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diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json
@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-09-03T01:04:35","documenter_version":"1.6.0"}}
+{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-10-03T21:20:30","documenter_version":"1.7.0"}}
diff --git a/dev/APIs/Bucket/index.html b/dev/APIs/Bucket/index.html
diff --git a/dev/APIs/ClimaLand/index.html b/dev/APIs/ClimaLand/index.html
diff --git a/dev/APIs/Regridder/index.html b/dev/APIs/Regridder/index.html
diff --git a/dev/APIs/Snow/index.html b/dev/APIs/Snow/index.html
diff --git a/dev/APIs/Soil/index.html b/dev/APIs/Soil/index.html
diff --git a/dev/APIs/SoilBiogeochemistry/index.html b/dev/APIs/SoilBiogeochemistry/index.html
diff --git a/dev/APIs/SurfaceWater/index.html b/dev/APIs/SurfaceWater/index.html
diff --git a/dev/APIs/canopy/AutotrophicRespiration/index.html b/dev/APIs/canopy/AutotrophicRespiration/index.html
diff --git a/dev/APIs/canopy/Canopy/index.html b/dev/APIs/canopy/Canopy/index.html
diff --git a/dev/APIs/canopy/CanopyEnergy/index.html b/dev/APIs/canopy/CanopyEnergy/index.html
diff --git a/dev/APIs/canopy/Photosynthesis/index.html b/dev/APIs/canopy/Photosynthesis/index.html
diff --git a/dev/APIs/canopy/PlantHydraulics/index.html b/dev/APIs/canopy/PlantHydraulics/index.html
diff --git a/dev/APIs/canopy/RadiativeTransfer/index.html b/dev/APIs/canopy/RadiativeTransfer/index.html
diff --git a/dev/APIs/canopy/StomatalConductance/index.html b/dev/APIs/canopy/StomatalConductance/index.html
diff --git a/dev/APIs/shared_utilities/index.html b/dev/APIs/shared_utilities/index.html
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diff --git a/dev/generated/standalone/Soil/richards_equation/index.html b/dev/generated/standalone/Soil/richards_equation/index.html
diff --git a/dev/generated/standalone/Soil/soil_energy_hydrology/index.html b/dev/generated/standalone/Soil/soil_energy_hydrology/index.html
diff --git a/dev/generated/standalone/Soil/sublimation/index.html b/dev/generated/standalone/Soil/sublimation/index.html
diff --git a/dev/generated/standalone/Soil/water_fluxes.png b/dev/generated/standalone/Soil/water_fluxes.png
diff --git a/dev/generated/standalone/Usage/LSM_single_column_tutorial/index.html b/dev/generated/standalone/Usage/LSM_single_column_tutorial/index.html
diff --git a/dev/generated/standalone/Usage/domain_tutorial/index.html b/dev/generated/standalone/Usage/domain_tutorial/index.html
diff --git a/dev/generated/standalone/Usage/model_tutorial/index.html b/dev/generated/standalone/Usage/model_tutorial/index.html
diff --git a/dev/getting_started/index.html b/dev/getting_started/index.html
diff --git a/dev/index.html b/dev/index.html
diff --git a/dev/objects.inv b/dev/objects.inv
diff --git a/dev/search_index.js b/dev/search_index.js
diff --git a/dev/standalone/README/index.html b/dev/standalone/README/index.html
diff --git a/dev/standalone/apps/leaf_an.jl b/dev/standalone/apps/leaf_an.jl
@@ -38,10 +38,11 @@ function ParamViz.parameterisation(
     Γstar = co2_compensation(Γstar25, ΔHΓstar, T, To, R)
     medlynt = 1 + g1 / sqrt(VPD)
     ci = intercellular_co2(ca, Γstar, medlynt)
-    Aj = light_assimilation(Canopy.C3(), J, ci, Γstar)
+    is_c3 = 1.0
+    Aj = light_assimilation(is_c3, J, ci, Γstar)
