fix: use total atom counts for defect energies

[njzjz-bot]

Summary

• Count atoms across every species in autotest result data.
• Use total task and equilibrium atom counts for vacancy and interstitial formation energies.
• Add multi-species atom-count regression coverage.

Tests

• python -m unittest tests.auto_test.test_property_atom_count -v
• ruff check dpgen/auto_test/Property.py dpgen/auto_test/Vacancy.py dpgen/auto_test/Interstitial.py tests/auto_test/test_property_atom_count.py
• ruff format --check dpgen/auto_test/Property.py dpgen/auto_test/Vacancy.py dpgen/auto_test/Interstitial.py tests/auto_test/test_property_atom_count.py

Fixes #1901

Coding agent: Codex
Codex version: codex-cli 0.149.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

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📥 Commits

Reviewing files that changed from the base of the PR and between d5ce577 and 7534dfa.

📒 Files selected for processing (4)

• dpgen/auto_test/Interstitial.py
• dpgen/auto_test/Property.py
• dpgen/auto_test/Vacancy.py
• tests/auto_test/test_property_atom_count.py

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[codecov]

Codecov Report

❌ Patch coverage is 50.00000% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 49.81%. Comparing base (d5ce577) to head (7534dfa).

Files with missing lines	Patch %	Lines
dpgen/auto_test/Interstitial.py	33.33%	2 Missing ⚠️
dpgen/auto_test/Vacancy.py	33.33%	2 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1941   +/-   ##
=======================================
  Coverage   49.80%   49.81%           
=======================================
  Files          83       83           
  Lines       14986    14988    +2     
=======================================
+ Hits         7464     7466    +2     
  Misses       7522     7522           

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