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v0.5.0: Improve package structure and docs (#1)
* rename internal files * rename ICMPBP to SolverCore * rename ICMBPData to AugmentedPBData * Add SciMLPublic * Ensure explicit imports * Move code from pluto notebook to normal files * Add lots of docs with help of Claude
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‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v5.0.0
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hooks:
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- id: check-added-large-files
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args: [--maxkb=8192]
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- id: check-merge-conflict
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- id: check-toml
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- id: check-yaml
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args: [--allow-multiple-documents]
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- id: no-commit-to-branch
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args: [--branch,master]
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- repo: https://github.com/gitleaks/gitleaks
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rev: v8.24.2
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hooks:
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- id: gitleaks
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- repo: https://github.com/fredrikekre/runic-pre-commit
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rev: v1.0.0
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hooks:
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- id: runic
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- repo: https://github.com/codespell-project/codespell
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rev: v2.4.1
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hooks:
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- id: codespell
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- repo: https://github.com/psf/black
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rev: 25.9.0
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hooks:
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- id: black
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language_version: python3
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- repo: https://github.com/pycqa/isort
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rev: 6.0.1
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hooks:
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- id: isort
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args: ["--profile", "black"]

‎Project.toml‎

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authors = ["Jürgen Fuhrmann <juergen-fuhrmann@web.de>, Jason Landini <landinjm@umich.edu>"]
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[deps]
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DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
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ExtendableGrids = "cfc395e8-590f-11e8-1f13-43a2532b2fa8"
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InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
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LessUnitful = "f29f6376-6e90-4d80-80c9-fb8ec61203d5"
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LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
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Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
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PreallocationTools = "d236fae5-4411-538c-8e31-a6e3d9e00b46"
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SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
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SciMLPublic = "431bcebd-1456-4ced-9d72-93c2757fff0b"
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Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
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VoronoiFVM = "82b139dc-5afc-11e9-35da-9b9bdfd336f3"
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[compat]
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DocStringExtensions = "0.9.5"
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ExplicitImports = "1.14.0"
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ExtendableGrids = "1.14.0"
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InteractiveUtils = "1.10.0"
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LessUnitful = "1.2.1"
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LinearAlgebra = "1.10.0"
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Markdown = "1.10.0"
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PreallocationTools = "0.4.34"
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SciMLBase = "2.127.0"
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SciMLPublic = "1.0.0"
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Unitful = "1.25.1"
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VoronoiFVM = "2.13.0"
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julia = "1.10"
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[extras]
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ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
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LessUnitful = "f29f6376-6e90-4d80-80c9-fb8ec61203d5"
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Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
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Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
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[targets]
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test = ["Test"]
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test = ["Test", "ExplicitImports", "Markdown", "LessUnitful"]

‎docs/Project.toml‎

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[deps]
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AugmentedPoissonBoltzmann = "d8b18f01-5396-498d-b34d-247825c18ff1"
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Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
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VoronoiFVM = "82b139dc-5afc-11e9-35da-9b9bdfd336f3"
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SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
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[sources]
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AugmentedPoissonBoltzmann = {rev = "main", url = ".."}
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AugmentedPoissonBoltzmann = {path = "/home/fuhrmann/Wias/work/julia/dev/AugmentedPoissonBoltzmann"}

‎docs/make.jl‎

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using Documenter, AugmentedPoissonBoltzmann
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using Documenter, AugmentedPoissonBoltzmann, AugmentedPoissonBoltzmann.SolverCore
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using VoronoiFVM, SciMLBase
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function mkdocs()
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makedocs(
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sitename = "AugmentedPoissonBoltzmann.jl",
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modules = [AugmentedPoissonBoltzmann],
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modules = [AugmentedPoissonBoltzmann, AugmentedPoissonBoltzmann.SolverCore],
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clean = false,
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doctest = false,
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warnonly = true,
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authors = "J. Fuhrmann, J. Landini",
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# warnonly = true,
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authors = "J. Fuhrmann, J. Landini, M. Landstorfer",
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repo = "https://github.com/IPAM-ECH2025/AugmentedPoissonBoltzmann.jl",
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pages = [
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"Home" => "index.md",
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"Python Access" => "pyapi.md",
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"Cells API" => "cells.md",
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"SolverCore API" => "solvercore.md",
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"Helpers" => "helpers.md",
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]
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)
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return if !isinteractive()

