replace JuliaMPBSolver by AugmentedPoissonBoltzmann

.github/workflows/ci.yml

@@ -48,6 +48,10 @@ jobs:
             ${{ runner.os }}-test-${{ env.cache-name }}-
             ${{ runner.os }}-test-
             ${{ runner.os }}-
+      - run: |
+          julia --project -e '
+            using Pkg
+            Pkg.Registry.add(url="https://github.com/j-fu/PackageNursery")'
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
         env:

Project.toml

@@ -1,9 +1,10 @@
 name = "PoissonBoltzmannIPAM2025"
 uuid = "480e0da0-c3fa-11f0-becb-6b90fb73a51e"
-authors = ["Jürgen Fuhrmann <juergen-fuhrmann@web.de>"]
 version = "0.1.0"
+authors = ["Jürgen Fuhrmann <juergen-fuhrmann@web.de>"]
 
 [deps]
+AugmentedPoissonBoltzmann = "d8b18f01-5396-498d-b34d-247825c18ff1"
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
 DoubleFloats = "497a8b3b-efae-58df-a0af-a86822472b78"
 DrWatson = "634d3b9d-ee7a-5ddf-bec9-22491ea816e1"
@@ -14,7 +15,6 @@ 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"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
@@ -31,10 +31,8 @@ UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 VoronoiFVM = "82b139dc-5afc-11e9-35da-9b9bdfd336f3"
 
-[sources]
-JuliaMPBSolver = {path = "packages/JuliaMPBSolver"}
-
 [compat]
+AugmentedPoissonBoltzmann = "0.4.1"
 DoubleFloats = "1"
 DynamicQuantities = "1.10.0"
 ExampleJuggler = "2.4.0"
@@ -57,9 +55,9 @@ julia = "1.11"
 
 [extras]
 ExampleJuggler = "3bbe58f8-ed81-4c4e-a134-03e85fcf4a1a"
-JuliaMPBSolver = "d8b18f01-5396-498d-b34d-247825c18ff0"
+AugmentedPoissonBoltzmann = "d8b18f01-5396-498d-b34d-247825c18ff1"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Pkg", "Test", "JuliaMPBSolver", "ExampleJuggler"]
+test = ["Pkg", "Test", "AugmentedPoissonBoltzmann", "ExampleJuggler"]

notebooks/HalfCellAppliedPotential.jl

@@ -21,7 +21,7 @@ begin
     using PythonPlot: pyplot
     using LaTeXStrings
     using Colors
-    using JuliaMPBSolver.ICMPBP: ICMPBP, ICMPBData, AppliedPotentialHalfCell, set_molarity!, calc_cmol, calc_c0mol, calc_χ, get_E, get_φ, get_p, get_c0,
+    using AugmentedPoissonBoltzmann.ICMPBP: ICMPBP, ICMPBData, AppliedPotentialHalfCell, set_molarity!, calc_cmol, calc_c0mol, calc_χ, get_E, get_φ, get_p, get_c0,
         set_κ!, set_φ!
     using DrWatson, PoissonBoltzmannIPAM2025
 

notebooks/ICMPBP-DD-Draft.jl

@@ -28,7 +28,7 @@ begin
     using LessUnitful
     using Test
     using PythonPlot
-    using JuliaMPBSolver.ICMPBP: ICMPBData, ICMPBSystem, L_Debye, set_molarity!, dlcap0, DerivedData, apply_charge!, ysum, qsweep, capscalc, calc_cmol, calc_c0mol, calc_χ, W, pramp
+    using AugmentedPoissonBoltzmann.ICMPBP: ICMPBData, ICMPBSystem, L_Debye, set_molarity!, dlcap0, DerivedData, apply_charge!, ysum, qsweep, capscalc, calc_cmol, calc_c0mol, calc_χ, W, pramp
 end
 
 # ╔═╡ ef660f6f-9de3-4896-a65e-13c60df5de1e

notebooks/ICMPBP-Draft.jl

@@ -19,7 +19,7 @@ begin
     using Test
     using PythonPlot
     using Colors
-    using JuliaMPBSolver.ICMPBP: ICMPBData, ICMPBSystem, L_Debye, set_molarity!, dlcap0, DerivedData, apply_charge!, ysum, qsweep, capscalc
+    using AugmentedPoissonBoltzmann.ICMPBP: ICMPBData, ICMPBSystem, L_Debye, set_molarity!, dlcap0, DerivedData, apply_charge!, ysum, qsweep, capscalc
 end
 
