Merge branch 'refactor/soil-module' into 'master'

Move Soil to Physics module and rename Water -> WaterBalance

See merge request sparcs/cryogrid/cryogridjulia!65

Project.toml

 name = "CryoGrid"
 uuid = "a535b82e-5f3d-4d97-8b0b-d6483f5bebd5"
 authors = ["Brian Groenke <brian.groenke@awi.de>", "Moritz Langer <moritz.langer@awi.de>"]
-version = "0.5.8"
+version = "0.6.0"
 
 [deps]
 ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"

docs/make.jl

@@ -7,10 +7,11 @@ const modules = [
        CryoGrid,
        CryoGrid.Utils,
        CryoGrid.Numerics,
-       CryoGrid.Layers,
        CryoGrid.Physics,
        CryoGrid.Boundaries,
        CryoGrid.HeatConduction,
+       CryoGrid.WaterBalance,
+       CryoGrid.Soils,
        CryoGrid.SEB,
        CryoGrid.Strat,
        CryoGrid.Presets,
@@ -34,6 +35,8 @@ makedocs(modules=modules,
                        "Utilities" => "api/utils.md",
                        "Physics" => [
                             "Heat Conduction" => "api/heat_conduction.md",
+                            "Water Balance" => "api/water_balance.md",
+                            "Soils" => "api/soils.md",
                             "Surface Energy Balance" => "api/seb.md",
                        ],
                        "Stratigraphy" => "api/strat.md",

docs/src/api/soils.md

+# Soils
+
+```@autodocs
+Modules = [Soils]
+Private = false
+Order = [:type, :function, :macro]
+```
\ No newline at end of file

docs/src/api/water_balance.md

+# Water balance
+
+```@autodocs
+Modules = [WaterBalance]
+Private = false
+Order = [:type, :function, :macro]
+```
\ No newline at end of file

src/CryoGrid.jl

@@ -22,7 +22,6 @@ include("methods.jl")
 # Submodules
 include("Utils/Utils.jl")
 include("Numerics/Numerics.jl")
-include("Layers/Layers.jl")
 include("Physics/Physics.jl")
 include("Strat/Strat.jl")
 include("IO/InputOutput.jl")
@@ -33,7 +32,6 @@ using .Utils
 # Re-exported submodules
 @reexport using .Numerics
 @reexport using .Utils: convert_tspan
-@reexport using .Layers
 @reexport using .Physics
 @reexport using .Strat
 @reexport using .Drivers

src/Layers/Layers.jl

-module Layers
-
-import CryoGrid: SubSurface
-import CryoGrid: initialcondition!, variables
-
-using CryoGrid.Numerics
-using CryoGrid.Utils
-
-using DimensionalData
-using IntervalSets
-using ModelParameters
-using Parameters
-using Unitful
-
-export Soil, SoilParameterization, SoilCharacteristicFractions, SoilProfile, SoilType, Sand, Silt, Clay
-export soilparameters, soilcomp, porosity
-include("soil.jl")
-
-end
\ No newline at end of file

src/Physics/HeatConduction/HeatConduction.jl

@@ -2,27 +2,20 @@ module HeatConduction
 
 import CryoGrid: SubSurfaceProcess, BoundaryStyle, Dirichlet, Neumann, BoundaryProcess, Layer, Top, Bottom, SubSurface, Callback
 import CryoGrid: diagnosticstep!, prognosticstep!, interact!, initialcondition!, boundaryflux, boundaryvalue, variables, callbacks, criterion, affect!
-import CryoGrid.Layers: Soil, totalwater, porosity, mineral, organic
 
 using CryoGrid.Physics
 using CryoGrid.Physics.Boundaries
-using CryoGrid.Physics.Water: VanGenuchten
 using CryoGrid.Numerics
 using CryoGrid.Numerics: nonlineardiffusion!, harmonicmean!, harmonicmean, heaviside
 using CryoGrid.Utils
 
 using Base: @propagate_inbounds
-using DimensionalData
 using IfElse
-using Interpolations: Linear, Flat
-using IntervalSets
 using ModelParameters
 using Parameters
 using SimulationLogs
 using Unitful
 
-import Flatten: @flattenable, flattenable
-
 export Heat, TemperatureProfile
 export FreeWater, FreezeCurve, freezecurve
 
@@ -53,11 +46,9 @@ variables(::SubSurface, ::Heat, ::FreezeCurve) = ()
 # Fallback (error) implementation for freeze curve
 (fc::FreezeCurve)(sub::SubSurface, heat::Heat, state) = error("freeze curve $(typeof(fc)) not implemented for $(typeof(heat)) on layer $(typeof(sub))")
 
-export heatconduction!, enthalpy, heatcapacity, heatcapacity!, thermalconductivity, thermalconductivity!
+export heatconduction!, enthalpy, totalwater, liquidwater, heatcapacity, heatcapacity!, thermalconductivity, thermalconductivity!
 include("heat.jl")
 export ConstantTemp, GeothermalHeatFlux, TemperatureGradient, NFactor, Damping
 include("heat_bc.jl")
-export SFCC, DallAmico, Westermann, McKenzie, SFCCNewtonSolver
-include("soil/soilheat.jl")
 
 end

src/Physics/Physics.jl

@@ -3,7 +3,6 @@ module Physics
 import CryoGrid: Process, CoupledProcesses, Coupled, Layer, Top, Bottom, SubSurface
 import CryoGrid: diagnosticstep!, initialcondition!, interact!, prognosticstep!, variables, callbacks, observe
 
