Refactor, get rid of excess NIVAFjord setups

dev_notes/todo.txt

@@ -2,6 +2,10 @@
 
 	*** High pri ***
 
+
+
+		# Need @else for options.
+
 
 		MobiView
 			If the plot x axis was set to nonsense since the first selected series was entirely NaN, it won't be fixed by selecting a non-NaN series.

models/modules/microplastic/mp_soil_column.txt

@@ -98,23 +98,28 @@ This is a module for transport of microplastic in a single *experimentally contr
 	z : property("Effective depth")
 	var(layer.z, [m m]) { dz*theta + z[vert.above] } @no_store
 
+
+	sat_lim : property("Saturation limiter")
+	var(layer.sat_lim, []) {
+		maxcap := dz * theta,
+		mincap := maxcap*fcs,
+		s_response(water, mincap, min(1.1*mincap, maxcap), 0, 1)
+	} @no_store
+
 	var(layer.water.side, [m m, day-1]) {
 		# TODO: This is wrong... Should compute gradient based on z and, z of outside and distance.
 		agrad := grad*(water_tot/z),
-		agrad*cond->>
+		sat_lim*agrad*cond->>
 	}
 
 	var(layer.water.perc, [m m, day-1]) {
-		maxcap := dz * theta,
 		maxcap_b := dz[vert.below] * theta[vert.below],
-
 		maxrate := cond->>,
-		mincap := maxcap*fcs,
 
-		maxperc := s_response(water, mincap, min(1.1*mincap, maxcap), 0, maxrate),
-		#s_response(water[vert.below], maxcap_b, 0.9*maxcap_b, 0, maxperc)
-		#1.1*mincap, mincap, 0, maxrate),      # Cut flow off when water saturation reaches field capacity
-		s_response(water[vert.below], 0.9*maxcap_b, maxcap_b, maxperc, 0)  # Cut flow off when water saturation below fills up
+		# Cut percolation off when water saturation goes below field capacity.
+		maxperc := sat_lim*maxrate,
+		# Cut percolation off when water saturation below fills up
+		s_response(water[vert.below], 0.9*maxcap_b, maxcap_b, maxperc, 0)
 
 		# TODO: Capillary action when water below is above fc and this layer is below fc?
 		# We could also compute forces on the water, but probably not necessary

models/modules/nivafjord/lake_basin.txt → models/modules/nivafjord/lake_discharge.txt

@@ -1,6 +1,6 @@
 
 
-module("NIVAFjord lake", version(0, 0, 1),
+module("NIVAFjord lake discharge", version(0, 0, 1),
 	river : compartment,
 	basin : compartment,
 	layer : compartment,

models/nivafjord_base.txt

@@ -1,18 +1,30 @@
 
 model("NIVAFjord") {
 
+	# NOTE: These configurations can be overruled by an extending model
+	has_boundaries : constant(true) 
+	default_airsea : constant(true)
+
 	basin_idx     : index_set("Basin index")
-	bnd_basin_idx : index_set("Boundary basin index")
-	all_basins    : index_set("All basins") @union(basin_idx, bnd_basin_idx)
-	e_idx         : index_set("Fjord connection index") @sub(basin_idx) # Ideally this should not be declared in this model, but then it sometimes is declared out of order.
-	layer_idx     : index_set("Layer index") @sub(all_basins)
+
+	option(has_boundaries) {
+		bnd_basin_idx : index_set("Boundary basin index")
+		all_basins    : index_set("All basins") @union(basin_idx, bnd_basin_idx)
+		e_idx         : index_set("Fjord connection index") @sub(basin_idx) # Ideally this should not be declared in this model, but then it sometimes is declared out of order.
+		layer_idx     : index_set("Layer index") @sub(all_basins)
+	} @otherwise {
+		layer_idx     : index_set("Layer index") @sub(basin_idx)
+	}
 
