chore: deprecate Atom class method

[stevenhua0320]

@sbillinge ready to review. Note that for these two functions we don't have test before. So I had a nice discussion with GPT with what isotropic and anisotropic means and designed the U matrix to test the behaviors.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.19%. Comparing base (279d29d) to head (d6d8525).
⚠️ Report is 9 commits behind head on v3.4.0.

Additional details and impacted files

@@            Coverage Diff             @@
##           v3.4.0     #181      +/-   ##
==========================================
+ Coverage   99.16%   99.19%   +0.02%     
==========================================
  Files          15       15              
  Lines        2400     2489      +89     
==========================================
+ Hits         2380     2469      +89     
  Misses         20       20              

Files with missing lines	Coverage Δ
tests/test_atom.py	98.96% <100.00%> (+1.09%)	⬆️

... and 2 files with indirect coverage changes

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[sbillinge]

these look good. The tests would be slightly better with empty lines closed up, vc name expanded with its full meaning, and our usual beloved case and expected comments.