     Kc = MM_Kc(Kc25, ΔHkc, T, To, R)
     Ko = MM_Ko(Ko25, ΔHko, T, To, R)
-    Ac = rubisco_assimilation(Canopy.C3(), Vcmax, ci, Γstar, Kc, Ko, oi)
+    Ac = rubisco_assimilation(is_c3, Vcmax, ci, Γstar, Kc, Ko, oi)
     Rd = dark_respiration(Vcmax25, β, f, ΔHRd, T, To, R)
     An = net_photosynthesis(Ac, Aj, Rd, β)
     return An
@@ -83,7 +84,7 @@ function An_app_f()
             "Ω", # Clumping index
             "Γstar25", # co2 compensation at 25c
             "ΔHΓstar", # a constant energy of activation
-            "To", # a standard temperature 
+            "To", # a standard temperature
             "R", # the universal gas constant
             "Vcmax25", # the maximum rate of carboxylation of Rubisco
             "ΔHJmax", # a constant

diff --git a/dev/standalone/apps/leaf_an_ci.jl b/dev/standalone/apps/leaf_an_ci.jl
@@ -36,8 +36,9 @@ function ParamViz.parameterisation(
     Γstar = co2_compensation(Γstar25, ΔHΓstar, T, To, R)
     Kc = MM_Kc(Kc25, ΔHkc, T, To, R)
     Ko = MM_Ko(Ko25, ΔHko, T, To, R)
-    Ac = rubisco_assimilation(Canopy.C3(), Vcmax, ci, Γstar, Kc, Ko, oi)
-    Aj = light_assimilation(Canopy.C3(), J, ci, Γstar)
+    is_c3 = 1.0
+    Ac = rubisco_assimilation(is_c3, Vcmax, ci, Γstar, Kc, Ko, oi)
+    Aj = light_assimilation(is_c3, J, ci, Γstar)
     Rd = dark_respiration(Vcmax25, β, f, ΔHRd, T, To, R)
     An = net_photosynthesis(Ac, Aj, Rd, β)
     return An
@@ -79,7 +80,7 @@ function An_ci_app_f()
             "Ω", # Clumping index
             "Γstar25", # co2 compensation at 25c
             "ΔHΓstar", # a constant energy of activation
-            "To", # a standard temperature 
+            "To", # a standard temperature
             "R", # the universal gas constant
             "ΔHJmax", # a constant
             "θj", # an empirical "curvature parameter"

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diff --git a/dev/standalone/pages/soil/hydrology/richards_model/index.html b/dev/standalone/pages/soil/hydrology/richards_model/index.html
diff --git a/dev/standalone/pages/surface_water/surface_water_model/index.html b/dev/standalone/pages/surface_water/surface_water_model/index.html
diff --git a/dev/standalone/pages/vegetation/photosynthesis/farquhar_model/index.html b/dev/standalone/pages/vegetation/photosynthesis/farquhar_model/index.html
diff --git a/dev/standalone/pages/vegetation/photosynthesis/optimality_model/index.html b/dev/standalone/pages/vegetation/photosynthesis/optimality_model/index.html
diff --git a/dev/standalone/pages/vegetation/plant_hydraulics/van_genuchten_model/index.html b/dev/standalone/pages/vegetation/plant_hydraulics/van_genuchten_model/index.html
diff --git a/dev/standalone/pages/vegetation/radiative_transfer/beer_model/index.html b/dev/standalone/pages/vegetation/radiative_transfer/beer_model/index.html
diff --git a/dev/standalone/pages/vegetation/radiative_transfer/twostream_model/index.html b/dev/standalone/pages/vegetation/radiative_transfer/twostream_model/index.html
diff --git a/dev/standalone/pages/vegetation/stomatal_conductance/medlyn_model/index.html b/dev/standalone/pages/vegetation/stomatal_conductance/medlyn_model/index.html
diff --git a/previews/PR621/.documenter-siteinfo.json b/previews/PR621/.documenter-siteinfo.json
