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Changes to naming in the TurbulenceClosures module #2752

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merged 20 commits into from
Jan 23, 2023
Merged

Changes to naming in the TurbulenceClosures module #2752

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7cd9be3
calc -> calc_nonlinear
tomchor Sep 25, 2022
769ca88
removed fallbacks for calc_nonlinear_κᶜᶜᶜ
tomchor Sep 25, 2022
fec38c4
added calc_nonlinear_kappa for Smag
tomchor Sep 26, 2022
cf46e2d
U -> velocities
tomchor Oct 2, 2022
148dad1
C -> tracers
tomchor Oct 2, 2022
590727b
c -> tracer
tomchor Oct 2, 2022
b3815fe
clo -> closure
tomchor Oct 2, 2022
6740bb9
improved support for horizontal and vertical viscosities
tomchor Oct 2, 2022
c71bc13
revert tuple treatment for viscosity()
tomchor Oct 9, 2022
71db8e2
dont sum tutple closures
tomchor Nov 4, 2022
f5947f7
oops
tomchor Nov 4, 2022
05acdb7
Merge branch 'main' into tc/turbulence_closures
tomchor Nov 4, 2022
37cd871
Merge branch 'main' into tc/turbulence_closures
tomchor Nov 15, 2022
ccf7bec
tracer -> c
tomchor Nov 15, 2022
f32dfff
closure bacl to clo
tomchor Nov 15, 2022
45b8111
Update src/TurbulenceClosures/turbulence_closure_implementations/leit…
tomchor Nov 15, 2022
e487f6a
nuke calc_nonlinear_κᶜᶜᶜ
tomchor Nov 15, 2022
479056a
Merge branch 'main' into tc/turbulence_closures
tomchor Jan 19, 2023
6296b1e
small cleanup
tomchor Jan 20, 2023
4260c69
fix typo
tomchor Jan 20, 2023
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4 changes: 2 additions & 2 deletions src/Models/ShallowWaterModels/shallow_water_diffusion_operators.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ import Oceananigans.TurbulenceClosures:
calculate_nonlinear_viscosity!,
viscosity,
with_tracers,
calc_νᶜᶜᶜ,
calc_nonlinear_νᶜᶜᶜ,
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Why this change?

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The rationale was to differentiate from calc_νᶜᶜᶜ() from νᶜᶜᶜ(), which at first seem to do the same thing. That said, I'm okay with other names. What would you suggest?

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Do we even need separate calc_νᶜᶜᶜ() and νᶜᶜᶜ() if they do the same thing?

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I don't know. I always assumed there was a reason to separate them. If we can use only one of them and get rid of the other, I'm all for it.

νᶜᶜᶜ

struct ShallowWaterScalarDiffusivity{N, X} <: AbstractScalarDiffusivity{ExplicitTimeDiscretization, ThreeDimensionalFormulation}
Expand All @@ -41,7 +41,7 @@ Adapt.adapt_structure(to, closure::ShallowWaterScalarDiffusivity) =
# The diffusivity for the shallow water model is calculated as h*ν in order to have a viscous term in the form
# h⁻¹ ∇ ⋅ (hν t) where t is the 2D stress tensor plus a trace => t = ∇u + (∇u)ᵀ - ξI⋅(∇⋅u)

@inline calc_νᶜᶜᶜ(i, j, k, grid, closure::ShallowWaterScalarDiffusivity, clock, fields) =
@inline calc_nonlinear_νᶜᶜᶜ(i, j, k, grid, closure::ShallowWaterScalarDiffusivity, clock, fields) =
fields.h[i, j, k] * νᶜᶜᶜ(i, j, k, grid, viscosity_location(closure), closure.ν, clock, fields)

function calculate_diffusivities!(diffusivity_fields, closure::ShallowWaterScalarDiffusivity, model)
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44 changes: 22 additions & 22 deletions src/TurbulenceClosures/abstract_scalar_biharmonic_diffusivity_closure.jl
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Expand Up @@ -16,7 +16,7 @@ const ASBD = AbstractScalarBiharmonicDiffusivity
#####