 # ╔═╡ ef660f6f-9de3-4896-a65e-13c60df5de1e

notebooks/ICMPBP-EndOfHackathon.jl

@@ -29,7 +29,7 @@ begin
     using Test
     using PythonPlot
     using Colors
-    using JuliaMPBSolver.ICMPBP: ICMPBData, ICMPBSystem, L_Debye, set_molarity!, dlcap0, DerivedData, apply_charge!, ysum, qsweep, capscalc, calc_cmol, calc_c0mol
+    using AugmentedPoissonBoltzmann.ICMPBP: ICMPBData, ICMPBSystem, L_Debye, set_molarity!, dlcap0, DerivedData, apply_charge!, ysum, qsweep, capscalc, calc_cmol, calc_c0mol
 end
 
 # ╔═╡ ef660f6f-9de3-4896-a65e-13c60df5de1e

notebooks/MPBP-Draft.jl

@@ -19,7 +19,7 @@ begin
     using Test
     using PythonPlot
     using Colors
-    using JuliaMPBSolver.ICMPBP: ICMPBData, ICMPBSystem, L_Debye, set_molarity!, dlcap0, DerivedData, apply_charge!, ysum, qsweep, capscalc
+    using AugmentedPoissonBoltzmann.ICMPBP: ICMPBData, ICMPBSystem, L_Debye, set_molarity!, dlcap0, DerivedData, apply_charge!, ysum, qsweep, capscalc
 end
 
 # ╔═╡ ef660f6f-9de3-4896-a65e-13c60df5de1e

notebooks/SymmetricCellSurfaceCharge.jl

@@ -22,7 +22,7 @@ begin
     using LaTeXStrings
     using Colors
     using DrWatson, PoissonBoltzmannIPAM2025
-    using JuliaMPBSolver.ICMPBP: ICMPBP, ICMPBData, SurfaceChargedSymmetricCell, AbstractSymmetricCell, set_molarity!, calc_cmol, calc_c0mol, calc_χ, get_E, get_φ, get_p, get_c0,
+    using AugmentedPoissonBoltzmann.ICMPBP: ICMPBP, ICMPBData, SurfaceChargedSymmetricCell, AbstractSymmetricCell, set_molarity!, calc_cmol, calc_c0mol, calc_χ, get_E, get_φ, get_p, get_c0,
         set_κ!, set_q!
 end
 

scripts/ICMPB-csv.jl

@@ -19,15 +19,15 @@ using DelimitedFiles
 using DrWatson
 
 using PoissonBoltzmannIPAM2025
-using JuliaMPBSolver
+using AugmentedPoissonBoltzmann
 
-const nel = 1.0 * JuliaMPBSolver.Units.el_surface_density # number of electrons/nm^2 at interfaces
+const nel = 1.0 * AugmentedPoissonBoltzmann.Units.el_surface_density # number of electrons/nm^2 at interfaces
 const M_bulk = 2.0 # (bulk) molarity at center of domain
-const E0 = 10JuliaMPBSolver.Units.V / JuliaMPBSolver.Units.nm # decrement parameter
+const E0 = 10AugmentedPoissonBoltzmann.Units.V / AugmentedPoissonBoltzmann.Units.nm # decrement parameter
 const a = 5.0 / E0^2 # decrement parameter in χ(E)
-const c̄ = 55.508JuliaMPBSolver.Units.M # summary molar concentration
+const c̄ = 55.508AugmentedPoissonBoltzmann.Units.M # summary molar concentration
 const z = [-1, 1]
-const c_bulk = [M_bulk / abs(z[1]), M_bulk / abs(z[2])] * JuliaMPBSolver.Units.M # bulk  concentrations
+const c_bulk = [M_bulk / abs(z[1]), M_bulk / abs(z[2])] * AugmentedPoissonBoltzmann.Units.M # bulk  concentrations
 
 const F = ph"N_A" * ph"e"
 const K = ufac"K"
@@ -46,8 +46,8 @@ const L = 2.278592867nm # computational domain size
 const N = length(z)
 
