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Update interface to use NQCBase.Structure type. #4

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Update interface to use NQCBase.Structure type. #4

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c60641c
Add NQCBase.Structure to interface
Alexsp32 Nov 27, 2025
115e76b
Update tests
Alexsp32 Nov 27, 2025
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4 changes: 2 additions & 2 deletions Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "NQCDInterfASE"
uuid = "4606675f-2246-4a0b-99d5-75b910de637b"
authors = ["Alexander Spears <alexander.spears@warwick.ac.uk> and contributors"]
version = "1.0.2"
version = "1.0.3"

[deps]
CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
Expand All @@ -13,7 +13,7 @@ UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"

[compat]
CondaPkg = "0.2.29"
NQCBase = "0.5, 1"
NQCBase = "1.1"
NQCModels = "0.10, 1"
PythonCall = "0.9"
Unitful = "1.22"
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11 changes: 9 additions & 2 deletions src/NQCDInterfASE.jl
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
module NQCDInterfASE

using PythonCall
using NQCBase: Atoms, AbstractCell, PeriodicCell, InfiniteCell
using NQCBase: Atoms, AbstractCell, PeriodicCell, InfiniteCell, Structure
import NQCModels
using Unitful, UnitfulAtomic

Expand Down Expand Up @@ -29,9 +29,16 @@ end
function convert_to_ase_atoms(atoms::Atoms, R::Vector{<:Matrix}, cell::AbstractCell)
convert_to_ase_atoms.(Ref(atoms), R, Ref(cell))
end
# Missing conversion of info to atoms["info"] because of type conversion for arbitrary types.
convert_to_ase_atoms(st::Structure) = convert_to_ase_atoms(st.atoms, st.positions, st.cell)

convert_from_ase_atoms(ase_atoms::PythonCall.Py) =
Atoms(ase_atoms), positions(ase_atoms), Cell(ase_atoms)
Structure(
Atoms(ase_atoms),
positions(ase_atoms),
Cell(ase_atoms),
PythonCall.pyconvert(Dict{String, Any}, ase_atoms["info"]) # Hopefully this conversion covers anything you might drop into the info.
)

Atoms(ase_atoms::PythonCall.Py) = Atoms{Float64}(Symbol.(PythonCall.PyList(ase_atoms.get_chemical_symbols())))

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23 changes: 16 additions & 7 deletions test/ase.jl
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Expand Up @@ -9,13 +9,13 @@ using PythonCall
R = rand(3, 4) .* 10

ase_atoms = convert_to_ase_atoms(atoms, R, cell)
new_atoms, new_R, new_cell = convert_from_ase_atoms(ase_atoms)
nqcd_structure = convert_from_ase_atoms(ase_atoms)

@test new_atoms == atoms
@test new_cell.vectors ≈ cell.vectors
@test new_cell.inverse ≈ cell.inverse
@test new_cell.periodicity ≈ cell.periodicity
@test new_R ≈ R
@test nqcd_structure.atoms == atoms
@test nqcd_structure.cell.vectors ≈ cell.vectors
@test nqcd_structure.cell.inverse ≈ cell.inverse
@test nqcd_structure.cell.periodicity ≈ cell.periodicity
@test nqcd_structure.positions ≈ R
end

@testset "Multiple frames" begin
Expand All @@ -25,5 +25,14 @@ end

ase_atoms = convert_to_ase_atoms(atoms, R, cell)
out = convert_from_ase_atoms.(ase_atoms)
@test out isa Vector{<:Tuple}
# Correct types
@test out isa Vector{<:NQCBase.Structure}
for frame in structure
nqcd_structure = frame
@test nqcd_structure.atoms == atoms
@test nqcd_structure.cell.vectors ≈ cell.vectors
@test nqcd_structure.cell.inverse ≈ cell.inverse
@test nqcd_structure.cell.periodicity ≈ cell.periodicity
@test nqcd_structure.positions ≈ R
end
end
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