrec->deform[XX][XX] == 0.0 && inputrec->deform[XX][YY] == 0.0
- && inputrec->deform[XX][ZZ] == 0.0 && inputrec->deform[YY][XX] == 0.0
- && inputrec->deform[YY][YY] == 0.0 && inputrec->deform[YY][ZZ] == 0.0
- && inputrec->deform[ZZ][XX] == 0.0 && inputrec->deform[ZZ][YY] == 0.0
- && inputrec->deform[ZZ][ZZ] == 0.0,
- "Deformation is not supported by the modular simulator.");
+ inputrec->deform[XX][XX] == 0.0 && inputrec->deform[XX][YY] == 0.0
+ && inputrec->deform[XX][ZZ] == 0.0 && inputrec->deform[YY][XX] == 0.0
+ && inputrec->deform[YY][YY] == 0.0 && inputrec->deform[YY][ZZ] == 0.0
+ && inputrec->deform[ZZ][XX] == 0.0 && inputrec->deform[ZZ][YY] == 0.0
+ && inputrec->deform[ZZ][ZZ] == 0.0,
+ "Deformation is not supported by the modular simulator.");
isInputCompatible =
isInputCompatible
&& conditionalAssert(gmx_mtop_interaction_count(globalTopology, IF_VSITE) == 0,
isInputCompatible =
isInputCompatible
&& conditionalAssert(
- gmx_mtop_ftype_count(globalTopology, F_ORIRES) == 0,
- "Orientation restraints are not supported by the modular simulator.");
+ gmx_mtop_ftype_count(globalTopology, F_ORIRES) == 0,
+ "Orientation restraints are not supported by the modular simulator.");
isInputCompatible =
isInputCompatible
&& conditionalAssert(ms == nullptr,
}
else
{
- auto distantRestraintEnsembleEnvVar = getenv("GMX_DISRE_ENSEMBLE_SIZE");
+ auto* distantRestraintEnsembleEnvVar = getenv("GMX_DISRE_ENSEMBLE_SIZE");
numEnsembleRestraintSystems =
(ms != nullptr && distantRestraintEnsembleEnvVar != nullptr)
? static_cast<int>(strtol(distantRestraintEnsembleEnvVar, nullptr, 10))
&& conditionalAssert(!doEssentialDynamics,
"Essential dynamics is not supported by the modular simulator.");
isInputCompatible = isInputCompatible
- && conditionalAssert(inputrec->eSwapCoords == eswapNO,
+ && conditionalAssert(inputrec->eSwapCoords == SwapType::No,
"Ion / water position swapping is not supported by "
"the modular simulator.");
isInputCompatible =
isInputCompatible =
isInputCompatible
&& conditionalAssert(
- getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") == nullptr,
- "Integration on the GPU is not supported by the modular simulator.");
+ getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") == nullptr,
+ "Integration on the GPU is not supported by the modular simulator.");
// Modular simulator is centered around NS updates
// TODO: think how to handle nstlist == 0
isInputCompatible = isInputCompatible
isInputCompatible = isInputCompatible
&& conditionalAssert(!GMX_FAHCORE,
"GMX_FAHCORE not supported by the modular simulator.");
- if (!isInputCompatible && (inputrec->eI == eiVV && inputrec->epc == epcPARRINELLORAHMAN))
+ if (!isInputCompatible
+ && (inputrec->eI == IntegrationAlgorithm::VV && inputrec->epc == PressureCoupling::ParrinelloRahman))
{
gmx_fatal(FARGS,
"Requested Parrinello-Rahman barostat with md-vv. This combination is only "
"only available in the legacy simulator. Use a different pressure control "
"algorithm.");
}
-
return isInputCompatible;
}
void ModularSimulator::checkInputForDisabledFunctionality()
{
- isInputCompatible(true, legacySimulatorData_->inputrec, legacySimulatorData_->mdrunOptions.rerun,
- *legacySimulatorData_->top_global, legacySimulatorData_->ms,
- legacySimulatorData_->replExParams, legacySimulatorData_->fr->fcdata.get(),
+ isInputCompatible(true,
+ legacySimulatorData_->inputrec,
+ legacySimulatorData_->mdrunOptions.rerun,
+ legacySimulatorData_->top_global,
+ legacySimulatorData_->ms,
+ legacySimulatorData_->replExParams,
+ legacySimulatorData_->fr->fcdata.get(),
opt2bSet("-ei", legacySimulatorData_->nfile, legacySimulatorData_->fnm),
legacySimulatorData_->membed != nullptr);
if (legacySimulatorData_->observablesHistory->edsamHistory)
"ModularSimulator::readCheckpointToTrxFrame can only read checkpoints "
"written by modular simulator.");
fr->bStep = true;
- fr->step =
- int64_to_int(checkpointHeaderContents.step, "conversion of checkpoint to trajectory");
+ fr->step = int64_to_int(checkpointHeaderContents.step, "conversion of checkpoint to trajectory");
fr->bTime = true;
fr->time = checkpointHeaderContents.t;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
template<typename T>
class ArrayRef;
-template<class Signaller>
-class SignallerBuilder;
-class NeighborSearchSignaller;
+class EnergySignaller;
class LastStepSignaller;
class LoggingSignaller;
+class NeighborSearchSignaller;
+enum class ScaleVelocities;
+template<class Signaller>
+class SignallerBuilder;
class TrajectorySignaller;
-class EnergySignaller;
//! \addtogroup module_modularsimulator
//! \{
typedef std::function<void(Step)> PropagatorCallback;
/*! \internal
- * \brief Information needed to connect a propagator to a thermostat
+ * \brief Strong type used to name propagators
*/
-struct PropagatorThermostatConnection
+struct PropagatorTag
{
- //! Function variable for setting velocity scaling variables.
- std::function<void(int)> setNumVelocityScalingVariables;
- //! Function variable for receiving view on velocity scaling.
- std::function<ArrayRef<real>()> getViewOnVelocityScaling;
- //! Function variable for callback.
- std::function<PropagatorCallback()> getVelocityScalingCallback;
+ //! Explicit constructor
+ explicit PropagatorTag(std::string_view name) : name_(name) {}
+ //! Can be used as string
+ operator const std::string&() const { return name_; }
+ //! Equality operator
+ bool operator==(const PropagatorTag& other) const { return name_ == other.name_; }
+ //! Inequality operator
+ bool operator!=(const PropagatorTag& other) const { return name_ != other.name_; }
+
+private:
+ //! The name of the propagator
+ const std::string name_;
+};
+
+/*! \internal
+ * \brief Strong type used to denote propagation time steps
+ */
+struct TimeStep
+{
+ //! Explicit constructor
+ explicit TimeStep(real timeStep) : timeStep_(timeStep) {}
+ //! Can be used as underlying type
+ operator const real&() const { return timeStep_; }
+
+private:
+ //! The time step
+ real timeStep_;
+};
+
+/*! \internal
+ * \brief Strong type used to denote scheduling offsets
+ */
+struct Offset
+{
+ //! Explicit constructor
+ explicit Offset(int offset) : offset_(offset) {}
+ //! Can be used as underlying type
+ operator const int&() const { return offset_; }
+
+private:
+ //! The offset
+ int offset_;
};
/*! \internal
- * \brief Information needed to connect a propagator to a barostat
+ * \brief Information needed to connect a propagator to a temperature and / or pressure coupling element
*/
-struct PropagatorBarostatConnection
+struct PropagatorConnection
{
- //! Function variable for receiving view on pressure scaling matrix.
+ //! The tag of the creating propagator
+ PropagatorTag tag;
+
+ //! Whether the propagator offers start velocity scaling
+ bool hasStartVelocityScaling() const
+ {
+ return setNumVelocityScalingVariables && getVelocityScalingCallback && getViewOnStartVelocityScaling;
+ }
+ //! Whether the propagator offers end velocity scaling
+ bool hasEndVelocityScaling() const
+ {
+ return setNumVelocityScalingVariables && getVelocityScalingCallback && getViewOnEndVelocityScaling;
+ }
+ //! Whether the propagator offers position scaling
+ bool hasPositionScaling() const
+ {
+ return setNumPositionScalingVariables && getPositionScalingCallback && getViewOnPositionScaling;
+ }
+ //! Whether the propagator offers Parrinello-Rahman scaling
+ bool hasParrinelloRahmanScaling() const
+ {
+ return getPRScalingCallback && getViewOnPRScalingMatrix;
+ }
+
+ //! Function object for setting velocity scaling variables
+ std::function<void(int, ScaleVelocities)> setNumVelocityScalingVariables;
+ //! Function object for setting velocity scaling variables
+ std::function<void(int)> setNumPositionScalingVariables;
+ //! Function object for receiving view on velocity scaling (before step)
+ std::function<ArrayRef<real>()> getViewOnStartVelocityScaling;
+ //! Function object for receiving view on velocity scaling (after step)
+ std::function<ArrayRef<real>()> getViewOnEndVelocityScaling;
+ //! Function object for receiving view on position scaling
+ std::function<ArrayRef<real>()> getViewOnPositionScaling;
+ //! Function object to request callback allowing to signal a velocity scaling step
+ std::function<PropagatorCallback()> getVelocityScalingCallback;
+ //! Function object to request callback allowing to signal a position scaling step
+ std::function<PropagatorCallback()> getPositionScalingCallback;
+ //! Function object for receiving view on pressure scaling matrix
std::function<ArrayRef<rvec>()> getViewOnPRScalingMatrix;
- //! Function variable for callback.
+ //! Function object to request callback allowing to signal a Parrinello-Rahman scaling step
std::function<PropagatorCallback()> getPRScalingCallback;
};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
boxVelocity_{ { 0 } },
statePropagatorData_(statePropagatorData),
energyData_(energyData),
+ nextEnergyCalculationStep_(-1),
fplog_(fplog),
inputrec_(inputrec),
mdAtoms_(mdAtoms)
{
- energyData->setParrinelloRahamnBarostat(this);
+ energyData->setParrinelloRahmanBoxVelocities([this]() { return boxVelocity_; });
+ energyData->addConservedEnergyContribution([this](Step gmx_used_in_debug step, Time /*unused*/) {
+ GMX_ASSERT(conservedEnergyContributionStep_ == step,
+ "Parrinello-Rahman conserved energy step mismatch.");
+ return conservedEnergyContribution_;
+ });
}
-void ParrinelloRahmanBarostat::connectWithPropagator(const PropagatorBarostatConnection& connectionData)
+void ParrinelloRahmanBarostat::connectWithMatchingPropagator(const PropagatorConnection& connectionData,
+ const PropagatorTag& propagatorTag)
{
- scalingTensor_ = connectionData.getViewOnPRScalingMatrix();
- propagatorCallback_ = connectionData.getPRScalingCallback();
+ if (connectionData.tag == propagatorTag)
+ {
+ GMX_RELEASE_ASSERT(connectionData.hasParrinelloRahmanScaling(),
+ "Connection data lacks Parrinello-Rahman scaling");
+ scalingTensor_ = connectionData.getViewOnPRScalingMatrix();
+ propagatorCallback_ = connectionData.getPRScalingCallback();
+ }
}
void ParrinelloRahmanBarostat::scheduleTask(Step step,
{
const bool scaleOnNextStep = do_per_step(step + nstpcouple_ + offset_ + 1, nstpcouple_);
const bool scaleOnThisStep = do_per_step(step + nstpcouple_ + offset_, nstpcouple_);
+ const bool contributeEnergyThisStep = (step == nextEnergyCalculationStep_);
+ if (contributeEnergyThisStep)
+ {
+ // For compatibility with legacy md, we store this before integrating the box velocities
+ registerRunFunction([this, step]() {
+ conservedEnergyContribution_ = conservedEnergyContribution();
+ conservedEnergyContributionStep_ = step;
+ });
+ }
if (scaleOnThisStep)
{
registerRunFunction([this]() { scaleBoxAndPositions(); });
void ParrinelloRahmanBarostat::integrateBoxVelocityEquations(Step step)
{
auto box = statePropagatorData_->constBox();
- parrinellorahman_pcoupl(fplog_, step, inputrec_, couplingTimeStep_, energyData_->pressure(step),
- box, boxRel_, boxVelocity_, scalingTensor_.data(), mu_, false);
+ parrinellorahman_pcoupl(fplog_,
+ step,
+ inputrec_,
+ couplingTimeStep_,
+ energyData_->pressure(step),
+ box,
+ boxRel_,
+ boxVelocity_,
+ scalingTensor_.data(),
+ mu_,
+ false);
// multiply matrix by the coupling time step to avoid having the propagator needing to know about that
msmul(scalingTensor_.data(), couplingTimeStep_, scalingTensor_.data());
}
throw MissingElementConnectionError(
"Parrinello-Rahman barostat was not connected to a propagator.\n"
"Connection to a propagator element is needed to scale the velocities.\n"
- "Use connectWithPropagator(...) before building the ModularSimulatorAlgorithm "
+ "Use connectWithMatchingPropagator(...) before building the "
+ "ModularSimulatorAlgorithm "
"object.");
}
if (inputrecPreserveShape(inputrec_))
{
auto box = statePropagatorData_->box();
- const int ndim = inputrec_->epct == epctSEMIISOTROPIC ? 2 : 3;
+ const int ndim = inputrec_->epct == PressureCouplingType::SemiIsotropic ? 2 : 3;
do_box_rel(ndim, inputrec_->deform, boxRel_, box, true);
}
// The call to parrinellorahman_pcoupl is using nullptr for fplog (since we don't expect any
// output here) and for the pressure (since it might not be calculated yet, and we don't need it).
auto box = statePropagatorData_->constBox();
- parrinellorahman_pcoupl(nullptr, initStep_, inputrec_, couplingTimeStep_, nullptr, box,
- boxRel_, boxVelocity_, scalingTensor_.data(), mu_, true);
+ parrinellorahman_pcoupl(nullptr,
+ initStep_,
+ inputrec_,
+ couplingTimeStep_,
+ nullptr,
+ box,
+ boxRel_,
+ boxVelocity_,
+ scalingTensor_.data(),
+ mu_,
+ true);
// multiply matrix by the coupling time step to avoid having the propagator needing to know about that
msmul(scalingTensor_.data(), couplingTimeStep_, scalingTensor_.data());
{
for (int j = 0; j <= i; j++)
{
- real invMass = PRESFAC * (4 * M_PI * M_PI * inputrec_->compress[i][j])
+ real invMass = c_presfac * (4 * M_PI * M_PI * inputrec_->compress[i][j])
/ (3 * inputrec_->tau_p * inputrec_->tau_p * maxBoxLength);
if (invMass > 0)
{
* track of unwrapped box diagonal elements. This case is
* excluded in integratorHasConservedEnergyQuantity().
*/
- energy += volume * trace(inputrec_->ref_p) / (DIM * PRESFAC);
+ energy += volume * trace(inputrec_->ref_p) / (DIM * c_presfac);
return energy;
}
return identifier_;
}
+std::optional<SignallerCallback> ParrinelloRahmanBarostat::registerEnergyCallback(EnergySignallerEvent event)
+{
+ if (event == EnergySignallerEvent::EnergyCalculationStep)
+ {
+ return [this](Step step, Time /*unused*/) { nextEnergyCalculationStep_ = step; };
+ }
+ return std::nullopt;
+}
+
ISimulatorElement* ParrinelloRahmanBarostat::getElementPointerImpl(
LegacySimulatorData* legacySimulatorData,
ModularSimulatorAlgorithmBuilderHelper* builderHelper,
EnergyData* energyData,
FreeEnergyPerturbationData gmx_unused* freeEnergyPerturbationData,
GlobalCommunicationHelper gmx_unused* globalCommunicationHelper,
- int offset)
+ Offset offset,
+ const PropagatorTag& propagatorTag)
{
auto* element = builderHelper->storeElement(std::make_unique<ParrinelloRahmanBarostat>(
- legacySimulatorData->inputrec->nstpcouple, offset,
+ legacySimulatorData->inputrec->nstpcouple,
+ offset,
legacySimulatorData->inputrec->delta_t * legacySimulatorData->inputrec->nstpcouple,
- legacySimulatorData->inputrec->init_step, statePropagatorData, energyData,
- legacySimulatorData->fplog, legacySimulatorData->inputrec, legacySimulatorData->mdAtoms));
+ legacySimulatorData->inputrec->init_step,
+ statePropagatorData,
+ energyData,
+ legacySimulatorData->fplog,
+ legacySimulatorData->inputrec,
+ legacySimulatorData->mdAtoms));
auto* barostat = static_cast<ParrinelloRahmanBarostat*>(element);
- builderHelper->registerBarostat([barostat](const PropagatorBarostatConnection& connection) {
- barostat->connectWithPropagator(connection);
- });
+ builderHelper->registerTemperaturePressureControl(
+ [barostat, propagatorTag](const PropagatorConnection& connection) {
+ barostat->connectWithMatchingPropagator(connection, propagatorTag);
+ });
return element;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* scaling factor, and
* * scales the box and the positions of the system.
*/
-class ParrinelloRahmanBarostat final : public ISimulatorElement, public ICheckpointHelperClient
+class ParrinelloRahmanBarostat final : public ISimulatorElement, public ICheckpointHelperClient, public IEnergySignallerClient
{
public:
//! Constructor
//! Getter for the box velocities
[[nodiscard]] const rvec* boxVelocities() const;
- //! Contribution to the conserved energy (called by energy data)
- [[nodiscard]] real conservedEnergyContribution() const;
//! Connect this to propagator
- void connectWithPropagator(const PropagatorBarostatConnection& connectionData);
+ void connectWithMatchingPropagator(const PropagatorConnection& connectionData,
+ const PropagatorTag& propagatorTag);
//! ICheckpointHelperClient write checkpoint implementation
void saveCheckpointState(std::optional<WriteCheckpointData> checkpointData, const t_commrec* cr) override;
* \param energyData Pointer to the \c EnergyData object
* \param freeEnergyPerturbationData Pointer to the \c FreeEnergyPerturbationData object
* \param globalCommunicationHelper Pointer to the \c GlobalCommunicationHelper object
+ * \param propagatorTag Tag of the propagator to connect to
* \param offset The step offset at which the barostat is applied
*
* \return Pointer to the element to be added. Element needs to have been stored using \c storeElement
*/
- static ISimulatorElement* getElementPointerImpl(LegacySimulatorData* legacySimulatorData,
- ModularSimulatorAlgorithmBuilderHelper* builderHelper,
- StatePropagatorData* statePropagatorData,
- EnergyData* energyData,
- FreeEnergyPerturbationData* freeEnergyPerturbationData,
- GlobalCommunicationHelper* globalCommunicationHelper,
- int offset);
+ static ISimulatorElement*
+ getElementPointerImpl(LegacySimulatorData* legacySimulatorData,
+ ModularSimulatorAlgorithmBuilderHelper* builderHelper,
+ StatePropagatorData* statePropagatorData,
+ EnergyData* energyData,
+ FreeEnergyPerturbationData gmx_unused* freeEnergyPerturbationData,
+ GlobalCommunicationHelper gmx_unused* globalCommunicationHelper,
+ Offset offset,
+ const PropagatorTag& propagatorTag);
private:
//! The frequency at which the barostat is applied
//! Box velocity
tensor boxVelocity_;
+ //! Current conserved energy contribution
+ real conservedEnergyContribution_;
+ //! Step of current conserved energy contribution
+ Step conservedEnergyContributionStep_;
+
// TODO: Clarify relationship to data objects and find a more robust alternative to raw pointers (#3583)
//! Pointer to the micro state
StatePropagatorData* statePropagatorData_;
template<CheckpointDataOperation operation>
void doCheckpointData(CheckpointData<operation>* checkpointData);
+ //! IEnergySignallerClient implementation
+ std::optional<SignallerCallback> registerEnergyCallback(EnergySignallerEvent event) override;
+ //! The next communicated energy calculation step
+ Step nextEnergyCalculationStep_;
+
+ //! Contribution to the conserved energy
+ [[nodiscard]] real conservedEnergyContribution() const;
+
// Access to ISimulator data
//! Handles logging.
FILE* fplog_;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const t_forcerec* fr)
{
return (mdrunOptions.tunePme && EEL_PME(fr->ic->eeltype) && !mdrunOptions.reproducible
- && inputrec->cutoff_scheme != ecutsGROUP);
+ && inputrec->cutoff_scheme != CutoffScheme::Group);
}
PmeLoadBalanceHelper::PmeLoadBalanceHelper(bool isVerbose,
auto box = statePropagatorData_->constBox();
GMX_RELEASE_ASSERT(box[0][0] != 0 && box[1][1] != 0 && box[2][2] != 0,
"PmeLoadBalanceHelper cannot be initialized with zero box.");
- pme_loadbal_init(&pme_loadbal_, cr_, mdlog_, *inputrec_, box, *fr_->ic, *fr_->nbv, fr_->pmedata,
- fr_->nbv->useGpu());
+ pme_loadbal_init(
+ &pme_loadbal_, cr_, mdlog_, *inputrec_, box, *fr_->ic, *fr_->nbv, fr_->pmedata, fr_->nbv->useGpu());
}
void PmeLoadBalanceHelper::run(gmx::Step step, gmx::Time gmx_unused time)
// PME grid + cut-off optimization with GPUs or PME nodes
// TODO pass SimulationWork object into this function, such that last argument can be set as
// simulationWork.useGpuPmePpCommunication as is done in main MD loop.
- pme_loadbal_do(pme_loadbal_, cr_, (isVerbose_ && MASTER(cr_)) ? stderr : nullptr, fplog_,
- mdlog_, *inputrec_, fr_, statePropagatorData_->constBox(),
- statePropagatorData_->constPositionsView().paddedArrayRef(), wcycle_, step,
- step - inputrec_->init_step, &bPMETunePrinting_, false);
+ pme_loadbal_do(pme_loadbal_,
+ cr_,
+ (isVerbose_ && MASTER(cr_)) ? stderr : nullptr,
+ fplog_,
+ mdlog_,
+ *inputrec_,
+ fr_,
+ statePropagatorData_->constBox(),
+ statePropagatorData_->constPositionsView().paddedArrayRef(),
+ wcycle_,
+ step,
+ step - inputrec_->init_step,
+ &bPMETunePrinting_,
+ false);
}
void PmeLoadBalanceHelper::teardown()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/timing/wallcycle.h"
-#include "gromacs/utility/fatalerror.h"
#include "modularsimulator.h"
#include "simulatoralgorithm.h"
namespace gmx
{
+namespace
+{
+// Names of integration steps, only used locally for error messages
+constexpr EnumerationArray<IntegrationStage, const char*> integrationStepNames = {
+ "IntegrationStage::PositionsOnly", "IntegrationStage::VelocitiesOnly",
+ "IntegrationStage::LeapFrog", "IntegrationStage::VelocityVerletPositionsAndVelocities",
+ "IntegrationStage::ScaleVelocities", "IntegrationStage::ScalePositions"
+};
+} // namespace
+
//! Update velocities
-template<NumVelocityScalingValues numVelocityScalingValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling>
+template<NumVelocityScalingValues numStartVelocityScalingValues,
+ ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling,
+ NumVelocityScalingValues numEndVelocityScalingValues>
static void inline updateVelocities(int a,
real dt,
- real lambda,
+ real lambdaStart,
+ real lambdaEnd,
const rvec* gmx_restrict invMassPerDim,
rvec* gmx_restrict v,
const rvec* gmx_restrict f,
for (int d = 0; d < DIM; d++)
{
// TODO: Extract this into policy classes
- if (numVelocityScalingValues != NumVelocityScalingValues::None
+ if (numStartVelocityScalingValues != NumVelocityScalingValues::None
&& parrinelloRahmanVelocityScaling == ParrinelloRahmanVelocityScaling::No)
{
- v[a][d] *= lambda;
+ v[a][d] *= lambdaStart;
}
- if (numVelocityScalingValues != NumVelocityScalingValues::None
+ if (numStartVelocityScalingValues != NumVelocityScalingValues::None
&& parrinelloRahmanVelocityScaling == ParrinelloRahmanVelocityScaling::Diagonal)
{
- v[a][d] *= (lambda - diagPR[d]);
+ v[a][d] *= (lambdaStart - diagPR[d]);
}
- if (numVelocityScalingValues != NumVelocityScalingValues::None
+ if (numStartVelocityScalingValues != NumVelocityScalingValues::None
&& parrinelloRahmanVelocityScaling == ParrinelloRahmanVelocityScaling::Full)
{
- v[a][d] = lambda * v[a][d] - iprod(matrixPR[d], v[a]);
+ v[a][d] = lambdaStart * v[a][d] - iprod(matrixPR[d], v[a]);
}
- if (numVelocityScalingValues == NumVelocityScalingValues::None
+ if (numStartVelocityScalingValues == NumVelocityScalingValues::None
&& parrinelloRahmanVelocityScaling == ParrinelloRahmanVelocityScaling::Diagonal)
{
v[a][d] *= (1 - diagPR[d]);
}
- if (numVelocityScalingValues == NumVelocityScalingValues::None
+ if (numStartVelocityScalingValues == NumVelocityScalingValues::None
&& parrinelloRahmanVelocityScaling == ParrinelloRahmanVelocityScaling::Full)
{
v[a][d] -= iprod(matrixPR[d], v[a]);
}
v[a][d] += f[a][d] * invMassPerDim[a][d] * dt;
+ if (numEndVelocityScalingValues != NumVelocityScalingValues::None)
+ {
+ v[a][d] *= lambdaEnd;
+ }
}
}
}
}
+//! Scale velocities
+template<NumVelocityScalingValues numStartVelocityScalingValues>
+static void inline scaleVelocities(int a, real lambda, rvec* gmx_restrict v)
+{
+ if (numStartVelocityScalingValues != NumVelocityScalingValues::None)
+ {
+ for (int d = 0; d < DIM; d++)
+ {
+ v[a][d] *= lambda;
+ }
+ }
+}
+
+//! Scale positions
+template<NumPositionScalingValues numPositionScalingValues>
+static void inline scalePositions(int a, real lambda, rvec* gmx_restrict x)
+{
+ if (numPositionScalingValues != NumPositionScalingValues::None)
+ {
+ for (int d = 0; d < DIM; d++)
+ {
+ x[a][d] *= lambda;
+ }
+ }
+}
+
//! Helper function diagonalizing the PR matrix if possible
template<ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling>
static inline bool diagonalizePRMatrix(matrix matrixPR, rvec diagPR)
//! Propagation (position only)
template<>
-template<NumVelocityScalingValues numVelocityScalingValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling>
-void Propagator<IntegrationStep::PositionsOnly>::run()
+template<NumVelocityScalingValues numStartVelocityScalingValues,
+ ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling,
+ NumVelocityScalingValues numEndVelocityScalingValues,
+ NumPositionScalingValues numPositionScalingValues>
+void Propagator<IntegrationStage::PositionsOnly>::run()
{
- wallcycle_start(wcycle_, ewcUPDATE);
+ wallcycle_start(wcycle_, WallCycleCounter::Update);
auto xp = as_rvec_array(statePropagatorData_->positionsView().paddedArrayRef().data());
- auto x = as_rvec_array(statePropagatorData_->constPreviousPositionsView().paddedArrayRef().data());
- auto v = as_rvec_array(statePropagatorData_->constVelocitiesView().paddedArrayRef().data());
+ auto x = as_rvec_array(statePropagatorData_->constPositionsView().paddedArrayRef().data());
+ auto v = as_rvec_array(statePropagatorData_->constVelocitiesView().paddedArrayRef().data());
- int nth = gmx_omp_nthreads_get(emntUpdate);
+ int nth = gmx_omp_nthreads_get(ModuleMultiThread::Update);
int homenr = mdAtoms_->mdatoms()->homenr;
#pragma omp parallel for num_threads(nth) schedule(static) default(none) shared(nth, homenr, x, xp, v)
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- wallcycle_stop(wcycle_, ewcUPDATE);
+ wallcycle_stop(wcycle_, WallCycleCounter::Update);
+}
+
+//! Propagation (scale position only)
+template<>
+template<NumVelocityScalingValues numStartVelocityScalingValues,
+ ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling,
+ NumVelocityScalingValues numEndVelocityScalingValues,
+ NumPositionScalingValues numPositionScalingValues>
+void Propagator<IntegrationStage::ScalePositions>::run()
+{
+ wallcycle_start(wcycle_, WallCycleCounter::Update);
+
+ auto* x = as_rvec_array(statePropagatorData_->positionsView().paddedArrayRef().data());
+
+ const real lambda =
+ (numPositionScalingValues == NumPositionScalingValues::Single) ? positionScaling_[0] : 1.0;
+
+ int nth = gmx_omp_nthreads_get(ModuleMultiThread::Update);
+ int homenr = mdAtoms_->mdatoms()->homenr;
+
+#pragma omp parallel for num_threads(nth) schedule(static) default(none) shared(nth, homenr, x) \
+ firstprivate(lambda)
+ for (int th = 0; th < nth; th++)
+ {
+ try
+ {
+ int start_th, end_th;
+ getThreadAtomRange(nth, th, homenr, &start_th, &end_th);
+
+ for (int a = start_th; a < end_th; a++)
+ {
+ scalePositions<numPositionScalingValues>(
+ a,
+ (numPositionScalingValues == NumPositionScalingValues::Multiple)
+ ? positionScaling_[mdAtoms_->mdatoms()->cTC[a]]
+ : lambda,
+ x);
+ }
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
+ }
+ wallcycle_stop(wcycle_, WallCycleCounter::Update);
}
//! Propagation (velocity only)
template<>
-template<NumVelocityScalingValues numVelocityScalingValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling>
-void Propagator<IntegrationStep::VelocitiesOnly>::run()
+template<NumVelocityScalingValues numStartVelocityScalingValues,
+ ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling,
+ NumVelocityScalingValues numEndVelocityScalingValues,
+ NumPositionScalingValues numPositionScalingValues>
+void Propagator<IntegrationStage::VelocitiesOnly>::run()
{
- wallcycle_start(wcycle_, ewcUPDATE);
+ wallcycle_start(wcycle_, WallCycleCounter::Update);
auto v = as_rvec_array(statePropagatorData_->velocitiesView().paddedArrayRef().data());
auto f = as_rvec_array(statePropagatorData_->constForcesView().force().data());
auto invMassPerDim = mdAtoms_->mdatoms()->invMassPerDim;
- const real lambda =
- (numVelocityScalingValues == NumVelocityScalingValues::Single) ? velocityScaling_[0] : 1.0;
+ const real lambdaStart = (numStartVelocityScalingValues == NumVelocityScalingValues::Single)
+ ? startVelocityScaling_[0]
+ : 1.0;
+ const real lambdaEnd = (numEndVelocityScalingValues == NumVelocityScalingValues::Single)
+ ? endVelocityScaling_[0]
+ : 1.0;
const bool isFullScalingMatrixDiagonal =
diagonalizePRMatrix<parrinelloRahmanVelocityScaling>(matrixPR_, diagPR_);
- const int nth = gmx_omp_nthreads_get(emntUpdate);
+ const int nth = gmx_omp_nthreads_get(ModuleMultiThread::Update);
const int homenr = mdAtoms_->mdatoms()->homenr;
// const variables could be shared, but gcc-8 & gcc-9 don't agree how to write that...
// https://www.gnu.org/software/gcc/gcc-9/porting_to.html -> OpenMP data sharing
-#pragma omp parallel for num_threads(nth) schedule(static) default(none) \
- shared(v, f, invMassPerDim) firstprivate(nth, homenr, lambda, isFullScalingMatrixDiagonal)
+#pragma omp parallel for num_threads(nth) schedule(static) default(none) shared(v, f, invMassPerDim) \
+ firstprivate(nth, homenr, lambdaStart, lambdaEnd, isFullScalingMatrixDiagonal)
for (int th = 0; th < nth; th++)
{
try
{
if (isFullScalingMatrixDiagonal)
{
- updateVelocities<numVelocityScalingValues, ParrinelloRahmanVelocityScaling::Diagonal>(
- a, timestep_,
- numVelocityScalingValues == NumVelocityScalingValues::Multiple
- ? velocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
- : lambda,
- invMassPerDim, v, f, diagPR_, matrixPR_);
+ updateVelocities<numStartVelocityScalingValues, ParrinelloRahmanVelocityScaling::Diagonal, numEndVelocityScalingValues>(
+ a,
+ timestep_,
+ numStartVelocityScalingValues == NumVelocityScalingValues::Multiple
+ ? startVelocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
+ : lambdaStart,
+ numEndVelocityScalingValues == NumVelocityScalingValues::Multiple
+ ? endVelocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
+ : lambdaEnd,
+ invMassPerDim,
+ v,
+ f,
+ diagPR_,
+ matrixPR_);
}
else
{
- updateVelocities<numVelocityScalingValues, parrinelloRahmanVelocityScaling>(
- a, timestep_,
- numVelocityScalingValues == NumVelocityScalingValues::Multiple
- ? velocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
- : lambda,
- invMassPerDim, v, f, diagPR_, matrixPR_);
+ updateVelocities<numStartVelocityScalingValues, parrinelloRahmanVelocityScaling, numEndVelocityScalingValues>(
+ a,
+ timestep_,
+ numStartVelocityScalingValues == NumVelocityScalingValues::Multiple
+ ? startVelocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
+ : lambdaStart,
+ numEndVelocityScalingValues == NumVelocityScalingValues::Multiple
+ ? endVelocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
+ : lambdaEnd,
+ invMassPerDim,
+ v,
+ f,
+ diagPR_,
+ matrixPR_);
}
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- wallcycle_stop(wcycle_, ewcUPDATE);
+ wallcycle_stop(wcycle_, WallCycleCounter::Update);
}
//! Propagation (leapfrog case - position and velocity)
template<>
-template<NumVelocityScalingValues numVelocityScalingValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling>
-void Propagator<IntegrationStep::LeapFrog>::run()
+template<NumVelocityScalingValues numStartVelocityScalingValues,
+ ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling,
+ NumVelocityScalingValues numEndVelocityScalingValues,
+ NumPositionScalingValues numPositionScalingValues>
+void Propagator<IntegrationStage::LeapFrog>::run()
{
- wallcycle_start(wcycle_, ewcUPDATE);
+ wallcycle_start(wcycle_, WallCycleCounter::Update);
auto xp = as_rvec_array(statePropagatorData_->positionsView().paddedArrayRef().data());
- auto x = as_rvec_array(statePropagatorData_->constPreviousPositionsView().paddedArrayRef().data());
- auto v = as_rvec_array(statePropagatorData_->velocitiesView().paddedArrayRef().data());
- auto f = as_rvec_array(statePropagatorData_->constForcesView().force().data());
+ auto x = as_rvec_array(statePropagatorData_->constPositionsView().paddedArrayRef().data());
+ auto v = as_rvec_array(statePropagatorData_->velocitiesView().paddedArrayRef().data());
+ auto f = as_rvec_array(statePropagatorData_->constForcesView().force().data());
auto invMassPerDim = mdAtoms_->mdatoms()->invMassPerDim;
- const real lambda =
- (numVelocityScalingValues == NumVelocityScalingValues::Single) ? velocityScaling_[0] : 1.0;
+ const real lambdaStart = (numStartVelocityScalingValues == NumVelocityScalingValues::Single)
+ ? startVelocityScaling_[0]
+ : 1.0;
+ const real lambdaEnd = (numEndVelocityScalingValues == NumVelocityScalingValues::Single)
+ ? endVelocityScaling_[0]
+ : 1.0;
const bool isFullScalingMatrixDiagonal =
diagonalizePRMatrix<parrinelloRahmanVelocityScaling>(matrixPR_, diagPR_);
- const int nth = gmx_omp_nthreads_get(emntUpdate);
+ const int nth = gmx_omp_nthreads_get(ModuleMultiThread::Update);
const int homenr = mdAtoms_->mdatoms()->homenr;
// const variables could be shared, but gcc-8 & gcc-9 don't agree how to write that...
// https://www.gnu.org/software/gcc/gcc-9/porting_to.html -> OpenMP data sharing
-#pragma omp parallel for num_threads(nth) schedule(static) default(none) shared( \
- x, xp, v, f, invMassPerDim) firstprivate(nth, homenr, lambda, isFullScalingMatrixDiagonal)
+#pragma omp parallel for num_threads(nth) schedule(static) default(none) \
+ shared(x, xp, v, f, invMassPerDim) \
+ firstprivate(nth, homenr, lambdaStart, lambdaEnd, isFullScalingMatrixDiagonal)
for (int th = 0; th < nth; th++)
{
try
{
if (isFullScalingMatrixDiagonal)
{
- updateVelocities<numVelocityScalingValues, ParrinelloRahmanVelocityScaling::Diagonal>(
- a, timestep_,
- numVelocityScalingValues == NumVelocityScalingValues::Multiple
- ? velocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
- : lambda,
- invMassPerDim, v, f, diagPR_, matrixPR_);
+ updateVelocities<numStartVelocityScalingValues, ParrinelloRahmanVelocityScaling::Diagonal, numEndVelocityScalingValues>(
+ a,
+ timestep_,
+ numStartVelocityScalingValues == NumVelocityScalingValues::Multiple
+ ? startVelocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
+ : lambdaStart,
+ numEndVelocityScalingValues == NumVelocityScalingValues::Multiple
+ ? endVelocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
+ : lambdaEnd,
+ invMassPerDim,
+ v,
+ f,
+ diagPR_,
+ matrixPR_);
}
else
{
- updateVelocities<numVelocityScalingValues, parrinelloRahmanVelocityScaling>(
- a, timestep_,
- numVelocityScalingValues == NumVelocityScalingValues::Multiple
- ? velocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
- : lambda,
- invMassPerDim, v, f, diagPR_, matrixPR_);
+ updateVelocities<numStartVelocityScalingValues, parrinelloRahmanVelocityScaling, numEndVelocityScalingValues>(
+ a,
+ timestep_,
+ numStartVelocityScalingValues == NumVelocityScalingValues::Multiple
+ ? startVelocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
+ : lambdaStart,
+ numEndVelocityScalingValues == NumVelocityScalingValues::Multiple
+ ? endVelocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
+ : lambdaEnd,
+ invMassPerDim,
+ v,
+ f,
+ diagPR_,
+ matrixPR_);
}
updatePositions(a, timestep_, x, xp, v);
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- wallcycle_stop(wcycle_, ewcUPDATE);
+ wallcycle_stop(wcycle_, WallCycleCounter::Update);
}
//! Propagation (velocity verlet stage 2 - velocity and position)
template<>
-template<NumVelocityScalingValues numVelocityScalingValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling>
-void Propagator<IntegrationStep::VelocityVerletPositionsAndVelocities>::run()
+template<NumVelocityScalingValues numStartVelocityScalingValues,
+ ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling,
+ NumVelocityScalingValues numEndVelocityScalingValues,
+ NumPositionScalingValues numPositionScalingValues>
+void Propagator<IntegrationStage::VelocityVerletPositionsAndVelocities>::run()
{
- wallcycle_start(wcycle_, ewcUPDATE);
+ wallcycle_start(wcycle_, WallCycleCounter::Update);
auto xp = as_rvec_array(statePropagatorData_->positionsView().paddedArrayRef().data());
- auto x = as_rvec_array(statePropagatorData_->constPreviousPositionsView().paddedArrayRef().data());
- auto v = as_rvec_array(statePropagatorData_->velocitiesView().paddedArrayRef().data());
- auto f = as_rvec_array(statePropagatorData_->constForcesView().force().data());
+ auto x = as_rvec_array(statePropagatorData_->constPositionsView().paddedArrayRef().data());
+ auto v = as_rvec_array(statePropagatorData_->velocitiesView().paddedArrayRef().data());
+ auto f = as_rvec_array(statePropagatorData_->constForcesView().force().data());
auto invMassPerDim = mdAtoms_->mdatoms()->invMassPerDim;
- const real lambda =
- (numVelocityScalingValues == NumVelocityScalingValues::Single) ? velocityScaling_[0] : 1.0;
+ const real lambdaStart = (numStartVelocityScalingValues == NumVelocityScalingValues::Single)
+ ? startVelocityScaling_[0]
+ : 1.0;
+ const real lambdaEnd = (numEndVelocityScalingValues == NumVelocityScalingValues::Single)
+ ? endVelocityScaling_[0]
+ : 1.0;
const bool isFullScalingMatrixDiagonal =
diagonalizePRMatrix<parrinelloRahmanVelocityScaling>(matrixPR_, diagPR_);
- const int nth = gmx_omp_nthreads_get(emntUpdate);
+ const int nth = gmx_omp_nthreads_get(ModuleMultiThread::Update);
const int homenr = mdAtoms_->mdatoms()->homenr;
// const variables could be shared, but gcc-8 & gcc-9 don't agree how to write that...
// https://www.gnu.org/software/gcc/gcc-9/porting_to.html -> OpenMP data sharing
-#pragma omp parallel for num_threads(nth) schedule(static) default(none) shared( \
- x, xp, v, f, invMassPerDim) firstprivate(nth, homenr, lambda, isFullScalingMatrixDiagonal)
+#pragma omp parallel for num_threads(nth) schedule(static) default(none) \
+ shared(x, xp, v, f, invMassPerDim) \
+ firstprivate(nth, homenr, lambdaStart, lambdaEnd, isFullScalingMatrixDiagonal)
for (int th = 0; th < nth; th++)
{
try
{
if (isFullScalingMatrixDiagonal)
{
- updateVelocities<numVelocityScalingValues, ParrinelloRahmanVelocityScaling::Diagonal>(
- a, 0.5 * timestep_,
- numVelocityScalingValues == NumVelocityScalingValues::Multiple
- ? velocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
- : lambda,
- invMassPerDim, v, f, diagPR_, matrixPR_);
+ updateVelocities<numStartVelocityScalingValues, ParrinelloRahmanVelocityScaling::Diagonal, numEndVelocityScalingValues>(
+ a,
+ 0.5 * timestep_,
+ numStartVelocityScalingValues == NumVelocityScalingValues::Multiple
+ ? startVelocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
+ : lambdaStart,
+ numEndVelocityScalingValues == NumVelocityScalingValues::Multiple
+ ? endVelocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
+ : lambdaEnd,
+ invMassPerDim,
+ v,
+ f,
+ diagPR_,
+ matrixPR_);
}
else
{
- updateVelocities<numVelocityScalingValues, parrinelloRahmanVelocityScaling>(
- a, 0.5 * timestep_,
- numVelocityScalingValues == NumVelocityScalingValues::Multiple
- ? velocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
- : lambda,
- invMassPerDim, v, f, diagPR_, matrixPR_);
+ updateVelocities<numStartVelocityScalingValues, parrinelloRahmanVelocityScaling, numEndVelocityScalingValues>(
+ a,
+ 0.5 * timestep_,
+ numStartVelocityScalingValues == NumVelocityScalingValues::Multiple
+ ? startVelocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
+ : lambdaStart,
+ numEndVelocityScalingValues == NumVelocityScalingValues::Multiple
+ ? endVelocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
+ : lambdaEnd,
+ invMassPerDim,
+ v,
+ f,
+ diagPR_,
+ matrixPR_);
}
updatePositions(a, timestep_, x, xp, v);
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- wallcycle_stop(wcycle_, ewcUPDATE);
+ wallcycle_stop(wcycle_, WallCycleCounter::Update);
+}
+
+//! Scaling (velocity scaling only)
+template<>
+template<NumVelocityScalingValues numStartVelocityScalingValues,
+ ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling,
+ NumVelocityScalingValues numEndVelocityScalingValues,
+ NumPositionScalingValues numPositionScalingValues>
+void Propagator<IntegrationStage::ScaleVelocities>::run()
+{
+ if (numStartVelocityScalingValues == NumVelocityScalingValues::None)
+ {
+ return;
+ }
+ wallcycle_start(wcycle_, WallCycleCounter::Update);
+
+ auto* v = as_rvec_array(statePropagatorData_->velocitiesView().paddedArrayRef().data());
+
+ const real lambdaStart = (numStartVelocityScalingValues == NumVelocityScalingValues::Single)
+ ? startVelocityScaling_[0]
+ : 1.0;
+
+ const int nth = gmx_omp_nthreads_get(ModuleMultiThread::Update);
+ const int homenr = mdAtoms_->mdatoms()->homenr;
+
+// const variables could be shared, but gcc-8 & gcc-9 don't agree how to write that...
+// https://www.gnu.org/software/gcc/gcc-9/porting_to.html -> OpenMP data sharing
+#pragma omp parallel for num_threads(nth) schedule(static) default(none) shared(v) \
+ firstprivate(nth, homenr, lambdaStart)
+ for (int th = 0; th < nth; th++)
+ {
+ try
+ {
+ int start_th = 0;
+ int end_th = 0;
+ getThreadAtomRange(nth, th, homenr, &start_th, &end_th);
+
+ for (int a = start_th; a < end_th; a++)
+ {
+ scaleVelocities<numStartVelocityScalingValues>(
+ a,
+ numStartVelocityScalingValues == NumVelocityScalingValues::Multiple
+ ? startVelocityScaling_[mdAtoms_->mdatoms()->cTC[a]]
+ : lambdaStart,
+ v);
+ }
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
+ }
+ wallcycle_stop(wcycle_, WallCycleCounter::Update);
}
-template<IntegrationStep algorithm>
-Propagator<algorithm>::Propagator(double timestep,
- StatePropagatorData* statePropagatorData,
- const MDAtoms* mdAtoms,
- gmx_wallcycle* wcycle) :
+template<IntegrationStage integrationStage>
+Propagator<integrationStage>::Propagator(double timestep,
+ StatePropagatorData* statePropagatorData,
+ const MDAtoms* mdAtoms,
+ gmx_wallcycle* wcycle) :
timestep_(timestep),
statePropagatorData_(statePropagatorData),
- doSingleVelocityScaling_(false),
- doGroupVelocityScaling_(false),
+ doSingleStartVelocityScaling_(false),
+ doGroupStartVelocityScaling_(false),
+ doSingleEndVelocityScaling_(false),
+ doGroupEndVelocityScaling_(false),
scalingStepVelocity_(-1),
diagPR_{ 0 },
matrixPR_{ { 0 } },
{
}
-template<IntegrationStep algorithm>
-void Propagator<algorithm>::scheduleTask(Step gmx_unused step,
- Time gmx_unused time,
- const RegisterRunFunction& registerRunFunction)
+template<IntegrationStage integrationStage>
+void Propagator<integrationStage>::scheduleTask(Step step,
+ Time gmx_unused time,
+ const RegisterRunFunction& registerRunFunction)
{
- const bool doSingleVScalingThisStep = (doSingleVelocityScaling_ && (step == scalingStepVelocity_));
- const bool doGroupVScalingThisStep = (doGroupVelocityScaling_ && (step == scalingStepVelocity_));
+ const bool doSingleVScalingThisStep =
+ (doSingleStartVelocityScaling_ && (step == scalingStepVelocity_));
+ const bool doGroupVScalingThisStep = (doGroupStartVelocityScaling_ && (step == scalingStepVelocity_));
- const bool doParrinelloRahmanThisStep = (step == scalingStepPR_);
+ if (integrationStage == IntegrationStage::ScaleVelocities)
+ {
+ // IntegrationStage::ScaleVelocities only needs to run if some kind of
+ // velocity scaling is needed on the current step.
+ if (!doSingleVScalingThisStep && !doGroupVScalingThisStep)
+ {
+ return;
+ }
+ }
- if (doSingleVScalingThisStep)
+ if (integrationStage == IntegrationStage::ScalePositions)
{
- if (doParrinelloRahmanThisStep)
+ // IntegrationStage::ScalePositions only needs to run if
+ // position scaling is needed on the current step.
+ if (step != scalingStepPosition_)
+ {
+ return;
+ }
+ // Since IntegrationStage::ScalePositions is the only stage for which position scaling
+ // is implemented we handle it here to avoid enlarging the decision tree below.
+ if (doSinglePositionScaling_)
{
registerRunFunction([this]() {
- run<NumVelocityScalingValues::Single, ParrinelloRahmanVelocityScaling::Full>();
+ run<NumVelocityScalingValues::None,
+ ParrinelloRahmanVelocityScaling::No,
+ NumVelocityScalingValues::None,
+ NumPositionScalingValues::Single>();
});
}
- else
+ else if (doGroupPositionScaling_)
{
registerRunFunction([this]() {
- run<NumVelocityScalingValues::Single, ParrinelloRahmanVelocityScaling::No>();
+ run<NumVelocityScalingValues::None,
+ ParrinelloRahmanVelocityScaling::No,
+ NumVelocityScalingValues::None,
+ NumPositionScalingValues::Multiple>();
});
}
}
+
+ const bool doParrinelloRahmanThisStep = (step == scalingStepPR_);
+
+ if (doSingleVScalingThisStep)
+ {
+ if (doParrinelloRahmanThisStep)
+ {
+ if (doSingleEndVelocityScaling_)
+ {
+ registerRunFunction([this]() {
+ run<NumVelocityScalingValues::Single,
+ ParrinelloRahmanVelocityScaling::Full,
+ NumVelocityScalingValues::Single,
+ NumPositionScalingValues::None>();
+ });
+ }
+ else
+ {
+ registerRunFunction([this]() {
+ run<NumVelocityScalingValues::Single,
+ ParrinelloRahmanVelocityScaling::Full,
+ NumVelocityScalingValues::None,
+ NumPositionScalingValues::None>();
+ });
+ }
+ }
+ else
+ {
+ if (doSingleEndVelocityScaling_)
+ {
+ registerRunFunction([this]() {
+ run<NumVelocityScalingValues::Single,
+ ParrinelloRahmanVelocityScaling::No,
+ NumVelocityScalingValues::Single,
+ NumPositionScalingValues::None>();
+ });
+ }
+ else
+ {
+ registerRunFunction([this]() {
+ run<NumVelocityScalingValues::Single,
+ ParrinelloRahmanVelocityScaling::No,
+ NumVelocityScalingValues::None,
+ NumPositionScalingValues::None>();
+ });
+ }
+ }
+ }
else if (doGroupVScalingThisStep)
{
if (doParrinelloRahmanThisStep)
{
- registerRunFunction([this]() {
- run<NumVelocityScalingValues::Multiple, ParrinelloRahmanVelocityScaling::Full>();
- });
+ if (doGroupEndVelocityScaling_)
+ {
+ registerRunFunction([this]() {
+ run<NumVelocityScalingValues::Multiple,
+ ParrinelloRahmanVelocityScaling::Full,
+ NumVelocityScalingValues::Multiple,
+ NumPositionScalingValues::None>();
+ });
+ }
+ else
+ {
+ registerRunFunction([this]() {
+ run<NumVelocityScalingValues::Multiple,
+ ParrinelloRahmanVelocityScaling::Full,
+ NumVelocityScalingValues::None,
+ NumPositionScalingValues::None>();
+ });
+ }
}
else
{
- registerRunFunction([this]() {
- run<NumVelocityScalingValues::Multiple, ParrinelloRahmanVelocityScaling::No>();
- });
+ if (doGroupEndVelocityScaling_)
+ {
+ registerRunFunction([this]() {
+ run<NumVelocityScalingValues::Multiple,
+ ParrinelloRahmanVelocityScaling::No,
+ NumVelocityScalingValues::Multiple,
+ NumPositionScalingValues::None>();
+ });
+ }
+ else
+ {
+ registerRunFunction([this]() {
+ run<NumVelocityScalingValues::Multiple,
+ ParrinelloRahmanVelocityScaling::No,
+ NumVelocityScalingValues::None,
+ NumPositionScalingValues::None>();
+ });
+ }
}
}
else
if (doParrinelloRahmanThisStep)
{
registerRunFunction([this]() {
- run<NumVelocityScalingValues::None, ParrinelloRahmanVelocityScaling::Full>();
+ run<NumVelocityScalingValues::None,
+ ParrinelloRahmanVelocityScaling::Full,
+ NumVelocityScalingValues::None,
+ NumPositionScalingValues::None>();
});
}
else
{
registerRunFunction([this]() {
- run<NumVelocityScalingValues::None, ParrinelloRahmanVelocityScaling::No>();
+ run<NumVelocityScalingValues::None,
+ ParrinelloRahmanVelocityScaling::No,
+ NumVelocityScalingValues::None,
+ NumPositionScalingValues::None>();
});
}
}
}
-template<IntegrationStep algorithm>
-void Propagator<algorithm>::setNumVelocityScalingVariables(int numVelocityScalingVariables)
+template<IntegrationStage integrationStage>
+constexpr bool hasStartVelocityScaling()
{
- if (algorithm == IntegrationStep::PositionsOnly)
- {
- gmx_fatal(FARGS, "Velocity scaling not implemented for IntegrationStep::PositionsOnly.");
- }
- GMX_ASSERT(velocityScaling_.empty(),
- "Number of velocity scaling variables cannot be changed once set.");
+ return (integrationStage == IntegrationStage::VelocitiesOnly
+ || integrationStage == IntegrationStage::LeapFrog
+ || integrationStage == IntegrationStage::VelocityVerletPositionsAndVelocities
+ || integrationStage == IntegrationStage::ScaleVelocities);
+}
- velocityScaling_.resize(numVelocityScalingVariables, 1.);
- doSingleVelocityScaling_ = numVelocityScalingVariables == 1;
- doGroupVelocityScaling_ = numVelocityScalingVariables > 1;
+template<IntegrationStage integrationStage>
+constexpr bool hasEndVelocityScaling()
+{
+ return (hasStartVelocityScaling<integrationStage>()
+ && integrationStage != IntegrationStage::ScaleVelocities);
}
-template<IntegrationStep algorithm>
-ArrayRef<real> Propagator<algorithm>::viewOnVelocityScaling()
+template<IntegrationStage integrationStage>
+constexpr bool hasPositionScaling()
{
- if (algorithm == IntegrationStep::PositionsOnly)
- {
- gmx_fatal(FARGS, "Velocity scaling not implemented for IntegrationStep::PositionsOnly.");
- }
- GMX_ASSERT(!velocityScaling_.empty(), "Number of velocity scaling variables not set.");
+ return (integrationStage == IntegrationStage::ScalePositions);
+}
- return velocityScaling_;
+template<IntegrationStage integrationStage>
+constexpr bool hasParrinelloRahmanScaling()
+{
+ return (integrationStage == IntegrationStage::VelocitiesOnly
+ || integrationStage == IntegrationStage::LeapFrog
+ || integrationStage == IntegrationStage::VelocityVerletPositionsAndVelocities);
}
-template<IntegrationStep algorithm>
-PropagatorCallback Propagator<algorithm>::velocityScalingCallback()
+template<IntegrationStage integrationStage>
+void Propagator<integrationStage>::setNumVelocityScalingVariables(int numVelocityScalingVariables,
+ ScaleVelocities scaleVelocities)
{
- if (algorithm == IntegrationStep::PositionsOnly)
+ GMX_RELEASE_ASSERT(
+ hasStartVelocityScaling<integrationStage>() || hasEndVelocityScaling<integrationStage>(),
+ formatString("Velocity scaling not implemented for %s", integrationStepNames[integrationStage])
+ .c_str());
+ GMX_RELEASE_ASSERT(startVelocityScaling_.empty(),
+ "Number of velocity scaling variables cannot be changed once set.");
+
+ const bool scaleEndVelocities = (scaleVelocities == ScaleVelocities::PreStepAndPostStep);
+ startVelocityScaling_.resize(numVelocityScalingVariables, 1.);
+ if (scaleEndVelocities)
{
- gmx_fatal(FARGS, "Velocity scaling not implemented for IntegrationStep::PositionsOnly.");
+ endVelocityScaling_.resize(numVelocityScalingVariables, 1.);
}
+ doSingleStartVelocityScaling_ = numVelocityScalingVariables == 1;
+ doGroupStartVelocityScaling_ = numVelocityScalingVariables > 1;
+ doSingleEndVelocityScaling_ = doSingleStartVelocityScaling_ && scaleEndVelocities;
+ doGroupEndVelocityScaling_ = doGroupStartVelocityScaling_ && scaleEndVelocities;
+}
- return [this](Step step) { scalingStepVelocity_ = step; };
+template<IntegrationStage integrationStage>
+void Propagator<integrationStage>::setNumPositionScalingVariables(int numPositionScalingVariables)
+{
+ GMX_RELEASE_ASSERT(hasPositionScaling<integrationStage>(),
+ formatString("Position scaling not implemented for %s",
+ integrationStepNames[integrationStage])
+ .c_str());
+ GMX_RELEASE_ASSERT(positionScaling_.empty(),
+ "Number of position scaling variables cannot be changed once set.");
+ positionScaling_.resize(numPositionScalingVariables, 1.);
+ doSinglePositionScaling_ = (numPositionScalingVariables == 1);
+ doGroupPositionScaling_ = (numPositionScalingVariables > 1);
}
-template<IntegrationStep algorithm>
-ArrayRef<rvec> Propagator<algorithm>::viewOnPRScalingMatrix()
+template<IntegrationStage integrationStage>
+ArrayRef<real> Propagator<integrationStage>::viewOnStartVelocityScaling()
+{
+ GMX_RELEASE_ASSERT(hasStartVelocityScaling<integrationStage>(),
+ formatString("Start velocity scaling not implemented for %s",
+ integrationStepNames[integrationStage])
+ .c_str());
+ GMX_RELEASE_ASSERT(!startVelocityScaling_.empty(),
+ "Number of velocity scaling variables not set.");
+
+ return startVelocityScaling_;
+}
+
+template<IntegrationStage integrationStage>
+ArrayRef<real> Propagator<integrationStage>::viewOnEndVelocityScaling()
+{
+ GMX_RELEASE_ASSERT(hasEndVelocityScaling<integrationStage>(),
+ formatString("End velocity scaling not implemented for %s",
+ integrationStepNames[integrationStage])
+ .c_str());
+ GMX_RELEASE_ASSERT(!endVelocityScaling_.empty(),
+ "Number of velocity scaling variables not set.");
+
+ return endVelocityScaling_;
+}
+
+template<IntegrationStage integrationStage>
+ArrayRef<real> Propagator<integrationStage>::viewOnPositionScaling()
+{
+ GMX_RELEASE_ASSERT(hasPositionScaling<integrationStage>(),
+ formatString("Position scaling not implemented for %s",
+ integrationStepNames[integrationStage])
+ .c_str());
+ GMX_RELEASE_ASSERT(!positionScaling_.empty(), "Number of position scaling variables not set.");
+
+ return positionScaling_;
+}
+
+template<IntegrationStage integrationStage>
+PropagatorCallback Propagator<integrationStage>::velocityScalingCallback()
{
GMX_RELEASE_ASSERT(
- algorithm != IntegrationStep::PositionsOnly,
- "Parrinello-Rahman scaling not implemented for IntegrationStep::PositionsOnly.");
+ hasStartVelocityScaling<integrationStage>() || hasEndVelocityScaling<integrationStage>(),
+ formatString("Velocity scaling not implemented for %s", integrationStepNames[integrationStage])
+ .c_str());
+
+ return [this](Step step) { scalingStepVelocity_ = step; };
+}
+
+template<IntegrationStage integrationStage>
+PropagatorCallback Propagator<integrationStage>::positionScalingCallback()
+{
+ GMX_RELEASE_ASSERT(hasPositionScaling<integrationStage>(),
+ formatString("Position scaling not implemented for %s",
+ integrationStepNames[integrationStage])
+ .c_str());
+
+ return [this](Step step) { scalingStepPosition_ = step; };
+}
+
+template<IntegrationStage integrationStage>
+ArrayRef<rvec> Propagator<integrationStage>::viewOnPRScalingMatrix()
+{
+ GMX_RELEASE_ASSERT(hasParrinelloRahmanScaling<integrationStage>(),
+ formatString("Parrinello-Rahman scaling not implemented for %s",
+ integrationStepNames[integrationStage])
+ .c_str());
clear_mat(matrixPR_);
// gcc-5 needs this to be explicit (all other tested compilers would be ok
return ArrayRef<rvec>(matrixPR_);
}
-template<IntegrationStep algorithm>
-PropagatorCallback Propagator<algorithm>::prScalingCallback()
+template<IntegrationStage integrationStage>
+PropagatorCallback Propagator<integrationStage>::prScalingCallback()
{
- GMX_RELEASE_ASSERT(
- algorithm != IntegrationStep::PositionsOnly,
- "Parrinello-Rahman scaling not implemented for IntegrationStep::PositionsOnly.");
+ GMX_RELEASE_ASSERT(hasParrinelloRahmanScaling<integrationStage>(),
+ formatString("Parrinello-Rahman scaling not implemented for %s",
+ integrationStepNames[integrationStage])
+ .c_str());
return [this](Step step) { scalingStepPR_ = step; };
}
-template<IntegrationStep algorithm>
-ISimulatorElement* Propagator<algorithm>::getElementPointerImpl(
+template<IntegrationStage integrationStage>
+static PropagatorConnection getConnection(Propagator<integrationStage> gmx_unused* propagator,
+ const PropagatorTag& propagatorTag)
+{
+ // gmx_unused is needed because gcc-7 & gcc-8 can't see that
+ // propagator is used for all IntegrationStage options
+
+ PropagatorConnection propagatorConnection{ propagatorTag };
+
+ // The clang-tidy version on our current CI throws 3 different warnings
+ // for the if constexpr lines, so disable linting for now. Also, this only
+ // works if the brace is on the same line, so turn off clang-format as well
+ // clang-format off
+ // NOLINTNEXTLINE
+ if constexpr (hasStartVelocityScaling<integrationStage>() || hasEndVelocityScaling<integrationStage>()) {
+ // clang-format on
+ propagatorConnection.setNumVelocityScalingVariables =
+ [propagator](int num, ScaleVelocities scaleVelocities) {
+ propagator->setNumVelocityScalingVariables(num, scaleVelocities);
+ };
+ propagatorConnection.getVelocityScalingCallback = [propagator]() {
+ return propagator->velocityScalingCallback();
+ };
+ }
+ // clang-format off
+ // NOLINTNEXTLINE
+ if constexpr (hasStartVelocityScaling<integrationStage>()) {
+ // clang-format on
+ propagatorConnection.getViewOnStartVelocityScaling = [propagator]() {
+ return propagator->viewOnStartVelocityScaling();
+ };
+ }
+ // clang-format off
+ // NOLINTNEXTLINE
+ if constexpr (hasEndVelocityScaling<integrationStage>()) {
+ // clang-format on
+ propagatorConnection.getViewOnEndVelocityScaling = [propagator]() {
+ return propagator->viewOnEndVelocityScaling();
+ };
+ }
+ // clang-format off
+ // NOLINTNEXTLINE
+ if constexpr (hasPositionScaling<integrationStage>()) {
+ // clang-format on
+ propagatorConnection.setNumPositionScalingVariables = [propagator](int num) {
+ propagator->setNumPositionScalingVariables(num);
+ };
+ propagatorConnection.getViewOnPositionScaling = [propagator]() {
+ return propagator->viewOnPositionScaling();
+ };
+ propagatorConnection.getPositionScalingCallback = [propagator]() {
+ return propagator->positionScalingCallback();
+ };
+ }
+ // clang-format off
+ // NOLINTNEXTLINE
+ if constexpr (hasParrinelloRahmanScaling<integrationStage>()) {
+ // clang-format on
+ propagatorConnection.getViewOnPRScalingMatrix = [propagator]() {
+ return propagator->viewOnPRScalingMatrix();
+ };
+ propagatorConnection.getPRScalingCallback = [propagator]() {
+ return propagator->prScalingCallback();
+ };
+ }
+
+ // NOLINTNEXTLINE(readability-misleading-indentation)
+ return propagatorConnection;
+}
+
+// doxygen is confused by the two definitions
+//! \cond
+template<IntegrationStage integrationStage>
+ISimulatorElement* Propagator<integrationStage>::getElementPointerImpl(
LegacySimulatorData* legacySimulatorData,
ModularSimulatorAlgorithmBuilderHelper* builderHelper,
StatePropagatorData* statePropagatorData,
EnergyData gmx_unused* energyData,
FreeEnergyPerturbationData gmx_unused* freeEnergyPerturbationData,
GlobalCommunicationHelper gmx_unused* globalCommunicationHelper,
- double timestep,
- RegisterWithThermostat registerWithThermostat,
- RegisterWithBarostat registerWithBarostat)
+ const PropagatorTag& propagatorTag,
+ TimeStep timestep)
{
- auto* element = builderHelper->storeElement(std::make_unique<Propagator<algorithm>>(
+ GMX_RELEASE_ASSERT(!(integrationStage == IntegrationStage::ScaleVelocities
+ || integrationStage == IntegrationStage::ScalePositions)
+ || (timestep == 0.0),
+ "Scaling elements don't propagate the system.");
+ auto* element = builderHelper->storeElement(std::make_unique<Propagator<integrationStage>>(
timestep, statePropagatorData, legacySimulatorData->mdAtoms, legacySimulatorData->wcycle));
- if (registerWithThermostat == RegisterWithThermostat::True)
- {
- auto* propagator = static_cast<Propagator<algorithm>*>(element);
- builderHelper->registerWithThermostat(
- { [propagator](int num) { propagator->setNumVelocityScalingVariables(num); },
- [propagator]() { return propagator->viewOnVelocityScaling(); },
- [propagator]() { return propagator->velocityScalingCallback(); } });
- }
- if (registerWithBarostat == RegisterWithBarostat::True)
- {
- auto* propagator = static_cast<Propagator<algorithm>*>(element);
- builderHelper->registerWithBarostat(
- { [propagator]() { return propagator->viewOnPRScalingMatrix(); },
- [propagator]() { return propagator->prScalingCallback(); } });
- }
+ auto* propagator = static_cast<Propagator<integrationStage>*>(element);
+ builderHelper->registerPropagator(getConnection<integrationStage>(propagator, propagatorTag));
return element;
}
+template<IntegrationStage integrationStage>
+ISimulatorElement* Propagator<integrationStage>::getElementPointerImpl(
+ LegacySimulatorData* legacySimulatorData,
+ ModularSimulatorAlgorithmBuilderHelper* builderHelper,
+ StatePropagatorData* statePropagatorData,
+ EnergyData* energyData,
+ FreeEnergyPerturbationData* freeEnergyPerturbationData,
+ GlobalCommunicationHelper* globalCommunicationHelper,
+ const PropagatorTag& propagatorTag)
+{
+ GMX_RELEASE_ASSERT(
+ integrationStage == IntegrationStage::ScaleVelocities
+ || integrationStage == IntegrationStage::ScalePositions,
+ "Adding a propagator without time step is only allowed for scaling elements");
+ return getElementPointerImpl(legacySimulatorData,
+ builderHelper,
+ statePropagatorData,
+ energyData,
+ freeEnergyPerturbationData,
+ globalCommunicationHelper,
+ propagatorTag,
+ TimeStep(0.0));
+}
+//! \endcond
+
// Explicit template initializations
-template class Propagator<IntegrationStep::PositionsOnly>;
-template class Propagator<IntegrationStep::VelocitiesOnly>;
-template class Propagator<IntegrationStep::LeapFrog>;
-template class Propagator<IntegrationStep::VelocityVerletPositionsAndVelocities>;
+template class Propagator<IntegrationStage::PositionsOnly>;
+template class Propagator<IntegrationStage::VelocitiesOnly>;
+template class Propagator<IntegrationStage::LeapFrog>;
+template class Propagator<IntegrationStage::VelocityVerletPositionsAndVelocities>;
+template class Propagator<IntegrationStage::ScaleVelocities>;
+template class Propagator<IntegrationStage::ScalePositions>;
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! \addtogroup module_modularsimulator
//! \{
-//! Whether built propagator should be registered with thermostat
-enum class RegisterWithThermostat
+//! Which velocities the thermostat scales
+enum class ScaleVelocities
{
- True,
- False
+ PreStepOnly,
+ PreStepAndPostStep
};
-//! Whether built propagator should be registered with barostat
-enum class RegisterWithBarostat
+
+//! The different integration types we know about
+enum class IntegrationStage
{
- True,
- False
+ PositionsOnly, //!< Moves the position vector by the given time step
+ VelocitiesOnly, //!< Moves the velocity vector by the given time step
+ LeapFrog, //!< Manual fusion of the previous two propagators
+ VelocityVerletPositionsAndVelocities, //!< Manual position (full dt) and velocity (half dt) fusion
+ ScaleVelocities, //!< Only scale velocities, don't propagate
+ ScalePositions, //!< Only scale positions, don't propagate
+ Count //!< The number of enum entries
};
-/*! \brief The different integration types we know about
- *
- * PositionsOnly:
- * Moves the position vector by the given time step
- * VelocitiesOnly:
- * Moves the velocity vector by the given time step
- * LeapFrog:
- * Is a manual fusion of the previous two propagators
- * VelocityVerletPositionsAndVelocities:
- * Is a manual fusion of VelocitiesOnly and PositionsOnly,
- * where VelocitiesOnly is only propagated by half the
- * time step of the positions.
- */
-enum class IntegrationStep
+//! Sets the number of different position scaling values
+enum class NumPositionScalingValues
{
- PositionsOnly,
- VelocitiesOnly,
- LeapFrog,
- VelocityVerletPositionsAndVelocities,
- Count
+ None, //!< No position scaling (either this step or ever)
+ Single, //!< Single scaling value (either one group or all values =1)
+ Multiple, //!< Multiple scaling values, need to use T-group indices
+ Count //!< The number of enum entries
};
//! Sets the number of different velocity scaling values
* functions allows to have performance comparable to fused update elements
* while keeping easily re-orderable single instructions.
*
- * \tparam algorithm The integration types
+ * \tparam integrationStep The integration types
*/
-template<IntegrationStep algorithm>
+template<IntegrationStage integrationStage>
class Propagator final : public ISimulatorElement
{
public:
gmx_wallcycle* wcycle);
/*! \brief Register run function for step / time
+ *
+ * This function will determine the required flavor of the run function to be registered
+ * for the current step. In case of the pure scaling integrator stage, it might also skip
+ * the function registration if no scaling is needed.
*
* \param step The step number
* \param time The time
void elementTeardown() override {}
//! Set the number of velocity scaling variables
- void setNumVelocityScalingVariables(int numVelocityScalingVariables);
- //! Get view on the velocity scaling vector
- ArrayRef<real> viewOnVelocityScaling();
+ void setNumVelocityScalingVariables(int numVelocityScalingVariables, ScaleVelocities scaleVelocities);
+ //! Set the number of position scaling variables
+ void setNumPositionScalingVariables(int numPositionScalingVariables);
+ //! Get view on the scaling vector applied to start of step velocities
+ ArrayRef<real> viewOnStartVelocityScaling();
+ //! Get view on the scaling vector applied to end of step velocities
+ ArrayRef<real> viewOnEndVelocityScaling();
+ //! Get view on the scaling vector applied to the positions
+ ArrayRef<real> viewOnPositionScaling();
//! Get velocity scaling callback
PropagatorCallback velocityScalingCallback();
+ //! Get position scaling callback
+ PropagatorCallback positionScalingCallback();
//! Get view on the full PR scaling matrix
ArrayRef<rvec> viewOnPRScalingMatrix();
* \param energyData Pointer to the \c EnergyData object
* \param freeEnergyPerturbationData Pointer to the \c FreeEnergyPerturbationData object
* \param globalCommunicationHelper Pointer to the \c GlobalCommunicationHelper object
+ * \param propagatorTag The name of the propagator to simplify connection
* \param timestep The time step the propagator uses
- * \param registerWithThermostat Whether this propagator should be registered with the thermostat
- * \param registerWithBarostat Whether this propagator should be registered with the barostat
*
* \return Pointer to the element to be added. Element needs to have been stored using \c storeElement
*/
EnergyData* energyData,
FreeEnergyPerturbationData* freeEnergyPerturbationData,
GlobalCommunicationHelper* globalCommunicationHelper,
- double timestep,
- RegisterWithThermostat registerWithThermostat,
- RegisterWithBarostat registerWithBarostat);
+ const PropagatorTag& propagatorTag,
+ TimeStep timestep);
+
+ /*! \brief Factory method implementation
+ *
+ * Version without time step for pure scaling elements
+ *
+ * \param legacySimulatorData Pointer allowing access to simulator level data
+ * \param builderHelper ModularSimulatorAlgorithmBuilder helper object
+ * \param statePropagatorData Pointer to the \c StatePropagatorData object
+ * \param energyData Pointer to the \c EnergyData object
+ * \param freeEnergyPerturbationData Pointer to the \c FreeEnergyPerturbationData object
+ * \param globalCommunicationHelper Pointer to the \c GlobalCommunicationHelper object
+ * \param propagatorTag The name of the propagator to simplify connection
+ *
+ * \return Pointer to the element to be added. Element needs to have been stored using \c storeElement
+ */
+ static ISimulatorElement* getElementPointerImpl(LegacySimulatorData* legacySimulatorData,
+ ModularSimulatorAlgorithmBuilderHelper* builderHelper,
+ StatePropagatorData* statePropagatorData,
+ EnergyData* energyData,
+ FreeEnergyPerturbationData* freeEnergyPerturbationData,
+ GlobalCommunicationHelper* globalCommunicationHelper,
+ const PropagatorTag& propagatorTag);
private:
//! The actual propagation
- template<NumVelocityScalingValues numVelocityScalingValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling>
+ template<NumVelocityScalingValues numStartVelocityScalingValues,
+ ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling,
+ NumVelocityScalingValues numEndVelocityScalingValues,
+ NumPositionScalingValues numPositionScalingValues>
void run();
//! The time step
//! Pointer to the micro state
StatePropagatorData* statePropagatorData_;
- //! Whether we're doing single-value velocity scaling
- bool doSingleVelocityScaling_;
- //! Wether we're doing group-wise velocity scaling
- bool doGroupVelocityScaling_;
+ //! Whether we're doing single-value velocity scaling (velocities at start of step)
+ bool doSingleStartVelocityScaling_;
+ //! Whether we're doing group-wise velocity scaling (velocities at start of step)
+ bool doGroupStartVelocityScaling_;
+ //! Whether we're doing single-value velocity scaling (velocities at end of step)
+ bool doSingleEndVelocityScaling_;
+ //! Wether we're doing group-wise velocity scaling (velocities at end of step)
+ bool doGroupEndVelocityScaling_;
+ //! Whether we're doing single-value position scaling
+ bool doSinglePositionScaling_;
+ //! Whether we're doing group-wise position scaling
+ bool doGroupPositionScaling_;
+ //! The vector of velocity scaling values
+ std::vector<real> startVelocityScaling_;
//! The vector of velocity scaling values
- std::vector<real> velocityScaling_;
+ std::vector<real> endVelocityScaling_;
+ //! The vector of position scaling values
+ std::vector<real> positionScaling_;
//! The next velocity scaling step
Step scalingStepVelocity_;
+ //! The next position scaling step
+ Step scalingStepPosition_;
//! The diagonal of the PR scaling matrix
rvec diagPR_;
std::vector<SignallerCallback> calculateFreeEnergyCallbacks,
int nstcalcenergy,
int nstcalcfreeenergy,
- int nstcalcvirial) :
+ int nstcalcvirial,
+ EnergySignallerVirialMode virialMode) :
calculateEnergyCallbacks_(std::move(calculateEnergyCallbacks)),
calculateVirialCallbacks_(std::move(calculateVirialCallbacks)),
calculateFreeEnergyCallbacks_(std::move(calculateFreeEnergyCallbacks)),
nstcalcenergy_(nstcalcenergy),
nstcalcfreeenergy_(nstcalcfreeenergy),
nstcalcvirial_(nstcalcvirial),
+ virialMode_(virialMode),
energyWritingStep_(-1),
trajectoryRegistrationDone_(false),
loggingStep_(-1),
void EnergySignaller::signal(Step step, Time time)
{
- bool calculateEnergy = do_per_step(step, nstcalcenergy_);
- bool calculateFreeEnergy = do_per_step(step, nstcalcfreeenergy_);
- bool calculateVirial = do_per_step(step, nstcalcvirial_);
- bool writeEnergy = energyWritingStep_ == step;
+ const bool writeEnergy = (energyWritingStep_ == step);
+ const bool writeLog = (loggingStep_ == step);
+ const bool calculateEnergy = writeEnergy || writeLog || do_per_step(step, nstcalcenergy_);
+ const bool calculateVirial = calculateEnergy
+ || ((virialMode_ == EnergySignallerVirialMode::OnStep
+ || virialMode_ == EnergySignallerVirialMode::OnStepAndNext)
+ && do_per_step(step, nstcalcvirial_))
+ || (virialMode_ == EnergySignallerVirialMode::OnStepAndNext
+ && do_per_step(step - 1, nstcalcvirial_));
+ const bool calculateFreeEnergy = do_per_step(step, nstcalcfreeenergy_);
- if (calculateEnergy || writeEnergy || step == loggingStep_)
+ if (calculateEnergy)
{
runAllCallbacks(calculateEnergyCallbacks_, step, time);
}
- if (calculateEnergy || writeEnergy || step == loggingStep_ || calculateVirial)
+ if (calculateVirial)
{
runAllCallbacks(calculateVirialCallbacks_, step, time);
}
std::optional<SignallerCallback> registerLastStepCallback() override;
};
+//! When we calculate virial
+enum class EnergySignallerVirialMode
+{
+ Off, //!< No specific virial calculation - calculate when energy is calculated
+ OnStep, //!< Calculate on virial frequency steps
+ OnStepAndNext, //!< Calculate on virial frequency steps and on step after
+ Count //!< The number of entries
+};
+
/*! \internal
* \ingroup module_modularsimulator
* \brief Element signalling energy related special steps
* \param nstcalcenergy The energy calculation frequency
* \param nstcalcfreeenergy The free energy calculation frequency
* \param nstcalcvirial The free energy calculation frequency
+ * \param virialMode Indicates which steps will calculate virial
*/
EnergySignaller(std::vector<SignallerCallback> calculateEnergyCallbacks,
std::vector<SignallerCallback> calculateVirialCallbacks,
std::vector<SignallerCallback> calculateFreeEnergyCallbacks,
int nstcalcenergy,
int nstcalcfreeenergy,
- int nstcalcvirial);
+ int nstcalcvirial,
+ EnergySignallerVirialMode virialMode);
//! Client callbacks
//! {
const int nstcalcfreeenergy_;
//! The virial calculation frequency
const int nstcalcvirial_;
+ //! The virial calculation mode
+ const EnergySignallerVirialMode virialMode_;
//! ITrajectorySignallerClient implementation
std::optional<SignallerCallback> registerTrajectorySignallerCallback(TrajectoryEvent event) override;
auto calculateFreeEnergyCallbacks =
buildCallbackVector(EnergySignallerEvent::FreeEnergyCalculationStep);
// NOLINTNEXTLINE(modernize-make-unique): make_unique does not work with private constructor
- return std::unique_ptr<EnergySignaller>(new EnergySignaller(
- std::move(calculateEnergyCallbacks), std::move(calculateVirialCallbacks),
- std::move(calculateFreeEnergyCallbacks), std::forward<Args>(args)...));
+ return std::unique_ptr<EnergySignaller>(new EnergySignaller(std::move(calculateEnergyCallbacks),
+ std::move(calculateVirialCallbacks),
+ std::move(calculateFreeEnergyCallbacks),
+ std::forward<Args>(args)...));
}
//! Helper function to get the callbacks from the clients
#include "energydata.h"
#include "freeenergyperturbationdata.h"
#include "modularsimulator.h"
-#include "parrinellorahmanbarostat.h"
#include "pmeloadbalancehelper.h"
#include "propagator.h"
#include "statepropagatordata.h"
-#include "velocityscalingtemperaturecoupling.h"
namespace gmx
{
t_commrec* cr,
const MDLogger& mdlog,
const MdrunOptions& mdrunOptions,
- t_inputrec* inputrec,
+ const t_inputrec* inputrec,
t_nrnb* nrnb,
gmx_wallcycle* wcycle,
t_forcerec* fr,
fprintf(stderr, "starting mdrun '%s'\n", topologyName_.c_str());
if (inputrec->nsteps >= 0)
{
- timeString = formatString("%8.1f", static_cast<double>(inputrec->init_step + inputrec->nsteps)
- * inputrec->delta_t);
+ timeString = formatString(
+ "%8.1f", static_cast<double>(inputrec->init_step + inputrec->nsteps) * inputrec->delta_t);
}
else
{
}
if (inputrec->init_step > 0)
{
- fprintf(stderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
- gmx_step_str(inputrec->init_step + inputrec->nsteps, sbuf), timeString.c_str(),
- gmx_step_str(inputrec->init_step, sbuf2), inputrec->init_step * inputrec->delta_t);
+ fprintf(stderr,
+ "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
+ gmx_step_str(inputrec->init_step + inputrec->nsteps, sbuf),
+ timeString.c_str(),
+ gmx_step_str(inputrec->init_step, sbuf2),
+ inputrec->init_step * inputrec->delta_t);
}
else
{
- fprintf(stderr, "%s steps, %s ps.\n", gmx_step_str(inputrec->nsteps, sbuf),
- timeString.c_str());
+ fprintf(stderr, "%s steps, %s ps.\n", gmx_step_str(inputrec->nsteps, sbuf), timeString.c_str());
}
fprintf(fplog, "\n");
}
walltime_accounting_start_time(walltime_accounting);
- wallcycle_start(wcycle, ewcRUN);
+ wallcycle_start(wcycle, WallCycleCounter::Run);
print_start(fplog, cr, walltime_accounting, "mdrun");
step_ = inputrec->init_step;
stophandlerCurrentStep_ = step;
stopHandler_->setSignal();
- wallcycle_start(wcycle, ewcSTEP);
+ wallcycle_start(wcycle, WallCycleCounter::Step);
}
void ModularSimulatorAlgorithm::postStep(Step step, Time gmx_unused time)
print_time(stderr, walltime_accounting, step, inputrec, cr);
}
- double cycles = wallcycle_stop(wcycle, ewcSTEP);
+ double cycles = wallcycle_stop(wcycle, WallCycleCounter::Step);
if (DOMAINDECOMP(cr) && wcycle)
{
dd_cycles_add(cr->dd, static_cast<float>(cycles), ddCyclStep);
}
- resetHandler_->resetCounters(
- step, step - inputrec->init_step, mdlog, fplog, cr, fr->nbv.get(), nrnb, fr->pmedata,
- pmeLoadBalanceHelper_ ? pmeLoadBalanceHelper_->loadBalancingObject() : nullptr, wcycle,
- walltime_accounting);
+ resetHandler_->resetCounters(step,
+ step - inputrec->init_step,
+ mdlog,
+ fplog,
+ cr,
+ fr->nbv.get(),
+ nrnb,
+ fr->pmedata,
+ pmeLoadBalanceHelper_ ? pmeLoadBalanceHelper_->loadBalancingObject() : nullptr,
+ wcycle,
+ walltime_accounting);
}
void ModularSimulatorAlgorithm::populateTaskQueue()
legacySimulatorData->startingBehavior,
legacySimulatorData->cr)
{
- if (legacySimulatorData->inputrec->efep != efepNO)
+ if (legacySimulatorData->inputrec->efep != FreeEnergyPerturbationType::No)
{
freeEnergyPerturbationData_ = std::make_unique<FreeEnergyPerturbationData>(
- legacySimulatorData->fplog, legacySimulatorData->inputrec, legacySimulatorData->mdAtoms);
+ legacySimulatorData->fplog, *legacySimulatorData->inputrec, legacySimulatorData->mdAtoms);
}
statePropagatorData_ = std::make_unique<StatePropagatorData>(
- legacySimulatorData->top_global->natoms, legacySimulatorData->fplog, legacySimulatorData->cr,
- legacySimulatorData->state_global, legacySimulatorData->fr->nbv->useGpu(),
- legacySimulatorData->fr->bMolPBC, legacySimulatorData->mdrunOptions.writeConfout,
- opt2fn("-c", legacySimulatorData->nfile, legacySimulatorData->fnm), legacySimulatorData->inputrec,
- legacySimulatorData->mdAtoms->mdatoms(), legacySimulatorData->top_global);
+ legacySimulatorData->top_global.natoms,
+ legacySimulatorData->fplog,
+ legacySimulatorData->cr,
+ legacySimulatorData->state_global,
+ legacySimulatorData->fr->nbv->useGpu(),
+ legacySimulatorData->fr->bMolPBC,
+ legacySimulatorData->mdrunOptions.writeConfout,
+ opt2fn("-c", legacySimulatorData->nfile, legacySimulatorData->fnm),
+ legacySimulatorData->inputrec,
+ legacySimulatorData->mdAtoms->mdatoms(),
+ legacySimulatorData->top_global);
// Multi sim is turned off
const bool simulationsShareState = false;
- energyData_ = std::make_unique<EnergyData>(
- statePropagatorData_.get(), freeEnergyPerturbationData_.get(), legacySimulatorData->top_global,
- legacySimulatorData->inputrec, legacySimulatorData->mdAtoms, legacySimulatorData->enerd,
- legacySimulatorData->ekind, legacySimulatorData->constr, legacySimulatorData->fplog,
- legacySimulatorData->fr->fcdata.get(), legacySimulatorData->mdModulesNotifier,
- MASTER(legacySimulatorData->cr), legacySimulatorData->observablesHistory,
- legacySimulatorData->startingBehavior, simulationsShareState);
+ energyData_ = std::make_unique<EnergyData>(statePropagatorData_.get(),
+ freeEnergyPerturbationData_.get(),
+ legacySimulatorData->top_global,
+ legacySimulatorData->inputrec,
+ legacySimulatorData->mdAtoms,
+ legacySimulatorData->enerd,
+ legacySimulatorData->ekind,
+ legacySimulatorData->constr,
+ legacySimulatorData->fplog,
+ legacySimulatorData->fr->fcdata.get(),
+ legacySimulatorData->mdModulesNotifiers,
+ MASTER(legacySimulatorData->cr),
+ legacySimulatorData->observablesHistory,
+ legacySimulatorData->startingBehavior,
+ simulationsShareState);
}
ModularSimulatorAlgorithm ModularSimulatorAlgorithmBuilder::build()
algorithmHasBeenBuilt_ = true;
// Connect propagators with thermostat / barostat
- for (const auto& thermostatRegistration : thermostatRegistrationFunctions_)
+ for (const auto& registrationFunction : pressureTemperatureControlRegistrationFunctions_)
{
- for (const auto& connection : propagatorThermostatConnections_)
+ for (const auto& connection : propagatorConnections_)
{
- thermostatRegistration(connection);
- }
- }
- for (const auto& barostatRegistration : barostatRegistrationFunctions_)
- {
- for (const auto& connection : propagatorBarostatConnections_)
- {
- barostatRegistration(connection);
+ registrationFunction(connection);
}
}
- ModularSimulatorAlgorithm algorithm(
- *(legacySimulatorData_->top_global->name), legacySimulatorData_->fplog,
- legacySimulatorData_->cr, legacySimulatorData_->mdlog, legacySimulatorData_->mdrunOptions,
- legacySimulatorData_->inputrec, legacySimulatorData_->nrnb, legacySimulatorData_->wcycle,
- legacySimulatorData_->fr, legacySimulatorData_->walltime_accounting);
+ ModularSimulatorAlgorithm algorithm(*(legacySimulatorData_->top_global.name),
+ legacySimulatorData_->fplog,
+ legacySimulatorData_->cr,
+ legacySimulatorData_->mdlog,
+ legacySimulatorData_->mdrunOptions,
+ legacySimulatorData_->inputrec,
+ legacySimulatorData_->nrnb,
+ legacySimulatorData_->wcycle,
+ legacySimulatorData_->fr,
+ legacySimulatorData_->walltime_accounting);
registerWithInfrastructureAndSignallers(algorithm.signalHelper_.get());
algorithm.statePropagatorData_ = std::move(statePropagatorData_);
algorithm.energyData_ = std::move(energyData_);
algorithm.stopHandler_ = legacySimulatorData_->stopHandlerBuilder->getStopHandlerMD(
compat::not_null<SimulationSignal*>(
&(*globalCommunicationHelper_.simulationSignals())[eglsSTOPCOND]),
- simulationsShareState, MASTER(legacySimulatorData_->cr),
- legacySimulatorData_->inputrec->nstlist, legacySimulatorData_->mdrunOptions.reproducible,
- globalCommunicationHelper_.nstglobalcomm(), legacySimulatorData_->mdrunOptions.maximumHoursToRun,
- legacySimulatorData_->inputrec->nstlist == 0, legacySimulatorData_->fplog,
- algorithm.stophandlerCurrentStep_, algorithm.stophandlerIsNSStep_,
+ simulationsShareState,
+ MASTER(legacySimulatorData_->cr),
+ legacySimulatorData_->inputrec->nstlist,
+ legacySimulatorData_->mdrunOptions.reproducible,
+ globalCommunicationHelper_.nstglobalcomm(),
+ legacySimulatorData_->mdrunOptions.maximumHoursToRun,
+ legacySimulatorData_->inputrec->nstlist == 0,
+ legacySimulatorData_->fplog,
+ algorithm.stophandlerCurrentStep_,
+ algorithm.stophandlerIsNSStep_,
legacySimulatorData_->walltime_accounting);
// Build reset handler
algorithm.resetHandler_ = std::make_unique<ResetHandler>(
compat::make_not_null<SimulationSignal*>(
&(*globalCommunicationHelper_.simulationSignals())[eglsRESETCOUNTERS]),
- simulationsShareResetCounters, legacySimulatorData_->inputrec->nsteps,
- MASTER(legacySimulatorData_->cr), legacySimulatorData_->mdrunOptions.timingOptions.resetHalfway,
- legacySimulatorData_->mdrunOptions.maximumHoursToRun, legacySimulatorData_->mdlog,
- legacySimulatorData_->wcycle, legacySimulatorData_->walltime_accounting);
+ simulationsShareResetCounters,
+ legacySimulatorData_->inputrec->nsteps,
+ MASTER(legacySimulatorData_->cr),
+ legacySimulatorData_->mdrunOptions.timingOptions.resetHalfway,
+ legacySimulatorData_->mdrunOptions.maximumHoursToRun,
+ legacySimulatorData_->mdlog,
+ legacySimulatorData_->wcycle,
+ legacySimulatorData_->walltime_accounting);
// Build topology holder
- algorithm.topologyHolder_ = topologyHolderBuilder_.build(
- *legacySimulatorData_->top_global, legacySimulatorData_->cr,
- legacySimulatorData_->inputrec, legacySimulatorData_->fr, legacySimulatorData_->mdAtoms,
- legacySimulatorData_->constr, legacySimulatorData_->vsite);
+ algorithm.topologyHolder_ = topologyHolderBuilder_.build(legacySimulatorData_->top_global,
+ legacySimulatorData_->cr,
+ legacySimulatorData_->inputrec,
+ legacySimulatorData_->fr,
+ legacySimulatorData_->mdAtoms,
+ legacySimulatorData_->constr,
+ legacySimulatorData_->vsite);
// Build PME load balance helper
if (PmeLoadBalanceHelper::doPmeLoadBalancing(legacySimulatorData_->mdrunOptions,
legacySimulatorData_->inputrec,
legacySimulatorData_->fr))
{
- algorithm.pmeLoadBalanceHelper_ = std::make_unique<PmeLoadBalanceHelper>(
- legacySimulatorData_->mdrunOptions.verbose, algorithm.statePropagatorData_.get(),
- legacySimulatorData_->fplog, legacySimulatorData_->cr, legacySimulatorData_->mdlog,
- legacySimulatorData_->inputrec, legacySimulatorData_->wcycle, legacySimulatorData_->fr);
+ algorithm.pmeLoadBalanceHelper_ =
+ std::make_unique<PmeLoadBalanceHelper>(legacySimulatorData_->mdrunOptions.verbose,
+ algorithm.statePropagatorData_.get(),
+ legacySimulatorData_->fplog,
+ legacySimulatorData_->cr,
+ legacySimulatorData_->mdlog,
+ legacySimulatorData_->inputrec,
+ legacySimulatorData_->wcycle,
+ legacySimulatorData_->fr);
registerWithInfrastructureAndSignallers(algorithm.pmeLoadBalanceHelper_.get());
}
// Build domdec helper
algorithm.domDecHelper_ = std::make_unique<DomDecHelper>(
legacySimulatorData_->mdrunOptions.verbose,
legacySimulatorData_->mdrunOptions.verboseStepPrintInterval,
- algorithm.statePropagatorData_.get(), algorithm.freeEnergyPerturbationData_.get(),
+ algorithm.statePropagatorData_.get(),
+ algorithm.freeEnergyPerturbationData_.get(),
algorithm.topologyHolder_.get(),
- globalCommunicationHelper_.moveCheckBondedInteractionsCallback(),
- globalCommunicationHelper_.nstglobalcomm(), legacySimulatorData_->fplog,
- legacySimulatorData_->cr, legacySimulatorData_->mdlog, legacySimulatorData_->constr,
- legacySimulatorData_->inputrec, legacySimulatorData_->mdAtoms, legacySimulatorData_->nrnb,
- legacySimulatorData_->wcycle, legacySimulatorData_->fr, legacySimulatorData_->vsite,
- legacySimulatorData_->imdSession, legacySimulatorData_->pull_work);
+ globalCommunicationHelper_.nstglobalcomm(),
+ legacySimulatorData_->fplog,
+ legacySimulatorData_->cr,
+ legacySimulatorData_->mdlog,
+ legacySimulatorData_->constr,
+ legacySimulatorData_->inputrec,
+ legacySimulatorData_->mdAtoms,
+ legacySimulatorData_->nrnb,
+ legacySimulatorData_->wcycle,
+ legacySimulatorData_->fr,
+ legacySimulatorData_->vsite,
+ legacySimulatorData_->imdSession,
+ legacySimulatorData_->pull_work);
registerWithInfrastructureAndSignallers(algorithm.domDecHelper_.get());
}
// Build trajectory element
- auto trajectoryElement = trajectoryElementBuilder_.build(
- legacySimulatorData_->fplog, legacySimulatorData_->nfile, legacySimulatorData_->fnm,
- legacySimulatorData_->mdrunOptions, legacySimulatorData_->cr,
- legacySimulatorData_->outputProvider, legacySimulatorData_->mdModulesNotifier,
- legacySimulatorData_->inputrec, legacySimulatorData_->top_global,
- legacySimulatorData_->oenv, legacySimulatorData_->wcycle,
- legacySimulatorData_->startingBehavior, simulationsShareState);
+ auto trajectoryElement = trajectoryElementBuilder_.build(legacySimulatorData_->fplog,
+ legacySimulatorData_->nfile,
+ legacySimulatorData_->fnm,
+ legacySimulatorData_->mdrunOptions,
+ legacySimulatorData_->cr,
+ legacySimulatorData_->outputProvider,
+ legacySimulatorData_->mdModulesNotifiers,
+ legacySimulatorData_->inputrec,
+ legacySimulatorData_->top_global,
+ legacySimulatorData_->oenv,
+ legacySimulatorData_->wcycle,
+ legacySimulatorData_->startingBehavior,
+ simulationsShareState);
registerWithInfrastructureAndSignallers(trajectoryElement.get());
// Build free energy element
{
checkpointHelperBuilder_.setCheckpointHandler(std::make_unique<CheckpointHandler>(
compat::make_not_null<SimulationSignal*>(&(*algorithm.signals_)[eglsCHKPT]),
- simulationsShareState, legacySimulatorData_->inputrec->nstlist == 0,
- MASTER(legacySimulatorData_->cr), legacySimulatorData_->mdrunOptions.writeConfout,
+ simulationsShareState,
+ legacySimulatorData_->inputrec->nstlist == 0,
+ MASTER(legacySimulatorData_->cr),
+ legacySimulatorData_->mdrunOptions.writeConfout,
legacySimulatorData_->mdrunOptions.checkpointOptions.period));
- algorithm.checkpointHelper_ = checkpointHelperBuilder_.build(
- legacySimulatorData_->inputrec->init_step, trajectoryElement.get(),
- legacySimulatorData_->fplog, legacySimulatorData_->cr,
- legacySimulatorData_->observablesHistory, legacySimulatorData_->walltime_accounting,
- legacySimulatorData_->state_global, legacySimulatorData_->mdrunOptions.writeConfout);
+ algorithm.checkpointHelper_ =
+ checkpointHelperBuilder_.build(legacySimulatorData_->inputrec->init_step,
+ trajectoryElement.get(),
+ legacySimulatorData_->fplog,
+ legacySimulatorData_->cr,
+ legacySimulatorData_->observablesHistory,
+ legacySimulatorData_->walltime_accounting,
+ legacySimulatorData_->state_global,
+ legacySimulatorData_->mdrunOptions.writeConfout);
registerWithInfrastructureAndSignallers(algorithm.checkpointHelper_.get());
}
registerWithInfrastructureAndSignallers(signaller.get());
algorithm.signallerList_.emplace(algorithm.signallerList_.begin(), std::move(signaller));
};
- const auto* inputrec = legacySimulatorData_->inputrec;
+ const auto* inputrec = legacySimulatorData_->inputrec;
+ auto virialMode = EnergySignallerVirialMode::Off;
+ if (inputrec->epc != PressureCoupling::No)
+ {
+ if (EI_VV(inputrec->eI))
+ {
+ virialMode = EnergySignallerVirialMode::OnStepAndNext;
+ }
+ else
+ {
+ virialMode = EnergySignallerVirialMode::OnStep;
+ }
+ }
addSignaller(energySignallerBuilder_.build(
- inputrec->nstcalcenergy, inputrec->fepvals->nstdhdl, inputrec->nstpcouple));
- addSignaller(trajectorySignallerBuilder_.build(
- inputrec->nstxout, inputrec->nstvout, inputrec->nstfout,
- inputrec->nstxout_compressed, trajectoryElement->tngBoxOut(),
- trajectoryElement->tngLambdaOut(), trajectoryElement->tngBoxOutCompressed(),
- trajectoryElement->tngLambdaOutCompressed(), inputrec->nstenergy));
- addSignaller(loggingSignallerBuilder_.build(inputrec->nstlog, inputrec->init_step,
- legacySimulatorData_->startingBehavior));
- addSignaller(lastStepSignallerBuilder_.build(inputrec->nsteps, inputrec->init_step,
- algorithm.stopHandler_.get()));
- addSignaller(neighborSearchSignallerBuilder_.build(inputrec->nstlist, inputrec->init_step,
- inputrec->init_t));
+ inputrec->nstcalcenergy, inputrec->fepvals->nstdhdl, inputrec->nstpcouple, virialMode));
+ addSignaller(trajectorySignallerBuilder_.build(inputrec->nstxout,
+ inputrec->nstvout,
+ inputrec->nstfout,
+ inputrec->nstxout_compressed,
+ trajectoryElement->tngBoxOut(),
+ trajectoryElement->tngLambdaOut(),
+ trajectoryElement->tngBoxOutCompressed(),
+ trajectoryElement->tngLambdaOutCompressed(),
+ inputrec->nstenergy));
+ addSignaller(loggingSignallerBuilder_.build(
+ inputrec->nstlog, inputrec->init_step, legacySimulatorData_->startingBehavior));
+ addSignaller(lastStepSignallerBuilder_.build(
+ inputrec->nsteps, inputrec->init_step, algorithm.stopHandler_.get()));
+ addSignaller(neighborSearchSignallerBuilder_.build(
+ inputrec->nstlist, inputrec->init_step, inputrec->init_t));
}
// Create element list
bool ModularSimulatorAlgorithmBuilder::elementExists(const ISimulatorElement* element) const
{
// Check whether element exists in element list
- if (std::any_of(elements_.begin(), elements_.end(),
- [element](auto& existingElement) { return element == existingElement.get(); }))
+ if (std::any_of(elements_.begin(), elements_.end(), [element](auto& existingElement) {
+ return element == existingElement.get();
+ }))
{
return true;
}
return simulationSignals_;
}
-void GlobalCommunicationHelper::setCheckBondedInteractionsCallback(CheckBondedInteractionsCallback callback)
-{
- checkBondedInteractionsCallback_ = std::move(callback);
-}
-
-CheckBondedInteractionsCallback GlobalCommunicationHelper::moveCheckBondedInteractionsCallback()
-{
- if (!checkBondedInteractionsCallback_)
- {
- throw SimulationAlgorithmSetupError(
- "Requested CheckBondedInteractionsCallback before it was set.");
- }
- return *checkBondedInteractionsCallback_;
-}
-
ModularSimulatorAlgorithmBuilderHelper::ModularSimulatorAlgorithmBuilderHelper(
ModularSimulatorAlgorithmBuilder* builder) :
builder_(builder)
}
}
-void ModularSimulatorAlgorithmBuilderHelper::registerThermostat(
- std::function<void(const PropagatorThermostatConnection&)> registrationFunction)
+void ModularSimulatorAlgorithmBuilderHelper::registerTemperaturePressureControl(
+ std::function<void(const PropagatorConnection&)> registrationFunction)
{
- builder_->thermostatRegistrationFunctions_.emplace_back(std::move(registrationFunction));
+ builder_->pressureTemperatureControlRegistrationFunctions_.emplace_back(std::move(registrationFunction));
}
-void ModularSimulatorAlgorithmBuilderHelper::registerBarostat(
- std::function<void(const PropagatorBarostatConnection&)> registrationFunction)
+void ModularSimulatorAlgorithmBuilderHelper::registerPropagator(PropagatorConnection connectionData)
{
- builder_->barostatRegistrationFunctions_.emplace_back(std::move(registrationFunction));
+ builder_->propagatorConnections_.emplace_back(std::move(connectionData));
}
-void ModularSimulatorAlgorithmBuilderHelper::registerWithThermostat(PropagatorThermostatConnection connectionData)
-{
- builder_->propagatorThermostatConnections_.emplace_back(std::move(connectionData));
-}
-
-void ModularSimulatorAlgorithmBuilderHelper::registerWithBarostat(PropagatorBarostatConnection connectionData)
-{
- builder_->propagatorBarostatConnections_.emplace_back(std::move(connectionData));
-}
-
-
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
namespace gmx
{
-enum class IntegrationStep;
+enum class IntegrationStage;
class EnergyData;
class ModularSimulator;
class ResetHandler;
-template<IntegrationStep algorithm>
+template<IntegrationStage integrationStage>
class Propagator;
class TopologyHolder;
t_commrec* cr,
const MDLogger& mdlog,
const MdrunOptions& mdrunOptions,
- t_inputrec* inputrec,
+ const t_inputrec* inputrec,
t_nrnb* nrnb,
gmx_wallcycle* wcycle,
t_forcerec* fr,
//! Contains command-line options to mdrun.
const MdrunOptions& mdrunOptions;
//! Contains user input mdp options.
- t_inputrec* inputrec;
+ const t_inputrec* inputrec;
//! Manages flop accounting.
t_nrnb* nrnb;
//! Manages wall cycle accounting.
//! Get a pointer to the signals vector
[[nodiscard]] SimulationSignals* simulationSignals();
- //! Set the callback to check the number of bonded interactions
- void setCheckBondedInteractionsCallback(CheckBondedInteractionsCallback callback);
- //! Move the callback to check the number of bonded interactions
- [[nodiscard]] CheckBondedInteractionsCallback moveCheckBondedInteractionsCallback();
-
private:
//! Compute globals communication period
const int nstglobalcomm_;
//! Signal vector (used by stop / reset / checkpointing signaller)
SimulationSignals* simulationSignals_;
- //! Callback to check the number of bonded interactions
- std::optional<CheckBondedInteractionsCallback> checkBondedInteractionsCallback_;
};
class ModularSimulatorAlgorithmBuilder;
void storeValue(const std::string& key, const ValueType& value);
//! Get previously stored data. Returns std::nullopt if key is not found.
std::optional<std::any> getStoredValue(const std::string& key) const;
- //! Register a thermostat that accepts propagator registrations
- void registerThermostat(std::function<void(const PropagatorThermostatConnection&)> registrationFunction);
- //! Register a barostat that accepts propagator registrations
- void registerBarostat(std::function<void(const PropagatorBarostatConnection&)> registrationFunction);
- //! Register a propagator to the thermostat used
- void registerWithThermostat(PropagatorThermostatConnection connectionData);
- //! Register a propagator to the barostat used
- void registerWithBarostat(PropagatorBarostatConnection connectionData);
+ //! Register temperature / pressure control algorithm to be matched with a propagator
+ void registerTemperaturePressureControl(std::function<void(const PropagatorConnection&)> registrationFunction);
+ //! Register a propagator to be used with a temperature / pressure control algorithm
+ void registerPropagator(PropagatorConnection connectionData);
private:
//! Pointer to the associated ModularSimulatorAlgorithmBuilder
*/
std::vector<ICheckpointHelperClient*> checkpointClients_;
- //! List of thermostat registration functions
- std::vector<std::function<void(const PropagatorThermostatConnection&)>> thermostatRegistrationFunctions_;
- //! List of barostat registration functions
- std::vector<std::function<void(const PropagatorBarostatConnection&)>> barostatRegistrationFunctions_;
- //! List of data to connect propagators to thermostats
- std::vector<PropagatorThermostatConnection> propagatorThermostatConnections_;
- //! List of data to connect propagators to barostats
- std::vector<PropagatorBarostatConnection> propagatorBarostatConnections_;
+ //! List of data to connect propagators to thermostats / barostats
+ std::vector<PropagatorConnection> propagatorConnections_;
+ //! List of temperature / pressure control registration functions
+ std::vector<std::function<void(const PropagatorConnection&)>> pressureTemperatureControlRegistrationFunctions_;
};
/*! \internal
GlobalCommunicationHelper* globalCommunicationHelper,
Args&&... args)
{
- return Element::getElementPointerImpl(legacySimulatorData, builderHelper, statePropagatorData,
- energyData, freeEnergyPerturbationData,
- globalCommunicationHelper, std::forward<Args>(args)...);
+ return Element::getElementPointerImpl(legacySimulatorData,
+ builderHelper,
+ statePropagatorData,
+ energyData,
+ freeEnergyPerturbationData,
+ globalCommunicationHelper,
+ std::forward<Args>(args)...);
}
template<typename Element, typename... Args>
}
// Get element from factory method
- auto* element = static_cast<Element*>(getElementPointer<Element>(
- legacySimulatorData_, &elementAdditionHelper_, statePropagatorData_.get(),
- energyData_.get(), freeEnergyPerturbationData_.get(), &globalCommunicationHelper_,
- std::forward<Args>(args)...));
+ auto* element = static_cast<Element*>(getElementPointer<Element>(legacySimulatorData_,
+ &elementAdditionHelper_,
+ statePropagatorData_.get(),
+ energyData_.get(),
+ freeEnergyPerturbationData_.get(),
+ &globalCommunicationHelper_,
+ std::forward<Args>(args)...));
// Make sure returned element pointer is owned by *this
// Ensuring this makes sure we can control the life time
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gmxpre.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "statepropagatordata.h"
#include "gromacs/commandline/filenm.h"
const std::string& finalConfigurationFilename,
const t_inputrec* inputrec,
const t_mdatoms* mdatoms,
- const gmx_mtop_t* globalTop) :
+ const gmx_mtop_t& globalTop) :
totalNumAtoms_(numAtoms),
localNAtoms_(0),
box_{ { 0 } },
if (DOMAINDECOMP(cr))
{
auto localState = std::make_unique<t_state>();
- dd_init_local_state(cr->dd, globalState, localState.get());
- stateHasVelocities = ((static_cast<unsigned int>(localState->flags) & (1U << estV)) != 0U);
+ dd_init_local_state(*cr->dd, globalState, localState.get());
+ stateHasVelocities = ((localState->flags & enumValueToBitMask(StateEntry::V)) != 0);
setLocalState(std::move(localState));
}
else
x_ = globalState->x;
v_ = globalState->v;
copy_mat(globalState->box, box_);
- stateHasVelocities = ((static_cast<unsigned int>(globalState->flags) & (1U << estV)) != 0U);
+ stateHasVelocities = ((globalState->flags & enumValueToBitMask(StateEntry::V)) != 0);
previousX_.resizeWithPadding(localNAtoms_);
ddpCount_ = globalState->ddp_count;
copyPosition();
// Set the velocities of vsites, shells and frozen atoms to zero
for (int i = 0; i < mdatoms->homenr; i++)
{
- if (mdatoms->ptype[i] == eptVSite || mdatoms->ptype[i] == eptShell)
+ if (mdatoms->ptype[i] == ParticleType::Shell)
{
clear_rvec(v[i]);
}
}
}
}
- if (inputrec->eI == eiVV)
+ if (inputrec->eI == IntegrationAlgorithm::VV)
{
vvResetVelocities_ = true;
}
std::unique_ptr<t_state> StatePropagatorData::localState()
{
auto state = std::make_unique<t_state>();
- state->flags = (1U << estX) | (1U << estV) | (1U << estBOX);
+ state->flags = enumValueToBitMask(StateEntry::X) | enumValueToBitMask(StateEntry::V)
+ | enumValueToBitMask(StateEntry::Box);
state_change_natoms(state.get(), localNAtoms_);
state->x = x_;
state->v = v_;
void StatePropagatorData::copyPosition()
{
- int nth = gmx_omp_nthreads_get(emntUpdate);
+ int nth = gmx_omp_nthreads_get(ModuleMultiThread::Update);
#pragma omp parallel for num_threads(nth) schedule(static) default(none) shared(nth)
for (int th = 0; th < nth; th++)
localStateBackup_ = statePropagatorData_->localState();
if (freeEnergyPerturbationData_)
{
- localStateBackup_->fep_state = freeEnergyPerturbationData_->currentFEPState();
- for (unsigned long i = 0; i < localStateBackup_->lambda.size(); ++i)
- {
- localStateBackup_->lambda[i] = freeEnergyPerturbationData_->constLambdaView()[i];
- }
- localStateBackup_->flags |= (1U << estLAMBDA) | (1U << estFEPSTATE);
+ localStateBackup_->fep_state = freeEnergyPerturbationData_->currentFEPState();
+ ArrayRef<const real> lambdaView = freeEnergyPerturbationData_->constLambdaView();
+ std::copy(lambdaView.begin(), lambdaView.end(), localStateBackup_->lambda.begin());
+ localStateBackup_->flags |=
+ enumValueToBitMask(StateEntry::Lambda) | enumValueToBitMask(StateEntry::FepState);
}
}
void StatePropagatorData::Element::write(gmx_mdoutf_t outf, Step currentStep, Time currentTime)
{
- wallcycle_start(mdoutf_get_wcycle(outf), ewcTRAJ);
+ wallcycle_start(mdoutf_get_wcycle(outf), WallCycleCounter::Traj);
unsigned int mdof_flags = 0;
if (do_per_step(currentStep, nstxout_))
{
if (mdof_flags == 0)
{
- wallcycle_stop(mdoutf_get_wcycle(outf), ewcTRAJ);
+ wallcycle_stop(mdoutf_get_wcycle(outf), WallCycleCounter::Traj);
return;
}
GMX_ASSERT(localStateBackup_, "Trajectory writing called, but no state saved.");
// TODO: This is only used for CPT - needs to be filled when we turn CPT back on
ObservablesHistory* observablesHistory = nullptr;
- mdoutf_write_to_trajectory_files(
- fplog_, cr_, outf, static_cast<int>(mdof_flags), statePropagatorData_->totalNumAtoms_,
- currentStep, currentTime, localStateBackup_.get(), statePropagatorData_->globalState_,
- observablesHistory, statePropagatorData_->f_.view().force(), &dummyCheckpointDataHolder_);
+ mdoutf_write_to_trajectory_files(fplog_,
+ cr_,
+ outf,
+ static_cast<int>(mdof_flags),
+ statePropagatorData_->totalNumAtoms_,
+ currentStep,
+ currentTime,
+ localStateBackup_.get(),
+ statePropagatorData_->globalState_,
+ observablesHistory,
+ statePropagatorData_->f_.view().force(),
+ &dummyCheckpointDataHolder_);
if (currentStep != lastStep_ || !isRegularSimulationEnd_)
{
localStateBackup_.reset();
}
- wallcycle_stop(mdoutf_get_wcycle(outf), ewcTRAJ);
+ wallcycle_stop(mdoutf_get_wcycle(outf), WallCycleCounter::Traj);
}
void StatePropagatorData::Element::elementSetup()
if (DOMAINDECOMP(cr))
{
// Collect state from all ranks into global vectors
- dd_collect_vec(cr->dd, statePropagatorData_->ddpCount_, statePropagatorData_->ddpCountCgGl_,
- statePropagatorData_->cgGl_, statePropagatorData_->x_,
+ dd_collect_vec(cr->dd,
+ statePropagatorData_->ddpCount_,
+ statePropagatorData_->ddpCountCgGl_,
+ statePropagatorData_->cgGl_,
+ statePropagatorData_->x_,
statePropagatorData_->xGlobal_);
- dd_collect_vec(cr->dd, statePropagatorData_->ddpCount_, statePropagatorData_->ddpCountCgGl_,
- statePropagatorData_->cgGl_, statePropagatorData_->v_,
+ dd_collect_vec(cr->dd,
+ statePropagatorData_->ddpCount_,
+ statePropagatorData_->ddpCountCgGl_,
+ statePropagatorData_->cgGl_,
+ statePropagatorData_->v_,
statePropagatorData_->vGlobal_);
}
else
// Everything is local - copy local vectors into global ones
statePropagatorData_->xGlobal_.resizeWithPadding(statePropagatorData_->totalNumAtoms());
statePropagatorData_->vGlobal_.resizeWithPadding(statePropagatorData_->totalNumAtoms());
- std::copy(statePropagatorData_->x_.begin(), statePropagatorData_->x_.end(),
+ std::copy(statePropagatorData_->x_.begin(),
+ statePropagatorData_->x_.end(),
statePropagatorData_->xGlobal_.begin());
- std::copy(statePropagatorData_->v_.begin(), statePropagatorData_->v_.end(),
+ std::copy(statePropagatorData_->v_.begin(),
+ statePropagatorData_->v_.end(),
statePropagatorData_->vGlobal_.begin());
}
if (MASTER(cr))
// Copy data to global state to be distributed by DD at setup stage
if (DOMAINDECOMP(cr) && MASTER(cr))
{
- updateGlobalState(statePropagatorData_->globalState_, statePropagatorData_->xGlobal_,
- statePropagatorData_->vGlobal_, statePropagatorData_->box_,
- statePropagatorData_->ddpCount_, statePropagatorData_->ddpCountCgGl_,
+ updateGlobalState(statePropagatorData_->globalState_,
+ statePropagatorData_->xGlobal_,
+ statePropagatorData_->vGlobal_,
+ statePropagatorData_->box_,
+ statePropagatorData_->ddpCount_,
+ statePropagatorData_->ddpCountCgGl_,
statePropagatorData_->cgGl_);
}
// Everything is local - copy global vectors to local ones
{
statePropagatorData_->x_.resizeWithPadding(statePropagatorData_->totalNumAtoms_);
statePropagatorData_->v_.resizeWithPadding(statePropagatorData_->totalNumAtoms_);
- std::copy(statePropagatorData_->xGlobal_.begin(), statePropagatorData_->xGlobal_.end(),
+ std::copy(statePropagatorData_->xGlobal_.begin(),
+ statePropagatorData_->xGlobal_.end(),
statePropagatorData_->x_.begin());
- std::copy(statePropagatorData_->vGlobal_.begin(), statePropagatorData_->vGlobal_.end(),
+ std::copy(statePropagatorData_->vGlobal_.begin(),
+ statePropagatorData_->vGlobal_.end(),
statePropagatorData_->v_.begin());
}
}
GMX_ASSERT(localStateBackup_, "Final trajectory writing called, but no state saved.");
- wallcycle_start(mdoutf_get_wcycle(outf), ewcTRAJ);
+ wallcycle_start(mdoutf_get_wcycle(outf), WallCycleCounter::Traj);
if (DOMAINDECOMP(cr_))
{
auto globalXRef =
MASTER(cr_) ? statePropagatorData_->globalState_->x : gmx::ArrayRef<gmx::RVec>();
- dd_collect_vec(cr_->dd, localStateBackup_->ddp_count, localStateBackup_->ddp_count_cg_gl,
- localStateBackup_->cg_gl, localStateBackup_->x, globalXRef);
+ dd_collect_vec(cr_->dd,
+ localStateBackup_->ddp_count,
+ localStateBackup_->ddp_count_cg_gl,
+ localStateBackup_->cg_gl,
+ localStateBackup_->x,
+ globalXRef);
auto globalVRef =
MASTER(cr_) ? statePropagatorData_->globalState_->v : gmx::ArrayRef<gmx::RVec>();
- dd_collect_vec(cr_->dd, localStateBackup_->ddp_count, localStateBackup_->ddp_count_cg_gl,
- localStateBackup_->cg_gl, localStateBackup_->v, globalVRef);
+ dd_collect_vec(cr_->dd,
+ localStateBackup_->ddp_count,
+ localStateBackup_->ddp_count_cg_gl,
+ localStateBackup_->cg_gl,
+ localStateBackup_->v,
+ globalVRef);
}
else
{
if (canMoleculesBeDistributedOverPBC_ && !systemHasPeriodicMolecules_)
{
// Make molecules whole only for confout writing
- do_pbc_mtop(pbcType_, localStateBackup_->box, top_global_,
+ do_pbc_mtop(pbcType_,
+ localStateBackup_->box,
+ &top_global_,
statePropagatorData_->globalState_->x.rvec_array());
}
- write_sto_conf_mtop(finalConfigurationFilename_.c_str(), *top_global_->name, top_global_,
+ write_sto_conf_mtop(finalConfigurationFilename_.c_str(),
+ *top_global_.name,
+ top_global_,
statePropagatorData_->globalState_->x.rvec_array(),
- statePropagatorData_->globalState_->v.rvec_array(), pbcType_,
+ statePropagatorData_->globalState_->v.rvec_array(),
+ pbcType_,
localStateBackup_->box);
}
- wallcycle_stop(mdoutf_get_wcycle(outf), ewcTRAJ);
+ wallcycle_stop(mdoutf_get_wcycle(outf), WallCycleCounter::Traj);
}
std::optional<SignallerCallback> StatePropagatorData::Element::registerLastStepCallback()
bool writeFinalConfiguration,
std::string finalConfigurationFilename,
const t_inputrec* inputrec,
- const gmx_mtop_t* globalTop) :
+ const gmx_mtop_t& globalTop) :
statePropagatorData_(statePropagatorData),
nstxout_(nstxout),
nstvout_(nstvout),
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const std::string& finalConfigurationFilename,
const t_inputrec* inputrec,
const t_mdatoms* mdatoms,
- const gmx_mtop_t* globalTop);
+ const gmx_mtop_t& globalTop);
// Allow access to state
//! Get write access to position vector
bool writeFinalConfiguration,
std::string finalConfigurationFilename,
const t_inputrec* inputrec,
- const gmx_mtop_t* globalTop);
+ const gmx_mtop_t& globalTop);
/*! \brief Register run function for step / time
*
//! Handles communication.
const t_commrec* cr_;
//! Full system topology.
- const gmx_mtop_t* top_global_;
+ const gmx_mtop_t& top_global_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
// Note: Legacy mdrun resizes the force buffer in mdAlgorithmsSetupAtomData()
// TopologyHolder has no access to the forces, so we are passing a nullptr
// TODO: Find a unique approach to resizing the forces in modular simulator (#3461)
- mdAlgorithmsSetupAtomData(cr, inputrec, globalTopology, localTopology_.get(), fr, nullptr,
- mdAtoms, constr, vsite, nullptr);
+ mdAlgorithmsSetupAtomData(
+ cr, *inputrec, globalTopology, localTopology_.get(), fr, nullptr, mdAtoms, constr, vsite, nullptr);
}
// Send copy of initial topology to clients
updateLocalTopology();
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const MdrunOptions& mdrunOptions,
const t_commrec* cr,
gmx::IMDOutputProvider* outputProvider,
- const MdModulesNotifier& mdModulesNotifier,
+ const MDModulesNotifiers& mdModulesNotifiers,
const t_inputrec* inputrec,
- const gmx_mtop_t* top_global,
+ const gmx_mtop_t& top_global,
const gmx_output_env_t* oenv,
gmx_wallcycle* wcycle,
StartingBehavior startingBehavior,
mdrunOptions,
cr,
outputProvider,
- mdModulesNotifier,
+ mdModulesNotifiers,
inputrec,
top_global,
oenv,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
namespace gmx
{
class IMDOutputProvider;
-struct MdModulesNotifier;
+struct MDModulesNotifiers;
struct MdrunOptions;
enum class StartingBehavior;
const MdrunOptions& mdrunOptions,
const t_commrec* cr,
IMDOutputProvider* outputProvider,
- const MdModulesNotifier& mdModulesNotifier,
+ const MDModulesNotifiers& mdModulesNotifiers,
const t_inputrec* inputrec,
- const gmx_mtop_t* top_global,
+ const gmx_mtop_t& top_global,
const gmx_output_env_t* oenv,
gmx_wallcycle* wcycle,
StartingBehavior startingBehavior,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/group.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/strconvert.h"
#include "modularsimulator.h"
#include "simulatoralgorithm.h"
{
public:
//! Allow access to the scaling vectors
- virtual void connectWithPropagator(const PropagatorThermostatConnection& connectionData,
- int numTemperatureGroups) = 0;
+ virtual void connectWithPropagator(const PropagatorConnection& connectionData,
+ int numTemperatureGroups) = 0;
/*! \brief Make a temperature control step
*
}
const real referenceKineticEnergy =
- 0.5 * temperatureCouplingData.referenceTemperature[temperatureGroup] * BOLTZ
+ 0.5 * temperatureCouplingData.referenceTemperature[temperatureGroup] * gmx::c_boltz
* temperatureCouplingData.numDegreesOfFreedom[temperatureGroup];
const real newKineticEnergy =
- vrescale_resamplekin(currentKineticEnergy, referenceKineticEnergy,
+ vrescale_resamplekin(currentKineticEnergy,
+ referenceKineticEnergy,
temperatureCouplingData.numDegreesOfFreedom[temperatureGroup],
temperatureCouplingData.couplingTime[temperatureGroup]
/ temperatureCouplingData.couplingTimeStep,
- step, seed_);
+ step,
+ seed_);
// Analytically newKineticEnergy >= 0, but we check for rounding errors
if (newKineticEnergy <= 0)
if (debug)
{
- fprintf(debug, "TC: group %d: Ekr %g, Ek %g, Ek_new %g, Lambda: %g\n", temperatureGroup,
- referenceKineticEnergy, currentKineticEnergy, newKineticEnergy,
+ fprintf(debug,
+ "TC: group %d: Ekr %g, Ek %g, Ek_new %g, Lambda: %g\n",
+ temperatureGroup,
+ referenceKineticEnergy,
+ currentKineticEnergy,
+ newKineticEnergy,
lambdaStartVelocities_[temperatureGroup]);
}
}
//! Connect with propagator - v-rescale only scales start step velocities
- void connectWithPropagator(const PropagatorThermostatConnection& connectionData,
- int numTemperatureGroups) override
+ void connectWithPropagator(const PropagatorConnection& connectionData, int numTemperatureGroups) override
{
- connectionData.setNumVelocityScalingVariables(numTemperatureGroups);
- lambdaStartVelocities_ = connectionData.getViewOnVelocityScaling();
+ GMX_RELEASE_ASSERT(connectionData.hasStartVelocityScaling(),
+ "V-Rescale requires start velocity scaling.");
+ connectionData.setNumVelocityScalingVariables(numTemperatureGroups, ScaleVelocities::PreStepOnly);
+ lambdaStartVelocities_ = connectionData.getViewOnStartVelocityScaling();
}
//! No data to write to checkpoint
std::max<real>(std::min<real>(lambda, 1.25_real), 0.8_real);
if (debug)
{
- fprintf(debug, "TC: group %d: T: %g, Lambda: %g\n", temperatureGroup,
- currentTemperature, lambdaStartVelocities_[temperatureGroup]);
+ fprintf(debug,
+ "TC: group %d: T: %g, Lambda: %g\n",
+ temperatureGroup,
+ currentTemperature,
+ lambdaStartVelocities_[temperatureGroup]);
}
return temperatureCouplingData.temperatureCouplingIntegral[temperatureGroup]
- (lambdaStartVelocities_[temperatureGroup] * lambdaStartVelocities_[temperatureGroup]
}
//! Connect with propagator - Berendsen only scales start step velocities
- void connectWithPropagator(const PropagatorThermostatConnection& connectionData,
- int numTemperatureGroups) override
+ void connectWithPropagator(const PropagatorConnection& connectionData, int numTemperatureGroups) override
{
- connectionData.setNumVelocityScalingVariables(numTemperatureGroups);
- lambdaStartVelocities_ = connectionData.getViewOnVelocityScaling();
+ GMX_RELEASE_ASSERT(connectionData.hasStartVelocityScaling(),
+ "Berendsen T-coupling requires start velocity scaling.");
+ connectionData.setNumVelocityScalingVariables(numTemperatureGroups, ScaleVelocities::PreStepOnly);
+ lambdaStartVelocities_ = connectionData.getViewOnStartVelocityScaling();
}
//! No data to write to checkpoint
ArrayRef<real> lambdaStartVelocities_;
};
+// Prepare NoseHooverTemperatureCoupling checkpoint data
+namespace
+{
+/*!
+ * \brief Enum describing the contents NoseHoover writes to modular checkpoint
+ *
+ * When changing the checkpoint content, add a new element just above Count, and adjust the
+ * checkpoint functionality.
+ */
+enum class NHCheckpointVersion
+{
+ Base, //!< First version of modular checkpointing
+ Count //!< Number of entries. Add new versions right above this!
+};
+constexpr auto c_nhCurrentVersion = NHCheckpointVersion(int(NHCheckpointVersion::Count) - 1);
+} // namespace
+
+/*! \internal
+ * \brief Implements the Nose-Hoover temperature coupling
+ */
+class NoseHooverTemperatureCoupling final : public ITemperatureCouplingImpl
+{
+public:
+ //! Apply the Nose-Hoover temperature control
+ real apply(Step gmx_unused step,
+ int temperatureGroup,
+ real currentKineticEnergy,
+ real currentTemperature,
+ const TemperatureCouplingData& thermostatData) override
+ {
+ return applyLeapFrog(
+ step, temperatureGroup, currentKineticEnergy, currentTemperature, thermostatData);
+ }
+
+ /*! \brief Apply for leap-frog
+ *
+ * This is called after the force calculation, before coordinate update
+ *
+ * We expect system to be at x(t), v(t-dt/2), f(t), T(t-dt/2)
+ * Internal variables are at xi(t-dt), v_xi(t-dt)
+ * Force on xi is calculated at time of system temperature
+ * After calling this, we will have xi(t), v_xi(t)
+ * The thermostat integral returned is a function of xi and v_xi,
+ * and hence at time t.
+ *
+ * This performs an update of the thermostat variables calculated as
+ * a_xi(t-dt/2) = (T_sys(t-dt/2) - T_ref) / mass_xi;
+ * v_xi(t) = v_xi(t-dt) + dt_xi * a_xi(t-dt/2);
+ * xi(t) = xi(t-dt) + dt_xi * (v_xi(t-dt) + v_xi(t))/2;
+ *
+ * This will be followed by leap-frog integration of coordinates, calculated as
+ * v(t-dt/2) *= - 0.5 * dt * v_xi(t); // scale previous velocities
+ * v(t+dt/2) = update_leapfrog_v(v(t-dt/2), f(t)); // do whatever LF does
+ * v(t+dt/2) *= 1 / (1 + 0.5 * dt * v_xi(t)) // scale new velocities
+ * x(t+dt) = update_leapfrog_x(x(t), v(t+dt/2)); // do whatever LF does
+ */
+ real applyLeapFrog(Step gmx_unused step,
+ int temperatureGroup,
+ real currentKineticEnergy,
+ real currentTemperature,
+ const TemperatureCouplingData& thermostatData)
+ {
+ if (!(thermostatData.couplingTime[temperatureGroup] >= 0
+ && thermostatData.numDegreesOfFreedom[temperatureGroup] > 0 && currentKineticEnergy > 0))
+ {
+ lambdaStartVelocities_[temperatureGroup] = 1.0;
+ lambdaEndVelocities_[temperatureGroup] = 1.0;
+ return thermostatData.temperatureCouplingIntegral[temperatureGroup];
+ }
+
+ const auto oldXiVelocity = xiVelocities_[temperatureGroup];
+ const auto xiAcceleration =
+ invXiMass_[temperatureGroup]
+ * (currentTemperature - thermostatData.referenceTemperature[temperatureGroup]);
+ xiVelocities_[temperatureGroup] += thermostatData.couplingTimeStep * xiAcceleration;
+ xi_[temperatureGroup] += thermostatData.couplingTimeStep
+ * (oldXiVelocity + xiVelocities_[temperatureGroup]) * 0.5;
+ lambdaStartVelocities_[temperatureGroup] =
+ (1 - 0.5 * thermostatData.couplingTimeStep * xiVelocities_[temperatureGroup]);
+ lambdaEndVelocities_[temperatureGroup] =
+ 1. / (1 + 0.5 * thermostatData.couplingTimeStep * xiVelocities_[temperatureGroup]);
+
+ // Current value of the thermostat integral
+ return 0.5 * c_boltz * thermostatData.numDegreesOfFreedom[temperatureGroup]
+ * (xiVelocities_[temperatureGroup] * xiVelocities_[temperatureGroup])
+ / invXiMass_[temperatureGroup]
+ + thermostatData.numDegreesOfFreedom[temperatureGroup] * xi_[temperatureGroup]
+ * c_boltz * thermostatData.referenceTemperature[temperatureGroup];
+ }
+
+ //! Connect with propagator - Nose-Hoover scales start and end step velocities
+ void connectWithPropagator(const PropagatorConnection& connectionData, int numTemperatureGroups) override
+ {
+ GMX_RELEASE_ASSERT(
+ connectionData.hasStartVelocityScaling() && connectionData.hasEndVelocityScaling(),
+ "Nose-Hoover T-coupling requires both start and end velocity scaling.");
+ connectionData.setNumVelocityScalingVariables(numTemperatureGroups,
+ ScaleVelocities::PreStepAndPostStep);
+ lambdaStartVelocities_ = connectionData.getViewOnStartVelocityScaling();
+ lambdaEndVelocities_ = connectionData.getViewOnEndVelocityScaling();
+ }
+
+ //! Constructor
+ NoseHooverTemperatureCoupling(int numTemperatureGroups,
+ ArrayRef<const real> referenceTemperature,
+ ArrayRef<const real> couplingTime)
+ {
+ xi_.resize(numTemperatureGroups, 0.0);
+ xiVelocities_.resize(numTemperatureGroups, 0.0);
+ invXiMass_.resize(numTemperatureGroups, 0.0);
+ for (auto temperatureGroup = 0; temperatureGroup < numTemperatureGroups; ++temperatureGroup)
+ {
+ if (referenceTemperature[temperatureGroup] > 0 && couplingTime[temperatureGroup] > 0)
+ {
+ // Note: This mass definition is equal to legacy md
+ // legacy md-vv divides the mass by ndof * kB
+ invXiMass_[temperatureGroup] = 1.0
+ / (gmx::square(couplingTime[temperatureGroup] / M_2PI)
+ * referenceTemperature[temperatureGroup]);
+ }
+ }
+ }
+
+ //! Helper function to read from / write to CheckpointData
+ template<CheckpointDataOperation operation>
+ void doCheckpointData(CheckpointData<operation>* checkpointData)
+ {
+ checkpointVersion(checkpointData, "Nose-Hoover version", c_nhCurrentVersion);
+ checkpointData->arrayRef("xi", makeCheckpointArrayRef<operation>(xi_));
+ checkpointData->arrayRef("xi velocities", makeCheckpointArrayRef<operation>(xiVelocities_));
+ }
+
+ //! Write thermostat dof to checkpoint
+ void writeCheckpoint(std::optional<WriteCheckpointData> checkpointData, const t_commrec* cr) override
+ {
+ if (MASTER(cr))
+ {
+ doCheckpointData(&checkpointData.value());
+ }
+ }
+ //! Read thermostat dof from checkpoint
+ void readCheckpoint(std::optional<ReadCheckpointData> checkpointData, const t_commrec* cr) override
+ {
+ if (MASTER(cr))
+ {
+ doCheckpointData(&checkpointData.value());
+ }
+ if (DOMAINDECOMP(cr))
+ {
+ dd_bcast(cr->dd, xi_.size() * sizeof(real), xi_.data());
+ dd_bcast(cr->dd, xiVelocities_.size() * sizeof(real), xiVelocities_.data());
+ }
+ }
+
+private:
+ //! The thermostat degree of freedom
+ std::vector<real> xi_;
+ //! Velocity of the thermostat dof
+ std::vector<real> xiVelocities_;
+ //! Inverse mass of the thermostat dof
+ std::vector<real> invXiMass_;
+
+ //! View on the scaling factor of the propagator (pre-step velocities)
+ ArrayRef<real> lambdaStartVelocities_;
+ //! View on the scaling factor of the propagator (post-step velocities)
+ ArrayRef<real> lambdaEndVelocities_;
+};
+
VelocityScalingTemperatureCoupling::VelocityScalingTemperatureCoupling(
int nstcouple,
int offset,
const real* couplingTime,
const real* numDegreesOfFreedom,
EnergyData* energyData,
- TemperatureCouplingType couplingType) :
+ TemperatureCoupling couplingType) :
nstcouple_(nstcouple),
offset_(offset),
useFullStepKE_(useFullStepKE),
couplingTime_(couplingTime, couplingTime + numTemperatureGroups),
numDegreesOfFreedom_(numDegreesOfFreedom, numDegreesOfFreedom + numTemperatureGroups),
temperatureCouplingIntegral_(numTemperatureGroups, 0.0),
- energyData_(energyData)
+ energyData_(energyData),
+ nextEnergyCalculationStep_(-1)
{
- if (reportPreviousConservedEnergy_ == ReportPreviousStepConservedEnergy::Yes)
- {
- temperatureCouplingIntegralPreviousStep_ = temperatureCouplingIntegral_;
- }
- energyData->setVelocityScalingTemperatureCoupling(this);
- if (couplingType == etcVRESCALE)
+ if (couplingType == TemperatureCoupling::VRescale)
{
temperatureCouplingImpl_ = std::make_unique<VRescaleTemperatureCoupling>(seed);
}
- else if (couplingType == etcBERENDSEN)
+ else if (couplingType == TemperatureCoupling::Berendsen)
{
temperatureCouplingImpl_ = std::make_unique<BerendsenTemperatureCoupling>();
}
+ else if (couplingType == TemperatureCoupling::NoseHoover)
+ {
+ temperatureCouplingImpl_ = std::make_unique<NoseHooverTemperatureCoupling>(
+ numTemperatureGroups_, referenceTemperature_, couplingTime_);
+ }
else
{
- throw NotImplementedError("Temperature coupling " + std::string(ETCOUPLTYPE(couplingType))
+ throw NotImplementedError("Temperature coupling " + std::string(enumValueToString(couplingType))
+ " is not implemented for modular simulator.");
}
+ energyData->addConservedEnergyContribution([this](Step gmx_used_in_debug step, Time /*unused*/) {
+ GMX_ASSERT(conservedEnergyContributionStep_ == step,
+ "VelocityScalingTemperatureCoupling conserved energy step mismatch.");
+ return conservedEnergyContribution_;
+ });
}
-void VelocityScalingTemperatureCoupling::connectWithPropagator(const PropagatorThermostatConnection& connectionData)
+void VelocityScalingTemperatureCoupling::connectWithMatchingPropagator(const PropagatorConnection& connectionData,
+ const PropagatorTag& propagatorTag)
{
- temperatureCouplingImpl_->connectWithPropagator(connectionData, numTemperatureGroups_);
- propagatorCallback_ = connectionData.getVelocityScalingCallback();
+ if (connectionData.tag == propagatorTag)
+ {
+ temperatureCouplingImpl_->connectWithPropagator(connectionData, numTemperatureGroups_);
+ propagatorCallback_ = connectionData.getVelocityScalingCallback();
+ }
}
void VelocityScalingTemperatureCoupling::elementSetup()
throw MissingElementConnectionError(
"Velocity scaling temperature coupling was not connected to a propagator.\n"
"Connection to a propagator element is needed to scale the velocities.\n"
- "Use connectWithPropagator(...) before building the ModularSimulatorAlgorithm "
+ "Use connectWithMatchingPropagator(...) before building the "
+ "ModularSimulatorAlgorithm "
"object.");
}
}
* of the kinetic energy is needed.
*
*/
+ if (step == nextEnergyCalculationStep_
+ && reportPreviousConservedEnergy_ == ReportPreviousStepConservedEnergy::Yes)
+ {
+ // add conserved energy before we do T-coupling
+ registerRunFunction([this, step]() {
+ conservedEnergyContribution_ = conservedEnergyContribution();
+ conservedEnergyContributionStep_ = step;
+ });
+ }
if (do_per_step(step + nstcouple_ + offset_, nstcouple_))
{
// do T-coupling this step
// Let propagator know that we want to do T-coupling
propagatorCallback_(step);
}
+ if (step == nextEnergyCalculationStep_
+ && reportPreviousConservedEnergy_ == ReportPreviousStepConservedEnergy::No)
+ {
+ // add conserved energy after we did T-coupling
+ registerRunFunction([this, step]() {
+ conservedEnergyContribution_ = conservedEnergyContribution();
+ conservedEnergyContributionStep_ = step;
+ });
+ }
}
void VelocityScalingTemperatureCoupling::setLambda(Step step)
{
- // if we report the previous energy, calculate before the step
- if (reportPreviousConservedEnergy_ == ReportPreviousStepConservedEnergy::Yes)
- {
- temperatureCouplingIntegralPreviousStep_ = temperatureCouplingIntegral_;
- }
-
const auto* ekind = energyData_->ekindata();
- TemperatureCouplingData thermostatData = { couplingTimeStep_, referenceTemperature_, couplingTime_,
- numDegreesOfFreedom_, temperatureCouplingIntegral_ };
+ TemperatureCouplingData thermostatData = {
+ couplingTimeStep_, referenceTemperature_, couplingTime_, numDegreesOfFreedom_, temperatureCouplingIntegral_
+ };
for (int temperatureGroup = 0; (temperatureGroup < numTemperatureGroups_); temperatureGroup++)
{
}
if (DOMAINDECOMP(cr))
{
- dd_bcast(cr->dd, ssize(temperatureCouplingIntegral_) * int(sizeof(double)),
+ dd_bcast(cr->dd,
+ ssize(temperatureCouplingIntegral_) * int(sizeof(double)),
temperatureCouplingIntegral_.data());
}
temperatureCouplingImpl_->readCheckpoint(
real VelocityScalingTemperatureCoupling::conservedEnergyContribution() const
{
- if (reportPreviousConservedEnergy_ == ReportPreviousStepConservedEnergy::Yes)
- {
- return std::accumulate(temperatureCouplingIntegralPreviousStep_.begin(),
- temperatureCouplingIntegralPreviousStep_.end(), 0.0);
- }
- else
+ return std::accumulate(temperatureCouplingIntegral_.begin(), temperatureCouplingIntegral_.end(), 0.0);
+}
+
+std::optional<SignallerCallback> VelocityScalingTemperatureCoupling::registerEnergyCallback(EnergySignallerEvent event)
+{
+ if (event == EnergySignallerEvent::EnergyCalculationStep)
{
- return std::accumulate(temperatureCouplingIntegral_.begin(),
- temperatureCouplingIntegral_.end(), 0.0);
+ return [this](Step step, Time /*unused*/) { nextEnergyCalculationStep_ = step; };
}
+ return std::nullopt;
}
ISimulatorElement* VelocityScalingTemperatureCoupling::getElementPointerImpl(
LegacySimulatorData* legacySimulatorData,
ModularSimulatorAlgorithmBuilderHelper* builderHelper,
StatePropagatorData gmx_unused* statePropagatorData,
- EnergyData gmx_unused* energyData,
+ EnergyData* energyData,
FreeEnergyPerturbationData gmx_unused* freeEnergyPerturbationData,
GlobalCommunicationHelper gmx_unused* globalCommunicationHelper,
- int offset,
+ Offset offset,
UseFullStepKE useFullStepKE,
- ReportPreviousStepConservedEnergy reportPreviousStepConservedEnergy)
+ ReportPreviousStepConservedEnergy reportPreviousStepConservedEnergy,
+ const PropagatorTag& propagatorTag)
{
// Element is now owned by the caller of this method, who will handle lifetime (see ModularSimulatorAlgorithm)
auto* element = builderHelper->storeElement(std::make_unique<VelocityScalingTemperatureCoupling>(
- legacySimulatorData->inputrec->nsttcouple, offset, useFullStepKE, reportPreviousStepConservedEnergy,
- legacySimulatorData->inputrec->ld_seed, legacySimulatorData->inputrec->opts.ngtc,
+ legacySimulatorData->inputrec->nsttcouple,
+ offset,
+ useFullStepKE,
+ reportPreviousStepConservedEnergy,
+ legacySimulatorData->inputrec->ld_seed,
+ legacySimulatorData->inputrec->opts.ngtc,
legacySimulatorData->inputrec->delta_t * legacySimulatorData->inputrec->nsttcouple,
- legacySimulatorData->inputrec->opts.ref_t, legacySimulatorData->inputrec->opts.tau_t,
- legacySimulatorData->inputrec->opts.nrdf, energyData, legacySimulatorData->inputrec->etc));
+ legacySimulatorData->inputrec->opts.ref_t,
+ legacySimulatorData->inputrec->opts.tau_t,
+ legacySimulatorData->inputrec->opts.nrdf,
+ energyData,
+ legacySimulatorData->inputrec->etc));
auto* thermostat = static_cast<VelocityScalingTemperatureCoupling*>(element);
// Capturing pointer is safe because lifetime is handled by caller
- builderHelper->registerThermostat([thermostat](const PropagatorThermostatConnection& connection) {
- thermostat->connectWithPropagator(connection);
- });
+ builderHelper->registerTemperaturePressureControl(
+ [thermostat, propagatorTag](const PropagatorConnection& connection) {
+ thermostat->connectWithMatchingPropagator(connection, propagatorTag);
+ });
return element;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
Count
};
-//! Typedef to match current use of ints as types.
-using TemperatureCouplingType = int;
-
/*! \internal
* \ingroup module_modularsimulator
* \brief Element implementing the a velocity-scaling thermostat
* implementations of the ITemperatureCouplingImpl interface, while the element
* handles the scheduling and interfacing with other elements.
*/
-class VelocityScalingTemperatureCoupling final : public ISimulatorElement, public ICheckpointHelperClient
+class VelocityScalingTemperatureCoupling final :
+ public ISimulatorElement,
+ public ICheckpointHelperClient,
+ public IEnergySignallerClient
{
public:
//! Constructor
const real* couplingTime,
const real* numDegreesOfFreedom,
EnergyData* energyData,
- TemperatureCouplingType couplingType);
+ TemperatureCoupling couplingType);
/*! \brief Register run function for step / time
*
//! No element teardown needed
void elementTeardown() override {}
- //! Contribution to the conserved energy (called by energy data)
- [[nodiscard]] real conservedEnergyContribution() const;
-
//! Connect this to propagator
- void connectWithPropagator(const PropagatorThermostatConnection& connectionData);
+ void connectWithMatchingPropagator(const PropagatorConnection& connectionData,
+ const PropagatorTag& propagatorTag);
//! ICheckpointHelperClient write checkpoint implementation
void saveCheckpointState(std::optional<WriteCheckpointData> checkpointData, const t_commrec* cr) override;
* \param energyData Pointer to the \c EnergyData object
* \param freeEnergyPerturbationData Pointer to the \c FreeEnergyPerturbationData object
* \param globalCommunicationHelper Pointer to the \c GlobalCommunicationHelper object
+ * \param propagatorTag Tag of the propagator to connect to
* \param offset The step offset at which the thermostat is applied
* \param useFullStepKE Whether full step or half step KE is used
* \param reportPreviousStepConservedEnergy Report the previous or the current step conserved energy
EnergyData* energyData,
FreeEnergyPerturbationData* freeEnergyPerturbationData,
GlobalCommunicationHelper* globalCommunicationHelper,
- int offset,
+ Offset offset,
UseFullStepKE useFullStepKE,
- ReportPreviousStepConservedEnergy reportPreviousStepConservedEnergy);
+ ReportPreviousStepConservedEnergy reportPreviousStepConservedEnergy,
+ const PropagatorTag& propagatorTag);
private:
//! The frequency at which the thermostat is applied
const std::vector<real> numDegreesOfFreedom_;
//! Work exerted by thermostat per group
std::vector<double> temperatureCouplingIntegral_;
- //! Work exerted by thermostat per group (backup from previous step)
- std::vector<double> temperatureCouplingIntegralPreviousStep_;
+
+ //! Current conserved energy contribution
+ real conservedEnergyContribution_;
+ //! Step of current conserved energy contribution
+ Step conservedEnergyContributionStep_;
// TODO: Clarify relationship to data objects and find a more robust alternative to raw pointers (#3583)
//! Pointer to the energy data (for ekindata)
//! Set new lambda value (at T-coupling steps)
void setLambda(Step step);
+ //! Contribution to the conserved energy
+ [[nodiscard]] real conservedEnergyContribution() const;
//! The temperature coupling implementation
std::unique_ptr<ITemperatureCouplingImpl> temperatureCouplingImpl_;
//! Helper function to read from / write to CheckpointData
template<CheckpointDataOperation operation>
void doCheckpointData(CheckpointData<operation>* checkpointData);
+
+ //! IEnergySignallerClient implementation
+ std::optional<SignallerCallback> registerEnergyCallback(EnergySignallerEvent event) override;
+ //! The next communicated energy calculation step
+ Step nextEnergyCalculationStep_;
};
} // namespace gmx
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(nbnxm INTERFACE)
+
add_subdirectory(kernels_simd_4xm)
add_subdirectory(kernels_simd_2xmm)
gmx_add_libgromacs_sources(nbnxm_gpu_data_mgmt.cpp)
_gmx_add_files_to_property(CUDA_SOURCES
nbnxm_gpu_data_mgmt.cpp
- )
+ )
endif()
if(GMX_GPU_OPENCL)
gmx_add_libgromacs_sources(nbnxm_gpu_data_mgmt.cpp)
endif()
+if(GMX_GPU_SYCL)
+ add_subdirectory(sycl)
+ gmx_add_libgromacs_sources(nbnxm_gpu_data_mgmt.cpp)
+ _gmx_add_files_to_property(SYCL_SOURCES nbnxm_gpu_data_mgmt.cpp nbnxm.cpp)
+endif()
+
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${NBNXM_SOURCES} PARENT_SCOPE)
+
+
+# Source files have the following private module dependencies.
+target_link_libraries(nbnxm PRIVATE
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(nbnxm PUBLIC
+target_include_directories(nbnxm INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(nbnxm PUBLIC
+target_link_libraries(nbnxm INTERFACE
+ legacy_api
+ )
+
+# TODO: when nbnxm is an OBJECT target
+#target_link_libraries(nbnxm PUBLIC legacy_api)
+#target_link_libraries(nbnxm PRIVATE common)
+
+# Module dependencies
+# nbnxm interfaces convey transitive dependence on these modules.
+#target_link_libraries(nbnxm PUBLIC
+target_link_libraries(nbnxm INTERFACE
+ utility
+ )
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "atomdata.h"
-#include <cassert>
#include <cmath>
#include <cstdlib>
#include <cstring>
#include <algorithm>
-#include "thread_mpi/atomic.h"
-
#include "gromacs/math/functions.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdtypes/forcerec.h" // only for GET_CGINFO_*
+#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/nbnxm/nbnxm.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/simd/simd.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxomp.h"
#include "gromacs/utility/logger.h"
-#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strconvert.h"
#include "gromacs/utility/stringutil.h"
using namespace gmx; // TODO: Remove when this file is moved into gmx namespace
+
+const char* enumValueToString(LJCombinationRule enumValue)
+{
+ static constexpr gmx::EnumerationArray<LJCombinationRule, const char*> s_ljCombinationRuleNames = {
+ "Geometric", "Lorentz-Berthelot", "None"
+ };
+ return s_ljCombinationRuleNames[enumValue];
+}
+
void nbnxn_atomdata_t::resizeCoordinateBuffer(int numAtoms)
{
numAtoms_ = numAtoms;
Vvdw({}, { pinningPolicy }),
Vc({}, { pinningPolicy })
{
- fshift.resize(SHIFTS * DIM);
+ fshift.resize(gmx::c_numShiftVectors * DIM);
Vvdw.resize(numEnergyGroups * numEnergyGroups);
Vc.resize(numEnergyGroups * numEnergyGroups);
static void copy_int_to_nbat_int(const int* a, int na, int na_round, const int* in, int fill, int* innb)
{
- int i, j;
-
- j = 0;
- for (i = 0; i < na; i++)
+ int j = 0;
+ for (int i = 0; i < na; i++)
{
innb[j++] = in[a[i]];
}
/* Complete the partially filled last cell with fill */
- for (; i < na_round; i++)
+ for (int i = na; i < na_round; i++)
{
innb[j++] = fill;
}
*/
const real farAway = -1000000;
- int i, j, c;
-
- switch (nbatFormat)
+ if (nbatFormat == nbatXYZ)
{
- case nbatXYZ:
- j = a0 * STRIDE_XYZ;
- for (i = 0; i < na; i++)
- {
- xnb[j++] = x[a[i]][XX];
- xnb[j++] = x[a[i]][YY];
- xnb[j++] = x[a[i]][ZZ];
- }
- /* Complete the partially filled last cell with farAway elements */
- for (; i < na_round; i++)
- {
- xnb[j++] = farAway;
- xnb[j++] = farAway;
- xnb[j++] = farAway;
- }
- break;
- case nbatXYZQ:
- j = a0 * STRIDE_XYZQ;
- for (i = 0; i < na; i++)
- {
- xnb[j++] = x[a[i]][XX];
- xnb[j++] = x[a[i]][YY];
- xnb[j++] = x[a[i]][ZZ];
- j++;
- }
- /* Complete the partially filled last cell with zeros */
- for (; i < na_round; i++)
- {
- xnb[j++] = farAway;
- xnb[j++] = farAway;
- xnb[j++] = farAway;
- j++;
- }
- break;
- case nbatX4:
- j = atom_to_x_index<c_packX4>(a0);
- c = a0 & (c_packX4 - 1);
- for (i = 0; i < na; i++)
+ int i = 0;
+ int j = a0 * STRIDE_XYZ;
+ for (; i < na; i++)
+ {
+ xnb[j++] = x[a[i]][XX];
+ xnb[j++] = x[a[i]][YY];
+ xnb[j++] = x[a[i]][ZZ];
+ }
+ /* Complete the partially filled last cell with farAway elements */
+ for (; i < na_round; i++)
+ {
+ xnb[j++] = farAway;
+ xnb[j++] = farAway;
+ xnb[j++] = farAway;
+ }
+ }
+ else if (nbatFormat == nbatXYZQ)
+ {
+ int i = 0;
+ int j = a0 * STRIDE_XYZQ;
+ for (; i < na; i++)
+ {
+ xnb[j++] = x[a[i]][XX];
+ xnb[j++] = x[a[i]][YY];
+ xnb[j++] = x[a[i]][ZZ];
+ j++;
+ }
+ /* Complete the partially filled last cell with zeros */
+ for (; i < na_round; i++)
+ {
+ xnb[j++] = farAway;
+ xnb[j++] = farAway;
+ xnb[j++] = farAway;
+ j++;
+ }
+ }
+ else if (nbatFormat == nbatX4)
+ {
+ int i = 0;
+ int j = atom_to_x_index<c_packX4>(a0);
+ int c = a0 & (c_packX4 - 1);
+ for (; i < na; i++)
+ {
+ xnb[j + XX * c_packX4] = x[a[i]][XX];
+ xnb[j + YY * c_packX4] = x[a[i]][YY];
+ xnb[j + ZZ * c_packX4] = x[a[i]][ZZ];
+ j++;
+ c++;
+ if (c == c_packX4)
{
- xnb[j + XX * c_packX4] = x[a[i]][XX];
- xnb[j + YY * c_packX4] = x[a[i]][YY];
- xnb[j + ZZ * c_packX4] = x[a[i]][ZZ];
- j++;
- c++;
- if (c == c_packX4)
- {
- j += (DIM - 1) * c_packX4;
- c = 0;
- }
+ j += (DIM - 1) * c_packX4;
+ c = 0;
}
- /* Complete the partially filled last cell with zeros */
- for (; i < na_round; i++)
+ }
+ /* Complete the partially filled last cell with zeros */
+ for (; i < na_round; i++)
+ {
+ xnb[j + XX * c_packX4] = farAway;
+ xnb[j + YY * c_packX4] = farAway;
+ xnb[j + ZZ * c_packX4] = farAway;
+ j++;
+ c++;
+ if (c == c_packX4)
{
- xnb[j + XX * c_packX4] = farAway;
- xnb[j + YY * c_packX4] = farAway;
- xnb[j + ZZ * c_packX4] = farAway;
- j++;
- c++;
- if (c == c_packX4)
- {
- j += (DIM - 1) * c_packX4;
- c = 0;
- }
+ j += (DIM - 1) * c_packX4;
+ c = 0;
}
- break;
- case nbatX8:
- j = atom_to_x_index<c_packX8>(a0);
- c = a0 & (c_packX8 - 1);
- for (i = 0; i < na; i++)
+ }
+ }
+ else if (nbatFormat == nbatX8)
+ {
+ int i = 0;
+ int j = atom_to_x_index<c_packX8>(a0);
+ int c = a0 & (c_packX8 - 1);
+ for (; i < na; i++)
+ {
+ xnb[j + XX * c_packX8] = x[a[i]][XX];
+ xnb[j + YY * c_packX8] = x[a[i]][YY];
+ xnb[j + ZZ * c_packX8] = x[a[i]][ZZ];
+ j++;
+ c++;
+ if (c == c_packX8)
{
- xnb[j + XX * c_packX8] = x[a[i]][XX];
- xnb[j + YY * c_packX8] = x[a[i]][YY];
- xnb[j + ZZ * c_packX8] = x[a[i]][ZZ];
- j++;
- c++;
- if (c == c_packX8)
- {
- j += (DIM - 1) * c_packX8;
- c = 0;
- }
+ j += (DIM - 1) * c_packX8;
+ c = 0;
}
- /* Complete the partially filled last cell with zeros */
- for (; i < na_round; i++)
+ }
+ /* Complete the partially filled last cell with zeros */
+ for (; i < na_round; i++)
+ {
+ xnb[j + XX * c_packX8] = farAway;
+ xnb[j + YY * c_packX8] = farAway;
+ xnb[j + ZZ * c_packX8] = farAway;
+ j++;
+ c++;
+ if (c == c_packX8)
{
- xnb[j + XX * c_packX8] = farAway;
- xnb[j + YY * c_packX8] = farAway;
- xnb[j + ZZ * c_packX8] = farAway;
- j++;
- c++;
- if (c == c_packX8)
- {
- j += (DIM - 1) * c_packX8;
- c = 0;
- }
+ j += (DIM - 1) * c_packX8;
+ c = 0;
}
- break;
- default: gmx_incons("Unsupported nbnxn_atomdata_t format");
+ }
+ }
+ else
+ {
+ gmx_incons("Unsupported nbnxn_atomdata_t format");
}
}
* not per pair of atom types.
*/
params->nbfp_comb.resize(nt * 2);
- switch (params->comb_rule)
+ switch (params->ljCombinationRule)
{
- case ljcrGEOM:
- params->comb_rule = ljcrGEOM;
-
+ case LJCombinationRule::Geometric:
for (int i = 0; i < nt; i++)
{
/* Store the sqrt of the diagonal from the nbfp matrix */
params->nbfp_comb[i * 2 + 1] = std::sqrt(params->nbfp[(i * nt + i) * 2 + 1]);
}
break;
- case ljcrLB:
+ case LJCombinationRule::LorentzBerthelot:
for (int i = 0; i < nt; i++)
{
/* Get 6*C6 and 12*C12 from the diagonal of the nbfp matrix */
}
}
break;
- case ljcrNONE:
+ case LJCombinationRule::None:
/* We always store the full matrix (see code above) */
break;
default: gmx_incons("Unknown combination rule");
/* Set the diagonal cluster pair exclusion mask setup data.
* In the kernel we check 0 < j - i to generate the masks.
* Here we store j - i for generating the mask for the first i,
- * we substract 0.5 to avoid rounding issues.
+ * we subtract 0.5 to avoid rounding issues.
* In the kernel we can subtract 1 to generate the subsequent mask.
*/
const int simd_4xn_diag_size = std::max(c_nbnxnCpuIClusterSize, simd_width);
{
}
-nbnxn_atomdata_t::nbnxn_atomdata_t(gmx::PinningPolicy pinningPolicy) :
- params_(pinningPolicy),
- numAtoms_(0),
- natoms_local(0),
- shift_vec({}, { pinningPolicy }),
- x_({}, { pinningPolicy }),
- simdMasks(),
- bUseBufferFlags(FALSE),
- bUseTreeReduce(FALSE)
-{
-}
-
/* Initializes an nbnxn_atomdata_t::Params data structure */
static void nbnxn_atomdata_params_init(const gmx::MDLogger& mdlog,
nbnxn_atomdata_t::Params* params,
ArrayRef<const real> nbfp,
int n_energygroups)
{
- real c6, c12, tol;
- char* ptr;
- gmx_bool simple, bCombGeom, bCombLB, bSIMD;
-
if (debug)
{
fprintf(debug, "There are %d atom types in the system, adding one for nbnxn_atomdata_t\n", ntype);
/* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
* force-field floating point parameters.
*/
- tol = 1e-5;
- ptr = getenv("GMX_LJCOMB_TOL");
- if (ptr != nullptr)
+ real tol = 1e-5;
+ const char* tolOverrideString = getenv("GMX_LJCOMB_TOL");
+ if (tolOverrideString != nullptr)
{
- double dbl;
-
- sscanf(ptr, "%lf", &dbl);
- tol = dbl;
+ double tolOverride = std::strtod(tolOverrideString, nullptr);
+ tol = tolOverride;
}
- bCombGeom = TRUE;
- bCombLB = TRUE;
+ bool bCombGeom = true;
+ bool bCombLB = true;
/* Temporarily fill params->nbfp_comb with sigma and epsilon
* to check for the LB rule.
*/
for (int i = 0; i < ntype; i++)
{
- c6 = nbfp[(i * ntype + i) * 2] / 6.0;
- c12 = nbfp[(i * ntype + i) * 2 + 1] / 12.0;
+ const real c6 = nbfp[(i * ntype + i) * 2] / 6.0;
+ const real c12 = nbfp[(i * ntype + i) * 2 + 1] / 12.0;
if (c6 > 0 && c12 > 0)
{
params->nbfp_comb[i * 2] = gmx::sixthroot(c12 / c6);
else
{
/* Can not use LB rule with only dispersion or repulsion */
- bCombLB = FALSE;
+ bCombLB = false;
}
}
/* fr->nbfp has been updated, so that array too now stores c6/c12 including
* the 6.0/12.0 prefactors to save 2 flops in the most common case (force-only).
*/
- c6 = nbfp[(i * ntype + j) * 2];
- c12 = nbfp[(i * ntype + j) * 2 + 1];
+ real c6 = nbfp[(i * ntype + j) * 2];
+ real c12 = nbfp[(i * ntype + j) * 2 + 1];
+
params->nbfp[(i * params->numTypes + j) * 2] = c6;
params->nbfp[(i * params->numTypes + j) * 2 + 1] = c12;
/* Compare 6*C6 and 12*C12 for geometric cobination rule */
bCombGeom =
bCombGeom
- && gmx_within_tol(c6 * c6,
- nbfp[(i * ntype + i) * 2] * nbfp[(j * ntype + j) * 2], tol)
+ && gmx_within_tol(c6 * c6, nbfp[(i * ntype + i) * 2] * nbfp[(j * ntype + j) * 2], tol)
&& gmx_within_tol(c12 * c12,
nbfp[(i * ntype + i) * 2 + 1] * nbfp[(j * ntype + j) * 2 + 1],
tol);
&& ((c6 == 0 && c12 == 0
&& (params->nbfp_comb[i * 2 + 1] == 0 || params->nbfp_comb[j * 2 + 1] == 0))
|| (c6 > 0 && c12 > 0
- && gmx_within_tol(
- gmx::sixthroot(c12 / c6),
- 0.5 * (params->nbfp_comb[i * 2] + params->nbfp_comb[j * 2]), tol)
+ && gmx_within_tol(gmx::sixthroot(c12 / c6),
+ 0.5 * (params->nbfp_comb[i * 2] + params->nbfp_comb[j * 2]),
+ tol)
&& gmx_within_tol(0.25 * c6 * c6 / c12,
std::sqrt(params->nbfp_comb[i * 2 + 1]
* params->nbfp_comb[j * 2 + 1]),
}
if (debug)
{
- fprintf(debug, "Combination rules: geometric %s Lorentz-Berthelot %s\n",
- gmx::boolToString(bCombGeom), gmx::boolToString(bCombLB));
+ fprintf(debug,
+ "Combination rules: geometric %s Lorentz-Berthelot %s\n",
+ gmx::boolToString(bCombGeom),
+ gmx::boolToString(bCombLB));
}
- simple = Nbnxm::kernelTypeUsesSimplePairlist(kernelType);
+ const bool simple = Nbnxm::kernelTypeUsesSimplePairlist(kernelType);
switch (enbnxninitcombrule)
{
case enbnxninitcombruleDETECT:
- /* We prefer the geometic combination rule,
+ /* We prefer the geometric combination rule,
* as that gives a slightly faster kernel than the LB rule.
*/
if (bCombGeom)
{
- params->comb_rule = ljcrGEOM;
+ params->ljCombinationRule = LJCombinationRule::Geometric;
}
else if (bCombLB)
{
- params->comb_rule = ljcrLB;
+ params->ljCombinationRule = LJCombinationRule::LorentzBerthelot;
}
else
{
- params->comb_rule = ljcrNONE;
+ params->ljCombinationRule = LJCombinationRule::None;
params->nbfp_comb.clear();
}
{
std::string mesg;
- if (params->comb_rule == ljcrNONE)
+ if (params->ljCombinationRule == LJCombinationRule::None)
{
mesg = "Using full Lennard-Jones parameter combination matrix";
}
else
{
- mesg = gmx::formatString(
- "Using %s Lennard-Jones combination rule",
- params->comb_rule == ljcrGEOM ? "geometric" : "Lorentz-Berthelot");
+ mesg = gmx::formatString("Using %s Lennard-Jones combination rule",
+ enumValueToString(params->ljCombinationRule));
}
GMX_LOG(mdlog.info).asParagraph().appendText(mesg);
}
break;
- case enbnxninitcombruleGEOM: params->comb_rule = ljcrGEOM; break;
- case enbnxninitcombruleLB: params->comb_rule = ljcrLB; break;
+ case enbnxninitcombruleGEOM:
+ params->ljCombinationRule = LJCombinationRule::Geometric;
+ break;
+ case enbnxninitcombruleLB:
+ params->ljCombinationRule = LJCombinationRule::LorentzBerthelot;
+ break;
case enbnxninitcombruleNONE:
- params->comb_rule = ljcrNONE;
+ params->ljCombinationRule = LJCombinationRule::None;
params->nbfp_comb.clear();
break;
default: gmx_incons("Unknown enbnxninitcombrule");
}
- bSIMD = Nbnxm::kernelTypeIsSimd(kernelType);
+ const bool bSIMD = Nbnxm::kernelTypeIsSimd(kernelType);
set_lj_parameter_data(params, bSIMD);
}
/* Initializes an nbnxn_atomdata_t data structure */
-void nbnxn_atomdata_init(const gmx::MDLogger& mdlog,
- nbnxn_atomdata_t* nbat,
- const Nbnxm::KernelType kernelType,
- int enbnxninitcombrule,
- int ntype,
- ArrayRef<const real> nbfp,
- int n_energygroups,
- int nout)
+nbnxn_atomdata_t::nbnxn_atomdata_t(gmx::PinningPolicy pinningPolicy,
+ const gmx::MDLogger& mdlog,
+ const Nbnxm::KernelType kernelType,
+ int enbnxninitcombrule,
+ int ntype,
+ ArrayRef<const real> nbfp,
+ int n_energygroups,
+ int nout) :
+ params_(pinningPolicy),
+ numAtoms_(0),
+ natoms_local(0),
+ shift_vec({}, { pinningPolicy }),
+ x_({}, { pinningPolicy }),
+ simdMasks(),
+ bUseBufferFlags(FALSE)
{
- nbnxn_atomdata_params_init(mdlog, &nbat->paramsDeprecated(), kernelType, enbnxninitcombrule,
- ntype, nbfp, n_energygroups);
+ nbnxn_atomdata_params_init(
+ mdlog, ¶msDeprecated(), kernelType, enbnxninitcombrule, ntype, nbfp, n_energygroups);
const bool simple = Nbnxm::kernelTypeUsesSimplePairlist(kernelType);
const bool bSIMD = Nbnxm::kernelTypeIsSimd(kernelType);
if (simple)
{
- int pack_x;
-
if (bSIMD)
{
- pack_x = std::max(c_nbnxnCpuIClusterSize, Nbnxm::JClusterSizePerKernelType[kernelType]);
+ int pack_x = std::max(c_nbnxnCpuIClusterSize, Nbnxm::JClusterSizePerKernelType[kernelType]);
switch (pack_x)
{
- case 4: nbat->XFormat = nbatX4; break;
- case 8: nbat->XFormat = nbatX8; break;
+ case 4: XFormat = nbatX4; break;
+ case 8: XFormat = nbatX8; break;
default: gmx_incons("Unsupported packing width");
}
}
else
{
- nbat->XFormat = nbatXYZ;
+ XFormat = nbatXYZ;
}
- nbat->FFormat = nbat->XFormat;
+ FFormat = XFormat;
}
else
{
- nbat->XFormat = nbatXYZQ;
- nbat->FFormat = nbatXYZ;
+ XFormat = nbatXYZQ;
+ FFormat = nbatXYZ;
}
- nbat->shift_vec.resize(SHIFTS);
+ shift_vec.resize(gmx::c_numShiftVectors);
- nbat->xstride = (nbat->XFormat == nbatXYZQ ? STRIDE_XYZQ : DIM);
- nbat->fstride = (nbat->FFormat == nbatXYZQ ? STRIDE_XYZQ : DIM);
+ xstride = (XFormat == nbatXYZQ ? STRIDE_XYZQ : DIM);
+ fstride = (FFormat == nbatXYZQ ? STRIDE_XYZQ : DIM);
/* Initialize the output data structures */
for (int i = 0; i < nout; i++)
{
- const auto& pinningPolicy = nbat->params().type.get_allocator().pinningPolicy();
- nbat->out.emplace_back(kernelType, nbat->params().nenergrp, 1 << nbat->params().neg_2log,
- pinningPolicy);
- }
-
- nbat->buffer_flags.clear();
-
- const int nth = gmx_omp_nthreads_get(emntNonbonded);
-
- const char* ptr = getenv("GMX_USE_TREEREDUCE");
- if (ptr != nullptr)
- {
- nbat->bUseTreeReduce = (strtol(ptr, nullptr, 10) != 0);
- }
-#if defined __MIC__
- else if (nth > 8) /*on the CPU we currently don't benefit even at 32*/
- {
- nbat->bUseTreeReduce = 1;
+ const auto& pinningPolicy = params().type.get_allocator().pinningPolicy();
+ out.emplace_back(kernelType, params().nenergrp, 1 << params().neg_2log, pinningPolicy);
}
-#endif
- else
- {
- nbat->bUseTreeReduce = false;
- }
- if (nbat->bUseTreeReduce)
- {
- GMX_LOG(mdlog.info).asParagraph().appendText("Using tree force reduction");
- nbat->syncStep = new tMPI_Atomic[nth];
- }
+ buffer_flags.clear();
}
template<int packSize>
const int atomOffset = grid.firstAtomInColumn(i);
copy_int_to_nbat_int(gridSet.atomIndices().data() + atomOffset,
- grid.numAtomsInColumn(i), numAtoms, atomTypes.data(),
- params->numTypes - 1, params->type.data() + atomOffset);
+ grid.numAtomsInColumn(i),
+ numAtoms,
+ atomTypes.data(),
+ params->numTypes - 1,
+ params->type.data() + atomOffset);
}
}
}
{
params->lj_comb.resize(gridSet.numGridAtomsTotal() * 2);
- if (params->comb_rule != ljcrNONE)
+ if (params->ljCombinationRule != LJCombinationRule::None)
{
for (const Nbnxm::Grid& grid : gridSet.grids())
{
if (XFormat == nbatX4)
{
copy_lj_to_nbat_lj_comb<c_packX4>(params->nbfp_comb,
- params->type.data() + atomOffset, numAtoms,
+ params->type.data() + atomOffset,
+ numAtoms,
params->lj_comb.data() + atomOffset * 2);
}
else if (XFormat == nbatX8)
{
copy_lj_to_nbat_lj_comb<c_packX8>(params->nbfp_comb,
- params->type.data() + atomOffset, numAtoms,
+ params->type.data() + atomOffset,
+ numAtoms,
params->lj_comb.data() + atomOffset * 2);
}
else if (XFormat == nbatXYZQ)
{
- copy_lj_to_nbat_lj_comb<1>(params->nbfp_comb, params->type.data() + atomOffset,
- numAtoms, params->lj_comb.data() + atomOffset * 2);
+ copy_lj_to_nbat_lj_comb<1>(params->nbfp_comb,
+ params->type.data() + atomOffset,
+ numAtoms,
+ params->lj_comb.data() + atomOffset * 2);
}
}
}
if (nbat->XFormat == nbatXYZQ)
{
real* q = nbat->x().data() + atomOffset * STRIDE_XYZQ + ZZ + 1;
- int i;
- for (i = 0; i < numAtoms; i++)
+ for (int i = 0; i < numAtoms; i++)
{
*q = charges[gridSet.atomIndices()[atomOffset + i]];
q += STRIDE_XYZQ;
}
/* Complete the partially filled last cell with zeros */
- for (; i < paddedNumAtoms; i++)
+ for (int i = numAtoms; i < paddedNumAtoms; i++)
{
*q = 0;
q += STRIDE_XYZQ;
else
{
real* q = nbat->paramsDeprecated().q.data() + atomOffset;
- int i;
- for (i = 0; i < numAtoms; i++)
+ for (int i = 0; i < numAtoms; i++)
{
*q = charges[gridSet.atomIndices()[atomOffset + i]];
q++;
}
/* Complete the partially filled last cell with zeros */
- for (; i < paddedNumAtoms; i++)
+ for (int i = numAtoms; i < paddedNumAtoms; i++)
{
*q = 0;
q++;
static void nbnxn_atomdata_mask_fep(nbnxn_atomdata_t* nbat, const Nbnxm::GridSet& gridSet)
{
nbnxn_atomdata_t::Params& params = nbat->paramsDeprecated();
- real* q;
- int stride_q;
- if (nbat->XFormat == nbatXYZQ)
- {
- q = nbat->x().data() + ZZ + 1;
- stride_q = STRIDE_XYZQ;
- }
- else
- {
- q = params.q.data();
- stride_q = 1;
- }
+ const bool formatIsXYZQ = (nbat->XFormat == nbatXYZQ);
+
+ real* q = formatIsXYZQ ? (nbat->x().data() + ZZ + 1) : params.q.data();
+ int stride_q = formatIsXYZQ ? STRIDE_XYZQ : 1;
for (const Nbnxm::Grid& grid : gridSet.grids())
{
- int nsubc;
- if (grid.geometry().isSimple)
- {
- nsubc = 1;
- }
- else
- {
- nsubc = c_gpuNumClusterPerCell;
- }
+ const int nsubc = (grid.geometry().isSimple) ? 1 : c_gpuNumClusterPerCell;
- int c_offset = grid.firstAtomInColumn(0);
+ const int c_offset = grid.firstAtomInColumn(0);
/* Loop over all columns and copy and fill */
for (int c = 0; c < grid.numCells() * nsubc; c++)
static void
copy_egp_to_nbat_egps(const int* a, int na, int na_round, int na_c, int bit_shift, const int* in, int* innb)
{
- int i;
- int comb;
-
- int j = 0;
- for (i = 0; i < na; i += na_c)
+ int i = 0, j = 0;
+ for (; i < na; i += na_c)
{
/* Store na_c energy group numbers into one int */
- comb = 0;
+ int comb = 0;
for (int sa = 0; sa < na_c; sa++)
{
int at = a[i + sa];
const int numAtoms = grid.paddedNumAtomsInColumn(i);
const int atomOffset = grid.firstAtomInColumn(i);
- copy_egp_to_nbat_egps(gridSet.atomIndices().data() + atomOffset, grid.numAtomsInColumn(i),
- numAtoms, c_nbnxnCpuIClusterSize, params->neg_2log, atomInfo.data(),
+ copy_egp_to_nbat_egps(gridSet.atomIndices().data() + atomOffset,
+ grid.numAtomsInColumn(i),
+ numAtoms,
+ c_nbnxnCpuIClusterSize,
+ params->neg_2log,
+ atomInfo.data(),
params->energrp.data() + grid.atomToCluster(atomOffset));
}
}
}
/* Copies the shift vector array to nbnxn_atomdata_t */
-void nbnxn_atomdata_copy_shiftvec(gmx_bool bDynamicBox, rvec* shift_vec, nbnxn_atomdata_t* nbat)
+void nbnxn_atomdata_copy_shiftvec(gmx_bool bDynamicBox, gmx::ArrayRef<gmx::RVec> shift_vec, nbnxn_atomdata_t* nbat)
{
- int i;
-
nbat->bDynamicBox = bDynamicBox;
- for (i = 0; i < SHIFTS; i++)
- {
- copy_rvec(shift_vec[i], nbat->shift_vec[i]);
- }
+ std::copy(shift_vec.begin(), shift_vec.end(), nbat->shift_vec.begin());
}
// This is slightly different from nbnxn_get_atom_range(...) at the end of the file
/* Copies (and reorders) the coordinates to nbnxn_atomdata_t */
void nbnxn_atomdata_copy_x_to_nbat_x(const Nbnxm::GridSet& gridSet,
const gmx::AtomLocality locality,
- bool fillLocal,
const rvec* coordinates,
nbnxn_atomdata_t* nbat)
{
int gridEnd = 0;
getAtomRanges(gridSet, locality, &gridBegin, &gridEnd);
- if (fillLocal)
- {
- nbat->natoms_local = gridSet.grids()[0].atomIndexEnd();
- }
-
- const int nth = gmx_omp_nthreads_get(emntPairsearch);
+ const int nth = gmx_omp_nthreads_get(ModuleMultiThread::Pairsearch);
#pragma omp parallel for num_threads(nth) schedule(static)
for (int th = 0; th < nth; th++)
{
const int na = grid.numAtomsInColumn(cxy);
const int ash = grid.firstAtomInColumn(cxy);
- int na_fill;
- if (g == 0 && fillLocal)
- {
- na_fill = grid.paddedNumAtomsInColumn(cxy);
- }
- else
- {
- /* We fill only the real particle locations.
- * We assume the filling entries at the end have been
- * properly set before during pair-list generation.
- */
- na_fill = na;
- }
- copy_rvec_to_nbat_real(gridSet.atomIndices().data() + ash, na, na_fill,
- coordinates, nbat->XFormat, nbat->x().data(), ash);
+ copy_rvec_to_nbat_real(gridSet.atomIndices().data() + ash,
+ na,
+ na,
+ coordinates,
+ nbat->XFormat,
+ nbat->x().data(),
+ ash);
}
}
}
/* Copies (and reorders) the coordinates to nbnxn_atomdata_t on the GPU*/
void nbnxn_atomdata_x_to_nbat_x_gpu(const Nbnxm::GridSet& gridSet,
const gmx::AtomLocality locality,
- bool fillLocal,
NbnxmGpu* gpu_nbv,
DeviceBuffer<RVec> d_x,
GpuEventSynchronizer* xReadyOnDevice)
{
+ GMX_ASSERT(xReadyOnDevice != nullptr, "Need a valid GpuEventSynchronizer object");
int gridBegin = 0;
int gridEnd = 0;
for (int g = gridBegin; g < gridEnd; g++)
{
- nbnxn_gpu_x_to_nbat_x(gridSet.grids()[g], fillLocal && g == 0, gpu_nbv, d_x, xReadyOnDevice,
- locality, g, gridSet.numColumnsMax());
+ nbnxn_gpu_x_to_nbat_x(gridSet.grids()[g],
+ gpu_nbv,
+ d_x,
+ (g == gridBegin) ? xReadyOnDevice : nullptr, // Sync on first iteration only
+ locality,
+ g,
+ gridSet.numColumnsMax(),
+ (g == gridEnd - 1));
}
}
}
else
{
- /* The destination buffer is unitialized, set it first */
+ /* The destination buffer is uninitialized, set it first */
for (int i = i0; i < i1; i++)
{
dest[i] = src[0][i];
}
}
-static inline unsigned char reverse_bits(unsigned char b)
-{
- /* http://graphics.stanford.edu/~seander/bithacks.html#ReverseByteWith64BitsDiv */
- return (b * 0x0202020202ULL & 0x010884422010ULL) % 1023;
-}
-
-static void nbnxn_atomdata_add_nbat_f_to_f_treereduce(nbnxn_atomdata_t* nbat, int nth)
-{
- gmx::ArrayRef<const gmx_bitmask_t> flags = nbat->buffer_flags;
-
- int next_pow2 = 1 << (gmx::log2I(nth - 1) + 1);
-
- const int numOutputBuffers = nbat->out.size();
- GMX_ASSERT(numOutputBuffers == nth,
- "tree-reduce currently only works for numOutputBuffers==nth");
-
- memset(nbat->syncStep, 0, sizeof(*(nbat->syncStep)) * nth);
-
-#pragma omp parallel num_threads(nth)
- {
- try
- {
- int b0, b1, b;
- int i0, i1;
- int group_size, th;
-
- th = gmx_omp_get_thread_num();
-
- for (group_size = 2; group_size < 2 * next_pow2; group_size *= 2)
- {
- int index[2], group_pos, partner_pos, wu;
- int partner_th = th ^ (group_size / 2);
-
- if (group_size > 2)
- {
-#ifdef TMPI_ATOMICS
- /* wait on partner thread - replaces full barrier */
- int sync_th, sync_group_size;
-
-# if defined(__clang__) && __clang_major__ >= 8
- // Suppress warnings that the use of memory_barrier may be excessive
- // Only exists beginning with clang-8
-# pragma clang diagnostic push
-# pragma clang diagnostic ignored "-Watomic-implicit-seq-cst"
-# endif
-
- tMPI_Atomic_memory_barrier(); /* guarantee data is saved before marking work as done */
- tMPI_Atomic_set(&(nbat->syncStep[th]), group_size / 2); /* mark previous step as completed */
-
- /* find thread to sync with. Equal to partner_th unless nth is not a power of two. */
- for (sync_th = partner_th, sync_group_size = group_size;
- sync_th >= nth && sync_group_size > 2; sync_group_size /= 2)
- {
- sync_th &= ~(sync_group_size / 4);
- }
- if (sync_th < nth) /* otherwise nothing to sync index[1] will be >=nout */
- {
- /* wait on the thread which computed input data in previous step */
- while (tMPI_Atomic_get(static_cast<volatile tMPI_Atomic_t*>(&(nbat->syncStep[sync_th])))
- < group_size / 2)
- {
- gmx_pause();
- }
- /* guarantee that no later load happens before wait loop is finisehd */
- tMPI_Atomic_memory_barrier();
- }
-# if defined(__clang__) && __clang_major__ >= 8
-# pragma clang diagnostic pop
-# endif
-#else /* TMPI_ATOMICS */
-# pragma omp barrier
-#endif
- }
-
- /* Calculate buffers to sum (result goes into first buffer) */
- group_pos = th % group_size;
- index[0] = th - group_pos;
- index[1] = index[0] + group_size / 2;
-
- /* If no second buffer, nothing to do */
- if (index[1] >= numOutputBuffers && group_size > 2)
- {
- continue;
- }
-
-#if NBNXN_BUFFERFLAG_MAX_THREADS > 256
-# error reverse_bits assumes max 256 threads
-#endif
- /* Position is permuted so that one of the 2 vectors being added was computed on the same thread in the previous step.
- This improves locality and enables to sync with just a single thread between steps (=the levels in the btree).
- The permutation which allows this corresponds to reversing the bits of the group position.
- */
- group_pos = reverse_bits(group_pos) / (256 / group_size);
-
- partner_pos = group_pos ^ 1;
-
- /* loop over two work-units (own and partner) */
- for (wu = 0; wu < 2; wu++)
- {
- if (wu == 1)
- {
- if (partner_th < nth)
- {
- break; /* partner exists we don't have to do his work */
- }
- else
- {
- group_pos = partner_pos;
- }
- }
-
- /* Calculate the cell-block range for our thread */
- b0 = (flags.size() * group_pos) / group_size;
- b1 = (flags.size() * (group_pos + 1)) / group_size;
-
- for (b = b0; b < b1; b++)
- {
- i0 = b * NBNXN_BUFFERFLAG_SIZE * nbat->fstride;
- i1 = (b + 1) * NBNXN_BUFFERFLAG_SIZE * nbat->fstride;
-
- if (bitmask_is_set(flags[b], index[1]) || group_size > 2)
- {
- const real* fIndex1 = nbat->out[index[1]].f.data();
-#if GMX_SIMD
- nbnxn_atomdata_reduce_reals_simd
-#else
- nbnxn_atomdata_reduce_reals
-#endif
- (nbat->out[index[0]].f.data(),
- bitmask_is_set(flags[b], index[0]) || group_size > 2, &fIndex1,
- 1, i0, i1);
- }
- else if (!bitmask_is_set(flags[b], index[0]))
- {
- nbnxn_atomdata_clear_reals(nbat->out[index[0]].f, i0, i1);
- }
- }
- }
- }
- }
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
- }
-}
-
-
-static void nbnxn_atomdata_add_nbat_f_to_f_stdreduce(nbnxn_atomdata_t* nbat, int nth)
+static void nbnxn_atomdata_add_nbat_f_to_f_reduce(nbnxn_atomdata_t* nbat, int nth)
{
#pragma omp parallel for num_threads(nth) schedule(static)
for (int th = 0; th < nth; th++)
{
try
{
- int nfptr;
const real* fptr[NBNXN_BUFFERFLAG_MAX_THREADS];
gmx::ArrayRef<const gmx_bitmask_t> flags = nbat->buffer_flags;
/* Calculate the cell-block range for our thread */
- int b0 = (flags.size() * th) / nth;
- int b1 = (flags.size() * (th + 1)) / nth;
+ const int b0 = (flags.size() * th) / nth;
+ const int b1 = (flags.size() * (th + 1)) / nth;
for (int b = b0; b < b1; b++)
{
- int i0 = b * NBNXN_BUFFERFLAG_SIZE * nbat->fstride;
- int i1 = (b + 1) * NBNXN_BUFFERFLAG_SIZE * nbat->fstride;
+ const int i0 = b * NBNXN_BUFFERFLAG_SIZE * nbat->fstride;
+ const int i1 = (b + 1) * NBNXN_BUFFERFLAG_SIZE * nbat->fstride;
- nfptr = 0;
+ int nfptr = 0;
for (gmx::index out = 1; out < gmx::ssize(nbat->out); out++)
{
if (bitmask_is_set(flags[b], out))
return;
}
- int nth = gmx_omp_nthreads_get(emntNonbonded);
+ int nth = gmx_omp_nthreads_get(ModuleMultiThread::Nonbonded);
if (nbat->out.size() > 1)
{
/* Reduce the force thread output buffers into buffer 0, before adding
* them to the, differently ordered, "real" force buffer.
*/
- if (nbat->bUseTreeReduce)
- {
- nbnxn_atomdata_add_nbat_f_to_f_treereduce(nbat, nth);
- }
- else
- {
- nbnxn_atomdata_add_nbat_f_to_f_stdreduce(nbat, nth);
- }
+ nbnxn_atomdata_add_nbat_f_to_f_reduce(nbat, nth);
}
#pragma omp parallel for num_threads(nth) schedule(static)
for (int th = 0; th < nth; th++)
{
try
{
- nbnxn_atomdata_add_nbat_f_to_f_part(gridSet, *nbat, nbat->out[0], a0 + ((th + 0) * na) / nth,
- a0 + ((th + 1) * na) / nth, f);
+ nbnxn_atomdata_add_nbat_f_to_f_part(
+ gridSet, *nbat, nbat->out[0], a0 + ((th + 0) * na) / nth, a0 + ((th + 1) * na) / nth, f);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
{
gmx::ArrayRef<const nbnxn_atomdata_output_t> outputBuffers = nbat.out;
- for (int s = 0; s < SHIFTS; s++)
+ for (int s = 0; s < gmx::c_numShiftVectors; s++)
{
rvec sum;
clear_rvec(sum);
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gpu_utils/hostallocator.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/locality.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/bitmask.h"
#include "gromacs/utility/real.h"
struct NbnxmGpu;
struct nbnxn_atomdata_t;
struct nonbonded_verlet_t;
-struct tMPI_Atomic;
class GpuEventSynchronizer;
//! f, size natoms*fstride
gmx::HostVector<real> f;
- //! Shift force array, size SHIFTS*DIM
+ //! Shift force array, size c_numShiftVectors*DIM
gmx::HostVector<real> fshift;
//! Temporary Van der Waals group energy storage
gmx::HostVector<real> Vvdw;
#define NBNXN_BUFFERFLAG_MAX_THREADS (BITMASK_SIZE)
-/*! \brief LJ combination rules: geometric, Lorentz-Berthelot, none */
-enum
+//! LJ combination rules
+enum class LJCombinationRule : int
{
- ljcrGEOM,
- ljcrLB,
- ljcrNONE,
- ljcrNR
+ //! Geometric
+ Geometric,
+ //! Lorentz-Berthelot
+ LorentzBerthelot,
+ //! No rule
+ None,
+ //! Size of the enum
+ Count
};
+//! String corresponding to LJ combination rule
+const char* enumValueToString(LJCombinationRule enumValue);
+
/*! \internal
* \brief Struct that stores atom related data for the nbnxn module
*
//! Lennard-Jone 6*C6 and 12*C12 parameters, size numTypes*2*2
gmx::HostVector<real> nbfp;
//! Combination rule, see enum defined above
- int comb_rule;
+ LJCombinationRule ljCombinationRule;
//! LJ parameters per atom type, size numTypes*2
gmx::HostVector<real> nbfp_comb;
//! As nbfp, but with a stride for the present SIMD architecture
/*! \brief Constructor
*
- * \param[in] pinningPolicy Sets the pinning policy for all data that might be transfered to a GPU
+ * \param[in] pinningPolicy Sets the pinning policy for all data that might be transferred
+ * to a GPU
+ * \param[in] mdlog The logger
+ * \param[in] kernelType Nonbonded NxN kernel type
+ * \param[in] enbnxninitcombrule LJ combination rule
+ * \param[in] ntype Number of atom types
+ * \param[in] nbfp Non-bonded force parameters
+ * \param[in] n_energygroups Number of energy groups
+ * \param[in] nout Number of output data structures
*/
- nbnxn_atomdata_t(gmx::PinningPolicy pinningPolicy);
+ nbnxn_atomdata_t(gmx::PinningPolicy pinningPolicy,
+ const gmx::MDLogger& mdlog,
+ Nbnxm::KernelType kernelType,
+ int enbnxninitcombrule,
+ int ntype,
+ gmx::ArrayRef<const real> nbfp,
+ int n_energygroups,
+ int nout);
//! Returns a const reference to the parameters
const Params& params() const { return params_; }
//! The format of f, enum
int FFormat;
//! Do we need to update shift_vec every step?
- gmx_bool bDynamicBox;
+ bool bDynamicBox;
//! Shift vectors, copied from t_forcerec
gmx::HostVector<gmx::RVec> shift_vec;
//! stride for a coordinate in x (usually 3 or 4)
//! Reduction related data
//! \{
//! Use the flags or operate on all atoms
- gmx_bool bUseBufferFlags;
+ bool bUseBufferFlags;
//! Flags for buffer zeroing+reduc.
std::vector<gmx_bitmask_t> buffer_flags;
- //! Use tree for force reduction
- gmx_bool bUseTreeReduce;
- //! Synchronization step for tree reduce
- tMPI_Atomic* syncStep;
//! \}
};
enbnxninitcombruleNONE
};
-/*! \brief Initialize the non-bonded atom data structure.
- *
- * The enum for nbatXFormat is in the file defining nbnxn_atomdata_t.
- * Copy the ntypes*ntypes*2 sized nbfp non-bonded parameter list
- * to the atom data structure.
- * enbnxninitcombrule sets what combination rule data gets stored in nbat.
- */
-void nbnxn_atomdata_init(const gmx::MDLogger& mdlog,
- nbnxn_atomdata_t* nbat,
- Nbnxm::KernelType kernelType,
- int enbnxninitcombrule,
- int ntype,
- gmx::ArrayRef<const real> nbfp,
- int n_energygroups,
- int nout);
-
//! Sets the atomdata after pair search
void nbnxn_atomdata_set(nbnxn_atomdata_t* nbat,
const Nbnxm::GridSet& gridSet,
gmx::ArrayRef<const int> atomInfo);
//! Copy the shift vectors to nbat
-void nbnxn_atomdata_copy_shiftvec(gmx_bool dynamic_box, rvec* shift_vec, nbnxn_atomdata_t* nbat);
+void nbnxn_atomdata_copy_shiftvec(bool dynamic_box, gmx::ArrayRef<gmx::RVec> shift_vec, nbnxn_atomdata_t* nbat);
/*! \brief Transform coordinates to xbat layout
*
*
* \param[in] gridSet The grids data.
* \param[in] locality If the transformation should be applied to local or non local coordinates.
- * \param[in] fillLocal Tells if the local filler particle coordinates should be zeroed.
* \param[in] coordinates Coordinates in plain rvec format.
* \param[in,out] nbat Data in NBNXM format, used for mapping formats and to locate the output buffer.
*/
void nbnxn_atomdata_copy_x_to_nbat_x(const Nbnxm::GridSet& gridSet,
gmx::AtomLocality locality,
- bool fillLocal,
const rvec* coordinates,
nbnxn_atomdata_t* nbat);
*
* \param[in] gridSet The grids data.
* \param[in] locality If the transformation should be applied to local or non local coordinates.
- * \param[in] fillLocal Tells if the local filler particle coordinates should be zeroed.
* \param[in,out] gpu_nbv The NBNXM GPU data structure.
* \param[in] d_x Coordinates to be copied (in plain rvec format).
* \param[in] xReadyOnDevice Event synchronizer indicating that the coordinates are ready in the device memory.
*/
void nbnxn_atomdata_x_to_nbat_x_gpu(const Nbnxm::GridSet& gridSet,
gmx::AtomLocality locality,
- bool fillLocal,
NbnxmGpu* gpu_nbv,
DeviceBuffer<gmx::RVec> d_x,
GpuEventSynchronizer* xReadyOnDevice);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <optional>
#include "gromacs/gmxlib/nrnb.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vectypes.h"
#include "gromacs/mdlib/dispersioncorrection.h"
#include "gromacs/mdlib/force_flags.h"
#include "gromacs/mdlib/forcerec.h"
{
interaction_const_t ic;
- ic.vdwtype = evdwCUT;
- ic.vdw_modifier = eintmodPOTSHIFT;
+ ic.vdwtype = VanDerWaalsType::Cut;
+ ic.vdw_modifier = InteractionModifiers::PotShift;
ic.rvdw = options.pairlistCutoff;
- ic.eeltype = (options.coulombType == BenchMarkCoulomb::Pme ? eelPME : eelRF);
- ic.coulomb_modifier = eintmodPOTSHIFT;
+ ic.eeltype = (options.coulombType == BenchMarkCoulomb::Pme ? CoulombInteractionType::Pme
+ : CoulombInteractionType::RF);
+ ic.coulomb_modifier = InteractionModifiers::PotShift;
ic.rcoulomb = options.pairlistCutoff;
- // Reaction-field with epsilon_rf=inf
+ // Reaction-field with reactionFieldPermitivity=inf
// TODO: Replace by calc_rffac() after refactoring that
- ic.k_rf = 0.5 * std::pow(ic.rcoulomb, -3);
- ic.c_rf = 1 / ic.rcoulomb + ic.k_rf * ic.rcoulomb * ic.rcoulomb;
+ ic.reactionFieldCoefficient = 0.5 * std::pow(ic.rcoulomb, -3);
+ ic.reactionFieldShift = 1 / ic.rcoulomb + ic.reactionFieldCoefficient * ic.rcoulomb * ic.rcoulomb;
if (EEL_PME_EWALD(ic.eeltype))
{
PairlistParams pairlistParams(kernelSetup.kernelType, false, options.pairlistCutoff, false);
- GridSet gridSet(PbcType::Xyz, false, nullptr, nullptr, pairlistParams.pairlistType, false,
- numThreads, pinPolicy);
+ GridSet gridSet(
+ PbcType::Xyz, false, nullptr, nullptr, pairlistParams.pairlistType, false, numThreads, pinPolicy);
auto pairlistSets = std::make_unique<PairlistSets>(pairlistParams, false, 0);
- auto pairSearch =
- std::make_unique<PairSearch>(PbcType::Xyz, false, nullptr, nullptr,
- pairlistParams.pairlistType, false, numThreads, pinPolicy);
+ auto pairSearch = std::make_unique<PairSearch>(
+ PbcType::Xyz, false, nullptr, nullptr, pairlistParams.pairlistType, false, numThreads, pinPolicy);
- auto atomData = std::make_unique<nbnxn_atomdata_t>(pinPolicy);
+ auto atomData = std::make_unique<nbnxn_atomdata_t>(pinPolicy,
+ gmx::MDLogger(),
+ kernelSetup.kernelType,
+ combinationRule,
+ system.numAtomTypes,
+ system.nonbondedParameters,
+ 1,
+ numThreads);
// Put everything together
- auto nbv = std::make_unique<nonbonded_verlet_t>(std::move(pairlistSets), std::move(pairSearch),
- std::move(atomData), kernelSetup, nullptr, nullptr);
-
- nbnxn_atomdata_init(gmx::MDLogger(), nbv->nbat.get(), kernelSetup.kernelType, combinationRule,
- system.numAtomTypes, system.nonbondedParameters, 1, numThreads);
+ auto nbv = std::make_unique<nonbonded_verlet_t>(
+ std::move(pairlistSets), std::move(pairSearch), std::move(atomData), kernelSetup, nullptr, nullptr);
t_nrnb nrnb;
const real atomDensity = system.coordinates.size() / det(system.box);
- nbnxn_put_on_grid(nbv.get(), system.box, 0, lowerCorner, upperCorner, nullptr,
- { 0, int(system.coordinates.size()) }, atomDensity, atomInfo,
- system.coordinates, 0, nullptr);
+ nbnxn_put_on_grid(nbv.get(),
+ system.box,
+ 0,
+ lowerCorner,
+ upperCorner,
+ nullptr,
+ { 0, int(system.coordinates.size()) },
+ atomDensity,
+ atomInfo,
+ system.coordinates,
+ 0,
+ nullptr);
nbv->constructPairlist(gmx::InteractionLocality::Local, system.excls, 0, &nrnb);
stepWork.computeEnergy = true;
}
- const gmx::EnumerationArray<BenchMarkKernels, std::string> kernelNames = { "auto", "no", "4xM",
- "2xMM" };
+ const gmx::EnumerationArray<BenchMarkKernels, std::string> kernelNames = {
+ "auto", "no", "4xM", "2xMM"
+ };
- const gmx::EnumerationArray<BenchMarkCombRule, std::string> combruleNames = { "geom.", "LB",
+ const gmx::EnumerationArray<BenchMarkCombRule, std::string> combruleNames = { "geom.",
+ "LB",
"none" };
if (!doWarmup)
{
- fprintf(stdout, "%-7s %-4s %-5s %-4s ",
+ fprintf(stdout,
+ "%-7s %-4s %-5s %-4s ",
options.coulombType == BenchMarkCoulomb::Pme ? "Ewald" : "RF",
options.useHalfLJOptimization ? "half" : "all",
- combruleNames[options.ljCombinationRule].c_str(), kernelNames[options.nbnxmSimd].c_str());
+ combruleNames[options.ljCombinationRule].c_str(),
+ kernelNames[options.nbnxmSimd].c_str());
if (!options.outputFile.empty())
{
fprintf(system.csv,
#else
0,
#endif
- system.coordinates.size(), options.pairlistCutoff, options.numThreads,
- options.numIterations, options.computeVirialAndEnergy ? "yes" : "no",
+ system.coordinates.size(),
+ options.pairlistCutoff,
+ options.numThreads,
+ options.numIterations,
+ options.computeVirialAndEnergy ? "yes" : "no",
(options.coulombType != BenchMarkCoulomb::ReactionField)
? ((options.nbnxmSimd == BenchMarkKernels::SimdNo || options.useTabulatedEwaldCorr)
? "table"
// Run pre-iteration to avoid cache misses
for (int iter = 0; iter < options.numPreIterations; iter++)
{
- nbv->dispatchNonbondedKernel(gmx::InteractionLocality::Local, ic, stepWork, enbvClearFYes,
- system.forceRec, &enerd, &nrnb);
+ nbv->dispatchNonbondedKernel(
+ gmx::InteractionLocality::Local,
+ ic,
+ stepWork,
+ enbvClearFYes,
+ system.forceRec.shift_vec,
+ enerd.grpp.energyGroupPairTerms[system.forceRec.haveBuckingham ? NonBondedEnergyTerms::BuckinghamSR
+ : NonBondedEnergyTerms::LJSR],
+ enerd.grpp.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR],
+ &nrnb);
}
const int numIterations = (doWarmup ? options.numWarmupIterations : options.numIterations);
for (int iter = 0; iter < numIterations; iter++)
{
// Run the kernel without force clearing
- nbv->dispatchNonbondedKernel(gmx::InteractionLocality::Local, ic, stepWork, enbvClearFNo,
- system.forceRec, &enerd, &nrnb);
+ nbv->dispatchNonbondedKernel(
+ gmx::InteractionLocality::Local,
+ ic,
+ stepWork,
+ enbvClearFNo,
+ system.forceRec.shift_vec,
+ enerd.grpp.energyGroupPairTerms[system.forceRec.haveBuckingham ? NonBondedEnergyTerms::BuckinghamSR
+ : NonBondedEnergyTerms::LJSR],
+ enerd.grpp.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR],
+ &nrnb);
}
cycles = gmx_cycles_read() - cycles;
if (!doWarmup)
const double uSec = static_cast<double>(cycles) * gmx_cycles_calibrate(1.0) * 1.e6;
if (options.cyclesPerPair)
{
- fprintf(stdout, "%13.2f %13.3f %10.3f %10.3f\n", uSec, uSec / options.numIterations,
+ fprintf(stdout,
+ "%13.2f %13.3f %10.3f %10.3f\n",
+ uSec,
+ uSec / options.numIterations,
uSec / (options.numIterations * numPairs),
uSec / (options.numIterations * numUsefulPairs));
if (!options.outputFile.empty())
{
- fprintf(system.csv, "\"%.3f\",\"%.4f\",\"%.4f\",\"%.4f\"\n", uSec,
- uSec / options.numIterations, uSec / (options.numIterations * numPairs),
+ fprintf(system.csv,
+ "\"%.3f\",\"%.4f\",\"%.4f\",\"%.4f\"\n",
+ uSec,
+ uSec / options.numIterations,
+ uSec / (options.numIterations * numPairs),
uSec / (options.numIterations * numUsefulPairs));
}
}
else
{
- fprintf(stdout, "%13.2f %13.3f %10.3f %10.3f\n", uSec, uSec / options.numIterations,
+ fprintf(stdout,
+ "%13.2f %13.3f %10.3f %10.3f\n",
+ uSec,
+ uSec / options.numIterations,
options.numIterations * numPairs / uSec,
options.numIterations * numUsefulPairs / uSec);
if (!options.outputFile.empty())
{
- fprintf(system.csv, "\"%.3f\",\"%.4f\",\"%.4f\",\"%.4f\"\n", uSec,
- uSec / options.numIterations, options.numIterations * numPairs / uSec,
+ fprintf(system.csv,
+ "\"%.3f\",\"%.4f\",\"%.4f\",\"%.4f\"\n",
+ uSec,
+ uSec / options.numIterations,
+ options.numIterations * numPairs / uSec,
options.numIterations * numUsefulPairs / uSec);
}
}
const double dCycles = static_cast<double>(cycles);
if (options.cyclesPerPair)
{
- fprintf(stdout, "%10.3f %10.4f %8.4f %8.4f\n", cycles * 1e-6,
+ fprintf(stdout,
+ "%10.3f %10.4f %8.4f %8.4f\n",
+ cycles * 1e-6,
dCycles / options.numIterations * 1e-6,
dCycles / (options.numIterations * numPairs),
dCycles / (options.numIterations * numUsefulPairs));
}
else
{
- fprintf(stdout, "%10.3f %10.4f %8.4f %8.4f\n", dCycles * 1e-6,
- dCycles / options.numIterations * 1e-6, options.numIterations * numPairs / dCycles,
+ fprintf(stdout,
+ "%10.3f %10.4f %8.4f %8.4f\n",
+ dCycles * 1e-6,
+ dCycles / options.numIterations * 1e-6,
+ options.numIterations * numPairs / dCycles,
options.numIterations * numUsefulPairs / dCycles);
}
}
void bench(const int sizeFactor, const KernelBenchOptions& options)
{
// We don't want to call gmx_omp_nthreads_init(), so we init what we need
- gmx_omp_nthreads_set(emntPairsearch, options.numThreads);
- gmx_omp_nthreads_set(emntNonbonded, options.numThreads);
+ gmx_omp_nthreads_set(ModuleMultiThread::Pairsearch, options.numThreads);
+ gmx_omp_nthreads_set(ModuleMultiThread::Nonbonded, options.numThreads);
const gmx::BenchmarkSystem system(sizeFactor, options.outputFile);
fprintf(stdout, "Compute energies: %s\n", options.computeVirialAndEnergy ? "yes" : "no");
if (options.coulombType != BenchMarkCoulomb::ReactionField)
{
- fprintf(stdout, "Ewald excl. corr.: %s\n",
+ fprintf(stdout,
+ "Ewald excl. corr.: %s\n",
options.nbnxmSimd == BenchMarkKernels::SimdNo || options.useTabulatedEwaldCorr
? "table"
: "analytical");
if (options.reportTime)
{
- fprintf(stdout, "Coulomb LJ comb. SIMD usec usec/it. %s\n",
+ fprintf(stdout,
+ "Coulomb LJ comb. SIMD usec usec/it. %s\n",
options.cyclesPerPair ? "usec/pair" : "pairs/usec");
if (!options.outputFile.empty())
{
}
else
{
- fprintf(stdout, "Coulomb LJ comb. SIMD Mcycles Mcycles/it. %s\n",
+ fprintf(stdout,
+ "Coulomb LJ comb. SIMD Mcycles Mcycles/it. %s\n",
options.cyclesPerPair ? "cycles/pair" : "pairs/cycle");
if (!options.outputFile.empty())
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
// A fatal error is generated when this is not the case.
static void generateCoordinates(int multiplicationFactor, std::vector<gmx::RVec>* coordinates, matrix box)
{
- if (multiplicationFactor < 1 || (multiplicationFactor & (multiplicationFactor - 1)) != 0)
+ if (!gmx::isPowerOfTwo(multiplicationFactor))
{
gmx_fatal(FARGS, "The size factor has to be a power of 2");
}
dim = 0;
}
}
- printf("Stacking a box of %zu atoms %d x %d x %d times\n", coordinates1000.size(), factors[XX],
- factors[YY], factors[ZZ]);
+ printf("Stacking a box of %zu atoms %d x %d x %d times\n",
+ coordinates1000.size(),
+ factors[XX],
+ factors[YY],
+ factors[ZZ]);
coordinates->resize(factors[XX] * factors[YY] * factors[ZZ] * coordinates1000.size());
forceRec.ntype = numAtomTypes;
forceRec.nbfp = nonbondedParameters;
- snew(forceRec.shift_vec, SHIFTS);
+ forceRec.shift_vec.resize(gmx::c_numShiftVectors);
calc_shifts(box, forceRec.shift_vec);
if (!outputFile.empty())
{
#elif GMX_SIMD && GMX_SIMD_REAL_WIDTH == 8
return ClusterDistanceKernelType::CpuSimd_2xMM;
#else
- GMX_RELEASE_ASSERT(false,
- "Expect 4-wide or 8-wide SIMD with 4x4 list and nbat SIMD layout");
+ GMX_RELEASE_ASSERT(false, "Expect 4-wide or 8-wide SIMD with 4x4 list and nbat SIMD layout");
#endif
}
else
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \param[in] numColumns Extent of cell-level parallelism.
* \param[out] gm_xq Coordinates buffer in nbnxm layout.
- * \tparam setFillerCoords Whether to set the coordinates of the filler particles.
* \param[in] gm_x Coordinates buffer.
* \param[in] gm_atomIndex Atom index mapping.
* \param[in] gm_numAtoms Array of number of atoms.
* \param[in] cellOffset First cell.
* \param[in] numAtomsPerCell Number of atoms per cell.
*/
-template<bool setFillerCoords>
static __global__ void nbnxn_gpu_x_to_nbat_x_kernel(int numColumns,
float4* __restrict__ gm_xq,
const float3* __restrict__ gm_x,
const int numAtoms = gm_numAtoms[cxy];
const int offset = (cellOffset + gm_cellIndex[cxy]) * numAtomsPerCell;
- int numAtomsRounded;
- if (setFillerCoords)
- {
- // TODO: This can be done more efficiently
- numAtomsRounded = (gm_cellIndex[cxy + 1] - gm_cellIndex[cxy]) * numAtomsPerCell;
- }
- else
- {
- // We fill only the real particle locations.
- // We assume the filling entries at the end have been
- // properly set before during pair-list generation.
- numAtomsRounded = numAtoms;
- }
const int threadIndex = blockIdx.x * blockDim.x + threadIdx.x;
float3* gm_xqDest = (float3*)&gm_xq[threadIndex + offset];
// Perform layout conversion of each element.
- if (threadIndex < numAtomsRounded)
+ if (threadIndex < numAtoms)
{
if (threadIndex < numAtoms)
{
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
constexpr static int c_bufOpsThreadsPerBlock = 128;
/*! Nonbonded kernel function pointer type */
-typedef void (*nbnxn_cu_kfunc_ptr_t)(const cu_atomdata_t, const NBParamGpu, const gpu_plist, bool);
+typedef void (*nbnxn_cu_kfunc_ptr_t)(const NBAtomDataGpu, const NBParamGpu, const gpu_plist, bool);
/*********************************/
"Watch out, the input system is too large to simulate!\n"
"The number of nonbonded work units (=number of super-clusters) exceeds the"
"maximum grid size in x dimension (%d > %d)!",
- nwork_units, max_grid_x_size);
+ nwork_units,
+ max_grid_x_size);
}
return nwork_units;
*/
/*! Force-only kernel function pointers. */
-static const nbnxn_cu_kfunc_ptr_t nb_kfunc_noener_noprune_ptr[eelTypeNR][evdwTypeNR] = {
- { nbnxn_kernel_ElecCut_VdwLJ_F_cuda, nbnxn_kernel_ElecCut_VdwLJCombGeom_F_cuda,
- nbnxn_kernel_ElecCut_VdwLJCombLB_F_cuda, nbnxn_kernel_ElecCut_VdwLJFsw_F_cuda,
- nbnxn_kernel_ElecCut_VdwLJPsw_F_cuda, nbnxn_kernel_ElecCut_VdwLJEwCombGeom_F_cuda,
+static const nbnxn_cu_kfunc_ptr_t nb_kfunc_noener_noprune_ptr[c_numElecTypes][c_numVdwTypes] = {
+ { nbnxn_kernel_ElecCut_VdwLJ_F_cuda,
+ nbnxn_kernel_ElecCut_VdwLJCombGeom_F_cuda,
+ nbnxn_kernel_ElecCut_VdwLJCombLB_F_cuda,
+ nbnxn_kernel_ElecCut_VdwLJFsw_F_cuda,
+ nbnxn_kernel_ElecCut_VdwLJPsw_F_cuda,
+ nbnxn_kernel_ElecCut_VdwLJEwCombGeom_F_cuda,
nbnxn_kernel_ElecCut_VdwLJEwCombLB_F_cuda },
- { nbnxn_kernel_ElecRF_VdwLJ_F_cuda, nbnxn_kernel_ElecRF_VdwLJCombGeom_F_cuda,
- nbnxn_kernel_ElecRF_VdwLJCombLB_F_cuda, nbnxn_kernel_ElecRF_VdwLJFsw_F_cuda,
- nbnxn_kernel_ElecRF_VdwLJPsw_F_cuda, nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_cuda,
+ { nbnxn_kernel_ElecRF_VdwLJ_F_cuda,
+ nbnxn_kernel_ElecRF_VdwLJCombGeom_F_cuda,
+ nbnxn_kernel_ElecRF_VdwLJCombLB_F_cuda,
+ nbnxn_kernel_ElecRF_VdwLJFsw_F_cuda,
+ nbnxn_kernel_ElecRF_VdwLJPsw_F_cuda,
+ nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_cuda,
nbnxn_kernel_ElecRF_VdwLJEwCombLB_F_cuda },
- { nbnxn_kernel_ElecEwQSTab_VdwLJ_F_cuda, nbnxn_kernel_ElecEwQSTab_VdwLJCombGeom_F_cuda,
- nbnxn_kernel_ElecEwQSTab_VdwLJCombLB_F_cuda, nbnxn_kernel_ElecEwQSTab_VdwLJFsw_F_cuda,
- nbnxn_kernel_ElecEwQSTab_VdwLJPsw_F_cuda, nbnxn_kernel_ElecEwQSTab_VdwLJEwCombGeom_F_cuda,
+ { nbnxn_kernel_ElecEwQSTab_VdwLJ_F_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJCombGeom_F_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJCombLB_F_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJFsw_F_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJPsw_F_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJEwCombGeom_F_cuda,
nbnxn_kernel_ElecEwQSTab_VdwLJEwCombLB_F_cuda },
- { nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJ_F_cuda, nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJCombGeom_F_cuda,
- nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJCombLB_F_cuda, nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJFsw_F_cuda,
- nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJPsw_F_cuda, nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombGeom_F_cuda,
+ { nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJ_F_cuda,
+ nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJCombGeom_F_cuda,
+ nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJCombLB_F_cuda,
+ nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJFsw_F_cuda,
+ nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJPsw_F_cuda,
+ nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombGeom_F_cuda,
nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombLB_F_cuda },
- { nbnxn_kernel_ElecEw_VdwLJ_F_cuda, nbnxn_kernel_ElecEw_VdwLJCombGeom_F_cuda,
- nbnxn_kernel_ElecEw_VdwLJCombLB_F_cuda, nbnxn_kernel_ElecEw_VdwLJFsw_F_cuda,
- nbnxn_kernel_ElecEw_VdwLJPsw_F_cuda, nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_cuda,
+ { nbnxn_kernel_ElecEw_VdwLJ_F_cuda,
+ nbnxn_kernel_ElecEw_VdwLJCombGeom_F_cuda,
+ nbnxn_kernel_ElecEw_VdwLJCombLB_F_cuda,
+ nbnxn_kernel_ElecEw_VdwLJFsw_F_cuda,
+ nbnxn_kernel_ElecEw_VdwLJPsw_F_cuda,
+ nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_cuda,
nbnxn_kernel_ElecEw_VdwLJEwCombLB_F_cuda },
- { nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_cuda, nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_cuda,
- nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_cuda, nbnxn_kernel_ElecEwTwinCut_VdwLJFsw_F_cuda,
- nbnxn_kernel_ElecEwTwinCut_VdwLJPsw_F_cuda, nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_cuda,
+ { nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_cuda,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_cuda,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_cuda,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJFsw_F_cuda,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJPsw_F_cuda,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_cuda,
nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombLB_F_cuda }
};
/*! Force + energy kernel function pointers. */
-static const nbnxn_cu_kfunc_ptr_t nb_kfunc_ener_noprune_ptr[eelTypeNR][evdwTypeNR] = {
- { nbnxn_kernel_ElecCut_VdwLJ_VF_cuda, nbnxn_kernel_ElecCut_VdwLJCombGeom_VF_cuda,
- nbnxn_kernel_ElecCut_VdwLJCombLB_VF_cuda, nbnxn_kernel_ElecCut_VdwLJFsw_VF_cuda,
- nbnxn_kernel_ElecCut_VdwLJPsw_VF_cuda, nbnxn_kernel_ElecCut_VdwLJEwCombGeom_VF_cuda,
+static const nbnxn_cu_kfunc_ptr_t nb_kfunc_ener_noprune_ptr[c_numElecTypes][c_numVdwTypes] = {
+ { nbnxn_kernel_ElecCut_VdwLJ_VF_cuda,
+ nbnxn_kernel_ElecCut_VdwLJCombGeom_VF_cuda,
+ nbnxn_kernel_ElecCut_VdwLJCombLB_VF_cuda,
+ nbnxn_kernel_ElecCut_VdwLJFsw_VF_cuda,
+ nbnxn_kernel_ElecCut_VdwLJPsw_VF_cuda,
+ nbnxn_kernel_ElecCut_VdwLJEwCombGeom_VF_cuda,
nbnxn_kernel_ElecCut_VdwLJEwCombLB_VF_cuda },
- { nbnxn_kernel_ElecRF_VdwLJ_VF_cuda, nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_cuda,
- nbnxn_kernel_ElecRF_VdwLJCombLB_VF_cuda, nbnxn_kernel_ElecRF_VdwLJFsw_VF_cuda,
- nbnxn_kernel_ElecRF_VdwLJPsw_VF_cuda, nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_cuda,
+ { nbnxn_kernel_ElecRF_VdwLJ_VF_cuda,
+ nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_cuda,
+ nbnxn_kernel_ElecRF_VdwLJCombLB_VF_cuda,
+ nbnxn_kernel_ElecRF_VdwLJFsw_VF_cuda,
+ nbnxn_kernel_ElecRF_VdwLJPsw_VF_cuda,
+ nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_cuda,
nbnxn_kernel_ElecRF_VdwLJEwCombLB_VF_cuda },
- { nbnxn_kernel_ElecEwQSTab_VdwLJ_VF_cuda, nbnxn_kernel_ElecEwQSTab_VdwLJCombGeom_VF_cuda,
- nbnxn_kernel_ElecEwQSTab_VdwLJCombLB_VF_cuda, nbnxn_kernel_ElecEwQSTab_VdwLJFsw_VF_cuda,
- nbnxn_kernel_ElecEwQSTab_VdwLJPsw_VF_cuda, nbnxn_kernel_ElecEwQSTab_VdwLJEwCombGeom_VF_cuda,
+ { nbnxn_kernel_ElecEwQSTab_VdwLJ_VF_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJCombGeom_VF_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJCombLB_VF_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJFsw_VF_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJPsw_VF_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJEwCombGeom_VF_cuda,
nbnxn_kernel_ElecEwQSTab_VdwLJEwCombLB_VF_cuda },
- { nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJ_VF_cuda, nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJCombGeom_VF_cuda,
- nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJCombLB_VF_cuda, nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJFsw_VF_cuda,
- nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJPsw_VF_cuda, nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombGeom_VF_cuda,
+ { nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJ_VF_cuda,
+ nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJCombGeom_VF_cuda,
+ nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJCombLB_VF_cuda,
+ nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJFsw_VF_cuda,
+ nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJPsw_VF_cuda,
+ nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombGeom_VF_cuda,
nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombLB_VF_cuda },
- { nbnxn_kernel_ElecEw_VdwLJ_VF_cuda, nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_cuda,
- nbnxn_kernel_ElecEw_VdwLJCombLB_VF_cuda, nbnxn_kernel_ElecEw_VdwLJFsw_VF_cuda,
- nbnxn_kernel_ElecEw_VdwLJPsw_VF_cuda, nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_cuda,
+ { nbnxn_kernel_ElecEw_VdwLJ_VF_cuda,
+ nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_cuda,
+ nbnxn_kernel_ElecEw_VdwLJCombLB_VF_cuda,
+ nbnxn_kernel_ElecEw_VdwLJFsw_VF_cuda,
+ nbnxn_kernel_ElecEw_VdwLJPsw_VF_cuda,
+ nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_cuda,
nbnxn_kernel_ElecEw_VdwLJEwCombLB_VF_cuda },
- { nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_cuda, nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_cuda,
- nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_cuda, nbnxn_kernel_ElecEwTwinCut_VdwLJFsw_VF_cuda,
- nbnxn_kernel_ElecEwTwinCut_VdwLJPsw_VF_cuda, nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_cuda,
+ { nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_cuda,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_cuda,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_cuda,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJFsw_VF_cuda,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJPsw_VF_cuda,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_cuda,
nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombLB_VF_cuda }
};
/*! Force + pruning kernel function pointers. */
-static const nbnxn_cu_kfunc_ptr_t nb_kfunc_noener_prune_ptr[eelTypeNR][evdwTypeNR] = {
- { nbnxn_kernel_ElecCut_VdwLJ_F_prune_cuda, nbnxn_kernel_ElecCut_VdwLJCombGeom_F_prune_cuda,
- nbnxn_kernel_ElecCut_VdwLJCombLB_F_prune_cuda, nbnxn_kernel_ElecCut_VdwLJFsw_F_prune_cuda,
- nbnxn_kernel_ElecCut_VdwLJPsw_F_prune_cuda, nbnxn_kernel_ElecCut_VdwLJEwCombGeom_F_prune_cuda,
+static const nbnxn_cu_kfunc_ptr_t nb_kfunc_noener_prune_ptr[c_numElecTypes][c_numVdwTypes] = {
+ { nbnxn_kernel_ElecCut_VdwLJ_F_prune_cuda,
+ nbnxn_kernel_ElecCut_VdwLJCombGeom_F_prune_cuda,
+ nbnxn_kernel_ElecCut_VdwLJCombLB_F_prune_cuda,
+ nbnxn_kernel_ElecCut_VdwLJFsw_F_prune_cuda,
+ nbnxn_kernel_ElecCut_VdwLJPsw_F_prune_cuda,
+ nbnxn_kernel_ElecCut_VdwLJEwCombGeom_F_prune_cuda,
nbnxn_kernel_ElecCut_VdwLJEwCombLB_F_prune_cuda },
- { nbnxn_kernel_ElecRF_VdwLJ_F_prune_cuda, nbnxn_kernel_ElecRF_VdwLJCombGeom_F_prune_cuda,
- nbnxn_kernel_ElecRF_VdwLJCombLB_F_prune_cuda, nbnxn_kernel_ElecRF_VdwLJFsw_F_prune_cuda,
- nbnxn_kernel_ElecRF_VdwLJPsw_F_prune_cuda, nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_prune_cuda,
+ { nbnxn_kernel_ElecRF_VdwLJ_F_prune_cuda,
+ nbnxn_kernel_ElecRF_VdwLJCombGeom_F_prune_cuda,
+ nbnxn_kernel_ElecRF_VdwLJCombLB_F_prune_cuda,
+ nbnxn_kernel_ElecRF_VdwLJFsw_F_prune_cuda,
+ nbnxn_kernel_ElecRF_VdwLJPsw_F_prune_cuda,
+ nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_prune_cuda,
nbnxn_kernel_ElecRF_VdwLJEwCombLB_F_prune_cuda },
- { nbnxn_kernel_ElecEwQSTab_VdwLJ_F_prune_cuda, nbnxn_kernel_ElecEwQSTab_VdwLJCombGeom_F_prune_cuda,
- nbnxn_kernel_ElecEwQSTab_VdwLJCombLB_F_prune_cuda, nbnxn_kernel_ElecEwQSTab_VdwLJFsw_F_prune_cuda,
- nbnxn_kernel_ElecEwQSTab_VdwLJPsw_F_prune_cuda, nbnxn_kernel_ElecEwQSTab_VdwLJEwCombGeom_F_prune_cuda,
+ { nbnxn_kernel_ElecEwQSTab_VdwLJ_F_prune_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJCombGeom_F_prune_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJCombLB_F_prune_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJFsw_F_prune_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJPsw_F_prune_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJEwCombGeom_F_prune_cuda,
nbnxn_kernel_ElecEwQSTab_VdwLJEwCombLB_F_prune_cuda },
{ nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJ_F_prune_cuda,
nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJCombGeom_F_prune_cuda,
nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJCombLB_F_prune_cuda,
- nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJFsw_F_prune_cuda, nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJPsw_F_prune_cuda,
+ nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJFsw_F_prune_cuda,
+ nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJPsw_F_prune_cuda,
nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombGeom_F_prune_cuda,
nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombLB_F_prune_cuda },
- { nbnxn_kernel_ElecEw_VdwLJ_F_prune_cuda, nbnxn_kernel_ElecEw_VdwLJCombGeom_F_prune_cuda,
- nbnxn_kernel_ElecEw_VdwLJCombLB_F_prune_cuda, nbnxn_kernel_ElecEw_VdwLJFsw_F_prune_cuda,
- nbnxn_kernel_ElecEw_VdwLJPsw_F_prune_cuda, nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_prune_cuda,
+ { nbnxn_kernel_ElecEw_VdwLJ_F_prune_cuda,
+ nbnxn_kernel_ElecEw_VdwLJCombGeom_F_prune_cuda,
+ nbnxn_kernel_ElecEw_VdwLJCombLB_F_prune_cuda,
+ nbnxn_kernel_ElecEw_VdwLJFsw_F_prune_cuda,
+ nbnxn_kernel_ElecEw_VdwLJPsw_F_prune_cuda,
+ nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_prune_cuda,
nbnxn_kernel_ElecEw_VdwLJEwCombLB_F_prune_cuda },
- { nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_prune_cuda, nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_prune_cuda,
- nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_prune_cuda, nbnxn_kernel_ElecEwTwinCut_VdwLJFsw_F_prune_cuda,
- nbnxn_kernel_ElecEwTwinCut_VdwLJPsw_F_prune_cuda, nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_prune_cuda,
+ { nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_prune_cuda,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_prune_cuda,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_prune_cuda,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJFsw_F_prune_cuda,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJPsw_F_prune_cuda,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_prune_cuda,
nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombLB_F_prune_cuda }
};
/*! Force + energy + pruning kernel function pointers. */
-static const nbnxn_cu_kfunc_ptr_t nb_kfunc_ener_prune_ptr[eelTypeNR][evdwTypeNR] = {
- { nbnxn_kernel_ElecCut_VdwLJ_VF_prune_cuda, nbnxn_kernel_ElecCut_VdwLJCombGeom_VF_prune_cuda,
- nbnxn_kernel_ElecCut_VdwLJCombLB_VF_prune_cuda, nbnxn_kernel_ElecCut_VdwLJFsw_VF_prune_cuda,
- nbnxn_kernel_ElecCut_VdwLJPsw_VF_prune_cuda, nbnxn_kernel_ElecCut_VdwLJEwCombGeom_VF_prune_cuda,
+static const nbnxn_cu_kfunc_ptr_t nb_kfunc_ener_prune_ptr[c_numElecTypes][c_numVdwTypes] = {
+ { nbnxn_kernel_ElecCut_VdwLJ_VF_prune_cuda,
+ nbnxn_kernel_ElecCut_VdwLJCombGeom_VF_prune_cuda,
+ nbnxn_kernel_ElecCut_VdwLJCombLB_VF_prune_cuda,
+ nbnxn_kernel_ElecCut_VdwLJFsw_VF_prune_cuda,
+ nbnxn_kernel_ElecCut_VdwLJPsw_VF_prune_cuda,
+ nbnxn_kernel_ElecCut_VdwLJEwCombGeom_VF_prune_cuda,
nbnxn_kernel_ElecCut_VdwLJEwCombLB_VF_prune_cuda },
- { nbnxn_kernel_ElecRF_VdwLJ_VF_prune_cuda, nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_prune_cuda,
- nbnxn_kernel_ElecRF_VdwLJCombLB_VF_prune_cuda, nbnxn_kernel_ElecRF_VdwLJFsw_VF_prune_cuda,
- nbnxn_kernel_ElecRF_VdwLJPsw_VF_prune_cuda, nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_prune_cuda,
+ { nbnxn_kernel_ElecRF_VdwLJ_VF_prune_cuda,
+ nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_prune_cuda,
+ nbnxn_kernel_ElecRF_VdwLJCombLB_VF_prune_cuda,
+ nbnxn_kernel_ElecRF_VdwLJFsw_VF_prune_cuda,
+ nbnxn_kernel_ElecRF_VdwLJPsw_VF_prune_cuda,
+ nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_prune_cuda,
nbnxn_kernel_ElecRF_VdwLJEwCombLB_VF_prune_cuda },
- { nbnxn_kernel_ElecEwQSTab_VdwLJ_VF_prune_cuda, nbnxn_kernel_ElecEwQSTab_VdwLJCombGeom_VF_prune_cuda,
- nbnxn_kernel_ElecEwQSTab_VdwLJCombLB_VF_prune_cuda, nbnxn_kernel_ElecEwQSTab_VdwLJFsw_VF_prune_cuda,
- nbnxn_kernel_ElecEwQSTab_VdwLJPsw_VF_prune_cuda, nbnxn_kernel_ElecEwQSTab_VdwLJEwCombGeom_VF_prune_cuda,
+ { nbnxn_kernel_ElecEwQSTab_VdwLJ_VF_prune_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJCombGeom_VF_prune_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJCombLB_VF_prune_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJFsw_VF_prune_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJPsw_VF_prune_cuda,
+ nbnxn_kernel_ElecEwQSTab_VdwLJEwCombGeom_VF_prune_cuda,
nbnxn_kernel_ElecEwQSTab_VdwLJEwCombLB_VF_prune_cuda },
{ nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJ_VF_prune_cuda,
nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJCombGeom_VF_prune_cuda,
nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJPsw_VF_prune_cuda,
nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombGeom_VF_prune_cuda,
nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombLB_VF_prune_cuda },
- { nbnxn_kernel_ElecEw_VdwLJ_VF_prune_cuda, nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_prune_cuda,
- nbnxn_kernel_ElecEw_VdwLJCombLB_VF_prune_cuda, nbnxn_kernel_ElecEw_VdwLJFsw_VF_prune_cuda,
- nbnxn_kernel_ElecEw_VdwLJPsw_VF_prune_cuda, nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_prune_cuda,
+ { nbnxn_kernel_ElecEw_VdwLJ_VF_prune_cuda,
+ nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_prune_cuda,
+ nbnxn_kernel_ElecEw_VdwLJCombLB_VF_prune_cuda,
+ nbnxn_kernel_ElecEw_VdwLJFsw_VF_prune_cuda,
+ nbnxn_kernel_ElecEw_VdwLJPsw_VF_prune_cuda,
+ nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_prune_cuda,
nbnxn_kernel_ElecEw_VdwLJEwCombLB_VF_prune_cuda },
- { nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_prune_cuda, nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_prune_cuda,
+ { nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_prune_cuda,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_prune_cuda,
nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_prune_cuda,
- nbnxn_kernel_ElecEwTwinCut_VdwLJFsw_VF_prune_cuda, nbnxn_kernel_ElecEwTwinCut_VdwLJPsw_VF_prune_cuda,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJFsw_VF_prune_cuda,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJPsw_VF_prune_cuda,
nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_prune_cuda,
nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombLB_VF_prune_cuda }
};
/*! Return a pointer to the kernel version to be executed at the current step. */
-static inline nbnxn_cu_kfunc_ptr_t select_nbnxn_kernel(int eeltype,
- int evdwtype,
+static inline nbnxn_cu_kfunc_ptr_t select_nbnxn_kernel(enum ElecType elecType,
+ enum VdwType vdwType,
bool bDoEne,
bool bDoPrune,
const DeviceInformation gmx_unused* deviceInfo)
{
- nbnxn_cu_kfunc_ptr_t res;
+ const int elecTypeIdx = static_cast<int>(elecType);
+ const int vdwTypeIdx = static_cast<int>(vdwType);
- GMX_ASSERT(eeltype < eelTypeNR,
+ GMX_ASSERT(elecTypeIdx < c_numElecTypes,
"The electrostatics type requested is not implemented in the CUDA kernels.");
- GMX_ASSERT(evdwtype < evdwTypeNR,
+ GMX_ASSERT(vdwTypeIdx < c_numVdwTypes,
"The VdW type requested is not implemented in the CUDA kernels.");
/* assert assumptions made by the kernels */
{
if (bDoPrune)
{
- res = nb_kfunc_ener_prune_ptr[eeltype][evdwtype];
+ return nb_kfunc_ener_prune_ptr[elecTypeIdx][vdwTypeIdx];
}
else
{
- res = nb_kfunc_ener_noprune_ptr[eeltype][evdwtype];
+ return nb_kfunc_ener_noprune_ptr[elecTypeIdx][vdwTypeIdx];
}
}
else
{
if (bDoPrune)
{
- res = nb_kfunc_noener_prune_ptr[eeltype][evdwtype];
+ return nb_kfunc_noener_prune_ptr[elecTypeIdx][vdwTypeIdx];
}
else
{
- res = nb_kfunc_noener_noprune_ptr[eeltype][evdwtype];
+ return nb_kfunc_noener_noprune_ptr[elecTypeIdx][vdwTypeIdx];
}
}
-
- return res;
}
/*! \brief Calculates the amount of shared memory required by the nonbonded kernel in use. */
/* cj in shared memory, for each warp separately */
shmem += num_threads_z * c_nbnxnGpuClusterpairSplit * c_nbnxnGpuJgroupSize * sizeof(int);
- if (nbp->vdwtype == evdwTypeCUTCOMBGEOM || nbp->vdwtype == evdwTypeCUTCOMBLB)
+ if (nbp->vdwType == VdwType::CutCombGeom || nbp->vdwType == VdwType::CutCombLB)
{
/* i-atom LJ combination parameters in shared memory */
shmem += c_nbnxnGpuNumClusterPerSupercluster * c_clSize * sizeof(float2);
return shmem;
}
-/*! \brief Sync the nonlocal stream with dependent tasks in the local queue.
- *
- * As the point where the local stream tasks can be considered complete happens
- * at the same call point where the nonlocal stream should be synced with the
- * the local, this function records the event if called with the local stream as
- * argument and inserts in the GPU stream a wait on the event on the nonlocal.
- */
-void nbnxnInsertNonlocalGpuDependency(const NbnxmGpu* nb, const InteractionLocality interactionLocality)
-{
- const DeviceStream& deviceStream = *nb->deviceStreams[interactionLocality];
-
- /* When we get here all misc operations issued in the local stream as well as
- the local xq H2D are done,
- so we record that in the local stream and wait for it in the nonlocal one.
- This wait needs to precede any PP tasks, bonded or nonbonded, that may
- compute on interactions between local and nonlocal atoms.
- */
- if (nb->bUseTwoStreams)
- {
- if (interactionLocality == InteractionLocality::Local)
- {
- cudaError_t stat = cudaEventRecord(nb->misc_ops_and_local_H2D_done, deviceStream.stream());
- CU_RET_ERR(stat, "cudaEventRecord on misc_ops_and_local_H2D_done failed");
- }
- else
- {
- cudaError_t stat =
- cudaStreamWaitEvent(deviceStream.stream(), nb->misc_ops_and_local_H2D_done, 0);
- CU_RET_ERR(stat, "cudaStreamWaitEvent on misc_ops_and_local_H2D_done failed");
- }
- }
-}
-
-/*! \brief Launch asynchronously the xq buffer host to device copy. */
-void gpu_copy_xq_to_gpu(NbnxmGpu* nb, const nbnxn_atomdata_t* nbatom, const AtomLocality atomLocality)
-{
- GMX_ASSERT(nb, "Need a valid nbnxn_gpu object");
-
- GMX_ASSERT(atomLocality == AtomLocality::Local || atomLocality == AtomLocality::NonLocal,
- "Only local and non-local xq transfers are supported");
-
- const InteractionLocality iloc = gpuAtomToInteractionLocality(atomLocality);
-
- int adat_begin, adat_len; /* local/nonlocal offset and length used for xq and f */
-
- cu_atomdata_t* adat = nb->atdat;
- gpu_plist* plist = nb->plist[iloc];
- cu_timers_t* t = nb->timers;
- const DeviceStream& deviceStream = *nb->deviceStreams[iloc];
-
- bool bDoTime = nb->bDoTime;
-
- /* Don't launch the non-local H2D copy if there is no dependent
- work to do: neither non-local nor other (e.g. bonded) work
- to do that has as input the nbnxn coordaintes.
- Doing the same for the local kernel is more complicated, since the
- local part of the force array also depends on the non-local kernel.
- So to avoid complicating the code and to reduce the risk of bugs,
- we always call the local local x+q copy (and the rest of the local
- work in nbnxn_gpu_launch_kernel().
- */
- if ((iloc == InteractionLocality::NonLocal) && !haveGpuShortRangeWork(*nb, iloc))
- {
- plist->haveFreshList = false;
-
- return;
- }
-
- /* calculate the atom data index range based on locality */
- if (atomLocality == AtomLocality::Local)
- {
- adat_begin = 0;
- adat_len = adat->natoms_local;
- }
- else
- {
- adat_begin = adat->natoms_local;
- adat_len = adat->natoms - adat->natoms_local;
- }
-
- /* HtoD x, q */
- /* beginning of timed HtoD section */
- if (bDoTime)
- {
- t->xf[atomLocality].nb_h2d.openTimingRegion(deviceStream);
- }
-
- static_assert(sizeof(adat->xq[0]) == sizeof(float4),
- "The size of the xyzq buffer element should be equal to the size of float4.");
- copyToDeviceBuffer(&adat->xq, reinterpret_cast<const float4*>(nbatom->x().data()) + adat_begin,
- adat_begin, adat_len, deviceStream, GpuApiCallBehavior::Async, nullptr);
-
- if (bDoTime)
- {
- t->xf[atomLocality].nb_h2d.closeTimingRegion(deviceStream);
- }
-
- /* When we get here all misc operations issued in the local stream as well as
- the local xq H2D are done,
- so we record that in the local stream and wait for it in the nonlocal one.
- This wait needs to precede any PP tasks, bonded or nonbonded, that may
- compute on interactions between local and nonlocal atoms.
- */
- nbnxnInsertNonlocalGpuDependency(nb, iloc);
-}
-
/*! As we execute nonbonded workload in separate streams, before launching
the kernel we need to make sure that he following operations have completed:
- atomdata allocation and related H2D transfers (every nstlist step);
*/
void gpu_launch_kernel(NbnxmGpu* nb, const gmx::StepWorkload& stepWork, const InteractionLocality iloc)
{
- cu_atomdata_t* adat = nb->atdat;
+ NBAtomDataGpu* adat = nb->atdat;
NBParamGpu* nbp = nb->nbparam;
gpu_plist* plist = nb->plist[iloc];
- cu_timers_t* t = nb->timers;
+ Nbnxm::GpuTimers* timers = nb->timers;
const DeviceStream& deviceStream = *nb->deviceStreams[iloc];
bool bDoTime = nb->bDoTime;
/* beginning of timed nonbonded calculation section */
if (bDoTime)
{
- t->interaction[iloc].nb_k.openTimingRegion(deviceStream);
+ timers->interaction[iloc].nb_k.openTimingRegion(deviceStream);
}
/* Kernel launch config:
"Non-bonded GPU launch configuration:\n\tThread block: %zux%zux%zu\n\t"
"\tGrid: %zux%zu\n\t#Super-clusters/clusters: %d/%d (%d)\n"
"\tShMem: %zu\n",
- config.blockSize[0], config.blockSize[1], config.blockSize[2], config.gridSize[0],
- config.gridSize[1], plist->nsci * c_nbnxnGpuNumClusterPerSupercluster,
- c_nbnxnGpuNumClusterPerSupercluster, plist->na_c, config.sharedMemorySize);
- }
-
- auto* timingEvent = bDoTime ? t->interaction[iloc].nb_k.fetchNextEvent() : nullptr;
+ config.blockSize[0],
+ config.blockSize[1],
+ config.blockSize[2],
+ config.gridSize[0],
+ config.gridSize[1],
+ plist->nsci * c_nbnxnGpuNumClusterPerSupercluster,
+ c_nbnxnGpuNumClusterPerSupercluster,
+ plist->na_c,
+ config.sharedMemorySize);
+ }
+
+ auto* timingEvent = bDoTime ? timers->interaction[iloc].nb_k.fetchNextEvent() : nullptr;
const auto kernel =
- select_nbnxn_kernel(nbp->eeltype, nbp->vdwtype, stepWork.computeEnergy,
+ select_nbnxn_kernel(nbp->elecType,
+ nbp->vdwType,
+ stepWork.computeEnergy,
(plist->haveFreshList && !nb->timers->interaction[iloc].didPrune),
&nb->deviceContext_->deviceInfo());
const auto kernelArgs =
if (bDoTime)
{
- t->interaction[iloc].nb_k.closeTimingRegion(deviceStream);
+ timers->interaction[iloc].nb_k.closeTimingRegion(deviceStream);
}
if (GMX_NATIVE_WINDOWS)
void gpu_launch_kernel_pruneonly(NbnxmGpu* nb, const InteractionLocality iloc, const int numParts)
{
- cu_atomdata_t* adat = nb->atdat;
+ NBAtomDataGpu* adat = nb->atdat;
NBParamGpu* nbp = nb->nbparam;
gpu_plist* plist = nb->plist[iloc];
- cu_timers_t* t = nb->timers;
+ Nbnxm::GpuTimers* timers = nb->timers;
const DeviceStream& deviceStream = *nb->deviceStreams[iloc];
bool bDoTime = nb->bDoTime;
GpuRegionTimer* timer = nullptr;
if (bDoTime)
{
- timer = &(plist->haveFreshList ? t->interaction[iloc].prune_k : t->interaction[iloc].rollingPrune_k);
+ timer = &(plist->haveFreshList ? timers->interaction[iloc].prune_k
+ : timers->interaction[iloc].rollingPrune_k);
}
/* beginning of timed prune calculation section */
* and j-cluster concurrency, in x, y, and z, respectively.
* - The 1D block-grid contains as many blocks as super-clusters.
*/
- int num_threads_z = c_cudaPruneKernelJ4Concurrency;
+ int num_threads_z = c_pruneKernelJ4Concurrency;
int nblock = calc_nb_kernel_nblock(numSciInPart, &nb->deviceContext_->deviceInfo());
KernelLaunchConfig config;
config.blockSize[0] = c_clSize;
"Pruning GPU kernel launch configuration:\n\tThread block: %zux%zux%zu\n\t"
"\tGrid: %zux%zu\n\t#Super-clusters/clusters: %d/%d (%d)\n"
"\tShMem: %zu\n",
- config.blockSize[0], config.blockSize[1], config.blockSize[2], config.gridSize[0],
- config.gridSize[1], numSciInPart * c_nbnxnGpuNumClusterPerSupercluster,
- c_nbnxnGpuNumClusterPerSupercluster, plist->na_c, config.sharedMemorySize);
+ config.blockSize[0],
+ config.blockSize[1],
+ config.blockSize[2],
+ config.gridSize[0],
+ config.gridSize[1],
+ numSciInPart * c_nbnxnGpuNumClusterPerSupercluster,
+ c_nbnxnGpuNumClusterPerSupercluster,
+ plist->na_c,
+ config.sharedMemorySize);
}
auto* timingEvent = bDoTime ? timer->fetchNextEvent() : nullptr;
}
}
-void gpu_launch_cpyback(NbnxmGpu* nb,
- nbnxn_atomdata_t* nbatom,
- const gmx::StepWorkload& stepWork,
- const AtomLocality atomLocality)
-{
- GMX_ASSERT(nb, "Need a valid nbnxn_gpu object");
-
- cudaError_t stat;
- int adat_begin, adat_len; /* local/nonlocal offset and length used for xq and f */
-
- /* determine interaction locality from atom locality */
- const InteractionLocality iloc = gpuAtomToInteractionLocality(atomLocality);
-
- /* extract the data */
- cu_atomdata_t* adat = nb->atdat;
- cu_timers_t* t = nb->timers;
- bool bDoTime = nb->bDoTime;
- const DeviceStream& deviceStream = *nb->deviceStreams[iloc];
-
- /* don't launch non-local copy-back if there was no non-local work to do */
- if ((iloc == InteractionLocality::NonLocal) && !haveGpuShortRangeWork(*nb, iloc))
- {
- return;
- }
-
- getGpuAtomRange(adat, atomLocality, &adat_begin, &adat_len);
-
- /* beginning of timed D2H section */
- if (bDoTime)
- {
- t->xf[atomLocality].nb_d2h.openTimingRegion(deviceStream);
- }
-
- /* With DD the local D2H transfer can only start after the non-local
- kernel has finished. */
- if (iloc == InteractionLocality::Local && nb->bUseTwoStreams)
- {
- stat = cudaStreamWaitEvent(deviceStream.stream(), nb->nonlocal_done, 0);
- CU_RET_ERR(stat, "cudaStreamWaitEvent on nonlocal_done failed");
- }
-
- /* DtoH f
- * Skip if buffer ops / reduction is offloaded to the GPU.
- */
- if (!stepWork.useGpuFBufferOps)
- {
- static_assert(
- sizeof(adat->f[0]) == sizeof(float3),
- "The size of the force buffer element should be equal to the size of float3.");
- copyFromDeviceBuffer(reinterpret_cast<float3*>(nbatom->out[0].f.data()) + adat_begin, &adat->f,
- adat_begin, adat_len, deviceStream, GpuApiCallBehavior::Async, nullptr);
- }
-
- /* After the non-local D2H is launched the nonlocal_done event can be
- recorded which signals that the local D2H can proceed. This event is not
- placed after the non-local kernel because we want the non-local data
- back first. */
- if (iloc == InteractionLocality::NonLocal)
- {
- stat = cudaEventRecord(nb->nonlocal_done, deviceStream.stream());
- CU_RET_ERR(stat, "cudaEventRecord on nonlocal_done failed");
- }
-
- /* only transfer energies in the local stream */
- if (iloc == InteractionLocality::Local)
- {
- /* DtoH fshift when virial is needed */
- if (stepWork.computeVirial)
- {
- static_assert(sizeof(nb->nbst.fshift[0]) == sizeof(adat->fshift[0]),
- "Sizes of host- and device-side shift vectors should be the same.");
- copyFromDeviceBuffer(nb->nbst.fshift, &adat->fshift, 0, SHIFTS, deviceStream,
- GpuApiCallBehavior::Async, nullptr);
- }
-
- /* DtoH energies */
- if (stepWork.computeEnergy)
- {
- static_assert(sizeof(nb->nbst.e_lj[0]) == sizeof(adat->e_lj[0]),
- "Sizes of host- and device-side LJ energy terms should be the same.");
- copyFromDeviceBuffer(nb->nbst.e_lj, &adat->e_lj, 0, 1, deviceStream,
- GpuApiCallBehavior::Async, nullptr);
- static_assert(sizeof(nb->nbst.e_el[0]) == sizeof(adat->e_el[0]),
- "Sizes of host- and device-side electrostatic energy terms should be the "
- "same.");
- copyFromDeviceBuffer(nb->nbst.e_el, &adat->e_el, 0, 1, deviceStream,
- GpuApiCallBehavior::Async, nullptr);
- }
- }
-
- if (bDoTime)
- {
- t->xf[atomLocality].nb_d2h.closeTimingRegion(deviceStream);
- }
-}
-
void cuda_set_cacheconfig()
{
cudaError_t stat;
- for (int i = 0; i < eelTypeNR; i++)
+ for (int i = 0; i < c_numElecTypes; i++)
{
- for (int j = 0; j < evdwTypeNR; j++)
+ for (int j = 0; j < c_numVdwTypes; j++)
{
/* Default kernel 32/32 kB Shared/L1 */
cudaFuncSetCacheConfig(nb_kfunc_ener_prune_ptr[i][j], cudaFuncCachePreferEqual);
/* X buffer operations on GPU: performs conversion from rvec to nb format. */
void nbnxn_gpu_x_to_nbat_x(const Nbnxm::Grid& grid,
- bool setFillerCoords,
NbnxmGpu* nb,
DeviceBuffer<gmx::RVec> d_x,
GpuEventSynchronizer* xReadyOnDevice,
const Nbnxm::AtomLocality locality,
int gridId,
- int numColumnsMax)
+ int numColumnsMax,
+ bool mustInsertNonLocalDependency)
{
GMX_ASSERT(nb, "Need a valid nbnxn_gpu object");
- cu_atomdata_t* adat = nb->atdat;
+ NBAtomDataGpu* adat = nb->atdat;
const int numColumns = grid.numColumns();
const int cellOffset = grid.cellOffset();
const int numAtomsPerCell = grid.numAtomsPerCell();
- Nbnxm::InteractionLocality interactionLoc = gpuAtomToInteractionLocality(locality);
+ Nbnxm::InteractionLocality interactionLoc = atomToInteractionLocality(locality);
const DeviceStream& deviceStream = *nb->deviceStreams[interactionLoc];
+ if (xReadyOnDevice != nullptr)
+ {
+ // We only need to wait on the first iteration of the loop
+ xReadyOnDevice->enqueueWaitEvent(deviceStream);
+ }
+
int numAtoms = grid.srcAtomEnd() - grid.srcAtomBegin();
// avoid empty kernel launch, skip to inserting stream dependency
if (numAtoms != 0)
// TODO: This will only work with CUDA
GMX_ASSERT(d_x, "Need a valid device pointer");
- // ensure that coordinates are ready on the device before launching the kernel
- GMX_ASSERT(xReadyOnDevice, "Need a valid GpuEventSynchronizer object");
- xReadyOnDevice->enqueueWaitEvent(deviceStream);
KernelLaunchConfig config;
config.blockSize[0] = c_bufOpsThreadsPerBlock;
"Can not have empty grid, early return above avoids this");
config.sharedMemorySize = 0;
- auto kernelFn = setFillerCoords ? nbnxn_gpu_x_to_nbat_x_kernel<true>
- : nbnxn_gpu_x_to_nbat_x_kernel<false>;
+ auto kernelFn = nbnxn_gpu_x_to_nbat_x_kernel;
float4* d_xq = adat->xq;
float3* d_xFloat3 = asFloat3(d_x);
const int* d_atomIndices = nb->atomIndices;
const int* d_cxy_na = &nb->cxy_na[numColumnsMax * gridId];
const int* d_cxy_ind = &nb->cxy_ind[numColumnsMax * gridId];
- const auto kernelArgs = prepareGpuKernelArguments(kernelFn, config, &numColumns, &d_xq,
- &d_xFloat3, &d_atomIndices, &d_cxy_na,
- &d_cxy_ind, &cellOffset, &numAtomsPerCell);
+ const auto kernelArgs = prepareGpuKernelArguments(kernelFn,
+ config,
+ &numColumns,
+ &d_xq,
+ &d_xFloat3,
+ &d_atomIndices,
+ &d_cxy_na,
+ &d_cxy_ind,
+ &cellOffset,
+ &numAtomsPerCell);
launchGpuKernel(kernelFn, config, deviceStream, nullptr, "XbufferOps", kernelArgs);
}
- // TODO: note that this is not necessary when there astreamre no local atoms, that is:
- // (numAtoms == 0 && interactionLoc == InteractionLocality::Local)
- // but for now we avoid that optimization
- nbnxnInsertNonlocalGpuDependency(nb, interactionLoc);
+ if (mustInsertNonLocalDependency)
+ {
+ Nbnxm::nbnxnInsertNonlocalGpuDependency(nb, interactionLoc);
+ }
}
-void* getGpuForces(NbnxmGpu* nb)
+DeviceBuffer<Float3> getGpuForces(NbnxmGpu* nb)
{
return nb->atdat->f;
}
// TODO Remove this comment when the above order issue is resolved
#include "gromacs/gpu_utils/cudautils.cuh"
#include "gromacs/gpu_utils/device_context.h"
-#include "gromacs/gpu_utils/device_stream_manager.h"
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/gpu_utils/gpueventsynchronizer.cuh"
-#include "gromacs/gpu_utils/pmalloc_cuda.h"
+#include "gromacs/gpu_utils/pmalloc.h"
#include "gromacs/hardware/device_information.h"
#include "gromacs/hardware/device_management.h"
#include "gromacs/math/vectypes.h"
*/
static unsigned int gpu_min_ci_balanced_factor = 44;
-/* Fw. decl. */
-static void nbnxn_cuda_clear_e_fshift(NbnxmGpu* nb);
-
-/*! Initializes the atomdata structure first time, it only gets filled at
- pair-search. */
-static void init_atomdata_first(cu_atomdata_t* ad, int ntypes, const DeviceContext& deviceContext)
-{
- ad->ntypes = ntypes;
- allocateDeviceBuffer(&ad->shift_vec, SHIFTS, deviceContext);
- ad->bShiftVecUploaded = false;
-
- allocateDeviceBuffer(&ad->fshift, SHIFTS, deviceContext);
- allocateDeviceBuffer(&ad->e_lj, 1, deviceContext);
- allocateDeviceBuffer(&ad->e_el, 1, deviceContext);
-
- /* initialize to nullptr poiters to data that is not allocated here and will
- need reallocation in nbnxn_cuda_init_atomdata */
- ad->xq = nullptr;
- ad->f = nullptr;
-
- /* size -1 indicates that the respective array hasn't been initialized yet */
- ad->natoms = -1;
- ad->nalloc = -1;
-}
-
-/*! Initializes the nonbonded parameter data structure. */
-static void init_nbparam(NBParamGpu* nbp,
- const interaction_const_t* ic,
- const PairlistParams& listParams,
- const nbnxn_atomdata_t::Params& nbatParams,
- const DeviceContext& deviceContext)
+void gpu_init_platform_specific(NbnxmGpu* /* nb */)
{
- int ntypes;
-
- ntypes = nbatParams.numTypes;
-
- set_cutoff_parameters(nbp, ic, listParams);
-
- /* The kernel code supports LJ combination rules (geometric and LB) for
- * all kernel types, but we only generate useful combination rule kernels.
- * We currently only use LJ combination rule (geometric and LB) kernels
- * for plain cut-off LJ. On Maxwell the force only kernels speed up 15%
- * with PME and 20% with RF, the other kernels speed up about half as much.
- * For LJ force-switch the geometric rule would give 7% speed-up, but this
- * combination is rarely used. LJ force-switch with LB rule is more common,
- * but gives only 1% speed-up.
- */
- if (ic->vdwtype == evdwCUT)
- {
- switch (ic->vdw_modifier)
- {
- case eintmodNONE:
- case eintmodPOTSHIFT:
- switch (nbatParams.comb_rule)
- {
- case ljcrNONE: nbp->vdwtype = evdwTypeCUT; break;
- case ljcrGEOM: nbp->vdwtype = evdwTypeCUTCOMBGEOM; break;
- case ljcrLB: nbp->vdwtype = evdwTypeCUTCOMBLB; break;
- default:
- gmx_incons(
- "The requested LJ combination rule is not implemented in the CUDA "
- "GPU accelerated kernels!");
- }
- break;
- case eintmodFORCESWITCH: nbp->vdwtype = evdwTypeFSWITCH; break;
- case eintmodPOTSWITCH: nbp->vdwtype = evdwTypePSWITCH; break;
- default:
- gmx_incons(
- "The requested VdW interaction modifier is not implemented in the CUDA GPU "
- "accelerated kernels!");
- }
- }
- else if (ic->vdwtype == evdwPME)
- {
- if (ic->ljpme_comb_rule == ljcrGEOM)
- {
- assert(nbatParams.comb_rule == ljcrGEOM);
- nbp->vdwtype = evdwTypeEWALDGEOM;
- }
- else
- {
- assert(nbatParams.comb_rule == ljcrLB);
- nbp->vdwtype = evdwTypeEWALDLB;
- }
- }
- else
- {
- gmx_incons(
- "The requested VdW type is not implemented in the CUDA GPU accelerated kernels!");
- }
-
- if (ic->eeltype == eelCUT)
- {
- nbp->eeltype = eelTypeCUT;
- }
- else if (EEL_RF(ic->eeltype))
- {
- nbp->eeltype = eelTypeRF;
- }
- else if ((EEL_PME(ic->eeltype) || ic->eeltype == eelEWALD))
- {
- nbp->eeltype = nbnxn_gpu_pick_ewald_kernel_type(*ic, deviceContext.deviceInfo());
- }
- else
- {
- /* Shouldn't happen, as this is checked when choosing Verlet-scheme */
- gmx_incons(
- "The requested electrostatics type is not implemented in the CUDA GPU accelerated "
- "kernels!");
- }
-
- /* generate table for PME */
- nbp->coulomb_tab = nullptr;
- if (nbp->eeltype == eelTypeEWALD_TAB || nbp->eeltype == eelTypeEWALD_TAB_TWIN)
- {
- GMX_RELEASE_ASSERT(ic->coulombEwaldTables, "Need valid Coulomb Ewald correction tables");
- init_ewald_coulomb_force_table(*ic->coulombEwaldTables, nbp, deviceContext);
- }
-
- /* set up LJ parameter lookup table */
- if (!useLjCombRule(nbp->vdwtype))
- {
- initParamLookupTable(&nbp->nbfp, &nbp->nbfp_texobj, nbatParams.nbfp.data(),
- 2 * ntypes * ntypes, deviceContext);
- }
-
- /* set up LJ-PME parameter lookup table */
- if (ic->vdwtype == evdwPME)
- {
- initParamLookupTable(&nbp->nbfp_comb, &nbp->nbfp_comb_texobj, nbatParams.nbfp_comb.data(),
- 2 * ntypes, deviceContext);
- }
-}
-
-/*! Initializes simulation constant data. */
-static void cuda_init_const(NbnxmGpu* nb,
- const interaction_const_t* ic,
- const PairlistParams& listParams,
- const nbnxn_atomdata_t::Params& nbatParams)
-{
- init_atomdata_first(nb->atdat, nbatParams.numTypes, *nb->deviceContext_);
- init_nbparam(nb->nbparam, ic, listParams, nbatParams, *nb->deviceContext_);
-
- /* clear energy and shift force outputs */
- nbnxn_cuda_clear_e_fshift(nb);
-}
-
-NbnxmGpu* gpu_init(const gmx::DeviceStreamManager& deviceStreamManager,
- const interaction_const_t* ic,
- const PairlistParams& listParams,
- const nbnxn_atomdata_t* nbat,
- bool bLocalAndNonlocal)
-{
- cudaError_t stat;
-
- auto nb = new NbnxmGpu();
- nb->deviceContext_ = &deviceStreamManager.context();
- snew(nb->atdat, 1);
- snew(nb->nbparam, 1);
- snew(nb->plist[InteractionLocality::Local], 1);
- if (bLocalAndNonlocal)
- {
- snew(nb->plist[InteractionLocality::NonLocal], 1);
- }
-
- nb->bUseTwoStreams = bLocalAndNonlocal;
-
- nb->timers = new cu_timers_t();
- snew(nb->timings, 1);
-
- /* init nbst */
- pmalloc((void**)&nb->nbst.e_lj, sizeof(*nb->nbst.e_lj));
- pmalloc((void**)&nb->nbst.e_el, sizeof(*nb->nbst.e_el));
- pmalloc((void**)&nb->nbst.fshift, SHIFTS * sizeof(*nb->nbst.fshift));
-
- init_plist(nb->plist[InteractionLocality::Local]);
-
- /* local/non-local GPU streams */
- GMX_RELEASE_ASSERT(deviceStreamManager.streamIsValid(gmx::DeviceStreamType::NonBondedLocal),
- "Local non-bonded stream should be initialized to use GPU for non-bonded.");
- nb->deviceStreams[InteractionLocality::Local] =
- &deviceStreamManager.stream(gmx::DeviceStreamType::NonBondedLocal);
- if (nb->bUseTwoStreams)
- {
- init_plist(nb->plist[InteractionLocality::NonLocal]);
-
- /* Note that the device we're running on does not have to support
- * priorities, because we are querying the priority range which in this
- * case will be a single value.
- */
- GMX_RELEASE_ASSERT(deviceStreamManager.streamIsValid(gmx::DeviceStreamType::NonBondedNonLocal),
- "Non-local non-bonded stream should be initialized to use GPU for "
- "non-bonded with domain decomposition.");
- nb->deviceStreams[InteractionLocality::NonLocal] =
- &deviceStreamManager.stream(gmx::DeviceStreamType::NonBondedNonLocal);
- ;
- }
-
- /* init events for sychronization (timing disabled for performance reasons!) */
- stat = cudaEventCreateWithFlags(&nb->nonlocal_done, cudaEventDisableTiming);
- CU_RET_ERR(stat, "cudaEventCreate on nonlocal_done failed");
- stat = cudaEventCreateWithFlags(&nb->misc_ops_and_local_H2D_done, cudaEventDisableTiming);
- CU_RET_ERR(stat, "cudaEventCreate on misc_ops_and_local_H2D_done failed");
-
- nb->xNonLocalCopyD2HDone = new GpuEventSynchronizer();
-
- /* WARNING: CUDA timings are incorrect with multiple streams.
- * This is the main reason why they are disabled by default.
- */
- // TODO: Consider turning on by default when we can detect nr of streams.
- nb->bDoTime = (getenv("GMX_ENABLE_GPU_TIMING") != nullptr);
-
- if (nb->bDoTime)
- {
- init_timings(nb->timings);
- }
-
/* set the kernel type for the current GPU */
/* pick L1 cache configuration */
cuda_set_cacheconfig();
-
- cuda_init_const(nb, ic, listParams, nbat->params());
-
- nb->atomIndicesSize = 0;
- nb->atomIndicesSize_alloc = 0;
- nb->ncxy_na = 0;
- nb->ncxy_na_alloc = 0;
- nb->ncxy_ind = 0;
- nb->ncxy_ind_alloc = 0;
-
- if (debug)
- {
- fprintf(debug, "Initialized CUDA data structures.\n");
- }
-
- return nb;
-}
-
-void gpu_upload_shiftvec(NbnxmGpu* nb, const nbnxn_atomdata_t* nbatom)
-{
- cu_atomdata_t* adat = nb->atdat;
- const DeviceStream& localStream = *nb->deviceStreams[InteractionLocality::Local];
-
- /* only if we have a dynamic box */
- if (nbatom->bDynamicBox || !adat->bShiftVecUploaded)
- {
- static_assert(sizeof(adat->shift_vec[0]) == sizeof(nbatom->shift_vec[0]),
- "Sizes of host- and device-side shift vectors should be the same.");
- copyToDeviceBuffer(&adat->shift_vec, reinterpret_cast<const float3*>(nbatom->shift_vec.data()),
- 0, SHIFTS, localStream, GpuApiCallBehavior::Async, nullptr);
- adat->bShiftVecUploaded = true;
- }
-}
-
-/*! Clears the first natoms_clear elements of the GPU nonbonded force output array. */
-static void nbnxn_cuda_clear_f(NbnxmGpu* nb, int natoms_clear)
-{
- cu_atomdata_t* adat = nb->atdat;
- const DeviceStream& localStream = *nb->deviceStreams[InteractionLocality::Local];
- clearDeviceBufferAsync(&adat->f, 0, natoms_clear, localStream);
-}
-
-/*! Clears nonbonded shift force output array and energy outputs on the GPU. */
-static void nbnxn_cuda_clear_e_fshift(NbnxmGpu* nb)
-{
- cu_atomdata_t* adat = nb->atdat;
- const DeviceStream& localStream = *nb->deviceStreams[InteractionLocality::Local];
-
- clearDeviceBufferAsync(&adat->fshift, 0, SHIFTS, localStream);
- clearDeviceBufferAsync(&adat->e_lj, 0, 1, localStream);
- clearDeviceBufferAsync(&adat->e_el, 0, 1, localStream);
-}
-
-void gpu_clear_outputs(NbnxmGpu* nb, bool computeVirial)
-{
- nbnxn_cuda_clear_f(nb, nb->atdat->natoms);
- /* clear shift force array and energies if the outputs were
- used in the current step */
- if (computeVirial)
- {
- nbnxn_cuda_clear_e_fshift(nb);
- }
}
-void gpu_init_atomdata(NbnxmGpu* nb, const nbnxn_atomdata_t* nbat)
+void gpu_free_platform_specific(NbnxmGpu* /* nb */)
{
- int nalloc, natoms;
- bool realloced;
- bool bDoTime = nb->bDoTime;
- cu_timers_t* timers = nb->timers;
- cu_atomdata_t* d_atdat = nb->atdat;
- const DeviceContext& deviceContext = *nb->deviceContext_;
- const DeviceStream& localStream = *nb->deviceStreams[InteractionLocality::Local];
-
- natoms = nbat->numAtoms();
- realloced = false;
-
- if (bDoTime)
- {
- /* time async copy */
- timers->atdat.openTimingRegion(localStream);
- }
-
- /* need to reallocate if we have to copy more atoms than the amount of space
- available and only allocate if we haven't initialized yet, i.e d_atdat->natoms == -1 */
- if (natoms > d_atdat->nalloc)
- {
- nalloc = over_alloc_small(natoms);
-
- /* free up first if the arrays have already been initialized */
- if (d_atdat->nalloc != -1)
- {
- freeDeviceBuffer(&d_atdat->f);
- freeDeviceBuffer(&d_atdat->xq);
- freeDeviceBuffer(&d_atdat->atom_types);
- freeDeviceBuffer(&d_atdat->lj_comb);
- }
-
- allocateDeviceBuffer(&d_atdat->f, nalloc, deviceContext);
- allocateDeviceBuffer(&d_atdat->xq, nalloc, deviceContext);
- if (useLjCombRule(nb->nbparam->vdwtype))
- {
- allocateDeviceBuffer(&d_atdat->lj_comb, nalloc, deviceContext);
- }
- else
- {
- allocateDeviceBuffer(&d_atdat->atom_types, nalloc, deviceContext);
- }
-
- d_atdat->nalloc = nalloc;
- realloced = true;
- }
-
- d_atdat->natoms = natoms;
- d_atdat->natoms_local = nbat->natoms_local;
-
- /* need to clear GPU f output if realloc happened */
- if (realloced)
- {
- nbnxn_cuda_clear_f(nb, nalloc);
- }
-
- if (useLjCombRule(nb->nbparam->vdwtype))
- {
- static_assert(sizeof(d_atdat->lj_comb[0]) == sizeof(float2),
- "Size of the LJ parameters element should be equal to the size of float2.");
- copyToDeviceBuffer(&d_atdat->lj_comb,
- reinterpret_cast<const float2*>(nbat->params().lj_comb.data()), 0,
- natoms, localStream, GpuApiCallBehavior::Async, nullptr);
- }
- else
- {
- static_assert(sizeof(d_atdat->atom_types[0]) == sizeof(nbat->params().type[0]),
- "Sizes of host- and device-side atom types should be the same.");
- copyToDeviceBuffer(&d_atdat->atom_types, nbat->params().type.data(), 0, natoms, localStream,
- GpuApiCallBehavior::Async, nullptr);
- }
-
- if (bDoTime)
- {
- timers->atdat.closeTimingRegion(localStream);
- }
-}
-
-void gpu_free(NbnxmGpu* nb)
-{
- cudaError_t stat;
- cu_atomdata_t* atdat;
- NBParamGpu* nbparam;
-
- if (nb == nullptr)
- {
- return;
- }
-
- atdat = nb->atdat;
- nbparam = nb->nbparam;
-
- if ((!nbparam->coulomb_tab)
- && (nbparam->eeltype == eelTypeEWALD_TAB || nbparam->eeltype == eelTypeEWALD_TAB_TWIN))
- {
- destroyParamLookupTable(&nbparam->coulomb_tab, nbparam->coulomb_tab_texobj);
- }
-
- stat = cudaEventDestroy(nb->nonlocal_done);
- CU_RET_ERR(stat, "cudaEventDestroy failed on timers->nonlocal_done");
- stat = cudaEventDestroy(nb->misc_ops_and_local_H2D_done);
- CU_RET_ERR(stat, "cudaEventDestroy failed on timers->misc_ops_and_local_H2D_done");
-
- delete nb->timers;
-
- if (!useLjCombRule(nb->nbparam->vdwtype))
- {
- destroyParamLookupTable(&nbparam->nbfp, nbparam->nbfp_texobj);
- }
-
- if (nbparam->vdwtype == evdwTypeEWALDGEOM || nbparam->vdwtype == evdwTypeEWALDLB)
- {
- destroyParamLookupTable(&nbparam->nbfp_comb, nbparam->nbfp_comb_texobj);
- }
-
- freeDeviceBuffer(&atdat->shift_vec);
- freeDeviceBuffer(&atdat->fshift);
-
- freeDeviceBuffer(&atdat->e_lj);
- freeDeviceBuffer(&atdat->e_el);
-
- freeDeviceBuffer(&atdat->f);
- freeDeviceBuffer(&atdat->xq);
- freeDeviceBuffer(&atdat->atom_types);
- freeDeviceBuffer(&atdat->lj_comb);
-
- /* Free plist */
- auto* plist = nb->plist[InteractionLocality::Local];
- freeDeviceBuffer(&plist->sci);
- freeDeviceBuffer(&plist->cj4);
- freeDeviceBuffer(&plist->imask);
- freeDeviceBuffer(&plist->excl);
- sfree(plist);
- if (nb->bUseTwoStreams)
- {
- auto* plist_nl = nb->plist[InteractionLocality::NonLocal];
- freeDeviceBuffer(&plist_nl->sci);
- freeDeviceBuffer(&plist_nl->cj4);
- freeDeviceBuffer(&plist_nl->imask);
- freeDeviceBuffer(&plist_nl->excl);
- sfree(plist_nl);
- }
-
- /* Free nbst */
- pfree(nb->nbst.e_lj);
- nb->nbst.e_lj = nullptr;
-
- pfree(nb->nbst.e_el);
- nb->nbst.e_el = nullptr;
-
- pfree(nb->nbst.fshift);
- nb->nbst.fshift = nullptr;
-
- sfree(atdat);
- sfree(nbparam);
- sfree(nb->timings);
- delete nb;
-
- if (debug)
- {
- fprintf(debug, "Cleaned up CUDA data structures.\n");
- }
+ // Nothing specific in CUDA
}
int gpu_min_ci_balanced(NbnxmGpu* nb)
{
assert(nb);
- return reinterpret_cast<DeviceBuffer<gmx::RVec>>(nb->atdat->fshift);
-}
-
-/* Initialization for X buffer operations on GPU. */
-/* TODO Remove explicit pinning from host arrays from here and manage in a more natural way*/
-void nbnxn_gpu_init_x_to_nbat_x(const Nbnxm::GridSet& gridSet, NbnxmGpu* gpu_nbv)
-{
- const DeviceStream& deviceStream = *gpu_nbv->deviceStreams[InteractionLocality::Local];
- bool bDoTime = gpu_nbv->bDoTime;
- const int maxNumColumns = gridSet.numColumnsMax();
-
- reallocateDeviceBuffer(&gpu_nbv->cxy_na, maxNumColumns * gridSet.grids().size(),
- &gpu_nbv->ncxy_na, &gpu_nbv->ncxy_na_alloc, *gpu_nbv->deviceContext_);
- reallocateDeviceBuffer(&gpu_nbv->cxy_ind, maxNumColumns * gridSet.grids().size(),
- &gpu_nbv->ncxy_ind, &gpu_nbv->ncxy_ind_alloc, *gpu_nbv->deviceContext_);
-
- for (unsigned int g = 0; g < gridSet.grids().size(); g++)
- {
-
- const Nbnxm::Grid& grid = gridSet.grids()[g];
-
- const int numColumns = grid.numColumns();
- const int* atomIndices = gridSet.atomIndices().data();
- const int atomIndicesSize = gridSet.atomIndices().size();
- const int* cxy_na = grid.cxy_na().data();
- const int* cxy_ind = grid.cxy_ind().data();
-
- reallocateDeviceBuffer(&gpu_nbv->atomIndices, atomIndicesSize, &gpu_nbv->atomIndicesSize,
- &gpu_nbv->atomIndicesSize_alloc, *gpu_nbv->deviceContext_);
-
- if (atomIndicesSize > 0)
- {
-
- if (bDoTime)
- {
- gpu_nbv->timers->xf[AtomLocality::Local].nb_h2d.openTimingRegion(deviceStream);
- }
-
- copyToDeviceBuffer(&gpu_nbv->atomIndices, atomIndices, 0, atomIndicesSize, deviceStream,
- GpuApiCallBehavior::Async, nullptr);
-
- if (bDoTime)
- {
- gpu_nbv->timers->xf[AtomLocality::Local].nb_h2d.closeTimingRegion(deviceStream);
- }
- }
-
- if (numColumns > 0)
- {
- if (bDoTime)
- {
- gpu_nbv->timers->xf[AtomLocality::Local].nb_h2d.openTimingRegion(deviceStream);
- }
-
- int* destPtr = &gpu_nbv->cxy_na[maxNumColumns * g];
- copyToDeviceBuffer(&destPtr, cxy_na, 0, numColumns, deviceStream,
- GpuApiCallBehavior::Async, nullptr);
-
- if (bDoTime)
- {
- gpu_nbv->timers->xf[AtomLocality::Local].nb_h2d.closeTimingRegion(deviceStream);
- }
-
- if (bDoTime)
- {
- gpu_nbv->timers->xf[AtomLocality::Local].nb_h2d.openTimingRegion(deviceStream);
- }
-
- destPtr = &gpu_nbv->cxy_ind[maxNumColumns * g];
- copyToDeviceBuffer(&destPtr, cxy_ind, 0, numColumns, deviceStream,
- GpuApiCallBehavior::Async, nullptr);
-
- if (bDoTime)
- {
- gpu_nbv->timers->xf[AtomLocality::Local].nb_h2d.closeTimingRegion(deviceStream);
- }
- }
- }
-
- // The above data is transferred on the local stream but is a
- // dependency of the nonlocal stream (specifically the nonlocal X
- // buf ops kernel). We therefore set a dependency to ensure
- // that the nonlocal stream waits on the local stream here.
- // This call records an event in the local stream:
- nbnxnInsertNonlocalGpuDependency(gpu_nbv, Nbnxm::InteractionLocality::Local);
- // ...and this call instructs the nonlocal stream to wait on that event:
- nbnxnInsertNonlocalGpuDependency(gpu_nbv, Nbnxm::InteractionLocality::NonLocal);
-
- return;
+ return reinterpret_cast<DeviceBuffer<gmx::RVec>>(nb->atdat->fShift);
}
} // namespace Nbnxm
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gpu_utils/cuda_arch_utils.cuh"
#include "gromacs/gpu_utils/cuda_kernel_utils.cuh"
+#include "gromacs/gpu_utils/typecasts.cuh"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/pbcutil/ishift.h"
/* Note that floating-point constants in CUDA code should be suffixed
__global__ void NB_KERNEL_FUNC_NAME(nbnxn_kernel, _F_cuda)
# endif /* CALC_ENERGIES */
#endif /* PRUNE_NBL */
- (const cu_atomdata_t atdat, const NBParamGpu nbparam, const Nbnxm::gpu_plist plist, bool bCalcFshift)
+ (const NBAtomDataGpu atdat, const NBParamGpu nbparam, const Nbnxm::gpu_plist plist, bool bCalcFshift)
#ifdef FUNCTION_DECLARATION_ONLY
; /* Only do function declaration, omit the function body. */
#else
nbnxn_cj4_t* pl_cj4 = plist.cj4;
const nbnxn_excl_t* excl = plist.excl;
# ifndef LJ_COMB
- const int* atom_types = atdat.atom_types;
- int ntypes = atdat.ntypes;
+ const int* atom_types = atdat.atomTypes;
+ int ntypes = atdat.numTypes;
# else
- const float2* lj_comb = atdat.lj_comb;
+ const float2* lj_comb = atdat.ljComb;
float2 ljcp_i, ljcp_j;
# endif
const float4* xq = atdat.xq;
- float3* f = atdat.f;
- const float3* shift_vec = atdat.shift_vec;
+ float3* f = asFloat3(atdat.f);
+ const float3* shift_vec = asFloat3(atdat.shiftVec);
float rcoulomb_sq = nbparam.rcoulomb_sq;
# ifdef VDW_CUTOFF_CHECK
float rvdw_sq = nbparam.rvdw_sq;
float beta = nbparam.ewald_beta;
float ewald_shift = nbparam.sh_ewald;
# else
- float c_rf = nbparam.c_rf;
+ float reactionFieldShift = nbparam.c_rf;
# endif /* EL_EWALD_ANY */
- float* e_lj = atdat.e_lj;
- float* e_el = atdat.e_el;
+ float* e_lj = atdat.eLJ;
+ float* e_el = atdat.eElec;
# endif /* CALC_ENERGIES */
/* thread/block/warp id-s */
E_el = 0.0f;
# ifdef EXCLUSION_FORCES /* Ewald or RF */
- if (nb_sci.shift == CENTRAL && pl_cj4[cij4_start].cj[0] == sci * c_nbnxnGpuNumClusterPerSupercluster)
+ if (nb_sci.shift == gmx::c_centralShiftIndex
+ && pl_cj4[cij4_start].cj[0] == sci * c_nbnxnGpuNumClusterPerSupercluster)
{
/* we have the diagonal: add the charge and LJ self interaction energy term */
for (i = 0; i < c_nbnxnGpuNumClusterPerSupercluster; i++)
# endif
# ifdef LJ_EWALD
-# if DISABLE_CUDA_TEXTURES
- E_lj += LDG(&nbparam.nbfp[atom_types[(sci * c_nbnxnGpuNumClusterPerSupercluster + i) * c_clSize + tidxi]
- * (ntypes + 1) * 2]);
-# else
- E_lj += tex1Dfetch<float>(
- nbparam.nbfp_texobj,
- atom_types[(sci * c_nbnxnGpuNumClusterPerSupercluster + i) * c_clSize + tidxi]
- * (ntypes + 1) * 2);
-# endif
+ // load only the first 4 bytes of the parameter pair (equivalent with nbfp[idx].x)
+ E_lj += LDG((float*)&nbparam.nbfp[atom_types[(sci * c_nbnxnGpuNumClusterPerSupercluster + i) * c_clSize + tidxi]
+ * (ntypes + 1)]);
# endif
}
/* Correct for epsfac^2 due to adding qi^2 */
E_el /= nbparam.epsfac * c_clSize * NTHREAD_Z;
# if defined EL_RF || defined EL_CUTOFF
- E_el *= -0.5f * c_rf;
+ E_el *= -0.5f * reactionFieldShift;
# else
E_el *= -beta * M_FLOAT_1_SQRTPI; /* last factor 1/sqrt(pi) */
# endif
# endif /* CALC_ENERGIES */
# ifdef EXCLUSION_FORCES
- const int nonSelfInteraction = !(nb_sci.shift == CENTRAL & tidxj <= tidxi);
+ const int nonSelfInteraction = !(nb_sci.shift == gmx::c_centralShiftIndex & tidxj <= tidxi);
# endif
/* loop over the j clusters = seen by any of the atoms in the current super-cluster;
# ifdef LJ_EWALD
# ifdef LJ_EWALD_COMB_GEOM
# ifdef CALC_ENERGIES
- calculate_lj_ewald_comb_geom_F_E(nbparam, typei, typej, r2, inv_r2,
- lje_coeff2, lje_coeff6_6, int_bit,
- &F_invr, &E_lj_p);
+ calculate_lj_ewald_comb_geom_F_E(
+ nbparam, typei, typej, r2, inv_r2, lje_coeff2, lje_coeff6_6, int_bit, &F_invr, &E_lj_p);
# else
- calculate_lj_ewald_comb_geom_F(nbparam, typei, typej, r2, inv_r2,
- lje_coeff2, lje_coeff6_6, &F_invr);
+ calculate_lj_ewald_comb_geom_F(
+ nbparam, typei, typej, r2, inv_r2, lje_coeff2, lje_coeff6_6, &F_invr);
# endif /* CALC_ENERGIES */
# elif defined LJ_EWALD_COMB_LB
- calculate_lj_ewald_comb_LB_F_E(nbparam, typei, typej, r2, inv_r2,
- lje_coeff2, lje_coeff6_6,
+ calculate_lj_ewald_comb_LB_F_E(nbparam,
+ typei,
+ typej,
+ r2,
+ inv_r2,
+ lje_coeff2,
+ lje_coeff6_6,
# ifdef CALC_ENERGIES
- int_bit, &F_invr, &E_lj_p
+ int_bit,
+ &F_invr,
+ &E_lj_p
# else
- 0, &F_invr, nullptr
+ 0,
+ &F_invr,
+ nullptr
# endif /* CALC_ENERGIES */
);
# endif /* LJ_EWALD_COMB_GEOM */
# ifdef CALC_ENERGIES
# ifdef EL_CUTOFF
- E_el += qi * qj_f * (int_bit * inv_r - c_rf);
+ E_el += qi * qj_f * (int_bit * inv_r - reactionFieldShift);
# endif
# ifdef EL_RF
- E_el += qi * qj_f * (int_bit * inv_r + 0.5f * two_k_rf * r2 - c_rf);
+ E_el += qi * qj_f
+ * (int_bit * inv_r + 0.5f * two_k_rf * r2 - reactionFieldShift);
# endif
# ifdef EL_EWALD_ANY
/* 1.0f - erff is faster than erfcf */
}
/* skip central shifts when summing shift forces */
- if (nb_sci.shift == CENTRAL)
+ if (nb_sci.shift == gmx::c_centralShiftIndex)
{
bCalcFshift = false;
}
/* add up local shift forces into global mem, tidxj indexes x,y,z */
if (bCalcFshift && (tidxj & 3) < 3)
{
- atomicAdd(&(atdat.fshift[nb_sci.shift].x) + (tidxj & 3), fshift_buf);
+ float3* fShift = asFloat3(atdat.fShift);
+ atomicAdd(&(fShift[nb_sci.shift].x) + (tidxj & 3), fshift_buf);
}
# ifdef CALC_ENERGIES
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef FUNCTION_DECLARATION_ONLY
/* Instantiate external template functions */
template __global__ void
-nbnxn_kernel_prune_cuda<false>(const cu_atomdata_t, const NBParamGpu, const Nbnxm::gpu_plist, int, int);
+nbnxn_kernel_prune_cuda<false>(const NBAtomDataGpu, const NBParamGpu, const Nbnxm::gpu_plist, int, int);
template __global__ void
-nbnxn_kernel_prune_cuda<true>(const cu_atomdata_t, const NBParamGpu, const Nbnxm::gpu_plist, int, int);
+nbnxn_kernel_prune_cuda<true>(const NBAtomDataGpu, const NBParamGpu, const Nbnxm::gpu_plist, int, int);
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gmxpre.h"
#include "gromacs/gpu_utils/cuda_arch_utils.cuh"
+#include "gromacs/gpu_utils/typecasts.cuh"
#include "gromacs/math/utilities.h"
#include "gromacs/pbcutil/ishift.h"
*/
template<bool haveFreshList>
__launch_bounds__(THREADS_PER_BLOCK, MIN_BLOCKS_PER_MP) __global__
- void nbnxn_kernel_prune_cuda(const cu_atomdata_t atdat,
+ void nbnxn_kernel_prune_cuda(const NBAtomDataGpu atdat,
const NBParamGpu nbparam,
const Nbnxm::gpu_plist plist,
int numParts,
// Add extern declarations so each translation unit understands that
// there will be a definition provided.
extern template __global__ void
-nbnxn_kernel_prune_cuda<true>(const cu_atomdata_t, const NBParamGpu, const Nbnxm::gpu_plist, int, int);
+nbnxn_kernel_prune_cuda<true>(const NBAtomDataGpu, const NBParamGpu, const Nbnxm::gpu_plist, int, int);
extern template __global__ void
-nbnxn_kernel_prune_cuda<false>(const cu_atomdata_t, const NBParamGpu, const Nbnxm::gpu_plist, int, int);
+nbnxn_kernel_prune_cuda<false>(const NBAtomDataGpu, const NBParamGpu, const Nbnxm::gpu_plist, int, int);
#else
{
const nbnxn_sci_t* pl_sci = plist.sci;
nbnxn_cj4_t* pl_cj4 = plist.cj4;
const float4* xq = atdat.xq;
- const float3* shift_vec = atdat.shift_vec;
+ const float3* shift_vec = asFloat3(atdat.shiftVec);
float rlistOuter_sq = nbparam.rlistOuter_sq;
float rlistInner_sq = nbparam.rlistInner_sq;
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static __forceinline__ __device__ float calculate_lj_ewald_c6grid(const NBParamGpu nbparam, int typei, int typej)
{
# if DISABLE_CUDA_TEXTURES
- return LDG(&nbparam.nbfp_comb[2 * typei]) * LDG(&nbparam.nbfp_comb[2 * typej]);
+ float c6_i = LDG(&nbparam.nbfp_comb[typei]).x;
+ float c6_j = LDG(&nbparam.nbfp_comb[typej]).x;
# else
- return tex1Dfetch<float>(nbparam.nbfp_comb_texobj, 2 * typei)
- * tex1Dfetch<float>(nbparam.nbfp_comb_texobj, 2 * typej);
+ float c6_i = tex1Dfetch<float2>(nbparam.nbfp_comb_texobj, typei).x;
+ float c6_j = tex1Dfetch<float2>(nbparam.nbfp_comb_texobj, typej).x;
# endif /* DISABLE_CUDA_TEXTURES */
+ return c6_i * c6_j;
}
*/
static __forceinline__ __device__ float2 fetch_nbfp_comb_c6_c12(const NBParamGpu nbparam, int type)
{
- float2 c6c12;
# if DISABLE_CUDA_TEXTURES
- /* Force an 8-byte fetch to save a memory instruction. */
- float2* nbfp_comb = (float2*)nbparam.nbfp_comb;
- c6c12 = LDG(&nbfp_comb[type]);
+ return LDG(&nbparam.nbfp_comb[type]);
# else
- /* NOTE: as we always do 8-byte aligned loads, we could
- fetch float2 here too just as above. */
- c6c12.x = tex1Dfetch<float>(nbparam.nbfp_comb_texobj, 2 * type);
- c6c12.y = tex1Dfetch<float>(nbparam.nbfp_comb_texobj, 2 * type + 1);
+ return tex1Dfetch<float2>(nbparam.nbfp_comb_texobj, type);
# endif /* DISABLE_CUDA_TEXTURES */
-
- return c6c12;
}
d.x = LDG(&nbparam.coulomb_tab[index]);
d.y = LDG(&nbparam.coulomb_tab[index + 1]);
# else
- d.x = tex1Dfetch<float>(nbparam.coulomb_tab_texobj, index);
- d.y = tex1Dfetch<float>(nbparam.coulomb_tab_texobj, index + 1);
+ d.x = tex1Dfetch<float>(nbparam.coulomb_tab_texobj, index);
+ d.y = tex1Dfetch<float>(nbparam.coulomb_tab_texobj, index + 1);
# endif // DISABLE_CUDA_TEXTURES
return d;
*/
static __forceinline__ __device__ void fetch_nbfp_c6_c12(float& c6, float& c12, const NBParamGpu nbparam, int baseIndex)
{
+ float2 c6c12;
# if DISABLE_CUDA_TEXTURES
- /* Force an 8-byte fetch to save a memory instruction. */
- float2* nbfp = (float2*)nbparam.nbfp;
- float2 c6c12;
- c6c12 = LDG(&nbfp[baseIndex]);
- c6 = c6c12.x;
- c12 = c6c12.y;
+ c6c12 = LDG(&nbparam.nbfp[baseIndex]);
# else
- /* NOTE: as we always do 8-byte aligned loads, we could
- fetch float2 here too just as above. */
- c6 = tex1Dfetch<float>(nbparam.nbfp_texobj, 2 * baseIndex);
- c12 = tex1Dfetch<float>(nbparam.nbfp_texobj, 2 * baseIndex + 1);
+ c6c12 = tex1Dfetch<float2>(nbparam.nbfp_texobj, baseIndex);
# endif // DISABLE_CUDA_TEXTURES
+ c6 = c6c12.x;
+ c12 = c6c12.y;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2012, The GROMACS development team.
- * Copyright (c) 2013-2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013-2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gpu_utils/cudautils.cuh"
#include "gromacs/gpu_utils/devicebuffer.h"
#include "gromacs/gpu_utils/devicebuffer_datatype.h"
+#include "gromacs/gpu_utils/gpueventsynchronizer.cuh"
#include "gromacs/gpu_utils/gputraits.cuh"
#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/nbnxm/gpu_types_common.h"
#include "gromacs/timing/gpu_timing.h"
#include "gromacs/utility/enumerationhelpers.h"
-/*! \brief Macro definining default for the prune kernel's j4 processing concurrency.
- *
- * The GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY macro allows compile-time override.
- */
-#ifndef GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY
-# define GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY 4
-#endif
-/*! \brief Default for the prune kernel's j4 processing concurrency.
- *
- * Initialized using the #GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY macro which allows compile-time override.
- */
-const int c_cudaPruneKernelJ4Concurrency = GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY;
-
/* TODO: consider moving this to kernel_utils */
/* Convenience defines */
/*! \brief cluster size = number of atoms per cluster. */
static constexpr int c_clSize = c_nbnxnGpuClusterSize;
-/* All structs prefixed with "cu_" hold data used in GPU calculations and
- * are passed to the kernels, except cu_timers_t. */
-/*! \cond */
-typedef struct cu_atomdata cu_atomdata_t;
-/*! \endcond */
-
-
-/** \internal
- * \brief Staging area for temporary data downloaded from the GPU.
- *
- * The energies/shift forces get downloaded here first, before getting added
- * to the CPU-side aggregate values.
- */
-struct nb_staging_t
-{
- //! LJ energy
- float* e_lj = nullptr;
- //! electrostatic energy
- float* e_el = nullptr;
- //! shift forces
- float3* fshift = nullptr;
-};
-
-/** \internal
- * \brief Nonbonded atom data - both inputs and outputs.
- */
-struct cu_atomdata
-{
- //! number of atoms
- int natoms;
- //! number of local atoms
- int natoms_local;
- //! allocation size for the atom data (xq, f)
- int nalloc;
-
- //! atom coordinates + charges, size natoms
- DeviceBuffer<float4> xq;
- //! force output array, size natoms
- DeviceBuffer<float3> f;
-
- //! LJ energy output, size 1
- DeviceBuffer<float> e_lj;
- //! Electrostatics energy input, size 1
- DeviceBuffer<float> e_el;
-
- //! shift forces
- DeviceBuffer<float3> fshift;
-
- //! number of atom types
- int ntypes;
- //! atom type indices, size natoms
- DeviceBuffer<int> atom_types;
- //! sqrt(c6),sqrt(c12) size natoms
- DeviceBuffer<float2> lj_comb;
-
- //! shifts
- DeviceBuffer<float3> shift_vec;
- //! true if the shift vector has been uploaded
- bool bShiftVecUploaded;
-};
-
-/** \internal
- * \brief Typedef of actual timer type.
- */
-typedef struct Nbnxm::gpu_timers_t cu_timers_t;
-
-class GpuEventSynchronizer;
-
/*! \internal
* \brief Main data structure for CUDA nonbonded force calculations.
*/
const DeviceContext* deviceContext_;
/*! \brief true if doing both local/non-local NB work on GPU */
bool bUseTwoStreams = false;
+ //! true indicates that the nonlocal_done event was marked
+ bool bNonLocalStreamDoneMarked = false;
+
/*! \brief atom data */
- cu_atomdata_t* atdat = nullptr;
+ NBAtomDataGpu* atdat = nullptr;
/*! \brief array of atom indices */
int* atomIndices = nullptr;
/*! \brief size of atom indices */
/*! \brief pair-list data structures (local and non-local) */
gmx::EnumerationArray<Nbnxm::InteractionLocality, Nbnxm::gpu_plist*> plist = { { nullptr } };
/*! \brief staging area where fshift/energies get downloaded */
- nb_staging_t nbst;
+ NBStagingData nbst;
/*! \brief local and non-local GPU streams */
gmx::EnumerationArray<Nbnxm::InteractionLocality, const DeviceStream*> deviceStreams;
- /*! \brief Events used for synchronization */
- /*! \{ */
/*! \brief Event triggered when the non-local non-bonded
* kernel is done (and the local transfer can proceed) */
- cudaEvent_t nonlocal_done = nullptr;
+ GpuEventSynchronizer nonlocal_done;
/*! \brief Event triggered when the tasks issued in the local
* stream that need to precede the non-local force or buffer
* operation calculations are done (e.g. f buffer 0-ing, local
* x/q H2D, buffer op initialization in local stream that is
* required also by nonlocal stream ) */
- cudaEvent_t misc_ops_and_local_H2D_done = nullptr;
- /*! \} */
+ GpuEventSynchronizer misc_ops_and_local_H2D_done;
/*! \brief True if there is work for the current domain in the
* respective locality.
* will be true. */
gmx::EnumerationArray<Nbnxm::InteractionLocality, bool> haveWork = { { false } };
- /*! \brief Event triggered when non-local coordinate buffer
- * has been copied from device to host. */
- GpuEventSynchronizer* xNonLocalCopyD2HDone = nullptr;
-
/* NOTE: With current CUDA versions (<=5.0) timing doesn't work with multiple
* concurrent streams, so we won't time if both l/nl work is done on GPUs.
* Timer init/uninit is still done even with timing off so only the condition
/*! \brief True if event-based timing is enabled. */
bool bDoTime = false;
/*! \brief CUDA event-based timers. */
- cu_timers_t* timers = nullptr;
+ Nbnxm::GpuTimers* timers = nullptr;
/*! \brief Timing data. TODO: deprecate this and query timers for accumulated data instead */
gmx_wallclock_gpu_nbnxn_t* timings = nullptr;
};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
# include "opencl/nbnxm_ocl_types.h"
#endif
+#if GMX_GPU_SYCL
+# include "sycl/nbnxm_sycl_types.h"
+#endif
+
#include "gromacs/gpu_utils/gpu_utils.h"
-#include "gromacs/listed_forces/gpubonded.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/simulation_workload.h"
#include "gromacs/nbnxm/nbnxm.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/timing/gpu_timing.h"
#include "gromacs/timing/wallcycle.h"
-#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/stringutil.h"
#include "gpu_common_utils.h"
namespace Nbnxm
{
-/*! \brief Check that atom locality values are valid for the GPU module.
- *
- * In the GPU module atom locality "all" is not supported, the local and
- * non-local ranges are treated separately.
- *
- * \param[in] atomLocality atom locality specifier
- */
-static inline void validateGpuAtomLocality(const AtomLocality atomLocality)
-{
- std::string str = gmx::formatString(
- "Invalid atom locality passed (%d); valid here is only "
- "local (%d) or nonlocal (%d)",
- static_cast<int>(atomLocality), static_cast<int>(AtomLocality::Local),
- static_cast<int>(AtomLocality::NonLocal));
-
- GMX_ASSERT(atomLocality == AtomLocality::Local || atomLocality == AtomLocality::NonLocal, str.c_str());
-}
-
-/*! \brief Convert atom locality to interaction locality.
- *
- * In the current implementation the this is straightforward conversion:
- * local to local, non-local to non-local.
- *
- * \param[in] atomLocality Atom locality specifier
- * \returns Interaction locality corresponding to the atom locality passed.
- */
-static inline InteractionLocality gpuAtomToInteractionLocality(const AtomLocality atomLocality)
-{
- validateGpuAtomLocality(atomLocality);
-
- /* determine interaction locality from atom locality */
- if (atomLocality == AtomLocality::Local)
- {
- return InteractionLocality::Local;
- }
- else if (atomLocality == AtomLocality::NonLocal)
- {
- return InteractionLocality::NonLocal;
- }
- else
- {
- gmx_incons("Wrong locality");
- }
-}
-
-
-//NOLINTNEXTLINE(misc-definitions-in-headers)
-void setupGpuShortRangeWork(NbnxmGpu* nb, const gmx::GpuBonded* gpuBonded, const gmx::InteractionLocality iLocality)
-{
- GMX_ASSERT(nb, "Need a valid nbnxn_gpu object");
-
- // There is short-range work if the pair list for the provided
- // interaction locality contains entries or if there is any
- // bonded work (as this is not split into local/nonlocal).
- nb->haveWork[iLocality] = ((nb->plist[iLocality]->nsci != 0)
- || (gpuBonded != nullptr && gpuBonded->haveInteractions()));
-}
-
-/*! \brief Returns true if there is GPU short-range work for the given interaction locality.
