Change default output array type for JLD2OutputWriter to Array{Float64}

Project.toml

@@ -1,7 +1,7 @@
 name = "Oceananigans"
 uuid = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
 authors = ["Climate Modeling Alliance and contributors"]
-version = "0.79.1"
+version = "0.79.2"
 
 [deps]
 AMGX = "c963dde9-0319-47f5-bf0c-b07d3c80ffa6"

docs/src/model_setup/output_writers.md

@@ -30,7 +30,7 @@ Other important keyword arguments are
   portion of model data is saved to disk.
 
 * `array_type` for specifying the type of the array that holds outputted field data. The default is
-  `Array{Float32}`, or arrays of single-precision floating point numbers.
+  `Array{Float64}`, or arrays of single-precision floating point numbers.
 
 Once an `OutputWriter` is created, it can be used to write output by adding it the
 ordered dictionary `simulation.output_writers`. prior to calling `run!(simulation)`.
@@ -70,7 +70,7 @@ NetCDFOutputWriter scheduled on TimeInterval(1 minute):
 ├── filepath: ./more_fields.nc
 ├── dimensions: zC(16), zF(17), xC(16), yF(16), xF(16), yC(16), time(0)
 ├── 2 outputs: (c, u)
-└── array type: Array{Float32}
+└── array type: Array{Float64}
 ```
 
 ```jldoctest netcdf1
@@ -83,7 +83,7 @@ NetCDFOutputWriter scheduled on TimeInterval(1 minute):
 ├── filepath: ./another_surface_xy_slice.nc
 ├── dimensions: zC(1), zF(1), xC(16), yF(16), xF(16), yC(16), time(0)
 ├── 2 outputs: (c, u)
-└── array type: Array{Float32}
+└── array type: Array{Float64}
 ```
 
 ```jldoctest netcdf1
@@ -98,7 +98,7 @@ NetCDFOutputWriter scheduled on TimeInterval(1 minute):
 ├── filepath: ./another_averaged_z_profile.nc
 ├── dimensions: zC(16), zF(17), xC(1), yF(1), xF(1), yC(1), time(0)
 ├── 2 outputs: (c, u) averaged on AveragedTimeInterval(window=20 seconds, stride=1, interval=1 minute)
-└── array type: Array{Float32}
+└── array type: Array{Float64}
 ```
 
 `NetCDFOutputWriter` also accepts output functions that write scalars and arrays to disk,
@@ -140,7 +140,7 @@ NetCDFOutputWriter scheduled on IterationInterval(1):
 ├── filepath: ./some_things.nc
 ├── dimensions: zC(16), zF(17), xC(16), yF(16), xF(16), yC(16), time(0)
 ├── 3 outputs: (profile, slice, scalar)
-└── array type: Array{Float32}
+└── array type: Array{Float64}
 ```
 
