More module factoring

dev_notes/todo.txt

@@ -3,14 +3,12 @@
 	*** 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.
 				Should not be considered as was_auto_resized if it was entirely NaN, so that the autoresize can trigger again.
 			If the parameter search is already selected, it doesn't react to clicks.
+
+			We could allow editing option_group parameters in MobiView (use the same recompile system as for constant parameters).
 
 		Dataset no longer checks if the correct amount of parameter values were provided?
 			May be intentional, but then it breaks when saving it again.
@@ -54,9 +52,16 @@
 
 
 		Specific models
+
+			Use options to combine airsea_fpv and airsea_fpv_simple
+				Put them in the main airsea file.
 
 			Maybe factor out common phyto module for EasyChem and FjordChem.
-			Also for O2 (found a difficulty with that earlier, but maybe we could resolve it?)
+			Also airsea_gas (found a difficulty with that earlier, but maybe we could resolve it now?)
+
+			Lots of duplication between the different airsea things in general.
+
+			DIC in nivafjord boundary (but how?)
 
 			NIVAFjord
 

models/modules/airsea_fpv_simple.txt

@@ -57,9 +57,6 @@ Authors: Francois Clayer, Magnus D. Norling
 	}
 
 	par_group("FPV", fpv) {
-		#FPV_alb    : par_real("FPV albedo", [], 0.2, 0, 1)
-		#FPV_eff    : par_real("FPV efficiency", [], 0.18)
-		#length_FPV : par_real("Length of FPV module", [m], 0.5)
 		swr_reduc  : par_real("Reduction in SWR by FPV", [], 0.45, 0, 1) ## rest of SWR is reaching the water surface as heat
 		lwr_reduc  : par_real("Reduction in LW back radiation by FPV", [], 0.55, 0, 1)
 	}

models/modules/airsea_gas.txt

@@ -4,7 +4,6 @@ module("AirSeaGas", version(0, 0, 0),
 	layer : compartment,
 	basin : compartment,
 	water : quantity,
-	ice : quantity,
 	o2 : quantity,
 	co2 : quantity,
 	ch4 : quantity,
@@ -14,66 +13,61 @@ module("AirSeaGas", version(0, 0, 0),
 	o2satconc : property,
 	ice_ind : loc,
 	vert : connection,
-	dims : preamble
+	dims : preamble,
+	compute_dic : par_bool
 ) {
 
 	load("stdlib/seawater.txt", library("Sea oxygen"))
 	load("stdlib/physiochemistry.txt", library("Chemistry"))
 
 	p_vel     : property("O₂ piston velocity")
-	pco2_vel  : property("CO₂ piston velocity")
-	pch4_vel  : property("CH4 piston velocity")
 
 	var(basin.p_vel, [c m, hr-1]) {
 		o2_piston_velocity(air.wind, layer.water.temp[vert.top])
 	}
 
-	## TO DO: decide whether to add this in the stdlib together with p_vel for O2.
-	var(basin.pco2_vel, [c m, hr-1]) {
-		wnd := air.wind => [],
-		k_600 := 2.07 + 0.215* (wnd^1.7) => [],
-		t := layer.water.temp[vert.top] =>[],
-		schmidt := 1923.6-125.06*t +4.3773*t^2 -0.085681*t^3+0.00070284*t^4,
-		k_600* min(2.5,(schmidt/600)^(-0.666)) => [c m, hr-1]
-	}
-
-	## TO DO: decide whether to add this in the stdlib together with p_vel for O2.
-	var(basin.pch4_vel, [c m, hr-1]) {
-		wnd := air.wind => [],
-		k_600 := 2.07 + 0.215* (wnd^1.7) => [],
-		t := layer.water.temp[vert.top] =>[],
-		schmidt := 1909.4-120.78*t +4.1555*t^2 -0.080578*t^3+0.00065777*t^4,
-		k_600* min(2.5,(schmidt/600)^(-0.666)) => [c m, hr-1]
-	}
-
 	flux(out, layer.water.o2[vert.top], [k g, day-1], "Precipitation O₂") {
 		precip_saturation := 0.9, # Probably ok estimate? Not extremely important in any case.
-		cnc := precip_saturation*o2_saturation(air.temp, 0)*o2_mol_mass,
+		cnc := precip_saturation*o2_saturation_concentration(air.temp, 0)*o2_mol_mass,
 		air.precip*A[vert.top]*cnc->>
 	}
 
 	flux(layer.water.o2[vert.top], out,  [k g, day-1], "O₂ gas exchange at surface") {
 		(!ice_ind) * basin.p_vel*(conc(o2[vert.top]) - o2satconc[vert.top])*A[vert.top] ->>
 	}
 
