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@nathanaelbosch
nathanaelbosch committed Nov 3, 2023
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Showing 8 changed files with 1,379 additions and 1,386 deletions.
1 change: 1 addition & 0 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ DiffEqDevTools = "f3b72e0c-5b89-59e1-b016-84e28bfd966d"
ExponentialUtilities = "d4d017d3-3776-5f7e-afef-a10c40355c18"
FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898"
FastGaussQuadrature = "442a2c76-b920-505d-bb47-c5924d526838"
FiniteHorizonGramians = "b59a298d-d283-4a37-9369-85a9f9a111a5"
ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
FunctionWrappersWrappers = "77dc65aa-8811-40c2-897b-53d922fa7daf"
GaussianDistributions = "43dcc890-d446-5863-8d1a-14597580bb8d"
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24 changes: 10 additions & 14 deletions benchmarks/hodgkinhuxley.jmd
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Original file line number Diff line number Diff line change
Expand Up @@ -77,21 +77,19 @@ plot(test_sol,
DENSE = SAVE_EVERYSTEP = false

_setups = [
"EK0(2)" => Dict(:alg=>EK0(order=2, smooth=DENSE))
"EK0(3)" => Dict(:alg=>EK0(order=3, smooth=DENSE))
"EK0(5)" => Dict(:alg=>EK0(order=5, smooth=DENSE))
"EK1(2)" => Dict(:alg=>EK1(order=2, smooth=DENSE))
"EK1(3)" => Dict(:alg=>EK1(order=3, smooth=DENSE))
"EK1(5)" => Dict(:alg=>EK1(order=5, smooth=DENSE))
"EK1(8)" => Dict(:alg=>EK1(order=8, smooth=DENSE))
"RosenbrockExpEK1(2)" => Dict(:alg=>RosenbrockExpEK(order=2, smooth=DENSE))
"RosenbrockExpEK1(3)" => Dict(:alg=>RosenbrockExpEK(order=3, smooth=DENSE))
"RosenbrockExpEK1(5)" => Dict(:alg=>RosenbrockExpEK(order=5, smooth=DENSE))
"RosenbrockExpEK1(8)" => Dict(:alg=>RosenbrockExpEK(order=8, smooth=DENSE))
]

labels = first.(_setups)
setups = last.(_setups)
colors = [1 1 1 2 2 2 2 3 3 3]
colors = [1 1 2 2 2 3 3 3]

abstols = 1.0 ./ 10.0 .^ (6:10)
reltols = 1.0 ./ 10.0 .^ (3:7)
Expand Down Expand Up @@ -124,21 +122,19 @@ plot(
DENSE = SAVE_EVERYSTEP = true

_setups = [
"EK0(2)" => Dict(:alg=>EK0(order=2, smooth=DENSE))
"EK0(3)" => Dict(:alg=>EK0(order=3, smooth=DENSE))
"EK0(5)" => Dict(:alg=>EK0(order=5, smooth=DENSE))
"EK1(2)" => Dict(:alg=>EK1(order=2, smooth=DENSE))
"EK1(3)" => Dict(:alg=>EK1(order=3, smooth=DENSE))
"EK1(5)" => Dict(:alg=>EK1(order=5, smooth=DENSE))
"EK1(8)" => Dict(:alg=>EK1(order=8, smooth=DENSE))
"RosenbrockExpEK1(2)" => Dict(:alg=>RosenbrockExpEK(order=2, smooth=DENSE))
"RosenbrockExpEK1(3)" => Dict(:alg=>RosenbrockExpEK(order=3, smooth=DENSE))
"RosenbrockExpEK1(5)" => Dict(:alg=>RosenbrockExpEK(order=5, smooth=DENSE))
"RosenbrockExpEK1(8)" => Dict(:alg=>RosenbrockExpEK(order=8, smooth=DENSE))
]

labels = first.(_setups)
setups = last.(_setups)
colors = [1 1 1 2 2 2 2 3 3 3]
colors = [1 1 2 2 2 3 3 3]

abstols = 1.0 ./ 10.0 .^ (6:10)
reltols = 1.0 ./ 10.0 .^ (3:7)
Expand Down Expand Up @@ -176,9 +172,9 @@ abstols = reltols = repeat([missing], length(dts))

