Change diffusivity_fields to closure_fields (#4925)

* Change diffusivity_fields to closure_fields

* Update src/Models/HydrostaticFreeSurfaceModels/hydrostatic_free_surface_model.jl

* Update src/Models/HydrostaticFreeSurfaceModels/hydrostatic_free_surface_model.jl

* Update src/Models/NonhydrostaticModels/nonhydrostatic_model.jl

* Update src/Models/NonhydrostaticModels/nonhydrostatic_model.jl

* Update src/Models/ShallowWaterModels/shallow_water_model.jl

* Update src/Models/ShallowWaterModels/shallow_water_model.jl

* Update src/Models/ShallowWaterModels/shallow_water_model.jl

* rename file

Author: glwagner

examples/ocean_wind_mixing_and_convection.jl

@@ -205,7 +205,7 @@ add_callback!(simulation, progress_message, IterationInterval(40))
 # `ocean_wind_mixing_and_convection.jld2`.
 
 ## Create a NamedTuple with eddy viscosity
-eddy_viscosity = (; νₑ = model.diffusivity_fields.νₑ)
+eddy_viscosity = (; νₑ = model.closure_fields.νₑ)
 
 filename = "ocean_wind_mixing_and_convection"
 

src/BoundaryConditions/discrete_boundary_function.jl

@@ -12,7 +12,7 @@ where `i, j` are the indices along the boundary,
 where `grid` is `model.grid`, `clock.time` is the current simulation time and
 `clock.iteration` is the current model iteration, and
 `model_fields` is a `NamedTuple` with `u, v, w`, the fields in `model.tracers`,
-and the fields in `model.diffusivity_fields`, each of which is an `OffsetArray`s (or `NamedTuple`s
+and the fields in `model.closure_fields`, each of which is an `OffsetArray`s (or `NamedTuple`s
 of `OffsetArray`s depending on the turbulence closure) of field data.
 
 When `parameters` is not `nothing`, the boundary condition `func` is called with

src/Forcings/forcing.jl

@@ -53,7 +53,7 @@ func(i, j, k, grid, clock, model_fields)
 where `i, j, k` is the grid point at which the forcing is applied, `grid` is `model.grid`,
 `clock.time` is the current simulation time and `clock.iteration` is the current model iteration,
 and `model_fields` is a `NamedTuple` with `u, v, w`, the fields in `model.tracers`,
-and the fields in `model.diffusivity_fields`, each of which is an `OffsetArray`s (or `NamedTuple`s
+and the fields in `model.closure_fields`, each of which is an `OffsetArray`s (or `NamedTuple`s
 of `OffsetArray`s depending on the turbulence closure) of field data.
 
 When `discrete_form=true` and `parameters` _is_ specified, `func` must be callable with the signature

src/Models/HydrostaticFreeSurfaceModels/compute_hydrostatic_free_surface_tendencies.jl

@@ -78,7 +78,7 @@ function compute_hydrostatic_free_surface_tendency_contributions!(model, kernel_
                      model.velocities,
                      model.free_surface,
                      model.tracers,
-                     model.diffusivity_fields,
+                     model.closure_fields,
                      model.auxiliary_fields,
                      model.clock,
                      c_forcing)
@@ -114,7 +114,7 @@ function compute_hydrostatic_momentum_tendencies!(model, velocities, kernel_para
                                 model.free_surface,
                                 model.tracers,
                                 model.buoyancy,
-                                model.diffusivity_fields,
+                                model.closure_fields,
                                 model.pressure.pHY′,
                                 model.auxiliary_fields,
                                 model.vertical_coordinate,

src/Models/HydrostaticFreeSurfaceModels/hydrostatic_free_surface_ab2_step.jl

@@ -48,7 +48,7 @@ function ab2_step_velocities!(velocities, model, Δt, χ)
         implicit_step!(velocity_field,
                        model.timestepper.implicit_solver,
                        model.closure,
-                       model.diffusivity_fields,
+                       model.closure_fields,
                        nothing,
                        model.clock, 
                        fields(model),
@@ -97,7 +97,7 @@ function ab2_step_tracers!(tracers, model, Δt, χ)
             implicit_step!(tracer_field,
                            model.timestepper.implicit_solver,
                            closure,
-                           model.diffusivity_fields,
+                           model.closure_fields,
                            Val(tracer_index),
                            model.clock,
                            fields(model),

