Update rest of the tests

test/regression_tests/ocean_large_eddy_simulation_regression_test.jl

@@ -55,9 +55,12 @@ function run_ocean_large_eddy_simulation_regression_test(arch, closure)
     S_bcs = HorizontallyPeriodicBCs(    top = BoundaryCondition(Flux, 5e-8)     )
 
     # Model instantiation
+    grid = RegularCartesianGrid(size=(16, 16, 16), length=(16, 16, 16),
+                                topology=(Periodic, Periodic, Bounded))
+
     model = Model(
              architecture = arch,
-                 grid = RegularCartesianGrid(size=(16, 16, 16), length=(16, 16, 16)),
+                     grid = grid,
                  coriolis = FPlane(f=1e-4),
                  buoyancy = SeawaterBuoyancy(equation_of_state=LinearEquationOfState(α=2e-4, β=8e-4)),
                   closure = closure,

test/regression_tests/rayleigh_benard_regression_test.jl

@@ -29,9 +29,11 @@ function run_rayleigh_benard_regression_test(arch)
     bbcs = HorizontallyPeriodicBCs(   top = BoundaryCondition(Value, 0.0),
                                    bottom = BoundaryCondition(Value, Δb))
 
+    grid = RegularCartesianGrid(size=(Nx, Ny, Nz), length=(Lx, Ly, Lz),
+                                topology=(Periodic, Periodic, Bounded))
     model = Model(
                architecture = arch,
-                       grid = RegularCartesianGrid(size=(Nx, Ny, Nz), length=(Lx, Ly, Lz)),
+                       grid = grid,
                     closure = ConstantIsotropicDiffusivity(ν=ν, κ=κ),
                     tracers = (:b, :c),
                    buoyancy = BuoyancyTracer(),

test/regression_tests/thermal_bubble_regression_test.jl

@@ -3,7 +3,8 @@ function run_thermal_bubble_regression_test(arch)
     Lx, Ly, Lz = 100, 100, 100
     Δt = 6
 
-    grid = RegularCartesianGrid(size=(Nx, Ny, Nz), length=(Lx, Ly, Lz))
+    grid = RegularCartesianGrid(size=(Nx, Ny, Nz), length=(Lx, Ly, Lz),
+                                topology=(Periodic, Periodic, Bounded))
     closure = ConstantIsotropicDiffusivity(ν=4e-2, κ=4e-2)
     model = Model(architecture=arch, grid=grid, closure=closure, coriolis=FPlane(f=1e-4))
 

test/test_abstract_operations.jl

@@ -50,7 +50,7 @@ function z_derivative(a)
 end
 
 function x_derivative_cell(FT, arch)
-    grid = RegularCartesianGrid(FT, size=(3, 3, 3), length=(3, 3, 3))
+    grid = RegularCartesianGrid(FT, size=(3, 3, 3), length=(3, 3, 3), topology=DT)
     a = Field(Cell, Cell, Cell, arch, grid)
     dx_a = ∂x(a)
 
@@ -232,7 +232,7 @@ end
 
     for FT in float_types
         arch = CPU()
-        grid = RegularCartesianGrid(FT, size=(3, 3, 3), length=(3, 3, 3))
+        grid = RegularCartesianGrid(FT, size=(3, 3, 3), length=(3, 3, 3), topology=DT)
         u, v, w = VelocityFields(arch, grid)
         c = Field(Cell, Cell, Cell, arch, grid)
 
