lineshape_tools 0.1.0__tar.gz

lineshape_tools-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Mark E. Turiansky
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

lineshape_tools-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: lineshape_tools
+Version: 0.1.0
+Summary: Software to evaluate the optical lineshape function of a defect.
+Keywords: defect,luminescence,absorption,electron-phonon coupling,density functional theory
+Author-Email: "Mark E. Turiansky" <mark.e.turiansky.ctr@us.navy.mil>
+License: MIT
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Project-URL: Homepage, https://github.com/mturiansky/lineshape_tools
+Project-URL: Documentation, https://lineshape_tools.readthedocs.io/en/latest
+Project-URL: Repository, https://github.com/mturiansky/lineshape_tools.git
+Project-URL: Issues, https://github.com/mturiansky/lineshape_tools/issues
+Requires-Python: <3.14,>=3.10
+Requires-Dist: mace-torch>=0.3.10
+Requires-Dist: numpy>=1.26.4
+Requires-Dist: numba>=0.61.0
+Requires-Dist: rocket-fft>=0.2.5
+Requires-Dist: cyclopts>=3.16.1
+Requires-Dist: ase>=3.25.0
+Requires-Dist: scipy>=1.15.3
+Requires-Dist: tqdm>=4.67.1
+Provides-Extra: extra
+Requires-Dist: phonopy>=2.42.0; extra == "extra"
+Requires-Dist: matplotlib>=3.10.5; extra == "extra"
+Description-Content-Type: text/markdown
+
+# lineshape_tools
+<!-- index start -->
+
+`lineshape_tools` is a Python software that implements the formulation for evaluating the effects of electron-phonon coupling on the optical properties of defects.
+In particular, it implements the approach pioneered by [Alkauskas *et al.*](https://doi.org/10.1088/1367-2630/16/7/073026) to compute the lineshape function within Huang-Rhys theory.
+The code interfaces with [`mace`](https://mace-docs.readthedocs.io/en/latest/) and [`phonopy`](https://phonopy.github.io/phonopy/) to evaluate the dynamical matrix and obtain the phonons of a defect-containing supercell.
+
+### Installation
+<!-- install start -->
+To install the latest version of `lineshape_tools`, create a new virtual environment and run
+```
+pip install lineshape_tools
+```
+<!-- install end -->
+For more installation information and some performance considerations, see the [Installation page]().
+
+### Usage 
+`lineshape_tools` provides a command-line interface for interacting with the code. See
+```
+lineshape_tools --help
+```
+Detailed usage information can be found in the [Tutorials page]().
+
+### How to Cite
+<!-- cite start -->
+If you use this code, please consider citing
+```bibtex
+@misc{turiansky_machine_2025,
+  title = {Machine Learning for Fast and Accurate Optical Lineshapes of Defects},
+  author = {Turiansky, Mark E. and Lyons, John L., and Bernstein, Noam},
+  year = {2025},
+  number = {arXiv:XXXX.XXXXX},
+  eprint = {XXXX.XXXXX},
+  primaryclass = {cond-mat},
+  publisher = {arXiv},
+  doi = {},
+  urldate = {},
+  archiveprefix = {arXiv},
+}
+```
+<!-- cite end -->
+Please also consider citing the foundational works that made this code possible on the [Citation page]().
+
+<!-- index end -->

lineshape_tools-0.1.0/README.md

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+# lineshape_tools
+<!-- index start -->
+
+`lineshape_tools` is a Python software that implements the formulation for evaluating the effects of electron-phonon coupling on the optical properties of defects.
+In particular, it implements the approach pioneered by [Alkauskas *et al.*](https://doi.org/10.1088/1367-2630/16/7/073026) to compute the lineshape function within Huang-Rhys theory.
+The code interfaces with [`mace`](https://mace-docs.readthedocs.io/en/latest/) and [`phonopy`](https://phonopy.github.io/phonopy/) to evaluate the dynamical matrix and obtain the phonons of a defect-containing supercell.
+
+### Installation
+<!-- install start -->
+To install the latest version of `lineshape_tools`, create a new virtual environment and run
+```
+pip install lineshape_tools
+```
+<!-- install end -->
+For more installation information and some performance considerations, see the [Installation page]().
+
+### Usage 
+`lineshape_tools` provides a command-line interface for interacting with the code. See
+```
+lineshape_tools --help
+```
+Detailed usage information can be found in the [Tutorials page]().
+
+### How to Cite
+<!-- cite start -->
+If you use this code, please consider citing
+```bibtex
+@misc{turiansky_machine_2025,
+  title = {Machine Learning for Fast and Accurate Optical Lineshapes of Defects},
+  author = {Turiansky, Mark E. and Lyons, John L., and Bernstein, Noam},
+  year = {2025},
+  number = {arXiv:XXXX.XXXXX},
+  eprint = {XXXX.XXXXX},
+  primaryclass = {cond-mat},
+  publisher = {arXiv},
+  doi = {},
+  urldate = {},
+  archiveprefix = {arXiv},
+}
+```
+<!-- cite end -->
+Please also consider citing the foundational works that made this code possible on the [Citation page]().
+
+<!-- index end -->

