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Keep a reference to the Frame when returning position/velocities view #40

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Jun 24, 2020
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Keep a reference to the Frame when returning position/velocities view #40

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21 changes: 19 additions & 2 deletions src/Frame.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,21 @@ export distance, dihedral, out_of_plane
__ptr(frame::Frame) = __ptr(frame.__handle)
__const_ptr(frame::Frame) = __const_ptr(frame.__handle)

# A small wrapper around Array{Float64, 2}, keeping a reference to the
# corresponding frame to prevent garbage collection (see issue
# https://github.com/chemfiles/Chemfiles.jl/issues/37)
struct ChemfilesArray <: AbstractArray{Float64, 2}
data::Array{Float64, 2}
parent::Frame
end

# Implement the Array interface for ChemfilesArray
@inline Base.size(A::ChemfilesArray) = size(A.data)
@inline Base.getindex(A::ChemfilesArray, I::Int) = getindex(A.data, I)
@inline Base.getindex(A::ChemfilesArray, I::Int...) = getindex(A.data, I...)
@inline Base.setindex!(A::ChemfilesArray, v, I::Int) = setindex!(A.data, v, I)
@inline Base.setindex!(A::ChemfilesArray, v, I::Int...) = setindex!(A.data, v, I...)

"""
Frame()

Expand Down Expand Up @@ -63,7 +78,8 @@ function positions(frame::Frame)
ptr = Ref{Ptr{Float64}}()
natoms = Ref{UInt64}(0)
__check(lib.chfl_frame_positions(__ptr(frame), ptr, natoms))
return unsafe_wrap(Array{Float64, 2}, ptr[], (3, Int(natoms[])); own=false)
data = unsafe_wrap(Array{Float64, 2}, ptr[], (3, Int(natoms[])); own=false)
return ChemfilesArray(data, frame)
end


Expand All @@ -81,7 +97,8 @@ function velocities(frame::Frame)
ptr = Ref{Ptr{Float64}}()
natoms = Ref{UInt64}(0)
__check(lib.chfl_frame_velocities(__ptr(frame), ptr, natoms))
return unsafe_wrap(Array{Float64, 2}, ptr[], (3, Int(natoms[])); own=false)
data = unsafe_wrap(Array{Float64, 2}, ptr[], (3, Int(natoms[])); own=false)
return ChemfilesArray(data, frame)
end


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1 change: 1 addition & 0 deletions test/Frame.jl
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Expand Up @@ -5,6 +5,7 @@

resize!(frame, 4)
@test size(frame) == 4
@test length(frame) == 4

pos = positions(frame)
expected = Array{Float64}(undef, 3, 4)
Expand Down