Factoring out some models

docs/gettingstarted/gettingstarted.md

@@ -23,15 +23,15 @@ You can also download a zip archive of the repository from its github front page
 
 ### 2. Get the MobiView2 program.
 
-For now we only support MobiView2 on Windows. It is technically possible to compile it on Linux, so if you need that, please contact us.
+For now we only support MobiView2 on Windows. It is theoretically possible to compile it on Linux, so if you need that, please contact us.
 
 Open ftp://mobiserver.niva.no/Mobius2 in a file explorer (not a web browser), then download the entire MobiView2 folder by copying it over to somewhere on your machine.
 
-In your local copy, edit MobiView2/config.txt so that the "Mobius2 base path" field contains the location where you put Mobius2 repository, e.g. `"C:/Data/Mobius2"`.
+In your local copy, edit MobiView2/config.txt so that the "Mobius2 base path" field contains the location where you put the Mobius2 repository, e.g. `"C:/Data/Mobius2"`.
 
-You can now run MobiView2.exe. Click the ![Open](../img/toolbar/Open.png) open icon in the top left and select e.g. `"Mobius2/models/simplyq.txt"`, then `"Mobius2/models/data/simplyq_simple.dat"`. If the model loaded correctly you can now run it by clicking the ![Run](../img/toolbar/Run.png) runner icon in the MobiView2 toolbar. You can then select series to plot in the result and input series selections in the bottom right.
+You can now run MobiView2.exe. Click the ![Open](../img/toolbar/Open.png) open icon in the top left and select e.g. `"Mobius2/models/simplyq.txt"`, then `"Mobius2/models/data/simplyq_simple.dat"`. If the model loaded correctly you can now run it by clicking the ![Run](../img/toolbar/Run.png) runner icon in the MobiView2 toolbar. You can then select the series to plot in the result and input series selections in the bottom right.
 
-If you chose simplyq.txt, you are running [SimplyQ](../existingmodels/simply.html#simplyq), which is a simple hydrology model for predicting river discharge.
+If you chose `simplyq.txt`, you are running [SimplyQ](../existingmodels/simply.html#simplyq), which is a simple hydrology model for predicting river discharge.
 
 ![MobiView2](../img/mobiview_gettingstarted.png)
 
@@ -74,4 +74,4 @@ The [Guide](../mobius2docs/guide.html) is a good place to start.
 
 ### Involve yourself with feedback to the developer team, or become a developer.
 
-Please use the github issues tracker to report bugs. You can also contact us at `magnus.norling@niva.no`
+Please use the [github issues tracker](https://github.com/NIVANorge/Mobius2/issues) to report bugs. You can also contact us at `magnus.norling@niva.no`

docs/index.md

@@ -44,7 +44,7 @@ Mobius2 also provides special support for transport along directed graphs and gr
 
 ## Authors and acknowledgement
 
-The Mobius2 framework is developed by Magnus Dahler Norling for [The Norwegian Institute for Water Research](https://www.niva.no/en) (NIVA).
+The Mobius2 framework is developed by Magnus Dahler Norling for [the Norwegian Institute for Water Research](https://www.niva.no/en) (NIVA).
 
 Additional contributions:
 Leah Jackson-Blake (Simply models, general testing), François Clayer (EasyLake model, general testing).

models/modules/hbv_snow.txt

@@ -12,9 +12,9 @@ module("HBVSnow", version(1, 0, 0),
 """
 This is an adaption of the snow module from HBV-Nordic (Sælthun 1995)
 
-[NVE home page](https://www.nve.no/vann-og-vassdrag/vannets-kretslop/analysemetoder-og-modeller/hbv-modellen/)
+[NVE home page](https://www.nve.no/vann-og-vassdrag/vannets-kretsloep/analysemetoder-og-modeller/hbv-modellen/)
 
-[Model description](https://www.uio.no/studier/emner/matnat/geofag/nedlagte-emner/GEO4430/v06/undervisningsmateriale/HBVMOD.PDF)
+[Model description](https://publikasjoner.nve.no/publication/1996/publication1996_07.pdf)
 
 Authors: Magnus D. Norling
 """

models/modules/nivafjord/basin.txt

@@ -35,6 +35,7 @@ module("NIVAFjord basin", version(0, 0, 3),
 	area      : property,
 	freeze_temp : property,
 	sw        : property,
+	ice_ind   : loc,
 	vert      : connection,
 	sw_vert   : connection,
 	sw_sed    : loc,
@@ -85,6 +86,7 @@ Authors: Magnus D. Norling
 
 	par_group("Layer specific mixing", layer) {
 		K0     : par_real("Mixing factor reference", [m 2, s-1], 0.5e-4, "Mixing factor when the B-V frequency is equal to the reference")
+		K0ice  : par_real("Mixing factor reference under ice", [m 2, s-1], 0.5e-4)
 	}
 
 	par_group("Initial layer physical", layer) {
@@ -178,7 +180,7 @@ Authors: Magnus D. Norling
 