 	air       : compartment("Atmosphere")
 	basin     : compartment("Basin",          basin_idx)
 	layer     : compartment("Fjord layer",    basin_idx, layer_idx)
 	sediment  : compartment("Fjord sediment", basin_idx, layer_idx)
-	bnd_basin : compartment("Boundary basin", bnd_basin_idx)
-	bnd_layer : compartment("Boundary layer", bnd_basin_idx, layer_idx)
+
+	option(has_boundaries) {
+		bnd_basin : compartment("Boundary basin", bnd_basin_idx)
+		bnd_layer : compartment("Boundary layer", bnd_basin_idx, layer_idx)
+	}
 
 	water : quantity("Water")
 	ice   : quantity("Ice")
@@ -53,20 +65,29 @@ model("NIVAFjord") {
 	load("modules/atmospheric.txt",
 		module("Atmospheric", air, temp, wind, g_rad, pressure, a_hum, rho, lwd, cos_z, a_vap, s_vap))
 
-	load("modules/airsea.txt",
-		module("AirSea", "AirSea Fjord", air, basin, ice, heat, temp, precip, wind, g_rad, pressure, rho, a_hum, lwd, sw, attn, indicator,
-							evap, cos_z, loc(basin.freeze_t), loc(basin.area), loc(layer.water[vert.top]), loc(layer.water.heat[sw_vert.top])))
-
-	all_layer : compartment("All layers", all_basins, layer_idx) # This is not used for anything other than to force a par group to distribute over all_basin
+	option(default_airsea) {
+		load("modules/airsea.txt",
+			module("AirSea", "AirSea Fjord", air, basin, ice, heat, temp, precip, wind, g_rad, pressure, rho, a_hum, lwd, sw, attn, indicator,
+								evap, cos_z, loc(basin.freeze_t), loc(basin.area), loc(layer.water[vert.top]), loc(layer.water.heat[sw_vert.top])))
+	}
 
+	option(has_boundaries) {
+		all_layer : compartment("All layers", all_basins, layer_idx) # This is not used for anything other than to force a par group to distribute over all_basin
+		load("modules/nivafjord/basin.txt", dims : preamble("NIVAFjord dimensions", all_layer, layer))
+	} @otherwise {
+		load("modules/nivafjord/basin.txt", dims : preamble("NIVAFjord dimensions", layer, layer))
+	}
+
 	load("modules/nivafjord/basin.txt",
-		dims : preamble("NIVAFjord dimensions", all_layer, layer),
 		module("NIVAFjord basin", air, basin, layer, water, salt, heat, temp, salinity, pressure, wind, g_rad, rho, attn, z, dz, h, area, freeze_t, sw, loc(basin.ice.indicator), vert, sw_vert, loc(sediment.heat), dims))
 
-	load("modules/nivafjord/boundary_basin.txt",
-		module("NIVAFjord boundary", bnd_basin, bnd_layer, water, heat, salt, temp, salinity, dz, h, rho, pressure, vert, dims))
+	option(has_boundaries) {
+		load("modules/nivafjord/boundary_basin.txt",
+			module("NIVAFjord boundary", bnd_basin, bnd_layer, water, heat, salt, temp, salinity, dz, h, rho, pressure, vert, dims))
+
+		solve(sol, bnd_basin.h)
+	}
 
 	sol : solver("NIVAFjord solver", inca_dascru, solver_h, solver_hmin)
 	solve(sol, layer.water, basin.ice)
-	solve(sol, bnd_basin.h)
 }

models/nivafjord_chem_base.txt

@@ -10,13 +10,13 @@ This won't run as its own model, it is just a base for model extension.
 
 	phyt_type : index_set("Phytoplankton type")
 
-	edge       : compartment("Basin edge",       basin_idx, e_idx)
-	edge_layer : compartment("Basin edge layer", basin_idx, e_idx, layer_idx)
 
