Add IsotropicMTKNPT to _md.py

[Andrew-S-Rosen]

Summary

This PR adds support for IsotropicMTKNPT simulations. Closes #87.

In doing so, I have added the "npt_isotropic_mtk" option to the list of supported ensembles. I have also added keyword arguments for tchain, pchain, tloop, and ploop.

A unit test has been added for the npt_isotropic_mtk ensemble. Note that I updated the test by relying on the default values of taut and taup instead of 0.1 for both, as the latter results in a nan with npt_isotropic_mtk. Since it is usually the case that taut is 100 * timestep and taup * 1000 timestep, this is perhaps not too surprising.

Checklist

• Google format doc strings added. Check with ruff.
• Type annotations included. Check with mypy.
• Tests added for new features/fixes.
• If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)

Tip: Install pre-commit hooks to auto-check types and linting before every commit:

pip install -U pre-commit
pre-commit install

[Andrew-S-Rosen]

@shyuep: Is there a way for you to approve workflows on this PR? I am having some trouble testing locally and might need a few iterations here before I'm confident in the outcome.

[Andrew-S-Rosen]

Alright, this should be ready for review @shyuep. If you don't like the change made to the test suite, just let me know. There should be no breaking changes in this PR.

[shyuep]

Thanks!

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 96.28%. Comparing base (c75fb3a) to head (b902145).
⚠️ Report is 6 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #88      +/-   ##
==========================================
+ Coverage   96.26%   96.28%   +0.02%     
==========================================
  Files          22       22              
  Lines        1151     1158       +7     
==========================================
+ Hits         1108     1115       +7     
  Misses         43       43              

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