Merge pull request #100 from ranocha/hr/trixi

Interfacing with Trixi and general cleanup

NEWS.md

@@ -6,6 +6,15 @@ used in the Julia ecosystem. Notable changes will be documented in this file
 for human readability.
 
 
+## Changes in the v0.5 lifecycle
+
+#### Deprecated
+
+- The (keyword) argument `parallel::Union{Val{:serial}, Val{:threads}}`
+  is deprecated in favor of `mode` with possible values
+  `FastMode()` (default), `SafeMode()`, and `ThreadedMode()`
+
+
 ## Breaking changes from v0.4.x to v0.5
 
 - Switch from British English to American English consistently, e.g.,

Project.toml

@@ -5,8 +5,8 @@ version = "0.5.3-pre"
 
 [deps]
 ArgCheck = "dce04be8-c92d-5529-be00-80e4d2c0e197"
+ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
-DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
@@ -23,7 +23,6 @@ Unrolled = "9602ed7d-8fef-5bc8-8597-8f21381861e8"
 [compat]
 ArgCheck = "1, 2.0"
 DiffEqBase = "6"
-DiffEqCallbacks = "2.6"
 FFTW = "1"
 LoopVectorization = "0.12.22"
 PolynomialBases = "0.4.5"

README.md

@@ -49,14 +49,11 @@ julia> using Plots: plot, plot!
 
 julia> D = periodic_derivative_operator(derivative_order=1, accuracy_order=2,
                                         xmin=0.0, xmax=2.0, N=20)
-Periodic 1st derivative operator of order 2 {T=Float64, Parallel=Val{:serial}}
-on a grid in [0.0, 2.0] using 20 nodes,
-stencils with 1 nodes to the left, 1 nodes to the right, and coefficients from
-  Fornberg (1998)
+Periodic first-derivative operator of order 2 on a grid in [0.0, 2.0] using 20 nodes,
+stencils with 1 nodes to the left, 1 nodes to the right, and coefficients of Fornberg (1998)
   Calculation of Weights in Finite Difference Formulas.
   SIAM Rev. 40.3, pp. 685-691.
 
-
 julia> x = grid(D); u = sinpi.(x);
 
 julia> plot(x, D * u, label="numerical")
@@ -78,15 +75,12 @@ julia> using Plots: plot, plot!
 
 julia> D = derivative_operator(MattssonNordström2004(), derivative_order=1, accuracy_order=2,
                                xmin=0.0, xmax=1.0, N=21)
-SBP 1st derivative operator of order 2 {T=Float64, Parallel=Val{:serial}}
-on a grid in [0.0, 1.0] using 21 nodes
-and coefficients given in
-  Mattsson, Nordström (2004)
+SBP first-derivative operator of order 2 on a grid in [0.0, 1.0] using 21 nodes
+and coefficients of Mattsson, Nordström (2004)
   Summation by parts operators for finite difference approximations of second
     derivatives.
   Journal of Computational Physics 199, pp. 503-540.
 
-
 julia> x = grid(D); u = exp.(x);
 
 julia> plot(x, D * u, label="numerical")
@@ -112,18 +106,18 @@ supported.
 
 ### Periodic domains
 
-- `periodic_derivative_operator(derivative_order, accuracy_order, xmin, xmax, N)`
+- `periodic_derivative_operator(; derivative_order, accuracy_order, xmin, xmax, N)`
 
   These are classical central finite difference operators using `N` nodes on the
   interval `[xmin, xmax]`.
 
-- `periodic_derivative_operator(Holoborodko2008(), derivative_order, accuracy_order, xmin, xmax, N)`
+- `periodic_derivative_operator(Holoborodko2008(); derivative_order, accuracy_order, xmin, xmax, N)`
 
   These are central finite difference operators using `N` nodes on the
   interval `[xmin, xmax]` and the coefficients of
   [Pavel Holoborodko](http://www.holoborodko.com/pavel/numerical-methods/numerical-derivative/smooth-low-noise-differentiators/).
 
-- `fourier_derivative_operator(xmin, xmax, N)`
+- `fourier_derivative_operator(; xmin, xmax, N)`
 
   Fourier derivative operators are implemented using the fast Fourier transform of
   [FFTW.jl](https://github.com/JuliaMath/FFTW.jl).
@@ -135,14 +129,14 @@ e.g. to solve elliptic problems of the form `u = (D^2 + I) \ f`.
 
