phonopy 2.45.1__tar.gz

phonopy-2.45.1/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.20)
+
+if(NOT SKBUILD_PROJECT_NAME)
+    set(SKBUILD_PROJECT_NAME phonopy)
+endif()
+
+if(PHONOPY_LIBS)
+    project(phonopy LANGUAGES C)
+    set(CMAKE_MACOSX_RPATH 1)
+    set(CMAKE_C_FLAGS_RELEASE "-Wall -O2")
+    set(CMAKE_C_FLAGS_DEBUG "-g -DTHMWARNING")
+    include(GNUInstallDirs)
+
+    # Version numbers
+    file(READ ${PROJECT_SOURCE_DIR}/phonopy/version.py VERSION_FILE)
+    string(REGEX MATCH "__version__.*([0-9]+)[.]([0-9]+)[.]([0-9]+)" phonopy_version
+                 ${VERSION_FILE})
+    set(PHONOPY_MAJOR_VERSION ${CMAKE_MATCH_1})
+    set(PHONOPY_MINOR_VERSION ${CMAKE_MATCH_2})
+    set(PHONOPY_MICRO_VERSION ${CMAKE_MATCH_3})
+    set(SERIAL
+        "${PHONOPY_MAJOR_VERSION}.${PHONOPY_MINOR_VERSION}.${PHONOPY_MICRO_VERSION}")
+    set(SOSERIAL "1")
+else()
+    project(${SKBUILD_PROJECT_NAME})
+    set(DEV_MODULE Development.Module)
+    find_package(
+        Python 3.9 REQUIRED
+        COMPONENTS Interpreter ${DEV_MODULE}
+        OPTIONAL_COMPONENTS Development.SABIModule)
+endif()
+
+cmake_policy(SET CMP0007 NEW)
+
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+    set(CMAKE_BUILD_TYPE
+        Release
+        CACHE STRING "Choose the type of build." FORCE)
+    set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
+                                                 "MinSizeRel" "RelWithDebInfo")
+endif()
+
+option(PHONOPY_USE_OMP "Build with OpenMP support" ON)
+
+message(STATUS "Build type: ${CMAKE_BUILD_TYPE}")
+message(STATUS "CMAKE_SYSTEM_PREFIX_PATH: ${CMAKE_SYSTEM_PREFIX_PATH}")
+
+if(PHONOPY_USE_OMP)
+    find_package(OpenMP)
+
+    if(OpenMP_FOUND)
+        message(STATUS "OpenMP libs: ${OpenMP_C_LIBRARIES}")
+        message(STATUS "OpenMP flags: ${OpenMP_C_FLAGS}")
+    endif()
+else()
+    message(STATUS "OpenMP is not used.")
+    set(OpenMP_FOUND OFF) # cmake-lint: disable=C0103
+endif()
+
+set(SOURCES_PHONOPY
+    ${PROJECT_SOURCE_DIR}/c/phonopy.c ${PROJECT_SOURCE_DIR}/c/dynmat.c
+    ${PROJECT_SOURCE_DIR}/c/derivative_dynmat.c ${PROJECT_SOURCE_DIR}/c/rgrid.c
+    ${PROJECT_SOURCE_DIR}/c/tetrahedron_method.c)
+
+if(BUILD_SHARED_LIBS)
+    # Shared library
+    add_library(phonopy_libs SHARED ${SOURCES_PHONOPY})
+
+    if(OpenMP_FOUND)
+        target_link_libraries(phonopy_libs PRIVATE OpenMP::OpenMP_C)
+    endif()
+
+    target_compile_definitions(phonopy_libs PRIVATE THM_EPSILON=1e-10)
+else()
+    # Static link library
+    add_library(phonopy_libs STATIC ${SOURCES_PHONOPY})
+
+    if(OpenMP_FOUND)
+        target_link_libraries(phonopy_libs PRIVATE OpenMP::OpenMP_C)
+    endif()
+
+    target_compile_definitions(phonopy_libs PRIVATE THM_EPSILON=1e-10)
+endif()
+
+if(PHONOPY_LIBS)
+    install(FILES ${PROJECT_SOURCE_DIR}/c/phonopy.h
+            DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+
+    if(BUILD_SHARED_LIBS)
+        install(TARGETS phonopy_libs LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
+        set_property(TARGET phonopy_libs PROPERTY VERSION ${SERIAL})
+        set_property(TARGET phonopy_libs PROPERTY SOVERSION ${SOSERIAL})
+    else()
+        install(TARGETS phonopy_libs ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+        set_property(TARGET phonopy_libs PROPERTY VERSION ${SERIAL})
+        set_property(TARGET phonopy_libs PROPERTY SOVERSION ${SOSERIAL})
+        set_property(TARGET phonopy_libs PROPERTY OUTPUT_NAME phonopy_libs)
+    endif()
+else()
+    set_target_properties(phonopy_libs PROPERTIES POSITION_INDEPENDENT_CODE ON)
+
+    execute_process(
+        COMMAND "${Python_EXECUTABLE}" -m nanobind --cmake_dir
+        OUTPUT_STRIP_TRAILING_WHITESPACE
+        OUTPUT_VARIABLE NB_DIR)
+    list(APPEND CMAKE_PREFIX_PATH "${NB_DIR}")
+    find_package(nanobind CONFIG REQUIRED)
+    nanobind_add_module(_phonopy STABLE_ABI ${PROJECT_SOURCE_DIR}/c/phonopy.h
+                        ${PROJECT_SOURCE_DIR}/c/_phonopy.cpp)
+
+    if(OpenMP_FOUND)
+        target_link_libraries(_phonopy PRIVATE phonopy_libs OpenMP::OpenMP_C)
+    else()
+        target_link_libraries(_phonopy PRIVATE phonopy_libs)
+    endif()
+
+    target_compile_definitions(_phonopy PRIVATE THM_EPSILON=1e-10)
+    install(TARGETS _phonopy LIBRARY DESTINATION ${SKBUILD_PROJECT_NAME})
+endif()

