Add BioPreDyn-bench B1, B2, B4, B5 benchmarks

.typos.toml

@@ -12,4 +12,6 @@ myu = "myu"
 ND = "ND"
 nd = "nd"
 ned = "ned"
-sitl = "sitl"
+sitl = "sitl"
+Ser = "Ser"
+inh = "inh"

benchmarks/Bio/BioPreDynB4.jmd

@@ -0,0 +1,161 @@
+---
+title: BioPreDyn-bench B4 Work-Precision Diagrams
+author: Chris Rackauckas
+---
+
+The following benchmark is of 35 ODEs modeling the metabolism of Chinese
+Hamster Ovary (CHO) cells from the
+[BioPreDyn-bench](https://doi.org/10.1186/s12918-015-0144-4) benchmark suite
+(Problem B4). The model describes a batch fermentation process with 32
+reactions including glycolysis, TCA cycle, amino acid metabolism, and product
+protein formation. The kinetics use log-linear elasticity coefficients with
+117 parameters.
+
+The model is manually translated from the original BioPreDyn-bench Matlab/C
+files since the SBML representation uses rate rules rather than reactions.
+
+```julia
+using OrdinaryDiffEq, DiffEqDevTools, Sundials, Plots,
+      LSODA, LinearAlgebra, BenchmarkTools,
+      SciMLBenchmarks
+
+gr()
+```
+
+## Load the model
+
+```julia
+include(joinpath(@__DIR__, "Models", "BioPreDyn", "b4_model.jl"))
+
+prob = ODEProblem{true, SciMLBase.FullSpecialize}(
+    biopredyn_b4!, B4_U0, B4_TSPAN, B4_NOMINAL_PARAMETERS)
+@show length(prob.u0)
+```
+
+## Picture of the solution
+
+```julia
+sol = solve(prob, Rodas5P(), abstol = 1e-8, reltol = 1e-8)
+plot(sol; legend = false, fmt = :png,
+     title = "BioPreDyn B4: CHO Cell Metabolism (35 ODEs)")
+```
+
+## Generate Reference Solution
+
+```julia
+@time sol = solve(prob, Rodas5P(), abstol = 1/10^14, reltol = 1/10^14)
+test_sol = TestSolution(sol);
+```
+
+## Setups
+
+```julia
+default(legendfontsize = 7, framestyle = :box, gridalpha = 0.3, gridlinewidth = 2.5)
+```
+
+## Work-Precision Diagrams (High Tolerances)
+
+```julia
+abstols = 1.0 ./ 10.0 .^ (5:8)
+reltols = 1.0 ./ 10.0 .^ (1:4)
+
+setups = [
+    Dict(:alg => Rosenbrock23()),
+    Dict(:alg => TRBDF2()),
+    Dict(:alg => FBDF()),
+    Dict(:alg => QNDF()),
+    Dict(:alg => Rodas4()),
+    Dict(:alg => Rodas5()),
+    Dict(:alg => RadauIIA5()),
+    Dict(:alg => lsoda()),
+    Dict(:alg => CVODE_BDF()),
+]
+
+wp = WorkPrecisionSet(prob, abstols, reltols, setups; error_estimate = :l2,
+    saveat = B4_TSPAN[2]/1000.0, appxsol = test_sol, maxiters = Int(1e5), numruns = 10)
+
+names = ["Rosenbrock23" "TRBDF2" "FBDF" "QNDF" "Rodas4" "Rodas5" "RadauIIA5" "lsoda" "CVODE_BDF"]
+plot(wp; label = names, title = "BioPreDyn B4: High Tolerances")
+```
+
+## Work-Precision Diagrams (Low Tolerances)
+
+```julia
+abstols = 1.0 ./ 10.0 .^ (7:12)
+reltols = 1.0 ./ 10.0 .^ (4:9)
+
+setups = [
+    Dict(:alg => FBDF()),
+    Dict(:alg => QNDF()),
+    Dict(:alg => Rodas4()),
+    Dict(:alg => Rodas5P()),
+    Dict(:alg => KenCarp4()),
+    Dict(:alg => KenCarp47()),
+    Dict(:alg => Kvaerno5()),
+    Dict(:alg => CVODE_BDF()),
+    Dict(:alg => lsoda()),
+    Dict(:alg => RadauIIA5()),
+]
+
+wp = WorkPrecisionSet(prob, abstols, reltols, setups; error_estimate = :l2,
+    saveat = B4_TSPAN[2]/1000.0, appxsol = test_sol, maxiters = Int(1e5), numruns = 10)
+
+names = ["FBDF" "QNDF" "Rodas4" "Rodas5P" "KenCarp4" "KenCarp47" "Kvaerno5" "CVODE_BDF" "lsoda" "RadauIIA5"]
+plot(wp; label = names, title = "BioPreDyn B4: Low Tolerances")
+```
+
+## Work-Precision Diagrams (SDIRK Methods)
+
+```julia
+abstols = 1.0 ./ 10.0 .^ (5:10)
+reltols = 1.0 ./ 10.0 .^ (2:7)
+
+setups = [
+    Dict(:alg => KenCarp3()),
+    Dict(:alg => KenCarp4()),
+    Dict(:alg => KenCarp5()),
+    Dict(:alg => Kvaerno3()),
+    Dict(:alg => Kvaerno4()),
+    Dict(:alg => Kvaerno5()),
+    Dict(:alg => TRBDF2()),
+    Dict(:alg => RadauIIA5()),
+]
+
+wp = WorkPrecisionSet(prob, abstols, reltols, setups; error_estimate = :l2,
+    saveat = B4_TSPAN[2]/1000.0, appxsol = test_sol, maxiters = Int(1e5), numruns = 10)
+
+names = ["KenCarp3" "KenCarp4" "KenCarp5" "Kvaerno3" "Kvaerno4" "Kvaerno5" "TRBDF2" "RadauIIA5"]
+plot(wp; label = names, title = "BioPreDyn B4: SDIRK Methods")
+```
+
+## Summary of Results
+
+```julia
+abstols = 1.0 ./ 10.0 .^ (5:12)
+reltols = 1.0 ./ 10.0 .^ (2:9)
+
+setups = [
+    Dict(:alg => CVODE_BDF()),
+    Dict(:alg => QNDF()),
+    Dict(:alg => FBDF()),
+    Dict(:alg => Rodas4()),
+    Dict(:alg => Rodas5P()),
+    Dict(:alg => KenCarp4()),
+    Dict(:alg => lsoda()),
+    Dict(:alg => RadauIIA5()),
+]
+
+wp = WorkPrecisionSet(prob, abstols, reltols, setups; error_estimate = :l2,
+    saveat = B4_TSPAN[2]/1000.0, appxsol = test_sol, maxiters = Int(1e5), numruns = 10)
+
+names = ["CVODE_BDF" "QNDF" "FBDF" "Rodas4" "Rodas5P" "KenCarp4" "lsoda" "RadauIIA5"]
+plot(wp; label = names, title = "BioPreDyn B4: Summary",
+    left_margin = 10Plots.mm, right_margin = 10Plots.mm,
+    legendfontsize = 10, tickfontsize = 10, guidefontsize = 10,
+    legend = :topright, lw = 2, markersize = 6, size = (800, 600))
+```
+
+```julia, echo = false
+using SciMLBenchmarks
+SciMLBenchmarks.bench_footer(WEAVE_ARGS[:folder], WEAVE_ARGS[:file])
+```