Phosphorus, N2, POM, and PX

examples/dev_sandbox/DOX_sat_test.py

@@ -25,15 +25,15 @@ def DOs_atm_alpha(
 
 def DOX_sat(
     TwaterK: xr.DataArray,
-    pressure_atm: xr.DataArray,
+    pressure_mb: xr.DataArray,
     pwv: xr.DataArray,
     DOs_atm_alpha: xr.DataArray
 ) -> xr.DataArray:
     """Calculate DO saturation value
 
     Args:
         TwaterK: Water temperature kelvin
-        pressure_atm: Atmospheric pressure (atm)
+        pressure_mb: Atmospheric pressure (mb)
         pwv: Patrial pressure of water vapor (atm)
         DOs_atm_alpha: DO saturation atmospheric correction coefficient
     """
@@ -44,8 +44,8 @@ def DOX_sat(
 
     DOX_sat_uncorrected = -139.34410 + ( 1.575701E05 / TwaterK ) - ( 6.642308E07 / (TwaterK**2.0) ) + ( 1.243800E10 / (TwaterK**3.0) ) - ( 8.621949E11 / (TwaterK**4.0) )
 
-    DOX_sat_corrected = DOX_sat_uncorrected * pressure_atm * \
-        (1 - pwv / pressure_atm) * (1 - DOs_atm_alpha * pressure_atm) / \
+    DOX_sat_corrected = DOX_sat_uncorrected * pressure_mb * \
+        (1 - pwv / pressure_mb) * (1 - DOs_atm_alpha * pressure_mb) / \
         ((1 - pwv) * (1 - DOs_atm_alpha))
 
     print(no_exp)

examples/dev_sandbox/prof_nsm.py

@@ -163,7 +163,7 @@
     'topwidth': 1,
     'slope': 2,
     'shear_velocity': 4,
-    'pressure_atm': 2,
+    'pressure_mb': 2026.5,
     'wind_speed': 4,
     'q_solar': 4,
     'Solid': 1, 

src/clearwater_modules/nsm1/constants.py

@@ -98,7 +98,7 @@ class BalgaeStaticVariables(TypedDict):
     krb_20=0.2,
     kdb_20=0.3,
     mub_max_theta = 1.047,
-    krb_theta = 1.047,
+    krb_theta = 1.06,
     kdb_theta = 1.047,
     b_growth_rate_option=1,
     b_light_limitation_option=1,
@@ -130,11 +130,11 @@ class NitrogenStaticVariables(TypedDict):
     kdnit_20=0.002,
     rnh4_20=0,
     vno3_20=0,
-    knit_theta= 1.047, ## Check values RAS/Kelsey's
-    kon_theta= 1.047,
-    kdnit_theta= 1.047,
+    knit_theta= 1.083,
+    kon_theta= 1.074,
+    kdnit_theta= 1.08,
     rnh4_theta= 1.047,
-    vno3_theta= 1.047,
+    vno3_theta= 1.045,
     KsOxdn=0.1,
     PN=0.5,
     PNb=0.5
@@ -156,10 +156,10 @@ class CarbonStaticVariables(TypedDict):
 DEFAULT_CARBON = CarbonStaticVariables(
     f_pocp = 0.9,
     kdoc_20= 0.01,
-    kdoc_theta = 1.047,
     f_pocb=0.9,
     kpoc_20= 0.005,
     kpoc_theta = 1.047,
+    kdoc_theta = 1.047,
     KsOxmc=1.0,
     pCO2 = 383.0,
     FCO2 = 0.2,
@@ -200,10 +200,12 @@ class N2StaticVariables(TypedDict):
 
 class POMStaticVariables(TypedDict):
     kpom_20: float
+    h2: float
     kpom_theta: float
 
 DEFAULT_POM = POMStaticVariables(
     kpom_20 = 0.1,
+    h2=0.1,
     kpom_theta = 1.047
 )
 
@@ -216,7 +218,7 @@ class PathogenStaticVariables(TypedDict):
 
 DEFAULT_PATHOGEN = PathogenStaticVariables(
     kdx_20=0.8,
-    kdx_theta = 1.047,
+    kdx_theta = 1.07,
     apx=1,
     vx=1
 )
@@ -232,7 +234,7 @@ class PhosphorusStaticVariables(TypedDict):
     kop_20 = 0.1,
     rpo4_20 =0,
     kop_theta = 1.047,
-    rpo4_theta = 1.047,
+    rpo4_theta = 1.074,
     kdpo4 = 0.0,
 )
 
@@ -299,7 +301,7 @@ class GlobalVars(TypedDict):
     topwidth: float
     slope: float
     shear_velocity: float
-    pressure_atm: float
+    pressure_mb: float
     wind_speed: float
     q_solar: float
     Solid: int
@@ -319,24 +321,24 @@ class GlobalVars(TypedDict):
     vs = 999,
     SOD_20 = 999,
     SOD_theta = 999,
+    theta=1.047,
     vb = 0.01,
     fcom = 0.4,
     kaw_20_user = 999,
     kah_20_user = 999,
-    kaw_theta = 1.047,
-    kah_theta = 1.047,
-    hydraulic_reaeration_option = 2,
-    wind_reaeration_option = 2,  
+    kaw_theta = 1.024,
+    kah_theta = 1.024,
+    hydraulic_reaeration_option = 1,
+    wind_reaeration_option = 1,  
     dt = 1,    #TODO Dynamic or static?
     depth = 1.5,         #TODO Dynamic or static?
     TwaterC = 20,
-    theta = 1.047,
     velocity = 1,
     flow = 2,
     topwidth = 1,
     slope = 2,
     shear_velocity = 4,
-    pressure_atm = 2,
+    pressure_mb = 2026.5,
     wind_speed = 4,
     q_solar = 500,
     Solid = 1,

src/clearwater_modules/nsm1/dynamic_variables.py

@@ -1371,14 +1371,6 @@ class Variable(base.Variable):
     process=processes.KHN2_tc
 )
 
-Variable(
-    name='P_wv',
-    long_name='Partial pressure water vapor',
-    units='atm',
-    description='Partial pressure water vapor',
-    use='dynamic',
-    process=processes.P_wv
-)
 
 Variable(
     name='N2sat',