Fix links after transition to WIAS-PDELib

WIAS-PDELib · Nov 1, 2024 · 22f811e · 22f811e
1 parent 68e11a5
commit 22f811e
Show file tree

Hide file tree

Showing 18 changed files with 37 additions and 38 deletions.
diff --git a/CITATION.cff b/CITATION.cff
@@ -1,6 +1,5 @@
 cff-version: 1.2.0
-title: "VoronoiFVM.jl - Finite volume solver for coupled nonlinear partial d
-ifferential equations"
+title: "VoronoiFVM.jl - Finite volume solver for coupled nonlinear partial differential equations"
 abstract: "Solution of nonlinear multiphysics partial differential equation systems using the Voronoi finite volume method"
 message: "If you use this software, please cite it using the  metadata from this file."
 type: software
@@ -26,4 +25,4 @@ authors:
     family-names: Liero
 doi: "10.5281/zenodo.3529808"
 license: MIT
-repository-code: "https://github.com/j-fu/VoronoiFVM.jl"
+repository-code: "https://github.com/WIAS-PDELib/VoronoiFVM.jl"
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "VoronoiFVM"
 uuid = "82b139dc-5afc-11e9-35da-9b9bdfd336f3"
 authors = ["Jürgen Fuhrmann <[email protected]>", "Patrick Jaap", "Daniel Runge", "Dilara Abdel", "Jan Weidner", "Alexander Seiler", "Patricio Farrell", "Matthias Liero"]
-version = "2.2"
+version = "2.2.1"
 
 [deps]
 BandedMatrices = "aae01518-5342-5314-be14-df237901396f"

diff --git a/README.md b/README.md
@@ -17,15 +17,15 @@ It uses automatic differentiation via [ForwardDiff.jl](https://github.com/JuliaD
 Please look up the list of recent [changes](https://WIAS-PDELib.github.io/VoronoiFVM.jl/stable/changes)
 
 ## Accompanying packages
-- [ExtendableSparse.jl](https://github.com/j-fu/ExtendableSparse.jl): convenient and efficient sparse matrix assembly
-- [ExtendableGrids.jl](https://github.com/j-fu/ExtendableGrids.jl): unstructured grid management library
-- [SimplexGridFactory.jl](https://github.com/j-fu/SimplexGridFactory.jl): unified high level  mesh generator interface
+- [ExtendableSparse.jl](https://github.com/WIAS-PDELib/ExtendableSparse.jl): convenient and efficient sparse matrix assembly
+- [ExtendableGrids.jl](https://github.com/WIAS-PDELib/ExtendableGrids.jl): unstructured grid management library
+- [SimplexGridFactory.jl](https://github.com/WIAS-PDELib/SimplexGridFactory.jl): unified high level  mesh generator interface
 - [Triangulate.jl](https://github.com/JuliaGeometry/Triangulate.jl):  Julia wrapper for the [Triangle](https://www.cs.cmu.edu/~quake/triangle.html) triangle mesh generator by J. Shewchuk
 - [TetGen.jl](https://github.com/JuliaGeometry/TetGen.jl):  Julia wrapper for the [TetGen](http://www.tetgen.org) tetrahedral mesh generator by H. Si.
-- [GridVisualize.jl](https://github.com/j-fu/GridVisualize.jl): grid and function visualization related to ExtendableGrids.jl
-- [PlutoVista.jl](https://github.com/j-fu/PlutoVista.jl): backend for [GridVisualize.jl](https://github.com/j-fu/GridVisualize.jl) for use in Pluto notebooks.
+- [GridVisualize.jl](https://github.com/WIAS-PDELib/GridVisualize.jl): grid and function visualization related to ExtendableGrids.jl
+- [PlutoVista.jl](https://github.com/j-fu/PlutoVista.jl): backend for [GridVisualize.jl](https://github.com/WIAS-PDELib/GridVisualize.jl) for use in Pluto notebooks.
 
