Saving solution data from ODEIntegrator types

General Usage
1

Hi all,

I’m not getting the output I expect when following the I/O: Saving and Loading Solution Data section of the DifferentialEquations.jl docs.

I’ve solved my ODE via the integrator interface, so my type looks like this:

julia> typeof(model.lake)
OrdinaryDiffEq.ODEIntegrator{OrdinaryDiffEq.Tsit5, true, Vector{Float64}, Nothing, Float64, LimnoSES.MartinParameters, Float64, Float64, Float64, Vector{Vector{Float64}}, SciMLBase.ODESolution{Float64, 2, Vector{Vector{Float64}}, Nothing, Nothing, Vector{Float64}, Vector{Vector{Vector{Float64}}}, SciMLBase.ODEProblem{Vector{Float64}, Tuple{Float64, Float64}, true, LimnoSES.MartinParameters, SciMLBase.ODEFunction{true, typeof(LimnoSES.lake_dynamics!), LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED), Nothing}, Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}, SciMLBase.StandardODEProblem}, OrdinaryDiffEq.Tsit5, OrdinaryDiffEq.InterpolationData{SciMLBase.ODEFunction{true, typeof(LimnoSES.lake_dynamics!), LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED), Nothing}, Vector{Vector{Float64}}, Vector{Float64}, Vector{Vector{Vector{Float64}}}, OrdinaryDiffEq.Tsit5Cache{Vector{Float64}, Vector{Float64}, Vector{Float64}, OrdinaryDiffEq.Tsit5ConstantCache{Float64, Float64}}}, DiffEqBase.DEStats}, SciMLBase.ODEFunction{true, typeof(LimnoSES.lake_dynamics!), LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED), Nothing}, OrdinaryDiffEq.Tsit5Cache{Vector{Float64}, Vector{Float64}, Vector{Float64}, OrdinaryDiffEq.Tsit5ConstantCache{Float64, Float64}}, OrdinaryDiffEq.DEOptions{Float64, Float64, Float64, Float64, typeof(DiffEqBase.ODE_DEFAULT_NORM), typeof(LinearAlgebra.opnorm), DiffEqBase.CallbackSet{Tuple{}, Tuple{}}, typeof(DiffEqBase.ODE_DEFAULT_ISOUTOFDOMAIN), typeof(DiffEqBase.ODE_DEFAULT_PROG_MESSAGE), typeof(DiffEqBase.ODE_DEFAULT_UNSTABLE_CHECK), DataStructures.BinaryMinHeap{Float64}, DataStructures.BinaryMinHeap{Float64}, Nothing, Nothing, Int64, Tuple{}, Tuple{}, Tuple{}}, Vector{Float64}, Float64, Nothing, OrdinaryDiffEq.DefaultInit}

julia> typeof(model.lake.sol)
SciMLBase.ODESolution{Float64, 2, Vector{Vector{Float64}}, Nothing, Nothing, Vector{Float64}, Vector{Vector{Vector{Float64}}}, SciMLBase.ODEProblem{Vector{Float64}, Tuple{Float64, Float64}, true, LimnoSES.MartinParameters, SciMLBase.ODEFunction{true, typeof(LimnoSES.lake_dynamics!), LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED), Nothing}, Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}, SciMLBase.StandardODEProblem}, OrdinaryDiffEq.Tsit5, OrdinaryDiffEq.InterpolationData{SciMLBase.ODEFunction{true, typeof(LimnoSES.lake_dynamics!), LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED), Nothing}, Vector{Vector{Float64}}, Vector{Float64}, Vector{Vector{Vector{Float64}}}, OrdinaryDiffEq.Tsit5Cache{Vector{Float64}, Vector{Float64}, Vector{Float64}, OrdinaryDiffEq.Tsit5ConstantCache{Float64, Float64}}}, DiffEqBase.DEStats}

When I try df = DataFrame(model.lake.sol), rather than the timestamp and values of the solution, the dataframe looks like this:

3×13 DataFrame
 Row │ x1       x2       x3       x4       x5       x6       x7       x8       x9       x10       ⋯
     │ Float64  Float64  Float64  Float64  Float64  Float64  Float64  Float64  Float64  Float64   ⋯
─────┼─────────────────────────────────────────────────────────────────────────────────────────────
   1 │ 20.5172  20.5172  20.5172  20.5172  20.5172  20.5172  20.5172  20.5172  20.5172  20.5172   ⋯
   2 │  1.7865   1.7865   1.7865   1.7865   1.7865   1.7865   1.7865   1.7865   1.7865   1.7865
   3 │ 56.8443  56.8443  56.8443  56.8443  56.8443  56.8443  56.8443  56.8443  56.8444  56.8444
                                                                                  3 columns omitted

It’s not obvious what I should do to get this to work as intended.

2

It’s a DataFrames.jl bug fixed in DataFrames.jl 1.0, or so I hear from the DF devs.

2 Likes
3

Great! Thanks Chis. Will wait for the next release.