Overhaul of finite-differences (#41)

* Implemented hashing of bases

* Finite-differences stencils now generated when needed

In-progress support for non-uniform implicit finite-differences
Coulomb fix at r=0 no longer part of type, but instantiated via
special CoulombDerivative operator

* Also compare indices when comparing restricted bases

* Print spacing variation for non-uniform finite-differences

* Disambiguate various finite-differences in hash

* Implemented R'D'QuasiDiagonal*D*R for StaggeredFiniteDifferences

* Derivative errors computed in R and not in Hilbert space

* Also test on Julia 1.6

* Fixed finite-differences test errors due to API breakage

* Update compat entries

* v0.3.0

* Fixed docs plots

* Ensure implicit finite-differences work in restricted bases

* Type alias

* Update CI.yml; 1.6 released, don't test on Windows due to memory issue (?)

* Updated CI to skip Windows/1.5 only and avoid Doctest error -> fail

Author: jagot

.github/workflows/CI.yml

@@ -11,14 +11,17 @@ jobs:
       matrix:
         version:
           - '1.5'
-          # - '1.6'
+          - '1.6'
           - 'nightly'
         os:
           - ubuntu-latest
           - macOS-latest
           - windows-latest
         arch:
           - x64
+        exclude:
+          - os: windows-latest
+            version: '1.5'
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
@@ -74,7 +77,10 @@ jobs:
             using Pkg
             Pkg.develop(PackageSpec(path=pwd()))
             Pkg.instantiate()'
-      - run: |
+      - name: Run Doctests
+        # See https://github.com/actions/toolkit/issues/399
+        continue-on-error: true
+        run: |
           julia --project=docs -e '
             using Documenter: DocMeta, doctest
             using CompactBases

Project.toml

@@ -1,7 +1,7 @@
 name = "CompactBases"
 uuid = "2c0377a8-7469-4ebd-be0f-82e501f20078"
 authors = ["Stefanos Carlström <[email protected]>"]
-version = "0.2.0"
+version = "0.3.0"
 
 [deps]
 BandedMatrices = "aae01518-5342-5314-be14-df237901396f"
@@ -21,14 +21,14 @@ SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 [compat]
 BandedMatrices = "0.16"
 BlockBandedMatrices = "0.10"
-ContinuumArrays = "0.6.4"
+ContinuumArrays = "0.6.4,0.7"
 FastGaussQuadrature = "0.4"
 FillArrays = "0.11"
 Formatting = "0.4"
 IntervalSets = "0.5.1"
 LazyArrays = "0.20,0.21"
 OffsetArrays = "1.1"
-QuasiArrays = "0.4.9"
+QuasiArrays = "0.4.9,0.5"
 RecipesBase = "1.0"
 julia = "1.5"
 

docs/plots.jl

@@ -135,7 +135,7 @@ function densities()
     rr = 10.0 .^ range(-2, stop=log10(rmax), length=3000)
 
     for R in [FiniteDifferences(N, ρ),
-              StaggeredFiniteDifferences(ρmin, ρmax, α, rmax, 0.0),
+              StaggeredFiniteDifferences(ρmin, ρmax, α, rmax),
               FEDVR(range(0, stop=rmax, length=Nn), k),
               BSpline(LinearKnotSet(k, 0, rmax, Nn))]
         r = axes(R,1)
@@ -203,12 +203,12 @@ function diagonal_operators()
 
     ρ = 0.1/Z
     N = ceil(Int, rmax/ρ)
-    ufd = StaggeredFiniteDifferences(N, ρ, Z)
+    ufd = StaggeredFiniteDifferences(N, ρ)
 
     ρmin=0.1/Z
     ρmax=0.6
     α=0.002
-    nufd = StaggeredFiniteDifferences(ρmin, ρmax, α, rmax, Z)
+    nufd = StaggeredFiniteDifferences(ρmin, ρmax, α, rmax)
 
     fedvr = FEDVR(range(0, stop=rmax, length=20),
                   vcat(10,fill(7,18)))[:,2:end-1]

src/CompactBases.jl

@@ -10,7 +10,7 @@ import ContinuumArrays: Basis, ℵ₁, Derivative, Inclusion, @simplify, simplif
 using QuasiArrays
 import QuasiArrays: AbstractQuasiMatrix, QuasiAdjoint, MulQuasiArray,
     PInvQuasiMatrix, InvQuasiMatrix, QuasiDiagonal,
-    BroadcastQuasiArray, SubQuasiArray
+    BroadcastQuasiArray, SubQuasiArray, LazyQuasiMatrix
 
 using IntervalSets
 
@@ -43,6 +43,8 @@ include("skewtridiag.jl")
 
 include("materialize_dsl.jl")
 
+include("coulomb_derivative.jl")
+
 include("fornberg.jl")
 include("finite_differences.jl")
 include("fd_operators.jl")

src/bsplines.jl

@@ -123,6 +123,7 @@ BSpline(t::AbstractKnotSet; k′=3) = BSpline(t, num_quadrature_points(order(t),
 axes(B::BSpline) = (Inclusion(first(B.t)..last(B.t)), Base.OneTo(numfunctions(B.t)))
 size(B::BSpline) = (ℵ₁, numfunctions(B.t))
 ==(A::BSpline,B::BSpline) = A.t == B.t
+Base.hash(B::BSpline, h::UInt) = hash(B.t, h)
 
 distribution(B::BSpline) = distribution(B.t)
 

src/coulomb_derivative.jl

@@ -0,0 +1,22 @@
+"""
+    CoulombDerivative(D, Z, ℓ)
+
+Helper operator wrapping the `Derivative` operator in the case of a
+Coulomb potential of charge `Z` and centrifugal potential
+``ℓ(ℓ+1)/2r²``. Its main use is to correctly apply boundary conditions
+at ``r=0``, when materializing derivatives.
+"""
+struct CoulombDerivative{T,Der<:Derivative{T},U<:Number} <: LazyQuasiMatrix{T}
+    D::Der
+    Z::U
+    ℓ::Int
+end
+
+axes(D::CoulombDerivative) = axes(D.D)
+==(a::CoulombDerivative, b::CoulombDerivative) = a.D == b.D && a.Z == b.Z && a.ℓ == b.ℓ
+copy(D::CoulombDerivative) = CoulombDerivative(copy(D.D), D.Z, D.ℓ)
+
+Base.show(io::IO, D::CoulombDerivative) =
+    write(io, "CoulombDerivative($(D.D), Z = $(D.Z), ℓ = $(D.ℓ))")
+
+export CoulombDerivative