Optimization of D3 calculation

[awvwgk]

• move redundant calculations out of inner loops
• additional caching in ASE calculator to avoid object reconstruction
• match default in Python API with CLI to require opt-in for ATM

Closes #171

[codecov]

Codecov Report

❌ Patch coverage is 77.27273% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 65.84%. Comparing base (87efc01) to head (fe758db).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
python/dftd3/ase.py	66.66%	10 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #172      +/-   ##
==========================================
+ Coverage   65.78%   65.84%   +0.05%     
==========================================
  Files          34       34              
  Lines        4782     4793      +11     
  Branches     1668     1670       +2     
==========================================
+ Hits         3146     3156      +10     
  Misses        683      683              
- Partials      953      954       +1     

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