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AtomsBase v0.5 update #13

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AtomsBase v0.5 update #13

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8 changes: 4 additions & 4 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,13 +11,13 @@ StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"

[compat]
AtomsBase = "0.4"
AtomsBase = "0.5"
JSON = "0.21.4"
LinearAlgebra = "1.9.0, 1.10.0"
Random = "1.9.0, 1.10.0"
LinearAlgebra = "1.9"
Random = "1.9"
StaticArrays = "1.9"
Unitful = "1.19"
julia = "1.9.0, 1.10.0"
julia = "1.9"

[extras]
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
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14 changes: 7 additions & 7 deletions src/utils.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ function _flexible_system(positions, elements, cell, pbc)
bc = pbc isa Bool ? (pbc, pbc, pbc) : tuple(pbc...)
bb = tuple([cell[i, :] for i = 1:3]...)
return FlexibleSystem(atoms;
bounding_box = bb,
cell_vectors = bb,
periodicity = bc)
end

Expand All @@ -38,7 +38,7 @@ function set_positions(at::FlexibleSystem,
particles = [ _set_position(at.particles[i], X[i])
for i in 1:length(at) ]
return FlexibleSystem(particles,
bounding_box = bounding_box(at),
cell_vectors = cell_vectors(at),
periodicity = periodicity(at))
end

Expand All @@ -48,7 +48,7 @@ function set_elements(at::FlexibleSystem, Z::AbstractVector)
particles = [ Atom(Z[i], position(x), velocity(x))
for (i, x) in enumerate(at.particles) ]
return FlexibleSystem(particles,
bounding_box = bounding_box(at),
cell_vectors = cell_vectors(at),
periodicity = periodicity(at))
end

Expand All @@ -72,7 +72,7 @@ at = bulk(:) * (3, 2, 4)
```
"""
function Base.repeat(at::FlexibleSystem, n::NTuple{3})
c1, c2, c3 = bounding_box(at)
c1, c2, c3 = cell_vectors(at)

particles = eltype(at.particles)[]
for a in CartesianIndices( (1:n[1], 1:n[2], 1:n[3]) )
Expand All @@ -85,7 +85,7 @@ function Base.repeat(at::FlexibleSystem, n::NTuple{3})
end

bb = (c1 * n[1], c2 * n[2], c3 * n[3])
return FlexibleSystem(particles; bounding_box = bb,
return FlexibleSystem(particles; cell_vectors = bb,
periodicity = periodicity(at))
end

Expand Down Expand Up @@ -173,9 +173,9 @@ takes the union of two particle systems provided their cells are identical.
"""
function union(sys1::FlexibleSystem, sys2::FlexibleSystem)
@assert periodicity(sys1) == periodicity(sys2)
@assert bounding_box(sys1) == bounding_box(sys2)
@assert cell_vectors(sys1) == cell_vectors(sys2)
return FlexibleSystem(union(sys1.particles, sys2.particles),
bounding_box = bounding_box(at),
cell_vectors = cell_vectors(at),
periodicit = periodicity(at) )
end

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2 changes: 1 addition & 1 deletion test/test_bulk.jl
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Expand Up @@ -12,7 +12,7 @@ test_systems = JSON.parsefile(joinpath(@__DIR__(), "..", "data", "test_systems.j
_ustripvecvec(X) = [ ustrip.(x) for x in X ]

compare_system(sys_f, sys_j) = (
all( ustrip.( hcat(bounding_box(sys_f)...) ) .≈ hcat(sys_j["cell"]...)' ) &&
all( ustrip.( hcat(cell_vectors(sys_f)...) ) .≈ hcat(sys_j["cell"]...)' ) &&
all( AtomsBuilder._convert_pbc(sys_j["pbc"]) .== periodicity(sys_f) ) &&
all( atomic_number(sys_f, :) .== sys_j["Z"] ) &&
all( _ustripvecvec(position(sys_f, :)) .≈ sys_j["X"] ) )
Expand Down