diff --git a/.clang-format.ignore b/.clang-format.ignore deleted file mode 100644 index ea50abb3..00000000 --- a/.clang-format.ignore +++ /dev/null @@ -1 +0,0 @@ -external/** diff --git a/.git_archival.txt b/.git_archival.txt new file mode 100644 index 00000000..0376d2ec --- /dev/null +++ b/.git_archival.txt @@ -0,0 +1,5 @@ +node: $Format:%H$ +node-date: $Format:%cI$ +describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$ +ref-names: $Format:%D$ + diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 00000000..d619e54d --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +.git_archival.txt export-subst + diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 00000000..9fcab7c4 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,12 @@ +version: 2 +updates: + # Maintain dependencies for GitHub Actions + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "weekly" + ignore: + # cibuildwheel updates often and cannot be tracked by + # a major version tag like 'v1'. Mute updates since + # this is not a critical component + - dependency-name: "pypa/cibuildwheel*" diff --git a/.github/environment.yml b/.github/environment.yml index b60af515..bb7ccc01 100644 --- a/.github/environment.yml +++ b/.github/environment.yml @@ -2,14 +2,6 @@ name: cppe-gha channels: - conda-forge dependencies: - - cmake - cxx-compiler - eigen - - h5py - - ninja - - numpy - - pandas - pip - - pybind11 - - pytest - - scipy diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 03c5bfc0..0600287b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -10,19 +10,17 @@ on: branches: - master -env: - BUILD_TYPE: Release - concurrency: group: ${{ github.workflow }}-${{ github.ref }} cancel-in-progress: true +env: + FORCE_COLOR: 3 + jobs: build: runs-on: ${{ matrix.os }} - continue-on-error: true - strategy: fail-fast: false matrix: @@ -32,84 +30,64 @@ jobs: - windows-latest python-version: - "3.8" - - "3.11" + - "3.12" defaults: run: - shell: bash -l {0} - - steps: - - uses: actions/checkout@v3 - - # this will set the system compiler; - # This must be done *before* setting up miniconda, see: - # https://github.com/ilammy/msvc-dev-cmd/issues/34 - - name: Set Windows env - if: matrix.os == 'windows-latest' - uses: ilammy/msvc-dev-cmd@v1 + shell: bash -el {0} - - name: Cache conda - uses: actions/cache@v3 - env: - # Increase this value to reset cache if .github/environment.yml has not changed - CACHE_NUMBER: 1 - with: - path: ~/conda_pkgs_dir - key: - ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('.github/environment.yml') }} + env: + NINJA_STATUS: "[Built edge %f of %t in %e sec] " - - uses: conda-incubator/setup-miniconda@v2 - with: - mamba-version: "*" - auto-update-conda: true - auto-activate-base: false - activate-environment: cppe-gha - environment-file: .github/environment.yml - channel-priority: strict - python-version: ${{ matrix.python-version }} - - - name: Select CMake CLI options - run: | - echo "We are running on ${{ matrix.os }}" - if [ "${{ matrix.os }}" == "ubuntu-latest" ]; then - echo "CXX=g++" >> $GITHUB_ENV - elif [ "${{ matrix.os }}" == "macos-latest" ]; then - echo "CXX=clang++" >> $GITHUB_ENV - else - echo "CXX=clang-cl" >> $GITHUB_ENV - fi - - - name: Configure - run: | - cmake -S. \ - -Bbuild \ - -GNinja \ - -DCMAKE_BUILD_TYPE=${{ env.BUILD_TYPE }} \ - -DCMAKE_CXX_COMPILER=${CXX} \ - -DCMAKE_INSTALL_PREFIX=~/Software - - - name: Build and install - run: | - cmake --build build --config ${{ env.BUILD_TYPE }} --target install -- -v -d stats - - - name: Test - run: | - python -m pip install git+https://gitlab.com/robertodr/polarizationsolver.git@master - - cd - - if [ "${{ matrix.os }}" == "windows-latest" ]; then - export KMP_DUPLICATE_LIB_OK=TRUE - export PYTHONPATH=Software/Lib/site-packages - python -m pytest --capture=no --log-cli-level=INFO --color=yes --pyargs cppe - else - export PYTHONPATH=$PYTHONPATH:Software/lib/python${{ matrix.python-version }}/site-packages - python -m pytest --capture=no --log-cli-level=INFO --color=yes --pyargs cppe - fi - - # TODO move to separate workflow - #- name: Build and Test Setuptools - # run: | - # rm -rf build - # python setup.py install - # py.test + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 # such that setuptools_scm can do its job correctly + + # this will set the system compiler; + # This must be done *before* setting up miniconda, see: + # https://github.com/ilammy/msvc-dev-cmd/issues/34 + - name: Set Windows env + if: matrix.os == 'windows-latest' + uses: ilammy/msvc-dev-cmd@v1 + env: + KMP_DUPLICATE_LIB_OK: "TRUE" + + - name: Cache conda + uses: actions/cache@v4 + env: + # Increase this value to reset cache if .github/environment.yml has not changed + CACHE_NUMBER: 2 + with: + path: ~/conda_pkgs_dir + key: + ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('.github/environment.yml') }} + + - uses: conda-incubator/setup-miniconda@v3 + with: + python-version: ${{ matrix.python-version }} + auto-update-conda: true + auto-activate-base: false + channels: conda-forge + channel-priority: true + activate-environment: cppe-gha + environment-file: .github/environment.yml + + - name: Select CMake CLI options + run: | + echo "We are running on ${{ matrix.os }}" + if [ "${{ matrix.os }}" == "ubuntu-latest" ]; then + echo "SKBUILD_CMAKE_ARGS=-DCMAKE_CXX_COMPILER=g++;-GNinja" >> $GITHUB_ENV + elif [ "${{ matrix.os }}" == "macos-latest" ]; then + echo "SKBUILD_CMAKE_ARGS=-DCMAKE_CXX_COMPILER=clang++;-GNinja" >> $GITHUB_ENV + else + echo "SKBUILD_CMAKE_ARGS=-DCMAKE_CXX_COMPILER=clang-cl;-GNinja" >> $GITHUB_ENV + fi + + - name: Configure, build, install + run: | + python -m pip install -v .[test] + + - name: Test + run: | + python -m pytest -vvv --ignore=tests/test_fields.py --ignore=tests/test_functionality.py --ignore=tests/test_gradients.py --ignore=tests/test_solver.py diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 7653a670..a8c053c0 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -1,31 +1,140 @@ name: Publish package on: - push: - branches: [master] workflow_dispatch: + pull_request: + push: + branches: + - master + release: + types: + - published + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +env: + FORCE_COLOR: 3 jobs: - publish: + build_sdist: + name: Build source distribution runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 - - uses: actions/setup-python@v1 + - uses: actions/checkout@v4 with: - python-version: '3.7' - - name: Install setuptools and wheel - run: | - python -m pip install --user setuptools wheel - - name: Build a source tarball + fetch-depth: 0 # such that setuptools_scm can do its job correctly + + - name: Build SDist + run: pipx run build --sdist + + - uses: actions/upload-artifact@v4 + with: + name: cibw-sdist + path: dist/*.tar.gz + + generate-wheels-matrix: + name: Generate wheels matrix + runs-on: ubuntu-latest + outputs: + include: ${{ steps.set-matrix.outputs.include }} + steps: + - uses: actions/checkout@v4 + - name: Install cibuildwheel + run: pipx install cibuildwheel==2.19.2 + - id: set-matrix