brainandforce / Electrum.jl

A Julian toolkit for solid-state chemical theory.
MIT License
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Enormous atom refactor #141

Closed brainandforce closed 1 year ago

brainandforce commented 1 year ago

@xamberl you're being tagged in this because this could break stuff you're working on.

The most important things to note with this: AtomList has all of its functionality in the PeriodicAtomList type, and all mentions of AtomList in external code should be changed PeriodicAtomList. (The new AtomList refers to absolute positions in space without respect to a crystal basis.) Similarly, AtomPosition has now been changed to two different types: CartesianAtomPosition and FractionalAtomPosition, which comprise AtomList and PeriodicAtomList respectively.

I'll also add that the NamedAtom type exists, which associates an atomic number with an atom name, which is the element's symbol by default, but can be changed if needed.

Hopefully, this will cut down on the confusion that some of the functions and types were producing.

codecov[bot] commented 1 year ago

Codecov Report

Base: 31.87% // Head: 31.96% // Increases project coverage by +0.09% :tada:

Coverage data is based on head (2c659fa) compared to base (aeba6ea). Patch coverage: 42.26% of modified lines in pull request are covered.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #141 +/- ## ========================================== + Coverage 31.87% 31.96% +0.09% ========================================== Files 16 16 Lines 1418 1414 -4 ========================================== Hits 452 452 + Misses 966 962 -4 ``` | [Impacted Files](https://codecov.io/gh/brainandforce/Electrum.jl/pull/141?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Brandon+Flores) | Coverage Δ | | |---|---|---| | [src/Electrum.jl](https://codecov.io/gh/brainandforce/Electrum.jl/pull/141?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Brandon+Flores#diff-c3JjL0VsZWN0cnVtLmps) | `50.00% <ø> (ø)` | | | [src/data/atomic.jl](https://codecov.io/gh/brainandforce/Electrum.jl/pull/141?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Brandon+Flores#diff-c3JjL2RhdGEvYXRvbWljLmps) | `0.00% <ø> (ø)` | | | [src/data/reciprocalspace.jl](https://codecov.io/gh/brainandforce/Electrum.jl/pull/141?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Brandon+Flores#diff-c3JjL2RhdGEvcmVjaXByb2NhbHNwYWNlLmps) | `12.21% <ø> (ø)` | | | [src/lattices.jl](https://codecov.io/gh/brainandforce/Electrum.jl/pull/141?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Brandon+Flores#diff-c3JjL2xhdHRpY2VzLmps) | `66.66% <ø> (ø)` | | | [src/show.jl](https://codecov.io/gh/brainandforce/Electrum.jl/pull/141?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Brandon+Flores#diff-c3JjL3Nob3cuamw=) | `0.00% <0.00%> (-6.84%)` | :arrow_down: | | [src/software/lammps.jl](https://codecov.io/gh/brainandforce/Electrum.jl/pull/141?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Brandon+Flores#diff-c3JjL3NvZnR3YXJlL2xhbW1wcy5qbA==) | `0.00% <0.00%> (ø)` | | | [src/filetypes.jl](https://codecov.io/gh/brainandforce/Electrum.jl/pull/141?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Brandon+Flores#diff-c3JjL2ZpbGV0eXBlcy5qbA==) | `41.47% <23.52%> (ø)` | | | [src/software/vasp.jl](https://codecov.io/gh/brainandforce/Electrum.jl/pull/141?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Brandon+Flores#diff-c3JjL3NvZnR3YXJlL3Zhc3Auamw=) | `12.38% <33.33%> (ø)` | | | [src/math.jl](https://codecov.io/gh/brainandforce/Electrum.jl/pull/141?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Brandon+Flores#diff-c3JjL21hdGguamw=) | `43.75% <42.85%> (-0.70%)` | :arrow_down: | | [src/crystals.jl](https://codecov.io/gh/brainandforce/Electrum.jl/pull/141?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Brandon+Flores#diff-c3JjL2NyeXN0YWxzLmps) | `35.89% <46.66%> (-8.84%)` | :arrow_down: | | ... and [3 more](https://codecov.io/gh/brainandforce/Electrum.jl/pull/141?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Brandon+Flores) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Brandon+Flores). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Brandon+Flores)

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