@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-09-03T16:56:48","documenter_version":"1.6.0"}}
+{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-10-03T22:38:19","documenter_version":"1.7.0"}}
diff --git a/previews/PR621/APIs/Bucket/index.html b/previews/PR621/APIs/Bucket/index.html
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diff --git a/previews/PR621/APIs/SoilBiogeochemistry/index.html b/previews/PR621/APIs/SoilBiogeochemistry/index.html
diff --git a/previews/PR621/APIs/SurfaceWater/index.html b/previews/PR621/APIs/SurfaceWater/index.html
diff --git a/previews/PR621/APIs/canopy/AutotrophicRespiration/index.html b/previews/PR621/APIs/canopy/AutotrophicRespiration/index.html
diff --git a/previews/PR621/APIs/canopy/Canopy/index.html b/previews/PR621/APIs/canopy/Canopy/index.html
diff --git a/previews/PR621/APIs/canopy/CanopyEnergy/index.html b/previews/PR621/APIs/canopy/CanopyEnergy/index.html
diff --git a/previews/PR621/APIs/canopy/Photosynthesis/index.html b/previews/PR621/APIs/canopy/Photosynthesis/index.html
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diff --git a/previews/PR621/generated/standalone/Usage/LSM_single_column_tutorial/index.html b/previews/PR621/generated/standalone/Usage/LSM_single_column_tutorial/index.html
diff --git a/previews/PR621/generated/standalone/Usage/domain_tutorial/index.html b/previews/PR621/generated/standalone/Usage/domain_tutorial/index.html
diff --git a/previews/PR621/generated/standalone/Usage/model_tutorial/index.html b/previews/PR621/generated/standalone/Usage/model_tutorial/index.html
diff --git a/previews/PR621/getting_started/index.html b/previews/PR621/getting_started/index.html
diff --git a/previews/PR621/index.html b/previews/PR621/index.html
diff --git a/previews/PR621/objects.inv b/previews/PR621/objects.inv
diff --git a/previews/PR621/search_index.js b/previews/PR621/search_index.js
diff --git a/previews/PR621/standalone/README/index.html b/previews/PR621/standalone/README/index.html
diff --git a/previews/PR621/standalone/apps/leaf_an.jl b/previews/PR621/standalone/apps/leaf_an.jl
@@ -38,10 +38,11 @@ function ParamViz.parameterisation(
     Γstar = co2_compensation(Γstar25, ΔHΓstar, T, To, R)
     medlynt = 1 + g1 / sqrt(VPD)
     ci = intercellular_co2(ca, Γstar, medlynt)
-    Aj = light_assimilation(Canopy.C3(), J, ci, Γstar)
+    is_c3 = 1.0
+    Aj = light_assimilation(is_c3, J, ci, Γstar)
     Kc = MM_Kc(Kc25, ΔHkc, T, To, R)
     Ko = MM_Ko(Ko25, ΔHko, T, To, R)
-    Ac = rubisco_assimilation(Canopy.C3(), Vcmax, ci, Γstar, Kc, Ko, oi)
+    Ac = rubisco_assimilation(is_c3, Vcmax, ci, Γstar, Kc, Ko, oi)
     Rd = dark_respiration(Vcmax25, β, f, ΔHRd, T, To, R)
     An = net_photosynthesis(Ac, Aj, Rd, β)
     return An
@@ -83,7 +84,7 @@ function An_app_f()
             "Ω", # Clumping index
             "Γstar25", # co2 compensation at 25c
             "ΔHΓstar", # a constant energy of activation
-            "To", # a standard temperature 
+            "To", # a standard temperature
             "R", # the universal gas constant
             "Vcmax25", # the maximum rate of carboxylation of Rubisco
             "ΔHJmax", # a constant

diff --git a/previews/PR621/standalone/apps/leaf_an_ci.jl b/previews/PR621/standalone/apps/leaf_an_ci.jl