const ccc = (Center(), Center(), Center())
@inline νᶜᶜᶜ(i, j, k, grid, closure::ASBD, K, clock, fields) = νᶜᶜᶜ(i, j, k, grid, ccc, viscosity(closure, K), clock, fields)
@inline νᶜᶜᶜ(i, j, k, grid, closure::ASBD, K, clock, fields) = νᶜᶜᶜ(i, j, k, grid, ccc, viscosity(closure, K), clock, fields)
@inline νᶠᶠᶜ(i, j, k, grid, closure::ASBD, K, clock, fields) = νᶠᶠᶜ(i, j, k, grid, ccc, viscosity(closure, K), clock, fields)
@inline νᶠᶜᶠ(i, j, k, grid, closure::ASBD, K, clock, fields) = νᶠᶜᶠ(i, j, k, grid, ccc, viscosity(closure, K), clock, fields)
@inline νᶜᶠᶠ(i, j, k, grid, closure::ASBD, K, clock, fields) = νᶜᶠᶠ(i, j, k, grid, ccc, viscosity(closure, K), clock, fields)
Expand All @@ -34,27 +34,27 @@ const AHBD = AbstractScalarBiharmonicDiffusivity{<:HorizontalFormulation}
const ADBD = AbstractScalarBiharmonicDiffusivity{<:HorizontalDivergenceFormulation}
const AVBD = AbstractScalarBiharmonicDiffusivity{<:VerticalFormulation}

@inline viscous_flux_ux(i, j, k, grid, clo::AIBD, K, clk, fields, b) = + ν_σᶜᶜᶜ(i, j, k, grid, clo, K, clk, fields, ∂xᶜᶜᶜ, biharmonic_mask_x, ∇²ᶠᶜᶜ, fields.u)
@inline viscous_flux_vx(i, j, k, grid, clo::AIBD, K, clk, fields, b) = + ν_σᶠᶠᶜ(i, j, k, grid, clo, K, clk, fields, biharmonic_mask_x, ∂xᶠᶠᶜ, ∇²ᶜᶠᶜ, fields.v)
@inline viscous_flux_wx(i, j, k, grid, clo::AIBD, K, clk, fields, b) = + ν_σᶠᶜᶠ(i, j, k, grid, clo, K, clk, fields, biharmonic_mask_x, ∂xᶠᶜᶠ, ∇²ᶜᶜᶠ, fields.w)
@inline viscous_flux_uy(i, j, k, grid, clo::AIBD, K, clk, fields, b) = + ν_σᶠᶠᶜ(i, j, k, grid, clo, K, clk, fields, biharmonic_mask_y, ∂yᶠᶠᶜ, ∇²ᶠᶜᶜ, fields.u)
@inline viscous_flux_vy(i, j, k, grid, clo::AIBD, K, clk, fields, b) = + ν_σᶜᶜᶜ(i, j, k, grid, clo, K, clk, fields, ∂yᶜᶜᶜ, biharmonic_mask_y, ∇²ᶜᶠᶜ, fields.v)
@inline viscous_flux_wy(i, j, k, grid, clo::AIBD, K, clk, fields, b) = + ν_σᶜᶠᶠ(i, j, k, grid, clo, K, clk, fields, biharmonic_mask_y, ∂yᶜᶠᶠ, ∇²ᶜᶜᶠ, fields.w)
