Fix failing tests and remove Presets submodule

README.md

@@ -51,12 +51,12 @@ using Plots: plot
 # The forcing file will be automatically downloaded to the input/ folder if not already present.
 forcings = loadforcings(CryoGrid.Forcings.Samoylov_ERA_obs_fitted_1979_2014_spinup_extended_2044);
 # get preset soil and initial temperature profile for Samoylov
-soilprofile, tempprofile = CryoGrid.Presets.SamoylovDefault
+soilprofile, tempprofile = CryoGrid.SamoylovDefault
 initT = initializer(:T, tempprofile)
 # choose grid with 5cm spacing
-grid = CryoGrid.Presets.DefaultGrid_5cm
+grid = CryoGrid.DefaultGrid_5cm
 # build a default Tile with heat conduction on the given soil profile
-tile = CryoGrid.Presets.SoilHeatTile(
+tile = CryoGrid.SoilHeatTile(
     TemperatureBC(forcings.Tair),
     GeothermalHeatFlux(0.053u"W/m^2"),
     soilprofile,

docs/src/manual/architecture.md

@@ -65,7 +65,7 @@ using CryoGrid
 using CryoGrid.Diagnostics
 
 soil = Ground()
-grid = CryoGrid.Presets.DefaultGrid_5cm
+grid = CryoGrid.DefaultGrid_5cm
 state = Diagnostics.build_dummy_state(grid, soil)
 
 @which CryoGrid.computediagnostic!(soil, state)

docs/src/manual/overview.md

@@ -18,7 +18,7 @@ strat = Stratigraphy(
     0.0u"m" => Ground(soilprofile, HeatBalance(:H; freezecurve=DallAmico())),
     1000.0u"m" => Bottom(GeothermalHeatFlux(0.053u"J/s/m^2"))
 );
-grid = CryoGrid.Presets.DefaultGrid_5cm
+grid = CryoGrid.DefaultGrid_5cm
 # define initial conditions for temperature using a given profile;
 # The default initializer linearly interpolates between profile points.
 initT = initializer(:T, tempprofile)

