Merge pull request #1323 from CliMA/js/integ-tutorials

minor fixes: docs typos, output writer closing, FrequencyBasedCallback

Author: juliasloan25

docs/src/tutorials/integrated/snowy_land_fluxnet_tutorial.jl

@@ -1,12 +1,13 @@
 # # Fluxnet simulations with the full land model: snow, soil, canopy
 
 # In the
-# [SoilCanopyModel tutorial](docs/src/tutorials/integrated/soil_canopy_fluxnet_tutorial.md),
+# [SoilCanopyModel tutorial](docs/src/tutorials/integrated/soil_canopy_fluxnet_tutorial.jl),
 # we demonstrated how to run the an integrated model with a soil and
 # canopy component at the US-MOz fluxnet site.
 # Here we add in a snow component, and run the site at the Niwot Ridge site instead.
 # The forcing data was obtained from
 # AmeriFlux FLUXNET: https://doi.org/10.17190/AMF/1871141
+
 # Citation: Peter D. Blanken, Russel K. Monson, Sean P. Burns,
 # David R. Bowling, Andrew A. Turnipseed (2022),
 # AmeriFlux FLUXNET-1F US-NR1 Niwot Ridge Forest (LTER NWT1),
@@ -15,7 +16,8 @@
 # The focus of this tutorial is to learn the steps towards setting up and
 # running an integrated simulation, and less on the parameterization
 # choices. As such, the default parameters are implicitly set.
-# To experiment with modularity in the parameters and parameterizations, please see the [canopy parameterizations tutorial](docs/src/tutorials/standalone/Canopy/changing_canopy_parameterizations.md) or the [soiil parameterizations tutorial](docs/src/tutorials/standalone/Soil/changing_soil_parameterizations.md).
+# To experiment with modularity in the parameters and parameterizations, please see the [canopy parameterizations tutorial](docs/src/tutorials/standalone/Canopy/changing_canopy_parameterizations.jl)
+# or the [soil parameterizations tutorial](docs/src/tutorials/standalone/Soil/changing_soil_parameterizations.jl).
 
 # # Preliminary Setup
 using Dates
@@ -40,7 +42,7 @@ earth_param_set = LP.LandParameters(FT);
 # US-NR1 tower.  We also
 # read in the MODIS LAI and let that vary in time in a prescribed manner.
 site_ID = "US-NR1";
-site_ID_val = FluxnetSimulations.replace_hyphen(site_ID)
+site_ID_val = FluxnetSimulations.replace_hyphen(site_ID);
 # Get the latitude and longitude in degrees, as well as the
 # time offset in hours of local time from UTC
 (; time_offset, lat, long) =
@@ -106,7 +108,7 @@ diagnostics = ClimaLand.default_diagnostics(
     average_period = :hourly,
 );
 
-# How often we want to update the forcing.
+# Choose how often we want to update the forcing.
 data_dt = Second(FluxnetSimulations.get_data_dt(site_ID));
 updateat = Array(start_date:data_dt:stop_date);
 

docs/src/tutorials/integrated/soil_canopy_fluxnet_tutorial.jl

@@ -1,7 +1,7 @@
 # # Fluxnet simulations with an integrated soil and canopy model
 
 # In the
-# [standalone canopy tutorial](docs/src/tutorials/standalone/Canopy/canopy_tutorial.md),
+# [standalone canopy tutorial](docs/src/tutorials/standalone/Canopy/canopy_tutorial.jl),
 # we demonstrated how to run the canopy model in
 # standalone mode using a prescribed soil moisture
 # and ground temperature. ClimaLand can also
@@ -14,13 +14,15 @@
 # located within an oak-hickory forest in Ozark, Missouri, USA.
 # The forcing data was obtained from
 # AmeriFlux FLUXNET: https://doi.org/10.17190/AMF/1854370
+
 # Citation: Jeffrey Wood, Lianhong Gu (2025), AmeriFlux FLUXNET-1F US-MOz Missouri Ozark
 # Site, Ver. 5-7, AmeriFlux AMP, (Dataset). https://doi.org/10.17190/AMF/1854370
 
 # The focus of this tutorial is to learn the steps towards setting up and
 # running an integrated simulation, and less on the parameterization
 # choices. As such, the default parameters are implicitly set.
-# To experiment with modularity in the parameters and parameterizations, please see the [canopy parameterizations tutorial](docs/src/tutorials/standalone/Canopy/changing_canopy_parameterizations.md) or the [soiil parameterizations tutorial](docs/src/tutorials/standalone/Soil/changing_soil_parameterizations.md).
+# To experiment with modularity in the parameters and parameterizations, please see the [canopy parameterizations tutorial](docs/src/tutorials/standalone/Canopy/changing_canopy_parameterizations.jl)
+# or the [soil parameterizations tutorial](docs/src/tutorials/standalone/Soil/changing_soil_parameterizations.jl).
 
