Merge pull request #269 from SpeedyWeather/mk/heldsuarez

Boundary layer scheme from Held and Suarez

src/SpeedyWeather.jl

@@ -1,143 +1,151 @@
 module SpeedyWeather
 
-    # STRUCTURE
-    import Parameters: @unpack
-
-    # NUMERICS
-    import Random
-    import FastGaussQuadrature
-    import LinearAlgebra: LinearAlgebra, Diagonal
-
-    # GPU, PARALLEL
-    import Base.Threads: Threads, @threads
-    import FLoops: FLoops, @floop
-    import KernelAbstractions
-    import CUDA
-    import CUDAKernels
-    import Adapt: Adapt, adapt, adapt_structure
-
-    # INPUT OUTPUT
-    import TOML
-    import Dates: Dates, DateTime
-    import Printf: @sprintf
-    import NetCDF: NetCDF, NcFile, NcDim, NcVar
-    import JLD2: jldopen
-    import CodecZlib
-    import BitInformation: round, round!
-    import UnicodePlots
-    import ProgressMeter
-
-    # EXPORT MAIN INTERFACE TO SPEEDY
-    export  run_speedy,
-            run_speedy!,
-            initialize_speedy
-
-    # EXPORT MODELS
-    export  Barotropic,
-            BarotropicModel,
-            ShallowWater,
-            ShallowWaterModel,
-            PrimitiveEquation,
-            PrimitiveDryCore,
-            PrimitiveWetCore,
-            PrimitiveDryCoreModel,
-            PrimitiveWetCoreModel
-
-    # EXPORT GRIDS
-    export  LowerTriangularMatrix,
-            FullClenshawGrid,
-            FullGaussianGrid,
-            FullHEALPixGrid,
-            FullOctaHEALPixGrid,
-            OctahedralGaussianGrid,
-            OctahedralClenshawGrid,
-            HEALPixGrid,
-            OctaHEALPixGrid
-
-    # EXPORT OROGRAPHIES
-    export  NoOrography,
-            EarthOrography,
-            ZonalRidge
-
-    # EXPORT INITIAL CONDITIONS
-    export  StartFromFile,
-            StartFromRest,
-            ZonalJet,
-            ZonalWind,
-            StartWithVorticity
-
-    # EXPORT STRUCTS
-    export  Parameters,
-            DynamicsConstants,
-            ParameterizationConstants,
-            Geometry,
-            SpectralTransform,
-            Boundaries,
-            PrognosticVariables,
-            DiagnosticVariables,
-            ColumnVariables
-
-    # EXPORT SPECTRAL FUNCTIONS
-    export  spectral,
-            gridded,
-            spectral_truncation
-
-    include("utility_functions.jl")
-    include("abstract_types.jl")
-
-    # LowerTriangularMatrices for spherical harmonics
-    export LowerTriangularMatrices
-    include("LowerTriangularMatrices/LowerTriangularMatrices.jl")
-    using .LowerTriangularMatrices
-
-    # RingGrids
-    export RingGrids
-    include("RingGrids/RingGrids.jl")
-    using .RingGrids
-
-    # SpeedyTransforms
-    export SpeedyTransforms
-    include("SpeedyTransforms/SpeedyTransforms.jl")
-    using .SpeedyTransforms
+# STRUCTURE
+import Parameters: @unpack
+
+# NUMERICS
+import Random
+import FastGaussQuadrature
+import LinearAlgebra: LinearAlgebra, Diagonal
+
+# GPU, PARALLEL
+import Base.Threads: Threads, @threads
+import FLoops: FLoops, @floop
+import KernelAbstractions
+import CUDA
+import CUDAKernels
+import Adapt: Adapt, adapt, adapt_structure
+
+# INPUT OUTPUT
+import TOML
+import Dates: Dates, DateTime
+import Printf: @sprintf
+import NetCDF: NetCDF, NcFile, NcDim, NcVar
+import JLD2: jldopen
+import CodecZlib
+import BitInformation: round, round!
+import UnicodePlots
+import ProgressMeter
+
+# EXPORT MAIN INTERFACE TO SPEEDY
+export  run_speedy,
+        run_speedy!,
+        initialize_speedy
+
+# EXPORT MODELS
+export  Barotropic,
+        BarotropicModel,
+        ShallowWater,
+        ShallowWaterModel,
+        PrimitiveEquation,
+        PrimitiveDryCore,
+        PrimitiveWetCore,
+        PrimitiveDryCoreModel,
+        PrimitiveWetCoreModel
+
+# EXPORT GRIDS
+export  LowerTriangularMatrix,
+        FullClenshawGrid,
+        FullGaussianGrid,
+        FullHEALPixGrid,
+        FullOctaHEALPixGrid,
+        OctahedralGaussianGrid,
+        OctahedralClenshawGrid,
+        HEALPixGrid,
+        OctaHEALPixGrid
+
+# EXPORT OROGRAPHIES
+export  NoOrography,
+        EarthOrography,
+        ZonalRidge
+
+# EXPORT INITIAL CONDITIONS
+export  StartFromFile,
+        StartFromRest,
+        ZonalJet,
+        ZonalJetCoefs,
+        ZonalWind,
+        ZonalWindCoefs,
+        StartWithVorticity
+
+# EXPORT BOUNDARY LAYER SCHEMES
+export  BoundaryLayer,
+        NoBoundaryLayer,
+        LinearDrag
+
+# EXPORT STRUCTS
+export  Parameters,
+        DynamicsConstants,
+        ParameterizationConstants,
+        Geometry,
+        SpectralTransform,
+        Boundaries,
+        PrognosticVariables,
+        DiagnosticVariables,
+        ColumnVariables
+
+# EXPORT SPECTRAL FUNCTIONS
+export  spectral,
+        gridded,
+        spectral_truncation
 