 ### Finite (nonperiodic) domains
 
-- `derivative_operator(source_of_coefficients, derivative_order, accuracy_order, xmin, xmax, N)`
+- `derivative_operator(source_of_coefficients; derivative_order, accuracy_order, xmin, xmax, N)`
 
   Finite difference SBP operators for first and second derivatives can be obtained
   by using `MattssonNordström2004()` as `source_of_coefficients`.
   Other sources of coefficients are implemented as well. To obtain a full list
   of all operators, use `subtypes(SourceOfCoefficients)`.
 
-- `legendre_derivative_operator(xmin, xmax, N)`
+- `legendre_derivative_operator(; xmin, xmax, N)`
 
   Use Lobatto Legendre polynomial collocation schemes on `N`, i.e.
   polynomials of degree `N-1`, implemented via
@@ -181,15 +175,14 @@ of the operators. Therefore, some conversion functions are supplied, e.g.
 ```julia
 julia> using SummationByPartsOperators
 
-julia> D = derivative_operator(MattssonNordström2004(), 1, 2, 0., 1., 5)
-SBP 1st derivative operator of order 2 {T=Float64, Parallel=Val{:serial}}
-on a grid in [0.0, 1.0] using 5 nodes
-and coefficients given in
-  Mattsson, Nordström (2004)
+julia> D = derivative_operator(MattssonNordström2004(),
+                               derivative_order=1, accuracy_order=2,
+                               xmin=0.0, xmax=1.0, N=5)
+SBP first-derivative operator of order 2 on a grid in [0.0, 1.0] using 5 nodes
+and coefficients of Mattsson, Nordström (2004)
   Summation by parts operators for finite difference approximations of second
     derivatives.
-  Journal of Computational Physics 199, pp.503-540.
-
+  Journal of Computational Physics 199, pp. 503-540.
 
 julia> Matrix(D)
 5×5 Array{Float64,2}:

docs/src/index.md

@@ -32,14 +32,11 @@ julia> using Plots: plot, plot!
 
 julia> D = periodic_derivative_operator(derivative_order=1, accuracy_order=2,
                                         xmin=0.0, xmax=2.0, N=20)
-Periodic 1st derivative operator of order 2 {T=Float64, Parallel=Val{:serial}}
-on a grid in [0.0, 2.0] using 20 nodes,
-stencils with 1 nodes to the left, 1 nodes to the right, and coefficients from
-  Fornberg (1998)
+Periodic first-derivative operator of order 2 on a grid in [0.0, 2.0] using 20 nodes,
+stencils with 1 nodes to the left, 1 nodes to the right, and coefficients of Fornberg (1998)
   Calculation of Weights in Finite Difference Formulas.
   SIAM Rev. 40.3, pp. 685-691.
 
-
 julia> x = grid(D); u = sinpi.(x);
 
 julia> plot(x, D * u, label="numerical")
@@ -59,15 +56,12 @@ julia> using Plots: plot, plot!
 
 julia> D = derivative_operator(MattssonNordström2004(), derivative_order=1, accuracy_order=2,
                                xmin=0.0, xmax=1.0, N=21)
-SBP 1st derivative operator of order 2 {T=Float64, Parallel=Val{:serial}}
-on a grid in [0.0, 1.0] using 21 nodes
-and coefficients given in
-  Mattsson, Nordström (2004)
+SBP first-derivative operator of order 2 on a grid in [0.0, 1.0] using 21 nodes
+and coefficients of Mattsson, Nordström (2004)
   Summation by parts operators for finite difference approximations of second
     derivatives.
   Journal of Computational Physics 199, pp. 503-540.
 
-
 julia> x = grid(D); u = exp.(x);
 
 julia> plot(x, D * u, label="numerical")

docs/src/introduction.md

@@ -44,14 +44,11 @@ julia> using SummationByPartsOperators, LinearAlgebra
 
 julia> D = periodic_derivative_operator(derivative_order=1, accuracy_order=2,
                                         xmin=0.0, xmax=2.0, N=20)
-Periodic 1st derivative operator of order 2 {T=Float64, Parallel=Val{:serial}}
-on a grid in [0.0, 2.0] using 20 nodes,
-stencils with 1 nodes to the left, 1 nodes to the right, and coefficients from
-  Fornberg (1998)
+Periodic first-derivative operator of order 2 on a grid in [0.0, 2.0] using 20 nodes,
+stencils with 1 nodes to the left, 1 nodes to the right, and coefficients of Fornberg (1998)
   Calculation of Weights in Finite Difference Formulas.
   SIAM Rev. 40.3, pp. 685-691.
 
-