@@ -36,8 +36,9 @@ function ParamViz.parameterisation(
     Γstar = co2_compensation(Γstar25, ΔHΓstar, T, To, R)
     Kc = MM_Kc(Kc25, ΔHkc, T, To, R)
     Ko = MM_Ko(Ko25, ΔHko, T, To, R)
-    Ac = rubisco_assimilation(Canopy.C3(), Vcmax, ci, Γstar, Kc, Ko, oi)
-    Aj = light_assimilation(Canopy.C3(), J, ci, Γstar)
+    is_c3 = 1.0
+    Ac = rubisco_assimilation(is_c3, Vcmax, ci, Γstar, Kc, Ko, oi)
+    Aj = light_assimilation(is_c3, J, ci, Γstar)
     Rd = dark_respiration(Vcmax25, β, f, ΔHRd, T, To, R)
     An = net_photosynthesis(Ac, Aj, Rd, β)
     return An
@@ -79,7 +80,7 @@ function An_ci_app_f()
             "Ω", # Clumping index
             "Γstar25", # co2 compensation at 25c
             "ΔHΓstar", # a constant energy of activation
-            "To", # a standard temperature 
+            "To", # a standard temperature
             "R", # the universal gas constant
             "ΔHJmax", # a constant
             "θj", # an empirical "curvature parameter"

diff --git a/previews/PR621/standalone/pages/snow/snow_model/index.html b/previews/PR621/standalone/pages/snow/snow_model/index.html
diff --git a/previews/PR621/standalone/pages/soil/biogeochemistry/DAMM_model/index.html b/previews/PR621/standalone/pages/soil/biogeochemistry/DAMM_model/index.html
diff --git a/previews/PR621/standalone/pages/soil/energy/energy_model/index.html b/previews/PR621/standalone/pages/soil/energy/energy_model/index.html
diff --git a/previews/PR621/standalone/pages/soil/hydrology/richards_model/index.html b/previews/PR621/standalone/pages/soil/hydrology/richards_model/index.html
diff --git a/previews/PR621/standalone/pages/surface_water/surface_water_model/index.html b/previews/PR621/standalone/pages/surface_water/surface_water_model/index.html
diff --git a/previews/PR621/standalone/pages/vegetation/photosynthesis/farquhar_model/index.html b/previews/PR621/standalone/pages/vegetation/photosynthesis/farquhar_model/index.html
diff --git a/previews/PR621/standalone/pages/vegetation/photosynthesis/optimality_model/index.html b/previews/PR621/standalone/pages/vegetation/photosynthesis/optimality_model/index.html
diff --git a/previews/PR621/standalone/pages/vegetation/plant_hydraulics/van_genuchten_model/index.html b/previews/PR621/standalone/pages/vegetation/plant_hydraulics/van_genuchten_model/index.html
diff --git a/previews/PR621/standalone/pages/vegetation/radiative_transfer/beer_model/index.html b/previews/PR621/standalone/pages/vegetation/radiative_transfer/beer_model/index.html
diff --git a/previews/PR621/standalone/pages/vegetation/radiative_transfer/twostream_model/index.html b/previews/PR621/standalone/pages/vegetation/radiative_transfer/twostream_model/index.html
diff --git a/previews/PR621/standalone/pages/vegetation/stomatal_conductance/medlyn_model/index.html b/previews/PR621/standalone/pages/vegetation/stomatal_conductance/medlyn_model/index.html
diff --git a/previews/PR629/.documenter-siteinfo.json b/previews/PR629/.documenter-siteinfo.json
@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-25T20:20:18","documenter_version":"1.5.0"}}
+{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-09-18T18:08:24","documenter_version":"1.6.0"}}
diff --git a/previews/PR629/APIs/Bucket/index.html b/previews/PR629/APIs/Bucket/index.html
