Tutorial: Solution of a stratospheric reaction problem
This tutorial is about the efficient solution of a stiff non-autonomous and non-conservative production-destruction systems (PDS) with a small number of differential equations. We will compare the use of standard arrays and static arrays from StaticArrays.jl and assess their efficiency.
Definition of the production-destruction system
This stratospheric reaction problem was described by Adrian Sandu in Positive Numerical Integration Methods for Chemical Kinetic Systems, see also the paper Positivity-preserving adaptive Runge–Kutta methods by Stefan Nüßlein, Hendrik Ranocha and David I. Ketcheson. The governing equations are
\[\begin{aligned} \frac{dO^{1D}}{dt} &= r_5 - r_6 - r_7,\\ \frac{dO}{dt} &= 2r_1 - r_2 + r_3 - r_4 + r_6 - r_9 + r_{10} - r_{11},\\ \frac{dO_3}{dt} &= r_2 - r_3 - r_4 - r_5 - r_7 - r_8,\\ \frac{dO_2}{dt} &= -r_1 -r_2 + r_3 + 2r_4+r_5+2r_7+r_8+r_9,\\ \frac{dNO}{dt} &= -r_8+r_9+r_{10}-r_{11},\\ \frac{dNO_2}{dt} &= r_8-r_9-r_{10}+r_{11}, \end{aligned}\]
with reaction rates
\[\begin{aligned} r_1 &=2.643⋅ 10^{-10}σ^3 O_2, & r_2 &=8.018⋅10^{-17}O O_2 , & r_3 &=6.12⋅10^{-4}σ O_3,\\ r_4 &=1.567⋅10^{-15}O_3 O , & r_5 &= 1.07⋅ 10^{-3}σ^2O_3, & r_6 &= 7.11⋅10^{-11}⋅ 8.12⋅10^6 O^{1D},\\ r_7 &= 1.2⋅10^{-10}O^{1D} O_3, & r_8 &= 6.062⋅10^{-15}O_3 NO, & r_9 &= 1.069⋅10^{-11}NO_2 O,\\ r_{10} &= 1.289⋅10^{-2}σ NO_2, & r_{11} &= 10^{-8}NO O, \end{aligned}\]
where
\[\begin{aligned} T &= t/3600 \mod 24,\quad T_r=4.5,\quad T_s = 19.5,\\ σ(T) &= \begin{cases}1, & T_r≤ T≤ T_s,\\0, & \text{otherwise}.\end{cases} \end{aligned}\]
Setting $\mathbf u = (O^{1D}, O, O_3, O_2, NO, NO_2)$ the initial value is $\mathbf{u}_0 = (9.906⋅10^1, 6.624⋅10^8, 5.326⋅10^{11}, 1.697⋅10^{16}, 4⋅10^6, 1.093⋅10^9)^T$. The time domain in seconds is $[4.32⋅10^{4}, 3.024⋅10^5]$, which corresponds to $[12.0, 84.0]$ in hours. There are two independent linear invariants, e.g. $u_1+u_2+3u_3+2u_4+u_5+2u_6=(1,1,3,2,1,2)\cdot\mathbf{u}_0$ and $u_5+u_6 = 1.097⋅10^9$.
The stratospheric reaction problem can be represented as a (non-conservative) PDS with production terms
\[\begin{aligned} p_{13} &= r_5, & p_{21} &= r_6, & p_{22} &= r_1+r_{10},\\ p_{23} &= r_3, & p_{24} &= r_1,& p_{32} &= r_2,\\ p_{41} &= r_7, & p_{42}&= r_4+r_9, & p_{43}&= r_4+r_7+r_8,\\ p_{44} &= r_3+r_5, & p_{56}&=r_9+r_{10}, & p_{65}&=r_8+r_{11}. \end{aligned}\]
and additional destruction terms
\[\begin{aligned} d_{22}&= r_{11}, & d_{44}&=r_2. \end{aligned}\]
In addition, all production and destruction terms not listed have the value zero.
Solution of the production-destruction system
Now we are ready to define a PDSProblem and to solve this problem with a method of PositiveIntegrators.jl or OrdinaryDiffEq.jl.
As mentioned above, we will try different approaches to solve this PDS and compare their efficiency. These are
- an out-of-place implementation with standard (dynamic) matrices and vectors,
- an in-place implementation with standard (dynamic) matrices and vectors,
- an out-of-place implementation with static matrices and vectors from StaticArrays.jl.
