Change vegetation model parameters

Rename these parameters to standard names.
 Additionally, made a start with standard name mapping (external standard name => internal model name). It makes use of `Wflow.param` functionality as much as possible, allowing to write any model output variable with the former TOML keys.

server/test/sbm_config.toml

@@ -75,6 +75,13 @@ soil_water_sat-zone_bottom__max_leakage_volume_flux = "MaxLeakage"
 "soil_root~wet__sigmoid_function_shape_parameter" = "rootdistpar"
 soil__thickness = "SoilThickness"
 
+vegetation_canopy_water__mean_evaporation-to-mean_precipitation_ratio = "EoverR"
+vegetation__leaf-area_index = "LAI"
+vegetation_canopy__light-extinction_coefficient = "Kext"
+vegetation__specific-leaf_storage = "Sl"
+vegetation_woody-part__storage_capacity = "Swood"
+vegetation_root__depth = "RootingDepth"
+
 # specify the internal IDs of the parameters which vary over time
 # the external name mapping needs to be below together with the other mappings
 forcing = [
@@ -83,14 +90,7 @@ forcing = [
   "vertical.atmospheric_forcing.potential_evaporation",
 ]
 
-cyclic = ["vertical.vegetation_parameter_set.leaf_area_index"]
-
-[input.vertical.vegetation_parameter_set]
-leaf_area_index = "LAI"
-kext = "Kext"
-storage_specific_leaf = "Sl"
-storage_wood = "Swood"
-rootingdepth = "RootingDepth"
+cyclic = ["vegetation__leaf-area_index"]
 
 [input.vertical.runoff.parameters]
 waterfrac = "WaterFrac"
@@ -103,20 +103,6 @@ potential_evaporation = "pet"
 precipitation = "precip"
 temperature = "temp"
 
-[input.vertical.soil.parameters]
-c = "c"
-cf_soil = "cf_soil"
-f = "f"
-infiltcappath = "InfiltCapPath"
-infiltcapsoil = "InfiltCapSoil"
-water_holding_capacity = "WHC"
-theta_r = "thetaR"
-theta_s = "thetaS"
-maxleakage = "MaxLeakage"
-pathfrac = "PathFrac"
-rootdistpar = "rootdistpar"
-soilthickness = "SoilThickness"
-
 [input.soil_surface_water__vertical_saturated_hydraulic_conductivity]
 netcdf.variable.name = "KsatVer"
 scale = 1.0

src/Wflow.jl

@@ -112,6 +112,7 @@ function Clock(config, reader)
     return Clock(starttime, 0, dt)
 end
 
+include("standard_name.jl")
 include("io.jl")
 
 """

src/io.jl

@@ -26,6 +26,7 @@ function param(obj, fields, default)
         return default
     end
 end
+get_fields(name) = haskey(standard_name_map, name) ? standard_name_map[name] : name
 
 """
     Config(path::AbstractString)
@@ -718,8 +719,8 @@ function prepare_reader(config)
         cyclic_parameters = Dict{Tuple{Symbol, Vararg{Symbol}}, NamedTuple}()
         cyclic_times = Dict{Tuple{Symbol, Vararg{Symbol}}, Vector{Tuple{Int, Int}}}()
         for par in config.input.cyclic
-            fields = symbols(par)
-            ncname, mod = ncvar_name_modifier(param(config.input, fields))
+            fields = symbols(get_fields(par)) #TODO: make this more restrict (only allow variables in `standard_name_map`)
+            ncname, mod = ncvar_name_modifier(param(config.input, par))
             i = findfirst(x -> startswith(x, "time"), dimnames(cyclic_dataset[ncname]))
             dimname = dimnames(cyclic_dataset[ncname])[i]
             cyclic_nc_times = collect(cyclic_dataset[dimname])