diff --git a/previews/PR629/APIs/ClimaLand/index.html b/previews/PR629/APIs/ClimaLand/index.html
diff --git a/previews/PR629/APIs/Regridder/index.html b/previews/PR629/APIs/Regridder/index.html
diff --git a/previews/PR629/APIs/Snow/index.html b/previews/PR629/APIs/Snow/index.html
diff --git a/previews/PR629/APIs/Soil/index.html b/previews/PR629/APIs/Soil/index.html
diff --git a/previews/PR629/APIs/SoilBiogeochemistry/index.html b/previews/PR629/APIs/SoilBiogeochemistry/index.html
diff --git a/previews/PR629/APIs/SurfaceWater/index.html b/previews/PR629/APIs/SurfaceWater/index.html
diff --git a/previews/PR629/APIs/canopy/AutotrophicRespiration/index.html b/previews/PR629/APIs/canopy/AutotrophicRespiration/index.html
diff --git a/previews/PR629/APIs/canopy/Canopy/index.html b/previews/PR629/APIs/canopy/Canopy/index.html
diff --git a/previews/PR629/APIs/canopy/CanopyEnergy/index.html b/previews/PR629/APIs/canopy/CanopyEnergy/index.html
diff --git a/previews/PR629/APIs/canopy/Photosynthesis/index.html b/previews/PR629/APIs/canopy/Photosynthesis/index.html
diff --git a/previews/PR629/APIs/canopy/PlantHydraulics/index.html b/previews/PR629/APIs/canopy/PlantHydraulics/index.html
diff --git a/previews/PR629/APIs/canopy/RadiativeTransfer/index.html b/previews/PR629/APIs/canopy/RadiativeTransfer/index.html
diff --git a/previews/PR629/APIs/canopy/StomatalConductance/index.html b/previews/PR629/APIs/canopy/StomatalConductance/index.html
diff --git a/previews/PR629/APIs/shared_utilities/index.html b/previews/PR629/APIs/shared_utilities/index.html
diff --git a/previews/PR629/Contributing/index.html b/previews/PR629/Contributing/index.html
diff --git a/previews/PR629/assets/documenter.js b/previews/PR629/assets/documenter.js
diff --git a/previews/PR629/diagnostics/available_diagnostics/index.html b/previews/PR629/diagnostics/available_diagnostics/index.html
diff --git a/previews/PR629/diagnostics/developers_diagnostics/index.html b/previews/PR629/diagnostics/developers_diagnostics/index.html
diff --git a/previews/PR629/diagnostics/make_diagnostic_table.jl b/previews/PR629/diagnostics/make_diagnostic_table.jl
@@ -16,7 +16,14 @@ for d in values(CL.Diagnostics.ALL_DIAGNOSTICS)
     push!(comments, d.comments)
     push!(standard_names, d.standard_name)
 end
-data = hcat(short_names, long_names, units, comments, standard_names)
+i = sortperm(short_names) # indices of short_names sorted alphabetically
+data = hcat(
+    short_names[i],
+    long_names[i],
+    units[i],
+    comments[i],
+    standard_names[i],
+)
 pretty_table(
     data;
     autowrap = true,

diff --git a/previews/PR629/diagnostics/users_diagnostics/index.html b/previews/PR629/diagnostics/users_diagnostics/index.html
diff --git a/previews/PR629/folderstructure/index.html b/previews/PR629/folderstructure/index.html
diff --git a/previews/PR629/generated/integrated/ozark_canopy_flux_test.png b/previews/PR629/generated/integrated/ozark_canopy_flux_test.png
diff --git a/previews/PR629/generated/integrated/ozark_soil_plant_flux.png b/previews/PR629/generated/integrated/ozark_soil_plant_flux.png
diff --git a/previews/PR629/generated/integrated/ozark_soil_test.png b/previews/PR629/generated/integrated/ozark_soil_test.png
diff --git a/previews/PR629/generated/integrated/soil_canopy_tutorial/index.html b/previews/PR629/generated/integrated/soil_canopy_tutorial/index.html