-VoronoiFVM.jl and most of these packages are  part of the meta package [PDELib.jl](https://github.com/WIAS-BERLIN/PDELib.jl).
+VoronoiFVM.jl and most of these packages are  part of the meta package [PDELib.jl](https://github.com/WIAS-PDELib/PDELib.jl).
 
 
 
@@ -49,4 +49,4 @@ VoronoiFVM.jl and most of these packages are  part of the meta package [PDELib.j
 
 ## Citation
 
-If you use this package in your work, please cite it according to [CITATION.cff](https://raw.githubusercontent.com/j-fu/VoronoiFVM.jl/master/CITATION.cff)
+If you use this package in your work, please cite it according to [CITATION.cff](https://raw.githubusercontent.com/WIAS-PDELib/VoronoiFVM.jl/master/CITATION.cff)
diff --git a/docs/make.jl b/docs/make.jl
@@ -79,7 +79,7 @@ function make(; with_examples = true,
              clean = false,
              doctest = false,
              authors = "J. Fuhrmann",
-             repo = "https://github.com/j-fu/VoronoiFVM.jl",
+             repo = "https://github.com/WIAS-PDELib/VoronoiFVM.jl",
              format = Documenter.HTML(; size_threshold_ignore,
                                        assets=String["assets/citations.css"],
                                       mathengine = MathJax3()),
@@ -89,7 +89,7 @@ function make(; with_examples = true,
     cleanexamples()
 
     if !isinteractive()
-        deploydocs(; repo = "github.com/j-fu/VoronoiFVM.jl.git")
+        deploydocs(; repo = "github.com/WIAS-PDELib/VoronoiFVM.jl.git")
     end
 end
 

diff --git a/docs/src/method.md b/docs/src/method.md
@@ -3,7 +3,7 @@ The Voronoi finite volume method
 
 ## Construction of control volumes
 
-- Start with a boundary conforming Delaunay triangulation of a polygonal domain (intervals in 1D, triangles in 2D, tetrahedra in   3D). Such a triangulation can be generated by e.g. by the mesh generators triangle and TetGen. These are available in Julia via [Triangulate.jl](https://github.com/JuliaGeometry/Triangulate.jl) and [TetGen.jl](https://github.com/JuliaGeometry/TetGen.jl). For simple geometries -- tensor products of lower dimensional grids -- such triangulation can be created more easily. The package [ExtendableGrids.jl](https://github.com/j-fu/ExtendableGrids.jl) manages the grid data structure which is used in this package. [SimplexGridFactory.jl](https://github.com/j-fu/SimplexGridFactory.jl) interfaces this grid structure with  [Triangulate.jl](https://github.com/JuliaGeometry/Triangulate.jl) and [TetGen.jl](https://github.com/JuliaGeometry/TetGen.jl) and provides an API for incrementally setting up geometry descriptions.
+- Start with a boundary conforming Delaunay triangulation of a polygonal domain (intervals in 1D, triangles in 2D, tetrahedra in   3D). Such a triangulation can be generated by e.g. by the mesh generators triangle and TetGen. These are available in Julia via [Triangulate.jl](https://github.com/JuliaGeometry/Triangulate.jl) and [TetGen.jl](https://github.com/JuliaGeometry/TetGen.jl). For simple geometries -- tensor products of lower dimensional grids -- such triangulation can be created more easily. The package [ExtendableGrids.jl](https://github.com/WIAS-PDELib/ExtendableGrids.jl) manages the grid data structure which is used in this package. [SimplexGridFactory.jl](https://github.com/WIAS-PDELib/SimplexGridFactory.jl) interfaces this grid structure with  [Triangulate.jl](https://github.com/JuliaGeometry/Triangulate.jl) and [TetGen.jl](https://github.com/JuliaGeometry/TetGen.jl) and provides an API for incrementally setting up geometry descriptions.
 