phonopy-2.45.1/LICENSE

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+Copyright (c) 2014-2024, Phonopy. All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions
+are met:
+
+* Redistributions of source code must retain the above copyright
+  notice, this list of conditions and the following disclaimer.
+* 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.
+* Neither the name of the phonopy project 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 THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"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 <COPYRIGHT
+HOLDER> 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.

phonopy-2.45.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: phonopy
+Version: 2.45.1
+Summary: This is the phonopy module.
+Author-Email: Atsushi Togo <atz.togo@gmail.com>
+License-Expression: BSD-3-Clause
+License-File: LICENSE
+Project-URL: Homepage, https://phonopy.github.io/phonopy/
+Project-URL: Repository, https://github.com/phonopy/phonopy
+Requires-Python: >=3.9
+Requires-Dist: numpy>=1.17.0
+Requires-Dist: PyYAML>=5.3
+Requires-Dist: matplotlib>=2.2.2
+Requires-Dist: h5py>=3.0
+Requires-Dist: spglib>=2.5
+Requires-Dist: symfc>=1.5
+Provides-Extra: cp2k
+Requires-Dist: cp2k-input-tools; extra == "cp2k"
+Provides-Extra: seekpath
+Requires-Dist: seekpath; extra == "seekpath"
+Provides-Extra: pypolymlp
+Requires-Dist: pypolymlp>=0.10.0; extra == "pypolymlp"
+Provides-Extra: tools
+Requires-Dist: seekpath; extra == "tools"
+Requires-Dist: pypolymlp>=0.10.0; extra == "tools"
+Description-Content-Type: text/markdown
+
+[![Version Badge](https://anaconda.org/conda-forge/phonopy/badges/version.svg)](https://anaconda.org/conda-forge/phonopy)
+[![Downloads Badge](https://anaconda.org/conda-forge/phonopy/badges/downloads.svg)](https://anaconda.org/conda-forge/phonopy)
+[![PyPI](https://img.shields.io/pypi/dm/phonopy.svg?maxAge=2592000)](https://pypi.python.org/pypi/phonopy)
+[![codecov](https://codecov.io/gh/phonopy/phonopy/branch/develop/graph/badge.svg)](https://codecov.io/gh/phonopy/phonopy)
+
+# Phonopy
+
+Phonon code mainly written in python. Phonopy user documentation is found at
+http://phonopy.github.io/phonopy/
+
+## Installation
+
+See https://phonopy.github.io/phonopy/install.html.
+
+## Mailing list for questions
+
+Usual phonopy questions should be sent to phonopy mailing list
+(https://sourceforge.net/p/phonopy/mailman/).
+
+## Development
+
+The development of phonopy is managed on the `develop` branch of github phonopy
+repository.
+
+- Github issues is the place to discuss about phonopy issues.
+- Github pull request is the place to request merging source code.
+
+### Formatting
+
+Formatting rules are found in `pyproject.toml`.
+
+### pre-commit
+
+Pre-commit (https://pre-commit.com/) is mainly used for applying the formatting
+rules automatically. Therefore, it is strongly encouraged to use it at or before
+git-commit. Pre-commit is set-up and used in the following way:
+
+- Installed by `pip install pre-commit`, `conda install pre_commit` or see
+  https://pre-commit.com/#install.
+- pre-commit hook is installed by `pre-commit install`.
+- pre-commit hook is run by `pre-commit run --all-files`.
+
+Unless running pre-commit, pre-commit.ci may push the fix at PR by github
+action. In this case, the fix should be merged by the contributor's repository.
+
+### VSCode setting
+- Not strictly, but VSCode's `settings.json` may be written like below
+
+  ```json
+  "ruff.lint.args": [
+      "--config=${workspaceFolder}/pyproject.toml",
+  ],
+  "[python]": {
+      "editor.defaultFormatter": "charliermarsh.ruff",
+      "editor.codeActionsOnSave": {
+          "source.organizeImports": "explicit"
+      }
+  },
+  ```
+
+## Documentation
+
+Phonopy user documentation is written using python sphinx. The source files are
+stored in `doc` directory. Please see how to write the documentation at
+`doc/README.md`.
+
+## How to run tests
+
+Tests are written using pytest. To run tests, pytest has to be installed. The
+tests can be run by
+
+```bash
+% pytest
+```

