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Change the scale of the figures in the spatial benchmark. #742

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Change the scale of the figures in the spatial benchmark. #742

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45d3ded
Change the scale of the sanft spatial model.
Vilin97 Sep 23, 2023
71ca3eb
Change the scale of the second figure.
Vilin97 Sep 23, 2023
d82c4bf
Fix typo.
Vilin97 Sep 25, 2023
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22 changes: 16 additions & 6 deletions benchmarks/Jumps/Spatial_Signaling_Sanft.jmd
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Original file line number Diff line number Diff line change
Expand Up @@ -195,23 +195,32 @@ function fetch_and_plot(bench_dict, domain_len)
end
len = length(medtimes[i])
plot!(plt1, Nv[1:len], medtimes[i], marker = :hex, label = name, lw = 2)
plot!(plt2, (Nv.^3)[1:len], medtimes[i], marker = :hex, label = name, lw = 2)
plot!(plt2, num_channels.(Nv[1:len]), medtimes[i], marker = :hex, label = name, lw = 2)
end

plot!(plt1, xlabel = "number of sites per edge", ylabel = "median time in seconds",
xticks = Nv, legend = :bottomright)
plot!(plt2, xlabel = "total number of sites", ylabel = "median time in seconds",
xticks = (Nv.^3, string.(Nv.^3)), legend = :bottomright)
plot(plt1, plt2; size = (1200,800), legendtitle = "SSAs",
plot_title="3D RDME, domain length = $domain_len", left_margin=5Plots.mm)
plot!(plt2, xlabel = "total number of channels", ylabel = "median time in seconds",
xticks = (num_channels.(Nv), string.(num_channels.(Nv))), legend = :bottomright)
plot(plt1, plt2; size = (1200,1200), legendtitle = "SSAs",
plot_title="3D RDME, domain length = $domain_len", left_margin=5Plots.mm, layout = (2, 1))
end

function num_channels(N::Int)
num_species = 8
num_sites = N^3
num_rxs = 12*num_sites
sum_outdegrees = (6*N^3 - 6*N^2)
num_species * sum_outdegrees + 12*num_rxs
end

```
We are now ready to run the benchmarks and plot the results. We start with a
domain length of `12` μm, analogous to Fig. 6 in [^1]:
```julia
bench_dict = Dict{Tuple{String, Int}, BenchmarkTools.Trial}()
algs = [NSM(), DirectCRDirect()]
Nv = [20, 30, 40, 50, 60, 90, 120, 240, 360]
Nv = 10:5:35
end_times = 20000.0 * ones(length(Nv))
domain_len = 12.0
benchmark_and_save!(bench_dict, end_times, Nv, algs, domain_len)
Expand All @@ -222,6 +231,7 @@ plt=fetch_and_plot(bench_dict, domain_len)
We next consider a domain of length `6` μm, analogous to Fig. 7 in [^1].
```julia
bench_dict = Dict{Tuple{String, Int}, BenchmarkTools.Trial}()
Nv = 10:5:60
domain_len = 6.0
benchmark_and_save!(bench_dict, end_times, Nv, algs, domain_len)
```
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