 - Join triangle circumcenters by lines $\rightarrow$ create Voronoi cells which can serve as control volumes, akin to representative elementary volumes (REV) used to derive conservation laws. 
 

diff --git a/docs/src/physics.md b/docs/src/physics.md
@@ -29,7 +29,7 @@ ramp
 These are characterized by the `boutflow` physics callback and 
 and the `outflowboundaries` keyword argument in the system
 resp. physics constructor. See also the 
-[corresponding notebook](https://j-fu.github.io/VoronoiFVM.jl/dev/nbhtml/outflow/)
+[corresponding notebook](https://WIAS-PDELib.github.io/VoronoiFVM.jl/dev/nbhtml/outflow/)
 
 ```@docs
 hasoutflownode

diff --git a/docs/src/post.md b/docs/src/post.md
@@ -2,7 +2,7 @@
 
 ## Plotting
 
-Plotting can be performed using the package [GridVisualize.jl](https://github.com/j-fu/GridVisualize.jl).
+Plotting can be performed using the package [GridVisualize.jl](https://github.com/WIAS-PDELib/GridVisualize.jl).
 This package extends the API with a couple of methods:
 
 ```@docs

diff --git a/docs/src/system.md b/docs/src/system.md
@@ -3,8 +3,8 @@
 The computational grid required is assumed to correspond to a domain
 ``\Omega=\cup_{r=1}^{n_\Omega} \Omega_r`` 
 
-Grids for VoronoiFVM are managed by the packages [ExtendableGrids.jl](https://github.com/j-fu/ExtendableGrids.jl)
-and [SimplexGridFactory.jl](https://github.com/j-fu/SimplexGridFactory.jl)
+Grids for VoronoiFVM are managed by the packages [ExtendableGrids.jl](https://github.com/WIAS-PDELib/ExtendableGrids.jl)
+and [SimplexGridFactory.jl](https://github.com/WIAS-PDELib/SimplexGridFactory.jl)
 
 
 with boundary  ``\partial\Omega=\Gamma=\cup_{b=1}^{n_\Gamma} \Gamma_b``.

diff --git a/pluto-examples/api-update.jl b/pluto-examples/api-update.jl
@@ -37,7 +37,7 @@ end;
 md"""
 # API updates 
 
-[Source](https://github.com/j-fu/VoronoiFVM.jl/blob/master/pluto-examples/api-updates.jl)
+[Source](https://github.com/WIAS-PDELib/VoronoiFVM.jl/blob/master/pluto-examples/api-updates.jl)
 """
 
 # ╔═╡ 3e6b4ffa-7b33-4b94-9fd6-75b030d5a115

diff --git a/pluto-examples/heterogeneous-catalysis.jl b/pluto-examples/heterogeneous-catalysis.jl
@@ -54,7 +54,7 @@ md"""
 # ╔═╡ 32eca884-3ed2-4b03-b2d9-871e00e4c0b1
 md"""
 How to model and simulate heterogeneous catalysis with [Catalyst.jl](http://github.com/SciML/Catalyst.jl)
-and [VoronoiFVM.jl](https://github.com/j-fu/VoronoiFVM.jl).
+and [VoronoiFVM.jl](https://github.com/WIAS-PDELib/VoronoiFVM.jl).
 """
 
 # ╔═╡ c8462f8e-9618-489e-9e02-7e2316c0e621

diff --git a/pluto-examples/interfaces1d.jl b/pluto-examples/interfaces1d.jl
@@ -28,7 +28,7 @@ TableOfContents(; title = "", aside = false)
 # ╔═╡ 3fa189e4-9e1c-470c-bf26-15b631945d2d
 md"""
 # Interface conditions in 1D
-[Source](https://github.com/j-fu/VoronoiFVM.jl/blob/master/pluto-examples/interfaces1d.jl)
+[Source](https://github.com/WIAS-PDELib/VoronoiFVM.jl/blob/master/pluto-examples/interfaces1d.jl)
 
