Convert all animations in Docs from mp4 to gifs

docs/src/index.md

@@ -4,20 +4,15 @@
 
 `GeophysicalFlows.jl` is a collection of modules which leverage the 
 [FourierFlows.jl](https://github.com/FourierFlows/FourierFlows.jl) framework to provide
-solvers for problems in Geophysical Fluid Dynamics, on periodic domains and using Fourier-based pseudospectral methods.
+solvers for problems in Geophysical Fluid Dynamics, on periodic domains using Fourier-based pseudospectral methods.
 
 ## Examples
 
 Examples aim to demonstrate the main functionalities of each module. Have a look at our Examples collection!
 
-!!! warning "Animations and Mac OS X Safari"
-    Often animations included the documentation, e.g., those in the [2D Navier-Stokes decaying turbulence example](generated/twodnavierstokes_decaying/)
-    don't show up in Safari. Until this issue is fixed we suggest using alternative browsers 
-    to view the documentation.
-
 ## Developers
 
-GeophysicalFlows is currently being developed by [Navid C. Constantinou](http://www.navidconstantinou.com) and [Gregory L. Wagner](https://glwagner.github.io).
+GeophysicalFlows.jl is currently being developed by [Navid C. Constantinou](http://www.navidconstantinou.com) and [Gregory L. Wagner](https://glwagner.github.io).
 
 ## Cite
 

examples/barotropicqg_betadecay.jl

@@ -71,7 +71,7 @@ qih *= sqrt(E₀ / Ein)             # normalize qi to have energy E₀
 qi = irfft(qih, grid.nx)
 
 BarotropicQG.set_zeta!(prob, qi)
-nothing #hide
+nothing # hide
 
 # Let's plot the initial vorticity field:
 
@@ -234,7 +234,7 @@ anim = @animate for j = 0:round(Int, nsteps/nsubs)
 
 end
 
-mp4(anim, "barotropicqg_betadecay.mp4", fps=12)
+gif(anim, "barotropicqg_betadecay.gif", fps=12)
 
 # ## Save
 

examples/barotropicqg_betaforced.jl

@@ -227,7 +227,7 @@ function plot_output(prob)
             xlabel = "μt")
 
   l = @layout Plots.grid(2, 3)
-  p = plot(pζ, pζm, pE, pψ, pum, pZ, layout=l, size = (1000, 600), dpi=150)
+  p = plot(pζ, pζm, pE, pψ, pum, pZ, layout=l, size = (1000, 600))
 
   return p
 end
@@ -265,7 +265,7 @@ anim = @animate for j = 0:Int(nsteps / nsubs)
   BarotropicQG.updatevars!(prob)
 end
 
-mp4(anim, "barotropicqg_betaforced.mp4", fps=18)
+gif(anim, "barotropicqg_betaforced.gif", fps=18)
 
 
 # ## Save

examples/barotropicqg_decay_topography.jl

@@ -88,7 +88,7 @@ qih *= sqrt(E₀ / energy(qih, grid))             # normalize qi to have energy
 qi = irfft(qih, grid.nx)
 
 BarotropicQG.set_zeta!(prob, qi)
-nothing #hide
+nothing # hide
 
 # Let's plot the initial vorticity field:
 
@@ -231,4 +231,4 @@ anim = @animate for j = 0:round(Int, nsteps/nsubs)
   BarotropicQG.updatevars!(prob)
 end
 
-mp4(anim, "barotropicqg_decay_topography.mp4", fps=12)
+gif(anim, "barotropicqg_decay_topography.gif", fps=12)

examples/barotropicqgql_betaforced.jl

@@ -243,7 +243,7 @@ function plot_output(prob)
             xlabel = "μt")
 
   l = @layout Plots.grid(2, 3)
-  p = plot(pζ, pζm, pE, pψ, pum, pZ, layout=l, size = (1000, 600), dpi=150)
+  p = plot(pζ, pζm, pE, pψ, pum, pZ, layout=l, size = (1000, 600))
 
   return p
 end
@@ -280,7 +280,7 @@ anim = @animate for j = 0:round(Int, nsteps / nsubs)
   BarotropicQGQL.updatevars!(prob)
 end
 
-mp4(anim, "barotropicqgql_betaforced.mp4", fps=18)
+gif(anim, "barotropicqgql_betaforced.gif", fps=18)
 
 
 # ## Save

examples/multilayerqg_2layer.jl

@@ -10,6 +10,7 @@
 using FourierFlows, Plots, Printf
 
 using FFTW: rfft, irfft
+using Random: seed!
 import GeophysicalFlows.MultilayerQG
 import GeophysicalFlows.MultilayerQG: energies
 
@@ -22,9 +23,7 @@ nothing # hide
 
 # ## Numerical parameters and time-stepping parameters
 
-nx = 128        # 2D resolution = nx^2
-ny = nx
-
+n = 128                  # 2D resolution = n²
 stepper = "FilteredRK4"  # timestepper
      dt = 6e-3           # timestep
  nsteps = 7000           # total number of time-steps
@@ -33,14 +32,14 @@ nothing # hide
 
 
 # ## Physical parameters
-Lx = 2π         # domain size
- μ = 5e-2       # bottom drag
- β = 5          # the y-gradient of planetary PV
+ L = 2π                  # domain size
+ μ = 5e-2                # bottom drag
+ β = 5                   # the y-gradient of planetary PV
 