-	load("modules/nivafjord/horizontal_fluxes.txt",
-		module("NIVAFjord horizontal fluxes", basin, bnd_basin, layer, bnd_layer, river, edge, edge_layer, water, salt, temp, salinity, flow, rho, pressure, dz, h, horz, vert, dims),
-		module("NIVAFjord simple realignment", basin, layer, water, dz, vert, dims)
-	)
+	sed : quantity("Sediments")
+	oc : quantity("Organic carbon")
+	on : quantity("Organic nitrogen")
+	op : quantity("Organic phosphorous")
+	din : quantity("Nitrate")
+	phos : quantity("Phosphate")
 
 	# Called 'fjord_phyt' to distinguish from freshwater in the version of the model that also has EasyLake
 	fjord_phyt : quantity("Fjord phytoplankton")#, phyt_type)
@@ -31,33 +31,25 @@ This won't run as its own model, it is just a base for model extension.
 	load("modules/nivafjord/fjordchem.txt",
 		chem_par : preamble("NIVAFjord chemistry rates", fjord_phyt),
 		module("NIVAFjord chemistry", air, basin, layer, sediment, water, o2, co2, ch4, ice, oc, din, on, phos, op, sed, fjord_phyt, zoo, chl_a, temp, salinity, wind, z, dz, indicator, attn, precip, area, cos_z, sw, o2satconc, vert, chem_par, dims))
-
-	load("modules/airsea_gas.txt",
-		module("AirSeaGas", air, layer, basin, water, ice, o2, co2, ch4, temp, wind, precip, o2satconc, loc(basin.ice.indicator), vert, dims)) 
+
+	option(default_airsea) {
+		load("modules/airsea_gas.txt",
+			module("AirSeaGas", air, layer, basin, water, ice, o2, co2, ch4, temp, wind, precip, o2satconc, loc(basin.ice.indicator), vert, dims)) 
+	}
 
 	load("modules/nivafjord/sediment.txt",
 		module("NIVAFjord sediments", layer, sediment, water, o2, co2, ch4, salinity, sed, oc, din, on, phos, op, heat, area, temp, dz, z, vert, chem_par, dims))
 
-	load("modules/nivafjord/boudary_chem.txt",
-		module("NIVAFjord boundary chemistry", bnd_layer, water, o2, oc, din, on, phos, op, fjord_phyt, chl_a, sed, chem_par))
+	option(has_boundaries) {
+		load("modules/nivafjord/boudary_chem.txt",
+			module("NIVAFjord boundary chemistry", bnd_layer, water, o2, oc, din, on, phos, op, fjord_phyt, chl_a, sed, chem_par))
+	}
 
 	load("modules/nivafjord/point_sources.txt",
 		module("NIVAFjord point sources", layer, water, din, on, phos, sed, oc, o2, heat, temp))
 
-	load("modules/easychem.txt",
-		module("Simple River O₂", river, water, o2, temp))
-
-	solve(sol, sediment.sed, sediment.heat)
-	solve(sol, air.cos_z)
-
-	wb_index : index_set("Water body") @union(sc, basin_idx)
 
-	downstream : connection("Downstream") @directed_graph {
-		river+
-	} @no_cycles
-
-	horz : connection("Fjord horizontal") @directed_graph(e_idx) { 
-		(river? layer+ bnd_layer?) | river
-	} @no_cycles
+	solve(sol, sediment.sed, sediment.heat)
+	solve(sol, air.cos_z, air.g_rad)
 }
 

models/nivafjord_easylake_simplycnp_model.txt

@@ -10,6 +10,12 @@ model("NIVAFjord-EasyLake-SimplyCNP") {
 		heat : quantity,
 		ice : quantity,
 		o2  : quantity,
+		sed : quantity,
+		oc : quantity,
+		din : quantity,
+		on : quantity,
+		phos : quantity,
+		op : quantity,
 		temp : property,
 		precip : property,
 		wind : property,

models/nivafjord_isolated_basin_fpv_model.txt

@@ -9,7 +9,14 @@ It is also currently without horizontal exchange between basins, so it only work
 
