think I've fixed particles and sediment together

OceanBioME · Jul 13, 2023 · 1ec431a · 1ec431a
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commit 1ec431a
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Showing 5 changed files with 11 additions and 14 deletions.
diff --git a/src/Boundaries/Sediments/Sediments.jl b/src/Boundaries/Sediments/Sediments.jl
@@ -11,19 +11,18 @@ using Oceananigans.Advection: div_Uc
 using Oceananigans.Units: day
 using Oceananigans.Fields: CenterField, Face
 using Oceananigans.Biogeochemistry: biogeochemical_drift_velocity
+using Oceananigans.Grids: zspacing
 
-import Oceananigans.Biogeochemistry: update_tendencies!
 import Adapt: adapt_structure, adapt
 
 abstract type AbstractSediment end
 abstract type FlatSediment <: AbstractSediment end
 
 sediment_fields(::AbstractSediment) = ()
 
-@inline update_tendencies!(bgc::ContinuousFormBiogeochemistry{<:Any, <:FlatSediment, <:Any}, model) = update_tendencies!(bgc, bgc.sediment_model, model)
-@inline update_tendencies!(bgc, sediment, model) = nothing
+@inline update_sediment_tendencies!(bgc, sediment, model) = nothing
 
-function update_tendencies!(bgc, sediment::FlatSediment, model)
+function update_sediment_tendencies!(bgc, sediment::FlatSediment, model)
     arch = model.grid.architecture
 
     for (i, tracer) in enumerate(sediment_tracers(sediment))

diff --git a/src/Boundaries/Sediments/simple_multi_G.jl b/src/Boundaries/Sediments/simple_multi_G.jl
@@ -98,7 +98,7 @@ function SimpleMultiG(; grid,
                                                depth = depth)) where {FT, P1, P2, P3, P4}
 
     @warn "Sediment models are an experimental feature and have not yet been validated"
-    @info "This sediment model is only compatible with models providing NH₄, NO₃, O₂ and DIC"
+    @info "This sediment model is currently only compatible with models providing NH₄, NO₃, O₂ and DIC"
 
     tracer_names = (:C_slow, :C_fast, :N_slow, :N_fast, :C_ref, :N_ref)
 

diff --git a/src/Models/Individuals/SLatissima.jl b/src/Models/Individuals/SLatissima.jl
@@ -31,7 +31,7 @@ using Oceananigans.Grids: AbstractGrid
 using Oceananigans.Fields: fractional_indices, _interpolate, datatuple
 
 import Adapt: adapt_structure, adapt
-import Oceananigans.Biogeochemistry: update_tendencies!
+import OceanBioME.Particles: update_particles_tendencies!
 import Oceananigans.Models.LagrangianParticleTracking: update_lagrangian_particle_properties!, _advect_particles!
 
 @inline no_dynamics(args...) = nothing

diff --git a/src/Models/Models.jl b/src/Models/Models.jl
@@ -1,14 +1,14 @@
-using OceanBioME.Particles: BiogeochemicalParticles
-using OceanBioME.Boundaries.Sediments: AbstractSediment
+using OceanBioME.Boundaries.Sediments: update_sediment_tendencies!
+using OceanBioME.Particles: update_particles_tendencies!
 
 import Oceananigans.Biogeochemistry: update_tendencies!
 
 include("AdvectedPopulations/LOBSTER/LOBSTER.jl")
 include("AdvectedPopulations/NPZD.jl")
 include("Individuals/SLatissima.jl")
 
-@inline function update_tendencies!(bgc::ContinuousFormBiogeochemistry{<:Any, <:AbstractSediment, <:BiogeochemicalParticles}, model)
-    update_tendencies!(bgc, bgc.sediment_model, model)
-    update_tendencies!(bgc, bgc.particles, model)
+@inline function update_tendencies!(bgc::ContinuousFormBiogeochemistry, model)
+    update_sediment_tendencies!(bgc, bgc.sediment_model, model)
+    update_particles_tendencies!(bgc, bgc.particles, model)
     return nothing
 end
diff --git a/src/Particles/Particles.jl b/src/Particles/Particles.jl
@@ -4,7 +4,6 @@ using OceanBioME: ContinuousFormBiogeochemistry
 using Oceananigans: NonhydrostaticModel, HydrostaticFreeSurfaceModel
 
 import Oceananigans.Models.LagrangianParticleTracking: update_lagrangian_particle_properties!, step_lagrangian_particles!
-import Oceananigans.Biogeochemistry: update_tendencies!
 import Oceananigans.OutputWriters: fetch_output
 import Base: length, size, show, summary
 
@@ -27,8 +26,7 @@ abstract type BiogeochemicalParticles end
     update_lagrangian_particle_properties!(bgc.particles, model, bgc, Δt)
 
 update_lagrangian_particle_properties!(::BiogeochemicalParticles, model, bgc, Δt) = nothing
-update_tendencies!(bgc::ContinuousFormBiogeochemistry{<:Any, <:Any, <:BiogeochemicalParticles}, model) = update_tendencies!(bgc, bgc.particles, model)
-update_tendencies!(bgc, ::BiogeochemicalParticles, model) = nothing
+update_particles_tendencies!(bgc, particles, model) = nothing
 
 size(particles::BiogeochemicalParticles) = size(particles.x)
 length(particles::BiogeochemicalParticles) = length(particles.x)