+	option(compute_dic) {
 
-	flux(layer.water.co2[vert.top], out, [k g, day-1], "CO₂ gas exchange at surface") {
-		top_t := (layer.water.temp[vert.top]->[K]) =>[],
-		lKh := 108.3865 + 0.01985076 * top_t -6919.53 / top_t-40.45154 * log10(top_t)+669365 /(top_t^2), ## Weyhenmeyer et al., 2012
-		Kh := 10 ^ (lKh=>[]),
-
-		co2_eq := 0.012[m g, l-1] *450 * (Kh * 1.013[] * 0.987[]), ## pco2 in ppm : 450 ppm, co2_eq in mgC/L
+		pco2_vel  : property("CO₂ piston velocity")
+		pch4_vel  : property("CH₄ piston velocity")
 
-		(!ice_ind) *  basin.pco2_vel * (conc(layer.water.co2[vert.top]) - co2_eq ) *A[vert.top] ->>	
-	}
-
-	flux(layer.water.ch4[vert.top], out, [k g, day-1], "CH4 gas exchange at surface") {
-		top_t := (layer.water.temp[vert.top]->[K]) =>[],
+		var(basin.pco2_vel, [c m, hr-1]) {
+			co2_piston_velocity(air.wind, layer.water.temp[vert.top])
+		}
 
-		Kh := exp( (-365.183 + 18103.7/top_t + 49.7554*ln(top_t) - 0.000285033*top_t)/1.9872)/55.556,
+		var(basin.pch4_vel, [c m, hr-1]) {
+			ch4_piston_velocity(air.wind, layer.water.temp[vert.top])
+		}
+
+		flux(layer.water.co2[vert.top], out, [k g, day-1], "CO₂ gas exchange at surface") {
+			#top_t := (layer.water.temp[vert.top]->[K]) =>[],
+			#lKh := 108.3865 + 0.01985076 * top_t -6919.53 / top_t-40.45154 * log10(top_t)+669365 /(top_t^2), ## Weyhenmeyer et al., 2012
+			#Kh := 10 ^ (lKh=>[]),
+			#co2_eq := 0.012[m g, l-1] *450 * (Kh * 1.013[] * 0.987[]), ## pco2 in ppm : 450 ppm, co2_eq in mgC/L
+
+			co2_eq := co2_saturation_concentration(layer.water.temp[vert.top]),
+
+			(!ice_ind) *  basin.pco2_vel * (conc(layer.water.co2[vert.top]) - co2_eq ) *A[vert.top] ->>	
+		}
+
+		flux(layer.water.ch4[vert.top], out, [k g, day-1], "CH₄ gas exchange at surface") {
+			top_t := (layer.water.temp[vert.top]->[K]) =>[],
+
+			Kh := exp( (-365.183 + 18103.7/top_t + 49.7554*ln(top_t) - 0.000285033*top_t)/1.9872)/55.556,
 
-		ch4_eq := 0.016[m g, l-1] * Kh * 2.3, ### ch4_eq in mgCH4/L, 2.3 being in ppm
-		(!ice_ind) * basin.pch4_vel * (conc(layer.water.ch4[vert.top]) - ch4_eq) * A[vert.top] ->>
+			ch4_eq := 0.016[m g, l-1] * Kh * 2.3, ### ch4_eq in mgCH4/L, 2.3 being in ppm
+			(!ice_ind) * basin.pch4_vel * (conc(layer.water.ch4[vert.top]) - ch4_eq) * A[vert.top] ->>
+		}
 	}
 }
 

models/modules/easychem.txt

@@ -22,7 +22,7 @@ Authors: Magnus D. Norling
 	var(river.water.o2, [k g], [m g, l-1], "River oxygen") 
 
 	flux(out, river.water.o2, [k g, day-1], "River oxygen from catchment") {
-		catch_conc := f_o2sat*o2_saturation(temp, 0) * o2_mol_mass,
+		catch_conc := f_o2sat*o2_saturation_concentration(temp, 0) * o2_mol_mass,
 		in_flux(water)*catch_conc->>
 	}
 }
@@ -125,8 +125,8 @@ Authors: François Clayer, Magnus D. Norling
 
 	f_par     : constant("Fraction of PAR in SW radiation", [], 0.45)  # Photosynthetically available radiation
 