 	# TODO: FPV cover does not dynamically affect wind mixing (not sure to how large a degree that would happen).
 
-	extend("nivafjord_lake_base.txt")
+	# Overrule configs for nivafjord_base
+	has_boundaries : constant(false)
+	default_airsea : constant(false)
+
+	extend("nivafjord_chem_base.txt") @exclude(
+		has_boundaries : constant,
+		default_airsea : constant,
+	)
 
 	tox_index : index_set("Contaminant type")
 
@@ -39,10 +46,6 @@ It is also currently without horizontal exchange between basins, so it only work
 		module("SimplyTox partitioning", "SimplyTox fjord layer", layer, water, oc, tox, temp, loc(layer.water.sed.oc), [n g], constant(true), phys)
 	)
 
-	#load("modules/nivafjord/tox.txt",
-	#	module("NIVAFjord tox air-water", basin, layer, air, water, tox, temp, area, vert, loc(basin.ice.indicator), dims, phys)
-	#)
-
 	load("modules/nivafjord/horizontal_fluxes.txt",
 		module("NIVAFjord simple realignment", basin, layer, water, dz, vert, dims))
 

models/nivafjord_lake_simplytox_model.txt

@@ -17,27 +17,23 @@ TODO: Maybe we want a simpler biochemistry model for this one, not the entire NI
 		wind : property,
 		sol : solver
 	)
+
+	has_boundaries : constant(false)
 
-	extend("nivafjord_lake_base.txt")
+	extend("nivafjord_chem_base.txt") @exclude(has_boundaries : constant) # Overrule the has_boundaries from the base model.
 
 	downstream : connection("Downstream") @directed_graph { river+ } @no_cycles
 
 	river_lake : connection("River-lake") @directed_graph { river+ layer } @no_cycles
-
-	load("modules/airsea.txt",
-		module("AirSea", "AirSea Fjord", air, basin, ice, heat, temp, precip, wind, g_rad, pressure, rho, a_hum, lwd, sw, attn, indicator,
-							evap, cos_z, loc(basin.freeze_t), loc(basin.area), loc(layer.water[vert.top]), loc(layer.water.heat[sw_vert.top]))
-	)
 
-	load("modules/nivafjord/lake_basin.txt",
-		module("NIVAFjord lake", river, basin, layer, water, flow, dz, river_lake, vert, dims)
+	load("modules/nivafjord/lake_discharge.txt",
+		module("NIVAFjord lake discharge", river, basin, layer, water, flow, dz, river_lake, vert, dims)
 	)
 
 	load("modules/simplytox.txt",
 		module("SimplyTox partitioning", "SimplyTox fjord layer", layer, water, oc, tox, temp, loc(layer.water.sed.oc), [n g], constant(true), phys),
 		module("SimplyTox partitioning", "SimplyTox fjord sediments", sediment, water, oc, tox, temp, loc(sediment.sed.oc), [n g], constant(false), phys),
 		module("SimplyTox air-water",    "SimplyTox lake air-water", air, basin, water, tox, temp, wind, loc(basin.area), phys)
-		#module("SimplyTox partitioning", "SimplyTox lake sediments", lake_sed, water, oc, tox, temp, loc(lake_sed.sed.oc), [n g, m-2], constant(false), phys)
 	)
 
 	load("modules/nivafjord/tox.txt",
@@ -48,6 +44,10 @@ TODO: Maybe we want a simpler biochemistry model for this one, not the entire NI
 	load("modules/nivafjord/horizontal_fluxes.txt",
 		module("NIVAFjord simple realignment", basin, layer, water, dz, vert, dims))
 
+	load("modules/easychem.txt",
+		module("Simple River O₂", river, water, o2, temp))
+
+	# This could maybe go into the main NIVAFjord model (put in same file as point_sources). It is relevant for different applications.
 	module("NIVAFjord extraction", version(0, 0, 1)) {
 
 		par_group("Extraction", layer) {
@@ -58,4 +58,6 @@ TODO: Maybe we want a simpler biochemistry model for this one, not the entire NI
 			ext
 		}
 	}
+
+	solve(sol, sediment.water)
 }