Merge pull request #85 from EcohydrologyTeam/KW_NitrogenTesting

Balgae Testing (and one Nitrogen Test)
EcohydrologyTeam · May 13, 2024 · 190c12a · 190c12a
2 parents ec0d3d0 + 0ff1eff
commit 190c12a
Show file tree

Hide file tree

Showing 39 changed files with 2,537 additions and 7 deletions.
diff --git a/...er_modules/nsm1/CBOD/dynamic_variables.py → ...odules/nsm1/old/CBOD/dynamic_variables.py b/...er_modules/nsm1/CBOD/dynamic_variables.py → ...odules/nsm1/old/CBOD/dynamic_variables.py
diff --git a/...clearwater_modules/nsm1/CBOD/processes.py → ...rwater_modules/nsm1/old/CBOD/processes.py b/...clearwater_modules/nsm1/CBOD/processes.py → ...rwater_modules/nsm1/old/CBOD/processes.py
diff --git a/...ter_modules/nsm1/CBOD/static_variables.py → ...modules/nsm1/old/CBOD/static_variables.py b/...ter_modules/nsm1/CBOD/static_variables.py → ...modules/nsm1/old/CBOD/static_variables.py
diff --git a/...ter_modules/nsm1/DOX/dynamic_variables.py → ...modules/nsm1/old/DOX/dynamic_variables.py b/...ter_modules/nsm1/DOX/dynamic_variables.py → ...modules/nsm1/old/DOX/dynamic_variables.py
diff --git a/src/clearwater_modules/nsm1/DOX/processes.py → ...arwater_modules/nsm1/old/DOX/processes.py b/src/clearwater_modules/nsm1/DOX/processes.py → ...arwater_modules/nsm1/old/DOX/processes.py
diff --git a/...ater_modules/nsm1/DOX/static_variables.py → ..._modules/nsm1/old/DOX/static_variables.py b/...ater_modules/nsm1/DOX/static_variables.py → ..._modules/nsm1/old/DOX/static_variables.py
diff --git a/...ter_modules/nsm1/POM/dynamic_variables.py → ...modules/nsm1/old/POM/dynamic_variables.py b/...ter_modules/nsm1/POM/dynamic_variables.py → ...modules/nsm1/old/POM/dynamic_variables.py
diff --git a/src/clearwater_modules/nsm1/POM/processes.py → ...arwater_modules/nsm1/old/POM/processes.py b/src/clearwater_modules/nsm1/POM/processes.py → ...arwater_modules/nsm1/old/POM/processes.py
diff --git a/...ater_modules/nsm1/POM/static_variables.py → ..._modules/nsm1/old/POM/static_variables.py b/...ater_modules/nsm1/POM/static_variables.py → ..._modules/nsm1/old/POM/static_variables.py
diff --git a/...r_modules/nsm1/algae/dynamic_variables.py → ...dules/nsm1/old/algae/dynamic_variables.py b/...r_modules/nsm1/algae/dynamic_variables.py → ...dules/nsm1/old/algae/dynamic_variables.py
diff --git a/...learwater_modules/nsm1/algae/processes.py → ...water_modules/nsm1/old/algae/processes.py b/...learwater_modules/nsm1/algae/processes.py → ...water_modules/nsm1/old/algae/processes.py
diff --git a/...er_modules/nsm1/algae/static_variables.py → ...odules/nsm1/old/algae/static_variables.py b/...er_modules/nsm1/algae/static_variables.py → ...odules/nsm1/old/algae/static_variables.py
diff --git a/...ules/nsm1/alkalinity/dynamic_variables.py → .../nsm1/old/alkalinity/dynamic_variables.py b/...ules/nsm1/alkalinity/dynamic_variables.py → .../nsm1/old/alkalinity/dynamic_variables.py
diff --git a/...ater_modules/nsm1/alkalinity/processes.py → ..._modules/nsm1/old/alkalinity/processes.py b/...ater_modules/nsm1/alkalinity/processes.py → ..._modules/nsm1/old/alkalinity/processes.py
diff --git a/...dules/nsm1/alkalinity/static_variables.py → ...s/nsm1/old/alkalinity/static_variables.py b/...dules/nsm1/alkalinity/static_variables.py → ...s/nsm1/old/alkalinity/static_variables.py
diff --git a/..._modules/nsm1/balgae/dynamic_variables.py → ...ules/nsm1/old/balgae/dynamic_variables.py b/..._modules/nsm1/balgae/dynamic_variables.py → ...ules/nsm1/old/balgae/dynamic_variables.py
diff --git a/...earwater_modules/nsm1/balgae/processes.py → ...ater_modules/nsm1/old/balgae/processes.py b/...earwater_modules/nsm1/balgae/processes.py → ...ater_modules/nsm1/old/balgae/processes.py
@@ -15,7 +15,7 @@ def mub_max_tc(
     """Calculate mub_max_tc: Maximum benthic algal growth rate with temperature correction (1/d).
 