@@ -277,7 +277,7 @@ end
         for FT in float_types
             num1 = FT(π)
             num2 = FT(42)
-            grid = RegularCartesianGrid(FT, size=(3, 3, 3), length=(3, 3, 3))
+            grid = RegularCartesianGrid(FT, size=(3, 3, 3), length=(3, 3, 3), topology=DT)
 
             u, v, w = VelocityFields(arch, grid)
             T, S = TracerFields(arch, grid, (:T, :S))
@@ -296,7 +296,7 @@ end
         arch = CPU()
         @info "  Testing derivatives..."
         for FT in float_types
-            grid = RegularCartesianGrid(FT, size=(3, 3, 3), length=(3, 3, 3))
+            grid = RegularCartesianGrid(FT, size=(3, 3, 3), length=(3, 3, 3), topology=DT)
 
             u, v, w = VelocityFields(arch, grid)
             T, S = TracerFields(arch, grid, (:T, :S))
@@ -314,7 +314,7 @@ end
         arch = CPU()
         Nx = 3 # Δx=1, xC = 0.5, 1.5, 2.5
         for FT in float_types
-            grid = RegularCartesianGrid(FT, size=(Nx, Nx, Nx), length=(Nx, Nx, Nx))
+            grid = RegularCartesianGrid(FT, size=(Nx, Nx, Nx), length=(Nx, Nx, Nx), topology=DT)
             a, b = (Field(Cell, Cell, Cell, arch, grid) for i in 1:2)
 
             set!(b, 2)
@@ -357,7 +357,7 @@ end
                 model = Model(
                     architecture = arch,
                       float_type = FT,
-                            grid = RegularCartesianGrid(FT, size=(16, 16, 16), length=(1, 1, 1))
+                            grid = RegularCartesianGrid(FT, size=(16, 16, 16), length=(1, 1, 1), topology=DT)
                 )
 
                 @testset "Derivative computations [$FT, $(typeof(arch))]" begin

test/test_boundary_conditions.jl

@@ -9,12 +9,12 @@ function test_z_boundary_condition_simple(arch, FT, fldname, bctype, bc, Nx, Ny)
     fieldbcs = HorizontallyPeriodicBCs(top=bc)
     modelbcs = HorizontallyPeriodicSolutionBCs(; Dict(fldname=>fieldbcs)...)
 
-    model = Model(grid=RegularCartesianGrid(FT; size=(Nx, Ny, Nz), length=(0.1, 0.2, 0.3)), architecture=arch,
-                  float_type=FT, boundary_conditions=modelbcs)
+    grid = RegularCartesianGrid(FT, size=(Nx, Ny, Nz), length=(0.1, 0.2, 0.3), topology=DT)
+    model = Model(grid=grid, architecture=arch, float_type=FT, boundary_conditions=modelbcs)
 
     time_step!(model, 1, 1e-16)
 
-    return typeof(model) <: Model
+    return model isa Model
 end
 
 function test_z_boundary_condition_top_bottom_alias(arch, FT, fldname)
@@ -24,8 +24,8 @@ function test_z_boundary_condition_top_bottom_alias(arch, FT, fldname)
     fieldbcs = HorizontallyPeriodicBCs(top=top_bc, bottom=bottom_bc)
     modelbcs = HorizontallyPeriodicSolutionBCs(; Dict(fldname=>fieldbcs)...)
 
-    model = Model(grid=RegularCartesianGrid(FT; size=(N, N, N), length=(0.1, 0.2, 0.3)), architecture=arch,
-                  float_type=FT, boundary_conditions=modelbcs)
+    grid = RegularCartesianGrid(FT, size=(N, N, N), length=(0.1, 0.2, 0.3), topology=DT)
+    model = Model(grid=grid, architecture=arch, float_type=FT, boundary_conditions=modelbcs)
 
     bcs = getfield(model.boundary_conditions.solution, fldname)
 
@@ -47,8 +47,8 @@ function test_z_boundary_condition_array(arch, FT, fldname)
     fieldbcs = HorizontallyPeriodicBCs(top=value_bc)
     modelbcs = HorizontallyPeriodicSolutionBCs(; Dict(fldname=>fieldbcs)...)
 