- *
- * Note that as, unlike nonbonded tasks, bonded tasks are not split into local/nonlocal,
- * and therefore if there are GPU offloaded bonded interactions, this function will return
- * true for all interaction localities.
- *
- * \param[inout] nb Pointer to the nonbonded GPU data structure
- * \param[in] iLocality Interaction locality identifier
- */
-static bool haveGpuShortRangeWork(const NbnxmGpu& nb, const gmx::InteractionLocality iLocality)
-{
- return nb.haveWork[iLocality];
-}
-
-//NOLINTNEXTLINE(misc-definitions-in-headers)
-bool haveGpuShortRangeWork(const NbnxmGpu* nb, const gmx::AtomLocality aLocality)
-{
- GMX_ASSERT(nb, "Need a valid nbnxn_gpu object");
-
- return haveGpuShortRangeWork(*nb, gpuAtomToInteractionLocality(aLocality));
-}
-
-
-/*! \brief Calculate atom range and return start index and length.
- *
- * \param[in] atomData Atom descriptor data structure
- * \param[in] atomLocality Atom locality specifier
- * \param[out] atomRangeBegin Starting index of the atom range in the atom data array.
- * \param[out] atomRangeLen Atom range length in the atom data array.
- */
-template<typename AtomDataT>
-static inline void getGpuAtomRange(const AtomDataT* atomData,
- const AtomLocality atomLocality,
- int* atomRangeBegin,
- int* atomRangeLen)
-{
- assert(atomData);
- validateGpuAtomLocality(atomLocality);
-
- /* calculate the atom data index range based on locality */
- if (atomLocality == AtomLocality::Local)
- {
- *atomRangeBegin = 0;
- *atomRangeLen = atomData->natoms_local;
- }
- else
- {
- *atomRangeBegin = atomData->natoms_local;
- *atomRangeLen = atomData->natoms - atomData->natoms_local;
- }
-}
-
-
/*! \brief Count pruning kernel time if either kernel has been triggered
*
* We do the accounting for either of the two pruning kernel flavors:
* - 1st pass prune: ran during the current step (prior to the force kernel);
* - rolling prune: ran at the end of the previous step (prior to the current step H2D xq);
*
- * Note that the resetting of cu_timers_t::didPrune and cu_timers_t::didRollingPrune should happen
- * after calling this function.
+ * Note that the resetting of Nbnxm::GpuTimers::didPrune and Nbnxm::GpuTimers::didRollingPrune
+ * should happen after calling this function.
*
* \param[in] timers structs with GPU timer objects
* \param[inout] timings GPU task timing data
* \param[in] iloc interaction locality
*/
-template<typename GpuTimers>
-static void countPruneKernelTime(GpuTimers* timers,
+static void countPruneKernelTime(Nbnxm::GpuTimers* timers,
gmx_wallclock_gpu_nbnxn_t* timings,
const InteractionLocality iloc)
{
- gpu_timers_t::Interaction& iTimers = timers->interaction[iloc];
+ GpuTimers::Interaction& iTimers = timers->interaction[iloc];
// We might have not done any pruning (e.g. if we skipped with empty domains).
if (!iTimers.didPrune && !iTimers.didRollingPrune)
* Note that this function should always be called after the transfers into the
* staging buffers has completed.
*
- * \tparam StagingData Type of staging data
* \param[in] nbst Nonbonded staging data
* \param[in] iLocality Interaction locality specifier
* \param[in] reduceEnergies True if energy reduction should be done
* \param[out] e_el Variable to accumulate electrostatic energy into
* \param[out] fshift Pointer to the array of shift forces to accumulate into
*/
-template<typename StagingData>
-static inline void gpu_reduce_staged_outputs(const StagingData& nbst,
+static inline void gpu_reduce_staged_outputs(const NBStagingData& nbst,
const InteractionLocality iLocality,
const bool reduceEnergies,
const bool reduceFshift,
{
if (reduceEnergies)
{
- *e_lj += *nbst.e_lj;
- *e_el += *nbst.e_el;
+ *e_lj += *nbst.eLJ;
+ *e_el += *nbst.eElec;
}
if (reduceFshift)
{
- for (int i = 0; i < SHIFTS; i++)
+ for (int i = 0; i < gmx::c_numShiftVectors; i++)
{
- rvec_inc(fshift[i], nbst.fshift[i]);
+ rvec_inc(fshift[i], nbst.fShift[i]);
}
}
}
* counters could end up being inconsistent due to not being incremented
* on some of the node when this is skipped on empty local domains!
*
- * \tparam GpuTimers GPU timers type
* \tparam GpuPairlist Pair list type
* \param[out] timings Pointer to the NB GPU timings data
* \param[in] timers Pointer to GPU timers data
* \param[in] doTiming True if timing is enabled.
*
*/
-template<typename GpuTimers, typename GpuPairlist>
+template<typename GpuPairlist>
static inline void gpu_accumulate_timings(gmx_wallclock_gpu_nbnxn_t* timings,
- GpuTimers* timers,
+ Nbnxm::GpuTimers* timers,
const GpuPairlist* plist,
AtomLocality atomLocality,
const gmx::StepWorkload& stepWork,
}
/* determine interaction locality from atom locality */
- const InteractionLocality iLocality = gpuAtomToInteractionLocality(atomLocality);
+ const InteractionLocality iLocality = atomToInteractionLocality(atomLocality);
const bool didEnergyKernels = stepWork.computeEnergy;
/* only increase counter once (at local F wait) */
GMX_ASSERT(nb, "Need a valid nbnxn_gpu object");
/* determine interaction locality from atom locality */
- const InteractionLocality iLocality = gpuAtomToInteractionLocality(aloc);
+ const InteractionLocality iLocality = atomToInteractionLocality(aloc);
// Transfers are launched and therefore need to be waited on if:
// We skip when during the non-local phase there was actually no work to do.
// This is consistent with nbnxn_gpu_launch_kernel but it also considers possible
// bonded GPU work.
- if ((iLocality == InteractionLocality::Local) || haveGpuShortRangeWork(*nb, iLocality))
+ if ((iLocality == InteractionLocality::Local) || haveGpuShortRangeWork(nb, iLocality))
{
// Query the state of the GPU stream and return early if we're not done
if (completionKind == GpuTaskCompletion::Check)
// we start without counting and only when the task finished we issue a
// start/stop to increment.
// GpuTaskCompletion::Wait mode the timing is expected to be done in the caller.
- wallcycle_start_nocount(wcycle, ewcWAIT_GPU_NB_L);
+ wallcycle_start_nocount(wcycle, WallCycleCounter::WaitGpuNbL);
if (!haveStreamTasksCompleted(*nb->deviceStreams[iLocality]))
{
- wallcycle_stop(wcycle, ewcWAIT_GPU_NB_L);
+ wallcycle_stop(wcycle, WallCycleCounter::WaitGpuNbL);
// Early return to skip the steps below that we have to do only
// after the NB task completed
return false;
}
- wallcycle_increment_event_count(wcycle, ewcWAIT_GPU_NB_L);
+ wallcycle_increment_event_count(wcycle, WallCycleCounter::WaitGpuNbL);
}
else if (haveResultToWaitFor)
{
if (stepWork.computeEnergy || stepWork.computeVirial)
{
- gpu_reduce_staged_outputs(nb->nbst, iLocality, stepWork.computeEnergy, stepWork.computeVirial,
- e_lj, e_el, as_rvec_array(shiftForces.data()));
+ gpu_reduce_staged_outputs(nb->nbst,
+ iLocality,
+ stepWork.computeEnergy,
+ stepWork.computeVirial,
+ e_lj,
+ e_el,
+ as_rvec_array(shiftForces.data()));
}
}
- /* Always reset both pruning flags (doesn't hurt doing it even when timing is off). */
- nb->timers->interaction[iLocality].didPrune =
- nb->timers->interaction[iLocality].didRollingPrune = false;
+ /* Reset both pruning flags. */
+ if (nb->bDoTime)
+ {
+ nb->timers->interaction[iLocality].didPrune =
+ nb->timers->interaction[iLocality].didRollingPrune = false;
+ }
/* Turn off initial list pruning (doesn't hurt if this is not pair-search step). */
nb->plist[iLocality]->haveFreshList = false;
gmx::ArrayRef<gmx::RVec> shiftForces,
gmx_wallcycle* wcycle)
{
- auto cycleCounter = (gpuAtomToInteractionLocality(aloc) == InteractionLocality::Local)
- ? ewcWAIT_GPU_NB_L
- : ewcWAIT_GPU_NB_NL;
+ auto cycleCounter = (atomToInteractionLocality(aloc) == InteractionLocality::Local)
+ ? WallCycleCounter::WaitGpuNbL
+ : WallCycleCounter::WaitGpuNbNL;
wallcycle_start(wcycle, cycleCounter);
gpu_try_finish_task(nb, stepWork, aloc, e_lj, e_el, shiftForces, GpuTaskCompletion::Wait, wcycle);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_NBNXM_GPU_COMMON_UTILS_H
#define GMX_NBNXM_GPU_COMMON_UTILS_H
-#include "config.h"
-
-#include "gromacs/nbnxm/nbnxm.h"
-
-#if GMX_GPU_CUDA
-# include "cuda/nbnxm_cuda_types.h"
-#endif
-
-#if GMX_GPU_OPENCL
-# include "opencl/nbnxm_ocl_types.h"
-#endif
+#include "gromacs/listed_forces/gpubonded.h"
+#include "gromacs/mdtypes/locality.h"
+#include "gromacs/nbnxm/gpu_types_common.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/range.h"
namespace Nbnxm
{
return (iloc == InteractionLocality::NonLocal && nb.plist[iloc]->nsci == 0);
}
+/*! \brief Calculate atom range and return start index and length.
+ *
+ * \param[in] atomData Atom descriptor data structure
+ * \param[in] atomLocality Atom locality specifier
+ * \returns Range of indexes for selected locality.
+ */
+static inline gmx::Range<int> getGpuAtomRange(const NBAtomDataGpu* atomData, const AtomLocality atomLocality)
+{
+ assert(atomData);
+
+ /* calculate the atom data index range based on locality */
+ if (atomLocality == AtomLocality::Local)
+ {
+ return gmx::Range<int>(0, atomData->numAtomsLocal);
+ }
+ else if (atomLocality == AtomLocality::NonLocal)
+ {
+ return gmx::Range<int>(atomData->numAtomsLocal, atomData->numAtoms);
+ }
+ else
+ {
+ GMX_THROW(gmx::InconsistentInputError(
+ "Only Local and NonLocal atom locities can be used to get atom ranges in NBNXM."));
+ }
+}
+
} // namespace Nbnxm
#endif
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2014,2015,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gpu_utils/gpu_macros.h"
#include "gromacs/mdtypes/locality.h"
+#include "nbnxm.h"
+
struct NbnxmGpu;
struct DeviceInformation;
struct gmx_wallclock_gpu_nbnxn_t;
*/
GPU_FUNC_QUALIFIER
void gpu_pme_loadbal_update_param(const struct nonbonded_verlet_t gmx_unused* nbv,
- const interaction_const_t gmx_unused* ic) GPU_FUNC_TERM;
+ const interaction_const_t gmx_unused& ic) GPU_FUNC_TERM;
/** Uploads shift vector to the GPU if the box is dynamic (otherwise just returns). */
GPU_FUNC_QUALIFIER
GPU_FUNC_QUALIFIER
bool gpu_is_kernel_ewald_analytical(const NbnxmGpu gmx_unused* nb) GPU_FUNC_TERM_WITH_RETURN(FALSE);
-/** Returns an opaque pointer to the GPU command stream
- * Note: CUDA only.
- */
-CUDA_FUNC_QUALIFIER
-const DeviceStream* gpu_get_command_stream(NbnxmGpu gmx_unused* nb, gmx::InteractionLocality gmx_unused iloc)
- CUDA_FUNC_TERM_WITH_RETURN(nullptr);
-
/** Returns an opaque pointer to the GPU coordinate+charge array
* Note: CUDA only.
*/
#include "config.h"
+#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/mdtypes/locality.h"
#include "gromacs/utility/enumerationhelpers.h"
+#include "nbnxm.h"
#include "pairlist.h"
#if GMX_GPU_OPENCL
# include "gromacs/gpu_utils/gpuregiontimer.cuh"
#endif
+#if GMX_GPU_SYCL
+# include "gromacs/gpu_utils/gpuregiontimer_sycl.h"
+#endif
+
+/*! \brief Macro definining default for the prune kernel's j4 processing concurrency.
+ *
+ * The GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY macro allows compile-time override with the default value of 4.
+ */
+#ifndef GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY
+# define GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY 4
+#endif
+//! Default for the prune kernel's j4 processing concurrency.
+static constexpr int c_pruneKernelJ4Concurrency = GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY;
+
+/*! \internal
+ * \brief Staging area for temporary data downloaded from the GPU.
+ *
+ * Since SYCL buffers already have host-side storage, this is a bit redundant.
+ * But it allows prefetching of the data from GPU, and brings GPU backends closer together.
+ */
+struct NBStagingData
+{
+ //! LJ energy
+ float* eLJ = nullptr;
+ //! electrostatic energy
+ float* eElec = nullptr;
+ //! shift forces
+ Float3* fShift = nullptr;
+};
+
+/** \internal
+ * \brief Nonbonded atom data - both inputs and outputs.
+ */
+struct NBAtomDataGpu
+{
+ //! number of atoms
+ int numAtoms;
+ //! number of local atoms
+ int numAtomsLocal;
+ //! allocation size for the atom data (xq, f)
+ int numAtomsAlloc;
+
+ //! atom coordinates + charges, size \ref numAtoms
+ DeviceBuffer<Float4> xq;
+ //! force output array, size \ref numAtoms
+ DeviceBuffer<Float3> f;
+
+ //! LJ energy output, size 1
+ DeviceBuffer<float> eLJ;
+ //! Electrostatics energy input, size 1
+ DeviceBuffer<float> eElec;
+
+ //! shift forces
+ DeviceBuffer<Float3> fShift;
+
+ //! number of atom types
+ int numTypes;
+ //! atom type indices, size \ref numAtoms
+ DeviceBuffer<int> atomTypes;
+ //! sqrt(c6),sqrt(c12) size \ref numAtoms
+ DeviceBuffer<Float2> ljComb;
+
+ //! shifts
+ DeviceBuffer<Float3> shiftVec;
+ //! true if the shift vector has been uploaded
+ bool shiftVecUploaded;
+};
+
/** \internal
* \brief Parameters required for the GPU nonbonded calculations.
*/
struct NBParamGpu
{
- //! type of electrostatics, takes values from #eelType
- int eeltype;
- //! type of VdW impl., takes values from #evdwType
- int vdwtype;
+ //! type of electrostatics
+ enum Nbnxm::ElecType elecType;
+ //! type of VdW impl.
+ enum Nbnxm::VdwType vdwType;
//! charge multiplication factor
float epsfac;
float two_k_rf;
//! Ewald/PME parameter
float ewald_beta;
- //! Ewald/PME correction term substracted from the direct-space potential
+ //! Ewald/PME correction term subtracted from the direct-space potential
float sh_ewald;
//! LJ-Ewald/PME correction term added to the correction potential
float sh_lj_ewald;
switch_consts_t vdw_switch;
/* LJ non-bonded parameters - accessed through texture memory */
- //! nonbonded parameter table with C6/C12 pairs per atom type-pair, 2*ntype^2 elements
- DeviceBuffer<float> nbfp;
+ //! nonbonded parameter table with 6*C6/12*C12 pairs per atom type-pair, ntype^2 elements
+ DeviceBuffer<Float2> nbfp{};
//! texture object bound to nbfp
DeviceTexture nbfp_texobj;
- //! nonbonded parameter table per atom type, 2*ntype elements
- DeviceBuffer<float> nbfp_comb;
+ //! nonbonded parameter table per atom type, ntype elements
+ DeviceBuffer<Float2> nbfp_comb{};
//! texture object bound to nbfp_comb
DeviceTexture nbfp_comb_texobj;
//! table scale/spacing
float coulomb_tab_scale;
//! pointer to the table in the device memory
- DeviceBuffer<float> coulomb_tab;
+ DeviceBuffer<float> coulomb_tab{};
//! texture object bound to coulomb_tab
DeviceTexture coulomb_tab_texobj;
};
* The two-sized arrays hold the local and non-local values and should always
* be indexed with eintLocal/eintNonlocal.
*/
-struct gpu_timers_t
+struct GpuTimers
{
/*! \internal
* \brief Timers for local or non-local coordinate/force transfers
//! timers for coordinate/force transfers (every step)
gmx::EnumerationArray<AtomLocality, XFTransfers> xf;
//! timers for interaction related transfers
- gmx::EnumerationArray<InteractionLocality, Nbnxm::gpu_timers_t::Interaction> interaction;
+ gmx::EnumerationArray<InteractionLocality, Nbnxm::GpuTimers::Interaction> interaction;
};
/*! \internal
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return static_cast<real>(numAtoms) / (size[XX] * size[YY] * size[ZZ]);
}
+// Get approximate dimensions of each cell. Returns the length along X and Y.
+static std::array<real, DIM - 1> getTargetCellLength(const Grid::Geometry& geometry, const real atomDensity)
+{
+ if (geometry.isSimple)
+ {
+ /* To minimize the zero interactions, we should make
+ * the largest of the i/j cell cubic.
+ */
+ int numAtomsInCell = std::max(geometry.numAtomsICluster, geometry.numAtomsJCluster);
+
+ /* Approximately cubic cells */
+ real tlen = std::cbrt(numAtomsInCell / atomDensity);
+ return { tlen, tlen };
+ }
+ else
+ {
+ /* Approximately cubic sub cells */
+ real tlen = std::cbrt(geometry.numAtomsICluster / atomDensity);
+ return { tlen * c_gpuNumClusterPerCellX, tlen * c_gpuNumClusterPerCellY };
+ }
+}
+
+static int getMaxNumCells(const Grid::Geometry& geometry, const int numAtoms, const int numColumns)
+{
+ if (geometry.numAtomsJCluster <= geometry.numAtomsICluster)
+ {
+ return numAtoms / geometry.numAtomsPerCell + numColumns;
+ }
+ else
+ {
+ return numAtoms / geometry.numAtomsPerCell
+ + numColumns * geometry.numAtomsJCluster / geometry.numAtomsICluster;
+ }
+}
+
void Grid::setDimensions(const int ddZone,
const int numAtoms,
gmx::RVec lowerCorner,
GMX_ASSERT(atomDensity > 0, "With one or more atoms, the density should be positive");
/* target cell length */
- real tlen_x;
- real tlen_y;
- if (geometry_.isSimple)
- {
- /* To minimize the zero interactions, we should make
- * the largest of the i/j cell cubic.
- */
- int numAtomsInCell = std::max(geometry_.numAtomsICluster, geometry_.numAtomsJCluster);
+ const std::array<real, DIM - 1> tlen = getTargetCellLength(geometry_, atomDensity);
- /* Approximately cubic cells */
- real tlen = std::cbrt(numAtomsInCell / atomDensity);
- tlen_x = tlen;
- tlen_y = tlen;
- }
- else
- {
- /* Approximately cubic sub cells */
- real tlen = std::cbrt(geometry_.numAtomsICluster / atomDensity);
- tlen_x = tlen * c_gpuNumClusterPerCellX;
- tlen_y = tlen * c_gpuNumClusterPerCellY;
- }
/* We round ncx and ncy down, because we get less cell pairs
* in the pairlist when the fixed cell dimensions (x,y) are
* larger than the variable one (z) than the other way around.
*/
- dimensions_.numCells[XX] = std::max(1, static_cast<int>(size[XX] / tlen_x));
- dimensions_.numCells[YY] = std::max(1, static_cast<int>(size[YY] / tlen_y));
+ dimensions_.numCells[XX] = std::max(1, static_cast<int>(size[XX] / tlen[XX]));
+ dimensions_.numCells[YY] = std::max(1, static_cast<int>(size[YY] / tlen[YY]));
}
else
{
changePinningPolicy(&cxy_ind_, pinningPolicy);
/* Worst case scenario of 1 atom in each last cell */
- int maxNumCells;
- if (geometry_.numAtomsJCluster <= geometry_.numAtomsICluster)
- {
- maxNumCells = numAtoms / geometry_.numAtomsPerCell + numColumns();
- }
- else
- {
- maxNumCells = numAtoms / geometry_.numAtomsPerCell
- + numColumns() * geometry_.numAtomsJCluster / geometry_.numAtomsICluster;
- }
+ const int maxNumCells = getMaxNumCells(geometry_, numAtoms, numColumns());
if (!geometry_.isSimple)
{
/* As we can have rounding effect, we use > iso >= here */
if (relevantAtomsAreWithinGridBounds && (zi < 0 || (dd_zone == 0 && zi > n_per_h * c_sortGridRatio)))
{
- gmx_fatal(FARGS, "(int)((x[%d][%c]=%f - %f)*%f) = %d, not in 0 - %d*%d\n", a[i],
- 'x' + dim, x[a[i]][dim], h0, invh, zi, n_per_h, c_sortGridRatio);
+ gmx_fatal(FARGS,
+ "(int)((x[%d][%c]=%f - %f)*%f) = %d, not in 0 - %d*%d\n",
+ a[i],
+ 'x' + dim,
+ x[a[i]][dim],
+ h0,
+ invh,
+ zi,
+ n_per_h,
+ c_sortGridRatio);
}
#endif
if (zi < 0)
zi = 0;
}
- /* In a non-local domain, particles communcated for bonded interactions
+ /* In a non-local domain, particles communicated for bonded interactions
* can be far beyond the grid size, which is set by the non-bonded
* cut-off distance. We sort such particles into the last cell.
*/
//! Computes the bounding box for na coordinates in order x,y,z, bb order xyz0
static void calc_bounding_box(int na, int stride, const real* x, BoundingBox* bb)
{
- int i;
- real xl, xh, yl, yh, zl, zh;
-
- i = 0;
- xl = x[i + XX];
- xh = x[i + XX];
- yl = x[i + YY];
- yh = x[i + YY];
- zl = x[i + ZZ];
- zh = x[i + ZZ];
+ int i = 0;
+ real xl = x[i + XX];
+ real xh = x[i + XX];
+ real yl = x[i + YY];
+ real yh = x[i + YY];
+ real zl = x[i + ZZ];
+ real zh = x[i + ZZ];
i += stride;
for (int j = 1; j < na; j++)
{
/*! \brief Computes the bounding box for na packed coordinates, bb order xyz0 */
static void calc_bounding_box_x_x4(int na, const real* x, BoundingBox* bb)
{
- real xl, xh, yl, yh, zl, zh;
-
- xl = x[XX * c_packX4];
- xh = x[XX * c_packX4];
- yl = x[YY * c_packX4];
- yh = x[YY * c_packX4];
- zl = x[ZZ * c_packX4];
- zh = x[ZZ * c_packX4];
+ real xl = x[XX * c_packX4];
+ real xh = x[XX * c_packX4];
+ real yl = x[YY * c_packX4];
+ real yh = x[YY * c_packX4];
+ real zl = x[ZZ * c_packX4];
+ real zh = x[ZZ * c_packX4];
for (int j = 1; j < na; j++)
{
xl = std::min(xl, x[j + XX * c_packX4]);
/*! \brief Computes the bounding box for na coordinates, bb order xyz0 */
static void calc_bounding_box_x_x8(int na, const real* x, BoundingBox* bb)
{
- real xl, xh, yl, yh, zl, zh;
-
- xl = x[XX * c_packX8];
- xh = x[XX * c_packX8];
- yl = x[YY * c_packX8];
- yh = x[YY * c_packX8];
- zl = x[ZZ * c_packX8];
- zh = x[ZZ * c_packX8];
+ real xl = x[XX * c_packX8];
+ real xh = x[XX * c_packX8];
+ real yl = x[YY * c_packX8];
+ real yh = x[YY * c_packX8];
+ real zl = x[ZZ * c_packX8];
+ real zh = x[ZZ * c_packX8];
for (int j = 1; j < na; j++)
{
xl = std::min(xl, x[j + XX * c_packX8]);
/*! \brief Computes the bounding box for na coordinates in order xyz, bb order xxxxyyyyzzzz */
static void calc_bounding_box_xxxx(int na, int stride, const real* x, float* bb)
{
- int i;
- real xl, xh, yl, yh, zl, zh;
-
- i = 0;
- xl = x[i + XX];
- xh = x[i + XX];
- yl = x[i + YY];
- yh = x[i + YY];
- zl = x[i + ZZ];
- zh = x[i + ZZ];
+ int i = 0;
+ real xl = x[i + XX];
+ real xh = x[i + XX];
+ real yl = x[i + YY];
+ real yh = x[i + YY];
+ real zl = x[i + ZZ];
+ real zh = x[i + ZZ];
i += stride;
for (int j = 1; j < na; j++)
{
const int sc2 = grid.firstCellInColumn(i) >> 1;
/* For odd numbers skip the last bb here */
const int nc2 = (grid.numAtomsInColumn(i) + 3) >> (2 + 1);
- int c2;
- for (c2 = sc2; c2 < sc2 + nc2; c2++)
+ for (int c2 = sc2; c2 < sc2 + nc2; c2++)
{
#if NBNXN_SEARCH_BB_SIMD4
Simd4Float min_S, max_S;
if (((grid.numAtomsInColumn(i) + 3) >> 2) & 1)
{
/* The bb count in this column is odd: duplicate the last bb */
+ int c2 = sc2 + nc2;
bbj[c2].lower = bb[c2 * 2].lower;
bbj[c2].upper = bb[c2 * 2].upper;
}
/ (dims.atomDensity * dims.cellSize[XX] * dims.cellSize[YY])
: 0.0);
- fprintf(fp, "ns bb: grid %4.2f %4.2f %4.2f abs %4.2f %4.2f %4.2f rel %4.2f %4.2f %4.2f\n",
- dims.cellSize[XX], dims.cellSize[YY], avgCellSizeZ, ba[XX], ba[YY], ba[ZZ],
- ba[XX] * dims.invCellSize[XX], ba[YY] * dims.invCellSize[YY],
+ fprintf(fp,
+ "ns bb: grid %4.2f %4.2f %4.2f abs %4.2f %4.2f %4.2f rel %4.2f %4.2f %4.2f\n",
+ dims.cellSize[XX],
+ dims.cellSize[YY],
+ avgCellSizeZ,
+ ba[XX],
+ ba[YY],
+ ba[ZZ],
+ ba[XX] * dims.invCellSize[XX],
+ ba[YY] * dims.invCellSize[YY],
dims.atomDensity > 0 ? ba[ZZ] / avgCellSizeZ : 0.0);
}
/*! \brief Prints the average bb size, used for debug output */
static void print_bbsizes_supersub(FILE* fp, const Grid& grid)
{
- int ns;
dvec ba;
clear_dvec(ba);
- ns = 0;
+ int ns = 0;
for (int c = 0; c < grid.numCells(); c++)
{
#if NBNXN_BBXXXX
* dims.cellSize[YY] * c_gpuNumClusterPerCellZ)
: 0.0);
- fprintf(fp, "ns bb: grid %4.2f %4.2f %4.2f abs %4.2f %4.2f %4.2f rel %4.2f %4.2f %4.2f\n",
+ fprintf(fp,
+ "ns bb: grid %4.2f %4.2f %4.2f abs %4.2f %4.2f %4.2f rel %4.2f %4.2f %4.2f\n",
dims.cellSize[XX] / c_gpuNumClusterPerCellX,
- dims.cellSize[YY] / c_gpuNumClusterPerCellY, avgClusterSizeZ, ba[XX], ba[YY], ba[ZZ],
+ dims.cellSize[YY] / c_gpuNumClusterPerCellY,
+ avgClusterSizeZ,
+ ba[XX],
+ ba[YY],
+ ba[ZZ],
ba[XX] * c_gpuNumClusterPerCellX * dims.invCellSize[XX],
ba[YY] * c_gpuNumClusterPerCellY * dims.invCellSize[YY],
dims.atomDensity > 0 ? ba[ZZ] / avgClusterSizeZ : 0.0);
* Then sort_cluster_on_flag will only set the flags and the sorting
* will not affect the atom order.
*/
- sort_cluster_on_flag(geometry_.numAtomsICluster, atomStart, atomEnd, atinfo, atomIndices,
+ sort_cluster_on_flag(geometry_.numAtomsICluster,
+ atomStart,
+ atomEnd,
+ atinfo,
+ atomIndices,
flags_.data() + atomToCluster(atomStart) - cellOffset_);
}
cells[atomIndices[at]] = at;
}
- copy_rvec_to_nbat_real(atomIndices.data() + atomStart, numAtoms, geometry_.numAtomsICluster,
- as_rvec_array(x.data()), nbat->XFormat, nbat->x().data(), atomStart);
+ copy_rvec_to_nbat_real(atomIndices.data() + atomStart,
+ numAtoms,
+ geometry_.numAtomsICluster,
+ as_rvec_array(x.data()),
+ nbat->XFormat,
+ nbat->x().data(),
+ atomStart);
if (nbat->XFormat == nbatX4)
{
{
calc_bounding_box_x_x4_halves(numAtoms,
nbat->x().data() + atom_to_x_index<c_packX4>(atomStart),
- bb_ptr, bbj_.data() + offset * 2);
+ bb_ptr,
+ bbj_.data() + offset * 2);
}
else
#endif
if (nbat->XFormat == nbatXYZQ)
{
GMX_ASSERT(bb_work_aligned != nullptr, "Must have valid aligned work structure");
- calc_bounding_box_xxxx_simd4(numAtoms, nbat->x().data() + atomStart * nbat->xstride,
- bb_work_aligned, pbb_ptr);
+ calc_bounding_box_xxxx_simd4(
+ numAtoms, nbat->x().data() + atomStart * nbat->xstride, bb_work_aligned, pbb_ptr);
}
else
# endif
{
- calc_bounding_box_xxxx(numAtoms, nbat->xstride,
- nbat->x().data() + atomStart * nbat->xstride, pbb_ptr);
+ calc_bounding_box_xxxx(
+ numAtoms, nbat->xstride, nbat->x().data() + atomStart * nbat->xstride, pbb_ptr);
}
if (gmx_debug_at)
{
- fprintf(debug, "cell %4d bb %5.2f %5.2f %5.2f %5.2f %5.2f %5.2f\n",
- atomToCluster(atomStart), pbb_ptr[0 * c_packedBoundingBoxesDimSize],
- pbb_ptr[3 * c_packedBoundingBoxesDimSize], pbb_ptr[1 * c_packedBoundingBoxesDimSize],
- pbb_ptr[4 * c_packedBoundingBoxesDimSize], pbb_ptr[2 * c_packedBoundingBoxesDimSize],
+ fprintf(debug,
+ "cell %4d bb %5.2f %5.2f %5.2f %5.2f %5.2f %5.2f\n",
+ atomToCluster(atomStart),
+ pbb_ptr[0 * c_packedBoundingBoxesDimSize],
+ pbb_ptr[3 * c_packedBoundingBoxesDimSize],
+ pbb_ptr[1 * c_packedBoundingBoxesDimSize],
+ pbb_ptr[4 * c_packedBoundingBoxesDimSize],
+ pbb_ptr[2 * c_packedBoundingBoxesDimSize],
pbb_ptr[5 * c_packedBoundingBoxesDimSize]);
}
}
if (gmx_debug_at)
{
int bbo = atomToCluster(atomStart - cellOffset_ * geometry_.numAtomsPerCell);
- fprintf(debug, "cell %4d bb %5.2f %5.2f %5.2f %5.2f %5.2f %5.2f\n",
- atomToCluster(atomStart), bb_[bbo].lower.x, bb_[bbo].lower.y, bb_[bbo].lower.z,
- bb_[bbo].upper.x, bb_[bbo].upper.y, bb_[bbo].upper.z);
+ fprintf(debug,
+ "cell %4d bb %5.2f %5.2f %5.2f %5.2f %5.2f %5.2f\n",
+ atomToCluster(atomStart),
+ bb_[bbo].lower.x,
+ bb_[bbo].lower.y,
+ bb_[bbo].lower.z,
+ bb_[bbo].upper.x,
+ bb_[bbo].upper.y,
+ bb_[bbo].upper.z);
}
}
}
{
if (debug)
{
- fprintf(debug, "cell_offset %d sorting columns %d - %d\n", cellOffset_,
- *columnRange.begin(), *columnRange.end());
+ fprintf(debug,
+ "cell_offset %d sorting columns %d - %d\n",
+ cellOffset_,
+ *columnRange.begin(),
+ *columnRange.end());
}
const bool relevantAtomsAreWithinGridBounds = (dimensions_.maxAtomGroupRadius == 0);
const int atomOffset = firstAtomInColumn(cxy);
/* Sort the atoms within each x,y column on z coordinate */
- sort_atoms(ZZ, FALSE, dd_zone, relevantAtomsAreWithinGridBounds,
- gridSetData->atomIndices.data() + atomOffset, numAtoms, x, dimensions_.lowerCorner[ZZ],
- 1.0 / dimensions_.gridSize[ZZ], numCellsZ * numAtomsPerCell, sort_work);
+ sort_atoms(ZZ,
+ FALSE,
+ dd_zone,
+ relevantAtomsAreWithinGridBounds,
+ gridSetData->atomIndices.data() + atomOffset,
+ numAtoms,
+ x,
+ dimensions_.lowerCorner[ZZ],
+ 1.0 / dimensions_.gridSize[ZZ],
+ numCellsZ * numAtomsPerCell,
+ sort_work);
/* Fill the ncz cells in this column */
const int firstCell = firstCellInColumn(cxy);
{
const int cell = firstCell + cellZ;
- const int atomOffsetCell = atomOffset + cellZ * numAtomsPerCell;
- const int numAtomsCell = std::min(numAtomsPerCell, numAtoms - (atomOffsetCell - atomOffset));
+ const int atomOffsetCell = atomOffset + cellZ * numAtomsPerCell;
+ const int numAtomsLeftInColumn = std::max(numAtoms - (atomOffsetCell - atomOffset), 0);
+ const int numAtomsCell = std::min(numAtomsPerCell, numAtomsLeftInColumn);
fillCell(gridSetData, nbat, atomOffsetCell, atomOffsetCell + numAtomsCell, atinfo, x, nullptr);
const gmx::Range<int> columnRange,
gmx::ArrayRef<int> sort_work)
{
- BoundingBox bb_work_array[2];
- BoundingBox* bb_work_aligned = reinterpret_cast<BoundingBox*>(
+ BoundingBox bb_work_array[2];
+ auto* bb_work_aligned = reinterpret_cast<BoundingBox*>(
(reinterpret_cast<std::size_t>(bb_work_array + 1)) & (~(static_cast<std::size_t>(15))));
if (debug)
{
- fprintf(debug, "cell_offset %d sorting columns %d - %d\n", cellOffset_,
- *columnRange.begin(), *columnRange.end());
+ fprintf(debug,
+ "cell_offset %d sorting columns %d - %d\n",
+ cellOffset_,
+ *columnRange.begin(),
+ *columnRange.end());
}
const bool relevantAtomsAreWithinGridBounds = (dimensions_.maxAtomGroupRadius == 0);
const int atomOffset = firstAtomInColumn(cxy);
/* Sort the atoms within each x,y column on z coordinate */
- sort_atoms(ZZ, FALSE, dd_zone, relevantAtomsAreWithinGridBounds,
- atomIndices.data() + atomOffset, numAtomsInColumn, x, dimensions_.lowerCorner[ZZ],
- 1.0 / dimensions_.gridSize[ZZ], numCellsInColumn * numAtomsPerCell, sort_work);
+ sort_atoms(ZZ,
+ FALSE,
+ dd_zone,
+ relevantAtomsAreWithinGridBounds,
+ atomIndices.data() + atomOffset,
+ numAtomsInColumn,
+ x,
+ dimensions_.lowerCorner[ZZ],
+ 1.0 / dimensions_.gridSize[ZZ],
+ numCellsInColumn * numAtomsPerCell,
+ sort_work);
/* This loop goes over the cells and clusters along z at once */
for (int sub_z = 0; sub_z < numCellsInColumn * c_gpuNumClusterPerCellZ; sub_z++)
const int numAtoms =
std::min(numAtomsPerCell, numAtomsInColumn - (atomOffsetZ - atomOffset));
- numClusters_[cell] =
- std::min(c_gpuNumClusterPerCell, (numAtoms + geometry_.numAtomsICluster - 1)
- / geometry_.numAtomsICluster);
+ numClusters_[cell] = std::min(
+ c_gpuNumClusterPerCell,
+ (numAtoms + geometry_.numAtomsICluster - 1) / geometry_.numAtomsICluster);
/* Store the z-boundaries of the bounding box of the cell */
bbcz_[cell].lower = x[atomIndices[atomOffsetZ]][ZZ];
if (c_gpuNumClusterPerCellY > 1)
{
/* Sort the atoms along y */
- sort_atoms(YY, (sub_z & 1) != 0, dd_zone, relevantAtomsAreWithinGridBounds,
- atomIndices.data() + atomOffsetZ, numAtomsZ, x,
+ sort_atoms(YY,
+ (sub_z & 1) != 0,
+ dd_zone,
+ relevantAtomsAreWithinGridBounds,
+ atomIndices.data() + atomOffsetZ,
+ numAtomsZ,
+ x,
dimensions_.lowerCorner[YY] + gridY * dimensions_.cellSize[YY],
- dimensions_.invCellSize[YY], subdiv_z, sort_work);
+ dimensions_.invCellSize[YY],
+ subdiv_z,
+ sort_work);
}
for (int sub_y = 0; sub_y < c_gpuNumClusterPerCellY; sub_y++)
if (c_gpuNumClusterPerCellX > 1)
{
/* Sort the atoms along x */
- sort_atoms(XX, ((cz * c_gpuNumClusterPerCellY + sub_y) & 1) != 0, dd_zone,
- relevantAtomsAreWithinGridBounds, atomIndices.data() + atomOffsetY, numAtomsY,
- x, dimensions_.lowerCorner[XX] + gridX * dimensions_.cellSize[XX],
- dimensions_.invCellSize[XX], subdiv_y, sort_work);
+ sort_atoms(XX,
+ ((cz * c_gpuNumClusterPerCellY + sub_y) & 1) != 0,
+ dd_zone,
+ relevantAtomsAreWithinGridBounds,
+ atomIndices.data() + atomOffsetY,
+ numAtomsY,
+ x,
+ dimensions_.lowerCorner[XX] + gridX * dimensions_.cellSize[XX],
+ dimensions_.invCellSize[XX],
+ subdiv_y,
+ sort_work);
}
for (int sub_x = 0; sub_x < c_gpuNumClusterPerCellX; sub_x++)
const int numAtomsX =
std::min(subdiv_x, numAtomsInColumn - (atomOffsetX - atomOffset));
- fillCell(gridSetData, nbat, atomOffsetX, atomOffsetX + numAtomsX, atinfo, x,
- bb_work_aligned);
+ fillCell(gridSetData, nbat, atomOffsetX, atomOffsetX + numAtomsX, atinfo, x, bb_work_aligned);
}
}
}
gmx_fatal(FARGS,
"grid cell cx %d cy %d out of range (max %d %d)\n"
"atom %f %f %f, grid->c0 %f %f",
- cx, cy, gridDims.numCells[XX], gridDims.numCells[YY], x[i][XX],
- x[i][YY], x[i][ZZ], gridDims.lowerCorner[XX], gridDims.lowerCorner[YY]);
+ cx,
+ cy,
+ gridDims.numCells[XX],
+ gridDims.numCells[YY],
+ x[i][XX],
+ x[i][YY],
+ x[i][ZZ],
+ gridDims.lowerCorner[XX],
+ gridDims.lowerCorner[YY]);
}
#endif
- /* Take care of potential rouding issues */
+ /* Take care of potential rounding issues */
cx = std::min(cx, gridDims.numCells[XX] - 1);
cy = std::min(cy, gridDims.numCells[YY] - 1);
srcAtomBegin_ = *atomRange.begin();
srcAtomEnd_ = *atomRange.end();
- const int nthread = gmx_omp_nthreads_get(emntPairsearch);
+ const int nthread = gmx_omp_nthreads_get(ModuleMultiThread::Pairsearch);
const int numAtomsPerCell = geometry_.numAtomsPerCell;
if (debug)
{
- fprintf(debug, "ns na_sc %d na_c %d super-cells: %d x %d y %d z %.1f maxz %d\n",
- numAtomsPerCell, geometry_.numAtomsICluster, numCellsTotal_, dimensions_.numCells[XX],
- dimensions_.numCells[YY], numCellsTotal_ / (static_cast<double>(numColumns())), ncz_max);
+ fprintf(debug,
+ "ns na_sc %d na_c %d super-cells: %d x %d y %d z %.1f maxz %d\n",
+ numAtomsPerCell,
+ geometry_.numAtomsICluster,
+ numCellsTotal_,
+ dimensions_.numCells[XX],
+ dimensions_.numCells[YY],
+ numCellsTotal_ / (static_cast<double>(numColumns())),
+ ncz_max);
if (gmx_debug_at)
{
int i = 0;
((thread + 1) * numColumns()) / nthread);
if (geometry_.isSimple)
{
- sortColumnsCpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
- gridWork[thread].sortBuffer);
+ sortColumnsCpuGeometry(
+ gridSetData, ddZone, atinfo, x, nbat, columnRange, gridWork[thread].sortBuffer);
}
else
{
- sortColumnsGpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
- gridWork[thread].sortBuffer);
+ sortColumnsGpuGeometry(
+ gridSetData, ddZone, atinfo, x, nbat, columnRange, gridWork[thread].sortBuffer);
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
else
{
- fprintf(debug, "ns non-zero sub-cells: %d average atoms %.2f\n", numClustersTotal_,
+ fprintf(debug,
+ "ns non-zero sub-cells: %d average atoms %.2f\n",
+ numClustersTotal_,
atomRange.size() / static_cast<double>(numClustersTotal_));
print_bbsizes_supersub(debug, *this);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/range.h"
-struct gmx_domdec_zones_t;
struct nbnxn_atomdata_t;
-struct nbnxn_search;
enum class PairlistType;
namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! Returns the number of search grids
static int numGrids(const GridSet::DomainSetup& domainSetup)
{
- int numGrids;
+ // One grid for the test particle, one for the rest
+ static constexpr int sc_numGridsForTestParticleInsertion = 2;
if (domainSetup.doTestParticleInsertion)
{
- numGrids = 2;
+ return sc_numGridsForTestParticleInsertion;
}
else
{
- numGrids = 1;
+ int numGrids = 1;
for (auto haveDD : domainSetup.haveMultipleDomainsPerDim)
{
if (haveDD)
numGrids *= 2;
}
}
+ return numGrids;
}
-
- return numGrids;
}
GridSet::DomainSetup::DomainSetup(const PbcType pbcType,
}
}
+static int getGridOffset(gmx::ArrayRef<const Grid> grids, int gridIndex)
+{
+ if (gridIndex == 0)
+ {
+ return 0;
+ }
+ else
+ {
+ const Nbnxm::Grid& previousGrid = grids[gridIndex - 1];
+ return previousGrid.atomIndexEnd() / previousGrid.geometry().numAtomsPerCell;
+ }
+}
+
void GridSet::putOnGrid(const matrix box,
const int gridIndex,
const rvec lowerCorner,
const int* move,
nbnxn_atomdata_t* nbat)
{
- Nbnxm::Grid& grid = grids_[gridIndex];
-
- int cellOffset;
- if (gridIndex == 0)
- {
- cellOffset = 0;
- }
- else
- {
- const Nbnxm::Grid& previousGrid = grids_[gridIndex - 1];
- cellOffset = previousGrid.atomIndexEnd() / previousGrid.geometry().numAtomsPerCell;
- }
-
- const int n = atomRange.size();
+ Nbnxm::Grid& grid = grids_[gridIndex];
+ const int cellOffset = getGridOffset(grids_, gridIndex);
+ const int n = atomRange.size();
+ real maxAtomGroupRadius = NAN;
- real maxAtomGroupRadius;
if (gridIndex == 0)
{
copy_mat(box, box_);
const int ddZone = (domainSetup_.doTestParticleInsertion ? 0 : gridIndex);
// grid data used in GPU transfers inherits the gridset pinning policy
auto pinPolicy = gridSetData_.cells.get_allocator().pinningPolicy();
- grid.setDimensions(ddZone, n - numAtomsMoved, lowerCorner, upperCorner, atomDensity,
- maxAtomGroupRadius, haveFep_, pinPolicy);
+ grid.setDimensions(
+ ddZone, n - numAtomsMoved, lowerCorner, upperCorner, atomDensity, maxAtomGroupRadius, haveFep_, pinPolicy);
for (GridWork& work : gridWork_)
{
/* Make space for the new cell indices */
gridSetData_.cells.resize(*atomRange.end());
- const int nthread = gmx_omp_nthreads_get(emntPairsearch);
+ const int nthread = gmx_omp_nthreads_get(ModuleMultiThread::Pairsearch);
GMX_ASSERT(nthread > 0, "We expect the OpenMP thread count to be set");
#pragma omp parallel for num_threads(nthread) schedule(static)
{
try
{
- Grid::calcColumnIndices(grid.dimensions(), updateGroupsCog, atomRange, x, ddZone, move, thread,
- nthread, gridSetData_.cells, gridWork_[thread].numAtomsPerColumn);
+ Grid::calcColumnIndices(grid.dimensions(),
+ updateGroupsCog,
+ atomRange,
+ x,
+ ddZone,
+ move,
+ thread,
+ nthread,
+ gridSetData_.cells,
+ gridWork_[thread].numAtomsPerColumn);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
/* Copy the already computed cell indices to the grid and sort, when needed */
- grid.setCellIndices(ddZone, cellOffset, &gridSetData_, gridWork_, atomRange, atomInfo.data(), x,
- numAtomsMoved, nbat);
+ grid.setCellIndices(
+ ddZone, cellOffset, &gridSetData_, gridWork_, atomRange, atomInfo.data(), x, numAtomsMoved, nbat);
if (gridIndex == 0)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "grid.h"
#include "gridsetdata.h"
-
+struct gmx_domdec_zones_t;
struct nbnxn_atomdata_t;
enum class PairlistType;
enum class PbcType : int;
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static void clearBufferFlagged(const nbnxn_atomdata_t& nbat, int outputIndex, gmx::ArrayRef<real> buffer)
{
gmx::ArrayRef<const gmx_bitmask_t> flags = nbat.buffer_flags;
- gmx_bitmask_t our_flag;
+ gmx_bitmask_t our_flag; // NOLINT(cppcoreguidelines-init-variables)
bitmask_init_bit(&our_flag, outputIndex);
constexpr size_t numComponentsPerBlock = NBNXN_BUFFERFLAG_SIZE * numComponentsPerElement;
void clear_fshift(real* fshift)
{
- int i;
-
- for (i = 0; i < SHIFTS * DIM; i++)
+ for (int i = 0; i < gmx::c_numShiftVectors * DIM; i++)
{
fshift[i] = 0;
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
-#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
#include "gromacs/gmxlib/nonbonded/nonbonded.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdlib/enerdata_utils.h"
#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/mdtypes/nblist.h"
#include "gromacs/mdtypes/simulation_workload.h"
#include "gromacs/nbnxm/gpu_data_mgmt.h"
#include "gromacs/nbnxm/nbnxm.h"
#include "gromacs/simd/simd.h"
#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/enumerationhelpers.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/real.h"
#include "kernel_common.h"
#include "nbnxm_gpu.h"
-#include "nbnxm_gpu_data_mgmt.h"
#include "nbnxm_simd.h"
#include "pairlistset.h"
#include "pairlistsets.h"
}
}
-/*! \brief Dispatches the non-bonded N versus M atom cluster CPU kernels.
- *
- * OpenMP parallelization is performed within this function.
- * Energy reduction, but not force and shift force reduction, is performed
- * within this function.
- *
- * \param[in] pairlistSet Pairlists with local or non-local interactions to compute
- * \param[in] kernelSetup The non-bonded kernel setup
- * \param[in,out] nbat The atomdata for the interactions
- * \param[in] ic Non-bonded interaction constants
- * \param[in] shiftVectors The PBC shift vectors
- * \param[in] stepWork Flags that tell what to compute
- * \param[in] clearF Enum that tells if to clear the force output buffer
- * \param[out] vCoulomb Output buffer for Coulomb energies
- * \param[out] vVdw Output buffer for Van der Waals energies
- * \param[in] wcycle Pointer to cycle counting data structure.
- */
-static void nbnxn_kernel_cpu(const PairlistSet& pairlistSet,
- const Nbnxm::KernelSetup& kernelSetup,
- nbnxn_atomdata_t* nbat,
- const interaction_const_t& ic,
- rvec* shiftVectors,
- const gmx::StepWorkload& stepWork,
- int clearF,
- real* vCoulomb,
- real* vVdw,
- gmx_wallcycle* wcycle)
+static int getCoulombKernelType(const Nbnxm::KernelSetup& kernelSetup, const interaction_const_t& ic)
{
- int coulkt;
- if (EEL_RF(ic.eeltype) || ic.eeltype == eelCUT)
+ if (EEL_RF(ic.eeltype) || ic.eeltype == CoulombInteractionType::Cut)
{
- coulkt = coulktRF;
+ return coulktRF;
}
else
{
{
if (ic.rcoulomb == ic.rvdw)
{
- coulkt = coulktTAB;
+ return coulktTAB;
}
else
{
- coulkt = coulktTAB_TWIN;
+ return coulktTAB_TWIN;
}
}
else
{
if (ic.rcoulomb == ic.rvdw)
{
- coulkt = coulktEWALD;
+ return coulktEWALD;
}
else
{
- coulkt = coulktEWALD_TWIN;
+ return coulktEWALD_TWIN;
}
}
}
+}
- const nbnxn_atomdata_t::Params& nbatParams = nbat->params();
-
- int vdwkt = 0;
- if (ic.vdwtype == evdwCUT)
+static int getVdwKernelType(const Nbnxm::KernelSetup& kernelSetup,
+ const nbnxn_atomdata_t::Params& nbatParams,
+ const interaction_const_t& ic)
+{
+ if (ic.vdwtype == VanDerWaalsType::Cut)
{
switch (ic.vdw_modifier)
{
- case eintmodNONE:
- case eintmodPOTSHIFT:
- switch (nbatParams.comb_rule)
+ case InteractionModifiers::None:
+ case InteractionModifiers::PotShift:
+ switch (nbatParams.ljCombinationRule)
{
- case ljcrGEOM: vdwkt = vdwktLJCUT_COMBGEOM; break;
- case ljcrLB: vdwkt = vdwktLJCUT_COMBLB; break;
- case ljcrNONE: vdwkt = vdwktLJCUT_COMBNONE; break;
- default: GMX_RELEASE_ASSERT(false, "Unknown combination rule");
+ case LJCombinationRule::Geometric: return vdwktLJCUT_COMBGEOM;
+ case LJCombinationRule::LorentzBerthelot: return vdwktLJCUT_COMBLB;
+ case LJCombinationRule::None: return vdwktLJCUT_COMBNONE;
+ default: gmx_incons("Unknown combination rule");
}
- break;
- case eintmodFORCESWITCH: vdwkt = vdwktLJFORCESWITCH; break;
- case eintmodPOTSWITCH: vdwkt = vdwktLJPOTSWITCH; break;
- default: GMX_RELEASE_ASSERT(false, "Unsupported VdW interaction modifier");
+ case InteractionModifiers::ForceSwitch: return vdwktLJFORCESWITCH;
+ case InteractionModifiers::PotSwitch: return vdwktLJPOTSWITCH;
+ default:
+ std::string errorMsg =
+ gmx::formatString("Unsupported VdW interaction modifier %s (%d)",
+ enumValueToString(ic.vdw_modifier),
+ static_cast<int>(ic.vdw_modifier));
+ gmx_incons(errorMsg);
}
}
- else if (ic.vdwtype == evdwPME)
+ else if (ic.vdwtype == VanDerWaalsType::Pme)
{
- if (ic.ljpme_comb_rule == eljpmeGEOM)
+ if (ic.ljpme_comb_rule == LongRangeVdW::Geom)
{
- vdwkt = vdwktLJEWALDCOMBGEOM;
+ return vdwktLJEWALDCOMBGEOM;
}
else
{
- vdwkt = vdwktLJEWALDCOMBLB;
/* At setup we (should have) selected the C reference kernel */
GMX_RELEASE_ASSERT(kernelSetup.kernelType == Nbnxm::KernelType::Cpu4x4_PlainC,
"Only the C reference nbnxn SIMD kernel supports LJ-PME with LB "
"combination rules");
+ return vdwktLJEWALDCOMBLB;
}
}
else
{
- GMX_RELEASE_ASSERT(false, "Unsupported VdW interaction type");
+ std::string errorMsg = gmx::formatString("Unsupported VdW interaction type %s (%d)",
+ enumValueToString(ic.vdwtype),
+ static_cast<int>(ic.vdwtype));
+ gmx_incons(errorMsg);
}
+}
+
+/*! \brief Dispatches the non-bonded N versus M atom cluster CPU kernels.
+ *
+ * OpenMP parallelization is performed within this function.
+ * Energy reduction, but not force and shift force reduction, is performed
+ * within this function.
+ *
+ * \param[in] pairlistSet Pairlists with local or non-local interactions to compute
+ * \param[in] kernelSetup The non-bonded kernel setup
+ * \param[in,out] nbat The atomdata for the interactions
+ * \param[in] ic Non-bonded interaction constants
+ * \param[in] shiftVectors The PBC shift vectors
+ * \param[in] stepWork Flags that tell what to compute
+ * \param[in] clearF Enum that tells if to clear the force output buffer
+ * \param[out] vCoulomb Output buffer for Coulomb energies
+ * \param[out] vVdw Output buffer for Van der Waals energies
+ * \param[in] wcycle Pointer to cycle counting data structure.
+ */
+static void nbnxn_kernel_cpu(const PairlistSet& pairlistSet,
+ const Nbnxm::KernelSetup& kernelSetup,
+ nbnxn_atomdata_t* nbat,
+ const interaction_const_t& ic,
+ gmx::ArrayRef<const gmx::RVec> shiftVectors,
+ const gmx::StepWorkload& stepWork,
+ int clearF,
+ real* vCoulomb,
+ real* vVdw,
+ gmx_wallcycle* wcycle)
+{
+
+ const nbnxn_atomdata_t::Params& nbatParams = nbat->params();
+
+ const int coulkt = getCoulombKernelType(kernelSetup, ic);
+ const int vdwkt = getVdwKernelType(kernelSetup, nbatParams, ic);
gmx::ArrayRef<const NbnxnPairlistCpu> pairlists = pairlistSet.cpuLists();
- int gmx_unused nthreads = gmx_omp_nthreads_get(emntNonbonded);
- wallcycle_sub_start(wcycle, ewcsNONBONDED_CLEAR);
+ const auto* shiftVecPointer = as_rvec_array(shiftVectors.data());
+
+ int gmx_unused nthreads = gmx_omp_nthreads_get(ModuleMultiThread::Nonbonded);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::NonbondedClear);
#pragma omp parallel for schedule(static) num_threads(nthreads)
for (gmx::index nb = 0; nb < pairlists.ssize(); nb++)
{
if (nb == 0)
{
- wallcycle_sub_stop(wcycle, ewcsNONBONDED_CLEAR);
- wallcycle_sub_start(wcycle, ewcsNONBONDED_KERNEL);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::NonbondedClear);
+ wallcycle_sub_start(wcycle, WallCycleSubCounter::NonbondedKernel);
}
// TODO: Change to reference
switch (kernelSetup.kernelType)
{
case Nbnxm::KernelType::Cpu4x4_PlainC:
- nbnxn_kernel_noener_ref[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
+ nbnxn_kernel_noener_ref[coulkt][vdwkt](pairlist, nbat, &ic, shiftVecPointer, out);
break;
#ifdef GMX_NBNXN_SIMD_2XNN
case Nbnxm::KernelType::Cpu4xN_Simd_2xNN:
- nbnxm_kernel_noener_simd_2xmm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
+ nbnxm_kernel_noener_simd_2xmm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVecPointer, out);
break;
#endif
#ifdef GMX_NBNXN_SIMD_4XN
case Nbnxm::KernelType::Cpu4xN_Simd_4xN:
- nbnxm_kernel_noener_simd_4xm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
+ nbnxm_kernel_noener_simd_4xm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVecPointer, out);
break;
#endif
default: GMX_RELEASE_ASSERT(false, "Unsupported kernel architecture");
switch (kernelSetup.kernelType)
{
case Nbnxm::KernelType::Cpu4x4_PlainC:
- nbnxn_kernel_ener_ref[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
+ nbnxn_kernel_ener_ref[coulkt][vdwkt](pairlist, nbat, &ic, shiftVecPointer, out);
break;
#ifdef GMX_NBNXN_SIMD_2XNN
case Nbnxm::KernelType::Cpu4xN_Simd_2xNN:
- nbnxm_kernel_ener_simd_2xmm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
+ nbnxm_kernel_ener_simd_2xmm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVecPointer, out);
break;
#endif
#ifdef GMX_NBNXN_SIMD_4XN
case Nbnxm::KernelType::Cpu4xN_Simd_4xN:
- nbnxm_kernel_ener_simd_4xm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
+ nbnxm_kernel_ener_simd_4xm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVecPointer, out);
break;
#endif
default: GMX_RELEASE_ASSERT(false, "Unsupported kernel architecture");
{
case Nbnxm::KernelType::Cpu4x4_PlainC:
unrollj = c_nbnxnCpuIClusterSize;
- nbnxn_kernel_energrp_ref[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
+ nbnxn_kernel_energrp_ref[coulkt][vdwkt](pairlist, nbat, &ic, shiftVecPointer, out);
break;
#ifdef GMX_NBNXN_SIMD_2XNN
case Nbnxm::KernelType::Cpu4xN_Simd_2xNN:
unrollj = GMX_SIMD_REAL_WIDTH / 2;
- nbnxm_kernel_energrp_simd_2xmm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
+ nbnxm_kernel_energrp_simd_2xmm[coulkt][vdwkt](
+ pairlist, nbat, &ic, shiftVecPointer, out);
break;
#endif
#ifdef GMX_NBNXN_SIMD_4XN
case Nbnxm::KernelType::Cpu4xN_Simd_4xN:
unrollj = GMX_SIMD_REAL_WIDTH;
- nbnxm_kernel_energrp_simd_4xm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
+ nbnxm_kernel_energrp_simd_4xm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVecPointer, out);
break;
#endif
default: GMX_RELEASE_ASSERT(false, "Unsupported kernel architecture");
}
}
}
- wallcycle_sub_stop(wcycle, ewcsNONBONDED_KERNEL);
+ wallcycle_sub_stop(wcycle, WallCycleSubCounter::NonbondedKernel);
if (stepWork.computeEnergy)
{
{
const bool usingGpuKernels = nbv.useGpu();
- int enr_nbnxn_kernel_ljc;
- if (EEL_RF(ic.eeltype) || ic.eeltype == eelCUT)
+ int enr_nbnxn_kernel_ljc = eNRNB;
+ if (EEL_RF(ic.eeltype) || ic.eeltype == CoulombInteractionType::Cut)
{
enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_RF;
}
/* The Coulomb-only kernels are offset -eNR_NBNXN_LJ_RF+eNR_NBNXN_RF */
inc_nrnb(nrnb, enr_nbnxn_kernel_ljc - eNR_NBNXN_LJ_RF + eNR_NBNXN_RF, pairlistSet.natpair_q_);
- if (ic.vdw_modifier == eintmodFORCESWITCH)
+ if (ic.vdw_modifier == InteractionModifiers::ForceSwitch)
{
/* We add up the switch cost separately */
- inc_nrnb(nrnb, eNR_NBNXN_ADD_LJ_FSW + (stepWork.computeEnergy ? 1 : 0),
+ inc_nrnb(nrnb,
+ eNR_NBNXN_ADD_LJ_FSW + (stepWork.computeEnergy ? 1 : 0),
pairlistSet.natpair_ljq_ + pairlistSet.natpair_lj_);
}
- if (ic.vdw_modifier == eintmodPOTSWITCH)
+ if (ic.vdw_modifier == InteractionModifiers::PotSwitch)
{
/* We add up the switch cost separately */
- inc_nrnb(nrnb, eNR_NBNXN_ADD_LJ_PSW + (stepWork.computeEnergy ? 1 : 0),
+ inc_nrnb(nrnb,
+ eNR_NBNXN_ADD_LJ_PSW + (stepWork.computeEnergy ? 1 : 0),
pairlistSet.natpair_ljq_ + pairlistSet.natpair_lj_);
}
- if (ic.vdwtype == evdwPME)
+ if (ic.vdwtype == VanDerWaalsType::Pme)
{
/* We add up the LJ Ewald cost separately */
- inc_nrnb(nrnb, eNR_NBNXN_ADD_LJ_EWALD + (stepWork.computeEnergy ? 1 : 0),
+ inc_nrnb(nrnb,
+ eNR_NBNXN_ADD_LJ_EWALD + (stepWork.computeEnergy ? 1 : 0),
pairlistSet.natpair_ljq_ + pairlistSet.natpair_lj_);
}
}
-void nonbonded_verlet_t::dispatchNonbondedKernel(gmx::InteractionLocality iLocality,
- const interaction_const_t& ic,
- const gmx::StepWorkload& stepWork,
- int clearF,
- const t_forcerec& fr,
- gmx_enerdata_t* enerd,
- t_nrnb* nrnb)
+void nonbonded_verlet_t::dispatchNonbondedKernel(gmx::InteractionLocality iLocality,
+ const interaction_const_t& ic,
+ const gmx::StepWorkload& stepWork,
+ int clearF,
+ gmx::ArrayRef<const gmx::RVec> shiftvec,
+ gmx::ArrayRef<real> repulsionDispersionSR,
+ gmx::ArrayRef<real> CoulombSR,
+ t_nrnb* nrnb) const
{
const PairlistSet& pairlistSet = pairlistSets().pairlistSet(iLocality);
case Nbnxm::KernelType::Cpu4x4_PlainC:
case Nbnxm::KernelType::Cpu4xN_Simd_4xN:
case Nbnxm::KernelType::Cpu4xN_Simd_2xNN:
- nbnxn_kernel_cpu(pairlistSet, kernelSetup(), nbat.get(), ic, fr.shift_vec, stepWork,
- clearF, enerd->grpp.ener[egCOULSR].data(),
- fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data(),
+ nbnxn_kernel_cpu(pairlistSet,
+ kernelSetup(),
+ nbat.get(),
+ ic,
+ shiftvec,
+ stepWork,
+ clearF,
+ CoulombSR.data(),
+ repulsionDispersionSR.data(),
wcycle_);
break;
break;
case Nbnxm::KernelType::Cpu8x8x8_PlainC:
- nbnxn_kernel_gpu_ref(
- pairlistSet.gpuList(), nbat.get(), &ic, fr.shift_vec, stepWork, clearF,
- nbat->out[0].f, nbat->out[0].fshift.data(), enerd->grpp.ener[egCOULSR].data(),
- fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data());
+ nbnxn_kernel_gpu_ref(pairlistSet.gpuList(),
+ nbat.get(),
+ &ic,
+ shiftvec,
+ stepWork,
+ clearF,
+ nbat->out[0].f,
+ nbat->out[0].fshift.data(),
+ CoulombSR.data(),
+ repulsionDispersionSR.data());
break;
default: GMX_RELEASE_ASSERT(false, "Invalid nonbonded kernel type passed!");
accountFlops(nrnb, pairlistSet, *this, ic, stepWork);
}
-void nonbonded_verlet_t::dispatchFreeEnergyKernel(gmx::InteractionLocality iLocality,
- const t_forcerec* fr,
- rvec x[],
+void nonbonded_verlet_t::dispatchFreeEnergyKernel(gmx::InteractionLocality iLocality,
+ const t_forcerec& fr,
+ gmx::ArrayRef<const gmx::RVec> coords,
gmx::ForceWithShiftForces* forceWithShiftForces,
- const t_mdatoms& mdatoms,
+ gmx::ArrayRef<const real> chargeA,
+ gmx::ArrayRef<const real> chargeB,
+ gmx::ArrayRef<const int> typeA,
+ gmx::ArrayRef<const int> typeB,
t_lambda* fepvals,
- gmx::ArrayRef<real const> lambda,
+ gmx::ArrayRef<const real> lambda,
gmx_enerdata_t* enerd,
const gmx::StepWorkload& stepWork,
t_nrnb* nrnb)
donb_flags |= GMX_NONBONDED_DO_POTENTIAL;
}
- nb_kernel_data_t kernel_data;
- real dvdl_nb[efptNR] = { 0 };
- kernel_data.flags = donb_flags;
- kernel_data.lambda = lambda.data();
- kernel_data.dvdl = dvdl_nb;
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real> dvdl_nb = { 0 };
+ int kernelFlags = donb_flags;
+ gmx::ArrayRef<const real> kernelLambda = lambda;
+ gmx::ArrayRef<real> kernelDvdl = dvdl_nb;
- kernel_data.energygrp_elec = enerd->grpp.ener[egCOULSR].data();
- kernel_data.energygrp_vdw = enerd->grpp.ener[egLJSR].data();
+ gmx::ArrayRef<real> energygrp_elec = enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR];
+ gmx::ArrayRef<real> energygrp_vdw = enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::LJSR];
- GMX_ASSERT(gmx_omp_nthreads_get(emntNonbonded) == nbl_fep.ssize(),
+ GMX_ASSERT(gmx_omp_nthreads_get(ModuleMultiThread::Nonbonded) == nbl_fep.ssize(),
"Number of lists should be same as number of NB threads");
- wallcycle_sub_start(wcycle_, ewcsNONBONDED_FEP);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::NonbondedFep);
#pragma omp parallel for schedule(static) num_threads(nbl_fep.ssize())
for (gmx::index th = 0; th < nbl_fep.ssize(); th++)
{
try
{
- gmx_nb_free_energy_kernel(nbl_fep[th].get(), x, forceWithShiftForces, fr, &mdatoms,
- &kernel_data, nrnb);
+ gmx_nb_free_energy_kernel(*nbl_fep[th],
+ coords,
+ forceWithShiftForces,
+ fr.use_simd_kernels,
+ fr.ntype,
+ fr.rlist,
+ *fr.ic,
+ fr.shift_vec,
+ fr.nbfp,
+ fr.ljpme_c6grid,
+ chargeA,
+ chargeB,
+ typeA,
+ typeB,
+ kernelFlags,
+ kernelLambda,
+ kernelDvdl,
+ energygrp_elec,
+ energygrp_vdw,
+ nrnb);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
if (fepvals->sc_alpha != 0)
{
- enerd->dvdl_nonlin[efptVDW] += dvdl_nb[efptVDW];
- enerd->dvdl_nonlin[efptCOUL] += dvdl_nb[efptCOUL];
+ enerd->dvdl_nonlin[FreeEnergyPerturbationCouplingType::Vdw] +=
+ dvdl_nb[FreeEnergyPerturbationCouplingType::Vdw];
+ enerd->dvdl_nonlin[FreeEnergyPerturbationCouplingType::Coul] +=
+ dvdl_nb[FreeEnergyPerturbationCouplingType::Coul];
}
else
{
- enerd->dvdl_lin[efptVDW] += dvdl_nb[efptVDW];
- enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL];
+ enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Vdw] +=
+ dvdl_nb[FreeEnergyPerturbationCouplingType::Vdw];
+ enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Coul] +=
+ dvdl_nb[FreeEnergyPerturbationCouplingType::Coul];
}
/* If we do foreign lambda and we have soft-core interactions
*/
if (fepvals->n_lambda > 0 && stepWork.computeDhdl && fepvals->sc_alpha != 0)
{
- real lam_i[efptNR];
- kernel_data.flags = (donb_flags & ~(GMX_NONBONDED_DO_FORCE | GMX_NONBONDED_DO_SHIFTFORCE))
- | GMX_NONBONDED_DO_FOREIGNLAMBDA;
- kernel_data.lambda = lam_i;
- kernel_data.dvdl = dvdl_nb;
- kernel_data.energygrp_elec = enerd->foreign_grpp.ener[egCOULSR].data();
- kernel_data.energygrp_vdw = enerd->foreign_grpp.ener[egLJSR].data();
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real> lam_i;
+ kernelFlags = (donb_flags & ~(GMX_NONBONDED_DO_FORCE | GMX_NONBONDED_DO_SHIFTFORCE))
+ | GMX_NONBONDED_DO_FOREIGNLAMBDA;
+ kernelLambda = lam_i;
+ kernelDvdl = dvdl_nb;
+ gmx::ArrayRef<real> energygrp_elec =
+ enerd->foreign_grpp.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR];
+ gmx::ArrayRef<real> energygrp_vdw =
+ enerd->foreign_grpp.energyGroupPairTerms[NonBondedEnergyTerms::LJSR];
for (gmx::index i = 0; i < 1 + enerd->foreignLambdaTerms.numLambdas(); i++)
{
std::fill(std::begin(dvdl_nb), std::end(dvdl_nb), 0);
- for (int j = 0; j < efptNR; j++)
+ for (int j = 0; j < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); j++)
{
lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i - 1]);
}
{
try
{
- gmx_nb_free_energy_kernel(nbl_fep[th].get(), x, forceWithShiftForces, fr,
- &mdatoms, &kernel_data, nrnb);
+ gmx_nb_free_energy_kernel(*nbl_fep[th],
+ coords,
+ forceWithShiftForces,
+ fr.use_simd_kernels,
+ fr.ntype,
+ fr.rlist,
+ *fr.ic,
+ fr.shift_vec,
+ fr.nbfp,
+ fr.ljpme_c6grid,
+ chargeA,
+ chargeB,
+ typeA,
+ typeB,
+ kernelFlags,
+ kernelLambda,
+ kernelDvdl,
+ energygrp_elec,
+ energygrp_vdw,
+ nrnb);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- sum_epot(enerd->foreign_grpp, enerd->foreign_term);
- enerd->foreignLambdaTerms.accumulate(i, enerd->foreign_term[F_EPOT],
- dvdl_nb[efptVDW] + dvdl_nb[efptCOUL]);
+ sum_epot(enerd->foreign_grpp, enerd->foreign_term.data());
+ enerd->foreignLambdaTerms.accumulate(
+ i,
+ enerd->foreign_term[F_EPOT],
+ dvdl_nb[FreeEnergyPerturbationCouplingType::Vdw]
+ + dvdl_nb[FreeEnergyPerturbationCouplingType::Coul]);
}
}
- wallcycle_sub_stop(wcycle_, ewcsNONBONDED_FEP);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::NonbondedFep);
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <algorithm>
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/interaction_const.h"
static constexpr int c_clSize = c_nbnxnGpuClusterSize;
-void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu* nbl,
- const nbnxn_atomdata_t* nbat,
- const interaction_const_t* iconst,
- rvec* shift_vec,
- const gmx::StepWorkload& stepWork,
- int clearF,
- gmx::ArrayRef<real> f,
- real* fshift,
- real* Vc,
- real* Vvdw)
+void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu* nbl,
+ const nbnxn_atomdata_t* nbat,
+ const interaction_const_t* iconst,
+ gmx::ArrayRef<const gmx::RVec> shiftvec,
+ const gmx::StepWorkload& stepWork,
+ int clearF,
+ gmx::ArrayRef<real> f,
+ real* fshift,
+ real* Vc,
+ real* Vvdw)
{
- gmx_bool bEwald;
- const real* Ftab = nullptr;
- real rcut2, rvdw2, rlist2;
- int ntype;
- real facel;
- int ish3;
- int sci;
- int cj4_ind0, cj4_ind1, cj4_ind;
- int ci, cj;
- int ic, jc, ia, ja, is, ifs, js, jfs, im, jm;
- int n0;
- int ggid;
- real shX, shY, shZ;
- real fscal, tx, ty, tz;
- real rinvsq;
- real iq;
- real qq, vcoul = 0, krsq, vctot;
- int nti;
- int tj;
- real rt, r, eps;
- real rinvsix;
- real Vvdwtot;
- real Vvdw_rep, Vvdw_disp;
- real ix, iy, iz, fix, fiy, fiz;
- real jx, jy, jz;
- real dx, dy, dz, rsq, rinv;
- real int_bit;
- real fexcl;
- real c6, c12;
+ real fscal = NAN;
+ real vcoul = 0;
const nbnxn_excl_t* excl[2];
- int npair_tot, npair;
- int nhwu, nhwu_pruned;
-
if (nbl->na_ci != c_clSize)
{
gmx_fatal(FARGS,
"The neighborlist cluster size in the GPU reference kernel is %d, expected it to "
"be %d",
- nbl->na_ci, c_clSize);
+ nbl->na_ci,
+ c_clSize);
}
if (clearF == enbvClearFYes)
}
}
- bEwald = EEL_FULL(iconst->eeltype);
- if (bEwald)
- {
- Ftab = iconst->coulombEwaldTables->tableF.data();
- }
+ const bool bEwald = EEL_FULL(iconst->eeltype);
- rcut2 = iconst->rcoulomb * iconst->rcoulomb;
- rvdw2 = iconst->rvdw * iconst->rvdw;
+ const real rcut2 = iconst->rcoulomb * iconst->rcoulomb;
+ const real rvdw2 = iconst->rvdw * iconst->rvdw;
- rlist2 = nbl->rlist * nbl->rlist;
+ const real rlist2 = nbl->rlist * nbl->rlist;
- const int* type = nbat->params().type.data();
- facel = iconst->epsfac;
- const real* shiftvec = shift_vec[0];
+ const int* type = nbat->params().type.data();
+ const real facel = iconst->epsfac;
const real* vdwparam = nbat->params().nbfp.data();
- ntype = nbat->params().numTypes;
+ const int ntype = nbat->params().numTypes;
const real* x = nbat->x().data();
- npair_tot = 0;
- nhwu = 0;
- nhwu_pruned = 0;
+ int npair_tot = 0;
+ int nhwu = 0;
+ int nhwu_pruned = 0;
for (const nbnxn_sci_t& nbln : nbl->sci)
{
- ish3 = 3 * nbln.shift;
- shX = shiftvec[ish3];
- shY = shiftvec[ish3 + 1];
- shZ = shiftvec[ish3 + 2];
- cj4_ind0 = nbln.cj4_ind_start;
- cj4_ind1 = nbln.cj4_ind_end;
- sci = nbln.sci;
- vctot = 0;
- Vvdwtot = 0;
-
- if (nbln.shift == CENTRAL && nbl->cj4[cj4_ind0].cj[0] == sci * c_nbnxnGpuNumClusterPerSupercluster)
+ const int ish = nbln.shift;
+ const int ish3 = DIM * ish;
+ const real shX = shiftvec[ish][XX];
+ const real shY = shiftvec[ish][YY];
+ const real shZ = shiftvec[ish][ZZ];
+ const int cj4_ind0 = nbln.cj4_ind_start;
+ const int cj4_ind1 = nbln.cj4_ind_end;
+ const int sci = nbln.sci;
+ real vctot = 0;
+ real Vvdwtot = 0;
+
+ if (nbln.shift == gmx::c_centralShiftIndex
+ && nbl->cj4[cj4_ind0].cj[0] == sci * c_nbnxnGpuNumClusterPerSupercluster)
{
/* we have the diagonal:
* add the charge self interaction energy term
*/
- for (im = 0; im < c_nbnxnGpuNumClusterPerSupercluster; im++)
+ for (int im = 0; im < c_nbnxnGpuNumClusterPerSupercluster; im++)
{
- ci = sci * c_nbnxnGpuNumClusterPerSupercluster + im;
- for (ic = 0; ic < c_clSize; ic++)
+ const int ci = sci * c_nbnxnGpuNumClusterPerSupercluster + im;
+ for (int ic = 0; ic < c_clSize; ic++)
{
- ia = ci * c_clSize + ic;
- iq = x[ia * nbat->xstride + 3];
+ const int ia = ci * c_clSize + ic;
+ real iq = x[ia * nbat->xstride + 3];
vctot += iq * iq;
}
}
if (!bEwald)
{
- vctot *= -facel * 0.5 * iconst->c_rf;
+ vctot *= -facel * 0.5 * iconst->reactionFieldShift;
}
else
{
}
}
- for (cj4_ind = cj4_ind0; (cj4_ind < cj4_ind1); cj4_ind++)
+ for (int cj4_ind = cj4_ind0; (cj4_ind < cj4_ind1); cj4_ind++)
{
excl[0] = &nbl->excl[nbl->cj4[cj4_ind].imei[0].excl_ind];
excl[1] = &nbl->excl[nbl->cj4[cj4_ind].imei[1].excl_ind];
- for (jm = 0; jm < c_nbnxnGpuJgroupSize; jm++)
+ for (int jm = 0; jm < c_nbnxnGpuJgroupSize; jm++)
{
- cj = nbl->cj4[cj4_ind].cj[jm];
+ const int cj = nbl->cj4[cj4_ind].cj[jm];
- for (im = 0; im < c_nbnxnGpuNumClusterPerSupercluster; im++)
+ for (int im = 0; im < c_nbnxnGpuNumClusterPerSupercluster; im++)
{
/* We're only using the first imask,
* but here imei[1].imask is identical.
if ((nbl->cj4[cj4_ind].imei[0].imask >> (jm * c_nbnxnGpuNumClusterPerSupercluster + im))
& 1)
{
- gmx_bool within_rlist;
-
- ci = sci * c_nbnxnGpuNumClusterPerSupercluster + im;
+ const int ci = sci * c_nbnxnGpuNumClusterPerSupercluster + im;
- within_rlist = FALSE;
- npair = 0;
- for (ic = 0; ic < c_clSize; ic++)
+ bool within_rlist = false;
+ int npair = 0;
+ for (int ic = 0; ic < c_clSize; ic++)
{
- ia = ci * c_clSize + ic;
+ const int ia = ci * c_clSize + ic;
- is = ia * nbat->xstride;
- ifs = ia * nbat->fstride;
- ix = shX + x[is + 0];
- iy = shY + x[is + 1];
- iz = shZ + x[is + 2];
- iq = facel * x[is + 3];
- nti = ntype * 2 * type[ia];
+ const int is = ia * nbat->xstride;
+ const int ifs = ia * nbat->fstride;
+ const real ix = shX + x[is + 0];
+ const real iy = shY + x[is + 1];
+ const real iz = shZ + x[is + 2];
+ const real iq = facel * x[is + 3];
+ const int nti = ntype * 2 * type[ia];
- fix = 0;
- fiy = 0;
- fiz = 0;
+ real fix = 0;
+ real fiy = 0;
+ real fiz = 0;
- for (jc = 0; jc < c_clSize; jc++)
+ for (int jc = 0; jc < c_clSize; jc++)
{
- ja = cj * c_clSize + jc;
+ const int ja = cj * c_clSize + jc;
- if (nbln.shift == CENTRAL && ci == cj && ja <= ia)
+ if (nbln.shift == gmx::c_centralShiftIndex && ci == cj && ja <= ia)
{
continue;
}
constexpr int clusterPerSplit =
c_nbnxnGpuClusterSize / c_nbnxnGpuClusterpairSplit;
- int_bit = static_cast<real>(
+ const real int_bit = static_cast<real>(
(excl[jc / clusterPerSplit]->pair[(jc & (clusterPerSplit - 1)) * c_clSize + ic]
>> (jm * c_nbnxnGpuNumClusterPerSupercluster + im))
& 1);
- js = ja * nbat->xstride;
- jfs = ja * nbat->fstride;
- jx = x[js + 0];
- jy = x[js + 1];
- jz = x[js + 2];
- dx = ix - jx;
- dy = iy - jy;
- dz = iz - jz;
- rsq = dx * dx + dy * dy + dz * dz;
+ int js = ja * nbat->xstride;
+ int jfs = ja * nbat->fstride;
+ const real jx = x[js + 0];
+ const real jy = x[js + 1];
+ const real jz = x[js + 2];
+ const real dx = ix - jx;
+ const real dy = iy - jy;
+ const real dz = iz - jz;
+ real rsq = dx * dx + dy * dy + dz * dz;
if (rsq < rlist2)
{
- within_rlist = TRUE;
+ within_rlist = true;
}
if (rsq >= rcut2)
{
// Ensure distance do not become so small that r^-12 overflows
rsq = std::max(rsq, c_nbnxnMinDistanceSquared);
- rinv = gmx::invsqrt(rsq);
- rinvsq = rinv * rinv;
+ const real rinv = gmx::invsqrt(rsq);
+ const real rinvsq = rinv * rinv;
- qq = iq * x[js + 3];
+ const real qq = iq * x[js + 3];
if (!bEwald)
{
/* Reaction-field */
- krsq = iconst->k_rf * rsq;
- fscal = qq * (int_bit * rinv - 2 * krsq) * rinvsq;
+ const real krsq = iconst->reactionFieldCoefficient * rsq;
+ fscal = qq * (int_bit * rinv - 2 * krsq) * rinvsq;
if (stepWork.computeEnergy)
{
- vcoul = qq * (int_bit * rinv + krsq - iconst->c_rf);
+ vcoul = qq * (int_bit * rinv + krsq - iconst->reactionFieldShift);
}
}
else
{
- r = rsq * rinv;
- rt = r * iconst->coulombEwaldTables->scale;
- n0 = static_cast<int>(rt);
- eps = rt - static_cast<real>(n0);
+ const real r = rsq * rinv;
+ const real rt = r * iconst->coulombEwaldTables->scale;
+ const int n0 = static_cast<int>(rt);
+ const real eps = rt - static_cast<real>(n0);
+ const real* Ftab = iconst->coulombEwaldTables->tableF.data();
- fexcl = (1 - eps) * Ftab[n0] + eps * Ftab[n0 + 1];
+ const real fexcl = (1 - eps) * Ftab[n0] + eps * Ftab[n0 + 1];
fscal = qq * (int_bit * rinvsq - fexcl) * rinv;
if (rsq < rvdw2)
{
- tj = nti + 2 * type[ja];
+ const int tj = nti + 2 * type[ja];
/* Vanilla Lennard-Jones cutoff */
- c6 = vdwparam[tj];
- c12 = vdwparam[tj + 1];
+ const real c6 = vdwparam[tj];
+ const real c12 = vdwparam[tj + 1];
- rinvsix = int_bit * rinvsq * rinvsq * rinvsq;
- Vvdw_disp = c6 * rinvsix;
- Vvdw_rep = c12 * rinvsix * rinvsix;
+ const real rinvsix = int_bit * rinvsq * rinvsq * rinvsq;
+ const real Vvdw_disp = c6 * rinvsix;
+ const real Vvdw_rep = c12 * rinvsix * rinvsix;
fscal += (Vvdw_rep - Vvdw_disp) * rinvsq;
if (stepWork.computeEnergy)
}
}
- tx = fscal * dx;
- ty = fscal * dy;
- tz = fscal * dz;
- fix = fix + tx;
- fiy = fiy + ty;
- fiz = fiz + tz;
+ real tx = fscal * dx;
+ real ty = fscal * dy;
+ real tz = fscal * dz;
+ fix = fix + tx;
+ fiy = fiy + ty;
+ fiz = fiz + tz;
f[jfs + 0] -= tx;
f[jfs + 1] -= ty;
f[jfs + 2] -= tz;
nhwu_pruned++;
}
- within_rlist = FALSE;
+ within_rlist = false;
npair = 0;
}
}
if (stepWork.computeEnergy)
{
- ggid = 0;
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
+ const int ggid = 0;
+ Vc[ggid] = Vc[ggid] + vctot;
+ Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
}
}
if (debug)
{
- fprintf(debug, "number of half %dx%d atom pairs: %d after pruning: %d fraction %4.2f\n",
- nbl->na_ci, nbl->na_ci, nhwu, nhwu_pruned, nhwu_pruned / static_cast<double>(nhwu));
- fprintf(debug, "generic kernel pair interactions: %d\n",
- nhwu * nbl->na_ci / 2 * nbl->na_ci);
- fprintf(debug, "generic kernel post-prune pair interactions: %d\n",
+ fprintf(debug,
+ "number of half %dx%d atom pairs: %d after pruning: %d fraction %4.2f\n",
+ nbl->na_ci,
+ nbl->na_ci,
+ nhwu,
+ nhwu_pruned,
+ nhwu_pruned / static_cast<double>(nhwu));
+ fprintf(debug, "generic kernel pair interactions: %d\n", nhwu * nbl->na_ci / 2 * nbl->na_ci);
+ fprintf(debug,
+ "generic kernel post-prune pair interactions: %d\n",
nhwu_pruned * nbl->na_ci / 2 * nbl->na_ci);
fprintf(debug, "generic kernel non-zero pair interactions: %d\n", npair_tot);
- fprintf(debug, "ratio non-zero/post-prune pair interactions: %4.2f\n",
+ fprintf(debug,
+ "ratio non-zero/post-prune pair interactions: %4.2f\n",
npair_tot / static_cast<double>(nhwu_pruned * gmx::exactDiv(nbl->na_ci, 2) * nbl->na_ci));
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
//! Reference (slow) kernel for nb n vs n GPU type pair lists
-void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu* nbl,
- const nbnxn_atomdata_t* nbat,
- const interaction_const_t* iconst,
- rvec* shift_vec,
- const gmx::StepWorkload& stepWork,
- int clearF,
- gmx::ArrayRef<real> f,
- real* fshift,
- real* Vc,
- real* Vvdw);
+void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu* nbl,
+ const nbnxn_atomdata_t* nbat,
+ const interaction_const_t* iconst,
+ gmx::ArrayRef<const gmx::RVec> shiftvec,
+ const gmx::StepWorkload& stepWork,
+ int clearF,
+ gmx::ArrayRef<real> f,
+ real* fshift,
+ real* Vc,
+ real* Vvdw);
#endif
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2017 The GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* advantage in using combination rules, so we (re-)use the same kernel.
*/
//! \{
-static p_nbk_func_noener nbnxn_kernel_noener_ref[coulktNR][vdwktNR_ref] = {
- { nbnxn_kernel_ElecRF_VdwLJ_F_ref, nbnxn_kernel_ElecRF_VdwLJ_F_ref, nbnxn_kernel_ElecRF_VdwLJ_F_ref,
- nbnxn_kernel_ElecRF_VdwLJFsw_F_ref, nbnxn_kernel_ElecRF_VdwLJPsw_F_ref,
- nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_ref, nbnxn_kernel_ElecRF_VdwLJEwCombLB_F_ref },
- { nbnxn_kernel_ElecQSTab_VdwLJ_F_ref, nbnxn_kernel_ElecQSTab_VdwLJ_F_ref, nbnxn_kernel_ElecQSTab_VdwLJ_F_ref,
- nbnxn_kernel_ElecQSTab_VdwLJFsw_F_ref, nbnxn_kernel_ElecQSTab_VdwLJPsw_F_ref,
- nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_ref, nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_F_ref },
- { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_F_ref,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref,
+static const p_nbk_func_noener nbnxn_kernel_noener_ref[coulktNR][vdwktNR_ref] = {
+ { nbnxn_kernel_ElecRF_VdwLJ_F_ref,
+ nbnxn_kernel_ElecRF_VdwLJ_F_ref,
+ nbnxn_kernel_ElecRF_VdwLJ_F_ref,
+ nbnxn_kernel_ElecRF_VdwLJFsw_F_ref,
+ nbnxn_kernel_ElecRF_VdwLJPsw_F_ref,
+ nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_ref,
+ nbnxn_kernel_ElecRF_VdwLJEwCombLB_F_ref },
+ { nbnxn_kernel_ElecQSTab_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJFsw_F_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJPsw_F_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_F_ref },
+ { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref,
nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref },
- { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_F_ref,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref,
+ { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref,
nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref },
- { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_F_ref,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref,
+ { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref,
nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref }
};
-static p_nbk_func_ener nbnxn_kernel_ener_ref[coulktNR][vdwktNR_ref] = {
- { nbnxn_kernel_ElecRF_VdwLJ_VF_ref, nbnxn_kernel_ElecRF_VdwLJ_VF_ref, nbnxn_kernel_ElecRF_VdwLJ_VF_ref,
- nbnxn_kernel_ElecRF_VdwLJFsw_VF_ref, nbnxn_kernel_ElecRF_VdwLJPsw_VF_ref,
- nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_ref, nbnxn_kernel_ElecRF_VdwLJEwCombLB_VF_ref },
- { nbnxn_kernel_ElecQSTab_VdwLJ_VF_ref, nbnxn_kernel_ElecQSTab_VdwLJ_VF_ref,
- nbnxn_kernel_ElecQSTab_VdwLJ_VF_ref, nbnxn_kernel_ElecQSTab_VdwLJFsw_VF_ref,
- nbnxn_kernel_ElecQSTab_VdwLJPsw_VF_ref, nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_ref,
+static const p_nbk_func_ener nbnxn_kernel_ener_ref[coulktNR][vdwktNR_ref] = {
+ { nbnxn_kernel_ElecRF_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecRF_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecRF_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecRF_VdwLJFsw_VF_ref,
+ nbnxn_kernel_ElecRF_VdwLJPsw_VF_ref,
+ nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_ref,
+ nbnxn_kernel_ElecRF_VdwLJEwCombLB_VF_ref },
+ { nbnxn_kernel_ElecQSTab_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJFsw_VF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJPsw_VF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_ref,
nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_VF_ref },
- { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VF_ref,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref,
+ { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref,
nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref },
- { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VF_ref,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref,
+ { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref,
nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref },
- { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VF_ref,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref,
+ { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref,
nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref }
};
-static p_nbk_func_ener nbnxn_kernel_energrp_ref[coulktNR][vdwktNR_ref] = {
- { nbnxn_kernel_ElecRF_VdwLJ_VgrpF_ref, nbnxn_kernel_ElecRF_VdwLJ_VgrpF_ref,
- nbnxn_kernel_ElecRF_VdwLJ_VgrpF_ref, nbnxn_kernel_ElecRF_VdwLJFsw_VgrpF_ref,
- nbnxn_kernel_ElecRF_VdwLJPsw_VgrpF_ref, nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_ref,
+static const p_nbk_func_ener nbnxn_kernel_energrp_ref[coulktNR][vdwktNR_ref] = {
+ { nbnxn_kernel_ElecRF_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecRF_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecRF_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecRF_VdwLJFsw_VgrpF_ref,
+ nbnxn_kernel_ElecRF_VdwLJPsw_VgrpF_ref,
+ nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_ref,
nbnxn_kernel_ElecRF_VdwLJEwCombLB_VgrpF_ref },
- { nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_ref, nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_ref,
- nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_ref, nbnxn_kernel_ElecQSTab_VdwLJFsw_VgrpF_ref,
- nbnxn_kernel_ElecQSTab_VdwLJPsw_VgrpF_ref, nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref,
+ { nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJFsw_VgrpF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJPsw_VgrpF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref,
nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_VgrpF_ref },
- { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref,
+ { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref,
nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref },
- { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref,
+ { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref,
nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref },
- { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref,
+ { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref,
nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref }
};
//! \}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#endif
{
- int cj;
-#ifdef ENERGY_GROUPS
- int egp_cj;
-#endif
- int i;
-
- cj = l_cj[cjind].cj;
+ const int cj = l_cj[cjind].cj;
#ifdef ENERGY_GROUPS
- egp_cj = nbatParams.energrp[cj];
+ const int egp_cj = nbatParams.energrp[cj];
#endif
- for (i = 0; i < UNROLLI; i++)
+ for (int i = 0; i < UNROLLI; i++)
{
- int ai;
- int type_i_off;
- int j;
-
- ai = ci * UNROLLI + i;
+ const int ai = ci * UNROLLI + i;
- type_i_off = type[ai] * ntype2;
+ const int type_i_off = type[ai] * ntype2;
- for (j = 0; j < UNROLLJ; j++)
+ for (int j = 0; j < UNROLLJ; j++)
{
- int aj;
- real dx, dy, dz;
- real rsq, rinv;
- real rinvsq, rinvsix;
- real c6, c12;
real FrLJ6 = 0, FrLJ12 = 0, frLJ = 0;
- real VLJ gmx_unused;
-#if defined LJ_FORCE_SWITCH || defined LJ_POT_SWITCH
- real r, rsw;
-#endif
-
-#ifdef CALC_COULOMB
- real qq;
- real fcoul;
-# ifdef CALC_COUL_TAB
- real rs, frac;
- int ri;
- real fexcl;
-# endif
-# ifdef CALC_ENERGIES
- real vcoul;
-# endif
-#endif
- real fscal;
- real fx, fy, fz;
/* A multiply mask used to zero an interaction
* when either the distance cutoff is exceeded, or
* (if appropriate) the i and j indices are
* unsuitable for this kind of inner loop. */
- real skipmask;
-
#ifdef CHECK_EXCLS
/* A multiply mask used to zero an interaction
* when that interaction should be excluded
* (e.g. because of bonding). */
- real interact = static_cast<real>((l_cj[cjind].excl >> (i * UNROLLI + j)) & 1);
+ const real interact = static_cast<real>((l_cj[cjind].excl >> (i * UNROLLI + j)) & 1);
# ifndef EXCL_FORCES
- skipmask = interact;
+ real skipmask = interact;
# else
- skipmask = (cj == ci_sh && j <= i) ? 0.0 : 1.0;
+ real skipmask = (cj == ci_sh && j <= i) ? 0.0 : 1.0;
# endif
#else
constexpr real interact = 1.0;
- skipmask = interact;
+ real skipmask = interact;
#endif
- VLJ = 0;
+ real gmx_unused VLJ = 0;
- aj = cj * UNROLLJ + j;
+ const int aj = cj * UNROLLJ + j;
- dx = xi[i * XI_STRIDE + XX] - x[aj * X_STRIDE + XX];
- dy = xi[i * XI_STRIDE + YY] - x[aj * X_STRIDE + YY];
- dz = xi[i * XI_STRIDE + ZZ] - x[aj * X_STRIDE + ZZ];
+ const real dx = xi[i * XI_STRIDE + XX] - x[aj * X_STRIDE + XX];
+ const real dy = xi[i * XI_STRIDE + YY] - x[aj * X_STRIDE + YY];
+ const real dz = xi[i * XI_STRIDE + ZZ] - x[aj * X_STRIDE + ZZ];
- rsq = dx * dx + dy * dy + dz * dz;
+ real rsq = dx * dx + dy * dy + dz * dz;
/* Prepare to enforce the cut-off. */
skipmask = (rsq >= rcut2) ? 0 : skipmask;
npair++;
#endif
- rinv = gmx::invsqrt(rsq);
+ real rinv = gmx::invsqrt(rsq);
/* 5 flops for invsqrt */
/* Partially enforce the cut-off (and perhaps
* the Coulomb table during lookup. */
rinv = rinv * skipmask;
- rinvsq = rinv * rinv;
+ const real rinvsq = rinv * rinv;
#ifdef HALF_LJ
if (i < UNROLLI / 2)
#endif
{
- c6 = nbfp[type_i_off + type[aj] * 2];
- c12 = nbfp[type_i_off + type[aj] * 2 + 1];
+ const real c6 = nbfp[type_i_off + type[aj] * 2];
+ const real c12 = nbfp[type_i_off + type[aj] * 2 + 1];
#if defined LJ_CUT || defined LJ_FORCE_SWITCH || defined LJ_POT_SWITCH
- rinvsix = interact * rinvsq * rinvsq * rinvsq;
- FrLJ6 = c6 * rinvsix;
- FrLJ12 = c12 * rinvsix * rinvsix;
- frLJ = FrLJ12 - FrLJ6;
+ real rinvsix = interact * rinvsq * rinvsq * rinvsq;
+ FrLJ6 = c6 * rinvsix;
+ FrLJ12 = c12 * rinvsix * rinvsix;
+ frLJ = FrLJ12 - FrLJ6;
/* 7 flops for r^-2 + LJ force */
# if defined CALC_ENERGIES || defined LJ_POT_SWITCH
VLJ = (FrLJ12 + c12 * ic->repulsion_shift.cpot) / 12
#if defined LJ_FORCE_SWITCH || defined LJ_POT_SWITCH
/* Force or potential switching from ic->rvdw_switch */
- r = rsq * rinv;
- rsw = r - ic->rvdw_switch;
- rsw = (rsw >= 0.0 ? rsw : 0.0);
+ real r = rsq * rinv;
+ real rsw = r - ic->rvdw_switch;
+ rsw = (rsw >= 0.0 ? rsw : 0.0);
#endif
#ifdef LJ_FORCE_SWITCH
frLJ += -c6 * (ic->dispersion_shift.c2 + ic->dispersion_shift.c3 * rsw) * rsw * rsw * r
#ifdef LJ_POT_SWITCH
{
- real sw, dsw;
-
- sw = 1.0 + (swV3 + (swV4 + swV5 * rsw) * rsw) * rsw * rsw * rsw;
- dsw = (swF2 + (swF3 + swF4 * rsw) * rsw) * rsw * rsw;
+ const real sw = 1.0 + (swV3 + (swV4 + swV5 * rsw) * rsw) * rsw * rsw * rsw;
+ const real dsw = (swF2 + (swF3 + swF4 * rsw) * rsw) * rsw * rsw;
frLJ = frLJ * sw - r * VLJ * dsw;
VLJ *= sw;
#ifdef LJ_EWALD
{
- real c6grid, rinvsix_nm, cr2, expmcr2, poly;
-# ifdef CALC_ENERGIES
- real sh_mask;
-# endif
-
# ifdef LJ_EWALD_COMB_GEOM
- c6grid = ljc[type[ai] * 2] * ljc[type[aj] * 2];
+ const real c6grid = ljc[type[ai] * 2] * ljc[type[aj] * 2];
# elif defined LJ_EWALD_COMB_LB
+ real c6grid = NAN;
{
- real sigma, sigma2, epsilon;
-
/* These sigma and epsilon are scaled to give 6*C6 */
- sigma = ljc[type[ai] * 2] + ljc[type[aj] * 2];
- epsilon = ljc[type[ai] * 2 + 1] * ljc[type[aj] * 2 + 1];
+ const real sigma = ljc[type[ai] * 2] + ljc[type[aj] * 2];
+ const real epsilon = ljc[type[ai] * 2 + 1] * ljc[type[aj] * 2 + 1];
- sigma2 = sigma * sigma;
- c6grid = epsilon * sigma2 * sigma2 * sigma2;
+ const real sigma2 = sigma * sigma;
+ c6grid = epsilon * sigma2 * sigma2 * sigma2;
}
# else
# error "No LJ Ewald combination rule defined"
# ifdef CHECK_EXCLS
/* Recalculate rinvsix without exclusion mask */
- rinvsix_nm = rinvsq * rinvsq * rinvsq;
+ const real rinvsix_nm = rinvsq * rinvsq * rinvsq;
# else
- rinvsix_nm = rinvsix;
+ const real rinvsix_nm = rinvsix;
# endif
- cr2 = lje_coeff2 * rsq;
+ const real cr2 = lje_coeff2 * rsq;
# if GMX_DOUBLE
- expmcr2 = exp(-cr2);
+ const real expmcr2 = exp(-cr2);
# else
- expmcr2 = expf(-cr2);
+ const real expmcr2 = expf(-cr2);
# endif
- poly = 1 + cr2 + 0.5 * cr2 * cr2;
+ const real poly = 1 + cr2 + 0.5 * cr2 * cr2;
/* Subtract the grid force from the total LJ force */
frLJ += c6grid * (rinvsix_nm - expmcr2 * (rinvsix_nm * poly + lje_coeff6_6));
# ifdef CALC_ENERGIES
/* Shift should only be applied to real LJ pairs */
- sh_mask = lje_vc * interact;
+ const real sh_mask = lje_vc * interact;
VLJ += c6grid / 6 * (rinvsix_nm * (1 - expmcr2 * poly) + sh_mask);
# endif
#ifdef VDW_CUTOFF_CHECK
/* Mask for VdW cut-off shorter than Coulomb cut-off */
{
- real skipmask_rvdw;
-
- skipmask_rvdw = (rsq < rvdw2) ? 1.0 : 0.0;
+ real skipmask_rvdw = (rsq < rvdw2) ? 1.0 : 0.0;
frLJ *= skipmask_rvdw;
# ifdef CALC_ENERGIES
VLJ *= skipmask_rvdw;
* to the force and potential, and the easiest way
* to do this is to zero the charges in
* advance. */
- qq = skipmask * qi[i] * q[aj];
+ const real qq = skipmask * qi[i] * q[aj];
# ifdef CALC_COUL_RF
- fcoul = qq * (interact * rinv * rinvsq - k_rf2);
+ real fcoul = qq * (interact * rinv * rinvsq - k_rf2);
/* 4 flops for RF force */
# ifdef CALC_ENERGIES
- vcoul = qq * (interact * rinv + k_rf * rsq - c_rf);
+ real vcoul = qq * (interact * rinv + reactionFieldCoefficient * rsq - reactionFieldShift);
/* 4 flops for RF energy */
# endif
# endif
# ifdef CALC_COUL_TAB
- rs = rsq * rinv * tab_coul_scale;
- ri = int(rs);
- frac = rs - static_cast<real>(ri);
+ const real rs = rsq * rinv * tab_coul_scale;
+ const int ri = int(rs);
+ const real frac = rs - static_cast<real>(ri);
# if !GMX_DOUBLE
/* fexcl = F_i + frac * (F_(i+1)-F_i) */
- fexcl = tab_coul_FDV0[ri * 4] + frac * tab_coul_FDV0[ri * 4 + 1];
+ const real fexcl = tab_coul_FDV0[ri * 4] + frac * tab_coul_FDV0[ri * 4 + 1];
# else
/* fexcl = (1-frac) * F_i + frac * F_(i+1) */
- fexcl = (1 - frac) * tab_coul_F[ri] + frac * tab_coul_F[ri + 1];
+ const real fexcl = (1 - frac) * tab_coul_F[ri] + frac * tab_coul_F[ri + 1];
# endif
- fcoul = interact * rinvsq - fexcl;
+ real fcoul = interact * rinvsq - fexcl;
/* 7 flops for float 1/r-table force */
# ifdef CALC_ENERGIES
# if !GMX_DOUBLE
- vcoul = qq
+ real vcoul =
+ qq
* (interact * (rinv - ic->sh_ewald)
- (tab_coul_FDV0[ri * 4 + 2] - halfsp * frac * (tab_coul_FDV0[ri * 4] + fexcl)));
/* 7 flops for float 1/r-table energy (8 with excls) */
# else
- vcoul = qq
- * (interact * (rinv - ic->sh_ewald)
- - (tab_coul_V[ri] - halfsp * frac * (tab_coul_F[ri] + fexcl)));
+ real vcoul = qq
+ * (interact * (rinv - ic->sh_ewald)
+ - (tab_coul_V[ri] - halfsp * frac * (tab_coul_F[ri] + fexcl)));
# endif
# endif
fcoul *= qq * rinv;
#endif
#ifdef CALC_COULOMB
+ static constexpr bool sc_halfLJ =
# ifdef HALF_LJ
- if (i < UNROLLI / 2)
-# endif
- {
- fscal = frLJ * rinvsq + fcoul;
- /* 2 flops for scalar LJ+Coulomb force */
- }
-# ifdef HALF_LJ
- else
- {
- fscal = fcoul;
- }
+ true;
+# else
+ false;
# endif
+ /* 2 flops for scalar LJ+Coulomb force if !HALF_LJ || (i < UNROLLI / 2) */
+ const real fscal = (!sc_halfLJ || (i < UNROLLI / 2)) ? frLJ * rinvsq + fcoul : fcoul;
#else
- fscal = frLJ * rinvsq;
+ const real fscal = frLJ * rinvsq;
#endif
- fx = fscal * dx;
- fy = fscal * dy;
- fz = fscal * dz;
+ const real fx = fscal * dx;
+ const real fy = fscal * dy;
+ const real fz = fscal * dz;
/* Increment i-atom force */
fi[i * FI_STRIDE + XX] += fx;
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
real* Vc = out->Vc.data();
#endif
- const nbnxn_cj_t* l_cj;
- real rcut2;
-#ifdef VDW_CUTOFF_CHECK
- real rvdw2;
-#endif
- int ntype2;
- real facel;
- int ci, ci_sh;
- int ish, ishf;
- gmx_bool do_LJ, half_LJ, do_coul;
- int cjind0, cjind1, cjind;
-
real xi[UNROLLI * XI_STRIDE];
real fi[UNROLLI * FI_STRIDE];
real qi[UNROLLI];
-#ifdef CALC_ENERGIES
-# ifndef ENERGY_GROUPS
-
- real Vvdw_ci, Vc_ci;
-# else
- int egp_mask;
- int egp_sh_i[UNROLLI];
-# endif
-#endif
-#ifdef LJ_POT_SWITCH
- real swV3, swV4, swV5;
- real swF2, swF3, swF4;
-#endif
-#ifdef LJ_EWALD
- real lje_coeff2, lje_coeff6_6;
-# ifdef CALC_ENERGIES
- real lje_vc;
-# endif
-#endif
-
-#ifdef CALC_COUL_RF
- real k_rf2;
-# ifdef CALC_ENERGIES
- real k_rf, c_rf;
-# endif
-#endif
-#ifdef CALC_COUL_TAB
-# ifdef CALC_ENERGIES
- real halfsp;
-# endif
-# if !GMX_DOUBLE
- const real* tab_coul_FDV0;
-# else
- const real* tab_coul_F;
- const real gmx_unused* tab_coul_V;
-# endif
-#endif
-
#ifdef COUNT_PAIRS
int npair = 0;
#endif
#ifdef LJ_POT_SWITCH
- swV3 = ic->vdw_switch.c3;
- swV4 = ic->vdw_switch.c4;
- swV5 = ic->vdw_switch.c5;
- swF2 = 3 * ic->vdw_switch.c3;
- swF3 = 4 * ic->vdw_switch.c4;
- swF4 = 5 * ic->vdw_switch.c5;
+ const real swV3 = ic->vdw_switch.c3;
+ const real swV4 = ic->vdw_switch.c4;
+ const real swV5 = ic->vdw_switch.c5;
+ const real swF2 = 3 * ic->vdw_switch.c3;
+ const real swF3 = 4 * ic->vdw_switch.c4;
+ const real swF4 = 5 * ic->vdw_switch.c5;
#endif
const nbnxn_atomdata_t::Params& nbatParams = nbat->params();
#ifdef LJ_EWALD
- lje_coeff2 = ic->ewaldcoeff_lj * ic->ewaldcoeff_lj;
- lje_coeff6_6 = lje_coeff2 * lje_coeff2 * lje_coeff2 / 6.0;
+ const real lje_coeff2 = ic->ewaldcoeff_lj * ic->ewaldcoeff_lj;
+ const real lje_coeff6_6 = lje_coeff2 * lje_coeff2 * lje_coeff2 / 6.0;
# ifdef CALC_ENERGIES
- lje_vc = ic->sh_lj_ewald;
+ const real lje_vc = ic->sh_lj_ewald;
# endif
const real* ljc = nbatParams.nbfp_comb.data();
#endif
#ifdef CALC_COUL_RF
- k_rf2 = 2 * ic->k_rf;
+ const real k_rf2 = 2 * ic->reactionFieldCoefficient;
# ifdef CALC_ENERGIES
- k_rf = ic->k_rf;
- c_rf = ic->c_rf;
+ const real reactionFieldCoefficient = ic->reactionFieldCoefficient;
+ const real reactionFieldShift = ic->reactionFieldShift;
# endif
#endif
#ifdef CALC_COUL_TAB
const real tab_coul_scale = ic->coulombEwaldTables->scale;
# ifdef CALC_ENERGIES
- halfsp = 0.5 / tab_coul_scale;
+ const real halfsp = 0.5 / tab_coul_scale;
# endif
# if !GMX_DOUBLE
- tab_coul_FDV0 = ic->coulombEwaldTables->tableFDV0.data();
+ const real* tab_coul_FDV0 = ic->coulombEwaldTables->tableFDV0.data();
# else
- tab_coul_F = ic->coulombEwaldTables->tableF.data();
- tab_coul_V = ic->coulombEwaldTables->tableV.data();
+ const real* tab_coul_F = ic->coulombEwaldTables->tableF.data();
+# ifdef CALC_ENERGIES
+ const real* tab_coul_V = ic->coulombEwaldTables->tableV.data();
+# endif
# endif
#endif
#ifdef ENERGY_GROUPS
- egp_mask = (1 << nbatParams.neg_2log) - 1;
+ const int egp_mask = (1 << nbatParams.neg_2log) - 1;
#endif
- rcut2 = ic->rcoulomb * ic->rcoulomb;
+ const real rcut2 = ic->rcoulomb * ic->rcoulomb;
#ifdef VDW_CUTOFF_CHECK
- rvdw2 = ic->rvdw * ic->rvdw;
+ const real rvdw2 = ic->rvdw * ic->rvdw;
#endif
- ntype2 = nbatParams.numTypes * 2;
+ const int ntype2 = nbatParams.numTypes * 2;
const real* nbfp = nbatParams.nbfp.data();
const real* q = nbatParams.q.data();
const int* type = nbatParams.type.data();
- facel = ic->epsfac;
+ const real facel = ic->epsfac;
const real* shiftvec = shift_vec[0];
const real* x = nbat->x().data();
- l_cj = nbl->cj.data();
+ const nbnxn_cj_t* l_cj = nbl->cj.data();
for (const nbnxn_ci_t& ciEntry : nbl->ci)
{
- int i, d;
-
- ish = (ciEntry.shift & NBNXN_CI_SHIFT);
+ const int ish = (ciEntry.shift & NBNXN_CI_SHIFT);
/* x, f and fshift are assumed to be stored with stride 3 */
- ishf = ish * DIM;
- cjind0 = ciEntry.cj_ind_start;
- cjind1 = ciEntry.cj_ind_end;
+ const int ishf = ish * DIM;
+ const int cjind0 = ciEntry.cj_ind_start;
+ const int cjind1 = ciEntry.cj_ind_end;
/* Currently only works super-cells equal to sub-cells */
- ci = ciEntry.ci;
- ci_sh = (ish == CENTRAL ? ci : -1);
+ const int ci = ciEntry.ci;
+ const int ci_sh = (ish == gmx::c_centralShiftIndex ? ci : -1);
/* We have 5 LJ/C combinations, but use only three inner loops,
* as the other combinations are unlikely and/or not much faster:
* inner LJ + C for full-LJ + C
* inner LJ for full-LJ + no-C / half-LJ + no-C
*/
- do_LJ = ((ciEntry.shift & NBNXN_CI_DO_LJ(0)) != 0);
- do_coul = ((ciEntry.shift & NBNXN_CI_DO_COUL(0)) != 0);
- half_LJ = (((ciEntry.shift & NBNXN_CI_HALF_LJ(0)) != 0) || !do_LJ) && do_coul;
+ const bool do_LJ = ((ciEntry.shift & NBNXN_CI_DO_LJ(0)) != 0);
+ const bool do_coul = ((ciEntry.shift & NBNXN_CI_DO_COUL(0)) != 0);
+ const bool half_LJ = (((ciEntry.shift & NBNXN_CI_HALF_LJ(0)) != 0) || !do_LJ) && do_coul;
#ifdef CALC_ENERGIES
# ifdef LJ_EWALD
- gmx_bool do_self = TRUE;
+ const bool do_self = true;
# else
- gmx_bool do_self = do_coul;
+ const bool do_self = do_coul;
# endif
# ifndef ENERGY_GROUPS
- Vvdw_ci = 0;
- Vc_ci = 0;
+ real Vvdw_ci = 0;
+ real Vc_ci = 0;
# else
- for (i = 0; i < UNROLLI; i++)
+ int egp_sh_i[UNROLLI];
+ for (int i = 0; i < UNROLLI; i++)
{
egp_sh_i[i] = ((nbatParams.energrp[ci] >> (i * nbatParams.neg_2log)) & egp_mask)
* nbatParams.nenergrp;
# endif
#endif
- for (i = 0; i < UNROLLI; i++)
+ for (int i = 0; i < UNROLLI; i++)
{
- for (d = 0; d < DIM; d++)
+ for (int d = 0; d < DIM; d++)
{
xi[i * XI_STRIDE + d] = x[(ci * UNROLLI + i) * X_STRIDE + d] + shiftvec[ishf + d];
fi[i * FI_STRIDE + d] = 0;
#ifdef CALC_ENERGIES
if (do_self)
{
- real Vc_sub_self;
-
# ifdef CALC_COUL_RF
- Vc_sub_self = 0.5 * c_rf;
+ const real Vc_sub_self = 0.5 * reactionFieldShift;
# endif
# ifdef CALC_COUL_TAB
# if GMX_DOUBLE
- Vc_sub_self = 0.5 * tab_coul_V[0];
+ const real Vc_sub_self = 0.5 * tab_coul_V[0];
# else
- Vc_sub_self = 0.5 * tab_coul_FDV0[2];
+ const real Vc_sub_self = 0.5 * tab_coul_FDV0[2];
# endif
# endif
if (l_cj[ciEntry.cj_ind_start].cj == ci_sh)
{
- for (i = 0; i < UNROLLI; i++)
+ for (int i = 0; i < UNROLLI; i++)
{
- int egp_ind;
# ifdef ENERGY_GROUPS
- egp_ind = egp_sh_i[i]
- + ((nbatParams.energrp[ci] >> (i * nbatParams.neg_2log)) & egp_mask);
+ const int egp_ind =
+ egp_sh_i[i] + ((nbatParams.energrp[ci] >> (i * nbatParams.neg_2log)) & egp_mask);
# else
- egp_ind = 0;
+ const int egp_ind = 0;
# endif
/* Coulomb self interaction */
Vc[egp_ind] -= qi[i] * q[ci * UNROLLI + i] * Vc_sub_self;
}
#endif /* CALC_ENERGIES */
- cjind = cjind0;
+ int cjind = cjind0;
while (cjind < cjind1 && nbl->cj[cjind].excl != 0xffff)
{
#define CHECK_EXCLS
}
/* Add accumulated i-forces to the force array */
- for (i = 0; i < UNROLLI; i++)
+ for (int i = 0; i < UNROLLI; i++)
{
- for (d = 0; d < DIM; d++)
+ for (int d = 0; d < DIM; d++)
{
f[(ci * UNROLLI + i) * F_STRIDE + d] += fi[i * FI_STRIDE + d];
}
if (fshift != nullptr)
{
/* Add i forces to shifted force list */
- for (i = 0; i < UNROLLI; i++)
+ for (int i = 0; i < UNROLLI; i++)
{
- for (d = 0; d < DIM; d++)
+ for (int d = 0; d < DIM; d++)
{
fshift[ishf + d] += fi[i * FI_STRIDE + d];
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/gmxassert.h"
/* Prune a single NbnxnPairlistCpu entry with distance rlistInner */
-void nbnxn_kernel_prune_ref(NbnxnPairlistCpu* nbl,
- const nbnxn_atomdata_t* nbat,
- const rvec* gmx_restrict shift_vec,
- real rlistInner)
+void nbnxn_kernel_prune_ref(NbnxnPairlistCpu* nbl,
+ const nbnxn_atomdata_t* nbat,
+ gmx::ArrayRef<const gmx::RVec> shiftvec,
+ real rlistInner)
{
/* We avoid push_back() for efficiency reasons and resize after filling */
nbl->ci.resize(nbl->ciOuter.size());
const nbnxn_cj_t* gmx_restrict cjOuter = nbl->cjOuter.data();
nbnxn_cj_t* gmx_restrict cjInner = nbl->cj.data();
- const real* gmx_restrict shiftvec = shift_vec[0];
- const real* gmx_restrict x = nbat->x().data();
+ const real* gmx_restrict x = nbat->x().data();
const real rlist2 = rlistInner * rlistInner;
{
for (int d = 0; d < DIM; d++)
{
- xi[i * c_xiStride + d] =
- x[(ci * c_iUnroll + i) * c_xStride + d] + shiftvec[ish * DIM + d];
+ xi[i * c_xiStride + d] = x[(ci * c_iUnroll + i) * c_xStride + d] + shiftvec[ish][d];
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct nbnxn_atomdata_t;
struct NbnxnPairlistCpu;
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
/*! \brief Prune a single NbnxnPairlistCpu entry with distance \p rlistInner
*
* Reads a cluster pairlist \p nbl->ciOuter, \p nbl->cjOuter and writes
* all cluster pairs within \p rlistInner to \p nbl->ci, \p nbl->cj.
*/
-void nbnxn_kernel_prune_ref(NbnxnPairlistCpu* nbl,
- const nbnxn_atomdata_t* nbat,
- const rvec* gmx_restrict shift_vec,
- real rlistInner);
+void nbnxn_kernel_prune_ref(NbnxnPairlistCpu* nbl,
+ const nbnxn_atomdata_t* nbat,
+ gmx::ArrayRef<const gmx::RVec> shiftvec,
+ real rlistInner);
for (int jj = 0; jj < (UNROLLJ / 2); jj++)
{
incrDualHsimd(v0 + offset_jj[jj] + jj * GMX_SIMD_REAL_WIDTH / 2,
- v1 + offset_jj[jj] + jj * GMX_SIMD_REAL_WIDTH / 2, e_S);
+ v1 + offset_jj[jj] + jj * GMX_SIMD_REAL_WIDTH / 2,
+ e_S);
}
}
#endif
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#endif
{
- int cj, aj, ajx, ajy, ajz;
-
#ifdef ENERGY_GROUPS
/* Energy group indices for two atoms packed into one int */
int egp_jj[UNROLLJ / 2];
SimdReal c6s_j_S, c12s_j_S;
# endif
-# if defined LJ_COMB_GEOM || defined LJ_COMB_LB || defined LJ_EWALD_GEOM
- /* Index for loading LJ parameters, complicated when interleaving */
- int aj2;
-# endif
-
/* Intermediate variables for LJ calculation */
# ifndef LJ_COMB_LB
SimdReal rinvsix_S0;
#endif /* CALC_LJ */
/* j-cluster index */
- cj = l_cj[cjind].cj;
+ const int cj = l_cj[cjind].cj;
/* Atom indices (of the first atom in the cluster) */
- aj = cj * UNROLLJ;
+ const int aj = cj * UNROLLJ;
#if defined CALC_LJ && (defined LJ_COMB_GEOM || defined LJ_COMB_LB || defined LJ_EWALD_GEOM)
- aj2 = aj * 2;
+ /* Index for loading LJ parameters, complicated when interleaving */
+ const int aj2 = aj * 2;
#endif
- ajx = aj * DIM;
- ajy = ajx + STRIDE;
- ajz = ajy + STRIDE;
+ const int ajx = aj * DIM;
+ const int ajy = ajx + STRIDE;
+ const int ajz = ajy + STRIDE;
#ifdef CHECK_EXCLS
- gmx_load_simd_2xnn_interactions(static_cast<int>(l_cj[cjind].excl), filter_S0, filter_S2,
- &interact_S0, &interact_S2);
+ gmx_load_simd_2xnn_interactions(
+ static_cast<int>(l_cj[cjind].excl), filter_S0, filter_S2, &interact_S0, &interact_S2);
#endif /* CHECK_EXCLS */
/* load j atom coordinates */
c6_S2 * fma(sixth_S, rinvsix_S2, v_fswitch_pr(rsw_S2, rsw2_S2, p6_6cpot_S, p6_vc3_S, p6_vc4_S));
# endif
SimdReal VLJ12_S0 = c12_S0
- * fma(twelveth_S, rinvsix_S0 * rinvsix_S0,
+ * fma(twelveth_S,
+ rinvsix_S0 * rinvsix_S0,
v_fswitch_pr(rsw_S0, rsw2_S0, p12_12cpot_S, p12_vc3_S, p12_vc4_S));
# ifndef HALF_LJ
SimdReal VLJ12_S2 = c12_S2
- * fma(twelveth_S, rinvsix_S2 * rinvsix_S2,
+ * fma(twelveth_S,
+ rinvsix_S2 * rinvsix_S2,
v_fswitch_pr(rsw_S2, rsw2_S2, p12_12cpot_S, p12_vc3_S, p12_vc4_S));
# endif
# undef v_fswitch_pr
* r^-6*cexp*(1 + cr2 + cr2^2/2 + cr2^3/6) = cexp*(r^-6*poly + c^6/6)
*/
frLJ_S0 = fma(c6grid_S0,
- fnma(expmcr2_S0, fma(rinvsix_nm_S0, poly_S0, lje_c6_6_S), rinvsix_nm_S0), frLJ_S0);
+ fnma(expmcr2_S0, fma(rinvsix_nm_S0, poly_S0, lje_c6_6_S), rinvsix_nm_S0),
+ frLJ_S0);
# ifndef HALF_LJ
frLJ_S2 = fma(c6grid_S2,
- fnma(expmcr2_S2, fma(rinvsix_nm_S2, poly_S2, lje_c6_6_S), rinvsix_nm_S2), frLJ_S2);
+ fnma(expmcr2_S2, fma(rinvsix_nm_S2, poly_S2, lje_c6_6_S), rinvsix_nm_S2),
+ frLJ_S2);
# endif
# ifdef CALC_ENERGIES
# endif
VLJ_S0 = fma(sixth_S * c6grid_S0,
- fma(rinvsix_nm_S0, fnma(expmcr2_S0, poly_S0, one_S), sh_mask_S0), VLJ_S0);
+ fma(rinvsix_nm_S0, fnma(expmcr2_S0, poly_S0, one_S), sh_mask_S0),
+ VLJ_S0);
# ifndef HALF_LJ
VLJ_S2 = fma(sixth_S * c6grid_S2,
- fma(rinvsix_nm_S2, fnma(expmcr2_S2, poly_S2, one_S), sh_mask_S2), VLJ_S2);
+ fma(rinvsix_nm_S2, fnma(expmcr2_S2, poly_S2, one_S), sh_mask_S2),
+ VLJ_S2);
# endif
# endif /* CALC_ENERGIES */
}
* complicated when the i- and j-cluster size don't match.
*/
{
- int egps_j;
# if UNROLLJ == 2
- egps_j = nbatParams.energrp[cj >> 1];
- egp_jj[0] = ((egps_j >> ((cj & 1) * egps_jshift)) & egps_jmask) * egps_jstride;
+ const int egps_j = nbatParams.energrp[cj >> 1];
+ egp_jj[0] = ((egps_j >> ((cj & 1) * egps_jshift)) & egps_jmask) * egps_jstride;
# else
/* We assume UNROLLI <= UNROLLJ */
- int jdi;
- for (jdi = 0; jdi < UNROLLJ / UNROLLI; jdi++)
+ for (int jdi = 0; jdi < UNROLLJ / UNROLLI; jdi++)
{
- int jj;
- egps_j = nbatParams.energrp[cj * (UNROLLJ / UNROLLI) + jdi];
- for (jj = 0; jj < (UNROLLI / 2); jj++)
+ const int egps_j = nbatParams.energrp[cj * (UNROLLJ / UNROLLI) + jdi];
+ for (int jj = 0; jj < (UNROLLI / 2); jj++)
{
egp_jj[jdi * (UNROLLI / 2) + jj] =
((egps_j >> (jj * egps_jshift)) & egps_jmask) * egps_jstride;
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
real* Vvdw = out->VSvdw.data();
real* Vc = out->VSc.data();
# else
- real* Vvdw = out->Vvdw.data();
- real* Vc = out->Vc.data();
+ real* Vvdw = out->Vvdw.data();
+ real* Vc = out->Vc.data();
# endif
#endif
- const nbnxn_cj_t* l_cj;
- int ci, ci_sh;
- int ish, ish3;
- gmx_bool do_LJ, half_LJ, do_coul;
- int cjind0, cjind1, cjind;
-
-#ifdef ENERGY_GROUPS
- int Vstride_i;
- int egps_ishift, egps_imask;
- int egps_jshift, egps_jmask, egps_jstride;
- int egps_i;
- real* vvdwtp[UNROLLI];
- real* vctp[UNROLLI];
-#endif
-
SimdReal shX_S;
SimdReal shY_S;
SimdReal shZ_S;
#ifdef CALC_COUL_TAB
/* Coulomb table variables */
- SimdReal invtsp_S;
- const real* tab_coul_F;
-# if defined CALC_ENERGIES && !defined TAB_FDV0
- const real* tab_coul_V;
-# endif
+ SimdReal invtsp_S;
# ifdef CALC_ENERGIES
SimdReal mhalfsp_S;
# endif
#endif
#ifdef LJ_EWALD_GEOM
- real lj_ewaldcoeff2, lj_ewaldcoeff6_6;
SimdReal half_S, lje_c2_S, lje_c6_6_S;
#endif
SimdReal rcvdw2_S;
#endif
- int ninner;
-
#ifdef COUNT_PAIRS
int npair = 0;
#endif
#ifdef CALC_COUL_RF
/* Reaction-field constants */
- mrc_3_S = SimdReal(-2 * ic->k_rf);
+ mrc_3_S = SimdReal(-2 * ic->reactionFieldCoefficient);
# ifdef CALC_ENERGIES
- hrc_3_S = SimdReal(ic->k_rf);
- moh_rc_S = SimdReal(-ic->c_rf);
+ hrc_3_S = SimdReal(ic->reactionFieldCoefficient);
+ moh_rc_S = SimdReal(-ic->reactionFieldShift);
# endif
#endif
# endif
# ifdef TAB_FDV0
- tab_coul_F = ic->coulombEwaldTables->tableFDV0.data();
+ const real* tab_coul_F = ic->coulombEwaldTables->tableFDV0.data();
# else
- tab_coul_F = ic->coulombEwaldTables->tableF.data();
+ const real* tab_coul_F = ic->coulombEwaldTables->tableF.data();
# ifdef CALC_ENERGIES
- tab_coul_V = ic->coulombEwaldTables->tableV.data();
+ const real* tab_coul_V = ic->coulombEwaldTables->tableV.data();
# endif
# endif
#endif /* CALC_COUL_TAB */
# endif
#endif
#ifdef LJ_EWALD_GEOM
- half_S = SimdReal(0.5);
- lj_ewaldcoeff2 = ic->ewaldcoeff_lj * ic->ewaldcoeff_lj;
- lj_ewaldcoeff6_6 = lj_ewaldcoeff2 * lj_ewaldcoeff2 * lj_ewaldcoeff2 / 6;
- lje_c2_S = SimdReal(lj_ewaldcoeff2);
- lje_c6_6_S = SimdReal(lj_ewaldcoeff6_6);
+ half_S = SimdReal(0.5);
+ const real lj_ewaldcoeff2 = ic->ewaldcoeff_lj * ic->ewaldcoeff_lj;
+ const real lj_ewaldcoeff6_6 = lj_ewaldcoeff2 * lj_ewaldcoeff2 * lj_ewaldcoeff2 / 6;
+ lje_c2_S = SimdReal(lj_ewaldcoeff2);
+ lje_c6_6_S = SimdReal(lj_ewaldcoeff6_6);
# ifdef CALC_ENERGIES
/* Determine the grid potential at the cut-off */
SimdReal lje_vc_S = SimdReal(ic->sh_lj_ewald);
#endif /* FIX_LJ_C */
#ifdef ENERGY_GROUPS
- egps_ishift = nbatParams.neg_2log;
- egps_imask = (1 << egps_ishift) - 1;
- egps_jshift = 2 * nbatParams.neg_2log;
- egps_jmask = (1 << egps_jshift) - 1;
- egps_jstride = (UNROLLJ >> 1) * UNROLLJ;
+ const int egps_ishift = nbatParams.neg_2log;
+ const int egps_imask = (1 << egps_ishift) - 1;
+ const int egps_jshift = 2 * nbatParams.neg_2log;
+ const int egps_jmask = (1 << egps_jshift) - 1;
+ const int egps_jstride = (UNROLLJ >> 1) * UNROLLJ;
/* Major division is over i-particle energy groups, determine the stride */
- Vstride_i = nbatParams.nenergrp * (1 << nbatParams.neg_2log) * egps_jstride;
+ const int Vstride_i = nbatParams.nenergrp * (1 << nbatParams.neg_2log) * egps_jstride;
#endif
- l_cj = nbl->cj.data();
+ const nbnxn_cj_t* l_cj = nbl->cj.data();
- ninner = 0;
+ int ninner = 0;
for (const nbnxn_ci_t& ciEntry : nbl->ci)
{
- ish = (ciEntry.shift & NBNXN_CI_SHIFT);
- ish3 = ish * 3;
- cjind0 = ciEntry.cj_ind_start;
- cjind1 = ciEntry.cj_ind_end;
- ci = ciEntry.ci;
- ci_sh = (ish == CENTRAL ? ci : -1);
+ const int ish = (ciEntry.shift & NBNXN_CI_SHIFT);
+ const int ish3 = ish * 3;
+ const int cjind0 = ciEntry.cj_ind_start;
+ const int cjind1 = ciEntry.cj_ind_end;
+ const int ci = ciEntry.ci;
+ const int ci_sh = (ish == gmx::c_centralShiftIndex ? ci : -1);
shX_S = SimdReal(shiftvec[ish3]);
shY_S = SimdReal(shiftvec[ish3 + 1]);
* inner LJ + C for full-LJ + C
* inner LJ for full-LJ + no-C / half-LJ + no-C
*/
- do_LJ = ((ciEntry.shift & NBNXN_CI_DO_LJ(0)) != 0);
- do_coul = ((ciEntry.shift & NBNXN_CI_DO_COUL(0)) != 0);
- half_LJ = (((ciEntry.shift & NBNXN_CI_HALF_LJ(0)) != 0) || !do_LJ) && do_coul;
+ const bool do_LJ = ((ciEntry.shift & NBNXN_CI_DO_LJ(0)) != 0);
+ const bool do_coul = ((ciEntry.shift & NBNXN_CI_DO_COUL(0)) != 0);
+ const bool half_LJ = (((ciEntry.shift & NBNXN_CI_HALF_LJ(0)) != 0) || !do_LJ) && do_coul;
#ifdef ENERGY_GROUPS
- egps_i = nbatParams.energrp[ci];
+ const int egps_i = nbatParams.energrp[ci];
+ real* vvdwtp[UNROLLI];
+ real* vctp[UNROLLI];
{
- int ia, egp_ia;
-
- for (ia = 0; ia < UNROLLI; ia++)
+ for (int ia = 0; ia < UNROLLI; ia++)
{
- egp_ia = (egps_i >> (ia * egps_ishift)) & egps_imask;
+ int egp_ia = (egps_i >> (ia * egps_ishift)) & egps_imask;
vvdwtp[ia] = Vvdw + egp_ia * Vstride_i;
vctp[ia] = Vc + egp_ia * Vstride_i;
}
{
if (do_coul)
{
- real Vc_sub_self;
- int ia;
-
# ifdef CALC_COUL_RF
- Vc_sub_self = 0.5 * ic->c_rf;
+ const real Vc_sub_self = 0.5 * ic->reactionFieldShift;
# endif
# ifdef CALC_COUL_TAB
# ifdef TAB_FDV0
- Vc_sub_self = 0.5 * tab_coul_F[2];
+ const real Vc_sub_self = 0.5 * tab_coul_F[2];
# else
- Vc_sub_self = 0.5 * tab_coul_V[0];
+ const real Vc_sub_self = 0.5 * tab_coul_V[0];
# endif
# endif
# ifdef CALC_COUL_EWALD
/* beta/sqrt(pi) */
- Vc_sub_self = 0.5 * ic->ewaldcoeff_q * M_2_SQRTPI;
+ const real Vc_sub_self = 0.5 * ic->ewaldcoeff_q * M_2_SQRTPI;
# endif
- for (ia = 0; ia < UNROLLI; ia++)
+ for (int ia = 0; ia < UNROLLI; ia++)
{
- real qi;
-
- qi = q[sci + ia];
+ const real qi = q[sci + ia];
# ifdef ENERGY_GROUPS
vctp[ia][((egps_i >> (ia * egps_ishift)) & egps_imask) * egps_jstride]
# else
# ifdef LJ_EWALD_GEOM
{
- int ia;
-
- for (ia = 0; ia < UNROLLI; ia++)
+ for (int ia = 0; ia < UNROLLI; ia++)
{
- real c6_i;
-
- c6_i = nbatParams.nbfp[nbatParams.type[sci + ia] * (nbatParams.numTypes + 1) * 2]
- / 6;
+ const real c6_i =
+ nbatParams.nbfp[nbatParams.type[sci + ia] * (nbatParams.numTypes + 1) * 2]
+ / 6;
# ifdef ENERGY_GROUPS
vvdwtp[ia][((egps_i >> (ia * egps_ishift)) & egps_imask) * egps_jstride]
# else
fiz_S0 = setZero();
fiz_S2 = setZero();
- cjind = cjind0;
+ int cjind = cjind0;
/* Currently all kernels use (at least half) LJ */
#define CALC_LJ
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#endif
/* Prune a single nbnxn_pairtlist_t entry with distance rlistInner */
-void nbnxn_kernel_prune_2xnn(NbnxnPairlistCpu* nbl,
- const nbnxn_atomdata_t* nbat,
- const rvec* gmx_restrict shift_vec,
- real rlistInner)
+void nbnxn_kernel_prune_2xnn(NbnxnPairlistCpu* nbl,
+ const nbnxn_atomdata_t* nbat,
+ gmx::ArrayRef<const gmx::RVec> shiftvec,
+ real rlistInner)
{
#ifdef GMX_NBNXN_SIMD_2XNN
using namespace gmx;
const nbnxn_cj_t* gmx_restrict cjOuter = nbl->cjOuter.data();
nbnxn_cj_t* gmx_restrict cjInner = nbl->cj.data();
- const real* gmx_restrict shiftvec = shift_vec[0];
- const real* gmx_restrict x = nbat->x().data();
+ const real* gmx_restrict x = nbat->x().data();
const SimdReal rlist2_S(rlistInner * rlistInner);
ciInner[nciInner].cj_ind_start = ncjInner;
/* Extract shift data */
- int ish = (ciEntry->shift & NBNXN_CI_SHIFT);
- int ish3 = ish * 3;
- int ci = ciEntry->ci;
+ int ish = (ciEntry->shift & NBNXN_CI_SHIFT);
+ int ci = ciEntry->ci;
- SimdReal shX_S = SimdReal(shiftvec[ish3]);
- SimdReal shY_S = SimdReal(shiftvec[ish3 + 1]);
- SimdReal shZ_S = SimdReal(shiftvec[ish3 + 2]);
+ SimdReal shX_S = SimdReal(shiftvec[ish][XX]);
+ SimdReal shY_S = SimdReal(shiftvec[ish][YY]);
+ SimdReal shZ_S = SimdReal(shiftvec[ish][ZZ]);
# if UNROLLJ <= 4
int scix = ci * STRIDE * DIM;
GMX_UNUSED_VALUE(nbl);
GMX_UNUSED_VALUE(nbat);
- GMX_UNUSED_VALUE(shift_vec);
+ GMX_UNUSED_VALUE(shiftvec);
GMX_UNUSED_VALUE(rlistInner);
#endif /* GMX_NBNXN_SIMD_2XNN */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct nbnxn_atomdata_t;
struct NbnxnPairlistCpu;
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
/*! \brief Prune a single NbnxnPairlistCpu entry with distance \p rlistInner
*
* Reads a cluster pairlist \p nbl->ciOuter, \p nbl->cjOuter and writes
* all cluster pairs within \p rlistInner to \p nbl->ci, \p nbl->cj.
*/
-void nbnxn_kernel_prune_2xnn(NbnxnPairlistCpu* nbl,
- const nbnxn_atomdata_t* nbat,
- const rvec* gmx_restrict shift_vec,
- real rlistInner);
+void nbnxn_kernel_prune_2xnn(NbnxnPairlistCpu* nbl,
+ const nbnxn_atomdata_t* nbat,
+ gmx::ArrayRef<const gmx::RVec> shift_vec,
+ real rlistInner);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2019 by the GROMACS development team.
+ * Copyright (c) 2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* The minor index of the array goes over both the LJ combination rules,
* which is only supported by plain cut-off, and the LJ switch/PME functions.
*/
-static p_nbk_func_noener nbnxm_kernel_noener_simd_2xmm[coulktNR][vdwktNR] = {
+static const p_nbk_func_noener nbnxm_kernel_noener_simd_2xmm[coulktNR][vdwktNR] = {
{
nbnxm_kernel_ElecRF_VdwLJCombGeom_F_2xmm,
nbnxm_kernel_ElecRF_VdwLJCombLB_F_2xmm,
},
};
-static p_nbk_func_ener nbnxm_kernel_ener_simd_2xmm[coulktNR][vdwktNR] = {
+static const p_nbk_func_ener nbnxm_kernel_ener_simd_2xmm[coulktNR][vdwktNR] = {
{
nbnxm_kernel_ElecRF_VdwLJCombGeom_VF_2xmm,
nbnxm_kernel_ElecRF_VdwLJCombLB_VF_2xmm,
},
};
-static p_nbk_func_ener nbnxm_kernel_energrp_simd_2xmm[coulktNR][vdwktNR] = {
+static const p_nbk_func_ener nbnxm_kernel_energrp_simd_2xmm[coulktNR][vdwktNR] = {
{
nbnxm_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xmm,
nbnxm_kernel_ElecRF_VdwLJCombLB_VgrpF_2xmm,
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static inline void add_ener_grp(gmx::SimdReal e_S, real* v, const int* offset_jj)
{
using namespace gmx;
- int jj;
/* We need to balance the number of store operations with
* the rapidly increases number of combinations of energy groups.
* We add to a temporary buffer for 1 i-group vs 2 j-groups.
*/
- for (jj = 0; jj < (UNROLLJ / 2); jj++)
+ for (int jj = 0; jj < (UNROLLJ / 2); jj++)
{
SimdReal v_S;
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
# endif
{
- int cj, ajx, ajy, ajz;
- int gmx_unused aj;
# ifdef ENERGY_GROUPS
/* Energy group indices for two atoms packed into one int */
SimdReal c6s_j_S, c12s_j_S;
# endif
-# if defined LJ_COMB_GEOM || defined LJ_COMB_LB || defined LJ_EWALD_GEOM
- /* Index for loading LJ parameters, complicated when interleaving */
- int aj2;
-# endif
-
/* Intermediate variables for LJ calculation */
# ifndef LJ_COMB_LB
SimdReal rinvsix_S0;
# endif /* CALC_LJ */
/* j-cluster index */
- cj = l_cj[cjind].cj;
+ const int cj = l_cj[cjind].cj;
/* Atom indices (of the first atom in the cluster) */
- aj = cj * UNROLLJ;
+ const int aj = cj * UNROLLJ;
# if defined CALC_LJ && (defined LJ_COMB_GEOM || defined LJ_COMB_LB || defined LJ_EWALD_GEOM)
+ /* Index for loading LJ parameters, complicated when interleaving */
# if UNROLLJ == STRIDE
- aj2 = aj * 2;
+ const int aj2 = aj * 2;
# else
- aj2 = (cj >> 1) * 2 * STRIDE + (cj & 1) * UNROLLJ;
+ const int aj2 = (cj >> 1) * 2 * STRIDE + (cj & 1) * UNROLLJ;
# endif
# endif
# if UNROLLJ == STRIDE
- ajx = aj * DIM;
+ const int ajx = aj * DIM;
# else
- ajx = (cj >> 1) * DIM * STRIDE + (cj & 1) * UNROLLJ;
+ const int ajx = (cj >> 1) * DIM * STRIDE + (cj & 1) * UNROLLJ;
# endif
- ajy = ajx + STRIDE;
- ajz = ajy + STRIDE;
+ const int ajy = ajx + STRIDE;
+ const int ajz = ajy + STRIDE;
# ifdef CHECK_EXCLS
- gmx_load_simd_4xn_interactions(static_cast<int>(l_cj[cjind].excl), filter_S0, filter_S1,
- filter_S2, filter_S3, nbat->simdMasks.interaction_array.data(),
- &interact_S0, &interact_S1, &interact_S2, &interact_S3);
+ gmx_load_simd_4xn_interactions(static_cast<int>(l_cj[cjind].excl),
+ filter_S0,
+ filter_S1,
+ filter_S2,
+ filter_S3,
+ nbat->simdMasks.interaction_array.data(),
+ &interact_S0,
+ &interact_S1,
+ &interact_S2,
+ &interact_S3);
# endif /* CHECK_EXCLS */
/* load j atom coordinates */
c6_S3 * fma(sixth_S, rinvsix_S3, v_fswitch_r(rsw_S3, rsw2_S3, p6_6cpot_S, p6_vc3_S, p6_vc4_S));
# endif
SimdReal VLJ12_S0 = c12_S0
- * fma(twelveth_S, rinvsix_S0 * rinvsix_S0,
+ * fma(twelveth_S,
+ rinvsix_S0 * rinvsix_S0,
v_fswitch_r(rsw_S0, rsw2_S0, p12_12cpot_S, p12_vc3_S, p12_vc4_S));
SimdReal VLJ12_S1 = c12_S1
- * fma(twelveth_S, rinvsix_S1 * rinvsix_S1,
+ * fma(twelveth_S,
+ rinvsix_S1 * rinvsix_S1,
v_fswitch_r(rsw_S1, rsw2_S1, p12_12cpot_S, p12_vc3_S, p12_vc4_S));
# ifndef HALF_LJ
SimdReal VLJ12_S2 = c12_S2
- * fma(twelveth_S, rinvsix_S2 * rinvsix_S2,
+ * fma(twelveth_S,
+ rinvsix_S2 * rinvsix_S2,
v_fswitch_r(rsw_S2, rsw2_S2, p12_12cpot_S, p12_vc3_S, p12_vc4_S));
SimdReal VLJ12_S3 = c12_S3
- * fma(twelveth_S, rinvsix_S3 * rinvsix_S3,
+ * fma(twelveth_S,
+ rinvsix_S3 * rinvsix_S3,
v_fswitch_r(rsw_S3, rsw2_S3, p12_12cpot_S, p12_vc3_S, p12_vc4_S));
# endif
# undef v_fswitch_r
* r^-6*cexp*(1 + cr2 + cr2^2/2 + cr2^3/6) = cexp*(r^-6*poly + c^6/6)
*/
frLJ_S0 = fma(c6grid_S0,
- fnma(expmcr2_S0, fma(rinvsix_nm_S0, poly_S0, lje_c6_6_S), rinvsix_nm_S0), frLJ_S0);
+ fnma(expmcr2_S0, fma(rinvsix_nm_S0, poly_S0, lje_c6_6_S), rinvsix_nm_S0),
+ frLJ_S0);
frLJ_S1 = fma(c6grid_S1,
- fnma(expmcr2_S1, fma(rinvsix_nm_S1, poly_S1, lje_c6_6_S), rinvsix_nm_S1), frLJ_S1);
+ fnma(expmcr2_S1, fma(rinvsix_nm_S1, poly_S1, lje_c6_6_S), rinvsix_nm_S1),
+ frLJ_S1);
# ifndef HALF_LJ
frLJ_S2 = fma(c6grid_S2,
- fnma(expmcr2_S2, fma(rinvsix_nm_S2, poly_S2, lje_c6_6_S), rinvsix_nm_S2), frLJ_S2);
+ fnma(expmcr2_S2, fma(rinvsix_nm_S2, poly_S2, lje_c6_6_S), rinvsix_nm_S2),
+ frLJ_S2);
frLJ_S3 = fma(c6grid_S3,
- fnma(expmcr2_S3, fma(rinvsix_nm_S3, poly_S3, lje_c6_6_S), rinvsix_nm_S3), frLJ_S3);
+ fnma(expmcr2_S3, fma(rinvsix_nm_S3, poly_S3, lje_c6_6_S), rinvsix_nm_S3),
+ frLJ_S3);
# endif
# ifdef CALC_ENERGIES
# endif
VLJ_S0 = fma(sixth_S * c6grid_S0,
- fma(rinvsix_nm_S0, fnma(expmcr2_S0, poly_S0, one_S), sh_mask_S0), VLJ_S0);
+ fma(rinvsix_nm_S0, fnma(expmcr2_S0, poly_S0, one_S), sh_mask_S0),
+ VLJ_S0);
VLJ_S1 = fma(sixth_S * c6grid_S1,
- fma(rinvsix_nm_S1, fnma(expmcr2_S1, poly_S1, one_S), sh_mask_S1), VLJ_S1);
+ fma(rinvsix_nm_S1, fnma(expmcr2_S1, poly_S1, one_S), sh_mask_S1),
+ VLJ_S1);
# ifndef HALF_LJ
VLJ_S2 = fma(sixth_S * c6grid_S2,
- fma(rinvsix_nm_S2, fnma(expmcr2_S2, poly_S2, one_S), sh_mask_S2), VLJ_S2);
+ fma(rinvsix_nm_S2, fnma(expmcr2_S2, poly_S2, one_S), sh_mask_S2),
+ VLJ_S2);
VLJ_S3 = fma(sixth_S * c6grid_S3,
- fma(rinvsix_nm_S3, fnma(expmcr2_S3, poly_S3, one_S), sh_mask_S3), VLJ_S3);
+ fma(rinvsix_nm_S3, fnma(expmcr2_S3, poly_S3, one_S), sh_mask_S3),
+ VLJ_S3);
# endif
# endif /* CALC_ENERGIES */
}
* complicated when the i- and j-cluster size don't match.
*/
{
- int egps_j;
# if UNROLLJ == 2
- egps_j = nbatParams.energrp[cj >> 1];
- egp_jj[0] = ((egps_j >> ((cj & 1) * egps_jshift)) & egps_jmask) * egps_jstride;
+ const int egps_j = nbatParams.energrp[cj >> 1];
+ egp_jj[0] = ((egps_j >> ((cj & 1) * egps_jshift)) & egps_jmask) * egps_jstride;
# else
/* We assume UNROLLI <= UNROLLJ */
- int jdi;
- for (jdi = 0; jdi < UNROLLJ / UNROLLI; jdi++)
+ for (int jdi = 0; jdi < UNROLLJ / UNROLLI; jdi++)
{
- int jj;
- egps_j = nbatParams.energrp[cj * (UNROLLJ / UNROLLI) + jdi];
- for (jj = 0; jj < (UNROLLI / 2); jj++)
+ const int egps_j = nbatParams.energrp[cj * (UNROLLJ / UNROLLI) + jdi];
+ for (int jj = 0; jj < (UNROLLI / 2); jj++)
{
egp_jj[jdi * (UNROLLI / 2) + jj] =
((egps_j >> (jj * egps_jshift)) & egps_jmask) * egps_jstride;
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
real* Vvdw = out->VSvdw.data();
real* Vc = out->VSc.data();
# else
- real* Vvdw = out->Vvdw.data();
- real* Vc = out->Vc.data();
+ real* Vvdw = out->Vvdw.data();
+ real* Vc = out->Vc.data();
# endif
#endif
- const nbnxn_cj_t* l_cj;
- int ci, ci_sh;
- int ish, ish3;
- gmx_bool do_LJ, half_LJ, do_coul;
- int cjind0, cjind1, cjind;
-
-#ifdef ENERGY_GROUPS
- int Vstride_i;
- int egps_ishift, egps_imask;
- int egps_jshift, egps_jmask, egps_jstride;
- int egps_i;
- real* vvdwtp[UNROLLI];
- real* vctp[UNROLLI];
-#endif
-
SimdReal shX_S;
SimdReal shY_S;
SimdReal shZ_S;
#ifdef CALC_COUL_TAB
/* Coulomb table variables */
- SimdReal invtsp_S;
- const real* tab_coul_F;
-# if defined CALC_ENERGIES && !defined TAB_FDV0
- const real gmx_unused* tab_coul_V;
-# endif
+ SimdReal invtsp_S;
# ifdef CALC_ENERGIES
SimdReal mhalfsp_S;
# endif
# endif
#endif
#ifdef LJ_EWALD_GEOM
- real lj_ewaldcoeff2, lj_ewaldcoeff6_6;
SimdReal half_S, lje_c2_S, lje_c6_6_S;
#endif
SimdReal rcvdw2_S;
#endif
- int ninner;
-
#ifdef COUNT_PAIRS
int npair = 0;
#endif
#ifdef CALC_COUL_RF
/* Reaction-field constants */
- mrc_3_S = SimdReal(-2 * ic->k_rf);
+ mrc_3_S = SimdReal(-2 * ic->reactionFieldCoefficient);
# ifdef CALC_ENERGIES
- hrc_3_S = SimdReal(ic->k_rf);
- moh_rc_S = SimdReal(-ic->c_rf);
+ hrc_3_S = SimdReal(ic->reactionFieldCoefficient);
+ moh_rc_S = SimdReal(-ic->reactionFieldShift);
# endif
#endif
# endif
# ifdef TAB_FDV0
- tab_coul_F = ic->coulombEwaldTables->tableFDV0.data();
+ const real* tab_coul_F = ic->coulombEwaldTables->tableFDV0.data();
# else
- tab_coul_F = ic->coulombEwaldTables->tableF.data();
+ const real* tab_coul_F = ic->coulombEwaldTables->tableF.data();
# ifdef CALC_ENERGIES
- tab_coul_V = ic->coulombEwaldTables->tableV.data();
+ const real* tab_coul_V = ic->coulombEwaldTables->tableV.data();
# endif
# endif
#endif /* CALC_COUL_TAB */
# endif
#endif
#ifdef LJ_EWALD_GEOM
- half_S = SimdReal(0.5);
- lj_ewaldcoeff2 = ic->ewaldcoeff_lj * ic->ewaldcoeff_lj;
- lj_ewaldcoeff6_6 = lj_ewaldcoeff2 * lj_ewaldcoeff2 * lj_ewaldcoeff2 / 6;
- lje_c2_S = SimdReal(lj_ewaldcoeff2);
- lje_c6_6_S = SimdReal(lj_ewaldcoeff6_6);
+ half_S = SimdReal(0.5);
+ const real lj_ewaldcoeff2 = ic->ewaldcoeff_lj * ic->ewaldcoeff_lj;
+ const real lj_ewaldcoeff6_6 = lj_ewaldcoeff2 * lj_ewaldcoeff2 * lj_ewaldcoeff2 / 6;
+ lje_c2_S = SimdReal(lj_ewaldcoeff2);
+ lje_c6_6_S = SimdReal(lj_ewaldcoeff6_6);
# ifdef CALC_ENERGIES
/* Determine the grid potential at the cut-off */
SimdReal lje_vc_S(ic->sh_lj_ewald);
#endif /* FIX_LJ_C */
#ifdef ENERGY_GROUPS
- egps_ishift = nbatParams.neg_2log;
- egps_imask = (1 << egps_ishift) - 1;
- egps_jshift = 2 * nbatParams.neg_2log;
- egps_jmask = (1 << egps_jshift) - 1;
- egps_jstride = (UNROLLJ >> 1) * UNROLLJ;
+ const int egps_ishift = nbatParams.neg_2log;
+ const int egps_imask = (1 << egps_ishift) - 1;
+ const int egps_jshift = 2 * nbatParams.neg_2log;
+ const int egps_jmask = (1 << egps_jshift) - 1;
+ const int egps_jstride = (UNROLLJ >> 1) * UNROLLJ;
/* Major division is over i-particle energy groups, determine the stride */
- Vstride_i = nbatParams.nenergrp * (1 << nbatParams.neg_2log) * egps_jstride;
+ const int Vstride_i = nbatParams.nenergrp * (1 << nbatParams.neg_2log) * egps_jstride;
#endif
- l_cj = nbl->cj.data();
+ const nbnxn_cj_t* l_cj = nbl->cj.data();
- ninner = 0;
+ int ninner = 0;
for (const nbnxn_ci_t& ciEntry : nbl->ci)
{
- ish = (ciEntry.shift & NBNXN_CI_SHIFT);
- ish3 = ish * 3;
- cjind0 = ciEntry.cj_ind_start;
- cjind1 = ciEntry.cj_ind_end;
- ci = ciEntry.ci;
- ci_sh = (ish == CENTRAL ? ci : -1);
+ const int ish = (ciEntry.shift & NBNXN_CI_SHIFT);
+ const int ish3 = ish * 3;
+ const int cjind0 = ciEntry.cj_ind_start;
+ const int cjind1 = ciEntry.cj_ind_end;
+ const int ci = ciEntry.ci;
+ const int ci_sh = (ish == gmx::c_centralShiftIndex ? ci : -1);
shX_S = SimdReal(shiftvec[ish3]);
shY_S = SimdReal(shiftvec[ish3 + 1]);
* inner LJ + C for full-LJ + C
* inner LJ for full-LJ + no-C / half-LJ + no-C
*/
- do_LJ = ((ciEntry.shift & NBNXN_CI_DO_LJ(0)) != 0);
- do_coul = ((ciEntry.shift & NBNXN_CI_DO_COUL(0)) != 0);
- half_LJ = (((ciEntry.shift & NBNXN_CI_HALF_LJ(0)) != 0) || !do_LJ) && do_coul;
+ const bool do_LJ = ((ciEntry.shift & NBNXN_CI_DO_LJ(0)) != 0);
+ const bool do_coul = ((ciEntry.shift & NBNXN_CI_DO_COUL(0)) != 0);
+ const bool half_LJ = (((ciEntry.shift & NBNXN_CI_HALF_LJ(0)) != 0) || !do_LJ) && do_coul;
#ifdef ENERGY_GROUPS
- egps_i = nbatParams.energrp[ci];
+ real* vvdwtp[UNROLLI];
+ real* vctp[UNROLLI];
+ const int egps_i = nbatParams.energrp[ci];
{
- int ia, egp_ia;
-
- for (ia = 0; ia < UNROLLI; ia++)
+ for (int ia = 0; ia < UNROLLI; ia++)
{
- egp_ia = (egps_i >> (ia * egps_ishift)) & egps_imask;
+ int egp_ia = (egps_i >> (ia * egps_ishift)) & egps_imask;
vvdwtp[ia] = Vvdw + egp_ia * Vstride_i;
vctp[ia] = Vc + egp_ia * Vstride_i;
}
#ifdef CALC_ENERGIES
# ifdef LJ_EWALD_GEOM
- gmx_bool do_self = TRUE;
+ const bool do_self = true;
# else
- gmx_bool do_self = do_coul;
+ const bool do_self = do_coul;
# endif
# if UNROLLJ == 4
if (do_self && l_cj[ciEntry.cj_ind_start].cj == ci_sh)
{
if (do_coul)
{
- real Vc_sub_self;
- int ia;
-
# ifdef CALC_COUL_RF
- Vc_sub_self = 0.5 * ic->c_rf;
+ const real Vc_sub_self = 0.5 * ic->reactionFieldShift;
# endif
# ifdef CALC_COUL_TAB
# ifdef TAB_FDV0
- Vc_sub_self = 0.5 * tab_coul_F[2];
+ const real Vc_sub_self = 0.5 * tab_coul_F[2];
# else
- Vc_sub_self = 0.5 * tab_coul_V[0];
+ const real Vc_sub_self = 0.5 * tab_coul_V[0];
# endif
# endif
# ifdef CALC_COUL_EWALD
/* beta/sqrt(pi) */
- Vc_sub_self = 0.5 * ic->ewaldcoeff_q * M_2_SQRTPI;
+ const real Vc_sub_self = 0.5 * ic->ewaldcoeff_q * M_2_SQRTPI;
# endif
- for (ia = 0; ia < UNROLLI; ia++)
+ for (int ia = 0; ia < UNROLLI; ia++)
{
- real qi;
-
- qi = q[sci + ia];
+ const real qi = q[sci + ia];
# ifdef ENERGY_GROUPS
vctp[ia][((egps_i >> (ia * egps_ishift)) & egps_imask) * egps_jstride]
# else
# ifdef LJ_EWALD_GEOM
{
- int ia;
-
- for (ia = 0; ia < UNROLLI; ia++)
+ for (int ia = 0; ia < UNROLLI; ia++)
{
- real c6_i;
-
- c6_i = nbatParams.nbfp[nbatParams.type[sci + ia] * (nbatParams.numTypes + 1) * 2]
- / 6;
+ real c6_i =
+ nbatParams.nbfp[nbatParams.type[sci + ia] * (nbatParams.numTypes + 1) * 2]
+ / 6;
# ifdef ENERGY_GROUPS
vvdwtp[ia][((egps_i >> (ia * egps_ishift)) & egps_imask) * egps_jstride]
# else
#endif
/* Load i atom data */
- int sciy = scix + STRIDE;
- int sciz = sciy + STRIDE;
- ix_S0 = SimdReal(x[scix]) + shX_S;
- ix_S1 = SimdReal(x[scix + 1]) + shX_S;
- ix_S2 = SimdReal(x[scix + 2]) + shX_S;
- ix_S3 = SimdReal(x[scix + 3]) + shX_S;
- iy_S0 = SimdReal(x[sciy]) + shY_S;
- iy_S1 = SimdReal(x[sciy + 1]) + shY_S;
- iy_S2 = SimdReal(x[sciy + 2]) + shY_S;
- iy_S3 = SimdReal(x[sciy + 3]) + shY_S;
- iz_S0 = SimdReal(x[sciz]) + shZ_S;
- iz_S1 = SimdReal(x[sciz + 1]) + shZ_S;
- iz_S2 = SimdReal(x[sciz + 2]) + shZ_S;
- iz_S3 = SimdReal(x[sciz + 3]) + shZ_S;
+ const int sciy = scix + STRIDE;
+ const int sciz = sciy + STRIDE;
+ ix_S0 = SimdReal(x[scix]) + shX_S;
+ ix_S1 = SimdReal(x[scix + 1]) + shX_S;
+ ix_S2 = SimdReal(x[scix + 2]) + shX_S;
+ ix_S3 = SimdReal(x[scix + 3]) + shX_S;
+ iy_S0 = SimdReal(x[sciy]) + shY_S;
+ iy_S1 = SimdReal(x[sciy + 1]) + shY_S;
+ iy_S2 = SimdReal(x[sciy + 2]) + shY_S;
+ iy_S3 = SimdReal(x[sciy + 3]) + shY_S;
+ iz_S0 = SimdReal(x[sciz]) + shZ_S;
+ iz_S1 = SimdReal(x[sciz + 1]) + shZ_S;
+ iz_S2 = SimdReal(x[sciz + 2]) + shZ_S;
+ iz_S3 = SimdReal(x[sciz + 3]) + shZ_S;
if (do_coul)
{
fiz_S2 = setZero();
fiz_S3 = setZero();
- cjind = cjind0;
+ int cjind = cjind0;
/* Currently all kernels use (at least half) LJ */
#define CALC_LJ
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#endif
/* Prune a single nbnxn_pairtlist_t entry with distance rlistInner */
-void nbnxn_kernel_prune_4xn(NbnxnPairlistCpu* nbl,
- const nbnxn_atomdata_t* nbat,
- const rvec* gmx_restrict shift_vec,
- real rlistInner)
+void nbnxn_kernel_prune_4xn(NbnxnPairlistCpu* nbl,
+ const nbnxn_atomdata_t* nbat,
+ gmx::ArrayRef<const gmx::RVec> shiftvec,
+ real rlistInner)
{
#ifdef GMX_NBNXN_SIMD_4XN
using namespace gmx;
const nbnxn_cj_t* gmx_restrict cjOuter = nbl->cjOuter.data();
nbnxn_cj_t* gmx_restrict cjInner = nbl->cj.data();
- const real* gmx_restrict shiftvec = shift_vec[0];
- const real* gmx_restrict x = nbat->x().data();
+ const real* gmx_restrict x = nbat->x().data();
const SimdReal rlist2_S(rlistInner * rlistInner);
ciInner[nciInner].cj_ind_start = ncjInner;
/* Extract shift data */
- int ish = (ciEntry->shift & NBNXN_CI_SHIFT);
- int ish3 = ish * 3;
- int ci = ciEntry->ci;
+ int ish = (ciEntry->shift & NBNXN_CI_SHIFT);
+ int ci = ciEntry->ci;
- SimdReal shX_S = SimdReal(shiftvec[ish3]);
- SimdReal shY_S = SimdReal(shiftvec[ish3 + 1]);
- SimdReal shZ_S = SimdReal(shiftvec[ish3 + 2]);
+ SimdReal shX_S = SimdReal(shiftvec[ish][XX]);
+ SimdReal shY_S = SimdReal(shiftvec[ish][YY]);
+ SimdReal shZ_S = SimdReal(shiftvec[ish][ZZ]);
# if UNROLLJ <= 4
int scix = ci * STRIDE * DIM;
GMX_UNUSED_VALUE(nbl);
GMX_UNUSED_VALUE(nbat);
- GMX_UNUSED_VALUE(shift_vec);
+ GMX_UNUSED_VALUE(shiftvec);
GMX_UNUSED_VALUE(rlistInner);
#endif /* GMX_NBNXN_SIMD_4XN */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct nbnxn_atomdata_t;
struct NbnxnPairlistCpu;
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
/*! \brief Prune a single NbnxnPairlistCpu entry with distance \p rlistInner
*
* Reads a cluster pairlist \p nbl->ciOuter, \p nbl->cjOuter and writes
* all cluster pairs within \p rlistInner to \p nbl->ci, \p nbl->cj.
*/
-void nbnxn_kernel_prune_4xn(NbnxnPairlistCpu* nbl,
- const nbnxn_atomdata_t* nbat,
- const rvec* gmx_restrict shift_vec,
- real rlistInner);
+void nbnxn_kernel_prune_4xn(NbnxnPairlistCpu* nbl,
+ const nbnxn_atomdata_t* nbat,
+ gmx::ArrayRef<const gmx::RVec> shiftvec,
+ real rlistInner);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2019 by the GROMACS development team.
+ * Copyright (c) 2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* The minor index of the array goes over both the LJ combination rules,
* which is only supported by plain cut-off, and the LJ switch/PME functions.
*/
-static p_nbk_func_noener nbnxm_kernel_noener_simd_4xm[coulktNR][vdwktNR] = {
+static const p_nbk_func_noener nbnxm_kernel_noener_simd_4xm[coulktNR][vdwktNR] = {
{
nbnxm_kernel_ElecRF_VdwLJCombGeom_F_4xm,
nbnxm_kernel_ElecRF_VdwLJCombLB_F_4xm,
},
};
-static p_nbk_func_ener nbnxm_kernel_ener_simd_4xm[coulktNR][vdwktNR] = {
+static const p_nbk_func_ener nbnxm_kernel_ener_simd_4xm[coulktNR][vdwktNR] = {
{
nbnxm_kernel_ElecRF_VdwLJCombGeom_VF_4xm,
nbnxm_kernel_ElecRF_VdwLJCombLB_VF_4xm,
},
};
-static p_nbk_func_ener nbnxm_kernel_energrp_simd_4xm[coulktNR][vdwktNR] = {
+static const p_nbk_func_ener nbnxm_kernel_energrp_simd_4xm[coulktNR][vdwktNR] = {
{
nbnxm_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xm,
nbnxm_kernel_ElecRF_VdwLJCombLB_VgrpF_4xm,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int numAtomsMoved,
const int* move)
{
- nb_verlet->pairSearch_->putOnGrid(box, gridIndex, lowerCorner, upperCorner, updateGroupsCog,
- atomRange, atomDensity, atomInfo, x, numAtomsMoved, move,
+ nb_verlet->pairSearch_->putOnGrid(box,
+ gridIndex,
+ lowerCorner,
+ upperCorner,
+ updateGroupsCog,
+ atomRange,
+ atomDensity,
+ atomInfo,
+ x,
+ numAtomsMoved,
+ move,
nb_verlet->nbat.get());
}
c1[d] = zones->size[zone].bb_x1[d];
}
- nbnxn_put_on_grid(nbv, nullptr, zone, c0, c1, nullptr,
- { zones->cg_range[zone], zones->cg_range[zone + 1] }, -1, atomInfo, x, 0,
+ nbnxn_put_on_grid(nbv,
+ nullptr,
+ zone,
+ c0,
+ c1,
+ nullptr,
+ { zones->cg_range[zone], zones->cg_range[zone + 1] },
+ -1,
+ atomInfo,
+ x,
+ 0,
nullptr);
}
}
return gmx::constArrayRefFromArray(pairSearch_->gridSet().atomIndices().data(), numIndices);
}
-void nonbonded_verlet_t::setLocalAtomOrder()
+void nonbonded_verlet_t::setLocalAtomOrder() const
{
pairSearch_->setLocalAtomOrder();
}
void nonbonded_verlet_t::setAtomProperties(gmx::ArrayRef<const int> atomTypes,
gmx::ArrayRef<const real> atomCharges,
- gmx::ArrayRef<const int> atomInfo)
+ gmx::ArrayRef<const int> atomInfo) const
{
nbnxn_atomdata_set(nbat.get(), pairSearch_->gridSet(), atomTypes, atomCharges, atomInfo);
}
void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality locality,
- const bool fillLocal,
gmx::ArrayRef<const gmx::RVec> coordinates)
{
- wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
- wallcycle_sub_start(wcycle_, ewcsNB_X_BUF_OPS);
+ wallcycle_start(wcycle_, WallCycleCounter::NbXFBufOps);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::NBXBufOps);
- nbnxn_atomdata_copy_x_to_nbat_x(pairSearch_->gridSet(), locality, fillLocal,
- as_rvec_array(coordinates.data()), nbat.get());
+ nbnxn_atomdata_copy_x_to_nbat_x(
+ pairSearch_->gridSet(), locality, as_rvec_array(coordinates.data()), nbat.get());
- wallcycle_sub_stop(wcycle_, ewcsNB_X_BUF_OPS);
- wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::NBXBufOps);
+ wallcycle_stop(wcycle_, WallCycleCounter::NbXFBufOps);
}
void nonbonded_verlet_t::convertCoordinatesGpu(const gmx::AtomLocality locality,
- const bool fillLocal,
DeviceBuffer<gmx::RVec> d_x,
GpuEventSynchronizer* xReadyOnDevice)
{
- wallcycle_start(wcycle_, ewcLAUNCH_GPU);
- wallcycle_sub_start(wcycle_, ewcsLAUNCH_GPU_NB_X_BUF_OPS);
+ wallcycle_start(wcycle_, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::LaunchGpuNBXBufOps);
- nbnxn_atomdata_x_to_nbat_x_gpu(pairSearch_->gridSet(), locality, fillLocal, gpu_nbv, d_x, xReadyOnDevice);
+ nbnxn_atomdata_x_to_nbat_x_gpu(pairSearch_->gridSet(), locality, gpu_nbv, d_x, xReadyOnDevice);
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_GPU_NB_X_BUF_OPS);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchGpuNBXBufOps);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
}
gmx::ArrayRef<const int> nonbonded_verlet_t::getGridIndices() const
/* Skip the reduction if there was no short-range GPU work to do
* (either NB or both NB and bonded work). */
- if (!pairlistIsSimple() && !Nbnxm::haveGpuShortRangeWork(gpu_nbv, locality))
+ if (!pairlistIsSimple() && !Nbnxm::haveGpuShortRangeWork(gpu_nbv, atomToInteractionLocality(locality)))
{
return;
}
- wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
- wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
+ wallcycle_start(wcycle_, WallCycleCounter::NbXFBufOps);
+ wallcycle_sub_start(wcycle_, WallCycleSubCounter::NBFBufOps);
reduceForces(nbat.get(), locality, pairSearch_->gridSet(), as_rvec_array(force.data()));
- wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
- wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::NBFBufOps);
+ wallcycle_stop(wcycle_, WallCycleCounter::NbXFBufOps);
}
-int nonbonded_verlet_t::getNumAtoms(const gmx::AtomLocality locality)
+int nonbonded_verlet_t::getNumAtoms(const gmx::AtomLocality locality) const
{
int numAtoms = 0;
switch (locality)
return numAtoms;
}
-void* nonbonded_verlet_t::getGpuForces()
+DeviceBuffer<gmx::RVec> nonbonded_verlet_t::getGpuForces() const
{
return Nbnxm::getGpuForces(gpu_nbv);
}
return pairlistSets_->params().rlistOuter;
}
-void nonbonded_verlet_t::changePairlistRadii(real rlistOuter, real rlistInner)
+void nonbonded_verlet_t::changePairlistRadii(real rlistOuter, real rlistInner) const
{
pairlistSets_->changePairlistRadii(rlistOuter, rlistInner);
}
void nonbonded_verlet_t::setupGpuShortRangeWork(const gmx::GpuBonded* gpuBonded,
- const gmx::InteractionLocality iLocality)
+ const gmx::InteractionLocality iLocality) const
{
if (useGpu() && !emulateGpu())
{
}
}
-void nonbonded_verlet_t::atomdata_init_copy_x_to_nbat_x_gpu()
+void nonbonded_verlet_t::atomdata_init_copy_x_to_nbat_x_gpu() const
{
Nbnxm::nbnxn_gpu_init_x_to_nbat_x(pairSearch_->gridSet(), gpu_nbv);
}
-void nonbonded_verlet_t::insertNonlocalGpuDependency(const gmx::InteractionLocality interactionLocality)
-{
- Nbnxm::nbnxnInsertNonlocalGpuDependency(gpu_nbv, interactionLocality);
-}
-
/*! \endcond */
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct NbnxmGpu;
struct gmx_wallcycle;
struct interaction_const_t;
+enum class LJCombinationRule;
struct nbnxn_atomdata_t;
struct nonbonded_verlet_t;
class PairSearch;
class PairlistSets;
struct t_commrec;
struct t_lambda;
-struct t_mdatoms;
struct t_nrnb;
struct t_forcerec;
struct t_inputrec;
class UpdateGroupsCog;
} // namespace gmx
+//! Namespace for non-bonded kernels
namespace Nbnxm
{
enum class KernelType;
-}
-namespace Nbnxm
+/*! \brief Nbnxm electrostatic GPU kernel flavors.
+ *
+ * Types of electrostatics implementations available in the GPU non-bonded
+ * force kernels. These represent both the electrostatics types implemented
+ * by the kernels (cut-off, RF, and Ewald - a subset of what's defined in
+ * enums.h) as well as encode implementation details analytical/tabulated
+ * and single or twin cut-off (for Ewald kernels).
+ * Note that the cut-off and RF kernels have only analytical flavor and unlike
+ * in the CPU kernels, the tabulated kernels are ATM Ewald-only.
+ *
+ * The row-order of pointers to different electrostatic kernels defined in
+ * nbnxn_cuda.cu by the nb_*_kfunc_ptr function pointer table
+ * should match the order of enumerated types below.
+ */
+enum class ElecType : int
+{
+ Cut, //!< Plain cut-off
+ RF, //!< Reaction field
+ EwaldTab, //!< Tabulated Ewald with single cut-off
+ EwaldTabTwin, //!< Tabulated Ewald with twin cut-off
+ EwaldAna, //!< Analytical Ewald with single cut-off
+ EwaldAnaTwin, //!< Analytical Ewald with twin cut-off
+ Count //!< Number of valid values
+};
+
+//! Number of possible \ref ElecType values.
+constexpr int c_numElecTypes = static_cast<int>(ElecType::Count);
+
+/*! \brief Nbnxm VdW GPU kernel flavors.
+ *
+ * The enumerates values correspond to the LJ implementations in the GPU non-bonded
+ * kernels.
+ *
+ * The column-order of pointers to different electrostatic kernels defined in
+ * nbnxn_cuda_ocl.cpp/.cu by the nb_*_kfunc_ptr function pointer table
+ * should match the order of enumerated types below.
+ */
+enum class VdwType : int
{
+ Cut, //!< Plain cut-off
+ CutCombGeom, //!< Cut-off with geometric combination rules
+ CutCombLB, //!< Cut-off with Lorentz-Berthelot combination rules
+ FSwitch, //!< Smooth force switch
+ PSwitch, //!< Smooth potential switch
+ EwaldGeom, //!< Ewald with geometric combination rules
+ EwaldLB, //!< Ewald with Lorentz-Berthelot combination rules
+ Count //!< Number of valid values
+};
+
+//! Number of possible \ref VdwType values.
+constexpr int c_numVdwTypes = static_cast<int>(VdwType::Count);
/*! \brief Nonbonded NxN kernel types: plain C, CPU SIMD, GPU, GPU emulation */
enum class KernelType : int
//! Return whether the pairlist is of simple, CPU type
bool pairlistIsSimple() const { return !useGpu() && !emulateGpu(); }
- //! Initialize the pair list sets, TODO this should be private
- void initPairlistSets(bool haveMultipleDomains);
//! Returns the order of the local atoms on the grid
gmx::ArrayRef<const int> getLocalAtomOrder() const;
//! Sets the order of the local atoms to the order grid atom ordering
- void setLocalAtomOrder();
+ void setLocalAtomOrder() const;
//! Returns the index position of the atoms on the search grid
gmx::ArrayRef<const int> getGridIndices() const;
void constructPairlist(gmx::InteractionLocality iLocality,
const gmx::ListOfLists<int>& exclusions,
int64_t step,
- t_nrnb* nrnb);
+ t_nrnb* nrnb) const;
//! Updates all the atom properties in Nbnxm
void setAtomProperties(gmx::ArrayRef<const int> atomTypes,
gmx::ArrayRef<const real> atomCharges,
- gmx::ArrayRef<const int> atomInfo);
+ gmx::ArrayRef<const int> atomInfo) const;
/*!\brief Convert the coordinates to NBNXM format for the given locality.
*
* The API function for the transformation of the coordinates from one layout to another.
*
* \param[in] locality Whether coordinates for local or non-local atoms should be
- * transformed. \param[in] fillLocal If the coordinates for filler particles should be
- * zeroed. \param[in] coordinates Coordinates in plain rvec format to be transformed.
+ * transformed. \param[in] coordinates Coordinates in plain rvec format to be transformed.
*/
- void convertCoordinates(gmx::AtomLocality locality, bool fillLocal, gmx::ArrayRef<const gmx::RVec> coordinates);
+ void convertCoordinates(gmx::AtomLocality locality, gmx::ArrayRef<const gmx::RVec> coordinates);
/*!\brief Convert the coordinates to NBNXM format on the GPU for the given locality
*
* The API function for the transformation of the coordinates from one layout to another in the GPU memory.
*
* \param[in] locality Whether coordinates for local or non-local atoms should be transformed.
- * \param[in] fillLocal If the coordinates for filler particles should be zeroed.
* \param[in] d_x GPU coordinates buffer in plain rvec format to be transformed.
* \param[in] xReadyOnDevice Event synchronizer indicating that the coordinates are ready in the device memory.
*/
void convertCoordinatesGpu(gmx::AtomLocality locality,
- bool fillLocal,
DeviceBuffer<gmx::RVec> d_x,
GpuEventSynchronizer* xReadyOnDevice);
//! Init for GPU version of setup coordinates in Nbnxm
- void atomdata_init_copy_x_to_nbat_x_gpu();
-
- //! Sync the nonlocal GPU stream with dependent tasks in the local queue.
- void insertNonlocalGpuDependency(gmx::InteractionLocality interactionLocality);
+ void atomdata_init_copy_x_to_nbat_x_gpu() const;
//! Returns a reference to the pairlist sets
const PairlistSets& pairlistSets() const { return *pairlistSets_; }
bool isDynamicPruningStepGpu(int64_t step) const;
//! Dispatches the dynamic pruning kernel for the given locality, for CPU lists
- void dispatchPruneKernelCpu(gmx::InteractionLocality iLocality, const rvec* shift_vec);
+ void dispatchPruneKernelCpu(gmx::InteractionLocality iLocality,
+ gmx::ArrayRef<const gmx::RVec> shift_vec) const;
//! Dispatches the dynamic pruning kernel for GPU lists
void dispatchPruneKernelGpu(int64_t step);
//! \brief Executes the non-bonded kernel of the GPU or launches it on the GPU
- void dispatchNonbondedKernel(gmx::InteractionLocality iLocality,
- const interaction_const_t& ic,
- const gmx::StepWorkload& stepWork,
- int clearF,
- const t_forcerec& fr,
- gmx_enerdata_t* enerd,
- t_nrnb* nrnb);
+ void dispatchNonbondedKernel(gmx::InteractionLocality iLocality,
+ const interaction_const_t& ic,
+ const gmx::StepWorkload& stepWork,
+ int clearF,
+ gmx::ArrayRef<const gmx::RVec> shiftvec,
+ gmx::ArrayRef<real> repulsionDispersionSR,
+ gmx::ArrayRef<real> CoulombSR,
+ t_nrnb* nrnb) const;
//! Executes the non-bonded free-energy kernel, always runs on the CPU
- void dispatchFreeEnergyKernel(gmx::InteractionLocality iLocality,
- const t_forcerec* fr,
- rvec x[],
- gmx::ForceWithShiftForces* forceWithShiftForces,
- const t_mdatoms& mdatoms,
- t_lambda* fepvals,
- gmx::ArrayRef<const real> lambda,
- gmx_enerdata_t* enerd,
- const gmx::StepWorkload& stepWork,
- t_nrnb* nrnb);
+ void dispatchFreeEnergyKernel(gmx::InteractionLocality iLocality,
+ const t_forcerec& fr,
+ gmx::ArrayRef<const gmx::RVec> coords,
+ gmx::ForceWithShiftForces* forceWithShiftForces,
+ gmx::ArrayRef<const real> chargeA,
+ gmx::ArrayRef<const real> chargeB,
+ gmx::ArrayRef<const int> typeA,
+ gmx::ArrayRef<const int> typeB,
+ t_lambda* fepvals,
+ gmx::ArrayRef<const real> lambda,
+ gmx_enerdata_t* enerd,
+ const gmx::StepWorkload& stepWork,
+ t_nrnb* nrnb);
/*! \brief Add the forces stored in nbat to f, zeros the forces in nbat
* \param [in] locality Local or non-local
*/
void atomdata_add_nbat_f_to_f(gmx::AtomLocality locality, gmx::ArrayRef<gmx::RVec> force);
- /*! \brief Add the forces stored in nbat to total force using GPU buffer opse
- *
- * \param [in] locality Local or non-local
- * \param [in,out] totalForcesDevice Force to be added to
- * \param [in] forcesPmeDevice Device buffer with PME forces
- * \param[in] dependencyList List of synchronizers that represent the dependencies the reduction task needs to sync on.
- * \param [in] useGpuFPmeReduction Whether PME forces should be added
- * \param [in] accumulateForce If the total force buffer already contains data
- */
- void atomdata_add_nbat_f_to_f_gpu(gmx::AtomLocality locality,
- DeviceBuffer<gmx::RVec> totalForcesDevice,
- void* forcesPmeDevice,
- gmx::ArrayRef<GpuEventSynchronizer* const> dependencyList,
- bool useGpuFPmeReduction,
- bool accumulateForce);
-
/*! \brief Get the number of atoms for a given locality
*
* \param [in] locality Local or non-local
* \returns The number of atoms for given locality
*/
- int getNumAtoms(gmx::AtomLocality locality);
+ int getNumAtoms(gmx::AtomLocality locality) const;
/*! \brief Get the pointer to the GPU nonbonded force buffer
*
* \returns A pointer to the force buffer in GPU memory
*/
- void* getGpuForces();
+ DeviceBuffer<gmx::RVec> getGpuForces() const;
//! Return the kernel setup
const Nbnxm::KernelSetup& kernelSetup() const { return kernelSetup_; }
real pairlistOuterRadius() const;
//! Changes the pair-list outer and inner radius
- void changePairlistRadii(real rlistOuter, real rlistInner);
+ void changePairlistRadii(real rlistOuter, real rlistInner) const;
//! Set up internal flags that indicate what type of short-range work there is.
- void setupGpuShortRangeWork(const gmx::GpuBonded* gpuBonded, gmx::InteractionLocality iLocality);
+ void setupGpuShortRangeWork(const gmx::GpuBonded* gpuBonded, gmx::InteractionLocality iLocality) const;
// TODO: Make all data members private
-public:
//! All data related to the pair lists
std::unique_ptr<PairlistSets> pairlistSets_;
//! Working data for constructing the pairlists
/*! \brief Creates an Nbnxm object */
std::unique_ptr<nonbonded_verlet_t> init_nb_verlet(const gmx::MDLogger& mdlog,
- const t_inputrec* ir,
- const t_forcerec* fr,
- const t_commrec* cr,
+ const t_inputrec& inputrec,
+ const t_forcerec& forcerec,
+ const t_commrec* commrec,
const gmx_hw_info_t& hardwareInfo,
bool useGpuForNonbonded,
const gmx::DeviceStreamManager* deviceStreamManager,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
matrix box,
gmx_wallcycle* wcycle);
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
static inline int get_2log(int n)
{
- int log2;
-
- log2 = 0;
- while ((1 << log2) < n)
- {
- log2++;
- }
- if ((1 << log2) != n)
+ if (!gmx::isPowerOfTwo(n))
{
gmx_fatal(FARGS, "nbnxn na_c (%d) is not a power of 2", n);
}
- return log2;
+ return gmx::log2I(n);
}
namespace Nbnxm
/*! \brief The nbnxn i-cluster size in atoms for each nbnxn kernel type */
static constexpr gmx::EnumerationArray<KernelType, int> IClusterSizePerKernelType = {
- { 0, c_nbnxnCpuIClusterSize, c_nbnxnCpuIClusterSize, c_nbnxnCpuIClusterSize,
- c_nbnxnGpuClusterSize, c_nbnxnGpuClusterSize }
+ { 0, c_nbnxnCpuIClusterSize, c_nbnxnCpuIClusterSize, c_nbnxnCpuIClusterSize, c_nbnxnGpuClusterSize, c_nbnxnGpuClusterSize }
};
/*! \brief The nbnxn j-cluster size in atoms for each nbnxn kernel type */
static constexpr gmx::EnumerationArray<KernelType, int> JClusterSizePerKernelType = {
- { 0, c_nbnxnCpuIClusterSize,
+ { 0,
+ c_nbnxnCpuIClusterSize,
#if GMX_SIMD
- GMX_SIMD_REAL_WIDTH, GMX_SIMD_REAL_WIDTH / 2,
+ GMX_SIMD_REAL_WIDTH,
+ GMX_SIMD_REAL_WIDTH / 2,
#else
- 0, 0,
+ 0,
+ 0,
#endif
- c_nbnxnGpuClusterSize, c_nbnxnGpuClusterSize / 2 }
+ c_nbnxnGpuClusterSize,
+ c_nbnxnGpuClusterSize / 2 }
};
/*! \brief Returns whether the pair-list corresponding to nb_kernel_type is simple */
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
+#include "nbnxm.h"
+
struct interaction_const_t;
struct nbnxn_atomdata_t;
struct gmx_wallcycle;
class StepWorkload;
} // namespace gmx
-/*! \brief Nbnxm electrostatic GPU kernel flavors.
- *
- * Types of electrostatics implementations available in the GPU non-bonded
- * force kernels. These represent both the electrostatics types implemented
- * by the kernels (cut-off, RF, and Ewald - a subset of what's defined in
- * enums.h) as well as encode implementation details analytical/tabulated
- * and single or twin cut-off (for Ewald kernels).
- * Note that the cut-off and RF kernels have only analytical flavor and unlike
- * in the CPU kernels, the tabulated kernels are ATM Ewald-only.
- *
- * The row-order of pointers to different electrostatic kernels defined in
- * nbnxn_cuda.cu by the nb_*_kfunc_ptr function pointer table
- * should match the order of enumerated types below.
- */
-enum eelType : int
-{
- eelTypeCUT,
- eelTypeRF,
- eelTypeEWALD_TAB,
- eelTypeEWALD_TAB_TWIN,
- eelTypeEWALD_ANA,
- eelTypeEWALD_ANA_TWIN,
- eelTypeNR
-};
-
-/*! \brief Nbnxm VdW GPU kernel flavors.
- *
- * The enumerates values correspond to the LJ implementations in the GPU non-bonded
- * kernels.
- *
- * The column-order of pointers to different electrostatic kernels defined in
- * nbnxn_cuda_ocl.cpp/.cu by the nb_*_kfunc_ptr function pointer table
- * should match the order of enumerated types below.
- */
-enum evdwType : int
-{
- evdwTypeCUT,
- evdwTypeCUTCOMBGEOM,
- evdwTypeCUTCOMBLB,
- evdwTypeFSWITCH,
- evdwTypePSWITCH,
- evdwTypeEWALDGEOM,
- evdwTypeEWALDLB,
- evdwTypeNR
-};
-
namespace Nbnxm
{
/*! \brief Returns true if LJ combination rules are used in the non-bonded kernels.
*
- * \param[in] vdwType The VdW interaction/implementation type as defined by evdwType
+ * \param[in] vdwType The VdW interaction/implementation type as defined by VdwType
* enumeration.
*
* \returns Whether combination rules are used by the run.
*/
-static inline bool useLjCombRule(const int vdwType)
+static inline bool useLjCombRule(const enum VdwType vdwType)
{
- return (vdwType == evdwTypeCUTCOMBGEOM || vdwType == evdwTypeCUTCOMBLB);
+ return (vdwType == VdwType::CutCombGeom || vdwType == VdwType::CutCombLB);
}
/*! \brief
/*! \brief Initialization for X buffer operations on GPU.
* Called on the NS step and performs (re-)allocations and memory copies. !*/
-CUDA_FUNC_QUALIFIER
+GPU_FUNC_QUALIFIER
void nbnxn_gpu_init_x_to_nbat_x(const Nbnxm::GridSet gmx_unused& gridSet,
- NbnxmGpu gmx_unused* gpu_nbv) CUDA_FUNC_TERM;
+ NbnxmGpu gmx_unused* gpu_nbv) GPU_FUNC_TERM;
/*! \brief X buffer operations on GPU: performs conversion from rvec to nb format.
*
* \param[in] grid Grid to be converted.
- * \param[in] setFillerCoords If the filler coordinates are used.
* \param[in,out] gpu_nbv The nonbonded data GPU structure.
* \param[in] d_x Device-side coordinates in plain rvec format.
* \param[in] xReadyOnDevice Event synchronizer indicating that the coordinates are ready in
* \param[in] locality Copy coordinates for local or non-local atoms.
* \param[in] gridId Index of the grid being converted.
* \param[in] numColumnsMax Maximum number of columns in the grid.
+ * \param[in] mustInsertNonLocalDependency Whether synchronization between local and non-local
+ * streams should be added. Typically, true if and only if that is the last grid in gridset.
*/
CUDA_FUNC_QUALIFIER
void nbnxn_gpu_x_to_nbat_x(const Nbnxm::Grid gmx_unused& grid,
- bool gmx_unused setFillerCoords,
NbnxmGpu gmx_unused* gpu_nbv,
DeviceBuffer<gmx::RVec> gmx_unused d_x,
GpuEventSynchronizer gmx_unused* xReadyOnDevice,
gmx::AtomLocality gmx_unused locality,
int gmx_unused gridId,
- int gmx_unused numColumnsMax) CUDA_FUNC_TERM;
+ int gmx_unused numColumnsMax,
+ bool gmx_unused mustInsertNonLocalDependency) CUDA_FUNC_TERM;
/*! \brief Sync the nonlocal stream with dependent tasks in the local queue.
+ *
+ * As the point where the local stream tasks can be considered complete happens
+ * at the same call point where the nonlocal stream should be synced with the
+ * the local, this function records the event if called with the local stream as
+ * argument and inserts in the GPU stream a wait on the event on the nonlocal.
+ *
* \param[in] nb The nonbonded data GPU structure
* \param[in] interactionLocality Local or NonLocal sync point
*/
-CUDA_FUNC_QUALIFIER
-void nbnxnInsertNonlocalGpuDependency(const NbnxmGpu gmx_unused* nb,
- gmx::InteractionLocality gmx_unused interactionLocality) CUDA_FUNC_TERM;
+GPU_FUNC_QUALIFIER
+void nbnxnInsertNonlocalGpuDependency(NbnxmGpu gmx_unused* nb,
+ gmx::InteractionLocality gmx_unused interactionLocality) GPU_FUNC_TERM;
/*! \brief Set up internal flags that indicate what type of short-range work there is.
*
const gmx::GpuBonded gmx_unused* gpuBonded,
gmx::InteractionLocality gmx_unused iLocality) GPU_FUNC_TERM;
-/*! \brief Returns true if there is GPU short-range work for the given atom locality.
+/*! \brief Returns true if there is GPU short-range work for the given interaction locality.
*
* Note that as, unlike nonbonded tasks, bonded tasks are not split into local/nonlocal,
* and therefore if there are GPU offloaded bonded interactions, this function will return
* true for both local and nonlocal atom range.
*
- * \param[inout] nb Pointer to the nonbonded GPU data structure
- * \param[in] aLocality Atom locality identifier
+ * \param[inout] nb Pointer to the nonbonded GPU data structure
+ * \param[in] interactionLocality Interaction locality identifier
+ *
+ * \return Whether there is short range work for a given locality.
*/
GPU_FUNC_QUALIFIER
-bool haveGpuShortRangeWork(const NbnxmGpu gmx_unused* nb, gmx::AtomLocality gmx_unused aLocality)
+bool haveGpuShortRangeWork(const NbnxmGpu gmx_unused* nb, gmx::InteractionLocality gmx_unused interactionLocality)
GPU_FUNC_TERM_WITH_RETURN(false);
-/*! \brief sync CPU thread on coordinate copy to device
- * \param[in] nb The nonbonded data GPU structure
- */
-CUDA_FUNC_QUALIFIER
-void nbnxn_wait_x_on_device(NbnxmGpu gmx_unused* nb) CUDA_FUNC_TERM;
-
/*! \brief Get the pointer to the GPU nonbonded force buffer
*
* \param[in] nb The nonbonded data GPU structure
* \returns A pointer to the force buffer in GPU memory
*/
CUDA_FUNC_QUALIFIER
-void* getGpuForces(NbnxmGpu gmx_unused* nb) CUDA_FUNC_TERM_WITH_RETURN(nullptr);
+DeviceBuffer<gmx::RVec> getGpuForces(NbnxmGpu gmx_unused* nb)
+ CUDA_FUNC_TERM_WITH_RETURN(DeviceBuffer<gmx::RVec>{});
} // namespace Nbnxm
#endif
# include "opencl/nbnxm_ocl_types.h"
#endif
+#if GMX_GPU_SYCL
+# include "sycl/nbnxm_sycl_types.h"
+#endif
+
#include "nbnxm_gpu_data_mgmt.h"
+#include "gromacs/gpu_utils/device_stream_manager.h"
+#include "gromacs/gpu_utils/gputraits.h"
+#include "gromacs/gpu_utils/pmalloc.h"
#include "gromacs/hardware/device_information.h"
+#include "gromacs/mdtypes/interaction_const.h"
+#include "gromacs/mdtypes/simulation_workload.h"
+#include "gromacs/nbnxm/gpu_common_utils.h"
#include "gromacs/nbnxm/gpu_data_mgmt.h"
+#include "gromacs/nbnxm/gridset.h"
+#include "gromacs/pbcutil/ishift.h"
#include "gromacs/timing/gpu_timing.h"
+#include "gromacs/pbcutil/ishift.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
#include "nbnxm_gpu.h"
#include "pairlistsets.h"
namespace Nbnxm
{
-void init_ewald_coulomb_force_table(const EwaldCorrectionTables& tables,
- NBParamGpu* nbp,
- const DeviceContext& deviceContext)
+static inline void issueClFlushInStream(const DeviceStream& deviceStream)
{
- if (nbp->coulomb_tab)
+#if GMX_GPU_OPENCL
+ /* Based on the v1.2 section 5.13 of the OpenCL spec, a flush is needed
+ * in the stream after marking an event in it in order to be able to sync with
+ * the event from another stream.
+ */
+ cl_int cl_error = clFlush(deviceStream.stream());
+ if (cl_error != CL_SUCCESS)
{
- destroyParamLookupTable(&nbp->coulomb_tab, nbp->coulomb_tab_texobj);
+ GMX_THROW(gmx::InternalError("clFlush failed: " + ocl_get_error_string(cl_error)));
}
-
- nbp->coulomb_tab_scale = tables.scale;
- initParamLookupTable(&nbp->coulomb_tab, &nbp->coulomb_tab_texobj, tables.tableF.data(),
- tables.tableF.size(), deviceContext);
+#else
+ GMX_UNUSED_VALUE(deviceStream);
+#endif
}
-void inline printEnvironmentVariableDeprecationMessage(bool isEnvironmentVariableSet,
- const std::string& environmentVariableSuffix)
+static inline void init_ewald_coulomb_force_table(const EwaldCorrectionTables& tables,
+ NBParamGpu* nbp,
+ const DeviceContext& deviceContext)
{
- if (isEnvironmentVariableSet)
+ if (nbp->coulomb_tab)
{
- fprintf(stderr,
- "Environment variables GMX_CUDA_%s and GMX_OCL_%s are deprecated and will be\n"
- "removed in release 2022, please use GMX_GPU_%s instead.",
- environmentVariableSuffix.c_str(), environmentVariableSuffix.c_str(),
- environmentVariableSuffix.c_str());
+ destroyParamLookupTable(&nbp->coulomb_tab, nbp->coulomb_tab_texobj);
}
+
+ nbp->coulomb_tab_scale = tables.scale;
+ initParamLookupTable(
+ &nbp->coulomb_tab, &nbp->coulomb_tab_texobj, tables.tableF.data(), tables.tableF.size(), deviceContext);
}
-int nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t& ic,
- const DeviceInformation gmx_unused& deviceInfo)
+static inline ElecType nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t& ic,
+ const DeviceInformation gmx_unused& deviceInfo)
{
bool bTwinCut = (ic.rcoulomb != ic.rvdw);
- int kernel_type;
/* Benchmarking/development environment variables to force the use of
analytical or tabulated Ewald kernel. */
-
- // Remove these when old environment variables are deprecated
- const bool forceAnalyticalEwaldLegacy = (getenv("GMX_CUDA_NB_ANA_EWALD") != nullptr)
- || (getenv("GMX_OCL_NB_ANA_EWALD") != nullptr);
- const bool forceTabulatedEwaldLegacy = (getenv("GMX_CUDA_NB_TAB_EWALD") != nullptr)
- || (getenv("GMX_OCL_NB_TAB_EWALD") != nullptr);
- const bool forceTwinCutoffEwaldLegacy = (getenv("GMX_CUDA_NB_EWALD_TWINCUT") != nullptr)
- || (getenv("GMX_OCL_NB_EWALD_TWINCUT") != nullptr);
-
- printEnvironmentVariableDeprecationMessage(forceAnalyticalEwaldLegacy, "NB_ANA_EWALD");
- printEnvironmentVariableDeprecationMessage(forceTabulatedEwaldLegacy, "NB_TAB_EWALD");
- printEnvironmentVariableDeprecationMessage(forceTwinCutoffEwaldLegacy, "NB_EWALD_TWINCUT");
-
- const bool forceAnalyticalEwald =
- (getenv("GMX_GPU_NB_ANA_EWALD") != nullptr) || forceAnalyticalEwaldLegacy;
- const bool forceTabulatedEwald =
- (getenv("GMX_GPU_NB_TAB_EWALD") != nullptr) || forceTabulatedEwaldLegacy;
- const bool forceTwinCutoffEwald =
- (getenv("GMX_GPU_NB_EWALD_TWINCUT") != nullptr) || forceTwinCutoffEwaldLegacy;
+ const bool forceAnalyticalEwald = (getenv("GMX_GPU_NB_ANA_EWALD") != nullptr);
+ const bool forceTabulatedEwald = (getenv("GMX_GPU_NB_TAB_EWALD") != nullptr);
+ const bool forceTwinCutoffEwald = (getenv("GMX_GPU_NB_EWALD_TWINCUT") != nullptr);
if (forceAnalyticalEwald && forceTabulatedEwald)
{
forces it (use it for debugging/benchmarking only). */
if (!bTwinCut && !forceTwinCutoffEwald)
{
- kernel_type = bUseAnalyticalEwald ? eelTypeEWALD_ANA : eelTypeEWALD_TAB;
+ return bUseAnalyticalEwald ? ElecType::EwaldAna : ElecType::EwaldTab;
}
else
{
- kernel_type = bUseAnalyticalEwald ? eelTypeEWALD_ANA_TWIN : eelTypeEWALD_TAB_TWIN;
+ return bUseAnalyticalEwald ? ElecType::EwaldAnaTwin : ElecType::EwaldTabTwin;
}
-
- return kernel_type;
}
-void set_cutoff_parameters(NBParamGpu* nbp, const interaction_const_t* ic, const PairlistParams& listParams)
+static inline void set_cutoff_parameters(NBParamGpu* nbp,
+ const interaction_const_t& ic,
+ const PairlistParams& listParams)
{
- nbp->ewald_beta = ic->ewaldcoeff_q;
- nbp->sh_ewald = ic->sh_ewald;
- nbp->epsfac = ic->epsfac;
- nbp->two_k_rf = 2.0 * ic->k_rf;
- nbp->c_rf = ic->c_rf;
- nbp->rvdw_sq = ic->rvdw * ic->rvdw;
- nbp->rcoulomb_sq = ic->rcoulomb * ic->rcoulomb;
+ nbp->ewald_beta = ic.ewaldcoeff_q;
+ nbp->sh_ewald = ic.sh_ewald;
+ nbp->epsfac = ic.epsfac;
+ nbp->two_k_rf = 2.0 * ic.reactionFieldCoefficient;
+ nbp->c_rf = ic.reactionFieldShift;
+ nbp->rvdw_sq = ic.rvdw * ic.rvdw;
+ nbp->rcoulomb_sq = ic.rcoulomb * ic.rcoulomb;
nbp->rlistOuter_sq = listParams.rlistOuter * listParams.rlistOuter;
nbp->rlistInner_sq = listParams.rlistInner * listParams.rlistInner;
nbp->useDynamicPruning = listParams.useDynamicPruning;
- nbp->sh_lj_ewald = ic->sh_lj_ewald;
- nbp->ewaldcoeff_lj = ic->ewaldcoeff_lj;
+ nbp->sh_lj_ewald = ic.sh_lj_ewald;
+ nbp->ewaldcoeff_lj = ic.ewaldcoeff_lj;
- nbp->rvdw_switch = ic->rvdw_switch;
- nbp->dispersion_shift = ic->dispersion_shift;
- nbp->repulsion_shift = ic->repulsion_shift;
- nbp->vdw_switch = ic->vdw_switch;
+ nbp->rvdw_switch = ic.rvdw_switch;
+ nbp->dispersion_shift = ic.dispersion_shift;
+ nbp->repulsion_shift = ic.repulsion_shift;
+ nbp->vdw_switch = ic.vdw_switch;
}
-void gpu_pme_loadbal_update_param(const nonbonded_verlet_t* nbv, const interaction_const_t* ic)
-{
- if (!nbv || !nbv->useGpu())
- {
- return;
- }
- NbnxmGpu* nb = nbv->gpu_nbv;
- NBParamGpu* nbp = nb->nbparam;
-
- set_cutoff_parameters(nbp, ic, nbv->pairlistSets().params());
-
- nbp->eeltype = nbnxn_gpu_pick_ewald_kernel_type(*ic, nb->deviceContext_->deviceInfo());
-
- GMX_RELEASE_ASSERT(ic->coulombEwaldTables, "Need valid Coulomb Ewald correction tables");
- init_ewald_coulomb_force_table(*ic->coulombEwaldTables, nbp, *nb->deviceContext_);
-}
-
-void init_plist(gpu_plist* pl)
+static inline void init_plist(gpu_plist* pl)
{
/* initialize to nullptr pointers to data that is not allocated here and will
need reallocation in nbnxn_gpu_init_pairlist */
pl->rollingPruningPart = 0;
}
-void init_timings(gmx_wallclock_gpu_nbnxn_t* t)
+static inline void init_timings(gmx_wallclock_gpu_nbnxn_t* t)
{
- int i, j;
-
t->nb_h2d_t = 0.0;
t->nb_d2h_t = 0.0;
t->nb_c = 0;
t->pl_h2d_t = 0.0;
t->pl_h2d_c = 0;
- for (i = 0; i < 2; i++)
+ for (int i = 0; i < 2; i++)
{
- for (j = 0; j < 2; j++)
+ for (int j = 0; j < 2; j++)
{
t->ktime[i][j].t = 0.0;
t->ktime[i][j].c = 0;
t->dynamicPruneTime.t = 0.0;
}
+/*! \brief Initialize \p atomdata first time; it only gets filled at pair-search. */
+static inline void initAtomdataFirst(NBAtomDataGpu* atomdata,
+ int numTypes,
+ const DeviceContext& deviceContext,
+ const DeviceStream& localStream)
+{
+ atomdata->numTypes = numTypes;
+ allocateDeviceBuffer(&atomdata->shiftVec, gmx::c_numShiftVectors, deviceContext);
+ atomdata->shiftVecUploaded = false;
+
+ allocateDeviceBuffer(&atomdata->fShift, gmx::c_numShiftVectors, deviceContext);
+ allocateDeviceBuffer(&atomdata->eLJ, 1, deviceContext);
+ allocateDeviceBuffer(&atomdata->eElec, 1, deviceContext);
+
+ clearDeviceBufferAsync(&atomdata->fShift, 0, gmx::c_numShiftVectors, localStream);
+ clearDeviceBufferAsync(&atomdata->eElec, 0, 1, localStream);
+ clearDeviceBufferAsync(&atomdata->eLJ, 0, 1, localStream);
+
+ /* initialize to nullptr pointers to data that is not allocated here and will
+ need reallocation in later */
+ atomdata->xq = nullptr;
+ atomdata->f = nullptr;
+
+ /* size -1 indicates that the respective array hasn't been initialized yet */
+ atomdata->numAtoms = -1;
+ atomdata->numAtomsAlloc = -1;
+}
+
+static inline VdwType nbnxmGpuPickVdwKernelType(const interaction_const_t& ic,
+ LJCombinationRule ljCombinationRule)
+{
+ if (ic.vdwtype == VanDerWaalsType::Cut)
+ {
+ switch (ic.vdw_modifier)
+ {
+ case InteractionModifiers::None:
+ case InteractionModifiers::PotShift:
+ switch (ljCombinationRule)
+ {
+ case LJCombinationRule::None: return VdwType::Cut;
+ case LJCombinationRule::Geometric: return VdwType::CutCombGeom;
+ case LJCombinationRule::LorentzBerthelot: return VdwType::CutCombLB;
+ default:
+ GMX_THROW(gmx::InconsistentInputError(gmx::formatString(
+ "The requested LJ combination rule %s is not implemented in "
+ "the GPU accelerated kernels!",
+ enumValueToString(ljCombinationRule))));
+ }
+ case InteractionModifiers::ForceSwitch: return VdwType::FSwitch;
+ case InteractionModifiers::PotSwitch: return VdwType::PSwitch;
+ default:
+ GMX_THROW(gmx::InconsistentInputError(
+ gmx::formatString("The requested VdW interaction modifier %s is not "
+ "implemented in the GPU accelerated kernels!",
+ enumValueToString(ic.vdw_modifier))));
+ }
+ }
+ else if (ic.vdwtype == VanDerWaalsType::Pme)
+ {
+ if (ic.ljpme_comb_rule == LongRangeVdW::Geom)
+ {
+ GMX_RELEASE_ASSERT(
+ ljCombinationRule == LJCombinationRule::Geometric,
+ "Combination rules for long- and short-range interactions should match.");
+ return VdwType::EwaldGeom;
+ }
+ else
+ {
+ GMX_RELEASE_ASSERT(
+ ljCombinationRule == LJCombinationRule::LorentzBerthelot,
+ "Combination rules for long- and short-range interactions should match.");
+ return VdwType::EwaldLB;
+ }
+ }
+ else
+ {
+ GMX_THROW(gmx::InconsistentInputError(gmx::formatString(
+ "The requested VdW type %s is not implemented in the GPU accelerated kernels!",
+ enumValueToString(ic.vdwtype))));
+ }
+}
+
+static inline ElecType nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t& ic,
+ const DeviceInformation& deviceInfo)
+{
+ if (ic.eeltype == CoulombInteractionType::Cut)
+ {
+ return ElecType::Cut;
+ }
+ else if (EEL_RF(ic.eeltype))
+ {
+ return ElecType::RF;
+ }
+ else if ((EEL_PME(ic.eeltype) || ic.eeltype == CoulombInteractionType::Ewald))
+ {
+ return nbnxn_gpu_pick_ewald_kernel_type(ic, deviceInfo);
+ }
+ else
+ {
+ /* Shouldn't happen, as this is checked when choosing Verlet-scheme */
+ GMX_THROW(gmx::InconsistentInputError(
+ gmx::formatString("The requested electrostatics type %s is not implemented in "
+ "the GPU accelerated kernels!",
+ enumValueToString(ic.eeltype))));
+ }
+}
+
+/*! \brief Initialize the nonbonded parameter data structure. */
+static inline void initNbparam(NBParamGpu* nbp,
+ const interaction_const_t& ic,
+ const PairlistParams& listParams,
+ const nbnxn_atomdata_t::Params& nbatParams,
+ const DeviceContext& deviceContext)
+{
+ const int numTypes = nbatParams.numTypes;
+
+ set_cutoff_parameters(nbp, ic, listParams);
+
+ nbp->vdwType = nbnxmGpuPickVdwKernelType(ic, nbatParams.ljCombinationRule);
+ nbp->elecType = nbnxmGpuPickElectrostaticsKernelType(ic, deviceContext.deviceInfo());
+
+ if (ic.vdwtype == VanDerWaalsType::Pme)
+ {
+ if (ic.ljpme_comb_rule == LongRangeVdW::Geom)
+ {
+ GMX_ASSERT(nbatParams.ljCombinationRule == LJCombinationRule::Geometric,
+ "Combination rule mismatch!");
+ }
+ else
+ {
+ GMX_ASSERT(nbatParams.ljCombinationRule == LJCombinationRule::LorentzBerthelot,
+ "Combination rule mismatch!");
+ }
+ }
+
+ /* generate table for PME */
+ if (nbp->elecType == ElecType::EwaldTab || nbp->elecType == ElecType::EwaldTabTwin)
+ {
+ GMX_RELEASE_ASSERT(ic.coulombEwaldTables, "Need valid Coulomb Ewald correction tables");
+ init_ewald_coulomb_force_table(*ic.coulombEwaldTables, nbp, deviceContext);
+ }
+
+ /* set up LJ parameter lookup table */
+ if (!useLjCombRule(nbp->vdwType))
+ {
+ static_assert(sizeof(decltype(nbp->nbfp)) == 2 * sizeof(decltype(*nbatParams.nbfp.data())),
+ "Mismatch in the size of host / device data types");
+ initParamLookupTable(&nbp->nbfp,
+ &nbp->nbfp_texobj,
+ reinterpret_cast<const Float2*>(nbatParams.nbfp.data()),
+ numTypes * numTypes,
+ deviceContext);
+ }
+
+ /* set up LJ-PME parameter lookup table */
+ if (ic.vdwtype == VanDerWaalsType::Pme)
+ {
+ static_assert(sizeof(decltype(nbp->nbfp_comb))
+ == 2 * sizeof(decltype(*nbatParams.nbfp_comb.data())),
+ "Mismatch in the size of host / device data types");
+ initParamLookupTable(&nbp->nbfp_comb,
+ &nbp->nbfp_comb_texobj,
+ reinterpret_cast<const Float2*>(nbatParams.nbfp_comb.data()),
+ numTypes,
+ deviceContext);
+ }
+}
+
+NbnxmGpu* gpu_init(const gmx::DeviceStreamManager& deviceStreamManager,
+ const interaction_const_t* ic,
+ const PairlistParams& listParams,
+ const nbnxn_atomdata_t* nbat,
+ const bool bLocalAndNonlocal)
+{
+ auto* nb = new NbnxmGpu();
+ nb->deviceContext_ = &deviceStreamManager.context();
+ nb->atdat = new NBAtomDataGpu;
+ nb->nbparam = new NBParamGpu;
+ nb->plist[InteractionLocality::Local] = new Nbnxm::gpu_plist;
+ if (bLocalAndNonlocal)
+ {
+ nb->plist[InteractionLocality::NonLocal] = new Nbnxm::gpu_plist;
+ }
+
+ nb->bUseTwoStreams = bLocalAndNonlocal;
+
+ nb->timers = new Nbnxm::GpuTimers();
+ snew(nb->timings, 1);
+
+ /* WARNING: CUDA timings are incorrect with multiple streams.
+ * This is the main reason why they are disabled by default.
+ * Can be enabled by setting GMX_ENABLE_GPU_TIMING environment variable.
+ * TODO: Consider turning on by default when we can detect nr of streams.
+ *
+ * OpenCL timing is enabled by default and can be disabled by
+ * GMX_DISABLE_GPU_TIMING environment variable.
+ *
+ * Timing is disabled in SYCL.
+ */
+ nb->bDoTime = (GMX_GPU_CUDA && (getenv("GMX_ENABLE_GPU_TIMING") != nullptr))
+ || (GMX_GPU_OPENCL && (getenv("GMX_DISABLE_GPU_TIMING") == nullptr));
+
+ if (nb->bDoTime)
+ {
+ init_timings(nb->timings);
+ }
+
+ /* init nbst */
+ pmalloc(reinterpret_cast<void**>(&nb->nbst.eLJ), sizeof(*nb->nbst.eLJ));
+ pmalloc(reinterpret_cast<void**>(&nb->nbst.eElec), sizeof(*nb->nbst.eElec));
+ pmalloc(reinterpret_cast<void**>(&nb->nbst.fShift), gmx::c_numShiftVectors * sizeof(*nb->nbst.fShift));
+
+ init_plist(nb->plist[InteractionLocality::Local]);
+
+ /* local/non-local GPU streams */
+ GMX_RELEASE_ASSERT(deviceStreamManager.streamIsValid(gmx::DeviceStreamType::NonBondedLocal),
+ "Local non-bonded stream should be initialized to use GPU for non-bonded.");
+ const DeviceStream& localStream = deviceStreamManager.stream(gmx::DeviceStreamType::NonBondedLocal);
+ nb->deviceStreams[InteractionLocality::Local] = &localStream;
+ // In general, it's not strictly necessary to use 2 streams for SYCL, since they are
+ // out-of-order. But for the time being, it will be less disruptive to keep them.
+ if (nb->bUseTwoStreams)
+ {
+ init_plist(nb->plist[InteractionLocality::NonLocal]);
+
+ GMX_RELEASE_ASSERT(deviceStreamManager.streamIsValid(gmx::DeviceStreamType::NonBondedNonLocal),
+ "Non-local non-bonded stream should be initialized to use GPU for "
+ "non-bonded with domain decomposition.");
+ nb->deviceStreams[InteractionLocality::NonLocal] =
+ &deviceStreamManager.stream(gmx::DeviceStreamType::NonBondedNonLocal);
+ }
+
+ const nbnxn_atomdata_t::Params& nbatParams = nbat->params();
+ const DeviceContext& deviceContext = *nb->deviceContext_;
+
+ initNbparam(nb->nbparam, *ic, listParams, nbatParams, deviceContext);
+ initAtomdataFirst(nb->atdat, nbatParams.numTypes, deviceContext, localStream);
+
+ gpu_init_platform_specific(nb);
+
+ if (debug)
+ {
+ fprintf(debug, "Initialized NBNXM GPU data structures.\n");
+ }
+
+ return nb;
+}
+
+void gpu_pme_loadbal_update_param(const nonbonded_verlet_t* nbv, const interaction_const_t& ic)
+{
+ if (!nbv || !nbv->useGpu())
+ {
+ return;
+ }
+ NbnxmGpu* nb = nbv->gpu_nbv;
+ NBParamGpu* nbp = nb->nbparam;
+
+ set_cutoff_parameters(nbp, ic, nbv->pairlistSets().params());
+
+ nbp->elecType = nbnxn_gpu_pick_ewald_kernel_type(ic, nb->deviceContext_->deviceInfo());
+
+ GMX_RELEASE_ASSERT(ic.coulombEwaldTables, "Need valid Coulomb Ewald correction tables");
+ init_ewald_coulomb_force_table(*ic.coulombEwaldTables, nbp, *nb->deviceContext_);
+}
+
+void gpu_upload_shiftvec(NbnxmGpu* nb, const nbnxn_atomdata_t* nbatom)
+{
+ NBAtomDataGpu* adat = nb->atdat;
+ const DeviceStream& localStream = *nb->deviceStreams[InteractionLocality::Local];
+
+ /* only if we have a dynamic box */
+ if (nbatom->bDynamicBox || !adat->shiftVecUploaded)
+ {
+ copyToDeviceBuffer(&adat->shiftVec,
+ gmx::asGenericFloat3Pointer(nbatom->shift_vec),
+ 0,
+ gmx::c_numShiftVectors,
+ localStream,
+ GpuApiCallBehavior::Async,
+ nullptr);
+ adat->shiftVecUploaded = true;
+ }
+}
+
//! This function is documented in the header file
void gpu_init_pairlist(NbnxmGpu* nb, const NbnxnPairlistGpu* h_plist, const InteractionLocality iloc)
{
{
if (d_plist->na_c != h_plist->na_ci)
{
- sprintf(sbuf, "In init_plist: the #atoms per cell has changed (from %d to %d)",
- d_plist->na_c, h_plist->na_ci);
+ sprintf(sbuf,
+ "In init_plist: the #atoms per cell has changed (from %d to %d)",
+ d_plist->na_c,
+ h_plist->na_ci);
gmx_incons(sbuf);
}
}
- gpu_timers_t::Interaction& iTimers = nb->timers->interaction[iloc];
+ GpuTimers::Interaction& iTimers = nb->timers->interaction[iloc];
if (bDoTime)
{
// TODO most of this function is same in CUDA and OpenCL, move into the header
const DeviceContext& deviceContext = *nb->deviceContext_;
- reallocateDeviceBuffer(&d_plist->sci, h_plist->sci.size(), &d_plist->nsci, &d_plist->sci_nalloc,
- deviceContext);
- copyToDeviceBuffer(&d_plist->sci, h_plist->sci.data(), 0, h_plist->sci.size(), deviceStream,
- GpuApiCallBehavior::Async, bDoTime ? iTimers.pl_h2d.fetchNextEvent() : nullptr);
+ reallocateDeviceBuffer(
+ &d_plist->sci, h_plist->sci.size(), &d_plist->nsci, &d_plist->sci_nalloc, deviceContext);
+ copyToDeviceBuffer(&d_plist->sci,
+ h_plist->sci.data(),
+ 0,
+ h_plist->sci.size(),
+ deviceStream,
+ GpuApiCallBehavior::Async,
+ bDoTime ? iTimers.pl_h2d.fetchNextEvent() : nullptr);
- reallocateDeviceBuffer(&d_plist->cj4, h_plist->cj4.size(), &d_plist->ncj4, &d_plist->cj4_nalloc,
- deviceContext);
- copyToDeviceBuffer(&d_plist->cj4, h_plist->cj4.data(), 0, h_plist->cj4.size(), deviceStream,
- GpuApiCallBehavior::Async, bDoTime ? iTimers.pl_h2d.fetchNextEvent() : nullptr);
+ reallocateDeviceBuffer(
+ &d_plist->cj4, h_plist->cj4.size(), &d_plist->ncj4, &d_plist->cj4_nalloc, deviceContext);
+ copyToDeviceBuffer(&d_plist->cj4,
+ h_plist->cj4.data(),
+ 0,
+ h_plist->cj4.size(),
+ deviceStream,
+ GpuApiCallBehavior::Async,
+ bDoTime ? iTimers.pl_h2d.fetchNextEvent() : nullptr);
- reallocateDeviceBuffer(&d_plist->imask, h_plist->cj4.size() * c_nbnxnGpuClusterpairSplit,
- &d_plist->nimask, &d_plist->imask_nalloc, deviceContext);
+ reallocateDeviceBuffer(&d_plist->imask,
+ h_plist->cj4.size() * c_nbnxnGpuClusterpairSplit,
+ &d_plist->nimask,
+ &d_plist->imask_nalloc,
+ deviceContext);
- reallocateDeviceBuffer(&d_plist->excl, h_plist->excl.size(), &d_plist->nexcl,
- &d_plist->excl_nalloc, deviceContext);
- copyToDeviceBuffer(&d_plist->excl, h_plist->excl.data(), 0, h_plist->excl.size(), deviceStream,
- GpuApiCallBehavior::Async, bDoTime ? iTimers.pl_h2d.fetchNextEvent() : nullptr);
+ reallocateDeviceBuffer(
+ &d_plist->excl, h_plist->excl.size(), &d_plist->nexcl, &d_plist->excl_nalloc, deviceContext);
+ copyToDeviceBuffer(&d_plist->excl,
+ h_plist->excl.data(),
+ 0,
+ h_plist->excl.size(),
+ deviceStream,
+ GpuApiCallBehavior::Async,
+ bDoTime ? iTimers.pl_h2d.fetchNextEvent() : nullptr);
if (bDoTime)
{
d_plist->haveFreshList = true;
}
+void gpu_init_atomdata(NbnxmGpu* nb, const nbnxn_atomdata_t* nbat)
+{
+ bool bDoTime = nb->bDoTime;
+ Nbnxm::GpuTimers* timers = bDoTime ? nb->timers : nullptr;
+ NBAtomDataGpu* atdat = nb->atdat;
+ const DeviceContext& deviceContext = *nb->deviceContext_;
+ const DeviceStream& localStream = *nb->deviceStreams[InteractionLocality::Local];
+
+ int numAtoms = nbat->numAtoms();
+ bool realloced = false;
+
+ if (bDoTime)
+ {
+ /* time async copy */
+ timers->atdat.openTimingRegion(localStream);
+ }
+
+ /* need to reallocate if we have to copy more atoms than the amount of space
+ available and only allocate if we haven't initialized yet, i.e atdat->natoms == -1 */
+ if (numAtoms > atdat->numAtomsAlloc)
+ {
+ int numAlloc = over_alloc_small(numAtoms);
+
+ /* free up first if the arrays have already been initialized */
+ if (atdat->numAtomsAlloc != -1)
+ {
+ freeDeviceBuffer(&atdat->f);
+ freeDeviceBuffer(&atdat->xq);
+ if (useLjCombRule(nb->nbparam->vdwType))
+ {
+ freeDeviceBuffer(&atdat->ljComb);
+ }
+ else
+ {
+ freeDeviceBuffer(&atdat->atomTypes);
+ }
+ }
+
+
+ allocateDeviceBuffer(&atdat->f, numAlloc, deviceContext);
+ allocateDeviceBuffer(&atdat->xq, numAlloc, deviceContext);
+
+ if (useLjCombRule(nb->nbparam->vdwType))
+ {
+ // Two Lennard-Jones parameters per atom
+ allocateDeviceBuffer(&atdat->ljComb, numAlloc, deviceContext);
+ }
+ else
+ {
+ allocateDeviceBuffer(&atdat->atomTypes, numAlloc, deviceContext);
+ }
+
+ atdat->numAtomsAlloc = numAlloc;
+ realloced = true;
+ }
+
+ atdat->numAtoms = numAtoms;
+ atdat->numAtomsLocal = nbat->natoms_local;
+
+ /* need to clear GPU f output if realloc happened */
+ if (realloced)
+ {
+ clearDeviceBufferAsync(&atdat->f, 0, atdat->numAtomsAlloc, localStream);
+ }
+
+ if (useLjCombRule(nb->nbparam->vdwType))
+ {
+ static_assert(
+ sizeof(Float2) == 2 * sizeof(*nbat->params().lj_comb.data()),
+ "Size of a pair of LJ parameters elements should be equal to the size of Float2.");
+ copyToDeviceBuffer(&atdat->ljComb,
+ reinterpret_cast<const Float2*>(nbat->params().lj_comb.data()),
+ 0,
+ numAtoms,
+ localStream,
+ GpuApiCallBehavior::Async,
+ bDoTime ? timers->atdat.fetchNextEvent() : nullptr);
+ }
+ else
+ {
+ static_assert(sizeof(int) == sizeof(*nbat->params().type.data()),
+ "Sizes of host- and device-side atom types should be the same.");
+ copyToDeviceBuffer(&atdat->atomTypes,
+ nbat->params().type.data(),
+ 0,
+ numAtoms,
+ localStream,
+ GpuApiCallBehavior::Async,
+ bDoTime ? timers->atdat.fetchNextEvent() : nullptr);
+ }
+
+ if (bDoTime)
+ {
+ timers->atdat.closeTimingRegion(localStream);
+ }
+
+ /* kick off the tasks enqueued above to ensure concurrency with the search */
+ issueClFlushInStream(localStream);
+}
+
+void gpu_clear_outputs(NbnxmGpu* nb, bool computeVirial)
+{
+ NBAtomDataGpu* adat = nb->atdat;
+ const DeviceStream& localStream = *nb->deviceStreams[InteractionLocality::Local];
+ // Clear forces
+ clearDeviceBufferAsync(&adat->f, 0, nb->atdat->numAtoms, localStream);
+ // Clear shift force array and energies if the outputs were used in the current step
+ if (computeVirial)
+ {
+ clearDeviceBufferAsync(&adat->fShift, 0, gmx::c_numShiftVectors, localStream);
+ clearDeviceBufferAsync(&adat->eLJ, 0, 1, localStream);
+ clearDeviceBufferAsync(&adat->eElec, 0, 1, localStream);
+ }
+ issueClFlushInStream(localStream);
+}
+
//! This function is documented in the header file
gmx_wallclock_gpu_nbnxn_t* gpu_get_timings(NbnxmGpu* nb)
{
bool gpu_is_kernel_ewald_analytical(const NbnxmGpu* nb)
{
- return ((nb->nbparam->eeltype == eelTypeEWALD_ANA) || (nb->nbparam->eeltype == eelTypeEWALD_ANA_TWIN));
+ return ((nb->nbparam->elecType == ElecType::EwaldAna)
+ || (nb->nbparam->elecType == ElecType::EwaldAnaTwin));
+}
+
+void setupGpuShortRangeWork(NbnxmGpu* nb, const gmx::GpuBonded* gpuBonded, const gmx::InteractionLocality iLocality)
+{
+ GMX_ASSERT(nb, "Need a valid nbnxn_gpu object");
+
+ // There is short-range work if the pair list for the provided
+ // interaction locality contains entries or if there is any
+ // bonded work (as this is not split into local/nonlocal).
+ nb->haveWork[iLocality] = ((nb->plist[iLocality]->nsci != 0)
+ || (gpuBonded != nullptr && gpuBonded->haveInteractions()));
+}
+
+bool haveGpuShortRangeWork(const NbnxmGpu* nb, const gmx::InteractionLocality interactionLocality)
+{
+ GMX_ASSERT(nb, "Need a valid nbnxn_gpu object");
+
+ return nb->haveWork[interactionLocality];
+}
+
+/*! \brief
+ * Launch asynchronously the download of nonbonded forces from the GPU
+ * (and energies/shift forces if required).
+ */
+void gpu_launch_cpyback(NbnxmGpu* nb,
+ struct nbnxn_atomdata_t* nbatom,
+ const gmx::StepWorkload& stepWork,
+ const AtomLocality atomLocality)
+{
+ GMX_ASSERT(nb, "Need a valid nbnxn_gpu object");
+
+ /* determine interaction locality from atom locality */
+ const InteractionLocality iloc = atomToInteractionLocality(atomLocality);
+ GMX_ASSERT(iloc == InteractionLocality::Local
+ || (iloc == InteractionLocality::NonLocal && nb->bNonLocalStreamDoneMarked == false),
+ "Non-local stream is indicating that the copy back event is enqueued at the "
+ "beginning of the copy back function.");
+
+ /* extract the data */
+ NBAtomDataGpu* adat = nb->atdat;
+ Nbnxm::GpuTimers* timers = nb->timers;
+ bool bDoTime = nb->bDoTime;
+ const DeviceStream& deviceStream = *nb->deviceStreams[iloc];
+
+ /* don't launch non-local copy-back if there was no non-local work to do */
+ if ((iloc == InteractionLocality::NonLocal) && !haveGpuShortRangeWork(nb, iloc))
+ {
+ /* TODO An alternative way to signal that non-local work is
+ complete is to use a clEnqueueMarker+clEnqueueBarrier
+ pair. However, the use of bNonLocalStreamDoneMarked has the
+ advantage of being local to the host, so probably minimizes
+ overhead. Curiously, for NVIDIA OpenCL with an empty-domain
+ test case, overall simulation performance was higher with
+ the API calls, but this has not been tested on AMD OpenCL,
+ so could be worth considering in future. */
+ nb->bNonLocalStreamDoneMarked = false;
+ return;
+ }
+
+ /* local/nonlocal offset and length used for xq and f */
+ auto atomsRange = getGpuAtomRange(adat, atomLocality);
+
+ /* beginning of timed D2H section */
+ if (bDoTime)
+ {
+ timers->xf[atomLocality].nb_d2h.openTimingRegion(deviceStream);
+ }
+
+ /* With DD the local D2H transfer can only start after the non-local
+ has been launched. */
+ if (iloc == InteractionLocality::Local && nb->bNonLocalStreamDoneMarked)
+ {
+ nb->nonlocal_done.enqueueWaitEvent(deviceStream);
+ nb->bNonLocalStreamDoneMarked = false;
+ }
+
+ /* DtoH f */
+ if (!stepWork.useGpuFBufferOps)
+ {
+ static_assert(
+ sizeof(*nbatom->out[0].f.data()) == sizeof(float),
+ "The host force buffer should be in single precision to match device data size.");
+ copyFromDeviceBuffer(reinterpret_cast<Float3*>(nbatom->out[0].f.data()) + atomsRange.begin(),
+ &adat->f,
+ atomsRange.begin(),
+ atomsRange.size(),
+ deviceStream,
+ GpuApiCallBehavior::Async,
+ bDoTime ? timers->xf[atomLocality].nb_d2h.fetchNextEvent() : nullptr);
+
+ issueClFlushInStream(deviceStream);
+ }
+
+ /* After the non-local D2H is launched the nonlocal_done event can be
+ recorded which signals that the local D2H can proceed. This event is not
+ placed after the non-local kernel because we first need the non-local
+ data back first. */
+ if (iloc == InteractionLocality::NonLocal)
+ {
+ nb->nonlocal_done.markEvent(deviceStream);
+ nb->bNonLocalStreamDoneMarked = true;
+ }
+
+ /* only transfer energies in the local stream */
+ if (iloc == InteractionLocality::Local)
+ {
+ /* DtoH fshift when virial is needed */
+ if (stepWork.computeVirial)
+ {
+ static_assert(
+ sizeof(*nb->nbst.fShift) == sizeof(Float3),
+ "Sizes of host- and device-side shift vector elements should be the same.");
+ copyFromDeviceBuffer(nb->nbst.fShift,
+ &adat->fShift,
+ 0,
+ gmx::c_numShiftVectors,
+ deviceStream,
+ GpuApiCallBehavior::Async,
+ bDoTime ? timers->xf[atomLocality].nb_d2h.fetchNextEvent() : nullptr);
+ }
+
+ /* DtoH energies */
+ if (stepWork.computeEnergy)
+ {
+ static_assert(sizeof(*nb->nbst.eLJ) == sizeof(float),
+ "Sizes of host- and device-side LJ energy terms should be the same.");
+ copyFromDeviceBuffer(nb->nbst.eLJ,
+ &adat->eLJ,
+ 0,
+ 1,
+ deviceStream,
+ GpuApiCallBehavior::Async,
+ bDoTime ? timers->xf[atomLocality].nb_d2h.fetchNextEvent() : nullptr);
+ static_assert(sizeof(*nb->nbst.eElec) == sizeof(float),
+ "Sizes of host- and device-side electrostatic energy terms should be the "
+ "same.");
+ copyFromDeviceBuffer(nb->nbst.eElec,
+ &adat->eElec,
+ 0,
+ 1,
+ deviceStream,
+ GpuApiCallBehavior::Async,
+ bDoTime ? timers->xf[atomLocality].nb_d2h.fetchNextEvent() : nullptr);
+ }
+ }
+
+ if (bDoTime)
+ {
+ timers->xf[atomLocality].nb_d2h.closeTimingRegion(deviceStream);
+ }
+}
+
+void nbnxnInsertNonlocalGpuDependency(NbnxmGpu* nb, const InteractionLocality interactionLocality)
+{
+ const DeviceStream& deviceStream = *nb->deviceStreams[interactionLocality];
+
+ /* When we get here all misc operations issued in the local stream as well as
+ the local xq H2D are done,
+ so we record that in the local stream and wait for it in the nonlocal one.
+ This wait needs to precede any PP tasks, bonded or nonbonded, that may
+ compute on interactions between local and nonlocal atoms.
+ */
+ if (nb->bUseTwoStreams)
+ {
+ if (interactionLocality == InteractionLocality::Local)
+ {
+ nb->misc_ops_and_local_H2D_done.markEvent(deviceStream);
+ issueClFlushInStream(deviceStream);
+ }
+ else
+ {
+ nb->misc_ops_and_local_H2D_done.enqueueWaitEvent(deviceStream);
+ }
+ }
+}
+
+/*! \brief Launch asynchronously the xq buffer host to device copy. */
+void gpu_copy_xq_to_gpu(NbnxmGpu* nb, const nbnxn_atomdata_t* nbatom, const AtomLocality atomLocality)
+{
+ GMX_ASSERT(nb, "Need a valid nbnxn_gpu object");
+
+ const InteractionLocality iloc = atomToInteractionLocality(atomLocality);
+
+ NBAtomDataGpu* adat = nb->atdat;
+ gpu_plist* plist = nb->plist[iloc];
+ Nbnxm::GpuTimers* timers = nb->timers;
+ const DeviceStream& deviceStream = *nb->deviceStreams[iloc];
+
+ const bool bDoTime = nb->bDoTime;
+
+ /* Don't launch the non-local H2D copy if there is no dependent
+ work to do: neither non-local nor other (e.g. bonded) work
+ to do that has as input the nbnxn coordaintes.
+ Doing the same for the local kernel is more complicated, since the
+ local part of the force array also depends on the non-local kernel.
+ So to avoid complicating the code and to reduce the risk of bugs,
+ we always call the local local x+q copy (and the rest of the local
+ work in nbnxn_gpu_launch_kernel().
+ */
+ if ((iloc == InteractionLocality::NonLocal) && !haveGpuShortRangeWork(nb, iloc))
+ {
+ plist->haveFreshList = false;
+
+ // The event is marked for Local interactions unconditionally,
+ // so it has to be released here because of the early return
+ // for NonLocal interactions.
+ nb->misc_ops_and_local_H2D_done.reset();
+
+ return;
+ }
+
+ /* local/nonlocal offset and length used for xq and f */
+ const auto atomsRange = getGpuAtomRange(adat, atomLocality);
+
+ /* beginning of timed HtoD section */
+ if (bDoTime)
+ {
+ timers->xf[atomLocality].nb_h2d.openTimingRegion(deviceStream);
+ }
+
+ /* HtoD x, q */
+ GMX_ASSERT(nbatom->XFormat == nbatXYZQ,
+ "The coordinates should be in xyzq format to copy to the Float4 device buffer.");
+ copyToDeviceBuffer(&adat->xq,
+ reinterpret_cast<const Float4*>(nbatom->x().data()) + atomsRange.begin(),
+ atomsRange.begin(),
+ atomsRange.size(),
+ deviceStream,
+ GpuApiCallBehavior::Async,
+ nullptr);
+
+ if (bDoTime)
+ {
+ timers->xf[atomLocality].nb_h2d.closeTimingRegion(deviceStream);
+ }
+
+ /* When we get here all misc operations issued in the local stream as well as
+ the local xq H2D are done,
+ so we record that in the local stream and wait for it in the nonlocal one.
+ This wait needs to precede any PP tasks, bonded or nonbonded, that may
+ compute on interactions between local and nonlocal atoms.
+ */
+ nbnxnInsertNonlocalGpuDependency(nb, iloc);
+}
+
+
+/* Initialization for X buffer operations on GPU. */
+void nbnxn_gpu_init_x_to_nbat_x(const Nbnxm::GridSet& gridSet, NbnxmGpu* gpu_nbv)
+{
+ const DeviceStream& localStream = *gpu_nbv->deviceStreams[InteractionLocality::Local];
+ const bool bDoTime = gpu_nbv->bDoTime;
+ const int maxNumColumns = gridSet.numColumnsMax();
+
+ reallocateDeviceBuffer(&gpu_nbv->cxy_na,
+ maxNumColumns * gridSet.grids().size(),
+ &gpu_nbv->ncxy_na,
+ &gpu_nbv->ncxy_na_alloc,
+ *gpu_nbv->deviceContext_);
+ reallocateDeviceBuffer(&gpu_nbv->cxy_ind,
+ maxNumColumns * gridSet.grids().size(),
+ &gpu_nbv->ncxy_ind,
+ &gpu_nbv->ncxy_ind_alloc,
+ *gpu_nbv->deviceContext_);
+
+ for (unsigned int g = 0; g < gridSet.grids().size(); g++)
+ {
+ const Nbnxm::Grid& grid = gridSet.grids()[g];
+
+ const int numColumns = grid.numColumns();
+ const int* atomIndices = gridSet.atomIndices().data();
+ const int atomIndicesSize = gridSet.atomIndices().size();
+ const int* cxy_na = grid.cxy_na().data();
+ const int* cxy_ind = grid.cxy_ind().data();
+
+ auto* timerH2D = bDoTime ? &gpu_nbv->timers->xf[AtomLocality::Local].nb_h2d : nullptr;
+
+ reallocateDeviceBuffer(&gpu_nbv->atomIndices,
+ atomIndicesSize,
+ &gpu_nbv->atomIndicesSize,
+ &gpu_nbv->atomIndicesSize_alloc,
+ *gpu_nbv->deviceContext_);
+
+ if (atomIndicesSize > 0)
+ {
+ if (bDoTime)
+ {
+ timerH2D->openTimingRegion(localStream);
+ }
+
+ copyToDeviceBuffer(&gpu_nbv->atomIndices,
+ atomIndices,
+ 0,
+ atomIndicesSize,
+ localStream,
+ GpuApiCallBehavior::Async,
+ bDoTime ? timerH2D->fetchNextEvent() : nullptr);
+
+ if (bDoTime)
+ {
+ timerH2D->closeTimingRegion(localStream);
+ }
+ }
+
+ if (numColumns > 0)
+ {
+ if (bDoTime)
+ {
+ timerH2D->openTimingRegion(localStream);
+ }
+
+ copyToDeviceBuffer(&gpu_nbv->cxy_na,
+ cxy_na,
+ maxNumColumns * g,
+ numColumns,
+ localStream,
+ GpuApiCallBehavior::Async,
+ bDoTime ? timerH2D->fetchNextEvent() : nullptr);
+
+ if (bDoTime)
+ {
+ timerH2D->closeTimingRegion(localStream);
+ }
+
+ if (bDoTime)
+ {
+ timerH2D->openTimingRegion(localStream);
+ }
+
+ copyToDeviceBuffer(&gpu_nbv->cxy_ind,
+ cxy_ind,
+ maxNumColumns * g,
+ numColumns,
+ localStream,
+ GpuApiCallBehavior::Async,
+ bDoTime ? timerH2D->fetchNextEvent() : nullptr);
+
+ if (bDoTime)
+ {
+ timerH2D->closeTimingRegion(localStream);
+ }
+ }
+ }
+
+ // The above data is transferred on the local stream but is a
+ // dependency of the nonlocal stream (specifically the nonlocal X
+ // buf ops kernel). We therefore set a dependency to ensure
+ // that the nonlocal stream waits on the local stream here.
+ // This call records an event in the local stream:
+ nbnxnInsertNonlocalGpuDependency(gpu_nbv, Nbnxm::InteractionLocality::Local);
+ // ...and this call instructs the nonlocal stream to wait on that event:
+ nbnxnInsertNonlocalGpuDependency(gpu_nbv, Nbnxm::InteractionLocality::NonLocal);
+}
+
+//! This function is documented in the header file
+void gpu_free(NbnxmGpu* nb)
+{
+ if (nb == nullptr)
+ {
+ return;
+ }
+
+ gpu_free_platform_specific(nb);
+
+ delete nb->timers;
+ sfree(nb->timings);
+
+ NBAtomDataGpu* atdat = nb->atdat;
+ NBParamGpu* nbparam = nb->nbparam;
+
+ /* Free atdat */
+ freeDeviceBuffer(&(nb->atdat->xq));
+ freeDeviceBuffer(&(nb->atdat->f));
+ freeDeviceBuffer(&(nb->atdat->eLJ));
+ freeDeviceBuffer(&(nb->atdat->eElec));
+ freeDeviceBuffer(&(nb->atdat->fShift));
+ freeDeviceBuffer(&(nb->atdat->shiftVec));
+ if (useLjCombRule(nb->nbparam->vdwType))
+ {
+ freeDeviceBuffer(&atdat->ljComb);
+ }
+ else
+ {
+ freeDeviceBuffer(&atdat->atomTypes);
+ }
+
+ /* Free nbparam */
+ if (nbparam->elecType == ElecType::EwaldTab || nbparam->elecType == ElecType::EwaldTabTwin)
+ {
+ destroyParamLookupTable(&nbparam->coulomb_tab, nbparam->coulomb_tab_texobj);
+ }
+
+ if (!useLjCombRule(nb->nbparam->vdwType))
+ {
+ destroyParamLookupTable(&nbparam->nbfp, nbparam->nbfp_texobj);
+ }
+
+ if (nbparam->vdwType == VdwType::EwaldGeom || nbparam->vdwType == VdwType::EwaldLB)
+ {
+ destroyParamLookupTable(&nbparam->nbfp_comb, nbparam->nbfp_comb_texobj);
+ }
+
+ /* Free plist */
+ auto* plist = nb->plist[InteractionLocality::Local];
+ freeDeviceBuffer(&plist->sci);
+ freeDeviceBuffer(&plist->cj4);
+ freeDeviceBuffer(&plist->imask);
+ freeDeviceBuffer(&plist->excl);
+ delete plist;
+ if (nb->bUseTwoStreams)
+ {
+ auto* plist_nl = nb->plist[InteractionLocality::NonLocal];
+ freeDeviceBuffer(&plist_nl->sci);
+ freeDeviceBuffer(&plist_nl->cj4);
+ freeDeviceBuffer(&plist_nl->imask);
+ freeDeviceBuffer(&plist_nl->excl);
+ delete plist_nl;
+ }
+
+ /* Free nbst */
+ pfree(nb->nbst.eLJ);
+ nb->nbst.eLJ = nullptr;
+
+ pfree(nb->nbst.eElec);
+ nb->nbst.eElec = nullptr;
+
+ pfree(nb->nbst.fShift);
+ nb->nbst.fShift = nullptr;
+
+ delete atdat;
+ delete nbparam;
+ delete nb;
+
+ if (debug)
+ {
+ fprintf(debug, "Cleaned up NBNXM GPU data structures.\n");
+ }
}
} // namespace Nbnxm
#ifndef GMX_NBNXM_NBNXM_GPU_DATA_MGMT_H
#define GMX_NBNXM_NBNXM_GPU_DATA_MGMT_H
+class DeviceContext;
struct interaction_const_t;
struct NBParamGpu;
struct PairlistParams;
struct gpu_plist;
-/*! \brief Tabulates the Ewald Coulomb force and initializes the size/scale and the table GPU array.
- *
- * If called with an already allocated table, it just re-uploads the
- * table.
- */
-void init_ewald_coulomb_force_table(const EwaldCorrectionTables& tables,
- NBParamGpu* nbp,
- const DeviceContext& deviceContext);
-
-/*! \brief Selects the Ewald kernel type, analytical or tabulated, single or twin cut-off. */
-int nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t gmx_unused& ic,
- const DeviceInformation& deviceInfo);
-
-/*! \brief Copies all parameters related to the cut-off from ic to nbp
- */
-void set_cutoff_parameters(NBParamGpu* nbp, const interaction_const_t* ic, const PairlistParams& listParams);
-
-/*! \brief Initializes the pair list data structure.
- */
-void init_plist(gpu_plist* pl);
+/*! \brief Initializes the NBNXM GPU data structures. */
+void gpu_init_platform_specific(NbnxmGpu* nb);
-/*! \brief Initializes the timings data structure. */
-void init_timings(gmx_wallclock_gpu_nbnxn_t* t);
+/*! \brief Releases the NBNXM GPU data structures. */
+void gpu_free_platform_specific(NbnxmGpu* nb);
} // namespace Nbnxm
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* If the return value is FALSE and fplog/cr != NULL, prints a fallback
* message to fplog/stderr.
*/
-static gmx_bool nbnxn_simd_supported(const gmx::MDLogger& mdlog, const t_inputrec* ir)
+static bool nbnxn_simd_supported(const gmx::MDLogger& mdlog, const t_inputrec& inputrec)
{
- if (ir->vdwtype == evdwPME && ir->ljpme_combination_rule == eljpmeLB)
+ if (inputrec.vdwtype == VanDerWaalsType::Pme && inputrec.ljpme_combination_rule == LongRangeVdW::LB)
{
/* LJ PME with LB combination rule does 7 mesh operations.
* This so slow that we don't compile SIMD non-bonded kernels
}
/*! \brief Returns the most suitable CPU kernel type and Ewald handling */
-static KernelSetup pick_nbnxn_kernel_cpu(const t_inputrec gmx_unused* ir,
+static KernelSetup pick_nbnxn_kernel_cpu(const t_inputrec gmx_unused& inputrec,
const gmx_hw_info_t gmx_unused& hardwareInfo)
{
KernelSetup kernelSetup;
*/
kernelSetup.kernelType = KernelType::Cpu4xN_Simd_4xN;
- if (!GMX_SIMD_HAVE_FMA && (EEL_PME_EWALD(ir->coulombtype) || EVDW_PME(ir->vdwtype)))
+ if (!GMX_SIMD_HAVE_FMA && (EEL_PME_EWALD(inputrec.coulombtype) || EVDW_PME(inputrec.vdwtype)))
{
/* We have Ewald kernels without FMA (Intel Sandy/Ivy Bridge).
* There are enough instructions to make 2x(4+4) efficient.
const char* lookup_kernel_name(const KernelType kernelType)
{
- const char* returnvalue = nullptr;
switch (kernelType)
{
- case KernelType::NotSet: returnvalue = "not set"; break;
- case KernelType::Cpu4x4_PlainC: returnvalue = "plain C"; break;
+ case KernelType::NotSet: return "not set";
+ case KernelType::Cpu4x4_PlainC: return "plain C";
case KernelType::Cpu4xN_Simd_4xN:
case KernelType::Cpu4xN_Simd_2xNN:
#if GMX_SIMD
- returnvalue = "SIMD";
+ return "SIMD";
#else // GMX_SIMD
- returnvalue = "not available";
+ return "not available";
#endif // GMX_SIMD
- break;
- case KernelType::Gpu8x8x8: returnvalue = "GPU"; break;
- case KernelType::Cpu8x8x8_PlainC: returnvalue = "plain C"; break;
+ case KernelType::Gpu8x8x8: return "GPU";
+ case KernelType::Cpu8x8x8_PlainC: return "plain C";
default: gmx_fatal(FARGS, "Illegal kernel type selected");
}
- return returnvalue;
};
/*! \brief Returns the most suitable kernel type and Ewald handling */
gmx_bool use_simd_kernels,
const gmx_hw_info_t& hardwareInfo,
const NonbondedResource& nonbondedResource,
- const t_inputrec* ir)
+ const t_inputrec& inputrec)
{
KernelSetup kernelSetup;
}
else
{
- if (use_simd_kernels && nbnxn_simd_supported(mdlog, ir))
+ if (use_simd_kernels && nbnxn_simd_supported(mdlog, inputrec))
{
- kernelSetup = pick_nbnxn_kernel_cpu(ir, hardwareInfo);
+ kernelSetup = pick_nbnxn_kernel_cpu(inputrec, hardwareInfo);
}
else
{
params_(pairlistParams),
minimumIlistCountForGpuBalancing_(minimumIlistCountForGpuBalancing)
{
- localSet_ = std::make_unique<PairlistSet>(gmx::InteractionLocality::Local, params_);
+ localSet_ = std::make_unique<PairlistSet>(params_);
if (haveMultipleDomains)
{
- nonlocalSet_ = std::make_unique<PairlistSet>(gmx::InteractionLocality::NonLocal, params_);
+ nonlocalSet_ = std::make_unique<PairlistSet>(params_);
}
}
/*! \brief Gets and returns the minimum i-list count for balacing based on the GPU used or env.var. when set */
static int getMinimumIlistCountForGpuBalancing(NbnxmGpu* nbnxmGpu)
{
- int minimumIlistCount;
-
if (const char* env = getenv("GMX_NB_MIN_CI"))
{
- char* end;
+ char* end = nullptr;
- minimumIlistCount = strtol(env, &end, 10);
+ int minimumIlistCount = strtol(env, &end, 10);
if (!end || (*end != 0) || minimumIlistCount < 0)
{
- gmx_fatal(FARGS,
- "Invalid value passed in GMX_NB_MIN_CI=%s, non-negative integer required", env);
+ gmx_fatal(
+ FARGS, "Invalid value passed in GMX_NB_MIN_CI=%s, non-negative integer required", env);
}
if (debug)
{
- fprintf(debug, "Neighbor-list balancing parameter: %d (passed as env. var.)\n",
- minimumIlistCount);
+ fprintf(debug, "Neighbor-list balancing parameter: %d (passed as env. var.)\n", minimumIlistCount);
}
+ return minimumIlistCount;
}
else
{
- minimumIlistCount = gpu_min_ci_balanced(nbnxmGpu);
+ int minimumIlistCount = gpu_min_ci_balanced(nbnxmGpu);
if (debug)
{
fprintf(debug,
"multi-processors)\n",
minimumIlistCount);
}
+ return minimumIlistCount;
}
+}
- return minimumIlistCount;
+static int getENbnxnInitCombRule(const t_forcerec& forcerec)
+{
+ if (forcerec.ic->vdwtype == VanDerWaalsType::Cut
+ && (forcerec.ic->vdw_modifier == InteractionModifiers::None
+ || forcerec.ic->vdw_modifier == InteractionModifiers::PotShift)
+ && getenv("GMX_NO_LJ_COMB_RULE") == nullptr)
+ {
+ /* Plain LJ cut-off: we can optimize with combination rules */
+ return enbnxninitcombruleDETECT;
+ }
+ else if (forcerec.ic->vdwtype == VanDerWaalsType::Pme)
+ {
+ /* LJ-PME: we need to use a combination rule for the grid */
+ if (forcerec.ljpme_combination_rule == LongRangeVdW::Geom)
+ {
+ return enbnxninitcombruleGEOM;
+ }
+ else
+ {
+ return enbnxninitcombruleLB;
+ }
+ }
+ else
+ {
+ /* We use a full combination matrix: no rule required */
+ return enbnxninitcombruleNONE;
+ }
}
std::unique_ptr<nonbonded_verlet_t> init_nb_verlet(const gmx::MDLogger& mdlog,
- const t_inputrec* ir,
- const t_forcerec* fr,
- const t_commrec* cr,
+ const t_inputrec& inputrec,
+ const t_forcerec& forcerec,
+ const t_commrec* commrec,
const gmx_hw_info_t& hardwareInfo,
- const bool useGpuForNonbonded,
+ bool useGpuForNonbonded,
const gmx::DeviceStreamManager* deviceStreamManager,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
matrix box,
gmx_wallcycle* wcycle)
{
nonbondedResource = NonbondedResource::Cpu;
}
- Nbnxm::KernelSetup kernelSetup =
- pick_nbnxn_kernel(mdlog, fr->use_simd_kernels, hardwareInfo, nonbondedResource, ir);
+ Nbnxm::KernelSetup kernelSetup = pick_nbnxn_kernel(
+ mdlog, forcerec.use_simd_kernels, hardwareInfo, nonbondedResource, inputrec);
- const bool haveMultipleDomains = havePPDomainDecomposition(cr);
+ const bool haveMultipleDomains = havePPDomainDecomposition(commrec);
- bool bFEP_NonBonded = (fr->efep != efepNO) && haveFepPerturbedNBInteractions(*mtop);
- PairlistParams pairlistParams(kernelSetup.kernelType, bFEP_NonBonded, ir->rlist, haveMultipleDomains);
+ bool bFEP_NonBonded = (forcerec.efep != FreeEnergyPerturbationType::No)
+ && haveFepPerturbedNBInteractions(mtop);
+ PairlistParams pairlistParams(
+ kernelSetup.kernelType, bFEP_NonBonded, inputrec.rlist, haveMultipleDomains);
- setupDynamicPairlistPruning(mdlog, ir, mtop, box, fr->ic, &pairlistParams);
+ setupDynamicPairlistPruning(mdlog, inputrec, mtop, box, *forcerec.ic, &pairlistParams);
- int enbnxninitcombrule;
- if (fr->ic->vdwtype == evdwCUT
- && (fr->ic->vdw_modifier == eintmodNONE || fr->ic->vdw_modifier == eintmodPOTSHIFT)
- && getenv("GMX_NO_LJ_COMB_RULE") == nullptr)
- {
- /* Plain LJ cut-off: we can optimize with combination rules */
- enbnxninitcombrule = enbnxninitcombruleDETECT;
- }
- else if (fr->ic->vdwtype == evdwPME)
- {
- /* LJ-PME: we need to use a combination rule for the grid */
- if (fr->ljpme_combination_rule == eljpmeGEOM)
- {
- enbnxninitcombrule = enbnxninitcombruleGEOM;
- }
- else
- {
- enbnxninitcombrule = enbnxninitcombruleLB;
- }
- }
- else
- {
- /* We use a full combination matrix: no rule required */
- enbnxninitcombrule = enbnxninitcombruleNONE;
- }
+ const int enbnxninitcombrule = getENbnxnInitCombRule(forcerec);
auto pinPolicy = (useGpuForNonbonded ? gmx::PinningPolicy::PinnedIfSupported
: gmx::PinningPolicy::CannotBePinned);
- auto nbat = std::make_unique<nbnxn_atomdata_t>(pinPolicy);
-
- int mimimumNumEnergyGroupNonbonded = ir->opts.ngener;
- if (ir->opts.ngener - ir->nwall == 1)
+ int mimimumNumEnergyGroupNonbonded = inputrec.opts.ngener;
+ if (inputrec.opts.ngener - inputrec.nwall == 1)
{
/* We have only one non-wall energy group, we do not need energy group
* support in the non-bondeds kernels, since all non-bonded energy
*/
mimimumNumEnergyGroupNonbonded = 1;
}
- nbnxn_atomdata_init(mdlog, nbat.get(), kernelSetup.kernelType, enbnxninitcombrule, fr->ntype,
- fr->nbfp, mimimumNumEnergyGroupNonbonded,
- (useGpuForNonbonded || emulateGpu) ? 1 : gmx_omp_nthreads_get(emntNonbonded));
+
+ auto nbat = std::make_unique<nbnxn_atomdata_t>(
+ pinPolicy,
+ mdlog,
+ kernelSetup.kernelType,
+ enbnxninitcombrule,
+ forcerec.ntype,
+ forcerec.nbfp,
+ mimimumNumEnergyGroupNonbonded,
+ (useGpuForNonbonded || emulateGpu) ? 1 : gmx_omp_nthreads_get(ModuleMultiThread::Nonbonded));
NbnxmGpu* gpu_nbv = nullptr;
int minimumIlistCountForGpuBalancing = 0;
GMX_RELEASE_ASSERT(
(deviceStreamManager != nullptr),
"Device stream manager should be initialized in order to use GPU for non-bonded.");
- gpu_nbv = gpu_init(*deviceStreamManager, fr->ic, pairlistParams, nbat.get(), haveMultipleDomains);
+ gpu_nbv = gpu_init(
+ *deviceStreamManager, forcerec.ic.get(), pairlistParams, nbat.get(), haveMultipleDomains);
minimumIlistCountForGpuBalancing = getMinimumIlistCountForGpuBalancing(gpu_nbv);
}
- auto pairlistSets = std::make_unique<PairlistSets>(pairlistParams, haveMultipleDomains,
- minimumIlistCountForGpuBalancing);
-
- auto pairSearch = std::make_unique<PairSearch>(
- ir->pbcType, EI_TPI(ir->eI), DOMAINDECOMP(cr) ? &cr->dd->numCells : nullptr,
- DOMAINDECOMP(cr) ? domdec_zones(cr->dd) : nullptr, pairlistParams.pairlistType,
- bFEP_NonBonded, gmx_omp_nthreads_get(emntPairsearch), pinPolicy);
-
- return std::make_unique<nonbonded_verlet_t>(std::move(pairlistSets), std::move(pairSearch),
- std::move(nbat), kernelSetup, gpu_nbv, wcycle);
+ auto pairlistSets = std::make_unique<PairlistSets>(
+ pairlistParams, haveMultipleDomains, minimumIlistCountForGpuBalancing);
+
+ auto pairSearch =
+ std::make_unique<PairSearch>(inputrec.pbcType,
+ EI_TPI(inputrec.eI),
+ DOMAINDECOMP(commrec) ? &commrec->dd->numCells : nullptr,
+ DOMAINDECOMP(commrec) ? domdec_zones(commrec->dd) : nullptr,
+ pairlistParams.pairlistType,
+ bFEP_NonBonded,
+ gmx_omp_nthreads_get(ModuleMultiThread::Pairsearch),
+ pinPolicy);
+
+ return std::make_unique<nonbonded_verlet_t>(
+ std::move(pairlistSets), std::move(pairSearch), std::move(nbat), kernelSetup, gpu_nbv, wcycle);
}
} // namespace Nbnxm
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*! \brief The nbnxn SIMD 4xN and 2x(N+N) kernels can be added independently.
* Currently the 2xNN SIMD kernels only make sense with:
* 8-way SIMD: 4x4 setup, works with AVX-256 in single precision
- * 16-way SIMD: 4x8 setup, works with Intel MIC in single precision
+ * 16-way SIMD: 4x8 setup, not currently in use, but worked with Intel MIC
*/
# if GMX_SIMD_REAL_WIDTH == 2 || GMX_SIMD_REAL_WIDTH == 4 || GMX_SIMD_REAL_WIDTH == 8
# define GMX_NBNXN_SIMD_4XN
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2012,2013,2014,2015,2018 by the GROMACS development team.
-# Copyright (c) 2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
-DNBNXM_MIN_DISTANCE_SQUARED_VALUE_FLOAT=3.82e-07
-Dc_nbnxnGpuNumClusterPerSupercluster=8
-Dc_nbnxnGpuJgroupSize=4
+ -Dc_centralShiftIndex=22
-DIATYPE_SHMEM
-c -I ${CMAKE_SOURCE_DIR}/src -std=cl1.2
-Weverything -Wno-conversion -Wno-missing-variable-declarations -Wno-used-but-marked-unused
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
# include <limits>
#endif
-#include "thread_mpi/atomic.h"
-
#include "gromacs/gpu_utils/device_context.h"
#include "gromacs/gpu_utils/gputraits_ocl.h"
#include "gromacs/gpu_utils/oclutils.h"
#include "gromacs/nbnxm/nbnxm.h"
#include "gromacs/nbnxm/nbnxm_gpu.h"
#include "gromacs/nbnxm/pairlist.h"
-#include "gromacs/pbcutil/ishift.h"
#include "gromacs/timing/gpu_timing.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
"Watch out, the input system is too large to simulate!\n"
"The number of nonbonded work units (=number of super-clusters) exceeds the"
"device capabilities. Global work size limit exceeded (%zu > %zu)!",
- global_work_size[i], device_limit);
+ global_work_size[i],
+ device_limit);
}
}
}
*/
/*! \brief Force-only kernel function names. */
-static const char* nb_kfunc_noener_noprune_ptr[eelTypeNR][evdwTypeNR] = {
- { "nbnxn_kernel_ElecCut_VdwLJ_F_opencl", "nbnxn_kernel_ElecCut_VdwLJCombGeom_F_opencl",
- "nbnxn_kernel_ElecCut_VdwLJCombLB_F_opencl", "nbnxn_kernel_ElecCut_VdwLJFsw_F_opencl",
- "nbnxn_kernel_ElecCut_VdwLJPsw_F_opencl", "nbnxn_kernel_ElecCut_VdwLJEwCombGeom_F_opencl",
+static const char* nb_kfunc_noener_noprune_ptr[c_numElecTypes][c_numVdwTypes] = {
+ { "nbnxn_kernel_ElecCut_VdwLJ_F_opencl",
+ "nbnxn_kernel_ElecCut_VdwLJCombGeom_F_opencl",
+ "nbnxn_kernel_ElecCut_VdwLJCombLB_F_opencl",
+ "nbnxn_kernel_ElecCut_VdwLJFsw_F_opencl",
+ "nbnxn_kernel_ElecCut_VdwLJPsw_F_opencl",
+ "nbnxn_kernel_ElecCut_VdwLJEwCombGeom_F_opencl",
"nbnxn_kernel_ElecCut_VdwLJEwCombLB_F_opencl" },
- { "nbnxn_kernel_ElecRF_VdwLJ_F_opencl", "nbnxn_kernel_ElecRF_VdwLJCombGeom_F_opencl",
- "nbnxn_kernel_ElecRF_VdwLJCombLB_F_opencl", "nbnxn_kernel_ElecRF_VdwLJFsw_F_opencl",
- "nbnxn_kernel_ElecRF_VdwLJPsw_F_opencl", "nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_opencl",
+ { "nbnxn_kernel_ElecRF_VdwLJ_F_opencl",
+ "nbnxn_kernel_ElecRF_VdwLJCombGeom_F_opencl",
+ "nbnxn_kernel_ElecRF_VdwLJCombLB_F_opencl",
+ "nbnxn_kernel_ElecRF_VdwLJFsw_F_opencl",
+ "nbnxn_kernel_ElecRF_VdwLJPsw_F_opencl",
+ "nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_opencl",
"nbnxn_kernel_ElecRF_VdwLJEwCombLB_F_opencl" },
- { "nbnxn_kernel_ElecEwQSTab_VdwLJ_F_opencl", "nbnxn_kernel_ElecEwQSTab_VdwLJCombGeom_F_opencl",
- "nbnxn_kernel_ElecEwQSTab_VdwLJCombLB_F_opencl", "nbnxn_kernel_ElecEwQSTab_VdwLJFsw_F_opencl",
+ { "nbnxn_kernel_ElecEwQSTab_VdwLJ_F_opencl",
+ "nbnxn_kernel_ElecEwQSTab_VdwLJCombGeom_F_opencl",
+ "nbnxn_kernel_ElecEwQSTab_VdwLJCombLB_F_opencl",
+ "nbnxn_kernel_ElecEwQSTab_VdwLJFsw_F_opencl",
"nbnxn_kernel_ElecEwQSTab_VdwLJPsw_F_opencl",
"nbnxn_kernel_ElecEwQSTab_VdwLJEwCombGeom_F_opencl",
"nbnxn_kernel_ElecEwQSTab_VdwLJEwCombLB_F_opencl" },
"nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJPsw_F_opencl",
"nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombGeom_F_opencl",
"nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombLB_F_opencl" },
- { "nbnxn_kernel_ElecEw_VdwLJ_F_opencl", "nbnxn_kernel_ElecEw_VdwLJCombGeom_F_opencl",
- "nbnxn_kernel_ElecEw_VdwLJCombLB_F_opencl", "nbnxn_kernel_ElecEw_VdwLJFsw_F_opencl",
- "nbnxn_kernel_ElecEw_VdwLJPsw_F_opencl", "nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_opencl",
+ { "nbnxn_kernel_ElecEw_VdwLJ_F_opencl",
+ "nbnxn_kernel_ElecEw_VdwLJCombGeom_F_opencl",
+ "nbnxn_kernel_ElecEw_VdwLJCombLB_F_opencl",
+ "nbnxn_kernel_ElecEw_VdwLJFsw_F_opencl",
+ "nbnxn_kernel_ElecEw_VdwLJPsw_F_opencl",
+ "nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_opencl",
"nbnxn_kernel_ElecEw_VdwLJEwCombLB_F_opencl" },
{ "nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_opencl",
"nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_opencl",
"nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_opencl",
- "nbnxn_kernel_ElecEwTwinCut_VdwLJFsw_F_opencl", "nbnxn_kernel_ElecEwTwinCut_VdwLJPsw_F_opencl",
+ "nbnxn_kernel_ElecEwTwinCut_VdwLJFsw_F_opencl",
+ "nbnxn_kernel_ElecEwTwinCut_VdwLJPsw_F_opencl",
"nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_opencl",
"nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombLB_F_opencl" }
};
/*! \brief Force + energy kernel function pointers. */
-static const char* nb_kfunc_ener_noprune_ptr[eelTypeNR][evdwTypeNR] = {
- { "nbnxn_kernel_ElecCut_VdwLJ_VF_opencl", "nbnxn_kernel_ElecCut_VdwLJCombGeom_VF_opencl",
- "nbnxn_kernel_ElecCut_VdwLJCombLB_VF_opencl", "nbnxn_kernel_ElecCut_VdwLJFsw_VF_opencl",
- "nbnxn_kernel_ElecCut_VdwLJPsw_VF_opencl", "nbnxn_kernel_ElecCut_VdwLJEwCombGeom_VF_opencl",
+static const char* nb_kfunc_ener_noprune_ptr[c_numElecTypes][c_numVdwTypes] = {
+ { "nbnxn_kernel_ElecCut_VdwLJ_VF_opencl",
+ "nbnxn_kernel_ElecCut_VdwLJCombGeom_VF_opencl",
+ "nbnxn_kernel_ElecCut_VdwLJCombLB_VF_opencl",
+ "nbnxn_kernel_ElecCut_VdwLJFsw_VF_opencl",
+ "nbnxn_kernel_ElecCut_VdwLJPsw_VF_opencl",
+ "nbnxn_kernel_ElecCut_VdwLJEwCombGeom_VF_opencl",
"nbnxn_kernel_ElecCut_VdwLJEwCombLB_VF_opencl" },
- { "nbnxn_kernel_ElecRF_VdwLJ_VF_opencl", "nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_opencl",
- "nbnxn_kernel_ElecRF_VdwLJCombLB_VF_opencl", "nbnxn_kernel_ElecRF_VdwLJFsw_VF_opencl",
- "nbnxn_kernel_ElecRF_VdwLJPsw_VF_opencl", "nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_opencl",
+ { "nbnxn_kernel_ElecRF_VdwLJ_VF_opencl",
+ "nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_opencl",
+ "nbnxn_kernel_ElecRF_VdwLJCombLB_VF_opencl",
+ "nbnxn_kernel_ElecRF_VdwLJFsw_VF_opencl",
+ "nbnxn_kernel_ElecRF_VdwLJPsw_VF_opencl",
+ "nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_opencl",
"nbnxn_kernel_ElecRF_VdwLJEwCombLB_VF_opencl" },
- { "nbnxn_kernel_ElecEwQSTab_VdwLJ_VF_opencl", "nbnxn_kernel_ElecEwQSTab_VdwLJCombGeom_VF_opencl",
+ { "nbnxn_kernel_ElecEwQSTab_VdwLJ_VF_opencl",
+ "nbnxn_kernel_ElecEwQSTab_VdwLJCombGeom_VF_opencl",
"nbnxn_kernel_ElecEwQSTab_VdwLJCombLB_VF_opencl",
- "nbnxn_kernel_ElecEwQSTab_VdwLJFsw_VF_opencl", "nbnxn_kernel_ElecEwQSTab_VdwLJPsw_VF_opencl",
+ "nbnxn_kernel_ElecEwQSTab_VdwLJFsw_VF_opencl",
+ "nbnxn_kernel_ElecEwQSTab_VdwLJPsw_VF_opencl",
"nbnxn_kernel_ElecEwQSTab_VdwLJEwCombGeom_VF_opencl",
"nbnxn_kernel_ElecEwQSTab_VdwLJEwCombLB_VF_opencl" },
{ "nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJ_VF_opencl",
"nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJPsw_VF_opencl",
"nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombGeom_VF_opencl",
"nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombLB_VF_opencl" },
- { "nbnxn_kernel_ElecEw_VdwLJ_VF_opencl", "nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_opencl",
- "nbnxn_kernel_ElecEw_VdwLJCombLB_VF_opencl", "nbnxn_kernel_ElecEw_VdwLJFsw_VF_opencl",
- "nbnxn_kernel_ElecEw_VdwLJPsw_VF_opencl", "nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_opencl",
+ { "nbnxn_kernel_ElecEw_VdwLJ_VF_opencl",
+ "nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_opencl",
+ "nbnxn_kernel_ElecEw_VdwLJCombLB_VF_opencl",
+ "nbnxn_kernel_ElecEw_VdwLJFsw_VF_opencl",
+ "nbnxn_kernel_ElecEw_VdwLJPsw_VF_opencl",
+ "nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_opencl",
"nbnxn_kernel_ElecEw_VdwLJEwCombLB_VF_opencl" },
{ "nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_opencl",
"nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_opencl",
};
/*! \brief Force + pruning kernel function pointers. */
-static const char* nb_kfunc_noener_prune_ptr[eelTypeNR][evdwTypeNR] = {
+static const char* nb_kfunc_noener_prune_ptr[c_numElecTypes][c_numVdwTypes] = {
{ "nbnxn_kernel_ElecCut_VdwLJ_F_prune_opencl",
"nbnxn_kernel_ElecCut_VdwLJCombGeom_F_prune_opencl",
"nbnxn_kernel_ElecCut_VdwLJCombLB_F_prune_opencl",
- "nbnxn_kernel_ElecCut_VdwLJFsw_F_prune_opencl", "nbnxn_kernel_ElecCut_VdwLJPsw_F_prune_opencl",
+ "nbnxn_kernel_ElecCut_VdwLJFsw_F_prune_opencl",
+ "nbnxn_kernel_ElecCut_VdwLJPsw_F_prune_opencl",
"nbnxn_kernel_ElecCut_VdwLJEwCombGeom_F_prune_opencl",
"nbnxn_kernel_ElecCut_VdwLJEwCombLB_F_prune_opencl" },
- { "nbnxn_kernel_ElecRF_VdwLJ_F_prune_opencl", "nbnxn_kernel_ElecRF_VdwLJCombGeom_F_prune_opencl",
+ { "nbnxn_kernel_ElecRF_VdwLJ_F_prune_opencl",
+ "nbnxn_kernel_ElecRF_VdwLJCombGeom_F_prune_opencl",
"nbnxn_kernel_ElecRF_VdwLJCombLB_F_prune_opencl",
- "nbnxn_kernel_ElecRF_VdwLJFsw_F_prune_opencl", "nbnxn_kernel_ElecRF_VdwLJPsw_F_prune_opencl",
+ "nbnxn_kernel_ElecRF_VdwLJFsw_F_prune_opencl",
+ "nbnxn_kernel_ElecRF_VdwLJPsw_F_prune_opencl",
"nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_prune_opencl",
"nbnxn_kernel_ElecRF_VdwLJEwCombLB_F_prune_opencl" },
{ "nbnxn_kernel_ElecEwQSTab_VdwLJ_F_prune_opencl",
"nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJPsw_F_prune_opencl",
"nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombGeom_F_prune_opencl",
"nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombLB_F_prune_opencl" },
- { "nbnxn_kernel_ElecEw_VdwLJ_F_prune_opencl", "nbnxn_kernel_ElecEw_VdwLJCombGeom_F_prune_opencl",
+ { "nbnxn_kernel_ElecEw_VdwLJ_F_prune_opencl",
+ "nbnxn_kernel_ElecEw_VdwLJCombGeom_F_prune_opencl",
"nbnxn_kernel_ElecEw_VdwLJCombLB_F_prune_opencl",
- "nbnxn_kernel_ElecEw_VdwLJFsw_F_prune_opencl", "nbnxn_kernel_ElecEw_VdwLJPsw_F_prune_opencl",
+ "nbnxn_kernel_ElecEw_VdwLJFsw_F_prune_opencl",
+ "nbnxn_kernel_ElecEw_VdwLJPsw_F_prune_opencl",
"nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_prune_opencl",
"nbnxn_kernel_ElecEw_VdwLJEwCombLB_F_prune_opencl" },
{ "nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_prune_opencl",
};
/*! \brief Force + energy + pruning kernel function pointers. */
-static const char* nb_kfunc_ener_prune_ptr[eelTypeNR][evdwTypeNR] = {
+static const char* nb_kfunc_ener_prune_ptr[c_numElecTypes][c_numVdwTypes] = {
{ "nbnxn_kernel_ElecCut_VdwLJ_VF_prune_opencl",
"nbnxn_kernel_ElecCut_VdwLJCombGeom_VF_prune_opencl",
"nbnxn_kernel_ElecCut_VdwLJCombLB_VF_prune_opencl",
{ "nbnxn_kernel_ElecRF_VdwLJ_VF_prune_opencl",
"nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_prune_opencl",
"nbnxn_kernel_ElecRF_VdwLJCombLB_VF_prune_opencl",
- "nbnxn_kernel_ElecRF_VdwLJFsw_VF_prune_opencl", "nbnxn_kernel_ElecRF_VdwLJPsw_VF_prune_opencl",
+ "nbnxn_kernel_ElecRF_VdwLJFsw_VF_prune_opencl",
+ "nbnxn_kernel_ElecRF_VdwLJPsw_VF_prune_opencl",
"nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_prune_opencl",
"nbnxn_kernel_ElecRF_VdwLJEwCombLB_VF_prune_opencl" },
{ "nbnxn_kernel_ElecEwQSTab_VdwLJ_VF_prune_opencl",
{ "nbnxn_kernel_ElecEw_VdwLJ_VF_prune_opencl",
"nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_prune_opencl",
"nbnxn_kernel_ElecEw_VdwLJCombLB_VF_prune_opencl",
- "nbnxn_kernel_ElecEw_VdwLJFsw_VF_prune_opencl", "nbnxn_kernel_ElecEw_VdwLJPsw_VF_prune_opencl",
+ "nbnxn_kernel_ElecEw_VdwLJFsw_VF_prune_opencl",
+ "nbnxn_kernel_ElecEw_VdwLJPsw_VF_prune_opencl",
"nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_prune_opencl",
"nbnxn_kernel_ElecEw_VdwLJEwCombLB_VF_prune_opencl" },
{ "nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_prune_opencl",
* OpenCL kernel objects are cached in nb. If the requested kernel is not
* found in the cache, it will be created and the cache will be updated.
*/
-static inline cl_kernel select_nbnxn_kernel(NbnxmGpu* nb, int eeltype, int evdwtype, bool bDoEne, bool bDoPrune)
+static inline cl_kernel
+select_nbnxn_kernel(NbnxmGpu* nb, enum ElecType elecType, enum VdwType vdwType, bool bDoEne, bool bDoPrune)
{
const char* kernel_name_to_run;
cl_kernel* kernel_ptr;
cl_int cl_error;
- GMX_ASSERT(eeltype < eelTypeNR,
+ const int elecTypeIdx = static_cast<int>(elecType);
+ const int vdwTypeIdx = static_cast<int>(vdwType);
+
+ GMX_ASSERT(elecTypeIdx < c_numElecTypes,
"The electrostatics type requested is not implemented in the OpenCL kernels.");
- GMX_ASSERT(evdwtype < evdwTypeNR,
+ GMX_ASSERT(vdwTypeIdx < c_numVdwTypes,
"The VdW type requested is not implemented in the OpenCL kernels.");
if (bDoEne)
{
if (bDoPrune)
{
- kernel_name_to_run = nb_kfunc_ener_prune_ptr[eeltype][evdwtype];
- kernel_ptr = &(nb->kernel_ener_prune_ptr[eeltype][evdwtype]);
+ kernel_name_to_run = nb_kfunc_ener_prune_ptr[elecTypeIdx][vdwTypeIdx];
+ kernel_ptr = &(nb->kernel_ener_prune_ptr[elecTypeIdx][vdwTypeIdx]);
}
else
{
- kernel_name_to_run = nb_kfunc_ener_noprune_ptr[eeltype][evdwtype];
- kernel_ptr = &(nb->kernel_ener_noprune_ptr[eeltype][evdwtype]);
+ kernel_name_to_run = nb_kfunc_ener_noprune_ptr[elecTypeIdx][vdwTypeIdx];
+ kernel_ptr = &(nb->kernel_ener_noprune_ptr[elecTypeIdx][vdwTypeIdx]);
}
}
else
{
if (bDoPrune)
{
- kernel_name_to_run = nb_kfunc_noener_prune_ptr[eeltype][evdwtype];
- kernel_ptr = &(nb->kernel_noener_prune_ptr[eeltype][evdwtype]);
+ kernel_name_to_run = nb_kfunc_noener_prune_ptr[elecTypeIdx][vdwTypeIdx];
+ kernel_ptr = &(nb->kernel_noener_prune_ptr[elecTypeIdx][vdwTypeIdx]);
}
else
{
- kernel_name_to_run = nb_kfunc_noener_noprune_ptr[eeltype][evdwtype];
- kernel_ptr = &(nb->kernel_noener_noprune_ptr[eeltype][evdwtype]);
+ kernel_name_to_run = nb_kfunc_noener_noprune_ptr[elecTypeIdx][vdwTypeIdx];
+ kernel_ptr = &(nb->kernel_noener_noprune_ptr[elecTypeIdx][vdwTypeIdx]);
}
}
if (nullptr == kernel_ptr[0])
{
*kernel_ptr = clCreateKernel(nb->dev_rundata->program, kernel_name_to_run, &cl_error);
- GMX_ASSERT(cl_error == CL_SUCCESS, ("clCreateKernel failed: " + ocl_get_error_string(cl_error)
- + " for kernel named " + kernel_name_to_run)
- .c_str());
+ GMX_ASSERT(cl_error == CL_SUCCESS,
+ ("clCreateKernel failed: " + ocl_get_error_string(cl_error)
+ + " for kernel named " + kernel_name_to_run)
+ .c_str());
}
return *kernel_ptr;
/*! \brief Calculates the amount of shared memory required by the nonbonded kernel in use.
*/
-static inline int calc_shmem_required_nonbonded(int vdwType, bool bPrefetchLjParam)
+static inline int calc_shmem_required_nonbonded(enum VdwType vdwType, bool bPrefetchLjParam)
{
int shmem;
nbparams_params->coulomb_tab_scale = nbp->coulomb_tab_scale;
nbparams_params->c_rf = nbp->c_rf;
nbparams_params->dispersion_shift = nbp->dispersion_shift;
- nbparams_params->eeltype = nbp->eeltype;
+ nbparams_params->elecType = nbp->elecType;
nbparams_params->epsfac = nbp->epsfac;
nbparams_params->ewaldcoeff_lj = nbp->ewaldcoeff_lj;
nbparams_params->ewald_beta = nbp->ewald_beta;
nbparams_params->sh_ewald = nbp->sh_ewald;
nbparams_params->sh_lj_ewald = nbp->sh_lj_ewald;
nbparams_params->two_k_rf = nbp->two_k_rf;
- nbparams_params->vdwtype = nbp->vdwtype;
+ nbparams_params->vdwType = nbp->vdwType;
nbparams_params->vdw_switch = nbp->vdw_switch;
}
-/*! \brief Enqueues a wait for event completion.
- *
- * Then it releases the event and sets it to 0.
- * Don't use this function when more than one wait will be issued for the event.
- * Equivalent to Cuda Stream Sync. */
-static void sync_ocl_event(cl_command_queue stream, cl_event* ocl_event)
-{
- cl_int gmx_unused cl_error;
-
- /* Enqueue wait */
- cl_error = clEnqueueBarrierWithWaitList(stream, 1, ocl_event, nullptr);
- GMX_RELEASE_ASSERT(CL_SUCCESS == cl_error, ocl_get_error_string(cl_error).c_str());
-
- /* Release event and reset it to 0. It is ok to release it as enqueuewaitforevents performs implicit retain for events. */
- cl_error = clReleaseEvent(*ocl_event);
- GMX_ASSERT(cl_error == CL_SUCCESS,
- ("clReleaseEvent failed: " + ocl_get_error_string(cl_error)).c_str());
- *ocl_event = nullptr;
-}
-
-/*! \brief Launch asynchronously the xq buffer host to device copy. */
-void gpu_copy_xq_to_gpu(NbnxmGpu* nb, const nbnxn_atomdata_t* nbatom, const AtomLocality atomLocality)
-{
- GMX_ASSERT(nb, "Need a valid nbnxn_gpu object");
-
- const InteractionLocality iloc = gpuAtomToInteractionLocality(atomLocality);
-
- /* local/nonlocal offset and length used for xq and f */
- int adat_begin, adat_len;
-
- cl_atomdata_t* adat = nb->atdat;
- gpu_plist* plist = nb->plist[iloc];
- cl_timers_t* t = nb->timers;
- const DeviceStream& deviceStream = *nb->deviceStreams[iloc];
-
- bool bDoTime = nb->bDoTime;
-
- /* Don't launch the non-local H2D copy if there is no dependent
- work to do: neither non-local nor other (e.g. bonded) work
- to do that has as input the nbnxn coordinates.
- Doing the same for the local kernel is more complicated, since the
- local part of the force array also depends on the non-local kernel.
- So to avoid complicating the code and to reduce the risk of bugs,
- we always call the local local x+q copy (and the rest of the local
- work in nbnxn_gpu_launch_kernel().
- */
- if ((iloc == InteractionLocality::NonLocal) && !haveGpuShortRangeWork(*nb, iloc))
- {
- plist->haveFreshList = false;
-
- return;
- }
-
- /* calculate the atom data index range based on locality */
- if (atomLocality == AtomLocality::Local)
- {
- adat_begin = 0;
- adat_len = adat->natoms_local;
- }
- else
- {
- adat_begin = adat->natoms_local;
- adat_len = adat->natoms - adat->natoms_local;
- }
-
- /* beginning of timed HtoD section */
- if (bDoTime)
- {
- t->xf[atomLocality].nb_h2d.openTimingRegion(deviceStream);
- }
-
- /* HtoD x, q */
- GMX_ASSERT(sizeof(float) == sizeof(*nbatom->x().data()),
- "The size of the xyzq buffer element should be equal to the size of float4.");
- copyToDeviceBuffer(&adat->xq, nbatom->x().data() + adat_begin * 4, adat_begin * 4, adat_len * 4,
- deviceStream, GpuApiCallBehavior::Async,
- bDoTime ? t->xf[atomLocality].nb_h2d.fetchNextEvent() : nullptr);
-
- if (bDoTime)
- {
- t->xf[atomLocality].nb_h2d.closeTimingRegion(deviceStream);
- }
-
- /* When we get here all misc operations issues in the local stream as well as
- the local xq H2D are done,
- so we record that in the local stream and wait for it in the nonlocal one. */
- if (nb->bUseTwoStreams)
- {
- if (iloc == InteractionLocality::Local)
- {
- cl_int gmx_used_in_debug cl_error = clEnqueueMarkerWithWaitList(
- deviceStream.stream(), 0, nullptr, &(nb->misc_ops_and_local_H2D_done));
- GMX_ASSERT(cl_error == CL_SUCCESS,
- ("clEnqueueMarkerWithWaitList failed: " + ocl_get_error_string(cl_error)).c_str());
-
- /* Based on the v1.2 section 5.13 of the OpenCL spec, a flush is needed
- * in the local stream in order to be able to sync with the above event
- * from the non-local stream.
- */
- cl_error = clFlush(deviceStream.stream());
- GMX_ASSERT(cl_error == CL_SUCCESS,
- ("clFlush failed: " + ocl_get_error_string(cl_error)).c_str());
- }
- else
- {
- sync_ocl_event(deviceStream.stream(), &(nb->misc_ops_and_local_H2D_done));
- }
- }
-}
-
-
/*! \brief Launch GPU kernel
As we execute nonbonded workload in separate queues, before launching
*/
void gpu_launch_kernel(NbnxmGpu* nb, const gmx::StepWorkload& stepWork, const Nbnxm::InteractionLocality iloc)
{
- cl_atomdata_t* adat = nb->atdat;
+ NBAtomDataGpu* adat = nb->atdat;
NBParamGpu* nbp = nb->nbparam;
gpu_plist* plist = nb->plist[iloc];
- cl_timers_t* t = nb->timers;
+ Nbnxm::GpuTimers* timers = nb->timers;
const DeviceStream& deviceStream = *nb->deviceStreams[iloc];
bool bDoTime = nb->bDoTime;
/* beginning of timed nonbonded calculation section */
if (bDoTime)
{
- t->interaction[iloc].nb_k.openTimingRegion(deviceStream);
+ timers->interaction[iloc].nb_k.openTimingRegion(deviceStream);
}
/* kernel launch config */
KernelLaunchConfig config;
- config.sharedMemorySize = calc_shmem_required_nonbonded(nbp->vdwtype, nb->bPrefetchLjParam);
+ config.sharedMemorySize = calc_shmem_required_nonbonded(nbp->vdwType, nb->bPrefetchLjParam);
config.blockSize[0] = c_clSize;
config.blockSize[1] = c_clSize;
config.gridSize[0] = plist->nsci;
fprintf(debug,
"Non-bonded GPU launch configuration:\n\tLocal work size: %zux%zux%zu\n\t"
"Global work size : %zux%zu\n\t#Super-clusters/clusters: %d/%d (%d)\n",
- config.blockSize[0], config.blockSize[1], config.blockSize[2],
- config.blockSize[0] * config.gridSize[0], config.blockSize[1] * config.gridSize[1],
+ config.blockSize[0],
+ config.blockSize[1],
+ config.blockSize[2],
+ config.blockSize[0] * config.gridSize[0],
+ config.blockSize[1] * config.gridSize[1],
plist->nsci * c_nbnxnGpuNumClusterPerSupercluster,
- c_nbnxnGpuNumClusterPerSupercluster, plist->na_c);
+ c_nbnxnGpuNumClusterPerSupercluster,
+ plist->na_c);
}
fillin_ocl_structures(nbp, &nbparams_params);
- auto* timingEvent = bDoTime ? t->interaction[iloc].nb_k.fetchNextEvent() : nullptr;
+ auto* timingEvent = bDoTime ? timers->interaction[iloc].nb_k.fetchNextEvent() : nullptr;
constexpr char kernelName[] = "k_calc_nb";
const auto kernel =
- select_nbnxn_kernel(nb, nbp->eeltype, nbp->vdwtype, stepWork.computeEnergy,
+ select_nbnxn_kernel(nb,
+ nbp->elecType,
+ nbp->vdwType,
+ stepWork.computeEnergy,
(plist->haveFreshList && !nb->timers->interaction[iloc].didPrune));
// The OpenCL kernel takes int as second to last argument because bool is
// not supported as a kernel argument type (sizeof(bool) is implementation defined).
const int computeFshift = static_cast<int>(stepWork.computeVirial);
- if (useLjCombRule(nb->nbparam->vdwtype))
- {
- const auto kernelArgs = prepareGpuKernelArguments(
- kernel, config, &nbparams_params, &adat->xq, &adat->f, &adat->e_lj, &adat->e_el,
- &adat->fshift, &adat->lj_comb, &adat->shift_vec, &nbp->nbfp, &nbp->nbfp_comb,
- &nbp->coulomb_tab, &plist->sci, &plist->cj4, &plist->excl, &computeFshift);
+ if (useLjCombRule(nb->nbparam->vdwType))
+ {
+ const auto kernelArgs = prepareGpuKernelArguments(kernel,
+ config,
+ &nbparams_params,
+ &adat->xq,
+ &adat->f,
+ &adat->eLJ,
+ &adat->eElec,
+ &adat->fShift,
+ &adat->ljComb,
+ &adat->shiftVec,
+ &nbp->nbfp,
+ &nbp->nbfp_comb,
+ &nbp->coulomb_tab,
+ &plist->sci,
+ &plist->cj4,
+ &plist->excl,
+ &computeFshift);
launchGpuKernel(kernel, config, deviceStream, timingEvent, kernelName, kernelArgs);
}
else
{
- const auto kernelArgs = prepareGpuKernelArguments(
- kernel, config, &adat->ntypes, &nbparams_params, &adat->xq, &adat->f, &adat->e_lj,
- &adat->e_el, &adat->fshift, &adat->atom_types, &adat->shift_vec, &nbp->nbfp, &nbp->nbfp_comb,
- &nbp->coulomb_tab, &plist->sci, &plist->cj4, &plist->excl, &computeFshift);
+ const auto kernelArgs = prepareGpuKernelArguments(kernel,
+ config,
+ &adat->numTypes,
+ &nbparams_params,
+ &adat->xq,
+ &adat->f,
+ &adat->eLJ,
+ &adat->eElec,
+ &adat->fShift,
+ &adat->atomTypes,
+ &adat->shiftVec,
+ &nbp->nbfp,
+ &nbp->nbfp_comb,
+ &nbp->coulomb_tab,
+ &plist->sci,
+ &plist->cj4,
+ &plist->excl,
+ &computeFshift);
launchGpuKernel(kernel, config, deviceStream, timingEvent, kernelName, kernelArgs);
}
if (bDoTime)
{
- t->interaction[iloc].nb_k.closeTimingRegion(deviceStream);
+ timers->interaction[iloc].nb_k.closeTimingRegion(deviceStream);
}
}
*/
void gpu_launch_kernel_pruneonly(NbnxmGpu* nb, const InteractionLocality iloc, const int numParts)
{
- cl_atomdata_t* adat = nb->atdat;
+ NBAtomDataGpu* adat = nb->atdat;
NBParamGpu* nbp = nb->nbparam;
gpu_plist* plist = nb->plist[iloc];
- cl_timers_t* t = nb->timers;
+ Nbnxm::GpuTimers* timers = nb->timers;
const DeviceStream& deviceStream = *nb->deviceStreams[iloc];
bool bDoTime = nb->bDoTime;
GpuRegionTimer* timer = nullptr;
if (bDoTime)
{
- timer = &(plist->haveFreshList ? t->interaction[iloc].prune_k : t->interaction[iloc].rollingPrune_k);
+ timer = &(plist->haveFreshList ? timers->interaction[iloc].prune_k
+ : timers->interaction[iloc].rollingPrune_k);
}
/* beginning of timed prune calculation section */
* and j-cluster concurrency, in x, y, and z, respectively.
* - The 1D block-grid contains as many blocks as super-clusters.
*/
- int num_threads_z = c_oclPruneKernelJ4ConcurrencyDEFAULT;
-
-
+ int num_threads_z = c_pruneKernelJ4Concurrency;
/* kernel launch config */
KernelLaunchConfig config;
config.sharedMemorySize = calc_shmem_required_prune(num_threads_z);
"Pruning GPU kernel launch configuration:\n\tLocal work size: %zux%zux%zu\n\t"
"\tGlobal work size: %zux%zu\n\t#Super-clusters/clusters: %d/%d (%d)\n"
"\tShMem: %zu\n",
- config.blockSize[0], config.blockSize[1], config.blockSize[2],
- config.blockSize[0] * config.gridSize[0], config.blockSize[1] * config.gridSize[1],
+ config.blockSize[0],
+ config.blockSize[1],
+ config.blockSize[2],
+ config.blockSize[0] * config.gridSize[0],
+ config.blockSize[1] * config.gridSize[1],
plist->nsci * c_nbnxnGpuNumClusterPerSupercluster,
- c_nbnxnGpuNumClusterPerSupercluster, plist->na_c, config.sharedMemorySize);
+ c_nbnxnGpuNumClusterPerSupercluster,
+ plist->na_c,
+ config.sharedMemorySize);
}
cl_nbparam_params_t nbparams_params;
auto* timingEvent = bDoTime ? timer->fetchNextEvent() : nullptr;
constexpr char kernelName[] = "k_pruneonly";
const auto pruneKernel = selectPruneKernel(nb->kernel_pruneonly, plist->haveFreshList);
- const auto kernelArgs = prepareGpuKernelArguments(pruneKernel, config, &nbparams_params,
- &adat->xq, &adat->shift_vec, &plist->sci,
- &plist->cj4, &plist->imask, &numParts, &part);
+ const auto kernelArgs = prepareGpuKernelArguments(pruneKernel,
+ config,
+ &nbparams_params,
+ &adat->xq,
+ &adat->shiftVec,
+ &plist->sci,
+ &plist->cj4,
+ &plist->imask,
+ &numParts,
+ &part);
launchGpuKernel(pruneKernel, config, deviceStream, timingEvent, kernelName, kernelArgs);
if (plist->haveFreshList)
}
}
-/*! \brief
- * Launch asynchronously the download of nonbonded forces from the GPU
- * (and energies/shift forces if required).
- */
-void gpu_launch_cpyback(NbnxmGpu* nb,
- struct nbnxn_atomdata_t* nbatom,
- const gmx::StepWorkload& stepWork,
- const AtomLocality aloc)
-{
- GMX_ASSERT(nb, "Need a valid nbnxn_gpu object");
-
- cl_int gmx_unused cl_error;
- int adat_begin, adat_len; /* local/nonlocal offset and length used for xq and f */
-
- /* determine interaction locality from atom locality */
- const InteractionLocality iloc = gpuAtomToInteractionLocality(aloc);
-
- cl_atomdata_t* adat = nb->atdat;
- cl_timers_t* t = nb->timers;
- bool bDoTime = nb->bDoTime;
- const DeviceStream& deviceStream = *nb->deviceStreams[iloc];
-
- /* don't launch non-local copy-back if there was no non-local work to do */
- if ((iloc == InteractionLocality::NonLocal) && !haveGpuShortRangeWork(*nb, iloc))
- {
- /* TODO An alternative way to signal that non-local work is
- complete is to use a clEnqueueMarker+clEnqueueBarrier
- pair. However, the use of bNonLocalStreamActive has the
- advantage of being local to the host, so probably minimizes
- overhead. Curiously, for NVIDIA OpenCL with an empty-domain
- test case, overall simulation performance was higher with
- the API calls, but this has not been tested on AMD OpenCL,
- so could be worth considering in future. */
- nb->bNonLocalStreamActive = CL_FALSE;
- return;
- }
-
- getGpuAtomRange(adat, aloc, &adat_begin, &adat_len);
-
- /* beginning of timed D2H section */
- if (bDoTime)
- {
- t->xf[aloc].nb_d2h.openTimingRegion(deviceStream);
- }
-
- /* With DD the local D2H transfer can only start after the non-local
- has been launched. */
- if (iloc == InteractionLocality::Local && nb->bNonLocalStreamActive)
- {
- sync_ocl_event(deviceStream.stream(), &(nb->nonlocal_done));
- }
-
- /* DtoH f */
- GMX_ASSERT(sizeof(*nbatom->out[0].f.data()) == sizeof(float),
- "The host force buffer should be in single precision to match device data size.");
- copyFromDeviceBuffer(&nbatom->out[0].f[adat_begin * DIM], &adat->f, adat_begin * DIM,
- adat_len * DIM, deviceStream, GpuApiCallBehavior::Async,
- bDoTime ? t->xf[aloc].nb_d2h.fetchNextEvent() : nullptr);
-
- /* kick off work */
- cl_error = clFlush(deviceStream.stream());
- GMX_ASSERT(cl_error == CL_SUCCESS, ("clFlush failed: " + ocl_get_error_string(cl_error)).c_str());
-
- /* After the non-local D2H is launched the nonlocal_done event can be
- recorded which signals that the local D2H can proceed. This event is not
- placed after the non-local kernel because we first need the non-local
- data back first. */
- if (iloc == InteractionLocality::NonLocal)
- {
- cl_error = clEnqueueMarkerWithWaitList(deviceStream.stream(), 0, nullptr, &(nb->nonlocal_done));
- GMX_ASSERT(cl_error == CL_SUCCESS,
- ("clEnqueueMarkerWithWaitList failed: " + ocl_get_error_string(cl_error)).c_str());
- nb->bNonLocalStreamActive = CL_TRUE;
- }
-
- /* only transfer energies in the local stream */
- if (iloc == InteractionLocality::Local)
- {
- /* DtoH fshift when virial is needed */
- if (stepWork.computeVirial)
- {
- GMX_ASSERT(sizeof(*nb->nbst.fshift) == DIM * sizeof(float),
- "Sizes of host- and device-side shift vector elements should be the same.");
- copyFromDeviceBuffer(reinterpret_cast<float*>(nb->nbst.fshift), &adat->fshift, 0,
- SHIFTS * DIM, deviceStream, GpuApiCallBehavior::Async,
- bDoTime ? t->xf[aloc].nb_d2h.fetchNextEvent() : nullptr);
- }
-
- /* DtoH energies */
- if (stepWork.computeEnergy)
- {
- GMX_ASSERT(sizeof(*nb->nbst.e_lj) == sizeof(float),
- "Sizes of host- and device-side LJ energy terms should be the same.");
- copyFromDeviceBuffer(nb->nbst.e_lj, &adat->e_lj, 0, 1, deviceStream, GpuApiCallBehavior::Async,
- bDoTime ? t->xf[aloc].nb_d2h.fetchNextEvent() : nullptr);
- GMX_ASSERT(sizeof(*nb->nbst.e_el) == sizeof(float),
- "Sizes of host- and device-side electrostatic energy terms should be the "
- "same.");
- copyFromDeviceBuffer(nb->nbst.e_el, &adat->e_el, 0, 1, deviceStream, GpuApiCallBehavior::Async,
- bDoTime ? t->xf[aloc].nb_d2h.fetchNextEvent() : nullptr);
- }
- }
-
- if (bDoTime)
- {
- t->xf[aloc].nb_d2h.closeTimingRegion(deviceStream);
- }
-}
-
} // namespace Nbnxm
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Berk Hess <hess@kth.se>
* \ingroup module_nbnxm
*/
-#ifndef NBNXN_OPENCL_CONSTS_H
-#define NBNXN_OPENCL_CONSTS_H
+#ifndef NBNXN_OCL_CONSTS_H
+#define NBNXN_OCL_CONSTS_H
-/*! \internal \file
- * \brief Macros defining platform-dependent defaults for the prune kernel's j4 processing concurrency.