 # Parameters
-user_parameters = JuliaMPBSolver.Parameters.UserParameters(
-    273.15 + 25 * JuliaMPBSolver.Units.K,
+user_parameters = AugmentedPoissonBoltzmann.Parameters.UserParameters(
+    273.15 + 25 * AugmentedPoissonBoltzmann.Units.K,
     78.49 - 1,
     0.0,
     0.0,
@@ -63,15 +63,15 @@ user_parameters = JuliaMPBSolver.Parameters.UserParameters(
 )
 
 computed_parameters =
-    JuliaMPBSolver.Parameters.ComputedParameters(user_parameters)
+    AugmentedPoissonBoltzmann.Parameters.ComputedParameters(user_parameters)
 
-grid_parameters = JuliaMPBSolver.Grid.UniformGrid(
+grid_parameters = AugmentedPoissonBoltzmann.Grid.UniformGrid(
     domain_size = L,
     refinement = 4,
     n_points = 20,
     use_offset = false,
 )
-grid = JuliaMPBSolver.Grid.create_full_cell(grid_parameters)
+grid = AugmentedPoissonBoltzmann.Grid.create_full_cell(grid_parameters)
 
 const i3 = grid[BFaceNodes][1, 3] # Index  of grid midpoint
 
@@ -190,7 +190,7 @@ indata = (M = M_bulk, q = 1, L = L / nm, n = length(Z))
 
 savename(indata)
 
-c3_avg = fill(M_bulk * JuliaMPBSolver.Units.M, 2)
+c3_avg = fill(M_bulk * AugmentedPoissonBoltzmann.Units.M, 2)
 
 data3 = PBData(
     c_avg = c3_avg,
@@ -200,13 +200,13 @@ data3 = PBData(
 
 sys3 = ICMPBSystem(data = data3, generic = xreaction!)
 
-JuliaMPBSolver.Equations.add_boundary_charge!(
+AugmentedPoissonBoltzmann.Equations.add_boundary_charge!(
     sys3,
     1,
     2,
     -user_parameters.boundary_electron_density,
 )
-JuliaMPBSolver.Equations.add_boundary_charge!(
+AugmentedPoissonBoltzmann.Equations.add_boundary_charge!(
     sys3,
     1,
     1,
@@ -224,9 +224,9 @@ sol3 = solve!(state3; inival = inival3, verbose = "n", damp_initial = 0.5)
 
 conc =
     concentrations(sol3, data3, c_ref = extcref(sol3[2:N, i3], data3)) /
-    (JuliaMPBSolver.Units.M)
+    (AugmentedPoissonBoltzmann.Units.M)
 
-c0 = c̄ / (JuliaMPBSolver.Units.M) .- sum(conc, dims = 1)
+c0 = c̄ / (AugmentedPoissonBoltzmann.Units.M) .- sum(conc, dims = 1)
 
 reference_data_filename = resultsdir(savename("icmpb", indata, "hdf5"))
 print(reference_data_filename)
@@ -236,13 +236,13 @@ if !isfile(reference_data_filename)
 end
 
 (x_ref, c_solvent_ref) =
-    JuliaMPBSolver.DataOut.read_hdf5_data(reference_data_filename, "c_solvent")
+    AugmentedPoissonBoltzmann.DataOut.read_hdf5_data(reference_data_filename, "c_solvent")
 (x_ref, c_anion_ref) =
-    JuliaMPBSolver.DataOut.read_hdf5_data(reference_data_filename, "c_anion")
+    AugmentedPoissonBoltzmann.DataOut.read_hdf5_data(reference_data_filename, "c_anion")
 (x_ref, c_cation_ref) =
-    JuliaMPBSolver.DataOut.read_hdf5_data(reference_data_filename, "c_cation")
+    AugmentedPoissonBoltzmann.DataOut.read_hdf5_data(reference_data_filename, "c_cation")
 
-same_x = x_ref == JuliaMPBSolver.Grid.get_coordinates(grid)
+same_x = x_ref == AugmentedPoissonBoltzmann.Grid.get_coordinates(grid)
 if !same_x
     throw(ErrorException("Grid coordinates mismatch"))
 end

scripts/equilibrium.jl

@@ -12,7 +12,7 @@ using LessUnitful.MoreUnitful
 using Test
 using PythonPlot
 using Colors
-using JuliaMPBSolver
+using AugmentedPoissonBoltzmann
 
 function L_Debye(data)
     return sqrt(
@@ -379,15 +379,15 @@ begin
     L = 20nm
 end
 