 	#TODO: Make wind mixing instead dependent on the B-V frequency also? One issue is to determine how much energy gets "used" in each layer.
 	var(basin.emix, [J], "Total wind mixing energy") {
-		A[vert.top]*sqrt(stress^3/layer.water.rho[vert.top])*time.step_length_in_seconds
+		(!ice_ind)*A[vert.top]*sqrt(stress^3/layer.water.rho[vert.top])*time.step_length_in_seconds
 	}
 
 	var(layer.water.sumV, [m 3]) {
@@ -208,8 +210,9 @@ Authors: Magnus D. Norling
 	}
 
 	var(layer.water.v_t, [m, s-1]) {
+		K := { K0ice if ice_ind, K0 otherwise },
 		dz_ := 0.5*(dz + dz[vert.below]),
-		safe_divide(K0, dz_*(Nfreq/N0)^alpha)
+		safe_divide(K, dz_*(Nfreq/N0)^alpha)
 	}
 
 	var(layer.water.v_s, [m, s-1]) {

models/modules/nivafjord/fjordchem.txt

@@ -90,6 +90,7 @@ module("NIVAFjord chemistry", version(0, 0, 5),
 	chem_par : preamble
 ) {
 	#TODO: Would be nice to unify easychem and fjordchem a bit more, maybe some shared code.
+	# Esp. for surface O2 exchange
 
 	par_group("Initial chem", layer) {
 		init_O2  : par_real("Initial O₂ saturation", [], 1, 0, 1)
@@ -145,7 +146,7 @@ module("NIVAFjord chemistry", version(0, 0, 5),
 	}
 
 	var(layer.water.o2satconc, [m g, l-1]) {
-		o2_saturation(temp, salin)*o2_mol_mass -> [m g, l-1]
+		o2_saturation(temp, salin)*o2_mol_mass ->>
 	} #@no_store
 
 	var(layer.water.o2sat, []) {

models/nivafjord_isolated_basin_fpv_model.txt

@@ -0,0 +1,60 @@
+
+
+model("NIVAFjord Isolated Basin FPV") {
+"""
+NIVAFjord in a single basin without open boundary conditions. Also, you can cover basins with FPV (floating photovoltaics).
+
+It is also currently without horizontal exchange between basins, so it only works in a single one (or several isolated ones) for now.
+"""
+
+	# TODO: FPV cover does not dynamically affect wind mixing (not sure to how large a degree that would happen).
+	extend("nivafjord_lake_model.txt")
+
+	fpv       : compartment("FPV", basin_idx)
+
+	load("modules/airsea_fpv.txt",
+		module("AirSea FPV", air, basin, fpv, 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])))
+
+	module("Basin inflow", version(0, 0, 0)) {
+
+		var(air.precip, [m m, day-1], "Precipitation")
+		var(air.temp, [deg_c], "Air temperature")
+
+
+		load("stdlib/seawater.txt", library("Sea oxygen"))
+		load("stdlib/physiochemistry.txt", library("Chemistry"), library("Water utils"))
+
+		# Water
+
+		flow : property("Basin inflow")
+		var(basin.flow, [m 3, s-1]) # Input series
+
+		# Just directing the catchment runoff to the top layer instead of doing the density check.
+		flux(out, layer.water[vert.top], [m 3, s-1], "Discharge from land to basin") { basin.flow->> }
+
+		# O2
+
+		par_group("Inflow oxygen") {
+			f_o2sat    : par_real("Inflow O₂ saturation fraction", [], 0.9, 0, 1)
+		}
+
+		flux(out, layer.water.o2[vert.top], [k g, day-1], "Oxygen from land") {
+			inflow_t := air.temp, # Assume inflow temperature = air temperature (see also below)
+			land_conc := f_o2sat*o2_saturation(inflow_t, 0) * o2_mol_mass,
+			basin.flow*land_conc->>
+		}
+
+		# Heat / temperature
+
+		flux(out, layer.water.heat[vert.top], [J, day-1], "Heat from land") {
+			inflow_t := air.temp, # Assume inflow temperature = air temperature (see also above)
+			(water_temp_to_heat(basin.flow => [m 3], inflow_t) => [J, s-1]) ->>
+		}
+
+		# TODO: Add other substances that may be washed in.
+
+		# TODO: Also outflow?
+	}
+}
+

models/nivafjord_model.txt

@@ -59,7 +59,7 @@ model("NIVAFjord") {
 
 	load("modules/nivafjord/basin.txt",
 		dims : preamble("NIVAFjord dimensions", all_basins, layer_idx, 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, vert, sw_vert, loc(sediment.heat), dims))
+		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))