     Args:
-        mu_max_20: Maximum benthic algal growth rate at 20C (1/d)
+        mub_max_20: Maximum benthic algal growth rate at 20C (1/d)
         TwaterC: Water temperature (C)
     """
     return arrhenius_correction(TwaterC, mub_max_20, 1.047)
@@ -162,7 +162,7 @@ def FNb(
     """
     FNb = xr.where(use_NH4 or use_NO3, (NH4 + NO3) / (KsNb + NH4 + NO3),1)
     FNb = xr.where(math.isnan(FNb),0.0,
-          xr.where(FNb < 1.0, 1, FNb))
+          xr.where(FNb > 1.0, 1, FNb))
 
     return FNb
 
@@ -230,12 +230,12 @@ def mub(
         FPb: Benthic algae phosphorous limitation (unitless)
         FNb: Benthic algae nitrogen limitation (unitless)
         FSb: Benthic density attenuation (unitless),
-    """
+    """  
 
     # Benthic Local Specific Growth Rate
     return xr.where(b_growth_rate_option == 1, mub_max_tc * FLb * FPb * FNb * FSb, mub_max_tc * FLb * FSb * min(FPb, FNb))
 
-
+#TODO RAS WQ has an option for harmonic which the FORTAN code does not have 
 
 @numba.njit
 def AbGrowth(

diff --git a/...r_modules/nsm1/balgae/static_variables.py → ...dules/nsm1/old/balgae/static_variables.py b/...r_modules/nsm1/balgae/static_variables.py → ...dules/nsm1/old/balgae/static_variables.py
diff --git a/..._modules/nsm1/carbon/dynamic_variables.py → ...ules/nsm1/old/carbon/dynamic_variables.py b/..._modules/nsm1/carbon/dynamic_variables.py → ...ules/nsm1/old/carbon/dynamic_variables.py
diff --git a/...earwater_modules/nsm1/carbon/processes.py → ...ater_modules/nsm1/old/carbon/processes.py b/...earwater_modules/nsm1/carbon/processes.py → ...ater_modules/nsm1/old/carbon/processes.py
diff --git a/...r_modules/nsm1/carbon/static_variables.py → ...dules/nsm1/old/carbon/static_variables.py b/...r_modules/nsm1/carbon/static_variables.py → ...dules/nsm1/old/carbon/static_variables.py
diff --git a/...ater_modules/nsm1/n2/dynamic_variables.py → ..._modules/nsm1/old/n2/dynamic_variables.py b/...ater_modules/nsm1/n2/dynamic_variables.py → ..._modules/nsm1/old/n2/dynamic_variables.py
diff --git a/src/clearwater_modules/nsm1/n2/processes.py → ...earwater_modules/nsm1/old/n2/processes.py b/src/clearwater_modules/nsm1/n2/processes.py → ...earwater_modules/nsm1/old/n2/processes.py
diff --git a/...water_modules/nsm1/n2/static_variables.py → ...r_modules/nsm1/old/n2/static_variables.py b/...water_modules/nsm1/n2/static_variables.py → ...r_modules/nsm1/old/n2/static_variables.py
diff --git a/...odules/nsm1/nitrogen/dynamic_variables.py → ...es/nsm1/old/nitrogen/dynamic_variables.py b/...odules/nsm1/nitrogen/dynamic_variables.py → ...es/nsm1/old/nitrogen/dynamic_variables.py
diff --git a/...rwater_modules/nsm1/nitrogen/processes.py → ...er_modules/nsm1/old/nitrogen/processes.py b/...rwater_modules/nsm1/nitrogen/processes.py → ...er_modules/nsm1/old/nitrogen/processes.py
diff --git a/...modules/nsm1/nitrogen/static_variables.py → ...les/nsm1/old/nitrogen/static_variables.py b/...modules/nsm1/nitrogen/static_variables.py → ...les/nsm1/old/nitrogen/static_variables.py
diff --git a/...dules/nsm1/pathogens/dynamic_variables.py → ...s/nsm1/old/pathogens/dynamic_variables.py b/...dules/nsm1/pathogens/dynamic_variables.py → ...s/nsm1/old/pathogens/dynamic_variables.py
