Fix #7556 and #7558 in pyabacus - #8021
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…ted species Cell._save_stru() rebuilt species_dict[symbol] on every atom, resetting the species atom list each time. For multiple atoms of the same species only the last atom survived, and natom was tied to the pp_type branch instead of counting appended atoms. Initialize each species entry only once and increment natom for every appended atom independently of pp_type. Add a regression test that appends atoms of an existing species and checks the saved STRU reloads with the full atom list.
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…rlap_generator The PyABACUS wrapper exposes rcut_max and lmax as methods, not properties, and there is no lmax_ method. The old code treated them as attributes, so overlap generation failed before producing matrices. Use self.orb.rcut_max(), self.orb.lmax(), and self.orb.lmax(it).
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AsTonyshment
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Sep 25, 2026
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Fix #7556 and #7558
Cell._save_stru() rebuilt species_dict[symbol] on every atom, resetting the species atom list each time. For multiple atoms of the same species only the last atom survived, and natom was tied to the pp_type branch instead of counting appended atoms.
Initialize each species entry only once and increment natom for every appended atom independently of pp_type. Add a regression test that appends atoms of an existing species and checks the saved STRU reloads with the full atom list.
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AGENTS.mdanddocs/developers_guide/agent_governance.md.source/changes.Linked Issue
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Unit Tests and/or Case Tests for my changes
What's changed?
Governance Notes