Merge pull request #360 from FourierFlows/ncc-ap/filteredLSRK54

Add `FilteredLSRK54TimeStepper` + upgrades to Documenter v1

Author: navidcy

Project.toml

@@ -6,7 +6,7 @@ authors = ["Gregory L. Wagner <wagner.greg@gmail.com>", "Navid C. Constantinou <
 description = "Tools for building fast, hackable, pseudospectral partial differential equation solvers on periodic domains."
 documentation = "https://fourierflows.github.io/FourierFlowsDocumentation/stable/"
 repository = "https://github.com/FourierFlows/FourierFlows.jl"
-version = "0.10.3"
+version = "0.10.4"
 
 [deps]
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"

docs/Project.toml

@@ -9,4 +9,6 @@ Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
 [compat]
 CairoMakie = "0.10"
+Documenter = "1"
+DocumenterCitations = "1.1"
 Literate = "≥2.9.0"

docs/make.jl

@@ -62,15 +62,16 @@ pages = [
     "References" => "references.md",
 ]
 
-makedocs(bib, sitename = "FourierFlows.jl",
-               authors = "Gregory L. Wagner and Navid C. Constantinou and contributors",
-               modules = [FourierFlows],
-                format = format,
-                 pages = pages,
-               doctest = false,
-                strict = :doctest,
-                 clean = true,
-             checkdocs = :exports)
+makedocs(sitename = "FourierFlows.jl",
+          authors = "Gregory L. Wagner, Navid C. Constantinou, and contributors",
+          modules = [FourierFlows],
+           format = format,
+            pages = pages,
+          plugins = [bib],
+          doctest = true,
+         warnonly = [:cross_references],
+            clean = true,
+        checkdocs = :exports)
 
 @info "Cleaning up temporary .jld2 and .nc files created by doctests or literated examples..."
 

src/FourierFlows.jl

@@ -52,6 +52,7 @@ export
   RK4TimeStepper,
   FilteredRK4TimeStepper,
   LSRK54TimeStepper,
+  FilteredLSRK54TimeStepper,
   ETDRK4TimeStepper,
   FilteredETDRK4TimeStepper,
   AB3TimeStepper,

src/timesteppers.jl

@@ -34,14 +34,15 @@ function stepforward!(prob::Problem, diags, nsteps::Int)
   return nothing
 end
 
-const fullyexplicitsteppers= [
+const fullyexplicitsteppers = [
   :ForwardEuler,
   :RK4,
   :AB3,
+  :LSRK54,
   :FilteredForwardEuler,
   :FilteredRK4,
   :FilteredAB3,
-  :LSRK54
+  :FilteredLSRK54
 ]
 
 isexplicit(stepper) = any(Symbol(stepper) .== fullyexplicitsteppers)
@@ -75,6 +76,7 @@ end
 #   * RK4
 #   * Filtered RK4
 #   * LSRK54
+#   * Filtered LSRK54
 #   * ETDRK4
 #   * Filtered ETDRK4
 #   * AB3
@@ -350,15 +352,43 @@ function LSRK54TimeStepper(equation::Equation, dev::Device=CPU())
   return LSRK54TimeStepper(S², RHS, Tuple(A), Tuple(B), Tuple(C))
 end
 
+"""
+    struct FilteredLSRK54TimeStepper{T,V,Tf} <: AbstractTimeStepper{T}
+
+A 4th-order 5-stages low-storage Runge-Kutta timestepper with spectral filtering.
+See [`LSRK54TimeStepper`](@ref).
+"""
+struct FilteredLSRK54TimeStepper{T,V,Tf} <: AbstractTimeStepper{T}
+      S² :: T
+     RHS :: T
+       A :: V
+       B :: V
+       C :: V
+  filter :: Tf
+end
+
+"""
+    FilteredRK4TimeStepper(equation::Equation, dev::Device=CPU(); filterkwargs...)
+
+Construct a 4th-order 5-stages 2-storage Runge-Kutta timestepper with spectral filtering
+for `equation` on device `dev`.
+"""
+function FilteredLSRK54TimeStepper(equation::Equation, dev::Device=CPU(); filterkwargs...)
+  ts = LSRK54TimeStepper(equation, dev)
+  filter = makefilter(equation; filterkwargs...)
+
+  return FilteredLSRK54TimeStepper(getfield.(Ref(ts), fieldnames(typeof(ts)))..., filter)
+end
+
 function LSRK54update!(sol, clock, ts, equation, vars, params, grid, t, dt)
   @. ts.S² = 0
 
   for i = 1:5
-    equation.calcN!(ts.RHS, sol, t + ts.C[i] * dt , clock, vars, params, grid)
+    @inbounds equation.calcN!(ts.RHS, sol, t + ts.C[i] * dt , clock, vars, params, grid)
     addlinearterm!(ts.RHS, equation.L, sol)
 
-    @. ts.S² = ts.A[i] * ts.S² + dt * ts.RHS
-    @.  sol += ts.B[i] * ts.S²
+    @. ts.S² = @inbounds ts.A[i] * ts.S² + dt * ts.RHS
+    @.  sol += @inbounds ts.B[i] * ts.S²
   end
 
   return nothing
@@ -373,6 +403,16 @@ function stepforward!(sol, clock, ts::LSRK54TimeStepper, equation, vars, params,
   return nothing
 end
 
+function stepforward!(sol, clock, ts::FilteredLSRK54TimeStepper, equation, vars, params, grid)
+  LSRK54update!(sol, clock, ts, equation, vars, params, grid, clock.t, clock.dt)
+  @. sol *= ts.filter
+
+  clock.t += clock.dt
+  clock.step += 1
+
+  return nothing
+end
+
 # --
 # ETDRK4
 # --

test/runtests.jl

@@ -31,6 +31,7 @@ const steppers = [
   "AB3",
   "FilteredForwardEuler",
   "FilteredRK4",
+  "FilteredLSRK54",
   "FilteredETDRK4",
   "FilteredAB3"
 ]