fluxnet data handling in extension (#1238)

Author: kmdeck

NEWS.md

@@ -3,6 +3,7 @@ ClimaLand.jl Release Notes
 
 main
 -------
+- Add data handling tools to FluxnetSimulationsExt and use throughout docs and experiments PR[#1238](https://github.com/CliMA/ClimaLand.jl/pull/1238)
 - Add convenience constructors for CanopyModel and integrated models PR[#1255](https://github.com/CliMA/ClimaLand.jl/pull/1255)
 - Rename LandSimulationVisualization to LandSimulationVisualizationExt; add template for FluxnetSimulationsExt PR[#1259](https://github.com/CliMA/ClimaLand.jl/pull/1259)
 - Remove root_depths from the PrescribeGroundConditions struct, and treat these ground ``drivers" consistently with how we handle atmospheric forcing PR[#1199](https://github.com/CliMA/ClimaLand.jl/pull/1240)

docs/src/tutorials/integrated/soil_canopy_tutorial.jl

@@ -52,6 +52,9 @@ using ClimaLand.Canopy
 using ClimaLand.Canopy.PlantHydraulics
 import ClimaLand
 import ClimaLand.Parameters as LP
+using DelimitedFiles
+FluxnetSimulationsExt =
+    Base.get_extension(ClimaLand, :FluxnetSimulationsExt).FluxnetSimulationsExt;
 
 # Define the floating point precision desired (64 or 32 bit), and get the
 # parameter set holding constants used across CliMA Models:
@@ -65,8 +68,6 @@ nelements = 10
 zmin = FT(-2)
 zmax = FT(0)
 f_root_to_shoot = FT(3.5)
-SAI = FT(0.00242)
-maxLAI = FT(4.2)
 plant_ν = FT(2.46e-4)
 n_stem = Int64(1)
 n_leaf = Int64(1)
@@ -82,14 +83,12 @@ land_domain = Column(; zlim = (zmin, zmax), nelements = nelements);
 #   the simulation with atmospheric and radiative flux models. We also
 # read in the observed LAI and let that vary in time in a prescribed manner.
 
-# Use the data tools for reading FLUXNET data sets
-include(
-    joinpath(pkgdir(ClimaLand), "experiments/integrated/fluxnet/data_tools.jl"),
-);
 
 # First provide some information about the site
+site_ID = "US-MOz"
 # Timezone (offset from UTC in hrs)
 time_offset = 7
+start_date = DateTime(2010) + Hour(time_offset)
 
 # Site latitude and longitude
 lat = FT(38.7441) # degree
@@ -98,17 +97,17 @@ long = FT(-92.2000) # degree
 # Height of the sensor at the site
 atmos_h = FT(32) # m
 
-# Provide the site site ID and the path to the data file:
-site_ID = "US-MOz"
-data_link = "https://caltech.box.com/shared/static/7r0ci9pacsnwyo0o9c25mhhcjhsu6d72.csv"
-
-include(
-    joinpath(
-        pkgdir(ClimaLand),
-        "experiments/integrated/fluxnet/met_drivers_FLUXNET.jl",
-    ),
+# Forcing data
+(; atmos, radiation) = FluxnetSimulationsExt.prescribed_forcing_fluxnet(
+    site_ID,
+    lat,
+    long,
+    time_offset,
+    atmos_h,
+    start_date,
+    earth_param_set,
+    FT,
 );
-
 # # Setup the Coupled Canopy and Soil Physics Model
 
 # We want to simulate the canopy-soil system together, so the model type
@@ -224,9 +223,13 @@ photosynthesis_args =
     (; parameters = FarquharParameters(FT, is_c3; Vcmax25 = FT(5e-5)));
 
 K_sat_plant = FT(1.8e-8)
+(; LAI, maxLAI) =
+    FluxnetSimulationsExt.prescribed_LAI_fluxnet(site_ID, start_date)
+maxLAI = FT(maxLAI) # convert to the float type of our simulation
+SAI = FT(0.00242)
 RAI = (SAI + maxLAI) * f_root_to_shoot;
 # Note: LAIfunction was determined from data in the script we included above.
-ai_parameterization = PrescribedSiteAreaIndex{FT}(LAIfunction, SAI, RAI)
+ai_parameterization = PrescribedSiteAreaIndex{FT}(LAI, SAI, RAI)
 