diff --git a/previews/PR629/generated/shared_utilities/driver_tutorial/index.html b/previews/PR629/generated/shared_utilities/driver_tutorial/index.html
diff --git a/previews/PR629/generated/standalone/Bucket/bucket_tutorial/index.html b/previews/PR629/generated/standalone/Bucket/bucket_tutorial/index.html
diff --git a/previews/PR629/generated/standalone/Bucket/coupled_bucket/index.html b/previews/PR629/generated/standalone/Bucket/coupled_bucket/index.html
diff --git a/previews/PR629/generated/standalone/Canopy/canopy_tutorial/index.html b/previews/PR629/generated/standalone/Canopy/canopy_tutorial/index.html
diff --git a/previews/PR629/generated/standalone/Canopy/ozark_standalone_canopy_test.png b/previews/PR629/generated/standalone/Canopy/ozark_standalone_canopy_test.png
diff --git a/previews/PR629/generated/standalone/Snow/base_tutorial/index.html b/previews/PR629/generated/standalone/Snow/base_tutorial/index.html
diff --git a/previews/PR629/generated/standalone/Snow/base_tutorial_plot1.png b/previews/PR629/generated/standalone/Snow/base_tutorial_plot1.png
diff --git a/previews/PR629/generated/standalone/Snow/base_tutorial_plot2.png b/previews/PR629/generated/standalone/Snow/base_tutorial_plot2.png
diff --git a/previews/PR629/generated/standalone/Snow/data_tutorial/index.html b/previews/PR629/generated/standalone/Snow/data_tutorial/index.html
diff --git a/previews/PR629/generated/standalone/Soil/boundary_conditions/index.html b/previews/PR629/generated/standalone/Soil/boundary_conditions/index.html
diff --git a/previews/PR629/generated/standalone/Soil/evaporation/index.html b/previews/PR629/generated/standalone/Soil/evaporation/index.html
diff --git a/previews/PR629/generated/standalone/Soil/evaporation_gardner_fig1.png b/previews/PR629/generated/standalone/Soil/evaporation_gardner_fig1.png
diff --git a/previews/PR629/generated/standalone/Soil/evaporation_gilat_loess/index.html b/previews/PR629/generated/standalone/Soil/evaporation_gilat_loess/index.html
diff --git a/previews/PR629/generated/standalone/Soil/evaporation_lehmann2008_fig8b.png b/previews/PR629/generated/standalone/Soil/evaporation_lehmann2008_fig8b.png
diff --git a/previews/PR629/generated/standalone/Soil/evaporation_lehmann2024_figS6.png b/previews/PR629/generated/standalone/Soil/evaporation_lehmann2024_figS6.png
diff --git a/previews/PR629/generated/standalone/Soil/freezing_front/index.html b/previews/PR629/generated/standalone/Soil/freezing_front/index.html
diff --git a/previews/PR629/generated/standalone/Soil/layered_soil/index.html b/previews/PR629/generated/standalone/Soil/layered_soil/index.html
diff --git a/previews/PR629/generated/standalone/Soil/mizoguchi_data_comparison.png b/previews/PR629/generated/standalone/Soil/mizoguchi_data_comparison.png
diff --git a/previews/PR629/generated/standalone/Soil/profiles.png b/previews/PR629/generated/standalone/Soil/profiles.png
diff --git a/previews/PR629/generated/standalone/Soil/richards_equation/index.html b/previews/PR629/generated/standalone/Soil/richards_equation/index.html
diff --git a/previews/PR629/generated/standalone/Soil/soil_energy_hydrology/index.html b/previews/PR629/generated/standalone/Soil/soil_energy_hydrology/index.html