-    model = Model(grid=RegularCartesianGrid(FT; size=(Nx, Ny, Nz), length=(0.1, 0.2, 0.3)), architecture=arch,
-                  float_type=FT, boundary_conditions=modelbcs)
+    grid = RegularCartesianGrid(FT, size=(Nx, Ny, Nz), length=(0.1, 0.2, 0.3), topology=DT)
+    model = Model(grid=grid, architecture=arch, float_type=FT, boundary_conditions=modelbcs)
 
     bcs = getfield(model.boundary_conditions.solution, fldname)
 
@@ -65,7 +65,7 @@ function test_flux_budget(arch, FT, fldname)
     fieldbcs = HorizontallyPeriodicBCs(bottom=flux_bc)
     modelbcs = HorizontallyPeriodicSolutionBCs(; Dict(fldname=>fieldbcs)...)
 
-    grid = RegularCartesianGrid(FT; size=(N, N, N), length=(1, 1, Lz))
+    grid = RegularCartesianGrid(FT, size=(N, N, N), length=(1, 1, Lz), topology=DT)
     closure = ConstantIsotropicDiffusivity(FT; ν=κ, κ=κ)
     model = Model(grid=grid, closure=closure, architecture=arch,
                   float_type=FT, buoyancy=nothing, boundary_conditions=modelbcs)
@@ -100,7 +100,7 @@ function fluxes_with_diffusivity_boundary_conditions_are_correct(arch, FT)
     flux = - κ₀ * bz
 
     tracer_names = (:b,)
-    grid = RegularCartesianGrid(size=(16, 16, 16), length=(1, 1, Lz))
+    grid = RegularCartesianGrid(size=(16, 16, 16), length=(1, 1, Lz), topology=DT)
     closure = with_tracers(tracer_names, AnisotropicMinimumDissipation())
     diffusivities = TurbulentDiffusivities(arch, grid, tracer_names, closure)
 
@@ -111,7 +111,7 @@ function fluxes_with_diffusivity_boundary_conditions_are_correct(arch, FT)
     κₑ_bcs = HorizontallyPeriodicBCs(bottom=BoundaryCondition(Value, κ₀))
     diffusivities_bcs = (νₑ=νₑ_bcs, κₑ=(b=κₑ_bcs))
 
-    model_bcs = ModelBoundaryConditions(tracer_names, diffusivities, solution_bcs; 
+    model_bcs = ModelBoundaryConditions(tracer_names, diffusivities, solution_bcs;
                                         diffusivities=diffusivities_bcs)
 
     model = Model(grid=grid, architecture=arch, float_type=FT, tracers=tracer_names, buoyancy=BuoyancyTracer(),

test/test_diagnostics.jl

@@ -1,5 +1,5 @@
 function horizontal_average_is_correct(arch, FT)
-    grid = RegularCartesianGrid(size=(16, 16, 16), length=(100, 100, 100))
+    grid = RegularCartesianGrid(size=(16, 16, 16), length=(100, 100, 100), topology=DT)
     model = Model(grid=grid, architecture=arch, float_type=FT)
 
     T₀(x, y, z) = 20 + 0.01*z
@@ -13,7 +13,7 @@ function horizontal_average_is_correct(arch, FT)
 end
 
 function nan_checker_aborts_simulation(arch, FT)
-    grid=RegularCartesianGrid(size=(16, 16, 2), length=(1, 1, 1))
+    grid=RegularCartesianGrid(size=(16, 16, 2), length=(1, 1, 1), topology=DT)
     model = Model(grid=grid, architecture=arch, float_type=FT)
 
     # It checks for NaNs in w by default.
@@ -26,14 +26,14 @@ function nan_checker_aborts_simulation(arch, FT)
 end
 
 TestModel(::GPU, FT, ν=1.0, Δx=0.5) =
-    Model(grid = RegularCartesianGrid(FT; size=(16, 16, 16), length=(16Δx, 16Δx, 16Δx)),
+    Model(grid = RegularCartesianGrid(FT, size=(16, 16, 16), length=(16Δx, 16Δx, 16Δx), topology=DT),
        closure = ConstantIsotropicDiffusivity(FT; ν=ν, κ=ν),
   architecture = GPU(),
     float_type = FT
 )
 
