Add and apply codespell config

.codespellrc

@@ -0,0 +1,3 @@
+[codespell]
+ignore-words-list = missings,rcall,linke,strat,nd
+skip = CITATIONS.bib

CHANGELOG.md

@@ -4,7 +4,7 @@
   - Remove VoronoiFVM solver strategies
   - Stop re-exporting ForwardDiff.value
   - Try to remove type piracies
-  - Remove `params` from edge, node structs (appearantly never used)
+  - Remove `params` from edge, node structs (apparently never used)
 
 ## v2.5.0 November 17, 2024
   - update show methods for physics, grid
@@ -24,11 +24,11 @@
 
 ## October 28, 2024
 
-Moved repositiory from https://github.com/j-fu/VoronoiFVM.jl to https://github.com/WIAS-PDELib/VoronoiFVM.jl. [WIAS-PDELib](https://github.com/WIAS-PDELib/) is a github organization created to collectively manage the Julia packages developed under the lead of the [WIAS Numerical Mathematics and Scientific Computing](https://wias-berlin.de/research/rgs/fg3)  research group. According to the [github docs on repository transfer](https://docs.github.com/en/repositories/creating-and-managing-repositories/transferring-a-repository#whats-transferred-with-a-repository), all links to the previous repository location are automatically redirected to the new location, and all relationships with forks stay intact.
+Moved repository from https://github.com/j-fu/VoronoiFVM.jl to https://github.com/WIAS-PDELib/VoronoiFVM.jl. [WIAS-PDELib](https://github.com/WIAS-PDELib/) is a github organization created to collectively manage the Julia packages developed under the lead of the [WIAS Numerical Mathematics and Scientific Computing](https://wias-berlin.de/research/rgs/fg3)  research group. According to the [github docs on repository transfer](https://docs.github.com/en/repositories/creating-and-managing-repositories/transferring-a-repository#whats-transferred-with-a-repository), all links to the previous repository location are automatically redirected to the new location, and all relationships with forks stay intact.
 
 ## v2.1.0 October 23, 2024
   - Features:
-    - Add VoronoiFVMExtendableFEMBaseExt  extension allowing to use velocity fields caculated  with [ExtendableFEM](https://github.com/chmerdon/ExtendableFEM.jl) in convection-diffusion problems
+    - Add VoronoiFVMExtendableFEMBaseExt  extension allowing to use velocity fields calculated  with [ExtendableFEM](https://github.com/chmerdon/ExtendableFEM.jl) in convection-diffusion problems
 
 ## v2.0.2 October 12, 2024
   - Bugfixes
@@ -100,7 +100,7 @@ Moved repositiory from https://github.com/j-fu/VoronoiFVM.jl to https://github.c
 
 ## v1.15.0 Dec 1, 2023
 - Adjusted time/embedding stepping scheme, added `num_final_steps` to  [`VoronoiFVM.SolverControl`](@ref). This may lead to
-  sligthly different results when solving time dependent problems. Some unit test values have been adapted. Before,
+  slightly different results when solving time dependent problems. Some unit test values have been adapted. Before,
   accidentally, very small time steps at the end of an evolution were possible.
 
 ## v1.14.0 Nov 27, 2023
@@ -124,7 +124,7 @@ Moved repositiory from https://github.com/j-fu/VoronoiFVM.jl to https://github.c
 
 ## v1.9.0 June 27, 2023
 - With `control.handle_exceptions=true`, in case of a failing step,
-  time stepping and embeding now returns the solution calculated so far instead of
+  time stepping and embedding now returns the solution calculated so far instead of
   throwing an error
 
 ## v1.8.0 June 20, 2023

docs/src/devel.md

@@ -4,7 +4,7 @@ Here, a bit of development hints are given which mainly concern tests and docume
 ## Pluto notebooks
 The pluto notebooks in this package are "triple use":
 - As typical Pluto notebooks, they are self-contained in the senses that they contain their own Project and Manifest files. So users can just download and execute them.
-- If they run with the environmnet variable `PLUTO_PROJECT` set to some julia environment, this environment will activated at the start of the notebook. In particular, they use `Revise.jl` so they can be run during development of VoronoiFVM.jl. See also  https://github.com/fonsp/Pluto.jl/issues/1788 .
+- If they run with the environment variable `PLUTO_PROJECT` set to some julia environment, this environment will activated at the start of the notebook. In particular, they use `Revise.jl` so they can be run during development of VoronoiFVM.jl. See also  https://github.com/fonsp/Pluto.jl/issues/1788 .
 - During CI tests, they are run as scripts. For this purpose they are wrapped into temporary modules, and @test macros can be used in the notebooks.
 