run: | - pip install pytest numpy h5py scipy pandas scikit-build pybind11 - pip install git+https://gitlab.com/reinholdt/polarizationsolver.git@master - python setup.py install - pytest --pyargs cppe - python setup.py sdist - - name: Publish distribution 📦 to Test PyPI - if: startsWith(github.ref, 'refs/tags') - uses: pypa/gh-action-pypi-publish@master - with: - user: __token__ - password: ${{ secrets.pypi_password }} + MATRIX=$( + { + cibuildwheel --print-build-identifiers --platform linux \ + | jq -nRc '{"only": inputs, "os": "ubuntu-latest"}' \ + && cibuildwheel --print-build-identifiers --platform macos \ + | jq -nRc '{"only": inputs, "os": "macos-latest"}' \ + && cibuildwheel --print-build-identifiers --platform windows \ + | jq -nRc '{"only": inputs, "os": "windows-latest"}' + } | jq -sc + ) + echo "Full build matrix" + echo "$MATRIX" + echo "include=$MATRIX" >> $GITHUB_OUTPUT + env: + CIBW_ARCHS_LINUX: x86_64 # aarch64 # skipping as h5py stopped providing pre-build wheels for aarch64 on PyPI + CIBW_ARCHS_MACOS: x86_64 arm64 + CIBW_ARCHS_WINDOWS: AMD64 + # skip musl builds + CIBW_SKIP: "*-musllinux_*" + # disable free-threaded support + CIBW_FREE_THREADED_SUPPORT: False + # exclude latest Python beta + CIBW_PRERELEASE_PYTHONS: False + + build_wheels: + name: Build ${{ matrix.only }} + needs: generate-wheels-matrix + strategy: + matrix: + include: ${{ fromJson(needs.generate-wheels-matrix.outputs.include) }} + runs-on: ${{ matrix.os }} + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 # such that setuptools_scm can do its job correctly + + - name: Set up QEMU + if: runner.os == 'Linux' + uses: docker/setup-qemu-action@v3 + with: + platforms: all + + # this will set the system compiler + - name: Set Windows env + if: matrix.os == 'windows-latest' + uses: ilammy/msvc-dev-cmd@v1 + + - uses: pypa/cibuildwheel@v2.19.2 + env: + # skip testing PyPy builds + CIBW_TEST_SKIP: "pp*" + + CIBW_ENVIRONMENT_LINUX: > + SKBUILD_CMAKE_ARGS="-DENABLE_ARCH_FLAGS=OFF;-DENABLE_OPENMP=OFF" + + CIBW_ENVIRONMENT_MACOS: > + SKBUILD_CMAKE_ARGS="-DENABLE_ARCH_FLAGS=OFF;-DENABLE_OPENMP=OFF" + + CIBW_ENVIRONMENT_WINDOWS: > + SKBUILD_CMAKE_ARGS="-GNinja;-DCMAKE_CXX_COMPILER=clang-cl;-DENABLE_ARCH_FLAGS=OFF;-DENABLE_OPENMP=OFF" + with: + only: ${{ matrix.only }} + + - name: Verify clean directory + run: git diff --exit-code + shell: bash + + - uses: actions/upload-artifact@v4 + with: + name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }} + path: ./wheelhouse/*.whl + + upload_all: + name: Upload if release + needs: + - build_wheels + - build_sdist + environment: pypi + permissions: + id-token: write + runs-on: ubuntu-latest + #if: github.event_name == 'release' && github.event.action == 'published' + + steps: + - uses: actions/download-artifact@v4 + with: + pattern: cibw-* + path: dist + merge-multiple: true + + - uses: pypa/gh-action-pypi-publish@release/v1 + with: + repository-url: https://test.pypi.org/legacy/ diff --git a/.gitignore b/.gitignore index c0cfe4d8..79d452a0 100644 --- a/.gitignore +++ b/.gitignore @@ -42,3 +42,6 @@ __pycache__ *.egg-info *.eggs .ipynb_checkpoints/ + +# autogenerated by setuptools-scm +_version.py diff --git a/CMakeLists.txt b/CMakeLists.txt index eb9cca86..5a394d49 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -2,8 +2,32 @@ cmake_minimum_required(VERSION 3.16...3.20) # project name -project(cppe LANGUAGES CXX VERSION 0.3.2) +project(cppe LANGUAGES CXX) +if(NOT SKBUILD) + message(WARNING "\ + This CMake file is meant to be executed using 'scikit-build'. Running + it directly will almost certainly not produce the desired result. If + you are a user trying to install this package, please use the command + below, which will install all necessary build dependencies, compile + the package in an isolated environment, and then install it. + ===================================================================== + $ pip install . + ===================================================================== + If you are a software developer, and this is your own package, then + it is usually much more efficient to install the build dependencies + in your environment once and use the following command that avoids + a costly creation of a new virtual environment at every compilation: + ===================================================================== + $ pip install scikit-build-core[pyproject] cmake ninja pybind11 setuptools_scm + $ pip install --no-build-isolation -ve . + ===================================================================== + You may optionally add -Ceditable.rebuild=true to auto-rebuild when + the package is imported. Otherwise, you need to re-run the above + after editing C++ files.") +endif() + +# Try to import all Python components potentially needed by nanobind # do not rebuild if rules (compiler flags) change set(CMAKE_SKIP_RULE_DEPENDENCY TRUE) @@ -47,7 +71,6 @@ endmacro() option_with_print(ENABLE_OPENMP "Enables OpenMP parallelization" ON) # included cmake modules -include(${PROJECT_SOURCE_DIR}/cmake/downloaded/autocmake_default_build_paths.cmake) include(${PROJECT_SOURCE_DIR}/cmake/downloaded/autocmake_safeguards.cmake) include(${PROJECT_SOURCE_DIR}/cmake/compiler_flags/CXXFlags.cmake) diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 3123c8ff..00000000 --- a/MANIFEST.in +++ /dev/null @@ -1,13 +0,0 @@ -# Exclude test stuff -global-exclude test_*.py -exclude tests -exclude scripts - -include README.md -include LICENSE* - -recursive-include cppe *.hh -recursive-include cppe *.cc - -include external/eigen3/Eigen/* -recursive-include external/eigen3/Eigen/src *.h diff --git a/cmake/compiler_flags/CXXFlags.cmake b/cmake/compiler_flags/CXXFlags.cmake index a84a8af2..71882281 100644 --- a/cmake/compiler_flags/CXXFlags.cmake +++ b/cmake/compiler_flags/CXXFlags.cmake @@ -64,6 +64,9 @@ if(ENABLE_ARCH_FLAGS) set(ARCH_FLAG "-march=native") endif() endif() + if(CMAKE_CXX_COMPILER_ID MATCHES MSVC) + set(ARCH_FLAG "/arch:AVX2") + endif() if(CMAKE_CXX_COMPILER_ID MATCHES Intel) set(ARCH_FLAG "-xHost") endif() @@ -73,3 +76,4 @@ set(CPPE_CXX_FLAGS "") include(${CMAKE_CURRENT_LIST_DIR}/GNU.CXX.cmake) include(${CMAKE_CURRENT_LIST_DIR}/Intel.CXX.cmake) include(${CMAKE_CURRENT_LIST_DIR}/Clang.CXX.cmake) +include(${CMAKE_CURRENT_LIST_DIR}/MSVC.CXX.cmake) diff --git a/cmake/compiler_flags/MSVC.CXX.cmake b/cmake/compiler_flags/MSVC.CXX.cmake new file mode 100644 index 00000000..df065da2 --- /dev/null +++ b/cmake/compiler_flags/MSVC.CXX.cmake @@ -0,0 +1,6 @@ +if(CMAKE_CXX_COMPILER_ID MATCHES MSVC) + set(CPPE_CXX_FLAGS "/W3 /EHsc /bigobj") + set(CMAKE_CXX_FLAGS_RELEASE "/O2") + set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "/O2") + set(CMAKE_CXX_FLAGS_DEBUG "/Od /W4") +endif() diff --git a/cmake/downloaded/autocmake_default_build_paths.cmake b/cmake/downloaded/autocmake_default_build_paths.cmake deleted file mode 100644 index 9000882f..00000000 --- a/cmake/downloaded/autocmake_default_build_paths.cmake +++ /dev/null @@ -1,19 +0,0 @@ -# (c) https://github.com/dev-cafe/autocmake/blob/master/AUTHORS.md -# licensed under BSD-3: https://github.com/dev-cafe/autocmake/blob/master/LICENSE - -#.rst: -# -# Sets binary and library output directories to ${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_BINDIR} -# and ${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR}, respectively. -# -# Variables modified:: -# -# CMAKE_ARCHIVE_OUTPUT_DIRECTORY -# CMAKE_LIBRARY_OUTPUT_DIRECTORY -# CMAKE_RUNTIME_OUTPUT_DIRECTORY - -include(GNUInstallDirs) - -set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR}) -set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR}) -set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_BINDIR}) diff --git a/pyproject.toml b/pyproject.toml index 93976541..27f3508c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,107 @@ [build-system] -requires = ["setuptools", "wheel", "scikit-build", "cmake", "ninja"] +requires = ["scikit-build-core >=0.8", "pybind11"] +build-backend = "scikit_build_core.build" +[project] +name = "cppe" +dynamic = ["version"] +description = "C++ and Python library for Polarizable Embedding" +readme = "README.md" +requires-python = ">=3.8" +authors = [ + { name = "Maximilian Scheurer", email = "maximilian.scheurer@iwr.uni-heidelberg.de" }, + { name = "Peter Reinholdt" }, + { name = "Michael F. Herbst" }, + { name = "Lori A. Burns" }, +] +classifiers = [ + "Development Status :: 5 - Production/Stable", + "License :: OSI Approved :: GNU Lesser", + "General Public License v3 (LGPLv3)", + "License :: Free For Educational Use", + "Intended Audience :: Science/Research", + "Topic :: Education", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3 :: Only", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Topic :: Scientific/Engineering :: Chemistry", +] + +[project.optional-dependencies] +test = [ + "pytest", + "numpy", + "h5py", + "scipy", + "pandas", + "polarizationsolver@git+https://gitlab.com/robertodr/polarizationsolver.git", +] + +[project.urls] +Homepage = "https://github.com/maxscheurer/cppe" +Source = "https://github.com/maxscheurer/cppe" +"Bug Tracker" = "https://github.com/maxscheurer/cppe/issues" +Changelog = "https://github.com/org/maxscheurer/releases" + +[tool.scikit-build] +# Protect the configuration against future changes in scikit-build-core +minimum-version = "0.8" + +# Setuptools-style build caching in a local directory +build-dir = "build/{wheel_tag}" + +# Build stable ABI wheels for CPython 3.12+ +wheel.py-api = "cp312" + +cmake.verbose = true +cmake.version = ">=3.16" +ninja.make-fallback = false +logging.level = "INFO" +metadata.version.provider = "scikit_build_core.metadata.setuptools_scm" +sdist.cmake = true +sdist.exclude = [".github", "scripts"] +sdist.include = [ + "src/cppe/_version.py", + "eigen3", +] + +[tool.setuptools_scm] +write_to = "src/cppe/_version.py" +fallback_version = "0.3.2" + +[tool.pytest.ini_options] +minversion = "6.0" +addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"] +xfail_strict = true +filterwarnings = ["error"] +log_cli_level = "INFO" +testpaths = [ + "tests", +] + +[tool.cibuildwheel] +# Necessary to see build output from the actual compilation +build-verbosity = 1 + +# Run pytest to ensure that the package was correctly built +test-command = "pytest {project}/tests" +test-requires = [ + "pytest", + "numpy", + "h5py", + "scipy", + "pandas", + "polarizationsolver@git+https://gitlab.com/robertodr/polarizationsolver.git", +] + +[tool.cibuildwheel.environment] +NINJA_STATUS = "[Built edge %f of %t in %e sec] " + +# Needed for full C++17 support +[tool.cibuildwheel.macos.environment] +MACOSX_DEPLOYMENT_TARGET = "10.14" diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 3a396883..00000000 --- a/requirements.txt +++ /dev/null @@ -1,2 +0,0 @@ ---index-url https://pypi.python.org/simple/ --e . diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 2f03264c..00000000 --- a/setup.cfg +++ /dev/null @@ -1,10 +0,0 @@ -[bumpversion] -current_version = 0.3.2 -commit = True -tag = True - -[bumpversion:file:CMakeLists.txt] - -[bumpversion:file:src/metadata.cc] - -[bumpversion:file:setup.py] diff --git a/setup.py b/setup.py deleted file mode 100755 index 5ad80009..00000000 --- a/setup.py +++ /dev/null @@ -1,199 +0,0 @@ -#!/usr/bin/env python3 - -"""Setup for cppe""" -import sys -import glob -import setuptools - -from setuptools import Extension, setup -from setuptools.command.build_ext import build_ext as BuildCommand - -try: - from sphinx.setup_command import BuildDoc as BuildSphinxDoc -except ImportError: - # No sphinx found -> make a dummy class - class BuildSphinxDoc(setuptools.Command): - user_options = [] - - def initialize_options(self): - pass - - def finalize_options(self): - pass - - -__version__ = "0.3.2" - - -def strip_readme(): - with open("README.md") as fp: - return "".join([line for line in fp if not line.startswith("= 2.2"], - install_requires=["pybind11 >= 2.2"], - tests_require=[ - "pytest", "numpy", "h5py", "scipy", "pandas" - ], - # extras_require={ - # "build_docs": ["sphinx>=2", "breathe", "sphinxcontrib-bibtex", - # "sphinx-automodapi"], - # }, - cmdclass={"build_ext": BuildExt, - # "build_docs": BuildDocs, - }, -) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 6c9b7203..ad3a8d40 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -1,13 +1,3 @@ -# define object library for sources common to C library and Python bindings -add_library(cppe-objs - OBJECT - metadata.cc - ) - -# create empty list of CPPE private header files -add_subdirectory(utils) -add_subdirectory(core) - # OpenMP if(ENABLE_OPENMP) find_package(OpenMP COMPONENTS CXX) @@ -16,11 +6,21 @@ if(ENABLE_OPENMP) endif() endif() +# define object library for sources +add_library(cppe-objs + OBJECT + "" + ) + +# create empty list of CPPE private header files +add_subdirectory(utils) +add_subdirectory(core) + # report on compiler flags in use message(STATUS "Configuring a ${CMAKE_BUILD_TYPE} build") string(TOUPPER ${CMAKE_BUILD_TYPE} _cmake_build_type_upper) -message(STATUS "C++ compiler flags") +message(STATUS "Compiler flags for ${CMAKE_CXX_COMPILER_ID}") message(STATUS " From environment : ${CMAKE_CXX_FLAGS}") message(STATUS " Build-type-specific : ${CMAKE_CXX_FLAGS_${_cmake_build_type_upper}}") message(STATUS " Vectorization flag : ${ARCH_FLAG}") @@ -29,14 +29,13 @@ message(STATUS " User-appended : ${EXTRA_CXXFLAGS}") message(STATUS " OpenMP parallelization : ${OpenMP_CXX_FLAGS}") # transform CPPE_CXX_FLAGS and EXTRA_CXXFLAGS to ;-separated lists -string(REPLACE " " ";" CPPE_CXX_FLAGS ${CPPE_CXX_FLAGS}) +if(DEFINED CPPE_CXX_FLAGS) + string(REPLACE " " ";" CPPE_CXX_FLAGS ${CPPE_CXX_FLAGS}) +endif() if(DEFINED EXTRA_CXXFLAGS) string(REPLACE " " ";" EXTRA_CXXFLAGS ${EXTRA_CXXFLAGS}) endif() -# Eigen3 -find_package(Eigen3 3.4 CONFIG REQUIRED) - # flags to prepend target_compile_options(cppe-objs BEFORE @@ -60,13 +59,40 @@ if(WIN32) ) endif() +# Eigen3 +find_package(Eigen3 3.4 CONFIG QUIET) +if(TARGET Eigen3::Eigen) + message(STATUS "Using Eigen3: ${EIGEN3_ROOT_DIR} (version ${Eigen3_VERSION})") +else() + message(STATUS "Suitable Eigen3 could not be located. Fetching and building!") + include(FetchContent) + + if(NOT SKBUILD_STATE STREQUAL "sdist" + AND EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/eigen3/CMakeLists.txt") + message(STATUS "Using integrated Eigen3") + set(FETCHCONTENT_FULLY_DISCONNECTED ON) + endif() + + FetchContent_Declare(eigen3 + QUIET + URL + https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz + SOURCE_DIR + ${CMAKE_CURRENT_SOURCE_DIR}/eigen3 + ) + + set(CMAKE_POLICY_DEFAULT_CMP0077 NEW) + set(BUILD_TESTING OFF) + set(CMAKE_C_COMPILER_WORKS ON) + set(CMAKE_Fortran_COMPILER_WORKS ON) + FetchContent_MakeAvailable(eigen3) +endif() + + target_link_libraries(cppe-objs PUBLIC Eigen3::Eigen $<$,$>:OpenMP::OpenMP_CXX> ) -# standard locations of libraries, headers, etc. -include(GNUInstallDirs) - add_subdirectory(python_iface) diff --git a/src/core/bmatrix.cc b/src/core/bmatrix.cc index 9936bdfc..47be0e86 100644 --- a/src/core/bmatrix.cc +++ b/src/core/bmatrix.cc @@ -13,7 +13,7 @@ Eigen::VectorXd BMatrix::apply(const Eigen::VectorXd& induced_moments) { int order = m_options.tree_expansion_order; double theta = m_options.theta; std::vector S(3 * m_n_polsites); - for (int i = 0; i < m_n_polsites; ++i) { + for (decltype(m_n_polsites) i = 0; i < m_n_polsites; ++i) { int l = i * 3; Eigen::Vector3d s = induced_moments.segment<3>(l); S[i * 3 + 0] = s(0); @@ -42,7 +42,7 @@ Eigen::VectorXd BMatrix::apply(const Eigen::VectorXd& induced_moments) { Eigen::VectorXd BMatrix::apply_diagonal_inverse(const Eigen::VectorXd& in) { Eigen::VectorXd ret = Eigen::VectorXd::Zero(3 * m_n_polsites); #pragma omp parallel for - for (int i = 0; i < m_n_polsites; ++i) { + for (decltype(m_n_polsites) i = 0; i < m_n_polsites; ++i) { int l = i * 3; Polarizability& alpha_i = m_polsites[i].get_polarizability(); ret.segment<3>(l) = alpha_i.get_matrix() * in.segment<3>(l); @@ -54,7 +54,7 @@ Eigen::VectorXd BMatrix::apply_diagonal(const Eigen::VectorXd& in) { Eigen::VectorXd ret = Eigen::VectorXd::Zero(3 * m_n_polsites); #pragma omp parallel for - for (int i = 0; i < m_n_polsites; ++i) { + for (decltype(m_n_polsites) i = 0; i < m_n_polsites; ++i) { int l = i * 3; ret.segment<3>(l) = m_alpha_inverse[i] * in.segment<3>(l); } @@ -64,10 +64,10 @@ Eigen::VectorXd BMatrix::apply_diagonal(const Eigen::VectorXd& in) { Eigen::MatrixXd BMatrix::to_dense_matrix() { Eigen::MatrixXd B = Eigen::MatrixXd::Zero(m_n_polsites * 3, m_n_polsites * 3); #pragma omp parallel for - for (int i = 0; i < m_n_polsites; ++i) { + for (decltype(m_n_polsites) i = 0; i < m_n_polsites; ++i) { int l = i * 3; Potential& pot1 = m_polsites[i]; - for (int j = 0; j < m_n_polsites; ++j) { + for (decltype(m_n_polsites) j = 0; j < m_n_polsites; ++j) { int m = j * 3; Potential& pot2 = m_polsites[j]; if (pot1.excludes_site(pot2.index) || i == j) continue; diff --git a/src/core/bmatrix.hh b/src/core/bmatrix.hh index 8839dcc3..ad88279e 100644 --- a/src/core/bmatrix.hh +++ b/src/core/bmatrix.hh @@ -27,7 +27,7 @@ class BMatrix { return p.get_polarizability().get_matrix().inverse(); }); #pragma omp parallel for - for (int i = 0; i < m_n_polsites; ++i) { + for (decltype(m_n_polsites) i = 0; i < m_n_polsites; ++i) { Potential& pot1 = m_polsites[i]; m_positions[i * 3 + 0] = pot1.m_x; m_positions[i * 3 + 1] = pot1.m_y; diff --git a/src/core/cppe_state.cc b/src/core/cppe_state.cc index 698fac62..dfe0e681 100644 --- a/src/core/cppe_state.cc +++ b/src/core/cppe_state.cc @@ -40,14 +40,14 @@ void CppeState::set_potentials(std::vector potentials) { m_positions = Eigen::MatrixXd::Zero(m_potentials.size(), 3); m_positions_polarizable = Eigen::MatrixXd::Zero(m_polarizable_sites, 3); - for (int i = 0; i < m_potentials.size(); ++i) { + for (auto i = 0; i < m_potentials.size(); ++i) { m_positions(i, 0) = m_potentials[i].m_x; m_positions(i, 1) = m_potentials[i].m_y; m_positions(i, 2) = m_potentials[i].m_z; } auto m_potentials_polarizable = get_polarizable_sites(m_potentials); - for (int i = 0; i < m_polarizable_sites; ++i) { + for (auto i = 0; i < m_polarizable_sites; ++i) { m_positions_polarizable(i, 0) = m_potentials_polarizable[i].m_x; m_positions_polarizable(i, 1) = m_potentials_polarizable[i].m_y; m_positions_polarizable(i, 2) = m_potentials_polarizable[i].m_z; @@ -114,13 +114,13 @@ Eigen::MatrixXd CppeState::induced_moments_eef() { Eigen::MatrixXd ret = Eigen::MatrixXd::Zero(m_polarizable_sites * 3, 3); Eigen::MatrixXd Fdn = Eigen::MatrixXd::Zero(m_polarizable_sites * 3, 3); - for (int s = 0; s < m_polarizable_sites; ++s) { + for (auto s = 0; s < m_polarizable_sites; ++s) { int l = 3 * s; Fdn(l, 0) = 1; Fdn(l + 1, 1) = 1; Fdn(l + 2, 2) = 1; } - for (int a = 0; a < 3; ++a) { + for (auto a = 0; a < 3; ++a) { Eigen::VectorXd ind_mom = Eigen::VectorXd::Zero(m_polarizable_sites * 3); ret.col(a) = ind.compute(Fdn.col(a), ind_mom, true); } diff --git a/src/core/electric_fields.cc b/src/core/electric_fields.cc index fd8d2e5f..7b67ba4b 100644 --- a/src/core/electric_fields.cc +++ b/src/core/electric_fields.cc @@ -38,9 +38,9 @@ Eigen::VectorXd multipole_derivative(int k, int l, const Eigen::Vector3d& Rji, for (z = k + l; z > -1; z--) { if (x + y + z != k + l) continue; i = xyz2idx(x, y, z); - for (int a = x; a > -1; a--) { - for (int b = y; b > -1; b--) { - for (int c = z; c > -1; c--) { + for (auto a = x; a > -1; a--) { + for (auto b = y; b > -1; b--) { + for (auto c = z; c > -1; c--) { if (a + b + c != k) continue; j = xyz2idx(a, b, c); m = xyz2idx(x - a, y - b, z - c); @@ -58,7 +58,7 @@ Eigen::VectorXd multipole_derivative(int k, int l, const Eigen::Vector3d& Rji, Eigen::VectorXd NuclearFields::compute() { Eigen::VectorXd nuc_fields = Eigen::VectorXd::Zero(3 * m_n_polsites); #pragma omp parallel for - for (size_t i = 0; i < m_n_polsites; i++) { + for (auto i = 0; i < m_n_polsites; i++) { size_t site_counter = 3 * i; Potential& potential = m_polsites[i]; Eigen::Vector3d site_position = potential.get_site_position(); @@ -78,11 +78,11 @@ Eigen::MatrixXd NuclearFields::nuclear_gradient() { int natoms = m_mol.size(); Eigen::MatrixXd grad = Eigen::MatrixXd::Zero(3 * natoms, 3 * m_n_polsites); #pragma omp parallel for - for (size_t i = 0; i < m_n_polsites; i++) { + for (auto i = 0; i < m_n_polsites; i++) { size_t site_counter = 3 * i; Potential& potential = m_polsites[i]; Eigen::Vector3d site_position = potential.get_site_position(); - for (int ai = 0; ai < natoms; ++ai) { + for (auto ai = 0; ai < natoms; ++ai) { auto& atom = m_mol[ai]; Eigen::Vector3d core_position = atom.get_position(); Eigen::Vector3d diff = site_position - core_position; @@ -120,7 +120,7 @@ Eigen::VectorXd MultipoleFields::compute() { } int max_order = 0; - for (int i = 0; i < n_sites; ++i) { + for (auto i = 0; i < n_sites; ++i) { int max_multipole_order = m_potentials[i].max_multipole_order(); if (max_multipole_order > max_order) { max_order = max_multipole_order; @@ -210,7 +210,7 @@ Eigen::VectorXd InducedMoments::compute(const Eigen::VectorXd& rhs, Eigen::Vecto std::vector x{x0}; std::vector r{r0}; std::vector z{z0}; - for (int k = 0; k < m_options.maxiter; ++k) { + for (auto k = 0; k < m_options.maxiter; ++k) { Eigen::VectorXd Ap = bmat.apply(p); alpha_k = r[k].dot(z[k]) / p.dot(Ap); x_k1 = x[k] + alpha_k * p; diff --git a/src/core/fmm/calculate.cc b/src/core/fmm/calculate.cc index a4b4950b..3d6d2342 100644 --- a/src/core/fmm/calculate.cc +++ b/src/core/fmm/calculate.cc @@ -14,7 +14,7 @@ using namespace libcppe; void M_sanity_check(const std::vector& cells) { double M0 = 0; - for (size_t c = 1; c < cells.size(); c++) { + for (auto c = 1; c < cells.size(); c++) { if (cells[c].nchild == 0) { M0 += cells[c].M[0]; } @@ -31,9 +31,9 @@ void P2P_Cells(size_t A, size_t B, std::vector& cells, std::vector& particles, double* F) { // A - target // B - source - for (size_t p1 = 0; p1 < cells[A].nleaf; p1++) { + for (auto p1 = 0; p1 < cells[A].nleaf; p1++) { size_t l1 = cells[A].leaf[p1]; - for (size_t p2 = 0; p2 < cells[B].nleaf; p2++) { + for (auto p2 = 0; p2 < cells[B].nleaf; p2++) { size_t l2 = cells[B].leaf[p2]; if (l2 != l1 && !particles[l1].excludes_particle(l2)) { double dx = (particles[l1].r[0] - particles[l2].r[0]); @@ -50,9 +50,9 @@ void P2P_Cells_damping(size_t A, size_t B, std::vector& cells, std::vector& particles, double* F, double damping) { // A - target // B - source - for (size_t p1 = 0; p1 < cells[A].nleaf; p1++) { + for (auto p1 = 0; p1 < cells[A].nleaf; p1++) { size_t l1 = cells[A].leaf[p1]; - for (size_t p2 = 0; p2 < cells[B].nleaf; p2++) { + for (auto p2 = 0; p2 < cells[B].nleaf; p2++) { size_t l2 = cells[B].leaf[p2]; if (l2 != l1 && !particles[l1].excludes_particle(l2)) { double dx = (particles[l1].r[0] - particles[l2].r[0]); @@ -104,7 +104,7 @@ void interact_dehnen_lazy(const size_t A, const size_t B, const std::vector= cells[B].rmax && cells[A].nchild != 0)) { - for (int oa = 0; oa < 8; oa++) { + for (auto oa = 0; oa < 8; oa++) { // For all 8 children of A, if child exists if (cells[A].nchild & (1 << oa)) { int a = cells[A].child[oa]; @@ -115,7 +115,7 @@ void interact_dehnen_lazy(const size_t A, const size_t B, const std::vector& particles, std::vector& cells, si size_t ncrit, size_t exporder) { int sourcesize = multipole_components(m_order); #pragma omp for - for (size_t c = 0; c < cells.size(); c++) { + for (auto c = 0; c < cells.size(); c++) { // std::cout << "Cell " << c << std::endl; // std::cout << " Msize = " << Msize(exporder, FMMGEN_SOURCEORDER) << std::endl; size_t msize = Msize(exporder, m_order); double* M = new double[msize](); if (cells[c].nleaf < ncrit) { - for (size_t i = 0; i < cells[c].nleaf; i++) { + for (auto i = 0; i < cells[c].nleaf; i++) { size_t l = cells[c].leaf[i]; // Walter dehnen's definition: // (-1)^m / m! (x_a - z_a)^m double dx = (cells[c].x - particles[l].r[0]); double dy = (cells[c].y - particles[l].r[1]); double dz = (cells[c].z - particles[l].r[2]); - for (int k = 0; k < sourcesize; k++) { + for (auto k = 0; k < sourcesize; k++) { // std::cout << particles[l].S[k] << std::endl; M[k] = particles[l].S[k]; } @@ -174,7 +174,7 @@ void evaluate_M2M(std::vector& particles, std::vector& cells, // Dehnen definition: // M_m(z_p) = (z_p - z_c)^n / n! M_{m - n} - for (size_t c = cells.size() - 1; c > 0; c--) { + for (auto c = cells.size() - 1; c > 0; c--) { size_t p = cells[c].parent; double dx = (cells[p].x - cells[c].x); double dy = (cells[p].y - cells[c].y); @@ -187,7 +187,7 @@ template void evaluate_M2L_lazy(std::vector& cells, std::vector>& M2L_list, size_t order) { #pragma omp for - for (size_t i = 0; i < M2L_list.size(); i++) { + for (auto i = 0; i < M2L_list.size(); i++) { size_t B = M2L_list[i].first; size_t A = M2L_list[i].second; // Dehnen definition: @@ -209,14 +209,14 @@ void evaluate_P2P_lazy(std::vector& cells, std::vector& particle if (damping > 0.0) { #pragma omp for - for (size_t i = 0; i < P2P_list.size(); i++) { + for (auto i = 0; i < P2P_list.size(); i++) { size_t A = P2P_list[i].first; size_t B = P2P_list[i].second; P2P_Cells_damping(A, B, cells, particles, F, damping); } } else { #pragma omp for - for (size_t i = 0; i < P2P_list.size(); i++) { + for (auto i = 0; i < P2P_list.size(); i++) { size_t A = P2P_list[i].first; size_t B = P2P_list[i].second; P2P_Cells(A, B, cells, particles, F); @@ -228,8 +228,8 @@ template void evaluate_L2L(std::vector& cells, size_t exporder) { // Can't currently go down the tree in parallel! // needs to be recursive or summing not correct. - for (size_t p = 0; p < cells.size(); p++) { - for (int octant = 0; octant < 8; octant++) { + for (auto p = 0; p < cells.size(); p++) { + for (auto octant = 0; octant < 8; octant++) { if (cells[p].nchild & (1 << octant)) { // for child c in cell p size_t c = cells[p].child[octant]; @@ -246,9 +246,9 @@ template void evaluate_L2P(std::vector& particles, std::vector& cells, double* F, size_t ncrit, size_t exporder) { #pragma omp for schedule(runtime) - for (size_t i = 0; i < cells.size(); i++) { + for (auto i = 0; i < cells.size(); i++) { if (cells[i].nleaf < ncrit) { - for (size_t p = 0; p < cells[i].nleaf; p++) { + for (auto p = 0; p < cells[i].nleaf; p++) { size_t k = cells[i].leaf[p]; double dx = particles[k].r[0] - cells[i].x; double dy = particles[k].r[1] - cells[i].y; @@ -263,8 +263,8 @@ template void evaluate_direct(std::vector& particles, double* F) { int n = particles.size(); #pragma omp parallel for schedule(runtime) - for (size_t i = 0; i < n; i++) { - for (size_t j = 0; j < n; j++) { + for (auto i = 0; i < n; i++) { + for (auto j = 0; j < n; j++) { if (i != j && !particles[i].excludes_particle(j)) { double dx = particles[i].r[0] - particles[j].r[0]; double dy = particles[i].r[1] - particles[j].r[1]; @@ -280,8 +280,8 @@ void evaluate_direct_damping(std::vector& particles, double* F, double damping) { int n = particles.size(); #pragma omp parallel for schedule(runtime) - for (size_t i = 0; i < n; i++) { - for (size_t j = 0; j < n; j++) { + for (auto i = 0; i < n; i++) { + for (auto j = 0; j < n; j++) { if (i != j && !particles[i].excludes_particle(j)) { double dx = particles[i].r[0] - particles[j].r[0]; double dy = particles[i].r[1] - particles[j].r[1]; @@ -397,4 +397,4 @@ void evaluate_M2P_and_P2P(std::vector& particles, unsigned int p, INSTANTIATE(0, 3) INSTANTIATE(1, 3) -INSTANTIATE(2, 3) \ No newline at end of file +INSTANTIATE(2, 3) diff --git a/src/core/fmm/tree.cc b/src/core/fmm/tree.cc index 4c9e9ebf..69351fb0 100644 --- a/src/core/fmm/tree.cc +++ b/src/core/fmm/tree.cc @@ -63,20 +63,20 @@ Cell::Cell(Cell&& other) { } void printTreeParticles(std::vector& cells, size_t cell, size_t depth) { - for (size_t i = 0; i < depth; i++) { + for (auto i = 0; i < depth; i++) { std::cout << " "; } std::cout << cell << " (" << cells[cell].x << "," << cells[cell].y << "," << cells[cell].z << ") : ("; size_t nchild = 0; - for (size_t octant = 0; octant < 8; octant++) { + for (auto octant = 0; octant < 8; octant++) { if (cells[cell].nchild & (1 << octant)) { nchild += 1; } } if (nchild == 0) { - for (size_t i = 0; i < cells[cell].nleaf; i++) { + for (auto i = 0; i < cells[cell].nleaf; i++) { std::cout << cells[cell].leaf[i]; if (i != (cells[cell].nleaf - 1)) { std::cout << ","; @@ -84,7 +84,7 @@ void printTreeParticles(std::vector& cells, size_t cell, size_t depth) { } } std::cout << ")" << std::endl; - for (size_t octant = 0; octant < 8; octant++) { + for (auto octant = 0; octant < 8; octant++) { if (cells[cell].nchild & (1 << octant)) { printTreeParticles(cells, cells[cell].child[octant], depth + 1); } @@ -114,7 +114,7 @@ void split_cell(std::vector& cells, std::vector& particles, size // Do not change octant to size_t - otherwise the calculation // of x, y, z position in add_child is not correct! int octant; - for (size_t i = 0; i < cells[p].leaf.size(); i++) { + for (auto i = 0; i < cells[p].leaf.size(); i++) { l = cells[p].leaf[i]; octant = (particles[l].r[0] > cells[p].x) + ((particles[l].r[1] > cells[p].y) << 1) + ((particles[l].r[2] > cells[p].z) << 2); @@ -139,7 +139,7 @@ std::shared_ptr> build_shared_tree( int nparticles = potentials.size(); std::vector particles(nparticles); bool damping_enabled = damping > 0.0; - for (size_t i = 0; i < nparticles; i++) { + for (auto i = 0; i < nparticles; i++) { particles[i].r = potentials[i].ptr_position(); particles[i].S = &S[sourcesize * i]; particles[i].exclusions = potentials[i].get_exclusions(); @@ -157,7 +157,7 @@ std::shared_ptr> build_shared_tree( double xavg = 0; double yavg = 0; double zavg = 0; - for (size_t i = 0; i < particles.size(); i++) { + for (auto i = 0; i < particles.size(); i++) { xavg += particles[i].r[0]; yavg += particles[i].r[1]; zavg += particles[i].r[2]; @@ -174,7 +174,7 @@ std::shared_ptr> build_shared_tree( double ymax = 0; double zmax = 0; - for (size_t i = 0; i < particles.size(); i++) { + for (auto i = 0; i < particles.size(); i++) { double x = std::abs(particles[i].r[0] - xavg); double y = std::abs(particles[i].r[1] - yavg); double z = std::abs(particles[i].r[2] - zavg); @@ -189,7 +189,7 @@ std::shared_ptr> build_shared_tree( auto root = Cell(xavg, yavg, zavg, r, 0, order, 0, ncrit); cells.push_back(root); - for (size_t i = 0; i < particles.size(); i++) { + for (auto i = 0; i < particles.size(); i++) { curr = 0; while (cells[curr].nleaf >= ncrit) { cells[curr].nleaf += 1; @@ -229,7 +229,7 @@ std::shared_ptr> build_shared_tree( // Create memory into which each cell can point for the multipole arrays. tree->M.resize(tree->cells.size() * Msize(order, m_order), 0.0); tree->L.resize(tree->cells.size() * Lsize(order, m_order), 0.0); - for (size_t i = 0; i < tree->cells.size(); i++) { + for (auto i = 0; i < tree->cells.size(); i++) { tree->cells[i].M = &tree->M[i * Msize(order, m_order)]; tree->cells[i].L = &tree->L[i * Lsize(order, m_order)]; } @@ -243,7 +243,7 @@ std::shared_ptr> build_shared_tree( int sourcesize = multipole_components(m_order); // Create particles list for convenience std::vector particles(nparticles); - for (size_t i = 0; i < nparticles; i++) { + for (auto i = 0; i < nparticles; i++) { particles[i].r = &pos[3 * i]; particles[i].S = &S[sourcesize * i]; particles[i].exclusions = exclusion_lists[i]; @@ -258,7 +258,7 @@ std::shared_ptr> build_shared_tree( double xavg = 0; double yavg = 0; double zavg = 0; - for (size_t i = 0; i < particles.size(); i++) { + for (auto i = 0; i < particles.size(); i++) { xavg += particles[i].r[0]; yavg += particles[i].r[1]; zavg += particles[i].r[2]; @@ -275,7 +275,7 @@ std::shared_ptr> build_shared_tree( double ymax = 0; double zmax = 0; - for (size_t i = 0; i < particles.size(); i++) { + for (auto i = 0; i < particles.size(); i++) { double x = std::abs(particles[i].r[0] - xavg); double y = std::abs(particles[i].r[1] - yavg); double z = std::abs(particles[i].r[2] - zavg); @@ -290,7 +290,7 @@ std::shared_ptr> build_shared_tree( auto root = Cell(xavg, yavg, zavg, r, 0, order, 0, ncrit); cells.push_back(root); - for (size_t i = 0; i < particles.size(); i++) { + for (auto i = 0; i < particles.size(); i++) { curr = 0; while (cells[curr].nleaf >= ncrit) { cells[curr].nleaf += 1; @@ -329,7 +329,7 @@ std::shared_ptr> build_shared_tree( // Create memory into which each cell can point for the multipole arrays. tree->M.resize(tree->cells.size() * Msize(order, m_order), 0.0); tree->L.resize(tree->cells.size() * Lsize(order, m_order), 0.0); - for (size_t i = 0; i < tree->cells.size(); i++) { + for (auto i = 0; i < tree->cells.size(); i++) { tree->cells[i].M = &tree->M[i * Msize(order, m_order)]; tree->cells[i].L = &tree->L[i * Lsize(order, m_order)]; } @@ -351,7 +351,7 @@ void Tree::set_sources(double* S) { int sourcesize = multipole_components(m_order); clear_M(); clear_L(); - for (size_t i = 0; i < particles.size(); i++) { + for (auto i = 0; i < particles.size(); i++) { particles[i].S = &S[sourcesize * i]; } } @@ -359,7 +359,7 @@ void Tree::set_sources(double* S) { template void Tree::compute_field_fmm(double* F) { // std::cout << "Computing FMM fields." << std::endl; - for (size_t i = 0; i < osize * particles.size(); i++) { + for (auto i = 0; i < osize * particles.size(); i++) { F[i] = 0.0; } clear_M(); diff --git a/src/core/fmm/utils.cc b/src/core/fmm/utils.cc index 8391b282..bef8bad1 100644 --- a/src/core/fmm/utils.cc +++ b/src/core/fmm/utils.cc @@ -4,7 +4,7 @@ size_t TriangleNumbers(size_t n) { return (n * (n + 1)) / 2; } size_t Nterms(size_t p) { size_t result = 0; - for (size_t i = 0; i < p + 2; i++) { + for (auto i = 0; i < p + 2; i++) { result += TriangleNumbers(i); } return result; diff --git a/src/core/math.cc b/src/core/math.cc index 59b18356..23883b21 100644 --- a/src/core/math.cc +++ b/src/core/math.cc @@ -33,7 +33,7 @@ Eigen::VectorXd mat_to_triangle(Eigen::Matrix3d m) { double factorial(int n) { if (n < 2) return 1.0; double x = 1.0; - for (int i = 2; i <= n; i++) x *= double(i); + for (auto i = 2; i <= n; i++) x *= double(i); return x; } @@ -75,7 +75,7 @@ std::vector prefactors(unsigned k) { // changed signs here because electron charges are included downstream // (integral library) std::vector pref = symmetry_factors(k); - for (size_t i = 0; i < pref.size(); i++) { + for (auto i = 0; i < pref.size(); i++) { pref[i] *= taylor; } return pref; @@ -90,7 +90,7 @@ std::vector prefactors_nuclei(unsigned k) { } std::vector pf = symmetry_factors(k); - for (size_t i = 0; i < pf.size(); i++) { + for (auto i = 0; i < pf.size(); i++) { pf[i] *= taylor; } return pf; diff --git a/src/core/multipole_expansion.cc b/src/core/multipole_expansion.cc index 0988f93f..f9541bce 100644 --- a/src/core/multipole_expansion.cc +++ b/src/core/multipole_expansion.cc @@ -12,7 +12,7 @@ double MultipoleExpansion::interaction_energy() { int npots = m_potentials.size(); #pragma omp parallel for reduction(+ : total_energy) - for (size_t i = 0; i < npots; i++) { + for (auto i = 0; i < npots; i++) { Potential& potential = m_potentials[i]; Eigen::Vector3d site_position = potential.get_site_position(); for (auto& multipole : potential.get_multipoles()) { @@ -38,7 +38,7 @@ Eigen::MatrixXd MultipoleExpansion::nuclear_gradient() { Eigen::MatrixXd grad = Eigen::MatrixXd::Zero(natoms, 3); #pragma omp parallel for - for (size_t