 See [`NetCDFOutputWriter`](@ref) for more information.
@@ -187,7 +187,7 @@ simulation.output_writers[:velocities] = JLD2OutputWriter(model, model.velocitie
 JLD2OutputWriter scheduled on TimeInterval(20 minutes):
 ├── filepath: ./some_more_data.jld2
 ├── 3 outputs: (u, v, w)
-├── array type: Array{Float32}
+├── array type: Array{Float64}
 ├── including: [:grid, :coriolis, :buoyancy, :closure]
 └── max filesize: Inf YiB
 ```
@@ -204,7 +204,7 @@ simulation.output_writers[:avg_c] = JLD2OutputWriter(model, (; c=c_avg),
 JLD2OutputWriter scheduled on TimeInterval(20 minutes):
 ├── filepath: ./some_more_averaged_data.jld2
 ├── 1 outputs: c averaged on AveragedTimeInterval(window=5 minutes, stride=1, interval=20 minutes)
-├── array type: Array{Float32}
+├── array type: Array{Float64}
 ├── including: [:grid, :coriolis, :buoyancy, :closure]
 └── max filesize: Inf YiB
 ```
@@ -261,7 +261,7 @@ simulation.output_writers[:velocities] = JLD2OutputWriter(model, model.velocitie
 JLD2OutputWriter scheduled on TimeInterval(4 years):
 ├── filepath: ./even_more_averaged_velocity_data.jld2
 ├── 3 outputs: (u, v, w) averaged on AveragedTimeInterval(window=1 year, stride=2, interval=4 years)
-├── array type: Array{Float32}
+├── array type: Array{Float64}
 ├── including: [:grid, :coriolis, :buoyancy, :closure]
 └── max filesize: Inf YiB
 ```

src/OutputWriters/jld2_output_writer.jl

@@ -31,7 +31,7 @@ ext(::Type{JLD2OutputWriter}) = ".jld2"
                               dir = ".",
                           indices = (:, :, :),
                        with_halos = false,
-                       array_type = Array{Float32},
+                       array_type = Array{Float64},
                      max_filesize = Inf,
                overwrite_existing = false,
                              init = noinit,
@@ -76,7 +76,7 @@ Keyword arguments
                        you might need to set `with_halos = true`.
 
 - `array_type`: The array type to which output arrays are converted to prior to saving.
-                Default: `Array{Float32}`.
+                Default: `Array{Float64}`.
 
 ## File management
 
@@ -136,7 +136,7 @@ simulation.output_writers[:velocities] = JLD2OutputWriter(model, model.velocitie
 JLD2OutputWriter scheduled on TimeInterval(20 minutes):
 ├── filepath: ./some_data.jld2
 ├── 3 outputs: (u, v, w)
-├── array type: Array{Float32}
+├── array type: Array{Float64}
 ├── including: [:grid, :coriolis, :buoyancy, :closure]
 └── max filesize: Inf YiB
 ```
@@ -153,7 +153,7 @@ simulation.output_writers[:avg_c] = JLD2OutputWriter(model, (; c=c_avg),
 JLD2OutputWriter scheduled on TimeInterval(20 minutes):
 ├── filepath: ./some_averaged_data.jld2
 ├── 1 outputs: c averaged on AveragedTimeInterval(window=5 minutes, stride=1, interval=20 minutes)
-├── array type: Array{Float32}
+├── array type: Array{Float64}
 ├── including: [:grid, :coriolis, :buoyancy, :closure]
 └── max filesize: Inf YiB
 ```
@@ -162,7 +162,7 @@ function JLD2OutputWriter(model, outputs; filename, schedule,
                                    dir = ".",
                                indices = (:, :, :),
                             with_halos = false,
-                            array_type = Array{Float32},
+                            array_type = Array{Float64},
                           max_filesize = Inf,
                     overwrite_existing = false,
                                   init = noinit,

src/OutputWriters/netcdf_output_writer.jl

@@ -137,7 +137,7 @@ end
 """
     NetCDFOutputWriter(model, outputs; filename, schedule
                                           dir = ".",
-                                   array_type = Array{Float32},
+                                   array_type = Array{Float64},
                                       indices = nothing,
                                    with_halos = false,
                             global_attributes = Dict(),
@@ -178,7 +178,7 @@ Keyword arguments
                 you might need to set `with_halos = true`.
 
 - `array_type`: The array type to which output arrays are converted to prior to saving.
-                Default: `Array{Float32}`.
+                Default: `Array{Float64}`.
 
 - `dimensions`: A `Dict` of dimension tuples to apply to outputs (required for function outputs).
 
@@ -224,7 +224,7 @@ NetCDFOutputWriter scheduled on TimeInterval(1 minute):
 ├── filepath: ./fields.nc
 ├── dimensions: zC(16), zF(17), xC(16), yF(16), xF(16), yC(16), time(0)
 ├── 2 outputs: (c, u)
-└── array type: Array{Float32}
+└── array type: Array{Float64}
 ```
 
 ```jldoctest netcdf1
@@ -237,7 +237,7 @@ NetCDFOutputWriter scheduled on TimeInterval(1 minute):
 ├── filepath: ./surface_xy_slice.nc
 ├── dimensions: zC(1), zF(1), xC(16), yF(16), xF(16), yC(16), time(0)
 ├── 2 outputs: (c, u)
-└── array type: Array{Float32}
+└── array type: Array{Float64}
 ```
 
 ```jldoctest netcdf1
@@ -252,7 +252,7 @@ NetCDFOutputWriter scheduled on TimeInterval(1 minute):
 ├── filepath: ./averaged_z_profile.nc
 ├── dimensions: zC(16), zF(17), xC(1), yF(1), xF(1), yC(1), time(0)
 ├── 2 outputs: (c, u) averaged on AveragedTimeInterval(window=20 seconds, stride=1, interval=1 minute)
-└── array type: Array{Float32}
+└── array type: Array{Float64}
 ```
 