@inline viscous_flux_uz(i, j, k, grid, clo::AIBD, K, clk, fields, b) = + ν_σᶠᶜᶠ(i, j, k, grid, clo, K, clk, fields, biharmonic_mask_z, ∂zᶠᶜᶠ, ∇²ᶠᶜᶜ, fields.u)
@inline viscous_flux_vz(i, j, k, grid, clo::AIBD, K, clk, fields, b) = + ν_σᶜᶠᶠ(i, j, k, grid, clo, K, clk, fields, biharmonic_mask_z, ∂zᶜᶠᶠ, ∇²ᶜᶠᶜ, fields.v)
@inline viscous_flux_wz(i, j, k, grid, clo::AIBD, K, clk, fields, b) = + ν_σᶜᶜᶜ(i, j, k, grid, clo, K, clk, fields, ∂zᶜᶜᶜ, biharmonic_mask_z, ∇²ᶜᶜᶠ, fields.w)
@inline viscous_flux_ux(i, j, k, grid, clo::AHBD, K, clk, fields, b) = + ν_σᶜᶜᶜ(i, j, k, grid, clo, K, clk, fields, δ★ᶜᶜᶜ, fields.u, fields.v)
@inline viscous_flux_vx(i, j, k, grid, clo::AHBD, K, clk, fields, b) = + ν_σᶠᶠᶜ(i, j, k, grid, clo, K, clk, fields, ζ★ᶠᶠᶜ, fields.u, fields.v)
@inline viscous_flux_wx(i, j, k, grid, clo::AHBD, K, clk, fields, b) = + ν_σᶠᶜᶠ(i, j, k, grid, clo, K, clk, fields, biharmonic_mask_x, ∂xᶠᶜᶠ, ∇²ᶜᶜᶠ, fields.w)
@inline viscous_flux_uy(i, j, k, grid, clo::AHBD, K, clk, fields, b) = - ν_σᶠᶠᶜ(i, j, k, grid, clo, K, clk, fields, ζ★ᶠᶠᶜ, fields.u, fields.v)
@inline viscous_flux_vy(i, j, k, grid, clo::AHBD, K, clk, fields, b) = + ν_σᶜᶜᶜ(i, j, k, grid, clo, K, clk, fields, δ★ᶜᶜᶜ, fields.u, fields.v)
@inline viscous_flux_wy(i, j, k, grid, clo::AHBD, K, clk, fields, b) = + ν_σᶜᶠᶠ(i, j, k, grid, clo, K, clk, fields, biharmonic_mask_y, ∂yᶜᶠᶠ, ∇²ᶜᶜᶠ, fields.w)
@inline viscous_flux_uz(i, j, k, grid, clo::AVBD, K, clk, fields, b) = + ν_σᶠᶜᶠ(i, j, k, grid, clo, K, clk, fields, biharmonic_mask_z, ∂zᶠᶜᶠ, ∂²zᶠᶜᶜ, fields.u)
@inline viscous_flux_vz(i, j, k, grid, clo::AVBD, K, clk, fields, b) = + ν_σᶜᶠᶠ(i, j, k, grid, clo, K, clk, fields, biharmonic_mask_z, ∂zᶜᶠᶠ, ∂²zᶜᶠᶜ, fields.v)
@inline viscous_flux_wz(i, j, k, grid, clo::AVBD, K, clk, fields, b) = + ν_σᶜᶜᶜ(i, j, k, grid, clo, K, clk, fields, ∂zᶜᶜᶜ, biharmonic_mask_z, ∂²zᶜᶜᶠ, fields.w)

