Fix various bugs in auto adding bgc tracers and setting up field depe…

…ndant forcing (#3323)

* Fixed bug in auto adding of tracers

* Bug in regularizing user function

* keys not names

* measure once cut twice

* Same for hydrostatic

* tried to make tidier

* fixed hydrostatic model

* added error if a field dependancy does not exist

* Update src/Biogeochemistry.jl

Co-authored-by: Gregory L. Wagner <wagner.greg@gmail.com>

* Bump patch version

---------

Co-authored-by: Gregory L. Wagner <wagner.greg@gmail.com>

Project.toml

@@ -1,7 +1,7 @@
 name = "Oceananigans"
 uuid = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
 authors = ["Climate Modeling Alliance and contributors"]
-version = "0.89.1"
+version = "0.89.2"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"

src/Biogeochemistry.jl

@@ -126,7 +126,7 @@ tracernames(tracers) = keys(tracers)
 tracernames(tracers::Tuple) = tracers
 
 add_biogeochemical_tracer(tracers::Tuple, name, grid) = tuple(tracers..., name)
-add_biogeochemical_tracer(tracers::NamedTuple, name, grid) = merge(tracers, NamedTuple(name => CenterField(grid)))
+add_biogeochemical_tracer(tracers::NamedTuple, name, grid) = merge(tracers, (; name => CenterField(grid)))
 
 @inline function has_biogeochemical_tracers(fields, required_fields, grid)
     user_specified_tracers = [name in tracernames(fields) for name in required_fields]

src/Models/HydrostaticFreeSurfaceModels/hydrostatic_free_surface_model.jl

@@ -138,7 +138,7 @@ function HydrostaticFreeSurfaceModel(; grid,
                                          extract_boundary_conditions(diffusivity_fields))
 
     # Next, we form a list of default boundary conditions:
-    prognostic_field_names = (:u, :v, :η, tracernames(tracers)...)
+    prognostic_field_names = (:u, :v, :w, tracernames(tracers)..., :η, keys(auxiliary_fields)...)
     default_boundary_conditions = NamedTuple{prognostic_field_names}(Tuple(FieldBoundaryConditions() for name in prognostic_field_names))
 
     # Then we merge specified, embedded, and default boundary conditions. Specified boundary conditions
@@ -175,7 +175,7 @@ function HydrostaticFreeSurfaceModel(; grid,
                               G⁻ = HydrostaticFreeSurfaceTendencyFields(velocities, free_surface, grid, tracernames(tracers)))
 
     # Regularize forcing for model tracer and velocity fields.
-    model_fields = hydrostatic_prognostic_fields(velocities, free_surface, tracers)
+    model_fields = merge(hydrostatic_prognostic_fields(velocities, free_surface, tracers), auxiliary_fields)
     forcing = model_forcing(model_fields; forcing...)
 
     default_tracer_advection, tracer_advection = validate_tracer_advection(tracer_advection, grid)

src/Models/NonhydrostaticModels/nonhydrostatic_model.jl

@@ -158,7 +158,9 @@ function NonhydrostaticModel(;    grid,
                                          extract_boundary_conditions(diffusivity_fields))
 
     # Next, we form a list of default boundary conditions:
-    prognostic_field_names = (:u, :v, :w, tracernames(tracers)...)
+
+    # Next, we form a list of default boundary conditions:
+    prognostic_field_names = (:u, :v, :w, tracernames(tracers)..., keys(auxiliary_fields)...)
     default_boundary_conditions = NamedTuple{prognostic_field_names}(FieldBoundaryConditions() for name in prognostic_field_names)
 
     # Finally, we merge specified, embedded, and default boundary conditions. Specified boundary conditions

src/Operators/interpolation_utils.jl

@@ -106,6 +106,8 @@ function index_and_interp_dependencies(X, Y, Z, dependencies, model_field_names)
         findfirst(isequal(name), model_field_names)
     end
 
+    !any(isnothing.(indices)) || error("$dependencies are required to be model fields but only $model_field_names are present")
+
     return indices, interps
 end