docs/src/quickstart.md

 ## Quick start
 
-After [installing](installation.md) `CryoGrid.jl`, you can get started right away with a simple soil heat model. The [`Presets`](@ref) module (aliased `CryoGrid.Presets`) provides pre-specified model configurations that can be obtained with a single function call. It is also possible to provide a custom soil and temperature profile to `SoilHeatTile`; here the values given in `Presets.SamoylovDefault` is used.
+After [installing](installation.md) `CryoGrid.jl`, you can get started right away with a simple soil heat model. The [`Presets`](@ref) module (aliased `CryoGrid.Presets`) provides pre-specified model configurations that can be obtained with a single function call. It is also possible to provide a custom soil and temperature profile to `SoilHeatTile`; here the values given in `SamoylovDefault` is used.
 
 ```julia
 using CryoGrid
@@ -10,12 +10,12 @@ using Plots
 # The forcing file will be automatically downloaded to the input/ folder if not already present.
 forcings = loadforcings(CryoGrid.Forcings.Samoylov_ERA_obs_fitted_1979_2014_spinup_extended_2044, :Tair => u"°C");
 # get preset soil and initial temperature profile for Samoylov
-soilprofile, tempprofile = CryoGrid.Presets.SamoylovDefault
+soilprofile, tempprofile = CryoGrid.SamoylovDefault
 initT = initializer(:T, tempprofile)
 # choose grid with 5cm spacing
-grid = CryoGrid.Presets.DefaultGrid_5cm
+grid = CryoGrid.DefaultGrid_5cm
 # build Tile from the given soil and temperature profiles
-tile = CryoGrid.Presets.SoilHeatTile(TemperatureBC(forcings.Tair), GeothermalHeatFlux(0.053u"W/m^2"), soilprofile, initT, grid=grid)
+tile = CryoGrid.SoilHeatTile(TemperatureBC(forcings.Tair), GeothermalHeatFlux(0.053u"W/m^2"), soilprofile, initT, grid=grid)
 # define time span (1 year)
 tspan = (DateTime(2010,11,30),DateTime(2011,11,30))
 u0, du0 = initialcondition!(tile, tspan)

examples/cglite_parameter_ensembles.jl

@@ -42,7 +42,7 @@ strat = Stratigraphy(
     soil_layers,
     z_bot => Bottom(GeothermalHeatFlux(0.053u"W/m^2"))
 );
-modelgrid = CryoGrid.Presets.DefaultGrid_2cm
+modelgrid = CryoGrid.DefaultGrid_2cm
 tile = Tile(strat, modelgrid, ssinit);
 # Since the solver can take daily timesteps, we can easily specify longer simulation time spans at minimal cost.
 # Here we specify a time span of 10 years.

examples/heat_freeW_bucketW_samoylov.jl

@@ -6,7 +6,7 @@
 # Frist, load forcings and define boundary conditions.
 using CryoGrid
 forcings = loadforcings(CryoGrid.Forcings.Samoylov_ERA_obs_fitted_1979_2014_spinup_extended_2044);
-_, tempprofile = CryoGrid.Presets.SamoylovDefault;
+_, tempprofile = CryoGrid.SamoylovDefault;
 initT = initializer(:T, tempprofile)
 initsat = initializer(:sat, (l,state) -> state.sat .= l.para.sat);
 upperbc = WaterHeatBC(
@@ -23,7 +23,7 @@ strat = @Stratigraphy(
     2.0u"m" => Ground(SimpleSoil(por=0.10,sat=1.0,org=0.0), heat=HeatBalance(), water=WaterBalance(BucketScheme())),
     1000.0u"m" => Bottom(GeothermalHeatFlux(0.053u"W/m^2")),
 );
-modelgrid = CryoGrid.Presets.DefaultGrid_2cm
+modelgrid = CryoGrid.DefaultGrid_2cm
 tile = Tile(strat, modelgrid, forcings, initT, initsat);
 
 # Now we set up the problem and solve using the integrator interface.

examples/heat_freeW_lake_lite_implicit.jl