- *
- * The GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY macro allows compile-time override.
+/*! \brief Macro definining default for the prune kernel's j4 processing concurrency.
*
- * \ingroup module_nbnxm
+ * The GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY macro allows compile-time override with the default value of 4.
*/
-/*! @{ */
-#define GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY_DEFAULT 4
-// The following has to match getOclPruneKernelJ4Concurrency
-#define GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY_DEFAULT
-/*! @} */
+#ifndef GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY
+# define GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY 4
+#endif
+
#endif
#include <cmath>
-#include "gromacs/gpu_utils/device_stream_manager.h"
-#include "gromacs/gpu_utils/oclutils.h"
+#include "gromacs/gpu_utils/pmalloc.h"
#include "gromacs/hardware/device_information.h"
#include "gromacs/hardware/device_management.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/nbnxm/nbnxm_gpu.h"
#include "gromacs/nbnxm/nbnxm_gpu_data_mgmt.h"
#include "gromacs/nbnxm/pairlistsets.h"
-#include "gromacs/pbcutil/ishift.h"
#include "gromacs/timing/gpu_timing.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
*/
static unsigned int gpu_min_ci_balanced_factor = 50;
-
-/*! \brief Initializes the atomdata structure first time, it only gets filled at
- pair-search.
- */
-static void init_atomdata_first(cl_atomdata_t* ad, int ntypes, const DeviceContext& deviceContext)
-{
- ad->ntypes = ntypes;
-
- allocateDeviceBuffer(&ad->shift_vec, SHIFTS * DIM, deviceContext);
- ad->bShiftVecUploaded = CL_FALSE;
-
- allocateDeviceBuffer(&ad->fshift, SHIFTS * DIM, deviceContext);
- allocateDeviceBuffer(&ad->e_lj, 1, deviceContext);
- allocateDeviceBuffer(&ad->e_el, 1, deviceContext);
-
- /* initialize to nullptr pointers to data that is not allocated here and will
- need reallocation in nbnxn_gpu_init_atomdata */
- ad->xq = nullptr;
- ad->f = nullptr;
-
- /* size -1 indicates that the respective array hasn't been initialized yet */
- ad->natoms = -1;
- ad->nalloc = -1;
-}
-
-/*! \brief Returns the kinds of electrostatics and Vdw OpenCL
- * kernels that will be used.
- *
- * Respectively, these values are from enum eelOcl and enum
- * evdwOcl. */
-static void map_interaction_types_to_gpu_kernel_flavors(const interaction_const_t* ic,
- int combRule,
- int* gpu_eeltype,
- int* gpu_vdwtype,
- const DeviceContext& deviceContext)
-{
- if (ic->vdwtype == evdwCUT)
- {
- switch (ic->vdw_modifier)
- {
- case eintmodNONE:
- case eintmodPOTSHIFT:
- switch (combRule)
- {
- case ljcrNONE: *gpu_vdwtype = evdwTypeCUT; break;
- case ljcrGEOM: *gpu_vdwtype = evdwTypeCUTCOMBGEOM; break;
- case ljcrLB: *gpu_vdwtype = evdwTypeCUTCOMBLB; break;
- default:
- gmx_incons(
- "The requested LJ combination rule is not implemented in the "
- "OpenCL GPU accelerated kernels!");
- }
- break;
- case eintmodFORCESWITCH: *gpu_vdwtype = evdwTypeFSWITCH; break;
- case eintmodPOTSWITCH: *gpu_vdwtype = evdwTypePSWITCH; break;
- default:
- gmx_incons(
- "The requested VdW interaction modifier is not implemented in the GPU "
- "accelerated kernels!");
- }
- }
- else if (ic->vdwtype == evdwPME)
- {
- if (ic->ljpme_comb_rule == ljcrGEOM)
- {
- *gpu_vdwtype = evdwTypeEWALDGEOM;
- }
- else
- {
- *gpu_vdwtype = evdwTypeEWALDLB;
- }
- }
- else
- {
- gmx_incons("The requested VdW type is not implemented in the GPU accelerated kernels!");
- }
-
- if (ic->eeltype == eelCUT)
- {
- *gpu_eeltype = eelTypeCUT;
- }
- else if (EEL_RF(ic->eeltype))
- {
- *gpu_eeltype = eelTypeRF;
- }
- else if ((EEL_PME(ic->eeltype) || ic->eeltype == eelEWALD))
- {
- *gpu_eeltype = nbnxn_gpu_pick_ewald_kernel_type(*ic, deviceContext.deviceInfo());
- }
- else
- {
- /* Shouldn't happen, as this is checked when choosing Verlet-scheme */
- gmx_incons(
- "The requested electrostatics type is not implemented in the GPU accelerated "
- "kernels!");
- }
-}
-
-/*! \brief Initializes the nonbonded parameter data structure.
- */
-static void init_nbparam(NBParamGpu* nbp,
- const interaction_const_t* ic,
- const PairlistParams& listParams,
- const nbnxn_atomdata_t::Params& nbatParams,
- const DeviceContext& deviceContext)
-{
- set_cutoff_parameters(nbp, ic, listParams);
-
- map_interaction_types_to_gpu_kernel_flavors(ic, nbatParams.comb_rule, &(nbp->eeltype),
- &(nbp->vdwtype), deviceContext);
-
- if (ic->vdwtype == evdwPME)
- {
- if (ic->ljpme_comb_rule == ljcrGEOM)
- {
- GMX_ASSERT(nbatParams.comb_rule == ljcrGEOM, "Combination rule mismatch!");
- }
- else
- {
- GMX_ASSERT(nbatParams.comb_rule == ljcrLB, "Combination rule mismatch!");
- }
- }
- /* generate table for PME */
- nbp->coulomb_tab = nullptr;
- if (nbp->eeltype == eelTypeEWALD_TAB || nbp->eeltype == eelTypeEWALD_TAB_TWIN)
- {
- GMX_RELEASE_ASSERT(ic->coulombEwaldTables, "Need valid Coulomb Ewald correction tables");
- init_ewald_coulomb_force_table(*ic->coulombEwaldTables, nbp, deviceContext);
- }
- else
- {
- allocateDeviceBuffer(&nbp->coulomb_tab, 1, deviceContext);
- }
-
- const int nnbfp = 2 * nbatParams.numTypes * nbatParams.numTypes;
- const int nnbfp_comb = 2 * nbatParams.numTypes;
-
- {
- /* set up LJ parameter lookup table */
- DeviceBuffer<real> nbfp;
- initParamLookupTable(&nbfp, nullptr, nbatParams.nbfp.data(), nnbfp, deviceContext);
- nbp->nbfp = nbfp;
-
- if (ic->vdwtype == evdwPME)
- {
- DeviceBuffer<float> nbfp_comb;
- initParamLookupTable(&nbfp_comb, nullptr, nbatParams.nbfp_comb.data(), nnbfp_comb, deviceContext);
- nbp->nbfp_comb = nbfp_comb;
- }
- }
-}
-
/*! \brief Initializes the OpenCL kernel pointers of the nbnxn_ocl_ptr_t input data structure. */
static cl_kernel nbnxn_gpu_create_kernel(NbnxmGpu* nb, const char* kernel_name)
{
kernel = clCreateKernel(nb->dev_rundata->program, kernel_name, &cl_error);
if (CL_SUCCESS != cl_error)
{
- gmx_fatal(FARGS, "Failed to create kernel '%s' for GPU #%s: OpenCL error %d", kernel_name,
- nb->deviceContext_->deviceInfo().device_name, cl_error);
+ gmx_fatal(FARGS,
+ "Failed to create kernel '%s' for GPU #%s: OpenCL error %d",
+ kernel_name,
+ nb->deviceContext_->deviceInfo().device_name,
+ cl_error);
}
return kernel;
}
-/*! \brief Clears nonbonded shift force output array and energy outputs on the GPU.
- */
-static void nbnxn_ocl_clear_e_fshift(NbnxmGpu* nb)
-{
-
- cl_int cl_error;
- cl_atomdata_t* adat = nb->atdat;
- cl_command_queue ls = nb->deviceStreams[InteractionLocality::Local]->stream();
-
- size_t local_work_size[3] = { 1, 1, 1 };
- size_t global_work_size[3] = { 1, 1, 1 };
-
- cl_int shifts = SHIFTS * 3;
-
- cl_int arg_no;
-
- cl_kernel zero_e_fshift = nb->kernel_zero_e_fshift;
-
- local_work_size[0] = 64;
- // Round the total number of threads up from the array size
- global_work_size[0] = ((shifts + local_work_size[0] - 1) / local_work_size[0]) * local_work_size[0];
-
- arg_no = 0;
- cl_error = clSetKernelArg(zero_e_fshift, arg_no++, sizeof(cl_mem), &(adat->fshift));
- cl_error |= clSetKernelArg(zero_e_fshift, arg_no++, sizeof(cl_mem), &(adat->e_lj));
- cl_error |= clSetKernelArg(zero_e_fshift, arg_no++, sizeof(cl_mem), &(adat->e_el));
- cl_error |= clSetKernelArg(zero_e_fshift, arg_no++, sizeof(cl_uint), &shifts);
- GMX_ASSERT(cl_error == CL_SUCCESS, ocl_get_error_string(cl_error).c_str());
-
- cl_error = clEnqueueNDRangeKernel(ls, zero_e_fshift, 3, nullptr, global_work_size,
- local_work_size, 0, nullptr, nullptr);
- GMX_ASSERT(cl_error == CL_SUCCESS, ocl_get_error_string(cl_error).c_str());
-}
-
/*! \brief Initializes the OpenCL kernel pointers of the nbnxn_ocl_ptr_t input data structure. */
static void nbnxn_gpu_init_kernels(NbnxmGpu* nb)
{
nb->kernel_pruneonly[epruneFirst] = nbnxn_gpu_create_kernel(nb, "nbnxn_kernel_prune_opencl");
nb->kernel_pruneonly[epruneRolling] =
nbnxn_gpu_create_kernel(nb, "nbnxn_kernel_prune_rolling_opencl");
-
- /* Init auxiliary kernels */
- nb->kernel_zero_e_fshift = nbnxn_gpu_create_kernel(nb, "zero_e_fshift");
-}
-
-/*! \brief Initializes simulation constant data.
- *
- * Initializes members of the atomdata and nbparam structs and
- * clears e/fshift output buffers.
- */
-static void nbnxn_ocl_init_const(cl_atomdata_t* atomData,
- NBParamGpu* nbParams,
- const interaction_const_t* ic,
- const PairlistParams& listParams,
- const nbnxn_atomdata_t::Params& nbatParams,
- const DeviceContext& deviceContext)
-{
- init_atomdata_first(atomData, nbatParams.numTypes, deviceContext);
- init_nbparam(nbParams, ic, listParams, nbatParams, deviceContext);
}
-
-//! This function is documented in the header file
-NbnxmGpu* gpu_init(const gmx::DeviceStreamManager& deviceStreamManager,
- const interaction_const_t* ic,
- const PairlistParams& listParams,
- const nbnxn_atomdata_t* nbat,
- const bool bLocalAndNonlocal)
+void gpu_init_platform_specific(NbnxmGpu* nb)
{
- GMX_ASSERT(ic, "Need a valid interaction constants object");
-
- auto nb = new NbnxmGpu();
- nb->deviceContext_ = &deviceStreamManager.context();
- snew(nb->atdat, 1);
- snew(nb->nbparam, 1);
- snew(nb->plist[InteractionLocality::Local], 1);
- if (bLocalAndNonlocal)
- {
- snew(nb->plist[InteractionLocality::NonLocal], 1);
- }
-
- nb->bUseTwoStreams = bLocalAndNonlocal;
-
- nb->timers = new cl_timers_t();
- snew(nb->timings, 1);
-
/* set device info, just point it to the right GPU among the detected ones */
nb->dev_rundata = new gmx_device_runtime_data_t();
- /* init nbst */
- pmalloc(reinterpret_cast<void**>(&nb->nbst.e_lj), sizeof(*nb->nbst.e_lj));
- pmalloc(reinterpret_cast<void**>(&nb->nbst.e_el), sizeof(*nb->nbst.e_el));
- pmalloc(reinterpret_cast<void**>(&nb->nbst.fshift), SHIFTS * sizeof(*nb->nbst.fshift));
-
- init_plist(nb->plist[InteractionLocality::Local]);
-
- /* OpenCL timing disabled if GMX_DISABLE_GPU_TIMING is defined. */
- nb->bDoTime = (getenv("GMX_DISABLE_GPU_TIMING") == nullptr);
-
- /* local/non-local GPU streams */
- GMX_RELEASE_ASSERT(deviceStreamManager.streamIsValid(gmx::DeviceStreamType::NonBondedLocal),
- "Local non-bonded stream should be initialized to use GPU for non-bonded.");
- nb->deviceStreams[InteractionLocality::Local] =
- &deviceStreamManager.stream(gmx::DeviceStreamType::NonBondedLocal);
-
- if (nb->bUseTwoStreams)
- {
- init_plist(nb->plist[InteractionLocality::NonLocal]);
-
- GMX_RELEASE_ASSERT(deviceStreamManager.streamIsValid(gmx::DeviceStreamType::NonBondedNonLocal),
- "Non-local non-bonded stream should be initialized to use GPU for "
- "non-bonded with domain decomposition.");
- nb->deviceStreams[InteractionLocality::NonLocal] =
- &deviceStreamManager.stream(gmx::DeviceStreamType::NonBondedNonLocal);
- }
-
- if (nb->bDoTime)
- {
- init_timings(nb->timings);
- }
-
- nbnxn_ocl_init_const(nb->atdat, nb->nbparam, ic, listParams, nbat->params(), *nb->deviceContext_);
-
/* Enable LJ param manual prefetch for AMD or Intel or if we request through env. var.
* TODO: decide about NVIDIA
*/
*/
nbnxn_gpu_compile_kernels(nb);
nbnxn_gpu_init_kernels(nb);
-
- /* clear energy and shift force outputs */
- nbnxn_ocl_clear_e_fshift(nb);
-
- if (debug)
- {
- fprintf(debug, "Initialized OpenCL data structures.\n");
- }
-
- return nb;
-}
-
-/*! \brief Clears the first natoms_clear elements of the GPU nonbonded force output array.
- */
-static void nbnxn_ocl_clear_f(NbnxmGpu* nb, int natoms_clear)
-{
- if (natoms_clear == 0)
- {
- return;
- }
-
- cl_atomdata_t* atomData = nb->atdat;
- const DeviceStream& localStream = *nb->deviceStreams[InteractionLocality::Local];
-
- clearDeviceBufferAsync(&atomData->f, 0, natoms_clear * DIM, localStream);
-}
-
-//! This function is documented in the header file
-void gpu_clear_outputs(NbnxmGpu* nb, bool computeVirial)
-{
- nbnxn_ocl_clear_f(nb, nb->atdat->natoms);
- /* clear shift force array and energies if the outputs were
- used in the current step */
- if (computeVirial)
- {
- nbnxn_ocl_clear_e_fshift(nb);
- }
-
- /* kick off buffer clearing kernel to ensure concurrency with constraints/update */
- cl_int gmx_unused cl_error;
- cl_error = clFlush(nb->deviceStreams[InteractionLocality::Local]->stream());
- GMX_ASSERT(cl_error == CL_SUCCESS, ("clFlush failed: " + ocl_get_error_string(cl_error)).c_str());
-}
-
-//! This function is documented in the header file
-void gpu_upload_shiftvec(NbnxmGpu* nb, const nbnxn_atomdata_t* nbatom)
-{
- cl_atomdata_t* adat = nb->atdat;
- const DeviceStream& deviceStream = *nb->deviceStreams[InteractionLocality::Local];
-
- /* only if we have a dynamic box */
- if (nbatom->bDynamicBox || !adat->bShiftVecUploaded)
- {
- GMX_ASSERT(sizeof(float) * DIM == sizeof(*nbatom->shift_vec.data()),
- "Sizes of host- and device-side shift vectors should be the same.");
- copyToDeviceBuffer(&adat->shift_vec, reinterpret_cast<const float*>(nbatom->shift_vec.data()),
- 0, SHIFTS * DIM, deviceStream, GpuApiCallBehavior::Async, nullptr);
- adat->bShiftVecUploaded = CL_TRUE;
- }
-}
-
-//! This function is documented in the header file
-void gpu_init_atomdata(NbnxmGpu* nb, const nbnxn_atomdata_t* nbat)
-{
- cl_int cl_error;
- int nalloc, natoms;
- bool realloced;
- bool bDoTime = nb->bDoTime;
- cl_timers_t* timers = nb->timers;
- cl_atomdata_t* d_atdat = nb->atdat;
- const DeviceContext& deviceContext = *nb->deviceContext_;
- const DeviceStream& deviceStream = *nb->deviceStreams[InteractionLocality::Local];
-
- natoms = nbat->numAtoms();
- realloced = false;
-
- if (bDoTime)
- {
- /* time async copy */
- timers->atdat.openTimingRegion(deviceStream);
- }
-
- /* need to reallocate if we have to copy more atoms than the amount of space
- available and only allocate if we haven't initialized yet, i.e d_atdat->natoms == -1 */
- if (natoms > d_atdat->nalloc)
- {
- nalloc = over_alloc_small(natoms);
-
- /* free up first if the arrays have already been initialized */
- if (d_atdat->nalloc != -1)
- {
- freeDeviceBuffer(&d_atdat->f);
- freeDeviceBuffer(&d_atdat->xq);
- freeDeviceBuffer(&d_atdat->lj_comb);
- freeDeviceBuffer(&d_atdat->atom_types);
- }
-
-
- allocateDeviceBuffer(&d_atdat->f, nalloc * DIM, deviceContext);
- allocateDeviceBuffer(&d_atdat->xq, nalloc * (DIM + 1), deviceContext);
-
- if (useLjCombRule(nb->nbparam->vdwtype))
- {
- // Two Lennard-Jones parameters per atom
- allocateDeviceBuffer(&d_atdat->lj_comb, nalloc * 2, deviceContext);
- }
- else
- {
- allocateDeviceBuffer(&d_atdat->atom_types, nalloc, deviceContext);
- }
-
- d_atdat->nalloc = nalloc;
- realloced = true;
- }
-
- d_atdat->natoms = natoms;
- d_atdat->natoms_local = nbat->natoms_local;
-
- /* need to clear GPU f output if realloc happened */
- if (realloced)
- {
- nbnxn_ocl_clear_f(nb, nalloc);
- }
-
- if (useLjCombRule(nb->nbparam->vdwtype))
- {
- GMX_ASSERT(sizeof(float) == sizeof(*nbat->params().lj_comb.data()),
- "Size of the LJ parameters element should be equal to the size of float2.");
- copyToDeviceBuffer(&d_atdat->lj_comb, nbat->params().lj_comb.data(), 0, 2 * natoms,
- deviceStream, GpuApiCallBehavior::Async,
- bDoTime ? timers->atdat.fetchNextEvent() : nullptr);
- }
- else
- {
- GMX_ASSERT(sizeof(int) == sizeof(*nbat->params().type.data()),
- "Sizes of host- and device-side atom types should be the same.");
- copyToDeviceBuffer(&d_atdat->atom_types, nbat->params().type.data(), 0, natoms, deviceStream,
- GpuApiCallBehavior::Async, bDoTime ? timers->atdat.fetchNextEvent() : nullptr);
- }
-
- if (bDoTime)
- {
- timers->atdat.closeTimingRegion(deviceStream);
- }
-
- /* kick off the tasks enqueued above to ensure concurrency with the search */
- cl_error = clFlush(deviceStream.stream());
- GMX_RELEASE_ASSERT(cl_error == CL_SUCCESS,
- ("clFlush failed: " + ocl_get_error_string(cl_error)).c_str());
}
/*! \brief Releases an OpenCL kernel pointer */
static void free_kernel(cl_kernel* kernel_ptr)
{
- cl_int gmx_unused cl_error;
-
GMX_ASSERT(kernel_ptr, "Need a valid kernel pointer");
if (*kernel_ptr)
{
- cl_error = clReleaseKernel(*kernel_ptr);
+ cl_int cl_error = clReleaseKernel(*kernel_ptr);
GMX_RELEASE_ASSERT(cl_error == CL_SUCCESS,
("clReleaseKernel failed: " + ocl_get_error_string(cl_error)).c_str());
/*! \brief Releases a list of OpenCL kernel pointers */
static void free_kernels(cl_kernel* kernels, int count)
{
- int i;
-
- for (i = 0; i < count; i++)
+ for (int i = 0; i < count; i++)
{
free_kernel(kernels + i);
}
}
//! This function is documented in the header file
-void gpu_free(NbnxmGpu* nb)
+void gpu_free_platform_specific(NbnxmGpu* nb)
{
- if (nb == nullptr)
- {
- return;
- }
-
/* Free kernels */
// NOLINTNEXTLINE(bugprone-sizeof-expression)
int kernel_count = sizeof(nb->kernel_ener_noprune_ptr) / sizeof(nb->kernel_ener_noprune_ptr[0][0]);
kernel_count = sizeof(nb->kernel_noener_prune_ptr) / sizeof(nb->kernel_noener_prune_ptr[0][0]);
free_kernels(nb->kernel_noener_prune_ptr[0], kernel_count);
- free_kernel(&(nb->kernel_zero_e_fshift));
-
- /* Free atdat */
- freeDeviceBuffer(&(nb->atdat->xq));
- freeDeviceBuffer(&(nb->atdat->f));
- freeDeviceBuffer(&(nb->atdat->e_lj));
- freeDeviceBuffer(&(nb->atdat->e_el));
- freeDeviceBuffer(&(nb->atdat->fshift));
- freeDeviceBuffer(&(nb->atdat->lj_comb));
- freeDeviceBuffer(&(nb->atdat->atom_types));
- freeDeviceBuffer(&(nb->atdat->shift_vec));
- sfree(nb->atdat);
-
- /* Free nbparam */
- freeDeviceBuffer(&(nb->nbparam->nbfp));
- freeDeviceBuffer(&(nb->nbparam->nbfp_comb));
- freeDeviceBuffer(&(nb->nbparam->coulomb_tab));
- sfree(nb->nbparam);
-
- /* Free plist */
- auto* plist = nb->plist[InteractionLocality::Local];
- freeDeviceBuffer(&plist->sci);
- freeDeviceBuffer(&plist->cj4);
- freeDeviceBuffer(&plist->imask);
- freeDeviceBuffer(&plist->excl);
- sfree(plist);
- if (nb->bUseTwoStreams)
- {
- auto* plist_nl = nb->plist[InteractionLocality::NonLocal];
- freeDeviceBuffer(&plist_nl->sci);
- freeDeviceBuffer(&plist_nl->cj4);
- freeDeviceBuffer(&plist_nl->imask);
- freeDeviceBuffer(&plist_nl->excl);
- sfree(plist_nl);
- }
-
- /* Free nbst */
- pfree(nb->nbst.e_lj);
- nb->nbst.e_lj = nullptr;
-
- pfree(nb->nbst.e_el);
- nb->nbst.e_el = nullptr;
-
- pfree(nb->nbst.fshift);
- nb->nbst.fshift = nullptr;
-
- /* Free other events */
- if (nb->nonlocal_done)
- {
- clReleaseEvent(nb->nonlocal_done);
- nb->nonlocal_done = nullptr;
- }
- if (nb->misc_ops_and_local_H2D_done)
- {
- clReleaseEvent(nb->misc_ops_and_local_H2D_done);
- nb->misc_ops_and_local_H2D_done = nullptr;
- }
-
freeGpuProgram(nb->dev_rundata->program);
delete nb->dev_rundata;
-
- /* Free timers and timings */
- delete nb->timers;
- sfree(nb->timings);
- delete nb;
-
- if (debug)
- {
- fprintf(debug, "Cleaned up OpenCL data structures.\n");
- }
}
//! This function is documented in the header file
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*! \brief Returns a string with the compiler defines required to avoid all flavour generation
*
- * For example if flavour eelTypeRF with evdwTypeFSWITCH, the output will be such that the corresponding
+ * For example if flavour ElecType::RF with VdwType::FSwitch, the output will be such that the corresponding
* kernel flavour is generated:
* -DGMX_OCL_FASTGEN (will replace flavour generator nbnxn_ocl_kernels.clh with nbnxn_ocl_kernels_fastgen.clh)
- * -DEL_RF (The eelTypeRF flavour)
+ * -DEL_RF (The ElecType::RF flavour)
* -DEELNAME=_ElecRF (The first part of the generated kernel name )
- * -DLJ_EWALD_COMB_GEOM (The evdwTypeFSWITCH flavour)
+ * -DLJ_EWALD_COMB_GEOM (The VdwType::FSwitch flavour)
* -DVDWNAME=_VdwLJEwCombGeom (The second part of the generated kernel name )
*
* prune/energy are still generated as originally. It is only the flavour-level that has changed, so that
* only the required flavour for the simulation is compiled.
*
- * If eeltype is single-range Ewald, then we need to add the
+ * If elecType is single-range Ewald, then we need to add the
* twin-cutoff flavour kernels to the JIT, because PME tuning might
* need it. This path sets -DGMX_OCL_FASTGEN_ADD_TWINCUT, which
* triggers the use of nbnxn_ocl_kernels_fastgen_add_twincut.clh. This
* JIT defaults to compiling all kernel flavours.
*
* \param[in] bFastGen Whether FastGen should be used
- * \param[in] eeltype Electrostatics kernel flavour for FastGen
- * \param[in] vdwtype VDW kernel flavour for FastGen
+ * \param[in] elecType Electrostatics kernel flavour for FastGen
+ * \param[in] vdwType VDW kernel flavour for FastGen
* \return String with the defines if FastGen is active
*
* \throws std::bad_alloc if out of memory
*/
-static std::string makeDefinesForKernelTypes(bool bFastGen, int eeltype, int vdwtype)
+static std::string makeDefinesForKernelTypes(bool bFastGen,
+ enum Nbnxm::ElecType elecType,
+ enum Nbnxm::VdwType vdwType)
{
+ using Nbnxm::ElecType;
std::string defines_for_kernel_types;
if (bFastGen)
{
- bool bIsEwaldSingleCutoff = (eeltype == eelTypeEWALD_TAB || eeltype == eelTypeEWALD_ANA);
+ bool bIsEwaldSingleCutoff = (elecType == ElecType::EwaldTab || elecType == ElecType::EwaldAna);
if (bIsEwaldSingleCutoff)
{
nbnxn_ocl_kernels_fastgen.clh. */
defines_for_kernel_types += "-DGMX_OCL_FASTGEN";
}
- defines_for_kernel_types += kernel_electrostatic_family_definitions[eeltype];
- defines_for_kernel_types += kernel_VdW_family_definitions[vdwtype];
+ defines_for_kernel_types += kernel_electrostatic_family_definitions[static_cast<int>(elecType)];
+ defines_for_kernel_types += kernel_VdW_family_definitions[static_cast<int>(vdwType)];
}
return defines_for_kernel_types;
try
{
std::string extraDefines =
- makeDefinesForKernelTypes(bFastGen, nb->nbparam->eeltype, nb->nbparam->vdwtype);
+ makeDefinesForKernelTypes(bFastGen, nb->nbparam->elecType, nb->nbparam->vdwType);
/* Here we pass macros and static const/constexpr int variables defined
* in include files outside the opencl as macros, to avoid
" -DNBNXM_MIN_DISTANCE_SQUARED_VALUE_FLOAT=%g"
" -Dc_nbnxnGpuNumClusterPerSupercluster=%d"
" -Dc_nbnxnGpuJgroupSize=%d"
+ " -Dc_centralShiftIndex=%d"
"%s",
- c_nbnxnGpuClusterSize, c_nbnxnMinDistanceSquared, c_nbnxnGpuNumClusterPerSupercluster,
- c_nbnxnGpuJgroupSize, (nb->bPrefetchLjParam) ? " -DIATYPE_SHMEM" : "");
+ c_nbnxnGpuClusterSize,
+ c_nbnxnMinDistanceSquared,
+ c_nbnxnGpuNumClusterPerSupercluster,
+ c_nbnxnGpuJgroupSize,
+ gmx::c_centralShiftIndex,
+ (nb->bPrefetchLjParam) ? " -DIATYPE_SHMEM" : "");
try
{
/* TODO when we have a proper MPI-aware logging module,
the log output here should be written there */
- program = gmx::ocl::compileProgram(
- stderr, "gromacs/nbnxm/opencl", "nbnxm_ocl_kernels.cl", extraDefines,
- nb->deviceContext_->context(), nb->deviceContext_->deviceInfo().oclDeviceId,
- nb->deviceContext_->deviceInfo().deviceVendor);
+ program = gmx::ocl::compileProgram(stderr,
+ "gromacs/nbnxm/opencl",
+ "nbnxm_ocl_kernels.cl",
+ extraDefines,
+ nb->deviceContext_->context(),
+ nb->deviceContext_->deviceInfo().oclDeviceId,
+ nb->deviceContext_->deviceInfo().deviceVendor);
}
catch (gmx::GromacsException& e)
{
- e.prependContext(gmx::formatString(
- "Failed to compile/load nbnxm kernels for GPU #%d %s\n",
- nb->deviceContext_->deviceInfo().id, nb->deviceContext_->deviceInfo().device_name));
+ e.prependContext(
+ gmx::formatString("Failed to compile/load nbnxm kernels for GPU #%d %s\n",
+ nb->deviceContext_->deviceInfo().id,
+ nb->deviceContext_->deviceInfo().device_name));
throw;
}
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#else
const __global int* restrict atom_types, /* IN */
#endif
- const __global float* restrict shift_vec, /* IN stores float3 values */
- __constant const float* gmx_unused nbfp_climg2d, /* IN */
- __constant const float* gmx_unused nbfp_comb_climg2d, /* IN */
- __constant const float* gmx_unused coulomb_tab_climg2d, /* IN */
- const __global nbnxn_sci_t* pl_sci, /* IN */
+ const __global float* restrict shift_vec, /* IN stores float3 values */
+ __constant const float2* restrict gmx_unused nbfp, /* IN */
+ __constant const float2* restrict gmx_unused nbfp_comb, /* IN */
+ __constant const float* restrict gmx_unused coulomb_tab, /* IN */
+ const __global nbnxn_sci_t* pl_sci, /* IN */
#ifndef PRUNE_NBL
const
#endif
const int ai = ci * CL_SIZE + tidxi;
float4 xqbuf = xq[ai]
- + (float4)(shift_vec[3 * nb_sci.shift], shift_vec[3 * nb_sci.shift + 1],
- shift_vec[3 * nb_sci.shift + 2], 0.0F);
+ + (float4)(shift_vec[3 * nb_sci.shift],
+ shift_vec[3 * nb_sci.shift + 1],
+ shift_vec[3 * nb_sci.shift + 2],
+ 0.0F);
xqbuf.w *= nbparam->epsfac;
xqib[(tidxj + i) * CL_SIZE + tidxi] = xqbuf;
#ifdef IATYPE_SHMEM
float E_el = 0.0F;
# if defined EXCLUSION_FORCES /* Ewald or RF */
- if (nb_sci.shift == CENTRAL && pl_cj4[cij4_start].cj[0] == sci * c_nbnxnGpuNumClusterPerSupercluster)
+ if (nb_sci.shift == c_centralShiftIndex
+ && pl_cj4[cij4_start].cj[0] == sci * c_nbnxnGpuNumClusterPerSupercluster)
{
/* we have the diagonal: add the charge and LJ self interaction energy term */
for (int i = 0; i < c_nbnxnGpuNumClusterPerSupercluster; i++)
E_el += qi * qi;
# endif
# if defined LJ_EWALD
- E_lj += nbfp_climg2d[atom_types[(sci * c_nbnxnGpuNumClusterPerSupercluster + i) * CL_SIZE + tidxi]
- * (ntypes + 1) * 2];
+ E_lj += nbfp[atom_types[(sci * c_nbnxnGpuNumClusterPerSupercluster + i) * CL_SIZE + tidxi] * (ntypes + 1)]
+ .x;
# endif /* LJ_EWALD */
}
#endif /* CALC_ENERGIES */
#ifdef EXCLUSION_FORCES
- const int nonSelfInteraction = !(nb_sci.shift == CENTRAL & tidxj <= tidxi);
+ const int nonSelfInteraction = !(nb_sci.shift == c_centralShiftIndex & tidxj <= tidxi);
#endif
/* loop over the j clusters = seen by any of the atoms in the current super-cluster */
#endif /* IATYPE_SHMEM */
/* LJ 6*C6 and 12*C12 */
#ifndef LJ_COMB
- const float c6 = nbfp_climg2d[2 * (ntypes * typei + typej)];
- const float c12 = nbfp_climg2d[2 * (ntypes * typei + typej) + 1];
+ const float2 c6c12 = nbfp[ntypes * typei + typej];
+
+ const float c6 = c6c12.x;
+ const float c12 = c6c12.y;
#else /* LJ_COMB */
# ifdef LJ_COMB_GEOM
const float c6 = ljcp_i.x * ljcp_j.x;
#ifdef LJ_EWALD
# ifdef LJ_EWALD_COMB_GEOM
# ifdef CALC_ENERGIES
- calculate_lj_ewald_comb_geom_F_E(
- nbfp_comb_climg2d, nbparam, typei, typej, r2, inv_r2,
- lje_coeff2, lje_coeff6_6, int_bit, &F_invr, &E_lj_p);
+ calculate_lj_ewald_comb_geom_F_E(nbfp_comb,
+ nbparam,
+ typei,
+ typej,
+ r2,
+ inv_r2,
+ lje_coeff2,
+ lje_coeff6_6,
+ int_bit,
+ &F_invr,
+ &E_lj_p);
# else
- calculate_lj_ewald_comb_geom_F(nbfp_comb_climg2d, typei, typej, r2, inv_r2,
- lje_coeff2, lje_coeff6_6, &F_invr);
+ calculate_lj_ewald_comb_geom_F(
+ nbfp_comb, typei, typej, r2, inv_r2, lje_coeff2, lje_coeff6_6, &F_invr);
# endif /* CALC_ENERGIES */
# elif defined LJ_EWALD_COMB_LB
- calculate_lj_ewald_comb_LB_F_E(nbfp_comb_climg2d, nbparam, typei, typej,
- r2, inv_r2, lje_coeff2, lje_coeff6_6,
+ calculate_lj_ewald_comb_LB_F_E(nbfp_comb,
+ nbparam,
+ typei,
+ typej,
+ r2,
+ inv_r2,
+ lje_coeff2,
+ lje_coeff6_6,
# ifdef CALC_ENERGIES
- int_bit, true, &F_invr, &E_lj_p
+ int_bit,
+ true,
+ &F_invr,
+ &E_lj_p
# else
- 0, false, &F_invr, 0
+ 0,
+ false,
+ &F_invr,
+ 0
# endif /* CALC_ENERGIES */
);
# endif /* LJ_EWALD_COMB_GEOM */
#elif defined EL_EWALD_TAB
F_invr += qi * qj_f
* (int_bit * inv_r2
- - interpolate_coulomb_force_r(coulomb_tab_climg2d, r2 * inv_r,
- coulomb_tab_scale))
+ - interpolate_coulomb_force_r(
+ coulomb_tab, r2 * inv_r, coulomb_tab_scale))
* inv_r;
#endif /* EL_EWALD_ANA/TAB */
}
/* skip central shifts when summing shift forces */
- if (nb_sci.shift == CENTRAL)
+ if (nb_sci.shift == c_centralShiftIndex)
{
bCalcFshift = 0;
}
/* We don't need q, but using float4 in shmem avoids bank conflicts */
const float4 tmp = xq[ai];
const float4 xi = tmp
- + (float4)(shift_vec[3 * nb_sci.shift], shift_vec[3 * nb_sci.shift + 1],
- shift_vec[3 * nb_sci.shift + 2], 0.0F);
+ + (float4)(shift_vec[3 * nb_sci.shift],
+ shift_vec[3 * nb_sci.shift + 1],
+ shift_vec[3 * nb_sci.shift + 2],
+ 0.0F);
xib[(tidxj + i) * c_clSize + tidxi] = xi;
}
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gpu_utils/device_utils.clh"
#include "gromacs/gpu_utils/vectype_ops.clh"
-#include "gromacs/pbcutil/ishift.h"
#include "nbnxm_ocl_consts.h"
# ifdef __GNUC__
-/* GCC, clang, and some ICC pretending to be GCC */
+/* GCC, clang */
# define gmx_unused __attribute__((unused))
# else
# define gmx_unused
typedef struct cl_nbparam_params
{
- //! type of electrostatics, takes values from #eelCu
- int eeltype;
- //! type of VdW impl., takes values from #evdwCu
- int vdwtype;
+ //! type of electrostatics, takes values from #ElecType
+ int elecType;
+ //! type of VdW impl., takes values from #VdwType
+ int vdwType;
//! charge multiplication factor
float epsfac;
} nbnxn_excl_t;
/*! i-cluster interaction mask for a super-cluster with all c_nbnxnGpuNumClusterPerSupercluster bits set */
-__constant unsigned supercl_interaction_mask = ((1U << c_nbnxnGpuNumClusterPerSupercluster) - 1U);
+__constant const unsigned supercl_interaction_mask = ((1U << c_nbnxnGpuNumClusterPerSupercluster) - 1U);
/*! Minimum single precision threshold for r^2 to avoid r^-12 overflow. */
-__constant float c_nbnxnMinDistanceSquared = NBNXM_MIN_DISTANCE_SQUARED_VALUE_FLOAT;
+__constant const float c_nbnxnMinDistanceSquared = NBNXM_MIN_DISTANCE_SQUARED_VALUE_FLOAT;
gmx_opencl_inline void preloadCj4Generic(__local int* sm_cjPreload,
const __global int* gm_cj,
*E_lj *= sw;
}
+/*! \brief Fetch C6 grid contribution coefficients and return the product of these.
+ */
+gmx_opencl_inline float calculate_lj_ewald_c6grid(__constant const float2* nbfp_comb, int typei, int typej)
+{
+ const float c6_i = nbfp_comb[typei].x;
+ const float c6_j = nbfp_comb[typej].x;
+ return c6_i * c6_j;
+}
+
/*! Calculate LJ-PME grid force contribution with
* geometric combination rule.
*/
-gmx_opencl_inline void calculate_lj_ewald_comb_geom_F(__constant const float* nbfp_comb_climg2d,
- int typei,
- int typej,
- float r2,
- float inv_r2,
- float lje_coeff2,
- float lje_coeff6_6,
- float* F_invr)
+gmx_opencl_inline void calculate_lj_ewald_comb_geom_F(__constant const float2* nbfp_comb,
+ int typei,
+ int typej,
+ float r2,
+ float inv_r2,
+ float lje_coeff2,
+ float lje_coeff6_6,
+ float* F_invr)
{
- const float c6grid = nbfp_comb_climg2d[2 * typei] * nbfp_comb_climg2d[2 * typej];
+ const float c6grid = calculate_lj_ewald_c6grid(nbfp_comb, typei, typej);
/* Recalculate inv_r6 without exclusion mask */
const float inv_r6_nm = inv_r2 * inv_r2 * inv_r2;
/*! Calculate LJ-PME grid force + energy contribution with
* geometric combination rule.
*/
-gmx_opencl_inline void calculate_lj_ewald_comb_geom_F_E(__constant const float* nbfp_comb_climg2d,
+gmx_opencl_inline void calculate_lj_ewald_comb_geom_F_E(__constant const float2* nbfp_comb,
const cl_nbparam_params_t* nbparam,
int typei,
int typej,
float* F_invr,
float* E_lj)
{
- const float c6grid = nbfp_comb_climg2d[2 * typei] * nbfp_comb_climg2d[2 * typej];
+ const float c6grid = calculate_lj_ewald_c6grid(nbfp_comb, typei, typej);
/* Recalculate inv_r6 without exclusion mask */
const float inv_r6_nm = inv_r2 * inv_r2 * inv_r2;
* We use a single F+E kernel with conditional because the performance impact
* of this is pretty small and LB on the CPU is anyway very slow.
*/
-gmx_opencl_inline void calculate_lj_ewald_comb_LB_F_E(__constant const float* nbfp_comb_climg2d,
+gmx_opencl_inline void calculate_lj_ewald_comb_LB_F_E(__constant const float2* nbfp_comb,
const cl_nbparam_params_t* nbparam,
int typei,
int typej,
float* E_lj)
{
/* sigma and epsilon are scaled to give 6*C6 */
- const float sigma = nbfp_comb_climg2d[2 * typei] + nbfp_comb_climg2d[2 * typej];
-
- const float epsilon = nbfp_comb_climg2d[2 * typei + 1] * nbfp_comb_climg2d[2 * typej + 1];
+ const float2 c6c12_i = nbfp_comb[typei];
+ const float2 c6c12_j = nbfp_comb[typej];
+ const float sigma = c6c12_i.x + c6c12_j.x;
+ const float epsilon = c6c12_i.y * c6c12_j.y;
const float sigma2 = sigma * sigma;
const float c6grid = epsilon * sigma2 * sigma2 * sigma2;
/*! Interpolate Ewald coulomb force using the table through the tex_nbfp texture.
* Original idea: from the OpenMM project
*/
-gmx_opencl_inline float interpolate_coulomb_force_r(__constant const float* coulomb_tab_climg2d,
- float r,
- float scale)
+gmx_opencl_inline float interpolate_coulomb_force_r(__constant const float* coulomb_tab, float r, float scale)
{
float normalized = scale * r;
int index = (int)normalized;
float fract2 = normalized - (float)index;
float fract1 = 1.0F - fract2;
- return fract1 * coulomb_tab_climg2d[index] + fract2 * coulomb_tab_climg2d[index + 1];
+ return fract1 * coulomb_tab[index] + fract2 * coulomb_tab[index + 1];
}
/*! Calculate analytical Ewald correction term. */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/* Auxiliary kernels */
-
-/* Very few data */
-__kernel void zero_e_fshift(__global float* fshift, __global float* e_lj, __global float* e_el, const unsigned int Nbuf)
-{
- unsigned int tidx = get_global_id(0);
- if (tidx < Nbuf)
- {
- fshift[tidx] = 0.0F;
- }
- if (tidx == 0)
- {
- *e_lj = 0.0F;
- *e_el = 0.0F;
- }
-}
-
/* Generate pruning kernels. */
#define HAVE_FRESH_LIST 1
#include "nbnxm_ocl_kernel_pruneonly.clh"
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gpu_utils/devicebuffer.h"
#include "gromacs/gpu_utils/gmxopencl.h"
+#include "gromacs/gpu_utils/gpueventsynchronizer_ocl.h"
#include "gromacs/gpu_utils/gputraits_ocl.h"
#include "gromacs/gpu_utils/oclutils.h"
#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/real.h"
-#include "nbnxm_ocl_consts.h"
-
struct gmx_wallclock_gpu_nbnxn_t;
-/* kernel does #include "gromacs/math/utilities.h" */
-/* Move the actual useful stuff here: */
-
-//! Define 1/sqrt(pi)
-#define M_FLOAT_1_SQRTPI 0.564189583547756f
-
-/*! \brief Constants for platform-dependent defaults for the prune kernel's j4 processing concurrency.
- *
- * Initialized using macros that can be overridden at compile-time (using #GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY).
- */
-/*! @{ */
-const int c_oclPruneKernelJ4ConcurrencyDEFAULT = GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY_DEFAULT;
-/*! @} */
-
/*! \brief Pruning kernel flavors.
*
* The values correspond to the first call of the pruning post-list generation
ePruneNR
};
-/*! \internal
- * \brief Staging area for temporary data downloaded from the GPU.
- *
- * The energies/shift forces get downloaded here first, before getting added
- * to the CPU-side aggregate values.
- */
-struct nb_staging_t
-{
- //! LJ energy
- float* e_lj = nullptr;
- //! electrostatic energy
- float* e_el = nullptr;
- //! float3 buffer with shift forces
- float (*fshift)[3] = nullptr;
-};
-
-/*! \internal
- * \brief Nonbonded atom data - both inputs and outputs.
- */
-typedef struct cl_atomdata
-{
- //! number of atoms
- int natoms;
- //! number of local atoms
- int natoms_local;
- //! allocation size for the atom data (xq, f)
- int nalloc;
-
- //! float4 buffer with atom coordinates + charges, size natoms
- DeviceBuffer<float> xq;
-
- //! float3 buffer with force output array, size natoms
- DeviceBuffer<float> f;
-
- //! LJ energy output, size 1
- DeviceBuffer<float> e_lj;
- //! Electrostatics energy input, size 1
- DeviceBuffer<float> e_el;
-
- //! float3 buffer with shift forces
- DeviceBuffer<float> fshift;
-
- //! number of atom types
- int ntypes;
- //! int buffer with atom type indices, size natoms
- DeviceBuffer<int> atom_types;
- //! float2 buffer with sqrt(c6),sqrt(c12), size natoms
- DeviceBuffer<float> lj_comb;
-
- //! float3 buffer with shifts values
- DeviceBuffer<float> shift_vec;
-
- //! true if the shift vector has been uploaded
- bool bShiftVecUploaded;
-} cl_atomdata_t;
-
/*! \internal
* \brief Data structure shared between the OpenCL device code and OpenCL host code
*
typedef struct cl_nbparam_params
{
- //! type of electrostatics, takes values from #eelType
- int eeltype;
- //! type of VdW impl., takes values from #evdwType
- int vdwtype;
+ //! type of electrostatics
+ enum Nbnxm::ElecType elecType;
+ //! type of VdW impl.
+ enum Nbnxm::VdwType vdwType;
//! charge multiplication factor
float epsfac;
float two_k_rf;
//! Ewald/PME parameter
float ewald_beta;
- //! Ewald/PME correction term substracted from the direct-space potential
+ //! Ewald/PME correction term subtracted from the direct-space potential
float sh_ewald;
//! LJ-Ewald/PME correction term added to the correction potential
float sh_lj_ewald;
} cl_nbparam_params_t;
-/** \internal
- * \brief Typedef of actual timer type.
- */
-typedef struct Nbnxm::gpu_timers_t cl_timers_t;
-
/*! \internal
* \brief Main data structure for OpenCL nonbonded force calculations.
*/
/**< Pointers to non-bonded kernel functions
* organized similar with nb_kfunc_xxx arrays in nbnxn_ocl.cpp */
///@{
- cl_kernel kernel_noener_noprune_ptr[eelTypeNR][evdwTypeNR] = { { nullptr } };
- cl_kernel kernel_ener_noprune_ptr[eelTypeNR][evdwTypeNR] = { { nullptr } };
- cl_kernel kernel_noener_prune_ptr[eelTypeNR][evdwTypeNR] = { { nullptr } };
- cl_kernel kernel_ener_prune_ptr[eelTypeNR][evdwTypeNR] = { { nullptr } };
+ cl_kernel kernel_noener_noprune_ptr[Nbnxm::c_numElecTypes][Nbnxm::c_numVdwTypes] = { { nullptr } };
+ cl_kernel kernel_ener_noprune_ptr[Nbnxm::c_numElecTypes][Nbnxm::c_numVdwTypes] = { { nullptr } };
+ cl_kernel kernel_noener_prune_ptr[Nbnxm::c_numElecTypes][Nbnxm::c_numVdwTypes] = { { nullptr } };
+ cl_kernel kernel_ener_prune_ptr[Nbnxm::c_numElecTypes][Nbnxm::c_numVdwTypes] = { { nullptr } };
///@}
//! prune kernels, ePruneKind defined the kernel kinds
cl_kernel kernel_pruneonly[ePruneNR] = { nullptr };
/**< auxiliary kernels implementing memset-like functions */
///@{
- cl_kernel kernel_memset_f = nullptr;
- cl_kernel kernel_memset_f2 = nullptr;
- cl_kernel kernel_memset_f3 = nullptr;
- cl_kernel kernel_zero_e_fshift = nullptr;
+ cl_kernel kernel_memset_f = nullptr;
+ cl_kernel kernel_memset_f2 = nullptr;
+ cl_kernel kernel_memset_f3 = nullptr;
///@}
//! true if doing both local/non-local NB work on GPU
bool bUseTwoStreams = false;
- //! true indicates that the nonlocal_done event was enqueued
- bool bNonLocalStreamActive = false;
+ //! true indicates that the nonlocal_done event was marked
+ bool bNonLocalStreamDoneMarked = false;
//! atom data
- cl_atomdata_t* atdat = nullptr;
+ NBAtomDataGpu* atdat = nullptr;
//! parameters required for the non-bonded calc.
NBParamGpu* nbparam = nullptr;
//! pair-list data structures (local and non-local)
gmx::EnumerationArray<Nbnxm::InteractionLocality, Nbnxm::gpu_plist*> plist = { nullptr };
//! staging area where fshift/energies get downloaded
- nb_staging_t nbst;
+ NBStagingData nbst;
+
+ // Data for GPU-side coordinate conversion between integrator and NBNXM
+ /*! \brief array of atom indices */
+ DeviceBuffer<int> atomIndices;
+ /*! \brief size of atom indices */
+ int atomIndicesSize = 0;
+ /*! \brief size of atom indices allocated in device buffer */
+ int atomIndicesSize_alloc = 0;
+ /*! \brief x buf ops num of atoms */
+ DeviceBuffer<int> cxy_na;
+ /*! \brief number of elements in cxy_na */
+ int ncxy_na = 0;
+ /*! \brief number of elements allocated allocated in device buffer */
+ int ncxy_na_alloc = 0;
+ /*! \brief x buf ops cell index mapping */
+ DeviceBuffer<int> cxy_ind;
+ /*! \brief number of elements in cxy_ind */
+ int ncxy_ind = 0;
+ /*! \brief number of elements allocated allocated in device buffer */
+ int ncxy_ind_alloc = 0;
//! local and non-local GPU queues
gmx::EnumerationArray<Nbnxm::InteractionLocality, const DeviceStream*> deviceStreams;
/*! \{ */
/*! \brief Event triggered when the non-local non-bonded
* kernel is done (and the local transfer can proceed) */
- cl_event nonlocal_done = nullptr;
+ GpuEventSynchronizer nonlocal_done;
/*! \brief Event triggered when the tasks issued in the local
* stream that need to precede the non-local force or buffer
* operation calculations are done (e.g. f buffer 0-ing, local
* x/q H2D, buffer op initialization in local stream that is
* required also by nonlocal stream ) */
- cl_event misc_ops_and_local_H2D_done = nullptr;
+ GpuEventSynchronizer misc_ops_and_local_H2D_done;
/*! \} */
//! True if there has been local/nonlocal GPU work, either bonded or nonbonded, scheduled
//! True if event-based timing is enabled.
bool bDoTime = false;
//! OpenCL event-based timers.
- cl_timers_t* timers = nullptr;
+ Nbnxm::GpuTimers* timers = nullptr;
//! Timing data. TODO: deprecate this and query timers for accumulated data instead
gmx_wallclock_gpu_nbnxn_t* timings = nullptr;
};
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
using Grid = Nbnxm::Grid; // TODO: Remove when refactoring this file
-// Convience alias for partial Nbnxn namespace usage
+// Convenience alias for partial Nbnxn namespace usage
using InteractionLocality = gmx::InteractionLocality;
/* We shift the i-particles backward for PBC.
}
#endif // defined(GMX_NBNXN_SIMD_4XN) || defined(GMX_NBNXN_SIMD_2XNN)
-
-void nbnxn_init_pairlist_fep(t_nblist* nl)
-{
- nl->type = GMX_NBLIST_INTERACTION_FREE_ENERGY;
- nl->igeometry = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
- /* The interaction functions are set in the free energy kernel fuction */
- nl->ivdw = -1;
- nl->ivdwmod = -1;
- nl->ielec = -1;
- nl->ielecmod = -1;
-
- nl->maxnri = 0;
- nl->maxnrj = 0;
- nl->nri = 0;
- nl->nrj = 0;
- nl->iinr = nullptr;
- nl->gid = nullptr;
- nl->shift = nullptr;
- nl->jindex = nullptr;
- nl->jjnr = nullptr;
- nl->excl_fep = nullptr;
-}
-
static constexpr int sizeNeededForBufferFlags(const int numAtoms)
{
return (numAtoms + NBNXN_BUFFERFLAG_SIZE - 1) / NBNXN_BUFFERFLAG_SIZE;
static_assert(c_nbnxnGpuClusterSize == 8 || c_nbnxnGpuClusterSize == 4,
"A cluster is hard-coded to 4/8 atoms.");
- Simd4Real rc2_S = Simd4Real(rlist2);
+ Simd4Real rc2_S{ rlist2 };
const real* x_i = work.iSuperClusterData.xSimd.data();
}
// TODO: Move to pairlistset.cpp
-PairlistSet::PairlistSet(const InteractionLocality locality, const PairlistParams& pairlistParams) :
- locality_(locality),
- params_(pairlistParams)
+PairlistSet::PairlistSet(const PairlistParams& pairlistParams) :
+ params_(pairlistParams),
+ combineLists_(sc_isGpuPairListType[pairlistParams.pairlistType]), // Currently GPU lists are always combined
+ isCpuType_(!sc_isGpuPairListType[pairlistParams.pairlistType])
{
- isCpuType_ = (params_.pairlistType == PairlistType::Simple4x2
- || params_.pairlistType == PairlistType::Simple4x4
- || params_.pairlistType == PairlistType::Simple4x8);
- // Currently GPU lists are always combined
- combineLists_ = !isCpuType_;
- const int numLists = gmx_omp_nthreads_get(emntNonbonded);
+ const int numLists = gmx_omp_nthreads_get(ModuleMultiThread::Nonbonded);
if (!combineLists_ && numLists > NBNXN_BUFFERFLAG_MAX_THREADS)
{
"%d OpenMP threads were requested. Since the non-bonded force buffer reduction "
"is prohibitively slow with more than %d threads, we do not allow this. Use %d "
"or less OpenMP threads.",
- numLists, NBNXN_BUFFERFLAG_MAX_THREADS, NBNXN_BUFFERFLAG_MAX_THREADS);
+ numLists,
+ NBNXN_BUFFERFLAG_MAX_THREADS,
+ NBNXN_BUFFERFLAG_MAX_THREADS);
}
if (isCpuType_)
* impacts performance.
*/
fepLists_[i] = std::make_unique<t_nblist>();
- nbnxn_init_pairlist_fep(fepLists_[i].get());
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
fprintf(fp, "nbl nci %zu ncj %d\n", nbl.ci.size(), nbl.ncjInUse);
const int numAtomsJCluster = grid.geometry().numAtomsJCluster;
const double numAtomsPerCell = nbl.ncjInUse / static_cast<double>(grid.numCells()) * numAtomsJCluster;
- fprintf(fp, "nbl na_cj %d rl %g ncp %d per cell %.1f atoms %.1f ratio %.2f\n", nbl.na_cj, rl,
- nbl.ncjInUse, nbl.ncjInUse / static_cast<double>(grid.numCells()), numAtomsPerCell,
+ fprintf(fp,
+ "nbl na_cj %d rl %g ncp %d per cell %.1f atoms %.1f ratio %.2f\n",
+ nbl.na_cj,
+ rl,
+ nbl.ncjInUse,
+ nbl.ncjInUse / static_cast<double>(grid.numCells()),
+ numAtomsPerCell,
numAtomsPerCell
/ (0.5 * 4.0 / 3.0 * M_PI * rl * rl * rl * grid.numCells() * numAtomsJCluster
/ (dims.gridSize[XX] * dims.gridSize[YY] * dims.gridSize[ZZ])));
- fprintf(fp, "nbl average j cell list length %.1f\n",
+ fprintf(fp,
+ "nbl average j cell list length %.1f\n",
0.25 * nbl.ncjInUse / std::max(static_cast<double>(nbl.ci.size()), 1.0));
- int cs[SHIFTS] = { 0 };
- int npexcl = 0;
+ int cs[gmx::c_numShiftVectors] = { 0 };
+ int npexcl = 0;
for (const nbnxn_ci_t& ciEntry : nbl.ci)
{
cs[ciEntry.shift & NBNXN_CI_SHIFT] += ciEntry.cj_ind_end - ciEntry.cj_ind_start;
j++;
}
}
- fprintf(fp, "nbl cell pairs, total: %zu excl: %d %.1f%%\n", nbl.cj.size(), npexcl,
+ fprintf(fp,
+ "nbl cell pairs, total: %zu excl: %d %.1f%%\n",
+ nbl.cj.size(),
+ npexcl,
100 * npexcl / std::max(static_cast<double>(nbl.cj.size()), 1.0));
- for (int s = 0; s < SHIFTS; s++)
+ for (int s = 0; s < gmx::c_numShiftVectors; s++)
{
if (cs[s] > 0)
{
const Grid& grid = gridSet.grids()[0];
const Grid::Dimensions& dims = grid.dimensions();
- fprintf(fp, "nbl nsci %zu ncj4 %zu nsi %d excl4 %zu\n", nbl.sci.size(), nbl.cj4.size(),
- nbl.nci_tot, nbl.excl.size());
+ fprintf(fp,
+ "nbl nsci %zu ncj4 %zu nsi %d excl4 %zu\n",
+ nbl.sci.size(),
+ nbl.cj4.size(),
+ nbl.nci_tot,
+ nbl.excl.size());
const int numAtomsCluster = grid.geometry().numAtomsICluster;
const double numAtomsPerCell = nbl.nci_tot / static_cast<double>(grid.numClusters()) * numAtomsCluster;
- fprintf(fp, "nbl na_c %d rl %g ncp %d per cell %.1f atoms %.1f ratio %.2f\n", nbl.na_ci, rl,
- nbl.nci_tot, nbl.nci_tot / static_cast<double>(grid.numClusters()), numAtomsPerCell,
+ fprintf(fp,
+ "nbl na_c %d rl %g ncp %d per cell %.1f atoms %.1f ratio %.2f\n",
+ nbl.na_ci,
+ rl,
+ nbl.nci_tot,
+ nbl.nci_tot / static_cast<double>(grid.numClusters()),
+ numAtomsPerCell,
numAtomsPerCell
/ (0.5 * 4.0 / 3.0 * M_PI * rl * rl * rl * grid.numClusters() * numAtomsCluster
/ (dims.gridSize[XX] * dims.gridSize[YY] * dims.gridSize[ZZ])));
sum_nsp /= nbl.sci.size();
sum_nsp2 /= nbl.sci.size();
}
- fprintf(fp, "nbl #cluster-pairs: av %.1f stddev %.1f max %d\n", sum_nsp,
- std::sqrt(sum_nsp2 - sum_nsp * sum_nsp), nsp_max);
+ fprintf(fp,
+ "nbl #cluster-pairs: av %.1f stddev %.1f max %d\n",
+ sum_nsp,
+ std::sqrt(sum_nsp2 - sum_nsp * sum_nsp),
+ nsp_max);
if (!nbl.cj4.empty())
{
for (int b = 0; b <= c_gpuNumClusterPerCell; b++)
{
- fprintf(fp, "nbl j-list #i-subcell %d %7d %4.1f\n", b, c[b],
+ fprintf(fp,
+ "nbl j-list #i-subcell %d %7d %4.1f\n",
+ b,
+ c[b],
100.0 * c[b] / size_t{ nbl.cj4.size() * c_nbnxnGpuJgroupSize });
}
}
const BoundingBox* gmx_restrict bb_ci = nbl->work->iClusterData.bb.data();
const real* gmx_restrict x_ci = nbl->work->iClusterData.x.data();
- gmx_bool InRange;
-
- InRange = FALSE;
+ bool InRange = false;
while (!InRange && jclusterFirst <= jclusterLast)
{
real d2 = clusterBoundingBoxDistance2(bb_ci[0], jGrid.jBoundingBoxes()[jclusterFirst]);
*/
if (d2 < rbb2)
{
- InRange = TRUE;
+ InRange = true;
}
else if (d2 < rlist2)
{
return;
}
- InRange = FALSE;
+ InRange = false;
while (!InRange && jclusterLast > jclusterFirst)
{
real d2 = clusterBoundingBoxDistance2(bb_ci[0], jGrid.jBoundingBoxes()[jclusterLast]);
*/
if (d2 < rbb2)
{
- InRange = TRUE;
+ InRange = true;
}
else if (d2 < rlist2)
{
const int cj_gl = jGrid.cellOffset() * c_gpuNumClusterPerCell + cj;
- int ci1;
- if (excludeSubDiagonal && sci == scj)
- {
- ci1 = subc + 1;
- }
- else
- {
- ci1 = iGrid.numClustersPerCell()[sci];
- }
+ int ci1 = (excludeSubDiagonal && sci == scj) ? subc + 1 : iGrid.numClustersPerCell()[sci];
+
#if NBNXN_BBXXXX
/* Determine all ci1 bb distances in one call with SIMD4 */
const int offset = packedBoundingBoxesIndex(cj) + (cj & (c_packedBoundingBoxesDimSize - 1));
- clusterBoundingBoxDistance2_xxxx_simd4(jGrid.packedBoundingBoxes().data() + offset, ci1,
- pbb_ci, d2l);
+ clusterBoundingBoxDistance2_xxxx_simd4(
+ jGrid.packedBoundingBoxes().data() + offset, ci1, pbb_ci, d2l);
*numDistanceChecks += c_nbnxnGpuClusterSize * 2;
#endif
const JListRanges& ranges,
gmx::ArrayRef<const CjListType> cjList)
{
- int index;
-
if (jCluster < ranges.cjFirst + ranges.numDirect)
{
/* We can calculate the index directly using the offset */
- index = ranges.cjIndexStart + jCluster - ranges.cjFirst;
+ return ranges.cjIndexStart + jCluster - ranges.cjFirst;
}
else
{
/* Search for jCluster using bisection */
- index = -1;
+ int index = -1;
int rangeStart = ranges.cjIndexStart + ranges.numDirect;
int rangeEnd = ranges.cjIndexEnd;
- int rangeMiddle;
while (index == -1 && rangeStart < rangeEnd)
{
- rangeMiddle = (rangeStart + rangeEnd) >> 1;
+ int rangeMiddle = (rangeStart + rangeEnd) >> 1;
const int clusterMiddle = nblCj(cjList, rangeMiddle);
rangeStart = rangeMiddle + 1;
}
}
+ return index;
}
-
- return index;
}
// TODO: Get rid of the two functions below by renaming sci to ci (or something better)
/* Rellocate FEP list for size nl->maxnri, TODO: replace by C++ */
static void reallocate_nblist(t_nblist* nl)
{
- if (gmx_debug_at)
- {
- fprintf(debug,
- "reallocating neigborlist (ielec=%d, ivdw=%d, igeometry=%d, type=%d), maxnri=%d\n",
- nl->ielec, nl->ivdw, nl->igeometry, nl->type, nl->maxnri);
- }
- srenew(nl->iinr, nl->maxnri);
- srenew(nl->gid, nl->maxnri);
- srenew(nl->shift, nl->maxnri);
- srenew(nl->jindex, nl->maxnri + 1);
+ nl->iinr.resize(nl->maxnri);
+ nl->gid.resize(nl->maxnri);
+ nl->shift.resize(nl->maxnri);
+ nl->jindex.resize(nl->maxnri + 1);
}
/* For load balancing of the free-energy lists over threads, we set
const Grid& jGrid,
t_nblist* nlist)
{
- int ci, cj_ind_start, cj_ind_end, cja, cjr;
- int nri_max;
- int gid_i = 0, gid_j, gid;
- int egp_shift, egp_mask;
- int gid_cj = 0;
- int ind_i, ind_j, ai, aj;
- int nri;
- gmx_bool bFEP_i, bFEP_i_all;
+ int gid_i = 0;
+ int gid_cj = 0;
if (nbl_ci->cj_ind_end == nbl_ci->cj_ind_start)
{
return;
}
- ci = nbl_ci->ci;
+ const int ci = nbl_ci->ci;
- cj_ind_start = nbl_ci->cj_ind_start;
- cj_ind_end = nbl_ci->cj_ind_end;
+ const int cj_ind_start = nbl_ci->cj_ind_start;
+ const int cj_ind_end = nbl_ci->cj_ind_end;
/* In worst case we have alternating energy groups
* and create #atom-pair lists, which means we need the size
* of a cluster pair (na_ci*na_cj) times the number of cj's.
*/
- nri_max = nbl->na_ci * nbl->na_cj * (cj_ind_end - cj_ind_start);
+ const int nri_max = nbl->na_ci * nbl->na_cj * (cj_ind_end - cj_ind_start);
if (nlist->nri + nri_max > nlist->maxnri)
{
nlist->maxnri = over_alloc_large(nlist->nri + nri_max);
gmx_fatal(FARGS,
"The Verlet scheme with %dx%d kernels and free-energy only supports up to %zu "
"energy groups",
- iGrid.geometry().numAtomsICluster, numAtomsJCluster,
+ iGrid.geometry().numAtomsICluster,
+ numAtomsJCluster,
(sizeof(gid_cj) * 8) / numAtomsJCluster);
}
- egp_shift = nbatParams.neg_2log;
- egp_mask = (1 << egp_shift) - 1;
+ const int egp_shift = nbatParams.neg_2log;
+ const int egp_mask = (1 << egp_shift) - 1;
/* Loop over the atoms in the i sub-cell */
- bFEP_i_all = TRUE;
+ bool bFEP_i_all = true;
for (int i = 0; i < nbl->na_ci; i++)
{
- ind_i = ci * nbl->na_ci + i;
- ai = atomIndices[ind_i];
+ const int ind_i = ci * nbl->na_ci + i;
+ const int ai = atomIndices[ind_i];
if (ai >= 0)
{
- nri = nlist->nri;
+ int nri = nlist->nri;
nlist->jindex[nri + 1] = nlist->jindex[nri];
nlist->iinr[nri] = ai;
/* The actual energy group pair index is set later */
nlist->gid[nri] = 0;
nlist->shift[nri] = nbl_ci->shift & NBNXN_CI_SHIFT;
- bFEP_i = iGrid.atomIsPerturbed(ci - iGrid.cellOffset(), i);
+ bool bFEP_i = iGrid.atomIsPerturbed(ci - iGrid.cellOffset(), i);
bFEP_i_all = bFEP_i_all && bFEP_i;
if (nlist->nrj + (cj_ind_end - cj_ind_start) * nbl->na_cj > nlist->maxnrj)
{
nlist->maxnrj = over_alloc_small(nlist->nrj + (cj_ind_end - cj_ind_start) * nbl->na_cj);
- srenew(nlist->jjnr, nlist->maxnrj);
- srenew(nlist->excl_fep, nlist->maxnrj);
+ nlist->jjnr.resize(nlist->maxnrj);
+ nlist->excl_fep.resize(nlist->maxnrj);
}
if (ngid > 1)
for (int cj_ind = cj_ind_start; cj_ind < cj_ind_end; cj_ind++)
{
- unsigned int fep_cj;
+ unsigned int fep_cj = 0U;
+ gid_cj = 0;
- cja = nbl->cj[cj_ind].cj;
+ const int cja = nbl->cj[cj_ind].cj;
if (numAtomsJCluster == jGrid.geometry().numAtomsICluster)
{
- cjr = cja - jGrid.cellOffset();
- fep_cj = jGrid.fepBits(cjr);
+ const int cjr = cja - jGrid.cellOffset();
+ fep_cj = jGrid.fepBits(cjr);
if (ngid > 1)
{
gid_cj = nbatParams.energrp[cja];
}
else if (2 * numAtomsJCluster == jGrid.geometry().numAtomsICluster)
{
- cjr = cja - jGrid.cellOffset() * 2;
+ const int cjr = cja - jGrid.cellOffset() * 2;
/* Extract half of the ci fep/energrp mask */
fep_cj = (jGrid.fepBits(cjr >> 1) >> ((cjr & 1) * numAtomsJCluster))
& ((1 << numAtomsJCluster) - 1);
}
else
{
- cjr = cja - (jGrid.cellOffset() >> 1);
+ const int cjr = cja - (jGrid.cellOffset() >> 1);
/* Combine two ci fep masks/energrp */
fep_cj = jGrid.fepBits(cjr * 2)
+ (jGrid.fepBits(cjr * 2 + 1) << jGrid.geometry().numAtomsICluster);
for (int j = 0; j < nbl->na_cj; j++)
{
/* Is this interaction perturbed and not excluded? */
- ind_j = cja * nbl->na_cj + j;
- aj = atomIndices[ind_j];
+ const int ind_j = cja * nbl->na_cj + j;
+ const int aj = atomIndices[ind_j];
if (aj >= 0 && (bFEP_i || (fep_cj & (1 << j))) && (!bDiagRemoved || ind_j >= ind_i))
{
if (ngid > 1)
{
- gid_j = (gid_cj >> (j * egp_shift)) & egp_mask;
- gid = GID(gid_i, gid_j, ngid);
+ const int gid_j = (gid_cj >> (j * egp_shift)) & egp_mask;
+ const int gid = GID(gid_i, gid_j, ngid);
if (nlist->nrj > nlist->jindex[nri] && nlist->gid[nri] != gid)
{
const Grid& jGrid,
t_nblist* nlist)
{
- int nri_max;
- int c_abs;
- int ind_i, ind_j, ai, aj;
- int nri;
- gmx_bool bFEP_i;
- real xi, yi, zi;
- const nbnxn_cj4_t* cj4;
-
const int numJClusterGroups = nbl_sci->numJClusterGroups();
if (numJClusterGroups == 0)
{
* So for each of the na_sc i-atoms, we need max one FEP list
* for each max_nrj_fep j-atoms.
*/
- nri_max = nbl->na_sc * nbl->na_cj * (1 + (numJClusterGroups * c_nbnxnGpuJgroupSize) / max_nrj_fep);
+ const int nri_max =
+ nbl->na_sc * nbl->na_cj * (1 + (numJClusterGroups * c_nbnxnGpuJgroupSize) / max_nrj_fep);
if (nlist->nri + nri_max > nlist->maxnri)
{
nlist->maxnri = over_alloc_large(nlist->nri + nri_max);
/* Loop over the atoms in the i super-cluster */
for (int c = 0; c < c_gpuNumClusterPerCell; c++)
{
- c_abs = sci * c_gpuNumClusterPerCell + c;
+ const int c_abs = sci * c_gpuNumClusterPerCell + c;
for (int i = 0; i < nbl->na_ci; i++)
{
- ind_i = c_abs * nbl->na_ci + i;
- ai = atomIndices[ind_i];
+ const int ind_i = c_abs * nbl->na_ci + i;
+ const int ai = atomIndices[ind_i];
if (ai >= 0)
{
- nri = nlist->nri;
+ int nri = nlist->nri;
nlist->jindex[nri + 1] = nlist->jindex[nri];
nlist->iinr[nri] = ai;
/* With GPUs, energy groups are not supported */
nlist->gid[nri] = 0;
nlist->shift[nri] = nbl_sci->shift & NBNXN_CI_SHIFT;
- bFEP_i = iGrid.atomIsPerturbed(c_abs - iGrid.cellOffset() * c_gpuNumClusterPerCell, i);
+ const bool bFEP_i =
+ iGrid.atomIsPerturbed(c_abs - iGrid.cellOffset() * c_gpuNumClusterPerCell, i);
- xi = nbat->x()[ind_i * nbat->xstride + XX] + shx;
- yi = nbat->x()[ind_i * nbat->xstride + YY] + shy;
- zi = nbat->x()[ind_i * nbat->xstride + ZZ] + shz;
+ real xi = nbat->x()[ind_i * nbat->xstride + XX] + shx;
+ real yi = nbat->x()[ind_i * nbat->xstride + YY] + shy;
+ real zi = nbat->x()[ind_i * nbat->xstride + ZZ] + shz;
const int nrjMax = nlist->nrj + numJClusterGroups * c_nbnxnGpuJgroupSize * nbl->na_cj;
if (nrjMax > nlist->maxnrj)
{
nlist->maxnrj = over_alloc_small(nrjMax);
- srenew(nlist->jjnr, nlist->maxnrj);
- srenew(nlist->excl_fep, nlist->maxnrj);
+ nlist->jjnr.resize(nlist->maxnrj);
+ nlist->excl_fep.resize(nlist->maxnrj);
}
for (int cj4_ind = cj4_ind_start; cj4_ind < cj4_ind_end; cj4_ind++)
{
- cj4 = &nbl->cj4[cj4_ind];
+ const nbnxn_cj4_t* cj4 = &nbl->cj4[cj4_ind];
for (int gcj = 0; gcj < c_nbnxnGpuJgroupSize; gcj++)
{
for (int j = 0; j < nbl->na_cj; j++)
{
/* Is this interaction perturbed and not excluded? */
- ind_j = (jGrid.cellOffset() * c_gpuNumClusterPerCell + cjr) * nbl->na_cj + j;
- aj = atomIndices[ind_j];
+ const int ind_j =
+ (jGrid.cellOffset() * c_gpuNumClusterPerCell + cjr) * nbl->na_cj + j;
+ const int aj = atomIndices[ind_j];
if (aj >= 0 && (bFEP_i || jGrid.atomIsPerturbed(cjr, j))
&& (!bDiagRemoved || ind_j >= ind_i))
{
- int excl_pair;
- unsigned int excl_bit;
- real dx, dy, dz;
-
const int jHalf =
j / (c_nbnxnGpuClusterSize / c_nbnxnGpuClusterpairSplit);
nbnxn_excl_t& excl = get_exclusion_mask(nbl, cj4_ind, jHalf);
- excl_pair = a_mod_wj(j) * nbl->na_ci + i;
- excl_bit = (1U << (gcj * c_gpuNumClusterPerCell + c));
+ int excl_pair = a_mod_wj(j) * nbl->na_ci + i;
+ unsigned int excl_bit = (1U << (gcj * c_gpuNumClusterPerCell + c));
- dx = nbat->x()[ind_j * nbat->xstride + XX] - xi;
- dy = nbat->x()[ind_j * nbat->xstride + YY] - yi;
- dz = nbat->x()[ind_j * nbat->xstride + ZZ] - zi;
+ real dx = nbat->x()[ind_j * nbat->xstride + XX] - xi;
+ real dy = nbat->x()[ind_j * nbat->xstride + YY] - yi;
+ real dz = nbat->x()[ind_j * nbat->xstride + ZZ] - zi;
/* The unpruned GPU list has more than 2/3
* of the atom pairs beyond rlist. Using
* Note that here we can not use cj4_ind_end, since the last cj4
* can be only partially filled, so we use cj_ind.
*/
- const JListRanges ranges(iEntry.cj4_ind_start * c_nbnxnGpuJgroupSize, nbl->work->cj_ind,
+ const JListRanges ranges(iEntry.cj4_ind_start * c_nbnxnGpuJgroupSize,
+ nbl->work->cj_ind,
gmx::makeConstArrayRef(nbl->cj4));
GMX_ASSERT(nbl->na_ci == c_nbnxnGpuClusterSize, "na_ci should match the GPU cluster size");
int thread,
int nthread)
{
- int nsp_max;
+
+ int nsp_max = nsp_target_av;
if (progBal)
{
- float nsp_est;
-
/* Estimate the total numbers of ci's of the nblist combined
* over all threads using the target number of ci's.
*/
- nsp_est = (nsp_tot_est * thread) / nthread + nbl->nci_tot;
+ float nsp_est = (nsp_tot_est * thread) / nthread + nbl->nci_tot;
/* The first ci blocks should be larger, to avoid overhead.
* The last ci blocks should be smaller, to improve load balancing.
*/
nsp_max = static_cast<int>(nsp_target_av * (nsp_tot_est * 1.5 / (nsp_est + nsp_tot_est)));
}
- else
- {
- nsp_max = nsp_target_av;
- }
const int cj4_start = nbl->sci.back().cj4_ind_start;
const int cj4_end = nbl->sci.back().cj4_ind_end;
{
nl->nri = 0;
nl->nrj = 0;
- if (nl->jindex == nullptr)
+ if (nl->jindex.empty())
{
- snew(nl->jindex, 1);
+ nl->jindex.resize(1);
}
nl->jindex[0] = 0;
}
gmx_unused static void set_icell_bb(const Grid& iGrid, int ci, real shx, real shy, real shz, NbnxnPairlistGpuWork* work)
{
#if NBNXN_BBXXXX
- set_icell_bbxxxx_supersub(iGrid.packedBoundingBoxes(), ci, shx, shy, shz,
- work->iSuperClusterData.bbPacked.data());
+ set_icell_bbxxxx_supersub(
+ iGrid.packedBoundingBoxes(), ci, shx, shy, shz, work->iSuperClusterData.bbPacked.data());
#else
set_icell_bb_supersub(iGrid.iBoundingBoxes(), ci, shx, shy, shz, work->iSuperClusterData.bb.data());
#endif
/* Estimates the interaction volume^2 for non-local interactions */
static real nonlocal_vol2(const struct gmx_domdec_zones_t* zones, const rvec ls, real r)
{
- real cl, ca, za;
- real vold_est;
- real vol2_est_tot;
-
- vol2_est_tot = 0;
+ real vol2_est_tot = 0;
/* Here we simply add up the volumes of 1, 2 or 3 1D decomposition
* not home interaction volume^2. As these volumes are not additive,
{
if (zones->shift[z][XX] + zones->shift[z][YY] + zones->shift[z][ZZ] == 1)
{
- cl = 0;
- ca = 1;
- za = 1;
+ real cl = 0;
+ real ca = 1;
+ real za = 1;
for (int d = 0; d < DIM; d++)
{
if (zones->shift[z][d] == 0)
}
/* 4 octants of a sphere */
- vold_est = 0.25 * M_PI * r * r * r * r;
+ real vold_est = 0.25 * M_PI * r * r * r * r;
/* 4 quarter pie slices on the edges */
vold_est += 4 * cl * M_PI / 6.0 * r * r * r;
/* One rectangular volume on a face */
* Maxwell is less sensitive to the exact value.
*/
const int nsubpair_target_min = 36;
- real r_eff_sup, vol_est, nsp_est, nsp_est_nl;
const Grid& grid = gridSet.grids()[0];
ls[ZZ] = numAtomsCluster / (dims.atomDensity * ls[XX] * ls[YY]);
/* The formulas below are a heuristic estimate of the average nsj per si*/
- r_eff_sup = rlist + nbnxn_get_rlist_effective_inc(numAtomsCluster, ls);
+ const real r_eff_sup = rlist + nbnxn_get_rlist_effective_inc(numAtomsCluster, ls);
- if (!gridSet.domainSetup().haveMultipleDomains || gridSet.domainSetup().zones->n == 1)
- {
- nsp_est_nl = 0;
- }
- else
+ real nsp_est_nl = 0;
+ if (gridSet.domainSetup().haveMultipleDomains && gridSet.domainSetup().zones->n != 1)
{
nsp_est_nl = gmx::square(dims.atomDensity / numAtomsCluster)
* nonlocal_vol2(gridSet.domainSetup().zones, ls, r_eff_sup);
}
+ real nsp_est = nsp_est_nl;
if (iloc == InteractionLocality::Local)
{
/* Sub-cell interacts with itself */
- vol_est = ls[XX] * ls[YY] * ls[ZZ];
+ real vol_est = ls[XX] * ls[YY] * ls[ZZ];
/* 6/2 rectangular volume on the faces */
vol_est += (ls[XX] * ls[YY] + ls[XX] * ls[ZZ] + ls[YY] * ls[ZZ]) * r_eff_sup;
/* 12/2 quarter pie slices on the edges */
/* Subtract the non-local pair count */
nsp_est -= nsp_est_nl;
- /* For small cut-offs nsp_est will be an underesimate.
+ /* For small cut-offs nsp_est will be an underestimate.
* With DD nsp_est_nl is an overestimate so nsp_est can get negative.
* So to avoid too small or negative nsp_est we set a minimum of
* all cells interacting with all 3^3 direct neighbors (3^3-1)/2+1=14.
fprintf(debug, "nsp_est local %5.1f non-local %5.1f\n", nsp_est, nsp_est_nl);
}
}
- else
- {
- nsp_est = nsp_est_nl;
- }
/* Thus the (average) maximum j-list size should be as follows.
* Since there is overhead, we shouldn't make the lists too small
{
for (const nbnxn_ci_t& ciEntry : nbl.ci)
{
- fprintf(fp, "ci %4d shift %2d ncj %3d\n", ciEntry.ci, ciEntry.shift,
- ciEntry.cj_ind_end - ciEntry.cj_ind_start);
+ fprintf(fp, "ci %4d shift %2d ncj %3d\n", ciEntry.ci, ciEntry.shift, ciEntry.cj_ind_end - ciEntry.cj_ind_start);
for (int j = ciEntry.cj_ind_start; j < ciEntry.cj_ind_end; j++)
{
}
}
}
- fprintf(fp, "ci %4d shift %2d ncj4 %2d ncp %3d\n", sci.sci, sci.shift,
- sci.numJClusterGroups(), ncp);
+ fprintf(fp, "ci %4d shift %2d ncj4 %2d ncp %3d\n", sci.sci, sci.shift, sci.numJClusterGroups(), ncp);
}
}
int nsci = nblc->sci.size();
int ncj4 = nblc->cj4.size();
int nexcl = nblc->excl.size();
- for (auto& nbl : nbls)
+ for (const auto& nbl : nbls)
{
nsci += nbl.sci.size();
ncj4 += nbl.cj4.size();
/* Each thread should copy its own data to the combined arrays,
* as otherwise data will go back and forth between different caches.
*/
- const int gmx_unused nthreads = gmx_omp_nthreads_get(emntPairsearch);
+ const int gmx_unused nthreads = gmx_omp_nthreads_get(ModuleMultiThread::Pairsearch);
#pragma omp parallel for num_threads(nthreads) schedule(static)
for (gmx::index n = 0; n < nbls.ssize(); n++)
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- for (auto& nbl : nbls)
+ for (const auto& nbl : nbls)
{
nblc->nci_tot += nbl.nci_tot;
}
const int nrj_target = (nrj_tot + numLists - 1) / numLists;
- GMX_ASSERT(gmx_omp_nthreads_get(emntNonbonded) == numLists,
+ GMX_ASSERT(gmx_omp_nthreads_get(ModuleMultiThread::Nonbonded) == numLists,
"We should have as many work objects as FEP lists");
#pragma omp parallel for schedule(static) num_threads(numLists)
if (nri_tot > nbl->maxnri || nrj_tot > nbl->maxnrj)
{
nbl->maxnrj = over_alloc_small(nrj_tot);
- srenew(nbl->jjnr, nbl->maxnrj);
- srenew(nbl->excl_fep, nbl->maxnrj);
+ nbl->jjnr.resize(nbl->maxnrj);
+ nbl->excl_fep.resize(nbl->maxnrj);
}
clear_pairlist_fep(nbl);
for (int i = 0; i < nbls->nri; i++)
{
- int nrj;
-
/* The number of pairs in this i-entry */
- nrj = nbls->jindex[i + 1] - nbls->jindex[i];
+ const int nrj = nbls->jindex[i + 1] - nbls->jindex[i];
/* Decide if list th_dest is too large and we should procede
* to the next destination list.
* is only performed when only 1 out of 8 sub-cells in within range,
* this is because the GPU is much faster than the cpu.
*/
- real bbx, bby;
- real rbb2;
- bbx = 0.5 * (iGridDims.cellSize[XX] + jGridDims.cellSize[XX]);
- bby = 0.5 * (iGridDims.cellSize[YY] + jGridDims.cellSize[YY]);
+ real bbx = 0.5 * (iGridDims.cellSize[XX] + jGridDims.cellSize[XX]);
+ real bby = 0.5 * (iGridDims.cellSize[YY] + jGridDims.cellSize[YY]);
if (!simple)
{
bbx /= c_gpuNumClusterPerCellX;
bby /= c_gpuNumClusterPerCellY;
}
- rbb2 = std::max(0.0, rlist - 0.5 * std::sqrt(bbx * bbx + bby * bby));
- rbb2 = rbb2 * rbb2;
+ real rbb2 = std::max(0.0, rlist - 0.5 * std::sqrt(bbx * bbx + bby * bby));
+ rbb2 = rbb2 * rbb2;
#if !GMX_DOUBLE
return rbb2;
const int ci_block_enum = 5;
const int ci_block_denom = 11;
const int ci_block_min_atoms = 16;
- int ci_block;
/* Here we decide how to distribute the blocks over the threads.
* We use prime numbers to try to avoid that the grid size becomes
*/
GMX_ASSERT(iGrid.dimensions().numCells[XX] > 0, "Grid can't be empty");
GMX_ASSERT(numLists > 0, "We need at least one list");
- ci_block = (iGrid.numCells() * ci_block_enum)
- / (ci_block_denom * iGrid.dimensions().numCells[XX] * numLists);
+ int ci_block = (iGrid.numCells() * ci_block_enum)
+ / (ci_block_denom * iGrid.dimensions().numCells[XX] * numLists);
const int numAtomsPerCell = iGrid.geometry().numAtomsPerCell;
switch (kernelType)
{
case ClusterDistanceKernelType::CpuPlainC:
- makeClusterListSimple(jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal,
- nbat->x().data(), rlist2, rbb2, numDistanceChecks);
+ makeClusterListSimple(
+ jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal, nbat->x().data(), rlist2, rbb2, numDistanceChecks);
break;
#ifdef GMX_NBNXN_SIMD_4XN
case ClusterDistanceKernelType::CpuSimd_4xM:
- makeClusterListSimd4xn(jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal,
- nbat->x().data(), rlist2, rbb2, numDistanceChecks);
+ makeClusterListSimd4xn(
+ jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal, nbat->x().data(), rlist2, rbb2, numDistanceChecks);
break;
#endif
#ifdef GMX_NBNXN_SIMD_2XNN
case ClusterDistanceKernelType::CpuSimd_2xMM:
- makeClusterListSimd2xnn(jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal,
- nbat->x().data(), rlist2, rbb2, numDistanceChecks);
+ makeClusterListSimd2xnn(
+ jGrid, nbl, ci, firstCell, lastCell, excludeSubDiagonal, nbat->x().data(), rlist2, rbb2, numDistanceChecks);
break;
#endif
default: GMX_ASSERT(false, "Unhandled kernel type");
{
for (int cj = firstCell; cj <= lastCell; cj++)
{
- make_cluster_list_supersub(iGrid, jGrid, nbl, ci, cj, excludeSubDiagonal, nbat->xstride,
- nbat->x().data(), rlist2, rbb2, numDistanceChecks);
+ make_cluster_list_supersub(
+ iGrid, jGrid, nbl, ci, cj, excludeSubDiagonal, nbat->xstride, nbat->x().data(), rlist2, rbb2, numDistanceChecks);
}
}
T* nbl,
t_nblist* nbl_fep)
{
- int na_cj_2log;
matrix box;
real rl_fep2 = 0;
- float rbb2;
- int ci_b, ci, ci_x, ci_y, ci_xy;
ivec shp;
- real bx0, bx1, by0, by1, bz0, bz1;
- real bz1_frac;
- real d2cx, d2z, d2z_cx, d2z_cy, d2zx, d2zxy, d2xy;
- int cxf, cxl, cyf, cyf_x, cyl;
- int numDistanceChecks;
int gridi_flag_shift = 0, gridj_flag_shift = 0;
gmx_bitmask_t* gridj_flag = nullptr;
- int ncj_old_i, ncj_old_j;
if (jGrid.geometry().isSimple != pairlistIsSimple(*nbl)
|| iGrid.geometry().isSimple != pairlistIsSimple(*nbl))
sync_work(nbl);
GMX_ASSERT(nbl->na_ci == jGrid.geometry().numAtomsICluster,
"The cluster sizes in the list and grid should match");
- nbl->na_cj = JClusterSizePerListType[pairlistType];
- na_cj_2log = get_2log(nbl->na_cj);
+ nbl->na_cj = JClusterSizePerListType[pairlistType];
+ const int na_cj_2log = get_2log(nbl->na_cj);
nbl->rlist = rlist;
* We should not simply use rlist, since then we would not have
* the small, effective buffering of the NxN lists.
* The buffer is on overestimate, but the resulting cost for pairs
- * beyond rlist is neglible compared to the FEP pairs within rlist.
+ * beyond rlist is negligible compared to the FEP pairs within rlist.
*/
rl_fep2 = nbl->rlist + effective_buffer_1x1_vs_MxN(iGrid, jGrid);
const Grid::Dimensions& iGridDims = iGrid.dimensions();
const Grid::Dimensions& jGridDims = jGrid.dimensions();
- rbb2 = boundingbox_only_distance2(iGridDims, jGridDims, nbl->rlist, pairlistIsSimple(*nbl));
+ const float rbb2 =
+ boundingbox_only_distance2(iGridDims, jGridDims, nbl->rlist, pairlistIsSimple(*nbl));
if (debug)
{
if (debug)
{
- fprintf(debug, "nbl nc_i %d col.av. %.1f ci_block %d\n", iGrid.numCells(),
- iGrid.numCells() / static_cast<double>(iGrid.numColumns()), ci_block);
+ fprintf(debug,
+ "nbl nc_i %d col.av. %.1f ci_block %d\n",
+ iGrid.numCells(),
+ iGrid.numCells() / static_cast<double>(iGrid.numColumns()),
+ ci_block);
}
- numDistanceChecks = 0;
+ int numDistanceChecks = 0;
const real listRangeBBToJCell2 =
gmx::square(listRangeForBoundingBoxToGridCell(rlist, jGrid.dimensions()));
/* Initially ci_b and ci to 1 before where we want them to start,
* as they will both be incremented in next_ci.
*/
- ci_b = -1;
- ci = th * ci_block - 1;
- ci_x = 0;
- ci_y = 0;
+ int ci_b = -1;
+ int ci = th * ci_block - 1;
+ int ci_x = 0;
+ int ci_y = 0;
while (next_ci(iGrid, nth, ci_block, &ci_x, &ci_y, &ci_b, &ci))
{
if (bSimple && flags_i[ci] == 0)
{
continue;
}
- ncj_old_i = getNumSimpleJClustersInList(*nbl);
+ const int ncj_old_i = getNumSimpleJClustersInList(*nbl);
- d2cx = 0;
+ real d2cx = 0;
if (!isIntraGridList && shp[XX] == 0)
{
- if (bSimple)
- {
- bx1 = bb_i[ci].upper.x;
- }
- else
- {
- bx1 = iGridDims.lowerCorner[XX] + (real(ci_x) + 1) * iGridDims.cellSize[XX];
- }
+ const real bx1 =
+ bSimple ? bb_i[ci].upper.x
+ : iGridDims.lowerCorner[XX] + (real(ci_x) + 1) * iGridDims.cellSize[XX];
if (bx1 < jGridDims.lowerCorner[XX])
{
d2cx = gmx::square(jGridDims.lowerCorner[XX] - bx1);
}
}
- ci_xy = ci_x * iGridDims.numCells[YY] + ci_y;
+ int ci_xy = ci_x * iGridDims.numCells[YY] + ci_y;
/* Loop over shift vectors in three dimensions */
for (int tz = -shp[ZZ]; tz <= shp[ZZ]; tz++)
{
const real shz = real(tz) * box[ZZ][ZZ];
- bz0 = bbcz_i[ci].lower + shz;
- bz1 = bbcz_i[ci].upper + shz;
+ real bz0 = bbcz_i[ci].lower + shz;
+ real bz1 = bbcz_i[ci].upper + shz;
- if (tz == 0)
- {
- d2z = 0;
- }
- else if (tz < 0)
+ real d2z = 0;
+ if (tz < 0)
{
d2z = gmx::square(bz1);
}
- else
+ else if (tz > 0)
{
d2z = gmx::square(bz0 - box[ZZ][ZZ]);
}
- d2z_cx = d2z + d2cx;
+ const real d2z_cx = d2z + d2cx;
if (d2z_cx >= rlist2)
{
continue;
}
- bz1_frac = bz1 / real(iGrid.numCellsInColumn(ci_xy));
+ real bz1_frac = bz1 / real(iGrid.numCellsInColumn(ci_xy));
if (bz1_frac < 0)
{
bz1_frac = 0;
{
const real shy = real(ty) * box[YY][YY] + real(tz) * box[ZZ][YY];
- if (bSimple)
- {
- by0 = bb_i[ci].lower.y + shy;
- by1 = bb_i[ci].upper.y + shy;
- }
- else
- {
- by0 = iGridDims.lowerCorner[YY] + (real(ci_y)) * iGridDims.cellSize[YY] + shy;
- by1 = iGridDims.lowerCorner[YY] + (real(ci_y) + 1) * iGridDims.cellSize[YY] + shy;
- }
+ const real by0 = bSimple ? bb_i[ci].lower.y + shy
+ : iGridDims.lowerCorner[YY]
+ + (real(ci_y)) * iGridDims.cellSize[YY] + shy;
+ const real by1 = bSimple ? bb_i[ci].upper.y + shy
+ : iGridDims.lowerCorner[YY]
+ + (real(ci_y) + 1) * iGridDims.cellSize[YY] + shy;
+ int cyf, cyl; //NOLINT(cppcoreguidelines-init-variables)
get_cell_range<YY>(by0, by1, jGridDims, d2z_cx, rlist, &cyf, &cyl);
if (cyf > cyl)
continue;
}
- d2z_cy = d2z;
+ real d2z_cy = d2z;
if (by1 < jGridDims.lowerCorner[YY])
{
d2z_cy += gmx::square(jGridDims.lowerCorner[YY] - by1);
for (int tx = -shp[XX]; tx <= shp[XX]; tx++)
{
- const int shift = XYZ2IS(tx, ty, tz);
+ const int shift = xyzToShiftIndex(tx, ty, tz);
- const bool excludeSubDiagonal = (isIntraGridList && shift == CENTRAL);
+ const bool excludeSubDiagonal = (isIntraGridList && shift == gmx::c_centralShiftIndex);
- if (c_pbcShiftBackward && isIntraGridList && shift > CENTRAL)
+ if (c_pbcShiftBackward && isIntraGridList && shift > gmx::c_centralShiftIndex)
{
continue;
}
const real shx =
real(tx) * box[XX][XX] + real(ty) * box[YY][XX] + real(tz) * box[ZZ][XX];
- if (bSimple)
- {
- bx0 = bb_i[ci].lower.x + shx;
- bx1 = bb_i[ci].upper.x + shx;
- }
- else
- {
- bx0 = iGridDims.lowerCorner[XX] + (real(ci_x)) * iGridDims.cellSize[XX] + shx;
- bx1 = iGridDims.lowerCorner[XX] + (real(ci_x) + 1) * iGridDims.cellSize[XX] + shx;
- }
+ const real bx0 = bSimple ? bb_i[ci].lower.x + shx
+ : iGridDims.lowerCorner[XX]
+ + (real(ci_x)) * iGridDims.cellSize[XX] + shx;
+ const real bx1 = bSimple ? bb_i[ci].upper.x + shx
+ : iGridDims.lowerCorner[XX]
+ + (real(ci_x) + 1) * iGridDims.cellSize[XX] + shx;
+ int cxf, cxl; //NOLINT(cppcoreguidelines-init-variables)
get_cell_range<XX>(bx0, bx1, jGridDims, d2z_cy, rlist, &cxf, &cxl);
if (cxf > cxl)
set_icell_bb(iGrid, ci, shx, shy, shz, nbl->work.get());
- icell_set_x(cell0_i + ci, shx, shy, shz, nbat->xstride, nbat->x().data(),
- kernelType, nbl->work.get());
+ icell_set_x(cell0_i + ci,
+ shx,
+ shy,
+ shz,
+ nbat->xstride,
+ nbat->x().data(),
+ kernelType,
+ nbl->work.get());
for (int cx = cxf; cx <= cxl; cx++)
{
const real cx_real = cx;
- d2zx = d2z;
+ real d2zx = d2z;
if (jGridDims.lowerCorner[XX] + cx_real * jGridDims.cellSize[XX] > bx1)
{
d2zx += gmx::square(jGridDims.lowerCorner[XX]
+ (cx_real + 1) * jGridDims.cellSize[XX] - bx0);
}
- if (isIntraGridList && cx == 0 && (!c_pbcShiftBackward || shift == CENTRAL)
- && cyf < ci_y)
- {
- /* Leave the pairs with i > j.
- * Skip half of y when i and j have the same x.
- */
- cyf_x = ci_y;
- }
- else
- {
- cyf_x = cyf;
- }
+ /* When true, leave the pairs with i > j.
+ * Skip half of y when i and j have the same x.
+ */
+ const bool skipHalfY = (isIntraGridList && cx == 0
+ && (!c_pbcShiftBackward || shift == gmx::c_centralShiftIndex)
+ && cyf < ci_y);
+ const int cyf_x = skipHalfY ? ci_y : cyf;
for (int cy = cyf_x; cy <= cyl; cy++)
{
jGrid.firstCellInColumn(cx * jGridDims.numCells[YY] + cy + 1);
const real cy_real = cy;
- d2zxy = d2zx;
+ real d2zxy = d2zx;
if (jGridDims.lowerCorner[YY] + cy_real * jGridDims.cellSize[YY] > by1)
{
d2zxy += gmx::square(jGridDims.lowerCorner[YY]
midCell = columnEnd - 1;
}
- d2xy = d2zxy - d2z;
+ const real d2xy = d2zxy - d2z;
/* Find the lowest cell that can possibly
* be within range.
/* We want each atom/cell pair only once,
* only use cj >= ci.
*/
- if (!c_pbcShiftBackward || shift == CENTRAL)
+ if (!c_pbcShiftBackward || shift == gmx::c_centralShiftIndex)
{
firstCell = std::max(firstCell, ci);
}
"column");
/* For f buffer flags with simple lists */
- ncj_old_j = getNumSimpleJClustersInList(*nbl);
-
- makeClusterListWrapper(nbl, iGrid, ci, jGrid, firstCell, lastCell,
- excludeSubDiagonal, nbat, rlist2, rbb2,
- kernelType, &numDistanceChecks);
+ const int ncj_old_j = getNumSimpleJClustersInList(*nbl);
+
+ makeClusterListWrapper(nbl,
+ iGrid,
+ ci,
+ jGrid,
+ firstCell,
+ lastCell,
+ excludeSubDiagonal,
+ nbat,
+ rlist2,
+ rbb2,
+ kernelType,
+ &numDistanceChecks);
if (bFBufferFlag)
{
if (!exclusions.empty())
{
/* Set the exclusions for this ci list */
- setExclusionsForIEntry(gridSet, nbl, excludeSubDiagonal, na_cj_2log,
- *getOpenIEntry(nbl), exclusions);
+ setExclusionsForIEntry(
+ gridSet, nbl, excludeSubDiagonal, na_cj_2log, *getOpenIEntry(nbl), exclusions);
}
if (haveFep)
{
- make_fep_list(gridSet.atomIndices(), nbat, nbl, excludeSubDiagonal,
- getOpenIEntry(nbl), shx, shy, shz, rl_fep2, iGrid, jGrid, nbl_fep);
+ make_fep_list(gridSet.atomIndices(),
+ nbat,
+ nbl,
+ excludeSubDiagonal,
+ getOpenIEntry(nbl),
+ shx,
+ shy,
+ shz,
+ rl_fep2,
+ iGrid,
+ jGrid,
+ nbl_fep);
}
/* Close this ci list */
static void print_reduction_cost(gmx::ArrayRef<const gmx_bitmask_t> flags, int nout)
{
- int nelem, nkeep, ncopy, nred, out;
- gmx_bitmask_t mask_0;
+ int nelem = 0;
+ int nkeep = 0;
+ int ncopy = 0;
+ int nred = 0;
- nelem = 0;
- nkeep = 0;
- ncopy = 0;
- nred = 0;
+ gmx_bitmask_t mask_0; // NOLINT(cppcoreguidelines-init-variables)
bitmask_init_bit(&mask_0, 0);
for (const gmx_bitmask_t& flag_mask : flags)
{
else if (!bitmask_is_zero(flag_mask))
{
int c = 0;
- for (out = 0; out < nout; out++)
+ for (int out = 0; out < nout; out++)
{
if (bitmask_is_set(flag_mask, out))
{
const auto numFlags = static_cast<double>(flags.size());
fprintf(debug,
"nbnxn reduction: #flag %zu #list %d elem %4.2f, keep %4.2f copy %4.2f red %4.2f\n",
- flags.size(), nout, nelem / numFlags, nkeep / numFlags, ncopy / numFlags, nred / numFlags);
+ flags.size(),
+ nout,
+ nelem / numFlags,
+ nkeep / numFlags,
+ ncopy / numFlags,
+ nred / numFlags);
}
/* Copies the list entries from src to dest when cjStart <= *cjGlobal < cjEnd.
}
}
-#if defined(__GNUC__) && !defined(__clang__) && !defined(__ICC) && __GNUC__ == 7
+#if defined(__GNUC__) && !defined(__clang__) && __GNUC__ == 7
/* Avoid gcc 7 avx512 loop vectorization bug (actually only needed with -mavx512f) */
# pragma GCC push_options
# pragma GCC optimize("no-tree-vectorize")
return ncjTotal;
}
-#if defined(__GNUC__) && !defined(__clang__) && !defined(__ICC) && __GNUC__ == 7
+#if defined(__GNUC__) && !defined(__clang__) && __GNUC__ == 7
# pragma GCC pop_options
#endif
}
else
{
- copySelectedListRange<false>(srcCi, src, &dest, flag, iFlagShift,
- jFlagShift, t);
+ copySelectedListRange<false>(
+ srcCi, src, &dest, flag, iFlagShift, jFlagShift, t);
}
}
cjGlobal += ncj;
//! Prepares CPU lists produced by the search for dynamic pruning
static void prepareListsForDynamicPruning(gmx::ArrayRef<NbnxnPairlistCpu> lists);
-void PairlistSet::constructPairlists(const Nbnxm::GridSet& gridSet,
+void PairlistSet::constructPairlists(gmx::InteractionLocality locality,
+ const Nbnxm::GridSet& gridSet,
gmx::ArrayRef<PairsearchWork> searchWork,
nbnxn_atomdata_t* nbat,
const ListOfLists<int>& exclusions,
{
const real rlist = params_.rlistOuter;
- int nsubpair_target;
- float nsubpair_tot_est;
- int ci_block;
- gmx_bool progBal;
- int np_tot, np_noq, np_hlj, nap;
-
const int numLists = (isCpuType_ ? cpuLists_.size() : gpuLists_.size());
if (debug)
nbat->bUseBufferFlags = (nbat->out.size() > 1);
/* We should re-init the flags before making the first list */
- if (nbat->bUseBufferFlags && locality_ == InteractionLocality::Local)
+ if (nbat->bUseBufferFlags && locality == InteractionLocality::Local)
{
resizeAndZeroBufferFlags(&nbat->buffer_flags, nbat->numAtoms());
}
+ int nsubpair_target = 0;
+ float nsubpair_tot_est = 0.0F;
if (!isCpuType_ && minimumIlistCountForGpuBalancing > 0)
{
- get_nsubpair_target(gridSet, locality_, rlist, minimumIlistCountForGpuBalancing,
- &nsubpair_target, &nsubpair_tot_est);
- }
- else
- {
- nsubpair_target = 0;
- nsubpair_tot_est = 0;
+ get_nsubpair_target(
+ gridSet, locality, rlist, minimumIlistCountForGpuBalancing, &nsubpair_target, &nsubpair_tot_est);
}
/* Clear all pair-lists */
}
const gmx_domdec_zones_t* ddZones = gridSet.domainSetup().zones;
- GMX_ASSERT(locality_ == InteractionLocality::Local || ddZones != nullptr,
+ GMX_ASSERT(locality == InteractionLocality::Local || ddZones != nullptr,
"Nonlocal interaction locality with null ddZones.");
- const auto iZoneRange = getIZoneRange(gridSet.domainSetup(), locality_);
+ const auto iZoneRange = getIZoneRange(gridSet.domainSetup(), locality);
for (const int iZone : iZoneRange)
{
const Grid& iGrid = gridSet.grids()[iZone];
- const auto jZoneRange = getJZoneRange(ddZones, locality_, iZone);
+ const auto jZoneRange = getJZoneRange(ddZones, locality, iZone);
for (int jZone : jZoneRange)
{
searchCycleCounting->start(enbsCCsearch);
- ci_block = get_ci_block_size(iGrid, gridSet.domainSetup().haveMultipleDomains, numLists);
+ const int ci_block =
+ get_ci_block_size(iGrid, gridSet.domainSetup().haveMultipleDomains, numLists);
/* With GPU: generate progressively smaller lists for
* load balancing for local only or non-local with 2 zones.
*/
- progBal = (locality_ == InteractionLocality::Local || ddZones->n <= 2);
+ const bool progBal = (locality == InteractionLocality::Local || ddZones->n <= 2);
#pragma omp parallel for num_threads(numLists) schedule(static)
for (int th = 0; th < numLists; th++)
/* Divide the i cells equally over the pairlists */
if (isCpuType_)
{
- nbnxn_make_pairlist_part(gridSet, iGrid, jGrid, &work, nbat, exclusions, rlist,
- params_.pairlistType, ci_block, nbat->bUseBufferFlags,
- nsubpair_target, progBal, nsubpair_tot_est, th,
- numLists, &cpuLists_[th], fepListPtr);
+ nbnxn_make_pairlist_part(gridSet,
+ iGrid,
+ jGrid,
+ &work,
+ nbat,
+ exclusions,
+ rlist,
+ params_.pairlistType,
+ ci_block,
+ nbat->bUseBufferFlags,
+ nsubpair_target,
+ progBal,
+ nsubpair_tot_est,
+ th,
+ numLists,
+ &cpuLists_[th],
+ fepListPtr);
}
else
{
- nbnxn_make_pairlist_part(gridSet, iGrid, jGrid, &work, nbat, exclusions, rlist,
- params_.pairlistType, ci_block, nbat->bUseBufferFlags,
- nsubpair_target, progBal, nsubpair_tot_est, th,
- numLists, &gpuLists_[th], fepListPtr);
+ nbnxn_make_pairlist_part(gridSet,
+ iGrid,
+ jGrid,
+ &work,
+ nbat,
+ exclusions,
+ rlist,
+ params_.pairlistType,
+ ci_block,
+ nbat->bUseBufferFlags,
+ nsubpair_target,
+ progBal,
+ nsubpair_tot_est,
+ th,
+ numLists,
+ &gpuLists_[th],
+ fepListPtr);
}
work.cycleCounter.stop();
}
searchCycleCounting->stop(enbsCCsearch);
- np_tot = 0;
- np_noq = 0;
- np_hlj = 0;
+ int np_tot = 0;
+ int np_noq = 0;
+ int np_hlj = 0;
for (int th = 0; th < numLists; th++)
{
inc_nrnb(nrnb, eNR_NBNXN_DIST2, searchWork[th].ndistc);
np_tot += nbl.nci_tot;
}
}
- if (isCpuType_)
- {
- nap = cpuLists_[0].na_ci * cpuLists_[0].na_cj;
- }
- else
- {
- nap = gmx::square(gpuLists_[0].na_ci);
- }
+ const int nap = isCpuType_ ? cpuLists_[0].na_ci * cpuLists_[0].na_cj
+ : gmx::square(gpuLists_[0].na_ci);
+
natpair_ljq_ = (np_tot - np_noq) * nap - np_hlj * nap / 2;
natpair_lj_ = np_noq * nap;
natpair_q_ = np_hlj * nap / 2;
"exclusions should either be empty or the number of lists should match the number of "
"local i-atoms");
- pairlistSet(iLocality).constructPairlists(gridSet, pairSearch->work(), nbat, exclusions,
- minimumIlistCountForGpuBalancing_, nrnb,
+ pairlistSet(iLocality).constructPairlists(iLocality,
+ gridSet,
+ pairSearch->work(),
+ nbat,
+ exclusions,
+ minimumIlistCountForGpuBalancing_,
+ nrnb,
&pairSearch->cycleCounting_);
if (iLocality == InteractionLocality::Local)
void nonbonded_verlet_t::constructPairlist(const InteractionLocality iLocality,
const ListOfLists<int>& exclusions,
int64_t step,
- t_nrnb* nrnb)
+ t_nrnb* nrnb) const
{
pairlistSets_->construct(iLocality, pairSearch_.get(), nbat.get(), exclusions, step, nrnb);
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx_cache_protect_t cp1;
};
-//! Initializes a free-energy pair-list
-void nbnxn_init_pairlist_fep(t_nblist* nl);
-
#endif
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const real* x,
NbnxnPairlistCpuWork* work)
{
- int ia;
real* x_ci_simd = work->iClusterData.xSimd.data();
- ia = xIndexFromCi<NbnxnLayout::Simd2xNN>(ci);
+ const int ia = xIndexFromCi<NbnxnLayout::Simd2xNN>(ci);
store(x_ci_simd + 0 * GMX_SIMD_REAL_WIDTH,
loadU1DualHsimd(x + ia + 0 * c_xStride2xNN + 0) + SimdReal(shx));
/*! \brief SIMD code for checking and adding cluster-pairs to the list using coordinates in packed format.
*
- * Checks bouding box distances and possibly atom pair distances.
+ * Checks bounding box distances and possibly atom pair distances.
* This is an accelerated version of make_cluster_list_simple.
*
* \param[in] jGrid The j-grid
SimdReal rc2_S;
- gmx_bool InRange;
- float d2;
- int xind_f, xind_l;
-
int jclusterFirst = cjFromCi<NbnxnLayout::Simd2xNN, 0>(firstCell);
int jclusterLast = cjFromCi<NbnxnLayout::Simd2xNN, 1>(lastCell);
GMX_ASSERT(jclusterLast >= jclusterFirst,
rc2_S = SimdReal(rlist2);
- InRange = FALSE;
+ bool InRange = false;
while (!InRange && jclusterFirst <= jclusterLast)
{
- d2 = clusterBoundingBoxDistance2(bb_ci[0], jGrid.jBoundingBoxes()[jclusterFirst]);
+ const float d2 = clusterBoundingBoxDistance2(bb_ci[0], jGrid.jBoundingBoxes()[jclusterFirst]);
*numDistanceChecks += 2;
/* Check if the distance is within the distance where
*/
if (d2 < rbb2)
{
- InRange = TRUE;
+ InRange = true;
}
else if (d2 < rlist2)
{
- xind_f = xIndexFromCj<NbnxnLayout::Simd2xNN>(
+ const int xind_f = xIndexFromCj<NbnxnLayout::Simd2xNN>(
cjFromCi<NbnxnLayout::Simd2xNN, 0>(jGrid.cellOffset()) + jclusterFirst);
jx_S = loadDuplicateHsimd(x_j + xind_f + 0 * c_xStride2xNN);
return;
}
- InRange = FALSE;
+ InRange = false;
while (!InRange && jclusterLast > jclusterFirst)
{
- d2 = clusterBoundingBoxDistance2(bb_ci[0], jGrid.jBoundingBoxes()[jclusterLast]);
+ const float d2 = clusterBoundingBoxDistance2(bb_ci[0], jGrid.jBoundingBoxes()[jclusterLast]);
*numDistanceChecks += 2;
/* Check if the distance is within the distance where
*/
if (d2 < rbb2)
{
- InRange = TRUE;
+ InRange = true;
}
else if (d2 < rlist2)
{
- xind_l = xIndexFromCj<NbnxnLayout::Simd2xNN>(
+ const int xind_l = xIndexFromCj<NbnxnLayout::Simd2xNN>(
cjFromCi<NbnxnLayout::Simd2xNN, 0>(jGrid.cellOffset()) + jclusterLast);
jx_S = loadDuplicateHsimd(x_j + xind_l + 0 * c_xStride2xNN);
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const real* x,
NbnxnPairlistCpuWork* work)
{
- int ia;
real* x_ci_simd = work->iClusterData.xSimd.data();
- ia = xIndexFromCi<NbnxnLayout::Simd4xN>(ci);
+ const int ia = xIndexFromCi<NbnxnLayout::Simd4xN>(ci);
store(x_ci_simd + 0 * GMX_SIMD_REAL_WIDTH, SimdReal(x[ia + 0 * c_xStride4xN] + shx));
store(x_ci_simd + 1 * GMX_SIMD_REAL_WIDTH, SimdReal(x[ia + 1 * c_xStride4xN] + shy));
/*! \brief SIMD code for checking and adding cluster-pairs to the list using coordinates in packed format.
*
- * Checks bouding box distances and possibly atom pair distances.
+ * Checks bounding box distances and possibly atom pair distances.
* This is an accelerated version of make_cluster_list_simple.
*
* \param[in] jGrid The j-grid
SimdReal rc2_S;
- gmx_bool InRange;
- float d2;
- int xind_f, xind_l;
-
/* Convert the j-range from i-cluster size indexing to j-cluster indexing */
int jclusterFirst = cjFromCi<NbnxnLayout::Simd4xN, 0>(firstCell);
int jclusterLast = cjFromCi<NbnxnLayout::Simd4xN, 1>(lastCell);
rc2_S = SimdReal(rlist2);
- InRange = FALSE;
+ bool InRange = false;
while (!InRange && jclusterFirst <= jclusterLast)
{
- d2 = clusterBoundingBoxDistance2(bb_ci[0], jGrid.jBoundingBoxes()[jclusterFirst]);
+ const float d2 = clusterBoundingBoxDistance2(bb_ci[0], jGrid.jBoundingBoxes()[jclusterFirst]);
*numDistanceChecks += 2;
/* Check if the distance is within the distance where
*/
if (d2 < rbb2)
{
- InRange = TRUE;
+ InRange = true;
}
else if (d2 < rlist2)
{
- xind_f = xIndexFromCj<NbnxnLayout::Simd4xN>(
+ const int xind_f = xIndexFromCj<NbnxnLayout::Simd4xN>(
cjFromCi<NbnxnLayout::Simd4xN, 0>(jGrid.cellOffset()) + jclusterFirst);
jx_S = load<SimdReal>(x_j + xind_f + 0 * c_xStride4xN);
return;
}
- InRange = FALSE;
+ InRange = false;
while (!InRange && jclusterLast > jclusterFirst)
{
- d2 = clusterBoundingBoxDistance2(bb_ci[0], jGrid.jBoundingBoxes()[jclusterLast]);
+ const float d2 = clusterBoundingBoxDistance2(bb_ci[0], jGrid.jBoundingBoxes()[jclusterLast]);
*numDistanceChecks += 2;
/* Check if the distance is within the distance where
*/
if (d2 < rbb2)
{
- InRange = TRUE;
+ InRange = true;
}
else if (d2 < rlist2)
{
- xind_l = xIndexFromCj<NbnxnLayout::Simd4xN>(
+ const int xind_l = xIndexFromCj<NbnxnLayout::Simd4xN>(
cjFromCi<NbnxnLayout::Simd4xN, 0>(jGrid.cellOffset()) + jclusterLast);
jx_S = load<SimdReal>(x_j + xind_l + 0 * c_xStride4xN);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
static bool supportsDynamicPairlistGenerationInterval(const t_inputrec& ir)
{
- return ir.cutoff_scheme == ecutsVERLET && EI_DYNAMICS(ir.eI)
- && !(EI_MD(ir.eI) && ir.etc == etcNO) && ir.verletbuf_tol > 0;
+ return ir.cutoff_scheme == CutoffScheme::Verlet && EI_DYNAMICS(ir.eI)
+ && !(EI_MD(ir.eI) && ir.etc == TemperatureCoupling::No) && ir.verletbuf_tol > 0;
}
/*! \brief Cost of non-bonded kernels
return;
}
- float listfac_ok, listfac_max;
- int nstlist_orig, nstlist_prev;
- real rlist_inc, rlist_ok, rlist_max;
- real rlist_new, rlist_prev;
size_t nstlist_ind = 0;
- gmx_bool bBox, bDD, bCont;
const char* nstl_gpu =
"\nFor optimal performance with a GPU nstlist (now %d) should be larger.\nThe "
"optimum depends on your CPU and GPU resources.\nYou might want to try several "
}
}
- if (EI_MD(ir->eI) && ir->etc == etcNO)
+ if (EI_MD(ir->eI) && ir->etc == TemperatureCoupling::No)
{
if (MASTER(cr))
{
"In all cases that do not support dynamic nstlist, we should have returned "
"with an appropriate message above");
- if (useOrEmulateGpuForNonbondeds)
- {
- listfac_ok = c_nbnxnListSizeFactorGPU;
- }
- else if (cpuinfo.brandString().find("Xeon Phi") != std::string::npos)
- {
- listfac_ok = c_nbnxnListSizeFactorIntelXeonPhi;
- }
- else
- {
- listfac_ok = c_nbnxnListSizeFactorCpu;
- }
- listfac_max = listfac_ok + c_nbnxnListSizeFactorMargin;
+ const bool runningOnXeonPhi = (cpuinfo.brandString().find("Xeon Phi") != std::string::npos);
+ const float listfac_ok = useOrEmulateGpuForNonbondeds
+ ? c_nbnxnListSizeFactorGPU
+ : runningOnXeonPhi ? c_nbnxnListSizeFactorIntelXeonPhi
+ : c_nbnxnListSizeFactorCpu;
+ float listfac_max = listfac_ok + c_nbnxnListSizeFactorMargin;
- nstlist_orig = ir->nstlist;
+ const int nstlist_orig = ir->nstlist;
if (nstlist_cmdline > 0)
{
if (fp)
/* Allow rlist to make the list a given factor larger than the list
* would be with the reference value for nstlist (10*mtsFactor).
*/
- nstlist_prev = ir->nstlist;
- ir->nstlist = nbnxnReferenceNstlist * mtsFactor;
+ int nstlist_prev = ir->nstlist;
+ ir->nstlist = nbnxnReferenceNstlist * mtsFactor;
const real rlistWithReferenceNstlist =
calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, -1, listSetup);
ir->nstlist = nstlist_prev;
/* Determine the pair list size increase due to zero interactions */
- rlist_inc = nbnxn_get_rlist_effective_inc(listSetup.cluster_size_j, mtop->natoms / det(box));
- rlist_ok = (rlistWithReferenceNstlist + rlist_inc) * std::cbrt(listfac_ok) - rlist_inc;
- rlist_max = (rlistWithReferenceNstlist + rlist_inc) * std::cbrt(listfac_max) - rlist_inc;
+ real rlist_inc = nbnxn_get_rlist_effective_inc(listSetup.cluster_size_j, mtop->natoms / det(box));
+ real rlist_ok = (rlistWithReferenceNstlist + rlist_inc) * std::cbrt(listfac_ok) - rlist_inc;
+ real rlist_max = (rlistWithReferenceNstlist + rlist_inc) * std::cbrt(listfac_max) - rlist_inc;
if (debug)
{
- fprintf(debug, "nstlist tuning: rlist_inc %.3f rlist_ok %.3f rlist_max %.3f\n", rlist_inc,
- rlist_ok, rlist_max);
+ fprintf(debug, "nstlist tuning: rlist_inc %.3f rlist_ok %.3f rlist_max %.3f\n", rlist_inc, rlist_ok, rlist_max);
}
- nstlist_prev = nstlist_orig;
- rlist_prev = ir->rlist;
+ nstlist_prev = nstlist_orig;
+ real rlist_prev = ir->rlist;
+ real rlist_new = 0;
+ bool bBox = false, bDD = false, bCont = false;
do
{
if (nstlist_cmdline <= 0)
}
/* Set the pair-list buffer size in ir */
- rlist_new = calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - mtsFactor,
- -1, listSetup);
+ rlist_new = calcVerletBufferSize(
+ *mtop, det(box), *ir, ir->nstlist, ir->nstlist - mtsFactor, -1, listSetup);
/* Does rlist fit in the box? */
bBox = (gmx::square(rlist_new) < max_cutoff2(ir->pbcType, box));
- bDD = TRUE;
+ bDD = true;
if (bBox && DOMAINDECOMP(cr))
{
/* Currently (as of July 2020), the code in this if clause is never executed.
if (debug)
{
- fprintf(debug, "nstlist %d rlist %.3f bBox %s bDD %s\n", ir->nstlist, rlist_new,
- gmx::boolToString(bBox), gmx::boolToString(bDD));
+ fprintf(debug,
+ "nstlist %d rlist %.3f bBox %s bDD %s\n",
+ ir->nstlist,
+ rlist_new,
+ gmx::boolToString(bBox),
+ gmx::boolToString(bDD));
}
- bCont = FALSE;
+ bCont = false;
if (nstlist_cmdline <= 0)
{
/* Stick with the previous nstlist */
ir->nstlist = nstlist_prev;
rlist_new = rlist_prev;
- bBox = TRUE;
- bDD = TRUE;
+ bBox = true;
+ bDD = true;
}
}
}
else if (ir->nstlist != nstlist_orig || rlist_new != ir->rlist)
{
- sprintf(buf, "Changing nstlist from %d to %d, rlist from %g to %g", nstlist_orig,
- ir->nstlist, ir->rlist, rlist_new);
+ sprintf(buf,
+ "Changing nstlist from %d to %d, rlist from %g to %g",
+ nstlist_orig,
+ ir->nstlist,
+ ir->rlist,
+ rlist_new);
if (MASTER(cr))
{
fprintf(stderr, "%s\n\n", buf);
/*! \brief Set the dynamic pairlist pruning parameters in \p ic
*
- * \param[in] ir The input parameter record
+ * \param[in] inputrec The input parameter record
* \param[in] mtop The global topology
* \param[in] box The unit cell
* \param[in] useGpuList Tells if we are using a GPU type pairlist
* \param[in] listSetup The nbnxn pair list setup
* \param[in] userSetNstlistPrune The user set ic->nstlistPrune (using an env.var.)
- * \param[in] ic The nonbonded interactions constants
+ * \param[in] interactionConst The nonbonded interactions constants
* \param[in,out] listParams The list setup parameters
*/
-static void setDynamicPairlistPruningParameters(const t_inputrec* ir,
- const gmx_mtop_t* mtop,
+static void setDynamicPairlistPruningParameters(const t_inputrec& inputrec,
+ const gmx_mtop_t& mtop,
const matrix box,
const bool useGpuList,
const VerletbufListSetup& listSetup,
const bool userSetNstlistPrune,
- const interaction_const_t* ic,
+ const interaction_const_t& interactionConst,
PairlistParams* listParams)
{
/* When applying multiple time stepping to the non-bonded forces,
* we only compute them every mtsFactor steps, so all parameters here
* should be a multiple of mtsFactor.
*/
- listParams->mtsFactor = gmx::nonbondedMtsFactor(*ir);
+ listParams->mtsFactor = gmx::nonbondedMtsFactor(inputrec);
const int mtsFactor = listParams->mtsFactor;
- GMX_RELEASE_ASSERT(ir->nstlist % mtsFactor == 0, "nstlist should be a multiple of mtsFactor");
+ GMX_RELEASE_ASSERT(inputrec.nstlist % mtsFactor == 0,
+ "nstlist should be a multiple of mtsFactor");
- listParams->lifetime = ir->nstlist - mtsFactor;
+ listParams->lifetime = inputrec.nstlist - mtsFactor;
/* When nstlistPrune was set by the user, we need to execute one loop
* iteration to determine rlistInner.
* Otherwise we compute rlistInner and increase nstlist as long as
* we have a pairlist buffer of length 0 (i.e. rlistInner == cutoff).
*/
- const real interactionCutoff = std::max(ic->rcoulomb, ic->rvdw);
+ const real interactionCutoff = std::max(interactionConst.rcoulomb, interactionConst.rvdw);
int tunedNstlistPrune = listParams->nstlistPrune;
do
{
*/
int listLifetime = tunedNstlistPrune - (useGpuList ? 0 : mtsFactor);
listParams->nstlistPrune = tunedNstlistPrune;
- listParams->rlistInner = calcVerletBufferSize(*mtop, det(box), *ir, tunedNstlistPrune,
- listLifetime, -1, listSetup);
+ listParams->rlistInner = calcVerletBufferSize(
+ mtop, det(box), inputrec, tunedNstlistPrune, listLifetime, -1, listSetup);
/* On the GPU we apply the dynamic pruning in a rolling fashion
* every c_nbnxnGpuRollingListPruningInterval steps,
* so keep nstlistPrune a multiple of the interval.
*/
tunedNstlistPrune += (useGpuList ? c_nbnxnGpuRollingListPruningInterval : 1) * mtsFactor;
- } while (!userSetNstlistPrune && tunedNstlistPrune < ir->nstlist
+ } while (!userSetNstlistPrune && tunedNstlistPrune < inputrec.nstlist
&& listParams->rlistInner == interactionCutoff);
if (userSetNstlistPrune)
else
{
/* Determine the pair list size increase due to zero interactions */
- real rlistInc = nbnxn_get_rlist_effective_inc(listSetup.cluster_size_j, mtop->natoms / det(box));
+ real rlistInc = nbnxn_get_rlist_effective_inc(listSetup.cluster_size_j, mtop.natoms / det(box));
/* Dynamic pruning is only useful when the inner list is smaller than
* the outer. The factor 0.99 ensures at least 3% list size reduction.
std::string nstListFormat =
"%" + gmx::formatString("%zu", gmx::formatString("%d", nstListForSpacing).size()) + "d";
listSetup += gmx::formatString(nstListFormat.c_str(), nstList);
- listSetup += gmx::formatString(" steps, buffer %.3f nm, rlist %.3f nm\n",
- rList - interactionCutoff, rList);
+ listSetup += gmx::formatString(
+ " steps, buffer %.3f nm, rlist %.3f nm\n", rList - interactionCutoff, rList);
return listSetup;
}
void setupDynamicPairlistPruning(const gmx::MDLogger& mdlog,
- const t_inputrec* ir,
- const gmx_mtop_t* mtop,
+ const t_inputrec& inputrec,
+ const gmx_mtop_t& mtop,
matrix box,
- const interaction_const_t* ic,
+ const interaction_const_t& interactionConst,
PairlistParams* listParams)
{
GMX_RELEASE_ASSERT(listParams->rlistOuter > 0, "With the nbnxn setup rlist should be > 0");
JClusterSizePerListType[listParams->pairlistType] };
/* Currently emulation mode does not support dual pair-lists */
- const bool useGpuList = (listParams->pairlistType == PairlistType::HierarchicalNxN);
+ const bool useGpuList = sc_isGpuPairListType[listParams->pairlistType];
- if (supportsDynamicPairlistGenerationInterval(*ir) && getenv("GMX_DISABLE_DYNAMICPRUNING") == nullptr)
+ if (supportsDynamicPairlistGenerationInterval(inputrec) && getenv("GMX_DISABLE_DYNAMICPRUNING") == nullptr)
{
/* Note that nstlistPrune can have any value independently of nstlist.
* Actually applying rolling pruning is only useful when
if (userSetNstlistPrune)
{
- char* end;
+ char* end = nullptr;
listParams->nstlistPrune = strtol(env, &end, 10);
if (!end || (*end != 0)
- || !(listParams->nstlistPrune > 0 && listParams->nstlistPrune < ir->nstlist))
+ || !(listParams->nstlistPrune > 0 && listParams->nstlistPrune < inputrec.nstlist))
{
gmx_fatal(FARGS,
"Invalid value passed in GMX_NSTLIST_DYNAMICPRUNING=%s, should be > 0 "
listParams->nstlistPrune = c_nbnxnDynamicListPruningMinLifetime;
}
- setDynamicPairlistPruningParameters(ir, mtop, box, useGpuList, ls, userSetNstlistPrune, ic,
- listParams);
+ setDynamicPairlistPruningParameters(
+ inputrec, mtop, box, useGpuList, ls, userSetNstlistPrune, interactionConst, listParams);
if (listParams->useDynamicPruning && useGpuList)
{
* rolling pruning interval slightly shorter than nstlistTune,
* thus giving correct results, but a slightly lower efficiency.
*/
- GMX_RELEASE_ASSERT(listParams->nstlistPrune >= c_nbnxnGpuRollingListPruningInterval, ("With dynamic list pruning on GPUs pruning frequency must be at least as large as the rolling pruning interval ("
- + std::to_string(c_nbnxnGpuRollingListPruningInterval)
- + ").")
- .c_str());
+ GMX_RELEASE_ASSERT(listParams->nstlistPrune >= c_nbnxnGpuRollingListPruningInterval,
+ ("With dynamic list pruning on GPUs pruning frequency must be at "
+ "least as large as the rolling pruning interval ("
+ + std::to_string(c_nbnxnGpuRollingListPruningInterval) + ").")
+ .c_str());
listParams->numRollingPruningParts =
listParams->nstlistPrune / c_nbnxnGpuRollingListPruningInterval;
}
std::string mesg;
- const real interactionCutoff = std::max(ic->rcoulomb, ic->rvdw);
+ const real interactionCutoff = std::max(interactionConst.rcoulomb, interactionConst.rvdw);
if (listParams->useDynamicPruning)
{
mesg += gmx::formatString(
- "Using a dual %dx%d pair-list setup updated with dynamic%s pruning:\n", ls.cluster_size_i,
- ls.cluster_size_j, listParams->numRollingPruningParts > 1 ? ", rolling" : "");
- mesg += formatListSetup("outer", ir->nstlist, ir->nstlist, listParams->rlistOuter, interactionCutoff);
- mesg += formatListSetup("inner", listParams->nstlistPrune, ir->nstlist,
- listParams->rlistInner, interactionCutoff);
+ "Using a dual %dx%d pair-list setup updated with dynamic%s pruning:\n",
+ ls.cluster_size_i,
+ ls.cluster_size_j,
+ listParams->numRollingPruningParts > 1 ? ", rolling" : "");
+ mesg += formatListSetup(
+ "outer", inputrec.nstlist, inputrec.nstlist, listParams->rlistOuter, interactionCutoff);
+ mesg += formatListSetup(
+ "inner", listParams->nstlistPrune, inputrec.nstlist, listParams->rlistInner, interactionCutoff);
}
else
{
mesg += gmx::formatString("Using a %dx%d pair-list setup:\n", ls.cluster_size_i, ls.cluster_size_j);
- mesg += formatListSetup("", ir->nstlist, ir->nstlist, listParams->rlistOuter, interactionCutoff);
+ mesg += formatListSetup(
+ "", inputrec.nstlist, inputrec.nstlist, listParams->rlistOuter, interactionCutoff);
}
- if (supportsDynamicPairlistGenerationInterval(*ir))
+ if (supportsDynamicPairlistGenerationInterval(inputrec))
{
const VerletbufListSetup listSetup1x1 = { 1, 1 };
- const real rlistOuter = calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist,
- ir->nstlist - 1, -1, listSetup1x1);
- real rlistInner = rlistOuter;
+ const real rlistOuter = calcVerletBufferSize(
+ mtop, det(box), inputrec, inputrec.nstlist, inputrec.nstlist - 1, -1, listSetup1x1);
+ real rlistInner = rlistOuter;
if (listParams->useDynamicPruning)
{
int listLifeTime = listParams->nstlistPrune - (useGpuList ? 0 : 1);
- rlistInner = calcVerletBufferSize(*mtop, det(box), *ir, listParams->nstlistPrune,
- listLifeTime, -1, listSetup1x1);
+ rlistInner = calcVerletBufferSize(
+ mtop, det(box), inputrec, listParams->nstlistPrune, listLifeTime, -1, listSetup1x1);
}
mesg += gmx::formatString(
"At tolerance %g kJ/mol/ps per atom, equivalent classical 1x1 list would be:\n",
- ir->verletbuf_tol);
+ inputrec.verletbuf_tol);
if (listParams->useDynamicPruning)
{
- mesg += formatListSetup("outer", ir->nstlist, ir->nstlist, rlistOuter, interactionCutoff);
- mesg += formatListSetup("inner", listParams->nstlistPrune, ir->nstlist, rlistInner,
- interactionCutoff);
+ mesg += formatListSetup(
+ "outer", inputrec.nstlist, inputrec.nstlist, rlistOuter, interactionCutoff);
+ mesg += formatListSetup(
+ "inner", listParams->nstlistPrune, inputrec.nstlist, rlistInner, interactionCutoff);
}
else
{
- mesg += formatListSetup("", ir->nstlist, ir->nstlist, rlistOuter, interactionCutoff);
+ mesg += formatListSetup("", inputrec.nstlist, inputrec.nstlist, rlistOuter, interactionCutoff);
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2017,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*! \brief Set up the dynamic pairlist pruning
*
* \param[in,out] mdlog MD logger
- * \param[in] ir The input parameter record
+ * \param[in] inputrec The input parameter record
* \param[in] mtop The global topology
* \param[in] box The unit cell
- * \param[in] ic The nonbonded interactions constants
+ * \param[in] interactionConst The nonbonded interactions constants
* \param[in,out] listParams The list setup parameters
*/
void setupDynamicPairlistPruning(const gmx::MDLogger& mdlog,
- const t_inputrec* ir,
- const gmx_mtop_t* mtop,
+ const t_inputrec& inputrec,
+ const gmx_mtop_t& mtop,
matrix box,
- const interaction_const_t* ic,
+ const interaction_const_t& interactionConst,
PairlistParams* listParams);
#endif /* NBNXM_PAIRLIST_TUNING_H */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! The i-cluster size for CPU kernels, always 4 atoms
static constexpr int c_nbnxnCpuIClusterSize = 4;
-//! The i- and j-cluster size for GPU lists, 8 atoms for CUDA, set at compile time for OpenCL
-#if GMX_GPU_OPENCL
-static constexpr int c_nbnxnGpuClusterSize = GMX_OPENCL_NB_CLUSTER_SIZE;
+//! The i- and j-cluster size for GPU lists, 8 atoms for CUDA, set at compile time for OpenCL and SYCL
+#if GMX_GPU_OPENCL || GMX_GPU_SYCL
+static constexpr int c_nbnxnGpuClusterSize = GMX_GPU_NB_CLUSTER_SIZE;
#else
static constexpr int c_nbnxnGpuClusterSize = 8;
#endif
static constexpr gmx::EnumerationArray<PairlistType, int> JClusterSizePerListType = {
{ 2, 4, 8, c_nbnxnGpuClusterSize }
};
+//! True if given pairlist type is used on GPU, false if on CPU.
+static constexpr gmx::EnumerationArray<PairlistType, bool> sc_isGpuPairListType = {
+ { false, false, false, true }
+};
/*! \internal
* \brief The setup for generating and pruning the nbnxn pair list.
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
public:
//! Constructor: initializes the pairlist set as empty
- PairlistSet(gmx::InteractionLocality locality, const PairlistParams& listParams);
+ PairlistSet(const PairlistParams& listParams);
~PairlistSet();
//! Constructs the pairlists in the set using the coordinates in \p nbat
- void constructPairlists(const Nbnxm::GridSet& gridSet,
+ void constructPairlists(gmx::InteractionLocality locality,
+ const Nbnxm::GridSet& gridSet,
gmx::ArrayRef<PairsearchWork> searchWork,
nbnxn_atomdata_t* nbat,
const gmx::ListOfLists<int>& exclusions,
SearchCycleCounting* searchCycleCounting);
//! Dispatch the kernel for dynamic pairlist pruning
- void dispatchPruneKernel(const nbnxn_atomdata_t* nbat, const rvec* shift_vec);
-
- //! Returns the locality
- gmx::InteractionLocality locality() const { return locality_; }
+ void dispatchPruneKernel(const nbnxn_atomdata_t* nbat, gmx::ArrayRef<const gmx::RVec> shift_vec);
//! Returns the lists of CPU pairlists
gmx::ArrayRef<const NbnxnPairlistCpu> cpuLists() const { return cpuLists_; }
gmx::ArrayRef<const std::unique_ptr<t_nblist>> fepLists() const { return fepLists_; }
private:
- //! The locality of the pairlist set
- gmx::InteractionLocality locality_;
//! List of pairlists in CPU layout
std::vector<NbnxnPairlistCpu> cpuLists_;
//! List of working list for rebalancing CPU lists
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
t_nrnb* nrnb);
//! Dispatches the dynamic pruning kernel for the given locality
- void dispatchPruneKernel(gmx::InteractionLocality iLocality,
- const nbnxn_atomdata_t* nbat,
- const rvec* shift_vec);
+ void dispatchPruneKernel(gmx::InteractionLocality iLocality,
+ const nbnxn_atomdata_t* nbat,
+ gmx::ArrayRef<const gmx::RVec> shift_vec);
//! Returns the pair list parameters
const PairlistParams& params() const { return params_; }
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! Working data for the actual i-supercell during pair search \internal
struct NbnxnPairlistCpuWork
{
- //! Struct for storing coordinats and bounding box for an i-entry during search \internal
+ //! Struct for storing coordinates and bounding box for an i-entry during search \internal
struct IClusterData
{
IClusterData() :
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "pairsearch.h"
#include "gromacs/mdtypes/nblist.h"
-#include "gromacs/utility/smalloc.h"
#include "pairlist.h"
void SearchCycleCounting::printCycles(FILE* fp, gmx::ArrayRef<const PairsearchWork> work) const
{
fprintf(fp, "\n");
- fprintf(fp, "ns %4d grid %4.1f search %4.1f", cc_[enbsCCgrid].count(),
- cc_[enbsCCgrid].averageMCycles(), cc_[enbsCCsearch].averageMCycles());
+ fprintf(fp,
+ "ns %4d grid %4.1f search %4.1f",
+ cc_[enbsCCgrid].count(),
+ cc_[enbsCCgrid].averageMCycles(),
+ cc_[enbsCCsearch].averageMCycles());
if (work.size() > 1)
{
fprintf(fp, "\n");
}
-/*! \brief Frees the contents of a legacy t_nblist struct */
-static void free_nblist(t_nblist* nl)
-{
- sfree(nl->iinr);
- sfree(nl->gid);
- sfree(nl->shift);
- sfree(nl->jindex);
- sfree(nl->jjnr);
- sfree(nl->excl_fep);
-}
-
#ifndef DOXYGEN
-PairsearchWork::PairsearchWork() : cp0({ { 0 } }), ndistc(0), nbl_fep(new t_nblist), cp1({ { 0 } })
+PairsearchWork::PairsearchWork() :
+ cp0({ { 0 } }),
+ ndistc(0),
+ nbl_fep(std::make_unique<t_nblist>()),
+ cp1({ { 0 } })
{
- nbnxn_init_pairlist_fep(nbl_fep.get());
}
#endif // !DOXYGEN
-PairsearchWork::~PairsearchWork()
-{
- free_nblist(nbl_fep.get());
-}
+PairsearchWork::~PairsearchWork() = default;
PairSearch::PairSearch(const PbcType pbcType,
const bool doTestParticleInsertion,
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* The PairSearch class holds the domain setup, the search grids
* and helper object for the pair search. It manages the search work.
- * The actual gridding and pairlist generation is performeed by the
+ * The actual gridding and pairlist generation is performed by the
* GridSet/Grid and PairlistSet/Pairlist classes, respectively.
*
* \author Berk Hess <hess@kth.se>
#include <memory>
#include <vector>
-#include "gromacs/domdec/domdec.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/nbnxm/atomdata.h"
#include "gromacs/timing/cyclecounter.h"
~PairsearchWork();
- //! Buffer to avoid cache polution
+ //! Buffer to avoid cache pollution
gmx_cache_protect_t cp0;
//! Temporary buffer for sorting atoms within a grid column
{
cycleCounting_.start(enbsCCgrid);
- gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
- atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
+ gridSet_.putOnGrid(box,
+ ddZone,
+ lowerCorner,
+ upperCorner,
+ updateGroupsCog,
+ atomRange,
+ atomDensity,
+ atomInfo,
+ x,
+ numAtomsMoved,
+ move,
+ nbat);
cycleCounting_.stop(enbsCCgrid);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020 by the GROMACS development team.
+ * Copyright (c) 2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void PairlistSets::dispatchPruneKernel(const gmx::InteractionLocality iLocality,
const nbnxn_atomdata_t* nbat,
- const rvec* shift_vec)
+ gmx::ArrayRef<const gmx::RVec> shift_vec)
{
pairlistSet(iLocality).dispatchPruneKernel(nbat, shift_vec);
}
-void PairlistSet::dispatchPruneKernel(const nbnxn_atomdata_t* nbat, const rvec* shift_vec)
+void PairlistSet::dispatchPruneKernel(const nbnxn_atomdata_t* nbat, gmx::ArrayRef<const gmx::RVec> shift_vec)
{
const real rlistInner = params_.rlistInner;
GMX_ASSERT(cpuLists_[0].ciOuter.size() >= cpuLists_[0].ci.size(),
"Here we should either have an empty ci list or ciOuter should be >= ci");
- int gmx_unused nthreads = gmx_omp_nthreads_get(emntNonbonded);
+ int gmx_unused nthreads = gmx_omp_nthreads_get(ModuleMultiThread::Nonbonded);
GMX_ASSERT(nthreads == static_cast<gmx::index>(cpuLists_.size()),
"The number of threads should match the number of lists");
#pragma omp parallel for schedule(static) num_threads(nthreads)
}
}
-void nonbonded_verlet_t::dispatchPruneKernelCpu(const gmx::InteractionLocality iLocality, const rvec* shift_vec)
+void nonbonded_verlet_t::dispatchPruneKernelCpu(const gmx::InteractionLocality iLocality,
+ gmx::ArrayRef<const gmx::RVec> shift_vec) const
{
pairlistSets_->dispatchPruneKernel(iLocality, nbat.get(), shift_vec);
}
void nonbonded_verlet_t::dispatchPruneKernelGpu(int64_t step)
{
- wallcycle_start_nocount(wcycle_, ewcLAUNCH_GPU);
- wallcycle_sub_start_nocount(wcycle_, ewcsLAUNCH_GPU_NONBONDED);
+ wallcycle_start_nocount(wcycle_, WallCycleCounter::LaunchGpu);
+ wallcycle_sub_start_nocount(wcycle_, WallCycleSubCounter::LaunchGpuNonBonded);
const bool stepIsEven =
(pairlistSets().numStepsWithPairlist(step) % (2 * pairlistSets().params().mtsFactor) == 0);
Nbnxm::gpu_launch_kernel_pruneonly(
- gpu_nbv, stepIsEven ? gmx::InteractionLocality::Local : gmx::InteractionLocality::NonLocal,
+ gpu_nbv,
+ stepIsEven ? gmx::InteractionLocality::Local : gmx::InteractionLocality::NonLocal,
pairlistSets().params().numRollingPruningParts);
- wallcycle_sub_stop(wcycle_, ewcsLAUNCH_GPU_NONBONDED);
- wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
+ wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchGpuNonBonded);
+ wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
}
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-set(CMAKE_SYSTEM_NAME Linux)
-set(CMAKE_SYSTEM_PROCESSOR XeonPhi)
-if(NOT GMX_MPI)
- set(CMAKE_C_COMPILER "icc")
- set(CMAKE_CXX_COMPILER "icpc")
-else()
- set(CMAKE_C_COMPILER "mpiicc") #FindMPI doesn't work (#14991)
- set(CMAKE_CXX_COMPILER "mpiicpc")
+if (GMX_GPU_SYCL)
+ file(GLOB NBNXM_SYCL_SOURCES *.cpp)
+ set(NBNXM_SOURCES ${NBNXM_SOURCES} ${NBNXM_SYCL_SOURCES} PARENT_SCOPE)
+ _gmx_add_files_to_property(SYCL_SOURCES ${NBNXM_SYCL_SOURCES})
endif()
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief
+ * Data management and kernel launch functions for nbnxm sycl.
+ *
+ * \ingroup module_nbnxm
+ */
+#include "gmxpre.h"
+
+#include "gromacs/nbnxm/gpu_common.h"
+#include "gromacs/utility/exceptions.h"
+
+#include "nbnxm_sycl_kernel.h"
+#include "nbnxm_sycl_kernel_pruneonly.h"
+#include "nbnxm_sycl_types.h"
+
+namespace Nbnxm
+{
+
+void gpu_launch_kernel_pruneonly(NbnxmGpu* nb, const InteractionLocality iloc, const int numParts)
+{
+ gpu_plist* plist = nb->plist[iloc];
+
+ if (plist->haveFreshList)
+ {
+ GMX_ASSERT(numParts == 1, "With first pruning we expect 1 part");
+
+ /* Set rollingPruningNumParts to signal that it is not set */
+ plist->rollingPruningNumParts = 0;
+ plist->rollingPruningPart = 0;
+ }
+ else
+ {
+ if (plist->rollingPruningNumParts == 0)
+ {
+ plist->rollingPruningNumParts = numParts;
+ }
+ else
+ {
+ GMX_ASSERT(numParts == plist->rollingPruningNumParts,
+ "It is not allowed to change numParts in between list generation steps");
+ }
+ }
+
+ /* Use a local variable for part and update in plist, so we can return here
+ * without duplicating the part increment code.
+ */
+ const int part = plist->rollingPruningPart;
+
+ plist->rollingPruningPart++;
+ if (plist->rollingPruningPart >= plist->rollingPruningNumParts)
+ {
+ plist->rollingPruningPart = 0;
+ }
+
+ /* Compute the number of list entries to prune in this pass */
+ const int numSciInPart = (plist->nsci - part) / numParts;
+
+ /* Don't launch the kernel if there is no work to do */
+ if (numSciInPart <= 0)
+ {
+ plist->haveFreshList = false;
+ return;
+ }
+
+ launchNbnxmKernelPruneOnly(nb, iloc, numParts, part, numSciInPart);
+
+ if (plist->haveFreshList)
+ {
+ plist->haveFreshList = false;
+ nb->didPrune[iloc] = true; // Mark that pruning has been done
+ }
+ else
+ {
+ nb->didRollingPrune[iloc] = true; // Mark that rolling pruning has been done
+ }
+}
+
+void gpu_launch_kernel(NbnxmGpu* nb, const gmx::StepWorkload& stepWork, const Nbnxm::InteractionLocality iloc)
+{
+ const NBParamGpu* nbp = nb->nbparam;
+ gpu_plist* plist = nb->plist[iloc];
+
+ if (canSkipNonbondedWork(*nb, iloc))
+ {
+ plist->haveFreshList = false;
+ return;
+ }
+
+ if (nbp->useDynamicPruning && plist->haveFreshList)
+ {
+ // Prunes for rlistOuter and rlistInner, sets plist->haveFreshList=false
+ gpu_launch_kernel_pruneonly(nb, iloc, 1);
+ }
+
+ if (plist->nsci == 0)
+ {
+ /* Don't launch an empty local kernel */
+ return;
+ }
+
+ launchNbnxmKernel(nb, stepWork, iloc);
+}
+
+} // namespace Nbnxm
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief
+ * Stubs of functions that must be defined by nbnxm sycl implementation.
+ *
+ * \ingroup module_nbnxm
+ */
+#include "gmxpre.h"
+
+#include "gromacs/gpu_utils/pmalloc.h"
+#include "gromacs/hardware/device_information.h"
+#include "gromacs/mdtypes/interaction_const.h"
+#include "gromacs/nbnxm/atomdata.h"
+#include "gromacs/nbnxm/gpu_data_mgmt.h"
+#include "gromacs/nbnxm/nbnxm_gpu.h"
+#include "gromacs/nbnxm/nbnxm_gpu_data_mgmt.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/utility/exceptions.h"
+
+#include "nbnxm_sycl_types.h"
+
+namespace Nbnxm
+{
+
+void gpu_init_platform_specific(NbnxmGpu* /* nb */)
+{
+ // Nothing specific in SYCL
+}
+
+void gpu_free_platform_specific(NbnxmGpu* /* nb */)
+{
+ // Nothing specific in SYCL
+}
+
+int gpu_min_ci_balanced(NbnxmGpu* nb)
+{
+ // SYCL-TODO: Logic and magic values taken from OpenCL
+ static constexpr unsigned int balancedFactor = 50;
+ if (nb == nullptr)
+ {
+ return 0;
+ }
+ const cl::sycl::device device = nb->deviceContext_->deviceInfo().syclDevice;
+ const int numComputeUnits = device.get_info<cl::sycl::info::device::max_compute_units>();
+ return balancedFactor * numComputeUnits;
+}
+
+} // namespace Nbnxm
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief
+ * NBNXM SYCL kernels
+ *
+ * \ingroup module_nbnxm
+ */
+#include "gmxpre.h"
+
+#include "nbnxm_sycl_kernel.h"
+
+#include "gromacs/gpu_utils/devicebuffer.h"
+#include "gromacs/gpu_utils/gmxsycl.h"
+#include "gromacs/math/functions.h"
+#include "gromacs/mdtypes/simulation_workload.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/utility/template_mp.h"
+
+#include "nbnxm_sycl_kernel_utils.h"
+#include "nbnxm_sycl_types.h"
+
+namespace Nbnxm
+{
+
+//! \brief Set of boolean constants mimicking preprocessor macros.
+template<enum ElecType elecType, enum VdwType vdwType>
+struct EnergyFunctionProperties {
+ static constexpr bool elecCutoff = (elecType == ElecType::Cut); ///< EL_CUTOFF
+ static constexpr bool elecRF = (elecType == ElecType::RF); ///< EL_RF
+ static constexpr bool elecEwaldAna =
+ (elecType == ElecType::EwaldAna || elecType == ElecType::EwaldAnaTwin); ///< EL_EWALD_ANA
+ static constexpr bool elecEwaldTab =
+ (elecType == ElecType::EwaldTab || elecType == ElecType::EwaldTabTwin); ///< EL_EWALD_TAB
+ static constexpr bool elecEwaldTwin =
+ (elecType == ElecType::EwaldAnaTwin || elecType == ElecType::EwaldTabTwin);
+ static constexpr bool elecEwald = (elecEwaldAna || elecEwaldTab); ///< EL_EWALD_ANY
+ static constexpr bool vdwCombLB = (vdwType == VdwType::CutCombLB);
+ static constexpr bool vdwCombGeom = (vdwType == VdwType::CutCombGeom); ///< LJ_COMB_GEOM
+ static constexpr bool vdwComb = (vdwCombLB || vdwCombGeom); ///< LJ_COMB
+ static constexpr bool vdwEwaldCombGeom = (vdwType == VdwType::EwaldGeom); ///< LJ_EWALD_COMB_GEOM
+ static constexpr bool vdwEwaldCombLB = (vdwType == VdwType::EwaldLB); ///< LJ_EWALD_COMB_LB
+ static constexpr bool vdwEwald = (vdwEwaldCombGeom || vdwEwaldCombLB); ///< LJ_EWALD
+ static constexpr bool vdwFSwitch = (vdwType == VdwType::FSwitch); ///< LJ_FORCE_SWITCH
+ static constexpr bool vdwPSwitch = (vdwType == VdwType::PSwitch); ///< LJ_POT_SWITCH
+};
+
+//! \brief Templated constants to shorten kernel function declaration.
+//@{
+template<enum VdwType vdwType>
+constexpr bool ljComb = EnergyFunctionProperties<ElecType::Count, vdwType>().vdwComb;
+
+template<enum ElecType elecType> // Yes, ElecType
+constexpr bool vdwCutoffCheck = EnergyFunctionProperties<elecType, VdwType::Count>().elecEwaldTwin;
+
+template<enum ElecType elecType>
+constexpr bool elecEwald = EnergyFunctionProperties<elecType, VdwType::Count>().elecEwald;
+
+template<enum ElecType elecType>
+constexpr bool elecEwaldTab = EnergyFunctionProperties<elecType, VdwType::Count>().elecEwaldTab;
+
+template<enum VdwType vdwType>
+constexpr bool ljEwald = EnergyFunctionProperties<ElecType::Count, vdwType>().vdwEwald;
+//@}
+
+using cl::sycl::access::fence_space;
+using cl::sycl::access::mode;
+using cl::sycl::access::target;
+
+static inline Float2 convertSigmaEpsilonToC6C12(const float sigma, const float epsilon)
+{
+ const float sigma2 = sigma * sigma;
+ const float sigma6 = sigma2 * sigma2 * sigma2;
+ const float c6 = epsilon * sigma6;
+ const float c12 = c6 * sigma6;
+
+ return Float2(c6, c12);
+}
+
+template<bool doCalcEnergies>
+static inline void ljForceSwitch(const shift_consts_t dispersionShift,
+ const shift_consts_t repulsionShift,
+ const float rVdwSwitch,
+ const float c6,
+ const float c12,
+ const float rInv,
+ const float r2,
+ cl::sycl::private_ptr<float> fInvR,
+ cl::sycl::private_ptr<float> eLJ)
+{
+ /* force switch constants */
+ const float dispShiftV2 = dispersionShift.c2;
+ const float dispShiftV3 = dispersionShift.c3;
+ const float repuShiftV2 = repulsionShift.c2;
+ const float repuShiftV3 = repulsionShift.c3;
+
+ const float r = r2 * rInv;
+ const float rSwitch = cl::sycl::fdim(r, rVdwSwitch); // max(r - rVdwSwitch, 0)
+
+ *fInvR += -c6 * (dispShiftV2 + dispShiftV3 * rSwitch) * rSwitch * rSwitch * rInv
+ + c12 * (repuShiftV2 + repuShiftV3 * rSwitch) * rSwitch * rSwitch * rInv;
+
+ if constexpr (doCalcEnergies)
+ {
+ const float dispShiftF2 = dispShiftV2 / 3;
+ const float dispShiftF3 = dispShiftV3 / 4;
+ const float repuShiftF2 = repuShiftV2 / 3;
+ const float repuShiftF3 = repuShiftV3 / 4;
+ *eLJ += c6 * (dispShiftF2 + dispShiftF3 * rSwitch) * rSwitch * rSwitch * rSwitch
+ - c12 * (repuShiftF2 + repuShiftF3 * rSwitch) * rSwitch * rSwitch * rSwitch;
+ }
+}
+
+//! \brief Fetch C6 grid contribution coefficients and return the product of these.
+template<enum VdwType vdwType>
+static inline float calculateLJEwaldC6Grid(const DeviceAccessor<Float2, mode::read> a_nbfpComb,
+ const int typeI,
+ const int typeJ)
+{
+ if constexpr (vdwType == VdwType::EwaldGeom)
+ {
+ return a_nbfpComb[typeI][0] * a_nbfpComb[typeJ][0];
+ }
+ else
+ {
+ static_assert(vdwType == VdwType::EwaldLB);
+ /* sigma and epsilon are scaled to give 6*C6 */
+ const Float2 c6c12_i = a_nbfpComb[typeI];
+ const Float2 c6c12_j = a_nbfpComb[typeJ];
+
+ const float sigma = c6c12_i[0] + c6c12_j[0];
+ const float epsilon = c6c12_i[1] * c6c12_j[1];
+
+ const float sigma2 = sigma * sigma;
+ return epsilon * sigma2 * sigma2 * sigma2;
+ }
+}
+
+//! Calculate LJ-PME grid force contribution with geometric or LB combination rule.
+template<bool doCalcEnergies, enum VdwType vdwType>
+static inline void ljEwaldComb(const DeviceAccessor<Float2, mode::read> a_nbfpComb,
+ const float sh_lj_ewald,
+ const int typeI,
+ const int typeJ,
+ const float r2,
+ const float r2Inv,
+ const float lje_coeff2,
+ const float lje_coeff6_6,
+ const float int_bit,
+ cl::sycl::private_ptr<float> fInvR,
+ cl::sycl::private_ptr<float> eLJ)
+{
+ const float c6grid = calculateLJEwaldC6Grid<vdwType>(a_nbfpComb, typeI, typeJ);
+
+ /* Recalculate inv_r6 without exclusion mask */
+ const float inv_r6_nm = r2Inv * r2Inv * r2Inv;
+ const float cr2 = lje_coeff2 * r2;
+ const float expmcr2 = cl::sycl::exp(-cr2);
+ const float poly = 1.0F + cr2 + 0.5F * cr2 * cr2;
+
+ /* Subtract the grid force from the total LJ force */
+ *fInvR += c6grid * (inv_r6_nm - expmcr2 * (inv_r6_nm * poly + lje_coeff6_6)) * r2Inv;
+
+ if constexpr (doCalcEnergies)
+ {
+ /* Shift should be applied only to real LJ pairs */
+ const float sh_mask = sh_lj_ewald * int_bit;
+ *eLJ += c_oneSixth * c6grid * (inv_r6_nm * (1.0F - expmcr2 * poly) + sh_mask);
+ }
+}
+
+/*! \brief Apply potential switch. */
+template<bool doCalcEnergies>
+static inline void ljPotentialSwitch(const switch_consts_t vdwSwitch,
+ const float rVdwSwitch,
+ const float rInv,
+ const float r2,
+ cl::sycl::private_ptr<float> fInvR,
+ cl::sycl::private_ptr<float> eLJ)
+{
+ /* potential switch constants */
+ const float switchV3 = vdwSwitch.c3;
+ const float switchV4 = vdwSwitch.c4;
+ const float switchV5 = vdwSwitch.c5;
+ const float switchF2 = 3 * vdwSwitch.c3;
+ const float switchF3 = 4 * vdwSwitch.c4;
+ const float switchF4 = 5 * vdwSwitch.c5;
+
+ const float r = r2 * rInv;
+ const float rSwitch = r - rVdwSwitch;
+
+ if (rSwitch > 0.0F)
+ {
+ const float sw =
+ 1.0F + (switchV3 + (switchV4 + switchV5 * rSwitch) * rSwitch) * rSwitch * rSwitch * rSwitch;
+ const float dsw = (switchF2 + (switchF3 + switchF4 * rSwitch) * rSwitch) * rSwitch * rSwitch;
+
+ *fInvR = (*fInvR) * sw - rInv * (*eLJ) * dsw;
+ if constexpr (doCalcEnergies)
+ {
+ *eLJ *= sw;
+ }
+ }
+}
+
+
+/*! \brief Calculate analytical Ewald correction term. */
+static inline float pmeCorrF(const float z2)
+{
+ constexpr float FN6 = -1.7357322914161492954e-8F;
+ constexpr float FN5 = 1.4703624142580877519e-6F;
+ constexpr float FN4 = -0.000053401640219807709149F;
+ constexpr float FN3 = 0.0010054721316683106153F;
+ constexpr float FN2 = -0.019278317264888380590F;
+ constexpr float FN1 = 0.069670166153766424023F;
+ constexpr float FN0 = -0.75225204789749321333F;
+
+ constexpr float FD4 = 0.0011193462567257629232F;
+ constexpr float FD3 = 0.014866955030185295499F;
+ constexpr float FD2 = 0.11583842382862377919F;
+ constexpr float FD1 = 0.50736591960530292870F;
+ constexpr float FD0 = 1.0F;
+
+ const float z4 = z2 * z2;
+
+ float polyFD0 = FD4 * z4 + FD2;
+ const float polyFD1 = FD3 * z4 + FD1;
+ polyFD0 = polyFD0 * z4 + FD0;
+ polyFD0 = polyFD1 * z2 + polyFD0;
+
+ polyFD0 = 1.0F / polyFD0;
+
+ float polyFN0 = FN6 * z4 + FN4;
+ float polyFN1 = FN5 * z4 + FN3;
+ polyFN0 = polyFN0 * z4 + FN2;
+ polyFN1 = polyFN1 * z4 + FN1;
+ polyFN0 = polyFN0 * z4 + FN0;
+ polyFN0 = polyFN1 * z2 + polyFN0;
+
+ return polyFN0 * polyFD0;
+}
+
+/*! \brief Linear interpolation using exactly two FMA operations.
+ *
+ * Implements numeric equivalent of: (1-t)*d0 + t*d1.
+ */
+template<typename T>
+static inline T lerp(T d0, T d1, T t)
+{
+ return fma(t, d1, fma(-t, d0, d0));
+}
+
+/*! \brief Interpolate Ewald coulomb force correction using the F*r table. */
+static inline float interpolateCoulombForceR(const DeviceAccessor<float, mode::read> a_coulombTab,
+ const float coulombTabScale,
+ const float r)
+{
+ const float normalized = coulombTabScale * r;
+ const int index = static_cast<int>(normalized);
+ const float fraction = normalized - index;
+
+ const float left = a_coulombTab[index];
+ const float right = a_coulombTab[index + 1];
+
+ return lerp(left, right, fraction); // TODO: cl::sycl::mix
+}
+
+/*! \brief Reduce c_clSize j-force components and atomically accumulate into a_f.
+ *
+ * c_clSize consecutive threads hold the force components of a j-atom which we
+ * reduced in log2(cl_Size) steps using shift and atomically accumulate them into \p a_f.
+ */
+static inline void reduceForceJShuffle(Float3 f,
+ const cl::sycl::nd_item<1> itemIdx,
+ const int tidxi,
+ const int aidx,
+ DeviceAccessor<float, mode_atomic> a_f)
+{
+ static_assert(c_clSize == 8 || c_clSize == 4);
+ sycl_2020::sub_group sg = itemIdx.get_sub_group();
+
+ f[0] += sycl_2020::shift_left(sg, f[0], 1);
+ f[1] += sycl_2020::shift_right(sg, f[1], 1);
+ f[2] += sycl_2020::shift_left(sg, f[2], 1);
+ if (tidxi & 1)
+ {
+ f[0] = f[1];
+ }
+
+ f[0] += sycl_2020::shift_left(sg, f[0], 2);
+ f[2] += sycl_2020::shift_right(sg, f[2], 2);
+ if (tidxi & 2)
+ {
+ f[0] = f[2];
+ }
+
+ if constexpr (c_clSize == 8)
+ {
+ f[0] += sycl_2020::shift_left(sg, f[0], 4);
+ }
+
+ if (tidxi < 3)
+ {
+ atomicFetchAdd(a_f, 3 * aidx + tidxi, f[0]);
+ }
+}
+
+
+/*! \brief Final i-force reduction.
+ *
+ * Reduce c_nbnxnGpuNumClusterPerSupercluster i-force componets stored in \p fCiBuf[]
+ * accumulating atomically into \p a_f.
+ * If \p calcFShift is true, further reduce shift forces and atomically accumulate into \p a_fShift.
+ *
+ * This implementation works only with power of two array sizes.
+ */
+static inline void reduceForceIAndFShift(cl::sycl::accessor<float, 1, mode::read_write, target::local> sm_buf,
+ const Float3 fCiBuf[c_nbnxnGpuNumClusterPerSupercluster],
+ const bool calcFShift,
+ const cl::sycl::nd_item<1> itemIdx,
+ const int tidxi,
+ const int tidxj,
+ const int sci,
+ const int shift,
+ DeviceAccessor<float, mode_atomic> a_f,
+ DeviceAccessor<float, mode_atomic> a_fShift)
+{
+ // must have power of two elements in fCiBuf
+ static_assert(gmx::isPowerOfTwo(c_nbnxnGpuNumClusterPerSupercluster));
+
+ static constexpr int bufStride = c_clSize * c_clSize;
+ static constexpr int clSizeLog2 = gmx::StaticLog2<c_clSize>::value;
+ const int tidx = tidxi + tidxj * c_clSize;
+ float fShiftBuf = 0;
+ for (int ciOffset = 0; ciOffset < c_nbnxnGpuNumClusterPerSupercluster; ciOffset++)
+ {
+ const int aidx = (sci * c_nbnxnGpuNumClusterPerSupercluster + ciOffset) * c_clSize + tidxi;
+ /* store i forces in shmem */
+ sm_buf[tidx] = fCiBuf[ciOffset][0];
+ sm_buf[bufStride + tidx] = fCiBuf[ciOffset][1];
+ sm_buf[2 * bufStride + tidx] = fCiBuf[ciOffset][2];
+ itemIdx.barrier(fence_space::local_space);
+
+ /* Reduce the initial c_clSize values for each i atom to half
+ * every step by using c_clSize * i threads. */
+ int i = c_clSize / 2;
+ for (int j = clSizeLog2 - 1; j > 0; j--)
+ {
+ if (tidxj < i)
+ {
+ sm_buf[tidxj * c_clSize + tidxi] += sm_buf[(tidxj + i) * c_clSize + tidxi];
+ sm_buf[bufStride + tidxj * c_clSize + tidxi] +=
+ sm_buf[bufStride + (tidxj + i) * c_clSize + tidxi];
+ sm_buf[2 * bufStride + tidxj * c_clSize + tidxi] +=
+ sm_buf[2 * bufStride + (tidxj + i) * c_clSize + tidxi];
+ }
+ i >>= 1;
+ itemIdx.barrier(fence_space::local_space);
+ }
+
+ /* i == 1, last reduction step, writing to global mem */
+ /* Split the reduction between the first 3 line threads
+ Threads with line id 0 will do the reduction for (float3).x components
+ Threads with line id 1 will do the reduction for (float3).y components
+ Threads with line id 2 will do the reduction for (float3).z components. */
+ if (tidxj < 3)
+ {
+ const float f =
+ sm_buf[tidxj * bufStride + tidxi] + sm_buf[tidxj * bufStride + c_clSize + tidxi];
+ atomicFetchAdd(a_f, 3 * aidx + tidxj, f);
+ if (calcFShift)
+ {
+ fShiftBuf += f;
+ }
+ }
+ itemIdx.barrier(fence_space::local_space);
+ }
+ /* add up local shift forces into global mem */
+ if (calcFShift)
+ {
+ /* Only threads with tidxj < 3 will update fshift.
+ The threads performing the update must be the same as the threads
+ storing the reduction result above. */
+ if (tidxj < 3)
+ {
+ atomicFetchAdd(a_fShift, 3 * shift + tidxj, fShiftBuf);
+ }
+ }
+}
+
+/*! \brief Main kernel for NBNXM.
+ *
+ */
+template<bool doPruneNBL, bool doCalcEnergies, enum ElecType elecType, enum VdwType vdwType>
+auto nbnxmKernel(cl::sycl::handler& cgh,
+ DeviceAccessor<Float4, mode::read> a_xq,
+ DeviceAccessor<float, mode_atomic> a_f,
+ DeviceAccessor<Float3, mode::read> a_shiftVec,
+ DeviceAccessor<float, mode_atomic> a_fShift,
+ OptionalAccessor<float, mode_atomic, doCalcEnergies> a_energyElec,
+ OptionalAccessor<float, mode_atomic, doCalcEnergies> a_energyVdw,
+ DeviceAccessor<nbnxn_cj4_t, doPruneNBL ? mode::read_write : mode::read> a_plistCJ4,
+ DeviceAccessor<nbnxn_sci_t, mode::read> a_plistSci,
+ DeviceAccessor<nbnxn_excl_t, mode::read> a_plistExcl,
+ OptionalAccessor<Float2, mode::read, ljComb<vdwType>> a_ljComb,
+ OptionalAccessor<int, mode::read, !ljComb<vdwType>> a_atomTypes,
+ OptionalAccessor<Float2, mode::read, !ljComb<vdwType>> a_nbfp,
+ OptionalAccessor<Float2, mode::read, ljEwald<vdwType>> a_nbfpComb,
+ OptionalAccessor<float, mode::read, elecEwaldTab<elecType>> a_coulombTab,
+ const int numTypes,
+ const float rCoulombSq,
+ const float rVdwSq,
+ const float twoKRf,
+ const float ewaldBeta,
+ const float rlistOuterSq,
+ const float ewaldShift,
+ const float epsFac,
+ const float ewaldCoeffLJ,
+ const float cRF,
+ const shift_consts_t dispersionShift,
+ const shift_consts_t repulsionShift,
+ const switch_consts_t vdwSwitch,
+ const float rVdwSwitch,
+ const float ljEwaldShift,
+ const float coulombTabScale,
+ const bool calcShift)
+{
+ static constexpr EnergyFunctionProperties<elecType, vdwType> props;
+
+ cgh.require(a_xq);
+ cgh.require(a_f);
+ cgh.require(a_shiftVec);
+ cgh.require(a_fShift);
+ if constexpr (doCalcEnergies)
+ {
+ cgh.require(a_energyElec);
+ cgh.require(a_energyVdw);
+ }
+ cgh.require(a_plistCJ4);
+ cgh.require(a_plistSci);
+ cgh.require(a_plistExcl);
+ if constexpr (!props.vdwComb)
+ {
+ cgh.require(a_atomTypes);
+ cgh.require(a_nbfp);
+ }
+ else
+ {
+ cgh.require(a_ljComb);
+ }
+ if constexpr (props.vdwEwald)
+ {
+ cgh.require(a_nbfpComb);
+ }
+ if constexpr (props.elecEwaldTab)
+ {
+ cgh.require(a_coulombTab);
+ }
+
+ // shmem buffer for i x+q pre-loading
+ cl::sycl::accessor<Float4, 2, mode::read_write, target::local> sm_xq(
+ cl::sycl::range<2>(c_nbnxnGpuNumClusterPerSupercluster, c_clSize), cgh);
+
+ // shmem buffer for force reduction
+ // SYCL-TODO: Make into 3D; section 4.7.6.11 of SYCL2020 specs
+ cl::sycl::accessor<float, 1, mode::read_write, target::local> sm_reductionBuffer(
+ cl::sycl::range<1>(c_clSize * c_clSize * DIM), cgh);
+
+ auto sm_atomTypeI = [&]() {
+ if constexpr (!props.vdwComb)
+ {
+ return cl::sycl::accessor<int, 2, mode::read_write, target::local>(
+ cl::sycl::range<2>(c_nbnxnGpuNumClusterPerSupercluster, c_clSize), cgh);
+ }
+ else
+ {
+ return nullptr;
+ }
+ }();
+
+ auto sm_ljCombI = [&]() {
+ if constexpr (props.vdwComb)
+ {
+ return cl::sycl::accessor<Float2, 2, mode::read_write, target::local>(
+ cl::sycl::range<2>(c_nbnxnGpuNumClusterPerSupercluster, c_clSize), cgh);
+ }
+ else
+ {
+ return nullptr;
+ }
+ }();
+
+ /* Flag to control the calculation of exclusion forces in the kernel
+ * We do that with Ewald (elec/vdw) and RF. Cut-off only has exclusion
+ * energy terms. */
+ constexpr bool doExclusionForces =
+ (props.elecEwald || props.elecRF || props.vdwEwald || (props.elecCutoff && doCalcEnergies));
+
+ // The post-prune j-i cluster-pair organization is linked to how exclusion and interaction mask data is stored.
+ // Currently this is ideally suited for 32-wide subgroup size but slightly less so for others,
+ // e.g. subGroupSize > prunedClusterPairSize on AMD GCN / CDNA.
+ // Hence, the two are decoupled.
+ constexpr int prunedClusterPairSize = c_clSize * c_splitClSize;
+#if defined(HIPSYCL_PLATFORM_ROCM) // SYCL-TODO AMD RDNA/RDNA2 has 32-wide exec; how can we check for that?
+ gmx_unused constexpr int subGroupSize = c_clSize * c_clSize;
+#else
+ gmx_unused constexpr int subGroupSize = prunedClusterPairSize;
+#endif
+
+ return [=](cl::sycl::nd_item<1> itemIdx) [[intel::reqd_sub_group_size(subGroupSize)]]
+ {
+ /* thread/block/warp id-s */
+ const cl::sycl::id<3> localId = unflattenId<c_clSize, c_clSize>(itemIdx.get_local_id());
+ const unsigned tidxi = localId[0];
+ const unsigned tidxj = localId[1];
+ const unsigned tidx = tidxj * c_clSize + tidxi;
+ const unsigned tidxz = 0;
+
+ // Group indexing was flat originally, no need to unflatten it.
+ const unsigned bidx = itemIdx.get_group(0);
+
+ const sycl_2020::sub_group sg = itemIdx.get_sub_group();
+ // Could use sg.get_group_range to compute the imask & exclusion Idx, but too much of the logic relies on it anyway
+ // and in cases where prunedClusterPairSize != subGroupSize we can't use it anyway
+ const unsigned imeiIdx = tidx / prunedClusterPairSize;
+
+ Float3 fCiBuf[c_nbnxnGpuNumClusterPerSupercluster]; // i force buffer
+ for (int i = 0; i < c_nbnxnGpuNumClusterPerSupercluster; i++)
+ {
+ fCiBuf[i] = Float3(0.0F, 0.0F, 0.0F);
+ }
+
+ const nbnxn_sci_t nbSci = a_plistSci[bidx];
+ const int sci = nbSci.sci;
+ const int cij4Start = nbSci.cj4_ind_start;
+ const int cij4End = nbSci.cj4_ind_end;
+
+ // Only needed if props.elecEwaldAna
+ const float beta2 = ewaldBeta * ewaldBeta;
+ const float beta3 = ewaldBeta * ewaldBeta * ewaldBeta;
+
+ for (int i = 0; i < c_nbnxnGpuNumClusterPerSupercluster; i += c_clSize)
+ {
+ /* Pre-load i-atom x and q into shared memory */
+ const int ci = sci * c_nbnxnGpuNumClusterPerSupercluster + tidxj + i;
+ const int ai = ci * c_clSize + tidxi;
+ const cl::sycl::id<2> cacheIdx = cl::sycl::id<2>(tidxj + i, tidxi);
+
+ const Float3 shift = a_shiftVec[nbSci.shift];
+ Float4 xqi = a_xq[ai];
+ xqi += Float4(shift[0], shift[1], shift[2], 0.0F);
+ xqi[3] *= epsFac;
+ sm_xq[cacheIdx] = xqi;
+
+ if constexpr (!props.vdwComb)
+ {
+ // Pre-load the i-atom types into shared memory
+ sm_atomTypeI[cacheIdx] = a_atomTypes[ai];
+ }
+ else
+ {
+ // Pre-load the LJ combination parameters into shared memory
+ sm_ljCombI[cacheIdx] = a_ljComb[ai];
+ }
+ }
+ itemIdx.barrier(fence_space::local_space);
+
+ float ewaldCoeffLJ_2, ewaldCoeffLJ_6_6; // Only needed if (props.vdwEwald)
+ if constexpr (props.vdwEwald)
+ {
+ ewaldCoeffLJ_2 = ewaldCoeffLJ * ewaldCoeffLJ;
+ ewaldCoeffLJ_6_6 = ewaldCoeffLJ_2 * ewaldCoeffLJ_2 * ewaldCoeffLJ_2 * c_oneSixth;
+ }
+
+ float energyVdw, energyElec; // Only needed if (doCalcEnergies)
+ if constexpr (doCalcEnergies)
+ {
+ energyVdw = energyElec = 0.0F;
+ }
+ if constexpr (doCalcEnergies && doExclusionForces)
+ {
+ if (nbSci.shift == gmx::c_centralShiftIndex
+ && a_plistCJ4[cij4Start].cj[0] == sci * c_nbnxnGpuNumClusterPerSupercluster)
+ {
+ // we have the diagonal: add the charge and LJ self interaction energy term
+ for (int i = 0; i < c_nbnxnGpuNumClusterPerSupercluster; i++)
+ {
+ // TODO: Are there other options?
+ if constexpr (props.elecEwald || props.elecRF || props.elecCutoff)
+ {
+ const float qi = sm_xq[i][tidxi][3];
+ energyElec += qi * qi;
+ }
+ if constexpr (props.vdwEwald)
+ {
+ energyVdw +=
+ a_nbfp[a_atomTypes[(sci * c_nbnxnGpuNumClusterPerSupercluster + i) * c_clSize + tidxi]
+ * (numTypes + 1)][0];
+ }
+ }
+ /* divide the self term(s) equally over the j-threads, then multiply with the coefficients. */
+ if constexpr (props.vdwEwald)
+ {
+ energyVdw /= c_clSize;
+ energyVdw *= 0.5F * c_oneSixth * ewaldCoeffLJ_6_6; // c_OneTwelfth?
+ }
+ if constexpr (props.elecRF || props.elecCutoff)
+ {
+ // Correct for epsfac^2 due to adding qi^2 */
+ energyElec /= epsFac * c_clSize;
+ energyElec *= -0.5F * cRF;
+ }
+ if constexpr (props.elecEwald)
+ {
+ // Correct for epsfac^2 due to adding qi^2 */
+ energyElec /= epsFac * c_clSize;
+ energyElec *= -ewaldBeta * c_OneOverSqrtPi; /* last factor 1/sqrt(pi) */
+ }
+ } // (nbSci.shift == gmx::c_centralShiftIndex && a_plistCJ4[cij4Start].cj[0] == sci * c_nbnxnGpuNumClusterPerSupercluster)
+ } // (doCalcEnergies && doExclusionForces)
+
+ // Only needed if (doExclusionForces)
+ const bool nonSelfInteraction = !(nbSci.shift == gmx::c_centralShiftIndex & tidxj <= tidxi);
+
+ // loop over the j clusters = seen by any of the atoms in the current super-cluster
+ for (int j4 = cij4Start + tidxz; j4 < cij4End; j4 += 1)
+ {
+ unsigned imask = a_plistCJ4[j4].imei[imeiIdx].imask;
+ if (!doPruneNBL && !imask)
+ {
+ continue;
+ }
+ const int wexclIdx = a_plistCJ4[j4].imei[imeiIdx].excl_ind;
+ static_assert(gmx::isPowerOfTwo(prunedClusterPairSize));
+ const unsigned wexcl = a_plistExcl[wexclIdx].pair[tidx & (prunedClusterPairSize - 1)];
+ for (int jm = 0; jm < c_nbnxnGpuJgroupSize; jm++)
+ {
+ const bool maskSet =
+ imask & (superClInteractionMask << (jm * c_nbnxnGpuNumClusterPerSupercluster));
+ if (!maskSet)
+ {
+ continue;
+ }
+ unsigned maskJI = (1U << (jm * c_nbnxnGpuNumClusterPerSupercluster));
+ const int cj = a_plistCJ4[j4].cj[jm];
+ const int aj = cj * c_clSize + tidxj;
+
+ // load j atom data
+ const Float4 xqj = a_xq[aj];
+
+ const Float3 xj(xqj[0], xqj[1], xqj[2]);
+ const float qj = xqj[3];
+ int atomTypeJ; // Only needed if (!props.vdwComb)
+ Float2 ljCombJ; // Only needed if (props.vdwComb)
+ if constexpr (props.vdwComb)
+ {
+ ljCombJ = a_ljComb[aj];
+ }
+ else
+ {
+ atomTypeJ = a_atomTypes[aj];
+ }
+
+ Float3 fCjBuf(0.0F, 0.0F, 0.0F);
+
+ for (int i = 0; i < c_nbnxnGpuNumClusterPerSupercluster; i++)
+ {
+ if (imask & maskJI)
+ {
+ // i cluster index
+ const int ci = sci * c_nbnxnGpuNumClusterPerSupercluster + i;
+ // all threads load an atom from i cluster ci into shmem!
+ const Float4 xqi = sm_xq[i][tidxi];
+ const Float3 xi(xqi[0], xqi[1], xqi[2]);
+
+ // distance between i and j atoms
+ const Float3 rv = xi - xj;
+ float r2 = norm2(rv);
+
+ if constexpr (doPruneNBL)
+ {
+ /* If _none_ of the atoms pairs are in cutoff range,
+ * the bit corresponding to the current
+ * cluster-pair in imask gets set to 0. */
+ if (!sycl_2020::group_any_of(sg, r2 < rlistOuterSq))
+ {
+ imask &= ~maskJI;
+ }
+ }
+ const float pairExclMask = (wexcl & maskJI) ? 1.0F : 0.0F;
+
+ // cutoff & exclusion check
+
+ const bool notExcluded = doExclusionForces ? (nonSelfInteraction | (ci != cj))
+ : (wexcl & maskJI);
+
+ // SYCL-TODO: Check optimal way of branching here.
+ if ((r2 < rCoulombSq) && notExcluded)
+ {
+ const float qi = xqi[3];
+ int atomTypeI; // Only needed if (!props.vdwComb)
+ float sigma, epsilon;
+ Float2 c6c12;
+
+ if constexpr (!props.vdwComb)
+ {
+ /* LJ 6*C6 and 12*C12 */
+ atomTypeI = sm_atomTypeI[i][tidxi];
+ c6c12 = a_nbfp[numTypes * atomTypeI + atomTypeJ];
+ }
+ else
+ {
+ const Float2 ljCombI = sm_ljCombI[i][tidxi];
+ if constexpr (props.vdwCombGeom)
+ {
+ c6c12 = Float2(ljCombI[0] * ljCombJ[0], ljCombI[1] * ljCombJ[1]);
+ }
+ else
+ {
+ static_assert(props.vdwCombLB);
+ // LJ 2^(1/6)*sigma and 12*epsilon
+ sigma = ljCombI[0] + ljCombJ[0];
+ epsilon = ljCombI[1] * ljCombJ[1];
+ if constexpr (doCalcEnergies)
+ {
+ c6c12 = convertSigmaEpsilonToC6C12(sigma, epsilon);
+ }
+ } // props.vdwCombGeom
+ } // !props.vdwComb
+
+ // c6 and c12 are unused and garbage iff props.vdwCombLB && !doCalcEnergies
+ const float c6 = c6c12[0];
+ const float c12 = c6c12[1];
+
+ // Ensure distance do not become so small that r^-12 overflows
+ r2 = std::max(r2, c_nbnxnMinDistanceSquared);
+#if GMX_SYCL_HIPSYCL
+ // No fast/native functions in some compilation passes
+ const float rInv = cl::sycl::rsqrt(r2);
+#else
+ // SYCL-TODO: sycl::half_precision::rsqrt?
+ const float rInv = cl::sycl::native::rsqrt(r2);
+#endif
+ const float r2Inv = rInv * rInv;
+ float r6Inv, fInvR, energyLJPair;
+ if constexpr (!props.vdwCombLB || doCalcEnergies)
+ {
+ r6Inv = r2Inv * r2Inv * r2Inv;
+ if constexpr (doExclusionForces)
+ {
+ // SYCL-TODO: Check if true for SYCL
+ /* We could mask r2Inv, but with Ewald masking both
+ * r6Inv and fInvR is faster */
+ r6Inv *= pairExclMask;
+ }
+ fInvR = r6Inv * (c12 * r6Inv - c6) * r2Inv;
+ }
+ else
+ {
+ float sig_r = sigma * rInv;
+ float sig_r2 = sig_r * sig_r;
+ float sig_r6 = sig_r2 * sig_r2 * sig_r2;
+ if constexpr (doExclusionForces)
+ {
+ sig_r6 *= pairExclMask;
+ }
+ fInvR = epsilon * sig_r6 * (sig_r6 - 1.0F) * r2Inv;
+ } // (!props.vdwCombLB || doCalcEnergies)
+ if constexpr (doCalcEnergies || props.vdwPSwitch)
+ {
+ energyLJPair = pairExclMask
+ * (c12 * (r6Inv * r6Inv + repulsionShift.cpot) * c_oneTwelfth
+ - c6 * (r6Inv + dispersionShift.cpot) * c_oneSixth);
+ }
+ if constexpr (props.vdwFSwitch)
+ {
+ ljForceSwitch<doCalcEnergies>(
+ dispersionShift, repulsionShift, rVdwSwitch, c6, c12, rInv, r2, &fInvR, &energyLJPair);
+ }
+ if constexpr (props.vdwEwald)
+ {
+ ljEwaldComb<doCalcEnergies, vdwType>(a_nbfpComb,
+ ljEwaldShift,
+ atomTypeI,
+ atomTypeJ,
+ r2,
+ r2Inv,
+ ewaldCoeffLJ_2,
+ ewaldCoeffLJ_6_6,
+ pairExclMask,
+ &fInvR,
+ &energyLJPair);
+ } // (props.vdwEwald)
+ if constexpr (props.vdwPSwitch)
+ {
+ ljPotentialSwitch<doCalcEnergies>(
+ vdwSwitch, rVdwSwitch, rInv, r2, &fInvR, &energyLJPair);
+ }
+ if constexpr (props.elecEwaldTwin)
+ {
+ // Separate VDW cut-off check to enable twin-range cut-offs
+ // (rVdw < rCoulomb <= rList)
+ const float vdwInRange = (r2 < rVdwSq) ? 1.0F : 0.0F;
+ fInvR *= vdwInRange;
+ if constexpr (doCalcEnergies)
+ {
+ energyLJPair *= vdwInRange;
+ }
+ }
+ if constexpr (doCalcEnergies)
+ {
+ energyVdw += energyLJPair;
+ }
+
+ if constexpr (props.elecCutoff)
+ {
+ if constexpr (doExclusionForces)
+ {
+ fInvR += qi * qj * pairExclMask * r2Inv * rInv;
+ }
+ else
+ {
+ fInvR += qi * qj * r2Inv * rInv;
+ }
+ }
+ if constexpr (props.elecRF)
+ {
+ fInvR += qi * qj * (pairExclMask * r2Inv * rInv - twoKRf);
+ }
+ if constexpr (props.elecEwaldAna)
+ {
+ fInvR += qi * qj
+ * (pairExclMask * r2Inv * rInv + pmeCorrF(beta2 * r2) * beta3);
+ }
+ if constexpr (props.elecEwaldTab)
+ {
+ fInvR += qi * qj
+ * (pairExclMask * r2Inv
+ - interpolateCoulombForceR(
+ a_coulombTab, coulombTabScale, r2 * rInv))
+ * rInv;
+ }
+
+ if constexpr (doCalcEnergies)
+ {
+ if constexpr (props.elecCutoff)
+ {
+ energyElec += qi * qj * (pairExclMask * rInv - cRF);
+ }
+ if constexpr (props.elecRF)
+ {
+ energyElec +=
+ qi * qj * (pairExclMask * rInv + 0.5f * twoKRf * r2 - cRF);
+ }
+ if constexpr (props.elecEwald)
+ {
+ energyElec +=
+ qi * qj
+ * (rInv * (pairExclMask - cl::sycl::erf(r2 * rInv * ewaldBeta))
+ - pairExclMask * ewaldShift);
+ }
+ }
+
+ const Float3 forceIJ = rv * fInvR;
+
+ /* accumulate j forces in registers */
+ fCjBuf -= forceIJ;
+ /* accumulate i forces in registers */
+ fCiBuf[i] += forceIJ;
+ } // (r2 < rCoulombSq) && notExcluded
+ } // (imask & maskJI)
+ /* shift the mask bit by 1 */
+ maskJI += maskJI;
+ } // for (int i = 0; i < c_nbnxnGpuNumClusterPerSupercluster; i++)
+ /* reduce j forces */
+ reduceForceJShuffle(fCjBuf, itemIdx, tidxi, aj, a_f);
+ } // for (int jm = 0; jm < c_nbnxnGpuJgroupSize; jm++)
+ if constexpr (doPruneNBL)
+ {
+ /* Update the imask with the new one which does not contain the
+ * out of range clusters anymore. */
+ a_plistCJ4[j4].imei[imeiIdx].imask = imask;
+ }
+ } // for (int j4 = cij4Start; j4 < cij4End; j4 += 1)
+
+ /* skip central shifts when summing shift forces */
+ const bool doCalcShift = (calcShift && !(nbSci.shift == gmx::c_centralShiftIndex));
+
+ reduceForceIAndFShift(
+ sm_reductionBuffer, fCiBuf, doCalcShift, itemIdx, tidxi, tidxj, sci, nbSci.shift, a_f, a_fShift);
+
+ if constexpr (doCalcEnergies)
+ {
+ const float energyVdwGroup = sycl_2020::group_reduce(
+ itemIdx.get_group(), energyVdw, 0.0F, sycl_2020::plus<float>());
+ const float energyElecGroup = sycl_2020::group_reduce(
+ itemIdx.get_group(), energyElec, 0.0F, sycl_2020::plus<float>());
+
+ if (tidx == 0)
+ {
+ atomicFetchAdd(a_energyVdw, 0, energyVdwGroup);
+ atomicFetchAdd(a_energyElec, 0, energyElecGroup);
+ }
+ }
+ };
+}
+
+// SYCL 1.2.1 requires providing a unique type for a kernel. Should not be needed for SYCL2020.
+template<bool doPruneNBL, bool doCalcEnergies, enum ElecType elecType, enum VdwType vdwType>
+class NbnxmKernelName;
+
+template<bool doPruneNBL, bool doCalcEnergies, enum ElecType elecType, enum VdwType vdwType, class... Args>
+cl::sycl::event launchNbnxmKernel(const DeviceStream& deviceStream, const int numSci, Args&&... args)
+{
+ // Should not be needed for SYCL2020.
+ using kernelNameType = NbnxmKernelName<doPruneNBL, doCalcEnergies, elecType, vdwType>;
+
+ /* Kernel launch config:
+ * - The thread block dimensions match the size of i-clusters, j-clusters,
+ * and j-cluster concurrency, in x, y, and z, respectively.
+ * - The 1D block-grid contains as many blocks as super-clusters.
+ */
+ const int numBlocks = numSci;
+ const cl::sycl::range<3> blockSize{ c_clSize, c_clSize, 1 };
+ const cl::sycl::range<3> globalSize{ numBlocks * blockSize[0], blockSize[1], blockSize[2] };
+ const cl::sycl::nd_range<3> range{ globalSize, blockSize };
+
+ cl::sycl::queue q = deviceStream.stream();
+
+ cl::sycl::event e = q.submit([&](cl::sycl::handler& cgh) {
+ auto kernel = nbnxmKernel<doPruneNBL, doCalcEnergies, elecType, vdwType>(
+ cgh, std::forward<Args>(args)...);
+ cgh.parallel_for<kernelNameType>(flattenNDRange(range), kernel);
+ });
+
+ return e;
+}
+
+template<class... Args>
+cl::sycl::event chooseAndLaunchNbnxmKernel(bool doPruneNBL,
+ bool doCalcEnergies,
+ enum ElecType elecType,
+ enum VdwType vdwType,
+ Args&&... args)
+{
+ return gmx::dispatchTemplatedFunction(
+ [&](auto doPruneNBL_, auto doCalcEnergies_, auto elecType_, auto vdwType_) {
+ return launchNbnxmKernel<doPruneNBL_, doCalcEnergies_, elecType_, vdwType_>(
+ std::forward<Args>(args)...);
+ },
+ doPruneNBL,
+ doCalcEnergies,
+ elecType,
+ vdwType);
+}
+
+void launchNbnxmKernel(NbnxmGpu* nb, const gmx::StepWorkload& stepWork, const InteractionLocality iloc)
+{
+ NBAtomDataGpu* adat = nb->atdat;
+ NBParamGpu* nbp = nb->nbparam;
+ gpu_plist* plist = nb->plist[iloc];
+ const bool doPruneNBL = (plist->haveFreshList && !nb->didPrune[iloc]);
+ const DeviceStream& deviceStream = *nb->deviceStreams[iloc];
+
+ // Casting to float simplifies using atomic ops in the kernel
+ cl::sycl::buffer<Float3, 1> f(*adat->f.buffer_);
+ auto fAsFloat = f.reinterpret<float, 1>(f.get_count() * DIM);
+ cl::sycl::buffer<Float3, 1> fShift(*adat->fShift.buffer_);
+ auto fShiftAsFloat = fShift.reinterpret<float, 1>(fShift.get_count() * DIM);
+
+ cl::sycl::event e = chooseAndLaunchNbnxmKernel(doPruneNBL,
+ stepWork.computeEnergy,
+ nbp->elecType,
+ nbp->vdwType,
+ deviceStream,
+ plist->nsci,
+ adat->xq,
+ fAsFloat,
+ adat->shiftVec,
+ fShiftAsFloat,
+ adat->eElec,
+ adat->eLJ,
+ plist->cj4,
+ plist->sci,
+ plist->excl,
+ adat->ljComb,
+ adat->atomTypes,
+ nbp->nbfp,
+ nbp->nbfp_comb,
+ nbp->coulomb_tab,
+ adat->numTypes,
+ nbp->rcoulomb_sq,
+ nbp->rvdw_sq,
+ nbp->two_k_rf,
+ nbp->ewald_beta,
+ nbp->rlistOuter_sq,
+ nbp->sh_ewald,
+ nbp->epsfac,
+ nbp->ewaldcoeff_lj,
+ nbp->c_rf,
+ nbp->dispersion_shift,
+ nbp->repulsion_shift,
+ nbp->vdw_switch,
+ nbp->rvdw_switch,
+ nbp->sh_lj_ewald,
+ nbp->coulomb_tab_scale,
+ stepWork.computeVirial);
+}
+
+} // namespace Nbnxm
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/*! \libinternal \file
+/*! \internal \file
* \brief
- * Declares C++11-style basic threading primitives
- * (gmx::Mutex, gmx::lock_guard).
+ * Declares nbnxn sycl helper functions
*
- * For now, the implementation is imported from thread-MPI.
- *
- * \author Teemu Murtola <teemu.murtola@gmail.com>
- * \inlibraryapi
- * \ingroup module_utility
+ * \ingroup module_nbnxm
*/
-#ifndef GMX_THREADING_MUTEX_H
-#define GMX_THREADING_MUTEX_H
-
-#include "thread_mpi/mutex.h"
+#ifndef GMX_NBNXM_SYCL_NBNXM_SYCL_KERNEL_H
+#define GMX_NBNXM_SYCL_NBNXM_SYCL_KERNEL_H
+// Forward declarations
namespace gmx
{
+enum class InteractionLocality;
+class StepWorkload;
+} // namespace gmx
+struct NbnxmGpu;
-//! \cond libapi
-/*! \libinternal \brief
- * C++11-compatible basic mutex.
- */
-typedef tMPI::mutex Mutex;
-//! \endcond
-using tMPI::lock_guard;
+namespace Nbnxm
+{
+using gmx::InteractionLocality;
-} // namespace gmx
+void launchNbnxmKernel(NbnxmGpu* nb, const gmx::StepWorkload& stepWork, const InteractionLocality iloc);
+
+} // namespace Nbnxm
-#endif
+#endif // GMX_NBNXM_SYCL_NBNXM_SYCL_KERNEL_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief
+ * NBNXM SYCL kernels
+ *
+ * \ingroup module_nbnxm
+ */
+#include "gmxpre.h"
+
+#include "nbnxm_sycl_kernel_pruneonly.h"
+
+#include "gromacs/gpu_utils/devicebuffer.h"
+#include "gromacs/gpu_utils/gmxsycl.h"
+#include "gromacs/utility/template_mp.h"
+
+#include "nbnxm_sycl_kernel_utils.h"
+#include "nbnxm_sycl_types.h"
+
+using cl::sycl::access::fence_space;
+using cl::sycl::access::mode;
+using cl::sycl::access::target;
+
+namespace Nbnxm
+{
+
+/*! \brief Prune-only kernel for NBNXM.
+ *
+ */
+template<bool haveFreshList>
+auto nbnxmKernelPruneOnly(cl::sycl::handler& cgh,
+ DeviceAccessor<Float4, mode::read> a_xq,
+ DeviceAccessor<Float3, mode::read> a_shiftVec,
+ DeviceAccessor<nbnxn_cj4_t, mode::read_write> a_plistCJ4,
+ DeviceAccessor<nbnxn_sci_t, mode::read> a_plistSci,
+ DeviceAccessor<unsigned int, haveFreshList ? mode::write : mode::read> a_plistIMask,
+ const float rlistOuterSq,
+ const float rlistInnerSq,
+ const int numParts,
+ const int part)
+{
+ cgh.require(a_xq);
+ cgh.require(a_shiftVec);
+ cgh.require(a_plistCJ4);
+ cgh.require(a_plistSci);
+ cgh.require(a_plistIMask);
+
+ /* shmem buffer for i x+q pre-loading */
+ cl::sycl::accessor<Float4, 2, mode::read_write, target::local> sm_xq(
+ cl::sycl::range<2>(c_nbnxnGpuNumClusterPerSupercluster, c_clSize), cgh);
+
+ constexpr int warpSize = c_clSize * c_clSize / 2;
+
+ /* Somewhat weird behavior inherited from OpenCL.
+ * With clSize == 4, we use sub_group size of 16 (not enforced in OpenCL implementation, but chosen
+ * by the IGC compiler), however for data layout we consider it to be 8.
+ * Setting sub_group size to 8 slows down the prune-only kernel 1.5-2 times.
+ * For clSize == But we need to set specific sub_group size >= 32 for clSize == 8 for correctness,
+ * but it causes very poor performance.
+ */
+ constexpr int gmx_unused requiredSubGroupSize = (c_clSize == 4) ? 16 : warpSize;
+
+ /* Requirements:
+ * Work group (block) must have range (c_clSize, c_clSize, ...) (for localId calculation, easy
+ * to change). */
+ return [=](cl::sycl::nd_item<1> itemIdx) [[intel::reqd_sub_group_size(requiredSubGroupSize)]]
+ {
+ const cl::sycl::id<3> localId = unflattenId<c_clSize, c_clSize>(itemIdx.get_local_id());
+ // thread/block/warp id-s
+ const unsigned tidxi = localId[0];
+ const unsigned tidxj = localId[1];
+ const int tidx = tidxj * c_clSize + tidxi;
+ const unsigned tidxz = localId[2];
+ const unsigned bidx = itemIdx.get_group(0);
+
+ const sycl_2020::sub_group sg = itemIdx.get_sub_group();
+ const unsigned widx = tidx / warpSize;
+
+ // my i super-cluster's index = sciOffset + current bidx * numParts + part
+ const nbnxn_sci_t nbSci = a_plistSci[bidx * numParts + part];
+ const int sci = nbSci.sci; /* super-cluster */
+ const int cij4Start = nbSci.cj4_ind_start; /* first ...*/
+ const int cij4End = nbSci.cj4_ind_end; /* and last index of j clusters */
+
+ if (tidxz == 0)
+ {
+ for (int i = 0; i < c_nbnxnGpuNumClusterPerSupercluster; i += c_clSize)
+ {
+ /* Pre-load i-atom x and q into shared memory */
+ const int ci = sci * c_nbnxnGpuNumClusterPerSupercluster + tidxj + i;
+ const int ai = ci * c_clSize + tidxi;
+
+ /* We don't need q, but using float4 in shmem avoids bank conflicts.
+ (but it also wastes L2 bandwidth). */
+ const Float4 xq = a_xq[ai];
+ const Float3 shift = a_shiftVec[nbSci.shift];
+ const Float4 xi(xq[0] + shift[0], xq[1] + shift[1], xq[2] + shift[2], xq[3]);
+ sm_xq[tidxj + i][tidxi] = xi;
+ }
+ }
+ itemIdx.barrier(fence_space::local_space);
+
+ /* loop over the j clusters = seen by any of the atoms in the current super-cluster.
+ * The loop stride c_syclPruneKernelJ4Concurrency ensures that consecutive warps-pairs are
+ * assigned consecutive j4's entries. */
+ for (int j4 = cij4Start + tidxz; j4 < cij4End; j4 += c_syclPruneKernelJ4Concurrency)
+ {
+ unsigned imaskFull, imaskCheck, imaskNew;
+
+ if constexpr (haveFreshList)
+ {
+ /* Read the mask from the list transferred from the CPU */
+ imaskFull = a_plistCJ4[j4].imei[widx].imask;
+ /* We attempt to prune all pairs present in the original list */
+ imaskCheck = imaskFull;
+ imaskNew = 0;
+ }
+ else
+ {
+ /* Read the mask from the "warp-pruned" by rlistOuter mask array */
+ imaskFull = a_plistIMask[j4 * c_nbnxnGpuClusterpairSplit + widx];
+ /* Read the old rolling pruned mask, use as a base for new */
+ imaskNew = a_plistCJ4[j4].imei[widx].imask;
+ /* We only need to check pairs with different mask */
+ imaskCheck = (imaskNew ^ imaskFull);
+ }
+
+ if (imaskCheck)
+ {
+ for (int jm = 0; jm < c_nbnxnGpuJgroupSize; jm++)
+ {
+ if (imaskCheck & (superClInteractionMask << (jm * c_nbnxnGpuNumClusterPerSupercluster)))
+ {
+ unsigned mask_ji = (1U << (jm * c_nbnxnGpuNumClusterPerSupercluster));
+ // SYCL-TODO: Reevaluate prefetching methods
+ const int cj = a_plistCJ4[j4].cj[jm];
+ const int aj = cj * c_clSize + tidxj;
+
+ /* load j atom data */
+ const Float4 tmp = a_xq[aj];
+ const Float3 xj(tmp[0], tmp[1], tmp[2]);
+
+ for (int i = 0; i < c_nbnxnGpuNumClusterPerSupercluster; i++)
+ {
+ if (imaskCheck & mask_ji)
+ {
+ // load i-cluster coordinates from shmem
+ const Float4 xi = sm_xq[i][tidxi];
+ // distance between i and j atoms
+ Float3 rv(xi[0], xi[1], xi[2]);
+ rv -= xj;
+ const float r2 = norm2(rv);
+
+ /* If _none_ of the atoms pairs are in rlistOuter
+ * range, the bit corresponding to the current
+ * cluster-pair in imask gets set to 0. */
+ if (haveFreshList && !(sycl_2020::group_any_of(sg, r2 < rlistOuterSq)))
+ {
+ imaskFull &= ~mask_ji;
+ }
+ /* If any atom pair is within range, set the bit
+ * corresponding to the current cluster-pair. */
+ if (sycl_2020::group_any_of(sg, r2 < rlistInnerSq))
+ {
+ imaskNew |= mask_ji;
+ }
+ } // (imaskCheck & mask_ji)
+ /* shift the mask bit by 1 */
+ mask_ji += mask_ji;
+ } // (int i = 0; i < c_nbnxnGpuNumClusterPerSupercluster; i++)
+ } // (imaskCheck & (superClInteractionMask << (jm * c_nbnxnGpuNumClusterPerSupercluster)))
+ } // for (int jm = 0; jm < c_nbnxnGpuJgroupSize; jm++)
+
+ if constexpr (haveFreshList)
+ {
+ /* copy the list pruned to rlistOuter to a separate buffer */
+ a_plistIMask[j4 * c_nbnxnGpuClusterpairSplit + widx] = imaskFull;
+ }
+ /* update the imask with only the pairs up to rlistInner */
+ a_plistCJ4[j4].imei[widx].imask = imaskNew;
+ } // (imaskCheck)
+ } // for (int j4 = cij4_start + tidxz; j4 < cij4_end; j4 += c_syclPruneKernelJ4Concurrency)
+ };
+}
+
+// SYCL 1.2.1 requires providing a unique type for a kernel. Should not be needed for SYCL2020.
+template<bool haveFreshList>
+class NbnxmKernelPruneOnlyName;
+
+template<bool haveFreshList, class... Args>
+cl::sycl::event launchNbnxmKernelPruneOnly(const DeviceStream& deviceStream,
+ const int numSciInPart,
+ Args&&... args)
+{
+ // Should not be needed for SYCL2020.
+ using kernelNameType = NbnxmKernelPruneOnlyName<haveFreshList>;
+
+ /* Kernel launch config:
+ * - The thread block dimensions match the size of i-clusters, j-clusters,
+ * and j-cluster concurrency, in x, y, and z, respectively.
+ * - The 1D block-grid contains as many blocks as super-clusters.
+ */
+ const unsigned long numBlocks = numSciInPart;
+ const cl::sycl::range<3> blockSize{ c_clSize, c_clSize, c_syclPruneKernelJ4Concurrency };
+ const cl::sycl::range<3> globalSize{ numBlocks * blockSize[0], blockSize[1], blockSize[2] };
+ const cl::sycl::nd_range<3> range{ globalSize, blockSize };
+
+ cl::sycl::queue q = deviceStream.stream();
+
+ cl::sycl::event e = q.submit([&](cl::sycl::handler& cgh) {
+ auto kernel = nbnxmKernelPruneOnly<haveFreshList>(cgh, std::forward<Args>(args)...);
+ cgh.parallel_for<kernelNameType>(flattenNDRange(range), kernel);
+ });
+
+ return e;
+}
+
+template<class... Args>
+cl::sycl::event chooseAndLaunchNbnxmKernelPruneOnly(bool haveFreshList, Args&&... args)
+{
+ return gmx::dispatchTemplatedFunction(
+ [&](auto haveFreshList_) {
+ return launchNbnxmKernelPruneOnly<haveFreshList_>(std::forward<Args>(args)...);
+ },
+ haveFreshList);
+}
+
+void launchNbnxmKernelPruneOnly(NbnxmGpu* nb,
+ const InteractionLocality iloc,
+ const int numParts,
+ const int part,
+ const int numSciInPart)
+{
+ NBAtomDataGpu* adat = nb->atdat;
+ NBParamGpu* nbp = nb->nbparam;
+ gpu_plist* plist = nb->plist[iloc];
+ const bool haveFreshList = plist->haveFreshList;
+ const DeviceStream& deviceStream = *nb->deviceStreams[iloc];
+
+ cl::sycl::event e = chooseAndLaunchNbnxmKernelPruneOnly(haveFreshList,
+ deviceStream,
+ numSciInPart,
+ adat->xq,
+ adat->shiftVec,
+ plist->cj4,
+ plist->sci,
+ plist->imask,
+ nbp->rlistOuter_sq,
+ nbp->rlistInner_sq,
+ numParts,
+ part);
+}
+
+} // namespace Nbnxm
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \internal \file
+ * \brief
+ * Declares nbnxn sycl helper functions
+ *
+ * \ingroup module_nbnxm
+ */
+#ifndef GMX_NBNXM_SYCL_NBNXM_SYCL_KERNEL_PRUNEONLY_H
+#define GMX_NBNXM_SYCL_NBNXM_SYCL_KERNEL_PRUNEONLY_H
-#ifndef GMX_SIMD_IMPLEMENTATION_IBM_VMX_GENERAL_H
-#define GMX_SIMD_IMPLEMENTATION_IBM_VMX_GENERAL_H
-
+// Forward declarations
namespace gmx
{
+enum class InteractionLocality;
+}
+struct NbnxmGpu;
-static inline void simdPrefetch(const void* m)
+namespace Nbnxm
{
-#if defined(__ibmxl__) || defined(__xlC__)
- __dcbt(m);
-#elif defined __GNUC__
- __builtin_prefetch(m);
-#endif
-}
+using gmx::InteractionLocality;
+
+void launchNbnxmKernelPruneOnly(NbnxmGpu* nb,
+ const InteractionLocality iloc,
+ const int numParts,
+ const int part,
+ const int numSciInPart);
-} // namespace gmx
+} // namespace Nbnxm
-#endif // GMX_SIMD_IMPLEMENTATION_IBM_VMX_GENERAL_H
+#endif // GMX_NBNXM_SYCL_NBNXM_SYCL_KERNEL_PRUNEONLY_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Helper functions and constants for SYCL NBNXM kernels
+ *
+ * \ingroup module_nbnxm
+ */
+#ifndef GMX_NBNXM_SYCL_NBNXN_SYCL_KERNEL_UTILS_H
+#define GMX_NBNXM_SYCL_NBNXN_SYCL_KERNEL_UTILS_H
+
+#include "gromacs/gpu_utils/sycl_kernel_utils.h"
+#include "gromacs/nbnxm/pairlist.h"
+#include "gromacs/nbnxm/pairlistparams.h"
+
+namespace Nbnxm
+{
+
+#ifndef GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY
+# define GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY 4
+#endif
+/*! \brief Macro defining default for the prune kernel's j4 processing concurrency.
+ *
+ * The GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY macro allows compile-time override.
+ */
+static constexpr int c_syclPruneKernelJ4Concurrency = GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY;
+
+/* Convenience constants */
+/*! \cond */
+// cluster size = number of atoms per cluster.
+static constexpr int c_clSize = c_nbnxnGpuClusterSize;
+// j-cluster size after split (4 in the current implementation).
+static constexpr int c_splitClSize = c_clSize / c_nbnxnGpuClusterpairSplit;
+// i-cluster interaction mask for a super-cluster with all c_nbnxnGpuNumClusterPerSupercluster=8 bits set.
+static constexpr unsigned superClInteractionMask = ((1U << c_nbnxnGpuNumClusterPerSupercluster) - 1U);
+
+// 1/sqrt(pi), same value as \c M_FLOAT_1_SQRTPI in other NB kernels.
+static constexpr float c_OneOverSqrtPi = 0.564189583547756F;
+// 1/6, same value as in other NB kernels.
+static constexpr float c_oneSixth = 0.16666667F;
+// 1/12, same value as in other NB kernels.
+static constexpr float c_oneTwelfth = 0.08333333F;
+/*! \endcond */
+
+/* The following functions are necessary because on some versions of Intel OpenCL RT, subgroups
+ * do not properly work (segfault or create subgroups of size 1) if used in kernels
+ * with non-1-dimensional workgroup. */
+//! \brief Convert 3D range to 1D
+static inline cl::sycl::range<1> flattenRange(cl::sycl::range<3> range3d)
+{
+ return cl::sycl::range<1>(range3d.size());
+}
+
+//! \brief Convert 3D nd_range to 1D
+static inline cl::sycl::nd_range<1> flattenNDRange(cl::sycl::nd_range<3> nd_range3d)
+{
+ return cl::sycl::nd_range<1>(flattenRange(nd_range3d.get_global_range()),
+ flattenRange(nd_range3d.get_local_range()));
+}
+
+//! \brief Convert flattened 1D index to 3D
+template<int rangeX, int rangeY>
+static inline cl::sycl::id<3> unflattenId(cl::sycl::id<1> id1d)
+{
+ constexpr unsigned rangeXY = rangeX * rangeY;
+ const unsigned id = id1d[0];
+ const unsigned z = id / rangeXY;
+ const unsigned xy = id % rangeXY;
+ return cl::sycl::id<3>(xy % rangeX, xy / rangeX, z);
+}
+
+} // namespace Nbnxm
+
+#endif // GMX_NBNXM_SYCL_NBNXN_SYCL_KERNEL_UTILS_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief
+ * Data types used internally in the nbnxm_sycl module.
+ *
+ * \ingroup module_nbnxm
+ */
+
+#ifndef NBNXM_SYCL_TYPES_H
+#define NBNXM_SYCL_TYPES_H
+
+#include "gromacs/gpu_utils/devicebuffer.h"
+#include "gromacs/gpu_utils/devicebuffer_sycl.h"
+#include "gromacs/gpu_utils/gmxsycl.h"
+#include "gromacs/gpu_utils/gpueventsynchronizer_sycl.h"
+#include "gromacs/gpu_utils/gputraits.h"
+#include "gromacs/gpu_utils/syclutils.h"
+#include "gromacs/nbnxm/gpu_types_common.h"
+#include "gromacs/nbnxm/nbnxm.h"
+#include "gromacs/nbnxm/pairlist.h"
+#include "gromacs/timing/gpu_timing.h"
+#include "gromacs/utility/enumerationhelpers.h"
+
+class GpuEventSynchronizer;
+
+/*! \internal
+ * \brief Main data structure for SYCL nonbonded force calculations.
+ */
+struct NbnxmGpu
+{
+ /*! \brief GPU device context.
+ *
+ * \todo Make it constant reference, once NbnxmGpu is a proper class.
+ */
+ const DeviceContext* deviceContext_;
+ /*! \brief true if doing both local/non-local NB work on GPU */
+ bool bUseTwoStreams = false;
+ /*! \brief true indicates that the nonlocal_done event was marked */
+ bool bNonLocalStreamDoneMarked = false;
+ /*! \brief atom data */
+ NBAtomDataGpu* atdat = nullptr;
+
+ // Data for GPU-side coordinate conversion between integrator and NBNXM
+ /*! \brief array of atom indices */
+ DeviceBuffer<int> atomIndices;
+ /*! \brief size of atom indices */
+ int atomIndicesSize = 0;
+ /*! \brief size of atom indices allocated in device buffer */
+ int atomIndicesSize_alloc = 0;
+ /*! \brief x buf ops num of atoms */
+ DeviceBuffer<int> cxy_na;
+ /*! \brief number of elements in cxy_na */
+ int ncxy_na = 0;
+ /*! \brief number of elements allocated allocated in device buffer */
+ int ncxy_na_alloc = 0;
+ /*! \brief x buf ops cell index mapping */
+ DeviceBuffer<int> cxy_ind;
+ /*! \brief number of elements in cxy_ind */
+ int ncxy_ind = 0;
+ /*! \brief number of elements allocated allocated in device buffer */
+ int ncxy_ind_alloc = 0;
+
+ NBParamGpu* nbparam = nullptr;
+ /*! \brief pair-list data structures (local and non-local) */
+ gmx::EnumerationArray<Nbnxm::InteractionLocality, Nbnxm::gpu_plist*> plist = { { nullptr } };
+ /*! \brief staging area where fshift/energies get downloaded. Will be removed in SYCL. */
+ NBStagingData nbst;
+ /*! \brief local and non-local GPU streams */
+ gmx::EnumerationArray<Nbnxm::InteractionLocality, const DeviceStream*> deviceStreams;
+
+ /*! \brief True if event-based timing is enabled. Always false for SYCL. */
+ bool bDoTime = false;
+ /*! \brief Dummy timers. */
+ Nbnxm::GpuTimers* timers = nullptr;
+ /*! \brief Dummy timing data. */
+ gmx_wallclock_gpu_nbnxn_t* timings = nullptr;
+
+ //! true when a pair-list transfer has been done at this step
+ gmx::EnumerationArray<Nbnxm::InteractionLocality, bool> didPairlistH2D = { { false } };
+ //! true when we we did pruning on this step
+ gmx::EnumerationArray<Nbnxm::InteractionLocality, bool> didPrune = { { false } };
+ //! true when we did rolling pruning (at the previous step)
+ gmx::EnumerationArray<Nbnxm::InteractionLocality, bool> didRollingPrune = { { false } };
+
+ /*! \brief Event triggered when the non-local non-bonded
+ * kernel is done (and the local transfer can proceed) */
+ GpuEventSynchronizer nonlocal_done;
+ /*! \brief Event triggered when the tasks issued in the local
+ * stream that need to precede the non-local force or buffer
+ * operation calculations are done (e.g. f buffer 0-ing, local
+ * x/q H2D, buffer op initialization in local stream that is
+ * required also by nonlocal stream ) */
+ GpuEventSynchronizer misc_ops_and_local_H2D_done;
+
+ /*! \brief True if there is work for the current domain in the
+ * respective locality.
+ *
+ * This includes local/nonlocal GPU work, either bonded or
+ * nonbonded, scheduled to be executed in the current
+ * domain. As long as bonded work is not split up into
+ * local/nonlocal, if there is bonded GPU work, both flags
+ * will be true. */
+ gmx::EnumerationArray<Nbnxm::InteractionLocality, bool> haveWork = { { false } };
+
+ /*! \brief Pointer to event synchronizer triggered when the local
+ * GPU buffer ops / reduction is complete. Would be deprecated in SYCL.
+ *
+ * \note That the synchronizer is managed outside of this module
+ * in StatePropagatorDataGpu.
+ */
+ GpuEventSynchronizer* localFReductionDone = nullptr;
+};
+
+#endif /* NBNXM_SYCL_TYPES_H */
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(onlinehelp INTERFACE)
file(GLOB ONLINEHELP_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${ONLINEHELP_SOURCES} PARENT_SCOPE)
+# Source files have the following dependencies on library infrastructure.
+#target_link_libraries(onlinehelp PRIVATE
+# common
+# legacy_modules
+#)
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(onlinehelp PUBLIC
+target_include_directories(onlinehelp INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(onlinehelp PUBLIC
+target_link_libraries(onlinehelp INTERFACE
+ legacy_api
+ )
+
+# TODO: when onlinehelp is an OBJECT target
+#target_link_libraries(onlinehelp PUBLIC legacy_api)
+#target_link_libraries(onlinehelp PRIVATE common)
+
+# Module dependencies
+# onlinehelp interfaces convey transitive dependence on these modules.
+#target_link_libraries(onlinehelp PUBLIC
+target_link_libraries(onlinehelp INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(onlinehelp PRIVATE NOTHING)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(onlinehelp PRIVATE legacy_modules)
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2016,2017 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/onlinehelp/helpwritercontext.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/basedefinitions.h"
namespace gmx
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_ONLINEHELP_HELPFORMAT_H
#define GMX_ONLINEHELP_HELPFORMAT_H
+#include <memory>
#include <string>
-#include "gromacs/utility/classhelpers.h"
-
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
else
{
- GMX_THROW(InvalidInputError(formatString("Help topic '%s' has no subtopic '%s'",
- impl_->currentTopicAsString().c_str(), name)));
+ GMX_THROW(InvalidInputError(formatString(
+ "Help topic '%s' has no subtopic '%s'", impl_->currentTopicAsString().c_str(), name)));
}
}
impl_->topicStack_.push_back(newTopic);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_ONLINEHELP_HELPMANAGER_H
#define GMX_ONLINEHELP_HELPMANAGER_H
+#include <memory>
#include <string>
-#include "gromacs/utility/classhelpers.h"
-
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <memory>
#include "gromacs/onlinehelp/ihelptopic.h"
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/stringutil.h"
namespace gmx
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
/*! \cond libapi */
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
#include "gromacs/onlinehelp/helpformat.h"
+#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/programcontext.h"
if (state_->links_ != nullptr)
{
HelpLinks::Impl::LinkList::const_iterator link;
- for (link = state_->links_->impl_->links_.begin();
- link != state_->links_->impl_->links_.end(); ++link)
+ for (link = state_->links_->impl_->links_.begin(); link != state_->links_->impl_->links_.end(); ++link)
{
result = replaceAllWords(result, link->linkName, link->replacement);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_ONLINEHELP_HELPWRITERCONTEXT_H
#define GMX_ONLINEHELP_HELPWRITERCONTEXT_H
+#include <memory>
#include <string>
#include <vector>
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
//! Allows the context to use the links.
friend class HelpWriterContext;
*/
explicit HelpWriterContext(Impl* impl);
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
GMX_DISALLOW_ASSIGN(HelpWriterContext);
};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_ONLINEHELP_RSTPARSER_H
#define GMX_ONLINEHELP_RSTPARSER_H
+#include <memory>
#include <string>
#include "gromacs/utility/classhelpers.h"
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
gmx_add_unit_test_library(onlinehelp-test-shared
mock_helptopic.cpp)
+target_link_libraries(onlinehelp-test-shared PUBLIC common)
gmx_add_unit_test(OnlineHelpUnitTests onlinehelp-test
CPP_SOURCE_FILES
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(options INTERFACE)
+
gmx_add_libgromacs_sources(
abstractoption.cpp
abstractsection.cpp
DESTINATION include/gromacs/options)
endif()
+# Source files have the following private module dependencies.
+target_link_libraries(options PRIVATE
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(options PUBLIC
+target_include_directories(options INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(options PUBLIC
+target_link_libraries(options INTERFACE
+ legacy_api
+ )
+
+# TODO: when options is an OBJECT target
+#target_link_libraries(options PUBLIC legacy_api)
+#target_link_libraries(options PRIVATE common)
+
+# Module dependencies
+# options interfaces convey transitive dependence on these modules.
+#target_link_libraries(options PUBLIC
+target_link_libraries(options INTERFACE
+ utility
+ )
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2017, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_OPTIONS_ABSTRACTOPTION_H
#define GMX_OPTIONS_ABSTRACTOPTION_H
+#include <memory>
#include <string>
#include <vector>
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2014,2015 by the GROMACS development team.
- * Copyright (c) 2016,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_OPTIONS_ABSTRACTOPTIONSTORAGE_H
#define GMX_OPTIONS_ABSTRACTOPTIONSTORAGE_H
+#include <memory>
#include <string>
#include <vector>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_OPTIONS_ABSTRACTSECTION_H
#define GMX_OPTIONS_ABSTRACTSECTION_H
+#include <memory>
+
#include "gromacs/options/ioptionscontainerwithsections.h"
#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/gmxassert.h"
AbstractOptionStorage* createStorage(const OptionManagerContainer& /*managers*/) const override
{
// TODO: Implement storeCount() if necessary.
- return internal::createEnumOptionStorage(*this, enumValues_, enumValuesCount_,
+ return internal::createEnumOptionStorage(*this,
+ enumValues_,
+ enumValuesCount_,
convertToInt(MyBase::defaultValue()),
convertToInt(MyBase::defaultValueIfSet()),
std::make_unique<internal::EnumIndexStore<EnumType>>(
AbstractOptionStorage* createStorage(const OptionManagerContainer& /*managers*/) const override
{
// TODO: Implement storeCount() if necessary.
- return internal::createEnumOptionStorage(*this, enumValues_, enumValuesCount_,
+ return internal::createEnumOptionStorage(*this,
+ enumValues_,
+ enumValuesCount_,
convertToInt(MyBase::defaultValue()),
convertToInt(MyBase::defaultValueIfSet()),
std::make_unique<internal::EnumIndexStore<EnumType>>(
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/options/filenameoptionmanager.h"
#include "gromacs/options/optionmanagercontainer.h"
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/stringutil.h"
};
//! Mappings from OptionFileType to file types in filetypes.h.
-const FileTypeMapping c_fileTypeMapping[] = { { eftTopology, efTPS }, { eftRunInput, efTPR },
- { eftTrajectory, efTRX }, { eftEnergy, efEDR },
- { eftPDB, efPDB }, { eftIndex, efNDX },
- { eftPlot, efXVG }, { eftGenericData, efDAT },
- { eftCsv, efCSV } };
+constexpr EnumerationArray<OptionFileType, int> sc_fileTypeMapping = { efTPS, efTPR, efTRX,
+ efEDR, efPDB, efNDX,
+ efXVG, efDAT, efCSV };
/********************************************************************
* FileTypeHandler
{
GMX_RELEASE_ASSERT(!hasFlag(efOption_MultipleTimes),
"allowMultiple() is not supported for file name options");
- if (settings.optionType_ == eftUnknown && settings.legacyType_ >= 0)
+ if (settings.optionType_ == OptionFileType::Count && settings.legacyType_ >= 0)
{
fileType_ = settings.legacyType_;
}
else
{
- ArrayRef<const FileTypeMapping> map(c_fileTypeMapping);
- ArrayRef<const FileTypeMapping>::const_iterator i;
- for (i = map.begin(); i != map.end(); ++i)
+ for (auto i : keysOf(sc_fileTypeMapping))
{
- if (i->optionType == settings.optionType_)
+ if (i == settings.optionType_)
{
- fileType_ = i->fileType;
+ fileType_ = sc_fileTypeMapping[i];
break;
}
}
"File '%s' cannot be used by GROMACS because it "
"does not have a recognizable extension.\n"
"The following extensions are possible for this option:\n %s",
- value.c_str(), joinStrings(extensions(), ", ").c_str());
+ value.c_str(),
+ joinStrings(extensions(), ", ").c_str());
GMX_THROW(InvalidInputError(message));
}
else if (!isValidType(fileType))
std::string message = formatString(
"File name '%s' cannot be used for this option.\n"
"Only the following extensions are possible:\n %s",
- value.c_str(), joinStrings(extensions(), ", ").c_str());
+ value.c_str(),
+ joinStrings(extensions(), ", ").c_str());
GMX_THROW(InvalidInputError(message));
}
return value;
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! Initializes an option with the given name.
explicit FileNameOption(const char* name) :
MyBase(name),
- optionType_(eftUnknown),
+ optionType_(OptionFileType::Count),
legacyType_(-1),
defaultBasename_(nullptr),
defaultType_(-1),
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
else if (fileType == efNR)
{
- const std::string processedValue = findExistingExtension(value, option, impl_->redirector_);
+ std::string processedValue = findExistingExtension(value, option, impl_->redirector_);
if (!processedValue.empty())
{
return processedValue;
std::string message = formatString(
"File '%s' does not exist or is not accessible.\n"
"The following extensions were tried to complete the file name:\n %s",
- value.c_str(), joinStrings(option.extensions(), ", ").c_str());
+ value.c_str(),
+ joinStrings(option.extensions(), ", ").c_str());
GMX_THROW(InvalidInputError(message));
}
}
const std::string realPrefix = !impl_->defaultFileName_.empty() ? impl_->defaultFileName_ : prefix;
if (bInput && !impl_->bInputCheckingDisabled_)
{
- const std::string completedName = findExistingExtension(realPrefix, option, impl_->redirector_);
+ std::string completedName = findExistingExtension(realPrefix, option, impl_->redirector_);
if (!completedName.empty())
{
return completedName;
"No file name was provided, and the default file "
"'%s' does not exist or is not accessible.\n"
"The following extensions were tried to complete the file name:\n %s",
- prefix.c_str(), joinStrings(option.extensions(), ", ").c_str());
+ prefix.c_str(),
+ joinStrings(option.extensions(), ", ").c_str());
GMX_THROW(InvalidInputError(message));
}
else if (option.isRequired())
"Required option was not provided, and the default file "
"'%s' does not exist or is not accessible.\n"
"The following extensions were tried to complete the file name:\n %s",
- prefix.c_str(), joinStrings(option.extensions(), ", ").c_str());
+ prefix.c_str(),
+ joinStrings(option.extensions(), ", ").c_str());
GMX_THROW(InvalidInputError(message));
}
// We get here with the legacy optional behavior.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_OPTIONS_FILENAMEOPTIONMANAGER_H
#define GMX_OPTIONS_FILENAMEOPTIONMANAGER_H
+#include <memory>
#include <string>
#include "gromacs/options/options.h"
-#include "gromacs/utility/classhelpers.h"
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2015,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2015,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* \ingroup module_options
*/
-enum OptionFileType
+enum class OptionFileType : int
{
- eftUnknown,
- eftTopology,
- eftRunInput,
- eftTrajectory,
- eftEnergy,
- eftPDB,
- eftIndex,
- eftPlot,
- eftGenericData,
- eftCsv,
- eftOptionFileType_NR
+ Topology,
+ RunInput,
+ Trajectory,
+ Energy,
+ PDB,
+ Index,
+ Plot,
+ GenericData,
+ Csv,
+ Count
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_OPTIONS_OPTIONMANAGERCONTAINER_H
#define GMX_OPTIONS_OPTIONMANAGERCONTAINER_H
+#include <memory>
#include <vector>
#include "gromacs/utility/classhelpers.h"
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2014,2015 by the GROMACS development team.
- * Copyright (c) 2016,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_OPTIONS_OPTIONS_H
#define GMX_OPTIONS_OPTIONS_H
+#include <memory>
#include <string>
#include "gromacs/options/ioptionscontainerwithsections.h"
-#include "gromacs/utility/classhelpers.h"
namespace gmx
{
// From IOptionsContainer
OptionInfo* addOptionImpl(const AbstractOption& settings) override;
- PrivateImplPointer<internal::OptionsImpl> impl_;
+ std::unique_ptr<internal::OptionsImpl> impl_;
//! Needed to be able to extend the interface of this object.
friend class OptionsAssigner;
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/options/optionmanagercontainer.h"
#include "gromacs/options/options.h"
#include "gromacs/options/optionsection.h"
+#include "gromacs/utility/classhelpers.h"
#include "isectionstorage.h"
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
- * Copyright (c) 2015,2016,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_OPTIONS_OPTIONSASSIGNER_H
#define GMX_OPTIONS_OPTIONSASSIGNER_H
+#include <memory>
#include <string>
-#include "gromacs/utility/classhelpers.h"
-
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_OPTIONS_OPTIONSECTION_H
#define GMX_OPTIONS_OPTIONSECTION_H
-#include "gromacs/utility/classhelpers.h"
+#include <memory>
#include "abstractsection.h"
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2014,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstddef>
+#include <memory>
#include <string>
#include "gromacs/options/abstractoption.h"
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
gmx::Options options;
std::string value;
- ASSERT_NO_THROW_GMX(options.addOption(
- FileNameOption("f").store(&value).required().filetype(gmx::eftGenericData).outputFile().defaultBasename("testfile")));
+ ASSERT_NO_THROW_GMX(options.addOption(FileNameOption("f")
+ .store(&value)
+ .required()
+ .filetype(gmx::OptionFileType::GenericData)
+ .outputFile()
+ .defaultBasename("testfile")));
EXPECT_EQ("testfile.dat", value);
gmx::OptionsAssigner assigner(&options);
{
gmx::Options options;
std::string value;
- ASSERT_NO_THROW_GMX(options.addOption(
- FileNameOption("f").store(&value).required().filetype(gmx::eftGenericData).outputFile().defaultBasename("testfile")));
+ ASSERT_NO_THROW_GMX(options.addOption(FileNameOption("f")
+ .store(&value)
+ .required()
+ .filetype(gmx::OptionFileType::GenericData)
+ .outputFile()
+ .defaultBasename("testfile")));
EXPECT_EQ("testfile.dat", value);
gmx::OptionsAssigner assigner(&options);
gmx::Options options;
std::string value;
ASSERT_NO_THROW_GMX(options.addOption(
- FileNameOption("f").store(&value).filetype(gmx::eftTrajectory).outputFile().defaultBasename("testfile")));
+ FileNameOption("f").store(&value).filetype(gmx::OptionFileType::Trajectory).outputFile().defaultBasename("testfile")));
EXPECT_TRUE(value.empty());
gmx::OptionsAssigner assigner(&options);
gmx::Options options;
std::string value;
ASSERT_NO_THROW_GMX(options.addOption(
- FileNameOption("f").store(&value).filetype(gmx::eftIndex).outputFile().defaultBasename("testfile")));
+ FileNameOption("f").store(&value).filetype(gmx::OptionFileType::Index).outputFile().defaultBasename("testfile")));
EXPECT_TRUE(value.empty());
gmx::OptionsAssigner assigner(&options);
ASSERT_NO_THROW_GMX(options.addOption(FileNameOption("f")
.store(&value)
.required()
- .filetype(gmx::eftTrajectory)
+ .filetype(gmx::OptionFileType::Trajectory)
.outputFile()
.defaultBasename("testfile")
.defaultType(efPDB)));
std::string value;
ASSERT_NO_THROW_GMX(options.addOption(FileNameOption("f")
.store(&value)
- .filetype(gmx::eftTrajectory)
+ .filetype(gmx::OptionFileType::Trajectory)
.outputFile()
.defaultBasename("testfile")
.defaultType(efPDB)));
{
gmx::Options options;
std::string value;
- ASSERT_NO_THROW_GMX(
- options.addOption(FileNameOption("f").store(&value).filetype(gmx::eftIndex).outputFile()));
+ ASSERT_NO_THROW_GMX(options.addOption(
+ FileNameOption("f").store(&value).filetype(gmx::OptionFileType::Index).outputFile()));
EXPECT_TRUE(value.empty());
gmx::OptionsAssigner assigner(&options);
gmx::Options options;
std::string value;
ASSERT_NO_THROW_GMX(options.addOption(
- FileNameOption("f").store(&value).filetype(gmx::eftTrajectory).outputFile()));
+ FileNameOption("f").store(&value).filetype(gmx::OptionFileType::Trajectory).outputFile()));
EXPECT_TRUE(value.empty());
gmx::OptionsAssigner assigner(&options);
{
gmx::Options options;
std::string value;
- ASSERT_NO_THROW_GMX(options.addOption(
- FileNameOption("f").store(&value).required().filetype(gmx::eftCsv).outputFile().defaultBasename("testfile")));
+ ASSERT_NO_THROW_GMX(options.addOption(FileNameOption("f")
+ .store(&value)
+ .required()
+ .filetype(gmx::OptionFileType::Csv)
+ .outputFile()
+ .defaultBasename("testfile")));
EXPECT_EQ("testfile.csv", value);
gmx::OptionsAssigner assigner(&options);
{
gmx::Options options;
std::string value;
- ASSERT_NO_THROW_GMX(options.addOption(
- FileNameOption("f").store(&value).required().filetype(gmx::eftCsv).outputFile().defaultBasename("testfile")));
+ ASSERT_NO_THROW_GMX(options.addOption(FileNameOption("f")
+ .store(&value)
+ .required()
+ .filetype(gmx::OptionFileType::Csv)
+ .outputFile()
+ .defaultBasename("testfile")));
EXPECT_EQ("testfile.csv", value);
gmx::OptionsAssigner assigner(&options);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
std::string value;
ASSERT_NO_THROW_GMX(options_.addOption(
- FileNameOption("f").store(&value).filetype(gmx::eftTrajectory).outputFile()));
+ FileNameOption("f").store(&value).filetype(gmx::OptionFileType::Trajectory).outputFile()));
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
{
std::string value;
ASSERT_NO_THROW_GMX(options_.addOption(
- FileNameOption("f").store(&value).filetype(gmx::eftTrajectory).outputFile().defaultType(efPDB)));
+ FileNameOption("f").store(&value).filetype(gmx::OptionFileType::Trajectory).outputFile().defaultType(efPDB)));
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
TEST_F(FileNameOptionManagerTest, GivesErrorOnMissingInputFile)
{
std::string value;
- ASSERT_NO_THROW_GMX(
- options_.addOption(FileNameOption("f").store(&value).filetype(gmx::eftIndex).inputFile()));
+ ASSERT_NO_THROW_GMX(options_.addOption(
+ FileNameOption("f").store(&value).filetype(gmx::OptionFileType::Index).inputFile()));
EXPECT_TRUE(value.empty());
gmx::OptionsAssigner assigner(&options_);
{
std::string value;
ASSERT_NO_THROW_GMX(options_.addOption(
- FileNameOption("f").store(&value).filetype(gmx::eftTrajectory).inputFile()));
+ FileNameOption("f").store(&value).filetype(gmx::OptionFileType::Trajectory).inputFile()));
EXPECT_TRUE(value.empty());
gmx::OptionsAssigner assigner(&options_);
{
std::string value;
ASSERT_NO_THROW_GMX(options_.addOption(
- FileNameOption("f").store(&value).filetype(gmx::eftIndex).inputFile().defaultBasename("missing")));
+ FileNameOption("f").store(&value).filetype(gmx::OptionFileType::Index).inputFile().defaultBasename("missing")));
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
TEST_F(FileNameOptionManagerTest, GivesErrorOnMissingRequiredInputFile)
{
std::string value;
- ASSERT_NO_THROW_GMX(options_.addOption(
- FileNameOption("f").store(&value).required().filetype(gmx::eftIndex).inputFile().defaultBasename("missing")));
+ ASSERT_NO_THROW_GMX(options_.addOption(FileNameOption("f")
+ .store(&value)
+ .required()
+ .filetype(gmx::OptionFileType::Index)
+ .inputFile()
+ .defaultBasename("missing")));
EXPECT_EQ("missing.ndx", value);
gmx::OptionsAssigner assigner(&options_);
{
std::string value;
ASSERT_NO_THROW_GMX(options_.addOption(
- FileNameOption("f").store(&value).filetype(gmx::eftIndex).inputFile().allowMissing()));
+ FileNameOption("f").store(&value).filetype(gmx::OptionFileType::Index).inputFile().allowMissing()));
EXPECT_TRUE(value.empty());
gmx::OptionsAssigner assigner(&options_);
std::string value;
ASSERT_NO_THROW_GMX(options_.addOption(FileNameOption("f")
.store(&value)
- .filetype(gmx::eftIndex)
+ .filetype(gmx::OptionFileType::Index)
.inputFile()
.defaultBasename("missing")
.allowMissing()));
ASSERT_NO_THROW_GMX(options_.addOption(FileNameOption("f")
.store(&value)
.required()
- .filetype(gmx::eftIndex)
+ .filetype(gmx::OptionFileType::Index)
.inputFile()
.defaultBasename("missing")
.allowMissing()));
std::string value;
ASSERT_NO_THROW_GMX(options_.addOption(
- FileNameOption("f").store(&value).filetype(gmx::eftTrajectory).inputFile()));
+ FileNameOption("f").store(&value).filetype(gmx::OptionFileType::Trajectory).inputFile()));
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
addExistingFile("testfile.trr");
std::string value;
- ASSERT_NO_THROW_GMX(options_.addOption(
- FileNameOption("f").store(&value).required().filetype(gmx::eftTrajectory).inputFile().defaultBasename("testfile")));
+ ASSERT_NO_THROW_GMX(options_.addOption(FileNameOption("f")
+ .store(&value)
+ .required()
+ .filetype(gmx::OptionFileType::Trajectory)
+ .inputFile()
+ .defaultBasename("testfile")));
EXPECT_EQ("testfile.xtc", value);
gmx::OptionsAssigner assigner(&options_);
std::string value;
ASSERT_NO_THROW_GMX(options_.addOption(
- FileNameOption("f").store(&value).filetype(gmx::eftTrajectory).inputFile().defaultBasename("testfile")));
+ FileNameOption("f").store(&value).filetype(gmx::OptionFileType::Trajectory).inputFile().defaultBasename("testfile")));
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
addExistingFile("testfile.trr");
std::string value;
- ASSERT_NO_THROW_GMX(options_.addOption(
- FileNameOption("f").store(&value).required().filetype(gmx::eftTrajectory).inputFile().defaultBasename("foo")));
+ ASSERT_NO_THROW_GMX(options_.addOption(FileNameOption("f")
+ .store(&value)
+ .required()
+ .filetype(gmx::OptionFileType::Trajectory)
+ .inputFile()
+ .defaultBasename("foo")));
ASSERT_NO_THROW_GMX(manager_.addDefaultFileNameOption(&options_, "deffnm"));
EXPECT_EQ("foo.xtc", value);
std::string value;
ASSERT_NO_THROW_GMX(options_.addOption(
- FileNameOption("f").store(&value).filetype(gmx::eftTrajectory).inputFile().defaultBasename("foo")));
+ FileNameOption("f").store(&value).filetype(gmx::OptionFileType::Trajectory).inputFile().defaultBasename("foo")));
ASSERT_NO_THROW_GMX(manager_.addDefaultFileNameOption(&options_, "deffnm"));
gmx::OptionsAssigner assigner(&options_);
ASSERT_NO_THROW_GMX(options_.addOption(FileNameOption("f")
.store(&value)
.required()
- .filetype(gmx::eftIndex)
+ .filetype(gmx::OptionFileType::Index)
.inputFile()
.defaultBasename("default")
.allowMissing()));
*
* These must correspond to the TimeUnit enum in the header!
*/
-const EnumerationArray<TimeUnit, const char*> c_timeUnitNames = { { "fs", "ps", "ns", "us", "ms",
- "s" } };
+const EnumerationArray<TimeUnit, const char*> c_timeUnitNames = {
+ { "fs", "ps", "ns", "us", "ms", "s" }
+};
/*! \brief
* Scaling factors from each time unit to internal units (=picoseconds).
*
"Time unit provided with environment variable GMXTIMEUNIT=%s "
"is not recognized as a valid time unit.\n"
"Possible values are: %s",
- value, joinStrings(c_timeUnitNames, ", ").c_str());
+ value,
+ joinStrings(c_timeUnitNames, ", ").c_str());
GMX_THROW(InvalidInputError(message));
}
setTimeUnit(result);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_OPTIONS_TIMEUNITMANAGER_H
#define GMX_OPTIONS_TIMEUNITMANAGER_H
+#include <memory>
+
#include "gromacs/fileio/oenv.h"
#include "gromacs/options/ioptionsbehavior.h"
#include "gromacs/utility/classhelpers.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
if (currentObject_->keyExists(name))
{
currentKnownNames_->insert(name);
- auto parentObject = currentObject_;
- auto parentKnownNames = currentKnownNames_;
+ const auto* parentObject = currentObject_;
+ auto* parentKnownNames = currentKnownNames_;
// TODO: Consider what to do with mismatching types.
currentObject_ = &(*currentObject_)[name].asObject();
currentPath_.append(name);
{
const std::string& name = section.name();
auto parentBuilder = currentObjectBuilder_;
- auto parentObject = currentSourceObject_;
+ const auto* parentObject = currentSourceObject_;
currentObjectBuilder_ = currentObjectBuilder_.addObject(name);
currentSourceObject_ = (currentSourceObject_ != nullptr && currentSourceObject_->keyExists(name)
? &(*currentSourceObject_)[name].asObject()
helper.processOptionSection(options.rootSection());
if (helper.hasUnknownPaths())
{
- std::string paths(formatAndJoin(helper.unknownPaths(), "\n ",
- [](const KeyValueTreePath& path) { return path.toString(); }));
+ std::string paths(formatAndJoin(helper.unknownPaths(), "\n ", [](const KeyValueTreePath& path) {
+ return path.toString();
+ }));
std::string message("Unknown input values:\n " + paths);
GMX_THROW(InvalidInputError(message));
}
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(pbcutil INTERFACE)
file(GLOB PBCUTIL_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${PBCUTIL_SOURCES} PARENT_SCOPE)
+# Source files have the following dependencies on library infrastructure.
+#target_link_libraries(pbcutil PRIVATE
+# common
+# legacy_modules
+#)
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(pbcutil PUBLIC
+target_include_directories(pbcutil INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(pbcutil PUBLIC
+target_link_libraries(pbcutil INTERFACE
+ legacy_api
+ )
+
+# TODO: when pbcutil is an OBJECT target
+#target_link_libraries(pbcutil PUBLIC legacy_api)
+#target_link_libraries(pbcutil PRIVATE common)
+
+# Module dependencies
+# pbcutil interfaces convey transitive dependence on these modules.
+#target_link_libraries(pbcutil PUBLIC
+target_link_libraries(pbcutil INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(pbcutil PRIVATE NOTHING)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(pbcutil PRIVATE legacy_modules)
+
if(GMX_INSTALL_LEGACY_API)
install(FILES
pbc.h
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_PBCUTIL_COM_H
#include <algorithm>
+#include <memory>
#include "gromacs/math/vec.h"
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/classhelpers.h"
#include "pbcenums.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2019, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_PBCUTIL_ISHIFT_H
#define GMX_PBCUTIL_ISHIFT_H
-#define D_BOX_Z 1
-#define D_BOX_Y 1
-#define D_BOX_X 2
-#define N_BOX_Z (2 * D_BOX_Z + 1)
-#define N_BOX_Y (2 * D_BOX_Y + 1)
-#define N_BOX_X (2 * D_BOX_X + 1)
-#define N_IVEC (N_BOX_Z * N_BOX_Y * N_BOX_X)
-#define CENTRAL (N_IVEC / 2)
-#define SHIFTS N_IVEC
+namespace gmx
+{
+//! Maximum dimensions of grid expressing shifts across PBC
+//! \{
+constexpr int c_dBoxZ = 1;
+constexpr int c_dBoxY = 1;
+constexpr int c_dBoxX = 2;
+//! \}
+namespace detail
+{
+constexpr int c_nBoxZ = 2 * gmx::c_dBoxZ + 1;
+constexpr int c_nBoxY = 2 * gmx::c_dBoxY + 1;
+constexpr int c_nBoxX = 2 * gmx::c_dBoxX + 1;
+constexpr int c_numIvecs = detail::c_nBoxZ * detail::c_nBoxY * detail::c_nBoxX;
+} // namespace detail
-#define XYZ2IS(x, y, z) (N_BOX_X * (N_BOX_Y * ((z) + D_BOX_Z) + (y) + D_BOX_Y) + (x) + D_BOX_X)
-#define IVEC2IS(iv) (XYZ2IS((iv)[XX], (iv)[YY], (iv)[ZZ]))
-#define IS2X(iv) (((iv) % N_BOX_X) - D_BOX_X)
-#define IS2Y(iv) ((((iv) / N_BOX_X) % N_BOX_Y) - D_BOX_Y)
-#define IS2Z(iv) ((iv) / (N_BOX_X * N_BOX_Y) - D_BOX_Z)
+constexpr int c_centralShiftIndex = detail::c_numIvecs / 2;
+constexpr int c_numShiftVectors = detail::c_numIvecs;
+//! Convert grid coordinates to shift index
+static inline int xyzToShiftIndex(int x, int y, int z)
+{
+ return (detail::c_nBoxX * (detail::c_nBoxY * ((z) + gmx::c_dBoxZ) + (y) + gmx::c_dBoxY) + (x)
+ + gmx::c_dBoxX);
+}
+
+//! Convert grid coordinates to shift index
+static inline int ivecToShiftIndex(ivec iv)
+{
+ return (xyzToShiftIndex((iv)[XX], (iv)[YY], (iv)[ZZ]));
+}
+
+//! Return the shift in the X dimension of grid space corresponding to \c iv
+static inline int shiftIndexToXDim(int iv)
+{
+ return (((iv) % detail::c_nBoxX) - gmx::c_dBoxX);
+}
+} // namespace gmx
#endif
"You are probably trying to use a trajectory which does "
"not match the first %d atoms of the run input file.\n"
"You can make a matching run input file with gmx convert-tpr.",
- at_end, at_end);
+ at_end,
+ at_end);
}
if (ftype == F_SETTLE)
{
{
if (!g->edges[i].empty())
{
- fprintf(log, "%5d%7d%7d%7d %1s%5zu", g->edgeAtomBegin + i + 1,
- g->ishift[g->edgeAtomBegin + i][XX], g->ishift[g->edgeAtomBegin + i][YY],
+ fprintf(log,
+ "%5d%7d%7d%7d %1s%5zu",
+ g->edgeAtomBegin + i + 1,
+ g->ishift[g->edgeAtomBegin + i][XX],
+ g->ishift[g->edgeAtomBegin + i][YY],
g->ishift[g->edgeAtomBegin + i][ZZ],
- (!g->edgeColor.empty()) ? cc[g->edgeColor[i]] : " ", g->edges[i].size());
+ (!g->edgeColor.empty()) ? cc[g->edgeColor[i]] : " ",
+ g->edges[i].size());
for (const int edge : g->edges[i])
{
fprintf(log, " %5d", edge + 1);
}
if (debug)
{
- fprintf(debug, "graph partNr[] numAtomsChanged=%d, bMultiPart=%s\n", numAtomsChanged,
+ fprintf(debug,
+ "graph partNr[] numAtomsChanged=%d, bMultiPart=%s\n",
+ numAtomsChanged,
gmx::boolToString(haveMultipleParts));
}
} while (numAtomsChanged > 0);
"mk_grey: shifts for atom %d due to atom %d\n"
"are (%d,%d,%d), should be (%d,%d,%d)\n"
"dx = (%g,%g,%g)\n",
- aj + 1, ai + 1, is_aj[XX], is_aj[YY], is_aj[ZZ], g->ishift[aj][XX],
- g->ishift[aj][YY], g->ishift[aj][ZZ], dx[XX], dx[YY], dx[ZZ]);
+ aj + 1,
+ ai + 1,
+ is_aj[XX],
+ is_aj[YY],
+ is_aj[ZZ],
+ g->ishift[aj][XX],
+ g->ishift[aj][YY],
+ g->ishift[aj][ZZ],
+ dx[XX],
+ dx[YY],
+ dx[ZZ]);
}
(*nerror)++;
}
"There are inconsistent shifts over periodic boundaries in a molecule type "
"consisting of %d atoms. The longest distance involved in such interactions is "
"%.3f nm which is %s half the box length.",
- g->shiftAtomEnd, maxDistance, maxDistance >= 0.5 * minBoxSize ? "above" : "close to");
+ g->shiftAtomEnd,
+ maxDistance,
+ maxDistance >= 0.5 * minBoxSize ? "above" : "close to");
switch (g->parts)
{
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
-const gmx::EnumerationArray<PbcType, std::string> c_pbcTypeNames = { { "xyz", "no", "xy", "screw",
- "unset" } };
+const gmx::EnumerationArray<PbcType, std::string> c_pbcTypeNames = {
+ { "xyz", "no", "xy", "screw", "unset" }
+};
/* Skip 0 so we have more chance of detecting if we forgot to call set_pbc. */
enum
void matrix_convert(matrix box, const rvec vec, const rvec angleInDegrees)
{
rvec angle;
- svmul(DEG2RAD, angleInDegrees, angle);
+ svmul(gmx::c_deg2Rad, angleInDegrees, angle);
box[XX][XX] = vec[XX];
box[YY][XX] = vec[YY] * cos(angle[ZZ]);
box[YY][YY] = vec[YY] * sin(angle[ZZ]);
}
//! Set to true if warning has been printed
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static gmx_bool bWarnedGuess = FALSE;
PbcType guessPbcType(const matrix box)
fprintf(stderr,
"WARNING: Unsupported box diagonal %f %f %f, "
"will not use periodic boundary conditions\n\n",
- box[XX][XX], box[YY][YY], box[ZZ][ZZ]);
+ box[XX][XX],
+ box[YY][YY],
+ box[ZZ][ZZ]);
bWarnedGuess = TRUE;
}
pbcType = PbcType::No;
fprintf(debug,
" tricvec %2d = %2d %2d %2d %5.2f %5.2f "
"%5.2f %5.2f %5.2f %5.2f %5.2f %5.2f\n",
- pbc->ntric_vec, i, j, k, sqrt(d2old),
- sqrt(d2new), trial[XX], trial[YY], trial[ZZ],
- pos[XX], pos[YY], pos[ZZ]);
+ pbc->ntric_vec,
+ i,
+ j,
+ k,
+ sqrt(d2old),
+ sqrt(d2new),
+ trial[XX],
+ trial[YY],
+ trial[ZZ],
+ pos[XX],
+ pos[YY],
+ pos[ZZ]);
}
}
}
"Internal error in pbc_dx_aiuc, set_pbc_dd or set_pbc has not been called");
}
- is = IVEC2IS(ishift);
+ is = gmx::ivecToShiftIndex(ishift);
if (debug)
{
- range_check_mesg(is, 0, SHIFTS, "PBC shift vector index range check.");
+ range_check_mesg(is, 0, gmx::c_numShiftVectors, "PBC shift vector index range check.");
}
return is;
}
}
-void calc_shifts(const matrix box, rvec shift_vec[])
+void calc_shifts(const matrix box, gmx::ArrayRef<gmx::RVec> shift_vec)
{
- for (int n = 0, m = -D_BOX_Z; m <= D_BOX_Z; m++)
+ for (int n = 0, m = -gmx::c_dBoxZ; m <= gmx::c_dBoxZ; m++)
{
- for (int l = -D_BOX_Y; l <= D_BOX_Y; l++)
+ for (int l = -gmx::c_dBoxY; l <= gmx::c_dBoxY; l++)
{
- for (int k = -D_BOX_X; k <= D_BOX_X; k++, n++)
+ for (int k = -gmx::c_dBoxX; k <= gmx::c_dBoxX; k++, n++)
{
for (int d = 0; d < DIM; d++)
{
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2012,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/real.h"
struct gmx_domdec_t;
struct gmx_mtop_t;
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+} // namespace gmx
+
//! Enumeration that contains all supported periodic boundary setups.
enum class PbcType : int
{
* \param[in] box The simulation cell
* \return TRUE when the box was corrected.
*/
-gmx_bool correct_box(FILE* fplog, int step, tensor box);
+bool correct_box(FILE* fplog, int step, tensor box);
/*! \brief Initiate the periodic boundary condition algorithms.
*
* \param[in] box The box tensor
* \return the pbc structure when pbc operations are required, NULL otherwise.
*/
-t_pbc* set_pbc_dd(t_pbc* pbc, PbcType pbcType, const ivec domdecCells, gmx_bool bSingleDir, const matrix box);
+t_pbc* set_pbc_dd(t_pbc* pbc, PbcType pbcType, const ivec domdecCells, bool bSingleDir, const matrix box);
/*! \brief Compute distance with PBC
*
* \param[in] x2 Coordinates for particle 2
* \param[out] dx Distance vector
* \return the ishift required to shift x1 at closest distance to x2;
- * i.e. if 0<=ishift<SHIFTS then x1 - x2 + shift_vec[ishift] = dx
+ * i.e. if 0<=ishift<c_numShiftVectors then x1 - x2 + shift_vec[ishift] = dx
* (see calc_shifts below on how to obtain shift_vec)
*/
int pbc_dx_aiuc(const t_pbc* pbc, const rvec x1, const rvec x2, rvec dx);
* \param[in] box The simulation box
* \param[out] shift_vec The shifting vectors
*/
-void calc_shifts(const matrix box, rvec shift_vec[]);
+void calc_shifts(const matrix box, gmx::ArrayRef<gmx::RVec> shift_vec);
/*! \brief Calculates the center of the box.
*
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_PBCUTIL_PBC_AIUC_CUDA_CUH
#include "gromacs/gpu_utils/vectype_ops.cuh"
+#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/pbc_aiuc.h"
+static inline __device__ int xyzToShiftIndex(int x, int y, int z)
+{
+ return (gmx::detail::c_nBoxX * (gmx::detail::c_nBoxY * ((z) + gmx::c_dBoxZ) + (y) + gmx::c_dBoxY)
+ + (x) + gmx::c_dBoxX);
+}
+
+static inline __device__ int int3ToShiftIndex(int3 iv)
+{
+ return (xyzToShiftIndex(iv.x, iv.y, iv.z));
+}
+
/*! \brief Computes the vector between two points taking PBC into account.
*
* Computes the vector dr between points r2 and r1, taking into account the
if (returnShift)
{
- ivec ishift;
+ int3 ishift;
- ishift[XX] = -__float2int_rn(shx);
- ishift[YY] = -__float2int_rn(shy);
- ishift[ZZ] = -__float2int_rn(shz);
+ ishift.x = -__float2int_rn(shx);
+ ishift.y = -__float2int_rn(shy);
+ ishift.z = -__float2int_rn(shz);
- return IVEC2IS(ishift);
+ return int3ToShiftIndex(ishift);
}
else
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
namespace gmx
{
-/*! \brief Names for different centering types.
- *
- * Those names need to be in sync with the CenteringType enum class
- * and reflect the same fields there.
- */
-static EnumerationArray<CenteringType, const char*> c_centeringTypeShortNames = {
- { "Triclinic", "Rectangular", "Zero-Based" }
-};
-
-/*! \brief Names for different centering types.
- *
- * Those names need to be in sync with the UnitCellType enum class
- * and reflect the same fields there.
- */
-static EnumerationArray<UnitCellType, const char*> c_unitCellTypeShortNames = {
- { "Triclinic", "Rectangular", "Compact" }
-};
-
const char* centerTypeNames(CenteringType type)
{
+ constexpr EnumerationArray<CenteringType, const char*> c_centeringTypeShortNames = {
+ "Triclinic", "Rectangular", "Zero-Based"
+ };
return c_centeringTypeShortNames[type];
}
const char* unitCellTypeNames(UnitCellType type)
{
+ constexpr EnumerationArray<UnitCellType, const char*> c_unitCellTypeShortNames = {
+ "Triclinic", "Rectangular", "Compact"
+ };
return c_unitCellTypeShortNames[type];
}
gmx_fatal(FARGS,
"Molecule %d marked for clustering but not atom %d in it - check your "
"index!",
- i + 1, j + 1);
+ i + 1,
+ j + 1);
}
else if (!bMol[i] && bTmp[j])
{
gmx_fatal(FARGS,
"Atom %d marked for clustering but not molecule %d - this is an internal "
"error...",
- j + 1, i + 1);
+ j + 1,
+ i + 1);
}
else if (bMol[i])
{
fprintf(debug,
"\nShifting position of molecule %d "
"by %8.3f %8.3f %8.3f\n",
- i + 1, shift[XX], shift[YY], shift[ZZ]);
+ i + 1,
+ shift[XX],
+ shift[YY],
+ shift[ZZ]);
}
for (j = mols->index[i]; (j < mols->index[i + 1] && j < natoms); j++)
{
fprintf(debug,
"\nShifting position of residue %d (atoms %d-%d) "
"by %g,%g,%g\n",
- atom[res_start].resind + 1, res_start + 1, res_end + 1, shift[XX],
- shift[YY], shift[ZZ]);
+ atom[res_start].resind + 1,
+ res_start + 1,
+ res_end + 1,
+ shift[XX],
+ shift[YY],
+ shift[ZZ]);
}
for (j = res_start; j < res_end; j++)
{
{
gmx_fatal(FARGS,
"Structure or trajectory file has more atoms (%d) than the topology (%d)",
- natoms, gpbc->natoms_init);
+ natoms,
+ gpbc->natoms_init);
}
gpbc->ngraph++;
srenew(gpbc->graph, gpbc->ngraph);
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
auto unitcell = std::get<0>(params);
auto center = std::get<1>(params);
auto pbcType = std::get<2>(params);
- placeCoordinatesWithCOMInBox(pbcType, unitcell, center, box, testCoordinates_, testTopology_,
- COMShiftType::Molecule);
+ placeCoordinatesWithCOMInBox(
+ pbcType, unitcell, center, box, testCoordinates_, testTopology_, COMShiftType::Molecule);
std::string testString = "Molecule " + std::string(unitCellTypeNames(unitcell))
+ std::string(centerTypeNames(center)) + c_pbcTypeNames[pbcType]
+ c_pbcTypeNames[guessPbcType(box)];
auto unitcell = std::get<0>(params);
auto center = std::get<1>(params);
auto pbcType = std::get<2>(params);
- placeCoordinatesWithCOMInBox(pbcType, unitcell, center, box, testCoordinates_, testTopology_,
- COMShiftType::Residue);
+ placeCoordinatesWithCOMInBox(
+ pbcType, unitcell, center, box, testCoordinates_, testTopology_, COMShiftType::Residue);
std::string testString = "Residue " + std::string(unitCellTypeNames(unitcell))
+ std::string(centerTypeNames(center)) + c_pbcTypeNames[pbcType]
+ c_pbcTypeNames[guessPbcType(box)];
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vectypes.h"
#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/utility/arrayref.h"
#include "testutils/refdata.h"
// Choose box vector entries whose magnitudes will lead to unique
// shift vector values when the largest box shift in any dimension
// is two.
- const matrix box = { { 0.01, 1, -100 }, { 300, -0.03, 3 }, { -6, -600, 0.06 } };
- rvec shiftVectors[SHIFTS];
+ const matrix box = { { 0.01, 1, -100 }, { 300, -0.03, 3 }, { -6, -600, 0.06 } };
+ std::vector<gmx::RVec> shiftVectors(c_numShiftVectors);
calc_shifts(box, shiftVectors);
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2016,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(pulling INTERFACE)
file(GLOB PULLING_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${PULLING_SOURCES} PARENT_SCOPE)
+# Source files have the following dependencies on library infrastructure.
+#target_link_libraries(pulling PRIVATE
+# common
+# legacy_modules
+#)
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(pulling PUBLIC
+target_include_directories(pulling INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(pulling PUBLIC
+target_link_libraries(pulling INTERFACE
+ legacy_api
+ )
+
+# TODO: when pulling is an OBJECT target
+#target_link_libraries(pulling PUBLIC legacy_api)
+#target_link_libraries(pulling PRIVATE common)
+
+# Module dependencies
+# pulling interfaces convey transitive dependence on these modules.
+#target_link_libraries(pulling PUBLIC
+target_link_libraries(pulling INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(pulling PRIVATE NOTHING)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(pulling PRIVATE legacy_modules)
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
pcrdHistory.dr23[m] += pcrd.spatialData.dr23[m];
pcrdHistory.dr45[m] += pcrd.spatialData.dr45[m];
}
- if (pcrd.params.eGeom == epullgCYL)
+ if (pcrd.params.eGeom == PullGroupGeometry::Cylinder)
{
for (int m = 0; m < DIM; m++)
{
- pcrdHistory.dynaX[m] += pull->dyna[c].x[m];
+ pcrdHistory.dynaX[m] += pcrd.dynamicGroup0->x[m];
}
}
}
double referenceValue,
const int numValuesInSum)
{
- const double unit_factor = pull_conversion_factor_internal2userinput(&coordParams);
+ const double unit_factor = pull_conversion_factor_internal2userinput(coordParams);
fprintf(out, "\t%g", pcrdData.value * unit_factor / numValuesInSum);
- if (pullParams.bPrintRefValue && coordParams.eType != epullEXTERNAL)
+ if (pullParams.bPrintRefValue && coordParams.eType != PullingAlgorithm::External)
{
fprintf(out, "\t%g", referenceValue * unit_factor / numValuesInSum);
}
pcrdHistory = &pull->coordForceHistory->pullCoordinateSums[c];
numValuesInSum = pull->coordForceHistory->numValuesInXSum;
- pull_print_coord_dr(out, pull->params, pcrd.params, *pcrdHistory, pcrdHistory->valueRef,
- numValuesInSum);
+ pull_print_coord_dr(
+ out, pull->params, pcrd.params, *pcrdHistory, pcrdHistory->valueRef, numValuesInSum);
}
else
{
- pull_print_coord_dr(out, pull->params, pcrd.params, pcrd.spatialData, pcrd.value_ref,
- numValuesInSum);
+ pull_print_coord_dr(
+ out, pull->params, pcrd.params, pcrd.spatialData, pcrd.value_ref, numValuesInSum);
}
if (pull->params.bPrintCOM)
{
- if (pcrd.params.eGeom == epullgCYL)
+ if (pcrd.params.eGeom == PullGroupGeometry::Cylinder)
{
for (int m = 0; m < DIM; m++)
{
}
else
{
- fprintf(out, "\t%g", pull->dyna[c].x[m]);
+ fprintf(out, "\t%g", pcrd.dynamicGroup0->x[m]);
}
}
}
{
if (pull->bXOutAverage)
{
- fprintf(out, "\t%g",
+ fprintf(out,
+ "\t%g",
pull->coordForceHistory->pullGroupSums[pcrd.params.group[0]].x[m]
/ numValuesInSum);
}
{
if (pull->bXOutAverage)
{
- fprintf(out, "\t%g",
+ fprintf(out,
+ "\t%g",
pull->coordForceHistory->pullGroupSums[pcrd.params.group[g]].x[m]
/ numValuesInSum);
}
{
for (size_t c = 0; c < pull->coord.size(); c++)
{
- fprintf(out, "\t%g",
+ fprintf(out,
+ "\t%g",
pull->coordForceHistory->pullCoordinateSums[c].scalarForce
/ pull->coordForceHistory->numValuesInFSum);
}
* the group COMs for all the groups (+ ngroups_max*DIM)
* and the components of the distance vectors can be printed (+ (ngroups_max/2)*DIM).
*/
- snew(setname, pull->coord.size()
- * (1 + 1 + c_pullCoordNgroupMax * DIM + c_pullCoordNgroupMax / 2 * DIM));
+ snew(setname,
+ pull->coord.size() * (1 + 1 + c_pullCoordNgroupMax * DIM + c_pullCoordNgroupMax / 2 * DIM));
nsets = 0;
for (size_t c = 0; c < pull->coord.size(); c++)
sprintf(buf, "%zu", c + 1);
setname[nsets] = gmx_strdup(buf);
nsets++;
- if (pull->params.bPrintRefValue && pull->coord[c].params.eType != epullEXTERNAL)
+ if (pull->params.bPrintRefValue && pull->coord[c].params.eType != PullingAlgorithm::External)
{
sprintf(buf, "%zu ref", c + 1);
setname[nsets] = gmx_strdup(buf);
#include <algorithm>
#include <memory>
+#include <mutex>
#include "gromacs/commandline/filenm.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
-#include "gromacs/utility/mutex.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strconvert.h"
+#include "gromacs/utility/stringutil.h"
#include "pull_internal.h"
extern template LocalAtomSet LocalAtomSetManager::add<void, void>(ArrayRef<const int> globalAtomIndex);
} // namespace gmx
+using gmx::ArrayRef;
+using gmx::RVec;
+
+/*! \brief Tells whether the pull geometry is an angle type */
+constexpr gmx::EnumerationArray<PullGroupGeometry, bool> sc_isAngleType = {
+ { false, false, false, false, false, true, true, true }
+};
+
static int groupPbcFromParams(const t_pull_group& params, bool setPbcRefToPrevStepCOM)
{
if (params.ind.size() <= 1)
*/
pull_group_work_t::pull_group_work_t(const t_pull_group& params,
gmx::LocalAtomSet atomSet,
- bool bSetPbcRefToPrevStepCOM) :
+ bool bSetPbcRefToPrevStepCOM,
+ int maxNumThreads) :
params(params),
epgrppbc(groupPbcFromParams(params, bSetPbcRefToPrevStepCOM)),
+ maxNumThreads(maxNumThreads),
needToCalcCom(false),
atomSet(atomSet),
mwscale(0),
clear_dvec(xp);
};
-bool pull_coordinate_is_angletype(const t_pull_coord* pcrd)
-{
- return (pcrd->eGeom == epullgANGLE || pcrd->eGeom == epullgDIHEDRAL || pcrd->eGeom == epullgANGLEAXIS);
-}
-
static bool pull_coordinate_is_directional(const t_pull_coord* pcrd)
{
- return (pcrd->eGeom == epullgDIR || pcrd->eGeom == epullgDIRPBC
- || pcrd->eGeom == epullgDIRRELATIVE || pcrd->eGeom == epullgCYL);
+ return (pcrd->eGeom == PullGroupGeometry::Direction || pcrd->eGeom == PullGroupGeometry::DirectionPBC
+ || pcrd->eGeom == PullGroupGeometry::DirectionRelative
+ || pcrd->eGeom == PullGroupGeometry::Cylinder);
}
-const char* pull_coordinate_units(const t_pull_coord* pcrd)
+const char* pull_coordinate_units(const t_pull_coord& pcrd)
{
- return pull_coordinate_is_angletype(pcrd) ? "deg" : "nm";
+ return sc_isAngleType[pcrd.eGeom] ? "deg" : "nm";
}
-double pull_conversion_factor_userinput2internal(const t_pull_coord* pcrd)
+double pull_conversion_factor_userinput2internal(const t_pull_coord& pcrd)
{
- if (pull_coordinate_is_angletype(pcrd))
+ if (sc_isAngleType[pcrd.eGeom])
{
- return DEG2RAD;
+ return gmx::c_deg2Rad;
}
else
{
}
}
-double pull_conversion_factor_internal2userinput(const t_pull_coord* pcrd)
+double pull_conversion_factor_internal2userinput(const t_pull_coord& pcrd)
{
- if (pull_coordinate_is_angletype(pcrd))
+ if (sc_isAngleType[pcrd.eGeom])
{
- return RAD2DEG;
+ return gmx::c_rad2Deg;
}
else
{
}
/* Apply forces in a mass weighted fashion for part of the pull group */
-static void apply_forces_grp_part(const pull_group_work_t* pgrp,
+static void apply_forces_grp_part(const pull_group_work_t& pgrp,
int ind_start,
int ind_end,
- const real* masses,
+ ArrayRef<const real> masses,
const dvec f_pull,
- int sign,
+ const int sign,
rvec* f)
{
- double inv_wm = pgrp->mwscale;
+ const double inv_wm = pgrp.mwscale;
- auto localAtomIndices = pgrp->atomSet.localIndex();
+ auto localAtomIndices = pgrp.atomSet.localIndex();
for (int i = ind_start; i < ind_end; i++)
{
int ii = localAtomIndices[i];
double wmass = masses[ii];
- if (!pgrp->localWeights.empty())
+ if (!pgrp.localWeights.empty())
{
- wmass *= pgrp->localWeights[i];
+ wmass *= pgrp.localWeights[i];
}
for (int d = 0; d < DIM; d++)
}
/* Apply forces in a mass weighted fashion */
-static void apply_forces_grp(const pull_group_work_t* pgrp,
- const real* masses,
+static void apply_forces_grp(const pull_group_work_t& pgrp,
+ ArrayRef<const real> masses,
const dvec f_pull,
- int sign,
- rvec* f,
- int nthreads)
+ const int sign,
+ rvec* f)
{
- auto localAtomIndices = pgrp->atomSet.localIndex();
+ auto localAtomIndices = pgrp.atomSet.localIndex();
- if (pgrp->params.ind.size() == 1 && pgrp->atomSet.numAtomsLocal() == 1)
+ if (pgrp.params.ind.size() == 1 && pgrp.atomSet.numAtomsLocal() == 1)
{
/* Only one atom and our rank has this atom: we can skip
* the mass weighting, which means that this code also works
}
else
{
- if (localAtomIndices.size() <= c_pullMaxNumLocalAtomsSingleThreaded)
+ const int numThreads = pgrp.numThreads();
+ if (numThreads == 1)
{
apply_forces_grp_part(pgrp, 0, localAtomIndices.size(), masses, f_pull, sign, f);
}
else
{
-#pragma omp parallel for num_threads(nthreads) schedule(static)
- for (int th = 0; th < nthreads; th++)
+#pragma omp parallel for num_threads(numThreads) schedule(static)
+ for (int th = 0; th < numThreads; th++)
{
- int ind_start = (localAtomIndices.size() * (th + 0)) / nthreads;
- int ind_end = (localAtomIndices.size() * (th + 1)) / nthreads;
+ int ind_start = (localAtomIndices.size() * (th + 0)) / numThreads;
+ int ind_end = (localAtomIndices.size() * (th + 1)) / numThreads;
apply_forces_grp_part(pgrp, ind_start, ind_end, masses, f_pull, sign, f);
}
}
}
/* Apply forces in a mass weighted fashion to a cylinder group */
-static void apply_forces_cyl_grp(const pull_group_work_t* pgrp,
+static void apply_forces_cyl_grp(const pull_group_work_t& pgrp,
const double dv_corr,
- const real* masses,
+ ArrayRef<const real> masses,
const dvec f_pull,
double f_scal,
- int sign,
- rvec* f,
- int gmx_unused nthreads)
+ const int sign,
+ rvec* f)
{
- double inv_wm = pgrp->mwscale;
+ const double inv_wm = pgrp.mwscale;
- auto localAtomIndices = pgrp->atomSet.localIndex();
+ auto localAtomIndices = pgrp.atomSet.localIndex();
/* The cylinder group is always a slab in the system, thus large.
* Therefore we always thread-parallelize this group.
*/
- int numAtomsLocal = localAtomIndices.size();
-#pragma omp parallel for num_threads(nthreads) schedule(static)
+ const int numAtomsLocal = localAtomIndices.size();
+ const int gmx_unused numThreads = pgrp.numThreads();
+#pragma omp parallel for num_threads(numThreads) schedule(static)
for (int i = 0; i < numAtomsLocal; i++)
{
- double weight = pgrp->localWeights[i];
+ double weight = pgrp.localWeights[i];
if (weight == 0)
{
continue;
* to be corrected for an offset (dv_corr), which was unknown when
* we calculated dv.
*/
- double dv_com = pgrp->dv[i] + dv_corr;
+ double dv_com = pgrp.dv[i] + dv_corr;
/* Here we not only add the pull force working along vec (f_pull),
* but also a radial component, due to the dependence of the weights
*/
for (int m = 0; m < DIM; m++)
{
- f[ii][m] += sign * inv_wm * (mass * weight * f_pull[m] + pgrp->mdw[i][m] * dv_com * f_scal);
+ f[ii][m] += sign * inv_wm * (mass * weight * f_pull[m] + pgrp.mdw[i][m] * dv_com * f_scal);
}
}
}
/* Apply torque forces in a mass weighted fashion to the groups that define
* the pull vector direction for pull coordinate pcrd.
*/
-static void apply_forces_vec_torque(const struct pull_t* pull,
- const pull_coord_work_t* pcrd,
- const real* masses,
- rvec* f)
+static void apply_forces_vec_torque(const pull_coord_work_t& pcrd,
+ ArrayRef<const pull_group_work_t> pullGroups,
+ ArrayRef<const real> masses,
+ rvec* f)
{
- const PullCoordSpatialData& spatialData = pcrd->spatialData;
+ const PullCoordSpatialData& spatialData = pcrd.spatialData;
/* The component inpr along the pull vector is accounted for in the usual
* way. Here we account for the component perpendicular to vec.
dvec f_perp;
for (int m = 0; m < DIM; m++)
{
- f_perp[m] = (spatialData.dr01[m] - inpr * spatialData.vec[m]) / spatialData.vec_len * pcrd->scalarForce;
+ f_perp[m] = (spatialData.dr01[m] - inpr * spatialData.vec[m]) / spatialData.vec_len * pcrd.scalarForce;
}
/* Apply the force to the groups defining the vector using opposite signs */
- apply_forces_grp(&pull->group[pcrd->params.group[2]], masses, f_perp, -1, f, pull->nthreads);
- apply_forces_grp(&pull->group[pcrd->params.group[3]], masses, f_perp, 1, f, pull->nthreads);
+ apply_forces_grp(pullGroups[pcrd.params.group[2]], masses, f_perp, -1, f);
+ apply_forces_grp(pullGroups[pcrd.params.group[3]], masses, f_perp, 1, f);
}
/* Apply forces in a mass weighted fashion */
-static void apply_forces_coord(struct pull_t* pull,
- int coord,
- const PullCoordVectorForces& forces,
- const real* masses,
- rvec* f)
+static void apply_forces_coord(const pull_coord_work_t& pcrd,
+ ArrayRef<const pull_group_work_t> pullGroups,
+ const PullCoordVectorForces& forces,
+ ArrayRef<const real> masses,
+ rvec* f)
{
/* Here it would be more efficient to use one large thread-parallel
* region instead of potential parallel regions within apply_forces_grp.
* to data races.
*/
- const pull_coord_work_t& pcrd = pull->coord[coord];
-
- if (pcrd.params.eGeom == epullgCYL)
+ if (pcrd.params.eGeom == PullGroupGeometry::Cylinder)
{
- apply_forces_cyl_grp(&pull->dyna[coord], pcrd.spatialData.cyl_dev, masses, forces.force01,
- pcrd.scalarForce, -1, f, pull->nthreads);
+ apply_forces_cyl_grp(
+ *pcrd.dynamicGroup0, pcrd.spatialData.cyl_dev, masses, forces.force01, pcrd.scalarForce, -1, f);
/* Sum the force along the vector and the radial force */
dvec f_tot;
{
f_tot[m] = forces.force01[m] + pcrd.scalarForce * pcrd.spatialData.ffrad[m];
}
- apply_forces_grp(&pull->group[pcrd.params.group[1]], masses, f_tot, 1, f, pull->nthreads);
+ apply_forces_grp(pullGroups[pcrd.params.group[1]], masses, f_tot, 1, f);
}
else
{
- if (pcrd.params.eGeom == epullgDIRRELATIVE)
+ if (pcrd.params.eGeom == PullGroupGeometry::DirectionRelative)
{
/* We need to apply the torque forces to the pull groups
* that define the pull vector.
*/
- apply_forces_vec_torque(pull, &pcrd, masses, f);
+ apply_forces_vec_torque(pcrd, pullGroups, masses, f);
}
- if (!pull->group[pcrd.params.group[0]].params.ind.empty())
+ if (!pullGroups[pcrd.params.group[0]].params.ind.empty())
{
- apply_forces_grp(&pull->group[pcrd.params.group[0]], masses, forces.force01, -1, f,
- pull->nthreads);
+ apply_forces_grp(pullGroups[pcrd.params.group[0]], masses, forces.force01, -1, f);
}
- apply_forces_grp(&pull->group[pcrd.params.group[1]], masses, forces.force01, 1, f, pull->nthreads);
+ apply_forces_grp(pullGroups[pcrd.params.group[1]], masses, forces.force01, 1, f);
if (pcrd.params.ngroup >= 4)
{
- apply_forces_grp(&pull->group[pcrd.params.group[2]], masses, forces.force23, -1, f,
- pull->nthreads);
- apply_forces_grp(&pull->group[pcrd.params.group[3]], masses, forces.force23, 1, f,
- pull->nthreads);
+ apply_forces_grp(pullGroups[pcrd.params.group[2]], masses, forces.force23, -1, f);
+ apply_forces_grp(pullGroups[pcrd.params.group[3]], masses, forces.force23, 1, f);
}
if (pcrd.params.ngroup >= 6)
{
- apply_forces_grp(&pull->group[pcrd.params.group[4]], masses, forces.force45, -1, f,
- pull->nthreads);
- apply_forces_grp(&pull->group[pcrd.params.group[5]], masses, forces.force45, 1, f,
- pull->nthreads);
+ apply_forces_grp(pullGroups[pcrd.params.group[4]], masses, forces.force45, -1, f);
+ apply_forces_grp(pullGroups[pcrd.params.group[5]], masses, forces.force45, 1, f);
}
}
}
* \param[in] max_dist2 The maximum distance squared
* \param[out] dr The distance vector
*/
-static void low_get_pull_coord_dr(const struct pull_t* pull,
+static void low_get_pull_coord_dr(const pull_t& pull,
const pull_coord_work_t* pcrd,
const t_pbc* pbc,
const dvec xg,
- dvec xref,
+ const dvec xref,
const int groupIndex0,
const int groupIndex1,
const double max_dist2,
dvec dr)
{
- const pull_group_work_t* pgrp0 = &pull->group[pcrd->params.group[0]];
+ const pull_group_work_t& pgrp0 = pull.group[pcrd->params.group[0]];
+
+ // Group coordinate, to be updated with the reference position
+ dvec xrefr;
/* Only the first group can be an absolute reference, in that case nat=0 */
- if (pgrp0->params.ind.empty())
+ if (pgrp0.params.ind.empty())
{
for (int m = 0; m < DIM; m++)
{
- xref[m] = pcrd->params.origin[m];
+ xrefr[m] = pcrd->params.origin[m];
}
}
-
- dvec xrefr;
- copy_dvec(xref, xrefr);
+ else
+ {
+ copy_dvec(xref, xrefr);
+ }
dvec dref = { 0, 0, 0 };
- if (pcrd->params.eGeom == epullgDIRPBC)
+ if (pcrd->params.eGeom == PullGroupGeometry::DirectionPBC)
{
for (int m = 0; m < DIM; m++)
{
gmx_fatal(FARGS,
"Distance between pull groups %d and %d (%f nm) is larger than 0.49 times the "
"box size (%f).\n%s",
- pcrd->params.group[groupIndex0], pcrd->params.group[groupIndex1], sqrt(dr2),
- sqrt(0.98 * 0.98 * max_dist2), pcrd->params.eGeom == epullgDIR ? "You might want to consider using \"pull-geometry = direction-periodic\" instead.\n" : "");
+ pcrd->params.group[groupIndex0],
+ pcrd->params.group[groupIndex1],
+ sqrt(dr2),
+ sqrt(0.98 * 0.98 * max_dist2),
+ pcrd->params.eGeom == PullGroupGeometry::Direction
+ ? "You might want to consider using \"pull-geometry = "
+ "direction-periodic\" instead.\n"
+ : "");
}
- if (pcrd->params.eGeom == epullgDIRPBC)
+ if (pcrd->params.eGeom == PullGroupGeometry::DirectionPBC)
{
dvec_inc(dr, dref);
}
/* This function returns the distance based on the contents of the pull struct.
* pull->coord[coord_ind].dr, and potentially vector, are updated.
*/
-static void get_pull_coord_dr(struct pull_t* pull, int coord_ind, const t_pbc* pbc)
+static void get_pull_coord_dr(const pull_t& pull, pull_coord_work_t* pcrd, const t_pbc* pbc)
{
- pull_coord_work_t* pcrd = &pull->coord[coord_ind];
+ const int coord_ind = pcrd->params.coordIndex;
+
PullCoordSpatialData& spatialData = pcrd->spatialData;
double md2;
/* With AWH pulling we allow for periodic pulling with geometry=direction.
* TODO: Store a periodicity flag instead of checking for external pull provider.
*/
- if (pcrd->params.eGeom == epullgDIRPBC
- || (pcrd->params.eGeom == epullgDIR && pcrd->params.eType == epullEXTERNAL))
+ if (pcrd->params.eGeom == PullGroupGeometry::DirectionPBC
+ || (pcrd->params.eGeom == PullGroupGeometry::Direction
+ && pcrd->params.eType == PullingAlgorithm::External))
{
md2 = -1;
}
md2 = static_cast<double>(max_pull_distance2(pcrd, pbc));
}
- if (pcrd->params.eGeom == epullgDIRRELATIVE)
+ if (pcrd->params.eGeom == PullGroupGeometry::DirectionRelative)
{
/* We need to determine the pull vector */
dvec vec;
int m;
- const pull_group_work_t& pgrp2 = pull->group[pcrd->params.group[2]];
- const pull_group_work_t& pgrp3 = pull->group[pcrd->params.group[3]];
+ const pull_group_work_t& pgrp2 = pull.group[pcrd->params.group[2]];
+ const pull_group_work_t& pgrp3 = pull.group[pcrd->params.group[3]];
pbc_dx_d(pbc, pgrp3.x, pgrp2.x, vec);
}
if (debug)
{
- fprintf(debug, "pull coord %d vector: %6.3f %6.3f %6.3f normalized: %6.3f %6.3f %6.3f\n",
- coord_ind, vec[XX], vec[YY], vec[ZZ], spatialData.vec[XX], spatialData.vec[YY],
+ fprintf(debug,
+ "pull coord %d vector: %6.3f %6.3f %6.3f normalized: %6.3f %6.3f %6.3f\n",
+ coord_ind,
+ vec[XX],
+ vec[YY],
+ vec[ZZ],
+ spatialData.vec[XX],
+ spatialData.vec[YY],
spatialData.vec[ZZ]);
}
}
- pull_group_work_t* pgrp0 = &pull->group[pcrd->params.group[0]];
- pull_group_work_t* pgrp1 = &pull->group[pcrd->params.group[1]];
+ const pull_group_work_t& pgrp0 = pull.group[pcrd->params.group[0]];
+ const pull_group_work_t& pgrp1 = pull.group[pcrd->params.group[1]];
- low_get_pull_coord_dr(pull, pcrd, pbc, pgrp1->x,
- pcrd->params.eGeom == epullgCYL ? pull->dyna[coord_ind].x : pgrp0->x, 0,
- 1, md2, spatialData.dr01);
+ low_get_pull_coord_dr(
+ pull,
+ pcrd,
+ pbc,
+ pgrp1.x,
+ pcrd->params.eGeom == PullGroupGeometry::Cylinder ? pcrd->dynamicGroup0->x : pgrp0.x,
+ 0,
+ 1,
+ md2,
+ spatialData.dr01);
if (pcrd->params.ngroup >= 4)
{
- pull_group_work_t *pgrp2, *pgrp3;
- pgrp2 = &pull->group[pcrd->params.group[2]];
- pgrp3 = &pull->group[pcrd->params.group[3]];
+ const pull_group_work_t& pgrp2 = pull.group[pcrd->params.group[2]];
+ const pull_group_work_t& pgrp3 = pull.group[pcrd->params.group[3]];
- low_get_pull_coord_dr(pull, pcrd, pbc, pgrp3->x, pgrp2->x, 2, 3, md2, spatialData.dr23);
+ low_get_pull_coord_dr(pull, pcrd, pbc, pgrp3.x, pgrp2.x, 2, 3, md2, spatialData.dr23);
}
if (pcrd->params.ngroup >= 6)
{
- pull_group_work_t *pgrp4, *pgrp5;
- pgrp4 = &pull->group[pcrd->params.group[4]];
- pgrp5 = &pull->group[pcrd->params.group[5]];
+ const pull_group_work_t& pgrp4 = pull.group[pcrd->params.group[4]];
+ const pull_group_work_t& pgrp5 = pull.group[pcrd->params.group[5]];
- low_get_pull_coord_dr(pull, pcrd, pbc, pgrp5->x, pgrp4->x, 4, 5, md2, spatialData.dr45);
+ low_get_pull_coord_dr(pull, pcrd, pbc, pgrp5.x, pgrp4.x, 4, 5, md2, spatialData.dr45);
}
}
}
}
-/* This function should always be used to modify pcrd->value_ref */
-static void low_set_pull_coord_reference_value(pull_coord_work_t* pcrd, int coord_ind, double value_ref)
+/* This function should always be used to get values for setting value_ref in pull_coord_work_t */
+static double sanitizePullCoordReferenceValue(const t_pull_coord& pcrdParams, double value_ref)
{
- GMX_ASSERT(pcrd->params.eType != epullEXTERNAL,
+ GMX_ASSERT(pcrdParams.eType != PullingAlgorithm::External,
"The pull coord reference value should not be used with type external-potential");
- if (pcrd->params.eGeom == epullgDIST)
+ if (pcrdParams.eGeom == PullGroupGeometry::Distance)
{
if (value_ref < 0)
{
gmx_fatal(FARGS,
"Pull reference distance for coordinate %d (%f) needs to be non-negative",
- coord_ind + 1, value_ref);
+ pcrdParams.coordIndex + 1,
+ value_ref);
}
}
- else if (pcrd->params.eGeom == epullgANGLE || pcrd->params.eGeom == epullgANGLEAXIS)
+ else if (pcrdParams.eGeom == PullGroupGeometry::Angle || pcrdParams.eGeom == PullGroupGeometry::AngleAxis)
{
if (value_ref < 0 || value_ref > M_PI)
{
gmx_fatal(FARGS,
"Pull reference angle for coordinate %d (%f) needs to be in the allowed "
"interval [0,180] deg",
- coord_ind + 1,
- value_ref * pull_conversion_factor_internal2userinput(&pcrd->params));
+ pcrdParams.coordIndex + 1,
+ value_ref * pull_conversion_factor_internal2userinput(pcrdParams));
}
}
- else if (pcrd->params.eGeom == epullgDIHEDRAL)
+ else if (pcrdParams.eGeom == PullGroupGeometry::Dihedral)
{
/* Allow pulling to be periodic for dihedral angles by remapping the reference value to the interval [-pi, pi). */
make_periodic_2pi(&value_ref);
}
- pcrd->value_ref = value_ref;
+ return value_ref;
}
-static void update_pull_coord_reference_value(pull_coord_work_t* pcrd, int coord_ind, double t)
+static void updatePullCoordReferenceValue(double* referenceValue, const t_pull_coord& pcrdParams, double t)
{
+ GMX_ASSERT(referenceValue, "Need a valid reference value object");
+
/* With zero rate the reference value is set initially and doesn't change */
- if (pcrd->params.rate != 0)
+ if (pcrdParams.rate != 0)
{
- double value_ref = (pcrd->params.init + pcrd->params.rate * t)
- * pull_conversion_factor_userinput2internal(&pcrd->params);
- low_set_pull_coord_reference_value(pcrd, coord_ind, value_ref);
+ const double inputValue = (pcrdParams.init + pcrdParams.rate * t)
+ * pull_conversion_factor_userinput2internal(pcrdParams);
+ *referenceValue = sanitizePullCoordReferenceValue(pcrdParams, inputValue);
}
}
/* Calculates pull->coord[coord_ind].value.
* This function also updates pull->coord[coord_ind].dr.
*/
-static void get_pull_coord_distance(struct pull_t* pull, int coord_ind, const t_pbc* pbc)
+static void get_pull_coord_distance(const pull_t& pull, pull_coord_work_t* pcrd, const t_pbc* pbc)
{
- pull_coord_work_t* pcrd;
- int m;
-
- pcrd = &pull->coord[coord_ind];
-
- get_pull_coord_dr(pull, coord_ind, pbc);
+ get_pull_coord_dr(pull, pcrd, pbc);
PullCoordSpatialData& spatialData = pcrd->spatialData;
switch (pcrd->params.eGeom)
{
- case epullgDIST:
+ case PullGroupGeometry::Distance:
/* Pull along the vector between the com's */
spatialData.value = dnorm(spatialData.dr01);
break;
- case epullgDIR:
- case epullgDIRPBC:
- case epullgDIRRELATIVE:
- case epullgCYL:
+ case PullGroupGeometry::Direction:
+ case PullGroupGeometry::DirectionPBC:
+ case PullGroupGeometry::DirectionRelative:
+ case PullGroupGeometry::Cylinder:
/* Pull along vec */
spatialData.value = 0;
- for (m = 0; m < DIM; m++)
+ for (int m = 0; m < DIM; m++)
{
spatialData.value += spatialData.vec[m] * spatialData.dr01[m];
}
break;
- case epullgANGLE:
+ case PullGroupGeometry::Angle:
spatialData.value = gmx_angle_between_dvecs(spatialData.dr01, spatialData.dr23);
break;
- case epullgDIHEDRAL: spatialData.value = get_dihedral_angle_coord(&spatialData); break;
- case epullgANGLEAXIS:
+ case PullGroupGeometry::Dihedral:
+ spatialData.value = get_dihedral_angle_coord(&spatialData);
+ break;
+ case PullGroupGeometry::AngleAxis:
spatialData.value = gmx_angle_between_dvecs(spatialData.dr01, spatialData.vec);
break;
default: gmx_incons("Unsupported pull type in get_pull_coord_distance");
/* Returns the deviation from the reference value.
* Updates pull->coord[coord_ind].dr, .value and .value_ref.
*/
-static double get_pull_coord_deviation(struct pull_t* pull, int coord_ind, const t_pbc* pbc, double t)
+static double get_pull_coord_deviation(const pull_t& pull, pull_coord_work_t* pcrd, const t_pbc* pbc, double t)
{
- pull_coord_work_t* pcrd;
- double dev = 0;
-
- pcrd = &pull->coord[coord_ind];
+ double dev = 0;
/* Update the reference value before computing the distance,
* since it is used in the distance computation with periodic pulling.
*/
- update_pull_coord_reference_value(pcrd, coord_ind, t);
+ updatePullCoordReferenceValue(&pcrd->value_ref, pcrd->params, t);
- get_pull_coord_distance(pull, coord_ind, pbc);
+ get_pull_coord_distance(pull, pcrd, pbc);
- get_pull_coord_distance(pull, coord_ind, pbc);
+ get_pull_coord_distance(pull, pcrd, pbc);
/* Determine the deviation */
dev = pcrd->spatialData.value - pcrd->value_ref;
/* Check that values are allowed */
- if (pcrd->params.eGeom == epullgDIST && pcrd->spatialData.value == 0)
+ if (pcrd->params.eGeom == PullGroupGeometry::Distance && pcrd->spatialData.value == 0)
{
/* With no vector we can not determine the direction for the force,
* so we set the force to zero.
*/
dev = 0;
}
- else if (pcrd->params.eGeom == epullgDIHEDRAL)
+ else if (pcrd->params.eGeom == PullGroupGeometry::Dihedral)
{
/* The reference value is in [-pi, pi). The coordinate value is in (-pi, pi].
Thus, the unwrapped deviation is here in (-2pi, 2pi].
return dev;
}
-double get_pull_coord_value(struct pull_t* pull, int coord_ind, const t_pbc* pbc)
+double get_pull_coord_value(pull_t* pull, int coord_ind, const t_pbc* pbc)
{
- get_pull_coord_distance(pull, coord_ind, pbc);
+ get_pull_coord_distance(*pull, &pull->coord[coord_ind], pbc);
return pull->coord[coord_ind].spatialData.value;
}
}
/* Apply constraint using SHAKE */
-static void
-do_constraint(struct pull_t* pull, t_pbc* pbc, rvec* x, rvec* v, gmx_bool bMaster, tensor vir, double dt, double t)
+static void do_constraint(struct pull_t* pull,
+ t_pbc* pbc,
+ ArrayRef<RVec> x,
+ ArrayRef<RVec> v,
+ gmx_bool bMaster,
+ tensor vir,
+ double dt,
+ double t)
{
dvec* r_ij; /* x[i] com of i in prev. step. Obeys constr. -> r_ij[i] */
pcrd = &pull->coord[c];
- if (pcrd->params.eType != epullCONSTRAINT)
+ if (pcrd->params.eType != PullingAlgorithm::Constraint)
{
continue;
}
* We don't modify dr and value anymore, so these values are also used
* for printing.