 `NetCDFOutputWriter` also accepts output functions that write scalars and arrays to disk,
@@ -296,12 +296,12 @@ NetCDFOutputWriter scheduled on IterationInterval(1):
 ├── filepath: ./things.nc
 ├── dimensions: zC(16), zF(17), xC(16), yF(16), xF(16), yC(16), time(0)
 ├── 3 outputs: (profile, slice, scalar)
-└── array type: Array{Float32}
+└── array type: Array{Float64}
 ```
 """
 function NetCDFOutputWriter(model, outputs; filename, schedule,
                                           dir = ".",
-                                   array_type = Array{Float32},
+                                   array_type = Array{Float64},
                                       indices = (:, :, :),
                                    with_halos = false,
                             global_attributes = Dict(),

src/OutputWriters/windowed_time_average.jl

@@ -76,7 +76,7 @@ simulation.output_writers[:velocities] = JLD2OutputWriter(model, model.velocitie
 JLD2OutputWriter scheduled on TimeInterval(4 years):
 ├── filepath: ./averaged_velocity_data.jld2
 ├── 3 outputs: (u, v, w) averaged on AveragedTimeInterval(window=1 year, stride=2, interval=4 years)
-├── array type: Array{Float32}
+├── array type: Array{Float64}
 ├── including: [:grid, :coriolis, :buoyancy, :closure]
 └── max filesize: Inf YiB
 ```

test/test_netcdf_output_writer.jl

@@ -137,12 +137,12 @@ function test_thermal_bubble_netcdf_output(arch)
 
     @test eltype(ds3["time"]) == eltype(model.clock.time)
 
-    @test eltype(ds3["xC"]) == Float32
-    @test eltype(ds3["xF"]) == Float32
-    @test eltype(ds3["yC"]) == Float32
-    @test eltype(ds3["yF"]) == Float32
-    @test eltype(ds3["zC"]) == Float32
-    @test eltype(ds3["zF"]) == Float32
+    @test eltype(ds3["xC"]) == Float64
+    @test eltype(ds3["xF"]) == Float64
+    @test eltype(ds3["yC"]) == Float64
+    @test eltype(ds3["yF"]) == Float64
+    @test eltype(ds3["zC"]) == Float64
+    @test eltype(ds3["zF"]) == Float64
 
     @test length(ds3["xC"]) == Nx
     @test length(ds3["yC"]) == Ny
@@ -165,11 +165,11 @@ function test_thermal_bubble_netcdf_output(arch)
     @test ds3["zC"][end] == grid.zᵃᵃᶜ[Nz]
     @test ds3["zF"][end] == grid.zᵃᵃᶠ[Nz+1]  # z is Bounded
 
-    @test eltype(ds3["u"]) == Float32
-    @test eltype(ds3["v"]) == Float32
-    @test eltype(ds3["w"]) == Float32
-    @test eltype(ds3["T"]) == Float32
-    @test eltype(ds3["S"]) == Float32
+    @test eltype(ds3["u"]) == Float64
+    @test eltype(ds3["v"]) == Float64
+    @test eltype(ds3["w"]) == Float64
+    @test eltype(ds3["T"]) == Float64
+    @test eltype(ds3["S"]) == Float64
 
     u = ds3["u"][:, :, :, end]
     v = ds3["v"][:, :, :, end]
@@ -268,6 +268,7 @@ function test_thermal_bubble_netcdf_output_with_halos(arch)
     view(model.tracers.T, i1:i2, j1:j2, k1:k2) .+= 0.01
 
     nc_filepath = "test_dump_with_halos_$(typeof(arch)).nc"
+
     nc_writer = NetCDFOutputWriter(model, merge(model.velocities, model.tracers),
                                    filename = nc_filepath,
                                    schedule = IterationInterval(10),
@@ -288,12 +289,13 @@ function test_thermal_bubble_netcdf_output_with_halos(arch)
 
     @test eltype(ds["time"]) == eltype(model.clock.time)
 
-    @test eltype(ds["xC"]) == Float32
-    @test eltype(ds["xF"]) == Float32
-    @test eltype(ds["yC"]) == Float32
-    @test eltype(ds["yF"]) == Float32
-    @test eltype(ds["zC"]) == Float32
-    @test eltype(ds["zF"]) == Float32
+    # Using default array_type = Array{Float64}
+    @test eltype(ds["xC"]) == Float64
+    @test eltype(ds["xF"]) == Float64
+    @test eltype(ds["yC"]) == Float64
+    @test eltype(ds["yF"]) == Float64
+    @test eltype(ds["zC"]) == Float64
+    @test eltype(ds["zF"]) == Float64
 
     Hx, Hy, Hz = grid.Hx, grid.Hy, grid.Hz
     @test length(ds["xC"]) == Nx+2Hx
@@ -317,11 +319,11 @@ function test_thermal_bubble_netcdf_output_with_halos(arch)
     @test ds["zC"][end] == grid.zᵃᵃᶜ[Nz+Hz]
     @test ds["zF"][end] == grid.zᵃᵃᶠ[Nz+Hz+1]  # z is Bounded
 