-grid_parameters = JuliaMPBSolver.Grid.GeometricGrid(
+grid_parameters = AugmentedPoissonBoltzmann.Grid.GeometricGrid(
     domain_size = L,
     refinement = 0,
     hmin = 0.05 * nm,
     hmax = 0.5 * nm,
     use_offset = false,
 )
-grid = JuliaMPBSolver.Grid.create_half_cell(grid_parameters)
-X = JuliaMPBSolver.Grid.get_coordinates(grid)
+grid = AugmentedPoissonBoltzmann.Grid.create_half_cell(grid_parameters)
+X = AugmentedPoissonBoltzmann.Grid.get_coordinates(grid)
 
 sys_sy = create_equilibrium_system(grid, equidata)
 

scripts/simplecell-bsk.jl

@@ -6,20 +6,20 @@ using LinearAlgebra
 using Interpolations
 using VoronoiFVM
 using PythonPlot
-using JuliaMPBSolver
+using AugmentedPoissonBoltzmann
 using JLD2
 
-const nel = 20.0 * JuliaMPBSolver.Units.el_surface_density # number of electrons/nm^2 at interfaces
+const nel = 20.0 * AugmentedPoissonBoltzmann.Units.el_surface_density # number of electrons/nm^2 at interfaces
 const M_bulk = 1 # (bulk) molarity at center of domain
-const E0 = 10JuliaMPBSolver.Units.V / JuliaMPBSolver.Units.nm # decrement parameter
+const E0 = 10AugmentedPoissonBoltzmann.Units.V / AugmentedPoissonBoltzmann.Units.nm # decrement parameter
 const a = 5.0 / E0^2 # decrement parameter in χ(E)
-const c̄ = 55.508JuliaMPBSolver.Units.M # summary molar concentration
+const c̄ = 55.508AugmentedPoissonBoltzmann.Units.M # summary molar concentration
 const z = [-1, 1]
-const c_bulk = [M_bulk / abs(z[1]), M_bulk / abs(z[2])] * JuliaMPBSolver.Units.M # bulk  concentrations
+const c_bulk = [M_bulk / abs(z[1]), M_bulk / abs(z[2])] * AugmentedPoissonBoltzmann.Units.M # bulk  concentrations
 
 # Parameters
-user_parameters = JuliaMPBSolver.Parameters.UserParameters(
-    273.15 + 25 * JuliaMPBSolver.Units.K,
+user_parameters = AugmentedPoissonBoltzmann.Parameters.UserParameters(
+    273.15 + 25 * AugmentedPoissonBoltzmann.Units.K,
     78.49 - 1,
     0.0,
     0.0,
@@ -31,22 +31,22 @@ user_parameters = JuliaMPBSolver.Parameters.UserParameters(
     true,
     false,
     true,
-    1 * JuliaMPBSolver.Units.nm,
+    1 * AugmentedPoissonBoltzmann.Units.nm,
 )
 
 computed_parameters =
-    JuliaMPBSolver.Parameters.ComputedParameters(user_parameters)
+    AugmentedPoissonBoltzmann.Parameters.ComputedParameters(user_parameters)
 
-grid_parameters = JuliaMPBSolver.Grid.GeometricGrid(
-    domain_size = 10.0 * JuliaMPBSolver.Units.nm,
+grid_parameters = AugmentedPoissonBoltzmann.Grid.GeometricGrid(
+    domain_size = 10.0 * AugmentedPoissonBoltzmann.Units.nm,
     refinement = 4,
-    hmin = 1.0e-1 * JuliaMPBSolver.Units.nm,
-    hmax = 1.0 * JuliaMPBSolver.Units.nm,
+    hmin = 1.0e-1 * AugmentedPoissonBoltzmann.Units.nm,
+    hmax = 1.0 * AugmentedPoissonBoltzmann.Units.nm,
     use_offset = false,
 )
 
 solution, X, nv, ε_r =
-    JuliaMPBSolver.Equations.create_and_run_full_cell_problem(
+    AugmentedPoissonBoltzmann.Equations.create_and_run_full_cell_problem(
     grid_parameters,
     user_parameters,
     computed_parameters,

scripts/simplecell.jl

@@ -6,20 +6,20 @@ using LinearAlgebra
 using Interpolations
 using VoronoiFVM
 using PythonPlot
-using JuliaMPBSolver
+using AugmentedPoissonBoltzmann
 using JLD2
 