 This notebooks discusses handling of internal interfaces with VoronoiFVM.jl.
 

diff --git a/pluto-examples/nonlinear-solvers.jl b/pluto-examples/nonlinear-solvers.jl
@@ -23,7 +23,7 @@ end;
 # ╔═╡ 4ed0c302-26e4-468a-a40d-0e6406f802d0
 md"""
 # Nonlinear solver control
-[Source](https://github.com/j-fu/VoronoiFVM.jl/blob/master/pluto-examples/nonlinear-solvers.jl)
+[Source](https://github.com/WIAS-PDELib/VoronoiFVM.jl/blob/master/pluto-examples/nonlinear-solvers.jl)
 
 """
 

diff --git a/pluto-examples/outflow.jl b/pluto-examples/outflow.jl
@@ -24,7 +24,7 @@ end
 md"""
 # Outflow boundary conditions
 
-[Source](https://github.com/j-fu/VoronoiFVM.jl/blob/master/pluto-examples/outflow.jl)
+[Source](https://github.com/WIAS-PDELib/VoronoiFVM.jl/blob/master/pluto-examples/outflow.jl)
 """
 
 # ╔═╡ 0d1b7d24-4dc7-4f1d-944f-e279e18f151c

diff --git a/pluto-examples/problemcase.jl b/pluto-examples/problemcase.jl
@@ -32,7 +32,7 @@ end;
 # ╔═╡ 5e13b3db-570c-4159-939a-7e2268f0a102
 md"""
 # Some problems with Voronoi FVM
-[Source](https://github.com/j-fu/VoronoiFVM.jl/blob/master/pluto-examples/problemcase.jl)
+[Source](https://github.com/WIAS-PDELib/VoronoiFVM.jl/blob/master/pluto-examples/problemcase.jl)
 
 Draft. J. Fuhrmann, Oct. 29. 2021. Updated Dec 19, 2021.
 

diff --git a/src/vfvm_diffeq_interface.jl b/src/vfvm_diffeq_interface.jl
@@ -133,7 +133,7 @@ in [mass matrix form](https://diffeq.sciml.ai/stable/solvers/dae_solve/#Ordinary
 to be handeled by ODE solvers from [DifferentialEquations.jl](https://github.com/SciML/DifferentialEquations.jl).
 
 Parameters:
-- `system`: A [`VoronoiFVM.System`](https://j-fu.github.io/VoronoiFVM.jl/stable/system/#VoronoiFVM.System-Tuple{ExtendableGrid})
+- `system`: A [`VoronoiFVM.System`](https://WIAS-PDELib.github.io/VoronoiFVM.jl/stable/system/#VoronoiFVM.System-Tuple{ExtendableGrid})
 - `jacval` (optional): Initial value. Default is a zero vector. Consider to  pass a stationary solution at time `tjac`.
 - `tjac` (optional): tjac, Default: 0
 
@@ -166,7 +166,7 @@ in [mass matrix form](https://diffeq.sciml.ai/stable/solvers/dae_solve/#Ordinary
 which can  be handeled by ODE solvers from [DifferentialEquations.jl](https://github.com/SciML/DifferentialEquations.jl).
 
 Parameters:
-- `system`: A [`VoronoiFVM.System`](https://j-fu.github.io/VoronoiFVM.jl/stable/system/#VoronoiFVM.System-Tuple{ExtendableGrid})
+- `system`: A [`VoronoiFVM.System`](https://WIAS-PDELib.github.io/VoronoiFVM.jl/stable/system/#VoronoiFVM.System-Tuple{ExtendableGrid})
 - `inival`: Initial value. Consider to  pass a stationary solution at `tspan[1]`.
 - `tspan`: Time interval 
 - `callback` : (optional) [callback](https://diffeq.sciml.ai/stable/features/callback_functions/#Using-Callbacks) for ODE solver 

diff --git a/src/vfvm_functions.jl b/src/vfvm_functions.jl
@@ -44,7 +44,7 @@ it's derivative calculated via `ForwardDiff.jl` is not,
 so we use the polynomial approximation in the  
 interval `(-bernoulli_small_threshold, bernoulli_small_threshold)`. 
 