 

docs/src/impedance-derivation.tex

@@ -173,7 +173,7 @@ \section{Impedance spectroscopy in nonlinear evolution equations}
 \end{equation}
 
 \subsection{Excited Dirichlet boundary condition}
-This dicussion is based on the idea to implement Dirichlet boundary conditions using the
+This discussion is based on the idea to implement Dirichlet boundary conditions using the
 penalty method and provides an easy way to handle deriviatives with respect to
 the Dirichlet boundary value. We assume that our problem corresponds to a (discretized) PDE
 in a domain $\Omega$ with boundary $\Gamma=\partial\Omega$.

docs/src/method.md

@@ -31,7 +31,7 @@ makes it easy to use these Voronoi cells as REVs aka control volumes aka finite
 
 ```@raw html
 <center>
-<img src="../vor.png" width="50%">
+<img src="../voro.png" width="50%">
 </center>
 ```
 

docs/src/runexamples.md

@@ -28,7 +28,7 @@ If you want to modify the example, consider using `Revise.jl` and `includet`.
 
 ## Performance with closures
 
-VoronoiFVM provides two flavors of calbacks for constitutive
+VoronoiFVM provides two flavors of callbacks for constitutive
 functions: 
 
 - Callbacks with `data` parameoter. `data` is declared as part of `Physics` and

pluto-examples/heterogeneous-catalysis.jl

@@ -83,7 +83,7 @@ or equivalently,
 ∑_{i=1}^n α_{i}^j S_i  \underset{k_j^+}{\stackrel{k_j^-}{\longrightleftharpoons}} ∑_{i=1}^n β_i^j S_i 
 ```
 The rate of these reactions depend on the concentrations
-``[S_i]`` of the species. Within ``Catalyst.jl``, due to consistency whith the derivation
+``[S_i]`` of the species. Within ``Catalyst.jl``, due to consistency with the derivation
 from stochastic approaches, the  default "combinatoric rate law" is
 ```math
     r_j=k_j^+ ∏_{i=1}^n \frac{[S_i]^{α_i^j}}{α_i^j!} - k_j^- ∏_{i=1}^n \frac{[S_i]^{β_i^j}}{β_i^j!}  
@@ -388,8 +388,8 @@ the surface reaction network.
 
 ### Problem specification
 Assume ``\Omega=(0,1)`` where a catalytic reaction takes place at ``x=0``. 
-We assume that the educts A, B, and the product AB2 are bulk species transported to te domain.
-At ``x=1`` we set Dirichlet boudary conditions providing A,B and removing AB2.
+We assume that the educts A, B, and the product AB2 are bulk species transported to the domain.
+At ``x=1`` we set Dirichlet boundary conditions providing A,B and removing AB2.
 
 A, B can adsorb  at the catalyst at ``x=0`` and  react to AB2 while adsorbed. 
 The product desorbs and is released to the bulk. So we have 

pluto-examples/ode-diffusion1d.jl

@@ -38,7 +38,7 @@ Solve the nonlinear diffusion equation
 ```math
 \partial_t u -\Delta u^m = 0
 ```
-in $\Omega=(-1,1)$ with homogeneous Neumann boundary conditons using the implicit Euler method.
+in $\Omega=(-1,1)$ with homogeneous Neumann boundary conditions using the implicit Euler method.
 
 This equation is also called  "porous medium equation". 
 The Barenblatt solution 

pluto-examples/ode-wave1d.jl

@@ -48,7 +48,7 @@ u_{tt}- c^2 \Delta u = 0
 ```
 
 
-We can create a system of first oder in time PDEs out of this:
+We can create a system of first order in time PDEs out of this:
 
 ```math 
     \begin{aligned}

pluto-examples/outflow.jl

@@ -29,7 +29,7 @@ md"""
 
 # ╔═╡ 0d1b7d24-4dc7-4f1d-944f-e279e18f151c
 md"""
-We show how to implment outflow boundary conditions when the velocities at the boundary are calculated by another equation in the system. A typical case is solute transport in porous media where fluid flow is calculated by Darcy's law which defines the convective velocity in the solute transport equation.
+We show how to implement outflow boundary conditions when the velocities at the boundary are calculated by another equation in the system. A typical case is solute transport in porous media where fluid flow is calculated by Darcy's law which defines the convective velocity in the solute transport equation.
 """
 
 # ╔═╡ f951520e-3edc-4353-910c-7f6ad5678e6b

src/vfvm_diffeq_interface.jl

@@ -130,7 +130,7 @@ end
     
 Create an [ODEFunction](https://diffeq.sciml.ai/stable/basics/overview/#Defining-Problems)
 in [mass matrix form](https://diffeq.sciml.ai/stable/solvers/dae_solve/#OrdinaryDiffEq.jl-(Mass-Matrix))
-to be handeled by ODE solvers from [DifferentialEquations.jl](https://github.com/SciML/DifferentialEquations.jl).
+to be handled by ODE solvers from [DifferentialEquations.jl](https://github.com/SciML/DifferentialEquations.jl).
 
 Parameters:
 - `system`: A [`VoronoiFVM.System`](https://WIAS-PDELib.github.io/VoronoiFVM.jl/stable/system/#VoronoiFVM.System-Tuple{ExtendableGrid})
@@ -163,7 +163,7 @@ end
     
 Create an [ODEProblem](https://diffeq.sciml.ai/stable/basics/overview/#Defining-Problems)
 in [mass matrix form](https://diffeq.sciml.ai/stable/solvers/dae_solve/#OrdinaryDiffEq.jl-(Mass-Matrix))
-which can  be handeled by ODE solvers from [DifferentialEquations.jl](https://github.com/SciML/DifferentialEquations.jl).
+which can  be handled by ODE solvers from [DifferentialEquations.jl](https://github.com/SciML/DifferentialEquations.jl).
 