 ψ63 = FT(-4 / 0.0098)
 Weibull_param = FT(4)

docs/src/tutorials/standalone/Canopy/canopy_tutorial.jl

@@ -52,6 +52,9 @@ using ClimaLand.Canopy
 using ClimaLand.Canopy.PlantHydraulics
 import ClimaLand
 import ClimaLand.Parameters as LP
+using DelimitedFiles
+FluxnetSimulationsExt =
+    Base.get_extension(ClimaLand, :FluxnetSimulationsExt).FluxnetSimulationsExt;
 
 # Define the floating point precision desired (64 or 32 bit), and get the
 # parameter set holding constants used across CliMA Models:
@@ -81,8 +84,6 @@ nelements = 10
 zmin = FT(-2)
 zmax = FT(0)
 f_root_to_shoot = FT(3.5)
-SAI = FT(0.00242)
-maxLAI = FT(4.2)
 plant_ν = FT(2.46e-4) # kg/m^2
 n_stem = Int64(1)
 n_leaf = Int64(1)
@@ -98,31 +99,30 @@ land_domain = Point(; z_sfc = FT(0.0))
 #   the simulation with atmospheric and radiative flux models. We also
 # read in the observed LAI and let that vary in time in a prescribed manner.
 
-# Use the data tools for reading FLUXNET data sets
-include(
-    joinpath(pkgdir(ClimaLand), "experiments/integrated/fluxnet/data_tools.jl"),
-);
-
 # First provide some information about the site
 # Timezone (offset from UTC in hrs)
 time_offset = 7
+start_date = DateTime(2010) + Hour(time_offset)
 
 # Site latitude and longitude
 lat = FT(38.7441) # degree
 long = FT(-92.2000) # degree
 
 # Height of the sensor at the site
 atmos_h = FT(32)
-
-# Provide the site site ID and the path to the data file:
-site_ID = "US-MOz"
-data_link = "https://caltech.box.com/shared/static/7r0ci9pacsnwyo0o9c25mhhcjhsu6d72.csv"
-
-include(
-    joinpath(
-        pkgdir(ClimaLand),
-        "experiments/integrated/fluxnet/met_drivers_FLUXNET.jl",
-    ),
+# Site ID
+site_ID = "US-MOz";
+
+# Forcing data
+(; atmos, radiation) = FluxnetSimulationsExt.prescribed_forcing_fluxnet(
+    site_ID,
+    lat,
+    long,
+    time_offset,
+    atmos_h,
+    start_date,
+    earth_param_set,
+    FT,
 );
 
 # Populate the SharedCanopyParameters struct, which holds the parameters
@@ -185,13 +185,12 @@ AR_model = AutotrophicRespirationModel{FT}(AR_params);
 # Begin by providing general plant parameters. For the area
 # indices of the canopy, we choose a `PrescribedSiteAreaIndex`,
 # which supports LAI as a function of time, with RAI and SAI as constant.
-LAI = 4.2
-LAIfunction = (t) -> LAI
+(; LAI, maxLAI) =
+    FluxnetSimulationsExt.prescribed_LAI_fluxnet(site_ID, start_date)
 SAI = FT(0.00242)
 f_root_to_shoot = FT(3.5)
-RAI = FT((SAI + LAI) * f_root_to_shoot)
-ai_parameterization =
-    PrescribedSiteAreaIndex{FT}(TimeVaryingInput(LAIfunction), SAI, RAI)
+RAI = FT((SAI + maxLAI) * f_root_to_shoot)
+ai_parameterization = PrescribedSiteAreaIndex{FT}(LAI, SAI, RAI)
 rooting_depth = FT(1.0);
 
 

experiments/integrated/fluxnet/data_tools.jl

@@ -1,7 +1,6 @@
 """This file contains the site-generic time variables for running ClimaLand on
 fluxtower sites. These work in tandem with the site-specific timing parameters
 found in the {site-ID}_simulation.jl files in each site directory."""
-
 N_spinup_days = 15
 N_days = N_spinup_days + 340