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Generalise system properties type check #49

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merged 2 commits into from
Jun 28, 2024
Merged

Generalise system properties type check #49

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c068234
Generalise type checks
mfherbst May 27, 2024
b10fcda
Also atom vectors suported
mfherbst May 27, 2024
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13 changes: 9 additions & 4 deletions src/atoms.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ function Atoms(system::AbstractSystem{D})
atoms_base_keys = (:charge, :covalent_radius, :vdw_radius,
:magnetic_moment, :pseudopotential)
v = system[1, k]
if k in atoms_base_keys || v isa ExtxyzType
if k in atoms_base_keys || v isa ExtxyzType || v isa AbstractVector{<: ExtxyzType}
# These are either Unitful quantities, which are uniformly supported
# across all of AtomsBase or the value has a type that Extxyz can write
# losslessly, so we can just write them no matter the value
Expand All @@ -79,7 +79,7 @@ function Atoms(system::AbstractSystem{D})
system_data = Dict{Symbol,Any}()
for (k, v) in pairs(system)
atoms_base_keys = (:charge, :multiplicity, :boundary_conditions, :bounding_box)
if k in atoms_base_keys || v isa ExtxyzType
if k in atoms_base_keys || v isa ExtxyzType || v isa AbstractArray{<: ExtxyzType}
# These are either Unitful quantities, which are uniformly supported
# across all of AtomsBase or the value has a type that Extxyz can write
# losslessly, so we can just write them no matter the value
Expand Down Expand Up @@ -136,7 +136,7 @@ function Atoms(dict::Dict{String, Any})
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]) ]
atom_data[Symbol(key)] = [ collect(col) for col in eachcol(arrays[key]) ]
else
atom_data[Symbol(key)] = arrays[key]
end
Expand Down Expand Up @@ -225,7 +225,12 @@ function write_dict(atoms::Atoms)
elseif v isa ExtxyzType
info[string(k)] = v
elseif v isa AbstractArray{<:ExtxyzType}
info[string(k)] = convert(Array, v)
if size(v, 1) != 3
@warn("Writing Array data with a first leading dimension " *
"different from 3 not supported.") # Else leads to segfaults
else
info[string(k)] = convert(Array, v)
end
else
@warn "Writing quantities of type $(typeof(v)) is not supported in write_dict."
end
Expand Down
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