Separate config to store just transport fluxes.

dev_notes/todo.txt

@@ -4,16 +4,15 @@
 
 		Add forums on github page? (github Discussions)
 
-		Would like to be able to use in_flux in initial code (for e.g. setting initial steady states easily), but then we also need to be able to compute initial values for fluxes. With in_flux_connection it could be tricky to determine what initial fluxes must be computed (?).
+		Would like to be able to use in_flux in initial code (for e.g. setting initial steady states easily), but then we also need to be able to compute initial values for fluxes. With in_flux_connection it could be tricky to determine what initial fluxes must be computed (Not tricky, maybe, but a lot of work.. ?).
 
 		Made it possible to add properties to solvers manually, but it could be error prone.
 			Fix errors if they appear.
 
 		Specific models
-
-			Keep better track of what elevation different models want wind speed. Maybe convert between different elevations if necessary.
 
 			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?)
 
 			NIVAFjord!
 
@@ -92,7 +91,7 @@
 				Alternatively, in the ODE codegen, directly make a subtraction of the flux (on condition of correct index).
 					This is maybe the easiest, but is still a bit of work for this special case.
 
-				Actually in grid1d the connection aggregate is always unnecessary unless it is referenced. Would be better to remove it as a default and only generate it if it is referenced by in_flux(connection).
+				Actually in grid1d the connection aggregate is always unnecessary unless it is referenced. Would it be better to remove it as a default and only generate it if it is referenced in code by in_flux(connection)?
 
 
 			.specific target:

docs/existingmodels/existingmodels.md

@@ -16,7 +16,7 @@ The Mobius2 framework comes with several existing modules and models that can be
 If desired, the above models can be coupled together into a full catchment-to-coast system, or you can use them separately to study smaller sub-systems.
 
 The following model is stand-alone:
-- [MAGIC](magic.html). This is a longer-timescale model for development of soil water chemistry (with a focus on acidity) in smaller catchment.
+- [MAGIC](magic.html). This is a longer-timescale model for development of soil water chemistry (with a focus on acidity) in smaller catchments.
 
 In addition to these, Mobius2 comes with modules for other processes that are convenient to include into larger models, for instance
 - [Snow pack and melt](autogen/auxiliary.html#hbvsnow)

docs/mobius2docs/guide_chapters/07_layered_lake.md

@@ -72,8 +72,9 @@ var(layer.water.N2freq, [s-2]) {
 Note how we can reference a value below us along a `grid1d` connection by using a square bracket.
 
 The `@no_store` directive just tells Mobius2 to not store the time series of this variable. This can be useful for a couple of reasons
-	- It saves memory. This is especially important for variables in compartments that are distributed over large index sets.
-	- Too many variables can clutter up the user interface, and not all of them are interesting in themselves.
+
+- It saves memory. This is especially important for variables in compartments that are distributed over large index sets.
+- Too many variables can clutter up the user interface, and not all of them are interesting in themselves.
 
 The mixing coefficient $$K$$ is (as in MyLake) given by
 

example_notebooks/basic_python.ipynb

@@ -36,7 +36,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0x20a1c881340>"
+       "<matplotlib.legend.Legend at 0x1c818f6eae0>"
       ]
      },
      "execution_count": 3,
@@ -249,6 +249,14 @@
     "app.run()\n",
     "app.var('Reach flow flux')['Coull'].plot(figsize=(10, 5), legend=True)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4a9a5de3-9040-4c9c-bee7-e51c9b921a9e",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

mobipy/__init__.py

@@ -68,6 +68,13 @@ class Mobius_Entity_Metadata(ctypes.Structure) :
 		("min", Parameter_Value),
 		("max", Parameter_Value)
 	]
+
+class Mobius_Base_Config(ctypes.Structure) :
+	_fields_ = [
+		("store_transport_fluxes", ctypes.c_bool),
+		("store_all_series", ctypes.c_bool),
+		("developer_mode", ctypes.c_bool),
+	]
 
 def mobius2_path() :
 	#NOTE: We have to add a trailing slash to the path for Mobius2 to understand it.
@@ -106,7 +113,7 @@ def load_dll() :
 	dll.mobius_encountered_log.argtypes = [ctypes.c_char_p, ctypes.c_int64]
 	dll.mobius_encountered_log.restype = ctypes.c_int64
 
-	dll.mobius_build_from_model_and_data_file.argtypes = [ctypes.c_char_p, ctypes.c_char_p, ctypes.c_char_p, ctypes.c_bool, ctypes.c_bool]
+	dll.mobius_build_from_model_and_data_file.argtypes = [ctypes.c_char_p, ctypes.c_char_p, ctypes.c_char_p, ctypes.POINTER(Mobius_Base_Config)]
 	dll.mobius_build_from_model_and_data_file.restype  = ctypes.c_void_p
 
 	dll.mobius_delete_application.argtypes = [ctypes.c_void_p]
@@ -391,9 +398,20 @@ def __exit__(self, type, value, tb) :
 		self.__del__()
 