DM = FixedDiffusion()
_setups = [
"EK0(2)" => Dict(:alg=>EK0(order=2, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"EK1(2)" => Dict(:alg=>EK1(order=2, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"RosenbrockExpEK1(2)" => Dict(:alg=>RosenbrockExpEK(order=2, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"EK0(3)" => Dict(:alg=>EK0(order=3, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"EK1(3)" => Dict(:alg=>EK1(order=3, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"RosenbrockExpEK1(3)" => Dict(:alg=>RosenbrockExpEK(order=3, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
]

labels = first.(_setups)
Expand Down Expand Up @@ -218,9 +214,9 @@ dts = 10.0 .^ range(-2, -3, length=length(abstols))

DM = FixedDiffusion()
_setups = [
"EK0(2)" => Dict(:alg=>EK0(order=2, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"EK1(2)" => Dict(:alg=>EK1(order=2, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"RosenbrockExpEK1(2)" => Dict(:alg=>RosenbrockExpEK(order=2, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"EK0(3)" => Dict(:alg=>EK0(order=3, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"EK1(3)" => Dict(:alg=>EK1(order=3, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"RosenbrockExpEK1(3)" => Dict(:alg=>RosenbrockExpEK(order=3, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
]

labels = first.(_setups)
Expand Down
834 changes: 417 additions & 417 deletions docs/src/benchmarks/figures/hodgkinhuxley_2_1.svg
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494 changes: 238 additions & 256 deletions docs/src/benchmarks/figures/hodgkinhuxley_3_1.svg
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486 changes: 232 additions & 254 deletions docs/src/benchmarks/figures/hodgkinhuxley_4_1.svg
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450 changes: 234 additions & 216 deletions docs/src/benchmarks/figures/hodgkinhuxley_5_1.svg
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444 changes: 233 additions & 211 deletions docs/src/benchmarks/figures/hodgkinhuxley_6_1.svg
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32 changes: 14 additions & 18 deletions docs/src/benchmarks/hodgkinhuxley.md
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Original file line number Diff line number Diff line change
Expand Up @@ -84,21 +84,19 @@ plot(test_sol,
DENSE = SAVE_EVERYSTEP = false

_setups = [
"EK0(2)" => Dict(:alg=>EK0(order=2, smooth=DENSE))
"EK0(3)" => Dict(:alg=>EK0(order=3, smooth=DENSE))
"EK0(5)" => Dict(:alg=>EK0(order=5, smooth=DENSE))
"EK1(2)" => Dict(:alg=>EK1(order=2, smooth=DENSE))
"EK1(3)" => Dict(:alg=>EK1(order=3, smooth=DENSE))
"EK1(5)" => Dict(:alg=>EK1(order=5, smooth=DENSE))
"EK1(8)" => Dict(:alg=>EK1(order=8, smooth=DENSE))
"RosenbrockExpEK1(2)" => Dict(:alg=>RosenbrockExpEK(order=2, smooth=DENSE))
"RosenbrockExpEK1(3)" => Dict(:alg=>RosenbrockExpEK(order=3, smooth=DENSE))
"RosenbrockExpEK1(5)" => Dict(:alg=>RosenbrockExpEK(order=5, smooth=DENSE))
"RosenbrockExpEK1(8)" => Dict(:alg=>RosenbrockExpEK(order=8, smooth=DENSE))
]

labels = first.(_setups)
setups = last.(_setups)
colors = [1 1 1 2 2 2 2 3 3 3]
colors = [1 1 2 2 2 3 3 3]

abstols = 1.0 ./ 10.0 .^ (6:10)
reltols = 1.0 ./ 10.0 .^ (3:7)
Expand All @@ -118,7 +116,7 @@ wp = WorkPrecisionSet(

plot(
wp,
title = "Hodgkin-Huxley with adaptive steps",
title = "Adaptive steps - no smoothing",
color = colors,
xticks = 10.0 .^ (-16:1:5),
yticks = 10.0 .^ (-6:1:5),
Expand All @@ -135,21 +133,19 @@ plot(
DENSE = SAVE_EVERYSTEP = true