-    include("gpu.jl")                       # defines utility for GPU / KernelAbstractions
-    include("default_parameters.jl")        # defines Parameters
-
-    # DYNAMICS
-    include("dynamics/constants.jl")                # defines DynamicsConstants
-    include("dynamics/geometry.jl")                 # defines Geometry
-    include("dynamics/boundaries.jl")               # defines Boundaries
-    include("dynamics/define_diffusion.jl")         # defines HorizontalDiffusion
-    include("dynamics/define_implicit.jl")          # defines ImplicitShallowWater, ImplicitPrimitiveEq
-    include("dynamics/parameter_structs.jl")        # defines GenLogisticCoefs
-    include("dynamics/models.jl")                   # defines ModelSetups
-    include("dynamics/prognostic_variables.jl")     # defines PrognosticVariables
-    include("dynamics/diagnostic_variables.jl")     # defines DiagnosticVariables
-    include("dynamics/initial_conditions.jl")
-    include("dynamics/scaling.jl")
-    include("dynamics/geopotential.jl")
-    include("dynamics/tendencies_dynamics.jl")
-    include("dynamics/tendencies.jl")
-    include("dynamics/implicit.jl")
-    include("dynamics/diffusion.jl")
-    include("dynamics/time_integration.jl")
-
-    # PHYSICS
-    include("physics/constants.jl")                 # defines Parameterization Constants
-    include("physics/parameter_structs.jl")         # defines MagnusCoefs, RadiationCoefs
-    include("physics/column_variables.jl")          # defines ColumnVariables
-    include("physics/thermodynamics.jl")
-    include("physics/tendencies_parametrizations.jl")
-    include("physics/convection.jl")
-    include("physics/large_scale_condensation.jl")
-    include("physics/longwave_radiation.jl")
-    include("physics/shortwave_radiation.jl")
-
-    # OUTPUT
-    include("output/output.jl")                     # defines Output
-    include("output/feedback.jl")                   # defines Feedback
-    include("output/pretty_printing.jl")
+include("utility_functions.jl")
+include("abstract_types.jl")
+
+# LowerTriangularMatrices for spherical harmonics
+export LowerTriangularMatrices
+include("LowerTriangularMatrices/LowerTriangularMatrices.jl")
+using .LowerTriangularMatrices
+
+# RingGrids
+export RingGrids
+include("RingGrids/RingGrids.jl")
+using .RingGrids
+
+# SpeedyTransforms
+export SpeedyTransforms
+include("SpeedyTransforms/SpeedyTransforms.jl")
+using .SpeedyTransforms
 
-    # INTERFACE
-    include("run_speedy.jl")
+include("gpu.jl")                       # defines utility for GPU / KernelAbstractions
+include("default_parameters.jl")        # defines Parameters
+
+# DYNAMICS
+include("dynamics/constants.jl")                # defines DynamicsConstants
+include("dynamics/geometry.jl")                 # defines Geometry
+include("dynamics/boundaries.jl")               # defines Boundaries
+include("dynamics/define_diffusion.jl")         # defines HorizontalDiffusion
+include("dynamics/define_implicit.jl")          # defines ImplicitShallowWater, ImplicitPrimitiveEq
+include("dynamics/parameter_structs.jl")        # defines GenLogisticCoefs
+include("dynamics/models.jl")                   # defines ModelSetups
+include("dynamics/prognostic_variables.jl")     # defines PrognosticVariables
+include("dynamics/diagnostic_variables.jl")     # defines DiagnosticVariables
+include("dynamics/initial_conditions.jl")
+include("dynamics/scaling.jl")
+include("dynamics/geopotential.jl")
+include("dynamics/tendencies_dynamics.jl")
+include("dynamics/tendencies.jl")
+include("dynamics/implicit.jl")
+include("dynamics/diffusion.jl")
+include("dynamics/time_integration.jl")
+
+# PHYSICS
+include("physics/constants.jl")                 # defines Parameterization Constants
+include("physics/parameter_structs.jl")         # defines MagnusCoefs, RadiationCoefs
+include("physics/column_variables.jl")          # defines ColumnVariables
+include("physics/thermodynamics.jl")
+include("physics/tendencies.jl")
+include("physics/convection.jl")
+include("physics/large_scale_condensation.jl")
+include("physics/longwave_radiation.jl")
+include("physics/shortwave_radiation.jl")
+include("physics/boundary_layer.jl")
+
+# OUTPUT
+include("output/output.jl")                     # defines Output
+include("output/feedback.jl")                   # defines Feedback
+include("output/pretty_printing.jl")
+
+# INTERFACE
+include("run_speedy.jl")
 end

src/abstract_types.jl

@@ -25,6 +25,9 @@ abstract type AbstractBoundaries{NF} end
 # ATMOSPHERIC COLUMN FOR PARAMETERIZATIONS
 abstract type AbstractColumnVariables{NF} end
 
