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Merged
landinjm merged 3 commits into from
Dec 6, 2025
Merged

Cleanup of script testing #62

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895eea3
some more elegant tests for the scripts
landinjm Dec 5, 2025
ed72fcd
missed a little
landinjm Dec 5, 2025
343ce92
with bsk
landinjm Dec 5, 2025
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4 changes: 3 additions & 1 deletion Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "PoissonBoltzmannIPAM2025"
uuid = "480e0da0-c3fa-11f0-becb-6b90fb73a51e"
version = "0.1.0"
authors = ["Jürgen Fuhrmann <juergen-fuhrmann@web.de>"]
version = "0.1.0"

[deps]
Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
Expand All @@ -13,6 +13,7 @@ ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
HypertextLiteral = "ac1192a8-f4b3-4bfe-ba22-af5b92cd3ab2"
InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
JuliaMPBSolver = "d8b18f01-5396-498d-b34d-247825c18ff0"
LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
LessUnitful = "f29f6376-6e90-4d80-80c9-fb8ec61203d5"
Expand Down Expand Up @@ -42,6 +43,7 @@ ForwardDiff = "1"
HypertextLiteral = "0.9"
InteractiveUtils = "1.11.0"
Interpolations = "0.16"
JLD2 = "0.6.3"
LaTeXStrings = "1.0.1"
LessUnitful = "1"
Markdown = "1.11.0"
Expand Down
34 changes: 0 additions & 34 deletions draftnotebooks/demo-notebook.jl
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119 changes: 2 additions & 117 deletions scripts/simplecell-bsk.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ using Interpolations
using VoronoiFVM
using PythonPlot
using JuliaMPBSolver
using JLD2

const nel = 20.0 * JuliaMPBSolver.Units.el_surface_density # number of electrons/nm^2 at interfaces
const M_bulk = 1 # (bulk) molarity at center of domain
Expand Down Expand Up @@ -51,120 +52,4 @@ solution, X, nv, ε_r =
computed_parameters,
)

function bee!(y, ϕ)
N = length(user_parameters.charge_numbers)
for i in 1:N
y[i] =
JuliaMPBSolver.Units.thermal_energy(user_parameters.temperature) *
log(c_bulk[i] / computed_parameters.bulk_solvent_concentration) /
JuliaMPBSolver.Units.F - user_parameters.charge_numbers[i] * ϕ
end
return nothing
end

function bee(sol)
n = size(sol, 2)
N = length(user_parameters.charge_numbers)
e = zeros(N, n)
y = zeros(N)
for i in 1:n
bee!(y, sol[1, i])
for j in 1:N
e[j, i] = y[j]
end
end
return e
end

function plotsol(sol; size = (600, 400))
PythonPlot.clf()
fig, ax = pyplot.subplots(2, 1)
ax1 = ax[0]
ax2 = ax[1]
ax1.grid()
ax1r = ax1.twinx()

c = JuliaMPBSolver.Postprocess.compute_concentrations(
sol[1, :],
user_parameters,
computed_parameters,
)
cm = c[1, :] ⋅ nv / (JuliaMPBSolver.Units.M) / grid_parameters.domain_size
cp = c[2, :] ⋅ nv / (JuliaMPBSolver.Units.M) / grid_parameters.domain_size
c0 = -(sum(c, dims = 1) .- c̄)
e = bee(sol)
ax1.set_title(
"ϕ∈$(round.(Float64.(extrema(sol[1, :])), sigdigits = 3)), ε_r ∈$(round.(Float64.(extrema(ε_r)), sigdigits = 3))",
)
ax1.plot(
X / JuliaMPBSolver.Units.nm,
sol[1, :],
color = "green",
linewidth = 2,
label = "ϕ",
)
ax1.plot(
X / JuliaMPBSolver.Units.nm,
e[1, :],
color = "blue",
linewidth = 2,
label = L"ψ^+",
linestyle = "dotted",
)
ax1.plot(
X / JuliaMPBSolver.Units.nm,
e[2, :],
color = "red",
linewidth = 2,
linestyle = "dotted",
label = L"ψ^+",
)
ax1r.plot(
X[1:(end - 1)] / JuliaMPBSolver.Units.nm,
ε_r,
color = "pink",
linewidth = 3,
label = L"ε_r",
)
ax1.set_ylim(-10, 10)
ax1.set_xlabel("z/nm")
ax1.set_ylabel("ϕ/V")
ax1.legend(loc = (0.1, 0.1))
ax1r.legend(loc = (0.8, 0.1))
ax1r.set_ylim(0, 80)

ax2.grid()
ax2.set_title("M_avg=$(round.((cm, cp), sigdigits = 3))")
ax2.set_xlabel("z/nm")
ax2.set_ylabel("c/(mol/L)")
ax2.set_ylim(0, 60)

ax2.plot(
X / JuliaMPBSolver.Units.nm,
c[1, :] / (JuliaMPBSolver.Units.M),
color = "blue",
linewidth = 2,
label = L"c^-",
)
ax2.plot(
X / JuliaMPBSolver.Units.nm,
c[2, :] / (JuliaMPBSolver.Units.M),
color = "red",
linewidth = 2,
label = L"c^+",
)
ax2.plot(
X / JuliaMPBSolver.Units.nm,
c0[1, :] / (JuliaMPBSolver.Units.M),
color = "green",
linewidth = 2,
label = L"c_{solvent}",
)
ax2.legend(loc = (0.4, 0.1))

tight_layout()
savefig("simplecell-bsk.jpg", dpi = 300)
return PythonPlot.gcf()
end