-	var(epi.water.o2, [k g], [m g, l-1], "Epilimnion O₂")  @initial_conc { o2_saturation(temp, 0)*init_O2*o2_mol_mass->> }
-	var(hyp.water.o2, [k g], [m g, l-1], "Hypolimnion O₂") @initial_conc { o2_saturation(temp, 0)*init_O2*o2_mol_mass->> }  
+	var(epi.water.o2, [k g], [m g, l-1], "Epilimnion O₂")  @initial_conc { o2_saturation_concentration(temp, 0)*init_O2*o2_mol_mass->> }
+	var(hyp.water.o2, [k g], [m g, l-1], "Hypolimnion O₂") @initial_conc { o2_saturation_concentration(temp, 0)*init_O2*o2_mol_mass->> }  
 
 	var(epi.water.oc, [k g], [m g, l-1], "Epilimnion DOC")  @initial_conc { init_c }
 	var(hyp.water.oc, [k g], [m g, l-1], "Hypolimnion DOC") @initial_conc { init_c }
@@ -167,11 +167,11 @@ Authors: François Clayer, Magnus D. Norling
 
 	o2sat : property("O₂ saturation concentration")
 	var(epi.water.o2sat, [m g, l-1]) {
-		o2_saturation(temp, 0)*o2_mol_mass -> [m g, l-1]
+		o2_saturation_concentration(temp, 0)*o2_mol_mass -> [m g, l-1]
 	}
 
 	flux(out, epi.water.o2, [k g, day-1], "Precipitation O₂") {
-		cnc := 0.9*o2_saturation(air.temp, 0)*o2_mol_mass -> [m g, l-1],  #Not sure what the fraction should be..
+		cnc := 0.9*o2_saturation_concentration(air.temp, 0)*o2_mol_mass -> [m g, l-1],  #Not sure what the fraction should be..
 		air.precip*area*cnc->>
 	}
 

models/modules/nivafjord/fjordchem.txt

@@ -59,38 +59,35 @@ preamble("NIVAFjord chemistry rates", version(0, 0, 0),
 
 module("NIVAFjord chemistry", version(0, 0, 5),
 	air   : compartment,
-	basin : compartment,
+	#basin : compartment,
 	layer : compartment,
 	sediment : compartment,
 	water : quantity,
 	o2    : quantity,
 	co2   : quantity,
 	ch4   : quantity,
-	ice   : quantity,
 	oc    : quantity,
 	din   : quantity,
 	on    : quantity,
 	phos  : quantity,
 	op    : quantity,
 	sed   : quantity,
 	phyt  : quantity,
-	zoo   : quantity,
 	chl_a : property,
 	temp  : property,
 	salin : property,
-	wind  : property,
 	z     : property,
 	dz    : property,
-	indicator : property,
 	attn  : property,
-	precip : property,
 	area   : property,
 	cos_z : property,
 	sw    : property,
 	o2satconc : property,
 	vert  : connection,
 	chem_par : preamble,
-	dims     : preamble
+	dims     : preamble,
+
+	compute_dic : par_bool,
 ) {
 	#TODO: Would be nice to unify easychem and fjordchem a bit more, maybe some shared code.
 	# Esp. for surface O2 exchange and maybe microbes and phyto (into separate modules).
@@ -120,13 +117,15 @@ module("NIVAFjord chemistry", version(0, 0, 5),
 
