fix: copy AtomicSystem arrays and carry energy, virial, stress - #189
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fix: copy AtomicSystem arrays and carry energy, virial, stress#189galjos wants to merge 1 commit into
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copy() forwarded only pos, vel, forces, charges, cell and topology by reference, so the copy aliased the source arrays and silently dropped energy, virial and stress. Mutating the copy, for example via center() or randomize_positions(), therefore corrupted the original system. The arrays are now copied and every field is carried over.
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## dev #189 +/- ##
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Coverage 93.94% 93.94%
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Files 177 177
Lines 9227 9227
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Hits 8668 8668
Misses 559 559
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copy()aliased the position, velocity, force, and charge arrays and dropped energy, virial, and stress, so mutating the copy (for examplecenter()) corrupted the source and property values vanished. The arrays are now copied and all three fields carried over.The added test covers value round-trip, aliasing, mutation isolation, and the empty system.
Fixes #188.