@inline viscous_flux_ux(i, j, k, grid, clo::ADBD, K, clk, fields, b) = + ν_σᶜᶜᶜ(i, j, k, grid, clo, K, clk, fields, δ★ᶜᶜᶜ, fields.u, fields.v)
@inline viscous_flux_vy(i, j, k, grid, clo::ADBD, K, clk, fields, b) = + ν_σᶜᶜᶜ(i, j, k, grid, clo, K, clk, fields, δ★ᶜᶜᶜ, fields.u, fields.v)
@inline viscous_flux_ux(i, j, k, grid, closure::AIBD, K, clk, fields, b) = + ν_σᶜᶜᶜ(i, j, k, grid, closure, K, clk, fields, ∂xᶜᶜᶜ, biharmonic_mask_x, ∇²ᶠᶜᶜ, fields.u)
@inline viscous_flux_vx(i, j, k, grid, closure::AIBD, K, clk, fields, b) = + ν_σᶠᶠᶜ(i, j, k, grid, closure, K, clk, fields, biharmonic_mask_x, ∂xᶠᶠᶜ, ∇²ᶜᶠᶜ, fields.v)
@inline viscous_flux_wx(i, j, k, grid, closure::AIBD, K, clk, fields, b) = + ν_σᶠᶜᶠ(i, j, k, grid, closure, K, clk, fields, biharmonic_mask_x, ∂xᶠᶜᶠ, ∇²ᶜᶜᶠ, fields.w)
@inline viscous_flux_uy(i, j, k, grid, closure::AIBD, K, clk, fields, b) = + ν_σᶠᶠᶜ(i, j, k, grid, closure, K, clk, fields, biharmonic_mask_y, ∂yᶠᶠᶜ, ∇²ᶠᶜᶜ, fields.u)
@inline viscous_flux_vy(i, j, k, grid, closure::AIBD, K, clk, fields, b) = + ν_σᶜᶜᶜ(i, j, k, grid, closure, K, clk, fields, ∂yᶜᶜᶜ, biharmonic_mask_y, ∇²ᶜᶠᶜ, fields.v)
@inline viscous_flux_wy(i, j, k, grid, closure::AIBD, K, clk, fields, b) = + ν_σᶜᶠᶠ(i, j, k, grid, closure, K, clk, fields, biharmonic_mask_y, ∂yᶜᶠᶠ, ∇²ᶜᶜᶠ, fields.w)
@inline viscous_flux_uz(i, j, k, grid, closure::AIBD, K, clk, fields, b) = + ν_σᶠᶜᶠ(i, j, k, grid, closure, K, clk, fields, biharmonic_mask_z, ∂zᶠᶜᶠ, ∇²ᶠᶜᶜ, fields.u)
@inline viscous_flux_vz(i, j, k, grid, closure::AIBD, K, clk, fields, b) = + ν_σᶜᶠᶠ(i, j, k, grid, closure, K, clk, fields, biharmonic_mask_z, ∂zᶜᶠᶠ, ∇²ᶜᶠᶜ, fields.v)
@inline viscous_flux_wz(i, j, k, grid, closure::AIBD, K, clk, fields, b) = + ν_σᶜᶜᶜ(i, j, k, grid, closure, K, clk, fields, ∂zᶜᶜᶜ, biharmonic_mask_z, ∇²ᶜᶜᶠ, fields.w)
@inline viscous_flux_ux(i, j, k, grid, closure::AHBD, K, clk, fields, b) = + ν_σᶜᶜᶜ(i, j, k, grid, closure, K, clk, fields, δ★ᶜᶜᶜ, fields.u, fields.v)
@inline viscous_flux_vx(i, j, k, grid, closure::AHBD, K, clk, fields, b) = + ν_σᶠᶠᶜ(i, j, k, grid, closure, K, clk, fields, ζ★ᶠᶠᶜ, fields.u, fields.v)
@inline viscous_flux_wx(i, j, k, grid, closure::AHBD, K, clk, fields, b) = + ν_σᶠᶜᶠ(i, j, k, grid, closure, K, clk, fields, biharmonic_mask_x, ∂xᶠᶜᶠ, ∇²ᶜᶜᶠ, fields.w)
@inline viscous_flux_uy(i, j, k, grid, closure::AHBD, K, clk, fields, b) = - ν_σᶠᶠᶜ(i, j, k, grid, closure, K, clk, fields, ζ★ᶠᶠᶜ, fields.u, fields.v)
@inline viscous_flux_vy(i, j, k, grid, closure::AHBD, K, clk, fields, b) = + ν_σᶜᶜᶜ(i, j, k, grid, closure, K, clk, fields, δ★ᶜᶜᶜ, fields.u, fields.v)
@inline viscous_flux_wy(i, j, k, grid, closure::AHBD, K, clk, fields, b) = + ν_σᶜᶠᶠ(i, j, k, grid, closure, K, clk, fields, biharmonic_mask_y, ∂yᶜᶠᶠ, ∇²ᶜᶜᶠ, fields.w)
@inline viscous_flux_uz(i, j, k, grid, closure::AVBD, K, clk, fields, b) = + ν_σᶠᶜᶠ(i, j, k, grid, closure, K, clk, fields, biharmonic_mask_z, ∂zᶠᶜᶠ, ∂²zᶠᶜᶜ, fields.u)
@inline viscous_flux_vz(i, j, k, grid, closure::AVBD, K, clk, fields, b) = + ν_σᶜᶠᶠ(i, j, k, grid, closure, K, clk, fields, biharmonic_mask_z, ∂zᶜᶠᶠ, ∂²zᶜᶠᶜ, fields.v)
@inline viscous_flux_wz(i, j, k, grid, closure::AVBD, K, clk, fields, b) = + ν_σᶜᶜᶜ(i, j, k, grid, closure, K, clk, fields, ∂zᶜᶜᶜ, biharmonic_mask_z, ∂²zᶜᶜᶠ, fields.w)

@inline viscous_flux_ux(i, j, k, grid, closure::ADBD, K, clk, fields, b) = + ν_σᶜᶜᶜ(i, j, k, grid, closure, K, clk, fields, δ★ᶜᶜᶜ, fields.u, fields.v)
@inline viscous_flux_vy(i, j, k, grid, closure::ADBD, K, clk, fields, b) = + ν_σᶜᶜᶜ(i, j, k, grid, closure, K, clk, fields, δ★ᶜᶜᶜ, fields.u, fields.v)

#####
##### Diffusive fluxes
Expand Down
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