refactor: Add general Structure class#2420
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trisyoungs wants to merge 8 commits intodevelop2from
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I have just realised that a number of functions were declared but not implemented. I'll be moving these over in a follow-up PR. |
RobBuchananCompPhys
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May 5, 2026
| Atom::Presence Atom::presence() const | ||
| { | ||
| return Z_ == Elements::Phantom ? Presence::Phantom : Presence::Physical; | ||
| ; |
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| ; | |
| #include "classes/structure.h" | ||
| #include "classes/species.h" | ||
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| Structure::Structure() { box_ = std::make_unique<SingleImageBox>(); } |
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This could all go into the initialiser list, in structure.h
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| Structure::Structure() { box_ = std::make_unique<SingleImageBox>(); } | |
| Structure::Structure() : box_(std::make_unique<SingleImageBox>()) {} |
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With plans in mind for introducing the capability for a
Speciesto be created within a graph from source geometry and forcefield terms, this PR introduces a fairly lightweightStructureclass. It is envisaged that this will be used to store, e.g. data read from XYZ files, data read from CIF files, etc. Since its focus is on utility rather than strictly protected data relationships (as is the case withSpecies) both atoms and bonds are represented as vectors of unique ptrs, rather than trying to emulate the reference-based system inSpecieswhich requires a bunch of copy / move constructor magic to maintain it. Thoughts on this welcome!A little pre-emptive tidying of
Speciesis done along the way to remove some unused stuff.