‎docs/src/cells.md‎

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# Electrochemical cells
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## Cell Types
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### Abstract Types
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```@docs
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AugmentedPoissonBoltzmann.SolverCore.AbstractAugmentedPBCell
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AugmentedPoissonBoltzmann.SolverCore.AbstractHalfCell
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AugmentedPoissonBoltzmann.SolverCore.AbstractSymmetricCell
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```
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### Concrete Cell Types
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```@docs
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AugmentedPoissonBoltzmann.SolverCore.AppliedPotentialHalfCell
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AugmentedPoissonBoltzmann.SolverCore.AppliedPotentialSymmetricCell
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AugmentedPoissonBoltzmann.SolverCore.SurfaceChargedHalfCell
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AugmentedPoissonBoltzmann.SolverCore.SurfaceChargedSymmetricCell
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```
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## Cell Constructors
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```@docs
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AugmentedPoissonBoltzmann.SolverCore.AppliedPotentialHalfCell(grid, data; dielectric_decrement=false, valuetype=Float64)
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AugmentedPoissonBoltzmann.SolverCore.SurfaceChargedSymmetricCell(grid, data; dielectric_decrement=false, valuetype=Float64)
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```
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## Solving and Initialization
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```@docs
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VoronoiFVM.unknowns(cell::AbstractAugmentedPBCell)
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SciMLBase.solve(cell::AbstractAugmentedPBCell; inival=unknowns(cell), verbose="", damp_initial=0.1, kwargs...)
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```
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## Helper Functions
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### Data Access
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```@docs
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AugmentedPoissonBoltzmann.SolverCore.apbdata
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```
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### Calculation Functions
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```@docs
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AugmentedPoissonBoltzmann.SolverCore.calc_cmol(sol, cell::AbstractAugmentedPBCell)
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AugmentedPoissonBoltzmann.SolverCore.calc_c0mol(sol, cell::AbstractAugmentedPBCell)
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AugmentedPoissonBoltzmann.SolverCore.calc_χ(sol, cell::AbstractAugmentedPBCell)
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```
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### Getter Functions
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```@docs
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AugmentedPoissonBoltzmann.SolverCore.get_E
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AugmentedPoissonBoltzmann.SolverCore.get_φ
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AugmentedPoissonBoltzmann.SolverCore.get_p
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```
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### Setter Functions
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```@docs
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AugmentedPoissonBoltzmann.SolverCore.set_κ!
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AugmentedPoissonBoltzmann.SolverCore.set_molarity!(cell::AbstractAugmentedPBCell, M)
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AugmentedPoissonBoltzmann.SolverCore.set_φ!
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AugmentedPoissonBoltzmann.SolverCore.set_q!
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```
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## Analysis Functions
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```@docs
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AugmentedPoissonBoltzmann.SolverCore.dlcapsweep
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```
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## Boundary Conditions (Internal)
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```@docs
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AugmentedPoissonBoltzmann.SolverCore.halfcell_applied_potential_bcondition!
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AugmentedPoissonBoltzmann.SolverCore.symmcell_surfacecharge_bcondition!
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```
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‎docs/src/helpers.md‎

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```@docs
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AugmentedPoissonBoltzmann.SolverCore.pramp
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```
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‎docs/src/pyapi.md‎

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# Python Access
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```@docs
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mpbpsolve
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icmpbpsolve
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```
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## Internal
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```@docs
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AugmentedPoissonBoltzmann.prepare_grid
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```
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‎docs/src/solvercore.md‎