-nlayers = 2      # number of layers
-f₀, g = 1, 1     # Coriolis parameter and gravitational constant
- H = [0.2, 0.8]  # the rest depths of each layer
- ρ = [4.0, 5.0]  # the density of each layer
+nlayers = 2              # number of layers
+f₀, g = 1, 1             # Coriolis parameter and gravitational constant
+ H = [0.2, 0.8]          # the rest depths of each layer
+ ρ = [4.0, 5.0]          # the density of each layer
 
  U = zeros(nlayers) # the imposed mean zonal flow in each layer
  U[1] = 1.0
@@ -50,7 +49,7 @@ nothing # hide
 
 # ## Problem setup
 # We initialize a `Problem` by providing a set of keyword arguments,
-prob = MultilayerQG.Problem(nlayers, dev; nx=nx, Lx=Lx, f₀=f₀, g=g, H=H, ρ=ρ, U=U, dt=dt, stepper=stepper, μ=μ, β=β)
+prob = MultilayerQG.Problem(nlayers, dev; nx=n, Lx=L, f₀=f₀, g=g, H=H, ρ=ρ, U=U, dt=dt, stepper=stepper, μ=μ, β=β)
 nothing # hide
 
 # and define some shortcuts.
@@ -64,7 +63,8 @@ nothing # hide
 # Our initial condition is some small amplitude random noise. We smooth our initial
 # condidtion using the `timestepper`'s high-wavenumber `filter`.
 
-q_i  = 4e-3randn((nx, ny, nlayers))
+seed!(1234) # reset of the random number generator for reproducibility
+q_i  = 4e-3randn((grid.nx, grid.ny, nlayers))
 qh_i = prob.timestepper.filter .* rfft(q_i, (1, 2)) # only apply rfft in dims=1, 2
 q_i  = irfft(qh_i, grid.nx, (1, 2)) # only apply irfft in dims=1, 2
 
@@ -108,7 +108,7 @@ function get_u(prob)
 end
 
 out = Output(prob, filename, (:sol, get_sol), (:u, get_u))
-nothing #hide
+nothing # hide
 
 
 # ## Visualizing the simulation
@@ -122,15 +122,15 @@ function plot_output(prob)
   Lx, Ly = prob.grid.Lx, prob.grid.Ly
 
   l = @layout Plots.grid(2, 3)
-  p = plot(layout=l, size = (1000, 600), dpi=150)
+  p = plot(layout=l, size = (1000, 600))
 
   for m in 1:nlayers
     heatmap!(p[(m-1) * 3 + 1], x, y, vars.q[:, :, m]',
          aspectratio = 1,
               legend = false,
                    c = :balance,
-               xlims = (-Lx / 2, Lx / 2),
-               ylims = (-Ly / 2, Ly / 2),
+               xlims = (-Lx/2, Lx/2),
+               ylims = (-Ly/2, Ly/2),
                clims = symlims,
               xticks = -3:3,
               yticks = -3:3,
@@ -144,8 +144,8 @@ function plot_output(prob)
          aspectratio = 1,
               legend = false,
                    c = :viridis,
-               xlims = (-Lx / 2, Lx / 2),
-               ylims = (-Ly / 2, Ly / 2),
+               xlims = (-Lx/2, Lx/2),
+               ylims = (-Ly/2, Ly/2),
                clims = symlims,
               xticks = -3:3,
               yticks = -3:3,
@@ -212,7 +212,7 @@ anim = @animate for j = 0:round(Int, nsteps / nsubs)
   MultilayerQG.updatevars!(prob)
 end
 
-mp4(anim, "multilayerqg_2layer.mp4", fps=18)
+gif(anim, "multilayerqg_2layer.gif", fps=18)
 
 
 # ## Save

examples/surfaceqg_decaying.jl

@@ -158,7 +158,7 @@ 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), dpi=150)
+  p = plot(pbₛ, pKE, pb², layout=layout, size = (900, 500))
 
   return p
 end
@@ -195,7 +195,7 @@ anim = @animate for j = 0:round(Int, nsteps/nsubs)
   SurfaceQG.updatevars!(prob)
 end
 
-mp4(anim, "sqg_ellipticalvortex.mp4", fps=14)
+gif(anim, "sqg_ellipticalvortex.gif", fps=14)
 
 # Let's see how all flow fields look like at the end of the simulation.
 
@@ -243,4 +243,3 @@ layout = @layout [a{0.5h}; b{0.5w} c{0.5w}]
 plot_final = plot(pb, pu, pv, layout=layout, size = (800, 800))
 
 # Last we can save the output by calling `saveoutput(out)`.
-

examples/twodnavierstokes_decaying.jl

@@ -159,7 +159,7 @@ anim = @animate for j = 0:Int(nsteps/nsubs)
   TwoDNavierStokes.updatevars!(prob)  
 end
 
-mp4(anim, "twodturb.mp4", fps=18)
+gif(anim, "twodturb.gif", fps=18)
 
 
 # Last we save the output.
@@ -168,7 +168,7 @@ saveoutput(out)
 
 # ## Radial energy spectrum
 
-# After the simulation is done we plot the radial energy spectrum to illustrate
+# After the simulation is done we plot the instantaneous radial energy spectrum to illustrate
 # how `FourierFlows.radialspectrum` can be used,
 
 E  = @. 0.5 * (vars.u^2 + vars.v^2) # energy density

examples/twodnavierstokes_stochasticforcing.jl

@@ -175,4 +175,4 @@ anim = @animate for j = 0:round(Int, nsteps / nsubs)
   TwoDNavierStokes.updatevars!(prob)  
 end
 
-mp4(anim, "twodturb_forced.mp4", fps=18)
+gif(anim, "twodturb_forced.gif", fps=18)