Standard out-of-place implementation
Here we create an out-of-place function to compute the production matrix with return type Matrix{Float64} and a second out-of-place function for the destruction vector with return type Vector{Float64}.
using PositiveIntegrators # load PDSProblem
function prod(u, p, t)
O1D, O, O3, O2, NO, NO2 = u
Tr = 4.5
Ts = 19.5
T = mod(t / 3600, 24)
if (Tr <= T) && (T <= Ts)
Tfrac = (2 * T - Tr - Ts) / (Ts - Tr)
sigma = 0.5 + 0.5 * cos(pi * abs(Tfrac) * Tfrac)
else
sigma = 0.0
end
M = 8.120e16
k1 = 2.643e-10 * sigma^3
k2 = 8.018e-17
k3 = 6.120e-4 * sigma
k4 = 1.567e-15
k5 = 1.070e-3 * sigma^2
k6 = 7.110e-11
k7 = 1.200e-10
k8 = 6.062e-15
k9 = 1.069e-11
k10 = 1.289e-2 * sigma
k11 = 1.0e-8
r1 = k1 * O2
r2 = k2 * O * O2
r3 = k3 * O3
r4 = k4 * O3 * O
r5 = k5 * O3
r6 = k6 * M * O1D
r7 = k7 * O1D * O3
r8 = k8 * O3 * NO
r9 = k9 * NO2 * O
r10 = k10 * NO2
r11 = k11 * NO * O
return [0.0 0.0 r5 0.0 0.0 0.0;
r6 r1+r10 r3 r1 0.0 0.0;
0.0 r2 0.0 0.0 0.0 0.0;
r7 r4+r9 r4+r7+r8 r3+r5 0.0 0.0;
0.0 0.0 0.0 0.0 0.0 r9+r10;
0.0 0.0 0.0 0.0 r8+r11 0.0]
end
function dest(u, p, t)
O1D, O, O3, O2, NO, NO2 = u
k2 = 8.018e-17
k11 = 1.0e-8
r2 = k2 * O * O2
r11 = k11 * NO * O
return [0.0, r11, 0.0, r2, 0.0, 0.0]
endThe solution of the stratospheric reaction problem can now be computed as follows.
u0 = [9.906e1, 6.624e8, 5.326e11, 1.697e16, 4e6, 1.093e9] # initial values
tspan = (4.32e4, 3.024e5) # time domain
prob_oop = PDSProblem(prod, dest, u0, tspan) # create the PDS
sol_oop = solve(prob_oop, MPRK43I(1.0, 0.5))Plotting the solution shows that the components $O¹ᴰ$, $O$ and $NO$ are in danger of becoming negative.
using Plots
plot(sol_oop,
layout=(3,2),
xguide = "t [h]",
xguidefontsize = 8,
xticks = (range(first(tspan), last(tspan), 4), range(12.0, 84.0, 4)),
yguide=["O¹ᴰ" "O" "O₃" "O₂" "NO" "NO₂"],
tickfontsize = 7,
legend = :none,
widen = true
)
PositiveIntegrators.jl provides the function isnonnegative (and also isnegative) to check if the solution is actually nonnegative, as expected from an MPRK scheme.
isnonnegative(sol_oop)trueStandard in-place implementation
Next we create in-place functions for the production matrix and the destruction vector.
function prod!(P, u, p, t)
O1D, O, O3, O2, NO, NO2 = u
Tr = 4.5
Ts = 19.5
T = mod(t / 3600, 24)
if (Tr <= T) && (T <= Ts)
Tfrac = (2 * T - Tr - Ts) / (Ts - Tr)
sigma = 0.5 + 0.5 * cos(pi * abs(Tfrac) * Tfrac)
else
sigma = 0.0
end
M = 8.120e16
k1 = 2.643e-10 * sigma^3
k2 = 8.018e-17
k3 = 6.120e-4 * sigma
k4 = 1.567e-15
k5 = 1.070e-3 * sigma^2
k6 = 7.110e-11
k7 = 1.200e-10
k8 = 6.062e-15
k9 = 1.069e-11
k10 = 1.289e-2 * sigma
k11 = 1.0e-8
r1 = k1 * O2
r2 = k2 * O * O2
r3 = k3 * O3
r4 = k4 * O3 * O
r5 = k5 * O3
r6 = k6 * M * O1D
r7 = k7 * O1D * O3
r8 = k8 * O3 * NO
r9 = k9 * NO2 * O
r10 = k10 * NO2
r11 = k11 * NO * O
fill!(P, zero(eltype(P)))
P[1, 3] = r5
P[2, 1] = r6
P[2, 2] = r1 + r10
P[2, 3] = r3
P[2, 4] = r1
P[3, 2] = r2
P[4, 1] = r7
P[4, 2] = r4 + r9
P[4, 3] = r4 + r7 + r8
P[4, 4] = r3 + r5
P[5, 6] = r9 + r10
P[6, 5] = r8 + r11
return nothing
end
function dest!(D, u, p, t)
O1D, O, O3, O2, NO, NO2 = u
k2 = 8.018e-17
k11 = 1.0e-8
r2 = k2 * O * O2
r11 = k11 * NO * O
fill!(D, zero(eltype(D)))
D[2] = r11
D[4] = r2
return nothing
endThe solution of the in-place implementation of the stratospheric reaction problem can now be computed as follows.