-using CryoGrid.Layers
 using CryoGrid.Numerics
 using CryoGrid.Utils
 
@@ -13,13 +12,15 @@ using Unitful
 
 include("coupled.jl")
 include("Boundaries/Boundaries.jl")
-include("Water/Water.jl")
+include("WaterBalance/WaterBalance.jl")
 include("HeatConduction/HeatConduction.jl")
+include("Soils/Soils.jl")
 include("SEB/SEB.jl")
 include("Sources/Sources.jl")
 
 @reexport using .Boundaries
 @reexport using .HeatConduction
+@reexport using .Soils
 @reexport using .SEB
 @reexport using .Sources
 

src/Physics/SEB/SEB.jl

@@ -3,7 +3,7 @@ module SEB
 using ..HeatConduction: Heat
 using ..Physics
 using ..Boundaries
-using CryoGrid.Layers: Soil
+using CryoGrid.Physics.Soils
 using CryoGrid.Numerics
 using CryoGrid.Utils
 

src/Layers/soil.jl → src/Physics/Soils/Soils.jl

+module Soils
+
+import CryoGrid: SubSurface
+import CryoGrid: initialcondition!, variables
+import CryoGrid.Physics.HeatConduction: Enthalpy, Temperature, totalwater, liquidwater, thermalconductivity, heatcapacity
+
+using CryoGrid.Numerics
+using CryoGrid.Numerics: heaviside
+using CryoGrid.Physics.HeatConduction
+using CryoGrid.Physics.WaterBalance
+using CryoGrid.Utils
+
+using Base: @propagate_inbounds
+using IfElse
+using ModelParameters
+using Parameters
+using Unitful
+
+import Flatten: @flattenable, flattenable
+
+export Soil, SoilParameterization, SoilCharacteristicFractions, SoilProfile, SoilType, Sand, Silt, Clay
+export soilparameters, soilcomp, porosity, mineral, organic
+
 """
 Represents the texture classification of the soil. Sand, Silt, and Clay are provided by default.
 """
@@ -69,3 +92,8 @@ totalwater(soil::Soil{T,<:SoilCharacteristicFractions}) where T = soilcomp(Val{:
 porosity(soil::Soil{T,<:SoilCharacteristicFractions}) where T = soilcomp(Val{:θp}(), soil.para)
 mineral(soil::Soil{T,<:SoilCharacteristicFractions}) where T = soilcomp(Val{:θm}(), soil.para)
 organic(soil::Soil{T,<:SoilCharacteristicFractions}) where T = soilcomp(Val{:θo}(), soil.para)
+
+export SFCC, DallAmico, Westermann, McKenzie, SFCCNewtonSolver
+include("soilheat.jl")
+
+end
\ No newline at end of file

src/Physics/Water/Water.jl → src/Physics/WaterBalance/WaterBalance.jl

-module Water
+module WaterBalance
 
 import CryoGrid: BoundaryStyle, diagnosticstep!, prognosticstep!, interact!, initialcondition!, variables
 

src/Strat/Strat.jl

@@ -3,7 +3,6 @@ module Strat
 import CryoGrid: Layer, Top, Bottom, SubSurface, Process, SubSurfaceProcess, BoundaryProcess, CoupledProcesses
 import CryoGrid: variables, initialcondition!, prognosticstep!, diagnosticstep!, interact!, observe
 
-using CryoGrid.Layers
 using CryoGrid.Numerics
 using CryoGrid.Physics
 using CryoGrid.Utils

test/Physics/HeatConduction/sfcc_tests.jl

@@ -7,10 +7,10 @@ using ComponentArrays
     Tₘ = 0.0
     θres = 0.0
     soil = Soil(para=soilparameters())
-    θw = Layers.soilcomp(Val{:θw}(), soil.para)
-    θp = Layers.soilcomp(Val{:θp}(), soil.para)
-    θm = Layers.soilcomp(Val{:θm}(), soil.para)
-    θo = Layers.soilcomp(Val{:θo}(), soil.para)
+    θw = Soils.soilcomp(Val{:θw}(), soil.para)
+    θp = Soils.soilcomp(Val{:θp}(), soil.para)
+    θm = Soils.soilcomp(Val{:θm}(), soil.para)
+    θo = Soils.soilcomp(Val{:θo}(), soil.para)
     @testset "McKenzie freeze curve" begin
         @testset "Sanity checks" begin
             f = McKenzie()
@@ -244,10 +244,10 @@ function benchmarksfcc()
     L = heat.L
     # set up multi-grid-cell state vars
     T = [-15.0 for i in 1:10]
-    θw = Layers.soilcomp(Val{:θw}(), soil.para)
-    θp = Layers.soilcomp(Val{:θp}(), soil.para)
-    θm = Layers.soilcomp(Val{:θm}(), soil.para)
-    θo = Layers.soilcomp(Val{:θo}(), soil.para)
+    θw = Soils.soilcomp(Val{:θw}(), soil.para)
+    θp = Soils.soilcomp(Val{:θp}(), soil.para)
+    θm = Soils.soilcomp(Val{:θm}(), soil.para)
+    θo = Soils.soilcomp(Val{:θo}(), soil.para)
     θl = f.(T,Tₘ,θres,θp,θw,L,α,n) # set liquid water content according to freeze curve
     C = heatcapacity.(soil,θw,θl,θm,θo)
     H = let T = T.+14.999,