src/Models/HydrostaticFreeSurfaceModels/hydrostatic_free_surface_model.jl

@@ -12,7 +12,7 @@ using Oceananigans.Grids: AbstractCurvilinearGrid, AbstractHorizontallyCurviline
 using Oceananigans.ImmersedBoundaries: ImmersedBoundaryGrid
 using Oceananigans.Models: AbstractModel, validate_model_halo, validate_tracer_advection, extract_boundary_conditions, initialization_update_state!
 using Oceananigans.TimeSteppers: Clock, TimeStepper, update_state!, AbstractLagrangianParticles, SplitRungeKutta3TimeStepper
-using Oceananigans.TurbulenceClosures: validate_closure, with_tracers, build_diffusivity_fields, add_closure_specific_boundary_conditions
+using Oceananigans.TurbulenceClosures: validate_closure, with_tracers, build_closure_fields, add_closure_specific_boundary_conditions
 using Oceananigans.TurbulenceClosures: time_discretization, implicit_diffusion_solver
 using Oceananigans.Utils: tupleit
 
@@ -51,7 +51,7 @@ mutable struct HydrostaticFreeSurfaceModel{TS, E, A<:AbstractArchitecture, S,
     velocities :: U             # Container for velocity fields `u`, `v`, and `w`
     tracers :: C                # Container for tracer fields
     pressure :: Φ               # Container for hydrostatic pressure
-    diffusivity_fields :: K     # Container for turbulent diffusivities
+    closure_fields :: K         # Container for auxiliary fields for closures
     timestepper :: TS           # Object containing timestepper fields and parameters
     auxiliary_fields :: AF      # User-specified auxiliary fields for forcing functions and boundary conditions
     vertical_coordinate :: Z    # Rulesets that define the time-evolution of the grid
@@ -80,7 +80,7 @@ default_free_surface(grid; gravitational_acceleration=defaults.gravitational_acc
                                 biogeochemistry::AbstractBGCOrNothing = nothing,
                                 velocities = nothing,
                                 pressure = nothing,
-                                diffusivity_fields = nothing,
+                                closure_fields = nothing,
                                 auxiliary_fields = NamedTuple(),
                                 vertical_coordinate = default_vertical_coordinate(grid))
 
@@ -112,7 +112,7 @@ Keyword arguments
   - `biogeochemistry`: Biogeochemical model for `tracers`.
   - `velocities`: The model velocities. Default: `nothing`.
   - `pressure`: Hydrostatic pressure field. Default: `nothing`.
-  - `diffusivity_fields`: Diffusivity fields. Default: `nothing`.
+  - `closure_fields`: Closure fields. Default: `nothing`.
   - `auxiliary_fields`: `NamedTuple` of auxiliary fields. Default: `nothing`.
   - `vertical_coordinate`: Algorithm for grid evolution: `ZStarCoordinate()` or `ZCoordinate(grid)`.
                            Default: `default_vertical_coordinate(grid)`, which returns `ZStarCoordinate(grid)`
@@ -135,7 +135,7 @@ function HydrostaticFreeSurfaceModel(; grid,
     biogeochemistry::AbstractBGCOrNothing = nothing,
     velocities = nothing,
     pressure = nothing,
-    diffusivity_fields = nothing,
+    closure_fields = nothing,
     auxiliary_fields = NamedTuple(),
     vertical_coordinate = default_vertical_coordinate(grid))
 
@@ -175,7 +175,7 @@ function HydrostaticFreeSurfaceModel(; grid,
     embedded_boundary_conditions = merge(extract_boundary_conditions(velocities),
                                          extract_boundary_conditions(tracers),
                                          extract_boundary_conditions(pressure),
-                                         extract_boundary_conditions(diffusivity_fields))
+                                         extract_boundary_conditions(closure_fields))
 
