(0.93.0) Use with_halos=true default for JLD2OutputWriter

examples/horizontal_convection.jl

@@ -179,10 +179,6 @@ b_timeseries = FieldTimeSeries(saved_output_filename, "b")
 ζ_timeseries = FieldTimeSeries(saved_output_filename, "ζ")
 
 times = b_timeseries.times
-
-## Coordinate arrays
-xc, yc, zc = nodes(b_timeseries[1])
-xζ, yζ, zζ = nodes(ζ_timeseries[1])
 nothing #hide
 
 χ_timeseries = deepcopy(b_timeseries)
@@ -329,4 +325,3 @@ lines!(ax_Nu, t, Nu; linewidth = 3)
 
 current_figure() #hide
 fig
-

examples/internal_tide.jl

@@ -206,20 +206,6 @@ wmax = maximum(abs, w_t[end])
 times = u′_t.times
 nothing #hide
 
-# We retrieve each field's coordinates and convert from meters to kilometers.
-
-xu,  _, zu  = nodes(u′_t[1])
-xw,  _, zw  = nodes(w_t[1])
-xN², _, zN² = nodes(N²_t[1])
-
-xu  = xu  ./ 1e3
-xw  = xw  ./ 1e3
-xN² = xN² ./ 1e3
-zu  = zu  ./ 1e3
-zw  = zw  ./ 1e3
-zN² = zN² ./ 1e3
-nothing #hide
-
 # ## Visualize
 
 # Now we can visualize our resutls! We use `CairoMakie` here. On a system with OpenGL
@@ -235,29 +221,29 @@ n = Observable(1)
 title = @lift @sprintf("t = %1.2f days = %1.2f T₂",
                        round(times[$n] / day, digits=2) , round(times[$n] / T₂, digits=2))
 
-u′n = @lift u′_t[$n]
- wn = @lift  w_t[$n]
-N²n = @lift N²_t[$n]
+u′ₙ = @lift u′_t[$n]
+ wₙ = @lift  w_t[$n]
+N²ₙ = @lift N²_t[$n]
 
-axis_kwargs = (xlabel = "x [km]",
-               ylabel = "z [km]",
-               limits = ((-grid.Lx/2e3, grid.Lx/2e3), (-grid.Lz/1e3, 0)), # note conversion to kilometers
+axis_kwargs = (xlabel = "x [m]",
+               ylabel = "z [m]",
+               limits = ((-grid.Lx/2, grid.Lx/2), (-grid.Lz, 0)),
                titlesize = 20)
 
 fig = Figure(size = (700, 900))
 
 fig[1, :] = Label(fig, title, fontsize=24, tellwidth=false)
 
 ax_u = Axis(fig[2, 1]; title = "u'-velocity", axis_kwargs...)
-hm_u = heatmap!(ax_u, xu, zu, u′n; nan_color=:gray, colorrange=(-umax, umax), colormap=:balance)
+hm_u = heatmap!(ax_u, u′ₙ; nan_color=:gray, colorrange=(-umax, umax), colormap=:balance)
 Colorbar(fig[2, 2], hm_u, label = "m s⁻¹")
 
 ax_w = Axis(fig[3, 1]; title = "w-velocity", axis_kwargs...)
-hm_w = heatmap!(ax_w, xw, zw, wn; nan_color=:gray, colorrange=(-wmax, wmax), colormap=:balance)
+hm_w = heatmap!(ax_w, wₙ; nan_color=:gray, colorrange=(-wmax, wmax), colormap=:balance)
 Colorbar(fig[3, 2], hm_w, label = "m s⁻¹")
 
 ax_N² = Axis(fig[4, 1]; title = "stratification N²", axis_kwargs...)
-hm_N² = heatmap!(ax_N², xN², zN², N²n; nan_color=:gray, colorrange=(0.9Nᵢ², 1.1Nᵢ²), colormap=:magma)
+hm_N² = heatmap!(ax_N², N²ₙ; nan_color=:gray, colorrange=(0.9Nᵢ², 1.1Nᵢ²), colormap=:magma)
 Colorbar(fig[4, 2], hm_N², label = "s⁻²")
 
 fig

examples/langmuir_turbulence.jl

@@ -254,8 +254,6 @@ time_series = (;
     wv = FieldTimeSeries("langmuir_turbulence_averages.jld2", "wv"))
 
 times = time_series.w.times
-xw, yw, zw = nodes(time_series.w)
-xu, yu, zu = nodes(time_series.u)
 nothing #hide
 