@@ -20,7 +20,7 @@ tempprofile_linear = TemperatureProfile(
     10.0u"m" => -10.0u"°C", 
     1000.0u"m" => 10.2u"°C"
 )
-modelgrid = Grid(vcat(-1.0u"m":0.02u"m":-0.02u"m", CryoGrid.Presets.DefaultGrid_2cm))
+modelgrid = Grid(vcat(-1.0u"m":0.02u"m":-0.02u"m", CryoGrid.DefaultGrid_2cm))
 z_top = -1.0u"m"
 z_sub = keys(soilprofile)
 z_bot = modelgrid[end]

examples/heat_freeW_lite_implicit.jl

@@ -36,7 +36,7 @@ strat = @Stratigraphy(
     soil_layers...,
     z_bot => Bottom(GeothermalHeatFlux(0.053u"W/m^2"))
 );
-modelgrid = Grid(vcat(z_top:0.02u"m":-0.02u"m", CryoGrid.Presets.DefaultGrid_2cm))
+modelgrid = Grid(vcat(z_top:0.02u"m":-0.02u"m", CryoGrid.DefaultGrid_2cm))
 tile = Tile(strat, modelgrid, forcings, ssinit);
 
 # Since the solver can take daily timesteps, we can easily specify longer simulation time spans at minimal cost.

examples/heat_freeW_samoylov.jl

@@ -23,14 +23,14 @@ soilprofile = SoilProfile(
 );
 
 # We construct a state variable initializer for temperature `T` from the temperature profile preset for Samoylov.
-initT = initializer(:T, CryoGrid.Presets.SamoylovDefault.tempprofile);
+initT = initializer(:T, CryoGrid.SamoylovDefault.tempprofile);
 
 # We choose the default grid discretization with 5 cm spacing at the surface.
 grid = CryoGrid.DefaultGrid_5cm;
 
 # Now we construct the Tile using the built-in model configuration `SoilHeatTile` which defines a
 # standalone soil straigraphy with only heat conduction and no water flow.
-tile = CryoGrid.Presets.SoilHeatTile(
+tile = CryoGrid.SoilHeatTile(
     :H,
     TemperatureBC(Input(:Tair), NFactor(nf=Param(0.6), nt=Param(0.9))),
     GeothermalHeatFlux(0.053u"W/m^2"),
@@ -59,7 +59,4 @@ out = CryoGridOutput(sol)
 import Plots
 zs = [1,10,20,30,50,100,200,500,1000]u"cm"
 cg = Plots.cgrad(:copper,rev=true);
-Plots.plot(out.T[Z(Near(zs))], color=cg[LinRange(0.0,1.0,length(zs))]', ylabel="Temperature", leg=false, size=(800,500), dpi=150)
-
-using BenchmarkTools
-@profview @btime $tile($du0, $u0, $prob.p, $prob.tspan[1])
+Plots.plot(out.T[Z(Near(zs))], color=cg[LinRange(0.0,1.0,length(zs))]', ylabel="Temperature", leg=false, size=(800,500), dpi=150)
\ No newline at end of file

examples/heat_freeW_seb_snow_bucketW_samoylov.jl

@@ -8,7 +8,7 @@ using CryoGrid
 using OrdinaryDiffEq
 
 # First, load the forcings and construct the Tile.
-modelgrid = CryoGrid.Presets.DefaultGrid_2cm;
+modelgrid = CryoGrid.DefaultGrid_2cm;
 soilprofile = SoilProfile(
     0.0u"m" => SimpleSoil(por=0.80,sat=1.0,org=0.75),
     0.1u"m" => SimpleSoil(por=0.80,sat=1.0,org=0.25),
@@ -17,9 +17,9 @@ soilprofile = SoilProfile(
     10.0u"m" => SimpleSoil(por=0.30,sat=1.0,org=0.0),
 );
 ## mid-winter temperature profile
-tempprofile = CryoGrid.Presets.SamoylovDefault.tempprofile
+tempprofile = CryoGrid.SamoylovDefault.tempprofile
 forcings = loadforcings(CryoGrid.Forcings.Samoylov_ERA_obs_fitted_1979_2014_spinup_extended_2044);
-tempprofile = CryoGrid.Presets.SamoylovDefault.tempprofile
+tempprofile = CryoGrid.SamoylovDefault.tempprofile
 initT = initializer(:T, tempprofile)
 seb = SurfaceEnergyBalance()
 swb = SurfaceWaterBalance()

examples/heat_freeW_snow_samoylov.jl

@@ -15,7 +15,7 @@ soilprofile = SoilProfile(
     3.0u"m" => SimpleSoil(por=0.50,sat=1.0,org=0.0),
     10.0u"m" => SimpleSoil(por=0.30,sat=1.0,org=0.0),
 );
-initT = initializer(:T, CryoGrid.Presets.SamoylovDefault.tempprofile)
+initT = initializer(:T, CryoGrid.SamoylovDefault.tempprofile)
 initsat = initializer(:sat, 1.0)
 z_top = -2.0u"m"
 z_sub = keys(soilprofile)
@@ -39,7 +39,7 @@ strat = @Stratigraphy(
     ground_layers...,
     z_bot => Bottom(GeothermalHeatFlux(0.053u"J/s/m^2"))
 );
-modelgrid = CryoGrid.Presets.DefaultGrid_5cm
+modelgrid = CryoGrid.DefaultGrid_5cm
 tile = Tile(strat, modelgrid, forcings, initT, initsat)
 # define time span, 2 years + 3 months
 tspan = (DateTime(2010,9,30), DateTime(2012,9,30))

examples/heat_sfcc_constantbc.jl

@@ -8,7 +8,7 @@
 using CryoGrid
 
 # Select default grid and initial temperature profile.
-grid = CryoGrid.Presets.DefaultGrid_10cm
+grid = CryoGrid.DefaultGrid_10cm
 tempprofile = TemperatureProfile(
     0.0u"m" => -20.0u"°C",
     1000.0u"m" => 10.0u"°C",
@@ -31,7 +31,7 @@ Plots.plot(-2.0u"°C":0.01u"K":0.0u"°C", sfcc)
 # specified.
 heatop = Heat.Diffusion1D(:H)
 initT = initializer(:T, tempprofile)
-tile = CryoGrid.Presets.SoilHeatTile(
+tile = CryoGrid.SoilHeatTile(
     heatop,
     ## 10 W/m^2 in and out, i.e. net zero flux
     ConstantBC(HeatBalance, CryoGrid.Neumann, 10.0u"W/m^2"),

examples/heat_sfcc_richardseq_samoylov.jl

@@ -38,7 +38,7 @@ strat = @Stratigraphy(
     2.0u"m" => Ground(SimpleSoil(por=0.10,sat=1.0,org=0.0,freezecurve=sfcc); heat, water),
     1000.0u"m" => Bottom(GeothermalHeatFlux(0.053u"W/m^2"))
 );
-grid = CryoGrid.Presets.DefaultGrid_2cm
+grid = CryoGrid.DefaultGrid_2cm
 tile = Tile(strat, grid, forcings, initT);
 u0, du0 = @time initialcondition!(tile, tspan)
 prob = CryoGridProblem(tile, u0, tspan, saveat=3*3600, savevars=(:T,:θw,:θwi,:kw));

examples/heat_sfcc_salt_constantbc.jl

@@ -14,7 +14,7 @@ strat = @Stratigraphy(
     0.0u"m" => SalineGround(SimpleSoil(freezecurve=sfcc), heat=HeatBalance(:T), salt=SaltMassBalance()),
     1000.0u"m" => Bottom(GeothermalHeatFlux(0.053u"W/m^2"))
 );
-modelgrid = CryoGrid.Presets.DefaultGrid_10cm
+modelgrid = CryoGrid.DefaultGrid_10cm
 tile = Tile(strat, modelgrid, initT, initsalt, initpor)
 tspan = (DateTime(1990,1,1),DateTime(2000,12,31))
 u0, du0 = initialcondition!(tile, tspan)

examples/heat_sfcc_samoylov.jl

@@ -5,14 +5,15 @@
 
 using CryoGrid
 
-# First we set up the soil heat model:
+# First we set up the soil heat model. Note that the default soil profile
+# for Samoylov already includes the appropriate freeze curves.
 forcings = loadforcings(CryoGrid.Forcings.Samoylov_ERA5_fitted_daily_1979_2020);
-grid = CryoGrid.Presets.DefaultGrid_5cm
-soilprofile, tempprofile = CryoGrid.Presets.SamoylovDefault
+grid = CryoGrid.DefaultGrid_5cm
+soilprofile, tempprofile = CryoGrid.SamoylovDefault
 initT = initializer(:T, tempprofile)
 upperbc = TemperatureBC(Input(:Tair), NFactor(nf=0.6, nt=0.9))
 lowerbc = GeothermalHeatFlux(0.053u"W/m^2")
-tile = CryoGrid.Presets.SoilHeatTile(upperbc, lowerbc, soilprofile, forcings, initT; grid=grid)
+tile = CryoGrid.SoilHeatTile(upperbc, lowerbc, soilprofile, forcings, initT; grid=grid)
 tspan = (DateTime(2010,10,30),DateTime(2011,10,30))
 u0, du0 = @time initialcondition!(tile, tspan)
