Update examples and verification experiments

examples/eady_turbulence.jl

@@ -132,8 +132,11 @@ output_filename_prefix = string("eady_turb_Nh", Nh, "_Nz", Nz)
 # Our use of biharmonic diffusivity means we must instantiate the model grid
 # with halos of size `(2, 2, 2)` in `(x, y, z)`.
 
-model = Model( grid = RegularCartesianGrid(size=(Nh, Nh, Nz), halo=(2, 2, 2),
-                                           x=(-Lh/2, Lh/2), y=(-Lh/2, Lh/2), z=(-Lz, 0)),
+grid = RegularCartesianGrid(size=(Nh, Nh, Nz), halo=(2, 2, 2),
+                            topology=(Periodic, Periodic, Bounded),
+                            x=(-Lh/2, Lh/2), y=(-Lh/2, Lh/2), z=(-Lz, 0))
+
+model = Model( grid = grid,
        architecture = CPU(),
            coriolis = FPlane(f=f),
            buoyancy = BuoyancyTracer(), tracers = :b,

examples/internal_wave.jl

@@ -69,8 +69,11 @@ nothing # hide
 # use temperature as a buoyancy tracer, and use a small constant viscosity
 # and diffusivity to stabilize the model.
 
+grid = RegularCartesianGrid(size=(Nx, 1, Nx), length=(Lx, Lx, Lx),
+                            topology=(Periodic, Singleton, Bounded))
+
 model = Model(
-        grid = RegularCartesianGrid(size=(Nx, 1, Nx), length=(Lx, Lx, Lx)),
+        grid = grid,
      closure = ConstantIsotropicDiffusivity(ν=1e-6, κ=1e-6),
     coriolis = FPlane(f=f),
      tracers = :b,

examples/langmuir_turbulence.jl

@@ -1,9 +1,9 @@
 # # Langmuir turbulence example
 #
 # This example implements the Langmuir turbulence simulation reported in section
-# 4 of McWilliams, J. C. et al., "Langmuir Turbulence in the ocean," Journal of 
+# 4 of McWilliams, J. C. et al., "Langmuir Turbulence in the ocean," Journal of
 # Fluid Mechanics (1997). This example demonstrates:
-#   
+#
 #   * how to run a simulation with surface wave effects via the Craik-Leibovich
 #     approximation
 #
@@ -17,7 +17,7 @@ using Oceananigans.SurfaceWaves: UniformStokesDrift
 # ## Model parameters
 #
 # Here we use an anisotropic grid with `Nh` horizontal grid points, `Nz` vertical
-# grid points, `Δh` horizontal grid spacing, and `Δz` vertical grid spacing. 
+# grid points, `Δh` horizontal grid spacing, and `Δz` vertical grid spacing.
 # We specify fluxes of buouyancy and momentum that match the specifications in
 # McWilliams and Sullivan (1997) via
 #
@@ -39,7 +39,7 @@ using Oceananigans.SurfaceWaves: UniformStokesDrift
        f = 1e-4     # [s⁻¹] Coriolis parameter
 end_time = 2hour    # [s] End time for the simulation
 
-# Surface wave stokes drift profile: 
+# Surface wave stokes drift profile:
 #
 # $ uˢ(z) = Uˢ exp(2kˢʷ z) $
 #
@@ -61,7 +61,7 @@ const aˢʷ = 0.8      # [m] Surface wave amplitude
 const Uˢ = aˢʷ^2 * kˢʷ * sqrt(g_Earth * kˢʷ)
 
 ## Oceananigans
-∂z_uˢ(z, t) = 2kˢʷ * Uˢ * exp(2kˢʷ * z) 
+∂z_uˢ(z, t) = 2kˢʷ * Uˢ * exp(2kˢʷ * z)
 
 # We use the Stokes drift profile for the initial condition
 uˢ(z) = Uˢ * exp(2kˢʷ * z)
@@ -75,19 +75,20 @@ uˢ(z) = Uˢ * exp(2kˢʷ * z)
 
 u_bcs = HorizontallyPeriodicBCs(top = BoundaryCondition(Flux, Qᵘ))
 
-b_bcs = HorizontallyPeriodicBCs(top = BoundaryCondition(Flux, Qᵇ), 
+b_bcs = HorizontallyPeriodicBCs(top = BoundaryCondition(Flux, Qᵇ),
                                 bottom = BoundaryCondition(Gradient, N²))
 
 # ## Model instantiation
 #
 # We instantiate a horizontally-periodic `Model` on the CPU with on a `RegularCartesianGrid`,
-# using a `FPlane` model for rotation (constant rotation rate), the Anisotropic Minimum 
-# Dissipation closure to model the effects of unresolved turbulence, and the previously defined 
+# using a `FPlane` model for rotation (constant rotation rate), the Anisotropic Minimum
+# Dissipation closure to model the effects of unresolved turbulence, and the previously defined
 # boundary conditions for `u` and `b`.
 
 model = Model(
          architecture = CPU(),
-                 grid = RegularCartesianGrid(size=(Nh, Nh, Nz), length=(Δh*Nh, Δh*Nh, Δz*Nz)),
+                 grid = RegularCartesianGrid(size=(Nh, Nh, Nz), length=(Δh*Nh, Δh*Nh, Δz*Nz),
+                                             topology=(Periodic, Periodic, Bounded)),
              buoyancy = BuoyancyTracer(), tracers = :b,
               closure = AnisotropicMinimumDissipation(),
         surface_waves = UniformStokesDrift(∂z_uˢ=∂z_uˢ),
@@ -106,8 +107,8 @@ model = Model(
 b₀(x, y, z) = N² * z + 1e-1 * Ξ(z) * N² * model.grid.Lz
 