src/parameters.jl

@@ -24,40 +24,40 @@ function VegetationParameters(dataset, config, indices)
     rootingdepth = ncread(
         dataset,
         config,
-        "vertical.vegetation_parameter_set.rootingdepth";
+        "vegetation_root__depth";
         sel = indices,
         defaults = 750.0,
         type = Float,
     )
     kc = ncread(
         dataset,
         config,
-        "vertical.vegetation_parameter_set.kc";
+        "vegetation__crop_factor";
         sel = indices,
         defaults = 1.0,
         type = Float,
     )
-    if haskey(config.input.vertical.vegetation_parameter_set, "leaf_area_index")
+    if haskey(config.input, "vegetation__leaf-area_index")
         storage_specific_leaf = ncread(
             dataset,
             config,
-            "vertical.vegetation_parameter_set.storage_specific_leaf";
+            "vegetation__specific-leaf_storage";
             optional = false,
             sel = indices,
             type = Float,
         )
         storage_wood = ncread(
             dataset,
             config,
-            "vertical.vegetation_parameter_set.storage_wood";
+            "vegetation_woody-part__storage_capacity";
             optional = false,
             sel = indices,
             type = Float,
         )
         kext = ncread(
             dataset,
             config,
-            "vertical.vegetation_parameter_set.kext";
+            "vegetation_canopy__light-extinction_coefficient";
             optional = false,
             sel = indices,
             type = Float,
@@ -76,15 +76,15 @@ function VegetationParameters(dataset, config, indices)
         canopygapfraction = ncread(
             dataset,
             config,
-            "vertical.vegetation_parameter_set.canopygapfraction";
+            "vegetation_canopy__gap_fraction";
             sel = indices,
             defaults = 0.1,
             type = Float,
         )
         cmax = ncread(
             dataset,
             config,
-            "vertical.vegetation_parameter_set.cmax";
+            "vegetation_water__storage_capacity";
             sel = indices,
             defaults = 1.0,
             type = Float,

src/standard_name.jl

@@ -0,0 +1,5 @@
+
+const standard_name_map = Dict{String,String}(
+    "vegetation__leaf-area_index" => "vertical.vegetation_parameter_set.leaf_area_index",
+    "river_water__volume_inflow_rate"=> "lateral.river.boundary_conditions.inflow",
+)

src/vegetation/canopy.jl

@@ -43,7 +43,7 @@ function GashInterceptionModel(dataset, config, indices, vegetation_parameter_se
     e_r = ncread(
         dataset,
         config,
-        "vertical.interception.parameters.e_r";
+        "vegetation_canopy_water__mean_evaporation-to-mean_precipitation_ratio";
         sel = indices,
         defaults = 0.1,
         type = Float,

test/run_sbm.jl

@@ -185,7 +185,7 @@ config.input.vertical.atmospheric_forcing.potential_evaporation = Dict(
     "offset" => 1.50,
     "netcdf" => Dict("variable" => Dict("name" => "pet")),
 )
-config.input.vertical.vegetation_parameter_set.leaf_area_index =
+config.input["vegetation__leaf-area_index"] =
     Dict("scale" => 1.6, "netcdf" => Dict("variable" => Dict("name" => "LAI")))
 
 model = Wflow.initialize_sbm_model(config)
@@ -208,10 +208,10 @@ tomlpath = joinpath(@__DIR__, "sbm_config.toml")
 config = Wflow.Config(tomlpath)
 
 config.input.cyclic = [
-    "vertical.vegetation_parameter_set.leaf_area_index",
-    "lateral.river.boundary_conditions.inflow",
+    "vegetation__leaf-area_index",
+    "river_water__volume_inflow_rate",
 ]
-Dict(config.input.lateral.river)["boundary_conditions"] = Dict("inflow" => "inflow")
+config.input.river_water__volume_inflow_rate = "inflow"
 
 model = Wflow.initialize_sbm_model(config)
 Wflow.run_timestep!(model)

test/sbm_config.toml

@@ -75,6 +75,13 @@ soil_water_sat-zone_bottom__max_leakage_volume_flux = "MaxLeakage"
 "soil_root~wet__sigmoid_function_shape_parameter" = "rootdistpar"
 soil__thickness = "SoilThickness"
 
+vegetation_canopy_water__mean_evaporation-to-mean_precipitation_ratio = "EoverR"
+vegetation__leaf-area_index = "LAI"
+vegetation_canopy__light-extinction_coefficient = "Kext"
+vegetation__specific-leaf_storage = "Sl"
+vegetation_woody-part__storage_capacity = "Swood"
+vegetation_root__depth = "RootingDepth"
+
 # specify the internal IDs of the parameters which vary over time
 # the external name mapping needs to be below together with the other mappings
 forcing = [
@@ -83,21 +90,11 @@ forcing = [
   "vertical.atmospheric_forcing.potential_evaporation",
 ]
 