 TestModel(::CPU, FT, ν=1.0, Δx=0.5) =
-    Model(grid = RegularCartesianGrid(FT; size=(3, 3, 3), length=(3Δx, 3Δx, 3Δx)),
+    Model(grid = RegularCartesianGrid(FT, size=(3, 3, 3), length=(3Δx, 3Δx, 3Δx), topology=DT),
        closure = ConstantIsotropicDiffusivity(FT; ν=ν, κ=ν),
   architecture = CPU(),
     float_type = FT

test/test_dynamics.jl

@@ -14,7 +14,7 @@ function relative_error(u_num, u, time)
 end
 
 function test_diffusion_simple(fieldname)
-    grid = RegularCartesianGrid(size=(1, 1, 16), length=(1, 1, 1))
+    grid = RegularCartesianGrid(size=(1, 1, 16), length=(1, 1, 1), topology=DT)
     closure = ConstantIsotropicDiffusivity(ν=1, κ=1)
     model = Model(grid=grid, closure=closure, buoyancy=nothing)
     field = getmodelfield(fieldname, model)
@@ -27,7 +27,7 @@ function test_diffusion_simple(fieldname)
 end
 
 function test_diffusion_budget_default(fieldname)
-    grid = RegularCartesianGrid(size=(1, 1, 16), length=(1, 1, 1))
+    grid = RegularCartesianGrid(size=(1, 1, 16), length=(1, 1, 1), topology=DT)
     closure = ConstantIsotropicDiffusivity(ν=1, κ=1)
     model = Model(grid=grid, closure=closure, buoyancy=nothing)
     field = getmodelfield(fieldname, model)
@@ -39,7 +39,7 @@ function test_diffusion_budget_default(fieldname)
 end
 
 function test_diffusion_budget_channel(fieldname)
-    grid = RegularCartesianGrid(size=(1, 16, 4), length=(1, 1, 1))
+    grid = RegularCartesianGrid(size=(1, 16, 4), length=(1, 1, 1), topology=DT)
     closure = ConstantIsotropicDiffusivity(ν=1, κ=1)
     model = ChannelModel(grid=grid, closure=closure, buoyancy=nothing)
     field = getmodelfield(fieldname, model)
@@ -58,7 +58,7 @@ end
 
 function test_diffusion_cosine(fieldname)
     Nz, Lz, κ, m = 128, π/2, 1, 2
-    grid = RegularCartesianGrid(size=(1, 1, Nz), length=(1, 1, Lz))
+    grid = RegularCartesianGrid(size=(1, 1, Nz), length=(1, 1, Lz), topology=DT)
     closure = ConstantIsotropicDiffusivity(ν=κ, κ=κ)
     model = Model(grid=grid, closure=closure, buoyancy=nothing)
     field = getmodelfield(fieldname, model)
@@ -111,7 +111,7 @@ function internal_wave_test(; N=128, Nt=10)
     b₀(x, y, z) = b(x, y, z, 0)
 
     # Create a model where temperature = buoyancy.
-    grid = RegularCartesianGrid(size=(N, 1, N), length=(L, L, L))
+    grid = RegularCartesianGrid(size=(N, 1, N), length=(L, L, L), topology=DT)
     closure = ConstantIsotropicDiffusivity(ν=ν, κ=κ)
     model = Model(grid=grid, closure=closure, buoyancy=BuoyancyTracer(), tracers=:b, coriolis=FPlane(f=f))
 
@@ -134,7 +134,7 @@ function passive_tracer_advection_test(; N=128, κ=1e-12, Nt=100)
     v₀(x, y, z) = V
     T₀(x, y, z) = T(x, y, z, 0)
 
-    grid = RegularCartesianGrid(size=(N, N, 2), length=(L, L, L))
+    grid = RegularCartesianGrid(size=(N, N, 2), length=(L, L, L), topology=DT)
     closure = ConstantIsotropicDiffusivity(ν=κ, κ=κ)
     model = Model(grid=grid, closure=closure)
 
