Changes ExponentialCoordinate to ExponentialDiscretization (#638)

* Changed `ExponentialCoordinate` to `ExponentialDiscretization` in ClimaOcean.jl

* Update vertical_grids.md with ExponentialDiscretization

* Update download_glorys_data.jl

* Update arctic_simulation.jl

* Update one_degree_simulation.jl

* Update ocean_sea_ice_coupled_simulation.jl

* Update near_global_ocean_simulation.jl

* Update one_degree_simulation.jl

* Update Oceananigans compat to 0.100

* Apply suggestions from code review

* Update one_degree_simulation.jl

* Update ClimaSeaIce version to 0.3.8

* use mutable kwarg

---------

Co-authored-by: Navid C. Constantinou <[email protected]>
Co-authored-by: Simone Silvestri <[email protected]>

Author: 3 people

Project.toml

@@ -46,7 +46,7 @@ ClimaOceanReactantExt = "Reactant"
 Adapt = "4"
 CFTime = "0.1, 0.2"
 CUDA = "4, 5"
-ClimaSeaIce = "0.3.7"
+ClimaSeaIce = "0.3.8"
 CondaPkg = "0.2.28"
 CubicSplines = "0.2"
 DataDeps = "0.7"
@@ -59,7 +59,7 @@ KernelAbstractions = "0.9"
 MPI = "0.20"
 MeshArrays = "0.3"
 NCDatasets = "0.12, 0.13, 0.14"
-Oceananigans = "0.97.6, 0.98, 0.99"
+Oceananigans = "0.100"
 OffsetArrays = "1.14"
 PrecompileTools = "1"
 PythonCall = "0.9"

docs/src/vertical_grids.md

@@ -1,7 +1,7 @@
 # Vertical grids
 
-We construct vertical coordinates using `Oceananigans.ExponentialCoordinate` and
-`Oceananigans.ConstantToStretchedCoordinate`. The 
+We construct vertical coordinates using `Oceananigans.ExponentialDiscretization` and
+`Oceananigans.ReferenceToStretchedDiscretization`. The 
 [Grids section](https://clima.github.io/OceananigansDocumentation/dev/grids/#Coordinate-helper-utilities)
 in the Oceananigans Documentation includes a mini-tutorial on how the above-mentioned methods
 can be used to generate a coordinate of your liking.

examples/download_glorys_data.jl

@@ -8,7 +8,7 @@ Ny = 20 * 12
 Nz = 50
 
 depth = 6000
-z = ExponentialCoordinate(Nz, -depth, 0; scale=depth/4.5)
+z = ExponentialDiscretization(Nz, -depth, 0; scale=depth/4.5)
 
 grid = LatitudeLongitudeGrid(arch;
                              size = (Nx, Ny, Nz),

examples/near_global_ocean_simulation.jl

@@ -37,8 +37,7 @@ Ny = 600
 Nz = 40
 
 depth = 6000meters
-z = ExponentialCoordinate(Nz, -depth, 0)
-z = Oceananigans.Grids.MutableVerticalDiscretization(z)
+z = ExponentialDiscretization(Nz, -depth, 0, mutable=true)
 
 grid = LatitudeLongitudeGrid(arch;
                              size = (Nx, Ny, Nz),

examples/one_degree_simulation.jl

@@ -27,7 +27,7 @@ Ny = 180
 Nz = 50
 
 depth = 5000meters
-z = ExponentialCoordinate(Nz, -depth, 0; scale = depth/4)
+z = ExponentialDiscretization(Nz, -depth, 0; scale = depth/4)
 
 underlying_grid = TripolarGrid(arch; size = (Nx, Ny, Nz), halo = (5, 5, 4), z)
 

experiments/arctic_simulation.jl

@@ -15,8 +15,7 @@ arch = GPU()
 
 depth = 2000meters
 Nz = 30
-z = ExponentialCoordinate(Nz, -depth, 0; scale=depth/3)
-z = MutableVerticalDiscretization(z)
+z = ExponentialDiscretization(Nz, -depth, 0; scale=depth/3, mutable=true)
 
 Nx = 180 # longitudinal direction -> 250 points is about 1.5ᵒ resolution
 Ny = 180 # meridional direction -> same thing, 48 points is about 1.5ᵒ resolution

experiments/coupled_simulation/ocean_sea_ice_coupled_simulation.jl

@@ -22,8 +22,7 @@ Ny = 128 # meridional direction -> same thing, 48 points is about 1.5ᵒ resolut
 Nz = 10
 depth = 1000meters
 
-z = ExponentialCoordinate(Nz, -depth, 0; scale=0.3*depth)
-z = MutableVerticalDiscretization(z)
+z = ExponentialDiscretization(Nz, -depth, 0; scale=0.3*depth, mutable=true)
 
 grid = TripolarGrid(arch, Float64; size=(Nx, Ny, Nz), z)
 sea_ice_grid = TripolarGrid(arch, Float64; size=(Nx, Ny, 1), z = (-10, 0))
@@ -153,4 +152,4 @@ run!(earth)
 # ## Visualizing the results
 #
 # We can visualize the results using CairoMakie. We record a video of surface variables and fluxes.
-# To load the data we can use Oceananigans' `FieldTimeSeries` object.
+# To load the data we can use Oceananigans' `FieldTimeSeries` object.

experiments/one_degree_simulation/one_degree_simulation.jl

@@ -8,12 +8,12 @@ using GLMakie
 
 Oceananigans.defaults.FloatType = Float64
 arch = CPU()
-Nx = 256
-Ny = 128
+Nx = 360
+Ny = 180
 Nz = 32
 
 depth = 6000meters
-z = ExponentialCoordinate(Nz, -depth, 0, scale=(34/Nz)*depth)
+z = ExponentialDiscretization(Nz, -depth, 0, scale=(34/Nz)*depth)
 underlying_grid = TripolarGrid(arch; size=(Nx, Ny, Nz), z)
 
 bottom_height = regrid_bathymetry(underlying_grid; minimum_depth=30, interpolation_passes=20, major_basins=1)

src/ClimaOcean.jl

@@ -108,7 +108,7 @@ using PrecompileTools: @setup_workload, @compile_workload
     Nx, Ny, Nz = 32, 32, 10
     @compile_workload begin
         depth = 6000
-        z = Oceananigans.Grids.ExponentialCoordinate(Nz, -depth, 0)
+        z = Oceananigans.Grids.ExponentialDiscretization(Nz, -depth, 0)
         grid = Oceananigans.OrthogonalSphericalShellGrids.TripolarGrid(CPU(); size=(Nx, Ny, Nz), halo=(7, 7, 7), z)
         grid = ImmersedBoundaryGrid(grid, GridFittedBottom((x, y) -> -5000))
         # ocean = ocean_simulation(grid)