prob_ip = PDSProblem(prod!, dest!, u0, tspan) # create the PDS
sol_ip = solve(prob_ip, MPRK43I(1.0, 0.5))plot(sol_ip,
layout=(3,2),
xguide = "t [h]",
xguidefontsize = 8,
xticks = (range(first(tspan), last(tspan), 4), range(12.0, 84.0, 4)),
yguide=["O¹ᴰ" "O" "O₃" "O₂" "NO" "NO₂"],
tickfontsize = 7,
legend = :none,
widen = true
)
We also check that the in-place and out-of-place solutions are equivalent.
sol_oop.t ≈ sol_ip.t && sol_oop.u ≈ sol_ip.utrueUsing static arrays
For PDS with a small number of differential equations like the stratospheric reaction model the use of static arrays will be more efficient. To create a function which computes the production matrix and returns a static matrix, we only need to add the @SMatrix macro. Accordingly, we use the @SVector macro for the destruction vector.
using StaticArrays
function prod_static(u, p, t)
O1D, O, O3, O2, NO, NO2 = u
Tr = 4.5
Ts = 19.5
T = mod(t / 3600, 24)
if (Tr <= T) && (T <= Ts)
Tfrac = (2 * T - Tr - Ts) / (Ts - Tr)
sigma = 0.5 + 0.5 * cos(pi * abs(Tfrac) * Tfrac)
else
sigma = 0.0
end
M = 8.120e16
k1 = 2.643e-10 * sigma^3
k2 = 8.018e-17
k3 = 6.120e-4 * sigma
k4 = 1.567e-15
k5 = 1.070e-3 * sigma^2
k6 = 7.110e-11
k7 = 1.200e-10
k8 = 6.062e-15
k9 = 1.069e-11
k10 = 1.289e-2 * sigma
k11 = 1.0e-8
r1 = k1 * O2
r2 = k2 * O * O2
r3 = k3 * O3
r4 = k4 * O3 * O
r5 = k5 * O3
r6 = k6 * M * O1D
r7 = k7 * O1D * O3
r8 = k8 * O3 * NO
r9 = k9 * NO2 * O
r10 = k10 * NO2
r11 = k11 * NO * O
return @SMatrix [0.0 0.0 r5 0.0 0.0 0.0;
r6 r1+r10 r3 r1 0.0 0.0;
0.0 r2 0.0 0.0 0.0 0.0;
r7 r4+r9 r4+r7+r8 r3+r5 0.0 0.0;
0.0 0.0 0.0 0.0 0.0 r9+r10;
0.0 0.0 0.0 0.0 r8+r11 0.0]
end
function dest_static(u, p, t)
O1D, O, O3, O2, NO, NO2 = u
k2 = 8.018e-17
k11 = 1.0e-8
r2 = k2 * O * O2
r11 = k11 * NO * O
return @SVector [0.0, r11, 0.0, r2, 0.0, 0.0]
endIn addition we also want to use a static vector to hold the initial conditions.
u0_static = @SVector [9.906e1, 6.624e8, 5.326e11, 1.697e16, 4e6, 1.093e9] # initial values
prob_static = PDSProblem(prod_static, dest_static, u0_static, tspan) # create the PDS
sol_static = solve(prob_static, MPRK43I(1.0, 0.5))This solution is also nonnegative.
isnonnegative(sol_static)trueusing Plots
plot(sol_static,
layout=(3,2),
xguide = "t [h]",
xguidefontsize = 8,
xticks = (range(first(tspan), last(tspan), 4), range(12.0, 84.0, 4)),
yguide=["O¹ᴰ" "O" "O₃" "O₂" "NO" "NO₂"],
tickfontsize = 7,
legend = :none,
widen = true
)
The above implementation of the stratospheric reaction problem using StaticArrays can also be found in the Example Problems as prob_pds_stratreac.