 	# TODO: Initial states for all these:
 	# Main variables:
-	var(layer.water.o2, [k g], [m g, l-1], "Layer O₂") @initial_conc { o2_saturation(temp, salin)*init_O2*o2_mol_mass->> }
+	var(layer.water.o2, [k g], [m g, l-1], "Layer O₂") @initial_conc { o2_saturation_concentration(temp, salin)*init_O2*o2_mol_mass->> }
 
 	var(layer.water.oc, [k g], [m g, l-1], "Layer DOC") @initial_conc { init_DOC }
 
-	var(layer.water.co2, [k g], [m g, l-1], "Layer CO₂")
-
-	var(layer.water.ch4, [k g], [m g, l-1], "Layer CH4")
+	option(compute_dic) {
+		var(layer.water.co2, [k g], [m g, l-1], "Layer CO₂")
+
+		var(layer.water.ch4, [k g], [m g, l-1], "Layer CH₄")
+	}
 
 	var(layer.water.din, [k g], [m g, l-1], "Layer DIN")
 
@@ -149,7 +148,7 @@ module("NIVAFjord chemistry", version(0, 0, 5),
 	o2sat     : property("O₂ saturation")
 
 	var(layer.water.o2satconc, [m g, l-1]) {
-		o2_saturation(temp, salin)*o2_mol_mass ->>
+		o2_saturation_concentration(temp, salin)*o2_mol_mass ->>
 	} #@no_store
 
 	var(layer.water.o2sat, []) {
@@ -347,8 +346,10 @@ module("NIVAFjord chemistry", version(0, 0, 5),
 		+ (on + sed.on)*min_rat*n_min*(o2_mol_mass/n_mol_mass)*1.5    # ON -> NH4 -> NO3   #TODO: Should the 1.5 be parametrizable?
 	}
 
-	flux(out, layer.water.co2, [k g, day-1], "Microbial CO2 production") {
-		(oc + sed.oc)*(min_rat+denit_rat) # NOTE: CO2 is in kg(C)
+	option(compute_dic) {
+		flux(out, layer.water.co2, [k g, day-1], "Microbial CO2 production") {
+			(oc + sed.oc)*(min_rat+denit_rat) # NOTE: CO2 is in kg(C)
+		}
 	}
 
 	var(layer.water.denit_rat, [day-1], "Denitrification rate") {

models/modules/nivafjord/point_sources.txt

@@ -37,7 +37,7 @@ This is a module for point source inputs to NIVAFjord.
 	flux(out, layer.water.o2, [k g, day-1], "Point source O2 to layer") {
 		eff_temp := layer.water.temp,
 		eff_salin := 0,
-		o2c := o2sat*o2_mol_mass*o2_saturation(eff_temp, eff_salin),
+		o2c := o2sat*o2_mol_mass*o2_saturation_concentration(eff_temp, eff_salin),
 		o2c*eff_q/time.days_this_year->>
 	}
 

models/modules/nivafjord/sediment.txt

@@ -20,7 +20,8 @@ module("NIVAFjord sediments", version(0, 0, 3),
 	z        : property,
 	vert     : connection,
 	dims     : preamble,
-	chem_par : preamble
+	chem_par : preamble,
+	compute_dic : par_bool,
 ) {
 
 	par_group("Sediments") {
@@ -79,7 +80,9 @@ module("NIVAFjord sediments", version(0, 0, 3),
 
 	var(sediment.sed.oc, [k g], [g, k g-1], "Sediment organic carbon") @initial_conc { init_c }
 
-	var(sediment.sed.ch4, [k g], [g, k g-1], "Sediment CH4") 
+	option(compute_dic) {
+		var(sediment.sed.ch4, [k g], [g, k g-1], "Sediment CH4")
+	}
 
 	var(sediment.sed.on, [k g], [g, k g-1], "Sediment organic N") @initial_conc { init_c / cn_molar_to_mass_ratio(sed_cn) }
 
@@ -124,37 +127,39 @@ module("NIVAFjord sediments", version(0, 0, 3),
 		+ (sediment.sed.on)*mr*n_min*(o2_mol_mass/n_mol_mass)*1.5    # ON -> NH4 -> NO3   #TODO: Should the 1.5 be parametrizable?
 	}
 