_setups = [
"EK0(2)" => Dict(:alg=>EK0(order=2, smooth=DENSE))
"EK0(3)" => Dict(:alg=>EK0(order=3, smooth=DENSE))
"EK0(5)" => Dict(:alg=>EK0(order=5, smooth=DENSE))
"EK1(2)" => Dict(:alg=>EK1(order=2, smooth=DENSE))
"EK1(3)" => Dict(:alg=>EK1(order=3, smooth=DENSE))
"EK1(5)" => Dict(:alg=>EK1(order=5, smooth=DENSE))
"EK1(8)" => Dict(:alg=>EK1(order=8, smooth=DENSE))
"RosenbrockExpEK1(2)" => Dict(:alg=>RosenbrockExpEK(order=2, smooth=DENSE))
"RosenbrockExpEK1(3)" => Dict(:alg=>RosenbrockExpEK(order=3, smooth=DENSE))
"RosenbrockExpEK1(5)" => Dict(:alg=>RosenbrockExpEK(order=5, smooth=DENSE))
"RosenbrockExpEK1(8)" => Dict(:alg=>RosenbrockExpEK(order=8, smooth=DENSE))
]

labels = first.(_setups)
setups = last.(_setups)
colors = [1 1 1 2 2 2 2 3 3 3]
colors = [1 1 2 2 2 3 3 3]

abstols = 1.0 ./ 10.0 .^ (6:10)
reltols = 1.0 ./ 10.0 .^ (3:7)
Expand All @@ -169,7 +165,7 @@ wp = WorkPrecisionSet(

plot(
wp,
title = "Hodgkin-Huxley with adaptive steps",
title = "Adaptive steps - with smoothing",
color = colors,
xticks = 10.0 .^ (-16:1:5),
yticks = 10.0 .^ (-6:1:5),
Expand All @@ -191,9 +187,9 @@ abstols = reltols = repeat([missing], length(dts))

DM = FixedDiffusion()
_setups = [
"EK0(2)" => Dict(:alg=>EK0(order=2, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"EK1(2)" => Dict(:alg=>EK1(order=2, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"RosenbrockExpEK1(2)" => Dict(:alg=>RosenbrockExpEK(order=2, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"EK0(3)" => Dict(:alg=>EK0(order=3, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"EK1(3)" => Dict(:alg=>EK1(order=3, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"RosenbrockExpEK1(3)" => Dict(:alg=>RosenbrockExpEK(order=3, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
]

labels = first.(_setups)
Expand All @@ -216,7 +212,7 @@ wp = WorkPrecisionSet(

plot(
wp,
title = "Hodgkin-Huxley with fixed steps",
title = "Fixed steps - no smoothing",
color = colors,
xticks = 10.0 .^ (-16:1:5),
yticks = 10.0 .^ (-6:1:5),
Expand All @@ -237,9 +233,9 @@ dts = 10.0 .^ range(-2, -3, length=length(abstols))

DM = FixedDiffusion()
_setups = [
"EK0(2)" => Dict(:alg=>EK0(order=2, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"EK1(2)" => Dict(:alg=>EK1(order=2, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"RosenbrockExpEK1(2)" => Dict(:alg=>RosenbrockExpEK(order=2, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"EK0(3)" => Dict(:alg=>EK0(order=3, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"EK1(3)" => Dict(:alg=>EK1(order=3, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
"RosenbrockExpEK1(3)" => Dict(:alg=>RosenbrockExpEK(order=3, diffusionmodel=DM, smooth=DENSE), :dts=>dts)
]

labels = first.(_setups)
Expand All @@ -262,7 +258,7 @@ wp = WorkPrecisionSet(

plot(
wp,
title = "Hodgkin-Huxley with fixed steps",
title = "Fixed steps - with smoothing",
color = colors,
xticks = 10.0 .^ (-16:1:5),
yticks = 10.0 .^ (-6:1:5),
Expand Down

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