+# PARAMETERIZATIONS
+abstract type BoundaryLayer end
+
 # INPUT/OUTPUT
 abstract type AbstractFeedback end
 abstract type AbstractOutput end

src/default_parameters.jl

@@ -95,6 +95,9 @@ Base.@kwdef struct Parameters{Model<:ModelSetup} <: AbstractParameters{Model}
     # Radiation
     radiation_coefs::Coefficients = RadiationCoefs{NF}()
 
+    # BOUNDARY LAYER
+    boundary_layer::BoundaryLayer = LinearDrag{NF}()
+
     # TIME STEPPING
     startdate::DateTime = DateTime(2000,1,1)    # time at which the integration starts
     n_days::Float64 = 10                        # number of days to integrate for

src/dynamics/tendencies.jl

@@ -1,23 +1,24 @@
 """
-    get_tendencies!(diagn,model)
+    dynamics_tendencies!(diagn,model)
 
 Calculate all tendencies for the BarotropicModel."""
-function get_tendencies!(   diagn::DiagnosticVariablesLayer,
-                            model::BarotropicModel)
+function dynamics_tendencies!(  diagn::DiagnosticVariablesLayer,
+                                model::BarotropicModel)
 
     # only (absolute) vorticity advection for the barotropic model
     vorticity_flux_divcurl!(diagn,model,curl=false)         # = -∇⋅(u(ζ+f),v(ζ+f))
 end
 
 """
-    get_tendencies!(diagn,surface,pres,time,model)
+    dynamics_tendencies!(diagn,surface,pres,time,model)
 
 Calculate all tendencies for the ShallowWaterModel."""
-function get_tendencies!(   diagn::DiagnosticVariablesLayer,
-                            surface::SurfaceVariables,
-                            pres::LowerTriangularMatrix,    # spectral pressure/η for geopotential
-                            time::DateTime,                 # time to evaluate the tendencies at
-                            model::ShallowWaterModel)       # struct containing all constants
+function dynamics_tendencies!(  diagn::DiagnosticVariablesLayer,
+                                surface::SurfaceVariables,
+                                pres::LowerTriangularMatrix,    # spectral pressure/η for geopotential
+                                time::DateTime,                 # time to evaluate the tendencies at
+                                model::ShallowWaterModel)       # struct containing all constants
+
     S,C = model.spectral_transform, model.constants
 
     # for compatibility with other ModelSetups pressure pres = interface displacement η here
@@ -33,23 +34,17 @@ function get_tendencies!(   diagn::DiagnosticVariablesLayer,
 end
 
 """
-    get_tendencies!(diagn,surface,pres,time,model)
+    dynamics_tendencies!(diagn,surface,pres,time,model)
 
 Calculate all tendencies for the primitive equation model (wet or dry)."""
-function get_tendencies!(   diagn::DiagnosticVariables,
-                            progn::PrognosticVariables,
-                            time::DateTime,
-                            model::PrimitiveEquation,
-                            lf::Int=2               # leapfrog index for tendencies
-                            )
+function dynamics_tendencies!(  diagn::DiagnosticVariables,
+                                progn::PrognosticVariables,
+                                model::PrimitiveEquation,
+                                lf::Int=2)               # leapfrog index for tendencies
 
     B, G, S = model.boundaries, model.geometry, model.spectral_transform
     @unpack surface = diagn
 
-    # PARAMETERIZATIONS
-    # parameterization_tendencies!(diagn,time,model)
-
-    # DYNAMICS
     # for semi-implicit corrections (α >= 0.5) linear gravity-wave related tendencies are
     # evaluated at previous timestep i-1 (i.e. lf=1 leapfrog time step) 
     # nonlinear terms and parameterizations are always evaluated at lf

src/dynamics/tendencies_dynamics.jl

@@ -297,7 +297,9 @@ function _vertical_advection!(  ξ_tend::Grid,           # tendency of quantity
                                 Δσₖ::NF                 # layer thickness on σ levels
                                 ) where {NF<:AbstractFloat,Grid<:AbstractGrid{NF}}
     Δσₖ2⁻¹ = -1/2Δσₖ                                    # precompute
-    @. ξ_tend = Δσₖ2⁻¹ * (σ_tend_below*(ξ_below - ξ) + σ_tend_above*(ξ - ξ_above))
+
+    # += as the tendencies already contain the parameterizations
+    @. ξ_tend += Δσₖ2⁻¹ * (σ_tend_below*(ξ_below - ξ) + σ_tend_above*(ξ - ξ_above))
 end
 
 function vordiv_tendencies!(diagn::DiagnosticVariablesLayer,