 	@classmethod
-	def build_from_model_and_data_file(cls, model_file, data_file, store_all_series=False, dev_mode=False) :
+	def build_from_model_and_data_file(cls, model_file, data_file, 
+		store_all_series=False, dev_mode=False, store_transport_fluxes=False
+	) :
+
 		base_path = mobius2_path()
-		data_ptr = dll.mobius_build_from_model_and_data_file(_c_str(model_file), _c_str(data_file), _c_str(base_path), store_all_series, dev_mode)
+
+		# TODO: We could use the args as dict thing here to make this more dynamic.
+		config = Mobius_Base_Config()
+		config.store_all_series = store_all_series
+		config.dev_mode = dev_mode
+		config.store_transport_fluxes = store_transport_fluxes
+
+		cfgptr = ctypes.POINTER(Mobius_Base_Config)(config)
+		data_ptr = dll.mobius_build_from_model_and_data_file(_c_str(model_file), _c_str(data_file), _c_str(base_path), cfgptr)
 		_check_for_errors()
 		return cls(data_ptr, True)
 

mobius_jl/mobius.jl

@@ -66,6 +66,12 @@ struct Entity_Ref
 	entity_id::Entity_Id
 end
 
+struct Mobius_Base_Config
+	store_transport_fluxes::Cint
+	store_all_series::Cint
+	developer_mode::Cint
+end
+
 invalid_entity_id = Entity_Id(-1, -1)
 invalid_var       = Var_Id(-1, -1)
 no_index          = Mobius_Index_Value(C_NULL, 0)
@@ -97,11 +103,15 @@ function check_error()
 	end
 end
 
-function setup_model(model_file::String, data_file::String, store_series::Bool = false, dev_mode::Bool = false)::Model_Data
+function setup_model(model_file::String, data_file::String, ; store_transport_fluxes::Bool = false, store_all_series::Bool = false, dev_mode::Bool = false)::Model_Data
 	#mobius_path = string(dirname(dirname(Base.source_path())), "\\") # Doesn't work in IJulia
 	mobius_path = string(dirname(dirname(@__FILE__)), "\\")
-	result =  ccall(setup_model_h, Ptr{Cvoid}, (Cstring, Cstring, Cstring, Cint, Cint), 
-		model_file, data_file, mobius_path, store_series, dev_mode)
+
+	cfg = Mobius_Base_Config(store_transport_fluxes, store_all_series, dev_mode)
+	cfgptr = Ref(cfg)
+
+	result =  ccall(setup_model_h, Ptr{Cvoid}, (Cstring, Cstring, Cstring, Ptr{Mobius_Base_Config}), 
+		model_file, data_file, mobius_path, cfgptr)
 	check_error()
 	return Model_Data(result, true)
 end

models/modules/airsea_fpv.txt

@@ -174,8 +174,6 @@ Authors: Francois Clayer, Magnus D. Norling
 
 	/*
 
-	# TODO: Separate heat fluxes between FPV-surface (and FPV-air) ?
-
 	# TODO: Make the below work (and add the correct heat budget for the basin?)
 
 	k_vis    : property("Kinematic viscosity")
@@ -202,25 +200,26 @@ Authors: Francois Clayer, Magnus D. Norling
 
 		# TODO: Name the magic constants, and/or reference the formula
 
-		#T_front_final := air.temp->[K],
-		#need to iterate to updte T_front  (what is the breaking condition?)
-			T_front := top_water.temp->[K],
-			T_air := air.temp->[K],
-			T_sky := (0.0552 * (T_air=>[]^(1.5))) => [K],
-			T_water := top_water.temp -> [K],                 # Why is it the same as T_front?
-			h_air := (2.8 + 3*air.wind=>[]) => [W, m-2, K-1],
-			h_sky := (1/(1/0.88+1/0.80-1)) * 5.67e-8[W, m-2, K-4] * (T_front+T_sky)*(T_front^2 + T_sky^2),
-			B_back := A_both + h_water,
-			C_back := h_water * T_water,
+		T_air := air.temp->[K],
+		T_sky := (0.0552 * (T_air=>[]^1.5)) => [K],
+		T_water := top_water.temp -> [K],
+		h_air := (2.8 + 3*air.wind=>[]) => [W, m-2, K-1],
+		B_back := A_both + h_water,
+		C_back := h_water * T_water,
+
+		T_front := top_water.temp->[K] + 3[K],
+		eps := 0.001[K]
+		i:{
+			h_sky := (1/(1/0.88+1/0.80-1)) * 5.67e-8[W, m-2, K-4] * (T_front+T_sky)*(T_front^2 + T_sky^2),	
 			B_front := A_both + h_air + h_sky,
 			C_front := h_air*T_air + h_sky*T_sky,
 			numer :=  B_front*B_back*2*A_both - (A_both^2)*(B_front - B_back),
-			T_cell := (B_front*B_back*(1- FPV_alb) * (1-FPV_eff)*air.g_rad + A_both*B_back*C_front + A_both*B_front*C_back) / numer -> [deg_c],
-			#A_both * h_water / (A_both + h_water) + A_both / (A_both + h_air + h_sky)*(h_air + h_sky*(Tc - T_sky)/(Tc - T_air))
-			T_front_final := ((A_both =>[] * (T_cell->[K])=>[]) + C_front=>[]) / B_front=>[],
+			T_cell := (B_front*B_back*(1- FPV_alb)*(1-FPV_eff)*air.g_rad + A_both*(B_back*C_front + B_front*C_back)) / numer -> [deg_c],
+			T_front_update := ((A_both =>[] * (T_cell->[K])=>[]) + C_front=>[]) / B_front=>[K],
 
