Minor tweaks in Examples

docs/make.jl

@@ -32,7 +32,6 @@ examples = [
 ]
 
 for example in examples
-  example_filepath = joinpath(EXAMPLES_DIR, example)
   withenv("GITHUB_REPOSITORY" => "FourierFlows/GeophysicalFlowsDocumentation") do
     example_filepath = joinpath(EXAMPLES_DIR, example)
     Literate.markdown(example_filepath, OUTPUT_DIR, documenter=true)

examples/singlelayerqg_betadecay.jl

@@ -100,8 +100,8 @@ p2 = contourf(x, y, vars.ψ',
          title = "initial streamfunction ψ",
     framestyle = :box)
 
-l = @layout Plots.grid(1, 2)
-p = plot(p1, p2, layout=l, size = (900, 800))
+layout = @layout Plots.grid(1, 2)
+p = plot(p1, p2, layout = layout, size = (800, 360))
 
 
 # ## Diagnostics
@@ -193,8 +193,8 @@ function plot_output(prob)
             ylabel = "y")
   plot!(pum, 0*y, y, linestyle=:dash, linecolor=:black)
 
-  l = @layout Plots.grid(2, 2)
-  p = plot(pq, pqm, pψ, pum, layout = l, size = (900, 800))
+  layout = @layout Plots.grid(2, 2)
+  p = plot(pq, pqm, pψ, pum, layout = layout, size = (800, 720))
 
   return p
 end

examples/singlelayerqg_decay_topography.jl

@@ -108,8 +108,8 @@ p1 = heatmap(x, y, vars.q',
 p2 = contourf(x, y, vars.ψ',
         aspectratio = 1,
              c = :viridis,
-        levels = range(-0.35, stop=0.35, length=10), 
-          clim = (-0.35, 0.35),
+        levels = range(-0.25, stop=0.25, length=11), 
+          clim = (-0.25, 0.25),
          xlims = (-grid.Lx/2, grid.Lx/2),
          ylims = (-grid.Ly/2, grid.Ly/2),
         xticks = -3:3,
@@ -119,8 +119,8 @@ p2 = contourf(x, y, vars.ψ',
          title = "initial streamfunction ψ",
     framestyle = :box)
 
-l = @layout Plots.grid(1, 2)
-p = plot(p1, p2, layout=l, size=(900, 400))
+layout = @layout Plots.grid(1, 2)
+p = plot(p1, p2, layout=layout, size = (800, 360))
 
 
 # ## Diagnostics
@@ -180,13 +180,13 @@ function plot_output(prob)
   contour!(pq, x, y, η',
           levels=-2:0.5:-0.5,
           lw=2, c=:black, ls=:dash, alpha=0.7)
-    
+
   pψ = contourf(x, y, ψ',
        aspectratio = 1,
             legend = false,
                  c = :viridis,
-            levels = range(-0.7, stop=0.7, length=10), 
-              clim = (-0.7, 0.7),
+            levels = range(-0.75, stop=0.75, length=31),
+              clim = (-0.75, 0.75),
              xlims = (-grid.Lx/2, grid.Lx/2),
              ylims = (-grid.Ly/2, grid.Ly/2),
             xticks = -3:3,
@@ -197,7 +197,7 @@ function plot_output(prob)
         framestyle = :box)
 
   l = @layout Plots.grid(1, 2)
-  p = plot(pq, pψ, layout = l, size = (900, 400))
+  p = plot(pq, pψ, layout = l, size = (800, 360))
 
   return p
 end

examples/singlelayerqg_decaying_barotropic_equivalentbarotropic.jl

@@ -47,17 +47,20 @@ nothing # hide
 
 # ## Setting initial conditions
 
-# We choose an initial condition with most energy around total wavenumber ``k_0``.
+# For initial condition we construct a relative vorticity with energy most energy around total 
+# wavenumber ``k_0``.
 seed!(1234)
 k₀, E₀ = 6, 0.5
 ∇²ψ₀ = peakedisotropicspectrum(prob_bqg.grid, k₀, E₀, mask=prob_bqg.timestepper.filter)
 nothing # hide
 
 # `SingleLayerQG` allows us to set up the initial ``q`` for each problem via `set_q!()` function.
-# To initialize both `prob_bqg` and `prob_eqbqg` with the same flow, we first find the streamfunction
-# the corresponds to the relative vorticity structure we computed above,
+# To initialize both `prob_bqg` and `prob_eqbqg` with the same flow, we first use function 
+# `SingleLayerQG.streamfunctionfrompv!` to get the streamfunction that corresponds to the 
+# relative vorticity we computed above. This works in the purely barotropic problem, `prob_bqg`
+# since in that case the QGPV is simply the relative vorticity.
 ∇²ψ₀h = rfft(∇²ψ₀)
-ψ₀h = @. 0*∇²ψ₀h
+ψ₀h = @. 0 * ∇²ψ₀h
 SingleLayerQG.streamfunctionfrompv!(ψ₀h, ∇²ψ₀h, prob_bqg.params, prob_bqg.grid)
 nothing # hide
 

examples/surfaceqg_decaying.jl

@@ -52,7 +52,7 @@ nothing # hide
 # Let's define some shortcuts.
 sol, clock, vars, params, grid = prob.sol, prob.clock, prob.vars, prob.params, prob.grid
 x, y = grid.x, grid.y
-nothing # hide
+#md nothing # hide
 
 
 # ## Setting initial conditions
@@ -121,11 +121,9 @@ nothing # hide
 # kinetic energy and buoyancy variance.
 
 function plot_output(prob)
-  bₛ = prob.vars.b
-  uₛ = prob.vars.u
-  vₛ = prob.vars.v
+  b = prob.vars.b
 
-  pbₛ = heatmap(x, y, bₛ',
+  pb = heatmap(x, y, b',
        aspectratio = 1,
                  c = :deep,
               clim = (0, 1),
@@ -158,7 +156,7 @@ function plot_output(prob)
             xlabel = "t")
 
   layout = @layout [a{0.5w} Plots.grid(2, 1)]
-  p = plot(pbₛ, pKE, pb², layout=layout, size = (900, 500))
+  p = plot(pb, pKE, pb², layout=layout, size = (900, 500))
 
   return p
 end