lineshape_tools-0.1.0/pyproject.toml

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+[project]
+name = "lineshape_tools"
+description = "Software to evaluate the optical lineshape function of a defect."
+authors = [
+    { name = "Mark E. Turiansky", email = "mark.e.turiansky.ctr@us.navy.mil" },
+]
+dependencies = [
+    "mace-torch>=0.3.10",
+    "numpy>=1.26.4",
+    "numba>=0.61.0",
+    "rocket-fft>=0.2.5",
+    "cyclopts>=3.16.1",
+    "ase>=3.25.0",
+    "scipy>=1.15.3",
+    "tqdm>=4.67.1",
+]
+requires-python = ">=3.10,<3.14"
+readme = "README.md"
+dynamic = []
+keywords = [
+    "defect",
+    "luminescence",
+    "absorption",
+    "electron-phonon coupling",
+    "density functional theory",
+]
+classifiers = [
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Physics",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
+version = "0.1.0"
+
+[project.license]
+text = "MIT"
+
+[project.urls]
+Homepage = "https://github.com/mturiansky/lineshape_tools"
+Documentation = "https://lineshape_tools.readthedocs.io/en/latest"
+Repository = "https://github.com/mturiansky/lineshape_tools.git"
+Issues = "https://github.com/mturiansky/lineshape_tools/issues"
+
+[project.scripts]
+lineshape_tools = "lineshape_tools.__main__:app.meta"
+
+[project.optional-dependencies]
+extra = [
+    "phonopy>=2.42.0",
+    "matplotlib>=3.10.5",
+]
+
+[build-system]
+requires = [
+    "pdm-backend",
+]
+build-backend = "pdm.backend"
+
+[dependency-groups]
+dev = [
+    "pytest>=8.3.4",
+    "mypy>=1.15.0",
+    "ruff>=0.9.4",
+    "pytest-cov>=6.2.1",
+    "pytest-mock>=3.14.1",
+    "pytest-skip-slow>=0.0.5",
+]
+docs = [
+    "sphinx>=8.1.3",
+    "furo>=2024.8.6",
+    "sphinx-autoapi>=3.6.0",
+    "myst-parser>=4.0.1",
+    "sphinx-copybutton>=0.5.2",
+]
+
+[tool.ruff]
+line-length = 99
+
+[tool.ruff.lint]
+select = [
+    "A",
+    "B",
+    "D",
+    "E",
+    "F",
+    "I",
+    "NPY",
+    "PL",
+    "UP",
+    "W",
+]
+ignore = [
+    "PLR",
+    "D100",
+    "D101",
+    "D104",
+    "E731",
+    "NPY201",
+    "PLC0415",
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**.py" = [
+    "D102",
+    "D103",
+    "D107",
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+
+[tool.mypy]
+ignore_missing_imports = true
+
+[tool.pdm]
+distribution = true
+
+[tool.pdm.version]
+source = "file"
+path = "src/lineshape_tools/__init__.py"
+
+[tool.pytest.ini_options]
+addopts = [
+    "--import-mode=importlib",
+]
+testpaths = [
+    "tests",
+]

lineshape_tools-0.1.0/src/lineshape_tools/__init__.py

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+"""The lineshape_tools package."""
+
+__author__ = "Mark E. Turiansky"
+__email__ = "mark.e.turiansky.ctr@us.navy.mil"
+__version__ = "0.1.0"
+__copyright__ = "Copyright (c) 2025 Mark E. Turiansky"
+__license__ = "MIT"

lineshape_tools-0.1.0/src/lineshape_tools/__main__.py

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+import logging
+from typing import Annotated
+
+import cyclopts
+from cyclopts import Group, Parameter
+
+from lineshape_tools.cli import (
+    analyze_dynmat,
+    collect,
+    compute_dynmat,
+    compute_lineshape,
+    convert_from_phonopy,
+    gen_confs,
+    gen_ft_config,
+)
+
+app = cyclopts.App(help_format="md")
+app.meta.group_parameters = Group("Commands")
+
+for func in (
+    analyze_dynmat,
+    collect,
+    compute_dynmat,
+    compute_lineshape,
+    convert_from_phonopy,
+    gen_confs,
+    gen_ft_config,
+):
+    app.command()(func)
+
+
+@app.meta.default
+def _app_launcher(
+    *tokens: Annotated[str, Parameter(show=False, allow_leading_hyphen=True)],
+    verbose: Annotated[bool, Parameter(negative="--quiet")] = False,
+) -> None:
+    fmt = "%(asctime)s %(levelname)s %(name)s: %(message)s" if verbose else "[*] %(message)s"
+    log_level = logging.DEBUG if verbose else logging.INFO
+
+    logging.basicConfig(level=log_level, format=fmt, encoding="utf-8")
+
+    # remove logging from imported libraries, wow this is a monster of a line
+    logging.getLogger().handlers[0].addFilter(logging.Filter(name=__name__.split(".")[0]))
+
+    logging.getLogger(__name__).debug("starting application")
+    app(tokens)
+
+
+if __name__ == "__main__":
+    app.meta()