*/
- get_pull_coord_distance(pull, c, pbc);
+ get_pull_coord_distance(*pull, pcrd, pbc);
const PullCoordSpatialData& spatialData = pcrd->spatialData;
if (debug)
{
- fprintf(debug, "Pull coord %zu dr %f %f %f\n", c, spatialData.dr01[XX],
- spatialData.dr01[YY], spatialData.dr01[ZZ]);
+ fprintf(debug,
+ "Pull coord %zu dr %f %f %f\n",
+ c,
+ spatialData.dr01[XX],
+ spatialData.dr01[YY],
+ spatialData.dr01[ZZ]);
}
- if (pcrd->params.eGeom == epullgDIR || pcrd->params.eGeom == epullgDIRPBC)
+ if (pcrd->params.eGeom == PullGroupGeometry::Direction
+ || pcrd->params.eGeom == PullGroupGeometry::DirectionPBC)
{
/* Select the component along vec */
a = 0;
pcrd = &pull->coord[c];
- if (pcrd->params.eType != epullCONSTRAINT)
+ if (pcrd->params.eType != PullingAlgorithm::Constraint)
{
continue;
}
- update_pull_coord_reference_value(pcrd, c, t);
+ updatePullCoordReferenceValue(&pcrd->value_ref, pcrd->params, t);
pgrp0 = &pull->group[pcrd->params.group[0]];
pgrp1 = &pull->group[pcrd->params.group[1]];
/* Get the current difference vector */
- low_get_pull_coord_dr(pull, pcrd, pbc, rnew[pcrd->params.group[1]],
- rnew[pcrd->params.group[0]], 0, 1, -1, unc_ij);
+ low_get_pull_coord_dr(
+ *pull, pcrd, pbc, rnew[pcrd->params.group[1]], rnew[pcrd->params.group[0]], 0, 1, -1, unc_ij);
if (debug)
{
switch (pcrd->params.eGeom)
{
- case epullgDIST:
+ case PullGroupGeometry::Distance:
if (pcrd->value_ref <= 0)
{
gmx_fatal(
FARGS,
"The pull constraint reference distance for group %zu is <= 0 (%f)",
- c, pcrd->value_ref);
+ c,
+ pcrd->value_ref);
}
{
if (debug)
{
- fprintf(debug, "Pull ax^2+bx+c=0: a=%e b=%e c=%e lambda=%e\n", c_a, c_b,
- c_c, lambda);
+ fprintf(debug, "Pull ax^2+bx+c=0: a=%e b=%e c=%e lambda=%e\n", c_a, c_b, c_c, lambda);
}
}
dsvmul(lambda * rm * pgrp0->invtm, r_ij[c], dr0);
dr_tot[c] += -lambda * dnorm(r_ij[c]);
break;
- case epullgDIR:
- case epullgDIRPBC:
- case epullgCYL:
+ case PullGroupGeometry::Direction:
+ case PullGroupGeometry::DirectionPBC:
+ case PullGroupGeometry::Cylinder:
/* A 1-dimensional constraint along a vector */
a = 0;
for (m = 0; m < DIM; m++)
g0 = pcrd->params.group[0];
g1 = pcrd->params.group[1];
- low_get_pull_coord_dr(pull, pcrd, pbc, rnew[g1], rnew[g0], 0, 1, -1, tmp);
- low_get_pull_coord_dr(pull, pcrd, pbc, dr1, dr0, 0, 1, -1, tmp3);
- fprintf(debug, "Pull cur %8.5f %8.5f %8.5f j:%8.5f %8.5f %8.5f d: %8.5f\n", rnew[g0][0],
- rnew[g0][1], rnew[g0][2], rnew[g1][0], rnew[g1][1], rnew[g1][2], dnorm(tmp));
- fprintf(debug, "Pull ref %8s %8s %8s %8s %8s %8s d: %8.5f\n", "", "", "", "", "",
- "", pcrd->value_ref);
- fprintf(debug, "Pull cor %8.5f %8.5f %8.5f j:%8.5f %8.5f %8.5f d: %8.5f\n", dr0[0],
- dr0[1], dr0[2], dr1[0], dr1[1], dr1[2], dnorm(tmp3));
+ low_get_pull_coord_dr(*pull, pcrd, pbc, rnew[g1], rnew[g0], 0, 1, -1, tmp);
+ low_get_pull_coord_dr(*pull, pcrd, pbc, dr1, dr0, 0, 1, -1, tmp3);
+ fprintf(debug,
+ "Pull cur %8.5f %8.5f %8.5f j:%8.5f %8.5f %8.5f d: %8.5f\n",
+ rnew[g0][0],
+ rnew[g0][1],
+ rnew[g0][2],
+ rnew[g1][0],
+ rnew[g1][1],
+ rnew[g1][2],
+ dnorm(tmp));
+ fprintf(debug,
+ "Pull ref %8s %8s %8s %8s %8s %8s d: %8.5f\n",
+ "",
+ "",
+ "",
+ "",
+ "",
+ "",
+ pcrd->value_ref);
+ fprintf(debug,
+ "Pull cor %8.5f %8.5f %8.5f j:%8.5f %8.5f %8.5f d: %8.5f\n",
+ dr0[0],
+ dr0[1],
+ dr0[2],
+ dr1[0],
+ dr1[1],
+ dr1[2],
+ dnorm(tmp3));
} /* END DEBUG */
/* Update the COMs with dr */
/* Check if all constraints are fullfilled now */
for (pull_coord_work_t& coord : pull->coord)
{
- if (coord.params.eType != epullCONSTRAINT)
+ if (coord.params.eType != PullingAlgorithm::Constraint)
{
continue;
}
- low_get_pull_coord_dr(pull, &coord, pbc, rnew[coord.params.group[1]],
- rnew[coord.params.group[0]], 0, 1, -1, unc_ij);
+ low_get_pull_coord_dr(
+ *pull, &coord, pbc, rnew[coord.params.group[1]], rnew[coord.params.group[0]], 0, 1, -1, unc_ij);
switch (coord.params.eGeom)
{
- case epullgDIST:
+ case PullGroupGeometry::Distance:
bConverged = fabs(dnorm(unc_ij) - coord.value_ref) < pull->params.constr_tol;
break;
- case epullgDIR:
- case epullgDIRPBC:
- case epullgCYL:
+ case PullGroupGeometry::Direction:
+ case PullGroupGeometry::DirectionPBC:
+ case PullGroupGeometry::Cylinder:
for (m = 0; m < DIM; m++)
{
vec[m] = coord.spatialData.vec[m];
dsvmul(inpr, vec, unc_ij);
bConverged = fabs(diprod(unc_ij, vec) - coord.value_ref) < pull->params.constr_tol;
break;
+ default:
+ GMX_ASSERT(false,
+ gmx::formatString("Geometry %s not handled here",
+ enumValueToString(coord.params.eGeom))
+ .c_str());
}
if (!bConverged)
"Pull constraint not converged: "
"groups %d %d,"
"d_ref = %f, current d = %f\n",
- coord.params.group[0], coord.params.group[1], coord.value_ref, dnorm(unc_ij));
+ coord.params.group[0],
+ coord.params.group[1],
+ coord.value_ref,
+ dnorm(unc_ij));
}
bConverged_all = FALSE;
/* DONE ITERATING, NOW UPDATE COORDINATES AND CALC. CONSTRAINT FORCES */
- if (v)
+ if (!v.empty())
{
invdt = 1 / dt;
}
{
x[ii][m] += tmp[m];
}
- if (v)
+ if (!v.empty())
{
for (m = 0; m < DIM; m++)
{
pcrd = &pull->coord[c];
- if (pcrd->params.eType != epullCONSTRAINT)
+ if (pcrd->params.eType != PullingAlgorithm::Constraint)
{
continue;
}
* dt * dt);
pcrd->scalarForce += force;
- if (vir != nullptr && pcrd->params.eGeom != epullgDIRPBC && bMaster)
+ if (vir != nullptr && pcrd->params.eGeom != PullGroupGeometry::DirectionPBC && bMaster)
{
double f_invr;
/* Adds the pull contribution to the virial */
static void add_virial_coord(tensor vir, const pull_coord_work_t& pcrd, const PullCoordVectorForces& forces)
{
- if (vir != nullptr && pcrd.params.eGeom != epullgDIRPBC)
+ if (vir != nullptr && pcrd.params.eGeom != PullGroupGeometry::DirectionPBC)
{
/* Add the pull contribution for each distance vector to the virial. */
add_virial_coord_dr(vir, pcrd.spatialData.dr01, forces.force01);
switch (pcrd->params.eType)
{
- case epullUMBRELLA:
- case epullFLATBOTTOM:
- case epullFLATBOTTOMHIGH:
+ case PullingAlgorithm::Umbrella:
+ case PullingAlgorithm::FlatBottom:
+ case PullingAlgorithm::FlatBottomHigh:
/* The only difference between an umbrella and a flat-bottom
* potential is that a flat-bottom is zero above or below
the reference value.
*/
- if ((pcrd->params.eType == epullFLATBOTTOM && dev < 0)
- || (pcrd->params.eType == epullFLATBOTTOMHIGH && dev > 0))
+ if ((pcrd->params.eType == PullingAlgorithm::FlatBottom && dev < 0)
+ || (pcrd->params.eType == PullingAlgorithm::FlatBottomHigh && dev > 0))
{
dev = 0;
}
*V += 0.5 * k * gmx::square(dev);
*dVdl += 0.5 * dkdl * gmx::square(dev);
break;
- case epullCONST_F:
+ case PullingAlgorithm::ConstantForce:
pcrd->scalarForce = -k;
*V += k * pcrd->spatialData.value;
*dVdl += dkdl * pcrd->spatialData.value;
break;
- case epullEXTERNAL:
+ case PullingAlgorithm::External:
gmx_incons(
"the scalar pull force should not be calculated internally for pull type "
"external");
/* The geometry of the coordinate determines how the scalar force relates to the force on each group */
PullCoordVectorForces forces;
- if (params.eGeom == epullgDIST)
+ if (params.eGeom == PullGroupGeometry::Distance)
{
double invdr01 = spatialData.value > 0 ? 1. / spatialData.value : 0.;
for (int m = 0; m < DIM; m++)
forces.force01[m] = pcrd.scalarForce * spatialData.dr01[m] * invdr01;
}
}
- else if (params.eGeom == epullgANGLE)
+ else if (params.eGeom == PullGroupGeometry::Angle)
{
double cos_theta, cos_theta2;
clear_dvec(forces.force23);
}
}
- else if (params.eGeom == epullgANGLEAXIS)
+ else if (params.eGeom == PullGroupGeometry::AngleAxis)
{
double cos_theta, cos_theta2;
clear_dvec(forces.force01);
}
}
- else if (params.eGeom == epullgDIHEDRAL)
+ else if (params.eGeom == PullGroupGeometry::Dihedral)
{
double m2, n2, tol, sqrdist_32;
dvec dr32;
dist_32 = sqrdist_32 * inv_dist_32;
/* Forces on groups 0, 1 */
- a_01 = pcrd.scalarForce * dist_32 / m2; /* scalarForce is -dV/dphi */
- dsvmul(-a_01, spatialData.planevec_m,
- forces.force01); /* added sign to get force on group 1, not 0 */
+ a_01 = pcrd.scalarForce * dist_32 / m2; /* scalarForce is -dV/dphi */
+ dsvmul(-a_01, spatialData.planevec_m, forces.force01); /* added sign to get force on group 1, not 0 */
/* Forces on groups 4, 5 */
a_45 = -pcrd.scalarForce * dist_32 / n2;
* We could use a different, local mutex for each pull object, but the overhead
* is extremely small here and registration is only done during initialization.
*/
-static gmx::Mutex registrationMutex;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static std::mutex registrationMutex;
-using Lock = gmx::lock_guard<gmx::Mutex>;
+using Lock = std::lock_guard<std::mutex>;
void register_external_pull_potential(struct pull_t* pull, int coord_index, const char* provider)
{
gmx_fatal(FARGS,
"Module '%s' attempted to register an external potential for pull coordinate %d "
"which is out of the pull coordinate range %d - %zu\n",
- provider, coord_index + 1, 1, pull->coord.size());
+ provider,
+ coord_index + 1,
+ 1,
+ pull->coord.size());
}
pull_coord_work_t* pcrd = &pull->coord[coord_index];
- if (pcrd->params.eType != epullEXTERNAL)
+ if (pcrd->params.eType != PullingAlgorithm::External)
{
gmx_fatal(
FARGS,
"Module '%s' attempted to register an external potential for pull coordinate %d "
"which of type '%s', whereas external potentials are only supported with type '%s'",
- provider, coord_index + 1, epull_names[pcrd->params.eType], epull_names[epullEXTERNAL]);
+ provider,
+ coord_index + 1,
+ enumValueToString(pcrd->params.eType),
+ enumValueToString(PullingAlgorithm::External));
}
GMX_RELEASE_ASSERT(!pcrd->params.externalPotentialProvider.empty(),
gmx_fatal(FARGS,
"Module '%s' attempted to register an external potential for pull coordinate %d "
"which expects the external potential to be provided by a module named '%s'",
- provider, coord_index + 1, pcrd->params.externalPotentialProvider.c_str());
+ provider,
+ coord_index + 1,
+ pcrd->params.externalPotentialProvider.c_str());
}
/* Lock to avoid (extremely unlikely) simultaneous reading and writing of
gmx_fatal(FARGS,
"Module '%s' attempted to register an external potential for pull coordinate %d "
"more than once",
- provider, coord_index + 1);
+ provider,
+ coord_index + 1);
}
pcrd->bExternalPotentialProviderHasBeenRegistered = true;
size_t c;
for (c = 0; c < pull->coord.size(); c++)
{
- if (pull->coord[c].params.eType == epullEXTERNAL
+ if (pull->coord[c].params.eType == PullingAlgorithm::External
&& !pull->coord[c].bExternalPotentialProviderHasBeenRegistered)
{
break;
"No external provider for external pull potentials have been provided for %d "
"pull coordinates. The first coordinate without provider is number %zu, which "
"expects a module named '%s' to provide the external potential.",
- pull->numUnregisteredExternalPotentials, c + 1,
+ pull->numUnregisteredExternalPotentials,
+ c + 1,
pull->coord[c].params.externalPotentialProvider.c_str());
}
}
-
/* Pull takes care of adding the forces of the external potential.
* The external potential module has to make sure that the corresponding
* potential energy is added either to the pull term or to a term
void apply_external_pull_coord_force(struct pull_t* pull,
int coord_index,
double coord_force,
- const real* masses,
+ ArrayRef<const real> masses,
gmx::ForceWithVirial* forceWithVirial)
{
pull_coord_work_t* pcrd;
pcrd = &pull->coord[coord_index];
GMX_RELEASE_ASSERT(
- pcrd->params.eType == epullEXTERNAL,
+ pcrd->params.eType == PullingAlgorithm::External,
"The pull force can only be set externally on pull coordinates of external type");
GMX_ASSERT(pcrd->bExternalPotentialProviderHasBeenRegistered,
forceWithVirial->addVirialContribution(virial);
}
- apply_forces_coord(pull, coord_index, pullCoordForces, masses,
- as_rvec_array(forceWithVirial->force_.data()));
+ apply_forces_coord(
+ *pcrd, pull->group, pullCoordForces, masses, as_rvec_array(forceWithVirial->force_.data()));
}
pull->numExternalPotentialsStillToBeAppliedThisStep--;
/* Calculate the pull potential and scalar force for a pull coordinate.
* Returns the vector forces for the pull coordinate.
*/
-static PullCoordVectorForces do_pull_pot_coord(struct pull_t* pull,
- int coord_ind,
- t_pbc* pbc,
- double t,
- real lambda,
- real* V,
- tensor vir,
- real* dVdl)
+static PullCoordVectorForces do_pull_pot_coord(const pull_t& pull,
+ pull_coord_work_t* pcrd,
+ t_pbc* pbc,
+ double t,
+ real lambda,
+ real* V,
+ tensor vir,
+ real* dVdl)
{
- pull_coord_work_t& pcrd = pull->coord[coord_ind];
+ assert(pcrd->params.eType != PullingAlgorithm::Constraint);
- assert(pcrd.params.eType != epullCONSTRAINT);
+ double dev = get_pull_coord_deviation(pull, pcrd, pbc, t);
- double dev = get_pull_coord_deviation(pull, coord_ind, pbc, t);
+ calc_pull_coord_scalar_force_and_potential(pcrd, dev, lambda, V, dVdl);
- calc_pull_coord_scalar_force_and_potential(&pcrd, dev, lambda, V, dVdl);
+ PullCoordVectorForces pullCoordForces = calculateVectorForces(*pcrd);
- PullCoordVectorForces pullCoordForces = calculateVectorForces(pcrd);
-
- add_virial_coord(vir, pcrd, pullCoordForces);
+ add_virial_coord(vir, *pcrd, pullCoordForces);
return pullCoordForces;
}
real pull_potential(struct pull_t* pull,
- const real* masses,
+ ArrayRef<const real> masses,
t_pbc* pbc,
const t_commrec* cr,
double t,
real lambda,
- const rvec* x,
+ ArrayRef<const RVec> x,
gmx::ForceWithVirial* force,
real* dvdlambda)
{
{
real dVdl = 0;
- pull_calc_coms(cr, pull, masses, pbc, t, x, nullptr);
+ pull_calc_coms(cr, pull, masses, pbc, t, x, {});
rvec* f = as_rvec_array(force->force_.data());
matrix virial = { { 0 } };
/* For external potential the force is assumed to be given by an external module by a
call to apply_pull_coord_external_force */
- if (pcrd->params.eType == epullCONSTRAINT || pcrd->params.eType == epullEXTERNAL)
+ if (pcrd->params.eType == PullingAlgorithm::Constraint
+ || pcrd->params.eType == PullingAlgorithm::External)
{
continue;
}
PullCoordVectorForces pullCoordForces = do_pull_pot_coord(
- pull, c, pbc, t, lambda, &V, computeVirial ? virial : nullptr, &dVdl);
+ *pull, pcrd, pbc, t, lambda, &V, computeVirial ? virial : nullptr, &dVdl);
/* Distribute the force over the atoms in the pulled groups */
- apply_forces_coord(pull, c, pullCoordForces, masses, f);
+ apply_forces_coord(*pcrd, pull->group, pullCoordForces, masses, f);
}
if (MASTER(cr))
return (MASTER(cr) ? V : 0.0);
}
-void pull_constraint(struct pull_t* pull,
- const real* masses,
- t_pbc* pbc,
- const t_commrec* cr,
- double dt,
- double t,
- rvec* x,
- rvec* xp,
- rvec* v,
- tensor vir)
+void pull_constraint(struct pull_t* pull,
+ ArrayRef<const real> masses,
+ t_pbc* pbc,
+ const t_commrec* cr,
+ double dt,
+ double t,
+ ArrayRef<RVec> x,
+ ArrayRef<RVec> xp,
+ ArrayRef<RVec> v,
+ tensor vir)
{
assert(pull != nullptr);
if (debug && dd != nullptr)
{
- fprintf(debug, "Our DD rank (%3d) pull #atoms>0 or master: %s, will be part %s\n", dd->rank,
- gmx::boolToString(bMustParticipate), gmx::boolToString(bWillParticipate));
+ fprintf(debug,
+ "Our DD rank (%3d) pull #atoms>0 or master: %s, will be part %s\n",
+ dd->rank,
+ gmx::boolToString(bMustParticipate),
+ gmx::boolToString(bWillParticipate));
}
if (bWillParticipate)
pull_group_work_t* pg,
gmx_bool bConstraint,
const ivec pulldim_con,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const t_inputrec* ir,
real lambda)
{
* But we still want to have the correct mass-weighted COMs.
* So we store the real masses in the weights.
*/
- const bool setWeights =
- (!pg->params.weight.empty() || EI_ENERGY_MINIMIZATION(ir->eI) || ir->eI == eiBD);
+ const bool setWeights = (!pg->params.weight.empty() || EI_ENERGY_MINIMIZATION(ir->eI)
+ || ir->eI == IntegrationAlgorithm::BD);
/* In parallel, store we need to extract localWeights from weights at DD time */
std::vector<real>& weights = ((cr && PAR(cr)) ? pg->globalWeights : pg->localWeights);
- const SimulationGroups& groups = mtop->groups;
+ const SimulationGroups& groups = mtop.groups;
/* Count frozen dimensions and (weighted) mass */
int nfrozen = 0;
}
const t_atom& atom = mtopGetAtomParameters(mtop, ii, &molb);
real m;
- if (ir->efep == efepNO)
+ if (ir->efep == FreeEnergyPerturbationType::No)
{
m = atom.m;
}
w *= m;
m = 1;
}
- else if (ir->eI == eiBD)
+ else if (ir->eI == IntegrationAlgorithm::BD)
{
real mbd;
if (ir->bd_fric != 0.0F)
}
else
{
- gmx_fatal(FARGS, "The total%s mass of pull group %d is zero",
- !pg->params.weight.empty() ? " weighted" : "", g);
+ gmx_fatal(FARGS,
+ "The total%s mass of pull group %d is zero",
+ !pg->params.weight.empty() ? " weighted" : "",
+ g);
}
}
if (fplog)
{
fprintf(fplog, "Pull group %d: %5zu atoms, mass %9.3f", g, pg->params.ind.size(), tmass);
- if (!pg->params.weight.empty() || EI_ENERGY_MINIMIZATION(ir->eI) || ir->eI == eiBD)
+ if (!pg->params.weight.empty() || EI_ENERGY_MINIMIZATION(ir->eI)
+ || ir->eI == IntegrationAlgorithm::BD)
{
fprintf(fplog, ", weighted mass %9.3f", wmass * wmass / wwmass);
}
struct pull_t* init_pull(FILE* fplog,
const pull_params_t* pull_params,
const t_inputrec* ir,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const t_commrec* cr,
gmx::LocalAtomSetManager* atomSets,
real lambda)
/* Copy the pull parameters */
pull->params = *pull_params;
+ /* The gmx_omp_nthreads module might not be initialized here, so max(1,) */
+ const int maxNumThreads = std::max(1, gmx_omp_nthreads_get(ModuleMultiThread::Default));
+
for (int i = 0; i < pull_params->ngroup; ++i)
{
- pull->group.emplace_back(pull_params->group[i], atomSets->add(pull_params->group[i].ind),
- pull_params->bSetPbcRefToPrevStepCOM);
+ pull->group.emplace_back(pull_params->group[i],
+ atomSets->add(pull_params->group[i].ind),
+ pull_params->bSetPbcRefToPrevStepCOM,
+ maxNumThreads);
}
if (cr != nullptr && DOMAINDECOMP(cr))
for (int c = 0; c < pull->params.ncoord; c++)
{
+ GMX_RELEASE_ASSERT(pull_params->coord[c].coordIndex == c,
+ "The stored index should match the position in the vector");
+
/* Construct a pull coordinate, copying all coordinate parameters */
pull->coord.emplace_back(pull_params->coord[c]);
switch (pcrd->params.eGeom)
{
- case epullgDIST:
- case epullgDIRRELATIVE: /* Direction vector is determined at each step */
- case epullgANGLE:
- case epullgDIHEDRAL: break;
- case epullgDIR:
- case epullgDIRPBC:
- case epullgCYL:
- case epullgANGLEAXIS:
+ case PullGroupGeometry::Distance:
+ case PullGroupGeometry::DirectionRelative: /* Direction vector is determined at each step */
+ case PullGroupGeometry::Angle:
+ case PullGroupGeometry::Dihedral: break;
+ case PullGroupGeometry::Direction:
+ case PullGroupGeometry::DirectionPBC:
+ case PullGroupGeometry::Cylinder:
+ case PullGroupGeometry::AngleAxis:
copy_rvec_to_dvec(pull_params->coord[c].vec, pcrd->spatialData.vec);
break;
default:
*/
gmx_fatal(FARGS,
"Pull geometry not supported for pull coordinate %d. The geometry enum "
- "%d in the input is larger than that supported by the code (up to %d). "
+ "%s in the input is larger than that supported by the code (up to %d). "
"You are probably reading a tpr file generated with a newer version of "
- "Gromacs with an binary from an older version of Gromacs.",
- c + 1, pcrd->params.eGeom, epullgNR - 1);
+ "GROMACS with an binary from an older version of Gromacs.",
+ c + 1,
+ enumValueToString(pcrd->params.eGeom),
+ static_cast<int>(PullGroupGeometry::Count) - 1);
}
- if (pcrd->params.eType == epullCONSTRAINT)
+ if (pcrd->params.eType == PullingAlgorithm::Constraint)
{
/* Check restrictions of the constraint pull code */
- if (pcrd->params.eGeom == epullgCYL || pcrd->params.eGeom == epullgDIRRELATIVE
- || pcrd->params.eGeom == epullgANGLE || pcrd->params.eGeom == epullgDIHEDRAL
- || pcrd->params.eGeom == epullgANGLEAXIS)
+ if (pcrd->params.eGeom == PullGroupGeometry::Cylinder
+ || pcrd->params.eGeom == PullGroupGeometry::DirectionRelative
+ || pcrd->params.eGeom == PullGroupGeometry::Angle
+ || pcrd->params.eGeom == PullGroupGeometry::Dihedral
+ || pcrd->params.eGeom == PullGroupGeometry::AngleAxis)
{
gmx_fatal(FARGS,
"Pulling of type %s can not be combined with geometry %s. Consider using "
"pull type %s.",
- epull_names[pcrd->params.eType], epullg_names[pcrd->params.eGeom],
- epull_names[epullUMBRELLA]);
+ enumValueToString(pcrd->params.eType),
+ enumValueToString(pcrd->params.eGeom),
+ enumValueToString(PullingAlgorithm::Umbrella));
}
GMX_RELEASE_ASSERT(
pull->bPotential = TRUE;
}
- if (pcrd->params.eGeom == epullgCYL)
+ if (pcrd->params.eGeom == PullGroupGeometry::Cylinder)
{
pull->bCylinder = TRUE;
}
- else if (pcrd->params.eGeom == epullgANGLE || pcrd->params.eGeom == epullgDIHEDRAL
- || pcrd->params.eGeom == epullgANGLEAXIS)
+ else if (pcrd->params.eGeom == PullGroupGeometry::Angle
+ || pcrd->params.eGeom == PullGroupGeometry::Dihedral
+ || pcrd->params.eGeom == PullGroupGeometry::AngleAxis)
{
pull->bAngle = TRUE;
}
for (int i = 0; i < pcrd->params.ngroup; i++)
{
int groupIndex = pcrd->params.group[i];
- if (groupIndex > 0 && !(pcrd->params.eGeom == epullgCYL && i == 0))
+ if (groupIndex > 0 && !(pcrd->params.eGeom == PullGroupGeometry::Cylinder && i == 0))
{
pull->group[groupIndex].needToCalcCom = true;
}
if (pcrd->params.rate == 0)
{
/* Initialize the constant reference value */
- if (pcrd->params.eType != epullEXTERNAL)
+ if (pcrd->params.eType != PullingAlgorithm::External)
{
- low_set_pull_coord_reference_value(
- pcrd, c,
- pcrd->params.init * pull_conversion_factor_userinput2internal(&pcrd->params));
+ pcrd->value_ref = sanitizePullCoordReferenceValue(
+ pcrd->params,
+ pcrd->params.init * pull_conversion_factor_userinput2internal(pcrd->params));
}
else
{
}
}
- if (pcrd->params.eType == epullEXTERNAL)
+ if (pcrd->params.eType == PullingAlgorithm::External)
{
GMX_RELEASE_ASSERT(
pcrd->params.rate == 0,
int numRealGroups = pull->group.size() - 1;
GMX_RELEASE_ASSERT(numRealGroups > 0,
"The reference absolute position pull group should always be present");
- fprintf(fplog, "with %zu pull coordinate%s and %d group%s\n", pull->coord.size(),
- pull->coord.size() == 1 ? "" : "s", numRealGroups, numRealGroups == 1 ? "" : "s");
+ fprintf(fplog,
+ "with %zu pull coordinate%s and %d group%s\n",
+ pull->coord.size(),
+ pull->coord.size() == 1 ? "" : "s",
+ numRealGroups,
+ numRealGroups == 1 ? "" : "s");
if (bAbs)
{
fprintf(fplog, "with an absolute reference\n");
{
pulldim[m] = 1;
- if (coord.params.eType == epullCONSTRAINT)
+ if (coord.params.eType == PullingAlgorithm::Constraint)
{
bConstraint = TRUE;
pulldim_con[m] = 1;
/* If we use cylinder coordinates, do some initialising for them */
if (pull->bCylinder)
{
- for (const pull_coord_work_t& coord : pull->coord)
+ for (pull_coord_work_t& coord : pull->coord)
{
- if (coord.params.eGeom == epullgCYL)
+ if (coord.params.eGeom == PullGroupGeometry::Cylinder)
{
if (pull->group[coord.params.group[0]].params.ind.empty())
{
"reference!\n");
}
}
- const auto& referenceGroup = pull->group[coord.params.group[0]];
- pull->dyna.emplace_back(referenceGroup.params, referenceGroup.atomSet,
- pull->params.bSetPbcRefToPrevStepCOM);
+ const auto& group0 = pull->group[coord.params.group[0]];
+ coord.dynamicGroup0 = std::make_unique<pull_group_work_t>(
+ group0.params, group0.atomSet, pull->params.bSetPbcRefToPrevStepCOM, maxNumThreads);
}
}
- /* The gmx_omp_nthreads module might not be initialized here, so max(1,) */
- pull->nthreads = std::max(1, gmx_omp_nthreads_get(emntDefault));
- pull->comSums.resize(pull->nthreads);
+ pull->comSums.resize(maxNumThreads);
comm = &pull->comm;
delete pull;
}
-void preparePrevStepPullCom(const t_inputrec* ir,
- pull_t* pull_work,
- const real* masses,
- t_state* state,
- const t_state* state_global,
- const t_commrec* cr,
- bool startingFromCheckpoint)
+void preparePrevStepPullCom(const t_inputrec* ir,
+ pull_t* pull_work,
+ ArrayRef<const real> masses,
+ t_state* state,
+ const t_state* state_global,
+ const t_commrec* cr,
+ bool startingFromCheckpoint)
{
if (!ir->pull || !ir->pull->bSetPbcRefToPrevStepCOM)
{
{
/* Only the master rank has the checkpointed COM from the previous step */
gmx_bcast(sizeof(double) * state->pull_com_prev_step.size(),
- &state->pull_com_prev_step[0], cr->mpi_comm_mygroup);
+ &state->pull_com_prev_step[0],
+ cr->mpi_comm_mygroup);
}
setPrevStepPullComFromState(pull_work, state);
}
{
t_pbc pbc;
set_pbc(&pbc, ir->pbcType, state->box);
- initPullComFromPrevStep(cr, pull_work, masses, &pbc, state->x.rvec_array());
+ initPullComFromPrevStep(
+ cr, pull_work, masses, &pbc, state->x.arrayRefWithPadding().unpaddedArrayRef());
updatePrevStepPullCom(pull_work, state);
}
}
{
for (int c = 0; c < pullParameters.ncoord; c++)
{
- if (pullParameters.coord[c].eType == epullCONSTRAINT)
+ if (pullParameters.coord[c].eType == PullingAlgorithm::Constraint)
{
return true;
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
namespace gmx
{
+template<typename>
+class ArrayRef;
class ForceWithVirial;
class LocalAtomSetManager;
} // namespace gmx
-/*! \brief Returns if the pull coordinate is an angle
- *
- * \param[in] pcrd The pull coordinate to query the type for.
- * \returns a boolean telling if the coordinate is of angle type.
- */
-bool pull_coordinate_is_angletype(const t_pull_coord* pcrd);
-
/*! \brief Returns the units of the pull coordinate.
*
* \param[in] pcrd The pull coordinate to query the units for.
* \returns a string with the units of the coordinate.
*/
-const char* pull_coordinate_units(const t_pull_coord* pcrd);
+const char* pull_coordinate_units(const t_pull_coord& pcrd);
/*! \brief Returns the conversion factor from the pull coord init/rate unit to internal value unit.
*
* \param[in] pcrd The pull coordinate to get the conversion factor for.
* \returns the conversion factor.
*/
-double pull_conversion_factor_userinput2internal(const t_pull_coord* pcrd);
+double pull_conversion_factor_userinput2internal(const t_pull_coord& pcrd);
/*! \brief Returns the conversion factor from the pull coord internal value unit to the init/rate unit.
*
* \param[in] pcrd The pull coordinate to get the conversion factor for.
* \returns the conversion factor.
*/
-double pull_conversion_factor_internal2userinput(const t_pull_coord* pcrd);
+double pull_conversion_factor_internal2userinput(const t_pull_coord& pcrd);
/*! \brief Get the value for pull coord coord_ind.
*
* \param[in] masses Atoms masses.
* \param[in,out] forceWithVirial Force and virial buffers.
*/
-void apply_external_pull_coord_force(struct pull_t* pull,
- int coord_index,
- double coord_force,
- const real* masses,
- gmx::ForceWithVirial* forceWithVirial);
-
+void apply_external_pull_coord_force(struct pull_t* pull,
+ int coord_index,
+ double coord_force,
+ gmx::ArrayRef<const real> masses,
+ gmx::ForceWithVirial* forceWithVirial);
/*! \brief Set the all the pull forces to zero.
*
*
* \returns The pull potential energy.
*/
-real pull_potential(struct pull_t* pull,
- const real* masses,
- struct t_pbc* pbc,
- const t_commrec* cr,
- double t,
- real lambda,
- const rvec* x,
- gmx::ForceWithVirial* force,
- real* dvdlambda);
+real pull_potential(struct pull_t* pull,
+ gmx::ArrayRef<const real> masses,
+ struct t_pbc* pbc,
+ const t_commrec* cr,
+ double t,
+ real lambda,
+ gmx::ArrayRef<const gmx::RVec> x,
+ gmx::ForceWithVirial* force,
+ real* dvdlambda);
/*! \brief Constrain the coordinates xp in the directions in x
* \param[in,out] v Velocities, which may get a pull correction.
* \param[in,out] vir The virial, which, if != NULL, gets a pull correction.
*/
-void pull_constraint(struct pull_t* pull,
- const real* masses,
- struct t_pbc* pbc,
- const t_commrec* cr,
- double dt,
- double t,
- rvec* x,
- rvec* xp,
- rvec* v,
- tensor vir);
+void pull_constraint(struct pull_t* pull,
+ gmx::ArrayRef<const real> masses,
+ struct t_pbc* pbc,
+ const t_commrec* cr,
+ double dt,
+ double t,
+ gmx::ArrayRef<gmx::RVec> x,
+ gmx::ArrayRef<gmx::RVec> xp,
+ gmx::ArrayRef<gmx::RVec> v,
+ tensor vir);
/*! \brief Make a selection of the home atoms for all pull groups.
struct pull_t* init_pull(FILE* fplog,
const pull_params_t* pull_params,
const t_inputrec* ir,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const t_commrec* cr,
gmx::LocalAtomSetManager* atomSets,
real lambda);
* \param[in,out] xp Updated x, can be NULL.
*
*/
-void pull_calc_coms(const t_commrec* cr,
- pull_t* pull,
- const real* masses,
- t_pbc* pbc,
- double t,
- const rvec x[],
- rvec* xp);
+void pull_calc_coms(const t_commrec* cr,
+ pull_t* pull,
+ gmx::ArrayRef<const real> masses,
+ t_pbc* pbc,
+ double t,
+ gmx::ArrayRef<const gmx::RVec> x,
+ gmx::ArrayRef<gmx::RVec> xp);
/*! \brief Margin for checking pull group PBC distances compared to half the box size */
static constexpr real c_pullGroupPbcMargin = 0.9;
* \param[in] pbcMargin The minimum margin (as a fraction) to half the box size
* \returns -1 when all groups obey PBC or the first group index that fails PBC
*/
-int pullCheckPbcWithinGroups(const pull_t& pull, const rvec* x, const t_pbc& pbc, real pbcMargin);
+int pullCheckPbcWithinGroups(const pull_t& pull, gmx::ArrayRef<const gmx::RVec> x, const t_pbc& pbc, real pbcMargin);
/*! \brief Checks whether a specific group that uses a reference atom is within PBC restrictions
*
* \param[in] cr Struct for communication info.
* \param[in] startingFromCheckpoint Is the simulation starting from a checkpoint?
*/
-void preparePrevStepPullCom(const t_inputrec* ir,
- pull_t* pull_work,
- const real* masses,
- t_state* state,
- const t_state* state_global,
- const t_commrec* cr,
- bool startingFromCheckpoint);
+void preparePrevStepPullCom(const t_inputrec* ir,
+ pull_t* pull_work,
+ gmx::ArrayRef<const real> masses,
+ t_state* state,
+ const t_state* state_global,
+ const t_commrec* cr,
+ bool startingFromCheckpoint);
/*! \brief Initializes the COM of the previous step (set to initial COM)
*
* \param[in] pbc Information struct about periodicity.
* \param[in] x The local positions.
*/
-void initPullComFromPrevStep(const t_commrec* cr, pull_t* pull, const real* masses, t_pbc* pbc, const rvec x[]);
+void initPullComFromPrevStep(const t_commrec* cr,
+ pull_t* pull,
+ gmx::ArrayRef<const real> masses,
+ t_pbc* pbc,
+ gmx::ArrayRef<const gmx::RVec> x);
#endif
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \param[in] params The group parameters set by the user
* \param[in] atomSet The global to local atom set manager
* \param[in] setPbcRefToPrevStepCOM Does this pull group use the COM from the previous step as reference position?
+ * \param[in] maxNumThreads Use either this number of threads of 1 for operations on x and f
*/
- pull_group_work_t(const t_pull_group& params, gmx::LocalAtomSet atomSet, bool setPbcRefToPrevStepCOM);
+ pull_group_work_t(const t_pull_group& params,
+ gmx::LocalAtomSet atomSet,
+ bool setPbcRefToPrevStepCOM,
+ int maxNumThreads);
+
+ //! Returns the number of threads to use for local atom operations based on the local atom count
+ int numThreads() const
+ {
+ return atomSet.numAtomsLocal() <= c_pullMaxNumLocalAtomsSingleThreaded ? 1 : maxNumThreads;
+ }
/* Data only modified at initialization */
const t_pull_group params; /**< The pull group parameters */
const int epgrppbc; /**< The type of pbc for this pull group, see enum above */
- bool needToCalcCom; /**< Do we need to calculate the COM? (Not for group 0 or if only used as cylinder group) */
- std::vector<real> globalWeights; /**< Weights per atom set by the user and/or mass/friction coefficients, if empty all weights are equal */
+ const int maxNumThreads; /**< The maximum number of threads to use for operations on x and f */
+ bool needToCalcCom; /**< Do we need to calculate the COM? (Not for group 0 or if only used as cylinder group) */
+ std::vector<real> globalWeights; /**< Weights per atom set by the user and/or mass/friction coefficients, if empty all weights are equal */
/* Data modified only at init or at domain decomposition */
gmx::LocalAtomSet atomSet; /**< Global to local atom set mapper */
const t_pull_coord params; /* Pull coordinate parameters */
+ /* Dynamic pull group 0 for this coordinate with dynamic weights, only present when needed */
+ std::unique_ptr<pull_group_work_t> dynamicGroup0;
+
double value_ref; /* The reference value, usually init+rate*t, units of nm or rad */
PullCoordSpatialData spatialData; /* Data defining the current geometry */
/* Parameters + dynamic data for groups */
std::vector<pull_group_work_t> group; /* The pull group param and work data */
- std::vector<pull_group_work_t> dyna; /* Dynamic groups for geom=cylinder */
/* Parameters + dynamic data for coordinates */
std::vector<pull_coord_work_t> coord; /* The pull group param and work data */
/* Global dynamic data */
gmx_bool bSetPBCatoms; /* Do we need to set x_pbc for the groups? */
- int nthreads; /* Number of threads used by the pull code */
- std::vector<ComSums> comSums; /* Work array for summing for COM, 1 entry per thread */
+ std::vector<ComSums> comSums; /* Work array for summing for COM, 1 entry per thread */
pull_comm_t comm; /* Communication parameters, communicator and buffers */
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxlib/network.h"
#include "gromacs/linearalgebra/nrjac.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/groupcoord.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/smalloc.h"
-static char const* RotStr = { "Enforced rotation:" };
+static const std::string RotStr = { "Enforced rotation:" };
/* Set the minimum weight for the determination of the slab centers */
#define WEIGHT_MIN (10 * GMX_FLOAT_MIN)
/* Activate output of forces for correctness checks */
/* #define PRINT_FORCES */
#ifdef PRINT_FORCES
-# define PRINT_FORCE_J \
- fprintf(stderr, "f%d = %15.8f %15.8f %15.8f\n", erg->xc_ref_ind[j], erg->f_rot_loc[j][XX], \
- erg->f_rot_loc[j][YY], erg->f_rot_loc[j][ZZ]);
+# define PRINT_FORCE_J \
+ fprintf(stderr, \
+ "f%d = %15.8f %15.8f %15.8f\n", \
+ erg->xc_ref_ind[j], \
+ erg->f_rot_loc[j][XX], \
+ erg->f_rot_loc[j][YY], \
+ erg->f_rot_loc[j][ZZ]);
# define PRINT_POT_TAU \
if (MASTER(cr)) \
{ \
fprintf(stderr, \
"potential = %15.8f\n" \
"torque = %15.8f\n", \
- erg->V, erg->torque_v); \
+ erg->V, \
+ erg->torque_v); \
}
#else
# define PRINT_FORCE_J
#endif
/* Shortcuts for often used queries */
-#define ISFLEX(rg) \
- (((rg)->eType == erotgFLEX) || ((rg)->eType == erotgFLEXT) || ((rg)->eType == erotgFLEX2) \
- || ((rg)->eType == erotgFLEX2T))
-#define ISCOLL(rg) \
- (((rg)->eType == erotgFLEX) || ((rg)->eType == erotgFLEXT) || ((rg)->eType == erotgFLEX2) \
- || ((rg)->eType == erotgFLEX2T) || ((rg)->eType == erotgRMPF) || ((rg)->eType == erotgRM2PF))
+#define ISFLEX(rg) \
+ (((rg)->eType == EnforcedRotationGroupType::Flex) || ((rg)->eType == EnforcedRotationGroupType::Flext) \
+ || ((rg)->eType == EnforcedRotationGroupType::Flex2) \
+ || ((rg)->eType == EnforcedRotationGroupType::Flex2t))
+#define ISCOLL(rg) \
+ (((rg)->eType == EnforcedRotationGroupType::Flex) || ((rg)->eType == EnforcedRotationGroupType::Flext) \
+ || ((rg)->eType == EnforcedRotationGroupType::Flex2) \
+ || ((rg)->eType == EnforcedRotationGroupType::Flex2t) \
+ || ((rg)->eType == EnforcedRotationGroupType::Rmpf) \
+ || ((rg)->eType == EnforcedRotationGroupType::Rm2pf))
/* Does any of the rotation groups use slab decomposition? */
{
for (int g = 0; g < rot->ngrp; g++)
{
- if (erotgFitPOT == rot->grp[g].eFittype)
+ if (RotationGroupFitting::Pot == rot->grp[g].eFittype)
{
return TRUE;
}
/* Reduce potential angle fit data for this group at this time step? */
static inline gmx_bool bPotAngle(const gmx_enfrot* er, const t_rotgrp* rotg, int64_t step)
{
- return ((erotgFitPOT == rotg->eFittype)
+ return ((RotationGroupFitting::Pot == rotg->eFittype)
&& (do_per_step(step, er->nstsout) || do_per_step(step, er->nstrout)));
}
}
if (count > er->mpi_bufsize)
{
- gmx_fatal(FARGS, "%s MPI buffer overflow, please report this error.", RotStr);
+ gmx_fatal(FARGS, "%s MPI buffer overflow, please report this error.", RotStr.c_str());
}
#if GMX_MPI
- MPI_Reduce(er->mpi_inbuf, er->mpi_outbuf, count, GMX_MPI_REAL, MPI_SUM, MASTERRANK(cr),
- cr->mpi_comm_mygroup);
+ MPI_Reduce(er->mpi_inbuf, er->mpi_outbuf, count, GMX_MPI_REAL, MPI_SUM, MASTERRANK(cr), cr->mpi_comm_mygroup);
#endif
/* Copy back the reduced data from the buffer on the master */
/* Output to main rotation output file: */
if (do_per_step(step, er->nstrout))
{
- if (erotgFitPOT == rotg->eFittype)
+ if (RotationGroupFitting::Pot == rotg->eFittype)
{
fitangle = get_fitangle(erg);
}
}
/* Output to angles log file: */
- if (erotgFitPOT == rotg->eFittype)
+ if (RotationGroupFitting::Pot == rotg->eFittype)
{
fprintf(er->out_angles, "%12.3e%6d%12.4f", t, erg->groupIndex, erg->degangle);
/* Output energies at a set of angles around the reference angle */
/* Add the forces from enforced rotation potential to the local forces.
* Should be called after the SR forces have been evaluated */
-real add_rot_forces(gmx_enfrot* er, rvec f[], const t_commrec* cr, int64_t step, real t)
+real add_rot_forces(gmx_enfrot* er, gmx::ArrayRef<gmx::RVec> force, const t_commrec* cr, int64_t step, real t)
{
real Vrot = 0.0; /* If more than one rotation group is present, Vrot
assembles the local parts from all groups */
/* Get the right index of the local force */
int ii = localRotationGroupIndex[l];
/* Add */
- rvec_inc(f[ii], erg->f_rot_loc[l]);
+ rvec_inc(force[ii], erg->f_rot_loc[l]);
}
}
/* We can do the calculations ONLY if there is weight in the slab! */
if (erg->slab_weights[slabIndex] > WEIGHT_MIN)
{
- svmul(1.0 / erg->slab_weights[slabIndex], erg->slab_center[slabIndex],
- erg->slab_center[slabIndex]);
+ svmul(1.0 / erg->slab_weights[slabIndex], erg->slab_center[slabIndex], erg->slab_center[slabIndex]);
}
else
{
for (int j = erg->slab_first; j <= erg->slab_last; j++)
{
int slabIndex = j - erg->slab_first;
- fprintf(out_slabs, "%6d%12.3e%12.3e%12.3e", j, erg->slab_center[slabIndex][XX],
- erg->slab_center[slabIndex][YY], erg->slab_center[slabIndex][ZZ]);
+ fprintf(out_slabs,
+ "%6d%12.3e%12.3e%12.3e",
+ j,
+ erg->slab_center[slabIndex][XX],
+ erg->slab_center[slabIndex][YY],
+ erg->slab_center[slabIndex][ZZ]);
}
fprintf(out_slabs, "\n");
}
fp = gmx_ffopen(fn, "w");
- fprintf(fp, "# Output of %s is written in intervals of %d time step%s.\n#\n", what, steps,
- steps > 1 ? "s" : "");
+ fprintf(fp, "# Output of %s is written in intervals of %d time step%s.\n#\n", what, steps, steps > 1 ? "s" : "");
return fp;
}
gmx_enfrotgrp* erg = &ergRef;
if (ISFLEX(erg->rotg))
{
- fprintf(fp, "# Rotation group %d (%s), slab distance %f nm, %s.\n", erg->groupIndex,
- erotg_names[erg->rotg->eType], erg->rotg->slab_dist,
+ fprintf(fp,
+ "# Rotation group %d (%s), slab distance %f nm, %s.\n",
+ erg->groupIndex,
+ enumValueToString(erg->rotg->eType),
+ erg->rotg->slab_dist,
erg->rotg->bMassW ? "centers of mass" : "geometrical centers");
}
}
}
else
{
- fp = xvgropen(fn, "Rotation angles and energy", "Time (ps)",
- "angles (degrees) and energies (kJ/mol)", oenv);
+ fp = xvgropen(fn,
+ "Rotation angles and energy",
+ "Time (ps)",
+ "angles (degrees) and energies (kJ/mol)",
+ oenv);
fprintf(fp,
"# Output of enforced rotation data is written in intervals of %d time "
"step%s.\n#\n",
- er->nstrout, er->nstrout > 1 ? "s" : "");
+ er->nstrout,
+ er->nstrout > 1 ? "s" : "");
fprintf(fp,
"# The scalar tau is the torque (kJ/mol) in the direction of the rotation vector "
"v.\n");
bFlex = ISFLEX(rotg);
fprintf(fp, "#\n");
- fprintf(fp, "# ROTATION GROUP %d, potential type '%s':\n", g, erotg_names[rotg->eType]);
- fprintf(fp, "# rot-massw%d %s\n", g, yesno_names[rotg->bMassW]);
- fprintf(fp, "# rot-vec%d %12.5e %12.5e %12.5e\n", g, erg->vec[XX],
- erg->vec[YY], erg->vec[ZZ]);
+ fprintf(fp, "# ROTATION GROUP %d, potential type '%s':\n", g, enumValueToString(rotg->eType));
+ fprintf(fp, "# rot-massw%d %s\n", g, booleanValueToString(rotg->bMassW));
+ fprintf(fp,
+ "# rot-vec%d %12.5e %12.5e %12.5e\n",
+ g,
+ erg->vec[XX],
+ erg->vec[YY],
+ erg->vec[ZZ]);
fprintf(fp, "# rot-rate%d %12.5e degrees/ps\n", g, rotg->rate);
fprintf(fp, "# rot-k%d %12.5e kJ/(mol*nm^2)\n", g, rotg->k);
- if (rotg->eType == erotgISO || rotg->eType == erotgPM || rotg->eType == erotgRM
- || rotg->eType == erotgRM2)
+ if (rotg->eType == EnforcedRotationGroupType::Iso || rotg->eType == EnforcedRotationGroupType::Pm
+ || rotg->eType == EnforcedRotationGroupType::Rm
+ || rotg->eType == EnforcedRotationGroupType::Rm2)
{
- fprintf(fp, "# rot-pivot%d %12.5e %12.5e %12.5e nm\n", g, rotg->pivot[XX],
- rotg->pivot[YY], rotg->pivot[ZZ]);
+ fprintf(fp,
+ "# rot-pivot%d %12.5e %12.5e %12.5e nm\n",
+ g,
+ rotg->pivot[XX],
+ rotg->pivot[YY],
+ rotg->pivot[ZZ]);
}
if (bFlex)
}
/* Output the centers of the rotation groups for the pivot-free potentials */
- if ((rotg->eType == erotgISOPF) || (rotg->eType == erotgPMPF) || (rotg->eType == erotgRMPF)
- || (rotg->eType == erotgRM2PF || (rotg->eType == erotgFLEXT) || (rotg->eType == erotgFLEX2T)))
+ if ((rotg->eType == EnforcedRotationGroupType::Isopf)
+ || (rotg->eType == EnforcedRotationGroupType::Pmpf)
+ || (rotg->eType == EnforcedRotationGroupType::Rmpf)
+ || (rotg->eType == EnforcedRotationGroupType::Rm2pf
+ || (rotg->eType == EnforcedRotationGroupType::Flext)
+ || (rotg->eType == EnforcedRotationGroupType::Flex2t)))
{
- fprintf(fp, "# ref. grp. %d center %12.5e %12.5e %12.5e\n", g,
- erg->xc_ref_center[XX], erg->xc_ref_center[YY], erg->xc_ref_center[ZZ]);
+ fprintf(fp,
+ "# ref. grp. %d center %12.5e %12.5e %12.5e\n",
+ g,
+ erg->xc_ref_center[XX],
+ erg->xc_ref_center[YY],
+ erg->xc_ref_center[ZZ]);
- fprintf(fp, "# grp. %d init.center %12.5e %12.5e %12.5e\n", g, erg->xc_center[XX],
- erg->xc_center[YY], erg->xc_center[ZZ]);
+ fprintf(fp,
+ "# grp. %d init.center %12.5e %12.5e %12.5e\n",
+ g,
+ erg->xc_center[XX],
+ erg->xc_center[YY],
+ erg->xc_center[ZZ]);
}
- if ((rotg->eType == erotgRM2) || (rotg->eType == erotgFLEX2) || (rotg->eType == erotgFLEX2T))
+ if ((rotg->eType == EnforcedRotationGroupType::Rm2)
+ || (rotg->eType == EnforcedRotationGroupType::Flex2)
+ || (rotg->eType == EnforcedRotationGroupType::Flex2t))
{
fprintf(fp, "# rot-eps%d %12.5e nm^2\n", g, rotg->eps);
}
- if (erotgFitPOT == rotg->eFittype)
+ if (RotationGroupFitting::Pot == rotg->eFittype)
{
fprintf(fp, "#\n");
fprintf(fp,
"# theta_fit%d is determined by first evaluating the potential for %d "
"angles around theta_ref%d.\n",
- g, rotg->PotAngle_nstep, g);
+ g,
+ rotg->PotAngle_nstep,
+ g);
fprintf(fp,
"# The fit angle is the one with the smallest potential. It is given as "
"the deviation\n");
/* For flexible axis rotation we use RMSD fitting to determine the
* actual angle of the rotation group */
- if (bFlex || erotgFitPOT == rotg->eFittype)
+ if (bFlex || RotationGroupFitting::Pot == rotg->eFittype)
{
sprintf(buf, "theta_fit%d", g);
}
/* Output for this group happens only if potential type is flexible or
* if fit type is potential! */
- if (ISFLEX(rotg) || (erotgFitPOT == rotg->eFittype))
+ if (ISFLEX(rotg) || (RotationGroupFitting::Pot == rotg->eFittype))
{
if (ISFLEX(rotg))
{
buf[0] = '\0';
}
- fprintf(fp, "#\n# ROTATION GROUP %d '%s',%s fit type '%s'.\n", g,
- erotg_names[rotg->eType], buf, erotg_fitnames[rotg->eFittype]);
+ fprintf(fp,
+ "#\n# ROTATION GROUP %d '%s',%s fit type '%s'.\n",
+ g,
+ enumValueToString(rotg->eType),
+ buf,
+ enumValueToString(rotg->eFittype));
/* Special type of fitting using the potential minimum. This is
* done for the whole group only, not for the individual slabs. */
- if (erotgFitPOT == rotg->eFittype)
+ if (RotationGroupFitting::Pot == rotg->eFittype)
{
fprintf(fp,
"# To obtain theta_fit%d, the potential is evaluated for %d angles "
"around theta_ref%d\n",
- g, rotg->PotAngle_nstep, g);
+ g,
+ rotg->PotAngle_nstep,
+ g);
fprintf(fp,
"# The fit angle in the rotation standard outfile is the one with "
"minimal energy E(theta_fit) [kJ/mol].\n");
print_aligned_short(fp, "grp");
print_aligned(fp, "theta_ref");
- if (erotgFitPOT == rotg->eFittype)
+ if (RotationGroupFitting::Pot == rotg->eFittype)
{
/* Output the set of angles around the reference angle */
for (int i = 0; i < rotg->PotAngle_nstep; i++)
const gmx_enfrotgrp* erg = &er->enfrotgrp[g];
if (ISFLEX(rotg))
{
- fprintf(fp, "# Rotation group %d (%s), slab distance %f nm.\n", g,
- erotg_names[rotg->eType], rotg->slab_dist);
+ fprintf(fp,
+ "# Rotation group %d (%s), slab distance %f nm.\n",
+ g,
+ enumValueToString(rotg->eType),
+ rotg->slab_dist);
fprintf(fp,
"# The scalar tau is the torque (kJ/mol) in the direction of the rotation "
"vector.\n");
fprintf(fp, "# To obtain the vectorial torque, multiply tau with\n");
- fprintf(fp, "# rot-vec%d %10.3e %10.3e %10.3e\n", g, erg->vec[XX],
- erg->vec[YY], erg->vec[ZZ]);
+ fprintf(fp,
+ "# rot-vec%d %10.3e %10.3e %10.3e\n",
+ g,
+ erg->vec[XX],
+ erg->vec[YY],
+ erg->vec[ZZ]);
fprintf(fp, "#\n");
}
}
get_center(erg->xc, erg->mc_sorted, erg->rotg->nat, center);
/* === Determine the optimal fit angle for the rotation group === */
- if (erg->rotg->eFittype == erotgFitNORM)
+ if (erg->rotg->eFittype == RotationGroupFitting::Norm)
{
/* Normalize every position to it's reference length */
for (int i = 0; i < erg->rotg->nat; i++)
/* From the point of view of the current positions, the reference has rotated
* backwards. Since we output the angle relative to the fixed reference,
* we need the minus sign. */
- fitangle = -opt_angle_analytic(erg->xc_ref_sorted, fitcoords, erg->mc_sorted, erg->rotg->nat,
- erg->xc_ref_center, center, erg->vec);
+ fitangle = -opt_angle_analytic(
+ erg->xc_ref_sorted, fitcoords, erg->mc_sorted, erg->rotg->nat, erg->xc_ref_center, center, erg->vec);
return fitangle;
}
/* Get the center of the slabs reference and current positions */
get_center(sd->ref, sd->weight, sd->nat, ref_center);
get_center(sd->x, sd->weight, sd->nat, act_center);
- if (erg->rotg->eFittype == erotgFitNORM)
+ if (erg->rotg->eFittype == RotationGroupFitting::Norm)
{
/* Normalize every position to it's reference length
* prior to performing the fit */
clear_rvec(ref_center);
clear_rvec(act_center);
}
- fitangle = -opt_angle_analytic(sd->ref, sd->x, sd->weight, sd->nat, ref_center,
- act_center, erg->vec);
+ fitangle = -opt_angle_analytic(
+ sd->ref, sd->x, sd->weight, sd->nat, ref_center, act_center, erg->vec);
fprintf(fp, "%6d%6d%12.3f", n, sd->nat, fitangle);
}
}
}
-static real do_flex2_lowlevel(gmx_enfrotgrp* erg,
- real sigma, /* The Gaussian width sigma */
- rvec x[],
- gmx_bool bOutstepRot,
- gmx_bool bOutstepSlab,
- const matrix box)
+static real do_flex2_lowlevel(gmx_enfrotgrp* erg,
+ real sigma, /* The Gaussian width sigma */
+ gmx::ArrayRef<const gmx::RVec> coords,
+ gmx_bool bOutstepRot,
+ gmx_bool bOutstepSlab,
+ const matrix box)
{
int count, ii, iigrp;
rvec xj; /* position in the i-sum */
* them again for every atom */
flex2_precalc_inner_sum(erg);
- bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == erg->rotg->eFittype);
+ bCalcPotFit = (bOutstepRot || bOutstepSlab) && (RotationGroupFitting::Pot == erg->rotg->eFittype);
/********************************************************/
/* Main loop over all local atoms of the rotation group */
* Note that erg->xc_center contains the center of mass in case the flex2-t
* potential was chosen. For the flex2 potential erg->xc_center must be
* zero. */
- rvec_sub(x[ii], erg->xc_center, xj);
+ rvec_sub(coords[ii], erg->xc_center, xj);
/* Shift this atom such that it is near its reference */
shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
}
#ifdef SUM_PARTS
- fprintf(stderr, "sum1: %15.8f %15.8f %15.8f\n", -erg->rotg->k * sum1vec[XX],
- -erg->rotg->k * sum1vec[YY], -erg->rotg->k * sum1vec[ZZ]);
- fprintf(stderr, "sum2: %15.8f %15.8f %15.8f\n", erg->rotg->k * sum2vec[XX],
- erg->rotg->k * sum2vec[YY], erg->rotg->k * sum2vec[ZZ]);
- fprintf(stderr, "sum3: %15.8f %15.8f %15.8f\n", -erg->rotg->k * sum3vec[XX],
- -erg->rotg->k * sum3vec[YY], -erg->rotg->k * sum3vec[ZZ]);
- fprintf(stderr, "sum4: %15.8f %15.8f %15.8f\n", 0.5 * erg->rotg->k * sum4vec[XX],
- 0.5 * erg->rotg->k * sum4vec[YY], 0.5 * erg->rotg->k * sum4vec[ZZ]);
+ fprintf(stderr,
+ "sum1: %15.8f %15.8f %15.8f\n",
+ -erg->rotg->k * sum1vec[XX],
+ -erg->rotg->k * sum1vec[YY],
+ -erg->rotg->k * sum1vec[ZZ]);
+ fprintf(stderr,
+ "sum2: %15.8f %15.8f %15.8f\n",
+ erg->rotg->k * sum2vec[XX],
+ erg->rotg->k * sum2vec[YY],
+ erg->rotg->k * sum2vec[ZZ]);
+ fprintf(stderr,
+ "sum3: %15.8f %15.8f %15.8f\n",
+ -erg->rotg->k * sum3vec[XX],
+ -erg->rotg->k * sum3vec[YY],
+ -erg->rotg->k * sum3vec[ZZ]);
+ fprintf(stderr,
+ "sum4: %15.8f %15.8f %15.8f\n",
+ 0.5 * erg->rotg->k * sum4vec[XX],
+ 0.5 * erg->rotg->k * sum4vec[YY],
+ 0.5 * erg->rotg->k * sum4vec[ZZ]);
#endif
PRINT_FORCE_J
static real do_flex_lowlevel(gmx_enfrotgrp* erg,
- real sigma, /* The Gaussian width sigma */
- rvec x[],
- gmx_bool bOutstepRot,
- gmx_bool bOutstepSlab,
- const matrix box)
+ real sigma, /* The Gaussian width sigma */
+ gmx::ArrayRef<const gmx::RVec> coords,
+ gmx_bool bOutstepRot,
+ gmx_bool bOutstepSlab,
+ const matrix box)
{
int count, iigrp;
rvec xj, yj0; /* current and reference position */
* them again for every atom */
flex_precalc_inner_sum(erg);
- bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == erg->rotg->eFittype);
+ bCalcPotFit = (bOutstepRot || bOutstepSlab) && (RotationGroupFitting::Pot == erg->rotg->eFittype);
/********************************************************/
/* Main loop over all local atoms of the rotation group */
* Note that erg->xc_center contains the center of mass in case the flex-t
* potential was chosen. For the flex potential erg->xc_center must be
* zero. */
- rvec_sub(x[ii], erg->xc_center, xj);
+ rvec_sub(coords[ii], erg->xc_center, xj);
/* Shift this atom such that it is near its reference */
shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
/* Check whether we have reference data to compare against */
if (erg->slab_first < erg->slab_first_ref)
{
- gmx_fatal(FARGS, "%s No reference data for first slab (n=%d), unable to proceed.", RotStr,
+ gmx_fatal(FARGS,
+ "%s No reference data for first slab (n=%d), unable to proceed.",
+ RotStr.c_str(),
erg->slab_first);
}
/* Check whether we have reference data to compare against */
if (erg->slab_last > erg->slab_last_ref)
{
- gmx_fatal(FARGS, "%s No reference data for last slab (n=%d), unable to proceed.", RotStr,
+ gmx_fatal(FARGS,
+ "%s No reference data for last slab (n=%d), unable to proceed.",
+ RotStr.c_str(),
erg->slab_last);
}
}
static void do_flexible(gmx_bool bMaster,
gmx_enfrot* enfrot, /* Other rotation data */
gmx_enfrotgrp* erg,
- rvec x[], /* The local positions */
- const matrix box,
- double t, /* Time in picoseconds */
- gmx_bool bOutstepRot, /* Output to main rotation output file */
- gmx_bool bOutstepSlab) /* Output per-slab data */
+ gmx::ArrayRef<const gmx::RVec> coords, /* The local positions */
+ const matrix box,
+ double t, /* Time in picoseconds */
+ gmx_bool bOutstepRot, /* Output to main rotation output file */
+ gmx_bool bOutstepSlab) /* Output per-slab data */
{
int nslabs;
real sigma; /* The Gaussian width sigma */
}
/* Call the rotational forces kernel */
- if (erg->rotg->eType == erotgFLEX || erg->rotg->eType == erotgFLEXT)
+ if (erg->rotg->eType == EnforcedRotationGroupType::Flex
+ || erg->rotg->eType == EnforcedRotationGroupType::Flext)
{
- erg->V = do_flex_lowlevel(erg, sigma, x, bOutstepRot, bOutstepSlab, box);
+ erg->V = do_flex_lowlevel(erg, sigma, coords, bOutstepRot, bOutstepSlab, box);
}
- else if (erg->rotg->eType == erotgFLEX2 || erg->rotg->eType == erotgFLEX2T)
+ else if (erg->rotg->eType == EnforcedRotationGroupType::Flex2
+ || erg->rotg->eType == EnforcedRotationGroupType::Flex2t)
{
- erg->V = do_flex2_lowlevel(erg, sigma, x, bOutstepRot, bOutstepSlab, box);
+ erg->V = do_flex2_lowlevel(erg, sigma, coords, bOutstepRot, bOutstepSlab, box);
}
else
{
/* Determine angle by RMSD fit to the reference - Let's hope this */
/* only happens once in a while, since this is not parallelized! */
- if (bMaster && (erotgFitPOT != erg->rotg->eFittype))
+ if (bMaster && (RotationGroupFitting::Pot != erg->rotg->eFittype))
{
if (bOutstepRot)
{
gmx_bool bProject;
- bProject = (erg->rotg->eType == erotgPM) || (erg->rotg->eType == erotgPMPF);
- bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == erg->rotg->eFittype);
+ bProject = (erg->rotg->eType == EnforcedRotationGroupType::Pm)
+ || (erg->rotg->eType == EnforcedRotationGroupType::Pmpf);
+ bCalcPotFit = (bOutstepRot || bOutstepSlab) && (RotationGroupFitting::Pot == erg->rotg->eFittype);
N_M = erg->rotg->nat * erg->invmass;
const auto& collectiveRotationGroupIndex = erg->atomSet->collectiveIndex();
/* Rotate with the alternative angle. Like rotate_local_reference(),
* just for a single local atom */
- mvmul(erg->PotAngleFit->rotmat[ifit], erg->rotg->x_ref[jj],
- fit_xr_loc); /* fit_xr_loc = Omega*(y_i-y_c) */
+ mvmul(erg->PotAngleFit->rotmat[ifit], erg->rotg->x_ref[jj], fit_xr_loc); /* fit_xr_loc = Omega*(y_i-y_c) */
/* Calculate Omega*(y_i-y_c)-(x_i-x_c) */
rvec_sub(fit_xr_loc, xi_xc, dr);
real wj; /* Mass-weighting of the positions */
real N_M; /* N/M */
- bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == erg->rotg->eFittype);
+ bCalcPotFit = (bOutstepRot || bOutstepSlab) && (RotationGroupFitting::Pot == erg->rotg->eFittype);
N_M = erg->rotg->nat * erg->invmass;
const auto& collectiveRotationGroupIndex = erg->atomSet->collectiveIndex();
/* Rotate with the alternative angle. Like rotate_local_reference(),
* just for a single local atom */
- mvmul(erg->PotAngleFit->rotmat[ifit], erg->rotg->x_ref[jj],
- fit_tmpvec); /* fit_tmpvec = Omega*(yj0-u) */
+ mvmul(erg->PotAngleFit->rotmat[ifit], erg->rotg->x_ref[jj], fit_tmpvec); /* fit_tmpvec = Omega*(yj0-u) */
/* Calculate Omega.(yj0-u) */
cprod(erg->vec, fit_tmpvec, tmpvec); /* tmpvec = v x Omega.(yj0-u) */
/* Calculate the radial motion pivot-free potential and forces */
-static void do_radial_motion_pf(gmx_enfrotgrp* erg,
- rvec x[], /* The positions */
- const matrix box, /* The simulation box */
- gmx_bool bOutstepRot, /* Output to main rotation output file */
- gmx_bool bOutstepSlab) /* Output per-slab data */
+static void do_radial_motion_pf(gmx_enfrotgrp* erg,
+ gmx::ArrayRef<const gmx::RVec> coords, /* The positions */
+ const matrix box, /* The simulation box */
+ gmx_bool bOutstepRot, /* Output to main rotation output file */
+ gmx_bool bOutstepSlab) /* Output per-slab data */
{
rvec xj; /* Current position */
rvec xj_xc; /* xj - xc */
real mj, wi, wj; /* Mass-weighting of the positions */
real N_M; /* N/M */
- bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == erg->rotg->eFittype);
+ bCalcPotFit = (bOutstepRot || bOutstepSlab) && (RotationGroupFitting::Pot == erg->rotg->eFittype);
N_M = erg->rotg->nat * erg->invmass;
wj = N_M * mj;
/* Current position of this atom: x[ii][XX/YY/ZZ] */
- copy_rvec(x[ii], xj);
+ copy_rvec(coords[ii], xj);
/* Shift this atom such that it is near its reference */
shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
/* Calculate the radial motion 2 potential and forces */
-static void do_radial_motion2(gmx_enfrotgrp* erg,
- rvec x[], /* The positions */
- const matrix box, /* The simulation box */
+static void do_radial_motion2(gmx_enfrotgrp* erg,
+ gmx::ArrayRef<const gmx::RVec> coords, /* The positions */
+ const matrix box, /* The simulation box */
gmx_bool bOutstepRot, /* Output to main rotation output file */
gmx_bool bOutstepSlab) /* Output per-slab data */
{
rvec innersumvec;
gmx_bool bCalcPotFit;
- bPF = erg->rotg->eType == erotgRM2PF;
- bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == erg->rotg->eFittype);
+ bPF = erg->rotg->eType == EnforcedRotationGroupType::Rm2pf;
+ bCalcPotFit = (bOutstepRot || bOutstepSlab) && (RotationGroupFitting::Pot == erg->rotg->eFittype);
clear_rvec(yj0_yc0); /* Make the compiler happy */
mj = erg->mc[iigrp];
/* Current position of this atom: x[ii] */
- copy_rvec(x[ii], xj);
+ copy_rvec(coords[ii], xj);
/* Shift this atom such that it is near its reference */
shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
int iigrp = collectiveRotationGroupIndex[j];
/* Rotate with the alternative angle. Like rotate_local_reference(),
* just for a single local atom */
- mvmul(erg->PotAngleFit->rotmat[ifit], erg->rotg->x_ref[iigrp],
- fit_rj); /* fit_rj = Omega*(yj0-u) */
+ mvmul(erg->PotAngleFit->rotmat[ifit], erg->rotg->x_ref[iigrp], fit_rj); /* fit_rj = Omega*(yj0-u) */
}
fit_fac = iprod(v_xj_u, fit_rj); /* fac = (v x (xj-u)).fit_rj */
/* Add to the rotation potential for this angle: */
if ((nullptr != fplog) && bVerbose)
{
- fprintf(fplog, "%s allocating memory to store data for %d slabs (rotation group %d).\n",
- RotStr, nslabs, erg->groupIndex);
+ fprintf(fplog,
+ "%s allocating memory to store data for %d slabs (rotation group %d).\n",
+ RotStr.c_str(),
+ nslabs,
+ erg->groupIndex);
}
snew(erg->slab_center, nslabs);
snew(erg->slab_center_ref, nslabs);
}
-static void init_rot_group(FILE* fplog,
- const t_commrec* cr,
- gmx_enfrotgrp* erg,
- rvec* x,
- gmx_mtop_t* mtop,
- gmx_bool bVerbose,
- FILE* out_slabs,
- const matrix box,
- t_inputrec* ir,
- gmx_bool bOutputCenters)
+static void init_rot_group(FILE* fplog,
+ const t_commrec* cr,
+ gmx_enfrotgrp* erg,
+ rvec* x,
+ const gmx_mtop_t& mtop,
+ gmx_bool bVerbose,
+ FILE* out_slabs,
+ const matrix box,
+ t_inputrec* ir,
+ gmx_bool bOutputCenters)
{
rvec coord, xref, *xdum;
gmx_bool bFlex, bColl;
snew(erg->xc_eshifts, erg->rotg->nat);
snew(erg->xc_old, erg->rotg->nat);
- if (erg->rotg->eFittype == erotgFitNORM)
+ if (erg->rotg->eFittype == RotationGroupFitting::Norm)
{
snew(erg->xc_ref_length, erg->rotg->nat); /* in case fit type NORM is chosen */
snew(erg->xc_norm, erg->rotg->nat);
/* Make space for the calculation of the potential at other angles (used
* for fitting only) */
- if (erotgFitPOT == erg->rotg->eFittype)
+ if (RotationGroupFitting::Pot == erg->rotg->eFittype)
{
snew(erg->PotAngleFit, 1);
snew(erg->PotAngleFit->degangle, erg->rotg->PotAngle_nstep);
erg->invmass = 1.0 / totalmass;
/* Set xc_ref_center for any rotation potential */
- if ((erg->rotg->eType == erotgISO) || (erg->rotg->eType == erotgPM)
- || (erg->rotg->eType == erotgRM) || (erg->rotg->eType == erotgRM2))
+ if ((erg->rotg->eType == EnforcedRotationGroupType::Iso)
+ || (erg->rotg->eType == EnforcedRotationGroupType::Pm)
+ || (erg->rotg->eType == EnforcedRotationGroupType::Rm)
+ || (erg->rotg->eType == EnforcedRotationGroupType::Rm2))
{
/* Set the pivot point for the fixed, stationary-axis potentials. This
* won't change during the simulation */
#endif
}
- if ((erg->rotg->eType != erotgFLEX) && (erg->rotg->eType != erotgFLEX2))
+ if ((erg->rotg->eType != EnforcedRotationGroupType::Flex)
+ && (erg->rotg->eType != EnforcedRotationGroupType::Flex2))
{
/* Put the reference positions into origin: */
for (int i = 0; i < erg->rotg->nat; i++)
get_slab_centers(erg, erg->rotg->x_ref, erg->mc, -1, out_slabs, bOutputCenters, TRUE);
/* Length of each x_rotref vector from center (needed if fit routine NORM is chosen): */
- if (erg->rotg->eFittype == erotgFitNORM)
+ if (erg->rotg->eFittype == RotationGroupFitting::Norm)
{
for (int i = 0; i < erg->rotg->nat; i++)
{
}
/* Add space for the potentials at different angles: */
- if (erotgFitPOT == erg->rotg->eFittype)
+ if (RotationGroupFitting::Pot == erg->rotg->eFittype)
{
count_group += erg->rotg->PotAngle_nstep;
}
const t_commrec* cr,
gmx::LocalAtomSetManager* atomSets,
const t_state* globalState,
- gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const gmx_output_env_t* oenv,
const gmx::MdrunOptions& mdrunOptions,
const gmx::StartingBehavior startingBehavior)
if (MASTER(cr) && mdrunOptions.verbose)
{
- fprintf(stdout, "%s Initializing ...\n", RotStr);
+ fprintf(stdout, "%s Initializing ...\n", RotStr.c_str());
}
auto enforcedRotation = std::make_unique<gmx::EnforcedRotation>();
{
if (nullptr != fplog)
{
- fprintf(fplog, "%s rerun - will write rotation output every available step.\n", RotStr);
+ fprintf(fplog, "%s rerun - will write rotation output every available step.\n", RotStr.c_str());
}
er->nstrout = 1;
er->nstsout = 1;
{
/* Remove pbc, make molecule whole.
* When ir->bContinuation=TRUE this has already been done, but ok. */
- snew(x_pbc, mtop->natoms);
- copy_rvecn(globalState->x.rvec_array(), x_pbc, 0, mtop->natoms);
- do_pbc_first_mtop(nullptr, ir->pbcType, globalState->box, mtop, x_pbc);
+ snew(x_pbc, mtop.natoms);
+ copy_rvecn(globalState->x.rvec_array(), x_pbc, 0, mtop.natoms);
+ do_pbc_first_mtop(nullptr, ir->pbcType, globalState->box, &mtop, x_pbc);
/* All molecules will be whole now, but not necessarily in the home box.
* Additionally, if a rotation group consists of more than one molecule
* (e.g. two strands of DNA), each one of them can end up in a different
if (nullptr != fplog)
{
- fprintf(fplog, "%s group %d type '%s'\n", RotStr, groupIndex, erotg_names[erg->rotg->eType]);
+ fprintf(fplog,
+ "%s group %d type '%s'\n",
+ RotStr.c_str(),
+ groupIndex,
+ enumValueToString(erg->rotg->eType));
}
if (erg->rotg->nat > 0)
{
nat_max = std::max(nat_max, erg->rotg->nat);
- init_rot_group(fplog, cr, erg, x_pbc, mtop, mdrunOptions.verbose, er->out_slabs,
- MASTER(cr) ? globalState->box : nullptr, ir,
+ init_rot_group(fplog,
+ cr,
+ erg,
+ x_pbc,
+ mtop,
+ mdrunOptions.verbose,
+ er->out_slabs,
+ MASTER(cr) ? globalState->box : nullptr,
+ ir,
!er->restartWithAppending); /* Do not output the reference centers
* again if we are appending */
}
/* Select the PBC representation for each local x position and store that
* for later usage. We assume the right PBC image of an x is the one nearest to
* its rotated reference */
-static void choose_pbc_image(rvec x[], gmx_enfrotgrp* erg, const matrix box, int npbcdim)
+static void choose_pbc_image(gmx::ArrayRef<const gmx::RVec> coords, gmx_enfrotgrp* erg, const matrix box, int npbcdim)
{
const auto& localRotationGroupIndex = erg->atomSet->localIndex();
for (gmx::index i = 0; i < localRotationGroupIndex.ssize(); i++)
copy_rvec(erg->xr_loc[i], xref);
rvec_inc(xref, erg->xc_ref_center);
- copy_correct_pbc_image(x[ii], erg->x_loc_pbc[i], xref, box, npbcdim);
+ copy_correct_pbc_image(coords[ii], erg->x_loc_pbc[i], xref, box, npbcdim);
}
}
-void do_rotation(const t_commrec* cr, gmx_enfrot* er, const matrix box, rvec x[], real t, int64_t step, gmx_bool bNS)
+void do_rotation(const t_commrec* cr,
+ gmx_enfrot* er,
+ const matrix box,
+ gmx::ArrayRef<const gmx::RVec> coords,
+ real t,
+ int64_t step,
+ gmx_bool bNS)
{
gmx_bool outstep_slab, outstep_rot;
gmx_bool bColl;
/* Transfer the rotation group's positions such that every node has
* all of them. Every node contributes its local positions x and stores
* it in the collective erg->xc array. */
- communicate_group_positions(cr, erg->xc, erg->xc_shifts, erg->xc_eshifts, bNS, x,
- rotg->nat, erg->atomSet->numAtomsLocal(),
+ communicate_group_positions(cr,
+ erg->xc,
+ erg->xc_shifts,
+ erg->xc_eshifts,
+ bNS,
+ as_rvec_array(coords.data()),
+ rotg->nat,
+ erg->atomSet->numAtomsLocal(),
erg->atomSet->localIndex().data(),
- erg->atomSet->collectiveIndex().data(), erg->xc_old, box);
+ erg->atomSet->collectiveIndex().data(),
+ erg->xc_old,
+ box);
}
else
{
/* Choose the nearest PBC images of the group atoms with respect
* to the rotated reference positions */
- choose_pbc_image(x, erg, box, 3);
+ choose_pbc_image(coords, erg, box, 3);
/* Get the center of the rotation group */
- if ((rotg->eType == erotgISOPF) || (rotg->eType == erotgPMPF))
+ if ((rotg->eType == EnforcedRotationGroupType::Isopf)
+ || (rotg->eType == EnforcedRotationGroupType::Pmpf))
{
- get_center_comm(cr, erg->x_loc_pbc, erg->m_loc, erg->atomSet->numAtomsLocal(),
- rotg->nat, erg->xc_center);
+ get_center_comm(
+ cr, erg->x_loc_pbc, erg->m_loc, erg->atomSet->numAtomsLocal(), rotg->nat, erg->xc_center);
}
}
}
/* Calculate angles and rotation matrices for potential fitting: */
- if ((outstep_rot || outstep_slab) && (erotgFitPOT == rotg->eFittype))
+ if ((outstep_rot || outstep_slab) && (RotationGroupFitting::Pot == rotg->eFittype))
{
fit = erg->PotAngleFit;
for (int i = 0; i < rotg->PotAngle_nstep; i++)
switch (rotg->eType)
{
- case erotgISO:
- case erotgISOPF:
- case erotgPM:
- case erotgPMPF: do_fixed(erg, outstep_rot, outstep_slab); break;
- case erotgRM: do_radial_motion(erg, outstep_rot, outstep_slab); break;
- case erotgRMPF: do_radial_motion_pf(erg, x, box, outstep_rot, outstep_slab); break;
- case erotgRM2:
- case erotgRM2PF: do_radial_motion2(erg, x, box, outstep_rot, outstep_slab); break;
- case erotgFLEXT:
- case erotgFLEX2T:
+ case EnforcedRotationGroupType::Iso:
+ case EnforcedRotationGroupType::Isopf:
+ case EnforcedRotationGroupType::Pm:
+ case EnforcedRotationGroupType::Pmpf: do_fixed(erg, outstep_rot, outstep_slab); break;
+ case EnforcedRotationGroupType::Rm:
+ do_radial_motion(erg, outstep_rot, outstep_slab);
+ break;
+ case EnforcedRotationGroupType::Rmpf:
+ do_radial_motion_pf(erg, coords, box, outstep_rot, outstep_slab);
+ break;
+ case EnforcedRotationGroupType::Rm2:
+ case EnforcedRotationGroupType::Rm2pf:
+ do_radial_motion2(erg, coords, box, outstep_rot, outstep_slab);
+ break;
+ case EnforcedRotationGroupType::Flext:
+ case EnforcedRotationGroupType::Flex2t:
/* Subtract the center of the rotation group from the collective positions array
* Also store the center in erg->xc_center since it needs to be subtracted
* in the low level routines from the local coordinates as well */
get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
svmul(-1.0, erg->xc_center, transvec);
translate_x(erg->xc, rotg->nat, transvec);
- do_flexible(MASTER(cr), er, erg, x, box, t, outstep_rot, outstep_slab);
+ do_flexible(MASTER(cr), er, erg, coords, box, t, outstep_rot, outstep_slab);
break;
- case erotgFLEX:
- case erotgFLEX2:
+ case EnforcedRotationGroupType::Flex:
+ case EnforcedRotationGroupType::Flex2:
/* Do NOT subtract the center of mass in the low level routines! */
clear_rvec(erg->xc_center);
- do_flexible(MASTER(cr), er, erg, x, box, t, outstep_rot, outstep_slab);
+ do_flexible(MASTER(cr), er, erg, coords, box, t, outstep_rot, outstep_slab);
break;
default: gmx_fatal(FARGS, "No such rotation potential.");
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <memory>
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/classhelpers.h"
struct gmx_domdec_t;
struct gmx_enfrot;
enum class StartingBehavior;
class LocalAtomSetManager;
struct MdrunOptions;
+template<typename>
+class ArrayRef;
class EnforcedRotation
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
const t_commrec* cr,
gmx::LocalAtomSetManager* atomSets,
const t_state* globalState,
- gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const gmx_output_env_t* oenv,
const gmx::MdrunOptions& mdrunOptions,
gmx::StartingBehavior startingBehavior);
* \param cr Pointer to MPI communication data.
* \param er Pointer to the enforced rotation working data.
* \param box Simulation box, needed to make group whole.
- * \param x The positions of all the local particles.
+ * \param coords The positions of all the local particles.
* \param t Time.
* \param step The time step.
* \param bNS After domain decomposition / neighbor searching several
* local arrays have to be updated (masses, shifts)
*/
-void do_rotation(const t_commrec* cr, gmx_enfrot* er, const matrix box, rvec x[], real t, int64_t step, gmx_bool bNS);
+void do_rotation(const t_commrec* cr,
+ gmx_enfrot* er,
+ const matrix box,
+ gmx::ArrayRef<const gmx::RVec> coords,
+ real t,
+ int64_t step,
+ bool bNS);
/*! \brief Add the enforced rotation forces to the official force array.
* the potential, the angle of the group(s), and torques).
*
* \param er Pointer to the enforced rotation working data.
- * \param f The local forces to which the rotational forces have
+ * \param force The local forces to which the rotational forces have
* to be added.
* \param cr Pointer to MPI communication data.
* \param step The time step, used for output.
* \param t Time, used for output.
* \returns The potential energy of the rotation potentials.
*/
-real add_rot_forces(gmx_enfrot* er, rvec f[], const t_commrec* cr, int64_t step, real t);
+real add_rot_forces(gmx_enfrot* er, gmx::ArrayRef<gmx::RVec> force, const t_commrec* cr, int64_t step, real t);
#endif
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/confio.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
+#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "pull_internal.h"
+using gmx::ArrayRef;
+using gmx::RVec;
+
#if GMX_MPI
// Helper function to deduce MPI datatype from the type of data
{
/* Separate branch because gmx_sum uses cr->mpi_comm_mygroup */
#if GMX_MPI
-# if MPI_IN_PLACE_EXISTS
MPI_Allreduce(MPI_IN_PLACE, data, n, mpiDatatype(data), MPI_SUM, comm->mpi_comm_com);
-# else
- std::vector<T> buf(n);
-
- MPI_Allreduce(data, buf.data(), n, mpiDatatype(data), MPI_SUM, comm->mpi_comm_com);
-
- /* Copy the result from the buffer to the input/output data */
- for (int i = 0; i < n; i++)
- {
- data[i] = buf[i];
- }
-# endif
#else
gmx_incons("comm->bParticipateAll=FALSE without GMX_MPI");
#endif
/* Copies the coordinates of the PBC atom of pgrp to x_pbc.
* When those coordinates are not available on this rank, clears x_pbc.
*/
-static void setPbcAtomCoords(const pull_group_work_t& pgrp, const rvec* x, rvec x_pbc)
+static void setPbcAtomCoords(const pull_group_work_t& pgrp, ArrayRef<const RVec> x, rvec x_pbc)
{
if (pgrp.pbcAtomSet != nullptr)
{
}
}
-static void pull_set_pbcatoms(const t_commrec* cr, struct pull_t* pull, const rvec* x, gmx::ArrayRef<gmx::RVec> x_pbc)
+static void pull_set_pbcatoms(const t_commrec* cr, struct pull_t* pull, ArrayRef<const RVec> x, ArrayRef<RVec> x_pbc)
{
int numPbcAtoms = 0;
for (size_t g = 0; g < pull->group.size(); g++)
}
}
-static void
-make_cyl_refgrps(const t_commrec* cr, pull_t* pull, const real* masses, t_pbc* pbc, double t, const rvec* x)
+static void make_cyl_refgrps(const t_commrec* cr,
+ pull_t* pull,
+ ArrayRef<const real> masses,
+ t_pbc* pbc,
+ double t,
+ ArrayRef<const RVec> x)
{
pull_comm_t* comm = &pull->comm;
double inv_cyl_r2 = 1.0 / gmx::square(pull->params.cylinder_r);
/* loop over all groups to make a reference group for each*/
- for (size_t c = 0; c < pull->coord.size(); c++)
+ int bufferOffset = 0;
+ for (pull_coord_work_t& pcrd : pull->coord)
{
- pull_coord_work_t* pcrd;
- double sum_a, wmass, wwmass;
- dvec radf_fac0, radf_fac1;
-
- pcrd = &pull->coord[c];
+ double sum_a, wmass, wwmass;
+ dvec radf_fac0, radf_fac1;
sum_a = 0;
wmass = 0;
clear_dvec(radf_fac0);
clear_dvec(radf_fac1);
- if (pcrd->params.eGeom == epullgCYL)
+ if (pcrd.params.eGeom == PullGroupGeometry::Cylinder)
{
/* pref will be the same group for all pull coordinates */
- const pull_group_work_t& pref = pull->group[pcrd->params.group[0]];
- const pull_group_work_t& pgrp = pull->group[pcrd->params.group[1]];
- pull_group_work_t& pdyna = pull->dyna[c];
+ const pull_group_work_t& pref = pull->group[pcrd.params.group[0]];
+ const pull_group_work_t& pgrp = pull->group[pcrd.params.group[1]];
+ pull_group_work_t& pdyna = *pcrd.dynamicGroup0;
rvec direction;
- copy_dvec_to_rvec(pcrd->spatialData.vec, direction);
+ copy_dvec_to_rvec(pcrd.spatialData.vec, direction);
/* Since we have not calculated the COM of the cylinder group yet,
* we calculate distances with respect to location of the pull
* here we already have the COM of the pull group. This resolves
* any PBC issues and we don't need to use a PBC-atom here.
*/
- if (pcrd->params.rate != 0)
+ if (pcrd.params.rate != 0)
{
/* With rate=0, value_ref is set initially */
- pcrd->value_ref = pcrd->params.init + pcrd->params.rate * t;
+ pcrd.value_ref = pcrd.params.init + pcrd.params.rate * t;
}
rvec reference;
for (int m = 0; m < DIM; m++)
{
- reference[m] = pgrp.x[m] - pcrd->spatialData.vec[m] * pcrd->value_ref;
+ reference[m] = pgrp.x[m] - pcrd.spatialData.vec[m] * pcrd.value_ref;
}
auto localAtomIndices = pref.atomSet.localIndex();
}
}
- auto buffer = gmx::arrayRefFromArray(
- comm->cylinderBuffer.data() + c * c_cylinderBufferStride, c_cylinderBufferStride);
+ auto buffer = gmx::arrayRefFromArray(comm->cylinderBuffer.data() + bufferOffset,
+ c_cylinderBufferStride);
+ bufferOffset += c_cylinderBufferStride;
buffer[0] = wmass;
buffer[1] = wwmass;
pullAllReduce(cr, comm, pull->coord.size() * c_cylinderBufferStride, comm->cylinderBuffer.data());
}
- for (size_t c = 0; c < pull->coord.size(); c++)
+ bufferOffset = 0;
+ for (pull_coord_work_t& pcrd : pull->coord)
{
- pull_coord_work_t* pcrd;
-
- pcrd = &pull->coord[c];
-
- if (pcrd->params.eGeom == epullgCYL)
+ if (pcrd.params.eGeom == PullGroupGeometry::Cylinder)
{
- pull_group_work_t* pdyna = &pull->dyna[c];
- pull_group_work_t* pgrp = &pull->group[pcrd->params.group[1]];
- PullCoordSpatialData& spatialData = pcrd->spatialData;
-
- auto buffer = gmx::constArrayRefFromArray(
- comm->cylinderBuffer.data() + c * c_cylinderBufferStride, c_cylinderBufferStride);
- double wmass = buffer[0];
- double wwmass = buffer[1];
- pdyna->mwscale = 1.0 / wmass;
+ pull_group_work_t& dynamicGroup0 = *pcrd.dynamicGroup0;
+ pull_group_work_t& group1 = pull->group[pcrd.params.group[1]];
+ PullCoordSpatialData& spatialData = pcrd.spatialData;
+
+ auto buffer = gmx::constArrayRefFromArray(comm->cylinderBuffer.data() + bufferOffset,
+ c_cylinderBufferStride);
+ bufferOffset += c_cylinderBufferStride;
+ double wmass = buffer[0];
+ double wwmass = buffer[1];
+ dynamicGroup0.mwscale = 1.0 / wmass;
/* Cylinder pulling can't be used with constraints, but we set
* wscale and invtm anyhow, in case someone would like to use them.
*/
- pdyna->wscale = wmass / wwmass;
- pdyna->invtm = wwmass / (wmass * wmass);
+ dynamicGroup0.wscale = wmass / wwmass;
+ dynamicGroup0.invtm = wwmass / (wmass * wmass);
/* We store the deviation of the COM from the reference location
* used above, since we need it when we apply the radial forces
spatialData.cyl_dev = 0;
for (int m = 0; m < DIM; m++)
{
- double reference = pgrp->x[m] - spatialData.vec[m] * pcrd->value_ref;
- double dist = -spatialData.vec[m] * buffer[2] * pdyna->mwscale;
- pdyna->x[m] = reference - dist;
+ double reference = group1.x[m] - spatialData.vec[m] * pcrd.value_ref;
+ double dist = -spatialData.vec[m] * buffer[2] * dynamicGroup0.mwscale;
+ dynamicGroup0.x[m] = reference - dist;
spatialData.cyl_dev += dist;
}
/* Now we know the exact COM of the cylinder reference group,
if (debug)
{
- fprintf(debug, "Pull cylinder group %zu:%8.3f%8.3f%8.3f m:%8.3f\n", c, pdyna->x[0],
- pdyna->x[1], pdyna->x[2], 1.0 / pdyna->invtm);
- fprintf(debug, "ffrad %8.3f %8.3f %8.3f\n", spatialData.ffrad[XX],
- spatialData.ffrad[YY], spatialData.ffrad[ZZ]);
+ fprintf(debug,
+ "Pull cylinder group %d:%8.3f%8.3f%8.3f m:%8.3f\n",
+ pcrd.params.coordIndex,
+ dynamicGroup0.x[0],
+ dynamicGroup0.x[1],
+ dynamicGroup0.x[2],
+ 1.0 / dynamicGroup0.invtm);
+ fprintf(debug,
+ "ffrad %8.3f %8.3f %8.3f\n",
+ spatialData.ffrad[XX],
+ spatialData.ffrad[YY],
+ spatialData.ffrad[ZZ]);
}
}
}
static void sum_com_part(const pull_group_work_t* pgrp,
int ind_start,
int ind_end,
- const rvec* x,
- const rvec* xp,
- const real* mass,
+ ArrayRef<const RVec> x,
+ ArrayRef<const RVec> xp,
+ ArrayRef<const real> mass,
const t_pbc* pbc,
const rvec x_pbc,
ComSums* sum_com)
{
sum_wmx[d] += wm * x[ii][d];
}
- if (xp)
+ if (!xp.empty())
{
for (int d = 0; d < DIM; d++)
{
{
sum_wmx[d] += wm * dx[d];
}
- if (xp)
+ if (!xp.empty())
{
/* For xp add the difference between xp and x to dx,
* such that we use the same periodic image,
sum_com->sum_wm = sum_wm;
sum_com->sum_wwm = sum_wwm;
copy_dvec(sum_wmx, sum_com->sum_wmx);
- if (xp)
+ if (!xp.empty())
{
copy_dvec(sum_wmxp, sum_com->sum_wmxp);
}
int ind_end,
int cosdim,
real twopi_box,
- const rvec* x,
- const rvec* xp,
- const real* mass,
+ ArrayRef<const RVec> x,
+ ArrayRef<const RVec> xp,
+ ArrayRef<const real> mass,
ComSums* sum_com)
{
/* Cosine weighting geometry */
sum_csm += static_cast<double>(cw * sw * m);
sum_ssm += static_cast<double>(sw * sw * m);
- if (xp != nullptr)
+ if (!xp.empty())
{
real cw = std::cos(xp[ii][cosdim] * twopi_box);
real sw = std::sin(xp[ii][cosdim] * twopi_box);
}
/* calculates center of mass of selection index from all coordinates x */
-// Compiler segfault with 2019_update_5 and 2020_initial
-#if defined(__INTEL_COMPILER) \
- && ((__INTEL_COMPILER == 1900 && __INTEL_COMPILER_UPDATE >= 5) || __INTEL_COMPILER >= 1910)
-# pragma intel optimization_level 2
-#endif
-void pull_calc_coms(const t_commrec* cr, pull_t* pull, const real* masses, t_pbc* pbc, double t, const rvec x[], rvec* xp)
+void pull_calc_coms(const t_commrec* cr,
+ pull_t* pull,
+ ArrayRef<const real> masses,
+ t_pbc* pbc,
+ double t,
+ ArrayRef<const RVec> x,
+ ArrayRef<RVec> xp)
{
real twopi_box = 0;
pull_comm_t* comm;
if (pgrp->params.ind.size() == 1 && pgrp->atomSet.numAtomsLocal() == 1
&& masses[pgrp->atomSet.localIndex()[0]] == 0)
{
- GMX_ASSERT(xp == nullptr,
+ GMX_ASSERT(xp.empty(),
"We should not have groups with zero mass with constraints, i.e. "
- "xp!=NULL");
+ "xp not empty");
/* Copy the single atom coordinate */
for (int d = 0; d < DIM; d++)
}
else if (pgrp->atomSet.numAtomsLocal() <= c_pullMaxNumLocalAtomsSingleThreaded)
{
- sum_com_part(pgrp, 0, pgrp->atomSet.numAtomsLocal(), x, xp, masses, pbc, x_pbc,
- &comSumsTotal);
+ sum_com_part(pgrp, 0, pgrp->atomSet.numAtomsLocal(), x, xp, masses, pbc, x_pbc, &comSumsTotal);
}
else
{
-#pragma omp parallel for num_threads(pull->nthreads) schedule(static)
- for (int t = 0; t < pull->nthreads; t++)
+ const int numThreads = pgrp->numThreads();
+#pragma omp parallel for num_threads(numThreads) schedule(static)
+ for (int t = 0; t < numThreads; t++)
{
- int ind_start = (pgrp->atomSet.numAtomsLocal() * (t + 0)) / pull->nthreads;
- int ind_end = (pgrp->atomSet.numAtomsLocal() * (t + 1)) / pull->nthreads;
- sum_com_part(pgrp, ind_start, ind_end, x, xp, masses, pbc, x_pbc,
- &pull->comSums[t]);
+ int ind_start = (pgrp->atomSet.numAtomsLocal() * (t + 0)) / numThreads;
+ int ind_end = (pgrp->atomSet.numAtomsLocal() * (t + 1)) / numThreads;
+ sum_com_part(
+ pgrp, ind_start, ind_end, x, xp, masses, pbc, x_pbc, &pull->comSums[t]);
}
/* Reduce the thread contributions to sum_com[0] */
- for (int t = 1; t < pull->nthreads; t++)
+ for (int t = 1; t < numThreads; t++)
{
comSumsTotal.sum_wm += pull->comSums[t].sum_wm;
comSumsTotal.sum_wwm += pull->comSums[t].sum_wwm;
* This uses a slab of the system, thus we always have many
* atoms in the pull groups. Therefore, always use threads.
*/
-#pragma omp parallel for num_threads(pull->nthreads) schedule(static)
- for (int t = 0; t < pull->nthreads; t++)
+ const int numThreads = pgrp->numThreads();
+#pragma omp parallel for num_threads(numThreads) schedule(static)
+ for (int t = 0; t < numThreads; t++)
{
- int ind_start = (pgrp->atomSet.numAtomsLocal() * (t + 0)) / pull->nthreads;
- int ind_end = (pgrp->atomSet.numAtomsLocal() * (t + 1)) / pull->nthreads;
- sum_com_part_cosweight(pgrp, ind_start, ind_end, pull->cosdim, twopi_box, x, xp,
- masses, &pull->comSums[t]);
+ int ind_start = (pgrp->atomSet.numAtomsLocal() * (t + 0)) / numThreads;
+ int ind_end = (pgrp->atomSet.numAtomsLocal() * (t + 1)) / numThreads;
+ sum_com_part_cosweight(
+ pgrp, ind_start, ind_end, pull->cosdim, twopi_box, x, xp, masses, &pull->comSums[t]);
}
/* Reduce the thread contributions to comSums[0] */
ComSums& comSumsTotal = pull->comSums[0];
- for (int t = 1; t < pull->nthreads; t++)
+ for (int t = 1; t < numThreads; t++)
{
comSumsTotal.sum_cm += pull->comSums[t].sum_cm;
comSumsTotal.sum_sm += pull->comSums[t].sum_sm;
}
}
- pullAllReduce(cr, comm, pull->group.size() * c_comBufferStride * DIM,
+ pullAllReduce(cr,
+ comm,
+ pull->group.size() * c_comBufferStride * DIM,
static_cast<double*>(comm->comBuffer[0]));
for (size_t g = 0; g < pull->group.size(); g++)
for (m = 0; m < DIM; m++)
{
pgrp->x[m] = comBuffer[0][m] * pgrp->mwscale;
- if (xp)
+ if (!xp.empty())
{
pgrp->xp[m] = comBuffer[1][m] * pgrp->mwscale;
}
if (pgrp->epgrppbc == epgrppbcREFAT || pgrp->epgrppbc == epgrppbcPREVSTEPCOM)
{
pgrp->x[m] += comm->pbcAtomBuffer[g][m];
- if (xp)
+ if (!xp.empty())
{
pgrp->xp[m] += comm->pbcAtomBuffer[g][m];
}
pgrp->localWeights[i] = csw * std::cos(twopi_box * x[ii][pull->cosdim])
+ snw * std::sin(twopi_box * x[ii][pull->cosdim]);
}
- if (xp)
+ if (!xp.empty())
{
csw = comBuffer[2][0];
snw = comBuffer[2][1];
/* Returns whether the pull group obeys the PBC restrictions */
static bool pullGroupObeysPbcRestrictions(const pull_group_work_t& group,
const BoolVec& dimUsed,
- const rvec* x,
+ ArrayRef<const RVec> x,
const t_pbc& pbc,
- const gmx::RVec& x_pbc,
+ const RVec& x_pbc,
const real pbcMargin)
{
/* Determine which dimensions are relevant for PBC */
return true;
}
-int pullCheckPbcWithinGroups(const pull_t& pull, const rvec* x, const t_pbc& pbc, real pbcMargin)
+int pullCheckPbcWithinGroups(const pull_t& pull, ArrayRef<const RVec> x, const t_pbc& pbc, real pbcMargin)
{
if (pbc.pbcType == PbcType::No)
{
/* Determine what dimensions are used for each group by pull coordinates */
std::vector<BoolVec> dimUsed(pull.group.size(), { false, false, false });
- for (size_t c = 0; c < pull.coord.size(); c++)
+ for (const pull_coord_work_t& pcrd : pull.coord)
{
- const t_pull_coord& coordParams = pull.coord[c].params;
+ const t_pull_coord& coordParams = pcrd.params;
for (int groupIndex = 0; groupIndex < coordParams.ngroup; groupIndex++)
{
for (int d = 0; d < DIM; d++)
{
- if (coordParams.dim[d] && !(coordParams.eGeom == epullgCYL && groupIndex == 0))
+ if (coordParams.dim[d]
+ && !(coordParams.eGeom == PullGroupGeometry::Cylinder && groupIndex == 0))
{
dimUsed[coordParams.group[groupIndex]][d] = true;
}
return -1;
}
-bool pullCheckPbcWithinGroup(const pull_t& pull,
- gmx::ArrayRef<const gmx::RVec> x,
- const t_pbc& pbc,
- int groupNr,
- real pbcMargin)
+bool pullCheckPbcWithinGroup(const pull_t& pull, ArrayRef<const RVec> x, const t_pbc& pbc, int groupNr, real pbcMargin)
{
if (pbc.pbcType == PbcType::No)
{
/* Determine what dimensions are used for each group by pull coordinates */
BoolVec dimUsed = { false, false, false };
- for (size_t c = 0; c < pull.coord.size(); c++)
+ for (const pull_coord_work_t& pcrd : pull.coord)
{
- const t_pull_coord& coordParams = pull.coord[c].params;
+ const t_pull_coord& coordParams = pcrd.params;
for (int groupIndex = 0; groupIndex < coordParams.ngroup; groupIndex++)
{
if (coordParams.group[groupIndex] == groupNr)
{
for (int d = 0; d < DIM; d++)
{
- if (coordParams.dim[d] && !(coordParams.eGeom == epullgCYL && groupIndex == 0))
+ if (coordParams.dim[d]
+ && !(coordParams.eGeom == PullGroupGeometry::Cylinder && groupIndex == 0))
{
dimUsed[d] = true;
}
}
}
- return (pullGroupObeysPbcRestrictions(group, dimUsed, as_rvec_array(x.data()), pbc,
- pull.comm.pbcAtomBuffer[groupNr], pbcMargin));
+ return (pullGroupObeysPbcRestrictions(
+ group, dimUsed, x, pbc, pull.comm.pbcAtomBuffer[groupNr], pbcMargin));
}
void setPrevStepPullComFromState(struct pull_t* pull, const t_state* state)
}
}
-void initPullComFromPrevStep(const t_commrec* cr, pull_t* pull, const real* masses, t_pbc* pbc, const rvec x[])
+void initPullComFromPrevStep(const t_commrec* cr,
+ pull_t* pull,
+ ArrayRef<const real> masses,
+ t_pbc* pbc,
+ ArrayRef<const RVec> x)
{
pull_comm_t* comm = &pull->comm;
size_t ngroup = pull->group.size();
"Groups with no atoms, or only one atom, should not "
"use the COM from the previous step as reference.");
- rvec x_pbc = { 0, 0, 0 };
+ RVec x_pbc = { 0, 0, 0 };
copy_rvec(comm->pbcAtomBuffer[g], x_pbc);
if (debug)
if (pgrp->atomSet.numAtomsLocal() <= c_pullMaxNumLocalAtomsSingleThreaded)
{
- sum_com_part(pgrp, 0, pgrp->atomSet.numAtomsLocal(), x, nullptr, masses, pbc, x_pbc,
- &comSumsTotal);
+ sum_com_part(pgrp, 0, pgrp->atomSet.numAtomsLocal(), x, {}, masses, pbc, x_pbc, &comSumsTotal);
}
else
{
-#pragma omp parallel for num_threads(pull->nthreads) schedule(static)
- for (int t = 0; t < pull->nthreads; t++)
+ const int numThreads = pgrp->numThreads();
+#pragma omp parallel for num_threads(numThreads) schedule(static)
+ for (int t = 0; t < numThreads; t++)
{
- int ind_start = (pgrp->atomSet.numAtomsLocal() * (t + 0)) / pull->nthreads;
- int ind_end = (pgrp->atomSet.numAtomsLocal() * (t + 1)) / pull->nthreads;
- sum_com_part(pgrp, ind_start, ind_end, x, nullptr, masses, pbc, x_pbc,
- &pull->comSums[t]);
+ int ind_start = (pgrp->atomSet.numAtomsLocal() * (t + 0)) / numThreads;
+ int ind_end = (pgrp->atomSet.numAtomsLocal() * (t + 1)) / numThreads;
+ sum_com_part(pgrp, ind_start, ind_end, x, {}, masses, pbc, x_pbc, &pull->comSums[t]);
}
/* Reduce the thread contributions to sum_com[0] */
- for (int t = 1; t < pull->nthreads; t++)
+ for (int t = 1; t < numThreads; t++)
{
comSumsTotal.sum_wm += pull->comSums[t].sum_wm;
comSumsTotal.sum_wwm += pull->comSums[t].sum_wwm;
}
if (debug)
{
- fprintf(debug, "Pull group %zu wmass %f invtm %f\n", g, 1.0 / pgrp->mwscale,
- pgrp->invtm);
+ fprintf(debug, "Pull group %zu wmass %f invtm %f\n", g, 1.0 / pgrp->mwscale, pgrp->invtm);
fprintf(debug, "Initialising prev step COM of pull group %zu to", g);
for (int m = 0; m < DIM; m++)
{
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
// Distance pulling in all 3 dimensions
t_pull_coord params;
- params.eGeom = epullgDIST;
- params.dim[XX] = 1;
- params.dim[YY] = 1;
- params.dim[ZZ] = 1;
+ params.eGeom = PullGroupGeometry::Distance;
+ params.dim[XX] = 1;
+ params.dim[YY] = 1;
+ params.dim[ZZ] = 1;
+ params.coordIndex = 0;
pull_coord_work_t pcrd(params);
clear_dvec(pcrd.spatialData.vec);
{
minBoxSize2 = std::min(minBoxSize2, norm2(box[d]));
}
- EXPECT_REAL_EQ_TOL(0.25 * minBoxSize2, max_pull_distance2(&pcrd, &pbc),
- defaultRealTolerance());
+ EXPECT_REAL_EQ_TOL(
+ 0.25 * minBoxSize2, max_pull_distance2(&pcrd, &pbc), defaultRealTolerance());
}
{
// Distance pulling along Z
t_pull_coord params;
- params.eGeom = epullgDIST;
- params.dim[XX] = 0;
- params.dim[YY] = 0;
- params.dim[ZZ] = 1;
+ params.eGeom = PullGroupGeometry::Distance;
+ params.dim[XX] = 0;
+ params.dim[YY] = 0;
+ params.dim[ZZ] = 1;
+ params.coordIndex = 0;
pull_coord_work_t pcrd(params);
clear_dvec(pcrd.spatialData.vec);
- EXPECT_REAL_EQ_TOL(0.25 * boxSizeZSquared, max_pull_distance2(&pcrd, &pbc),
- defaultRealTolerance());
+ EXPECT_REAL_EQ_TOL(
+ 0.25 * boxSizeZSquared, max_pull_distance2(&pcrd, &pbc), defaultRealTolerance());
}
{
// Directional pulling along Z
t_pull_coord params;
- params.eGeom = epullgDIR;
- params.dim[XX] = 1;
- params.dim[YY] = 1;
- params.dim[ZZ] = 1;
+ params.eGeom = PullGroupGeometry::Direction;
+ params.dim[XX] = 1;
+ params.dim[YY] = 1;
+ params.dim[ZZ] = 1;
+ params.coordIndex = 0;
pull_coord_work_t pcrd(params);
clear_dvec(pcrd.spatialData.vec);
pcrd.spatialData.vec[ZZ] = 1;
- EXPECT_REAL_EQ_TOL(0.25 * boxSizeZSquared, max_pull_distance2(&pcrd, &pbc),
- defaultRealTolerance());
+ EXPECT_REAL_EQ_TOL(
+ 0.25 * boxSizeZSquared, max_pull_distance2(&pcrd, &pbc), defaultRealTolerance());
}
{
// Directional pulling along X
t_pull_coord params;
- params.eGeom = epullgDIR;
- params.dim[XX] = 1;
- params.dim[YY] = 1;
- params.dim[ZZ] = 1;
+ params.eGeom = PullGroupGeometry::Direction;
+ params.dim[XX] = 1;
+ params.dim[YY] = 1;
+ params.dim[ZZ] = 1;
+ params.coordIndex = 0;
pull_coord_work_t pcrd(params);
clear_dvec(pcrd.spatialData.vec);
pcrd.spatialData.vec[XX] = 1;
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015,2016,2019, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,2019,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(random INTERFACE)
file(GLOB RANDOM_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${RANDOM_SOURCES} PARENT_SCOPE)
+# Source files have the following dependencies on library infrastructure.
+#target_link_libraries(random PRIVATE
+# common
+# legacy_modules
+#)
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(random PUBLIC
+target_include_directories(random INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(random PUBLIC
+target_link_libraries(random INTERFACE
+ legacy_api
+ )
+
+# TODO: when random is an OBJECT target
+#target_link_libraries(random PUBLIC legacy_api)
+#target_link_libraries(random PRIVATE common)
+
+# Module dependencies
+# random interfaces convey transitive dependence on these modules.
+#target_link_libraries(random PUBLIC
+target_link_libraries(random INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(random PRIVATE NOTHING)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(random PRIVATE legacy_modules)
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cmath>
#include <limits>
+#include <memory>
#include "gromacs/random/uniformrealdistribution.h"
#include "gromacs/utility/classhelpers.h"
bool operator!=(const param_type& x) const { return !operator==(x); }
};
-public:
/*! \brief Construct new distribution with given floating-point parameter.
*
* \param lambda lambda/decay parameter
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cmath>
#include <limits>
+#include <memory>
#include "gromacs/random/exponentialdistribution.h"
#include "gromacs/random/uniformrealdistribution.h"
/*! \brief Gamma distribution
*
* The C++ standard library does provide a gamma distribution, but when
- * using libstdc++-4.4.7 with at least gcc-4.6 or icc-14.0 the headers
+ * using libstdc++-4.4.7 with at least gcc-4.6 the headers
* produce errors. Even for newer compilers, libstdc++ and libc++ appear to
* use different algorithms to generate it, which means their values differ
* in contrast to the uniform and normal distributions where they are
bool operator!=(const param_type& x) const { return !operator==(x); }
};
-public:
/*! \brief Construct new distribution with given floating-point parameters.
*
* \param alpha First parameter of gamma distribution
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cmath>
#include <limits>
+#include <memory>
#include "gromacs/random/uniformrealdistribution.h"
#include "gromacs/utility/classhelpers.h"
bool operator!=(const param_type& x) const { return !operator==(x); }
};
-public:
/*! \brief Construct new distribution with given floating-point parameters.
*
* \param mean Mean of normal distribution
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <array>
#include <limits>
+#include <memory>
#include "gromacs/math/functions.h"
#include "gromacs/math/utilities.h"
return table;
}
-public:
/*! \brief Construct new normal distribution with specified mean & stdddev.
*
* \param mean Mean value of tabulated normal distribution
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* The 2x64 flavors of ThreeFry64 will use the first four values, while
* the 4x64 version uses all eight.
*/
-const std::vector<uint64_t> bitsOne{ { 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL,
- 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL } };
+const std::vector<uint64_t> bitsOne{
+ { 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL }
+};
/*! \brief Constant array of integers with bitpattern from Pi.
*
* The 2x64 flavors of ThreeFry64 will use the first four values, while
* the 4x64 version uses all eight.
*/
-const std::vector<uint64_t> bitsPi{ { 0x243f6a8885a308d3ULL, 0x13198a2e03707344ULL,
- 0xa4093822299f31d0ULL, 0x082efa98ec4e6c89ULL } };
+const std::vector<uint64_t> bitsPi{
+ { 0x243f6a8885a308d3ULL, 0x13198a2e03707344ULL, 0xa4093822299f31d0ULL, 0x082efa98ec4e6c89ULL }
+};
// Test the known ansers for the ThreeFry random function when the argument
// is (1) all zero, (2) all ones, (3) the bits of pi, for a bunch of different flavors of ThreeFry.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <array>
#include <limits>
+#include <memory>
#include "gromacs/math/functions.h"
#include "gromacs/random/seed.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_RANDOM_UNIFORMINTDISTRIBUTION_H
#include <limits>
+#include <memory>
#include "gromacs/math/functions.h"
#include "gromacs/utility/basedefinitions.h"
bool operator!=(const param_type& x) const { return !operator==(x); }
};
-public:
/*! \brief Construct new distribution with given integer parameters.
*
* \param a Lower end of range (inclusive)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <algorithm>
#include <limits>
+#include <memory>
#include <type_traits>
#include "gromacs/math/functions.h"
+
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/gmxassert.h"
bool operator!=(const param_type& x) const { return !operator==(x); }
};
-public:
/*! \brief Construct new distribution with given floating-point parameters.
*
* \param a Lower end of range (inclusive)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
+# Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(restraint INTERFACE)
+file(GLOB RESTRAINT_SOURCES *.cpp)
+set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${RESTRAINT_SOURCES} PARENT_SCOPE)
-gmx_add_libgromacs_sources(
- manager.cpp
- restraintmdmodule.cpp
- )
-# TODO this is a hacky way to expose things for the API and needs to be changed to something proper
-install(FILES restraintpotential.h DESTINATION include/gromacs/restraint)
+# Source files have the following dependencies on library infrastructure.
+#target_link_libraries(restraint PRIVATE
+# common
+# legacy_modules
+#)
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(restraint PUBLIC
+target_include_directories(restraint INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(restraint PUBLIC
+target_link_libraries(restraint INTERFACE
+ legacy_api
+ )
+
+# TODO: when restraint is an OBJECT target
+#target_link_libraries(restraint PUBLIC legacy_api)
+#target_link_libraries(restraint PRIVATE common)
+
+# Module dependencies
+# restraint interfaces convey transitive dependence on these modules.
+#target_link_libraries(restraint PUBLIC
+target_link_libraries(restraint INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(restraint PRIVATE NOTHING)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(restraint PRIVATE legacy_modules)
if (BUILD_TESTING)
add_subdirectory(tests)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
private:
//! Regulate initialization of the shared resource when (re)initialized.
+ // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static std::mutex initializationMutex_;
};
// Initialize static members
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
std::mutex RestraintManager::Impl::initializationMutex_{};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
GMX_ASSERT(restraint_, "Restraint must be initialized.");
- const auto& mdatoms = forceProviderInput.mdatoms_;
- GMX_ASSERT(mdatoms.homenr >= 0, "number of home atoms must be non-negative.");
+ const int homenr = forceProviderInput.homenr_;
+ GMX_ASSERT(homenr >= 0, "number of home atoms must be non-negative.");
const auto& box = forceProviderInput.box_;
GMX_ASSERT(check_box(PbcType::Unset, box) == nullptr, "Invalid box.");
const auto& cr = forceProviderInput.cr_;
const auto& t = forceProviderInput.t_;
// Cooperatively get Cartesian coordinates for center of mass of each site
- RVec r1 = sites_[0].centerOfMass(cr, static_cast<size_t>(mdatoms.homenr), x, t);
+ RVec r1 = sites_[0].centerOfMass(cr, static_cast<size_t>(homenr), x, t);
// r2 is to be constructed as
// r2 = (site[N] - site[N-1]) + (site_{N-1} - site_{N-2}) + ... + (site_2 - site_1) + site_1
// where the minimum image convention is applied to each path but not to the overall sum.
// a big molecule in a small box.
for (size_t i = 0; i < sites_.size() - 1; ++i)
{
- RVec a = sites_[i].centerOfMass(cr, static_cast<size_t>(mdatoms.homenr), x, t);
- RVec b = sites_[i + 1].centerOfMass(cr, static_cast<size_t>(mdatoms.homenr), x, t);
+ RVec a = sites_[i].centerOfMass(cr, static_cast<size_t>(homenr), x, t);
+ RVec b = sites_[i + 1].centerOfMass(cr, static_cast<size_t>(homenr), x, t);
// dr = minimum_image_vector(b - a)
pbc_dx(&pbc, b, a, dr);
r2[0] += dr[0];
const int site1 = static_cast<int>(sites_.front().index());
const int* aLocal = &site1;
// Set forces using index `site1` if no domain decomposition, otherwise set with local index if available.
- auto& force = forceProviderOutput->forceWithVirial_.force_;
+ const auto& force = forceProviderOutput->forceWithVirial_.force_;
if ((cr.dd == nullptr) || (aLocal = cr.dd->ga2la->findHome(site1)))
{
force[static_cast<size_t>(*aLocal)] += result.force;
return newModule;
}
-void RestraintMDModule::subscribeToSimulationSetupNotifications(MdModulesNotifier* /*notifier*/) {}
+void RestraintMDModule::subscribeToSimulationSetupNotifications(MDModulesNotifiers* /*notifiers*/)
+{
+}
-void RestraintMDModule::subscribeToPreProcessingNotifications(MdModulesNotifier* /*notifier*/) {}
+void RestraintMDModule::subscribeToPreProcessingNotifications(MDModulesNotifiers* /*notifiers*/) {}
// private constructor to implement static create() method.
RestraintMDModule::RestraintMDModule(std::unique_ptr<RestraintMDModuleImpl> restraint) :
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
// Forward declaration to allow opaque pointer to library internal class.
class RestraintMDModuleImpl;
-struct MdModulesNotifier;
+struct MDModulesNotifiers;
/*! \libinternal \ingroup module_restraint
* \brief MDModule wrapper for Restraint implementations.
void initForceProviders(ForceProviders* forceProviders) override;
//! Subscribe to simulation setup notifications
- void subscribeToSimulationSetupNotifications(MdModulesNotifier* notifier) override;
+ void subscribeToSimulationSetupNotifications(MDModulesNotifiers* notifiers) override;
//! Subscribe to pre processing notifications
- void subscribeToPreProcessingNotifications(MdModulesNotifier* notifier) override;
+ void subscribeToPreProcessingNotifications(MDModulesNotifiers* notifiers) override;
private:
/*!
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
if (DOMAINDECOMP(&cr)) // Domain decomposition
{
// Get global-to-local indexing structure
- auto crossRef = cr.dd->ga2la;
+ auto* crossRef = cr.dd->ga2la;
GMX_ASSERT(crossRef, "Domain decomposition must provide global/local cross-reference.");
- if (const auto localIndex = crossRef->findHome(index_))
+ if (const auto* localIndex = crossRef->findHome(index_))
{
GMX_ASSERT(localIndex,
"Expect not to reach this point if findHome does not find index_.");
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -bugprone-reserved-identifier
+# Quite a large number of functions use the _FName style for naming
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# The selection code has a large amount of static or exported non-const
+# variables that are out of scope for quick rework
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion, -bugprone-reserved-identifier,
+ -cppcoreguidelines-avoid-non-const-global-variables
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(selection INTERFACE)
+
file(GLOB SELECTION_SOURCES *.cpp)
file(GLOB SCANNER_SOURCES scanner.cpp parser.cpp)
list(REMOVE_ITEM SELECTION_SOURCES ${SCANNER_SOURCES})
gmx_target_warning_suppression(scanner -Wno-missing-declarations HAS_NO_MISSING_DECLARATIONS)
gmx_target_warning_suppression(scanner -Wno-null-conversion HAS_NO_NULL_CONVERSIONS)
endif()
+target_link_libraries(scanner PRIVATE legacy_api)
+# TODO: Use explicit module dependencies.
+target_link_libraries(scanner PRIVATE legacy_modules)
+
list(APPEND libgromacs_object_library_dependencies scanner)
set(libgromacs_object_library_dependencies ${libgromacs_object_library_dependencies} PARENT_SCOPE)
+# Source files have the following dependencies on library infrastructure.
+#target_link_libraries(selection PRIVATE
+# common
+# legacy_modules
+#)
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(selection PUBLIC
+target_include_directories(selection INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(selection PUBLIC
+target_link_libraries(selection INTERFACE
+ legacy_api
+ )
+
+# TODO: when selection is an OBJECT target
+#target_link_libraries(selection PUBLIC legacy_api)
+#target_link_libraries(selection PRIVATE common)
+
+# Module dependencies
+# selection interfaces convey transitive dependence on these modules.
+#target_link_libraries(selection PUBLIC
+target_link_libraries(selection INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(selection PRIVATE NOTHING)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(selection PRIVATE legacy_modules)
+
if(GMX_INSTALL_LEGACY_API)
install(FILES
indexutil.h
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2009-2018, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
for (int m = 0; m < nrefat; ++m)
{
const int ai = index[m];
- const real mass = mtopGetAtomMass(top, ai, &molb);
+ const real mass = mtopGetAtomMass(*top, ai, &molb);
for (int j = 0; j < DIM; ++j)
{
xout[j] += mass * x[ai][j];
for (int m = 0; m < nrefat; ++m)
{
const int ai = index[m];
- const real mass = mtopGetAtomMass(top, ai, &molb);
+ const real mass = mtopGetAtomMass(*top, ai, &molb);
for (int j = 0; j < DIM; ++j)
{
fout[j] += f[ai][j] / mass;
for (int m = 0; m < nrefat; ++m)
{
const int ai = index[m];
- const real mass = mtopGetAtomMass(top, ai, &molb);
+ const real mass = mtopGetAtomMass(*top, ai, &molb);
for (int j = 0; j < DIM; ++j)
{
xout[j] += mass * x[ai][j];
{
rvec dx, xtest;
const int ai = index[m];
- const real mass = mtopGetAtomMass(top, ai, &molb) / mtot;
+ const real mass = mtopGetAtomMass(*top, ai, &molb) / mtot;
pbc_dx(pbc, x[ai], xout, dx);
rvec_add(xout, dx, xtest);
for (int j = 0; j < DIM; ++j)
for (int i = block->index[b]; i < block->index[b + 1]; ++i)
{
const int ai = index[i];
- const real mass = mtopGetAtomMass(top, ai, &molb);
+ const real mass = mtopGetAtomMass(*top, ai, &molb);
for (int d = 0; d < DIM; ++d)
{
xb[d] += mass * x[ai][d];
for (int i = block->index[b]; i < block->index[b + 1]; ++i)
{
const int ai = index[i];
- const real mass = mtopGetAtomMass(top, ai, &molb);
+ const real mass = mtopGetAtomMass(*top, ai, &molb);
for (int d = 0; d < DIM; ++d)
{
fb[d] += f[ai][d] / mass;
if (sel->u.expr.method->init && (bAtomVal || !(sel->flags & SEL_METHODINIT)))
{
sel->flags |= SEL_METHODINIT;
- sel->u.expr.method->init(top, sel->u.expr.method->nparams, sel->u.expr.method->param,
- sel->u.expr.mdata);
+ sel->u.expr.method->init(
+ top, sel->u.expr.method->nparams, sel->u.expr.method->param, sel->u.expr.mdata);
}
if (bAtomVal || !(sel->flags & SEL_OUTINIT))
{
for (i = 0; i < sc->sel.size(); ++i)
{
gmx::internal::SelectionData& sel = *sc->sel[i];
- init_pos_keyword_defaults(&sel.rootElement(), coll->impl_->spost_.c_str(),
- coll->impl_->rpost_.c_str(), &sel);
+ init_pos_keyword_defaults(
+ &sel.rootElement(), coll->impl_->spost_.c_str(), coll->impl_->rpost_.c_str(), &sel);
}
/* Remove any unused variables. */
expandValueForPositions(sel->v.u.r, &sel->v.nr, sel->u.expr.pos);
break;
default:
- GMX_RELEASE_ASSERT(false,
- "Unimplemented value type for position update method");
+ GMX_RELEASE_ASSERT(false, "Unimplemented value type for position update method");
}
}
}
*
* Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
bool IndexGroupsAndNames::containsGroupName(const std::string& groupName) const
{
- return std::any_of(
- std::begin(groupNames_), std::end(groupNames_),
- [&groupName](const std::string& name) { return equalCaseInsensitive(groupName, name); });
+ return std::any_of(std::begin(groupNames_), std::end(groupNames_), [&groupName](const std::string& name) {
+ return equalCaseInsensitive(groupName, name);
+ });
}
std::vector<index> IndexGroupsAndNames::indices(const std::string& groupName) const
"of grompp."));
}
const auto groupNamePosition = std::find_if(
- std::begin(groupNames_), std::end(groupNames_),
- [&groupName](const std::string& name) { return equalCaseInsensitive(groupName, name); });
+ std::begin(groupNames_), std::end(groupNames_), [&groupName](const std::string& name) {
+ return equalCaseInsensitive(groupName, name);
+ });
const auto groupIndex = std::distance(std::begin(groupNames_), groupNamePosition);
const auto groupSize = indexGroup_.index[groupIndex + 1] - indexGroup_.index[groupIndex];
std::vector<index> groupIndices(groupSize);
const auto startingIndex = indexGroup_.index[groupIndex];
std::iota(std::begin(groupIndices), std::end(groupIndices), startingIndex);
- std::transform(std::begin(groupIndices), std::end(groupIndices), std::begin(groupIndices),
+ std::transform(std::begin(groupIndices),
+ std::end(groupIndices),
+ std::begin(groupIndices),
[blockLookup = indexGroup_.a](auto i) { return blockLookup[i]; });
return groupIndices;
}
{
block = new_blocka();
// TODO: Propagate mtop further.
- t_atoms atoms = gmx_mtop_global_atoms(top);
+ t_atoms atoms = gmx_mtop_global_atoms(*top);
analyse(&atoms, block, &names, FALSE, FALSE);
done_atom(&atoms);
}
case INDEX_RES:
{
int resind, molb = 0;
- mtopGetAtomAndResidueName(top, atomIndex, &molb, nullptr, nullptr, nullptr, &resind);
+ mtopGetAtomAndResidueName(*top, atomIndex, &molb, nullptr, nullptr, nullptr, &resind);
*id = resind;
break;
}
case INDEX_MOL:
{
int molb = 0;
- *id = mtopGetMoleculeIndex(top, atomIndex, &molb);
+ *id = mtopGetMoleculeIndex(*top, atomIndex, &molb);
break;
}
case INDEX_UNKNOWN:
case INDEX_RES:
{
int molnr, atnr_mol;
- mtopGetMolblockIndex(top, ai, &molb, &molnr, &atnr_mol);
+ mtopGetMolblockIndex(*top, ai, &molb, &molnr, &atnr_mol);
const t_atoms& mol_atoms = top->moltype[top->molblock[molb].type].atoms;
int last_atom = atnr_mol + 1;
const int currentResid = mol_atoms.atom[atnr_mol].resind;
case INDEX_MOL:
{
int molnr, atnr_mol;
- mtopGetMolblockIndex(top, ai, &molb, &molnr, &atnr_mol);
+ mtopGetMolblockIndex(*top, ai, &molb, &molnr, &atnr_mol);
const MoleculeBlockIndices& blockIndices = top->moleculeBlockIndices[molb];
const int atomStart = blockIndices.globalAtomStart
+ (id - blockIndices.moleculeIndexStart)
* \param[in,out] molb The molecule block of atom a
* \returns true if atoms \p a and \p a + 1 are in different residues, false otherwise.
*/
-static bool is_at_residue_boundary(const gmx_mtop_t* top, int a, int* molb)
+static bool is_at_residue_boundary(const gmx_mtop_t& top, int a, int* molb)
{
- if (a == -1 || a + 1 == top->natoms)
+ if (a == -1 || a + 1 == top.natoms)
{
return true;
}
// Check if a is consecutive or on a residue boundary
if (a != aPrev + 1)
{
- if (!is_at_residue_boundary(top, aPrev, &molb))
+ if (!is_at_residue_boundary(*top, aPrev, &molb))
{
return false;
}
- if (!is_at_residue_boundary(top, a - 1, &molb))
+ if (!is_at_residue_boundary(*top, a - 1, &molb))
{
return false;
}
}
GMX_ASSERT(g->isize > 0, "We return above when isize=0");
const int a = g->index[g->isize - 1];
- if (!is_at_residue_boundary(top, a, &molb))
+ if (!is_at_residue_boundary(*top, a, &molb))
{
return false;
}
*
* Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstring>
#include <algorithm>
+#include <mutex>
#include <vector>
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/listoflists.h"
-#include "gromacs/utility/mutex.h"
#include "gromacs/utility/stringutil.h"
#include "position.h"
//! Data structure to hold the grid cell contents.
CellList cells_;
- Mutex createPairSearchMutex_;
+ std::mutex createPairSearchMutex_;
PairSearchList pairSearchList_;
friend class AnalysisNeighborhoodPairSearchImpl;
AnalysisNeighborhoodSearchImpl::PairSearchImplPointer AnalysisNeighborhoodSearchImpl::getPairSearch()
{
- lock_guard<Mutex> lock(createPairSearchMutex_);
+ std::lock_guard<std::mutex> lock(createPairSearchMutex_);
// TODO: Consider whether this needs to/can be faster, e.g., by keeping a
// separate pool of unused search objects.
PairSearchList::const_iterator i;
}
else if (bTryGrid_)
{
- bGrid_ = initGrid(pbc_, positions.count_, positions.x_,
- mode == AnalysisNeighborhood::eSearchMode_Grid);
+ bGrid_ = initGrid(
+ pbc_, positions.count_, positions.x_, mode == AnalysisNeighborhood::eSearchMode_Grid);
}
refIndices_ = positions.indices_;
if (bGrid_)
SearchImplPointer getSearch();
- Mutex createSearchMutex_;
+ std::mutex createSearchMutex_;
SearchList searchList_;
real cutoff_;
const ListOfLists<int>* excls_;
AnalysisNeighborhood::Impl::SearchImplPointer AnalysisNeighborhood::Impl::getSearch()
{
- lock_guard<Mutex> lock(createSearchMutex_);
+ std::lock_guard<std::mutex> lock(createSearchMutex_);
// TODO: Consider whether this needs to/can be faster, e.g., by keeping a
// separate pool of unused search objects.
SearchList::const_iterator i;
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2009-2018, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/real.h"
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
/*! \brief
*
* Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
/* Integers to floating point are easy */
if (value->type == INT_VALUE && type == REAL_VALUE)
{
- *value = SelectionParserValue::createRealRange(value->u.i.i1, value->u.i.i2,
- value->location());
+ *value = SelectionParserValue::createRealRange(
+ value->u.i.i1, value->u.i.i2, value->location());
return;
}
/* Reals that are integer-valued can also be converted */
/* Sort the ranges and merge consequent ones */
if (param->val.type == INT_VALUE)
{
- const auto range_data = reinterpret_cast<std::array<int, 2>*>(idata);
+ auto* range_data = reinterpret_cast<std::array<int, 2>*>(idata);
sort(range_data, range_data + n, cmp_range<int>);
for (i = j = 2; i < 2 * n; i += 2)
{
}
else
{
- const auto range_data = reinterpret_cast<std::array<real, 2>*>(rdata);
+ auto* range_data = reinterpret_cast<std::array<real, 2>*>(rdata);
sort(range_data, range_data + n, cmp_range<real>);
for (i = j = 2; i < 2 * n; i += 2)
{
GMX_RELEASE_ASSERT(false, "Variable-count value type not implemented");
}
}
- GMX_RELEASE_ASSERT(i == valueCount,
- "Inconsistent value count wrt. the actual value population");
+ GMX_RELEASE_ASSERT(i == valueCount, "Inconsistent value count wrt. the actual value population");
if (param->nvalptr)
{
*param->nvalptr = param->val.nr;
SelectionParserParameterList params;
params.push_back(SelectionParserParameter::createFromExpression(nullptr, child));
params.push_back(SelectionParserParameter::create(nullptr, std::move(args), location));
- _gmx_sel_parse_params(params, root->u.expr.method->nparams, root->u.expr.method->param,
- root, scanner);
+ _gmx_sel_parse_params(
+ params, root->u.expr.method->nparams, root->u.expr.method->param, root, scanner);
}
set_refpos_type(&sc->pcc, child, rpost);
root = modifier;
}
/* Process the parameters */
- _gmx_sel_parse_params(*params, modifier->u.expr.method->nparams, modifier->u.expr.method->param,
- modifier, scanner);
+ _gmx_sel_parse_params(
+ *params, modifier->u.expr.method->nparams, modifier->u.expr.method->param, modifier, scanner);
return root;
}
break;
default:
// TODO: It would probably be better to do this without the type casts.
- gmx_calc_comg_block(top, fr->x, reinterpret_cast<t_block*>(&pc->b), index.data(),
- bMass, p->x);
+ gmx_calc_comg_block(
+ top, fr->x, reinterpret_cast<t_block*>(&pc->b), index.data(), bMass, p->x);
if (p->v && fr->bV)
{
- gmx_calc_comg_block(top, fr->v, reinterpret_cast<t_block*>(&pc->b),
- index.data(), bMass, p->v);
+ gmx_calc_comg_block(
+ top, fr->v, reinterpret_cast<t_block*>(&pc->b), index.data(), bMass, p->v);
}
if (p->f && fr->bF)
{
- gmx_calc_comg_f_block(top, fr->f, reinterpret_cast<t_block*>(&pc->b),
- index.data(), bMass, p->f);
+ gmx_calc_comg_f_block(
+ top, fr->f, reinterpret_cast<t_block*>(&pc->b), index.data(), bMass, p->f);
}
break;
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2009-2016, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
-#include "gromacs/utility/classhelpers.h"
+#include <memory>
/*! \name Flags for position calculation.
* \anchor poscalc_flags
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
/*! \brief
* Needed to access the implementation class from the C code.
#if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
-/* C99 says to define __STDC_LIMIT_MACROS before including stdint.h,
- * if you want the limit (max/min) macros for int types.
- */
-#ifndef __STDC_LIMIT_MACROS
-#define __STDC_LIMIT_MACROS 1
-#endif
-
#include <inttypes.h>
typedef int8_t flex_int8_t;
typedef uint8_t flex_uint8_t;
// manually.
#define YY_BREAK
-#ifdef __INTEL_COMPILER
-// Ignore unused variables in generated code.
-#pragma warning(disable:593)
-#endif
#define YY_NO_UNISTD_H 1
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
- * Copyright (c) 2014,2015,2016,2020, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
// manually.
#define YY_BREAK
-#ifdef __INTEL_COMPILER
-// Ignore unused variables in generated code.
-#pragma warning(disable:593)
-#endif
%}
INTEGER [[:digit:]]+
#if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
-/* C99 says to define __STDC_LIMIT_MACROS before including stdint.h,
- * if you want the limit (max/min) macros for int types.
- */
-#ifndef __STDC_LIMIT_MACROS
-#define __STDC_LIMIT_MACROS 1
-#endif
-
#include <inttypes.h>
typedef int8_t flex_int8_t;
typedef uint8_t flex_uint8_t;
*
* Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
for (int i = pos.m.mapb.index[b]; i < pos.m.mapb.index[b + 1]; ++i)
{
const int index = pos.m.mapb.a[i];
- const t_atom& atom = mtopGetAtomParameters(top, index, &molb);
+ const t_atom& atom = mtopGetAtomParameters(*top, index, &molb);
mass += atom.m;
charge += atom.q;
}
std::string message = formatString(
"Cannot group selection '%s' into %s, because some "
"positions have atoms from more than one such group.",
- name(), type == INDEX_MOL ? "molecules" : "residues");
+ name(),
+ type == INDEX_MOL ? "molecules" : "residues");
GMX_THROW(InconsistentInputError(message));
}
}
void Selection::printInfo(FILE* fp) const
{
- fprintf(fp, "\"%s\" (%d position%s, %d atom%s%s)", name(), posCount(), posCount() == 1 ? "" : "s",
- atomCount(), atomCount() == 1 ? "" : "s", isDynamic() ? ", dynamic" : "");
+ fprintf(fp,
+ "\"%s\" (%d position%s, %d atom%s%s)",
+ name(),
+ posCount(),
+ posCount() == 1 ? "" : "s",
+ atomCount(),
+ atomCount() == 1 ? "" : "s",
+ isDynamic() ? ", dynamic" : "");
fprintf(fp, "\n");
}
*
* Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_SELECTION_SELECTION_H
#define GMX_SELECTION_SELECTION_H
+#include <memory>
#include <string>
#include <vector>
bool hasFlag(SelectionFlag flag) const { return flags_.test(flag); }
//! Sets the flags for this selection.
void setFlags(SelectionFlags flags) { flags_ = flags; }
+ //! Returns the current flags.
+ SelectionFlags flags() const { return flags_; }
//! \copydoc Selection::initCoveredFraction()
bool initCoveredFraction(e_coverfrac_t type);
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
#include <memory>
+#include <optional>
#include <string>
#include <vector>
#include "gromacs/options/ioptionscontainer.h"
#include "gromacs/selection/selection.h"
#include "gromacs/selection/selhelp.h"
-#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/utility/exceptions.h"
}
for (size_t i = firstSelection; i < sc->sel.size(); ++i)
{
- writer->writeString(formatString(" %2d. %s\n", static_cast<int>(i - firstSelection + 1),
- sc->sel[i]->selectionText()));
+ writer->writeString(formatString(
+ " %2d. %s\n", static_cast<int>(i - firstSelection + 1), sc->sel[i]->selectionText()));
}
if (maxCount > 0)
{
const int remaining = maxCount - static_cast<int>(sc->sel.size() - firstSelection);
- writer->writeString(formatString("(%d more selection%s required)\n", remaining,
- remaining > 1 ? "s" : ""));
+ writer->writeString(formatString(
+ "(%d more selection%s required)\n", remaining, remaining > 1 ? "s" : ""));
}
}
}
SelectionCollection::SelectionCollection() : impl_(new Impl) {}
-SelectionCollection::~SelectionCollection() {}
+SelectionCollection::~SelectionCollection() = default;
+SelectionCollection::SelectionCollection(const SelectionCollection& rhs) :
+ impl_(std::make_unique<Impl>())
+{
+ setReferencePosType(rhs.impl_->rpost_.empty() ? PositionCalculationCollection::typeEnumValues[0]
+ : rhs.impl_->rpost_.c_str());
+ setOutputPosType(rhs.impl_->spost_.empty() ? PositionCalculationCollection::typeEnumValues[0]
+ : rhs.impl_->spost_.c_str());
+ setDebugLevel(static_cast<int>(rhs.impl_->debugLevel_));
+
+ for (size_t i = 0; i < rhs.impl_->sc_.sel.size(); i++)
+ {
+ const auto& selectionOption = rhs.impl_->sc_.sel[i];
+ parseFromString(selectionOption->selectionText());
+ impl_->sc_.sel[i]->setFlags(selectionOption->flags());
+ }
+
+ // Topology has been initialized in rhs if top is non-null or natoms is set.
+ // Note this needs to be set after selections are parsed to register topology requirements properly.
+ if (rhs.impl_->sc_.top != nullptr || rhs.impl_->sc_.gall.isize > 0)
+ {
+ setTopology(rhs.impl_->sc_.top, rhs.impl_->sc_.gall.isize);
+ gmx_ana_index_copy(&impl_->sc_.gall, &rhs.impl_->sc_.gall, /*balloc=*/false);
+ }
+
+ if (rhs.impl_->grps_ != nullptr)
+ {
+ setIndexGroups(rhs.impl_->grps_);
+ }
+
+ // Only compile the selection if rhs is compiled.
+ if (rhs.impl_->sc_.mempool != nullptr)
+ {
+ compile();
+ }
+}
+
+SelectionCollection& SelectionCollection::operator=(SelectionCollection rhs)
+{
+ rhs.swap(*this);
+ return *this;
+}
+
+void SelectionCollection::swap(SelectionCollection& rhs)
+{
+ using std::swap;
+ swap(impl_, rhs.impl_);
+}
void SelectionCollection::initOptions(IOptionsContainer* options, SelectionTypeOption selectionTypeOption)
{
}
-void SelectionCollection::setTopology(gmx_mtop_t* top, int natoms)
+void SelectionCollection::setTopology(const gmx_mtop_t* top, int natoms)
{
GMX_RELEASE_ASSERT(natoms > 0 || top != nullptr,
"The number of atoms must be given if there is no topology");
SelectionList SelectionCollection::parseFromStdin(int count, bool bInteractive, const std::string& context)
{
StandardInputStream inputStream;
- return parseInteractive(count, &inputStream,
- bInteractive ? &TextOutputFile::standardError() : nullptr, context);
+ return parseInteractive(
+ count, &inputStream, bInteractive ? &TextOutputFile::standardError() : nullptr, context);
}
namespace
yyscan_t scanner;
const std::unique_ptr<TextWriter> statusWriter(initStatusWriter(statusStream));
- _gmx_sel_init_lexer(&scanner, &impl_->sc_, statusWriter.get(), count,
- impl_->bExternalGroupsSet_, impl_->grps_);
+ _gmx_sel_init_lexer(
+ &scanner, &impl_->sc_, statusWriter.get(), count, impl_->bExternalGroupsSet_, impl_->grps_);
return runParser(scanner, inputStream, true, count, context);
}
"Trajectory has less atoms (%d) than what is required for "
"evaluating the provided selections (atoms up to index %d "
"are required).",
- fr->natoms, maxAtomIndex + 1);
+ fr->natoms,
+ maxAtomIndex + 1);
GMX_THROW(InconsistentInputError(message));
}
}
evaluator.evaluateFinal(this, nframes);
}
+std::optional<Selection> SelectionCollection::selection(std::string_view selName) const
+{
+ const auto& selections = impl_->sc_.sel;
+ if (const auto foundIter = std::find_if(
+ selections.cbegin(),
+ selections.cend(),
+ [selName](const auto& selection) { return selection->name() == selName; });
+ foundIter != selections.end())
+ {
+ return Selection(foundIter->get());
+ }
+ return std::nullopt;
+}
+
void SelectionCollection::printTree(FILE* fp, bool bValues) const
{
std::fprintf(out, "#\n");
}
+void swap(SelectionCollection& lhs, SelectionCollection& rhs)
+{
+ lhs.swap(rhs);
+}
+
} // namespace gmx
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
- * Copyright (c) 2015,2016,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
+#include <memory>
+#include <optional>
#include <string>
#include <vector>
#include "gromacs/selection/selection.h" // For gmx::SelectionList
-#include "gromacs/utility/classhelpers.h"
struct gmx_ana_indexgrps_t;
struct gmx_mtop_t;
{
class IOptionsContainer;
-class SelectionCompiler;
class SelectionEvaluator;
class TextInputStream;
class TextOutputStream;
* setOutputPosType(). See these methods for more details on the
* initialization options.
*
+ * SelectionCollections can be copied. Copies retain the same pointers to external indices (if set)
+ * and the topology (if set), and are compiled if the copied collection is compiled. Selection
+ * objects created from a given SelectionCollection are tied only to the original collection, so
+ * a copy of a SelectionCollection will not update pre-existing Selections on evaluate() calls.
+ *
* After setting the default values, one or more selections can be parsed with
* one or more calls to parseInteractive(), parseFromStdin(), parseFromFile(), and/or
* parseFromString(). After all selections are parsed, the topology must be
SelectionCollection();
~SelectionCollection();
+ SelectionCollection(const SelectionCollection& rhs);
+ SelectionCollection& operator=(SelectionCollection rhs);
+ void swap(SelectionCollection& rhs);
+
/*! \brief
* Initializes options for setting global properties on the collection.
*
* Does not throw currently, but this is subject to change when more
* underlying code is converted to C++.
*/
- void setTopology(gmx_mtop_t* top, int natoms);
+ void setTopology(const gmx_mtop_t* top, int natoms);
/*! \brief
* Sets the external index groups to use for the selections.
*
* Does not throw.
*/
void evaluateFinal(int nframes);
-
+ /*! \brief
+ * Retrieves a Selection handle for the selection with the given name
+ *
+ * @param selName name of the selection to return
+ * @return The selection with the given name, or nullopt if no such selection exists.
+ */
+ [[nodiscard]] std::optional<Selection> selection(std::string_view selName) const;
/*! \brief
* Prints a human-readable version of the internal selection element
* tree.
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
// Needed for the compiler to freely modify the collection.
friend void compileSelection(SelectionCollection* coll);
friend class SelectionEvaluator;
};
+void swap(SelectionCollection& lhs, SelectionCollection& rhs);
+
} // namespace gmx
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
getMassesIfRequired(top);
}
- void getMassesIfRequired(gmx_mtop_t* top)
+ void getMassesIfRequired(gmx_mtop_t* top) const
{
const bool massRequired = selections_.requiredTopologyProperties().needsMasses;
if (!massRequired)
void SelectionOptionBehavior::initOptions(IOptionsContainer* options)
{
options->addOption(FileNameOption("n")
- .filetype(eftIndex)
+ .filetype(OptionFileType::Index)
.inputFile()
.store(&impl_->ndxfile_)
.defaultBasename("index")
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_SELECTION_SELECTIONOPTIONBEHAVIOR_H
#define GMX_SELECTION_SELECTIONOPTIONBEHAVIOR_H
+#include <memory>
#include <string>
#include "gromacs/options/ioptionsbehavior.h"
-#include "gromacs/utility/classhelpers.h"
struct gmx_mtop_t;
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
formatString("Too few selections provided for '%s': "
"Expected %d selections, but only %d left "
"after assigning the first %d to other selections.",
- request.name().c_str(), request.count(), remaining, assigned)));
+ request.name().c_str(),
+ request.count(),
+ remaining,
+ assigned)));
}
last = first + request.count();
}
"selections to be assigned to '%s'. "
"Resolution for such cases is not implemented, "
"and may be impossible.",
- name, conflictName, name, conflictName)));
+ name,
+ conflictName,
+ name,
+ conflictName)));
}
last = selections.end();
}
formatString("Too many selections provided: "
"Expected %d selections, but %d provided. "
"Last %d selections could not be assigned to any option.",
- assigned, count, remaining)));
+ assigned,
+ count,
+ remaining)));
}
}
for (i = impl_->requests_.begin(); i != impl_->requests_.end(); ++i)
{
const Impl::SelectionRequest& request = *i;
- std::string context = formatString("for option '%s'\n(%s)", request.name().c_str(),
- request.description().c_str());
+ std::string context = formatString(
+ "for option '%s'\n(%s)", request.name().c_str(), request.description().c_str());
SelectionList selections =
impl_->collection_.parseFromStdin(request.count(), bInteractive, context);
request.storage_->addSelections(selections, true);
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_SELECTION_SELECTIONOPTIONMANAGER_H
#define GMX_SELECTION_SELECTIONOPTIONMANAGER_H
+#include <memory>
#include <string>
#include "gromacs/options/options.h"
-#include "gromacs/utility/classhelpers.h"
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
/*! \brief
* Needed for handling delayed selection parsing requests.
"Group '%s' cannot be used in selections, because it "
"contains negative atom indices and/or references atoms "
"not present (largest allowed atom index is %d).",
- name().c_str(), natoms);
+ name().c_str(),
+ natoms);
GMX_THROW(InconsistentInputError(message));
}
}
{
int i;
- fprintf(fp, "%*c %s %s", level * 2 + 1, '*', _gmx_selelem_type_str(sel),
- _gmx_sel_value_type_str(&sel.v));
+ fprintf(fp, "%*c %s %s", level * 2 + 1, '*', _gmx_selelem_type_str(sel), _gmx_sel_value_type_str(&sel.v));
if (!sel.name().empty())
{
fprintf(fp, " \"%s\"", sel.name().c_str());
* segfaults when printing the selection tree. */
if (sel.v.u.p->x)
{
- fprintf(fp, "(%f, %f, %f)", sel.v.u.p->x[0][XX], sel.v.u.p->x[0][YY],
- sel.v.u.p->x[0][ZZ]);
+ fprintf(fp, "(%f, %f, %f)", sel.v.u.p->x[0][XX], sel.v.u.p->x[0][YY], sel.v.u.p->x[0][ZZ]);
}
else
{
*
* Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/onlinehelp/helptopic.h"
#include "gromacs/onlinehelp/helpwritercontext.h"
+#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/stringutil.h"
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2009-2018, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
if (param[i].val.type != INT_VALUE && param[i].val.type != REAL_VALUE)
{
- report_param_error(fp, name, param[i].name,
+ report_param_error(fp,
+ name,
+ param[i].name,
"error: SPAR_RANGES cannot be set for a non-numeric parameter");
bOk = false;
}
if (param[i].flags & SPAR_DYNAMIC)
{
- report_param_error(fp, name, param[i].name,
+ report_param_error(fp,
+ name,
+ param[i].name,
"warning: SPAR_DYNAMIC does not have effect with SPAR_RANGES");
param[i].flags &= ~SPAR_DYNAMIC;
}
if (!(param[i].flags & SPAR_VARNUM) && param[i].val.nr != 1)
{
report_param_error(
- fp, name, param[i].name,
+ fp,
+ name,
+ param[i].name,
"error: range should take either one or an arbitrary number of values");
bOk = false;
}
if (param[i].flags & SPAR_ATOMVAL)
{
- report_param_error(fp, name, param[i].name,
- "error: SPAR_RANGES and SPAR_ATOMVAL both set");
+ report_param_error(
+ fp, name, param[i].name, "error: SPAR_RANGES and SPAR_ATOMVAL both set");
bOk = false;
}
}
if ((param[i].flags & SPAR_VARNUM) && (param[i].flags & SPAR_ATOMVAL))
{
- report_param_error(fp, name, param[i].name,
- "error: SPAR_VARNUM and SPAR_ATOMVAL both set");
+ report_param_error(
+ fp, name, param[i].name, "error: SPAR_VARNUM and SPAR_ATOMVAL both set");
bOk = false;
}
if (param[i].flags & SPAR_ENUMVAL)
{
if (param[i].val.type != STR_VALUE)
{
- report_param_error(fp, name, param[i].name,
+ report_param_error(fp,
+ name,
+ param[i].name,
"error: SPAR_ENUMVAL can only be set for string parameters");
bOk = false;
}
if (param[i].val.nr != 1)
{
- report_param_error(fp, name, param[i].name,
+ report_param_error(fp,
+ name,
+ param[i].name,
"error: SPAR_ENUMVAL parameters should take exactly one value");
bOk = false;
}
if (param[i].flags & (SPAR_DYNAMIC | SPAR_VARNUM | SPAR_ATOMVAL))
{
- report_param_error(fp, name, param[i].name,
+ report_param_error(fp,
+ name,
+ param[i].name,
"error: only SPAR_OPTIONAL supported with SPAR_ENUMVAL");
bOk = false;
}
{
if (param[i].val.nr != 0)
{
- report_param_error(fp, name, param[i].name,
+ report_param_error(fp,
+ name,
+ param[i].name,
"error: number of values should be zero for boolean parameters");
bOk = false;
}
/* Any other flags should not be specified */
if (param[i].flags & ~SPAR_OPTIONAL)
{
- report_param_error(fp, name, param[i].name,
+ report_param_error(fp,
+ name,
+ param[i].name,
"error: boolean parameter should not have any flags set");
bOk = false;
}
if (param[i].val.nr != -1)
{
report_param_error(
- fp, name, param[i].name,
+ fp,
+ name,
+ param[i].name,
"warning: val.nr is not -1 although SPAR_VARNUM/SPAR_ATOMVAL is set");
}
param[i].val.nr = -1;
{
if (param[i].name[j] != '_' && !isalnum(param[i].name[j]))
{
- report_param_error(fp, name, param[i].name,
- "error: name contains non-alphanumeric characters");
+ report_param_error(
+ fp, name, param[i].name, "error: name contains non-alphanumeric characters");
bOk = false;
break;
}
/* Check that the name does not conflict with a method */
if (symtab.findSymbol(param[i].name) != nullptr)
{
- report_param_error(fp, name, param[i].name,
+ report_param_error(fp,
+ name,
+ param[i].name,
"error: name conflicts with another method or a keyword");
bOk = false;
}
gmx_ana_selparam_t* param = gmx_ana_selmethod_find_param(name, method);
if (param)
{
- report_param_error(fp, method->name, param->name,
+ report_param_error(fp,
+ method->name,
+ param->name,
"error: name conflicts with another method or a keyword");
bOk = false;
}
/* Make some checks on init_data and free */
if (method->nparams > 0 && !method->init_data)
{
- report_error(fp, method->name,
+ report_error(fp,
+ method->name,
"error: init_data should be provided because the method has parameters");
bOk = false;
}
/* Check presence of outinit for position-valued methods */
if (method->type == POS_VALUE && !method->outinit)
{
- report_error(fp, method->name,
+ report_error(fp,
+ method->name,
"error: outinit should be provided because the method has POS_VALUE");
bOk = false;
}
/* Check presence of outinit for variable output count methods */
if ((method->flags & SMETH_VARNUMVAL) && !method->outinit)
{
- report_error(fp, method->name,
+ report_error(fp,
+ method->name,
"error: outinit should be provided because the method has SMETH_VARNUMVAL");
bOk = false;
}
/* Check that conflicting flags are not present. */
if (method->flags & SMETH_VARNUMVAL)
{
- report_error(fp, method->name,
+ report_error(fp,
+ method->name,
"error: SMETH_VARNUMVAL cannot be set for group-valued methods");
bOk = false;
}
}
if ((method->flags & SMETH_CHARVAL) && method->type != STR_VALUE)
{
- report_error(fp, method->name,
+ report_error(fp,
+ method->name,
"error: SMETH_CHARVAL can only be specified for STR_VALUE methods");
bOk = false;
}
/* Check flags */
if (method->flags & (SMETH_SINGLEVAL | SMETH_VARNUMVAL))
{
- report_error(fp, method->name,
+ report_error(fp,
+ method->name,
"error: modifier should not have SMETH_SINGLEVAL or SMETH_VARNUMVAL set");
bOk = false;
}
*
* Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
&init_frame_insolidangle,
nullptr,
&evaluate_insolidangle,
- { "insolidangle center POS span POS_EXPR [cutoff REAL]", "Selecting atoms in a solid angle",
- asize(help_insolidangle), help_insolidangle },
+ { "insolidangle center POS span POS_EXPR [cutoff REAL]",
+ "Selecting atoms in a solid angle",
+ asize(help_insolidangle),
+ help_insolidangle },
};
static void* init_data_insolidangle(int /* npar */, gmx_ana_selparam_t* param)
GMX_THROW(gmx::InvalidInputError("Angle cutoff should be > 0"));
}
- surf->angcut *= DEG2RAD;
+ surf->angcut *= gmx::c_deg2Rad;
surf->distccut = -std::cos(surf->angcut);
surf->targetbinsize = surf->angcut / 2;
surf->ntbins = static_cast<int>(M_PI / surf->targetbinsize);
- surf->tbinsize = (180.0 / surf->ntbins) * DEG2RAD;
+ surf->tbinsize = (180.0 / surf->ntbins) * gmx::c_deg2Rad;
snew(surf->tbin, static_cast<int>(M_PI / surf->tbinsize) + 1);
surf->maxbins = 0;
{
out->u.p->m.type = d->p1.m.type;
}
- gmx_ana_pos_reserve_for_append(out->u.p, d->p1.count() + d->p2.count(),
- d->p1.m.b.nra + d->p2.m.b.nra, d->p1.v != nullptr, d->p1.f != nullptr);
+ gmx_ana_pos_reserve_for_append(out->u.p,
+ d->p1.count() + d->p2.count(),
+ d->p1.m.b.nra + d->p2.m.b.nra,
+ d->p1.v != nullptr,
+ d->p1.f != nullptr);
gmx_ana_pos_empty_init(out->u.p);
}
int i, j, b;
out->u.p->m.type = d->p.m.type;
- gmx_ana_pos_reserve_for_append(out->u.p, d->p.count(), d->p.m.b.nra, d->p.v != nullptr,
- d->p.f != nullptr);
+ gmx_ana_pos_reserve_for_append(
+ out->u.p, d->p.count(), d->p.m.b.nra, d->p.v != nullptr, d->p.f != nullptr);
gmx_ana_pos_empty_init(out->u.p);
for (i = 0; i < d->p.count(); i += d->n)
{
*
* Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int molb = 0;
for (int i = 0; i < g->isize; ++i)
{
- mtopGetAtomAndResidueName(context.top, g->index[i], &molb, nullptr, &out->u.i[i], nullptr, nullptr);
+ mtopGetAtomAndResidueName(*context.top, g->index[i], &molb, nullptr, &out->u.i[i], nullptr, nullptr);
}
}
for (int i = 0; i < g->isize; ++i)
{
int resind;
- mtopGetAtomAndResidueName(context.top, g->index[i], &molb, nullptr, nullptr, nullptr, &resind);
+ mtopGetAtomAndResidueName(*context.top, g->index[i], &molb, nullptr, nullptr, nullptr, &resind);
out->u.i[i] = resind + 1;
}
}
int molb = 0;
for (int i = 0; i < g->isize; ++i)
{
- out->u.i[i] = mtopGetMoleculeIndex(context.top, g->index[i], &molb) + 1;
+ out->u.i[i] = mtopGetMoleculeIndex(*context.top, g->index[i], &molb) + 1;
}
}
for (int i = 0; i < g->isize; ++i)
{
const char* atom_name;
- mtopGetAtomAndResidueName(context.top, g->index[i], &molb, &atom_name, nullptr, nullptr, nullptr);
+ mtopGetAtomAndResidueName(*context.top, g->index[i], &molb, &atom_name, nullptr, nullptr, nullptr);
out->u.s[i] = const_cast<char*>(atom_name);
}
}
int molb = 0;
for (int i = 0; i < g->isize; ++i)
{
- const char* s = mtopGetAtomPdbInfo(context.top, g->index[i], &molb).atomnm;
+ const char* s = mtopGetAtomPdbInfo(*context.top, g->index[i], &molb).atomnm;
while (std::isspace(*s))
{
++s;
for (int i = 0; i < g->isize; ++i)
{
int atomIndexInMolecule;
- mtopGetMolblockIndex(context.top, g->index[i], &molb, nullptr, &atomIndexInMolecule);
+ mtopGetMolblockIndex(*context.top, g->index[i], &molb, nullptr, &atomIndexInMolecule);
const gmx_moltype_t& moltype = context.top->moltype[context.top->molblock[molb].type];
out->u.s[i] = *moltype.atoms.atomtype[atomIndexInMolecule];
}
int molb = 0;
for (int i = 0; i < g->isize; ++i)
{
- out->u.s[i] = *mtopGetResidueInfo(context.top, g->index[i], &molb).name;
+ out->u.s[i] = *mtopGetResidueInfo(*context.top, g->index[i], &molb).name;
}
}
int molb = 0;
for (int i = 0; i < g->isize; ++i)
{
- out->u.s[i][0] = mtopGetResidueInfo(context.top, g->index[i], &molb).ic;
+ out->u.s[i][0] = mtopGetResidueInfo(*context.top, g->index[i], &molb).ic;
}
}
int molb = 0;
for (int i = 0; i < g->isize; ++i)
{
- out->u.s[i][0] = mtopGetResidueInfo(context.top, g->index[i], &molb).chainid;
+ out->u.s[i][0] = mtopGetResidueInfo(*context.top, g->index[i], &molb).chainid;
}
}
int molb = 0;
for (int i = 0; i < g->isize; ++i)
{
- out->u.r[i] = mtopGetAtomMass(context.top, g->index[i], &molb);
+ out->u.r[i] = mtopGetAtomMass(*context.top, g->index[i], &molb);
}
}
int molb = 0;
for (int i = 0; i < g->isize; ++i)
{
- out->u.r[i] = mtopGetAtomParameters(context.top, g->index[i], &molb).q;
+ out->u.r[i] = mtopGetAtomParameters(*context.top, g->index[i], &molb).q;
}
}
int molb = 0;
for (int i = 0; i < g->isize; ++i)
{
- out->u.s[i][0] = mtopGetAtomPdbInfo(context.top, g->index[i], &molb).altloc;
+ out->u.s[i][0] = mtopGetAtomPdbInfo(*context.top, g->index[i], &molb).altloc;
}
}
int molb = 0;
for (int i = 0; i < g->isize; ++i)
{
- out->u.r[i] = mtopGetAtomPdbInfo(context.top, g->index[i], &molb).occup;
+ out->u.r[i] = mtopGetAtomPdbInfo(*context.top, g->index[i], &molb).occup;
}
}
int molb = 0;
for (int i = 0; i < g->isize; ++i)
{
- out->u.r[i] = mtopGetAtomPdbInfo(context.top, g->index[i], &molb).bfac;
+ out->u.r[i] = mtopGetAtomPdbInfo(*context.top, g->index[i], &molb).bfac;
}
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2009-2017, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
SelectionParserSymbolIterator& SelectionParserSymbolIterator::operator=(const SelectionParserSymbolIterator& other)
{
- impl_.reset(new Impl(*other.impl_));
+ impl_ = std::make_unique<Impl>(*other.impl_);
return *this;
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
- * Copyright (c) 2014,2015,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_SELECTION_SYMREC_H
#include <iterator>
+#include <memory>
#include <string>
#include <boost/stl_interfaces/iterator_interface.hpp>
-#include "gromacs/utility/classhelpers.h"
-
#include "selelem.h"
struct gmx_ana_selmethod_t;
*/
explicit SelectionParserSymbol(Impl* impl);
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
/*! \brief
* Needed to call the constructor and for other initialization.
*/
explicit SelectionParserSymbolIterator(Impl* impl);
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
/*! \brief
* Needed to access the constructor.
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
/*! \brief
* Needed to access implementation types.
for (int i = 0; i < blocka_.nr; ++i)
{
gmx::test::TestReferenceChecker blockCompound(compound.checkCompound("Block", nullptr));
- blockCompound.checkSequence(&blocka_.a[blocka_.index[i]], &blocka_.a[blocka_.index[i + 1]],
- "Atoms");
+ blockCompound.checkSequence(
+ &blocka_.a[blocka_.index[i]], &blocka_.a[blocka_.index[i + 1]], "Atoms");
}
}
for (int i = 0; i < map_.mapb.nr; ++i)
{
gmx::test::TestReferenceChecker blockCompound(compound.checkCompound("Block", nullptr));
- blockCompound.checkSequence(&atoms[map_.mapb.index[i]], &atoms[map_.mapb.index[i + 1]],
- "Atoms");
+ blockCompound.checkSequence(
+ &atoms[map_.mapb.index[i]], &atoms[map_.mapb.index[i + 1]], "Atoms");
blockCompound.checkInteger(map_.refid[i], "RefId");
blockCompound.checkInteger(map_.mapid[i], "MapId");
int originalIdIndex = (map_.refid[i] != -1 ? map_.refid[i] : i);
addGroupToBlocka_(indicesGroupSecondA_);
addGroupToBlocka_(indicesGroupC_);
- const char* const namesAsConstCharArray[4] = { groupNames[0].c_str(), groupNames[1].c_str(),
- groupNames[2].c_str(), groupNames[3].c_str() };
+ const char* const namesAsConstCharArray[4] = {
+ groupNames[0].c_str(), groupNames[1].c_str(), groupNames[2].c_str(), groupNames[3].c_str()
+ };
indexGroupAndNames_ = std::make_unique<gmx::IndexGroupsAndNames>(blockA_, namesAsConstCharArray);
}
~IndexGroupsAndNamesTest() override { done_blocka(&blockA_); }
if (selfPairs)
{
searchPair = NeighborhoodSearchTestData::RefPair(testIndex, 0.0);
- const auto otherRefPair = std::lower_bound(refPairs[refIndex].begin(),
- refPairs[refIndex].end(), searchPair);
+ const auto otherRefPair = std::lower_bound(
+ refPairs[refIndex].begin(), refPairs[refIndex].end(), searchPair);
GMX_RELEASE_ASSERT(otherRefPair != refPairs[refIndex].end(),
"Precomputed reference data is not symmetric");
otherRefPair->bFound = true;
nb_.initSearch(&data.pbc_, data.refPositions().exclusionIds(helper.refPosIds()));
ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Simple, search.mode());
- testPairSearchFull(&search, data, data.testPositions().exclusionIds(helper.testPosIds()),
- helper.exclusions(), {}, {}, false);
+ testPairSearchFull(&search,
+ data,
+ data.testPositions().exclusionIds(helper.testPosIds()),
+ helper.exclusions(),
+ {},
+ {},
+ false);
}
TEST_F(NeighborhoodSearchTest, GridSearchExclusions)
nb_.initSearch(&data.pbc_, data.refPositions().exclusionIds(helper.refPosIds()));
ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Grid, search.mode());
- testPairSearchFull(&search, data, data.testPositions().exclusionIds(helper.testPosIds()),
- helper.exclusions(), {}, {}, false);
+ testPairSearchFull(&search,
+ data,
+ data.testPositions().exclusionIds(helper.testPosIds()),
+ helper.exclusions(),
+ {},
+ {},
+ false);
}
} // namespace
for (int i = 0; i < p->count(); ++i)
{
gmx::test::TestReferenceChecker posCompound(compound.checkCompound("Position", nullptr));
- posCompound.checkSequence(&p->m.mapb.a[p->m.mapb.index[i]],
- &p->m.mapb.a[p->m.mapb.index[i + 1]], "Atoms");
+ posCompound.checkSequence(
+ &p->m.mapb.a[p->m.mapb.index[i]], &p->m.mapb.a[p->m.mapb.index[i + 1]], "Atoms");
posCompound.checkInteger(p->m.refid[i], "RefId");
if (bCoordinates)
{
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <ParsedSelections Name="Parsed">
+ <ParsedSelection Name="Selection1">
+ <String Name="Input">group "GrpA"</String>
+ <String Name="Name">GrpA</String>
+ <String Name="Text">group "GrpA"</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection2">
+ <String Name="Input">GrpB</String>
+ <String Name="Name">GrpB</String>
+ <String Name="Text">GrpB</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection3">
+ <String Name="Input">1</String>
+ <String Name="Name">GrpB</String>
+ <String Name="Text">1</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection4">
+ <String Name="Input">group "GrpB" and resname RB</String>
+ <String Name="Name">group "GrpB" and resname RB</String>
+ <String Name="Text">group "GrpB" and resname RB</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection5">
+ <String Name="Input">group "GrpA" permute 5 3 2 1 4</String>
+ <String Name="Name">group "GrpA" permute 5 3 2 1 4</String>
+ <String Name="Text">group "GrpA" permute 5 3 2 1 4</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection6">
+ <String Name="Input">group "GrpA" plus group "GrpB"</String>
+ <String Name="Name">group "GrpA" plus group "GrpB"</String>
+ <String Name="Text">group "GrpA" plus group "GrpB"</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection7">
+ <String Name="Input">res_cog of group "GrpA"</String>
+ <String Name="Name">res_cog of group "GrpA"</String>
+ <String Name="Text">res_cog of group "GrpA"</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ </ParsedSelections>
+ <CompiledSelections Name="Compiled">
+ <Selection Name="Selection1">
+ <String Name="Name">GrpA</String>
+ <Sequence Name="Atoms">
+ <Int Name="Length">5</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection2">
+ <String Name="Name">GrpB</String>
+ <Sequence Name="Atoms">
+ <Int Name="Length">5</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection3">
+ <String Name="Name">GrpB</String>
+ <Sequence Name="Atoms">
+ <Int Name="Length">5</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection4">
+ <String Name="Name">group "GrpB" and resname RB</String>
+ <Sequence Name="Atoms">
+ <Int Name="Length">3</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection5">
+ <String Name="Name">group "GrpA" permute 5 3 2 1 4</String>
+ <Sequence Name="Atoms">
+ <Int Name="Length">5</Int>
+ <Int>3</Int>
+ <Int>2</Int>
+ <Int>1</Int>
+ <Int>4</Int>
+ <Int>0</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection6">
+ <String Name="Name">group "GrpA" plus group "GrpB"</String>
+ <Sequence Name="Atoms">
+ <Int Name="Length">10</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection7">
+ <String Name="Name">res_cog of group "GrpA"</String>
+ <Sequence Name="Atoms">
+ <Int Name="Length">5</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ </Sequence>
+ </Selection>
+ </CompiledSelections>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <ParsedSelections Name="Parsed">
+ <ParsedSelection Name="Selection1">
+ <String Name="Input">x > 2</String>
+ <String Name="Text">x > 2</String>
+ <Bool Name="Dynamic">true</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection2">
+ <String Name="Input">2 < x</String>
+ <String Name="Text">2 < x</String>
+ <Bool Name="Dynamic">true</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection3">
+ <String Name="Input">y > resnr</String>
+ <String Name="Text">y > resnr</String>
+ <Bool Name="Dynamic">true</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection4">
+ <String Name="Input">resnr < 2.5</String>
+ <String Name="Text">resnr < 2.5</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection5">
+ <String Name="Input">2.5 > resnr</String>
+ <String Name="Text">2.5 > resnr</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ </ParsedSelections>
+ <CompiledSelections Name="Compiled">
+ <Selection Name="Selection1">
+ <Sequence Name="Atoms">
+ <Int Name="Length">15</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection2">
+ <Sequence Name="Atoms">
+ <Int Name="Length">15</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection3">
+ <Sequence Name="Atoms">
+ <Int Name="Length">15</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection4">
+ <Sequence Name="Atoms">
+ <Int Name="Length">6</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection5">
+ <Sequence Name="Atoms">
+ <Int Name="Length">6</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ </Selection>
+ </CompiledSelections>
+ <EvaluatedSelections Name="Frame1">
+ <Selection Name="Selection1">
+ <Sequence Name="Atoms">
+ <Int Name="Length">7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">7</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection2">
+ <Sequence Name="Atoms">
+ <Int Name="Length">7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">7</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">3</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
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+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">4</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection3">
+ <Sequence Name="Atoms">
+ <Int Name="Length">4</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>7</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">4</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection4">
+ <Sequence Name="Atoms">
+ <Int Name="Length">6</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">6</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection5">
+ <Sequence Name="Atoms">
+ <Int Name="Length">6</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">6</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">3</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">1</Real>
+ <Real Name="Y">4</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">2</Real>
+ <Real Name="Y">2</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Position>
+ </Sequence>
+ </Selection>
+ </EvaluatedSelections>
+</ReferenceData>
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
sc_.setIndexGroups(grps_);
}
-
/********************************************************************
* Test fixture for interactive SelectionCollection tests
*/
{
helper_.setInputLines(inputLines);
// TODO: Check something about the returned selections as well.
- ASSERT_NO_THROW_GMX(sc_.parseInteractive(count, &helper_.inputStream(),
+ ASSERT_NO_THROW_GMX(sc_.parseInteractive(count,
+ &helper_.inputStream(),
bInteractive ? &helper_.outputStream() : nullptr,
"for test context"));
helper_.checkSession();
void runTest(int natoms, const gmx::ArrayRef<const char* const>& selections);
void runTest(const char* filename, const gmx::ArrayRef<const char* const>& selections);
+ void checkCompiled();
+
private:
static void checkSelection(gmx::test::TestReferenceChecker* checker,
const gmx::Selection& sel,
TestFlags flags);
- void checkCompiled();
gmx::test::TestReferenceData data_;
gmx::test::TestReferenceChecker checker_;
// TODO: Tests for more evaluation errors
+
+/********************************************************************
+ * Tests for retrieving selections.
+ */
+TEST_F(SelectionCollectionTest, RetrieveValidSelection)
+{
+ ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
+ const std::optional<gmx::Selection> retrievedSel = sc_.selection(sel_[0].name());
+ ASSERT_TRUE(retrievedSel.has_value());
+ EXPECT_STREQ(sel_[0].name(), retrievedSel->name());
+}
+
+TEST_F(SelectionCollectionTest, RetrieveInvalidSelection)
+{
+ ASSERT_FALSE(sc_.selection("some invalid key").has_value());
+}
+
+/********************************************************************
+ * Tests for assignment/copying.
+ */
+TEST_F(SelectionCollectionTest, CanCopyEmptyCollection)
+{
+ EXPECT_NO_THROW_GMX(gmx::SelectionCollection sc2(sc_));
+}
+
+TEST_F(SelectionCollectionTest, CopiedSelectionListsAreHandledSeparately)
+{
+ ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
+ EXPECT_FALSE(sc_.requiredTopologyProperties().hasAny());
+ ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
+ ASSERT_EQ(2U, sel_.size());
+ gmx::SelectionCollection sc2(sc_);
+ ASSERT_NO_THROW_GMX(sel_[1].setEvaluateVelocities(true));
+ ASSERT_NO_THROW_GMX(sel_[1].setEvaluateForces(true));
+ ASSERT_NO_THROW_GMX(sc2.compile());
+ // These would only be populated if sc_.compile() was called
+ EXPECT_FALSE(sel_[1].hasVelocities());
+ EXPECT_FALSE(sel_[1].hasForces());
+}
+
+
/********************************************************************
* Tests for interactive selection input
*/
TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
{
- static const char* const selections[] = { "atomnr 1 to 3 6 to 8", "atomnr 4 2 5 to 7",
+ static const char* const selections[] = { "atomnr 1 to 3 6 to 8",
+ "atomnr 4 2 5 to 7",
"atomnr <= 5" };
runTest(10, selections);
}
TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
{
- static const char* const selections[] = { "name HG21", "name 1HG2", "pdbname HG21 CB",
- "pdbatomname 1HG2" };
+ static const char* const selections[] = {
+ "name HG21", "name 1HG2", "pdbname HG21 CB", "pdbatomname 1HG2"
+ };
runTest("simple.pdb", selections);
}
TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
{
- static const char* const selections[] = { "cog of resnr 1 3", "res_cog of name CB and resnr 1 3",
+ static const char* const selections[] = { "cog of resnr 1 3",
+ "res_cog of name CB and resnr 1 3",
"whole_res_cog of name CB and resnr 1 3",
- "part_res_cog of x < 3", "dyn_res_cog of x < 3" };
+ "part_res_cog of x < 3",
+ "dyn_res_cog of x < 3" };
setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates | efTestPositionAtoms);
runTest("simple.gro", selections);
}
TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
{
static const char* const selections[] = {
- "name S2 plus name S1", "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
+ "name S2 plus name S1",
+ "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
"name S1 and y < 3 plus res_cog of x < 2.5"
};
setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates | efTestPositionAtoms
TEST_F(SelectionCollectionDataTest, HandlesFramesWithAtomSubsets)
{
const int index[] = { 0, 1, 2, 3, 4, 5, 9, 10, 11 };
- const char* const selections[] = { "resnr 1 4", "atomnr 1 2 5 11 and y > 2",
+ const char* const selections[] = { "resnr 1 4",
+ "atomnr 1 2 5 11 and y > 2",
"res_cog of atomnr 2 5 11" };
setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms);
ASSERT_NO_FATAL_FAILURE(runParser(selections));
TEST_F(SelectionCollectionDataTest, HandlesSelectionNames)
{
static const char* const selections[] = { "\"GroupSelection\" group \"GrpA\"",
- "\"DynamicSelection\" x < 5", "y < 3" };
+ "\"DynamicSelection\" x < 5",
+ "y < 3" };
setFlags(TestFlags() | efTestSelectionNames);
ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
runTest(10, selections);
TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelections)
{
- static const char* const selections[] = { "group \"GrpA\"", "GrpB", "1",
+ static const char* const selections[] = { "group \"GrpA\"",
+ "GrpB",
+ "1",
// These test that the name of the group is not too
// eagerly promoted to the name of the selection.
"group \"GrpB\" and resname RB",
TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelectionsDelayed)
{
- static const char* const selections[] = { "group \"GrpA\"", "GrpB", "1",
- "group \"GrpB\" and resname RB" };
+ static const char* const selections[] = {
+ "group \"GrpA\"", "GrpB", "1", "group \"GrpB\" and resname RB"
+ };
setFlags(TestFlags() | efTestSelectionNames);
ASSERT_NO_FATAL_FAILURE(runParser(selections));
ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
{
static const char* const selections[] = {
- "atomnr 1 to 5 and atomnr 2 to 7", "atomnr 1 to 5 or not atomnr 3 to 8",
+ "atomnr 1 to 5 and atomnr 2 to 7",
+ "atomnr 1 to 5 or not atomnr 3 to 8",
"not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
"atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
"x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
TEST_F(SelectionCollectionDataTest, HandlesEmptySelectionWithUnevaluatedExpressions)
{
- static const char* const selections[] = { "none and x > 2",
- "none and same resname as resnr 2" };
+ static const char* const selections[] = { "none and x > 2", "none and same resname as resnr 2" };
runTest("simple.gro", selections);
}
TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
{
- static const char* const selections[] = { "x > 2", "2 < x", "y > resnr", "resnr < 2.5",
- "2.5 > resnr" };
+ static const char* const selections[] = {
+ "x > 2", "2 < x", "y > resnr", "resnr < 2.5", "2.5 > resnr"
+ };
setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
runTest("simple.gro", selections);
}
TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
{
- static const char* const selections[] = { "value = x + y", "value <= 4", "index = resnr",
- "index < 3" };
+ static const char* const selections[] = {
+ "value = x + y", "value <= 4", "index = resnr", "index < 3"
+ };
setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
runTest("simple.gro", selections);
}
TEST_F(SelectionCollectionDataTest, HandlesPositionVariableInModifier)
{
- static const char* const selections[] = { "foo = cog of resnr 1", "cog of resnr 2 plus foo",
+ static const char* const selections[] = { "foo = cog of resnr 1",
+ "cog of resnr 2 plus foo",
"cog of resnr 3 plus foo" };
setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
runTest("simple.gro", selections);
TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
{
- static const char* const selections[] = { "constpos = [1.0, 2.5, 0.5]", "constpos",
+ static const char* const selections[] = { "constpos = [1.0, 2.5, 0.5]",
+ "constpos",
"within 2 of constpos" };
setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates | efTestPositionAtoms);
runTest("simple.gro", selections);
TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
{
- static const char* const selections[] = { "constint = 4", "constreal1 = 0.5", "constreal2 = 2.7",
- "resnr < constint", "x + constreal1 < constreal2" };
+ static const char* const selections[] = { "constint = 4",
+ "constreal1 = 0.5",
+ "constreal2 = 2.7",
+ "resnr < constint",
+ "x + constreal1 < constreal2" };
setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
runTest("simple.gro", selections);
}
TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
{
static const char* const selections[] = {
- "atomnr 1 to 5 and atomnr 2 to 7 and x < 2", "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
+ "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
+ "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
"atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
"atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
"atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
{
- static const char* const selections[] = { "unused1 = atomnr 1 to 3", "foo = atomnr 4 to 7",
- "atomnr 1 to 6 and foo", "unused2 = atomnr 3 to 5" };
+ static const char* const selections[] = { "unused1 = atomnr 1 to 3",
+ "foo = atomnr 4 to 7",
+ "atomnr 1 to 6 and foo",
+ "unused2 = atomnr 3 to 5" };
runTest(10, selections);
}
TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
{
static const char* const selections[] = { "foo = atomnr 4 to 7 and x < 2",
- "atomnr 1 to 5 and foo", "atomnr 3 to 7 and foo" };
+ "atomnr 1 to 5 and foo",
+ "atomnr 3 to 7 and foo" };
runTest(10, selections);
}
TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
{
- static const char* const selections[] = { "foo = atomnr 4 to 7 and x < 2",
- "atomnr 1 to 6 and foo", "within 1 of foo", "foo" };
+ static const char* const selections[] = {
+ "foo = atomnr 4 to 7 and x < 2", "atomnr 1 to 6 and foo", "within 1 of foo", "foo"
+ };
runTest(10, selections);
}
TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
{
static const char* const selections[] = { "foo = atomnr 1 to 8 and x < 10",
- "atomnr 1 to 5 and y < 10 and foo", "foo" };
+ "atomnr 1 to 5 and y < 10 and foo",
+ "foo" };
setFlags(TestFlags() | efTestEvaluation);
runTest("simple.gro", selections);
}
+/*******************************************************************
+ * Tests for copy validation.
+ *
+ * These tests ensure that copies of a SelectionCollection behave as the original while being
+ * independently evaluated.
+ */
+TEST_F(SelectionCollectionDataTest, CopiedSelectionWorksPreCompilation)
+{
+ static const char* const selections[] = {
+ "x > 2", "2 < x", "y > resnr", "resnr < 2.5", "2.5 > resnr"
+ };
+ setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
+ ASSERT_NO_FATAL_FAILURE(runParser(selections));
+ ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
+ std::vector<std::string> selNames;
+ for (const auto& sel : sel_)
+ {
+ selNames.emplace_back(sel.name());
+ }
+ // Swap copied selection with original and update selections, to reuse the testing machinery.
+ gmx::SelectionCollection sc2(sc_);
+ sc_ = sc2;
+ std::vector<gmx::Selection> sel2;
+ for (const std::string_view selName : selNames)
+ {
+ std::optional<gmx::Selection> maybeSel = sc_.selection(selName);
+ ASSERT_TRUE(maybeSel.has_value());
+ sel2.push_back(*maybeSel);
+ }
+ sel_ = std::move(sel2);
+
+ ASSERT_NO_FATAL_FAILURE(runCompiler());
+ ASSERT_NO_FATAL_FAILURE(runEvaluate());
+ ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
+}
+
+TEST_F(SelectionCollectionDataTest, CopiedSelectionWorksPostCompilation)
+{
+ static const char* const selections[] = {
+ "x > 2", "2 < x", "y > resnr", "resnr < 2.5", "2.5 > resnr"
+ };
+ setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
+ ASSERT_NO_FATAL_FAILURE(runParser(selections));
+ ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
+
+ ASSERT_NO_FATAL_FAILURE(runCompiler());
+ // Note the copy is made post-compilation.
+ std::vector<std::string> selNames;
+ for (const auto& sel : sel_)
+ {
+ selNames.emplace_back(sel.name());
+ }
+ gmx::SelectionCollection sc2(sc_);
+ sc_ = sc2;
+ std::vector<gmx::Selection> sel2;
+ for (const std::string_view selName : selNames)
+ {
+ std::optional<gmx::Selection> maybeSel = sc_.selection(selName);
+ ASSERT_TRUE(maybeSel.has_value());
+ sel2.push_back(*maybeSel);
+ }
+ sel_ = std::move(sel2);
+
+ ASSERT_NO_FATAL_FAILURE(runEvaluate());
+ ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
+}
+
+TEST_F(SelectionCollectionDataTest, CopiedSelectionsAreIndependent)
+{
+ static const char* const selections[] = {
+ "x > 2", "2 < x", "y > resnr", "resnr < 2.5", "2.5 > resnr"
+ };
+ setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
+ ASSERT_NO_FATAL_FAILURE(runParser(selections));
+ ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
+
+ ASSERT_NO_FATAL_FAILURE(runCompiler());
+ // Check that copy evaluation does not conflict with original.
+ gmx::SelectionCollection sc2(sc_);
+ ASSERT_NO_THROW_GMX(sc2.evaluate(topManager_.frame(), nullptr));
+
+ ASSERT_NO_FATAL_FAILURE(runEvaluate());
+ ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
+}
+
+TEST_F(SelectionCollectionDataTest, CopiedSelectionWithIndexPostCompilation)
+{
+ static const char* const selections[] = { "group \"GrpA\"",
+ "GrpB",
+ "1",
+ "group \"GrpB\" and resname RB",
+ "group \"GrpA\" permute 5 3 2 1 4",
+ "group \"GrpA\" plus group \"GrpB\"",
+ "res_cog of group \"GrpA\"" };
+ setFlags(TestFlags() | efTestSelectionNames);
+ ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
+ ASSERT_NO_FATAL_FAILURE(runParser(selections));
+ ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
+ ASSERT_NO_FATAL_FAILURE(runCompiler());
+ std::vector<std::string> selNames;
+ for (const auto& sel : sel_)
+ {
+ selNames.emplace_back(sel.name());
+ }
+ gmx::SelectionCollection sc2(sc_);
+ sc_ = sc2;
+ std::vector<gmx::Selection> sel2;
+ for (const std::string_view selName : selNames)
+ {
+ std::optional<gmx::Selection> maybeSel = sc_.selection(selName);
+ ASSERT_TRUE(maybeSel.has_value());
+ sel2.push_back(*maybeSel);
+ }
+ sel_ = std::move(sel2);
+ checkCompiled();
+}
} // namespace
GMX_RELEASE_ASSERT(mtop_ == nullptr, "Topology initialized more than once");
mtop_ = std::make_unique<gmx_mtop_t>();
- readConfAndTopology(gmx::test::TestFileManager::getInputFilePath(filename).c_str(), &fullTopology,
- mtop_.get(), &pbcType, frame_ != nullptr ? &xtop : nullptr, nullptr, box);
+ readConfAndTopology(gmx::test::TestFileManager::getInputFilePath(filename).c_str(),
+ &fullTopology,
+ mtop_.get(),
+ &pbcType,
+ frame_ != nullptr ? &xtop : nullptr,
+ nullptr,
+ box);
if (frame_ != nullptr)
{
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+add_library(simd INTERFACE)
file(GLOB SIMD_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${SIMD_SOURCES} PARENT_SCOPE)
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(simd PUBLIC
+target_include_directories(simd INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(simd PUBLIC
+target_link_libraries(simd INTERFACE
+ legacy_api
+ )
+
+# TODO: when simd is an OBJECT target
+#target_link_libraries(simd PUBLIC legacy_api)
+#target_link_libraries(simd PRIVATE common)
+
+# Module dependencies
+# simd interfaces convey transitive dependence on these modules.
+#target_link_libraries(simd PUBLIC
+target_link_libraries(simd INTERFACE
+ utility
+ )
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_SIMD_IMPL_ARM_NEON_H
-#define GMX_SIMD_IMPL_ARM_NEON_H
-
-#include "impl_arm_neon_definitions.h"
-#include "impl_arm_neon_general.h"
-// Arm/Neon cannot do double precision SIMD4
-#include "impl_arm_neon_simd4_float.h"
-// Arm/Neon cannot do double precision SIMD
-#include "impl_arm_neon_simd_float.h"
-// Arm/Neon cannot do double precision SIMD utilities
-#include "impl_arm_neon_util_float.h"
-
-#endif // GMX_SIMD_IMPL_ARM_NEON_H
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2017,2018,2019,2020, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_SIMD_IMPL_ARM_NEON_DEFINITIONS_H
-#define GMX_SIMD_IMPL_ARM_NEON_DEFINITIONS_H
-
-#define GMX_SIMD 1
-#define GMX_SIMD_HAVE_FLOAT 1
-#define GMX_SIMD_HAVE_DOUBLE 0
-#define GMX_SIMD_HAVE_LOADU 1
-#define GMX_SIMD_HAVE_STOREU 1
-#define GMX_SIMD_HAVE_LOGICAL 1
-#define GMX_SIMD_HAVE_FMA 1
-#define GMX_SIMD_HAVE_FINT32_EXTRACT 1
-#define GMX_SIMD_HAVE_FINT32_LOGICAL 1
-#define GMX_SIMD_HAVE_FINT32_ARITHMETICS 1
-#define GMX_SIMD_HAVE_DINT32_EXTRACT 0
-#define GMX_SIMD_HAVE_DINT32_LOGICAL 0
-#define GMX_SIMD_HAVE_DINT32_ARITHMETICS 0
-#define GMX_SIMD_HAVE_NATIVE_COPYSIGN_FLOAT 0
-#define GMX_SIMD_HAVE_NATIVE_RSQRT_ITER_FLOAT \
- 0 // Although there is support, it is disabled in GROMACS, because rsqrtIter does not work correctly for inputs near MAX_FLOAT
-#define GMX_SIMD_HAVE_NATIVE_RCP_ITER_FLOAT 1
-#define GMX_SIMD_HAVE_NATIVE_LOG_FLOAT 0
-#define GMX_SIMD_HAVE_NATIVE_EXP2_FLOAT 0
-#define GMX_SIMD_HAVE_NATIVE_EXP_FLOAT 0
-#define GMX_SIMD_HAVE_NATIVE_COPYSIGN_DOUBLE 0
-#define GMX_SIMD_HAVE_NATIVE_RSQRT_ITER_DOUBLE 0
-#define GMX_SIMD_HAVE_NATIVE_RCP_ITER_DOUBLE 0
-#define GMX_SIMD_HAVE_NATIVE_LOG_DOUBLE 0
-#define GMX_SIMD_HAVE_NATIVE_EXP2_DOUBLE 0
-#define GMX_SIMD_HAVE_NATIVE_EXP_DOUBLE 0
-#define GMX_SIMD_HAVE_GATHER_LOADU_BYSIMDINT_TRANSPOSE_FLOAT 1
-#define GMX_SIMD_HAVE_GATHER_LOADU_BYSIMDINT_TRANSPOSE_DOUBLE 0
-#define GMX_SIMD_HAVE_HSIMD_UTIL_FLOAT 0 // No need for half-simd, width is 4
-#define GMX_SIMD_HAVE_HSIMD_UTIL_DOUBLE 0
-
-#define GMX_SIMD4_HAVE_FLOAT 1
-#define GMX_SIMD4_HAVE_DOUBLE 0
-
-// Implementation details
-#define GMX_SIMD_FLOAT_WIDTH 4
-#undef GMX_SIMD_DOUBLE_WIDTH
-#define GMX_SIMD_FINT32_WIDTH 4
-#undef GMX_SIMD_DINT32_WIDTH
-#define GMX_SIMD4_WIDTH 4
-#define GMX_SIMD_ALIGNMENT 16 // Bytes (4*single)
-#define GMX_SIMD_RSQRT_BITS 8
-#define GMX_SIMD_RCP_BITS 8
-
-#endif // GMX_SIMD_IMPL_ARM_NEON_DEFINITIONS_H
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2019, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifndef GMX_SIMD_IMPL_ARM_NEON_SIMD4_FLOAT_H
-#define GMX_SIMD_IMPL_ARM_NEON_SIMD4_FLOAT_H
-
-#include "config.h"
-
-#include <cassert>
-#include <cstddef>
-
-#include <arm_neon.h>
-
-namespace gmx
-{
-
-class Simd4Float
-{
-public:
- Simd4Float() {}
-
- Simd4Float(float f) : simdInternal_(vdupq_n_f32(f)) {}
-
- // Internal utility constructor to simplify return statements
- Simd4Float(float32x4_t simd) : simdInternal_(simd) {}
-
- float32x4_t simdInternal_;
-};
-
-class Simd4FBool
-{
-public:
- Simd4FBool() {}
-
- //! \brief Construct from scalar bool
- Simd4FBool(bool b) : simdInternal_(vdupq_n_u32(b ? 0xFFFFFFFF : 0)) {}
-
- // Internal utility constructor to simplify return statements
- Simd4FBool(uint32x4_t simd) : simdInternal_(simd) {}
-
- uint32x4_t simdInternal_;
-};
-
-static inline Simd4Float gmx_simdcall load4(const float* m)
-{
- assert(size_t(m) % 16 == 0);
- return { vld1q_f32(m) };
-}
-
-static inline void gmx_simdcall store4(float* m, Simd4Float a)
-{
- assert(size_t(m) % 16 == 0);
- vst1q_f32(m, a.simdInternal_);
-}
-
-static inline Simd4Float gmx_simdcall load4U(const float* m)
-{
- return { vld1q_f32(m) };
-}
-
-static inline void gmx_simdcall store4U(float* m, Simd4Float a)
-{
- vst1q_f32(m, a.simdInternal_);
-}
-
-static inline Simd4Float gmx_simdcall simd4SetZeroF()
-{
- return { vdupq_n_f32(0.0F) };
-}
-
-static inline Simd4Float gmx_simdcall operator&(Simd4Float a, Simd4Float b)
-{
- return { vreinterpretq_f32_s32(vandq_s32(vreinterpretq_s32_f32(a.simdInternal_),
- vreinterpretq_s32_f32(b.simdInternal_))) };
-}
-
-static inline Simd4Float gmx_simdcall andNot(Simd4Float a, Simd4Float b)
-{
- return { vreinterpretq_f32_s32(vbicq_s32(vreinterpretq_s32_f32(b.simdInternal_),
- vreinterpretq_s32_f32(a.simdInternal_))) };
-}
-
-static inline Simd4Float gmx_simdcall operator|(Simd4Float a, Simd4Float b)
-{
- return { vreinterpretq_f32_s32(vorrq_s32(vreinterpretq_s32_f32(a.simdInternal_),
- vreinterpretq_s32_f32(b.simdInternal_))) };
-}
-
-static inline Simd4Float gmx_simdcall operator^(Simd4Float a, Simd4Float b)
-{
- return { vreinterpretq_f32_s32(veorq_s32(vreinterpretq_s32_f32(a.simdInternal_),
- vreinterpretq_s32_f32(b.simdInternal_))) };
-}
-
-static inline Simd4Float gmx_simdcall operator+(Simd4Float a, Simd4Float b)
-{
- return { vaddq_f32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall operator-(Simd4Float a, Simd4Float b)
-{
- return { vsubq_f32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall operator-(Simd4Float x)
-{
- return { vnegq_f32(x.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall operator*(Simd4Float a, Simd4Float b)
-{
- return { vmulq_f32(a.simdInternal_, b.simdInternal_) };
-}
-
-// Override for Neon-Asimd
-#if GMX_SIMD_ARM_NEON
-static inline Simd4Float gmx_simdcall fma(Simd4Float a, Simd4Float b, Simd4Float c)
-{
- return {
-# ifdef __ARM_FEATURE_FMA
- vfmaq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_)
-# else
- vmlaq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_)
-# endif
- };
-}
-
-static inline Simd4Float gmx_simdcall fms(Simd4Float a, Simd4Float b, Simd4Float c)
-{
- return {
-# ifdef __ARM_FEATURE_FMA
- vnegq_f32(vfmsq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_))
-# else
- vnegq_f32(vmlsq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_))
-# endif
- };
-}
-
-static inline Simd4Float gmx_simdcall fnma(Simd4Float a, Simd4Float b, Simd4Float c)
-{
- return {
-# ifdef __ARM_FEATURE_FMA
- vfmsq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_)
-# else
- vmlsq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_)
-# endif
- };
-}
-
-static inline Simd4Float gmx_simdcall fnms(Simd4Float a, Simd4Float b, Simd4Float c)
-{
- return {
-# ifdef __ARM_FEATURE_FMA
- vnegq_f32(vfmaq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_))
-# else
- vnegq_f32(vmlaq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_))
-# endif
- };
-}
-#endif
-
-static inline Simd4Float gmx_simdcall rsqrt(Simd4Float x)
-{
- return { vrsqrteq_f32(x.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall abs(Simd4Float x)
-{
- return { vabsq_f32(x.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall max(Simd4Float a, Simd4Float b)
-{
- return { vmaxq_f32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall min(Simd4Float a, Simd4Float b)
-{
- return { vminq_f32(a.simdInternal_, b.simdInternal_) };
-}
-
-// Override for Neon-Asimd
-#if GMX_SIMD_ARM_NEON
-static inline Simd4Float gmx_simdcall round(Simd4Float x)
-{
- // Convert x to nearest integer
- float32x4_t signBitOfX = vreinterpretq_f32_u32(
- vandq_u32(vdupq_n_u32(0x80000000), vreinterpretq_u32_f32(x.simdInternal_)));
- float32x4_t half = vdupq_n_f32(0.5F);
- float32x4_t corr = vreinterpretq_f32_u32(
- vorrq_u32(vreinterpretq_u32_f32(half), vreinterpretq_u32_f32(signBitOfX)));
-
- int32x4_t integerX = vcvtq_s32_f32(vaddq_f32(x.simdInternal_, corr));
-
- // Convert back to float
-
- return { vcvtq_f32_s32(integerX) };
-}
-
-static inline Simd4Float gmx_simdcall trunc(Simd4Float x)
-{
- return { vcvtq_f32_s32(vcvtq_s32_f32(x.simdInternal_)) };
-}
-#endif
-
-static inline void gmx_simdcall transpose(Simd4Float* v0, Simd4Float* v1, Simd4Float* v2, Simd4Float* v3)
-{
- float32x4x2_t t0 = vuzpq_f32(v0->simdInternal_, v2->simdInternal_);
- float32x4x2_t t1 = vuzpq_f32(v1->simdInternal_, v3->simdInternal_);
- float32x4x2_t t2 = vtrnq_f32(t0.val[0], t1.val[0]);
- float32x4x2_t t3 = vtrnq_f32(t0.val[1], t1.val[1]);
- v0->simdInternal_ = t2.val[0];
- v1->simdInternal_ = t3.val[0];
- v2->simdInternal_ = t2.val[1];
- v3->simdInternal_ = t3.val[1];
-}
-
-static inline Simd4FBool gmx_simdcall operator==(Simd4Float a, Simd4Float b)
-{
- return { vceqq_f32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4FBool gmx_simdcall operator!=(Simd4Float a, Simd4Float b)
-{
- return { vmvnq_u32(vceqq_f32(a.simdInternal_, b.simdInternal_)) };
-}
-
-static inline Simd4FBool gmx_simdcall operator<(Simd4Float a, Simd4Float b)
-{
- return { vcltq_f32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4FBool gmx_simdcall operator<=(Simd4Float a, Simd4Float b)
-{
- return { vcleq_f32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4FBool gmx_simdcall operator&&(Simd4FBool a, Simd4FBool b)
-{
- return { vandq_u32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4FBool gmx_simdcall operator||(Simd4FBool a, Simd4FBool b)
-{
- return { vorrq_u32(a.simdInternal_, b.simdInternal_) };
-}
-
-// Override for Neon-Asimd
-#if GMX_SIMD_ARM_NEON
-static inline bool gmx_simdcall anyTrue(Simd4FBool a)
-{
- uint32x4_t x = a.simdInternal_;
- uint32x4_t y = vextq_u32(x, x, 2);
-
- x = vorrq_u32(x, y);
- y = vextq_u32(x, x, 1);
- x = vorrq_u32(x, y);
- return (vgetq_lane_u32(x, 0) != 0);
-}
-#endif
-
-static inline Simd4Float gmx_simdcall selectByMask(Simd4Float a, Simd4FBool m)
-{
- return { vreinterpretq_f32_u32(vandq_u32(vreinterpretq_u32_f32(a.simdInternal_), m.simdInternal_)) };
-}
-
-static inline Simd4Float gmx_simdcall selectByNotMask(Simd4Float a, Simd4FBool m)
-{
- return { vreinterpretq_f32_u32(vbicq_u32(vreinterpretq_u32_f32(a.simdInternal_), m.simdInternal_)) };
-}
-
-static inline Simd4Float gmx_simdcall blend(Simd4Float a, Simd4Float b, Simd4FBool sel)
-{
- return { vbslq_f32(sel.simdInternal_, b.simdInternal_, a.simdInternal_) };
-}
-
-// Override for Neon-Asimd
-#if GMX_SIMD_ARM_NEON
-static inline float gmx_simdcall reduce(Simd4Float a)
-{
- float32x4_t x = a.simdInternal_;
- float32x4_t y = vextq_f32(x, x, 2);
-
- x = vaddq_f32(x, y);
- y = vextq_f32(x, x, 1);
- x = vaddq_f32(x, y);
- return vgetq_lane_f32(x, 0);
-}
-
-static inline float gmx_simdcall dotProduct(Simd4Float a, Simd4Float b)
-{
- Simd4Float c;
-
- c = a * b;
- /* set 4th element to 0, then add all of them */
- c.simdInternal_ = vsetq_lane_f32(0.0F, c.simdInternal_, 3);
- return reduce(c);
-}
-#endif
-
-} // namespace gmx
-
-#endif // GMX_SIMD_IMPL_ARM_NEON_SIMD4_FLOAT_H
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2016,2017,2019,2020, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifndef GMX_SIMD_IMPL_ARM_NEON_SIMD_FLOAT_H
-#define GMX_SIMD_IMPL_ARM_NEON_SIMD_FLOAT_H
-
-#include "config.h"
-
-#include <cassert>
-#include <cstddef>
-#include <cstdint>
-
-#include <arm_neon.h>
-
-#include "gromacs/math/utilities.h"
-
-namespace gmx
-{
-
-class SimdFloat
-{
-public:
- SimdFloat() {}
-
- SimdFloat(float f) : simdInternal_(vdupq_n_f32(f)) {}
-
- // Internal utility constructor to simplify return statements
- SimdFloat(float32x4_t simd) : simdInternal_(simd) {}
-
- float32x4_t simdInternal_;
-};
-
-class SimdFInt32
-{
-public:
- SimdFInt32() {}
-
- SimdFInt32(std::int32_t i) : simdInternal_(vdupq_n_s32(i)) {}
-
- // Internal utility constructor to simplify return statements
- SimdFInt32(int32x4_t simd) : simdInternal_(simd) {}
-
- int32x4_t simdInternal_;
-};
-
-class SimdFBool
-{
-public:
- SimdFBool() {}
-
- SimdFBool(bool b) : simdInternal_(vdupq_n_u32(b ? 0xFFFFFFFF : 0)) {}
-
- // Internal utility constructor to simplify return statements
- SimdFBool(uint32x4_t simd) : simdInternal_(simd) {}
-
- uint32x4_t simdInternal_;
-};
-
-class SimdFIBool
-{
-public:
- SimdFIBool() {}
-
- SimdFIBool(bool b) : simdInternal_(vdupq_n_u32(b ? 0xFFFFFFFF : 0)) {}
-
- // Internal utility constructor to simplify return statements
- SimdFIBool(uint32x4_t simd) : simdInternal_(simd) {}
-
- uint32x4_t simdInternal_;
-};
-
-static inline SimdFloat gmx_simdcall simdLoad(const float* m, SimdFloatTag = {})
-{
- assert(std::size_t(m) % 16 == 0);
- return { vld1q_f32(m) };
-}
-
-static inline void gmx_simdcall store(float* m, SimdFloat a)
-{
- assert(std::size_t(m) % 16 == 0);
- vst1q_f32(m, a.simdInternal_);
-}
-
-static inline SimdFloat gmx_simdcall simdLoadU(const float* m, SimdFloatTag = {})
-{
- return { vld1q_f32(m) };
-}
-
-static inline void gmx_simdcall storeU(float* m, SimdFloat a)
-{
- vst1q_f32(m, a.simdInternal_);
-}
-
-static inline SimdFloat gmx_simdcall setZeroF()
-{
- return { vdupq_n_f32(0.0F) };
-}
-
-static inline SimdFInt32 gmx_simdcall simdLoad(const std::int32_t* m, SimdFInt32Tag)
-{
- assert(std::size_t(m) % 16 == 0);
- return { vld1q_s32(m) };
-}
-
-static inline void gmx_simdcall store(std::int32_t* m, SimdFInt32 a)
-{
- assert(std::size_t(m) % 16 == 0);
- vst1q_s32(m, a.simdInternal_);
-}
-
-static inline SimdFInt32 gmx_simdcall simdLoadU(const std::int32_t* m, SimdFInt32Tag)
-{
- return { vld1q_s32(m) };
-}
-
-static inline void gmx_simdcall storeU(std::int32_t* m, SimdFInt32 a)
-{
- vst1q_s32(m, a.simdInternal_);
-}
-
-static inline SimdFInt32 gmx_simdcall setZeroFI()
-{
- return { vdupq_n_s32(0) };
-}
-
-template<int index>
-gmx_simdcall static inline std::int32_t extract(SimdFInt32 a)
-{
- return vgetq_lane_s32(a.simdInternal_, index);
-}
-
-static inline SimdFloat gmx_simdcall operator&(SimdFloat a, SimdFloat b)
-{
- return { vreinterpretq_f32_s32(vandq_s32(vreinterpretq_s32_f32(a.simdInternal_),
- vreinterpretq_s32_f32(b.simdInternal_))) };
-}
-
-static inline SimdFloat gmx_simdcall andNot(SimdFloat a, SimdFloat b)
-{
- return { vreinterpretq_f32_s32(vbicq_s32(vreinterpretq_s32_f32(b.simdInternal_),
- vreinterpretq_s32_f32(a.simdInternal_))) };
-}
-
-static inline SimdFloat gmx_simdcall operator|(SimdFloat a, SimdFloat b)
-{
- return { vreinterpretq_f32_s32(vorrq_s32(vreinterpretq_s32_f32(a.simdInternal_),
- vreinterpretq_s32_f32(b.simdInternal_))) };
-}
-
-static inline SimdFloat gmx_simdcall operator^(SimdFloat a, SimdFloat b)
-{
- return { vreinterpretq_f32_s32(veorq_s32(vreinterpretq_s32_f32(a.simdInternal_),
- vreinterpretq_s32_f32(b.simdInternal_))) };
-}
-
-static inline SimdFloat gmx_simdcall operator+(SimdFloat a, SimdFloat b)
-{
- return { vaddq_f32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall operator-(SimdFloat a, SimdFloat b)
-{
- return { vsubq_f32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall operator-(SimdFloat x)
-{
- return { vnegq_f32(x.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall operator*(SimdFloat a, SimdFloat b)
-{
- return { vmulq_f32(a.simdInternal_, b.simdInternal_) };
-}
-
-// Override for Neon-Asimd
-#if GMX_SIMD_ARM_NEON
-static inline SimdFloat gmx_simdcall fma(SimdFloat a, SimdFloat b, SimdFloat c)
-{
- return {
-# ifdef __ARM_FEATURE_FMA
- vfmaq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_)
-# else
- vmlaq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_)
-# endif
- };
-}
-
-static inline SimdFloat gmx_simdcall fms(SimdFloat a, SimdFloat b, SimdFloat c)
-{
- return {
-# ifdef __ARM_FEATURE_FMA
- vnegq_f32(vfmsq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_))
-# else
- vnegq_f32(vmlsq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_))
-# endif
- };
-}
-
-static inline SimdFloat gmx_simdcall fnma(SimdFloat a, SimdFloat b, SimdFloat c)
-{
- return {
-# ifdef __ARM_FEATURE_FMA
- vfmsq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_)
-# else
- vmlsq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_)
-# endif
- };
-}
-
-static inline SimdFloat gmx_simdcall fnms(SimdFloat a, SimdFloat b, SimdFloat c)
-{
- return {
-# ifdef __ARM_FEATURE_FMA
- vnegq_f32(vfmaq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_))
-# else
- vnegq_f32(vmlaq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_))
-# endif
- };
-}
-#endif
-
-static inline SimdFloat gmx_simdcall rsqrt(SimdFloat x)
-{
- return { vrsqrteq_f32(x.simdInternal_) };
-}
-
-// The SIMD implementation seems to overflow when we square lu for
-// values close to FLOAT_MAX, so we fall back on the version in
-// simd_math.h, which is probably slightly slower.
-#if GMX_SIMD_HAVE_NATIVE_RSQRT_ITER_FLOAT
-static inline SimdFloat gmx_simdcall rsqrtIter(SimdFloat lu, SimdFloat x)
-{
- return { vmulq_f32(lu.simdInternal_,
- vrsqrtsq_f32(vmulq_f32(lu.simdInternal_, lu.simdInternal_), x.simdInternal_)) };
-}
-#endif
-
-static inline SimdFloat gmx_simdcall rcp(SimdFloat x)
-{
- return { vrecpeq_f32(x.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall rcpIter(SimdFloat lu, SimdFloat x)
-{
- return { vmulq_f32(lu.simdInternal_, vrecpsq_f32(lu.simdInternal_, x.simdInternal_)) };
-}
-
-static inline SimdFloat gmx_simdcall maskAdd(SimdFloat a, SimdFloat b, SimdFBool m)
-{
- b.simdInternal_ =
- vreinterpretq_f32_u32(vandq_u32(vreinterpretq_u32_f32(b.simdInternal_), m.simdInternal_));
-
- return { vaddq_f32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall maskzMul(SimdFloat a, SimdFloat b, SimdFBool m)
-{
- SimdFloat tmp = a * b;
-
- return { vreinterpretq_f32_u32(vandq_u32(vreinterpretq_u32_f32(tmp.simdInternal_), m.simdInternal_)) };
-}
-
-static inline SimdFloat gmx_simdcall maskzFma(SimdFloat a, SimdFloat b, SimdFloat c, SimdFBool m)
-{
-#ifdef __ARM_FEATURE_FMA
- float32x4_t tmp = vfmaq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_);
-#else
- float32x4_t tmp = vmlaq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_);
-#endif
-
- return { vreinterpretq_f32_u32(vandq_u32(vreinterpretq_u32_f32(tmp), m.simdInternal_)) };
-}
-
-static inline SimdFloat gmx_simdcall maskzRsqrt(SimdFloat x, SimdFBool m)
-{
- // The result will always be correct since we mask the result with m, but
- // for debug builds we also want to make sure not to generate FP exceptions
-#ifndef NDEBUG
- x.simdInternal_ = vbslq_f32(m.simdInternal_, x.simdInternal_, vdupq_n_f32(1.0F));
-#endif
- return { vreinterpretq_f32_u32(
- vandq_u32(vreinterpretq_u32_f32(vrsqrteq_f32(x.simdInternal_)), m.simdInternal_)) };
-}
-
-static inline SimdFloat gmx_simdcall maskzRcp(SimdFloat x, SimdFBool m)
-{
- // The result will always be correct since we mask the result with m, but
- // for debug builds we also want to make sure not to generate FP exceptions
-#ifndef NDEBUG
- x.simdInternal_ = vbslq_f32(m.simdInternal_, x.simdInternal_, vdupq_n_f32(1.0F));
-#endif
- return { vreinterpretq_f32_u32(
- vandq_u32(vreinterpretq_u32_f32(vrecpeq_f32(x.simdInternal_)), m.simdInternal_)) };
-}
-
-static inline SimdFloat gmx_simdcall abs(SimdFloat x)
-{
- return { vabsq_f32(x.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall max(SimdFloat a, SimdFloat b)
-{
- return { vmaxq_f32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall min(SimdFloat a, SimdFloat b)
-{
- return { vminq_f32(a.simdInternal_, b.simdInternal_) };
-}
-
-// Round and trunc operations are defined at the end of this file, since they
-// need to use float-to-integer and integer-to-float conversions.
-
-template<MathOptimization opt = MathOptimization::Safe>
-static inline SimdFloat gmx_simdcall frexp(SimdFloat value, SimdFInt32* exponent)
-{
- const int32x4_t exponentMask = vdupq_n_s32(0x7F800000);
- const int32x4_t mantissaMask = vdupq_n_s32(0x807FFFFF);
- const int32x4_t exponentBias = vdupq_n_s32(126); // add 1 to make our definition identical to frexp()
- const float32x4_t half = vdupq_n_f32(0.5F);
- int32x4_t iExponent;
-
- iExponent = vandq_s32(vreinterpretq_s32_f32(value.simdInternal_), exponentMask);
- iExponent = vsubq_s32(vshrq_n_s32(iExponent, 23), exponentBias);
-
- float32x4_t result = vreinterpretq_f32_s32(
- vorrq_s32(vandq_s32(vreinterpretq_s32_f32(value.simdInternal_), mantissaMask),
- vreinterpretq_s32_f32(half)));
-
- if (opt == MathOptimization::Safe)
- {
- uint32x4_t valueIsZero = vceqq_f32(value.simdInternal_, vdupq_n_f32(0.0F));
- iExponent = vbicq_s32(iExponent, vreinterpretq_s32_u32(valueIsZero));
- result = vbslq_f32(valueIsZero, value.simdInternal_, result);
- }
-
- exponent->simdInternal_ = iExponent;
- return { result };
-}
-
-template<MathOptimization opt = MathOptimization::Safe>
-static inline SimdFloat gmx_simdcall ldexp(SimdFloat value, SimdFInt32 exponent)
-{
- const int32x4_t exponentBias = vdupq_n_s32(127);
- int32x4_t iExponent = vaddq_s32(exponent.simdInternal_, exponentBias);
-
- if (opt == MathOptimization::Safe)
- {
- // Make sure biased argument is not negative
- iExponent = vmaxq_s32(iExponent, vdupq_n_s32(0));
- }
-
- iExponent = vshlq_n_s32(iExponent, 23);
-
- return { vmulq_f32(value.simdInternal_, vreinterpretq_f32_s32(iExponent)) };
-}
-
-// Override for Neon-Asimd
-#if GMX_SIMD_ARM_NEON
-static inline float gmx_simdcall reduce(SimdFloat a)
-{
- float32x4_t x = a.simdInternal_;
- float32x4_t y = vextq_f32(x, x, 2);
-
- x = vaddq_f32(x, y);
- y = vextq_f32(x, x, 1);
- x = vaddq_f32(x, y);
- return vgetq_lane_f32(x, 0);
-}
-#endif
-
-static inline SimdFBool gmx_simdcall operator==(SimdFloat a, SimdFloat b)
-{
- return { vceqq_f32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFBool gmx_simdcall operator!=(SimdFloat a, SimdFloat b)
-{
- return { vmvnq_u32(vceqq_f32(a.simdInternal_, b.simdInternal_)) };
-}
-
-static inline SimdFBool gmx_simdcall operator<(SimdFloat a, SimdFloat b)
-{
- return { vcltq_f32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFBool gmx_simdcall operator<=(SimdFloat a, SimdFloat b)
-{
- return { vcleq_f32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFBool gmx_simdcall testBits(SimdFloat a)
-{
- uint32x4_t tmp = vreinterpretq_u32_f32(a.simdInternal_);
-
- return { vtstq_u32(tmp, tmp) };
-}
-
-static inline SimdFBool gmx_simdcall operator&&(SimdFBool a, SimdFBool b)
-{
-
- return { vandq_u32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFBool gmx_simdcall operator||(SimdFBool a, SimdFBool b)
-{
- return { vorrq_u32(a.simdInternal_, b.simdInternal_) };
-}
-
-// Override for Neon-Asimd
-#if GMX_SIMD_ARM_NEON
-static inline bool gmx_simdcall anyTrue(SimdFBool a)
-{
- uint32x4_t x = a.simdInternal_;
- uint32x4_t y = vextq_u32(x, x, 2);
-
- x = vorrq_u32(x, y);
- y = vextq_u32(x, x, 1);
- x = vorrq_u32(x, y);
- return (vgetq_lane_u32(x, 0) != 0);
-}
-#endif
-
-static inline SimdFloat gmx_simdcall selectByMask(SimdFloat a, SimdFBool m)
-{
- return { vreinterpretq_f32_u32(vandq_u32(vreinterpretq_u32_f32(a.simdInternal_), m.simdInternal_)) };
-}
-
-static inline SimdFloat gmx_simdcall selectByNotMask(SimdFloat a, SimdFBool m)
-{
- return { vreinterpretq_f32_u32(vbicq_u32(vreinterpretq_u32_f32(a.simdInternal_), m.simdInternal_)) };
-}
-
-static inline SimdFloat gmx_simdcall blend(SimdFloat a, SimdFloat b, SimdFBool sel)
-{
- return { vbslq_f32(sel.simdInternal_, b.simdInternal_, a.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall operator&(SimdFInt32 a, SimdFInt32 b)
-{
- return { vandq_s32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall andNot(SimdFInt32 a, SimdFInt32 b)
-{
- return { vbicq_s32(b.simdInternal_, a.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall operator|(SimdFInt32 a, SimdFInt32 b)
-{
- return { vorrq_s32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall operator^(SimdFInt32 a, SimdFInt32 b)
-{
- return { veorq_s32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall operator+(SimdFInt32 a, SimdFInt32 b)
-{
- return { vaddq_s32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall operator-(SimdFInt32 a, SimdFInt32 b)
-{
- return { vsubq_s32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall operator*(SimdFInt32 a, SimdFInt32 b)
-{
- return { vmulq_s32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFIBool gmx_simdcall operator==(SimdFInt32 a, SimdFInt32 b)
-{
- return { vceqq_s32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFIBool gmx_simdcall testBits(SimdFInt32 a)
-{
- return { vtstq_s32(a.simdInternal_, a.simdInternal_) };
-}
-
-static inline SimdFIBool gmx_simdcall operator<(SimdFInt32 a, SimdFInt32 b)
-{
- return { vcltq_s32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFIBool gmx_simdcall operator&&(SimdFIBool a, SimdFIBool b)
-{
- return { vandq_u32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFIBool gmx_simdcall operator||(SimdFIBool a, SimdFIBool b)
-{
- return { vorrq_u32(a.simdInternal_, b.simdInternal_) };
-}
-
-// Override for Neon-Asimd
-#if GMX_SIMD_ARM_NEON
-static inline bool gmx_simdcall anyTrue(SimdFIBool a)
-{
- uint32x4_t x = a.simdInternal_;
- uint32x4_t y = vextq_u32(x, x, 2);
-
- x = vorrq_u32(x, y);
- y = vextq_u32(x, x, 1);
- x = vorrq_u32(x, y);
- return (vgetq_lane_u32(x, 0) != 0);
-}
-#endif
-
-static inline SimdFInt32 gmx_simdcall selectByMask(SimdFInt32 a, SimdFIBool m)
-{
- return { vandq_s32(a.simdInternal_, vreinterpretq_s32_u32(m.simdInternal_)) };
-}
-
-static inline SimdFInt32 gmx_simdcall selectByNotMask(SimdFInt32 a, SimdFIBool m)
-{
- return { vbicq_s32(a.simdInternal_, vreinterpretq_s32_u32(m.simdInternal_)) };
-}
-
-static inline SimdFInt32 gmx_simdcall blend(SimdFInt32 a, SimdFInt32 b, SimdFIBool sel)
-{
- return { vbslq_s32(sel.simdInternal_, b.simdInternal_, a.simdInternal_) };
-}
-
-// Override for Neon-Asimd
-#if GMX_SIMD_ARM_NEON
-static inline SimdFInt32 gmx_simdcall cvtR2I(SimdFloat a)
-{
- float32x4_t signBitOfA = vreinterpretq_f32_u32(
- vandq_u32(vdupq_n_u32(0x80000000), vreinterpretq_u32_f32(a.simdInternal_)));
- float32x4_t half = vdupq_n_f32(0.5F);
- float32x4_t corr = vreinterpretq_f32_u32(
- vorrq_u32(vreinterpretq_u32_f32(half), vreinterpretq_u32_f32(signBitOfA)));
-
- return { vcvtq_s32_f32(vaddq_f32(a.simdInternal_, corr)) };
-}
-#endif
-
-static inline SimdFInt32 gmx_simdcall cvttR2I(SimdFloat a)
-{
- return { vcvtq_s32_f32(a.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall cvtI2R(SimdFInt32 a)
-{
- return { vcvtq_f32_s32(a.simdInternal_) };
-}
-
-static inline SimdFIBool gmx_simdcall cvtB2IB(SimdFBool a)
-{
- return { a.simdInternal_ };
-}
-
-static inline SimdFBool gmx_simdcall cvtIB2B(SimdFIBool a)
-{
- return { a.simdInternal_ };
-}
-
-// Override for Neon-Asimd
-#if GMX_SIMD_ARM_NEON
-static inline SimdFloat gmx_simdcall round(SimdFloat x)
-{
- return cvtI2R(cvtR2I(x));
-}
-
-static inline SimdFloat gmx_simdcall trunc(SimdFloat x)
-{
- return cvtI2R(cvttR2I(x));
-}
-#endif
-
-} // namespace gmx
-
-#endif // GMX_SIMD_IMPL_ARM_NEON_SIMD_FLOAT_H
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifndef GMX_SIMD_IMPL_ARM_NEON_UTIL_FLOAT_H
-#define GMX_SIMD_IMPL_ARM_NEON_UTIL_FLOAT_H
-
-#include "config.h"
-
-#include <cassert>
-#include <cstddef>
-#include <cstdint>
-
-#include <arm_neon.h>
-
-#include "gromacs/utility/basedefinitions.h"
-
-#include "impl_arm_neon_simd_float.h"
-
-
-namespace gmx
-{
-
-template<int align>
-static inline void gmx_simdcall gatherLoadTranspose(const float* base,
- const std::int32_t offset[],
- SimdFloat* v0,
- SimdFloat* v1,
- SimdFloat* v2,
- SimdFloat* v3)
-{
- assert(std::size_t(offset) % 16 == 0);
- assert(std::size_t(base) % 16 == 0);
- assert(align % 4 == 0);
-
- // Unfortunately we cannot use the beautiful Neon structured load
- // instructions since the data comes from four different memory locations.
- float32x4x2_t t0 =
- vuzpq_f32(vld1q_f32(base + align * offset[0]), vld1q_f32(base + align * offset[2]));
- float32x4x2_t t1 =
- vuzpq_f32(vld1q_f32(base + align * offset[1]), vld1q_f32(base + align * offset[3]));
- float32x4x2_t t2 = vtrnq_f32(t0.val[0], t1.val[0]);
- float32x4x2_t t3 = vtrnq_f32(t0.val[1], t1.val[1]);
- v0->simdInternal_ = t2.val[0];
- v1->simdInternal_ = t3.val[0];
- v2->simdInternal_ = t2.val[1];
- v3->simdInternal_ = t3.val[1];
-}
-
-template<int align>
-static inline void gmx_simdcall
- gatherLoadTranspose(const float* base, const std::int32_t offset[], SimdFloat* v0, SimdFloat* v1)
-{
- assert(std::size_t(offset) % 16 == 0);
- assert(std::size_t(base) % 8 == 0);
- assert(align % 2 == 0);
-
- v0->simdInternal_ =
- vcombine_f32(vld1_f32(base + align * offset[0]), vld1_f32(base + align * offset[2]));
- v1->simdInternal_ =
- vcombine_f32(vld1_f32(base + align * offset[1]), vld1_f32(base + align * offset[3]));
-
- float32x4x2_t tmp = vtrnq_f32(v0->simdInternal_, v1->simdInternal_);
-
- v0->simdInternal_ = tmp.val[0];
- v1->simdInternal_ = tmp.val[1];
-}
-
-static const int c_simdBestPairAlignmentFloat = 2;
-
-template<int align>
-static inline void gmx_simdcall gatherLoadUTranspose(const float* base,
- const std::int32_t offset[],
- SimdFloat* v0,
- SimdFloat* v1,
- SimdFloat* v2)
-{
- assert(std::size_t(offset) % 16 == 0);
-
- float32x4x2_t t0 =
- vuzpq_f32(vld1q_f32(base + align * offset[0]), vld1q_f32(base + align * offset[2]));
- float32x4x2_t t1 =
- vuzpq_f32(vld1q_f32(base + align * offset[1]), vld1q_f32(base + align * offset[3]));
- float32x4x2_t t2 = vtrnq_f32(t0.val[0], t1.val[0]);
- float32x4x2_t t3 = vtrnq_f32(t0.val[1], t1.val[1]);
- v0->simdInternal_ = t2.val[0];
- v1->simdInternal_ = t3.val[0];
- v2->simdInternal_ = t2.val[1];
-}
-
-
-template<int align>
-static inline void gmx_simdcall
- transposeScatterStoreU(float* base, const std::int32_t offset[], SimdFloat v0, SimdFloat v1, SimdFloat v2)
-{
- assert(std::size_t(offset) % 16 == 0);
-
- float32x4x2_t tmp = vtrnq_f32(v0.simdInternal_, v1.simdInternal_);
-
- vst1_f32(base + align * offset[0], vget_low_f32(tmp.val[0]));
- vst1_f32(base + align * offset[1], vget_low_f32(tmp.val[1]));
- vst1_f32(base + align * offset[2], vget_high_f32(tmp.val[0]));
- vst1_f32(base + align * offset[3], vget_high_f32(tmp.val[1]));
-
- vst1q_lane_f32(base + align * offset[0] + 2, v2.simdInternal_, 0);
- vst1q_lane_f32(base + align * offset[1] + 2, v2.simdInternal_, 1);
- vst1q_lane_f32(base + align * offset[2] + 2, v2.simdInternal_, 2);
- vst1q_lane_f32(base + align * offset[3] + 2, v2.simdInternal_, 3);
-}
-
-
-template<int align>
-static inline void gmx_simdcall
- transposeScatterIncrU(float* base, const std::int32_t offset[], SimdFloat v0, SimdFloat v1, SimdFloat v2)
-{
- assert(std::size_t(offset) % 16 == 0);
-
- if (align < 4)
- {
- float32x2_t t0, t1, t2, t3;
- float32x4x2_t tmp = vtrnq_f32(v0.simdInternal_, v1.simdInternal_);
-
- t0 = vget_low_f32(tmp.val[0]);
- t1 = vget_low_f32(tmp.val[1]);
- t2 = vget_high_f32(tmp.val[0]);
- t3 = vget_high_f32(tmp.val[1]);
-
- t0 = vadd_f32(t0, vld1_f32(base + align * offset[0]));
- vst1_f32(base + align * offset[0], t0);
- base[align * offset[0] + 2] += vgetq_lane_f32(v2.simdInternal_, 0);
-
- t1 = vadd_f32(t1, vld1_f32(base + align * offset[1]));
- vst1_f32(base + align * offset[1], t1);
- base[align * offset[1] + 2] += vgetq_lane_f32(v2.simdInternal_, 1);
-
- t2 = vadd_f32(t2, vld1_f32(base + align * offset[2]));
- vst1_f32(base + align * offset[2], t2);
- base[align * offset[2] + 2] += vgetq_lane_f32(v2.simdInternal_, 2);
-
- t3 = vadd_f32(t3, vld1_f32(base + align * offset[3]));
- vst1_f32(base + align * offset[3], t3);
- base[align * offset[3] + 2] += vgetq_lane_f32(v2.simdInternal_, 3);
- }
- else
- {
- // Extra elements means we can use full width-4 load/store operations
- float32x4x2_t t0 = vuzpq_f32(v0.simdInternal_, v2.simdInternal_);
- float32x4x2_t t1 = vuzpq_f32(v1.simdInternal_, vdupq_n_f32(0.0F));
- float32x4x2_t t2 = vtrnq_f32(t0.val[0], t1.val[0]);
- float32x4x2_t t3 = vtrnq_f32(t0.val[1], t1.val[1]);
- float32x4_t t4 = t2.val[0];
- float32x4_t t5 = t3.val[0];
- float32x4_t t6 = t2.val[1];
- float32x4_t t7 = t3.val[1];
-
- vst1q_f32(base + align * offset[0], vaddq_f32(t4, vld1q_f32(base + align * offset[0])));
- vst1q_f32(base + align * offset[1], vaddq_f32(t5, vld1q_f32(base + align * offset[1])));
- vst1q_f32(base + align * offset[2], vaddq_f32(t6, vld1q_f32(base + align * offset[2])));
- vst1q_f32(base + align * offset[3], vaddq_f32(t7, vld1q_f32(base + align * offset[3])));
- }
-}
-
-template<int align>
-static inline void gmx_simdcall
- transposeScatterDecrU(float* base, const std::int32_t offset[], SimdFloat v0, SimdFloat v1, SimdFloat v2)
-{
- assert(std::size_t(offset) % 16 == 0);
-
- if (align < 4)
- {
- float32x2_t t0, t1, t2, t3;
- float32x4x2_t tmp = vtrnq_f32(v0.simdInternal_, v1.simdInternal_);
-
- t0 = vget_low_f32(tmp.val[0]);
- t1 = vget_low_f32(tmp.val[1]);
- t2 = vget_high_f32(tmp.val[0]);
- t3 = vget_high_f32(tmp.val[1]);
-
- t0 = vsub_f32(vld1_f32(base + align * offset[0]), t0);
- vst1_f32(base + align * offset[0], t0);
- base[align * offset[0] + 2] -= vgetq_lane_f32(v2.simdInternal_, 0);
-
- t1 = vsub_f32(vld1_f32(base + align * offset[1]), t1);
- vst1_f32(base + align * offset[1], t1);
- base[align * offset[1] + 2] -= vgetq_lane_f32(v2.simdInternal_, 1);
-
- t2 = vsub_f32(vld1_f32(base + align * offset[2]), t2);
- vst1_f32(base + align * offset[2], t2);
- base[align * offset[2] + 2] -= vgetq_lane_f32(v2.simdInternal_, 2);
-
- t3 = vsub_f32(vld1_f32(base + align * offset[3]), t3);
- vst1_f32(base + align * offset[3], t3);
- base[align * offset[3] + 2] -= vgetq_lane_f32(v2.simdInternal_, 3);
- }
- else
- {
- // Extra elements means we can use full width-4 load/store operations
- float32x4x2_t t0 = vuzpq_f32(v0.simdInternal_, v2.simdInternal_);
- float32x4x2_t t1 = vuzpq_f32(v1.simdInternal_, vdupq_n_f32(0.0F));
- float32x4x2_t t2 = vtrnq_f32(t0.val[0], t1.val[0]);
- float32x4x2_t t3 = vtrnq_f32(t0.val[1], t1.val[1]);
- float32x4_t t4 = t2.val[0];
- float32x4_t t5 = t3.val[0];
- float32x4_t t6 = t2.val[1];
- float32x4_t t7 = t3.val[1];
-
- vst1q_f32(base + align * offset[0], vsubq_f32(vld1q_f32(base + align * offset[0]), t4));
- vst1q_f32(base + align * offset[1], vsubq_f32(vld1q_f32(base + align * offset[1]), t5));
- vst1q_f32(base + align * offset[2], vsubq_f32(vld1q_f32(base + align * offset[2]), t6));
- vst1q_f32(base + align * offset[3], vsubq_f32(vld1q_f32(base + align * offset[3]), t7));
- }
-}
-
-static inline void gmx_simdcall expandScalarsToTriplets(SimdFloat scalar,
- SimdFloat* triplets0,
- SimdFloat* triplets1,
- SimdFloat* triplets2)
-{
- float32x2_t lo, hi;
- float32x4_t t0, t1, t2, t3;
-
- lo = vget_low_f32(scalar.simdInternal_);
- hi = vget_high_f32(scalar.simdInternal_);
-
- t0 = vdupq_lane_f32(lo, 0);
- t1 = vdupq_lane_f32(lo, 1);
- t2 = vdupq_lane_f32(hi, 0);
- t3 = vdupq_lane_f32(hi, 1);
-
- triplets0->simdInternal_ = vextq_f32(t0, t1, 1);
- triplets1->simdInternal_ = vextq_f32(t1, t2, 2);
- triplets2->simdInternal_ = vextq_f32(t2, t3, 3);
-}
-
-
-template<int align>
-static inline void gmx_simdcall gatherLoadBySimdIntTranspose(const float* base,
- SimdFInt32 offset,
- SimdFloat* v0,
- SimdFloat* v1,
- SimdFloat* v2,
- SimdFloat* v3)
-{
- alignas(GMX_SIMD_ALIGNMENT) std::int32_t ioffset[GMX_SIMD_FINT32_WIDTH];
-
- assert(std::size_t(base) % 16 == 0);
- assert(align % 4 == 0);
-
- store(ioffset, offset);
- gatherLoadTranspose<align>(base, ioffset, v0, v1, v2, v3);
-}
-
-template<int align>
-static inline void gmx_simdcall
- gatherLoadBySimdIntTranspose(const float* base, SimdFInt32 offset, SimdFloat* v0, SimdFloat* v1)
-{
- alignas(GMX_SIMD_ALIGNMENT) std::int32_t ioffset[GMX_SIMD_FINT32_WIDTH];
-
- store(ioffset, offset);
- gatherLoadTranspose<align>(base, ioffset, v0, v1);
-}
-
-
-template<int align>
-static inline void gmx_simdcall
- gatherLoadUBySimdIntTranspose(const float* base, SimdFInt32 offset, SimdFloat* v0, SimdFloat* v1)
-{
- alignas(GMX_SIMD_ALIGNMENT) std::int32_t ioffset[GMX_SIMD_FINT32_WIDTH];
-
- store(ioffset, offset);
- v0->simdInternal_ =
- vcombine_f32(vld1_f32(base + align * ioffset[0]), vld1_f32(base + align * ioffset[2]));
- v1->simdInternal_ =
- vcombine_f32(vld1_f32(base + align * ioffset[1]), vld1_f32(base + align * ioffset[3]));
- float32x4x2_t tmp = vtrnq_f32(v0->simdInternal_, v1->simdInternal_);
- v0->simdInternal_ = tmp.val[0];
- v1->simdInternal_ = tmp.val[1];
-}
-
-static inline float gmx_simdcall reduceIncr4ReturnSum(float* m, SimdFloat v0, SimdFloat v1, SimdFloat v2, SimdFloat v3)
-{
- assert(std::size_t(m) % 16 == 0);
-
- float32x4x2_t t0 = vuzpq_f32(v0.simdInternal_, v2.simdInternal_);
- float32x4x2_t t1 = vuzpq_f32(v1.simdInternal_, v3.simdInternal_);
- float32x4x2_t t2 = vtrnq_f32(t0.val[0], t1.val[0]);
- float32x4x2_t t3 = vtrnq_f32(t0.val[1], t1.val[1]);
- v0.simdInternal_ = t2.val[0];
- v1.simdInternal_ = t3.val[0];
- v2.simdInternal_ = t2.val[1];
- v3.simdInternal_ = t3.val[1];
-
- v0 = v0 + v1;
- v2 = v2 + v3;
- v0 = v0 + v2;
- v2 = v0 + simdLoad(m);
- store(m, v2);
-
- return reduce(v0);
-}
-
-} // namespace gmx
-
-#endif // GMX_SIMD_IMPL_ARM_NEON_UTIL_FLOAT_H
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
#ifndef GMX_SIMD_IMPL_ARM_NEON_ASIMD_GENERAL_H
#define GMX_SIMD_IMPL_ARM_NEON_ASIMD_GENERAL_H
-#include "gromacs/simd/impl_arm_neon/impl_arm_neon_general.h"
+namespace gmx
+{
+
+static inline void simdPrefetch(void* m)
+{
+#ifdef __GNUC__
+ __builtin_prefetch(m);
+#endif
+}
+
+} // namespace gmx
#endif // GMX_SIMD_IMPL_ARM_NEON_ASIMD_GENERAL_H
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
#ifndef GMX_SIMD_IMPL_ARM_NEON_ASIMD_SIMD4_FLOAT_H
#define GMX_SIMD_IMPL_ARM_NEON_ASIMD_SIMD4_FLOAT_H
#include "config.h"
-#include <arm_neon.h>
+#include <cassert>
+#include <cstddef>
-#include "gromacs/simd/impl_arm_neon/impl_arm_neon_simd4_float.h"
+#include <arm_neon.h>
namespace gmx
{
+class Simd4Float
+{
+public:
+ Simd4Float() {}
+
+ Simd4Float(float f) : simdInternal_(vdupq_n_f32(f)) {}
+
+ // Internal utility constructor to simplify return statements
+ Simd4Float(float32x4_t simd) : simdInternal_(simd) {}
+
+ float32x4_t simdInternal_;
+};
+
+class Simd4FBool
+{
+public:
+ Simd4FBool() {}
+
+ //! \brief Construct from scalar bool
+ Simd4FBool(bool b) : simdInternal_(vdupq_n_u32(b ? 0xFFFFFFFF : 0)) {}
+
+ // Internal utility constructor to simplify return statements
+ Simd4FBool(uint32x4_t simd) : simdInternal_(simd) {}
+
+ uint32x4_t simdInternal_;
+};
+
+static inline Simd4Float gmx_simdcall load4(const float* m)
+{
+ assert(size_t(m) % 16 == 0);
+ return { vld1q_f32(m) };
+}
+
+static inline void gmx_simdcall store4(float* m, Simd4Float a)
+{
+ assert(size_t(m) % 16 == 0);
+ vst1q_f32(m, a.simdInternal_);
+}
+
+static inline Simd4Float gmx_simdcall load4U(const float* m)
+{
+ return { vld1q_f32(m) };
+}
+
+static inline void gmx_simdcall store4U(float* m, Simd4Float a)
+{
+ vst1q_f32(m, a.simdInternal_);
+}
+
+static inline Simd4Float gmx_simdcall simd4SetZeroF()
+{
+ return { vdupq_n_f32(0.0F) };
+}
+
+static inline Simd4Float gmx_simdcall operator&(Simd4Float a, Simd4Float b)
+{
+ return { vreinterpretq_f32_s32(vandq_s32(vreinterpretq_s32_f32(a.simdInternal_),
+ vreinterpretq_s32_f32(b.simdInternal_))) };
+}
+
+static inline Simd4Float gmx_simdcall andNot(Simd4Float a, Simd4Float b)
+{
+ return { vreinterpretq_f32_s32(vbicq_s32(vreinterpretq_s32_f32(b.simdInternal_),
+ vreinterpretq_s32_f32(a.simdInternal_))) };
+}
+
+static inline Simd4Float gmx_simdcall operator|(Simd4Float a, Simd4Float b)
+{
+ return { vreinterpretq_f32_s32(vorrq_s32(vreinterpretq_s32_f32(a.simdInternal_),
+ vreinterpretq_s32_f32(b.simdInternal_))) };
+}
+
+static inline Simd4Float gmx_simdcall operator^(Simd4Float a, Simd4Float b)
+{
+ return { vreinterpretq_f32_s32(veorq_s32(vreinterpretq_s32_f32(a.simdInternal_),
+ vreinterpretq_s32_f32(b.simdInternal_))) };
+}
+
+static inline Simd4Float gmx_simdcall operator+(Simd4Float a, Simd4Float b)
+{
+ return { vaddq_f32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline Simd4Float gmx_simdcall operator-(Simd4Float a, Simd4Float b)
+{
+ return { vsubq_f32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline Simd4Float gmx_simdcall operator-(Simd4Float x)
+{
+ return { vnegq_f32(x.simdInternal_) };
+}
+
+static inline Simd4Float gmx_simdcall operator*(Simd4Float a, Simd4Float b)
+{
+ return { vmulq_f32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline Simd4Float gmx_simdcall rsqrt(Simd4Float x)
+{
+ return { vrsqrteq_f32(x.simdInternal_) };
+}
+
+static inline Simd4Float gmx_simdcall abs(Simd4Float x)
+{
+ return { vabsq_f32(x.simdInternal_) };
+}
+
+static inline Simd4Float gmx_simdcall max(Simd4Float a, Simd4Float b)
+{
+ return { vmaxq_f32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline Simd4Float gmx_simdcall min(Simd4Float a, Simd4Float b)
+{
+ return { vminq_f32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline void gmx_simdcall transpose(Simd4Float* v0, Simd4Float* v1, Simd4Float* v2, Simd4Float* v3)
+{
+ float32x4x2_t t0 = vuzpq_f32(v0->simdInternal_, v2->simdInternal_);
+ float32x4x2_t t1 = vuzpq_f32(v1->simdInternal_, v3->simdInternal_);
+ float32x4x2_t t2 = vtrnq_f32(t0.val[0], t1.val[0]);
+ float32x4x2_t t3 = vtrnq_f32(t0.val[1], t1.val[1]);
+ v0->simdInternal_ = t2.val[0];
+ v1->simdInternal_ = t3.val[0];
+ v2->simdInternal_ = t2.val[1];
+ v3->simdInternal_ = t3.val[1];
+}
+
+static inline Simd4FBool gmx_simdcall operator==(Simd4Float a, Simd4Float b)
+{
+ return { vceqq_f32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline Simd4FBool gmx_simdcall operator!=(Simd4Float a, Simd4Float b)
+{
+ return { vmvnq_u32(vceqq_f32(a.simdInternal_, b.simdInternal_)) };
+}
+
+static inline Simd4FBool gmx_simdcall operator<(Simd4Float a, Simd4Float b)
+{
+ return { vcltq_f32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline Simd4FBool gmx_simdcall operator<=(Simd4Float a, Simd4Float b)
+{
+ return { vcleq_f32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline Simd4FBool gmx_simdcall operator&&(Simd4FBool a, Simd4FBool b)
+{
+ return { vandq_u32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline Simd4FBool gmx_simdcall operator||(Simd4FBool a, Simd4FBool b)
+{
+ return { vorrq_u32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline Simd4Float gmx_simdcall selectByMask(Simd4Float a, Simd4FBool m)
+{
+ return { vreinterpretq_f32_u32(vandq_u32(vreinterpretq_u32_f32(a.simdInternal_), m.simdInternal_)) };
+}
+
+static inline Simd4Float gmx_simdcall selectByNotMask(Simd4Float a, Simd4FBool m)
+{
+ return { vreinterpretq_f32_u32(vbicq_u32(vreinterpretq_u32_f32(a.simdInternal_), m.simdInternal_)) };
+}
+
+static inline Simd4Float gmx_simdcall blend(Simd4Float a, Simd4Float b, Simd4FBool sel)
+{
+ return { vbslq_f32(sel.simdInternal_, b.simdInternal_, a.simdInternal_) };
+}
+
static inline Simd4Float gmx_simdcall fma(Simd4Float a, Simd4Float b, Simd4Float c)
{
return { vfmaq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_) };
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2019,2020, by the GROMACS development team.
+ * Copyright (c) 2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
#ifndef GMX_SIMD_IMPL_ARM_NEON_ASIMD_SIMD_FLOAT_H
#define GMX_SIMD_IMPL_ARM_NEON_ASIMD_SIMD_FLOAT_H
#include "config.h"
+#include <cassert>
+#include <cstddef>
+#include <cstdint>
+
#include <arm_neon.h>
-#include "gromacs/simd/impl_arm_neon/impl_arm_neon_simd_float.h"
+#include "gromacs/math/utilities.h"
namespace gmx
{
+class SimdFloat
+{
+public:
+ SimdFloat() {}
+
+ SimdFloat(float f) : simdInternal_(vdupq_n_f32(f)) {}
+
+ // Internal utility constructor to simplify return statements
+ SimdFloat(float32x4_t simd) : simdInternal_(simd) {}
+
+ float32x4_t simdInternal_;
+};
+
+class SimdFInt32
+{
+public:
+ SimdFInt32() {}
+
+ SimdFInt32(std::int32_t i) : simdInternal_(vdupq_n_s32(i)) {}
+
+ // Internal utility constructor to simplify return statements
+ SimdFInt32(int32x4_t simd) : simdInternal_(simd) {}
+
+ int32x4_t simdInternal_;
+};
+
+class SimdFBool
+{
+public:
+ SimdFBool() {}
+
+ SimdFBool(bool b) : simdInternal_(vdupq_n_u32(b ? 0xFFFFFFFF : 0)) {}
+
+ // Internal utility constructor to simplify return statements
+ SimdFBool(uint32x4_t simd) : simdInternal_(simd) {}
+
+ uint32x4_t simdInternal_;
+};
+
+class SimdFIBool
+{
+public:
+ SimdFIBool() {}
+
+ SimdFIBool(bool b) : simdInternal_(vdupq_n_u32(b ? 0xFFFFFFFF : 0)) {}
+
+ // Internal utility constructor to simplify return statements
+ SimdFIBool(uint32x4_t simd) : simdInternal_(simd) {}
+
+ uint32x4_t simdInternal_;
+};
+
+static inline SimdFloat gmx_simdcall simdLoad(const float* m, SimdFloatTag = {})
+{
+ assert(std::size_t(m) % 16 == 0);
+ return { vld1q_f32(m) };
+}
+
+static inline void gmx_simdcall store(float* m, SimdFloat a)
+{
+ assert(std::size_t(m) % 16 == 0);
+ vst1q_f32(m, a.simdInternal_);
+}
+
+static inline SimdFloat gmx_simdcall simdLoadU(const float* m, SimdFloatTag = {})
+{
+ return { vld1q_f32(m) };
+}
+
+static inline void gmx_simdcall storeU(float* m, SimdFloat a)
+{
+ vst1q_f32(m, a.simdInternal_);
+}
+
+static inline SimdFloat gmx_simdcall setZeroF()
+{
+ return { vdupq_n_f32(0.0F) };
+}
+
+static inline SimdFInt32 gmx_simdcall simdLoad(const std::int32_t* m, SimdFInt32Tag)
+{
+ assert(std::size_t(m) % 16 == 0);
+ return { vld1q_s32(m) };
+}
+
+static inline void gmx_simdcall store(std::int32_t* m, SimdFInt32 a)
+{
+ assert(std::size_t(m) % 16 == 0);
+ vst1q_s32(m, a.simdInternal_);
+}
+
+static inline SimdFInt32 gmx_simdcall simdLoadU(const std::int32_t* m, SimdFInt32Tag)
+{
+ return { vld1q_s32(m) };
+}
+
+static inline void gmx_simdcall storeU(std::int32_t* m, SimdFInt32 a)
+{
+ vst1q_s32(m, a.simdInternal_);
+}
+
+static inline SimdFInt32 gmx_simdcall setZeroFI()
+{
+ return { vdupq_n_s32(0) };
+}
+
+template<int index>
+gmx_simdcall static inline std::int32_t extract(SimdFInt32 a)
+{
+ return vgetq_lane_s32(a.simdInternal_, index);
+}
+
+static inline SimdFloat gmx_simdcall operator&(SimdFloat a, SimdFloat b)
+{
+ return { vreinterpretq_f32_s32(vandq_s32(vreinterpretq_s32_f32(a.simdInternal_),
+ vreinterpretq_s32_f32(b.simdInternal_))) };
+}
+
+static inline SimdFloat gmx_simdcall andNot(SimdFloat a, SimdFloat b)
+{
+ return { vreinterpretq_f32_s32(vbicq_s32(vreinterpretq_s32_f32(b.simdInternal_),
+ vreinterpretq_s32_f32(a.simdInternal_))) };
+}
+
+static inline SimdFloat gmx_simdcall operator|(SimdFloat a, SimdFloat b)
+{
+ return { vreinterpretq_f32_s32(vorrq_s32(vreinterpretq_s32_f32(a.simdInternal_),
+ vreinterpretq_s32_f32(b.simdInternal_))) };
+}
+
+static inline SimdFloat gmx_simdcall operator^(SimdFloat a, SimdFloat b)
+{
+ return { vreinterpretq_f32_s32(veorq_s32(vreinterpretq_s32_f32(a.simdInternal_),
+ vreinterpretq_s32_f32(b.simdInternal_))) };
+}
+
+static inline SimdFloat gmx_simdcall operator+(SimdFloat a, SimdFloat b)
+{
+ return { vaddq_f32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFloat gmx_simdcall operator-(SimdFloat a, SimdFloat b)
+{
+ return { vsubq_f32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFloat gmx_simdcall operator-(SimdFloat x)
+{
+ return { vnegq_f32(x.simdInternal_) };
+}
+
+static inline SimdFloat gmx_simdcall operator*(SimdFloat a, SimdFloat b)
+{
+ return { vmulq_f32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFloat gmx_simdcall rsqrt(SimdFloat x)
+{
+ return { vrsqrteq_f32(x.simdInternal_) };
+}
+
+// The SIMD implementation seems to overflow when we square lu for
+// values close to FLOAT_MAX, so we fall back on the version in
+// simd_math.h, which is probably slightly slower.
+#if GMX_SIMD_HAVE_NATIVE_RSQRT_ITER_FLOAT
+static inline SimdFloat gmx_simdcall rsqrtIter(SimdFloat lu, SimdFloat x)
+{
+ return { vmulq_f32(lu.simdInternal_,
+ vrsqrtsq_f32(vmulq_f32(lu.simdInternal_, lu.simdInternal_), x.simdInternal_)) };
+}
+#endif
+
+static inline SimdFloat gmx_simdcall rcp(SimdFloat x)
+{
+ return { vrecpeq_f32(x.simdInternal_) };
+}
+
+static inline SimdFloat gmx_simdcall rcpIter(SimdFloat lu, SimdFloat x)
+{
+ return { vmulq_f32(lu.simdInternal_, vrecpsq_f32(lu.simdInternal_, x.simdInternal_)) };
+}
+
+static inline SimdFloat gmx_simdcall maskAdd(SimdFloat a, SimdFloat b, SimdFBool m)
+{
+ b.simdInternal_ =
+ vreinterpretq_f32_u32(vandq_u32(vreinterpretq_u32_f32(b.simdInternal_), m.simdInternal_));
+
+ return { vaddq_f32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFloat gmx_simdcall maskzMul(SimdFloat a, SimdFloat b, SimdFBool m)
+{
+ SimdFloat tmp = a * b;
+
+ return { vreinterpretq_f32_u32(vandq_u32(vreinterpretq_u32_f32(tmp.simdInternal_), m.simdInternal_)) };
+}
+
+static inline SimdFloat gmx_simdcall maskzFma(SimdFloat a, SimdFloat b, SimdFloat c, SimdFBool m)
+{
+#ifdef __ARM_FEATURE_FMA
+ float32x4_t tmp = vfmaq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_);
+#else
+ float32x4_t tmp = vmlaq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_);
+#endif
+
+ return { vreinterpretq_f32_u32(vandq_u32(vreinterpretq_u32_f32(tmp), m.simdInternal_)) };
+}
+
+static inline SimdFloat gmx_simdcall maskzRsqrt(SimdFloat x, SimdFBool m)
+{
+ // The result will always be correct since we mask the result with m, but
+ // for debug builds we also want to make sure not to generate FP exceptions
+#ifndef NDEBUG
+ x.simdInternal_ = vbslq_f32(m.simdInternal_, x.simdInternal_, vdupq_n_f32(1.0F));
+#endif
+ return { vreinterpretq_f32_u32(
+ vandq_u32(vreinterpretq_u32_f32(vrsqrteq_f32(x.simdInternal_)), m.simdInternal_)) };
+}
+
+static inline SimdFloat gmx_simdcall maskzRcp(SimdFloat x, SimdFBool m)
+{
+ // The result will always be correct since we mask the result with m, but
+ // for debug builds we also want to make sure not to generate FP exceptions
+#ifndef NDEBUG
+ x.simdInternal_ = vbslq_f32(m.simdInternal_, x.simdInternal_, vdupq_n_f32(1.0F));
+#endif
+ return { vreinterpretq_f32_u32(
+ vandq_u32(vreinterpretq_u32_f32(vrecpeq_f32(x.simdInternal_)), m.simdInternal_)) };
+}
+
+static inline SimdFloat gmx_simdcall abs(SimdFloat x)
+{
+ return { vabsq_f32(x.simdInternal_) };
+}
+
+static inline SimdFloat gmx_simdcall max(SimdFloat a, SimdFloat b)
+{
+ return { vmaxq_f32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFloat gmx_simdcall min(SimdFloat a, SimdFloat b)
+{
+ return { vminq_f32(a.simdInternal_, b.simdInternal_) };
+}
+
+// Round and trunc operations are defined at the end of this file, since they
+// need to use float-to-integer and integer-to-float conversions.
+
+template<MathOptimization opt = MathOptimization::Safe>
+static inline SimdFloat gmx_simdcall frexp(SimdFloat value, SimdFInt32* exponent)
+{
+ const int32x4_t exponentMask = vdupq_n_s32(0x7F800000);
+ const int32x4_t mantissaMask = vdupq_n_s32(0x807FFFFF);
+ const int32x4_t exponentBias = vdupq_n_s32(126); // add 1 to make our definition identical to frexp()
+ const float32x4_t half = vdupq_n_f32(0.5F);
+ int32x4_t iExponent;
+
+ iExponent = vandq_s32(vreinterpretq_s32_f32(value.simdInternal_), exponentMask);
+ iExponent = vsubq_s32(vshrq_n_s32(iExponent, 23), exponentBias);
+
+ float32x4_t result = vreinterpretq_f32_s32(
+ vorrq_s32(vandq_s32(vreinterpretq_s32_f32(value.simdInternal_), mantissaMask),
+ vreinterpretq_s32_f32(half)));
+
+ if (opt == MathOptimization::Safe)
+ {
+ uint32x4_t valueIsZero = vceqq_f32(value.simdInternal_, vdupq_n_f32(0.0F));
+ iExponent = vbicq_s32(iExponent, vreinterpretq_s32_u32(valueIsZero));
+ result = vbslq_f32(valueIsZero, value.simdInternal_, result);
+ }
+
+ exponent->simdInternal_ = iExponent;
+ return { result };
+}
+
+template<MathOptimization opt = MathOptimization::Safe>
+static inline SimdFloat gmx_simdcall ldexp(SimdFloat value, SimdFInt32 exponent)
+{
+ const int32x4_t exponentBias = vdupq_n_s32(127);
+ int32x4_t iExponent = vaddq_s32(exponent.simdInternal_, exponentBias);
+
+ if (opt == MathOptimization::Safe)
+ {
+ // Make sure biased argument is not negative
+ iExponent = vmaxq_s32(iExponent, vdupq_n_s32(0));
+ }
+
+ iExponent = vshlq_n_s32(iExponent, 23);
+
+ return { vmulq_f32(value.simdInternal_, vreinterpretq_f32_s32(iExponent)) };
+}
+
+static inline SimdFBool gmx_simdcall operator==(SimdFloat a, SimdFloat b)
+{
+ return { vceqq_f32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFBool gmx_simdcall operator!=(SimdFloat a, SimdFloat b)
+{
+ return { vmvnq_u32(vceqq_f32(a.simdInternal_, b.simdInternal_)) };
+}
+
+static inline SimdFBool gmx_simdcall operator<(SimdFloat a, SimdFloat b)
+{
+ return { vcltq_f32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFBool gmx_simdcall operator<=(SimdFloat a, SimdFloat b)
+{
+ return { vcleq_f32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFBool gmx_simdcall testBits(SimdFloat a)
+{
+ uint32x4_t tmp = vreinterpretq_u32_f32(a.simdInternal_);
+
+ return { vtstq_u32(tmp, tmp) };
+}
+
+static inline SimdFBool gmx_simdcall operator&&(SimdFBool a, SimdFBool b)
+{
+
+ return { vandq_u32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFBool gmx_simdcall operator||(SimdFBool a, SimdFBool b)
+{
+ return { vorrq_u32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFloat gmx_simdcall selectByMask(SimdFloat a, SimdFBool m)
+{
+ return { vreinterpretq_f32_u32(vandq_u32(vreinterpretq_u32_f32(a.simdInternal_), m.simdInternal_)) };
+}
+
+static inline SimdFloat gmx_simdcall selectByNotMask(SimdFloat a, SimdFBool m)
+{
+ return { vreinterpretq_f32_u32(vbicq_u32(vreinterpretq_u32_f32(a.simdInternal_), m.simdInternal_)) };
+}
+
+static inline SimdFloat gmx_simdcall blend(SimdFloat a, SimdFloat b, SimdFBool sel)
+{
+ return { vbslq_f32(sel.simdInternal_, b.simdInternal_, a.simdInternal_) };
+}
+
+static inline SimdFInt32 gmx_simdcall operator&(SimdFInt32 a, SimdFInt32 b)
+{
+ return { vandq_s32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFInt32 gmx_simdcall andNot(SimdFInt32 a, SimdFInt32 b)
+{
+ return { vbicq_s32(b.simdInternal_, a.simdInternal_) };
+}
+
+static inline SimdFInt32 gmx_simdcall operator|(SimdFInt32 a, SimdFInt32 b)
+{
+ return { vorrq_s32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFInt32 gmx_simdcall operator^(SimdFInt32 a, SimdFInt32 b)
+{
+ return { veorq_s32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFInt32 gmx_simdcall operator+(SimdFInt32 a, SimdFInt32 b)
+{
+ return { vaddq_s32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFInt32 gmx_simdcall operator-(SimdFInt32 a, SimdFInt32 b)
+{
+ return { vsubq_s32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFInt32 gmx_simdcall operator*(SimdFInt32 a, SimdFInt32 b)
+{
+ return { vmulq_s32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFIBool gmx_simdcall operator==(SimdFInt32 a, SimdFInt32 b)
+{
+ return { vceqq_s32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFIBool gmx_simdcall testBits(SimdFInt32 a)
+{
+ return { vtstq_s32(a.simdInternal_, a.simdInternal_) };
+}
+
+static inline SimdFIBool gmx_simdcall operator<(SimdFInt32 a, SimdFInt32 b)
+{
+ return { vcltq_s32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFIBool gmx_simdcall operator&&(SimdFIBool a, SimdFIBool b)
+{
+ return { vandq_u32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFIBool gmx_simdcall operator||(SimdFIBool a, SimdFIBool b)
+{
+ return { vorrq_u32(a.simdInternal_, b.simdInternal_) };
+}
+
+static inline SimdFInt32 gmx_simdcall selectByMask(SimdFInt32 a, SimdFIBool m)
+{
+ return { vandq_s32(a.simdInternal_, vreinterpretq_s32_u32(m.simdInternal_)) };
+}
+
+static inline SimdFInt32 gmx_simdcall selectByNotMask(SimdFInt32 a, SimdFIBool m)
+{
+ return { vbicq_s32(a.simdInternal_, vreinterpretq_s32_u32(m.simdInternal_)) };
+}
+
+static inline SimdFInt32 gmx_simdcall blend(SimdFInt32 a, SimdFInt32 b, SimdFIBool sel)
+{
+ return { vbslq_s32(sel.simdInternal_, b.simdInternal_, a.simdInternal_) };
+}
+
+static inline SimdFInt32 gmx_simdcall cvttR2I(SimdFloat a)
+{
+ return { vcvtq_s32_f32(a.simdInternal_) };
+}
+
+static inline SimdFloat gmx_simdcall cvtI2R(SimdFInt32 a)
+{
+ return { vcvtq_f32_s32(a.simdInternal_) };
+}
+
+static inline SimdFIBool gmx_simdcall cvtB2IB(SimdFBool a)
+{
+ return { a.simdInternal_ };
+}
+
+static inline SimdFBool gmx_simdcall cvtIB2B(SimdFIBool a)
+{
+ return { a.simdInternal_ };
+}
+
static inline SimdFloat gmx_simdcall fma(SimdFloat a, SimdFloat b, SimdFloat c)
{
return { vfmaq_f32(c.simdInternal_, b.simdInternal_, a.simdInternal_) };
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
#ifndef GMX_SIMD_IMPL_ARM_NEON_ASIMD_UTIL_FLOAT_H
#define GMX_SIMD_IMPL_ARM_NEON_ASIMD_UTIL_FLOAT_H
-#include "gromacs/simd/impl_arm_neon/impl_arm_neon_util_float.h"
+#include "config.h"
+
+#include <cassert>
+#include <cstddef>
+#include <cstdint>
+
+#include <arm_neon.h>
+
+#include "gromacs/utility/basedefinitions.h"
+
+
+namespace gmx
+{
+
+template<int align>
+static inline void gmx_simdcall gatherLoadTranspose(const float* base,
+ const std::int32_t offset[],
+ SimdFloat* v0,
+ SimdFloat* v1,
+ SimdFloat* v2,
+ SimdFloat* v3)
+{
+ assert(std::size_t(offset) % 16 == 0);
+ assert(std::size_t(base) % 16 == 0);
+ assert(align % 4 == 0);
+
+ // Unfortunately we cannot use the beautiful Neon structured load
+ // instructions since the data comes from four different memory locations.
+ float32x4x2_t t0 =
+ vuzpq_f32(vld1q_f32(base + align * offset[0]), vld1q_f32(base + align * offset[2]));
+ float32x4x2_t t1 =
+ vuzpq_f32(vld1q_f32(base + align * offset[1]), vld1q_f32(base + align * offset[3]));
+ float32x4x2_t t2 = vtrnq_f32(t0.val[0], t1.val[0]);
+ float32x4x2_t t3 = vtrnq_f32(t0.val[1], t1.val[1]);
+ v0->simdInternal_ = t2.val[0];
+ v1->simdInternal_ = t3.val[0];
+ v2->simdInternal_ = t2.val[1];
+ v3->simdInternal_ = t3.val[1];
+}
+
+template<int align>
+static inline void gmx_simdcall
+ gatherLoadTranspose(const float* base, const std::int32_t offset[], SimdFloat* v0, SimdFloat* v1)
+{
+ assert(std::size_t(offset) % 16 == 0);
+ assert(std::size_t(base) % 8 == 0);
+ assert(align % 2 == 0);
+
+ v0->simdInternal_ =
+ vcombine_f32(vld1_f32(base + align * offset[0]), vld1_f32(base + align * offset[2]));
+ v1->simdInternal_ =
+ vcombine_f32(vld1_f32(base + align * offset[1]), vld1_f32(base + align * offset[3]));
+
+ float32x4x2_t tmp = vtrnq_f32(v0->simdInternal_, v1->simdInternal_);
+
+ v0->simdInternal_ = tmp.val[0];
+ v1->simdInternal_ = tmp.val[1];
+}
+
+static const int c_simdBestPairAlignmentFloat = 2;
+
+template<int align>
+static inline void gmx_simdcall gatherLoadUTranspose(const float* base,
+ const std::int32_t offset[],
+ SimdFloat* v0,
+ SimdFloat* v1,
+ SimdFloat* v2)
+{
+ assert(std::size_t(offset) % 16 == 0);
+
+ float32x4x2_t t0 =
+ vuzpq_f32(vld1q_f32(base + align * offset[0]), vld1q_f32(base + align * offset[2]));
+ float32x4x2_t t1 =
+ vuzpq_f32(vld1q_f32(base + align * offset[1]), vld1q_f32(base + align * offset[3]));
+ float32x4x2_t t2 = vtrnq_f32(t0.val[0], t1.val[0]);
+ float32x4x2_t t3 = vtrnq_f32(t0.val[1], t1.val[1]);
+ v0->simdInternal_ = t2.val[0];
+ v1->simdInternal_ = t3.val[0];
+ v2->simdInternal_ = t2.val[1];
+}
+
+
+template<int align>
+static inline void gmx_simdcall
+ transposeScatterStoreU(float* base, const std::int32_t offset[], SimdFloat v0, SimdFloat v1, SimdFloat v2)
+{
+ assert(std::size_t(offset) % 16 == 0);
+
+ float32x4x2_t tmp = vtrnq_f32(v0.simdInternal_, v1.simdInternal_);
+
+ vst1_f32(base + align * offset[0], vget_low_f32(tmp.val[0]));
+ vst1_f32(base + align * offset[1], vget_low_f32(tmp.val[1]));
+ vst1_f32(base + align * offset[2], vget_high_f32(tmp.val[0]));
+ vst1_f32(base + align * offset[3], vget_high_f32(tmp.val[1]));
+
+ vst1q_lane_f32(base + align * offset[0] + 2, v2.simdInternal_, 0);
+ vst1q_lane_f32(base + align * offset[1] + 2, v2.simdInternal_, 1);
+ vst1q_lane_f32(base + align * offset[2] + 2, v2.simdInternal_, 2);
+ vst1q_lane_f32(base + align * offset[3] + 2, v2.simdInternal_, 3);
+}
+
+
+template<int align>
+static inline void gmx_simdcall
+ transposeScatterIncrU(float* base, const std::int32_t offset[], SimdFloat v0, SimdFloat v1, SimdFloat v2)
+{
+ assert(std::size_t(offset) % 16 == 0);
+
+ if (align < 4)
+ {
+ float32x2_t t0, t1, t2, t3;
+ float32x4x2_t tmp = vtrnq_f32(v0.simdInternal_, v1.simdInternal_);
+
+ t0 = vget_low_f32(tmp.val[0]);
+ t1 = vget_low_f32(tmp.val[1]);
+ t2 = vget_high_f32(tmp.val[0]);
+ t3 = vget_high_f32(tmp.val[1]);
+
+ t0 = vadd_f32(t0, vld1_f32(base + align * offset[0]));
+ vst1_f32(base + align * offset[0], t0);
+ base[align * offset[0] + 2] += vgetq_lane_f32(v2.simdInternal_, 0);
+
+ t1 = vadd_f32(t1, vld1_f32(base + align * offset[1]));
+ vst1_f32(base + align * offset[1], t1);
+ base[align * offset[1] + 2] += vgetq_lane_f32(v2.simdInternal_, 1);
+
+ t2 = vadd_f32(t2, vld1_f32(base + align * offset[2]));
+ vst1_f32(base + align * offset[2], t2);
+ base[align * offset[2] + 2] += vgetq_lane_f32(v2.simdInternal_, 2);
+
+ t3 = vadd_f32(t3, vld1_f32(base + align * offset[3]));
+ vst1_f32(base + align * offset[3], t3);
+ base[align * offset[3] + 2] += vgetq_lane_f32(v2.simdInternal_, 3);
+ }
+ else
+ {
+ // Extra elements means we can use full width-4 load/store operations
+ float32x4x2_t t0 = vuzpq_f32(v0.simdInternal_, v2.simdInternal_);
+ float32x4x2_t t1 = vuzpq_f32(v1.simdInternal_, vdupq_n_f32(0.0F));
+ float32x4x2_t t2 = vtrnq_f32(t0.val[0], t1.val[0]);
+ float32x4x2_t t3 = vtrnq_f32(t0.val[1], t1.val[1]);
+ float32x4_t t4 = t2.val[0];
+ float32x4_t t5 = t3.val[0];
+ float32x4_t t6 = t2.val[1];
+ float32x4_t t7 = t3.val[1];
+
+ vst1q_f32(base + align * offset[0], vaddq_f32(t4, vld1q_f32(base + align * offset[0])));
+ vst1q_f32(base + align * offset[1], vaddq_f32(t5, vld1q_f32(base + align * offset[1])));
+ vst1q_f32(base + align * offset[2], vaddq_f32(t6, vld1q_f32(base + align * offset[2])));
+ vst1q_f32(base + align * offset[3], vaddq_f32(t7, vld1q_f32(base + align * offset[3])));
+ }
+}
+
+template<int align>
+static inline void gmx_simdcall
+ transposeScatterDecrU(float* base, const std::int32_t offset[], SimdFloat v0, SimdFloat v1, SimdFloat v2)
+{
+ assert(std::size_t(offset) % 16 == 0);
+
+ if (align < 4)
+ {
+ float32x2_t t0, t1, t2, t3;
+ float32x4x2_t tmp = vtrnq_f32(v0.simdInternal_, v1.simdInternal_);
+
+ t0 = vget_low_f32(tmp.val[0]);
+ t1 = vget_low_f32(tmp.val[1]);
+ t2 = vget_high_f32(tmp.val[0]);
+ t3 = vget_high_f32(tmp.val[1]);
+
+ t0 = vsub_f32(vld1_f32(base + align * offset[0]), t0);
+ vst1_f32(base + align * offset[0], t0);
+ base[align * offset[0] + 2] -= vgetq_lane_f32(v2.simdInternal_, 0);
+
+ t1 = vsub_f32(vld1_f32(base + align * offset[1]), t1);
+ vst1_f32(base + align * offset[1], t1);
+ base[align * offset[1] + 2] -= vgetq_lane_f32(v2.simdInternal_, 1);
+
+ t2 = vsub_f32(vld1_f32(base + align * offset[2]), t2);
+ vst1_f32(base + align * offset[2], t2);
+ base[align * offset[2] + 2] -= vgetq_lane_f32(v2.simdInternal_, 2);
+
+ t3 = vsub_f32(vld1_f32(base + align * offset[3]), t3);
+ vst1_f32(base + align * offset[3], t3);
+ base[align * offset[3] + 2] -= vgetq_lane_f32(v2.simdInternal_, 3);
+ }
+ else
+ {
+ // Extra elements means we can use full width-4 load/store operations
+ float32x4x2_t t0 = vuzpq_f32(v0.simdInternal_, v2.simdInternal_);
+ float32x4x2_t t1 = vuzpq_f32(v1.simdInternal_, vdupq_n_f32(0.0F));
+ float32x4x2_t t2 = vtrnq_f32(t0.val[0], t1.val[0]);
+ float32x4x2_t t3 = vtrnq_f32(t0.val[1], t1.val[1]);
+ float32x4_t t4 = t2.val[0];
+ float32x4_t t5 = t3.val[0];
+ float32x4_t t6 = t2.val[1];
+ float32x4_t t7 = t3.val[1];
+
+ vst1q_f32(base + align * offset[0], vsubq_f32(vld1q_f32(base + align * offset[0]), t4));
+ vst1q_f32(base + align * offset[1], vsubq_f32(vld1q_f32(base + align * offset[1]), t5));
+ vst1q_f32(base + align * offset[2], vsubq_f32(vld1q_f32(base + align * offset[2]), t6));
+ vst1q_f32(base + align * offset[3], vsubq_f32(vld1q_f32(base + align * offset[3]), t7));
+ }
+}
+
+static inline void gmx_simdcall expandScalarsToTriplets(SimdFloat scalar,
+ SimdFloat* triplets0,
+ SimdFloat* triplets1,
+ SimdFloat* triplets2)
+{
+ float32x2_t lo, hi;
+ float32x4_t t0, t1, t2, t3;
+
+ lo = vget_low_f32(scalar.simdInternal_);
+ hi = vget_high_f32(scalar.simdInternal_);
+
+ t0 = vdupq_lane_f32(lo, 0);
+ t1 = vdupq_lane_f32(lo, 1);
+ t2 = vdupq_lane_f32(hi, 0);
+ t3 = vdupq_lane_f32(hi, 1);
+
+ triplets0->simdInternal_ = vextq_f32(t0, t1, 1);
+ triplets1->simdInternal_ = vextq_f32(t1, t2, 2);
+ triplets2->simdInternal_ = vextq_f32(t2, t3, 3);
+}
+
+
+template<int align>
+static inline void gmx_simdcall gatherLoadBySimdIntTranspose(const float* base,
+ SimdFInt32 offset,
+ SimdFloat* v0,
+ SimdFloat* v1,
+ SimdFloat* v2,
+ SimdFloat* v3)
+{
+ alignas(GMX_SIMD_ALIGNMENT) std::int32_t ioffset[GMX_SIMD_FINT32_WIDTH];
+
+ assert(std::size_t(base) % 16 == 0);
+ assert(align % 4 == 0);
+
+ store(ioffset, offset);
+ gatherLoadTranspose<align>(base, ioffset, v0, v1, v2, v3);
+}
+
+template<int align>
+static inline void gmx_simdcall
+ gatherLoadBySimdIntTranspose(const float* base, SimdFInt32 offset, SimdFloat* v0, SimdFloat* v1)
+{
+ alignas(GMX_SIMD_ALIGNMENT) std::int32_t ioffset[GMX_SIMD_FINT32_WIDTH];
+
+ store(ioffset, offset);
+ gatherLoadTranspose<align>(base, ioffset, v0, v1);
+}
+
+
+template<int align>
+static inline void gmx_simdcall
+ gatherLoadUBySimdIntTranspose(const float* base, SimdFInt32 offset, SimdFloat* v0, SimdFloat* v1)
+{
+ alignas(GMX_SIMD_ALIGNMENT) std::int32_t ioffset[GMX_SIMD_FINT32_WIDTH];
+
+ store(ioffset, offset);
+ v0->simdInternal_ =
+ vcombine_f32(vld1_f32(base + align * ioffset[0]), vld1_f32(base + align * ioffset[2]));
+ v1->simdInternal_ =
+ vcombine_f32(vld1_f32(base + align * ioffset[1]), vld1_f32(base + align * ioffset[3]));
+ float32x4x2_t tmp = vtrnq_f32(v0->simdInternal_, v1->simdInternal_);
+ v0->simdInternal_ = tmp.val[0];
+ v1->simdInternal_ = tmp.val[1];
+}
+
+static inline float gmx_simdcall reduceIncr4ReturnSum(float* m, SimdFloat v0, SimdFloat v1, SimdFloat v2, SimdFloat v3)
+{
+ assert(std::size_t(m) % 16 == 0);
+
+ float32x4x2_t t0 = vuzpq_f32(v0.simdInternal_, v2.simdInternal_);
+ float32x4x2_t t1 = vuzpq_f32(v1.simdInternal_, v3.simdInternal_);
+ float32x4x2_t t2 = vtrnq_f32(t0.val[0], t1.val[0]);
+ float32x4x2_t t3 = vtrnq_f32(t0.val[1], t1.val[1]);
+ v0.simdInternal_ = t2.val[0];
+ v1.simdInternal_ = t3.val[0];
+ v2.simdInternal_ = t2.val[1];
+ v3.simdInternal_ = t3.val[1];
+
+ v0 = v0 + v1;
+ v2 = v2 + v3;
+ v0 = v0 + v2;
+ v2 = v0 + simdLoad(m);
+ store(m, v2);
+
+ return reduce(v0);
+}
+
+} // namespace gmx
#endif // GMX_SIMD_IMPL_ARM_NEON_ASIMD_UTIL_FLOAT_H
static inline Simd4Double gmx_simdcall operator&(Simd4Double a, Simd4Double b)
{
svbool_t pg = svptrue_b64();
- return { svreinterpret_f64_s64(svand_s64_z(pg, svreinterpret_s64_f64(a.simdInternal_),
- svreinterpret_s64_f64(b.simdInternal_))) };
+ return { svreinterpret_f64_s64(svand_s64_z(
+ pg, svreinterpret_s64_f64(a.simdInternal_), svreinterpret_s64_f64(b.simdInternal_))) };
}
static inline Simd4Double gmx_simdcall andNot(Simd4Double a, Simd4Double b)
{
svbool_t pg = svptrue_b64();
- return { svreinterpret_f64_s64(svbic_s64_z(pg, svreinterpret_s64_f64(b.simdInternal_),
- svreinterpret_s64_f64(a.simdInternal_))) };
+ return { svreinterpret_f64_s64(svbic_s64_z(
+ pg, svreinterpret_s64_f64(b.simdInternal_), svreinterpret_s64_f64(a.simdInternal_))) };
}
static inline Simd4Double gmx_simdcall operator|(Simd4Double a, Simd4Double b)
{
svbool_t pg = svptrue_b64();
- return { svreinterpret_f64_s64(svorr_s64_z(pg, svreinterpret_s64_f64(a.simdInternal_),
- svreinterpret_s64_f64(b.simdInternal_))) };
+ return { svreinterpret_f64_s64(svorr_s64_z(
+ pg, svreinterpret_s64_f64(a.simdInternal_), svreinterpret_s64_f64(b.simdInternal_))) };
}
static inline Simd4Double gmx_simdcall operator^(Simd4Double a, Simd4Double b)
{
svbool_t pg = svptrue_b64();
- return { svreinterpret_f64_s64(sveor_s64_z(pg, svreinterpret_s64_f64(a.simdInternal_),
- svreinterpret_s64_f64(b.simdInternal_))) };
+ return { svreinterpret_f64_s64(sveor_s64_z(
+ pg, svreinterpret_s64_f64(a.simdInternal_), svreinterpret_s64_f64(b.simdInternal_))) };
}
static inline Simd4Double gmx_simdcall operator+(Simd4Double a, Simd4Double b)
{
assert(0 == (std::size_t(m) % GMX_SIMD_ALIGNMENT));
svbool_t pg = svwhilelt_b32(0, (int32_t)GMX_SIMD_DINT32_WIDTH);
- svst1_s32(pg, m,
- svuzp1(svreinterpret_s32_s64(a.simdInternal_), svreinterpret_s32_s64(a.simdInternal_)));
+ svst1_s32(pg, m, svuzp1(svreinterpret_s32_s64(a.simdInternal_), svreinterpret_s32_s64(a.simdInternal_)));
}
static inline SimdDInt32 gmx_simdcall simdLoadU(const std::int32_t* m, SimdDInt32Tag)
static inline void gmx_simdcall storeU(std::int32_t* m, SimdDInt32 a)
{
svbool_t pg = svwhilelt_b32(0, (int32_t)GMX_SIMD_DINT32_WIDTH);
- svst1_s32(pg, m,
- svuzp1(svreinterpret_s32_s64(a.simdInternal_), svreinterpret_s32_s64(a.simdInternal_)));
+ svst1_s32(pg, m, svuzp1(svreinterpret_s32_s64(a.simdInternal_), svreinterpret_s32_s64(a.simdInternal_)));
}
static inline SimdDInt32 gmx_simdcall setZeroDI()
static inline SimdDouble gmx_simdcall operator&(SimdDouble a, SimdDouble b)
{
svbool_t pg = svptrue_b64();
- return { svreinterpret_f64_s64(svand_s64_x(pg, svreinterpret_s64_f64(a.simdInternal_),
- svreinterpret_s64_f64(b.simdInternal_))) };
+ return { svreinterpret_f64_s64(svand_s64_x(
+ pg, svreinterpret_s64_f64(a.simdInternal_), svreinterpret_s64_f64(b.simdInternal_))) };
}
static inline SimdDouble gmx_simdcall andNot(SimdDouble a, SimdDouble b)
{
svbool_t pg = svptrue_b64();
- return { svreinterpret_f64_s64(svbic_s64_x(pg, svreinterpret_s64_f64(b.simdInternal_),
- svreinterpret_s64_f64(a.simdInternal_))) };
+ return { svreinterpret_f64_s64(svbic_s64_x(
+ pg, svreinterpret_s64_f64(b.simdInternal_), svreinterpret_s64_f64(a.simdInternal_))) };
}
static inline SimdDouble gmx_simdcall operator|(SimdDouble a, SimdDouble b)
{
svbool_t pg = svptrue_b64();
- return { svreinterpret_f64_s64(svorr_s64_x(pg, svreinterpret_s64_f64(a.simdInternal_),
- svreinterpret_s64_f64(b.simdInternal_))) };
+ return { svreinterpret_f64_s64(svorr_s64_x(
+ pg, svreinterpret_s64_f64(a.simdInternal_), svreinterpret_s64_f64(b.simdInternal_))) };
}
static inline SimdDouble gmx_simdcall operator^(SimdDouble a, SimdDouble b)
{
svbool_t pg = svptrue_b64();
- return { svreinterpret_f64_s64(sveor_s64_x(pg, svreinterpret_s64_f64(a.simdInternal_),
- svreinterpret_s64_f64(b.simdInternal_))) };
+ return { svreinterpret_f64_s64(sveor_s64_x(
+ pg, svreinterpret_s64_f64(a.simdInternal_), svreinterpret_s64_f64(b.simdInternal_))) };
}
static inline SimdDouble gmx_simdcall operator+(SimdDouble a, SimdDouble b)
pg, svreinterpret_s64_u64(svlsr_n_u64_x(pg, svreinterpret_u64_s64(iExponent), 52)), exponentBias);
- svfloat64_t result = svreinterpret_f64_s64(svorr_s64_x(
- pg, svand_s64_x(pg, svreinterpret_s64_f64(value.simdInternal_), mantissaMask),
- svreinterpret_s64_f64(half)));
+ svfloat64_t result = svreinterpret_f64_s64(
+ svorr_s64_x(pg,
+ svand_s64_x(pg, svreinterpret_s64_f64(value.simdInternal_), mantissaMask),
+ svreinterpret_s64_f64(half)));
if (opt == MathOptimization::Safe)
{
static inline SimdFloat gmx_simdcall operator&(SimdFloat a, SimdFloat b)
{
svbool_t pg = svptrue_b32();
- return { svreinterpret_f32_s32(svand_s32_x(pg, svreinterpret_s32_f32(a.simdInternal_),
- svreinterpret_s32_f32(b.simdInternal_))) };
+ return { svreinterpret_f32_s32(svand_s32_x(
+ pg, svreinterpret_s32_f32(a.simdInternal_), svreinterpret_s32_f32(b.simdInternal_))) };
}
static inline SimdFloat gmx_simdcall andNot(SimdFloat a, SimdFloat b)
{
svbool_t pg = svptrue_b32();
- return { svreinterpret_f32_s32(svbic_s32_x(pg, svreinterpret_s32_f32(b.simdInternal_),
- svreinterpret_s32_f32(a.simdInternal_))) };
+ return { svreinterpret_f32_s32(svbic_s32_x(
+ pg, svreinterpret_s32_f32(b.simdInternal_), svreinterpret_s32_f32(a.simdInternal_))) };
}
static inline SimdFloat gmx_simdcall operator|(SimdFloat a, SimdFloat b)
{
svbool_t pg = svptrue_b32();
- return { svreinterpret_f32_s32(svorr_s32_x(pg, svreinterpret_s32_f32(a.simdInternal_),
- svreinterpret_s32_f32(b.simdInternal_))) };
+ return { svreinterpret_f32_s32(svorr_s32_x(
+ pg, svreinterpret_s32_f32(a.simdInternal_), svreinterpret_s32_f32(b.simdInternal_))) };
}
static inline SimdFloat gmx_simdcall operator^(SimdFloat a, SimdFloat b)
{
svbool_t pg = svptrue_b32();
- return { svreinterpret_f32_s32(sveor_s32_x(pg, svreinterpret_s32_f32(a.simdInternal_),
- svreinterpret_s32_f32(b.simdInternal_))) };
+ return { svreinterpret_f32_s32(sveor_s32_x(
+ pg, svreinterpret_s32_f32(a.simdInternal_), svreinterpret_s32_f32(b.simdInternal_))) };
}
static inline SimdFloat gmx_simdcall operator+(SimdFloat a, SimdFloat b)
iExponent = svsub_s32_x(
pg, svreinterpret_s32_u32(svlsr_n_u32_x(pg, svreinterpret_u32_s32(iExponent), 23)), exponentBias);
-
- svfloat32_t result = svreinterpret_f32_s32(svorr_s32_x(
- pg, svand_s32_x(pg, svreinterpret_s32_f32(value.simdInternal_), mantissaMask),
- svreinterpret_s32_f32(half)));
+ svfloat32_t result = svreinterpret_f32_s32(
+ svorr_s32_x(pg,
+ svand_s32_x(pg, svreinterpret_s32_f32(value.simdInternal_), mantissaMask),
+ svreinterpret_s32_f32(half)));
if (opt == MathOptimization::Safe)
{
svint64_t offsets;
svbool_t pg = svptrue_b64();
offsets = svmul_n_s64_x(
- pg, svunpklo_s64(svld1_s32(svwhilelt_b32(0, (int32_t)GMX_SIMD_DINT32_WIDTH), offset)),
+ pg,
+ svunpklo_s64(svld1_s32(svwhilelt_b32(0, (int32_t)GMX_SIMD_DINT32_WIDTH), offset)),
align * sizeof(double));
v0->simdInternal_ = svld1_gather_s64offset_f64(pg, base, offsets);
offsets = svadd_n_s64_x(pg, offsets, sizeof(double));
svint64_t offsets;
svbool_t pg = svptrue_b64();
offsets = svmul_n_s64_x(
- pg, svunpklo_s64(svld1_s32(svwhilelt_b32(0, (int32_t)GMX_SIMD_DINT32_WIDTH), offset)),
+ pg,
+ svunpklo_s64(svld1_s32(svwhilelt_b32(0, (int32_t)GMX_SIMD_DINT32_WIDTH), offset)),
align * sizeof(double));
v0->simdInternal_ = svld1_gather_s64offset_f64(pg, base, offsets);
offsets = svadd_n_s64_x(pg, offsets, sizeof(double));
svint64_t offsets;
svbool_t pg = svptrue_b64();
offsets = svmul_n_s64_x(
- pg, svunpklo_s64(svld1_s32(svwhilelt_b32(0, (int32_t)GMX_SIMD_DINT32_WIDTH), offset)),
+ pg,
+ svunpklo_s64(svld1_s32(svwhilelt_b32(0, (int32_t)GMX_SIMD_DINT32_WIDTH), offset)),
align * sizeof(double));
svst1_scatter_s64offset_f64(pg, base, offsets, v0.simdInternal_);
offsets = svadd_n_s64_x(pg, offsets, sizeof(double));
svbool_t pg = svwhilelt_b64(0, (int32_t)GMX_SIMD_DOUBLE_WIDTH / 2);
svfloat64_t _v0, _v1;
offsets = svmul_n_s64_x(
- pg, svunpklo(svld1_s32(svwhilelt_b32(0, (int32_t)GMX_SIMD_DINT32_WIDTH / 2), offset)),
+ pg,
+ svunpklo(svld1_s32(svwhilelt_b32(0, (int32_t)GMX_SIMD_DINT32_WIDTH / 2), offset)),
align * sizeof(double));
_v0 = svld1_gather_s64offset_f64(pg, base0, offsets);
_v1 = svld1_gather_s64offset_f64(pg, base1, offsets);
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_SIMD_IMPLEMENTATION_IBM_VMX_H
-#define GMX_SIMD_IMPLEMENTATION_IBM_VMX_H
-
-#include "impl_ibm_vmx_definitions.h"
-#include "impl_ibm_vmx_general.h"
-// No double precision available for VMX
-#include "impl_ibm_vmx_simd4_float.h"
-#include "impl_ibm_vmx_simd_float.h"
-#include "impl_ibm_vmx_util_float.h"
-
-#endif // GMX_SIMD_IMPLEMENTATION_IBM_VMX_H
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2017,2018,2019,2020, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_SIMD_IMPLEMENTATION_IBM_VMX_DEFINITIONS_H
-#define GMX_SIMD_IMPLEMENTATION_IBM_VMX_DEFINITIONS_H
-
-#include <altivec.h>
-
-#if defined(__GNUC__) && !defined(__ibmxl__) && !defined(__xlC__)
-// According to G++ documentation, when using altivec in C++ we
-// must undefine vector & bool macros after including altivec.h
-# undef vector
-# undef bool
-# define vmxBool __bool
-#else
-// We cannot undefine bool on xlc, but somehow it works anyway
-# define vmxBool bool
-#endif
-
-#define GMX_SIMD 1
-#define GMX_SIMD_HAVE_FLOAT 1
-#define GMX_SIMD_HAVE_DOUBLE 0
-#define GMX_SIMD_HAVE_LOADU 0
-#define GMX_SIMD_HAVE_STOREU 0
-
-#define GMX_SIMD_HAVE_LOGICAL 1
-#define GMX_SIMD_HAVE_FMA 1
-#define GMX_SIMD_HAVE_FINT32_EXTRACT 0
-#define GMX_SIMD_HAVE_FINT32_LOGICAL 1
-#define GMX_SIMD_HAVE_FINT32_ARITHMETICS 1
-#define GMX_SIMD_HAVE_DINT32_EXTRACT 0
-#define GMX_SIMD_HAVE_DINT32_LOGICAL 0
-#define GMX_SIMD_HAVE_DINT32_ARITHMETICS 0
-#define GMX_SIMD_HAVE_NATIVE_COPYSIGN_FLOAT 0
-#define GMX_SIMD_HAVE_NATIVE_RSQRT_ITER_FLOAT 0
-#define GMX_SIMD_HAVE_NATIVE_RCP_ITER_FLOAT 0
-#define GMX_SIMD_HAVE_NATIVE_LOG_FLOAT 0
-#define GMX_SIMD_HAVE_NATIVE_EXP2_FLOAT 0
-#define GMX_SIMD_HAVE_NATIVE_EXP_FLOAT 0
-#define GMX_SIMD_HAVE_NATIVE_COPYSIGN_DOUBLE 0
-#define GMX_SIMD_HAVE_NATIVE_RSQRT_ITER_DOUBLE 0
-#define GMX_SIMD_HAVE_NATIVE_RCP_ITER_DOUBLE 0
-#define GMX_SIMD_HAVE_NATIVE_LOG_DOUBLE 0
-#define GMX_SIMD_HAVE_NATIVE_EXP2_DOUBLE 0
-#define GMX_SIMD_HAVE_NATIVE_EXP_DOUBLE 0
-#define GMX_SIMD_HAVE_GATHER_LOADU_BYSIMDINT_TRANSPOSE_FLOAT 0
-#define GMX_SIMD_HAVE_GATHER_LOADU_BYSIMDINT_TRANSPOSE_DOUBLE 0
-#define GMX_SIMD_HAVE_HSIMD_UTIL_FLOAT 0 // No need for half-simd, width is 4
-#define GMX_SIMD_HAVE_HSIMD_UTIL_DOUBLE 0
-
-#define GMX_SIMD4_HAVE_FLOAT 1
-#define GMX_SIMD4_HAVE_DOUBLE 0
-
-// Implementation details
-#define GMX_SIMD_FLOAT_WIDTH 4
-#undef GMX_SIMD_DOUBLE_WIDTH
-#define GMX_SIMD_FINT32_WIDTH 4
-#undef GMX_SIMD_DINT32_WIDTH
-#define GMX_SIMD4_WIDTH 4
-#define GMX_SIMD_ALIGNMENT 16 // Bytes (4*single)
-#define GMX_SIMD_RSQRT_BITS 14
-#define GMX_SIMD_RCP_BITS 14
-
-#endif // GMX_SIMD_IMPLEMENTATION_IBM_VMX_DEFINITIONS_H
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2019, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_SIMD_IMPLEMENTATION_IBM_VMX_SIMD4_FLOAT_H
-#define GMX_SIMD_IMPLEMENTATION_IBM_VMX_SIMD4_FLOAT_H
-
-#include "config.h"
-
-#include "gromacs/utility/basedefinitions.h"
-
-#include "impl_ibm_vmx_definitions.h"
-
-namespace gmx
-{
-
-class Simd4Float
-{
-public:
- Simd4Float() {}
-
- Simd4Float(float f)
- {
- __vector unsigned char perm;
-
- simdInternal_ = vec_lde(0, const_cast<float*>(&f));
- perm = vec_lvsl(0, const_cast<float*>(&f));
- simdInternal_ = vec_perm(simdInternal_, simdInternal_, perm);
- simdInternal_ = vec_splat(simdInternal_, 0);
- }
-
- // Internal utility constructor to simplify return statements
- Simd4Float(__vector float simd) : simdInternal_(simd) {}
-
- __vector float simdInternal_;
-};
-
-class Simd4FBool
-{
-public:
- Simd4FBool() {}
-
- Simd4FBool(bool b)
- {
- simdInternal_ = reinterpret_cast<__vector vmxBool int>(vec_splat_u32(b ? 0xFFFFFFFF : 0));
- }
-
- // Internal utility constructor to simplify return statements
- Simd4FBool(__vector vmxBool int simd) : simdInternal_(simd) {}
-
- __vector vmxBool int simdInternal_;
-};
-
-static inline Simd4Float gmx_simdcall load4(const float* m)
-{
- return { vec_ld(0, const_cast<float*>(m)) };
-}
-
-static inline void gmx_simdcall store4(float* m, Simd4Float a)
-{
- vec_st(a.simdInternal_, 0, const_cast<float*>(m));
-}
-
-static inline Simd4Float gmx_simdcall simd4SetZeroF()
-{
- return { reinterpret_cast<__vector float>(vec_splat_u32(0)) };
-}
-
-static inline Simd4Float gmx_simdcall operator&(Simd4Float a, Simd4Float b)
-{
- return { vec_and(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall andNot(Simd4Float a, Simd4Float b)
-{
- return { vec_andc(b.simdInternal_, a.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall operator|(Simd4Float a, Simd4Float b)
-{
- return { vec_or(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall operator^(Simd4Float a, Simd4Float b)
-{
- return { vec_xor(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall operator+(Simd4Float a, Simd4Float b)
-{
- return { vec_add(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall operator-(Simd4Float a, Simd4Float b)
-{
- return { vec_sub(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall operator-(Simd4Float x)
-{
- return { vec_xor(x.simdInternal_,
- reinterpret_cast<__vector float>(vec_sl(vec_splat_u32(-1), vec_splat_u32(-1)))) };
-}
-
-static inline Simd4Float gmx_simdcall operator*(Simd4Float a, Simd4Float b)
-{
- return { vec_madd(a.simdInternal_, b.simdInternal_,
- reinterpret_cast<__vector float>(vec_splat_u32(0))) };
-}
-
-static inline Simd4Float gmx_simdcall fma(Simd4Float a, Simd4Float b, Simd4Float c)
-{
- return { vec_madd(a.simdInternal_, b.simdInternal_, c.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall fms(Simd4Float a, Simd4Float b, Simd4Float c)
-{
- return { vec_madd(a.simdInternal_, b.simdInternal_, -c.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall fnma(Simd4Float a, Simd4Float b, Simd4Float c)
-{
- return { vec_nmsub(a.simdInternal_, b.simdInternal_, c.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall fnms(Simd4Float a, Simd4Float b, Simd4Float c)
-{
- return { -vec_madd(a.simdInternal_, b.simdInternal_, c.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall rsqrt(Simd4Float x)
-{
- return { vec_rsqrte(x.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall abs(Simd4Float x)
-{
- return { vec_abs(x.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall max(Simd4Float a, Simd4Float b)
-{
- return { vec_max(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall min(Simd4Float a, Simd4Float b)
-{
- return { vec_min(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall round(Simd4Float x)
-{
- return { vec_round(x.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall trunc(Simd4Float x)
-{
- return { vec_trunc(x.simdInternal_) };
-}
-
-static inline float gmx_simdcall dotProduct(Simd4Float a, Simd4Float b)
-{
- float res;
-
- __vector float c = vec_madd(a.simdInternal_, b.simdInternal_,
- reinterpret_cast<__vector float>(vec_splat_u32(0)));
- // Keep only elements 0,1,2 by shifting in zero from right (xor of a vector with itself is 0)
- c = vec_sld(c, vec_xor(a.simdInternal_, a.simdInternal_), 4);
- // calculate sum
- c = vec_add(c, vec_sld(c, c, 8));
- c = vec_add(c, vec_sld(c, c, 4));
- vec_ste(c, 0, &res);
- return res;
-}
-
-static inline void gmx_simdcall transpose(Simd4Float* v0, Simd4Float* v1, Simd4Float* v2, Simd4Float* v3)
-{
- __vector float t0 = vec_mergeh(v0->simdInternal_, v2->simdInternal_);
- __vector float t1 = vec_mergel(v0->simdInternal_, v2->simdInternal_);
- __vector float t2 = vec_mergeh(v1->simdInternal_, v3->simdInternal_);
- __vector float t3 = vec_mergel(v1->simdInternal_, v3->simdInternal_);
- v0->simdInternal_ = vec_mergeh(t0, t2);
- v1->simdInternal_ = vec_mergel(t0, t2);
- v2->simdInternal_ = vec_mergeh(t1, t3);
- v3->simdInternal_ = vec_mergel(t1, t3);
-}
-
-static inline Simd4FBool gmx_simdcall operator==(Simd4Float a, Simd4Float b)
-{
- return { vec_cmpeq(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4FBool gmx_simdcall operator!=(Simd4Float a, Simd4Float b)
-{
- return { vec_or(vec_cmpgt(a.simdInternal_, b.simdInternal_),
- vec_cmplt(a.simdInternal_, b.simdInternal_)) };
-}
-
-static inline Simd4FBool gmx_simdcall operator<(Simd4Float a, Simd4Float b)
-{
- return { vec_cmplt(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4FBool gmx_simdcall operator<=(Simd4Float a, Simd4Float b)
-{
- return { vec_cmple(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4FBool gmx_simdcall operator&&(Simd4FBool a, Simd4FBool b)
-{
- return { vec_and(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4FBool gmx_simdcall operator||(Simd4FBool a, Simd4FBool b)
-{
- return { vec_or(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline bool gmx_simdcall anyTrue(Simd4FBool a)
-{
- return vec_any_ne(a.simdInternal_, reinterpret_cast<__vector vmxBool int>(vec_splat_u32(0)));
-}
-
-static inline Simd4Float gmx_simdcall selectByMask(Simd4Float a, Simd4FBool m)
-{
- return { vec_and(a.simdInternal_, reinterpret_cast<__vector float>(m.simdInternal_)) };
-}
-
-static inline Simd4Float gmx_simdcall selectByNotMask(Simd4Float a, Simd4FBool m)
-{
- return { vec_andc(a.simdInternal_, reinterpret_cast<__vector float>(m.simdInternal_)) };
-}
-
-static inline Simd4Float gmx_simdcall blend(Simd4Float a, Simd4Float b, Simd4FBool sel)
-{
- return { vec_sel(a.simdInternal_, b.simdInternal_, sel.simdInternal_) };
-}
-
-static inline float gmx_simdcall reduce(Simd4Float a)
-{
- __vector float c = a.simdInternal_;
- float res;
-
- // calculate sum
- c = vec_add(c, vec_sld(c, c, 8));
- c = vec_add(c, vec_sld(c, c, 4));
- vec_ste(c, 0, &res);
- return res;
-}
-
-} // namespace gmx
-
-#endif // GMX_SIMD_IMPLEMENTATION_IBM_VMX_SIMD4_FLOAT_H
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2016,2017,2019,2020, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_SIMD_IMPLEMENTATION_IBM_VMX_SIMD_FLOAT_H
-#define GMX_SIMD_IMPLEMENTATION_IBM_VMX_SIMD_FLOAT_H
-
-#include "config.h"
-
-#include <cstdint>
-
-#include "gromacs/math/utilities.h"
-#include "gromacs/utility/basedefinitions.h"
-
-#include "impl_ibm_vmx_definitions.h"
-
-namespace gmx
-{
-
-class SimdFloat
-{
-public:
- SimdFloat() {}
-
- SimdFloat(float f)
- {
- __vector unsigned char perm;
-
- simdInternal_ = vec_lde(0, const_cast<float*>(&f));
- perm = vec_lvsl(0, const_cast<float*>(&f));
- simdInternal_ = vec_perm(simdInternal_, simdInternal_, perm);
- simdInternal_ = vec_splat(simdInternal_, 0);
- }
-
- // Internal utility constructor to simplify return statements
- SimdFloat(__vector float simd) : simdInternal_(simd) {}
-
- __vector float simdInternal_;
-};
-
-class SimdFInt32
-{
-public:
- SimdFInt32() {}
-
- SimdFInt32(std::int32_t i)
- {
- __vector unsigned char perm;
-
- simdInternal_ = vec_lde(0, const_cast<int*>(&i));
- perm = vec_lvsl(0, const_cast<int*>(&i));
- simdInternal_ = vec_perm(simdInternal_, simdInternal_, perm);
- simdInternal_ = vec_splat(simdInternal_, 0);
- }
-
-
- // Internal utility constructor to simplify return statements
- SimdFInt32(__vector signed int simd) : simdInternal_(simd) {}
-
- __vector signed int simdInternal_;
-};
-
-class SimdFBool
-{
-public:
- SimdFBool() {}
-
- SimdFBool(bool b) :
- simdInternal_(reinterpret_cast<__vector vmxBool int>(vec_splats(b ? 0xFFFFFFFF : 0)))
- {
- }
-
- // Internal utility constructor to simplify return statements
- SimdFBool(__vector vmxBool int simd) : simdInternal_(simd) {}
-
- __vector vmxBool int simdInternal_;
-};
-
-class SimdFIBool
-{
-public:
- SimdFIBool() {}
-
- SimdFIBool(bool b) :
- simdInternal_(reinterpret_cast<__vector vmxBool int>(vec_splat_u32(b ? 0xFFFFFFFF : 0)))
- {
- }
-
- // Internal utility constructor to simplify return statements
- SimdFIBool(__vector vmxBool int simd) : simdInternal_(simd) {}
-
- __vector vmxBool int simdInternal_;
-};
-
-static inline SimdFloat gmx_simdcall simdLoad(const float* m, SimdFloatTag = {})
-{
- return { vec_ld(0, const_cast<float*>(m)) };
-}
-
-static inline void gmx_simdcall store(float* m, SimdFloat a)
-{
- vec_st(a.simdInternal_, 0, const_cast<float*>(m));
-}
-
-static inline SimdFloat gmx_simdcall setZeroF()
-{
- return { reinterpret_cast<__vector float>(vec_splat_u32(0)) };
-}
-
-static inline SimdFInt32 gmx_simdcall simdLoad(const std::int32_t* m, SimdFInt32Tag)
-{
- return { vec_ld(0, const_cast<int*>(m)) };
-}
-
-static inline void gmx_simdcall store(std::int32_t* m, SimdFInt32 a)
-{
- vec_st(a.simdInternal_, 0, const_cast<int*>(m));
-}
-
-static inline SimdFInt32 gmx_simdcall setZeroFI()
-{
- return { vec_splat_s32(0) };
-}
-
-static inline SimdFloat gmx_simdcall operator&(SimdFloat a, SimdFloat b)
-{
- return { vec_and(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall andNot(SimdFloat a, SimdFloat b)
-{
- return { vec_andc(b.simdInternal_, a.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall operator|(SimdFloat a, SimdFloat b)
-{
- return { vec_or(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall operator^(SimdFloat a, SimdFloat b)
-{
- return { vec_xor(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall operator+(SimdFloat a, SimdFloat b)
-{
- return { vec_add(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall operator-(SimdFloat a, SimdFloat b)
-{
- return { vec_sub(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall operator-(SimdFloat x)
-{
- return { vec_xor(x.simdInternal_,
- reinterpret_cast<__vector float>(vec_sl(vec_splat_u32(-1), vec_splat_u32(-1)))) };
-}
-
-static inline SimdFloat gmx_simdcall operator*(SimdFloat a, SimdFloat b)
-{
- return { vec_madd(a.simdInternal_, b.simdInternal_,
- reinterpret_cast<__vector float>(vec_splat_u32(0))) };
-}
-
-static inline SimdFloat gmx_simdcall fma(SimdFloat a, SimdFloat b, SimdFloat c)
-{
- return { vec_madd(a.simdInternal_, b.simdInternal_, c.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall fms(SimdFloat a, SimdFloat b, SimdFloat c)
-{
- return { vec_madd(a.simdInternal_, b.simdInternal_, -c.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall fnma(SimdFloat a, SimdFloat b, SimdFloat c)
-{
- return { vec_nmsub(a.simdInternal_, b.simdInternal_, c.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall fnms(SimdFloat a, SimdFloat b, SimdFloat c)
-{
- return { -vec_madd(a.simdInternal_, b.simdInternal_, c.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall rsqrt(SimdFloat x)
-{
- return { vec_rsqrte(x.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall rcp(SimdFloat x)
-{
- return { vec_re(x.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall maskAdd(SimdFloat a, SimdFloat b, SimdFBool m)
-{
- return { vec_add(a.simdInternal_,
- vec_and(b.simdInternal_, reinterpret_cast<__vector float>(m.simdInternal_))) };
-}
-
-static inline SimdFloat gmx_simdcall maskzMul(SimdFloat a, SimdFloat b, SimdFBool m)
-{
- SimdFloat prod = a * b;
-
- return { vec_and(prod.simdInternal_, reinterpret_cast<__vector float>(m.simdInternal_)) };
-}
-
-static inline SimdFloat gmx_simdcall maskzFma(SimdFloat a, SimdFloat b, SimdFloat c, SimdFBool m)
-{
- SimdFloat prod = fma(a, b, c);
-
- return { vec_and(prod.simdInternal_, reinterpret_cast<__vector float>(m.simdInternal_)) };
-}
-
-static inline SimdFloat gmx_simdcall maskzRsqrt(SimdFloat x, SimdFBool m)
-{
-#ifndef NDEBUG
- SimdFloat one(1.0F);
- x.simdInternal_ = vec_sel(one.simdInternal_, x.simdInternal_, m.simdInternal_);
-#endif
- return { vec_and(vec_rsqrte(x.simdInternal_), reinterpret_cast<__vector float>(m.simdInternal_)) };
-}
-
-static inline SimdFloat gmx_simdcall maskzRcp(SimdFloat x, SimdFBool m)
-{
-#ifndef NDEBUG
- SimdFloat one(1.0F);
- x.simdInternal_ = vec_sel(one.simdInternal_, x.simdInternal_, m.simdInternal_);
-#endif
- return { vec_and(vec_re(x.simdInternal_), reinterpret_cast<__vector float>(m.simdInternal_)) };
-}
-
-static inline SimdFloat gmx_simdcall abs(SimdFloat x)
-{
- return { vec_abs(x.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall max(SimdFloat a, SimdFloat b)
-{
- return { vec_max(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall min(SimdFloat a, SimdFloat b)
-{
- return { vec_min(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall round(SimdFloat x)
-{
- return { vec_round(x.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall trunc(SimdFloat x)
-{
- return { vec_trunc(x.simdInternal_) };
-}
-
-template<MathOptimization opt = MathOptimization::Safe>
-static inline SimdFloat gmx_simdcall frexp(SimdFloat value, SimdFInt32* exponent)
-{
- // Generate constants without memory operations
- const __vector signed int exponentMask =
- vec_sl(vec_add(vec_splat_s32(15), vec_sl(vec_splat_s32(15), vec_splat_u32(4))),
- vec_add(vec_splat_u32(15), vec_splat_u32(8))); // 0x7F800000
- const __vector signed int exponentBias =
- vec_sub(vec_sl(vec_splat_s32(1), vec_splat_u32(7)), vec_splat_s32(2)); // 126
- const SimdFloat half(0.5F);
- __vector signed int iExponent;
-
- __vector vmxBool int valueIsZero =
- vec_cmpeq(value.simdInternal_, reinterpret_cast<__vector float>(vec_splat_u32(0)));
-
- iExponent = vec_and(reinterpret_cast<__vector signed int>(value.simdInternal_), exponentMask);
- iExponent = vec_sr(iExponent, vec_add(vec_splat_u32(15), vec_splat_u32(8)));
- iExponent = vec_sub(iExponent, exponentBias);
- iExponent = vec_andc(iExponent, reinterpret_cast<__vector int>(valueIsZero));
-
- __vector float result =
- vec_or(vec_andc(value.simdInternal_, reinterpret_cast<__vector float>(exponentMask)),
- half.simdInternal_);
- result = vec_sel(result, value.simdInternal_, valueIsZero);
-
- exponent->simdInternal_ = iExponent;
-
- return { result };
-}
-
-template<MathOptimization opt = MathOptimization::Safe>
-static inline SimdFloat gmx_simdcall ldexp(SimdFloat value, SimdFInt32 exponent)
-{
- const __vector signed int exponentBias =
- vec_sub(vec_sl(vec_splat_s32(1), vec_splat_u32(7)), vec_splat_s32(1)); // 127
- __vector signed int iExponent;
-
- iExponent = vec_add(exponent.simdInternal_, exponentBias);
-
- if (opt == MathOptimization::Safe)
- {
- // Make sure biased argument is not negative
- iExponent = vec_max(iExponent, vec_splat_s32(0));
- }
-
- iExponent = vec_sl(iExponent, vec_add(vec_splat_u32(15), vec_splat_u32(8)));
-
- return { vec_madd(value.simdInternal_, reinterpret_cast<__vector float>(iExponent),
- reinterpret_cast<__vector float>(vec_splat_u32(0))) };
-}
-
-static inline float gmx_simdcall reduce(SimdFloat a)
-{
- __vector float c = a.simdInternal_;
- float res;
-
- // calculate sum
- c = vec_add(c, vec_sld(c, c, 8));
- c = vec_add(c, vec_sld(c, c, 4));
- vec_ste(c, 0, &res);
- return res;
-}
-
-static inline SimdFBool gmx_simdcall operator==(SimdFloat a, SimdFloat b)
-{
- return { vec_cmpeq(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFBool gmx_simdcall operator!=(SimdFloat a, SimdFloat b)
-{
- return { vec_or(vec_cmpgt(a.simdInternal_, b.simdInternal_),
- vec_cmplt(a.simdInternal_, b.simdInternal_)) };
-}
-
-static inline SimdFBool gmx_simdcall operator<(SimdFloat a, SimdFloat b)
-{
- return { vec_cmplt(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFBool gmx_simdcall operator<=(SimdFloat a, SimdFloat b)
-{
- return { vec_cmple(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFBool gmx_simdcall testBits(SimdFloat a)
-{
- return { vec_cmpgt(reinterpret_cast<__vector unsigned int>(a.simdInternal_), vec_splat_u32(0)) };
-}
-
-static inline SimdFBool gmx_simdcall operator&&(SimdFBool a, SimdFBool b)
-{
- return { vec_and(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFBool gmx_simdcall operator||(SimdFBool a, SimdFBool b)
-{
- return { vec_or(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline bool gmx_simdcall anyTrue(SimdFBool a)
-{
- return vec_any_ne(a.simdInternal_, reinterpret_cast<__vector vmxBool int>(vec_splat_u32(0)));
-}
-
-static inline SimdFloat gmx_simdcall selectByMask(SimdFloat a, SimdFBool m)
-{
- return { vec_and(a.simdInternal_, reinterpret_cast<__vector float>(m.simdInternal_)) };
-}
-
-static inline SimdFloat gmx_simdcall selectByNotMask(SimdFloat a, SimdFBool m)
-{
- return { vec_andc(a.simdInternal_, reinterpret_cast<__vector float>(m.simdInternal_)) };
-}
-
-static inline SimdFloat gmx_simdcall blend(SimdFloat a, SimdFloat b, SimdFBool sel)
-{
- return { vec_sel(a.simdInternal_, b.simdInternal_, sel.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall operator&(SimdFInt32 a, SimdFInt32 b)
-{
- return { vec_and(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall andNot(SimdFInt32 a, SimdFInt32 b)
-{
- return { vec_andc(b.simdInternal_, a.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall operator|(SimdFInt32 a, SimdFInt32 b)
-{
- return { vec_or(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall operator^(SimdFInt32 a, SimdFInt32 b)
-{
- return { vec_xor(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall operator+(SimdFInt32 a, SimdFInt32 b)
-{
- return { vec_add(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall operator-(SimdFInt32 a, SimdFInt32 b)
-{
- return { vec_sub(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall operator*(SimdFInt32 a, SimdFInt32 b)
-{
- return { a.simdInternal_ * b.simdInternal_ };
-}
-
-static inline SimdFIBool gmx_simdcall operator==(SimdFInt32 a, SimdFInt32 b)
-{
- return { vec_cmpeq(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFIBool gmx_simdcall testBits(SimdFInt32 a)
-{
- return { vec_cmpgt(reinterpret_cast<__vector unsigned int>(a.simdInternal_), vec_splat_u32(0)) };
-}
-
-static inline SimdFIBool gmx_simdcall operator<(SimdFInt32 a, SimdFInt32 b)
-{
- return { vec_cmplt(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFIBool gmx_simdcall operator&&(SimdFIBool a, SimdFIBool b)
-{
- return { vec_and(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFIBool gmx_simdcall operator||(SimdFIBool a, SimdFIBool b)
-{
- return { vec_or(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline bool gmx_simdcall anyTrue(SimdFIBool a)
-{
- return vec_any_ne(a.simdInternal_, reinterpret_cast<__vector vmxBool int>(vec_splat_u32(0)));
-}
-
-static inline SimdFInt32 gmx_simdcall selectByMask(SimdFInt32 a, SimdFIBool m)
-{
- return { vec_and(a.simdInternal_, reinterpret_cast<__vector signed int>(m.simdInternal_)) };
-}
-
-static inline SimdFInt32 gmx_simdcall selectByNotMask(SimdFInt32 a, SimdFIBool m)
-{
- return { vec_andc(a.simdInternal_, reinterpret_cast<__vector signed int>(m.simdInternal_)) };
-}
-
-static inline SimdFInt32 gmx_simdcall blend(SimdFInt32 a, SimdFInt32 b, SimdFIBool sel)
-{
- return { vec_sel(a.simdInternal_, b.simdInternal_, sel.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall cvtR2I(SimdFloat a)
-{
- return { vec_cts(vec_round(a.simdInternal_), 0) };
-}
-
-static inline SimdFInt32 gmx_simdcall cvttR2I(SimdFloat a)
-{
- return { vec_cts(a.simdInternal_, 0) };
-}
-
-static inline SimdFloat gmx_simdcall cvtI2R(SimdFInt32 a)
-{
- return { vec_ctf(a.simdInternal_, 0) };
-}
-
-static inline SimdFIBool gmx_simdcall cvtB2IB(SimdFBool a)
-{
- return { a.simdInternal_ };
-}
-
-static inline SimdFBool gmx_simdcall cvtIB2B(SimdFIBool a)
-{
- return { a.simdInternal_ };
-}
-
-} // namespace gmx
-
-#endif // GMX_SIMD_IMPLEMENTATION_IBM_VMX_SIMD_FLOAT_H
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifndef GMX_SIMD_IMPL_IBM_VMX_UTIL_FLOAT_H
-#define GMX_SIMD_IMPL_IBM_VMX_UTIL_FLOAT_H
-
-#include "config.h"
-
-#include <cstddef>
-#include <cstdint>
-
-#include "gromacs/utility/basedefinitions.h"
-
-#include "impl_ibm_vmx_definitions.h"
-#include "impl_ibm_vmx_simd_float.h"
-
-namespace gmx
-{
-
-template<int align>
-static inline void gmx_simdcall gatherLoadTranspose(const float* base,
- const std::int32_t offset[],
- SimdFloat* v0,
- SimdFloat* v1,
- SimdFloat* v2,
- SimdFloat* v3)
-{
- *v0 = simdLoad(base + align * offset[0]);
- *v1 = simdLoad(base + align * offset[1]);
- *v2 = simdLoad(base + align * offset[2]);
- *v3 = simdLoad(base + align * offset[3]);
-
- __vector float t0 = vec_mergeh(v0->simdInternal_, v2->simdInternal_);
- __vector float t1 = vec_mergel(v0->simdInternal_, v2->simdInternal_);
- __vector float t2 = vec_mergeh(v1->simdInternal_, v3->simdInternal_);
- __vector float t3 = vec_mergel(v1->simdInternal_, v3->simdInternal_);
- v0->simdInternal_ = vec_mergeh(t0, t2);
- v1->simdInternal_ = vec_mergel(t0, t2);
- v2->simdInternal_ = vec_mergeh(t1, t3);
- v3->simdInternal_ = vec_mergel(t1, t3);
-}
-
-template<int align>
-static inline void gmx_simdcall
- gatherLoadTranspose(const float* base, const std::int32_t offset[], SimdFloat* v0, SimdFloat* v1)
-{
- if (align % 4 == 0)
- {
- SimdFloat t2, t3;
-
- gatherLoadTranspose<align>(base, offset, v0, v1, &t2, &t3);
- }
- else
- {
- __vector float t0, t1, t2, t3, t4, t5, t6, t7;
- __vector unsigned char p0, p1, p2, p3;
-
- // This is REALLY slow, since we have no choice but to load individual
- // elements when we cannot guarantee that we can access beyond the end of
- // the memory. Fortunately, 99% of the usage should be the aligned-to-4
- // case above instead.
