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Fix a bug in AtomsBase interface #38

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Sep 20, 2023
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Merged

Fix a bug in AtomsBase interface #38

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4 changes: 4 additions & 0 deletions src/atoms.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -135,6 +135,8 @@ function Atoms(dict::Dict{String, Any})
atom_data[Symbol(key)] = arrays[key] * u"Å"
elseif key in ("charge", ) # Add charge unit
atom_data[Symbol(key)] = arrays[key] * u"e_au"
elseif typeof(arrays[key]) <: AbstractMatrix
atom_data[Symbol(key)] = [ collect(col) for col in eachcol(arrays[key]) ]
else
atom_data[Symbol(key)] = arrays[key]
end
Expand Down Expand Up @@ -198,6 +200,8 @@ function write_dict(atoms::Atoms)
arrays[string(k)] = ustrip.(u"e_au", v)
elseif v isa AbstractVector{<:ExtxyzType}
arrays[string(k)] = v # These can be written losslessly
elseif v isa AbstractArray && eltype(v) <: AbstractVector{<:ExtxyzType}
arrays[string(k)] = reduce(hcat, v)
else
@warn "Writing quantities of type $(typeof(v)) is not supported in write_dict."
end
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25 changes: 25 additions & 0 deletions test/atomsbase.jl
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Expand Up @@ -88,3 +88,28 @@ end
end
test_approx_eq(system, io_system; rtol=1e-4)
end

@testset "Extra variables for atoms" begin
text = """2
Lattice="2.614036117884091 0.0 0.0 0.0 2.6528336296738044 0.0 0.0 0.0 3.8250280122051756" Properties=species:S:1:pos:R:3:force:R:3:tags:I:1 config_type=FLD_TiAl spacegroup="P 1" virial="5.072173561696366 0.1220123768779895 0.6518229755809941 0.1220123768779895 4.667636799854875 0.5969893898844183 0.6518229755809941 0.5969893898844183 4.700422750506493" energy=-1703.64063822 unit_cell=conventional n_minim_iter=2 pbc="T T T"
Ti 1.30924260 1.32316179 1.62637131 0.86219000 0.78737000 2.65969000 0
Al 0.11095015 0.09471147 -0.05013464 -0.86219000 -0.78737000 -2.65969000 1
"""
infile = tempname()
outfile = tempname()
open(infile, "w") do io
print(io, text)
end
frame = read_frame(infile)
atoms = Atoms(frame)
@test all( atoms[1][:force] .== [0.86219000, 0.78737000, 2.65969000] )
@test all( atoms[2][:force] .== [-0.86219000, -0.78737000, -2.65969000] )
@test atoms[1][:tags] == 0
@test atoms[2][:tags] == 1
ExtXYZ.save(outfile, atoms)
new_atoms = ExtXYZ.load(outfile)
@test all( atoms[1][:force] .== new_atoms[1][:force] )
@test all( atoms[2][:force] .== new_atoms[2][:force] )
@test atoms[1][:tags] == new_atoms[1][:tags]
@test atoms[2][:tags] == new_atoms[2][:tags]
end
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