From 22f811e58084b22bda3edc37828f30e534579123 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BCrgen=20Fuhrmann?= Date: Fri, 1 Nov 2024 16:54:52 +0100 Subject: [PATCH] Fix links after transition to WIAS-PDELib --- CITATION.cff | 5 ++--- Project.toml | 2 +- README.md | 14 +++++++------- docs/make.jl | 4 ++-- docs/src/method.md | 2 +- docs/src/physics.md | 2 +- docs/src/post.md | 2 +- docs/src/system.md | 4 ++-- pluto-examples/api-update.jl | 2 +- pluto-examples/heterogeneous-catalysis.jl | 2 +- pluto-examples/interfaces1d.jl | 2 +- pluto-examples/nonlinear-solvers.jl | 2 +- pluto-examples/outflow.jl | 2 +- pluto-examples/problemcase.jl | 2 +- src/vfvm_diffeq_interface.jl | 4 ++-- src/vfvm_functions.jl | 2 +- src/vfvm_linsolve.jl | 16 ++++++++-------- src/vfvm_system.jl | 6 +++--- 18 files changed, 37 insertions(+), 38 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index d66101c83..de4482c38 100644 --- 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 index a0aa5a1a8..b21ac62da 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "VoronoiFVM" uuid = "82b139dc-5afc-11e9-35da-9b9bdfd336f3" authors = ["Jürgen Fuhrmann ", "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 index a4c09d506..4994c71b3 100644 --- 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 index 7acb4b29b..b46345619 100644 --- 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 index ca91184de..00ae3a1be 100644 --- 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 index 65c38b97a..b21712659 100644 --- 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 index 67e06cccb..b1b908711 100644 --- 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 index fd5f3f102..c06e7c6c0 100644 --- 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 index c030de33c..d57b1d168 100644 --- 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 index a5e044256..33c7ae9b6 100644 --- 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 index f9cc700f9..d9ca6cc3a 100644 --- 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 index 06f23e497..f208d45cf 100644 --- 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 index f26b137f0..37e24b8b5 100644 --- 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 index c4474745b..41b433cd1 100644 --- 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 index 837e5a889..bd80b86f9 100644 --- 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 index e8b958305..357327e54 100644 --- 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 index b21d0fec0..3c19852d2 100644 --- 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 index 86f324186..d8ebe3470 100644 --- a/src/vfvm_system.jl +++ b/src/vfvm_system.jl @@ -257,7 +257,7 @@ 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...) @@ -265,7 +265,7 @@ 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...) @@ -273,7 +273,7 @@ System(X::AbstractVector, Y::AbstractVector; kwargs...) = System(simplexgrid(X, ```` 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...)