-Also, see the discussion in [#117](https://github.com/j-fu/VoronoiFVM.jl/issues/117).
+Also, see the discussion in [#117](https://github.com/WIAS-PDELib/VoronoiFVM.jl/issues/117).
 """
 function fbernoulli(x)
     if x < -bernoulli_large_threshold

diff --git a/src/vfvm_linsolve.jl b/src/vfvm_linsolve.jl
@@ -35,22 +35,22 @@ Currently available strategies are:
 Notable LU Factorizations/direct solvers are:
 - [`UMFPACKFactorization`](https://docs.sciml.ai/LinearSolve/stable/solvers/solvers/#SuiteSparse.jl)  (`using LinearSolve`)
 - [`KLUFactorization`](https://docs.sciml.ai/LinearSolve/stable/solvers/solvers/#SuiteSparse.jl) (`using LinearSolve`)
-- [`SparspakFactorization`](https://docs.sciml.ai/LinearSolve/stable/solvers/solvers/#Sparspak.jl)  (`using LinearSolve`), [`SparspakLU`](https://j-fu.github.io/ExtendableSparse.jl/stable/iter/#ExtendableSparse.SparspakLU) (`using ExtendableSparse,Sparspak`)
-- [`MKLPardisoLU`](https://j-fu.github.io/ExtendableSparse.jl/stable/iter/#ExtendableSparse.MKLPardisoLU) (`using ExtendableSparse, Pardiso`), openmp parallel
+- [`SparspakFactorization`](https://docs.sciml.ai/LinearSolve/stable/solvers/solvers/#Sparspak.jl)  (`using LinearSolve`), [`SparspakLU`](https://WIAS-PDELib.github.io/ExtendableSparse.jl/stable/iter/#ExtendableSparse.SparspakLU) (`using ExtendableSparse,Sparspak`)
+- [`MKLPardisoLU`](https://WIAS-PDELib.github.io/ExtendableSparse.jl/stable/iter/#ExtendableSparse.MKLPardisoLU) (`using ExtendableSparse, Pardiso`), openmp parallel
 - [`AMGSolver`](https://j-fu.github.io/AMGCLWrap.jl/stable/solvers/#AMGCLWrap.AMGSolver) (`using AMGCLWrap`), openmp parallel
 - [`RLXSolver`](https://j-fu.github.io/AMGCLWrap.jl/stable/solvers/#AMGCLWrap.RLXSolver) (`using AMGCLWrap`), openmp parallel
 
