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…in general assignment
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… electron perception
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Pull request overview
This pull request fixes a crash in the electron perception logic when processing isolated metal atoms (e.g., Au, transition metals) that lack predefined valence electron counts. The fix introduces a graceful fallback that defaults to zero valence electrons for isolated atoms (degree 0) while maintaining the existing error behavior for bonded atoms with unknown valence.
Key Changes
- Modified
assign_generalto check atom degree before erroring on unknown valence - Isolated atoms with unknown valence now default to 0 valence electrons instead of crashing
- Added comprehensive test coverage for both isolated and bonded unknown-valence cases
Reviewed changes
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| File | Description |
|---|---|
| src/perception/electrons.rs | Updated valence assignment logic to handle isolated atoms gracefully; added unit tests for isolated Au and bonded Au-H cases |
| docs/02_perception.md | Updated electron assignment documentation to describe the new degree-0 fallback behavior |
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TKanX
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Summary:
Updated the electron perception logic to prevent crashes when encountering isolated metal atoms (e.g., ions like Na+, Ca2+, or noble metals like Au) that have no predefined valence electron count. Previously,
assign_generalwould return an error for any element without a valence definition, regardless of its bonding state. Now, the system safely defaults to zero valence electrons for isolated atoms (degree 0), allowing them to be processed correctly. Bonded atoms with unknown valence will still trigger an error to ensure chemical correctness.Changes:
assign_generalinelectrons.rsto check the atom's degree.valence_electrons()returnsNonebut the atom is isolated (degree == 0), the valence is now defaulted to 0 instead of returning an error.isolated_unknown_valence_metal_defaults_to_zero: Verifies that an isolated Gold (Au) atom is processed without error.bonded_unknown_valence_metal_errors: Confirms that a bonded Gold atom still raises aPerceptionError, maintaining safety for bonded systems.