- t0 = vec_lde(0, base + align * offset[0]);
- t1 = vec_lde(0, base + align * offset[1]);
- t2 = vec_lde(0, base + align * offset[2]);
- t3 = vec_lde(0, base + align * offset[3]);
- p0 = vec_lvsl(0, base + align * offset[0]);
- p1 = vec_lvsl(0, base + align * offset[1]);
- p2 = vec_lvsl(0, base + align * offset[2]);
- p3 = vec_lvsl(0, base + align * offset[3]);
- t0 = vec_perm(t0, t0, p0);
- t1 = vec_perm(t1, t1, p1);
- t2 = vec_perm(t2, t2, p2);
- t3 = vec_perm(t3, t3, p3);
- t0 = vec_mergeh(t0, t2);
- t1 = vec_mergeh(t1, t3);
- v0->simdInternal_ = vec_mergeh(t0, t1);
-
- t4 = vec_lde(0, base + align * offset[0] + 1);
- t5 = vec_lde(0, base + align * offset[1] + 1);
- t6 = vec_lde(0, base + align * offset[2] + 1);
- t7 = vec_lde(0, base + align * offset[3] + 1);
- p0 = vec_lvsl(0, base + align * offset[0] + 1);
- p1 = vec_lvsl(0, base + align * offset[1] + 1);
- p2 = vec_lvsl(0, base + align * offset[2] + 1);
- p3 = vec_lvsl(0, base + align * offset[3] + 1);
- t4 = vec_perm(t4, t4, p0);
- t5 = vec_perm(t5, t5, p1);
- t6 = vec_perm(t6, t6, p2);
- t7 = vec_perm(t7, t7, p3);
- t4 = vec_mergeh(t4, t6);
- t5 = vec_mergeh(t5, t7);
- v1->simdInternal_ = vec_mergeh(t4, t5);
- }
-}
-
-static const int c_simdBestPairAlignmentFloat = 2;
-
-template<int align>
-static inline void gmx_simdcall gatherLoadUTranspose(const float* base,
- const std::int32_t offset[],
- SimdFloat* v0,
- SimdFloat* v1,
- SimdFloat* v2)
-{
- if (align % 4 == 0)
- {
- SimdFloat t3;
- gatherLoadTranspose<align>(base, offset, v0, v1, v2, &t3);
- }
- else
- {
- __vector float t0, t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11;
- __vector unsigned char p0, p1, p2, p3;
-
- // This is REALLY slow, since we have no choice but to load individual
- // elements when we cannot guarantee that we can access beyond the end of
- // the memory. Unfortunately this is likely the most common case.
- t0 = vec_lde(0, base + align * offset[0]);
- t1 = vec_lde(0, base + align * offset[1]);
- t2 = vec_lde(0, base + align * offset[2]);
- t3 = vec_lde(0, base + align * offset[3]);
- p0 = vec_lvsl(0, base + align * offset[0]);
- p1 = vec_lvsl(0, base + align * offset[1]);
- p2 = vec_lvsl(0, base + align * offset[2]);
- p3 = vec_lvsl(0, base + align * offset[3]);
- t0 = vec_perm(t0, t0, p0);
- t1 = vec_perm(t1, t1, p1);
- t2 = vec_perm(t2, t2, p2);
- t3 = vec_perm(t3, t3, p3);
- t0 = vec_mergeh(t0, t2);
- t1 = vec_mergeh(t1, t3);
- v0->simdInternal_ = vec_mergeh(t0, t1);
-
- t4 = vec_lde(0, base + align * offset[0] + 1);
- t5 = vec_lde(0, base + align * offset[1] + 1);
- t6 = vec_lde(0, base + align * offset[2] + 1);
- t7 = vec_lde(0, base + align * offset[3] + 1);
- p0 = vec_lvsl(0, base + align * offset[0] + 1);
- p1 = vec_lvsl(0, base + align * offset[1] + 1);
- p2 = vec_lvsl(0, base + align * offset[2] + 1);
- p3 = vec_lvsl(0, base + align * offset[3] + 1);
- t4 = vec_perm(t4, t4, p0);
- t5 = vec_perm(t5, t5, p1);
- t6 = vec_perm(t6, t6, p2);
- t7 = vec_perm(t7, t7, p3);
- t4 = vec_mergeh(t4, t6);
- t5 = vec_mergeh(t5, t7);
- v1->simdInternal_ = vec_mergeh(t4, t5);
-
- t8 = vec_lde(0, base + align * offset[0] + 2);
- t9 = vec_lde(0, base + align * offset[1] + 2);
- t10 = vec_lde(0, base + align * offset[2] + 2);
- t11 = vec_lde(0, base + align * offset[3] + 2);
- p0 = vec_lvsl(0, base + align * offset[0] + 2);
- p1 = vec_lvsl(0, base + align * offset[1] + 2);
- p2 = vec_lvsl(0, base + align * offset[2] + 2);
- p3 = vec_lvsl(0, base + align * offset[3] + 2);
- t8 = vec_perm(t8, t8, p0);
- t9 = vec_perm(t9, t9, p1);
- t10 = vec_perm(t10, t10, p2);
- t11 = vec_perm(t11, t11, p3);
- t8 = vec_mergeh(t8, t10);
- t9 = vec_mergeh(t9, t11);
- v2->simdInternal_ = vec_mergeh(t8, t9);
- }
-}
-
-
-template<int align>
-static inline void gmx_simdcall
- transposeScatterStoreU(float* base, const std::int32_t offset[], SimdFloat v0, SimdFloat v1, SimdFloat v2)
-{
- __vector unsigned char p0, p1, p2, p3;
-
- __vector float t0 = vec_mergeh(v0.simdInternal_, v2.simdInternal_);
- __vector float t1 = vec_mergel(v0.simdInternal_, v2.simdInternal_);
- __vector float t2 = vec_mergeh(v1.simdInternal_, v2.simdInternal_);
- __vector float t3 = vec_mergel(v1.simdInternal_, v2.simdInternal_);
- __vector float t4 = vec_mergeh(t0, t2);
- __vector float t5 = vec_mergel(t0, t2);
- __vector float t6 = vec_mergeh(t1, t3);
- __vector float t7 = vec_mergel(t1, t3);
-
- p0 = vec_lvsr(0, base + align * offset[0]);
- p1 = vec_lvsr(0, base + align * offset[1]);
- p2 = vec_lvsr(0, base + align * offset[2]);
- p3 = vec_lvsr(0, base + align * offset[3]);
-
- t4 = vec_perm(t4, t4, p0);
- t5 = vec_perm(t5, t5, p1);
- t6 = vec_perm(t6, t6, p2);
- t7 = vec_perm(t7, t7, p3);
-
- vec_ste(t4, 0, base + align * offset[0]);
- vec_ste(t4, 4, base + align * offset[0]);
- vec_ste(t4, 8, base + align * offset[0]);
- vec_ste(t5, 0, base + align * offset[1]);
- vec_ste(t5, 4, base + align * offset[1]);
- vec_ste(t5, 8, base + align * offset[1]);
- vec_ste(t6, 0, base + align * offset[2]);
- vec_ste(t6, 4, base + align * offset[2]);
- vec_ste(t6, 8, base + align * offset[2]);
- vec_ste(t7, 0, base + align * offset[3]);
- vec_ste(t7, 4, base + align * offset[3]);
- vec_ste(t7, 8, base + align * offset[3]);
-}
-
-
-template<int align>
-static inline void gmx_simdcall
- transposeScatterIncrU(float* base, const std::int32_t offset[], SimdFloat v0, SimdFloat v1, SimdFloat v2)
-{
- if (align % 4 == 0)
- {
- __vector float zero = reinterpret_cast<__vector float>(vec_splat_u32(0));
- __vector float t0 = vec_mergeh(v0.simdInternal_, v2.simdInternal_);
- __vector float t1 = vec_mergel(v0.simdInternal_, v2.simdInternal_);
- __vector float t2 = vec_mergeh(v1.simdInternal_, zero);
- __vector float t3 = vec_mergel(v1.simdInternal_, zero);
- __vector float t4 = vec_mergeh(t0, t2);
- __vector float t5 = vec_mergel(t0, t2);
- __vector float t6 = vec_mergeh(t1, t3);
- __vector float t7 = vec_mergel(t1, t3);
-
- vec_st(vec_add(vec_ld(0, base + align * offset[0]), t4), 0, base + align * offset[0]);
- vec_st(vec_add(vec_ld(0, base + align * offset[1]), t5), 0, base + align * offset[1]);
- vec_st(vec_add(vec_ld(0, base + align * offset[2]), t6), 0, base + align * offset[2]);
- vec_st(vec_add(vec_ld(0, base + align * offset[3]), t7), 0, base + align * offset[3]);
- }
- else
- {
- alignas(GMX_SIMD_ALIGNMENT) float rdata0[GMX_SIMD_FLOAT_WIDTH];
- alignas(GMX_SIMD_ALIGNMENT) float rdata1[GMX_SIMD_FLOAT_WIDTH];
- alignas(GMX_SIMD_ALIGNMENT) float rdata2[GMX_SIMD_FLOAT_WIDTH];
-
- vec_st(v0.simdInternal_, 0, rdata0);
- vec_st(v1.simdInternal_, 0, rdata1);
- vec_st(v2.simdInternal_, 0, rdata2);
-
- base[align * offset[0] + 0] += rdata0[0];
- base[align * offset[0] + 1] += rdata1[0];
- base[align * offset[0] + 2] += rdata2[0];
- base[align * offset[1] + 0] += rdata0[1];
- base[align * offset[1] + 1] += rdata1[1];
- base[align * offset[1] + 2] += rdata2[1];
- base[align * offset[2] + 0] += rdata0[2];
- base[align * offset[2] + 1] += rdata1[2];
- base[align * offset[2] + 2] += rdata2[2];
- base[align * offset[3] + 0] += rdata0[3];
- base[align * offset[3] + 1] += rdata1[3];
- base[align * offset[3] + 2] += rdata2[3];
- }
-}
-
-template<int align>
-static inline void gmx_simdcall
- transposeScatterDecrU(float* base, const std::int32_t offset[], SimdFloat v0, SimdFloat v1, SimdFloat v2)
-{
- if (align % 4 == 0)
- {
- __vector float zero = reinterpret_cast<__vector float>(vec_splat_u32(0));
- __vector float t0 = vec_mergeh(v0.simdInternal_, v2.simdInternal_);
- __vector float t1 = vec_mergel(v0.simdInternal_, v2.simdInternal_);
- __vector float t2 = vec_mergeh(v1.simdInternal_, zero);
- __vector float t3 = vec_mergel(v1.simdInternal_, zero);
- __vector float t4 = vec_mergeh(t0, t2);
- __vector float t5 = vec_mergel(t0, t2);
- __vector float t6 = vec_mergeh(t1, t3);
- __vector float t7 = vec_mergel(t1, t3);
-
- vec_st(vec_sub(vec_ld(0, base + align * offset[0]), t4), 0, base + align * offset[0]);
- vec_st(vec_sub(vec_ld(0, base + align * offset[1]), t5), 0, base + align * offset[1]);
- vec_st(vec_sub(vec_ld(0, base + align * offset[2]), t6), 0, base + align * offset[2]);
- vec_st(vec_sub(vec_ld(0, base + align * offset[3]), t7), 0, base + align * offset[3]);
- }
- else
- {
- alignas(GMX_SIMD_ALIGNMENT) float rdata0[GMX_SIMD_FLOAT_WIDTH];
- alignas(GMX_SIMD_ALIGNMENT) float rdata1[GMX_SIMD_FLOAT_WIDTH];
- alignas(GMX_SIMD_ALIGNMENT) float rdata2[GMX_SIMD_FLOAT_WIDTH];
-
- vec_st(v0.simdInternal_, 0, rdata0);
- vec_st(v1.simdInternal_, 0, rdata1);
- vec_st(v2.simdInternal_, 0, rdata2);
-
- base[align * offset[0] + 0] -= rdata0[0];
- base[align * offset[0] + 1] -= rdata1[0];
- base[align * offset[0] + 2] -= rdata2[0];
- base[align * offset[1] + 0] -= rdata0[1];
- base[align * offset[1] + 1] -= rdata1[1];
- base[align * offset[1] + 2] -= rdata2[1];
- base[align * offset[2] + 0] -= rdata0[2];
- base[align * offset[2] + 1] -= rdata1[2];
- base[align * offset[2] + 2] -= rdata2[2];
- base[align * offset[3] + 0] -= rdata0[3];
- base[align * offset[3] + 1] -= rdata1[3];
- base[align * offset[3] + 2] -= rdata2[3];
- }
-}
-
-static inline void gmx_simdcall expandScalarsToTriplets(SimdFloat scalar,
- SimdFloat* triplets0,
- SimdFloat* triplets1,
- SimdFloat* triplets2)
-{
- const __vector unsigned char perm0 = { 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 4, 5, 6, 7 };
- const __vector unsigned char perm1 = { 4, 5, 6, 7, 4, 5, 6, 7, 8, 9, 10, 11, 8, 9, 10, 11 };
- const __vector unsigned char perm2 = { 8, 9, 10, 11, 12, 13, 14, 15,
- 12, 13, 14, 15, 12, 13, 14, 15 };
-
- triplets0->simdInternal_ = vec_perm(scalar.simdInternal_, scalar.simdInternal_, perm0);
- triplets1->simdInternal_ = vec_perm(scalar.simdInternal_, scalar.simdInternal_, perm1);
- triplets2->simdInternal_ = vec_perm(scalar.simdInternal_, scalar.simdInternal_, perm2);
-}
-
-
-template<int align>
-static inline void gmx_simdcall gatherLoadBySimdIntTranspose(const float* base,
- SimdFInt32 offset,
- SimdFloat* v0,
- SimdFloat* v1,
- SimdFloat* v2,
- SimdFloat* v3)
-{
- alignas(GMX_SIMD_ALIGNMENT) std::int32_t ioffset[GMX_SIMD_FINT32_WIDTH];
-
- vec_st(offset.simdInternal_, 0, ioffset);
- gatherLoadTranspose<align>(base, ioffset, v0, v1, v2, v3);
-}
-
-template<int align>
-static inline void gmx_simdcall
- gatherLoadBySimdIntTranspose(const float* base, SimdFInt32 offset, SimdFloat* v0, SimdFloat* v1)
-{
- alignas(GMX_SIMD_ALIGNMENT) std::int32_t ioffset[GMX_SIMD_FINT32_WIDTH];
-
- vec_st(offset.simdInternal_, 0, ioffset);
- gatherLoadTranspose<align>(base, ioffset, v0, v1);
-}
-
-
-static inline float gmx_simdcall reduceIncr4ReturnSum(float* m, SimdFloat v0, SimdFloat v1, SimdFloat v2, SimdFloat v3)
-{
- __vector float t0 = vec_mergeh(v0.simdInternal_, v2.simdInternal_);
- __vector float t1 = vec_mergel(v0.simdInternal_, v2.simdInternal_);
- __vector float t2 = vec_mergeh(v1.simdInternal_, v3.simdInternal_);
- __vector float t3 = vec_mergel(v1.simdInternal_, v3.simdInternal_);
- v0.simdInternal_ = vec_mergeh(t0, t2);
- v1.simdInternal_ = vec_mergel(t0, t2);
- v2.simdInternal_ = vec_mergeh(t1, t3);
- v3.simdInternal_ = vec_mergel(t1, t3);
-
- v0 = v0 + v1;
- v2 = v2 + v3;
- v0 = v0 + v2;
- v2 = v0 + simdLoad(m);
- store(m, v2);
-
- return reduce(v0);
-}
-
-} // namespace gmx
-
-#endif // GMX_SIMD_IMPL_IBM_VMX_UTIL_FLOAT_H
const __vector unsigned char perm = { 8, 9, 10, 11, 12, 13, 14, 15, 0, 1, 2, 3, 4, 5, 6, 7 };
#ifdef __xlC__
/* old xlc version 12 does not understand vec_perm() with double arguments */
- x.simdInternal_ = vec_add(
- x.simdInternal_, reinterpret_cast<__vector double>(vec_perm(
- reinterpret_cast<__vector signed int>(x.simdInternal_),
- reinterpret_cast<__vector signed int>(x.simdInternal_), perm)));
+ x.simdInternal_ = vec_add(x.simdInternal_,
+ reinterpret_cast<__vector double>(vec_perm(
+ reinterpret_cast<__vector signed int>(x.simdInternal_),
+ reinterpret_cast<__vector signed int>(x.simdInternal_),
+ perm)));
#else
x.simdInternal_ = vec_add(x.simdInternal_, vec_perm(x.simdInternal_, x.simdInternal_, perm));
#endif
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_SIMD_IMPL_SPARC64_HPC_ACE_H
-#define GMX_SIMD_IMPL_SPARC64_HPC_ACE_H
-
-#include "impl_sparc64_hpc_ace_simd_double.h"
-#include "impl_sparc64_hpc_ace_simd_float.h"
-/* No SIMD4 support, since both single & double are only 2-wide */
-
-#endif /* GMX_SIMD_IMPL_SPARC64_HPC_ACE_H */
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2018,2019, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_SIMD_IMPL_SPARC64_HPC_ACE_COMMON_H
-#define GMX_SIMD_IMPL_SPARC64_HPC_ACE_COMMON_H
-
-/* Capability definitions for Sparc64 HPC-ACE */
-/* HPC-ACE is actually double-only on the register level, but we also implement
- * a single-precision interface where we only offer single-precision accuracy
- * in math functions - this can save quite a few cycles.
- */
-#define GMX_SIMD 1
-#define GMX_SIMD_HAVE_FLOAT 1
-#define GMX_SIMD_HAVE_DOUBLE 1
-#define GMX_SIMD_HAVE_LOADU 0
-#define GMX_SIMD_HAVE_STOREU 0
-#define GMX_SIMD_HAVE_LOGICAL 1
-#define GMX_SIMD_HAVE_FMA 1
-#define GMX_SIMD_HAVE_FINT32_EXTRACT 1
-#define GMX_SIMD_HAVE_FINT32_LOGICAL 1
-#define GMX_SIMD_HAVE_FINT32_ARITHMETICS 0
-#define GMX_SIMD_HAVE_DINT32_EXTRACT 1
-#define GMX_SIMD_HAVE_DINT32_LOGICAL 1
-#define GMX_SIMD_HAVE_DINT32_ARITHMETICS 0
-#define GMX_SIMD4_HAVE_FLOAT 0
-#define GMX_SIMD4_HAVE_DOUBLE 0
-
-/* Implementation details */
-#define GMX_SIMD_FLOAT_WIDTH 2
-#define GMX_SIMD_DOUBLE_WIDTH 2
-#define GMX_SIMD_FINT32_WIDTH 2
-#define GMX_SIMD_DINT32_WIDTH 2
-/* No SIMD4 support in either single or double */
-#define GMX_SIMD_RSQRT_BITS 10
-#define GMX_SIMD_RCP_BITS 9
-
-#endif /* GMX_SIMD_IMPL_SPARC64_HPC_ACE_COMMON_H */
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2019, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_SIMD_IMPL_SPARC64_HPC_ACE_SIMD_DOUBLE_H
-#define GMX_SIMD_IMPL_SPARC64_HPC_ACE_SIMD_DOUBLE_H
-
-/* Fujitsu header borrows the name from SSE2, since some instructions have aliases.
- * Environment/compiler version GM-1.2.0-17 seems to be buggy; when -Xg is
- * defined to enable GNUC extensions, this sets _ISOC99_SOURCE, which in
- * turn causes all intrinsics to be declared inline _instead_ of static. This
- * leads to duplicate symbol errors at link time.
- * To work around this we unset this before including the HPC-ACE header, and
- * reset the value afterwards.
- */
-#ifdef _ISOC99_SOURCE
-# undef _ISOC99_SOURCE
-# define SAVE_ISOC99_SOURCE
-#endif
-
-#include <emmintrin.h>
-
-#ifdef SAVE_ISOC99_SOURCE
-# define _ISOC99_SOURCE
-# undef SAVE_ISOC99_SOURCE
-#endif
-
-#include <cmath>
-#include <cstdint>
-
-#include "impl_sparc64_hpc_ace_common.h"
-
-/****************************************************
- * DOUBLE PRECISION SIMD IMPLEMENTATION *
- ****************************************************/
-#define SimdDouble _fjsp_v2r8
-#define simdLoadD _fjsp_load_v2r8
-#define simdLoad1D(m) _fjsp_set_v2r8((*m), (*m))
-#define simdSet1D(a) _fjsp_set_v2r8(a, a)
-#define simdStoreD _fjsp_store_v2r8
-#define simdLoadUD simdLoadD
-/* No unaligned store of SimdDouble */
-#define simdSetZeroD _fjsp_setzero_v2r8
-#define simdAddD _fjsp_add_v2r8
-#define simdSubD _fjsp_sub_v2r8
-#define simdMulD _fjsp_mul_v2r8
-#define simdFmaddD(a, b, c) _fjsp_madd_v2r8(a, b, c)
-#define simdFmsubD(a, b, c) _fjsp_msub_v2r8(a, b, c)
-#define simdFnmaddD(a, b, c) _fjsp_nmsub_v2r8(a, b, c)
-#define simdFnmsubD(a, b, c) _fjsp_nmadd_v2r8(a, b, c)
-#define simdAndD _fjsp_and_v2r8
-#define simdAndNotD _fjsp_andnot1_v2r8
-#define simdOrD _fjsp_or_v2r8
-#define simdXorD _fjsp_xor_v2r8
-#define simdRsqrtD(x) _fjsp_rsqrta_v2r8(x)
-#define simdRcpD(x) _fjsp_rcpa_v2r8(x)
-#define simdAbsD(x) _fjsp_abs_v2r8(x)
-#define simdNegD(x) _fjsp_neg_v2r8(x)
-#define simdMaxD _fjsp_max_v2r8
-#define simdMinD _fjsp_min_v2r8
-#define simdRoundD(x) simdCvtI2D(simdCvtD2I(x))
-#define simdTruncD(x) simdCvtI2D(simdCvttD2I(x))
-#define simdFractionD(x) simdSubD(x, simdTruncD(x))
-#define simdGetExponentD simdGetExponentD_sparc64_hpc_ace
-#define simdGetMantissaD simdGetMantissaD_sparc64_hpc_ace
-#define simdSetExponentD simdSetExponentD_sparc64_hpc_ace
-/* integer datatype corresponding to double: SimdDInt32 */
-#define SimdDInt32 _fjsp_v2r8
-#define simdLoadDI(m) simdLoadDI_sparc64_hpc_ace(m)
-#define simdSet1DI(i) simdSet1DI_sparc64_hpc_ace(i)
-#define simdStoreDI(m, x) simdStoreDI_sparc64_hpc_ace(m, x)
-#define simdLoadUDI simdLoadDI
-/* No unaligned store of SimdDInt32 */
-#define simdSetZeroDI _fjsp_setzero_v2r8
-#define simdCvtD2I simdCvtD2I_sparc64_hpc_ace
-#define simdCvttD2I _fjsp_dtox_v2r8
-#define simdCvtI2D _fjsp_xtod_v2r8
-#define simdExtractDI simdExtractDI_sparc64_hpc_ace
-/* Integer logical ops on SimdDInt32 */
-#define simdSlliDI simdSlliDI_sparc64_hpc_ace
-#define simdSrliDI simdSrliDI_sparc64_hpc_ace
-#define simdAndDI _fjsp_and_v2r8
-#define simdAndNotDI _fjsp_andnot1_v2r8
-#define simdOrDI _fjsp_or_v2r8
-#define simdXorDI _fjsp_xor_v2r8
-/* Integer arithmetic ops on integer datatype corresponding to double */
-/* Boolean & comparison operations on SimdDouble */
-#define SimdDBool _fjsp_v2r8
-#define simdCmpEqD _fjsp_cmpeq_v2r8
-#define simdCmpLtD _fjsp_cmplt_v2r8
-#define simdCmpLeD _fjsp_cmple_v2r8
-#define simdAndDB _fjsp_and_v2r8
-#define simdOrDB _fjsp_or_v2r8
-#define simdAnyTrueDB gmx_simd_anytrue_d_sparc64_hpc_ace
-#define simdMaskD _fjsp_and_v2r8
-#define simdMaskNotD(a, sel) _fjsp_andnot1_v2r8(sel, a)
-#define simdBlendD(a, b, sel) _fjsp_selmov_v2r8(b, a, sel)
-#define simdReduceD(a) simdReduceD_sparc64_hpc_ace(a)
-
-/* No boolean & comparison operations on SimdDInt32 */
-/* Float/double conversion */
-#define simdCvtF2D(f) (f)
-#define simdCvtD2F(d) (d)
-
-
-/****************************************************
- * DOUBLE PRECISION IMPLEMENTATION HELPER FUNCTIONS *
- ****************************************************/
-static inline SimdDInt32 simdLoadDI_sparc64_hpc_ace(const int* m)
-{
- union {
- _fjsp_v2r8 simd;
- long long int i[2];
- } conv;
-
- conv.i[0] = m[0];
- conv.i[1] = m[1];
-
- return _fjsp_load_v2r8((double*)&(conv.simd));
-}
-
-static inline void simdStoreDI_sparc64_hpc_ace(int* m, SimdDInt32 x)
-{
- union {
- _fjsp_v2r8 simd;
- long long int i[2];
- } conv;
-
- _fjsp_store_v2r8((double*)&(conv.simd), x);
-
- m[0] = conv.i[0];
- m[1] = conv.i[1];
-}
-
-static inline SimdDInt32 simdSet1DI_sparc64_hpc_ace(int i)
-{
- union {
- _fjsp_v2r8 simd;
- long long int i[2];
- } conv;
-
- conv.i[0] = i;
- conv.i[1] = i;
-
- return _fjsp_load_v2r8((double*)&(conv.simd));
-}
-
-static inline int simdExtractDI_sparc64_hpc_ace(SimdDInt32 x, int i)
-{
- long long int res;
- /* This conditional should be optimized away at compile time */
- if (i == 0)
- {
- _fjsp_storel_v2r8((double*)&res, x);
- }
- else
- {
- _fjsp_storeh_v2r8((double*)&res, x);
- }
- return (int)res;
-}
-
-static inline SimdDInt32 simdSlliDI_sparc64_hpc_ace(SimdDInt32 x, int i)
-{
- _fjsp_v2i8 ix = *((_fjsp_v2i8*)&x);
- ix = _fjsp_slli_v2i8(ix, i);
- x = *((_fjsp_v2r8*)&ix);
- return x;
-}
-
-static inline SimdDInt32 simdSrliDI_sparc64_hpc_ace(SimdDInt32 x, int i)
-{
- _fjsp_v2i8 ix = *((_fjsp_v2i8*)&x);
- ix = _fjsp_srli_v2i8(ix, i);
- x = *((_fjsp_v2r8*)&ix);
- return x;
-}
-
-static inline SimdDInt32 simdCvtD2I_sparc64_hpc_ace(SimdDouble x)
-{
- _fjsp_v2r8 signbit = _fjsp_set_v2r8(-0.0, -0.0);
- _fjsp_v2r8 half = _fjsp_set_v2r8(0.5, 0.5);
-
- x = _fjsp_add_v2r8(x, _fjsp_or_v2r8(_fjsp_and_v2r8(signbit, x), half));
- return _fjsp_dtox_v2r8(x);
-}
-
-static inline int gmx_simd_anytrue_d_sparc64_hpc_ace(SimdDBool x)
-{
- long long int i;
- x = _fjsp_or_v2r8(x, _fjsp_unpackhi_v2r8(x, x));
- _fjsp_storel_v2r8((double*)&i, x);
- return (i != 0LL);
-}
-
-static inline double simdReduceD_sparc64_hpc_ace(SimdDouble x)
-{
- double d;
- x = _fjsp_add_v2r8(x, _fjsp_unpackhi_v2r8(x, x));
- _fjsp_storel_v2r8(&d, x);
- return d;
-}
-
-
-static inline SimdDouble simdGetExponentD_sparc64_hpc_ace(SimdDouble x)
-{
- /* HPC-ACE cannot cast _fjsp_v2r8 to _fjsp_v4i4, so to perform shifts we
- * would need to store and reload. Since we are only operating on two
- * numbers it is likely more efficient to do the operations directly on
- * normal registers.
- */
- const std::int64_t expmask = 0x7ff0000000000000LL;
- const std::int64_t expbias = 1023LL;
-
- union {
- _fjsp_v2r8 simd;
- long long int i[2];
- } conv;
-
- _fjsp_store_v2r8((double*)&conv.simd, x);
- conv.i[0] = ((conv.i[0] & expmask) >> 52) - expbias;
- conv.i[1] = ((conv.i[1] & expmask) >> 52) - expbias;
- x = _fjsp_load_v2r8((double*)&conv.simd);
- return _fjsp_xtod_v2r8(x);
-}
-
-static inline SimdDouble simdGetMantissaD_sparc64_hpc_ace(SimdDouble x)
-{
- std::int64_t mantmask[2] = { 0x000fffffffffffffLL, 0x000fffffffffffffLL };
- SimdDouble one = _fjsp_set_v2r8(1.0, 1.0);
-
- x = _fjsp_and_v2r8(x, _fjsp_load_v2r8((double*)mantmask));
- return _fjsp_or_v2r8(x, one);
-}
-
-static inline SimdDouble simdSetExponentD_sparc64_hpc_ace(SimdDouble x)
-{
- const std::int64_t expbias = 1023;
- union {
- _fjsp_v2r8 simd;
- long long int i[2];
- } conv;
-
-
- _fjsp_store_v2r8((double*)&conv.simd, simdCvtD2I_sparc64_hpc_ace(x));
- conv.i[0] = (conv.i[0] + expbias) << 52;
- conv.i[1] = (conv.i[1] + expbias) << 52;
-
- return _fjsp_load_v2r8((double*)&conv.simd);
-}
-
-#endif /* GMX_SIMD_IMPL_SPARC64_HPC_ACE_SIMD_DOUBLE_H */
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2019, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_SIMD_IMPL_SPARC64_HPC_ACE_SIMD_FLOAT_H
-#define GMX_SIMD_IMPL_SPARC64_HPC_ACE_SIMD_FLOAT_H
-
-/* Fujitsu header borrows the name from SSE2, since some instructions have aliases.
- * Environment/compiler version GM-1.2.0-17 seems to be buggy; when -Xg is
- * defined to enable GNUC extensions, this sets _ISOC99_SOURCE, which in
- * turn causes all intrinsics to be declared inline _instead_ of static. This
- * leads to duplicate symbol errors at link time.
- * To work around this we unset this before including the HPC-ACE header, and
- * reset the value afterwards.
- */
-#ifdef _ISOC99_SOURCE
-# undef _ISOC99_SOURCE
-# define SAVE_ISOC99_SOURCE
-#endif
-
-#include <emmintrin.h>
-
-#ifdef SAVE_ISOC99_SOURCE
-# define _ISOC99_SOURCE
-# undef SAVE_ISOC99_SOURCE
-#endif
-
-#include <math.h>
-
-#include "impl_sparc64_hpc_ace_common.h"
-
-/* HPC-ACE is a bit strange; some instructions like
- * shifts only work on _integer_ versions of SIMD
- * registers, but there are no intrinsics to load
- * or convert, or even to cast. The only way to use
- * them is to declare unions with the SIMD integer
- * type. However, this will lead to extra load ops,
- * and the normal real-to-int and int-to-real
- * conversions work purely on the v2r8 fp regs.
- * Since our most common usage is to convert and
- * then extract the result for table lookups, we
- * define the SimdFInt32 datatype to use
- * the v2r8 rather than v2i8 SIMD type.
- */
-
-/****************************************************
- * SINGLE PRECISION SIMD IMPLEMENTATION *
- ****************************************************/
-#define SimdFloat _fjsp_v2r8
-#define simdLoadF simdLoadF_sparc64_hpc_ace
-#define simdLoad1F(m) _fjsp_set_v2r8((*m), (*m))
-#define simdSet1F(a) _fjsp_set_v2r8(a, a)
-#define simdStoreF simdStoreF_sparc64_hpc_ace
-#define simdLoadUF simdLoadF
-/* No unaligned store of SimdFloat */
-#define simdSetZeroF _fjsp_setzero_v2r8
-#define simdAddF _fjsp_add_v2r8
-#define simdSubF _fjsp_sub_v2r8
-#define simdMulF _fjsp_mul_v2r8
-#define simdFmaddF(a, b, c) _fjsp_madd_v2r8(a, b, c)
-#define simdFmsubF(a, b, c) _fjsp_msub_v2r8(a, b, c)
-#define simdFnmaddF(a, b, c) _fjsp_nmsub_v2r8(a, b, c)
-#define simdFnmsubF(a, b, c) _fjsp_nmadd_v2r8(a, b, c)
-#define simdAndF _fjsp_and_v2r8
-#define simdAndNotF _fjsp_andnot1_v2r8
-#define simdOrF _fjsp_or_v2r8
-#define simdXorF _fjsp_xor_v2r8
-#define simdRsqrtF _fjsp_rsqrta_v2r8
-#define simdRcpF _fjsp_rcpa_v2r8
-#define simdAbsF(x) _fjsp_abs_v2r8(x)
-#define simdNegF(x) _fjsp_neg_v2r8(x)
-#define simdMaxF _fjsp_max_v2r8
-#define simdMinF _fjsp_min_v2r8
-#define simdRoundF(x) simdRoundD(x)
-#define simdTruncF(x) simdTruncD(x)
-#define simdFractionF(x) simdSubF(x, simdTruncF(x))
-#define simdGetExponentF simdGetExponentD_sparc64_hpc_ace
-#define simdGetMantissaF simdGetMantissaD_sparc64_hpc_ace
-#define simdSetExponentF simdSetExponentD_sparc64_hpc_ace
-/* integer datatype corresponding to float: SimdFInt32 */
-#define SimdFInt32 _fjsp_v2r8
-#define simdLoadFI(m) simdLoadDI_sparc64_hpc_ace(m)
-#define simdSet1FI(i) simdSet1DI_sparc64_hpc_ace(i)
-#define simdStoreFI(m, x) simdStoreDI_sparc64_hpc_ace(m, x)
-#define simdLoadUFI simdLoadFI
-/* No unaligned store of SimdFInt32 */
-#define simdSetZeroFI _fjsp_setzero_v2r8
-#define simdCvtF2I simdCvtD2I
-#define simdCvttF2I _fjsp_dtox_v2r8
-#define simdCvtI2F _fjsp_xtod_v2r8
-#define simdExtractFI simdExtractDI_sparc64_hpc_ace
-/* Integer logical ops on SimdFInt32 */
-/* Shifts are horrible since they require memory re-loads. */
-#define simdSlliFI simdSlliDI_sparc64_hpc_ace
-#define simdSrliFI simdSrliDI_sparc64_hpc_ace
-#define simdAndFI _fjsp_and_v2r8
-#define simdAndNotFI(a, b) _fjsp_andnot1_v2r8(a, b)
-#define simdOrFI _fjsp_or_v2r8
-#define simdXorFI _fjsp_xor_v2r8
-/* No integer arithmetic ops on SimdFInt32 */
-/* Boolean & comparison operations on SimdFloat */
-#define SimdFBool _fjsp_v2r8
-#define simdCmpEqF _fjsp_cmpeq_v2r8
-#define simdCmpLtF _fjsp_cmplt_v2r8
-#define simdCmpLeF _fjsp_cmple_v2r8
-#define simdAndFB _fjsp_and_v2r8
-#define simdOrFB _fjsp_or_v2r8
-#define simdAnyTrueFB gmx_simd_anytrue_d_sparc64_hpc_ace
-#define simdMaskF _fjsp_and_v2r8
-#define simdMaskNotF(a, sel) _fjsp_andnot1_v2r8(sel, a)
-#define simdBlendF(a, b, s) _fjsp_selmov_v2r8(b, a, s)
-#define simdReduceF(a) simdReduceD_sparc64_hpc_ace(a)
-/* No boolean & comparison operations on SimdFInt32 */
-/* No conversions between different booleans */
-
-/****************************************************
- * SINGLE PRECISION IMPLEMENTATION HELPER FUNCTIONS *
- ****************************************************/
-static inline SimdFloat simdLoadF_sparc64_hpc_ace(const float* m)
-{
- /* We are not allowed to cast single-to-double registers, but we can
- * masquerade the memory location as a variable of type _fjsp_v2r4.
- */
- const _fjsp_v2r4* p = (const _fjsp_v2r4*)m;
- _fjsp_v2r4 simd;
-
- simd = *p;
- return _fjsp_stod_v2r8(simd);
-}
-
-static inline void simdStoreF_sparc64_hpc_ace(float* m, SimdFloat x)
-{
- /* We are not allowed to cast single-to-double registers, but we can
- * masquerade the memory location as a variable of type _fjsp_v2r4.
- */
- _fjsp_v2r4* p = (_fjsp_v2r4*)m;
- *p = _fjsp_dtos_v2r4(x);
-}
-
-/* Note that some single precision defines refer to the double precision helpers */
-
-#endif /* GMX_SIMD_IMPL_SPARC64_HPC_ACE_SIMD_FLOAT_H */
// precision fields, but a bit below we'll need a corresponding integer variable with 4x
// 32-bit fields. Since AVX1 does not support shuffling across the upper/lower 128-bit
// lanes, we need to extract those first, and then shuffle between two 128-bit variables.
- __m128i iValueIsZero = _mm_castps_si128(_mm_shuffle_ps(
- _mm256_extractf128_ps(_mm256_castpd_ps(valueIsZero), 0x0),
- _mm256_extractf128_ps(_mm256_castpd_ps(valueIsZero), 0x1), _MM_SHUFFLE(2, 0, 2, 0)));
+ __m128i iValueIsZero = _mm_castps_si128(
+ _mm_shuffle_ps(_mm256_extractf128_ps(_mm256_castpd_ps(valueIsZero), 0x0),
+ _mm256_extractf128_ps(_mm256_castpd_ps(valueIsZero), 0x1),
+ _MM_SHUFFLE(2, 0, 2, 0)));
// Set exponent to 0 when input value was zero
iExponentLow = _mm_andnot_si128(iValueIsZero, iExponentLow);
// we can use aligned loads since base should also be aligned in this case
assert(std::size_t(base) % 16 == 0);
t1 = _mm256_insertf128_ps(_mm256_castps128_ps256(_mm_load_ps(base + align * offset[0])),
- _mm_load_ps(base + align * offset[4]), 0x1);
+ _mm_load_ps(base + align * offset[4]),
+ 0x1);
t2 = _mm256_insertf128_ps(_mm256_castps128_ps256(_mm_load_ps(base + align * offset[1])),
- _mm_load_ps(base + align * offset[5]), 0x1);
+ _mm_load_ps(base + align * offset[5]),
+ 0x1);
t3 = _mm256_insertf128_ps(_mm256_castps128_ps256(_mm_load_ps(base + align * offset[2])),
- _mm_load_ps(base + align * offset[6]), 0x1);
+ _mm_load_ps(base + align * offset[6]),
+ 0x1);
t4 = _mm256_insertf128_ps(_mm256_castps128_ps256(_mm_load_ps(base + align * offset[3])),
- _mm_load_ps(base + align * offset[7]), 0x1);
+ _mm_load_ps(base + align * offset[7]),
+ 0x1);
}
else
{
// Use unaligned loads
t1 = _mm256_insertf128_ps(_mm256_castps128_ps256(_mm_loadu_ps(base + align * offset[0])),
- _mm_loadu_ps(base + align * offset[4]), 0x1);
+ _mm_loadu_ps(base + align * offset[4]),
+ 0x1);
t2 = _mm256_insertf128_ps(_mm256_castps128_ps256(_mm_loadu_ps(base + align * offset[1])),
- _mm_loadu_ps(base + align * offset[5]), 0x1);
+ _mm_loadu_ps(base + align * offset[5]),
+ 0x1);
t3 = _mm256_insertf128_ps(_mm256_castps128_ps256(_mm_loadu_ps(base + align * offset[2])),
- _mm_loadu_ps(base + align * offset[6]), 0x1);
+ _mm_loadu_ps(base + align * offset[6]),
+ 0x1);
t4 = _mm256_insertf128_ps(_mm256_castps128_ps256(_mm_loadu_ps(base + align * offset[3])),
- _mm_loadu_ps(base + align * offset[7]), 0x1);
+ _mm_loadu_ps(base + align * offset[7]),
+ 0x1);
}
t5 = _mm256_unpacklo_ps(t1, t2);
_mm_add_ps(_mm_load_ps(base + align * offset[2]), _mm256_castps256_ps128(t7)));
_mm_store_ps(base + align * offset[3],
_mm_add_ps(_mm_load_ps(base + align * offset[3]), _mm256_castps256_ps128(t8)));
- _mm_store_ps(base + align * offset[4], _mm_add_ps(_mm_load_ps(base + align * offset[4]),
- _mm256_extractf128_ps(t5, 0x1)));
- _mm_store_ps(base + align * offset[5], _mm_add_ps(_mm_load_ps(base + align * offset[5]),
- _mm256_extractf128_ps(t6, 0x1)));
- _mm_store_ps(base + align * offset[6], _mm_add_ps(_mm_load_ps(base + align * offset[6]),
- _mm256_extractf128_ps(t7, 0x1)));
- _mm_store_ps(base + align * offset[7], _mm_add_ps(_mm_load_ps(base + align * offset[7]),
- _mm256_extractf128_ps(t8, 0x1)));
+ _mm_store_ps(base + align * offset[4],
+ _mm_add_ps(_mm_load_ps(base + align * offset[4]), _mm256_extractf128_ps(t5, 0x1)));
+ _mm_store_ps(base + align * offset[5],
+ _mm_add_ps(_mm_load_ps(base + align * offset[5]), _mm256_extractf128_ps(t6, 0x1)));
+ _mm_store_ps(base + align * offset[6],
+ _mm_add_ps(_mm_load_ps(base + align * offset[6]), _mm256_extractf128_ps(t7, 0x1)));
+ _mm_store_ps(base + align * offset[7],
+ _mm_add_ps(_mm_load_ps(base + align * offset[7]), _mm256_extractf128_ps(t8, 0x1)));
}
else
{
// alignment >=5, but not a multiple of 4
- _mm_storeu_ps(base + align * offset[0], _mm_add_ps(_mm_loadu_ps(base + align * offset[0]),
- _mm256_castps256_ps128(t5)));
- _mm_storeu_ps(base + align * offset[1], _mm_add_ps(_mm_loadu_ps(base + align * offset[1]),
- _mm256_castps256_ps128(t6)));
- _mm_storeu_ps(base + align * offset[2], _mm_add_ps(_mm_loadu_ps(base + align * offset[2]),
- _mm256_castps256_ps128(t7)));
- _mm_storeu_ps(base + align * offset[3], _mm_add_ps(_mm_loadu_ps(base + align * offset[3]),
- _mm256_castps256_ps128(t8)));
- _mm_storeu_ps(base + align * offset[4], _mm_add_ps(_mm_loadu_ps(base + align * offset[4]),
- _mm256_extractf128_ps(t5, 0x1)));
- _mm_storeu_ps(base + align * offset[5], _mm_add_ps(_mm_loadu_ps(base + align * offset[5]),
- _mm256_extractf128_ps(t6, 0x1)));
- _mm_storeu_ps(base + align * offset[6], _mm_add_ps(_mm_loadu_ps(base + align * offset[6]),
- _mm256_extractf128_ps(t7, 0x1)));
- _mm_storeu_ps(base + align * offset[7], _mm_add_ps(_mm_loadu_ps(base + align * offset[7]),
- _mm256_extractf128_ps(t8, 0x1)));
+ _mm_storeu_ps(base + align * offset[0],
+ _mm_add_ps(_mm_loadu_ps(base + align * offset[0]), _mm256_castps256_ps128(t5)));
+ _mm_storeu_ps(base + align * offset[1],
+ _mm_add_ps(_mm_loadu_ps(base + align * offset[1]), _mm256_castps256_ps128(t6)));
+ _mm_storeu_ps(base + align * offset[2],
+ _mm_add_ps(_mm_loadu_ps(base + align * offset[2]), _mm256_castps256_ps128(t7)));
+ _mm_storeu_ps(base + align * offset[3],
+ _mm_add_ps(_mm_loadu_ps(base + align * offset[3]), _mm256_castps256_ps128(t8)));
+ _mm_storeu_ps(
+ base + align * offset[4],
+ _mm_add_ps(_mm_loadu_ps(base + align * offset[4]), _mm256_extractf128_ps(t5, 0x1)));
+ _mm_storeu_ps(
+ base + align * offset[5],
+ _mm_add_ps(_mm_loadu_ps(base + align * offset[5]), _mm256_extractf128_ps(t6, 0x1)));
+ _mm_storeu_ps(
+ base + align * offset[6],
+ _mm_add_ps(_mm_loadu_ps(base + align * offset[6]), _mm256_extractf128_ps(t7, 0x1)));
+ _mm_storeu_ps(
+ base + align * offset[7],
+ _mm_add_ps(_mm_loadu_ps(base + align * offset[7]), _mm256_extractf128_ps(t8, 0x1)));
}
}
}
_mm_sub_ps(_mm_load_ps(base + align * offset[2]), _mm256_castps256_ps128(t7)));
_mm_store_ps(base + align * offset[3],
_mm_sub_ps(_mm_load_ps(base + align * offset[3]), _mm256_castps256_ps128(t8)));
- _mm_store_ps(base + align * offset[4], _mm_sub_ps(_mm_load_ps(base + align * offset[4]),
- _mm256_extractf128_ps(t5, 0x1)));
- _mm_store_ps(base + align * offset[5], _mm_sub_ps(_mm_load_ps(base + align * offset[5]),
- _mm256_extractf128_ps(t6, 0x1)));
- _mm_store_ps(base + align * offset[6], _mm_sub_ps(_mm_load_ps(base + align * offset[6]),
- _mm256_extractf128_ps(t7, 0x1)));
- _mm_store_ps(base + align * offset[7], _mm_sub_ps(_mm_load_ps(base + align * offset[7]),
- _mm256_extractf128_ps(t8, 0x1)));
+ _mm_store_ps(base + align * offset[4],
+ _mm_sub_ps(_mm_load_ps(base + align * offset[4]), _mm256_extractf128_ps(t5, 0x1)));
+ _mm_store_ps(base + align * offset[5],
+ _mm_sub_ps(_mm_load_ps(base + align * offset[5]), _mm256_extractf128_ps(t6, 0x1)));
+ _mm_store_ps(base + align * offset[6],
+ _mm_sub_ps(_mm_load_ps(base + align * offset[6]), _mm256_extractf128_ps(t7, 0x1)));
+ _mm_store_ps(base + align * offset[7],
+ _mm_sub_ps(_mm_load_ps(base + align * offset[7]), _mm256_extractf128_ps(t8, 0x1)));
}
else
{
// alignment >=5, but not a multiple of 4
- _mm_storeu_ps(base + align * offset[0], _mm_sub_ps(_mm_loadu_ps(base + align * offset[0]),
- _mm256_castps256_ps128(t5)));
- _mm_storeu_ps(base + align * offset[1], _mm_sub_ps(_mm_loadu_ps(base + align * offset[1]),
- _mm256_castps256_ps128(t6)));
- _mm_storeu_ps(base + align * offset[2], _mm_sub_ps(_mm_loadu_ps(base + align * offset[2]),
- _mm256_castps256_ps128(t7)));
- _mm_storeu_ps(base + align * offset[3], _mm_sub_ps(_mm_loadu_ps(base + align * offset[3]),
- _mm256_castps256_ps128(t8)));
- _mm_storeu_ps(base + align * offset[4], _mm_sub_ps(_mm_loadu_ps(base + align * offset[4]),
- _mm256_extractf128_ps(t5, 0x1)));
- _mm_storeu_ps(base + align * offset[5], _mm_sub_ps(_mm_loadu_ps(base + align * offset[5]),
- _mm256_extractf128_ps(t6, 0x1)));
- _mm_storeu_ps(base + align * offset[6], _mm_sub_ps(_mm_loadu_ps(base + align * offset[6]),
- _mm256_extractf128_ps(t7, 0x1)));
- _mm_storeu_ps(base + align * offset[7], _mm_sub_ps(_mm_loadu_ps(base + align * offset[7]),
- _mm256_extractf128_ps(t8, 0x1)));
+ _mm_storeu_ps(base + align * offset[0],
+ _mm_sub_ps(_mm_loadu_ps(base + align * offset[0]), _mm256_castps256_ps128(t5)));
+ _mm_storeu_ps(base + align * offset[1],
+ _mm_sub_ps(_mm_loadu_ps(base + align * offset[1]), _mm256_castps256_ps128(t6)));
+ _mm_storeu_ps(base + align * offset[2],
+ _mm_sub_ps(_mm_loadu_ps(base + align * offset[2]), _mm256_castps256_ps128(t7)));
+ _mm_storeu_ps(base + align * offset[3],
+ _mm_sub_ps(_mm_loadu_ps(base + align * offset[3]), _mm256_castps256_ps128(t8)));
+ _mm_storeu_ps(
+ base + align * offset[4],
+ _mm_sub_ps(_mm_loadu_ps(base + align * offset[4]), _mm256_extractf128_ps(t5, 0x1)));
+ _mm_storeu_ps(
+ base + align * offset[5],
+ _mm_sub_ps(_mm_loadu_ps(base + align * offset[5]), _mm256_extractf128_ps(t6, 0x1)));
+ _mm_storeu_ps(
+ base + align * offset[6],
+ _mm_sub_ps(_mm_loadu_ps(base + align * offset[6]), _mm256_extractf128_ps(t7, 0x1)));
+ _mm_storeu_ps(
+ base + align * offset[7],
+ _mm_sub_ps(_mm_loadu_ps(base + align * offset[7]), _mm256_extractf128_ps(t8, 0x1)));
}
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static inline Simd4DBool gmx_simdcall operator==(Simd4Double a, Simd4Double b)
{
- return { _mm512_mask_cmp_pd_mask(avx512Int2Mask(0xF), _mm512_castpd256_pd512(a.simdInternal_),
- _mm512_castpd256_pd512(b.simdInternal_), _CMP_EQ_OQ) };
+ return { _mm512_mask_cmp_pd_mask(avx512Int2Mask(0xF),
+ _mm512_castpd256_pd512(a.simdInternal_),
+ _mm512_castpd256_pd512(b.simdInternal_),
+ _CMP_EQ_OQ) };
}
static inline Simd4DBool gmx_simdcall operator!=(Simd4Double a, Simd4Double b)
{
- return { _mm512_mask_cmp_pd_mask(avx512Int2Mask(0xF), _mm512_castpd256_pd512(a.simdInternal_),
- _mm512_castpd256_pd512(b.simdInternal_), _CMP_NEQ_OQ) };
+ return { _mm512_mask_cmp_pd_mask(avx512Int2Mask(0xF),
+ _mm512_castpd256_pd512(a.simdInternal_),
+ _mm512_castpd256_pd512(b.simdInternal_),
+ _CMP_NEQ_OQ) };
}
static inline Simd4DBool gmx_simdcall operator<(Simd4Double a, Simd4Double b)
{
- return { _mm512_mask_cmp_pd_mask(avx512Int2Mask(0xF), _mm512_castpd256_pd512(a.simdInternal_),
- _mm512_castpd256_pd512(b.simdInternal_), _CMP_LT_OQ) };
+ return { _mm512_mask_cmp_pd_mask(avx512Int2Mask(0xF),
+ _mm512_castpd256_pd512(a.simdInternal_),
+ _mm512_castpd256_pd512(b.simdInternal_),
+ _CMP_LT_OQ) };
}
static inline Simd4DBool gmx_simdcall operator<=(Simd4Double a, Simd4Double b)
{
- return { _mm512_mask_cmp_pd_mask(avx512Int2Mask(0xF), _mm512_castpd256_pd512(a.simdInternal_),
- _mm512_castpd256_pd512(b.simdInternal_), _CMP_LE_OQ) };
+ return { _mm512_mask_cmp_pd_mask(avx512Int2Mask(0xF),
+ _mm512_castpd256_pd512(a.simdInternal_),
+ _mm512_castpd256_pd512(b.simdInternal_),
+ _CMP_LE_OQ) };
}
static inline Simd4DBool gmx_simdcall operator&&(Simd4DBool a, Simd4DBool b)
static inline Simd4Double gmx_simdcall selectByMask(Simd4Double a, Simd4DBool m)
{
- return { _mm512_castpd512_pd256(_mm512_mask_mov_pd(_mm512_setzero_pd(), m.simdInternal_,
- _mm512_castpd256_pd512(a.simdInternal_))) };
+ return { _mm512_castpd512_pd256(_mm512_mask_mov_pd(
+ _mm512_setzero_pd(), m.simdInternal_, _mm512_castpd256_pd512(a.simdInternal_))) };
}
static inline Simd4Double gmx_simdcall selectByNotMask(Simd4Double a, Simd4DBool m)
{
- return { _mm512_castpd512_pd256(_mm512_mask_mov_pd(_mm512_castpd256_pd512(a.simdInternal_),
- m.simdInternal_, _mm512_setzero_pd())) };
+ return { _mm512_castpd512_pd256(_mm512_mask_mov_pd(
+ _mm512_castpd256_pd512(a.simdInternal_), m.simdInternal_, _mm512_setzero_pd())) };
}
static inline Simd4Double gmx_simdcall blend(Simd4Double a, Simd4Double b, Simd4DBool sel)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static inline Simd4FBool gmx_simdcall operator==(Simd4Float a, Simd4Float b)
{
- return { _mm512_mask_cmp_ps_mask(avx512Int2Mask(0xF), _mm512_castps128_ps512(a.simdInternal_),
- _mm512_castps128_ps512(b.simdInternal_), _CMP_EQ_OQ) };
+ return { _mm512_mask_cmp_ps_mask(avx512Int2Mask(0xF),
+ _mm512_castps128_ps512(a.simdInternal_),
+ _mm512_castps128_ps512(b.simdInternal_),
+ _CMP_EQ_OQ) };
}
static inline Simd4FBool gmx_simdcall operator!=(Simd4Float a, Simd4Float b)
{
- return { _mm512_mask_cmp_ps_mask(avx512Int2Mask(0xF), _mm512_castps128_ps512(a.simdInternal_),
- _mm512_castps128_ps512(b.simdInternal_), _CMP_NEQ_OQ) };
+ return { _mm512_mask_cmp_ps_mask(avx512Int2Mask(0xF),
+ _mm512_castps128_ps512(a.simdInternal_),
+ _mm512_castps128_ps512(b.simdInternal_),
+ _CMP_NEQ_OQ) };
}
static inline Simd4FBool gmx_simdcall operator<(Simd4Float a, Simd4Float b)
{
- return { _mm512_mask_cmp_ps_mask(avx512Int2Mask(0xF), _mm512_castps128_ps512(a.simdInternal_),
- _mm512_castps128_ps512(b.simdInternal_), _CMP_LT_OQ) };
+ return { _mm512_mask_cmp_ps_mask(avx512Int2Mask(0xF),
+ _mm512_castps128_ps512(a.simdInternal_),
+ _mm512_castps128_ps512(b.simdInternal_),
+ _CMP_LT_OQ) };
}
static inline Simd4FBool gmx_simdcall operator<=(Simd4Float a, Simd4Float b)
{
- return { _mm512_mask_cmp_ps_mask(avx512Int2Mask(0xF), _mm512_castps128_ps512(a.simdInternal_),
- _mm512_castps128_ps512(b.simdInternal_), _CMP_LE_OQ) };
+ return { _mm512_mask_cmp_ps_mask(avx512Int2Mask(0xF),
+ _mm512_castps128_ps512(a.simdInternal_),
+ _mm512_castps128_ps512(b.simdInternal_),
+ _CMP_LE_OQ) };
}
static inline Simd4FBool gmx_simdcall operator&&(Simd4FBool a, Simd4FBool b)
static inline Simd4Float gmx_simdcall selectByMask(Simd4Float a, Simd4FBool m)
{
- return { _mm512_castps512_ps128(_mm512_mask_mov_ps(_mm512_setzero_ps(), m.simdInternal_,
- _mm512_castps128_ps512(a.simdInternal_))) };
+ return { _mm512_castps512_ps128(_mm512_mask_mov_ps(
+ _mm512_setzero_ps(), m.simdInternal_, _mm512_castps128_ps512(a.simdInternal_))) };
}
static inline Simd4Float gmx_simdcall selectByNotMask(Simd4Float a, Simd4FBool m)
{
- return { _mm512_castps512_ps128(_mm512_mask_mov_ps(_mm512_castps128_ps512(a.simdInternal_),
- m.simdInternal_, _mm512_setzero_ps())) };
+ return { _mm512_castps512_ps128(_mm512_mask_mov_ps(
+ _mm512_castps128_ps512(a.simdInternal_), m.simdInternal_, _mm512_setzero_ps())) };
}
static inline Simd4Float gmx_simdcall blend(Simd4Float a, Simd4Float b, Simd4FBool sel)
iExponent = _mm256_add_epi32(iExponent, _mm256_set1_epi32(1));
// Set result to value (+-0) when it is zero.
- result = _mm512_mask_getmant_pd(value.simdInternal_, valueIsNonZero, value.simdInternal_,
- _MM_MANT_NORM_p5_1, _MM_MANT_SIGN_src);
+ result = _mm512_mask_getmant_pd(
+ value.simdInternal_, valueIsNonZero, value.simdInternal_, _MM_MANT_NORM_p5_1, _MM_MANT_SIGN_src);
}
else
{
{
return { _mm512_castsi512_pd(_mm512_ternarylogic_epi64(_mm512_castpd_si512(a.simdInternal_),
_mm512_castpd_si512(b.simdInternal_),
- _mm512_set1_epi64(INT64_MIN), 0xD8)) };
+ _mm512_set1_epi64(INT64_MIN),
+ 0xD8)) };
}
static inline SimdDInt32 gmx_simdcall operator&(SimdDInt32 a, SimdDInt32 b)
static inline SimdDIBool gmx_simdcall operator==(SimdDInt32 a, SimdDInt32 b)
{
- return { _mm512_mask_cmp_epi32_mask(avx512Int2Mask(0xFF), _mm512_castsi256_si512(a.simdInternal_),
- _mm512_castsi256_si512(b.simdInternal_), _MM_CMPINT_EQ) };
+ return { _mm512_mask_cmp_epi32_mask(avx512Int2Mask(0xFF),
+ _mm512_castsi256_si512(a.simdInternal_),
+ _mm512_castsi256_si512(b.simdInternal_),
+ _MM_CMPINT_EQ) };
}
static inline SimdDIBool gmx_simdcall testBits(SimdDInt32 a)
{
- return { _mm512_mask_test_epi32_mask(avx512Int2Mask(0xFF), _mm512_castsi256_si512(a.simdInternal_),
+ return { _mm512_mask_test_epi32_mask(avx512Int2Mask(0xFF),
+ _mm512_castsi256_si512(a.simdInternal_),
_mm512_castsi256_si512(a.simdInternal_)) };
}
static inline SimdDIBool gmx_simdcall operator<(SimdDInt32 a, SimdDInt32 b)
{
- return { _mm512_mask_cmp_epi32_mask(avx512Int2Mask(0xFF), _mm512_castsi256_si512(a.simdInternal_),
- _mm512_castsi256_si512(b.simdInternal_), _MM_CMPINT_LT) };
+ return { _mm512_mask_cmp_epi32_mask(avx512Int2Mask(0xFF),
+ _mm512_castsi256_si512(a.simdInternal_),
+ _mm512_castsi256_si512(b.simdInternal_),
+ _MM_CMPINT_LT) };
}
static inline SimdDIBool gmx_simdcall operator&&(SimdDIBool a, SimdDIBool b)
static inline SimdDInt32 gmx_simdcall blend(SimdDInt32 a, SimdDInt32 b, SimdDIBool sel)
{
- return { _mm512_castsi512_si256(
- _mm512_mask_blend_epi32(sel.simdInternal_, _mm512_castsi256_si512(a.simdInternal_),
- _mm512_castsi256_si512(b.simdInternal_))) };
+ return { _mm512_castsi512_si256(_mm512_mask_blend_epi32(sel.simdInternal_,
+ _mm512_castsi256_si512(a.simdInternal_),
+ _mm512_castsi256_si512(b.simdInternal_))) };
}
static inline SimdDInt32 gmx_simdcall cvtR2I(SimdDouble a)
iExponent = _mm512_mask_add_epi32(iExponent, valueIsNonZero, iExponent, _mm512_set1_epi32(1));
// Set result to input value when the latter is +-0
- result = _mm512_mask_getmant_ps(value.simdInternal_, valueIsNonZero, value.simdInternal_,
- _MM_MANT_NORM_p5_1, _MM_MANT_SIGN_src);
+ result = _mm512_mask_getmant_ps(
+ value.simdInternal_, valueIsNonZero, value.simdInternal_, _MM_MANT_NORM_p5_1, _MM_MANT_SIGN_src);
}
else
{
{
return { _mm512_castsi512_ps(_mm512_ternarylogic_epi32(_mm512_castps_si512(a.simdInternal_),
_mm512_castps_si512(b.simdInternal_),
- _mm512_set1_epi32(INT32_MIN), 0xD8)) };
+ _mm512_set1_epi32(INT32_MIN),
+ 0xD8)) };
}
static inline SimdFInt32 gmx_simdcall operator&(SimdFInt32 a, SimdFInt32 b)
__m512d t[4], t5, t6, t7, t8;
alignas(GMX_SIMD_ALIGNMENT) std::int64_t o[8];
// TODO: should use fastMultiply
- _mm512_store_epi64(o, _mm512_cvtepi32_epi64(_mm256_mullo_epi32(
- _mm256_load_si256((const __m256i*)(offset)), _mm256_set1_epi32(align))));
+ _mm512_store_epi64(o,
+ _mm512_cvtepi32_epi64(_mm256_mullo_epi32(
+ _mm256_load_si256((const __m256i*)(offset)), _mm256_set1_epi32(align))));
t5 = _mm512_unpacklo_pd(v0.simdInternal_, v1.simdInternal_);
t6 = _mm512_unpackhi_pd(v0.simdInternal_, v1.simdInternal_);
t7 = _mm512_unpacklo_pd(v2.simdInternal_, _mm512_setzero_pd());
{
for (int i = 0; i < 4; i++)
{
- _mm512_mask_storeu_pd(base + o[0 + i], avx512Int2Mask(7),
+ _mm512_mask_storeu_pd(base + o[0 + i],
+ avx512Int2Mask(7),
_mm512_castpd256_pd512(_mm256_add_pd(_mm256_loadu_pd(base + o[0 + i]),
_mm512_castpd512_pd256(t[i]))));
_mm512_mask_storeu_pd(
- base + o[4 + i], avx512Int2Mask(7),
+ base + o[4 + i],
+ avx512Int2Mask(7),
_mm512_castpd256_pd512(_mm256_add_pd(_mm256_loadu_pd(base + o[4 + i]),
_mm512_extractf64x4_pd(t[i], 1))));
}
{
for (int i = 0; i < 4; i++)
{
- _mm256_store_pd(base + o[0 + i], _mm256_add_pd(_mm256_load_pd(base + o[0 + i]),
- _mm512_castpd512_pd256(t[i])));
- _mm256_store_pd(base + o[4 + i], _mm256_add_pd(_mm256_load_pd(base + o[4 + i]),
- _mm512_extractf64x4_pd(t[i], 1)));
+ _mm256_store_pd(
+ base + o[0 + i],
+ _mm256_add_pd(_mm256_load_pd(base + o[0 + i]), _mm512_castpd512_pd256(t[i])));
+ _mm256_store_pd(base + o[4 + i],
+ _mm256_add_pd(_mm256_load_pd(base + o[4 + i]),
+ _mm512_extractf64x4_pd(t[i], 1)));
}
}
else
{
for (int i = 0; i < 4; i++)
{
- _mm256_storeu_pd(base + o[0 + i], _mm256_add_pd(_mm256_loadu_pd(base + o[0 + i]),
- _mm512_castpd512_pd256(t[i])));
- _mm256_storeu_pd(base + o[4 + i], _mm256_add_pd(_mm256_loadu_pd(base + o[4 + i]),
- _mm512_extractf64x4_pd(t[i], 1)));
+ _mm256_storeu_pd(
+ base + o[0 + i],
+ _mm256_add_pd(_mm256_loadu_pd(base + o[0 + i]), _mm512_castpd512_pd256(t[i])));
+ _mm256_storeu_pd(base + o[4 + i],
+ _mm256_add_pd(_mm256_loadu_pd(base + o[4 + i]),
+ _mm512_extractf64x4_pd(t[i], 1)));
}
}
}
__m512d t[4], t5, t6, t7, t8;
alignas(GMX_SIMD_ALIGNMENT) std::int64_t o[8];
// TODO: should use fastMultiply
- _mm512_store_epi64(o, _mm512_cvtepi32_epi64(_mm256_mullo_epi32(
- _mm256_load_si256((const __m256i*)(offset)), _mm256_set1_epi32(align))));
+ _mm512_store_epi64(o,
+ _mm512_cvtepi32_epi64(_mm256_mullo_epi32(
+ _mm256_load_si256((const __m256i*)(offset)), _mm256_set1_epi32(align))));
t5 = _mm512_unpacklo_pd(v0.simdInternal_, v1.simdInternal_);
t6 = _mm512_unpackhi_pd(v0.simdInternal_, v1.simdInternal_);
t7 = _mm512_unpacklo_pd(v2.simdInternal_, _mm512_setzero_pd());
{
for (int i = 0; i < 4; i++)
{
- _mm512_mask_storeu_pd(base + o[0 + i], avx512Int2Mask(7),
+ _mm512_mask_storeu_pd(base + o[0 + i],
+ avx512Int2Mask(7),
_mm512_castpd256_pd512(_mm256_sub_pd(_mm256_loadu_pd(base + o[0 + i]),
_mm512_castpd512_pd256(t[i]))));
_mm512_mask_storeu_pd(
- base + o[4 + i], avx512Int2Mask(7),
+ base + o[4 + i],
+ avx512Int2Mask(7),
_mm512_castpd256_pd512(_mm256_sub_pd(_mm256_loadu_pd(base + o[4 + i]),
_mm512_extractf64x4_pd(t[i], 1))));
}
{
for (int i = 0; i < 4; i++)
{
- _mm256_store_pd(base + o[0 + i], _mm256_sub_pd(_mm256_load_pd(base + o[0 + i]),
- _mm512_castpd512_pd256(t[i])));
- _mm256_store_pd(base + o[4 + i], _mm256_sub_pd(_mm256_load_pd(base + o[4 + i]),
- _mm512_extractf64x4_pd(t[i], 1)));
+ _mm256_store_pd(
+ base + o[0 + i],
+ _mm256_sub_pd(_mm256_load_pd(base + o[0 + i]), _mm512_castpd512_pd256(t[i])));
+ _mm256_store_pd(base + o[4 + i],
+ _mm256_sub_pd(_mm256_load_pd(base + o[4 + i]),
+ _mm512_extractf64x4_pd(t[i], 1)));
}
}
else
{
for (int i = 0; i < 4; i++)
{
- _mm256_storeu_pd(base + o[0 + i], _mm256_sub_pd(_mm256_loadu_pd(base + o[0 + i]),
- _mm512_castpd512_pd256(t[i])));
- _mm256_storeu_pd(base + o[4 + i], _mm256_sub_pd(_mm256_loadu_pd(base + o[4 + i]),
- _mm512_extractf64x4_pd(t[i], 1)));
+ _mm256_storeu_pd(
+ base + o[0 + i],
+ _mm256_sub_pd(_mm256_loadu_pd(base + o[0 + i]), _mm512_castpd512_pd256(t[i])));
+ _mm256_storeu_pd(base + o[4 + i],
+ _mm256_sub_pd(_mm256_loadu_pd(base + o[4 + i]),
+ _mm512_extractf64x4_pd(t[i], 1)));
}
}
}
t0 = _mm512_add_pd(v0.simdInternal_, _mm512_permute_pd(v0.simdInternal_, 0x55));
t2 = _mm512_add_pd(v2.simdInternal_, _mm512_permute_pd(v2.simdInternal_, 0x55));
- t0 = _mm512_mask_add_pd(t0, avx512Int2Mask(0xAA), v1.simdInternal_,
- _mm512_permute_pd(v1.simdInternal_, 0x55));
- t2 = _mm512_mask_add_pd(t2, avx512Int2Mask(0xAA), v3.simdInternal_,
- _mm512_permute_pd(v3.simdInternal_, 0x55));
+ t0 = _mm512_mask_add_pd(
+ t0, avx512Int2Mask(0xAA), v1.simdInternal_, _mm512_permute_pd(v1.simdInternal_, 0x55));
+ t2 = _mm512_mask_add_pd(
+ t2, avx512Int2Mask(0xAA), v3.simdInternal_, _mm512_permute_pd(v3.simdInternal_, 0x55));
t0 = _mm512_add_pd(t0, _mm512_shuffle_f64x2(t0, t0, 0x4E));
t0 = _mm512_mask_add_pd(t0, avx512Int2Mask(0xF0), t2, _mm512_shuffle_f64x2(t2, t2, 0x4E));
t0 = _mm512_add_pd(t0, _mm512_shuffle_f64x2(t0, t0, 0xB1));
static inline SimdDouble gmx_simdcall loadU1DualHsimd(const double* m)
{
- return { _mm512_insertf64x4(_mm512_broadcastsd_pd(_mm_load_sd(m)),
- _mm256_broadcastsd_pd(_mm_load_sd(m + 1)), 1) };
+ return { _mm512_insertf64x4(
+ _mm512_broadcastsd_pd(_mm_load_sd(m)), _mm256_broadcastsd_pd(_mm_load_sd(m + 1)), 1) };
}
assert(std::size_t(m) % 32 == 0);
t0 = _mm512_add_pd(v0.simdInternal_, _mm512_permutex_pd(v0.simdInternal_, 0x4E));
- t0 = _mm512_mask_add_pd(t0, avx512Int2Mask(0xCC), v1.simdInternal_,
- _mm512_permutex_pd(v1.simdInternal_, 0x4E));
+ t0 = _mm512_mask_add_pd(
+ t0, avx512Int2Mask(0xCC), v1.simdInternal_, _mm512_permutex_pd(v1.simdInternal_, 0x4E));
t0 = _mm512_add_pd(t0, _mm512_permutex_pd(t0, 0xB1));
t0 = _mm512_mask_shuffle_f64x2(t0, avx512Int2Mask(0xAA), t0, t0, 0xEE);
static inline SimdDouble gmx_simdcall loadU4NOffset(const double* m, int offset)
{
- return { _mm512_insertf64x4(_mm512_castpd256_pd512(_mm256_loadu_pd(m)),
- _mm256_loadu_pd(m + offset), 1) };
+ return { _mm512_insertf64x4(
+ _mm512_castpd256_pd512(_mm256_loadu_pd(m)), _mm256_loadu_pd(m + offset), 1) };
}
} // namespace gmx
t[3] = _mm512_shuffle_ps(t6, v2.simdInternal_, _MM_SHUFFLE(3, 3, 3, 2));
for (i = 0; i < 4; i++)
{
- _mm512_mask_storeu_ps(base + o[i], avx512Int2Mask(7),
+ _mm512_mask_storeu_ps(base + o[i],
+ avx512Int2Mask(7),
_mm512_castps128_ps512(_mm_add_ps(_mm_loadu_ps(base + o[i]),
_mm512_castps512_ps128(t[i]))));
- _mm512_mask_storeu_ps(base + o[4 + i], avx512Int2Mask(7),
+ _mm512_mask_storeu_ps(base + o[4 + i],
+ avx512Int2Mask(7),
_mm512_castps128_ps512(_mm_add_ps(_mm_loadu_ps(base + o[4 + i]),
_mm512_extractf32x4_ps(t[i], 1))));
- _mm512_mask_storeu_ps(base + o[8 + i], avx512Int2Mask(7),
+ _mm512_mask_storeu_ps(base + o[8 + i],
+ avx512Int2Mask(7),
_mm512_castps128_ps512(_mm_add_ps(_mm_loadu_ps(base + o[8 + i]),
_mm512_extractf32x4_ps(t[i], 2))));
- _mm512_mask_storeu_ps(base + o[12 + i], avx512Int2Mask(7),
+ _mm512_mask_storeu_ps(base + o[12 + i],
+ avx512Int2Mask(7),
_mm512_castps128_ps512(_mm_add_ps(_mm_loadu_ps(base + o[12 + i]),
_mm512_extractf32x4_ps(t[i], 3))));
}
_mm_add_ps(_mm_load_ps(base + o[4 + i]), _mm512_extractf32x4_ps(t[i], 1)));
_mm_store_ps(base + o[8 + i],
_mm_add_ps(_mm_load_ps(base + o[8 + i]), _mm512_extractf32x4_ps(t[i], 2)));
- _mm_store_ps(base + o[12 + i], _mm_add_ps(_mm_load_ps(base + o[12 + i]),
- _mm512_extractf32x4_ps(t[i], 3)));
+ _mm_store_ps(base + o[12 + i],
+ _mm_add_ps(_mm_load_ps(base + o[12 + i]), _mm512_extractf32x4_ps(t[i], 3)));
}
}
else
{
_mm_storeu_ps(base + o[i],
_mm_add_ps(_mm_loadu_ps(base + o[i]), _mm512_castps512_ps128(t[i])));
- _mm_storeu_ps(base + o[4 + i], _mm_add_ps(_mm_loadu_ps(base + o[4 + i]),
- _mm512_extractf32x4_ps(t[i], 1)));
- _mm_storeu_ps(base + o[8 + i], _mm_add_ps(_mm_loadu_ps(base + o[8 + i]),
- _mm512_extractf32x4_ps(t[i], 2)));
- _mm_storeu_ps(base + o[12 + i], _mm_add_ps(_mm_loadu_ps(base + o[12 + i]),
- _mm512_extractf32x4_ps(t[i], 3)));
+ _mm_storeu_ps(base + o[4 + i],
+ _mm_add_ps(_mm_loadu_ps(base + o[4 + i]), _mm512_extractf32x4_ps(t[i], 1)));
+ _mm_storeu_ps(base + o[8 + i],
+ _mm_add_ps(_mm_loadu_ps(base + o[8 + i]), _mm512_extractf32x4_ps(t[i], 2)));
+ _mm_storeu_ps(base + o[12 + i],
+ _mm_add_ps(_mm_loadu_ps(base + o[12 + i]), _mm512_extractf32x4_ps(t[i], 3)));
}
}
}
t[3] = _mm512_shuffle_ps(t6, v2.simdInternal_, _MM_SHUFFLE(3, 3, 3, 2));
for (i = 0; i < 4; i++)
{
- _mm512_mask_storeu_ps(base + o[i], avx512Int2Mask(7),
+ _mm512_mask_storeu_ps(base + o[i],
+ avx512Int2Mask(7),
_mm512_castps128_ps512(_mm_sub_ps(_mm_loadu_ps(base + o[i]),
_mm512_castps512_ps128(t[i]))));
- _mm512_mask_storeu_ps(base + o[4 + i], avx512Int2Mask(7),
+ _mm512_mask_storeu_ps(base + o[4 + i],
+ avx512Int2Mask(7),
_mm512_castps128_ps512(_mm_sub_ps(_mm_loadu_ps(base + o[4 + i]),
_mm512_extractf32x4_ps(t[i], 1))));
- _mm512_mask_storeu_ps(base + o[8 + i], avx512Int2Mask(7),
+ _mm512_mask_storeu_ps(base + o[8 + i],
+ avx512Int2Mask(7),
_mm512_castps128_ps512(_mm_sub_ps(_mm_loadu_ps(base + o[8 + i]),
_mm512_extractf32x4_ps(t[i], 2))));
- _mm512_mask_storeu_ps(base + o[12 + i], avx512Int2Mask(7),
+ _mm512_mask_storeu_ps(base + o[12 + i],
+ avx512Int2Mask(7),
_mm512_castps128_ps512(_mm_sub_ps(_mm_loadu_ps(base + o[12 + i]),
_mm512_extractf32x4_ps(t[i], 3))));
}
_mm_sub_ps(_mm_load_ps(base + o[4 + i]), _mm512_extractf32x4_ps(t[i], 1)));
_mm_store_ps(base + o[8 + i],
_mm_sub_ps(_mm_load_ps(base + o[8 + i]), _mm512_extractf32x4_ps(t[i], 2)));
- _mm_store_ps(base + o[12 + i], _mm_sub_ps(_mm_load_ps(base + o[12 + i]),
- _mm512_extractf32x4_ps(t[i], 3)));
+ _mm_store_ps(base + o[12 + i],
+ _mm_sub_ps(_mm_load_ps(base + o[12 + i]), _mm512_extractf32x4_ps(t[i], 3)));
}
}
else
{
_mm_storeu_ps(base + o[i],
_mm_sub_ps(_mm_loadu_ps(base + o[i]), _mm512_castps512_ps128(t[i])));
- _mm_storeu_ps(base + o[4 + i], _mm_sub_ps(_mm_loadu_ps(base + o[4 + i]),
- _mm512_extractf32x4_ps(t[i], 1)));
- _mm_storeu_ps(base + o[8 + i], _mm_sub_ps(_mm_loadu_ps(base + o[8 + i]),
- _mm512_extractf32x4_ps(t[i], 2)));
- _mm_storeu_ps(base + o[12 + i], _mm_sub_ps(_mm_loadu_ps(base + o[12 + i]),
- _mm512_extractf32x4_ps(t[i], 3)));
+ _mm_storeu_ps(base + o[4 + i],
+ _mm_sub_ps(_mm_loadu_ps(base + o[4 + i]), _mm512_extractf32x4_ps(t[i], 1)));
+ _mm_storeu_ps(base + o[8 + i],
+ _mm_sub_ps(_mm_loadu_ps(base + o[8 + i]), _mm512_extractf32x4_ps(t[i], 2)));
+ _mm_storeu_ps(base + o[12 + i],
+ _mm_sub_ps(_mm_loadu_ps(base + o[12 + i]), _mm512_extractf32x4_ps(t[i], 3)));
}
}
}
assert(std::size_t(m) % 16 == 0);
t0 = _mm512_add_ps(v0.simdInternal_, _mm512_permute_ps(v0.simdInternal_, 0x4E));
- t0 = _mm512_mask_add_ps(t0, avx512Int2Mask(0xCCCC), v2.simdInternal_,
- _mm512_permute_ps(v2.simdInternal_, 0x4E));
+ t0 = _mm512_mask_add_ps(
+ t0, avx512Int2Mask(0xCCCC), v2.simdInternal_, _mm512_permute_ps(v2.simdInternal_, 0x4E));
t1 = _mm512_add_ps(v1.simdInternal_, _mm512_permute_ps(v1.simdInternal_, 0x4E));
- t1 = _mm512_mask_add_ps(t1, avx512Int2Mask(0xCCCC), v3.simdInternal_,
- _mm512_permute_ps(v3.simdInternal_, 0x4E));
+ t1 = _mm512_mask_add_ps(
+ t1, avx512Int2Mask(0xCCCC), v3.simdInternal_, _mm512_permute_ps(v3.simdInternal_, 0x4E));
t2 = _mm512_add_ps(t0, _mm512_permute_ps(t0, 0xB1));
t2 = _mm512_mask_add_ps(t2, avx512Int2Mask(0xAAAA), t1, _mm512_permute_ps(t1, 0xB1));
return { _mm512_castpd_ps(_mm512_insertf64x4(
_mm512_castpd256_pd512(_mm256_load_pd(reinterpret_cast<const double*>(m0))),
- _mm256_load_pd(reinterpret_cast<const double*>(m1)), 1)) };
+ _mm256_load_pd(reinterpret_cast<const double*>(m1)),
+ 1)) };
}
static inline SimdFloat gmx_simdcall loadDuplicateHsimd(const float* m)
static inline SimdFloat gmx_simdcall loadU1DualHsimd(const float* m)
{
- return { _mm512_shuffle_f32x4(_mm512_broadcastss_ps(_mm_load_ss(m)),
- _mm512_broadcastss_ps(_mm_load_ss(m + 1)), 0x44) };
+ return { _mm512_shuffle_f32x4(
+ _mm512_broadcastss_ps(_mm_load_ss(m)), _mm512_broadcastss_ps(_mm_load_ss(m + 1)), 0x44) };
}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_SIMD_IMPL_X86_MIC_H
-#define GMX_SIMD_IMPL_X86_MIC_H
-
-#include "impl_x86_mic_definitions.h"
-#include "impl_x86_mic_general.h"
-#include "impl_x86_mic_simd4_double.h"
-#include "impl_x86_mic_simd4_float.h"
-#include "impl_x86_mic_simd_double.h"
-#include "impl_x86_mic_simd_float.h"
-#include "impl_x86_mic_util_double.h"
-#include "impl_x86_mic_util_float.h"
-
-#endif // GMX_SIMD_IMPL_X86_MIC_H
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2017,2018,2019,2020, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_SIMD_IMPL_X86_MIC_DEFINITIONS_H
-#define GMX_SIMD_IMPL_X86_MIC_DEFINITIONS_H
-
-#define GMX_SIMD 1
-#define GMX_SIMD_HAVE_FLOAT 1
-#define GMX_SIMD_HAVE_DOUBLE 1
-#define GMX_SIMD_HAVE_LOADU 1
-#define GMX_SIMD_HAVE_STOREU 1
-#define GMX_SIMD_HAVE_LOGICAL 1
-#define GMX_SIMD_HAVE_FMA 1
-#define GMX_SIMD_HAVE_FINT32_EXTRACT 1
-#define GMX_SIMD_HAVE_FINT32_LOGICAL 1
-#define GMX_SIMD_HAVE_FINT32_ARITHMETICS 1
-#define GMX_SIMD_HAVE_DINT32_EXTRACT 1
-#define GMX_SIMD_HAVE_DINT32_LOGICAL 1
-#define GMX_SIMD_HAVE_DINT32_ARITHMETICS 1
-#define GMX_SIMD_HAVE_NATIVE_COPYSIGN_FLOAT 0
-#define GMX_SIMD_HAVE_NATIVE_RSQRT_ITER_FLOAT 0
-#define GMX_SIMD_HAVE_NATIVE_RCP_ITER_FLOAT 0
-#define GMX_SIMD_HAVE_NATIVE_LOG_FLOAT 1
-#define GMX_SIMD_HAVE_NATIVE_EXP2_FLOAT 1
-#define GMX_SIMD_HAVE_NATIVE_EXP_FLOAT 1
-#define GMX_SIMD_HAVE_NATIVE_COPYSIGN_DOUBLE 0
-#define GMX_SIMD_HAVE_NATIVE_RSQRT_ITER_DOUBLE 0
-#define GMX_SIMD_HAVE_NATIVE_RCP_ITER_DOUBLE 0
-#define GMX_SIMD_HAVE_NATIVE_LOG_DOUBLE 0
-#define GMX_SIMD_HAVE_NATIVE_EXP2_DOUBLE 0
-#define GMX_SIMD_HAVE_NATIVE_EXP_DOUBLE 0
-#define GMX_SIMD_HAVE_GATHER_LOADU_BYSIMDINT_TRANSPOSE_FLOAT 1
-#define GMX_SIMD_HAVE_GATHER_LOADU_BYSIMDINT_TRANSPOSE_DOUBLE 1
-#define GMX_SIMD_HAVE_HSIMD_UTIL_FLOAT 1
-#define GMX_SIMD_HAVE_HSIMD_UTIL_DOUBLE 1
-
-#define GMX_SIMD4_HAVE_FLOAT 1
-#define GMX_SIMD4_HAVE_DOUBLE 1
-
-// Implementation details
-#define GMX_SIMD_FLOAT_WIDTH 16
-#define GMX_SIMD_DOUBLE_WIDTH 8
-#define GMX_SIMD_FINT32_WIDTH 16
-#define GMX_SIMD_DINT32_WIDTH 8
-#define GMX_SIMD4_WIDTH 4
-#define GMX_SIMD_ALIGNMENT 64 // Bytes (16*single or 8*double)
-#define GMX_SIMD_RSQRT_BITS 23
-#define GMX_SIMD_RCP_BITS 23
-
-#endif // GMX_SIMD_IMPL_X86_MIC_DEFINITIONS_H
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2017,2019, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_SIMD_IMPL_X86_MIC_SIMD4_DOUBLE_H
-#define GMX_SIMD_IMPL_X86_MIC_SIMD4_DOUBLE_H
-
-#include "config.h"
-
-#include <cassert>
-
-#include <immintrin.h>
-
-#include "gromacs/utility/basedefinitions.h"
-
-#include "impl_x86_mic_simd_double.h"
-
-namespace gmx
-{
-
-class Simd4Double
-{
-public:
- Simd4Double() {}
-
- Simd4Double(double d) : simdInternal_(_mm512_set1_pd(d)) {}
-
- // Internal utility constructor to simplify return statements
- Simd4Double(__m512d simd) : simdInternal_(simd) {}
-
- __m512d simdInternal_;
-};
-
-class Simd4DBool
-{
-public:
- Simd4DBool() {}
-
- // Internal utility constructor to simplify return statements
- Simd4DBool(__mmask16 simd) : simdInternal_(simd) {}
-
- __mmask16 simdInternal_;
-};
-
-static inline Simd4Double gmx_simdcall load4(const double* m)
-{
- assert(size_t(m) % 32 == 0);
- return { _mm512_mask_extload_pd(_mm512_undefined_pd(), _mm512_int2mask(0xF), m,
- _MM_UPCONV_PD_NONE, _MM_BROADCAST_4X8, _MM_HINT_NONE) };
-}
-
-static inline void gmx_simdcall store4(double* m, Simd4Double a)
-{
- assert(size_t(m) % 32 == 0);
- _mm512_mask_packstorelo_pd(m, _mm512_int2mask(0xF), a.simdInternal_);
-}
-
-static inline Simd4Double gmx_simdcall load4U(const double* m)
-{
- return { _mm512_mask_loadunpackhi_pd(
- _mm512_mask_loadunpacklo_pd(_mm512_undefined_pd(), _mm512_int2mask(0xF), m),
- _mm512_int2mask(0xF), m + 8) };
-}
-
-static inline void gmx_simdcall store4U(double* m, Simd4Double a)
-{
- _mm512_mask_packstorelo_pd(m, _mm512_int2mask(0xF), a.simdInternal_);
- _mm512_mask_packstorehi_pd(m + 8, _mm512_int2mask(0xF), a.simdInternal_);
-}
-
-static inline Simd4Double gmx_simdcall simd4SetZeroD()
-{
- return { _mm512_setzero_pd() };
-}
-
-static inline Simd4Double gmx_simdcall operator&(Simd4Double a, Simd4Double b)
-{
- return { _mm512_castsi512_pd(_mm512_mask_and_epi32(
- _mm512_undefined_epi32(), _mm512_int2mask(0x00FF), _mm512_castpd_si512(a.simdInternal_),
- _mm512_castpd_si512(b.simdInternal_))) };
-}
-
-static inline Simd4Double gmx_simdcall andNot(Simd4Double a, Simd4Double b)
-{
- return { _mm512_castsi512_pd(_mm512_mask_andnot_epi32(
- _mm512_undefined_epi32(), _mm512_int2mask(0x00FF), _mm512_castpd_si512(a.simdInternal_),
- _mm512_castpd_si512(b.simdInternal_))) };
-}
-
-static inline Simd4Double gmx_simdcall operator|(Simd4Double a, Simd4Double b)
-{
- return { _mm512_castsi512_pd(_mm512_mask_or_epi32(
- _mm512_undefined_epi32(), _mm512_int2mask(0x00FF), _mm512_castpd_si512(a.simdInternal_),
- _mm512_castpd_si512(b.simdInternal_))) };
-}
-
-static inline Simd4Double gmx_simdcall operator^(Simd4Double a, Simd4Double b)
-{
- return { _mm512_castsi512_pd(_mm512_mask_xor_epi32(
- _mm512_undefined_epi32(), _mm512_int2mask(0x00FF), _mm512_castpd_si512(a.simdInternal_),
- _mm512_castpd_si512(b.simdInternal_))) };
-}
-
-static inline Simd4Double gmx_simdcall operator+(Simd4Double a, Simd4Double b)
-{
- return { _mm512_mask_add_pd(_mm512_undefined_pd(), _mm512_int2mask(0xF), a.simdInternal_,
- b.simdInternal_) };
-}
-
-static inline Simd4Double gmx_simdcall operator-(Simd4Double a, Simd4Double b)
-{
- return { _mm512_mask_sub_pd(_mm512_undefined_pd(), _mm512_int2mask(0xF), a.simdInternal_,
- b.simdInternal_) };
-}
-
-static inline Simd4Double gmx_simdcall operator-(Simd4Double x)
-{
- return { _mm512_mask_addn_pd(_mm512_undefined_pd(), _mm512_int2mask(0xF), x.simdInternal_,
- _mm512_setzero_pd()) };
-}
-
-static inline Simd4Double gmx_simdcall operator*(Simd4Double a, Simd4Double b)
-{
- return { _mm512_mask_mul_pd(_mm512_undefined_pd(), _mm512_int2mask(0xF), a.simdInternal_,
- b.simdInternal_) };
-}
-
-static inline Simd4Double gmx_simdcall fma(Simd4Double a, Simd4Double b, Simd4Double c)
-{
- return { _mm512_mask_fmadd_pd(a.simdInternal_, _mm512_int2mask(0xF), b.simdInternal_, c.simdInternal_) };
-}
-
-static inline Simd4Double gmx_simdcall fms(Simd4Double a, Simd4Double b, Simd4Double c)
-{
- return { _mm512_mask_fmsub_pd(a.simdInternal_, _mm512_int2mask(0xF), b.simdInternal_, c.simdInternal_) };
-}
-
-static inline Simd4Double gmx_simdcall fnma(Simd4Double a, Simd4Double b, Simd4Double c)
-{
- return { _mm512_mask_fnmadd_pd(a.simdInternal_, _mm512_int2mask(0xF), b.simdInternal_, c.simdInternal_) };
-}
-
-static inline Simd4Double gmx_simdcall fnms(Simd4Double a, Simd4Double b, Simd4Double c)
-{
- return { _mm512_mask_fnmsub_pd(a.simdInternal_, _mm512_int2mask(0xF), b.simdInternal_, c.simdInternal_) };
-}
-
-static inline Simd4Double gmx_simdcall rsqrt(Simd4Double x)
-{
- return { _mm512_mask_cvtpslo_pd(
- _mm512_undefined_pd(), _mm512_int2mask(0xF),
- _mm512_mask_rsqrt23_ps(_mm512_undefined_ps(), _mm512_int2mask(0xF),
- _mm512_mask_cvtpd_pslo(_mm512_undefined_ps(),
- _mm512_int2mask(0xF), x.simdInternal_))) };
-}
-
-static inline Simd4Double gmx_simdcall abs(Simd4Double x)
-{
- return { _mm512_castsi512_pd(_mm512_mask_andnot_epi32(
- _mm512_undefined_epi32(), _mm512_int2mask(0x00FF),
- _mm512_castpd_si512(_mm512_set1_pd(GMX_DOUBLE_NEGZERO)), _mm512_castpd_si512(x.simdInternal_)))
-
- };
-}
-
-static inline Simd4Double gmx_simdcall max(Simd4Double a, Simd4Double b)
-{
- return { _mm512_mask_gmax_pd(_mm512_undefined_pd(), _mm512_int2mask(0xF), a.simdInternal_,
- b.simdInternal_) };
-}
-
-static inline Simd4Double gmx_simdcall min(Simd4Double a, Simd4Double b)
-{
- return { _mm512_mask_gmin_pd(_mm512_undefined_pd(), _mm512_int2mask(0xF), a.simdInternal_,
- b.simdInternal_) };
-}
-
-static inline Simd4Double gmx_simdcall round(Simd4Double x)
-{
- return { _mm512_mask_roundfxpnt_adjust_pd(_mm512_undefined_pd(), _mm512_int2mask(0xF), x.simdInternal_,
- _MM_FROUND_TO_NEAREST_INT, _MM_EXPADJ_NONE) };
-}
-
-static inline Simd4Double gmx_simdcall trunc(Simd4Double x)
-{
- return { _mm512_mask_roundfxpnt_adjust_pd(_mm512_undefined_pd(), _mm512_int2mask(0xF),
- x.simdInternal_, _MM_FROUND_TO_ZERO, _MM_EXPADJ_NONE) };
-}
-
-static inline double gmx_simdcall dotProduct(Simd4Double a, Simd4Double b)
-{
- return _mm512_mask_reduce_add_pd(_mm512_int2mask(7),
- _mm512_mask_mul_pd(_mm512_undefined_pd(), _mm512_int2mask(7),
- a.simdInternal_, b.simdInternal_));
-}
-
-static inline void gmx_simdcall transpose(Simd4Double* v0, Simd4Double* v1, Simd4Double* v2, Simd4Double* v3)
-{
- __m512i t0 = _mm512_mask_permute4f128_epi32(_mm512_castpd_si512(v0->simdInternal_), 0xFF00,
- _mm512_castpd_si512(v1->simdInternal_), _MM_PERM_BABA);
- __m512i t1 = _mm512_mask_permute4f128_epi32(_mm512_castpd_si512(v2->simdInternal_), 0xFF00,
- _mm512_castpd_si512(v3->simdInternal_), _MM_PERM_BABA);
-
- t0 = _mm512_permutevar_epi32(
- _mm512_set_epi32(15, 14, 7, 6, 13, 12, 5, 4, 11, 10, 3, 2, 9, 8, 1, 0), t0);
- t1 = _mm512_permutevar_epi32(
- _mm512_set_epi32(15, 14, 7, 6, 13, 12, 5, 4, 11, 10, 3, 2, 9, 8, 1, 0), t1);
-
- v0->simdInternal_ = _mm512_mask_swizzle_pd(_mm512_castsi512_pd(t0), _mm512_int2mask(0xCC),
- _mm512_castsi512_pd(t1), _MM_SWIZ_REG_BADC);
- v1->simdInternal_ = _mm512_mask_swizzle_pd(_mm512_castsi512_pd(t1), _mm512_int2mask(0x33),
- _mm512_castsi512_pd(t0), _MM_SWIZ_REG_BADC);
-
- v2->simdInternal_ =
- _mm512_castps_pd(_mm512_permute4f128_ps(_mm512_castpd_ps(v0->simdInternal_), _MM_PERM_DCDC));
- v3->simdInternal_ =
- _mm512_castps_pd(_mm512_permute4f128_ps(_mm512_castpd_ps(v1->simdInternal_), _MM_PERM_DCDC));
-}
-
-// Picky, picky, picky:
-// icc-16 complains about "Illegal value of immediate argument to intrinsic"
-// unless we use
-// 1) Ordered-quiet for ==
-// 2) Unordered-quiet for !=
-// 3) Ordered-signaling for < and <=
-
-static inline Simd4DBool gmx_simdcall operator==(Simd4Double a, Simd4Double b)
-{
- return { _mm512_mask_cmp_pd_mask(_mm512_int2mask(0xF), a.simdInternal_, b.simdInternal_, _CMP_EQ_OQ) };
-}
-
-static inline Simd4DBool gmx_simdcall operator!=(Simd4Double a, Simd4Double b)
-{
- return { _mm512_mask_cmp_pd_mask(_mm512_int2mask(0xF), a.simdInternal_, b.simdInternal_, _CMP_NEQ_UQ) };
-}
-
-static inline Simd4DBool gmx_simdcall operator<(Simd4Double a, Simd4Double b)
-{
- return { _mm512_mask_cmp_pd_mask(_mm512_int2mask(0xF), a.simdInternal_, b.simdInternal_, _CMP_LT_OS) };
-}
-
-static inline Simd4DBool gmx_simdcall operator<=(Simd4Double a, Simd4Double b)
-{
- return { _mm512_mask_cmp_pd_mask(_mm512_int2mask(0xF), a.simdInternal_, b.simdInternal_, _CMP_LE_OS) };
-}
-
-static inline Simd4DBool gmx_simdcall operator&&(Simd4DBool a, Simd4DBool b)
-{
- return { _mm512_kand(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4DBool gmx_simdcall operator||(Simd4DBool a, Simd4DBool b)
-{
- return { _mm512_kor(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline bool gmx_simdcall anyTrue(Simd4DBool a)
-{
- return (_mm512_mask2int(a.simdInternal_) & 0xF) != 0;
-}
-
-static inline Simd4Double gmx_simdcall selectByMask(Simd4Double a, Simd4DBool m)
-{
- return { _mm512_mask_mov_pd(_mm512_setzero_pd(), m.simdInternal_, a.simdInternal_) };
-}
-
-static inline Simd4Double gmx_simdcall selectByNotMask(Simd4Double a, Simd4DBool m)
-{
- return { _mm512_mask_mov_pd(_mm512_setzero_pd(), _mm512_knot(m.simdInternal_), a.simdInternal_) };
-}
-
-static inline Simd4Double gmx_simdcall blend(Simd4Double a, Simd4Double b, Simd4DBool sel)
-{
- return { _mm512_mask_blend_pd(sel.simdInternal_, a.simdInternal_, b.simdInternal_) };
-}
-
-static inline double gmx_simdcall reduce(Simd4Double a)
-{
- return _mm512_mask_reduce_add_pd(_mm512_int2mask(0xF), a.simdInternal_);
-}
-
-} // namespace gmx
-
-#endif // GMX_SIMD_IMPL_X86_MIC_SIMD4_DOUBLE_H
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2019, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_SIMD_IMPL_X86_MIC_SIMD4_FLOAT_H
-#define GMX_SIMD_IMPL_X86_MIC_SIMD4_FLOAT_H
-
-#include "config.h"
-
-#include <cassert>
-
-#include <immintrin.h>
-
-#include "gromacs/utility/basedefinitions.h"
-
-#include "impl_x86_mic_simd_float.h"
-
-namespace gmx
-{
-
-class Simd4Float
-{
-public:
- Simd4Float() {}
-
- Simd4Float(float f) : simdInternal_(_mm512_set1_ps(f)) {}
-
- // Internal utility constructor to simplify return statements
- Simd4Float(__m512 simd) : simdInternal_(simd) {}
-
- __m512 simdInternal_;
-};
-
-class Simd4FBool
-{
-public:
- Simd4FBool() {}
-
- // Internal utility constructor to simplify return statements
- Simd4FBool(__mmask16 simd) : simdInternal_(simd) {}
-
- __mmask16 simdInternal_;
-};
-
-static inline Simd4Float gmx_simdcall load4(const float* m)
-{
- assert(size_t(m) % 16 == 0);
- return { _mm512_mask_extload_ps(_mm512_undefined_ps(), _mm512_int2mask(0xF), m,
- _MM_UPCONV_PS_NONE, _MM_BROADCAST_4X16, _MM_HINT_NONE) };
-}
-
-static inline void gmx_simdcall store4(float* m, Simd4Float a)
-{
- assert(size_t(m) % 16 == 0);
- _mm512_mask_packstorelo_ps(m, _mm512_int2mask(0xF), a.simdInternal_);
-}
-
-static inline Simd4Float gmx_simdcall load4U(const float* m)
-{
- return { _mm512_mask_loadunpackhi_ps(
- _mm512_mask_loadunpacklo_ps(_mm512_undefined_ps(), _mm512_int2mask(0xF), m),
- _mm512_int2mask(0xF), m + 16) };
-}
-
-static inline void gmx_simdcall store4U(float* m, Simd4Float a)
-{
- _mm512_mask_packstorelo_ps(m, _mm512_int2mask(0xF), a.simdInternal_);
- _mm512_mask_packstorehi_ps(m + 16, _mm512_int2mask(0xF), a.simdInternal_);
-}
-
-static inline Simd4Float gmx_simdcall simd4SetZeroF()
-{
- return { _mm512_setzero_ps() };
-}
-
-static inline Simd4Float gmx_simdcall operator&(Simd4Float a, Simd4Float b)
-{
- return { _mm512_castsi512_ps(_mm512_mask_and_epi32(_mm512_undefined_epi32(), _mm512_int2mask(0xF),
- _mm512_castps_si512(a.simdInternal_),
- _mm512_castps_si512(b.simdInternal_))) };
-}
-
-static inline Simd4Float gmx_simdcall andNot(Simd4Float a, Simd4Float b)
-{
- return { _mm512_castsi512_ps(_mm512_mask_andnot_epi32(
- _mm512_undefined_epi32(), _mm512_int2mask(0xF), _mm512_castps_si512(a.simdInternal_),
- _mm512_castps_si512(b.simdInternal_))) };
-}
-
-static inline Simd4Float gmx_simdcall operator|(Simd4Float a, Simd4Float b)
-{
- return { _mm512_castsi512_ps(_mm512_mask_or_epi32(_mm512_undefined_epi32(), _mm512_int2mask(0xF),
- _mm512_castps_si512(a.simdInternal_),
- _mm512_castps_si512(b.simdInternal_))) };
-}
-
-static inline Simd4Float gmx_simdcall operator^(Simd4Float a, Simd4Float b)
-{
- return { _mm512_castsi512_ps(_mm512_mask_xor_epi32(_mm512_undefined_epi32(), _mm512_int2mask(0xF),
- _mm512_castps_si512(a.simdInternal_),
- _mm512_castps_si512(b.simdInternal_))) };
-}
-
-static inline Simd4Float gmx_simdcall operator+(Simd4Float a, Simd4Float b)
-{
- return { _mm512_mask_add_ps(_mm512_undefined_ps(), _mm512_int2mask(0xF), a.simdInternal_,
- b.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall operator-(Simd4Float a, Simd4Float b)
-{
- return { _mm512_mask_sub_ps(_mm512_undefined_ps(), _mm512_int2mask(0xF), a.simdInternal_,
- b.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall operator-(Simd4Float x)
-{
- return { _mm512_mask_addn_ps(_mm512_undefined_ps(), _mm512_int2mask(0xF), x.simdInternal_,
- _mm512_setzero_ps()) };
-}
-
-static inline Simd4Float gmx_simdcall operator*(Simd4Float a, Simd4Float b)
-{
- return { _mm512_mask_mul_ps(_mm512_undefined_ps(), _mm512_int2mask(0xF), a.simdInternal_,
- b.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall fma(Simd4Float a, Simd4Float b, Simd4Float c)
-{
- return { _mm512_mask_fmadd_ps(a.simdInternal_, _mm512_int2mask(0xF), b.simdInternal_, c.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall fms(Simd4Float a, Simd4Float b, Simd4Float c)
-{
- return { _mm512_mask_fmsub_ps(a.simdInternal_, _mm512_int2mask(0xF), b.simdInternal_, c.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall fnma(Simd4Float a, Simd4Float b, Simd4Float c)
-{
- return { _mm512_mask_fnmadd_ps(a.simdInternal_, _mm512_int2mask(0xF), b.simdInternal_, c.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall fnms(Simd4Float a, Simd4Float b, Simd4Float c)
-{
- return { _mm512_mask_fnmsub_ps(a.simdInternal_, _mm512_int2mask(0xF), b.simdInternal_, c.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall rsqrt(Simd4Float x)
-{
- return { _mm512_mask_rsqrt23_ps(_mm512_undefined_ps(), _mm512_int2mask(0xF), x.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall abs(Simd4Float x)
-{
- return { _mm512_castsi512_ps(_mm512_mask_andnot_epi32(
- _mm512_undefined_epi32(), _mm512_int2mask(0xF),
- _mm512_castps_si512(_mm512_set1_ps(GMX_FLOAT_NEGZERO)), _mm512_castps_si512(x.simdInternal_))) };
-}
-
-static inline Simd4Float gmx_simdcall max(Simd4Float a, Simd4Float b)
-{
- return { _mm512_mask_gmax_ps(_mm512_undefined_ps(), _mm512_int2mask(0xF), a.simdInternal_,
- b.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall min(Simd4Float a, Simd4Float b)
-{
- return { _mm512_mask_gmin_ps(_mm512_undefined_ps(), _mm512_int2mask(0xF), a.simdInternal_,
- b.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall round(Simd4Float x)
-{
- return { _mm512_mask_round_ps(_mm512_undefined_ps(), _mm512_int2mask(0xF), x.simdInternal_,
- _MM_FROUND_TO_NEAREST_INT, _MM_EXPADJ_NONE) };
-}
-
-static inline Simd4Float gmx_simdcall trunc(Simd4Float x)
-{
- return { _mm512_mask_round_ps(_mm512_undefined_ps(), _mm512_int2mask(0xF), x.simdInternal_,
- _MM_FROUND_TO_ZERO, _MM_EXPADJ_NONE) };
-}
-
-static inline float gmx_simdcall dotProduct(Simd4Float a, Simd4Float b)
-{
- __m512 x = _mm512_mask_mul_ps(_mm512_setzero_ps(), _mm512_int2mask(0x7), a.simdInternal_,
- b.simdInternal_);
- x = _mm512_add_ps(x, _mm512_swizzle_ps(x, _MM_SWIZ_REG_BADC));
- x = _mm512_add_ps(x, _mm512_swizzle_ps(x, _MM_SWIZ_REG_CDAB));
- float f;
- _mm512_mask_packstorelo_ps(&f, _mm512_mask2int(0x1), x);
- return f;
-}
-
-static inline void gmx_simdcall transpose(Simd4Float* v0, Simd4Float* v1, Simd4Float* v2, Simd4Float* v3)
-{
- v0->simdInternal_ = _mm512_mask_permute4f128_ps(v0->simdInternal_, _mm512_int2mask(0x00F0),
- v1->simdInternal_, _MM_PERM_AAAA);
- v2->simdInternal_ = _mm512_mask_permute4f128_ps(v2->simdInternal_, _mm512_int2mask(0x00F0),
- v3->simdInternal_, _MM_PERM_AAAA);
- v0->simdInternal_ = _mm512_mask_permute4f128_ps(v0->simdInternal_, _mm512_int2mask(0xFF00),
- v2->simdInternal_, _MM_PERM_BABA);
- v0->simdInternal_ = _mm512_castsi512_ps(_mm512_permutevar_epi32(
- _mm512_set_epi32(15, 11, 7, 3, 14, 10, 6, 2, 13, 9, 5, 1, 12, 8, 4, 0),
- _mm512_castps_si512(v0->simdInternal_)));
- v1->simdInternal_ = _mm512_mask_permute4f128_ps(_mm512_setzero_ps(), _mm512_int2mask(0x000F),
- v0->simdInternal_, _MM_PERM_BBBB);
- v2->simdInternal_ = _mm512_mask_permute4f128_ps(_mm512_setzero_ps(), _mm512_int2mask(0x000F),
- v0->simdInternal_, _MM_PERM_CCCC);
- v3->simdInternal_ = _mm512_mask_permute4f128_ps(_mm512_setzero_ps(), _mm512_int2mask(0x000F),
- v0->simdInternal_, _MM_PERM_DDDD);
-}
-
-// Picky, picky, picky:
-// icc-16 complains about "Illegal value of immediate argument to intrinsic"
-// unless we use
-// 1) Ordered-quiet for ==
-// 2) Unordered-quiet for !=
-// 3) Ordered-signaling for < and <=
-
-static inline Simd4FBool gmx_simdcall operator==(Simd4Float a, Simd4Float b)
-{
- return { _mm512_mask_cmp_ps_mask(_mm512_int2mask(0xF), a.simdInternal_, b.simdInternal_, _CMP_EQ_OQ) };
-}
-
-static inline Simd4FBool gmx_simdcall operator!=(Simd4Float a, Simd4Float b)
-{
- return { _mm512_mask_cmp_ps_mask(_mm512_int2mask(0xF), a.simdInternal_, b.simdInternal_, _CMP_NEQ_UQ) };
-}
-
-static inline Simd4FBool gmx_simdcall operator<(Simd4Float a, Simd4Float b)
-{
- return { _mm512_mask_cmp_ps_mask(_mm512_int2mask(0xF), a.simdInternal_, b.simdInternal_, _CMP_LT_OS) };
-}
-
-static inline Simd4FBool gmx_simdcall operator<=(Simd4Float a, Simd4Float b)
-{
- return { _mm512_mask_cmp_ps_mask(_mm512_int2mask(0xF), a.simdInternal_, b.simdInternal_, _CMP_LE_OS) };
-}
-
-static inline Simd4FBool gmx_simdcall operator&&(Simd4FBool a, Simd4FBool b)
-{
- return { _mm512_kand(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline Simd4FBool gmx_simdcall operator||(Simd4FBool a, Simd4FBool b)
-{
- return { _mm512_kor(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline bool gmx_simdcall anyTrue(Simd4FBool a)
-{
- return (_mm512_mask2int(a.simdInternal_) & 0xF) != 0;
-}
-
-static inline Simd4Float gmx_simdcall selectByMask(Simd4Float a, Simd4FBool m)
-{
- return { _mm512_mask_mov_ps(_mm512_setzero_ps(), m.simdInternal_, a.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall selectByNotMask(Simd4Float a, Simd4FBool m)
-{
- return { _mm512_mask_mov_ps(_mm512_setzero_ps(), _mm512_knot(m.simdInternal_), a.simdInternal_) };
-}
-
-static inline Simd4Float gmx_simdcall blend(Simd4Float a, Simd4Float b, Simd4FBool sel)
-{
- return { _mm512_mask_blend_ps(sel.simdInternal_, a.simdInternal_, b.simdInternal_) };
-}
-
-static inline float gmx_simdcall reduce(Simd4Float a)
-{
- __m512 x = a.simdInternal_;
- x = _mm512_add_ps(x, _mm512_swizzle_ps(x, _MM_SWIZ_REG_BADC));
- x = _mm512_add_ps(x, _mm512_swizzle_ps(x, _MM_SWIZ_REG_CDAB));
- float f;
- _mm512_mask_packstorelo_ps(&f, _mm512_mask2int(0x1), x);
- return f;
-}
-
-} // namespace gmx
-
-#endif // GMX_SIMD_IMPL_X86_MIC_SIMD4_FLOAT_H
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2016,2017,2019,2020, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_SIMD_IMPL_X86_MIC_SIMD_DOUBLE_H
-#define GMX_SIMD_IMPL_X86_MIC_SIMD_DOUBLE_H
-
-#include "config.h"
-
-#include <cassert>
-#include <cstdint>
-
-#include <immintrin.h>
-
-#include "gromacs/math/utilities.h"
-#include "gromacs/utility/basedefinitions.h"
-
-#include "impl_x86_mic_simd_float.h"
-
-namespace gmx
-{
-
-class SimdDouble
-{
-public:
- SimdDouble() {}
-
- SimdDouble(double d) : simdInternal_(_mm512_set1_pd(d)) {}
-
- // Internal utility constructor to simplify return statements
- SimdDouble(__m512d simd) : simdInternal_(simd) {}
-
- __m512d simdInternal_;
-};
-
-class SimdDInt32
-{
-public:
- SimdDInt32() {}
-
- SimdDInt32(std::int32_t i) : simdInternal_(_mm512_set1_epi32(i)) {}
-
- // Internal utility constructor to simplify return statements
- SimdDInt32(__m512i simd) : simdInternal_(simd) {}
-
- __m512i simdInternal_;
-};
-
-class SimdDBool
-{
-public:
- SimdDBool() {}
-
- // Internal utility constructor to simplify return statements
- SimdDBool(__mmask8 simd) : simdInternal_(simd) {}
-
- __mmask8 simdInternal_;
-};
-
-class SimdDIBool
-{
-public:
- SimdDIBool() {}
-
- // Internal utility constructor to simplify return statements
- SimdDIBool(__mmask16 simd) : simdInternal_(simd) {}
-
- __mmask16 simdInternal_;
-};
-
-static inline SimdDouble gmx_simdcall simdLoad(const double* m, SimdDoubleTag = {})
-{
- assert(std::size_t(m) % 64 == 0);
- return { _mm512_load_pd(m) };
-}
-
-static inline void gmx_simdcall store(double* m, SimdDouble a)
-{
- assert(std::size_t(m) % 64 == 0);
- _mm512_store_pd(m, a.simdInternal_);
-}
-
-static inline SimdDouble gmx_simdcall simdLoadU(const double* m, SimdDoubleTag = {})
-{
- return { _mm512_loadunpackhi_pd(_mm512_loadunpacklo_pd(_mm512_undefined_pd(), m), m + 8) };
-}
-
-static inline void gmx_simdcall storeU(double* m, SimdDouble a)
-{
- _mm512_packstorelo_pd(m, a.simdInternal_);
- _mm512_packstorehi_pd(m + 8, a.simdInternal_);
-}
-
-static inline SimdDouble gmx_simdcall setZeroD()
-{
- return { _mm512_setzero_pd() };
-}
-
-static inline SimdDInt32 gmx_simdcall simdLoad(const std::int32_t* m, SimdDInt32Tag)
-{
- assert(std::size_t(m) % 32 == 0);
- return { _mm512_extload_epi64(m, _MM_UPCONV_EPI64_NONE, _MM_BROADCAST_4X8, _MM_HINT_NONE) };
-}
-
-static inline void gmx_simdcall store(std::int32_t* m, SimdDInt32 a)
-{
- assert(std::size_t(m) % 32 == 0);
- _mm512_mask_packstorelo_epi32(m, _mm512_int2mask(0x00FF), a.simdInternal_);
-}
-
-static inline SimdDInt32 gmx_simdcall simdLoadU(const std::int32_t* m, SimdDInt32Tag)
-{
- return { _mm512_mask_loadunpackhi_epi32(
- _mm512_mask_loadunpacklo_epi32(_mm512_undefined_epi32(), _mm512_int2mask(0x00FF), m),
- _mm512_int2mask(0x00FF), m + 16) };
-}
-
-static inline void gmx_simdcall storeU(std::int32_t* m, SimdDInt32 a)
-{
- _mm512_mask_packstorelo_epi32(m, _mm512_int2mask(0x00FF), a.simdInternal_);
- _mm512_mask_packstorehi_epi32(m + 16, _mm512_int2mask(0x00FF), a.simdInternal_);
-}
-
-static inline SimdDInt32 gmx_simdcall setZeroDI()
-{
- return { _mm512_setzero_epi32() };
-}
-
-template<int index>
-static inline std::int32_t gmx_simdcall extract(SimdDInt32 a)
-{
- int r;
- _mm512_mask_packstorelo_epi32(&r, _mm512_mask2int(1 << index), a.simdInternal_);
- return r;
-}
-
-static inline SimdDouble gmx_simdcall operator&(SimdDouble a, SimdDouble b)
-{
- return { _mm512_castsi512_pd(_mm512_and_epi32(_mm512_castpd_si512(a.simdInternal_),
- _mm512_castpd_si512(b.simdInternal_))) };
-}
-
-static inline SimdDouble gmx_simdcall andNot(SimdDouble a, SimdDouble b)
-{
- return { _mm512_castsi512_pd(_mm512_andnot_epi32(_mm512_castpd_si512(a.simdInternal_),
- _mm512_castpd_si512(b.simdInternal_))) };
-}
-
-static inline SimdDouble gmx_simdcall operator|(SimdDouble a, SimdDouble b)
-{
- return { _mm512_castsi512_pd(_mm512_or_epi32(_mm512_castpd_si512(a.simdInternal_),
- _mm512_castpd_si512(b.simdInternal_))) };
-}
-
-static inline SimdDouble gmx_simdcall operator^(SimdDouble a, SimdDouble b)
-{
- return { _mm512_castsi512_pd(_mm512_xor_epi32(_mm512_castpd_si512(a.simdInternal_),
- _mm512_castpd_si512(b.simdInternal_))) };
-}
-
-static inline SimdDouble gmx_simdcall operator+(SimdDouble a, SimdDouble b)
-{
- return { _mm512_add_pd(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdDouble gmx_simdcall operator-(SimdDouble a, SimdDouble b)
-{
- return { _mm512_sub_pd(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdDouble gmx_simdcall operator-(SimdDouble x)
-{
- return { _mm512_addn_pd(x.simdInternal_, _mm512_setzero_pd()) };
-}
-
-static inline SimdDouble gmx_simdcall operator*(SimdDouble a, SimdDouble b)
-{
- return { _mm512_mul_pd(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdDouble gmx_simdcall fma(SimdDouble a, SimdDouble b, SimdDouble c)
-{
- return { _mm512_fmadd_pd(a.simdInternal_, b.simdInternal_, c.simdInternal_) };
-}
-
-static inline SimdDouble gmx_simdcall fms(SimdDouble a, SimdDouble b, SimdDouble c)
-{
- return { _mm512_fmsub_pd(a.simdInternal_, b.simdInternal_, c.simdInternal_) };
-}
-
-static inline SimdDouble gmx_simdcall fnma(SimdDouble a, SimdDouble b, SimdDouble c)
-{
- return { _mm512_fnmadd_pd(a.simdInternal_, b.simdInternal_, c.simdInternal_) };
-}
-
-static inline SimdDouble gmx_simdcall fnms(SimdDouble a, SimdDouble b, SimdDouble c)
-{
- return { _mm512_fnmsub_pd(a.simdInternal_, b.simdInternal_, c.simdInternal_) };
-}
-
-static inline SimdDouble gmx_simdcall rsqrt(SimdDouble x)
-{
- return { _mm512_cvtpslo_pd(_mm512_rsqrt23_ps(_mm512_cvtpd_pslo(x.simdInternal_))) };
-}
-
-static inline SimdDouble gmx_simdcall rcp(SimdDouble x)
-{
- return { _mm512_cvtpslo_pd(_mm512_rcp23_ps(_mm512_cvtpd_pslo(x.simdInternal_))) };
-}
-
-static inline SimdDouble gmx_simdcall maskAdd(SimdDouble a, SimdDouble b, SimdDBool m)
-{
- return { _mm512_mask_add_pd(a.simdInternal_, m.simdInternal_, a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdDouble gmx_simdcall maskzMul(SimdDouble a, SimdDouble b, SimdDBool m)
-{
- return { _mm512_mask_mul_pd(_mm512_setzero_pd(), m.simdInternal_, a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdDouble gmx_simdcall maskzFma(SimdDouble a, SimdDouble b, SimdDouble c, SimdDBool m)
-{
- return { _mm512_mask_mov_pd(_mm512_setzero_pd(), m.simdInternal_,
- _mm512_fmadd_pd(a.simdInternal_, b.simdInternal_, c.simdInternal_)) };
-}
-
-static inline SimdDouble gmx_simdcall maskzRsqrt(SimdDouble x, SimdDBool m)
-{
- return { _mm512_cvtpslo_pd(_mm512_mask_rsqrt23_ps(_mm512_setzero_ps(), m.simdInternal_,
- _mm512_cvtpd_pslo(x.simdInternal_))) };
-}
-
-static inline SimdDouble gmx_simdcall maskzRcp(SimdDouble x, SimdDBool m)
-{
- return { _mm512_cvtpslo_pd(_mm512_mask_rcp23_ps(_mm512_setzero_ps(), m.simdInternal_,
- _mm512_cvtpd_pslo(x.simdInternal_))) };
-}
-
-static inline SimdDouble gmx_simdcall abs(SimdDouble x)
-{
- return { _mm512_castsi512_pd(_mm512_andnot_epi32(_mm512_castpd_si512(_mm512_set1_pd(GMX_DOUBLE_NEGZERO)),
- _mm512_castpd_si512(x.simdInternal_))) };
-}
-
-static inline SimdDouble gmx_simdcall max(SimdDouble a, SimdDouble b)
-{
- return { _mm512_gmax_pd(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdDouble gmx_simdcall min(SimdDouble a, SimdDouble b)
-{
- return { _mm512_gmin_pd(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdDouble gmx_simdcall round(SimdDouble x)
-{
- return { _mm512_roundfxpnt_adjust_pd(x.simdInternal_, _MM_FROUND_TO_NEAREST_INT, _MM_EXPADJ_NONE) };
-}
-
-static inline SimdDouble gmx_simdcall trunc(SimdDouble x)
-{
- return { _mm512_roundfxpnt_adjust_pd(x.simdInternal_, _MM_FROUND_TO_ZERO, _MM_EXPADJ_NONE) };
-}
-
-template<MathOptimization opt = MathOptimization::Safe>
-static inline SimdDouble frexp(SimdDouble value, SimdDInt32* exponent)
-{
- __m512d rExponent;
- __m512i iExponent;
- __m512d result;
-
- if (opt == MathOptimization::Safe)
- {
- // For the safe branch, we use the masked operations to only assign results if the
- // input value was nonzero, and otherwise set exponent to 0, and the fraction to the input (+-0).
- __mmask8 valueIsNonZero =
- _mm512_cmp_pd_mask(_mm512_setzero_pd(), value.simdInternal_, _CMP_NEQ_OQ);
- rExponent = _mm512_mask_getexp_pd(_mm512_setzero_pd(), valueIsNonZero, value.simdInternal_);
-
- // Create an integer -1 value, and use masking in the conversion as the result for
- // zero-value input. When we later add 1 to all fields, the fields that were formerly -1
- // (corresponding to zero exponent) will be assigned -1 + 1 = 0.
- iExponent = _mm512_mask_cvtfxpnt_roundpd_epi32lo(_mm512_set_epi32(-1), valueIsNonZero,
- rExponent, _MM_FROUND_TO_NEAREST_INT);
- iExponent = _mm512__add_epi32(iExponent, _mm512_set1_epi32(1));
-
- // Set result to value (+-0) when it is zero.
- result = _mm512_mask_getmant_pd(value.simdInternal_, valueIsNonZero, value.simdInternal_,
- _MM_MANT_NORM_p5_1, _MM_MANT_SIGN_src);
- }
- else
- {
- rExponent = _mm512_getexp_pd(value.simdInternal_);
- iExponent = _mm512_cvtfxpnt_roundpd_epi32lo(rExponent, _MM_FROUND_TO_NEAREST_INT);
- iExponent = _mm512_add_epi32(iExponent, _mm512_set1_epi32(1));
- result = _mm512_getmant_pd(value.simdInternal_, _MM_MANT_NORM_p5_1, _MM_MANT_SIGN_src);
- }
-
- exponent->simdInternal_ = iExponent;
-
- return { result };
-}
-
-template<MathOptimization opt = MathOptimization::Safe>
-static inline SimdDouble ldexp(SimdDouble value, SimdDInt32 exponent)
-{
- const __m512i exponentBias = _mm512_set1_epi32(1023);
- __m512i iExponent = _mm512_add_epi32(exponent.simdInternal_, exponentBias);
-
- if (opt == MathOptimization::Safe)
- {
- // Make sure biased argument is not negative
- iExponent = _mm512_max_epi32(iExponent, _mm512_setzero_epi32());
- }
-
- iExponent = _mm512_permutevar_epi32(
- _mm512_set_epi32(7, 7, 6, 6, 5, 5, 4, 4, 3, 3, 2, 2, 1, 1, 0, 0), iExponent);
- iExponent = _mm512_mask_slli_epi32(_mm512_setzero_epi32(), _mm512_int2mask(0xAAAA), iExponent, 20);
- return _mm512_mul_pd(_mm512_castsi512_pd(iExponent), value.simdInternal_);
-}
-
-static inline double gmx_simdcall reduce(SimdDouble a)
-{
- return _mm512_reduce_add_pd(a.simdInternal_);
-}
-
-// Picky, picky, picky:
-// icc-16 complains about "Illegal value of immediate argument to intrinsic"
-// unless we use
-// 1) Ordered-quiet for ==
-// 2) Unordered-quiet for !=
-// 3) Ordered-signaling for < and <=
-
-static inline SimdDBool gmx_simdcall operator==(SimdDouble a, SimdDouble b)
-{
- return { _mm512_cmp_pd_mask(a.simdInternal_, b.simdInternal_, _CMP_EQ_OQ) };
-}
-
-static inline SimdDBool gmx_simdcall operator!=(SimdDouble a, SimdDouble b)
-{
- return { _mm512_cmp_pd_mask(a.simdInternal_, b.simdInternal_, _CMP_NEQ_UQ) };
-}
-
-static inline SimdDBool gmx_simdcall operator<(SimdDouble a, SimdDouble b)
-{
- return { _mm512_cmp_pd_mask(a.simdInternal_, b.simdInternal_, _CMP_LT_OS) };
-}
-
-static inline SimdDBool gmx_simdcall operator<=(SimdDouble a, SimdDouble b)
-{
- return { _mm512_cmp_pd_mask(a.simdInternal_, b.simdInternal_, _CMP_LE_OS) };
-}
-
-static inline SimdDBool gmx_simdcall testBits(SimdDouble a)
-{
- // This is a bit problematic since Knight's corner does not have any 64-bit integer comparisons,
- // and we cannot use floating-point since values with just a single bit set can evaluate to 0.0.
- // Instead, we do it as
- // 1) Do a logical or of the high/low 32 bits
- // 2) Do a permute so we have the low 32 bits of each value in the low 8 32-bit elements
- // 3) Do an integer comparison, and cast so we just keep the low 8 bits of the mask.
- //
- // By default we will use integers for the masks in the nonbonded kernels, so this shouldn't
- // have any significant performance drawbacks.
-
- __m512i ia = _mm512_castpd_si512(a.simdInternal_);
-
- ia = _mm512_or_epi32(ia, _mm512_swizzle_epi32(ia, _MM_SWIZ_REG_CDAB));
- ia = _mm512_permutevar_epi32(
- _mm512_set_epi32(15, 13, 11, 9, 7, 5, 3, 1, 14, 12, 10, 8, 6, 4, 2, 0), ia);
-
- return { static_cast<__mmask8>(_mm512_cmp_epi32_mask(ia, _mm512_setzero_si512(), _MM_CMPINT_NE)) };
-}
-
-static inline SimdDBool gmx_simdcall operator&&(SimdDBool a, SimdDBool b)
-{
- return { static_cast<__mmask8>(_mm512_kand(a.simdInternal_, b.simdInternal_)) };
-}
-
-static inline SimdDBool gmx_simdcall operator||(SimdDBool a, SimdDBool b)
-{
- return { static_cast<__mmask8>(_mm512_kor(a.simdInternal_, b.simdInternal_)) };
-}
-
-static inline bool gmx_simdcall anyTrue(SimdDBool a)
-{
- return _mm512_mask2int(a.simdInternal_) != 0;
-}
-
-static inline SimdDouble gmx_simdcall selectByMask(SimdDouble a, SimdDBool m)
-{
- return { _mm512_mask_mov_pd(_mm512_setzero_pd(), m.simdInternal_, a.simdInternal_) };
-}
-
-static inline SimdDouble gmx_simdcall selectByNotMask(SimdDouble a, SimdDBool m)
-{
- return { _mm512_mask_mov_pd(a.simdInternal_, m.simdInternal_, _mm512_setzero_pd()) };
-}
-
-static inline SimdDouble gmx_simdcall blend(SimdDouble a, SimdDouble b, SimdDBool sel)
-{
- return { _mm512_mask_blend_pd(sel.simdInternal_, a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdDInt32 gmx_simdcall operator&(SimdDInt32 a, SimdDInt32 b)
-{
- return { _mm512_and_epi32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdDInt32 gmx_simdcall andNot(SimdDInt32 a, SimdDInt32 b)
-{
- return { _mm512_andnot_epi32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdDInt32 gmx_simdcall operator|(SimdDInt32 a, SimdDInt32 b)
-{
- return { _mm512_or_epi32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdDInt32 gmx_simdcall operator^(SimdDInt32 a, SimdDInt32 b)
-{
- return { _mm512_xor_epi32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdDInt32 gmx_simdcall operator+(SimdDInt32 a, SimdDInt32 b)
-{
- return { _mm512_add_epi32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdDInt32 gmx_simdcall operator-(SimdDInt32 a, SimdDInt32 b)
-{
- return { _mm512_sub_epi32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdDInt32 gmx_simdcall operator*(SimdDInt32 a, SimdDInt32 b)
-{
- return { _mm512_mullo_epi32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdDIBool gmx_simdcall operator==(SimdDInt32 a, SimdDInt32 b)
-{
- return { _mm512_cmp_epi32_mask(a.simdInternal_, b.simdInternal_, _MM_CMPINT_EQ) };
-}
-
-static inline SimdDIBool gmx_simdcall testBits(SimdDInt32 a)
-{
- return { _mm512_cmp_epi32_mask(a.simdInternal_, _mm512_setzero_si512(), _MM_CMPINT_NE) };
-}
-
-static inline SimdDIBool gmx_simdcall operator<(SimdDInt32 a, SimdDInt32 b)
-{
- return { _mm512_cmp_epi32_mask(a.simdInternal_, b.simdInternal_, _MM_CMPINT_LT) };
-}
-
-static inline SimdDIBool gmx_simdcall operator&&(SimdDIBool a, SimdDIBool b)
-{
- return { _mm512_kand(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdDIBool gmx_simdcall operator||(SimdDIBool a, SimdDIBool b)
-{
- return { _mm512_kor(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline bool gmx_simdcall anyTrue(SimdDIBool a)
-{
- return (_mm512_mask2int(a.simdInternal_) & 0xFF) != 0;
-}
-
-static inline SimdDInt32 gmx_simdcall selectByMask(SimdDInt32 a, SimdDIBool m)
-{
- return { _mm512_mask_mov_epi32(_mm512_setzero_epi32(), m.simdInternal_, a.simdInternal_) };
-}
-
-static inline SimdDInt32 gmx_simdcall selectByNotMask(SimdDInt32 a, SimdDIBool m)
-{
- return { _mm512_mask_mov_epi32(a.simdInternal_, m.simdInternal_, _mm512_setzero_epi32()) };
-}
-
-static inline SimdDInt32 gmx_simdcall blend(SimdDInt32 a, SimdDInt32 b, SimdDIBool sel)
-{
- return { _mm512_mask_blend_epi32(sel.simdInternal_, a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdDInt32 gmx_simdcall cvtR2I(SimdDouble a)
-{
- return { _mm512_cvtfxpnt_roundpd_epi32lo(a.simdInternal_, _MM_FROUND_TO_NEAREST_INT) };
-}
-
-static inline SimdDInt32 gmx_simdcall cvttR2I(SimdDouble a)
-{
- return { _mm512_cvtfxpnt_roundpd_epi32lo(a.simdInternal_, _MM_FROUND_TO_ZERO) };
-}
-
-static inline SimdDouble gmx_simdcall cvtI2R(SimdDInt32 a)
-{
- return { _mm512_cvtepi32lo_pd(a.simdInternal_) };
-}
-
-static inline SimdDIBool gmx_simdcall cvtB2IB(SimdDBool a)
-{
- return { a.simdInternal_ };
-}
-
-static inline SimdDBool gmx_simdcall cvtIB2B(SimdDIBool a)
-{
- return { static_cast<__mmask8>(a.simdInternal_) };
-}
-
-static inline void gmx_simdcall cvtF2DD(SimdFloat f, SimdDouble* d0, SimdDouble* d1)
-{
- __m512i i1 = _mm512_permute4f128_epi32(_mm512_castps_si512(f.simdInternal_), _MM_PERM_DCDC);
-
- *d0 = _mm512_cvtpslo_pd(f.simdInternal_);
- *d1 = _mm512_cvtpslo_pd(_mm512_castsi512_ps(i1));
-}
-
-static inline SimdFloat gmx_simdcall cvtDD2F(SimdDouble d0, SimdDouble d1)
-{
- __m512 f0 = _mm512_cvtpd_pslo(d0.simdInternal_);
- __m512 f1 = _mm512_cvtpd_pslo(d1.simdInternal_);
- return { _mm512_mask_permute4f128_ps(f0, _mm512_int2mask(0xFF00), f1, _MM_PERM_BABA) };
-}
-
-} // namespace gmx
-
-#endif // GMX_SIMD_IMPL_X86_MIC_SIMD_DOUBLE_H
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2016,2017,2019,2020, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_SIMD_IMPL_X86_MIC_SIMD_FLOAT_H
-#define GMX_SIMD_IMPL_X86_MIC_SIMD_FLOAT_H
-
-#include "config.h"
-
-#include <cassert>
-#include <cstdint>
-
-#include <immintrin.h>
-
-#include "gromacs/math/utilities.h"
-
-namespace gmx
-{
-
-class SimdFloat
-{
-public:
- SimdFloat() {}
-
- SimdFloat(float f) : simdInternal_(_mm512_set1_ps(f)) {}
-
- // Internal utility constructor to simplify return statements
- SimdFloat(__m512 simd) : simdInternal_(simd) {}
-
- __m512 simdInternal_;
-};
-
-class SimdFInt32
-{
-public:
- SimdFInt32() {}
-
- SimdFInt32(std::int32_t i) : simdInternal_(_mm512_set1_epi32(i)) {}
-
- // Internal utility constructor to simplify return statements
- SimdFInt32(__m512i simd) : simdInternal_(simd) {}
-
- __m512i simdInternal_;
-};
-
-class SimdFBool
-{
-public:
- SimdFBool() {}
-
- SimdFBool(bool b) : simdInternal_(_mm512_int2mask(b ? 0xFFFF : 0)) {}
-
- // Internal utility constructor to simplify return statements
- SimdFBool(__mmask16 simd) : simdInternal_(simd) {}
-
- __mmask16 simdInternal_;
-};
-
-class SimdFIBool
-{
-public:
- SimdFIBool() {}
-
- SimdFIBool(bool b) : simdInternal_(_mm512_int2mask(b ? 0xFFFF : 0)) {}
-
- // Internal utility constructor to simplify return statements
- SimdFIBool(__mmask16 simd) : simdInternal_(simd) {}
-
- __mmask16 simdInternal_;
-};
-
-static inline SimdFloat gmx_simdcall simdLoad(const float* m, SimdFloatTag = {})
-{
- assert(std::size_t(m) % 64 == 0);
- return { _mm512_load_ps(m) };
-}
-
-static inline void gmx_simdcall store(float* m, SimdFloat a)
-{
- assert(std::size_t(m) % 64 == 0);
- _mm512_store_ps(m, a.simdInternal_);
-}
-
-static inline SimdFloat gmx_simdcall simdLoadU(const float* m, SimdFloatTag = {})
-{
- return { _mm512_loadunpackhi_ps(_mm512_loadunpacklo_ps(_mm512_undefined_ps(), m), m + 16) };
-}
-
-static inline void gmx_simdcall storeU(float* m, SimdFloat a)
-{
- _mm512_packstorelo_ps(m, a.simdInternal_);
- _mm512_packstorehi_ps(m + 16, a.simdInternal_);
-}
-
-static inline SimdFloat gmx_simdcall setZeroF()
-{
- return { _mm512_setzero_ps() };
-}
-
-static inline SimdFInt32 gmx_simdcall simdLoad(const std::int32_t* m, SimdFInt32Tag)
-{
- assert(std::size_t(m) % 64 == 0);
- return { _mm512_load_epi32(m) };
-}
-
-static inline void gmx_simdcall store(std::int32_t* m, SimdFInt32 a)
-{
- assert(std::size_t(m) % 64 == 0);
- _mm512_store_epi32(m, a.simdInternal_);
-}
-
-static inline SimdFInt32 gmx_simdcall simdLoadU(const std::int32_t* m, SimdFInt32Tag)
-{
- return { _mm512_loadunpackhi_epi32(_mm512_loadunpacklo_epi32(_mm512_undefined_epi32(), m), m + 16) };
-}
-
-static inline void gmx_simdcall storeU(std::int32_t* m, SimdFInt32 a)
-{
- _mm512_packstorelo_epi32(m, a.simdInternal_);
- _mm512_packstorehi_epi32(m + 16, a.simdInternal_);
-}
-
-static inline SimdFInt32 gmx_simdcall setZeroFI()
-{
- return { _mm512_setzero_si512() };
-}
-
-
-template<int index>
-static inline std::int32_t gmx_simdcall extract(SimdFInt32 a)
-{
- int r;
- _mm512_mask_packstorelo_epi32(&r, _mm512_mask2int(1 << index), a.simdInternal_);
- return r;
-}
-
-static inline SimdFloat gmx_simdcall operator&(SimdFloat a, SimdFloat b)
-{
- return { _mm512_castsi512_ps(_mm512_and_epi32(_mm512_castps_si512(a.simdInternal_),
- _mm512_castps_si512(b.simdInternal_))) };
-}
-
-static inline SimdFloat gmx_simdcall andNot(SimdFloat a, SimdFloat b)
-{
- return { _mm512_castsi512_ps(_mm512_andnot_epi32(_mm512_castps_si512(a.simdInternal_),
- _mm512_castps_si512(b.simdInternal_))) };
-}
-
-static inline SimdFloat gmx_simdcall operator|(SimdFloat a, SimdFloat b)
-{
- return { _mm512_castsi512_ps(_mm512_or_epi32(_mm512_castps_si512(a.simdInternal_),
- _mm512_castps_si512(b.simdInternal_))) };
-}
-
-static inline SimdFloat gmx_simdcall operator^(SimdFloat a, SimdFloat b)
-{
- return { _mm512_castsi512_ps(_mm512_xor_epi32(_mm512_castps_si512(a.simdInternal_),
- _mm512_castps_si512(b.simdInternal_))) };
-}
-
-static inline SimdFloat gmx_simdcall operator+(SimdFloat a, SimdFloat b)
-{
- return { _mm512_add_ps(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall operator-(SimdFloat a, SimdFloat b)
-{
- return { _mm512_sub_ps(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall operator-(SimdFloat x)
-{
- return { _mm512_addn_ps(x.simdInternal_, _mm512_setzero_ps()) };
-}
-
-static inline SimdFloat gmx_simdcall operator*(SimdFloat a, SimdFloat b)
-{
- return { _mm512_mul_ps(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall fma(SimdFloat a, SimdFloat b, SimdFloat c)
-{
- return { _mm512_fmadd_ps(a.simdInternal_, b.simdInternal_, c.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall fms(SimdFloat a, SimdFloat b, SimdFloat c)
-{
- return { _mm512_fmsub_ps(a.simdInternal_, b.simdInternal_, c.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall fnma(SimdFloat a, SimdFloat b, SimdFloat c)
-{
- return { _mm512_fnmadd_ps(a.simdInternal_, b.simdInternal_, c.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall fnms(SimdFloat a, SimdFloat b, SimdFloat c)
-{
- return { _mm512_fnmsub_ps(a.simdInternal_, b.simdInternal_, c.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall rsqrt(SimdFloat x)
-{
- return { _mm512_rsqrt23_ps(x.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall rcp(SimdFloat x)
-{
- return { _mm512_rcp23_ps(x.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall maskAdd(SimdFloat a, SimdFloat b, SimdFBool m)
-{
- return { _mm512_mask_add_ps(a.simdInternal_, m.simdInternal_, a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall maskzMul(SimdFloat a, SimdFloat b, SimdFBool m)
-{
- return { _mm512_mask_mul_ps(_mm512_setzero_ps(), m.simdInternal_, a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall maskzFma(SimdFloat a, SimdFloat b, SimdFloat c, SimdFBool m)
-{
- return { _mm512_mask_mov_ps(_mm512_setzero_ps(), m.simdInternal_,
- _mm512_fmadd_ps(a.simdInternal_, b.simdInternal_, c.simdInternal_)) };
-}
-
-static inline SimdFloat gmx_simdcall maskzRsqrt(SimdFloat x, SimdFBool m)
-{
- return { _mm512_mask_rsqrt23_ps(_mm512_setzero_ps(), m.simdInternal_, x.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall maskzRcp(SimdFloat x, SimdFBool m)
-{
- return { _mm512_mask_rcp23_ps(_mm512_setzero_ps(), m.simdInternal_, x.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall abs(SimdFloat x)
-{
- return { _mm512_castsi512_ps(_mm512_andnot_epi32(_mm512_castps_si512(_mm512_set1_ps(GMX_FLOAT_NEGZERO)),
- _mm512_castps_si512(x.simdInternal_))) };
-}
-
-static inline SimdFloat gmx_simdcall max(SimdFloat a, SimdFloat b)
-{
- return { _mm512_gmax_ps(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall min(SimdFloat a, SimdFloat b)
-{
- return { _mm512_gmin_ps(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall round(SimdFloat x)
-{
- return { _mm512_round_ps(x.simdInternal_, _MM_FROUND_TO_NEAREST_INT, _MM_EXPADJ_NONE) };
-}
-
-static inline SimdFloat gmx_simdcall trunc(SimdFloat x)
-{
- return { _mm512_round_ps(x.simdInternal_, _MM_FROUND_TO_ZERO, _MM_EXPADJ_NONE) };
-}
-
-template<MathOptimization opt = MathOptimization::Safe>
-static inline SimdFloat gmx_simdcall frexp(SimdFloat value, SimdFInt32* exponent)
-{
- __m512 rExponent;
- __m512i iExponent;
- __m512 result;
-
- if (opt == MathOptimization::Safe)
- {
- // For the safe branch, we use the masked operations to only assign results if the
- // input value was nonzero, and otherwise set exponent to 0, and the fraction to the input (+-0).
- __mmask16 valueIsNonZero =
- _mm512_cmp_ps_mask(_mm512_setzero_ps(), value.simdInternal_, _CMP_NEQ_OQ);
- rExponent = _mm512_mask_getexp_ps(_mm512_setzero_ps(), valueIsNonZero, value.simdInternal_);
- iExponent = _mm512_cvtfxpnt_round_adjustps_epi32(rExponent, _MM_FROUND_TO_NEAREST_INT,
- _MM_EXPADJ_NONE);
- iExponent = _mm512_mask_add_epi32(iExponent, valueIsNonZero, iExponent, _mm512_set1_epi32(1));
-
- // Set result to input value when the latter is +-0
- result = _mm512_mask_getmant_ps(value.simdInternal_, valueIsNonZero, value.simdInternal_,
- _MM_MANT_NORM_p5_1, _MM_MANT_SIGN_src);
- }
- else
- {
- rExponent = _mm512_getexp_ps(value.simdInternal_);
- iExponent = _mm512_cvtfxpnt_round_adjustps_epi32(rExponent, _MM_FROUND_TO_NEAREST_INT,
- _MM_EXPADJ_NONE);
- iExponent = _mm512_add_epi32(iExponent, _mm512_set1_epi32(1));
- result = _mm512_getmant_ps(value.simdInternal_, _MM_MANT_NORM_p5_1, _MM_MANT_SIGN_src);
- }
-
- exponent->simdInternal_ = iExponent;
-
- return { result };
-}
-
-template<MathOptimization opt = MathOptimization::Safe>
-static inline SimdFloat gmx_simdcall ldexp(SimdFloat value, SimdFInt32 exponent)
-{
- const __m512i exponentBias = _mm512_set1_epi32(127);
- __m512i iExponent = _mm512_add_epi32(exponent.simdInternal_, exponentBias);
-
- if (opt == MathOptimization::Safe)
- {
- // Make sure biased argument is not negative
- iExponent = _mm512_max_epi32(iExponent, _mm512_setzero_epi32());
- }
-
- iExponent = _mm512_slli_epi32(iExponent, 23);
-
- return { _mm512_mul_ps(value.simdInternal_, _mm512_castsi512_ps(iExponent)) };
-}
-
-static inline float gmx_simdcall reduce(SimdFloat a)
-{
- return _mm512_reduce_add_ps(a.simdInternal_);
-}
-
-// Picky, picky, picky:
-// icc-16 complains about "Illegal value of immediate argument to intrinsic"
-// unless we use
-// 1) Ordered-quiet for ==
-// 2) Unordered-quiet for !=
-// 3) Ordered-signaling for < and <=
-
-static inline SimdFBool gmx_simdcall operator==(SimdFloat a, SimdFloat b)
-{
- return { _mm512_cmp_ps_mask(a.simdInternal_, b.simdInternal_, _CMP_EQ_OQ) };
-}
-
-static inline SimdFBool gmx_simdcall operator!=(SimdFloat a, SimdFloat b)
-{
- return { _mm512_cmp_ps_mask(a.simdInternal_, b.simdInternal_, _CMP_NEQ_UQ) };
-}
-
-static inline SimdFBool gmx_simdcall operator<(SimdFloat a, SimdFloat b)
-{
- return { _mm512_cmp_ps_mask(a.simdInternal_, b.simdInternal_, _CMP_LT_OS) };
-}
-
-static inline SimdFBool gmx_simdcall operator<=(SimdFloat a, SimdFloat b)
-{
- return { _mm512_cmp_ps_mask(a.simdInternal_, b.simdInternal_, _CMP_LE_OS) };
-}
-
-static inline SimdFBool gmx_simdcall testBits(SimdFloat a)
-{
- return { _mm512_test_epi32_mask(_mm512_castps_si512(a.simdInternal_),
- _mm512_castps_si512(a.simdInternal_)) };
-}
-
-static inline SimdFBool gmx_simdcall operator&&(SimdFBool a, SimdFBool b)
-{
- return { _mm512_kand(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFBool gmx_simdcall operator||(SimdFBool a, SimdFBool b)
-{
- return { _mm512_kor(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline bool gmx_simdcall anyTrue(SimdFBool a)
-{
- return _mm512_mask2int(a.simdInternal_) != 0;
-}
-
-static inline SimdFloat gmx_simdcall selectByMask(SimdFloat a, SimdFBool m)
-{
- return { _mm512_mask_mov_ps(_mm512_setzero_ps(), m.simdInternal_, a.simdInternal_) };
-}
-
-static inline SimdFloat gmx_simdcall selectByNotMask(SimdFloat a, SimdFBool m)
-{
- return { _mm512_mask_mov_ps(a.simdInternal_, m.simdInternal_, _mm512_setzero_ps()) };
-}
-
-static inline SimdFloat gmx_simdcall blend(SimdFloat a, SimdFloat b, SimdFBool sel)
-{
- return { _mm512_mask_blend_ps(sel.simdInternal_, a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall operator&(SimdFInt32 a, SimdFInt32 b)
-{
- return { _mm512_and_epi32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall andNot(SimdFInt32 a, SimdFInt32 b)
-{
- return { _mm512_andnot_epi32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall operator|(SimdFInt32 a, SimdFInt32 b)
-{
- return { _mm512_or_epi32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall operator^(SimdFInt32 a, SimdFInt32 b)
-{
- return { _mm512_xor_epi32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall operator+(SimdFInt32 a, SimdFInt32 b)
-{
- return { _mm512_add_epi32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall operator-(SimdFInt32 a, SimdFInt32 b)
-{
- return { _mm512_sub_epi32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall operator*(SimdFInt32 a, SimdFInt32 b)
-{
- return { _mm512_mullo_epi32(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFIBool gmx_simdcall operator==(SimdFInt32 a, SimdFInt32 b)
-{
- return { _mm512_cmp_epi32_mask(a.simdInternal_, b.simdInternal_, _MM_CMPINT_EQ) };
-}
-
-static inline SimdFIBool gmx_simdcall testBits(SimdFInt32 a)
-{
- return { _mm512_test_epi32_mask(a.simdInternal_, a.simdInternal_) };
-}
-
-static inline SimdFIBool gmx_simdcall operator<(SimdFInt32 a, SimdFInt32 b)
-{
- return { _mm512_cmp_epi32_mask(a.simdInternal_, b.simdInternal_, _MM_CMPINT_LT) };
-}
-
-static inline SimdFIBool gmx_simdcall operator&&(SimdFIBool a, SimdFIBool b)
-{
- return { _mm512_kand(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFIBool gmx_simdcall operator||(SimdFIBool a, SimdFIBool b)
-{
- return { _mm512_kor(a.simdInternal_, b.simdInternal_) };
-}
-
-static inline bool gmx_simdcall anyTrue(SimdFIBool a)
-{
- return _mm512_mask2int(a.simdInternal_) != 0;
-}
-
-static inline SimdFInt32 gmx_simdcall selectByMask(SimdFInt32 a, SimdFIBool m)
-{
- return { _mm512_mask_mov_epi32(_mm512_setzero_epi32(), m.simdInternal_, a.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall selectByNotMask(SimdFInt32 a, SimdFIBool m)
-{
- return { _mm512_mask_mov_epi32(a.simdInternal_, m.simdInternal_, _mm512_setzero_epi32()) };
-}
-
-static inline SimdFInt32 gmx_simdcall blend(SimdFInt32 a, SimdFInt32 b, SimdFIBool sel)
-{
- return { _mm512_mask_blend_epi32(sel.simdInternal_, a.simdInternal_, b.simdInternal_) };
-}
-
-static inline SimdFInt32 gmx_simdcall cvtR2I(SimdFloat a)
-{
- return { _mm512_cvtfxpnt_round_adjustps_epi32(a.simdInternal_, _MM_FROUND_TO_NEAREST_INT,
- _MM_EXPADJ_NONE) };
-}
-
-static inline SimdFInt32 gmx_simdcall cvttR2I(SimdFloat a)
-{
- return { _mm512_cvtfxpnt_round_adjustps_epi32(a.simdInternal_, _MM_FROUND_TO_ZERO, _MM_EXPADJ_NONE) };
-}
-
-static inline SimdFloat gmx_simdcall cvtI2R(SimdFInt32 a)
-{
- return { _mm512_cvtfxpnt_round_adjustepi32_ps(a.simdInternal_, _MM_FROUND_TO_NEAREST_INT,
- _MM_EXPADJ_NONE) };
-}
-
-static inline SimdFIBool gmx_simdcall cvtB2IB(SimdFBool a)
-{
- return { a.simdInternal_ };
-}
-
-static inline SimdFBool gmx_simdcall cvtIB2B(SimdFIBool a)
-{
- return { a.simdInternal_ };
-}
-
-
-template<MathOptimization opt = MathOptimization::Safe>
-static inline SimdFloat gmx_simdcall exp2(SimdFloat x)
-{
- return { _mm512_exp223_ps(_mm512_cvtfxpnt_round_adjustps_epi32(
- x.simdInternal_, _MM_ROUND_MODE_NEAREST, _MM_EXPADJ_24)) };
-}
-
-template<MathOptimization opt = MathOptimization::Safe>
-static inline SimdFloat gmx_simdcall exp(SimdFloat x)
-{
- const __m512 argscale = _mm512_set1_ps(1.44269504088896341F);
- const __m512 invargscale = _mm512_set1_ps(-0.69314718055994528623F);
-
- if (opt == MathOptimization::Safe)
- {
- // Set the limit to gurantee flush to zero
- const SimdFloat smallArgLimit(-88.f);
- // Since we multiply the argument by 1.44, for the safe version we need to make
- // sure this doesn't result in overflow
- x = max(x, smallArgLimit);
- }
-
- __m512 xscaled = _mm512_mul_ps(x.simdInternal_, argscale);
- __m512 r = _mm512_exp223_ps(
- _mm512_cvtfxpnt_round_adjustps_epi32(xscaled, _MM_ROUND_MODE_NEAREST, _MM_EXPADJ_24));
-
- // exp2a23_ps provides 23 bits of accuracy, but we ruin some of that with our argument
- // scaling. To correct this, we find the difference between the scaled argument and
- // the true one (extended precision arithmetics does not appear to be necessary to
- // fulfill our accuracy requirements) and then multiply by the exponent of this
- // correction since exp(a+b)=exp(a)*exp(b).
- // Note that this only adds two instructions (and maybe some constant loads).
-
- // find the difference
- x = _mm512_fmadd_ps(invargscale, xscaled, x.simdInternal_);
- // x will now be a _very_ small number, so approximate exp(x)=1+x.
- // We should thus apply the correction as r'=r*(1+x)=r+r*x
- r = _mm512_fmadd_ps(r, x.simdInternal_, r);
- return { r };
-}
-
-static inline SimdFloat gmx_simdcall log(SimdFloat x)
-{
- return { _mm512_mul_ps(_mm512_set1_ps(0.693147180559945286226764F),
- _mm512_log2ae23_ps(x.simdInternal_)) };
-}
-
-} // namespace gmx
-
-#endif // GMX_SIMD_IMPL_X86_MIC_SIMD_FLOAT_H
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_SIMD_IMPL_X86_MIC_UTIL_DOUBLE_H
-#define GMX_SIMD_IMPL_X86_MIC_UTIL_DOUBLE_H
-
-#include "config.h"
-
-#include <cassert>
-#include <cstdint>
-
-#include <immintrin.h>
-
-#include "gromacs/utility/basedefinitions.h"
-
-#include "impl_x86_mic_simd_double.h"
-
-namespace gmx
-{
-
-namespace
-{
-/* This is an internal helper function used by decr3Hsimd(...).
- */
-inline void gmx_simdcall decrHsimd(double* m, SimdDouble a)
-{
- __m512d t;
-
- assert(std::size_t(m) % 32 == 0);
-
- t = _mm512_extload_pd(m, _MM_UPCONV_PD_NONE, _MM_BROADCAST_4X8, _MM_HINT_NONE);
- a.simdInternal_ = _mm512_add_pd(
- a.simdInternal_,
- _mm512_castps_pd(_mm512_permute4f128_ps(_mm512_castpd_ps(a.simdInternal_), _MM_PERM_BADC)));
- t = _mm512_sub_pd(t, a.simdInternal_);
- _mm512_mask_packstorelo_pd(m, _mm512_int2mask(0x0F), t);
-}
-} // namespace
-
-// On MIC it is better to use scatter operations, so we define the load routines
-// that use a SIMD offset variable first.
-
-template<int align>
-static inline void gmx_simdcall gatherLoadBySimdIntTranspose(const double* base,
- SimdDInt32 simdoffset,
- SimdDouble* v0,
- SimdDouble* v1,
- SimdDouble* v2,
- SimdDouble* v3)
-{
- assert((size_t)base % 32 == 0);
- assert(align % 4 == 0);
-
- // All instructions might be latency ~4 on MIC, so we use shifts where we
- // only need a single instruction (since the shift parameter is an immediate),
- // but multiplication otherwise.
- if (align == 4)
- {
- simdoffset.simdInternal_ = _mm512_slli_epi32(simdoffset.simdInternal_, 2);
- }
- else if (align == 8)
- {
- simdoffset.simdInternal_ = _mm512_slli_epi32(simdoffset.simdInternal_, 3);
- }
- else
- {
- simdoffset = simdoffset * SimdDInt32(align);
- }
-
- v0->simdInternal_ = _mm512_i32logather_pd(simdoffset.simdInternal_, base, sizeof(double));
- v1->simdInternal_ = _mm512_i32logather_pd(simdoffset.simdInternal_, base + 1, sizeof(double));
- v2->simdInternal_ = _mm512_i32logather_pd(simdoffset.simdInternal_, base + 2, sizeof(double));
- v3->simdInternal_ = _mm512_i32logather_pd(simdoffset.simdInternal_, base + 3, sizeof(double));
-}
-
-template<int align>
-static inline void gmx_simdcall gatherLoadUBySimdIntTranspose(const double* base,
- SimdDInt32 simdoffset,
- SimdDouble* v0,
- SimdDouble* v1)
-{
- // All instructions might be latency ~4 on MIC, so we use shifts where we
- // only need a single instruction (since the shift parameter is an immediate),
- // but multiplication otherwise.
- if (align == 2)
- {
- simdoffset.simdInternal_ = _mm512_slli_epi32(simdoffset.simdInternal_, 1);
- }
- else if (align == 4)
- {
- simdoffset.simdInternal_ = _mm512_slli_epi32(simdoffset.simdInternal_, 2);
- }
- else if (align == 8)
- {
- simdoffset.simdInternal_ = _mm512_slli_epi32(simdoffset.simdInternal_, 3);
- }
- else
- {
- simdoffset = simdoffset * SimdDInt32(align);
- }
-
- v0->simdInternal_ = _mm512_i32logather_pd(simdoffset.simdInternal_, base, sizeof(double));
- v1->simdInternal_ = _mm512_i32logather_pd(simdoffset.simdInternal_, base + 1, sizeof(double));
-}
-
-template<int align>
-static inline void gmx_simdcall gatherLoadBySimdIntTranspose(const double* base,
- SimdDInt32 simdoffset,
- SimdDouble* v0,
- SimdDouble* v1)
-{
- assert(std::size_t(base) % 16 == 0);
- assert(align % 2 == 0);
- gatherLoadUBySimdIntTranspose<align>(base, simdoffset, v0, v1);
-}
-
-
-template<int align>
-static inline void gmx_simdcall gatherLoadTranspose(const double* base,
- const std::int32_t offset[],
- SimdDouble* v0,
- SimdDouble* v1,
- SimdDouble* v2,
- SimdDouble* v3)
-{
- gatherLoadBySimdIntTranspose<align>(base, simdLoad(offset, SimdDInt32Tag()), v0, v1, v2, v3);
-}
-
-template<int align>
-static inline void gmx_simdcall
- gatherLoadTranspose(const double* base, const std::int32_t offset[], SimdDouble* v0, SimdDouble* v1)
-{
- gatherLoadBySimdIntTranspose<align>(base, simdLoad(offset, SimdDInt32Tag()), v0, v1);
-}
-
-static const int c_simdBestPairAlignmentDouble = 2;
-
-template<int align>
-static inline void gmx_simdcall gatherLoadUTranspose(const double* base,
- const std::int32_t offset[],
- SimdDouble* v0,
- SimdDouble* v1,
- SimdDouble* v2)
-{
- SimdDInt32 simdoffset;
-
- assert(std::size_t(offset) % 32 == 0);
-
- simdoffset = simdLoad(offset, SimdDInt32Tag());
-
- // All instructions might be latency ~4 on MIC, so we use shifts where we
- // only need a single instruction (since the shift parameter is an immediate),
- // but multiplication otherwise.
- if (align == 4)
- {
- simdoffset.simdInternal_ = _mm512_slli_epi32(simdoffset.simdInternal_, 2);
- }
- else if (align == 8)
- {
- simdoffset.simdInternal_ = _mm512_slli_epi32(simdoffset.simdInternal_, 3);
- }
- else
- {
- simdoffset = simdoffset * SimdDInt32(align);
- }
-
- v0->simdInternal_ = _mm512_i32logather_pd(simdoffset.simdInternal_, base, sizeof(double));
- v1->simdInternal_ = _mm512_i32logather_pd(simdoffset.simdInternal_, base + 1, sizeof(double));
- v2->simdInternal_ = _mm512_i32logather_pd(simdoffset.simdInternal_, base + 2, sizeof(double));
-}
-
-template<int align>
-static inline void gmx_simdcall transposeScatterStoreU(double* base,
- const std::int32_t offset[],
- SimdDouble v0,
- SimdDouble v1,
- SimdDouble v2)
-{
- SimdDInt32 simdoffset;
-
- assert(std::size_t(offset) % 32 == 0);
-
- simdoffset = simdLoad(offset, SimdDInt32Tag());
-
- // All instructions might be latency ~4 on MIC, so we use shifts where we
- // only need a single instruction (since the shift parameter is an immediate),
- // but multiplication otherwise.
- if (align == 4)
- {
- simdoffset.simdInternal_ = _mm512_slli_epi32(simdoffset.simdInternal_, 2);
- }
- else if (align == 8)
- {
- simdoffset.simdInternal_ = _mm512_slli_epi32(simdoffset.simdInternal_, 3);
- }
- else
- {
- simdoffset = simdoffset * SimdDInt32(align);
- }
-
- _mm512_i32loscatter_pd(base, simdoffset.simdInternal_, v0.simdInternal_, sizeof(double));
- _mm512_i32loscatter_pd(base + 1, simdoffset.simdInternal_, v1.simdInternal_, sizeof(double));
- _mm512_i32loscatter_pd(base + 2, simdoffset.simdInternal_, v2.simdInternal_, sizeof(double));
-}
-
-template<int align>
-static inline void gmx_simdcall
- transposeScatterIncrU(double* base, const std::int32_t offset[], SimdDouble v0, SimdDouble v1, SimdDouble v2)
-{
- alignas(GMX_SIMD_ALIGNMENT) double rdata0[GMX_SIMD_DOUBLE_WIDTH];
- alignas(GMX_SIMD_ALIGNMENT) double rdata1[GMX_SIMD_DOUBLE_WIDTH];
- alignas(GMX_SIMD_ALIGNMENT) double rdata2[GMX_SIMD_DOUBLE_WIDTH];
-
- store(rdata0, v0);
- store(rdata1, v1);
- store(rdata2, v2);
-
- for (int i = 0; i < GMX_SIMD_DOUBLE_WIDTH; i++)
- {
- base[align * offset[i] + 0] += rdata0[i];
- base[align * offset[i] + 1] += rdata1[i];
- base[align * offset[i] + 2] += rdata2[i];
- }
-}
-
-template<int align>
-static inline void gmx_simdcall
- transposeScatterDecrU(double* base, const std::int32_t offset[], SimdDouble v0, SimdDouble v1, SimdDouble v2)
-{
- alignas(GMX_SIMD_ALIGNMENT) double rdata0[GMX_SIMD_DOUBLE_WIDTH];
- alignas(GMX_SIMD_ALIGNMENT) double rdata1[GMX_SIMD_DOUBLE_WIDTH];
- alignas(GMX_SIMD_ALIGNMENT) double rdata2[GMX_SIMD_DOUBLE_WIDTH];
-
- store(rdata0, v0);
- store(rdata1, v1);
- store(rdata2, v2);
-
- for (int i = 0; i < GMX_SIMD_DOUBLE_WIDTH; i++)
- {
- base[align * offset[i] + 0] -= rdata0[i];
- base[align * offset[i] + 1] -= rdata1[i];
- base[align * offset[i] + 2] -= rdata2[i];
- }
-}
-
-static inline void gmx_simdcall expandScalarsToTriplets(SimdDouble scalar,
- SimdDouble* triplets0,
- SimdDouble* triplets1,
- SimdDouble* triplets2)
-{
- triplets0->simdInternal_ = _mm512_castsi512_pd(
- _mm512_permutevar_epi32(_mm512_set_epi32(5, 4, 5, 4, 3, 2, 3, 2, 3, 2, 1, 0, 1, 0, 1, 0),
- _mm512_castpd_si512(scalar.simdInternal_)));
- triplets1->simdInternal_ = _mm512_castsi512_pd(_mm512_permutevar_epi32(
- _mm512_set_epi32(11, 10, 9, 8, 9, 8, 9, 8, 7, 6, 7, 6, 7, 6, 5, 4),
- _mm512_castpd_si512(scalar.simdInternal_)));
- triplets2->simdInternal_ = _mm512_castsi512_pd(_mm512_permutevar_epi32(
- _mm512_set_epi32(15, 14, 15, 14, 15, 14, 13, 12, 13, 12, 13, 12, 11, 10, 11, 10),
- _mm512_castpd_si512(scalar.simdInternal_)));
-}
-
-
-static inline double gmx_simdcall
- reduceIncr4ReturnSum(double* m, SimdDouble v0, SimdDouble v1, SimdDouble v2, SimdDouble v3)
-{
- double d;
- __m512d t0, t1, t2, t3;
-
- assert(std::size_t(m) % 32 == 0);
-
- t0 = _mm512_swizzle_pd(_mm512_mask_blend_pd(_mm512_int2mask(0x33), v0.simdInternal_, v2.simdInternal_),
- _MM_SWIZ_REG_BADC);
- t2 = _mm512_mask_blend_pd(_mm512_int2mask(0x33), v2.simdInternal_, v0.simdInternal_);
- t1 = _mm512_swizzle_pd(_mm512_mask_blend_pd(_mm512_int2mask(0x33), v1.simdInternal_, v3.simdInternal_),
- _MM_SWIZ_REG_BADC);
- t3 = _mm512_mask_blend_pd(_mm512_int2mask(0x33), v3.simdInternal_, v1.simdInternal_);
- t0 = _mm512_add_pd(t0, t2);
- t1 = _mm512_add_pd(t1, t3);
-
- t2 = _mm512_swizzle_pd(_mm512_mask_blend_pd(_mm512_int2mask(0b01010101), t0, t1), _MM_SWIZ_REG_CDAB);
- t3 = _mm512_mask_blend_pd(_mm512_int2mask(0b01010101), t1, t0);
- t2 = _mm512_add_pd(t2, t3);
-
- t2 = _mm512_add_pd(t2, _mm512_castps_pd(_mm512_permute4f128_ps(_mm512_castpd_ps(t2), _MM_PERM_BADC)));
-
- t0 = _mm512_mask_extload_pd(_mm512_undefined_pd(), _mm512_int2mask(0xF), m, _MM_UPCONV_PD_NONE,
- _MM_BROADCAST_4X8, _MM_HINT_NONE);
- t0 = _mm512_add_pd(t0, t2);
- _mm512_mask_packstorelo_pd(m, _mm512_int2mask(0xF), t0);
-
- t2 = _mm512_add_pd(t2, _mm512_swizzle_pd(t2, _MM_SWIZ_REG_BADC));
- t2 = _mm512_add_pd(t2, _mm512_swizzle_pd(t2, _MM_SWIZ_REG_CDAB));
-
- _mm512_mask_packstorelo_pd(&d, _mm512_mask2int(0x01), t2);
- return d;
-}
-
-static inline SimdDouble gmx_simdcall loadDualHsimd(const double* m0, const double* m1)
-{
- assert(std::size_t(m0) % 32 == 0);
- assert(std::size_t(m1) % 32 == 0);
-
- return _mm512_mask_extload_pd(
- _mm512_extload_pd(m0, _MM_UPCONV_PD_NONE, _MM_BROADCAST_4X8, _MM_HINT_NONE),
- _mm512_int2mask(0xF0), m1, _MM_UPCONV_PD_NONE, _MM_BROADCAST_4X8, _MM_HINT_NONE);
-}
-
-static inline SimdDouble gmx_simdcall loadDuplicateHsimd(const double* m)
-{
- assert(std::size_t(m) % 32 == 0);
-
- return _mm512_extload_pd(m, _MM_UPCONV_PD_NONE, _MM_BROADCAST_4X8, _MM_HINT_NONE);
-}
-
-static inline SimdDouble gmx_simdcall loadU1DualHsimd(const double* m)
-{
- return _mm512_mask_extload_pd(
- _mm512_extload_pd(m, _MM_UPCONV_PD_NONE, _MM_BROADCAST_1X8, _MM_HINT_NONE),
- _mm512_int2mask(0xF0), m + 1, _MM_UPCONV_PD_NONE, _MM_BROADCAST_1X8, _MM_HINT_NONE);
-}
-
-
-static inline void gmx_simdcall storeDualHsimd(double* m0, double* m1, SimdDouble a)
-{
- assert(std::size_t(m0) % 32 == 0);
- assert(std::size_t(m1) % 32 == 0);
-
- _mm512_mask_packstorelo_pd(m0, _mm512_int2mask(0x0F), a.simdInternal_);
- _mm512_mask_packstorelo_pd(m1, _mm512_int2mask(0xF0), a.simdInternal_);
-}
-
-static inline void gmx_simdcall incrDualHsimd(double* m0, double* m1, SimdDouble a)
-{
- assert(std::size_t(m0) % 32 == 0);
- assert(std::size_t(m1) % 32 == 0);
-
- __m512d x;
-
- // Update lower half
- x = _mm512_extload_pd(m0, _MM_UPCONV_PD_NONE, _MM_BROADCAST_4X8, _MM_HINT_NONE);
- x = _mm512_add_pd(x, a.simdInternal_);
- _mm512_mask_packstorelo_pd(m0, _mm512_int2mask(0x0F), x);
-
- // Update upper half
- x = _mm512_extload_pd(m1, _MM_UPCONV_PD_NONE, _MM_BROADCAST_4X8, _MM_HINT_NONE);
- x = _mm512_add_pd(x, a.simdInternal_);
- _mm512_mask_packstorelo_pd(m1, _mm512_int2mask(0xF0), x);
-}
-
-static inline void gmx_simdcall decr3Hsimd(double* m, SimdDouble a0, SimdDouble a1, SimdDouble a2)
-{
- assert(std::size_t(m) % 32 == 0);
- decrHsimd(m, a0);
- decrHsimd(m + GMX_SIMD_DOUBLE_WIDTH / 2, a1);
- decrHsimd(m + GMX_SIMD_DOUBLE_WIDTH, a2);
-}
-
-
-template<int align>
-static inline void gmx_simdcall gatherLoadTransposeHsimd(const double* base0,
- const double* base1,
- const std::int32_t offset[],
- SimdDouble* v0,
- SimdDouble* v1)
-{
- __m512i idx0, idx1, idx;
- __m512d tmp1, tmp2;
-
- assert(std::size_t(offset) % 16 == 0);
- assert(std::size_t(base0) % 16 == 0);
- assert(std::size_t(base1) % 16 == 0);
- assert(std::size_t(align) % 2 == 0);
-
- idx0 = _mm512_extload_epi32(offset, _MM_UPCONV_EPI32_NONE, _MM_BROADCAST_4X16, _MM_HINT_NONE);
-
- idx0 = _mm512_mullo_epi32(idx0, _mm512_set1_epi32(align));
- idx1 = _mm512_add_epi32(idx0, _mm512_set1_epi32(1));
-
- idx = _mm512_mask_permute4f128_epi32(idx0, _mm512_int2mask(0x00F0), idx1, _MM_PERM_AAAA);
-
- tmp1 = _mm512_i32logather_pd(idx, base0, sizeof(double));
- tmp2 = _mm512_i32logather_pd(idx, base1, sizeof(double));
-
- v0->simdInternal_ = _mm512_castps_pd(_mm512_mask_permute4f128_ps(
- _mm512_castpd_ps(tmp1), _mm512_int2mask(0xFF00), _mm512_castpd_ps(tmp2), _MM_PERM_BABA));
- v1->simdInternal_ = _mm512_castps_pd(_mm512_mask_permute4f128_ps(
- _mm512_castpd_ps(tmp2), _mm512_int2mask(0x00FF), _mm512_castpd_ps(tmp1), _MM_PERM_DCDC));
-}
-
-static inline double gmx_simdcall reduceIncr4ReturnSumHsimd(double* m, SimdDouble v0, SimdDouble v1)
-{
- double d;
- __m512d t0, t1;
-
- assert(std::size_t(m) % 32 == 0);
-
- t0 = _mm512_add_pd(v0.simdInternal_, _mm512_swizzle_pd(v0.simdInternal_, _MM_SWIZ_REG_BADC));
- t0 = _mm512_mask_add_pd(t0, _mm512_int2mask(0xCC), v1.simdInternal_,
- _mm512_swizzle_pd(v1.simdInternal_, _MM_SWIZ_REG_BADC));
- t0 = _mm512_add_pd(t0, _mm512_swizzle_pd(t0, _MM_SWIZ_REG_CDAB));
- t0 = _mm512_castps_pd(_mm512_mask_permute4f128_ps(_mm512_castpd_ps(t0), _mm512_int2mask(0xCCCC),
- _mm512_castpd_ps(t0), _MM_PERM_DCDC));
-
- t1 = _mm512_mask_extload_pd(_mm512_undefined_pd(), _mm512_int2mask(0xF), m, _MM_UPCONV_PD_NONE,
- _MM_BROADCAST_4X8, _MM_HINT_NONE);
- t1 = _mm512_add_pd(t1, t0);
- _mm512_mask_packstorelo_pd(m, _mm512_int2mask(0xF), t1);
-
- t0 = _mm512_add_pd(t0, _mm512_swizzle_pd(t0, _MM_SWIZ_REG_BADC));
- t0 = _mm512_add_pd(t0, _mm512_swizzle_pd(t0, _MM_SWIZ_REG_CDAB));
-
- _mm512_mask_packstorelo_pd(&d, _mm512_mask2int(0x03), t0);
- return d;
-}
-
-} // namespace gmx
-
-#endif // GMX_SIMD_IMPL_X86_MIC_UTIL_DOUBLE_H
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_SIMD_IMPL_X86_MIC_UTIL_FLOAT_H
-#define GMX_SIMD_IMPL_X86_MIC_UTIL_FLOAT_H
-
-#include "config.h"
-
-#include <cassert>
-#include <cstdint>
-
-#include <immintrin.h>
-
-#include "gromacs/utility/basedefinitions.h"
-
-#include "impl_x86_mic_simd_float.h"
-
-namespace gmx
-{
-
-namespace
-{
-/* This is an internal helper function used by decr3Hsimd(...).
- */
-inline void gmx_simdcall decrHsimd(float* m, SimdFloat a)
-{
- __m512 t;
-
- assert(std::size_t(m) % 32 == 0);
-
- t = _mm512_castpd_ps(_mm512_extload_pd(reinterpret_cast<const double*>(m), _MM_UPCONV_PD_NONE,
- _MM_BROADCAST_4X8, _MM_HINT_NONE));
- a = _mm512_add_ps(a.simdInternal_, _mm512_permute4f128_ps(a.simdInternal_, _MM_PERM_BADC));
- t = _mm512_sub_ps(t, a.simdInternal_);
- _mm512_mask_packstorelo_ps(m, _mm512_int2mask(0x00FF), t);
-}
-} // namespace
-
-// On MIC it is better to use scatter operations, so we define the load routines
-// that use a SIMD offset variable first.
-
-template<int align>
-static inline void gmx_simdcall gatherLoadBySimdIntTranspose(const float* base,
- SimdFInt32 simdoffset,
- SimdFloat* v0,
- SimdFloat* v1,
- SimdFloat* v2,
- SimdFloat* v3)
-{
- assert(std::size_t(base) % 16 == 0);
- assert(align % 4 == 0);
-
- // All instructions might be latency ~4 on MIC, so we use shifts where we
- // only need a single instruction (since the shift parameter is an immediate),
- // but multiplication otherwise.
- if (align == 4)
- {
- simdoffset.simdInternal_ = _mm512_slli_epi32(simdoffset.simdInternal_, 2);
- }
- else if (align == 8)
- {
- simdoffset.simdInternal_ = _mm512_slli_epi32(simdoffset.simdInternal_, 3);
- }
- else
- {
- simdoffset = simdoffset * SimdFInt32(align);
- }
-
- v0->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base, sizeof(float));
- v1->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base + 1, sizeof(float));
- v2->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base + 2, sizeof(float));
- v3->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base + 3, sizeof(float));
-}
-
-template<int align>
-static inline void gmx_simdcall
- gatherLoadUBySimdIntTranspose(const float* base, SimdFInt32 simdoffset, SimdFloat* v0, SimdFloat* v1)
-{
- // All instructions might be latency ~4 on MIC, so we use shifts where we
- // only need a single instruction (since the shift parameter is an immediate),
- // but multiplication otherwise.
- // For align == 2 we can merge the constant into the scale parameter,
- // which can take constants up to 8 in total.
- if (align == 2)
- {
- v0->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base, align * sizeof(float));
- v1->simdInternal_ =
- _mm512_i32gather_ps(simdoffset.simdInternal_, base + 1, align * sizeof(float));
- }
- else
- {
- if (align == 4)
- {
- simdoffset.simdInternal_ = _mm512_slli_epi32(simdoffset.simdInternal_, 2);
- }
- else if (align == 8)
- {
- simdoffset.simdInternal_ = _mm512_slli_epi32(simdoffset.simdInternal_, 3);
- }
- else
- {
- simdoffset = simdoffset * SimdFInt32(align);
- }
- v0->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base, sizeof(float));
- v1->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base + 1, sizeof(float));
- }
-}
-
-template<int align>
-static inline void gmx_simdcall
- gatherLoadBySimdIntTranspose(const float* base, SimdFInt32 simdoffset, SimdFloat* v0, SimdFloat* v1)
-{
- assert(std::size_t(base) % 8 == 0);
- assert(align % 2 == 0);
- gatherLoadUBySimdIntTranspose<align>(base, simdoffset, v0, v1);
-}
-
-template<int align>
-static inline void gmx_simdcall gatherLoadTranspose(const float* base,
- const std::int32_t offset[],
- SimdFloat* v0,
- SimdFloat* v1,
- SimdFloat* v2,
- SimdFloat* v3)
-{
- gatherLoadBySimdIntTranspose<align>(base, simdLoad(offset, SimdFInt32Tag()), v0, v1, v2, v3);
-}
-
-template<int align>
-static inline void gmx_simdcall
- gatherLoadTranspose(const float* base, const std::int32_t offset[], SimdFloat* v0, SimdFloat* v1)
-{
- gatherLoadBySimdIntTranspose<align>(base, simdLoad(offset, SimdFInt32Tag()), v0, v1);
-}
-
-static const int c_simdBestPairAlignmentFloat = 2;
-
-template<int align>
-static inline void gmx_simdcall gatherLoadUTranspose(const float* base,
- const std::int32_t offset[],
- SimdFloat* v0,
- SimdFloat* v1,
- SimdFloat* v2)
-{
- SimdFInt32 simdoffset;
-
- assert(std::size_t(offset) % 64 == 0);
-
- simdoffset = simdLoad(offset, SimdFInt32Tag());
-
- // All instructions might be latency ~4 on MIC, so we use shifts where we
- // only need a single instruction (since the shift parameter is an immediate),
- // but multiplication otherwise.
- if (align == 4)
- {
- simdoffset.simdInternal_ = _mm512_slli_epi32(simdoffset.simdInternal_, 2);
- }
- else if (align == 8)
- {
- simdoffset.simdInternal_ = _mm512_slli_epi32(simdoffset.simdInternal_, 3);
- }
- else
- {
- simdoffset = simdoffset * SimdFInt32(align);
- }
-
- v0->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base, sizeof(float));
- v1->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base + 1, sizeof(float));
- v2->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base + 2, sizeof(float));
-}
-
-
-template<int align>
-static inline void gmx_simdcall
- transposeScatterStoreU(float* base, const std::int32_t offset[], SimdFloat v0, SimdFloat v1, SimdFloat v2)
-{
- SimdFInt32 simdoffset;
-
- assert(std::size_t(offset) % 64 == 0);
-
- simdoffset = simdLoad(offset, SimdFInt32Tag());
-
- // All instructions might be latency ~4 on MIC, so we use shifts where we
- // only need a single instruction (since the shift parameter is an immediate),
- // but multiplication otherwise.
- if (align == 4)
- {
- simdoffset.simdInternal_ = _mm512_slli_epi32(simdoffset.simdInternal_, 2);
- }
- else if (align == 8)
- {
- simdoffset.simdInternal_ = _mm512_slli_epi32(simdoffset.simdInternal_, 3);
- }
- else
- {
- simdoffset = simdoffset * SimdFInt32(align);
- }
-
- _mm512_i32scatter_ps(base, simdoffset.simdInternal_, v0.simdInternal_, sizeof(float));
- _mm512_i32scatter_ps(base + 1, simdoffset.simdInternal_, v1.simdInternal_, sizeof(float));
- _mm512_i32scatter_ps(base + 2, simdoffset.simdInternal_, v2.simdInternal_, sizeof(float));
-}
-
-
-template<int align>
-static inline void gmx_simdcall
- transposeScatterIncrU(float* base, const std::int32_t offset[], SimdFloat v0, SimdFloat v1, SimdFloat v2)
-{
- alignas(GMX_SIMD_ALIGNMENT) float rdata0[GMX_SIMD_FLOAT_WIDTH];
- alignas(GMX_SIMD_ALIGNMENT) float rdata1[GMX_SIMD_FLOAT_WIDTH];
- alignas(GMX_SIMD_ALIGNMENT) float rdata2[GMX_SIMD_FLOAT_WIDTH];
-
- store(rdata0, v0);
- store(rdata1, v1);
- store(rdata2, v2);
-
- for (int i = 0; i < GMX_SIMD_FLOAT_WIDTH; i++)
- {
- base[align * offset[i] + 0] += rdata0[i];
- base[align * offset[i] + 1] += rdata1[i];
- base[align * offset[i] + 2] += rdata2[i];
- }
-}
-
-template<int align>
-static inline void gmx_simdcall
- transposeScatterDecrU(float* base, const std::int32_t offset[], SimdFloat v0, SimdFloat v1, SimdFloat v2)
-{
- alignas(GMX_SIMD_ALIGNMENT) float rdata0[GMX_SIMD_FLOAT_WIDTH];
- alignas(GMX_SIMD_ALIGNMENT) float rdata1[GMX_SIMD_FLOAT_WIDTH];
- alignas(GMX_SIMD_ALIGNMENT) float rdata2[GMX_SIMD_FLOAT_WIDTH];
-
- store(rdata0, v0);
- store(rdata1, v1);
- store(rdata2, v2);
-
- for (int i = 0; i < GMX_SIMD_FLOAT_WIDTH; i++)
- {
- base[align * offset[i] + 0] -= rdata0[i];
- base[align * offset[i] + 1] -= rdata1[i];
- base[align * offset[i] + 2] -= rdata2[i];
- }
-}
-
-static inline void gmx_simdcall expandScalarsToTriplets(SimdFloat scalar,
- SimdFloat* triplets0,
- SimdFloat* triplets1,
- SimdFloat* triplets2)
-{
- triplets0->simdInternal_ = _mm512_castsi512_ps(
- _mm512_permutevar_epi32(_mm512_set_epi32(5, 4, 4, 4, 3, 3, 3, 2, 2, 2, 1, 1, 1, 0, 0, 0),
- _mm512_castps_si512(scalar.simdInternal_)));
- triplets1->simdInternal_ = _mm512_castsi512_ps(_mm512_permutevar_epi32(
- _mm512_set_epi32(10, 10, 9, 9, 9, 8, 8, 8, 7, 7, 7, 6, 6, 6, 5, 5),
- _mm512_castps_si512(scalar.simdInternal_)));
- triplets2->simdInternal_ = _mm512_castsi512_ps(_mm512_permutevar_epi32(
- _mm512_set_epi32(15, 15, 15, 14, 14, 14, 13, 13, 13, 12, 12, 12, 11, 11, 11, 10),
- _mm512_castps_si512(scalar.simdInternal_)));
-}
-
-
-static inline float gmx_simdcall reduceIncr4ReturnSum(float* m, SimdFloat v0, SimdFloat v1, SimdFloat v2, SimdFloat v3)
-{
- float f;
- __m512 t0, t1, t2, t3;
-
- assert(std::size_t(m) % 16 == 0);
-
- t0 = _mm512_add_ps(v0.simdInternal_, _mm512_swizzle_ps(v0.simdInternal_, _MM_SWIZ_REG_BADC));
- t0 = _mm512_mask_add_ps(t0, _mm512_int2mask(0xCCCC), v2.simdInternal_,
- _mm512_swizzle_ps(v2.simdInternal_, _MM_SWIZ_REG_BADC));
- t1 = _mm512_add_ps(v1.simdInternal_, _mm512_swizzle_ps(v1.simdInternal_, _MM_SWIZ_REG_BADC));
- t1 = _mm512_mask_add_ps(t1, _mm512_int2mask(0xCCCC), v3.simdInternal_,
- _mm512_swizzle_ps(v3.simdInternal_, _MM_SWIZ_REG_BADC));
- t2 = _mm512_add_ps(t0, _mm512_swizzle_ps(t0, _MM_SWIZ_REG_CDAB));
- t2 = _mm512_mask_add_ps(t2, _mm512_int2mask(0xAAAA), t1, _mm512_swizzle_ps(t1, _MM_SWIZ_REG_CDAB));
-
- t2 = _mm512_add_ps(t2, _mm512_permute4f128_ps(t2, _MM_PERM_BADC));
- t2 = _mm512_add_ps(t2, _mm512_permute4f128_ps(t2, _MM_PERM_CDAB));
-
- t0 = _mm512_mask_extload_ps(_mm512_undefined_ps(), _mm512_int2mask(0xF), m, _MM_UPCONV_PS_NONE,
- _MM_BROADCAST_4X16, _MM_HINT_NONE);
- t0 = _mm512_add_ps(t0, t2);
- _mm512_mask_packstorelo_ps(m, _mm512_int2mask(0xF), t0);
-
- t2 = _mm512_add_ps(t2, _mm512_swizzle_ps(t2, _MM_SWIZ_REG_BADC));
- t2 = _mm512_add_ps(t2, _mm512_swizzle_ps(t2, _MM_SWIZ_REG_CDAB));
-
- _mm512_mask_packstorelo_ps(&f, _mm512_mask2int(0x1), t2);
- return f;
-}
-
-static inline SimdFloat gmx_simdcall loadDualHsimd(const float* m0, const float* m1)
-{
- assert(std::size_t(m0) % 32 == 0);
- assert(std::size_t(m1) % 32 == 0);
-
- return _mm512_castpd_ps(_mm512_mask_extload_pd(
- _mm512_extload_pd(reinterpret_cast<const double*>(m0), _MM_UPCONV_PD_NONE,
- _MM_BROADCAST_4X8, _MM_HINT_NONE),
- _mm512_int2mask(0xF0), reinterpret_cast<const double*>(m1), _MM_UPCONV_PD_NONE,
- _MM_BROADCAST_4X8, _MM_HINT_NONE));
-}
-
-static inline SimdFloat gmx_simdcall loadDuplicateHsimd(const float* m)
-{
- assert(std::size_t(m) % 32 == 0);
-
- return _mm512_castpd_ps(_mm512_extload_pd(reinterpret_cast<const double*>(m),
- _MM_UPCONV_PD_NONE, _MM_BROADCAST_4X8, _MM_HINT_NONE));
-}
-
-static inline SimdFloat gmx_simdcall loadU1DualHsimd(const float* m)
-{
- return _mm512_mask_extload_ps(
- _mm512_extload_ps(m, _MM_UPCONV_PS_NONE, _MM_BROADCAST_1X16, _MM_HINT_NONE),
- _mm512_int2mask(0xFF00), m + 1, _MM_UPCONV_PS_NONE, _MM_BROADCAST_1X16, _MM_HINT_NONE);
-}
-
-
-static inline void gmx_simdcall storeDualHsimd(float* m0, float* m1, SimdFloat a)
-{
- __m512 t0;
-
- assert(std::size_t(m0) % 32 == 0);
- assert(std::size_t(m1) % 32 == 0);
-
- _mm512_mask_packstorelo_ps(m0, _mm512_int2mask(0x00FF), a.simdInternal_);
- _mm512_mask_packstorelo_ps(m1, _mm512_int2mask(0xFF00), a.simdInternal_);
-}
-
-static inline void gmx_simdcall incrDualHsimd(float* m0, float* m1, SimdFloat a)
-{
- assert(std::size_t(m0) % 32 == 0);
- assert(std::size_t(m1) % 32 == 0);
-
- __m512 x;
-
- // Update lower half
- x = _mm512_castpd_ps(_mm512_extload_pd(reinterpret_cast<const double*>(m0), _MM_UPCONV_PD_NONE,
- _MM_BROADCAST_4X8, _MM_HINT_NONE));
- x = _mm512_add_ps(x, a.simdInternal_);
- _mm512_mask_packstorelo_ps(m0, _mm512_int2mask(0x00FF), x);
-
- // Update upper half
- x = _mm512_castpd_ps(_mm512_extload_pd(reinterpret_cast<const double*>(m1), _MM_UPCONV_PD_NONE,
- _MM_BROADCAST_4X8, _MM_HINT_NONE));
- x = _mm512_add_ps(x, a.simdInternal_);
- _mm512_mask_packstorelo_ps(m1, _mm512_int2mask(0xFF00), x);
-}
-
-static inline void gmx_simdcall decr3Hsimd(float* m, SimdFloat a0, SimdFloat a1, SimdFloat a2)
-{
- assert(std::size_t(m) % 32 == 0);
- decrHsimd(m, a0);
- decrHsimd(m + GMX_SIMD_FLOAT_WIDTH / 2, a1);
- decrHsimd(m + GMX_SIMD_FLOAT_WIDTH, a2);
-}
-
-
-template<int align>
-static inline void gmx_simdcall gatherLoadTransposeHsimd(const float* base0,
- const float* base1,
- const std::int32_t offset[],
- SimdFloat* v0,
- SimdFloat* v1)
-{
- __m512i idx0, idx1, idx;
- __m512 tmp1, tmp2;
-
- assert(std::size_t(offset) % 32 == 0);
- assert(std::size_t(base0) % 8 == 0);
- assert(std::size_t(base1) % 8 == 0);
- assert(std::size_t(align) % 2 == 0);
-
- idx0 = _mm512_loadunpacklo_epi32(_mm512_undefined_epi32(), offset);
-
- idx0 = _mm512_mullo_epi32(idx0, _mm512_set1_epi32(align));
- idx1 = _mm512_add_epi32(idx0, _mm512_set1_epi32(1));
-
- idx = _mm512_mask_permute4f128_epi32(idx0, _mm512_int2mask(0xFF00), idx1, _MM_PERM_BABA);
-
- tmp1 = _mm512_i32gather_ps(idx, base0, sizeof(float));
- tmp2 = _mm512_i32gather_ps(idx, base1, sizeof(float));
-
- v0->simdInternal_ = _mm512_mask_permute4f128_ps(tmp1, _mm512_int2mask(0xFF00), tmp2, _MM_PERM_BABA);
- v1->simdInternal_ = _mm512_mask_permute4f128_ps(tmp2, _mm512_int2mask(0x00FF), tmp1, _MM_PERM_DCDC);
-}
-
-static inline float gmx_simdcall reduceIncr4ReturnSumHsimd(float* m, SimdFloat v0, SimdFloat v1)
-{
- float f;
- __m512 t0, t1;
-
- assert(std::size_t(m) % 32 == 0);
-
- t0 = _mm512_add_ps(v0.simdInternal_, _mm512_swizzle_ps(v0.simdInternal_, _MM_SWIZ_REG_BADC));
- t0 = _mm512_mask_add_ps(t0, _mm512_int2mask(0xCCCC), v1.simdInternal_,
- _mm512_swizzle_ps(v1.simdInternal_, _MM_SWIZ_REG_BADC));
- t0 = _mm512_add_ps(t0, _mm512_swizzle_ps(t0, _MM_SWIZ_REG_CDAB));
- t0 = _mm512_add_ps(t0, _mm512_castpd_ps(_mm512_swizzle_pd(_mm512_castps_pd(t0), _MM_SWIZ_REG_BADC)));
- t0 = _mm512_mask_permute4f128_ps(t0, _mm512_int2mask(0xAAAA), t0, _MM_PERM_BADC);
- t1 = _mm512_mask_extload_ps(_mm512_undefined_ps(), _mm512_int2mask(0xF), m, _MM_UPCONV_PS_NONE,
- _MM_BROADCAST_4X16, _MM_HINT_NONE);
- t1 = _mm512_add_ps(t1, t0);
- _mm512_mask_packstorelo_ps(m, _mm512_int2mask(0xF), t1);
-
- t0 = _mm512_add_ps(t0, _mm512_swizzle_ps(t0, _MM_SWIZ_REG_BADC));
- t0 = _mm512_add_ps(t0, _mm512_swizzle_ps(t0, _MM_SWIZ_REG_CDAB));
-
- _mm512_mask_packstorelo_ps(&f, _mm512_mask2int(0x1), t0);
- return f;
-}
-
-} // namespace gmx
-
-#endif // GMX_SIMD_IMPL_X86_MIC_UTIL_FLOAT_H
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return m != 0.0F ? (a * b + c) : 0.0F;
}
+/*! \brief Float 1.0/x, masked version.
+ *
+ * \param x Argument, x>0 for entries where mask is true.
+ * \param m Mask
+ * \return 1/x. The result for masked-out entries will be 0.0.
+ *
+ * \note This function might be superficially meaningless, but it helps us to
+ * write templated SIMD/non-SIMD code. For clarity it should not be used
+ * outside such code.
+ */
+static inline float gmx_simdcall maskzRcp(float x, float m)
+{
+ return m != 0.0F ? 1.0F / x : 0.0F;
+}
+
/*! \brief Float Floating-point abs().
*
* \param a any floating point values
return m != 0.0 ? (a * b + c) : 0.0;
}
+/*! \brief Double 1.0/x, masked version.
+ *
+ * \param x Argument, x>0 for entries where mask is true.
+ * \param m Mask
+ * \return Approximation of 1/x. The result for masked-out entries will be 0.0.
+ *
+ * \note This function might be superficially meaningless, but it helps us to
+ * write templated SIMD/non-SIMD code. For clarity it should not be used
+ * outside such code.
+ */
+static inline double gmx_simdcall maskzRcp(double x, double m)
+{
+ return m != 0.0 ? 1.0 / x : 0.0;
+}
+
/*! \brief double doubleing-point abs().
*
* \param a any doubleing point values
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return std::sqrt(x);
}
+/*! \brief Float cbrt(x). This is the cubic root.
+ *
+ * \param x Argument, should be >= 0.
+ * \result The cubic root of x. Undefined if argument is invalid.
+ *
+ * \note This function might be superficially meaningless, but it helps us to
+ * write templated SIMD/non-SIMD code. For clarity it should not be used
+ * outside such code.
+ */
+template<MathOptimization opt = MathOptimization::Safe>
+static inline float cbrt(float x)
+{
+ return std::cbrt(x);
+}
+
/*! \brief Float log(x). This is the natural logarithm.
*
* \param x Argument, should be >0.
return std::sqrt(x);
}
+/*! \brief Double cbrt(x). This is the cubic root.
+ *
+ * \param x Argument, should be >= 0.
+ * \result The cubic root of x. Undefined if argument is invalid.
+ *
+ * \note This function might be superficially meaningless, but it helps us to
+ * write templated SIMD/non-SIMD code. For clarity it should not be used
+ * outside such code.
+ */
+template<MathOptimization opt = MathOptimization::Safe>
+static inline double cbrt(double x)
+{
+ return std::cbrt(x);
+}
+
/*! \brief Double log(x). This is the natural logarithm.
*
* \param x Argument, should be >0.
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdint>
#include <array>
+#include <memory>
#include <type_traits>
#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/real.h"
//! \cond libapi
# include "impl_x86_avx2_256/impl_x86_avx2_256.h"
#elif GMX_SIMD_X86_AVX2_128
# include "impl_x86_avx2_128/impl_x86_avx2_128.h"
-#elif GMX_SIMD_X86_MIC
-# include "impl_x86_mic/impl_x86_mic.h"
#elif GMX_SIMD_X86_AVX_512
# include "impl_x86_avx_512/impl_x86_avx_512.h"
#elif GMX_SIMD_X86_AVX_512_KNL
# include "impl_x86_avx_512_knl/impl_x86_avx_512_knl.h"
-#elif GMX_SIMD_ARM_NEON
-# include "impl_arm_neon/impl_arm_neon.h"
#elif GMX_SIMD_ARM_NEON_ASIMD
# include "impl_arm_neon_asimd/impl_arm_neon_asimd.h"
#elif GMX_SIMD_ARM_SVE
# include "impl_arm_sve/impl_arm_sve.h"
-#elif GMX_SIMD_IBM_VMX
-# include "impl_ibm_vmx/impl_ibm_vmx.h"
#elif GMX_SIMD_IBM_VSX
# include "impl_ibm_vsx/impl_ibm_vsx.h"
#elif (GMX_SIMD_REFERENCE || defined DOXYGEN)
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <limits>
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/simd/simd.h"
#include "gromacs/utility/basedefinitions.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
private:
- pointer const m_; //!< The pointer used to load memory
+ pointer m_; //!< The pointer used to load memory
};
template<typename T>
template<typename U>
friend class SimdArrayRef;
- pointer const begin_;
- pointer const end_;
+ pointer begin_;
+ pointer end_;
};
} // namespace internal
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const std::string& simdString(SimdType s)
{
- static const std::map<SimdType, std::string> name = {
- { SimdType::None, "None" },
- { SimdType::Reference, "Reference" },
- { SimdType::Generic, "Generic" },
- { SimdType::X86_Sse2, "SSE2" },
- { SimdType::X86_Sse4_1, "SSE4.1" },
- { SimdType::X86_Avx128Fma, "AVX_128_FMA" },
- { SimdType::X86_Avx, "AVX_256" },
- { SimdType::X86_Avx2, "AVX2_256" },
- { SimdType::X86_Avx2_128, "AVX2_128" },
- { SimdType::X86_Avx512, "AVX_512" },
- { SimdType::X86_Avx512Knl, "AVX_512_KNL" },
- { SimdType::X86_Mic, "X86_MIC" },
- { SimdType::Arm_Neon, "ARM_NEON" },
- { SimdType::Arm_NeonAsimd, "ARM_NEON_ASIMD" },
- { SimdType::Arm_Sve, "ARM_SVE" },
- { SimdType::Ibm_Vmx, "IBM_VMX" },
- { SimdType::Ibm_Vsx, "IBM_VSX" },
- { SimdType::Fujitsu_HpcAce, "Fujitsu HPC-ACE" }
- };
+ static const std::map<SimdType, std::string> name = { { SimdType::None, "None" },
+ { SimdType::Reference, "Reference" },
+ { SimdType::Generic, "Generic" },
+ { SimdType::X86_Sse2, "SSE2" },
+ { SimdType::X86_Sse4_1, "SSE4.1" },
+ { SimdType::X86_Avx128Fma, "AVX_128_FMA" },
+ { SimdType::X86_Avx, "AVX_256" },
+ { SimdType::X86_Avx2, "AVX2_256" },
+ { SimdType::X86_Avx2_128, "AVX2_128" },
+ { SimdType::X86_Avx512, "AVX_512" },
+ { SimdType::X86_Avx512Knl, "AVX_512_KNL" },
+ { SimdType::Arm_NeonAsimd,
+ "ARM_NEON_ASIMD" },
+ { SimdType::Arm_Sve, "ARM_SVE" },
+ { SimdType::Ibm_Vsx, "IBM_VSX" } };
return name.at(s);
}
-namespace
-{
-
-
-//! Helper to detect correct AMD Zen architecture.
-bool cpuIsAmdZen1(const CpuInfo& cpuInfo)
-{
- // Both Zen/Zen+/Zen2 have family==23
- // Model numbers for Zen:
- // 1) Naples, Whitehaven, Summit ridge, and Snowy Owl
- // 17) Raven ridge
- // Model numbers for Zen+:
- // 8) Pinnacle Ridge
- // 24) Picasso
- return (cpuInfo.vendor() == gmx::CpuInfo::Vendor::Amd && cpuInfo.family() == 23
- && (cpuInfo.model() == 1 || cpuInfo.model() == 17 || cpuInfo.model() == 8
- || cpuInfo.model() == 24));
-}
-
-} // namespace
-
-
SimdType simdSuggested(const CpuInfo& c)
{
SimdType suggested = SimdType::None;
}
else if (c.feature(CpuInfo::Feature::Arm_Neon))
{
- suggested = SimdType::Arm_Neon;
+ suggested = SimdType::None;
}
break;
case CpuInfo::Vendor::Ibm:
}
else if (c.feature(CpuInfo::Feature::Ibm_Vmx))
{
- suggested = SimdType::Ibm_Vmx;
+ suggested = SimdType::None;
}
break;
case CpuInfo::Vendor::Fujitsu:
if (c.feature(CpuInfo::Feature::Fujitsu_HpcAce))
{
- suggested = SimdType::Fujitsu_HpcAce;
+ suggested = SimdType::None;
}
break;
default: break;
return SimdType::X86_Avx512Knl;
#elif GMX_SIMD_X86_AVX_512
return SimdType::X86_Avx512;
-#elif GMX_SIMD_X86_MIC
- return SimdType::X86_Mic;
#elif GMX_SIMD_X86_AVX2_256
return SimdType::X86_Avx2;
#elif GMX_SIMD_X86_AVX2_128
return SimdType::X86_Sse4_1;
#elif GMX_SIMD_X86_SSE2
return SimdType::X86_Sse2;
-#elif GMX_SIMD_ARM_NEON
- return SimdType::Arm_Neon;
#elif GMX_SIMD_ARM_NEON_ASIMD
return SimdType::Arm_NeonAsimd;
#elif GMX_SIMD_ARM_SVE
return SimdType::Arm_Sve;
-#elif GMX_SIMD_IBM_VMX
- return SimdType::Ibm_Vmx;
#elif GMX_SIMD_IBM_VSX
return SimdType::Ibm_Vsx;
-#elif GMX_SIMD_SPARC64_HPC_ACE
- return SimdType::Fujitsu_HpcAce;
#elif GMX_SIMD_REFERENCE
return SimdType::Reference;
#else
"which could influence performance. This build might have been configured on "
"a login node with only a single AVX-512 FMA unit (in which case AVX2 is faster), "
"while the node you are running on has dual AVX-512 FMA units.",
- simdString(wanted).c_str(), simdString(compiled).c_str()));
+ simdString(wanted).c_str(),
+ simdString(compiled).c_str()));
warnMsg = wrapper.wrapToString(formatString(
"Compiled SIMD: %s, but for this host/run %s might be better (see log).",
- simdString(compiled).c_str(), simdString(wanted).c_str()));
+ simdString(compiled).c_str(),
+ simdString(wanted).c_str()));
}
else if (compiled == SimdType::X86_Avx512 && wanted == SimdType::X86_Avx2
&& identifyAvx512FmaUnits() == 1)
"which could influence performance."
"This host supports AVX-512, but since it only has 1 AVX-512"
"FMA unit, it would be faster to use AVX2 instead.",
- simdString(wanted).c_str(), simdString(compiled).c_str()));
+ simdString(wanted).c_str(),
+ simdString(compiled).c_str()));
warnMsg = wrapper.wrapToString(formatString(
"Compiled SIMD: %s, but for this host/run %s might be better (see log).",
- simdString(compiled).c_str(), simdString(wanted).c_str()));
+ simdString(compiled).c_str(),
+ simdString(wanted).c_str()));
}
else if (compiled == SimdType::X86_Avx2 && wanted == SimdType::X86_Avx2_128)
{
formatString("Highest SIMD level requested by all nodes in run: %s\n"
"SIMD instructions selected at compile time: %s\n"
"Compiled SIMD newer than requested; program might crash.",
- simdString(wanted).c_str(), simdString(compiled).c_str()));
+ simdString(wanted).c_str(),
+ simdString(compiled).c_str()));
warnMsg = logMsg;
}
else if (wanted != compiled)
"SIMD instructions selected at compile time: %s\n"
"This program was compiled for different hardware than you are running on, "
"which could influence performance.",
- simdString(wanted).c_str(), simdString(compiled).c_str()));
+ simdString(wanted).c_str(),
+ simdString(compiled).c_str()));
warnMsg = wrapper.wrapToString(formatString(
"Compiled SIMD: %s, but for this host/run %s might be better (see log).",
- simdString(compiled).c_str(), simdString(wanted).c_str()));
+ simdString(compiled).c_str(),
+ simdString(wanted).c_str()));
#if GMX_SIMD_ARM_SVE
}
else if ((compiled == SimdType::Arm_Sve) && (svcntb() != GMX_SIMD_ARM_SVE_LENGTH_VALUE / 8))
"This program was compiled for different hardware than you are running on, "
"which will lead to incorrect behavior.\n"
"Aborting",
- GMX_SIMD_ARM_SVE_LENGTH_VALUE, svcntb() * 8));
+ GMX_SIMD_ARM_SVE_LENGTH_VALUE,
+ svcntb() * 8));
warnMsg = wrapper.wrapToString(formatString(
"Compiled SVE Length: %d, but for this process requires %ld (see log).",
- GMX_SIMD_ARM_SVE_LENGTH_VALUE, svcntb() * 8));
+ GMX_SIMD_ARM_SVE_LENGTH_VALUE,
+ svcntb() * 8));
#endif
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team.
+ * Copyright (c) 2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
X86_Avx2_128, //!< 128-bit AVX2, better than 256-bit for AMD Ryzen
X86_Avx512, //!< AVX_512
X86_Avx512Knl, //!< AVX_512_KNL
- X86_Mic, //!< Knight's corner
- Arm_Neon, //!< 32-bit ARM NEON
Arm_NeonAsimd, //!< 64-bit ARM AArch64 Advanced SIMD
Arm_Sve, //!< ARM Scalable Vector Extensions
- Ibm_Vmx, //!< IBM VMX SIMD (Altivec on Power6 and later)
- Ibm_Vsx, //!< IBM VSX SIMD (Power7 and later)
- Fujitsu_HpcAce //!< Fujitsu K-computer
+ Ibm_Vsx //!< IBM VSX SIMD (Power7 and later)
};
/*! \libinternal \brief Return a string with the name of a SIMD type
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
::testing::AssertionResult SimdBaseTest::compareVectorRealUlp(const char* refExpr,
const char* tstExpr,
const std::vector<real>& ref,
- const std::vector<real>& tst)
+ const std::vector<real>& tst) const
{
std::vector<real> absDiff(tst.size());
std::vector<std::int64_t> ulpDiff(tst.size());
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
::testing::AssertionResult compareVectorRealUlp(const char* refExpr,
const char* tstExpr,
const std::vector<real>& ref,
- const std::vector<real>& tst);
+ const std::vector<real>& tst) const;
/*! \brief Compare std::vectors for exact equality.
*
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <gtest/gtest.h>
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/simd/simd.h"
#include "gromacs/utility/basedefinitions.h"
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cmath>
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/simd/simd.h"
#include "gromacs/utility/basedefinitions.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/simd/simd.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
Simd4Real simdX = rSimd4_c0c1c2;
Simd4Real simdY = rSimd4_c3c4c5;
Simd4Real simdZ = rSimd4_c6c7c8;
- Simd4Real simdR2 = setSimd4RealFrom3R(c0 * c0 + c3 * c3 + c6 * c6, c1 * c1 + c4 * c4 + c7 * c7,
- c2 * c2 + c5 * c5 + c8 * c8);
+ Simd4Real simdR2 = setSimd4RealFrom3R(
+ c0 * c0 + c3 * c3 + c6 * c6, c1 * c1 + c4 * c4 + c7 * c7, c2 * c2 + c5 * c5 + c8 * c8);
setUlpTol(2);
GMX_EXPECT_SIMD4_REAL_NEAR(simdR2, norm2(simdX, simdY, simdZ));
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <array>
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/simd/simd.h"
#include "gromacs/utility/basedefinitions.h"
fraction = frexp(rSimd_Exp, &exponent);
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(0.609548660288905419513128, 0.5833690139241746175358116,
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(0.609548660288905419513128,
+ 0.5833690139241746175358116,
-0.584452007502232362412542),
fraction);
GMX_EXPECT_SIMD_INT_EQ(setSimdIntFrom3I(61, -40, 55), exponent);
// Test the unsafe flavor too, in case they use different branches
fraction = frexp<MathOptimization::Unsafe>(rSimd_Exp, &exponent);
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(0.609548660288905419513128, 0.5833690139241746175358116,
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(0.609548660288905419513128,
+ 0.5833690139241746175358116,
-0.584452007502232362412542),
fraction);
GMX_EXPECT_SIMD_INT_EQ(setSimdIntFrom3I(61, -40, 55), exponent);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
mem0_[j] = refmem[j] = (1000.0 + j) * (1.0 + 100 * GMX_REAL_EPS);
}
-# ifdef __INTEL_COMPILER // Bug in (at least) 19u1 and 18u5 (03424712)
-# pragma novector
-# endif
for (std::size_t j = 0; j < GMX_SIMD_REAL_WIDTH; j++)
{
// Subtract values from _reference_ memory (we will then test with mem0_, and compare)
real data[GMX_SIMD_REAL_WIDTH / 4];
std::iota(data, data + GMX_SIMD_REAL_WIDTH / 4, 1);
-# if defined __ICC && __ICC == 1800 || defined __ICL && __ICL == 1800
-# pragma novector /* Work-around for incorrect vectorization for AVX_512(_KNL) */
-# endif
for (i = 0; i < GMX_SIMD_REAL_WIDTH / 4; i++)
{
val0_[i * 4] = val0_[i * 4 + 1] = val0_[i * 4 + 2] = val0_[i * 4 + 3] = data[i];
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <utility>
#include <vector>
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/simd/simd.h"
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp2, exp2, settings);
// Subnormal range, require matching, but DTZ is fine
- settings = { Range(lowestRealThatProducesDenormal, lowestRealThatProducesNormal), ulpTol_,
- absTol_, MatchRule::Dtz };
+ settings = { Range(lowestRealThatProducesDenormal, lowestRealThatProducesNormal),
+ ulpTol_,
+ absTol_,
+ MatchRule::Dtz };
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp2, exp2, settings);
// Normal range, standard result expected
- settings = { Range(lowestRealThatProducesNormal, highestRealThatProducesNormal), ulpTol_,
- absTol_, MatchRule::Normal };
+ settings = { Range(lowestRealThatProducesNormal, highestRealThatProducesNormal),
+ ulpTol_,
+ absTol_,
+ MatchRule::Normal };
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp2, exp2, settings);
}
- 1; // adding the significant corresponds to one more unit in exponent
CompareSettings settings{ Range(lowestRealThatProducesNormal, highestRealThatProducesNormal),
- ulpTol_, absTol_, MatchRule::Normal };
+ ulpTol_,
+ absTol_,
+ MatchRule::Normal };
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp2, exp2<MathOptimization::Unsafe>, settings);
}
const real lowestReal = -std::numeric_limits<real>::max();
// In theory the smallest value should be (min_exponent-1)*log(2), but rounding after the multiplication will cause this
// value to be a single ulp too low. This might cause failed tests on CPUs that use different DTZ modes for SIMD vs.
- // non-SIMD arithmetics (ARM v7), so multiply by (1.0-eps) to increase it by a single ulp.
+ // non-SIMD arithmetics (e.g. ARM v7), so multiply by (1.0-eps) to increase it by a single ulp.
const real lowestRealThatProducesNormal = (std::numeric_limits<real>::min_exponent - 1)
* std::log(2.0)
* (1 - std::numeric_limits<real>::epsilon());
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp, exp, settings);
// Subnormal range, require matching, but DTZ is fine
- settings = { Range(lowestRealThatProducesDenormal, lowestRealThatProducesNormal), ulpTol_,
- absTol_, MatchRule::Dtz };
+ settings = { Range(lowestRealThatProducesDenormal, lowestRealThatProducesNormal),
+ ulpTol_,
+ absTol_,
+ MatchRule::Dtz };
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp, exp, settings);
// Normal range, standard result expected
- settings = { Range(lowestRealThatProducesNormal, highestRealThatProducesNormal), ulpTol_,
- absTol_, MatchRule::Normal };
+ settings = { Range(lowestRealThatProducesNormal, highestRealThatProducesNormal),
+ ulpTol_,
+ absTol_,
+ MatchRule::Normal };
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp, exp, settings);
}
(std::numeric_limits<real>::max_exponent - 1) * std::log(2.0);
CompareSettings settings{ Range(lowestRealThatProducesNormal, highestRealThatProducesNormal),
- ulpTol_, absTol_, MatchRule::Normal };
+ ulpTol_,
+ absTol_,
+ MatchRule::Normal };
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp, exp<MathOptimization::Unsafe>, settings);
}
TEST_F(SimdMathTest, erfc)
{
// Our erfc algorithm has 4 ulp accuracy, so relax tolerance a bit to 4*ulpTol
- CompareSettings settings{ Range(-9, 9), 4 * ulpTol_, std::numeric_limits<real>::min(),
- MatchRule::Normal };
+ CompareSettings settings{ Range(-9, 9), 4 * ulpTol_, std::numeric_limits<real>::min(), MatchRule::Normal };
GMX_EXPECT_SIMD_FUNC_NEAR(refErfc, erfc, settings);
}
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp2, exp2SingleAccuracy, settings);
// Subnormal range, require matching, but DTZ is fine
- settings = { Range(lowestRealThatProducesDenormal, lowestRealThatProducesNormal), ulpTol_,
- absTol_, MatchRule::Dtz };
+ settings = { Range(lowestRealThatProducesDenormal, lowestRealThatProducesNormal),
+ ulpTol_,
+ absTol_,
+ MatchRule::Dtz };
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp2, exp2SingleAccuracy, settings);
// Normal range, standard result expected
- settings = { Range(lowestRealThatProducesNormal, highestRealThatProducesNormal), ulpTol_,
- absTol_, MatchRule::Normal };
+ settings = { Range(lowestRealThatProducesNormal, highestRealThatProducesNormal),
+ ulpTol_,
+ absTol_,
+ MatchRule::Normal };
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp2, exp2SingleAccuracy, settings);
}
setUlpTolSingleAccuracy(ulpTol_);
CompareSettings settings{ Range(lowestRealThatProducesNormal, highestRealThatProducesNormal),
- ulpTol_, absTol_, MatchRule::Normal };
+ ulpTol_,
+ absTol_,
+ MatchRule::Normal };
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp2, exp2SingleAccuracy<MathOptimization::Unsafe>, settings);
}
const real lowestReal = -std::numeric_limits<real>::max();
// In theory the smallest value should be (min_exponent-1)*log(2), but rounding after the multiplication will cause this
// value to be a single ulp too low. This might cause failed tests on CPUs that use different DTZ modes for SIMD vs.
- // non-SIMD arithmetics (ARM v7), so multiply by (1.0-eps) to increase it by a single ulp.
+ // non-SIMD arithmetics (e.g. ARM v7), so multiply by (1.0-eps) to increase it by a single ulp.
const real lowestRealThatProducesNormal = (std::numeric_limits<real>::min_exponent - 1)
* std::log(2.0)
* (1.0 - std::numeric_limits<real>::epsilon());
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp, expSingleAccuracy, settings);
// Subnormal range, require matching, but DTZ is fine
- settings = { Range(lowestRealThatProducesDenormal, lowestRealThatProducesNormal), ulpTol_,
- absTol_, MatchRule::Dtz };
+ settings = { Range(lowestRealThatProducesDenormal, lowestRealThatProducesNormal),
+ ulpTol_,
+ absTol_,
+ MatchRule::Dtz };
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp, expSingleAccuracy, settings);
// Normal range, standard result expected
- settings = { Range(lowestRealThatProducesNormal, highestRealThatProducesNormal), ulpTol_,
- absTol_, MatchRule::Normal };
+ settings = { Range(lowestRealThatProducesNormal, highestRealThatProducesNormal),
+ ulpTol_,
+ absTol_,
+ MatchRule::Normal };
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp, expSingleAccuracy, settings);
}
setUlpTolSingleAccuracy(ulpTol_);
CompareSettings settings{ Range(lowestRealThatProducesNormal, highestRealThatProducesNormal),
- ulpTol_, absTol_, MatchRule::Normal };
+ ulpTol_,
+ absTol_,
+ MatchRule::Normal };
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp, expSingleAccuracy<MathOptimization::Unsafe>, settings);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
SimdReal bX = rSimd_c3c0c4;
SimdReal bY = rSimd_c4c6c8;
SimdReal bZ = rSimd_c7c2c3;
- SimdReal iprodRef = setSimdRealFrom3R(c0 * c3 + c3 * c4 + c6 * c7, c1 * c0 + c4 * c6 + c7 * c2,
- c2 * c4 + c5 * c8 + c8 * c3);
+ SimdReal iprodRef = setSimdRealFrom3R(
+ c0 * c3 + c3 * c4 + c6 * c7, c1 * c0 + c4 * c6 + c7 * c2, c2 * c4 + c5 * c8 + c8 * c3);
setUlpTol(2);
GMX_EXPECT_SIMD_REAL_NEAR(iprodRef, iprod(aX, aY, aZ, bX, bY, bZ));
SimdReal simdX = rSimd_c0c1c2;
SimdReal simdY = rSimd_c3c4c5;
SimdReal simdZ = rSimd_c6c7c8;
- SimdReal norm2Ref = setSimdRealFrom3R(c0 * c0 + c3 * c3 + c6 * c6, c1 * c1 + c4 * c4 + c7 * c7,
- c2 * c2 + c5 * c5 + c8 * c8);
+ SimdReal norm2Ref = setSimdRealFrom3R(
+ c0 * c0 + c3 * c3 + c6 * c6, c1 * c1 + c4 * c4 + c7 * c7, c2 * c2 + c5 * c5 + c8 * c8);
setUlpTol(2);
GMX_EXPECT_SIMD_REAL_NEAR(norm2Ref, norm2(simdX, simdY, simdZ));
// The SIMD version might use FMA. If we don't force FMA for the reference value, the compiler is free to use FMA
// for either product. If the compiler uses FMA for one product and the SIMD version uses FMA for the other, the
// rounding error of each product adds up and the total possible ulp-error is 12.
- SimdReal refcX = setSimdRealFrom3R(std::fma(-c6, c4, c3 * c7), std::fma(-c7, c6, c4 * c2),
- std::fma(-c8, c8, c5 * c3));
- SimdReal refcY = setSimdRealFrom3R(std::fma(-c0, c7, c6 * c3), std::fma(-c1, c2, c7 * c0),
- std::fma(-c2, c3, c8 * c4));
- SimdReal refcZ = setSimdRealFrom3R(std::fma(-c3, c3, c0 * c4), std::fma(-c4, c0, c1 * c6),
- std::fma(-c5, c4, c2 * c8));
+ SimdReal refcX = setSimdRealFrom3R(
+ std::fma(-c6, c4, c3 * c7), std::fma(-c7, c6, c4 * c2), std::fma(-c8, c8, c5 * c3));
+ SimdReal refcY = setSimdRealFrom3R(
+ std::fma(-c0, c7, c6 * c3), std::fma(-c1, c2, c7 * c0), std::fma(-c2, c3, c8 * c4));
+ SimdReal refcZ = setSimdRealFrom3R(
+ std::fma(-c3, c3, c0 * c4), std::fma(-c4, c0, c1 * c6), std::fma(-c5, c4, c2 * c8));
SimdReal cX, cY, cZ;
// The test assumes that cprod uses FMA on architectures which have FMA so that the compiler
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(statistics INTERFACE)
file(GLOB STATISTICS_SOURCES *.cpp)
-
set(LIBGROMACS_SOURCES
${LIBGROMACS_SOURCES} ${STATISTICS_SOURCES} PARENT_SCOPE)
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(statistics PUBLIC
+target_include_directories(statistics INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(statistics PUBLIC
+target_link_libraries(statistics INTERFACE
+ legacy_api
+ )
+
+# TODO: when statistics is an OBJECT target
+#target_link_libraries(statistics PUBLIC legacy_api)
+#target_link_libraries(statistics PRIVATE common)
+
+# Module dependencies
+# statistics interfaces convey transitive dependence on these modules.
+#target_link_libraries(statistics PUBLIC
+target_link_libraries(statistics INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(statistics PRIVATE NOTHING)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(statistics PRIVATE legacy_modules)
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2012,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "statistics.h"
#include <cmath>
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
-static int gmx_dnint(double x)
-{
- return gmx::roundToInt(x);
-}
typedef struct gmx_stats
{
return static_cast<gmx_stats_t>(stats);
}
-int gmx_stats_get_npoints(gmx_stats_t gstats, int* N)
-{
- gmx_stats* stats = static_cast<gmx_stats*>(gstats);
-
- *N = stats->np;
-
- return estatsOK;
-}
-
void gmx_stats_free(gmx_stats_t gstats)
{
gmx_stats* stats = static_cast<gmx_stats*>(gstats);
sfree(stats);
}
-int gmx_stats_add_point(gmx_stats_t gstats, double x, double y, double dx, double dy)
+StatisticsStatus gmx_stats_add_point(gmx_stats_t gstats, double x, double y, double dx, double dy)
{
gmx_stats* stats = gstats;
stats->np++;
stats->computed = 0;
- return estatsOK;
+ return StatisticsStatus::Ok;
}
-int gmx_stats_get_point(gmx_stats_t gstats, real* x, real* y, real* dx, real* dy, real level)
-{
- gmx_stats* stats = gstats;
- int ok, outlier;
- real rmsd, r;
-
- if ((ok = gmx_stats_get_rmsd(gstats, &rmsd)) != estatsOK)
- {
- return ok;
- }
- outlier = 0;
- while ((outlier == 0) && (stats->np_c < stats->np))
- {
- r = std::abs(stats->x[stats->np_c] - stats->y[stats->np_c]);
- outlier = static_cast<int>(r > rmsd * level);
- if (outlier)
- {
- if (nullptr != x)
- {
- *x = stats->x[stats->np_c];
- }
- if (nullptr != y)
- {
- *y = stats->y[stats->np_c];
- }
- if (nullptr != dx)
- {
- *dx = stats->dx[stats->np_c];
- }
- if (nullptr != dy)
- {
- *dy = stats->dy[stats->np_c];
- }
- }
- stats->np_c++;
-
- if (outlier)
- {
- return estatsOK;
- }
- }
-
- stats->np_c = 0;
-
- return estatsNO_POINTS;
-}
-
-int gmx_stats_add_points(gmx_stats_t gstats, int n, real* x, real* y, real* dx, real* dy)
-{
- for (int i = 0; (i < n); i++)
- {
- int ok;
- if ((ok = gmx_stats_add_point(gstats, x[i], y[i], (nullptr != dx) ? dx[i] : 0,
- (nullptr != dy) ? dy[i] : 0))
- != estatsOK)
- {
- return ok;
- }
- }
- return estatsOK;
-}
-
-static int gmx_stats_compute(gmx_stats* stats, int weight)
+static StatisticsStatus gmx_stats_compute(gmx_stats* stats, int weight)
{
double yy, yx, xx, sx, sy, dy, chi2, chi2aa, d2;
double ssxx, ssyy, ssxy;
{
if (N < 1)
{
- return estatsNO_POINTS;
+ return StatisticsStatus::NoPoints;
}
xx = xx_nw = 0;
stats->computed = 1;
}
- return estatsOK;
+ return StatisticsStatus::Ok;
}
-int gmx_stats_get_ab(gmx_stats_t gstats, int weight, real* a, real* b, real* da, real* db, real* chi2, real* Rfit)
+StatisticsStatus
+gmx_stats_get_ab(gmx_stats_t gstats, int weight, real* a, real* b, real* da, real* db, real* chi2, real* Rfit)
{
- gmx_stats* stats = gstats;
- int ok;
+ gmx_stats* stats = gstats;
+ StatisticsStatus ok;
- if ((ok = gmx_stats_compute(stats, weight)) != estatsOK)
+ if ((ok = gmx_stats_compute(stats, weight)) != StatisticsStatus::Ok)
{
return ok;
}
*Rfit = stats->Rfit;
}
- return estatsOK;
-}
-
-int gmx_stats_get_a(gmx_stats_t gstats, int weight, real* a, real* da, real* chi2, real* Rfit)
-{
- gmx_stats* stats = gstats;
- int ok;
-
- if ((ok = gmx_stats_compute(stats, weight)) != estatsOK)
- {
- return ok;
- }
- if (nullptr != a)
- {
- *a = stats->aa;
- }
- if (nullptr != da)
- {
- *da = stats->sigma_aa;
- }
- if (nullptr != chi2)
- {
- *chi2 = stats->chi2aa;
- }
- if (nullptr != Rfit)
- {
- *Rfit = stats->Rfitaa;
- }
-
- return estatsOK;
+ return StatisticsStatus::Ok;
}
-int gmx_stats_get_average(gmx_stats_t gstats, real* aver)
+StatisticsStatus gmx_stats_get_average(gmx_stats_t gstats, real* aver)
{
- gmx_stats* stats = gstats;
- int ok;
+ gmx_stats* stats = gstats;
+ StatisticsStatus ok;
- if ((ok = gmx_stats_compute(stats, elsqWEIGHT_NONE)) != estatsOK)
+ if ((ok = gmx_stats_compute(stats, elsqWEIGHT_NONE)) != StatisticsStatus::Ok)
{
return ok;
}
*aver = stats->aver;
- return estatsOK;
+ return StatisticsStatus::Ok;
}
-int gmx_stats_get_ase(gmx_stats_t gstats, real* aver, real* sigma, real* error)
+StatisticsStatus gmx_stats_get_ase(gmx_stats_t gstats, real* aver, real* sigma, real* error)
{
- gmx_stats* stats = gstats;
- int ok;
+ gmx_stats* stats = gstats;
+ StatisticsStatus ok;
- if ((ok = gmx_stats_compute(stats, elsqWEIGHT_NONE)) != estatsOK)
+ if ((ok = gmx_stats_compute(stats, elsqWEIGHT_NONE)) != StatisticsStatus::Ok)
{
return ok;
}
*error = stats->error;
}
- return estatsOK;
-}
-
-int gmx_stats_get_sigma(gmx_stats_t gstats, real* sigma)
-{
- gmx_stats* stats = gstats;
- int ok;
-
- if ((ok = gmx_stats_compute(stats, elsqWEIGHT_NONE)) != estatsOK)
- {
- return ok;
- }
-
- *sigma = stats->sigma_aver;
-
- return estatsOK;
-}
-
-int gmx_stats_get_error(gmx_stats_t gstats, real* error)
-{
- gmx_stats* stats = gstats;
- int ok;
-
- if ((ok = gmx_stats_compute(stats, elsqWEIGHT_NONE)) != estatsOK)
- {
- return ok;
- }
-
- *error = stats->error;
-
- return estatsOK;
-}
-
-int gmx_stats_get_corr_coeff(gmx_stats_t gstats, real* R)
-{
- gmx_stats* stats = gstats;
- int ok;
-
- if ((ok = gmx_stats_compute(stats, elsqWEIGHT_NONE)) != estatsOK)
- {
- return ok;
- }
-
- *R = stats->Rdata;
-
- return estatsOK;
-}
-
-int gmx_stats_get_rmsd(gmx_stats_t gstats, real* rmsd)
-{
- gmx_stats* stats = gstats;
- int ok;
-
- if ((ok = gmx_stats_compute(stats, elsqWEIGHT_NONE)) != estatsOK)
- {
- return ok;
- }
-
- *rmsd = stats->rmsd;
-
- return estatsOK;
-}
-
-int gmx_stats_dump_xy(gmx_stats_t gstats, FILE* fp)
-{
- gmx_stats* stats = gstats;
-
- for (int i = 0; (i < stats->np); i++)
- {
- fprintf(fp, "%12g %12g %12g %12g\n", stats->x[i], stats->y[i], stats->dx[i], stats->dy[i]);
- }
-
- return estatsOK;
-}
-
-int gmx_stats_remove_outliers(gmx_stats_t gstats, double level)
-{
- gmx_stats* stats = gstats;
- int iter = 1, done = 0, ok;
- real rmsd, r;
-
- while ((stats->np >= 10) && !done)
- {
- if ((ok = gmx_stats_get_rmsd(gstats, &rmsd)) != estatsOK)
- {
- return ok;
- }
- done = 1;
- for (int i = 0; (i < stats->np);)
- {
- r = std::abs(stats->x[i] - stats->y[i]);
- if (r > level * rmsd)
- {
- fprintf(stderr, "Removing outlier, iter = %d, rmsd = %g, x = %g, y = %g\n", iter,
- rmsd, stats->x[i], stats->y[i]);
- if (i < stats->np - 1)
- {
- stats->x[i] = stats->x[stats->np - 1];
- stats->y[i] = stats->y[stats->np - 1];
- stats->dx[i] = stats->dx[stats->np - 1];
- stats->dy[i] = stats->dy[stats->np - 1];
- }
- stats->np--;
- done = 0;
- }
- else
- {
- i++;
- }
- }
- iter++;
- }
-
- return estatsOK;
-}
-
-int gmx_stats_make_histogram(gmx_stats_t gstats, real binwidth, int* nb, int ehisto, int normalized, real** x, real** y)
-{
- gmx_stats* stats = gstats;
- int index = 0, nbins = *nb, *nindex;
- double minx, maxx, maxy, miny, delta, dd, minh;
-
- if (((binwidth <= 0) && (nbins <= 0)) || ((binwidth > 0) && (nbins > 0)))
- {
- return estatsINVALID_INPUT;
- }
- if (stats->np <= 2)
- {
- return estatsNO_POINTS;
- }
- minx = maxx = stats->x[0];
- miny = maxy = stats->y[0];
- for (int i = 1; (i < stats->np); i++)
- {
- miny = (stats->y[i] < miny) ? stats->y[i] : miny;
- maxy = (stats->y[i] > maxy) ? stats->y[i] : maxy;
- minx = (stats->x[i] < minx) ? stats->x[i] : minx;
- maxx = (stats->x[i] > maxx) ? stats->x[i] : maxx;
- }
- if (ehisto == ehistoX)
- {
- delta = maxx - minx;
- minh = minx;
- }
- else if (ehisto == ehistoY)
- {
- delta = maxy - miny;
- minh = miny;
- }
- else
- {
- return estatsINVALID_INPUT;
- }
-
- if (binwidth == 0)
- {
- binwidth = (delta) / nbins;
- }
- else
- {
- nbins = gmx_dnint((delta) / binwidth + 0.5);
- }
- snew(*x, nbins);
- snew(nindex, nbins);
- for (int i = 0; (i < nbins); i++)
- {
- (*x)[i] = minh + binwidth * (i + 0.5);
- }
- if (normalized == 0)
- {
- dd = 1;
- }
- else
- {
- dd = 1.0 / (binwidth * stats->np);
- }
-
- snew(*y, nbins);
- for (int i = 0; (i < stats->np); i++)
- {
- if (ehisto == ehistoY)
- {
- index = static_cast<int>((stats->y[i] - miny) / binwidth);
- }
- else if (ehisto == ehistoX)
- {
- index = static_cast<int>((stats->x[i] - minx) / binwidth);
- }
- if (index < 0)
- {
- index = 0;
- }
- if (index > nbins - 1)
- {
- index = nbins - 1;
- }
- (*y)[index] += dd;
- nindex[index]++;
- }
- if (*nb == 0)
- {
- *nb = nbins;
- }
- for (int i = 0; (i < nbins); i++)
- {
- if (nindex[i] > 0)
- {
- (*y)[i] /= nindex[i];
- }
- }
-
- sfree(nindex);
-
- return estatsOK;
+ return StatisticsStatus::Ok;
}
-static const char* stats_error[estatsNR] = { "All well in STATS land", "No points",
- "Not enough memory", "Invalid histogram input",
- "Unknown error", "Not implemented yet" };
-
-const char* gmx_stats_message(int estats)
+static const char* enumValueToString(StatisticsStatus enumValue)
{
- if ((estats >= 0) && (estats < estatsNR))
- {
- return stats_error[estats];
- }
- else
- {
- return stats_error[estatsERROR];
- }
+ constexpr gmx::EnumerationArray<StatisticsStatus, const char*> statisticsStatusNames = {
+ "All well in STATS land", "No points", "Not enough memory",
+ "Invalid histogram input", "Unknown error", "Not implemented yet"
+ };
+ return statisticsStatusNames[enumValue];
}
-/* Old convenience functions, should be merged with the core
- statistics above. */
-int lsq_y_ax(int n, real x[], real y[], real* a)
+void gmx_stats_message([[maybe_unused]] StatisticsStatus estats)
{
- gmx_stats_t lsq = gmx_stats_init();
- int ok;
- real da, chi2, Rfit;
-
- gmx_stats_add_points(lsq, n, x, y, nullptr, nullptr);
- ok = gmx_stats_get_a(lsq, elsqWEIGHT_NONE, a, &da, &chi2, &Rfit);
- gmx_stats_free(lsq);
-
- return ok;
+ GMX_ASSERT(estats == StatisticsStatus::Ok, enumValueToString(estats));
}
-static int low_lsq_y_ax_b(int n, const real* xr, const double* xd, real yr[], real* a, real* b, real* r, real* chi2)
+static StatisticsStatus
+low_lsq_y_ax_b(int n, const real* xr, const double* xd, real yr[], real* a, real* b, real* r, real* chi2)
{
- gmx_stats_t lsq = gmx_stats_init();
- int ok;
+ gmx_stats_t lsq = gmx_stats_init();
+ StatisticsStatus ok;
for (int i = 0; (i < n); i++)
{
gmx_incons("Either xd or xr has to be non-NULL in low_lsq_y_ax_b()");
}
- if ((ok = gmx_stats_add_point(lsq, pt, yr[i], 0, 0)) != estatsOK)
+ if ((ok = gmx_stats_add_point(lsq, pt, yr[i], 0, 0)) != StatisticsStatus::Ok)
{
gmx_stats_free(lsq);
return ok;
return ok;
}
-int lsq_y_ax_b(int n, real x[], real y[], real* a, real* b, real* r, real* chi2)
+StatisticsStatus lsq_y_ax_b(int n, real x[], real y[], real* a, real* b, real* r, real* chi2)
{
return low_lsq_y_ax_b(n, x, nullptr, y, a, b, r, chi2);
}
-int lsq_y_ax_b_xdouble(int n, double x[], real y[], real* a, real* b, real* r, real* chi2)
+StatisticsStatus lsq_y_ax_b_xdouble(int n, double x[], real y[], real* a, real* b, real* r, real* chi2)
{
return low_lsq_y_ax_b(n, nullptr, x, y, a, b, r, chi2);
}
-int lsq_y_ax_b_error(int n, real x[], real y[], real dy[], real* a, real* b, real* da, real* db, real* r, real* chi2)
+StatisticsStatus
+lsq_y_ax_b_error(int n, real x[], real y[], real dy[], real* a, real* b, real* da, real* db, real* r, real* chi2)
{
- gmx_stats_t lsq = gmx_stats_init();
- int ok;
+ gmx_stats_t lsq = gmx_stats_init();
+ StatisticsStatus ok;
for (int i = 0; (i < n); i++)
{
ok = gmx_stats_add_point(lsq, x[i], y[i], 0, dy[i]);
- if (ok != estatsOK)
+ if (ok != StatisticsStatus::Ok)
{
gmx_stats_free(lsq);
return ok;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2010,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
typedef struct gmx_stats* gmx_stats_t;
//! Error codes returned by the routines
-enum
+enum class StatisticsStatus : int
{
- estatsOK,
- estatsNO_POINTS,
- estatsNO_MEMORY,
- estatsERROR,
- estatsINVALID_INPUT,
- estatsNOT_IMPLEMENTED,
- estatsNR
+ Ok,
+ NoPoints,
+ NoMemory,
+ Error,
+ InvalidInput,
+ NotImplemented,
+ Count
};
//! Enum for statistical weights
elsqWEIGHT_NR
};
-//! Enum determining which coordinate to histogram
-enum
-{
- ehistoX,
- ehistoY,
- ehistoNR
-};
-
/*! \brief
* Initiate a data structure
* \return the data structure
*/
void gmx_stats_free(gmx_stats_t stats);
-/*! \brief
- * Remove outliers from a straight line, where level in units of
- * sigma. Level needs to be larger than one obviously.
- * \param[in] stats The data structure
- * \param[in] level The sigma level
- * \return error code
- */
-int gmx_stats_remove_outliers(gmx_stats_t stats, double level);
-
/*! \brief
* Add a point to the data set
* \param[in] stats The data structure
* \param[in] dy The error in the y value
* \return error code
*/
-int gmx_stats_add_point(gmx_stats_t stats, double x, double y, double dx, double dy);
-
-/*! \brief
- * Add a series of datapoints at once. The arrays dx and dy may
- * be NULL in that case zero uncertainties will be assumed.
- *
- * \param[in] stats The data structure
- * \param[in] n Number of points
- * \param[in] x The array of x values
- * \param[in] y The array of y values
- * \param[in] dx The error in the x value
- * \param[in] dy The error in the y value
- * \return error code
- */
-int gmx_stats_add_points(gmx_stats_t stats, int n, real* x, real* y, real* dx, real* dy);
-
-/*! \brief
- * Delivers data points from the statistics.
- *
- * Should be used in a while loop. Variables for either
- * pointer may be NULL, in which case the routine can be used as an
- * expensive point counter.
- * Return the data points one by one. Return estatsOK while there are
- * more points, and returns estatsNOPOINTS when the last point has
- * been returned.
- * If level > 0 then the outliers outside level*sigma are reported
- * only.
- * \param[in] stats The data structure
- * \param[out] x The array of x values
- * \param[out] y The array of y values
- * \param[out] dx The error in the x value
- * \param[out] dy The error in the y value
- * \param[in] level sigma level (see above)
- * \return error code
- */
-int gmx_stats_get_point(gmx_stats_t stats, real* x, real* y, real* dx, real* dy, real level);
+StatisticsStatus gmx_stats_add_point(gmx_stats_t stats, double x, double y, double dx, double dy);
/*! \brief
* Fit the data to y = ax + b, possibly weighted, if uncertainties
* \param[out] Rfit correlation coefficient
* \return error code
*/
-int gmx_stats_get_ab(gmx_stats_t stats, int weight, real* a, real* b, real* da, real* db, real* chi2, real* Rfit);
-
-/*! \brief
- * Fit the data to y = ax, possibly weighted, if uncertainties have
- * have been input. da and db may be NULL.
- * \param[in] stats The data structure
- * \param[in] weight type of weighting
- * \param[out] a slope
- * \param[out] da sigma in a
- * \param[out] chi2 normalized quality of fit
- * \param[out] Rfit correlation coefficient
- * \return error code
- */
-int gmx_stats_get_a(gmx_stats_t stats, int weight, real* a, real* da, real* chi2, real* Rfit);
-
-/*! \brief
- * Get the correlation coefficient.
- * \param[in] stats The data structure
- * \param[out] R the correlation coefficient between the data (x and y) as input to the structure.
- * \return error code
- */
-int gmx_stats_get_corr_coeff(gmx_stats_t stats, real* R);
-
-/*! \brief
- * Get the root mean square deviation.
- * \param[in] stats The data structure
- * \param[out] rmsd the root mean square deviation between x and y values.
- * \return error code
- */
-int gmx_stats_get_rmsd(gmx_stats_t stats, real* rmsd);
-
-/*! \brief
- * Get the number of points.
- * \param[in] stats The data structure
- * \param[out] N number of data points
- * \return error code
- */
-int gmx_stats_get_npoints(gmx_stats_t stats, int* N);
+StatisticsStatus
+gmx_stats_get_ab(gmx_stats_t stats, int weight, real* a, real* b, real* da, real* db, real* chi2, real* Rfit);
/*! \brief
* Computes and returns the average value.
* \param[out] aver Average value
* \return error code
*/
-int gmx_stats_get_average(gmx_stats_t stats, real* aver);
-
-/*! \brief
- * Computes and returns the standard deviation.
- * \param[in] stats The data structure
- * \param[out] sigma Standard deviation
- * \return error code
- */
-int gmx_stats_get_sigma(gmx_stats_t stats, real* sigma);
-
-/*! \brief
- * Computes and returns the standard error.
- * \param[in] stats The data structure
- * \param[out] error Standard error
- * \return error code
- */
-int gmx_stats_get_error(gmx_stats_t stats, real* error);
+StatisticsStatus gmx_stats_get_average(gmx_stats_t stats, real* aver);
/*! \brief
* Pointers may be null, in which case no assignment will be done.
* \param[out] error Standard error
* \return error code
*/
-int gmx_stats_get_ase(gmx_stats_t stats, real* aver, real* sigma, real* error);
-
-/*! \brief
- * Dump the x, y, dx, dy data to a text file
- * \param[in] stats The data structure
- * \param[in] fp File pointer
- * \return error code
- */
-int gmx_stats_dump_xy(gmx_stats_t stats, FILE* fp);
+StatisticsStatus gmx_stats_get_ase(gmx_stats_t stats, real* aver, real* sigma, real* error);
-/*! \brief
- * Make a histogram of the data present.
+/*! \brief Assert that statistics are OK
*
- * Uses either binwidth to
- * determine the number of bins, or nbins to determine the binwidth,
- * therefore one of these should be zero, but not the other. If *nbins = 0
- * the number of bins will be returned in this variable. ehisto should be one of
- * ehistoX or ehistoY. If
- * normalized not equal to zero, the integral of the histogram will be
- * normalized to one. The output is in two arrays, *x and *y, to which
- * you should pass a pointer. Memory for the arrays will be allocated
- * as needed. Function returns one of the estats codes.
- * \param[in] stats The data structure
- * \param[in] binwidth For the histogram
- * \param[in] nbins Number of bins
- * \param[in] ehisto Type (see enum above)
- * \param[in] normalized see above
- * \param[out] x see above
- * \param[out] y see above
- * \return error code
- */
-int gmx_stats_make_histogram(gmx_stats_t stats,
- real binwidth,
- int* nbins,
- int ehisto,
- int normalized,
- real** x,
- real** y);
-
-/*! \brief
- * Return message belonging to error code
* \param[in] estats error code
*/
-const char* gmx_stats_message(int estats);
+void gmx_stats_message([[maybe_unused]] StatisticsStatus estats);
/****************************************************
* Some statistics utilities for convenience: useful when a complete data
* set is available already from another source, e.g. an xvg file.
****************************************************/
-/*! \brief
- * Fit a straight line y=ax thru the n data points x, y, return the
- * slope in *a.
- * \param[in] n number of points
- * \param[in] x data points x
- * \param[in] y data point y
- * \param[out] a slope
- * \return error code
- */
-int lsq_y_ax(int n, real x[], real y[], real* a);
/*! \brief
* Fit a straight line y=ax+b thru the n data points x, y.
* \param[out] chi2 quality of fit
* \return error code
*/
-int lsq_y_ax_b(int n, real x[], real y[], real* a, real* b, real* r, real* chi2);
+StatisticsStatus lsq_y_ax_b(int n, real x[], real y[], real* a, real* b, real* r, real* chi2);
/*! \copydoc lsq_y_ax_b
*/
-int lsq_y_ax_b_xdouble(int n, double x[], real y[], real* a, real* b, real* r, real* chi2);
+StatisticsStatus lsq_y_ax_b_xdouble(int n, double x[], real y[], real* a, real* b, real* r, real* chi2);
/*! \brief
* Fit a straight line y=ax+b thru the n data points x, y.
* \param[out] chi2 quality of fit
* \return error code
*/
-int lsq_y_ax_b_error(int n, real x[], real y[], real dy[], real* a, real* b, real* da, real* db, real* r, real* chi2);
+StatisticsStatus
+lsq_y_ax_b_error(int n, real x[], real y[], real dy[], real* a, real* b, real* da, real* db, real* r, real* chi2);
#endif
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(swap INTERFACE)
file(GLOB SWAP_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${SWAP_SOURCES} PARENT_SCOPE)
+# Source files have the following dependencies on library infrastructure.
+#target_link_libraries(swap PRIVATE
+# common
+# legacy_modules
+#)
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(swap PUBLIC
+target_include_directories(swap INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(swap PUBLIC
+target_link_libraries(swap INTERFACE
+ legacy_api
+ )
+
+# TODO: when swap is an OBJECT target
+#target_link_libraries(swap PUBLIC legacy_api)
+#target_link_libraries(swap PRIVATE common)
+
+# Module dependencies
+# swap interfaces convey transitive dependence on these modules.
+#target_link_libraries(swap PUBLIC
+target_link_libraries(swap INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(swap PRIVATE NOTHING)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(swap PRIVATE legacy_modules)
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "swapcoords.h"
#include <cstdio>
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/snprintf.h"
-static const char* SwS = { "SWAP:" }; /**< For output that comes from the swap module */
-static const char* SwSEmpty = { " " }; /**< Placeholder for multi-line output */
-static const char* CompStr[eCompNR] = { "A", "B" }; /**< Compartment name */
-static const char* SwapStr[eSwapTypesNR + 1] = { "", "X-", "Y-", "Z-",
- nullptr }; /**< Name for the swap types. */
-static const char* DimStr[DIM + 1] = { "X", "Y", "Z", nullptr }; /**< Name for the swap dimension. */
+static const std::string SwS = { "SWAP:" }; /**< For output that comes from the swap module */
+static const std::string SwSEmpty = { " " }; /**< Placeholder for multi-line output */
+static constexpr gmx::EnumerationArray<Compartment, const char*> CompStr = { "A", "B" }; /**< Compartment name */
+static constexpr gmx::EnumerationArray<SwapType, const char*> SwapStr = { "", "X-", "Y-", "Z-" }; /**< Name for the swap types. */
+static const char* const DimStr[DIM + 1] = { "X", "Y", "Z", nullptr }; /**< Name for the swap dimension. */
/** Keep track of through which channel the ions have passed */
-enum eChannelHistory
+enum class ChannelHistory : int
{
- eChHistPassedNone,
- eChHistPassedCh0,
- eChHistPassedCh1,
- eChHistNr
+ None,
+ Ch0,
+ Ch1,
+ Count
};
-static const char* ChannelString[eChHistNr] = { "none", "channel0", "channel1" }; /**< Name for the channels */
+static constexpr gmx::EnumerationArray<ChannelHistory, const char*> ChannelString = { "none",
+ "channel0",
+ "channel1" }; /**< Name for the channels */
/*! \brief Domain identifier.
*
* Keeps track of from which compartment the ions came before passing the
* channel.
*/
-enum eDomain
+enum class Domain : int
{
- eDomainNotset,
- eDomainA,
- eDomainB,
- eDomainNr
+ Notset,
+ A,
+ B,
+ Count
};
-static const char* DomainString[eDomainNr] = { "not_assigned", "Domain_A",
- "Domain_B" }; /**< Name for the domains */
+static constexpr gmx::EnumerationArray<Domain, const char*> DomainString = { "not_assigned",
+ "Domain_A",
+ "Domain_B" }; /**< Name for the domains */
namespace gmx
{
IMdpOptionProvider* mdpOptionProvider() override { return nullptr; }
IMDOutputProvider* outputProvider() override { return nullptr; }
void initForceProviders(ForceProviders* /* forceProviders */) override {}
- void subscribeToSimulationSetupNotifications(MdModulesNotifier* /* notifier */) override {}
- void subscribeToPreProcessingNotifications(MdModulesNotifier* /* notifier */) override {}
+ void subscribeToSimulationSetupNotifications(MDModulesNotifiers* /* notifiers */) override {}
+ void subscribeToPreProcessingNotifications(MDModulesNotifiers* /* notifiers */) override {}
};
std::unique_ptr<IMDModule> createSwapCoordinatesModule()
int apm = 0; /**< Number of atoms in each molecule */
gmx::LocalAtomSet atomset; /**< The atom indices in the swap group */
rvec* xc = nullptr; /**< Collective array of group atom positions (size nat) */
- ivec* xc_shifts = nullptr; /**< Current (collective) shifts (size nat) */
- ivec* xc_eshifts = nullptr; /**< Extra shifts since last DD step (size nat) */
- rvec* xc_old = nullptr; /**< Old (collective) positions (size nat) */
- real q = 0.; /**< Total charge of one molecule of this group */
- real* m = nullptr; /**< Masses (can be omitted, size apm) */
- unsigned char* comp_from = nullptr; /**< (Collective) Stores from which compartment this
- molecule has come. This way we keep track of
- through which channel an ion permeates
- (size nMol = nat/apm) */
- unsigned char* comp_now = nullptr; /**< In which compartment this ion is now (size nMol) */
- unsigned char* channel_label = nullptr; /**< Which channel was passed at last by this ion?
+ ivec* xc_shifts = nullptr; /**< Current (collective) shifts (size nat) */
+ ivec* xc_eshifts = nullptr; /**< Extra shifts since last DD step (size nat) */
+ rvec* xc_old = nullptr; /**< Old (collective) positions (size nat) */
+ real q = 0.; /**< Total charge of one molecule of this group */
+ real* m = nullptr; /**< Masses (can be omitted, size apm) */
+ Domain* comp_from = nullptr; /**< (Collective) Stores from which compartment this
+ molecule has come. This way we keep track of
+ through which channel an ion permeates
+ (size nMol = nat/apm) */
+ Domain* comp_now = nullptr; /**< In which compartment this ion is now (size nMol) */
+ ChannelHistory* channel_label = nullptr; /**< Which channel was passed at last by this ion?
(size nMol) */
- rvec center; /**< Center of the group; COM if masses are used */
- t_compartment comp[eCompNR]; /**< Distribution of particles of this group across
- the two compartments */
- real vacancy[eCompNR]; /**< How many molecules need to be swapped in? */
- int fluxfromAtoB[eChanNR]; /**< Net flux of ions per channel */
- int nCyl[eChanNR]; /**< Number of ions residing in a channel */
- int nCylBoth = 0; /**< Ions assigned to cyl0 and cyl1. Not good. */
+ rvec center; /**< Center of the group; COM if masses are used */
+ gmx::EnumerationArray<Compartment, t_compartment> comp; /**< Distribution of particles of this
+ group across the two compartments */
+ gmx::EnumerationArray<Compartment, real> vacancy; /**< How many molecules need to be swapped in? */
+ gmx::EnumerationArray<Channel, int> fluxfromAtoB; /**< Net flux of ions per channel */
+ gmx::EnumerationArray<Channel, int> nCyl; /**< Number of ions residing in a channel */
+ int nCylBoth = 0; /**< Ions assigned to cyl0 and cyl1. Not good. */
} t_swapgrp;
t_swapgrp::swap_group(const gmx::LocalAtomSet& atomset) : atomset{ atomset }
center[0] = 0;
center[1] = 0;
center[2] = 0;
- for (int compartment = eCompA; compartment < eCompNR; ++compartment)
+ for (auto compartment : keysOf(comp))
{
comp[compartment] = {};
vacancy[compartment] = 0;
}
- for (int channel = eChan0; channel < eChanNR; ++channel)
+ for (auto channel : keysOf(fluxfromAtoB))
{
fluxfromAtoB[channel] = 0;
nCyl[channel] = 0;
// Output number of molecules and difference to reference counts for each
// compartment and ion type
- for (int iComp = 0; iComp < eCompNR; iComp++)
+ for (auto iComp : gmx::EnumerationWrapper<Compartment>{})
{
- for (int ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < s->ngrp; ig++)
{
t_compartment* comp = &s->group[ig].comp[iComp];
}
// Output center of split groups
- fprintf(s->fpout, "%10g%10g", s->group[eGrpSplit0].center[s->swapdim],
- s->group[eGrpSplit1].center[s->swapdim]);
+ fprintf(s->fpout,
+ "%10g%10g",
+ s->group[static_cast<int>(SwapGroupSplittingType::Split0)].center[s->swapdim],
+ s->group[static_cast<int>(SwapGroupSplittingType::Split1)].center[s->swapdim]);
// Output ion flux for each channel and ion type
- for (int iChan = 0; iChan < eChanNR; iChan++)
+ for (auto iChan : gmx::EnumerationWrapper<Channel>{})
{
- for (int ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < s->ngrp; ig++)
{
t_swapgrp* g = &s->group[ig];
fprintf(s->fpout, "%10d", g->fluxfromAtoB[iChan]);
/*! \brief Determine the compartment boundaries from the channel centers. */
-static void get_compartment_boundaries(int c, t_swap* s, const matrix box, real* left, real* right)
+static void get_compartment_boundaries(Compartment c, t_swap* s, const matrix box, real* left, real* right)
{
real pos0, pos1;
real leftpos, rightpos, leftpos_orig;
- if (c >= eCompNR)
+ if (c >= Compartment::Count)
{
- gmx_fatal(FARGS, "No compartment %c.", c + 'A');
+ gmx_fatal(FARGS, "Compartment out of range");
}
- pos0 = s->group[eGrpSplit0].center[s->swapdim];
- pos1 = s->group[eGrpSplit1].center[s->swapdim];
+ pos0 = s->group[static_cast<int>(SwapGroupSplittingType::Split0)].center[s->swapdim];
+ pos1 = s->group[static_cast<int>(SwapGroupSplittingType::Split1)].center[s->swapdim];
if (pos0 < pos1)
{
}
/* This gets us the other compartment: */
- if (c == eCompB)
+ if (c == Compartment::B)
{
leftpos_orig = leftpos;
leftpos = rightpos;
*
* \endcode
*/
-static void detect_flux_per_channel(t_swapgrp* g,
- int iAtom,
- int comp,
- rvec atomPosition,
- unsigned char* comp_now,
- unsigned char* comp_from,
- unsigned char* channel_label,
- t_swapcoords* sc,
- t_swap* s,
- real cyl0_r2,
- real cyl1_r2,
- int64_t step,
- gmx_bool bRerun,
- FILE* fpout)
+static void detect_flux_per_channel(t_swapgrp* g,
+ int iAtom,
+ Compartment comp,
+ rvec atomPosition,
+ Domain* comp_now,
+ Domain* comp_from,
+ ChannelHistory* channel_label,
+ const t_swapcoords* sc,
+ t_swap* s,
+ real cyl0_r2,
+ real cyl1_r2,
+ int64_t step,
+ gmx_bool bRerun,
+ FILE* fpout)
{
int sd, chan_nr;
gmx_bool in_cyl0, in_cyl1;
sd = s->swapdim;
/* Check whether ion is inside any of the channels */
- in_cyl0 = is_in_channel(atomPosition, s->group[eGrpSplit0].center, sc->cyl0u, sc->cyl0l,
- cyl0_r2, s->pbc, sd);
- in_cyl1 = is_in_channel(atomPosition, s->group[eGrpSplit1].center, sc->cyl1u, sc->cyl1l,
- cyl1_r2, s->pbc, sd);
+ in_cyl0 = is_in_channel(atomPosition,
+ s->group[static_cast<int>(SwapGroupSplittingType::Split0)].center,
+ sc->cyl0u,
+ sc->cyl0l,
+ cyl0_r2,
+ s->pbc,
+ sd);
+ in_cyl1 = is_in_channel(atomPosition,
+ s->group[static_cast<int>(SwapGroupSplittingType::Split1)].center,
+ sc->cyl1u,
+ sc->cyl1l,
+ cyl1_r2,
+ s->pbc,
+ sd);
if (in_cyl0 && in_cyl1)
{
/* Ion appears to be in both channels. Something is severely wrong! */
g->nCylBoth++;
- *comp_now = eDomainNotset;
- *comp_from = eDomainNotset;
- *channel_label = eChHistPassedNone;
+ *comp_now = Domain::Notset;
+ *comp_from = Domain::Notset;
+ *channel_label = ChannelHistory::None;
}
else if (in_cyl0)
{
/* Ion is in channel 0 now */
- *channel_label = eChHistPassedCh0;
- *comp_now = eDomainNotset;
- g->nCyl[eChan0]++;
+ *channel_label = ChannelHistory::Ch0;
+ *comp_now = Domain::Notset;
+ g->nCyl[Channel::Zero]++;
}
else if (in_cyl1)
{
/* Ion is in channel 1 now */
- *channel_label = eChHistPassedCh1;
- *comp_now = eDomainNotset;
- g->nCyl[eChan1]++;
+ *channel_label = ChannelHistory::Ch1;
+ *comp_now = Domain::Notset;
+ g->nCyl[Channel::One]++;
}
else
{
/* Ion is not in any of the channels, so it must be in domain A or B */
- if (eCompA == comp)
+ if (Compartment::A == comp)
{
- *comp_now = eDomainA;
+ *comp_now = Domain::A;
}
else
{
- *comp_now = eDomainB;
+ *comp_now = Domain::B;
}
}
/* Only take action, if ion is now in domain A or B, and was before
* in the other domain!
*/
- if (eDomainNotset == *comp_from)
+ if (Domain::Notset == *comp_from)
{
/* Maybe we can set the domain now */
- *comp_from = *comp_now; /* Could still be eDomainNotset, though */
+ *comp_from = *comp_now; /* Could still be Domain::Notset, though */
}
- else if ((*comp_now != eDomainNotset) /* if in channel */
+ else if ((*comp_now != Domain::Notset) /* if in channel */
&& (*comp_from != *comp_now))
{
/* Obviously the ion changed its domain.
* Count this for the channel through which it has passed. */
switch (*channel_label)
{
- case eChHistPassedNone:
+ case ChannelHistory::None:
++s->fluxleak;
- fprintf(stderr, " %s Warning! Step %s, ion %d moved from %s to %s\n", SwS,
- gmx_step_str(step, buf), iAtom, DomainString[*comp_from],
+ fprintf(stderr,
+ " %s Warning! Step %s, ion %d moved from %s to %s\n",
+ SwS.c_str(),
+ gmx_step_str(step, buf),
+ iAtom,
+ DomainString[*comp_from],
DomainString[*comp_now]);
if (bRerun)
{
fprintf(s->fpout,
" # Warning: step %s, ion %d moved from %s to %s (probably through the "
"membrane)\n",
- gmx_step_str(step, buf), iAtom, DomainString[*comp_from],
+ gmx_step_str(step, buf),
+ iAtom,
+ DomainString[*comp_from],
DomainString[*comp_now]);
}
break;
- case eChHistPassedCh0:
- case eChHistPassedCh1:
- if (*channel_label == eChHistPassedCh0)
+ case ChannelHistory::Ch0:
+ case ChannelHistory::Ch1:
+ if (*channel_label == ChannelHistory::Ch0)
{
chan_nr = 0;
}
chan_nr = 1;
}
- if (eDomainA == *comp_from)
+ if (Domain::A == *comp_from)
{
g->fluxfromAtoB[chan_nr]++;
}
{
g->fluxfromAtoB[chan_nr]--;
}
- fprintf(fpout, "# Atom nr. %d finished passing %s.\n", iAtom,
- ChannelString[*channel_label]);
+ fprintf(fpout, "# Atom nr. %d finished passing %s.\n", iAtom, ChannelString[*channel_label]);
break;
default:
- gmx_fatal(FARGS, "%s Unknown channel history entry for ion type '%s'\n", SwS, g->molname);
+ gmx_fatal(FARGS, "%s Unknown channel history entry for ion type '%s'\n", SwS.c_str(), g->molname);
}
/* This ion has moved to the _other_ compartment ... */
*comp_from = *comp_now;
/* ... and it did not pass any channel yet */
- *channel_label = eChHistPassedNone;
+ *channel_label = ChannelHistory::None;
}
}
/*! \brief Determines which ions or solvent molecules are in compartment A and B */
-static void sortMoleculesIntoCompartments(t_swapgrp* g,
- t_commrec* cr,
- t_swapcoords* sc,
- t_swap* s,
- const matrix box,
- int64_t step,
- FILE* fpout,
- gmx_bool bRerun,
- gmx_bool bIsSolvent)
+static void sortMoleculesIntoCompartments(t_swapgrp* g,
+ t_commrec* cr,
+ const t_swapcoords* sc,
+ t_swap* s,
+ const matrix box,
+ int64_t step,
+ FILE* fpout,
+ gmx_bool bRerun,
+ gmx_bool bIsSolvent)
{
- int nMolNotInComp[eCompNR]; /* consistency check */
- real cyl0_r2 = sc->cyl0r * sc->cyl0r;
- real cyl1_r2 = sc->cyl1r * sc->cyl1r;
+ gmx::EnumerationArray<Compartment, int> nMolNotInComp; /* consistency check */
+ real cyl0_r2 = sc->cyl0r * sc->cyl0r;
+ real cyl1_r2 = sc->cyl1r * sc->cyl1r;
/* Get us a counter that cycles in the range of [0 ... sc->nAverage[ */
int replace = (step / sc->nstswap) % sc->nAverage;
- for (int comp = eCompA; comp <= eCompB; comp++)
+ for (auto comp : gmx::EnumerationWrapper<Compartment>{})
{
real left, right;
int sd = s->swapdim;
/* Is this first atom of the molecule in the compartment that we look at? */
- if (compartment_contains_atom(left, right, g->xc[iAtom][sd], box[sd][sd],
- sc->bulkOffset[comp], &dist))
+ if (compartment_contains_atom(
+ left, right, g->xc[iAtom][sd], box[sd][sd], sc->bulkOffset[comp], &dist))
{
/* Add the first atom of this molecule to the list of molecules in this compartment */
add_to_list(iAtom, &g->comp[comp], dist);
if (MASTER(cr) && (g->comp_now != nullptr) && !bIsSolvent)
{
int globalAtomNr = g->atomset.globalIndex()[iAtom] + 1; /* PDB index starts at 1 ... */
- detect_flux_per_channel(g, globalAtomNr, comp, g->xc[iAtom], &g->comp_now[iMol],
- &g->comp_from[iMol], &g->channel_label[iMol], sc, s,
- cyl0_r2, cyl1_r2, step, bRerun, fpout);
+ detect_flux_per_channel(g,
+ globalAtomNr,
+ comp,
+ g->xc[iAtom],
+ &g->comp_now[iMol],
+ &g->comp_from[iMol],
+ &g->channel_label[iMol],
+ sc,
+ s,
+ cyl0_r2,
+ cyl1_r2,
+ step,
+ bRerun,
+ fpout);
}
}
else
"split\n"
"%s cylinder is way too large, or one compartment has collapsed (step "
"%" PRId64 ")\n",
- SwS, g->nCylBoth, SwS, step);
+ SwS.c_str(),
+ g->nCylBoth,
+ SwS.c_str(),
+ step);
fprintf(s->fpout, "Warning: %d atoms were assigned to both channels!\n", g->nCylBoth);
if (bIsSolvent && nullptr != fpout)
{
- fprintf(fpout, "# Solv. molecules in comp.%s: %d comp.%s: %d\n", CompStr[eCompA],
- g->comp[eCompA].nMol, CompStr[eCompB], g->comp[eCompB].nMol);
+ fprintf(fpout,
+ "# Solv. molecules in comp.%s: %d comp.%s: %d\n",
+ CompStr[Compartment::A],
+ g->comp[Compartment::A].nMol,
+ CompStr[Compartment::B],
+ g->comp[Compartment::B].nMol);
}
/* Consistency checks */
const auto numMolecules = static_cast<int>(g->atomset.numAtomsGlobal() / g->apm);
- if (nMolNotInComp[eCompA] + nMolNotInComp[eCompB] != numMolecules)
+ if (nMolNotInComp[Compartment::A] + nMolNotInComp[Compartment::B] != numMolecules)
{
fprintf(stderr,
"%s Warning: Inconsistency while assigning '%s' molecules to compartments. !inA: "
"%d, !inB: %d, total molecules %d\n",
- SwS, g->molname, nMolNotInComp[eCompA], nMolNotInComp[eCompB], numMolecules);
+ SwS.c_str(),
+ g->molname,
+ nMolNotInComp[Compartment::A],
+ nMolNotInComp[Compartment::B],
+ numMolecules);
}
- int sum = g->comp[eCompA].nMol + g->comp[eCompB].nMol;
+ int sum = g->comp[Compartment::A].nMol + g->comp[Compartment::B].nMol;
if (sum != numMolecules)
{
fprintf(stderr,
"%s Warning: %d molecules are in group '%s', but altogether %d have been assigned "
"to the compartments.\n",
- SwS, numMolecules, g->molname, sum);
+ SwS.c_str(),
+ numMolecules,
+ g->molname,
+ sum);
}
}
sc = ir->swap;
/* Loop over the user-defined (ion) groups */
- for (int ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < s->ngrp; ig++)
{
g = &s->group[ig];
sortMoleculesIntoCompartments(g, cr, sc, s, box, 0, s->fpout, bRerun, FALSE);
/* Set initial molecule counts if requested (as signaled by "-1" value) */
- for (int ic = 0; ic < eCompNR; ic++)
+ for (auto ic : gmx::EnumerationWrapper<Compartment>{})
{
int requested = sc->grp[ig].nmolReq[ic];
if (requested < 0)
}
/* Check whether the number of requested molecules adds up to the total number */
- int req = g->comp[eCompA].nMolReq + g->comp[eCompB].nMolReq;
- int tot = g->comp[eCompA].nMol + g->comp[eCompB].nMol;
+ int req = g->comp[Compartment::A].nMolReq + g->comp[Compartment::B].nMolReq;
+ int tot = g->comp[Compartment::A].nMol + g->comp[Compartment::B].nMol;
if ((req != tot))
{
"Mismatch of the number of %s ions summed over both compartments.\n"
"You requested a total of %d ions (%d in A and %d in B),\n"
"but there are a total of %d ions of this type in the system.\n",
- g->molname, req, g->comp[eCompA].nMolReq, g->comp[eCompB].nMolReq, tot);
+ g->molname,
+ req,
+ g->comp[Compartment::A].nMolReq,
+ g->comp[Compartment::B].nMolReq,
+ tot);
}
/* Initialize time-averaging:
* Write initial concentrations to all time bins to start with */
- for (int ic = 0; ic < eCompNR; ic++)
+ for (auto ic : gmx::EnumerationWrapper<Compartment>{})
{
g->comp[ic].nMolAv = g->comp[ic].nMol;
for (int i = 0; i < sc->nAverage; i++)
/* Copy the past values from the checkpoint values that have been read in already */
if (bVerbose)
{
- fprintf(stderr, "%s Copying values from checkpoint\n", SwS);
+ fprintf(stderr, "%s Copying values from checkpoint\n", SwS.c_str());
}
- for (int ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < s->ngrp; ig++)
{
g = &s->group[ig];
- gs = &swapstate->ionType[ig - eSwapFixedGrpNR];
+ gs = &swapstate->ionType[ig - static_cast<int>(SwapGroupSplittingType::Count)];
- for (int ic = 0; ic < eCompNR; ic++)
+ for (auto ic : gmx::EnumerationWrapper<Compartment>{})
{
g->comp[ic].nMolReq = gs->nMolReq[ic];
g->comp[ic].inflow_net = gs->inflow_net[ic];
if (bVerbose)
{
- fprintf(stderr, "%s ... Influx netto: %d Requested: %d Past values: ", SwS,
- g->comp[ic].inflow_net, g->comp[ic].nMolReq);
+ fprintf(stderr,
+ "%s ... Influx netto: %d Requested: %d Past values: ",
+ SwS.c_str(),
+ g->comp[ic].inflow_net,
+ g->comp[ic].nMolReq);
}
for (int j = 0; j < sc->nAverage; j++)
/*! \brief The master lets all others know about the initial ion counts. */
static void bc_initial_concentrations(t_commrec* cr, t_swapcoords* swap, t_swap* s)
{
- int ic, ig;
- t_swapgrp* g;
-
-
- for (ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < s->ngrp; ig++)
{
- g = &s->group[ig];
+ t_swapgrp* g = &s->group[ig];
- for (ic = 0; ic < eCompNR; ic++)
+ for (auto ic : gmx::EnumerationWrapper<Compartment>{})
{
gmx_bcast(sizeof(g->comp[ic].nMolReq), &(g->comp[ic].nMolReq), cr->mpi_comm_mygroup);
gmx_bcast(sizeof(g->comp[ic].nMol), &(g->comp[ic].nMol), cr->mpi_comm_mygroup);
- gmx_bcast(swap->nAverage * sizeof(g->comp[ic].nMolPast[0]), g->comp[ic].nMolPast,
- cr->mpi_comm_mygroup);
+ gmx_bcast(swap->nAverage * sizeof(g->comp[ic].nMolPast[0]), g->comp[ic].nMolPast, cr->mpi_comm_mygroup);
}
}
}
if (bVerbose)
{
- fprintf(stderr, "%s Making sure each atom belongs to at most one of the swap groups.\n", SwS);
+ fprintf(stderr, "%s Making sure each atom belongs to at most one of the swap groups.\n", SwS.c_str());
}
/* Add one to the group count of atoms belonging to a swap group: */
"groups, or the solvent.\n"
"%s Check the .mdp file settings regarding the swap index groups or the index "
"groups themselves.\n",
- SwS, nMultiple, (1 == nMultiple) ? " is" : "s are", SwSEmpty, SwSEmpty);
+ SwS.c_str(),
+ nMultiple,
+ (1 == nMultiple) ? " is" : "s are",
+ SwSEmpty.c_str(),
+ SwSEmpty.c_str());
}
}
*
* Also ensure that all the molecules in this group have this number of atoms.
*/
-static int get_group_apm_check(int igroup, t_swap* s, gmx_bool bVerbose, gmx_mtop_t* mtop)
+static int get_group_apm_check(int igroup, t_swap* s, gmx_bool bVerbose, const gmx_mtop_t& mtop)
{
t_swapgrp* g = &s->group[igroup];
const int* ind = s->group[igroup].atomset.globalIndex().data();
* first solvent atom: */
int molb = 0;
mtopGetMolblockIndex(mtop, ind[0], &molb, nullptr, nullptr);
- int apm = mtop->moleculeBlockIndices[molb].numAtomsPerMolecule;
+ int apm = mtop.moleculeBlockIndices[molb].numAtomsPerMolecule;
if (bVerbose)
{
- fprintf(stderr, "%s Checking whether all %s molecules consist of %d atom%s\n", SwS,
- g->molname, apm, apm > 1 ? "s" : "");
+ fprintf(stderr,
+ "%s Checking whether all %s molecules consist of %d atom%s\n",
+ SwS.c_str(),
+ g->molname,
+ apm,
+ apm > 1 ? "s" : "");
}
/* Check whether this is also true for all other solvent atoms */
for (int i = 1; i < nat; i++)
{
mtopGetMolblockIndex(mtop, ind[i], &molb, nullptr, nullptr);
- if (apm != mtop->moleculeBlockIndices[molb].numAtomsPerMolecule)
+ if (apm != mtop.moleculeBlockIndices[molb].numAtomsPerMolecule)
{
gmx_fatal(FARGS, "Not all molecules of swap group %d consist of %d atoms.", igroup, apm);
}
int count = 0;
char buf[STRLEN];
- int nIonTypes = ir->swap->ngrp - eSwapFixedGrpNR;
- snew(legend, eCompNR * nIonTypes * 3 + 2 + eChanNR * nIonTypes + 1);
+ int nIonTypes = ir->swap->ngrp - static_cast<int>(SwapGroupSplittingType::Count);
+ snew(legend,
+ static_cast<int>(Compartment::Count) * nIonTypes * 3 + 2
+ + static_cast<int>(Channel::Count) * nIonTypes + 1);
// Number of molecules and difference to reference counts for each
// compartment and ion type
- for (int ic = count = 0; ic < eCompNR; ic++)
+ for (auto ic : gmx::EnumerationWrapper<Compartment>{})
{
- for (int ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < s->ngrp; ig++)
{
t_swapGroup* g = &ir->swap->grp[ig];
real q = s->group[ig].q;
snprintf(buf, STRLEN, "%s %s ions (charge %s%g)", CompStr[ic], g->molname, q > 0 ? "+" : "", q);
legend[count++] = gmx_strdup(buf);
- snprintf(buf, STRLEN, "%s av. mismatch to %d %s ions", CompStr[ic],
- s->group[ig].comp[ic].nMolReq, g->molname);
+ snprintf(buf,
+ STRLEN,
+ "%s av. mismatch to %d %s ions",
+ CompStr[ic],
+ s->group[ig].comp[ic].nMolReq,
+ g->molname);
legend[count++] = gmx_strdup(buf);
snprintf(buf, STRLEN, "%s net %s ion influx", CompStr[ic], g->molname);
}
// Center of split groups
- snprintf(buf, STRLEN, "%scenter of %s of split group 0", SwapStr[ir->eSwapCoords],
- (nullptr != s->group[eGrpSplit0].m) ? "mass" : "geometry");
+ snprintf(buf,
+ STRLEN,
+ "%scenter of %s of split group 0",
+ SwapStr[ir->eSwapCoords],
+ (nullptr != s->group[static_cast<int>(SwapGroupSplittingType::Split0)].m) ? "mass" : "geometry");
legend[count++] = gmx_strdup(buf);
- snprintf(buf, STRLEN, "%scenter of %s of split group 1", SwapStr[ir->eSwapCoords],
- (nullptr != s->group[eGrpSplit1].m) ? "mass" : "geometry");
+ snprintf(buf,
+ STRLEN,
+ "%scenter of %s of split group 1",
+ SwapStr[ir->eSwapCoords],
+ (nullptr != s->group[static_cast<int>(SwapGroupSplittingType::Split1)].m) ? "mass" : "geometry");
legend[count++] = gmx_strdup(buf);
// Ion flux for each channel and ion type
- for (int ic = 0; ic < eChanNR; ic++)
+ for (auto ic : gmx::EnumerationWrapper<Channel>{})
{
- for (int ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < s->ngrp; ig++)
{
t_swapGroup* g = &ir->swap->grp[ig];
- snprintf(buf, STRLEN, "A->ch%d->B %s permeations", ic, g->molname);
+ snprintf(buf, STRLEN, "A->ch%d->B %s permeations", static_cast<int>(ic), g->molname);
legend[count++] = gmx_strdup(buf);
}
}
return;
}
- for (int ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < s->ngrp; ig++)
{
g = &s->group[ig];
- gs = &swapstate->ionType[ig - eSwapFixedGrpNR];
+ gs = &swapstate->ionType[ig - static_cast<int>(SwapGroupSplittingType::Count)];
/******************************************************/
/* Channel and domain history for the individual ions */
/* Initialize the channel and domain history counters */
for (size_t i = 0; i < g->atomset.numAtomsGlobal() / g->apm; i++)
{
- g->comp_now[i] = eDomainNotset;
+ g->comp_now[i] = Domain::Notset;
if (!isRestart)
{
- g->comp_from[i] = eDomainNotset;
- g->channel_label[i] = eChHistPassedNone;
+ g->comp_from[i] = Domain::Notset;
+ g->channel_label[i] = ChannelHistory::None;
}
}
/************************************/
/* Channel fluxes for both channels */
/************************************/
- g->nCyl[eChan0] = 0;
- g->nCyl[eChan1] = 0;
- g->nCylBoth = 0;
+ g->nCyl[Channel::Zero] = 0;
+ g->nCyl[Channel::One] = 0;
+ g->nCylBoth = 0;
}
if (isRestart)
{
- fprintf(stderr, "%s Copying channel fluxes from checkpoint file data\n", SwS);
+ fprintf(stderr, "%s Copying channel fluxes from checkpoint file data\n", SwS.c_str());
}
// Loop over ion types (and both channels)
- for (int ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < s->ngrp; ig++)
{
g = &s->group[ig];
- gs = &swapstate->ionType[ig - eSwapFixedGrpNR];
+ gs = &swapstate->ionType[ig - static_cast<int>(SwapGroupSplittingType::Count)];
- for (int ic = 0; ic < eChanNR; ic++)
+ for (auto ic : gmx::EnumerationWrapper<Channel>{})
{
- fprintf(stderr, "%s Channel %d flux history for ion type %s (charge %g): ", SwS, ic,
- g->molname, g->q);
+ fprintf(stderr,
+ "%s Channel %d flux history for ion type %s (charge %g): ",
+ SwS.c_str(),
+ static_cast<int>(ic),
+ g->molname,
+ g->q);
if (isRestart)
{
g->fluxfromAtoB[ic] = gs->fluxfromAtoB[ic];
/* Set pointers for checkpoint writing */
swapstate->fluxleak_p = &s->fluxleak;
- for (int ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < s->ngrp; ig++)
{
g = &s->group[ig];
- gs = &swapstate->ionType[ig - eSwapFixedGrpNR];
+ gs = &swapstate->ionType[ig - static_cast<int>(SwapGroupSplittingType::Count)];
- for (int ic = 0; ic < eChanNR; ic++)
+ for (auto ic : gmx::EnumerationWrapper<Channel>{})
{
gs->fluxfromAtoB_p[ic] = &g->fluxfromAtoB[ic];
}
* If this is not correct, the ion counts per channel will be very likely
* wrong.