     # Next, we form a list of default boundary conditions:
     field_names = constructor_field_names(velocities, tracers, free_surface, auxiliary_fields, biogeochemistry, grid)
@@ -204,7 +204,7 @@ function HydrostaticFreeSurfaceModel(; grid,
     velocities         = hydrostatic_velocity_fields(velocities, grid, clock, boundary_conditions)
     tracers            = TracerFields(tracers, grid, boundary_conditions)
     pressure           = PressureField(grid)
-    diffusivity_fields = build_diffusivity_fields(diffusivity_fields, grid, clock, tracernames(tracers), boundary_conditions, closure)
+    closure_fields = build_closure_fields(closure_fields, grid, clock, tracernames(tracers), boundary_conditions, closure)
 
     @apply_regionally validate_velocity_boundary_conditions(grid, velocities)
 
@@ -228,7 +228,7 @@ function HydrostaticFreeSurfaceModel(; grid,
 
     model = HydrostaticFreeSurfaceModel(arch, grid, clock, advection, buoyancy, coriolis,
                                         free_surface, forcing, closure, particles, biogeochemistry, velocities, tracers,
-                                        pressure, diffusivity_fields, timestepper, auxiliary_fields, vertical_coordinate)
+                                        pressure, closure_fields, timestepper, auxiliary_fields, vertical_coordinate)
 
     initialization_update_state!(model; compute_tendencies=false)
 

src/Models/HydrostaticFreeSurfaceModels/hydrostatic_free_surface_rk3_step.jl

@@ -44,7 +44,7 @@ function rk3_substep_velocities!(velocities, model, Δt)
         implicit_step!(velocity_field,
                        model.timestepper.implicit_solver,
                        model.closure,
-                       model.diffusivity_fields,
+                       model.closure_fields,
                        nothing,
                        model.clock, 
                        fields(model),
@@ -84,7 +84,7 @@ function rk3_substep_tracers!(tracers, model, Δt)
             implicit_step!(c,
                            model.timestepper.implicit_solver,
                            closure,
-                           model.diffusivity_fields,
+                           model.closure_fields,
                            Val(tracer_index),
                            model.clock,
                            fields(model),

src/Models/HydrostaticFreeSurfaceModels/single_column_model_mode.jl

@@ -73,9 +73,9 @@ function update_state!(model::HydrostaticFreeSurfaceModel, grid::SingleColumnGri
     compute_auxiliary_fields!(model.auxiliary_fields)
 
     # Calculate diffusivities
-    compute_diffusivities!(model.diffusivity_fields, model.closure, model)
+    compute_diffusivities!(model.closure_fields, model.closure, model)
 
-    fill_halo_regions!(model.diffusivity_fields, model.clock, fields(model))
+    fill_halo_regions!(model.closure_fields, model.clock, fields(model))
 
     for callback in callbacks
         callback.callsite isa UpdateStateCallsite && callback(model)

src/Models/HydrostaticFreeSurfaceModels/update_hydrostatic_free_surface_model_state.jl

@@ -44,7 +44,7 @@ function update_state!(model::HydrostaticFreeSurfaceModel, grid, callbacks; comp
 
     @apply_regionally compute_auxiliaries!(model)
 
-    fill_halo_regions!(model.diffusivity_fields; only_local_halos=true)
+    fill_halo_regions!(model.closure_fields; only_local_halos=true)
 
     [callback(model) for callback in callbacks if callback.callsite isa UpdateStateCallsite]
 
@@ -78,7 +78,7 @@ function compute_auxiliaries!(model::HydrostaticFreeSurfaceModel; w_parameters =
     grid        = model.grid
     closure     = model.closure
     tracers     = model.tracers
-    diffusivity = model.diffusivity_fields
+    diffusivity = model.closure_fields
     buoyancy    = model.buoyancy
 
     P    = model.pressure.pHY′

src/Models/Models.jl

@@ -130,7 +130,7 @@ function possible_field_time_series(model::OceananigansModels)
     forcing = model.forcing
     model_fields = fields(model)
     # Note: we may need to include other objects in the tuple below,
-    # such as model.diffusivity_fields
+    # such as model.closure_fields
     return tuple(model_fields, forcing)
 end