 # Velocity initial condition: note that McWilliams and Sullivan (1997) use a model
-# that is formulated in terms of the Eulerian-mean velocity field. Due to this, 
-# their 'resting' initial condition actually consists of a sheared and 
+# that is formulated in terms of the Eulerian-mean velocity field. Due to this,
+# their 'resting' initial condition actually consists of a sheared and
 # unbalanced Lagrangian-mean velocity field uˢ(z). To this we add noise.
 u₀(x, y, z) = uˢ(z) + sqrt(abs(Qᵘ)) * 1e-1 * Ξ(z)
 

examples/netcdf_ouput_example.jl

@@ -8,8 +8,9 @@ Nx, Ny, Nz = 16, 16, 16       # No. of grid points in x, y, and z, respectively.
 Lx, Ly, Lz = 100, 100, 100    # Length of the domain in x, y, and z, respectively (m).
 tf = 5000                     # Length of the simulation (s)
 
-model = Model(grid=RegularCartesianGrid(size=(Nx, Ny, Nz), length=(Lx, Ly, Lz)),
-              closure=ConstantIsotropicDiffusivity())
+grid = RegularCartesianGrid(size=(Nx, Ny, Nz), length=(Lx, Ly, Lz),
+                            topology=(Periodic, Periodic, Bounded))
+model = Model(grid=grid, closure=ConstantIsotropicDiffusivity())
 
 # Add a cube-shaped warm temperature anomaly that takes up the middle 50%
 # of the domain volume.

examples/ocean_convection_with_plankton.jl

@@ -54,8 +54,10 @@ nothing # hide
 growth_and_decay = SimpleForcing((x, y, z, t) -> exp(z/16))
 
 ## Instantiate the model
-model = Model(
-                   grid = RegularCartesianGrid(size = (Nz, 1, Nz), length = (Lz, Lz, Lz)),
+grid = RegularCartesianGrid(size=(Nz, 1, Nz), length=(Lz, Lz, Lz),
+                            topology=(Periodic, Periodic, Bounded))
+
+model = Model(     grid = grid,
                 closure = ConstantIsotropicDiffusivity(ν=1e-4, κ=1e-4),
                coriolis = FPlane(f=1e-4),
                 tracers = (:b, :plankton),

examples/ocean_wind_mixing_and_convection.jl

@@ -82,9 +82,12 @@ nothing # hide
 # model.parameters for use in the boundary condition function that calculates the salinity
 # flux.
 
+grid = RegularCartesianGrid(size=(Nz, Nz, Nz), length=(Δz*Nz, Δz*Nz, Δz*Nz),
+                            topology=(Periodic, Periodic, Bounded))
+
 model = Model(
          architecture = CPU(),
-                 grid = RegularCartesianGrid(size=(Nz, Nz, Nz), length=(Δz*Nz, Δz*Nz, Δz*Nz)),
+                 grid = grid,
              coriolis = FPlane(f=f),
              buoyancy = SeawaterBuoyancy(equation_of_state=LinearEquationOfState(α=α, β=β)),
               closure = AnisotropicMinimumDissipation(),

examples/one_dimensional_diffusion.jl

@@ -26,7 +26,8 @@ using Plots, Printf
 # `Model` constructor:
 
 model = Model(
-    grid = RegularCartesianGrid(size = (1, 1, 128), x = (0, 1), y = (0, 1), z = (-0.5, 0.5)),
+    grid = RegularCartesianGrid(size=(1, 1, 128), x=(0, 1), y=(0, 1), z=(-0.5, 0.5),
+                                topology=(Singleton, Singleton, Bounded)),
     closure = ConstantIsotropicDiffusivity(κ = 1.0)
 )
 nothing # hide

examples/two_dimensional_turbulence.jl

@@ -24,8 +24,11 @@ using Oceananigans: Face, Cell
 # `Face` and `Cell` represent "locations" on the staggered grid. We instantiate the
 # model with a simple isotropic diffusivity.
 
+grid = RegularCartesianGrid(size=(128, 128, 1), length=(2π, 2π, 2π),
+                            topology=(Periodic, Periodic, Singleton))
+
 model = Model(
-        grid = RegularCartesianGrid(size=(128, 128, 1), length=(2π, 2π, 2π)),
+        grid = grid,
     buoyancy = nothing,
      tracers = nothing,
      closure = ConstantIsotropicDiffusivity(ν=1e-3, κ=1e-3)

verification/stratified_couette_flow/stratified_couette_flow.jl

@@ -109,9 +109,12 @@ function simulate_stratified_couette_flow(; Nxy, Nz, arch=GPU(), h=1, U_wall=1,
     ##### Non-dimensional model setup
     #####
 
+    grid = RegularCartesianGrid(size=(Nxy, Nxy, Nz), length=(4π*h, 2π*h, 2h),
+                                topology=(Periodic, Periodic, Bounded))
+
     model = Model(
        architecture = arch,
-               grid = RegularCartesianGrid(size = (Nxy, Nxy, Nz), length = (4π*h, 2π*h, 2h)),
+               grid = grid,
            buoyancy = SeawaterBuoyancy(equation_of_state=LinearEquationOfState(α=1.0, β=0.0)),
             closure = AnisotropicMinimumDissipation(ν=ν, κ=κ),
 boundary_conditions = HorizontallyPeriodicSolutionBCs(u=ubcs, v=vbcs, T=Tbcs),