*/
-static void outputStartStructureIfWanted(gmx_mtop_t* mtop, rvec* x, PbcType pbcType, const matrix box)
+static void outputStartStructureIfWanted(const gmx_mtop_t& mtop, rvec* x, PbcType pbcType, const matrix box)
{
char* env = getenv("GMX_COMPELDUMP");
"whole.\n"
"%s In case of multimeric channels, please check whether they have the correct PBC "
"representation.\n",
- SwS, SwSEmpty);
+ SwS.c_str(),
+ SwSEmpty.c_str());
- write_sto_conf_mtop("CompELAssumedWholeConfiguration.pdb", *mtop->name, mtop, x, nullptr,
- pbcType, box);
+ write_sto_conf_mtop(
+ "CompELAssumedWholeConfiguration.pdb", *mtop.name, mtop, x, nullptr, pbcType, box);
}
}
static void init_swapstate(swaphistory_t* swapstate,
t_swapcoords* sc,
t_swap* s,
- gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const rvec* x, /* the initial positions */
const matrix box,
const t_inputrec* ir)
if (swapstate->bFromCpt)
{
/* Copy the last whole positions of each channel from .cpt */
- g = &(s->group[eGrpSplit0]);
+ g = &(s->group[static_cast<int>(SwapGroupSplittingType::Split0)]);
for (size_t i = 0; i < g->atomset.numAtomsGlobal(); i++)
{
- copy_rvec(swapstate->xc_old_whole[eChan0][i], g->xc_old[i]);
+ copy_rvec(swapstate->xc_old_whole[Channel::Zero][i], g->xc_old[i]);
}
- g = &(s->group[eGrpSplit1]);
+ g = &(s->group[static_cast<int>(SwapGroupSplittingType::Split1)]);
for (size_t i = 0; i < g->atomset.numAtomsGlobal(); i++)
{
- copy_rvec(swapstate->xc_old_whole[eChan1][i], g->xc_old[i]);
+ copy_rvec(swapstate->xc_old_whole[Channel::One][i], g->xc_old[i]);
}
}
else
swapstate->eSwapCoords = ir->eSwapCoords;
/* Set the number of ion types and allocate memory for checkpointing */
- swapstate->nIonTypes = s->ngrp - eSwapFixedGrpNR;
+ swapstate->nIonTypes = s->ngrp - static_cast<int>(SwapGroupSplittingType::Count);
snew(swapstate->ionType, swapstate->nIonTypes);
/* Store the total number of ions of each type in the swapstateIons
for (int ii = 0; ii < swapstate->nIonTypes; ii++)
{
swapstateIons_t* gs = &swapstate->ionType[ii];
- gs->nMol = sc->grp[ii + eSwapFixedGrpNR].nat;
+ gs->nMol = sc->grp[ii + static_cast<int>(SwapGroupSplittingType::Count)].nat;
}
/* Extract the initial split group positions. */
/* Remove pbc, make molecule whole. */
- snew(x_pbc, mtop->natoms);
- copy_rvecn(x, x_pbc, 0, mtop->natoms);
+ snew(x_pbc, mtop.natoms);
+ copy_rvecn(x, x_pbc, 0, mtop.natoms);
/* This can only make individual molecules whole, not multimers */
- do_pbc_mtop(ir->pbcType, box, mtop, x_pbc);
+ do_pbc_mtop(ir->pbcType, box, &mtop, x_pbc);
/* Output the starting structure? */
outputStartStructureIfWanted(mtop, x_pbc, ir->pbcType, box);
/* If this is the first run (i.e. no checkpoint present) we assume
* that the starting positions give us the correct PBC representation */
- for (int ig = eGrpSplit0; ig <= eGrpSplit1; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Split0);
+ ig <= static_cast<int>(SwapGroupSplittingType::Split1);
+ ig++)
{
g = &(s->group[ig]);
for (size_t i = 0; i < g->atomset.numAtomsGlobal(); i++)
sfree(x_pbc);
/* Prepare swapstate arrays for later checkpoint writing */
- swapstate->nat[eChan0] = s->group[eGrpSplit0].atomset.numAtomsGlobal();
- swapstate->nat[eChan1] = s->group[eGrpSplit1].atomset.numAtomsGlobal();
+ swapstate->nat[Channel::Zero] =
+ s->group[static_cast<int>(SwapGroupSplittingType::Split0)].atomset.numAtomsGlobal();
+ swapstate->nat[Channel::One] =
+ s->group[static_cast<int>(SwapGroupSplittingType::Split1)].atomset.numAtomsGlobal();
}
/* For subsequent checkpoint writing, set the swapstate pointers to the xc_old
* arrays that get updated at every swapping step */
- swapstate->xc_old_whole_p[eChan0] = &s->group[eGrpSplit0].xc_old;
- swapstate->xc_old_whole_p[eChan1] = &s->group[eGrpSplit1].xc_old;
+ swapstate->xc_old_whole_p[Channel::Zero] =
+ &s->group[static_cast<int>(SwapGroupSplittingType::Split0)].xc_old;
+ swapstate->xc_old_whole_p[Channel::One] =
+ &s->group[static_cast<int>(SwapGroupSplittingType::Split1)].xc_old;
}
/*! \brief Determine the total charge imbalance resulting from the swap groups */
static real getRequestedChargeImbalance(t_swap* s)
{
- int ig;
- real DeltaQ = 0.0;
- t_swapgrp* g;
- real particle_charge;
- real particle_number[eCompNR];
+ int ig;
+ real DeltaQ = 0.0;
+ t_swapgrp* g;
+ real particle_charge;
+ gmx::EnumerationArray<Compartment, real> particle_number;
- // s->deltaQ = ( (-1) * s->comp[eCompA][eIonNEG].nat_req + s->comp[eCompA][eIonPOS].nat_req )
- // - ( (-1) * s->comp[eCompB][eIonNEG].nat_req + s->comp[eCompB][eIonPOS].nat_req );
-
- for (ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
+ for (ig = static_cast<int>(SwapGroupSplittingType::Count); ig < s->ngrp; ig++)
{
g = &s->group[ig];
- particle_charge = g->q;
- particle_number[eCompA] = g->comp[eCompA].nMolReq;
- particle_number[eCompB] = g->comp[eCompB].nMolReq;
+ particle_charge = g->q;
+ particle_number[Compartment::A] = g->comp[Compartment::A].nMolReq;
+ particle_number[Compartment::B] = g->comp[Compartment::B].nMolReq;
- DeltaQ += particle_charge * (particle_number[eCompA] - particle_number[eCompB]);
+ DeltaQ += particle_charge * (particle_number[Compartment::A] - particle_number[Compartment::B]);
}
return DeltaQ;
/* If explicit ion counts were requested in the .mdp file
* (by setting positive values for the number of ions),
* we can make an additional consistency check here */
- if ((g->nmolReq[eCompA] < 0) && (g->nmolReq[eCompB] < 0))
+ if ((g->nmolReq[Compartment::A] < 0) && (g->nmolReq[Compartment::B] < 0))
{
- if (g->nat != (g->nmolReq[eCompA] + g->nmolReq[eCompB]))
+ if (g->nat != (g->nmolReq[Compartment::A] + g->nmolReq[Compartment::B]))
{
- gmx_fatal_collective(FARGS, cr->mpi_comm_mysim, MASTER(cr),
+ gmx_fatal_collective(FARGS,
+ cr->mpi_comm_mysim,
+ MASTER(cr),
"%s Inconsistency while importing swap-related data from an old "
"input file version.\n"
"%s The requested ion counts in compartments A (%d) and B (%d)\n"
"%s do not add up to the number of ions (%d) of this type for the "
"group '%s'.\n",
- SwS, SwSEmpty, g->nmolReq[eCompA], g->nmolReq[eCompB], SwSEmpty,
- g->nat, g->molname);
+ SwS.c_str(),
+ SwSEmpty.c_str(),
+ g->nmolReq[Compartment::A],
+ g->nmolReq[Compartment::B],
+ SwSEmpty.c_str(),
+ g->nat,
+ g->molname);
}
}
* #4 cations - empty before conversion
*
*/
-static void convertOldToNewGroupFormat(t_swapcoords* sc, gmx_mtop_t* mtop, gmx_bool bVerbose, t_commrec* cr)
+static void convertOldToNewGroupFormat(t_swapcoords* sc, const gmx_mtop_t& mtop, gmx_bool bVerbose, t_commrec* cr)
{
t_swapGroup* g = &sc->grp[3];
if (bVerbose)
{
- fprintf(stdout, "%s Sorted %d ions into separate groups of %d anions and %d cations.\n",
- SwS, g->nat, nAnions, nCations);
+ fprintf(stdout,
+ "%s Sorted %d ions into separate groups of %d anions and %d cations.\n",
+ SwS.c_str(),
+ g->nat,
+ nAnions,
+ nCations);
}
t_swap* init_swapcoords(FILE* fplog,
const t_inputrec* ir,
const char* fn,
- gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const t_state* globalState,
ObservablesHistory* oh,
t_commrec* cr,
gmx_fatal(FARGS, "Position swapping is only implemented for domain decomposition!");
}
- auto sc = ir->swap;
- auto s = new t_swap();
+ auto* sc = ir->swap;
+ auto* s = new t_swap();
if (mdrunOptions.rerun)
{
gmx_fatal(FARGS,
"%s This module does not support reruns in parallel\nPlease request a serial "
"run with -nt 1 / -np 1\n",
- SwS);
+ SwS.c_str());
}
- fprintf(stderr, "%s Rerun - using every available frame\n", SwS);
+ fprintf(stderr, "%s Rerun - using every available frame\n", SwS.c_str());
sc->nstswap = 1;
sc->nAverage = 1; /* averaging makes no sense for reruns */
}
switch (ir->eSwapCoords)
{
- case eswapX: s->swapdim = XX; break;
- case eswapY: s->swapdim = YY; break;
- case eswapZ: s->swapdim = ZZ; break;
+ case SwapType::X: s->swapdim = XX; break;
+ case SwapType::Y: s->swapdim = YY; break;
+ case SwapType::Z: s->swapdim = ZZ; break;
default: s->swapdim = -1; break;
}
}
/* Check for overlapping atoms */
- check_swap_groups(s, mtop->natoms, bVerbose && MASTER(cr));
+ check_swap_groups(s, mtop.natoms, bVerbose && MASTER(cr));
/* Allocate space for the collective arrays for all groups */
/* For the collective position array */
/* For the split groups (the channels) we need some extra memory to
* be able to make the molecules whole even if they span more than
* half of the box size. */
- if ((i == eGrpSplit0) || (i == eGrpSplit1))
+ if ((i == static_cast<int>(SwapGroupSplittingType::Split0))
+ || (i == static_cast<int>(SwapGroupSplittingType::Split1)))
{
snew(g->xc_shifts, g->atomset.numAtomsGlobal());
snew(g->xc_eshifts, g->atomset.numAtomsGlobal());
* channels. Now transfer that to all nodes */
if (PAR(cr))
{
- for (int ig = eGrpSplit0; ig <= eGrpSplit1; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Split0);
+ ig <= static_cast<int>(SwapGroupSplittingType::Split1);
+ ig++)
{
g = &(s->group[ig]);
- gmx_bcast((g->atomset.numAtomsGlobal()) * sizeof((g->xc_old)[0]), g->xc_old,
- cr->mpi_comm_mygroup);
+ gmx_bcast((g->atomset.numAtomsGlobal()) * sizeof((g->xc_old)[0]), g->xc_old, cr->mpi_comm_mygroup);
}
}
/* Make sure that all molecules in the solvent and ion groups contain the
* same number of atoms each */
- for (int ig = eGrpSolvent; ig < s->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Solvent); ig < s->ngrp; ig++)
{
real charge;
/* Need mass-weighted center of split group? */
- for (int j = eGrpSplit0; j <= eGrpSplit1; j++)
+ for (int j = static_cast<int>(SwapGroupSplittingType::Split0);
+ j <= static_cast<int>(SwapGroupSplittingType::Split1);
+ j++)
{
g = &(s->group[j]);
if (sc->massw_split[j])
{
if (bVerbose)
{
- fprintf(stderr, "%s Opening output file %s%s\n", SwS, fn,
+ fprintf(stderr,
+ "%s Opening output file %s%s\n",
+ SwS.c_str(),
+ fn,
restartWithAppending ? " for appending" : "");
}
for (int ig = 0; ig < s->ngrp; ig++)
{
- g = &(s->group[ig]);
- fprintf(s->fpout, "# %s group '%s' contains %d atom%s",
- ig < eSwapFixedGrpNR ? eSwapFixedGrp_names[ig] : "Ion", g->molname,
+ auto enumValue = static_cast<SwapGroupSplittingType>(ig);
+ g = &(s->group[ig]);
+ fprintf(s->fpout,
+ "# %s group '%s' contains %d atom%s",
+ ig < static_cast<int>(SwapGroupSplittingType::Count) ? enumValueToString(enumValue)
+ : "Ion",
+ g->molname,
static_cast<int>(g->atomset.numAtomsGlobal()),
(g->atomset.numAtomsGlobal() > 1) ? "s" : "");
- if (!(eGrpSplit0 == ig || eGrpSplit1 == ig))
+ if (!(SwapGroupSplittingType::Split0 == enumValue
+ || SwapGroupSplittingType::Split1 == enumValue))
{
- fprintf(s->fpout, " with %d atom%s in each molecule of charge %g", g->apm,
- (g->apm > 1) ? "s" : "", g->q);
+ fprintf(s->fpout,
+ " with %d atom%s in each molecule of charge %g",
+ g->apm,
+ (g->apm > 1) ? "s" : "",
+ g->q);
}
fprintf(s->fpout, ".\n");
}
fprintf(s->fpout, "#\n# Initial positions of split groups:\n");
}
- for (int j = eGrpSplit0; j <= eGrpSplit1; j++)
+ for (int j = static_cast<int>(SwapGroupSplittingType::Split0);
+ j <= static_cast<int>(SwapGroupSplittingType::Split1);
+ j++)
{
- g = &(s->group[j]);
+ auto enumValue = static_cast<SwapGroupSplittingType>(j);
+ g = &(s->group[j]);
for (size_t i = 0; i < g->atomset.numAtomsGlobal(); i++)
{
copy_rvec(globalState->x[sc->grp[j].ind[i]], g->xc[i]);
get_center(g->xc, g->m, g->atomset.numAtomsGlobal(), g->center);
if (!restartWithAppending)
{
- fprintf(s->fpout, "# %s group %s-center %5f nm\n", eSwapFixedGrp_names[j],
- DimStr[s->swapdim], g->center[s->swapdim]);
+ fprintf(s->fpout,
+ "# %s group %s-center %5f nm\n",
+ enumValueToString(enumValue),
+ DimStr[s->swapdim],
+ g->center[s->swapdim]);
}
}
if (!restartWithAppending)
{
- if ((0 != sc->bulkOffset[eCompA]) || (0 != sc->bulkOffset[eCompB]))
+ if ((0 != sc->bulkOffset[Compartment::A]) || (0 != sc->bulkOffset[Compartment::B]))
{
fprintf(s->fpout, "#\n");
fprintf(s->fpout,
fprintf(s->fpout,
"# are not midway (= at 0.0) between the compartment-defining layers (at "
"+/- 1.0).\n");
- fprintf(s->fpout, "# bulk-offsetA = %g\n", sc->bulkOffset[eCompA]);
- fprintf(s->fpout, "# bulk-offsetB = %g\n", sc->bulkOffset[eCompB]);
+ fprintf(s->fpout, "# bulk-offsetA = %g\n", sc->bulkOffset[Compartment::A]);
+ fprintf(s->fpout, "# bulk-offsetB = %g\n", sc->bulkOffset[Compartment::B]);
}
fprintf(s->fpout, "#\n");
- fprintf(s->fpout, "# Split0 cylinder radius %f nm, up %f nm, down %f nm\n", sc->cyl0r,
- sc->cyl0u, sc->cyl0l);
- fprintf(s->fpout, "# Split1 cylinder radius %f nm, up %f nm, down %f nm\n", sc->cyl1r,
- sc->cyl1u, sc->cyl1l);
+ fprintf(s->fpout,
+ "# Split0 cylinder radius %f nm, up %f nm, down %f nm\n",
+ sc->cyl0r,
+ sc->cyl0u,
+ sc->cyl0l);
+ fprintf(s->fpout,
+ "# Split1 cylinder radius %f nm, up %f nm, down %f nm\n",
+ sc->cyl1r,
+ sc->cyl1u,
+ sc->cyl1l);
fprintf(s->fpout, "#\n");
if (!mdrunOptions.rerun)
fprintf(s->fpout,
"# Coupling constant (number of swap attempt steps to average over): %d "
"(translates to %f ps).\n",
- sc->nAverage, sc->nAverage * sc->nstswap * ir->delta_t);
+ sc->nAverage,
+ sc->nAverage * sc->nstswap * ir->delta_t);
fprintf(s->fpout, "# Threshold is %f\n", sc->threshold);
fprintf(s->fpout, "#\n");
fprintf(s->fpout,
}
/* Allocate memory to remember the past particle counts for time averaging */
- for (int ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < s->ngrp; ig++)
{
g = &(s->group[ig]);
- for (int ic = 0; ic < eCompNR; ic++)
+ for (auto ic : keysOf(g->comp))
{
snew(g->comp[ic].nMolPast, sc->nAverage);
}
}
else
{
- fprintf(stderr, "%s Determining initial numbers of ions per compartment.\n", SwS);
- get_initial_ioncounts(ir, s, globalState->x.rvec_array(), globalState->box, cr,
- mdrunOptions.rerun);
+ fprintf(stderr, "%s Determining initial numbers of ions per compartment.\n", SwS.c_str());
+ get_initial_ioncounts(
+ ir, s, globalState->x.rvec_array(), globalState->box, cr, mdrunOptions.rerun);
}
/* Prepare (further) checkpoint writes ... */
/* Consistency check */
if (swapstate->nAverage != sc->nAverage)
{
- gmx_fatal(FARGS, "%s Ion count averaging steps mismatch! checkpoint: %d, tpr: %d",
- SwS, swapstate->nAverage, sc->nAverage);
+ gmx_fatal(FARGS,
+ "%s Ion count averaging steps mismatch! checkpoint: %d, tpr: %d",
+ SwS.c_str(),
+ swapstate->nAverage,
+ sc->nAverage);
}
}
else
{
swapstate->nAverage = sc->nAverage;
}
- fprintf(stderr, "%s Setting pointers for checkpoint writing\n", SwS);
- for (int ic = 0; ic < eCompNR; ic++)
+ fprintf(stderr, "%s Setting pointers for checkpoint writing\n", SwS.c_str());
+ for (auto ic : gmx::EnumerationWrapper<Compartment>{})
{
- for (int ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < s->ngrp; ig++)
{
g = &s->group[ig];
- gs = &swapstate->ionType[ig - eSwapFixedGrpNR];
+ gs = &swapstate->ionType[ig - static_cast<int>(SwapGroupSplittingType::Count)];
gs->nMolReq_p[ic] = &(g->comp[ic].nMolReq);
gs->nMolPast_p[ic] = &(g->comp[ic].nMolPast[0]);
if (bVerbose)
{
- fprintf(stderr, "%s Requested charge imbalance is Q(A) - Q(B) = %g e.\n", SwS, s->deltaQ);
+ fprintf(stderr, "%s Requested charge imbalance is Q(A) - Q(B) = %g e.\n", SwS.c_str(), s->deltaQ);
}
if (!restartWithAppending)
{
}
/* Update the time-averaged number of molecules for all groups and compartments */
- for (int ig = eSwapFixedGrpNR; ig < sc->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < sc->ngrp; ig++)
{
g = &s->group[ig];
- for (int ic = 0; ic < eCompNR; ic++)
+ for (auto ic : keysOf(g->comp))
{
update_time_window(&g->comp[ic], sc->nAverage, -1);
}
* From the requested and average molecule counts we determine whether a swap is needed
* at this time step.
*/
-static gmx_bool need_swap(t_swapcoords* sc, t_swap* s)
+static gmx_bool need_swap(const t_swapcoords* sc, t_swap* s)
{
- int ic, ig;
- t_swapgrp* g;
-
- for (ig = eSwapFixedGrpNR; ig < sc->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < sc->ngrp; ig++)
{
- g = &s->group[ig];
+ t_swapgrp* g = &s->group[ig];
- for (ic = 0; ic < eCompNR; ic++)
+ for (auto ic : keysOf(g->comp))
{
if (g->comp[ic].nMolReq - g->comp[ic].nMolAv >= sc->threshold)
{
gmx_fatal(FARGS,
"Could not get index of %s atom. Compartment contains %d %s molecules before "
"swaps.",
- molname, comp->nMolBefore, molname);
+ molname,
+ comp->nMolBefore,
+ molname);
}
/* Set the distance of this index to infinity such that it won't get selected again in
}
-gmx_bool do_swapcoords(t_commrec* cr,
- int64_t step,
- double t,
- t_inputrec* ir,
- t_swap* s,
- gmx_wallcycle* wcycle,
- rvec x[],
- matrix box,
- gmx_bool bVerbose,
- gmx_bool bRerun)
+gmx_bool do_swapcoords(t_commrec* cr,
+ int64_t step,
+ double t,
+ const t_inputrec* ir,
+ t_swap* s,
+ gmx_wallcycle* wcycle,
+ rvec x[],
+ matrix box,
+ gmx_bool bVerbose,
+ gmx_bool bRerun)
{
- t_swapcoords* sc;
- int j, ic, ig, nswaps;
- int thisC, otherC; /* Index into this compartment and the other one */
- gmx_bool bSwap = FALSE;
- t_swapgrp * g, *gsol;
- int isol, iion;
- rvec com_solvent, com_particle; /* solvent and swap molecule's center of mass */
+ const t_swapcoords* sc = ir->swap;
+ gmx_bool bSwap = FALSE;
+ t_swapgrp* gsol;
+ int isol, iion;
+ rvec com_solvent, com_particle; /* solvent and swap molecule's center of mass */
- wallcycle_start(wcycle, ewcSWAP);
-
- sc = ir->swap;
+ wallcycle_start(wcycle, WallCycleCounter::Swap);
set_pbc(s->pbc, ir->pbcType, box);
* Here we also pass a shifts array to communicate_group_positions(), so that it can make
* the molecules whole even in cases where they span more than half of the box in
* any dimension */
- for (ig = eGrpSplit0; ig <= eGrpSplit1; ig++)
- {
- g = &(s->group[ig]);
- communicate_group_positions(cr, g->xc, g->xc_shifts, g->xc_eshifts, TRUE, x,
- g->atomset.numAtomsGlobal(), g->atomset.numAtomsLocal(),
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Split0);
+ ig <= static_cast<int>(SwapGroupSplittingType::Split1);
+ ig++)
+ {
+ t_swapgrp* g = &(s->group[ig]);
+ communicate_group_positions(cr,
+ g->xc,
+ g->xc_shifts,
+ g->xc_eshifts,
+ TRUE,
+ x,
+ g->atomset.numAtomsGlobal(),
+ g->atomset.numAtomsLocal(),
g->atomset.localIndex().data(),
- g->atomset.collectiveIndex().data(), g->xc_old, box);
+ g->atomset.collectiveIndex().data(),
+ g->xc_old,
+ box);
get_center(g->xc, g->m, g->atomset.numAtomsGlobal(), g->center); /* center of split groups == channels */
}
/* Assemble the positions of the ions (ig = 3, 4, ...). These molecules should
* be small and we can always make them whole with a simple distance check.
* Therefore we pass NULL as third argument. */
- for (ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
- {
- g = &(s->group[ig]);
- communicate_group_positions(cr, g->xc, nullptr, nullptr, FALSE, x, g->atomset.numAtomsGlobal(),
- g->atomset.numAtomsLocal(), g->atomset.localIndex().data(),
- g->atomset.collectiveIndex().data(), nullptr, nullptr);
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < s->ngrp; ig++)
+ {
+ t_swapgrp* g = &(s->group[ig]);
+ communicate_group_positions(cr,
+ g->xc,
+ nullptr,
+ nullptr,
+ FALSE,
+ x,
+ g->atomset.numAtomsGlobal(),
+ g->atomset.numAtomsLocal(),
+ g->atomset.localIndex().data(),
+ g->atomset.collectiveIndex().data(),
+ nullptr,
+ nullptr);
/* Determine how many ions of this type each compartment contains */
sortMoleculesIntoCompartments(g, cr, sc, s, box, step, s->fpout, bRerun, FALSE);
{
/* Since we here know that we have to perform ion/water position exchanges,
* we now assemble the solvent positions */
- g = &(s->group[eGrpSolvent]);
- communicate_group_positions(cr, g->xc, nullptr, nullptr, FALSE, x, g->atomset.numAtomsGlobal(),
- g->atomset.numAtomsLocal(), g->atomset.localIndex().data(),
- g->atomset.collectiveIndex().data(), nullptr, nullptr);
+ t_swapgrp* g = &(s->group[static_cast<int>(SwapGroupSplittingType::Solvent)]);
+ communicate_group_positions(cr,
+ g->xc,
+ nullptr,
+ nullptr,
+ FALSE,
+ x,
+ g->atomset.numAtomsGlobal(),
+ g->atomset.numAtomsLocal(),
+ g->atomset.localIndex().data(),
+ g->atomset.collectiveIndex().data(),
+ nullptr,
+ nullptr);
/* Determine how many molecules of solvent each compartment contains */
sortMoleculesIntoCompartments(g, cr, sc, s, box, step, s->fpout, bRerun, TRUE);
/* Save number of solvent molecules per compartment prior to any swaps */
- g->comp[eCompA].nMolBefore = g->comp[eCompA].nMol;
- g->comp[eCompB].nMolBefore = g->comp[eCompB].nMol;
+ g->comp[Compartment::A].nMolBefore = g->comp[Compartment::A].nMol;
+ g->comp[Compartment::B].nMolBefore = g->comp[Compartment::B].nMol;
- for (ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < s->ngrp; ig++)
{
- g = &(s->group[ig]);
+ t_swapgrp* g = &(s->group[ig]);
- for (ic = 0; ic < eCompNR; ic++)
+ for (auto ic : keysOf(g->comp))
{
/* Determine in which compartment ions are missing and where they are too many */
g->vacancy[ic] = g->comp[ic].nMolReq - g->comp[ic].nMolAv;
}
/* Now actually perform the particle exchanges, one swap group after another */
- gsol = &s->group[eGrpSolvent];
- for (ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
+ gsol = &s->group[static_cast<int>(SwapGroupSplittingType::Solvent)];
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < s->ngrp; ig++)
{
- nswaps = 0;
- g = &s->group[ig];
- for (thisC = 0; thisC < eCompNR; thisC++)
+ int nswaps = 0;
+ t_swapgrp* g = &s->group[ig];
+ for (auto thisC : gmx::EnumerationWrapper<Compartment>{})
{
/* Index to the other compartment */
- otherC = (thisC + 1) % eCompNR;
+ auto otherC = thisC == Compartment::A ? Compartment::B : Compartment::A;
while (g->vacancy[thisC] >= sc->threshold)
{
/* Correct the past time window to still get the right averages from now on */
g->comp[thisC].nMolAv++;
g->comp[otherC].nMolAv--;
- for (j = 0; j < sc->nAverage; j++)
+ for (int j = 0; j < sc->nAverage; j++)
{
g->comp[thisC].nMolPast[j]++;
g->comp[otherC].nMolPast[j]--;
if (MASTER(cr))
{
int iMol = iion / g->apm;
- g->channel_label[iMol] = eChHistPassedNone;
- g->comp_from[iMol] = eDomainNotset;
+ g->channel_label[iMol] = ChannelHistory::None;
+ g->comp_from[iMol] = Domain::Notset;
}
/* That was the swap */
nswaps++;
if (nswaps && bVerbose)
{
- fprintf(stderr, "%s Performed %d swap%s in step %" PRId64 " for iontype %s.\n", SwS,
- nswaps, nswaps > 1 ? "s" : "", step, g->molname);
+ fprintf(stderr,
+ "%s Performed %d swap%s in step %" PRId64 " for iontype %s.\n",
+ SwS.c_str(),
+ nswaps,
+ nswaps > 1 ? "s" : "",
+ step,
+ g->molname);
}
}
/* For the solvent and user-defined swap groups, each rank writes back its
* (possibly modified) local positions to the official position array. */
- for (ig = eGrpSolvent; ig < s->ngrp; ig++)
+ for (int ig = static_cast<int>(SwapGroupSplittingType::Solvent); ig < s->ngrp; ig++)
{
- g = &s->group[ig];
+ t_swapgrp* g = &s->group[ig];
apply_modified_positions(g, x);
}
} /* end of if(bSwap) */
- wallcycle_stop(wcycle, ewcSWAP);
+ wallcycle_stop(wcycle, WallCycleCounter::Swap);
return bSwap;
}
*
* Copyright (c) 2013, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
t_swap* init_swapcoords(FILE* fplog,
const t_inputrec* ir,
const char* fn,
- gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const t_state* globalState,
ObservablesHistory* oh,
t_commrec* cr,
*
* \returns Whether at least one pair of molecules was swapped.
*/
-gmx_bool do_swapcoords(t_commrec* cr,
- int64_t step,
- double t,
- t_inputrec* ir,
- t_swap* s,
- gmx_wallcycle* wcycle,
- rvec x[],
- matrix box,
- gmx_bool bVerbose,
- gmx_bool bRerun);
+gmx_bool do_swapcoords(t_commrec* cr,
+ int64_t step,
+ double t,
+ const t_inputrec* ir,
+ t_swap* s,
+ gmx_wallcycle* wcycle,
+ rvec x[],
+ matrix box,
+ gmx_bool bVerbose,
+ gmx_bool bRerun);
#endif
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,200, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(tables INTERFACE)
file(GLOB TABLE_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${TABLE_SOURCES} PARENT_SCOPE)
+# Source files have the following dependencies on library infrastructure.
+#target_link_libraries(tables PRIVATE
+# common
+# legacy_modules
+#)
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(tables PUBLIC
+target_include_directories(tables INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(tables PUBLIC
+target_link_libraries(tables INTERFACE
+ legacy_api
+ )
+
+# TODO: when tables is an OBJECT target
+#target_link_libraries(tables PUBLIC legacy_api)
+#target_link_libraries(tables PRIVATE common)
+
+# Module dependencies
+# tables interfaces convey transitive dependence on these modules.
+#target_link_libraries(tables PUBLIC
+target_link_libraries(tables INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(tables PRIVATE NOTHING)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(tables PRIVATE legacy_modules)
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
double Y, F, G, H;
- calculateCubicSplineCoefficients(functionValue0, functionValue1, derivativeValue0,
- derivativeValue1, spacing, &Y, &F, &G, &H);
+ calculateCubicSplineCoefficients(
+ functionValue0, functionValue1, derivativeValue0, derivativeValue1, spacing, &Y, &F, &G, &H);
double Fp = fma(fma(H, eps, G), eps, F);
if (functionIsInRange)
{
- calculateCubicSplineCoefficients(tmpFunctionValue, nextHigherFunction, tmpDerivativeValue,
- nextHigherDerivative, spacing, &Y, &F, &G, &H);
+ calculateCubicSplineCoefficients(tmpFunctionValue,
+ nextHigherFunction,
+ tmpDerivativeValue,
+ nextHigherDerivative,
+ spacing,
+ &Y,
+ &F,
+ &G,
+ &H);
lastIndexInRange--;
}
else
if (functionIsInRange)
{
- cubicSplineInterpolationFromFunctionAndDerivative(
- function[index], function[index + 1], derivative[index], derivative[index + 1],
- inputSpacing, eps, &(tmpFunction[i]), &(tmpDerivative[i]));
+ cubicSplineInterpolationFromFunctionAndDerivative(function[index],
+ function[index + 1],
+ derivative[index],
+ derivative[index + 1],
+ inputSpacing,
+ eps,
+ &(tmpFunction[i]),
+ &(tmpDerivative[i]));
lastIndexInRange--;
}
else
double nextFunction = ((i + 1) < endIndex) ? tmpFunction[i + 1] : 0.0;
double nextDerivative = ((i + 1) < endIndex) ? tmpDerivative[i + 1] : 0.0;
- calculateCubicSplineCoefficients(tmpFunction[i], nextFunction, tmpDerivative[i],
- nextDerivative, spacing, &Y, &F, &G, &H);
+ calculateCubicSplineCoefficients(
+ tmpFunction[i], nextFunction, tmpDerivative[i], nextDerivative, spacing, &Y, &F, &G, &H);
(*yfghTableData)[4 * i] = Y;
(*yfghTableData)[4 * i + 1] = F;
(*yfghTableData)[4 * i + 2] = G;
{
std::vector<real> tmpYfghTableData;
- fillSingleCubicSplineTableData(thisFuncInput.function, thisFuncInput.derivative, range_,
- spacing, &tmpYfghTableData);
+ fillSingleCubicSplineTableData(
+ thisFuncInput.function, thisFuncInput.derivative, range_, spacing, &tmpYfghTableData);
- internal::fillMultiplexedTableData(tmpYfghTableData, &yfghMultiTableData_, 4,
- numFuncInTable_, funcIndex);
+ internal::fillMultiplexedTableData(
+ tmpYfghTableData, &yfghMultiTableData_, 4, numFuncInTable_, funcIndex);
funcIndex++;
}
std::vector<real> tmpYfghTableData;
- fillSingleCubicSplineTableData(thisFuncInput.function, thisFuncInput.derivative,
- thisFuncInput.spacing, range, spacing, &tmpYfghTableData);
+ fillSingleCubicSplineTableData(thisFuncInput.function,
+ thisFuncInput.derivative,
+ thisFuncInput.spacing,
+ range,
+ spacing,
+ &tmpYfghTableData);
- internal::fillMultiplexedTableData(tmpYfghTableData, &yfghMultiTableData_, 4,
- numFuncInTable_, funcIndex);
+ internal::fillMultiplexedTableData(
+ tmpYfghTableData, &yfghMultiTableData_, 4, numFuncInTable_, funcIndex);
funcIndex++;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_TABLES_CUBICSPLINETABLE_H
#include <initializer_list>
+#include <memory>
#include <vector>
#include "gromacs/simd/simd.h"
// Load Derivative, Delta, Function, and Zero values for each table point.
// The 4 refers to these four values - not any SIMD width.
- gatherLoadBySimdIntTranspose<4 * numFuncInTable>(yfghMultiTableData_.data() + 4 * funcIndex,
- tabIndex, &Y, &F, &G, &H);
+ gatherLoadBySimdIntTranspose<4 * numFuncInTable>(
+ yfghMultiTableData_.data() + 4 * funcIndex, tabIndex, &Y, &F, &G, &H);
*functionValue = fma(fma(fma(H, eps, G), eps, F), eps, Y);
*derivativeValue = tableScale_ * fma(fma(T(3.0) * H, eps, T(2.0) * G), eps, F);
}
// Load Derivative, Delta, Function, and Zero values for each table point.
// The 4 refers to these four values - not any SIMD width.
- gatherLoadBySimdIntTranspose<4 * numFuncInTable>(yfghMultiTableData_.data() + 4 * funcIndex,
- tabIndex, &Y, &F, &G, &H);
+ gatherLoadBySimdIntTranspose<4 * numFuncInTable>(
+ yfghMultiTableData_.data() + 4 * funcIndex, tabIndex, &Y, &F, &G, &H);
*derivativeValue = tableScale_ * fma(fma(T(3.0) * H, eps, T(2.0) * G), eps, F);
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/multidimarray.h"
#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
-#include "gromacs/math/vec.h"
#include "gromacs/mdspan/extensions.h"
#include "gromacs/mdtypes/fcdata.h"
#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
-#include "gromacs/utility/smalloc.h"
/* All the possible (implemented) table functions */
enum
{ "COULSwitch", TRUE }, { "EXPMIN", FALSE }, { "USER", FALSE },
};
-typedef struct
+struct t_tabledata
{
- int nx, nx0;
- double tabscale;
- double *x, *v, *f;
-} t_tabledata;
+ t_tabledata() = default;
+ t_tabledata(int n, int nx0, double tabscale, bool bAlloc);
+ int nx;
+ int nx0;
+ double tabscale;
+ std::vector<double> x;
+ std::vector<double> v;
+ std::vector<double> f;
+};
double v_q_ewald_lr(double beta, double r)
{
{
GMX_RELEASE_ASSERT(!generateCoulombTables || EEL_PME_EWALD(ic.eeltype),
"Can only use tables with Ewald");
- GMX_RELEASE_ASSERT(!generateVdwTables || EVDW_PME(ic.vdwtype),
- "Can only use tables with Ewald");
+ GMX_RELEASE_ASSERT(!generateVdwTables || EVDW_PME(ic.vdwtype), "Can only use tables with Ewald");
real sc = 0;
return sc;
}
-static void copy2table(int n,
- int offset,
- int stride,
- const double x[],
- const double Vtab[],
- const double Ftab[],
- real scalefactor,
- real dest[])
+static void copy2table(int n,
+ int offset,
+ int stride,
+ gmx::ArrayRef<const double> x,
+ gmx::ArrayRef<const double> Vtab,
+ gmx::ArrayRef<const double> Ftab,
+ real scalefactor,
+ gmx::ArrayRef<real> dest)
{
/* Use double prec. for the intermediary variables
* and temporary x/vtab/vtab2 data to avoid unnecessary
}
}
-static void init_table(int n, int nx0, double tabscale, t_tabledata* td, gmx_bool bAlloc)
+t_tabledata::t_tabledata(int n, int nx0, double tabscale, bool bAlloc) :
+ nx(n),
+ nx0(nx0),
+ tabscale(tabscale)
{
- td->nx = n;
- td->nx0 = nx0;
- td->tabscale = tabscale;
if (bAlloc)
{
- snew(td->x, td->nx);
- snew(td->v, td->nx);
- snew(td->f, td->nx);
+ x.resize(nx);
+ v.resize(nx);
+ f.resize(nx);
}
}
{
int start, end, i;
double v3, b_s, b_e, b;
- double beta, *gamma;
+ double beta;
/* Formulas can be found in:
* H.J.C. Berendsen, Simulating the Physical World, Cambridge 2007
end = nx - 1;
}
- snew(gamma, nx);
+ std::vector<double> gamma(nx);
beta = (bS3 ? 1 : 4);
/* For V'' fitting */
{
f[i] -= gamma[i + 1] * f[i + 1];
}
- sfree(gamma);
/* Correct for the minus sign and the spacing */
for (i = start; i < end; i++)
if (fp)
{
- fprintf(fp, "Generating forces for table %d, boundary conditions: V''' at %g, %s at %g\n",
- table + 1, start * h, end == nx ? "V'''" : "V'=0", (end - 1) * h);
+ fprintf(fp,
+ "Generating forces for table %d, boundary conditions: V''' at %g, %s at %g\n",
+ table + 1,
+ start * h,
+ end == nx ? "V'''" : "V'=0",
+ (end - 1) * h);
}
spline_forces(end - start, h, v + start, TRUE, end == nx, f + start);
}
-static void read_tables(FILE* fp, const char* filename, int ntab, int angle, t_tabledata td[])
+static std::vector<t_tabledata> read_tables(FILE* fp, const char* filename, int ntab, int angle)
{
char buf[STRLEN];
double start, end, dx0, dx1, ssd, vm, vp, f, numf;
int numColumns = xvgData.extent(0);
if (numColumns != nny)
{
- gmx_fatal(FARGS, "Trying to read file %s, but nr columns = %d, should be %d", libfn.c_str(),
- numColumns, nny);
+ gmx_fatal(FARGS, "Trying to read file %s, but nr columns = %d, should be %d", libfn.c_str(), numColumns, nny);
}
int numRows = xvgData.extent(1);
{
if (yy[0][0] != 0.0)
{
- gmx_fatal(FARGS, "The first distance in file %s is %f nm instead of %f nm",
- libfn.c_str(), yy[0][0], 0.0);
+ gmx_fatal(FARGS,
+ "The first distance in file %s is %f nm instead of %f nm",
+ libfn.c_str(),
+ yy[0][0],
+ 0.0);
}
}
else
end = 180.0;
if (yy[0][0] != start || yy[0][numRows - 1] != end)
{
- gmx_fatal(FARGS, "The angles in file %s should go from %f to %f instead of %f to %f\n",
- libfn.c_str(), start, end, yy[0][0], yy[0][numRows - 1]);
+ gmx_fatal(FARGS,
+ "The angles in file %s should go from %f to %f instead of %f to %f\n",
+ libfn.c_str(),
+ start,
+ end,
+ yy[0][0],
+ yy[0][numRows - 1]);
}
}
{
gmx_fatal(FARGS,
"In table file '%s' the x values are not equally spaced: %f %f %f",
- filename, yy[0][i - 2], yy[0][i - 1], yy[0][i]);
+ filename,
+ yy[0][i - 2],
+ yy[0][i - 1],
+ yy[0][i]);
}
}
if (yy[1 + k * 2][i] != 0)
}
if (yy[1 + k * 2][i] > 0.01 * GMX_REAL_MAX || yy[1 + k * 2][i] < -0.01 * GMX_REAL_MAX)
{
- gmx_fatal(FARGS, "Out of range potential value %g in file '%s'",
- yy[1 + k * 2][i], filename);
+ gmx_fatal(FARGS, "Out of range potential value %g in file '%s'", yy[1 + k * 2][i], filename);
}
}
if (yy[1 + k * 2 + 1][i] != 0)
}
if (yy[1 + k * 2 + 1][i] > 0.01 * GMX_REAL_MAX || yy[1 + k * 2 + 1][i] < -0.01 * GMX_REAL_MAX)
{
- gmx_fatal(FARGS, "Out of range force value %g in file '%s'",
- yy[1 + k * 2 + 1][i], filename);
+ gmx_fatal(FARGS, "Out of range force value %g in file '%s'", yy[1 + k * 2 + 1][i], filename);
}
}
}
if (!bZeroV && bZeroF)
{
- set_forces(fp, angle, numRows, 1 / tabscale, yy[1 + k * 2].data(),
- yy[1 + k * 2 + 1].data(), k);
+ set_forces(fp, angle, numRows, 1 / tabscale, yy[1 + k * 2].data(), yy[1 + k * 2 + 1].data(), k);
}
else
{
"For the %d non-zero entries for table %d in %s the forces deviate on "
"average %" PRId64
"%% from minus the numerical derivative of the potential\n",
- ns, k, libfn.c_str(), gmx::roundToInt64(100 * ssd));
+ ns,
+ k,
+ libfn.c_str(),
+ gmx::roundToInt64(100 * ssd));
if (debug)
{
fprintf(debug, "%s", buf);
fprintf(fp, "\nNOTE: All elements in table %s are zero\n\n", libfn.c_str());
}
+ std::vector<t_tabledata> td;
for (k = 0; (k < ntab); k++)
{
- init_table(numRows, nx0, tabscale, &(td[k]), TRUE);
+ td.emplace_back(t_tabledata(numRows, nx0, tabscale, true));
for (i = 0; (i < numRows); i++)
{
td[k].x[i] = yy[0][i];
td[k].f[i] = yy[2 * k + 2][i];
}
}
-}
-
-static void done_tabledata(t_tabledata* td)
-{
- if (!td)
- {
- return;
- }
-
- sfree(td->x);
- sfree(td->v);
- sfree(td->f);
+ return td;
}
static void fill_table(t_tabledata* td, int tp, const interaction_const_t* ic, gmx_bool b14only)
}
else
{
- bPotentialSwitch = ((tp == etabLJ6Switch) || (tp == etabLJ12Switch) || (tp == etabCOULSwitch)
- || (tp == etabEwaldSwitch) || (tp == etabEwaldUserSwitch)
- || (tprops[tp].bCoulomb && (ic->coulomb_modifier == eintmodPOTSWITCH))
- || (!tprops[tp].bCoulomb && (ic->vdw_modifier == eintmodPOTSWITCH)));
- bForceSwitch = ((tp == etabLJ6Shift) || (tp == etabLJ12Shift) || (tp == etabShift)
- || (tprops[tp].bCoulomb && (ic->coulomb_modifier == eintmodFORCESWITCH))
- || (!tprops[tp].bCoulomb && (ic->vdw_modifier == eintmodFORCESWITCH)));
- bPotentialShift = ((tprops[tp].bCoulomb && (ic->coulomb_modifier == eintmodPOTSHIFT))
- || (!tprops[tp].bCoulomb && (ic->vdw_modifier == eintmodPOTSHIFT)));
+ bPotentialSwitch =
+ ((tp == etabLJ6Switch) || (tp == etabLJ12Switch) || (tp == etabCOULSwitch)
+ || (tp == etabEwaldSwitch) || (tp == etabEwaldUserSwitch)
+ || (tprops[tp].bCoulomb && (ic->coulomb_modifier == InteractionModifiers::PotSwitch))
+ || (!tprops[tp].bCoulomb && (ic->vdw_modifier == InteractionModifiers::PotSwitch)));
+ bForceSwitch =
+ ((tp == etabLJ6Shift) || (tp == etabLJ12Shift) || (tp == etabShift)
+ || (tprops[tp].bCoulomb && (ic->coulomb_modifier == InteractionModifiers::ForceSwitch))
+ || (!tprops[tp].bCoulomb && (ic->vdw_modifier == InteractionModifiers::ForceSwitch)));
+ bPotentialShift =
+ ((tprops[tp].bCoulomb && (ic->coulomb_modifier == InteractionModifiers::PotShift))
+ || (!tprops[tp].bCoulomb && (ic->vdw_modifier == InteractionModifiers::PotShift)));
}
reppow = ic->reppow;
gmx_fatal(FARGS,
"Cannot apply new potential-shift modifier to interaction type '%s' yet. "
"(%s,%d)",
- tprops[tp].name, __FILE__, __LINE__);
+ tprops[tp].name,
+ __FILE__,
+ __LINE__);
}
}
break;
case etabRF:
case etabRF_ZERO:
- Vtab = 1.0 / r + ic->k_rf * r2 - ic->c_rf;
- Ftab = 1.0 / r2 - 2 * ic->k_rf * r;
+ Vtab = 1.0 / r + ic->reactionFieldCoefficient * r2 - ic->reactionFieldShift;
+ Ftab = 1.0 / r2 - 2 * ic->reactionFieldCoefficient * r;
if (tp == etabRF_ZERO && r >= rc)
{
Vtab = 0;
static void set_table_type(int tabsel[], const interaction_const_t* ic, gmx_bool b14only)
{
- int eltype, vdwtype;
-
/* Set the different table indices.
* Coulomb first.
*/
+ CoulombInteractionType eltype;
+ VanDerWaalsType vdwtype;
if (b14only)
{
switch (ic->eeltype)
{
- case eelUSER:
- case eelPMEUSER:
- case eelPMEUSERSWITCH: eltype = eelUSER; break;
- default: eltype = eelCUT;
+ case CoulombInteractionType::User:
+ case CoulombInteractionType::PmeUser:
+ case CoulombInteractionType::PmeUserSwitch:
+ eltype = CoulombInteractionType::User;
+ break;
+ default: eltype = CoulombInteractionType::Cut;
}
}
else
switch (eltype)
{
- case eelCUT: tabsel[etiCOUL] = etabCOUL; break;
- case eelPOISSON: tabsel[etiCOUL] = etabShift; break;
- case eelSHIFT:
+ case CoulombInteractionType::Cut: tabsel[etiCOUL] = etabCOUL; break;
+ case CoulombInteractionType::Poisson: tabsel[etiCOUL] = etabShift; break;
+ case CoulombInteractionType::Shift:
if (ic->rcoulomb > ic->rcoulomb_switch)
{
tabsel[etiCOUL] = etabShift;
tabsel[etiCOUL] = etabCOUL;
}
break;
- case eelEWALD:
- case eelPME:
- case eelP3M_AD: tabsel[etiCOUL] = etabEwald; break;
- case eelPMESWITCH: tabsel[etiCOUL] = etabEwaldSwitch; break;
- case eelPMEUSER: tabsel[etiCOUL] = etabEwaldUser; break;
- case eelPMEUSERSWITCH: tabsel[etiCOUL] = etabEwaldUserSwitch; break;
- case eelRF:
- case eelRF_ZERO: tabsel[etiCOUL] = etabRF_ZERO; break;
- case eelSWITCH: tabsel[etiCOUL] = etabCOULSwitch; break;
- case eelUSER: tabsel[etiCOUL] = etabUSER; break;
- default: gmx_fatal(FARGS, "Invalid eeltype %d", eltype);
+ case CoulombInteractionType::Ewald:
+ case CoulombInteractionType::Pme:
+ case CoulombInteractionType::P3mAD: tabsel[etiCOUL] = etabEwald; break;
+ case CoulombInteractionType::PmeSwitch: tabsel[etiCOUL] = etabEwaldSwitch; break;
+ case CoulombInteractionType::PmeUser: tabsel[etiCOUL] = etabEwaldUser; break;
+ case CoulombInteractionType::PmeUserSwitch: tabsel[etiCOUL] = etabEwaldUserSwitch; break;
+ case CoulombInteractionType::RF:
+ case CoulombInteractionType::RFZero: tabsel[etiCOUL] = etabRF_ZERO; break;
+ case CoulombInteractionType::Switch: tabsel[etiCOUL] = etabCOULSwitch; break;
+ case CoulombInteractionType::User: tabsel[etiCOUL] = etabUSER; break;
+ default: gmx_fatal(FARGS, "Invalid eeltype %s", enumValueToString(eltype));
}
/* Van der Waals time */
}
else
{
- if (b14only && ic->vdwtype != evdwUSER)
+ if (b14only && ic->vdwtype != VanDerWaalsType::User)
{
- vdwtype = evdwCUT;
+ vdwtype = VanDerWaalsType::Cut;
}
else
{
switch (vdwtype)
{
- case evdwSWITCH:
+ case VanDerWaalsType::Switch:
tabsel[etiLJ6] = etabLJ6Switch;
tabsel[etiLJ12] = etabLJ12Switch;
break;
- case evdwSHIFT:
+ case VanDerWaalsType::Shift:
tabsel[etiLJ6] = etabLJ6Shift;
tabsel[etiLJ12] = etabLJ12Shift;
break;
- case evdwUSER:
+ case VanDerWaalsType::User:
tabsel[etiLJ6] = etabUSER;
tabsel[etiLJ12] = etabUSER;
break;
- case evdwCUT:
+ case VanDerWaalsType::Cut:
tabsel[etiLJ6] = etabLJ6;
tabsel[etiLJ12] = etabLJ12;
break;
- case evdwPME:
+ case VanDerWaalsType::Pme:
tabsel[etiLJ6] = etabLJ6Ewald;
tabsel[etiLJ12] = etabLJ12;
break;
default:
- gmx_fatal(FARGS, "Invalid vdwtype %d in %s line %d", vdwtype, __FILE__, __LINE__);
+ gmx_fatal(FARGS, "Invalid vdwtype %s in %s line %d", enumValueToString(vdwtype), __FILE__, __LINE__);
}
- if (!b14only && ic->vdw_modifier != eintmodNONE)
+ if (!b14only && ic->vdw_modifier != InteractionModifiers::None)
{
- if (ic->vdw_modifier != eintmodPOTSHIFT && ic->vdwtype != evdwCUT)
+ if (ic->vdw_modifier != InteractionModifiers::PotShift && ic->vdwtype != VanDerWaalsType::Cut)
{
gmx_incons(
"Potential modifiers other than potential-shift are only implemented for "
/* LJ-PME and other (shift-only) modifiers are handled by applying the modifiers
* to the original interaction forms when we fill the table, so we only check cutoffs here.
*/
- if (ic->vdwtype == evdwCUT)
+ if (ic->vdwtype == VanDerWaalsType::Cut)
{
switch (ic->vdw_modifier)
{
- case eintmodNONE:
- case eintmodPOTSHIFT:
- case eintmodEXACTCUTOFF:
+ case InteractionModifiers::None:
+ case InteractionModifiers::PotShift:
+ case InteractionModifiers::ExactCutoff:
/* No modification */
break;
- case eintmodPOTSWITCH:
+ case InteractionModifiers::PotSwitch:
tabsel[etiLJ6] = etabLJ6Switch;
tabsel[etiLJ12] = etabLJ12Switch;
break;
- case eintmodFORCESWITCH:
+ case InteractionModifiers::ForceSwitch:
tabsel[etiLJ6] = etabLJ6Shift;
tabsel[etiLJ12] = etabLJ12Shift;
break;
}
}
-t_forcetable* make_tables(FILE* out, const interaction_const_t* ic, const char* fn, real rtab, int flags)
+std::unique_ptr<t_forcetable>
+make_tables(FILE* fp, const interaction_const_t* ic, const char* fn, real rtab, int flags)
{
- t_tabledata* td;
- gmx_bool b14only, useUserTable;
- int nx0, tabsel[etiNR];
- real scalefactor;
+ gmx_bool b14only, useUserTable;
+ int nx0, tabsel[etiNR];
+ real scalefactor;
- t_forcetable* table = new t_forcetable(GMX_TABLE_INTERACTION_ELEC_VDWREP_VDWDISP,
- GMX_TABLE_FORMAT_CUBICSPLINE_YFGH);
+ auto table = std::make_unique<t_forcetable>(GMX_TABLE_INTERACTION_ELEC_VDWREP_VDWDISP,
+ GMX_TABLE_FORMAT_CUBICSPLINE_YFGH);
b14only = ((flags & GMX_MAKETABLES_14ONLY) != 0);
{
set_table_type(tabsel, ic, b14only);
}
- snew(td, etiNR);
+ std::vector<t_tabledata> td;
table->r = rtab;
table->scale = 0;
table->n = 0;
}
if (useUserTable)
{
- read_tables(out, fn, etiNR, 0, td);
+ td = read_tables(fp, fn, etiNR, 0);
if (rtab == 0 || (flags & GMX_MAKETABLES_14ONLY))
{
table->n = td[0].nx;
gmx_fatal(FARGS,
"Tables in file %s not long enough for cut-off:\n"
"\tshould be at least %f nm\n",
- fn, rtab);
+ fn,
+ rtab);
}
table->n = gmx::roundToInt(rtab * td[0].tabscale);
}
}
else
{
+ td.resize(etiNR);
// No tables are read
#if GMX_DOUBLE
table->scale = 2000.0;
{
scale /= ic->buckinghamBMax;
}
- init_table(table->n, nx0, scale, &(td[k]), !useUserTable);
+ td[k] = t_tabledata(table->n, nx0, scale, !useUserTable);
fill_table(&(td[k]), tabsel[k], ic, b14only);
- if (out)
+ if (fp)
{
- fprintf(out,
+ fprintf(fp,
"Generated table with %d data points for %s%s.\n"
"Tabscale = %g points/nm\n",
- td[k].nx, b14only ? "1-4 " : "", tprops[tabsel[k]].name, td[k].tabscale);
+ td[k].nx,
+ b14only ? "1-4 " : "",
+ tprops[tabsel[k]].name,
+ td[k].tabscale);
}
}
scalefactor = 1.0;
}
- copy2table(table->n, k * table->formatsize, table->stride, td[k].x, td[k].v, td[k].f,
- scalefactor, table->data.data());
-
- done_tabledata(&(td[k]));
+ copy2table(table->n, k * table->formatsize, table->stride, td[k].x, td[k].v, td[k].f, scalefactor, table->data);
}
- sfree(td);
return table;
}
bondedtable_t make_bonded_table(FILE* fplog, const char* fn, int angle)
{
- t_tabledata td;
int i;
bondedtable_t tab;
int stride = 4;
- read_tables(fplog, fn, 1, angle, &td);
+ t_tabledata td = read_tables(fplog, fn, 1, angle)[0];
if (angle > 0)
{
/* Convert the table from degrees to radians */
for (i = 0; i < td.nx; i++)
{
- td.x[i] *= DEG2RAD;
- td.f[i] *= RAD2DEG;
+ td.x[i] *= gmx::c_deg2Rad;
+ td.f[i] *= gmx::c_rad2Deg;
}
- td.tabscale *= RAD2DEG;
+ td.tabscale *= gmx::c_rad2Deg;
}
tab.n = td.nx;
tab.scale = td.tabscale;
tab.data.resize(tab.n * stride);
- copy2table(tab.n, 0, stride, td.x, td.v, td.f, 1.0, tab.data.data());
- done_tabledata(&td);
+ copy2table(tab.n, 0, stride, td.x, td.v, td.f, 1.0, tab.data);
return tab;
}
std::unique_ptr<t_forcetable>
makeDispersionCorrectionTable(FILE* fp, const interaction_const_t* ic, real rtab, const char* tabfn)
{
- GMX_RELEASE_ASSERT(ic->vdwtype != evdwUSER || tabfn,
+ GMX_RELEASE_ASSERT(ic->vdwtype != VanDerWaalsType::User || tabfn,
"With VdW user tables we need a table file name");
- t_forcetable* fullTable = make_tables(fp, ic, tabfn, rtab, 0);
+ std::unique_ptr<t_forcetable> fullTable = make_tables(fp, ic, tabfn, rtab, 0);
/* Copy the contents of the table to one that has just dispersion
* and repulsion, to improve cache performance. We want the table
* data to be aligned to 32-byte boundaries.
dispersionCorrectionTable->data[8 * i + j] = fullTable->data[12 * i + 4 + j];
}
}
- delete fullTable;
return dispersionCorrectionTable;
}
stride(0)
{
}
+
+t_forcetable::~t_forcetable() = default;
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* \return Pointer to inner loop table structure
*/
-t_forcetable* make_tables(FILE* fp, const interaction_const_t* ic, const char* fn, real rtab, int flags);
+std::unique_ptr<t_forcetable>
+make_tables(FILE* fp, const interaction_const_t* ic, const char* fn, real rtab, int flags);
/*! \brief Return a table for bonded interactions,
*
const std::vector<real>& derivativeTableData,
std::vector<real>* ddfzTableData)
{
- GMX_ASSERT(functionTableData.size() == derivativeTableData.size(),
- "Mismatching vector lengths");
+ GMX_ASSERT(functionTableData.size() == derivativeTableData.size(), "Mismatching vector lengths");
std::size_t points = functionTableData.size();
std::vector<real> tmpDerTableData;
std::vector<real> tmpDdfzTableData;
- fillSingleQuadraticSplineTableData(thisFuncInput.function, thisFuncInput.derivative,
- range_, spacing, &tmpFuncTableData, &tmpDerTableData);
+ fillSingleQuadraticSplineTableData(thisFuncInput.function,
+ thisFuncInput.derivative,
+ range_,
+ spacing,
+ &tmpFuncTableData,
+ &tmpDerTableData);
fillDdfzTableData(tmpFuncTableData, tmpDerTableData, &tmpDdfzTableData);
- internal::fillMultiplexedTableData(tmpDerTableData, &derivativeMultiTableData_, 1,
- numFuncInTable_, funcIndex);
+ internal::fillMultiplexedTableData(
+ tmpDerTableData, &derivativeMultiTableData_, 1, numFuncInTable_, funcIndex);
- internal::fillMultiplexedTableData(tmpDdfzTableData, &ddfzMultiTableData_, 4,
- numFuncInTable_, funcIndex);
+ internal::fillMultiplexedTableData(
+ tmpDdfzTableData, &ddfzMultiTableData_, 4, numFuncInTable_, funcIndex);
funcIndex++;
}
std::vector<real> tmpDerTableData;
std::vector<real> tmpDdfzTableData;
- fillSingleQuadraticSplineTableData(thisFuncInput.function, thisFuncInput.derivative,
- thisFuncInput.spacing, range, spacing,
- &tmpFuncTableData, &tmpDerTableData);
+ fillSingleQuadraticSplineTableData(thisFuncInput.function,
+ thisFuncInput.derivative,
+ thisFuncInput.spacing,
+ range,
+ spacing,
+ &tmpFuncTableData,
+ &tmpDerTableData);
fillDdfzTableData(tmpFuncTableData, tmpDerTableData, &tmpDdfzTableData);
- internal::fillMultiplexedTableData(tmpDerTableData, &derivativeMultiTableData_, 1,
- numFuncInTable_, funcIndex);
+ internal::fillMultiplexedTableData(
+ tmpDerTableData, &derivativeMultiTableData_, 1, numFuncInTable_, funcIndex);
- internal::fillMultiplexedTableData(tmpDdfzTableData, &ddfzMultiTableData_, 4,
- numFuncInTable_, funcIndex);
+ internal::fillMultiplexedTableData(
+ tmpDdfzTableData, &ddfzMultiTableData_, 4, numFuncInTable_, funcIndex);
funcIndex++;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <functional>
#include <initializer_list>
+#include <memory>
#include <vector>
#include "gromacs/simd/simd.h"
// Load Derivative, Delta, Function, and Zero values for each table point.
// The 4 refers to these four values - not any SIMD width.
- gatherLoadBySimdIntTranspose<4 * numFuncInTable>(ddfzMultiTableData_.data() + 4 * funcIndex,
- tabIndex, &t0, &t1, &t2, &t3);
+ gatherLoadBySimdIntTranspose<4 * numFuncInTable>(
+ ddfzMultiTableData_.data() + 4 * funcIndex, tabIndex, &t0, &t1, &t2, &t3);
t1 = t0 + eps * t1;
*functionValue = fma(eps * T(halfSpacing_), t0 + t1, t2);
if (numFuncInTable == 1)
{
- gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex,
- tabIndex, &t0, &t1); // works for scalar T too
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(
+ derivativeMultiTableData_.data() + funcIndex, tabIndex, &t0, &t1); // works for scalar T too
}
else
{
// This is not ideal, but we need a version of gatherLoadUBySimdIntTranspose that
// only loads a single value from memory to implement it better (will be written)
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(
+ derivativeMultiTableData_.data() + funcIndex, tabIndex, &t0, &t2); // works for scalar T too
gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex,
- tabIndex, &t0, &t2); // works for scalar T too
- gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex,
- tabIndex + T(1), &t1,
+ tabIndex + T(1),
+ &t1,
&t2); // works for scalar T too
}
if (numFuncInTable == 2 && funcIndex0 == 0 && funcIndex1 == 1)
{
T t0A, t0B, t1A, t1B;
- gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data(), tabIndex,
- &t0A, &t0B); // works for scalar T too
- gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + 2, tabIndex,
- &t1A, &t1B); // works for scalar T too
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(
+ derivativeMultiTableData_.data(), tabIndex, &t0A, &t0B); // works for scalar T too
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(
+ derivativeMultiTableData_.data() + 2, tabIndex, &t1A, &t1B); // works for scalar T too
*derivativeValue1 = fma(t1A - t0A, eps, t0A);
*derivativeValue2 = fma(t1B - t0B, eps, t0B);
}
T t0, t1, t2;
// This is not ideal, but we need a version of gatherLoadUBySimdIntTranspose that
// only loads a single value from memory to implement it better (will be written)
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(
+ derivativeMultiTableData_.data() + funcIndex0, tabIndex, &t0, &t2); // works for scalar T too
gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex0,
- tabIndex, &t0, &t2); // works for scalar T too
- gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex0,
- tabIndex + T(1), &t1,
+ tabIndex + T(1),
+ &t1,
&t2); // works for scalar T too
*derivativeValue1 = fma(t1 - t0, eps, t0);
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(
+ derivativeMultiTableData_.data() + funcIndex1, tabIndex, &t0, &t2); // works for scalar T too
gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex1,
- tabIndex, &t0, &t2); // works for scalar T too
- gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex1,
- tabIndex + T(1), &t1,
+ tabIndex + T(1),
+ &t1,
&t2); // works for scalar T too
*derivativeValue2 = fma(t1 - t0, eps, t0);
}
if (numFuncInTable == 3 && funcIndex0 == 0 && funcIndex1 == 1 && funcIndex2 == 2)
{
T t0A, t0B, t0C, t1A, t1B, t1C;
- gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data(),
- tabIndex, &t0A, &t0B);
- gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + 2,
- tabIndex, &t0C, &t1A);
- gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + 4,
- tabIndex, &t1B, &t1C);
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(
+ derivativeMultiTableData_.data(), tabIndex, &t0A, &t0B);
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(
+ derivativeMultiTableData_.data() + 2, tabIndex, &t0C, &t1A);
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(
+ derivativeMultiTableData_.data() + 4, tabIndex, &t1B, &t1C);
*derivativeValue1 = fma(t1A - t0A, eps, t0A);
*derivativeValue2 = fma(t1B - t0B, eps, t0B);
*derivativeValue3 = fma(t1C - t0C, eps, t0C);
T t0, t1, t2;
// This is not ideal, but we need a version of gatherLoadUBySimdIntTranspose that
// only loads a single value from memory to implement it better (will be written)
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(
+ derivativeMultiTableData_.data() + funcIndex0, tabIndex, &t0, &t2); // works for scalar T too
gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex0,
- tabIndex, &t0, &t2); // works for scalar T too
- gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex0,
- tabIndex + T(1), &t1,
+ tabIndex + T(1),
+ &t1,
&t2); // works for scalar T too
*derivativeValue1 = fma(t1 - t0, eps, t0);
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(
+ derivativeMultiTableData_.data() + funcIndex1, tabIndex, &t0, &t2); // works for scalar T too
gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex1,
- tabIndex, &t0, &t2); // works for scalar T too
- gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex1,
- tabIndex + T(1), &t1,
+ tabIndex + T(1),
+ &t1,
&t2); // works for scalar T too
*derivativeValue2 = fma(t1 - t0, eps, t0);
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(
+ derivativeMultiTableData_.data() + funcIndex2, tabIndex, &t0, &t2); // works for scalar T too
gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex2,
- tabIndex, &t0, &t2); // works for scalar T too
- gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex2,
- tabIndex + T(1), &t1,
+ tabIndex + T(1),
+ &t1,
&t2); // works for scalar T too
*derivativeValue3 = fma(t1 - t0, eps, t0);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
if (!isConsistent)
{
- GMX_THROW(InconsistentInputError(
- formatString("Derivative inconsistent with numerical vector for elements %zu-%zu",
- minFail + 1, maxFail + 1)));
+ GMX_THROW(InconsistentInputError(formatString(
+ "Derivative inconsistent with numerical vector for elements %zu-%zu", minFail + 1, maxFail + 1)));
}
}
for (std::size_t i = firstIndex + 1; (i + 1) < lastIndex; i++)
{
- minQuotient = std::min(
- minQuotient, quotientOfFunctionAndSecondDerivative(function[i - 1], function[i],
- function[i + 1], inputSpacing));
+ minQuotient = std::min(minQuotient,
+ quotientOfFunctionAndSecondDerivative(
+ function[i - 1], function[i], function[i + 1], inputSpacing));
}
return static_cast<real>(minQuotient);
}
for (double x = newRange.first; x <= newRange.second; x += dx)
{
minQuotient = std::min(minQuotient,
- quotientOfFunctionAndThirdDerivative(f(x - 2 * h), f(x - h), f(x),
- f(x + h), f(x + 2 * h), h));
+ quotientOfFunctionAndThirdDerivative(
+ f(x - 2 * h), f(x - h), f(x), f(x + h), f(x + 2 * h), h));
}
return static_cast<real>(minQuotient);
}
for (std::size_t i = firstIndex + 2; (i + 2) < lastIndex; i++)
{
- minQuotient = std::min(minQuotient, quotientOfFunctionAndThirdDerivative(
- function[i - 2], function[i - 1], function[i],
- function[i + 1], function[i + 2], inputSpacing));
+ minQuotient = std::min(
+ minQuotient,
+ quotientOfFunctionAndThirdDerivative(
+ function[i - 2], function[i - 1], function[i], function[i + 1], function[i + 2], inputSpacing));
}
return static_cast<real>(minQuotient);
}
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <gtest/gtest.h>
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/ioptionscontainer.h"
real testFuncValue;
real testDerValue;
- table.template evaluateFunctionAndDerivative<numFuncInTable, funcIndex>(x, &testFuncValue,
- &testDerValue);
+ table.template evaluateFunctionAndDerivative<numFuncInTable, funcIndex>(
+ x, &testFuncValue, &testDerValue);
// Check that we get the same values from function/derivative-only methods
real tmpFunc, tmpDer;
TypeParam pmeCorrTable({ { "PMECorr", pmeCorrFunction, pmeCorrDerivative } }, range, tolerance);
TestFixture::setTolerance(tolerance);
- TestFixture::testSplineTableAgainstFunctions("PMECorr", pmeCorrFunction, pmeCorrDerivative,
- pmeCorrTable, range);
+ TestFixture::testSplineTableAgainstFunctions(
+ "PMECorr", pmeCorrFunction, pmeCorrDerivative, pmeCorrTable, range);
}
derivativeValues.push_back(pmeCorrDerivative(x));
}
- TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
- range, tolerance);
+ TypeParam pmeCorrTable(
+ { { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } }, range, tolerance);
TestFixture::setTolerance(tolerance);
- TestFixture::testSplineTableAgainstFunctions("NumericalPMECorr", pmeCorrFunction,
- pmeCorrDerivative, pmeCorrTable, range);
+ TestFixture::testSplineTableAgainstFunctions(
+ "NumericalPMECorr", pmeCorrFunction, pmeCorrDerivative, pmeCorrTable, range);
}
TYPED_TEST(SplineTableTest, TwoFunctions)
range);
// Test entire range for each function. This will use the method that interpolates a single function
- TestFixture::template testSplineTableAgainstFunctions<2, 0>("LJ6", lj6Function, lj6Derivative,
- table, range);
- TestFixture::template testSplineTableAgainstFunctions<2, 1>("LJ12", lj12Function,
- lj12Derivative, table, range);
+ TestFixture::template testSplineTableAgainstFunctions<2, 0>(
+ "LJ6", lj6Function, lj6Derivative, table, range);
+ TestFixture::template testSplineTableAgainstFunctions<2, 1>(
+ "LJ12", lj12Function, lj12Derivative, table, range);
// Test the methods that evaluated both functions for one value
real x = 0.5 * (range.first + range.second);
range);
// Test entire range for each function
- TestFixture::template testSplineTableAgainstFunctions<3, 0>("Coulomb", coulombFunction,
- coulombDerivative, table, range);
- TestFixture::template testSplineTableAgainstFunctions<3, 1>("LJ6", lj6Function, lj6Derivative,
- table, range);
- TestFixture::template testSplineTableAgainstFunctions<3, 2>("LJ12", lj12Function,
- lj12Derivative, table, range);
+ TestFixture::template testSplineTableAgainstFunctions<3, 0>(
+ "Coulomb", coulombFunction, coulombDerivative, table, range);
+ TestFixture::template testSplineTableAgainstFunctions<3, 1>(
+ "LJ6", lj6Function, lj6Derivative, table, range);
+ TestFixture::template testSplineTableAgainstFunctions<3, 2>(
+ "LJ12", lj12Function, lj12Derivative, table, range);
// Test the methods that evaluated both functions for one value
real x = 0.5 * (range.first + range.second);
EXPECT_EQ(tstDer1, tmpDer1);
// Test that scrambled order interpolation methods work
- table.template evaluateFunctionAndDerivative<3, 2, 1, 0>(x, &tstFunc2, &tstDer2, &tstFunc1,
- &tstDer1, &tstFunc0, &tstDer0);
+ table.template evaluateFunctionAndDerivative<3, 2, 1, 0>(
+ x, &tstFunc2, &tstDer2, &tstFunc1, &tstDer1, &tstFunc0, &tstDer0);
EXPECT_EQ(tstFunc0, tmpFunc0);
EXPECT_EQ(tstFunc1, tmpFunc1);
EXPECT_EQ(tstFunc2, tmpFunc2);
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(taskassignment INTERFACE)
+file(GLOB TASKASSIGNMENT_SOURCES *.cpp)
+set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${TASKASSIGNMENT_SOURCES} PARENT_SCOPE)
+
# Note that this is a higher-level module that should not need
# special compilation to suit e.g. GPU or MPI dependencies.
# If you find you want to do that, consider a preliminary
# refactoring.
-gmx_add_libgromacs_sources(
- decidegpuusage.cpp
- decidesimulationworkload.cpp
- findallgputasks.cpp
- reportgpuusage.cpp
- resourcedivision.cpp
- taskassignment.cpp
- usergpuids.cpp
- )
+
+# Source files have the following dependencies on library infrastructure.
+#target_link_libraries(taskassignment PRIVATE
+# common
+# legacy_modules
+#)
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(taskassignment PUBLIC
+target_include_directories(taskassignment INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(taskassignment PUBLIC
+target_link_libraries(taskassignment INTERFACE
+ legacy_api
+ )
+
+# TODO: when taskassignment is an OBJECT target
+#target_link_libraries(taskassignment PUBLIC legacy_api)
+#target_link_libraries(taskassignment PRIVATE common)
+
+# Module dependencies
+# taskassignment interfaces convey transitive dependence on these modules.
+#target_link_libraries(taskassignment PUBLIC
+target_link_libraries(taskassignment INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(taskassignment PRIVATE NOTHING)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(taskassignment PRIVATE legacy_modules)
if (BUILD_TESTING)
add_subdirectory(tests)
{
//! Helper variable to localise the text of an often repeated message.
-const char* g_specifyEverythingFormatString =
+const char* const g_specifyEverythingFormatString =
"When you use mdrun -gputasks, %s must be set to non-default "
"values, so that the device IDs can be interpreted correctly."
#if GMX_GPU
} // namespace
bool decideWhetherToUseGpusForNonbondedWithThreadMpi(const TaskTarget nonbondedTarget,
- const int numDevicesToUse,
+ const bool haveAvailableDevices,
const std::vector<int>& userGpuTaskAssignment,
const EmulateGpuNonbonded emulateGpuNonbonded,
const bool buildSupportsNonbondedOnGpu,
// all potential ranks can use, and can use that in a global
// decision that will later be consistent.
// If we get here, then the user permitted or required GPUs.
- return (numDevicesToUse > 0);
+ return haveAvailableDevices;
}
bool decideWhetherToUseGpusForPmeWithThreadMpi(const bool useGpuForNonbonded,
errorMessage += "Multiple time stepping is not supported.\n";
}
- if (inputrec.eConstrAlg == econtSHAKE && hasAnyConstraints && gmx_mtop_ftype_count(mtop, F_CONSTR) > 0)
+ if (inputrec.eConstrAlg == ConstraintAlgorithm::Shake && hasAnyConstraints
+ && gmx_mtop_ftype_count(mtop, F_CONSTR) > 0)
{
errorMessage += "SHAKE constraints are not supported.\n";
}
{
errorMessage += "Only a CUDA build is supported.\n";
}
- if (inputrec.eI != eiMD)
+ if (inputrec.eI != IntegrationAlgorithm::MD)
{
errorMessage += "Only the md integrator is supported.\n";
}
- if (inputrec.etc == etcNOSEHOOVER)
+ if (inputrec.etc == TemperatureCoupling::NoseHoover)
{
errorMessage += "Nose-Hoover temperature coupling is not supported.\n";
}
- if (!(inputrec.epc == epcNO || inputrec.epc == epcPARRINELLORAHMAN
- || inputrec.epc == epcBERENDSEN || inputrec.epc == epcCRESCALE))
+ if (!(inputrec.epc == PressureCoupling::No || inputrec.epc == PressureCoupling::ParrinelloRahman
+ || inputrec.epc == PressureCoupling::Berendsen || inputrec.epc == PressureCoupling::CRescale))
{
errorMessage +=
"Only Parrinello-Rahman, Berendsen, and C-rescale pressure coupling are "
// The graph is needed, but not supported
errorMessage += "Orientation restraints are not supported.\n";
}
- if (inputrec.efep != efepNO && (haveFepPerturbedMasses(mtop) || havePerturbedConstraints(mtop)))
+ if (inputrec.efep != FreeEnergyPerturbationType::No
+ && (haveFepPerturbedMasses(mtop) || havePerturbedConstraints(mtop)))
{
errorMessage += "Free energy perturbation for mass and constraints are not supported.\n";
}
const auto particleTypes = gmx_mtop_particletype_count(mtop);
- if (particleTypes[eptShell] > 0)
+ if (particleTypes[ParticleType::Shell] > 0)
{
errorMessage += "Shells are not supported.\n";
}
{
errorMessage += "Replica exchange simulations are not supported.\n";
}
- if (inputrec.eSwapCoords != eswapNO)
+ if (inputrec.eSwapCoords != SwapType::No)
{
errorMessage += "Swapping the coordinates is not supported.\n";
}
bool enableGpuHaloExchange = false;
//! True if the PME PP direct communication GPU development feature is enabled
bool enableGpuPmePPComm = false;
+ //! True if the CUDA-aware MPI is being used for GPU direct communication feature
+ bool usingCudaAwareMpi = false;
};
*
* \param[in] nonbondedTarget The user's choice for mdrun -nb for where to assign
* short-ranged nonbonded interaction tasks.
- * \param[in] numDevicesToUse Number of compatible GPUs that the user permitted
- * us to use.
+ * \param[in] haveAvailableDevices Whether there are available devices.
* \param[in] userGpuTaskAssignment The user-specified assignment of GPU tasks to device IDs.
* \param[in] emulateGpuNonbonded Whether we will emulate GPU calculation of nonbonded
* interactions.
* \throws std::bad_alloc If out of memory
* InconsistentInputError If the user requirements are inconsistent. */
bool decideWhetherToUseGpusForNonbondedWithThreadMpi(TaskTarget nonbondedTarget,
- int numDevicesToUse,
+ bool haveAvailableDevices,
const std::vector<int>& userGpuTaskAssignment,
EmulateGpuNonbonded emulateGpuNonbonded,
bool buildSupportsNonbondedOnGpu,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
// to compile warning-free with all versions of MPI headers.
//
// TODO Make an allgather template to deal with this nonsense.
- MPI_Gather(const_cast<int*>(&input), 1, MPI_INT, const_cast<int*>(result.data()), 1,
- MPI_INT, root, communicator);
+ MPI_Gather(const_cast<int*>(&input), 1, MPI_INT, const_cast<int*>(result.data()), 1, MPI_INT, root, communicator);
MPI_Bcast(const_cast<int*>(result.data()), result.size(), MPI_INT, root, communicator);
#else
GMX_UNUSED_VALUE(communicator);
{
std::vector<int> displacements(numRanks + 1);
displacements[0] = 0;
- std::partial_sum(std::begin(extentOnEachRank), std::end(extentOnEachRank),
- std::begin(displacements) + 1);
+ std::partial_sum(
+ std::begin(extentOnEachRank), std::end(extentOnEachRank), std::begin(displacements) + 1);
return displacements;
}
int root = 0;
// Calling a C API with the const T * from data() doesn't seem to compile reliably.
// TODO Make an allgatherv template to deal with this nonsense.
- MPI_Gatherv(const_cast<GpuTask*>(input.data()), input.size(), MPI_INT,
- const_cast<GpuTask*>(result.data()), const_cast<int*>(extentOnEachRank.data()),
- const_cast<int*>(displacementForEachRank.data()), MPI_INT, root, communicator);
+ MPI_Gatherv(const_cast<GpuTask*>(input.data()),
+ input.size(),
+ MPI_INT,
+ const_cast<GpuTask*>(result.data()),
+ const_cast<int*>(extentOnEachRank.data()),
+ const_cast<int*>(displacementForEachRank.data()),
+ MPI_INT,
+ root,
+ communicator);
MPI_Bcast(const_cast<GpuTask*>(result.data()), result.size(), MPI_INT, root, communicator);
#else
GMX_UNUSED_VALUE(communicator);
* the vector. */
auto displacementsForEachRank =
computeDisplacements(numGpuTasksOnEachRankOfThisNode, numRanksOnThisNode);
- auto gpuTasksOnThisNode = allgatherv(gpuTasksOnThisRank, numGpuTasksOnEachRankOfThisNode,
- displacementsForEachRank, communicator);
+ auto gpuTasksOnThisNode = allgatherv(
+ gpuTasksOnThisRank, numGpuTasksOnEachRankOfThisNode, displacementsForEachRank, communicator);
/* Next, we re-use the displacements to break up the vector
* of GPU tasks into something that can be indexed like
do
{
gpuTasksOnRanksOfThisNode.emplace_back(std::vector<GpuTask>());
- for (auto taskOnThisRankIndex = *currentDisplacementIt;
- taskOnThisRankIndex != *nextDisplacementIt; ++taskOnThisRankIndex)
+ for (auto taskOnThisRankIndex = *currentDisplacementIt; taskOnThisRankIndex != *nextDisplacementIt;
+ ++taskOnThisRankIndex)
{
gpuTasksOnRanksOfThisNode.back().push_back(gpuTasksOnThisNode[taskOnThisRankIndex]);
}
output += gmx::formatString(
"%zu GPU%s selected for this run.\n"
"Mapping of GPU IDs to the %zu GPU task%s in the %zu rank%s on this node:\n %s\n",
- numGpusInUse, bPluralGpus ? "s" : "", numGpuTasksOnThisNode,
- (numGpuTasksOnThisNode > 1) ? "s" : "", numRanks, (numRanks > 1) ? "s" : "",
+ numGpusInUse,
+ bPluralGpus ? "s" : "",
+ numGpuTasksOnThisNode,
+ (numGpuTasksOnThisNode > 1) ? "s" : "",
+ numRanks,
+ (numRanks > 1) ? "s" : "",
gpuIdsString.c_str());
// Because there is a GPU in use, there must be a PP task on a GPU.
output += gmx::formatString(
bool nonbondedOnGpu,
bool pmeOnGpu,
const t_inputrec* inputrec,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const gmx::MDLogger& mdlog,
bool doMembed)
{
// had to define a function that returns such requirements,
// and a description string.
SingleRankChecker checker;
- checker.applyConstraint(inputrec->eI == eiLBFGS, "L-BFGS minimization");
- checker.applyConstraint(inputrec->coulombtype == eelEWALD, "Plain Ewald electrostatics");
+ checker.applyConstraint(inputrec->eI == IntegrationAlgorithm::LBFGS, "L-BFGS minimization");
+ checker.applyConstraint(inputrec->coulombtype == CoulombInteractionType::Ewald,
+ "Plain Ewald electrostatics");
checker.applyConstraint(doMembed, "Membrane embedding");
bool useOrientationRestraints = (gmx_mtop_ftype_count(mtop, F_ORIRES) > 0);
checker.applyConstraint(useOrientationRestraints, "Orientation restraints");
nrank = get_tmpi_omp_thread_division(hwinfo, *hw_opt, nthreads_tot_max, ngpu);
- if (inputrec->eI == eiNM || EI_TPI(inputrec->eI))
+ if (inputrec->eI == IntegrationAlgorithm::NM || EI_TPI(inputrec->eI))
{
/* Dims/steps are divided over the nodes iso splitting the atoms.
* With NM we can't have more ranks than #atoms*#dim. With TPI it's
}
}
- if (mtop->natoms / nrank < min_atoms_per_mpi_rank)
+ if (mtop.natoms / nrank < min_atoms_per_mpi_rank)
{
int nrank_new;
/* the rank number was chosen automatically, but there are too few
atoms per rank, so we need to reduce the rank count */
- nrank_new = std::max(1, mtop->natoms / min_atoms_per_mpi_rank);
+ nrank_new = std::max(1, mtop.natoms / min_atoms_per_mpi_rank);
/* Avoid partial use of Hyper-Threading */
if (gmxSmtIsEnabled(hwTop) && nrank_new > nthreads_hw / 2 && nrank_new < nthreads_hw)
GMX_RELEASE_ASSERT(nthreads_omp_faster_default >= nthreads_omp_mpi_ok_max,
"Inconsistent OpenMP thread count default values");
}
- GMX_RELEASE_ASSERT(gmx_omp_nthreads_get(emntDefault) >= 1,
+ GMX_RELEASE_ASSERT(gmx_omp_nthreads_get(ModuleMultiThread::Default) >= 1,
"Must have at least one OpenMP thread");
- nth_omp_max = gmx_omp_nthreads_get(emntDefault);
+ nth_omp_max = gmx_omp_nthreads_get(ModuleMultiThread::Default);
bool anyRankIsUsingGpus = willUsePhysicalGpu;
/* Thread-MPI seems to have a bug with reduce on 1 node, so use a cond. */
"threads per rank, which is most likely inefficient. The optimum is usually "
"between %d and"
" %d threads per rank.",
- nth_omp_max, nthreads_omp_mpi_ok_min, nthreads_omp_mpi_target_max);
+ nth_omp_max,
+ nthreads_omp_mpi_ok_min,
+ nthreads_omp_mpi_target_max);
if (bNtOmpOptionSet)
{
"%s If you want to run with this setup, specify the -ntomp option. But "
"we suggest to "
"change the number of MPI ranks%s.",
- buf, mpi_option);
+ buf,
+ mpi_option);
}
}
}
//! Dump a \c hw_opt to \c fp.
static void print_hw_opt(FILE* fp, const gmx_hw_opt_t* hw_opt)
{
- fprintf(fp, "hw_opt: nt %d ntmpi %d ntomp %d ntomp_pme %d gpu_id '%s' gputasks '%s'\n",
- hw_opt->nthreads_tot, hw_opt->nthreads_tmpi, hw_opt->nthreads_omp, hw_opt->nthreads_omp_pme,
- hw_opt->gpuIdsAvailable.c_str(), hw_opt->userGpuTaskAssignment.c_str());
+ fprintf(fp,
+ "hw_opt: nt %d ntmpi %d ntomp %d ntomp_pme %d gpu_id '%s' gputasks '%s'\n",
+ hw_opt->nthreads_tot,
+ hw_opt->nthreads_tmpi,
+ hw_opt->nthreads_omp,
+ hw_opt->nthreads_omp_pme,
+ hw_opt->devicesSelectedByUser.c_str(),
+ hw_opt->userGpuTaskAssignment.c_str());
}
void checkAndUpdateHardwareOptions(const gmx::MDLogger& mdlog,
"The total number of threads requested (%d) does not match the thread-MPI "
"ranks (%d) "
"times the OpenMP threads (%d) requested",
- hw_opt->nthreads_tot, hw_opt->nthreads_tmpi, hw_opt->nthreads_omp);
+ hw_opt->nthreads_tot,
+ hw_opt->nthreads_tmpi,
+ hw_opt->nthreads_omp);
}
if (hw_opt->nthreads_tmpi > 0 && hw_opt->nthreads_tot % hw_opt->nthreads_tmpi != 0)
"The total number of threads requested (%d) is not divisible by the number "
"of thread-MPI "
"ranks requested (%d)",
- hw_opt->nthreads_tot, hw_opt->nthreads_tmpi);
+ hw_opt->nthreads_tot,
+ hw_opt->nthreads_tmpi);
}
if (hw_opt->nthreads_omp > 0 && hw_opt->nthreads_tot % hw_opt->nthreads_omp != 0)
"The total number of threads requested (%d) is not divisible by the number "
"of OpenMP "
"threads requested (%d)",
- hw_opt->nthreads_tot, hw_opt->nthreads_omp);
+ hw_opt->nthreads_tot,
+ hw_opt->nthreads_omp);
}
}
"You requested %d OpenMP threads with %d total threads. Choose a total "
"number of threads "
"that is a multiple of the number of OpenMP threads.",
- hw_opt->nthreads_omp, hw_opt->nthreads_tot);
+ hw_opt->nthreads_omp,
+ hw_opt->nthreads_tot);
}
if (hw_opt->nthreads_tmpi > hw_opt->nthreads_tot)
"You requested %d thread-MPI ranks with %d total threads. Choose a total "
"number of "
"threads that is a multiple of the number of thread-MPI ranks.",
- hw_opt->nthreads_tmpi, hw_opt->nthreads_tot);
+ hw_opt->nthreads_tmpi,
+ hw_opt->nthreads_tot);
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
bool nonbondedOnGpu,
bool pmeOnGpu,
const t_inputrec* inputrec,
- const gmx_mtop_t* mtop,
+ const gmx_mtop_t& mtop,
const gmx::MDLogger& mdlog,
bool doMembed);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
} // namespace
-void GpuTaskAssignments::logPerformanceHints(const MDLogger& mdlog, size_t numCompatibleGpusOnThisNode)
+void GpuTaskAssignments::logPerformanceHints(const MDLogger& mdlog, size_t numAvailableDevicesOnThisNode)
{
- if (numCompatibleGpusOnThisNode > numGpuTasksOnThisNode_)
+ if (numAvailableDevicesOnThisNode > numGpuTasksOnThisNode_)
{
/* TODO In principle, this warning could be warranted only on
* some nodes, but we lack the infrastructure to do a good job
GpuTaskAssignmentsBuilder::GpuTaskAssignmentsBuilder() = default;
-GpuTaskAssignments GpuTaskAssignmentsBuilder::build(const std::vector<int>& gpuIdsToUse,
- const std::vector<int>& userGpuTaskAssignment,
- const gmx_hw_info_t& hardwareInfo,
- MPI_Comm gromacsWorldComm,
+GpuTaskAssignments GpuTaskAssignmentsBuilder::build(const gmx::ArrayRef<const int> availableDevices,
+ const gmx::ArrayRef<const int> userGpuTaskAssignment,
+ const gmx_hw_info_t& hardwareInfo,
+ MPI_Comm gromacsWorldComm,
const PhysicalNodeCommunicator& physicalNodeComm,
const TaskTarget nonbondedTarget,
const TaskTarget pmeTarget,
bool rankHasPmeTask)
{
size_t numRanksOnThisNode = physicalNodeComm.size_;
- std::vector<GpuTask> gpuTasksOnThisRank = findGpuTasksOnThisRank(
- !gpuIdsToUse.empty(), nonbondedTarget, pmeTarget, bondedTarget, updateTarget,
- useGpuForNonbonded, useGpuForPme, rankHasPpTask, rankHasPmeTask);
+ std::vector<GpuTask> gpuTasksOnThisRank = findGpuTasksOnThisRank(!availableDevices.empty(),
+ nonbondedTarget,
+ pmeTarget,
+ bondedTarget,
+ updateTarget,
+ useGpuForNonbonded,
+ useGpuForPme,
+ rankHasPpTask,
+ rankHasPmeTask);
/* Communicate among ranks on this node to find each task that can
* be executed on a GPU, on each rank. */
auto gpuTasksOnRanksOfThisNode = findAllGpuTasksOnThisNode(gpuTasksOnThisRank, physicalNodeComm);
std::exception_ptr exceptionPtr;
std::vector<GpuTaskAssignment> taskAssignmentOnRanksOfThisNode;
+ std::vector<int> deviceIdAssignment;
try
{
// Use the GPU IDs from the user if they supplied
// runtime, and subject to environment modification such as
// with CUDA_VISIBLE_DEVICES) that will be used for the
// GPU-suitable tasks on all of the ranks of that node.
- ArrayRef<const int> gpuIdsForTaskAssignment;
- std::vector<int> generatedGpuIds;
+ std::vector<int> generatedGpuIds;
if (userGpuTaskAssignment.empty())
{
- ArrayRef<const int> compatibleGpusToUse = gpuIdsToUse;
+ ArrayRef<const int> compatibleGpusToUse = availableDevices;
// enforce the single device/rank restriction
if (numRanksOnThisNode == 1 && !compatibleGpusToUse.empty())
// but we don't have any way to do a better job reliably.
generatedGpuIds = makeGpuIds(compatibleGpusToUse, numGpuTasksOnThisNode);
- if ((numGpuTasksOnThisNode > gpuIdsToUse.size())
- && (numGpuTasksOnThisNode % gpuIdsToUse.size() != 0))
+ if ((numGpuTasksOnThisNode > availableDevices.size())
+ && (numGpuTasksOnThisNode % availableDevices.size() != 0))
{
// TODO Decorating the message with hostname should be
// the job of an error-reporting module.
"You should reconsider your GPU task assignment, "
"number of ranks, or your use of the -nb, -pme, and -npme options, "
"perhaps after measuring the performance you can get.",
- numGpuTasksOnThisNode, host, gpuIdsToUse.size())));
+ numGpuTasksOnThisNode,
+ host,
+ availableDevices.size())));
}
- gpuIdsForTaskAssignment = generatedGpuIds;
+ deviceIdAssignment = generatedGpuIds;
}
else
{
"There were %zu GPU tasks assigned on node %s, but %zu GPU tasks were "
"identified, and these must match. Reconsider your GPU task assignment, "
"number of ranks, or your use of the -nb, -pme, and -npme options.",
- userGpuTaskAssignment.size(), host, numGpuTasksOnThisNode)));
+ userGpuTaskAssignment.size(),
+ host,
+ numGpuTasksOnThisNode)));
}
// Did the user choose compatible GPUs?
- checkUserGpuIds(hardwareInfo.deviceInfoList, gpuIdsToUse, userGpuTaskAssignment);
+ checkUserGpuIds(hardwareInfo.deviceInfoList, availableDevices, userGpuTaskAssignment);
- gpuIdsForTaskAssignment = userGpuTaskAssignment;
+ deviceIdAssignment = gmx::copyOf(userGpuTaskAssignment);
}
taskAssignmentOnRanksOfThisNode =
- buildTaskAssignment(gpuTasksOnRanksOfThisNode, gpuIdsForTaskAssignment);
+ buildTaskAssignment(gpuTasksOnRanksOfThisNode, deviceIdAssignment);
}
catch (...)
{
gpuTaskAssignments.indexOfThisRank_ = physicalNodeComm.rank_;
gpuTaskAssignments.numGpuTasksOnThisNode_ = numGpuTasksOnThisNode;
gpuTaskAssignments.numRanksOnThisNode_ = numRanksOnThisNode;
+ gpuTaskAssignments.deviceIdsAssigned_ = deviceIdAssignment;
+ std::sort(gpuTaskAssignments.deviceIdsAssigned_.begin(), gpuTaskAssignments.deviceIdsAssigned_.end());
+ gpuTaskAssignments.deviceIdsAssigned_.erase(unique(gpuTaskAssignments.deviceIdsAssigned_.begin(),
+ gpuTaskAssignments.deviceIdsAssigned_.end()),
+ gpuTaskAssignments.deviceIdsAssigned_.end());
return gpuTaskAssignments;
}
PmeRunMode pmeRunMode,
bool useGpuForUpdate)
{
- gmx::reportGpuUsage(mdlog, assignmentForAllRanksOnThisNode_, numGpuTasksOnThisNode_,
- numRanksOnThisNode_, printHostName, useGpuForBonded, pmeRunMode, useGpuForUpdate);
+ gmx::reportGpuUsage(mdlog,
+ assignmentForAllRanksOnThisNode_,
+ numGpuTasksOnThisNode_,
+ numRanksOnThisNode_,
+ printHostName,
+ useGpuForBonded,
+ pmeRunMode,
+ useGpuForUpdate);
}
/*! \brief Function for whether the task of \c mapping has value \c TaskType.
{
const GpuTaskAssignment& gpuTaskAssignment = assignmentForAllRanksOnThisNode_[indexOfThisRank_];
- auto pmeGpuTaskMapping = std::find_if(gpuTaskAssignment.begin(), gpuTaskAssignment.end(),
- hasTaskType<GpuTask::Pme>);
+ auto pmeGpuTaskMapping = std::find_if(
+ gpuTaskAssignment.begin(), gpuTaskAssignment.end(), hasTaskType<GpuTask::Pme>);
const bool thisRankHasPmeGpuTask = (pmeGpuTaskMapping != gpuTaskAssignment.end());
return thisRankHasPmeGpuTask;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxmpi.h"
* the ranks of that node. It throws InconsistentInputError
* when a/the useful GPU task assignment is not possible.
*
- * \param[in] gpuIdsToUse The compatible GPUs that the user permitted us to use.
+ * \param[in] availableDevices The compatible devices that the user permitted us to use.
* \param[in] userGpuTaskAssignment The user-specified assignment of GPU tasks to device IDs.
* \param[in] hardwareInfo The detected hardware
* \param[in] gromacsWorldComm MPI communicator for all ranks in the current GROMACS run
* \throws std::bad_alloc If out of memory.
* InconsistentInputError If user and/or detected inputs are inconsistent.
*/
- static GpuTaskAssignments build(const std::vector<int>& gpuIdsToUse,
- const std::vector<int>& userGpuTaskAssignment,
+ static GpuTaskAssignments build(ArrayRef<const int> availableDevices,
+ ArrayRef<const int> userGpuTaskAssignment,
const gmx_hw_info_t& hardwareInfo,
MPI_Comm gromacsWorldComm,
const PhysicalNodeCommunicator& physicalNodeComm,
//! Number of ranks on this physical node.
size_t numRanksOnThisNode_ = 0;
+ //! Vector of device IDs assigned to this node
+ std::vector<int> deviceIdsAssigned_;
+
public:
/*! \brief Log a report on how GPUs are being used on
* the ranks of the physical node of rank 0 of the simulation.
* learn how to let mdrun make a task assignment that runs
* faster.
*
- * \param[in] mdlog Logging object.
- * \param[in] numCompatibleGpusOnThisNode The number of compatible GPUs on this node.
+ * \param[in] mdlog Logging object.
+ * \param[in] numAvailableDevicesOnThisNode The number of compatible devices on this node
+ * that the user permitted us to use.
* */
- void logPerformanceHints(const MDLogger& mdlog, size_t numCompatibleGpusOnThisNode);
+ void logPerformanceHints(const MDLogger& mdlog, size_t numAvailableDevicesOnThisNode);
/*! \brief Return handle to the initialized GPU to use in the this rank.
*
* \param[out] deviceId Index of the assigned device.
bool thisRankHasPmeGpuTask() const;
//! Return whether this rank has any task running on a GPU
bool thisRankHasAnyGpuTask() const;
+ //! Get the list of unique devices that have been assigned tasks on this physical node
+ std::vector<int> deviceIdsAssigned() { return deviceIdsAssigned_; }
};
} // namespace gmx
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return digits;
}
-std::vector<int> makeGpuIdsToUse(const std::vector<std::unique_ptr<DeviceInformation>>& deviceInfoList,
- const std::string& gpuIdsAvailableString)
+std::vector<int> makeListOfAvailableDevices(gmx::ArrayRef<const std::unique_ptr<DeviceInformation>> deviceInfoList,
+ const std::string& devicesSelectedByUserString)
{
- std::vector<int> gpuIdsAvailable = parseUserGpuIdString(gpuIdsAvailableString);
+ std::vector<int> devicesSelectedByUser = parseUserGpuIdString(devicesSelectedByUserString);
- if (gpuIdsAvailable.empty())
+ if (devicesSelectedByUser.empty())
{
- // The user didn't restrict the choice, so we use all compatible GPUs
+ // The user didn't restrict the choice, so we use all compatible devices.
return getCompatibleDeviceIds(deviceInfoList);
}
- std::vector<int> gpuIdsToUse;
- gpuIdsToUse.reserve(gpuIdsAvailable.size());
- std::vector<int> availableGpuIdsThatAreIncompatible;
- for (const int& availableGpuId : gpuIdsAvailable)
+ std::vector<int> availableDevices;
+ availableDevices.reserve(devicesSelectedByUser.size());
+ std::vector<int> incompatibleDevicesSelectedByUser;
+ for (const int& selectedDeviceId : devicesSelectedByUser)
{
- if (deviceIdIsCompatible(deviceInfoList, availableGpuId))
+ if (deviceIdIsCompatible(deviceInfoList, selectedDeviceId))
{
- gpuIdsToUse.push_back(availableGpuId);
+ availableDevices.push_back(selectedDeviceId);
}
else
{
- // Prepare data for an error message about all incompatible available GPU IDs.
- availableGpuIdsThatAreIncompatible.push_back(availableGpuId);
+ // Prepare data for an error message about all incompatible devices that were selected by the user.
+ incompatibleDevicesSelectedByUser.push_back(selectedDeviceId);
}
}
- if (!availableGpuIdsThatAreIncompatible.empty())
+ if (!incompatibleDevicesSelectedByUser.empty())
{
- auto message = "You requested mdrun to use GPUs with IDs " + gpuIdsAvailableString
- + ", but that includes the following incompatible GPUs: "
- + formatAndJoin(availableGpuIdsThatAreIncompatible, ",", StringFormatter("%d"))
- + ". Request only compatible GPUs.";
+ auto message = "You requested mdrun to use GPU devices with IDs " + devicesSelectedByUserString
+ + ", but that includes the following incompatible devices: "
+ + formatAndJoin(incompatibleDevicesSelectedByUser, ",", StringFormatter("%d"))
+ + ". Request only compatible devices.";
GMX_THROW(InvalidInputError(message));
}
- return gpuIdsToUse;
+ return availableDevices;
}
std::vector<int> parseUserTaskAssignmentString(const std::string& gpuIdString)
return formatAndJoin(resultGpuIds, ",", StringFormatter("%d"));
}
-void checkUserGpuIds(const std::vector<std::unique_ptr<DeviceInformation>>& deviceInfoList,
- const std::vector<int>& compatibleGpus,
- const std::vector<int>& gpuIds)
+void checkUserGpuIds(const ArrayRef<const std::unique_ptr<DeviceInformation>> deviceInfoList,
+ const ArrayRef<const int> compatibleGpus,
+ const ArrayRef<const int> gpuIds)
{
bool foundIncompatibleGpuIds = false;
std::string message =
if (std::find(compatibleGpus.begin(), compatibleGpus.end(), gpuId) == compatibleGpus.end())
{
foundIncompatibleGpuIds = true;
- message += gmx::formatString(" GPU #%d: %s\n", gpuId,
+ message += gmx::formatString(" GPU #%d: %s\n",
+ gpuId,
getDeviceCompatibilityDescription(deviceInfoList, gpuId).c_str());
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* all compatible GPUs on this physical node. Otherwise, check the
* user specified compatible GPUs and return their IDs.
*
- * \param[in] deviceInfoList Information on the GPUs on this physical node.
- * \param[in] gpuIdsAvailableString String like "013" or "0,1,3" typically
- * supplied by the user to mdrun -gpu_id.
- * Must contain only unique decimal digits, or only decimal
- * digits separated by comma delimiters. A terminal
- * comma is accceptable (and required to specify a
- * single ID that is larger than 9).
+ * \param[in] deviceInfoList Information on the GPUs on this physical node.
+ * \param[in] devicesSelectedByUserString String like "013" or "0,1,3" typically
+ * supplied by the user to mdrun -gpu_id.
+ * Must contain only unique decimal digits, or only decimal
+ * digits separated by comma delimiters. A terminal
+ * comma is accceptable (and required to specify a
+ * single ID that is larger than 9).
*
* \returns A vector of unique compatible GPU IDs on this physical node.
*
* \throws std::bad_alloc If out of memory.
* InvalidInputError If an invalid character is found (ie not a digit or ',') or if
* identifiers are duplicated in the specifier list.
- * InvalidInputError If gpuIdsAvailableString specifies GPU IDs that are
+ * InvalidInputError If devicesSelectedByUserString specifies IDs of the devices that are
* not compatible.
*/
-std::vector<int> makeGpuIdsToUse(const std::vector<std::unique_ptr<DeviceInformation>>& deviceInfoList,
- const std::string& gpuIdsAvailableString);
+std::vector<int> makeListOfAvailableDevices(gmx::ArrayRef<const std::unique_ptr<DeviceInformation>> deviceInfoList,
+ const std::string& devicesSelectedByUserString);
/*! \brief Parse a GPU ID specifier string into a container describing device ID to task mapping.
*
* \throws std::bad_alloc If out of memory
* InconsistentInputError If the assigned GPUs are not valid
*/
-void checkUserGpuIds(const std::vector<std::unique_ptr<DeviceInformation>>& deviceInfoList,
- const std::vector<int>& compatibleGpus,
- const std::vector<int>& gpuIds);
+void checkUserGpuIds(ArrayRef<const std::unique_ptr<DeviceInformation>> deviceInfoList,
+ ArrayRef<const int> compatibleGpus,
+ ArrayRef<const int> gpuIds);
} // namespace gmx
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014,2015,2019, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015,2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(timing INTERFACE)
file(GLOB TIMING_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${TIMING_SOURCES} PARENT_SCOPE)
+# Source files have the following dependencies on library infrastructure.
+#target_link_libraries(timing PRIVATE
+# common
+# legacy_modules
+#)
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(timing PUBLIC
+target_include_directories(timing INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(timing PUBLIC
+target_link_libraries(timing INTERFACE
+ legacy_api
+ )
+
+# TODO: when timing is an OBJECT target
+#target_link_libraries(timing PUBLIC legacy_api)
+#target_link_libraries(timing PRIVATE common)
+
+# Module dependencies
+# timing interfaces convey transitive dependence on these modules.
+#target_link_libraries(timing PUBLIC
+target_link_libraries(timing INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(timing PRIVATE NOTHING)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(timing PRIVATE legacy_modules)
+
if (BUILD_TESTING)
-# add_subdirectory(tests)
+ add_subdirectory(tests)
endif()
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TIMING_GPU_TIMING_H
#define GMX_TIMING_GPU_TIMING_H
+#include "gromacs/utility/enumerationhelpers.h"
+
/*! \internal \brief GPU kernel time and call count. */
struct gmx_kernel_timing_data_t
{
/*! \internal \brief
* PME GPU stages timing events indices, corresponding to the string in PMEStageNames in wallcycle.cpp.
*/
-enum
+enum class PmeStage : int
{
- gtPME_SPLINE = 0,
- gtPME_SPREAD,
- gtPME_SPLINEANDSPREAD,
- gtPME_FFT_R2C,
- gtPME_SOLVE,
- gtPME_FFT_C2R,
- gtPME_GATHER,
- gtPME_EVENT_COUNT /* not a stage ID but a static array size */
+ Spline = 0,
+ Spread,
+ SplineAndSpread,
+ FftTransformR2C,
+ Solve,
+ FftTransformC2R,
+ Gather,
+ Count /* not a stage ID but a static array size */
};
/*! \internal \brief GPU timings for PME. */
* TODO: devise a better GPU timing data structuring.
*/
/*! \brief Array of PME GPU timing data. */
- gmx_kernel_timing_data_t timing[gtPME_EVENT_COUNT];
+ gmx::EnumerationArray<PmeStage, gmx_kernel_timing_data_t> timing;
};
/*! \internal \brief GPU NB timings for kernels and H2d/D2H transfers. */
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-# the name of the target operating system
-set(CMAKE_SYSTEM_NAME Linux CACHE STRING "Cross-compiling for Fujitsu Sparc64, with MPI")
-set(CMAKE_SYSTEM_PROCESSOR "s64fx")
-
-set_property(GLOBAL PROPERTY TARGET_SUPPORTS_SHARED_LIBS FALSE)
-
-# set the compiler
-set(CMAKE_C_COMPILER mpifccpx)
-set(CMAKE_CXX_COMPILER mpiFCCpx)
-
-# Prevent CMake from adding GNU-specific linker flags (-rdynamic)
-set(CMAKE_C_COMPILER_ID "Fujitsu" CACHE STRING "Fujitsu C cross-compiler" FORCE)
-set(CMAKE_CXX_COMPILER_ID "Fujitsu" CACHE STRING "Fujitsu C++ cross-compiler" FORCE)
-
-# FindOpenMP.cmake does not try -Kopenmp,but the package will try specific
-# flags based on the compier ID.
-set(OMP_FLAG_Fujitsu "-Kopenmp")
+gmx_add_unit_test(GmxTimingTests timing-test
+ CPP_SOURCE_FILES
+ timing.cpp
+ )
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * This implements tests for timing function wrappers and decorators
+ *
+ * \author Sebastian Keller <keller@cscs.ch>
+ */
+
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include <chrono>
+#include <memory>
+#include <thread>
+
+#include "gromacs/timing/cyclecounter.h"
+#include "gromacs/timing/wallcycle.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+
+constexpr bool useCycleSubcounters = GMX_CYCLE_SUBCOUNTERS;
+
+//! Test function
+void sleepForMilliseconds(int msecs)
+{
+ std::this_thread::sleep_for(std::chrono::milliseconds(msecs));
+}
+
+//! Test Fixture for timing tests
+class TimingTest : public ::testing::Test
+{
+public:
+ TimingTest() : wcycle(wallcycle_init(nullptr, 0, nullptr)) {}
+
+protected:
+ const int delayInMilliseconds = 1;
+ std::unique_ptr<gmx_wallcycle> wcycle;
+};
+
+
+//! Test whether the we can run the cycle counter.
+TEST_F(TimingTest, RunWallCycle)
+{
+ WallCycleCounter probe = WallCycleCounter::Run, ref = WallCycleCounter::Step;
+ int n1, n2;
+ double c1, c2;
+
+ //! credit cycles from enclosing call to the ref field of wcycle
+ wallcycle_start(wcycle.get(), ref);
+ //! cycles from the probe call
+ wallcycle_start(wcycle.get(), probe);
+ sleepForMilliseconds(delayInMilliseconds);
+ wallcycle_stop(wcycle.get(), probe);
+ wallcycle_stop(wcycle.get(), ref);
+ //! extract both
+ wallcycle_get(wcycle.get(), probe, &n1, &c1);
+ wallcycle_get(wcycle.get(), ref, &n2, &c2);
+
+ EXPECT_EQ(n1, n2);
+ EXPECT_DOUBLE_EQ_TOL(c1, c2, relativeToleranceAsFloatingPoint(c1, 5e-3));
+ EXPECT_GE(c2, c1);
+}
+
+//! Test whether the subcyclecounter runs
+TEST_F(TimingTest, RunWallCycleSub)
+{
+ if (useCycleSubcounters)
+ {
+ WallCycleSubCounter probe = WallCycleSubCounter::DDRedist;
+ WallCycleSubCounter ref = WallCycleSubCounter::DDGrid;
+ int n1, n2;
+ double c1, c2;
+ wallcycle_sub_start(wcycle.get(), ref);
+ wallcycle_sub_start(wcycle.get(), probe);
+ sleepForMilliseconds(delayInMilliseconds);
+ wallcycle_sub_stop(wcycle.get(), probe);
+ wallcycle_sub_stop(wcycle.get(), ref);
+ wallcycle_sub_get(wcycle.get(), probe, &n1, &c1);
+ wallcycle_sub_get(wcycle.get(), ref, &n2, &c2);
+
+ EXPECT_EQ(n1, n2);
+ EXPECT_DOUBLE_EQ_TOL(c1, c2, relativeToleranceAsFloatingPoint(c1, 5e-3));
+ EXPECT_GE(c2, c1);
+ }
+}
+
+} // namespace
+} // namespace test
+} // namespace gmx
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdlib>
#include <array>
+#include <memory>
#include <vector>
#include "gromacs/math/functions.h"
#include "gromacs/timing/cyclecounter.h"
#include "gromacs/timing/gpu_timing.h"
#include "gromacs/timing/wallcyclereporting.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/snprintf.h"
+#include "gromacs/utility/stringutil.h"
-static const bool useCycleSubcounters = GMX_CYCLE_SUBCOUNTERS;
-
-#ifndef DEBUG_WCYCLE
-/*! \brief Enables consistency checking for the counters.
- *
- * If the macro is set to 1, code checks if you stop a counter different from the last
- * one that was opened and if you do nest too deep.
- */
-# define DEBUG_WCYCLE 0
-#endif
//! Whether wallcycle debugging is enabled
constexpr bool gmx_unused enableWallcycleDebug = (DEBUG_WCYCLE != 0);
//! True if only the master rank should print debugging output
# include "gromacs/utility/fatalerror.h"
#endif
-typedef struct
+/* Each name should not exceed 19 printing characters
+ (ie. terminating null can be twentieth) */
+static const char* enumValuetoString(WallCycleCounter enumValue)
{
- int n;
- gmx_cycles_t c;
- gmx_cycles_t start;
-} wallcc_t;
+ constexpr gmx::EnumerationArray<WallCycleCounter, const char*> wallCycleCounterNames = {
+ "Run",
+ "Step",
+ "PP during PME",
+ "Domain decomp.",
+ "DD comm. load",
+ "DD comm. bounds",
+ "Vsite constr.",
+ "Send X to PME",
+ "Neighbor search",
+ "Launch GPU ops.",
+ "Comm. coord.",
+ "Force",
+ "Wait + Comm. F",
+ "PME mesh",
+ "PME redist. X/F",
+ "PME spread",
+ "PME gather",
+ "PME 3D-FFT",
+ "PME 3D-FFT Comm.",
+ "PME solve LJ",
+ "PME solve Elec",
+ "PME wait for PP",
+ "Wait + Recv. PME F",
+ "Wait PME GPU spread",
+ "PME 3D-FFT",
+ "PME solve", /* the strings for FFT/solve are repeated here for mixed mode counters */
+ "Wait PME GPU gather",
+ "Wait Bonded GPU",
+ "Reduce GPU PME F",
+ "Wait GPU NB nonloc.",
+ "Wait GPU NB local",
+ "Wait GPU state copy",
+ "NB X/F buffer ops.",
+ "Vsite spread",
+ "COM pull force",
+ "AWH",
+ "Write traj.",
+ "Update",
+ "Constraints",
+ "Comm. energies",
+ "Enforced rotation",
+ "Add rot. forces",
+ "Position swapping",
+ "IMD",
+ "Test"
+ };
+ return wallCycleCounterNames[enumValue];
+}
-struct gmx_wallcycle
+static const char* enumValuetoString(WallCycleSubCounter enumValue)
{
- wallcc_t* wcc;
- /* did we detect one or more invalid cycle counts */
- gmx_bool haveInvalidCount;
- /* variables for testing/debugging */
- gmx_bool wc_barrier;
- wallcc_t* wcc_all;
- int wc_depth;
-#if DEBUG_WCYCLE
-# define DEPTH_MAX 6
- int counterlist[DEPTH_MAX];
- int count_depth;
- bool isMasterRank;
-#endif
- int ewc_prev;
- gmx_cycles_t cycle_prev;
- int64_t reset_counters;
-#if GMX_MPI
- MPI_Comm mpi_comm_mygroup;
-#endif
- wallcc_t* wcsc;
-};
-
-/* Each name should not exceed 19 printing characters
- (ie. terminating null can be twentieth) */
-static const char* wcn[ewcNR] = { "Run",
- "Step",
- "PP during PME",
- "Domain decomp.",
- "DD comm. load",
- "DD comm. bounds",
- "Vsite constr.",
- "Send X to PME",
- "Neighbor search",
- "Launch GPU ops.",
- "Comm. coord.",
- "Force",
- "Wait + Comm. F",
- "PME mesh",
- "PME redist. X/F",
- "PME spread",
- "PME gather",
- "PME 3D-FFT",
- "PME 3D-FFT Comm.",
- "PME solve LJ",
- "PME solve Elec",
- "PME wait for PP",
- "Wait + Recv. PME F",
- "Wait PME GPU spread",
- "PME 3D-FFT",
- "PME solve", /* the strings for FFT/solve are repeated here for mixed mode counters */
- "Wait PME GPU gather",
- "Wait Bonded GPU",
- "Reduce GPU PME F",
- "Wait GPU NB nonloc.",
- "Wait GPU NB local",
- "Wait GPU state copy",
- "NB X/F buffer ops.",
- "Vsite spread",
- "COM pull force",
- "AWH",
- "Write traj.",
- "Update",
- "Constraints",
- "Comm. energies",
- "Enforced rotation",
- "Add rot. forces",
- "Position swapping",
- "IMD",
- "Test" };
-
-static const char* wcsn[ewcsNR] = {
- "DD redist.",
- "DD NS grid + sort",
- "DD setup comm.",
- "DD make top.",
- "DD make constr.",
- "DD top. other",
- "DD GPU ops.",
- "NS grid local",
- "NS grid non-loc.",
- "NS search local",
- "NS search non-loc.",
- "Bonded F",
- "Bonded-FEP F",
- "Restraints F",
- "Listed buffer ops.",
- "Nonbonded pruning",
- "Nonbonded F kernel",
- "Nonbonded F clear",
- "Nonbonded FEP",
- "Launch NB GPU tasks",
- "Launch Bonded GPU tasks",
- "Launch PME GPU tasks",
- "Launch state copy",
- "Ewald F correction",
- "NB X buffer ops.",
- "NB F buffer ops.",
- "Clear force buffer",
- "Launch GPU NB X buffer ops.",
- "Launch GPU NB F buffer ops.",
- "Launch GPU Comm. coord.",
- "Launch GPU Comm. force.",
- "Launch GPU update",
- "Test subcounter",
-};
+ constexpr gmx::EnumerationArray<WallCycleSubCounter, const char*> wallCycleSubCounterNames = {
+ "DD redist.",
+ "DD NS grid + sort",
+ "DD setup comm.",
+ "DD make top.",
+ "DD make constr.",
+ "DD top. other",
+ "DD GPU ops.",
+ "NS grid local",
+ "NS grid non-loc.",
+ "NS search local",
+ "NS search non-loc.",
+ "Bonded F",
+ "Bonded-FEP F",
+ "Restraints F",
+ "Listed buffer ops.",
+ "Nonbonded pruning",
+ "Nonbonded F kernel",
+ "Nonbonded F clear",
+ "Nonbonded FEP",
+ "Launch NB GPU tasks",
+ "Launch Bonded GPU tasks",
+ "Launch PME GPU tasks",
+ "Launch state copy",
+ "Ewald F correction",
+ "NB X buffer ops.",
+ "NB F buffer ops.",
+ "Clear force buffer",
+ "Launch GPU NB X buffer ops.",
+ "Launch GPU NB F buffer ops.",
+ "Launch GPU Comm. coord.",
+ "Launch GPU Comm. force.",
+ "Launch GPU update",
+ "Test subcounter"
+ };
+ return wallCycleSubCounterNames[enumValue];
+}
/* PME GPU timing events' names - correspond to the enum in the gpu_timing.h */
-static const char* PMEStageNames[] = {
- "PME spline", "PME spread", "PME spline + spread", "PME 3D-FFT r2c",
- "PME solve", "PME 3D-FFT c2r", "PME gather",
+static const char* enumValuetoString(PmeStage enumValue)
+{
+ constexpr gmx::EnumerationArray<PmeStage, const char*> pmeStageNames = {
+ "PME spline", "PME spread", "PME spline + spread", "PME 3D-FFT r2c",
+ "PME solve", "PME 3D-FFT c2r", "PME gather"
+ };
+ return pmeStageNames[enumValue];
};
-gmx_bool wallcycle_have_counter()
+bool wallcycle_have_counter()
{
return gmx_cycles_have_counter();
}
-gmx_wallcycle_t wallcycle_init(FILE* fplog, int resetstep, t_commrec gmx_unused* cr)
+std::unique_ptr<gmx_wallcycle> wallcycle_init(FILE* fplog, int resetstep, const t_commrec* cr)
{
- gmx_wallcycle_t wc;
+ std::unique_ptr<gmx_wallcycle> wc;
if (!wallcycle_have_counter())
{
- return nullptr;
+ return wc;
}
- snew(wc, 1);
+ wc = std::make_unique<gmx_wallcycle>();
- wc->haveInvalidCount = FALSE;
- wc->wc_barrier = FALSE;
- wc->wcc_all = nullptr;
+ wc->haveInvalidCount = false;
+ wc->wc_barrier = false;
wc->wc_depth = 0;
- wc->ewc_prev = -1;
+ wc->ewc_prev = WallCycleCounter::Count;
wc->reset_counters = resetstep;
+ wc->cr = cr;
#if GMX_MPI
- if (PAR(cr) && getenv("GMX_CYCLE_BARRIER") != nullptr)
+ if (cr != nullptr && PAR(cr) && getenv("GMX_CYCLE_BARRIER") != nullptr)
{
if (fplog)
{
fprintf(fplog, "\nWill call MPI_Barrier before each cycle start/stop call\n\n");
}
- wc->wc_barrier = TRUE;
- wc->mpi_comm_mygroup = cr->mpi_comm_mygroup;
+ wc->wc_barrier = true;
}
#endif
- snew(wc->wcc, ewcNR);
if (getenv("GMX_CYCLE_ALL") != nullptr)
{
if (fplog)
{
fprintf(fplog, "\nWill time all the code during the run\n\n");
}
- snew(wc->wcc_all, ewcNR * ewcNR);
- }
-
- if (useCycleSubcounters)
- {
- snew(wc->wcsc, ewcsNR);
+ wc->wcc_all.resize(sc_numWallCycleCountersSquared);
}
#if DEBUG_WCYCLE
return wc;
}
-void wallcycle_destroy(gmx_wallcycle_t wc)
-{
- if (wc == nullptr)
- {
- return;
- }
-
- if (wc->wcc != nullptr)
- {
- sfree(wc->wcc);
- }
- if (wc->wcc_all != nullptr)
- {
- sfree(wc->wcc_all);
- }
- if (wc->wcsc != nullptr)
- {
- sfree(wc->wcsc);
- }
- sfree(wc);
-}
-
-static void wallcycle_all_start(gmx_wallcycle_t wc, int ewc, gmx_cycles_t cycle)
-{
- wc->ewc_prev = ewc;
- wc->cycle_prev = cycle;
-}
-
-static void wallcycle_all_stop(gmx_wallcycle_t wc, int ewc, gmx_cycles_t cycle)
-{
- wc->wcc_all[wc->ewc_prev * ewcNR + ewc].n += 1;
- wc->wcc_all[wc->ewc_prev * ewcNR + ewc].c += cycle - wc->cycle_prev;
-}
-
-
#if DEBUG_WCYCLE
-static void debug_start_check(gmx_wallcycle_t wc, int ewc)
+static void debug_start_check(gmx_wallcycle* wc, WallCycleCounter ewc)
{
- if (wc->count_depth < 0 || wc->count_depth >= DEPTH_MAX)
+ if (wc->count_depth < 0 || wc->count_depth >= c_MaxWallCycleDepth)
{
gmx_fatal(FARGS, "wallcycle counter depth out of range: %d", wc->count_depth + 1);
}
if (debugPrintDepth && (!onlyMasterDebugPrints || wc->isMasterRank))
{
std::string indentStr(4 * wc->count_depth, ' ');
- fprintf(stderr, "%swcycle_start depth %d, %s\n", indentStr.c_str(), wc->count_depth, wcn[ewc]);
+ fprintf(stderr, "%swcycle_start depth %d, %s\n", indentStr.c_str(), wc->count_depth, enumValuetoString(ewc));
}
}
-static void debug_stop_check(gmx_wallcycle_t wc, int ewc)
+static void debug_stop_check(gmx_wallcycle* wc, WallCycleCounter ewc)
{
if (debugPrintDepth && (!onlyMasterDebugPrints || wc->isMasterRank))
{
std::string indentStr(4 * wc->count_depth, ' ');
- fprintf(stderr, "%swcycle_stop depth %d, %s\n", indentStr.c_str(), wc->count_depth, wcn[ewc]);
+ fprintf(stderr, "%swcycle_stop depth %d, %s\n", indentStr.c_str(), wc->count_depth, enumValuetoString(ewc));
}
wc->count_depth--;
if (wc->count_depth < 0)
{
- gmx_fatal(FARGS, "wallcycle counter depth out of range when stopping %s: %d", wcn[ewc],
+ gmx_fatal(FARGS,
+ "wallcycle counter depth out of range when stopping %s: %d",
+ enumValuetoString(ewc),
wc->count_depth);
}
if (wc->counterlist[wc->count_depth] != ewc)
{
- gmx_fatal(FARGS, "wallcycle mismatch at stop, start %s, stop %s",
- wcn[wc->counterlist[wc->count_depth]], wcn[ewc]);
+ gmx_fatal(FARGS,
+ "wallcycle mismatch at stop, start %s, stop %s",
+ enumValuetoString(wc->counterlist[wc->count_depth]),
+ enumValuetoString(ewc));
}
}
#endif
-void wallcycle_start(gmx_wallcycle_t wc, int ewc)
+void wallcycle_get(gmx_wallcycle* wc, WallCycleCounter ewc, int* n, double* c)
{
- gmx_cycles_t cycle;
-
- if (wc == nullptr)
- {
- return;
- }
-
-#if GMX_MPI
- if (wc->wc_barrier)
- {
- MPI_Barrier(wc->mpi_comm_mygroup);
- }
-#endif
-
-#if DEBUG_WCYCLE
- debug_start_check(wc, ewc);
-#endif
-
- cycle = gmx_cycles_read();
- wc->wcc[ewc].start = cycle;
- if (wc->wcc_all != nullptr)
- {
- wc->wc_depth++;
- if (ewc == ewcRUN)
- {
- wallcycle_all_start(wc, ewc, cycle);
- }
- else if (wc->wc_depth == 3)
- {
- wallcycle_all_stop(wc, ewc, cycle);
- }
- }
-}
-
-void wallcycle_increment_event_count(gmx_wallcycle_t wc, int ewc)
-{
- if (wc == nullptr)
- {
- return;
- }
- wc->wcc[ewc].n++;
-}
-
-void wallcycle_start_nocount(gmx_wallcycle_t wc, int ewc)
-{
- if (wc == nullptr)
- {
- return;
- }
-
- wallcycle_start(wc, ewc);
- wc->wcc[ewc].n--;
+ *n = wc->wcc[ewc].n;
+ *c = static_cast<double>(wc->wcc[ewc].c);
}
-double wallcycle_stop(gmx_wallcycle_t wc, int ewc)
+void wallcycle_sub_get(gmx_wallcycle* wc, WallCycleSubCounter ewcs, int* n, double* c)
{
- gmx_cycles_t cycle, last;
-
- if (wc == nullptr)
+ if (sc_useCycleSubcounters && wc != nullptr)
{
- return 0;
+ *n = wc->wcsc[ewcs].n;
+ *c = static_cast<double>(wc->wcsc[ewcs].c);
}
-
-#if GMX_MPI
- if (wc->wc_barrier)
- {
- MPI_Barrier(wc->mpi_comm_mygroup);
- }
-#endif
-
-#if DEBUG_WCYCLE
- debug_stop_check(wc, ewc);
-#endif
-
- /* When processes or threads migrate between cores, the cycle counting
- * can get messed up if the cycle counter on different cores are not
- * synchronized. When this happens we expect both large negative and
- * positive cycle differences. We can detect negative cycle differences.
- * Detecting too large positive counts if difficult, since count can be
- * large, especially for ewcRUN. If we detect a negative count,
- * we will not print the cycle accounting table.
- */
- cycle = gmx_cycles_read();
- if (cycle >= wc->wcc[ewc].start)
- {
- last = cycle - wc->wcc[ewc].start;
- }
- else
- {
- last = 0;
- wc->haveInvalidCount = TRUE;
- }
- wc->wcc[ewc].c += last;
- wc->wcc[ewc].n++;
- if (wc->wcc_all)
- {
- wc->wc_depth--;
- if (ewc == ewcRUN)
- {
- wallcycle_all_stop(wc, ewc, cycle);
- }
- else if (wc->wc_depth == 2)
- {
- wallcycle_all_start(wc, ewc, cycle);
- }
- }
-
- return last;
}
-void wallcycle_get(gmx_wallcycle_t wc, int ewc, int* n, double* c)
+void wallcycle_reset_all(gmx_wallcycle* wc)
{
- *n = wc->wcc[ewc].n;
- *c = static_cast<double>(wc->wcc[ewc].c);
-}
-
-void wallcycle_reset_all(gmx_wallcycle_t wc)
-{
- int i;
-
if (wc == nullptr)
{
return;
}
- for (i = 0; i < ewcNR; i++)
+ for (auto& counter : wc->wcc)
{
- wc->wcc[i].n = 0;
- wc->wcc[i].c = 0;
+ counter.n = 0;
+ counter.c = 0;
}
- wc->haveInvalidCount = FALSE;
+ wc->haveInvalidCount = false;
- if (wc->wcc_all)
+ if (!wc->wcc_all.empty())
{
- for (i = 0; i < ewcNR * ewcNR; i++)
+ for (int i = 0; i < sc_numWallCycleCountersSquared; i++)
{
wc->wcc_all[i].n = 0;
wc->wcc_all[i].c = 0;
}
}
- if (wc->wcsc)
+ for (auto& counter : wc->wcsc)
{
- for (i = 0; i < ewcsNR; i++)
- {
- wc->wcsc[i].n = 0;
- wc->wcsc[i].c = 0;
- }
+ counter.n = 0;
+ counter.c = 0;
}
}
-static gmx_bool is_pme_counter(int ewc)
+static bool is_pme_counter(WallCycleCounter ewc)
{
- return (ewc >= ewcPMEMESH && ewc <= ewcPMEWAITCOMM);
+ return (ewc >= WallCycleCounter::PmeMesh && ewc <= WallCycleCounter::PmeWaitComm);
}
-static gmx_bool is_pme_subcounter(int ewc)
+static bool is_pme_subcounter(WallCycleCounter ewc)
{
- return (ewc >= ewcPME_REDISTXF && ewc < ewcPMEWAITCOMM);
+ return (ewc >= WallCycleCounter::PmeRedistXF && ewc < WallCycleCounter::PmeWaitComm);
+}
+
+void wallcycleBarrier(gmx_wallcycle* wc)
+{
+#if GMX_MPI
+ if (wc->wc_barrier)
+ {
+ MPI_Barrier(wc->cr->mpi_comm_mygroup);
+ }
+#else
+ GMX_UNUSED_VALUE(wc);
+#endif
}
/* Subtract counter ewc_sub timed inside a timing block for ewc_main */
-static void subtract_cycles(wallcc_t* wcc, int ewc_main, int ewc_sub)
+// NOLINTNEXTLINE(google-runtime-references)
+static void subtract_cycles(gmx::EnumerationArray<WallCycleCounter, wallcc_t>& wcc,
+ WallCycleCounter ewc_main,
+ WallCycleCounter ewc_sub)
{
if (wcc[ewc_sub].n > 0)
{
}
}
-void wallcycle_scale_by_num_threads(gmx_wallcycle_t wc, bool isPmeRank, int nthreads_pp, int nthreads_pme)
+void wallcycle_scale_by_num_threads(gmx_wallcycle* wc, bool isPmeRank, int nthreads_pp, int nthreads_pme)
{
if (wc == nullptr)
{
return;
}
- for (int i = 0; i < ewcNR; i++)
+ for (auto key : keysOf(wc->wcc))
{
- if (is_pme_counter(i) || (i == ewcRUN && isPmeRank))
+ if (is_pme_counter(key) || (key == WallCycleCounter::Run && isPmeRank))
{
- wc->wcc[i].c *= nthreads_pme;
+ wc->wcc[key].c *= nthreads_pme;
- if (wc->wcc_all)
+ if (!wc->wcc_all.empty())
{
- for (int j = 0; j < ewcNR; j++)
+ const int current = static_cast<int>(key);
+ for (int j = 0; j < sc_numWallCycleCounters; j++)
{
- wc->wcc_all[i * ewcNR + j].c *= nthreads_pme;
+ wc->wcc_all[current * sc_numWallCycleCounters + j].c *= nthreads_pme;
}
}
}
else
{
- wc->wcc[i].c *= nthreads_pp;
+ wc->wcc[key].c *= nthreads_pp;
- if (wc->wcc_all)
+ if (!wc->wcc_all.empty())
{
- for (int j = 0; j < ewcNR; j++)
+ const int current = static_cast<int>(key);
+ for (int j = 0; j < sc_numWallCycleCounters; j++)
{
- wc->wcc_all[i * ewcNR + j].c *= nthreads_pp;
+ wc->wcc_all[current * sc_numWallCycleCounters + j].c *= nthreads_pp;
}
}
}
}
- if (useCycleSubcounters && wc->wcsc && !isPmeRank)
+ if (sc_useCycleSubcounters && !isPmeRank)
{
- for (int i = 0; i < ewcsNR; i++)
+ for (auto counter : wc->wcsc)
{
- wc->wcsc[i].c *= nthreads_pp;
+ counter.c *= nthreads_pp;
}
}
}
* wcc_all are unused by the GPU reporting, but it is not satisfactory
* for the future. Also, there's no need for MPI_Allreduce, since
* only MASTERRANK uses any of the results. */
-WallcycleCounts wallcycle_sum(const t_commrec* cr, gmx_wallcycle_t wc)
+WallcycleCounts wallcycle_sum(const t_commrec* cr, gmx_wallcycle* wc)
{
- WallcycleCounts cycles_sum;
- wallcc_t* wcc;
- double cycles[int(ewcNR) + int(ewcsNR)];
+ WallcycleCounts cycles_sum;
+ gmx::EnumerationArray<WallCycleCounter, double> cyclesMain;
+ gmx::EnumerationArray<WallCycleSubCounter, double> cyclesSub;
#if GMX_MPI
- double cycles_n[int(ewcNR) + int(ewcsNR) + 1];
+ gmx::EnumerationArray<WallCycleCounter, double> cyclesMainOnNode;
+ gmx::EnumerationArray<WallCycleSubCounter, double> cyclesSubOnNode;
#endif
- int i;
- int nsum;
if (wc == nullptr)
{
/* Default construction of std::array of non-class T can leave
- the values indeterminate, just like a C array, and icc
- warns about it. */
+ the values indeterminate, just like a C array */
cycles_sum.fill(0);
return cycles_sum;
}
- wcc = wc->wcc;
+ auto& wcc = wc->wcc;
- subtract_cycles(wcc, ewcDOMDEC, ewcDDCOMMLOAD);
- subtract_cycles(wcc, ewcDOMDEC, ewcDDCOMMBOUND);
+ subtract_cycles(wcc, WallCycleCounter::Domdec, WallCycleCounter::DDCommLoad);
+ subtract_cycles(wcc, WallCycleCounter::Domdec, WallCycleCounter::DDCommBound);
- subtract_cycles(wcc, ewcPME_FFT, ewcPME_FFTCOMM);
+ subtract_cycles(wcc, WallCycleCounter::PmeFft, WallCycleCounter::PmeFftComm);
if (cr->npmenodes == 0)
{
/* All nodes do PME (or no PME at all) */
- subtract_cycles(wcc, ewcFORCE, ewcPMEMESH);
+ subtract_cycles(wcc, WallCycleCounter::Force, WallCycleCounter::PmeMesh);
}
else
{
/* The are PME-only nodes */
- if (wcc[ewcPMEMESH].n > 0)
+ if (wcc[WallCycleCounter::PmeMesh].n > 0)
{
/* This must be a PME only node, calculate the Wait + Comm. time */
- GMX_ASSERT(wcc[ewcRUN].c >= wcc[ewcPMEMESH].c,
+ GMX_ASSERT(wcc[WallCycleCounter::Run].c >= wcc[WallCycleCounter::PmeMesh].c,
"Total run ticks must be greater than PME-only ticks");
- wcc[ewcPMEWAITCOMM].c = wcc[ewcRUN].c - wcc[ewcPMEMESH].c;
+ wcc[WallCycleCounter::PmeWaitComm].c =
+ wcc[WallCycleCounter::Run].c - wcc[WallCycleCounter::PmeMesh].c;
}
}
/* Store the cycles in a double buffer for summing */
- for (i = 0; i < ewcNR; i++)
+ for (auto key : keysOf(wcc))
{
#if GMX_MPI
- cycles_n[i] = static_cast<double>(wcc[i].n);
+ cyclesMainOnNode[key] = static_cast<double>(wcc[key].n);
#endif
- cycles[i] = static_cast<double>(wcc[i].c);
+ cyclesMain[key] = static_cast<double>(wcc[key].c);
}
- nsum = ewcNR;
- if (wc->wcsc)
+ if (sc_useCycleSubcounters)
{
- for (i = 0; i < ewcsNR; i++)
+ for (auto key : keysOf(wc->wcsc))
{
#if GMX_MPI
- cycles_n[ewcNR + i] = static_cast<double>(wc->wcsc[i].n);
+ cyclesSubOnNode[key] = static_cast<double>(wc->wcsc[key].n);
#endif
- cycles[ewcNR + i] = static_cast<double>(wc->wcsc[i].c);
+ cyclesSub[key] = static_cast<double>(wc->wcsc[key].c);
}
- nsum += ewcsNR;
}
#if GMX_MPI
if (cr->nnodes > 1)
{
- double buf[int(ewcNR) + int(ewcsNR) + 1];
+ gmx::EnumerationArray<WallCycleCounter, double> bufMain;
+ gmx::EnumerationArray<WallCycleSubCounter, double> bufSub;
// TODO this code is used only at the end of the run, so we
// can just do a simple reduce of haveInvalidCount in
// wallcycle_print, and avoid bugs
- cycles_n[nsum] = (wc->haveInvalidCount ? 1 : 0);
+ double haveInvalidCount = (wc->haveInvalidCount ? 1 : 0);
// TODO Use MPI_Reduce
- MPI_Allreduce(cycles_n, buf, nsum + 1, MPI_DOUBLE, MPI_MAX, cr->mpi_comm_mysim);
- for (i = 0; i < ewcNR; i++)
+ MPI_Allreduce(cyclesMainOnNode.data(), bufMain.data(), bufMain.size(), MPI_DOUBLE, MPI_MAX, cr->mpi_comm_mysim);
+ if (sc_useCycleSubcounters)
{
- wcc[i].n = gmx::roundToInt(buf[i]);
+ MPI_Allreduce(cyclesSubOnNode.data(), bufSub.data(), bufSub.size(), MPI_DOUBLE, MPI_MAX, cr->mpi_comm_mysim);
}
- wc->haveInvalidCount = (buf[nsum] > 0);
- if (wc->wcsc)
+ MPI_Allreduce(MPI_IN_PLACE, &haveInvalidCount, 1, MPI_DOUBLE, MPI_MAX, cr->mpi_comm_mysim);
+ for (auto key : keysOf(wcc))
{
- for (i = 0; i < ewcsNR; i++)
+ wcc[key].n = gmx::roundToInt(bufMain[key]);
+ }
+ wc->haveInvalidCount = (haveInvalidCount > 0);
+ if (sc_useCycleSubcounters)
+ {
+ for (auto key : keysOf(wc->wcsc))
{
- wc->wcsc[i].n = gmx::roundToInt(buf[ewcNR + i]);
+ wc->wcsc[key].n = gmx::roundToInt(bufSub[key]);
}
}
// TODO Use MPI_Reduce
- MPI_Allreduce(cycles, cycles_sum.data(), nsum, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
+ MPI_Allreduce(cyclesMain.data(), cycles_sum.data(), cyclesMain.size(), MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
+ if (sc_useCycleSubcounters)
+ {
+ MPI_Allreduce(cyclesSub.data(),
+ cycles_sum.data() + sc_numWallCycleCounters,
+ cyclesSub.size(),
+ MPI_DOUBLE,
+ MPI_SUM,
+ cr->mpi_comm_mysim);
+ }
- if (wc->wcc_all != nullptr)
+ if (!wc->wcc_all.empty())
{
- double *buf_all, *cyc_all;
+ std::array<double, sc_numWallCycleCountersSquared> cyc_all;
+ std::array<double, sc_numWallCycleCountersSquared> buf_all;
- snew(cyc_all, ewcNR * ewcNR);
- snew(buf_all, ewcNR * ewcNR);
- for (i = 0; i < ewcNR * ewcNR; i++)
+ for (int i = 0; i < sc_numWallCycleCountersSquared; i++)
{
cyc_all[i] = wc->wcc_all[i].c;
}
// TODO Use MPI_Reduce
- MPI_Allreduce(cyc_all, buf_all, ewcNR * ewcNR, MPI_DOUBLE, MPI_SUM, cr->mpi_comm_mysim);
- for (i = 0; i < ewcNR * ewcNR; i++)
+ MPI_Allreduce(cyc_all.data(),
+ buf_all.data(),
+ sc_numWallCycleCountersSquared,
+ MPI_DOUBLE,
+ MPI_SUM,
+ cr->mpi_comm_mysim);
+ for (int i = 0; i < sc_numWallCycleCountersSquared; i++)
{
wc->wcc_all[i].c = static_cast<gmx_cycles_t>(buf_all[i]);
}
- sfree(buf_all);
- sfree(cyc_all);
}
}
else
#endif
{
- for (i = 0; i < nsum; i++)
+ for (auto key : keysOf(cyclesMain))
{
- cycles_sum[i] = cycles[i];
+ cycles_sum[static_cast<int>(key)] = cyclesMain[key];
+ }
+ if (sc_useCycleSubcounters)
+ {
+ for (auto key : keysOf(cyclesSub))
+ {
+ const int offset = static_cast<int>(key) + sc_numWallCycleCounters;
+ cycles_sum[offset] = cyclesSub[key];
+ }
}
}
/* Convert the cycle count to wallclock time for this task */
wallt = c_sum * c2t;
- fprintf(fplog, " %-19.19s %4s %4s %10s %10.3f %14.3f %5.1f\n", name, nnodes_str,
- nthreads_str, ncalls_str, wallt, c_sum * 1e-9, percentage);
+ fprintf(fplog,
+ " %-19.19s %4s %4s %10s %10.3f %14.3f %5.1f\n",
+ name,
+ nnodes_str,
+ nthreads_str,
+ ncalls_str,
+ wallt,
+ c_sum * 1e-9,
+ percentage);
}
}
int nth_pp,
int nth_pme,
double realtime,
- gmx_wallcycle_t wc,
+ gmx_wallcycle* wc,
const WallcycleCounts& cyc_sum,
const gmx_wallclock_gpu_nbnxn_t* gpu_nbnxn_t,
const gmx_wallclock_gpu_pme_t* gpu_pme_t)
{
double tot, tot_for_pp, tot_for_rest, tot_cpu_overlap, gpu_cpu_ratio;
double c2t, c2t_pp, c2t_pme = 0;
- int i, j, npp, nth_tot;
+ int npp, nth_tot;
char buf[STRLEN];
const char* hline =
"-----------------------------------------------------------------------------";
/* When using PME-only nodes, the next line is valid for both
PP-only and PME-only nodes because they started ewcRUN at the
same time. */
- tot = cyc_sum[ewcRUN];
+ tot = cyc_sum[static_cast<int>(WallCycleCounter::Run)];
tot_for_pp = 0;
if (tot <= 0.0)
print_header(fplog, npp, nth_pp, npme, nth_pme);
fprintf(fplog, "%s\n", hline);
- for (i = ewcPPDURINGPME + 1; i < ewcNR; i++)
+ gmx::EnumerationWrapper<WallCycleCounter> iter;
+ for (auto key = gmx::EnumerationIterator<WallCycleCounter>(WallCycleCounter::Domdec);
+ key != iter.end();
+ ++key)
{
- if (is_pme_subcounter(i))
+
+ if (is_pme_subcounter(*key))
{
/* Do not count these at all */
}
- else if (npme > 0 && is_pme_counter(i))
+ else if (npme > 0 && is_pme_counter(*key))
{
/* Print timing information for PME-only nodes, but add an
* asterisk so the reader of the table can know that the
* walltimes are not meant to add up. The asterisk still
* fits in the required maximum of 19 characters. */
- char buffer[STRLEN];
- snprintf(buffer, STRLEN, "%s *", wcn[i]);
- print_cycles(fplog, c2t_pme, buffer, npme, nth_pme, wc->wcc[i].n, cyc_sum[i], tot);
+ std::string message = gmx::formatString("%s *", enumValuetoString(*key));
+ print_cycles(fplog,
+ c2t_pme,
+ message.c_str(),
+ npme,
+ nth_pme,
+ wc->wcc[*key].n,
+ cyc_sum[static_cast<int>(*key)],
+ tot);
}
else
{
/* Print timing information when it is for a PP or PP+PME
node */
- print_cycles(fplog, c2t_pp, wcn[i], npp, nth_pp, wc->wcc[i].n, cyc_sum[i], tot);
- tot_for_pp += cyc_sum[i];
+ print_cycles(fplog,
+ c2t_pp,
+ enumValuetoString(*key),
+ npp,
+ nth_pp,
+ wc->wcc[*key].n,
+ cyc_sum[static_cast<int>(*key)],
+ tot);
+ tot_for_pp += cyc_sum[static_cast<int>(*key)];
}
}
- if (wc->wcc_all != nullptr)
+ if (!wc->wcc_all.empty())
{
- for (i = 0; i < ewcNR; i++)
+ for (auto i : keysOf(wc->wcc))
{
- for (j = 0; j < ewcNR; j++)
+ const int countI = static_cast<int>(i);
+ for (auto j : keysOf(wc->wcc))
{
- snprintf(buf, 20, "%-9.9s %-9.9s", wcn[i], wcn[j]);
- print_cycles(fplog, c2t_pp, buf, npp, nth_pp, wc->wcc_all[i * ewcNR + j].n,
- wc->wcc_all[i * ewcNR + j].c, tot);
+ const int countJ = static_cast<int>(j);
+ snprintf(buf, 20, "%-9.9s %-9.9s", enumValuetoString(i), enumValuetoString(j));
+ print_cycles(fplog,
+ c2t_pp,
+ buf,
+ npp,
+ nth_pp,
+ wc->wcc_all[countI * sc_numWallCycleCounters + countJ].n,
+ wc->wcc_all[countI * sc_numWallCycleCounters + countJ].c,
+ tot);
}
}
}
hline);
}
- if (wc->wcc[ewcPMEMESH].n > 0)
+ if (wc->wcc[WallCycleCounter::PmeMesh].n > 0)
{
// A workaround to not print breakdown when no subcounters were recorded.
// TODO: figure out and record PME GPU counters (what to do with the waiting ones?)
- std::vector<int> validPmeSubcounterIndices;
- for (i = ewcPPDURINGPME + 1; i < ewcNR; i++)
+ std::vector<WallCycleCounter> validPmeSubcounterIndices;
+ for (auto key = gmx::EnumerationIterator<WallCycleCounter>(WallCycleCounter::Domdec);
+ key != iter.end();
+ key++)
{
- if (is_pme_subcounter(i) && wc->wcc[i].n > 0)
+ if (is_pme_subcounter(*key) && wc->wcc[*key].n > 0)
{
- validPmeSubcounterIndices.push_back(i);
+ validPmeSubcounterIndices.push_back(*key);
}
}
fprintf(fplog, "%s\n", hline);
for (auto i : validPmeSubcounterIndices)
{
- print_cycles(fplog, npme > 0 ? c2t_pme : c2t_pp, wcn[i], npme > 0 ? npme : npp,
- nth_pme, wc->wcc[i].n, cyc_sum[i], tot);
+ print_cycles(fplog,
+ npme > 0 ? c2t_pme : c2t_pp,
+ enumValuetoString(i),
+ npme > 0 ? npme : npp,
+ nth_pme,
+ wc->wcc[i].n,
+ cyc_sum[static_cast<int>(i)],
+ tot);
}
fprintf(fplog, "%s\n", hline);
}
}
- if (useCycleSubcounters && wc->wcsc)
+ if (sc_useCycleSubcounters)
{
fprintf(fplog, " Breakdown of PP computation\n");
fprintf(fplog, "%s\n", hline);
- for (i = 0; i < ewcsNR; i++)
+ for (auto key : keysOf(wc->wcsc))
{
- print_cycles(fplog, c2t_pp, wcsn[i], npp, nth_pp, wc->wcsc[i].n, cyc_sum[ewcNR + i], tot);
+ print_cycles(fplog,
+ c2t_pp,
+ enumValuetoString(key),
+ npp,
+ nth_pp,
+ wc->wcsc[key].n,
+ cyc_sum[sc_numWallCycleCounters + static_cast<int>(key)],
+ tot);
}
fprintf(fplog, "%s\n", hline);
}
double tot_gpu = 0.0;
if (gpu_pme_t)
{
- for (size_t k = 0; k < gtPME_EVENT_COUNT; k++)
+ for (auto key : keysOf(gpu_pme_t->timing))
{
- tot_gpu += gpu_pme_t->timing[k].t;
+ tot_gpu += gpu_pme_t->timing[key].t;
}
}
if (gpu_nbnxn_t)
tot_gpu += gpu_nbnxn_t->pl_h2d_t + gpu_nbnxn_t->nb_h2d_t + gpu_nbnxn_t->nb_d2h_t;
/* add up the kernel timings */
- for (i = 0; i < 2; i++)
+ for (int i = 0; i < 2; i++)
{
- for (j = 0; j < 2; j++)
+ for (int j = 0; j < 2; j++)
{
tot_gpu += gpu_nbnxn_t->ktime[i][j].t;
}
}
tot_gpu += gpu_nbnxn_t->pruneTime.t;
- tot_cpu_overlap = wc->wcc[ewcFORCE].c;
- if (wc->wcc[ewcPMEMESH].n > 0)
+ tot_cpu_overlap = wc->wcc[WallCycleCounter::Force].c;
+ if (wc->wcc[WallCycleCounter::PmeMesh].n > 0)
{
- tot_cpu_overlap += wc->wcc[ewcPMEMESH].c;
+ tot_cpu_overlap += wc->wcc[WallCycleCounter::PmeMesh].c;
}
tot_cpu_overlap *= realtime * 1000 / tot; /* convert s to ms */
fprintf(fplog, "\n GPU timings\n%s\n", hline);
fprintf(fplog,
- " Computing: Count Wall t (s) ms/step %c\n", '%');
+ " Computing: Count Wall t (s) ms/step %c\n",
+ '%');
fprintf(fplog, "%s\n", hline);
print_gputimes(fplog, "Pair list H2D", gpu_nbnxn_t->pl_h2d_c, gpu_nbnxn_t->pl_h2d_t, tot_gpu);
print_gputimes(fplog, "X / q H2D", gpu_nbnxn_t->nb_c, gpu_nbnxn_t->nb_h2d_t, tot_gpu);
- for (i = 0; i < 2; i++)
+ for (int i = 0; i < 2; i++)
{
- for (j = 0; j < 2; j++)
+ for (int j = 0; j < 2; j++)
{
if (gpu_nbnxn_t->ktime[i][j].c)
{
- print_gputimes(fplog, k_log_str[i][j], gpu_nbnxn_t->ktime[i][j].c,
- gpu_nbnxn_t->ktime[i][j].t, tot_gpu);
+ print_gputimes(fplog,
+ k_log_str[i][j],
+ gpu_nbnxn_t->ktime[i][j].c,
+ gpu_nbnxn_t->ktime[i][j].t,
+ tot_gpu);
}
}
}
if (gpu_pme_t)
{
- for (size_t k = 0; k < gtPME_EVENT_COUNT; k++)
+ for (auto key : keysOf(gpu_pme_t->timing))
{
- if (gpu_pme_t->timing[k].c)
+ if (gpu_pme_t->timing[key].c)
{
- print_gputimes(fplog, PMEStageNames[k], gpu_pme_t->timing[k].c,
- gpu_pme_t->timing[k].t, tot_gpu);
+ print_gputimes(fplog,
+ enumValuetoString(key),
+ gpu_pme_t->timing[key].c,
+ gpu_pme_t->timing[key].t,
+ tot_gpu);
}
}
}
if (gpu_nbnxn_t->pruneTime.c)
{
- print_gputimes(fplog, "Pruning kernel", gpu_nbnxn_t->pruneTime.c,
- gpu_nbnxn_t->pruneTime.t, tot_gpu);
+ print_gputimes(fplog, "Pruning kernel", gpu_nbnxn_t->pruneTime.c, gpu_nbnxn_t->pruneTime.t, tot_gpu);
}
print_gputimes(fplog, "F D2H", gpu_nbnxn_t->nb_c, gpu_nbnxn_t->nb_d2h_t, tot_gpu);
fprintf(fplog, "%s\n", hline);
* and avoid adding it to tot_gpu as this is not in the force
* overlap. We print the fraction as relative to the rest.
*/
- print_gputimes(fplog, "*Dynamic pruning", gpu_nbnxn_t->dynamicPruneTime.c,
- gpu_nbnxn_t->dynamicPruneTime.t, tot_gpu);
+ print_gputimes(fplog,
+ "*Dynamic pruning",
+ gpu_nbnxn_t->dynamicPruneTime.c,
+ gpu_nbnxn_t->dynamicPruneTime.t,
+ tot_gpu);
fprintf(fplog, "%s\n", hline);
}
gpu_cpu_ratio = tot_gpu / tot_cpu_overlap;
- if (gpu_nbnxn_t->nb_c > 0 && wc->wcc[ewcFORCE].n > 0)
+ if (gpu_nbnxn_t->nb_c > 0 && wc->wcc[WallCycleCounter::Force].n > 0)
{
fprintf(fplog,
"\nAverage per-step force GPU/CPU evaluation time ratio: %.3f ms/%.3f ms = "
"%.3f\n",
- tot_gpu / gpu_nbnxn_t->nb_c, tot_cpu_overlap / wc->wcc[ewcFORCE].n, gpu_cpu_ratio);
+ tot_gpu / gpu_nbnxn_t->nb_c,
+ tot_cpu_overlap / wc->wcc[WallCycleCounter::Force].n,
+ gpu_cpu_ratio);
}
/* only print notes related to CPU-GPU load balance with PME */
- if (wc->wcc[ewcPMEMESH].n > 0)
+ if (wc->wcc[WallCycleCounter::PmeMesh].n > 0)
{
fprintf(fplog, "For optimal resource utilization this ratio should be close to 1\n");
"call, so timings are not those of real runs.");
}
- if (wc->wcc[ewcNB_XF_BUF_OPS].n > 0 && (cyc_sum[ewcDOMDEC] > tot * 0.1 || cyc_sum[ewcNS] > tot * 0.1))
+ if (wc->wcc[WallCycleCounter::NbXFBufOps].n > 0
+ && (cyc_sum[static_cast<int>(WallCycleCounter::Domdec)] > tot * 0.1
+ || cyc_sum[static_cast<int>(WallCycleCounter::NS)] > tot * 0.1))
{
/* Only the sim master calls this function, so always print to stderr */
- if (wc->wcc[ewcDOMDEC].n == 0)
+ if (wc->wcc[WallCycleCounter::Domdec].n == 0)
{
GMX_LOG(mdlog.warning)
.asParagraph()
"NOTE: %d %% of the run time was spent in pair search,\n"
" you might want to increase nstlist (this has no effect on "
"accuracy)\n",
- gmx::roundToInt(100 * cyc_sum[ewcNS] / tot));
+ gmx::roundToInt(100 * cyc_sum[static_cast<int>(WallCycleCounter::NS)] / tot));
}
else
{
" %d %% of the run time was spent in pair search,\n"
" you might want to increase nstlist (this has no effect on "
"accuracy)\n",
- gmx::roundToInt(100 * cyc_sum[ewcDOMDEC] / tot),
- gmx::roundToInt(100 * cyc_sum[ewcNS] / tot));
+ gmx::roundToInt(100 * cyc_sum[static_cast<int>(WallCycleCounter::Domdec)] / tot),
+ gmx::roundToInt(100 * cyc_sum[static_cast<int>(WallCycleCounter::NS)] / tot));
}
}
- if (cyc_sum[ewcMoveE] > tot * 0.05)
+ if (cyc_sum[static_cast<int>(WallCycleCounter::MoveE)] > tot * 0.05)
{
GMX_LOG(mdlog.warning)
.asParagraph()
.appendTextFormatted(
"NOTE: %d %% of the run time was spent communicating energies,\n"
" you might want to increase some nst* mdp options\n",
- gmx::roundToInt(100 * cyc_sum[ewcMoveE] / tot));
+ gmx::roundToInt(100 * cyc_sum[static_cast<int>(WallCycleCounter::MoveE)] / tot));
}
}
-extern int64_t wcycle_get_reset_counters(gmx_wallcycle_t wc)
+int64_t wcycle_get_reset_counters(gmx_wallcycle* wc)
{
if (wc == nullptr)
{
return -1;
}
-
return wc->reset_counters;
}
-extern void wcycle_set_reset_counters(gmx_wallcycle_t wc, int64_t reset_counters)
+void wcycle_set_reset_counters(gmx_wallcycle* wc, int64_t reset_counters)
{
if (wc == nullptr)
{
return;
}
-
wc->reset_counters = reset_counters;
}
-
-void wallcycle_sub_start(gmx_wallcycle_t wc, int ewcs)
-{
- if (useCycleSubcounters && wc != nullptr)
- {
- wc->wcsc[ewcs].start = gmx_cycles_read();
- }
-}
-
-void wallcycle_sub_start_nocount(gmx_wallcycle_t wc, int ewcs)
-{
- if (useCycleSubcounters && wc != nullptr)
- {
- wallcycle_sub_start(wc, ewcs);
- wc->wcsc[ewcs].n--;
- }
-}
-
-void wallcycle_sub_stop(gmx_wallcycle_t wc, int ewcs)
-{
- if (useCycleSubcounters && wc != nullptr)
- {
- wc->wcsc[ewcs].c += gmx_cycles_read() - wc->wcsc[ewcs].start;
- wc->wcsc[ewcs].n++;
- }
-}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <stdio.h>
+#include <array>
+#include <memory>
+#include <vector>
+
+#include "gromacs/timing/cyclecounter.h"
#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/enumerationhelpers.h"
+
+#ifndef DEBUG_WCYCLE
+/*! \brief Enables consistency checking for the counters.
+ *
+ * If the macro is set to 1, code checks if you stop a counter different from the last
+ * one that was opened and if you do nest too deep.
+ */
+# define DEBUG_WCYCLE 0
+#endif
-typedef struct gmx_wallcycle* gmx_wallcycle_t;
struct t_commrec;
-static constexpr gmx_wallcycle* nullWallcycle = nullptr;
-enum
+#ifndef DEBUG_WCYCLE
+/*! \brief Enables consistency checking for the counters.
+ *
+ * If the macro is set to 1, code checks if you stop a counter different from the last
+ * one that was opened and if you do nest too deep.
+ */
+# define DEBUG_WCYCLE 0
+#endif
+
+enum class WallCycleCounter : int
{
- ewcRUN,
- ewcSTEP,
- ewcPPDURINGPME,
- ewcDOMDEC,
- ewcDDCOMMLOAD,
- ewcDDCOMMBOUND,
- ewcVSITECONSTR,
- ewcPP_PMESENDX,
- ewcNS,
- ewcLAUNCH_GPU,
- ewcMOVEX,
- ewcFORCE,
- ewcMOVEF,
- ewcPMEMESH,
- ewcPME_REDISTXF,
- ewcPME_SPREAD,
- ewcPME_GATHER,
- ewcPME_FFT,
- ewcPME_FFTCOMM,
- ewcLJPME,
- ewcPME_SOLVE,
- ewcPMEWAITCOMM,
- ewcPP_PMEWAITRECVF,
- ewcWAIT_GPU_PME_SPREAD,
- ewcPME_FFT_MIXED_MODE,
- ewcPME_SOLVE_MIXED_MODE,
- ewcWAIT_GPU_PME_GATHER,
- ewcWAIT_GPU_BONDED,
- ewcPME_GPU_F_REDUCTION,
- ewcWAIT_GPU_NB_NL,
- ewcWAIT_GPU_NB_L,
- ewcWAIT_GPU_STATE_PROPAGATOR_DATA,
- ewcNB_XF_BUF_OPS,
- ewcVSITESPREAD,
- ewcPULLPOT,
- ewcAWH,
- ewcTRAJ,
- ewcUPDATE,
- ewcCONSTR,
- ewcMoveE,
- ewcROT,
- ewcROTadd,
- ewcSWAP,
- ewcIMD,
- ewcTEST,
- ewcNR
+ Run,
+ Step,
+ PpDuringPme,
+ Domdec,
+ DDCommLoad,
+ DDCommBound,
+ VsiteConstr,
+ PpPmeSendX,
+ NS,
+ LaunchGpu,
+ MoveX,
+ Force,
+ MoveF,
+ PmeMesh,
+ PmeRedistXF,
+ PmeSpread,
+ PmeGather,
+ PmeFft,
+ PmeFftComm,
+ LJPme,
+ PmeSolve,
+ PmeWaitComm,
+ PpPmeWaitRecvF,
+ WaitGpuPmeSpread,
+ PmeFftMixedMode,
+ PmeSolveMixedMode,
+ WaitGpuPmeGather,
+ WaitGpuBonded,
+ PmeGpuFReduction,
+ WaitGpuNbNL,
+ WaitGpuNbL,
+ WaitGpuStatePropagatorData,
+ NbXFBufOps,
+ VsiteSpread,
+ PullPot,
+ Awh,
+ Traj,
+ Update,
+ Constr,
+ MoveE,
+ Rot,
+ RotAdd,
+ Swap,
+ Imd,
+ Test,
+ Count
};
-enum
+enum class WallCycleSubCounter : int
{
- ewcsDD_REDIST,
- ewcsDD_GRID,
- ewcsDD_SETUPCOMM,
- ewcsDD_MAKETOP,
- ewcsDD_MAKECONSTR,
- ewcsDD_TOPOTHER,
- ewcsDD_GPU,
- ewcsNBS_GRID_LOCAL,
- ewcsNBS_GRID_NONLOCAL,
- ewcsNBS_SEARCH_LOCAL,
- ewcsNBS_SEARCH_NONLOCAL,
- ewcsLISTED,
- ewcsLISTED_FEP,
- ewcsRESTRAINTS,
- ewcsLISTED_BUF_OPS,
- ewcsNONBONDED_PRUNING,
- ewcsNONBONDED_KERNEL,
- ewcsNONBONDED_CLEAR,
- ewcsNONBONDED_FEP,
- ewcsLAUNCH_GPU_NONBONDED,
- ewcsLAUNCH_GPU_BONDED,
- ewcsLAUNCH_GPU_PME,
- ewcsLAUNCH_STATE_PROPAGATOR_DATA,
- ewcsEWALD_CORRECTION,
- ewcsNB_X_BUF_OPS,
- ewcsNB_F_BUF_OPS,
- ewcsCLEAR_FORCE_BUFFER,
- ewcsLAUNCH_GPU_NB_X_BUF_OPS,
- ewcsLAUNCH_GPU_NB_F_BUF_OPS,
- ewcsLAUNCH_GPU_MOVEX,
- ewcsLAUNCH_GPU_MOVEF,
- ewcsLAUNCH_GPU_UPDATE_CONSTRAIN,
- ewcsTEST,
- ewcsNR
+ DDRedist,
+ DDGrid,
+ DDSetupComm,
+ DDMakeTop,
+ DDMakeConstr,
+ DDTopOther,
+ DDGpu,
+ NBSGridLocal,
+ NBSGridNonLocal,
+ NBSSearchLocal,
+ NBSSearchNonLocal,
+ Listed,
+ ListedFep,
+ Restraints,
+ ListedBufOps,
+ NonbondedPruning,
+ NonbondedKernel,
+ NonbondedClear,
+ NonbondedFep,
+ LaunchGpuNonBonded,
+ LaunchGpuBonded,
+ LaunchGpuPme,
+ LaunchStatePropagatorData,
+ EwaldCorrection,
+ NBXBufOps,
+ NBFBufOps,
+ ClearForceBuffer,
+ LaunchGpuNBXBufOps,
+ LaunchGpuNBFBufOps,
+ LaunchGpuMoveX,
+ LaunchGpuMoveF,
+ LaunchGpuUpdateConstrain,
+ Test,
+ Count
};
-gmx_bool wallcycle_have_counter();
-/* Returns if cycle counting is supported */
+static constexpr int sc_numWallCycleCounters = static_cast<int>(WallCycleCounter::Count);
+static constexpr int sc_numWallCycleSubCounters = static_cast<int>(WallCycleSubCounter::Count);
+static constexpr int sc_numWallCycleCountersSquared = sc_numWallCycleCounters * sc_numWallCycleCounters;
+static constexpr bool sc_useCycleSubcounters = GMX_CYCLE_SUBCOUNTERS;
-gmx_wallcycle_t wallcycle_init(FILE* fplog, int resetstep, struct t_commrec* cr);
-/* Returns the wall cycle structure.
- * Returns NULL when cycle counting is not supported.
- */
+struct wallcc_t
+{
+ int n;
+ gmx_cycles_t c;
+ gmx_cycles_t start;
+};
+
+#if DEBUG_WCYCLE
+static constexpr int c_MaxWallCycleDepth = 6;
+#endif
+
+
+struct gmx_wallcycle
+{
+ gmx::EnumerationArray<WallCycleCounter, wallcc_t> wcc;
+ /* did we detect one or more invalid cycle counts */
+ bool haveInvalidCount;
+ /* variables for testing/debugging */
+ bool wc_barrier;
+ std::vector<wallcc_t> wcc_all;
+ int wc_depth;
+#if DEBUG_WCYCLE
+ std::array<WallCycleCounter, c_MaxWallCycleDepth> counterlist;
+ int count_depth;
+ bool isMasterRank;
+#endif
+ WallCycleCounter ewc_prev;
+ gmx_cycles_t cycle_prev;
+ int64_t reset_counters;
+ const t_commrec* cr;
+ gmx::EnumerationArray<WallCycleSubCounter, wallcc_t> wcsc;
+};
+
+//! Returns if cycle counting is supported
+bool wallcycle_have_counter();
+
+//! Returns the wall cycle structure.
+std::unique_ptr<gmx_wallcycle> wallcycle_init(FILE* fplog, int resetstep, const t_commrec* cr);
-/* cleans up wallcycle structure */
-void wallcycle_destroy(gmx_wallcycle_t wc);
+//! Adds custom barrier for wallcycle counting.
+void wallcycleBarrier(gmx_wallcycle* wc);
-void wallcycle_start(gmx_wallcycle_t wc, int ewc);
-/* Starts the cycle counter (and increases the call count) */
+void wallcycle_sub_get(gmx_wallcycle* wc, WallCycleSubCounter ewcs, int* n, double* c);
+/* Returns the cumulative count and sub cycle count for ewcs */
-void wallcycle_start_nocount(gmx_wallcycle_t wc, int ewc);
-/* Starts the cycle counter without increasing the call count */
+inline void wallcycle_all_start(gmx_wallcycle* wc, WallCycleCounter ewc, gmx_cycles_t cycle)
+{
+ wc->ewc_prev = ewc;
+ wc->cycle_prev = cycle;
+}
-double wallcycle_stop(gmx_wallcycle_t wc, int ewc);
-/* Stop the cycle count for ewc, returns the last cycle count */
+inline void wallcycle_all_stop(gmx_wallcycle* wc, WallCycleCounter ewc, gmx_cycles_t cycle)
+{
+ const int prev = static_cast<int>(wc->ewc_prev);
+ const int current = static_cast<int>(ewc);
+ wc->wcc_all[prev * sc_numWallCycleCounters + current].n += 1;
+ wc->wcc_all[prev * sc_numWallCycleCounters + current].c += cycle - wc->cycle_prev;
+}
-void wallcycle_increment_event_count(gmx_wallcycle_t wc, int ewc);
-/* Only increment call count for ewc by one */
+//! Starts the cycle counter (and increases the call count)
+inline void wallcycle_start(gmx_wallcycle* wc, WallCycleCounter ewc)
+{
+ if (wc == nullptr)
+ {
+ return;
+ }
-void wallcycle_get(gmx_wallcycle_t wc, int ewc, int* n, double* c);
-/* Returns the cumulative count and cycle count for ewc */
+ wallcycleBarrier(wc);
-void wallcycle_reset_all(gmx_wallcycle_t wc);
-/* Resets all cycle counters to zero */
+#if DEBUG_WCYCLE
+ debug_start_check(wc, ewc);
+#endif
+ gmx_cycles_t cycle = gmx_cycles_read();
+ wc->wcc[ewc].start = cycle;
+ if (!wc->wcc_all.empty())
+ {
+ wc->wc_depth++;
+ if (ewc == WallCycleCounter::Run)
+ {
+ wallcycle_all_start(wc, ewc, cycle);
+ }
+ else if (wc->wc_depth == 3)
+ {
+ wallcycle_all_stop(wc, ewc, cycle);
+ }
+ }
+}
-void wallcycle_scale_by_num_threads(gmx_wallcycle_t wc, bool isPmeRank, int nthreads_pp, int nthreads_pme);
-/* Scale the cycle counts to reflect how many threads run for that number of cycles */
+//! Starts the cycle counter without increasing the call count
+inline void wallcycle_start_nocount(gmx_wallcycle* wc, WallCycleCounter ewc)
+{
+ if (wc == nullptr)
+ {
+ return;
+ }
+ wc->wcc[ewc].n++;
+}
-int64_t wcycle_get_reset_counters(gmx_wallcycle_t wc);
-/* Return reset_counters from wc struct */
+//! Stop the cycle count for ewc , returns the last cycle count
+inline double wallcycle_stop(gmx_wallcycle* wc, WallCycleCounter ewc)
+{
+ gmx_cycles_t cycle, last;
-void wcycle_set_reset_counters(gmx_wallcycle_t wc, int64_t reset_counters);
-/* Set reset_counters */
+ if (wc == nullptr)
+ {
+ return 0;
+ }
-void wallcycle_sub_start(gmx_wallcycle_t wc, int ewcs);
-/* Set the start sub cycle count for ewcs */
+ wallcycleBarrier(wc);
-void wallcycle_sub_start_nocount(gmx_wallcycle_t wc, int ewcs);
-/* Set the start sub cycle count for ewcs without increasing the call count */
+#if DEBUG_WCYCLE
+ debug_stop_check(wc, ewc);
+#endif
+
+ /* When processes or threads migrate between cores, the cycle counting
+ * can get messed up if the cycle counter on different cores are not
+ * synchronized. When this happens we expect both large negative and
+ * positive cycle differences. We can detect negative cycle differences.
+ * Detecting too large positive counts if difficult, since count can be
+ * large, especially for ewcRUN. If we detect a negative count,
+ * we will not print the cycle accounting table.
+ */
+ cycle = gmx_cycles_read();
+ if (cycle >= wc->wcc[ewc].start)
+ {
+ last = cycle - wc->wcc[ewc].start;
+ }
+ else
+ {
+ last = 0;
+ wc->haveInvalidCount = true;
+ }
+ wc->wcc[ewc].c += last;
+ wc->wcc[ewc].n++;
+ if (!wc->wcc_all.empty())
+ {
+ wc->wc_depth--;
+ if (ewc == WallCycleCounter::Run)
+ {
+ wallcycle_all_stop(wc, ewc, cycle);
+ }
+ else if (wc->wc_depth == 2)
+ {
+ wallcycle_all_start(wc, ewc, cycle);
+ }
+ }
+
+ return last;
+}
+
+//! Only increment call count for ewc by one
+inline void wallcycle_increment_event_count(gmx_wallcycle* wc, WallCycleCounter ewc)
+{
+ if (wc == nullptr)
+ {
+ return;
+ }
+ wc->wcc[ewc].n++;
+}
-void wallcycle_sub_stop(gmx_wallcycle_t wc, int ewcs);
-/* Stop the sub cycle count for ewcs */
+//! Returns the cumulative count and cycle count for ewc
+void wallcycle_get(gmx_wallcycle* wc, WallCycleCounter ewc, int* n, double* c);
+
+//! Resets all cycle counters to zero
+void wallcycle_reset_all(gmx_wallcycle* wc);
+
+//! Scale the cycle counts to reflect how many threads run for that number of cycles
+void wallcycle_scale_by_num_threads(gmx_wallcycle* wc, bool isPmeRank, int nthreads_pp, int nthreads_pme);
+
+//! Return reset_counters from wc struct
+int64_t wcycle_get_reset_counters(gmx_wallcycle* wc);
+
+//! Set reset_counters
+void wcycle_set_reset_counters(gmx_wallcycle* wc, int64_t reset_counters);
+
+//! Set the start sub cycle count for ewcs
+inline void wallcycle_sub_start(gmx_wallcycle* wc, WallCycleSubCounter ewcs)
+{
+ if (sc_useCycleSubcounters && wc != nullptr)
+ {
+ wc->wcsc[ewcs].start = gmx_cycles_read();
+ }
+}
+
+//! Set the start sub cycle count for ewcs without increasing the call count
+inline void wallcycle_sub_start_nocount(gmx_wallcycle* wc, WallCycleSubCounter ewcs)
+{
+ if (sc_useCycleSubcounters && wc != nullptr)
+ {
+ wc->wcsc[ewcs].start = gmx_cycles_read();
+ }
+}
+
+//! Stop the sub cycle count for ewcs
+inline void wallcycle_sub_stop(gmx_wallcycle* wc, WallCycleSubCounter ewcs)
+{
+ if (sc_useCycleSubcounters && wc != nullptr)
+ {
+ wc->wcsc[ewcs].c += gmx_cycles_read() - wc->wcsc[ewcs].start;
+ wc->wcsc[ewcs].n++;
+ }
+}
#endif
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <array>
+#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/basedefinitions.h"
struct t_commrec;
class MDLogger;
}
-typedef struct gmx_wallcycle* gmx_wallcycle_t;
struct gmx_wallclock_gpu_nbnxn_t;
struct gmx_wallclock_gpu_pme_t;
-typedef std::array<double, int(ewcNR) + int(ewcsNR)> WallcycleCounts;
+using WallcycleCounts = std::array<double, sc_numWallCycleCounters + sc_numWallCycleSubCounters>;
/* Convenience typedef */
-WallcycleCounts wallcycle_sum(const t_commrec* cr, gmx_wallcycle_t wc);
+WallcycleCounts wallcycle_sum(const t_commrec* cr, gmx_wallcycle* wc);
/* Return a vector of the sum of cycle counts over the nodes in
cr->mpi_comm_mysim. */
int nth_pp,
int nth_pme,
double realtime,
- gmx_wallcycle_t wc,
+ gmx_wallcycle* wc,
const WallcycleCounts& cyc_sum,
const gmx_wallclock_gpu_nbnxn_t* gpu_nbnxn_t,
const gmx_wallclock_gpu_pme_t* gpu_pme_t);
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015,2018, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2018,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(tools INTERFACE)
file(GLOB TOOLS_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${TOOLS_SOURCES} PARENT_SCOPE)
+# Source files have the following dependencies on library infrastructure.
+#target_link_libraries(tools PRIVATE
+# common
+# legacy_modules
+#)
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(tools PUBLIC
+target_include_directories(tools INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(tools PUBLIC
+target_link_libraries(tools INTERFACE
+ legacy_api
+ )
+
+# TODO: when tools is an OBJECT target
+#target_link_libraries(tools PUBLIC legacy_api)
+#target_link_libraries(tools PRIVATE common)
+
+# Module dependencies
+# tools interfaces convey transitive dependence on these modules.
+#target_link_libraries(tools PUBLIC
+target_link_libraries(tools INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(tools PRIVATE NOTHING)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(tools PRIVATE legacy_modules)
+
+
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
else
{
- if (ir[0]->efep == efepNO)
+ if (ir[0]->efep == FreeEnergyPerturbationType::No)
{
- fprintf(stdout, "inputrec->efep = %s\n", efep_names[ir[0]->efep]);
+ fprintf(stdout, "inputrec->efep = %s\n", enumValueToString(ir[0]->efep));
}
else
{
deviation = gmx::square(blen - b0);
if (std::sqrt(deviation / gmx::square(b0)) > tol)
{
- fprintf(stderr, "Distance between atoms %d and %d is %.3f, should be %.3f\n",
- ai + 1, aj + 1, blen, b0);
+ fprintf(stderr,
+ "Distance between atoms %d and %d is %.3f, should be %.3f\n",
+ ai + 1,
+ aj + 1,
+ blen,
+ b0);
}
}
}
{
read_tpx_state(tpr, &ir, &state, &mtop);
top = std::make_unique<gmx_localtop_t>(mtop.ffparams);
- gmx_mtop_generate_local_top(mtop, top.get(), ir.efep != efepNO);
+ gmx_mtop_generate_local_top(mtop, top.get(), ir.efep != FreeEnergyPerturbationType::No);
}
new_natoms = -1;
natoms = -1;
> 0.1 * (std::fabs(fr.time - old_t1) + std::fabs(old_t1 - old_t2)))
{
bShowTimestep = FALSE;
- fprintf(stderr, "%sTimesteps at t=%g don't match (%g, %g)\n", newline ? "\n" : "",
- old_t1, old_t1 - old_t2, fr.time - old_t1);
+ fprintf(stderr,
+ "%sTimesteps at t=%g don't match (%g, %g)\n",
+ newline ? "\n" : "",
+ old_t1,
+ old_t1 - old_t2,
+ fr.time - old_t1);
}
}
natoms = new_natoms;
ekin += 0.5 * atoms->atom[i].m * v[i][j] * v[i][j];
}
}
- temp1 = (2.0 * ekin) / (natom * DIM * BOLTZ);
- temp2 = (2.0 * ekin) / (natom * (DIM - 1) * BOLTZ);
+ temp1 = (2.0 * ekin) / (natom * DIM * gmx::c_boltz);
+ temp2 = (2.0 * ekin) / (natom * (DIM - 1) * gmx::c_boltz);
fprintf(stderr, "Kinetic energy: %g (kJ/mol)\n", ekin);
fprintf(stderr,
"Assuming the number of degrees of freedom to be "
"Natoms * %d or Natoms * %d,\n"
"the velocities correspond to a temperature of the system\n"
"of %g K or %g K respectively.\n\n",
- DIM, DIM - 1, temp1, temp2);
+ DIM,
+ DIM - 1,
+ temp1,
+ temp2);
}
/* check coordinates */
fprintf(stderr,
"Checking for atoms closer than %g and not between %g and %g,\n"
"relative to sum of Van der Waals distance:\n",
- vdw_fac, bon_lo, bon_hi);
+ vdw_fac,
+ bon_lo,
+ bon_hi);
snew(atom_vdw, natom);
AtomProperties aps;
for (i = 0; (i < natom); i++)
{
- aps.setAtomProperty(epropVDW, *(atoms->resinfo[atoms->atom[i].resind].name),
- *(atoms->atomname[i]), &(atom_vdw[i]));
+ aps.setAtomProperty(epropVDW,
+ *(atoms->resinfo[atoms->atom[i].resind].name),
+ *(atoms->atomname[i]),
+ &(atom_vdw[i]));
if (debug)
{
- fprintf(debug, "%5d %4s %4s %7g\n", i + 1, *(atoms->resinfo[atoms->atom[i].resind].name),
- *(atoms->atomname[i]), atom_vdw[i]);
+ fprintf(debug,
+ "%5d %4s %4s %7g\n",
+ i + 1,
+ *(atoms->resinfo[atoms->atom[i].resind].name),
+ *(atoms->atomname[i]),
+ atom_vdw[i]);
}
}
if (bB)
{
if (bFirst)
{
- fprintf(stderr, "\r%5s %4s %8s %5s %5s %4s %8s %5s %6s\n", "atom#", "name",
- "residue", "r_vdw", "atom#", "name", "residue", "r_vdw", "distance");
+ fprintf(stderr,
+ "\r%5s %4s %8s %5s %5s %4s %8s %5s %6s\n",
+ "atom#",
+ "name",
+ "residue",
+ "r_vdw",
+ "atom#",
+ "name",
+ "residue",
+ "r_vdw",
+ "distance");
bFirst = FALSE;
}
- fprintf(stderr, "\r%5d %4s %4s%4d %-5.3g %5d %4s %4s%4d %-5.3g %-6.4g\n", i + 1,
- *(atoms->atomname[i]), *(atoms->resinfo[atoms->atom[i].resind].name),
- atoms->resinfo[atoms->atom[i].resind].nr, atom_vdw[i], j + 1,
- *(atoms->atomname[j]), *(atoms->resinfo[atoms->atom[j].resind].name),
- atoms->resinfo[atoms->atom[j].resind].nr, atom_vdw[j], std::sqrt(r2));
+ fprintf(stderr,
+ "\r%5d %4s %4s%4d %-5.3g %5d %4s %4s%4d %-5.3g %-6.4g\n",
+ i + 1,
+ *(atoms->atomname[i]),
+ *(atoms->resinfo[atoms->atom[i].resind].name),
+ atoms->resinfo[atoms->atom[i].resind].nr,
+ atom_vdw[i],
+ j + 1,
+ *(atoms->atomname[j]),
+ *(atoms->resinfo[atoms->atom[j].resind].name),
+ atoms->resinfo[atoms->atom[j].resind].nr,
+ atom_vdw[j],
+ std::sqrt(r2));
}
}
}
"):\n"
"(These may occur often and are normally not a problem)\n"
"%5s %4s %8s %5s %s\n",
- "atom#", "name", "residue", "r_vdw", "coordinate");
+ "atom#",
+ "name",
+ "residue",
+ "r_vdw",
+ "coordinate");
bFirst = FALSE;
}
- fprintf(stderr, "%5d %4s %4s%4d %-5.3g", i, *(atoms->atomname[i]),
+ fprintf(stderr,
+ "%5d %4s %4s%4d %-5.3g",
+ i,
+ *(atoms->atomname[i]),
*(atoms->resinfo[atoms->atom[i].resind].name),
- atoms->resinfo[atoms->atom[i].resind].nr, atom_vdw[i]);
+ atoms->resinfo[atoms->atom[i].resind].nr,
+ atom_vdw[i]);
for (j = 0; (j < DIM); j++)
{
fprintf(stderr, " %6.3g", x[i][j]);
printf("Nr. Group #Entries First Last\n");
for (i = 0; (i < grps->nr); i++)
{
- printf("%4d %-20s%8d%8d%8d\n", i, grpname[i], grps->index[i + 1] - grps->index[i],
- grps->a[grps->index[i]] + 1, grps->a[grps->index[i + 1] - 1] + 1);
+ printf("%4d %-20s%8d%8d%8d\n",
+ i,
+ grpname[i],
+ grps->index[i + 1] - grps->index[i],
+ grps->a[grps->index[i]] + 1,
+ grps->a[grps->index[i + 1] - 1] + 1);
}
}
for (i = 0; (i < grps->nr); i++)
> 0.1 * (fabs(fr->t - old_t1) + std::fabs(old_t1 - old_t2)))
{
bShowTStep = FALSE;
- fprintf(stderr, "\nTimesteps at t=%g don't match (%g, %g)\n", old_t1,
- old_t1 - old_t2, fr->t - old_t1);
+ fprintf(stderr, "\nTimesteps at t=%g don't match (%g, %g)\n", old_t1, old_t1 - old_t2, fr->t - old_t1);
}
}
old_t2 = old_t1;
}
if (fnr == 0)
{
- fprintf(stderr, "\rframe: %6s (index %6d), t: %10.3f\n", gmx_step_str(fr->step, buf),
- fnr, fr->t);
+ fprintf(stderr, "\rframe: %6s (index %6d), t: %10.3f\n", gmx_step_str(fr->step, buf), fnr, fr->t);
}
fnr++;
}
const char *fn1 = nullptr, *fn2 = nullptr, *tex = nullptr;
gmx_output_env_t* oenv;
- static real vdw_fac = 0.8;
- static real bon_lo = 0.4;
- static real bon_hi = 0.7;
- static gmx_bool bRMSD = FALSE;
- static real ftol = 0.001;
- static real abstol = 0.001;
- static gmx_bool bCompAB = FALSE;
- static char* lastener = nullptr;
+ real vdw_fac = 0.8;
+ real bon_lo = 0.4;
+ real bon_hi = 0.7;
+ gmx_bool bRMSD = FALSE;
+ real ftol = 0.001;
+ real abstol = 0.001;
+ gmx_bool bCompAB = FALSE;
+ char* lastener = nullptr;
static t_pargs pa[] = {
{ "-vdwfac",
FALSE,
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx_fatal(FARGS,
"Your index file contains atomnumbers (e.g. %d)\nthat are larger than the number "
"of atoms in the tpr file (%d)",
- (numberInIndexFile), (maxAtomNumber));
+ (numberInIndexFile),
+ (maxAtomNumber));
}
}
}
}
- fprintf(stderr, "Reduced block %8s from %6zu to %6zu index-, %6d to %6d a-entries\n", name,
- src.size(), lists.size(), src.numElements(), lists.numElements());
+ fprintf(stderr,
+ "Reduced block %8s from %6zu to %6zu index-, %6d to %6d a-entries\n",
+ name,
+ src.size(),
+ lists.size(),
+ src.numElements(),
+ lists.numElements());
return lists;
}
ilReduced.push_back(il->iatoms[i], nratoms, newAtoms.data());
}
}
- fprintf(stderr, "Reduced ilist %8s from %6d to %6d entries\n", name,
- il->size() / (nratoms + 1), ilReduced.size() / (nratoms + 1));
+ fprintf(stderr,
+ "Reduced ilist %8s from %6d to %6d entries\n",
+ name,
+ il->size() / (nratoms + 1),
+ ilReduced.size() / (nratoms + 1));
*il = std::move(ilReduced);
}
{
gmx_localtop_t top(mtop->ffparams);
gmx_mtop_generate_local_top(*mtop, &top, false);
- t_atoms atoms = gmx_mtop_global_atoms(mtop);
+ t_atoms atoms = gmx_mtop_global_atoms(*mtop);
const std::vector<bool> bKeep = bKeepIt(gnx, atoms.nr, index);
const std::vector<int> invindex = invind(gnx, atoms.nr, index);
for (int i = 0; (i < F_NRE); i++)
{
- reduce_ilist(invindex, bKeep, &(top.idef.il[i]), interaction_function[i].nratoms,
+ reduce_ilist(invindex,
+ bKeep,
+ &(top.idef.il[i]),
+ interaction_function[i].nratoms,
interaction_function[i].name);
}
settings->setHelpText(desc);
options->addOption(FileNameOption("s")
- .filetype(eftTopology)
+ .filetype(OptionFileType::Topology)
.inputFile()
.required()
.store(&inputTprFileName_)
.defaultBasename("topol")
.description("Run input file to modify"));
options->addOption(FileNameOption("n")
- .filetype(eftIndex)
+ .filetype(OptionFileType::Index)
.inputFile()
.store(&inputIndexFileName_)
.storeIsSet(&haveReadIndexFile_)
.defaultBasename("index")
.description("File containing additional index groups"));
options->addOption(FileNameOption("o")
- .filetype(eftTopology)
+ .filetype(OptionFileType::Topology)
.outputFile()
.store(&outputTprFileName_)
.defaultBasename("tprout")
{
ir->nsteps = ir->nsteps - (currentMaxStep - ir->init_step)
+ gmx::roundToInt64(extendTime_ / ir->delta_t);
- printf("Extending remaining runtime of by %g ps (now %s steps)\n", extendTime_,
+ printf("Extending remaining runtime of by %g ps (now %s steps)\n",
+ extendTime_,
gmx_step_str(ir->nsteps, buf));
}
else if (runToMaxTimeIsSet_)
{
printf("nsteps = %s, run_step = %s, current_t = %g, until = %g\n",
- gmx_step_str(ir->nsteps, buf), gmx_step_str(currentMaxStep, buf2),
- currentRunTime, runToMaxTime_);
+ gmx_step_str(ir->nsteps, buf),
+ gmx_step_str(currentMaxStep, buf2),
+ currentRunTime,
+ runToMaxTime_);
ir->nsteps = gmx::roundToInt64((currentMaxRunTime - currentRunTime) / ir->delta_t);
- printf("Extending remaining runtime until %g ps (now %s steps)\n", currentMaxRunTime,
+ printf("Extending remaining runtime until %g ps (now %s steps)\n",
+ currentMaxRunTime,
gmx_step_str(ir->nsteps, buf));
}
else
{
ir->nsteps -= currentMaxStep - ir->init_step;
/* Print message */
- printf("%s steps (%g ps) remaining from first run.\n", gmx_step_str(ir->nsteps, buf),
+ printf("%s steps (%g ps) remaining from first run.\n",
+ gmx_step_str(ir->nsteps, buf),
ir->nsteps * ir->delta_t);
}
}
if (haveReadIndexFile_ || !(maxStepsIsSet_ || extendTimeIsSet_ || runToMaxTimeIsSet_))
{
- atoms = gmx_mtop_global_atoms(&mtop);
+ atoms = gmx_mtop_global_atoms(mtop);
int gnx = 0;
int* index = nullptr;
char* grpname = nullptr;
fprintf(stderr,
"Will write subset %s of original tpx containing %d "
"atoms\n",
- grpname, gnx);
+ grpname,
+ gnx);
reduce_topology_x(gnx, index, &mtop, state.x.rvec_array(), state.v.rvec_array());
state.natoms = gnx;
}
}
double stateTime = ir->init_t + ir->init_step * ir->delta_t;
- sprintf(buf, "Writing statusfile with starting step %s%s and length %s%s steps...\n", "%10",
- PRId64, "%10", PRId64);
+ sprintf(buf,
+ "Writing statusfile with starting step %s%s and length %s%s steps...\n",
+ "%10",
+ PRId64,
+ "%10",
+ PRId64);
fprintf(stderr, buf, ir->init_step, ir->nsteps);
- fprintf(stderr, " time %10.3f and length %10.3f ps\n",
- stateTime, ir->nsteps * ir->delta_t);
- write_tpx_state(outputTprFileName_.c_str(), ir, &state, &mtop);
+ fprintf(stderr,
+ " time %10.3f and length %10.3f ps\n",
+ stateTime,
+ ir->nsteps * ir->delta_t);
+ write_tpx_state(outputTprFileName_.c_str(), ir, &state, mtop);
}
else
{
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
for (auto group : keysOf(gcount))
{
+ if (group == SimulationAtomGroupType::AccelerationUnused)
+ {
+ continue;
+ }
gcount[group][getGroupType(groups, group, i)]++;
}
}
snew(x, trrheader.natoms);
snew(v, trrheader.natoms);
snew(f, trrheader.natoms);
- if (gmx_trr_read_frame_data(fpread, &trrheader, trrheader.box_size ? box : nullptr,
- trrheader.x_size ? x : nullptr, trrheader.v_size ? v : nullptr,
+ if (gmx_trr_read_frame_data(fpread,
+ &trrheader,
+ trrheader.box_size ? box : nullptr,
+ trrheader.x_size ? x : nullptr,
+ trrheader.v_size ? v : nullptr,
trrheader.f_size ? f : nullptr))
{
sprintf(buf, "%s frame %d", fn, nframe);
indent = 0;
indent = pr_title(stdout, indent, buf);
pr_indent(stdout, indent);
- fprintf(stdout, "natoms=%10d step=%10" PRId64 " time=%12.7e lambda=%10g\n",
- trrheader.natoms, trrheader.step, trrheader.t, trrheader.lambda);
+ fprintf(stdout,
+ "natoms=%10d step=%10" PRId64 " time=%12.7e lambda=%10g\n",
+ trrheader.natoms,
+ trrheader.step,
+ trrheader.t,
+ trrheader.lambda);
if (trrheader.box_size)
{
pr_rvecs(stdout, indent, "box", box, DIM);
indent = 0;
indent = pr_title(stdout, indent, buf);
pr_indent(stdout, indent);
- fprintf(stdout, "natoms=%10d step=%10" PRId64 " time=%12.7e prec=%10g\n", natoms, step,
- time, prec);
+ fprintf(stdout, "natoms=%10d step=%10" PRId64 " time=%12.7e prec=%10g\n", natoms, step, time, prec);
pr_rvecs(stdout, indent, "box", box, DIM);
pr_rvecs(stdout, indent, "x", x, natoms);
nframe++;
int64_t n_values_per_frame, n_atoms;
char block_name[STRLEN];
- gmx_get_tng_data_next_frame_of_block_type(tng, block_ids[i], &values, &step,
- &frame_time, &n_values_per_frame, &n_atoms,
- &prec, block_name, STRLEN, &bOK);
+ gmx_get_tng_data_next_frame_of_block_type(tng,
+ block_ids[i],
+ &values,
+ &step,
+ &frame_time,
+ &n_values_per_frame,
+ &n_atoms,
+ &prec,
+ block_name,
+ STRLEN,
+ &bOK);
if (!bOK)
{
/* Can't write any output because we don't know what
arrays are valid. */
- fprintf(stderr, "\nWARNING: Incomplete frame at time %g, will not write output\n",
- frame_time);
+ fprintf(stderr, "\nWARNING: Incomplete frame at time %g, will not write output\n", frame_time);
}
else
{
- list_tng_inner(fn, (0 == i), values, step, frame_time, n_values_per_frame, n_atoms,
- prec, nframe, block_name);
+ list_tng_inner(
+ fn, (0 == i), values, step, frame_time, n_values_per_frame, n_atoms, prec, nframe, block_name);
}
}
nframe++;
- } while (gmx_get_tng_data_block_types_of_next_frame(tng, step, 0, nullptr, &step, &ndatablocks,
- &block_ids));
+ } while (gmx_get_tng_data_block_types_of_next_frame(
+ tng, step, 0, nullptr, &step, &ndatablocks, &block_ids));
if (block_ids)
{
case efTRR: list_trr(fn); break;
case efTNG: list_tng(fn); break;
default:
- fprintf(stderr, "File %s is of an unsupported type. Try using the command\n 'less %s'\n",
- fn, fn);
+ fprintf(stderr, "File %s is of an unsupported type. Try using the command\n 'less %s'\n", fn, fn);
}
}
{
printf("\n%24s %12.5e %12s %12s\n", "time:", fr->t, "step:", gmx_step_str(fr->step, buf));
printf("%24s %12s %12s %12s\n", "", "", "nsteps:", gmx_step_str(fr->nsteps, buf));
- printf("%24s %12.5e %12s %12s\n", "delta_t:", fr->dt,
- "sum steps:", gmx_step_str(fr->nsum, buf));
+ printf("%24s %12.5e %12s %12s\n", "delta_t:", fr->dt, "sum steps:", gmx_step_str(fr->nsum, buf));
if (fr->nre == nre)
{
- printf("%24s %12s %12s %12s\n", "Component", "Energy", "Av. Energy",
+ printf("%24s %12s %12s %12s\n",
+ "Component",
+ "Energy",
+ "Av. Energy",
"Sum Energy");
if (fr->nsum > 0)
{
for (i = 0; (i < nre); i++)
{
- printf("%24s %12.5e %12.5e %12.5e\n", enm[i].name, fr->ener[i].e,
- fr->ener[i].eav, fr->ener[i].esum);
+ printf("%24s %12.5e %12.5e %12.5e\n",
+ enm[i].name,
+ fr->ener[i].e,
+ fr->ener[i].eav,
+ fr->ener[i].esum);
}
}
else
for (i = 0; i < eb->nsub; i++)
{
t_enxsubblock* sb = &(eb->sub[i]);
- printf(" Sub block %3d (%5d elems, type=%s) values:\n", i, sb->nr,
- xdr_datatype_names[sb->type]);
+ printf(" Sub block %3d (%5d elems, type=%s) values:\n",
+ i,
+ sb->nr,
+ enumValueToString(sb->type));
switch (sb->type)
{
- case xdr_datatype_float:
+ case XdrDataType::Float:
for (j = 0; j < sb->nr; j++)
{
printf("%14d %8.4f\n", j, sb->fval[j]);
}
break;
- case xdr_datatype_double:
+ case XdrDataType::Double:
for (j = 0; j < sb->nr; j++)
{
printf("%14d %10.6f\n", j, sb->dval[j]);
}
break;
- case xdr_datatype_int:
+ case XdrDataType::Int:
for (j = 0; j < sb->nr; j++)
{
printf("%14d %10d\n", j, sb->ival[j]);
}
break;
- case xdr_datatype_int64:
+ case XdrDataType::Int64:
for (j = 0; j < sb->nr; j++)
{
printf("%14d %s\n", j, gmx_step_str(sb->lval[j], buf));
}
break;
- case xdr_datatype_char:
+ case XdrDataType::Char:
for (j = 0; j < sb->nr; j++)
{
printf("%14d %1c\n", j, sb->cval[j]);
}
break;
- case xdr_datatype_string:
+ case XdrDataType::String:
for (j = 0; j < sb->nr; j++)
{
printf("%14d %80s\n", j, sb->sval[j]);
// fix it or block that run path:
// Position restraint output from -sys -s is broken
- options->addOption(
- FileNameOption("s").filetype(eftRunInput).inputFile().store(&inputTprFilename_).description("Run input file to dump"));
+ options->addOption(FileNameOption("s")
+ .filetype(OptionFileType::RunInput)
+ .inputFile()
+ .store(&inputTprFilename_)
+ .description("Run input file to dump"));
options->addOption(FileNameOption("f")
- .filetype(eftTrajectory)
+ .filetype(OptionFileType::Trajectory)
.inputFile()
.store(&inputTrajectoryFilename_)
.description("Trajectory file to dump"));
- options->addOption(
- FileNameOption("e").filetype(eftEnergy).inputFile().store(&inputEnergyFilename_).description("Energy file to dump"));
+ options->addOption(FileNameOption("e")
+ .filetype(OptionFileType::Energy)
+ .inputFile()
+ .store(&inputEnergyFilename_)
+ .description("Energy file to dump"));
options->addOption(
FileNameOption("cp").legacyType(efCPT).inputFile().store(&inputCheckpointFilename_).description("Checkpoint file to dump"));
options->addOption(
{
if (!inputTprFilename_.empty())
{
- list_tpr(inputTprFilename_.c_str(), bShowNumbers_, bShowParams_,
- outputMdpFilename_.empty() ? nullptr : outputMdpFilename_.c_str(), bSysTop_,
+ list_tpr(inputTprFilename_.c_str(),
+ bShowNumbers_,
+ bShowParams_,
+ outputMdpFilename_.empty() ? nullptr : outputMdpFilename_.c_str(),
+ bSysTop_,
bOriginalInputrec_);
}
else if (!inputTrajectoryFilename_.empty())
fprintf(stderr,
"Energy files don't match, different number of energies:\n"
" %s: %d\n %s: %d\n",
- files[f - 1].c_str(), nresav, files[f].c_str(), fr->nre);
+ files[f - 1].c_str(),
+ nresav,
+ files[f].c_str(),
+ fr->nre);
fprintf(stderr,
"\nContinue conversion using only the first %d terms (n/y)?\n"
"(you should be sure that the energy terms match)\n",
{ "-error", FALSE, etBOOL, { &bError }, "Stop on errors in the file" }
};
- if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa, asize(desc), desc,
- asize(bugs), bugs, &oenv))
+ if (!parse_common_args(
+ &argc, argv, 0, NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
if (debug)
{
- fprintf(debug, "fr->step %s, fr->t %.4f, fro->step %s fro->t %.4f, w %s\n",
- gmx_step_str(fr->step, buf), fr->t, gmx_step_str(fro->step, buf2), fro->t,
+ fprintf(debug,
+ "fr->step %s, fr->t %.4f, fro->step %s fro->t %.4f, w %s\n",
+ gmx_step_str(fr->step, buf),
+ fr->t,
+ gmx_step_str(fro->step, buf2),
+ fro->t,
gmx::boolToString(bWrite));
}
if (bNewOutput)
{
bNewOutput = FALSE;
- fprintf(stderr, "\nContinue writing frames from t=%g, step=%s\n", fro->t,
+ fprintf(stderr,
+ "\nContinue writing frames from t=%g, step=%s\n",
+ fro->t,
gmx_step_str(fro->step, buf));
}
"samples away.\n"
" Use g_energy -odh option to extract these "
"samples.\n",
- files[f].c_str(), size);
+ files[f].c_str(),
+ size);
warned_about_dh = TRUE;
break;
}
{
f--;
}
- printf("\nLast step written from %s: t %g, step %s\n", files[f].c_str(), last_t,
+ printf("\nLast step written from %s: t %g, step %s\n",
+ files[f].c_str(),
+ last_t,
gmx_step_str(laststep, buf));
lastfilestep = laststep;
}
else
{
- fprintf(stderr, "Last frame written was at step %s, time %f\n",
- gmx_step_str(fro->step, buf), fro->t);
+ fprintf(stderr, "Last frame written was at step %s, time %f\n", gmx_step_str(fro->step, buf), fro->t);
fprintf(stderr, "Wrote %d frames\n", noutfr);
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "gromacs/utility/arrayref.h"
#include "make_ndx.h"
+#include <array>
#include <cctype>
#include <cstring>
#include <algorithm>
+#include <array>
+#include <vector>
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/topology/index.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#define NAME_LEN 1024
static const int NOTSET = -92637;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static gmx_bool bCase = FALSE;
static int or_groups(int nr1, const int* at1, int nr2, const int* at2, int* nr, int* at)
return (c != '\0' && std::strchr(spec, c) == nullptr);
}
-static int parse_names(char** string, int* n_names, char** names)
+static int parse_names(char** string, int* n_names, gmx::ArrayRef<char*> names)
{
int i;
return *n_names;
}
-static gmx_bool parse_int_char(char** string, int* nr, char* c)
+static gmx_bool parse_int_char(char** string, int* nr, unsigned char* c)
{
char* orig;
gmx_bool bRet;
static gmx_bool parse_int(char** string, int* nr)
{
- char * orig, c;
- gmx_bool bRet;
+ char* orig;
+ unsigned char c;
+ gmx_bool bRet;
orig = *string;
bRet = parse_int_char(string, nr, &c);
return *nr;
}
-static int select_residuenumbers(char** string, const t_atoms* atoms, int n1, char c, int* nr, int* index, char* gname)
+static int
+select_residuenumbers(char** string, const t_atoms* atoms, int n1, unsigned char c, int* nr, int* index, char* gname)
{
char buf[STRLEN];
int i, j, up;
return *nr;
}
-static int select_residueindices(char** string, const t_atoms* atoms, int n1, char c, int* nr, int* index, char* gname)
+static int
+select_residueindices(char** string, const t_atoms* atoms, int n1, unsigned char c, int* nr, int* index, char* gname)
{
/*this should be similar to select_residuenumbers except select by index (sequential numbering in file)*/
/*resind+1 for 1-indexing*/
return matches;
}
-static int select_chainnames(const t_atoms* atoms, int n_names, char** names, int* nr, int* index)
+static int select_chainnames(const t_atoms* atoms, int n_names, gmx::ArrayRef<char*> names, int* nr, int* index)
{
char name[2];
int j;
return *nr;
}
-static int select_atomnames(const t_atoms* atoms, int n_names, char** names, int* nr, int* index, gmx_bool bType)
+static int select_atomnames(const t_atoms* atoms, int n_names, gmx::ArrayRef<char*> names, int* nr, int* index, gmx_bool bType)
{
char* name;
int j;
return *nr;
}
-static int select_residuenames(const t_atoms* atoms, int n_names, char** names, int* nr, int* index)
+static int select_residuenames(const t_atoms* atoms, int n_names, gmx::ArrayRef<char*> names, int* nr, int* index)
{
char* name;
int j;
}
}
-static void make_gname(int n, char** names, char* gname)
+static void make_gname(int n, gmx::ArrayRef<char*> names, char* gname)
{
int i;
}
}
-static gmx_bool parse_entry(char** string,
- int natoms,
- const t_atoms* atoms,
- t_blocka* block,
- char*** gn,
- int* nr,
- int* index,
- char* gname)
+static gmx_bool parse_entry(char** string,
+ int natoms,
+ const t_atoms* atoms,
+ t_blocka* block,
+ char*** gn,
+ int* nr,
+ int* index,
+ char* gname,
+ gmx::ArrayRef<char*> entryNames)
{
- static char ** names, *ostring;
- static gmx_bool bFirst = TRUE;
- int j, n_names, sel_nr1;
- int i, nr1, *index1;
- char c;
- gmx_bool bRet, bCompl;
-
- if (bFirst)
- {
- bFirst = FALSE;
- snew(names, MAXNAMES);
- for (i = 0; i < MAXNAMES; i++)
- {
- snew(names[i], NAME_LEN + 1);
- }
- }
+ char* ostring;
+ int j, n_names, sel_nr1;
+ int i, nr1, *index1;
+ unsigned char c;
+ gmx_bool bRet, bCompl;
bRet = FALSE;
sel_nr1 = NOTSET;
{
bRet = (select_atomnumbers(string, atoms, sel_nr1, nr, index, gname) != 0);
}
- else if (parse_names(string, &n_names, names))
+ else if (parse_names(string, &n_names, entryNames))
{
- bRet = (select_atomnames(atoms, n_names, names, nr, index, FALSE) != 0);
- make_gname(n_names, names, gname);
+ bRet = (select_atomnames(atoms, n_names, entryNames, nr, index, FALSE) != 0);
+ make_gname(n_names, entryNames, gname);
}
}
}
else if ((*string)[0] == 't')
{
(*string)++;
- if (check_have_atoms(atoms, ostring) && parse_names(string, &n_names, names))
+ if (check_have_atoms(atoms, ostring) && parse_names(string, &n_names, entryNames))
{
if (!(atoms->haveType))
{
}
else
{
- bRet = (select_atomnames(atoms, n_names, names, nr, index, TRUE) != 0);
- make_gname(n_names, names, gname);
+ bRet = (select_atomnames(atoms, n_names, entryNames, nr, index, TRUE) != 0);
+ make_gname(n_names, entryNames, gname);
}
}
}
{
bRet = (select_residuenumbers(string, atoms, sel_nr1, c, nr, index, gname) != 0);
}
- else if (parse_names(string, &n_names, names))
+ else if (parse_names(string, &n_names, entryNames))
{
- bRet = (select_residuenames(atoms, n_names, names, nr, index) != 0);
- make_gname(n_names, names, gname);
+ bRet = (select_residuenames(atoms, n_names, entryNames, nr, index) != 0);
+ make_gname(n_names, entryNames, gname);
}
}
}
else if (std::strncmp(*string, "chain", 5) == 0)
{
(*string) += 5;
- if (check_have_atoms(atoms, ostring) && parse_names(string, &n_names, names))
+ if (check_have_atoms(atoms, ostring) && parse_names(string, &n_names, entryNames))
{
- bRet = (select_chainnames(atoms, n_names, names, nr, index) != 0);
- sprintf(gname, "ch%s", names[0]);
+ bRet = (select_chainnames(atoms, n_names, entryNames, nr, index) != 0);
+ sprintf(gname, "ch%s", entryNames[0]);
for (i = 1; i < n_names; i++)
{
- std::strcat(gname, names[i]);
+ std::strcat(gname, entryNames[i]);
}
}
}
static void edit_index(int natoms, const t_atoms* atoms, const rvec* x, t_blocka* block, char*** gn, gmx_bool bVerbose)
{
- static char ** atnames, *ostring;
- static gmx_bool bFirst = TRUE;
- char inp_string[STRLEN], *string;
- char gname[STRLEN * 3], gname1[STRLEN], gname2[STRLEN];
- int i, i0, i1, sel_nr, sel_nr2, newgroup;
- int nr, nr1, nr2, *index, *index1, *index2;
- gmx_bool bAnd, bOr, bPrintOnce;
-
- if (bFirst)
- {
- bFirst = FALSE;
- snew(atnames, MAXNAMES);
- for (i = 0; i < MAXNAMES; i++)
- {
- snew(atnames[i], NAME_LEN + 1);
- }
- }
+ char* ostring;
+ char inp_string[STRLEN], *string;
+ char gname[STRLEN * 3], gname1[STRLEN], gname2[STRLEN];
+ int i, i0, i1, sel_nr, sel_nr2, newgroup;
+ int nr, nr1, nr2, *index, *index1, *index2;
+ gmx_bool bAnd, bOr, bPrintOnce;
string = nullptr;
newgroup = NOTSET;
bPrintOnce = TRUE;
+ std::array<char*, MAXNAMES> entryNames;
+ for (auto& name : entryNames)
+ {
+ snew(name, NAME_LEN + 1);
+ }
+
do
{
gname1[0] = '\0';
else if (string[0] != 'q')
{
nr2 = -1;
- if (parse_entry(&string, natoms, atoms, block, gn, &nr, index, gname))
+ if (parse_entry(&string, natoms, atoms, block, gn, &nr, index, gname, entryNames))
{
do
{
index1[i] = index[i];
}
std::strcpy(gname1, gname);
- if (parse_entry(&string, natoms, atoms, block, gn, &nr2, index2, gname2))
+ if (parse_entry(&string, natoms, atoms, block, gn, &nr2, index2, gname2, entryNames))
{
if (bOr)
{
}
} while (string[0] != 'q');
+ for (auto& name : entryNames)
+ {
+ sfree(name);
+ }
sfree(index);
sfree(index1);
sfree(index2);
bool haveFullTopology = false;
fprintf(stderr, "\nReading structure file\n");
readConfAndTopology(stxfile, &haveFullTopology, &mtop, &pbcType, &x, &v, box);
- atoms = gmx_mtop_global_atoms(&mtop);
+ atoms = gmx_mtop_global_atoms(mtop);
if (atoms.pdbinfo == nullptr)
{
snew(atoms.pdbinfo, atoms.nr);
natoms = block2natoms(block);
printf("Counted atom numbers up to %d in index file\n", natoms);
}
-
edit_index(natoms, &atoms, x, block, &gnames, bVerbose);
write_index(ndxoutfile, block, gnames, bDuplicate, natoms);
switch (ftype)
{
case F_ANGLES:
- sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
+ sprintf(buf,
+ "Theta=%.1f_%.2f",
+ idef->iparams[i].harmonic.rA,
idef->iparams[i].harmonic.krA);
break;
case F_G96ANGLES:
- sprintf(buf, "Cos_th=%.1f_%.2f", idef->iparams[i].harmonic.rA,
+ sprintf(buf,
+ "Cos_th=%.1f_%.2f",
+ idef->iparams[i].harmonic.rA,
idef->iparams[i].harmonic.krA);
break;
case F_UREY_BRADLEY:
- sprintf(buf, "UB_th=%.1f_%.2f2f", idef->iparams[i].u_b.thetaA,
+ sprintf(buf,
+ "UB_th=%.1f_%.2f2f",
+ idef->iparams[i].u_b.thetaA,
idef->iparams[i].u_b.kthetaA);
break;
case F_QUARTIC_ANGLES:
- sprintf(buf, "Q_th=%.1f_%.2f_%.2f", idef->iparams[i].qangle.theta,
- idef->iparams[i].qangle.c[0], idef->iparams[i].qangle.c[1]);
+ sprintf(buf,
+ "Q_th=%.1f_%.2f_%.2f",
+ idef->iparams[i].qangle.theta,
+ idef->iparams[i].qangle.c[0],
+ idef->iparams[i].qangle.c[1]);
break;
case F_TABANGLES:
- sprintf(buf, "Table=%d_%.2f", idef->iparams[i].tab.table,
+ sprintf(buf,
+ "Table=%d_%.2f",
+ idef->iparams[i].tab.table,
idef->iparams[i].tab.kA);
break;
case F_PDIHS:
- sprintf(buf, "Phi=%.1f_%d_%.2f", idef->iparams[i].pdihs.phiA,
- idef->iparams[i].pdihs.mult, idef->iparams[i].pdihs.cpA);
+ sprintf(buf,
+ "Phi=%.1f_%d_%.2f",
+ idef->iparams[i].pdihs.phiA,
+ idef->iparams[i].pdihs.mult,
+ idef->iparams[i].pdihs.cpA);
break;
case F_IDIHS:
- sprintf(buf, "Xi=%.1f_%.2f", idef->iparams[i].harmonic.rA,
+ sprintf(buf,
+ "Xi=%.1f_%.2f",
+ idef->iparams[i].harmonic.rA,
idef->iparams[i].harmonic.krA);
break;
case F_RBDIHS:
case F_RESTRANGLES:
// Fall through intended
case F_RESTRDIHS:
- sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
+ sprintf(buf,
+ "Theta=%.1f_%.2f",
+ idef->iparams[i].harmonic.rA,
idef->iparams[i].harmonic.krA);
break;
case F_CBTDIHS:
break;
default:
- gmx_fatal(FARGS, "Unsupported function type '%s' selected",
+ gmx_fatal(FARGS,
+ "Unsupported function type '%s' selected",
interaction_function[ftype].longname);
}
grpnames[ind] = gmx_strdup(buf);
*
* Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
* Copyright (c) 2015,2016,2017,2018,2019 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
fprintf(stderr,
"Molecule %2d (%5d atoms) q2_mol=%10.3e nr.mol.charges=%5d (%6dx) q2_all=%10.3e "
"tot.charges=%d\n",
- imol, molecule.atoms.nr, q2_mol, nrq_mol, molblock.nmol, q2_all, nrq_all);
+ imol,
+ molecule.atoms.nr,
+ q2_mol,
+ nrq_mol,
+ molblock.nmol,
+ q2_all,
+ nrq_all);
#endif
}
e_dir = 2.0 * info->q2all * gmx::invsqrt(info->q2allnr * r_coulomb * info->volume);
e_dir *= std::exp(-beta * beta * r_coulomb * r_coulomb);
- return ONE_4PI_EPS0 * e_dir;
+ return gmx::c_one4PiEps0 * e_dir;
}
#define SUMORDER 6
}
if (MASTER(cr))
{
- fprintf(stderr, "\rCalculating reciprocal error part 1 ... %3.0f%%",
+ fprintf(stderr,
+ "\rCalculating reciprocal error part 1 ... %3.0f%%",
100.0 * (nx - startlocal + 1) / (x_per_core));
fflush(stderr);
}
if (bVerbose && MASTER(cr))
{
- fprintf(stdout, "Using %d sample%s to approximate the self interaction error term",
- xtot, xtot == 1 ? "" : "s");
+ fprintf(stdout,
+ "Using %d sample%s to approximate the self interaction error term",
+ xtot,
+ xtot == 1 ? "" : "s");
if (PAR(cr))
{
fprintf(stdout, " (%d sample%s per rank)", x_per_core, x_per_core == 1 ? "" : "s");
e_rec = std::sqrt(e_rec1 + e_rec2 + e_rec3);
- return ONE_4PI_EPS0 * e_rec;
+ return gmx::c_one4PiEps0 * e_rec;
}
fprintf(fp_out, "Ewald_rtol : %g\n", info->ewald_rtol[0]);
fprintf(fp_out, "Ewald parameter beta : %g\n", info->ewald_beta[0]);
fprintf(fp_out, "Interpolation order : %d\n", info->pme_order[0]);
- fprintf(fp_out, "Fourier grid (nx,ny,nz) : %d x %d x %d\n", info->nkx[0], info->nky[0],
- info->nkz[0]);
+ fprintf(fp_out, "Fourier grid (nx,ny,nz) : %d x %d x %d\n", info->nkx[0], info->nky[0], info->nkz[0]);
fflush(fp_out);
}
if (MASTER(cr))
{
i++;
- fprintf(stderr, "difference between real and rec. space error (step %d): %g\n", i,
+ fprintf(stderr,
+ "difference between real and rec. space error (step %d): %g\n",
+ i,
std::abs(derr));
fprintf(stderr, "old beta: %f\n", beta0);
fprintf(stderr, "new beta: %f\n", beta);
t_commrec* cr = commrecHandle.get();
PCA_Flags = PCA_NOEXIT_ON_ARGS;
- if (!parse_common_args(&argc, argv, PCA_Flags, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0,
- nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_Flags, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
info.nkx[0] = 0;
info.nky[0] = 0;
info.nkz[0] = 0;
- calcFftGrid(stdout, state.box, info.fourier_sp[0], minimalPmeGridSize(info.pme_order[0]),
- &(info.nkx[0]), &(info.nky[0]), &(info.nkz[0]));
+ calcFftGrid(stdout,
+ state.box,
+ info.fourier_sp[0],
+ minimalPmeGridSize(info.pme_order[0]),
+ &(info.nkx[0]),
+ &(info.nky[0]),
+ &(info.nkz[0]));
if ((ir.nkx != info.nkx[0]) || (ir.nky != info.nky[0]) || (ir.nkz != info.nkz[0]))
{
gmx_fatal(FARGS,
"Wrong fourierspacing %f nm, input file grid = %d x %d x %d, computed grid = "
"%d x %d x %d",
- fs, ir.nkx, ir.nky, ir.nkz, info.nkx[0], info.nky[0], info.nkz[0]);
+ fs,
+ ir.nkx,
+ ir.nky,
+ ir.nkz,
+ info.nkx[0],
+ info.nky[0],
+ info.nkz[0]);
}
}
if (opt2bSet("-so", NFILE, fnm) || bTUNE)
{
ir.ewald_rtol = info.ewald_rtol[0];
- write_tpx_state(opt2fn("-so", NFILE, fnm), &ir, &state, &mtop);
+ write_tpx_state(opt2fn("-so", NFILE, fnm), &ir, &state, mtop);
}
please_cite(fp, "Wang2010");
fclose(fp);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const t_atom* atom;
writeHeader(writer, "Simulation system", "subsection", writeFormattedText);
- aloop = gmx_mtop_atomloop_block_init(&top);
+ aloop = gmx_mtop_atomloop_block_init(top);
while (gmx_mtop_atomloop_block_next(aloop, &atom, &nmol))
{
- if (atom->ptype == eptVSite)
+ if (atom->ptype == ParticleType::VSite)
{
nvsite += nmol;
}
}
{
writer->writeLine(formatString("A system of %d molecules (%d atoms) was simulated.",
- gmx_mtop_num_molecules(top), top.natoms - nvsite));
+ gmx_mtop_num_molecules(top),
+ top.natoms - nvsite));
}
if (nvsite)
{
{
writeHeader(writer, "Simulation settings", "subsection", writeFormattedText);
writer->writeLine(formatString("A total of %g ns were simulated with a time step of %g fs.",
- ir.nsteps * ir.delta_t * 0.001, 1000 * ir.delta_t));
+ ir.nsteps * ir.delta_t * 0.001,
+ 1000 * ir.delta_t));
writer->writeLine(formatString("Neighbor searching was performed every %d steps.", ir.nstlist));
writer->writeLine(formatString("The %s algorithm was used for electrostatic interactions.",
- EELTYPE(ir.coulombtype)));
+ enumValueToString(ir.coulombtype)));
writer->writeLine(formatString("with a cut-off of %g nm.", ir.rcoulomb));
- if (ir.coulombtype == eelPME)
+ if (ir.coulombtype == CoulombInteractionType::Pme)
{
writer->writeLine(
formatString("A reciprocal grid of %d x %d x %d cells was used with %dth order "
"B-spline interpolation.",
- ir.nkx, ir.nky, ir.nkz, ir.pme_order));
+ ir.nkx,
+ ir.nky,
+ ir.nkz,
+ ir.pme_order));
}
writer->writeLine(formatString(
"A single cut-off of %g nm was used for Van der Waals interactions.", ir.rlist));
- if (ir.etc != 0)
+ if (ir.etc != TemperatureCoupling::No)
{
writer->writeLine(formatString("Temperature coupling was done with the %s algorithm.",
- etcoupl_names[ir.etc]));
+ enumValueToString(ir.etc)));
}
- if (ir.epc != 0)
+ if (ir.epc != PressureCoupling::No)
{
writer->writeLine(formatString("Pressure coupling was done with the %s algorithm.",
- epcoupl_names[ir.epc]));
+ enumValueToString(ir.epc)));
}
writer->ensureEmptyLine();
}
settings->setHelpText(desc);
options->addOption(FileNameOption("s")
- .filetype(eftTopology)
+ .filetype(OptionFileType::Topology)
.inputFile()
.required()
.store(&inputTopology_)
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
TEST_F(DumpTest, WorksWithTprAndMdpWriting)
{
- TestFileManager fileManager;
- std::string mdpName = fileManager.getTemporaryFilePath("output.mdp");
- const char* const command[] = { "dump", "-s", s_tprFileHandle->tprName().c_str(), "-om",
- mdpName.c_str() };
- CommandLine cmdline(command);
+ TestFileManager fileManager;
+ std::string mdpName = fileManager.getTemporaryFilePath("output.mdp");
+ const char* const command[] = { "dump", "-s", s_tprFileHandle->tprName().c_str(), "-om", mdpName.c_str() };
+ CommandLine cmdline(command);
runTest(&cmdline);
}
{
const char* const command[] = { "report-methods", "-s", s_tprFileHandle->tprName().c_str() };
CommandLine cmdline(command);
- EXPECT_EQ(0, gmx::test::CommandLineTestHelper::runModuleFactory(&gmx::ReportMethodsInfo::create,
- &cmdline));
+ EXPECT_EQ(0, gmx::test::CommandLineTestHelper::runModuleFactory(&gmx::ReportMethodsInfo::create, &cmdline));
}
} // namespace test
fprintf(stderr,
" File Current start (%s) New start (%s)\n"
"---------------------------------------------------------\n",
- timeUnit.c_str(), timeUnit.c_str());
+ timeUnit.c_str(),
+ timeUnit.c_str());
for (gmx::index i = 0; i < files.ssize(); i++)
{
- fprintf(stderr, "%25s %10.3f %s ", files[i].c_str(),
- output_env_conv_time(oenv, readtime[i]), timeUnit.c_str());
+ fprintf(stderr,
+ "%25s %10.3f %s ",
+ files[i].c_str(),
+ output_env_conv_time(oenv, readtime[i]),
+ timeUnit.c_str());
ok = FALSE;
do
{
switch (cont_type[i])
{
case TIME_EXPLICIT:
- fprintf(stderr, "%25s %10.3f %s %10.3f %s", files[i].c_str(),
- output_env_conv_time(oenv, settime[i]), timeUnit.c_str(),
- output_env_conv_time(oenv, timestep[i]), timeUnit.c_str());
+ fprintf(stderr,
+ "%25s %10.3f %s %10.3f %s",
+ files[i].c_str(),
+ output_env_conv_time(oenv, settime[i]),
+ timeUnit.c_str(),
+ output_env_conv_time(oenv, timestep[i]),
+ timeUnit.c_str());
if (i > 0 && cont_type[i - 1] == TIME_EXPLICIT && settime[i] == settime[i - 1])
{
fprintf(stderr, " WARNING: same Start time as previous");
}
else if (natoms != trx[i].natoms)
{
- gmx_fatal(FARGS, "Trajectory file %s has %d atoms while previous trajs had %d atoms",
- inFiles[i].c_str(), trx[i].natoms, natoms);
+ gmx_fatal(FARGS,
+ "Trajectory file %s has %d atoms while previous trajs had %d atoms",
+ inFiles[i].c_str(),
+ trx[i].natoms,
+ natoms);
}
if (t == -1)
{
}
else if (t != trx[i].time)
{
- gmx_fatal(FARGS, "Trajectory file %s has time %f while previous trajs had time %f",
- inFiles[i].c_str(), trx[i].time, t);
+ gmx_fatal(FARGS,
+ "Trajectory file %s has time %f while previous trajs had time %f",
+ inFiles[i].c_str(),
+ trx[i].time,
+ t);
}
}
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_TIME_UNIT, NFILE, fnm, asize(pa), pa, asize(desc), desc,
- 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_TIME_UNIT, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
{
nset = 0;
dt_remd = 0;
- val = read_xvg_time(opt2fn("-demux", NFILE, fnm), TRUE, opt2parg_bSet("-b", npargs, pa),
- begin, opt2parg_bSet("-e", npargs, pa), end, 1, &nset, &n, &dt_remd, &t);
+ val = read_xvg_time(opt2fn("-demux", NFILE, fnm),
+ TRUE,
+ opt2parg_bSet("-b", npargs, pa),
+ begin,
+ opt2parg_bSet("-e", npargs, pa),
+ end,
+ 1,
+ &nset,
+ &n,
+ &dt_remd,
+ &t);
printf("Read %d sets of %d points, dt = %g\n\n", nset, n, dt_remd);
if (debug)
{
if (bDeMux && ssize(inFiles) != nset)
{
- gmx_fatal(FARGS, "You have specified %td files and %d entries in the demux table",
- inFiles.ssize(), nset);
+ gmx_fatal(FARGS, "You have specified %td files and %d entries in the demux table", inFiles.ssize(), nset);
}
ftpin = fn2ftp(inFiles[0].c_str());
}
else if (bDeMux && ssize(outFiles) != nset && outFiles.size() != 1)
{
- gmx_fatal(FARGS, "Number of output files should be 1 or %d (#input files), not %td", nset,
+ gmx_fatal(FARGS,
+ "Number of output files should be 1 or %d (#input files), not %td",
+ nset,
outFiles.ssize());
}
if (bDeMux)
}
else if (n_append != -1)
{
- gmx_fatal(FARGS, "Can only append to the first file which is %s (not %s)",
- inFilesEdited[0].c_str(), out_file);
+ gmx_fatal(FARGS,
+ "Can only append to the first file which is %s (not %s)",
+ inFilesEdited[0].c_str(),
+ out_file);
}
/* Not checking input format, could be dangerous :-) */
}
if (bIndex)
{
- trxout = trjtools_gmx_prepare_tng_writing(
- out_file, 'w', nullptr, inFilesEdited[0].c_str(), isize, nullptr,
- gmx::arrayRefFromArray(index, isize), grpname);
+ trxout = trjtools_gmx_prepare_tng_writing(out_file,
+ 'w',
+ nullptr,
+ inFilesEdited[0].c_str(),
+ isize,
+ nullptr,
+ gmx::arrayRefFromArray(index, isize),
+ grpname);
}
else
{
read_next_frame(oenv, status, &fr);
if (std::abs(searchtime - fr.time) > timest[0] * 0.5)
{
- gmx_fatal(FARGS, "Error seeking: attempted to seek to %f but got %f.",
- searchtime, fr.time);
+ gmx_fatal(FARGS, "Error seeking: attempted to seek to %f but got %f.", searchtime, fr.time);
}
lasttime = fr.time;
lastTimeSet = TRUE;
"spacing than the rest,\n"
"might be a gap or overlap that couldn't be corrected "
"automatically.\n",
- output_env_conv_time(oenv, frout.time), timeUnit.c_str());
+ output_env_conv_time(oenv, frout.time),
+ timeUnit.c_str());
}
}
}
"\nContinue writing frames from %s t=%g %s, "
"frame=%d \n",
inFilesEdited[i].c_str(),
- output_env_conv_time(oenv, frout.time), timeUnit.c_str(), frame);
+ output_env_conv_time(oenv, frout.time),
+ timeUnit.c_str(),
+ frame);
bNewFile = FALSE;
}
}
if (((frame % 10) == 0) || (frame < 10))
{
- fprintf(stderr, " -> frame %6d time %8.3f %s \r", frame_out,
- output_env_conv_time(oenv, frout.time), timeUnit.c_str());
+ fprintf(stderr,
+ " -> frame %6d time %8.3f %s \r",
+ frame_out,
+ output_env_conv_time(oenv, frout.time),
+ timeUnit.c_str());
fflush(stderr);
}
}
{
close_trx(trxout);
}
- fprintf(stderr, "\nLast frame written was %d, time %f %s\n", frame,
- output_env_conv_time(oenv, last_ok_t), timeUnit.c_str());
+ fprintf(stderr,
+ "\nLast frame written was %d, time %f %s\n",
+ frame,
+ output_env_conv_time(oenv, last_ok_t),
+ timeUnit.c_str());
}
return 0;
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
fprintf(stderr,
"Do you REALLY want to truncate this trajectory (%s) at:\n"
"frame %d, time %g, bytes %ld ??? (type YES if so)\n",
- fn, j, t, static_cast<long int>(fpos));
+ fn,
+ j,
+ t,
+ static_cast<long int>(fpos));
if (1 != scanf("%s", yesno))
{
gmx_fatal(FARGS, "Error reading user input");
const char* fit[efNR + 1] = { nullptr, "none", "rot+trans", "rotxy+transxy",
"translation", "transxy", "progressive", nullptr };
- static gmx_bool bSeparate = FALSE, bVels = TRUE, bForce = FALSE, bCONECT = FALSE;
- static gmx_bool bCenter = FALSE;
- static int skip_nr = 1, ndec = 3, nzero = 0;
- static real tzero = 0, delta_t = 0, timestep = 0, ttrunc = -1, tdump = -1, split_t = 0;
- static rvec newbox = { 0, 0, 0 }, shift = { 0, 0, 0 }, trans = { 0, 0, 0 };
- static char* exec_command = nullptr;
- static real dropunder = 0, dropover = 0;
- static gmx_bool bRound = FALSE;
+ gmx_bool bSeparate = FALSE, bVels = TRUE, bForce = FALSE, bCONECT = FALSE;
+ gmx_bool bCenter = FALSE;
+ int skip_nr = 1, ndec = 3, nzero = 0;
+ real tzero = 0, delta_t = 0, timestep = 0, ttrunc = -1, tdump = -1, split_t = 0;
+ rvec newbox = { 0, 0, 0 }, shift = { 0, 0, 0 }, trans = { 0, 0, 0 };
+ char* exec_command = nullptr;
+ real dropunder = 0, dropover = 0;
+ gmx_bool bRound = FALSE;
t_pargs pa[] = {
{ "-skip", FALSE, etINT, { &skip_nr }, "Only write every nr-th frame" },
{ efXVG, "-drop", "drop", ffOPTRD } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc,
+ argv,
+ PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT,
+ NFILE,
+ fnm,
+ NPA,
+ pa,
+ asize(desc),
+ desc,
+ 0,
+ nullptr,
+ &oenv))
{
return 0;
}
"WARNING: Option for unitcell representation (-ur %s)\n"
" only has effect in combination with -pbc %s, %s or %s.\n"
" Ingoring unitcell representation.\n\n",
- unitcell_opt[0], pbc_opt[2], pbc_opt[3], pbc_opt[4]);
+ unitcell_opt[0],
+ pbc_opt[2],
+ pbc_opt[3],
+ pbc_opt[4]);
}
}
if (bFit && bPBC)
if (0 == top->mols.nr && (bCluster || bPBCcomMol))
{
- gmx_fatal(FARGS, "Option -pbc %s requires a .tpr file for the -s option",
- pbc_opt[pbc_enum]);
+ gmx_fatal(FARGS, "Option -pbc %s requires a .tpr file for the -s option", pbc_opt[pbc_enum]);
}
/* top_title is only used for gro and pdb,
"Index[%d] %d is larger than the number of atoms in the\n"
"trajectory file (%d). There is a mismatch in the contents\n"
"of your -f, -s and/or -n files.",
- i, index[i] + 1, natoms);
+ i,
+ index[i] + 1,
+ natoms);
}
bCopy = bCopy || (i != index[i]);
}
switch (ftp)
{
case efTNG:
- trxout = trjtools_gmx_prepare_tng_writing(
- out_file, filemode[0], trxin, nullptr, nout, mtop.get(),
- gmx::arrayRefFromArray(index, nout), grpnm);
+ trxout = trjtools_gmx_prepare_tng_writing(out_file,
+ filemode[0],
+ trxin,
+ nullptr,
+ nout,
+ mtop.get(),
+ gmx::arrayRefFromArray(index, nout),
+ grpnm);
break;
case efXTC:
case efTRR:
if (bTDump)
{
- fprintf(stderr, "\nDumping frame at t= %g %s\n",
+ fprintf(stderr,
+ "\nDumping frame at t= %g %s\n",
output_env_conv_time(oenv, frout_time),
output_env_get_time_unit(oenv).c_str());
}
else
{
/* round() is not C89 compatible, so we do this: */
- bDoIt = bRmod(std::floor(frout_time + 0.5), std::floor(tzero + 0.5),
+ bDoIt = bRmod(std::floor(frout_time + 0.5),
+ std::floor(tzero + 0.5),
std::floor(delta_t + 0.5));
}
}
/* print sometimes */
if (((outframe % SKIP) == 0) || (outframe < SKIP))
{
- fprintf(stderr, " -> frame %6d time %8.3f \r", outframe,
+ fprintf(stderr,
+ " -> frame %6d time %8.3f \r",
+ outframe,
output_env_conv_time(oenv, frout_time));
fflush(stderr);
}
put_atoms_in_triclinic_unitcell(ecenter, fr.box, positionsArrayRef);
break;
case euCompact:
- put_atoms_in_compact_unitcell(pbcType, ecenter, fr.box,
- positionsArrayRef);
+ put_atoms_in_compact_unitcell(
+ pbcType, ecenter, fr.box, positionsArrayRef);
break;
}
}
if (bPBCcomRes)
{
- put_residue_com_in_box(unitcell_enum, ecenter, natoms, atoms->atom,
- pbcType, fr.box, fr.x);
+ put_residue_com_in_box(
+ unitcell_enum, ecenter, natoms, atoms->atom, pbcType, fr.box, fr.x);
}
if (bPBCcomMol)
{
- put_molecule_com_in_box(unitcell_enum, ecenter, &top->mols, natoms,
- atoms->atom, pbcType, fr.box, fr.x);
+ put_molecule_com_in_box(
+ unitcell_enum, ecenter, &top->mols, natoms, atoms->atom, pbcType, fr.box, fr.x);
}
/* Copy the input trxframe struct to the output trxframe struct */
frout = fr;
/* round() is not C89 compatible, so we do this: */
bSplitHere = bSplit
&& bRmod(std::floor(frout.time + 0.5),
- std::floor(tzero + 0.5), std::floor(split_t + 0.5));
+ std::floor(tzero + 0.5),
+ std::floor(split_t + 0.5));
}
if (bSeparate || bSplitHere)
{
switch (ftp)
{
case efGRO:
- write_hconf_p(out, title.c_str(), &useatoms, frout.x,
- frout.bV ? frout.v : nullptr, frout.box);
+ write_hconf_p(out,
+ title.c_str(),
+ &useatoms,
+ frout.x,
+ frout.bV ? frout.v : nullptr,
+ frout.box);
break;
case efPDB:
fprintf(out, "REMARK GENERATED BY TRJCONV\n");
{
model_nr++;
}
- write_pdbfile(out, title.c_str(), &useatoms, frout.x,
- frout.pbcType, frout.box, ' ', model_nr, gc);
+ write_pdbfile(out,
+ title.c_str(),
+ &useatoms,
+ frout.x,
+ frout.pbcType,
+ frout.box,
+ ' ',
+ model_nr,
+ gc);
break;
case efG96:
const char* outputTitle = "";
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2009-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
fprintf(stderr,
"WARNING: Time step counters were reset at step %s,\n"
" though they were supposed to be reset at step %s!\n",
- dumstring, dumstring2);
+ dumstring,
+ dumstring2);
}
}
}
/* Look for domain decomp grid and separate PME nodes: */
if (str_starts(line, matchstrdd))
{
- sscanf(line, "Domain decomposition grid %d x %d x %d, separate PME ranks %d",
- &(perfdata->nx), &(perfdata->ny), &(perfdata->nz), &npme);
+ sscanf(line,
+ "Domain decomposition grid %d x %d x %d, separate PME ranks %d",
+ &(perfdata->nx),
+ &(perfdata->ny),
+ &(perfdata->nz),
+ &npme);
if (perfdata->nPMEnodes == -1)
{
perfdata->guessPME = npme;
s /= (nrepeats - 1);
s = std::sqrt(s);
- fprintf(fp, "%4d %3d %4d%s %12.3f %12.3f %12.3f %s", line, k, pd->nPMEnodes,
- strbuf, pd->Gcycles_Av, s, pd->ns_per_day_Av, str_PME_f_load);
+ fprintf(fp,
+ "%4d %3d %4d%s %12.3f %12.3f %12.3f %s",
+ line,
+ k,
+ pd->nPMEnodes,
+ strbuf,
+ pd->Gcycles_Av,
+ s,
+ pd->ns_per_day_Av,
+ str_PME_f_load);
if (nnodes > 1)
{
fprintf(fp, " %3d %3d %3d", pd->nx, pd->ny, pd->nz);
if (bRefinedCoul)
{
- fprintf(fp, " New Coulomb radius: %f nm (was %f nm)\n", info->rcoulomb[k_win],
- info->rcoulomb[0]);
+ fprintf(fp, " New Coulomb radius: %f nm (was %f nm)\n", info->rcoulomb[k_win], info->rcoulomb[0]);
}
if (bRefinedVdW)
if (bRefinedGrid)
{
- fprintf(fp, " New Fourier grid xyz: %d %d %d (was %d %d %d)\n", info->nkx[k_win],
- info->nky[k_win], info->nkz[k_win], info->nkx[0], info->nky[0], info->nkz[0]);
+ fprintf(fp,
+ " New Fourier grid xyz: %d %d %d (was %d %d %d)\n",
+ info->nkx[k_win],
+ info->nky[k_win],
+ info->nkz[k_win],
+ info->nkx[0],
+ info->nky[0],
+ info->nkz[0]);
}
if (bCanUseOrigTPR && ntprs > 1)
}
else
{
- snew(command, std::strlen(cmd_mpirun) + std::strlen(cmd_np) + std::strlen(cmd_mdrun)
- + std::strlen(filename) + 50);
+ snew(command,
+ std::strlen(cmd_mpirun) + std::strlen(cmd_np) + std::strlen(cmd_mdrun)
+ + std::strlen(filename) + 50);
sprintf(command, "%s%s%s -version -maxh 0.001 1> %s 2>&1", cmd_mpirun, cmd_np, cmd_mdrun, filename);
}
fprintf(stdout, "Trying '%s' ... ", command);
/* Make enough space for the system call command,
* (200 extra chars for -npme ... etc. options should suffice): */
- snew(command, std::strlen(cmd_mpirun) + std::strlen(cmd_mdrun) + std::strlen(cmd_np)
- + std::strlen(args_for_mdrun) + std::strlen(simulation_tpr) + 200);
+ snew(command,
+ std::strlen(cmd_mpirun) + std::strlen(cmd_mdrun) + std::strlen(cmd_np)
+ + std::strlen(args_for_mdrun) + std::strlen(simulation_tpr) + 200);
auto cmd_gpu_ids = make_gpu_id_command_line(eligible_gpu_ids);
* of the command line string */
if (bThreads)
{
- sprintf(command, "%s%s-npme %d -s %s %s %s", cmd_mdrun, cmd_np, nPMEnodes, simulation_tpr,
- args_for_mdrun, cmd_gpu_ids.c_str());
+ sprintf(command,
+ "%s%s-npme %d -s %s %s %s",
+ cmd_mdrun,
+ cmd_np,
+ nPMEnodes,
+ simulation_tpr,
+ args_for_mdrun,
+ cmd_gpu_ids.c_str());
}
else
{
- sprintf(command, "%s%s%s -npme %d -s %s %s %s", cmd_mpirun, cmd_np, cmd_mdrun, nPMEnodes,
- simulation_tpr, args_for_mdrun, cmd_gpu_ids.c_str());
+ sprintf(command,
+ "%s%s%s -npme %d -s %s %s %s",
+ cmd_mpirun,
+ cmd_np,
+ cmd_mdrun,
+ nPMEnodes,
+ simulation_tpr,
+ args_for_mdrun,
+ cmd_gpu_ids.c_str());
}
- fprintf(fp, "%s this command line to launch the simulation:\n\n%s",
- bLaunch ? "Using" : "Please use", command);
+ fprintf(fp, "%s this command line to launch the simulation:\n\n%s", bLaunch ? "Using" : "Please use", command);
sep_line(fp);
fflush(fp);
sprintf(buf, "Writing optimized simulation file %s with nsteps=%s.\n", fn_sim_tpr, "%" PRId64);
fprintf(stdout, buf, ir->nsteps);
fflush(stdout);
- write_tpx_state(fn_sim_tpr, ir, &state, &mtop);
+ write_tpx_state(fn_sim_tpr, ir, &state, mtop);
}
-static gmx_bool can_scale_rvdw(int vdwtype)
+static gmx_bool can_scale_rvdw(VanDerWaalsType vdwtype)
{
- return (evdwCUT == vdwtype || evdwPME == vdwtype);
+ return (VanDerWaalsType::Cut == vdwtype || VanDerWaalsType::Pme == vdwtype);
}
-#define EPME_SWITCHED(e) ((e) == eelPMESWITCH || (e) == eelPMEUSERSWITCH)
+#define EPME_SWITCHED(e) \
+ ((e) == CoulombInteractionType::PmeSwitch || (e) == CoulombInteractionType::PmeUserSwitch)
/* Make additional TPR files with more computational load for the
* direct space processors: */
real fourierspacing; /* Basic fourierspacing from tpr */
- sprintf(buf, "Making benchmark tpr file%s with %s time step%s", *ntprs > 1 ? "s" : "",
- "%" PRId64, benchsteps > 1 ? "s" : "");
+ sprintf(buf,
+ "Making benchmark tpr file%s with %s time step%s",
+ *ntprs > 1 ? "s" : "",
+ "%" PRId64,
+ benchsteps > 1 ? "s" : "");
fprintf(stdout, buf, benchsteps);
if (statesteps > 0)
{
/* Check if some kind of PME was chosen */
if (EEL_PME(ir->coulombtype) == FALSE)
{
- gmx_fatal(FARGS, "Can only do optimizations for simulations with %s electrostatics.",
- EELTYPE(eelPME));
+ gmx_fatal(FARGS,
+ "Can only do optimizations for simulations with %s electrostatics.",
+ enumValueToString(CoulombInteractionType::Pme));
}
/* Check if rcoulomb == rlist, which is necessary for plain PME. */
- if ((ir->cutoff_scheme != ecutsVERLET) && (eelPME == ir->coulombtype) && !(ir->rcoulomb == ir->rlist))
+ if ((ir->cutoff_scheme != CutoffScheme::Verlet)
+ && (CoulombInteractionType::Pme == ir->coulombtype) && !(ir->rcoulomb == ir->rlist))
{
- gmx_fatal(FARGS, "%s requires rcoulomb (%f) to be equal to rlist (%f).", EELTYPE(eelPME),
- ir->rcoulomb, ir->rlist);
+ gmx_fatal(FARGS,
+ "%s requires rcoulomb (%f) to be equal to rlist (%f).",
+ enumValueToString(CoulombInteractionType::Pme),
+ ir->rcoulomb,
+ ir->rlist);
}
/* For other PME types, rcoulomb is allowed to be smaller than rlist */
else if (ir->rcoulomb > ir->rlist)
{
- gmx_fatal(FARGS, "%s requires rcoulomb (%f) to be equal to or smaller than rlist (%f)",
- EELTYPE(ir->coulombtype), ir->rcoulomb, ir->rlist);
+ gmx_fatal(FARGS,
+ "%s requires rcoulomb (%f) to be equal to or smaller than rlist (%f)",
+ enumValueToString(ir->coulombtype),
+ ir->rcoulomb,
+ ir->rlist);
}
if (bScaleRvdw && ir->rvdw != ir->rcoulomb)
fourierspacing = std::max(std::max(info->fsx[0], info->fsy[0]), info->fsz[0]);
}
- fprintf(stdout, "Calculating PME grid points on the basis of a fourierspacing of %f nm\n",
- fourierspacing);
+ fprintf(stdout, "Calculating PME grid points on the basis of a fourierspacing of %f nm\n", fourierspacing);
/* For performance comparisons the number of particles is useful to have */
fprintf(fp, " Number of particles : %d\n", mtop.natoms);
/* Print information about settings of which some are potentially modified: */
- fprintf(fp, " Coulomb type : %s\n", EELTYPE(ir->coulombtype));
- fprintf(fp, " Grid spacing x y z : %f %f %f\n", box_size[XX] / ir->nkx,
- box_size[YY] / ir->nky, box_size[ZZ] / ir->nkz);
- fprintf(fp, " Van der Waals type : %s\n", EVDWTYPE(ir->vdwtype));
+ fprintf(fp, " Coulomb type : %s\n", enumValueToString(ir->coulombtype));
+ fprintf(fp,
+ " Grid spacing x y z : %f %f %f\n",
+ box_size[XX] / ir->nkx,
+ box_size[YY] / ir->nky,
+ box_size[ZZ] / ir->nkz);
+ fprintf(fp, " Van der Waals type : %s\n", enumValueToString(ir->vdwtype));
if (ir_vdw_switched(ir))
{
fprintf(fp, " rvdw_switch : %f nm\n", ir->rvdw_switch);
/* Scale the Fourier grid spacing */
ir->nkx = ir->nky = ir->nkz = 0;
- calcFftGrid(nullptr, state.box, fourierspacing * fac, minimalPmeGridSize(ir->pme_order),
- &ir->nkx, &ir->nky, &ir->nkz);
+ calcFftGrid(nullptr,
+ state.box,
+ fourierspacing * fac,
+ minimalPmeGridSize(ir->pme_order),
+ &ir->nkx,
+ &ir->nky,
+ &ir->nkz);
/* Adjust other radii since various conditions need to be fulfilled */
- if (eelPME == ir->coulombtype)
+ if (CoulombInteractionType::Pme == ir->coulombtype)
{
/* plain PME, rcoulomb must be equal to rlist TODO only in the group scheme? */
ir->rlist = ir->rcoulomb;
if (bScaleRvdw && can_scale_rvdw(ir->vdwtype))
{
- if (ecutsVERLET == ir->cutoff_scheme || evdwPME == ir->vdwtype)
+ if (CutoffScheme::Verlet == ir->cutoff_scheme || VanDerWaalsType::Pme == ir->vdwtype)
{
/* With either the Verlet cutoff-scheme or LJ-PME,
the van der Waals radius must always equal the
fprintf(stdout, ", unmodified settings\n");
}
- write_tpx_state(fn_bench_tprs[j], ir, &state, &mtop);
+ write_tpx_state(fn_bench_tprs[j], ir, &state, mtop);
/* Write information about modified tpr settings to log file */
fprintf(fp, "%4d%10f%10f", j, fac, ir->rcoulomb);
* the -passall (if set) options requires cmd_args_bench to be
* at the end of the command line string */
snew(pd->mdrun_cmd_line, cmdline_length);
- sprintf(pd->mdrun_cmd_line, "%s-npme %d -s %s %s %s", cmd_stub, pd->nPMEnodes,
- tpr_names[k], cmd_args_bench, cmd_gpu_ids.c_str());
+ sprintf(pd->mdrun_cmd_line,
+ "%s-npme %d -s %s %s %s",
+ cmd_stub,
+ pd->nPMEnodes,
+ tpr_names[k],
+ cmd_args_bench,
+ cmd_gpu_ids.c_str());
/* To prevent that all benchmarks fail due to a show-stopper argument
* on the mdrun command line, we make a quick check first.
do for this check, but it'll be easier to
implement that after some refactoring of how
the number of MPI ranks is managed. */
- sprintf(temporary_cmd_line, "%s-npme 0 -nb cpu -s %s %s", cmd_stub,
- tpr_names[k], cmd_args_bench);
+ sprintf(temporary_cmd_line, "%s-npme 0 -nb cpu -s %s %s", cmd_stub, tpr_names[k], cmd_args_bench);
make_sure_it_runs(temporary_cmd_line, cmdline_length, fp, fnm, nfile);
}
bFirst = FALSE;
{
buf[0] = '\0';
}
- fprintf(stdout, "\n=== Progress %2.0f%%, tpr %d/%d, run %d/%d%s:\n",
- (100.0 * count) / totaltests, k + 1, nr_tprs, i + 1, *pmeentries, buf);
+ fprintf(stdout,
+ "\n=== Progress %2.0f%%, tpr %d/%d, run %d/%d%s:\n",
+ (100.0 * count) / totaltests,
+ k + 1,
+ nr_tprs,
+ i + 1,
+ *pmeentries,
+ buf);
make_backup(opt2fn("-err", nfile, fnm));
sprintf(command, "%s 1> /dev/null 2>%s", pd->mdrun_cmd_line, opt2fn("-err", nfile, fnm));
fprintf(stdout, "%s\n", pd->mdrun_cmd_line);
/* Collect the performance data from the log file; also check stderr
* for fatal errors */
- ret = parse_logfile(opt2fn("-bg", nfile, fnm), opt2fn("-err", nfile, fnm), pd, nr,
- presteps, cpt_steps, nnodes);
+ ret = parse_logfile(
+ opt2fn("-bg", nfile, fnm), opt2fn("-err", nfile, fnm), pd, nr, presteps, cpt_steps, nnodes);
if ((presteps > 0) && (ret == eParselogResetProblem))
{
bResetProblem = TRUE;
}
/* Write the data we got to disk */
- fprintf(fp, "%4d%s %12.3f %12.3f %s %s", pd->nPMEnodes, buf, pd->Gcycles[nr],
- pd->ns_per_day[nr], str_PME_f_load, ParseLog[ret]);
+ fprintf(fp,
+ "%4d%s %12.3f %12.3f %s %s",
+ pd->nPMEnodes,
+ buf,
+ pd->Gcycles[nr],
+ pd->ns_per_day[nr],
+ str_PME_f_load,
+ ParseLog[ret]);
if (!(ret == eParselogOK || ret == eParselogNoDDGrid || ret == eParselogNotFound))
{
fprintf(fp, " Check %s file for problems.", ret == eParselogFatal ? "err" : "log");
gmx_fatal(FARGS,
"Please choose the Coulomb radii such that rmin <= rmax.\n"
"rmin = %g, rmax = %g, actual rcoul from .tpr file = %g\n",
- *rmin, *rmax, rcoulomb);
+ *rmin,
+ *rmax,
+ rcoulomb);
}
/* Add test scenarios if rmin or rmax were set */
if (*ntprs <= 2)
{
fprintf(stderr, "WARNING: steps=");
fprintf(stderr, "%" PRId64, bench_nsteps);
- fprintf(stderr, ". Are you sure you want to perform so %s steps for each benchmark?\n",
+ fprintf(stderr,
+ ". Are you sure you want to perform so %s steps for each benchmark?\n",
(bench_nsteps < 100) ? "few" : "many");
}
gmx_fatal(FARGS,
"Cannot have more than %d PME-only ranks for a total of %d ranks (you chose "
"%d).\n",
- nnodes / 2, nnodes, npme_fixed);
+ nnodes / 2,
+ nnodes,
+ npme_fixed);
}
if ((npme_fixed > 0) && (5 * npme_fixed < nnodes))
{
t_inputrec irInstance;
t_inputrec* ir = &irInstance;
read_tpx_state(opt2fn("-s", nfile, fnm), ir, &state, &mtop);
- bFree = (efepNO != ir->efep);
- bNM = (eiNM == ir->eI);
- bSwap = (eswapNO != ir->eSwapCoords);
+ bFree = (FreeEnergyPerturbationType::No != ir->efep);
+ bNM = (IntegrationAlgorithm::NM == ir->eI);
+ bSwap = (SwapType::No != ir->eSwapCoords);
bTpi = EI_TPI(ir->eI);
/* Set these output files on the tuning command-line */
"[THISMODULE] needs to call [gmx-mdrun] and so requires that you",
"specify how to call mdrun with the argument to the [TT]-mdrun[tt]",
"parameter. Depending how you have built GROMACS, values such as",
- "'gmx mdrun', 'gmx_d mdrun', or 'mdrun_mpi' might be needed.[PAR]",
+ "'gmx mdrun', 'gmx_d mdrun', or 'gmx_mpi mdrun' might be needed.[PAR]",
"The program that runs MPI programs can be set in the environment variable",
"MPIRUN (defaults to 'mpirun'). Note that for certain MPI frameworks,",
"you need to provide a machine- or hostfile. This can also be passed",
FALSE,
etSTR,
{ &cmd_mdrun },
- "Command line to run a simulation, e.g. 'gmx mdrun' or 'mdrun_mpi'" },
+ "Command line to run a simulation, e.g. 'gmx mdrun' or 'gmx_mpi mdrun'" },
{ "-np",
FALSE,
etINT,
seconds = gmx_gettime();
- if (!parse_common_args(&argc, argv, PCA_NOEXIT_ON_ARGS, NFILE, fnm, asize(pa), pa, asize(desc),
- desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_NOEXIT_ON_ARGS, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
cmd_np = bbuf;
- create_command_line_snippets(bAppendFiles, bKeepAndNumCPT, bResetCountersHalfWay, presteps,
- NFILE, fnm, &cmd_args_bench, &cmd_args_launch, ExtraArgs, deffnm);
+ create_command_line_snippets(bAppendFiles,
+ bKeepAndNumCPT,
+ bResetCountersHalfWay,
+ presteps,
+ NFILE,
+ fnm,
+ &cmd_args_bench,
+ &cmd_args_launch,
+ ExtraArgs,
+ deffnm);
/* Prepare to use checkpoint file if requested */
sim_part = 1;
fp = gmx_ffopen(opt2fn("-p", NFILE, fnm), "w");
/* Make a quick consistency check of command line parameters */
- check_input(nnodes, repeats, &ntprs, &rmin, rcoulomb, &rmax, maxPMEfraction, minPMEfraction,
- npme_fixed, bench_nsteps, fnm, NFILE, sim_part, presteps, asize(pa), pa);
+ check_input(nnodes,
+ repeats,
+ &ntprs,
+ &rmin,
+ rcoulomb,
+ &rmax,
+ maxPMEfraction,
+ minPMEfraction,
+ npme_fixed,
+ bench_nsteps,
+ fnm,
+ NFILE,
+ sim_part,
+ presteps,
+ asize(pa),
+ pa);
/* Determine the maximum and minimum number of PME nodes to test,
* the actual list of settings is build in do_the_tests(). */
/* It can be that ntprs is reduced by make_benchmark_tprs if not enough
* different grids could be found. */
- make_benchmark_tprs(opt2fn("-s", NFILE, fnm), tpr_names, bench_nsteps + presteps, cpt_steps,
- rmin, rmax, bScaleRvdw, &ntprs, info, fp);
+ make_benchmark_tprs(opt2fn("-s", NFILE, fnm),
+ tpr_names,
+ bench_nsteps + presteps,
+ cpt_steps,
+ rmin,
+ rmax,
+ bScaleRvdw,
+ &ntprs,
+ info,
+ fp);
/********************************************************************************/
/* Main loop over all scenarios we need to test: tpr files, PME nodes, repeats */
{
GMX_RELEASE_ASSERT(npmevalues_opt[0] != nullptr,
"Options inconsistency; npmevalues_opt[0] is NULL");
- do_the_tests(fp, tpr_names, maxPMEnodes, minPMEnodes, npme_fixed, npmevalues_opt[0], perfdata,
- &pmeentries, repeats, nnodes, ntprs, bThreads, cmd_mpirun, cmd_np, cmd_mdrun,
- cmd_args_bench, fnm, NFILE, presteps, cpt_steps, bCheck, eligible_gpu_ids);
+ do_the_tests(fp,
+ tpr_names,
+ maxPMEnodes,
+ minPMEnodes,
+ npme_fixed,
+ npmevalues_opt[0],
+ perfdata,
+ &pmeentries,
+ repeats,
+ nnodes,
+ ntprs,
+ bThreads,
+ cmd_mpirun,
+ cmd_np,
+ cmd_mdrun,
+ cmd_args_bench,
+ fnm,
+ NFILE,
+ presteps,
+ cpt_steps,
+ bCheck,
+ eligible_gpu_ids);
fprintf(fp, "\nTuning took%8.1f minutes.\n", (gmx_gettime() - seconds) / 60.0);
/* Analyse the results and give a suggestion for optimal settings: */
- bKeepTPR = analyze_data(fp, opt2fn("-p", NFILE, fnm), perfdata, nnodes, ntprs, pmeentries,
- repeats, info, &best_tpr, &best_npme);
+ bKeepTPR = analyze_data(
+ fp, opt2fn("-p", NFILE, fnm), perfdata, nnodes, ntprs, pmeentries, repeats, info, &best_tpr, &best_npme);
/* Take the best-performing tpr file and enlarge nsteps to original value */
if (bKeepTPR && !bOverwrite)
{
simulation_tpr = opt2fn("-so", NFILE, fnm);
modify_PMEsettings(bOverwrite ? (new_sim_nsteps + cpt_steps) : info->orig_sim_steps,
- info->orig_init_step, tpr_names[best_tpr], simulation_tpr);
+ info->orig_init_step,
+ tpr_names[best_tpr],
+ simulation_tpr);
}
/* Let's get rid of the temporary benchmark input files */
}
/* Now start the real simulation if the user requested it ... */
- launch_simulation(bLaunch, fp, bThreads, cmd_mpirun, cmd_np, cmd_mdrun, cmd_args_launch,
- simulation_tpr, best_npme, eligible_gpu_ids);
+ launch_simulation(
+ bLaunch, fp, bThreads, cmd_mpirun, cmd_np, cmd_mdrun, cmd_args_launch, simulation_tpr, best_npme, eligible_gpu_ids);
}
gmx_ffclose(fp);
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(topology INTERFACE)
+
file(GLOB TOPOLOGY_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${TOPOLOGY_SOURCES} PARENT_SCOPE)
-if (BUILD_TESTING)
- add_subdirectory(tests)
-endif()
-
if(GMX_INSTALL_LEGACY_API)
install(FILES
atomprop.h
- atoms.h
- block.h
- forcefieldparameters.h
- idef.h
- ifunc.h
+ atoms.h
+ block.h
+ forcefieldparameters.h
+ idef.h
+ ifunc.h
index.h
- symtab.h
- topology.h
- DESTINATION include/gromacs/topology)
+ symtab.h
+ topology.h
+ DESTINATION include/gromacs/topology)
endif()
+
+# Source files have the following private module dependencies.
+target_link_libraries(options PRIVATE
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(topology PUBLIC
+target_include_directories(topology INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(topology PUBLIC
+target_link_libraries(topology INTERFACE
+ legacy_api
+ )
+
+# TODO: when topology is an OBJECT target
+#target_link_libraries(topology PUBLIC legacy_api)
+#target_link_libraries(topology PRIVATE common)
+
+# Module dependencies
+# topology interfaces convey transitive dependence on these modules.
+#target_link_libraries(topology PUBLIC
+target_link_libraries(topology INTERFACE
+ utility
+ )
+
+if (BUILD_TESTING)
+ add_subdirectory(tests)
+endif()
\ No newline at end of file
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
else
{
- fprintf(debug, " match: %4s %4s\n", ap->entry[j].residueName.c_str(),
+ fprintf(debug,
+ " match: %4s %4s\n",
+ ap->entry[j].residueName.c_str(),
ap->entry[j].atomName.c_str());
}
}
real propValue,
int line)
{
- bool bExact;
- int j = findPropertyIndex(ap, restype, residueName, atomName, &bExact);
+ bool bExact = false;
+ int j = findPropertyIndex(ap, restype, residueName, atomName, &bExact);
if (!bExact)
{
{
if (ap->entry[j].value == propValue)
{
- fprintf(stderr, "Warning double identical entries for %s %s %g on line %d in file %s\n",
- residueName.c_str(), atomName.c_str(), propValue, line, ap->db.c_str());
+ fprintf(stderr,
+ "Warning double identical entries for %s %s %g on line %d in file %s\n",
+ residueName.c_str(),
+ atomName.c_str(),
+ propValue,
+ line,
+ ap->db.c_str());
}
else
{
fprintf(stderr,
"Warning double different entries %s %s %g and %g on line %d in file %s\n"
"Using last entry (%g)\n",
- residueName.c_str(), atomName.c_str(), propValue, ap->entry[j].value, line,
- ap->db.c_str(), propValue);
+ residueName.c_str(),
+ atomName.c_str(),
+ propValue,
+ ap->entry[j].value,
+ line,
+ ap->db.c_str(),
+ propValue);
ap->entry[j].value = propValue;
}
}
while (get_a_line(fp.get(), line, STRLEN))
{
line_no++;
- double pp;
+ double pp = 0.0;
if (sscanf(line, "%31s %31s %20lf", resnm, atomnm, &pp) == 3)
{
pp *= factor;
*/
static bool setProperties(AtomProperty* ap, ResidueType* restype, int eprop, bool haveBeenWarned)
{
- const char* fns[epropNR] = { "atommass.dat", "vdwradii.dat", "dgsolv.dat", "electroneg.dat",
- "elements.dat" };
- double fac[epropNR] = { 1.0, 1.0, 418.4, 1.0, 1.0 };
- double def[epropNR] = { 12.011, 0.14, 0.0, 2.2, -1 };
+ const char* fns[epropNR] = {
+ "atommass.dat", "vdwradii.dat", "dgsolv.dat", "electroneg.dat", "elements.dat"
+ };
+ double fac[epropNR] = { 1.0, 1.0, 418.4, 1.0, 1.0 };
+ double def[epropNR] = { 12.011, 0.14, 0.0, 2.2, -1 };
bool printWarning = false;
if (!ap->isSet)
{
if (nullptr != fp)
{
- fprintf(fp, "NOTE: From version 5.0 %s uses the Van der Waals radii\n",
+ fprintf(fp,
+ "NOTE: From version 5.0 %s uses the Van der Waals radii\n",
gmx::getProgramContext().displayName());
fprintf(fp, "from the source below. This means the results may be different\n");
fprintf(fp, "compared to previous GROMACS versions.\n");
const std::string& atomName,
real* value)
{
- int j;
std::string tmpAtomName, tmpResidueName;
- gmx_bool bExact;
+ bool bExact = false;
if (setProperties(prop(eprop), restype(), eprop, impl_->bWarned))
{
{
tmpAtomName = atomName;
}
- j = findPropertyIndex(&(impl_->prop[eprop]), &impl_->restype, residueName, tmpAtomName, &bExact);
+ const int j = findPropertyIndex(
+ &(impl_->prop[eprop]), &impl_->restype, residueName, tmpAtomName, &bExact);
if (eprop == epropVDW && !impl_->bWarnVDW)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TOPOLOGY_ATOMPROP_H
#define GMX_TOPOLOGY_ATOMPROP_H
+#include <memory>
#include <string>
#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/real.h"
enum
//! Implementation pointer.
class Impl;
- gmx::PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
#endif
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/topology/atomprop.h"
#include "gromacs/topology/symtab.h"
#include "gromacs/utility/compare.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/txtdump.h"
-const char* ptype_str[eptNR + 1] = { "Atom", "Nucleus", "Shell", "Bond", "VSite", nullptr };
+const char* enumValueToString(ParticleType enumValue)
+{
+ static constexpr gmx::EnumerationArray<ParticleType, const char*> particleTypeNames = {
+ "Atom", "Nucleus", "Shell", "Bond", "VSite"
+ };
+ return particleTypeNames[enumValue];
+}
void init_atom(t_atoms* at)
{
void add_t_atoms(t_atoms* atoms, int natom_extra, int nres_extra)
{
- int i;
-
if (natom_extra > 0)
{
srenew(atoms->atomname, atoms->nr + natom_extra);
{
srenew(atoms->atomtypeB, atoms->nr + natom_extra);
}
- for (i = atoms->nr; (i < atoms->nr + natom_extra); i++)
+ for (int i = atoms->nr; (i < atoms->nr + natom_extra); i++)
{
atoms->atomname[i] = nullptr;
memset(&atoms->atom[i], 0, sizeof(atoms->atom[i]));
if (nres_extra > 0)
{
srenew(atoms->resinfo, atoms->nres + nres_extra);
- for (i = atoms->nres; (i < atoms->nres + nres_extra); i++)
+ for (int i = atoms->nres; (i < atoms->nres + nres_extra); i++)
{
std::memset(&atoms->resinfo[i], 0, sizeof(atoms->resinfo[i]));
}
void gmx_pdbinfo_init_default(t_pdbinfo* pdbinfo)
{
- pdbinfo->type = epdbATOM;
+ pdbinfo->type = PdbRecordType::Atom;
pdbinfo->atomnr = 0;
pdbinfo->altloc = ' ';
pdbinfo->atomnm[0] = '\0';
t_atoms* copy_t_atoms(const t_atoms* src)
{
- t_atoms* dst;
- int i;
+ t_atoms* dst = nullptr;
snew(dst, 1);
init_t_atoms(dst, src->nr, (nullptr != src->pdbinfo));
{
snew(dst->atomtypeB, src->nr);
}
- for (i = 0; (i < src->nr); i++)
+ for (int i = 0; (i < src->nr); i++)
{
dst->atom[i] = src->atom[i];
if (nullptr != src->pdbinfo)
dst->havePdbInfo = src->havePdbInfo;
dst->haveType = src->haveType;
dst->nres = src->nres;
- for (i = 0; (i < src->nres); i++)
+ for (int i = 0; (i < src->nres); i++)
{
dst->resinfo[i] = src->resinfo[i];
}
int chainnum,
char chainid)
{
- t_resinfo* ri;
-
- ri = &atoms->resinfo[atoms->atom[atom_ind].resind];
- ri->name = put_symtab(symtab, resname);
- ri->rtp = nullptr;
- ri->nr = resnr;
- ri->ic = ic;
- ri->chainnum = chainnum;
- ri->chainid = chainid;
+ t_resinfo* ri = &atoms->resinfo[atoms->atom[atom_ind].resind];
+ ri->name = put_symtab(symtab, resname);
+ ri->rtp = nullptr;
+ ri->nr = resnr;
+ ri->ic = ic;
+ ri->chainnum = chainnum;
+ ri->chainid = chainid;
}
static void pr_atom(FILE* fp, int indent, const char* title, const t_atom* atom, int n)
{
- int i;
-
if (available(fp, atom, indent, title))
{
indent = pr_title_n(fp, indent, title, n);
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
pr_indent(fp, indent);
fprintf(fp,
"%s[%6d]={type=%3hu, typeB=%3hu, ptype=%8s, m=%12.5e, "
"q=%12.5e, mB=%12.5e, qB=%12.5e, resind=%5d, atomnumber=%3d}\n",
- title, i, atom[i].type, atom[i].typeB, ptype_str[atom[i].ptype], atom[i].m,
- atom[i].q, atom[i].mB, atom[i].qB, atom[i].resind, atom[i].atomnumber);
+ title,
+ i,
+ atom[i].type,
+ atom[i].typeB,
+ enumValueToString(atom[i].ptype),
+ atom[i].m,
+ atom[i].q,
+ atom[i].mB,
+ atom[i].qB,
+ atom[i].resind,
+ atom[i].atomnumber);
}
}
}
static void pr_strings2(FILE* fp, int indent, const char* title, char*** nm, char*** nmB, int n, gmx_bool bShowNumbers)
{
- int i;
-
if (available(fp, nm, indent, title))
{
indent = pr_title_n(fp, indent, title, n);
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
pr_indent(fp, indent);
- fprintf(fp, "%s[%d]={name=\"%s\",nameB=\"%s\"}\n", title, bShowNumbers ? i : -1,
- *(nm[i]), *(nmB[i]));
+ fprintf(fp, "%s[%d]={name=\"%s\",nameB=\"%s\"}\n", title, bShowNumbers ? i : -1, *(nm[i]), *(nmB[i]));
}
}
}
static void pr_resinfo(FILE* fp, int indent, const char* title, const t_resinfo* resinfo, int n, gmx_bool bShowNumbers)
{
- int i;
-
if (available(fp, resinfo, indent, title))
{
indent = pr_title_n(fp, indent, title, n);
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
pr_indent(fp, indent);
- fprintf(fp, "%s[%d]={name=\"%s\", nr=%d, ic='%c'}\n", title, bShowNumbers ? i : -1,
- *(resinfo[i].name), resinfo[i].nr, (resinfo[i].ic == '\0') ? ' ' : resinfo[i].ic);
+ fprintf(fp,
+ "%s[%d]={name=\"%s\", nr=%d, ic='%c'}\n",
+ title,
+ bShowNumbers ? i : -1,
+ *(resinfo[i].name),
+ resinfo[i].nr,
+ (resinfo[i].ic == '\0') ? ' ' : resinfo[i].ic);
}
}
}
void pr_atomtypes(FILE* fp, int indent, const char* title, const t_atomtypes* atomtypes, gmx_bool bShowNumbers)
{
- int i;
if (available(fp, atomtypes, indent, title))
{
indent = pr_title(fp, indent, title);
- for (i = 0; i < atomtypes->nr; i++)
+ for (int i = 0; i < atomtypes->nr; i++)
{
pr_indent(fp, indent);
- fprintf(fp, "atomtype[%3d]={atomnumber=%4d}\n", bShowNumbers ? i : -1,
- atomtypes->atomnumber[i]);
+ fprintf(fp, "atomtype[%3d]={atomnumber=%4d}\n", bShowNumbers ? i : -1, atomtypes->atomnumber[i]);
}
}
}
if (a2)
{
cmp_us(fp, "atom.type", index, a1->type, a2->type);
- cmp_us(fp, "atom.ptype", index, a1->ptype, a2->ptype);
+ cmpEnum<ParticleType>(fp, "atom.ptype", a1->ptype, a2->ptype);
cmp_int(fp, "atom.resind", index, a1->resind, a2->resind);
cmp_int(fp, "atom.atomnumber", index, a1->atomnumber, a2->atomnumber);
cmp_real(fp, "atom.m", index, a1->m, a2->m, relativeTolerance, absoluteTolerance);
real absoluteTolerance)
{
fprintf(fp, "comparing t_pdbinfo\n");
- cmp_int(fp, "type", pdb, pdb1.type, pdb2.type);
+ cmpEnum<PdbRecordType>(fp, "type", pdb1.type, pdb2.type);
cmp_int(fp, "atomnr", pdb, pdb1.atomnr, pdb2.atomnr);
cmp_uc(fp, "altloc", pdb, pdb1.altloc, pdb2.altloc);
cmp_str(fp, "atomnm", pdb, pdb1.atomnm, pdb2.atomnm);
bool haveMass = true;
for (int i = 0; i < atoms->nr; i++)
{
- if (!aps.setAtomProperty(epropMass, *atoms->resinfo[atoms->atom[i].resind].name,
- *atoms->atomname[i], &atoms->atom[i].m))
+ if (!aps.setAtomProperty(epropMass,
+ *atoms->resinfo[atoms->atom[i].resind].name,
+ *atoms->atomname[i],
+ &atoms->atom[i].m))
{
haveMass = false;
if (numWarn < maxWarn)
{
- fprintf(stderr, "Can not find mass in database for atom %s in residue %d %s\n",
- *atoms->atomname[i], atoms->resinfo[atoms->atom[i].resind].nr,
+ fprintf(stderr,
+ "Can not find mass in database for atom %s in residue %d %s\n",
+ *atoms->atomname[i],
+ atoms->resinfo[atoms->atom[i].resind].nr,
*atoms->resinfo[atoms->atom[i].resind].name);
numWarn++;
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2012,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct t_symtab;
/* The particle type */
-enum
+enum class ParticleType : int
{
- eptAtom,
- eptNucleus,
- eptShell,
- eptBond,
- eptVSite,
- eptNR
+ Atom,
+ Nucleus,
+ Shell,
+ Bond,
+ VSite,
+ Count
};
/* The particle type names */
-extern const char* ptype_str[eptNR + 1];
+const char* enumValueToString(ParticleType enumValue);
/* Enumerated type for pdb records. The other entries are ignored
* when reading a pdb file
*/
-enum PDB_record
+enum class PdbRecordType : int
{
- epdbATOM,
- epdbHETATM,
- epdbANISOU,
- epdbCRYST1,
- epdbCOMPND,
- epdbMODEL,
- epdbENDMDL,
- epdbTER,
- epdbHEADER,
- epdbTITLE,
- epdbREMARK,
- epdbCONECT,
- epdbNR
+ Atom,
+ Hetatm,
+ Anisou,
+ Cryst1,
+ Compound,
+ Model,
+ EndModel,
+ Ter,
+ Header,
+ Title,
+ Remark,
+ Conect,
+ Count
};
+const char* enumValueToString(PdbRecordType enumValue);
+
typedef struct t_atom
{
real m, q; /* Mass and charge */
real mB, qB; /* Mass and charge for Free Energy calc */
unsigned short type; /* Atom type */
unsigned short typeB; /* Atom type for Free Energy calc */
- int ptype; /* Particle type */
+ ParticleType ptype; /* Particle type */
int resind; /* Index into resinfo (in t_atoms) */
int atomnumber; /* Atomic Number or 0 */
char elem[4]; /* Element name */
typedef struct t_pdbinfo
{
- int type; /* PDB record name */
- int atomnr; /* PDB atom number */
- char altloc; /* Alternate location indicator */
- char atomnm[6]; /* True atom name including leading spaces */
- real occup; /* Occupancy */
- real bfac; /* B-factor */
- gmx_bool bAnisotropic; /* (an)isotropic switch */
- int uij[6]; /* Anisotropic B-factor */
+ PdbRecordType type; /* PDB record name */
+ int atomnr; /* PDB atom number */
+ char altloc; /* Alternate location indicator */
+ char atomnm[6]; /* True atom name including leading spaces */
+ real occup; /* Occupancy */
+ real bfac; /* B-factor */
+ gmx_bool bAnisotropic; /* (an)isotropic switch */
+ int uij[6]; /* Anisotropic B-factor */
} t_pdbinfo;
//! Contains indices into group names for different groups.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TOPOLOGY_ATOMSBUILDER_H
#define GMX_TOPOLOGY_ATOMSBUILDER_H
+#include <memory>
#include <vector>
#include "gromacs/math/vectypes.h"
+
#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/real.h"
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
t_blocka* new_blocka()
{
- t_blocka* block;
+ t_blocka* block = nullptr;
snew(block, 1);
snew(block->index, 1);
static void low_pr_blocka(FILE* fp, int indent, const char* title, const t_blocka* block, gmx_bool bShowNumbers)
{
- int i;
-
if (available(fp, block, indent, title))
{
indent = pr_blocka_title(fp, indent, title, block);
- for (i = 0; i <= block->nr; i++)
+ for (int i = 0; i <= block->nr; i++)
{
pr_indent(fp, indent + INDENT);
fprintf(fp, "%s->index[%d]=%d\n", title, bShowNumbers ? i : -1, block->index[i]);
}
- for (i = 0; i < block->nra; i++)
+ for (int i = 0; i < block->nra; i++)
{
pr_indent(fp, indent + INDENT);
fprintf(fp, "%s->a[%d]=%d\n", title, bShowNumbers ? i : -1, block->a[i]);
void pr_block(FILE* fp, int indent, const char* title, const t_block* block, gmx_bool bShowNumbers)
{
- int i, start;
-
if (available(fp, block, indent, title))
{
- indent = pr_block_title(fp, indent, title, block);
- start = 0;
+ indent = pr_block_title(fp, indent, title, block);
+ int start = 0;
if (block->index[start] != 0)
{
fprintf(fp, "block->index[%d] should be 0\n", start);
}
else
{
- for (i = 0; i < block->nr; i++)
+ for (int i = 0; i < block->nr; i++)
{
int end = block->index[i + 1];
pr_indent(fp, indent);
}
else
{
- fprintf(fp, "%s[%d]={%d..%d}\n", title, bShowNumbers ? i : -1,
- bShowNumbers ? start : -1, bShowNumbers ? end - 1 : -1);
+ fprintf(fp,
+ "%s[%d]={%d..%d}\n",
+ title,
+ bShowNumbers ? i : -1,
+ bShowNumbers ? start : -1,
+ bShowNumbers ? end - 1 : -1);
}
start = end;
}
void pr_blocka(FILE* fp, int indent, const char* title, const t_blocka* block, gmx_bool bShowNumbers)
{
- int i, j, ok, size, start, end;
+ bool ok = false;
if (available(fp, block, indent, title))
{
- indent = pr_blocka_title(fp, indent, title, block);
- start = 0;
- end = start;
- if ((ok = static_cast<int>(block->index[start] == 0)) == 0)
+ indent = pr_blocka_title(fp, indent, title, block);
+ int start = 0;
+ int end = start;
+ ok = (block->index[start] == 0);
+ if (!ok)
{
fprintf(fp, "block->index[%d] should be 0\n", start);
}
else
{
- for (i = 0; i < block->nr; i++)
+ for (int i = 0; i < block->nr; i++)
{
- end = block->index[i + 1];
- size = pr_indent(fp, indent);
+ end = block->index[i + 1];
+ int size = pr_indent(fp, indent);
if (end <= start)
{
size += fprintf(fp, "%s[%d]={", title, i);
}
else
{
- size += fprintf(fp, "%s[%d][%d..%d]={", title, bShowNumbers ? i : -1,
- bShowNumbers ? start : -1, bShowNumbers ? end - 1 : -1);
+ size += fprintf(fp,
+ "%s[%d][%d..%d]={",
+ title,
+ bShowNumbers ? i : -1,
+ bShowNumbers ? start : -1,
+ bShowNumbers ? end - 1 : -1);
}
- for (j = start; j < end; j++)
+ for (int j = start; j < end; j++)
{
if (j > start)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/range.h"
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static void pr_cmap(FILE* fp, int indent, const char* title, const gmx_cmap_t* cmap_grid, gmx_bool bShowNumbers)
{
- int j, nelem;
- real dx, idx;
+ const real dx = cmap_grid->grid_spacing != 0 ? 360.0 / cmap_grid->grid_spacing : 0;
- if (cmap_grid->grid_spacing != 0)
- {
- dx = 360.0 / cmap_grid->grid_spacing;
- }
- else
- {
- dx = 0;
- }
- nelem = cmap_grid->grid_spacing * cmap_grid->grid_spacing;
+ const int nelem = cmap_grid->grid_spacing * cmap_grid->grid_spacing;
if (available(fp, cmap_grid, indent, title))
{
for (gmx::index i = 0; i < gmx::ssize(cmap_grid->cmapdata); i++)
{
- idx = -180.0;
+ real idx = -180.0;
fprintf(fp, "%8s %8s %8s %8s\n", "V", "dVdx", "dVdy", "d2dV");
fprintf(fp, "grid[%3zd]={\n", bShowNumbers ? i : -1);
- for (j = 0; j < nelem; j++)
+ for (int j = 0; j < nelem; j++)
{
if ((j % cmap_grid->grid_spacing) == 0)
{
void pr_ffparams(FILE* fp, int indent, const char* title, const gmx_ffparams_t* ffparams, gmx_bool bShowNumbers)
{
- int i;
-
indent = pr_title(fp, indent, title);
pr_indent(fp, indent);
fprintf(fp, "atnr=%d\n", ffparams->atnr);
pr_indent(fp, indent);
fprintf(fp, "ntypes=%d\n", ffparams->numTypes());
- for (i = 0; i < ffparams->numTypes(); i++)
+ for (int i = 0; i < ffparams->numTypes(); i++)
{
pr_indent(fp, indent + INDENT);
- fprintf(fp, "functype[%d]=%s, ", bShowNumbers ? i : -1,
+ fprintf(fp,
+ "functype[%d]=%s, ",
+ bShowNumbers ? i : -1,
interaction_function[ffparams->functype[i]].name);
pr_iparams(fp, ffparams->functype[i], ffparams->iparams[i]);
}
const char* r,
const char* kr)
{
- writer->writeLineFormatted("%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e", r,
- iparams.harmonic.rA, kr, iparams.harmonic.krA, r,
- iparams.harmonic.rB, kr, iparams.harmonic.krB);
+ writer->writeLineFormatted("%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e",
+ r,
+ iparams.harmonic.rA,
+ kr,
+ iparams.harmonic.krA,
+ r,
+ iparams.harmonic.rB,
+ kr,
+ iparams.harmonic.krB);
}
void pr_iparams(FILE* fp, t_functype ftype, const t_iparams& iparams)
case F_ANGLES:
case F_G96ANGLES: printHarmonicInteraction(writer, iparams, "th", "ct"); break;
case F_CROSS_BOND_BONDS:
- writer->writeLineFormatted("r1e=%15.8e, r2e=%15.8e, krr=%15.8e", iparams.cross_bb.r1e,
- iparams.cross_bb.r2e, iparams.cross_bb.krr);
+ writer->writeLineFormatted("r1e=%15.8e, r2e=%15.8e, krr=%15.8e",
+ iparams.cross_bb.r1e,
+ iparams.cross_bb.r2e,
+ iparams.cross_bb.krr);
break;
case F_CROSS_BOND_ANGLES:
writer->writeLineFormatted("r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e",
- iparams.cross_ba.r1e, iparams.cross_ba.r2e,
- iparams.cross_ba.r3e, iparams.cross_ba.krt);
+ iparams.cross_ba.r1e,
+ iparams.cross_ba.r2e,
+ iparams.cross_ba.r3e,
+ iparams.cross_ba.krt);
break;
case F_LINEAR_ANGLES:
writer->writeLineFormatted("klinA=%15.8e, aA=%15.8e, klinB=%15.8e, aB=%15.8e",
- iparams.linangle.klinA, iparams.linangle.aA,
- iparams.linangle.klinB, iparams.linangle.aB);
+ iparams.linangle.klinA,
+ iparams.linangle.aA,
+ iparams.linangle.klinB,
+ iparams.linangle.aB);
break;
case F_UREY_BRADLEY:
writer->writeLineFormatted(
"thetaA=%15.8e, kthetaA=%15.8e, r13A=%15.8e, kUBA=%15.8e, thetaB=%15.8e, "
"kthetaB=%15.8e, r13B=%15.8e, kUBB=%15.8e",
- iparams.u_b.thetaA, iparams.u_b.kthetaA, iparams.u_b.r13A, iparams.u_b.kUBA,
- iparams.u_b.thetaB, iparams.u_b.kthetaB, iparams.u_b.r13B, iparams.u_b.kUBB);
+ iparams.u_b.thetaA,
+ iparams.u_b.kthetaA,
+ iparams.u_b.r13A,
+ iparams.u_b.kUBA,
+ iparams.u_b.thetaB,
+ iparams.u_b.kthetaB,
+ iparams.u_b.r13B,
+ iparams.u_b.kUBB);
break;
case F_QUARTIC_ANGLES:
writer->writeStringFormatted("theta=%15.8e", iparams.qangle.theta);
writer->ensureLineBreak();
break;
case F_BHAM:
- writer->writeLineFormatted("a=%15.8e, b=%15.8e, c=%15.8e", iparams.bham.a,
- iparams.bham.b, iparams.bham.c);
+ writer->writeLineFormatted(
+ "a=%15.8e, b=%15.8e, c=%15.8e", iparams.bham.a, iparams.bham.b, iparams.bham.c);
break;
case F_BONDS:
case F_G96BONDS:
case F_MORSE:
writer->writeLineFormatted(
"b0A=%15.8e, cbA=%15.8e, betaA=%15.8e, b0B=%15.8e, cbB=%15.8e, betaB=%15.8e",
- iparams.morse.b0A, iparams.morse.cbA, iparams.morse.betaA, iparams.morse.b0B,
- iparams.morse.cbB, iparams.morse.betaB);
+ iparams.morse.b0A,
+ iparams.morse.cbA,
+ iparams.morse.betaA,
+ iparams.morse.b0B,
+ iparams.morse.cbB,
+ iparams.morse.betaB);
break;
case F_CUBICBONDS:
- writer->writeLineFormatted("b0=%15.8e, kb=%15.8e, kcub=%15.8e", iparams.cubic.b0,
- iparams.cubic.kb, iparams.cubic.kcub);
+ writer->writeLineFormatted("b0=%15.8e, kb=%15.8e, kcub=%15.8e",
+ iparams.cubic.b0,
+ iparams.cubic.kb,
+ iparams.cubic.kcub);
break;
case F_CONNBONDS: writer->ensureEmptyLine(); break;
case F_FENEBONDS:
writer->writeLineFormatted(
"lowA=%15.8e, up1A=%15.8e, up2A=%15.8e, kA=%15.8e, lowB=%15.8e, up1B=%15.8e, "
"up2B=%15.8e, kB=%15.8e,",
- iparams.restraint.lowA, iparams.restraint.up1A, iparams.restraint.up2A,
- iparams.restraint.kA, iparams.restraint.lowB, iparams.restraint.up1B,
- iparams.restraint.up2B, iparams.restraint.kB);
+ iparams.restraint.lowA,
+ iparams.restraint.up1A,
+ iparams.restraint.up2A,
+ iparams.restraint.kA,
+ iparams.restraint.lowB,
+ iparams.restraint.up1B,
+ iparams.restraint.up2B,
+ iparams.restraint.kB);
break;
case F_TABBONDS:
case F_TABBONDSNC:
case F_TABANGLES:
case F_TABDIHS:
- writer->writeLineFormatted("tab=%d, kA=%15.8e, kB=%15.8e", iparams.tab.table,
- iparams.tab.kA, iparams.tab.kB);
+ writer->writeLineFormatted(
+ "tab=%d, kA=%15.8e, kB=%15.8e", iparams.tab.table, iparams.tab.kA, iparams.tab.kB);
break;
case F_POLARIZATION:
writer->writeLineFormatted("alpha=%15.8e", iparams.polarize.alpha);
break;
case F_ANHARM_POL:
writer->writeLineFormatted("alpha=%15.8e drcut=%15.8e khyp=%15.8e",
- iparams.anharm_polarize.alpha, iparams.anharm_polarize.drcut,
+ iparams.anharm_polarize.alpha,
+ iparams.anharm_polarize.drcut,
iparams.anharm_polarize.khyp);
break;
case F_THOLE_POL:
writer->writeLineFormatted("a=%15.8e, alpha1=%15.8e, alpha2=%15.8e, rfac=%15.8e",
- iparams.thole.a, iparams.thole.alpha1, iparams.thole.alpha2,
+ iparams.thole.a,
+ iparams.thole.alpha1,
+ iparams.thole.alpha2,
iparams.thole.rfac);
break;
case F_WATER_POL:
writer->writeLineFormatted(
"al_x=%15.8e, al_y=%15.8e, al_z=%15.8e, rOH=%9.6f, rHH=%9.6f, rOD=%9.6f",
- iparams.wpol.al_x, iparams.wpol.al_y, iparams.wpol.al_z, iparams.wpol.rOH,
- iparams.wpol.rHH, iparams.wpol.rOD);
+ iparams.wpol.al_x,
+ iparams.wpol.al_y,
+ iparams.wpol.al_z,
+ iparams.wpol.rOH,
+ iparams.wpol.rHH,
+ iparams.wpol.rOD);
break;
case F_LJ:
writer->writeLineFormatted("c6=%15.8e, c12=%15.8e", iparams.lj.c6, iparams.lj.c12);
break;
case F_LJ14:
writer->writeLineFormatted("c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e",
- iparams.lj14.c6A, iparams.lj14.c12A, iparams.lj14.c6B,
+ iparams.lj14.c6A,
+ iparams.lj14.c12A,
+ iparams.lj14.c6B,
iparams.lj14.c12B);
break;
case F_LJC14_Q:
writer->writeLineFormatted("fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e",
- iparams.ljc14.fqq, iparams.ljc14.qi, iparams.ljc14.qj,
- iparams.ljc14.c6, iparams.ljc14.c12);
+ iparams.ljc14.fqq,
+ iparams.ljc14.qi,
+ iparams.ljc14.qj,
+ iparams.ljc14.c6,
+ iparams.ljc14.c12);
break;
case F_LJC_PAIRS_NB:
- writer->writeLineFormatted("qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e", iparams.ljcnb.qi,
- iparams.ljcnb.qj, iparams.ljcnb.c6, iparams.ljcnb.c12);
+ writer->writeLineFormatted("qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e",
+ iparams.ljcnb.qi,
+ iparams.ljcnb.qj,
+ iparams.ljcnb.c6,
+ iparams.ljcnb.c12);
break;
case F_PDIHS:
case F_PIDIHS:
case F_ANGRES:
case F_ANGRESZ:
writer->writeLineFormatted("phiA=%15.8e, cpA=%15.8e, phiB=%15.8e, cpB=%15.8e, mult=%d",
- iparams.pdihs.phiA, iparams.pdihs.cpA, iparams.pdihs.phiB,
- iparams.pdihs.cpB, iparams.pdihs.mult);
+ iparams.pdihs.phiA,
+ iparams.pdihs.cpA,
+ iparams.pdihs.phiB,
+ iparams.pdihs.cpB,
+ iparams.pdihs.mult);
break;
case F_DISRES:
writer->writeLineFormatted(
"label=%4d, type=%1d, low=%15.8e, up1=%15.8e, up2=%15.8e, fac=%15.8e)",
- iparams.disres.label, iparams.disres.type, iparams.disres.low,
- iparams.disres.up1, iparams.disres.up2, iparams.disres.kfac);
+ iparams.disres.label,
+ iparams.disres.type,
+ iparams.disres.low,
+ iparams.disres.up1,
+ iparams.disres.up2,
+ iparams.disres.kfac);
break;
case F_ORIRES:
writer->writeLineFormatted(
"ex=%4d, label=%d, power=%4d, c=%15.8e, obs=%15.8e, kfac=%15.8e)",
- iparams.orires.ex, iparams.orires.label, iparams.orires.power, iparams.orires.c,
- iparams.orires.obs, iparams.orires.kfac);
+ iparams.orires.ex,
+ iparams.orires.label,
+ iparams.orires.power,
+ iparams.orires.c,
+ iparams.orires.obs,
+ iparams.orires.kfac);
break;
case F_DIHRES:
writer->writeLineFormatted(
"phiA=%15.8e, dphiA=%15.8e, kfacA=%15.8e, phiB=%15.8e, dphiB=%15.8e, "
"kfacB=%15.8e",
- iparams.dihres.phiA, iparams.dihres.dphiA, iparams.dihres.kfacA,
- iparams.dihres.phiB, iparams.dihres.dphiB, iparams.dihres.kfacB);
+ iparams.dihres.phiA,
+ iparams.dihres.dphiA,
+ iparams.dihres.kfacA,
+ iparams.dihres.phiB,
+ iparams.dihres.dphiB,
+ iparams.dihres.kfacB);
break;
case F_POSRES:
writer->writeLineFormatted(
"pos0A=(%15.8e,%15.8e,%15.8e), fcA=(%15.8e,%15.8e,%15.8e), "
"pos0B=(%15.8e,%15.8e,%15.8e), fcB=(%15.8e,%15.8e,%15.8e)",
- iparams.posres.pos0A[XX], iparams.posres.pos0A[YY], iparams.posres.pos0A[ZZ],
- iparams.posres.fcA[XX], iparams.posres.fcA[YY], iparams.posres.fcA[ZZ],
- iparams.posres.pos0B[XX], iparams.posres.pos0B[YY], iparams.posres.pos0B[ZZ],
- iparams.posres.fcB[XX], iparams.posres.fcB[YY], iparams.posres.fcB[ZZ]);
+ iparams.posres.pos0A[XX],
+ iparams.posres.pos0A[YY],
+ iparams.posres.pos0A[ZZ],
+ iparams.posres.fcA[XX],
+ iparams.posres.fcA[YY],
+ iparams.posres.fcA[ZZ],
+ iparams.posres.pos0B[XX],
+ iparams.posres.pos0B[YY],
+ iparams.posres.pos0B[ZZ],
+ iparams.posres.fcB[XX],
+ iparams.posres.fcB[YY],
+ iparams.posres.fcB[ZZ]);
break;
case F_FBPOSRES:
writer->writeLineFormatted(
"pos0=(%15.8e,%15.8e,%15.8e), geometry=%d, r=%15.8e, k=%15.8e",
- iparams.fbposres.pos0[XX], iparams.fbposres.pos0[YY], iparams.fbposres.pos0[ZZ],
- iparams.fbposres.geom, iparams.fbposres.r, iparams.fbposres.k);
+ iparams.fbposres.pos0[XX],
+ iparams.fbposres.pos0[YY],
+ iparams.fbposres.pos0[ZZ],
+ iparams.fbposres.geom,
+ iparams.fbposres.r,
+ iparams.fbposres.k);
break;
case F_RBDIHS:
for (int i = 0; i < NR_RBDIHS; i++)
{
- writer->writeStringFormatted("%srbcA[%d]=%15.8e", i == 0 ? "" : ", ", i,
- iparams.rbdihs.rbcA[i]);
+ writer->writeStringFormatted(
+ "%srbcA[%d]=%15.8e", i == 0 ? "" : ", ", i, iparams.rbdihs.rbcA[i]);
}
writer->ensureLineBreak();
for (int i = 0; i < NR_RBDIHS; i++)
{
- writer->writeStringFormatted("%srbcB[%d]=%15.8e", i == 0 ? "" : ", ", i,
- iparams.rbdihs.rbcB[i]);
+ writer->writeStringFormatted(
+ "%srbcB[%d]=%15.8e", i == 0 ? "" : ", ", i, iparams.rbdihs.rbcB[i]);
}
writer->ensureLineBreak();
break;
case F_VSITE3OUT:
case F_VSITE4FD:
case F_VSITE4FDN:
- writer->writeLineFormatted("a=%15.8e, b=%15.8e, c=%15.8e", iparams.vsite.a,
- iparams.vsite.b, iparams.vsite.c);
+ writer->writeLineFormatted(
+ "a=%15.8e, b=%15.8e, c=%15.8e", iparams.vsite.a, iparams.vsite.b, iparams.vsite.c);
break;
case F_VSITEN:
writer->writeLineFormatted("n=%2d, a=%15.8e", iparams.vsiten.n, iparams.vsiten.a);
writer->ensureLineBreak();
break;
default:
- gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d", ftype,
- interaction_function[ftype].name, __FILE__, __LINE__);
+ gmx_fatal(FARGS,
+ "unknown function type %d (%s) in %s line %d",
+ ftype,
+ interaction_function[ftype].name,
+ __FILE__,
+ __LINE__);
}
}
gmx_bool bShowParameters,
const t_iparams* iparams)
{
- int i, j, k, type, ftype;
-
indent = pr_title(fp, indent, title);
pr_indent(fp, indent);
fprintf(fp, "nr: %d\n", ilist.size());
{
pr_indent(fp, indent);
fprintf(fp, "iatoms:\n");
- for (i = j = 0; i < ilist.size();)
+ int j = 0;
+ for (int i = 0; i < ilist.size();)
{
pr_indent(fp, indent + INDENT);
- type = ilist.iatoms[i];
- ftype = functype[type];
+ const int type = ilist.iatoms[i];
+ const int ftype = functype[type];
if (bShowNumbers)
{
fprintf(fp, "%d type=%d ", j, type);
}
j++;
printf("(%s)", interaction_function[ftype].name);
- for (k = 0; k < interaction_function[ftype].nratoms; k++)
+ for (int k = 0; k < interaction_function[ftype].nratoms; k++)
{
fprintf(fp, " %3d", ilist.iatoms[i + 1 + k]);
}
void pr_idef(FILE* fp, int indent, const char* title, const t_idef* idef, gmx_bool bShowNumbers, gmx_bool bShowParameters)
{
- int i, j;
-
if (available(fp, idef, indent, title))
{
indent = pr_title(fp, indent, title);
fprintf(fp, "atnr=%d\n", idef->atnr);
pr_indent(fp, indent);
fprintf(fp, "ntypes=%d\n", idef->ntypes);
- for (i = 0; i < idef->ntypes; i++)
+ for (int i = 0; i < idef->ntypes; i++)
{
pr_indent(fp, indent + INDENT);
- fprintf(fp, "functype[%d]=%s, ", bShowNumbers ? i : -1,
+ fprintf(fp,
+ "functype[%d]=%s, ",
+ bShowNumbers ? i : -1,
interaction_function[idef->functype[i]].name);
pr_iparams(fp, idef->functype[i], idef->iparams[i]);
}
pr_real(fp, indent, "fudgeQQ", idef->fudgeQQ);
- for (j = 0; (j < F_NRE); j++)
+ for (int j = 0; (j < F_NRE); j++)
{
- printIlist(fp, indent, interaction_function[j].longname, idef->functype, idef->il[j],
- bShowNumbers, bShowParameters, idef->iparams);
+ printIlist(fp,
+ indent,
+ interaction_function[j].longname,
+ idef->functype,
+ idef->il[j],
+ bShowNumbers,
+ bShowParameters,
+ idef->iparams);
}
}
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/ifunc.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
struct gmx_ffparams_t;
const char* title,
const t_functype* functype,
const InteractionList& ilist,
- gmx_bool bShowNumbers,
- gmx_bool bShowParameters,
+ bool bShowNumbers,
+ bool bShowParameters,
const t_iparams* iparams);
-void pr_idef(FILE* fp, int indent, const char* title, const t_idef* idef, gmx_bool bShowNumbers, gmx_bool bShowParameters);
+void pr_idef(FILE* fp, int indent, const char* title, const t_idef* idef, bool bShowNumbers, bool bShowParameters);
/*! \brief
* Properly initialize idef struct.