 julia> M = mass_matrix(D)
 UniformScaling{Float64}
 0.1*I
@@ -61,8 +58,7 @@ julia> M * Matrix(D) + Matrix(D)' * M |> norm
 
 julia> D = fourier_derivative_operator(xmin=0.0, xmax=2.0, N=20)
 Periodic 1st derivative Fourier operator {T=Float64}
-on a grid in [0.0, 2.0] using 20 nodes and 11 modes.
-
+on a grid in [0.0, 2.0] using 20 nodes and 11 modes
 
 julia> M = mass_matrix(D)
 UniformScaling{Float64}
@@ -111,15 +107,12 @@ julia> using SummationByPartsOperators, LinearAlgebra
 
 julia> D = derivative_operator(MattssonNordström2004(), derivative_order=1, accuracy_order=2,
                                xmin=0//1, xmax=1//1, N=9)
-SBP 1st derivative operator of order 2 {T=Rational{Int64}, Parallel=Val{:serial}}
-on a grid in [0//1, 1//1] using 9 nodes
-and coefficients given in
-  Mattsson, Nordström (2004)
+SBP first-derivative operator of order 2 on a grid in [0//1, 1//1] using 9 nodes
+and coefficients of Mattsson, Nordström (2004)
   Summation by parts operators for finite difference approximations of second
     derivatives.
   Journal of Computational Physics 199, pp. 503-540.
 
-
 julia> tL = zeros(eltype(D), size(D, 1)); tL[1] = 1; tL'
 1×9 adjoint(::Vector{Rational{Int64}}) with eltype Rational{Int64}:
  1//1  0//1  0//1  0//1  0//1  0//1  0//1  0//1  0//1
@@ -186,15 +179,12 @@ julia> using SummationByPartsOperators, LinearAlgebra
 
 julia> D = derivative_operator(MattssonNordström2004(), derivative_order=2, accuracy_order=2,
                                xmin=0//1, xmax=1//1, N=9)
-SBP 2nd derivative operator of order 2 {T=Rational{Int64}, Parallel=Val{:serial}}
-on a grid in [0//1, 1//1] using 9 nodes
-and coefficients given in
-  Mattsson, Nordström (2004)
+SBP second-derivative operator of order 2 on a grid in [0//1, 1//1] using 9 nodes
+and coefficients of Mattsson, Nordström (2004)
   Summation by parts operators for finite difference approximations of second
     derivatives.
   Journal of Computational Physics 199, pp. 503-540.
 
-
 julia> M = mass_matrix(D)
 9×9 Diagonal{Rational{Int64}, Vector{Rational{Int64}}}:
  1//16   ⋅     ⋅     ⋅     ⋅     ⋅     ⋅     ⋅     ⋅
@@ -262,25 +252,19 @@ julia> using SummationByPartsOperators, LinearAlgebra
 
 julia> Dp = derivative_operator(Mattsson2017(:plus), derivative_order=1, accuracy_order=2,
                                 xmin=0//1, xmax=1//1, N=9)
-SBP 1st derivative operator of order 2 {T=Rational{Int64}, Parallel=Val{:serial}}
-on a grid in [0//1, 1//1] using 9 nodes
-and coefficients given in
-  Upwind coefficients (plus) of
-  Mattsson (2017)
+SBP first-derivative operator of order 2 on a grid in [0//1, 1//1] using 9 nodes
+and coefficients of Mattsson (2017)
   Diagonal-norm upwind SBP operators.
   Journal of Computational Physics 335, pp. 283-310.
-
+  (upwind coefficients plus)
 
 julia> Dm = derivative_operator(Mattsson2017(:minus), derivative_order=1, accuracy_order=2,
                                 xmin=0//1, xmax=1//1, N=9)
-SBP 1st derivative operator of order 2 {T=Rational{Int64}, Parallel=Val{:serial}}
-on a grid in [0//1, 1//1] using 9 nodes
-and coefficients given in
-  Upwind coefficients (minus) of
-  Mattsson (2017)
+SBP first-derivative operator of order 2 on a grid in [0//1, 1//1] using 9 nodes
+and coefficients of Mattsson (2017)
   Diagonal-norm upwind SBP operators.
   Journal of Computational Physics 335, pp. 283-310.
-
+  (upwind coefficients minus)
 
 julia> M = mass_matrix(Dp)
 9×9 Diagonal{Rational{Int64}, Vector{Rational{Int64}}}:
@@ -324,11 +308,8 @@ julia> using SummationByPartsOperators, LinearAlgebra
 julia> D = couple_continuously(
                legendre_derivative_operator(xmin=-1.0, xmax=1.0, N=3),
                UniformMesh1D(xmin=0.0, xmax=1.0, Nx=3))
-First derivative operator {T=Float64}
-on the Lobatto Legendre nodes in [-1.0, 1.0] using 3 nodes
-coupled continuously on the mesh
-UniformMesh1D{Float64} with 3 cells in (0.0, 1.0)
-
+First derivative operator {T=Float64} on 3 Lobatto Legendre nodes in [-1.0, 1.0]