-cyclic = ["vertical.vegetation_parameter_set.leaf_area_index"]
-
-[input.vertical.vegetation_parameter_set]
-leaf_area_index = "LAI"
-kext = "Kext"
-storage_specific_leaf = "Sl"
-storage_wood = "Swood"
-rootingdepth = "RootingDepth"
+cyclic = ["vegetation__leaf-area_index"]
 
 [input.vertical.runoff.parameters]
 waterfrac = "WaterFrac"
 
-[input.vertical.interception.parameters]
-e_r = "EoverR"
-
 [input.vertical.atmospheric_forcing]
 potential_evaporation = "pet"
 precipitation = "precip"

test/sbm_gw.toml

@@ -58,6 +58,25 @@ atmosphere_air__snowfall_temperature_interval = "TTI"
 snowpack__melting_temperature_threshold = "TTM"
 snowpack__degree-day_coefficient = "Cfmax"
 
+soil_water__brooks-corey_epsilon_parameter = "c"
+soil_surface_water__infiltration_reduction_parameter = "cf_soil"
+soil_water__vertical_saturated_hydraulic_conductivity_scale_parameter = "f"
+"soil~compacted_surface_water__infiltration_capacity" = "InfiltCapPath"
+"soil~non-compacted_surface_water__infiltration_capacity" = "InfiltCapSoil"
+soil_water__residual_volume_fraction = "thetaR"
+soil_water__saturated_volume_fraction = "thetaS"
+soil_water_sat-zone_bottom__max_leakage_volume_flux = "MaxLeakage"
+"soil~compacted__area_fraction" = "PathFrac"
+"soil_root~wet__sigmoid_function_shape_parameter" = "rootdistpar"
+soil__thickness = "SoilThickness"
+
+vegetation_canopy_water__mean_evaporation-to-mean_precipitation_ratio = "EoverR"
+vegetation__leaf-area_index = "LAI"
+vegetation_canopy__light-extinction_coefficient = "Kext"
+vegetation__specific-leaf_storage = "Sl"
+vegetation_woody-part__storage_capacity = "Swood"
+vegetation_root__depth = "RootingDepth"
+
 # specify the internal IDs of the parameters which vary over time
 # the external name mapping needs to be below together with the other mappings
 forcing = [
@@ -66,40 +85,16 @@ forcing = [
   "vertical.atmospheric_forcing.potential_evaporation",
 ]
 
-cyclic = ["vertical.vegetation_parameter_set.leaf_area_index"]
+cyclic = ["vegetation__leaf-area_index"]
 
 [input.vertical.atmospheric_forcing]
 potential_evaporation = "pet"
 precipitation = "precip"
 temperature = "temp"
 
-[input.vertical.vegetation_parameter_set]
-leaf_area_index = "LAI"
-kext = "Kext"
-storage_specific_leaf = "Sl"
-storage_wood = "Swood"
-rootingdepth = "RootingDepth"
-
 [input.vertical.runoff.parameters]
 waterfrac = "WaterFrac"
 
-[input.vertical.soil.parameters]
-c = "c"
-cf_soil = "cf_soil"
-cfmax = "Cfmax"
-e_r = "EoverR"
-f = "f"
-infiltcappath = "InfiltCapPath"
-infiltcapsoil = "InfiltCapSoil"
-kv_0 = "KsatVer"
-maxleakage = "MaxLeakage"
-pathfrac = "PathFrac"
-rootdistpar = "rootdistpar"
-rootingdepth = "RootingDepth"
-soilthickness = "SoilThickness"
-theta_r = "thetaR"
-theta_s = "thetaS"
-
 [input.lateral.river]
 length = "wflow_riverlength"
 mannings_n = "N_River"

test/sbm_gwf_config.toml

@@ -55,21 +55,18 @@ soil_water__saturated_volume_fraction = "thetaS"
 "soil~compacted__area_fraction" = "PathFrac"
 soil__thickness = "soilthickness"
 
+vegetation_canopy_water__mean_evaporation-to-mean_precipitation_ratio = "EoverR"
+vegetation_root__depth = "rootingdepth"
+vegetation_canopy__gap_fraction = "canopygapfraction"
+vegetation_water__storage_capacity = "cmax"
+
 # specify the internal IDs of the parameters which vary over time
 # the external name mapping needs to be below together with the other mappings
 forcing = [
   "vertical.atmospheric_forcing.precipitation",
   "vertical.atmospheric_forcing.potential_evaporation",
 ]
 