-		T_cell
-
+			T_cell                                if abs(T_front - T_front_update) < eps,
+			{T_front <- T_front_update, iterate i} otherwise	
+		}
 	}
 
 	var(fpv.T_s_back, [deg_c]) {

models/modules/pet.txt

@@ -87,7 +87,8 @@ Authors: Magnus D. Norling
 		# Also, the energy balance should take snow melt into account.
 		net_rad := net_sw + air.lwd - lwu,
 
-		u := max(0.5[m, s-1], air.wind),
+		w := air.wind * 0.75, # Convert from 10m to 2m altitude
+		u := max(0.5[m, s-1], w),
 		# Modified psychrometric constant
 		psy_corr := {
 			psy                             if pt,

src/c_abi.cpp

@@ -79,12 +79,10 @@ mobius_encountered_log(char *msg_out, s64 buf_len) {
 }
 
 DLLEXPORT Model_Data *
-mobius_build_from_model_and_data_file(char * model_file, char * data_file, char *base_path, bool store_series, bool dev_mode) {
+mobius_build_from_model_and_data_file(char * model_file, char * data_file, char *base_path, Mobius_Base_Config *cfg) {
 
-	Mobius_Config config;
+	Mobius_Config config = *cfg;
 	config.mobius_base_path = base_path;
-	config.store_all_series = store_series;
-	config.developer_mode   = dev_mode;
 
 	try {
 		Mobius_Model *model = load_model(model_file, &config);

src/c_abi.h

@@ -62,7 +62,7 @@ DLLEXPORT s64
 mobius_encountered_log(char *msg_out, s64 buf_len);
 
 DLLEXPORT Model_Data *
-mobius_build_from_model_and_data_file(char * model_file, char * data_file, char *base_path, bool store_series, bool dev_mode);
+mobius_build_from_model_and_data_file(char * model_file, char * data_file, char *base_path, Mobius_Base_Config *cfg);
 
 DLLEXPORT void
 mobius_delete_application(Model_Data *data);

src/model_composition.cpp

@@ -931,7 +931,7 @@ prelim_compose(Model_Application *app, std::vector<std::string> &input_names) {
 			sprintf(varname, "carried_flux(%s, %s)", var_name.data(), flux_name.data());
 
 			// It is just much cleaner in MobiView if this is off, but on the other hand we do want to know some of these fluxes quite often. Make a more granular way to specify which ones to store?
-			bool no_store = true;
+			bool no_store = !model->config.store_transport_fluxes;
 
 			Var_Id gen_flux_id = register_state_variable<State_Var::Type::dissolved_flux>(app, invalid_entity_id, false, varname, no_store);
 			auto gen_flux = as<State_Var::Type::dissolved_flux>(app->vars[gen_flux_id]);

src/model_declaration.cpp

@@ -1466,19 +1466,24 @@ load_config(String_View file_name) {
 			match_declaration(decl, {{Token_Type::quoted_string, Token_Type::boolean}}, false);
 
 			config.developer_mode = single_arg(decl, 1)->val_bool;
-
-			log_print(Log_Mode::dev, file_name, ": Configured to developer mode.\n");
 		} else if(item == "Just store all the series") {
 			match_declaration(decl, {{Token_Type::quoted_string, Token_Type::boolean}}, false);
 
 			config.store_all_series = single_arg(decl, 1)->val_bool;
+		} else if(item == "Store transport fluxes") {
+			match_declaration(decl, {{Token_Type::quoted_string, Token_Type::boolean}}, false);
+
+			config.store_transport_fluxes = single_arg(decl, 1)->val_bool;
 		} else {
 			decl->source_loc.print_error_header();
 			fatal_error("Unknown config option \"", item, "\".");
 		}
 		delete decl;
 	}
 
+	if(config.developer_mode)
+		log_print(Log_Mode::dev, file_name, ": Configured to developer mode.\n");
+
 	return std::move(config);
 }
 

src/model_declaration.h

@@ -274,12 +274,20 @@ Solver_Function_Registration : Registration_Base {
 };
 
 struct
-Mobius_Config {
-	std::string mobius_base_path;
+Mobius_Base_Config {
+	bool store_transport_fluxes = false;
 	bool store_all_series = false;
 	bool developer_mode   = false;
 };
 
+struct
+Mobius_Config : Mobius_Base_Config {
+	std::string mobius_base_path;
+
+	Mobius_Config() = default;
+	Mobius_Config(const Mobius_Base_Config &c) : Mobius_Base_Config(c) {}
+};
+
 struct
 Mobius_Model : Catalog {