+coupled continuously on UniformMesh1D{Float64} with 3 cells in (0.0, 1.0)
 
 julia> Matrix(D)
 7×7 Matrix{Float64}:
@@ -363,11 +344,8 @@ julia> D = couple_discontinuously(
                legendre_derivative_operator(xmin=-1.0, xmax=1.0, N=3),
                UniformPeriodicMesh1D(xmin=0.0, xmax=1.0, Nx=3),
                Val(:central))
-First derivative operator {T=Float64}
-on the Lobatto Legendre nodes in [-1.0, 1.0] using 3 nodes
-coupled discontinuously (upwind: Val{:central}()) on the mesh
-UniformPeriodicMesh1D{Float64} with 3 cells in (0.0, 1.0)
-
+First derivative operator {T=Float64} on 3 Lobatto Legendre nodes in [-1.0, 1.0]
+coupled discontinuously (upwind: Val{:central}()) on UniformPeriodicMesh1D{Float64} with 3 cells in (0.0, 1.0)
 
 julia> M = mass_matrix(D);
 

src/SBP_coefficients/Mattsson2012.jl

@@ -3,37 +3,41 @@
     Mattsson2012()
 
 Coefficients of the SBP operators given in
-  Mattsson (2012)
+- Mattsson (2012)
   Summation by Parts Operators for Finite Difference Approximations of
     Second-Derivatives with Variable Coefficients.
   Journal of Scientific Computing 51, pp. 650-682.
 """
 struct Mattsson2012 <: SourceOfCoefficients end
 
-function Base.show(io::IO, ::Mattsson2012)
-    print(io,
-        "  Mattsson (2012) \n",
-        "  Summation by Parts Operators for Finite Difference Approximations of\n",
-        "    Second-Derivatives with Variable Coefficients. \n",
-        "  Journal of Scientific Computing 51, pp. 650-682. \n",
-        "See also (first derivatives) \n",
-        "  Mattsson, Nordström (2004) \n",
-        "  Summation by parts operators for finite difference approximations of second \n",
-        "    derivatives. \n",
-        "  Journal of Computational Physics 199, pp. 503-540. \n")
+function Base.show(io::IO, source::Mattsson2012)
+  if get(io, :compact, false)
+    summary(io, source)
+  else
+      print(io,
+          "Mattsson (2012) \n",
+          "  Summation by Parts Operators for Finite Difference Approximations of\n",
+          "    Second-Derivatives with Variable Coefficients. \n",
+          "  Journal of Scientific Computing 51, pp. 650-682. \n",
+          "See also (first derivatives) \n",
+          "  Mattsson, Nordström (2004) \n",
+          "  Summation by parts operators for finite difference approximations of second \n",
+          "    derivatives. \n",
+          "  Journal of Computational Physics 199, pp. 503-540.")
+  end
 end
 
 
-@inline function first_derivative_coefficients(source::Mattsson2012, order::Int, T=Float64, parallel=Val{:serial}())
-    first_derivative_coefficients(MattssonNordström2004(), order, T, parallel)
+@inline function first_derivative_coefficients(source::Mattsson2012, order::Int, T=Float64, mode=FastMode())
+    first_derivative_coefficients(MattssonNordström2004(), order, T, mode)
 end
 
-@inline function second_derivative_coefficients(source::Mattsson2012, order::Int, T=Float64, parallel=Val{:serial}())
-    second_derivative_coefficients(MattssonNordström2004(), order, T, parallel)
+@inline function second_derivative_coefficients(source::Mattsson2012, order::Int, T=Float64, mode=FastMode())
+    second_derivative_coefficients(MattssonNordström2004(), order, T, mode)
 end
 
 
-function var_coef_derivative_coefficients(source::Mattsson2012, derivative_order::Int, accuracy_order::Int, grid, parallel=Val{:serial}())
+function var_coef_derivative_coefficients(source::Mattsson2012, derivative_order::Int, accuracy_order::Int, grid, mode=FastMode())
     @argcheck derivative_order == 2
     T = eltype(grid)
     if accuracy_order == 2
@@ -61,7 +65,7 @@ function var_coef_derivative_coefficients(source::Mattsson2012, derivative_order
     end
 
     VarCoefDerivativeCoefficients(coefficient_cache, left_weights, right_weights,
-                                  parallel, derivative_order, accuracy_order, source)
+                                  mode, derivative_order, accuracy_order, source)
 end