/* this MUST correspond to the enum in src/gromacs/topology/ifunc.h */
const t_interaction_function interaction_function[F_NRE] = {
- def_bond("BONDS", "Bond", 2, 2, 2), def_bond("G96BONDS", "G96Bond", 2, 2, 2),
- def_bond("MORSE", "Morse", 2, 3, 3), def_bond("CUBICBONDS", "Cubic Bonds", 2, 3, 0),
+ def_bond("BONDS", "Bond", 2, 2, 2),
+ def_bond("G96BONDS", "G96Bond", 2, 2, 2),
+ def_bond("MORSE", "Morse", 2, 3, 3),
+ def_bond("CUBICBONDS", "Cubic Bonds", 2, 3, 0),
def_bondnb("CONNBONDS", "Connect Bonds", 2, 0, 0),
- def_bonded("HARMONIC", "Harmonic Pot.", 2, 2, 2), def_bondnb("FENEBONDS", "FENE Bonds", 2, 2, 0),
- def_bondt("TABBONDS", "Tab. Bonds", 2, 2, 2), def_bondedtz("TABBONDSNC", "Tab. Bonds NC", 2, 2, 2),
- def_bonded("RESTRAINTPOT", "Restraint Pot.", 2, 4, 4), def_angle("ANGLES", "Angle", 3, 2, 2),
- def_angle("G96ANGLES", "G96Angle", 3, 2, 2), def_angle("RESTRANGLES", "Restricted Angles", 3, 2, 2),
+ def_bonded("HARMONIC", "Harmonic Pot.", 2, 2, 2),
+ def_bondnb("FENEBONDS", "FENE Bonds", 2, 2, 0),
+ def_bondt("TABBONDS", "Tab. Bonds", 2, 2, 2),
+ def_bondedtz("TABBONDSNC", "Tab. Bonds NC", 2, 2, 2),
+ def_bonded("RESTRAINTPOT", "Restraint Pot.", 2, 4, 4),
+ def_angle("ANGLES", "Angle", 3, 2, 2),
+ def_angle("G96ANGLES", "G96Angle", 3, 2, 2),
+ def_angle("RESTRANGLES", "Restricted Angles", 3, 2, 2),
def_angle("LINEAR_ANGLES", "Lin. Angle", 3, 2, 2),
def_bonded("CROSS_BOND_BOND", "Bond-Cross", 3, 3, 0),
- def_bonded("CROSS_BOND_ANGLE", "BA-Cross", 3, 4, 0), def_angle("UREY_BRADLEY", "U-B", 3, 4, 4),
- def_angle("QANGLES", "Quartic Angles", 3, 6, 0), def_bondedt("TABANGLES", "Tab. Angles", 3, 2, 2),
- def_dihedral("PDIHS", "Proper Dih.", 4, 3, 3), def_dihedral("RBDIHS", "Ryckaert-Bell.", 4, 6, 6),
+ def_bonded("CROSS_BOND_ANGLE", "BA-Cross", 3, 4, 0),
+ def_angle("UREY_BRADLEY", "U-B", 3, 4, 4),
+ def_angle("QANGLES", "Quartic Angles", 3, 6, 0),
+ def_bondedt("TABANGLES", "Tab. Angles", 3, 2, 2),
+ def_dihedral("PDIHS", "Proper Dih.", 4, 3, 3),
+ def_dihedral("RBDIHS", "Ryckaert-Bell.", 4, 6, 6),
def_dihedral("RESTRDIHS", "Restricted Dih.", 4, 2, 2),
- def_dihedral("CBTDIHS", "CBT Dih.", 4, 6, 6), def_dihedral("FOURDIHS", "Fourier Dih.", 4, 4, 4),
- def_dihedral("IDIHS", "Improper Dih.", 4, 2, 2), def_dihedral("PIDIHS", "Improper Dih.", 4, 3, 3),
+ def_dihedral("CBTDIHS", "CBT Dih.", 4, 6, 6),
+ def_dihedral("FOURDIHS", "Fourier Dih.", 4, 4, 4),
+ def_dihedral("IDIHS", "Improper Dih.", 4, 2, 2),
+ def_dihedral("PIDIHS", "Improper Dih.", 4, 3, 3),
def_dihedral_tabulated("TABDIHS", "Tab. Dih.", 4, 2, 2),
- def_dihedral("CMAP", "CMAP Dih.", 5, -1, -1), def_nofc("GB12", "GB 1-2 Pol. (unused)"),
- def_nofc("GB13", "GB 1-3 Pol. (unused)"), def_nofc("GB14", "GB 1-4 Pol. (unused)"),
- def_nofc("GBPOL", "GB Polarization (unused)"), def_nofc("NPSOLVATION", "Nonpolar Sol. (unused)"),
- def_pair("LJ14", "LJ-14", 2, 2, 2), def_nofc("COUL14", "Coulomb-14"),
- def_pair("LJC14_Q", "LJC-14 q", 2, 5, 0), def_pair("LJC_NB", "LJC Pairs NB", 2, 4, 0),
- def_nb("LJ_SR", "LJ (SR)", 2, 2), def_nb("BHAM", "Buck.ham (SR)", 2, 3),
- def_nofc("LJ_LR", "LJ (unused)"), def_nofc("BHAM_LR", "B.ham (unused)"),
- def_nofc("DISPCORR", "Disper. corr."), def_nofc("COUL_SR", "Coulomb (SR)"),
- def_nofc("COUL_LR", "Coul (unused)"), def_nofc("RF_EXCL", "RF excl."),
- def_nofc("COUL_RECIP", "Coul. recip."), def_nofc("LJ_RECIP", "LJ recip."),
- def_nofc("DPD", "DPD"), def_bondnb("POLARIZATION", "Polarization", 2, 1, 0),
- def_bonded("WATERPOL", "Water Pol.", 5, 6, 0), def_bonded("THOLE", "Thole Pol.", 4, 3, 0),
- def_bondnb("ANHARM_POL", "Anharm. Pol.", 2, 3, 0), def_bonded("POSRES", "Position Rest.", 1, 3, 3),
- def_bonded("FBPOSRES", "Flat-bottom posres", 1, 3, 0), def_bonded("DISRES", "Dis. Rest.", 2, 6, 0),
- def_nofc("DISRESVIOL", "D.R.Viol. (nm)"), def_bonded("ORIRES", "Orient. Rest.", 2, 6, 0),
- def_nofc("ORDEV", "Ori. R. RMSD"), def_bonded("ANGRES", "Angle Rest.", 4, 3, 3),
- def_bonded("ANGRESZ", "Angle Rest. Z", 2, 3, 3), def_bonded("DIHRES", "Dih. Rest.", 4, 3, 3),
+ def_dihedral("CMAP", "CMAP Dih.", 5, -1, -1),
+ def_nofc("GB12", "GB 1-2 Pol. (unused)"),
+ def_nofc("GB13", "GB 1-3 Pol. (unused)"),
+ def_nofc("GB14", "GB 1-4 Pol. (unused)"),
+ def_nofc("GBPOL", "GB Polarization (unused)"),
+ def_nofc("NPSOLVATION", "Nonpolar Sol. (unused)"),
+ def_pair("LJ14", "LJ-14", 2, 2, 2),
+ def_nofc("COUL14", "Coulomb-14"),
+ def_pair("LJC14_Q", "LJC-14 q", 2, 5, 0),
+ def_pair("LJC_NB", "LJC Pairs NB", 2, 4, 0),
+ def_nb("LJ_SR", "LJ (SR)", 2, 2),
+ def_nb("BHAM", "Buck.ham (SR)", 2, 3),
+ def_nofc("LJ_LR", "LJ (unused)"),
+ def_nofc("BHAM_LR", "B.ham (unused)"),
+ def_nofc("DISPCORR", "Disper. corr."),
+ def_nofc("COUL_SR", "Coulomb (SR)"),
+ def_nofc("COUL_LR", "Coul (unused)"),
+ def_nofc("RF_EXCL", "RF excl."),
+ def_nofc("COUL_RECIP", "Coul. recip."),
+ def_nofc("LJ_RECIP", "LJ recip."),
+ def_nofc("DPD", "DPD"),
+ def_bondnb("POLARIZATION", "Polarization", 2, 1, 0),
+ def_bonded("WATERPOL", "Water Pol.", 5, 6, 0),
+ def_bonded("THOLE", "Thole Pol.", 4, 3, 0),
+ def_bondnb("ANHARM_POL", "Anharm. Pol.", 2, 3, 0),
+ def_bonded("POSRES", "Position Rest.", 1, 3, 3),
+ def_bonded("FBPOSRES", "Flat-bottom posres", 1, 3, 0),
+ def_bonded("DISRES", "Dis. Rest.", 2, 6, 0),
+ def_nofc("DISRESVIOL", "D.R.Viol. (nm)"),
+ def_bonded("ORIRES", "Orient. Rest.", 2, 6, 0),
+ def_nofc("ORDEV", "Ori. R. RMSD"),
+ def_bonded("ANGRES", "Angle Rest.", 4, 3, 3),
+ def_bonded("ANGRESZ", "Angle Rest. Z", 2, 3, 3),
+ def_bonded("DIHRES", "Dih. Rest.", 4, 3, 3),
def_nofc("DIHRESVIOL", "Dih. Rest. Viol."), /* obsolete */
- def_shkcb("CONSTR", "Constraint", 2, 1, 1), def_shk("CONSTRNC", "Constr. No Conn.", 2, 1, 1),
- def_shkcb("SETTLE", "Settle", 3, 2, 0), def_vsite("VSITE1", "Virtual site 1", 2, 0),
- def_vsite("VSITE2", "Virtual site 2", 3, 1), def_vsite("VSITE2FD", "Virtual site 2fd", 3, 1),
- def_vsite("VSITE3", "Virtual site 3", 4, 2), def_vsite("VSITE3FD", "Virtual site 3fd", 4, 2),
+ def_shkcb("CONSTR", "Constraint", 2, 1, 1),
+ def_shk("CONSTRNC", "Constr. No Conn.", 2, 1, 1),
+ def_shkcb("SETTLE", "Settle", 3, 2, 0),
+ def_vsite("VSITE1", "Virtual site 1", 2, 0),
+ def_vsite("VSITE2", "Virtual site 2", 3, 1),
+ def_vsite("VSITE2FD", "Virtual site 2fd", 3, 1),
+ def_vsite("VSITE3", "Virtual site 3", 4, 2),
+ def_vsite("VSITE3FD", "Virtual site 3fd", 4, 2),
def_vsite("VSITE3FAD", "Virtual site 3fad", 4, 2),
- def_vsite("VSITE3OUT", "Virtual site 3out", 4, 3), def_vsite("VSITE4FD", "Virtual site 4fd", 5, 3),
- def_vsite("VSITE4FDN", "Virtual site 4fdn", 5, 3), def_vsite("VSITEN", "Virtual site N", 2, 2),
- def_nofc("COM_PULL", "COM Pull En."), def_nofc("DENSITYFIT", "Density fitting"),
- def_nofc("EQM", "Quantum En."), def_nofc("EPOT", "Potential"), def_nofc("EKIN", "Kinetic En."),
- def_nofc("ETOT", "Total Energy"), def_nofc("ECONS", "Conserved En."),
- def_nofc("TEMP", "Temperature"), def_nofc("VTEMP", "Vir. Temp. (not used)"),
+ def_vsite("VSITE3OUT", "Virtual site 3out", 4, 3),
+ def_vsite("VSITE4FD", "Virtual site 4fd", 5, 3),
+ def_vsite("VSITE4FDN", "Virtual site 4fdn", 5, 3),
+ def_vsite("VSITEN", "Virtual site N", 2, 2),
+ def_nofc("COM_PULL", "COM Pull En."),
+ def_nofc("DENSITYFIT", "Density fitting"),
+ def_nofc("EQM", "Quantum En."),
+ def_nofc("EPOT", "Potential"),
+ def_nofc("EKIN", "Kinetic En."),
+ def_nofc("ETOT", "Total Energy"),
+ def_nofc("ECONS", "Conserved En."),
+ def_nofc("TEMP", "Temperature"),
+ def_nofc("VTEMP", "Vir. Temp. (not used)"),
/* Note that pressure names can not be more than 8 char's,
* because " (bar)" is appended to them.
*/
- def_nofc("PDISPCORR", "Pres. DC"), def_nofc("PRES", "Pressure"),
+ def_nofc("PDISPCORR", "Pres. DC"),
+ def_nofc("PRES", "Pressure"),
def_nofc("DH/DL_CON", "dH/dl constr."), /* obsolete */
- def_nofc("DV/DL", "dVremain/dl"), def_nofc("DK/DL", "dEkin/dl"), def_nofc("DVC/DL", "dVcoul/dl"),
- def_nofc("DVV/DL", "dVvdw/dl"), def_nofc("DVB/DL", "dVbonded/dl"),
- def_nofc("DVR/DL", "dVrestraint/dl"), def_nofc("DVT/DL", "dVtemperature/dl")
+ def_nofc("DV/DL", "dVremain/dl"),
+ def_nofc("DK/DL", "dEkin/dl"),
+ def_nofc("DVC/DL", "dVcoul/dl"),
+ def_nofc("DVV/DL", "dVvdw/dl"),
+ def_nofc("DVB/DL", "dVbonded/dl"),
+ def_nofc("DVR/DL", "dVrestraint/dl"),
+ def_nofc("DVT/DL", "dVtemperature/dl")
};
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstring>
#include <algorithm>
+#include <numeric>
#include "gromacs/topology/atoms.h"
#include "gromacs/topology/block.h"
static gmx_bool gmx_ask_yesno(gmx_bool bASK)
{
- char c;
+ char c = 0;
if (bASK)
{
void write_index(const char* outf, t_blocka* b, char** gnames, gmx_bool bDuplicate, int natoms)
{
- FILE* out;
- int i, j, k;
-
- out = gmx_ffopen(outf, "w");
+ FILE* out = gmx_ffopen(outf, "w");
/* fprintf(out,"%5d %5d\n",b->nr,b->nra); */
- for (i = 0; (i < b->nr); i++)
+ for (int i = 0; (i < b->nr); i++)
{
fprintf(out, "[ %s ]", gnames[i]);
- for (k = 0, j = b->index[i]; j < b->index[i + 1]; j++, k++)
+ for (int k = 0, j = b->index[i]; j < b->index[i + 1]; j++, k++)
{
const char sep = (k % 15 == 0 ? '\n' : ' ');
fprintf(out, "%c%4d", sep, b->a[j] + 1);
if (bDuplicate)
{
fprintf(stderr, "Duplicating the whole system with an atom offset of %d atoms.\n", natoms);
- for (i = 0; (i < b->nr); i++)
+ for (int i = 0; (i < b->nr); i++)
{
fprintf(out, "[ %s_copy ]", gnames[i]);
- for (k = 0, j = b->index[i]; j < b->index[i + 1]; j++, k++)
+ for (int k = 0, j = b->index[i]; j < b->index[i + 1]; j++, k++)
{
const char sep = (k % 15 == 0 ? '\n' : ' ');
fprintf(out, "%c%4d", sep, b->a[j] + 1 + natoms);
gmx_bool bASK,
gmx_bool bVerb)
{
- restp_t* restp = nullptr;
- char** attp = nullptr;
- char * rname, *aname;
- int i, resind, natp, nrestp = 0;
+ std::vector<restp_t> restp;
+ int i = 0;
- for (i = 0; (i < atoms->nres); i++)
+ for (; (i < atoms->nres); i++)
{
if (gmx_strcasecmp(restype[i].c_str(), "Protein")
&& gmx_strcasecmp(restype[i].c_str(), "DNA") && gmx_strcasecmp(restype[i].c_str(), "RNA")
}
for (int k = 0; (k < atoms->nr); k++)
{
- resind = atoms->atom[k].resind;
- rname = *atoms->resinfo[resind].name;
+ int resind = atoms->atom[k].resind;
+ const char* rname = *atoms->resinfo[resind].name;
if (gmx_strcasecmp(restype[resind].c_str(), "Protein")
&& gmx_strcasecmp(restype[resind].c_str(), "DNA")
&& gmx_strcasecmp(restype[resind].c_str(), "RNA")
&& gmx_strcasecmp(restype[resind].c_str(), "Water"))
{
- int l;
- for (l = 0; (l < nrestp); l++)
- {
- assert(restp);
- if (strcmp(restp[l].rname, rname) == 0)
- {
- break;
- }
- }
- if (l == nrestp)
+ auto found = std::find_if(restp.begin(), restp.end(), [rname](const auto& entry) {
+ return strcmp(entry.rname, rname) == 0;
+ });
+ if (found == restp.end())
{
- srenew(restp, nrestp + 1);
- restp[nrestp].rname = gmx_strdup(rname);
- restp[nrestp].bNeg = FALSE;
- restp[nrestp].gname = gmx_strdup(rname);
- nrestp++;
+ restp.emplace_back();
+ auto& last = restp.back();
+ last.rname = gmx_strdup(rname);
+ last.bNeg = false;
+ last.gname = gmx_strdup(rname);
}
}
}
- for (int i = 0; (i < nrestp); i++)
+ for (int i = 0; (i < gmx::ssize(restp)); i++)
{
std::vector<int> aid;
for (int j = 0; (j < atoms->nr); j++)
{
- rname = *atoms->resinfo[atoms->atom[j].resind].name;
+ const char* rname = *atoms->resinfo[atoms->atom[j].resind].name;
if ((strcmp(restp[i].rname, rname) == 0 && !restp[i].bNeg)
|| (strcmp(restp[i].rname, rname) != 0 && restp[i].bNeg))
{
fflush(stdout);
if (gmx_ask_yesno(bASK))
{
- natp = 0;
+ std::vector<const char*> attp;
for (size_t k = 0; (k < aid.size()); k++)
{
- aname = *atoms->atomname[aid[k]];
- int l;
- for (l = 0; (l < natp); l++)
- {
- if (strcmp(aname, attp[l]) == 0)
- {
- break;
- }
- }
- if (l == natp)
+ const char* aname = *atoms->atomname[aid[k]];
+ auto found = std::find_if(attp.begin(), attp.end(), [aname](const char* entry) {
+ return strcmp(aname, entry) == 0;
+ });
+ if (found == attp.end())
{
- srenew(attp, ++natp);
- attp[natp - 1] = aname;
+ attp.emplace_back(aname);
}
}
- if (natp > 1)
+ if (attp.size() > 1)
{
+ const int natp = attp.size();
for (int l = 0; (l < natp); l++)
{
std::vector<int> aaid;
for (size_t k = 0; (k < aid.size()); k++)
{
- aname = *atoms->atomname[aid[k]];
+ const char* aname = *atoms->atomname[aid[k]];
if (strcmp(aname, attp[l]) == 0)
{
aaid.push_back(aid[k]);
add_grp(gb, gn, aaid, attp[l]);
}
}
- sfree(attp);
- attp = nullptr;
}
}
sfree(restp[i].rname);
sfree(restp[i].gname);
}
- sfree(restp);
}
}
};
const int num_index_groups = asize(constructing_data);
- int n, j;
- int npres;
- gmx_bool match;
- char ndx_name[STRLEN], *atnm;
- int i;
+ char ndx_name[STRLEN];
if (bVerb)
{
std::vector<int> aid;
/* calculate the number of protein residues */
- npres = 0;
- for (i = 0; (i < atoms->nres); i++)
+ int npres = 0;
+ for (int i = 0; (i < atoms->nres); i++)
{
if (0 == gmx_strcasecmp(restype[i].c_str(), "Protein"))
{
}
}
/* find matching or complement atoms */
- for (i = 0; (i < num_index_groups); i++)
+ for (int i = 0; (i < num_index_groups); i++)
{
- for (n = 0; (n < atoms->nr); n++)
+ for (int n = 0; (n < atoms->nr); n++)
{
if (0 == gmx_strcasecmp(restype[atoms->atom[n].resind].c_str(), "Protein"))
{
- match = FALSE;
- for (j = 0; (j < constructing_data[i].num_defining_atomnames); j++)
+ bool match = false;
+ for (int j = 0; (j < constructing_data[i].num_defining_atomnames); j++)
{
/* skip digits at beginning of atomname, e.g. 1H */
- atnm = *atoms->atomname[n];
+ char* atnm = *atoms->atomname[n];
while (isdigit(atnm[0]))
{
atnm++;
{
if (0 == gmx_strcasecmp(constructing_data[i].defining_atomnames[j], atnm))
{
- match = TRUE;
+ match = true;
}
}
else
{
if (0
- == gmx_strncasecmp(constructing_data[i].defining_atomnames[j], atnm,
+ == gmx_strncasecmp(constructing_data[i].defining_atomnames[j],
+ atnm,
strlen(constructing_data[i].defining_atomnames[j])))
{
- match = TRUE;
+ match = true;
}
}
}
if (bASK)
{
- for (i = 0; (i < num_index_groups); i++)
+ for (int i = 0; (i < num_index_groups); i++)
{
printf("Split %12s into %5d residues (y/n) ? ", constructing_data[i].group_name, npres);
if (gmx_ask_yesno(bASK))
{
- int resind;
aid.clear();
- for (n = 0; ((atoms->atom[n].resind < npres) && (n < atoms->nr));)
+ for (int n = 0; ((atoms->atom[n].resind < npres) && (n < atoms->nr));)
{
- resind = atoms->atom[n].resind;
+ int resind = atoms->atom[n].resind;
for (; ((atoms->atom[n].resind == resind) && (n < atoms->nr)); n++)
{
- match = FALSE;
- for (j = 0; (j < constructing_data[i].num_defining_atomnames); j++)
+ bool match = false;
+ for (int j = 0; (j < constructing_data[i].num_defining_atomnames); j++)
{
if (0
== gmx_strcasecmp(constructing_data[i].defining_atomnames[j],
*atoms->atomname[n]))
{
- match = TRUE;
+ match = true;
}
}
if (constructing_data[i].bTakeComplement != match)
/* copy the residuename to the tail of the groupname */
if (!aid.empty())
{
- t_resinfo* ri;
- ri = &atoms->resinfo[resind];
- sprintf(ndx_name, "%s_%s%d%c", constructing_data[i].group_name, *ri->name,
- ri->nr, ri->ic == ' ' ? '\0' : ri->ic);
+ t_resinfo* ri = &atoms->resinfo[resind];
+ sprintf(ndx_name,
+ "%s_%s%d%c",
+ constructing_data[i].group_name,
+ *ri->name,
+ ri->nr,
+ ri->ic == ' ' ? '\0' : ri->ic);
add_grp(gb, gn, aid, ndx_name);
aid.clear();
}
void analyse(const t_atoms* atoms, t_blocka* gb, char*** gn, gmx_bool bASK, gmx_bool bVerb)
{
- char* resnm;
- int i;
- int iwater, iion;
- int nwater, nion;
-
if (bVerb)
{
printf("Analysing residue names:\n");
}
/* Create system group, every single atom */
std::vector<int> aid(atoms->nr);
- for (i = 0; i < atoms->nr; i++)
- {
- aid[i] = i;
- }
+ std::iota(aid.begin(), aid.end(), 0);
add_grp(gb, gn, aid, "System");
/* For every residue, get a pointer to the residue type name */
std::vector<std::string> previousTypename;
if (atoms->nres > 0)
{
- int i = 0;
-
- resnm = *atoms->resinfo[i].name;
+ const char* resnm = *atoms->resinfo[0].name;
restype.emplace_back(rt.typeOfNamedDatabaseResidue(resnm));
previousTypename.push_back(restype.back());
- for (i = 1; i < atoms->nres; i++)
+ for (int i = 1; i < atoms->nres; i++)
{
- resnm = *atoms->resinfo[i].name;
+ const char* resnm = *atoms->resinfo[i].name;
restype.emplace_back(rt.typeOfNamedDatabaseResidue(resnm));
/* Note that this does not lead to a N*N loop, but N*K, where
for (gmx::index k = 0; k < gmx::ssize(previousTypename); k++)
{
- aid = mk_aid(atoms, restype, previousTypename[k], TRUE);
+ std::vector<int> aid = mk_aid(atoms, restype, previousTypename[k], TRUE);
/* Check for special types to do fancy stuff with */
analyse_prot(restype, atoms, gb, gn, bASK, bVerb);
/* Create a Non-Protein group */
- aid = mk_aid(atoms, restype, "Protein", FALSE);
+ std::vector<int> aid = mk_aid(atoms, restype, "Protein", FALSE);
if ((!aid.empty()) && (gmx::ssize(aid) < atoms->nr))
{
add_grp(gb, gn, aid, "non-Protein");
/* Solvent, create a negated group too */
- aid = mk_aid(atoms, restype, "Water", FALSE);
+ std::vector<int> aid = mk_aid(atoms, restype, "Water", FALSE);
if ((!aid.empty()) && (gmx::ssize(aid) < atoms->nr))
{
add_grp(gb, gn, aid, "non-Water");
/* Create a merged water_and_ions group */
- iwater = -1;
- iion = -1;
- nwater = 0;
- nion = 0;
+ int iwater = -1;
+ int iion = -1;
+ int nwater = 0;
+ int nion = 0;
- for (i = 0; i < gb->nr; i++)
+ for (int i = 0; i < gb->nr; i++)
{
if (!gmx_strcasecmp((*gn)[i], "Water"))
{
srenew(gb->a, gb->nra + nwater + nion);
if (nwater > 0)
{
- for (i = gb->index[iwater]; i < gb->index[iwater + 1]; i++)
+ for (int i = gb->index[iwater]; i < gb->index[iwater + 1]; i++)
{
gb->a[gb->nra++] = gb->a[i];
}
}
if (nion > 0)
{
- for (i = gb->index[iion]; i < gb->index[iion + 1]; i++)
+ for (int i = gb->index[iion]; i < gb->index[iion + 1]; i++)
{
gb->a[gb->nra++] = gb->a[i];
}
void check_index(const char* gname, int n, int index[], const char* traj, int natoms)
{
- int i;
-
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
if (index[i] >= natoms)
{
gmx_fatal(FARGS,
"%s atom number (index[%d]=%d) is larger than the number of atoms in %s (%d)",
- gname ? gname : "Index", i + 1, index[i] + 1, traj ? traj : "the trajectory",
+ gname ? gname : "Index",
+ i + 1,
+ index[i] + 1,
+ traj ? traj : "the trajectory",
natoms);
}
else if (index[i] < 0)
{
- gmx_fatal(FARGS, "%s atom number (index[%d]=%d) is less than zero",
- gname ? gname : "Index", i + 1, index[i] + 1);
+ gmx_fatal(FARGS,
+ "%s atom number (index[%d]=%d) is less than zero",
+ gname ? gname : "Index",
+ i + 1,
+ index[i] + 1);
}
}
}
t_blocka* init_index(const char* gfile, char*** grpname)
{
- FILE* in;
- t_blocka* b;
- int maxentries;
- int i, j;
- char line[STRLEN], *pt, str[STRLEN];
+ t_blocka* b = nullptr;
+ char line[STRLEN], str[STRLEN];
- in = gmx_ffopen(gfile, "r");
+ FILE* in = gmx_ffopen(gfile, "r");
snew(b, 1);
- b->nr = 0;
- b->index = nullptr;
- b->nra = 0;
- b->a = nullptr;
- *grpname = nullptr;
- maxentries = 0;
+ b->nr = 0;
+ b->index = nullptr;
+ b->nra = 0;
+ b->a = nullptr;
+ *grpname = nullptr;
+ int maxentries = 0;
while (get_a_line(in, line, STRLEN))
{
if (get_header(line, str))
{
gmx_fatal(FARGS, "The first header of your indexfile is invalid");
}
- pt = line;
+ char* pt = line;
while (sscanf(pt, "%s", str) == 1)
{
- i = b->index[b->nr];
+ int i = b->index[b->nr];
if (i >= maxentries)
{
maxentries += 1024;
}
gmx_ffclose(in);
- for (i = 0; (i < b->nr); i++)
+ for (int i = 0; (i < b->nr); i++)
{
assert(b->a != nullptr); // for clang analyzer
- for (j = b->index[i]; (j < b->index[i + 1]); j++)
+ for (int j = b->index[i]; (j < b->index[i + 1]); j++)
{
if (b->a[j] < 0)
{
static void minstring(char* str)
{
- int i;
-
- for (i = 0; (i < static_cast<int>(strlen(str))); i++)
+ for (int i = 0; (i < static_cast<int>(strlen(str))); i++)
{
if (str[i] == '-')
{
int find_group(const char* s, int ngrps, char** grpname)
{
- int aa, i, n;
- char string[STRLEN];
- gmx_bool bMultiple;
- bMultiple = FALSE;
- n = strlen(s);
- aa = -1;
+ char string[STRLEN];
+ bool bMultiple = false;
+ const int n = strlen(s);
+ int aa = -1;
/* first look for whole name match */
{
- for (i = 0; i < ngrps; i++)
+ for (int i = 0; i < ngrps; i++)
{
if (gmx_strcasecmp_min(s, grpname[i]) == 0)
{
if (aa != -1)
{
- bMultiple = TRUE;
+ bMultiple = true;
}
aa = i;
}
/* second look for first string match */
if (aa == -1)
{
- for (i = 0; i < ngrps; i++)
+ for (int i = 0; i < ngrps; i++)
{
if (gmx_strncasecmp_min(s, grpname[i], n) == 0)
{
key[STRLEN - 1] = '\0';
upstring(key);
minstring(key);
- for (i = 0; i < ngrps; i++)
+ for (int i = 0; i < ngrps; i++)
{
strncpy(string, grpname[i], STRLEN - 1);
upstring(string);
static int qgroup(int* a, int ngrps, char** grpname)
{
- char s[STRLEN];
- int aa;
- gmx_bool bInRange;
- char* end;
+ char s[STRLEN];
+ int aa = 0;
+ bool bInRange = false;
+ char* end = nullptr;
do
{
static void
rd_groups(t_blocka* grps, char** grpname, char* gnames[], int ngrps, int isize[], int* index[], int grpnr[])
{
- int i, j, gnr1;
-
if (grps->nr == 0)
{
gmx_fatal(FARGS, "Error: no groups in indexfile");
}
- for (i = 0; (i < grps->nr); i++)
+ for (int i = 0; (i < grps->nr); i++)
{
- fprintf(stderr, "Group %5d (%15s) has %5d elements\n", i, grpname[i],
- grps->index[i + 1] - grps->index[i]);
+ fprintf(stderr, "Group %5d (%15s) has %5d elements\n", i, grpname[i], grps->index[i + 1] - grps->index[i]);
}
- for (i = 0; (i < ngrps); i++)
+ for (int i = 0; (i < ngrps); i++)
{
+ int gnr1 = 0;
if (grps->nr > 1)
{
do
gnames[i] = gmx_strdup(grpname[gnr1]);
isize[i] = grps->index[gnr1 + 1] - grps->index[gnr1];
snew(index[i], isize[i]);
- for (j = 0; (j < isize[i]); j++)
+ for (int j = 0; (j < isize[i]); j++)
{
index[i][j] = grps->a[grps->index[gnr1] + j];
}
void rd_index(const char* statfile, int ngrps, int isize[], int* index[], char* grpnames[])
{
- char** gnames;
- t_blocka* grps;
- int* grpnr;
+ char** gnames = nullptr;
+ int* grpnr = nullptr;
snew(grpnr, ngrps);
if (!statfile)
{
gmx_fatal(FARGS, "No index file specified");
}
- grps = init_index(statfile, &gnames);
+ t_blocka* grps = init_index(statfile, &gnames);
rd_groups(grps, gnames, grpnames, ngrps, isize, index, grpnr);
for (int i = 0; i < grps->nr; i++)
{
void get_index(const t_atoms* atoms, const char* fnm, int ngrps, int isize[], int* index[], char* grpnames[])
{
- char*** gnames;
- t_blocka* grps = nullptr;
- int* grpnr;
+ char*** gnames = nullptr;
+ t_blocka* grps = nullptr;
+ int* grpnr = nullptr;
snew(grpnr, ngrps);
snew(gnames, 1);
t_cluster_ndx* cluster_index(FILE* fplog, const char* ndx)
{
- t_cluster_ndx* c;
- int i;
+ t_cluster_ndx* c = nullptr;
snew(c, 1);
c->clust = init_index(ndx, &c->grpname);
c->maxframe = -1;
- for (i = 0; (i < c->clust->nra); i++)
+ for (int i = 0; (i < c->clust->nra); i++)
{
c->maxframe = std::max(c->maxframe, c->clust->a[i]);
}
fprintf(fplog ? fplog : stdout,
- "There are %d clusters containing %d structures, highest framenr is %d\n", c->clust->nr,
- c->clust->nra, c->maxframe);
+ "There are %d clusters containing %d structures, highest framenr is %d\n",
+ c->clust->nr,
+ c->clust->nra,
+ c->maxframe);
if (debug)
{
pr_blocka(debug, 0, "clust", c->clust, TRUE);
- for (i = 0; (i < c->clust->nra); i++)
+ for (int i = 0; (i < c->clust->nra); i++)
{
if ((c->clust->a[i] < 0) || (c->clust->a[i] > c->maxframe))
{
gmx_fatal(FARGS,
"Range check error for c->clust->a[%d] = %d\n"
"should be within 0 and %d",
- i, c->clust->a[i], c->maxframe + 1);
+ i,
+ c->clust->a[i],
+ c->maxframe + 1);
}
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int* make_invblock(const t_block* block, int nr)
{
- int i, j;
- int* invblock;
+ int* invblock = nullptr;
snew(invblock, nr + 1);
/* Mark unused numbers */
- for (i = 0; i <= nr; i++)
+ for (int i = 0; i <= nr; i++)
{
invblock[i] = -1;
}
- for (i = 0; (i < block->nr); i++)
+ for (int i = 0; (i < block->nr); i++)
{
- for (j = block->index[i]; (j < block->index[i + 1]); j++)
+ for (int j = block->index[i]; (j < block->index[i + 1]); j++)
{
if (invblock[j] == -1)
{
gmx_fatal(FARGS,
"Double entries in block structure. Item %d is in blocks %d and %d\n"
" Cannot make an unambiguous inverse block.",
- j, i, invblock[j]);
+ j,
+ i,
+ invblock[j]);
}
}
}
int* make_invblocka(const t_blocka* block, int nr)
{
- int i, j;
- int* invblock;
+ int* invblock = nullptr;
snew(invblock, nr + 1);
/* Mark unused numbers */
- for (i = 0; i <= nr; i++)
+ for (int i = 0; i <= nr; i++)
{
invblock[i] = -1;
}
- for (i = 0; (i < block->nr); i++)
+ for (int i = 0; (i < block->nr); i++)
{
- for (j = block->index[i]; (j < block->index[i + 1]); j++)
+ for (int j = block->index[i]; (j < block->index[i + 1]); j++)
{
if (invblock[block->a[j]] == -1)
{
gmx_fatal(FARGS,
"Double entries in block structure. Item %d is in blocks %d and %d\n"
" Cannot make an unambiguous inverse block.",
- j, i, invblock[block->a[j]]);
+ j,
+ i,
+ invblock[block->a[j]]);
}
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \param[out] moleculeIndex The index of the molecule in the block, can be NULL
* \param[out] atomIndexInMolecule The atom index in the molecule, can be NULL
*/
-static inline void mtopGetMolblockIndex(const gmx_mtop_t* mtop,
+static inline void mtopGetMolblockIndex(const gmx_mtop_t& mtop,
int globalAtomIndex,
int* moleculeBlock,
int* moleculeIndex,
int* atomIndexInMolecule)
{
GMX_ASSERT(globalAtomIndex >= 0, "The atom index to look up should not be negative");
- GMX_ASSERT(globalAtomIndex < mtop->natoms, "The atom index to look up should be within range");
+ GMX_ASSERT(globalAtomIndex < mtop.natoms, "The atom index to look up should be within range");
GMX_ASSERT(moleculeBlock != nullptr, "molBlock can not be NULL");
- GMX_ASSERT(!mtop->moleculeBlockIndices.empty(), "The moleculeBlockIndices should not be empty");
+ GMX_ASSERT(!mtop.moleculeBlockIndices.empty(), "The moleculeBlockIndices should not be empty");
GMX_ASSERT(*moleculeBlock >= 0,
"The starting molecule block index for the search should not be negative");
- GMX_ASSERT(*moleculeBlock < gmx::ssize(mtop->moleculeBlockIndices),
+ GMX_ASSERT(*moleculeBlock < gmx::ssize(mtop.moleculeBlockIndices),
"The starting molecule block index for the search should be within range");
/* Search the molecule block index using bisection */
int molBlock0 = -1;
- int molBlock1 = mtop->molblock.size();
+ int molBlock1 = mtop.molblock.size();
- int globalAtomStart;
+ int globalAtomStart = 0;
while (TRUE)
{
- globalAtomStart = mtop->moleculeBlockIndices[*moleculeBlock].globalAtomStart;
+ globalAtomStart = mtop.moleculeBlockIndices[*moleculeBlock].globalAtomStart;
if (globalAtomIndex < globalAtomStart)
{
molBlock1 = *moleculeBlock;
}
- else if (globalAtomIndex >= mtop->moleculeBlockIndices[*moleculeBlock].globalAtomEnd)
+ else if (globalAtomIndex >= mtop.moleculeBlockIndices[*moleculeBlock].globalAtomEnd)
{
molBlock0 = *moleculeBlock;
}
}
int molIndex = (globalAtomIndex - globalAtomStart)
- / mtop->moleculeBlockIndices[*moleculeBlock].numAtomsPerMolecule;
+ / mtop.moleculeBlockIndices[*moleculeBlock].numAtomsPerMolecule;
if (moleculeIndex != nullptr)
{
*moleculeIndex = molIndex;
if (atomIndexInMolecule != nullptr)
{
*atomIndexInMolecule = globalAtomIndex - globalAtomStart
- - molIndex * mtop->moleculeBlockIndices[*moleculeBlock].numAtomsPerMolecule;
+ - molIndex * mtop.moleculeBlockIndices[*moleculeBlock].numAtomsPerMolecule;
}
}
* \param[in] globalAtomIndex The global atom index to look up
* \param[in,out] moleculeBlock The molecule block index in \p mtop
*/
-static inline int mtopGetMoleculeIndex(const gmx_mtop_t* mtop, int globalAtomIndex, int* moleculeBlock)
+static inline int mtopGetMoleculeIndex(const gmx_mtop_t& mtop, int globalAtomIndex, int* moleculeBlock)
{
- int localMoleculeIndex;
+ int localMoleculeIndex = 0;
mtopGetMolblockIndex(mtop, globalAtomIndex, moleculeBlock, &localMoleculeIndex, nullptr);
- return mtop->moleculeBlockIndices[*moleculeBlock].moleculeIndexStart + localMoleculeIndex;
+ return mtop.moleculeBlockIndices[*moleculeBlock].moleculeIndexStart + localMoleculeIndex;
}
/*! \brief Returns the atom data for an atom based on global atom index
* \param[in] globalAtomIndex The global atom index to look up
* \param[in,out] moleculeBlock The molecule block index in \p mtop
*/
-static inline const t_atom& mtopGetAtomParameters(const gmx_mtop_t* mtop, int globalAtomIndex, int* moleculeBlock)
+static inline const t_atom& mtopGetAtomParameters(const gmx_mtop_t& mtop, int globalAtomIndex, int* moleculeBlock)
{
- int atomIndexInMolecule;
+ int atomIndexInMolecule = 0;
mtopGetMolblockIndex(mtop, globalAtomIndex, moleculeBlock, nullptr, &atomIndexInMolecule);
- const gmx_moltype_t& moltype = mtop->moltype[mtop->molblock[*moleculeBlock].type];
+ const gmx_moltype_t& moltype = mtop.moltype[mtop.molblock[*moleculeBlock].type];
return moltype.atoms.atom[atomIndexInMolecule];
}
* \param[in] globalAtomIndex The global atom index to look up
* \param[in,out] moleculeBlock The molecule block index in \p mtop
*/
-static inline real mtopGetAtomMass(const gmx_mtop_t* mtop, int globalAtomIndex, int* moleculeBlock)
+static inline real mtopGetAtomMass(const gmx_mtop_t& mtop, int globalAtomIndex, int* moleculeBlock)
{
const t_atom& atom = mtopGetAtomParameters(mtop, globalAtomIndex, moleculeBlock);
return atom.m;
* \param[out] residueName The residue name, input can be NULL
* \param[out] globalResidueIndex The gobal residue index, input can be NULL
*/
-static inline void mtopGetAtomAndResidueName(const gmx_mtop_t* mtop,
+static inline void mtopGetAtomAndResidueName(const gmx_mtop_t& mtop,
int globalAtomIndex,
int* moleculeBlock,
const char** atomName,
const char** residueName,
int* globalResidueIndex)
{
- int moleculeIndex;
- int atomIndexInMolecule;
+ int moleculeIndex = 0;
+ int atomIndexInMolecule = 0;
mtopGetMolblockIndex(mtop, globalAtomIndex, moleculeBlock, &moleculeIndex, &atomIndexInMolecule);
- const gmx_molblock_t& molb = mtop->molblock[*moleculeBlock];
- const t_atoms& atoms = mtop->moltype[molb.type].atoms;
- const MoleculeBlockIndices& indices = mtop->moleculeBlockIndices[*moleculeBlock];
+ const gmx_molblock_t& molb = mtop.molblock[*moleculeBlock];
+ const t_atoms& atoms = mtop.moltype[molb.type].atoms;
+ const MoleculeBlockIndices& indices = mtop.moleculeBlockIndices[*moleculeBlock];
if (atomName != nullptr)
{
*atomName = *(atoms.atomname[atomIndexInMolecule]);
}
if (residueNumber != nullptr)
{
- if (atoms.nres > mtop->maxResiduesPerMoleculeToTriggerRenumber())
+ if (atoms.nres > mtop.maxResiduesPerMoleculeToTriggerRenumber())
{
*residueNumber = atoms.resinfo[atoms.atom[atomIndexInMolecule].resind].nr;
}
}
}
-//! \copydoc mtopGetAtomAndResidueName()
-static inline void mtopGetAtomAndResidueName(const gmx_mtop_t& mtop,
- int globalAtomIndex,
- int* moleculeBlock,
- const char** atomName,
- int* residueNumber,
- const char** residueName,
- int* globalResidueIndex)
-{
- mtopGetAtomAndResidueName(&mtop, globalAtomIndex, moleculeBlock, atomName, residueNumber,
- residueName, globalResidueIndex);
-}
-
/*! \brief Returns residue information for an atom based on global atom index
*
* The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
* \param[in] globalAtomIndex The global atom index to look up
* \param[in,out] moleculeBlock The molecule block index in \p mtop
*/
-static inline const t_resinfo& mtopGetResidueInfo(const gmx_mtop_t* mtop, int globalAtomIndex, int* moleculeBlock)
+static inline const t_resinfo& mtopGetResidueInfo(const gmx_mtop_t& mtop, int globalAtomIndex, int* moleculeBlock)
{
- int atomIndexInMolecule;
+ int atomIndexInMolecule = 0;
mtopGetMolblockIndex(mtop, globalAtomIndex, moleculeBlock, nullptr, &atomIndexInMolecule);
- const gmx_moltype_t& moltype = mtop->moltype[mtop->molblock[*moleculeBlock].type];
+ const gmx_moltype_t& moltype = mtop.moltype[mtop.molblock[*moleculeBlock].type];
const int resind = moltype.atoms.atom[atomIndexInMolecule].resind;
return moltype.atoms.resinfo[resind];
}
* \param[in] globalAtomIndex The global atom index to look up
* \param[in,out] moleculeBlock The molecule block index in \p mtop
*/
-static inline const t_pdbinfo& mtopGetAtomPdbInfo(const gmx_mtop_t* mtop, int globalAtomIndex, int* moleculeBlock)
+static inline const t_pdbinfo& mtopGetAtomPdbInfo(const gmx_mtop_t& mtop, int globalAtomIndex, int* moleculeBlock)
{
- int atomIndexInMolecule;
+ int atomIndexInMolecule = 0;
mtopGetMolblockIndex(mtop, globalAtomIndex, moleculeBlock, nullptr, &atomIndexInMolecule);
- const gmx_moltype_t& moltype = mtop->moltype[mtop->molblock[*moleculeBlock].type];
+ const gmx_moltype_t& moltype = mtop.moltype[mtop.molblock[*moleculeBlock].type];
GMX_ASSERT(moltype.atoms.havePdbInfo, "PDB information not present when requested");
return moltype.atoms.pdbinfo[atomIndexInMolecule];
}
#include "gromacs/topology/topology.h"
#include "gromacs/topology/topsort.h"
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
-void gmx_mtop_count_atomtypes(const gmx_mtop_t* mtop, int state, int typecount[])
+void gmx_mtop_count_atomtypes(const gmx_mtop_t& mtop, int state, int typecount[])
{
- for (int i = 0; i < mtop->ffparams.atnr; ++i)
+ for (int i = 0; i < mtop.ffparams.atnr; ++i)
{
typecount[i] = 0;
}
- for (const gmx_molblock_t& molb : mtop->molblock)
+ for (const gmx_molblock_t& molb : mtop.molblock)
{
- const t_atoms& atoms = mtop->moltype[molb.type].atoms;
+ const t_atoms& atoms = mtop.moltype[molb.type].atoms;
for (int i = 0; i < atoms.nr; ++i)
{
- int tpi;
- if (state == 0)
- {
- tpi = atoms.atom[i].type;
- }
- else
- {
- tpi = atoms.atom[i].typeB;
- }
+ const int tpi = (state == 0) ? atoms.atom[i].type : atoms.atom[i].typeB;
typecount[tpi] += molb.nmol;
}
}
return numMolecules;
}
-int gmx_mtop_nres(const gmx_mtop_t* mtop)
+int gmx_mtop_nres(const gmx_mtop_t& mtop)
{
int nres = 0;
- for (const gmx_molblock_t& molb : mtop->molblock)
+ for (const gmx_molblock_t& molb : mtop.molblock)
{
- nres += molb.nmol * mtop->moltype[molb.type].atoms.nres;
+ nres += molb.nmol * mtop.moltype[molb.type].atoms.nres;
}
return nres;
}
return it_->localAtomNumber_;
}
-typedef struct gmx_mtop_atomloop_block
+struct gmx_mtop_atomloop_block
{
const gmx_mtop_t* mtop;
size_t mblock;
const t_atoms* atoms;
int at_local;
-} t_gmx_mtop_atomloop_block;
+};
-gmx_mtop_atomloop_block_t gmx_mtop_atomloop_block_init(const gmx_mtop_t* mtop)
+gmx_mtop_atomloop_block_t gmx_mtop_atomloop_block_init(const gmx_mtop_t& mtop)
{
- struct gmx_mtop_atomloop_block* aloop;
+ struct gmx_mtop_atomloop_block* aloop = nullptr;
snew(aloop, 1);
- aloop->mtop = mtop;
+ aloop->mtop = &mtop;
aloop->mblock = 0;
- aloop->atoms = &mtop->moltype[mtop->molblock[aloop->mblock].type].atoms;
+ aloop->atoms = &mtop.moltype[mtop.molblock[aloop->mblock].type].atoms;
aloop->at_local = -1;
return aloop;
return TRUE;
}
-typedef struct gmx_mtop_ilistloop
+IListIterator::IListIterator(const gmx_mtop_t& mtop, size_t molblock) :
+ mtop_(&mtop), mblock_(molblock)
{
- const gmx_mtop_t* mtop;
- int mblock;
-} t_gmx_mtop_ilist;
+}
-gmx_mtop_ilistloop_t gmx_mtop_ilistloop_init(const gmx_mtop_t* mtop)
+IListIterator& IListIterator::operator++()
{
- struct gmx_mtop_ilistloop* iloop;
-
- snew(iloop, 1);
-
- iloop->mtop = mtop;
- iloop->mblock = -1;
-
- return iloop;
+ mblock_++;
+ return *this;
}
-gmx_mtop_ilistloop_t gmx_mtop_ilistloop_init(const gmx_mtop_t& mtop)
+bool IListIterator::operator==(const IListIterator& o) const
{
- return gmx_mtop_ilistloop_init(&mtop);
+ return mtop_ == o.mtop_ && mblock_ == o.mblock_;
}
-static void gmx_mtop_ilistloop_destroy(gmx_mtop_ilistloop_t iloop)
+const InteractionLists& IListProxy::list() const
{
- sfree(iloop);
+ // one past the end means we want to take the
+ // intermolecular list instead.
+ if (it_->mblock_ == it_->mtop_->molblock.size())
+ {
+ return *it_->mtop_->intermolecular_ilist;
+ }
+ else
+ {
+ return it_->mtop_->moltype[it_->mtop_->molblock[it_->mblock_].type].ilist;
+ }
}
-const InteractionLists* gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop, int* nmol)
+int IListProxy::nmol() const
{
- if (iloop == nullptr)
+ // one past the end means we want to take the
+ // intermolecular list instead.
+ if (it_->mblock_ == it_->mtop_->molblock.size())
{
- gmx_incons("gmx_mtop_ilistloop_next called without calling gmx_mtop_ilistloop_init");
+ return 1;
}
-
- iloop->mblock++;
- if (iloop->mblock >= gmx::ssize(iloop->mtop->molblock))
+ else
{
- if (iloop->mblock == gmx::ssize(iloop->mtop->molblock) && iloop->mtop->bIntermolecularInteractions)
- {
- *nmol = 1;
- return iloop->mtop->intermolecular_ilist.get();
- }
-
- gmx_mtop_ilistloop_destroy(iloop);
- return nullptr;
+ return it_->mtop_->molblock[it_->mblock_].nmol;
}
-
- *nmol = iloop->mtop->molblock[iloop->mblock].nmol;
-
- return &iloop->mtop->moltype[iloop->mtop->molblock[iloop->mblock].type].ilist;
}
-typedef struct gmx_mtop_ilistloop_all
-{
- const gmx_mtop_t* mtop;
- size_t mblock;
- int mol;
- int a_offset;
-} t_gmx_mtop_ilist_all;
-int gmx_mtop_ftype_count(const gmx_mtop_t* mtop, int ftype)
+IListRange::IListRange(const gmx_mtop_t& mtop) : begin_(mtop), end_(mtop, mtop.molblock.size())
{
- gmx_mtop_ilistloop_t iloop;
- int n, nmol;
+ if (mtop.bIntermolecularInteractions)
+ {
+ end_ = IListIterator(mtop, mtop.molblock.size() + 1);
+ }
+}
- n = 0;
+int gmx_mtop_ftype_count(const gmx_mtop_t& mtop, int ftype)
+{
+ int n = 0;
- iloop = gmx_mtop_ilistloop_init(mtop);
- while (const InteractionLists* il = gmx_mtop_ilistloop_next(iloop, &nmol))
+ for (const IListProxy il : IListRange(mtop))
{
- n += nmol * (*il)[ftype].size() / (1 + NRAL(ftype));
+ n += il.nmol() * il.list()[ftype].size() / (1 + NRAL(ftype));
}
- if (mtop->bIntermolecularInteractions)
+ if (mtop.bIntermolecularInteractions)
{
- n += (*mtop->intermolecular_ilist)[ftype].size() / (1 + NRAL(ftype));
+ n += (*mtop.intermolecular_ilist)[ftype].size() / (1 + NRAL(ftype));
}
return n;
}
-int gmx_mtop_ftype_count(const gmx_mtop_t& mtop, int ftype)
-{
- return gmx_mtop_ftype_count(&mtop, ftype);
-}
-
int gmx_mtop_interaction_count(const gmx_mtop_t& mtop, const int unsigned if_flags)
{
int n = 0;
- gmx_mtop_ilistloop_t iloop = gmx_mtop_ilistloop_init(mtop);
- int nmol;
- while (const InteractionLists* il = gmx_mtop_ilistloop_next(iloop, &nmol))
+ for (const IListProxy il : IListRange(mtop))
{
for (int ftype = 0; ftype < F_NRE; ftype++)
{
if ((interaction_function[ftype].flags & if_flags) == if_flags)
{
- n += nmol * (*il)[ftype].size() / (1 + NRAL(ftype));
+ n += il.nmol() * il.list()[ftype].size() / (1 + NRAL(ftype));
}
}
}
return n;
}
-std::array<int, eptNR> gmx_mtop_particletype_count(const gmx_mtop_t& mtop)
+gmx::EnumerationArray<ParticleType, int> gmx_mtop_particletype_count(const gmx_mtop_t& mtop)
{
- std::array<int, eptNR> count = { { 0 } };
+ gmx::EnumerationArray<ParticleType, int> count = { { 0 } };
for (const auto& molblock : mtop.molblock)
{
static void atomcat(t_atoms* dest, const t_atoms* src, int copies, int maxres_renum, int* maxresnr)
{
- int i, j, l, size;
+ int i = 0, j = 0, l = 0, size = 0;
int srcnr = src->nr;
int destnr = dest->nr;
/* residue information */
for (l = dest->nres, j = 0; (j < copies); j++, l += src->nres)
{
- memcpy(reinterpret_cast<char*>(&(dest->resinfo[l])), reinterpret_cast<char*>(&(src->resinfo[0])),
+ memcpy(reinterpret_cast<char*>(&(dest->resinfo[l])),
+ reinterpret_cast<char*>(&(src->resinfo[0])),
static_cast<size_t>(src->nres * sizeof(src->resinfo[0])));
}
for (l = destnr, j = 0; (j < copies); j++, l += srcnr)
{
- memcpy(reinterpret_cast<char*>(&(dest->atom[l])), reinterpret_cast<char*>(&(src->atom[0])),
+ memcpy(reinterpret_cast<char*>(&(dest->atom[l])),
+ reinterpret_cast<char*>(&(src->atom[0])),
static_cast<size_t>(srcnr * sizeof(src->atom[0])));
memcpy(reinterpret_cast<char*>(&(dest->atomname[l])),
reinterpret_cast<char*>(&(src->atomname[0])),
dest->nr += copies * src->nr;
}
-t_atoms gmx_mtop_global_atoms(const gmx_mtop_t* mtop)
+t_atoms gmx_mtop_global_atoms(const gmx_mtop_t& mtop)
{
t_atoms atoms;
init_t_atoms(&atoms, 0, FALSE);
- int maxresnr = mtop->maxResNumberNotRenumbered();
- for (const gmx_molblock_t& molb : mtop->molblock)
+ int maxresnr = mtop.maxResNumberNotRenumbered();
+ for (const gmx_molblock_t& molb : mtop.molblock)
{
- atomcat(&atoms, &mtop->moltype[molb.type].atoms, molb.nmol,
- mtop->maxResiduesPerMoleculeToTriggerRenumber(), &maxresnr);
+ atomcat(&atoms,
+ &mtop.moltype[molb.type].atoms,
+ molb.nmol,
+ mtop.maxResiduesPerMoleculeToTriggerRenumber(),
+ &maxresnr);
}
return atoms;
static void ilistcat(int ftype, InteractionList* dest, const InteractionList& src, int copies, int dnum, int snum)
{
- int nral, c, i, a;
-
- nral = NRAL(ftype);
+ const int nral = NRAL(ftype);
size_t destIndex = dest->iatoms.size();
dest->iatoms.resize(dest->iatoms.size() + copies * src.size());
- for (c = 0; c < copies; c++)
+ for (int c = 0; c < copies; c++)
{
- for (i = 0; i < src.size();)
+ for (int i = 0; i < src.size();)
{
dest->iatoms[destIndex++] = src.iatoms[i++];
- for (a = 0; a < nral; a++)
+ for (int a = 0; a < nral; a++)
{
dest->iatoms[destIndex++] = dnum + src.iatoms[i++];
}
static void ilistcat(int ftype, t_ilist* dest, const InteractionList& src, int copies, int dnum, int snum)
{
- int nral, c, i, a;
-
- nral = NRAL(ftype);
+ const int nral = NRAL(ftype);
dest->nalloc = dest->nr + copies * src.size();
srenew(dest->iatoms, dest->nalloc);
- for (c = 0; c < copies; c++)
+ for (int c = 0; c < copies; c++)
{
- for (i = 0; i < src.size();)
+ for (int i = 0; i < src.size();)
{
dest->iatoms[dest->nr++] = src.iatoms[i++];
- for (a = 0; a < nral; a++)
+ for (int a = 0; a < nral; a++)
{
dest->iatoms[dest->nr++] = dnum + src.iatoms[i++];
}
template<typename IdefType>
static void set_posres_params(IdefType* idef, const gmx_molblock_t* molb, int i0, int a_offset)
{
- int i1, i, a_molb;
- t_iparams* ip;
-
auto* il = &idef->il[F_POSRES];
- i1 = il->size() / 2;
+ int i1 = il->size() / 2;
resizeIParams(&idef->iparams_posres, i1);
- for (i = i0; i < i1; i++)
+ for (int i = i0; i < i1; i++)
{
- ip = &idef->iparams_posres[i];
+ t_iparams* ip = &idef->iparams_posres[i];
/* Copy the force constants */
- *ip = getIparams(*idef, il->iatoms[i * 2]);
- a_molb = il->iatoms[i * 2 + 1] - a_offset;
+ *ip = getIparams(*idef, il->iatoms[i * 2]);
+ int a_molb = il->iatoms[i * 2 + 1] - a_offset;
if (molb->posres_xA.empty())
{
gmx_incons("Position restraint coordinates are missing");
template<typename IdefType>
static void set_fbposres_params(IdefType* idef, const gmx_molblock_t* molb, int i0, int a_offset)
{
- int i1, i, a_molb;
- t_iparams* ip;
-
auto* il = &idef->il[F_FBPOSRES];
- i1 = il->size() / 2;
+ int i1 = il->size() / 2;
resizeIParams(&idef->iparams_fbposres, i1);
- for (i = i0; i < i1; i++)
+ for (int i = i0; i < i1; i++)
{
- ip = &idef->iparams_fbposres[i];
+ t_iparams* ip = &idef->iparams_fbposres[i];
/* Copy the force constants */
- *ip = getIparams(*idef, il->iatoms[i * 2]);
- a_molb = il->iatoms[i * 2 + 1] - a_offset;
+ *ip = getIparams(*idef, il->iatoms[i * 2]);
+ int a_molb = il->iatoms[i * 2 + 1] - a_offset;
if (molb->posres_xA.empty())
{
gmx_incons("Position restraint coordinates are missing");
*/
for (int mol = 0; mol < molb.nmol; mol++)
{
- ilistcat(ftype, &idef->il[F_CONSTR], molt.ilist[F_CONSTR], 1,
- destnr + mol * srcnr, srcnr);
- ilistcat(ftype, &idef->il[F_CONSTR], molt.ilist[F_CONSTRNC], 1,
- destnr + mol * srcnr, srcnr);
+ ilistcat(ftype, &idef->il[F_CONSTR], molt.ilist[F_CONSTR], 1, destnr + mol * srcnr, srcnr);
+ ilistcat(ftype, &idef->il[F_CONSTR], molt.ilist[F_CONSTRNC], 1, destnr + mol * srcnr, srcnr);
}
}
else if (!(mergeConstr && ftype == F_CONSTRNC))
if (mtop.atomtypes.atomnumber)
{
snew(atomtypes->atomnumber, mtop.atomtypes.nr);
- std::copy(mtop.atomtypes.atomnumber, mtop.atomtypes.atomnumber + mtop.atomtypes.nr,
+ std::copy(mtop.atomtypes.atomnumber,
+ mtop.atomtypes.atomnumber + mtop.atomtypes.nr,
atomtypes->atomnumber);
}
else
copyIListsFromMtop(mtop, &top->idef, bMergeConstr);
top->name = mtop.name;
- top->atoms = gmx_mtop_global_atoms(&mtop);
+ top->atoms = gmx_mtop_global_atoms(mtop);
top->mols = gmx_mtop_molecules_t_block(mtop);
top->bIntermolecularInteractions = mtop.bIntermolecularInteractions;
top->symtab = mtop.symtab;
return top;
}
-std::vector<int> get_atom_index(const gmx_mtop_t* mtop)
+std::vector<int> get_atom_index(const gmx_mtop_t& mtop)
{
std::vector<int> atom_index;
- for (const AtomProxy atomP : AtomRange(*mtop))
+ for (const AtomProxy atomP : AtomRange(mtop))
{
const t_atom& local = atomP.atom();
int index = atomP.globalAtomNumber();
- if (local.ptype == eptAtom)
+ if (local.ptype == ParticleType::Atom)
{
atom_index.push_back(index);
}
#include <boost/stl_interfaces/iterator_interface.hpp>
#include "gromacs/topology/topology.h"
-#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/enumerationhelpers.h"
struct gmx_localtop_t;
struct t_atom;
* state A and 1 for state B types. typecount should have at
* least mtop->ffparams.atnr elements.
*/
-void gmx_mtop_count_atomtypes(const gmx_mtop_t* mtop, int state, int typecount[]);
+void gmx_mtop_count_atomtypes(const gmx_mtop_t& mtop, int state, int typecount[]);
/*!\brief Returns the total number of molecules in mtop
*
int gmx_mtop_num_molecules(const gmx_mtop_t& mtop);
/* Returns the total number of residues in mtop. */
-int gmx_mtop_nres(const gmx_mtop_t* mtop);
+int gmx_mtop_nres(const gmx_mtop_t& mtop);
class AtomIterator;
AtomIterator begin_, end_;
};
+class IListIterator;
+
+//! Proxy object returned from IListIterator
+class IListProxy
+{
+public:
+ //! Default constructor.
+ IListProxy(const IListIterator* it) : it_(it) {}
+ //! Access current global atom number.
+ const InteractionLists& list() const;
+ //! Access current molecule.
+ int nmol() const;
+
+private:
+ const IListIterator* it_;
+};
+
+/*! \brief
+ * Object that allows looping over all atoms in an mtop.
+ */
+class IListIterator :
+ public boost::stl_interfaces::proxy_iterator_interface<IListIterator, std::forward_iterator_tag, InteractionLists, IListProxy>
+{
+ using Base =
+ boost::stl_interfaces::proxy_iterator_interface<IListIterator, std::forward_iterator_tag, InteractionLists, IListProxy>;
+
+public:
+ //! Construct from topology.
+ explicit IListIterator(const gmx_mtop_t& mtop, size_t mblock = 0);
+
+ //! Prefix increment.
+ IListIterator& operator++();
+ using Base:: operator++;
+
+ //! Equality comparison.
+ bool operator==(const IListIterator& o) const;
+
+ //! Dereference operator. Returns proxy.
+ IListProxy operator*() const { return { this }; }
+
+private:
+ //! Global topology.
+ const gmx_mtop_t* mtop_;
+ //! Index of molecule block corresponding to the current location.
+ size_t mblock_;
+
+ friend class IListProxy;
+};
+
+
+/*! \brief
+ * Range over all interaction lists of topology.
+ *
+ * Includes the intermolecular interactions as the final element in the
+ * range if present.
+ */
+class IListRange
+{
+public:
+ //! Default constructor.
+ explicit IListRange(const gmx_mtop_t& mtop);
+ //! Iterator to begin of range.
+ IListIterator& begin() { return begin_; }
+ //! Iterator to end of range.
+ IListIterator& end() { return end_; }
+
+private:
+ IListIterator begin_, end_;
+};
+
/* Abstract type for atom loop over atoms in all molecule blocks */
typedef struct gmx_mtop_atomloop_block* gmx_mtop_atomloop_block_t;
/* Initialize an atom loop over atoms in all molecule blocks the system.
*/
-gmx_mtop_atomloop_block_t gmx_mtop_atomloop_block_init(const gmx_mtop_t* mtop);
+gmx_mtop_atomloop_block_t gmx_mtop_atomloop_block_init(const gmx_mtop_t& mtop);
/* Loop to the next atom.
* When not at the end:
gmx_bool gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop, const t_atom** atom, int* nmol);
-/* Abstract type for ilist loop over all ilists */
-typedef struct gmx_mtop_ilistloop* gmx_mtop_ilistloop_t;
-
-/* Initialize an ilist loop over all molecule types in the system. */
-gmx_mtop_ilistloop_t gmx_mtop_ilistloop_init(const gmx_mtop_t* mtop);
-
-/* Initialize an ilist loop over all molecule types in the system. */
-gmx_mtop_ilistloop_t gmx_mtop_ilistloop_init(const gmx_mtop_t& mtop);
-
-/* Loop to the next molecule,
- * When not at the end:
- * returns a valid pointer to the next array ilist_mol[F_NRE],
- * writes the number of molecules for this ilist in *nmol.
- * When at the end, destroys iloop and returns nullptr.
- */
-const InteractionLists* gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop, int* nmol);
-
-/* Returns the total number of interactions in the system of type ftype */
-int gmx_mtop_ftype_count(const gmx_mtop_t* mtop, int ftype);
-
/* Returns the total number of interactions in the system of type ftype */
int gmx_mtop_ftype_count(const gmx_mtop_t& mtop, int ftype);
int gmx_mtop_interaction_count(const gmx_mtop_t& mtop, int unsigned if_flags);
/* Returns the count of atoms for each particle type */
-std::array<int, eptNR> gmx_mtop_particletype_count(const gmx_mtop_t& mtop);
+gmx::EnumerationArray<ParticleType, int> gmx_mtop_particletype_count(const gmx_mtop_t& mtop);
/* Returns a single t_atoms struct for the whole system */
-t_atoms gmx_mtop_global_atoms(const gmx_mtop_t* mtop);
+t_atoms gmx_mtop_global_atoms(const gmx_mtop_t& mtop);
/*! \brief
* \param[in] mtop Molecular topology
* \returns Vector that will be filled with the atom indices
*/
-std::vector<int> get_atom_index(const gmx_mtop_t* mtop);
+std::vector<int> get_atom_index(const gmx_mtop_t& mtop);
/*! \brief Converts a t_atoms struct to an mtop struct
*
fprintf(stderr,
"Warning: Residue '%s' already present with type '%s' in database, ignoring "
"new type '%s'.\n",
- residueName.c_str(), (*foundIt)->residueType.c_str(), residueType.c_str());
+ residueName.c_str(),
+ (*foundIt)->residueType.c_str(),
+ residueType.c_str());
}
}
else
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2014,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TOPOLOGY_RESIDUETYPES_H
#define GMX_TOPOLOGY_RESIDUETYPES_H
+#include <memory>
#include <optional>
#include <string>
#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/classhelpers.h"
struct ResidueTypeEntry;
//! Implementation pointer.
class Impl;
- gmx::PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
#endif
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
StringTable::StringTable(gmx::ISerializer* serializer)
{
- GMX_RELEASE_ASSERT(serializer->reading(),
- "Can not use writing serializer to read string table");
+ GMX_RELEASE_ASSERT(serializer->reading(), "Can not use writing serializer to read string table");
int nr = 0;
serializer->doInt(&nr);
table_.resize(nr);
StringTableEntry readStringTableEntry(gmx::ISerializer* serializer, const StringTable& table)
{
- GMX_RELEASE_ASSERT(serializer->reading(),
- "Can not use writing serializer to read string index");
+ GMX_RELEASE_ASSERT(serializer->reading(), "Can not use writing serializer to read string index");
int entry = 0;
serializer->doInt(&entry);
return table.at(entry);
*/
static char* trim_string(const char* s, char* out, int maxlen)
{
- int len, i;
+ int len = 0, i = 0;
if (strlen(s) > static_cast<size_t>(maxlen - 1))
{
int lookup_symtab(t_symtab* symtab, char** name)
{
- int base;
- t_symbuf* symbuf;
-
- base = 0;
- symbuf = symtab->symbuf;
+ int base = 0;
+ t_symbuf* symbuf = symtab->symbuf;
while (symbuf != nullptr)
{
const int index = name - symbuf->buf;
char** get_symtab_handle(t_symtab* symtab, int name)
{
- t_symbuf* symbuf;
-
- symbuf = symtab->symbuf;
+ t_symbuf* symbuf = symtab->symbuf;
while (symbuf != nullptr)
{
if (name < symbuf->bufsize)
//! Returns a new initialized entry into the symtab linked list.
static t_symbuf* new_symbuf()
{
- t_symbuf* symbuf;
+ t_symbuf* symbuf = nullptr;
snew(symbuf, 1);
symbuf->bufsize = c_maxBufSize;
*/
static char** enter_buf(t_symtab* symtab, char* name)
{
- int i;
- t_symbuf* symbuf;
- gmx_bool bCont;
+ bool bCont = false;
if (symtab->symbuf == nullptr)
{
symtab->symbuf = new_symbuf();
}
- symbuf = symtab->symbuf;
+ t_symbuf* symbuf = symtab->symbuf;
do
{
- for (i = 0; (i < symbuf->bufsize); i++)
+ for (int i = 0; (i < symbuf->bufsize); i++)
{
if (symbuf->buf[i] == nullptr)
{
// std::list<std::vector<std::string>>> for t_symtab.
t_symtab* duplicateSymtab(const t_symtab* symtab)
{
- t_symtab* copySymtab;
+ t_symtab* copySymtab = nullptr;
snew(copySymtab, 1);
open_symtab(copySymtab);
t_symbuf* symbuf = symtab->symbuf;
void done_symtab(t_symtab* symtab)
{
- int i;
- t_symbuf *symbuf, *freeptr;
-
close_symtab(symtab);
- symbuf = symtab->symbuf;
+ t_symbuf* symbuf = symtab->symbuf;
while (symbuf != nullptr)
{
- for (i = 0; (i < symbuf->bufsize) && (i < symtab->nr); i++)
+ int i = 0;
+ for (; (i < symbuf->bufsize) && (i < symtab->nr); i++)
{
sfree(symbuf->buf[i]);
}
symtab->nr -= i;
sfree(symbuf->buf);
- freeptr = symbuf;
- symbuf = symbuf->next;
+ t_symbuf* freeptr = symbuf;
+ symbuf = symbuf->next;
sfree(freeptr);
}
symtab->symbuf = nullptr;
void free_symtab(t_symtab* symtab)
{
- t_symbuf *symbuf, *freeptr;
-
close_symtab(symtab);
- symbuf = symtab->symbuf;
+ t_symbuf* symbuf = symtab->symbuf;
while (symbuf != nullptr)
{
symtab->nr -= std::min(symbuf->bufsize, symtab->nr);
- freeptr = symbuf;
- symbuf = symbuf->next;
+ t_symbuf* freeptr = symbuf;
+ symbuf = symbuf->next;
sfree(freeptr);
}
symtab->symbuf = nullptr;
void pr_symtab(FILE* fp, int indent, const char* title, t_symtab* symtab)
{
- int i, j, nr;
- t_symbuf* symbuf;
-
if (available(fp, symtab, indent, title))
{
- indent = pr_title_n(fp, indent, title, symtab->nr);
- i = 0;
- nr = symtab->nr;
- symbuf = symtab->symbuf;
+ indent = pr_title_n(fp, indent, title, symtab->nr);
+ int i = 0;
+ int nr = symtab->nr;
+ t_symbuf* symbuf = symtab->symbuf;
while (symbuf != nullptr)
{
- for (j = 0; (j < symbuf->bufsize) && (j < nr); j++)
+ int j = 0;
+ for (; (j < symbuf->bufsize) && (j < nr); j++)
{
pr_indent(fp, indent);
(void)fprintf(fp, "%s[%d]=\"%s\"\n", title, i++, symbuf->buf[j]);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <unordered_map>
#include <vector>
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"
struct t_commrec;
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int pos = 0;
while (symbuf != nullptr)
{
- int i;
- for (i = 0; (i < symbuf->bufsize) && (i < nr); i++)
+ int i = 0;
+ for (; (i < symbuf->bufsize) && (i < nr); i++)
{
symtabDump.emplace_back(formatString("Symtab[%d]=\"%s\"", pos++, symbuf->buf[i]));
}
TEST_F(LegacySymtabTest, AddSingleEntry)
{
- auto fooSymbol = put_symtab(symtab(), "Foo");
+ auto* fooSymbol = put_symtab(symtab(), "Foo");
ASSERT_EQ(1, symtab()->nr);
compareSymtabLookupAndHandle(symtab(), fooSymbol);
EXPECT_STREQ("Foo", *fooSymbol);
TEST_F(LegacySymtabTest, AddTwoDistinctEntries)
{
- auto fooSymbol = put_symtab(symtab(), "Foo");
- auto barSymbol = put_symtab(symtab(), "Bar");
+ auto* fooSymbol = put_symtab(symtab(), "Foo");
+ auto* barSymbol = put_symtab(symtab(), "Bar");
ASSERT_EQ(2, symtab()->nr);
compareSymtabLookupAndHandle(symtab(), fooSymbol);
TEST_F(LegacySymtabTest, TryToAddDuplicates)
{
- auto fooSymbol = put_symtab(symtab(), "Foo");
- auto barSymbol = put_symtab(symtab(), "Bar");
+ auto* fooSymbol = put_symtab(symtab(), "Foo");
+ auto* barSymbol = put_symtab(symtab(), "Bar");
ASSERT_EQ(2, symtab()->nr);
compareSymtabLookupAndHandle(symtab(), fooSymbol);
EXPECT_STREQ("Bar", *barSymbol);
// Insert a duplicate element
- auto anotherFooSymbol = put_symtab(symtab(), "Foo");
+ auto* anotherFooSymbol = put_symtab(symtab(), "Foo");
ASSERT_EQ(2, symtab()->nr);
// Check for correct post-conditions
compareSymtabLookupAndHandle(symtab(), symbolsAdded[i]);
}
// Add something unrelated and check that indices still work afterward.
- auto foobarSymbol = put_symtab(symtab(), "foobar");
+ auto* foobarSymbol = put_symtab(symtab(), "foobar");
ASSERT_EQ(numStringsToAdd + 1, symtab()->nr);
for (int i = 0; i < numStringsToAdd; ++i)
{
ASSERT_EQ(halfOfStringsToAdd, symtab()->nr);
// We now try to mess around in the symtab.
- auto bazSymbol = put_symtab(symtab(), "baz");
+ auto* bazSymbol = put_symtab(symtab(), "baz");
ASSERT_EQ(halfOfStringsToAdd + 1, symtab()->nr);
compareSymtabLookupAndHandle(symtab(), bazSymbol);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "topology.h"
#include <cstdio>
#include "gromacs/utility/strconvert.h"
#include "gromacs/utility/txtdump.h"
-static gmx::EnumerationArray<SimulationAtomGroupType, const char*> c_simulationAtomGroupTypeShortNames = {
- { "T-Coupling", "Energy Mon.", "Acceleration", "Freeze", "User1", "User2", "VCM",
- "Compressed X", "Or. Res. Fit", "QMMM" }
-};
-
const char* shortName(SimulationAtomGroupType type)
{
- return c_simulationAtomGroupTypeShortNames[type];
+ constexpr gmx::EnumerationArray<SimulationAtomGroupType, const char*> sc_simulationAtomGroupTypeShortNames = {
+ { "T-Coupling",
+ "Energy Mon.",
+ "Acc. not used",
+ "Freeze",
+ "User1",
+ "User2",
+ "VCM",
+ "Compressed X",
+ "Or. Res. Fit",
+ "QMMM" }
+ };
+
+ return sc_simulationAtomGroupTypeShortNames[type];
}
void init_top(t_topology* top)
int index = 0;
for (const auto& group : grps)
{
- fprintf(fp, "%s[%-12s] nr=%zu, name=[", title, c_simulationAtomGroupTypeShortNames[index],
+ fprintf(fp,
+ "%s[%-12s] nr=%zu, name=[",
+ title,
+ shortName(static_cast<SimulationAtomGroupType>(index)),
group.size());
for (const auto& entry : group)
{
static void pr_groups(FILE* fp, int indent, const SimulationGroups& groups, gmx_bool bShowNumbers)
{
pr_grps(fp, "grp", groups.groups, const_cast<char***>(groups.groupNames.data()));
- pr_strings(fp, indent, "grpname", const_cast<char***>(groups.groupNames.data()),
- groups.groupNames.size(), bShowNumbers);
+ pr_strings(fp,
+ indent,
+ "grpname",
+ const_cast<char***>(groups.groupNames.data()),
+ groups.groupNames.size(),
+ bShowNumbers);
pr_indent(fp, indent);
fprintf(fp, "groups ");
- for (const auto& group : c_simulationAtomGroupTypeShortNames)
+ for (const auto group : gmx::EnumerationWrapper<SimulationAtomGroupType>{})
{
- printf(" %5.5s", group);
+ printf(" %5.5s", shortName(group));
}
printf("\n");
fprintf(fp, "groupnr[%5d] =", i);
for (auto group : keysOf(groups.groups))
{
- fprintf(fp, " %3d ",
+ fprintf(fp,
+ " %3d ",
!groups.groupNumbers[group].empty() ? groups.groupNumbers[group][i] : 0);
}
fprintf(fp, "\n");
gmx_bool bShowNumbers,
gmx_bool bShowParameters)
{
- int j;
-
indent = pr_title_n(fp, indent, title, n);
pr_indent(fp, indent);
fprintf(fp, "name=\"%s\"\n", *(molt->name));
pr_atoms(fp, indent, "atoms", &(molt->atoms), bShowNumbers);
pr_listoflists(fp, indent, "excls", &molt->excls, bShowNumbers);
- for (j = 0; (j < F_NRE); j++)
+ for (int j = 0; (j < F_NRE); j++)
{
- pr_ilist(fp, indent, interaction_function[j].longname, ffparams->functype.data(),
- molt->ilist[j], bShowNumbers, bShowParameters, ffparams->iparams.data());
+ pr_ilist(fp,
+ indent,
+ interaction_function[j].longname,
+ ffparams->functype.data(),
+ molt->ilist[j],
+ bShowNumbers,
+ bShowParameters,
+ ffparams->iparams.data());
}
}
{
pr_molblock(fp, indent, "molblock", &mtop->molblock[mb], mb, mtop->moltype);
}
- pr_str(fp, indent, "bIntermolecularInteractions",
- gmx::boolToString(mtop->bIntermolecularInteractions));
+ pr_str(fp, indent, "bIntermolecularInteractions", gmx::boolToString(mtop->bIntermolecularInteractions));
if (mtop->bIntermolecularInteractions)
{
for (int j = 0; j < F_NRE; j++)
{
- pr_ilist(fp, indent, interaction_function[j].longname,
- mtop->ffparams.functype.data(), (*mtop->intermolecular_ilist)[j],
- bShowNumbers, bShowParameters, mtop->ffparams.iparams.data());
+ pr_ilist(fp,
+ indent,
+ interaction_function[j].longname,
+ mtop->ffparams.functype.data(),
+ (*mtop->intermolecular_ilist)[j],
+ bShowNumbers,
+ bShowParameters,
+ mtop->ffparams.iparams.data());
}
}
pr_ffparams(fp, indent, "ffparams", &(mtop->ffparams), bShowNumbers);
pr_atomtypes(fp, indent, "atomtypes", &(mtop->atomtypes), bShowNumbers);
for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
{
- pr_moltype(fp, indent, "moltype", &mtop->moltype[mt], mt, &mtop->ffparams, bShowNumbers,
- bShowParameters);
+ pr_moltype(fp, indent, "moltype", &mtop->moltype[mt], mt, &mtop->ffparams, bShowNumbers, bShowParameters);
}
pr_groups(fp, indent, mtop->groups, bShowNumbers);
}
pr_atoms(fp, indent, "atoms", &(top->atoms), bShowNumbers);
pr_atomtypes(fp, indent, "atomtypes", &(top->atomtypes), bShowNumbers);
pr_block(fp, indent, "mols", &top->mols, bShowNumbers);
- pr_str(fp, indent, "bIntermolecularInteractions",
- gmx::boolToString(top->bIntermolecularInteractions));
+ pr_str(fp, indent, "bIntermolecularInteractions", gmx::boolToString(top->bIntermolecularInteractions));
pr_idef(fp, indent, "idef", &top->idef, bShowNumbers, bShowParameters);
}
}
real relativeTolerance,
real absoluteTolerance)
{
- int i;
- gmx_bool bDiff;
-
- bDiff = FALSE;
- for (i = 0; i < MAXFORCEPARAM && !bDiff; i++)
+ bool bDiff = false;
+ for (int i = 0; i < MAXFORCEPARAM && !bDiff; i++)
{
bDiff = !equal_real(ip1.generic.buf[i], ip2.generic.buf[i], relativeTolerance, absoluteTolerance);
}
static void cmp_iparm_AB(FILE* fp, const char* s, t_functype ft, const t_iparams& ip1, real relativeTolerance, real absoluteTolerance)
{
- int nrfpA, nrfpB, p0, i;
- gmx_bool bDiff;
-
/* Normally the first parameter is perturbable */
- p0 = 0;
- nrfpA = interaction_function[ft].nrfpA;
- nrfpB = interaction_function[ft].nrfpB;
+ int p0 = 0;
+ int nrfpA = interaction_function[ft].nrfpA;
+ int nrfpB = interaction_function[ft].nrfpB;
if (ft == F_PDIHS)
{
nrfpB = 2;
p0 = 1;
nrfpB = 1;
}
- bDiff = FALSE;
- for (i = 0; i < nrfpB && !bDiff; i++)
+ bool bDiff = false;
+ for (int i = 0; i < nrfpB && !bDiff; i++)
{
- bDiff = !equal_real(ip1.generic.buf[p0 + i], ip1.generic.buf[nrfpA + i], relativeTolerance,
- absoluteTolerance);
+ bDiff = !equal_real(
+ ip1.generic.buf[p0 + i], ip1.generic.buf[nrfpA + i], relativeTolerance, absoluteTolerance);
}
if (bDiff)
{
{
for (size_t g = 0; g < cmap1->cmapdata.size(); g++)
{
- int i;
-
fprintf(fp, "comparing cmap %zu\n", g);
- for (i = 0; i < 4 * cmap1->grid_spacing * cmap1->grid_spacing; i++)
+ for (int i = 0; i < 4 * cmap1->grid_spacing * cmap1->grid_spacing; i++)
{
- cmp_real(fp, "", i, cmap1->cmapdata[g].cmap[i], cmap2->cmapdata[g].cmap[i],
- relativeTolerance, absoluteTolerance);
+ cmp_real(fp, "", i, cmap1->cmapdata[g].cmap[i], cmap2->cmapdata[g].cmap[i], relativeTolerance, absoluteTolerance);
}
}
}
std::string buf = gmx::formatString("ffparams->functype[%d]", i);
cmp_int(fp, buf.c_str(), i, ff1.functype[i], ff2.functype[i]);
buf = gmx::formatString("ffparams->iparams[%d]", i);
- cmp_iparm(fp, buf.c_str(), ff1.functype[i], ff1.iparams[i], ff2.iparams[i],
- relativeTolerance, absoluteTolerance);
+ cmp_iparm(fp, buf.c_str(), ff1.functype[i], ff1.iparams[i], ff2.iparams[i], relativeTolerance, absoluteTolerance);
}
}
fprintf(fp, "comparing mtop topology\n");
cmp_str(fp, "Name", -1, *mtop1.name, *mtop2.name);
cmp_int(fp, "natoms", -1, mtop1.natoms, mtop2.natoms);
- cmp_int(fp, "maxres_renum", -1, mtop1.maxResiduesPerMoleculeToTriggerRenumber(),
+ cmp_int(fp,
+ "maxres_renum",
+ -1,
+ mtop1.maxResiduesPerMoleculeToTriggerRenumber(),
mtop2.maxResiduesPerMoleculeToTriggerRenumber());
cmp_int(fp, "maxresnr", -1, mtop1.maxResNumberNotRenumbered(), mtop2.maxResNumberNotRenumbered());
- cmp_bool(fp, "bIntermolecularInteractions", -1, mtop1.bIntermolecularInteractions,
- mtop2.bIntermolecularInteractions);
+ cmp_bool(fp, "bIntermolecularInteractions", -1, mtop1.bIntermolecularInteractions, mtop2.bIntermolecularInteractions);
cmp_bool(fp, "haveMoleculeIndices", -1, mtop1.haveMoleculeIndices, mtop2.haveMoleculeIndices);
compareFfparams(fp, mtop1.ffparams, mtop2.ffparams, relativeTolerance, absoluteTolerance);
compareInteractionLists(fp, mtop1.intermolecular_ilist.get(), mtop2.intermolecular_ilist.get());
compareAtomtypes(fp, mtop1.atomtypes, mtop2.atomtypes);
compareAtomGroups(fp, mtop1.groups, mtop2.groups, mtop1.natoms, mtop2.natoms);
- compareIntermolecularExclusions(fp, mtop1.intermolecularExclusionGroup,
- mtop2.intermolecularExclusionGroup);
+ compareIntermolecularExclusions(
+ fp, mtop1.intermolecularExclusionGroup, mtop2.intermolecularExclusionGroup);
compareBlockIndices(fp, mtop1.moleculeBlockIndices, mtop2.moleculeBlockIndices);
}
for (gmx::index j = 0; j < gmx::ssize(g0.groups[group]); j++)
{
buf = gmx::formatString("grps[%d].name[%zd]", static_cast<int>(group), j);
- cmp_str(fp, buf.c_str(), -1, *g0.groupNames[g0.groups[group][j]],
+ cmp_str(fp,
+ buf.c_str(),
+ -1,
+ *g0.groupNames[g0.groups[group][j]],
*g1.groupNames[g1.groups[group][j]]);
}
}
- cmp_int(fp, "ngrpnr", static_cast<int>(group), g0.numberOfGroupNumbers(group),
+ cmp_int(fp,
+ "ngrpnr",
+ static_cast<int>(group),
+ g0.numberOfGroupNumbers(group),
g1.numberOfGroupNumbers(group));
if (g0.numberOfGroupNumbers(group) == g1.numberOfGroupNumbers(group) && natoms0 == natoms1
&& (!g0.groupNumbers[group].empty() || !g1.groupNumbers[group].empty()))
{
for (int j = 0; j < natoms0; j++)
{
- cmp_int(fp, c_simulationAtomGroupTypeShortNames[group], j,
- getGroupType(g0, group, j), getGroupType(g1, group, j));
+ cmp_int(fp, shortName(group), j, getGroupType(g0, group, j), getGroupType(g1, group, j));
}
}
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2011,2014,2015,2016,2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
TemperatureCoupling,
EnergyOutput,
- Acceleration,
+ AccelerationUnused,
Freeze,
User1,
User2,
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static gmx_bool ip_pert(int ftype, const t_iparams* ip)
{
- gmx_bool bPert;
- int i;
-
if (NRFPB(ftype) == 0)
{
return FALSE;
}
+ bool bPert = false;
switch (ftype)
{
case F_BONDS:
break;
case F_RBDIHS:
bPert = FALSE;
- for (i = 0; i < NR_RBDIHS; i++)
+ for (int i = 0; i < NR_RBDIHS; i++)
{
if (ip->rbdihs.rbcA[i] != ip->rbdihs.rbcB[i])
{
case F_TABDIHS: bPert = (ip->tab.kA != ip->tab.kB); break;
case F_POSRES:
bPert = FALSE;
- for (i = 0; i < DIM; i++)
+ for (int i = 0; i < DIM; i++)
{
if (ip->posres.pos0A[i] != ip->posres.pos0B[i] || ip->posres.fcA[i] != ip->posres.fcB[i])
{
case F_RESTRANGLES:
case F_RESTRDIHS:
case F_CBTDIHS:
- gmx_fatal(FARGS, "Function type %s does not support currentely free energy calculations",
+ gmx_fatal(FARGS,
+ "Function type %s does not support currentely free energy calculations",
interaction_function[ftype].longname);
default:
- gmx_fatal(FARGS, "Function type %s not implemented in ip_pert",
+ gmx_fatal(FARGS,
+ "Function type %s not implemented in ip_pert",
interaction_function[ftype].longname);
}
void gmx_sort_ilist_fe(InteractionDefinitions* idef, const real* qA, const real* qB)
{
- int ftype, nral, i, ic, ib, a;
- t_iatom* iabuf;
- int iabuf_nalloc;
-
if (qB == nullptr)
{
qB = qA;
bool havePerturbedInteractions = false;
- iabuf_nalloc = 0;
- iabuf = nullptr;
+ int iabuf_nalloc = 0;
+ t_iatom* iabuf = nullptr;
- for (ftype = 0; ftype < F_NRE; ftype++)
+ for (int ftype = 0; ftype < F_NRE; ftype++)
{
if (interaction_function[ftype].flags & IF_BOND)
{
InteractionList* ilist = &idef->il[ftype];
int* iatoms = ilist->iatoms.data();
- nral = NRAL(ftype);
- ic = 0;
- ib = 0;
- i = 0;
+ const int nral = NRAL(ftype);
+ int ic = 0;
+ int ib = 0;
+ int i = 0;
while (i < ilist->size())
{
/* Check if this interaction is perturbed */
iabuf_nalloc = over_alloc_large(ib + 1 + nral);
srenew(iabuf, iabuf_nalloc);
}
- for (a = 0; a < 1 + nral; a++)
+ for (int a = 0; a < 1 + nral; a++)
{
iabuf[ib++] = iatoms[i++];
}
else
{
/* Copy in place */
- for (a = 0; a < 1 + nral; a++)
+ for (int a = 0; a < 1 + nral; a++)
{
iatoms[ic++] = iatoms[i++];
}
idef->numNonperturbedInteractions[ftype] = ic;
/* Copy the buffer with perturbed interactions to the ilist */
- for (a = 0; a < ib; a++)
+ for (int a = 0; a < ib; a++)
{
iatoms[ic++] = iabuf[a];
}
if (debug)
{
const int numNonperturbed = idef->numNonperturbedInteractions[ftype];
- fprintf(debug, "%s non-pert %d pert %d\n", interaction_function[ftype].longname,
- numNonperturbed, ilist->size() - numNonperturbed);
+ fprintf(debug,
+ "%s non-pert %d pert %d\n",
+ interaction_function[ftype].longname,
+ numNonperturbed,
+ ilist->size() - numNonperturbed);
}
}
}
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015,2016,2018,2019, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,2018,2019,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-gmx_add_libgromacs_sources(
- energyframe.cpp
- trajectoryframe.cpp
- )
+# Set up the module library
+add_library(trajectory INTERFACE)
+file(GLOB TRAJECTORY_SOURCES *.cpp)
+set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${TRAJECTORY_SOURCES} PARENT_SCOPE)
+
+# Source files have the following dependencies on library infrastructure.
+#target_link_libraries(trajectory PRIVATE
+# common
+# legacy_modules
+#)
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(trajectory PUBLIC
+target_include_directories(trajectory INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(trajectory PUBLIC
+target_link_libraries(trajectory INTERFACE
+ legacy_api
+ )
+
+# TODO: when trajectory is an OBJECT target
+#target_link_libraries(trajectory PUBLIC legacy_api)
+#target_link_libraries(trajectory PRIVATE common)
+
+# Module dependencies
+# trajectory interfaces convey transitive dependence on these modules.
+#target_link_libraries(trajectory PUBLIC
+target_link_libraries(trajectory INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(trajectory PRIVATE NOTHING)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(trajectory PRIVATE legacy_modules)
if(GMX_INSTALL_LEGACY_API)
install(FILES trajectoryframe.h
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
step_(enxframe.step),
time_(enxframe.t)
{
- for (auto& index : indicesOfEnergyFields)
+ for (const auto& index : indicesOfEnergyFields)
{
if (index.second >= enxframe.nre)
{
GMX_THROW(InternalError(formatString(
"Index %d for energy %s not present in energy frame with %d energies",
- index.second, index.first.c_str(), enxframe.nre)));
+ index.second,
+ index.first.c_str(),
+ enxframe.nre)));
}
values_[index.first] = enxframe.ener[index.second].e;
}
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int64_t step; /* MD step */
int64_t nsteps; /* The number of steps between frames */
double dt; /* The MD time step */
- int nsum; /* The number of terms for the sums in ener */
+ int nsum; /* The number of terms for the sums in energyGroupPairTerms */
int nre; /* Number of energies */
int e_size; /* Size (in bytes) of energies */
- int e_alloc; /* Allocated size (in elements) of ener */
+ int e_alloc; /* Allocated size (in elements) of energyGroupPairTerms */
t_energy* ener; /* The energies */
int nblock; /* Number of following energy blocks */
t_enxblock* block; /* The blocks */
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# Set up the module library
+add_library(trajectoryanalysis INTERFACE)
file(GLOB TRAJECTORYANALYSIS_SOURCES *.cpp modules/*.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${TRAJECTORYANALYSIS_SOURCES} PARENT_SCOPE)
+# Source files have the following dependencies on library infrastructure.
+#target_link_libraries(trajectoryanalysis PRIVATE
+# common
+# legacy_modules
+#)
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(trajectoryanalysis PUBLIC
+target_include_directories(trajectoryanalysis INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(trajectoryanalysis PUBLIC
+target_link_libraries(trajectoryanalysis INTERFACE
+ legacy_api
+ )
+
+# TODO: when trajectoryanalysis is an OBJECT target
+#target_link_libraries(trajectoryanalysis PUBLIC legacy_api)
+#target_link_libraries(trajectoryanalysis PRIVATE common)
+
+# Module dependencies
+# trajectoryanalysis interfaces convey transitive dependence on these modules.
+#target_link_libraries(trajectoryanalysis PUBLIC
+target_link_libraries(trajectoryanalysis INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(trajectoryanalysis PRIVATE NOTHING)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(trajectoryanalysis PRIVATE legacy_modules)
+
if(GMX_INSTALL_LEGACY_API)
install(FILES
analysismodule.h
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/analysisdata/analysisdata.h"
#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selectioncollection.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/stringutil.h"
namespace gmx
{
Selection TrajectoryAnalysisModuleData::parallelSelection(const Selection& selection)
{
- // TODO: Implement properly.
- return selection;
+ std::optional<Selection> sel = impl_->selections_.selection(selection.name());
+ // Selections should never be missing in an analysis module, so this is an internal consistency check.
+ GMX_RELEASE_ASSERT(sel.has_value(),
+ gmx::formatString("invalid selection %s", selection.name()).c_str());
+ return sel.value();
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
- * Copyright (c) 2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
#include "gromacs/selection/selection.h" // For gmx::SelectionList
-#include "gromacs/utility/classhelpers.h"
struct t_pbc;
struct t_trxframe;
*
* Does not throw.
*/
- static Selection parallelSelection(const Selection& selection);
+ Selection parallelSelection(const Selection& selection);
/*! \brief
* Returns a set of selection that corresponds to the given selections.
*
*
* \see parallelSelection()
*/
- static SelectionList parallelSelections(const SelectionList& selections);
+ SelectionList parallelSelections(const SelectionList& selections);
protected:
/*! \brief
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
//! Smart pointer to manage a TrajectoryAnalysisModuleData object.
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
/*! \brief
* Needed to access the registered analysis data sets.
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TRAJECTORYANALYSIS_ANALYSISSETTINGS_H
#define GMX_TRAJECTORYANALYSIS_ANALYSISSETTINGS_H
+#include <memory>
#include <string>
#include "gromacs/options/timeunitmanager.h"
-#include "gromacs/utility/classhelpers.h"
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
friend class TrajectoryAnalysisRunnerCommon;
};
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
- * Copyright (c) 2016,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "modules/distance.h"
#include "modules/extract_cluster.h"
#include "modules/freevolume.h"
+#include "modules/msd.h"
#include "modules/pairdist.h"
#include "modules/rdf.h"
#include "modules/sasa.h"
registerModule<DistanceInfo>(manager, group);
registerModule<ExtractClusterInfo>(manager, group);
registerModule<FreeVolumeInfo>(manager, group);
+ registerModule<MsdInfo>(manager, group);
registerModule<PairDistanceInfo>(manager, group);
registerModule<RdfInfo>(manager, group);
registerModule<SasaInfo>(manager, group);
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2011-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/analysisdata/modules/histogram.h"
#include "gromacs/analysisdata/modules/plot.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/trajectoryanalysis/analysissettings.h"
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
Count
};
//! String values corresponding to Group1Type.
-const EnumerationArray<Group1Type, const char*> c_group1TypeEnumNames = { { "angle", "dihedral",
- "vector", "plane" } };
+const EnumerationArray<Group1Type, const char*> c_group1TypeEnumNames = {
+ { "angle", "dihedral", "vector", "plane" }
+};
//! String values corresponding to Group2Type.
const EnumerationArray<Group2Type, const char*> c_group2TypeEnumNames = {
{ "none", "vector", "plane", "t0", "z", "sphnorm" }
settings->setHelpText(desc);
options->addOption(FileNameOption("oav")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnAverage_)
.defaultBasename("angaver")
.description("Average angles as a function of time"));
options->addOption(FileNameOption("oall")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnAll_)
.defaultBasename("angles")
.description("All angles as a function of time"));
options->addOption(FileNameOption("oh")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnHistogram_)
.defaultBasename("anghist")
{
GMX_THROW(InconsistentInputError(formatString(
"Number of positions in selection %d in the first group not divisible by %d",
- static_cast<int>(g + 1), natoms1_)));
+ static_cast<int>(g + 1),
+ natoms1_)));
}
const int angleCount1 = posCount1 / natoms1_;
int angleCount = angleCount1;
GMX_THROW(InconsistentInputError(
formatString("Number of positions in selection %d in the second group not "
"divisible by %d",
- static_cast<int>(g + 1), natoms2_)));
+ static_cast<int>(g + 1),
+ natoms2_)));
}
if (g2type_ == Group2Type::SphereNormal && posCount2 != 1)
{
void Angle::analyzeFrame(int frnr, const t_trxframe& fr, t_pbc* pbc, TrajectoryAnalysisModuleData* pdata)
{
AnalysisDataHandle dh = pdata->dataHandle(angles_);
- const SelectionList& sel1 = TrajectoryAnalysisModuleData::parallelSelections(sel1_);
- const SelectionList& sel2 = TrajectoryAnalysisModuleData::parallelSelections(sel2_);
+ const SelectionList& sel1 = pdata->parallelSelections(sel1_);
+ const SelectionList& sel2 = pdata->parallelSelections(sel2_);
checkSelections(sel1, sel2);
// read), but unsurprisingly the static analyzer chokes a bit on that.
clear_rvecs(4, x);
- real angle;
+ real angle = 0;
// checkSelections() ensures that this reflects all the involved
// positions.
const bool bPresent = iter1.currentValuesSelected() && iter2.currentValuesSelected();
break;
default: GMX_THROW(InternalError("invalid -g1 value"));
}
- dh.setPoint(n, angle * RAD2DEG, bPresent);
+ dh.setPoint(n, angle * gmx::c_rad2Deg, bPresent);
}
}
dh.finishFrame();
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"Selection of particles to write to the file"));
options->addOption(FileNameOption("o")
- .filetype(eftTrajectory)
+ .filetype(OptionFileType::Trajectory)
.outputFile()
.store(&name_)
.defaultBasename("trajout")
void ConvertTrj::initAnalysis(const TrajectoryAnalysisSettings& /*settings*/, const TopologyInformation& top)
{
- output_ = createTrajectoryFrameWriter(top.mtop(), sel_, name_,
+ output_ = createTrajectoryFrameWriter(top.mtop(),
+ sel_,
+ name_,
top.hasTopology() ? top.copyAtoms() : nullptr,
requirementsBuilder_.process());
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
settings->setHelpText(desc);
options->addOption(FileNameOption("oav")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnAverage_)
.defaultBasename("distave")
.description("Average distances as function of time"));
options->addOption(FileNameOption("oall")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnAll_)
.defaultBasename("dist")
.description("All distances as function of time"));
options->addOption(FileNameOption("oxyz")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnXYZ_)
.defaultBasename("distxyz")
.description("Distance components as function of time"));
options->addOption(FileNameOption("oh")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnHistogram_)
.defaultBasename("disthist")
.description("Histogram of the distances"));
options->addOption(FileNameOption("oallstat")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnAllStats_)
.defaultBasename("diststat")
std::string message = formatString(
"Selection '%s' does not evaluate into an even number of positions "
"(there are %d positions)",
- sel[g].name(), sel[g].posCount());
+ sel[g].name(),
+ sel[g].posCount());
GMX_THROW(InconsistentInputError(message));
}
if (sel[g].isDynamic())
{
AnalysisDataHandle distHandle = pdata->dataHandle(distances_);
AnalysisDataHandle xyzHandle = pdata->dataHandle(xyz_);
- const SelectionList& sel = TrajectoryAnalysisModuleData::parallelSelections(sel_);
+ const SelectionList& sel = pdata->parallelSelections(sel_);
checkSelections(sel);
void Distance::writeOutput()
{
SelectionList::const_iterator sel;
- int index;
- for (sel = sel_.begin(), index = 0; sel != sel_.end(); ++sel, ++index)
+ int index = 0;
+ for (sel = sel_.begin(); sel != sel_.end(); ++sel, ++index)
{
printf("%s:\n", sel->name());
printf(" Number of samples: %d\n", summaryStatsModule_->sampleCount(index, 0));
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
options->addOption(FileNameOption("clusters")
- .filetype(eftIndex)
+ .filetype(OptionFileType::Index)
.inputFile()
.required()
.store(&indexFileName_)
"Selection of atoms to write to the file"));
options->addOption(FileNameOption("o")
- .filetype(eftTrajectory)
+ .filetype(OptionFileType::Trajectory)
.outputFile()
.store(&outputNamePrefix_)
.defaultBasename("trajout")
{
std::string outputName = Path::concatenateBeforeExtension(
outputNamePrefix_, formatString("_%s", clusterIndex_->grpname[i]));
- writers_.emplace_back(createTrajectoryFrameWriter(top.mtop(), sel_, outputName,
+ writers_.emplace_back(createTrajectoryFrameWriter(top.mtop(),
+ sel_,
+ outputName,
top.hasTopology() ? top.copyAtoms() : nullptr,
requirementsBuilder_.process()));
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
// Add option for optional output file
options->addOption(FileNameOption("o")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnFreevol_)
.defaultBasename("freevolume")
for (ArrayRef<const int>::iterator ai = atomind.begin(); (ai < atomind.end()); ++ai)
{
// Dereference the iterator to obtain an atom number
- int i = *ai;
- real value;
+ int i = *ai;
+ real value = 0;
// Lookup the Van der Waals radius of this atom
int resnr = atoms->atom[i].resind;
nnovdw++;
if (nnovdw < maxnovdw)
{
- fprintf(stderr, "Could not determine VDW radius for %s-%s. Set to zero.\n",
- *(atoms->resinfo[resnr].name), *(atoms->atomname[i]));
+ fprintf(stderr,
+ "Could not determine VDW radius for %s-%s. Set to zero.\n",
+ *(atoms->resinfo[resnr].name),
+ *(atoms->atomname[i]));
}
vdw_radius_.push_back(0.0);
}
void FreeVolume::analyzeFrame(int frnr, const t_trxframe& fr, t_pbc* pbc, TrajectoryAnalysisModuleData* pdata)
{
AnalysisDataHandle dh = pdata->dataHandle(data_);
- const Selection& sel = TrajectoryAnalysisModuleData::parallelSelection(sel_);
+ const Selection& sel = pdata->parallelSelection(sel_);
gmx::UniformRealDistribution<real> dist;
GMX_RELEASE_ASSERT(nullptr != pbc, "You have no periodic boundary conditions");
printf("Total volume %.2f +/- %.2f nm^3\n", Vaver, Verror);
printf("Number of molecules %d total mass %.2f Dalton\n", nmol_, mtot_);
- double RhoAver = mtot_ / (Vaver * 1e-24 * AVOGADRO);
+ double RhoAver = mtot_ / (Vaver * 1e-24 * gmx::c_avogadro);
double RhoError = gmx::square(RhoAver / Vaver) * Verror;
printf("Average molar mass: %.2f Dalton\n", mtot_ / nmol_);
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Defines the trajectory analysis module for mean squared displacement calculations.
+ *
+ * \author Kevin Boyd <kevin44boyd@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+
+#include "gmxpre.h"
+
+#include "msd.h"
+
+#include <numeric>
+#include <optional>
+
+#include "gromacs/analysisdata/analysisdata.h"
+#include "gromacs/analysisdata/modules/average.h"
+#include "gromacs/analysisdata/modules/plot.h"
+#include "gromacs/analysisdata/paralleloptions.h"
+#include "gromacs/fileio/oenv.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/math/functions.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/ioptionscontainer.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/selection/selectionoption.h"
+#include "gromacs/statistics/statistics.h"
+#include "gromacs/trajectoryanalysis/analysissettings.h"
+#include "gromacs/trajectoryanalysis/topologyinformation.h"
+#include "gromacs/trajectory/trajectoryframe.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility.h"
+
+namespace gmx
+{
+namespace analysismodules
+{
+
+namespace
+{
+
+//! Convert nm^2/ps to 10e-5 cm^2/s
+constexpr double c_diffusionConversionFactor = 1000.0;
+//! Three dimensional diffusion coefficient multiplication constant.
+constexpr double c_3DdiffusionDimensionFactor = 6.0;
+//! Two dimensional diffusion coefficient multiplication constant.
+constexpr double c_2DdiffusionDimensionFactor = 4.0;
+//! One dimensional diffusion coefficient multiplication constant.
+constexpr double c_1DdiffusionDimensionFactor = 2.0;
+
+
+/*! \brief Mean Squared Displacement data accumulator
+ *
+ * This class is used to accumulate individual MSD data points
+ * and emit tau-averaged results once data is finished collecting. Displacements at each observed
+ * time difference (tau) are recorded from the trajectory. Because it is not known in advance which
+ * time differences will be observed from the trajectory, this data structure is built adaptively.
+ * New columns corresponding to observed time differences are added as needed, and additional
+ * observations at formerly observed time differences are added to those columns. Separate time lags
+ * will likely have differing total data points.
+ *
+ * Data columns per tau are accessed via operator[], which always guarantees
+ * a column is initialized and returns an MsdColumProxy to the column that can push data.
+ */
+class MsdData
+{
+public:
+ //! Proxy to a MsdData tau column vector. Supports only push_back.
+ class MsdColumnProxy
+ {
+ public:
+ MsdColumnProxy(std::vector<double>* column) : column_(column) {}
+
+ void push_back(double value) { column_->push_back(value); }
+
+ private:
+ std::vector<double>* column_;
+ };
+ //! Returns a proxy to the column for the given tau index. Guarantees that the column is initialized.
+ MsdColumnProxy operator[](size_t index)
+ {
+ if (msds_.size() <= index)
+ {
+ msds_.resize(index + 1);
+ }
+ return MsdColumnProxy(&msds_[index]);
+ }
+ /*! \brief Compute per-tau MSDs averaged over all added points.
+ *
+ * The resulting vector is size(max tau index). Any indices
+ * that have no data points have MSD set to 0.
+ *
+ * \return Average MSD per tau
+ */
+ [[nodiscard]] std::vector<real> averageMsds() const;
+
+private:
+ //! Results - first indexed by tau, then data points
+ std::vector<std::vector<double>> msds_;
+};
+
+
+std::vector<real> MsdData::averageMsds() const
+{
+ std::vector<real> msdSums;
+ msdSums.reserve(msds_.size());
+ for (gmx::ArrayRef<const double> msdValues : msds_)
+ {
+ if (msdValues.empty())
+ {
+ msdSums.push_back(0.0);
+ continue;
+ }
+ msdSums.push_back(std::accumulate(msdValues.begin(), msdValues.end(), 0.0, std::plus<>())
+ / msdValues.size());
+ }
+ return msdSums;
+}
+
+/*! \brief Calculates 1,2, or 3D distance for two vectors.
+ *
+ * \todo Remove NOLINTs once clang-tidy is updated to v11, it should be able to handle constexpr.
+ *
+ * \tparam x If true, calculate x dimension of displacement
+ * \tparam y If true, calculate y dimension of displacement
+ * \tparam z If true, calculate z dimension of displacement
+ * \param[in] c1 First point
+ * \param[in] c2 Second point
+ * \return Euclidian distance for the given dimension.
+ */
+template<bool x, bool y, bool z>
+inline double calcSingleSquaredDistance(const RVec c1, const RVec c2)
+{
+ static_assert(x || y || z, "zero-dimensional MSD selected");
+ const DVec firstCoords = c1.toDVec();
+ const DVec secondCoords = c2.toDVec();
+ double result = 0;
+ if constexpr (x) // NOLINT // NOLINTNEXTLINE
+ {
+ result += (firstCoords[XX] - secondCoords[XX]) * (firstCoords[XX] - secondCoords[XX]);
+ }
+ if constexpr (y) // NOLINT // NOLINTNEXTLINE
+ {
+ result += (firstCoords[YY] - secondCoords[YY]) * (firstCoords[YY] - secondCoords[YY]);
+ }
+ if constexpr (z) // NOLINT // NOLINTNEXTLINE
+ {
+ result += (firstCoords[ZZ] - secondCoords[ZZ]) * (firstCoords[ZZ] - secondCoords[ZZ]);
+ }
+ return result; // NOLINT
+}
+
+/*! \brief Calculate average displacement between sets of points
+ *
+ * Each displacement c1[i] - c2[i] is calculated and the distances
+ * are averaged.
+ *
+ * \tparam x If true, calculate x dimension of displacement
+ * \tparam y If true, calculate y dimension of displacement
+ * \tparam z If true, calculate z dimension of displacement
+ * \param[in] c1 First vector
+ * \param[in] c2 Second vector
+ * \return Per-particle averaged distance
+ */
+template<bool x, bool y, bool z>
+double calcAverageDisplacement(ArrayRef<const RVec> c1, ArrayRef<const RVec> c2)
+{
+ double result = 0;
+ for (size_t i = 0; i < c1.size(); i++)
+ {
+ result += calcSingleSquaredDistance<x, y, z>(c1[i], c2[i]);
+ }
+ return result / c1.size();
+}
+
+
+//! Describes 1D MSDs, in the given dimension.
+enum class SingleDimDiffType : int
+{
+ X = 0,
+ Y,
+ Z,
+ Unused,
+ Count,
+};
+
+//! Describes 2D MSDs, in the plane normal to the given dimension.
+enum class TwoDimDiffType : int
+{
+ NormalToX = 0,
+ NormalToY,
+ NormalToZ,
+ Unused,
+ Count,
+};
+
+/*! \brief Removes jumps across periodic boundaries for currentFrame, based on the positions in
+ * previousFrame. Updates currentCoords in place.
+ */
+void removePbcJumps(ArrayRef<RVec> currentCoords, ArrayRef<const RVec> previousCoords, t_pbc* pbc)
+{
+ // There are two types of "pbc removal" in gmx msd. The first happens in the trajectoryanalysis
+ // framework, which makes molecules whole across periodic boundaries and is done
+ // automatically where the inputs support it. This lambda performs the second PBC correction, where
+ // any "jump" across periodic boundaries BETWEEN FRAMES is put back. The order of these
+ // operations is important - since the first transformation may only apply to part of a
+ // molecule (e.g., one half in/out of the box is put on one side of the box), the
+ // subsequent step needs to be applied to the molecule COM rather than individual atoms, or
+ // we'd have a clash where the per-mol PBC removal moves an atom that gets put back into
+ // it's original position by the second transformation. Therefore, this second transformation
+ // is applied *after* per molecule coordinates have been consolidated into COMs.
+ auto pbcRemover = [pbc](RVec in, RVec prev) {
+ rvec dx;
+ pbc_dx(pbc, in, prev, dx);
+ return prev + dx;
+ };
+ std::transform(
+ currentCoords.begin(), currentCoords.end(), previousCoords.begin(), currentCoords.begin(), pbcRemover);
+}
+
+//! Holds data needed for MSD calculations for a single molecule, if requested.
+struct MoleculeData
+{
+ //! Number of atoms in the molecule.
+ int atomCount = 0;
+ //! Total mass.
+ double mass = 0;
+ //! MSD accumulator and calculator for the molecule
+ MsdData msdData;
+ //! Calculated diffusion coefficient
+ real diffusionCoefficient = 0;
+};
+
+/*! \brief Handles coordinate operations for MSD calculations.
+ *
+ * Can be used to hold coordinates for individual atoms as well as molecules COMs. Handles PBC
+ * jump removal between consecutive frames.
+ *
+ * Only previous_ contains valid data between calls to buildCoordinates(), although both vectors
+ * are maintained at the correct size for the number of coordinates needed.
+ */
+class MsdCoordinateManager
+{
+public:
+ MsdCoordinateManager(const int numAtoms,
+ ArrayRef<const MoleculeData> molecules,
+ ArrayRef<const int> moleculeIndexMapping) :
+ current_(numAtoms),
+ previous_(numAtoms),
+ molecules_(molecules),
+ moleculeIndexMapping_(moleculeIndexMapping)
+ {
+ }
+ /*! \brief Prepares coordinates for the current frame.
+ *
+ * Reads in selection data, and returns an ArrayRef of the particle positions or molecule
+ * centers of mass (if the molecules input is not empty). Removes jumps across periodic
+ * boundaries based on the previous frame coordinates, except for the first frame built with
+ * builtCoordinates(), which has no previous frame as a reference.
+ *
+ * \param[in] sel The selection object which holds coordinates
+ * \param[in] pbc Information about periodicity.
+ * \returns The current frames coordinates in proper format.
+ */
+ ArrayRef<const RVec> buildCoordinates(const Selection& sel, t_pbc* pbc);
+
+private:
+ //! The current coordinates.
+ std::vector<RVec> current_;
+ //! The previous frame's coordinates.
+ std::vector<RVec> previous_;
+ //! Molecule data.
+ ArrayRef<const MoleculeData> molecules_;
+ //! Mapping of atom indices to molecle indices;
+ ArrayRef<const int> moleculeIndexMapping_;
+ //! Tracks if a previous frame exists to compare with for PBC handling.
+ bool containsPreviousFrame_ = false;
+};
+
+ArrayRef<const RVec> MsdCoordinateManager::buildCoordinates(const Selection& sel, t_pbc* pbc)
+{
+
+ if (molecules_.empty())
+ {
+ std::copy(sel.coordinates().begin(), sel.coordinates().end(), current_.begin());
+ }
+ else
+ {
+ // Prepare for molecule COM calculation, then sum up all positions per molecule.
+
+ std::fill(current_.begin(), current_.end(), RVec(0, 0, 0));
+ gmx::ArrayRef<const real> masses = sel.masses();
+ for (int i = 0; i < sel.posCount(); i++)
+ {
+ const int moleculeIndex = moleculeIndexMapping_[i];
+ // accumulate ri * mi, and do division at the end to minimize number of divisions.
+ current_[moleculeIndex] += RVec(sel.position(i).x()) * masses[i];
+ }
+ // Divide accumulated mass * positions to get COM.
+ std::transform(current_.begin(),
+ current_.end(),
+ molecules_.begin(),
+ current_.begin(),
+ [](const RVec& position, const MoleculeData& molecule) -> RVec {
+ return position / molecule.mass;
+ });
+ }
+
+ if (containsPreviousFrame_)
+ {
+ removePbcJumps(current_, previous_, pbc);
+ }
+ else
+ {
+ containsPreviousFrame_ = true;
+ }
+
+ // Previous is no longer needed, swap with current and return "current" coordinates which
+ // now reside in previous.
+ current_.swap(previous_);
+ return previous_;
+}
+
+
+//! Holds per-group coordinates, analysis, and results.
+struct MsdGroupData
+{
+ explicit MsdGroupData(const Selection& inputSel,
+ ArrayRef<const MoleculeData> molecules,
+ ArrayRef<const int> moleculeAtomMapping) :
+ sel(inputSel),
+ coordinateManager_(molecules.empty() ? sel.posCount() : molecules.size(), molecules, moleculeAtomMapping)
+ {
+ }
+
+ //! Selection associated with this group.
+ const Selection& sel;
+
+ //! Stored coordinates, indexed by frame then atom number.
+ std::vector<std::vector<RVec>> frames;
+
+ //! MSD result accumulator
+ MsdData msds;
+ //! Coordinate handler for the group.
+ MsdCoordinateManager coordinateManager_;
+ //! Collector for processed MSD averages per tau
+ std::vector<real> msdSums;
+ //! Fitted diffusion coefficient
+ real diffusionCoefficient = 0.0;
+ //! Uncertainty of diffusion coefficient
+ double sigma = 0.0;
+};
+
+} // namespace
+
+/*! \brief Implements the gmx msd module
+ *
+ * \todo Implement -(no)mw. Right now, all calculations are mass-weighted with -mol, and not otherwise
+ * \todo Implement -tensor for full MSD tensor calculation
+ * \todo Implement -rmcomm for total-frame COM removal
+ * \todo Implement -pdb for molecule B factors
+ * \todo Implement -maxtau option proposed at https://gitlab.com/gromacs/gromacs/-/issues/3870
+ * \todo Update help text as options are added and clarifications decided on at https://gitlab.com/gromacs/gromacs/-/issues/3869
+ */
+class Msd : public TrajectoryAnalysisModule
+{
+public:
+ Msd();
+
+ void initOptions(IOptionsContainer* options, TrajectoryAnalysisSettings* settings) override;
+ void optionsFinished(TrajectoryAnalysisSettings* settings) override;
+ void initAfterFirstFrame(const TrajectoryAnalysisSettings& settings, const t_trxframe& fr) override;
+ void initAnalysis(const TrajectoryAnalysisSettings& settings, const TopologyInformation& top) override;
+ void analyzeFrame(int frameNumber,
+ const t_trxframe& frame,
+ t_pbc* pbc,
+ TrajectoryAnalysisModuleData* pdata) override;
+ void finishAnalysis(int nframes) override;
+ void writeOutput() override;
+
+private:
+ //! Selections for MSD output
+ SelectionList selections_;
+
+ //! MSD type information, for -type {x,y,z}
+ SingleDimDiffType singleDimType_ = SingleDimDiffType::Unused;
+ //! MSD type information, for -lateral {x,y,z}
+ TwoDimDiffType twoDimType_ = TwoDimDiffType::Unused;
+ //! Diffusion coefficient conversion factor
+ double diffusionCoefficientDimensionFactor_ = c_3DdiffusionDimensionFactor;
+ //! Method used to calculate MSD - changes based on dimensonality.
+ std::function<double(ArrayRef<const RVec>, ArrayRef<const RVec>)> calcMsd_ =
+ calcAverageDisplacement<true, true, true>;
+
+ //! Picoseconds between restarts
+ double trestart_ = 10.0;
+ //! Initial time
+ double t0_ = 0;
+ //! Inter-frame delta-t
+ std::optional<double> dt_ = std::nullopt;
+
+ //! First tau value to fit from for diffusion coefficient, defaults to 0.1 * max tau
+ real beginFit_ = -1.0;
+ //! Final tau value to fit to for diffusion coefficient, defaults to 0.9 * max tau
+ real endFit_ = -1.0;
+
+ //! All selection group-specific data stored here.
+ std::vector<MsdGroupData> groupData_;
+
+ //! Time of all frames.
+ std::vector<double> times_;
+ //! Taus for output - won't know the size until the end.
+ std::vector<double> taus_;
+ //! Tau indices for fitting.
+ size_t beginFitIndex_ = 0;
+ size_t endFitIndex_ = 0;
+
+ // MSD per-molecule stuff
+ //! Are we doing molecule COM-based MSDs?
+ bool molSelected_ = false;
+ //! Per molecule topology information and MSD accumulators.
+ std::vector<MoleculeData> molecules_;
+ //! Atom index -> mol index map
+ std::vector<int> moleculeIndexMappings_;
+
+ // Output stuff
+ AnalysisData msdPlotData_;
+ AnalysisData msdMoleculePlotData_;
+
+ AnalysisDataPlotSettings plotSettings_;
+ //! Per-tau MSDs for each selected group
+ std::string output_;
+ //! Per molecule diffusion coefficients if -mol is selected.
+ std::string moleculeOutput_;
+};
+
+
+Msd::Msd() = default;
+
+void Msd::initOptions(IOptionsContainer* options, TrajectoryAnalysisSettings* settings)
+{
+ static const char* const desc[] = {
+ "[THISMODULE] computes the mean square displacement (MSD) of atoms from",
+ "a set of initial positions. This provides an easy way to compute",
+ "the diffusion constant using the Einstein relation.",
+ "The time between the reference points for the MSD calculation",
+ "is set with [TT]-trestart[tt].",
+ "The diffusion constant is calculated by least squares fitting a",
+ "straight line (D*t + c) through the MSD(t) from [TT]-beginfit[tt] to",
+ "[TT]-endfit[tt] (note that t is time from the reference positions,",
+ "not simulation time). An error estimate given, which is the difference",
+ "of the diffusion coefficients obtained from fits over the two halves",
+ "of the fit interval.[PAR]",
+ "There are three, mutually exclusive, options to determine different",
+ "types of mean square displacement: [TT]-type[tt], [TT]-lateral[tt]",
+ "and [TT]-ten[tt]. Option [TT]-ten[tt] writes the full MSD tensor for",
+ "each group, the order in the output is: trace xx yy zz yx zx zy.[PAR]",
+ "If [TT]-mol[tt] is set, [THISMODULE] plots the MSD for individual molecules",
+ "(including making molecules whole across periodic boundaries): ",
+ "for each individual molecule a diffusion constant is computed for ",
+ "its center of mass. The chosen index group will be split into ",
+ "molecules. With -mol, only one index group can be selected.[PAR]",
+ "The diffusion coefficient is determined by linear regression of the MSD.",
+ "When [TT]-beginfit[tt] is -1, fitting starts at 10%",
+ "and when [TT]-endfit[tt] is -1, fitting goes to 90%.",
+ "Using this option one also gets an accurate error estimate",
+ "based on the statistics between individual molecules.",
+ "Note that this diffusion coefficient and error estimate are only",
+ "accurate when the MSD is completely linear between",
+ "[TT]-beginfit[tt] and [TT]-endfit[tt].[PAR]",
+ };
+ settings->setHelpText(desc);
+
+ // Selections
+ options->addOption(SelectionOption("sel")
+ .storeVector(&selections_)
+ .required()
+ .onlyStatic()
+ .multiValue()
+ .description("Selections to compute MSDs for from the reference"));
+
+ // Select MSD type - defaults to 3D if neither option is selected.
+ EnumerationArray<SingleDimDiffType, const char*> enumTypeNames = { "x", "y", "z", "unused" };
+ EnumerationArray<TwoDimDiffType, const char*> enumLateralNames = { "x", "y", "z", "unused" };
+ options->addOption(EnumOption<SingleDimDiffType>("type")
+ .enumValue(enumTypeNames)
+ .store(&singleDimType_)
+ .defaultValue(SingleDimDiffType::Unused));
+ options->addOption(EnumOption<TwoDimDiffType>("lateral")
+ .enumValue(enumLateralNames)
+ .store(&twoDimType_)
+ .defaultValue(TwoDimDiffType::Unused));
+
+ options->addOption(DoubleOption("trestart")
+ .description("Time between restarting points in trajectory (ps)")
+ .defaultValue(10.0)
+ .store(&trestart_));
+ options->addOption(
+ RealOption("beginfit").description("Time point at which to start fitting.").store(&beginFit_));
+ options->addOption(RealOption("endfit").description("End time for fitting.").store(&endFit_));
+
+ // Output options
+ options->addOption(FileNameOption("o")
+ .filetype(OptionFileType::Plot)
+ .outputFile()
+ .store(&output_)
+ .defaultBasename("msdout")
+ .description("MSD output"));
+ options->addOption(
+ FileNameOption("mol")
+ .filetype(OptionFileType::Plot)
+ .outputFile()
+ .store(&moleculeOutput_)
+ .storeIsSet(&molSelected_)
+ .defaultBasename("diff_mol")
+ .description("Report diffusion coefficients for each molecule in selection"));
+}
+
+void Msd::optionsFinished(TrajectoryAnalysisSettings gmx_unused* settings)
+{
+ if (singleDimType_ != SingleDimDiffType::Unused && twoDimType_ != TwoDimDiffType::Unused)
+ {
+ std::string errorMessage =
+ "Options -type and -lateral are mutually exclusive. Choose one or neither (for 3D "
+ "MSDs).";
+ GMX_THROW(InconsistentInputError(errorMessage.c_str()));
+ }
+ if (selections_.size() > 1 && molSelected_)
+ {
+ std::string errorMessage =
+ "Cannot have multiple groups selected with -sel when using -mol.";
+ GMX_THROW(InconsistentInputError(errorMessage.c_str()));
+ }
+}
+
+
+void Msd::initAnalysis(const TrajectoryAnalysisSettings& settings, const TopologyInformation& top)
+{
+ plotSettings_ = settings.plotSettings();
+
+ // Enumeration helpers for dispatching the right MSD calculation type.
+ const EnumerationArray<SingleDimDiffType, decltype(&calcAverageDisplacement<true, true, true>)>
+ oneDimensionalMsdFunctions = { &calcAverageDisplacement<true, false, false>,
+ &calcAverageDisplacement<false, true, false>,
+ &calcAverageDisplacement<false, false, true> };
+ const EnumerationArray<TwoDimDiffType, decltype(&calcAverageDisplacement<true, true, true>)>
+ twoDimensionalMsdFunctions = { calcAverageDisplacement<false, true, true>,
+ calcAverageDisplacement<true, false, true>,
+ calcAverageDisplacement<true, true, false> };
+
+ // Parse dimensionality and assign the MSD calculating function.
+ // Note if we don't hit either of these cases, we're computing 3D MSDs.
+ if (singleDimType_ != SingleDimDiffType::Unused)
+ {
+ calcMsd_ = oneDimensionalMsdFunctions[singleDimType_];
+ diffusionCoefficientDimensionFactor_ = c_1DdiffusionDimensionFactor;
+ }
+ else if (twoDimType_ != TwoDimDiffType::Unused)
+ {
+ calcMsd_ = twoDimensionalMsdFunctions[twoDimType_];
+ diffusionCoefficientDimensionFactor_ = c_2DdiffusionDimensionFactor;
+ }
+
+ // TODO validate that we have mol info and not atom only - and masses, and topology.
+ if (molSelected_)
+ {
+ Selection& sel = selections_[0];
+ const int nMol = sel.initOriginalIdsToGroup(top.mtop(), INDEX_MOL);
+
+ gmx::ArrayRef<const int> mappedIds = selections_[0].mappedIds();
+ moleculeIndexMappings_.resize(selections_[0].posCount());
+ std::copy(mappedIds.begin(), mappedIds.end(), moleculeIndexMappings_.begin());
+
+ // Precalculate each molecules mass for speeding up COM calculations.
+ ArrayRef<const real> masses = sel.masses();
+
+ molecules_.resize(nMol);
+ for (int i = 0; i < sel.posCount(); i++)
+ {
+ molecules_[mappedIds[i]].atomCount++;
+ molecules_[mappedIds[i]].mass += masses[i];
+ }
+ }
+
+ // Accumulated frames and results
+ for (const Selection& sel : selections_)
+ {
+ groupData_.emplace_back(sel, molecules_, moleculeIndexMappings_);
+ }
+}
+
+void Msd::initAfterFirstFrame(const TrajectoryAnalysisSettings gmx_unused& settings, const t_trxframe& fr)
+{
+ t0_ = std::round(fr.time);
+}
+
+
+void Msd::analyzeFrame(int gmx_unused frameNumber,
+ const t_trxframe& frame,
+ t_pbc* pbc,
+ TrajectoryAnalysisModuleData* pdata)
+{
+ const real time = std::round(frame.time);
+ // Need to populate dt on frame 2;
+ if (!dt_.has_value() && !times_.empty())
+ {
+ dt_ = time - times_[0];
+ }
+
+ // Each frame gets an entry in times, but frameTimes only updates if we're at a restart.
+ times_.push_back(time);
+
+ // Each frame will get a tau between it and frame 0, and all other frame combos should be
+ // covered by this.
+ // \todo this will no longer hold exactly when maxtau is added
+ taus_.push_back(time - times_[0]);
+
+ for (MsdGroupData& msdData : groupData_)
+ {
+ const Selection& sel = pdata->parallelSelection(msdData.sel);
+
+ ArrayRef<const RVec> coords = msdData.coordinateManager_.buildCoordinates(sel, pbc);
+
+ // For each preceding frame, calculate tau and do comparison.
+ for (size_t i = 0; i < msdData.frames.size(); i++)
+ {
+ // If dt > trestart, the tau increment will be dt rather than trestart.
+ double tau = time - (t0_ + std::max<double>(trestart_, *dt_) * i);
+ int64_t tauIndex = gmx::roundToInt64(tau / *dt_);
+ msdData.msds[tauIndex].push_back(calcMsd_(coords, msdData.frames[i]));
+
+ for (size_t molInd = 0; molInd < molecules_.size(); molInd++)
+ {
+ molecules_[molInd].msdData[tauIndex].push_back(
+ calcMsd_(arrayRefFromArray(&coords[molInd], 1),
+ arrayRefFromArray(&msdData.frames[i][molInd], 1)));
+ }
+ }
+
+
+ // We only store the frame for the future if it's a restart per -trestart.
+ if (bRmod(time, t0_, trestart_))
+ {
+ msdData.frames.emplace_back(coords.begin(), coords.end());
+ }
+ }
+}
+
+//! Calculate the tau index for fitting. If userFitTau < 0, uses the default fraction of max tau.
+static size_t calculateFitIndex(const int userFitTau,
+ const double defaultTauFraction,
+ const int numTaus,
+ const double dt)
+{
+ if (userFitTau < 0)
+ {
+ return gmx::roundToInt((numTaus - 1) * defaultTauFraction);
+ }
+ return std::min<size_t>(numTaus - 1, gmx::roundToInt(static_cast<double>(userFitTau) / dt));
+}
+
+
+void Msd::finishAnalysis(int gmx_unused nframes)
+{
+ static constexpr double c_defaultStartFitIndexFraction = 0.1;
+ static constexpr double c_defaultEndFitIndexFraction = 0.9;
+ beginFitIndex_ = calculateFitIndex(beginFit_, c_defaultStartFitIndexFraction, taus_.size(), *dt_);
+ endFitIndex_ = calculateFitIndex(endFit_, c_defaultEndFitIndexFraction, taus_.size(), *dt_);
+ const int numTausForFit = 1 + endFitIndex_ - beginFitIndex_;
+
+ // These aren't used, except for correlationCoefficient, which is used to estimate error if
+ // enough points are available.
+ real b = 0.0, correlationCoefficient = 0.0, chiSquared = 0.0;
+
+ for (MsdGroupData& msdData : groupData_)
+ {
+ msdData.msdSums = msdData.msds.averageMsds();
+
+ if (numTausForFit >= 4)
+ {
+ const int halfNumTaus = numTausForFit / 2;
+ const int secondaryStartIndex = beginFitIndex_ + halfNumTaus;
+ // Split the fit in 2, and compare the results of each fit;
+ real a = 0.0, a2 = 0.0;
+ lsq_y_ax_b_xdouble(halfNumTaus,
+ &taus_[beginFitIndex_],
+ &msdData.msdSums[beginFitIndex_],
+ &a,
+ &b,
+ &correlationCoefficient,
+ &chiSquared);
+ lsq_y_ax_b_xdouble(halfNumTaus,
+ &taus_[secondaryStartIndex],
+ &msdData.msdSums[secondaryStartIndex],
+ &a2,
+ &b,
+ &correlationCoefficient,
+ &chiSquared);
+ msdData.sigma = std::abs(a - a2);
+ }
+ lsq_y_ax_b_xdouble(numTausForFit,
+ &taus_[beginFitIndex_],
+ &msdData.msdSums[beginFitIndex_],
+ &msdData.diffusionCoefficient,
+ &b,
+ &correlationCoefficient,
+ &chiSquared);
+ msdData.diffusionCoefficient *= c_diffusionConversionFactor / diffusionCoefficientDimensionFactor_;
+ msdData.sigma *= c_diffusionConversionFactor / diffusionCoefficientDimensionFactor_;
+ }
+
+ for (MoleculeData& molecule : molecules_)
+ {
+ std::vector<real> msds = molecule.msdData.averageMsds();
+ lsq_y_ax_b_xdouble(numTausForFit,
+ &taus_[beginFitIndex_],
+ &msds[beginFitIndex_],
+ &molecule.diffusionCoefficient,
+ &b,
+ &correlationCoefficient,
+ &chiSquared);
+ molecule.diffusionCoefficient *= c_diffusionConversionFactor / diffusionCoefficientDimensionFactor_;
+ }
+}
+
+void Msd::writeOutput()
+{
+ // AnalysisData currently doesn't support changing column counts after analysis has started.
+ // We can't determine the number of tau values until the trajectory is fully read, so analysis
+ // data construction and plotting are done here.
+ AnalysisDataPlotModulePointer msdPlotModule(new AnalysisDataPlotModule(plotSettings_));
+ msdPlotModule->setFileName(output_);
+ msdPlotModule->setTitle("Mean Squared Displacement");
+ msdPlotModule->setXLabel("tau (ps)");
+ msdPlotModule->setYLabel(R"(MSD (nm\\S2\\N))");
+ msdPlotModule->setYFormat(10, 6, 'g');
+ for (const auto& group : groupData_)
+ {
+ const real D = group.diffusionCoefficient;
+ if (D > 0.01 && D < 1e4)
+ {
+ msdPlotModule->appendLegend(formatString(
+ "D[%10s] = %.4f (+/- %.4f) (1e-5 cm^2/s)", group.sel.name(), D, group.sigma));
+ }
+ else
+ {
+ msdPlotModule->appendLegend(formatString(
+ "D[%10s] = %.4g (+/- %.4f) (1e-5 cm^2/s)", group.sel.name(), D, group.sigma));
+ }
+ }
+ msdPlotData_.addModule(msdPlotModule);
+ msdPlotData_.setDataSetCount(groupData_.size());
+ for (size_t i = 0; i < groupData_.size(); i++)
+ {
+ msdPlotData_.setColumnCount(i, 1);
+ }
+ AnalysisDataHandle dh = msdPlotData_.startData({});
+ for (size_t tauIndex = 0; tauIndex < taus_.size(); tauIndex++)
+ {
+ dh.startFrame(tauIndex, taus_[tauIndex]);
+ for (size_t dataSetIndex = 0; dataSetIndex < groupData_.size(); dataSetIndex++)
+ {
+ dh.selectDataSet(dataSetIndex);
+ dh.setPoint(0, groupData_[dataSetIndex].msdSums[tauIndex]);
+ }
+ dh.finishFrame();
+ }
+ dh.finishData();
+
+ if (molSelected_)
+ {
+ AnalysisDataPlotModulePointer molPlotModule(new AnalysisDataPlotModule(plotSettings_));
+ molPlotModule->setFileName(moleculeOutput_);
+ molPlotModule->setTitle("Mean Squared Displacement / Molecule");
+ molPlotModule->setXLabel("Molecule");
+ molPlotModule->setYLabel("D(1e-5 cm^2/s)");
+ molPlotModule->setYFormat(10, 0, 'g');
+ msdMoleculePlotData_.addModule(molPlotModule);
+ msdMoleculePlotData_.setDataSetCount(1);
+ msdMoleculePlotData_.setColumnCount(0, 1);
+ AnalysisDataHandle molDh = msdMoleculePlotData_.startData({});
+ for (size_t moleculeIndex = 0; moleculeIndex < molecules_.size(); moleculeIndex++)
+ {
+ molDh.startFrame(moleculeIndex, moleculeIndex);
+ molDh.setPoint(0, molecules_[moleculeIndex].diffusionCoefficient);
+ molDh.finishFrame();
+ }
+ molDh.finishData();
+ }
+}
+
+
+const char MsdInfo::name[] = "msd";
+const char MsdInfo::shortDescription[] = "Compute mean squared displacements";
+TrajectoryAnalysisModulePointer MsdInfo::create()
+{
+ return TrajectoryAnalysisModulePointer(new Msd);
+}
+
+
+} // namespace analysismodules
+} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \internal \file
+ * \brief
+ * Declares trajectory analysis module for Mean Squared Displacement calculations.
+ *
+ * \author Kevin Boyd <kevin44boyd@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+#ifndef GMX_TRAJECTORYANALYSIS_MODULES_MSD_H
+#define GMX_TRAJECTORYANALYSIS_MODULES_MSD_H
-#ifndef GMX_SIMD_IMPL_X86_MIC_GENERAL_H
-#define GMX_SIMD_IMPL_X86_MIC_GENERAL_H
-
-#include <immintrin.h>
+#include "gromacs/trajectoryanalysis/analysismodule.h"
-namespace gmx
+namespace gmx::analysismodules
{
-static inline void simdPrefetch(const void* m)
+class MsdInfo
{
- _mm_prefetch((const char*)m, _MM_HINT_T0);
-}
+public:
+ static const char name[];
+ static const char shortDescription[];
+ static TrajectoryAnalysisModulePointer create();
+};
-} // namespace gmx
+} // namespace gmx::analysismodules
-#endif // GMX_SIMD_IMPL_X86_MIC_OTHER_H
+#endif // GMX_TRAJECTORYANALYSIS_MODULES_MSD_H
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! Strings corresponding to DistanceType.
const EnumerationArray<DistanceType, const char*> c_distanceTypeNames = { { "min", "max" } };
//! Strings corresponding to GroupType.
-const EnumerationArray<GroupType, const char*> c_groupTypeNames = { { "all", "res", "mol",
- "none" } };
+const EnumerationArray<GroupType, const char*> c_groupTypeNames = {
+ { "all", "res", "mol", "none" }
+};
/*! \brief
* Implements `gmx pairdist` trajectory analysis module.
settings->setHelpText(desc);
options->addOption(FileNameOption("o")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.required()
.store(&fnDist_)
void PairDistance::analyzeFrame(int frnr, const t_trxframe& fr, t_pbc* pbc, TrajectoryAnalysisModuleData* pdata)
{
AnalysisDataHandle dh = pdata->dataHandle(distances_);
- const Selection& refSel = TrajectoryAnalysisModuleData::parallelSelection(refSel_);
- const SelectionList& sel = TrajectoryAnalysisModuleData::parallelSelections(sel_);
+ const Selection& refSel = pdata->parallelSelection(refSel_);
+ const SelectionList& sel = pdata->parallelSelections(sel_);
PairDistanceModuleData& frameData = *static_cast<PairDistanceModuleData*>(pdata);
std::vector<real>& distArray = frameData.distArray_;
std::vector<int>& countArray = frameData.countArray_;
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/analysisdata/modules/histogram.h"
#include "gromacs/analysisdata/modules/plot.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/options/basicoptions.h"
settings->setHelpText(desc);
options->addOption(FileNameOption("o")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.required()
.store(&fnRdf_)
.defaultBasename("rdf")
.description("Computed RDFs"));
options->addOption(FileNameOption("cn")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnCumulative_)
.defaultBasename("rdf_cn")
{
AnalysisDataHandle dh = pdata->dataHandle(pairDist_);
AnalysisDataHandle nh = pdata->dataHandle(normFactors_);
- const Selection& refSel = TrajectoryAnalysisModuleData::parallelSelection(refSel_);
- const SelectionList& sel = TrajectoryAnalysisModuleData::parallelSelections(sel_);
+ const Selection& refSel = pdata->parallelSelection(refSel_);
+ const SelectionList& sel = pdata->parallelSelections(sel_);
RdfModuleData& frameData = *static_cast<RdfModuleData*>(pdata);
const bool bSurface = !frameData.surfaceDist2_.empty();
real prevSphereVolume = 0.0;
for (int i = 0; i < nbin; ++i)
{
- const real r = (i + 0.5) * binwidth_;
- real sphereVolume;
- if (bXY_)
- {
- sphereVolume = M_PI * r * r;
- }
- else
- {
- sphereVolume = (4.0 / 3.0) * M_PI * r * r * r;
- }
- const real binVolume = sphereVolume - prevSphereVolume;
- invBinVolume[i] = 1.0 / binVolume;
- prevSphereVolume = sphereVolume;
+ const real r = (i + 0.5) * binwidth_;
+ const real sphereVolume = (bXY_) ? M_PI * r * r : (4.0 / 3.0) * M_PI * r * r * r;
+ const real binVolume = sphereVolume - prevSphereVolume;
+ invBinVolume[i] = 1.0 / binVolume;
+ prevSphereVolume = sphereVolume;
}
finalRdf->scaleAllByVector(invBinVolume.data());
* Copyright (c) 2001-2006, The GROMACS development team.
* Copyright (c) 2008,2009,2010,2011,2012 by the GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
void do_conect(const char* fn, int n, rvec x[])
{
- FILE* fp;
- int i, j;
- t_conect* c;
- rvec dx;
- real d2;
+ t_conect* c = nullptr;
fprintf(stderr, "Building CONECT records\n");
snew(c, n);
- for (i = 0; (i < n); i++)
+ for (int i = 0; (i < n); i++)
{
c[i].aa = c[i].ab = -1;
}
- for (i = 0; (i < n); i++)
+ for (int i = 0; (i < n); i++)
{
- for (j = i + 1; (j < n); j++)
+ for (int j = i + 1; (j < n); j++)
{
+ rvec dx;
rvec_sub(x[i], x[j], dx);
- d2 = iprod(dx, dx);
+ const real d2 = iprod(dx, dx);
add_rec(c, i, j, d2);
add_rec(c, j, i, d2);
}
}
- fp = gmx_ffopen(fn, "a");
- for (i = 0; (i < n); i++)
+ FILE* fp = gmx_ffopen(fn, "a");
+ for (int i = 0; (i < n); i++)
{
if ((c[i].aa == -1) || (c[i].ab == -1))
{
const char* const resnm = "DOT";
const char* const title = "Connolly Dot Surface Generated by gmx sasa";
- int i, i0, r0, ii0, k;
- rvec* xnew;
- t_atoms aaa;
+ rvec* xnew = nullptr;
if (bIncludeSolute)
{
- i0 = atoms->nr;
- r0 = atoms->nres;
+ int i0 = atoms->nr;
+ int r0 = atoms->nres;
srenew(atoms->atom, atoms->nr + ndots);
memset(&atoms->atom[i0], 0, sizeof(*atoms->atom) * ndots);
srenew(atoms->atomname, atoms->nr + ndots);
srenew(atoms->pdbinfo, atoms->nr + ndots);
}
snew(xnew, atoms->nr + ndots);
- for (i = 0; (i < atoms->nr); i++)
+ for (int i = 0; (i < atoms->nr); i++)
{
copy_rvec(x[i], xnew[i]);
}
- for (i = k = 0; (i < ndots); i++)
+ int k = 0;
+ for (int i = 0; (i < ndots); i++)
{
- ii0 = i0 + i;
+ int ii0 = i0 + i;
atoms->atomname[ii0] = put_symtab(symtab, atomnm);
atoms->atom[ii0].resind = r0;
xnew[ii0][XX] = dots[k++];
xnew[ii0][ZZ] = dots[k++];
if (atoms->pdbinfo != nullptr)
{
- atoms->pdbinfo[ii0].type = epdbATOM;
+ atoms->pdbinfo[ii0].type = PdbRecordType::Atom;
atoms->pdbinfo[ii0].atomnr = ii0;
atoms->pdbinfo[ii0].bfac = 0.0;
atoms->pdbinfo[ii0].occup = 0.0;
}
else
{
+ t_atoms aaa;
init_t_atoms(&aaa, ndots, TRUE);
aaa.atom[0].resind = 0;
t_atoms_set_resinfo(&aaa, 0, symtab, resnm, 1, ' ', 0, ' ');
snew(xnew, ndots);
- for (i = k = 0; (i < ndots); i++)
+ int k = 0;
+ for (int i = 0; (i < ndots); i++)
{
- ii0 = i;
+ int ii0 = i;
aaa.atomname[ii0] = put_symtab(symtab, atomnm);
- aaa.pdbinfo[ii0].type = epdbATOM;
+ aaa.pdbinfo[ii0].type = PdbRecordType::Atom;
aaa.pdbinfo[ii0].atomnr = ii0;
aaa.atom[ii0].resind = 0;
xnew[ii0][XX] = dots[k++];
"from the full surface.[PAR]",
"The average and standard deviation of the area over the trajectory",
- "can be calculated per residue and atom (options [TT]-or[tt] and", "[TT]-oa[tt]).[PAR]",
+ "can be calculated per residue and atom (options [TT]-or[tt] and",
+ "[TT]-oa[tt]).[PAR]",
//"In combination with the latter option an [REF].itp[ref] file can be",
//"generated (option [TT]-i[tt])",
//"which can be used to restrain surface atoms.[PAR]",
settings->setHelpText(desc);
options->addOption(FileNameOption("o")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.required()
.store(&fnArea_)
.description("Total area as a function of time"));
options->addOption(
FileNameOption("odg")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnDGSolv_)
.defaultBasename("dgsolv")
.description("Estimated solvation free energy as a function of time"));
options->addOption(FileNameOption("or")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnResidueArea_)
.defaultBasename("resarea")
.description("Average area per residue"));
options->addOption(FileNameOption("oa")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnAtomArea_)
.defaultBasename("atomarea")
.description("Average area per atom"));
options->addOption(FileNameOption("tv")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnVolume_)
.defaultBasename("volume")
.description("Total volume and density as a function of time"));
options->addOption(FileNameOption("q")
- .filetype(eftPDB)
+ .filetype(OptionFileType::PDB)
.outputFile()
.store(&fnConnolly_)
.defaultBasename("connolly")
.description("PDB file for Connolly surface"));
- // options->addOption(FileNameOption("i").filetype(eftITP).outputFile()
- // .store(&fnRestraints_).defaultBasename("surfat")
- // .description("Topology file for position restraings on surface atoms"));
-
options->addOption(
DoubleOption("probe").store(&solsize_).description("Radius of the solvent probe (nm)"));
options->addOption(IntegerOption("ndots").store(&ndots_).description(
"Number of dots per sphere, more dots means more accuracy"));
- // options->addOption(DoubleOption("minarea").store(&minarea_)
- // .description("The minimum area (nm^2) to count an atom as a surface atom when writing a position restraint file (see help)"));
options->addOption(
BooleanOption("prot").store(&bIncludeSolute_).description("Output the protein to the Connolly [REF].pdb[ref] file too"));
options->addOption(
}
please_cite(stderr, "Eisenhaber95");
- // if ((top.pbcType() != PbcType::Xyz) || (TRICLINIC(fr.box)))
- //{
- // fprintf(stderr, "\n\nWARNING: non-rectangular boxes may give erroneous results or crashes.\n"
- // "Analysis based on vacuum simulations (with the possibility of evaporation)\n"
- // "will certainly crash the analysis.\n\n");
- //}
if (bDGsol)
{
{
const int ii = atomIndices[i];
const int resind = atoms_->atom[ii].resind;
- real radius;
+ real radius = 0;
if (!aps.setAtomProperty(epropVDW, *(atoms_->resinfo[resind].name), *(atoms_->atomname[ii]), &radius))
{
ndefault++;
radii_.push_back(radius + solsize_);
if (bDGsol)
{
- real dgsFactor;
- if (!aps.setAtomProperty(epropDGsol, *(atoms_->resinfo[resind].name),
- *(atoms_->atomtype[ii]), &dgsFactor))
+ real dgsFactor = 0;
+ if (!aps.setAtomProperty(
+ epropDGsol, *(atoms_->resinfo[resind].name), *(atoms_->atomtype[ii]), &dgsFactor))
{
dgsFactor = dgsDefault_;
}
"Output selection '%s' is not a subset of "
"the surface selection (atom %d is the first "
"atom not in the surface selection)",
- outputSel_[g].name(), outputIndices[i] + 1);
+ outputSel_[g].name(),
+ outputIndices[i] + 1);
GMX_THROW(InconsistentInputError(message));
}
outputSel_[g].setOriginalId(i, j);
AnalysisDataHandle aah = pdata->dataHandle(atomArea_);
AnalysisDataHandle rah = pdata->dataHandle(residueArea_);
AnalysisDataHandle vh = pdata->dataHandle(volume_);
- const Selection& surfaceSel = TrajectoryAnalysisModuleData::parallelSelection(surfaceSel_);
- const SelectionList& outputSel = TrajectoryAnalysisModuleData::parallelSelections(outputSel_);
+ const Selection& surfaceSel = pdata->parallelSelection(surfaceSel_);
+ const SelectionList& outputSel = pdata->parallelSelections(outputSel_);
SasaModuleData& frameData = *static_cast<SasaModuleData*>(pdata);
const bool bResAt = !frameData.res_a_.empty();
// area array contains the per-atom areas for the selected positions.
// surfacedots contains nsurfacedots entries, and contains the actual
// points.
- real totarea, totvolume;
+ real totarea = 0;
+ real totvolume = 0;
real *area = nullptr, *surfacedots = nullptr;
- int nsurfacedots;
- calculator_.calculate(surfaceSel.coordinates().data(), pbc, frameData.index_.size(),
- frameData.index_.data(), flag, &totarea, &totvolume, &area, &surfacedots,
+ int nsurfacedots = 0;
+ calculator_.calculate(surfaceSel.coordinates().data(),
+ pbc,
+ frameData.index_.size(),
+ frameData.index_.data(),
+ flag,
+ &totarea,
+ &totvolume,
+ &area,
+ &surfacedots,
&nsurfacedots);
// Unpack the atomwise areas into the frameData.atomAreas_ array for easier
// indexing in the case of dynamic surfaceSel.
// structures. But since it is only used in the first frame, and no
// one else uses the topology after initialization, it may just work
// even with future parallelization.
- connolly_plot(fnConnolly_.c_str(), nsurfacedots, surfacedots, fr.x, atoms_.get(),
- &mtop_->symtab, fr.pbcType, fr.box, bIncludeSolute_);
+ connolly_plot(fnConnolly_.c_str(),
+ nsurfacedots,
+ surfacedots,
+ fr.x,
+ atoms_.get(),
+ &mtop_->symtab,
+ fr.pbcType,
+ fr.box,
+ bIncludeSolute_);
}
ah.startFrame(frnr, fr.time);
ah.setPoint(0, totarea);
- real totalArea, dgsolv;
+ real totalArea = 0;
+ real dgsolv = 0;
if (bResAt || bDGsol)
{
- computeAreas(surfaceSel, surfaceSel, frameData.atomAreas_, dgsFactor_, &totalArea, &dgsolv,
- aah, rah, &frameData.res_a_);
+ computeAreas(surfaceSel,
+ surfaceSel,
+ frameData.atomAreas_,
+ dgsFactor_,
+ &totalArea,
+ &dgsolv,
+ aah,
+ rah,
+ &frameData.res_a_);
if (bDGsol)
{
dgh.setPoint(0, dgsolv);
aah.selectDataSet(g + 1);
rah.selectDataSet(g + 1);
}
- computeAreas(surfaceSel, outputSel[g], frameData.atomAreas_, dgsFactor_, &totalArea,
- &dgsolv, aah, rah, &frameData.res_a_);
+ computeAreas(surfaceSel,
+ outputSel[g],
+ frameData.atomAreas_,
+ dgsFactor_,
+ &totalArea,
+ &dgsolv,
+ aah,
+ rah,
+ &frameData.res_a_);
ah.setPoint(g + 1, totalArea);
if (bDGsol)
{
{
totmass += surfaceSel.position(i).mass();
}
- const real density = totmass * AMU / (totvolume * NANO * NANO * NANO);
+ const real density = totmass * gmx::c_amu / (totvolume * gmx::c_nano * gmx::c_nano * gmx::c_nano);
vh.startFrame(frnr, fr.time);
vh.setPoint(0, totvolume);
vh.setPoint(1, density);
}
}
-void Sasa::finishAnalysis(int /*nframes*/)
-{
- // if (bITP)
- //{
- // fp3 = ftp2FILE(efITP, nfile, fnm, "w");
- // fprintf(fp3, "[ position_restraints ]\n"
- // "#define FCX 1000\n"
- // "#define FCY 1000\n"
- // "#define FCZ 1000\n"
- // "; Atom Type fx fy fz\n");
- // for (i = 0; i < nx[0]; i++)
- // {
- // if (atom_area[i] > minarea)
- // {
- // fprintf(fp3, "%5d 1 FCX FCX FCZ\n", ii+1);
- // }
- // }
- // ffclose(fp3);
- //}
-}
+void Sasa::finishAnalysis(int /*nframes*/) {}
void Sasa::writeOutput() {}
*
* Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const EnumerationArray<ResidueNumbering, const char*> c_residueNumberingTypeNames = { { "number",
"index" } };
//! String values corresponding to PdbAtomsSelection.
-const EnumerationArray<PdbAtomsSelection, const char*> c_pdbAtomsTypeNames = { { "all", "maxsel",
- "selected" } };
+const EnumerationArray<PdbAtomsSelection, const char*> c_pdbAtomsTypeNames = {
+ { "all", "maxsel", "selected" }
+};
class Select : public TrajectoryAnalysisModule
{
settings->setHelpText(desc);
options->addOption(FileNameOption("os")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnSize_)
.defaultBasename("size")
.description("Number of positions in each selection"));
options->addOption(FileNameOption("oc")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnFrac_)
.defaultBasename("cfrac")
.description("Covered fraction for each selection"));
options->addOption(FileNameOption("oi")
- .filetype(eftGenericData)
+ .filetype(OptionFileType::GenericData)
.outputFile()
.store(&fnIndex_)
.defaultBasename("index")
.description("Indices selected by each selection"));
options->addOption(FileNameOption("on")
- .filetype(eftIndex)
+ .filetype(OptionFileType::Index)
.outputFile()
.store(&fnNdx_)
.defaultBasename("index")
.description("Index file from the selection"));
options->addOption(FileNameOption("om")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnMask_)
.defaultBasename("mask")
.description("Mask for selected positions"));
options->addOption(FileNameOption("of")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnOccupancy_)
.defaultBasename("occupancy")
.description("Occupied fraction for selected positions"));
options->addOption(
FileNameOption("ofpdb")
- .filetype(eftPDB)
+ .filetype(OptionFileType::PDB)
.outputFile()
.store(&fnPDB_)
.defaultBasename("occupancy")
.description("PDB file with occupied fraction for selected positions"));
options->addOption(FileNameOption("olt")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnLifetime_)
.defaultBasename("lifetime")
AnalysisDataHandle cdh = pdata->dataHandle(cdata_);
AnalysisDataHandle idh = pdata->dataHandle(idata_);
AnalysisDataHandle mdh = pdata->dataHandle(mdata_);
- const SelectionList& sel = TrajectoryAnalysisModuleData::parallelSelections(sel_);
+ const SelectionList& sel = pdata->parallelSelections(sel_);
sdh.startFrame(frnr, fr.time);
for (size_t g = 0; g < sel.size(); ++g)
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2007, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
divarc(real x1, real y1, real z1, real x2, real y2, real z2, int div1, int div2, real* xr, real* yr, real* zr)
{
- real xd, yd, zd, dd, d1, d2, s, x, y, z;
- real phi, sphi, cphi;
-
- xd = y1 * z2 - y2 * z1;
- yd = z1 * x2 - z2 * x1;
- zd = x1 * y2 - x2 * y1;
- dd = std::sqrt(xd * xd + yd * yd + zd * zd);
+ const real xd = y1 * z2 - y2 * z1;
+ const real yd = z1 * x2 - z2 * x1;
+ const real zd = x1 * y2 - x2 * y1;
+ const real dd = std::sqrt(xd * xd + yd * yd + zd * zd);
GMX_ASSERT(dd >= DP_TOL, "Rotation axis vector too short");
- d1 = x1 * x1 + y1 * y1 + z1 * z1;
- d2 = x2 * x2 + y2 * y2 + z2 * z2;
+ const real d1 = x1 * x1 + y1 * y1 + z1 * z1;
+ const real d2 = x2 * x2 + y2 * y2 + z2 * z2;
GMX_ASSERT(d1 >= 0.5, "Vector 1 too short");
GMX_ASSERT(d2 >= 0.5, "Vector 2 too short");
- phi = safe_asin(dd / std::sqrt(d1 * d2));
- phi = phi * (static_cast<real>(div1)) / (static_cast<real>(div2));
- sphi = sin(phi);
- cphi = cos(phi);
- s = (x1 * xd + y1 * yd + z1 * zd) / dd;
-
- x = xd * s * (1. - cphi) / dd + x1 * cphi + (yd * z1 - y1 * zd) * sphi / dd;
- y = yd * s * (1. - cphi) / dd + y1 * cphi + (zd * x1 - z1 * xd) * sphi / dd;
- z = zd * s * (1. - cphi) / dd + z1 * cphi + (xd * y1 - x1 * yd) * sphi / dd;
- dd = std::sqrt(x * x + y * y + z * z);
- *xr = x / dd;
- *yr = y / dd;
- *zr = z / dd;
+ real phi = safe_asin(dd / std::sqrt(d1 * d2));
+ phi = phi * (static_cast<real>(div1)) / (static_cast<real>(div2));
+ const real sphi = sin(phi);
+ const real cphi = cos(phi);
+ const real s = (x1 * xd + y1 * yd + z1 * zd) / dd;
+
+ const real x = xd * s * (1. - cphi) / dd + x1 * cphi + (yd * z1 - y1 * zd) * sphi / dd;
+ const real y = yd * s * (1. - cphi) / dd + y1 * cphi + (zd * x1 - z1 * xd) * sphi / dd;
+ const real z = zd * s * (1. - cphi) / dd + z1 * cphi + (xd * y1 - x1 * yd) * sphi / dd;
+ const real dd2 = std::sqrt(x * x + y * y + z * z);
+ *xr = x / dd2;
+ *yr = y / dd2;
+ *zr = z / dd2;
}
/* densit...required dots per unit sphere */
/* dot distribution on a unit sphere based on an icosaeder *
* great circle average refining of icosahedral face */
- int i, j, k, tl, tl2, tn;
- real a, d, x, y, z, x2, y2, z2, x3, y3, z3;
- real xij, yij, zij, xji, yji, zji, xik, yik, zik, xki, yki, zki, xjk, yjk, zjk, xkj, ykj, zkj;
+ real x2 = NAN, y2 = NAN, z2 = NAN, x3 = NAN, y3 = NAN, z3 = NAN;
+ real xij = NAN, yij = NAN, zij = NAN, xji = NAN, yji = NAN, zji = NAN, xik = NAN, yik = NAN,
+ zik = NAN, xki = NAN, yki = NAN, zki = NAN, xjk = NAN, yjk = NAN, zjk = NAN, xkj = NAN,
+ ykj = NAN, zkj = NAN;
/* calculate tessalation level */
- a = std::sqrt(((static_cast<real>(densit)) - 2.) / 10.);
- const int tess = static_cast<int>(ceil(a));
- const int ndot = 10 * tess * tess + 2;
+ const real a = std::sqrt(((static_cast<real>(densit)) - 2.) / 10.);
+ const int tess = static_cast<int>(ceil(a));
+ const int ndot = 10 * tess * tess + 2;
GMX_RELEASE_ASSERT(ndot >= densit, "Inconsistent surface dot formula");
std::vector<real> xus(3 * ndot);
if (tess > 1)
{
- tn = 12;
- a = rh * rh * 2. * (1. - cos(TORAD(72.)));
+ int tn = 12;
+ const real a = rh * rh * 2. * (1. - cos(TORAD(72.)));
/* calculate tessalation of icosaeder edges */
- for (i = 0; i < 11; i++)
+ for (int i = 0; i < 11; i++)
{
- for (j = i + 1; j < 12; j++)
+ for (int j = i + 1; j < 12; j++)
{
- x = xus[3 * i] - xus[3 * j];
- y = xus[1 + 3 * i] - xus[1 + 3 * j];
- z = xus[2 + 3 * i] - xus[2 + 3 * j];
- d = x * x + y * y + z * z;
+ const real x = xus[3 * i] - xus[3 * j];
+ const real y = xus[1 + 3 * i] - xus[1 + 3 * j];
+ const real z = xus[2 + 3 * i] - xus[2 + 3 * j];
+ const real d = x * x + y * y + z * z;
if (std::fabs(a - d) > DP_TOL)
{
continue;
}
- for (tl = 1; tl < tess; tl++)
+ for (int tl = 1; tl < tess; tl++)
{
GMX_ASSERT(tn < ndot, "Inconsistent precomputed surface dot count");
- divarc(xus[3 * i], xus[1 + 3 * i], xus[2 + 3 * i], xus[3 * j], xus[1 + 3 * j],
- xus[2 + 3 * j], tl, tess, &xus[3 * tn], &xus[1 + 3 * tn], &xus[2 + 3 * tn]);
+ divarc(xus[3 * i],
+ xus[1 + 3 * i],
+ xus[2 + 3 * i],
+ xus[3 * j],
+ xus[1 + 3 * j],
+ xus[2 + 3 * j],
+ tl,
+ tess,
+ &xus[3 * tn],
+ &xus[1 + 3 * tn],
+ &xus[2 + 3 * tn]);
tn++;
}
}
}
/* calculate tessalation of icosaeder faces */
- for (i = 0; i < 10; i++)
+ for (int i = 0; i < 10; i++)
{
- for (j = i + 1; j < 11; j++)
+ for (int j = i + 1; j < 11; j++)
{
- x = xus[3 * i] - xus[3 * j];
- y = xus[1 + 3 * i] - xus[1 + 3 * j];
- z = xus[2 + 3 * i] - xus[2 + 3 * j];
- d = x * x + y * y + z * z;
+ real x = xus[3 * i] - xus[3 * j];
+ real y = xus[1 + 3 * i] - xus[1 + 3 * j];
+ real z = xus[2 + 3 * i] - xus[2 + 3 * j];
+ real d = x * x + y * y + z * z;
if (std::fabs(a - d) > DP_TOL)
{
continue;
}
- for (k = j + 1; k < 12; k++)
+ for (int k = j + 1; k < 12; k++)
{
x = xus[3 * i] - xus[3 * k];
y = xus[1 + 3 * i] - xus[1 + 3 * k];
{
continue;
}
- for (tl = 1; tl < tess - 1; tl++)
+ for (int tl = 1; tl < tess - 1; tl++)
{
- divarc(xus[3 * j], xus[1 + 3 * j], xus[2 + 3 * j], xus[3 * i],
- xus[1 + 3 * i], xus[2 + 3 * i], tl, tess, &xji, &yji, &zji);
- divarc(xus[3 * k], xus[1 + 3 * k], xus[2 + 3 * k], xus[3 * i],
- xus[1 + 3 * i], xus[2 + 3 * i], tl, tess, &xki, &yki, &zki);
-
- for (tl2 = 1; tl2 < tess - tl; tl2++)
+ divarc(xus[3 * j],
+ xus[1 + 3 * j],
+ xus[2 + 3 * j],
+ xus[3 * i],
+ xus[1 + 3 * i],
+ xus[2 + 3 * i],
+ tl,
+ tess,
+ &xji,
+ &yji,
+ &zji);
+ divarc(xus[3 * k],
+ xus[1 + 3 * k],
+ xus[2 + 3 * k],
+ xus[3 * i],
+ xus[1 + 3 * i],
+ xus[2 + 3 * i],
+ tl,
+ tess,
+ &xki,
+ &yki,
+ &zki);
+
+ for (int tl2 = 1; tl2 < tess - tl; tl2++)
{
- divarc(xus[3 * i], xus[1 + 3 * i], xus[2 + 3 * i], xus[3 * j],
- xus[1 + 3 * j], xus[2 + 3 * j], tl2, tess, &xij, &yij, &zij);
- divarc(xus[3 * k], xus[1 + 3 * k], xus[2 + 3 * k], xus[3 * j],
- xus[1 + 3 * j], xus[2 + 3 * j], tl2, tess, &xkj, &ykj, &zkj);
- divarc(xus[3 * i], xus[1 + 3 * i], xus[2 + 3 * i], xus[3 * k], xus[1 + 3 * k],
- xus[2 + 3 * k], tess - tl - tl2, tess, &xik, &yik, &zik);
- divarc(xus[3 * j], xus[1 + 3 * j], xus[2 + 3 * j], xus[3 * k], xus[1 + 3 * k],
- xus[2 + 3 * k], tess - tl - tl2, tess, &xjk, &yjk, &zjk);
+ divarc(xus[3 * i],
+ xus[1 + 3 * i],
+ xus[2 + 3 * i],
+ xus[3 * j],
+ xus[1 + 3 * j],
+ xus[2 + 3 * j],
+ tl2,
+ tess,
+ &xij,
+ &yij,
+ &zij);
+ divarc(xus[3 * k],
+ xus[1 + 3 * k],
+ xus[2 + 3 * k],
+ xus[3 * j],
+ xus[1 + 3 * j],
+ xus[2 + 3 * j],
+ tl2,
+ tess,
+ &xkj,
+ &ykj,
+ &zkj);
+ divarc(xus[3 * i],
+ xus[1 + 3 * i],
+ xus[2 + 3 * i],
+ xus[3 * k],
+ xus[1 + 3 * k],
+ xus[2 + 3 * k],
+ tess - tl - tl2,
+ tess,
+ &xik,
+ &yik,
+ &zik);
+ divarc(xus[3 * j],
+ xus[1 + 3 * j],
+ xus[2 + 3 * j],
+ xus[3 * k],
+ xus[1 + 3 * k],
+ xus[2 + 3 * k],
+ tess - tl - tl2,
+ tess,
+ &xjk,
+ &yjk,
+ &zjk);
divarc(xki, yki, zki, xji, yji, zji, tl2, tess - tl, &x, &y, &z);
divarc(xkj, ykj, zkj, xij, yij, zij, tl, tess - tl2, &x2, &y2, &z2);
divarc(xjk, yjk, zjk, xik, yik, zik, tl, tl + tl2, &x3, &y3, &z3);
/* dot distribution on a unit sphere based on an icosaeder *
* great circle average refining of icosahedral face */
- int i, j, k, tl, tl2, tn, tess, j1, j2;
- real a, d, x, y, z, x2, y2, z2, x3, y3, z3, ai_d, adod;
- real xij, yij, zij, xji, yji, zji, xik, yik, zik, xki, yki, zki, xjk, yjk, zjk, xkj, ykj, zkj;
+ real x2 = NAN, y2 = NAN, z2 = NAN, x3 = NAN, y3 = NAN, z3 = NAN;
+ real xij = NAN, yij = NAN, zij = NAN, xji = NAN, yji = NAN, zji = NAN, xik = NAN, yik = NAN,
+ zik = NAN, xki = NAN, yki = NAN, zki = NAN, xjk = NAN, yjk = NAN, zjk = NAN, xkj = NAN,
+ ykj = NAN, zkj = NAN;
/* calculate tesselation level */
- a = std::sqrt(((static_cast<real>(densit)) - 2.) / 30.);
- tess = std::max(static_cast<int>(ceil(a)), 1);
+ real a = std::sqrt(((static_cast<real>(densit)) - 2.) / 30.);
+ const int tess = std::max(static_cast<int>(ceil(a)), 1);
const int ndot = 30 * tess * tess + 2;
GMX_RELEASE_ASSERT(ndot >= densit, "Inconsistent surface dot formula");
std::vector<real> xus(3 * ndot);
const real rh = icosaeder_vertices(xus.data());
- tn = 12;
+ int tn = 12;
/* square of the edge of an icosaeder */
a = rh * rh * 2. * (1. - cos(TORAD(72.)));
/* dodecaeder vertices */
- for (i = 0; i < 10; i++)
+ for (int i = 0; i < 10; i++)
{
- for (j = i + 1; j < 11; j++)
+ for (int j = i + 1; j < 11; j++)
{
- x = xus[3 * i] - xus[3 * j];
- y = xus[1 + 3 * i] - xus[1 + 3 * j];
- z = xus[2 + 3 * i] - xus[2 + 3 * j];
- d = x * x + y * y + z * z;
+ const real x = xus[3 * i] - xus[3 * j];
+ const real y = xus[1 + 3 * i] - xus[1 + 3 * j];
+ const real z = xus[2 + 3 * i] - xus[2 + 3 * j];
+ const real d = x * x + y * y + z * z;
if (std::fabs(a - d) > DP_TOL)
{
continue;
}
- for (k = j + 1; k < 12; k++)
+ for (int k = j + 1; k < 12; k++)
{
- x = xus[3 * i] - xus[3 * k];
- y = xus[1 + 3 * i] - xus[1 + 3 * k];
- z = xus[2 + 3 * i] - xus[2 + 3 * k];
- d = x * x + y * y + z * z;
- if (std::fabs(a - d) > DP_TOL)
{
- continue;
+ const real x = xus[3 * i] - xus[3 * k];
+ const real y = xus[1 + 3 * i] - xus[1 + 3 * k];
+ const real z = xus[2 + 3 * i] - xus[2 + 3 * k];
+ const real d = x * x + y * y + z * z;
+ if (std::fabs(a - d) > DP_TOL)
+ {
+ continue;
+ }
}
- x = xus[3 * j] - xus[3 * k];
- y = xus[1 + 3 * j] - xus[1 + 3 * k];
- z = xus[2 + 3 * j] - xus[2 + 3 * k];
- d = x * x + y * y + z * z;
- if (std::fabs(a - d) > DP_TOL)
{
- continue;
+ const real x = xus[3 * j] - xus[3 * k];
+ const real y = xus[1 + 3 * j] - xus[1 + 3 * k];
+ const real z = xus[2 + 3 * j] - xus[2 + 3 * k];
+ const real d = x * x + y * y + z * z;
+ if (std::fabs(a - d) > DP_TOL)
+ {
+ continue;
+ }
}
- x = xus[3 * i] + xus[3 * j] + xus[3 * k];
- y = xus[1 + 3 * i] + xus[1 + 3 * j] + xus[1 + 3 * k];
- z = xus[2 + 3 * i] + xus[2 + 3 * j] + xus[2 + 3 * k];
- d = std::sqrt(x * x + y * y + z * z);
+ const real x = xus[3 * i] + xus[3 * j] + xus[3 * k];
+ const real y = xus[1 + 3 * i] + xus[1 + 3 * j] + xus[1 + 3 * k];
+ const real z = xus[2 + 3 * i] + xus[2 + 3 * j] + xus[2 + 3 * k];
+ const real d = std::sqrt(x * x + y * y + z * z);
xus[3 * tn] = x / d;
xus[1 + 3 * tn] = y / d;
xus[2 + 3 * tn] = z / d;
if (tess > 1)
{
- tn = 32;
+ int tn = 32;
/* square of the edge of an dodecaeder */
- adod = 4. * (cos(TORAD(108.)) - cos(TORAD(120.))) / (1. - cos(TORAD(120.)));
+ const real adod = 4. * (cos(TORAD(108.)) - cos(TORAD(120.))) / (1. - cos(TORAD(120.)));
/* square of the distance of two adjacent vertices of ico- and dodecaeder */
- ai_d = 2. * (1. - std::sqrt(1. - a / 3.));
+ const real ai_d = 2. * (1. - std::sqrt(1. - a / 3.));
/* calculate tessalation of mixed edges */
- for (i = 0; i < 31; i++)
+ for (int i = 0; i < 31; i++)
{
- j1 = 12;
- j2 = 32;
- a = ai_d;
+ int j1 = 12;
+ int j2 = 32;
+ a = ai_d;
if (i >= 12)
{
j1 = i + 1;
a = adod;
}
- for (j = j1; j < j2; j++)
+ for (int j = j1; j < j2; j++)
{
- x = xus[3 * i] - xus[3 * j];
- y = xus[1 + 3 * i] - xus[1 + 3 * j];
- z = xus[2 + 3 * i] - xus[2 + 3 * j];
- d = x * x + y * y + z * z;
+ const real x = xus[3 * i] - xus[3 * j];
+ const real y = xus[1 + 3 * i] - xus[1 + 3 * j];
+ const real z = xus[2 + 3 * i] - xus[2 + 3 * j];
+ const real d = x * x + y * y + z * z;
if (std::fabs(a - d) > DP_TOL)
{
continue;
}
- for (tl = 1; tl < tess; tl++)
+ for (int tl = 1; tl < tess; tl++)
{
GMX_ASSERT(tn < ndot, "Inconsistent precomputed surface dot count");
- divarc(xus[3 * i], xus[1 + 3 * i], xus[2 + 3 * i], xus[3 * j], xus[1 + 3 * j],
- xus[2 + 3 * j], tl, tess, &xus[3 * tn], &xus[1 + 3 * tn], &xus[2 + 3 * tn]);
+ divarc(xus[3 * i],
+ xus[1 + 3 * i],
+ xus[2 + 3 * i],
+ xus[3 * j],
+ xus[1 + 3 * j],
+ xus[2 + 3 * j],
+ tl,
+ tess,
+ &xus[3 * tn],
+ &xus[1 + 3 * tn],
+ &xus[2 + 3 * tn]);
tn++;
}
}
}
/* calculate tessalation of pentakisdodecahedron faces */
- for (i = 0; i < 12; i++)
+ for (int i = 0; i < 12; i++)
{
- for (j = 12; j < 31; j++)
+ for (int j = 12; j < 31; j++)
{
- x = xus[3 * i] - xus[3 * j];
- y = xus[1 + 3 * i] - xus[1 + 3 * j];
- z = xus[2 + 3 * i] - xus[2 + 3 * j];
- d = x * x + y * y + z * z;
+ const real x = xus[3 * i] - xus[3 * j];
+ const real y = xus[1 + 3 * i] - xus[1 + 3 * j];
+ const real z = xus[2 + 3 * i] - xus[2 + 3 * j];
+ const real d = x * x + y * y + z * z;
if (std::fabs(ai_d - d) > DP_TOL)
{
continue;
}
- for (k = j + 1; k < 32; k++)
+ for (int k = j + 1; k < 32; k++)
{
- x = xus[3 * i] - xus[3 * k];
- y = xus[1 + 3 * i] - xus[1 + 3 * k];
- z = xus[2 + 3 * i] - xus[2 + 3 * k];
- d = x * x + y * y + z * z;
+ real x = xus[3 * i] - xus[3 * k];
+ real y = xus[1 + 3 * i] - xus[1 + 3 * k];
+ real z = xus[2 + 3 * i] - xus[2 + 3 * k];
+ real d = x * x + y * y + z * z;
if (std::fabs(ai_d - d) > DP_TOL)
{
continue;
{
continue;
}
- for (tl = 1; tl < tess - 1; tl++)
+ for (int tl = 1; tl < tess - 1; tl++)
{
- divarc(xus[3 * j], xus[1 + 3 * j], xus[2 + 3 * j], xus[3 * i],
- xus[1 + 3 * i], xus[2 + 3 * i], tl, tess, &xji, &yji, &zji);
- divarc(xus[3 * k], xus[1 + 3 * k], xus[2 + 3 * k], xus[3 * i],
- xus[1 + 3 * i], xus[2 + 3 * i], tl, tess, &xki, &yki, &zki);
-
- for (tl2 = 1; tl2 < tess - tl; tl2++)
+ divarc(xus[3 * j],
+ xus[1 + 3 * j],
+ xus[2 + 3 * j],
+ xus[3 * i],
+ xus[1 + 3 * i],
+ xus[2 + 3 * i],
+ tl,
+ tess,
+ &xji,
+ &yji,
+ &zji);
+ divarc(xus[3 * k],
+ xus[1 + 3 * k],
+ xus[2 + 3 * k],
+ xus[3 * i],
+ xus[1 + 3 * i],
+ xus[2 + 3 * i],
+ tl,
+ tess,
+ &xki,
+ &yki,
+ &zki);
+
+ for (int tl2 = 1; tl2 < tess - tl; tl2++)
{
- divarc(xus[3 * i], xus[1 + 3 * i], xus[2 + 3 * i], xus[3 * j],
- xus[1 + 3 * j], xus[2 + 3 * j], tl2, tess, &xij, &yij, &zij);
- divarc(xus[3 * k], xus[1 + 3 * k], xus[2 + 3 * k], xus[3 * j],
- xus[1 + 3 * j], xus[2 + 3 * j], tl2, tess, &xkj, &ykj, &zkj);
- divarc(xus[3 * i], xus[1 + 3 * i], xus[2 + 3 * i], xus[3 * k], xus[1 + 3 * k],
- xus[2 + 3 * k], tess - tl - tl2, tess, &xik, &yik, &zik);
- divarc(xus[3 * j], xus[1 + 3 * j], xus[2 + 3 * j], xus[3 * k], xus[1 + 3 * k],
- xus[2 + 3 * k], tess - tl - tl2, tess, &xjk, &yjk, &zjk);
+ divarc(xus[3 * i],
+ xus[1 + 3 * i],
+ xus[2 + 3 * i],
+ xus[3 * j],
+ xus[1 + 3 * j],
+ xus[2 + 3 * j],
+ tl2,
+ tess,
+ &xij,
+ &yij,
+ &zij);
+ divarc(xus[3 * k],
+ xus[1 + 3 * k],
+ xus[2 + 3 * k],
+ xus[3 * j],
+ xus[1 + 3 * j],
+ xus[2 + 3 * j],
+ tl2,
+ tess,
+ &xkj,
+ &ykj,
+ &zkj);
+ divarc(xus[3 * i],
+ xus[1 + 3 * i],
+ xus[2 + 3 * i],
+ xus[3 * k],
+ xus[1 + 3 * k],
+ xus[2 + 3 * k],
+ tess - tl - tl2,
+ tess,
+ &xik,
+ &yik,
+ &zik);
+ divarc(xus[3 * j],
+ xus[1 + 3 * j],
+ xus[2 + 3 * j],
+ xus[3 * k],
+ xus[1 + 3 * k],
+ xus[2 + 3 * k],
+ tess - tl - tl2,
+ tess,
+ &xjk,
+ &yjk,
+ &zjk);
divarc(xki, yki, zki, xji, yji, zji, tl2, tess - tl, &x, &y, &z);
divarc(xkj, ykj, zkj, xij, yij, zij, tl, tess - tl2, &x2, &y2, &z2);
divarc(xjk, yjk, zjk, xik, yik, zik, tl, tl + tl2, &x3, &y3, &z3);
static int unsp_type(int densit)
{
- int i1, i2;
- i1 = 1;
+ int i1 = 1;
while (10 * i1 * i1 + 2 < densit)
{
i1++;
}
- i2 = 1;
+ int i2 = 1;
while (30 * i2 * i2 + 2 < densit)
{
i2++;
static std::vector<real> make_unsp(int densit, int cubus)
{
- int *ico_wk, *ico_pt;
- int ico_cube, ico_cube_cb, i, j, k, l, ijk, tn, tl, tl2;
- int* work;
- real x, y, z;
+ int ico_cube = 0;
int mode = unsp_type(densit);
std::vector<real> xus;
}
else
{
- i = 1;
+ int i = 1;
while (i * i * i * 2 < ndot)
{
i++;
}
ico_cube = std::max(i - 1, 0);
}
- ico_cube_cb = ico_cube * ico_cube * ico_cube;
- const real del_cube = 2. / (static_cast<real>(ico_cube));
- snew(work, ndot);
- for (l = 0; l < ndot; l++)
+ int ico_cube_cb = ico_cube * ico_cube * ico_cube;
+ const real del_cube = 2. / (static_cast<real>(ico_cube));
+ std::vector<int> work;
+ for (int l = 0; l < ndot; l++)
{
- i = std::max(static_cast<int>(floor((1. + xus[3 * l]) / del_cube)), 0);
+ int i = std::max(static_cast<int>(floor((1. + xus[3 * l]) / del_cube)), 0);
if (i >= ico_cube)
{
i = ico_cube - 1;
}
- j = std::max(static_cast<int>(floor((1. + xus[1 + 3 * l]) / del_cube)), 0);
+ int j = std::max(static_cast<int>(floor((1. + xus[1 + 3 * l]) / del_cube)), 0);
if (j >= ico_cube)
{
j = ico_cube - 1;
}
- k = std::max(static_cast<int>(floor((1. + xus[2 + 3 * l]) / del_cube)), 0);
+ int k = std::max(static_cast<int>(floor((1. + xus[2 + 3 * l]) / del_cube)), 0);
if (k >= ico_cube)
{
k = ico_cube - 1;
}
- ijk = i + j * ico_cube + k * ico_cube * ico_cube;
- work[l] = ijk;
+ int ijk = i + j * ico_cube + k * ico_cube * ico_cube;
+ work.emplace_back(ijk);
}
- snew(ico_wk, 2 * ico_cube_cb + 1);
+ std::vector<int> ico_wk(2 * ico_cube_cb + 1);
- ico_pt = ico_wk + ico_cube_cb;
- for (l = 0; l < ndot; l++)
+ int* ico_pt = ico_wk.data() + ico_cube_cb;
+ for (int l = 0; l < ndot; l++)
{
ico_wk[work[l]]++; /* dots per elementary cube */
}
/* reordering of the coordinate array in accordance with box number */
- tn = 0;
- for (i = 0; i < ico_cube; i++)
+ int tn = 0;
+ for (int i = 0; i < ico_cube; i++)
{
- for (j = 0; j < ico_cube; j++)
+ for (int j = 0; j < ico_cube; j++)
{
- for (k = 0; k < ico_cube; k++)
+ for (int k = 0; k < ico_cube; k++)
{
- tl = 0;
- tl2 = tn;
- ijk = i + ico_cube * j + ico_cube * ico_cube * k;
+ int tl = 0;
+ int tl2 = tn;
+ int ijk = i + ico_cube * j + ico_cube * ico_cube * k;
*(ico_pt + ijk) = tn;
- for (l = tl2; l < ndot; l++)
+ for (int l = tl2; l < ndot; l++)
{
if (ijk == work[l])
{
- x = xus[3 * l];
- y = xus[1 + 3 * l];
- z = xus[2 + 3 * l];
+ const real x = xus[3 * l];
+ const real y = xus[1 + 3 * l];
+ const real z = xus[2 + 3 * l];
xus[3 * l] = xus[3 * tn];
xus[1 + 3 * l] = xus[1 + 3 * tn];
xus[2 + 3 * l] = xus[2 + 3 * tn];
tl++;
}
}
- *(ico_wk + ijk) = tl;
+ *(ico_wk.data() + ijk) = tl;
} /* cycle k */
} /* cycle j */
} /* cycle i */
- sfree(ico_wk);
- sfree(work);
return xus;
}
{
*n_dots = 0;
}
- nsc_dclm_pbc(x, impl_->radius_, nat, &impl_->unitSphereDots_[0], impl_->unitSphereDots_.size() / 3,
- flags, area, at_area, volume, lidots, n_dots, index, &impl_->nb_, pbc);
+ nsc_dclm_pbc(x,
+ impl_->radius_,
+ nat,
+ &impl_->unitSphereDots_[0],
+ impl_->unitSphereDots_.size() / 3,
+ flags,
+ area,
+ at_area,
+ volume,
+ lidots,
+ n_dots,
+ index,
+ &impl_->nb_,
+ pbc);
}
} // namespace gmx
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TRAJECTORYANALYSIS_SURFACEAREA_H
#define GMX_TRAJECTORYANALYSIS_SURFACEAREA_H
+#include <memory>
+
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/real.h"
struct t_pbc;
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
settings->setHelpText(desc);
options->addOption(FileNameOption("ox")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnX_)
.defaultBasename("coord")
.description("Coordinates for each position as a function of time"));
options->addOption(FileNameOption("ov")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnV_)
.defaultBasename("veloc")
.description("Velocities for each position as a function of time"));
options->addOption(FileNameOption("of")
- .filetype(eftPlot)
+ .filetype(OptionFileType::Plot)
.outputFile()
.store(&fnF_)
.defaultBasename("force")
void Trajectory::analyzeFrame(int frnr, const t_trxframe& fr, t_pbc* /* pbc */, TrajectoryAnalysisModuleData* pdata)
{
AnalysisDataHandle dh = pdata->dataHandle(xdata_);
- const SelectionList& sel = TrajectoryAnalysisModuleData::parallelSelections(sel_);
+ const SelectionList& sel = pdata->parallelSelections(sel_);
analyzeFrameImpl(frnr, fr, &dh, sel, [](const SelectionPosition& pos) { return pos.x(); });
if (fr.bV)
{
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
const std::string message =
formatString("Trajectory (%d atoms) does not match topology (%d atoms)",
- fr->natoms, topologyAtomCount);
+ fr->natoms,
+ topologyAtomCount);
GMX_THROW(InconsistentInputError(message));
}
}
const std::string message = formatString(
"Selection specified with -fgroup has %d atoms, but "
"the trajectory (-f) has %d atoms.",
- trajectoryGroup_.atomCount(), fr->natoms);
+ trajectoryGroup_.atomCount(),
+ fr->natoms);
GMX_THROW(InconsistentInputError(message));
}
fr->bIndex = TRUE;
// Add common file name arguments.
options->addOption(FileNameOption("f")
- .filetype(eftTrajectory)
+ .filetype(OptionFileType::Trajectory)
.inputFile()
.store(&impl_->trjfile_)
.defaultBasename("traj")
.description("Input trajectory or single configuration"));
options->addOption(FileNameOption("s")
- .filetype(eftTopology)
+ .filetype(OptionFileType::Topology)
.inputFile()
.store(&impl_->topfile_)
.defaultBasename("topol")
if (impl_->bStartTimeSet_)
{
- setTimeValue(TBEGIN, impl_->startTime_);
+ setTimeValue(TimeControl::Begin, impl_->startTime_);
}
if (impl_->bEndTimeSet_)
{
- setTimeValue(TEND, impl_->endTime_);
+ setTimeValue(TimeControl::End, impl_->endTime_);
}
if (impl_->bDeltaTimeSet_)
{
- setTimeValue(TDELTA, impl_->deltaTime_);
+ setTimeValue(TimeControl::Delta, impl_->deltaTime_);
}
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
- * Copyright (c) 2015,2016,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TRAJECTORYANALYSIS_RUNNERCOMMON_H
#define GMX_TRAJECTORYANALYSIS_RUNNERCOMMON_H
-#include "gromacs/utility/classhelpers.h"
+#include <memory>
struct t_trxframe;
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2010,2012,2013,2014,2015 by the GROMACS development team.
-# Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
distance.cpp
extract_cluster.cpp
freevolume.cpp
+ msd.cpp
pairdist.cpp
rdf.cpp
sasa.cpp
)
gmx_register_gtest_test(TrajectoryAnalysisUnitTests trajectoryanalysis-test SLOW_TEST)
target_link_libraries(trajectoryanalysis-test PRIVATE analysisdata-test-shared)
+target_link_libraries(trajectoryanalysis-test PRIVATE common)
add_executable(test_selection ${UNITTEST_TARGET_OPTIONS} test_selection.cpp)
-target_link_libraries(test_selection PRIVATE libgromacs ${GMX_EXE_LINKER_FLAGS})
+target_link_libraries(test_selection PRIVATE
+ common
+ libgromacs
+ ${GMX_EXE_LINKER_FLAGS})
+# TODO: Explicitly link to module dependencies.
+target_link_libraries(test_selection PRIVATE legacy_modules)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
TEST_F(ConvertTrjModuleTest, WorksWithAtomsAndSelection)
{
- const char* const cmdline[] = { "convert-trj", "-atoms", "always-from-structure", "-select",
- "not resname = CO2" };
+ const char* const cmdline[] = {
+ "convert-trj", "-atoms", "always-from-structure", "-select", "not resname = CO2"
+ };
// TODO check output structures once this is supported.
setTopology("clustsize.tpr");
setInputFile("-f", "clustsize.pdb");
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
TEST_F(ExtractClusterModuleTest, WorksWithAtomSubset)
{
std::string realFileName = TestFileManager::getTestSpecificFileName("test.g96");
- const char* const cmdline[] = { "extract-cluster", "-o", realFileName.c_str(), "-select",
- "atomnr 1 2" };
+ const char* const cmdline[] = {
+ "extract-cluster", "-o", realFileName.c_str(), "-select", "atomnr 1 2"
+ };
runTest(CommandLine(cmdline));
compareFiles();
{
const char* const name = dataset->first.c_str();
AbstractAnalysisData& data = module.datasetFromName(name);
- AnalysisDataTestFixture::addReferenceCheckerModule(dataChecker, name, &data,
- dataset->second.tolerance);
+ AnalysisDataTestFixture::addReferenceCheckerModule(
+ dataChecker, name, &data, dataset->second.tolerance);
}
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TRAJECTORYANALYSIS_TESTS_MODULETEST_H
#define GMX_TRAJECTORYANALYSIS_TESTS_MODULETEST_H
+#include <memory>
+
#include <gtest/gtest.h>
#include "gromacs/trajectoryanalysis/analysismodule.h"
-#include "gromacs/utility/classhelpers.h"
#include "testutils/cmdlinetest.h"
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
/*! \internal \brief
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for functionality of the "msd" trajectory analysis module.
+ *
+ * \author Kevin Boyd <kevin44boyd@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+#include "gmxpre.h"
+
+#include "gromacs/trajectoryanalysis/modules/msd.h"
+
+#include <gtest/gtest.h>
+
+#include "gromacs/gmxpreprocess/grompp.h"
+#include "gromacs/utility/path.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/textstream.h"
+#include "gromacs/utility/textwriter.h"
+
+#include "testutils/cmdlinetest.h"
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+#include "testutils/testfilemanager.h"
+#include "testutils/textblockmatchers.h"
+
+#include "moduletest.h"
+
+namespace gmx::test
+{
+
+namespace
+{
+
+using gmx::test::CommandLine;
+
+/*! \brief Returns whether or not we care about a header line in an xvg file, for matching purposes.
+ *
+ * \todo This is mostly taken from xvgtest.cpp. We could probably create some modular checker
+ * functionality where each line is compared against a set of subcheckers automatically. Then we
+ * could build matchers like this out of the modular components.
+ */
+bool isRelevantXvgHeader(const std::string& line)
+{
+ return startsWith(line, "@")
+ && (contains(line, " title ") || contains(line, " subtitle ") || contains(line, " label ")
+ || contains(line, "@TYPE ") || contains(line, " legend \""));
+}
+
+//! Helper function to check a single xvg value in a sequence.
+void checkXvgDataPoint(TestReferenceChecker* checker, const std::string& value)
+{
+ checker->checkRealFromString(value, nullptr);
+}
+
+/*! \brief MsdMatcher is effectively an extension of XvgMatcher for gmx msd results.
+ *
+ * In addition to the usual fields XvgMatcher checks, MsdMatcher checks for properly reported
+ * diffusion coefficients.
+ */
+class MsdMatcher : public ITextBlockMatcher
+{
+public:
+ MsdMatcher() = default;
+
+ void checkStream(TextInputStream* stream, TestReferenceChecker* checker) override
+ {
+ checker->setDefaultTolerance(
+ gmx::test::FloatingPointTolerance(gmx::test::absoluteTolerance(1.0e-5)));
+ TestReferenceChecker dCoefficientChecker(
+ checker->checkCompound("XvgLegend", "DiffusionCoefficient"));
+ TestReferenceChecker legendChecker(checker->checkCompound("XvgLegend", "Legend"));
+ TestReferenceChecker dataChecker(checker->checkCompound("XvgData", "Data"));
+ std::string line;
+ int rowCount = 0;
+ while (stream->readLine(&line))
+ {
+ // Legend and titles.
+ if (isRelevantXvgHeader(line))
+ {
+ legendChecker.checkString(stripString(line.substr(1)), nullptr);
+ continue;
+ }
+ // All other comment lines we don't care about.
+ if (startsWith(line, "#") || startsWith(line, "@"))
+ {
+ continue;
+ }
+ // Actual data.
+ const std::vector<std::string> columns = splitString(line);
+ const std::string id = formatString("Row%d", rowCount);
+ dataChecker.checkSequence(columns.begin(), columns.end(), id.c_str(), &checkXvgDataPoint);
+ rowCount++;
+ }
+ }
+};
+
+class MsdMatch : public ITextBlockMatcherSettings
+{
+public:
+ [[nodiscard]] TextBlockMatcherPointer createMatcher() const override
+ {
+ return std::make_unique<MsdMatcher>();
+ }
+};
+
+class MsdModuleTest : public gmx::test::TrajectoryAnalysisModuleTestFixture<gmx::analysismodules::MsdInfo>
+{
+public:
+ MsdModuleTest() { setOutputFile("-o", "msd.xvg", MsdMatch()); }
+ // Creates a TPR for the given starting structure and topology. Builds an mdp in place prior
+ // to calling grompp. sets the -s input to the generated tpr
+ void createTpr(const std::string& structure, const std::string& topology, const std::string& index)
+ {
+ std::string tpr = fileManager().getTemporaryFilePath(".tpr");
+ std::string mdp = fileManager().getTemporaryFilePath(".mdp");
+ std::string mdpFileContents = gmx::formatString(
+ "cutoff-scheme = verlet\n"
+ "rcoulomb = 0.85\n"
+ "rvdw = 0.85\n"
+ "rlist = 0.85\n");
+ gmx::TextWriter::writeFileFromString(mdp, mdpFileContents);
+
+ // Prepare a .tpr file
+ CommandLine caller;
+ const auto* simDB = gmx::test::TestFileManager::getTestSimulationDatabaseDirectory();
+ caller.append("grompp");
+ caller.addOption("-maxwarn", 0);
+ caller.addOption("-f", mdp.c_str());
+ std::string gro = gmx::Path::join(simDB, structure);
+ caller.addOption("-c", gro.c_str());
+ std::string top = gmx::Path::join(simDB, topology);
+ caller.addOption("-p", top.c_str());
+ std::string ndx = gmx::Path::join(simDB, index);
+ caller.addOption("-n", ndx.c_str());
+ caller.addOption("-o", tpr.c_str());
+ ASSERT_EQ(0, gmx_grompp(caller.argc(), caller.argv()));
+
+ // setInputFile() doesn't like the temporary tpr path.
+ CommandLine& cmdline = commandLine();
+ cmdline.addOption("-s", tpr.c_str());
+ }
+
+ // Convenience function to set input trajectory, tpr, and index, if all of the input files
+ // share a common prefix.
+ void setAllInputs(const std::string& prefix)
+ {
+ setInputFile("-f", prefix + ".xtc");
+ setInputFile("-n", prefix + ".ndx");
+ createTpr(prefix + ".gro", prefix + ".top", prefix + ".ndx");
+ }
+};
+
+// ----------------------------------------------
+// These tests check the basic MSD and diffusion coefficient reporting capabilities on toy systems.
+// Trestart is set to larger than the size of the trajectory so that all frames are only compared
+// against the first frame and diffusion coefficients can be predicted exactly.
+// ----------------------------------------------
+
+// for 3D, (8 + 4 + 0) / 3 should yield 4 cm^2 / s
+TEST_F(MsdModuleTest, threeDimensionalDiffusion)
+{
+ setInputFile("-f", "msd_traj.xtc");
+ setInputFile("-s", "msd_coords.gro");
+ setInputFile("-n", "msd.ndx");
+ const char* const cmdline[] = {
+ "-trestart",
+ "200",
+ "-sel",
+ "0",
+ };
+ runTest(CommandLine(cmdline));
+}
+
+// for lateral z, (8 + 4) / 2 should yield 6 cm^2 /s
+TEST_F(MsdModuleTest, twoDimensionalDiffusion)
+{
+ setInputFile("-f", "msd_traj.xtc");
+ setInputFile("-s", "msd_coords.gro");
+ setInputFile("-n", "msd.ndx");
+ const char* const cmdline[] = { "-trestart", "200", "-lateral", "z", "-sel", "0" };
+ runTest(CommandLine(cmdline));
+}
+
+// for type x, should yield 8 cm^2 / s
+TEST_F(MsdModuleTest, oneDimensionalDiffusion)
+{
+ setInputFile("-f", "msd_traj.xtc");
+ setInputFile("-s", "msd_coords.gro");
+ setInputFile("-n", "msd.ndx");
+ const char* const cmdline[] = { "-trestart", "200", "-type", "x", "-sel", "0" };
+ runTest(CommandLine(cmdline));
+}
+
+// -------------------------------------------------------------------------
+// These tests operate on a more realistic trajectory, with a solvated protein,
+// with 20 frames at a 2 ps dt. Note that this box is also non-square, so we're validating
+// non-trivial pbc removal.
+
+// Group 1 = protein, 2 = all waters, 3 = a subset of 6 water molecules
+// ------------------------------------------------------------------------
+TEST_F(MsdModuleTest, multipleGroupsWork)
+{
+ setAllInputs("alanine_vsite_solvated");
+ // Restart every frame, select protein and water separately. Note that the reported diffusion
+ // coefficient for protein is not well-sampled and doesn't correspond to anything physical.
+ const char* const cmdline[] = { "-trestart", "2", "-sel", "1;2" };
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(MsdModuleTest, trestartLessThanDt)
+{
+ setAllInputs("alanine_vsite_solvated");
+ const char* const cmdline[] = { "-trestart", "1", "-sel", "2" };
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(MsdModuleTest, trestartGreaterThanDt)
+{
+ setAllInputs("alanine_vsite_solvated");
+ const char* const cmdline[] = { "-trestart", "10", "-sel", "2" };
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(MsdModuleTest, molTest)
+{
+ setAllInputs("alanine_vsite_solvated");
+ setOutputFile("-mol", "diff_mol.xvg", MsdMatch());
+ const char* const cmdline[] = { "-trestart", "10", "-sel", "3" };
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(MsdModuleTest, beginFit)
+{
+ setAllInputs("alanine_vsite_solvated");
+ const char* const cmdline[] = { "-trestart", "2", "-sel", "3", "-beginfit", "20" };
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(MsdModuleTest, endFit)
+{
+ setAllInputs("alanine_vsite_solvated");
+ const char* const cmdline[] = { "-trestart", "2", "-sel", "3", "-endfit", "25" };
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(MsdModuleTest, notEnoughPointsForFitErrorEstimate)
+{
+ setAllInputs("alanine_vsite_solvated");
+ const char* const cmdline[] = { "-trestart", "2", "-beginfit", "5", "-endfit",
+ "9", "-lateral", "x", "-sel", "all" };
+ runTest(CommandLine(cmdline));
+}
+
+} // namespace
+
+} // namespace gmx::test
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
TEST_F(RdfModuleTest, SelectionsSolelyFromIndexFileWork)
{
- const char* const cmdline[] = { "rdf", "-bin", "0.05",
+ const char* const cmdline[] = { "rdf",
+ "-bin",
+ "0.05",
// Use selection that names a group in the index file
- "-ref", "name_OW",
+ "-ref",
+ "name_OW",
// Use selections that name groups in the index file
- "-sel", "name_OW", "not_name_OW" };
+ "-sel",
+ "name_OW",
+ "not_name_OW" };
// Note not supplying a topology file to -s
setTrajectory("spc216.gro");
setInputFile("-n", "index.ndx");
TEST_F(RdfModuleTest, SelectionsFromBothTopologyFileAndIndexFileWork)
{
- const char* const cmdline[] = { "rdf", "-bin", "0.05",
+ const char* const cmdline[] = { "rdf",
+ "-bin",
+ "0.05",
// Use selection whose parsing requires topology file
- "-ref", "name OW",
+ "-ref",
+ "name OW",
// Use selections that name groups in the index file
- "-sel", "name_OW", "not_name_OW" };
+ "-sel",
+ "name_OW",
+ "not_name_OW" };
// Note supplying a topology file to -s
setTopology("spc216.gro");
setInputFile("-n", "index.ndx");
--- /dev/null
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+ <Real>3.000</Real>
<Real>0.072</Real>
</Sequence>
<Sequence Name="Row4">
<Int Name="Length">2</Int>
- <Real>4</Real>
+ <Real>4.000</Real>
<Real>0.096</Real>
</Sequence>
<Sequence Name="Row5">
<Int Name="Length">2</Int>
- <Real>5</Real>
+ <Real>5.000</Real>
<Real>0.12</Real>
</Sequence>
<Sequence Name="Row6">
<Int Name="Length">2</Int>
- <Real>6</Real>
+ <Real>6.000</Real>
<Real>0.144</Real>
</Sequence>
<Sequence Name="Row7">
<Int Name="Length">2</Int>
- <Real>7</Real>
+ <Real>7.000</Real>
<Real>0.168</Real>
</Sequence>
<Sequence Name="Row8">
<Int Name="Length">2</Int>
- <Real>8</Real>
+ <Real>8.000</Real>
<Real>0.192</Real>
</Sequence>
<Sequence Name="Row9">
<Int Name="Length">2</Int>
- <Real>9</Real>
+ <Real>9.000</Real>
<Real>0.216</Real>
</Sequence>
</XvgData>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
TEST_F(SelectModuleTest, WritesResidueIndices)
{
- const char* const cmdline[] = { "select", "-select", "res_com of resname RA RD", "-resnr",
- "index" };
+ const char* const cmdline[] = {
+ "select", "-select", "res_com of resname RA RD", "-resnr", "index"
+ };
setTopology("simple.gro");
includeDataset("index");
runTest(CommandLine(cmdline));
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <gtest/gtest.h>
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
for (int i = 0; i < count; ++i)
{
rvec x;
- real radius;
+ real radius = 0;
generateRandomPosition(x, &radius);
addSphere(x[XX], x[YY], x[ZZ], radius);
}
gmx::SurfaceAreaCalculator calculator;
calculator.setDotCount(ndots);
calculator.setRadii(radius_);
- calculator.calculate(as_rvec_array(x_.data()), bPBC ? &pbc : nullptr, index_.size(),
- index_.data(), flags, &area_, &volume_, &atomArea_, &dots_, &dotCount_);
+ calculator.calculate(as_rvec_array(x_.data()),
+ bPBC ? &pbc : nullptr,
+ index_.size(),
+ index_.data(),
+ flags,
+ &area_,
+ &volume_,
+ &atomArea_,
+ &dots_,
+ &dotCount_);
}
real resultArea() const { return area_; }
real resultVolume() const { return volume_; }
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
for (size_t g = 0; g < selections_.size(); ++g)
{
const Selection& sel = selections_[g];
- int n;
fprintf(stderr, " Atoms (%d pcs):", sel.atomCount());
- n = sel.atomCount();
+ int n = sel.atomCount();
if (nmaxind_ >= 0 && n > nmaxind_)
{
n = nmaxind_;
for (int i = 0; i < n; ++i)
{
const SelectionPosition& p = sel.position(i);
- fprintf(stderr, " (%.2f,%.2f,%.2f) r=%d, m=%d, n=%d\n", p.x()[XX], p.x()[YY],
- p.x()[ZZ], p.refId(), p.mappedId(), p.atomCount());
+ fprintf(stderr,
+ " (%.2f,%.2f,%.2f) r=%d, m=%d, n=%d\n",
+ p.x()[XX],
+ p.x()[YY],
+ p.x()[ZZ],
+ p.refId(),
+ p.mappedId(),
+ p.atomCount());
}
if (n < sel.posCount())
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
EXPECT_TRUE(atoms2);
// Must be different pointer to a deep copy.
EXPECT_NE(atoms1.get(), atoms2.get());
- auto atoms = topInfo.atoms();
+ const auto* atoms = topInfo.atoms();
// Must be a pointer to a different instance.
EXPECT_NE(atoms1.get(), atoms);
EXPECT_NE(atoms2.get(), atoms);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
// t_atoms that we'd keep, which we currently can't do.
// TODO Once there are fewer callers of the file-reading
// functionality, make them read directly into std::vector.
- rvec *x, *v;
+ rvec *x = nullptr, *v = nullptr;
readConfAndTopology(filename.c_str(), &bTop_, mtop_.get(), &pbcType_, &x, &v, boxtop_);
xtop_.assign(x, x + mtop_->natoms);
vtop_.assign(v, v + mtop_->natoms);
AtomsDataPtr atoms(new t_atoms);
if (top_.hasTopology())
{
- *atoms = gmx_mtop_global_atoms(top_.mtop());
+ *atoms = gmx_mtop_global_atoms(*top_.mtop());
}
else
{
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* compiler-specific attributes, and ::GMX_UNUSED_VALUE and ::GMX_IGNORE_RETURN_VALUE
* for handling warnings about unused values.
*
- * The header classhelpers.h implements a gmx::PrivateImplPointer template for easily
- * writing classes that use the private implementation idiom. This header also
- * declares ::GMX_DISALLOW_COPY_AND_ASSIGN and ::GMX_DISALLOW_ASSIGN macros for
- * class declarations.
+ * The header classhelpers.h declares ::GMX_DISALLOW_COPY_AND_ASSIGN,
+ * ::GMX_DISALLOW_COPY_MOVE_AND_ASSIGN, ::GMX_DISALLOW_ASSIGN, and
+ * ::GMX_DEFAULT_CONSTRUCTORS macros for class declarations.
*
* The header flags.h implements a gmx::FlagsTemplate template for better type
* safety when using bit flag fields.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+add_library(utility INTERFACE)
+
file(GLOB UTILITY_SOURCES *.cpp)
if (GMX_GPU_CUDA)
gmx_add_libgromacs_sources(cuda_version_information.cu)
endif()
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${UTILITY_SOURCES} PARENT_SCOPE)
-# TODO: (https://gitlab.com/gromacs/gromacs/-/issues/988) Find a new convention for defining public API.
-install(FILES
- basedefinitions.h
- current_function.h
- gmxassert.h
- real.h
- DESTINATION include/gromacs/utility)
-
if(GMX_INSTALL_LEGACY_API)
install(FILES
- arrayref.h
baseversion.h
classhelpers.h
enumerationhelpers.h
- exceptions.h
- listoflists.h
fileptr.h
futil.h
flags.h
DESTINATION include/gromacs/utility)
endif()
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(utility PUBLIC
+target_include_directories(utility INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(utility PUBLIC
+target_link_libraries(utility INTERFACE
+ legacy_api
+ )
+
+# TODO: when utility is an OBJECT target
+#target_link_libraries(utility PUBLIC legacy_api)
+#target_link_libraries(utility PRIVATE common)
+
+# Source files have the following private module dependencies.
+# TODO: Explicitly link specific modules.
+#target_link_libraries(utility PRIVATE legacy_modules)
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \note This is an internal routine that should only be called from
* gmx::alignedMalloc(). Just like system-provided routines, it provides
* memory that is aligned - but not padded.
+ *
+ * \note This functionality is provided by C++17 std::aligned_alloc,
+ * and it would be preferable to use that instead, however it is not
+ * yet widely enough available to depend on. See #3968.
*/
gmx_unused void* alignedMallocGeneric(std::size_t bytes, std::size_t alignment)
{
//! Implement malloc of \c bytes of memory, aligned to \c alignment.
void* mallocImpl(std::size_t bytes, std::size_t alignment)
{
- void* p;
+ void* p = nullptr;
#if HAVE__MM_MALLOC
p = _mm_malloc(bytes, alignment);
//! \todo Move this function into sysinfo.cpp where other OS-specific code/includes live
static std::size_t getPageSize()
{
- long pageSize;
+ long pageSize = 0;
#if GMX_NATIVE_WINDOWS
SYSTEM_INFO si;
GetNativeSystemInfo(&si);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2017,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
/*! \libinternal \brief
- * Represents a dynamically typed value of an arbitrary type.
+ * Represents a dynamically typed value of an arbitrary type - deprecated.
*
- * To create a any, either initialize it as empty, or with the create()
+ * New uses of this type should be avoided - prefer std::any or
+ * std::variant.
+ *
+ * To create an Any, either initialize it as empty, or with the create()
* method (or the equivalent constructor, if the type parameter can be deduced
* and is clear to the reader from the context).
*
*
* This provides essentially the same functionality as boost::any.
*
+ * It would be good to replace the current uses of this type with
+ * std::any or std::variant, but see
+ * https://gitlab.com/gromacs/gromacs/-/issues/3951 for discussion
+ * about the things that have blocked such attempts.
+ *
* \ingroup module_utility
*/
class Any
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#if !GMX_MPI
return false;
#else
- int n;
+ int n = 0;
MPI_Initialized(&n);
return n != 0;
return 1;
}
# endif
- int i;
+ int i = 0;
(void)MPI_Comm_size(MPI_COMM_WORLD, &i);
return i;
#endif
return 0;
}
# endif
- int i;
+ int i = 0;
(void)MPI_Comm_rank(MPI_COMM_WORLD, &i);
return i;
#endif
static int mpi_hostname_hash()
{
- int hash_int;
+ int hash_int = 0;
#if GMX_LIB_MPI
int resultlen;
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2012,2014,2015,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gromacs/utility/baseversion_gen.h"
-const char _gmx_ver_string[] = "@GMX_VERSION_STRING_FULL@";
-const char _gmx_full_git_hash[] = "@GMX_VERSION_FULL_HASH@";
-const char _gmx_central_base_hash[] = "@GMX_VERSION_CENTRAL_BASE_HASH@";
+const char gmx_ver_string[] = "@GMX_VERSION_STRING_FULL@";
+const char gmx_full_git_hash[] = "@GMX_VERSION_FULL_HASH@";
+const char gmx_central_base_hash[] = "@GMX_VERSION_CENTRAL_BASE_HASH@";
const char gmxSourceDoiString[] = "@GMX_SOURCE_DOI@";
const char gmxReleaseSourceFileChecksum[] = "@GMX_RELEASE_SOURCE_FILE_CHECKSUM@";
const char gmxCurrentSourceFileChecksum[] = "@GMX_CURRENT_SOURCE_FILE_CHECKSUM@";
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const char* gmx_version()
{
- return _gmx_ver_string;
+ return gmx_ver_string;
}
const char* gmx_version_git_full_hash()
{
- return _gmx_full_git_hash;
+ return gmx_full_git_hash;
}
const char* gmx_version_git_central_base_hash()
{
- return _gmx_central_base_hash;
+ return gmx_central_base_hash;
}
const char* gmxDOI()
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2010,2012,2013,2014,2015 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! \{
//! Version string, containing the version, date, and abbreviated hash.
-extern const char _gmx_ver_string[];
+extern const char gmx_ver_string[];
//! Full git hash of the latest commit.
-extern const char _gmx_full_git_hash[];
+extern const char gmx_full_git_hash[];
//! Full git hash of the latest commit in a central \Gromacs repository.
-extern const char _gmx_central_base_hash[];
+extern const char gmx_central_base_hash[];
/*! \brief
* DOI string for the \Gromacs source code populated by CMake.
*
"Aldert van Buuren",
"Rudi van Drunen",
"Anton Feenstra",
+ "Gaurav Garg",
"Gilles Gouaillardet",
"Alan Gray",
"Gerrit Groenhof",
static const char* const CopyrightText[] = {
"Copyright (c) 1991-2000, University of Groningen, The Netherlands.",
"Copyright (c) 2001-2019, The GROMACS development team at",
- "Uppsala University, Stockholm University and", "the Royal Institute of Technology, Sweden.",
+ "Uppsala University, Stockholm University and",
+ "the Royal Institute of Technology, Sweden.",
"check out http://www.gromacs.org for more information."
};
#if GMX_THREAD_MPI
writer->writeLine("MPI library: thread_mpi");
#elif GMX_MPI
+# if HAVE_CUDA_AWARE_MPI
+ writer->writeLine("MPI library: MPI (CUDA-aware)");
+# else
writer->writeLine("MPI library: MPI");
+# endif
#else
writer->writeLine("MPI library: none");
#endif
#if HAVE_EXTRAE
unsigned major, minor, revision;
Extrae_get_version(&major, &minor, &revision);
- writer->writeLine(formatString("Tracing support: enabled. Using Extrae-%d.%d.%d", major,
- minor, revision));
+ writer->writeLine(formatString(
+ "Tracing support: enabled. Using Extrae-%d.%d.%d", major, minor, revision));
#else
writer->writeLine("Tracing support: disabled");
#endif
* them. Can wait for later, as the master branch has ready code to do all
* that. */
writer->writeLine(formatString("C compiler: %s", BUILD_C_COMPILER));
- writer->writeLine(formatString("C compiler flags: %s %s", BUILD_CFLAGS,
- CMAKE_BUILD_CONFIGURATION_C_FLAGS));
+ writer->writeLine(formatString(
+ "C compiler flags: %s %s", BUILD_CFLAGS, CMAKE_BUILD_CONFIGURATION_C_FLAGS));
writer->writeLine(formatString("C++ compiler: %s", BUILD_CXX_COMPILER));
- writer->writeLine(formatString("C++ compiler flags: %s %s", BUILD_CXXFLAGS,
- CMAKE_BUILD_CONFIGURATION_CXX_FLAGS));
+ writer->writeLine(formatString(
+ "C++ compiler flags: %s %s", BUILD_CXXFLAGS, CMAKE_BUILD_CONFIGURATION_CXX_FLAGS));
#ifdef HAVE_LIBMKL
/* MKL might be used for LAPACK/BLAS even if FFTs use FFTW, so keep it separate */
- writer->writeLine(formatString("Linked with Intel MKL version %d.%d.%d.", __INTEL_MKL__,
- __INTEL_MKL_MINOR__, __INTEL_MKL_UPDATE__));
+ writer->writeLine(formatString(
+ "Linked with Intel MKL version %d.%d.%d.", __INTEL_MKL__, __INTEL_MKL_MINOR__, __INTEL_MKL_UPDATE__));
#endif
#if GMX_GPU_OPENCL
writer->writeLine(formatString("OpenCL include dir: %s", OPENCL_INCLUDE_DIR));
#endif
#if GMX_GPU_CUDA
writer->writeLine(formatString("CUDA compiler: %s", CUDA_COMPILER_INFO));
- writer->writeLine(formatString("CUDA compiler flags:%s %s", CUDA_COMPILER_FLAGS,
- CMAKE_BUILD_CONFIGURATION_CXX_FLAGS));
+ writer->writeLine(formatString(
+ "CUDA compiler flags:%s %s", CUDA_COMPILER_FLAGS, CMAKE_BUILD_CONFIGURATION_CXX_FLAGS));
writer->writeLine("CUDA driver: " + gmx::getCudaDriverVersionString());
writer->writeLine("CUDA runtime: " + gmx::getCudaRuntimeVersionString());
#endif
// necessary to read stuff above the copyright notice.
// The line above the copyright notice puts the copyright notice is
// context, though.
- writer->writeLine(formatString("%sGROMACS: %s, version %s%s%s", prefix, name,
- gmx_version(), precisionString, suffix));
+ writer->writeLine(formatString(
+ "%sGROMACS: %s, version %s%s%s", prefix, name, gmx_version(), precisionString, suffix));
}
const char* const binaryPath = programContext.fullBinaryPath();
if (!gmx::isNullOrEmpty(binaryPath))
const gmx::InstallationPrefixInfo installPrefix = programContext.installationPrefix();
if (!gmx::isNullOrEmpty(installPrefix.path))
{
- writer->writeLine(formatString("%sData prefix: %s%s%s", prefix, installPrefix.path,
- installPrefix.bSourceLayout ? " (source tree)" : "", suffix));
+ writer->writeLine(formatString("%sData prefix: %s%s%s",
+ prefix,
+ installPrefix.path,
+ installPrefix.bSourceLayout ? " (source tree)" : "",
+ suffix));
}
const std::string workingDir = Path::getWorkingDirectory();
if (!workingDir.empty())
const char* const commandLine = programContext.commandLine();
if (!gmx::isNullOrEmpty(commandLine))
{
- writer->writeLine(formatString("%sCommand line:%s\n%s %s%s", prefix, suffix, prefix,
- commandLine, suffix));
+ writer->writeLine(formatString(
+ "%sCommand line:%s\n%s %s%s", prefix, suffix, prefix, commandLine, suffix));
}
if (settings.bExtendedInfo_)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
inline static bool bitmask_is_disjoint(gmx_bitmask_t a, gmx_bitmask_t b)
{
- int i;
bool r = true;
- for (i = 0; i < BITMASK_ALEN; i++)
+ for (int i = 0; i < BITMASK_ALEN; i++)
{
r = r && ((a[i] & b[i]) == 0U);
}
inline static bool bitmask_is_equal(gmx_bitmask_t a, gmx_bitmask_t b)
{
- int i;
bool r = true;
- for (i = 0; i < BITMASK_ALEN; i++)
+ for (int i = 0; i < BITMASK_ALEN; i++)
{
r = r && (a[i] == b[i]);
}
inline static bool bitmask_is_zero(gmx_bitmask_t m)
{
- int i;
bool r = true;
- for (i = 0; i < BITMASK_ALEN; i++)
+ for (int i = 0; i < BITMASK_ALEN; i++)
{
r = r && (m[i] == 0U);
}
inline static void bitmask_union(gmx_bitmask_t* a, gmx_bitmask_t b)
{
- int i;
- for (i = 0; i < BITMASK_ALEN; i++)
+ for (int i = 0; i < BITMASK_ALEN; i++)
{
(*a)[i] |= b[i];
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_UTILITY_CLASSHELPERS_H
#define GMX_UTILITY_CLASSHELPERS_H
-#include <memory>
-
namespace gmx
{
#endif
//clang-format on
-/*! \brief
- * Helper class to manage a pointer to a private implementation class.
- *
- * This helper provides the following benefits (all but the last could also be
- * achieved with std::unique_ptr):
- * - Automatic memory management: the implementation pointer is freed in
- * the destructor automatically. If the destructor is not declared or is
- * defined inline in the header file, a compilation error occurs instead
- * of a memory leak or undefined behavior.
- * - Exception safety in constructors: the implementation pointer is freed
- * correctly even if the constructor of the containing class throws after
- * the implementation class is constructed.
- * - Copy and/or assignment is automatically disallowed if explicit copy
- * constructor and/or assignment operator is not provided.
- * - Compiler helps to manage const-correctness: in const methods, it is not
- * possible to change the implementation class.
- *
- * Move construction and assignment are also disallowed, but can be enabled by
- * providing explicit move constructor and/or assignment.
- *
- * Intended use:
- * \code
- // In exampleclass.h
- class ExampleClass
- {
- public:
- ExampleClass();
- ~ExampleClass(); // Must be defined, must not be defined inline
-
- // <...>
-
- private:
- class Impl;
-
- PrivateImplPointer<Impl> impl_;
- };
-
- // In exampleclass.cpp
-
- // <definition of ExampleClass::Impl>
-
- ExampleClass::ExampleClass()
- : impl_(new Impl)
- {
- }
-
- ExampleClass::~ExampleClass()
- {
- }
- \endcode
- *
- * Note that ExampleClass::~ExampleClass cannot be declared inline (or
- * generated by the compiler) because the implementation of impl_
- * requires that ExampleClass::Impl be known in size, whereas it has
- * only been forward declared. Only the translation unit where
- * ExampleClass::Impl is declared can define the destructor for
- * ExampleClass (which may be defaulted).
- *
- * \inlibraryapi
- * \ingroup module_utility
- */
-template<class Impl>
-class PrivateImplPointer
-{
-public:
- //! Allow implicit initialization from nullptr to support comparison.
- PrivateImplPointer(std::nullptr_t) : ptr_(nullptr) {}
- //! Initialize with the given implementation class.
- explicit PrivateImplPointer(Impl* ptr) : ptr_(ptr) {}
- //! \cond
- // Explicitly declared to work around MSVC problems.
- PrivateImplPointer(PrivateImplPointer&& other) noexcept : ptr_(std::move(other.ptr_)) {}
- PrivateImplPointer& operator=(PrivateImplPointer&& other) noexcept
- {
- ptr_ = std::move(other.ptr_);
- return *this;
- }
- //! \endcond
-
- /*! \brief
- * Sets a new implementation class and destructs the previous one.
- *
- * Needed, e.g., to implement lazily initializable or copy-assignable
- * classes.
- */
- void reset(Impl* ptr) { ptr_.reset(ptr); }
- //! Access the raw pointer.
- Impl* get() { return ptr_.get(); }
- //! Access the implementation class as with a raw pointer.
- Impl* operator->() { return ptr_.get(); }
- //! Access the implementation class as with a raw pointer.
- Impl& operator*() { return *ptr_; }
- //! Access the implementation class as with a raw pointer.
- const Impl* operator->() const { return ptr_.get(); }
- //! Access the implementation class as with a raw pointer.
- const Impl& operator*() const { return *ptr_; }
-
- //! Allows testing whether the implementation is initialized.
- explicit operator bool() const { return ptr_ != nullptr; }
-
- //! Tests for equality (mainly useful against nullptr).
- bool operator==(const PrivateImplPointer& other) const { return ptr_ == other.ptr_; }
- //! Tests for inequality (mainly useful against nullptr).
- bool operator!=(const PrivateImplPointer& other) const { return ptr_ != other.ptr_; }
-
-private:
- std::unique_ptr<Impl> ptr_;
-
- // Copy construction and assignment disabled by the unique_ptr member.
-};
-
} // namespace gmx
#endif
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
+#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
//! Compares two doubles and prints differences.
void cmp_double(FILE* fp, const char* s, int index, double i1, double i2, double ftol, double abstol);
+//! Compare two enums of generic type and print differences.
+template<typename EnumType>
+void cmpEnum(FILE* fp, const char* s, EnumType value1, EnumType value2)
+{
+ if (value1 != value2)
+ {
+ fprintf(fp, "%s (", s);
+ fprintf(fp, "%s", enumValueToString(value1));
+ fprintf(fp, " - ");
+ fprintf(fp, "%s", enumValueToString(value2));
+ fprintf(fp, ")\n");
+ }
+}
+
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{ "Disturb the Peace of a John Q Citizen", "Urban Dance Squad" },
{ "Wicky-wicky Wa-wild West", "Will Smith" },
{ "This is Tense !", "Star Wars Episode I The Phantom Menace" },
- { "Fly to the Court of England and Unfold",
- "Macbeth, Act 3, Scene 6, William Shakespeare" },
+ { "Fly to the Court of England and Unfold", "Macbeth, Act 3, Scene 6, William Shakespeare" },
{ "Why, how now, Claudio ! Whence Comes this Restraint ?",
"Lucio in Measure for measure, Act 1, Scene 4, William Shakespeare" },
{ "In the End Science Comes Down to Praying", "P. v.d. Berg" },
{ "Nobody Never Learnt No-Nothing from No History", "Gogol Bordello" },
{ "I'd be Safe and Warm if I was in L.A.", "The Mamas and the Papas" },
{ "It's Unacceptable That Chocolate Makes You Fat", "MI 3" },
- { "My Brothers are Protons (Protons!), My Sisters are Neurons (Neurons)",
- "Gogol Bordello" },
+ { "My Brothers are Protons (Protons!), My Sisters are Neurons (Neurons)", "Gogol Bordello" },
{ "Put Me Inside SSC, Let's Test Superstring Theory, Oh Yoi Yoi Accelerate the Protons",
"Gogol Bordello" },
{ "Do You Have Sex Maniacs or Schizophrenics or Astrophysicists in Your Family?",
{ "The scientific method is an integral part of human intelligence, and when it has once "
"been set at work it can only be dismissed by dismissing the intelligence itself",
"George H. Mead" },
- { "Der Ball ist rund, das Spiel dauert 90 minuten, alles andere ist Theorie",
- "Lola rennt" },
+ { "Der Ball ist rund, das Spiel dauert 90 minuten, alles andere ist Theorie", "Lola rennt" },
{ "Life in the streets is not easy", "Marky Mark" },
{ "How will I know it's working right?", "MGMT" },
{ "There was no preconception on what to do", "Daft Punk" },
{ "All sorts of things can happen when you're open to new ideas and playing around with "
"things.",
"Stephanie Kwolek, inventor of Kevlar" },
- { "As always in life, people want a simple answer... and it's always wrong.",
- "Marie Daly" },
+ { "As always in life, people want a simple answer... and it's always wrong.", "Marie Daly" },
{ "For a research worker the unforgotten moments of his life are those rare ones which "
"come after years of plodding work, when the veil over natures secret seems suddenly to "
"lift & when what was dark & chaotic appears in a clear & beautiful light & pattern.",
"3-phosphoshikimate-carboxyvinyl transferase?' Shopkeeper: 'You mean Roundup?' "
"Scientist: 'Yeah, that's it. I can never remember that dang name!'",
"John Pickett" },
- { "It is not clear that intelligence has any long-term survival value.",
- "Stephen Hawking" },
+ { "It is not clear that intelligence has any long-term survival value.", "Stephen Hawking" },
{ "The greatest shortcoming of the human race is our inability to understand the "
"exponential function.",
"Albert Bartlett" },
"married, it never occurred to him to verify this statement by examining his wives' "
"mouths.",
"Bertrand Russell" },
- { "I had trouble with physics in college. When I signed up I thought it said psychics.",
- "Greg Tamblyn" },
{ "I don't believe in astrology; I'm a Sagittarian and we're skeptical.",
"Arthur C. Clarke" },
{ "I see they found out the universe is 80 million years older than we thought. It's also "
"attempted.",
"Anonymous" },
{ "If my PhD doesn't allow me to be right on the internet, what is it even good for?",
- "Martin Vögele" }
+ "Martin Vögele" },
+ { "A little less conversation, a little more action, please.", "Elvis Presley" },
+ { "Friends don't let friends use Berendsen!", "John Chodera (on Twitter)" }
};
if (beCool())
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int continuing(char* s)
{
- int sl;
assert(s);
rtrim(s);
- sl = strlen(s);
+ int sl = strlen(s);
if ((sl > 0) && (s[sl - 1] == CONTINUE))
{
s[sl - 1] = 0;
char* fgets2(char* line, int n, FILE* stream)
{
- char* c;
+ char* c = nullptr;
if (fgets(line, n, stream) == nullptr)
{
return nullptr;
gmx_fatal(FARGS,
"An input file contains a line longer than %d characters, while the buffer "
"passed to fgets2 has size %d. The line starts with: '%20.20s'",
- n, n, line);
+ n,
+ n,
+ line);
}
}
if ((c = strchr(line, '\r')) != nullptr)
void strip_comment(char* line)
{
- char* c;
+ char* c = nullptr;
if (!line)
{
void upstring(char* str)
{
- int i;
-
- for (i = 0; (i < static_cast<int>(strlen(str))); i++)
+ for (int i = 0; (i < static_cast<int>(strlen(str))); i++)
{
str[i] = toupper(str[i]);
}
void ltrim(char* str)
{
- int i, c;
-
if (nullptr == str)
{
return;
}
- c = 0;
+ int c = 0;
while (('\0' != str[c]) && isspace(str[c]))
{
c++;
}
if (c > 0)
{
- for (i = c; ('\0' != str[i]); i++)
+ int i = c;
+ for (; ('\0' != str[i]); i++)
{
str[i - c] = str[i];
}
void rtrim(char* str)
{
- int nul;
-
if (nullptr == str)
{
return;
}
- nul = strlen(str) - 1;
+ int nul = strlen(str) - 1;
while ((nul > 0) && ((str[nul] == ' ') || (str[nul] == '\t')))
{
str[nul] = '\0';
int gmx_strcasecmp_min(const char* str1, const char* str2)
{
- char ch1, ch2;
+ char ch1 = 0, ch2 = 0;
do
{
int gmx_strncasecmp_min(const char* str1, const char* str2, int n)
{
- char ch1, ch2;
- char *stri1, *stri2;
+ char ch1 = 0, ch2 = 0;
- stri1 = const_cast<char*>(str1);
- stri2 = const_cast<char*>(str2);
+ const char* stri1 = str1;
+ const char* stri2 = str2;
do
{
do
int gmx_strcasecmp(const char* str1, const char* str2)
{
- char ch1, ch2;
+ char ch1 = 0, ch2 = 0;
do
{
int gmx_strncasecmp(const char* str1, const char* str2, int n)
{
- char ch1, ch2;
+ char ch1 = 0, ch2 = 0;
if (n == 0)
{
char* gmx_strdup(const char* src)
{
- char* dest;
+ char* dest = nullptr;
auto length = strlen(src) + 1;
snew(dest, length);
char* gmx_strndup(const char* src, int n)
{
- int len;
- char* dest;
+ char* dest = nullptr;
- len = strlen(src);
+ int len = strlen(src);
if (len > n)
{
len = n;
unsigned int gmx_string_fullhash_func(const char* s, unsigned int hash_init)
{
- int c;
+ char c = 0;
while ((c = (*s++)) != '\0')
{
unsigned int gmx_string_hash_func(const char* s, unsigned int hash_init)
{
- int c;
+ int c = 0;
while ((c = toupper(*s++)) != '\0')
{
* since we have processed them above. */
if (*pattern == *str)
{
- int rc;
/* Match the suffix, and return if a match or an error */
- rc = gmx_wcmatch(pattern, str);
+ int rc = gmx_wcmatch(pattern, str);
if (rc != GMX_NO_WCMATCH)
{
return rc;
char* wrap_lines(const char* buf, int line_width, int indent, gmx_bool bIndentFirst)
{
- char* b2;
- int i, i0, i2, j, b2len, lspace = 0, l2space = 0;
- gmx_bool bFirst, bFitsOnLine;
+ int i = 0;
/* characters are copied from buf to b2 with possible spaces changed
* into newlines and extra space added for indentation.
* the current line (where it also won't fit, but looks better)
*/
- b2 = nullptr;
- b2len = strlen(buf) + 1 + indent;
+ char* b2 = nullptr;
+ int b2len = strlen(buf) + 1 + indent;
snew(b2, b2len);
- i0 = i2 = 0;
+ int i0 = 0;
+ int i2 = 0;
if (bIndentFirst)
{
for (i2 = 0; (i2 < indent); i2++)
b2[i2] = ' ';
}
}
- bFirst = TRUE;
+ bool bFirst = true;
do
{
- l2space = -1;
+ int lspace = 0;
+ int l2space = -1;
/* find the last space before end of line */
for (i = i0; ((i - i0 < line_width) || (l2space == -1)) && (buf[i]); i++)
{
b2len += indent;
srenew(b2, b2len);
/* add indentation after the newline */
- for (j = 0; (j < indent); j++)
+ for (int j = 0; (j < indent); j++)
{
b2[i2++] = ' ';
}
if (buf[i])
{
/* check if one word does not fit on the line */
- bFitsOnLine = (i - i0 <= line_width);
+ bool bFitsOnLine = (i - i0 <= line_width);
/* reset line counters to just after the space */
i0 = lspace + 1;
i2 = l2space + 1;
}
b2len += indent;
srenew(b2, b2len);
- for (j = 0; (j < indent); j++)
+ for (int j = 0; (j < indent); j++)
{
b2[i2++] = ' ';
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
if (!impl_)
{
- impl_.reset(new Impl());
+ impl_ = std::make_unique<Impl>();
}
impl_->envName_ = envVarName;
const char* const lib = getenv(envVarName);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
+#include <memory>
#include <string>
#include <vector>
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/fileptr.h"
namespace gmx
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
}
else
{
- GMX_THROW_WITH_ERRNO(FileIOError("Failed to list files in a directory"),
- "_findnext", errno);
+ GMX_THROW_WITH_ERRNO(
+ FileIOError("Failed to list files in a directory"), "_findnext", errno);
}
}
*filename = finddata.name;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_UTILITY_DIRECTORYENUMERATOR_H
#define GMX_UTILITY_DIRECTORYENUMERATOR_H
+#include <memory>
#include <string>
#include <vector>
-#include "gromacs/utility/classhelpers.h"
-
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* See file documentation for usage example.
*
+ * Note that if clang-tidy gives strange errors referring to the line
+ * number of the struct declaration, these likely refer to the
+ * compiler-generated constructors. Simplification of the calling code
+ * might eliminate that call and thus the clang-tidy error.
+ *
* \tparam EnumType The enum (class) type.
* \tparam DataType Type of the data stored in the array.
* \tparam ArraySize Size in entries of the array.
*/
-template<typename EnumType, // The enum (class) type.
- typename DataType, // Type of the data stored in the array.
- EnumType ArraySize = EnumType::Count // Size in entries of the array.
- >
-struct EnumerationArray final
+template<typename EnumType, typename DataType, EnumType ArraySize = EnumType::Count>
+struct EnumerationArray final // NOLINT
{
//! Convenience alias
using EnumerationWrapperType = EnumerationWrapper<EnumType, ArraySize>;
+ //! Convenience alias
+ using value_type = DataType;
+
/*! \brief Data for names.
*
* Data is kept public so we can use direct aggregate
//! Returns an object that provides iterators over the keys.
static constexpr EnumerationWrapperType keys() { return EnumerationWrapperType{}; }
//! Returns the size of the enumeration.
- static constexpr std::size_t size() { return std::size_t(ArraySize); }
+ constexpr std::size_t size() const { return std::size_t(ArraySize); }
/*!@{*/
//! Array access with asserts:
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2011-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "exceptions.h"
+#include "gromacs/utility/exceptions.h"
#include <cstring>
#include <stdexcept>
#include <typeinfo>
-#include "thread_mpi/system_error.h"
-
#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
std::fprintf(fp_, "%*sReason: %s\n", indent, "", std::strerror(errorNumber));
if (funcName != nullptr)
{
- std::fprintf(fp_, "%*s(call to %s() returned error code %d)\n", indent, "", funcName,
- errorNumber);
+ std::fprintf(fp_, "%*s(call to %s() returned error code %d)\n", indent, "", funcName, errorNumber);
}
}
if (errorNumber != nullptr && *errorNumber != 0)
{
const char* const* funcName = gmxEx->getInfo<ExceptionInfoApiFunction>();
- writer->writeErrNoInfo(*errorNumber, funcName != nullptr ? *funcName : nullptr,
- (indent + 1) * 2);
+ writer->writeErrNoInfo(
+ *errorNumber, funcName != nullptr ? *funcName : nullptr, (indent + 1) * 2);
bAnythingWritten = true;
}
{
title = getErrorCodeString(gmxEx->errorCode());
}
- else if (dynamic_cast<const tMPI::system_error*>(&ex) != nullptr)
- {
- title = "System error in thread synchronization";
- }
else if (dynamic_cast<const std::bad_alloc*>(&ex) != nullptr)
{
title = "Memory allocation failed";
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017, The GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstring>
#include <exception>
+#include <mutex>
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/baseversion.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/futil.h"
-#include "gromacs/utility/mutex.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/stringutil.h"
#include "errorformat.h"
-static bool bDebug = false;
+static bool bDebug = false; // NOLINT(cppcoreguidelines-avoid-non-const-global-variables)
-FILE* debug = nullptr;
-gmx_bool gmx_debug_at = FALSE;
+FILE* debug = nullptr; // NOLINT(cppcoreguidelines-avoid-non-const-global-variables)
+bool gmx_debug_at = false; // NOLINT(cppcoreguidelines-avoid-non-const-global-variables)
-static FILE* log_file = nullptr;
-static gmx::Mutex error_mutex;
+static FILE* log_file = nullptr; // NOLINT(cppcoreguidelines-avoid-non-const-global-variables)
+static std::mutex error_mutex; // NOLINT(cppcoreguidelines-avoid-non-const-global-variables)
-using Lock = gmx::lock_guard<gmx::Mutex>;
+using Lock = std::lock_guard<std::mutex>;
void gmx_init_debug(const int dbglevel, const char* dbgfile)
{
gmx::internal::printFatalErrorFooter(stderr);
}
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static gmx_error_handler_t gmx_error_handler = default_error_handler;
void gmx_set_error_handler(gmx_error_handler_t func)
va_end(ap);
}
-void _gmx_error(const char* key, const std::string& msg, const char* file, int line)
+void gmx_error_function(const char* key, const std::string& msg, const char* file, int line)
{
call_error_handler(key, file, line, msg);
gmx_exit_on_fatal_error(ExitType_Abort, 1);
}
-void _range_check(int n, int n_min, int n_max, const char* warn_str, const char* var, const char* file, int line)
+void range_check_function(int n, int n_min, int n_max, const char* warn_str, const char* var, const char* file, int line)
{
if ((n < n_min) || (n >= n_max))
{
buf += gmx::formatString(
"Variable %s has value %d. It should have been "
"within [ %d .. %d ]\n",
- var, n, n_min, n_max);
+ var,
+ n,
+ n_min,
+ n_max);
- _gmx_error("range", buf, file, line);
+ gmx_error_function("range", buf, file, line);
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
\endcode
*/
-extern FILE* debug;
+extern FILE* debug; //NOLINT(cppcoreguidelines-avoid-non-const-global-variables,-warnings-as-errors)
/** Whether extra debugging is enabled. */
-extern gmx_bool gmx_debug_at;
+extern gmx_bool gmx_debug_at; //NOLINT(cppcoreguidelines-avoid-non-const-global-variables,-warnings-as-errors)
/*! \brief
* Initializes debugging variables.
*
* This is used to implement gmx_fatal_collective() (which cannot be declared
* here, since it would bring with it mdrun-specific dependencies).
+ *
+ * This function is deprecated and no new calls should be made to it.
*/
[[noreturn]] void gmx_fatal_mpi_va(int fatal_errno,
const char* file,
* use gmx_fatal_collective(), declared in network.h,
* to avoid having as many error messages as processes.
*
+ * This function is deprecated and no new calls should be made to it.
+ *
* The first three parameters can be provided through ::FARGS:
* \code
gmx_fatal(FARGS, fmt, ...);
/** Helper macro to pass first three parameters to gmx_fatal(). */
#define FARGS 0, __FILE__, __LINE__
-/** Implementation for gmx_error(). */
-[[noreturn]] void _gmx_error(const char* key, const std::string& msg, const char* file, int line);
+/*! \brief Implementation for gmx_error().
+ *
+ * This function is deprecated and no new calls should be made to it. */
+[[noreturn]] void gmx_error_function(const char* key, const std::string& msg, const char* file, int line);
/*! \brief
* Alternative fatal error routine with canned messages.
*
* This works as gmx_fatal(), except that a generic error message is added
* based on a string key, and printf-style formatting is not supported.
* Should not typically be called directly, but through gmx_call() etc.
+ *
+ * This macro is deprecated and no new calls should be made to it.
*/
-#define gmx_error(key, msg) _gmx_error(key, msg, __FILE__, __LINE__)
+#define gmx_error(key, msg) gmx_error_function(key, msg, __FILE__, __LINE__)
/*! \name Fatal error routines for certain types of errors
*
* These wrap gmx_error() and provide the \p key parameter as one of the
* recognized strings.
+ *
+ * These macros are deprecated and no new calls should be made to them.
*/
/*! \{ */
#define gmx_call(msg) gmx_error("call", msg)
*
* \p warn_str can be NULL.
*/
-void _range_check(int n, int n_min, int n_max, const char* warn_str, const char* var, const char* file, int line);
+void range_check_function(int n, int n_min, int n_max, const char* warn_str, const char* var, const char* file, int line);
/*! \brief
* Checks that a variable is within a range.
* \p n_min is inclusive, but \p n_max is not.
*/
#define range_check_mesg(n, n_min, n_max, str) \
- _range_check(n, n_min, n_max, str, #n, __FILE__, __LINE__)
+ range_check_function(n, n_min, n_max, str, #n, __FILE__, __LINE__)
/*! \brief
* Checks that a variable is within a range.
*
* This works as range_check_mesg(), but with a default error message.
*/
-#define range_check(n, n_min, n_max) _range_check(n, n_min, n_max, NULL, #n, __FILE__, __LINE__)
+#define range_check(n, n_min, n_max) \
+ range_check_function(n, n_min, n_max, NULL, #n, __FILE__, __LINE__)
/*! \brief
* Prints a warning message to stderr.
fp_ = std::fopen(filename, mode);
if (fp_ == nullptr)
{
- GMX_THROW_WITH_ERRNO(FileIOError(formatString("Could not open file '%s'", filename)),
- "fopen", errno);
+ GMX_THROW_WITH_ERRNO(
+ FileIOError(formatString("Could not open file '%s'", filename)), "fopen", errno);
}
}
~FileStreamImpl()
FilePtr fp(fopen(filename, "r"));
if (fp == nullptr)
{
- GMX_THROW_WITH_ERRNO(FileIOError(formatString("Could not open file '%s'", filename)),
- "fopen", errno);
+ GMX_THROW_WITH_ERRNO(
+ FileIOError(formatString("Could not open file '%s'", filename)), "fopen", errno);
}
return fp;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
+#include <memory>
#include <string>
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/fileptr.h"
#include "gromacs/utility/textstream.h"
void close() override;
private:
- PrivateImplPointer<internal::FileStreamImpl> impl_;
+ std::unique_ptr<internal::FileStreamImpl> impl_;
};
/*! \libinternal \brief
static TextOutputFile& standardError();
private:
- PrivateImplPointer<internal::FileStreamImpl> impl_;
+ std::unique_ptr<internal::FileStreamImpl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <array>
#include <stdexcept>
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"
namespace gmx
#include <cstdlib>
#include <cstring>
+#include <mutex>
#include <tuple>
#include <fcntl.h>
#include "gromacs/utility/dir_separator.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/mutex.h"
#include "gromacs/utility/path.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
struct t_pstack* prev;
} t_pstack;
-static t_pstack* pstack = nullptr;
-static bool bUnbuffered = false;
-static int s_maxBackupCount = 0;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static t_pstack* pstack = nullptr;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static bool bUnbuffered = false;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static int s_maxBackupCount = 0;
/* this linked list is an intrinsically globally shared object, so we have
to protect it with mutexes */
-static gmx::Mutex pstack_mutex;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static std::mutex pstack_mutex;
-using Lock = gmx::lock_guard<gmx::Mutex>;
+using Lock = std::lock_guard<std::mutex>;
namespace gmx
{
namespace
{
//! Global library file finder; stores the object set with setLibraryFileFinder().
-const DataFileFinder* g_libFileFinder;
+const DataFileFinder* g_libFileFinder; //NOLINT(cppcoreguidelines-avoid-non-const-global-variables)
//! Default library file finder if nothing is set.
const DataFileFinder g_defaultLibFileFinder;
} // namespace
static void push_ps(FILE* fp)
{
- t_pstack* ps;
+ t_pstack* ps = nullptr;
Lock pstackLock(pstack_mutex);
int gmx_ffclose(FILE* fp)
{
- t_pstack *ps, *tmp;
- int ret = 0;
+ int ret = 0;
Lock pstackLock(pstack_mutex);
- ps = pstack;
+ t_pstack* ps = pstack;
if (ps == nullptr)
{
if (fp != nullptr)
{
ret = pclose(ps->prev->fp);
}
- tmp = ps->prev;
- ps->prev = ps->prev->prev;
+ t_pstack* tmp = ps->prev;
+ ps->prev = ps->prev->prev;
sfree(tmp);
}
else
static FILE* uncompress(const std::string& fn, const char* mode)
{
- FILE* fp;
+ FILE* fp = nullptr;
std::string buf = "uncompress -c < " + fn;
fprintf(stderr, "Going to execute '%s'\n", buf.c_str());
if ((fp = popen(buf.c_str(), mode)) == nullptr)
static FILE* gunzip(const std::string& fn, const char* mode)
{
- FILE* fp;
+ FILE* fp = nullptr;
std::string buf = "gunzip -c < ";
buf += fn;
fprintf(stderr, "Going to execute '%s'\n", buf.c_str());
gmx_bool gmx_fexist(const std::string& fname)
{
- FILE* test;
-
if (fname.empty())
{
return FALSE;
}
- test = fopen(fname.c_str(), "r");
+ FILE* test = fopen(fname.c_str(), "r");
if (test == nullptr)
{
/*Windows doesn't allow fopen of directory - so we need to check this seperately */
gmx_fatal(FARGS,
"Won't make more than %d backups of %s for you.\n"
"The env.var. GMX_MAXBACKUP controls this maximum, -1 disables backups.",
- s_maxBackupCount, fn.c_str());
+ s_maxBackupCount,
+ fn.c_str());
}
return buf;
FILE* gmx_ffopen(const std::string& file, const char* mode)
{
- FILE* ff = nullptr;
- gmx_bool bRead;
- int bs;
+ FILE* ff = nullptr;
if (file.empty())
{
make_backup(file);
}
- bRead = (mode[0] == 'r' && mode[1] != '+');
+ bool bRead = (mode[0] == 'r' && mode[1] != '+');
if (!bRead || gmx_fexist(file))
{
if ((ff = fopen(file.c_str(), mode)) == nullptr)
if (bUnbuffered || ((bufsize = getenv("GMX_LOG_BUFFER")) != nullptr))
{
/* Check whether to use completely unbuffered */
- if (bUnbuffered)
- {
- bs = 0;
- }
- else
- {
- bs = strtol(bufsize, nullptr, 10);
- }
+ const int bs = bUnbuffered ? 0 : strtol(bufsize, nullptr, 10);
if (bs <= 0)
{
setbuf(ff, nullptr);
}
else
{
- char* ptr;
+ char* ptr = nullptr;
snew(ptr, bs + 8);
if (setvbuf(ff, ptr, _IOFBF, bs) != 0)
{
/*! \brief Use mkstemp (or similar function to make a new temporary
* file and (on non-Windows systems) return a file descriptor to it.
*
+ * Note: not thread-safe on non-Windows systems
+ *
* \todo Use std::string and std::vector<char>. */
static int makeTemporaryFilename(char* buf)
{
- int len;
+ int len = 0;
if ((len = strlen(buf)) < 7)
{
* since windows doesnt support it we have to separate the cases.
* 20090307: mktemp deprecated, use iso c++ _mktemp instead.
*/
- int fd;
#if GMX_NATIVE_WINDOWS
_mktemp(buf);
if (buf == NULL)
{
gmx_fatal(FARGS, "Error creating temporary file %s: %s", buf, strerror(errno));
}
- fd = 0;
+ int fd = 0;
#else
- fd = mkstemp(buf);
+ int fd = mkstemp(buf);
/* mkstemp creates 0600 files - respect umask instead */
mode_t currUmask = umask(0);
while (!feof(in.get()))
{
- size_t nread;
-
- nread = fread(buf.data(), sizeof(char), FILECOPY_BUFSIZE, in.get());
+ size_t nread = fread(buf.data(), sizeof(char), FILECOPY_BUFSIZE, in.get());
if (nread > 0)
{
- size_t ret;
+ size_t ret = 0;
if (!out)
{
/* so this is where we open when copy_if_empty is false:
int rc = 0;
{
- int fn;
-
/* get the file number */
#if HAVE_FILENO
- fn = fileno(fp);
+ int fn = fileno(fp);
#elif HAVE__FILENO
- fn = _fileno(fp);
+ int fn = _fileno(fp);
#else
GMX_UNUSED_VALUE(fp);
- fn = -1;
+ int fn = -1;
#endif
/* do the actual fsync */
#endif
if (rc != 0)
{
- auto message = gmx::formatString("Cannot change directory to '%s'. Reason: %s", directory,
- strerror(errno));
+ auto message = gmx::formatString(
+ "Cannot change directory to '%s'. Reason: %s", directory, strerror(errno));
GMX_THROW(gmx::FileIOError(message));
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2014,2015,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "gmxassert.h"
+#include "gromacs/utility/gmxassert.h"
#include <cstdio>
#include <cstdlib>
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#endif
}
-gmx_bool gmx_omp_check_thread_affinity(char** message)
+bool gmx_omp_check_thread_affinity(char** message)
{
bool shouldSetAffinity = true;
/* We assume that the affinity setting is available on all platforms
* gcc supports. Even if this is not the case (e.g. Mac OS) the user
* will only get a warning. */
-# if defined(__GNUC__) || defined(__INTEL_COMPILER)
+# if defined(__GNUC__)
const char* programName;
try
{
" setting as the two can conflict and cause performance degradation.\n"
" To keep using the %s internal affinity setting, unset the\n"
" GOMP_CPU_AFFINITY environment variable.",
- programName, programName);
+ programName,
+ programName);
*message = gmx_strdup(buf.c_str());
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
shouldSetAffinity = false;
}
-# endif /* __GNUC__ || __INTEL_COMPILER */
-
-# if defined(__INTEL_COMPILER)
- const char* const kmp_env = getenv("KMP_AFFINITY");
- const bool bKmpAffinitySet = (kmp_env != NULL);
-
- // turn off internal pinning if KMP_AFFINITY is set but does not contain
- // the settings 'disabled' or 'none'.
- if (bKmpAffinitySet && (strstr(kmp_env, "disabled") == NULL) && (strstr(kmp_env, "none") == NULL))
- {
- try
- {
- std::string buf = gmx::formatString(
- "NOTE: KMP_AFFINITY set, will turn off %s internal affinity\n"
- " setting as the two can conflict and cause performance degradation.\n"
- " To keep using the %s internal affinity setting, unset the\n"
- " KMP_AFFINITY environment variable or set it to 'none' or 'disabled'.",
- programName, programName);
- *message = gmx_strdup(buf.c_str());
- }
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
- shouldSetAffinity = false;
- }
-# endif /* __INTEL_COMPILER */
+# endif /* __GNUC__ */
#endif /* GMX_OPENMP */
return shouldSetAffinity;
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_UTILITY_OMP_H
#define GMX_UTILITY_OMP_H
-#include "config.h"
-
-#include <stdio.h>
-
-#if GMX_NATIVE_WINDOWS
-# include <windows.h>
-#elif HAVE_XMMINTRIN_H
-# include <xmmintrin.h>
-#endif
-
-#include "gromacs/utility/basedefinitions.h"
-
/*! \addtogroup module_utility
* \{
*/
* allocated for \p *message.
* If the return value is `true`, \p *message is NULL.
*/
-gmx_bool gmx_omp_check_thread_affinity(char** message);
-
-/*! \brief
- * Pause for use in a spin-wait loop.
- */
-static inline void gmx_pause()
-{
-#if GMX_NATIVE_WINDOWS
- YieldProcessor();
-#elif HAVE_XMMINTRIN_H
- _mm_pause();
-#elif defined __MIC__
- _mm_delay_32(32);
-#else
- // No wait for unknown architecture
-#endif
-}
+bool gmx_omp_check_thread_affinity(char** message);
/*! \} */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
void doString(std::string* value)
{
- uint64_t size;
+ uint64_t size = 0;
doValue<uint64_t>(&size);
*value = std::string(&buffer_[pos_], size);
pos_ += size;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstddef>
+#include <memory>
#include <vector>
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/iserializer.h"
namespace gmx
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
class InMemoryDeserializer : public ISerializer
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int int64_to_int(int64_t step, const char* warn)
{
- int i;
-
- i = static_cast<int>(step);
+ int i = static_cast<int>(step);
if (warn != nullptr && (static_cast<int64_t>(i) != step))
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
}
///@}
+
+ //! Serialize enum value with underlying type int
+ template<typename EnumType>
+ void doEnumAsInt(EnumType* enumValue)
+ {
+ static_assert(std::is_same<std::underlying_type_t<EnumType>, int>::value,
+ "Only enums with underlying type int are supported.");
+ auto castedValue = static_cast<int>(*enumValue);
+ doInt(&castedValue);
+ *enumValue = static_cast<EnumType>(castedValue);
+ }
+
+ //! Serialize array of enum values with underlying type.
+ template<typename EnumType>
+ void doEnumArrayAsInt(EnumType* values, int elements)
+ {
+ for (int i = 0; i < elements; i++)
+ {
+ doEnumAsInt<EnumType>(&(values[i]));
+ }
+ }
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
writer->wrapperSettings().setIndent(oldIndent);
}
else if (value.isArray()
- && std::all_of(value.asArray().values().begin(), value.asArray().values().end(),
+ && std::all_of(value.asArray().values().begin(),
+ value.asArray().values().end(),
[](const auto& elem) { return elem.isObject(); }))
{
// Array containing only objects
abstol_(abstol)
{
}
-
void compareObjects(const KeyValueTreeObject& obj1, const KeyValueTreeObject& obj2)
{
for (const auto& prop1 : obj1.properties())
else if (!areSimpleValuesOfSameTypeEqual(value1, value2))
{
writer_->writeString(currentPath_.toString());
- writer_->writeLine(formatString(" (%s - %s)", simpleValueToString(value1).c_str(),
+ writer_->writeLine(formatString(" (%s - %s)",
+ simpleValueToString(value1).c_str(),
simpleValueToString(value2).c_str()));
}
}
}
}
- bool areSimpleValuesOfSameTypeEqual(const KeyValueTreeValue& value1, const KeyValueTreeValue& value2)
+ bool areSimpleValuesOfSameTypeEqual(const KeyValueTreeValue& value1, const KeyValueTreeValue& value2) const
{
GMX_ASSERT(value1.type() == value2.type(), "Caller should ensure that types are equal");
if (value1.isType<bool>())
void handleMissingKeyInFirstObject(const KeyValueTreeValue& value)
{
- const std::string message = formatString("%s (missing - %s)", currentPath_.toString().c_str(),
+ const std::string message = formatString("%s (missing - %s)",
+ currentPath_.toString().c_str(),
formatValueForMissingMessage(value).c_str());
writer_->writeLine(message);
}
void handleMissingKeyInSecondObject(const KeyValueTreeValue& value)
{
- const std::string message = formatString("%s (%s - missing)", currentPath_.toString().c_str(),
+ const std::string message = formatString("%s (%s - missing)",
+ currentPath_.toString().c_str(),
formatValueForMissingMessage(value).c_str());
writer_->writeLine(message);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "keyvaluetreeserializer.h"
+#include <mutex>
+
#include "gromacs/utility/iserializer.h"
#include "gromacs/utility/keyvaluetree.h"
#include "gromacs/utility/keyvaluetreebuilder.h"
-#include "gromacs/utility/mutex.h"
namespace gmx
{
SerializerFunction serialize;
DeserializerFunction deserialize;
};
-
- static Mutex s_initMutex;
- static std::map<std::type_index, Serializer> s_serializers;
+ // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+ static std::mutex s_initMutex;
+ // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+ static std::map<std::type_index, Serializer> s_serializers;
+ // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static std::map<unsigned char, DeserializerFunction> s_deserializers;
};
-Mutex ValueSerializer::s_initMutex;
-std::map<std::type_index, ValueSerializer::Serializer> ValueSerializer::s_serializers;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+std::mutex ValueSerializer::s_initMutex;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+std::map<std::type_index, ValueSerializer::Serializer> ValueSerializer::s_serializers;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
std::map<unsigned char, ValueSerializer::DeserializerFunction> ValueSerializer::s_deserializers;
template<typename T>
}
static void deserializeObject(KeyValueTreeObjectBuilder* builder, ISerializer* serializer)
{
- int count;
+ int count = 0;
std::string key;
serializer->doInt(&count);
for (int i = 0; i < count; ++i)
static void deserialize(KeyValueTreeValueBuilder* value, ISerializer* serializer)
{
KeyValueTreeArrayBuilder builder(value->createArray());
- int count;
+ int count = 0;
serializer->doInt(&count);
for (int i = 0; i < count; ++i)
{
static void serialize(bool value, ISerializer* serializer) { serializer->doBool(&value); }
static void deserialize(KeyValueTreeValueBuilder* builder, ISerializer* serializer)
{
- bool value;
+ bool value = false;
serializer->doBool(&value);
builder->setValue<bool>(value);
}
static void serialize(int value, ISerializer* serializer) { serializer->doInt(&value); }
static void deserialize(KeyValueTreeValueBuilder* builder, ISerializer* serializer)
{
- int value;
+ int value = 0;
serializer->doInt(&value);
builder->setValue<int>(value);
}
static void serialize(int64_t value, ISerializer* serializer) { serializer->doInt64(&value); }
static void deserialize(KeyValueTreeValueBuilder* builder, ISerializer* serializer)
{
- int64_t value;
+ int64_t value = 0;
serializer->doInt64(&value);
builder->setValue<int64_t>(value);
}
static void serialize(float value, ISerializer* serializer) { serializer->doFloat(&value); }
static void deserialize(KeyValueTreeValueBuilder* builder, ISerializer* serializer)
{
- float value;
+ float value = 0;
serializer->doFloat(&value);
builder->setValue<float>(value);
}
static void serialize(double value, ISerializer* serializer) { serializer->doDouble(&value); }
static void deserialize(KeyValueTreeValueBuilder* builder, ISerializer* serializer)
{
- double value;
+ double value = 0;
serializer->doDouble(&value);
builder->setValue<double>(value);
}
// static
void ValueSerializer::initSerializers()
{
- lock_guard<Mutex> lock(s_initMutex);
+ std::lock_guard<std::mutex> lock(s_initMutex);
if (!s_serializers.empty())
{
return;
KeyValueTreeValue ValueSerializer::deserialize(ISerializer* serializer)
{
- unsigned char typeTag;
+ unsigned char typeTag = 0;
serializer->doUChar(&typeTag);
auto iter = s_deserializers.find(typeTag);
GMX_RELEASE_ASSERT(iter != s_deserializers.end(), "Unknown type tag for deserializization");
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_UTILITY_KEYVALUETREETRANSFORM_H
#include <functional>
+#include <memory>
#include <string>
#include <typeindex>
#include <vector>
#include "gromacs/utility/any.h"
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/keyvaluetree.h"
namespace gmx
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
/*! \libinternal \brief
IKeyValueTreeErrorHandler* errorHandler) const;
private:
- PrivateImplPointer<internal::KeyValueTreeTransformerImpl> impl_;
+ std::unique_ptr<internal::KeyValueTreeTransformerImpl> impl_;
};
class IKeyValueTreeBackMapping
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <memory>
#include <string>
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/logger.h"
namespace gmx
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
/*! \libinternal \brief
LoggerOwner(std::unique_ptr<Impl> impl);
- PrivateImplPointer<Impl> impl_;
- const MDLogger* logger_;
+ std::unique_ptr<Impl> impl_;
+ const MDLogger* logger_;
friend class LoggerBuilder;
};
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2020, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*! \libinternal \file
- * \brief
- * Declares gmx::MdModuleNotification.
- *
- * \author Christian Blau <blau@kth.se>
- * \inlibraryapi
- * \ingroup module_utility
- */
-
-#ifndef GMX_UTILITY_MDMODULENOTIFICATION_IMPL_H
-#define GMX_UTILITY_MDMODULENOTIFICATION_IMPL_H
-
-#include <functional>
-#include <vector>
-
-namespace gmx
-{
-
-/*! \libinternal \brief
- * Subscribe and trigger notification functions.
- *
- * Extends MdModuleNotificationBase with new notification function and routine
- * to subscribe new listeners.
- *
- * To create a class of this type that provides callbacks, e.g., for events
- * EventA, and EventB use registerMdModuleNotification<EventA, EventB>::type.
- *
- * \tparam CallParameter of the function to be notified
- * \tparam MdModuleNotificationBase class to be extended with a notification
- * with CallParameter
- *
- * \note All added subscribers are required to out-live the MdModuleNotification
- *
- */
-template<class CallParameter, class MdModuleNotificationBase>
-class MdModuleNotification : public MdModuleNotificationBase
-{
-public:
- //! Make base class notification trigger available to this class
- using MdModuleNotificationBase::notify;
- //! Make base class subscription available to this class
- using MdModuleNotificationBase::subscribe;
-
- /*! \brief Trigger the subscribed notifications.
- * \param[in] callParameter of the function to be called back
- */
- void notify(CallParameter callParameter) const
- {
- for (auto& callBack : callBackFunctions_)
- {
- callBack(callParameter);
- }
- }
-
- /*! \brief
- * Add callback function to be called when notification is triggered.
- *
- * Notifications are distinguished by their call signature.
- *
- * \param[in] callBackFunction to be called from this class
- */
- void subscribe(std::function<void(CallParameter)> callBackFunction)
- {
- callBackFunctions_.emplace_back(callBackFunction);
- }
-
-private:
- std::vector<std::function<void(CallParameter)>> callBackFunctions_;
-};
-
-/*! \internal
- * \brief Aide to avoid nested MdModuleNotification definition.
- *
- * Instead of
- * MdModuleNotification<CallParameterA, MdModuleNotification<CallParameterB, etc ... >>
- * this allows to write
- * registerMdModuleNotification<CallParameterA, CallParameterB, ...>::type
- *
- * \tparam CallParameter all the event types to be registered
- */
-template<class... CallParameter>
-struct registerMdModuleNotification;
-
-/*! \internal \brief Template specialization to end parameter unpacking recursion.
- */
-template<>
-struct registerMdModuleNotification<>
-{
- /*! \internal
- * \brief Do nothing but be base class of MdModuleNotification.
- *
- * Required so that using MdModuleNotificationBase::notify and
- * MdModuleNotificationBase::subscribe are valid in derived class.
- */
- class NoCallParameter
- {
- public:
- //! Do nothing but provide MdModuleNotification::notify to derived class
- void notify() {}
- //! Do nothing but provide MdModuleNotification::subscribe to derived class
- void subscribe() {}
- };
- /*! \brief Defines a type if no notifications are managed.
- *
- * This ensures that code works with MdModuleCallParameterManagement that
- * does not manage any notifications.
- */
- using type = NoCallParameter;
-};
-
-/*! \libinternal
- * \brief Template specialization to assemble MdModuleNotification.
- *
- * Assembly of MdModuleNotification is performed by recursively taking off the
- * front of the CallParameter parameter pack and constructing the nested type
- * definition of MdModuleNotification base classes.
- *
- * \tparam CurrentCallParameter front of the template parameter pack
- * \tparam CallParameter rest of the event types
- */
-template<class CurrentCallParameter, class... CallParameter>
-struct registerMdModuleNotification<CurrentCallParameter, CallParameter...>
-{
- // private:
- //! The next type with rest of the arguments with the front parameter removed.
- using next_type = typename registerMdModuleNotification<CallParameter...>::type;
- //! The type of the MdModuleNotification
- using type = MdModuleNotification<CurrentCallParameter, next_type>;
-};
-
-} // namespace gmx
-
-#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares gmx::MDModulesNotifier and builder.
+ *
+ * \author Christian Blau <blau@kth.se>
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+
+#ifndef GMX_UTILITY_MDMODULESNOTIFIER_H
+#define GMX_UTILITY_MDMODULESNOTIFIER_H
+
+#include <functional>
+#include <vector>
+
+namespace gmx
+{
+
+/*! \libinternal
+ * \brief Organizes notifications about an event of interest to modules.
+ *
+ * An object of this type permits modules to subscribe to the
+ * corresponding event. The template types of this type encode what
+ * information is available when the event occurs. Modules \c
+ * subscribe() by providing a callback function that accepts a single
+ * parameter of such an event type. The code that handles that event
+ * has the responsibilty to call \c notify() afterwards. The
+ * subscribed modules then receive the callback with the requested
+ * event type as an argument.
+ *
+ * See gmx::MDModulesNotifiers for sequence diagrams for an example.
+ *
+ * This suits scenarios where several objects are built (or re-built)
+ * and one or more modules need to know when one or more of such
+ * objects are available (or updated), so they can adapt their
+ * internal state accordingly. Examples include responding to loading
+ * input data, or to changes related to a recurring process like
+ * checkpointing or partitioning. The coupling between these modules
+ * is now expressed indirectly. This improves the modularity and
+ * testability of those modules.
+ *
+ * The implementation provides the necessary flexibility to be
+ * parameterized with multiple event types and provide \c callback()
+ * and \b notify() methods corresponding to each related event. This
+ * is done by inheriting from a series of base classes, each of which
+ * handles a single type of event. BuildMDModulesNotifier implements
+ * the details. To create a class of this type that provides two
+ * events with callbacks that receive respectively types TypeA and
+ * TypeB, use BuildMDModulesNotifier<TypeA, TypeB>::type.
+ *
+ * \tparam CallParameter of the function to be notified
+ * \tparam MDModulesNotifierBase class to be extended with a notification
+ * with CallParameter
+ *
+ * \note All added subscribers are required to out-live the MDModulesNotifier
+ *
+ */
+template<class CallParameter, class MDModulesNotifierBase>
+class MDModulesNotifier : public MDModulesNotifierBase
+{
+public:
+ //! Make base class notification trigger available to this class
+ using MDModulesNotifierBase::notify;
+ //! Make base class subscription available to this class
+ using MDModulesNotifierBase::subscribe;
+
+ /*! \brief Notifies subscribers of the event described by \c
+ * callbackParameter.
+ *
+ * \param[in] callParameter of the function to be called back
+ */
+ void notify(CallParameter callParameter) const
+ {
+ for (auto& callBack : callBackFunctions_)
+ {
+ callBack(callParameter);
+ }
+ }
+
+ /*! \brief
+ * Add callback function to be called when \c notify() is called
+ *
+ * \param[in] callBackFunction to be called
+ */
+ void subscribe(std::function<void(CallParameter)> callBackFunction)
+ {
+ callBackFunctions_.emplace_back(callBackFunction);
+ }
+
+private:
+ std::vector<std::function<void(CallParameter)>> callBackFunctions_;
+};
+
+/*! \internal
+ * \brief Aide to avoid nested MDModulesNotifier definition.
+ *
+ * Instead of
+ * MDModulesNotifier<CallParameterA, MDModulesNotifier<CallParameterB, etc ... >>
+ * this allows to write
+ * BuildMDModulesNotifier<CallParameterA, CallParameterB, ...>::type
+ *
+ * \tparam CallParameter all the callback types to be registered
+ */
+template<class... CallParameter>
+struct BuildMDModulesNotifier;
+
+/*! \internal \brief Template specialization to end parameter unpacking recursion.
+ */
+template<>
+struct BuildMDModulesNotifier<>
+{
+ /*! \internal
+ * \brief Do nothing but be base class of MDModulesNotifier.
+ *
+ * Required so that using MDModulesNotifierBase::notify and
+ * MDModulesNotifierBase::subscribe are valid in derived class.
+ */
+ class NoCallParameter
+ {
+ public:
+ //! Do nothing but provide MDModulesNotifier::notify to derived class
+ void notify() {}
+ //! Do nothing but provide MDModulesNotifier::subscribe to derived class
+ void subscribe() {}
+ };
+ /*! \brief Defines a type if no notifications are managed.
+ *
+ * This ensures that code works with MDModuleCallParameterManagement that
+ * does not manage any notifications.
+ */
+ using type = NoCallParameter;
+};
+
+/*! \libinternal
+ * \brief Template specialization to assemble MDModulesNotifier.
+ *
+ * Assembly of MDModulesNotifier is performed by recursively taking off the
+ * front of the CallParameter parameter pack and constructing the nested type
+ * definition of MDModulesNotifier base classes.
+ *
+ * \tparam CurrentCallParameter front of the template parameter pack
+ * \tparam CallParameter rest of the callback types
+ */
+template<class CurrentCallParameter, class... CallParameter>
+struct BuildMDModulesNotifier<CurrentCallParameter, CallParameter...>
+{
+ // private:
+ //! The next type with rest of the arguments with the front parameter removed.
+ using next_type = typename BuildMDModulesNotifier<CallParameter...>::type;
+ //! The type of the MDModulesNotifier
+ using type = MDModulesNotifier<CurrentCallParameter, next_type>;
+};
+
+} // namespace gmx
+
+#endif
*/
/*! \libinternal \file
* \brief
- * Declares gmx::MdModulesNotifier.
+ * Declares gmx::MDModulesNotifiers.
*
* \author Christian Blau <blau@kth.se>
* \inlibraryapi
* \ingroup module_utility
*/
-#ifndef GMX_UTILITY_MDMODULENOTIFICATION_H
-#define GMX_UTILITY_MDMODULENOTIFICATION_H
+#ifndef GMX_UTILITY_MDMODULESNOTIFIERS_H
+#define GMX_UTILITY_MDMODULESNOTIFIERS_H
#include <string>
#include <vector>
-#include "gromacs/utility/mdmodulenotification-impl.h"
+#include "gromacs/utility/mdmodulesnotifier.h"
struct t_commrec;
+struct gmx_mtop_t;
enum class PbcType : int;
namespace gmx
class KeyValueTreeObjectBuilder;
class LocalAtomSetManager;
class IndexGroupsAndNames;
-struct MdModulesCheckpointReadingDataOnMaster;
-struct MdModulesCheckpointReadingBroadcast;
-struct MdModulesWriteCheckpointData;
+class SeparatePmeRanksPermitted;
+struct MDModulesCheckpointReadingDataOnMaster;
+struct MDModulesCheckpointReadingBroadcast;
+struct MDModulesWriteCheckpointData;
/*! \libinternal \brief Check if module outputs energy to a specific field.
*
* Ensures that energy is output for this module.
*/
-struct MdModulesEnergyOutputToDensityFittingRequestChecker
+struct MDModulesEnergyOutputToDensityFittingRequestChecker
{
//! Trigger output to density fitting energy field
bool energyOutputToDensityFitting_ = false;
};
/*! \libinternal
- * \brief Collection of callbacks to MDModules at differnt run-times.
+ * \brief Group of notifers to organize that MDModules
+ * can receive callbacks they subscribe to.
*
- * MDModules use members of this struct to sign up for callback functionality.
- *
- * The members of the struct represent callbacks at these run-times:
- *
- * When pre-processing the simulation data
- * When reading and writing check-pointing data
- * When setting up simulation after reading in the tpr file
+ * MDModules use members of this struct to subscribe to notifications
+ * of particular events. When the event occurs, the callback provided
+ * by a particular MDModule will be passed a parameter of the
+ * particular type they are interested in.
*
+ * Typically, during the setup phase, modules subscribe to notifiers
+ * that interest them by passing callbacks that expect a single parameter
+ * that describes the event. These are stored for later use. See the
+ * sequence diagram that follows:
\msc
- wordwraparcs=true,
- hscale="2";
-
- runner [label="runner:\nMdrunner"],
- CallParameter [label = "eventA:\nCallParameter"],
- MOD [label = "mdModules_:\nMdModules"],
- ModuleA [label="moduleA"],
- ModuleB [label="moduleB"],
- MdModuleNotification [label="notifier_:\nMdModuleNotification"];
-
- MOD box MdModuleNotification [label = "mdModules_ owns notifier_ and moduleA/B"];
- MOD =>> ModuleA [label="instantiates(notifier_)"];
- ModuleA =>> MdModuleNotification [label="subscribe(otherfunc)"];
- ModuleA =>> MOD;
- MOD =>> ModuleB [label="instantiates(notifier_)"];
- ModuleB =>> MdModuleNotification [label="subscribe(func)"];
- ModuleB =>> MOD;
- runner =>> CallParameter [label="instantiate"];
- CallParameter =>> runner ;
- runner =>> MOD [label="notify(eventA)"];
- MOD =>> MdModuleNotification [label="notify(eventA)"];
- MdModuleNotification =>> ModuleA [label="notify(eventA)"];
- ModuleA -> ModuleA [label="func(eventA)"];
- MdModuleNotification =>> ModuleB [label="notify(eventA)"];
- ModuleB -> ModuleB [label="otherfunc(eventA)"];
+wordwraparcs=true,
+hscale="2";
+
+modules [label = "mdModules:\nMDModules"],
+notifiers [label="notifiers\nMDModulesNotifiers"],
+notifier [label="exampleNotifier:\nBuildMDModulesNotifier\n<EventX, EventY>::type"],
+moduleA [label="moduleA"],
+moduleB [label="moduleB"],
+moduleC [label="moduleC"];
+
+modules box moduleC [label = "mdModules creates and owns moduleA, moduleB, and moduleC"];
+modules =>> notifiers [label="creates"];
+notifiers =>> notifier [label="creates"];
+notifier =>> notifiers [label="returns"];
+notifiers =>> modules [label="returns"];
+
+modules =>> moduleA [label="provides notifiers"];
+moduleA =>> moduleA [label="unpacks\nnotifiers.exampleNotifier"];
+moduleA =>> notifier [label="subscribes with\ncallback(EventX&)"];
+notifier =>> notifier [label="records subscription\nto EventX"];
+moduleA =>> notifier [label="subscribes with\ncallback(EventY&)"];
+notifier =>> notifier [label="records subscription\nto EventY"];
+moduleA =>> modules [label="returns"];
+
+modules =>> moduleB [label="provides notifiers"];
+moduleB =>> moduleB [label="unpacks\nnotifiers.exampleNotifier"];
+moduleA =>> notifier [label="subscribes with\ncallback(EventY&)"];
+notifier =>> notifier [label="records subscription\nto EventY"];
+moduleB =>> modules [label="returns"];
+
+modules =>> moduleC [label="provides notifiers"];
+moduleC =>> moduleC [label="unpacks and keeps\nnotifiers.exampleNotifier"];
+moduleC =>> modules [label="returns"];
\endmsc
+
+ * When the event occurs later on, the stored callbacks are used to
+ * allow the modules to react. See the following sequence diagram,
+ * which assumes that exampleNotifier was configured as in the
+ * previous sequence diagram.
+
+ \msc
+wordwraparcs=true,
+hscale="2";
+
+moduleC [label="moduleC"],
+notifier [label="exampleNotifier:\nBuildMDModulesNotifier\n<EventX, EventY>::type"],
+moduleA [label="moduleA"],
+moduleB [label="moduleB"];
+
+moduleC box moduleB [label = "Later, when ModuleC is doing work"];
+moduleC =>> moduleC [label="generates EventX"];
+moduleC =>> moduleC [label="generates EventY"];
+moduleC =>> notifier [label="calls notify(eventX)"];
+notifier =>> moduleA [label="calls callback(eventX)"];
+moduleA =>> moduleA [label="reacts to eventX"];
+moduleA =>> notifier [label="returns"];
+
+notifier =>> moduleC [label="returns"];
+moduleC =>> notifier [label="calls notify(eventY)"];
+notifier =>> moduleA [label="calls callback(eventY)"];
+moduleA =>> moduleA [label="reacts to eventY"];
+moduleA =>> notifier [label="returns"];
+notifier =>> moduleB [label="calls callback(eventY)"];
+moduleB =>> moduleB [label="reacts to eventY"];
+moduleB =>> notifier [label="returns"];
+notifier =>> moduleC [label="returns"];
+ \endmsc
*
- * The template arguments to the members of this struct directly reflect
- * the callback function signature. Arguments passed as pointers are always
- * meant to be modified, but never meant to be stored (in line with the policy
+ * The template arguments to the members of this struct are the
+ * parameters passed to the callback functions, one type per
+ * callback. Arguments passed as pointers are always meant to be
+ * modified, but never meant to be stored (in line with the policy
* everywhere else).
+ *
*/
-struct MdModulesNotifier
+struct MDModulesNotifiers
{
- /*! \brief Pre-processing callback functions.
+ /*! \brief Handles subscribing and calling pre-processing callback functions.
*
* EnergyCalculationFrequencyErrors* allows modules to check if they match
* their required calculation frequency
* KeyValueTreeObjectBuilder enables writing of module internal data to
* .tpr files.
*/
- registerMdModuleNotification<EnergyCalculationFrequencyErrors*, const IndexGroupsAndNames&, KeyValueTreeObjectBuilder>::type preProcessingNotifications_;
+ BuildMDModulesNotifier<EnergyCalculationFrequencyErrors*, const IndexGroupsAndNames&, KeyValueTreeObjectBuilder>::type preProcessingNotifier_;
- /*! \brief Checkpointing callback functions.
+ /*! \brief Handles subscribing and calling checkpointing callback functions.
*
- * MdModulesCheckpointReadingDataOnMaster provides modules with their
+ * MDModulesCheckpointReadingDataOnMaster provides modules with their
* checkpointed data on the master
* node and checkpoint file version
- * MdModulesCheckpointReadingBroadcast provides modules with a communicator
+ * MDModulesCheckpointReadingBroadcast provides modules with a communicator
* and the checkpoint file version to
* distribute their data
- * MdModulesWriteCheckpointData provides the modules with a key-value-tree
+ * MDModulesWriteCheckpointData provides the modules with a key-value-tree
* builder to store their checkpoint data and
* the checkpoint file version
*/
- registerMdModuleNotification<MdModulesCheckpointReadingDataOnMaster,
- MdModulesCheckpointReadingBroadcast,
- MdModulesWriteCheckpointData>::type checkpointingNotifications_;
+ BuildMDModulesNotifier<MDModulesCheckpointReadingDataOnMaster, MDModulesCheckpointReadingBroadcast, MDModulesWriteCheckpointData>::type
+ checkpointingNotifier_;
- /*! \brief Callbacks during simulation setup.
+ /*! \brief Handles subscribing and calling callbacks during simulation setup.
*
* const KeyValueTreeObject& provides modules with the internal data they
* wrote to .tpr files
* LocalAtomSetManager* enables modules to add atom indices to local atom sets
* to be managed
- * MdModulesEnergyOutputToDensityFittingRequestChecker* enables modules to
+ * const gmx_mtop_t& provides the topology of the system to the modules
+ * MDModulesEnergyOutputToDensityFittingRequestChecker* enables modules to
* report if they want to write their energy output
* to the density fitting field in the energy files
+ * SeparatePmeRanksPermitted* enables modules to report if they want
+ * to disable dedicated PME ranks
* const PbcType& provides modules with the periodic boundary condition type
* that is used during the simulation
* const SimulationTimeStep& provides modules with the simulation time-step
* const t_commrec& provides a communicator to the modules during simulation
* setup
*/
- registerMdModuleNotification<const KeyValueTreeObject&,
- LocalAtomSetManager*,
- MdModulesEnergyOutputToDensityFittingRequestChecker*,
- const PbcType&,
- const SimulationTimeStep&,
- const t_commrec&>::type simulationSetupNotifications_;
+ BuildMDModulesNotifier<const KeyValueTreeObject&,
+ LocalAtomSetManager*,
+ const gmx_mtop_t&,
+ MDModulesEnergyOutputToDensityFittingRequestChecker*,
+ SeparatePmeRanksPermitted*,
+ const PbcType&,
+ const SimulationTimeStep&,
+ const t_commrec&>::type simulationSetupNotifier_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013,2014,2019, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_UTILITY_MESSAGESTRINGCOLLECTOR_H
#define GMX_UTILITY_MESSAGESTRINGCOLLECTOR_H
+#include <memory>
#include <string>
#include "gromacs/utility/classhelpers.h"
void clear();
/*! \brief
- * Returns true if any messages have been added.
+ * Returns false if any messages have been added.
*
- * \returns true if append() has been called at least once.
+ * \returns false if append() has been called at least once.
*
* The return value is identical to `toString().empty()`.
- * Calls to startContext() or finishContext() only do not cause this
- * function to return true.
+ * Calls to startContext() or finishContext() do not affect the
+ * return value of this function.
*/
bool isEmpty() const;
/*! \brief
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
/*! \libinternal \brief
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#include "gromacs/utility/mpiinfo.h"
+
+// need to include gmxapi.h here as mpi.h needs to be included before mpi-ext.h
+#include "gromacs/utility/gmxmpi.h"
+
+#if HAVE_CUDA_AWARE_MPI
+# include <mpi-ext.h>
+#endif
+
+namespace gmx
+{
+
+CudaAwareMpiStatus checkMpiCudaAwareSupport()
+{
+#if defined(MPIX_CUDA_AWARE_SUPPORT)
+ // With OMPI version <=4.x, this function doesn't check if UCX PML is built with CUDA-support
+ // or if CUDA is disabled at runtime.
+ // Expect this function to work only if OMPI uses OB1 PML
+ // This is a known issue (https://github.com/open-mpi/ompi/issues/7963) and fix for this is
+ // expected soon (written March 2021)
+ CudaAwareMpiStatus status = (MPIX_Query_cuda_support() == 1) ? CudaAwareMpiStatus::Supported
+ : CudaAwareMpiStatus::NotSupported;
+#else
+ CudaAwareMpiStatus status = CudaAwareMpiStatus::NotKnown;
+#endif
+
+ return status;
+}
+
+} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef GMX_SIMD_IMPL_ARM_NEON_GENERAL_H
-#define GMX_SIMD_IMPL_ARM_NEON_GENERAL_H
+#ifndef GMX_UTILITY_MPI_INFO_H
+#define GMX_UTILITY_MPI_INFO_H
namespace gmx
{
-
-static inline void simdPrefetch(void* m)
+/*! \brief Enum describing CUDA-aware support in underlying MPI library.
+ */
+enum class CudaAwareMpiStatus : int
{
-#ifdef __GNUC__
- __builtin_prefetch(m);
-#endif
-}
+ Supported, //!< CUDA-aware support available.
+ NotSupported, //!< CUDA-aware support NOT available.
+ NotKnown //!< CUDA-aware support status not known.