 Parameters:
 - `system`: A [`VoronoiFVM.System`](https://WIAS-PDELib.github.io/VoronoiFVM.jl/stable/system/#VoronoiFVM.System-Tuple{ExtendableGrid})

src/vfvm_formfactors.jl

@@ -298,7 +298,7 @@ function bfacefactors!(T::Type{Triangle2D}, ::Type{<:Cartesian3D}, coord, bfacen
 
     dd = (epar[1], epar[2], epar[3])
 
-    # Kanten-Flaechenanteile (ohne Abschneiden); epar als Hilfsfeld benutzt
+    # Kanten-Flaechenanteile (ohne Abschneiden); epar -> Hilfsfeld
     epar[1] = (dd[2] + dd[3] - dd[1]) * dd[1]
     epar[2] = (dd[3] + dd[1] - dd[2]) * dd[2]
     epar[3] = (dd[1] + dd[2] - dd[3]) * dd[3]

src/vfvm_geometryitems.jl

@@ -52,7 +52,7 @@ Base.getindex(p::DParameters, i) = @inbounds p.val[p.offset + i]
 """
     parameters(edge_or_node)
 
-Return abstract vector of parameters passed via vector of unknonws. 
+Return abstract vector of parameters passed via vector of unknowns. 
 This allows differentiation with respect to these parameters.
 """
 function parameters(u::AbstractNodeData)

src/vfvm_impedance.jl

@@ -245,7 +245,7 @@ function measurement_derivative(system::AbstractSystem, measurement_functional,
 
     # See https://github.com/JuliaDiff/SparseDiffTools.jl
 
-    # Color the matrix for automtic differentiation
+    # Color the matrix for automatic differentiation
     colors = matrix_colors(jac)
 
     # Use Julia automatic differentiation for the calculation of the Jacobian

src/vfvm_linsolve.jl

@@ -8,7 +8,7 @@ function Random.rand(rng::AbstractRNG,
     ForwardDiff.Dual{T, V, N}(rand(rng, V))
 end
 
-# TODO: these may be not anymore neded
+# TODO: these may be not anymore needed
 canonical_matrix(A) = A
 canonical_matrix(A::AbstractExtendableSparseMatrixCSC) = SparseMatrixCSC(A)
 

src/vfvm_physics.jl

@@ -166,7 +166,7 @@ mutable struct Physics{Flux <: Function,
     boutflow::BOutflow
 
     """
-    List (Vector) of boundary regions which carry outflow bondary conditions.
+    List (Vector) of boundary regions which carry outflow boundary conditions.
     Influences when `boutflow` is called.
     """
     outflowboundaries::Vector{Int}

src/vfvm_postprocess.jl

@@ -228,7 +228,7 @@ end
 """
     $(SIGNATURES)
 
-Calculate weigthed discrete ``L^2(\\Omega)`` norm of a solution vector.
+Calculate weighted discrete ``L^2(\\Omega)`` norm of a solution vector.
 """
 function l2norm(sys, u, species_weights = ones(num_species(sys)))
     _complete!(sys)

src/vfvm_solvercontrol.jl

@@ -200,7 +200,7 @@ Base.@kwdef mutable struct SolverControl
     Δu_opt::Float64 = 0.1
 
     """
-    Control maximum  sice of update `Δu` for time stepping and embeding relative to
+    Control maximum  sice of update `Δu` for time stepping and embedding relative to
     `Δu_opt`. Time steps with `Δu > Δu_max_factor*Δu_opt` will be rejected.
     """
     Δu_max_factor::Float64 = 1.2

src/vfvm_sparsesolution.jl

@@ -139,7 +139,7 @@ function Base.setindex!(a::SparseSolutionArray, v, ispec::Int, inode::Int)
         return a
     end
     # TODO: what is the right reacton here ?
-    # Ignoring seems to be better, so we can broacast etc.
+    # Ignoring seems to be better, so we can broadcast etc.
     # throw(DomainError("undefined degree of freedom"))
 end
 

src/vfvm_system.jl

@@ -165,9 +165,9 @@ Keyword arguments:
 - `assembly`: either `:cellwise` (default) or `:edgewise`. Determine, how the assembly loop is organized.
    `:cellwise` means that the outer loop goes over grid cells (triangles, tetrahedra), and contributions to
    edge fluxes and node reactions are calculated for each cell. As a consequence, e.g. im 2D for all interior
-   edges, flux functions are callled twice, once for each adjacent cell. Especially in 3D, this becomes a significant
+   edges, flux functions are called twice, once for each adjacent cell. Especially in 3D, this becomes a significant
    overhead. With `:edgewise`, geometry factors of these edges are pre-assembled, and the outer assembly loops
-   go over all grid edges resp. nodes, still with separate calls if neigboring cells belong to different regions.
+   go over all grid edges resp. nodes, still with separate calls if neighboring cells belong to different regions.
 !!! note
     It is planned to make `:edgewise` the default in a later version.