tau2 1.0.0__tar.gz

tau2-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: tau2
+Version: 1.0.0
+Summary: A package for calculating magnetic relaxation rates
+Home-page: https://gitlab.com/chilton-group/tau2
+Author: Ben Atkinson
+Author-email: benjamin.atkinson@anu.edu.au
+Project-URL: Bug Tracker, https://gitlab.com/chilton-group/tau2/issues
+Project-URL: Documentation, https://chilton-group.gitlab.io/tau2
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: h5py
+Requires-Dist: dask[distributed]
+Requires-Dist: matplotlib
+Requires-Dist: numba
+Requires-Dist: python-flint
+Requires-Dist: mpmath
+Requires-Dist: argcomplete
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: project-url
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# tau2
+
+`tau2` is a python package for simulating magnetic relaxation.
+
+# Installation via `pip`
+
+Install `tau2` using `pip` (if using a shared machine, add the `--user` argument after `install`)
+
+```
+pip install tau2
+```
+
+# Updating
+
+Update the code using `pip` (if using a shared machine, add the `--user` argument after `install`)
+
+```
+pip install tau2 --upgrade
+```
+
+# Installation with `pip` editable install
+
+**Only do this if you are developing (i.e. changing) the code.**
+
+Clone a copy of this repository, preferably while within a directory called git
+
+```
+mkdir -p git; cd git
+git clone https://gitlab.com/chilton-group/tau2
+```
+
+Navigate to the package directory
+
+```
+cd tau2/packages
+```
+
+and install the package in editable mode (if using a shared machine, add the `--user` argument after `install`)
+
+```
+pip install -e .
+```
+
+When you're done developing (i.e. your changes have been merged to the master), 
+or if you just want to use the current release version of the package, uninstall using `pip`
+
+```
+pip uninstall tau2
+```
+
+and follow the Installation via `pip` instructions above.
+
+# Usage
+
+The `tau2` command line interface can be invoked with 
+
+```
+tau2 -h
+```
+
+which prints a list of available subprograms.
+
+Additional options for the `raman` and `orbach` programs can be viewed with `--advanced_help`.
+
+# Documentation
+
+The [documentation](https://chilton-group.gitlab.io/tau2/) for this package is hosted by gitlab, and is automatically generated whenever new code is committed to the `main` branch. The automatic generation of this documentation relies on a common layout for comments and docstrings within the code, see [contributing](https://gitlab.com/chilton-group/group-wiki/-/wikis/Contributing:-General) for more information.
+
+# Development
+
+Before making changes to this repository, please follow the steps outlined in the [Chilton group wiki](https://gitlab.com/chilton-group/group-wiki/-/wikis/Contributing:-General).
+
+# Bugs
+
+If you believe you have a bug, *please check that you are using the most up to date version of the code*. 
+
+If that does not fix the problem, please create an issue on GitLab detailing the following:
+ - The commands you entered
+ - The error message
+
+Remember to simplify the problem as much as possible in order to provide a minimum working example, e.g. an example for a small molecule rather than one with 100000 atoms.
+
+Then, look at the code, try and figure out what you think is wrong if possible, and include this in your issue.

tau2-1.0.0/README.md

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+# tau2
+
+`tau2` is a python package for simulating magnetic relaxation.
+
+# Installation via `pip`
+
+Install `tau2` using `pip` (if using a shared machine, add the `--user` argument after `install`)
+
+```
+pip install tau2
+```
+
+# Updating
+
+Update the code using `pip` (if using a shared machine, add the `--user` argument after `install`)
+
+```
+pip install tau2 --upgrade
+```
+
+# Installation with `pip` editable install
+
+**Only do this if you are developing (i.e. changing) the code.**
+
+Clone a copy of this repository, preferably while within a directory called git
+
+```
+mkdir -p git; cd git
+git clone https://gitlab.com/chilton-group/tau2
+```
+
+Navigate to the package directory
+
+```
+cd tau2/packages
+```
+
+and install the package in editable mode (if using a shared machine, add the `--user` argument after `install`)
+
+```
+pip install -e .
+```
+
+When you're done developing (i.e. your changes have been merged to the master), 
+or if you just want to use the current release version of the package, uninstall using `pip`
+
+```
+pip uninstall tau2
+```
+
+and follow the Installation via `pip` instructions above.
+
+# Usage
+
+The `tau2` command line interface can be invoked with 
+
+```
+tau2 -h
+```
+
+which prints a list of available subprograms.
+
+Additional options for the `raman` and `orbach` programs can be viewed with `--advanced_help`.
+
+# Documentation
+
+The [documentation](https://chilton-group.gitlab.io/tau2/) for this package is hosted by gitlab, and is automatically generated whenever new code is committed to the `main` branch. The automatic generation of this documentation relies on a common layout for comments and docstrings within the code, see [contributing](https://gitlab.com/chilton-group/group-wiki/-/wikis/Contributing:-General) for more information.
+
+# Development
+
+Before making changes to this repository, please follow the steps outlined in the [Chilton group wiki](https://gitlab.com/chilton-group/group-wiki/-/wikis/Contributing:-General).
+
+# Bugs
+
+If you believe you have a bug, *please check that you are using the most up to date version of the code*. 
+
+If that does not fix the problem, please create an issue on GitLab detailing the following:
+ - The commands you entered
+ - The error message
+
+Remember to simplify the problem as much as possible in order to provide a minimum working example, e.g. an example for a small molecule rather than one with 100000 atoms.
+
+Then, look at the code, try and figure out what you think is wrong if possible, and include this in your issue.

tau2-1.0.0/pyproject.toml

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+[tool.semantic_release]
+version_variables = [
+    'setup.py:__version__',
+    'tau2/__version__.py:__version__'
+    ]
+upload_to_pypi=true
+branch = "main"
+hvcs="gitlab"
+
+[tool.semantic_release.branches.main]
+match = "(master|main)"
+
+[tool.semantic_release.changelog]
+template_dir = "templates"
+exclude_commit_patterns = []
+
+[tool.semantic_release.default_templates]
+changelog_file = "CHANGELOG.md"
+
+[tool.semantic_release.commit_author]
+env = "GIT_COMMIT_AUTHOR"
+default = "semantic-release <semantic-release>"
+
+[tool.semantic_release.commit_parser_options]
+allowed_tags = ["build", "chore", "ci", "docs", "feat", "fix", "perf", "style", "refactor", "test"]
+minor_tags = ["feat"]
+patch_tags = ["fix", "perf"]
+
+[tool.semantic_release.remote]
+name = "origin"
+type = "gitlab"
+ignore_token_for_push = false
+hvcs = "gitlab"
+
+[tool.semantic_release.remote.token]
+env = "GL_TOKEN"
+
+[tool.semantic_release.publish]
+dist_glob_patterns = ["dist/*"]
+upload_to_vcs_release = true

tau2-1.0.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

tau2-1.0.0/setup.py

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+import setuptools
+  
+with open("README.md", "r", encoding="utf-8") as fh:
+    long_description = fh.read()
+
+# DO NOT EDIT THIS NUMBER!
+# IT IS AUTOMATICALLY CHANGED BY python-semantic-release
+__version__ = "1.0.0"
+
+setuptools.setup(
+    name="tau2",
+    version=__version__,
+    author="Ben Atkinson",
+    author_email="benjamin.atkinson@anu.edu.au",
+    description="A package for calculating magnetic relaxation rates", # noqa
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://gitlab.com/chilton-group/tau2",
+    project_urls={
+        "Bug Tracker": "https://gitlab.com/chilton-group/tau2/issues",
+        "Documentation": "https://chilton-group.gitlab.io/tau2"
+    },
+    classifiers=[
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
+        'License :: OSI Approved :: MIT License',
+        'Operating System :: OS Independent',
+        'Intended Audience :: Science/Research',
+        'Topic :: Scientific/Engineering :: Chemistry',
+        'Topic :: Scientific/Engineering :: Physics',
+    ],
+    package_dir={"":"."},
+    packages=setuptools.find_packages(),
+    entry_points={
+        'console_scripts': [
+            'tau2=tau2.__main__:main',
+        ],
+    },
+    python_requires=">=3.8",
+    install_requires=[
+        'numpy',
+        'scipy',
+        'h5py',
+        'dask[distributed]', 
+        'matplotlib',
+        'numba',
+        'python-flint',
+        'mpmath',
+        'argcomplete'
+    ],
+)