+};
+
+
+/*! \brief
+ * Wrapper on top of MPIX_Query_cuda_support()
+ * For MPI implementations which don't support this function, it returns NotKnown
+ * Even when an MPI implementation does support this function, MPI library might not be
+ * robust enough to detect CUDA-aware support at runtime correcly e.g. when UCX PML is used
+ * or CUDA is disabled at runtime
+ *
+ * \returns CUDA-aware status in MPI implementation */
+CudaAwareMpiStatus checkMpiCudaAwareSupport();
} // namespace gmx
-#endif // GMX_SIMD_IMPL_ARM_NEON_GENERAL_H
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void niceHeader(TextWriter* writer, const char* fn, char commentChar)
{
- int uid;
char userbuf[256];
char hostbuf[256];
writer->writeLine(formatString("%c", commentChar));
writer->writeLine(formatString("%c\tFile '%s' was generated", commentChar, fn ? fn : "unknown"));
- uid = gmx_getuid();
+ int uid = gmx_getuid();
gmx_getusername(userbuf, 256);
gmx_gethostname(hostbuf, 256);
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2011-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
// p2 is done first, so any error reported is for p1
// FixME: #1635
- handle_wrapper h2(CreateFile(path2.c_str(), 0, FILE_SHARE_DELETE | FILE_SHARE_READ | FILE_SHARE_WRITE,
- 0, OPEN_EXISTING, FILE_FLAG_BACKUP_SEMANTICS, 0));
-
- handle_wrapper h1(CreateFile(path1.c_str(), 0, FILE_SHARE_DELETE | FILE_SHARE_READ | FILE_SHARE_WRITE,
- 0, OPEN_EXISTING, FILE_FLAG_BACKUP_SEMANTICS, 0));
+ handle_wrapper h2(CreateFile(path2.c_str(),
+ 0,
+ FILE_SHARE_DELETE | FILE_SHARE_READ | FILE_SHARE_WRITE,
+ 0,
+ OPEN_EXISTING,
+ FILE_FLAG_BACKUP_SEMANTICS,
+ 0));
+
+ handle_wrapper h1(CreateFile(path1.c_str(),
+ 0,
+ FILE_SHARE_DELETE | FILE_SHARE_READ | FILE_SHARE_WRITE,
+ 0,
+ OPEN_EXISTING,
+ FILE_FLAG_BACKUP_SEMANTICS,
+ 0));
if (h1.handle == INVALID_HANDLE_VALUE || h2.handle == INVALID_HANDLE_VALUE)
{
// but if both are invalid then it is an error.
if (e1 != 0 && e2 != 0)
{
- GMX_THROW_WITH_ERRNO(FileIOError("Path::isEquivalent called with two invalid files"),
- "stat", errno);
+ GMX_THROW_WITH_ERRNO(
+ FileIOError("Path::isEquivalent called with two invalid files"), "stat", errno);
}
return false;
}
void Path::splitPathEnvironment(const std::string& pathEnv, std::vector<std::string>* result)
{
- size_t prevPos = 0;
- size_t separator;
+ size_t prevPos = 0;
+ size_t separator = 0;
do
{
separator = pathEnv.find(cPathSeparator, prevPos);
std::string result(path);
#if !GMX_NATIVE_WINDOWS
char buf[GMX_PATH_MAX];
- int length;
+ int length = 0;
while ((length = readlink(result.c_str(), buf, sizeof(buf) - 1)) > 0)
{
buf[length] = '\0';
void File::throwOnNotFound(const NotFoundInfo& info)
{
throwOnError(info);
- const std::string message = formatString("File '%s' does not exist or is not accessible.\n%s",
- info.filename, info.message);
+ const std::string message = formatString(
+ "File '%s' does not exist or is not accessible.\n%s", info.filename, info.message);
GMX_THROW_WITH_ERRNO(InvalidInputError(message), info.call, info.err);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
PhysicalNodeCommunicator::PhysicalNodeCommunicator(MPI_Comm world, int physicalNodeId)
{
#if GMX_MPI
- int isInitialized;
+ int isInitialized = 0;
MPI_Initialized(&isInitialized);
if (isInitialized)
{
- int sizeOfWorld;
+ int sizeOfWorld = 0;
MPI_Comm_size(world, &sizeOfWorld);
if (sizeOfWorld > 1)
{
- int rankWithinWorld;
+ int rankWithinWorld = 0;
MPI_Comm_rank(world, &rankWithinWorld);
MPI_Comm_split(world, physicalNodeId, rankWithinWorld, &comm_);
auto ptr = MPI_Comm_ptr(&comm_);
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const char* pages;
} t_citerec;
+static constexpr int sc_lineWidth = 79;
+
void please_cite(FILE* fp, const char* key)
{
static const t_citerec citedb[] = {
- { "Allen1987a", "M. P. Allen and D. J. Tildesley", "Computer simulation of liquids",
- "Oxford Science Publications", 1, 1987, "1" },
- { "Berendsen95a", "H. J. C. Berendsen, D. van der Spoel and R. van Drunen",
+ { "Allen1987a",
+ "M. P. Allen and D. J. Tildesley",
+ "Computer simulation of liquids",
+ "Oxford Science Publications",
+ 1,
+ 1987,
+ "1" },
+ { "Berendsen95a",
+ "H. J. C. Berendsen, D. van der Spoel and R. van Drunen",
"GROMACS: A message-passing parallel molecular dynamics implementation",
- "Comp. Phys. Comm.", 91, 1995, "43-56" },
- { "Berendsen84a", "H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak",
- "Molecular dynamics with coupling to an external bath", "J. Chem. Phys.", 81, 1984,
+ "Comp. Phys. Comm.",
+ 91,
+ 1995,
+ "43-56" },
+ { "Berendsen84a",
+ "H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak",
+ "Molecular dynamics with coupling to an external bath",
+ "J. Chem. Phys.",
+ 81,
+ 1984,
"3684-3690" },
- { "Ryckaert77a", "J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen",
+ { "Ryckaert77a",
+ "J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen",
"Numerical Integration of the Cartesian Equations of Motion of a System with "
"Constraints; Molecular Dynamics of n-Alkanes",
- "J. Comp. Phys.", 23, 1977, "327-341" },
- { "Miyamoto92a", "S. Miyamoto and P. A. Kollman",
+ "J. Comp. Phys.",
+ 23,
+ 1977,
+ "327-341" },
+ { "Miyamoto92a",
+ "S. Miyamoto and P. A. Kollman",
"SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models",
- "J. Comp. Chem.", 13, 1992, "952-962" },
- { "Cromer1968a", "D. T. Cromer & J. B. Mann",
+ "J. Comp. Chem.",
+ 13,
+ 1992,
+ "952-962" },
+ { "Cromer1968a",
+ "D. T. Cromer & J. B. Mann",
"X-ray scattering factors computed from numerical Hartree-Fock wave functions",
- "Acta Cryst. A", 24, 1968, "321" },
- { "Barth95a", "E. Barth and K. Kuczera and B. Leimkuhler and R. D. Skeel",
- "Algorithms for Constrained Molecular Dynamics", "J. Comp. Chem.", 16, 1995, "1192-1209" },
+ "Acta Cryst. A",
+ 24,
+ 1968,
+ "321" },
+ { "Barth95a",
+ "E. Barth and K. Kuczera and B. Leimkuhler and R. D. Skeel",
+ "Algorithms for Constrained Molecular Dynamics",
+ "J. Comp. Chem.",
+ 16,
+ 1995,
+ "1192-1209" },
{ "Essmann95a",
"U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen ",
- "A smooth particle mesh Ewald method", "J. Chem. Phys.", 103, 1995, "8577-8592" },
- { "Torda89a", "A. E. Torda and R. M. Scheek and W. F. van Gunsteren",
+ "A smooth particle mesh Ewald method",
+ "J. Chem. Phys.",
+ 103,
+ 1995,
+ "8577-8592" },
+ { "Torda89a",
+ "A. E. Torda and R. M. Scheek and W. F. van Gunsteren",
"Time-dependent distance restraints in molecular dynamics simulations",
- "Chem. Phys. Lett.", 157, 1989, "289-294" },
- { "Tironi95a", "I. G. Tironi and R. Sperb and P. E. Smith and W. F. van Gunsteren",
- "Generalized reaction field method for molecular dynamics simulations", "J. Chem. Phys",
- 102, 1995, "5451-5459" },
- { "Hess97a", "B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije",
- "LINCS: A Linear Constraint Solver for molecular simulations", "J. Comp. Chem.", 18, 1997,
+ "Chem. Phys. Lett.",
+ 157,
+ 1989,
+ "289-294" },
+ { "Tironi95a",
+ "I. G. Tironi and R. Sperb and P. E. Smith and W. F. van Gunsteren",
+ "Generalized reaction field method for molecular dynamics simulations",
+ "J. Chem. Phys",
+ 102,
+ 1995,
+ "5451-5459" },
+ { "Hess97a",
+ "B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije",
+ "LINCS: A Linear Constraint Solver for molecular simulations",
+ "J. Comp. Chem.",
+ 18,
+ 1997,
"1463-1472" },
- { "Hess2008a", "B. Hess",
+ { "Hess2008a",
+ "B. Hess",
"P-LINCS: A Parallel Linear Constraint Solver for molecular simulation",
- "J. Chem. Theory Comput.", 4, 2008, "116-122" },
- { "Hess2008b", "B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl",
+ "J. Chem. Theory Comput.",
+ 4,
+ 2008,
+ "116-122" },
+ { "Hess2008b",
+ "B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl",
"GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular "
"simulation",
- "J. Chem. Theory Comput.", 4, 2008, "435-447" },
- { "Hub2010", "J. S. Hub, B. L. de Groot and D. van der Spoel",
+ "J. Chem. Theory Comput.",
+ 4,
+ 2008,
+ "435-447" },
+ { "Hub2010",
+ "J. S. Hub, B. L. de Groot and D. van der Spoel",
"g_wham - A free weighted histogram analysis implementation including robust error and "
"autocorrelation estimates",
- "J. Chem. Theory Comput.", 6, 2010, "3713-3720" },
- { "In-Chul99a", "Y. In-Chul and M. L. Berkowitz",
- "Ewald summation for systems with slab geometry", "J. Chem. Phys.", 111, 1999,
+ "J. Chem. Theory Comput.",
+ 6,
+ 2010,
+ "3713-3720" },
+ { "In-Chul99a",
+ "Y. In-Chul and M. L. Berkowitz",
+ "Ewald summation for systems with slab geometry",
+ "J. Chem. Phys.",
+ 111,
+ 1999,
"3155-3162" },
{ "DeGroot97a",
"B. L. de Groot and D. M. F. van Aalten and R. M. Scheek and A. Amadei and G. Vriend and "
"H. J. C. Berendsen",
- "Prediction of Protein Conformational Freedom From Distance Constrains", "Proteins", 29,
- 1997, "240-251" },
- { "Spoel98a", "D. van der Spoel and P. J. van Maaren and H. J. C. Berendsen",
+ "Prediction of Protein Conformational Freedom From Distance Constrains",
+ "Proteins",
+ 29,
+ 1997,
+ "240-251" },
+ { "Spoel98a",
+ "D. van der Spoel and P. J. van Maaren and H. J. C. Berendsen",
"A systematic study of water models for molecular simulation. Derivation of models "
"optimized for use with a reaction-field.",
- "J. Chem. Phys.", 108, 1998, "10220-10230" },
- { "Wishart98a", "D. S. Wishart and A. M. Nip",
- "Protein Chemical Shift Analysis: A Practical Guide", "Biochem. Cell Biol.", 76, 1998,
+ "J. Chem. Phys.",
+ 108,
+ 1998,
+ "10220-10230" },
+ { "Wishart98a",
+ "D. S. Wishart and A. M. Nip",
+ "Protein Chemical Shift Analysis: A Practical Guide",
+ "Biochem. Cell Biol.",
+ 76,
+ 1998,
"153-163" },
- { "Maiorov95", "V. N. Maiorov and G. M. Crippen",
+ { "Maiorov95",
+ "V. N. Maiorov and G. M. Crippen",
"Size-Independent Comparison of Protein Three-Dimensional Structures",
- "PROTEINS: Struct. Funct. Gen.", 22, 1995, "273-283" },
- { "Feenstra99", "K. A. Feenstra and B. Hess and H. J. C. Berendsen",
+ "PROTEINS: Struct. Funct. Gen.",
+ 22,
+ 1995,
+ "273-283" },
+ { "Feenstra99",
+ "K. A. Feenstra and B. Hess and H. J. C. Berendsen",
"Improving Efficiency of Large Time-scale Molecular Dynamics Simulations of "
"Hydrogen-rich Systems",
- "J. Comput. Chem.", 20, 1999, "786-798" },
+ "J. Comput. Chem.",
+ 20,
+ 1999,
+ "786-798" },
{ "Lourenco2013a",
"Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David van der "
"Spoel and Luciano T. Costa",
"Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium "
"Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View",
- "Environ. Sci. Technol.", 47, 2013, "7421-7429" },
- { "Timneanu2004a", "N. Timneanu and C. Caleman and J. Hajdu and D. van der Spoel",
- "Auger Electron Cascades in Water and Ice", "Chem. Phys.", 299, 2004, "277-283" },
- { "Pascal2011a", "T. A. Pascal and S. T. Lin and W. A. Goddard III",
+ "Environ. Sci. Technol.",
+ 47,
+ 2013,
+ "7421-7429" },
+ { "Timneanu2004a",
+ "N. Timneanu and C. Caleman and J. Hajdu and D. van der Spoel",
+ "Auger Electron Cascades in Water and Ice",
+ "Chem. Phys.",
+ 299,
+ 2004,
+ "277-283" },
+ { "Pascal2011a",
+ "T. A. Pascal and S. T. Lin and W. A. Goddard III",
"Thermodynamics of liquids: standard molar entropies and heat capacities of common "
"solvents from 2PT molecular dynamics",
- "Phys. Chem. Chem. Phys.", 13, 2011, "169-181" },
- { "Caleman2008a", "C. Caleman and D. van der Spoel",
+ "Phys. Chem. Chem. Phys.",
+ 13,
+ 2011,
+ "169-181" },
+ { "Caleman2008a",
+ "C. Caleman and D. van der Spoel",
"Picosecond Melting of Ice by an Infrared Laser Pulse: A Simulation Study",
- "Angew. Chem. Int. Ed", 47, 2008, "1417-1420" },
+ "Angew. Chem. Int. Ed",
+ 47,
+ 2008,
+ "1417-1420" },
{ "Caleman2011b",
"C. Caleman and P. J. van Maaren and M. Hong and J. S. Hub and L. T. da Costa and D. van "
"der Spoel",
"Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat "
"Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion "
"Coefficient, and Dielectric Constant",
- "J. Chem. Theo. Comp.", 8, 2012, "61" },
- { "Lindahl2001a", "E. Lindahl and B. Hess and D. van der Spoel",
- "GROMACS 3.0: A package for molecular simulation and trajectory analysis", "J. Mol. Mod.",
- 7, 2001, "306-317" },
- { "Wang2001a", "J. Wang and W. Wang and S. Huo and M. Lee and P. A. Kollman",
- "Solvation model based on weighted solvent accessible surface area", "J. Phys. Chem. B",
- 105, 2001, "5055-5067" },
- { "Eisenberg86a", "D. Eisenberg and A. D. McLachlan",
- "Solvation energy in protein folding and binding", "Nature", 319, 1986, "199-203" },
- { "Bondi1964a", "A. Bondi", "van der Waals Volumes and Radii", "J. Phys. Chem.", 68, 1964,
+ "J. Chem. Theo. Comp.",
+ 8,
+ 2012,
+ "61" },
+ { "Lindahl2001a",
+ "E. Lindahl and B. Hess and D. van der Spoel",
+ "GROMACS 3.0: A package for molecular simulation and trajectory analysis",
+ "J. Mol. Mod.",
+ 7,
+ 2001,
+ "306-317" },
+ { "Wang2001a",
+ "J. Wang and W. Wang and S. Huo and M. Lee and P. A. Kollman",
+ "Solvation model based on weighted solvent accessible surface area",
+ "J. Phys. Chem. B",
+ 105,
+ 2001,
+ "5055-5067" },
+ { "Eisenberg86a",
+ "D. Eisenberg and A. D. McLachlan",
+ "Solvation energy in protein folding and binding",
+ "Nature",
+ 319,
+ 1986,
+ "199-203" },
+ { "Bondi1964a",
+ "A. Bondi",
+ "van der Waals Volumes and Radii",
+ "J. Phys. Chem.",
+ 68,
+ 1964,
"441-451" },
{ "Eisenhaber95",
"Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and Michael "
"Scharf",
"The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of "
"Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies",
- "J. Comp. Chem.", 16, 1995, "273-284" },
- { "Hess2002", "B. Hess, H. Saint-Martin and H.J.C. Berendsen",
+ "J. Comp. Chem.",
+ 16,
+ 1995,
+ "273-284" },
+ { "Hess2002",
+ "B. Hess, H. Saint-Martin and H.J.C. Berendsen",
"Flexible constraints: an adiabatic treatment of quantum degrees of freedom, with "
"application to the flexible and polarizable MCDHO model for water",
- "J. Chem. Phys.", 116, 2002, "9602-9610" },
- { "Hess2003", "B. Hess and R.M. Scheek",
+ "J. Chem. Phys.",
+ 116,
+ 2002,
+ "9602-9610" },
+ { "Hess2003",
+ "B. Hess and R.M. Scheek",
"Orientation restraints in molecular dynamics simulations using time and ensemble "
"averaging",
- "J. Magn. Res.", 164, 2003, "19-27" },
- { "Rappe1991a", "A. K. Rappe and W. A. Goddard III",
- "Charge Equillibration for Molecular Dynamics Simulations", "J. Phys. Chem.", 95, 1991,
+ "J. Magn. Res.",
+ 164,
+ 2003,
+ "19-27" },
+ { "Rappe1991a",
+ "A. K. Rappe and W. A. Goddard III",
+ "Charge Equillibration for Molecular Dynamics Simulations",
+ "J. Phys. Chem.",
+ 95,
+ 1991,
"3358-3363" },
- { "Mu2005a", "Y. Mu, P. H. Nguyen and G. Stock",
+ { "Mu2005a",
+ "Y. Mu, P. H. Nguyen and G. Stock",
"Energy landscape of a small peptide revelaed by dihedral angle principal component "
"analysis",
- "Prot. Struct. Funct. Bioinf.", 58, 2005, "45-52" },
- { "Okabe2001a", "T. Okabe and M. Kawata and Y. Okamoto and M. Mikami",
+ "Prot. Struct. Funct. Bioinf.",
+ 58,
+ 2005,
+ "45-52" },
+ { "Okabe2001a",
+ "T. Okabe and M. Kawata and Y. Okamoto and M. Mikami",
"Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble",
- "Chem. Phys. Lett.", 335, 2001, "435-439" },
- { "Hukushima96a", "K. Hukushima and K. Nemoto",
+ "Chem. Phys. Lett.",
+ 335,
+ 2001,
+ "435-439" },
+ { "Hukushima96a",
+ "K. Hukushima and K. Nemoto",
"Exchange Monte Carlo Method and Application to Spin Glass Simulations",
- "J. Phys. Soc. Jpn.", 65, 1996, "1604-1608" },
- { "Tropp80a", "J. Tropp",
+ "J. Phys. Soc. Jpn.",
+ 65,
+ 1996,
+ "1604-1608" },
+ { "Tropp80a",
+ "J. Tropp",
"Dipolar Relaxation and Nuclear Overhauser effects in nonrigid molecules: The effect of "
"fluctuating internuclear distances",
- "J. Chem. Phys.", 72, 1980, "6035-6043" },
+ "J. Chem. Phys.",
+ 72,
+ 1980,
+ "6035-6043" },
{ "Bultinck2002a",
"P. Bultinck and W. Langenaeker and P. Lahorte and F. De Proft and P. Geerlings and M. "
"Waroquier and J. P. Tollenaere",
"The electronegativity equalization method I: Parametrization and validation for atomic "
"charge calculations",
- "J. Phys. Chem. A", 106, 2002, "7887-7894" },
- { "Yang2006b", "Q. Y. Yang and K. A. Sharp",
+ "J. Phys. Chem. A",
+ 106,
+ 2002,
+ "7887-7894" },
+ { "Yang2006b",
+ "Q. Y. Yang and K. A. Sharp",
"Atomic charge parameters for the finite difference Poisson-Boltzmann method using "
"electronegativity neutralization",
- "J. Chem. Theory Comput.", 2, 2006, "1152-1167" },
+ "J. Chem. Theory Comput.",
+ 2,
+ 2006,
+ "1152-1167" },
{ "Spoel2005a",
"D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen",
- "GROMACS: Fast, Flexible and Free", "J. Comp. Chem.", 26, 2005, "1701-1719" },
- { "Spoel2006b", "D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu",
+ "GROMACS: Fast, Flexible and Free",
+ "J. Comp. Chem.",
+ 26,
+ 2005,
+ "1701-1719" },
+ { "Spoel2006b",
+ "D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu",
"Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media",
- "J. Phys. Chem. B", 110, 2006, "4393-4398" },
- { "Spoel2006d", "D. van der Spoel and M. M. Seibert",
+ "J. Phys. Chem. B",
+ 110,
+ 2006,
+ "4393-4398" },
+ { "Spoel2006d",
+ "D. van der Spoel and M. M. Seibert",
"Protein folding kinetics and thermodynamics from atomistic simulations",
- "Phys. Rev. Letters", 96, 2006, "238102" },
- { "Palmer94a", "B. J. Palmer",
+ "Phys. Rev. Letters",
+ 96,
+ 2006,
+ "238102" },
+ { "Palmer94a",
+ "B. J. Palmer",
"Transverse-current autocorrelation-function calculations of the shear viscosity for "
"molecular liquids",
- "Phys. Rev. E", 49, 1994, "359-366" },
- { "Bussi2007a", "G. Bussi, D. Donadio and M. Parrinello",
- "Canonical sampling through velocity rescaling", "J. Chem. Phys.", 126, 2007, "014101" },
- { "Hub2006", "J. S. Hub and B. L. de Groot", "Does CO2 permeate through Aquaporin-1?",
- "Biophys. J.", 91, 2006, "842-848" },
- { "Hub2008", "J. S. Hub and B. L. de Groot",
- "Mechanism of selectivity in aquaporins and aquaglyceroporins", "PNAS", 105, 2008,
+ "Phys. Rev. E",
+ 49,
+ 1994,
+ "359-366" },
+ { "Bussi2007a",
+ "G. Bussi, D. Donadio and M. Parrinello",
+ "Canonical sampling through velocity rescaling",
+ "J. Chem. Phys.",
+ 126,
+ 2007,
+ "014101" },
+ { "Hub2006",
+ "J. S. Hub and B. L. de Groot",
+ "Does CO2 permeate through Aquaporin-1?",
+ "Biophys. J.",
+ 91,
+ 2006,
+ "842-848" },
+ { "Hub2008",
+ "J. S. Hub and B. L. de Groot",
+ "Mechanism of selectivity in aquaporins and aquaglyceroporins",
+ "PNAS",
+ 105,
+ 2008,
"1198-1203" },
{ "Friedrich2009",
"M. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. LeGrand, A. L. Beberg, D. "
"L. Ensign, C. M. Bruns, and V. S. Pande",
"Accelerating Molecular Dynamic Simulation on Graphics Processing Units",
- "J. Comp. Chem.", 30, 2009, "864-872" },
- { "Engin2010", "O. Engin, A. Villa, M. Sayar and B. Hess",
+ "J. Comp. Chem.",
+ 30,
+ 2009,
+ "864-872" },
+ { "Engin2010",
+ "O. Engin, A. Villa, M. Sayar and B. Hess",
"Driving Forces for Adsorption of Amphiphilic Peptides to Air-Water Interface",
- "J. Phys. Chem. B", 114, 2010, "11093" },
- { "Wang2010", "H. Wang, F. Dommert, C.Holm",
+ "J. Phys. Chem. B",
+ 114,
+ 2010,
+ "11093" },
+ { "Wang2010",
+ "H. Wang, F. Dommert, C.Holm",
"Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of "
"accuracy and efficiency",
- "J. Chem. Phys. B", 133, 2010, "034117" },
- { "Sugita1999a", "Y. Sugita, Y. Okamoto",
- "Replica-exchange molecular dynamics method for protein folding", "Chem. Phys. Lett.",
- 314, 1999, "141-151" },
- { "Kutzner2011", "C. Kutzner and J. Czub and H. Grubmuller",
+ "J. Chem. Phys. B",
+ 133,
+ 2010,
+ "034117" },
+ { "Sugita1999a",
+ "Y. Sugita, Y. Okamoto",
+ "Replica-exchange molecular dynamics method for protein folding",
+ "Chem. Phys. Lett.",
+ 314,
+ 1999,
+ "141-151" },
+ { "Kutzner2011",
+ "C. Kutzner and J. Czub and H. Grubmuller",
"Keep it Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with "
"GROMACS",
- "J. Chem. Theory Comput.", 7, 2011, "1381-1393" },
+ "J. Chem. Theory Comput.",
+ 7,
+ 2011,
+ "1381-1393" },
{ "Hoefling2011",
"M. Hoefling, N. Lima, D. Haenni, C.A.M. Seidel, B. Schuler, H. Grubmuller",
"Structural Heterogeneity and Quantitative FRET Efficiency Distributions of Polyprolines "
"through a Hybrid Atomistic Simulation and Monte Carlo Approach",
- "PLoS ONE", 6, 2011, "e19791" },
- { "Hockney1988", "R. W. Hockney and J. W. Eastwood", "Computer simulation using particles",
- "IOP, Bristol", 1, 1988, "1" },
- { "Ballenegger2012", "V. Ballenegger, J.J. Cerda, and C. Holm",
+ "PLoS ONE",
+ 6,
+ 2011,
+ "e19791" },
+ { "Hockney1988",
+ "R. W. Hockney and J. W. Eastwood",
+ "Computer simulation using particles",
+ "IOP, Bristol",
+ 1,
+ 1988,
+ "1" },
+ { "Ballenegger2012",
+ "V. Ballenegger, J.J. Cerda, and C. Holm",
"How to Convert SPME to P3M: Influence Functions and Error Estimates",
- "J. Chem. Theory Comput.", 8, 2012, "936-947" },
+ "J. Chem. Theory Comput.",
+ 8,
+ 2012,
+ "936-947" },
{ "Garmay2012",
"Garmay Yu, Shvetsov A, Karelov D, Lebedev D, Radulescu A, Petukhov M, Isaev-Ivanov V",
"Correlated motion of protein subdomains and large-scale conformational flexibility of "
"RecA protein filament",
- "Journal of Physics: Conference Series", 340, 2012, "012094" },
- { "Kutzner2011b", "C. Kutzner, H. Grubmuller, B. L. de Groot, and U. Zachariae",
+ "Journal of Physics: Conference Series",
+ 340,
+ 2012,
+ "012094" },
+ { "Kutzner2011b",
+ "C. Kutzner, H. Grubmuller, B. L. de Groot, and U. Zachariae",
"Computational Electrophysiology: The Molecular Dynamics of Ion Channel Permeation and "
"Selectivity in Atomistic Detail",
- "Biophys. J.", 101, 2011, "809-817" },
+ "Biophys. J.",
+ 101,
+ 2011,
+ "809-817" },
{ "Lundborg2014",
"M. Lundborg, R. Apostolov, D. Spangberg, A. Gardenas, D. van der Spoel and E. Lindahl",
"An efficient and extensible format, library, and API for binary trajectory data from "
"molecular simulations",
- "J. Comput. Chem.", 35, 2014, "260-269" },
+ "J. Comput. Chem.",
+ 35,
+ 2014,
+ "260-269" },
{ "Goga2012",
"N. Goga and A. J. Rzepiela and A. H. de Vries and S. J. Marrink and H. J. C. Berendsen",
- "Efficient Algorithms for Langevin and DPD Dynamics", "J. Chem. Theory Comput.", 8, 2012,
+ "Efficient Algorithms for Langevin and DPD Dynamics",
+ "J. Chem. Theory Comput.",
+ 8,
+ 2012,
"3637--3649" },
{ "Pronk2013",
"S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. "
"C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl",
"GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation "
"toolkit",
- "Bioinformatics", 29, 2013, "845-54" },
- { "Pall2015", "S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl",
+ "Bioinformatics",
+ 29,
+ 2013,
+ "845-54" },
+ { "Pall2015",
+ "S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl",
"Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS",
- "In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale", 8759, 2015,
+ "In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale",
+ 8759,
+ 2015,
"3-27" },
{ "Abraham2015",
"M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. Lindahl",
"GROMACS: High performance molecular simulations through multi-level parallelism from "
"laptops to supercomputers",
- "SoftwareX", 1, 2015, "19-25" },
- { "Ballenegger2009", "V. Ballenegger, A. Arnold, J. J. Cerdà",
+ "SoftwareX",
+ 1,
+ 2015,
+ "19-25" },
+ { "Ballenegger2009",
+ "V. Ballenegger, A. Arnold, J. J. Cerdà",
"Simulations of non-neutral slab systems with long-range electrostatic interactions in "
"two-dimensional periodic boundary conditions",
- "J. Chem. Phys", 131, 2009, "094107" },
- { "Hub2014a", "J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof",
+ "J. Chem. Phys",
+ 131,
+ 2009,
+ "094107" },
+ { "Hub2014a",
+ "J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof",
"Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge",
- "J. Chem. Theory Comput.", 10, 2014, "381-393" },
- { "Spoel2018a", "D. van der Spoel, M. M. Ghahremanpour, J. Lemkul",
+ "J. Chem. Theory Comput.",
+ 10,
+ 2014,
+ "381-393" },
+ { "Spoel2018a",
+ "D. van der Spoel, M. M. Ghahremanpour, J. Lemkul",
"Small Molecule Thermochemistry: A Tool For Empirical Force Field Development",
- "J. Phys. Chem. A", 122, 2018, "8982-8988" },
- { "Lindahl2014", "V. Lindahl, J. Lidmar, B. Hess",
+ "J. Phys. Chem. A",
+ 122,
+ 2018,
+ "8982-8988" },
+ { "Lindahl2014",
+ "V. Lindahl, J. Lidmar, B. Hess",
"Accelerated weight histogram method for exploring free energy landscapes",
- "J. Chem. Phys.", 141, 2014, "044110" },
- { "Bernetti2020", "M. Bernetti, G. Bussi",
- "Pressure control using stochastic cell rescaling", "J. Chem. Phys.", 153, 2020,
+ "J. Chem. Phys.",
+ 141,
+ 2014,
+ "044110" },
+ { "Bernetti2020",
+ "M. Bernetti, G. Bussi",
+ "Pressure control using stochastic cell rescaling",
+ "J. Chem. Phys.",
+ 153,
+ 2020,
"114107" },
};
#define NSTR static_cast<int>(asize(citedb))
- int index;
- char* author;
- char* title;
-#define LINE_WIDTH 79
-
if (fp == nullptr)
{
return;
}
- for (index = 0; index < NSTR && (strcmp(citedb[index].key, key) != 0); index++) {}
+ int index = 0;
+ for (; index < NSTR && (strcmp(citedb[index].key, key) != 0); index++) {}
fprintf(fp, "\n++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n");
if (index < NSTR)
{
/* Insert newlines */
- author = wrap_lines(citedb[index].author, LINE_WIDTH, 0, FALSE);
- title = wrap_lines(citedb[index].title, LINE_WIDTH, 0, FALSE);
- fprintf(fp, "%s\n%s\n%s %d (%d) pp. %s\n", author, title, citedb[index].journal,
- citedb[index].volume, citedb[index].year, citedb[index].pages);
+ char* author = wrap_lines(citedb[index].author, sc_lineWidth, 0, FALSE);
+ char* title = wrap_lines(citedb[index].title, sc_lineWidth, 0, FALSE);
+ fprintf(fp,
+ "%s\n%s\n%s %d (%d) pp. %s\n",
+ author,
+ title,
+ citedb[index].journal,
+ citedb[index].volume,
+ citedb[index].year,
+ citedb[index].pages);
sfree(author);
sfree(title);
}
return;
}
gmx::TextLineWrapper wrapper;
- wrapper.settings().setLineLength(LINE_WIDTH);
+ wrapper.settings().setLineLength(sc_lineWidth);
wrapper.settings().setFirstLineIndent(0);
const std::string doiString = wrapper.wrapToString(gmxDOI());
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
//! Global program info; stores the object set with setProgramContext().
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
const IProgramContext* g_programContext;
//! Default program context if nothing is set.
const DefaultProgramContext g_defaultContext;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <type_traits>
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"
namespace gmx
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
#include <cstdlib>
-#ifdef WITH_DMALLOC
-# include <dmalloc.h>
-#endif
+#include <mutex>
#include <cstring>
-#include "thread_mpi/threads.h"
-
#include "gromacs/utility/alignedallocator.h"
-#include "gromacs/utility/dir_separator.h"
#include "gromacs/utility/fatalerror.h"
#ifdef PRINT_ALLOC_KB
# include "gromacs/utility/basenetwork.h"
# include "gromacs/utility/gmxmpi.h"
#endif
-static gmx_bool g_bOverAllocDD = FALSE;
-static tMPI_Thread_mutex_t g_over_alloc_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static bool g_bOverAllocDD = false;
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static std::mutex g_overAllocMutex;
void* save_malloc(const char* name, const char* file, int line, size_t size)
{
- void* p;
+ void* p = nullptr;
- p = nullptr;
if (size == 0)
{
p = nullptr;
{
if ((p = malloc(size)) == nullptr)
{
- gmx_fatal(errno, __FILE__, __LINE__,
+ gmx_fatal(errno,
+ __FILE__,
+ __LINE__,
"Not enough memory. Failed to malloc %" PRId64
" bytes for %s\n"
"(called from file %s, line %d)",
- static_cast<int64_t>(size), name, file, line);
+ static_cast<int64_t>(size),
+ name,
+ file,
+ line);
}
(void)memset(p, 0, size);
}
void* save_calloc(const char* name, const char* file, int line, size_t nelem, size_t elsize)
{
- void* p;
+ void* p = nullptr;
- p = nullptr;
if ((nelem == 0) || (elsize == 0))
{
p = nullptr;
{
int rank = gmx_node_rank();
printf("Allocating %.1f MB for %s (called from file %s, line %d on %d)\n",
- nelem * elsize / 1048576.0, name, file, line, rank);
+ nelem * elsize / 1048576.0,
+ name,
+ file,
+ line,
+ rank);
}
#endif
#if GMX_BROKEN_CALLOC
a broken calloc, e.g. in -lgmalloc on cray xt3. */
if ((p = malloc((size_t)nelem * (size_t)elsize)) == NULL)
{
- gmx_fatal(errno, __FILE__, __LINE__,
+ gmx_fatal(errno,
+ __FILE__,
+ __LINE__,
"Not enough memory. Failed to calloc %" PRId64 " elements of size %" PRId64
" for %s\n(called from file %s, line %d)",
- (int64_t)nelem, (int64_t)elsize, name, file, line);
+ (int64_t)nelem,
+ (int64_t)elsize,
+ name,
+ file,
+ line);
}
memset(p, 0, (size_t)(nelem * elsize));
#else
if ((p = calloc(nelem, elsize)) == nullptr)
{
- gmx_fatal(errno, __FILE__, __LINE__,
+ gmx_fatal(errno,
+ __FILE__,
+ __LINE__,
"Not enough memory. Failed to calloc %" PRId64 " elements of size %" PRId64
" for %s\n(called from file %s, line %d)",
- static_cast<int64_t>(nelem), static_cast<int64_t>(elsize), name, file, line);
+ static_cast<int64_t>(nelem),
+ static_cast<int64_t>(elsize),
+ name,
+ file,
+ line);
}
#endif
}
void* save_realloc(const char* name, const char* file, int line, void* ptr, size_t nelem, size_t elsize)
{
- void* p;
+ void* p = nullptr;
size_t size = nelem * elsize;
- p = nullptr;
if (size == 0)
{
save_free(name, file, line, ptr);
{
int rank = gmx_node_rank();
printf("Reallocating %.1f MB for %s (called from file %s, line %d on %d)\n",
- size / 1048576.0, name, file, line, rank);
+ size / 1048576.0,
+ name,
+ file,
+ line,
+ rank);
}
#endif
if (ptr == nullptr)
}
if (p == nullptr)
{
- gmx_fatal(errno, __FILE__, __LINE__,
+ gmx_fatal(errno,
+ __FILE__,
+ __LINE__,
"Not enough memory. Failed to realloc %zu bytes for %s, %s=%p\n"
"(called from file %s, line %d)",
- size, name, name, ptr, file, line);
+ size,
+ name,
+ name,
+ ptr,
+ file,
+ line);
}
}
return p;
* the necessary alignment. */
void* save_malloc_aligned(const char* name, const char* file, int line, size_t nelem, size_t elsize, size_t alignment)
{
- void* p;
+ void* p = nullptr;
if (alignment == 0)
{
- gmx_fatal(errno, __FILE__, __LINE__,
+ gmx_fatal(errno,
+ __FILE__,
+ __LINE__,
"Cannot allocate aligned memory with alignment of zero!\n(called from file %s, "
"line %d)",
- file, line);
+ file,
+ line);
}
size_t alignmentSize = gmx::AlignedAllocationPolicy::alignment();
if (alignment > alignmentSize)
{
- gmx_fatal(errno, __FILE__, __LINE__,
+ gmx_fatal(errno,
+ __FILE__,
+ __LINE__,
"Cannot allocate aligned memory with alignment > %zu bytes\n(called from file "
"%s, line %d)",
- alignmentSize, file, line);
+ alignmentSize,
+ file,
+ line);
}
{
int rank = gmx_node_rank();
printf("Allocating %.1f MB for %s (called from file %s, line %d on %d)\n",
- nelem * elsize / 1048576.0, name, file, line, rank);
+ nelem * elsize / 1048576.0,
+ name,
+ file,
+ line,
+ rank);
}
#endif
if (p == nullptr)
{
- gmx_fatal(errno, __FILE__, __LINE__,
+ gmx_fatal(errno,
+ __FILE__,
+ __LINE__,
"Not enough memory. Failed to allocate %zu aligned elements of size %zu for "
"%s\n(called from file %s, line %d)",
- nelem, elsize, name, file, line);
+ nelem,
+ elsize,
+ name,
+ file,
+ line);
}
}
return p;
gmx::AlignedAllocationPolicy::free(ptr);
}
-void set_over_alloc_dd(gmx_bool set)
+void set_over_alloc_dd(bool set)
{
- tMPI_Thread_mutex_lock(&g_over_alloc_mutex);
+ std::lock_guard<std::mutex> lock(g_overAllocMutex);
/* we just make sure that we don't set this at the same time.
We don't worry too much about reading this rarely-set variable */
g_bOverAllocDD = set;
- tMPI_Thread_mutex_unlock(&g_over_alloc_mutex);
}
int over_alloc_dd(int n)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019,2020, by the GROMACS development team.
+ * Copyright (c) 2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <stddef.h>
-#include "gromacs/utility/basedefinitions.h"
-
/*! \brief
* \Gromacs wrapper for malloc().
*
* This is mdrun-specific, so it might be better to put this and
* over_alloc_dd() much higher up.
*/
-void set_over_alloc_dd(gmx_bool set);
+void set_over_alloc_dd(bool set);
/*! \brief
* Returns new allocation count for domain decomposition allocations.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int intFromString(const char* str)
{
- errno = 0;
- char* endptr;
- const long int value = std::strtol(str, &endptr, 10);
+ errno = 0;
+ char* endptr = nullptr;
+ const long int value = std::strtol(str, &endptr, 10);
if (errno == ERANGE || value < std::numeric_limits<int>::min()
|| value > std::numeric_limits<int>::max())
{
int64_t int64FromString(const char* str)
{
- errno = 0;
- char* endptr;
- const int64_t value = str_to_int64_t(str, &endptr);
+ errno = 0;
+ char* endptr = nullptr;
+ const int64_t value = str_to_int64_t(str, &endptr);
if (errno == ERANGE)
{
GMX_THROW(InvalidInputError("Invalid value: '" + std::string(str)
float floatFromString(const char* str)
{
- errno = 0;
- char* endptr;
- const double value = std::strtod(str, &endptr);
+ errno = 0;
+ char* endptr = nullptr;
+ const double value = std::strtod(str, &endptr);
if (errno == ERANGE || value < -std::numeric_limits<float>::max()
|| value > std::numeric_limits<float>::max())
{
double doubleFromString(const char* str)
{
- errno = 0;
- char* endptr;
- const double value = std::strtod(str, &endptr);
+ errno = 0;
+ char* endptr = nullptr;
+ const double value = std::strtod(str, &endptr);
if (errno == ERANGE)
{
GMX_THROW(InvalidInputError("Invalid value: '" + std::string(str)
// will throw if any conversion from string to value fails
std::array<ValueType, NumExpectedValues> valuesAsArray;
- std::transform(std::begin(valuesAsStrings), std::end(valuesAsStrings), std::begin(valuesAsArray),
+ std::transform(std::begin(valuesAsStrings),
+ std::end(valuesAsStrings),
+ std::begin(valuesAsArray),
[](const std::string& split) { return fromString<ValueType>(split); });
return { valuesAsArray };
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx_bool get_a_line(FILE* fp, char line[], int n)
{
- char* line0;
- char* dum;
+ char* line0 = nullptr;
+ char* dum = nullptr;
snew(line0, n + 1);
else if (static_cast<int>(std::strlen(line0)) == n)
{
fprintf(stderr,
- "Warning: line length exceeds buffer length (%d), data might be corrupted\n", n);
+ "Warning: line length exceeds buffer length (%d), data might be corrupted\n",
+ n);
line0[n - 1] = '\0';
}
else
int search_str(int nstr, char** str, char* key)
{
- int i;
-
/* Linear search */
- for (i = 0; (i < nstr); i++)
+ for (int i = 0; (i < nstr); i++)
{
if (gmx_strcasecmp(str[i], key) == 0)
{
static int fget_lines(FILE* in, const char* db, char*** strings)
{
- char** ptr;
+ char** ptr = nullptr;
char buf[STRLEN];
- int i, nstr;
- char* pret;
+ int nstr = 0;
- pret = fgets(buf, STRLEN, in);
+ char* pret = fgets(buf, STRLEN, in);
if (pret == nullptr || sscanf(buf, "%d", &nstr) != 1)
{
gmx_warning("File is empty");
return 0;
}
snew(ptr, nstr);
- for (i = 0; (i < nstr); i++)
+ for (int i = 0; (i < nstr); i++)
{
if (fgets2(buf, STRLEN, in) == nullptr)
{
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief Defines helper function object for class enumerations
+ *
+ * This helper type facilitates efficient lookup of values from
+ * an enumeration identified by a string, given a pre-declared mapping of
+ * values to such strings.
+ *
+ * It is separated from enumerationhelpers.h because it is not as
+ * widely used and brings in several extra dependencies not needed by
+ * that header.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_STRINGTOENUMVALUECONVERTER_H
+#define GMX_UTILITY_STRINGTOENUMVALUECONVERTER_H
+
+#include <map>
+#include <optional>
+#include <string>
+
+#include "enumerationhelpers.h"
+#include "stringcompare.h"
+#include "stringutil.h"
+
+namespace gmx
+{
+
+/*! \brief Enum class for whether StringToEnumValueConverter will strip strings
+ * of leading and trailing whitespace before comparison. */
+enum class StripStrings : int
+{
+ //! Do not strip strings
+ No,
+ //! Strip strings
+ Yes
+};
+
+/*! \brief A class to convert a string to an enum value of type \c EnumType.
+ *
+ * It can be configured:
+ * - to match different enumerations,
+ * - to convert enumerations to strings in a custom way,
+ * - either strip strings of leading and trailing whitespace before
+ * comparison or not,
+ * - with different handling of how the string characters are compared.
+ *
+ * Usage example:
+ *
+ * enum class Foo : int {
+ * Fizz, Buzz, Count, Default = Fizz
+ * };
+ * StringToEnumValueConverter<Foo, enumValueToString> converter;
+ * Foo type = converter.valueFrom(theString);
+ *
+ * \tparam EnumType A class enum for which enumValueToString
+ * is defined and maps all values
+ * (except EnumType::Count) to a string.
+ * \tparam enumValueToStringFunction Function to convert EnumValue to string, which
+ * is typically enumValueToString, per convention
+ * \tparam stringCompareType Indicates how the string should be compared
+ * with respect to case, hyphens, underscores, etc.
+ * \tparam stripStrings Indicates whether strings should have leading
+ * and trailing whitespace removed before comparison
+ */
+template<typename EnumType,
+ const char*(enumValueToStringFunction)(EnumType),
+ StringCompareType stringCompareType = StringCompareType::Exact,
+ StripStrings stripStrings = StripStrings::No>
+class StringToEnumValueConverter
+{
+public:
+ StringToEnumValueConverter() : stringToEnumValue_(stringCompareType)
+ {
+ for (const auto type : EnumerationWrapper<EnumType>{})
+ {
+ GMX_RELEASE_ASSERT(type != EnumType::Count,
+ "EnumerationWrapper<EnumType> should never return EnumType::Count");
+ std::string stringFromType = enumValueToStringFunction(type);
+ if (stripStrings == StripStrings::Yes)
+ {
+ // Ensure leading and trailing spaces are removed
+ stringFromType = stripString(stringFromType);
+ }
+ stringToEnumValue_[stringFromType] = type;
+ }
+ }
+
+ //! Return an optional enum value identified from the \c s (which is never EnumType::Count)
+ std::optional<EnumType> valueFrom(const std::string& s) const
+ {
+ typename decltype(stringToEnumValue_)::const_iterator typeIt;
+ if (stripStrings == StripStrings::Yes)
+ {
+ // Ensure leading and trailing spaces are removed
+ typeIt = stringToEnumValue_.find(stripString(s));
+ }
+ else
+ {
+ typeIt = stringToEnumValue_.find(s);
+ }
+ return (typeIt != stringToEnumValue_.end()) ? std::make_optional(typeIt->second) : std::nullopt;
+ }
+
+private:
+ /*! \brief Map of strings to enumeration values.
+ *
+ * By construction, those values never include
+ * EnumType::Count. */
+ std::map<std::string, EnumType, StringCompare> stringToEnumValue_;
+};
+
+} // namespace gmx
+
+#endif
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2011-2018, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
std::vector<std::string> splitDelimitedString(const std::string& str, char delim)
{
std::vector<std::string> result;
- size_t currPos = 0;
- const size_t len = str.length();
+ const size_t len = str.length();
if (len > 0)
{
- size_t nextDelim;
+ size_t nextDelim = 0;
+ size_t currPos = 0;
do
{
nextDelim = str.find(delim, currPos);
}
comparisonEnd = source.begin() + maxLengthOfComparison;
}
- return std::equal(source.begin(), comparisonEnd, target.begin(),
- [](const char& s, const char& t) { return std::tolower(s) == std::tolower(t); });
+ return std::equal(source.begin(), comparisonEnd, target.begin(), [](const char& s, const char& t) {
+ return std::tolower(s) == std::tolower(t);
+ });
}
/********************************************************************
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/** \internal \brief Helper function to select appropriate template based on runtime values.
*
- * Can only use enums for template parameters.
+ * Can use enums or booleans for template parameters.
* These enums must have a member \c Count indicating the total number of valid values.
*
* Example usage:
Count = 2
};
- template<Options p1, Options p2>
+ template<bool p0, Options p1, Options p2>
bool foo(int i);
- bool bar(Options p1, Options p2, int i) {
+ bool bar(bool p0, Options p1, Options p2, int i) {
return dispatchTemplatedFunction(
- [=](auto p1, auto p2) {
- return foo<p1, p2>(i);
+ [=](auto p0, auto p1, auto p2) {
+ return foo<p0, p1, p2>(i);
},
- p1, p2);
+ p0, p1, p2);
}
* \endcode
*/
es...);
}
+template<class Function, class... Enums>
+auto dispatchTemplatedFunction(Function&& f, bool e, Enums... es)
+{
+ return dispatchTemplatedFunction(
+ [&](auto... es_) {
+ return compat::mp_with_index<2>(size_t(e), [&](auto e_) {
+ return std::forward<Function>(f)(std::bool_constant<static_cast<bool>(e_)>(), es_...);
+ });
+ },
+ es...);
+}
+
} // namespace gmx
#endif // GMX_UTILITY_TEMPLATE_MP_H
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
-# Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
keyvaluetreetransform.cpp
listoflists.cpp
logger.cpp
- mdmodulenotification-impl.cpp
- mutex.cpp
+ mdmodulesnotifier.cpp
path.cpp
physicalnodecommunicator.cpp
range.cpp
strconvert.cpp
+ stringtoenumvalueconverter.cpp
stringutil.cpp
template_mp.cpp
textreader.cpp
textwriter.cpp
typetraits.cpp
)
+# TODO: Explicitly link specific modules.
+target_link_libraries(utility-test PRIVATE legacy_modules)
gmx_add_mpi_unit_test(UtilityMpiUnitTests utility-mpi-test 4
CPP_SOURCE_FILES
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
BITMASK_TEST_P(SetAndClear) //NOLINT(misc-definitions-in-headers)
{
- gmx_bitmask_t m;
+ gmx_bitmask_t m; //NOLINT(cppcoreguidelines-init-variables)
int i = GetParam();
bitmask_clear(&m);
EXPECT_TRUE(bitmask_is_zero(m));
BITMASK_TEST_P(InitBit) //NOLINT(misc-definitions-in-headers)
{
- gmx_bitmask_t m1, m2;
+ gmx_bitmask_t m1, m2; //NOLINT(cppcoreguidelines-init-variables)
int i = GetParam();
bitmask_init_bit(&m1, i);
bitmask_clear(&m2);
BITMASK_TEST_P(InitLowBits) //NOLINT(misc-definitions-in-headers)
{
- gmx_bitmask_t m;
+ gmx_bitmask_t m; //NOLINT(cppcoreguidelines-init-variables)
int i = GetParam();
bitmask_init_low_bits(&m, i);
for (int j = 0; j < BITMASK_SIZE; j++)
BITMASK_TEST_P(Disjoint) //NOLINT(misc-definitions-in-headers)
{
- gmx_bitmask_t m1, m2;
+ gmx_bitmask_t m1, m2; //NOLINT(cppcoreguidelines-init-variables)
int i = GetParam();
bitmask_init_bit(&m1, i);
bitmask_init_bit(&m2, i);
BITMASK_TEST_P(Union) //NOLINT(misc-definitions-in-headers)
{
- gmx_bitmask_t m1, m2;
+ gmx_bitmask_t m1, m2; //NOLINT(cppcoreguidelines-init-variables)
int i = GetParam();
int j = (i + BITMASK_SIZE / 2) % BITMASK_SIZE;
bitmask_init_bit(&m1, i);
}
BITMASK_TEST_P(ToHex) //NOLINT(misc-definitions-in-headers)
{
- gmx_bitmask_t m;
+ gmx_bitmask_t m; //NOLINT(cppcoreguidelines-init-variables)
bitmask_clear(&m);
bitmask_set_bit(&m, BITMASK_SIZE - 1);
EXPECT_EQ(to_hex_string(m), "8" + std::string(BITMASK_SIZE / 4 - 1, '0'));
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
// Incrementing iterators works
- auto x = std::begin(fooStrings);
+ const auto* x = std::begin(fooStrings);
EXPECT_EQ(*x, "Bar");
++x;
EXPECT_EQ(*x, "Baz");
auto buffer = serializerWithSwap.finishAndGetBuffer();
- InMemoryDeserializer deserializerWithSwap(buffer, std::is_same_v<real, double>,
- EndianSwapBehavior::Swap);
+ InMemoryDeserializer deserializerWithSwap(
+ buffer, std::is_same_v<real, double>, EndianSwapBehavior::Swap);
SerializerValues deserialisedValues = deserialize(&deserializerWithSwap);
auto buffer = serializer.finishAndGetBuffer();
- InMemoryDeserializer deserializerWithSwap(buffer, std::is_same_v<real, double>,
- EndianSwapBehavior::Swap);
+ InMemoryDeserializer deserializerWithSwap(
+ buffer, std::is_same_v<real, double>, EndianSwapBehavior::Swap);
SerializerValues deserialisedValues = deserialize(&deserializerWithSwap);
checkSerializerValuesforEquality(endianessSwappedValues_, deserialisedValues);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx::test::TestReferenceChecker checker(data.rootChecker());
checker.checkKeyValueTreeObject(input, "Input");
auto mappedPaths = transform.mappedPaths();
- checker.checkSequence(mappedPaths.begin(), mappedPaths.end(), "MappedPaths",
- &TreeValueTransformTest::checkMappedPath);
+ checker.checkSequence(
+ mappedPaths.begin(), mappedPaths.end(), "MappedPaths", &TreeValueTransformTest::checkMappedPath);
checker.checkKeyValueTreeObject(object, "Tree");
checkBackMapping(&checker, object, result.backMapping());
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
/*! \internal \file
* \brief
- * Tests MdModuleNotification
+ * Tests MDModulesNotifier
*
* \author Christian Blau <blau@kth.se>
* \ingroup module_utility
*/
#include "gmxpre.h"
-#include "gromacs/utility/mdmodulenotification-impl.h"
+#include "gromacs/utility/mdmodulesnotifier.h"
#include <gmock/gmock.h>
public:
void callback(EventA /*a*/) { notifiedEventA_ = true; }
- bool notifiedEventA() { return notifiedEventA_; }
+ bool notifiedEventA() const { return notifiedEventA_; }
private:
bool notifiedEventA_ = false;
public:
void callback(EventB* /* bPointer */) { notifiedEventB_ = true; }
- bool notifiedEventB() { return notifiedEventB_; }
+ bool notifiedEventB() const { return notifiedEventB_; }
private:
bool notifiedEventB_ = false;
void callback(EventA /* a */) { notifiedEventA_ = true; }
- bool notifiedEventB() { return notifiedEventB_; }
- bool notifiedEventA() { return notifiedEventA_; }
+ bool notifiedEventB() const { return notifiedEventB_; }
+ bool notifiedEventA() const { return notifiedEventA_; }
private:
bool notifiedEventB_ = false;
bool notifiedEventA_ = false;
};
-TEST(MDModuleNotificationTest, addConsumer)
+TEST(MDModulesNotifierTest, AddConsumer)
{
- registerMdModuleNotification<EventA>::type notifications;
- EventACallee eventACallee;
+ BuildMDModulesNotifier<EventA>::type notifier;
+ EventACallee eventACallee;
EXPECT_FALSE(eventACallee.notifiedEventA());
- notifications.subscribe([&eventACallee](EventA eventA) { eventACallee.callback(eventA); });
- notifications.notify(EventA{});
+ notifier.subscribe([&eventACallee](EventA eventA) { eventACallee.callback(eventA); });
+ notifier.notify(EventA{});
EXPECT_TRUE(eventACallee.notifiedEventA());
}
-TEST(MDModuleNotificationTest, addConsumerWithPointerParameter)
+TEST(MDModulesNotifierTest, AddConsumerWithPointerParameter)
{
- registerMdModuleNotification<EventB*>::type notifications;
- EventBCallee eventBCallee;
+ BuildMDModulesNotifier<EventB*>::type notifier;
+ EventBCallee eventBCallee;
EXPECT_FALSE(eventBCallee.notifiedEventB());
- notifications.subscribe([&eventBCallee](EventB* eventB) { eventBCallee.callback(eventB); });
+ notifier.subscribe([&eventBCallee](EventB* eventB) { eventBCallee.callback(eventB); });
EventB* eventBPointer = nullptr;
- notifications.notify(eventBPointer);
+ notifier.notify(eventBPointer);
EXPECT_TRUE(eventBCallee.notifiedEventB());
}
-TEST(MDModuleNotificationTest, addTwoDifferentConsumers)
+TEST(MDModulesNotifierTest, AddTwoDifferentConsumers)
{
- registerMdModuleNotification<EventA, EventB*>::type notifications;
- EventBCallee eventBCallee;
- EventACallee eventACallee;
+ BuildMDModulesNotifier<EventA, EventB*>::type notifier;
+ EventBCallee eventBCallee;
+ EventACallee eventACallee;
EXPECT_FALSE(eventACallee.notifiedEventA());
EXPECT_FALSE(eventBCallee.notifiedEventB());
- notifications.subscribe([&eventBCallee](EventB* eventB) { eventBCallee.callback(eventB); });
- notifications.subscribe([&eventACallee](EventA eventA) { eventACallee.callback(eventA); });
+ notifier.subscribe([&eventBCallee](EventB* eventB) { eventBCallee.callback(eventB); });
+ notifier.subscribe([&eventACallee](EventA eventA) { eventACallee.callback(eventA); });
EventB* eventBPointer = nullptr;
- notifications.notify(eventBPointer);
+ notifier.notify(eventBPointer);
EXPECT_FALSE(eventACallee.notifiedEventA());
EXPECT_TRUE(eventBCallee.notifiedEventB());
- notifications.notify(EventA{});
+ notifier.notify(EventA{});
EXPECT_TRUE(eventACallee.notifiedEventA());
EXPECT_TRUE(eventBCallee.notifiedEventB());
}
-TEST(MDModuleNotificationTest, consumerOfTwoResources)
+TEST(MDModulesNotifierTest, AddConsumerOfTwoResources)
{
- registerMdModuleNotification<EventA, EventB*>::type notifications;
+ BuildMDModulesNotifier<EventA, EventB*>::type notifier;
EventAandBCallee callee;
EXPECT_FALSE(callee.notifiedEventA());
// requires a template parameter here, because call is ambiguous otherwise
- notifications.subscribe([&callee](EventA msg) { callee.callback(msg); });
- notifications.subscribe([&callee](EventB* msg) { callee.notify(msg); });
+ notifier.subscribe([&callee](EventA msg) { callee.callback(msg); });
+ notifier.subscribe([&callee](EventB* msg) { callee.notify(msg); });
EventB* eventBp = nullptr;
- notifications.notify(eventBp);
+ notifier.notify(eventBp);
EXPECT_FALSE(callee.notifiedEventA());
EXPECT_TRUE(callee.notifiedEventB());
- notifications.notify(EventA{});
+ notifier.notify(EventA{});
EXPECT_TRUE(callee.notifiedEventA());
EXPECT_TRUE(callee.notifiedEventB());
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*! \internal \file
- * \brief Tests for gmx::Mutex
- *
- * These tests ensure that basic mutual-exclusion properties hold.
- * Note that no testing can prove there isn't a bug, but if one
- * exists, then these tests might expose one.
- *
- * In particular, try_lock can be implemented differently on different
- * platforms, or with different default mutex types, so we should
- * check that the behaviour continues to conform with the thread-MPI
- * documentation.
- *
- * \author Mark Abraham <mark.j.abraham@gmail.com>
- * \ingroup module_utility
- */
-
-#include "gmxpre.h"
-
-#include "gromacs/utility/mutex.h"
-
-#include "config.h"
-
-#include <future>
-
-#include <gtest/gtest.h>
-
-
-namespace gmx
-{
-namespace test
-{
-namespace
-{
-
-//! Convenience definition.
-using Lock = gmx::lock_guard<Mutex>;
-
-TEST(MutexBasicTest, CanBeMade)
-{
- Mutex m;
-}
-
-TEST(MutexBasicTest, CanBeLocked)
-{
- Mutex m;
- ASSERT_NO_THROW(m.lock());
- m.unlock();
-}
-
-TEST(MutexBasicTest, CanBeTryLocked)
-{
- Mutex m;
- ASSERT_TRUE(m.try_lock());
- m.unlock();
-}
-
-TEST(MutexBasicTest, CanBeUsedInLockGuard)
-{
- Mutex m;
- Lock g(m);
-}
-
-//! A shared value for a mutex to protect
-int g_sharedValue;
-//! A mutex to protect a shared value
-Mutex g_sharedValueMutex;
-
-//! Function type for asynchronous tasks.
-using TaskType = std::function<int(void)>;
-
-//! A task that just does work.
-int updateSharedValue()
-{
- return ++g_sharedValue;
-}
-
-//! A task that does work after it gets the mutex.
-int updateSharedValueWithLock()
-{
- Lock guard(g_sharedValueMutex);
- return updateSharedValue();
-}
-
-//! A task that does work only if it can get the mutex immediately.
-int updateSharedValueWithTryLock()
-{
- // Special return value to signal when work was not done because
- // the lock was not acquired.
- int result = -1;
- if (g_sharedValueMutex.try_lock())
- {
- result = updateSharedValue();
- g_sharedValueMutex.unlock();
- }
- return result;
-}
-
-/*! \brief Parameterized test fixture.
- *
- * Checks that different launch policies work. In further tests of
- * mutual exclusion, we need to specify std::thread::async, to require
- * that a thread actually launched. The default policy permits the
- * std:: implementation to avoid launching a thread, and at least the
- * behaviour of thread-MPI try_lock also varies with the threading
- * implementation underlying it. */
-class DifferentTasksTest : public ::testing::TestWithParam<TaskType>
-{
-public:
- DifferentTasksTest() { g_sharedValue = 0; }
- //! Check the results
- void checkResults()
- {
- int result = 0;
- EXPECT_NO_THROW(result = futureResult_.get()) << "Future should not contain an exception";
- EXPECT_EQ(1, result) << "Task should have run";
- EXPECT_EQ(1, g_sharedValue) << "Shared value should be updated";
- }
- //! Contains the result the task returns.
- std::future<int> futureResult_;
-};
-
-TEST_P(DifferentTasksTest, StdAsyncWorksWithDefaultPolicy)
-{
- auto task = GetParam();
- EXPECT_NO_THROW(futureResult_ = std::async(task)) << "Async should succeed";
- checkResults();
-}
-
-TEST_P(DifferentTasksTest, StdAsyncWorksWithAsyncLaunchPolicy)
-{
- auto task = GetParam();
- EXPECT_NO_THROW(futureResult_ = std::async(std::launch::async, task)) << "Async should succeed";
- checkResults();
-}
-
-TEST_P(DifferentTasksTest, StdAsyncWorksWithDeferredLaunchPolicy)
-{
- auto task = GetParam();
- EXPECT_NO_THROW(futureResult_ = std::async(std::launch::deferred, task))
- << "Async should succeed";
- checkResults();
-}
-
-// Test that the different launch policies work with the different tasks
-INSTANTIATE_TEST_CASE_P(WithAndWithoutMutex,
- DifferentTasksTest,
- ::testing::Values(updateSharedValue,
- updateSharedValueWithLock,
- updateSharedValueWithTryLock));
-
-TEST(MutexTaskTest, MutualExclusionWorksWithLock)
-{
- g_sharedValue = 0;
- std::future<int> result;
- {
- // Hold the mutex, launch a lock attempt on another
- // thread, check that the shared value isn't changed, then
- // release the mutex by leaving the scope, after which the
- // other thread's lock can get the mutex.
- Lock guard(g_sharedValueMutex);
- result = std::async(std::launch::async, updateSharedValueWithLock);
- EXPECT_EQ(0, g_sharedValue) << "Task should not have run yet";
- }
- EXPECT_EQ(1, result.get()) << "Task should have run";
- EXPECT_EQ(1, g_sharedValue) << "Shared value should be updated";
-}
-
-TEST(MutexTaskTest, MutualExclusionWorksWithTryLockOnOtherThread)
-{
- g_sharedValue = 0;
- {
- // Hold the mutex, launch a try_lock attempt on another
- // thread, check that the shared value isn't changed, then
- // make sure the try_lock attempt has returned, double check
- // that the shared value isn't changed, and release the mutex
- // by leaving the scope.
- Lock guard(g_sharedValueMutex);
- auto result = std::async(std::launch::async, updateSharedValueWithTryLock);
- EXPECT_EQ(0, g_sharedValue) << "Data race detected";
- EXPECT_EQ(-1, result.get()) << "The try_lock should fail";
- EXPECT_EQ(0, g_sharedValue) << "Task should not have run";
- }
- EXPECT_EQ(0, g_sharedValue) << "Mutex release can't affect the protected value";
-}
-
-TEST(MutexTaskTest, MutualExclusionWorksWithTryLockOnSameThread)
-{
- g_sharedValue = 0;
- int finalSharedValue = GMX_NATIVE_WINDOWS ? 1 : 0;
- {
- // Hold the mutex and launch a try_lock attempt on this
- // thread. Behaviour then varies with the implementation
- // underlying thread-MPI.
- Lock guard(g_sharedValueMutex);
- int result = updateSharedValueWithTryLock();
- if (GMX_NATIVE_WINDOWS)
- {
- EXPECT_EQ(1, result) << "The try_lock should succeed";
- EXPECT_EQ(finalSharedValue, g_sharedValue) << "Task should have run";
- }
- else
- {
- EXPECT_EQ(-1, result) << "The try_lock should fail";
- EXPECT_EQ(finalSharedValue, g_sharedValue) << "Task should not have run";
- }
- }
- EXPECT_EQ(finalSharedValue, g_sharedValue) << "Mutex release can't affect the protected value";
-}
-
-} // namespace
-} // namespace test
-} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
gmx::test::TestReferenceData data;
gmx::test::TestReferenceChecker rootChecker(data.rootChecker());
- for (const std::string& input :
- { "", "md.log", "md", "/tmp/absolute.txt", "simpledir/traj.tng", "simpledir/traj",
- "windowsdir\\traj.tng", "complex.dir/traj.tng", "complex.dir/traj",
- "nested/dir/conf.pdb", "/tmp/absolutedir/conf.pdb" })
+ for (const std::string& input : { "",
+ "md.log",
+ "md",
+ "/tmp/absolute.txt",
+ "simpledir/traj.tng",
+ "simpledir/traj",
+ "windowsdir\\traj.tng",
+ "complex.dir/traj.tng",
+ "complex.dir/traj",
+ "nested/dir/conf.pdb",
+ "/tmp/absolutedir/conf.pdb" })
{
SCOPED_TRACE(std::string("for input '") + input + "'");
auto checker = rootChecker.checkCompound("PathToTest", input);
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief Tests for string-to-enum-value helper functor
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_utility
+ */
+#include "gmxpre.h"
+
+#include "gromacs/utility/stringtoenumvalueconverter.h"
+
+#include <gtest/gtest.h>
+
+namespace gmx
+{
+
+namespace
+{
+
+//! Type to use in testing
+enum class Foo : int
+{
+ Bar,
+ Ugh,
+ Fooz,
+ Weird,
+ Empty,
+ Count,
+ Default = Ugh
+};
+
+//! Declare the conventional conversion function
+const char* enumValueToString(Foo f)
+{
+ static constexpr gmx::EnumerationArray<Foo, const char*> toString = {
+ "Bar", "Ugh ", "Foo z", "We-i_rd", ""
+ };
+ return toString[f];
+}
+
+//! Declare an atypical conversion function
+const char* enumValueToLetterAsString(Foo f)
+{
+ static constexpr gmx::EnumerationArray<Foo, const char*> toString = { "B", "U", "F", "W", "" };
+ return toString[f];
+}
+
+//! Pretty-printer for GoogleTest to use
+::std::ostream& operator<<(::std::ostream& os, const std::optional<Foo>& f)
+{
+ if (f)
+ {
+ return os << enumValueToString(f.value());
+ }
+ else
+ {
+ return os << "Out-of-range Foo value";
+ }
+}
+
+TEST(StringToEnumValueConverterTest, ExactStringComparisonWorksWithoutStripping)
+{
+ StringToEnumValueConverter<Foo, enumValueToString, StringCompareType::Exact, StripStrings::No> converter;
+ EXPECT_EQ(converter.valueFrom("Bar"), Foo::Bar);
+ EXPECT_FALSE(converter.valueFrom("bar"));
+ EXPECT_EQ(converter.valueFrom("Ugh "), Foo::Ugh);
+ EXPECT_FALSE(converter.valueFrom("ugh "));
+ EXPECT_EQ(converter.valueFrom("Foo z"), Foo::Fooz);
+ EXPECT_FALSE(converter.valueFrom("foo z"));
+ EXPECT_EQ(converter.valueFrom("We-i_rd"), Foo::Weird);
+ EXPECT_FALSE(converter.valueFrom("we-i_rd"));
+ EXPECT_EQ(converter.valueFrom(""), Foo::Empty);
+ EXPECT_FALSE(converter.valueFrom("count"));
+ EXPECT_FALSE(converter.valueFrom("Unknown"));
+ EXPECT_FALSE(converter.valueFrom("BarFoo z"));
+ EXPECT_FALSE(converter.valueFrom("Ugh"));
+ EXPECT_FALSE(converter.valueFrom("Default"));
+}
+
+TEST(StringToEnumValueConverterTest, CaseInsensitiveStringComparisonWorksWithoutStripping)
+{
+ StringToEnumValueConverter<Foo, enumValueToString, StringCompareType::CaseInsensitive, StripStrings::No> converter;
+ EXPECT_EQ(converter.valueFrom("Bar"), Foo::Bar);
+ EXPECT_EQ(converter.valueFrom("bar"), Foo::Bar);
+ EXPECT_EQ(converter.valueFrom("Ugh "), Foo::Ugh);
+ EXPECT_EQ(converter.valueFrom("ugh "), Foo::Ugh);
+ EXPECT_EQ(converter.valueFrom("Foo z"), Foo::Fooz);
+ EXPECT_EQ(converter.valueFrom("foo z"), Foo::Fooz);
+ EXPECT_EQ(converter.valueFrom("We-i_rd"), Foo::Weird);
+ EXPECT_EQ(converter.valueFrom("we-i_rd"), Foo::Weird);
+ EXPECT_EQ(converter.valueFrom(""), Foo::Empty);
+ EXPECT_FALSE(converter.valueFrom("Count"));
+ EXPECT_FALSE(converter.valueFrom("count"));
+ EXPECT_FALSE(converter.valueFrom("Unknown"));
+ EXPECT_FALSE(converter.valueFrom("barfoo z"));
+ EXPECT_FALSE(converter.valueFrom("Ugh"));
+ EXPECT_FALSE(converter.valueFrom("Default"));
+}
+
+TEST(StringToEnumValueConverterTest, CaseAndDashInsensitiveStringComparisonWorksWithoutStripping)
+{
+ StringToEnumValueConverter<Foo, enumValueToString, StringCompareType::CaseAndDashInsensitive, StripStrings::No> converter;
+ EXPECT_EQ(converter.valueFrom("Bar"), Foo::Bar);
+ EXPECT_EQ(converter.valueFrom("b-ar"), Foo::Bar);
+ EXPECT_EQ(converter.valueFrom("Ugh "), Foo::Ugh);
+ EXPECT_EQ(converter.valueFrom("_ugh "), Foo::Ugh);
+ EXPECT_EQ(converter.valueFrom("Foo z"), Foo::Fooz);
+ EXPECT_EQ(converter.valueFrom("fo_o z"), Foo::Fooz);
+ EXPECT_EQ(converter.valueFrom("We-i_rd"), Foo::Weird);
+ EXPECT_EQ(converter.valueFrom("we-i_rd"), Foo::Weird);
+ EXPECT_EQ(converter.valueFrom(""), Foo::Empty);
+ EXPECT_FALSE(converter.valueFrom("Count"));
+ EXPECT_FALSE(converter.valueFrom("count"));
+ EXPECT_FALSE(converter.valueFrom("Unknown"));
+ EXPECT_FALSE(converter.valueFrom("Bar-Foo z"));
+ EXPECT_FALSE(converter.valueFrom("Ugh"));
+ EXPECT_FALSE(converter.valueFrom("Default"));
+}
+
+TEST(StringToEnumValueConverterTest, ExactStringComparisonWorksWithStripping)
+{
+ StringToEnumValueConverter<Foo, enumValueToString, StringCompareType::Exact, StripStrings::Yes> converter;
+ EXPECT_EQ(converter.valueFrom("Bar "), Foo::Bar);
+ EXPECT_FALSE(converter.valueFrom("Ba r"));
+ EXPECT_EQ(converter.valueFrom("Ugh"), Foo::Ugh);
+ EXPECT_FALSE(converter.valueFrom("ugh"));
+ EXPECT_EQ(converter.valueFrom(" Foo z "), Foo::Fooz);
+ EXPECT_FALSE(converter.valueFrom(" foo z"));
+ EXPECT_EQ(converter.valueFrom("We-i_rd "), Foo::Weird);
+ EXPECT_FALSE(converter.valueFrom(" we-i_rd "));
+ EXPECT_EQ(converter.valueFrom(""), Foo::Empty);
+ EXPECT_FALSE(converter.valueFrom(" Count"));
+ EXPECT_FALSE(converter.valueFrom("count "));
+ EXPECT_FALSE(converter.valueFrom("Unknown"));
+ EXPECT_FALSE(converter.valueFrom("Bar Foo z"));
+ EXPECT_EQ(converter.valueFrom(" Ugh"), Foo::Ugh);
+ EXPECT_FALSE(converter.valueFrom("Default"));
+}
+
+TEST(StringToEnumValueConverterTest, CaseInsensitiveStringComparisonWorksWithStripping)
+{
+ StringToEnumValueConverter<Foo, enumValueToString, StringCompareType::CaseInsensitive, StripStrings::Yes> converter;
+ EXPECT_EQ(converter.valueFrom("Bar "), Foo::Bar);
+ EXPECT_FALSE(converter.valueFrom("ba r"));
+ EXPECT_EQ(converter.valueFrom("Ugh "), Foo::Ugh);
+ EXPECT_EQ(converter.valueFrom(" ugh "), Foo::Ugh);
+ EXPECT_EQ(converter.valueFrom(" Foo z "), Foo::Fooz);
+ EXPECT_EQ(converter.valueFrom("foo z "), Foo::Fooz);
+ EXPECT_EQ(converter.valueFrom("We-i_rd "), Foo::Weird);
+ EXPECT_EQ(converter.valueFrom(" we-i_rd "), Foo::Weird);
+ EXPECT_EQ(converter.valueFrom(""), Foo::Empty);
+ EXPECT_FALSE(converter.valueFrom(" Count"));
+ EXPECT_FALSE(converter.valueFrom("count "));
+ EXPECT_FALSE(converter.valueFrom("Unknown"));
+ EXPECT_FALSE(converter.valueFrom(" barfoo z"));
+ EXPECT_EQ(converter.valueFrom(" Ugh"), Foo::Ugh);
+ EXPECT_FALSE(converter.valueFrom("Default"));
+}
+
+TEST(StringToEnumValueConverterTest, CaseAndDashInsensitiveStringComparisonWorksWithStripping)
+{
+ StringToEnumValueConverter<Foo, enumValueToString, StringCompareType::CaseAndDashInsensitive, StripStrings::Yes> converter;
+ EXPECT_EQ(converter.valueFrom("Bar "), Foo::Bar);
+ EXPECT_FALSE(converter.valueFrom("b-a r"));
+ EXPECT_EQ(converter.valueFrom("Ugh "), Foo::Ugh);
+ EXPECT_EQ(converter.valueFrom(" _ugh "), Foo::Ugh);
+ EXPECT_EQ(converter.valueFrom(" Foo z "), Foo::Fooz);
+ EXPECT_EQ(converter.valueFrom("fo_o z "), Foo::Fooz);
+ EXPECT_EQ(converter.valueFrom("We-i_rd "), Foo::Weird);
+ EXPECT_EQ(converter.valueFrom(" we-i_rd "), Foo::Weird);
+ EXPECT_EQ(converter.valueFrom(""), Foo::Empty);
+ EXPECT_FALSE(converter.valueFrom(" Count"));
+ EXPECT_FALSE(converter.valueFrom("coun-t "));
+ EXPECT_FALSE(converter.valueFrom("Unknown"));
+ EXPECT_FALSE(converter.valueFrom(" Bar-Foo z "));
+ EXPECT_EQ(converter.valueFrom("Ugh "), Foo::Ugh);
+ EXPECT_FALSE(converter.valueFrom("Default"));
+}
+
+TEST(StringToEnumValueConverterTest, CustomConverterWorks)
+{
+ StringToEnumValueConverter<Foo, enumValueToLetterAsString> converter;
+ EXPECT_EQ(converter.valueFrom("B"), Foo::Bar);
+ EXPECT_FALSE(converter.valueFrom("b"));
+ EXPECT_EQ(converter.valueFrom("U"), Foo::Ugh);
+ EXPECT_FALSE(converter.valueFrom("u"));
+ EXPECT_EQ(converter.valueFrom("F"), Foo::Fooz);
+ EXPECT_FALSE(converter.valueFrom("f"));
+ EXPECT_EQ(converter.valueFrom(""), Foo::Empty);
+ EXPECT_FALSE(converter.valueFrom("C"));
+ EXPECT_FALSE(converter.valueFrom("c"));
+ EXPECT_FALSE(converter.valueFrom("X"));
+ EXPECT_FALSE(converter.valueFrom("Default"));
+}
+
+} // namespace
+} // namespace gmx
{
const char* const words[] = { "The", "quick", "brown", "fox" };
EXPECT_EQ("The .quick .brown .fox ",
- gmx::formatAndJoin(gmx::ArrayRef<const char* const>(words), ".",
- gmx::StringFormatter("%-10s")));
+ gmx::formatAndJoin(
+ gmx::ArrayRef<const char* const>(words), ".", gmx::StringFormatter("%-10s")));
const int values[] = { 0, 1, 4 };
EXPECT_EQ("0,1,4",
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return 2 * int(i) + int(j) + k;
}
-TEST(TemplateMPTest, DispatchTemplatedFunction)
+template<bool doDoubling, Options i, Options j>
+static int testBoolEnumTwoIPlusJPlusK(int k)
+{
+ return (doDoubling ? 2 : 1) * int(i) + int(j) + k;
+}
+
+template<bool doDoubling>
+static int testBoolDoubleOrNot(int k)
+{
+ return (doDoubling ? 2 : 1) * k;
+}
+
+
+TEST(TemplateMPTest, DispatchTemplatedFunctionEnum)
+{
+ int five = 5;
+ int two1plus2plus5 = dispatchTemplatedFunction(
+ [=](auto p1, auto p2) { return testEnumTwoIPlusJPlusK<p1, p2>(five); }, Options::Op1, Options::Op2);
+ EXPECT_EQ(two1plus2plus5, 9);
+}
+
+TEST(TemplateMPTest, DispatchTemplatedFunctionBool)
+{
+ int five = 5;
+ int double5 = dispatchTemplatedFunction([=](auto p1) { return testBoolDoubleOrNot<p1>(five); }, true);
+ EXPECT_EQ(double5, 10);
+ int just5 = dispatchTemplatedFunction([=](auto p1) { return testBoolDoubleOrNot<p1>(five); }, false);
+ EXPECT_EQ(just5, 5);
+}
+
+TEST(TemplateMPTest, DispatchTemplatedFunctionEnumBool)
{
int five = 5;
int two1plus2plus5 = dispatchTemplatedFunction(
- [=](auto p1, auto p2) { return testEnumTwoIPlusJPlusK<p1, p2>(five); }, Options::Op1,
+ [=](auto p1, auto p2, auto p3) { return testBoolEnumTwoIPlusJPlusK<p1, p2, p3>(five); },
+ true,
+ Options::Op1,
Options::Op2);
EXPECT_EQ(two1plus2plus5, 9);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_UTILITY_TEXTREADER_H
#define GMX_UTILITY_TEXTREADER_H
+#include <memory>
#include <string>
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/textstream.h"
namespace gmx
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
+#include <memory>
#include <string>
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/textstream.h"
namespace gmx
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace gmx
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int pr_indent(FILE* fp, int n)
{
- int i;
-
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
fprintf(fp, " ");
}
void pr_reals(FILE* fp, int indent, const char* title, const real* vec, int n)
{
- int i;
-
if (available(fp, vec, indent, title))
{
pr_indent(fp, indent);
fprintf(fp, "%s:\t", title);
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
fprintf(fp, " %10g", vec[i]);
}
void pr_doubles(FILE* fp, int indent, const char* title, const double* vec, int n)
{
- int i;
-
if (available(fp, vec, indent, title))
{
pr_indent(fp, indent);
fprintf(fp, "%s:\t", title);
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
fprintf(fp, " %10g", vec[i]);
}
void pr_reals_of_dim(FILE* fp, int indent, const char* title, const real* vec, int n, int dim)
{
- int i, j;
const char* fshort = "%12.5e";
const char* flong = "%15.8e";
- const char* format;
-
- if (getenv("GMX_PRINT_LONGFORMAT") != nullptr)
- {
- format = flong;
- }
- else
- {
- format = fshort;
- }
+ const char* format = (getenv("GMX_PRINT_LONGFORMAT") != nullptr) ? flong : fshort;
if (available(fp, vec, indent, title))
{
indent = pr_title_nxn(fp, indent, title, n, dim);
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
pr_indent(fp, indent);
fprintf(fp, "%s[%5d]={", title, i);
- for (j = 0; j < dim; j++)
+ for (int j = 0; j < dim; j++)
{
if (j != 0)
{
void pr_strings(FILE* fp, int indent, const char* title, char*** nm, int n, gmx_bool bShowNumbers)
{
- int i;
-
if (available(fp, nm, indent, title))
{
indent = pr_title_n(fp, indent, title, n);
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
pr_indent(fp, indent);
fprintf(fp, "%s[%d]={name=\"%s\"}\n", title, bShowNumbers ? i : -1, *(nm[i]));
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
# define _GNU_SOURCE 1
#endif
-/* Some C++(?) compilers require these to be defined to get the integer limits
- * and format specifier macros from stdint.h and inttypes.h, respectively.
- * The macros are in C99 and C++11, but not in C++98...
- * As with _GNU_SOURCE, these need to be defined before these headers get first
- * included. Unlike _GNU_SOURCE, these headers are included indirectly in most
- * header and source files (even though the macros are not used that often), so
- * there is no easy alternative to defining them here, either.
- * If someone happens to use such a compiler to compile against the installed
- * Gromacs headers, they need for now take care to define the macros themselves
- * (as there is no way Gromacs can do that consistently).
- */
-#define __STDC_LIMIT_MACROS
-#define __STDC_FORMAT_MACROS
-
#if GMX_FAHCORE
# define FULLINDIRECT 1
# define USE_FAH_XDR 1
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
-# Copyright (c) 2015,2016,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,2018,2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
target_include_directories(mdrun_objlib SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
# Should be possible to remove this when resolving #3290
target_include_directories(mdrun_objlib SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
+target_link_libraries(mdrun_objlib PRIVATE common)
+target_link_libraries(mdrun_objlib PRIVATE legacy_api)
+# TODO: Explicitly link specific modules.
+target_link_libraries(mdrun_objlib PRIVATE legacy_modules)
if(GMX_FAHCORE)
# The lack of a real source file here alongside the object library
# may break some generators, according to CMake documentation. If
# so, we can consider adding some dummy file to make it work.
add_library(fahcore $<TARGET_OBJECTS:mdrun_objlib>)
- target_link_libraries(fahcore PRIVATE ${GMX_COMMON_LIBRARIES})
-elseif(GMX_BUILD_MDRUN_ONLY)
- message(STATUS "The mdrun-only build is deprecated")
- add_executable(mdrun $<TARGET_OBJECTS:mdrun_objlib> mdrun_main.cpp)
- gmx_target_compile_options(mdrun)
- target_include_directories(mdrun SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
- target_compile_definitions(mdrun PRIVATE HAVE_CONFIG_H)
- target_link_libraries(mdrun libgromacs
- ${GMX_COMMON_LIBRARIES}
- ${GMX_EXE_LINKER_FLAGS})
- set(BINARY_NAME "mdrun${GMX_BINARY_SUFFIX}")
- set_target_properties(mdrun PROPERTIES
- OUTPUT_NAME "${BINARY_NAME}")
- install(TARGETS mdrun DESTINATION ${CMAKE_INSTALL_BINDIR} COMPONENT mdrun)
- file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/gmx-completion-${BINARY_NAME}.bash
- "complete -o nospace -F _gmx_mdrun_compl ${BINARY_NAME}")
- install(FILES ${CMAKE_CURRENT_BINARY_DIR}/gmx-completion-${BINARY_NAME}.bash
- DESTINATION ${CMAKE_INSTALL_BINDIR} COMPONENT runtime)
+ target_link_libraries(fahcore PRIVATE ${GMX_COMMON_LIBRARIES} legacy_api)
else()
file(GLOB GMX_MAIN_SOURCES gmx.cpp legacymodules.cpp)
if(GMX_X11)
gmx_target_compile_options(view_objlib)
target_compile_definitions(view_objlib PRIVATE HAVE_CONFIG_H)
target_include_directories(view_objlib SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
+ target_link_libraries(view_objlib PRIVATE common legacy_api)
+ # TODO: Explicitly link specific modules.
+ target_link_libraries(view_objlib PRIVATE legacy_modules)
add_library(gmx_objlib OBJECT ${GMX_MAIN_SOURCES})
+ target_link_libraries(gmx_objlib PRIVATE common legacy_api)
+ # TODO: Explicitly link specific modules.
+ target_link_libraries(gmx_objlib PRIVATE legacy_modules)
target_include_directories(gmx_objlib SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
target_include_directories(gmx_objlib SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
add_executable(gmx
add_executable(Gromacs::gmx ALIAS gmx)
gmx_target_compile_options(gmx)
target_compile_definitions(gmx PRIVATE HAVE_CONFIG_H)
- target_link_libraries(gmx libgromacs
- ${GMX_COMMON_LIBRARIES}
- ${GMX_EXE_LINKER_FLAGS})
+ target_link_libraries(gmx PRIVATE
+ common
+ libgromacs
+ ${GMX_COMMON_LIBRARIES}
+ ${GMX_EXE_LINKER_FLAGS})
if(GMX_X11)
target_link_libraries(gmx ${X11_LIBRARIES})
endif()
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx::ICommandLineOptionsModule::registerModuleFactory(
manager, gmx::DumpInfo::name, gmx::DumpInfo::shortDescription, &gmx::DumpInfo::create);
registerModule(manager, &gmx_grompp, "grompp", "Make a run input file");
- gmx::ICommandLineOptionsModule::registerModuleFactory(manager, gmx::ConvertTprInfo::name,
+ gmx::ICommandLineOptionsModule::registerModuleFactory(manager,
+ gmx::ConvertTprInfo::name,
gmx::ConvertTprInfo::shortDescription,
&gmx::ConvertTprInfo::create);
registerObsoleteTool(manager, "tpbconv");
registerModule(manager, &gmx_x2top, "x2top", "Generate a primitive topology from coordinates");
registerModuleNoNice(
- manager, &gmx::gmx_mdrun, "mdrun",
+ manager,
+ &gmx::gmx_mdrun,
+ "mdrun",
"Perform a simulation, do a normal mode analysis or an energy minimization");
- gmx::ICommandLineOptionsModule::registerModuleFactory(
- manager, gmx::NonbondedBenchmarkInfo::name,
- gmx::NonbondedBenchmarkInfo::shortDescription, &gmx::NonbondedBenchmarkInfo::create);
+ gmx::ICommandLineOptionsModule::registerModuleFactory(manager,
+ gmx::NonbondedBenchmarkInfo::name,
+ gmx::NonbondedBenchmarkInfo::shortDescription,
+ &gmx::NonbondedBenchmarkInfo::create);
- gmx::ICommandLineOptionsModule::registerModuleFactory(manager, gmx::InsertMoleculesInfo::name(),
+ gmx::ICommandLineOptionsModule::registerModuleFactory(manager,
+ gmx::InsertMoleculesInfo::name(),
gmx::InsertMoleculesInfo::shortDescription(),
&gmx::InsertMoleculesInfo::create);
- gmx::ICommandLineOptionsModule::registerModuleFactory(manager, gmx::ReportMethodsInfo::name,
+ gmx::ICommandLineOptionsModule::registerModuleFactory(manager,
+ gmx::ReportMethodsInfo::name,
gmx::ReportMethodsInfo::shortDescription,
&gmx::ReportMethodsInfo::create);
- gmx::ICommandLineOptionsModule::registerModuleFactory(manager, gmx::pdb2gmxInfo::name,
- gmx::pdb2gmxInfo::shortDescription,
- &gmx::pdb2gmxInfo::create);
+ gmx::ICommandLineOptionsModule::registerModuleFactory(
+ manager, gmx::pdb2gmxInfo::name, gmx::pdb2gmxInfo::shortDescription, &gmx::pdb2gmxInfo::create);
// Modules from gmx_ana.h.
- registerModule(manager, &gmx_do_dssp, "do_dssp",
+ registerModule(manager,
+ &gmx_do_dssp,
+ "do_dssp",
"Assign secondary structure and calculate solvent accessible surface area");
registerModule(manager, &gmx_editconf, "editconf", "Convert and manipulates structure files");
registerModule(manager, &gmx_eneconv, "eneconv", "Convert energy files");
registerModule(manager, &gmx_solvate, "solvate", "Solvate a system");
registerObsoleteTool(manager, "genbox");
- registerModule(manager, &gmx_genconf, "genconf",
- "Multiply a conformation in 'random' orientations");
- registerModule(manager, &gmx_genion, "genion",
+ registerModule(
+ manager, &gmx_genconf, "genconf", "Multiply a conformation in 'random' orientations");
+ registerModule(manager,
+ &gmx_genion,
+ "genion",
"Generate monoatomic ions on energetically favorable positions");
- registerModule(manager, &gmx_genrestr, "genrestr",
+ registerModule(manager,
+ &gmx_genrestr,
+ "genrestr",
"Generate position restraints or distance restraints for index groups");
- registerModule(manager, &gmx_make_edi, "make_edi",
+ registerModule(manager,
+ &gmx_make_edi,
+ "make_edi",
"Generate input files for essential dynamics sampling");
registerModule(manager, &gmx_make_ndx, "make_ndx", "Make index files");
registerModule(manager, &gmx_mk_angndx, "mk_angndx", "Generate index files for 'gmx angle'");
registerModule(manager, &gmx_trjcat, "trjcat", "Concatenate trajectory files");
registerModule(manager, &gmx_trjconv, "trjconv", "Convert and manipulates trajectory files");
- registerModule(manager, &gmx_trjorder, "trjorder",
+ registerModule(manager,
+ &gmx_trjorder,
+ "trjorder",
"Order molecules according to their distance to a group");
- registerModule(manager, &gmx_xpm2ps, "xpm2ps",
- "Convert XPM (XPixelMap) matrices to postscript or XPM");
+ registerModule(
+ manager, &gmx_xpm2ps, "xpm2ps", "Convert XPM (XPixelMap) matrices to postscript or XPM");
registerModule(manager, &gmx_anaeig, "anaeig", "Analyze eigenvectors/normal modes");
registerModule(manager, &gmx_analyze, "analyze", "Analyze data sets");
- registerModule(manager, &gmx_g_angle, "angle",
+ registerModule(manager,
+ &gmx_g_angle,
+ "angle",
"Calculate distributions and correlations for angles and dihedrals");
- registerModule(manager, &gmx_awh, "awh",
- "Extract data from an accelerated weight histogram (AWH) run");
- registerModule(manager, &gmx_bar, "bar",
+ registerModule(
+ manager, &gmx_awh, "awh", "Extract data from an accelerated weight histogram (AWH) run");
+ registerModule(manager,
+ &gmx_bar,
+ "bar",
"Calculate free energy difference estimates through Bennett's acceptance ratio");
registerObsoleteTool(manager, "bond");
registerObsoleteTool(manager, "dist");
registerObsoleteTool(manager, "sgangle");
registerModule(manager, &gmx_bundle, "bundle", "Analyze bundles of axes, e.g., helices");
- registerModule(manager, &gmx_chi, "chi",
+ registerModule(manager,
+ &gmx_chi,
+ "chi",
"Calculate everything you want to know about chi and other dihedrals");
registerModule(manager, &gmx_cluster, "cluster", "Cluster structures");
- registerModule(manager, &gmx_clustsize, "clustsize",
- "Calculate size distributions of atomic clusters");
+ registerModule(
+ manager, &gmx_clustsize, "clustsize", "Calculate size distributions of atomic clusters");
registerModule(manager, &gmx_confrms, "confrms", "Fit two structures and calculates the RMSD");
registerModule(manager, &gmx_covar, "covar", "Calculate and diagonalize the covariance matrix");
- registerModule(manager, &gmx_current, "current",
+ registerModule(manager,
+ &gmx_current,
+ "current",
"Calculate dielectric constants and current autocorrelation function");
registerModule(manager, &gmx_density, "density", "Calculate the density of the system");
- registerModule(manager, &gmx_densmap, "densmap",
- "Calculate 2D planar or axial-radial density maps");
+ registerModule(
+ manager, &gmx_densmap, "densmap", "Calculate 2D planar or axial-radial density maps");
registerModule(manager, &gmx_densorder, "densorder", "Calculate surface fluctuations");
- registerModule(manager, &gmx_dielectric, "dielectric",
+ registerModule(manager,
+ &gmx_dielectric,
+ "dielectric",
"Calculate frequency dependent dielectric constants");
registerModule(manager, &gmx_dipoles, "dipoles", "Compute the total dipole plus fluctuations");
registerModule(manager, &gmx_disre, "disre", "Analyze distance restraints");
- registerModule(manager, &gmx_dos, "dos",
- "Analyze density of states and properties based on that");
+ registerModule(
+ manager, &gmx_dos, "dos", "Analyze density of states and properties based on that");
registerModule(manager, &gmx_dyecoupl, "dyecoupl", "Extract dye dynamics from trajectories");
registerModule(manager, &gmx_enemat, "enemat", "Extract an energy matrix from an energy file");
- registerModule(manager, &gmx_energy, "energy",
- "Writes energies to xvg files and display averages");
- registerModule(manager, &gmx_filter, "filter",
+ registerModule(
+ manager, &gmx_energy, "energy", "Writes energies to xvg files and display averages");
+ registerModule(manager,
+ &gmx_filter,
+ "filter",
"Frequency filter trajectories, useful for making smooth movies");
registerModule(manager, &gmx_gyrate, "gyrate", "Calculate the radius of gyration");
registerModule(manager, &gmx_h2order, "h2order", "Compute the orientation of water molecules");
registerModule(manager, &gmx_hbond, "hbond", "Compute and analyze hydrogen bonds");
registerModule(manager, &gmx_helix, "helix", "Calculate basic properties of alpha helices");
- registerModule(manager, &gmx_helixorient, "helixorient",
+ registerModule(manager,
+ &gmx_helixorient,
+ "helixorient",
"Calculate local pitch/bending/rotation/orientation inside helices");
- registerModule(manager, &gmx_hydorder, "hydorder",
+ registerModule(manager,
+ &gmx_hydorder,
+ "hydorder",
"Compute tetrahedrality parameters around a given atom");
registerModule(manager, &gmx_lie, "lie", "Estimate free energy from linear combinations");
registerModule(manager, &gmx_mdmat, "mdmat", "Calculate residue contact maps");
- registerModule(manager, &gmx_mindist, "mindist",
- "Calculate the minimum distance between two groups");
- registerModule(manager, &gmx_msd, "msd", "Calculates mean square displacements");
+ registerModule(
+ manager, &gmx_mindist, "mindist", "Calculate the minimum distance between two groups");
registerModule(manager, &gmx_nmeig, "nmeig", "Diagonalize the Hessian for normal mode analysis");
- registerModule(manager, &gmx_nmens, "nmens",
+ registerModule(manager,
+ &gmx_nmens,
+ "nmens",
"Generate an ensemble of structures from the normal modes");
- registerModule(manager, &gmx_nmr, "nmr",
+ registerModule(manager,
+ &gmx_nmr,
+ "nmr",
"Analyze nuclear magnetic resonance properties from an energy file");
- registerModule(manager, &gmx_nmtraj, "nmtraj",
+ registerModule(manager,
+ &gmx_nmtraj,
+ "nmtraj",
"Generate a virtual oscillating trajectory from an eigenvector");
- registerModule(manager, &gmx_order, "order",
- "Compute the order parameter per atom for carbon tails");
- registerModule(manager, &gmx_pme_error, "pme_error",
+ registerModule(
+ manager, &gmx_order, "order", "Compute the order parameter per atom for carbon tails");
+ registerModule(manager,
+ &gmx_pme_error,
+ "pme_error",
"Estimate the error of using PME with a given input file");
registerModule(manager, &gmx_polystat, "polystat", "Calculate static properties of polymers");
- registerModule(manager, &gmx_potential, "potential",
+ registerModule(manager,
+ &gmx_potential,
+ "potential",
"Calculate the electrostatic potential across the box");
- registerModule(manager, &gmx_principal, "principal",
+ registerModule(manager,
+ &gmx_principal,
+ "principal",
"Calculate principal axes of inertia for a group of atoms");
registerModule(manager, &gmx_rama, "rama", "Compute Ramachandran plots");
- registerModule(manager, &gmx_rms, "rms",
+ registerModule(manager,
+ &gmx_rms,
+ "rms",
"Calculate RMSDs with a reference structure and RMSD matrices");
- registerModule(manager, &gmx_rmsdist, "rmsdist",
+ registerModule(manager,
+ &gmx_rmsdist,
+ "rmsdist",
"Calculate atom pair distances averaged with power -2, -3 or -6");
registerModule(manager, &gmx_rmsf, "rmsf", "Calculate atomic fluctuations");
- registerModule(manager, &gmx_rotacf, "rotacf",
+ registerModule(manager,
+ &gmx_rotacf,
+ "rotacf",
"Calculate the rotational correlation function for molecules");
- registerModule(manager, &gmx_rotmat, "rotmat",
+ registerModule(manager,
+ &gmx_rotmat,
+ "rotmat",
"Plot the rotation matrix for fitting to a reference structure");
registerModule(manager, &gmx_saltbr, "saltbr", "Compute salt bridges");
registerModule(manager, &gmx_sans, "sans", "Compute small angle neutron scattering spectra");
registerModule(manager, &gmx_saxs, "saxs", "Compute small angle X-ray scattering spectra");
- registerModule(manager, &gmx_sham, "sham",
- "Compute free energies or other histograms from histograms");
- registerModule(manager, &gmx_sigeps, "sigeps",
+ registerModule(
+ manager, &gmx_sham, "sham", "Compute free energies or other histograms from histograms");
+ registerModule(manager,
+ &gmx_sigeps,
+ "sigeps",
"Convert c6/12 or c6/cn combinations to and from sigma/epsilon");
registerModule(manager, &gmx_sorient, "sorient", "Analyze solvent orientation around solutes");
registerModule(manager, &gmx_spatial, "spatial", "Calculate the spatial distribution function");
- registerModule(manager, &gmx_spol, "spol",
+ registerModule(manager,
+ &gmx_spol,
+ "spol",
"Analyze solvent dipole orientation and polarization around solutes");
registerModule(manager, &gmx_tcaf, "tcaf", "Calculate viscosities of liquids");
- registerModule(manager, &gmx_traj, "traj",
+ registerModule(manager,
+ &gmx_traj,
+ "traj",
"Plot x, v, f, box, temperature and rotational energy from trajectories");
- registerModule(manager, &gmx_tune_pme, "tune_pme",
+ registerModule(manager,
+ &gmx_tune_pme,
+ "tune_pme",
"Time mdrun as a function of PME ranks to optimize settings");
- registerModule(manager, &gmx_vanhove, "vanhove",
+ registerModule(manager,
+ &gmx_vanhove,
+ "vanhove",
"Compute Van Hove displacement and correlation functions");
registerModule(manager, &gmx_velacc, "velacc", "Calculate velocity autocorrelation functions");
- registerModule(manager, &gmx_wham, "wham",
+ registerModule(manager,
+ &gmx_wham,
+ "wham",
"Perform weighted histogram analysis after umbrella sampling");
registerModule(manager, &gmx_wheel, "wheel", "Plot helical wheels");
registerModuleNoNice(manager, &gmx_view, "view", "View a trajectory on an X-Windows terminal");
gmx::CommandLineModuleGroup group =
manager->addModuleGroup("Mass distribution properties over time");
group.addModule("gyrate");
- group.addModule("msd");
group.addModule("polystat");
group.addModule("rdf");
group.addModule("rotacf");
StartingBehavior startingBehavior = StartingBehavior::NewSimulation;
LogFilePtr logFileGuard = nullptr;
gmx_multisim_t* ms = simulationContext.multiSimulation_.get();
- std::tie(startingBehavior, logFileGuard) = handleRestart(
- findIsSimulationMasterRank(ms, communicator), communicator, ms,
- options.mdrunOptions.appendingBehavior, ssize(options.filenames), options.filenames.data());
+ std::tie(startingBehavior, logFileGuard) = handleRestart(findIsSimulationMasterRank(ms, communicator),
+ communicator,
+ ms,
+ options.mdrunOptions.appendingBehavior,
+ ssize(options.filenames),
+ options.filenames.data());
/* The named components for the builder exposed here are descriptive of the
* state of mdrun at implementation and are not intended to be prescriptive
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
options->addOption(
BooleanOption("time").store(&benchmarkOptions_.reportTime).description("Report micro-seconds instead of cycles"));
options->addOption(FileNameOption("o")
- .filetype(eftCsv)
+ .filetype(OptionFileType::Csv)
.outputFile()
.store(&benchmarkOptions_.outputFile)
.defaultBasename("nonbonded-benchmark")
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
-# Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
$<TARGET_OBJECTS:mdrun_objlib>
)
target_include_directories(mdrun_test_infrastructure SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
+target_link_libraries(mdrun_test_infrastructure PUBLIC legacy_api)
# To avoid running into test timeouts, some end-to-end tests of mdrun
# functionality are split off. This can be rearranged in future as we
orires.cpp
swapcoords.cpp
tabulated_bonded_interactions.cpp
+ freezegroups.cpp
# pseudo-library for code for mdrun
$<TARGET_OBJECTS:mdrun_objlib>
)
domain_decomposition.cpp
minimize.cpp
mimic.cpp
+ pmetest.cpp
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
+ )
+target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
+gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 2 OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS)
+
+# Multi sim only makes sense with real MPI, and ideally at least 4 ranks,
+# to allow for multiple simulations (>= 2 sims) each using DD (>= 2 ranks per sim)
+set(testname "MdrunMultiSimTests")
+set(exename "mdrun-multisim-test")
+
+gmx_add_gtest_executable(${exename} MPI
+ CPP_SOURCE_FILES
+ # files with code for tests
multisim.cpp
multisimtest.cpp
replicaexchange.cpp
- pmetest.cpp
# pseudo-library for code for mdrun
$<TARGET_OBJECTS:mdrun_objlib>
)
target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
-gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 2 OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS)
+gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 4 INTEGRATION_TEST IGNORE_LEAKS)
# Tests that only make sense to run with multiple ranks and/or real
# MPI are implemented here. Special case for slow PME tests
$<TARGET_OBJECTS:mdrun_objlib>
)
target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
+# TODO: Link specific modules: topology
+target_link_libraries(${exename} PRIVATE legacy_modules)
gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS)
# End-to-end tests comparing different simulator code paths
)
target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS)
+
+# Tests checking virtual sites - we want to run them with multiple ranks
+set(testname "MdrunVirtualSiteTests")
+set(exename "mdrun-vsites-test")
+
+gmx_add_gtest_executable(${exename} MPI
+ CPP_SOURCE_FILES
+ # files with code for tests
+ virtualsites.cpp
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
+ )
+target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
+gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 2 INTEGRATION_TEST IGNORE_LEAKS)
// 1/2 dt between checkpoint (top of the loop) and trajectory (full time step state)
trajectoryMatchSettings.velocitiesComparison = ComparisonConditions::NoComparison;
}
- const TrajectoryTolerances trajectoryTolerances{ defaultRealTolerance(), defaultRealTolerance(),
- defaultRealTolerance(), defaultRealTolerance() };
+ const TrajectoryTolerances trajectoryTolerances{
+ defaultRealTolerance(), defaultRealTolerance(), defaultRealTolerance(), defaultRealTolerance()
+ };
const auto mdpFieldValues =
prepareMdpFieldValues(simulationName, integrator, temperatureCoupling, pressureCoupling);
SCOPED_TRACE(formatString(
"Checking the sanity of the checkpointed coordinates using system '%s' "
"with integrator '%s', '%s' temperature coupling, and '%s' pressure coupling ",
- simulationName.c_str(), integrator.c_str(), temperatureCoupling.c_str(),
+ simulationName.c_str(),
+ integrator.c_str(),
+ temperatureCoupling.c_str(),
pressureCoupling.c_str()));
SCOPED_TRACE("End of trajectory sanity");
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{ interaction_function[F_EKIN].longname, relativeToleranceAsUlp(10.0, 50) },
// The pressure is very strongly affected by summation errors,
// so we need a large tolerance.
- // The value of 15000 is calibrated for running a small water box for 16 steps.
+ // The value of 17000 is calibrated for running a small water box for 16 steps.
// For a single frame for a water box a value of 150 could work.
- { interaction_function[F_PRES].longname, relativeToleranceAsUlp(10.0, 15000) },
+ { interaction_function[F_PRES].longname, relativeToleranceAsUlp(10.0, 17000) },
};
};
+ test.frameName());
for (auto referenceIt = reference.begin(); referenceIt != reference.end(); ++referenceIt)
{
- auto& energyName = referenceIt->first;
+ const auto& energyName = referenceIt->first;
SCOPED_TRACE("Comparing " + energyName + " between frames");
auto testIt = test.find(energyName);
if (testIt != test.end())
{
- auto& energyValueInReference = referenceIt->second;
- auto& energyValueInTest = testIt->second;
- EXPECT_REAL_EQ_TOL(energyValueInReference, energyValueInTest,
- energyTermsToCompare_.at(energyName));
+ const auto& energyValueInReference = referenceIt->second;
+ const auto& energyValueInTest = testIt->second;
+ EXPECT_REAL_EQ_TOL(
+ energyValueInReference, energyValueInTest, energyTermsToCompare_.at(energyName));
}
else
{
const EnergyTermsToCompare& energyTermsToCompare,
TestReferenceChecker* checker)
{
- checkEnergiesAgainstReferenceData(energyFilename, energyTermsToCompare, checker,
- MaxNumFrames::compareAllFrames());
+ checkEnergiesAgainstReferenceData(
+ energyFilename, energyTermsToCompare, checker, MaxNumFrames::compareAllFrames());
}
} // namespace test
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
std::string requiredEnergiesNotFound =
"Did not find the following required energies in mdrun output:\n";
- for (auto& name : namesOfRequiredEnergyTerms)
+ for (const auto& name : namesOfRequiredEnergyTerms)
{
auto possibleIndex = indicesOfEnergyTerms.find(name);
if (possibleIndex == indicesOfEnergyTerms.end())
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
fprintf(stdout,
"Test system '%s' cannot run with %d ranks.\n"
"The supported numbers are %s 1.\n",
- simulationName.c_str(), numRanksAvailable, numRanksAvailable == 1 ? ">" : "=");
+ simulationName.c_str(),
+ numRanksAvailable,
+ numRanksAvailable == 1 ? ">" : "=");
return;
}
auto frame = reader.frame();
auto force = frame.f();
int atom = 0;
- for (auto& f : force)
+ for (const auto& f : force)
{
std::string forceName = frame.frameName() + " F[" + toString(atom) + "]";
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
fprintf(stdout,
"Test system '%s' cannot run with %d ranks.\n"
"The supported numbers are: %s\n",
- simulationName.c_str(), numRanksAvailable,
+ simulationName.c_str(),
+ numRanksAvailable,
reportNumbersOfPpRanksSupported(simulationName).c_str());
return;
}
SCOPED_TRACE(
formatString("Comparing normal and two-part run of simulation '%s' "
"with integrator '%s'",
- simulationName.c_str(), integrator.c_str()));
+ simulationName.c_str(),
+ integrator.c_str()));
- auto mdpFieldValues = prepareMdpFieldValues(simulationName.c_str(), integrator.c_str(),
- temperatureCoupling.c_str(), pressureCoupling.c_str());
+ auto mdpFieldValues = prepareMdpFieldValues(simulationName.c_str(),
+ integrator.c_str(),
+ temperatureCoupling.c_str(),
+ pressureCoupling.c_str());
// The exact lambda state choice is unimportant, so long as there
// is one when using an FEP input.
- mdpFieldValues["other"] += formatString("\ninit-lambda-state = %d", 3);
- mdpFieldValues["nsteps"] = "16";
+ mdpFieldValues["init-lambda-state"] = "3";
+ mdpFieldValues["nsteps"] = "16";
// Forces on GPUs are generally not reproducible enough for a tight
// tolerance. Similarly, the propagation of sd and bd are not as
if (pressureCoupling == "parrinello-rahman")
{
- energyTermsToCompare.insert(
- { "Box-Vel-XX", relativeToleranceAsPrecisionDependentUlp(1e-12, ulpToleranceInMixed,
- ulpToleranceInDouble) });
- energyTermsToCompare.insert(
- { "Box-Vel-YY", relativeToleranceAsPrecisionDependentUlp(1e-12, ulpToleranceInMixed,
- ulpToleranceInDouble) });
- energyTermsToCompare.insert(
- { "Box-Vel-ZZ", relativeToleranceAsPrecisionDependentUlp(1e-12, ulpToleranceInMixed,
- ulpToleranceInDouble) });
+ energyTermsToCompare.insert({ "Box-Vel-XX",
+ relativeToleranceAsPrecisionDependentUlp(
+ 1e-12, ulpToleranceInMixed, ulpToleranceInDouble) });
+ energyTermsToCompare.insert({ "Box-Vel-YY",
+ relativeToleranceAsPrecisionDependentUlp(
+ 1e-12, ulpToleranceInMixed, ulpToleranceInDouble) });
+ energyTermsToCompare.insert({ "Box-Vel-ZZ",
+ relativeToleranceAsPrecisionDependentUlp(
+ 1e-12, ulpToleranceInMixed, ulpToleranceInDouble) });
}
int numWarningsToTolerate = 1;
- runTest(&fileManager_, &runner_, simulationName, numWarningsToTolerate, mdpFieldValues,
- energyTermsToCompare);
+ runTest(&fileManager_, &runner_, simulationName, numWarningsToTolerate, mdpFieldValues, energyTermsToCompare);
}
// TODO The time for OpenCL kernel compilation means these tests time
fprintf(stdout,
"The FEP tests cannot run with %d ranks.\n"
"The maximum number of ranks supported is %d.",
- numRanksAvailable, maxNumRanks);
+ numRanksAvailable,
+ maxNumRanks);
return;
}
// Check that the trajectories agree with the refdata within tolerance.
if (testTwoTrajectoryFrames)
{
- checkTrajectoryAgainstReferenceData(simulationTrajectoryFileName, trajectoryComparison,
- &rootChecker, MaxNumFrames(2));
+ checkTrajectoryAgainstReferenceData(
+ simulationTrajectoryFileName, trajectoryComparison, &rootChecker, MaxNumFrames(2));
}
else if (testOneTrajectoryFrame)
{
- checkTrajectoryAgainstReferenceData(simulationTrajectoryFileName, trajectoryComparison,
- &rootChecker, MaxNumFrames(1));
+ checkTrajectoryAgainstReferenceData(
+ simulationTrajectoryFileName, trajectoryComparison, &rootChecker, MaxNumFrames(1));
}
else
{
- checkTrajectoryAgainstReferenceData(simulationTrajectoryFileName, trajectoryComparison,
- &rootChecker, MaxNumFrames(0));
+ checkTrajectoryAgainstReferenceData(
+ simulationTrajectoryFileName, trajectoryComparison, &rootChecker, MaxNumFrames(0));
}
if (File::exists(simulationDhdlFileName, File::returnFalseOnError))
{
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief End-to-end tests checking sanity of results of simulations
+ * containing freeze groups
+ *
+ * \author Pascal Merz <pascal.merz@me.com>
+ * \ingroup module_mdrun_integration_tests
+ */
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include "gromacs/topology/ifunc.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/mpitest.h"
+#include "testutils/simulationdatabase.h"
+#include "testutils/testmatchers.h"
+
+#include "moduletest.h"
+#include "simulatorcomparison.h"
+#include "trajectoryreader.h"
+
+namespace gmx::test
+{
+namespace
+{
+/*! \brief Test fixture checking sanity of freeze group results
+ *
+ * This tests the sanity of simulation results containing fully and partially
+ * frozen atoms. For fully frozen atoms, it checks that their reported position
+ * is identical for all steps, and that their velocity is zero. For partially
+ * frozen atoms (for simplicity only in z-direction), it checks that their
+ * position is identical in the frozen dimension for all steps, and that their
+ * velocity is zero in the frozen dimension.
+ */
+using FreezeGroupTestParams = std::tuple<std::string, std::string, std::string>;
+class FreezeGroupTest : public MdrunTestFixture, public ::testing::WithParamInterface<FreezeGroupTestParams>
+{
+public:
+ //! Check that the frozen positions don't change and velocities are zero
+ static void checkFreezeGroups(const std::string& trajectoryName,
+ ArrayRef<const unsigned int> fullyFrozenAtoms,
+ ArrayRef<const unsigned int> partiallyFrozenAtomsDimZ,
+ const TrajectoryTolerances& tolerances)
+ {
+ auto [fullyFrozenPositions, fullyFrozenVelocities] =
+ getFrozenPositionsAndVelocities(trajectoryName, fullyFrozenAtoms);
+ auto [partiallyFrozenPositions, partiallyFrozenVelocities] =
+ getFrozenPositionsAndVelocities(trajectoryName, partiallyFrozenAtomsDimZ);
+ GMX_RELEASE_ASSERT(fullyFrozenPositions.size() == fullyFrozenVelocities.size(),
+ "Position and velocity trajectory don't have the same length.");
+ GMX_RELEASE_ASSERT(partiallyFrozenPositions.size() == partiallyFrozenVelocities.size(),
+ "Position and velocity trajectory don't have the same length.");
+ GMX_RELEASE_ASSERT(fullyFrozenPositions.size() == partiallyFrozenPositions.size(),
+ "Fully and partially frozen trajectory don't have the same length.");
+ const auto trajectorySize = fullyFrozenPositions.size();
+
+ for (auto frameIdx = decltype(trajectorySize){ 0 }; frameIdx < trajectorySize; frameIdx++)
+ {
+ SCOPED_TRACE(formatString("Checking frame %lu", frameIdx + 1));
+ if (frameIdx > 0)
+ {
+ checkFullyFrozenPositions(
+ fullyFrozenPositions[frameIdx], fullyFrozenPositions[frameIdx - 1], tolerances);
+ checkZDimFrozenPositions(partiallyFrozenPositions[frameIdx],
+ partiallyFrozenPositions[frameIdx - 1],
+ tolerances);
+ }
+ checkFullyFrozenVelocities(fullyFrozenVelocities[frameIdx], tolerances);
+ checkZDimFrozenVelocities(partiallyFrozenVelocities[frameIdx], tolerances);
+ }
+ }
+
+ //! Check that fully frozen frame velocities are zero
+ static void checkFullyFrozenVelocities(ArrayRef<const RVec> velocities,
+ const TrajectoryTolerances& tolerances)
+ {
+ SCOPED_TRACE("Checking fully frozen velocity frame");
+ std::vector<RVec> zeroVelocities(velocities.size(), RVec{ 0, 0, 0 });
+ EXPECT_THAT(zeroVelocities, Pointwise(RVecEq(tolerances.velocities), velocities));
+ }
+ //! Check that z-dimension frozen frame velocities are zero
+ static void checkZDimFrozenVelocities(ArrayRef<const RVec> velocities,
+ const TrajectoryTolerances& tolerances)
+ {
+ SCOPED_TRACE("Checking z-dimension frozen velocity frame");
+ std::vector<real> zVelocities;
+ for (const auto& v : velocities)
+ {
+ zVelocities.emplace_back(v[ZZ]);
+ }
+ std::vector<real> zeroVelocities(zVelocities.size(), 0);
+ EXPECT_THAT(zeroVelocities, Pointwise(RealEq(tolerances.velocities), zVelocities));
+ }
+ //! Check that fully frozen frame positions are static
+ static void checkFullyFrozenPositions(ArrayRef<const RVec> positions,
+ ArrayRef<const RVec> previousPositions,
+ const TrajectoryTolerances& tolerances)
+ {
+ SCOPED_TRACE("Checking fully frozen position frame");
+ EXPECT_THAT(previousPositions, Pointwise(RVecEq(tolerances.coordinates), positions));
+ }
+ //! Check that z-dimension frozen frame positions are zero
+ static void checkZDimFrozenPositions(ArrayRef<const RVec> positions,
+ ArrayRef<const RVec> previousPositions,
+ const TrajectoryTolerances& tolerances)
+ {
+ SCOPED_TRACE("Checking z-dimension frozen position frame");
+ std::vector<real> zPositions;
+ for (const auto& p : positions)
+ {
+ zPositions.emplace_back(p[ZZ]);
+ }
+ std::vector<real> zPrevPositions;
+ for (const auto& p : previousPositions)
+ {
+ zPrevPositions.emplace_back(p[ZZ]);
+ }
+ EXPECT_THAT(zPrevPositions, Pointwise(RealEq(tolerances.coordinates), zPositions));
+ }
+
+ static std::tuple<std::vector<std::vector<RVec>>, std::vector<std::vector<RVec>>>
+ getFrozenPositionsAndVelocities(const std::string& trajectoryName, ArrayRef<const unsigned int> frozenAtoms)
+ {
+ std::vector<std::vector<RVec>> positions;
+ std::vector<std::vector<RVec>> velocities;
+
+ TrajectoryFrameReader trajectoryFrameReader(trajectoryName);
+ while (trajectoryFrameReader.readNextFrame())
+ {
+ const auto frame = trajectoryFrameReader.frame();
+ positions.emplace_back();
+ velocities.emplace_back();
+ for (const auto& index : frozenAtoms)
+ {
+ positions.back().emplace_back(frame.x().at(index));
+ velocities.back().emplace_back(frame.v().at(index));
+ }
+ }
+
+ return { std::move(positions), std::move(velocities) };
+ }
+};
+
+TEST_P(FreezeGroupTest, WithinTolerances)
+{
+ const auto& params = GetParam();
+ const auto& integrator = std::get<0>(params);
+ const auto& tcoupling = std::get<1>(params);
+ const auto& pcoupling = std::get<2>(params);
+ const auto& simulationName = "alanine_vacuo";
+
+ constexpr std::array<unsigned int, 5> backbone = { 4, 6, 8, 14, 16 };
+ constexpr std::array<unsigned int, 13> sideChainH = { 0, 1, 2, 3, 9, 10, 11,
+ 12, 13, 18, 19, 20, 21 };
+
+ if (integrator == "md-vv" && pcoupling == "parrinello-rahman")
+ {
+ // Parrinello-Rahman is not implemented in md-vv
+ return;
+ }
+
+ // Prepare mdp input
+ auto mdpFieldValues = prepareMdpFieldValues(simulationName, integrator, tcoupling, pcoupling);
+ mdpFieldValues["nsteps"] = "8";
+ mdpFieldValues["nstxout"] = "4";
+ mdpFieldValues["nstvout"] = "4";
+ mdpFieldValues["freezegrps"] = "Backbone SideChain";
+ mdpFieldValues["freezedim"] = "Y Y Y N N Y";
+ mdpFieldValues["constraints"] = "all-bonds";
+
+ // Run grompp
+ runner_.useTopGroAndNdxFromDatabase(simulationName);
+ runner_.useStringAsMdpFile(prepareMdpFileContents(mdpFieldValues));
+ // Allow one warning for COMM removal + partially frozen atoms
+ runGrompp(&runner_, { SimulationOptionTuple("-maxwarn", "1") });
+ // Run mdrun
+ runMdrun(&runner_);
+
+ // Check frozen atoms
+ checkFreezeGroups(runner_.fullPrecisionTrajectoryFileName_,
+ backbone,
+ sideChainH,
+ TrajectoryComparison::s_defaultTrajectoryTolerances);
+}
+
+INSTANTIATE_TEST_CASE_P(FreezeWorks,
+ FreezeGroupTest,
+ ::testing::Combine(::testing::Values("md", "md-vv", "sd", "bd"),
+ ::testing::Values("no"),
+ ::testing::Values("no")));
+} // namespace
+} // namespace gmx::test
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
const int nsteps = 1;
const float timestep = 0.001;
- auto integrator = GetParam();
+ const auto* integrator = GetParam();
const std::string integratorName(integrator);
SCOPED_TRACE("Integrating with " + integratorName);
const std::string theMdpFile = formatString(
"integrator = %s\n"
"nsteps = %d\n"
"dt = %f\n",
- integratorName.c_str(), nsteps, timestep);
+ integratorName.c_str(),
+ nsteps,
+ timestep);
runner_.useStringAsMdpFile(theMdpFile);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
auto simulationName = std::get<0>(params);
auto minimizer = std::get<1>(params);
SCOPED_TRACE(formatString("Comparing '%s' energy minimization for simulation '%s'",
- minimizer.c_str(), simulationName.c_str()));
+ minimizer.c_str(),
+ simulationName.c_str()));
// TODO At some point we should also test PME-only ranks.
int numRanksAvailable = getNumberOfTestMpiRanks();
fprintf(stdout,
"Test system '%s' cannot run with %d ranks.\n"
"The supported numbers are: %s\n",
- simulationName.c_str(), numRanksAvailable,
+ simulationName.c_str(),
+ numRanksAvailable,
reportNumbersOfPpRanksSupported(simulationName).c_str());
return;
}
"glycine_no_constraints_vacuo" };
std::vector<std::string> minimizersToTest_g = { "steep", "cg", "l-bfgs" };
-std::vector<std::string> constrainedSystemsToTest_g = { "tip3p5", "glycine_vacuo",
+std::vector<std::string> constrainedSystemsToTest_g = { "tip3p5",
+ "glycine_vacuo",
"alanine_vsite_vacuo" };
std::vector<std::string> minimizersToTestWithConstraints_g = { "steep", "cg" };
//! \}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#if GMX_OPENMP || defined(DOXYGEN)
//! Number of OpenMP threads for child mdrun call.
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
int g_numOpenMPThreads = 1;
#endif
//! \cond
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
GMX_TEST_OPTIONS(MdrunTestOptions, options)
{
GMX_UNUSED_VALUE(options);
mdpInputContents_ = mdpString;
}
-void SimulationRunner::useStringAsNdxFile(const char* ndxString)
+void SimulationRunner::useStringAsNdxFile(const char* ndxString) const
{
gmx::TextWriter::writeFileFromString(ndxFileName_, ndxString);
}
return callGrompp(CommandLine());
}
-int SimulationRunner::changeTprNsteps(int nsteps)
+int SimulationRunner::changeTprNsteps(int nsteps) const
{
CommandLine caller;
caller.append("convert-tpr");
return gmx::test::CommandLineTestHelper::runModuleFactory(&gmx::ConvertTprInfo::create, &caller);
}
-int SimulationRunner::callNmeig()
+int SimulationRunner::callNmeig() const
{
/* Conforming to style guide by not passing a non-const reference
to this function. Passing a non-const reference might make it
caller.addOption("-ntomp", g_numOpenMPThreads);
#endif
- return gmx_mdrun(MdrunTestFixtureBase::communicator_, *MdrunTestFixtureBase::hwinfo_,
- caller.argc(), caller.argv());
+ return gmx_mdrun(MdrunTestFixtureBase::communicator_,
+ *MdrunTestFixtureBase::hwinfo_,
+ caller.argc(),
+ caller.argv());
}
int SimulationRunner::callMdrun()
// ====
// static
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
MPI_Comm MdrunTestFixtureBase::communicator_ = MPI_COMM_NULL;
// static
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
std::unique_ptr<gmx_hw_info_t> MdrunTestFixtureBase::hwinfo_;
// static
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <gtest/gtest.h>
+#include <memory>
+
#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/gmxmpi.h"
//! Use a given string as input to grompp
void useStringAsMdpFile(const std::string& mdpString);
//! Use a string as -n input to grompp
- void useStringAsNdxFile(const char* ndxString);
+ void useStringAsNdxFile(const char* ndxString) const;
//! Use a standard .top and .g96 file as input to grompp
void useTopG96AndNdxFromDatabase(const std::string& name);
//! Use a standard .top and .gro file as input to grompp
//! Convenience wrapper for a default call to \c callGromppOnThisRank
int callGromppOnThisRank();
//! Calls nmeig for testing
- int callNmeig();
+ int callNmeig() const;
//! Calls mdrun for testing with a customized command line
int callMdrun(const CommandLine& callerRef);
/*! \brief Convenience wrapper for calling mdrun for testing
* with default command line */
int callMdrun();
//! Calls convert-tpr on this rank to set a new number of steps in the tpr.
- int changeTprNsteps(int nsteps);
+ int changeTprNsteps(int nsteps) const;
//@{
/*! \name Names for frequently used grompp and mdrun output files
~MdrunTestFixtureBase() override;
//! Communicator over which the test fixture works
+ // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static MPI_Comm communicator_;
/*! \brief Hardware information object
*
* Detected within \c communicator_ and available to re-use
* over all tests in the test case of this text fixture. */
+ // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
static std::unique_ptr<gmx_hw_info_t> hwinfo_;
};
auto mtsScheme = std::get<1>(params);
// Note that there should be no relevant limitation on MPI ranks and OpenMP threads
- SCOPED_TRACE(formatString("Comparing for '%s' no MTS with MTS scheme '%s'",
- simulationName.c_str(), mtsScheme.c_str()));
+ SCOPED_TRACE(formatString(
+ "Comparing for '%s' no MTS with MTS scheme '%s'", simulationName.c_str(), mtsScheme.c_str()));
const bool isPullTest = (mtsScheme.find("pull") != std::string::npos);
"rcoulomb = 0.9\n"
"rvdw = 0.9\n"
"constraints = h-bonds\n",
- numSteps, isPullTest ? "reaction-field" : "PME");
+ numSteps,
+ isPullTest ? "reaction-field" : "PME");
if (isPullTest)
{
"nstxout = 0\n"
"nstvout = 0\n"
"nstfout = %d\n",
- numSteps, numSteps, nstfout);
+ numSteps,
+ numSteps,
+ nstfout);
auto mtsMdpOptions = sharedMdpOptions
+ gmx::formatString(
"nstxout = 0\n"
"nstvout = 0\n"
"nstfout = %d\n",
- mtsScheme.c_str(), numSteps, numSteps, nstfout);
+ mtsScheme.c_str(),
+ numSteps,
+ numSteps,
+ nstfout);
// At step 0 the energy and virial should only differ due to rounding errors
EnergyTermsToCompare energyTermsToCompareStep0 = energyTermsToCompare(0.001, 0.01);
runMdrun(&runner_);
// Compare simulation results at step 0, which should be indentical
- compareEnergies(simulator1EdrFileName, simulator2EdrFileName, energyTermsToCompareStep0,
- MaxNumFrames(1));
+ compareEnergies(
+ simulator1EdrFileName, simulator2EdrFileName, energyTermsToCompareStep0, MaxNumFrames(1));
compareTrajectories(simulator1TrajectoryFileName, simulator2TrajectoryFileName, trajectoryComparison);
// Compare energies at the last step (and step 0 again) with lower tolerance
- compareEnergies(simulator1EdrFileName, simulator2EdrFileName, energyTermsToCompareAllSteps,
+ compareEnergies(simulator1EdrFileName,
+ simulator2EdrFileName,
+ energyTermsToCompareAllSteps,
MaxNumFrames::compareAllFrames());
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <gtest/gtest.h>
+#include "gromacs/mdtypes/md_enums.h"
+
#include "multisimtest.h"
namespace gmx
* that it is disabled. There's no elegant way to conditionally
* disable a test at run time, so currently there is no feedback if
* only one rank is available. However, the test harness knows to run
- * this test with more than one rank.
- *
- * Strictly, this test does not need to be parameterized, but
- * conditionally disabling it with respect to GMX_LIB_MPI is easier if
- * it is parameterized. */
+ * this test with more than one rank. */
TEST_P(MultiSimTest, ExitsNormally)
{
runExitsNormallyTest();
TEST_P(MultiSimTest, ExitsNormallyWithDifferentNumbersOfStepsPerSimulation)
{
- if (size_ <= 1)
+ if (!mpiSetupValid())
{
- /* Can't test multi-sim without multiple ranks. */
+ // MPI setup is not suitable for multi-sim
return;
}
SimulationRunner runner(&fileManager_);
runner.useTopGroAndNdxFromDatabase("spc2");
- const char* pcoupl = GetParam();
// Do some different small numbers of steps in each simulation
- int numSteps = rank_ % 4;
- organizeMdpFile(&runner, pcoupl, numSteps);
- /* Call grompp on every rank - the standard callGrompp() only runs
- grompp on rank 0. */
- EXPECT_EQ(0, runner.callGromppOnThisRank());
+ int numSteps = simulationNumber_ % 4;
+ runGrompp(&runner, numSteps);
ASSERT_EQ(0, runner.callMdrun(*mdrunCaller_));
}
/* Note, not all preprocessor implementations nest macro expansions
the same way / at all, if we would try to duplicate less code. */
#if GMX_LIB_MPI
-INSTANTIATE_TEST_CASE_P(InNvt, MultiSimTest, ::testing::Values("pcoupl = no"));
+INSTANTIATE_TEST_CASE_P(InNvt,
+ MultiSimTest,
+ ::testing::Combine(::testing::Values(NumRanksPerSimulation(1),
+ NumRanksPerSimulation(2)),
+ ::testing::Values(IntegrationAlgorithm::MD),
+ ::testing::Values(TemperatureCoupling::VRescale),
+ ::testing::Values(PressureCoupling::No)));
#else
// Test needs real MPI to run
-INSTANTIATE_TEST_CASE_P(DISABLED_InNvt, MultiSimTest, ::testing::Values("pcoupl = no"));
+INSTANTIATE_TEST_CASE_P(DISABLED_InNvt,
+ MultiSimTest,
+ ::testing::Combine(::testing::Values(NumRanksPerSimulation(1),
+ NumRanksPerSimulation(2)),
+ ::testing::Values(IntegrationAlgorithm::MD),
+ ::testing::Values(TemperatureCoupling::VRescale),
+ ::testing::Values(PressureCoupling::No)));
#endif
//! Convenience typedef
typedef MultiSimTest MultiSimTerminationTest;
-TEST_F(MultiSimTerminationTest, WritesCheckpointAfterMaxhTerminationAndThenRestarts)
+TEST_P(MultiSimTerminationTest, WritesCheckpointAfterMaxhTerminationAndThenRestarts)
{
runMaxhTest();
}
+INSTANTIATE_TEST_CASE_P(InNvt,
+ MultiSimTerminationTest,
+ ::testing::Combine(::testing::Values(NumRanksPerSimulation(1),
+ NumRanksPerSimulation(2)),
+ ::testing::Values(IntegrationAlgorithm::MD),
+ ::testing::Values(TemperatureCoupling::VRescale),
+ ::testing::Values(PressureCoupling::No)));
+
} // namespace test
} // namespace gmx
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <gtest/gtest.h>
+#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/path.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/stringutil.h"
MultiSimTest::MultiSimTest() :
size_(gmx_node_num()),
rank_(gmx_node_rank()),
+ numRanksPerSimulation_(std::get<0>(GetParam())),
+ simulationNumber_(rank_ / numRanksPerSimulation_),
mdrunCaller_(new CommandLine)
{
+ // Zero or less ranks doesn't make sense
+ GMX_RELEASE_ASSERT(numRanksPerSimulation_ > 0, "Invalid number of ranks per simulation.");
+
const char* directoryNameFormat = "sim_%d";
// Modify the file manager to have a temporary directory unique to
// constructed it.
std::string originalTempDirectory = fileManager_.getOutputTempDirectory();
std::string newTempDirectory =
- Path::join(originalTempDirectory, formatString(directoryNameFormat, rank_));
- Directory::create(newTempDirectory);
+ Path::join(originalTempDirectory, formatString(directoryNameFormat, simulationNumber_));
+ if (rank_ % numRanksPerSimulation_ == 0)
+ {
+ // Only one rank per simulation creates directory
+ Directory::create(newTempDirectory);
+ }
+#if GMX_LIB_MPI
+ // Make sure directories got created.
+ MPI_Barrier(MdrunTestFixtureBase::communicator_);
+#endif
fileManager_.setOutputTempDirectory(newTempDirectory);
mdrunCaller_->append("mdrun");
mdrunCaller_->addOption("-multidir");
- for (int i = 0; i != size_; ++i)
+ for (int i = 0; i < size_ / numRanksPerSimulation_; ++i)
{
mdrunCaller_->append(Path::join(originalTempDirectory, formatString(directoryNameFormat, i)));
}
}
-void MultiSimTest::organizeMdpFile(SimulationRunner* runner, const char* controlVariable, int numSteps)
+bool MultiSimTest::mpiSetupValid() const
+{
+ // Single simulation case is not implemented in multi-sim
+ const bool haveAtLeastTwoSimulations = ((size_ / numRanksPerSimulation_) >= 2);
+ // Mdrun will throw error if simulations don't have identical number of ranks
+ const bool simulationsHaveIdenticalRankNumber = ((size_ % numRanksPerSimulation_) == 0);
+
+ return (haveAtLeastTwoSimulations && simulationsHaveIdenticalRankNumber);
+}
+
+void MultiSimTest::organizeMdpFile(SimulationRunner* runner,
+ IntegrationAlgorithm integrator,
+ TemperatureCoupling tcoupl,
+ PressureCoupling pcoupl,
+ int numSteps,
+ bool doRegression) const
{
+ GMX_RELEASE_ASSERT(mpiSetupValid(), "Creating the mdp file without valid MPI setup is useless.");
const real baseTemperature = 298;
const real basePressure = 1;
std::string mdpFileContents = formatString(
+ "integrator = %s\n"
+ "tcoupl = %s\n"
+ "pcoupl = %s\n"
"nsteps = %d\n"
"nstlog = 1\n"
"nstcalcenergy = 1\n"
- "tcoupl = v-rescale\n"
"tc-grps = System\n"
"tau-t = 1\n"
"ref-t = %f\n"
// pressure coupling (if active)
- "tau-p = 1\n"
+ "tau-p = 2\n"
"ref-p = %f\n"
"compressibility = 4.5e-5\n"
// velocity generation
"gen-vel = yes\n"
"gen-temp = %f\n"
- // control variable specification
- "%s\n",
- numSteps, baseTemperature + 0.0001 * rank_, basePressure * std::pow(1.01, rank_),
+ "gen-seed = %d\n"
+ // v-rescale and c-rescale use ld-seed
+ "ld-seed = %d\n"
+ // Two systems are used: spc2 non-interacting also at cutoff 1nm
+ // tip3p5 has box length of 1.86
+ "rcoulomb = 0.7\n"
+ "rvdw = 0.7\n"
+ // Trajectory output if required
+ "nstxout = %d\n"
+ "nstvout = %d\n"
+ "nstfout = %d\n"
+ "nstenergy = %d\n",
+ enumValueToString(integrator),
+ enumValueToString(tcoupl),
+ enumValueToString(pcoupl),
+ numSteps,
+ baseTemperature + 0.0001 * rank_,
+ basePressure * std::pow(1.01, rank_),
/* Set things up so that the initial KE decreases with
increasing replica number, so that the (identical)
starting PE decreases on the first step more for the
replicas with higher number, which will tend to force
replica exchange to occur. */
- std::max(baseTemperature - 10 * rank_, real(0)), controlVariable);
+ std::max(baseTemperature - 10 * rank_, real(0)),
+ // If we do regression, we need reproducible velocity
+ // generation, which can be different per simulation
+ (doRegression ? 671324 + simulationNumber_ : -1),
+ // If we do regression, we need reproducible temperature and
+ // pressure coupling, which can be different per simulation
+ (doRegression ? 51203 + simulationNumber_ : -1),
+ // If we do regression, write one intermediate point
+ (doRegression ? int(numSteps / 2) : 0),
+ (doRegression ? int(numSteps / 2) : 0),
+ (doRegression ? int(numSteps / 2) : 0),
+ // If we do regression, print energies every step so
+ // we're sure to catch the replica exchange steps
+ (doRegression ? 1 : 1000));
runner->useStringAsMdpFile(mdpFileContents);
}
+void MultiSimTest::runGrompp(SimulationRunner* runner, int numSteps, bool doRegression, int maxWarnings) const
+{
+ // Call grompp once per simulation
+ if (rank_ % numRanksPerSimulation_ == 0)
+ {
+ const auto& simulator = std::get<1>(GetParam());
+ const auto& tcoupl = std::get<2>(GetParam());
+ const auto& pcoupl = std::get<3>(GetParam());
+ organizeMdpFile(runner, simulator, tcoupl, pcoupl, numSteps, doRegression);
+ CommandLine caller;
+ caller.addOption("-maxwarn", maxWarnings);
+ EXPECT_EQ(0, runner->callGromppOnThisRank(caller));
+ }
+
+#if GMX_LIB_MPI
+ // Make sure simulation masters have written the .tpr file before other ranks try to read it.
+ MPI_Barrier(MdrunTestFixtureBase::communicator_);
+#endif
+}
+
void MultiSimTest::runExitsNormallyTest()
{
- if (size_ <= 1)
+ if (!mpiSetupValid())
{
- /* Can't test multi-sim without multiple ranks. */
+ // Can't test multi-sim without multiple simulations
return;
}
SimulationRunner runner(&fileManager_);
runner.useTopGroAndNdxFromDatabase("spc2");
- const char* pcoupl = GetParam();
- organizeMdpFile(&runner, pcoupl);
- /* Call grompp on every rank - the standard callGrompp() only runs
- grompp on rank 0. */
- EXPECT_EQ(0, runner.callGromppOnThisRank());
+ runGrompp(&runner);
ASSERT_EQ(0, runner.callMdrun(*mdrunCaller_));
}
void MultiSimTest::runMaxhTest()
{
- if (size_ <= 1)
+ if (!mpiSetupValid())
{
- /* Can't test replica exchange without multiple ranks. */
+ // Can't test multi-sim without multiple simulations
return;
}
TerminationHelper helper(&fileManager_, mdrunCaller_.get(), &runner);
// Make sure -maxh has a chance to propagate
int numSteps = 100;
- organizeMdpFile(&runner, "pcoupl = no", numSteps);
- /* Call grompp on every rank - the standard callGrompp() only runs
- grompp on rank 0. */
- EXPECT_EQ(0, runner.callGromppOnThisRank());
+ runGrompp(&runner, numSteps);
helper.runFirstMdrun(runner.cptFileName_);
helper.runSecondMdrun();
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "moduletest.h"
+enum class IntegrationAlgorithm : int;
+enum class PressureCoupling : int;
+enum class TemperatureCoupling : int;
+
namespace gmx
{
namespace test
//! Convenience typedef
typedef std::unique_ptr<CommandLine> CommandLinePointer;
+/*! \internal
+ * \brief Test flag setting the number of ranks per simulation
+ */
+class NumRanksPerSimulation final
+{
+public:
+ //! Explicit constructor
+ explicit NumRanksPerSimulation(int value) : value_(value) {}
+ //! Implicit conversion to int
+ operator int() const { return value_; }
+
+private:
+ //! Internal state
+ int value_;
+};
+
+//! The parameters of the MultiSimTest class
+typedef std::tuple<NumRanksPerSimulation, IntegrationAlgorithm, TemperatureCoupling, PressureCoupling> MultiSimTestParams;
+
/*! \internal
* \brief Test fixture for multi-sim functionality.
*
*
* \ingroup module_mdrun_integration_tests
*/
-class MultiSimTest : public MdrunTestFixtureBase, public ::testing::WithParamInterface<const char*>
+class MultiSimTest : public MdrunTestFixtureBase, public ::testing::WithParamInterface<MultiSimTestParams>
{
public:
MultiSimTest();
+ /*! \brief Check whether the MPI setup is valid
+ *
+ * Excludes MPI setups which are not supported by multi-sim
+ */
+ bool mpiSetupValid() const;
+
/*! \brief Organize the .mdp file for this rank
*
* For testing multi-simulation, this .mdp file is more
* and doing it this way allows this function to be re-used
* for testing replica-exchange.
*
- * \param runner The simulation runner that uses the
- * mdp file that is organized.
- * \param controlVariable Allows parameterization to work with
+ * The mdp options, specifically the temperature and pressure
+ * coupling, allow parameterization to work with
* T, P or (later) lambda as the control variable, by passing a
- * string with "mdp-param = value" such that different paths
- * in init_replica_exchange() are followed.
- * \param numSteps Number of MD steps to perform.
+ * string with a value for the respective mdp option such that
+ * different paths in init_replica_exchange() are followed.
+ *
+ * \param runner The simulation runner that uses the
+ * mdp file that is organized.
+ * \param integrator Value for the mdp option `integrator`
+ * \param tcoupl Value for the mdp option `tcoupl`
+ * \param pcoupl Value for the mdp option `pcoupl`
+ * \param numSteps Number of MD steps to perform.
+ * \param doRegression Whether the mdp file will be used for
+ * regression tests, request use of
+ * reproducible parameters
+ */
+ void organizeMdpFile(SimulationRunner* runner,
+ IntegrationAlgorithm integrator,
+ TemperatureCoupling tcoupl,
+ PressureCoupling pcoupl,
+ int numSteps,
+ bool doRegression) const;
+
+ /*! \brief Run grompp on the ranks that need to run it
+ *
+ * Adds an MPI barrier to ensure that all ranks have written before returning
+ *
+ * \param runner The simulation runner to run grompp on
+ * \param numSteps Number of MD steps to perform
+ * \param doRegression Whether to write trajectories during the simulation
+ * \param maxWarnings Number of grompp warning tolerated
*/
- void organizeMdpFile(SimulationRunner* runner, const char* controlVariable, int numSteps = 2);
+ void runGrompp(SimulationRunner* runner, int numSteps = 2, bool doRegression = false, int maxWarnings = 0) const;
//! Test that a basic simulation works
void runExitsNormallyTest();
//! Test that mdrun -maxh and restart works
int size_;
//! MPI rank of this process
int rank_;
+ //! Number of ranks per simulation
+ int numRanksPerSimulation_;
+ //! The simulation this rank belongs to (equal to `int( rank_ / numRanksPerSimulation_)`)
+ int simulationNumber_;
//! Object for building the mdrun command line
CommandLinePointer mdrunCaller_;
//! Manages temporary files during the test.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const char* const command[] = { "nonbonded-benchmark" };
CommandLine cmdline(command);
cmdline.addOption("-iter", 1);
- EXPECT_EQ(0, gmx::test::CommandLineTestHelper::runModuleFactory(
- &gmx::NonbondedBenchmarkInfo::create, &cmdline));
+ EXPECT_EQ(0,
+ gmx::test::CommandLineTestHelper::runModuleFactory(
+ &gmx::NonbondedBenchmarkInfo::create, &cmdline));
}
} // namespace
fprintf(stdout,
"Test system '%s' cannot run with %d ranks.\n"
"The supported numbers are: %s\n",
- simulationName.c_str(), numRanksAvailable,
+ simulationName.c_str(),
+ numRanksAvailable,
reportNumbersOfPpRanksSupported(simulationName).c_str());
return;
}
//! Containers of systems and integrators to test.
//! \{
-std::vector<std::string> systemsToTest_g = { "scaled-water", "villin", "spc-dimer", "one-tip5p",
+std::vector<std::string> systemsToTest_g = { "scaled-water",
+ "villin",
+ "spc-dimer",
+ "one-tip5p",
"sw-dimer" };
std::vector<std::string> integratorsToTest_g = { "nm" };
SCOPED_TRACE(
formatString("Checking for presence of expected output files using "
"simulation '%s' with integrator '%s'",
- simulationName.c_str(), integrator.c_str()));
+ simulationName.c_str(),
+ integrator.c_str()));
// Prepare the .tpr file
{
}
// Check if expected files are present
{
- for (const auto& file : { runner_.fullPrecisionTrajectoryFileName_, runner_.logFileName_,
- runner_.edrFileName_, fileManager_.getTemporaryFilePath("state.gro"),
+ for (const auto& file : { runner_.fullPrecisionTrajectoryFileName_,
+ runner_.logFileName_,
+ runner_.edrFileName_,
+ fileManager_.getTemporaryFilePath("state.gro"),
fileManager_.getTemporaryFilePath("state.cpt") })
{
EXPECT_TRUE(File::exists(file, File::returnFalseOnError))
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
auto propagation = std::get<0>(GetParam());
SCOPED_TRACE(
formatString("Doing %s simulation with %s integrator, %s tcoupling and %s pcoupling\n",
- propagation["simulationName"].c_str(), propagation["integrator"].c_str(),
- propagation["tcoupl"].c_str(), propagation["pcoupl"].c_str()));
- auto mdpFieldValues = prepareMdpFieldValues(propagation["simulationName"], propagation["integrator"],
- propagation["tcoupl"], propagation["pcoupl"]);
- mdpFieldValues.insert(propagation.begin(), propagation.end());
- mdpFieldValues.insert(output.begin(), output.end());
+ propagation["simulationName"].c_str(),
+ propagation["integrator"].c_str(),
+ propagation["tcoupl"].c_str(),
+ propagation["pcoupl"].c_str()));
+ auto mdpFieldValues = prepareMdpFieldValues(propagation["simulationName"],
+ propagation["integrator"],
+ propagation["tcoupl"],
+ propagation["pcoupl"]);
+
+ // This lambda writes all mdp options in `source` into `target`, overwriting options already
+ // present in `target`. It also filters out non-mdp option entries in the source maps
+ auto overWriteMdpMapValues = [](const MdpFieldValues& source, MdpFieldValues& target) {
+ for (auto const& [key, value] : source)
+ {
+ if (key == "simulationName" || key == "maxGromppWarningsTolerated" || key == "description")
+ {
+ // Remove non-mdp entries used in propagation and output
+ continue;
+ }
+ target[key] = value;
+ }
+ };
+ // Add options in propagation and output to the mdp options
+ overWriteMdpMapValues(propagation, mdpFieldValues);
+ overWriteMdpMapValues(output, mdpFieldValues);
// prepare the tpr file
{
{
auto propagation = std::get<0>(GetParam());
SCOPED_TRACE(formatString("Comparing two simulations of '%s' with integrator '%s'",
- propagation["simulationName"].c_str(), propagation["integrator"].c_str()));
+ propagation["simulationName"].c_str(),
+ propagation["integrator"].c_str()));
prepareReferenceData();
+ "' and test '" + runner_.edrFileName_ + "'");
shouldContinueComparing = shouldContinueComparing
&& compareFrames(referenceEnergyFrameReader.get(),
- testEnergyFrameReader.get(), energyComparison_);
+ testEnergyFrameReader.get(),
+ energyComparison_);
}
}
}
--- /dev/null
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+Repl There are 4 replicas:
+Replica-exchange molecular dynamics method for protein folding
+Repl Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl p 1.00 1.01 1.02 1.03
+Replica exchange interval: 4
+Replica random seed: 98714
+Replica exchange information below: ex and x = exchange, pr = probability
+Replica exchange at step 4 time 0.00400
+Repl 0 <-> 1 [ not checked ]
+Repl ex 0 x 1 2 x 3
+Repl pr 1.0 1.0
+Replica exchange at step 8 time 0.00800
+Repl 1 <-> 2 [ not checked ]
+Repl ex 0 1 x 2 3
+Repl pr 1.0
+Replica exchange at step 12 time 0.01200
+Repl 0 <-> 1 [ not checked ]
+Repl ex 0 x 1 2 x 3
+Repl pr 1.0 1.0
+Replica exchange statistics
+Repl 3 attempts, 2 odd, 1 even
+Repl average probabilities:
+Repl 0 1 2 3
+Repl 1.0 1.0 1.0
+Repl number of exchanges:
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+Repl Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
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+Repl ex 0 x 1 2 x 3
+Repl pr 1.0 1.0
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+Repl 1.0 1.0 1.0
+Repl number of exchanges:
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+Repl 2 1 2
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+Repl There are 2 replicas:
+Replica-exchange molecular dynamics method for protein folding
+Repl Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl p 1.00 1.02
+Replica exchange interval: 4
+Replica random seed: 98713
+Replica exchange information below: ex and x = exchange, pr = probability
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+Repl ex 0 x 1
+Repl pr 1.0
+Replica exchange at step 8 time 0.00800
+Repl ex 0 1
+Repl pr
+Replica exchange at step 12 time 0.01200
+Repl 0 <-> 1 [ not checked ]
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+Repl pr 1.0
+Replica exchange statistics
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+Repl 0 1
+Repl 1.0
+Repl number of exchanges:
+Repl 0 1
+Repl 2
+Repl average number of exchanges:
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+Replica-exchange molecular dynamics method for protein folding
+Repl Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl p 1.00 1.02
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+Repl 1.0
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+Replica-exchange molecular dynamics method for protein folding
+Repl Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
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+Repl ex 0 x 1 2 x 3
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+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
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+Replica-exchange molecular dynamics method for protein folding
+Repl Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl p 1.00 1.02
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+Repl pr 1.0
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+Repl pr
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+Repl 0 <-> 1 [ not checked ]
+Repl ex 0 x 1
+Repl pr 1.0
+Replica exchange statistics
+Repl 3 attempts, 2 odd, 1 even
+Repl average probabilities:
+Repl 0 1
+Repl 1.0
+Repl number of exchanges:
+Repl 0 1
+Repl 2
+Repl average number of exchanges:
+Repl 0 1
+Repl 1.0
+Repl Empirical Transition Matrix
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+Repl 0.3333 0.6667 0
+Repl 0.6667 0.3333 1
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+Replica-exchange molecular dynamics method for protein folding
+Repl Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
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+Repl There are 4 replicas:
+Replica-exchange molecular dynamics method for protein folding
+Repl Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl p 1.00 1.01 1.02 1.03
+Replica exchange interval: 4
+Replica random seed: 98714
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+Repl ex 0 1 x 2 3
+Repl pr 1.0
+Replica exchange at step 12 time 0.01200
+Repl 0 <-> 1 [ not checked ]
+Repl ex 0 x 1 2 x 3
+Repl pr 1.0 1.0
+Replica exchange statistics
+Repl 3 attempts, 2 odd, 1 even
+Repl average probabilities:
+Repl 0 1 2 3
+Repl 1.0 1.0 1.0
+Repl number of exchanges:
+Repl 0 1 2 3
+Repl 2 1 2
+Repl average number of exchanges:
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+Repl 1.0 1.0 1.0
+Repl Empirical Transition Matrix
+Repl 1 2 3 4
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+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
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+Replica-exchange molecular dynamics method for protein folding
+Repl Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
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+Repl 1.0
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+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
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+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
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+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
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+Replica-exchange molecular dynamics method for protein folding
+Repl Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
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+Repl 1.0
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+Replica-exchange molecular dynamics method for protein folding
+Replica exchange in temperature
+Replica exchange interval: 4
+Replica random seed: 98714
+Replica exchange information below: ex and x = exchange, pr = probability
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+Repl ex 0 1 x 2 3
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+Replica-exchange molecular dynamics method for protein folding
+Replica exchange in temperature
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+Replica exchange in temperature
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+Replica random seed: 98715
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+ </Vector>
+ <Vector>
+ <Real Name="X">-0.083593786</Real>
+ <Real Name="Y">-1.0349144</Real>
+ <Real Name="Z">2.229893</Real>
+ </Vector>
+ </Sequence>
+ <Sequence Name="Time 0.008000 Step 8 F">
+ <Int Name="Length">15</Int>
+ <Vector>
+ <Real Name="X">-64.500107</Real>
+ <Real Name="Y">-106.42567</Real>
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+ </Vector>
+ <Vector>
+ <Real Name="X">0.19950867</Real>
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+ </Vector>
+ <Vector>
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+ </Vector>
+ <Vector>
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+ </Vector>
+ <Vector>
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+ </Vector>
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+ </Vector>
+ <Vector>
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+ </Vector>
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+ </Vector>
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+ </Vector>
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+ </Vector>
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+ </Vector>
+ </Sequence>
+ <Real Name="Time 0.016000 Step 16 Box[0][0]">1.86206</Real>
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+ <Real Name="Time 0.016000 Step 16 Box[2][1]">0</Real>
+ <Real Name="Time 0.016000 Step 16 Box[2][2]">1.86206</Real>
+ <Sequence Name="Time 0.016000 Step 16 X">
+ <Int Name="Length">15</Int>
+ <Vector>
+ <Real Name="X">0.0014099475</Real>
+ <Real Name="Y">0.58940381</Real>
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+ </Vector>
+ <Vector>
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+ </Vector>
+ <Vector>
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+ </Vector>
+ <Vector>
+ <Real Name="X">0.98185748</Real>
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+ </Vector>
+ <Vector>
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+ </Vector>
+ <Vector>
+ <Real Name="X">0.94000816</Real>
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+ </Vector>
+ <Vector>
+ <Real Name="X">1.3893729</Real>
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+ </Vector>
+ <Vector>
+ <Real Name="X">1.3376812</Real>
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+ </Vector>
+ <Vector>
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+ </Vector>
+ <Vector>
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+ </Vector>
+ <Vector>
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+ </Vector>
+ <Vector>
+ <Real Name="X">1.6021434</Real>
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+ </Vector>
+ <Vector>
+ <Real Name="X">1.7750171</Real>
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+ </Vector>
+ <Vector>
+ <Real Name="X">1.7156733</Real>
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+ </Vector>
+ <Vector>
+ <Real Name="X">1.7890438</Real>
+ <Real Name="Y">0.48907131</Real>
+ <Real Name="Z">0.050391514</Real>
+ </Vector>
+ </Sequence>
+ <Sequence Name="Time 0.016000 Step 16 V">
+ <Int Name="Length">15</Int>
+ <Vector>
+ <Real Name="X">-0.20774576</Real>
+ <Real Name="Y">-0.57286853</Real>
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+ </Vector>
+ <Vector>
+ <Real Name="X">0.33856916</Real>
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+ </Vector>
+ <Vector>
+ <Real Name="X">2.4273114</Real>
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+ </Vector>
+ <Vector>
+ <Real Name="X">0.42057839</Real>
+ <Real Name="Y">-0.10071245</Real>
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+ </Vector>
+ <Vector>
+ <Real Name="X">1.570209</Real>
+ <Real Name="Y">0.80972606</Real>
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+ </Vector>
+ <Vector>
+ <Real Name="X">1.5919843</Real>
+ <Real Name="Y">0.45125833</Real>
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+ </Vector>
+ <Vector>
+ <Real Name="X">-0.52939558</Real>
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+ </Vector>
+ <Vector>
+ <Real Name="X">0.56629837</Real>
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+ <Real Name="Z">1.0528401</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.94382876</Real>
+ <Real Name="Y">-1.7395716</Real>
+ <Real Name="Z">2.3638034</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.23067445</Real>
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+ </Vector>
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+ <Vector>
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+ </Vector>
+ <Vector>
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+ </Vector>
+ <Vector>
+ <Real Name="X">-2.7428274</Real>
+ <Real Name="Y">0.28813386</Real>
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+ </Vector>
+ </Sequence>
+ <Sequence Name="Time 0.016000 Step 16 F">
+ <Int Name="Length">15</Int>
+ <Vector>
+ <Real Name="X">-71.80658</Real>
+ <Real Name="Y">68.801941</Real>
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+ </Vector>
+ <Vector>
+ <Real Name="X">3.7374649</Real>
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+ </Vector>
+ <Vector>
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+ <Vector>
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+ </Vector>
+ <Vector>
+ <Real Name="X">-5.6398582</Real>
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+ </Vector>
+ <Vector>
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+ </Vector>
+ <Vector>
+ <Real Name="X">-13.121216</Real>
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+ <Real Name="Z">18.122276</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-316.19507</Real>
+ <Real Name="Y">-133.0134</Real>
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+ <Vector>
+ <Real Name="X">244.08429</Real>
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+ <Vector>
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+ <Real Name="Y">60.946838</Real>
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+ </Vector>
+ <Vector>
+ <Real Name="X">-73.573181</Real>
+ <Real Name="Y">-317.42291</Real>
+ <Real Name="Z">-33.423706</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">19.039402</Real>
+ <Real Name="Y">56.988865</Real>
+ <Real Name="Z">25.400909</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-30.646835</Real>
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+ </Vector>
+ </Sequence>
+ </Simulation>
+</ReferenceData>
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "config.h"
+#include <regex>
+
#include <gtest/gtest.h>
+#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/topology/ifunc.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/filestream.h"
#include "gromacs/utility/path.h"
#include "gromacs/utility/stringutil.h"
+#include "testutils/refdata.h"
#include "testutils/testfilemanager.h"
+#include "energycomparison.h"
#include "multisimtest.h"
+#include "trajectorycomparison.h"
namespace gmx
{
/* Note, not all preprocessor implementations nest macro expansions
the same way / at all, if we would try to duplicate less code. */
+
#if GMX_LIB_MPI
-INSTANTIATE_TEST_CASE_P(WithDifferentControlVariables,
- ReplicaExchangeEnsembleTest,
- ::testing::Values("pcoupl = no", "pcoupl = Berendsen"));
+INSTANTIATE_TEST_CASE_P(
+ WithDifferentControlVariables,
+ ReplicaExchangeEnsembleTest,
+ ::testing::Combine(::testing::Values(NumRanksPerSimulation(1), NumRanksPerSimulation(2)),
+ ::testing::Values(IntegrationAlgorithm::MD),
+ ::testing::Values(TemperatureCoupling::VRescale),
+ ::testing::Values(PressureCoupling::No, PressureCoupling::Berendsen)));
#else
-INSTANTIATE_TEST_CASE_P(DISABLED_WithDifferentControlVariables,
- ReplicaExchangeEnsembleTest,
- ::testing::Values("pcoupl = no", "pcoupl = Berendsen"));
+INSTANTIATE_TEST_CASE_P(
+ DISABLED_WithDifferentControlVariables,
+ ReplicaExchangeEnsembleTest,
+ ::testing::Combine(::testing::Values(NumRanksPerSimulation(1), NumRanksPerSimulation(2)),
+ ::testing::Values(IntegrationAlgorithm::MD),
+ ::testing::Values(TemperatureCoupling::VRescale),
+ ::testing::Values(PressureCoupling::No, PressureCoupling::Berendsen)));
#endif
//! Convenience typedef
typedef MultiSimTest ReplicaExchangeTerminationTest;
-TEST_F(ReplicaExchangeTerminationTest, WritesCheckpointAfterMaxhTerminationAndThenRestarts)
+TEST_P(ReplicaExchangeTerminationTest, WritesCheckpointAfterMaxhTerminationAndThenRestarts)
{
mdrunCaller_->addOption("-replex", 1);
runMaxhTest();
}
+INSTANTIATE_TEST_CASE_P(InNvt,
+ ReplicaExchangeTerminationTest,
+ ::testing::Combine(::testing::Values(NumRanksPerSimulation(1)),
+ ::testing::Values(IntegrationAlgorithm::MD),
+ ::testing::Values(TemperatureCoupling::VRescale),
+ ::testing::Values(PressureCoupling::No)));
+
+/*! \brief Return replica exchange related output from logfile
+ *
+ * All replica exchange related output in log files start with 'Repl',
+ * making extraction easy. This function also removes the printing of
+ * energy differences, as the log files are compared exactly, and
+ * energy differences will slightly vary between runs.
+ *
+ * \param logFileName Name of log file
+ * \return Replica exchange related output in log file
+ */
+static std::string getReplicaExchangeOutputFromLogFile(const std::string& logFileName)
+{
+ TextInputFile logFile(logFileName);
+ std::string replExOutput;
+ std::string line;
+ while (logFile.readLine(&line))
+ {
+ // All replica exchange output lines starts with "Repl"
+ if (startsWith(line, "Repl"))
+ {
+ // This is an exact comparison, so we can't compare the energies which
+ // are slightly different per run. Energies are tested later.
+ const auto pos = line.find("dE_term");
+ if (pos != std::string::npos)
+ {
+ line.replace(line.begin() + pos, line.end(), "[ not checked ]\n");
+ }
+ replExOutput.append(line);
+ }
+ }
+ return replExOutput;
+}
+
+//! Convenience typedef
+typedef MultiSimTest ReplicaExchangeRegressionTest;
+
+/* Run replica exchange simulations, compare to reference data
+ *
+ * Reference data generated by
+ *
+ * GROMACS version: 2022-dev
+ * Precision: single and double (separate reference data)
+ * Memory model: 64 bit
+ * MPI library: MPI
+ * OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
+ * GPU support: disabled
+ * SIMD instructions: AVX2_256
+ * FFT library: fftw-3.3.9-sse2-avx
+ * RDTSCP usage: enabled
+ * TNG support: enabled
+ * Hwloc support: disabled
+ * Tracing support: disabled
+ * C compiler: /usr/local/bin/mpicc Clang 8.0.1
+ * C++ compiler: /usr/local/bin/mpic++ Clang 8.0.1
+ *
+ */
+TEST_P(ReplicaExchangeRegressionTest, WithinTolerances)
+{
+ if (!mpiSetupValid())
+ {
+ // Can't test multi-sim without multiple simulations
+ return;
+ }
+
+ if (size_ != 4)
+ {
+ // Results are depending on number of ranks, and we can't have reference
+ // data for all cases. Restricting the regression tests to runs with 4 ranks.
+ // This allows testing 4 replicas with single rank, or 2 replicas with 2 ranks each.
+ return;
+ }
+ const auto& tcoupl = std::get<2>(GetParam());
+ const auto& pcoupl = std::get<3>(GetParam());
+
+ const int numSteps = 16;
+ const int exchangePeriod = 4;
+ // grompp warns about generating velocities and using parrinello-rahman
+ const int maxWarnings = (pcoupl == PressureCoupling::ParrinelloRahman ? 1 : 0);
+
+ mdrunCaller_->addOption("-replex", exchangePeriod);
+ // Seeds need to be reproducible for regression, but can be different per simulation
+ mdrunCaller_->addOption("-reseed", 98713 + simulationNumber_);
+
+ SimulationRunner runner(&fileManager_);
+ runner.useTopGroAndNdxFromDatabase("tip3p5");
+
+ runGrompp(&runner, numSteps, true, maxWarnings);
+ ASSERT_EQ(0, runner.callMdrun(*mdrunCaller_));
+
+#if GMX_LIB_MPI
+ // Make sure all simulations are finished before checking the results.
+ MPI_Barrier(MdrunTestFixtureBase::communicator_);
+#endif
+
+ // We only test simulation results on one rank to avoid problems with reference file access.
+ if (rank_ == 0)
+ {
+ // Create reference data helper object
+ TestReferenceData refData;
+
+ // Specify how energy trajectory comparison must work
+ const auto hasConservedField =
+ !(tcoupl == TemperatureCoupling::No && pcoupl == PressureCoupling::No);
+ // Tolerances copied from simulator tests
+ EnergyTermsToCompare energyTermsToCompare{ {
+ { interaction_function[F_EPOT].longname,
+ relativeToleranceAsPrecisionDependentUlp(60.0, 200, 160) },
+ { interaction_function[F_EKIN].longname,
+ relativeToleranceAsPrecisionDependentUlp(60.0, 200, 160) },
+ } };
+ if (hasConservedField)
+ {
+ energyTermsToCompare.emplace(interaction_function[F_ECONSERVED].longname,
+ relativeToleranceAsPrecisionDependentUlp(50.0, 100, 80));
+ }
+ if (pcoupl != PressureCoupling::No)
+ {
+ energyTermsToCompare.emplace("Volume",
+ relativeToleranceAsPrecisionDependentUlp(10.0, 200, 160));
+ }
+
+ // Specify how trajectory frame matching must work.
+ const TrajectoryFrameMatchSettings trajectoryMatchSettings{ true,
+ true,
+ true,
+ ComparisonConditions::MustCompare,
+ ComparisonConditions::MustCompare,
+ ComparisonConditions::MustCompare,
+ MaxNumFrames::compareAllFrames() };
+ TrajectoryTolerances trajectoryTolerances = TrajectoryComparison::s_defaultTrajectoryTolerances;
+ // By default, velocity tolerance is MUCH tighter than force tolerance
+ trajectoryTolerances.velocities = trajectoryTolerances.forces;
+ // Build the functor that will compare reference and test
+ // trajectory frames in the chosen way.
+ TrajectoryComparison trajectoryComparison{ trajectoryMatchSettings, trajectoryTolerances };
+
+ // Loop over simulations
+ for (int simulationNumber = 0; simulationNumber < (size_ / numRanksPerSimulation_);
+ simulationNumber++)
+ {
+ TestReferenceChecker simulationChecker(refData.rootChecker().checkCompound(
+ "Simulation", formatString("Replica %d", simulationNumber)));
+
+ const auto logFileName =
+ std::regex_replace(runner.logFileName_,
+ std::regex(formatString("sim_%d", simulationNumber_)),
+ formatString("sim_%d", simulationNumber));
+ const auto energyFileName =
+ std::regex_replace(runner.edrFileName_,
+ std::regex(formatString("sim_%d", simulationNumber_)),
+ formatString("sim_%d", simulationNumber));
+ const auto trajectoryFileName =
+ std::regex_replace(runner.fullPrecisionTrajectoryFileName_,
+ std::regex(formatString("sim_%d", simulationNumber_)),
+ formatString("sim_%d", simulationNumber));
+
+ // Check log replica exchange related output (contains exchange statistics)
+ auto replicaExchangeOutputChecker =
+ simulationChecker.checkCompound("ReplExOutput", "Output");
+ const auto replExOutput = getReplicaExchangeOutputFromLogFile(logFileName);
+ replicaExchangeOutputChecker.checkTextBlock(replExOutput, "Replica Exchange Output");
+
+ // Check that the energies agree with the refdata within tolerance.
+ checkEnergiesAgainstReferenceData(energyFileName, energyTermsToCompare, &simulationChecker);
+
+ // Check that the trajectories agree with the refdata within tolerance.
+ checkTrajectoryAgainstReferenceData(trajectoryFileName, trajectoryComparison, &simulationChecker);
+
+ } // end loop over simulations
+ } // end testing simulations on one rank
+
+#if GMX_LIB_MPI
+ // Make sure testing is complete before returning - ranks delete temporary files on exit
+ MPI_Barrier(MdrunTestFixtureBase::communicator_);
+#endif
+}
+
+/*! \brief Helper struct printing custom test name
+ *
+ * Regression test results not only depend on the test parameters, but
+ * also on the total number of ranks and the precision. Names must
+ * reflect that to identify correct reference data.
+ */
+struct PrintReplicaExchangeParametersToString
+{
+ template<class ParamType>
+ std::string operator()(const testing::TestParamInfo<ParamType>& parameter) const
+ {
+ auto testIdentifier =
+ formatString("ReplExRegression_%s_%s_%s_%dRanks_%dRanksPerSimulation_%s",
+ enumValueToString(std::get<1>(parameter.param)),
+ enumValueToString(std::get<2>(parameter.param)),
+ enumValueToString(std::get<3>(parameter.param)),
+ gmx_node_num(),
+ static_cast<int>(std::get<0>(parameter.param)),
+ GMX_DOUBLE ? "d" : "s");
+ // Valid GTest names cannot include hyphens
+ testIdentifier.erase(std::remove(testIdentifier.begin(), testIdentifier.end(), '-'),
+ testIdentifier.end());
+ return testIdentifier;
+ }
+};
+
+#if GMX_LIB_MPI
+INSTANTIATE_TEST_CASE_P(
+ ReplicaExchangeIsEquivalentToReferenceLeapFrog,
+ ReplicaExchangeRegressionTest,
+ ::testing::Combine(::testing::Values(NumRanksPerSimulation(1), NumRanksPerSimulation(2)),
+ ::testing::Values(IntegrationAlgorithm::MD),
+ ::testing::Values(TemperatureCoupling::VRescale, TemperatureCoupling::NoseHoover),
+ ::testing::Values(PressureCoupling::CRescale, PressureCoupling::ParrinelloRahman)),
+ PrintReplicaExchangeParametersToString());
+INSTANTIATE_TEST_CASE_P(ReplicaExchangeIsEquivalentToReferenceVelocityVerlet,
+ ReplicaExchangeRegressionTest,
+ ::testing::Combine(::testing::Values(NumRanksPerSimulation(1),
+ NumRanksPerSimulation(2)),
+ ::testing::Values(IntegrationAlgorithm::VV),
+ ::testing::Values(TemperatureCoupling::NoseHoover),
+ ::testing::Values(PressureCoupling::No)),
+ PrintReplicaExchangeParametersToString());
+#else
+INSTANTIATE_TEST_CASE_P(
+ DISABLED_ReplicaExchangeIsEquivalentToReferenceLeapFrog,
+ ReplicaExchangeRegressionTest,
+ ::testing::Combine(::testing::Values(NumRanksPerSimulation(1), NumRanksPerSimulation(2)),
+ ::testing::Values(IntegrationAlgorithm::MD),
+ ::testing::Values(TemperatureCoupling::VRescale, TemperatureCoupling::NoseHoover),
+ ::testing::Values(PressureCoupling::CRescale, PressureCoupling::ParrinelloRahman)),
+ PrintReplicaExchangeParametersToString());
+INSTANTIATE_TEST_CASE_P(DISABLED_ReplicaExchangeIsEquivalentToReferenceVelocityVerlet,
+ ReplicaExchangeRegressionTest,
+ ::testing::Combine(::testing::Values(NumRanksPerSimulation(1),
+ NumRanksPerSimulation(2)),
+ ::testing::Values(IntegrationAlgorithm::VV),
+ ::testing::Values(TemperatureCoupling::NoseHoover),
+ ::testing::Values(PressureCoupling::No)),
+ PrintReplicaExchangeParametersToString());
+#endif
} // namespace test
} // namespace gmx
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "config.h"
#include "gromacs/topology/ifunc.h"
+#include "gromacs/utility/strconvert.h"
#include "gromacs/utility/stringutil.h"
#include "testutils/mpitest.h"
fprintf(stdout,
"Test system '%s' cannot run with %d ranks.\n"
"The supported numbers are: %s\n",
- simulationName.c_str(), numRanksAvailable,
+ simulationName.c_str(),
+ numRanksAvailable,
reportNumbersOfPpRanksSupported(simulationName).c_str());
return;
}
SCOPED_TRACE(
formatString("Comparing normal and rerun of simulation '%s' "
"with integrator '%s'",
- simulationName.c_str(), integrator.c_str()));
+ simulationName.c_str(),
+ integrator.c_str()));
auto mdpFieldValues =
prepareMdpFieldValues(simulationName.c_str(), integrator.c_str(), "no", "no");
const int toleranceScaleFactor = (integrator == "bd") ? 2 : 1;
EnergyTermsToCompare energyTermsToCompare{ {
{ interaction_function[F_EPOT].longname,
- relativeToleranceAsPrecisionDependentUlp(10.0, 24 * toleranceScaleFactor,
- 40 * toleranceScaleFactor) },
+ relativeToleranceAsPrecisionDependentUlp(
+ 10.0, 24 * toleranceScaleFactor, 40 * toleranceScaleFactor) },
} };
// Specify how trajectory frame matching must work
TrajectoryComparison::s_defaultTrajectoryTolerances };
int numWarningsToTolerate = 0;
- executeRerunTest(&fileManager_, &runner_, simulationName, numWarningsToTolerate, mdpFieldValues,
- energyTermsToCompare, trajectoryComparison);
+ executeRerunTest(&fileManager_,
+ &runner_,
+ simulationName,
+ numWarningsToTolerate,
+ mdpFieldValues,
+ energyTermsToCompare,
+ trajectoryComparison);
}
// TODO The time for OpenCL kernel compilation means these tests time
SCOPED_TRACE(
formatString("Comparing normal and rerun of simulation '%s' "
"with integrator '%s' for initial lambda state %d",
- simulationName.c_str(), integrator.c_str(), initLambdaState));
+ simulationName.c_str(),
+ integrator.c_str(),
+ initLambdaState));
auto mdpFieldValues =
prepareMdpFieldValues(simulationName.c_str(), integrator.c_str(), "no", "no");
- mdpFieldValues["other"] += formatString("\ninit-lambda-state = %d", initLambdaState);
+ mdpFieldValues["init-lambda-state"] = toString(initLambdaState);
EnergyTermsToCompare energyTermsToCompare{
{ { interaction_function[F_EPOT].longname, relativeToleranceAsPrecisionDependentUlp(10.0, 24, 32) },
// The md integrator triggers a warning for nearly decoupled
// states, which we need to suppress. TODO sometimes?
int numWarningsToTolerate = (integrator == "md") ? 1 : 0;
- executeRerunTest(&fileManager_, &runner_, simulationName, numWarningsToTolerate, mdpFieldValues,
- energyTermsToCompare, trajectoryComparison);
+ executeRerunTest(&fileManager_,
+ &runner_,
+ simulationName,
+ numWarningsToTolerate,
+ mdpFieldValues,
+ energyTermsToCompare,
+ trajectoryComparison);
}
// TODO The time for OpenCL kernel compilation means these tests time
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
fprintf(stdout,
"Test system '%s' cannot run with %d ranks.\n"
"The supported numbers are: %s\n",
- simulationName.c_str(), numRanksAvailable,
+ simulationName.c_str(),
+ numRanksAvailable,
reportNumbersOfPpRanksSupported(simulationName).c_str());
return;
}
auto frame = reader.frame();
auto force = frame.f();
int atom = 0;
- for (auto& f : force)
+ for (const auto& f : force)
{
std::string forceName = frame.frameName() + " F[" + toString(atom) + "]";
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
fprintf(stdout,
"Test system '%s' cannot run with %d ranks.\n"
"The supported numbers are: %s\n",
- simulationName.c_str(), numRanksAvailable,
+ simulationName.c_str(),
+ numRanksAvailable,
reportNumbersOfPpRanksSupported(simulationName).c_str());
return;
}
"Comparing two simulations of '%s' "
"with integrator '%s', '%s' temperature coupling, and '%s' pressure coupling "
"switching environment variable '%s'",
- simulationName.c_str(), integrator.c_str(), tcoupling.c_str(), pcoupling.c_str(),
+ simulationName.c_str(),
+ integrator.c_str(),
+ tcoupling.c_str(),
+ pcoupling.c_str(),
environmentVariable.c_str()));
- const auto mdpFieldValues = prepareMdpFieldValues(simulationName.c_str(), integrator.c_str(),
- tcoupling.c_str(), pcoupling.c_str());
+ const auto mdpFieldValues = prepareMdpFieldValues(
+ simulationName.c_str(), integrator.c_str(), tcoupling.c_str(), pcoupling.c_str());
EnergyTermsToCompare energyTermsToCompare{ {
{ interaction_function[F_EPOT].longname, relativeToleranceAsPrecisionDependentUlp(60.0, 200, 160) },
INSTANTIATE_TEST_CASE_P(
SimulatorsAreEquivalentDefaultLegacy,
SimulatorComparisonTest,
- ::testing::Combine(::testing::Combine(::testing::Values("argon12", "tip3p5"),
- ::testing::Values("md"),
- ::testing::Values("no", "v-rescale", "berendsen"),
- ::testing::Values("no", "Parrinello-Rahman")),
- ::testing::Values("GMX_USE_MODULAR_SIMULATOR")));
+ ::testing::Combine(
+ ::testing::Combine(::testing::Values("argon12", "tip3p5"),
+ ::testing::Values("md"),
+ ::testing::Values("no", "v-rescale", "berendsen", "nose-hoover"),
+ ::testing::Values("no", "Parrinello-Rahman")),
+ ::testing::Values("GMX_USE_MODULAR_SIMULATOR")));
#else
INSTANTIATE_TEST_CASE_P(
DISABLED_SimulatorsAreEquivalentDefaultModular,
INSTANTIATE_TEST_CASE_P(
DISABLED_SimulatorsAreEquivalentDefaultLegacy,
SimulatorComparisonTest,
- ::testing::Combine(::testing::Combine(::testing::Values("argon12", "tip3p5"),
- ::testing::Values("md"),
- ::testing::Values("no", "v-rescale", "berendsen"),
- ::testing::Values("no", "Parrinello-Rahman")),
- ::testing::Values("GMX_USE_MODULAR_SIMULATOR")));
+ ::testing::Combine(
+ ::testing::Combine(::testing::Values("argon12", "tip3p5"),
+ ::testing::Values("md"),
+ ::testing::Values("no", "v-rescale", "berendsen", "nose-hoover"),
+ ::testing::Values("no", "Parrinello-Rahman")),
+ ::testing::Values("GMX_USE_MODULAR_SIMULATOR")));
#endif
} // namespace
ASSERT_EQ(0, runner_.callMdrun(secondPart));
auto logFileContents = TextReader::readFileToString(runner_.logFileName_);
- EXPECT_NE(
- std::string::npos,
- logFileContents.find("Restarting from checkpoint, appending to previous log file"))
+ EXPECT_NE(std::string::npos, logFileContents.find("Restarting from checkpoint, appending to previous log file"))
<< "appending was not detected";
}
}
ASSERT_EQ(0, runner_.callMdrun(secondPart));
auto logFileContents = TextReader::readFileToString(runner_.logFileName_);
- EXPECT_EQ(
- std::string::npos,
- logFileContents.find("Restarting from checkpoint, appending to previous log file"))
+ EXPECT_EQ(std::string::npos, logFileContents.find("Restarting from checkpoint, appending to previous log file"))
<< "appending was not detected";
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
ref_t = 298
nsteps = %d
)",
- randomSeed, nsteps);
+ randomSeed,
+ nsteps);
runner_.useStringAsMdpFile(mdpFileContents);
runTest();
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
SCOPED_TRACE("Comparing positions");
if (shouldDoComparison(frame.x(), matchSettings.coordinatesComparison))
{
- auto positions = frame.x();
+ ArrayRef<const RVec> positions{};
+ std::vector<RVec> shiftedPositions{};
if (frame.hasBox() && (matchSettings.handlePbcIfPossible || matchSettings.requirePbcHandling))
{
- positions = putAtomsInBox(frame);
+ shiftedPositions = putAtomsInBox(frame);
+ positions = shiftedPositions;
}
+ else
+ {
+ positions = frame.x();
+ }
+
if (!frame.hasBox() && matchSettings.requirePbcHandling)
{
ADD_FAILURE() << "Comparing positions required PBC handling, "
const TrajectoryComparison& trajectoryComparison,
TestReferenceChecker* checker)
{
- checkTrajectoryAgainstReferenceData(trajectoryFilename, trajectoryComparison, checker,
- MaxNumFrames::compareAllFrames());
+ checkTrajectoryAgainstReferenceData(
+ trajectoryFilename, trajectoryComparison, checker, MaxNumFrames::compareAllFrames());
}
void checkTrajectoryAgainstReferenceData(const std::string& trajectoryFilename,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
t_trxstatus* trajectoryFile;
int flags = TRX_READ_X | TRX_READ_V | TRX_READ_F;
- nextFrameExists_ = read_first_frame(oenvGuard_.get(), &trajectoryFile, filename_.c_str(),
- trxframeGuard_.get(), flags);
+ nextFrameExists_ = read_first_frame(
+ oenvGuard_.get(), &trajectoryFile, filename_.c_str(), trxframeGuard_.get(), flags);
if (!trajectoryFile)
{
GMX_THROW(FileIOError("Could not open trajectory file " + filename_ + " for reading"));
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief Sanity checks for virtual sites
+ *
+ * The tests in this file test the virtual site implementation in two ways.
+ * 1) An artificial test system containing all virtual site types is run
+ * end-to-end. The virtual sites are recalculated using a reference
+ * implementation, and compared to the trajectory values. This ensures
+ * that no relevant (real or virtual) coordinates were changed between
+ * virtual site computation, and that the mdrun implementation agrees
+ * with the reference implementation. The latter has the advantage to
+ * be written closer to the analytical expressions, hence easier to
+ * check by eye. Unlike the mdrun implementation, it can also be unit-
+ * tested (see 2)). Since this is an end-to-end test, it also ensures
+ * that virtual sites can be processed by grompp and run by mdrun.
+ * 2) The reference implementation is tested to have corresponding positions
+ * and velocities. This is achieved by comparing virtual site positions
+ * calculated from propagated real positions to virtual site positions
+ * calculated by propagating virtual sites using the virtual velocities.
+ *
+ * Note, this only ensures that the position and velocity implementation
+ * match, not that they are actually correct. Some regression test systems
+ * include virtual sites, so there is some testing that no bugs are introduced.
+ * It would be good to have unit tests, though. This can either be achieved by
+ * refactoring the mdrun implementation, or adding them to the reference
+ * implementation here. See also #3911.
+ *
+ * \author Pascal Merz <pascal.merz@me.com>
+ * \ingroup module_mdrun_integration_tests
+ */
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/ifunc.h"
+#include "gromacs/trajectoryanalysis/topologyinformation.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/mpitest.h"
+#include "testutils/simulationdatabase.h"
+#include "testutils/testmatchers.h"
+
+#include "gromacs/utility/strconvert.h"
+
+#include "moduletest.h"
+#include "simulatorcomparison.h"
+#include "trajectoryreader.h"
+
+namespace gmx::test
+{
+namespace
+{
+using VirtualSiteTestParams = std::tuple<std::string, std::string, std::string>;
+class VirtualSiteTest : public MdrunTestFixture, public ::testing::WithParamInterface<VirtualSiteTestParams>
+{
+public:
+ struct VirtualSite;
+
+ /*! \brief Check against reference implementation
+ *
+ * Check that the positions and velocities of virtual sites are equal to the reference
+ * implementation, within a given tolerance. This loops over the trajectory, calculates
+ * the virtual site positions and velocities using a reference implementation, and
+ * compares it with the reported virtual site positions and velocities.
+ *
+ * The expectation is that the trajectory and the reference calculations are identical.
+ * This ensures that neither the real atoms nor the virtual sites are changed between
+ * virtual site calculation and trajectory printing. The reference implementation is
+ * also closer to the analytically derived equations than the mdrun implementation,
+ * making it easier to verify. Finally, the reference implementation is tested (within
+ * this file), which is a reasonable work-around for the fact that the actual implementation
+ * doesn't have unit tests.
+ *
+ * Note that the reference implementation does not take into account PBC. It's intended
+ * to be used with simple test cases in which molecules are ensured not to be broken
+ * across periodic boundaries.
+ */
+ static void checkVirtualSitesAgainstReferenceImplementation(const std::string& trajectoryName,
+ ArrayRef<const VirtualSite> virtualSites,
+ FloatingPointTolerance tolerance)
+ {
+ SCOPED_TRACE(
+ "Checking virtual site positions and velocities against reference implementation.");
+ TrajectoryFrameReader trajectoryFrameReader(trajectoryName);
+ while (trajectoryFrameReader.readNextFrame())
+ {
+ const auto frame = trajectoryFrameReader.frame();
+ SCOPED_TRACE(formatString("Checking frame %s", frame.frameName().c_str()));
+ std::vector<RVec> positions;
+ std::vector<RVec> velocities;
+ std::vector<RVec> refPositions;
+ std::vector<RVec> refVelocities;
+ for (const auto& vSite : virtualSites)
+ {
+ auto [refPosition, refVelocity] = vSite.calculate(frame.x(), frame.v());
+ refPositions.emplace_back(refPosition);
+ refVelocities.emplace_back(refVelocity);
+ positions.emplace_back(frame.x().at(vSite.atomIdx));
+ velocities.emplace_back(frame.v().at(vSite.atomIdx));
+ }
+ EXPECT_THAT(refPositions, Pointwise(RVecEq(tolerance), positions));
+ EXPECT_THAT(refVelocities, Pointwise(RVecEq(tolerance), velocities));
+ }
+ }
+
+ /*! \brief Check the reference implementation
+ *
+ * This tests that the reference implementation position and velocities correspond.
+ * This is done by
+ * a) generating real atom starting positions (x(t)) and half-step velocities (v(t+dt/2))
+ * b) propagating the real atoms positions by one time step x(t+dt) = x(t) + dt*v(t+dt/2)
+ * c) calculating the half-step positions x(t+dt/2) = 0.5 * (x(t) + x(t+dt))
+ * d) calculating the virtual position xv(t) := xv(x(t)) and xv1(t+dt) := xv(x(t+dt))
+ * using the reference implementation
+ * e) calculating the virtual velocity vv(t+dt/2) := vv(x(t+dt/2), v(t+dt/2))
+ * using the reference implementation
+ * f) calculating the virtual position xv2(t+dt) = xv(t) + dt*xv(t+dt/2)
+ * g) comparing xv1(t+dt) and xv2(t+dt)
+ * If the calculation of the virtual positions and velocities correspond, xv1 and xv2 will
+ * be identical up to some integration error.
+ *
+ * Maybe unused because this test runs only in double precision.
+ */
+ [[maybe_unused]] static void checkReferenceImplementation()
+ {
+ SCOPED_TRACE("Checking virtual site reference implementation.");
+ // Randomly generated real atom positions and velocities
+ std::vector<RVec> startPositions = { { 2.641321, 2.076298, 2.138602 },
+ { 3.776765, 3.154901, 1.556379 },
+ { 2.376669, 1.166706, 2.457044 },
+ { 3.242320, 2.142465, 2.023578 } };
+ std::vector<RVec> halfStepVelocities = { { 0.154667, 0.319010, 0.458749 },
+ { -0.010590, -0.191858, -0.096820 },
+ { -0.008609, 0.004656, 0.448852 },
+ { 0.411874, -0.038205, -0.151459 } };
+ // Virtual site definitions with randomly generated parameters
+ std::vector<VirtualSite> virtualSites = {
+ { F_VSITE1, 6, { 0 }, {} },
+ { F_VSITE2, 6, { 0, 1 }, { 0.710573 } },
+ { F_VSITE2FD, 6, { 0, 1 }, { 0.292430 } },
+ { F_VSITE3, 6, { 0, 1, 2 }, { 0.060990, 0.543636 } },
+ { F_VSITE3FD, 6, { 0, 1, 2 }, { 0.125024, 0.444587 } },
+ { F_VSITE3FAD, 6, { 0, 1, 2 }, { 0.414850, 0.349767 } },
+ { F_VSITE3OUT, 6, { 0, 1, 2 }, { 0.779323, 0.093773, 0.743164 } },
+ { F_VSITE4FDN, 6, { 0, 1, 2, 3 }, { 0.975111, 0.952180, 0.757594 } }
+ };
+
+ // Make integration step
+ const real timeStep = 1e-5;
+ std::vector<RVec> endPositions;
+ std::vector<RVec> halfStepPositions;
+ GMX_RELEASE_ASSERT(startPositions.size() == halfStepVelocities.size(),
+ "Need positions and velocities for every real atom.");
+ const auto numRealAtoms = startPositions.size();
+ for (auto idx = decltype(numRealAtoms){ 0 }; idx < numRealAtoms; idx++)
+ {
+ endPositions.emplace_back(startPositions[idx] + timeStep * halfStepVelocities[idx]);
+ halfStepPositions.emplace_back(startPositions[idx]
+ + real(0.5) * timeStep * halfStepVelocities[idx]);
+ }
+
+ // Check that displacement equals the calculated velocities
+ for (const auto& vSite : virtualSites)
+ {
+ SCOPED_TRACE(formatString("Checking %s", interaction_function[vSite.type].longname));
+
+ // GCC 7 falsely flags unused "variables" in structured bindings, GCC 8+ fixed this
+ // https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81767
+ // clang-format off
+ GCC_DIAGNOSTIC_IGNORE(-Wunused-variable)
+ // clang-format on
+ /* Calculate start and end virtual position
+ *
+ * The reference implementation always calculates the virtual velocity, but
+ * since we don't have real velocities at full steps, these virtual velocities
+ * are unprecise. We don't need them anyway, so we'll just ignore them.
+ */
+ const auto [startVPosition, vVelocityUnused1] =
+ vSite.calculate(startPositions, halfStepVelocities);
+ const auto [endVPosition1, vVelocityUnused2] =
+ vSite.calculate(endPositions, halfStepVelocities);
+
+ /* Calculate virtual velocity at half step using reference implementation
+ *
+ * The virtual positions are exact, but we don't need them.
+ */
+ const auto [halfStepVPositionUnused, halfStepVVelocity] =
+ vSite.calculate(halfStepPositions, halfStepVelocities);
+ GCC_DIAGNOSTIC_RESET
+
+ // We can now integrate the virtual positions using the half step velocity
+ const auto endVPosition2 = startVPosition + timeStep * halfStepVVelocity;
+
+ /* We can now calculate the displacement of the virtual site in two ways:
+ * (1) Using endVPosition1, calculated by advancing the real positions
+ * and calculating the virtual position from them.
+ * (2) Using endVPosition2, calculated by advancing the virtual position
+ * by the virtual velocity.
+ * Comparing the difference of the displacement with relative tolerance makes
+ * this at least somewhat independent of the choice of time step and coordinates -
+ * assuming that the displacement doesn't go to zero, of course!
+ */
+ const auto displacement1 = endVPosition1 - startVPosition;
+ const auto displacement2 = endVPosition2 - startVPosition;
+ ASSERT_GT(std::abs(displacement1[XX]), 0)
+ << "adjust choice of coordinates or time step.";
+ ASSERT_GT(std::abs(displacement1[YY]), 0)
+ << "adjust choice of coordinates or time step.";
+ ASSERT_GT(std::abs(displacement1[ZZ]), 0)
+ << "adjust choice of coordinates or time step.";
+
+ EXPECT_REAL_EQ_TOL(displacement1[XX],
+ displacement2[XX],
+ relativeToleranceAsFloatingPoint(displacement1[XX], 1e-9));
+ EXPECT_REAL_EQ_TOL(displacement1[YY],
+ displacement2[YY],
+ relativeToleranceAsFloatingPoint(displacement1[YY], 1e-9));
+ EXPECT_REAL_EQ_TOL(displacement1[ZZ],
+ displacement2[ZZ],
+ relativeToleranceAsFloatingPoint(displacement1[ZZ], 1e-9));
+ }
+ }
+
+ //! Holds parameters of virtual site and allows calculation
+ struct VirtualSite
+ {
+ //! Type of virtual site
+ int type;
+ //! Index of virtual site
+ int atomIdx;
+ //! Indices of constructing atoms
+ std::vector<int> constructingAtomIdx;
+ //! Construction parameters
+ std::vector<real> parameters;
+
+ //! Dispatch function to compute position and velocity of virtual site from reference implementation based on \p type
+ [[nodiscard]] std::tuple<RVec, RVec> calculate(ArrayRef<const RVec> constructingPositions,
+ ArrayRef<const RVec> constructingVelocities) const;
+
+ private:
+ //! Templated reference implementation of virtual site position and velocity calculation
+ template<int vsiteType>
+ [[nodiscard]] std::tuple<RVec, RVec> calculateVSite(ArrayRef<const RVec> positions,
+ ArrayRef<const RVec> velocities) const;
+ };
+
+ /*! \brief Helper function returning a list of virtual sites from the topology
+ *
+ * This also prints the indices of the virtual sites. If any tests fail, this
+ * can be used to understand which type is failing.
+ */
+ static std::vector<VirtualSite> vSiteList(const TopologyInformation& topologyInformation)
+ {
+ std::vector<VirtualSite> virtualSites;
+ const auto& localTopology = *topologyInformation.expandedTopology();
+ printf("Reading virtual site types...\n");
+ for (int vsiteType = F_VSITE1; vsiteType <= F_VSITEN; vsiteType++)
+ {
+ const auto& interactionList = localTopology.idef.il.at(vsiteType);
+ if (vsiteType == F_VSITE4FD || interactionList.empty())
+ {
+ // 4FD is deprecated. Interaction list empty means system doesn't contain this type.
+ continue;
+ }
+ const int numConstructingAtoms = interaction_function[vsiteType].nratoms - 1;
+ const int defaultIncrement = numConstructingAtoms + 2;
+ std::string indexString;
+
+ for (int i = 0; i < interactionList.size();)
+ {
+ const int parameterIdx = interactionList.iatoms[i];
+ const int virtualSiteIdx = interactionList.iatoms[i + 1];
+ if (!indexString.empty())
+ {
+ indexString += ", ";
+ }
+ indexString += toString(virtualSiteIdx);
+
+ if (vsiteType == F_VSITEN)
+ {
+ const int vSiteNConstructingAtoms =
+ localTopology.idef.iparams[parameterIdx].vsiten.n;
+ VirtualSite vSite{ vsiteType, virtualSiteIdx, { interactionList.iatoms[i + 2] }, {} };
+ for (int j = 3; j < 3 * vSiteNConstructingAtoms; j += 3)
+ {
+ vSite.constructingAtomIdx.push_back(interactionList.iatoms[j + 2]);
+ vSite.parameters.push_back(
+ localTopology.idef.iparams[interactionList.iatoms[j]].vsiten.a);
+ }
+ virtualSites.push_back(std::move(vSite));
+ i += 3 * vSiteNConstructingAtoms;
+ }
+ else
+ {
+ virtualSites.emplace_back(VirtualSite{
+ vsiteType,
+ virtualSiteIdx,
+ { &interactionList.iatoms[i + 2],
+ &interactionList.iatoms[i + 2 + numConstructingAtoms] },
+ { localTopology.idef.iparams[parameterIdx].generic.buf,
+ localTopology.idef.iparams[parameterIdx].generic.buf + MAXFORCEPARAM } });
+ i += defaultIncrement;
+ }
+ }
+ }
+ return virtualSites;
+ }
+};
+
+// check-source gets confused by these
+//! \cond
+template<>
+[[nodiscard]] std::tuple<RVec, RVec>
+VirtualSiteTest::VirtualSite::calculateVSite<F_VSITE1>(ArrayRef<const RVec> positions,
+ ArrayRef<const RVec> velocities) const
+{
+ return { positions[constructingAtomIdx.at(0)], velocities[constructingAtomIdx.at(0)] };
+}
+template<>
+[[nodiscard]] std::tuple<RVec, RVec>
+VirtualSiteTest::VirtualSite::calculateVSite<F_VSITE2>(ArrayRef<const RVec> positions,
+ ArrayRef<const RVec> velocities) const
+{
+ const auto& a = parameters[0];
+ return { (1 - a) * positions[constructingAtomIdx.at(0)] + a * positions[constructingAtomIdx.at(1)],
+ (1 - a) * velocities[constructingAtomIdx.at(0)] + a * velocities[constructingAtomIdx.at(1)] };
+}
+template<>
+[[nodiscard]] std::tuple<RVec, RVec>
+VirtualSiteTest::VirtualSite::calculateVSite<F_VSITE2FD>(ArrayRef<const RVec> positions,
+ ArrayRef<const RVec> velocities) const
+{
+ const auto& a = parameters[0];
+ const auto& ri = positions[constructingAtomIdx.at(0)];
+ const auto& rj = positions[constructingAtomIdx.at(1)];
+ const auto& vi = velocities[constructingAtomIdx.at(0)];
+ const auto& vj = velocities[constructingAtomIdx.at(1)];
+ const auto rij = rj - ri;
+ const auto vij = vj - vi;
+
+ return { ri + (a / rij.norm()) * rij,
+ vi + (a / rij.norm()) * (vij - rij * (vij.dot(rij) / rij.norm2())) };
+}
+template<>
+[[nodiscard]] std::tuple<RVec, RVec>
+VirtualSiteTest::VirtualSite::calculateVSite<F_VSITE3>(ArrayRef<const RVec> positions,
+ ArrayRef<const RVec> velocities) const
+{
+ const auto& a = parameters[0];
+ const auto& b = parameters[1];
+ const auto& ri = positions[constructingAtomIdx.at(0)];
+ const auto& rj = positions[constructingAtomIdx.at(1)];
+ const auto& rk = positions[constructingAtomIdx.at(2)];
+ const auto& vi = velocities[constructingAtomIdx.at(0)];
+ const auto& vj = velocities[constructingAtomIdx.at(1)];
+ const auto& vk = velocities[constructingAtomIdx.at(2)];
+
+ return { (1 - a - b) * ri + a * rj + b * rk, (1 - a - b) * vi + a * vj + b * vk };
+}
+template<>
+[[nodiscard]] std::tuple<RVec, RVec>
+VirtualSiteTest::VirtualSite::calculateVSite<F_VSITE3FD>(ArrayRef<const RVec> positions,
+ ArrayRef<const RVec> velocities) const
+{
+ const auto& a = parameters[0];
+ const auto& b = parameters[1];
+ const auto& ri = positions[constructingAtomIdx.at(0)];
+ const auto& rj = positions[constructingAtomIdx.at(1)];
+ const auto& rk = positions[constructingAtomIdx.at(2)];
+ const auto& vi = velocities[constructingAtomIdx.at(0)];
+ const auto& vj = velocities[constructingAtomIdx.at(1)];
+ const auto& vk = velocities[constructingAtomIdx.at(2)];
+ const auto rij = rj - ri;
+ const auto rjk = rk - rj;
+ const auto vij = vj - vi;
+ const auto vjk = vk - vj;
+
+ // TODO: Should be uncommented after resolution of #3909
+ const auto rijk = /*(1 - a) **/ rij + a * rjk;
+ const auto vijk = /*(1 - a) **/ vij + a * vjk;
+
+ return { ri + (b / rijk.norm()) * rijk,
+ vi + (b / rijk.norm()) * (vijk - rijk * (vijk.dot(rijk) / rijk.norm2())) };
+}
+template<>
+[[nodiscard]] std::tuple<RVec, RVec>
+VirtualSiteTest::VirtualSite::calculateVSite<F_VSITE3FAD>(ArrayRef<const RVec> positions,
+ ArrayRef<const RVec> velocities) const
+{
+ // Note: a = d * cos(theta)
+ // b = d * sin(theta)
+ const auto& a = parameters[0];
+ const auto& b = parameters[1];
+ const auto& ri = positions[constructingAtomIdx.at(0)];
+ const auto& rj = positions[constructingAtomIdx.at(1)];
+ const auto& rk = positions[constructingAtomIdx.at(2)];
+ const auto& vi = velocities[constructingAtomIdx.at(0)];
+ const auto& vj = velocities[constructingAtomIdx.at(1)];
+ const auto& vk = velocities[constructingAtomIdx.at(2)];
+ const auto rij = rj - ri;
+ const auto rjk = rk - rj;
+ const auto vij = vj - vi;
+ const auto vjk = vk - vj;
+
+ const auto rPerp = rjk - rij * (rij.dot(rjk) / rij.norm2());
+ const auto dtRijNormRij = (1 / rij.norm()) * (vij - rij * (vij.dot(rij) / rij.norm2()));
+ const auto vPerp = vjk
+ - rij
+ * ((vij.dot(rjk) + rij.dot(vjk)) / rij.norm2()
+ - 2 * rij.dot(rjk) * rij.dot(vij) / rij.norm2() / rij.norm2())
+ - vij * (rij.dot(rjk) / rij.norm2());
+ const auto dtRPerpNormRPerp =
+ (1 / rPerp.norm()) * (vPerp - rPerp * (vPerp.dot(rPerp) / rPerp.norm2()));
+
+ return { ri + (a / rij.norm()) * rij + (b / rPerp.norm()) * rPerp,
+ vi + a * dtRijNormRij + b * dtRPerpNormRPerp };
+}
+template<>
+[[nodiscard]] std::tuple<RVec, RVec>
+VirtualSiteTest::VirtualSite::calculateVSite<F_VSITE3OUT>(ArrayRef<const RVec> positions,
+ ArrayRef<const RVec> velocities) const
+{
+ const auto& a = parameters[0];
+ const auto& b = parameters[1];
+ const auto& c = parameters[2];
+ const auto& ri = positions[constructingAtomIdx.at(0)];
+ const auto& rj = positions[constructingAtomIdx.at(1)];
+ const auto& rk = positions[constructingAtomIdx.at(2)];
+ const auto& vi = velocities[constructingAtomIdx.at(0)];
+ const auto& vj = velocities[constructingAtomIdx.at(1)];
+ const auto& vk = velocities[constructingAtomIdx.at(2)];
+ const auto rij = rj - ri;
+ const auto rik = rk - ri;
+ const auto vij = vj - vi;
+ const auto vik = vk - vi;
+
+ return { ri + a * rij + b * rik + c * rij.cross(rik),
+ vi + a * vij + b * vik + c * (vij.cross(rik) + rij.cross(vik)) };
+}
+template<>
+[[nodiscard]] std::tuple<RVec, RVec>
+VirtualSiteTest::VirtualSite::calculateVSite<F_VSITE4FDN>(ArrayRef<const RVec> positions,
+ ArrayRef<const RVec> velocities) const
+{
+ const auto& a = parameters[0];
+ const auto& b = parameters[1];
+ const auto& c = parameters[2];
+ const auto& ri = positions[constructingAtomIdx.at(0)];
+ const auto& rj = positions[constructingAtomIdx.at(1)];
+ const auto& rk = positions[constructingAtomIdx.at(2)];
+ const auto& rl = positions[constructingAtomIdx.at(3)];
+ const auto& vi = velocities[constructingAtomIdx.at(0)];
+ const auto& vj = velocities[constructingAtomIdx.at(1)];
+ const auto& vk = velocities[constructingAtomIdx.at(2)];
+ const auto& vl = velocities[constructingAtomIdx.at(3)];
+ const auto rij = rj - ri;
+ const auto rik = rk - ri;
+ const auto ril = rl - ri;
+ const auto vij = vj - vi;
+ const auto vik = vk - vi;
+ const auto vil = vl - vi;
+
+ const auto rja = a * rik - rij;
+ const auto rjb = b * ril - rij;
+ const auto rm = rja.cross(rjb);
+
+ const auto vja = a * vik - vij;
+ const auto vjb = b * vil - vij;
+ const auto vm = vja.cross(rjb) + rja.cross(vjb);
+
+ return { ri + (c / rm.norm()) * rm, vi + (c / rm.norm()) * (vm - rm * (vm.dot(rm) / rm.norm2())) };
+}
+
+template<>
+[[nodiscard]] std::tuple<RVec, RVec>
+VirtualSiteTest::VirtualSite::calculateVSite<F_VSITEN>(ArrayRef<const RVec> positions,
+ ArrayRef<const RVec> velocities) const
+{
+ const auto& ri = positions[constructingAtomIdx.at(0)];
+ const auto& vi = velocities[constructingAtomIdx.at(0)];
+ GMX_RELEASE_ASSERT(constructingAtomIdx.size() == parameters.size() - 1,
+ "VSITEN atom / parameters mismatch.");
+
+ RVec rSum(0, 0, 0);
+ RVec vSum(0, 0, 0);
+
+ const auto parameterSize = parameters.size();
+ for (auto idx = decltype(parameterSize){ 0 }; idx < parameterSize; idx++)
+ {
+ rSum += parameters[idx] * (positions[constructingAtomIdx[idx + 1]] - ri);
+ vSum += parameters[idx] * (velocities[constructingAtomIdx[idx + 1]] - vi);
+ }
+
+ return { ri + rSum, vi + vSum };
+}
+
+[[nodiscard]] std::tuple<RVec, RVec>
+VirtualSiteTest::VirtualSite::calculate(ArrayRef<const RVec> constructingPositions,
+ ArrayRef<const RVec> constructingVelocities) const
+{
+ switch (type)
+ {
+ case F_VSITE1:
+ return calculateVSite<F_VSITE1>(constructingPositions, constructingVelocities);
+ case F_VSITE2:
+ return calculateVSite<F_VSITE2>(constructingPositions, constructingVelocities);
+ case F_VSITE2FD:
+ return calculateVSite<F_VSITE2FD>(constructingPositions, constructingVelocities);
+ case F_VSITE3:
+ return calculateVSite<F_VSITE3>(constructingPositions, constructingVelocities);
+ case F_VSITE3FD:
+ return calculateVSite<F_VSITE3FD>(constructingPositions, constructingVelocities);
+ case F_VSITE3FAD:
+ return calculateVSite<F_VSITE3FAD>(constructingPositions, constructingVelocities);
+ case F_VSITE3OUT:
+ return calculateVSite<F_VSITE3OUT>(constructingPositions, constructingVelocities);
+ case F_VSITE4FDN:
+ return calculateVSite<F_VSITE4FDN>(constructingPositions, constructingVelocities);
+ case F_VSITEN:
+ return calculateVSite<F_VSITEN>(constructingPositions, constructingVelocities);
+ default: throw NotImplementedError("Unknown virtual site type");
+ }
+}
+//! \endcond
+
+TEST(VirtualSiteVelocityTest, ReferenceIsCorrect)
+{
+ // Test is too sensitive to run in single precision
+ if constexpr (GMX_DOUBLE)
+ {
+ VirtualSiteTest::checkReferenceImplementation();
+ }
+}
+
+TEST_P(VirtualSiteTest, WithinToleranceOfReference)
+{
+ const auto& params = GetParam();
+ const auto& integrator = std::get<0>(params);
+ const auto& tcoupling = std::get<1>(params);
+ const auto& pcoupling = std::get<2>(params);
+ const real timeStep = 0.001;
+ const auto& simulationName = "vsite_test";
+
+ if (integrator == "md-vv" && pcoupling == "parrinello-rahman")
+ {
+ // Parrinello-Rahman is not implemented in md-vv
+ return;
+ }
+
+ if ((integrator == "sd" || integrator == "bd") && tcoupling != "no")
+ {
+ // bd and sd handle temperature coupling implicitly and would set tcoupling to "no" anyway
+ return;
+ }
+
+ // Prepare mdp input
+ auto mdpFieldValues = prepareMdpFieldValues(simulationName, integrator, tcoupling, pcoupling);
+ mdpFieldValues["nsteps"] = "8";
+ mdpFieldValues["nstxout"] = "4";
+ mdpFieldValues["nstvout"] = "4";
+ mdpFieldValues["dt"] = toString(timeStep);
+ mdpFieldValues["constraints"] = "none";
+ if (pcoupling == "parrinello-rahman")
+ {
+ mdpFieldValues["tau-p"] = "2";
+ }
+
+ // Run grompp
+ runner_.useTopGroAndNdxFromDatabase(simulationName);
+ runner_.useStringAsMdpFile(prepareMdpFileContents(mdpFieldValues));
+ runGrompp(&runner_);
+ // Run mdrun
+ runMdrun(&runner_);
+
+ TopologyInformation topologyInformation;
+ topologyInformation.fillFromInputFile(runner_.tprFileName_);
+ const auto virtualSites = vSiteList(topologyInformation);
+
+ // This is in line with other tests (e.g. exact continuation, rerun), which
+ // never reach the same reproducibility for BD as for the other integrators.
+ const auto tolerance =
+ (integrator == "bd") ? relativeToleranceAsUlp(1.0, 100) : defaultRealTolerance();
+
+ checkVirtualSitesAgainstReferenceImplementation(
+ runner_.fullPrecisionTrajectoryFileName_, virtualSites, tolerance);
+}
+
+INSTANTIATE_TEST_CASE_P(
+ VelocitiesConformToExpectations,
+ VirtualSiteTest,
+ ::testing::Combine(::testing::Values("md", "md-vv", "sd", "bd"),
+ ::testing::Values("no", "v-rescale", "nose-hoover"),
+ ::testing::Values("no", "c-rescale", "parrinello-rahman")));
+
+} // namespace
+} // namespace gmx::test
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2016,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int main(int argc, char* argv[])
{
- return gmx::CommandLineModuleManager::runAsMainCMainWithSettings(argc, argv, &gmx::gmx_mdrun,
- &initSettingsNoNice);
+ return gmx::CommandLineModuleManager::runAsMainCMainWithSettings(
+ argc, argv, &gmx::gmx_mdrun, &initSettingsNoNice);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* VBox holder */
y0 = XTextHeight(x11->font) + 2 * AIR + 2;
- InitWin(&vb->wd, 0, 0, vb->nbut * (play_width + AIR) + AIR, y0 + play_height + 2 * AIR, 1,
+ InitWin(&vb->wd,
+ 0,
+ 0,
+ vb->nbut * (play_width + AIR) + AIR,
+ y0 + play_height + 2 * AIR,
+ 1,
"VCR - Control");
- vb->wd.self = XCreateSimpleWindow(x11->disp, Parent, vb->wd.x, vb->wd.y, vb->wd.width,
- vb->wd.height, vb->wd.bwidth, fg, bg);
+ vb->wd.self = XCreateSimpleWindow(
+ x11->disp, Parent, vb->wd.x, vb->wd.y, vb->wd.width, vb->wd.height, vb->wd.bwidth, fg, bg);
x11->RegisterCallback(x11, vb->wd.self, Parent, VBCallBack, vb);
x11->SetInputMask(x11, vb->wd.self, ExposureMask);
default: fprintf(stderr, "Invalid bitmap in init_vbox %d\n", ID); std::exit(1);
}
/* Rely on the fact that all bitmaps are equal size */
- pm = XCreatePixmapFromBitmapData(x11->disp, x11->root, (char*)data, play_width, play_height,
- BLACK, LIGHTGREY, x11->depth);
+ pm = XCreatePixmapFromBitmapData(
+ x11->disp, x11->root, (char*)data, play_width, play_height, BLACK, LIGHTGREY, x11->depth);
vb->b[i].ID = ID;
vb->b[i].wd.Parent = SendTo;
- vb->b[i].wd.self = XCreateSimpleWindow(x11->disp, vb->wd.self, x, y0 + AIR, play_width,
- play_height, 0, WHITE, BLACK);
+ vb->b[i].wd.self = XCreateSimpleWindow(
+ x11->disp, vb->wd.self, x, y0 + AIR, play_width, play_height, 0, WHITE, BLACK);
XSetWindowBackgroundPixmap(x11->disp, vb->b[i].wd.self, pm);
x11->RegisterCallback(x11, vb->b[i].wd.self, vb->wd.self, ButtonCallBack, &(vb->b[i]));
InitWin(&(bbox->wd), 0, 0, /*width,(y0+AIR)*IDBUTNR+AIR+2*BORDER,*/ 1, 1, 1, "Button Box");
width -= 2 * AIR + 2 * BORDER;
- bbox->wd.self = XCreateSimpleWindow(x11->disp, Parent, bbox->wd.x, bbox->wd.y, bbox->wd.width,
- bbox->wd.height, bbox->wd.bwidth, fg, bg);
+ bbox->wd.self = XCreateSimpleWindow(
+ x11->disp, Parent, bbox->wd.x, bbox->wd.y, bbox->wd.width, bbox->wd.height, bbox->wd.bwidth, fg, bg);
x11->RegisterCallback(x11, bbox->wd.self, Parent, BBCallBack, bbox);
x11->SetInputMask(x11, bbox->wd.self, StructureNotifyMask);
h0 += y0 + AIR;
but->wd.Parent = SendTo;
but->ID = i;
- but->wd.self = XCreateSimpleWindow(x11->disp, DrawOn, but->wd.x, but->wd.y, but->wd.width,
- but->wd.height, but->wd.bwidth, bg, bg);
+ but->wd.self = XCreateSimpleWindow(
+ x11->disp, DrawOn, but->wd.x, but->wd.y, but->wd.width, but->wd.height, but->wd.bwidth, bg, bg);
x11->RegisterCallback(x11, but->wd.self, DrawOn, ButtonCallBack, but);
x11->SetInputMask(x11, but->wd.self, ExposureMask | ButtonPressMask | EnterLeave);
}
static t_dlg* about_mb(t_x11* x11, t_gmx* gmx)
{
- const char* lines[] = { " G R O M A C S", " Machine for Simulating Chemistry",
+ const char* lines[] = { " G R O M A C S",
+ " Machine for Simulating Chemistry",
" Copyright (c) 1992-2013",
" Berk Hess, David van der Spoel, Erik Lindahl",
" and many collaborators!" };
- return MessageBox(x11, gmx->wd->self, gmx->wd->text, asize(lines), lines,
- MB_OK | MB_ICONGMX | MBFLAGS, MBCallback, gmx);
+ return MessageBox(
+ x11, gmx->wd->self, gmx->wd->text, asize(lines), lines, MB_OK | MB_ICONGMX | MBFLAGS, MBCallback, gmx);
}
static void QuitCB(t_x11* x11, int dlg_mess, int /*item_id*/, char* set, void* data)
{
const char* lines[] = { " Do you really want to Quit ?" };
- return MessageBox(x11, gmx->wd->self, gmx->wd->text, asize(lines), lines,
- MB_YESNO | MB_ICONSTOP | MBFLAGS, QuitCB, gmx);
+ return MessageBox(
+ x11, gmx->wd->self, gmx->wd->text, asize(lines), lines, MB_YESNO | MB_ICONSTOP | MBFLAGS, QuitCB, gmx);
}
static t_dlg* help_mb(t_x11* x11, t_gmx* gmx)
{
const char* lines[] = { " Help will soon be added" };
- return MessageBox(x11, gmx->wd->self, gmx->wd->text, asize(lines), lines,
- MB_OK | MB_ICONINFORMATION | MBFLAGS, MBCallback, gmx);
+ return MessageBox(
+ x11, gmx->wd->self, gmx->wd->text, asize(lines), lines, MB_OK | MB_ICONINFORMATION | MBFLAGS, MBCallback, gmx);
}
static t_dlg* ni_mb(t_x11* x11, t_gmx* gmx)
{
const char* lines[] = { " This feature has not been", " implemented yet." };
- return MessageBox(x11, gmx->wd->self, gmx->wd->text, asize(lines), lines,
- MB_OK | MB_ICONEXCLAMATION | MBFLAGS, MBCallback, gmx);
+ return MessageBox(
+ x11, gmx->wd->self, gmx->wd->text, asize(lines), lines, MB_OK | MB_ICONEXCLAMATION | MBFLAGS, MBCallback, gmx);
}
enum
snew(gmx->dlgs, edNR);
for (int i = 0; (i < asize(di)); i++)
{
- gmx->dlgs[i] = ReadDlg(x11, gmx->wd->self, di[i].dlgfile, di[i].dlgfile, 0, 0, true, false,
- di[i].cb, gmx);
+ gmx->dlgs[i] = ReadDlg(
+ x11, gmx->wd->self, di[i].dlgfile, di[i].dlgfile, 0, 0, true, false, di[i].cb, gmx);
}
gmx->dlgs[edFilter] = select_filter(x11, gmx);
{
int i;
- std::printf(" type: %s, set: '%s', get: '%s', def: '%s', help: '%s'\n {", type[fitem->edlg],
- fitem->set, fitem->get, fitem->def, fitem->help);
+ std::printf(" type: %s, set: '%s', get: '%s', def: '%s', help: '%s'\n {",
+ type[fitem->edlg],
+ fitem->set,
+ fitem->get,
+ fitem->def,
+ fitem->help);
for (i = 0; (i < fitem->nname); i++)
{
std::printf(" '%s'", fitem->name[i]);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
if (!gmx->filter->bDisable[k])
{
- std::fprintf(tmp, "checkbox \"%s\" \"%d\" %s %s %s\n", gmx->filter->grpnames[k], k,
- dummy, dummy, dummy);
+ std::fprintf(
+ tmp, "checkbox \"%s\" \"%d\" %s %s %s\n", gmx->filter->grpnames[k], k, dummy, dummy, dummy);
}
else
{
- std::fprintf(tmp, "statictext { \" %s\" } \"%d\" %s %s %s\n",
- gmx->filter->grpnames[k], k, dummy, dummy, dummy);
+ std::fprintf(tmp,
+ "statictext { \" %s\" } \"%d\" %s %s %s\n",
+ gmx->filter->grpnames[k],
+ k,
+ dummy,
+ dummy,
+ dummy);
}
}
std::fprintf(tmp, "}\n\n");
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
XSetLineAttributes(x11->disp, x11->gc, 3, LineSolid, CapNotLast, JoinRound);
for (i = 0; (i < asize(lines)); i += 2)
{
- XDrawLine(x11->disp, wd->self, x11->gc, c[lines[i]].x, c[lines[i]].y,
- c[lines[i + 1]].x, c[lines[i + 1]].y);
+ XDrawLine(x11->disp,
+ wd->self,
+ x11->gc,
+ c[lines[i]].x,
+ c[lines[i]].y,
+ c[lines[i + 1]].x,
+ c[lines[i + 1]].y);
}
XSetLineAttributes(x11->disp, x11->gc, 1, LineSolid, CapNotLast, JoinRound);
for (i = 0; (i < asize(c)); i++)
XDrawRectangle(x11->disp, wd->self, x11->gc, 2, 2, wd->width - 5, wd->height - 5);
for (i = 0; (i < NMESS); i++)
{
- SpecialTextInRect(x11, Mess[i].fnt, wd->self, Mess[i].text, 0, Mess[i].y, wd->width,
- Mess[i].h, eXCenter, eYCenter);
+ SpecialTextInRect(
+ x11, Mess[i].fnt, wd->self, Mess[i].text, 0, Mess[i].y, wd->width, Mess[i].h, eXCenter, eYCenter);
}
XSetForeground(x11->disp, x11->gc, x11->fg);
break;
{
GetNamedColor(x11, newcol, &bg);
}
- logo->wd.self = XCreateSimpleWindow(x11->disp, parent, logo->wd.x, logo->wd.y, logo->wd.width,
- logo->wd.height, logo->wd.bwidth, WHITE, bg);
+ logo->wd.self = XCreateSimpleWindow(
+ x11->disp, parent, logo->wd.x, logo->wd.y, logo->wd.width, logo->wd.height, logo->wd.bwidth, WHITE, bg);
for (i = 0, logo->bigfont = nullptr; (i < NBF); i++)
{
if ((logo->bigfont = XLoadQueryFont(x11->disp, bfname[i])) != nullptr)
return;
}
XSetForeground(x11->disp, x11->gc, col);
- XDrawString(x11->disp, man->molw->wd.self, x11->gc, x + 2, y - 2, man->szLab[ai],
- std::strlen(man->szLab[ai]));
+ XDrawString(
+ x11->disp, man->molw->wd.self, x11->gc, x + 2, y - 2, man->szLab[ai], std::strlen(man->szLab[ai]));
XSetForeground(x11->disp, x11->gc, x11->fg);
}
}
gmx_fatal(FARGS,
"Topology %s (%d atoms) and trajectory %s (%d atoms) "
"do not match",
- status, man->top.atoms.nr, trajectory, man->natom);
+ status,
+ man->top.atoms.nr,
+ trajectory,
+ man->natom);
}
man->title.text =
man->bSort = true;
man->oenv = oenv;
InitWin(&(man->wd), x, y, width, height, 0, "Manager");
- man->wd.self = XCreateSimpleWindow(x11->disp, Parent, man->wd.x, man->wd.y, man->wd.width,
- man->wd.height, man->wd.bwidth, fg, bg);
+ man->wd.self = XCreateSimpleWindow(
+ x11->disp, Parent, man->wd.x, man->wd.y, man->wd.width, man->wd.height, man->wd.bwidth, fg, bg);
x11->RegisterCallback(x11, man->wd.self, Parent, ManCallBack, man);
x11->SetInputMask(x11, man->wd.self, StructureNotifyMask | ExposureMask | ButtonPressMask);
/* Title Window */
InitWin(&(man->title), 0, 0, 1, 1, 0, nullptr);
- man->title.self =
- XCreateSimpleWindow(x11->disp, man->molw->wd.self, man->title.x, man->title.y,
- man->title.width, man->title.height, man->title.bwidth, WHITE, BLUE);
+ man->title.self = XCreateSimpleWindow(x11->disp,
+ man->molw->wd.self,
+ man->title.x,
+ man->title.y,
+ man->title.width,
+ man->title.height,
+ man->title.bwidth,
+ WHITE,
+ BLUE);
x11->RegisterCallback(x11, man->title.self, man->molw->wd.self, TitleCallBack, &(man->title));
x11->SetInputMask(x11, man->title.self, ExposureMask | StructureNotifyMask);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
ps_color(ps, 0, 0, 0.5);
for (i = 0; (i < 12); i++)
{
- ps_line(ps, vec2[bonds[i][0]][XX], vec2[bonds[i][0]][YY], vec2[bonds[i][1]][XX],
- vec2[bonds[i][1]][YY]);
+ ps_line(ps, vec2[bonds[i][0]][XX], vec2[bonds[i][0]][YY], vec2[bonds[i][1]][XX], vec2[bonds[i][1]][YY]);
}
}
}
/* Draw the objects */
- draw_objects(x11->disp, win->self, x11->gc, nvis, man->obj, man->ix, man->x, man->col,
- man->size, mw->bShowHydrogen, mw->bond_type, man->bPlus);
+ draw_objects(x11->disp,
+ win->self,
+ x11->gc,
+ nvis,
+ man->obj,
+ man->ix,
+ man->x,
+ man->col,
+ man->size,
+ mw->bShowHydrogen,
+ mw->bond_type,
+ man->bPlus);
/* Draw the labels */
XSetForeground(x11->disp, x11->gc, WHITE);
{
if (man->bLabel[i] && man->bVis[i])
{
- XDrawString(x11->disp, win->self, x11->gc, vec2[i][XX] + 2, vec2[i][YY] - 2,
- man->szLab[i], std::strlen(man->szLab[i]));
+ XDrawString(x11->disp,
+ win->self,
+ x11->gc,
+ vec2[i][XX] + 2,
+ vec2[i][YY] - 2,
+ man->szLab[i],
+ std::strlen(man->szLab[i]));
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* Nothing to be done */
if (m->bGrabbed)
{
- m->bGrabbed = GrabOK(stderr, XGrabPointer(x11->disp, m->wd.self, True, ButtonReleaseMask,
- GrabModeAsync, GrabModeAsync, m->wd.self,
- None, CurrentTime));
+ m->bGrabbed = GrabOK(stderr,
+ XGrabPointer(x11->disp,
+ m->wd.self,
+ True,
+ ButtonReleaseMask,
+ GrabModeAsync,
+ GrabModeAsync,
+ m->wd.self,
+ None,
+ CurrentTime));
}
break;
case ButtonRelease: hide_menu(x11, m); break;
}
InitWin(&(m->wd), 10, 10, fcol * mlen, frows * mht, 1, "Menu");
snew(m->item, nent);
- m->wd.self = XCreateSimpleWindow(x11->disp, Parent, m->wd.x, m->wd.y, m->wd.width, m->wd.height,
- m->wd.bwidth, fg, bg);
+ m->wd.self = XCreateSimpleWindow(
+ x11->disp, Parent, m->wd.x, m->wd.y, m->wd.width, m->wd.height, m->wd.bwidth, fg, bg);
x11->RegisterCallback(x11, m->wd.self, Parent, MenuCallBack, m);
x11->SetInputMask(x11, m->wd.self, ExposureMask | OwnerGrabButtonMask | ButtonReleaseMask);
kid->Parent = Parent;
w = &(kid->wd);
InitWin(w, j * mlen, k * mht, mlen - 2, mht - 2, 1, nullptr);
- w->self = XCreateSimpleWindow(x11->disp, m->wd.self, w->x, w->y, w->width, w->height,
- w->bwidth, bg, bg);
+ w->self = XCreateSimpleWindow(
+ x11->disp, m->wd.self, w->x, w->y, w->width, w->height, w->bwidth, bg, bg);
x11->RegisterCallback(x11, w->self, m->wd.self, ChildCallBack, kid);
- x11->SetInputMask(x11, w->self,
+ x11->SetInputMask(x11,
+ w->self,
ButtonPressMask | ButtonReleaseMask | OwnerGrabButtonMask
| ExposureMask | EnterWindowMask | LeaveWindowMask);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
XDrawLine(x11->disp, w, x11->gc, 0, y - 1, pd->wd.width, y - 1);
for (i = 0; (i < pd->nmenu); i++)
{
- XDrawString(x11->disp, pd->wd.self, x11->gc, pd->xpos[i], x11->font->ascent,
- pd->title[i], std::strlen(pd->title[i]));
+ XDrawString(x11->disp,
+ pd->wd.self,
+ x11->gc,
+ pd->xpos[i],
+ x11->font->ascent,
+ pd->title[i],
+ std::strlen(pd->title[i]));
}
break;
case ButtonPress:
}
InitWin(&(pd->wd), 0, 0, width, XTextHeight(x11->font) + 2, 0, "PullDown");
- pd->wd.self = XCreateSimpleWindow(x11->disp, Parent, pd->wd.x, pd->wd.y, pd->wd.width,
- pd->wd.height, pd->wd.bwidth, fg, bg);
+ pd->wd.self = XCreateSimpleWindow(
+ x11->disp, Parent, pd->wd.x, pd->wd.y, pd->wd.width, pd->wd.height, pd->wd.bwidth, fg, bg);
x11->RegisterCallback(x11, pd->wd.self, Parent, PDCallBack, pd);
- x11->SetInputMask(x11, pd->wd.self,
- ExposureMask | ButtonPressMask | OwnerGrabButtonMask | ButtonReleaseMask);
+ x11->SetInputMask(
+ x11, pd->wd.self, ExposureMask | ButtonPressMask | OwnerGrabButtonMask | ButtonReleaseMask);
XMapWindow(x11->disp, pd->wd.self);
for (i = 0; (i < nmenu); i++)
case IDIMPORT:
case IDEXPORT: ShowDlg(gmx->dlgs[edExport]); break;
case IDDOEXPORT:
- write_sto_conf(gmx->confout, *gmx->man->top.name, &(gmx->man->top.atoms), gmx->man->x,
- nullptr, gmx->man->molw->pbcType, gmx->man->box);
+ write_sto_conf(gmx->confout,
+ *gmx->man->top.name,
+ &(gmx->man->top.atoms),
+ gmx->man->x,
+ nullptr,
+ gmx->man->molw->pbcType,
+ gmx->man->box);
break;
case IDQUIT: show_mb(gmx, emQuit); break;
case IDTERM: done_gmx(x11, gmx); return true;
w0 = DisplayWidth(x11->disp, x11->screen) - 132;
h0 = DisplayHeight(x11->disp, x11->screen) - 140;
InitWin(gmx->wd, 0, 0, w0, h0, 3, gmx::bromacs().c_str());
- gmx->wd->self = XCreateSimpleWindow(x11->disp, x11->root, gmx->wd->x, gmx->wd->y, gmx->wd->width,
- gmx->wd->height, gmx->wd->bwidth, WHITE, BLACK);
- pm = XCreatePixmapFromBitmapData(x11->disp, x11->root, (char*)gromacs_bits, gromacs_width,
- gromacs_height, WHITE, BLACK, 1);
+ gmx->wd->self = XCreateSimpleWindow(
+ x11->disp, x11->root, gmx->wd->x, gmx->wd->y, gmx->wd->width, gmx->wd->height, gmx->wd->bwidth, WHITE, BLACK);
+ pm = XCreatePixmapFromBitmapData(
+ x11->disp, x11->root, (char*)gromacs_bits, gromacs_width, gromacs_height, WHITE, BLACK, 1);
hints.flags = PMinSize;
hints.min_width = 2 * EWIDTH + 40;
hints.min_height = EHEIGHT + LDHEIGHT + LEGHEIGHT + 40;
XSetStandardProperties(x11->disp, gmx->wd->self, gmx->wd->text, program, pm, nullptr, 0, &hints);
x11->RegisterCallback(x11, gmx->wd->self, x11->root, MainCallBack, gmx);
- x11->SetInputMask(x11, gmx->wd->self,
+ x11->SetInputMask(x11,
+ gmx->wd->self,
ButtonPressMask | ButtonReleaseMask | OwnerGrabButtonMask | ExposureMask
| StructureNotifyMask);
map_man(x11, gmx->man);
/* Pull Down menu */
- gmx->pd = init_pd(x11, gmx->wd->self, gmx->wd->width, x11->fg, x11->bg, MSIZE, gmx_pd_size,
- gmx_pd, MenuTitle);
+ gmx->pd = init_pd(
+ x11, gmx->wd->self, gmx->wd->width, x11->fg, x11->bg, MSIZE, gmx_pd_size, gmx_pd, MenuTitle);
/* Dialogs & Filters */
{ efNDX, nullptr, nullptr, ffOPTRD } };
#define NFILE asize(fnm)
- if (parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm, 0, nullptr, asize(desc), desc,
- asize(bugs), bugs, &oenv))
+ if (parse_common_args(
+ &argc, argv, PCA_CAN_TIME, NFILE, fnm, 0, nullptr, asize(desc), desc, asize(bugs), bugs, &oenv))
{
#if !GMX_X11
std::fprintf(stderr, "Compiled without X-Windows - can not run viewer.\n");
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
else
{
/* We have real color! */
- std::fprintf(x11->console, "%s screen with depth %d.\n",
- (i == NCLASS) ? "Unknown" : v_name[i], x11->depth);
+ std::fprintf(x11->console,
+ "%s screen with depth %d.\n",
+ (i == NCLASS) ? "Unknown" : v_name[i],
+ x11->depth);
GetNamedColor(x11, "midnight blue", &BLUE);
GetNamedColor(x11, "DarkGreen", &GREEN);
GetNamedColor(x11, "SeaGreen", &CYAN);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
dlgitem->win.height = h;
}
#ifdef DEBUG
- std::fprintf(dlg->x11->console, "Size window from: %dx%d to %dx%d\n", old_w, old_h,
- dlgitem->win.width, dlgitem->win.height);
+ std::fprintf(dlg->x11->console,
+ "Size window from: %dx%d to %dx%d\n",
+ old_w,
+ old_h,
+ dlgitem->win.width,
+ dlgitem->win.height);
dlg->x11->Flush(dlg->x11);
#endif
if (dlgitem->win.self)
void NoHelp(t_dlg* dlg)
{
const char* lines[2] = { "Error", "No help for this item" };
- MessageBox(dlg->x11, dlg->wDad, "No Help", 2, lines, MB_OK | MB_ICONSTOP | MB_APPLMODAL,
- nullptr, nullptr);
+ MessageBox(dlg->x11, dlg->wDad, "No Help", 2, lines, MB_OK | MB_ICONSTOP | MB_APPLMODAL, nullptr, nullptr);
}
void HelpDlg(t_dlg* dlg)
{
const char* lines[] = { "Place the cursor over one of the items",
- "and press the F1 key to get more help.", "First press the OK button." };
- MessageBox(dlg->x11, dlg->win.self, "Help Dialogbox", 3, lines,
- MB_OK | MB_ICONINFORMATION | MB_APPLMODAL, nullptr, nullptr);
+ "and press the F1 key to get more help.",
+ "First press the OK button." };
+ MessageBox(dlg->x11, dlg->win.self, "Help Dialogbox", 3, lines, MB_OK | MB_ICONINFORMATION | MB_APPLMODAL, nullptr, nullptr);
}
void HelpNow(t_dlg* dlg, t_dlgitem* dlgitem)
}
}
} while (bCont);
- MessageBox(dlg->x11, dlg->wDad, "Help", nlines, lines,
- MB_OK | MB_ICONINFORMATION | MB_APPLMODAL, nullptr, nullptr);
+ MessageBox(dlg->x11, dlg->wDad, "Help", nlines, lines, MB_OK | MB_ICONINFORMATION | MB_APPLMODAL, nullptr, nullptr);
for (i = 0; (i < nlines); i++)
{
sfree(lines[i]);
{
if (dlg->flags & DLG_APPLMODAL)
{
- dlg->bGrab = GrabOK(dlg->x11->console,
- XGrabPointer(dlg->x11->disp, dlg->win.self, True, 0, GrabModeAsync,
- GrabModeAsync, dlg->win.self, None, CurrentTime));
+ dlg->bGrab = GrabOK(
+ dlg->x11->console,
+ XGrabPointer(
+ dlg->x11->disp, dlg->win.self, True, 0, GrabModeAsync, GrabModeAsync, dlg->win.self, None, CurrentTime));
}
dlg->x11->Flush(dlg->x11);
}
{
if ((dlg->dlgitem[i]->type == edlgBN) && (dlg->dlgitem[i]->u.button.bDefault))
{
- PushMouse(x11->disp, dlg->dlgitem[i]->win.self,
- dlg->dlgitem[i]->win.width / 2, dlg->dlgitem[i]->win.height / 2);
+ PushMouse(x11->disp,
+ dlg->dlgitem[i]->win.self,
+ dlg->dlgitem[i]->win.width / 2,
+ dlg->dlgitem[i]->win.height / 2);
break;
}
}
attr.save_under = True;
attr.cursor = XCreateFontCursor(dlg->x11->disp, XC_hand2);
Val = CWBackPixel | CWBorderPixel | CWOverrideRedirect | CWSaveUnder | CWCursor;
- dlg->win.self = XCreateWindow(dlg->x11->disp, dlg->wDad, dlg->win.x, dlg->win.y, dlg->win.width,
- dlg->win.height, dlg->win.bwidth, CopyFromParent, InputOutput,
- CopyFromParent, Val, &attr);
+ dlg->win.self = XCreateWindow(dlg->x11->disp,
+ dlg->wDad,
+ dlg->win.x,
+ dlg->win.y,
+ dlg->win.width,
+ dlg->win.height,
+ dlg->win.bwidth,
+ CopyFromParent,
+ InputOutput,
+ CopyFromParent,
+ Val,
+ &attr);
dlg->x11->RegisterCallback(dlg->x11, dlg->win.self, dlg->wDad, DlgCB, dlg);
dlg->x11->SetInputMask(dlg->x11, dlg->win.self, ExposureMask | ButtonPressMask | KeyPressMask);
{
gmx_fatal(FARGS, "dlgitem not allocated");
}
- item->win.self = XCreateSimpleWindow(dlg->x11->disp, dlg->win.self, item->win.x, item->win.y,
- item->win.width, item->win.height, item->win.bwidth,
- dlg->x11->fg, dlg->x11->bg);
+ item->win.self = XCreateSimpleWindow(dlg->x11->disp,
+ dlg->win.self,
+ item->win.x,
+ item->win.y,
+ item->win.width,
+ item->win.height,
+ item->win.bwidth,
+ dlg->x11->fg,
+ dlg->x11->bg);
CheckWindow(item->win.self);
dlg->x11->RegisterCallback(dlg->x11, item->win.self, dlg->win.self, DlgCB, dlg);
dlg->win.height = h;
#ifdef DEBUG
- std::fprintf(dlg->x11->console, "SetDlgSize: Dialog is %dx%d, at %d,%d\n", dlg->win.width,
- dlg->win.height, dlg->win.x, dlg->win.y);
+ std::fprintf(dlg->x11->console,
+ "SetDlgSize: Dialog is %dx%d, at %d,%d\n",
+ dlg->win.width,
+ dlg->win.height,
+ dlg->win.x,
+ dlg->win.y);
dlg->x11->Flush(dlg->x11);
#endif
if (dlg->win.self)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
switch (fitem->edlg)
{
case edlgBN:
- AddListItem(list, CreateButton(x11, fitem->name[0], fitem->bDef, (*ID)++, GroupID, x,
- (*y), 0, 0, 0));
+ AddListItem(list,
+ CreateButton(x11, fitem->name[0], fitem->bDef, (*ID)++, GroupID, x, (*y), 0, 0, 0));
break;
case edlgRB:
std::strcpy(buf, fitem->def);
for (i = 0; (i < fitem->nname); i++)
{
- AddListItem(list, CreateRadioButton(x11, fitem->name[i], (iSel == i), (*ID)++,
- GroupID, x, (*y), 0, 0, 0));
+ AddListItem(list,
+ CreateRadioButton(
+ x11, fitem->name[i], (iSel == i), (*ID)++, GroupID, x, (*y), 0, 0, 0));
(*y) += list->list[list->nitem - 1]->win.height + OFFS_Y;
(*w) = std::max((*w), list->list[list->nitem - 1]->win.width);
SetDlgitemOpts(list->list[list->nitem - 1], bUseMon, fitem->set, fitem->get, fitem->help);
bool bCheck;
bCheck = gmx_strcasecmp(fitem->def, "TRUE") == 0;
- AddListItem(list, CreateCheckBox(x11, fitem->name[0], bCheck, (*ID)++, GroupID, x, (*y),
- 0, 0, 0));
+ AddListItem(list,
+ CreateCheckBox(x11, fitem->name[0], bCheck, (*ID)++, GroupID, x, (*y), 0, 0, 0));
break;
}
case edlgST:
- AddListItem(list, CreateStaticText(x11, fitem->nname, fitem->name, (*ID)++, GroupID, x,
- (*y), 0, 0, 0));
+ AddListItem(list,
+ CreateStaticText(
+ x11, fitem->nname, fitem->name, (*ID)++, GroupID, x, (*y), 0, 0, 0));
break;
case edlgET:
slen = std::strlen(fitem->name[0]) + strlen(fitem->def);
- AddListItem(list, CreateEditText(x11, fitem->name[0], slen, fitem->def, (*ID)++,
- GroupID, x, (*y), 0, 0, 0));
+ AddListItem(list,
+ CreateEditText(
+ x11, fitem->name[0], slen, fitem->def, (*ID)++, GroupID, x, (*y), 0, 0, 0));
break;
case edlgPM:
case edlgGB:
{
ids[i] = GroupID + i + 1;
}
- item->list[0] = CreateGroupBox(x11, fgroup->name, GroupID, item->nitem - 1, ids, 2 * OFFS_X,
- 2 * OFFS_Y, w + 2 * OFFS_X, y, 0);
+ item->list[0] = CreateGroupBox(
+ x11, fgroup->name, GroupID, item->nitem - 1, ids, 2 * OFFS_X, 2 * OFFS_Y, w + 2 * OFFS_X, y, 0);
sfree(ids);
item->w = fgroup->w;
item->h = fgroup->h;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
case Expose:
XSetForeground(x11->disp, x11->gc, x11->fg);
- XDrawRoundRect(x11->disp, win->self, x11->gc, 0, y / 2, win->width - 1,
- win->height - y / 2 - 1);
+ XDrawRoundRect(
+ x11->disp, win->self, x11->gc, 0, y / 2, win->width - 1, win->height - y / 2 - 1);
XClearArea(x11->disp, win->self, OFFS_X, 0, x + OFFS_X, y, False);
TextInRect(x11, win->self, win->text, 2 * OFFS_X, 0, x, y, eXCenter, eYCenter);
break;
dy = XTextHeight(x11->font) + OFFS_Y;
for (i = 0; (i < st->nlines); i++)
{
- TextInRect(x11, win->self, st->lines[i], 0, OFFS_Y + i * dy, win->width, dy, eXLeft,
- eYCenter);
+ TextInRect(x11, win->self, st->lines[i], 0, OFFS_Y + i * dy, win->width, dy, eXLeft, eYCenter);
}
break;
default: return DefWndProc(x11, dlgitem, event);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
if (nicon > 0)
{
AddDlgItem(dlg,
- CreatePixmap(XCreatePixmapFromBitmapData(x11->disp, dlg->win.self, icon_bits, icon_width,
- icon_height, icon_fg, icon_bg, x11->depth),
- ID_ICON, ID_BOX, 2 * OFFS_X, 2 * OFFS_Y, icon_width, icon_height, 0));
+ CreatePixmap(
+ XCreatePixmapFromBitmapData(
+ x11->disp, dlg->win.self, icon_bits, icon_width, icon_height, icon_fg, icon_bg, x11->depth),
+ ID_ICON,
+ ID_BOX,
+ 2 * OFFS_X,
+ 2 * OFFS_Y,
+ icon_width,
+ icon_height,
+ 0));
x += QueryDlgItemW(dlg, ID_ICON) + 2 * OFFS_X;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
XSetLineAttributes(disp, gc, 1, LineOnOffDash, CapButt, JoinRound);
XSetForeground(disp, gc, color);
- XDrawRoundRect(disp, win->self, gc, offsx, offsy, win->width - 2 * offsx - 1,
- win->height - 2 * offsy - 1);
+ XDrawRoundRect(
+ disp, win->self, gc, offsx, offsy, win->width - 2 * offsx - 1, win->height - 2 * offsy - 1);
XSetLineAttributes(disp, gc, 1, LineSolid, CapButt, JoinRound);
}
--- /dev/null
+# List of rationales for check suppressions (where known).
+# This have to precede the list because inline comments are not
+# supported by clang-tidy.
+#
+# -cppcoreguidelines-non-private-member-variables-in-classes,
+# -misc-non-private-member-variables-in-classes,
+# We intend a gradual transition to conform to this guideline, but it
+# is not practical to implement yet.
+#
+# -readability-isolate-declaration,
+# Declarations like "int a, b;" are readable. Some forms are not, and
+# those might reasonably be suggested against during code review.
+#
+# -cppcoreguidelines-avoid-c-arrays,
+# C arrays are still necessary in many places with legacy code
+#
+# -cppcoreguidelines-avoid-magic-numbers,
+# -readability-magic-numbers,
+# We have many legitimate use cases for magic numbers
+#
+# -cppcoreguidelines-macro-usage,
+# We do use too many macros, and we should fix many of them, but there
+# is no reasonable way to suppress the check e.g. in src/config.h and
+# configuring the build is a major legitimate use of macros.
+#
+# -cppcoreguidelines-narrowing-conversions,
+# -bugprone-narrowing-conversions
+# We have many cases where int is converted to float and we don't care
+# enough about such potential loss of precision to use explicit casts
+# in large numbers of places.
+#
+# -google-readability-avoid-underscore-in-googletest-name
+# We need to use underscores for readability for our legacy types
+# and command-line parameter names
+#
+# -misc-no-recursion
+# We have way too many functions and methods relying on recursion
+#
+# -cppcoreguidelines-avoid-non-const-global-variables
+# There are quite a lot of static variables in the test code that
+# can not be replaced.
+#
+# -modernize-avoid-bind
+# Some code needs to use std::bind and can't be modernized quickly.
+Checks: clang-diagnostic-*,-clang-analyzer-*,-clang-analyzer-security.insecureAPI.strcpy,
+ bugprone-*,misc-*,readability-*,performance-*,mpi-*,
+ -readability-inconsistent-declaration-parameter-name,
+ -readability-function-size,-readability-else-after-return,
+ modernize-use-nullptr,modernize-use-emplace,
+ modernize-make-unique,modernize-make-shared,
+ modernize-avoid-bind,
+ modernize-use-override,
+ modernize-redundant-void-arg,modernize-use-bool-literals,
+ cppcoreguidelines-*,-cppcoreguidelines-pro-*,-cppcoreguidelines-owning-memory,
+ -cppcoreguidelines-no-malloc,-cppcoreguidelines-special-member-functions,
+ -cppcoreguidelines-avoid-goto,
+ google-*,-google-build-using-namespace,-google-explicit-constructor,
+ -google-readability-function-size,-google-readability-todo,-google-runtime-int,
+ -cppcoreguidelines-non-private-member-variables-in-classes,
+ -misc-non-private-member-variables-in-classes,
+ -readability-isolate-declaration,
+ -cppcoreguidelines-avoid-c-arrays,
+ -cppcoreguidelines-avoid-magic-numbers,
+ -readability-magic-numbers,
+ -cppcoreguidelines-macro-usage,
+ -cppcoreguidelines-narrowing-conversions,
+ -bugprone-narrowing-conversions,
+ -google-readability-avoid-underscore-in-googletest-name,
+ -cppcoreguidelines-init-variables,
+ -misc-no-recursion,
+ -cppcoreguidelines-avoid-non-const-global-variables,
+ -modernize-avoid-bind
+HeaderFilterRegex: .*
+CheckOptions:
+ - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+ value: 1
+ - key: modernize-make-unique.IncludeStyle
+ value: google
+ - key: modernize-make-shared.IncludeStyle
+ value: google
+ - key: readability-implicit-bool-conversion.AllowIntegerConditions
+ value: 1
+ - key: readability-implicit-bool-conversion.AllowPointerConditions
+ value: 1
+ - key: bugprone-dangling-handle.HandleClasses
+ value: std::basic_string_view; nonstd::sv_lite::basic_string_view
+# Permit passing shard pointers by value for sink parameters
+ - key: performance-unnecessary-copy-initialization.AllowedTypes
+ value: shared_ptr
+ - key: performance-unnecessary-value-param.AllowedTypes
+ value: shared_ptr
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2011,2012,2013,2014,2015 by the GROMACS development team.
-# Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2016,2017,2018,2019,2020 by the GROMACS development team.
+# Copyright (c) 2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
return()
endif()
-set(TESTUTILS_SOURCES
- cmdlinetest.cpp
- conftest.cpp
- filematchers.cpp
- interactivetest.cpp
- loggertest.cpp
- mpi_printer.cpp
- mpitest.cpp
- refdata.cpp
- refdata_xml.cpp
- simulationdatabase.cpp
- stdiohelper.cpp
- stringtest.cpp
- testasserts.cpp
- testfilemanager.cpp
- testfileredirector.cpp
- test_device.cpp
- test_hardware_environment.cpp
- testinit.cpp
- testmatchers.cpp
- testoptions.cpp
- textblockmatchers.cpp
- tprfilegenerator.cpp
- xvgtest.cpp
- )
-
-if(NOT HAVE_TINYXML2)
- list(APPEND TESTUTILS_SOURCES ../external/tinyxml2/tinyxml2.cpp)
-endif()
-
if (GMX_GPU_CUDA)
# Work around FindCUDA that prevents using target_link_libraries()
# with keywords otherwise...
set(CUDA_LIBRARIES PRIVATE ${CUDA_LIBRARIES})
if (NOT GMX_CLANG_CUDA)
- gmx_cuda_add_library(testutils ${TESTUTILS_SOURCES})
+ gmx_cuda_add_library(testutils)
else()
set_source_files_properties(test_device.cpp PROPERTIES CUDA_SOURCE_PROPERTY_FORMAT OBJ)
gmx_compile_cuda_file_with_clang(test_device.cpp)
endif()
target_link_libraries(testutils PRIVATE ${CUDA_CUFFT_LIBRARIES})
else()
- add_library(testutils STATIC ${UNITTEST_TARGET_OPTIONS} ${TESTUTILS_SOURCES})
+ add_library(testutils STATIC ${UNITTEST_TARGET_OPTIONS})
+endif()
+
+# Module interface / provided facilities
+target_include_directories(testutils PUBLIC include)
+
+# Executable targets for tests based on `testutils` acquire the source for
+# their entry point from unittest_main.cpp when linking to the `testutils` target.
+target_sources(testutils INTERFACE unittest_main.cpp)
+
+
+target_sources(testutils PRIVATE
+ cmdlinetest.cpp
+ conftest.cpp
+ filematchers.cpp
+ interactivetest.cpp
+ loggertest.cpp
+ mpi_printer.cpp
+ mpitest.cpp
+ refdata.cpp
+ refdata_xml.cpp
+ simulationdatabase.cpp
+ stdiohelper.cpp
+ stringtest.cpp
+ testasserts.cpp
+ testfilemanager.cpp
+ testfileredirector.cpp
+ test_device.cpp
+ test_hardware_environment.cpp
+ testinit.cpp
+ testmatchers.cpp
+ testoptions.cpp
+ textblockmatchers.cpp
+ tprfilegenerator.cpp
+ xvgtest.cpp
+ )
+
+
+if(HAVE_TINYXML2)
+ target_include_directories(testutils SYSTEM PRIVATE ${TinyXML2_INCLUDE_DIR})
+ target_link_libraries(testutils PRIVATE ${TinyXML2_LIBRARIES})
+else()
+ target_include_directories(testutils SYSTEM BEFORE PRIVATE ${CMAKE_SOURCE_DIR}/src/external/tinyxml2)
+ target_sources(testutils PRIVATE ${CMAKE_SOURCE_DIR}/src/external/tinyxml2/tinyxml2.cpp)
endif()
+target_include_directories(testutils PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
+
if (GMX_GPU_SYCL)
- set_source_files_properties(test_device.cpp
- PROPERTIES COMPILE_FLAGS "${SYCL_CXX_FLAGS}")
+ add_sycl_to_target(
+ TARGET testutils
+ SOURCES test_device.cpp
+ )
endif()
gmx_target_compile_options(testutils)
target_compile_definitions(testutils PRIVATE HAVE_CONFIG_H)
target_include_directories(testutils SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
target_link_libraries(testutils PRIVATE libgromacs ${GMX_COMMON_LIBRARIES} gmock)
+target_link_libraries(testutils PUBLIC common)
-if(HAVE_TINYXML2)
- include_directories(SYSTEM ${TinyXML2_INCLUDE_DIR})
- target_link_libraries(testutils PRIVATE ${TinyXML2_LIBRARIES})
-else()
- include_directories(BEFORE SYSTEM "../external/tinyxml2")
-endif()
+# GROMACS module dependencies.
+# Note that testutils conveys transitive dependencies on some modules.
+# TODO: Explicitly link specific modules with minimal exposure.
+target_link_libraries(testutils PUBLIC legacy_modules)
# TODO Use gmx_add_missing_tests_notice() instead of the messages below.
set(GMX_CAN_RUN_MPI_TESTS 1)
set(GMX_CAN_RUN_MPI_TESTS 0)
endif()
-set(TESTUTILS_DIR ${CMAKE_CURRENT_SOURCE_DIR})
-set(TESTUTILS_DIR ${TESTUTILS_DIR} PARENT_SCOPE)
set(GMX_CAN_RUN_MPI_TESTS ${GMX_CAN_RUN_MPI_TESTS} PARENT_SCOPE)
add_subdirectory(tests)
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2011,2012,2013,2014,2015 by the GROMACS development team.
-# Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2016,2017,2018,2019,2020 by the GROMACS development team.
+# Copyright (c) 2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
cuda_add_executable(${EXENAME} ${UNITTEST_TARGET_OPTIONS}
${ARG_CPP_SOURCE_FILES}
${ARG_CUDA_CU_SOURCE_FILES}
- ${ARG_GPU_CPP_SOURCE_FILES}
- ${TESTUTILS_DIR}/unittest_main.cpp)
+ ${ARG_GPU_CPP_SOURCE_FILES})
else()
add_executable(${EXENAME} ${UNITTEST_TARGET_OPTIONS}
- ${ARG_CPP_SOURCE_FILES}
- ${TESTUTILS_DIR}/unittest_main.cpp)
+ ${ARG_CPP_SOURCE_FILES})
endif()
if (GMX_GPU_CUDA)
endif()
elseif (GMX_GPU_SYCL)
target_sources(${EXENAME} PRIVATE ${ARG_SYCL_CPP_SOURCE_FILES} ${ARG_GPU_CPP_SOURCE_FILES})
- set_source_files_properties(${ARG_GPU_CPP_SOURCE_FILES} PROPERTIES COMPILE_FLAGS "${SYCL_CXX_FLAGS}")
- set_source_files_properties(${ARG_SYCL_CPP_SOURCE_FILES} PROPERTIES COMPILE_FLAGS "${SYCL_CXX_FLAGS}")
if(ARG_SYCL_CPP_SOURCE_FILES OR ARG_GPU_CPP_SOURCE_FILES)
- target_link_libraries(${EXENAME} PRIVATE ${SYCL_CXX_FLAGS})
+ add_sycl_to_target(
+ TARGET ${EXENAME}
+ SOURCES ${ARG_SYCL_CPP_SOURCE_FILES} ${ARG_GPU_CPP_SOURCE_FILES}
+ )
endif()
else()
target_sources(${EXENAME} PRIVATE ${ARG_NON_GPU_CPP_SOURCE_FILES} ${ARG_GPU_CPP_SOURCE_FILES})
endif()
target_link_libraries(${EXENAME} PRIVATE
- testutils libgromacs gmock
+ testutils common libgromacs gmock
${GMX_COMMON_LIBRARIES} ${GMX_EXE_LINKER_FLAGS})
if(GMX_CLANG_TIDY)
# Both OpenCL (from JIT) and ThreadSanitizer (from how it
# checks) can take signficantly more time than other
# configurations.
- if (GMX_GPU_OPENCL)
+ if (GMX_GPU_OPENCL OR GMX_GPU_SYCL)
set(_timeout 240)
elseif (${CMAKE_BUILD_TYPE} STREQUAL TSAN)
set(_timeout 300)
*/
#include "gmxpre.h"
-#include "cmdlinetest.h"
+#include "testutils/cmdlinetest.h"
#include <cstdlib>
#include <cstring>
std::vector<const char*> convertFromStringArrayRef(const ArrayRef<const std::string>& cmdline)
{
std::vector<const char*> v(cmdline.size());
- std::transform(cmdline.begin(), cmdline.end(), v.begin(),
- [](const std::string& s) { return s.c_str(); });
+ std::transform(
+ cmdline.begin(), cmdline.end(), v.begin(), [](const std::string& s) { return s.c_str(); });
return v;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019,2021, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "conftest.h"
+#include "testutils/conftest.h"
#include <cstdio>
#include <cstdlib>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "filematchers.h"
+#include "testutils/filematchers.h"
#include "gromacs/utility/filestream.h"
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
// arrayref.h is not strictly necessary for this header, but nearly all
// callers will need it to use the constructor that takes ArrayRef.
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/classhelpers.h"
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
/*! \libinternal \brief
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
/*! \libinternal \brief
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace test
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019,2021, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TESTUTILS_INTERACTIVETEST_H
#define GMX_TESTUTILS_INTERACTIVETEST_H
+#include <memory>
+
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/classhelpers.h"
namespace gmx
{
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace test
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TESTUTILS_LOGGERTEST_H
#define GMX_TESTUTILS_LOGGERTEST_H
-#include "gromacs/utility/classhelpers.h"
+#include <memory>
+
#include "gromacs/utility/logger.h"
namespace gmx
*/
void expectEntryMatchingRegex(gmx::MDLogger::LogLevel level, const char* re);
+ /*! \brief
+ * Expects that no log entries were made at a given level.
+ *
+ * If not called for a log level, all entries for that level are
+ * accepted.
+ */
+ void expectNoEntries(gmx::MDLogger::LogLevel level);
+
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace test
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \ingroup module_testutils
*/
#if GMX_THREAD_MPI
-# define GMX_MPI_TEST(expectedRankCount) \
- do \
- { \
- ASSERT_EQ(expectedRankCount, ::gmx::test::getNumberOfTestMpiRanks()); \
- using MyTestClass = std::remove_reference_t<decltype(*this)>; \
- if (!::gmx::test::threadMpiTestRunner(std::bind(&MyTestClass::TestBody, this))) \
- { \
- return; \
- } \
+# define GMX_MPI_TEST(expectedRankCount) \
+ do \
+ { \
+ ASSERT_EQ(expectedRankCount, ::gmx::test::getNumberOfTestMpiRanks()); \
+ using MyTestClass = std::remove_reference_t<decltype(*this)>; \
+ if (!::gmx::test::threadMpiTestRunner([this]() { this->MyTestClass::TestBody(); })) \
+ { \
+ return; \
+ } \
} while (0)
#else
# define GMX_MPI_TEST(expectedRankCount) \
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2011-2018, The GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
explicit TestReferenceChecker(Impl* impl);
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
/*! \brief
* Needed to expose the constructor only to TestReferenceData.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \inlibraryapi
* \ingroup module_testutils
*/
-#ifndef GMX_TESTUTILS__SIMULATIONDATABASE_H
-#define GMX_TESTUTILS__SIMULATIONDATABASE_H
+#ifndef GMX_TESTUTILS_SIMULATIONDATABASE_H
+#define GMX_TESTUTILS_SIMULATIONDATABASE_H
#include <map>
#include <string>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TESTUTILS_STDIOHELPER_H
#define GMX_TESTUTILS_STDIOHELPER_H
+#include <memory>
+
#include "gromacs/utility/classhelpers.h"
namespace gmx
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TESTUTILS_STRINGTEST_H
#define GMX_TESTUTILS_STRINGTEST_H
+#include <memory>
#include <string>
#include <gtest/gtest.h>
-#include "gromacs/utility/classhelpers.h"
-
namespace gmx
{
* \param[in] refFilename File with the expected contents.
* \param[in] testFilename File with the contents to be tested.
*/
- void testFilesEqual(const std::string& refFilename, const std::string& testFilename);
+ static void testFilesEqual(const std::string& refFilename, const std::string& testFilename);
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace test
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include <map>
+#include <memory>
#include <string>
#include <vector>
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/gmxassert.h"
class DeviceContext;
//! Implementation type.
class Impl;
//! Implementation object.
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace test
uint64_t doubleUlpDiff)
{
return FloatingPointTolerance(float(magnitude) * singleUlpDiff * GMX_FLOAT_EPS,
- magnitude * doubleUlpDiff * GMX_DOUBLE_EPS, 0.0, 0.0,
- singleUlpDiff, doubleUlpDiff, false);
+ magnitude * doubleUlpDiff * GMX_DOUBLE_EPS,
+ 0.0,
+ 0.0,
+ singleUlpDiff,
+ doubleUlpDiff,
+ false);
}
/*! \brief
static inline FloatingPointTolerance defaultFloatTolerance()
{
return relativeToleranceAsPrecisionDependentUlp(
- 1.0, detail::g_defaultUlpTolerance,
+ 1.0,
+ detail::g_defaultUlpTolerance,
static_cast<uint64_t>(detail::g_defaultUlpTolerance * (GMX_FLOAT_EPS / GMX_DOUBLE_EPS)));
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2015,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TESTUTILS_TESTFILEMANAGER_H
#define GMX_TESTUTILS_TESTFILEMANAGER_H
+#include <memory>
#include <string>
-#include "gromacs/utility/classhelpers.h"
-
namespace gmx
{
/*! \libinternal \brief
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace test
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TESTUTILS_TESTFILEREDIRECTOR_H
#define GMX_TESTUTILS_TESTFILEREDIRECTOR_H
+#include <memory>
#include <set>
#include <string>
private:
class Impl;
- PrivateImplPointer<Impl> impl_;
+ std::unique_ptr<Impl> impl_;
};
} // namespace test
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \param[in] name Name of the options provider (for ordering).
* \param[in] provider The provider to register.
* \throws std::bad_alloc if out of memory.
- * \throws tMPI::system_error on mutex failures.
*
* Typically not used directly in test code, but through the
* #GMX_TEST_OPTIONS macro.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "interactivetest.h"
+#include "testutils/interactivetest.h"
#include <string>
#include <utility>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "loggertest.h"
+#include "testutils/loggertest.h"
#include <gmock/gmock.h>
EXPECT_CALL(target, writeEntry(Field(&LogEntry::text, ContainsRegex(re))));
}
+void LoggerTestHelper::expectNoEntries(gmx::MDLogger::LogLevel level)
+{
+ auto& target = impl_->getTarget(level);
+ EXPECT_CALL(target, writeEntry(testing::_)).Times(0);
+}
+
} // namespace test
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "mpitest.h"
+#include "testutils/mpitest.h"
#include "config.h"
*/
#include "gmxpre.h"
-#include "refdata.h"
+#include "testutils/refdata.h"
#include <cctype>
#include <cstdlib>
#include "gromacs/utility/real.h"
#include "gromacs/utility/stringutil.h"
-#include "testutils/refdata_checkers.h"
-#include "testutils/refdata_impl.h"
-#include "testutils/refdata_xml.h"
#include "testutils/testasserts.h"
#include "testutils/testexceptions.h"
#include "testutils/testfilemanager.h"
+#include "refdata_checkers.h"
+#include "refdata_impl.h"
+#include "refdata_xml.h"
+
namespace gmx
{
namespace test
return TestReferenceChecker(new TestReferenceChecker::Impl(true));
}
impl_->compareRootEntry_->setChecked();
- return TestReferenceChecker(new TestReferenceChecker::Impl(
- "", impl_->compareRootEntry_.get(), impl_->outputRootEntry_.get(),
- impl_->updateMismatchingEntries_, impl_->bSelfTestMode_, defaultRealTolerance()));
+ return TestReferenceChecker(new TestReferenceChecker::Impl("",
+ impl_->compareRootEntry_.get(),
+ impl_->outputRootEntry_.get(),
+ impl_->updateMismatchingEntries_,
+ impl_->bSelfTestMode_,
+ defaultRealTolerance()));
}
{
impl_->outputRootEntry_->addChild(entry->cloneToOutputEntry());
}
- return TestReferenceChecker(new Impl(fullId, entry, entry->correspondingOutputEntry(),
- impl_->updateMismatchingEntries_, impl_->bSelfTestMode_,
+ return TestReferenceChecker(new Impl(fullId,
+ entry,
+ entry->correspondingOutputEntry(),
+ impl_->updateMismatchingEntries_,
+ impl_->bSelfTestMode_,
impl_->defaultTolerance_));
}
void TestReferenceChecker::checkBoolean(bool value, const char* id)
{
- EXPECT_PLAIN(impl_->processItem(Impl::cBooleanNodeName, id,
- ExactStringChecker(value ? "true" : "false")));
+ EXPECT_PLAIN(impl_->processItem(
+ Impl::cBooleanNodeName, id, ExactStringChecker(value ? "true" : "false")));
}
void TestReferenceChecker::checkUChar(unsigned char value, const char* id)
{
- EXPECT_PLAIN(impl_->processItem(Impl::cUCharNodeName, id,
- ExactStringChecker(formatString("%d", value))));
+ EXPECT_PLAIN(impl_->processItem(
+ Impl::cUCharNodeName, id, ExactStringChecker(formatString("%d", value))));
}
void TestReferenceChecker::checkInteger(int value, const char* id)
{
- EXPECT_PLAIN(impl_->processItem(Impl::cIntegerNodeName, id,
- ExactStringChecker(formatString("%d", value))));
+ EXPECT_PLAIN(impl_->processItem(
+ Impl::cIntegerNodeName, id, ExactStringChecker(formatString("%d", value))));
}
void TestReferenceChecker::checkInt32(int32_t value, const char* id)
{
- EXPECT_PLAIN(impl_->processItem(Impl::cInt32NodeName, id,
- ExactStringChecker(formatString("%" PRId32, value))));
+ EXPECT_PLAIN(impl_->processItem(
+ Impl::cInt32NodeName, id, ExactStringChecker(formatString("%" PRId32, value))));
}
void TestReferenceChecker::checkUInt32(uint32_t value, const char* id)
{
- EXPECT_PLAIN(impl_->processItem(Impl::cUInt32NodeName, id,
- ExactStringChecker(formatString("%" PRIu32, value))));
+ EXPECT_PLAIN(impl_->processItem(
+ Impl::cUInt32NodeName, id, ExactStringChecker(formatString("%" PRIu32, value))));
}
void TestReferenceChecker::checkInt64(int64_t value, const char* id)
{
- EXPECT_PLAIN(impl_->processItem(Impl::cInt64NodeName, id,
- ExactStringChecker(formatString("%" PRId64, value))));
+ EXPECT_PLAIN(impl_->processItem(
+ Impl::cInt64NodeName, id, ExactStringChecker(formatString("%" PRId64, value))));
}
void TestReferenceChecker::checkUInt64(uint64_t value, const char* id)
{
- EXPECT_PLAIN(impl_->processItem(Impl::cUInt64NodeName, id,
- ExactStringChecker(formatString("%" PRIu64, value))));
+ EXPECT_PLAIN(impl_->processItem(
+ Impl::cUInt64NodeName, id, ExactStringChecker(formatString("%" PRIu64, value))));
}
void TestReferenceChecker::checkDouble(double value, const char* id)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/strconvert.h"
#include "gromacs/utility/stringutil.h"
-#include "testutils/refdata_impl.h"
#include "testutils/testasserts.h"
#include "testutils/testexceptions.h"
+#include "refdata_impl.h"
+
namespace gmx
{
namespace test
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/exceptions.h"
-#include "testutils/refdata_impl.h"
#include "testutils/testexceptions.h"
+#include "refdata_impl.h"
+
namespace gmx
{
namespace test
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
-#include "testutils/refdata_impl.h"
+#include "refdata_impl.h"
namespace gmx
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "simulationdatabase.h"
+#include "testutils/simulationdatabase.h"
#include <algorithm>
#include <map>
{ { { "ref-t", "80" } },
{ // TODO This test case is not currently used, so we
// have not tested which rank counts work.
- 1, 2, 3, 4, 5, 6, 7, 8, 9 } } },
+ 1,
+ 2,
+ 3,
+ 4,
+ 5,
+ 6,
+ 7,
+ 8,
+ 9 } } },
// Simple system with 2 nearby water molecules
{ "spc2",
{ {},
{ // TODO This test case is not currently used, so we
// have not tested which rank counts work.
- 1, 2, 3, 4, 5, 6, 7, 8, 9 } } },
+ 1,
+ 2,
+ 3,
+ 4,
+ 5,
+ 6,
+ 7,
+ 8,
+ 9 } } },
// Simple system with 216 water molecules, condensed phase
{ "spc216",
{ {},
{
// TODO This test case is not currently used, so we
// have not tested which rank counts work.
- 1, 2, 3, 4, 5, 6, 7, 8, 9 // TODO tpi test
+ 1,
+ 2,
+ 3,
+ 4,
+ 5,
+ 6,
+ 7,
+ 8,
+ 9 // TODO tpi test
} } },
// Capped alanine peptide in vacuo with virtual sites
{ "alanine_vsite_vacuo",
{ { { "constraints", "all-bonds" }, { "compressibility", "5e-10" }, { "tau-p", "1000" } },
{ // TODO This test case is not currently used, so we
// have not tested which rank counts work.
- 1, 2, 3, 4, 5, 6, 7, 8, 9 } } },
+ 1,
+ 2,
+ 3,
+ 4,
+ 5,
+ 6,
+ 7,
+ 8,
+ 9 } } },
+ // Capped alanine peptide in vacuo (no virtual sites)
+ { "alanine_vacuo", { { { "constraints", "h-bonds" } }, { 1, 2, 3, 4, 5, 6, 7, 8, 9 } } },
// Zwitterionic glycine in vacuo
{ "glycine_vacuo", { { { "constraints", "h-bonds" } }, { 1, 2, 3, 4, 5, 6, 7, 8, 9 } } },
// Zwitterionic glycine in vacuo, without constraints
{ "compressibility", "5e-10" },
{ "tau-p", "1000" },
{ "constraints", "h-bonds" },
- { "other",
- R"(free-energy = yes
- sc-alpha = 0.5
- sc-r-power = 6
- mass-lambdas = 0.0 0.5 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
- bonded-lambdas = 0.0 0.0 0.0 0.5 1.0 1.0 1.0 1.0 1.0 1.0 1.0
- restraint-lambdas = 0.0 0.0 0.0 0.0 0.0 0.5 1.0 1.0 1.0 1.0 1.0
- vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.5 1.0 1.0 1.0
- coul-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.5 1.0
- ;couple-moltype = nonanol
- ;couple-lambda0 = none
- ;couple-lambda1 = vdw-q
- ;couple-intramol = yes)" } },
- { 1, 2, 3, 4, 5, 6, 8, 9 } } }
+ { "free-energy", "yes" },
+ { "sc-alpha", "0.5" },
+ { "sc-r-power", "6" },
+ { "mass-lambdas", "0.0 0.5 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0" },
+ { "bonded-lambdas", "0.0 0.0 0.0 0.5 1.0 1.0 1.0 1.0 1.0 1.0 1.0" },
+ { "restraint-lambdas", "0.0 0.0 0.0 0.0 0.0 0.5 1.0 1.0 1.0 1.0 1.0" },
+ { "vdw-lambdas", "0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.5 1.0 1.0 1.0" },
+ { "coul-lambdas", "0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.5 1.0" },
+ { ";couple-moltype", "nonanol" },
+ { ";couple-lambda0", "none" },
+ { ";couple-lambda1", "vdw-q" },
+ { ";couple-intramol", "yes" } },
+ { 1, 2, 3, 4, 5, 6, 8, 9 } } },
+ // Artificial test system including all virtual site types
+ { "vsite_test", { {}, { 1, 2, 3, 4, 5, 6, 7, 8, 9 } } },
};
/*! \brief Prepare default .mdp values
*
* \throws std::bad_alloc if out of memory
* std::out_of_range if \c simulationName is not in the database
- *
- * Note: Any mdp options that are not added here cannot be used
*/
MdpFieldValues prepareDefaultMdpFieldValues(const std::string& simulationName)
{
mdpFieldValues.insert(MdpField("nstpcouple", "4"));
mdpFieldValues.insert(MdpField("compressibility", "5e-5"));
mdpFieldValues.insert(MdpField("constraints", "none"));
- mdpFieldValues.insert(MdpField("other", ""));
mdpFieldValues.insert(MdpField("coulombtype", "Cut-off"));
mdpFieldValues.insert(MdpField("rcoulomb", "0.7"));
mdpFieldValues.insert(MdpField("vdwtype", "Cut-off"));
mdpFieldValues.insert(MdpField("rvdw", "0.7"));
mdpFieldValues.insert(MdpField("nstcalcenergy", "100"));
+ mdpFieldValues.insert(MdpField("rlist", "-1"));
+ mdpFieldValues.insert(MdpField("bd-fric", "1000"));
+ mdpFieldValues.insert(MdpField("verlet-buffer-tolerance", "0.000001"));
+ mdpFieldValues.insert(MdpField("nstlist", "8"));
+ mdpFieldValues.insert(MdpField("ld-seed", "234262"));
+ mdpFieldValues.insert(MdpField("tau-t", "1"));
+ mdpFieldValues.insert(MdpField("tc-grps", "System"));
+ mdpFieldValues.insert(MdpField("pcoupltype", "isotropic"));
+ mdpFieldValues.insert(MdpField("ref-p", "1"));
+ mdpFieldValues.insert(MdpField("constraint-algorithm", "lincs"));
+ mdpFieldValues.insert(MdpField("lincs-order", "2"));
+ mdpFieldValues.insert(MdpField("lincs-iter", "5"));
return mdpFieldValues;
}
std::string reportNumbersOfPpRanksSupported(const std::string& simulationName)
{
const auto& possibleNumbers = mdpFileValueDatabase_g.at(simulationName).validPpRankCounts;
- return formatAndJoin(std::begin(possibleNumbers), std::end(possibleNumbers), ",",
- StringFormatter("%d"));
+ return formatAndJoin(
+ std::begin(possibleNumbers), std::end(possibleNumbers), ",", StringFormatter("%d"));
}
MdpFieldValues prepareMdpFieldValues(const std::string& simulationName,
* currently have a good way to compare forces at steps where
* energies were not computed with those from rerun on the same
* coordinates.
- *
- * Note: Any mdp options that are not printed here cannot be used
*/
- return formatString(
- R"(coulombtype = %s
- rcoulomb = %s
- vdwtype = %s
- rvdw = %s
- rlist = -1
- bd-fric = 1000
- verlet-buffer-tolerance = 0.000001
- nsteps = %s
- nstenergy = %s
- nstxout = %s
- nstvout = %s
- nstfout = %s
- nstxout-compressed = %s
- nstdhdl = %s
- nstlist = 8
- integrator = %s
- ld-seed = 234262
- tcoupl = %s
- nsttcouple = %s
- ref-t = %s
- tau-t = 1
- tc-grps = System
- pcoupl = %s
- nstpcouple = %s
- pcoupltype = isotropic
- ref-p = 1
- tau-p = %s
- compressibility = %s
- constraints = %s
- constraint-algorithm = lincs
- lincs-order = 2
- lincs-iter = 5
- nstcalcenergy = %s
- comm-mode = %s
- nstcomm = %s
- %s)",
- mdpFieldValues.at("coulombtype").c_str(), mdpFieldValues.at("rcoulomb").c_str(),
- mdpFieldValues.at("vdwtype").c_str(), mdpFieldValues.at("rvdw").c_str(),
- mdpFieldValues.at("nsteps").c_str(), mdpFieldValues.at("nstenergy").c_str(),
- mdpFieldValues.at("nstxout").c_str(), mdpFieldValues.at("nstvout").c_str(),
- mdpFieldValues.at("nstfout").c_str(), mdpFieldValues.at("nstxout-compressed").c_str(),
- mdpFieldValues.at("nstdhdl").c_str(), mdpFieldValues.at("integrator").c_str(),
- mdpFieldValues.at("tcoupl").c_str(), mdpFieldValues.at("nsttcouple").c_str(),
- mdpFieldValues.at("ref-t").c_str(), mdpFieldValues.at("pcoupl").c_str(),
- mdpFieldValues.at("nstpcouple").c_str(), mdpFieldValues.at("tau-p").c_str(),
- mdpFieldValues.at("compressibility").c_str(), mdpFieldValues.at("constraints").c_str(),
- mdpFieldValues.at("nstcalcenergy").c_str(), mdpFieldValues.at("comm-mode").c_str(),
- mdpFieldValues.at("nstcomm").c_str(), mdpFieldValues.at("other").c_str());
+ std::string optionString;
+ for (auto const& [key, value] : mdpFieldValues)
+ {
+ optionString += formatString("%-24s = %s\n", key.c_str(), value.c_str());
+ }
+ return optionString;
}
} // namespace test
--- /dev/null
+Generated by trjconv : Alanine-dipeptide t= 1.25800
+ 22
+ 1ACE CH3 1 2.389 2.391 1.033 -0.7039 0.4613 0.0257
+ 1ACE HH31 2 2.354 2.463 0.960 0.5981 -0.1788 -1.3029
+ 1ACE HH32 3 2.440 2.450 1.109 -0.1149 0.3508 -0.2771
+ 1ACE HH33 4 2.460 2.325 0.982 -0.9598 0.6736 -0.6069
+ 1ACE C 5 2.272 2.319 1.095 0.2222 -0.0856 -0.2558
+ 1ACE O 6 2.221 2.357 1.199 0.2726 0.1210 -0.4387
+ 2ALA N 7 2.219 2.218 1.026 0.4241 -0.9217 0.8026
+ 2ALA H 8 2.266 2.192 0.941 1.5735 -0.8934 1.4029
+ 2ALA CA 9 2.096 2.154 1.056 0.0365 -0.2046 0.2115
+ 2ALA HA 10 2.105 2.106 1.153 -0.0104 0.7343 0.6916
+ 2ALA CB 11 1.968 2.244 1.045 -0.3611 0.0604 -0.0105
+ 2ALA HB1 12 1.950 2.276 0.942 -0.3033 1.7389 0.4634
+ 2ALA HB2 13 1.882 2.189 1.084 0.2534 -0.2994 0.8622
+ 2ALA HB3 14 1.984 2.333 1.106 -1.1497 0.4723 -0.3796
+ 2ALA C 15 2.076 2.046 0.948 -0.3002 -0.0866 -0.1169
+ 2ALA O 16 2.130 2.052 0.836 0.3392 0.2597 -0.0125
+ 3NME N 17 1.992 1.950 0.986 0.0586 0.0225 -0.1088
+ 3NME H 18 1.962 1.955 1.082 -0.6948 0.1462 -0.3441
+ 3NME CH3 19 1.964 1.834 0.902 -0.3035 0.0695 -0.1543
+ 3NME HH31 20 1.957 1.867 0.799 1.3131 1.1659 0.0471
+ 3NME HH32 21 2.050 1.768 0.911 -0.0987 0.4321 0.7448
+ 3NME HH33 22 1.876 1.782 0.939 -0.0292 -0.4463 -0.2141
+ 3.00000 3.00000 3.00000
--- /dev/null
+[ System ]
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+ 16 17 18 19 20 21 22
+[ Protein ]
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+ 16 17 18 19 20 21 22
+[ Protein-H ]
+ 1 5 6 7 9 11 15 16 17 19
+[ C-alpha ]
+ 9
+[ Backbone ]
+ 5 7 9 15 17
+[ MainChain ]
+ 5 6 7 9 15 16 17
+[ MainChain+Cb ]
+ 5 6 7 9 11 15 16 17
+[ MainChain+H ]
+ 5 6 7 8 9 15 16 17 18
+[ SideChain ]
+ 1 2 3 4 10 11 12 13 14 19 20 21 22
+[ SideChain-H ]
+ 1 11 19
+[ CA ]
+ 9
+[ C_&_r_1 ]
+ 5
+[ C_&_r_2 ]
+ 15
+[ N_&_r_2 ]
+ 7
+[ N_&_r_3 ]
+ 17
--- /dev/null
+#include "amber99sb-ildn.ff/forcefield.itp"
+
+[ moleculetype ]
+; Name nrexcl
+ALANINEDIPEPTIDE 3
+
+[ atoms ]
+; nr type resnr residue atom cgnr charge mass typeB chargeB massB
+; residue 1 ACE rtp ACE q 0.0
+ 1 CT 1 ACE CH3 1 -0.3662 12.01 ; qtot -0.3662
+ 2 HC 1 ACE HH31 2 0.1123 1.008 ; qtot -0.2539
+ 3 HC 1 ACE HH32 3 0.1123 1.008 ; qtot -0.1416
+ 4 HC 1 ACE HH33 4 0.1123 1.008 ; qtot -0.0293
+ 5 C 1 ACE C 5 0.5972 12.01 ; qtot 0.5679
+ 6 O 1 ACE O 6 -0.5679 16 ; qtot 0
+; residue 2 ALA rtp ALA q 0.0
+ 7 N 2 ALA N 7 -0.4157 14.01 ; qtot -0.4157
+ 8 H 2 ALA H 8 0.2719 1.008 ; qtot -0.1438
+ 9 CT 2 ALA CA 9 0.0337 12.01 ; qtot -0.1101
+ 10 H1 2 ALA HA 10 0.0823 1.008 ; qtot -0.0278
+ 11 CT 2 ALA CB 11 -0.1825 12.01 ; qtot -0.2103
+ 12 HC 2 ALA HB1 12 0.0603 1.008 ; qtot -0.15
+ 13 HC 2 ALA HB2 13 0.0603 1.008 ; qtot -0.0897
+ 14 HC 2 ALA HB3 14 0.0603 1.008 ; qtot -0.0294
+ 15 C 2 ALA C 15 0.5973 12.01 ; qtot 0.5679
+ 16 O 2 ALA O 16 -0.5679 16 ; qtot 0
+; residue 3 NME rtp NME q 0.0
+ 17 N 3 NME N 17 -0.4157 14.01 ; qtot -0.4157
+ 18 H 3 NME H 18 0.2719 1.008 ; qtot -0.1438
+ 19 CT 3 NME CH3 19 -0.149 12.01 ; qtot -0.2928
+ 20 H1 3 NME HH31 20 0.0976 1.008 ; qtot -0.1952
+ 21 H1 3 NME HH32 21 0.0976 1.008 ; qtot -0.0976
+ 22 H1 3 NME HH33 22 0.0976 1.008 ; qtot 0
+
+[ bonds ]
+; ai aj funct c0 c1 c2 c3
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 7 8 1
+ 7 9 1
+ 9 10 1
+ 9 11 1
+ 9 15 1
+ 11 12 1
+ 11 13 1
+ 11 14 1
+ 15 16 1
+ 15 17 1
+ 17 18 1
+ 17 19 1
+ 19 20 1
+ 19 21 1
+ 19 22 1
+
+[ pairs ]
+; ai aj funct c0 c1 c2 c3
+ 1 8 1
+ 1 9 1
+ 2 6 1
+ 2 7 1
+ 3 6 1
+ 3 7 1
+ 4 6 1
+ 4 7 1
+ 5 10 1
+ 5 11 1
+ 5 15 1
+ 6 8 1
+ 6 9 1
+ 7 12 1
+ 7 13 1
+ 7 14 1
+ 7 16 1
+ 7 17 1
+ 8 10 1
+ 8 11 1
+ 8 15 1
+ 9 18 1
+ 9 19 1
+ 10 12 1
+ 10 13 1
+ 10 14 1
+ 10 16 1
+ 10 17 1
+ 11 16 1
+ 11 17 1
+ 12 15 1
+ 13 15 1
+ 14 15 1
+ 15 20 1
+ 15 21 1
+ 15 22 1
+ 16 18 1
+ 16 19 1
+ 18 20 1
+ 18 21 1
+ 18 22 1
+
+[ angles ]
+; ai aj ak funct c0 c1 c2 c3
+ 2 1 3 1
+ 2 1 4 1
+ 2 1 5 1
+ 3 1 4 1
+ 3 1 5 1
+ 4 1 5 1
+ 1 5 6 1
+ 1 5 7 1
+ 6 5 7 1
+ 5 7 8 1
+ 5 7 9 1
+ 8 7 9 1
+ 7 9 10 1
+ 7 9 11 1
+ 7 9 15 1
+ 10 9 11 1
+ 10 9 15 1
+ 11 9 15 1
+ 9 11 12 1
+ 9 11 13 1
+ 9 11 14 1
+ 12 11 13 1
+ 12 11 14 1
+ 13 11 14 1
+ 9 15 16 1
+ 9 15 17 1
+ 16 15 17 1
+ 15 17 18 1
+ 15 17 19 1
+ 18 17 19 1
+ 17 19 20 1
+ 17 19 21 1
+ 17 19 22 1
+ 20 19 21 1
+ 20 19 22 1
+ 21 19 22 1
+
+[ dihedrals ]
+; ai aj ak al funct c0 c1 c2 c3 c4 c5
+ 2 1 5 6 9
+ 2 1 5 7 9
+ 3 1 5 6 9
+ 3 1 5 7 9
+ 4 1 5 6 9
+ 4 1 5 7 9
+ 1 5 7 8 9
+ 1 5 7 9 9
+ 6 5 7 8 9
+ 6 5 7 9 9
+ 5 7 9 10 9
+ 5 7 9 11 9
+ 5 7 9 15 9
+ 8 7 9 10 9
+ 8 7 9 11 9
+ 8 7 9 15 9
+ 7 9 11 12 9
+ 7 9 11 13 9
+ 7 9 11 14 9
+ 10 9 11 12 9
+ 10 9 11 13 9
+ 10 9 11 14 9
+ 15 9 11 12 9
+ 15 9 11 13 9
+ 15 9 11 14 9
+ 7 9 15 16 9
+ 7 9 15 17 9
+ 10 9 15 16 9
+ 10 9 15 17 9
+ 11 9 15 16 9
+ 11 9 15 17 9
+ 9 15 17 18 9
+ 9 15 17 19 9
+ 16 15 17 18 9
+ 16 15 17 19 9
+ 15 17 19 20 9
+ 15 17 19 21 9
+ 15 17 19 22 9
+ 18 17 19 20 9
+ 18 17 19 21 9
+ 18 17 19 22 9
+
+[ dihedrals ]
+; ai aj ak al funct c0 c1 c2 c3
+ 1 7 5 6 4
+ 5 9 7 8 4
+ 9 17 15 16 4
+ 15 19 17 18 4
+
+[ system ]
+; Name
+Alanine-dipeptide
+
+[ molecules ]
+; Compound #mols
+ALANINEDIPEPTIDE 1
[ System ]
- 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
- 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
- 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
- 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
- 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
- 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
- 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
- 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
- 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135
- 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150
- 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165
- 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180
- 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195
- 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210
- 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225
- 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240
- 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255
- 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270
- 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285
- 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300
- 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315
- 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330
- 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345
- 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360
- 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375
- 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390
- 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405
- 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420
- 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435
- 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450
- 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465
- 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480
- 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495
- 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510
- 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525
- 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540
- 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555
- 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570
- 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585
- 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600
- 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615
- 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630
- 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645
- 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660
- 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675
- 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690
- 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705
- 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720
- 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735
- 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750
- 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765
- 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780
- 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795
- 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810
- 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825
- 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840
- 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855
- 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870
- 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885
- 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900
- 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915
- 916 917 918 919 920 921 922 923
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+ 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
+ 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
+ 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
+ 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
+ 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
+ 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
+ 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
+ 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135
+ 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150
+ 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165
+ 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180
+ 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195
+ 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210
+ 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225
+ 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240
+ 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255
+ 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270
+ 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285
+ 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300
+ 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315
+ 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330
+ 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345
+ 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360
+ 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375
+ 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390
+ 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405
+ 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420
+ 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435
+ 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450
+ 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465
+ 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480
+ 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495
+ 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510
+ 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525
+ 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540
+ 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555
+ 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570
+ 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585
+ 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600
+ 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615
+ 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630
+ 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645
+ 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660
+ 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675
+ 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690
+ 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705
+ 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720
+ 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735
+ 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750
+ 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765
+ 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780
+ 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795
+ 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810
+ 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825
+ 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840
+ 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855
+ 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870
+ 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885
+ 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900
+ 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915
+ 916 917 918 919 920 921 922 923
+[ Protein ]
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+ 16 17 18 19 20 21 22 23 24 25 26 27 28 29
+[ Water ]
+ 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44
+ 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
+ 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74
+ 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89
+ 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104
+ 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
+ 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134
+ 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149
+ 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164
+ 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
+ 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194
+ 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209
+ 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224
+ 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
+ 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254
+ 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269
+ 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284
+ 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299
+ 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314
+ 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329
+ 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344
+ 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359
+ 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374
+ 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389
+ 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404
+ 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419
+ 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434
+ 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449
+ 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464
+ 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479
+ 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494
+ 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509
+ 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524
+ 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539
+ 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554
+ 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569
+ 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584
+ 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599
+ 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614
+ 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629
+ 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644
+ 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659
+ 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674
+ 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689
+ 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704
+ 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719
+ 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734
+ 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749
+ 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764
+ 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779
+ 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794
+ 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809
+ 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824
+ 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839
+ 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854
+ 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869
+ 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884
+ 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899
+ 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914
+ 915 916 917 918 919 920 921 922 923
+[ some_water_subset ]
+ 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44
+ 45 46 47
--- /dev/null
+[ particles ]
+1 2 3
--- /dev/null
+msd_beads
+ 3
+ 1A A 1 2.167 1.833 1.500
+ 2A A 2 0.000 0.000 0.000
+ 3A A 3 3.167 3.833 4.500
+ 5.00000 5.00000 5.00000
--- /dev/null
+UNITED ATOM STRUCTURE FOR MOLECULE VSTEST
+ 24
+ 1VSTST C1 1 1.537 2.466 2.499
+ 1VSTST C2 2 1.666 2.549 2.500
+ 1VSTST C3 3 1.793 2.464 2.500
+ 1VSTST C4 4 1.922 2.547 2.500
+ 1VSTST C5 5 2.050 2.462 2.501
+ 1VSTST C6 6 2.179 2.545 2.500
+ 1VSTST C7 7 2.307 2.460 2.500
+ 1VSTST C8 8 2.436 2.543 2.500
+ 1VSTST C9 9 2.564 2.457 2.500
+ 1VSTST C10 10 2.693 2.540 2.500
+ 1VSTST C11 11 2.821 2.455 2.500
+ 1VSTST C12 12 2.950 2.538 2.499
+ 1VSTST C13 13 3.078 2.453 2.500
+ 1VSTST C14 14 3.207 2.536 2.500
+ 1VSTST C15 15 3.334 2.451 2.500
+ 1VSTST C16 16 3.463 2.534 2.501
+ 1VSTST VS1 17 2.500 2.500 2.500
+ 1VSTST VS2 18 2.500 2.500 2.500
+ 1VSTST VS3 19 2.500 2.500 2.500
+ 1VSTST VS4 20 2.500 2.500 2.500
+ 1VSTST VS5 21 2.500 2.500 2.500
+ 1VSTST VS6 22 2.500 2.500 2.500
+ 1VSTST VS7 23 2.500 2.500 2.500
+ 1VSTST VS8 24 2.500 2.500 2.500
+ 5.00000 5.00000 5.00000
--- /dev/null
+[ System ]
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+ 16 17 18 19 20 21 22 23 24
--- /dev/null
+; Combination of a GROMOS54A7 hexadecane (from ATB) with some
+; added virtual sites for testing purposes. Not a physical system.
+
+[ defaults ]
+; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
+ 1 1 no 1.0 1.0
+[ atomtypes ]
+;name at.num mass charge ptype c6 c12
+ CH2 6 0.000 0.000 A 0.0074684164 3.3965584e-05
+ CH3 6 0.000 0.000 A 0.0096138025 2.6646244e-05
+ DUM 0 0.000 0.000 A 0 0
+[ nonbond_params ]
+; i j func c6 c12
+ CH3 CH2 1 8.473481E-03 3.008414E-05
+ DUM CH2 1 0.000000E+00 0.000000E+00
+ DUM CH3 1 0.000000E+00 0.000000E+00
+[ pairtypes ]
+; i j func c6 c12
+ CH2 CH2 1 4.723813E-03 4.741926E-06
+ CH3 CH2 1 5.689469E-03 5.347702E-06
+ CH3 CH3 1 6.852528E-03 6.030865E-06
+ DUM CH2 1 0.000000E+00 0.000000E+00
+ DUM CH3 1 0.000000E+00 0.000000E+00
+ DUM DUM 1 0.000000E+00 0.000000E+00
+
+
+[ moleculetype ]
+; Name nrexcl
+VSTEST 3
+
+[ atoms ]
+; nr type resnr resid atom cgnr charge mass
+ 1 CH3 1 VSTEST C1 1 -0.016 15.0350
+ 2 CH2 1 VSTEST C2 2 0.013 14.0270
+ 3 CH2 1 VSTEST C3 3 0.012 14.0270
+ 4 CH2 1 VSTEST C4 4 -0.010 14.0270
+ 5 CH2 1 VSTEST C5 5 -0.004 14.0270
+ 6 CH2 1 VSTEST C6 6 0.006 14.0270
+ 7 CH2 1 VSTEST C7 7 0.001 14.0270
+ 8 CH2 1 VSTEST C8 8 -0.002 14.0270
+ 9 CH2 1 VSTEST C9 9 -0.002 14.0270
+ 10 CH2 1 VSTEST C10 10 0.001 14.0270
+ 11 CH2 1 VSTEST C11 11 0.006 14.0270
+ 12 CH2 1 VSTEST C12 12 -0.004 14.0270
+ 13 CH2 1 VSTEST C13 13 -0.010 14.0270
+ 14 CH2 1 VSTEST C14 14 0.012 14.0270
+ 15 CH2 1 VSTEST C15 15 0.013 14.0270
+ 16 CH3 1 VSTEST C16 16 -0.016 15.0350
+ 17 DUM 1 VSTEST VS1 17 0.010 0.0
+ 18 DUM 1 VSTEST VS2 18 -0.010 0.0
+ 19 DUM 1 VSTEST VS3 19 0.010 0.0
+ 20 DUM 1 VSTEST VS4 20 -0.010 0.0
+ 21 DUM 1 VSTEST VS5 21 0.010 0.0
+ 22 DUM 1 VSTEST VS6 22 -0.010 0.0
+ 23 DUM 1 VSTEST VS7 23 0.010 0.0
+ 24 DUM 1 VSTEST VS8 24 -0.010 0.0
+; total charge of the molecule: 0.000
+[ bonds ]
+; ai aj funct c0 c1
+ 1 2 2 0.1530 7.1500e+06
+ 2 3 2 0.1530 7.1500e+06
+ 3 4 2 0.1530 7.1500e+06
+ 4 5 2 0.1530 7.1500e+06
+ 5 6 2 0.1530 7.1500e+06
+ 6 7 2 0.1530 7.1500e+06
+ 7 8 2 0.1530 7.1500e+06
+ 8 9 2 0.1530 7.1500e+06
+ 9 10 2 0.1530 7.1500e+06
+ 10 11 2 0.1530 7.1500e+06
+ 11 12 2 0.1530 7.1500e+06
+ 12 13 2 0.1530 7.1500e+06
+ 13 14 2 0.1530 7.1500e+06
+ 14 15 2 0.1530 7.1500e+06
+ 15 16 2 0.1530 7.1500e+06
+[ pairs ]
+; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp
+ 1 4 1
+ 2 5 1
+ 3 6 1
+ 4 7 1
+ 5 8 1
+ 6 9 1
+ 7 10 1
+ 8 11 1
+ 9 12 1
+ 10 13 1
+ 11 14 1
+ 12 15 1
+ 13 16 1
+[ angles ]
+; ai aj ak funct angle fc
+ 1 2 3 2 111.00 530.00
+ 2 3 4 2 111.00 530.00
+ 3 4 5 2 111.00 530.00
+ 4 5 6 2 111.00 530.00
+ 5 6 7 2 111.00 530.00
+ 6 7 8 2 111.00 530.00
+ 7 8 9 2 111.00 530.00
+ 8 9 10 2 111.00 530.00
+ 9 10 11 2 111.00 530.00
+ 10 11 12 2 111.00 530.00
+ 11 12 13 2 111.00 530.00
+ 12 13 14 2 111.00 530.00
+ 13 14 15 2 111.00 530.00
+ 14 15 16 2 111.00 530.00
+[ dihedrals ]
+; ai aj ak al funct ph0 cp mult
+ 1 2 3 4 1 0.00 5.92 3
+ 2 3 4 5 1 0.00 5.92 3
+ 3 4 5 6 1 0.00 5.92 3
+ 4 5 6 7 1 0.00 5.92 3
+ 5 6 7 8 1 0.00 5.92 3
+ 6 7 8 9 1 0.00 5.92 3
+ 7 8 9 10 1 0.00 5.92 3
+ 8 9 10 11 1 0.00 5.92 3
+ 9 10 11 12 1 0.00 5.92 3
+ 10 11 12 13 1 0.00 5.92 3
+ 11 12 13 14 1 0.00 5.92 3
+ 12 13 14 15 1 0.00 5.92 3
+ 13 14 15 16 1 0.00 5.92 3
+[ exclusions ]
+; ai aj funct ; GROMOS 1-4 exclusions
+[ virtual_sites1 ]
+; Site from funct
+ 17 1 1
+[ virtual_sites2 ]
+; Site from funct a
+ 18 2 3 1 0.7439756
+[ virtual_sites2 ]
+; Site from funct a
+ 19 3 4 2 0.7439756
+[ virtual_sites3 ]
+; Site from funct a b
+ 20 4 5 6 1 0.7439756 0.128012
+[ virtual_sites3 ]
+; Site from funct a d
+ 21 6 7 8 2 0.5 -0.105
+[ virtual_sites3 ]
+; Site from funct theta d
+ 22 8 9 10 3 120 0.5
+[ virtual_sites3 ]
+; Site from funct a b c
+ 23 10 11 12 4 -0.4 -0.4 6.9281
+[ virtual_sites4 ]
+; Site from funct a b c
+ 24 12 13 14 15 2 1.0 0.9 0.105
+
+[ system ]
+; Name
+Virtual sites test system in vacuo
+
+[ molecules ]
+; Compound #mols
+VSTEST 1
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "stdiohelper.h"
+#include "testutils/stdiohelper.h"
#include <cerrno>
#include <cstdio>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "stringtest.h"
+#include "testutils/stringtest.h"
#include <string>
*/
#include "gmxpre.h"
-#include "test_device.h"
+#include "testutils/test_device.h"
#include <memory>
#include "gmxpre.h"
-#include "test_hardware_environment.h"
+#include "testutils/test_hardware_environment.h"
#include <memory>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "testasserts.h"
+#include "testutils/testasserts.h"
#include <cmath>
#include <cstdio>
relDiffStr = formatString("Inf");
}
- return formatString("%g (%" PRIu64 " %s-prec. ULPs, rel. %s)%s", absoluteDifference_,
- ulpDifference_, isDouble() ? "double" : "single", relDiffStr.c_str(),
+ return formatString("%g (%" PRIu64 " %s-prec. ULPs, rel. %s)%s",
+ absoluteDifference_,
+ ulpDifference_,
+ isDouble() ? "double" : "single",
+ relDiffStr.c_str(),
bSignDifference_ ? ", signs differ" : "");
}
*/
#include "gmxpre.h"
-#include "testfilemanager.h"
+#include "testutils/testfilemanager.h"
#include <cstdio>
// Assume file is in global directory for simulation input files.
return Path::join(getTestSimulationDatabaseDirectory(), filename);
}
- else
- {
- // Assume file is present locally without full name (e.g. extension).
- return Path::join(getInputDataDirectory(), filename);
- }
+ // Assume file is present locally without full name (e.g. extension).
+ return Path::join(getInputDataDirectory(), filename);
}
std::string TestFileManager::getInputFilePath(const std::string& filename)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "testfileredirector.h"
+#include "testutils/testfileredirector.h"
#include <memory>
#include <set>
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "testinit.h"
+#include "testutils/testinit.h"
#include <cstdio>
#include <cstdlib>
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/textwriter.h"
-#include "testutils/mpi_printer.h"
#include "testutils/refdata.h"
#include "testutils/test_hardware_environment.h"
#include "testutils/testfilemanager.h"
#include "testutils/testoptions.h"
+#include "mpi_printer.h"
+
namespace gmx
{
namespace test
int* argc,
char*** argv)
{
-#if !defined NDEBUG \
- && !((defined __clang__ || (defined(__GNUC__) && !defined(__ICC) && __GNUC__ == 7)) \
- && defined __OPTIMIZE__)
- gmx_feenableexcept();
-#endif
+ if (gmxShouldEnableFPExceptions())
+ {
+ gmx_feenableexcept();
+ }
const CommandLineProgramContext& context = initForCommandLine(argc, argv);
try
{
"NOTE: You are running %s on %d MPI ranks, "
"but it is does not contain MPI-enabled tests. "
"The test will now exit.\n",
- context.programName(), gmx_node_num());
+ context.programName(),
+ gmx_node_num());
}
finalizeForCommandLine();
std::exit(1);
*/
#include "gmxpre.h"
-#include "testmatchers.h"
+#include "testutils/testmatchers.h"
#include <memory>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "testoptions.h"
+#include "testutils/testoptions.h"
#include <list>
+#include <mutex>
+#include <memory>
#include "gromacs/utility/classhelpers.h"
-#include "gromacs/utility/mutex.h"
namespace gmx
{
//! Adds a provider into the registry.
void add(const char* /*name*/, TestOptionsProvider* provider)
{
- lock_guard<Mutex> lock(listMutex_);
+ std::lock_guard<std::mutex> lock(listMutex_);
providerList_.push_back(provider);
}
typedef std::list<TestOptionsProvider*> ProviderList;
- Mutex listMutex_;
+ std::mutex listMutex_;
ProviderList providerList_;
GMX_DISALLOW_COPY_AND_ASSIGN(TestOptionsRegistry);
{
// TODO: Have some deterministic order for the options; now it depends on
// the order in which the global initializers are run.
- lock_guard<Mutex> lock(listMutex_);
+ std::lock_guard<std::mutex> lock(listMutex_);
ProviderList::const_iterator i;
for (i = providerList_.begin(); i != providerList_.end(); ++i)
{
testasserts_tests.cpp
xvgtest_tests.cpp
)
+target_link_libraries(testutils-test PRIVATE testutils)
gmx_add_mpi_unit_test(TestUtilsMpiUnitTests testutils-mpi-test 2
CPP_SOURCE_FILES
mpitest.cpp
)
+target_link_libraries(testutils-test PRIVATE testutils)
checkXvgFile(&sis, &checker, XvgMatchSettings());
}
{
- const char* const input[] = { "0 2905.86 -410.199", "0.2 6656.67 -430.437",
+ const char* const input[] = { "0 2905.86 -410.199",
+ "0.2 6656.67 -430.437",
"0.4 5262.44 -409.399" };
// Now check with missing data
TestReferenceData data(ReferenceDataMode::Compare);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "textblockmatchers.h"
+#include "testutils/textblockmatchers.h"
#include <memory>
#include <regex>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gmxpre.h"
-#include "tprfilegenerator.h"
+#include "testutils/tprfilegenerator.h"
#include "gromacs/gmxpreprocess/grompp.h"
#include "gromacs/utility/textwriter.h"
int main(int argc, char* argv[])
{
// Calls ::testing::InitGoogleMock()
- ::gmx::test::initTestUtils(TEST_DATA_PATH, TEST_TEMP_PATH, TEST_USES_MPI,
- TEST_USES_HARDWARE_DETECTION, &argc, &argv);
+ ::gmx::test::initTestUtils(
+ TEST_DATA_PATH, TEST_TEMP_PATH, TEST_USES_MPI, TEST_USES_HARDWARE_DETECTION, &argc, &argv);
int errcode = RUN_ALL_TESTS();
::gmx::test::finalizeTestUtils();
return errcode;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "xvgtest.h"
+#include "testutils/xvgtest.h"
#include <cerrno>
#include <cstdlib>
set(REGRESSIONTEST_DOWNLOAD OFF CACHE BOOL "Tests already downloaded. Set to yes to download again" FORCE)
endif()
-if(REGRESSIONTEST_PATH AND (CMAKE_CROSSCOMPILING OR CMAKE_CONFIGURATION_TYPES OR GMX_BUILD_MDRUN_ONLY))
+if(REGRESSIONTEST_PATH AND (CMAKE_CROSSCOMPILING OR CMAKE_CONFIGURATION_TYPES))
# TODO: It would be nicer to do these checks before potentially downloading the tests.
# Cross-compiling toolchains require us to compile both front-end and
# back-end binaries to run gmxtest.pl.
- # Testing an mdrun-only builds require supporting binaries from a full build
message(WARNING
- "With cross-compiling, multi-configuration generators (e.g. Visual Studio), or with mdrun-only builds, running regressiontests from build system is not supported. Please run gmxtest.pl directly.")
+ "With cross-compiling or multi-configuration generators (e.g. Visual Studio), running regressiontests from build system is not supported. Please run gmxtest.pl directly.")
set(REGRESSIONTEST_PATH OFF CACHE BOOL
"With cross-compiling or multi-configuration generators, running regressiontests from build system is not supported." FORCE)
endif()
list(APPEND ARGS -suffix ${GMX_BINARY_SUFFIX})
endif()
#crosscompile is only used to disable checking whether binaries work
- #given that we know they are there and that mdrun might not be exectuable
+ #given that we know they are there and that mdrun might not be executable
#(e.g. Cray) we enable it.
list(APPEND ARGS -crosscompile)
"GMX_PHYSICAL_VALIDATION set, but physical validation script not found in ${PHYSVALTEST_SOURCE_PATH}.")
endif()
- if(CMAKE_CROSSCOMPILING OR CMAKE_CONFIGURATION_TYPES OR GMX_BUILD_MDRUN_ONLY)
+ if(CMAKE_CROSSCOMPILING OR CMAKE_CONFIGURATION_TYPES)
# The following comment is copied from regression tests:
# Cross-compiling toolchains require us to compile both front-end and
# back-end binaries to run gmxtest.pl.
- # Testing an mdrun-only builds require supporting binaries from a full build
# TODO: Look into the details of this.
# For now, turn it off - our python-gmx interface is probably not that stable for special cases anyway
message(WARNING
- "With cross-compiling, multi-configuration generators (e.g. Visual Studio), or with mdrun-only builds,\
+ "With cross-compiling or multi-configuration generators (e.g. Visual Studio),\
running physical validation tests from build system is not supported.\
Please run physicalvalidation.py directly.")
set(GMX_PHYSICAL_VALIDATION OFF CACHE BOOL
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff