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Implement isolated system for AB (#32) #33

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Jan 13, 2025
Merged

Implement isolated system for AB (#32) #33

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05f6c61
implement #32
tjjarvinen Jan 9, 2025
12b83d4
clear code
tjjarvinen Jan 9, 2025
9d3365d
throw error for non 3D isolated systems
tjjarvinen Jan 11, 2025
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27 changes: 24 additions & 3 deletions src/atoms_base.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -4,13 +4,34 @@ using Unitful


function PairList(ab::AtomsBase.AbstractSystem, cutoff::Unitful.Length; length_unit=unit(cutoff))
cell = ustrip.(length_unit, hcat( cell_vectors(ab)... )' )
pbc = periodicity(ab)
r = map( 1:length(ab) ) do i
# Need to have SVector here for PairList to work
# if position does not give SVector
SVector( ustrip.(length_unit, position(ab,i))...)
end
nlist = PairList(r, ustrip(length_unit, cutoff), cell, pbc; int_type=Int)
tmp_cell = cell(ab)
if tmp_cell isa AtomsBase.IsolatedCell{3, <:Any}
# this only works in 3D
max_x = maximum(q->q[1], r)
max_y = maximum(q->q[2], r)
max_z = maximum(q->q[3], r)
min_x = minimum(q->q[1], r)
min_y = minimum(q->q[2], r)
min_z = minimum(q->q[3], r)
cell_matrix = SMatrix{3,3, typeof(max_x), 9}(
# add +1 for cell size
max_x - min_x + 1, 0., 0.,
0., max_y - min_y + 1, 0.,
0., 0., max_z - min_z + 1,
)
elseif tmp_cell isa AtomsBase.IsolatedCell
D = n_dimensions(ab)
throw( error("NeighbourLists.jl does not support $D-dimensional isolated AtomsBase systems yet.") )
else
cell_matrix = ustrip.(length_unit, hcat( cell_vectors(ab)... )' )
end
pbc = periodicity(ab)

nlist = PairList(r, ustrip(length_unit, cutoff), cell_matrix, pbc; int_type=Int)
return nlist
end
1 change: 1 addition & 0 deletions test/Project.toml
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@@ -1,4 +1,5 @@
[deps]
AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
AtomsBuilder = "f5cc8831-eeb7-4288-8d9f-d6c1ddb77004"
Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
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27 changes: 27 additions & 0 deletions test/test_atoms_base.jl
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@@ -1,4 +1,5 @@
#using ASEconvert
using AtomsBase
using AtomsBuilder
using NeighbourLists
using Test
Expand All @@ -12,6 +13,32 @@ using Unitful
id, r = neigs(nlist,1)

@test length(id) == 12

@testset "AtomsBase Isolated System" begin
isys = isolated_system([
:H => [0., 0., 0.]u"Å",
:H => [0., 0., 2.]u"Å",
:H => [0., 10., 0.]u"Å"
])
nlist = PairList(isys, 5.0u"Å")
id, r = neigs(nlist,1)
@test length(id) == 1
@test id[1] == 2
@test all( r[1] .≈ [0., 0., 2.] )
id, r = neigs(nlist,2)
@test length(id) == 1
@test id[1] == 1
@test all( r[1] .≈ [0., 0., -2.] )
id, r = neigs(nlist,3)
@test length(id) == 0

isys2d = isolated_system([
:H => [ 0., 0.]u"Å",
:H => [ 0., 2.]u"Å",
:H => [ 10., 0.]u"Å"
])
@test_throws ErrorException PairList(isys2d, 5.0u"Å")
end
end


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