 prob = CryoGridProblem(tile, u0, tspan, saveat=3*3600.0, savevars=(:T,));

examples/heat_simple_autodiff_grad.jl

@@ -7,10 +7,10 @@
 # Set up forcings and boundary conditions similarly to other examples:
 using CryoGrid
 forcings = loadforcings(CryoGrid.Forcings.Samoylov_ERA_obs_fitted_1979_2014_spinup_extended_2044);
-soilprofile, tempprofile = CryoGrid.Presets.SamoylovDefault
-grid = CryoGrid.Presets.DefaultGrid_5cm
+soilprofile, tempprofile = CryoGrid.SamoylovDefault
+grid = CryoGrid.DefaultGrid_5cm
 initT = initializer(:T, tempprofile)
-tile = CryoGrid.Presets.SoilHeatTile(
+tile = CryoGrid.SoilHeatTile(
     :T,
     TemperatureBC(Input(:Tair), NFactor(nf=Param(0.5), nt=Param(0.9))),
     GeothermalHeatFlux(0.053u"W/m^2"),

src/CryoGrid.jl

@@ -36,6 +36,8 @@ import Interpolations
 @reexport using Unitful
 @reexport using UnPack
 
+using SciMLBase: intervals # resolve name collision
+
 export Interpolations
 
 # Common types and methods
@@ -79,6 +81,7 @@ include("IO/InputOutput.jl")
 
 include("Tiles/Tiles.jl")
 @reexport using .Tiles
+using .Tiles: layers # resolve name collision
 parameters = Tiles.parameters
 
 export ConstantBC, PeriodicBC, ConstantValue, PeriodicValue, ConstantFlux, PeriodicFlux
@@ -99,8 +102,9 @@ include("problem.jl")
 export CGEuler, CryoGridIntegrator, CryoGridSolution
 include("Solvers/Solvers.jl")
 
-# Presets
-include("Presets/Presets.jl")
+# Built-in model definitions
+export SoilHeatTile, SamoylovDefault
+include("models.jl")
 
 using .InputOutput: Resource
 

src/IO/forcings/forcings_json.jl

@@ -41,7 +41,7 @@ function loadforcings(format::ForcingFormatJSON{1}, filename::String, kwargs...)
     end
     return Interpolated1D(DimStack((; forcings...)); kwargs...)
 end
-function loadforcings(format::ForcingFormatJSON{2}, filename::String)
+function loadforcings(format::ForcingFormatJSON{2}, filename::String; kwargs...)
     dict = open(filename, "r") do file; JSON3.read(file) end
     # convert JSON3 dict for data field to Julia dict
     data = Dict(dict[:data]...)

src/Physics/Soils/para/simple.jl

@@ -35,12 +35,12 @@ SoilThermalProperties(
     kh_i = ThermalProperties().kh_i,
     kh_a = ThermalProperties().kh_a,
     kh_o=Param(0.25, units=u"W/m/K", domain=0..Inf), # organic [Hillel (1982)]
-    kh_m=Param(3.8, untis=u"W/m/K", domain=0..Inf), # mineral [Hillel (1982)]
+    kh_m=Param(3.8, units=u"W/m/K", domain=0..Inf), # mineral [Hillel (1982)]
     ch_w = ThermalProperties().ch_w,
     ch_i = ThermalProperties().ch_i,
     ch_a = ThermalProperties().ch_a,
     ch_o=Param(2.5e6, units=u"J/K/m^3", domain=0..Inf), # heat capacity organic
-    ch_m=Param(2.0e6, untis=u"J/K/m^3", domain=0..Inf), # heat capacity mineral
+    ch_m=Param(2.0e6, units=u"J/K/m^3", domain=0..Inf), # heat capacity mineral
     kwargs...,
 ) = ThermalProperties(; kh_w, kh_i, kh_a, kh_m, kh_o, ch_w, ch_i, ch_a, ch_m, ch_o, kwargs...)
 

src/Physics/Surface/SEB/seb.jl

@@ -96,7 +96,7 @@ function SurfaceEnergyBalance(;
     stabfun::StabilityFunctions = HøgstrømSHEBA(),
 )
     inputs = (; Tair, Lin, Sin, pr, qh, wind)
-    SurfaceEnergyBalance(; inputs, para, solscheme, stabfun)
+    SurfaceEnergyBalance(inputs, para, solscheme, stabfun)
 end
 
 """