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## AugmentedPBSystem
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```@docs
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AugmentedPoissonBoltzmann.SolverCore.AugmentedPBSystem
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VoronoiFVM.unknowns
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AugmentedPoissonBoltzmann.SolverCore.calc_cnum
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AugmentedPoissonBoltzmann.SolverCore.calc_c0num
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AugmentedPoissonBoltzmann.SolverCore.calc_cmol
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AugmentedPoissonBoltzmann.SolverCore.calc_c0mol
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AugmentedPoissonBoltzmann.SolverCore.calc_χ
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AugmentedPoissonBoltzmann.SolverCore.calc_spacecharge
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AugmentedPoissonBoltzmann.SolverCore.ysum(::VoronoiFVM.System, sol)
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AugmentedPoissonBoltzmann.SolverCore.qsweep
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```
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## AugementedPBData
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```@docs
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AugmentedPoissonBoltzmann.SolverCore.AugmentedPBData
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AugmentedPoissonBoltzmann.SolverCore.apply_voltage!
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AugmentedPoissonBoltzmann.SolverCore.apply_charge!
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AugmentedPoissonBoltzmann.SolverCore.set_molarity!
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AugmentedPoissonBoltzmann.SolverCore.L_Debye
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AugmentedPoissonBoltzmann.SolverCore.dlcap0
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AugmentedPoissonBoltzmann.SolverCore.capscalc
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```
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## Internal: Constitutive model
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```@docs
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AugmentedPoissonBoltzmann.SolverCore.DerivedData
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AugmentedPoissonBoltzmann.SolverCore.DerivedData(data::AugmentedPBData)
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AugmentedPoissonBoltzmann.SolverCore.DerivedData(data::AugmentedPBData, n_E)
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AugmentedPoissonBoltzmann.SolverCore.makeδ
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AugmentedPoissonBoltzmann.SolverCore.W
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AugmentedPoissonBoltzmann.SolverCore.Λ
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AugmentedPoissonBoltzmann.SolverCore.y_α
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AugmentedPoissonBoltzmann.SolverCore.y0
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AugmentedPoissonBoltzmann.SolverCore.ysum(u, ::AugmentedPBData)
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AugmentedPoissonBoltzmann.SolverCore.spacecharge
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AugmentedPoissonBoltzmann.SolverCore.susceptibility
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AugmentedPoissonBoltzmann.SolverCore.c_num!
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AugmentedPoissonBoltzmann.SolverCore.c0_num
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```
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## Internal: System
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```@docs
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AugmentedPoissonBoltzmann.SolverCore.reaction!
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AugmentedPoissonBoltzmann.SolverCore.poisson_and_p_flux!
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AugmentedPoissonBoltzmann.SolverCore.bcondition!
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AugmentedPoissonBoltzmann.SolverCore.ionconservation!
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```

‎src/AugmentedPoissonBoltzmann.jl‎

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"""
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module AugmentedPoissonBoltzmann
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using ExtendableGrids: ExtendableGrids, bfacemask!
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using LessUnitful: LessUnitful, @ufac_str
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using VoronoiFVM: VoronoiFVM, solve, unknowns
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using LessUnitful: LessUnitful, @ufac_str
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include("units.jl")
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using .Units
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using .Equations
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module ICMPBP
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using LessUnitful
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using ExtendableGrids
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using VoronoiFVM
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using LinearAlgebra
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using SciMLBase
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module SolverCore
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using DocStringExtensions: TYPEDFIELDS
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using ExtendableGrids: ExtendableGrids, BFaceNodes, Coordinates, num_nodes
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using LessUnitful: LessUnitful, @ph_str, @ufac_str
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using SciMLBase: SciMLBase, solve, solve!
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using SciMLPublic: @public
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using VoronoiFVM: VoronoiFVM, boundary_dirichlet!, boundary_neumann!,
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enable_boundary_species!, enable_species!, nodevolumes,
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unknown_indices, unknowns
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include("pramp.jl")
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include("icmbp-p.jl")
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include("augmentedpbdata.jl")
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include("augmentedpbconstitutive.jl")
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include("augmentedpbsystem.jl")
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include("cells.jl")
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export pramp
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export set_molarity!, set_κ!, set_q!, set_φ
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@public L_debye, dlcap0
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export calc_cmol, calc_c0mol, calc_χ
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export get_E, get_φ, get_p
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export AbstractAugmentedPBCell, AbstractHalfCell, AbstractSymmetricCell
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export AugmentedPBData, SurfaceChargedSymmetricCell, AppliedPotentialHalfCell
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@public W, Λ
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end
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include("api.jl")
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include("pyapi.jl")
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export pramp
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export mpbpsolve
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export icmpbpsolve
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end

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