diff --git a/...water_modules/nsm1/pathogens/processes.py → ...r_modules/nsm1/old/pathogens/processes.py b/...water_modules/nsm1/pathogens/processes.py → ...r_modules/nsm1/old/pathogens/processes.py
diff --git a/...odules/nsm1/pathogens/static_variables.py → ...es/nsm1/old/pathogens/static_variables.py b/...odules/nsm1/pathogens/static_variables.py → ...es/nsm1/old/pathogens/static_variables.py
diff --git a/...ules/nsm1/phosphorus/dynamic_variables.py → .../nsm1/old/phosphorus/dynamic_variables.py b/...ules/nsm1/phosphorus/dynamic_variables.py → .../nsm1/old/phosphorus/dynamic_variables.py
diff --git a/...ater_modules/nsm1/phosphorus/processes.py → ..._modules/nsm1/old/phosphorus/processes.py b/...ater_modules/nsm1/phosphorus/processes.py → ..._modules/nsm1/old/phosphorus/processes.py
diff --git a/...dules/nsm1/phosphorus/static_variables.py → ...s/nsm1/old/phosphorus/static_variables.py b/...dules/nsm1/phosphorus/static_variables.py → ...s/nsm1/old/phosphorus/static_variables.py
diff --git a/...modules/nsm1/sedflux/dynamic_variables.py → ...les/nsm1/old/sedflux/dynamic_variables.py b/...modules/nsm1/sedflux/dynamic_variables.py → ...les/nsm1/old/sedflux/dynamic_variables.py
diff --git a/...arwater_modules/nsm1/sedflux/processes.py → ...ter_modules/nsm1/old/sedflux/processes.py b/...arwater_modules/nsm1/sedflux/processes.py → ...ter_modules/nsm1/old/sedflux/processes.py
diff --git a/...r_modules/nsm1/sedflux/static_variable.py → ...dules/nsm1/old/sedflux/static_variable.py b/...r_modules/nsm1/sedflux/static_variable.py → ...dules/nsm1/old/sedflux/static_variable.py
diff --git a/src/clearwater_modules/nsm1/processes.py b/src/clearwater_modules/nsm1/processes.py
@@ -704,7 +704,7 @@ def mub_max_tc(
     """Calculate mub_max_tc: Maximum benthic algal growth rate with temperature correction (1/d).
 
     Args:
-        mu_max_20: Maximum benthic algal growth rate at 20C (1/d)
+        mub_max_20: Maximum benthic algal growth rate at 20C (1/d)
         TwaterC: Water temperature (C)
     """
     return arrhenius_correction(TwaterC, mub_max_20, 1.047)
@@ -1169,7 +1169,7 @@ def kon_tc(
         kon_20: Decay rate of OrgN to NH4 (1/d)
     """
 
-    return arrhenius_correction(TwaterC, kon_20, 1.074)
+    return arrhenius_correction(TwaterC, kon_20, 1.047)
 
 
 
@@ -1490,6 +1490,8 @@ def NH4_ApGrowth(
 def NH4_AbRespiration(
     use_Balgae: bool,
     rnb: xr.DataArray,
+    Fb: xr.DataArray,
+    depth: xr.DataArray,
     AbRespiration: xr.DataArray,
 
 ) -> xr.DataArray:
@@ -1499,10 +1501,12 @@ def NH4_AbRespiration(
         use_Balgae: true/false to use benthic algae module (unitless),
         rnb: xr.DataArray,
         AbRespiration: Benthic algal respiration rate (g/m^2/d),
+        depth: water depth (m),
+        Fb: Fraction of bottom area for benthic algae (unitless),
     """
     # TODO changed the calculation for respiration from the inital FORTRAN due to conflict with the reference guide
 
-    return xr.where(use_Balgae, rnb * AbRespiration, 0.0 )
+    return xr.where(use_Balgae, (rnb * AbRespiration*Fb)/depth, 0.0 )
 
 def NH4_AbGrowth(
     use_Balgae: bool,