 # We are now ready to animate using Makie. We use Makie's `Observable` to animate
@@ -309,43 +307,43 @@ nothing #hide
 
 wₙ = @lift time_series.w[$n]
 uₙ = @lift time_series.u[$n]
-Bₙ = @lift time_series.B[$n][1, 1, :]
-Uₙ = @lift time_series.U[$n][1, 1, :]
-Vₙ = @lift time_series.V[$n][1, 1, :]
-wuₙ = @lift time_series.wu[$n][1, 1, :]
-wvₙ = @lift time_series.wv[$n][1, 1, :]
+Bₙ = @lift view(time_series.B[$n], 1, 1, :)
+Uₙ = @lift view(time_series.U[$n], 1, 1, :)
+Vₙ = @lift view(time_series.V[$n], 1, 1, :)
+wuₙ = @lift view(time_series.wu[$n], 1, 1, :)
+wvₙ = @lift view(time_series.wv[$n], 1, 1, :)
 
 k = searchsortedfirst(grid.zᵃᵃᶠ[:], -8)
-wxyₙ = @lift interior(time_series.w[$n], :, :, k)
-wxzₙ = @lift interior(time_series.w[$n], :, 1, :)
-uxzₙ = @lift interior(time_series.u[$n], :, 1, :)
+wxyₙ = @lift view(time_series.w[$n], :, :, k)
+wxzₙ = @lift view(time_series.w[$n], :, 1, :)
+uxzₙ = @lift view(time_series.u[$n], :, 1, :)
 
 wlims = (-0.03, 0.03)
 ulims = (-0.05, 0.05)
 
-lines!(ax_B, Bₙ, zu)
+lines!(ax_B, Bₙ)
 
-lines!(ax_U, Uₙ, zu; label = L"\bar{u}")
-lines!(ax_U, Vₙ, zu; label = L"\bar{v}")
+lines!(ax_U, Uₙ; label = L"\bar{u}")
+lines!(ax_U, Vₙ; label = L"\bar{v}")
 axislegend(ax_U; position = :rb)
 
-lines!(ax_fluxes, wuₙ, zw; label = L"mean $wu$")
-lines!(ax_fluxes, wvₙ, zw; label = L"mean $wv$")
+lines!(ax_fluxes, wuₙ; label = L"mean $wu$")
+lines!(ax_fluxes, wvₙ; label = L"mean $wv$")
 axislegend(ax_fluxes; position = :rb)
 
-hm_wxy = heatmap!(ax_wxy, xw, yw, wxyₙ;
+hm_wxy = heatmap!(ax_wxy, wxyₙ;
                   colorrange = wlims,
                   colormap = :balance)
 
 Colorbar(fig[1, 3], hm_wxy; label = "m s⁻¹")
 
-hm_wxz = heatmap!(ax_wxz, xw, zw, wxzₙ;
+hm_wxz = heatmap!(ax_wxz, wxzₙ;
                   colorrange = wlims,
                   colormap = :balance)
 
 Colorbar(fig[2, 3], hm_wxz; label = "m s⁻¹")
 
-ax_uxz = heatmap!(ax_uxz, xu, zu, uxzₙ;
+ax_uxz = heatmap!(ax_uxz, uxzₙ;
                   colorrange = ulims,
                   colormap = :balance)
 

src/OutputWriters/jld2_output_writer.jl

@@ -30,7 +30,7 @@ ext(::Type{JLD2OutputWriter}) = ".jld2"
     JLD2OutputWriter(model, outputs; filename, schedule,
                               dir = ".",
                           indices = (:, :, :),
-                       with_halos = false,
+                       with_halos = true,
                        array_type = Array{Float64},
                    file_splitting = NoFileSplitting(),
                overwrite_existing = false,
@@ -71,9 +71,7 @@ Keyword arguments
              will save xy-slices of the bottom-most index.
 
 - `with_halos` (Bool): Whether or not to slice halo regions from fields before writing output.
-                       Note, that to postprocess saved output (e.g., compute derivatives, etc)
-                       information about the boundary conditions is often crucial. In that case
-                       you might need to set `with_halos = true`.
+                       Preserving halo region data can be useful for postprocessing.
 
 - `array_type`: The array type to which output arrays are converted to prior to saving.
                 Default: `Array{Float64}`.
@@ -165,7 +163,7 @@ JLD2OutputWriter scheduled on TimeInterval(20 minutes):
 function JLD2OutputWriter(model, outputs; filename, schedule,
                                    dir = ".",
                                indices = (:, :, :),
-                            with_halos = false,
+                            with_halos = true,
                             array_type = Array{Float64},
                         file_splitting = NoFileSplitting(),
                     overwrite_existing = false,