 
 Notable incomplete factorizations/preconditioners
 - Incomplete LU factorizations written in Julia:
-    - [`ILUZeroPreconditioner`](https://j-fu.github.io/ExtendableSparse.jl/stable/iter/#ExtendableSparse.ILUZeroPreconditioner)
-    - [`ILUTPrecondidtioner`](https://j-fu.github.io/ExtendableSparse.jl/stable/iter/#ExtendableSparse.ILUTPreconditioner) (`using ExtendableSparse, IncompleteLU`)
+    - [`ILUZeroPreconditioner`](https://WIAS-PDELib.github.io/ExtendableSparse.jl/stable/iter/#ExtendableSparse.ILUZeroPreconditioner)
+    - [`ILUTPrecondidtioner`](https://WIAS-PDELib.github.io/ExtendableSparse.jl/stable/iter/#ExtendableSparse.ILUTPreconditioner) (`using ExtendableSparse, IncompleteLU`)
 - Algebraic multigrid written in Julia: (`using ExtendableSparse, AlgebraicMultigrid`)
-    - [`RS_AMGPreconditioner`](https://j-fu.github.io/ExtendableSparse.jl/stable/iter/#ExtendableSparse.RS_AMGPreconditioner)
-    - [`SA_AMGPreconditioner`](https://j-fu.github.io/ExtendableSparse.jl/stable/iter/#ExtendableSparse.SA_AMGPreconditioner)
+    - [`RS_AMGPreconditioner`](https://WIAS-PDELib.github.io/ExtendableSparse.jl/stable/iter/#ExtendableSparse.RS_AMGPreconditioner)
+    - [`SA_AMGPreconditioner`](https://WIAS-PDELib.github.io/ExtendableSparse.jl/stable/iter/#ExtendableSparse.SA_AMGPreconditioner)
 - AMGCL based preconditioners (`using ExtendableSparse, AMGCLWrap`), openmp parallel
-    - [`AMGCL_AMGPreconditioner`](https://j-fu.github.io/ExtendableSparse.jl/stable/iter/#ExtendableSparse.AMGCL_AMGPreconditioner)
-    - [`AMGCL_RLXPreconditioner`](https://j-fu.github.io/ExtendableSparse.jl/stable/iter/#ExtendableSparse.AMGCL_RLXPreconditioner)
+    - [`AMGCL_AMGPreconditioner`](https://WIAS-PDELib.github.io/ExtendableSparse.jl/stable/iter/#ExtendableSparse.AMGCL_AMGPreconditioner)
+    - [`AMGCL_RLXPreconditioner`](https://WIAS-PDELib.github.io/ExtendableSparse.jl/stable/iter/#ExtendableSparse.AMGCL_RLXPreconditioner)
 
 Blocking strategies are:
 - [`NoBlock`](@ref)

diff --git a/src/vfvm_system.jl b/src/vfvm_system.jl
@@ -257,23 +257,23 @@ end
 ````
 System(X; kwargs...)
 ````
-Create an [1D grid from vector X](https://j-fu.github.io/ExtendableGrids.jl/stable/gridconstructors/) and call  [`VoronoiFVM.System(grid::ExtendableGrid; kwargs...)`](@ref).
+Create an [1D grid from vector X](https://WIAS-PDELib.github.io/ExtendableGrids.jl/stable/gridconstructors/) and call  [`VoronoiFVM.System(grid::ExtendableGrid; kwargs...)`](@ref).
 """
 System(X::AbstractVector; kwargs...) = System(simplexgrid(X); kwargs...)
 
 """
 ````
 System(X,Y; kwargs...)
 ````
-Create a [2D grid from vectors X,Y ](https://j-fu.github.io/ExtendableGrids.jl/stable/gridconstructors/) and call  [`VoronoiFVM.System(grid::ExtendableGrid; kwargs...)`](@ref).
+Create a [2D grid from vectors X,Y ](https://WIAS-PDELib.github.io/ExtendableGrids.jl/stable/gridconstructors/) and call  [`VoronoiFVM.System(grid::ExtendableGrid; kwargs...)`](@ref).
 """
 System(X::AbstractVector, Y::AbstractVector; kwargs...) = System(simplexgrid(X, Y); kwargs...)
 
 """
 ````
 System(X,Y, Z; kwargs...)
 ````
-Create a [3D grid from vectors X,Y,Z ](https://j-fu.github.io/ExtendableGrids.jl/stable/gridconstructors/) and call  [`VoronoiFVM.System(grid::ExtendableGrid; kwargs...)`](@ref).
+Create a [3D grid from vectors X,Y,Z ](https://WIAS-PDELib.github.io/ExtendableGrids.jl/stable/gridconstructors/) and call  [`VoronoiFVM.System(grid::ExtendableGrid; kwargs...)`](@ref).
 """
 System(X::AbstractVector, Y::AbstractVector, Z::AbstractVector; kwargs...) = System(simplexgrid(X, Y, Z); kwargs...)