tau2-1.0.0/tau2/__main__.py

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+#!/usr/bin/env python3
+from tau2.main import main
+
+if __name__ == '__main__':
+    main()

tau2-1.0.0/tau2/__version__.py

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+# DO NOT EDIT THIS NUMBER!
+# IT IS AUTOMATICALLY CHANGED BY python-semantic-release
+__version__ = "1.0.0"

tau2-1.0.0/tau2/calculation_setup.py

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+import numpy as np
+from scipy.spatial.transform import Rotation
+
+from .constants import MU_B_CM_T, G_E
+
+def setup_field_orientation(args, angmom, spin, orientations=1):
+    """Determines the field direction and magnitudes for the calculation.
+
+    This function handles the g-tensor reorientation to align the calculation's
+    z-axis with the principal magnetic axis of the ground state doublet. It also
+    interprets user-provided field vectors and magnitudes from the command line.
+
+    Args:
+        args (argparse.Namespace): The parsed command-line arguments.
+        angmom (np.ndarray): The angular momentum matrices (L_x, L_y, L_z).
+        spin (np.ndarray): The spin matrices (S_x, S_y, S_z).
+        orientations (int): The number of orientations being calculated.
+
+    Returns:
+        tuple: A tuple containing:
+            - B_unit (np.ndarray): The normalised field direction vector for a single calculation.
+            - magnitudes_to_run (list): A list of field magnitudes (in Tesla).
+            - rotation_matrix (np.ndarray): The matrix to rotate from the input to the principal axis frame.
+    """
+    rotation_matrix = np.identity(3)
+    principal_frame_z_axis = np.array([0.0, 0.0, 1.0])
+
+    if  args.reorient:
+        print("\nReorienting: z-axis will be aligned with the principal g-tensor axis.")
+        mu_op = MU_B_CM_T * (angmom + G_E * spin)
+        mu_op_doublet = mu_op[:, 0:2, 0:2]
+        g_tensor = 2 * np.real(np.einsum('kab,lba->kl', mu_op_doublet, mu_op_doublet))
+        g_squared = g_tensor.T @ g_tensor
+        eigvals, eigvecs = np.linalg.eigh(g_squared)
+
+        principal_axis = eigvecs[:, np.argmax(eigvals)]
+        print(f"Principal g-axis in input frame: [{principal_axis[0]:.4f}, {principal_axis[1]:.4f}, {principal_axis[2]:.4f}]")
+
+        r, _ = Rotation.align_vectors([principal_axis], [principal_frame_z_axis])
+        rotation_matrix = r.as_matrix()
+
+    if args.field_direction:
+        if orientations == 1:
+            print("Using user-provided --field_direction relative to the principal axis frame.")
+        field_direction_principal_frame = np.array(args.field_direction)
+    else:
+        field_direction_principal_frame = principal_frame_z_axis
+
+    field_direction_input_frame = rotation_matrix @ field_direction_principal_frame
+    norm = np.linalg.norm(field_direction_principal_frame)
+
+    if norm < 1e-9:
+        if orientations == 1:
+            print("Warning: Field direction vector has zero magnitude. Using principal frame z-axis.")
+        B_unit = rotation_matrix.T @ principal_frame_z_axis
+        B_unit_principal = principal_frame_z_axis
+    else:
+        B_unit = field_direction_input_frame / np.linalg.norm(field_direction_input_frame)
+        B_unit_principal = field_direction_principal_frame / norm
+
+    if orientations == 1:
+        print("\nNormalised field direction:")
+        print(f"  principal axis frame:\t[{B_unit_principal[0]:.4f}, {B_unit_principal[1]:.4f}, {B_unit_principal[2]:.4f}]")
+        print(f"  input frame:\t\t[{B_unit[0]:.4f}, {B_unit[1]:.4f}, {B_unit[2]:.4f}]")
+
+    if args.field_magnitudes:
+        magnitudes_to_run = args.field_magnitudes
+    elif args.field_direction:
+        magnitudes_to_run = [norm]
+    else:
+        magnitudes_to_run = [0.0002]
+
+    return B_unit, magnitudes_to_run, rotation_matrix