-[input.vertical.vegetation_parameter_set]
-rootingdepth = "rootingdepth"
-canopygapfraction = "canopygapfraction"
-cmax = "cmax"
-
-[input.vertical.interception.parameters]
-e_r = "EoverR"
-
 [input.vertical.atmospheric_forcing]
 potential_evaporation = "PET"
 precipitation = "P"

test/sbm_gwf_piave_demand_config.toml

@@ -52,14 +52,21 @@ soil_water__vertical_saturated_hydraulic_conductivity_factor = "kvfrac"
 "vegetation_root__feddes_critial_pressure_head_h~3~high" = "h3_high"
 "vegetation_root__feddes_critial_pressure_head_h~3~low" = "h3_low"
 "vegetation_root__feddes_critial_pressure_head_h~4" = "h4"
+vegetation_canopy_water__mean_evaporation-to-mean_precipitation_ratio = "EoverR"
+vegetation__leaf-area_index = "LAI"
+vegetation_canopy__light-extinction_coefficient = "Kext"
+vegetation__specific-leaf_storage = "Sl"
+vegetation_woody-part__storage_capacity = "Swood"
+vegetation_root__depth = "RootingDepth"
+vegetation__crop_factor = "crop_factor"
 
 forcing = [
   "vertical.atmospheric_forcing.precipitation",
   "vertical.atmospheric_forcing.temperature",
   "vertical.atmospheric_forcing.potential_evaporation",
 ]
 cyclic = [ 
-    "vertical.vegetation_parameter_set.leaf_area_index", 
+    "vegetation__leaf-area_index", 
     "vertical.demand.domestic.demand.demand_gross", 
     "vertical.demand.domestic.demand.demand_net", 
     "vertical.demand.industry.demand.demand_gross", 
@@ -109,17 +116,6 @@ head = "head"
 [input.vertical.glacier.variables]
 glacier_store = "wflow_glacierstore"
 
-[input.vertical.vegetation_parameter_set]
-leaf_area_index = "LAI"
-kext = "Kext"
-storage_specific_leaf = "Sl"
-storage_wood = "Swood"
-rootingdepth = "RootingDepth"
-kc = "crop_factor"
-
-[input.vertical.interception.parameters]
-e_r = "EoverR"
-
 [input.vertical.atmospheric_forcing]
 potential_evaporation = "pet"
 precipitation = "precip"

test/sbm_piave_config.toml

@@ -49,14 +49,21 @@ soil__thickness = "SoilThickness"
 "vegetation_root__feddes_critial_pressure_head_h~3~high" = "h3_high"
 "vegetation_root__feddes_critial_pressure_head_h~3~low" = "h3_low"
 "vegetation_root__feddes_critial_pressure_head_h~4" = "h4"
+vegetation_canopy_water__mean_evaporation-to-mean_precipitation_ratio = "EoverR"
+vegetation__leaf-area_index = "LAI"
+vegetation_canopy__light-extinction_coefficient = "Kext"
+vegetation__specific-leaf_storage = "Sl"
+vegetation_woody-part__storage_capacity = "Swood"
+vegetation_root__depth = "RootingDepth"
+vegetation__crop_factor = "crop_factor"
 
 forcing = [
   "vertical.atmospheric_forcing.precipitation",
   "vertical.atmospheric_forcing.temperature",
   "vertical.atmospheric_forcing.potential_evaporation",
 ]
 
-cyclic = ["vertical.vegetation_parameter_set.leaf_area_index"]
+cyclic = ["vegetation__leaf-area_index"]
 
 [model]
 type = "sbm"
@@ -90,17 +97,6 @@ glacier_store = "glacierstore"
 [input.vertical.glacier.variables]
 glacier_store = "wflow_glacierstore"
 
-[input.vertical.vegetation_parameter_set]
-leaf_area_index = "LAI"
-kext = "Kext"
-storage_specific_leaf = "Sl"
-storage_wood = "Swood"
-rootingdepth = "RootingDepth"
-kc = "crop_factor"
-
-[input.vertical.interception.parameters]
-e_r = "EoverR"
-
 [input.vertical.atmospheric_forcing]
 potential_evaporation = "pet"
 precipitation = "precip"