-const nel = 20.0 * JuliaMPBSolver.Units.el_surface_density # number of electrons/nm^2 at interfaces
+const nel = 20.0 * AugmentedPoissonBoltzmann.Units.el_surface_density # number of electrons/nm^2 at interfaces
 const M_bulk = 1 # (bulk) molarity at center of domain
-const E0 = 10JuliaMPBSolver.Units.V / JuliaMPBSolver.Units.nm # decrement parameter
+const E0 = 10AugmentedPoissonBoltzmann.Units.V / AugmentedPoissonBoltzmann.Units.nm # decrement parameter
 const a = 5.0 / E0^2 # decrement parameter in χ(E)
-const c̄ = 55.508JuliaMPBSolver.Units.M # summary molar concentration
+const c̄ = 55.508AugmentedPoissonBoltzmann.Units.M # summary molar concentration
 const z = [-1, 1]
-const c_bulk = [M_bulk / abs(z[1]), M_bulk / abs(z[2])] * JuliaMPBSolver.Units.M # bulk  concentrations
+const c_bulk = [M_bulk / abs(z[1]), M_bulk / abs(z[2])] * AugmentedPoissonBoltzmann.Units.M # bulk  concentrations
 
 # Parameters
-user_parameters = JuliaMPBSolver.Parameters.UserParameters(
-    273.15 + 25 * JuliaMPBSolver.Units.K,
+user_parameters = AugmentedPoissonBoltzmann.Parameters.UserParameters(
+    273.15 + 25 * AugmentedPoissonBoltzmann.Units.K,
     78.49 - 1,
     0.0,
     0.0,
@@ -35,19 +35,19 @@ user_parameters = JuliaMPBSolver.Parameters.UserParameters(
 )
 
 computed_parameters =
-    JuliaMPBSolver.Parameters.ComputedParameters(user_parameters)
+    AugmentedPoissonBoltzmann.Parameters.ComputedParameters(user_parameters)
 
 # Grid generation
-grid_parameters = JuliaMPBSolver.Grid.GeometricGrid(
-    domain_size = 10.0 * JuliaMPBSolver.Units.nm,
+grid_parameters = AugmentedPoissonBoltzmann.Grid.GeometricGrid(
+    domain_size = 10.0 * AugmentedPoissonBoltzmann.Units.nm,
     refinement = 4,
-    hmin = 1.0e-1 * JuliaMPBSolver.Units.nm,
-    hmax = 1.0 * JuliaMPBSolver.Units.nm,
+    hmin = 1.0e-1 * AugmentedPoissonBoltzmann.Units.nm,
+    hmax = 1.0 * AugmentedPoissonBoltzmann.Units.nm,
     use_offset = false,
 )
 
 solution, X, nv, ε_r =
-    JuliaMPBSolver.Equations.create_and_run_full_cell_problem(
+    AugmentedPoissonBoltzmann.Equations.create_and_run_full_cell_problem(
     grid_parameters,
     user_parameters,
     computed_parameters,

src/PoissonBoltzmannIPAM2025.jl

@@ -6,7 +6,7 @@ using LessUnitful
 using ExtendableGrids
 using VoronoiFVM
 using Test
-using JuliaMPBSolver.ICMPBP: ICMPBP, SurfaceChargedSymmetricCell, AbstractHalfCell, AbstractSymmetricCell, set_molarity!, calc_cmol, calc_c0mol, calc_χ, get_E, get_φ, get_p, get_c0,
+using AugmentedPoissonBoltzmann.ICMPBP: ICMPBP, SurfaceChargedSymmetricCell, AbstractHalfCell, AbstractSymmetricCell, set_molarity!, calc_cmol, calc_c0mol, calc_χ, get_E, get_φ, get_p, get_c0,
     set_κ!, set_q!, set_φ!, pramp
 
 resultsdir(args...) = projectdir("results", args...)

test/runtests.jl

@@ -1,5 +1,5 @@
 using Pkg
-using JuliaMPBSolver
+using AugmentedPoissonBoltzmann
 using ExampleJuggler
 using Test
 using Markdown
@@ -42,5 +42,3 @@ end
     end
 
 end
-
-Pkg.test("JuliaMPBSolver")