From 3a0c45169c1575997d40bb54e478526c4cc4e634 Mon Sep 17 00:00:00 2001
From: Simone Silvestri <33547697+simone-silvestri@users.noreply.github.com>
Date: Tue, 27 Feb 2024 15:44:17 -0500
Subject: [PATCH] some updates

---
 src/bathymetry_and_forcings.jl | 6 +++---
 src/grid_load_balance.jl       | 2 +-
 src/near_global_simulation.jl  | 5 ++---
 3 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/src/bathymetry_and_forcings.jl b/src/bathymetry_and_forcings.jl
index d82ccdf..45629f0 100644
--- a/src/bathymetry_and_forcings.jl
+++ b/src/bathymetry_and_forcings.jl
@@ -142,19 +142,19 @@ end
 @inline v_linear_bottom_drag(i, j, grid, c, Φ, μ) = @inbounds - μ * Φ.v[i, j, 1]
 
 @inline function surface_stress_x(i, j, grid, clock, fields, p)
-    φ = φnode(j, grid, Center())
+    φ = φnode(j, grid.underlying_grid, Center())
     return wind_stress(φ, p)
 end
 
 @inline function surface_salinity_flux(i, j, grid, clock, fields, p)
-    φ = φnode(j, grid, Center())
+    φ = φnode(j, grid.underlying_grid, Center())
     return salinity_flux(φ, p)
 end
 
 @inline T_reference(φ) = max(0.0, 30.0 * cos(1.2 * π * φ / 180))
 
 @inline function T_relaxation(i, j, grid, clock, fields, λ)
-    φ = φnode(j, grid, Center())
+    φ = φnode(j, grid.underlying_grid, Center())
     return @inbounds λ * (fields.T[i, j, grid.Nz] - T_reference(φ))
 end
 
diff --git a/src/grid_load_balance.jl b/src/grid_load_balance.jl
index fd91d73..fcb1cf9 100644
--- a/src/grid_load_balance.jl
+++ b/src/grid_load_balance.jl
@@ -28,7 +28,7 @@ function load_balanced_grid(arch, precision, N, latitude, z_faces, resolution,
     return experiment == :RealisticOcean ? 
     	   ImmersedBoundaryGrid(underlying_grid, Bottom(realistic_bathymetry(underlying_grid, resolution)), active_cells_map = true) :
            experiment == :DoubleDrake ?
-           ImmersedBoundaryGrid(underlying_grid, GridFittedBottom(double_drake_bathymetry)) :
+           ImmersedBoundaryGrid(underlying_grid, GridFittedBottom(double_drake_bathymetry), active_cells_map = true) :
            underlying_grid
 end
 
diff --git a/src/near_global_simulation.jl b/src/near_global_simulation.jl
index 3e8a572..4e36d3f 100644
--- a/src/near_global_simulation.jl
+++ b/src/near_global_simulation.jl
@@ -49,8 +49,7 @@ function scaling_test_simulation(resolution, ranks, Δt, stop_time;
                                  boundary_layer_parameterization = RiBasedVerticalDiffusivity(precision)
                                  )
 
-    topo = (Periodic, Bounded, Bounded)
-    arch = Distributed(child_arch; topology = topo, partition = Partition(ranks...))
+    arch = Distributed(child_arch; partition = Partition(ranks...))
 
     min_Δt, max_Δt = Δt isa Number ? (Δt, Δt) : Δt
 
@@ -73,7 +72,7 @@ function scaling_test_simulation(resolution, ranks, Δt, stop_time;
 
     vertical_diffusivity = VerticalScalarDiffusivity(VerticallyImplicitTimeDiscretization(), precision; ν=νz, κ=κz)
     
-    tracer_advection   = Oceananigans.Advection.ThreeDimensionalTracerAdvection(;
+    tracer_advection   = Oceananigans.Advection.TracerAdvection(;
                                 x = WENO(precision; order = 7),
                                 y = WENO(precision; order = 7),
                                 z = Centered(precision))