-	# Simple CO2 release from the sediment = O2 sediment demand
-	flux(out, layer.water.co2, [k g, day-1], "CO₂ sediment microbial production") {
-		mr := layer.water.min_rat,
-		dr := layer.water.denit_rat,
-		(sediment.sed.oc)*(mr + dr)    
-	}
-
-	# Simple CH4 production in the sediment: fraction scaled to CO2 production
-	flux(out, sediment.sed.ch4, [k g, day-1], "CH4 sediment microbial production") {
-		mr := layer.water.min_rat,
-		(sediment.sed.oc) * mr * ch4_production_scaler    
-	}
-
-	ch4satconc : property("CH4 saturation concentration")
-
-	## Simplified model of CH4 sollubility as a function of water temp, ambient pressure and salinity: Duan and Mao, 2006, https://doi.org/10.1016/j.gca.2006.03.018
-	# TODO: Name the magic constants, and probably move to stdlib.
-	var(sediment.sed.ch4satconc, [g, k g-1]) {
-		ch4_mol_mass*((0.00247[mol, k g-1] - (0.00004033[mol, k g-1, deg_c-1] * sediment.temp))* (1-(0.2844-0.001775[deg_c-1]*sediment.temp) * (layer.water.salin/58.44)))* (1 + 44.6[m-1] * (layer.z[vert.above])/490)
-	}
-
-	## Simple CH4 bubble release from the sediment 
-	flux(sediment.sed.ch4, out, [k g, day-1], "CH4 sediment bubbling") {
-		max(0, bubble_ch4*(conc(ch4) - ch4satconc)*sediment.sed) ->>
-	}
-
-	## Simple CH4 diffusion release from the sediment; Diffusion coefficient from 
-	flux(sediment.sed.ch4, layer.water.ch4, [k g, day-1], "CH4 sediment diffusion release") {
-		# TODO: Use Mobius2 inbuilt unit conversion and use named constants (e.g. is 1000[g, l-1] rho_water?)
-		diff_coeff := (4.18e-11[m 2, s-1, deg_c-1]*sediment.temp + 8.06e-10[m 2, s-1])->[m 2, day-1],
-		diff_coeff  * (conc(sediment.sed.ch4)* 1000[g, l-1] *(porosity)- conc(layer.water.ch4)) * 0.001[k g, g-1] / 0.25 [m] * sediment.area
+	option(compute_dic) {
+		# Simple CO2 release from the sediment = O2 sediment demand
+		flux(out, layer.water.co2, [k g, day-1], "CO₂ sediment microbial production") {
+			mr := layer.water.min_rat,
+			dr := layer.water.denit_rat,
+			(sediment.sed.oc)*(mr + dr)    
+		}
+
+		# Simple CH4 production in the sediment: fraction scaled to CO2 production
+		flux(out, sediment.sed.ch4, [k g, day-1], "CH4 sediment microbial production") {
+			mr := layer.water.min_rat,
+			(sediment.sed.oc) * mr * ch4_production_scaler    
+		}
+
+		ch4satconc : property("CH4 saturation concentration")
+
+		## Simplified model of CH4 sollubility as a function of water temp, ambient pressure and salinity: Duan and Mao, 2006, https://doi.org/10.1016/j.gca.2006.03.018
+		# TODO: Name the magic constants, and probably move to stdlib.
+		var(sediment.sed.ch4satconc, [g, k g-1]) {
+			ch4_mol_mass*((0.00247[mol, k g-1] - (0.00004033[mol, k g-1, deg_c-1] * sediment.temp))* (1-(0.2844-0.001775[deg_c-1]*sediment.temp) * (layer.water.salin/58.44)))* (1 + 44.6[m-1] * (layer.z[vert.above])/490)
+		}
+
+		## Simple CH4 bubble release from the sediment 
+		flux(sediment.sed.ch4, out, [k g, day-1], "CH4 sediment bubbling") {
+			max(0, bubble_ch4*(conc(ch4) - ch4satconc)*sediment.sed) ->>
+		}
+
+		## Simple CH4 diffusion release from the sediment; Diffusion coefficient from 
+		flux(sediment.sed.ch4, layer.water.ch4, [k g, day-1], "CH4 sediment diffusion release") {
+			# TODO: Use Mobius2 inbuilt unit conversion and use named constants (e.g. is 1000[g, l-1] rho_water?)
+			diff_coeff := (4.18e-11[m 2, s-1, deg_c-1]*sediment.temp + 8.06e-10[m 2, s-1])->[m 2, day-1],
+			diff_coeff  * (conc(sediment.sed.ch4)* 1000[g, l-1] *(porosity)- conc(layer.water.ch4)) * 0.001[k g, g-1] / 0.25 [m] * sediment.area
+		}
 	}