refactor: Separate GMM parameter extraction and temperature conversion

[henry2004y]

Refactors the get_gmm_parameters method in AMReXParticleData to separate the core logic of extracting squared thermal velocities from the unit conversion to temperature.

• get_gmm_parameters now returns only the raw squared thermal velocities (variances) from the GMM's covariance matrix.
• A new method, get_gmm_temperatures, has been added to handle the conversion of these velocities to temperatures in Kelvin.
• The documentation notebook amrex_data.ipynb and the relevant tests in tests/test_gmm_parameters.py have been updated to reflect these changes.

[gemini-code-assist]

Summary of Changes

Hello @henry2004y, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request enhances the AMReXParticleData class by separating the concerns of extracting raw Gaussian Mixture Model (GMM) parameters from their physical unit conversion to temperature. This refactoring improves code modularity, making the parameter extraction logic clearer and more flexible for future extensions or alternative unit conversions.

Highlights

• Method Refactoring: The get_gmm_parameters method in AMReXParticleData has been refactored to solely extract raw squared thermal velocities from GMM covariance matrices, removing the particle_mass argument.
• New Temperature Conversion Method: A new static method, get_gmm_temperatures, has been introduced to handle the conversion of these extracted velocities into temperatures in Kelvin, taking particle_mass as an argument.
• Documentation Update: The amrex_data.ipynb notebook has been updated to reflect the usage of the new get_gmm_temperatures method and to demonstrate the raw velocity extraction.
• Test Suite Enhancement: The test suite (tests/test_gmm_parameters.py) has been updated with new tests for get_gmm_parameters and modified existing tests to validate get_gmm_temperatures.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 68.39%. Comparing base (399e168) to head (a3839b0).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #164      +/-   ##
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+ Coverage   68.31%   68.39%   +0.08%     
==========================================
  Files          25       25              
  Lines        4191     4202      +11     
==========================================
+ Hits         2863     2874      +11     
  Misses       1328     1328              

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[gemini-code-assist]

Code Review

This pull request is a well-executed refactoring that separates the extraction of GMM parameters from the physics-specific conversion to temperature. By introducing get_gmm_parameters for raw velocity variances and get_gmm_temperatures for the conversion, the code is now more modular and adheres better to the single-responsibility principle. The updates to the documentation notebook and tests are thorough and correctly reflect these changes. I have a couple of suggestions to make the new methods even more concise and Pythonic by using list comprehensions.