-    @test eltype(ds["u"]) == Float32
-    @test eltype(ds["v"]) == Float32
-    @test eltype(ds["w"]) == Float32
-    @test eltype(ds["T"]) == Float32
-    @test eltype(ds["S"]) == Float32
+    @test eltype(ds["u"]) == Float64
+    @test eltype(ds["v"]) == Float64
+    @test eltype(ds["w"]) == Float64
+    @test eltype(ds["T"]) == Float64
+    @test eltype(ds["S"]) == Float64
 
     u = ds["u"][:, :, :, end]
     v = ds["v"][:, :, :, end]
@@ -349,8 +351,7 @@ function test_netcdf_function_output(arch)
     iters = 3
 
     grid = RectilinearGrid(arch, size=(N, N, N), extent=(L, 2L, 3L))
-    model = NonhydrostaticModel(grid=grid,
-                                buoyancy=SeawaterBuoyancy(), tracers=(:T, :S))
+    model = NonhydrostaticModel(; grid, buoyancy=SeawaterBuoyancy(), tracers=(:T, :S))
 
     simulation = Simulation(model, Δt=Δt, stop_iteration=iters)
     grid = model.grid
@@ -377,19 +378,22 @@ function test_netcdf_function_output(arch)
     nc_filepath = "test_function_outputs_$(typeof(arch)).nc"
 
     simulation.output_writers[:food] =
-        NetCDFOutputWriter(model, outputs; filename=nc_filepath,
-                           schedule=TimeInterval(Δt), dimensions=dims, array_type=Array{Float64}, verbose=true,
-                           global_attributes=global_attributes, output_attributes=output_attributes)
+        NetCDFOutputWriter(model, outputs; global_attributes, output_attributes,
+                           filename = nc_filepath,
+                           schedule = TimeInterval(Δt),
+                           dimensions = dims,
+                           array_type = Array{Float64},
+                           verbose=true)
 
     run!(simulation)
 
     ds = Dataset(nc_filepath, "r")
 
-    @test haskey(ds.attrib, "date") && !isnothing(ds.attrib["date"])
-    @test haskey(ds.attrib, "Julia") && !isnothing(ds.attrib["Julia"])
-    @test haskey(ds.attrib, "Oceananigans") && !isnothing(ds.attrib["Oceananigans"])
-    @test haskey(ds.attrib, "schedule") && !isnothing(ds.attrib["schedule"])
-    @test haskey(ds.attrib, "interval") && !isnothing(ds.attrib["interval"])
+    @test haskey(ds.attrib, "date")                 && !isnothing(ds.attrib["date"])
+    @test haskey(ds.attrib, "Julia")                && !isnothing(ds.attrib["Julia"])
+    @test haskey(ds.attrib, "Oceananigans")         && !isnothing(ds.attrib["Oceananigans"])
+    @test haskey(ds.attrib, "schedule")             && !isnothing(ds.attrib["schedule"])
+    @test haskey(ds.attrib, "interval")             && !isnothing(ds.attrib["interval"])
     @test haskey(ds.attrib, "output time interval") && !isnothing(ds.attrib["output time interval"])
 
     @test eltype(ds["time"]) == eltype(model.clock.time)
@@ -467,9 +471,13 @@ function test_netcdf_function_output(arch)
     simulation = Simulation(model, Δt=Δt, stop_iteration=iters)
 
     simulation.output_writers[:food] =
-        NetCDFOutputWriter(model, outputs; filename=nc_filepath, overwrite_existing=false,
-                           schedule=IterationInterval(1), array_type=Array{Float64}, dimensions=dims, verbose=true,
-                           global_attributes=global_attributes, output_attributes=output_attributes)
+        NetCDFOutputWriter(model, outputs; global_attributes, output_attributes,
+                           filename = nc_filepath,
+                           overwrite_existing = false,
+                           schedule = IterationInterval(1),
+                           array_type = Array{Float64},
+                           dimensions = dims,
+                           verbose = true)
 
     run!(simulation)
 
@@ -510,15 +518,10 @@ function test_netcdf_time_averaging(arch)
     c1_forcing = Forcing(Fc1, field_dependencies=:c1)
     c2_forcing = Forcing(Fc2, field_dependencies=:c2)
 
-    model = NonhydrostaticModel(
-                grid = grid,
-         timestepper = :RungeKutta3,
-             tracers = (:c1, :c2),
-             forcing = (c1=c1_forcing, c2=c2_forcing),
-            coriolis = nothing,
-            buoyancy = nothing,
-             closure = nothing
-    )
+    model = NonhydrostaticModel(; grid,
+                                timestepper = :RungeKutta3,
+                                tracers = (:c1, :c2),
+                                forcing = (c1=c1_forcing, c2=c2_forcing))
 
     set!(model, c1=1, c2=1)