Preservation of linear invariants
As MPRK schemes do not preserve general linear invariants, especially when applied to non-conservative PDS, we compute and plot the relative errors with respect to both linear invariants to see how well these are preserved.
linear_invariant(a, u) = sum(a .* u)
function relerr_lininv(a, u0, sol)
c = linear_invariant(a, u0)
return abs.(c .- (x -> linear_invariant(a, x)).(sol.u))./c
end
a1 = [1; 1; 3; 2; 1; 2] # first linear invariant
a2 = [0; 0; 0; 0; 1; 1] # second linear invariant
p1 = plot(sol_oop.t, relerr_lininv(a1, u0, sol_oop))
p2 = plot(sol_oop.t, relerr_lininv(a2, u0, sol_oop))
plot(p1, p2,
xticks = (range(first(tspan), last(tspan), 4), range(12.0, 84.0, 4)),
legend = :none)
In contrast to MPRK schemes, Runge-Kutta and Rosenbrock methods preserve all linear invariants, but are not guaranteed to generate nonnegative solutions. One way to enforce nonnegative solutions of such schemes is passing isnegative to the solver option isoutofdomain. We show this using the Rosenbrock scheme Rosenbrock23 as an example.
using OrdinaryDiffEq
sol_tmp = solve(prob_oop, Rosenbrock23());
isnonnegative(sol_tmp)falsesol_Ros23 = solve(prob_oop, Rosenbrock23(), isoutofdomain = isnegative);
isnonnegative(sol_Ros23)truep3 = plot(sol_Ros23.t, relerr_lininv(a1, u0, sol_Ros23))
p4 = plot(sol_Ros23.t, relerr_lininv(a2, u0, sol_Ros23))
plot(p3, p4,
xticks = (range(first(tspan), last(tspan), 4), range(12.0, 84.0, 4)),
legend = :none)
Performance comparison
Finally, we use BenchmarkTools.jl to compare the different implementations and to show the benefit of using static arrays.
using BenchmarkTools
@benchmark solve(prob_oop, MPRK43I(1.0, 0.5))BenchmarkTools.Trial: 4 samples with 1 evaluation.
Range (min … max): 1.330 s … 1.426 s ┊ GC (min … max): 2.92% … 3.69%
Time (median): 1.383 s ┊ GC (median): 3.31%
Time (mean ± σ): 1.381 s ± 39.392 ms ┊ GC (mean ± σ): 3.34% ± 2.76%
█ █ █ █
█▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁█▁▁▁▁▁█▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁█ ▁
1.33 s Histogram: frequency by time 1.43 s <
Memory estimate: 390.12 MiB, allocs estimate: 4912678.using BenchmarkTools
@benchmark solve(prob_ip, MPRK43I(1.0, 0.5))BenchmarkTools.Trial: 64 samples with 1 evaluation.
Range (min … max): 63.879 ms … 134.440 ms ┊ GC (min … max): 0.00% … 47.80%
Time (median): 78.690 ms ┊ GC (median): 0.00%
Time (mean ± σ): 78.729 ms ± 11.682 ms ┊ GC (mean ± σ): 5.83% ± 10.27%
▂▅ ▂▅ ▂███
████▁█▅▁▁▅▁▅▅▁▅▅▁▁▅▁▅▁██▅█████▁▅▁▁▁▁▅▁▁▅▅▅▁▁▅▁▁▅▁▁▅▁▅▅▁▁▅▁▅█ ▁
63.9 ms Histogram: frequency by time 98.1 ms <
Memory estimate: 37.24 MiB, allocs estimate: 181827.@benchmark solve(prob_static, MPRK43I(1.0, 0.5))BenchmarkTools.Trial: 135 samples with 1 evaluation.
Range (min … max): 27.105 ms … 91.297 ms ┊ GC (min … max): 0.00% … 62.01%
Time (median): 36.713 ms ┊ GC (median): 0.00%
Time (mean ± σ): 37.103 ms ± 8.334 ms ┊ GC (mean ± σ): 7.76% ± 13.40%
▆ ▁▆█▁
█▆▇▁▁▁▅▁▅▆▆▅▆▁▁▅▅▁████▁▅▁▁▁▁▁▁▁▁▅▅▅▁▁▁▅▁▅▅▅▆▆▁▅▅▁▁▁▇▁▆▁▅▅▅▅ ▅
27.1 ms Histogram: log(frequency) by time 55.4 ms <
Memory estimate: 25.29 MiB, allocs estimate: 90923.Package versions
These results were obtained using the following versions.
using InteractiveUtils
versioninfo()
println()
using Pkg
Pkg.status(["PositiveIntegrators", "StaticArrays", "LinearSolve", "OrdinaryDiffEq"],
mode=PKGMODE_MANIFEST)Julia Version 1.10.5
Commit 6f3fdf7b362 (2024-08-27 14:19 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: 4 × AMD EPYC 7763 64-Core Processor
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)
Environment:
JULIA_PKG_SERVER_REGISTRY_PREFERENCE = eager
Status `~/work/PositiveIntegrators.jl/PositiveIntegrators.jl/docs/Manifest.toml`
[7ed4a6bd] LinearSolve v2.33.0
[1dea7af3] OrdinaryDiffEq v6.89.0
[d1b20bf0] PositiveIntegrators v0.2.6 `~/work/PositiveIntegrators.jl/PositiveIntegrators.jl`
[90137ffa] StaticArrays v1.9.7