Docstring rendering

docs/climaocean.bib

@@ -21,7 +21,7 @@ @article{large2009global
 
 @article{nishizawa2018surface,
   author = {Nishizawa, S. and Kitamura, Y.},
-  title = {A Surface Flux Scheme Based on the {Monin-Obukhov} Similarity for Finite Volume Models},
+  title = {A Surface Flux Scheme Based on the {Monin--Obukhov} Similarity for Finite Volume Models},
   journal = {Journal of Advances in Modeling Earth Systems},
   volume = {10},
   number = {12},
@@ -41,11 +41,11 @@ @article{stewart2020jra55
 }
 
 @article{tsujino2018jra,
-  title={JRA-55 based surface dataset for driving ocean--sea-ice models (JRA55-do)},
-  author={Tsujino, H and Urakawa, S and Nakano, H and Small, R J and Kim, W M and Yeager, S G and Danabasoglu, G and Suzuki, T and Bamber, J L and Bentsen, M and and B{\"o}ning, C and Bozec, A and Chassignet, E and Curchitser, E and Dias, F and Durack, P J and Griffies, S M and Harada, Y and Ilicak, M and Josey, S A and Kobayashi, C and Kobayashi, S and Komuro, Y and Large, W G and Sommer, J and Marsland, S J and Masina, S and Scheinert, M and Tomita, H and ValRdivieso, M and Yamazaki, D},
+  title={JRA-55 based surface dataset for driving ocean--sea-ice models ({JRA55-do})},
+  author={Tsujino, H and Urakawa, S and Nakano, H and Small, R J and Kim, W M and Yeager, S G and Danabasoglu, G and Suzuki, T and Bamber, J L and Bentsen, M and and B{\"o}ning, C and Bozec, A and Chassignet, E and Curchitser, E and Dias, F and Durack, P J and Griffies, S M and Harada, Y and Ilicak, M and Josey, S A and Kobayashi, C and Kobayashi, S and Komuro, Y and Large, W G and Sommer, J and Marsland, S J and Masina, S and Scheinert, M and Tomita, H and Valdivieso, M and Yamazaki, D},
   journal={Ocean Modelling},
   volume={130},
   pages={79--139},
   year={2018},
   doi={10.1016/j.ocemod.2018.07.002}
-}
+}

docs/src/index.md

@@ -3,7 +3,7 @@
 🌎 Realistic ocean-only and coupled ocean + sea-ice simulations driven by prescribed atmospheres and based on [Oceananigans](https://github.com/CliMA/Oceananigans.jl) and [ClimaSeaIce](https://github.com/CliMA/ClimaSeaIce.jl).
 
 ClimaOcean implements a framework for coupling prescribed or prognostic representations of the ocean, sea ice, and atmosphere state.
-Fluxes of heat, momentum, and freshwater are computed across the interfaces of its component models according to either Monin-Obukhov similarity theory,
+Fluxes of heat, momentum, and freshwater are computed across the interfaces of its component models according to either Monin--Obukhov similarity theory,
 or coefficient-based "bulk formula".
 ClimaOcean builds off Oceananigans, which provides tools for gridded finite volume computations on CPUs and GPUs and building ocean-flavored fluid dynamics simulations. ClimaSeaIce, which provides software for both stand-alone and coupled sea ice simulations, is also built with Oceananigans.
 

src/InitialConditions/InitialConditions.jl

@@ -72,4 +72,3 @@ end
 include("diffuse_tracers.jl")
 
 end # module
-

src/OceanSeaIceModels/InterfaceComputations/roughness_lengths.jl

@@ -180,14 +180,12 @@ struct ReynoldsScalingFunction{FT}
 end
 
 """
-    ReynoldsScalingFunction(FT=Float64; A=5.85e-5, b=0.72)
+    ReynoldsScalingFunction(FT = Oceananigans.defaults.FloatType; A = 5.85e-5, b = 0.72)
 
-
-Empirical fit of the scalar roughness length with roughness Reynolds number `R★ = u★ ℓu / ν`.
-Edson et al. (2013), equation (28).
+Empirical fit of the scalar roughness length with roughness Reynolds number `R_★ = u_★ ℓu / ν`.
 
 ```math
-    ℓs = A / R★ ^ b
+    ℓs = A / R_★ ^ b
 ```
 
 See equation (28) by [edson2013exchange](@citet).

src/OceanSeaIceModels/InterfaceComputations/similarity_theory_turbulent_fluxes.jl

@@ -67,7 +67,7 @@ end
                            solver_maxiter = 100)
 
 `SimilarityTheoryFluxes` contains parameters and settings to calculate
-air-interface turbulent fluxes using Monin-Obukhov similarity theory.
+air-interface turbulent fluxes using Monin--Obukhov similarity theory.
 