i = 0; i < npots; i++) { + for (auto i = 0; i < npots; i++) { Potential& potential = m_potentials[i]; Eigen::Vector3d site_position = potential.get_site_position(); for (auto& multipole : potential.get_multipoles()) { @@ -47,7 +47,7 @@ Eigen::MatrixXd MultipoleExpansion::nuclear_gradient() { Eigen::VectorXd pref_v = Eigen::Map(std::move(pref.data()), pref.size()); Eigen::VectorXd mul_v = multipole.get_values_vec(); - for (int ai = 0; ai < natoms; ++ai) { + for (auto ai = 0; ai < natoms; ++ai) { auto& atom = m_mol[ai]; Eigen::Vector3d core_position = atom.get_position(); Eigen::Vector3d diff = core_position - site_position; diff --git a/src/core/pot_manipulation.cc b/src/core/pot_manipulation.cc index 7198c1e5..613e44ec 100644 --- a/src/core/pot_manipulation.cc +++ b/src/core/pot_manipulation.cc @@ -73,7 +73,7 @@ std::vector PotManipulator::manipulate_border(const PeOptions& pe_opt neighbor_list.push_back(std::pair(pot.index, dist)); } sort(neighbor_list.begin(), neighbor_list.end(), sortbysec); - for (int k = 0; k < nredist; ++k) { + for (auto k = 0; k < nredist; ++k) { Potential& pot = m_potentials[neighbor_list[k].first]; if (pot.index == site) continue; m_printer(" to neighbor " + std::to_string(pot.index)); @@ -89,7 +89,7 @@ std::vector PotManipulator::manipulate_border(const PeOptions& pe_opt } else { // std::cout << "Before: " << std::endl; // std::cout << m.get_values_vec() << std::endl; - for (size_t i = 0; i < multipole_components(m.m_k); i++) { + for (auto i = 0; i < multipole_components(m.m_k); i++) { m.get_values()[i] += m_potentials[site].get_multipoles()[m_idx].get_values()[i] / static_cast(nredist); diff --git a/src/core/potfile_reader.cc b/src/core/potfile_reader.cc index 9c13fa05..aa10e5b4 100644 --- a/src/core/potfile_reader.cc +++ b/src/core/potfile_reader.cc @@ -57,7 +57,7 @@ std::vector PotfileReader::read() { throw std::runtime_error("Invalid unit for potential file."); } - for (size_t i = 0; i < num_sites; i++) { + for (auto i = 0; i < num_sites; i++) { Site site; getline(infile, line); std::vector temp = split(reduce(line), ' '); @@ -81,7 +81,7 @@ std::vector PotfileReader::read() { getline(infile, line); int num_multipoles = stoi(line); int site_before = -1; - for (size_t n_mul = 0; n_mul < num_multipoles; n_mul++) { + for (auto n_mul = 0; n_mul < num_multipoles; n_mul++) { getline(infile, line); temp = split(reduce(line), ' '); int site_num = stoi(temp[0]) - 1; @@ -89,9 +89,9 @@ std::vector PotfileReader::read() { // fill up the array if values were not defined for all sites if (site_num != site_before + 1) { int diff = site_num - site_before; - for (size_t d = 1; d < diff; d++) { + for (auto d = 1; d < diff; d++) { Multipole mul(order); - for (size_t vl = 1; vl <= multipole_components(order); vl++) { + for (auto vl = 1; vl <= multipole_components(order); vl++) { mul.add_value(0.0); } potentials[site_before + d].add_multipole(mul); @@ -99,7 +99,7 @@ std::vector PotfileReader::read() { } Multipole mul(order); - for (size_t vl = 1; vl <= multipole_components(order); vl++) { + for (auto vl = 1; vl <= multipole_components(order); vl++) { mul.add_value(stod(temp[vl])); } mul.remove_trace(); @@ -109,9 +109,9 @@ std::vector PotfileReader::read() { // check if multipoles at the end of the list are missing if ((n_mul == num_multipoles - 1) && site_num != (num_sites - 1)) { int diff = num_sites - site_num; - for (size_t d = 1; d < diff; d++) { + for (auto d = 1; d < diff; d++) { Multipole mul(order); - for (size_t vl = 1; vl <= multipole_components(order); vl++) { + for (auto vl = 1; vl <= multipole_components(order); vl++) { mul.add_value(0.0); } potentials[site_num + d].add_multipole(mul); @@ -128,14 +128,14 @@ std::vector PotfileReader::read() { } getline(infile, line); int num_polarizabilities = stoi(line); - for (size_t n_pol = 0; n_pol < num_polarizabilities; n_pol++) { + for (auto n_pol = 0; n_pol < num_polarizabilities; n_pol++) { getline(infile, line); temp = split(reduce(line), ' '); int site_num = stoi(temp[0]) - 1; // std::cout << site.x << " " << site.y << " " << site.z << " " << // site_num + 1 << std::endl; std::vector pol_tmp; - for (size_t vl = 1; vl <= multipole_components(order1 + order2); vl++) { + for (auto vl = 1; vl <= multipole_components(order1 + order2); vl++) { pol_tmp.push_back(stod(temp[vl])); } Polarizability pol{pol_tmp}; @@ -152,7 +152,7 @@ std::vector PotfileReader::read() { getline(infile, line); int num_excl = stoi(split(line, ' ')[0]); std::vector temp; - for (size_t i = 0; i < num_excl; i++) { + for (auto i = 0; i < num_excl; i++) { getline(infile, line); temp = split(reduce(line), ' '); int site_num = stoi(temp[0]) - 1; diff --git a/src/core/tensors/tensors_recursive.cc b/src/core/tensors/tensors_recursive.cc index 9288bb1b..727e2b6d 100644 --- a/src/core/tensors/tensors_recursive.cc +++ b/src/core/tensors/tensors_recursive.cc @@ -24,9 +24,9 @@ Eigen::VectorXd T_recursive(int k, const Eigen::Vector3d& Rij, double damping_fa int xyz2idx(int x, int y, int z) { int idx = 0; int k = x + y + z; - for (int a = k; a > -1; a--) { - for (int b = k; b > -1; b--) { - for (int c = k; c > -1; c--) { + for (auto a = k; a > -1; a--) { + for (auto b = k; b > -1; b--) { + for (auto c = k; c > -1; c--) { if (a + b + c != k) continue; if (a != x || b != y || c != z) { idx++; @@ -55,11 +55,11 @@ double T(const Eigen::Vector3d& Rij, int x, int y, int z, scr_facs = thole_screening_factors(R * damping_factor, k); } - for (size_t l = 0; l <= x; l++) { + for (auto l = 0; l <= x; l++) { Cx = Cijn[0](x, l) * pow((Rij(0) / R), l); - for (size_t m = 0; m <= y; m++) { + for (auto m = 0; m <= y; m++) { Cy = Cx * Cijn[l + x](y, m) * pow((Rij(1) / R), m); - for (size_t n = 0; n <= z; n++) { + for (auto n = 0; n <= z; n++) { Cz = Cy * Cijn[l + x + m + y](z, n) * pow((Rij(2) / R), n); int kk = l + m + n; // Thole damping @@ -116,7 +116,7 @@ std::vector thole_screening_factors(double v, int k) { std::vector Tk_coefficients(int max_order) { int maxi = 2 * max_order + 3; std::vector Cijn; - for (int n = 0; n < maxi; ++n) { + for (auto n = 0; n < maxi; ++n) { int k; Eigen::MatrixXi mat = Eigen::MatrixXi::Zero(max_order + 2, max_order + 2); mat(0, 0) = 1; @@ -124,13 +124,13 @@ std::vector Tk_coefficients(int max_order) { Cijn.push_back(mat); continue; } - for (size_t i = 1; i <= max_order + 1; i++) { + for (auto i = 1; i <= max_order + 1; i++) { if (i % 2 != 0) { k = i - 1; } else if (i % 2 == 0) { k = i; } - for (size_t j = 0; j <= i; j++) { + for (auto j = 0; j <= i; j++) { if ((i + j) % 2 != 0) continue; if (j == 0) { mat(i, j) = mat(i - 1, j + 1); diff --git a/src/cppe/__init__.py b/src/cppe/__init__.py new file mode 100644 index 00000000..293272cc --- /dev/null +++ b/src/cppe/__init__.py @@ -0,0 +1,8 @@ +from .pycppe import * +from .pycppe import __build_type__, __parallel__ +from .pycppe.tensors import * + +all = [ + "__build_type__", + "__parallel__", +] diff --git a/src/metadata.cc b/src/metadata.cc deleted file mode 100644 index 2f24dd7d..00000000 --- a/src/metadata.cc +++ /dev/null @@ -1,54 +0,0 @@ -#include "metadata.hh" -#include -#include - -namespace libcppe { -namespace { -static const std::string static_version_string = "0.3.2"; - -static const std::vector version_split = [](const std::string& in) { - std::vector parts; - std::stringstream ss(in); - std::string item; - while (std::getline(ss, item, '.')) parts.push_back(item); - return parts; -}(static_version_string); - -static int get_version_part(size_t part) { - int ret; - std::stringstream ss(version_split[part]); - ss >> ret; - return ret; -} -} // namespace - -int version::major_part() { return get_version_part(0); } -int version::minor_part() { return get_version_part(1); } -int version::patch_part() { return get_version_part(2); } -bool version::is_debug() { -#ifdef NDEBUG - return false; -#else - return true; -#endif // NDEBUG -} - -bool version::has_openmp() { -#ifdef _OPENMP - return true; -#else - return false; -#endif -} - -std::string version::version_string() { return static_version_string; } - -std::string __authors__() { return "Maximilian Scheurer"; } - -std::string __contributors__() { - return "Peter Reinholdt, Michael F. Herbst, Lori A. Burns"; -} - -std::string __email__() { return "maximilian.scheurer@iwr.uni-heidelberg.de"; } - -} // namespace libcppe \ No newline at end of file diff --git a/src/metadata.hh b/src/metadata.hh deleted file mode 100644 index ac8c87ed..00000000 --- a/src/metadata.hh +++ /dev/null @@ -1,36 +0,0 @@ -#pragma once -#include -#include - -namespace libcppe { - -struct version { - /** Return the major part of the version */ - static int major_part(); - - /** Return the minor part of the version */ - static int minor_part(); - - /** Return the patch part of the version */ - static int patch_part(); - - /** Is the compiled version a Debug version */ - static bool is_debug(); - - /** Is the compiled version using OpenMP */ - static bool has_openmp(); - - /** Return the version as a string */ - static std::string version_string(); -}; - -/** Return the authors string */ -std::string __authors__(); - -/** Return the contributors string */ -std::string __contributors__(); - -/** Return the email string */ -std::string __email__(); - -} // namespace libcppe diff --git a/src/python_iface/CMakeLists.txt b/src/python_iface/CMakeLists.txt index c54832bd..d09d7164 100644 --- a/src/python_iface/CMakeLists.txt +++ b/src/python_iface/CMakeLists.txt @@ -1,31 +1,13 @@ -find_package(Python 3.8 REQUIRED COMPONENTS Interpreter Development) - -# figure out where to put the Python module -if(NOT DEFINED PYMOD_INSTALL_FULLDIR) - if(NOT WIN32) - set(PYMOD_INSTALL_FULLDIR - "lib/python${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}/site-packages/cppe" - CACHE STRING - "Location under CMAKE_INSTALL_PREFIX to which Python modules are installed" - FORCE - ) - else() - set(PYMOD_INSTALL_FULLDIR - "Lib/site-packages/cppe" - CACHE STRING - "Location under CMAKE_INSTALL_PREFIX to which Python modules are installed" - FORCE - ) - endif() -endif() -message(STATUS "Setting PYMOD_INSTALL_FULLDIR: ${PYMOD_INSTALL_FULLDIR}") -file(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/${PYMOD_INSTALL_FULLDIR}) +find_package(Python 3.8 + REQUIRED COMPONENTS Interpreter Development.Module + OPTIONAL_COMPONENTS Development.SABIModule + ) find_package(pybind11 2.6 CONFIG REQUIRED) pybind11_add_module(pycppe MODULE - THIN_LTO + NO_EXTRAS export_molecule.cc export_potential.cc export_fields.cc @@ -42,62 +24,9 @@ target_link_libraries(pycppe cppe-objs ) -set_target_properties(pycppe - PROPERTIES - ARCHIVE_OUTPUT_DIRECTORY - ${PROJECT_BINARY_DIR}/${PYMOD_INSTALL_FULLDIR} - LIBRARY_OUTPUT_DIRECTORY - ${PROJECT_BINARY_DIR}/${PYMOD_INSTALL_FULLDIR} - RUNTIME_OUTPUT_DIRECTORY - ${PROJECT_BINARY_DIR}/${PYMOD_INSTALL_FULLDIR} - ) - -# we glob the Python files in this folder and let CMake add a rule such that -# the glob is repeated every time we rebuild. -# This is NOT RECOMMENDED by CMake -# (https://cmake.org/cmake/help/v3.16/command/file.html#filesystem) but you only -# live once! -file( - GLOB - _pys - LIST_DIRECTORIES - FALSE - CONFIGURE_DEPENDS - ${CMAKE_CURRENT_SOURCE_DIR}/*.py - ) - -# link the Python files under the build folder -foreach(_py IN LISTS _pys) - get_filename_component(__py ${_py} NAME) - file( - CREATE_LINK - ${_py} - ${PROJECT_BINARY_DIR}/${PYMOD_INSTALL_FULLDIR}/${__py} - COPY_ON_ERROR - SYMBOLIC - ) -endforeach() - install( TARGETS pycppe - DESTINATION - ${PYMOD_INSTALL_FULLDIR} - ) - -install( - FILES - ${_pys} - DESTINATION - ${PYMOD_INSTALL_FULLDIR} - ) - -# install the Python tests -install( - DIRECTORY - ${PROJECT_SOURCE_DIR}/tests/ - DESTINATION - ${PYMOD_INSTALL_FULLDIR}/tests - PATTERN "CMakeLists.txt" EXCLUDE - PATTERN "__pycache__" EXCLUDE + LIBRARY DESTINATION + cppe ) diff --git a/src/python_iface/__init__.py b/src/python_iface/__init__.py deleted file mode 100644 index 76ee7471..00000000 --- a/src/python_iface/__init__.py +++ /dev/null @@ -1,15 +0,0 @@ -from .pycppe import * -from .pycppe.tensors import * -from .pycppe import ( - __version__, __build_type__, __authors__, __contributors__, __email__, - __parallel__, -) - -all = [ - "__version__", - "__build_type__", - "__parallel__", - "__authors__", - "__contributors__", - "__email__", -] diff --git a/src/python_iface/export_cppe.cc b/src/python_iface/export_cppe.cc index 3d44e857..aaff9a82 100644 --- a/src/python_iface/export_cppe.cc +++ b/src/python_iface/export_cppe.cc @@ -1,4 +1,3 @@ -#include "../metadata.hh" #include namespace py = pybind11; @@ -13,13 +12,21 @@ void export_tensors(py::module&); void export_fmm(py::module&); PYBIND11_MODULE(pycppe, cppe) { - cppe.doc() = "Python interface for CPPE"; - cppe.attr("__version__") = libcppe::version::version_string(); - cppe.attr("__build_type__") = libcppe::version::is_debug() ? "Debug" : "Release"; - cppe.attr("__parallel__") = libcppe::version::has_openmp(); - cppe.attr("__authors__") = libcppe::__authors__(); - cppe.attr("__contributors__") = libcppe::__contributors__(); - cppe.attr("__email__") = libcppe::__email__(); + cppe.doc() = "Python interface for CPPE"; + cppe.attr("__build_type__") = [] { +#ifdef NDEBUG + return "Release"; +#else + return "Debug"; +#endif + }(); + cppe.attr("__parallel__") = [] { +#ifdef _OPENMP + return true; +#else + return false; +#endif + }(); export_molecule(cppe); export_multipole(cppe); @@ -29,4 +36,4 @@ PYBIND11_MODULE(pycppe, cppe) { export_math(cppe); export_tensors(cppe); export_fmm(cppe); -} \ No newline at end of file +} diff --git a/tests/test_math.py b/tests/test_math.py index 254c738a..f0a10150 100644 --- a/tests/test_math.py +++ b/tests/test_math.py @@ -1,5 +1,6 @@ import unittest import pytest +import math import numpy as np from cppe import T_recursive, xyz2idx, T, T_damp_thole from cppe import (factorial, prefactors, @@ -22,7 +23,7 @@ def test_basic_math(self): # factorial rng = np.arange(0, 10, 1) for a in rng: - assert factorial(a) == np.math.factorial(a) + assert factorial(a) == math.factorial(a) def test_prefactors(self): for k in range(3):