plotsol(solution)
save("simplecell-bsk.jld2", "solution", solution, "X", X, "nv", nv, "ε_r", ε_r)
119 changes: 2 additions & 117 deletions scripts/simplecell.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ using Interpolations
using VoronoiFVM
using PythonPlot
using JuliaMPBSolver
using JLD2

const nel = 20.0 * JuliaMPBSolver.Units.el_surface_density # number of electrons/nm^2 at interfaces
const M_bulk = 1 # (bulk) molarity at center of domain
Expand Down Expand Up @@ -52,120 +53,4 @@ solution, X, nv, ε_r =
computed_parameters,
)

function bee!(y, ϕ)
N = length(user_parameters.charge_numbers)
for i in 1:N
y[i] =
JuliaMPBSolver.Units.thermal_energy(user_parameters.temperature) *
log(c_bulk[i] / computed_parameters.bulk_solvent_concentration) /
JuliaMPBSolver.Units.F - user_parameters.charge_numbers[i] * ϕ
end
return nothing
end

function bee(sol)
n = size(sol, 2)
N = length(user_parameters.charge_numbers)
e = zeros(N, n)
y = zeros(N)
for i in 1:n
bee!(y, sol[1, i])
for j in 1:N
e[j, i] = y[j]
end
end
return e
end

function plotsol(sol; size = (600, 400))
PythonPlot.clf()
fig, ax = pyplot.subplots(2, 1)
ax1 = ax[0]
ax2 = ax[1]
ax1.grid()
ax1r = ax1.twinx()

c = JuliaMPBSolver.Postprocess.compute_concentrations(
sol[1, :],
user_parameters,
computed_parameters,
)
cm = c[1, :] ⋅ nv / (JuliaMPBSolver.Units.M) / grid_parameters.domain_size
cp = c[2, :] ⋅ nv / (JuliaMPBSolver.Units.M) / grid_parameters.domain_size
c0 = -(sum(c, dims = 1) .- c̄)
e = bee(sol)
ax1.set_title(
"ϕ∈$(round.(Float64.(extrema(sol[1, :])), sigdigits = 3)), ε_r ∈$(round.(Float64.(extrema(ε_r)), sigdigits = 3))",
)
ax1.plot(
X / JuliaMPBSolver.Units.nm,
sol[1, :],
color = "green",
linewidth = 2,
label = "ϕ",
)
ax1.plot(
X / JuliaMPBSolver.Units.nm,
e[1, :],
color = "blue",
linewidth = 2,
label = L"ψ^+",
linestyle = "dotted",
)
ax1.plot(
X / JuliaMPBSolver.Units.nm,
e[2, :],
color = "red",
linewidth = 2,
linestyle = "dotted",
label = L"ψ^+",
)
ax1r.plot(
X[1:(end - 1)] / JuliaMPBSolver.Units.nm,
ε_r,
color = "pink",
linewidth = 3,
label = L"ε_r",
)
ax1.set_ylim(-10, 10)
ax1.set_xlabel("z/nm")
ax1.set_ylabel("ϕ/V")
ax1.legend(loc = (0.1, 0.1))
ax1r.legend(loc = (0.8, 0.1))
ax1r.set_ylim(0, 80)

ax2.grid()
ax2.set_title("M_avg=$(round.((cm, cp), sigdigits = 3))")
ax2.set_xlabel("z/nm")
ax2.set_ylabel("c/(mol/L)")
ax2.set_ylim(0, 60)

ax2.plot(
X / JuliaMPBSolver.Units.nm,
c[1, :] / (JuliaMPBSolver.Units.M),
color = "blue",
linewidth = 2,
label = L"c^-",
)
ax2.plot(
X / JuliaMPBSolver.Units.nm,
c[2, :] / (JuliaMPBSolver.Units.M),
color = "red",
linewidth = 2,
label = L"c^+",
)
ax2.plot(
X / JuliaMPBSolver.Units.nm,
c0[1, :] / (JuliaMPBSolver.Units.M),
color = "green",
linewidth = 2,
label = L"c_{solvent}",
)
ax2.legend(loc = (0.4, 0.1))

tight_layout()
savefig("simplecell.jpg", dpi = 300)
return PythonPlot.gcf()
end

plotsol(solution)
save("simplecell.jld2", "solution", solution, "X", X, "nv", nv, "ε_r", ε_r)
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30 changes: 29 additions & 1 deletion test/runtests.jl
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@@ -1,4 +1,9 @@
using Pkg, JuliaMPBSolver, ExampleJuggler, Test, Markdown
using Pkg
using JuliaMPBSolver
using ExampleJuggler
using Test
using Markdown
using JLD2

ExampleJuggler.verbose!(true)

Expand All @@ -11,8 +16,31 @@ notebooks = [
"SymmetricCellSurfaceCharge.jl",
]

scripts = [
"simplecell.jl",
"simplecell-bsk.jl",
]

@testset "Notebooks" begin
@testscripts(joinpath(@__DIR__, "..", "notebooks"), notebooks)
end

@testset "Scripts" begin
@testscripts(joinpath(@__DIR__, "..", "scripts"), scripts)

for script in scripts
script_name = script[1:(end - 3)]
solution, X, nv, ε_r = load(script_name * ".jld2", "solution", "X", "nv", "ε_r")
solution_reference, X_reference, nv_reference, ε_r_reference = load(script_name * "-reference.jld2", "solution", "X", "nv", "ε_r")

@test solution ≈ solution_reference
@test X ≈ X_reference
@test nv ≈ nv_reference
@test ε_r ≈ ε_r_reference

rm(script_name * ".jld2")
end

end

Pkg.test("JuliaMPBSolver")
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