 Keyword Arguments
 ==================
@@ -127,21 +127,21 @@ end
 """
     LogarithmicSimilarityProfile()
 
-Represent the classic Monin-Obukhov similarity profile, which finds that
+Represent the classic Monin--Obukhov similarity profile, which finds that
 
 ```math
-ϕ(z) = Π(z) ϕ★ / ϰ
+ϕ(z) = Π(z) ϕ_★ / ϰ
 ```
 
-where ``ϰ`` is the Von Karman constant, ``ϕ★`` is the characteristic scale for ``ϕ``,
+where ``ϰ`` is the Von Karman constant, ``ϕ_★`` is the characteristic scale for ``ϕ``,
 and ``Π`` is the "similarity profile",
 
 ```math
-Π(h) = log(h / ℓ) - ψ(h / L) + ψ(ℓ / L)
+Π(h) = \\log(h / ℓ) - ψ(h / L) + ψ(ℓ / L)
 ```
 
 which is a logarithmic profile adjusted by the stability function ``ψ`` and dependent on
-the Monin-Obukhov length ``L`` and the roughness length ``ℓ``.
+the Monin--Obukhov length ``L`` and the roughness length ``ℓ``.
 """
 struct LogarithmicSimilarityProfile end
 struct COARELogarithmicSimilarityProfile end
@@ -189,7 +189,7 @@ function iterate_interface_fluxes(flux_formulation::SimilarityTheoryFluxes,
     # Compute surface thermodynamic state
     𝒬ₛ = AtmosphericThermodynamics.PhaseEquil_pTq(ℂₐ, 𝒬ₐ.p, Tₛ, qₛ)
 
-    # Compute Monin-Obukhov length scale depending on a `buoyancy flux`
+    # Compute Monin--Obukhov length scale depending on a `buoyancy flux`
     b★ = buoyancy_scale(θ★, q★, ℂₐ, 𝒬ₛ, g)
 
     # Buoyancy flux characteristic scale for gustiness (Edson et al. 2013)
@@ -231,30 +231,29 @@ end
 
 Return the characteristic buoyancy scale `b★` associated with
 the characteristic temperature `θ★`, specific humidity scale `q★`,
-surface thermodynamic state `𝒬`, thermodynamic
-parameters `ℂ`, and gravitational acceleration `g`.
+surface thermodynamic state `𝒬`, thermodynamic parameters `ℂ`,
+and gravitational acceleration `g`.
 
 The buoyancy scale is defined in terms of the interface buoyancy flux,
 
 ```math
-u★ b★ ≡ w′b′,
+u_★ b_★ ≡ w'b',
 ```
 
-where `u★` is the friction velocity.
+where `u_★` is the friction velocity.
 Using the definition of buoyancy for clear air without condensation, we find that
 
 ```math
-b★ = g / 𝒯ₛ * (θ★ * (1 + δ * qₐ) + δ * 𝒯ₛ * q★),
+b_★ = (g / 𝒯ₛ) [θ_★ (1 + δ qₐ) + δ 𝒯ₛ q_★] ,
 ```
-where ``𝒯ₐ`` is the virtual temperature at the surface,
-and ``δ = Rᵥ / R_d - 1``, where ``Rᵥ`` is the molar mass of water vapor and
-``R_d`` is the molar mass of dry air.
+where ``𝒯ₐ`` is the virtual temperature at the surface, and ``δ = Rᵥ / R_d - 1``,
+where ``Rᵥ`` is the molar mass of water vapor and ``R_d`` is the molar mass of dry air.
 
-Note that the Monin-Obukhov characteristic length scale is defined
-in terms of `b★` and additionally the Von Karman constant `ϰ`,
+Note that the Monin--Obukhov characteristic length scale is defined
+in terms of ``b_★`` and additionally the Von Karman constant ``ϰ``,
 
 ```math
-L★ = - u★² / ϰ b★ .
+L_★ = - u_★² / ϰ b_★ .
 ```
 """
 @inline function buoyancy_scale(θ★, q★, ℂ, 𝒬, g)