@@ -164,7 +164,7 @@ function taylor_green_vortex_test(arch; FT=Float64, N=64, Nt=10)
     @inline v(x, y, z, t) =  sin(2π*x) * exp(-4π^2 * ν * t)
 
     model = Model(architecture = arch,
-                          grid = RegularCartesianGrid(FT; size=(Nx, Ny, Nz), length=(Lx, Ly, Lz)),
+                          grid = RegularCartesianGrid(FT, size=(Nx, Ny, Nz), length=(Lx, Ly, Lz), topology=DT),
                        closure = ConstantIsotropicDiffusivity(FT; ν=1, κ=0),  # Turn off diffusivity.
                        tracers = nothing,
                       buoyancy = nothing) # turn off buoyancy

test/test_forcings.jl

@@ -14,7 +14,7 @@ function time_step_with_forcing_functions(arch)
 
     forcing = ModelForcing(u=Fu, v=Fv, w=Fw)
 
-    grid = RegularCartesianGrid(size=(16, 16, 16), length=(1, 1, 1))
+    grid = RegularCartesianGrid(size=(16, 16, 16), length=(1, 1, 1), topology=DT)
     model = Model(grid=grid, architecture=arch, forcing=forcing)
     time_step!(model, 1, 1)
     return true
@@ -27,7 +27,7 @@ function time_step_with_forcing_functions_params(arch)
 
     forcing = ModelForcing(u=Fu, v=Fv, w=Fw)
 
-    grid = RegularCartesianGrid(size=(16, 16, 16), length=(1, 1, 1))
+    grid = RegularCartesianGrid(size=(16, 16, 16), length=(1, 1, 1), topology=DT)
     model = Model(grid=grid, architecture=arch, forcing=forcing, parameters=(τ=60,))
     time_step!(model, 1, 1)
     return true
@@ -39,23 +39,23 @@ function time_step_with_forcing_functions_sin_exp(arch)
 
     forcing = ModelForcing(u=Fu, T=FT)
 
-    grid = RegularCartesianGrid(size=(16, 16, 16), length=(1, 1, 1))
+    grid = RegularCartesianGrid(size=(16, 16, 16), length=(1, 1, 1), topology=DT)
     model = Model(grid=grid, architecture=arch, forcing=forcing)
     time_step!(model, 1, 1)
     return true
 end
 
 function time_step_with_simple_forcing(arch)
     u_forcing = SimpleForcing((x, y, z, t) -> sin(x))
-    grid = RegularCartesianGrid(size=(16, 16, 16), length=(1, 1, 1))
+    grid = RegularCartesianGrid(size=(16, 16, 16), length=(1, 1, 1), topology=DT)
     model = Model(grid=grid, architecture=arch, forcing=ModelForcing(u=u_forcing))
     time_step!(model, 1, 1)
     return true
 end
 
 function time_step_with_simple_forcing_parameters(arch)
     u_forcing = SimpleForcing((x, y, z, t, p) -> sin(p.ω * x), parameters=(ω=π,))
-    grid = RegularCartesianGrid(size=(16, 16, 16), length=(1, 1, 1))
+    grid = RegularCartesianGrid(size=(16, 16, 16), length=(1, 1, 1), topology=DT)
     model = Model(grid=grid, architecture=arch, forcing=ModelForcing(u=u_forcing))
     time_step!(model, 1, 1)
     return true

test/test_models.jl

@@ -13,7 +13,7 @@ function set_velocity_tracer_fields(arch, grid, fieldname, value, answer)
 end
 
 function initial_conditions_correctly_set(arch, FT)
-    model = Model(grid=RegularCartesianGrid(FT; size=(16, 16, 8), length=(1, 2, 3)), 
+    model = Model(grid=RegularCartesianGrid(FT, size=(16, 16, 8), length=(1, 2, 3), topology=DT),
                   architecture=arch, float_type=FT)
 