 # # Preliminary Setup
 using Dates
@@ -44,7 +46,7 @@ earth_param_set = LP.LandParameters(FT);
 # We will use prescribed atmospheric and radiative forcing from the
 # US-MOz tower.
 site_ID = "US-MOz";
-site_ID_val = FluxnetSimulations.replace_hyphen(site_ID)
+site_ID_val = FluxnetSimulations.replace_hyphen(site_ID);
 # Get the latitude and longitude in degrees, as well as the
 # time offset in hours of local time from UTC
 (; time_offset, lat, long) =
@@ -110,10 +112,11 @@ diagnostics = ClimaLand.default_diagnostics(
     average_period = :hourly,
 );
 
-# How often we want to update the forcing.
+# Choose how often we want to update the forcing.
 data_dt = Second(FluxnetSimulations.get_data_dt(site_ID));
 updateat = Array(start_date:data_dt:stop_date);
 
+# Now we can construct the simulation object and solve it.
 simulation = Simulations.LandSimulation(
     start_date,
     stop_date,

experiments/integrated/fluxnet/ozark_pft.jl

@@ -347,7 +347,6 @@ simulation = LandSimulation(
 )
 sol = solve!(simulation)
 
-ClimaLand.Diagnostics.close_output_writers(diags)
 comparison_data = FluxnetSimulations.get_comparison_data(site_ID, time_offset)
 savedir =
     joinpath(pkgdir(ClimaLand), "experiments/integrated/fluxnet/US-MOz/pft/out")

experiments/integrated/fluxnet/run_fluxnet.jl

@@ -313,7 +313,6 @@ simulation = LandSimulation(
 )
 @time sol = solve!(simulation)
 
-ClimaLand.Diagnostics.close_output_writers(diags)
 comparison_data = FluxnetSimulations.get_comparison_data(site_ID, time_offset)
 savedir =
     joinpath(pkgdir(ClimaLand), "experiments/integrated/fluxnet/$(site_ID)/out")

experiments/integrated/global/global_soil_canopy.jl

@@ -146,7 +146,6 @@ simulation = LandSimulation(
     user_callbacks = (),
 )
 ClimaLand.Simulations.solve!(simulation)
-ClimaLand.Diagnostics.close_output_writers(diags)
 
 # ClimaAnalysis
 if ClimaComms.iamroot(context)

experiments/standalone/Bucket/bucket_era5.jl

@@ -204,7 +204,6 @@ sol = ClimaComms.@time ClimaComms.device() ClimaLand.Simulations.solve!(
     simulation,
 );
 
-ClimaLand.Diagnostics.close_output_writers(diags)
 
 simdir = ClimaAnalysis.SimDir(output_dir)
 short_names = ["rn", "tsfc", "qsfc", "lhf", "shf", "wsoil", "wsfc", "ssfc"]

experiments/standalone/Bucket/global_bucket_temporalmap.jl

@@ -213,7 +213,6 @@ simulation, saved_values, nc_writer =
 sol = ClimaComms.@time ClimaComms.device() ClimaLand.Simulations.solve!(
     simulation,
 );
-close(nc_writer)
 output_dir = nc_writer.output_dir
 
 simdir = ClimaAnalysis.SimDir(output_dir)
@@ -246,7 +245,6 @@ if PROFILING
     flame_file = joinpath(outdir, "flame_$device_suffix.html")
     ProfileCanvas.html_file(flame_file, results)
     @info "Save compute flame to $flame_file"
-    close(nc_writer)
 
     simulation, saved_values, nc_writer =
         setup_prob(start_date, start_date + Second(tf), Δt, outdir)
@@ -258,7 +256,6 @@ if PROFILING
     alloc_flame_file = joinpath(outdir, "alloc_flame_$device_suffix.html")
     ProfileCanvas.html_file(alloc_flame_file, profile)
     @info "Save allocation flame to $alloc_flame_file"
-    close(nc_writer)
 end
 
 # Interpolate to grid

src/shared_utilities/utils.jl

@@ -684,7 +684,7 @@ function NaNCheckCallback(
     end
     affect! = (integrator) -> call_count_nans_state(integrator.u; mask)
 
-    SciMLBase.DiscreteCallback(cond, affect!)
+    return SciMLBase.DiscreteCallback(cond, affect!)
 end
 
 # no date version
@@ -730,10 +730,10 @@ arguments at a specified frequency in simulation time.
     integrator as its first argument and kwargs specified in
     `func_args`. Typically, such a function will look something like:
         (integrator; func_args) -> do_some_update(integrator.p, integrator.u, ...)
-    Note that func_args can be empty. 
+    Note that func_args can be empty.
 
 The callback uses `ClimaDiagnostics.EveryCalendarDtSchedule` to determine when to
-call the function based on the `frequency`. 
+call the function based on the `frequency`.
 """
 function FrequencyBasedCallback(
     frequency::Union{AbstractFloat, Dates.Period},
@@ -766,8 +766,8 @@ function FrequencyBasedCallback(
     cond = let schedule = schedule
         (u, t, integrator) -> schedule(integrator)
     end
-    affect! = (integrator) -> call_count_nans_state(integrator.u; mask)
-    SciMLBase.DiscreteCallback(cond, affect!)
+    affect! = (integrator) -> func(integrator; func_args...)
+    return SciMLBase.DiscreteCallback(cond, affect!)
 end
 
 """