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Strange atom coloring #268

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kbarros opened this issue May 25, 2024 · 0 comments
Open

Strange atom coloring #268

kbarros opened this issue May 25, 2024 · 0 comments
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@kbarros
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kbarros commented May 25, 2024

The atom coloring can be confusing in this case:

using Sunny, GLMakie
positions = [[2/3, 1/3, 0],
             [1/3, 2/3, 0],
             [0, 0, 1/3],
             [1/3, 2/3, 1/3],
             [0, 0, 2/3],
             [2/3, 1/3, 2/3]]
lat_vecs = lattice_vectors(1, 1, 2, 90, 90, 120)
cryst = Crystal(lat_vecs, positions; types=["A", "A", "B", "B", "C", "C"])
view_crystal(cryst)

which infers

Crystal
Spacegroup 'P 3 m 1' (156)
Lattice params a=1, b=1, c=2, α=90°, β=90°, γ=120°
Cell volume 1.732
Type 'A', Wyckoff 1c (point group '3m.'):
   1. [2/3, 1/3, 0]
Type 'A', Wyckoff 1b (point group '3m.'):
   2. [1/3, 2/3, 0]
Type 'B', Wyckoff 1a (point group '3m.'):
   3. [0, 0, 1/3]
Type 'B', Wyckoff 1b (point group '3m.'):
   4. [1/3, 2/3, 1/3]
Type 'C', Wyckoff 1a (point group '3m.'):
   5. [0, 0, 2/3]
Type 'C', Wyckoff 1c (point group '3m.'):
   6. [2/3, 1/3, 2/3]

"B" and "C" are actual elements (boron and carbon), so they can get "real" colors. "A" is not an actual element, so then Sunny assigns the two "A" atoms distinct colors because they are symmetry-inequivalent sites.

image

Maybe if a type is specified, then we should always color by type, and not by symmetry equivalence.

@kbarros kbarros added the question Further information is requested label Nov 16, 2024
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