     # Set initial condition to some basic function we can easily check for.
@@ -52,7 +52,7 @@ end
     @testset "Doubly periodic model" begin
         @info "  Testing doubly periodic model construction..."
         for arch in archs, FT in float_types
-            model = Model(grid=RegularCartesianGrid(FT; size=(16, 16, 2), length=(1, 2, 3)), 
+            model = Model(grid=RegularCartesianGrid(FT, size=(16, 16, 2), length=(1, 2, 3), topology=DT),
                           architecture=arch, float_type=FT)
 
             # Just testing that a Model was constructed with no errors/crashes.
@@ -63,8 +63,8 @@ end
     @testset "Reentrant channel model" begin
         @info "  Testing reentrant channel model construction..."
         for arch in archs, FT in float_types
-            model = ChannelModel(grid=RegularCartesianGrid(FT; size=(16, 16, 2), length=(1, 2, 3)), 
-                                 architecture=arch, float_type=FT)
+            grid = RegularCartesianGrid(FT, size=(16, 16, 2), length=(1, 2, 3), topology=(Periodic, Bounded, Bounded))
+            model = ChannelModel(grid=grid, architecture=arch, float_type=FT)
 
             # Just testing that a ChannelModel was constructed with no errors/crashes.
             @test true
@@ -74,7 +74,7 @@ end
     @testset "Non-dimensional model" begin
         @info "  Testing non-dimensional model construction..."
         for arch in archs, FT in float_types
-            grid = RegularCartesianGrid(FT; size=(16, 16, 2), length=(3, 2, 1))
+            grid = RegularCartesianGrid(FT, size=(16, 16, 2), length=(3, 2, 1), topology=DT)
             model = NonDimensionalModel(architecture=arch, float_type=FT, grid=grid, Re=1, Pr=1, Ro=Inf)
 
             # Just testing that a NonDimensionalModel was constructed with no errors/crashes.
@@ -88,7 +88,7 @@ end
             N = (16, 16, 8)
             L = (2π, 3π, 5π)
 
-            grid = RegularCartesianGrid(FT; size=N, length=L)
+            grid = RegularCartesianGrid(FT, size=N, length=L, topology=DT)
             xF = reshape(grid.xF[1:end-1], N[1], 1, 1)
             yC = reshape(grid.yC, 1, N[2], 1)
             zC = reshape(grid.zC, 1, 1, N[3])

test/test_output_writers.jl

@@ -8,7 +8,7 @@ function run_thermal_bubble_netcdf_tests(arch)
     Lx, Ly, Lz = 100, 100, 100
     Δt = 6
 
-    grid = RegularCartesianGrid(size=(Nx, Ny, Nz), length=(Lx, Ly, Lz))
+    grid = RegularCartesianGrid(size=(Nx, Ny, Nz), length=(Lx, Ly, Lz), topology=DT)
     closure = ConstantIsotropicDiffusivity(ν=4e-2, κ=4e-2)
     model = Model(architecture=arch, grid=grid, closure=closure)
 
@@ -73,7 +73,7 @@ function run_thermal_bubble_netcdf_tests(arch)
 end
 
 function run_jld2_file_splitting_tests(arch)
-    model = Model(grid=RegularCartesianGrid(size=(16, 16, 16), length=(1, 1, 1)))
+    model = Model(grid=RegularCartesianGrid(size=(16, 16, 16), length=(1, 1, 1), topology=DT))
 
     u(model) = Array(model.velocities.u.data.parent)
     fields = Dict(:u => u)
@@ -120,7 +120,7 @@ function run_thermal_bubble_checkpointer_tests(arch)
     Lx, Ly, Lz = 100, 100, 100
     Δt = 6
 
-    grid = RegularCartesianGrid(size=(Nx, Ny, Nz), length=(Lx, Ly, Lz))
+    grid = RegularCartesianGrid(size=(Nx, Ny, Nz), length=(Lx, Ly, Lz), topology=DT)
     closure = ConstantIsotropicDiffusivity(ν=4e-2, κ=4e-2)
     true_model = Model(architecture=arch, grid=grid, closure=closure)