phonopy-2.45.1/README.md

@@ -0,0 +1,74 @@
+[![Version Badge](https://anaconda.org/conda-forge/phonopy/badges/version.svg)](https://anaconda.org/conda-forge/phonopy)
+[![Downloads Badge](https://anaconda.org/conda-forge/phonopy/badges/downloads.svg)](https://anaconda.org/conda-forge/phonopy)
+[![PyPI](https://img.shields.io/pypi/dm/phonopy.svg?maxAge=2592000)](https://pypi.python.org/pypi/phonopy)
+[![codecov](https://codecov.io/gh/phonopy/phonopy/branch/develop/graph/badge.svg)](https://codecov.io/gh/phonopy/phonopy)
+
+# Phonopy
+
+Phonon code mainly written in python. Phonopy user documentation is found at
+http://phonopy.github.io/phonopy/
+
+## Installation
+
+See https://phonopy.github.io/phonopy/install.html.
+
+## Mailing list for questions
+
+Usual phonopy questions should be sent to phonopy mailing list
+(https://sourceforge.net/p/phonopy/mailman/).
+
+## Development
+
+The development of phonopy is managed on the `develop` branch of github phonopy
+repository.
+
+- Github issues is the place to discuss about phonopy issues.
+- Github pull request is the place to request merging source code.
+
+### Formatting
+
+Formatting rules are found in `pyproject.toml`.
+
+### pre-commit
+
+Pre-commit (https://pre-commit.com/) is mainly used for applying the formatting
+rules automatically. Therefore, it is strongly encouraged to use it at or before
+git-commit. Pre-commit is set-up and used in the following way:
+
+- Installed by `pip install pre-commit`, `conda install pre_commit` or see
+  https://pre-commit.com/#install.
+- pre-commit hook is installed by `pre-commit install`.
+- pre-commit hook is run by `pre-commit run --all-files`.
+
+Unless running pre-commit, pre-commit.ci may push the fix at PR by github
+action. In this case, the fix should be merged by the contributor's repository.
+
+### VSCode setting
+- Not strictly, but VSCode's `settings.json` may be written like below
+
+  ```json
+  "ruff.lint.args": [
+      "--config=${workspaceFolder}/pyproject.toml",
+  ],
+  "[python]": {
+      "editor.defaultFormatter": "charliermarsh.ruff",
+      "editor.codeActionsOnSave": {
+          "source.organizeImports": "explicit"
+      }
+  },
+  ```
+
+## Documentation
+
+Phonopy user documentation is written using python sphinx. The source files are
+stored in `doc` directory. Please see how to write the documentation at
+`doc/README.md`.
+
+## How to run tests
+
+Tests are written using pytest. To run tests, pytest has to be installed. The
+tests can be run by
+
+```bash
+% pytest
+```